NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|446348356|ref|WP_000426211|]
View 

MULTISPECIES: Tex family protein [Bacillus]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
10-722 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


:

Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1255.31  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356  10 LMKMLVKELGFSEKQVRHVIQLTEEGNTVPFIARYRKEWTGSLDEVQIRAILERWQYMMQLEDRKEEVIRLIGEKGKLTG 89
Cdd:COG2183    5 IIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGKLTP 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356  90 ELRLQIVKATKLQEVEDLYRPYKEKRRTKATIAKEKGLEPLAEWLLLYKKEDPAKKAVEFINAEKEVQSAEEALQGAQDI 169
Cdd:COG2183   85 ELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEEKGVADVEAALDGARDI 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 170 IAEMISDEATYRSWIRNITFRKGIMSSSVKGEEKDEKNIYEMYYSYEEPLQKVVPHRVLAMNRGEKEDILRVSVVPPVDE 249
Cdd:COG2183  165 LAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPDEEE 244

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 250 ILNFLNKKVIRDNDSKSAHYVQLAIEDGYKRLIQSSIEREIRKELTETAEEQAIHIFSENLRNLLLQPPMKGKVVLAVDP 329
Cdd:COG2183  245 AEAYIARRFIKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVLGLDP 324

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 330 AYRTGCKLSVVDDTGKVLHIDVIYPHPPVRKYDDAKTKVLSIIDKYQVEMIAIGNGTASRETEEFIVDVLQSVKQEVFYI 409
Cdd:COG2183  325 GFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELDLKVQYV 404

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 410 IVNEAGASVYSASDLAREEFPNLQVEERSAVSIGRRLQDPLAELVKIDPKSVGVGQYQHDVSQKRLNESLTFVVETAVNQ 489
Cdd:COG2183  405 IVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCVNA 484

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 490 VGVNVNTASVALLQYVSGLSKTVAKNIVAKREEDGKFTKRTELKKIPRLGAKTYEQCIGFLRILEGANPLDRTGIHPEQY 569
Cdd:COG2183  485 VGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDNSAVHPESY 564

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 570 KNVELLLKSLGLSIDDVGQPqlQKRLEEVEISKLSQETrVGEPTLVDIIDALISPERDTRDELPKPLLKKGILKLEDLKR 649
Cdd:COG2183  565 PVVEKILKDLGVSVKDLIGN--KELLKKLDPEKYADEL-FGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLKIEDLKP 641

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446348356 650 GMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSMLPIE 722
Cdd:COG2183  642 GMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDD 714
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
10-722 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1255.31  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356  10 LMKMLVKELGFSEKQVRHVIQLTEEGNTVPFIARYRKEWTGSLDEVQIRAILERWQYMMQLEDRKEEVIRLIGEKGKLTG 89
Cdd:COG2183    5 IIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGKLTP 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356  90 ELRLQIVKATKLQEVEDLYRPYKEKRRTKATIAKEKGLEPLAEWLLLYKKEDPAKKAVEFINAEKEVQSAEEALQGAQDI 169
Cdd:COG2183   85 ELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEEKGVADVEAALDGARDI 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 170 IAEMISDEATYRSWIRNITFRKGIMSSSVKGEEKDEKNIYEMYYSYEEPLQKVVPHRVLAMNRGEKEDILRVSVVPPVDE 249
Cdd:COG2183  165 LAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPDEEE 244

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 250 ILNFLNKKVIRDNDSKSAHYVQLAIEDGYKRLIQSSIEREIRKELTETAEEQAIHIFSENLRNLLLQPPMKGKVVLAVDP 329
Cdd:COG2183  245 AEAYIARRFIKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVLGLDP 324

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 330 AYRTGCKLSVVDDTGKVLHIDVIYPHPPVRKYDDAKTKVLSIIDKYQVEMIAIGNGTASRETEEFIVDVLQSVKQEVFYI 409
Cdd:COG2183  325 GFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELDLKVQYV 404

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 410 IVNEAGASVYSASDLAREEFPNLQVEERSAVSIGRRLQDPLAELVKIDPKSVGVGQYQHDVSQKRLNESLTFVVETAVNQ 489
Cdd:COG2183  405 IVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCVNA 484

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 490 VGVNVNTASVALLQYVSGLSKTVAKNIVAKREEDGKFTKRTELKKIPRLGAKTYEQCIGFLRILEGANPLDRTGIHPEQY 569
Cdd:COG2183  485 VGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDNSAVHPESY 564

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 570 KNVELLLKSLGLSIDDVGQPqlQKRLEEVEISKLSQETrVGEPTLVDIIDALISPERDTRDELPKPLLKKGILKLEDLKR 649
Cdd:COG2183  565 PVVEKILKDLGVSVKDLIGN--KELLKKLDPEKYADEL-FGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLKIEDLKP 641

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446348356 650 GMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSMLPIE 722
Cdd:COG2183  642 GMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDD 714
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 14-198 1.84e-96

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: 295.85  E-value: 1.84e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356   14 LVKELGFSEKQVRHVIQLTEEGNTVPFIARYRKEWTGSLDEVQIRAILERWQYMMQLEDRKEEVIRLIGEKGKLTGELRL 93
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356   94 QIVKATKLQEVEDLYRPYKEKRRTKATIAKEKGLEPLAEWLLLYKkeDPAKKAVEFINAEKEVQSAEEALQGAQDIIAEM 173
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQP--DPEEEAAKYINPEKGVADVEEALAGARDIIAER 158

                         170       180
                  ....*....|....*....|....*
gi 446348356  174 ISDEATYRSWIRNITFRKGIMSSSV 198
Cdd:pfam09371 159 ISEDAELRKKLRELLWREGVIVSKV 183
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 650-717 1.13e-33

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


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 123.11  E-value: 1.13e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446348356 650 GMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALS 717
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 322-420 4.41e-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: 88.39  E-value: 4.41e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356   322 KVVLAVDPAyRTGCKLSVVDDTGKVLHIDVIYPHppvRKYDDAKTKVLSIIDKYQVEMIAIG-----NGTASRETEEFIV 396
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVIPR---TNKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFA 76

                           90       100
                   ....*....|....*....|....
gi 446348356   397 DVLQSvKQEVFYIIVNEAGASVYS 420
Cdd:smart00732  77 ELLKE-RFNLPVVLVDERLATVYA 99
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 644-718 1.89e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 88.01  E-value: 1.89e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446348356 644 LEDLKRGMELEGTVRNVVDFGAFVDVG-VkqDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:PRK06676 187 LSSLKEGDVVEGTVARLTDFGAFVDIGgV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSL 260
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 648-718 1.59e-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: 1.59e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446348356 648 KRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:NF040579   2 KIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSL 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 644-718 5.42e-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: 72.07  E-value: 5.42e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446348356  644 LEDLKRGMELEGTVRNVVDFGAFVDVGVkQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:TIGR00717 182 LENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255
 
Name Accession Description Interval E-value
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
10-722 0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 1255.31  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356  10 LMKMLVKELGFSEKQVRHVIQLTEEGNTVPFIARYRKEWTGSLDEVQIRAILERWQYMMQLEDRKEEVIRLIGEKGKLTG 89
Cdd:COG2183    5 IIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQGKLTP 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356  90 ELRLQIVKATKLQEVEDLYRPYKEKRRTKATIAKEKGLEPLAEWLLLYKKEDPAKKAVEFINAEKEVQSAEEALQGAQDI 169
Cdd:COG2183   85 ELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEEKGVADVEAALDGARDI 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 170 IAEMISDEATYRSWIRNITFRKGIMSSSVKGEEKDEKNIYEMYYSYEEPLQKVVPHRVLAMNRGEKEDILRVSVVPPVDE 249
Cdd:COG2183  165 LAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEPDEEE 244

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 250 ILNFLNKKVIRDNDSKSAHYVQLAIEDGYKRLIQSSIEREIRKELTETAEEQAIHIFSENLRNLLLQPPMKGKVVLAVDP 329
Cdd:COG2183  245 AEAYIARRFIKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLAAPAGGKVVLGLDP 324

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 330 AYRTGCKLSVVDDTGKVLHIDVIYPHPPVRKYDDAKTKVLSIIDKYQVEMIAIGNGTASRETEEFIVDVLQSVKQEVFYI 409
Cdd:COG2183  325 GFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKTLAALIKKYKVELIAIGNGTASRETEQFVAELIKELDLKVQYV 404

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 410 IVNEAGASVYSASDLAREEFPNLQVEERSAVSIGRRLQDPLAELVKIDPKSVGVGQYQHDVSQKRLNESLTFVVETAVNQ 489
Cdd:COG2183  405 IVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKLKRSLDAVVEDCVNA 484

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 490 VGVNVNTASVALLQYVSGLSKTVAKNIVAKREEDGKFTKRTELKKIPRLGAKTYEQCIGFLRILEGANPLDRTGIHPEQY 569
Cdd:COG2183  485 VGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDGDNPLDNSAVHPESY 564

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 570 KNVELLLKSLGLSIDDVGQPqlQKRLEEVEISKLSQETrVGEPTLVDIIDALISPERDTRDELPKPLLKKGILKLEDLKR 649
Cdd:COG2183  565 PVVEKILKDLGVSVKDLIGN--KELLKKLDPEKYADEL-FGLPTLRDILKELEKPGRDPRPEFKTPTFREGVLKIEDLKP 641

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446348356 650 GMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSMLPIE 722
Cdd:COG2183  642 GMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDD 714
Tex_N pfam09371
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 14-198 1.84e-96

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: 295.85  E-value: 1.84e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356   14 LVKELGFSEKQVRHVIQLTEEGNTVPFIARYRKEWTGSLDEVQIRAILERWQYMMQLEDRKEEVIRLIGEKGKLTGELRL 93
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356   94 QIVKATKLQEVEDLYRPYKEKRRTKATIAKEKGLEPLAEWLLLYKkeDPAKKAVEFINAEKEVQSAEEALQGAQDIIAEM 173
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQP--DPEEEAAKYINPEKGVADVEEALAGARDIIAER 158

                         170       180
                  ....*....|....*....|....*
gi 446348356  174 ISDEATYRSWIRNITFRKGIMSSSV 198
Cdd:pfam09371 159 ISEDAELRKKLRELLWREGVIVSKV 183
Tex_YqgF pfam16921
Tex protein YqgF-like domain; This is the YqgF-like domain of the bacterial Tex protein, which ...
 323-447 8.07e-80

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: 250.39  E-value: 8.07e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356  323 VVLAVDPAYRTGCKLSVVDDTGKVLHIDVIYPHPPVRKYDDAKTKVLSIIDKYQVEMIAIGNGTASRETEEFIVDVLQSV 402
Cdd:pfam16921   1 VVLGLDPGYRTGCKLAVVDETGKVLDTAVIYPHPPQNKVEEAKKKLKKLIKKYGVELIAIGNGTASRETEQFVAELIKEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 446348356  403 KQEVFYIIVNEAGASVYSASDLAREEFPNLQVEERSAVSIGRRLQ 447
Cdd:pfam16921  81 PLKVKYVIVSEAGASVYSASELAREEFPDLDVSLRGAVSIARRLQ 125
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 650-717 1.13e-33

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


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 123.11  E-value: 1.13e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446348356 650 GMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALS 717
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 489-550 1.84e-26

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


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 102.56  E-value: 1.84e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446348356  489 QVGVNVNTASVALLQYVSGLSKTVAKNIVAKREEDGKFTKRTELKKIPRLGAKTYEQCIGFL 550
Cdd:pfam12836   1 AVGVDINTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKTFEQLAGFL 62
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 322-420 4.41e-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: 88.39  E-value: 4.41e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356   322 KVVLAVDPAyRTGCKLSVVDDTGKVLHIDVIYPHppvRKYDDAKTKVLSIIDKYQVEMIAIG-----NGTASRETEEFIV 396
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVIPR---TNKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFA 76

                           90       100
                   ....*....|....*....|....
gi 446348356   397 DVLQSvKQEVFYIIVNEAGASVYS 420
Cdd:smart00732  77 ELLKE-RFNLPVVLVDERLATVYA 99
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 644-718 1.04e-20

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 94.34  E-value: 1.04e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446348356 644 LEDLKRGMELEGTVRNVVDFGAFVDV-GVkqDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:COG0539  184 LEKLEEGDVVEGTVKNITDFGAFVDLgGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSL 257
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 650-717 1.32e-20

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: 86.14  E-value: 1.32e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446348356 650 GMELEGTVRNVVDFGAFVDVGVKqDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALS 717
Cdd:cd05688    2 GDVVEGTVKSITDFGAFVDLGGV-DGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
HHH_9 pfam17674
HHH domain;
557-629 5.56e-19

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 81.43  E-value: 5.56e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446348356  557 NPLDRTGIHPEQYKNVELLLKSLGLSIDD-VGQPQLQKRLeevEISKLSQETrVGEPTLVDIIDALISPERDTR 629
Cdd:pfam17674   1 NPLDNTAIHPESYPLAEKILKDLGLDLKDlIGNSALLKKL---DPKKLAEEE-VGLPTLKDILEELAKPGRDPR 70
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 650-718 7.04e-19

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


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 91.22  E-value: 7.04e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446348356 650 GMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDtKKGRVALSM 718
Cdd:COG1185  617 GEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEID-DQGRIKLSR 684
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 644-718 1.89e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 88.01  E-value: 1.89e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446348356 644 LEDLKRGMELEGTVRNVVDFGAFVDVG-VkqDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:PRK06676 187 LSSLKEGDVVEGTVARLTDFGAFVDIGgV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSL 260
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 650-718 2.57e-18

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 89.34  E-value: 2.57e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446348356 650 GMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDtKKGRVALSM 718
Cdd:PRK11824 622 GEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSR 689
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 644-718 1.14e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 87.14  E-value: 1.14e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446348356 644 LEDLKRGMELEGTVRNVVDFGAFVDVGVkQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:PRK06299 196 LENLEEGQVVEGVVKNITDYGAFVDLGG-VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGL 269
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
648-718 2.21e-17

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 76.87  E-value: 2.21e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446348356   648 KRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 650-718 7.70e-17

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: 75.27  E-value: 7.70e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446348356 650 GMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDtKKGRVALSM 718
Cdd:cd04472    1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD-DRGRISLSR 68
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 650-718 2.27e-16

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: 73.86  E-value: 2.27e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446348356 650 GMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDtKKGRVALSM 718
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID-ARGRISLSI 68
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 645-718 3.43e-16

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: 80.47  E-value: 3.43e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446348356 645 EDLKRGMELEGTVRNVVDFGAFVDV--GVkqDGLVHISKLSK-QFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:COG0539  270 EKYPVGDVVKGKVTRLTDFGAFVELepGV--EGLVHISEMSWtKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSI 344
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 645-718 1.88e-15

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 73.29  E-value: 1.88e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446348356 645 EDLKRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDtKKGRVALSM 718
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSID-EDGKISLSI 73
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 645-718 2.05e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 78.76  E-value: 2.05e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446348356 645 EDLKRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:PRK06676 273 EKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSI 346
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
644-717 3.43e-15

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 79.22  E-value: 3.43e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446348356 644 LEDLKRGMELEGTVRNVVDFGAFVDV-GVkqDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALS 717
Cdd:PRK00087 472 WNSLEEGDVVEGEVKRLTDFGAFVDIgGV--DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLS 544
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 644-718 3.31e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 75.85  E-value: 3.31e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446348356 644 LEDLKRGMELEGTVRNVVDFGAFVDVGvKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:PRK07899 203 LNQLQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSL 276
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 650-718 6.69e-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: 66.93  E-value: 6.69e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446348356  650 GMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:pfam00575   4 GDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 654-718 1.46e-13

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: 66.49  E-value: 1.46e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446348356 654 EGTVRNVVDFGAFV---DVGVKQDGLVHISKLSKQ-FVKHPLDVVSVGQIVKVWVddIDTKKGRVALSM 718
Cdd:cd05684    5 KGKVTSIMDFGCFVqleGLKGRKEGLVHISQLSFEgRVANPSDVVKRGQKVKVKV--ISIQNGKISLSM 71
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 648-718 1.59e-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: 1.59e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446348356 648 KRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:NF040579   2 KIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSL 72
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 653-717 2.00e-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: 65.48  E-value: 2.00e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446348356 653 LEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALS 717
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PRK08059 PRK08059
general stress protein 13; Validated
 644-718 3.94e-13

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 66.61  E-value: 3.94e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446348356 644 LEDLKRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:PRK08059   2 MSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSI 76
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 644-718 5.42e-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: 72.07  E-value: 5.42e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446348356  644 LEDLKRGMELEGTVRNVVDFGAFVDVGVkQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:TIGR00717 182 LENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255
rpsA PRK13806
30S ribosomal protein S1; Provisional
 645-718 4.57e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 68.98  E-value: 4.57e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446348356 645 EDLKRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLS--KQFVKhPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:PRK13806 288 DRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSwtRRVNK-PEDVVAPGDAVAVKIKDIDPAKRRISLSL 362
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 645-718 8.67e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 68.27  E-value: 8.67e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446348356 645 EDLKRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLS-KQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:PRK06299 282 KKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGL 356
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
645-718 1.02e-11

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 68.05  E-value: 1.02e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446348356 645 EDLKRGMELEGTVRNVVDFGAFVDV--GVkqDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:PRK00087 558 EKYPVGSIVLGKVVRIAPFGAFVELepGV--DGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSI 631
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 650-716 6.35e-11

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 58.66  E-value: 6.35e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446348356 650 GMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLS-KQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVAL 716
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 648-720 1.37e-10

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: 57.72  E-value: 1.37e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446348356 648 KRGMELEGTVRNVVDFGAFVDV-GVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSMLP 720
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKA 74
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 643-718 2.15e-10

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: 57.60  E-value: 2.15e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446348356 643 KLEDLKRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:cd04461    8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 644-718 2.18e-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: 2.18e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446348356  644 LEDLKRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLS-KQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:TIGR00717 267 EKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGL 342
PRK05807 PRK05807
RNA-binding protein S1;
647-718 2.82e-10

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 58.60  E-value: 2.82e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446348356 647 LKRGMELEGTVRNVVDFGAFVDVGVKQdGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDtKKGRVALSM 718
Cdd:PRK05807   3 LKAGSILEGTVVNITNFGAFVEVEGKT-GLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISLSI 72
ComEA COG1555
DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]; ...
 492-545 2.89e-10

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


Pssm-ID: 441164 [Multi-domain]  Cd Length: 72  Bit Score: 56.79  E-value: 2.89e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446348356 492 VNVNTASVALLQYVSGLSKTVAKNIVAKREEDGKFTKRTELKKIPRLGAKTYEQ 545
Cdd:COG1555   13 VDINTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGIGPKTLEK 66
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 648-718 5.93e-10

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 62.49  E-value: 5.93e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446348356 648 KRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLS-KQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGI 443
PRK08582 PRK08582
RNA-binding protein S1;
650-717 6.23e-10

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 57.74  E-value: 6.23e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446348356 650 GMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDtKKGRVALS 717
Cdd:PRK08582   6 GSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE-DDGKIGLS 72
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 655-718 1.54e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 60.83  E-value: 1.54e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446348356 655 GTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:PRK07899 299 GKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSL 362
rpsA PRK13806
30S ribosomal protein S1; Provisional
 644-717 2.09e-09

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 60.51  E-value: 2.09e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446348356 644 LEDLKRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKG----RVALS 717
Cdd:PRK13806 197 METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLS 274
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 644-718 5.66e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 59.41  E-value: 5.66e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446348356 644 LEDLKRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:PRK06299 455 AKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSI 529
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 650-716 8.70e-09

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


Pssm-ID: 240194 [Multi-domain]  Cd Length: 72  Bit Score: 52.58  E-value: 8.70e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 650 GMELEGTVRNVVDFGAFVDVGVKQDGLVHISKL---SKQFvkHPLDVVSVGQIVKVWVDDIDTKKGRVAL 716
Cdd:cd05689    4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMdwtNKNI--HPSKVVSLGDEVEVMVLDIDEERRRISL 71
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 643-722 2.27e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 56.35  E-value: 2.27e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 643 KLEDLKRGMELEGTVRNVVDFGAFVDVGvKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSMLPIE 722
Cdd:PRK07400 190 KMNRLEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLE 268
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 653-718 1.39e-07

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


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 49.02  E-value: 1.39e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446348356 653 LEGTVRNVVDFGAFVDV-GVKQDGLVHISKLSKQFVKHPLDVVSVGQivKVWVDDIDTK-KGRVALSM 718
Cdd:cd05686    7 FKGEVASVTEYGAFVKIpGCRKQGLVHKSHMSSCRVDDPSEVVDVGE--KVWVKVIGREmKDKMKLSL 72
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
647-722 3.63e-07

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 49.31  E-value: 3.63e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446348356 647 LKRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSMLPIE 722
Cdd:PRK07252   1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLE 76
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 650-717 4.22e-07

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


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 47.61  E-value: 4.22e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 650 GMELEGTVRNVVDFGAFVDV--GVKqdGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALS 717
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFynNVK--GFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLS 68
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 655-718 8.57e-07

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 50.98  E-value: 8.57e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446348356 655 GTVRNVVDFGAFVDV---GVKQdGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:PRK03987  14 GTVKEVKDFGAFVTLdeyPGKE-GFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSL 79
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 648-717 1.39e-06

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: 51.66  E-value: 1.39e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356  648 KRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALS 717
Cdd:TIGR00717 445 KVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLS 514
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 650-717 1.52e-06

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: 46.13  E-value: 1.52e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446348356 650 GMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALS 717
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 655-718 3.23e-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: 45.27  E-value: 3.23e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446348356 655 GTVRNVVDFGAFVDVGVKQD--GLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:cd04452    9 VTVKSIADMGAYVSLLEYGNieGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSK 74
HHH_7 pfam14635
Helix-hairpin-helix motif;
457-552 7.32e-06

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 45.23  E-value: 7.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356  457 DPKSVGVGQYQHDVSQKRLNESLTFVVETAVNQVGVNVNTA-----SVALLQYVSGLSKTVAKNIVAK-REEDGKFTKRT 530
Cdd:pfam14635   2 DILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAiankyEAAILPYIAGLGPRKADHLLKIlAANNGRLDNRS 81

                          90       100
                  ....*....|....*....|..
gi 446348356  531 ELKKIPRLGAKTYEQCIGFLRI 552
Cdd:pfam14635  82 QLITKCIMGPKVFMNCAGFLII 103
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 644-717 1.10e-05

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 48.12  E-value: 1.10e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446348356 644 LEDLKRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKqfvKHPLDVVSVGQIVKVWVDDIDTKKGRVALS 717
Cdd:COG0539   13 LKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSD---EPGELEVKVGDEVEVYVEKVEDGEGEIVLS 83
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
646-717 2.08e-05

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 48.02  E-value: 2.08e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446348356 646 DLKRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALS 717
Cdd:PRK00087 299 QIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLS 370
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 653-717 3.83e-05

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


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 42.13  E-value: 3.83e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446348356 653 LEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALS 717
Cdd:cd05687    4 VKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLS 68
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 653-718 9.87e-05

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 45.86  E-value: 9.87e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446348356 653 LEGTVRNVVDFGAFVDVGvKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:PRK12269 497 VSGVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSL 561
TIGR00426 TIGR00426
competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...
 492-545 1.69e-04

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: 40.30  E-value: 1.69e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446348356  492 VNVNTASVALLQ-YVSGLSKTVAKNIVAKREEDGKFTKRTELKKIPRLGAKTYEQ 545
Cdd:TIGR00426   8 VNINTATAEELQrAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEK 62
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 653-718 2.20e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 44.70  E-value: 2.20e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446348356 653 LEGTVRNVVDFGAFVDVGVKQDGLVHISKLS-KQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALSM 718
Cdd:PRK12269 582 VKGRVTKIADFGAFIELAEGIEGLAHISEFSwVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGL 648
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 650-719 2.97e-04

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: 40.08  E-value: 2.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 650 GMELEGTVRNVVDFGAFV---DVGVkqDGLVHISKLSKQF-----VKHPLD------VVSVGQIVKVWVDDIDTKKGRVA 715
Cdd:cd04471    2 GEEFDGVISGVTSFGLFVeldNLTV--EGLVHVSTLGDDYyefdeENHALVgertgkVFRLGDKVKVRVVRVDLDRRKID 79


                 ....
gi 446348356 716 LSML 719
Cdd:cd04471   80 FELV 83
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 657-717 3.16e-04

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 44.11  E-value: 3.16e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446348356 657 VRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIdTKKGRVALS 717
Cdd:PLN00207 762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEV-NDKGQLRLS 821
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 645-717 4.66e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 43.33  E-value: 4.66e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446348356 645 EDLKRGMELEGTVRNVVDFGAFVDV-GVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALS 717
Cdd:PRK06676  13 KEVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLS 86
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 654-688 5.95e-04

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 41.35  E-value: 5.95e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 446348356 654 EGTVRNVVDFGAFVDVGVkQDGLVHISKLSKQFVK 688
Cdd:PRK08563  86 EGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYIS 119
T2SSK pfam03934
Type II secretion system (T2SS), protein K; Members of this family are involved in the Type II ...
 489-540 7.15e-04

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: 42.31  E-value: 7.15e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 446348356  489 QVGVNVNTASVALLQ-YVSGLSKTVAKNIVAKREEDGkFTKRTELKKIPRLGA 540
Cdd:pfam03934 183 RTPINVNTAPAEVLAaLFDGLSLDQAQALLAQRPADG-FESVDDFLAQPALGG 234
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 650-717 1.02e-03

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: 42.41  E-value: 1.02e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446348356  650 GMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLS-KQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVALS 717
Cdd:TIGR00717 360 GDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLG 428
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 654-718 1.11e-03

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: 38.81  E-value: 1.11e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 654 EGTVRNVVDFGAFVDVGvKQDGLVHISKLSKQFVKHPLD-----------VVSVGQIVKVWV-----DDIDTKKGRVALS 717
Cdd:cd04460    4 EGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKnkrligeetkrVLKVGDVVRARIvavslKERRPRESKIGLT 82


                 .
gi 446348356 718 M 718
Cdd:cd04460   83 M 83
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 644-722 1.32e-03

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: 42.13  E-value: 1.32e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446348356 644 LEDLKRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFvkhpldvvSVGQIVKVWVDDIdTKKGRVALSMLPIE 722
Cdd:COG1107   34 PDDLEPGRYYRGTVDGVADFGVFVDLNDHVTGLLHRSELDQDW--------EVGDEVFVQVKEV-RDNGNVDLGWVSID 103
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 650-716 1.36e-03

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: 37.60  E-value: 1.36e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446348356 650 GMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVDDIDTKKGRVAL 716
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVL 67
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 644-699 1.65e-03

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: 37.59  E-value: 1.65e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446348356 644 LEDLKRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISKLSKQF-VKHPLdVVSVGQI 699
Cdd:cd04473   11 MEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDYeVGDEV-IVQVTDI 66
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 381-452 1.75e-03

Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage


Pssm-ID: 258777  Cd Length: 150  Bit Score: 39.46  E-value: 1.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356  381 AIGNGTASRETEEFIVDVLQSVKQE--------VFYIIVNEAGASVYSASDLAREEFPNLQVEERSAVSIGRRLQDPLAE 452
Cdd:pfam14639  66 VIGVSGENRDAQKFYEDVQRVLHELeqdsrlhtIGVILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLE 145
VacB COG0557
Exoribonuclease R [Transcription];
625-722 3.36e-03

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 40.86  E-value: 3.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446348356 625 ERDTRDelpkplLKKgILKLEDlKRGMELEGTVRNVVDFGAFV---DVGVkqDGLVHISKLSKQF-----VKHPL----- 691
Cdd:COG0557  606 ERDVVD------LKK-AEYMKD-RVGEEFEGVISGVTSFGLFVeldELGV--EGLVHVSSLGDDYyeydeRRQALvgert 675

                         90       100       110
                 ....*....|....*....|....*....|..
gi 446348356 692 -DVVSVGQIVKVWVDDIDTKKGRVALSMLPIE 722
Cdd:COG0557  676 gKRYRLGDRVEVRVVRVDLDRRQIDFELVEGG 707
PulK COG3156
Type II secretory pathway, component PulK [Intracellular trafficking, secretion, and vesicular ...
 492-540 7.96e-03

Type II secretory pathway, component PulK [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442390 [Multi-domain]  Cd Length: 307  Bit Score: 38.83  E-value: 7.96e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 446348356 492 VNVNTASVALLQ-YVSGLSKTVAKNIVAKREEDGkFTKRTELKKIPRLGA 540
Cdd:COG3156  213 INVNTAPPEVLAaLLGGLSLDDAQALLAARPEKG-FADVADFLALLGLAG 261
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 647-718 8.62e-03

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


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 35.41  E-value: 8.62e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446348356 647 LKRGMELEGTVRNVV-DFGAFVDVGVKQDGLVHISKLSKQFVKHPLDVVSVGQIVKVWVddIDTKKGRVALSM 718
Cdd:cd05704    1 LEEGAVTLGMVTKVIpHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCI--LSKKDGKYQLSL 71
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 642-717 8.92e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 39.38  E-value: 8.92e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446348356 642 LKLEDLKRGMELEGTVRNVVDFGAFVDVGVKQDGLVHISklskQFVKHPLDV-VSVGQIVKVWVDDIDTKKGRVALS 717
Cdd:PRK06299  23 LKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLE----EFKNEQGELeVKVGDEVEVYVERIEDGFGETVLS 95
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH