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Conserved domains on  [gi|695750501|ref|WP_032676758|]
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Tex family protein [Enterobacter hormaechei]

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];
2-727 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


:

Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1382.43  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501   2 MKESLCRIIAGDIQARAEQVEAAVRLLDEGNTVPFIARYRKEVTGGLDDTQLRNLETRLGYLRELEDRRQAILKSIGEQG 81
Cdd:COG2183    1 MMMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501  82 KLTSDLEKAINGTLSKTELEDLYLPYKPKRRTRGQIAIEAGLEPLADLLWNEPSHDPETEAAKFIDAEKGVADTKAALDG 161
Cdd:COG2183   81 KLTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEEKGVADVEAALDG 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 162 ARYILMERFAEDAALLAKVRDYLWKNAHIVSTVVSGKEDEGAKFRDYFDHHEPISTAPSHRALAMFRGRNEGVLQLSLNA 241
Cdd:COG2183  161 ARDILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEP 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 242 DPQFdeppkeshCEQIIIDHLgLRLNNAPADSWRKGVVSWTWRIKVLMHLETELMGTVRERAEDEAINVFARNLHDLLMA 321
Cdd:COG2183  241 DEEE--------AEAYIARRF-IKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLA 311

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 322 APAGLRATMGLDPGLRTGVKVAVVDGTGKLVATDTIYPHTGQAAKA--AVVVAALCEKYNVELVAIGNGTASRETERFYL 399
Cdd:COG2183  312 APAGGKVVLGLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEeaAKTLAALIKKYKVELIAIGNGTASRETEQFVA 391

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 400 DVQKQFPKvTAQKVIVSEAGASVYSASELAAQEFPELDVSLRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVSQTQL 479
Cdd:COG2183  392 ELIKELDL-KVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKL 470

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 480 ARKLDAVVEDCVNAVGVDLNTASVPLLTRVAGLTRMMAQNIVAWRDENGQFQNRQQLLKVSRLGPKAFEQCAGFLRINHG 559
Cdd:COG2183  471 KRSLDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDG 550

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 560 DNPLDASTVHPEAYPVVERILAATQQALKDVMGDSSALRNLKAVDFTDEQFGVPTVTDIIKELEKPGRDPRPEFKTATFA 639
Cdd:COG2183  551 DNPLDNSAVHPESYPVVEKILKDLGVSVKDLIGNKELLKKLDPEKYADELFGLPTLRDILKELEKPGRDPRPEFKTPTFR 630

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 640 DGVETMNDLLPGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTM 719
Cdd:COG2183  631 EGVLKIEDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSM 710


                 ....*...
gi 695750501 720 RLDEQPGD 727
Cdd:COG2183  711 KLDDEAGA 718
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
2-727 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1382.43  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501   2 MKESLCRIIAGDIQARAEQVEAAVRLLDEGNTVPFIARYRKEVTGGLDDTQLRNLETRLGYLRELEDRRQAILKSIGEQG 81
Cdd:COG2183    1 MMMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501  82 KLTSDLEKAINGTLSKTELEDLYLPYKPKRRTRGQIAIEAGLEPLADLLWNEPSHDPETEAAKFIDAEKGVADTKAALDG 161
Cdd:COG2183   81 KLTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEEKGVADVEAALDG 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 162 ARYILMERFAEDAALLAKVRDYLWKNAHIVSTVVSGKEDEGAKFRDYFDHHEPISTAPSHRALAMFRGRNEGVLQLSLNA 241
Cdd:COG2183  161 ARDILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEP 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 242 DPQFdeppkeshCEQIIIDHLgLRLNNAPADSWRKGVVSWTWRIKVLMHLETELMGTVRERAEDEAINVFARNLHDLLMA 321
Cdd:COG2183  241 DEEE--------AEAYIARRF-IKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLA 311

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 322 APAGLRATMGLDPGLRTGVKVAVVDGTGKLVATDTIYPHTGQAAKA--AVVVAALCEKYNVELVAIGNGTASRETERFYL 399
Cdd:COG2183  312 APAGGKVVLGLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEeaAKTLAALIKKYKVELIAIGNGTASRETEQFVA 391

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 400 DVQKQFPKvTAQKVIVSEAGASVYSASELAAQEFPELDVSLRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVSQTQL 479
Cdd:COG2183  392 ELIKELDL-KVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKL 470

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 480 ARKLDAVVEDCVNAVGVDLNTASVPLLTRVAGLTRMMAQNIVAWRDENGQFQNRQQLLKVSRLGPKAFEQCAGFLRINHG 559
Cdd:COG2183  471 KRSLDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDG 550

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 560 DNPLDASTVHPEAYPVVERILAATQQALKDVMGDSSALRNLKAVDFTDEQFGVPTVTDIIKELEKPGRDPRPEFKTATFA 639
Cdd:COG2183  551 DNPLDNSAVHPESYPVVEKILKDLGVSVKDLIGNKELLKKLDPEKYADELFGLPTLRDILKELEKPGRDPRPEFKTPTFR 630

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 640 DGVETMNDLLPGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTM 719
Cdd:COG2183  631 EGVLKIEDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSM 710


                 ....*...
gi 695750501 720 RLDEQPGD 727
Cdd:COG2183  711 KLDDEAGA 718
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 10-194 2.92e-104

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: 317.42  E-value: 2.92e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501   10 IAGDIQARAEQVEAAVRLLDEGNTVPFIARYRKEVTGGLDDTQLRNLETRLGYLRELEDRRQAILKSIGEQGKLTSDLEK 89
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501   90 AINGTLSKTELEDLYLPYKPKRRTRGQIAIEAGLEPLADLLWNEPshDPETEAAKFIDAEKGVADTKAALDGARYILMER 169
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQP--DPEEEAAKYINPEKGVADVEEALAGARDIIAER 158

                         170       180
                  ....*....|....*....|....*
gi 695750501  170 FAEDAALLAKVRDYLWKNAHIVSTV 194
Cdd:pfam09371 159 ISEDAELRKKLRELLWREGVIVSKV 183
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 651-718 2.90e-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: 127.73  E-value: 2.90e-35
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALT 718
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
650-720 3.47e-23

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 93.44  E-value: 3.47e-23
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 695750501   650 PGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 643-726 3.40e-21

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 96.48  E-value: 3.40e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 643 ETMNDLLPGMVLEGAVTNVTNFGAFVDIG-VhqDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMRl 721
Cdd:PRK06676 185 ELLSSLKEGDVVEGTVARLTDFGAFVDIGgV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLK- 261


                 ....*
gi 695750501 722 DEQPG 726
Cdd:PRK06676 262 DTLPG 266
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 651-725 2.17e-20

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: 87.10  E-value: 2.17e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR-LDEQP 725
Cdd:NF040579   4 GDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSLRaLEEAP 79
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 643-725 1.01e-15

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: 80.93  E-value: 1.01e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501  643 ETMNDLLPGMVLEGAVTNVTNFGAFVDIGVhQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR-L 721
Cdd:TIGR00717 180 ELLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKqL 258


                  ....
gi 695750501  722 DEQP 725
Cdd:TIGR00717 259 GEDP 262
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
2-727 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1382.43  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501   2 MKESLCRIIAGDIQARAEQVEAAVRLLDEGNTVPFIARYRKEVTGGLDDTQLRNLETRLGYLRELEDRRQAILKSIGEQG 81
Cdd:COG2183    1 MMMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501  82 KLTSDLEKAINGTLSKTELEDLYLPYKPKRRTRGQIAIEAGLEPLADLLWNEPSHDPETEAAKFIDAEKGVADTKAALDG 161
Cdd:COG2183   81 KLTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEEKGVADVEAALDG 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 162 ARYILMERFAEDAALLAKVRDYLWKNAHIVSTVVSGKEDEGAKFRDYFDHHEPISTAPSHRALAMFRGRNEGVLQLSLNA 241
Cdd:COG2183  161 ARDILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEP 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 242 DPQFdeppkeshCEQIIIDHLgLRLNNAPADSWRKGVVSWTWRIKVLMHLETELMGTVRERAEDEAINVFARNLHDLLMA 321
Cdd:COG2183  241 DEEE--------AEAYIARRF-IKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLA 311

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 322 APAGLRATMGLDPGLRTGVKVAVVDGTGKLVATDTIYPHTGQAAKA--AVVVAALCEKYNVELVAIGNGTASRETERFYL 399
Cdd:COG2183  312 APAGGKVVLGLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEeaAKTLAALIKKYKVELIAIGNGTASRETEQFVA 391

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 400 DVQKQFPKvTAQKVIVSEAGASVYSASELAAQEFPELDVSLRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVSQTQL 479
Cdd:COG2183  392 ELIKELDL-KVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKL 470

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 480 ARKLDAVVEDCVNAVGVDLNTASVPLLTRVAGLTRMMAQNIVAWRDENGQFQNRQQLLKVSRLGPKAFEQCAGFLRINHG 559
Cdd:COG2183  471 KRSLDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDG 550

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 560 DNPLDASTVHPEAYPVVERILAATQQALKDVMGDSSALRNLKAVDFTDEQFGVPTVTDIIKELEKPGRDPRPEFKTATFA 639
Cdd:COG2183  551 DNPLDNSAVHPESYPVVEKILKDLGVSVKDLIGNKELLKKLDPEKYADELFGLPTLRDILKELEKPGRDPRPEFKTPTFR 630

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 640 DGVETMNDLLPGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTM 719
Cdd:COG2183  631 EGVLKIEDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSM 710


                 ....*...
gi 695750501 720 RLDEQPGD 727
Cdd:COG2183  711 KLDDEAGA 718
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 10-194 2.92e-104

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: 317.42  E-value: 2.92e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501   10 IAGDIQARAEQVEAAVRLLDEGNTVPFIARYRKEVTGGLDDTQLRNLETRLGYLRELEDRRQAILKSIGEQGKLTSDLEK 89
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501   90 AINGTLSKTELEDLYLPYKPKRRTRGQIAIEAGLEPLADLLWNEPshDPETEAAKFIDAEKGVADTKAALDGARYILMER 169
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQP--DPEEEAAKYINPEKGVADVEEALAGARDIIAER 158

                         170       180
                  ....*....|....*....|....*
gi 695750501  170 FAEDAALLAKVRDYLWKNAHIVSTV 194
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 ...
 328-451 2.01e-68

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: 221.12  E-value: 2.01e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501  328 ATMGLDPGLRTGVKVAVVDGTGKLVATDTIYPHTGQAAKAAVVV--AALCEKYNVELVAIGNGTASRETERFYLDVQKQF 405
Cdd:pfam16921   1 VVLGLDPGYRTGCKLAVVDETGKVLDTAVIYPHPPQNKVEEAKKklKKLIKKYGVELIAIGNGTASRETEQFVAELIKEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 695750501  406 PKvTAQKVIVSEAGASVYSASELAAQEFPELDVSLRGAVSIARRLQ 451
Cdd:pfam16921  81 PL-KVKYVIVSEAGASVYSASELAREEFPDLDVSLRGAVSIARRLQ 125
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 651-718 2.90e-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: 127.73  E-value: 2.90e-35
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALT 718
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 493-554 1.02e-30

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


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 114.50  E-value: 1.02e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 695750501  493 AVGVDLNTASVPLLTRVAGLTRMMAQNIVAWRDENGQFQNRQQLLKVSRLGPKAFEQCAGFL 554
Cdd:pfam12836   1 AVGVDINTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKTFEQLAGFL 62
HHH_9 pfam17674
HHH domain;
561-630 3.62e-29

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 110.32  E-value: 3.62e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501  561 NPLDASTVHPEAYPVVERILAATQQALKDVMGDSSALRNLKAVDFTDEQFGVPTVTDIIKELEKPGRDPR 630
Cdd:pfam17674   1 NPLDNTAIHPESYPLAEKILKDLGLDLKDLIGNSALLKKLDPKKLAEEEVGLPTLKDILEELAKPGRDPR 70
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
650-720 3.47e-23

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 93.44  E-value: 3.47e-23
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 695750501   650 PGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 651-720 7.04e-23

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: 92.73  E-value: 7.04e-23
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDlQRKRIALTMR 720
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID-ARGRISLSIK 69
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 651-719 9.56e-23

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: 92.35  E-value: 9.56e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 695750501  651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTM 719
Cdd:pfam00575   4 GDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 651-725 1.32e-22

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 94.09  E-value: 1.32e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDlQRKRIALTMR-LDEQP 725
Cdd:COG1098    6 GDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSID-EDGKISLSIKqAEEKP 80
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 643-725 1.47e-22

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: 99.73  E-value: 1.47e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 643 ETMNDLLPGMVLEGAVTNVTNFGAFVDI-GVhqDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR- 720
Cdd:COG0539  182 ELLEKLEEGDVVEGTVKNITDFGAFVDLgGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKq 259


                 ....*
gi 695750501 721 LDEQP 725
Cdd:COG0539  260 LQPDP 264
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 327-424 1.62e-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: 92.63  E-value: 1.62e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501   327 RATMGLDPGlRTGVKVAVVDGTGKLVATDTIYPHTgQAAKAAVVVAALCEKYNVELVAIG-----NGTASRETERFYLDV 401
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVIPRT-NKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFAEL 78

                           90       100
                   ....*....|....*....|...
gi 695750501   402 QKQFPKVtaQKVIVSEAGASVYS 424
Cdd:smart00732  79 LKERFNL--PVVLVDERLATVYA 99
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 643-726 3.40e-21

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 96.48  E-value: 3.40e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 643 ETMNDLLPGMVLEGAVTNVTNFGAFVDIG-VhqDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMRl 721
Cdd:PRK06676 185 ELLSSLKEGDVVEGTVARLTDFGAFVDIGgV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLK- 261


                 ....*
gi 695750501 722 DEQPG 726
Cdd:PRK06676 262 DTLPG 266
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 650-717 5.36e-21

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: 87.30  E-value: 5.36e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 695750501 650 PGMVLEGAVTNVTNFGAFVDIGVhQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIAL 717
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDLGG-VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISL 67
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 650-720 1.14e-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: 94.34  E-value: 1.14e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 695750501 650 PGMVLEGAVTNVTNFGAFVDI--GVhqDGLVHISSLA-DKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:COG0539  274 VGDVVKGKVTRLTDFGAFVELepGV--EGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 651-725 2.17e-20

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: 87.10  E-value: 2.17e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR-LDEQP 725
Cdd:NF040579   4 GDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSLRaLEEAP 79
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 640-725 1.19e-19

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 91.86  E-value: 1.19e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 640 DGVEtmNDLLPGMVLEGAVTNVTNFGAFVDI--GVhqDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIAL 717
Cdd:PRK06676 269 EGVE--EKLPEGDVIEGTVKRLTDFGAFVEVlpGV--EGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISL 344


                 ....*....
gi 695750501 718 TMR-LDEQP 725
Cdd:PRK06676 345 SIKaLEEAP 353
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 650-720 1.44e-18

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


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 90.45  E-value: 1.44e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 695750501 650 PGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDlQRKRIALTMR 720
Cdd:COG1185  616 VGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEID-DQGRIKLSRK 685
PRK08582 PRK08582
RNA-binding protein S1;
651-762 1.90e-18

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 82.39  E-value: 1.90e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDlQRKRIALTMRldeqpgdtna 730
Cdd:PRK08582   6 GSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE-DDGKIGLSIK---------- 74

                         90       100       110
                 ....*....|....*....|....*....|..
gi 695750501 731 rrggngggREQQRPAAKAAKPRGRDAQPAGNS 762
Cdd:PRK08582  75 --------KAKDRPKRQHDRPRHEDNRGGGND 98
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 651-720 8.66e-18

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 87.80  E-value: 8.66e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDlQRKRIALTMR 720
Cdd:PRK11824 622 GEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSRK 690
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 654-718 9.32e-18

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: 77.81  E-value: 9.32e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 695750501 654 LEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALT 718
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
651-728 1.21e-17

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 87.31  E-value: 1.21e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 651 GMVLEGAVTNVTNFGAFVDI--GVhqDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR-LDEQPGD 727
Cdd:PRK00087 563 GSIVLGKVVRIAPFGAFVELepGV--DGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKeVEEEPGD 640


                 .
gi 695750501 728 T 728
Cdd:PRK00087 641 I 641
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 651-719 1.24e-17

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


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 77.58  E-value: 1.24e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDlQRKRIALTM 719
Cdd:cd04472    1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD-DRGRISLSR 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 643-719 1.25e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 87.14  E-value: 1.25e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 695750501 643 ETMNDLLPGMVLEGAVTNVTNFGAFVDIGVhQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTM 719
Cdd:PRK06299 194 ELLENLEEGQVVEGVVKNITDYGAFVDLGG-VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGL 269
PRK08059 PRK08059
general stress protein 13; Validated
 651-753 5.40e-17

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 77.78  E-value: 5.40e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMRldeqpgdtnA 730
Cdd:PRK08059   8 GSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR---------A 78

                         90       100
                 ....*....|....*....|...
gi 695750501 731 RRGGNGGGREQQRPAAKAAKPRG 753
Cdd:PRK08059  79 TEEAPEAKRKKGKILIPNPSEQG 101
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
643-717 1.71e-16

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 83.84  E-value: 1.71e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 695750501 643 ETMNDLLPGMVLEGAVTNVTNFGAFVDI-GVhqDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIAL 717
Cdd:PRK00087 470 ETWNSLEEGDVVEGEVKRLTDFGAFVDIgGV--DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSL 543
PRK05807 PRK05807
RNA-binding protein S1;
651-720 5.96e-16

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 75.17  E-value: 5.96e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 695750501 651 GMVLEGAVTNVTNFGAFVDI-GvhQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDlQRKRIALTMR 720
Cdd:PRK05807   6 GSILEGTVVNITNFGAFVEVeG--KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISLSIK 73
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 643-720 6.15e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 81.24  E-value: 6.15e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 695750501 643 ETMNDLLPGMVLEGAVTNVTNFGAFVDIGvHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:PRK07899 201 EFLNQLQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLK 277
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 643-725 1.01e-15

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: 80.93  E-value: 1.01e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501  643 ETMNDLLPGMVLEGAVTNVTNFGAFVDIGVhQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR-L 721
Cdd:TIGR00717 180 ELLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKqL 258


                  ....
gi 695750501  722 DEQP 725
Cdd:TIGR00717 259 GEDP 262
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 650-720 2.27e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 79.70  E-value: 2.27e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 695750501 650 PGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLK 363
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 650-725 5.41e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 78.67  E-value: 5.41e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 695750501 650 PGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLA-DKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTM-RLDEQP 725
Cdd:PRK06299 373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIkQLEEDP 450
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 651-720 6.00e-15

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: 70.35  E-value: 6.00e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 695750501 651 GMVLEGAVTNVTNFGAFVDI---GVHQDGLVHISSL-ADKFVEDPHTVVKAGDIVKVKVLEVdlQRKRIALTMR 720
Cdd:cd05684    1 GKIYKGKVTSIMDFGCFVQLeglKGRKEGLVHISQLsFEGRVANPSDVVKRGQKVKVKVISI--QNGKISLSMK 72
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 651-720 3.00e-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: 68.12  E-value: 3.00e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 695750501 651 GMVLEGAVTNVTNFGAFVDI-GVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:cd05708    3 GQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 650-720 4.13e-14

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 75.54  E-value: 4.13e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 695750501  650 PGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLA-DKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:TIGR00717 272 VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 650-720 1.93e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 73.66  E-value: 1.93e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 695750501 650 PGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLA-DKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:PRK06299 286 VGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLK 357
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 645-727 3.80e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 70.98  E-value: 3.80e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 645 MNDLLPGMVLEGAVTNVTNFGAFVDIGvHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIAL-TMRLDE 723
Cdd:PRK07400 191 MNRLEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLsTKQLEP 269


                 ....
gi 695750501 724 QPGD 727
Cdd:PRK07400 270 EPGD 273
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 653-726 4.10e-13

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 68.31  E-value: 4.10e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 653 VLEGAVTNVTNFGAFVDIGVhQDGLVHISSLADKFV-----------EDPHTVVKAGDIVKVKVLEVDL-----QRKRIA 716
Cdd:PRK08563  84 VVEGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYIsydpkngrligKESKRVLKVGDVVRARIVAVSLkerrpRGSKIG 162

                         90
                 ....*....|
gi 695750501 717 LTMRldeQPG 726
Cdd:PRK08563 163 LTMR---QPG 169
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 651-717 1.49e-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: 63.28  E-value: 1.49e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLA-DKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIAL 717
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 496-549 3.32e-12

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


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 62.19  E-value: 3.32e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 695750501 496 VDLNTASVPLLTRVAGLTRMMAQNIVAWRDENGQFQNRQQLLKVSRLGPKAFEQ 549
Cdd:COG1555   13 VDINTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGIGPKTLEK 66
rpsA PRK13806
30S ribosomal protein S1; Provisional
 650-720 4.33e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 69.37  E-value: 4.33e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 695750501 650 PGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLA-DKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:PRK13806 292 AGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR 363
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 653-726 7.20e-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: 62.30  E-value: 7.20e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 653 VLEGAVTNVTNFGAFVDIGvHQDGLVHISSLADKFVE-DPHT----------VVKAGDIVKVKVLEVDL-----QRKRIA 716
Cdd:cd04460    2 VVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISyDPKNkrligeetkrVLKVGDVVRARIVAVSLkerrpRESKIG 80

                         90
                 ....*....|
gi 695750501 717 LTMRldeQPG 726
Cdd:cd04460   81 LTMR---QPG 87
rpsA PRK13806
30S ribosomal protein S1; Provisional
 645-728 9.25e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 68.21  E-value: 9.25e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 645 MNDLLPGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRK----RIALTMR 720
Cdd:PRK13806 197 METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIK 276


                 ....*....
gi 695750501 721 -LDEQPGDT 728
Cdd:PRK13806 277 qAGGDPWDT 285
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 644-719 1.01e-11

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 61.45  E-value: 1.01e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 695750501 644 TMNDLLPGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTM 719
Cdd:cd04461    8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 651-719 1.99e-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: 60.49  E-value: 1.99e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 651 GMVLEGAVTNVTNFGAFV---DIGVhqDGLVHISSLAD---KFVEDPHTVV--------KAGDIVKVKVLEVDLQRKRIA 716
Cdd:cd04471    2 GEEFDGVISGVTSFGLFVeldNLTV--EGLVHVSTLGDdyyEFDEENHALVgertgkvfRLGDKVKVRVVRVDLDRRKID 79


                 ...
gi 695750501 717 LTM 719
Cdd:cd04471   80 FEL 82
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 619-724 2.63e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 66.73  E-value: 2.63e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 619 IKELEKpgrDPRPEFktatfadgvETMNDllPGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAG 698
Cdd:PRK06299 443 IKQLEE---DPFEEF---------AKKHK--KGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVG 508

                         90       100
                 ....*....|....*....|....*..
gi 695750501 699 DIVKVKVLEVDLQRKRIALTMR-LDEQ 724
Cdd:PRK06299 509 DEVEAKVINIDRKNRRISLSIKaLDEA 535
VacB COG0557
Exoribonuclease R [Transcription];
651-719 4.29e-11

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 66.28  E-value: 4.29e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 651 GMVLEGAVTNVTNFGAFV---DIGVhqDGLVHISSLAD---KFVEDPHTVV--------KAGDIVKVKVLEVDLQRKRIA 716
Cdd:COG0557  623 GEEFEGVISGVTSFGLFVeldELGV--EGLVHVSSLGDdyyEYDERRQALVgertgkryRLGDRVEVRVVRVDLDRRQID 700


                 ...
gi 695750501 717 LTM 719
Cdd:COG0557  701 FEL 703
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 651-717 5.32e-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: 59.13  E-value: 5.32e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSL--ADKFVEdPHTVVKAGDIVKVKVLEVDLQRKRIAL 717
Cdd:cd05689    4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMdwTNKNIH-PSKVVSLGDEVEVMVLDIDEERRRISL 71
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 651-718 1.10e-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: 58.02  E-value: 1.10e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALT 718
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLT 68
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 648-720 1.59e-10

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: 57.65  E-value: 1.59e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 695750501 648 LLPGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:cd05706    1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 651-725 1.64e-10

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: 64.37  E-value: 1.64e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 695750501  651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLA-DKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR-LDEQP 725
Cdd:TIGR00717 360 GDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKqLTENP 436
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 653-719 3.49e-10

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: 56.72  E-value: 3.49e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 695750501 653 VLEGAVTNVTNFGAFVDI-GVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKrIALTM 719
Cdd:cd05686    6 IFKGEVASVTEYGAFVKIpGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDK-MKLSL 72
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 651-718 1.03e-09

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: 54.99  E-value: 1.03e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALT 718
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
HHH_7 pfam14635
Helix-hairpin-helix motif;
461-556 2.41e-09

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 55.24  E-value: 2.41e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501  461 DPKSIGVGQYQHDVSQTQLARKLDAVVEDCVNAVGVDLNTA-----SVPLLTRVAGLTRMMAQNIV-AWRDENGQFQNRQ 534
Cdd:pfam14635   2 DILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAiankyEAAILPYIAGLGPRKADHLLkILAANNGRLDNRS 81

                          90       100
                  ....*....|....*....|..
gi 695750501  535 QLLKVSRLGPKAFEQCAGFLRI 556
Cdd:pfam14635  82 QLITKCIMGPKVFMNCAGFLII 103
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
654-724 4.61e-08

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 52.01  E-value: 4.61e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 695750501 654 LEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR-LDEQ 724
Cdd:PRK07252   7 LKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRtLEEE 78
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 638-721 7.29e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 55.27  E-value: 7.29e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 638 FADGVETMNDLLPGMVLEGAVTNVTNFGAFVDI-GVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIA 716
Cdd:PRK06676   5 FEESLNSVKEVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLL 84


                 ....*
gi 695750501 717 LTMRL 721
Cdd:PRK06676  85 LSKRR 89
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 651-720 1.29e-07

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: 55.13  E-value: 1.29e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501  651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:TIGR00717 447 GSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 651-720 2.40e-07

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


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 48.38  E-value: 2.40e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 620-720 4.78e-07

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 53.56  E-value: 4.78e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 620 KELEKPGRDPRPEF-KTATFADGVEtmndllpgmvleGAVTNVTNFGAFVDIGVHqDGLVHISSLADKFVEDPHTVVKAG 698
Cdd:PRK12269 474 RYLEERARQAREEFfNSVHIEDSVS------------GVVKSFTSFGAFIDLGGF-DGLLHVNDMSWGHVARPREFVKKG 540

                         90       100
                 ....*....|....*....|..
gi 695750501 699 DIVKVKVLEVDLQRKRIALTMR 720
Cdd:PRK12269 541 QTIELKVIRLDQAEKRINLSLK 562
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 644-700 1.02e-06

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: 46.83  E-value: 1.02e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 695750501 644 TMNDLLPGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDI 700
Cdd:cd04473   10 TMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDYEVGDEVIVQVTDI 66
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 651-709 1.03e-06

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


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 46.75  E-value: 1.03e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVD 709
Cdd:cd05687    1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVE 59
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 651-720 1.11e-06

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


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 46.81  E-value: 1.11e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQD--GLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:cd04452    4 GELVVVTVKSIADMGAYVSLLEYGNieGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 650-720 1.29e-06

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 50.59  E-value: 1.29e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 695750501 650 PGMVLEGAVTNVTNFGAFVDI----GVhqDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:PRK03987   8 EGELVVGTVKEVKDFGAFVTLdeypGK--EGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 496-549 4.13e-06

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: 44.92  E-value: 4.13e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 695750501  496 VDLNTASVPLLTR-VAGLTRMMAQNIVAWRDENGQFQNRQQLLKVSRLGPKAFEQ 549
Cdd:TIGR00426   8 VNINTATAEELQRaMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEK 62
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 384-456 7.10e-06

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: 46.40  E-value: 7.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501  384 AIGNGTASRETERFYLDVQKQFPKVTAQK-------VIVSEAGASVYSASELAAQEFPELDVSLRGAVSIARRLQDPLAE 456
Cdd:pfam14639  66 VIGVSGENRDAQKFYEDVQRVLHELEQDSrlhtigvILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLE 145
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 643-709 7.62e-06

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: 48.89  E-value: 7.62e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 695750501 643 ETMNDLLPGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADkfvEDPHTVVKAGDIVKVKVLEVD 709
Cdd:COG0539   11 ESLKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSD---EPGELEVKVGDEVEVYVEKVE 74
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 653-720 1.12e-05

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 48.94  E-value: 1.12e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 695750501 653 VLEGAVTNVTNFGAFVDIGVHQDGLVHISSLA-DKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:PRK12269 581 VVKGRVTKIADFGAFIELAEGIEGLAHISEFSwVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLK 649
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 658-762 1.26e-05

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 48.74  E-value: 1.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 658 VTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVD----LQRKRIALTMRLDEQPGDTNARRG 733
Cdd:PLN00207 762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNdkgqLRLSRRALLPEANSEKSSQKQQGG 841

                         90       100
                 ....*....|....*....|....*....
gi 695750501 734 GNGGGREQQRPAAKAAKPRgRDAQPAGNS 762
Cdd:PLN00207 842 STKDKAPQKKYVNTSSRPR-RAAQAEKNS 869
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 644-708 1.53e-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: 48.29  E-value: 1.53e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 695750501 644 TMNDLLPGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFvedphtvvKAGDIVKVKVLEV 708
Cdd:COG1107   33 TPDDLEPGRYYRGTVDGVADFGVFVDLNDHVTGLLHRSELDQDW--------EVGDEVFVQVKEV 89
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 651-720 1.99e-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: 43.03  E-value: 1.99e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:cd05691    1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
643-715 5.29e-05

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 46.86  E-value: 5.29e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 643 ETMNDLLPGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVD-------LQRKRI 715
Cdd:PRK00087 295 ELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEdedgyvvLSKKEA 374
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 648-707 1.59e-04

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: 40.41  E-value: 1.59e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 695750501 648 LLPGMVLEGAVTNVT-NFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLE 707
Cdd:cd05704    1 LEEGAVTLGMVTKVIpHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILS 61
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 643-709 7.95e-04

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: 41.42  E-value: 7.95e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 695750501 643 ETMNDLLPGMVLEGAVTNVTNFGAFVDI----------GVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVD 709
Cdd:COG1096   58 KPPPVPKKGDIVIGEVVDVRESMALVKIyaiegnerelPSSFSGIIHISQVSDSYVKDLSDEFRVGDIVRAKVISTL 134
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 651-720 8.94e-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: 38.21  E-value: 8.94e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 695750501 651 GMVLEGAVTNVTNFGAFVDI-GVhqDGLVHISSLADKFVEDPHTVVkaGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:cd04465    1 GEIVEGKVTEKVKGGLIVDIeGV--RAFLPASQVDLRPVEDLDEYV--GKELKFKIIEIDRERNNIVLSRR 67
PRK04163 PRK04163
exosome complex protein Rrp4;
656-720 1.30e-03

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 41.03  E-value: 1.30e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 695750501 656 GAVTNVTNFGAFVDIGVHQDGLVHISSLADKFV----EDPHTVVKAGDIVKVKVLEVDLQRKRIaLTMR 720
Cdd:PRK04163  69 GKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVnvegTDLRKYLDIGDYIIAKVKDVDRTRDVV-LTLK 136
rpsA PRK13806
30S ribosomal protein S1; Provisional
 650-760 2.28e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 41.25  E-value: 2.28e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 650 PGMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMRLDEQPGDTN 729
Cdd:PRK13806 379 PGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAPAGAAGSGADD 458

                         90       100       110
                 ....*....|....*....|....*....|.
gi 695750501 730 arrggngggreqqrPAAKAAKPRGRDAQPAG 760
Cdd:PRK13806 459 --------------DDWKQFAPKKSAPASGG 475
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 656-720 2.48e-03

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: 37.53  E-value: 2.48e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 695750501 656 GAVTNVTNFGAFVDIGVHQDGLVHISSL----ADKFVEDPHTVVKAGDIVKVKVLEVDLQRKrIALTMR 720
Cdd:cd05789   12 GRVTEVGFKRWKVDINSPYDAVLPLSEVnlprTDEDELNMRSYLDEGDLIVAEVQSVDSDGS-VSLHTR 79
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 651-720 2.58e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 41.24  E-value: 2.58e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIGVHQDGLVHISSLADKFVEDPHTVVK---AGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:PRK12269 753 GSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPGEALRkyaVGDRVKAVIVDMNVKDRKVAFSVR 825
PRK11642 PRK11642
ribonuclease R;
651-761 6.23e-03

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 40.11  E-value: 6.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695750501 651 GMVLEGAVTNVTNFGAFVDIG-VHQDGLVHISSLADKFV-----------EDPHTVVKAGDIVKVKVLEVDLQRKRIALT 718
Cdd:PRK11642 644 GNVFKGVISSVTGFGFFVRLDdLFIDGLVHVSSLDNDYYrfdqvgqrligESSGQTYRLGDRVEVRVEAVNMDERKIDFS 723

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 695750501 719 M----RLDEQPGDTnarrggngGGREQQRPAAKAAKPRGRDAQPAGN 761
Cdd:PRK11642 724 LisseRAPRNVGKT--------AREKAKKGDAGKKGGKRRQVGKKVN 762
 
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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