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Conserved domains on  [gi|914776599|ref|WP_050719321|]
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Tex family protein [Aeromonas tecta]

Protein Classification

Tex family protein( domain architecture ID 11450661)

Tex (toxin expression) family protein is an RNA-binding transcriptional accessory protein; includes two functional domains, an N-terminal domain which may be a transcriptional factor, and a C-terminal S1 RNA-binding domain

Gene Ontology:  GO:0005829|GO:0003729|GO:0003676
PubMed:  17242308|8755871

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1-724 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


:

Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1411.32  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599   1 MNSIERQIATELNARPEQVEAAVRLLDEGSTVPFIARYRKEVTGGLDDSQLRTLESRLGYLRELSDRRQVILRSIEEQGK 80
Cdd:COG2183    2 MMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599  81 LTPELARDLNEADSKTRLEDLYLPYKPKRRTKGQMAIEAGLEPLANLLLTDPMRDPEQEAATFLNAEQGIADTKAALDGA 160
Cdd:COG2183   82 LTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEEKGVADVEAALDGA 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 161 RYILMERFAEQADLLEKLRDYLWHNATLRARVVAGKEQEGAKFKDYFEHDEPLHKAPSHRVLAMLRGRNEGILNLALVTG 240
Cdd:COG2183  162 RDILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPD 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 241 DDDsvspCEGIITHHLrLNLQSRPADKWLQGVVSWTWKIKLSLQMETELIGRVRESAEEEAIKVFAMNLQDLLMAAPAGM 320
Cdd:COG2183  242 EEE----AEAYIARRF-IKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGG 316

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 321 RCTMGLDPGIRTGVKVAVVDATGKLVDHATIYPFEPKKQVDQSLRTLNELCQKHKVELISIGNGTASRETDRLVSDLFER 400
Cdd:COG2183  317 KVVLGLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKE 396

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 401 YPAaKAQKIVVSEAGASVYSASELASQEFPDLDVSIRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVGQSQLARRLD 480
Cdd:COG2183  397 LDL-KVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLD 475

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 481 AVVEDCVNAVGVDVNTASVALLNRVSGLSQTMAQNIVAYRDDNGAFRNRQQLLKVSRLGPKAFEQCAGFLRIRGGSNPLD 560
Cdd:COG2183  476 AVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLD 555

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 561 GSAVHPESYPVVERILAQLQQQVENLLGNSSLLRGLKPADYTDERFGVPTVTDIIGELDKPGRDPRPEFKTATFKDGVEK 640
Cdd:COG2183  556 NSAVHPESYPVVEKILKDLGVSVKDLIGNKELLKKLDPEKYADELFGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLK 635

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 641 ISDLVPEMVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMRLDEK 720
Cdd:COG2183  636 IEDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDDE 715


                 ....
gi 914776599 721 AGEQ 724
Cdd:COG2183  716 AGAA 719
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1-724 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1411.32  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599   1 MNSIERQIATELNARPEQVEAAVRLLDEGSTVPFIARYRKEVTGGLDDSQLRTLESRLGYLRELSDRRQVILRSIEEQGK 80
Cdd:COG2183    2 MMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599  81 LTPELARDLNEADSKTRLEDLYLPYKPKRRTKGQMAIEAGLEPLANLLLTDPMRDPEQEAATFLNAEQGIADTKAALDGA 160
Cdd:COG2183   82 LTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEEKGVADVEAALDGA 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 161 RYILMERFAEQADLLEKLRDYLWHNATLRARVVAGKEQEGAKFKDYFEHDEPLHKAPSHRVLAMLRGRNEGILNLALVTG 240
Cdd:COG2183  162 RDILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPD 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 241 DDDsvspCEGIITHHLrLNLQSRPADKWLQGVVSWTWKIKLSLQMETELIGRVRESAEEEAIKVFAMNLQDLLMAAPAGM 320
Cdd:COG2183  242 EEE----AEAYIARRF-IKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGG 316

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 321 RCTMGLDPGIRTGVKVAVVDATGKLVDHATIYPFEPKKQVDQSLRTLNELCQKHKVELISIGNGTASRETDRLVSDLFER 400
Cdd:COG2183  317 KVVLGLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKE 396

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 401 YPAaKAQKIVVSEAGASVYSASELASQEFPDLDVSIRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVGQSQLARRLD 480
Cdd:COG2183  397 LDL-KVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLD 475

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 481 AVVEDCVNAVGVDVNTASVALLNRVSGLSQTMAQNIVAYRDDNGAFRNRQQLLKVSRLGPKAFEQCAGFLRIRGGSNPLD 560
Cdd:COG2183  476 AVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLD 555

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 561 GSAVHPESYPVVERILAQLQQQVENLLGNSSLLRGLKPADYTDERFGVPTVTDIIGELDKPGRDPRPEFKTATFKDGVEK 640
Cdd:COG2183  556 NSAVHPESYPVVEKILKDLGVSVKDLIGNKELLKKLDPEKYADELFGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLK 635

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 641 ISDLVPEMVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMRLDEK 720
Cdd:COG2183  636 IEDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDDE 715


                 ....
gi 914776599 721 AGEQ 724
Cdd:COG2183  716 AGAA 719
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 8-192 2.08e-101

Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss:Q45388. This protein defines a novel family of prokaryotic transcriptional accessory factors.


Pssm-ID: 462777  Cd Length: 183  Bit Score: 310.11  E-value: 2.08e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599    8 IATELNARPEQVEAAVRLLDEGSTVPFIARYRKEVTGGLDDSQLRTLESRLGYLRELSDRRQVILRSIEEQGKLTPELAR 87
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599   88 DLNEADSKTRLEDLYLPYKPKRRTKGQMAIEAGLEPLANLLLTDPmrDPEQEAATFLNAEQGIADTKAALDGARYILMER 167
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQP--DPEEEAAKYINPEKGVADVEEALAGARDIIAER 158

                         170       180
                  ....*....|....*....|....*
gi 914776599  168 FAEQADLLEKLRDYLWHNATLRARV 192
Cdd:pfam09371 159 ISEDAELRKKLRELLWREGVIVSKV 183
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 648-714 1.42e-35

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: 128.50  E-value: 1.42e-35
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 914776599 648 MVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLT 714
Cdd:cd05685    2 MVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 648-740 8.15e-23

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator.


Pssm-ID: 468553 [Multi-domain]  Cd Length: 113  Bit Score: 94.03  E-value: 8.15e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 648 MVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR-LDEKAGEQRG 726
Cdd:NF040579   5 DIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSLRaLEEAPEKHRK 84

                         90
                 ....*....|....
gi 914776599 727 PGRKPAEQRQSSAG 740
Cdd:NF040579  85 RRKHRWTNKRLKIG 98
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
648-716 1.17e-22

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 91.90  E-value: 1.17e-22
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 914776599   648 MVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:smart00316   4 DVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 632-724 8.41e-21

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 95.33  E-value: 8.41e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 632 ATFKDGVEKISDLVPE-MVLEGVVTNVTNFGAFVDI--GVhqDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPR 708
Cdd:PRK06676 262 DTLPGPWEGVEEKLPEgDVIEGTVKRLTDFGAFVEVlpGV--EGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEE 339

                         90
                 ....*....|....*..
gi 914776599 709 KRISLTMR-LDEKAGEQ 724
Cdd:PRK06676 340 KRISLSIKaLEEAPAEE 356
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 639-716 2.41e-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: 82.86  E-value: 2.41e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 914776599  639 EKISDLVPEMVLEGVVTNVTNFGAFVDIGVhQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:TIGR00717 180 ELLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLK 256
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1-724 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1411.32  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599   1 MNSIERQIATELNARPEQVEAAVRLLDEGSTVPFIARYRKEVTGGLDDSQLRTLESRLGYLRELSDRRQVILRSIEEQGK 80
Cdd:COG2183    2 MMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599  81 LTPELARDLNEADSKTRLEDLYLPYKPKRRTKGQMAIEAGLEPLANLLLTDPMRDPEQEAATFLNAEQGIADTKAALDGA 160
Cdd:COG2183   82 LTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEEKGVADVEAALDGA 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 161 RYILMERFAEQADLLEKLRDYLWHNATLRARVVAGKEQEGAKFKDYFEHDEPLHKAPSHRVLAMLRGRNEGILNLALVTG 240
Cdd:COG2183  162 RDILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPD 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 241 DDDsvspCEGIITHHLrLNLQSRPADKWLQGVVSWTWKIKLSLQMETELIGRVRESAEEEAIKVFAMNLQDLLMAAPAGM 320
Cdd:COG2183  242 EEE----AEAYIARRF-IKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGG 316

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 321 RCTMGLDPGIRTGVKVAVVDATGKLVDHATIYPFEPKKQVDQSLRTLNELCQKHKVELISIGNGTASRETDRLVSDLFER 400
Cdd:COG2183  317 KVVLGLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKE 396

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 401 YPAaKAQKIVVSEAGASVYSASELASQEFPDLDVSIRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVGQSQLARRLD 480
Cdd:COG2183  397 LDL-KVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLD 475

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 481 AVVEDCVNAVGVDVNTASVALLNRVSGLSQTMAQNIVAYRDDNGAFRNRQQLLKVSRLGPKAFEQCAGFLRIRGGSNPLD 560
Cdd:COG2183  476 AVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLD 555

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 561 GSAVHPESYPVVERILAQLQQQVENLLGNSSLLRGLKPADYTDERFGVPTVTDIIGELDKPGRDPRPEFKTATFKDGVEK 640
Cdd:COG2183  556 NSAVHPESYPVVEKILKDLGVSVKDLIGNKELLKKLDPEKYADELFGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLK 635

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 641 ISDLVPEMVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMRLDEK 720
Cdd:COG2183  636 IEDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDDE 715


                 ....
gi 914776599 721 AGEQ 724
Cdd:COG2183  716 AGAA 719
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 8-192 2.08e-101

Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss:Q45388. This protein defines a novel family of prokaryotic transcriptional accessory factors.


Pssm-ID: 462777  Cd Length: 183  Bit Score: 310.11  E-value: 2.08e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599    8 IATELNARPEQVEAAVRLLDEGSTVPFIARYRKEVTGGLDDSQLRTLESRLGYLRELSDRRQVILRSIEEQGKLTPELAR 87
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599   88 DLNEADSKTRLEDLYLPYKPKRRTKGQMAIEAGLEPLANLLLTDPmrDPEQEAATFLNAEQGIADTKAALDGARYILMER 167
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQP--DPEEEAAKYINPEKGVADVEEALAGARDIIAER 158

                         170       180
                  ....*....|....*....|....*
gi 914776599  168 FAEQADLLEKLRDYLWHNATLRARV 192
Cdd:pfam09371 159 ISEDAELRKKLRELLWREGVIVSKV 183
Tex_YqgF pfam16921
Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which ...
 323-447 1.95e-76

Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which is involved in transcriptional processes.


Pssm-ID: 465314  Cd Length: 125  Bit Score: 242.30  E-value: 1.95e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599  323 TMGLDPGIRTGVKVAVVDATGKLVDHATIYPFEPKKQVDQSLRTLNELCQKHKVELISIGNGTASRETDRLVSDLFERYP 402
Cdd:pfam16921   2 VLGLDPGYRTGCKLAVVDETGKVLDTAVIYPHPPQNKVEEAKKKLKKLIKKYGVELIAIGNGTASRETEQFVAELIKELP 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 914776599  403 aAKAQKIVVSEAGASVYSASELASQEFPDLDVSIRGAVSIARRLQ 447
Cdd:pfam16921  82 -LKVKYVIVSEAGASVYSASELAREEFPDLDVSLRGAVSIARRLQ 125
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 648-714 1.42e-35

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: 128.50  E-value: 1.42e-35
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 914776599 648 MVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLT 714
Cdd:cd05685    2 MVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 489-550 5.78e-32

Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 118.35  E-value: 5.78e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 914776599  489 AVGVDVNTASVALLNRVSGLSQTMAQNIVAYRDDNGAFRNRQQLLKVSRLGPKAFEQCAGFL 550
Cdd:pfam12836   1 AVGVDINTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKTFEQLAGFL 62
HHH_9 pfam17674
HHH domain;
557-626 4.73e-30

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 113.02  E-value: 4.73e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599  557 NPLDGSAVHPESYPVVERILAQLQQQVENLLGNSSLLRGLKPADYTDERFGVPTVTDIIGELDKPGRDPR 626
Cdd:pfam17674   1 NPLDNTAIHPESYPLAEKILKDLGLDLKDLIGNSALLKKLDPKKLAEEEVGLPTLKDILEELAKPGRDPR 70
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 648-741 4.44e-24

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 98.33  E-value: 4.44e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 648 MVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDaPRKRISLTMRldeKAGEQRGP 727
Cdd:COG1098    7 DIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSID-EDGKISLSIK---QAEEKPKR 82

                         90
                 ....*....|....
gi 914776599 728 GRKPAEQRQSSAGN 741
Cdd:COG1098   83 PPRPRRNSRPKAGF 96
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 639-716 2.47e-23

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: 102.04  E-value: 2.47e-23
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 914776599 639 EKISDLVPEMVLEGVVTNVTNFGAFVDI-GVhqDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:COG0539  182 ELLEKLEEGDVVEGTVKNITDFGAFVDLgGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLK 258
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 648-740 8.15e-23

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator.


Pssm-ID: 468553 [Multi-domain]  Cd Length: 113  Bit Score: 94.03  E-value: 8.15e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 648 MVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR-LDEKAGEQRG 726
Cdd:NF040579   5 DIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSLRaLEEAPEKHRK 84

                         90
                 ....*....|....
gi 914776599 727 PGRKPAEQRQSSAG 740
Cdd:NF040579  85 RRKHRWTNKRLKIG 98
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
648-716 1.17e-22

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 91.90  E-value: 1.17e-22
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 914776599   648 MVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:smart00316   4 DVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 646-713 1.58e-22

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: 91.54  E-value: 1.58e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 914776599 646 PEMVLEGVVTNVTNFGAFVDIGVhQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISL 713
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDLGG-VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISL 67
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 323-420 4.35e-22

Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.


Pssm-ID: 128971  Cd Length: 99  Bit Score: 91.47  E-value: 4.35e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599   323 TMGLDPGiRTGVKVAVVDATGKLVDHATIYPFepkKQVDQSLRTLNELCQKHKVELISIG-----NGTASRETDRLVSDL 397
Cdd:smart00732   3 VLGLDPG-RKGIGVAVVDETGKLADPLEVIPR---TNKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFAEL 78

                           90       100
                   ....*....|....*....|...
gi 914776599   398 FERYPaaKAQKIVVSEAGASVYS 420
Cdd:smart00732  79 LKERF--NLPVVLVDERLATVYA 99
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 649-716 2.08e-21

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: 88.50  E-value: 2.08e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 914776599 649 VLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDaPRKRISLTMR 716
Cdd:cd05692    3 VVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID-ARGRISLSIK 69
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 632-724 8.41e-21

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 95.33  E-value: 8.41e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 632 ATFKDGVEKISDLVPE-MVLEGVVTNVTNFGAFVDI--GVhqDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPR 708
Cdd:PRK06676 262 DTLPGPWEGVEEKLPEgDVIEGTVKRLTDFGAFVEVlpGV--EGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEE 339

                         90
                 ....*....|....*..
gi 914776599 709 KRISLTMR-LDEKAGEQ 724
Cdd:PRK06676 340 KRISLSIKaLEEAPAEE 356
PRK08059 PRK08059
general stress protein 13; Validated
 649-740 1.82e-20

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 87.79  E-value: 1.82e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 649 VLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMRLDEKAGEQRGPG 728
Cdd:PRK08059  10 VVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEAPEAKRKK 89

                         90
                 ....*....|..
gi 914776599 729 RKPAEQRQSSAG 740
Cdd:PRK08059  90 GKILIPNPSEQG 101
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 649-715 2.48e-20

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: 85.42  E-value: 2.48e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 914776599  649 VLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTM 715
Cdd:pfam00575   6 VVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 648-716 4.59e-20

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: 92.41  E-value: 4.59e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 914776599 648 MVLEGVVTNVTNFGAFVDI--GVhqDGLVHIS--SLTDRfIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:COG0539  276 DVVKGKVTRLTDFGAFVELepGV--EGLVHISemSWTKR-VAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 639-716 1.52e-19

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 91.48  E-value: 1.52e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 914776599 639 EKISDLVPEMVLEGVVTNVTNFGAFVDIG-VhqDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:PRK06676 185 ELLSSLKEGDVVEGTVARLTDFGAFVDIGgV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLK 261
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 638-716 3.32e-19

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


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 92.38  E-value: 3.32e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 638 VEKISDLVPE----MVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDaPRKRISL 713
Cdd:COG1185  604 IERIEGITAEpevgEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEID-DQGRIKL 682


                 ...
gi 914776599 714 TMR 716
Cdd:COG1185  683 SRK 685
PRK08582 PRK08582
RNA-binding protein S1;
650-745 4.35e-19

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 84.31  E-value: 4.35e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 650 LEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKrISLTMRldeKAGEQ-RGPG 728
Cdd:PRK08582   9 LQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGK-IGLSIK---KAKDRpKRQH 84

                         90
                 ....*....|....*..
gi 914776599 729 RKPAEQRQSSAGNSKPK 745
Cdd:PRK08582  85 DRPRHEDNRGGGNDVAP 101
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 650-714 6.57e-19

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: 81.27  E-value: 6.57e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 914776599 650 LEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLT 714
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PRK05807 PRK05807
RNA-binding protein S1;
649-746 7.24e-19

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 83.64  E-value: 7.24e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 649 VLEGVVTNVTNFGAFVDI-GvhQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDaPRKRISLTMRldeKAGEQRgP 727
Cdd:PRK05807   8 ILEGTVVNITNFGAFVEVeG--KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISLSIK---QAMKQK-K 80

                         90
                 ....*....|....*....
gi 914776599 728 GRKPAEQRQSSAGNSKPKS 746
Cdd:PRK05807  81 SVKPAEIDWQKEKNKNNNG 99
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 641-715 9.35e-19

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 90.61  E-value: 9.35e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 914776599 641 ISDLVPEMVLEGVVTNVTNFGAFVDIGVhQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTM 715
Cdd:PRK06299 196 LENLEEGQVVEGVVKNITDYGAFVDLGG-VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGL 269
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 638-716 1.13e-17

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 87.41  E-value: 1.13e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 638 VEKISDLV--PE--MVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDaPRKRISL 713
Cdd:PRK11824 609 KERIEGITaePEvgEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRL 687


                 ...
gi 914776599 714 TMR 716
Cdd:PRK11824 688 SRK 690
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
649-724 5.92e-17

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 85.00  E-value: 5.92e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 914776599 649 VLEGVVTNVTNFGAFVDI--GVhqDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR-LDEKAGEQ 724
Cdd:PRK00087 565 IVLGKVVRIAPFGAFVELepGV--DGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKeVEEEPGDI 641
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 639-716 2.41e-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: 82.86  E-value: 2.41e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 914776599  639 EKISDLVPEMVLEGVVTNVTNFGAFVDIGVhQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:TIGR00717 180 ELLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLK 256
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 649-713 4.39e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 82.13  E-value: 4.39e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 914776599 649 VLEGVVTNVTNFGAFVDIGVHQDGLVHISSLT-DRFIKDPREVVKAGDIVRVKVLEVDAPRKRISL 713
Cdd:PRK06299 376 VVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERISL 441
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 649-722 5.14e-16

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: 73.43  E-value: 5.14e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 914776599 649 VLEGVVTNVTNFGAFVDI---GVHQDGLVHISSLT-DRFIKDPREVVKAGDIVRVKVLEVDapRKRISLTMR-LDEKAG 722
Cdd:cd05684    3 IYKGKVTSIMDFGCFVQLeglKGRKEGLVHISQLSfEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMKdVDQDTG 79
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 649-716 6.08e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 81.24  E-value: 6.08e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 914776599 649 VLEGVVTNVTNFGAFVDIGvHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:PRK07899 211 VRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLK 277
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 649-715 6.23e-16

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: 72.58  E-value: 6.23e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 914776599 649 VLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDApRKRISLTM 715
Cdd:cd04472    3 IYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 570-716 1.25e-15

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 75.63  E-value: 1.25e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 570 PVVERILAQLQQQVENLLgnssllrglkpadytDERFG-VPTVTDI--IGEldkpGR----DP----RPEFKTATFKdgv 638
Cdd:PRK08563  21 DLEEAALEVLREKYEGRI---------------DKELGiIVAVLDVkvIGE----GKivpgDGatyhEVEFDALVFK--- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 639 ekisdlvPEM--VLEGVVTNVTNFGAFVDIGVhQDGLVHISSLTDRFI-----------KDPREVVKAGDIVRVKVLEV- 704
Cdd:PRK08563  79 -------PELqeVVEGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYIsydpkngrligKESKRVLKVGDVVRARIVAVs 150

                        170
                 ....*....|....*.
gi 914776599 705 -DAPRKR---ISLTMR 716
Cdd:PRK08563 151 lKERRPRgskIGLTMR 166
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 636-716 1.42e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 80.59  E-value: 1.42e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 636 DGVEKisDLVPEMVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLT-DRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLT 714
Cdd:PRK06299 278 EAIEK--KYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLG 355


                 ..
gi 914776599 715 MR 716
Cdd:PRK06299 356 LK 357
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
639-713 3.50e-15

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 79.61  E-value: 3.50e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 914776599 639 EKISDLVPEMVLEGVVTNVTNFGAFVDI-GVhqDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISL 713
Cdd:PRK00087 470 ETWNSLEEGDVVEGEVKRLTDFGAFVDIgGV--DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSL 543
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 649-716 1.45e-14

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


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 69.28  E-value: 1.45e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 914776599 649 VLEGVVTNVTNFGAFVDI-GVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:cd05708    5 KIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 492-545 9.21e-14

DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair];


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 66.81  E-value: 9.21e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 914776599 492 VDVNTASVALLNRVSGLSQTMAQNIVAYRDDNGAFRNRQQLLKVSRLGPKAFEQ 545
Cdd:COG1555   13 VDINTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGIGPKTLEK 66
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 639-716 4.87e-13

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 72.46  E-value: 4.87e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599  639 EKISDLVPE-MVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLT-DRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:TIGR00717 264 EAIEKKFPVgDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343
rpsA PRK13806
30S ribosomal protein S1; Provisional
 649-716 5.50e-13

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 72.06  E-value: 5.50e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 649 VLEGVVTNVTNFGAFVDIGVHQDGLVHIS--SLTDRFIKdPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:PRK13806 295 KVTGKVVRLAPFGAFVEILPGIEGLVHVSemSWTRRVNK-PEDVVAPGDAVAVKIKDIDPAKRRISLSLR 363
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 649-716 5.56e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 72.00  E-value: 5.56e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 914776599 649 VLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:PRK07899 296 IVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLK 363
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 640-715 8.73e-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: 64.15  E-value: 8.73e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 914776599 640 KISDLVPEMVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTM 715
Cdd:cd04461    8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 649-713 1.14e-12

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: 63.67  E-value: 1.14e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 914776599 649 VLEGVVTNVTNFGAFVDIGVHQDGLVHISSLT-DRFIKDPREVVKAGDIVRVKVLEVDAPRKRISL 713
Cdd:cd05690    3 VVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 649-716 1.89e-12

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


Pssm-ID: 239907 [Multi-domain]  Cd Length: 99  Bit Score: 63.85  E-value: 1.89e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 649 VLEGVVTNVTNFGAFVDIGvHQDGLVHISSLTDRFIK-DP----------REVVKAGDIVRVKVLEVDAP-----RKRIS 712
Cdd:cd04460    2 VVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISyDPknkrligeetKRVLKVGDVVRARIVAVSLKerrprESKIG 80


                 ....
gi 914776599 713 LTMR 716
Cdd:cd04460   81 LTMR 84
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 650-713 1.07e-11

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: 61.05  E-value: 1.07e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 914776599 650 LEGVVTNVTNFGAFVDIGVHQDGLVHISSL--TDRFIkDPREVVKAGDIVRVKVLEVDAPRKRISL 713
Cdd:cd05689    7 LFGKVTNLTDYGCFVELEEGVEGLVHVSEMdwTNKNI-HPSKVVSLGDEVEVMVLDIDEERRRISL 71
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 649-724 1.08e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 68.27  E-value: 1.08e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 914776599 649 VLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMRLDEKAGEQ 724
Cdd:PRK06299 463 IVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEAEEK 538
rpsA PRK13806
30S ribosomal protein S1; Provisional
 649-716 1.23e-11

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 67.83  E-value: 1.23e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 914776599 649 VLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRK----RISLTMR 716
Cdd:PRK13806 205 VVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIK 276
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 651-715 2.37e-11

S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.


Pssm-ID: 239917 [Multi-domain]  Cd Length: 83  Bit Score: 60.11  E-value: 2.37e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 914776599 651 EGVVTNVTNFGAFV---DIGVhqDGLVHISSLT-DRFIKDPRE----------VVKAGDIVRVKVLEVDAPRKRISLTM 715
Cdd:cd04471    6 DGVISGVTSFGLFVeldNLTV--EGLVHVSTLGdDYYEFDEENhalvgertgkVFRLGDKVKVRVVRVDLDRRKIDFEL 82
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 648-714 1.12e-10

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: 57.69  E-value: 1.12e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 914776599 648 MVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLT 714
Cdd:cd05707    2 DVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
VacB COG0557
Exoribonuclease R [Transcription];
638-715 1.20e-10

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 65.13  E-value: 1.20e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 638 VEKISDLVPEmVLEGVVTNVTNFGAFV---DIGVhqDGLVHISSLT-DRFIKDPRE----------VVKAGDIVRVKVLE 703
Cdd:COG0557  615 AEYMKDRVGE-EFEGVISGVTSFGLFVeldELGV--EGLVHVSSLGdDYYEYDERRqalvgertgkRYRLGDRVEVRVVR 691

                         90
                 ....*....|..
gi 914776599 704 VDAPRKRISLTM 715
Cdd:COG0557  692 VDLDRRQIDFEL 703
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 648-714 2.85e-10

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: 56.86  E-value: 2.85e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 914776599 648 MVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLT 714
Cdd:cd05697    2 QVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLT 68
HHH_7 pfam14635
Helix-hairpin-helix motif;
457-552 6.99e-10

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 56.78  E-value: 6.99e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599  457 DPKSIGVGQYQHDVGQSQLARRLDAVVEDCVNAVGVDVNTA-----SVALLNRVSGLSQTMAQNIV-AYRDDNGAFRNRQ 530
Cdd:pfam14635   2 DILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAiankyEAAILPYIAGLGPRKADHLLkILAANNGRLDNRS 81

                          90       100
                  ....*....|....*....|..
gi 914776599  531 QLLKVSRLGPKAFEQCAGFLRI 552
Cdd:pfam14635  82 QLITKCIMGPKVFMNCAGFLII 103
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 646-702 1.18e-09

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: 55.18  E-value: 1.18e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 646 PEM--VLEGVVTNVTNFGAFVDI-GVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVL 702
Cdd:cd05686    1 PALyqIFKGEVASVTEYGAFVKIpGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVI 60
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 648-716 1.26e-09

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: 54.95  E-value: 1.26e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 914776599 648 MVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:cd05706    5 DILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 649-713 4.16e-09

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: 59.75  E-value: 4.16e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 914776599  649 VLEGVVTNVTNFGAFVDIGVHQDGLVHISSLT-DRFIKDPREVVKAGDIVRVKVLEVDAPRKRISL 713
Cdd:TIGR00717 362 RVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRISL 427
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 618-716 4.94e-09

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 60.11  E-value: 4.94e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 618 LDKPGRDPRPEFKTATfkdgveKISDLVpemvlEGVVTNVTNFGAFVDIGVHqDGLVHISSLTDRFIKDPREVVKAGDIV 697
Cdd:PRK12269 476 LEERARQAREEFFNSV------HIEDSV-----SGVVKSFTSFGAFIDLGGF-DGLLHVNDMSWGHVARPREFVKKGQTI 543

                         90
                 ....*....|....*....
gi 914776599 698 RVKVLEVDAPRKRISLTMR 716
Cdd:PRK12269 544 ELKVIRLDQAEKRINLSLK 562
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 647-716 2.68e-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: 2.68e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 914776599 647 EMVLeGVVTNVTNFGAFVDIGVHQD--GLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:cd04452    5 ELVV-VTVKSIADMGAYVSLLEYGNieGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 652-716 4.02e-08

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 55.22  E-value: 4.02e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 914776599 652 GVVTNVTNFGAFVDI----GVhqDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:PRK03987  14 GTVKEVKDFGAFVTLdeypGK--EGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
650-719 4.26e-08

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 52.01  E-value: 4.26e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 914776599 650 LEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR-LDE 719
Cdd:PRK07252   7 LKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRtLEE 77
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 654-755 4.47e-08

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 56.83  E-value: 4.47e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 654 VTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVD------APRKRISLTMRLDEKAGEQR-G 726
Cdd:PLN00207 762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNdkgqlrLSRRALLPEANSEKSSQKQQgG 841

                         90       100
                 ....*....|....*....|....*....
gi 914776599 727 PGRKPAEQRQSSAGNSKPKSAAGNKPTPA 755
Cdd:PLN00207 842 STKDKAPQKKYVNTSSRPRRAAQAEKNSA 870
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 645-723 8.63e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 54.81  E-value: 8.63e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 645 VPEMVLeGVVTNVTNFGAFVDIGvHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISL-TMRLDEKAGE 723
Cdd:PRK07400 196 VGEVVV-GTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLsTKQLEPEPGD 273
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 652-716 1.39e-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: 49.15  E-value: 1.39e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 914776599 652 GVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:cd05698    6 GTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 649-705 2.26e-07

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


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 48.68  E-value: 2.26e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 914776599 649 VLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVD 705
Cdd:cd05687    3 IVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVE 59
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 492-545 9.39e-07

competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model. [Cellular processes, DNA transformation]


Pssm-ID: 129520 [Multi-domain]  Cd Length: 69  Bit Score: 46.85  E-value: 9.39e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 914776599  492 VDVNTASVALLNR-VSGLSQTMAQNIVAYRDDNGAFRNRQQLLKVSRLGPKAFEQ 545
Cdd:TIGR00426   8 VNINTATAEELQRaMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEK 62
rpsA PRK13806
30S ribosomal protein S1; Provisional
 651-774 2.44e-06

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 50.88  E-value: 2.44e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 651 EGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTmrldekageqrgpgrk 730
Cdd:PRK13806 384 TGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLA---------------- 447

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 914776599 731 PAEQRQSSAGNSKPKSAAGNKPTPAAPLGGAMGNAFAAALSKNK 774
Cdd:PRK13806 448 PAGAAGSGADDDDWKQFAPKKSAPASGGLGSLGQALQEAMKKKK 491
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 649-716 3.42e-06

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 50.50  E-value: 3.42e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 914776599  649 VLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:TIGR00717 449 VVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 634-725 4.34e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 49.87  E-value: 4.34e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 634 FKDGVEKISDLVPEMVLEGVVTNVTNFGAFVDI-GVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKris 712
Cdd:PRK06676   5 FEESLNSVKEVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEG--- 81

                         90
                 ....*....|...
gi 914776599 713 lTMRLDEKAGEQR 725
Cdd:PRK06676  82 -NLLLSKRRLEAE 93
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 649-719 9.49e-06

Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440713 [Multi-domain]  Cd Length: 191  Bit Score: 46.82  E-value: 9.49e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 649 VLEGVVTNVTNFGAFVDI----------GVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPrkrISLTMRLD 718
Cdd:COG1096   68 IVIGEVVDVRESMALVKIyaiegnerelPSSFSGIIHISQVSDSYVKDLSDEFRVGDIVRAKVISTLPP---IQLSIKEP 144


                 .
gi 914776599 719 E 719
Cdd:COG1096  145 D 145
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 652-716 1.15e-05

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


Pssm-ID: 240215 [Multi-domain]  Cd Length: 86  Bit Score: 44.08  E-value: 1.15e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 914776599 652 GVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFI----KDPREVVKAGDIVRVKVLEVDaPRKRISLTMR 716
Cdd:cd05789   12 GRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTdedeLNMRSYLDEGDLIVAEVQSVD-SDGSVSLHTR 79
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
649-722 1.47e-05

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 48.40  E-value: 1.47e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 914776599 649 VLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLT-MRLDEKAG 722
Cdd:PRK00087 305 IVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSkKEADREKA 379
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 641-696 1.62e-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: 43.36  E-value: 1.62e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 914776599 641 ISDLVPEMVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDI 696
Cdd:cd04473   11 MEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDYEVGDEVIVQVTDI 66
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 337-452 2.27e-05

Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage


Pssm-ID: 258777  Cd Length: 150  Bit Score: 45.24  E-value: 2.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599  337 AVVDATGKLVDHATIY--PFEPKKQvDQSLRTLNELCQKHKVELISIgNGTaSRETDRLVSDLfERYPAAKAQK------ 408
Cdd:pfam14639  24 VLVNGEGEVTDFLKLAwrEFDRENK-AQFEETLKKFLLSKKPHVIGV-SGE-NRDAQKFYEDV-QRVLHELEQDsrlhti 99

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 914776599  409 --IVVSEAGASVYSASELASQEFPDLDVSIRGAVSIARRLQDPLAE 452
Cdd:pfam14639 100 gvILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLE 145
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 641-704 2.79e-05

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


Pssm-ID: 440724 [Multi-domain]  Cd Length: 626  Bit Score: 47.52  E-value: 2.79e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 914776599 641 ISDLVPEMVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFikdprevvKAGDIVRVKVLEV 704
Cdd:COG1107   34 PDDLEPGRYYRGTVDGVADFGVFVDLNDHVTGLLHRSELDQDW--------EVGDEVFVQVKEV 89
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 649-716 3.88e-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: 42.26  E-value: 3.88e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 914776599 649 VLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:cd05691    3 IVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
PRK11642 PRK11642
ribonuclease R;
649-775 5.20e-05

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 46.66  E-value: 5.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 649 VLEGVVTNVTNFGAFVDIG-VHQDGLVHISSLTD----------RFIKDPR-EVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:PRK11642 646 VFKGVISSVTGFGFFVRLDdLFIDGLVHVSSLDNdyyrfdqvgqRLIGESSgQTYRLGDRVEVRVEAVNMDERKIDFSLI 725

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 717 LDEKAgeQRGPGRKPAEQ-RQSSAGNSKPKSAAGNKPTPAAPLGGAMGNAFAAALSKNKK 775
Cdd:PRK11642 726 SSERA--PRNVGKTAREKaKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKD 783
PRK04163 PRK04163
exosome complex protein Rrp4;
640-716 1.27e-04

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 44.11  E-value: 1.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 640 KISDLVPemvleGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFI----KDPREVVKAGDIVRVKVLEVDaPRKRISLTM 715
Cdd:PRK04163  62 KVGDLVI-----GKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVnvegTDLRKYLDIGDYIIAKVKDVD-RTRDVVLTL 135


                 .
gi 914776599 716 R 716
Cdd:PRK04163 136 K 136
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 639-705 1.29e-04

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: 45.04  E-value: 1.29e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 914776599 639 EKISDLVPEMVLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDrfikDPREV-VKAGDIVRVKVLEVD 705
Cdd:COG0539   11 ESLKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSD----EPGELeVKVGDEVEVYVEKVE 74
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 649-716 1.55e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 45.47  E-value: 1.55e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 914776599 649 VLEGVVTNVTNFGAFVDIGVHQDGLVHISSLT-DRFIKDPREVVKAGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:PRK12269 581 VVKGRVTKIADFGAFIELAEGIEGLAHISEFSwVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLK 649
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 649-716 7.19e-04

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: 38.59  E-value: 7.19e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 914776599 649 VLEGVVTNVTNFGAFVDI-GVhqDGLVHISSLTDRFIKDPREVVkaGDIVRVKVLEVDAPRKRISLTMR 716
Cdd:cd04465    3 IVEGKVTEKVKGGLIVDIeGV--RAFLPASQVDLRPVEDLDEYV--GKELKFKIIEIDRERNNIVLSRR 67
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 649-725 1.31e-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: 41.57  E-value: 1.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914776599 649 VLEGVVTNVTNFGAFVDI-GVhqDGLVHISSLTDRFIKDPREVVkaGDIVRVKVLEVDAPRKRISLTMR--LDEKAGEQR 725
Cdd:COG0539  105 PVEGKVKGVVKGGLIVDIgGV--RAFLPASQVDVRPVRDLDEYV--GKTLEFKIIKLDRKRNNVVVSRRavLEEEREEKR 180
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 644-716 2.08e-03

S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 239901 [Multi-domain]  Cd Length: 82  Bit Score: 37.91  E-value: 2.08e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 914776599 644 LVPEM--VLEGVVTNVTNFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLEVDaPRKRISLTMR 716
Cdd:cd04454    2 YLPDVgdIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLG-DDMNVLLTTA 75
RuvC cd16962
Crossover junction endodeoxyribonuclease RuvC; Crossover junction endodeoxyribonuclease RuvC ...
 324-381 3.12e-03

Crossover junction endodeoxyribonuclease RuvC; Crossover junction endodeoxyribonuclease RuvC is also called Holliday junction resolvase RuvC. It is part of the RuvABC pathway in Escherichia coli and other Gram-negative bacteria that is involved in processing Holliday junctions, which are formed by the reciprocal exchange of strands between two DNA duplexes. Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. RuvC is thought to bind either on the open, DNA exposed face of a single RuvA tetramer, or to replace one of the two tetramers. Binding is proposed to be mediated by an unstructured loop on RuvC, which becomes structured on binding RuvA. RuvC can be bound to the complex in either orientation, therefore resolving Holliday junctions in either a horizontal or vertical manner. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the Escherichia coli HJR. RuvC and its orthologs are homodimers and display structural similarity to RNase H and Hsp70.


Pssm-ID: 438562  Cd Length: 152  Bit Score: 38.95  E-value: 3.12e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 914776599 324 MGLDPGIR-TGvkVAVVDATG---KLVDHATIypfEPKKQVDQSLR------TLNELCQKHKVELISI 381
Cdd:cd16962    2 LGIDPGLRrTG--YGVIEVEGnklRLLDYGVI---RTPSKLSLPERlkeiydGLSELIEKYKPDEVAI 64
S1_RNAPII_Rpb7 cd04462
S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. ...
 649-706 3.45e-03

S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.


Pssm-ID: 239909 [Multi-domain]  Cd Length: 88  Bit Score: 37.24  E-value: 3.45e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 914776599 649 VLEGVVTNVTNFGAFVDIGVHQdglVHIS--SLTDRFIKDP-----------REVVKAGDIVRVKV--LEVDA 706
Cdd:cd04462    4 VVDAIVTSVNKTGFFAEVGPLS---IFISrhLIPSDMEFDPnasppcftsneDIVIKKDTEVRLKIigTRVDA 73
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 644-703 5.14e-03

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: 36.18  E-value: 5.14e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 914776599 644 LVPEMVLEGVVTNVT-NFGAFVDIGVHQDGLVHISSLTDRFIKDPREVVKAGDIVRVKVLE 703
Cdd:cd05704    1 LEEGAVTLGMVTKVIpHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILS 61
 
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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