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Conserved domains on  [gi|599131065|gb|EYE89893|]
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hypothetical protein Q428_00820, partial [Fervidicella metallireducens AeB]

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];
1-715 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


:

Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1284.20  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065   1 MSQIIKQLTEELNIKEWQVKNTIELIDSGNTIPFIARYRKEVTGELDDTTLRNFYERLTYLRNLEQKKEEVKRLIEAQGK 80
Cdd:COG2183    2 MMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065  81 LTEEIINNIDNALSITEVEDIYRPFRPKKRTRATIAKEKGLEPLAALIYSQDfTDDLLKIVEGYVNKELGVENHEDAIKG 160
Cdd:COG2183   82 LTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQP-TGDPEAEAAKYINEEKGVADVEAALDG 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 161 AMDIIAEDISDNPEYRKEIRRLTFREGLIVTK---GLKDETSPYEMYYKYSEAVNRIVSHRILAINRGEKEEFLSVKIEA 237
Cdd:COG2183  161 ARDILAERISEDAELRGKLRELLWKEGVLVSKvkkGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEP 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 238 PIEKILSFLENKVIKRSSKETS-YLLETIKDSYNRLIAPSVEREIRNELTEKAEEQAIKVFAANLKSLLMISPVKGKVVL 316
Cdd:COG2183  241 DEEEAEAYIARRFIKDQGRPADeWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVL 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 317 GFDPGFRTGCKVAVVDETGKLLDYATVYSTAPQNDIEGSKKILKELIYKYNVDIISLGNGTASRESEIFLAELIKEVEce 396
Cdd:COG2183  321 GLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELD-- 398

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 397 sgKKIYYVVVSEAGASVYSASEIAAKEFPDINVSIRGAISIARRLQDPLAELVKIDPKSIGVGQYQHDVSQKKLDESLKG 476
Cdd:COG2183  399 --LKVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDA 476

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 477 VVEDCVNSVGVDLNTASAPLLSYISGINAATAKNIVEYREENGKFRDRREILKVKRLGEKAFEQCAGFLRIPESENVLDN 556
Cdd:COG2183  477 VVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDN 556

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 557 TAVHPESYSAAENILEKLGYTIQDVKDKKlndidKKLDEYGVEKLSSETgVGIPTLRDIISELKKPGRDPRESLPQPIFM 636
Cdd:COG2183  557 SAVHPESYPVVEKILKDLGVSVKDLIGNK-----ELLKKLDPEKYADEL-FGLPTLRDILKELEKPGRDPRPEFKTPTFR 630

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 599131065 637 SGVMELEDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLT 715
Cdd:COG2183  631 EGVLKIEDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLS 709
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1-715 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1284.20  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065   1 MSQIIKQLTEELNIKEWQVKNTIELIDSGNTIPFIARYRKEVTGELDDTTLRNFYERLTYLRNLEQKKEEVKRLIEAQGK 80
Cdd:COG2183    2 MMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065  81 LTEEIINNIDNALSITEVEDIYRPFRPKKRTRATIAKEKGLEPLAALIYSQDfTDDLLKIVEGYVNKELGVENHEDAIKG 160
Cdd:COG2183   82 LTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQP-TGDPEAEAAKYINEEKGVADVEAALDG 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 161 AMDIIAEDISDNPEYRKEIRRLTFREGLIVTK---GLKDETSPYEMYYKYSEAVNRIVSHRILAINRGEKEEFLSVKIEA 237
Cdd:COG2183  161 ARDILAERISEDAELRGKLRELLWKEGVLVSKvkkGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEP 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 238 PIEKILSFLENKVIKRSSKETS-YLLETIKDSYNRLIAPSVEREIRNELTEKAEEQAIKVFAANLKSLLMISPVKGKVVL 316
Cdd:COG2183  241 DEEEAEAYIARRFIKDQGRPADeWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVL 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 317 GFDPGFRTGCKVAVVDETGKLLDYATVYSTAPQNDIEGSKKILKELIYKYNVDIISLGNGTASRESEIFLAELIKEVEce 396
Cdd:COG2183  321 GLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELD-- 398

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 397 sgKKIYYVVVSEAGASVYSASEIAAKEFPDINVSIRGAISIARRLQDPLAELVKIDPKSIGVGQYQHDVSQKKLDESLKG 476
Cdd:COG2183  399 --LKVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDA 476

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 477 VVEDCVNSVGVDLNTASAPLLSYISGINAATAKNIVEYREENGKFRDRREILKVKRLGEKAFEQCAGFLRIPESENVLDN 556
Cdd:COG2183  477 VVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDN 556

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 557 TAVHPESYSAAENILEKLGYTIQDVKDKKlndidKKLDEYGVEKLSSETgVGIPTLRDIISELKKPGRDPRESLPQPIFM 636
Cdd:COG2183  557 SAVHPESYPVVEKILKDLGVSVKDLIGNK-----ELLKKLDPEKYADEL-FGLPTLRDILKELEKPGRDPRPEFKTPTFR 630

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 599131065 637 SGVMELEDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLT 715
Cdd:COG2183  631 EGVLKIEDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLS 709
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 8-192 2.49e-94

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: 290.07  E-value: 2.49e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065    8 LTEELNIKEWQVKNTIELIDSGNTIPFIARYRKEVTGELDDTTLRNFYERLTYLRNLEQKKEEVKRLIEAQGKLTEEIIN 87
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065   88 NIDNALSITEVEDIYRPFRPKKRTRATIAKEKGLEPLAALIYSQdftDDLLKIVEGYVNKELGVENHEDAIKGAMDIIAE 167
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQ---PDPEEEAAKYINPEKGVADVEEALAGARDIIAE 157

                         170       180
                  ....*....|....*....|....*
gi 599131065  168 DISDNPEYRKEIRRLTFREGLIVTK 192
Cdd:pfam09371 158 RISEDAELRKKLRELLWREGVIVSK 182
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 648-715 2.09e-34

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 125.04  E-value: 2.09e-34
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 599131065 648 GMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLT 715
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 313-415 1.44e-24

Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.


Pssm-ID: 128971  Cd Length: 99  Bit Score: 98.41  E-value: 1.44e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065   313 KVVLGFDPGfRTGCKVAVVDETGKLLDYATVYstaPQNDIEGSKKILKELIYKYNVDIISLG-----NGTASRESEIFLA 387
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVI---PRTNKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFA 76

                           90       100
                   ....*....|....*....|....*...
gi 599131065   388 ELIKEvecesGKKIYYVVVSEAGASVYS 415
Cdd:smart00732  77 ELLKE-----RFNLPVVLVDERLATVYA 99
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 642-716 2.76e-21

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 98.31  E-value: 2.76e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 599131065 642 LEDLKPGMILKGTVRNVADFGAFVDIGVhQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:PRK06299 196 LENLEEGQVVEGVVKNITDYGAFVDLGG-VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGL 269
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 646-716 3.29e-18

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: 80.55  E-value: 3.29e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 599131065 646 KPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:NF040579   2 KIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSL 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 642-716 8.40e-17

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: 84.02  E-value: 8.40e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 599131065  642 LEDLKPGMILKGTVRNVADFGAFVDIGVhQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:TIGR00717 182 LENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1-715 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1284.20  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065   1 MSQIIKQLTEELNIKEWQVKNTIELIDSGNTIPFIARYRKEVTGELDDTTLRNFYERLTYLRNLEQKKEEVKRLIEAQGK 80
Cdd:COG2183    2 MMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065  81 LTEEIINNIDNALSITEVEDIYRPFRPKKRTRATIAKEKGLEPLAALIYSQDfTDDLLKIVEGYVNKELGVENHEDAIKG 160
Cdd:COG2183   82 LTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQP-TGDPEAEAAKYINEEKGVADVEAALDG 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 161 AMDIIAEDISDNPEYRKEIRRLTFREGLIVTK---GLKDETSPYEMYYKYSEAVNRIVSHRILAINRGEKEEFLSVKIEA 237
Cdd:COG2183  161 ARDILAERISEDAELRGKLRELLWKEGVLVSKvkkGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEP 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 238 PIEKILSFLENKVIKRSSKETS-YLLETIKDSYNRLIAPSVEREIRNELTEKAEEQAIKVFAANLKSLLMISPVKGKVVL 316
Cdd:COG2183  241 DEEEAEAYIARRFIKDQGRPADeWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVL 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 317 GFDPGFRTGCKVAVVDETGKLLDYATVYSTAPQNDIEGSKKILKELIYKYNVDIISLGNGTASRESEIFLAELIKEVEce 396
Cdd:COG2183  321 GLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELD-- 398

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 397 sgKKIYYVVVSEAGASVYSASEIAAKEFPDINVSIRGAISIARRLQDPLAELVKIDPKSIGVGQYQHDVSQKKLDESLKG 476
Cdd:COG2183  399 --LKVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDA 476

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 477 VVEDCVNSVGVDLNTASAPLLSYISGINAATAKNIVEYREENGKFRDRREILKVKRLGEKAFEQCAGFLRIPESENVLDN 556
Cdd:COG2183  477 VVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDN 556

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 557 TAVHPESYSAAENILEKLGYTIQDVKDKKlndidKKLDEYGVEKLSSETgVGIPTLRDIISELKKPGRDPRESLPQPIFM 636
Cdd:COG2183  557 SAVHPESYPVVEKILKDLGVSVKDLIGNK-----ELLKKLDPEKYADEL-FGLPTLRDILKELEKPGRDPRPEFKTPTFR 630

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 599131065 637 SGVMELEDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLT 715
Cdd:COG2183  631 EGVLKIEDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLS 709
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 8-192 2.49e-94

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: 290.07  E-value: 2.49e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065    8 LTEELNIKEWQVKNTIELIDSGNTIPFIARYRKEVTGELDDTTLRNFYERLTYLRNLEQKKEEVKRLIEAQGKLTEEIIN 87
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065   88 NIDNALSITEVEDIYRPFRPKKRTRATIAKEKGLEPLAALIYSQdftDDLLKIVEGYVNKELGVENHEDAIKGAMDIIAE 167
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQ---PDPEEEAAKYINPEKGVADVEEALAGARDIIAE 157

                         170       180
                  ....*....|....*....|....*
gi 599131065  168 DISDNPEYRKEIRRLTFREGLIVTK 192
Cdd:pfam09371 158 RISEDAELRKKLRELLWREGVIVSK 182
Tex_YqgF pfam16921
Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which ...
 314-442 3.93e-78

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: 245.77  E-value: 3.93e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065  314 VVLGFDPGFRTGCKVAVVDETGKLLDYATVYSTAPQNDIEGSKKILKELIYKYNVDIISLGNGTASRESEIFLAELIKev 393
Cdd:pfam16921   1 VVLGLDPGYRTGCKLAVVDETGKVLDTAVIYPHPPQNKVEEAKKKLKKLIKKYGVELIAIGNGTASRETEQFVAELIK-- 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 599131065  394 ecESGKKIYYVVVSEAGASVYSASEIAAKEFPDINVSIRGAISIARRLQ 442
Cdd:pfam16921  79 --ELPLKVKYVIVSEAGASVYSASELAREEFPDLDVSLRGAVSIARRLQ 125
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 648-715 2.09e-34

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 125.04  E-value: 2.09e-34
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 599131065 648 GMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLT 715
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 484-545 3.04e-30

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


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 113.35  E-value: 3.04e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 599131065  484 SVGVDLNTASAPLLSYISGINAATAKNIVEYREENGKFRDRREILKVKRLGEKAFEQCAGFL 545
Cdd:pfam12836   1 AVGVDINTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKTFEQLAGFL 62
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 642-716 1.22e-25

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: 108.98  E-value: 1.22e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 599131065 642 LEDLKPGMILKGTVRNVADFGAFVDIGvHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:COG0539  184 LEKLEEGDVVEGTVKNITDFGAFVDLG-GVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSL 257
HHH_9 pfam17674
HHH domain;
552-627 3.97e-25

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 98.76  E-value: 3.97e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 599131065  552 NVLDNTAVHPESYSAAENILEKLGYTIQDVkdKKLNDIDKKLDeygVEKLSSEtGVGIPTLRDIISELKKPGRDPR 627
Cdd:pfam17674   1 NPLDNTAIHPESYPLAEKILKDLGLDLKDL--IGNSALLKKLD---PKKLAEE-EVGLPTLKDILEELAKPGRDPR 70
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 313-415 1.44e-24

Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.


Pssm-ID: 128971  Cd Length: 99  Bit Score: 98.41  E-value: 1.44e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065   313 KVVLGFDPGfRTGCKVAVVDETGKLLDYATVYstaPQNDIEGSKKILKELIYKYNVDIISLG-----NGTASRESEIFLA 387
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVI---PRTNKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFA 76

                           90       100
                   ....*....|....*....|....*...
gi 599131065   388 ELIKEvecesGKKIYYVVVSEAGASVYS 415
Cdd:smart00732  77 ELLKE-----RFNLPVVLVDERLATVYA 99
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 647-714 3.40e-24

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


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 96.16  E-value: 3.40e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 599131065 647 PGMILKGTVRNVADFGAFVDIGVhQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISL 714
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDLGG-VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISL 67
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 643-716 2.15e-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: 102.04  E-value: 2.15e-23
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 599131065 643 EDLKPGMILKGTVRNVADFGAFVDI--GVhqDGLVHISELS-DKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:COG0539  270 EKYPVGDVVKGKVTRLTDFGAFVELepGV--EGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSI 344
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
646-716 2.48e-21

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 88.04  E-value: 2.48e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 599131065   646 KPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 642-716 2.76e-21

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 98.31  E-value: 2.76e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 599131065 642 LEDLKPGMILKGTVRNVADFGAFVDIGVhQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:PRK06299 196 LENLEEGQVVEGVVKNITDYGAFVDLGG-VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGL 269
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 642-716 3.09e-21

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 96.48  E-value: 3.09e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 599131065 642 LEDLKPGMILKGTVRNVADFGAFVDIG-VhqDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:PRK06676 187 LSSLKEGDVVEGTVARLTDFGAFVDIGgV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSL 260
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 643-716 3.79e-21

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 96.10  E-value: 3.79e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 599131065 643 EDLKPGMILKGTVRNVADFGAFVDI--GVhqDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:PRK06676 273 EKLPEGDVIEGTVKRLTDFGAFVEVlpGV--EGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSI 346
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 643-716 9.67e-21

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 96.77  E-value: 9.67e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 599131065 643 EDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELS-DKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:PRK06299 282 KKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGL 356
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 642-716 1.59e-20

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 95.50  E-value: 1.59e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 599131065 642 LEDLKPGMILKGTVRNVADFGAFVDIGvHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:PRK07899 203 LNQLQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSL 276
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 643-716 3.04e-20

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


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 95.46  E-value: 3.04e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 599131065 643 EDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDvRRRRISLTI 716
Cdd:COG1185  612 AEPEVGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEID-DQGRIKLSR 684
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 648-716 5.43e-20

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: 84.13  E-value: 5.43e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 599131065 648 GMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDvRRRRISLTI 716
Cdd:cd04472    1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD-DRGRISLSR 68
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 644-716 3.80e-19

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 92.03  E-value: 3.80e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 599131065 644 DLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDvRRRRISLTI 716
Cdd:PRK11824 618 EPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSR 689
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 648-716 3.91e-19

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: 81.95  E-value: 3.91e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 599131065 648 GMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDvRRRRISLTI 716
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID-ARGRISLSI 68
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 645-716 1.05e-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: 80.79  E-value: 1.05e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 599131065  645 LKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 643-716 1.06e-18

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 82.53  E-value: 1.06e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 599131065 643 EDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDvRRRRISLTI 716
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSID-EDGKISLSI 73
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
641-716 3.22e-18

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 88.85  E-value: 3.22e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 599131065 641 ELEDLKPGMILKGTVRNVADFGAFVDI-GVhqDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:PRK00087 471 TWNSLEEGDVVEGEVKRLTDFGAFVDIgGV--DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSL 545
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 646-716 3.29e-18

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: 80.55  E-value: 3.29e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 599131065 646 KPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:NF040579   2 KIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSL 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 646-716 4.02e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 88.30  E-value: 4.02e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 599131065 646 KPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELS-DKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGI 443
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 651-715 5.54e-18

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 78.58  E-value: 5.54e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 599131065 651 LKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLT 715
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
643-716 7.17e-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: 7.17e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 599131065 643 EDLKPGMILKGTVRNVADFGAFVDI--GVhqDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:PRK00087 558 EKYPVGSIVLGKVVRIAPFGAFVELepGV--DGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSI 631
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 642-716 8.40e-17

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: 84.02  E-value: 8.40e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 599131065  642 LEDLKPGMILKGTVRNVADFGAFVDIGVhQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:TIGR00717 182 LENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255
rpsA PRK13806
30S ribosomal protein S1; Provisional
 643-716 1.90e-16

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 82.85  E-value: 1.90e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 599131065 643 EDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELS-DKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:PRK13806 288 DRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSL 362
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 642-716 1.39e-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: 1.39e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 599131065  642 LEDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELS-DKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:TIGR00717 267 EKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGL 342
PRK08059 PRK08059
general stress protein 13; Validated
 642-716 3.85e-15

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 72.39  E-value: 3.85e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 599131065 642 LEDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:PRK08059   2 MSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSI 76
PRK08582 PRK08582
RNA-binding protein S1;
651-716 8.51e-15

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 71.99  E-value: 8.51e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 599131065 651 LKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDvRRRRISLTI 716
Cdd:PRK08582   9 LQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE-DDGKIGLSI 73
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 648-714 1.60e-14

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: 68.67  E-value: 1.60e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 599131065 648 GMILKGTVRNVADFGAFVDIGVHQDGLVHISELS-DKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISL 714
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 647-716 1.61e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 76.62  E-value: 1.61e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 647 PGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSL 362
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 646-714 2.18e-14

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 68.51  E-value: 2.18e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 646 KPGMILKGTVRNVADFGAFVDI-GVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISL 714
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISL 70
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 648-714 5.20e-14

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: 67.65  E-value: 5.20e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 599131065 648 GMILKGTVRNVADFGAFVDI---GVHQDGLVHISELS-DKYIKHPLEVVKVGDIVNVKVLevDVRRRRISL 714
Cdd:cd05684    1 GKIYKGKVTSIMDFGCFVQLeglKGRKEGLVHISQLSfEGRVANPSDVVKRGQKVKVKVI--SIQNGKISL 69
PRK05807 PRK05807
RNA-binding protein S1;
645-716 5.68e-14

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 69.39  E-value: 5.68e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 599131065 645 LKPGMILKGTVRNVADFGAFVDIGvHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDvRRRRISLTI 716
Cdd:PRK05807   3 LKAGSILEGTVVNITNFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISLSI 72
rpsA PRK13806
30S ribosomal protein S1; Provisional
 642-716 1.53e-13

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 73.61  E-value: 1.53e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 599131065 642 LEDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRR----RISLTI 716
Cdd:PRK13806 197 METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSI 275
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 648-714 2.39e-13

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: 65.68  E-value: 2.39e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 599131065 648 GMILKGTVRNVADFGAFVDIGVHQDGLVHISEL--SDKYIkHPLEVVKVGDIVNVKVLEVDVRRRRISL 714
Cdd:cd05689    4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMdwTNKNI-HPSKVVSLGDEVEVMVLDIDEERRRISL 71
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 648-715 2.71e-13

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: 65.34  E-value: 2.71e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 599131065 648 GMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLT 715
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLT 68
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 487-540 4.29e-13

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


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 64.88  E-value: 4.29e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 599131065 487 VDLNTASAPLLSYISGINAATAKNIVEYREENGKFRDRREILKVKRLGEKAFEQ 540
Cdd:COG1555   13 VDINTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGIGPKTLEK 66
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 641-716 2.33e-12

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: 62.99  E-value: 2.33e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 599131065 641 ELEDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:cd04461    8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 642-716 5.79e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 68.65  E-value: 5.79e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 599131065 642 LEDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:PRK06299 455 AKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSI 529
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 648-715 1.46e-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: 60.39  E-value: 1.46e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 599131065 648 GMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLT 715
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
comE TIGR01259
comEA protein; This model describes the ComEA protein in bacteria. The com E locus is ...
 473-547 1.10e-10

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


Pssm-ID: 213597 [Multi-domain]  Cd Length: 120  Bit Score: 59.53  E-value: 1.10e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 599131065  473 SLKGVVEDCVNSVGVDLNTASAPLLSYISGINAATAKNIVEYREENGKFRDRREILKVKRLGEKAFEQCAGFLRI 547
Cdd:TIGR01259  46 SQQGTQSSAGKLAAVNINAASLEELQALPGIGPAKAKAIIEYREENGAFKSVDDLTKVSGIGEKSLEKLKDYATV 120
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 650-703 2.13e-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: 57.11  E-value: 2.13e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 599131065 650 ILKGTVRNVADFGAFVDI-GVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVL 703
Cdd:cd05686    6 IFKGEVASVTEYGAFVKIpGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVI 60
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 645-715 2.72e-10

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 62.12  E-value: 2.72e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 599131065 645 LKPGMILKGTVRNVADFGAFVDIGvHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLT 715
Cdd:PRK07400 194 LEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLS 263
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 646-714 4.27e-10

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: 56.44  E-value: 4.27e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 599131065 646 KPGMILKGTVRNVADFGAFVDIGVHQD--GLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISL 714
Cdd:cd04452    2 EEGELVVVTVKSIADMGAYVSLLEYGNieGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDL 72
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 642-705 6.01e-10

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: 62.55  E-value: 6.01e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 599131065 642 LEDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYikhplevvKVGDIVNVKVLEV 705
Cdd:COG1107   34 PDDLEPGRYYRGTVDGVADFGVFVDLNDHVTGLLHRSELDQDW--------EVGDEVFVQVKEV 89
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 648-716 9.92e-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: 61.67  E-value: 9.92e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065  648 GMILKGTVRNVADFGAFVDIGVHQDGLVHISELS-DKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:TIGR00717 360 GDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGV 429
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 647-716 1.02e-09

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 59.84  E-value: 1.02e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 599131065 647 PGMILKGTVRNVADFGAFVDIGVHQD--GLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:PRK03987   8 EGELVVGTVKEVKDFGAFVTLDEYPGkeGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSL 79
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 648-715 4.24e-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: 53.38  E-value: 4.24e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 599131065 648 GMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLT 715
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLS 68
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 641-709 4.42e-09

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: 53.38  E-value: 4.42e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 599131065 641 ELEDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYikhplevvKVGDIVNVKVLEVDVRR 709
Cdd:cd04473   10 TMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDY--------EVGDEVIVQVTDIPENG 70
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 655-706 1.96e-08

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 57.98  E-value: 1.96e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 599131065 655 VRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVD 706
Cdd:PLN00207 762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVN 813
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 645-714 2.22e-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: 51.48  E-value: 2.22e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 645 LKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISL 714
Cdd:cd05706    1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIAL 70
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 635-707 2.42e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 56.81  E-value: 2.42e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 599131065 635 FMSGVMELEDLKPGMILKGTVRNVADFGAFVDI-GVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDV 707
Cdd:PRK06676   5 FEESLNSVKEVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVED 78
HHH_7 pfam14635
Helix-hairpin-helix motif;
452-548 2.86e-08

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 52.16  E-value: 2.86e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065  452 DPKSIGVGQYQHDVSQKKLDESLKGVVEDCVNSVGVDLNTA-----SAPLLSYISGINAATAKNIVE-YREENGKFRDRR 525
Cdd:pfam14635   2 DILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAiankyEAAILPYIAGLGPRKADHLLKiLAANNGRLDNRS 81

                          90       100
                  ....*....|....*....|...
gi 599131065  526 EILKVKRLGEKAFEQCAGFLRIP 548
Cdd:pfam14635  82 QLITKCIMGPKVFMNCAGFLIID 104
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 648-716 3.54e-08

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: 51.25  E-value: 3.54e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 648 GMILKGTVRNVADFGAFV---DIGVhqDGLVHISELSDKY-----IKHPL------EVVKVGDIVNVKVLEVDVRRRRIS 713
Cdd:cd04471    2 GEEFDGVISGVTSFGLFVeldNLTV--EGLVHVSTLGDDYyefdeENHALvgertgKVFRLGDKVKVRVVRVDLDRRKID 79


                 ...
gi 599131065 714 LTI 716
Cdd:cd04471   80 FEL 82
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 646-716 3.94e-08

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 56.28  E-value: 3.94e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 599131065  646 KPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:TIGR00717 445 KVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSV 515
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 650-715 5.20e-08

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: 51.13  E-value: 5.20e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 599131065 650 ILKGTVRNVADFGAFVDIGvHQDGLVHISELSDKYIKHPLE-----------VVKVGDIVNVKVLEVDVRRRRISLT 715
Cdd:cd04460    2 VVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKnkrligeetkrVLKVGDVVRARIVAVSLKERRPRES 77
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 650-715 5.80e-08

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 53.29  E-value: 5.80e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 650 ILKGTVRNVADFGAFVDIGVhQDGLVHISELSDKYIKHPLE-----------VVKVGD-----IVNVKVLEVDVRRRRIS 713
Cdd:PRK08563  84 VVEGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYISYDPKngrligkeskrVLKVGDvvrarIVAVSLKERRPRGSKIG 162


                 ..
gi 599131065 714 LT 715
Cdd:PRK08563 163 LT 164
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 648-706 1.18e-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: 49.06  E-value: 1.18e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 599131065 648 GMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVD 706
Cdd:cd05687    1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVE 59
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
645-716 1.31e-07

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 50.86  E-value: 1.31e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 599131065 645 LKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:PRK07252   1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSL 72
VacB COG0557
Exoribonuclease R [Transcription];
648-716 1.44e-07

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 54.73  E-value: 1.44e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 648 GMILKGTVRNVADFGAFV---DIGVhqDGLVHISELSDKY-----IKHPL------EVVKVGDIVNVKVLEVDVRRRRIS 713
Cdd:COG0557  623 GEEFEGVISGVTSFGLFVeldELGV--EGLVHVSSLGDDYyeydeRRQALvgertgKRYRLGDRVEVRVVRVDLDRRQID 700


                 ...
gi 599131065 714 LTI 716
Cdd:COG0557  701 FEL 703
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 650-714 1.64e-07

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 54.72  E-value: 1.64e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 599131065 650 ILKGTVRNVADFGAFVDIGVHQDGLVHISELS-DKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISL 714
Cdd:PRK12269 581 VVKGRVTKIADFGAFIELAEGIEGLAHISEFSwVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSL 646
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 651-716 3.14e-07

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 53.95  E-value: 3.14e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 599131065 651 LKGTVRNVADFGAFVDIGVHqDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:PRK12269 497 VSGVVKSFTSFGAFIDLGGF-DGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSL 561
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 648-716 3.64e-07

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


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 48.04  E-value: 3.64e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 599131065 648 GMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLTI 716
Cdd:cd05691    1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSI 69
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 641-706 3.70e-07

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: 52.74  E-value: 3.70e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 599131065 641 ELEDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDkyiKHPLEVVKVGDIVNVKVLEVD 706
Cdd:COG0539   12 SLKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSD---EPGELEVKVGDEVEVYVEKVE 74
rpsA PRK13806
30S ribosomal protein S1; Provisional
 643-715 6.16e-07

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 52.42  E-value: 6.16e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 599131065 643 EDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVDVRRRRISLT 715
Cdd:PRK13806 375 ERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLA 447
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 487-540 1.35e-06

competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model. [Cellular processes, DNA transformation]


Pssm-ID: 129520 [Multi-domain]  Cd Length: 69  Bit Score: 46.46  E-value: 1.35e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 599131065  487 VDLNTASAP-LLSYISGINAATAKNIVEYREENGKFRDRREILKVKRLGEKAFEQ 540
Cdd:TIGR00426   8 VNINTATAEeLQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEK 62
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
608-706 3.17e-06

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 50.33  E-value: 3.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 608 GIPTLRDIISE-LKKPGRDPRESLPQPIFMSGVMELED--LKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKY 684
Cdd:PRK00087 260 GASTPDWIIEEvIKKMSELDNMEEVEENEQLEYMNELEkqIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDE 339

                         90       100
                 ....*....|....*....|..
gi 599131065 685 IKHPLEVVKVGDIVNVKVLEVD 706
Cdd:PRK00087 340 ISSLKESVKVGDEIEVKVLKLE 361
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 645-704 7.71e-06

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: 44.26  E-value: 7.71e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 599131065 645 LKPGMILKGTV-RNVADFGAFVDIGVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLE 704
Cdd:cd05704    1 LEEGAVTLGMVtKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILS 61
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 648-711 1.87e-05

S1_Rrp5_repeat_hs11_sc8: 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 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 42.96  E-value: 1.87e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 599131065 648 GMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKY--IKHPLEVVKVGDIVNVKVLEV-DVRRRR 711
Cdd:cd05702    1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWpdGKNPLSKFKIGQKIKARVIGGhDAKTHR 67
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 644-715 4.79e-05

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


Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 41.85  E-value: 4.79e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 599131065 644 DLKPGMILKGTVRNVADFGAFVDIGVHQ-DGLVHISELSDKyikhplEVVKVGDIVNVKVLEVDVRRRRISLT 715
Cdd:cd05694    1 DLVEGMVLSGCVSSVEDHGYILDIGIPGtTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLS 67
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 346-447 2.23e-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: 42.16  E-value: 2.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065  346 TAPQNDIEGSKKILKELiyKYNVDIISLGNGTASRESEiFLAELIKEVECES-GKKIYYVVVSEAGASVYSASEIAAKEF 424
Cdd:pfam14639  46 ENKAQFEETLKKFLLSK--KPHVIGVSGENRDAQKFYE-DVQRVLHELEQDSrLHTIGVILVDDEVAILYQNSKRAEAEF 122

                          90       100
                  ....*....|....*....|...
gi 599131065  425 PDINVSIRGAISIARRLQDPLAE 447
Cdd:pfam14639 123 PDYPPLLRYCVALARYIQDPLLE 145
ASKHA_NBD_O66634-like_rpt2 cd24035
nucleotide-binding domain (NBD) of the second repeat of Aquifex aeolicus hypothetical protein ...
 315-377 1.60e-03

nucleotide-binding domain (NBD) of the second repeat of Aquifex aeolicus hypothetical protein O66634 and similar proteins; The family includes a group of uncharacterized proteins similar to Aquifex aeolicus hypothetical protein O66634, which contains two copies of the BcrAD/BadFG-like domain, suggesting that the family may structurally dimerize. The model corresponds to the second copy of the BcrAD/BadFG-like domain.


Pssm-ID: 466885  Cd Length: 258  Bit Score: 40.98  E-value: 1.60e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 599131065 315 VLGFDPGfRTGCKVAVVDETGKLLDyaTVYSTAPQNDIEGSKKILKELIYKYNVDIISLGNGT 377
Cdd:cd24035    1 YLGIDVG-STTTKAVLIDEDGEILA--SVYLRTKGNPIEAVKKGLKELREQLPEKVVIVGVGT 60
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 640-714 1.70e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 41.69  E-value: 1.70e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 599131065 640 MELEDLKPGMILKGTVRNVADFGAFVDIGVHQDGLVHISELSDKyiKHPLEvVKVGDIVNVKVLEVDVRRRRISL 714
Cdd:PRK06299  23 LKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNE--QGELE-VKVGDEVEVYVERIEDGFGETVL 94
T2SSK pfam03934
Type II secretion system (T2SS), protein K; Members of this family are involved in the Type II ...
 485-534 2.13e-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: 40.77  E-value: 2.13e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 599131065  485 VGVDLNTASAPLLS-YISGINAATAKNIVEYREENGkFRDRREILKVKRLG 534
Cdd:pfam03934 184 TPINVNTAPAEVLAaLFDGLSLDQAQALLAQRPADG-FESVDDFLAQPALG 233
S1_RNase_E cd04453
S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential ...
 648-702 3.88e-03

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


Pssm-ID: 239900 [Multi-domain]  Cd Length: 88  Bit Score: 37.19  E-value: 3.88e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 599131065 648 GMILKGTVRNVADF--GAFVDIGVHQDGLVHISELSDKYIKHPL---EVVKVGDIVNVKV 702
Cdd:cd04453    8 GNIYLGRVKKIVPGlqAAFVDIGLGKNGFLHLSDILPAYFKKHKkiaKLLKEGQEILVQV 67
Csl4 COG1096
Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...
 645-706 9.92e-03

Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440713 [Multi-domain]  Cd Length: 191  Bit Score: 37.96  E-value: 9.92e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 599131065 645 LKPGMILKGTVRNVADFGAFVDI----------GVHQDGLVHISELSDKYIKHPLEVVKVGDIVNVKVLEVD 706
Cdd:COG1096   63 PKKGDIVIGEVVDVRESMALVKIyaiegnerelPSSFSGIIHISQVSDSYVKDLSDEFRVGDIVRAKVISTL 134
 
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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