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Conserved domains on  [gi|1724454750|ref|WP_147197145|]
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MULTISPECIES: Tex family protein [Rummeliibacillus]

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];
3-717 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


:

Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1260.32  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750   3 TQKMHQLIAKEIGIRTQQVDQVIQLLEASNTVPFIARYRKEATGSLDEVQIKAIEDRYHYVMQLEQRKQEVLRIIEEQGK 82
Cdd:COG2183     2 MMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750  83 LTEELTKDINEATVLKRVEDLYRPYKQKRRTKATIAKDKGLEPLADSLLQFNQTEVETLALPFINE--NVESVEEALQGA 160
Cdd:COG2183    82 LTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEekGVADVEAALDGA 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 161 SDILAERFADDAAIRESIRQISWKQGVIQSTVKAKELDEKSVFEMYYDYQEPVNKIVPHRILAINRGEKEDILKIGIEVP 240
Cdd:COG2183   162 RDILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPD 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 241 TESIYQLMRKKWIVSTSSPSSKLVEVAIEDAYKRLIQPSIEREIRNELTDKAETQAIHIFSENLRNLLLQPPMKGKYVLG 320
Cdd:COG2183   242 EEEAEAYIARRFIKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVLG 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 321 VDPAYRTGCKLAVVDDTGKMLEISVIYPHTAKADINKSKSIFNDLLNRYPISIIAIGNGTASRETEQFVSECLNESNASA 400
Cdd:COG2183   322 LDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELDLKV 401

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 401 AYVIVNEAGASVYSASPIAREEFPDLQVEQRSAVSIARRLQDPLAELVKIEPKAVGVGQYQHDVSQKKLAEQLTFIVETA 480
Cdd:COG2183   402 QYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDC 481

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 481 VNQVGVDVNTASSSLLQYVSGLSKTVAENIVKTRGEQGKFTARTQLKKIPRLGAKTYEQAIGFLRIPNAKNPLDSTAIHP 560
Cdd:COG2183   482 VNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDNSAVHP 561

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 561 ESYDLANRILEAVGLDKKQIGTAEAeqAIANLNIKELSKEwEIGEVTLKDVIDSLMKPSRDPRDAFPQPLLKKDVLKMED 640
Cdd:COG2183   562 ESYPVVEKILKDLGVSVKDLIGNKE--LLKKLDPEKYADE-LFGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLKIED 638

                         650       660       670       680       690       700       710
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1724454750 641 LQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTMLPPNQ 717
Cdd:COG2183   639 LKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDDE 715
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
3-717 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1260.32  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750   3 TQKMHQLIAKEIGIRTQQVDQVIQLLEASNTVPFIARYRKEATGSLDEVQIKAIEDRYHYVMQLEQRKQEVLRIIEEQGK 82
Cdd:COG2183     2 MMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750  83 LTEELTKDINEATVLKRVEDLYRPYKQKRRTKATIAKDKGLEPLADSLLQFNQTEVETLALPFINE--NVESVEEALQGA 160
Cdd:COG2183    82 LTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEekGVADVEAALDGA 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 161 SDILAERFADDAAIRESIRQISWKQGVIQSTVKAKELDEKSVFEMYYDYQEPVNKIVPHRILAINRGEKEDILKIGIEVP 240
Cdd:COG2183   162 RDILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPD 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 241 TESIYQLMRKKWIVSTSSPSSKLVEVAIEDAYKRLIQPSIEREIRNELTDKAETQAIHIFSENLRNLLLQPPMKGKYVLG 320
Cdd:COG2183   242 EEEAEAYIARRFIKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVLG 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 321 VDPAYRTGCKLAVVDDTGKMLEISVIYPHTAKADINKSKSIFNDLLNRYPISIIAIGNGTASRETEQFVSECLNESNASA 400
Cdd:COG2183   322 LDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELDLKV 401

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 401 AYVIVNEAGASVYSASPIAREEFPDLQVEQRSAVSIARRLQDPLAELVKIEPKAVGVGQYQHDVSQKKLAEQLTFIVETA 480
Cdd:COG2183   402 QYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDC 481

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 481 VNQVGVDVNTASSSLLQYVSGLSKTVAENIVKTRGEQGKFTARTQLKKIPRLGAKTYEQAIGFLRIPNAKNPLDSTAIHP 560
Cdd:COG2183   482 VNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDNSAVHP 561

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 561 ESYDLANRILEAVGLDKKQIGTAEAeqAIANLNIKELSKEwEIGEVTLKDVIDSLMKPSRDPRDAFPQPLLKKDVLKMED 640
Cdd:COG2183   562 ESYPVVEKILKDLGVSVKDLIGNKE--LLKKLDPEKYADE-LFGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLKIED 638

                         650       660       670       680       690       700       710
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1724454750 641 LQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTMLPPNQ 717
Cdd:COG2183   639 LKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDDE 715
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 10-192 1.70e-91

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: 282.76  E-value: 1.70e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750  10 IAKEIGIRTQQVDQVIQLLEASNTVPFIARYRKEATGSLDEVQIKAIEDRYHYVMQLEQRKQEVLRIIEEQGKLTEELTK 89
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750  90 DINEATVLKRVEDLYRPYKQKRRTKATIAKDKGLEPLADSLLqfNQTEVETLALPFINE--NVESVEEALQGASDILAER 167
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAIL--AQPDPEEEAAKYINPekGVADVEEALAGARDIIAER 158

                         170       180
                  ....*....|....*....|....*
gi 1724454750 168 FADDAAIRESIRQISWKQGVIQSTV 192
Cdd:pfam09371 159 ISEDAELRKKLRELLWREGVIVSKV 183
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 644-711 5.74e-34

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: 123.88  E-value: 5.74e-34
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1724454750 644 GMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALT 711
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 316-414 8.45e-18

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: 79.15  E-value: 8.45e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750  316 KYVLGVDPAyRTGCKLAVVDDTGKMLEISVIYPHTakaDINKSKSIFNDLLNRYPISIIAIG-----NGTASRETEQFVS 390
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVIPRT---NKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFA 76

                           90       100
                   ....*....|....*....|....
gi 1724454750  391 ECLNEsNASAAYVIVNEAGASVYS 414
Cdd:smart00732  77 ELLKE-RFNLPVVLVDERLATVYA 99
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 632-712 3.72e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 84.16  E-value: 3.72e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 632 KKDVLKmEDLQPGMELQGTVRNVVDFGAFVDIG-VkqDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIAL 710
Cdd:PRK06676  182 KKEELL-SSLKEGDVVEGTVARLTDFGAFVDIGgV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISL 258


                  ..
gi 1724454750 711 TM 712
Cdd:PRK06676  259 SL 260
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 632-710 3.62e-13

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 72.46  E-value: 3.62e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1724454750 632 KKDVLKmEDLQPGMELQGTVRNVVDFGAFVDIGVkQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIAL 710
Cdd:TIGR00717 177 AREELL-ENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISL 253
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 644-712 2.35e-11

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: 61.29  E-value: 2.35e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1724454750 644 GMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:NF040579    4 GDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSL 72
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
3-717 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1260.32  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750   3 TQKMHQLIAKEIGIRTQQVDQVIQLLEASNTVPFIARYRKEATGSLDEVQIKAIEDRYHYVMQLEQRKQEVLRIIEEQGK 82
Cdd:COG2183     2 MMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750  83 LTEELTKDINEATVLKRVEDLYRPYKQKRRTKATIAKDKGLEPLADSLLQFNQTEVETLALPFINE--NVESVEEALQGA 160
Cdd:COG2183    82 LTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEekGVADVEAALDGA 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 161 SDILAERFADDAAIRESIRQISWKQGVIQSTVKAKELDEKSVFEMYYDYQEPVNKIVPHRILAINRGEKEDILKIGIEVP 240
Cdd:COG2183   162 RDILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPD 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 241 TESIYQLMRKKWIVSTSSPSSKLVEVAIEDAYKRLIQPSIEREIRNELTDKAETQAIHIFSENLRNLLLQPPMKGKYVLG 320
Cdd:COG2183   242 EEEAEAYIARRFIKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVLG 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 321 VDPAYRTGCKLAVVDDTGKMLEISVIYPHTAKADINKSKSIFNDLLNRYPISIIAIGNGTASRETEQFVSECLNESNASA 400
Cdd:COG2183   322 LDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELDLKV 401

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 401 AYVIVNEAGASVYSASPIAREEFPDLQVEQRSAVSIARRLQDPLAELVKIEPKAVGVGQYQHDVSQKKLAEQLTFIVETA 480
Cdd:COG2183   402 QYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDC 481

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 481 VNQVGVDVNTASSSLLQYVSGLSKTVAENIVKTRGEQGKFTARTQLKKIPRLGAKTYEQAIGFLRIPNAKNPLDSTAIHP 560
Cdd:COG2183   482 VNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDNSAVHP 561

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 561 ESYDLANRILEAVGLDKKQIGTAEAeqAIANLNIKELSKEwEIGEVTLKDVIDSLMKPSRDPRDAFPQPLLKKDVLKMED 640
Cdd:COG2183   562 ESYPVVEKILKDLGVSVKDLIGNKE--LLKKLDPEKYADE-LFGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLKIED 638

                         650       660       670       680       690       700       710
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1724454750 641 LQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTMLPPNQ 717
Cdd:COG2183   639 LKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDDE 715
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 10-192 1.70e-91

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: 282.76  E-value: 1.70e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750  10 IAKEIGIRTQQVDQVIQLLEASNTVPFIARYRKEATGSLDEVQIKAIEDRYHYVMQLEQRKQEVLRIIEEQGKLTEELTK 89
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750  90 DINEATVLKRVEDLYRPYKQKRRTKATIAKDKGLEPLADSLLqfNQTEVETLALPFINE--NVESVEEALQGASDILAER 167
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAIL--AQPDPEEEAAKYINPekGVADVEEALAGARDIIAER 158

                         170       180
                  ....*....|....*....|....*
gi 1724454750 168 FADDAAIRESIRQISWKQGVIQSTV 192
Cdd:pfam09371 159 ISEDAELRKKLRELLWREGVIVSKV 183
Tex_YqgF pfam16921
Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which ...
 318-441 1.92e-74

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: 236.14  E-value: 1.92e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 318 VLGVDPAYRTGCKLAVVDDTGKMLEISVIYPHTAKADINKSKSIFNDLLNRYPISIIAIGNGTASRETEQFVSECLNESN 397
Cdd:pfam16921   2 VLGLDPGYRTGCKLAVVDETGKVLDTAVIYPHPPQNKVEEAKKKLKKLIKKYGVELIAIGNGTASRETEQFVAELIKELP 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1724454750 398 ASAAYVIVNEAGASVYSASPIAREEFPDLQVEQRSAVSIARRLQ 441
Cdd:pfam16921  82 LKVKYVIVSEAGASVYSASELAREEFPDLDVSLRGAVSIARRLQ 125
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 644-711 5.74e-34

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: 123.88  E-value: 5.74e-34
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1724454750 644 GMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALT 711
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
HHH_9 pfam17674
HHH domain;
551-623 1.91e-25

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 99.92  E-value: 1.91e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1724454750 551 NPLDSTAIHPESYDLANRILEAVGLDKKQIGTAEAeqAIANLNIKELSKEwEIGEVTLKDVIDSLMKPSRDPR 623
Cdd:pfam17674   1 NPLDNTAIHPESYPLAEKILKDLGLDLKDLIGNSA--LLKKLDPKKLAEE-EVGLPTLKDILEELAKPGRDPR 70
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 483-544 3.37e-24

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


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 96.01  E-value: 3.37e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1724454750 483 QVGVDVNTASSSLLQYVSGLSKTVAENIVKTRGEQGKFTARTQLKKIPRLGAKTYEQAIGFL 544
Cdd:pfam12836   1 AVGVDINTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKTFEQLAGFL 62
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 643-710 1.94e-19

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: 82.68  E-value: 1.94e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1724454750 643 PGMELQGTVRNVVDFGAFVDIGVKqDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIAL 710
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDLGGV-DGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISL 67
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 638-712 3.07e-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: 89.72  E-value: 3.07e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1724454750 638 MEDLQPGMELQGTVRNVVDFGAFVDI-GVkqDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:COG0539   184 LEKLEEGDVVEGTVKNITDFGAFVDLgGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSL 257
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 316-414 8.45e-18

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: 79.15  E-value: 8.45e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750  316 KYVLGVDPAyRTGCKLAVVDDTGKMLEISVIYPHTakaDINKSKSIFNDLLNRYPISIIAIG-----NGTASRETEQFVS 390
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVIPRT---NKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFA 76

                           90       100
                   ....*....|....*....|....
gi 1724454750  391 ECLNEsNASAAYVIVNEAGASVYS 414
Cdd:smart00732  77 ELLKE-RFNLPVVLVDERLATVYA 99
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
642-712 1.03e-17

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 78.03  E-value: 1.03e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1724454750  642 QPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 632-712 3.72e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 84.16  E-value: 3.72e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 632 KKDVLKmEDLQPGMELQGTVRNVVDFGAFVDIG-VkqDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIAL 710
Cdd:PRK06676  182 KKEELL-SSLKEGDVVEGTVARLTDFGAFVDIGgV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISL 258


                  ..
gi 1724454750 711 TM 712
Cdd:PRK06676  259 SL 260
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 639-712 1.47e-16

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


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 83.90  E-value: 1.47e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1724454750 639 EDLQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEkDKGRIALTM 712
Cdd:COG1185   612 AEPEVGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEID-DQGRIKLSR 684
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 640-712 4.04e-15

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 79.32  E-value: 4.04e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1724454750 640 DLQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEkDKGRIALTM 712
Cdd:PRK11824  618 EPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSR 689
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 632-712 6.87e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 78.28  E-value: 6.87e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 632 KKDVLkMEDLQPGMELQGTVRNVVDFGAFVDIGVkQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALT 711
Cdd:PRK06299  191 EREEL-LENLEEGQVVEGVVKNITDYGAFVDLGG-VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLG 268


                  .
gi 1724454750 712 M 712
Cdd:PRK06299  269 L 269
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 639-712 9.35e-15

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 76.24  E-value: 9.35e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1724454750 639 EDLQPGMELQGTVRNVVDFGAFVDI--GVkqDGLVHISKL---KKgfVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:COG0539   270 EKYPVGDVVKGKVTRLTDFGAFVELepGV--EGLVHISEMswtKR--VAHPSDVVKVGDEVEVKVLDIDPEERRISLSI 344
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 644-712 1.89e-14

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: 68.34  E-value: 1.89e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1724454750 644 GMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEkDKGRIALTM 712
Cdd:cd04472     1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD-DRGRISLSR 68
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 639-712 2.71e-14

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 70.21  E-value: 2.71e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1724454750 639 EDLQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDkGRIALTM 712
Cdd:COG1098     1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDED-GKISLSI 73
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 641-712 2.79e-14

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: 68.08  E-value: 2.79e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1724454750 641 LQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
PRK08582 PRK08582
RNA-binding protein S1;
644-711 4.82e-14

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 69.68  E-value: 4.82e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1724454750 644 GMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDkGRIALT 711
Cdd:PRK08582    6 GSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDD-GKIGLS 72
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 644-712 7.31e-14

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 66.93  E-value: 7.31e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1724454750 644 GMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVeKDKGRIALTM 712
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSI-DARGRISLSI 68
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 632-710 3.62e-13

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 72.46  E-value: 3.62e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1724454750 632 KKDVLKmEDLQPGMELQGTVRNVVDFGAFVDIGVkQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIAL 710
Cdd:TIGR00717 177 AREELL-ENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISL 253
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 647-711 6.28e-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: 6.28e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1724454750 647 LQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALT 711
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
630-710 7.83e-13

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 71.90  E-value: 7.83e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 630 LLKKDVLKMED-----LQPGMELQGTVRNVVDFGAFVDI-GVkqDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEK 703
Cdd:PRK00087  459 ILEEEKEKKKEetwnsLEEGDVVEGEVKRLTDFGAFVDIgGV--DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDK 536


                  ....*..
gi 1724454750 704 DKGRIAL 710
Cdd:PRK00087  537 ENKKLSL 543
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 639-712 2.30e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 69.13  E-value: 2.30e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1724454750 639 EDLQPGMELQGTVRNVVDFGAFVDI--GVkqDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:PRK06676  273 EKLPEGDVIEGTVKRLTDFGAFVEVlpGV--EGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSI 346
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 641-712 1.32e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 67.38  E-value: 1.32e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1724454750 641 LQPGMELQGTVRNVVDFGAFVDIGvKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:PRK07899  206 LQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSL 276
PRK08059 PRK08059
general stress protein 13; Validated
 638-712 1.98e-11

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 61.60  E-value: 1.98e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1724454750 638 MEDLQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:PRK08059    2 MSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSI 76
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 644-712 2.35e-11

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: 61.29  E-value: 2.35e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1724454750 644 GMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:NF040579    4 GDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSL 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 639-712 2.86e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 66.73  E-value: 2.86e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1724454750 639 EDLQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKL---KKgfVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:PRK06299  282 KKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMswtKK--NKHPSKVVSVGQEVEVMVLEIDEEKRRISLGL 356
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 648-712 3.89e-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: 59.56  E-value: 3.89e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1724454750 648 QGTVRNVVDFGAFVDI-GVK--QDGLVHISKL-KKGFVKHPLDVVSLGDIVTVWVDNVEKDKgrIALTM 712
Cdd:cd05684     5 KGKVTSIMDFGCFVQLeGLKgrKEGLVHISQLsFEGRVANPSDVVKRGQKVKVKVISIQNGK--ISLSM 71
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
638-712 6.38e-10

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 62.27  E-value: 6.38e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1724454750 638 MEDLQPGMELQGTVRNVVDFGAFVDI--GVkqDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:PRK00087  557 EEKYPVGSIVLGKVVRIAPFGAFVELepGV--DGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSI 631
rpsA PRK13806
30S ribosomal protein S1; Provisional
 639-712 6.68e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 62.05  E-value: 6.68e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1724454750 639 EDLQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLK--KGFVKhPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:PRK13806  288 DRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSwtRRVNK-PEDVVAPGDAVAVKIKDIDPAKRRISLSL 362
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 644-710 8.00e-10

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: 55.58  E-value: 8.00e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1724454750 644 GMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLK-KGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIAL 710
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 632-712 1.13e-09

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: 55.29  E-value: 1.13e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 632 KKDVLKMEDLQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALT 711
Cdd:cd04461     3 GTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLS 82


                  .
gi 1724454750 712 M 712
Cdd:cd04461    83 L 83
rpsA PRK13806
30S ribosomal protein S1; Provisional
 638-711 1.41e-09

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 60.89  E-value: 1.41e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1724454750 638 MEDLQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKG----RIALT 711
Cdd:PRK13806  197 METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLS 274
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 644-710 2.83e-09

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: 54.12  E-value: 2.83e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 644 GMELQGTVRNVVDFGAFVDIGVKQDGLVHISKL---KKGFvkHPLDVVSLGDIVTVWVDNVEKDKGRIAL 710
Cdd:cd05689     4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMdwtNKNI--HPSKVVSLGDEVEVMVLDIDEERRRISL 71
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 642-710 3.83e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 59.79  E-value: 3.83e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1724454750 642 QPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKL---KKGfvKHPLDVVSLGDIVTVWVDNVEKDKGRIAL 710
Cdd:PRK06299  372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDIswdKKG--EEAVELYKKGDEVEAVVLKVDVEKERISL 441
PRK05807 PRK05807
RNA-binding protein S1;
641-712 7.90e-09

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 54.75  E-value: 7.90e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1724454750 641 LQPGMELQGTVRNVVDFGAFVDIGVKQdGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEkDKGRIALTM 712
Cdd:PRK05807    3 LKAGSILEGTVVNITNFGAFVEVEGKT-GLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISLSI 72
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 644-714 9.16e-09

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: 52.72  E-value: 9.16e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1724454750 644 GMELQGTVRNVVDFGAFVDI-GVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTMLP 714
Cdd:cd05708     3 GQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKA 74
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 486-545 1.23e-08

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


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 52.17  E-value: 1.23e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 486 VDVNTASSSLLQYVSGLSKTVAENIVKTRGEQGKFTARTQLKKIPRLGAKTYEQAIGFLR 545
Cdd:COG1555    13 VDINTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGIGPKTLEKLKPYLT 72
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 638-710 3.67e-08

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: 56.77  E-value: 3.67e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1724454750 638 MEDLQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLkkgfvKHPLDVvslGDIVTVWVDNVeKDKGRIAL 710
Cdd:COG1107    34 PDDLEPGRYYRGTVDGVADFGVFVDLNDHVTGLLHRSEL-----DQDWEV---GDEVFVQVKEV-RDNGNVDL 97
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 639-710 4.86e-08

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: 56.28  E-value: 4.86e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1724454750 639 EDLQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLK-KGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIAL 710
Cdd:TIGR00717 268 KKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSL 340
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 647-712 1.07e-07

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: 49.40  E-value: 1.07e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1724454750 647 LQGTVRNVVDFGAFVDI-GVKQDGLVHISKLKKGFVKHPLDVVSLGDIvtVWVDNVEKD-KGRIALTM 712
Cdd:cd05686     7 FKGEVASVTEYGAFVKIpGCRKQGLVHKSHMSSCRVDDPSEVVDVGEK--VWVKVIGREmKDKMKLSL 72
HHH_7 pfam14635
Helix-hairpin-helix motif;
460-547 1.75e-07

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 49.85  E-value: 1.75e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 460 YQHDVSQkklaEQLTFIVETA----VNQVGVDVNTA-----SSSLLQYVSGLSKTVAENIVKT-RGEQGKFTARTQLKKI 529
Cdd:pfam14635  11 LQELLPK----EELLKALETAfvdiVNLVGVDVNEAiankyEAAILPYIAGLGPRKADHLLKIlAANNGRLDNRSQLITK 86

                          90
                  ....*....|....*...
gi 1724454750 530 PRLGAKTYEQAIGFLRIP 547
Cdd:pfam14635  87 CIMGPKVFMNCAGFLIID 104
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 642-712 4.64e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 53.24  E-value: 4.64e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1724454750 642 QPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:PRK06299  459 KKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSI 529
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 642-712 6.87e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 52.35  E-value: 6.87e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1724454750 642 QPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:PRK07899  292 AIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSL 362
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 637-711 8.67e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 51.34  E-value: 8.67e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1724454750 637 KMEDLQPGMELQGTVRNVVDFGAFVDIGvKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALT 711
Cdd:PRK07400  190 KMNRLEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLS 263
VacB COG0557
Exoribonuclease R [Transcription];
631-713 1.02e-06

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 52.03  E-value: 1.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 631 LKKdVLKMEDlQPGMELQGTVRNVVDFGAFV---DIGVkqDGLVHISKLKKGF-----VKHPL------DVVSLGDIVTV 696
Cdd:COG0557   612 LKK-AEYMKD-RVGEEFEGVISGVTSFGLFVeldELGV--EGLVHVSSLGDDYyeydeRRQALvgertgKRYRLGDRVEV 687

                          90
                  ....*....|....*..
gi 1724454750 697 WVDNVEKDKGRIALTML 713
Cdd:COG0557   688 RVVRVDLDRRQIDFELV 704
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 644-713 3.83e-06

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: 45.47  E-value: 3.83e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 644 GMELQGTVRNVVDFGAFV---DIGVkqDGLVHISKLKKGF-----VKHPLD------VVSLGDIVTVWVDNVEKDKGRIA 709
Cdd:cd04471     2 GEEFDGVISGVTSFGLFVeldNLTV--EGLVHVSTLGDDYyefdeENHALVgertgkVFRLGDKVKVRVVRVDLDRRKID 79


                  ....
gi 1724454750 710 LTML 713
Cdd:cd04471    80 FELV 83
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 638-710 3.86e-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: 45.29  E-value: 3.86e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1724454750 638 MEDLQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFvkhpldvvSLGDIVTVWVDNVeKDKGRIAL 710
Cdd:cd04473    11 MEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDY--------EVGDEVIVQVTDI-PENGNIDL 74
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
644-712 5.80e-06

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 45.85  E-value: 5.80e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1724454750 644 GMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:PRK07252    4 GDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSL 72
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 648-715 7.50e-06

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: 44.97  E-value: 7.50e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 648 QGTVRNVVDFGAFVDIGvKQDGLVHISKLKKGFVKHPLDVVSL-----------GD-----IVTVWVDNVEKDKGRIALT 711
Cdd:cd04460     4 EGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLigeetkrvlkvGDvvrarIVAVSLKERRPRESKIGLT 82


                  ....
gi 1724454750 712 MLPP 715
Cdd:cd04460    83 MRQP 86
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 649-712 1.35e-05

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


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 43.73  E-value: 1.35e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1724454750 649 GTVRNVVDFGAFVDIGVKQD--GLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:cd04452     9 VTVKSIADMGAYVSLLEYGNieGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSK 74
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 638-710 1.78e-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: 47.35  E-value: 1.78e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1724454750 638 MEDLQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKgfvKHPLDVVSLGDIVTVWVDNVEKDKGRIAL 710
Cdd:COG0539    13 LKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSD---EPGELEVKVGDEVEVYVEKVEDGEGEIVL 82
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 649-710 1.92e-05

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 46.74  E-value: 1.92e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1724454750 649 GTVRNVVDFGAFVDI---GVKQdGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIAL 710
Cdd:PRK03987   14 GTVKEVKDFGAFVTLdeyPGKE-GFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDL 77
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 637-711 2.56e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 47.18  E-value: 2.56e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1724454750 637 KMEDLQPGMELQGTVRNVVDFGAFVDI-GVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALT 711
Cdd:PRK06676   11 SVKEVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLS 86
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 647-710 3.38e-05

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: 42.13  E-value: 3.38e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1724454750 647 LQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIAL 710
Cdd:cd05687     4 VKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVL 67
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 648-712 5.27e-05

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 44.43  E-value: 5.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 648 QGTVRNVVDFGAFVDIGVkQDGLVHISKLKKGFVKHPLD-----------VVSLGD-----IVTVWVDNVEKDKGRIALT 711
Cdd:PRK08563   86 EGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYISYDPKngrligkeskrVLKVGDvvrarIVAVSLKERRPRGSKIGLT 164


                  .
gi 1724454750 712 M 712
Cdd:PRK08563  165 M 165
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 644-711 6.13e-05

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: 41.45  E-value: 6.13e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1724454750 644 GMELQGTVRNVVDFGAFVDIGVKQDGLV---HISKLKkgfVKHPLDVVSLGDIVTVWVDNVEKDKGRIALT 711
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVppmHLADVR---LKHPEKKFKPGLKVKCRVLSVEPERKRLVLT 68
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 644-711 1.06e-04

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: 40.74  E-value: 1.06e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1724454750 644 GMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALT 711
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
631-710 1.56e-04

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 44.94  E-value: 1.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 631 LKKDVLKMEDLQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIAL 710
Cdd:PRK00087  290 LEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVL 369
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 644-711 2.06e-04

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: 39.90  E-value: 2.06e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724454750 644 GMELQGTVRNVVDFGAFVDI--GVKqdGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALT 711
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFynNVK--GFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLS 68
rpsA PRK13806
30S ribosomal protein S1; Provisional
 639-711 4.09e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 43.56  E-value: 4.09e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1724454750 639 EDLQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALT 711
Cdd:PRK13806  375 ERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLA 447
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 644-711 5.20e-04

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 43.18  E-value: 5.20e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1724454750 644 GMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALT 711
Cdd:TIGR00717 447 GSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLS 514
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 647-712 8.77e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 42.78  E-value: 8.77e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1724454750 647 LQGTVRNVVDFGAFVDIGvKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:PRK12269  497 VSGVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSL 561
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 634-710 9.41e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 42.46  E-value: 9.41e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1724454750 634 DVLKMEDLQPGMELQGTVRNVVDFGAFVDIGVKQDGLVHISKLK--KGFVKhpldvVSLGDIVTVWVDNVEKDKGRIAL 710
Cdd:PRK06299   21 ESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKneQGELE-----VKVGDEVEVYVERIEDGFGETVL 94
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 651-711 1.16e-03

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 42.19  E-value: 1.16e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1724454750 651 VRNVVDFGAFVDIGVKQDGLVHISKLKKGFVKHPLDVVSLGDIVTVWVDNVeKDKGRIALT 711
Cdd:PLN00207  762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEV-NDKGQLRLS 821
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 647-712 3.07e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 40.85  E-value: 3.07e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1724454750 647 LQGTVRNVVDFGAFVDIGVKQDGLVHISK---LKKgfVKHPLDVVSLGDIVTVWVDNVEKDKGRIALTM 712
Cdd:PRK12269  582 VKGRVTKIADFGAFIELAEGIEGLAHISEfswVKK--TSKPSDMVKIGDEVECMILGYDIQAGRVSLGL 648
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 394-446 3.67e-03

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: 38.69  E-value: 3.67e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1724454750 394 NESNASAAYVIVNEAGASVYSASPIAREEFPDLQVEQRSAVSIARRLQDPLAE 446
Cdd:pfam14639  93 DSRLHTIGVILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLE 145
 
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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