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Conserved domains on  [gi|489462214|ref|WP_003367415|]
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MULTISPECIES: Tex family protein [Pseudomonas]

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];
1-726 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


:

Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1411.70  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214   1 MDSINSRIAEELGVRPQQVAAAVALLDEGSTVPFISRYRKEVTGSLDDTQLRHLEERLRYLRELDERRVSILASIEEQGK 80
Cdd:COG2183    2 MMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214  81 LTPELARDIKLADTKTRLEDLYLPYKQKRRTKGQIALEAGLGELADGLFNDPSLAPEAEAARFVDAEKGVADVKAALEGA 160
Cdd:COG2183   82 LTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEEKGVADVEAALDGA 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 161 KYILMERFAEDASLLDKLRSFLKQEAVISARVVPGKEEEGAKFRDYFEHDEPLKSMPSHRALAIFRGRNEGFLSSALKVG 240
Cdd:COG2183  162 RDILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPD 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 241 EElpgamhPCELMIGERFgIQNQNRPADKWLAEVVRWTWKVKLYSHLETDLLGELRDGAETEAINVFAHNLHDLLLAAPA 320
Cdd:COG2183  242 EE------EAEAYIARRF-IKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPA 314

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 321 GQRATLGLDPGLRTGCKVAVVDATGKLLDYATVYPHVPKNQWDQTIAVLAALCAKHSVDLIAIGNGTASRETDKLAADLI 400
Cdd:COG2183  315 GGKVVLGLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELI 394

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 401 KKYPgLKMTKVMVSEAGASVYSASELAAKEFPDLDVSIRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVSQLKLARG 480
Cdd:COG2183  395 KELD-LKVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRS 473

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 481 LDAVVEDCVNAVGVDVNTASVALLARISGLNTTLAQNIVAHRDENGAFKTRAALKKVSRLGEKTFEQAAGFLRVMTGDNP 560
Cdd:COG2183  474 LDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNP 553

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 561 LDASAVHPEAYPLVQRIAAETDRDIRSLIGDASFLKRLDPKKFTDETFGLPTVTDILQELEKPGRDPRPEFKTAEFQDGV 640
Cdd:COG2183  554 LDNSAVHPESYPVVEKILKDLGVSVKDLIGNKELLKKLDPEKYADELFGLPTLRDILKELEKPGRDPRPEFKTPTFREGV 633

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 641 EDLKDLQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMRMS 720
Cdd:COG2183  634 LKIEDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLD 713


                 ....*.
gi 489462214 721 DTPGEK 726
Cdd:COG2183  714 DEAGAA 719
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1-726 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1411.70  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214   1 MDSINSRIAEELGVRPQQVAAAVALLDEGSTVPFISRYRKEVTGSLDDTQLRHLEERLRYLRELDERRVSILASIEEQGK 80
Cdd:COG2183    2 MMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214  81 LTPELARDIKLADTKTRLEDLYLPYKQKRRTKGQIALEAGLGELADGLFNDPSLAPEAEAARFVDAEKGVADVKAALEGA 160
Cdd:COG2183   82 LTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEEKGVADVEAALDGA 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 161 KYILMERFAEDASLLDKLRSFLKQEAVISARVVPGKEEEGAKFRDYFEHDEPLKSMPSHRALAIFRGRNEGFLSSALKVG 240
Cdd:COG2183  162 RDILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPD 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 241 EElpgamhPCELMIGERFgIQNQNRPADKWLAEVVRWTWKVKLYSHLETDLLGELRDGAETEAINVFAHNLHDLLLAAPA 320
Cdd:COG2183  242 EE------EAEAYIARRF-IKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPA 314

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 321 GQRATLGLDPGLRTGCKVAVVDATGKLLDYATVYPHVPKNQWDQTIAVLAALCAKHSVDLIAIGNGTASRETDKLAADLI 400
Cdd:COG2183  315 GGKVVLGLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELI 394

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 401 KKYPgLKMTKVMVSEAGASVYSASELAAKEFPDLDVSIRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVSQLKLARG 480
Cdd:COG2183  395 KELD-LKVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRS 473

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 481 LDAVVEDCVNAVGVDVNTASVALLARISGLNTTLAQNIVAHRDENGAFKTRAALKKVSRLGEKTFEQAAGFLRVMTGDNP 560
Cdd:COG2183  474 LDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNP 553

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 561 LDASAVHPEAYPLVQRIAAETDRDIRSLIGDASFLKRLDPKKFTDETFGLPTVTDILQELEKPGRDPRPEFKTAEFQDGV 640
Cdd:COG2183  554 LDNSAVHPESYPVVEKILKDLGVSVKDLIGNKELLKKLDPEKYADELFGLPTLRDILKELEKPGRDPRPEFKTPTFREGV 633

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 641 EDLKDLQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMRMS 720
Cdd:COG2183  634 LKIEDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLD 713


                 ....*.
gi 489462214 721 DTPGEK 726
Cdd:COG2183  714 DEAGAA 719
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 8-192 6.15e-99

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: 303.56  E-value: 6.15e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214    8 IAEELGVRPQQVAAAVALLDEGSTVPFISRYRKEVTGSLDDTQLRHLEERLRYLRELDERRVSILASIEEQGKLTPELAR 87
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214   88 DIKLADTKTRLEDLYLPYKQKRRTKGQIALEAGLGELADGLFNDPSlaPEAEAARFVDAEKGVADVKAALEGAKYILMER 167
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQPD--PEEEAAKYINPEKGVADVEEALAGARDIIAER 158

                         170       180
                  ....*....|....*....|....*
gi 489462214  168 FAEDASLLDKLRSFLKQEAVISARV 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 ...
 649-716 2.60e-36

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: 130.82  E-value: 2.60e-36
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLS 716
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 323-422 2.68e-27

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: 106.11  E-value: 2.68e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214   323 RATLGLDPGlRTGCKVAVVDATGKLLDYATVYPHvpkNQWDQTIAVLAALCAKHSVDLIAIG-----NGTASRETDKLAA 397
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVIPR---TNKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFA 76

                           90       100
                   ....*....|....*....|....*
gi 489462214   398 DLIKKYPGLKmtKVMVSEAGASVYS 422
Cdd:smart00732  77 ELLKERFNLP--VVLVDERLATVYA 99
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 643-718 1.52e-19

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 91.48  E-value: 1.52e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489462214 643 LKDLQLGMILEGVVTNVTNFGAFVDIG-VhqDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:PRK06676 187 LSSLKEGDVVEGTVARLTDFGAFVDIGgV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLK 261
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 649-718 2.38e-19

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: 84.02  E-value: 2.38e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:NF040579   4 GDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSLR 73
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 641-727 1.74e-15

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 80.16  E-value: 1.74e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214  641 EDLKDLQLGMILEGVVTNVTNFGAFVDIGVhQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMRMS 720
Cdd:TIGR00717 180 ELLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQL 258


                  ....*...
gi 489462214  721 D-TPGEKI 727
Cdd:TIGR00717 259 GeDPWEAI 266
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1-726 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1411.70  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214   1 MDSINSRIAEELGVRPQQVAAAVALLDEGSTVPFISRYRKEVTGSLDDTQLRHLEERLRYLRELDERRVSILASIEEQGK 80
Cdd:COG2183    2 MMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214  81 LTPELARDIKLADTKTRLEDLYLPYKQKRRTKGQIALEAGLGELADGLFNDPSLAPEAEAARFVDAEKGVADVKAALEGA 160
Cdd:COG2183   82 LTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEEKGVADVEAALDGA 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 161 KYILMERFAEDASLLDKLRSFLKQEAVISARVVPGKEEEGAKFRDYFEHDEPLKSMPSHRALAIFRGRNEGFLSSALKVG 240
Cdd:COG2183  162 RDILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPD 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 241 EElpgamhPCELMIGERFgIQNQNRPADKWLAEVVRWTWKVKLYSHLETDLLGELRDGAETEAINVFAHNLHDLLLAAPA 320
Cdd:COG2183  242 EE------EAEAYIARRF-IKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPA 314

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 321 GQRATLGLDPGLRTGCKVAVVDATGKLLDYATVYPHVPKNQWDQTIAVLAALCAKHSVDLIAIGNGTASRETDKLAADLI 400
Cdd:COG2183  315 GGKVVLGLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELI 394

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 401 KKYPgLKMTKVMVSEAGASVYSASELAAKEFPDLDVSIRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVSQLKLARG 480
Cdd:COG2183  395 KELD-LKVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRS 473

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 481 LDAVVEDCVNAVGVDVNTASVALLARISGLNTTLAQNIVAHRDENGAFKTRAALKKVSRLGEKTFEQAAGFLRVMTGDNP 560
Cdd:COG2183  474 LDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNP 553

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 561 LDASAVHPEAYPLVQRIAAETDRDIRSLIGDASFLKRLDPKKFTDETFGLPTVTDILQELEKPGRDPRPEFKTAEFQDGV 640
Cdd:COG2183  554 LDNSAVHPESYPVVEKILKDLGVSVKDLIGNKELLKKLDPEKYADELFGLPTLRDILKELEKPGRDPRPEFKTPTFREGV 633

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 641 EDLKDLQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMRMS 720
Cdd:COG2183  634 LKIEDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLD 713


                 ....*.
gi 489462214 721 DTPGEK 726
Cdd:COG2183  714 DEAGAA 719
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 8-192 6.15e-99

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: 303.56  E-value: 6.15e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214    8 IAEELGVRPQQVAAAVALLDEGSTVPFISRYRKEVTGSLDDTQLRHLEERLRYLRELDERRVSILASIEEQGKLTPELAR 87
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214   88 DIKLADTKTRLEDLYLPYKQKRRTKGQIALEAGLGELADGLFNDPSlaPEAEAARFVDAEKGVADVKAALEGAKYILMER 167
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQPD--PEEEAAKYINPEKGVADVEEALAGARDIIAER 158

                         170       180
                  ....*....|....*....|....*
gi 489462214  168 FAEDASLLDKLRSFLKQEAVISARV 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 ...
 324-449 2.41e-81

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: 255.40  E-value: 2.41e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214  324 ATLGLDPGLRTGCKVAVVDATGKLLDYATVYPHVPKNQWDQTIAVLAALCAKHSVDLIAIGNGTASRETDKLAADLIKKY 403
Cdd:pfam16921   1 VVLGLDPGYRTGCKLAVVDETGKVLDTAVIYPHPPQNKVEEAKKKLKKLIKKYGVELIAIGNGTASRETEQFVAELIKEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 489462214  404 PgLKMTKVMVSEAGASVYSASELAAKEFPDLDVSIRGAVSIARRLQ 449
Cdd:pfam16921  81 P-LKVKYVIVSEAGASVYSASELAREEFPDLDVSLRGAVSIARRLQ 125
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 649-716 2.60e-36

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: 130.82  E-value: 2.60e-36
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLS 716
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
HHH_9 pfam17674
HHH domain;
559-628 6.81e-34

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 123.80  E-value: 6.81e-34
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214  559 NPLDASAVHPEAYPLVQRIAAETDRDIRSLIGDASFLKRLDPKKFTDETFGLPTVTDILQELEKPGRDPR 628
Cdd:pfam17674   1 NPLDNTAIHPESYPLAEKILKDLGLDLKDLIGNSALLKKLDPKKLAEEEVGLPTLKDILEELAKPGRDPR 70
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 491-552 6.84e-30

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


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 112.19  E-value: 6.84e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489462214  491 AVGVDVNTASVALLARISGLNTTLAQNIVAHRDENGAFKTRAALKKVSRLGEKTFEQAAGFL 552
Cdd:pfam12836   1 AVGVDINTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKTFEQLAGFL 62
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 323-422 2.68e-27

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: 106.11  E-value: 2.68e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214   323 RATLGLDPGlRTGCKVAVVDATGKLLDYATVYPHvpkNQWDQTIAVLAALCAKHSVDLIAIG-----NGTASRETDKLAA 397
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVIPR---TNKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFA 76

                           90       100
                   ....*....|....*....|....*
gi 489462214   398 DLIKKYPGLKmtKVMVSEAGASVYS 422
Cdd:smart00732  77 ELLKERFNLP--VVLVDERLATVYA 99
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 643-728 1.07e-23

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 103.20  E-value: 1.07e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 643 LKDLQLGMILEGVVTNVTNFGAFVDI-GVhqDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR-MS 720
Cdd:COG0539  184 LEKLEEGDVVEGTVKNITDFGAFVDLgGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKqLQ 261


                 ....*...
gi 489462214 721 DTPGEKID 728
Cdd:COG0539  262 PDPWENIA 269
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 644-743 3.92e-23

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 95.25  E-value: 3.92e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 644 KDLQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDiPRKRVGLSMRmsDTP 723
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSID-EDGKISLSIK--QAE 77

                         90       100
                 ....*....|....*....|
gi 489462214 724 GEKIDGARGARPGSSPRQNN 743
Cdd:COG1098   78 EKPKRPPRPRRNSRPKAGFE 97
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 649-718 3.63e-22

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: 90.42  E-value: 3.63e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDiPRKRVGLSMR 718
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID-ARGRISLSIK 69
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 649-716 4.16e-22

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 90.38  E-value: 4.16e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVhQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLS 716
Cdd:cd05688    2 GDVVEGTVKSITDFGAFVDLGG-VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
647-718 1.63e-21

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 88.81  E-value: 1.63e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489462214   647 QLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 644-718 2.10e-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: 93.57  E-value: 2.10e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489462214 644 KDLQLGMILEGVVTNVTNFGAFVDI--GVhqDGLVHISALS-EKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:COG0539  270 EKYPVGDVVKGKVTRLTDFGAFVELepGV--EGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 643-718 1.52e-19

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 91.48  E-value: 1.52e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489462214 643 LKDLQLGMILEGVVTNVTNFGAFVDIG-VhqDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:PRK06676 187 LSSLKEGDVVEGTVARLTDFGAFVDIGgV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLK 261
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 649-718 2.38e-19

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: 84.02  E-value: 2.38e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:NF040579   4 GDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSLR 73
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 640-718 2.92e-19

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


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 92.76  E-value: 2.92e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 640 VEDL-KDLQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDiPRKRVGLSMR 718
Cdd:COG1185  607 IEGItAEPEVGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEID-DQGRIKLSRK 685
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 638-718 8.69e-19

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 89.16  E-value: 8.69e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 638 DGVEDlkDLQLGMILEGVVTNVTNFGAFVDI--GVhqDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGL 715
Cdd:PRK06676 269 EGVEE--KLPEGDVIEGTVKRLTDFGAFVEVlpGV--EGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISL 344


                 ...
gi 489462214 716 SMR 718
Cdd:PRK06676 345 SIK 347
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 643-718 2.54e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 88.95  E-value: 2.54e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489462214 643 LKDLQLGMILEGVVTNVTNFGAFVDIGvHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:PRK07899 203 LNQLQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLK 277
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 643-717 4.35e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 88.30  E-value: 4.35e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489462214 643 LKDLQLGMILEGVVTNVTNFGAFVDIGVhQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSM 717
Cdd:PRK06299 196 LENLEEGQVVEGVVKNITDYGAFVDLGG-VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGL 269
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 646-717 5.60e-18

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: 78.87  E-value: 5.60e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489462214  646 LQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSM 717
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
PRK05807 PRK05807
RNA-binding protein S1;
646-718 7.82e-18

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 80.56  E-value: 7.82e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489462214 646 LQLGMILEGVVTNVTNFGAFVDI-GvhQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDiPRKRVGLSMR 718
Cdd:PRK05807   3 LKAGSILEGTVVNITNFGAFVEVeG--KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISLSIK 73
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 640-718 1.22e-17

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 87.41  E-value: 1.22e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 640 VEDL-KDLQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDiPRKRVGLSMR 718
Cdd:PRK11824 612 IEGItAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSRK 690
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 652-716 2.27e-17

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: 76.65  E-value: 2.27e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489462214 652 LEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLS 716
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
647-718 4.95e-17

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 85.38  E-value: 4.95e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489462214 647 QLGMILEGVVTNVTNFGAFVDI--GVhqDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:PRK00087 561 PVGSIVLGKVVRIAPFGAFVELepGV--DGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIK 632
PRK08582 PRK08582
RNA-binding protein S1;
646-749 5.13e-17

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 78.15  E-value: 5.13e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 646 LQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKrVGLSMRMS-DTPg 724
Cdd:PRK08582   3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGK-IGLSIKKAkDRP- 80

                         90       100
                 ....*....|....*....|....*
gi 489462214 725 eKIDGARGARPGSSPRQNNAPRKET 749
Cdd:PRK08582  81 -KRQHDRPRHEDNRGGGNDVAPKED 104
PRK08059 PRK08059
general stress protein 13; Validated
 649-739 5.42e-17

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 77.78  E-value: 5.42e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR-MSDTPGEKI 727
Cdd:PRK08059   8 GSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRaTEEAPEAKR 87

                         90
                 ....*....|..
gi 489462214 728 DGARGARPGSSP 739
Cdd:PRK08059  88 KKGKILIPNPSE 99
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
641-728 8.62e-17

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 84.61  E-value: 8.62e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 641 EDLKDLQLGMILEGVVTNVTNFGAFVDI-GVhqDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR- 718
Cdd:PRK00087 470 ETWNSLEEGDVVEGEVKRLTDFGAFVDIgGV--DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKk 547

                         90
                 ....*....|
gi 489462214 719 MSDTPGEKID 728
Cdd:PRK00087 548 LLPDPWENVE 557
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 649-717 1.15e-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: 74.89  E-value: 1.15e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDiPRKRVGLSM 717
Cdd:cd04472    1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD-DRGRISLSR 68
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 649-721 1.20e-16

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


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 75.35  E-value: 1.20e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489462214 649 GMILEGVVTNVTNFGAFVDI---GVHQDGLVHISALS-EKFIKDPREAVKAGDVVKVKVMevDIPRKRVGLSMRMSD 721
Cdd:cd05684    1 GKIYKGKVTSIMDFGCFVQLeglKGRKEGLVHISQLSfEGRVANPSDVVKRGQKVKVKVI--SIQNGKISLSMKDVD 75
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 641-727 1.74e-15

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 80.16  E-value: 1.74e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214  641 EDLKDLQLGMILEGVVTNVTNFGAFVDIGVhQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMRMS 720
Cdd:TIGR00717 180 ELLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQL 258


                  ....*...
gi 489462214  721 D-TPGEKI 727
Cdd:TIGR00717 259 GeDPWEAI 266
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 649-718 1.91e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 76.74  E-value: 1.91e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVHQDGLVHISALS-EKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:PRK06299 374 GDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIK 444
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 494-553 3.14e-14

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


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 67.97  E-value: 3.14e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 494 VDVNTASVALLARISGLNTTLAQNIVAHRDENGAFKTRAALKKVSRLGEKTFEQAAGFLR 553
Cdd:COG1555   13 VDINTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGIGPKTLEKLKPYLT 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 643-718 7.75e-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: 74.77  E-value: 7.75e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489462214  643 LKDLQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALS-EKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:TIGR00717 267 EKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 638-718 9.22e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 74.82  E-value: 9.22e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 638 DGVEDlkDLQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALS-EKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLS 716
Cdd:PRK06299 278 EAIEK--KYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLG 355


                 ..
gi 489462214 717 MR 718
Cdd:PRK06299 356 LK 357
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 649-720 2.55e-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: 65.81  E-value: 2.55e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489462214 649 GMILEGVVTNVTNFGAFVDI-GVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMRMS 720
Cdd:cd05708    3 GQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 647-721 6.09e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 72.00  E-value: 6.09e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489462214 647 QLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMRMSD 721
Cdd:PRK07899 292 AIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQAN 366
rpsA PRK13806
30S ribosomal protein S1; Provisional
 646-718 1.84e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 70.52  E-value: 1.84e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489462214 646 LQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALS-EKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:PRK13806 290 LKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR 363
rpsA PRK13806
30S ribosomal protein S1; Provisional
 643-728 2.43e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 70.14  E-value: 2.43e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 643 LKDLQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRK----RVGLSMR 718
Cdd:PRK13806 197 METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIK 276

                         90
                 ....*....|....*
gi 489462214 719 MS-----DTPGEKID 728
Cdd:PRK13806 277 QAggdpwDTVGDRLK 291
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 651-719 8.40e-12

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 64.46  E-value: 8.40e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 651 ILEGVVTNVTNFGAFVDIGVhQDGLVHISALSEKFI-----------KDPREAVKAGDVVKVKVMEVDI----PRK-RVG 714
Cdd:PRK08563  84 VVEGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYIsydpkngrligKESKRVLKVGDVVRARIVAVSLkerrPRGsKIG 162


                 ....*
gi 489462214 715 LSMRM 719
Cdd:PRK08563 163 LTMRQ 167
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 642-717 1.28e-11

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


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 61.06  E-value: 1.28e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489462214 642 DLKDLQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSM 717
Cdd:cd04461    8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 641-726 1.68e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 67.50  E-value: 1.68e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 641 EDLKDLQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMRMS 720
Cdd:PRK06299 453 EFAKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKAL 532


                 ....*.
gi 489462214 721 DTPGEK 726
Cdd:PRK06299 533 DEAEEK 538
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 649-715 4.34e-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: 59.04  E-value: 4.34e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVHQDGLVHISALS-EKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGL 715
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 649-716 8.38e-11

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: 58.08  E-value: 8.38e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLS 716
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 647-717 1.47e-10

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


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 57.88  E-value: 1.47e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489462214 647 QLGMILEGVVTNVTNFGAFVDI-GVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIpRKRVGLSM 717
Cdd:cd05686    2 ALYQIFKGEVASVTEYGAFVKIpGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREM-KDKMKLSL 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 647-727 2.27e-10

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 63.60  E-value: 2.27e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214  647 QLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSekFIKDPREAV---KAGDVVKVKVMEVDIPRKRVGLSMR-MSDT 722
Cdd:TIGR00717 358 PVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDIS--WDKDGREADhlyKKGDEIEAVVLAVDKEKKRISLGVKqLTEN 435


                  ....*
gi 489462214  723 PGEKI 727
Cdd:TIGR00717 436 PWEKF 440
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 651-718 3.70e-10

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: 57.30  E-value: 3.70e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 651 ILEGVVTNVTNFGAFVDIGvHQDGLVHISALSEKFIK-DPREA----------VKAGDVVKVKVMEVDIP-----RKRVG 714
Cdd:cd04460    2 VVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISyDPKNKrligeetkrvLKVGDVVRARIVAVSLKerrprESKIG 80


                 ....
gi 489462214 715 LSMR 718
Cdd:cd04460   81 LTMR 84
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 620-718 7.82e-10

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 62.42  E-value: 7.82e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 620 LEKPGRDPRPEF-KTAEFQDGVEdlkdlqlgmileGVVTNVTNFGAFVDIGVHqDGLVHISALSEKFIKDPREAVKAGDV 698
Cdd:PRK12269 476 LEERARQAREEFfNSVHIEDSVS------------GVVKSFTSFGAFIDLGGF-DGLLHVNDMSWGHVARPREFVKKGQT 542

                         90       100
                 ....*....|....*....|
gi 489462214 699 VKVKVMEVDIPRKRVGLSMR 718
Cdd:PRK12269 543 IELKVIRLDQAEKRINLSLK 562
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 649-718 1.49e-09

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: 54.54  E-value: 1.49e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 648-713 2.71e-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: 54.33  E-value: 2.71e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 648 LGMILEGVVTNVTNFGAFV---DIGVhqDGLVHISALS-EKFIKDPRE----------AVKAGDVVKVKVMEVDIPRKRV 713
Cdd:cd04471    1 VGEEFDGVISGVTSFGLFVeldNLTV--EGLVHVSTLGdDYYEFDEENhalvgertgkVFRLGDKVKVRVVRVDLDRRKI 78
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 649-715 2.71e-09

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: 53.78  E-value: 2.71e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGL 715
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVL 67
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 649-715 4.70e-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: 53.35  E-value: 4.70e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVHQDGLVHISAL--SEKFIkDPREAVKAGDVVKVKVMEVDIPRKRVGL 715
Cdd:cd05689    4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMdwTNKNI-HPSKVVSLGDEVEVMVLDIDEERRRISL 71
VacB COG0557
Exoribonuclease R [Transcription];
630-717 6.28e-09

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 59.35  E-value: 6.28e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 630 EFKTAEFqdgvedLKDlQLGMILEGVVTNVTNFGAFV---DIGVhqDGLVHISALSEK-FIKDPREAV----------KA 695
Cdd:COG0557  611 DLKKAEY------MKD-RVGEEFEGVISGVTSFGLFVeldELGV--EGLVHVSSLGDDyYEYDERRQAlvgertgkryRL 681

                         90       100
                 ....*....|....*....|..
gi 489462214 696 GDVVKVKVMEVDIPRKRVGLSM 717
Cdd:COG0557  682 GDRVEVRVVRVDLDRRQIDFEL 703
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 646-718 1.02e-08

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: 52.25  E-value: 1.02e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489462214 646 LQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:cd05706    1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
646-718 8.12e-08

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 51.24  E-value: 8.12e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489462214 646 LQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:PRK07252   1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLR 73
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 494-547 9.64e-08

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: 49.54  E-value: 9.64e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 489462214  494 VDVNTASVALLAR-ISGLNTTLAQNIVAHRDENGAFKTRAALKKVSRLGEKTFEQ 547
Cdd:TIGR00426   8 VNINTATAEELQRaMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEK 62
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 649-718 1.69e-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: 54.74  E-value: 1.69e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214  649 GMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:TIGR00717 447 GSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 649-718 2.04e-07

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: 48.73  E-value: 2.04e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVHQD--GLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:cd04452    4 GELVVVTVKSIADMGAYVSLLEYGNieGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 646-725 3.52e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 52.88  E-value: 3.52e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 646 LQLGMILEGVVTNVTNFGAFVDIGvHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR-MSDTPG 724
Cdd:PRK07400 194 LEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKqLEPEPG 272


                 .
gi 489462214 725 E 725
Cdd:PRK07400 273 D 273
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 649-718 5.07e-07

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 51.75  E-value: 5.07e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVHQD--GLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:PRK03987   9 GELVVGTVKEVKDFGAFVTLDEYPGkeGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 649-718 5.07e-07

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


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 47.52  E-value: 5.07e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 649 GMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:cd05687    1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 635-722 5.30e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 52.57  E-value: 5.30e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 635 EFQDGVEDLKDLQLGMILEGVVTNVTNFGAFVDI-GVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRV 713
Cdd:PRK06676   4 EFEESLNSVKEVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNL 83


                 ....*....
gi 489462214 714 GLSMRMSDT 722
Cdd:PRK06676  84 LLSKRRLEA 92
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 656-707 9.68e-07

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 52.59  E-value: 9.68e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489462214 656 VTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVD 707
Cdd:PLN00207 762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVN 813
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 626-734 1.38e-06

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 52.02  E-value: 1.38e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 626 DPRPEFktaEFQDGVEDlkdlqlgmILEGVVTNVTNFGAFVDIGVHQDGLVHISALS-EKFIKDPREAVKAGDVVKVKVM 704
Cdd:PRK12269 567 DPWLEF---ENKFGVND--------VVKGRVTKIADFGAFIELAEGIEGLAHISEFSwVKKTSKPSDMVKIGDEVECMIL 635

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489462214 705 EVDIPRKRVGLSMR-MSDTPGEKID-----GARGAR 734
Cdd:PRK12269 636 GYDIQAGRVSLGLKqVTANPWEEIEarypvGARFTR 671
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 641-721 2.19e-06

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 50.43  E-value: 2.19e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 641 EDLKDLQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEkfiKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMRMS 720
Cdd:COG0539   11 ESLKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSD---EPGELEVKVGDEVEVYVEKVEDGEGEIVLSKKKA 87


                 .
gi 489462214 721 D 721
Cdd:COG0539   88 D 88
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 642-706 5.37e-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: 44.91  E-value: 5.37e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489462214 642 DLKDLQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFikdpreavKAGDVVKVKVMEV 706
Cdd:cd04473   10 TMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDY--------EVGDEVIVQVTDI 66
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
641-718 1.20e-05

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 48.79  E-value: 1.20e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489462214 641 EDLKDLQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:PRK00087 295 ELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKK 372
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 642-706 3.91e-05

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


Pssm-ID: 440724 [Multi-domain]  Cd Length: 626  Bit Score: 47.14  E-value: 3.91e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489462214 642 DLKDLQLGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFikdpreavKAGDVVKVKVMEV 706
Cdd:COG1107   33 TPDDLEPGRYYRGTVDGVADFGVFVDLNDHVTGLLHRSELDQDW--------EVGDEVFVQVKEV 89
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 648-748 4.18e-05

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 47.01  E-value: 4.18e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 648 LGMILEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFIKDPREAVK---AGDVVKVKVMEVDIPRKRVGLSMRmsdtpg 724
Cdd:PRK12269 752 VGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPGEALRkyaVGDRVKAVIVDMNVKDRKVAFSVR------ 825

                         90       100
                 ....*....|....*....|....
gi 489462214 725 ekiDGARGARPGSSPRQNNAPRKE 748
Cdd:PRK12269 826 ---DYQRKVQRDELSRYMSAPRGE 846
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 649-718 7.55e-05

S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 239911 [Multi-domain]  Cd Length: 67  Bit Score: 41.29  E-value: 7.55e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489462214 649 GMILEGVVTNVTNFGAFVDI-GVhqDGLVHISALSEKFIKDPREAVkaGDVVKVKVMEVDIPRKRVGLSMR 718
Cdd:cd04465    1 GEIVEGKVTEKVKGGLIVDIeGV--RAFLPASQVDLRPVEDLDEYV--GKELKFKIIEIDRERNNIVLSRR 67
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 411-454 1.01e-04

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: 43.32  E-value: 1.01e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 489462214  411 VMVSEAGASVYSASELAAKEFPDLDVSIRGAVSIARRLQDPLAE 454
Cdd:pfam14639 102 ILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLE 145
ASKHA_NBD_FGGY cd00366
nucleotide-binding domain (NBD) of the FGGY family of carbohydrate kinases; This family is ...
 325-383 1.91e-04

nucleotide-binding domain (NBD) of the FGGY family of carbohydrate kinases; This family is predominantly composed of glycerol kinase (GK) and similar carbohydrate kinases including rhamnulokinase (RhuK), xylulokinase (XK), gluconokinase (GntK), ribulokinase (RBK), and fuculokinase (FK). These enzymes catalyze the transfer of a phosphate group, usually from ATP, to their carbohydrate substrates. The monomer of FGGY proteins contains two large domains, which are separated by a deep cleft that forms the active site. One domain is primarily involved in sugar substrate binding, and the other is mainly responsible for ATP binding. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. Substrate-induced conformational changes and a divalent cation may be required for the catalytic activity. The FGGY family belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains.


Pssm-ID: 466787 [Multi-domain]  Cd Length: 392  Bit Score: 44.48  E-value: 1.91e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 325 TLGLDPGlRTGCKVAVVDATGKLLD-----YATVYPHV------PKNQWDQTIAVLAALCAKHSVDLIAI 383
Cdd:cd00366    2 LLGIDIG-TTSVKAALFDEDGNLVAsasreYPLIYPQPgwaeqdPEDWWQAVVEAIREVLAKAGIDPSDI 70
HHH_7 pfam14635
Helix-hairpin-helix motif;
459-554 3.36e-04

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 40.61  E-value: 3.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214  459 DPKSIGVGQYQHDVSQLKLARGLDAVVEDCVNAVGVDVNTA-----SVALLARISGLNTTLAQNIVAH-RDENGAFKTRA 532
Cdd:pfam14635   2 DILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAiankyEAAILPYIAGLGPRKADHLLKIlAANNGRLDNRS 81

                          90       100
                  ....*....|....*....|..
gi 489462214  533 ALKKVSRLGEKTFEQAAGFLRV 554
Cdd:pfam14635  82 QLITKCIMGPKVFMNCAGFLII 103
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 645-716 8.41e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 42.84  E-value: 8.41e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489462214 645 DLQLGMILEGVVTNVTNFGAFVDIGVHQDGLVhisALSEkFIKDPREA-VKAGDVVKVKVMEVDIPRKRVGLS 716
Cdd:PRK06299  27 ETREGSIVKGTVVAIDKDYVLVDVGLKSEGRI---PLEE-FKNEQGELeVKVGDEVEVYVERIEDGFGETVLS 95
PRK04163 PRK04163
exosome complex protein Rrp4;
654-718 9.40e-04

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 41.41  E-value: 9.40e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489462214 654 GVVTNVTNFGAFVDIGVHQDGLVHISALSEKFI----KDPREAVKAGDVVKVKVMEVDiPRKRVGLSMR 718
Cdd:PRK04163  69 GKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVnvegTDLRKYLDIGDYIIAKVKDVD-RTRDVVLTLK 136
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 654-718 1.15e-03

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


Pssm-ID: 240215 [Multi-domain]  Cd Length: 86  Bit Score: 38.68  E-value: 1.15e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489462214 654 GVVTNVTNFGAFVDIGVHQDGLVHISA-LSEKFIKD---PREAVKAGDVVKVKVMEVDiPRKRVGLSMR 718
Cdd:cd05789   12 GRVTEVGFKRWKVDINSPYDAVLPLSEvNLPRTDEDelnMRSYLDEGDLIVAEVQSVD-SDGSVSLHTR 79
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 646-721 2.77e-03

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 39.57  E-value: 2.77e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 646 LQLGMILEGVVTNVTNFGAFVDI----------GVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIPrkrVGL 715
Cdd:PRK09521  62 LKKGDIVYGRVVDVKEQRALVRIvsiegserelATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYTDP---LQL 138


                 ....*.
gi 489462214 716 SMRMSD 721
Cdd:PRK09521 139 STKGKD 144
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 646-718 2.87e-03

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


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 36.95  E-value: 2.87e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489462214 646 LQLGMILEGVVTNVT-NFGAFVDIGVHQDGLVHISALSEKFIKDPREAVKAGDVVKVKVMEVDIprKRVGLSMR 718
Cdd:cd05704    1 LEEGAVTLGMVTKVIpHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSLR 72
YqgF cd16964
putative pre-16S rRNA nuclease YqgF and RuvX family; Escherichia coli YqgF has been shown to ...
 326-403 2.93e-03

putative pre-16S rRNA nuclease YqgF and RuvX family; Escherichia coli YqgF has been shown to act as a pre-16S rRNA nuclease, presumably as a monomer. It is involved in the processing of pre-16S rRNA during ribosome maturation. The RuvX gene product from Mycobacterium tuberculosis was shown to act, in a dimeric form, as a Holliday junction resolvase (HJR). HJRs endonucleases specifically resolve Holliday junction DNA intermediates during homologous recombination. Holliday junctions are formed by the reciprocal exchange of strands between two DNA duplexes. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi; they may form homodimers and display structural similarity to RNase H and Hsp70.


Pssm-ID: 438564  Cd Length: 132  Bit Score: 38.62  E-value: 2.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 326 LGLDPGL-RTGckVAVVDATGKLldyATVYPHVPKNQWDQTIAVLAALCAKHSVDLIAIG-----NGTAS---RETDKLA 396
Cdd:cd16964    2 LGIDYGTkRIG--LAISDPLGII---ASPLETIERKNLEKLLEELKKIIKEEKIEKIVVGlplnmDGTESeqaEKVRKFA 76


                 ....*..
gi 489462214 397 ADLIKKY 403
Cdd:cd16964   77 EKLKKRF 83
DnaE COG0587
DNA polymerase III, alpha subunit [Replication, recombination and repair];
485-601 4.44e-03

DNA polymerase III, alpha subunit [Replication, recombination and repair];


Pssm-ID: 440352 [Multi-domain]  Cd Length: 1050  Bit Score: 40.44  E-value: 4.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214  485 VEDC----VNAVGVDVNtASVAL------------LARISGLNTTLAQNIVAHRDENGAFKT------RAALKKVSRlge 542
Cdd:COG0587   783 VQEArrhgIEVLPPDVN-ESDWDftvepggairlgLGAIKGVGEAAAEAIVAAREENGPFTSlfdfcrRVDLRKLNK--- 858

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489462214  543 KTFEQ--AAGFLRVMtGDNPLDASAVHPEAYPLVQRIAAETDRDIRSLIGDASFLKRLDPK 601
Cdd:COG0587   859 RVLEAliKAGAFDSL-GPNRRQLLWALEAALDAAQQAQKDKASGQLSLFGGAGDEEVAEPA 918
PRK11642 PRK11642
ribonuclease R;
647-741 6.91e-03

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 40.11  E-value: 6.91e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214 647 QLGMILEGVVTNVTNFGAFVDIG-VHQDGLVHISALS----------EKFIKDPR-EAVKAGDVVKVKVMEVDIPRKRVG 714
Cdd:PRK11642 642 QVGNVFKGVISSVTGFGFFVRLDdLFIDGLVHVSSLDndyyrfdqvgQRLIGESSgQTYRLGDRVEVRVEAVNMDERKID 721

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 489462214 715 LSMRMSD--------TPGEKIDGARGARPGSSPRQ 741
Cdd:PRK11642 722 FSLISSEraprnvgkTAREKAKKGDAGKKGGKRRQ 756
T2SSK pfam03934
Type II secretion system (T2SS), protein K; Members of this family are involved in the Type II ...
 471-541 9.35e-03

Type II secretion system (T2SS), protein K; Members of this family are involved in the Type II protein secretion system. The T2SK family includes proteins such as ExeK, PulK, OutX and XcpX.


Pssm-ID: 427597 [Multi-domain]  Cd Length: 283  Bit Score: 38.84  E-value: 9.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489462214  471 DVSQLKLARGLDAVVED------CV---NAVGVDVNTASVALL-ARISGLNTTLAQNIVAHRDENGaFKTRAALKKVSRL 540
Cdd:pfam03934 154 DVSELRLVLGFTPELYArlrpyvCAlpgDRTPINVNTAPAEVLaALFDGLSLDQAQALLAQRPADG-FESVDDFLAQPAL 232


                  .
gi 489462214  541 G 541
Cdd:pfam03934 233 G 233
 
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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