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Conserved domains on  [gi|501508023|ref|WP_012515960|]
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Tex family protein [Streptococcus equi]

Protein Classification

Tex family protein( domain architecture ID 11450661)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1-709 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


:

Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1080.43  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023   1 MENMNHQNISEALGVTPKQISQVLALTAEGNTIPFIARYRKEATGNLDEVVIKAIIDMDKSLTQLRERKDTILAKIEGQG 80
Cdd:COG2183    1 MMMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023  81 KLTAALKEAIEAADKLADLEELYLPYKEKRRTKATIAREAGISGLARLIL-QNAQDLETKAEAFITE--GFSDPQAALAG 157
Cdd:COG2183   81 KLTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLaQPTGDPEAEAAKYINEekGVADVEAALDG 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 158 AVDILVEAMSEDSRLRSWTYNEIWKYSRITSSLKEASLDDKRVFQIYYAFSETVSNMQGYRTLALNRGEKLGILKVSFEH 237
Cdd:COG2183  161 ARDILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEP 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 238 HIDKMLRFFSLRF-KEHNAYIDDVINQTI----KKKIVPAMERRIRTELTEMAEDGAIKLFSENLRHLLLISPLKGKMVL 312
Cdd:COG2183  241 DEEEAEAYIARRFiKDQGRPADEWLKEAVrdayKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVL 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 313 GFDPAFRTGAKLAVIDPTGKLLTTQVIYPVAPANQakIQAARVALAQLITDYQIDIIAIGNGTASRESEAFVAEVLKDFP 392
Cdd:COG2183  321 GLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNK--WEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELD 398

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 393 -ETSYVIVNESGASVYSASELARHEFPELTVEKRSAISIARRLQDPLAELVKIDPKAIGVGQYQHDVSQKKLSEHLDFVV 471
Cdd:COG2183  399 lKVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVV 478

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 472 DTVVNQVGVNINTASPALLAHVSGLNKTISENIVRYREENGEITSRAEIKKVPRLGAKAFEQAAGFLRIPNAKNILDNTG 551
Cdd:COG2183  479 EDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDNSA 558

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 552 VHPEAYPAVKKLFQLL--AIKDLDEPaRAKLQAVNLEEMAEQlTLGQETLKDIIADLLKPGRDLRDDFEAPVLRKDILSV 629
Cdd:COG2183  559 VHPESYPVVEKILKDLgvSVKDLIGN-KELLKKLDPEKYADE-LFGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLKI 636

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 630 KDLAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSLVPPRDA 709
Cdd:COG2183  637 EDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDDEA 716
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1-709 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1080.43  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023   1 MENMNHQNISEALGVTPKQISQVLALTAEGNTIPFIARYRKEATGNLDEVVIKAIIDMDKSLTQLRERKDTILAKIEGQG 80
Cdd:COG2183    1 MMMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023  81 KLTAALKEAIEAADKLADLEELYLPYKEKRRTKATIAREAGISGLARLIL-QNAQDLETKAEAFITE--GFSDPQAALAG 157
Cdd:COG2183   81 KLTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLaQPTGDPEAEAAKYINEekGVADVEAALDG 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 158 AVDILVEAMSEDSRLRSWTYNEIWKYSRITSSLKEASLDDKRVFQIYYAFSETVSNMQGYRTLALNRGEKLGILKVSFEH 237
Cdd:COG2183  161 ARDILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEP 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 238 HIDKMLRFFSLRF-KEHNAYIDDVINQTI----KKKIVPAMERRIRTELTEMAEDGAIKLFSENLRHLLLISPLKGKMVL 312
Cdd:COG2183  241 DEEEAEAYIARRFiKDQGRPADEWLKEAVrdayKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVL 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 313 GFDPAFRTGAKLAVIDPTGKLLTTQVIYPVAPANQakIQAARVALAQLITDYQIDIIAIGNGTASRESEAFVAEVLKDFP 392
Cdd:COG2183  321 GLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNK--WEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELD 398

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 393 -ETSYVIVNESGASVYSASELARHEFPELTVEKRSAISIARRLQDPLAELVKIDPKAIGVGQYQHDVSQKKLSEHLDFVV 471
Cdd:COG2183  399 lKVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVV 478

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 472 DTVVNQVGVNINTASPALLAHVSGLNKTISENIVRYREENGEITSRAEIKKVPRLGAKAFEQAAGFLRIPNAKNILDNTG 551
Cdd:COG2183  479 EDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDNSA 558

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 552 VHPEAYPAVKKLFQLL--AIKDLDEPaRAKLQAVNLEEMAEQlTLGQETLKDIIADLLKPGRDLRDDFEAPVLRKDILSV 629
Cdd:COG2183  559 VHPESYPVVEKILKDLgvSVKDLIGN-KELLKKLDPEKYADE-LFGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLKI 636

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 630 KDLAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSLVPPRDA 709
Cdd:COG2183  637 EDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDDEA 716
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 9-190 2.34e-76

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: 243.08  E-value: 2.34e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023    9 ISEALGVTPKQISQVLALTAEGNTIPFIARYRKEATGNLDEVVIKAIIDMDKSLTQLRERKDTILAKIEGQGKLTAALKE 88
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023   89 AIEAADKLADLEELYLPYKEKRRTKATIAREAGISGLARLILQNAqDLETKAEAFITE--GFSDPQAALAGAVDILVEAM 166
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQP-DPEEEAAKYINPekGVADVEEALAGARDIIAERI 159

                         170       180
                  ....*....|....*....|....
gi 501508023  167 SEDSRLRSWTYNEIWKYSRITSSL 190
Cdd:pfam09371 160 SEDAELRKKLRELLWREGVIVSKV 183
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 635-702 1.06e-32

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: 120.42  E-value: 1.06e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501508023 635 GQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLS 702
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 309-408 2.43e-24

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: 97.64  E-value: 2.43e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023   309 KMVLGFDPAfRTGAKLAVIDPTGKLLTTQVIYPVApanqaKIQAARVALAQLITDYQIDIIAIG-----NGTASRESEAF 383
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVIPRT-----NKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEA 74

                           90       100
                   ....*....|....*....|....*
gi 501508023   384 VAEVLKDFPETSYVIVNESGASVYS 408
Cdd:smart00732  75 FAELLKERFNLPVVLVDERLATVYA 99
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 623-703 1.09e-20

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 94.94  E-value: 1.09e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 623 RKDILSVkdLAVGQRLEGTVRNVVDFGAFVDIG-VheDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNL 701
Cdd:PRK06676 183 KEELLSS--LKEGDVVEGTVARLTDFGAFVDIGgV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISL 258


                 ..
gi 501508023 702 SL 703
Cdd:PRK06676 259 SL 260
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 634-703 1.15e-15

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: 73.23  E-value: 1.15e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 634 VGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:NF040579   3 IGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSL 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 632-703 3.96e-14

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 75.54  E-value: 3.96e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 501508023  632 LAVGQRLEGTVRNVVDFGAFVDIGVHeDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:TIGR00717 185 LKEGDVVKGVVKNITDFGAFVDLGGV-DGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1-709 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1080.43  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023   1 MENMNHQNISEALGVTPKQISQVLALTAEGNTIPFIARYRKEATGNLDEVVIKAIIDMDKSLTQLRERKDTILAKIEGQG 80
Cdd:COG2183    1 MMMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023  81 KLTAALKEAIEAADKLADLEELYLPYKEKRRTKATIAREAGISGLARLIL-QNAQDLETKAEAFITE--GFSDPQAALAG 157
Cdd:COG2183   81 KLTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLaQPTGDPEAEAAKYINEekGVADVEAALDG 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 158 AVDILVEAMSEDSRLRSWTYNEIWKYSRITSSLKEASLDDKRVFQIYYAFSETVSNMQGYRTLALNRGEKLGILKVSFEH 237
Cdd:COG2183  161 ARDILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEP 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 238 HIDKMLRFFSLRF-KEHNAYIDDVINQTI----KKKIVPAMERRIRTELTEMAEDGAIKLFSENLRHLLLISPLKGKMVL 312
Cdd:COG2183  241 DEEEAEAYIARRFiKDQGRPADEWLKEAVrdayKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVL 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 313 GFDPAFRTGAKLAVIDPTGKLLTTQVIYPVAPANQakIQAARVALAQLITDYQIDIIAIGNGTASRESEAFVAEVLKDFP 392
Cdd:COG2183  321 GLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNK--WEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELD 398

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 393 -ETSYVIVNESGASVYSASELARHEFPELTVEKRSAISIARRLQDPLAELVKIDPKAIGVGQYQHDVSQKKLSEHLDFVV 471
Cdd:COG2183  399 lKVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVV 478

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 472 DTVVNQVGVNINTASPALLAHVSGLNKTISENIVRYREENGEITSRAEIKKVPRLGAKAFEQAAGFLRIPNAKNILDNTG 551
Cdd:COG2183  479 EDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDNSA 558

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 552 VHPEAYPAVKKLFQLL--AIKDLDEPaRAKLQAVNLEEMAEQlTLGQETLKDIIADLLKPGRDLRDDFEAPVLRKDILSV 629
Cdd:COG2183  559 VHPESYPVVEKILKDLgvSVKDLIGN-KELLKKLDPEKYADE-LFGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLKI 636

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 630 KDLAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSLVPPRDA 709
Cdd:COG2183  637 EDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDDEA 716
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 9-190 2.34e-76

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: 243.08  E-value: 2.34e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023    9 ISEALGVTPKQISQVLALTAEGNTIPFIARYRKEATGNLDEVVIKAIIDMDKSLTQLRERKDTILAKIEGQGKLTAALKE 88
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023   89 AIEAADKLADLEELYLPYKEKRRTKATIAREAGISGLARLILQNAqDLETKAEAFITE--GFSDPQAALAGAVDILVEAM 166
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQP-DPEEEAAKYINPekGVADVEEALAGARDIIAERI 159

                         170       180
                  ....*....|....*....|....
gi 501508023  167 SEDSRLRSWTYNEIWKYSRITSSL 190
Cdd:pfam09371 160 SEDAELRKKLRELLWREGVIVSKV 183
Tex_YqgF pfam16921
Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which ...
 311-435 5.85e-71

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: 226.51  E-value: 5.85e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023  311 VLGFDPAFRTGAKLAVIDPTGKLLTTQVIYPVAPANqaKIQAARVALAQLITDYQIDIIAIGNGTASRESEAFVAEVLKD 390
Cdd:pfam16921   2 VLGLDPGYRTGCKLAVVDETGKVLDTAVIYPHPPQN--KVEEAKKKLKKLIKKYGVELIAIGNGTASRETEQFVAELIKE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 501508023  391 FP-ETSYVIVNESGASVYSASELARHEFPELTVEKRSAISIARRLQ 435
Cdd:pfam16921  80 LPlKVKYVIVSEAGASVYSASELAREEFPDLDVSLRGAVSIARRLQ 125
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 635-702 1.06e-32

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: 120.42  E-value: 1.06e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501508023 635 GQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLS 702
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 477-538 1.63e-27

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


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 105.26  E-value: 1.63e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 501508023  477 QVGVNINTASPALLAHVSGLNKTISENIVRYREENGEITSRAEIKKVPRLGAKAFEQAAGFL 538
Cdd:pfam12836   1 AVGVDINTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKTFEQLAGFL 62
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 309-408 2.43e-24

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: 97.64  E-value: 2.43e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023   309 KMVLGFDPAfRTGAKLAVIDPTGKLLTTQVIYPVApanqaKIQAARVALAQLITDYQIDIIAIG-----NGTASRESEAF 383
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVIPRT-----NKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEA 74

                           90       100
                   ....*....|....*....|....*
gi 501508023   384 VAEVLKDFPETSYVIVNESGASVYS 408
Cdd:smart00732  75 FAELLKERFNLPVVLVDERLATVYA 99
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 623-703 9.67e-24

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: 103.20  E-value: 9.67e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 623 RKDILSvkDLAVGQRLEGTVRNVVDFGAFVDI-GVheDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNL 701
Cdd:COG0539  180 REELLE--KLEEGDVVEGTVKNITDFGAFVDLgGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISL 255


                 ..
gi 501508023 702 SL 703
Cdd:COG0539  256 SL 257
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 634-702 9.83e-24

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: 95.00  E-value: 9.83e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501508023 634 VGQRLEGTVRNVVDFGAFVDIGVhEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLS 702
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDLGG-VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
HHH_9 pfam17674
HHH domain;
545-614 7.75e-21

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 86.82  E-value: 7.75e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 501508023  545 NILDNTGVHPEAYPAVKKLFQLLA--IKDLDePARAKLQAVNLEEMAEQlTLGQETLKDIIADLLKPGRDLR 614
Cdd:pfam17674   1 NPLDNTAIHPESYPLAEKILKDLGldLKDLI-GNSALLKKLDPKKLAEE-EVGLPTLKDILEELAKPGRDPR 70
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 623-703 1.09e-20

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 94.94  E-value: 1.09e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 623 RKDILSVkdLAVGQRLEGTVRNVVDFGAFVDIG-VheDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNL 701
Cdd:PRK06676 183 KEELLSS--LKEGDVVEGTVARLTDFGAFVDIGgV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISL 258


                 ..
gi 501508023 702 SL 703
Cdd:PRK06676 259 SL 260
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 603-703 4.29e-20

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 92.41  E-value: 4.29e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 603 IADLLKPGrdlrDDFEAPVLRKDI------LSVKDL------------AVGQRLEGTVRNVVDFGAFVDI--GVheDGLI 662
Cdd:COG0539  229 PSEVLKVG----DEVEVKVLKIDRekerisLSLKQLqpdpweniaekyPVGDVVKGKVTRLTDFGAFVELepGV--EGLV 302

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 501508023 663 HISEMS-EAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:COG0539  303 HISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSI 344
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 623-703 9.84e-20

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 93.31  E-value: 9.84e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 623 RKDILSvkDLAVGQRLEGTVRNVVDFGAFVDIGVhEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLS 702
Cdd:PRK06299 192 REELLE--NLEEGQVVEGVVKNITDYGAFVDLGG-VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLG 268


                 .
gi 501508023 703 L 703
Cdd:PRK06299 269 L 269
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 632-703 2.47e-19

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 91.64  E-value: 2.47e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 501508023 632 LAVGQRLEGTVRNVVDFGAFVDIG-VheDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:PRK07899 206 LQKGQVRKGVVSSIVNFGAFVDLGgV--DGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSL 276
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
634-703 6.83e-19

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 81.11  E-value: 6.83e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023   634 VGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
623-703 1.58e-17

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 86.92  E-value: 1.58e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 623 RKDILSV----------KDLAVGQRLEGTVRNVVDFGAFVDI-GVheDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSK 691
Cdd:PRK00087 456 RKAILEEekekkkeetwNSLEEGDVVEGEVKRLTDFGAFVDIgGV--DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILD 533

                         90
                 ....*....|..
gi 501508023 692 VDLDRHKVNLSL 703
Cdd:PRK00087 534 IDKENKKLSLSL 545
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 624-702 2.25e-17

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


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 86.21  E-value: 2.25e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 624 KDIlsVKDLAVGQRLEGTVRNVVDFGAFVDI--GVheDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDlDRHKVNL 701
Cdd:COG1185  608 EGI--TAEPEVGEIYEGKVVRIMDFGAFVEIlpGK--DGLVHISELADERVEKVEDVLKEGDEVKVKVLEID-DQGRIKL 682


                 .
gi 501508023 702 S 702
Cdd:COG1185  683 S 683
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 629-703 1.17e-16

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 83.95  E-value: 1.17e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 501508023 629 VKDLAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDlDRHKVNLSL 703
Cdd:PRK11824 616 TAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSR 689
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 630-703 1.80e-16

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 76.37  E-value: 1.80e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501508023 630 KDLAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDlDRHKVNLSL 703
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSID-EDGKISLSI 73
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 635-702 7.13e-16

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


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 72.58  E-value: 7.13e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501508023 635 GQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDlDRHKVNLS 702
Cdd:cd04472    1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD-DRGRISLS 67
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 634-703 1.15e-15

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: 73.23  E-value: 1.15e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 634 VGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:NF040579   3 IGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSL 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 632-703 4.50e-15

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: 70.39  E-value: 4.50e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 501508023  632 LAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 603-703 4.97e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 77.61  E-value: 4.97e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 603 IADLLKPGrdlrDDFEAPVLRKDI------LSVKD------------LAVGQRLEGTVRNVVDFGAFVDI--GVheDGLI 662
Cdd:PRK06676 232 PSEVVSVG----QEVEVKVLSIDWeterisLSLKDtlpgpwegveekLPEGDVIEGTVKRLTDFGAFVEVlpGV--EGLV 305

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 501508023 663 HISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:PRK06676 306 HISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSI 346
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 635-702 1.10e-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: 69.24  E-value: 1.10e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501508023 635 GQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDlDRHKVNLS 702
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID-ARGRISLS 67
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 638-702 1.73e-14

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: 68.56  E-value: 1.73e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 501508023 638 LEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLS 702
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 630-703 2.87e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 75.97  E-value: 2.87e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 501508023 630 KDLAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVN-HPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:PRK06299 282 KKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNkHPSKVVSVGQEVEVMVLEIDEEKRRISLGL 356
rpsA PRK13806
30S ribosomal protein S1; Provisional
 632-709 3.69e-14

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 75.53  E-value: 3.69e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501508023 632 LAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEA-FVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSLvppRDA 709
Cdd:PRK13806 290 LKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTrRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSL---RDA 365
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 632-703 3.96e-14

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 75.54  E-value: 3.96e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 501508023  632 LAVGQRLEGTVRNVVDFGAFVDIGVHeDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:TIGR00717 185 LKEGDVVKGVVKNITDFGAFVDLGGV-DGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 633-705 1.28e-13

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: 66.58  E-value: 1.28e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501508023 633 AVGQRLEGTVRNVVDFGAFVDI-GVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSLVP 705
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKA 74
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 633-703 1.32e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 73.93  E-value: 1.32e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 501508023 633 AVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:PRK07899 292 AIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSL 362
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 630-703 1.80e-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: 73.61  E-value: 1.80e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 501508023  630 KDLAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMS-EAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:TIGR00717 268 KKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGL 342
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 635-701 1.95e-12

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: 62.98  E-value: 1.95e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501508023 635 GQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVN-HPSQVVSVGDLVTVWVSKVDLDRHKVNL 701
Cdd:cd05689    4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNiHPSKVVSLGDEVEVMVLDIDEERRRISL 71
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 635-710 3.10e-12

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: 62.64  E-value: 3.10e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 635 GQRLEGTVRNVVDFGAFVDI-GVHE--DGLIHISEMS-EAFVNHPSQVVSVGDLVTVWVSKVdlDRHKVNLSLvppRDAD 710
Cdd:cd05684    1 GKIYKGKVTSIMDFGCFVQLeGLKGrkEGLVHISQLSfEGRVANPSDVVKRGQKVKVKVISI--QNGKISLSM---KDVD 75
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
623-703 5.52e-12

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 69.21  E-value: 5.52e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 623 RKDILSVKDL------------AVGQRLEGTVRNVVDFGAFVDI--GVheDGLIHISEMSEAFVNHPSQVVSVGDLVTVW 688
Cdd:PRK00087 539 KKLSLSLKKLlpdpwenveekyPVGSIVLGKVVRIAPFGAFVELepGV--DGLVHISQISWKRIDKPEDVLSEGEEVKAK 616

                         90
                 ....*....|....*
gi 501508023 689 VSKVDLDRHKVNLSL 703
Cdd:PRK00087 617 ILEVDPEEKRIRLSI 631
PRK08582 PRK08582
RNA-binding protein S1;
634-703 6.41e-12

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 63.51  E-value: 6.41e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 634 VGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDlDRHKVNLSL 703
Cdd:PRK08582   5 VGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE-DDGKIGLSI 73
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 480-539 3.22e-11

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


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 59.49  E-value: 3.22e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 480 VNINTASPALLAHVSGLNKTISENIVRYREENGEITSRAEIKKVPRLGAKAFEQAAGFLR 539
Cdd:COG1555   13 VDINTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGIGPKTLEKLKPYLT 72
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 635-701 3.47e-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: 3.47e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501508023 635 GQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMS-EAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNL 701
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 634-702 6.14e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 65.57  E-value: 6.14e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 634 VGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMS-EAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLS 702
Cdd:PRK06299 373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLG 442
PRK08059 PRK08059
general stress protein 13; Validated
 634-703 6.22e-11

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 60.06  E-value: 6.22e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 634 VGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:PRK08059   7 VGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSI 76
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 605-702 1.29e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 61.33  E-value: 1.29e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 605 DLLKPGrdlrDDFEAPVLRKDI------LSVKDL------------AVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISE 666
Cdd:PRK06299 417 ELYKKG----DEVEAVVLKVDVekerisLGIKQLeedpfeefakkhKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASE 492

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 501508023 667 MSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLS 702
Cdd:PRK06299 493 LSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLS 528
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 634-704 1.93e-09

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: 54.71  E-value: 1.93e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 634 VGQRLEGTVRNVVDFGAFV---DIGVheDGLIHISEMSE----------AFVNHPS-QVVSVGDLVTVWVSKVDLDRHKV 699
Cdd:cd04471    1 VGEEFDGVISGVTSFGLFVeldNLTV--EGLVHVSTLGDdyyefdeenhALVGERTgKVFRLGDKVKVRVVRVDLDRRKI 78


                 ....*
gi 501508023 700 NLSLV 704
Cdd:cd04471   79 DFELV 83
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 633-703 1.96e-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: 1.96e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 501508023 633 AVGQRLEGTVRNVVDFGAFVDI-GVHEDGLIHISEMSEAFVNHPSQVVSVGDlvTVWVSKVDLD-RHKVNLSL 703
Cdd:cd05686    2 ALYQIFKGEVASVTEYGAFVKIpGCRKQGLVHKSHMSSCRVDDPSEVVDVGE--KVWVKVIGREmKDKMKLSL 72
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 632-702 3.71e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 58.66  E-value: 3.71e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 501508023 632 LAVGQRLEGTVRNVVDFGAFVDIGvHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLS 702
Cdd:PRK07400 194 LEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLS 263
rpsA PRK13806
30S ribosomal protein S1; Provisional
 630-693 4.02e-09

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 59.74  E-value: 4.02e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501508023 630 KDLAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVD 693
Cdd:PRK13806 198 ETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIE 261
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
634-703 7.98e-09

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 54.32  E-value: 7.98e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 634 VGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:PRK07252   3 IGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSL 72
PRK05807 PRK05807
RNA-binding protein S1;
632-703 1.14e-08

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 53.98  E-value: 1.14e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 501508023 632 LAVGQRLEGTVRNVVDFGAFVDIGvHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDlDRHKVNLSL 703
Cdd:PRK05807   3 LKAGSILEGTVVNITNFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISLSI 72
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 628-696 8.00e-08

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: 49.91  E-value: 8.00e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501508023 628 SVKDLAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFvnhpsqvvSVGDLVTVWVSKVDLDR 696
Cdd:cd04473   10 TMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDY--------EVGDEVIVQVTDIPENG 70
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 631-703 1.17e-07

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


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 49.51  E-value: 1.17e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 501508023 631 DLAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:cd04461   11 DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
VacB COG0557
Exoribonuclease R [Transcription];
634-709 1.89e-07

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 54.34  E-value: 1.89e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 634 VGQRLEGTVRNVVDFGAFV---DIGVheDGLIHISEMSE----------AFVNHPS-QVVSVGDLVTVWVSKVDLDRHKV 699
Cdd:COG0557  622 VGEEFEGVISGVTSFGLFVeldELGV--EGLVHVSSLGDdyyeyderrqALVGERTgKRYRLGDRVEVRVVRVDLDRRQI 699

                         90
                 ....*....|
gi 501508023 700 NLSLVPPRDA 709
Cdd:COG0557  700 DFELVEGGSE 709
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 634-703 2.24e-07

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 53.97  E-value: 2.24e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 501508023  634 VGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMS-EAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:TIGR00717 359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGV 429
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 628-702 3.48e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 52.96  E-value: 3.48e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 501508023 628 SVKDLAVGQRLEGTVRNVVDFGAFVDI-GVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLS 702
Cdd:PRK06676  11 SVKEVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLS 86
comE TIGR01259
comEA protein; This model describes the ComEA protein in bacteria. The com E locus is ...
 480-540 3.87e-07

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: 49.52  E-value: 3.87e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 501508023  480 VNINTASPALLAHVSGLNKTISENIVRYREENGEITSRAEIKKVPRLGAKAFEQAAGFLRI 540
Cdd:TIGR01259  60 VNINAASLEELQALPGIGPAKAKAIIEYREENGAFKSVDDLTKVSGIGEKSLEKLKDYATV 120
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 640-703 6.08e-07

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


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 47.22  E-value: 6.08e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501508023 640 GTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:cd05698    6 GTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSC 69
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 640-703 1.07e-06

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


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 46.81  E-value: 1.07e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 501508023 640 GTVRNVVDFGAFVDIGVHED--GLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:cd04452    9 VTVKSIADMGAYVSLLEYGNieGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSK 74
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 635-702 1.87e-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: 45.98  E-value: 1.87e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501508023 635 GQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLS 702
Cdd:cd05687    1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLS 68
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 628-705 1.95e-06

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: 50.99  E-value: 1.95e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501508023 628 SVKDLAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFvnhpsqvvSVGDLVTVWVSKVdldRHKVNLSLVP 705
Cdd:COG1107   33 TPDDLEPGRYYRGTVDGVADFGVFVDLNDHVTGLLHRSELDQDW--------EVGDEVFVQVKEV---RDNGNVDLGW 99
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 623-703 2.89e-06

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 49.44  E-value: 2.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 623 RKDILSVKDLAVGqrlegTVRNVVDFGAFVDIGVHED--GLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVN 700
Cdd:PRK03987   2 RKEWPEEGELVVG-----TVKEVKDFGAFVTLDEYPGkeGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHID 76


                 ...
gi 501508023 701 LSL 703
Cdd:PRK03987  77 LSL 79
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 635-703 3.89e-06

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: 44.92  E-value: 3.89e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501508023 635 GQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
592-702 4.68e-06

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 49.95  E-value: 4.68e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 592 LTLGQETLKDIIADLLKPGRDL---RDDFEAPVLRKDILSVKDLAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMS 668
Cdd:PRK00087 257 VTAGASTPDWIIEEVIKKMSELdnmEEVEENEQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELT 336

                         90       100       110
                 ....*....|....*....|....*....|....
gi 501508023 669 EAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLS 702
Cdd:PRK00087 337 LDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLS 370
HHH_7 pfam14635
Helix-hairpin-helix motif;
442-541 5.81e-06

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 45.61  E-value: 5.81e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023  442 VKIDPkaigvgqYQHDVSQKKLSEHLDFVVDTVVNQVGVNINTA-----SPALLAHVSGLNKTISENIVRYREENGE-IT 515
Cdd:pfam14635   6 LSFHP-------LQELLPKEELLKALETAFVDIVNLVGVDVNEAiankyEAAILPYIAGLGPRKADHLLKILAANNGrLD 78

                          90       100
                  ....*....|....*....|....*.
gi 501508023  516 SRAEIKKVPRLGAKAFEQAAGFLRIP 541
Cdd:pfam14635  79 NRSQLITKCIMGPKVFMNCAGFLIID 104
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 638-703 5.82e-06

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 49.71  E-value: 5.82e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 501508023 638 LEGTVRNVVDFGAFVDIGVHeDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:PRK12269 497 VSGVVKSFTSFGAFIDLGGF-DGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSL 561
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 639-685 6.88e-06

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 47.13  E-value: 6.88e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 501508023 639 EGTVRNVVDFGAFVDIGVHeDGLIHISEMSEAFVNHPSQ-----------VVSVGDLV 685
Cdd:PRK08563  86 EGEVVEVVEFGAFVRIGPV-DGLLHISQIMDDYISYDPKngrligkeskrVLKVGDVV 142
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 628-693 1.87e-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: 1.87e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 501508023 628 SVKDLAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAfvnHPSQVVSVGDLVTVWVSKVD 693
Cdd:COG0539   12 SLKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSDE---PGELEVKVGDEVEVYVEKVE 74
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 634-703 2.31e-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: 47.42  E-value: 2.31e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023  634 VGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:TIGR00717 446 VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSV 515
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 480-533 2.38e-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: 42.61  E-value: 2.38e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 501508023  480 VNINTASPALLA-HVSGLNKTISENIVRYREENGEITSRAEIKKVPRLGAKAFEQ 533
Cdd:TIGR00426   8 VNINTATAEELQrAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEK 62
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 595-710 4.81e-05

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 46.81  E-value: 4.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 595 GQETLKDIIADLLKPGRDLRDDFEAPVLRKDILSVK-----------DLAVGQRLEGT-VRNVVDFGAFVDIGVHEDGLI 662
Cdd:PLN00207 703 GGKKVKSIIEETGVEAIDTQDDGTVKITAKDLSSLEkskaiissltmVPTVGDIYRNCeIKSIAPYGAFVEIAPGREGLC 782

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 501508023 663 HISEMSEAFVNHPSQVVSVGDLVTVWVSKVDlDRHKVNLS---LVPPRDAD 710
Cdd:PLN00207 783 HISELSSNWLAKPEDAFKVGDRIDVKLIEVN-DKGQLRLSrraLLPEANSE 832
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 639-695 1.04e-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: 1.04e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501508023 639 EGTVRNVVDFGAFVDIGvHEDGLIHISEMSEAFV-----------NHPSQVVSVGDLVTVWVSKVDLD 695
Cdd:cd04460    4 EGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYIsydpknkrligEETKRVLKVGDVVRARIVAVSLK 70
rpsA PRK13806
30S ribosomal protein S1; Provisional
 620-710 2.72e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 43.94  E-value: 2.72e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 620 PVLRKDILSVKD------------LAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTV 687
Cdd:PRK13806 353 PAKRRISLSLRDaegdpwadvaerFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTL 432

                         90       100
                 ....*....|....*....|...
gi 501508023 688 WVSKVDLDRHKVnlSLVPPRDAD 710
Cdd:PRK13806 433 VVEEIDTAKRKI--SLAPAGAAG 453
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 632-703 3.14e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 44.32  E-value: 3.14e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 501508023 632 LAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEA-FVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:PRK12269 576 FGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVkKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGL 648
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 635-703 3.41e-04

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


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 39.56  E-value: 3.41e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501508023 635 GQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:cd05691    1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSI 69
S1_RNase_E cd04453
S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential ...
 640-691 7.08e-04

S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain that is highly homologous to that of RNase E. RNase G not only shares sequence similarity with RNase E, but also functionally overlaps with RNase E. In Escherichia coli, RNase G is involved in the maturation of the 5' end of the 16S rRNA. RNase G plays a secondary role in mRNA decay.


Pssm-ID: 239900 [Multi-domain]  Cd Length: 88  Bit Score: 39.11  E-value: 7.08e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 501508023 640 GTVRNVVDF--GAFVDIGVHEDGLIHISEMSEAF---VNHPSQVVSVGDLVTVWVSK 691
Cdd:cd04453   13 GRVKKIVPGlqAAFVDIGLGKNGFLHLSDILPAYfkkHKKIAKLLKEGQEILVQVVK 69
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 635-680 7.24e-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: 38.43  E-value: 7.24e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 501508023 635 GQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVN------HPSQVVS 680
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKdwkkrfKVGQLVK 52
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 632-703 9.14e-04

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


Pssm-ID: 240211 [Multi-domain]  Cd Length: 73  Bit Score: 38.39  E-value: 9.14e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 501508023 632 LAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEMSEAFVNHPSQVVSVGDLVTVWVSKVDLDRHKVNLSL 703
Cdd:cd05706    1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSL 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 612-702 9.53e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 42.46  E-value: 9.53e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501508023 612 DLRDDFEApvLRKDILSVKDLAVGQRLEGTVRNVVDFGAFVDIGVHEDGLIHISEmseaFVNHPSQV-VSVGDLVTVWVS 690
Cdd:PRK06299  10 DMEESFAE--LFEESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEE----FKNEQGELeVKVGDEVEVYVE 83

                         90
                 ....*....|..
gi 501508023 691 KVDLDRHKVNLS 702
Cdd:PRK06299  84 RIEDGFGETVLS 95
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 386-440 3.27e-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: 3.27e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 501508023  386 EVLKDFPETSYVIVNESGASVYSASELARHEFPELTVEKRSAISIARRLQDPLAE 440
Cdd:pfam14639  91 EQDSRLHTIGVILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLE 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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