NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|613307357|gb|EZZ12449|]
View 

hypothetical protein U935_02440 [Staphylococcus aureus Sau 46]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1-712 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


:

Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1212.17  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357   1 MINSIIEKYQFSKKQIEAVLTLLEEKNTVPFIARYRKEQTGGLDEVQIKQIDDEYQYMVNLQKRKEEVIKNIEQQGLLTE 80
Cdd:COG2183    5 IIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGKLTP 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357  81 ELKKDILKQNKLQRVEDLYRPFKQKKKTRATEAKRKGLEPLAIWMKARKhEVSIEEKAQQFINEE--VQSVEDAIKGAQD 158
Cdd:COG2183   85 ELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQP-TGDPEAEAAKYINEEkgVADVEAALDGARD 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 159 IIAEQISDNPKYRTKILKDMYHQGVLTTSKKKNAEDEKGIFEMYYAYSEPIKRIANHRVLAVNRGEKEKVLSVKFEFDTT 238
Cdd:COG2183  164 ILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPDEE 243

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 239 AVEDFIARQEI-NHNNVNRSYILEAIKDSLKRLIVPSIEREIHADLTEKAENHAIDVFSENLRNLLLQPPMKGKQILGVD 317
Cdd:COG2183  244 EAEAYIARRFIkDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVLGLD 323

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 318 PAFRTGCKLAVINPFGTFIAKGVIYPHPPVSKKEAAEKDFVQMVKAYDVQLIAIGNGTASRETEQFVADLIKKHQLPVQF 397
Cdd:COG2183  324 PGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELDLKVQY 403

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 398 IIVNEAGASVYSASEIARDEFPDFQVEERSAVSIGRRVQDPLSELVKIDPKSIGVGQYQHDVNQKALENALTFVVETAVN 477
Cdd:COG2183  404 VIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCVN 483

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 478 QVGVDVNTASSSLLQYVSGLSSQIAKNIIAYREENGAIKHNKELSKIKRLGAKTFEQSIGFLRIVDGSEPLDNTSIHPES 557
Cdd:COG2183  484 AVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDNSAVHPES 563

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 558 YKVTYQLLDKLGFGGNDLGSDalKAKLNSLDMDELAIELqVGVPTLEDIIKSLKAPNRDPRDEFETPILKSDVLSIEDLK 637
Cdd:COG2183  564 YPVVEKILKDLGVSVKDLIGN--KELLKKLDPEKYADEL-FGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLKIEDLK 640

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 613307357 638 EGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTMIDPHE 712
Cdd:COG2183  641 PGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDDE 715
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1-712 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1212.17  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357   1 MINSIIEKYQFSKKQIEAVLTLLEEKNTVPFIARYRKEQTGGLDEVQIKQIDDEYQYMVNLQKRKEEVIKNIEQQGLLTE 80
Cdd:COG2183    5 IIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGKLTP 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357  81 ELKKDILKQNKLQRVEDLYRPFKQKKKTRATEAKRKGLEPLAIWMKARKhEVSIEEKAQQFINEE--VQSVEDAIKGAQD 158
Cdd:COG2183   85 ELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQP-TGDPEAEAAKYINEEkgVADVEAALDGARD 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 159 IIAEQISDNPKYRTKILKDMYHQGVLTTSKKKNAEDEKGIFEMYYAYSEPIKRIANHRVLAVNRGEKEKVLSVKFEFDTT 238
Cdd:COG2183  164 ILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPDEE 243

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 239 AVEDFIARQEI-NHNNVNRSYILEAIKDSLKRLIVPSIEREIHADLTEKAENHAIDVFSENLRNLLLQPPMKGKQILGVD 317
Cdd:COG2183  244 EAEAYIARRFIkDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVLGLD 323

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 318 PAFRTGCKLAVINPFGTFIAKGVIYPHPPVSKKEAAEKDFVQMVKAYDVQLIAIGNGTASRETEQFVADLIKKHQLPVQF 397
Cdd:COG2183  324 PGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELDLKVQY 403

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 398 IIVNEAGASVYSASEIARDEFPDFQVEERSAVSIGRRVQDPLSELVKIDPKSIGVGQYQHDVNQKALENALTFVVETAVN 477
Cdd:COG2183  404 VIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCVN 483

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 478 QVGVDVNTASSSLLQYVSGLSSQIAKNIIAYREENGAIKHNKELSKIKRLGAKTFEQSIGFLRIVDGSEPLDNTSIHPES 557
Cdd:COG2183  484 AVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDNSAVHPES 563

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 558 YKVTYQLLDKLGFGGNDLGSDalKAKLNSLDMDELAIELqVGVPTLEDIIKSLKAPNRDPRDEFETPILKSDVLSIEDLK 637
Cdd:COG2183  564 YPVVEKILKDLGVSVKDLIGN--KELLKKLDPEKYADEL-FGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLKIEDLK 640

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 613307357 638 EGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTMIDPHE 712
Cdd:COG2183  641 PGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDDE 715
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 5-188 4.51e-84

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: 263.50  E-value: 4.51e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357    5 IIEKYQFSKKQIEAVLTLLEEKNTVPFIARYRKEQTGGLDEVQIKQIDDEYQYMVNLQKRKEEVIKNIEQQGLLTEELKK 84
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357   85 DILKQNKLQRVEDLYRPFKQKKKTRATEAKRKGLEPLAIWMKARKhevSIEEKAQQFINEE--VQSVEDAIKGAQDIIAE 162
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQP---DPEEEAAKYINPEkgVADVEEALAGARDIIAE 157

                         170       180
                  ....*....|....*....|....*.
gi 613307357  163 QISDNPKYRTKILKDMYHQGVLTTSK 188
Cdd:pfam09371 158 RISEDAELRKKLRELLWREGVIVSKV 183
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 639-706 3.46e-30

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: 113.10  E-value: 3.46e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 613307357 639 GMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLT 706
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 311-409 8.15e-23

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: 93.40  E-value: 8.15e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357   311 KQILGVDPAfRTGCKLAVINPFGTFIAKGVIYPHppvSKKEAAEKDFVQMVKAYDVQLIAIG-----NGTASRETEQFVA 385
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVIPR---TNKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFA 76

                           90       100
                   ....*....|....*....|....
gi 613307357   386 DLIKKHqLPVQFIIVNEAGASVYS 409
Cdd:smart00732  77 ELLKER-FNLPVVLVDERLATVYA 99
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 634-709 1.83e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 88.01  E-value: 1.83e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 613307357 634 EDLKEGMKLSGTVRNVVDFGAFVDIG-VkqDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTMID 709
Cdd:PRK06676 188 SSLKEGDVVEGTVARLTDFGAFVDIGgV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKD 262
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 637-707 3.68e-13

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: 66.30  E-value: 3.68e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 613307357 637 KEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTM 707
Cdd:NF040579   2 KIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSL 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 632-707 5.88e-12

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: 68.61  E-value: 5.88e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 613307357  632 SIEDLKEGMKLSGTVRNVVDFGAFVDIGVkQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTM 707
Cdd:TIGR00717 181 LLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1-712 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1212.17  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357   1 MINSIIEKYQFSKKQIEAVLTLLEEKNTVPFIARYRKEQTGGLDEVQIKQIDDEYQYMVNLQKRKEEVIKNIEQQGLLTE 80
Cdd:COG2183    5 IIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGKLTP 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357  81 ELKKDILKQNKLQRVEDLYRPFKQKKKTRATEAKRKGLEPLAIWMKARKhEVSIEEKAQQFINEE--VQSVEDAIKGAQD 158
Cdd:COG2183   85 ELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQP-TGDPEAEAAKYINEEkgVADVEAALDGARD 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 159 IIAEQISDNPKYRTKILKDMYHQGVLTTSKKKNAEDEKGIFEMYYAYSEPIKRIANHRVLAVNRGEKEKVLSVKFEFDTT 238
Cdd:COG2183  164 ILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPDEE 243

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 239 AVEDFIARQEI-NHNNVNRSYILEAIKDSLKRLIVPSIEREIHADLTEKAENHAIDVFSENLRNLLLQPPMKGKQILGVD 317
Cdd:COG2183  244 EAEAYIARRFIkDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVLGLD 323

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 318 PAFRTGCKLAVINPFGTFIAKGVIYPHPPVSKKEAAEKDFVQMVKAYDVQLIAIGNGTASRETEQFVADLIKKHQLPVQF 397
Cdd:COG2183  324 PGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELDLKVQY 403

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 398 IIVNEAGASVYSASEIARDEFPDFQVEERSAVSIGRRVQDPLSELVKIDPKSIGVGQYQHDVNQKALENALTFVVETAVN 477
Cdd:COG2183  404 VIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCVN 483

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 478 QVGVDVNTASSSLLQYVSGLSSQIAKNIIAYREENGAIKHNKELSKIKRLGAKTFEQSIGFLRIVDGSEPLDNTSIHPES 557
Cdd:COG2183  484 AVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDNSAVHPES 563

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 558 YKVTYQLLDKLGFGGNDLGSDalKAKLNSLDMDELAIELqVGVPTLEDIIKSLKAPNRDPRDEFETPILKSDVLSIEDLK 637
Cdd:COG2183  564 YPVVEKILKDLGVSVKDLIGN--KELLKKLDPEKYADEL-FGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLKIEDLK 640

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 613307357 638 EGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTMIDPHE 712
Cdd:COG2183  641 PGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDDE 715
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 5-188 4.51e-84

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: 263.50  E-value: 4.51e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357    5 IIEKYQFSKKQIEAVLTLLEEKNTVPFIARYRKEQTGGLDEVQIKQIDDEYQYMVNLQKRKEEVIKNIEQQGLLTEELKK 84
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357   85 DILKQNKLQRVEDLYRPFKQKKKTRATEAKRKGLEPLAIWMKARKhevSIEEKAQQFINEE--VQSVEDAIKGAQDIIAE 162
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQP---DPEEEAAKYINPEkgVADVEEALAGARDIIAE 157

                         170       180
                  ....*....|....*....|....*.
gi 613307357  163 QISDNPKYRTKILKDMYHQGVLTTSK 188
Cdd:pfam09371 158 RISEDAELRKKLRELLWREGVIVSKV 183
Tex_YqgF pfam16921
Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which ...
 313-436 1.05e-75

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: 239.22  E-value: 1.05e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357  313 ILGVDPAFRTGCKLAVINPFGTFIAKGVIYPHPPVSKKEAAEKDFVQMVKAYDVQLIAIGNGTASRETEQFVADLIKKHQ 392
Cdd:pfam16921   2 VLGLDPGYRTGCKLAVVDETGKVLDTAVIYPHPPQNKVEEAKKKLKKLIKKYGVELIAIGNGTASRETEQFVAELIKELP 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 613307357  393 LPVQFIIVNEAGASVYSASEIARDEFPDFQVEERSAVSIGRRVQ 436
Cdd:pfam16921  82 LKVKYVIVSEAGASVYSASELAREEFPDLDVSLRGAVSIARRLQ 125
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 639-706 3.46e-30

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: 113.10  E-value: 3.46e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 613307357 639 GMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLT 706
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 478-539 2.19e-25

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


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 99.48  E-value: 2.19e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 613307357  478 QVGVDVNTASSSLLQYVSGLSSQIAKNIIAYREENGAIKHNKELSKIKRLGAKTFEQSIGFL 539
Cdd:pfam12836   1 AVGVDINTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKTFEQLAGFL 62
HHH_9 pfam17674
HHH domain;
546-618 5.46e-24

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 95.68  E-value: 5.46e-24
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 613307357  546 EPLDNTSIHPESYKVTYQLLDKLGFGGNDLGSDalKAKLNSLDMDELAiELQVGVPTLEDIIKSLKAPNRDPR 618
Cdd:pfam17674   1 NPLDNTAIHPESYPLAEKILKDLGLDLKDLIGN--SALLKKLDPKKLA-EEEVGLPTLKDILEELAKPGRDPR 70
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 311-409 8.15e-23

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: 93.40  E-value: 8.15e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357   311 KQILGVDPAfRTGCKLAVINPFGTFIAKGVIYPHppvSKKEAAEKDFVQMVKAYDVQLIAIG-----NGTASRETEQFVA 385
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVIPR---TNKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFA 76

                           90       100
                   ....*....|....*....|....
gi 613307357   386 DLIKKHqLPVQFIIVNEAGASVYS 409
Cdd:smart00732  77 ELLKER-FNLPVVLVDERLATVYA 99
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 638-705 8.68e-20

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: 83.45  E-value: 8.68e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 613307357 638 EGMKLSGTVRNVVDFGAFVDIGVKqDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSL 705
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDLGGV-DGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISL 67
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 633-707 1.56e-19

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: 90.49  E-value: 1.56e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 613307357 633 IEDLKEGMKLSGTVRNVVDFGAFVDI-GVkqDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTM 707
Cdd:COG0539  184 LEKLEEGDVVEGTVKNITDFGAFVDLgGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSL 257
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 634-709 1.83e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 88.01  E-value: 1.83e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 613307357 634 EDLKEGMKLSGTVRNVVDFGAFVDIG-VkqDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTMID 709
Cdd:PRK06676 188 SSLKEGDVVEGTVARLTDFGAFVDIGgV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKD 262
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 633-709 8.26e-17

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


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 84.67  E-value: 8.26e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 613307357 633 IEDLKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKnKDKVSLTMID 709
Cdd:COG1185  611 TAEPEVGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEIDD-QGRIKLSRKA 686
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 609-707 1.17e-16

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: 82.01  E-value: 1.17e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 609 SLKAPNRDPRDEFEtpilksdvlsiEDLKEGMKLSGTVRNVVDFGAFVDI--GVkqDGLVHVSKLSK-KFVKNPMDIVSV 685
Cdd:COG0539  256 SLKQLQPDPWENIA-----------EKYPVGDVVKGKVTRLTDFGAFVELepGV--EGLVHISEMSWtKRVAHPSDVVKV 322

                         90       100
                 ....*....|....*....|..
gi 613307357 686 GDIVDVWIYSIDKNKDKVSLTM 707
Cdd:COG0539  323 GDEVEVKVLDIDPEERRISLSI 344
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
637-707 1.70e-16

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 74.56  E-value: 1.70e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 613307357   637 KEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTM 707
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
633-705 1.89e-16

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 83.46  E-value: 1.89e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 613307357 633 IEDLKEGMKLSGTVRNVVDFGAFVDI-GVkqDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSL 705
Cdd:PRK00087 472 WNSLEEGDVVEGEVKRLTDFGAFVDIgGV--DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSL 543
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 633-707 2.82e-16

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 82.79  E-value: 2.82e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 613307357 633 IEDL----KEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDkNKDKVSLTM 707
Cdd:PRK11824 612 IEGItaepEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSR 689
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 633-707 4.27e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 82.13  E-value: 4.27e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 613307357 633 IEDLKEGMKLSGTVRNVVDFGAFVDIGVkQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTM 707
Cdd:PRK06299 196 LENLEEGQVVEGVVKNITDYGAFVDLGG-VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGL 269
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 639-707 2.87e-15

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: 70.78  E-value: 2.87e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 613307357 639 GMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKdKVSLTM 707
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARG-RISLSI 68
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 644-707 6.80e-15

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: 69.88  E-value: 6.80e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 613307357 644 GTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKnKDKVSLTM 707
Cdd:cd04472    6 GKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 634-707 7.85e-15

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 71.75  E-value: 7.85e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 613307357 634 EDLKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKdKVSLTM 707
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDG-KISLSI 73
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 609-707 1.87e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 76.74  E-value: 1.87e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 609 SLKAPNRDPRDEFEtpilksdvlsiEDLKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLS--KKfVKNPMDIVSVG 686
Cdd:PRK06299 268 GLKQLGEDPWEAIE-----------KKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSwtKK-NKHPSKVVSVG 335

                         90       100
                 ....*....|....*....|.
gi 613307357 687 DIVDVWIYSIDKNKDKVSLTM 707
Cdd:PRK06299 336 QEVEVMVLEIDEEKRRISLGL 356
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 578-707 2.19e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 72.60  E-value: 2.19e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 578 DALKAKLNSLDMDELAIELqvgvptlediikSLKAPNRDPRDEFEtpilksdvlsiEDLKEGMKLSGTVRNVVDFGAFVD 657
Cdd:PRK06676 240 QEVEVKVLSIDWETERISL------------SLKDTLPGPWEGVE-----------EKLPEGDVIEGTVKRLTDFGAFVE 296

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 613307357 658 IGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTM 707
Cdd:PRK06676 297 VLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSI 346
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 637-707 3.68e-13

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: 66.30  E-value: 3.68e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 613307357 637 KEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTM 707
Cdd:NF040579   2 KIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSL 72
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 644-706 6.74e-13

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: 63.94  E-value: 6.74e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 613307357 644 GTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLT 706
Cdd:cd00164    3 GKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA PRK13806
30S ribosomal protein S1; Provisional
 578-709 7.99e-13

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 71.29  E-value: 7.99e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 578 DALKAKLNSLDMDELAIELQVGVptlediikSLKAPNRDPRDEFEtpilksdvlsiEDLKEGMKLSGTVRNVVDFGAFVD 657
Cdd:PRK13806 251 DTVRVKVLGIERAKKGKGLRISL--------SIKQAGGDPWDTVG-----------DRLKAGDKVTGKVVRLAPFGAFVE 311

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 613307357 658 IGVKQDGLVHVSKLS-KKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTMID 709
Cdd:PRK13806 312 ILPGIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRD 364
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 636-710 4.05e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 68.92  E-value: 4.05e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 613307357 636 LKEGMKLSGTVRNVVDFGAFVDIGvKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSL----TMIDP 710
Cdd:PRK07899 206 LQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLslkaTQEDP 283
PRK08582 PRK08582
RNA-binding protein S1;
631-706 4.81e-12

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 63.90  E-value: 4.81e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 613307357 631 LSIEdlkEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNkDKVSLT 706
Cdd:PRK08582   1 MSIE---VGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDD-GKIGLS 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 632-707 5.88e-12

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: 68.61  E-value: 5.88e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 613307357  632 SIEDLKEGMKLSGTVRNVVDFGAFVDIGVkQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTM 707
Cdd:TIGR00717 181 LLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 606-705 6.58e-12

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: 68.61  E-value: 6.58e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357  606 IIKSLKAPNRDPRDEFEtpilksdvlsiEDLKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLS-KKFVKNPMDIVS 684
Cdd:TIGR00717 251 ISLSLKQLGEDPWEAIE-----------KKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVK 319

                          90       100
                  ....*....|....*....|.
gi 613307357  685 VGDIVDVWIYSIDKNKDKVSL 705
Cdd:TIGR00717 320 KGDEVEVMILDIDPERRRLSL 340
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 636-707 7.58e-12

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: 61.15  E-value: 7.58e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 613307357  636 LKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTM 707
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
634-707 9.15e-12

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 68.43  E-value: 9.15e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 613307357 634 EDLKEGMKLSGTVRNVVDFGAFVDI--GVkqDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTM 707
Cdd:PRK00087 558 EKYPVGSIVLGKVVRIAPFGAFVELepGV--DGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSI 631
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 638-705 1.04e-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: 60.67  E-value: 1.04e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 638 EGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKL--SKKFVkNPMDIVSVGDIVDVWIYSIDKNKDKVSL 705
Cdd:cd05689    3 EGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMdwTNKNI-HPSKVVSLGDEVEVMVLDIDEERRRISL 71
PRK08059 PRK08059
general stress protein 13; Validated
 636-707 1.12e-11

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 62.37  E-value: 1.12e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 613307357 636 LKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTM 707
Cdd:PRK08059   5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSI 76
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 637-707 1.53e-11

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: 60.42  E-value: 1.53e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 613307357 637 KEGMKLSGTVRNVVDFGAFVDI-GVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTM 707
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGL 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 609-705 1.53e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 67.50  E-value: 1.53e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 609 SLKAPNRDPRDEFEtpilksdvlsiEDLKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLS-KKFVKNPMDIVSVGD 687
Cdd:PRK06299 355 GLKQCKENPWEEFA-----------EKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGD 423

                         90
                 ....*....|....*...
gi 613307357 688 IVDVWIYSIDKNKDKVSL 705
Cdd:PRK06299 424 EVEAVVLKVDVEKERISL 441
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 639-705 2.89e-11

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


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 59.43  E-value: 2.89e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 613307357 639 GMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLS-KKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSL 705
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 643-709 4.97e-11

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 59.17  E-value: 4.97e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 613307357 643 SGTVRNVVDFGAFVDI-GVK--QDGLVHVSKLSKK-FVKNPMDIVSVGDIVDVWIYSIDKNkdKVSLTMID 709
Cdd:cd05684    5 KGKVTSIMDFGCFVQLeGLKgrKEGLVHISQLSFEgRVANPSDVVKRGQKVKVKVISIQNG--KISLSMKD 73
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 481-534 5.20e-11

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


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 58.72  E-value: 5.20e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 613307357 481 VDVNTASSSLLQYVSGLSSQIAKNIIAYREENGAIKHNKELSKIKRLGAKTFEQ 534
Cdd:COG1555   13 VDINTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGIGPKTLEK 66
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 627-707 3.66e-10

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: 56.83  E-value: 3.66e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 627 KSDVLSIEDLKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLT 706
Cdd:cd04461    3 GTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLS 82


                 .
gi 613307357 707 M 707
Cdd:cd04461   83 L 83
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 619-707 5.42e-10

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 62.49  E-value: 5.42e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 619 DEFETPILKSDV------LSIEDLKE------------GMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPM 680
Cdd:PRK06299 423 DEVEAVVLKVDVekerisLGIKQLEEdpfeefakkhkkGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDAT 502

                         90       100
                 ....*....|....*....|....*..
gi 613307357 681 DIVSVGDIVDVWIYSIDKNKDKVSLTM 707
Cdd:PRK06299 503 EVLKVGDEVEAKVINIDRKNRRISLSI 529
PRK05807 PRK05807
RNA-binding protein S1;
636-707 1.38e-09

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 56.68  E-value: 1.38e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 613307357 636 LKEGMKLSGTVRNVVDFGAFVDIGVKQdGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNkDKVSLTM 707
Cdd:PRK05807   3 LKAGSILEGTVVNITNFGAFVEVEGKT-GLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDN-GKISLSI 72
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 642-707 1.80e-09

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


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 54.41  E-value: 1.80e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 613307357 642 LSGTVRNVVDFGAFVDI-GVKQDGLVHVSKLSKKFVKNPMDIVSVGDIvdVWIYSIDKN-KDKVSLTM 707
Cdd:cd05686    7 FKGEVASVTEYGAFVKIpGCRKQGLVHKSHMSSCRVDDPSEVVDVGEK--VWVKVIGREmKDKMKLSL 72
rpsA PRK13806
30S ribosomal protein S1; Provisional
 633-710 2.05e-09

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 60.51  E-value: 2.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 633 IEDLKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKD----KVSLT-- 706
Cdd:PRK13806 197 METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSik 276


                 ....*.
gi 613307357 707 --MIDP 710
Cdd:PRK13806 277 qaGGDP 282
comE TIGR01259
comEA protein; This model describes the ComEA protein in bacteria. The com E locus is ...
 481-534 2.34e-08

comEA protein; This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation. [Cellular processes, DNA transformation]


Pssm-ID: 213597 [Multi-domain]  Cd Length: 120  Bit Score: 52.98  E-value: 2.34e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 613307357  481 VDVNTASSSLLQYVSGLSSQIAKNIIAYREENGAIKHNKELSKIKRLGAKTFEQ 534
Cdd:TIGR01259  60 VNINAASLEELQALPGIGPAKAKAIIEYREENGAFKSVDDLTKVSGIGEKSLEK 113
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 632-706 3.35e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 56.42  E-value: 3.35e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 613307357 632 SIEDLKEGMKLSGTVRNVVDFGAFVDI-GVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLT 706
Cdd:PRK06676  11 SVKEVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLS 86
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 609-707 9.11e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 55.05  E-value: 9.11e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 609 SLKAPNRDPRDEFEtpilksdvlsiEDLKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDI 688
Cdd:PRK07899 275 SLKATQEDPWQQFA-----------RTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDE 343

                         90
                 ....*....|....*....
gi 613307357 689 VDVWIYSIDKNKDKVSLTM 707
Cdd:PRK07899 344 VFVKVIDIDLERRRISLSL 362
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
636-707 6.70e-07

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 48.54  E-value: 6.70e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 613307357 636 LKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTM 707
Cdd:PRK07252   1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSL 72
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 644-707 7.72e-07

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 49.82  E-value: 7.72e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 644 GTVRNVVDFGAFVDIGVkQDGLVHVSKLSKKFV----KNPMDI-------VSVGDIVDVWIYSIDKNK-----DKVSLTM 707
Cdd:PRK08563  87 GEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYIsydpKNGRLIgkeskrvLKVGDVVRARIVAVSLKErrprgSKIGLTM 165
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 639-705 2.64e-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: 45.21  E-value: 2.64e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 613307357 639 GMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSL 705
Cdd:cd05687    1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVL 67
HHH_7 pfam14635
Helix-hairpin-helix motif;
446-541 3.51e-06

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 46.00  E-value: 3.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357  446 DPKSIGVGQYQHDVNQKALENALTFVVETAVNQVGVDVNTA-----SSSLLQYVSGLSSQIAKNII-AYREENGAIKHNK 519
Cdd:pfam14635   2 DILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAiankyEAAILPYIAGLGPRKADHLLkILAANNGRLDNRS 81

                          90       100
                  ....*....|....*....|..
gi 613307357  520 ELSKIKRLGAKTFEQSIGFLRI 541
Cdd:pfam14635  82 QLITKCIMGPKVFMNCAGFLII 103
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 609-707 3.68e-06

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 50.48  E-value: 3.68e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 609 SLKAPNRDPRDEFETPILKSDVLSiedlkegmklsGTVRNVVDFGAFVDIGVKQDGLVHVSKLS-KKFVKNPMDIVSVGD 687
Cdd:PRK12269 560 SLKHFQPDPWLEFENKFGVNDVVK-----------GRVTKIADFGAFIELAEGIEGLAHISEFSwVKKTSKPSDMVKIGD 628

                         90       100
                 ....*....|....*....|
gi 613307357 688 IVDVWIYSIDKNKDKVSLTM 707
Cdd:PRK12269 629 EVECMILGYDIQAGRVSLGL 648
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 355-441 5.53e-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: 46.78  E-value: 5.53e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357  355 KDFVQMVKAYdvqliAIGNGTASRETEQF---VADLIKKHQL-----PVQFIIVNEAGASVYSASEIARDEFPDFQVEER 426
Cdd:pfam14639  56 KKFLLSKKPH-----VIGVSGENRDAQKFyedVQRVLHELEQdsrlhTIGVILVDDEVAILYQNSKRAEAEFPDYPPLLR 130

                          90
                  ....*....|....*
gi 613307357  427 SAVSIGRRVQDPLSE 441
Cdd:pfam14639 131 YCVALARYIQDPLLE 145
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 636-706 7.18e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 48.64  E-value: 7.18e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 613307357 636 LKEGMKLSGTVRNVVDFGAFVDIGvKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLT 706
Cdd:PRK07400 194 LEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLS 263
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 608-707 1.31e-05

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 48.55  E-value: 1.31e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 608 KSLKAPNRDPRDEFETPIlksdvlSIEDlkegmKLSGTVRNVVDFGAFVDIGvKQDGLVHVSKLSKKFVKNPMDIVSVGD 687
Cdd:PRK12269 474 RYLEERARQAREEFFNSV------HIED-----SVSGVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQ 541

                         90       100
                 ....*....|....*....|
gi 613307357 688 IVDVWIYSIDKNKDKVSLTM 707
Cdd:PRK12269 542 TIELKVIRLDQAEKRINLSL 561
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 637-706 1.39e-05

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: 48.19  E-value: 1.39e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357  637 KEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLT 706
Cdd:TIGR00717 445 KVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLS 514
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 606-705 1.51e-05

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: 48.19  E-value: 1.51e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357  606 IIKSLKAPNRDPRDEFEtpilksdvlsiEDLKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLS-KKFVKNPMDIVS 684
Cdd:TIGR00717 338 LSLGLKQCKANPWEQFE-----------EKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYK 406

                          90       100
                  ....*....|....*....|.
gi 613307357  685 VGDIVDVWIYSIDKNKDKVSL 705
Cdd:TIGR00717 407 KGDEIEAVVLAVDKEKKRISL 427
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 639-706 1.69e-05

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


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 43.05  E-value: 1.69e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 613307357 639 GMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLT 706
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 639-706 1.78e-05

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: 42.98  E-value: 1.78e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 639 GMKLSGTVRNVVDFGAFVDI--GVKqdGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLT 706
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFynNVK--GFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLS 68
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 599-698 3.26e-05

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 47.20  E-value: 3.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 599 GVPTLEDIIKSLKAPNRDPRDEFETPILKSDVLSIEDLKE---GMKLSGTV----RN-----VVDFGAFVDIGVKQDGLV 666
Cdd:PLN00207 703 GGKKVKSIIEETGVEAIDTQDDGTVKITAKDLSSLEKSKAiisSLTMVPTVgdiyRNceiksIAPYGAFVEIAPGREGLC 782

                         90       100       110
                 ....*....|....*....|....*....|..
gi 613307357 667 HVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDK 698
Cdd:PLN00207 783 HISELSSNWLAKPEDAFKVGDRIDVKLIEVND 814
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 481-534 5.73e-05

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: 41.84  E-value: 5.73e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 613307357  481 VDVNTASSSLLQ-YVSGLSSQIAKNIIAYREENGAIKHNKELSKIKRLGAKTFEQ 534
Cdd:TIGR00426   8 VNINTATAEELQrAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEK 62
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 632-705 7.39e-05

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 45.42  E-value: 7.39e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 613307357 632 SIEDLKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKkfvKNPMDIVSVGDIVDVWIYSIDKNKDKVSL 705
Cdd:COG0539   12 SLKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSD---EPGELEVKVGDEVEVYVEKVEDGEGEIVL 82
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 632-688 9.62e-05

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


Pssm-ID: 239919 [Multi-domain]  Cd Length: 77  Bit Score: 41.05  E-value: 9.62e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 613307357 632 SIEDLKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDI 688
Cdd:cd04473   10 TMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDYEVGDEVIVQVTDI 66
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
626-705 9.63e-05

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 45.71  E-value: 9.63e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 626 LKSDVLSIEDLKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSL 705
Cdd:PRK00087 290 LEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVL 369
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 644-710 1.06e-04

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: 41.89  E-value: 1.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357 644 GTVRNVVDFGAFVDIGvKQDGLVHVSKLSKKFV-----------KNPMDIVSVGDIVDVWIYSIDKNKD-----KVSLTM 707
Cdd:cd04460    5 GEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYIsydpknkrligEETKRVLKVGDVVRARIVAVSLKERrpresKIGLTM 83


                 ...
gi 613307357 708 IDP 710
Cdd:cd04460   84 RQP 86
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 632-690 1.28e-04

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: 45.21  E-value: 1.28e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 613307357 632 SIEDLKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFvkNPMD--IVSVGDIVD 690
Cdd:COG1107   33 TPDDLEPGRYYRGTVDGVADFGVFVDLNDHVTGLLHRSELDQDW--EVGDevFVQVKEVRD 91
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 637-707 1.88e-04

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: 40.26  E-value: 1.88e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 613307357 637 KEGMKLSGTVRNVVDFGAFVDIGVKQD--GLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTM 707
Cdd:cd04452    2 EEGELVVVTVKSIADMGAYVSLLEYGNieGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSK 74
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 635-706 2.38e-04

S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 39.93  E-value: 2.38e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 613307357 635 DLKEGMKLSGTVRNVVDFGAFVDIGVKQ-DGLvhvskLSKKFVKNPMDIVsVGDIVDVWIYSIDKNKDKVSLT 706
Cdd:cd05694    1 DLVEGMVLSGCVSSVEDHGYILDIGIPGtTGF-----LPKKDAGNFSKLK-VGQLLLCVVEKVKDDGRVVSLS 67
PTZ00121 PTZ00121
MAEBL; Provisional
 10-298 2.08e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 41.67  E-value: 2.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357   10 QFSKKQIEAVLTLLEEKNTVPfIARYRKEQTGGLDEVQIKQIDDEYQYMVNLQKRKEEVIKNIEQ-------QGLLTEEL 82
Cdd:PTZ00121 1588 KAEEARIEEVMKLYEEEKKMK-AEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEElkkaeeeNKIKAAEE 1666

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357   83 KK----DILKQNKLQRVEDLYR------PFKQKKKTRATEAKRKGLEPLAIWMKARKHEVSIEEKAQQF---INEEVQSV 149
Cdd:PTZ00121 1667 AKkaeeDKKKAEEAKKAEEDEKkaaealKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAkkeAEEDKKKA 1746

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 613307357  150 EDAIK--GAQDIIAEQISDNPKYRTKILKD---MYHQGVLTTSKKKNAEDEKGIFEMyYAYSEPIKRIANHRVLAVNRGE 224
Cdd:PTZ00121 1747 EEAKKdeEEKKKIAHLKKEEEKKAEEIRKEkeaVIEEELDEEDEKRRMEVDKKIKDI-FDNFANIIEGGKEGNLVINDSK 1825

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 613307357  225 KEKVLSVKFEFDTTAVE----DFIARQEINHNNVN-RSYILEAIKDSLKRLIVPSIEREIHADLTEKAENHAIDVFSEN 298
Cdd:PTZ00121 1826 EMEDSAIKEVADSKNMQleeaDAFEKHKFNKNNENgEDGNKEADFNKEKDLKEDDEEEIEEADEIEKIDKDDIEREIPN 1904
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 644-712 2.91e-03

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 40.19  E-value: 2.91e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 613307357 644 GTVRNVVDFGAFVDI---GVKQdGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLTMIDPHE 712
Cdd:PRK03987  14 GTVKEVKDFGAFVTLdeyPGKE-GFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVNE 84
rpsA PRK13806
30S ribosomal protein S1; Provisional
 635-707 5.11e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 40.09  E-value: 5.11e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 613307357 635 DLKEGMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPmdiVSVGDIVDVWIYSIDKNKDKVSLTM 707
Cdd:PRK13806  31 ELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDADGELT---VAVGDEVELYVVSVNGQEIRLSKAL 100
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 639-706 5.76e-03

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


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 36.06  E-value: 5.76e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 613307357 639 GMKLSGTVRNVVDFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSLT 706
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLT 68
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 636-705 7.33e-03

S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 35.79  E-value: 7.33e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 613307357 636 LKEGMKLSGTVRNVV-DFGAFVDIGVKQDGLVHVSKLSKKFVKNPMDIVSVGDIVDVWIYSIDKNKDKVSL 705
Cdd:cd05704    1 LEEGAVTLGMVTKVIpHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGKYQLSL 71
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH