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Conserved domains on  [gi|1733400547|gb|QEK79885|]
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RNA-binding transcriptional accessory protein [Clostridioides difficile]

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];
1-713 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


:

Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1229.12  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547   1 MDINQILKKEFNLRDEQINNTLKLIDEGNTIPFIARYRKEMTGEMSDVTLREFYEKLMYLRNLQSRKDDVVRLIDEQGKL 80
Cdd:COG2183     3 MDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGKL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547  81 TDEITQNIEKAKTLQEVEDIYAPYKQKKRTRATIAKEKGLENLALSILENNLDNIEIEAKNYLDEEKEVLSIEDALKGAR 160
Cdd:COG2183    83 TPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEEKGVADVEAALDGAR 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 161 DIIAELVSDDAKIRKYIRELALREGMIVSK---SATDEKSVYDMYYDYSEAVKSMAPHRVLAINRGEKESFLKVKLEINN 237
Cdd:COG2183   163 DILAERISEDAELRGKLRELLWKEGVLVSKvkkGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPDE 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 238 DKVLNYIINEYVNDKNFKNKEEIVSSIEDSYKRLIFPSIEREIRNHLTEIAQERAISVFGKNVKSLLLQPPVKDKVVMGF 317
Cdd:COG2183   243 EEAEAYIARRFIKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVLGL 322

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 318 DPAFRTGCKIAVVDKNGKLLDYTTVYPTDPQNDVEGAKKVLKGLIEKYDIDIISIGNGTASRESETFVSEMIKEIDSEVQ 397
Cdd:COG2183   323 DPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELDLKVQ 402

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 398 YVIVSEAGASVYSASELANEEHPDINVSIRGAISIARRLQDPLAELVKIDPKSIGVGQYQHDLNKKRLEEVLDGVVEDSV 477
Cdd:COG2183   403 YVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCV 482

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 478 NSVGVDLNTASYSLLEHVAGISKAIAKNIIAYREENGDFTSRAQLKKVKRLGPQAFTQCAGFMRILEGKNPLDNTGVHPE 557
Cdd:COG2183   483 NAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDNSAVHPE 562

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 558 SYDICKKMIEIIGYSLDDVKNKnigeiDEKIKEIGLRELSEKLeVGQVTLKDIIAEIKKPGRDPREEGIKPILRTDVLKI 637
Cdd:COG2183   563 SYPVVEKILKDLGVSVKDLIGN-----KELLKKLDPEKYADEL-FGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLKI 636

                         650       660       670       680       690       700       710
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1733400547 638 EDIQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMKK 713
Cdd:COG2183   637 EDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKL 712
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1-713 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1229.12  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547   1 MDINQILKKEFNLRDEQINNTLKLIDEGNTIPFIARYRKEMTGEMSDVTLREFYEKLMYLRNLQSRKDDVVRLIDEQGKL 80
Cdd:COG2183     3 MDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGKL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547  81 TDEITQNIEKAKTLQEVEDIYAPYKQKKRTRATIAKEKGLENLALSILENNLDNIEIEAKNYLDEEKEVLSIEDALKGAR 160
Cdd:COG2183    83 TPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEEKGVADVEAALDGAR 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 161 DIIAELVSDDAKIRKYIRELALREGMIVSK---SATDEKSVYDMYYDYSEAVKSMAPHRVLAINRGEKESFLKVKLEINN 237
Cdd:COG2183   163 DILAERISEDAELRGKLRELLWKEGVLVSKvkkGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPDE 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 238 DKVLNYIINEYVNDKNFKNKEEIVSSIEDSYKRLIFPSIEREIRNHLTEIAQERAISVFGKNVKSLLLQPPVKDKVVMGF 317
Cdd:COG2183   243 EEAEAYIARRFIKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVLGL 322

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 318 DPAFRTGCKIAVVDKNGKLLDYTTVYPTDPQNDVEGAKKVLKGLIEKYDIDIISIGNGTASRESETFVSEMIKEIDSEVQ 397
Cdd:COG2183   323 DPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELDLKVQ 402

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 398 YVIVSEAGASVYSASELANEEHPDINVSIRGAISIARRLQDPLAELVKIDPKSIGVGQYQHDLNKKRLEEVLDGVVEDSV 477
Cdd:COG2183   403 YVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCV 482

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 478 NSVGVDLNTASYSLLEHVAGISKAIAKNIIAYREENGDFTSRAQLKKVKRLGPQAFTQCAGFMRILEGKNPLDNTGVHPE 557
Cdd:COG2183   483 NAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDNSAVHPE 562

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 558 SYDICKKMIEIIGYSLDDVKNKnigeiDEKIKEIGLRELSEKLeVGQVTLKDIIAEIKKPGRDPREEGIKPILRTDVLKI 637
Cdd:COG2183   563 SYPVVEKILKDLGVSVKDLIGN-----KELLKKLDPEKYADEL-FGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLKI 636

                         650       660       670       680       690       700       710
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1733400547 638 EDIQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMKK 713
Cdd:COG2183   637 EDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKL 712
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 7-190 1.90e-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: 290.46  E-value: 1.90e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547   7 LKKEFNLRDEQINNTLKLIDEGNTIPFIARYRKEMTGEMSDVTLREFYEKLMYLRNLQSRKDDVVRLIDEQGKLTDEITQ 86
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547  87 NIEKAKTLQEVEDIYAPYKQKKRTRATIAKEKGLENLALSILENnlDNIEIEAKNYLDEEKEVLSIEDALKGARDIIAEL 166
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQ--PDPEEEAAKYINPEKGVADVEEALAGARDIIAER 158

                         170       180
                  ....*....|....*....|....
gi 1733400547 167 VSDDAKIRKYIRELALREGMIVSK 190
Cdd:pfam09371 159 ISEDAELRKKLRELLWREGVIVSK 182
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 643-710 2.77e-29

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: 110.79  E-value: 2.77e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1733400547 643 GMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALS 710
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 312-410 1.12e-21

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: 89.93  E-value: 1.12e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547  312 KVVMGFDPAfRTGCKIAVVDKNGKLLDYTTVYPTdpqNDVEGAKKVLKGLIEKYDIDIISIG-----NGTASRESETFVS 386
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVIPR---TNKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFA 76

                           90       100
                   ....*....|....*....|....
gi 1733400547  387 EMIKEiDSEVQYVIVSEAGASVYS 410
Cdd:smart00732  77 ELLKE-RFNLPVVLVDERLATVYA 99
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 637-712 2.93e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 88.68  E-value: 2.93e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1733400547 637 IEDIQEGMTLKGTIRNVVDFGAFVDI-GIknDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:PRK06299  196 LENLEEGQVVEGVVKNITDYGAFVDLgGV--DGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLK 270
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 640-712 1.24e-13

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator.


Pssm-ID: 468553 [Multi-domain]  Cd Length: 113  Bit Score: 67.45  E-value: 1.24e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1733400547 640 IQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:NF040579    1 YKIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSLR 73
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 637-712 3.84e-13

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 72.46  E-value: 3.84e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1733400547 637 IEDIQEGMTLKGTIRNVVDFGAFVDIGIKnDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:TIGR00717 182 LENLKEGDVVKGVVKNITDFGAFVDLGGV-DGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLK 256
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1-713 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1229.12  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547   1 MDINQILKKEFNLRDEQINNTLKLIDEGNTIPFIARYRKEMTGEMSDVTLREFYEKLMYLRNLQSRKDDVVRLIDEQGKL 80
Cdd:COG2183     3 MDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGKL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547  81 TDEITQNIEKAKTLQEVEDIYAPYKQKKRTRATIAKEKGLENLALSILENNLDNIEIEAKNYLDEEKEVLSIEDALKGAR 160
Cdd:COG2183    83 TPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEEKGVADVEAALDGAR 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 161 DIIAELVSDDAKIRKYIRELALREGMIVSK---SATDEKSVYDMYYDYSEAVKSMAPHRVLAINRGEKESFLKVKLEINN 237
Cdd:COG2183   163 DILAERISEDAELRGKLRELLWKEGVLVSKvkkGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPDE 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 238 DKVLNYIINEYVNDKNFKNKEEIVSSIEDSYKRLIFPSIEREIRNHLTEIAQERAISVFGKNVKSLLLQPPVKDKVVMGF 317
Cdd:COG2183   243 EEAEAYIARRFIKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVLGL 322

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 318 DPAFRTGCKIAVVDKNGKLLDYTTVYPTDPQNDVEGAKKVLKGLIEKYDIDIISIGNGTASRESETFVSEMIKEIDSEVQ 397
Cdd:COG2183   323 DPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELDLKVQ 402

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 398 YVIVSEAGASVYSASELANEEHPDINVSIRGAISIARRLQDPLAELVKIDPKSIGVGQYQHDLNKKRLEEVLDGVVEDSV 477
Cdd:COG2183   403 YVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCV 482

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 478 NSVGVDLNTASYSLLEHVAGISKAIAKNIIAYREENGDFTSRAQLKKVKRLGPQAFTQCAGFMRILEGKNPLDNTGVHPE 557
Cdd:COG2183   483 NAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDNSAVHPE 562

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 558 SYDICKKMIEIIGYSLDDVKNKnigeiDEKIKEIGLRELSEKLeVGQVTLKDIIAEIKKPGRDPREEGIKPILRTDVLKI 637
Cdd:COG2183   563 SYPVVEKILKDLGVSVKDLIGN-----KELLKKLDPEKYADEL-FGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLKI 636

                         650       660       670       680       690       700       710
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1733400547 638 EDIQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMKK 713
Cdd:COG2183   637 EDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKL 712
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 7-190 1.90e-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: 290.46  E-value: 1.90e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547   7 LKKEFNLRDEQINNTLKLIDEGNTIPFIARYRKEMTGEMSDVTLREFYEKLMYLRNLQSRKDDVVRLIDEQGKLTDEITQ 86
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547  87 NIEKAKTLQEVEDIYAPYKQKKRTRATIAKEKGLENLALSILENnlDNIEIEAKNYLDEEKEVLSIEDALKGARDIIAEL 166
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQ--PDPEEEAAKYINPEKGVADVEEALAGARDIIAER 158

                         170       180
                  ....*....|....*....|....
gi 1733400547 167 VSDDAKIRKYIRELALREGMIVSK 190
Cdd:pfam09371 159 ISEDAELRKKLRELLWREGVIVSK 182
Tex_YqgF pfam16921
Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which ...
 313-437 2.65e-81

Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which is involved in transcriptional processes.


Pssm-ID: 465314  Cd Length: 125  Bit Score: 253.86  E-value: 2.65e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 313 VVMGFDPAFRTGCKIAVVDKNGKLLDYTTVYPTDPQNDVEGAKKVLKGLIEKYDIDIISIGNGTASRESETFVSEMIKEI 392
Cdd:pfam16921   1 VVLGLDPGYRTGCKLAVVDETGKVLDTAVIYPHPPQNKVEEAKKKLKKLIKKYGVELIAIGNGTASRETEQFVAELIKEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1733400547 393 DSEVQYVIVSEAGASVYSASELANEEHPDINVSIRGAISIARRLQ 437
Cdd:pfam16921  81 PLKVKYVIVSEAGASVYSASELAREEFPDLDVSLRGAVSIARRLQ 125
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 643-710 2.77e-29

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: 110.79  E-value: 2.77e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1733400547 643 GMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALS 710
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 479-539 1.60e-28

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


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 108.34  E-value: 1.60e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1733400547 479 SVGVDLNTASYSLLEHVAGISKAIAKNIIAYREENGDFTSRAQLKKVKRLGPQAFTQCAGF 539
Cdd:pfam12836   1 AVGVDINTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKTFEQLAGF 61
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 637-712 1.34e-22

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: 99.73  E-value: 1.34e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1733400547 637 IEDIQEGMTLKGTIRNVVDFGAFVDI-GIknDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:COG0539   184 LEKLEEGDVVEGTVKNITDFGAFVDLgGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLK 258
HHH_9 pfam17674
HHH domain;
547-622 9.14e-22

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 89.13  E-value: 9.14e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1733400547 547 NPLDNTGVHPESYDICKKMIEIIGYSLDDVKNKNigeidEKIKEIGLRELSEkLEVGQVTLKDIIAEIKKPGRDPR 622
Cdd:pfam17674   1 NPLDNTAIHPESYPLAEKILKDLGLDLKDLIGNS-----ALLKKLDPKKLAE-EEVGLPTLKDILEELAKPGRDPR 70
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 312-410 1.12e-21

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: 89.93  E-value: 1.12e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547  312 KVVMGFDPAfRTGCKIAVVDKNGKLLDYTTVYPTdpqNDVEGAKKVLKGLIEKYDIDIISIG-----NGTASRESETFVS 386
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVIPR---TNKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFA 76

                           90       100
                   ....*....|....*....|....
gi 1733400547  387 EMIKEiDSEVQYVIVSEAGASVYS 410
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 ...
 642-710 8.84e-19

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


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 80.75  E-value: 8.84e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1733400547 642 EGMTLKGTIRNVVDFGAFVDIGiKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALS 710
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 638-712 2.36e-18

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: 87.02  E-value: 2.36e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1733400547 638 EDIQEGMTLKGTIRNVVDFGAFVDI--GIknDGLVHKSEMS-NSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:COG0539   270 EKYPVGDVVKGKVTRLTDFGAFVELepGV--EGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 637-712 2.93e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 88.68  E-value: 2.93e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1733400547 637 IEDIQEGMTLKGTIRNVVDFGAFVDI-GIknDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:PRK06299  196 LENLEEGQVVEGVVKNITDYGAFVDLgGV--DGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLK 270
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 638-713 1.31e-17

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 79.45  E-value: 1.31e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1733400547 638 EDIQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDlNKKRVALSMKK 713
Cdd:COG1098     1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSID-EDGKISLSIKQ 75
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 638-712 1.74e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 84.93  E-value: 1.74e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1733400547 638 EDIQEGMTLKGTIRNVVDFGAFVDIGiKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:PRK06676  188 SSLKEGDVVEGTVARLTDFGAFVDIG-GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLK 261
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
641-712 1.81e-17

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 77.26  E-value: 1.81e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1733400547  641 QEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 637-712 1.93e-17

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


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 86.60  E-value: 1.93e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1733400547 637 IEDIQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDlNKKRVALSMK 712
Cdd:COG1185   611 TAEPEVGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEID-DQGRIKLSRK 685
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 636-712 2.50e-17

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 86.26  E-value: 2.50e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 636 KIEDI----QEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDlNKKRVALSM 711
Cdd:PRK11824  611 RIEGItaepEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSR 689


                  .
gi 1733400547 712 K 712
Cdd:PRK11824  690 K 690
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
637-713 1.90e-16

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 83.46  E-value: 1.90e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1733400547 637 IEDIQEGMTLKGTIRNVVDFGAFVDIGIKnDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMKK 713
Cdd:PRK00087  472 WNSLEEGDVVEGEVKRLTDFGAFVDIGGV-DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKK 547
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 643-712 3.23e-15

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


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 70.78  E-value: 3.23e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 643 GMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDlNKKRVALSMK 712
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID-ARGRISLSIK 69
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 643-711 1.07e-14

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


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 69.11  E-value: 1.07e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1733400547 643 GMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDlNKKRVALSM 711
Cdd:cd04472     1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD-DRGRISLSR 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 638-712 2.09e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 76.74  E-value: 2.09e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1733400547 638 EDIQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMS--NSfVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:PRK06299  282 KKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSwtKK-NKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLK 357
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 646-712 3.50e-14

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: 67.89  E-value: 3.50e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1733400547 646 LKGTIRNVVDFGAFVDI-GIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLnKKRVALSMK 712
Cdd:cd05686     7 FKGEVASVTEYGAFVKIpGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREM-KDKMKLSLS 73
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 641-711 3.82e-14

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 67.70  E-value: 3.82e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1733400547 641 QEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSM 711
Cdd:pfam00575   2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 642-712 3.97e-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: 67.74  E-value: 3.97e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1733400547 642 EGMTLKGTIRNVVDFGAFVDI-GIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:cd05708     2 VGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 640-712 1.24e-13

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator.


Pssm-ID: 468553 [Multi-domain]  Cd Length: 113  Bit Score: 67.45  E-value: 1.24e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1733400547 640 IQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:NF040579    1 YKIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSLR 73
PRK08582 PRK08582
RNA-binding protein S1;
640-713 1.47e-13

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 68.14  E-value: 1.47e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1733400547 640 IQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKrVALSMKK 713
Cdd:PRK08582    3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGK-IGLSIKK 75
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 482-535 2.86e-13

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


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 65.27  E-value: 2.86e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1733400547 482 VDLNTASYSLLEHVAGISKAIAKNIIAYREENGDFTSRAQLKKVKRLGPQAFTQ 535
Cdd:COG1555    13 VDINTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGIGPKTLEK 66
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 640-712 2.91e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 72.77  E-value: 2.91e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1733400547 640 IQEGMTLKGTIRNVVDFGAFVDIGiKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:PRK07899  206 LQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLK 277
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 646-710 3.54e-13

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 64.71  E-value: 3.54e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1733400547 646 LKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALS 710
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 637-712 3.84e-13

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 72.46  E-value: 3.84e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1733400547 637 IEDIQEGMTLKGTIRNVVDFGAFVDIGIKnDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:TIGR00717 182 LENLKEGDVVKGVVKNITDFGAFVDLGGV-DGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLK 256
PRK08059 PRK08059
general stress protein 13; Validated
 640-712 4.95e-13

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 66.22  E-value: 4.95e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1733400547 640 IQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:PRK08059    5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 631-711 1.48e-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: 63.38  E-value: 1.48e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 631 RTDVLKIEDIQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALS 710
Cdd:cd04461     3 GTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLS 82


                  .
gi 1733400547 711 M 711
Cdd:cd04461    83 L 83
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 594-712 1.96e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 70.19  E-value: 1.96e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 594 RELSEKLEVGQvTLKDIIAEIkkpgrDPREE----GIKPILRTDVLKIEDI-QEGMTLKGTIRNVVDFGAFVDIGIKNDG 668
Cdd:PRK06299  413 EEAVELYKKGD-EVEAVVLKV-----DVEKErislGIKQLEEDPFEEFAKKhKKGSIVTGTVTEVKDKGAFVELEDGVEG 486

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1733400547 669 LVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:PRK06299  487 LIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 638-712 2.49e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 69.13  E-value: 2.49e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1733400547 638 EDIQEGMTLKGTIRNVVDFGAFVDI--GIknDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:PRK06676  273 EKLPEGDVIEGTVKRLTDFGAFVEVlpGV--EGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIK 347
rpsA PRK13806
30S ribosomal protein S1; Provisional
 637-713 2.77e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 69.75  E-value: 2.77e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 637 IEDIQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKK----RVALSMK 712
Cdd:PRK13806  197 METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIK 276


                  .
gi 1733400547 713 K 713
Cdd:PRK13806  277 Q 277
rpsA PRK13806
30S ribosomal protein S1; Provisional
 638-712 5.83e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 68.60  E-value: 5.83e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1733400547 638 EDIQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNS-FVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:PRK13806  288 DRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTrRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR 363
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 641-712 1.09e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 67.88  E-value: 1.09e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1733400547 641 QEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMS-NSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:PRK06299  372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIK 444
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 643-713 1.92e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 66.99  E-value: 1.92e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1733400547 643 GMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMKK 713
Cdd:PRK07899  294 GQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQ 364
PRK05807 PRK05807
RNA-binding protein S1;
640-713 2.79e-11

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 61.69  E-value: 2.79e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1733400547 640 IQEGMTLKGTIRNVVDFGAFVDIGIKNdGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKrVALSMKK 713
Cdd:PRK05807    3 LKAGSILEGTVVNITNFGAFVEVEGKT-GLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGK-ISLSIKQ 74
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 647-712 1.55e-10

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: 57.63  E-value: 1.55e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 647 KGTIRNVVDFGAFVDI---GIKNDGLVHKSEMS-NSFVKDPMSIVTVGDIVDVKVIGIDLNKkrVALSMK 712
Cdd:cd05684     5 KGKVTSIMDFGCFVQLeglKGRKEGLVHISQLSfEGRVANPSDVVKRGQKVKVKVISIQNGK--ISLSMK 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 597-713 2.03e-10

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 63.60  E-value: 2.03e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 597 SEKLEVGQ-VTLKdIIAEIKKPGRdpREEGIKPILRTDVLKIED-IQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSE 674
Cdd:TIGR00717 228 SEYVKVGQeVKVK-VIKFDKEKGR--ISLSLKQLGEDPWEAIEKkFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSE 304

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1733400547 675 MS-NSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMKK 713
Cdd:TIGR00717 305 MSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQ 344
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
638-713 2.39e-10

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 63.81  E-value: 2.39e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1733400547 638 EDIQEGMTLKGTIRNVVDFGAFVDI--GIknDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMKK 713
Cdd:PRK00087  558 EKYPVGSIVLGKVVRIAPFGAFVELepGV--DGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKE 633
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 642-709 1.08e-09

S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240194 [Multi-domain]  Cd Length: 72  Bit Score: 55.28  E-value: 1.08e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 642 EGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEM--SNSFVkDPMSIVTVGDIVDVKVIGIDLNKKRVAL 709
Cdd:cd05689     3 EGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMdwTNKNI-HPSKVVSLGDEVEVMVLDIDEERRRISL 71
comE TIGR01259
comEA protein; This model describes the ComEA protein in bacteria. The com E locus is ...
 466-542 2.31e-09

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: 55.68  E-value: 2.31e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1733400547 466 EEVLDGVVEDSVNSVGVDLNTASYSLLEHVAGISKAIAKNIIAYREENGDFTSRAQLKKVKRLGPQAFTQCAGFMRI 542
Cdd:TIGR01259  44 AVSQQGTQSSAGKLAAVNINAASLEELQALPGIGPAKAKAIIEYREENGAFKSVDDLTKVSGIGEKSLEKLKDYATV 120
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 643-712 2.49e-09

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


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 54.15  E-value: 2.49e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1733400547 643 GMTLKGTIRNVVDFGAFVDI--GIKndGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFynNVK--GFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 643-709 5.10e-09

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: 53.27  E-value: 5.10e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1733400547 643 GMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMS-NSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVAL 709
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 637-705 5.99e-08

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


Pssm-ID: 239919 [Multi-domain]  Cd Length: 77  Bit Score: 50.30  E-value: 5.99e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1733400547 637 IEDIQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVkdpmsivtVGDIVDVKVIGIDLNKK 705
Cdd:cd04473    11 MEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDYE--------VGDEVIVQVTDIPENGN 71
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 636-713 7.54e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 55.27  E-value: 7.54e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1733400547 636 KIEDIQEGMTLKGTIRNVVDFGAFVDI-GIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMKK 713
Cdd:PRK06676   11 SVKEVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRR 89
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
580-713 8.68e-08

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 55.72  E-value: 8.68e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 580 NIGEIDEKI----KEIGLrelseklEVGQVTLKDIIAEIKKpgrdpREEGIKPILRT--------DVLKIEDIQEGMTLK 647
Cdd:PRK00087  240 NAGELPEEWfkgvKIIGV-------TAGASTPDWIIEEVIK-----KMSELDNMEEVeeneqleyMNELEKQIRRGDIVK 307

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1733400547 648 GTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMKK 713
Cdd:PRK00087  308 GTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKE 373
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 643-710 9.11e-08

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: 49.60  E-value: 9.11e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1733400547 643 GMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALS 710
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 636-713 1.41e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 54.04  E-value: 1.41e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1733400547 636 KIEDIQEGMTLKGTIRNVVDFGAFVDIGiKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMKK 713
Cdd:PRK07400  190 KMNRLEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQ 266
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 603-705 1.56e-07

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 54.90  E-value: 1.56e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 603 GQVTLKDIIAEIKKPGRDPREEGIKPILRTDVLKIE---DIQEGMTLKGT---------IRNVVDFGAFVDIGIKNDGLV 670
Cdd:PLN00207  703 GGKKVKSIIEETGVEAIDTQDDGTVKITAKDLSSLEkskAIISSLTMVPTvgdiyrnceIKSIAPYGAFVEIAPGREGLC 782

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1733400547 671 HKSEMSNSFVKDPMSIVTVGDIVDVKVigIDLNKK 705
Cdd:PLN00207  783 HISELSSNWLAKPEDAFKVGDRIDVKL--IEVNDK 815
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 614-712 2.29e-07

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 54.33  E-value: 2.29e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 614 IKKPGRDPREEGIKPIlrtdvlKIEDiqegmTLKGTIRNVVDFGAFVDIGiKNDGLVHKSEMSNSFVKDPMSIVTVGDIV 693
Cdd:PRK12269  476 LEERARQAREEFFNSV------HIED-----SVSGVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQTI 543

                          90
                  ....*....|....*....
gi 1733400547 694 DVKVIGIDLNKKRVALSMK 712
Cdd:PRK12269  544 ELKVIRLDQAEKRINLSLK 562
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 637-713 2.82e-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: 53.12  E-value: 2.82e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1733400547 637 IEDIQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSfvkDPMSIVTVGDIVDVKVIGIDLNKKRVALSMKK 713
Cdd:COG0539    13 LKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSDE---PGELEVKVGDEVEVYVEKVEDGEGEIVLSKKK 86
HHH_7 pfam14635
Helix-hairpin-helix motif;
447-542 3.34e-07

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 49.08  E-value: 3.34e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 447 DPKSIGVGQYQHDLNKKRLEEVLDGVVEDSVNSVGVDLNTA-----SYSLLEHVAGISKAIAKNII-AYREENGDFTSRA 520
Cdd:pfam14635   2 DILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAiankyEAAILPYIAGLGPRKADHLLkILAANNGRLDNRS 81

                          90       100
                  ....*....|....*....|..
gi 1733400547 521 QLKKVKRLGPQAFTQCAGFMRI 542
Cdd:pfam14635  82 QLITKCIMGPKVFMNCAGFLII 103
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 583-712 3.85e-07

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 50.98  E-value: 3.85e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 583 EIDEKIKEIGLRELSEKLEvgqvtlkdiiaeikkpGRDPREEGIkpILrtDVLKIEDIQEGMTL---------------- 646
Cdd:PRK08563   17 MFGEDLEEAALEVLREKYE----------------GRIDKELGI--IV--AVLDVKVIGEGKIVpgdgatyhevefdalv 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 647 ---------KGTIRNVVDFGAFVDIGiKNDGLVHKSEMSNSFVK-DPMS----------IVTVGDIVDVKVIGIDLNKK- 705
Cdd:PRK08563   77 fkpelqevvEGEVVEVVEFGAFVRIG-PVDGLLHISQIMDDYISyDPKNgrligkeskrVLKVGDVVRARIVAVSLKERr 155

                         170
                  ....*....|.
gi 1733400547 706 ----RVALSMK 712
Cdd:PRK08563  156 prgsKIGLTMR 166
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 643-712 4.65e-07

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 53.20  E-value: 4.65e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 643 GMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:TIGR00717 447 GSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 641-712 6.74e-07

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 52.43  E-value: 6.74e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1733400547 641 QEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMS-NSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:TIGR00717 358 PVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVK 430
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 643-712 1.95e-06

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


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 45.60  E-value: 1.95e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 643 GMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:cd05687     1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 642-713 2.20e-06

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


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 45.65  E-value: 2.20e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1733400547 642 EGMTLKGTIRNVVDFGAFVDIGIKND--GLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMKK 713
Cdd:cd04452     3 EGELVVVTVKSIADMGAYVSLLEYGNieGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 643-709 2.26e-06

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


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 45.69  E-value: 2.26e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1733400547 643 GMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVAL 709
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVL 67
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
643-712 2.46e-06

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 47.00  E-value: 2.46e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 643 GMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:PRK07252    4 GDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLR 73
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 637-700 3.62e-06

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


Pssm-ID: 440724 [Multi-domain]  Cd Length: 626  Bit Score: 50.22  E-value: 3.62e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1733400547 637 IEDIQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVkdpmsivtVGDIVDVKVIGI 700
Cdd:COG1107    34 PDDLEPGRYYRGTVDGVADFGVFVDLNDHVTGLLHRSELDQDWE--------VGDEVFVQVKEV 89
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 640-710 3.63e-06

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: 44.94  E-value: 3.63e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1733400547 640 IQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALS 710
Cdd:cd05706     1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALS 71
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 648-713 4.37e-06

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 48.67  E-value: 4.37e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1733400547 648 GTIRNVVDFGAFVDIGIKND--GLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMKK 713
Cdd:PRK03987   14 GTVKEVKDFGAFVTLDEYPGkeGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKR 81
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 648-712 5.46e-06

S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.


Pssm-ID: 239907 [Multi-domain]  Cd Length: 99  Bit Score: 45.36  E-value: 5.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 648 GTIRNVVDFGAFVDIGiKNDGLVHKSEMSNSFVK-DPMS----------IVTVGDIVDVKVIGIDLNKK-----RVALSM 711
Cdd:cd04460     5 GEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISyDPKNkrligeetkrVLKVGDVVRARIVAVSLKERrpresKIGLTM 83


                  .
gi 1733400547 712 K 712
Cdd:cd04460    84 R 84
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 646-713 5.75e-06

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 49.71  E-value: 5.75e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1733400547 646 LKGTIRNVVDFGAFVDIGIKNDGLVHKSEMsnSFVK---DPMSIVTVGDIVDVKVIGIDLNKKRVALSMKK 713
Cdd:PRK12269  582 VKGRVTKIADFGAFIELAEGIEGLAHISEF--SWVKktsKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQ 650
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 643-712 6.03e-06

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: 44.57  E-value: 6.03e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 643 GMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 633-713 7.09e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 45.93  E-value: 7.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1733400547 633 DVLKIEDIQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSfvkDPMSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:PRK06299   21 ESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNE---QGELEVKVGDEVEVYVERIEDGFGETVLSRE 97


                  .
gi 1733400547 713 K 713
Cdd:PRK06299   98 K 98
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 639-713 9.39e-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: 41.08  E-value: 9.39e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1733400547 639 DIQEGMTLKGTIRNVVDFGAFVDIGIKN-DGLVHKSEMSNSFVKDpmsivtVGDIVDVKVIGIDLNKKRVALSMKK 713
Cdd:cd05694     1 DLVEGMVLSGCVSSVEDHGYILDIGIPGtTGFLPKKDAGNFSKLK------VGQLLLCVVEKVKDDGRVVSLSADP 70
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 643-699 4.51e-04

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: 39.11  E-value: 4.51e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1733400547 643 GMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFV--KDPMSIVTVGDIVDVKVIG 699
Cdd:cd05702     1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPdgKNPLSKFKIGQKIKARVIG 59
rpsA PRK13806
30S ribosomal protein S1; Provisional
 639-711 7.24e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 42.79  E-value: 7.24e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1733400547 639 DIQEGMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNsfvKDPMSIVTVGDIVDVKVIGIDLNKKRVALSM 711
Cdd:PRK13806   31 ELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLD---ADGELTVAVGDEVELYVVSVNGQEIRLSKAL 100
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 482-533 1.77e-03

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: 37.60  E-value: 1.77e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1733400547 482 VDLNTASYSLLE-HVAGISKAIAKNIIAYREENGDFTSRAQLKKVKRLGPQAF 533
Cdd:TIGR00426   8 VNINTATAEELQrAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLV 60
rpsA PRK13806
30S ribosomal protein S1; Provisional
 643-710 3.30e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 40.48  E-value: 3.30e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1733400547 643 GMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDPMSIVTVGDIVDVKVIGIDLNKKRVALS 710
Cdd:PRK13806  380 GTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLA 447
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 643-712 7.60e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 39.70  E-value: 7.60e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1733400547 643 GMTLKGTIRNVVDFGAFVDIGIKNDGLVHKSEMSNSFVKDP---MSIVTVGDIVDVKVIGIDLNKKRVALSMK 712
Cdd:PRK12269  753 GSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPgeaLRKYAVGDRVKAVIVDMNVKDRKVAFSVR 825
 
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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