NCBI Conserved Domain Search

30S ribosomal protein S1; Reviewed

643-726

1.54e-22

30S ribosomal protein S1; Reviewed

Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 100.72 E-value: 1.54e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 643 ETMNDLQPGMILEGAVTNVTNFGAFVDIG-VhqDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMRl 721
Cdd:PRK06676  185 ELLSSLKEGDVVEGTVARLTDFGAFVDIGgV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLK- 261


                  ....*
gi 2786195043 722 DEQPG 726
Cdd:PRK06676  262 DTLPG 266

S1_dom_CvfD

NF040579

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...

651-732

6.18e-22

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: 91.33 E-value: 6.18e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 651 GMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR-LDEQPGETN 729
Cdd:NF040579    4 GDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSLRaLEEAPEKHR 83


                  ...
gi 2786195043 730 ARR 732
Cdd:NF040579   84 KRR 86

rpsA

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...

643-727

1.16e-16

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: 83.63 E-value: 1.16e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 643 ETMNDLQPGMILEGAVTNVTNFGAFVDIGVhQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR-L 721
Cdd:TIGR00717 180 ELLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKqL 258


                  ....*.
gi 2786195043 722 DEQPGE 727
Cdd:TIGR00717 259 GEDPWE 264

Name

Accession

Description

Interval

E-value

Tex

COG2183

Transcriptional accessory protein Tex/SPT6 [Transcription];

2-727

0e+00

Transcriptional accessory protein Tex/SPT6 [Transcription];

Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 1398.99 E-value: 0e+00

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043   2 MNDSFCRIIAGEIQARPEQVDAAVRLLDEGNTVPFIARYRKEITGGLDDTQLRNLETRLSYLRELEERRQAILKSISEQG 81
Cdd:COG2183     1 MMMDIIQRIAQELGLRPKQVEAAVELLDEGATVPFIARYRKEATGGLDEVQLRTIEERLTYLRELEKRRETILKSIEEQG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043  82 KLTDDLAKAINATLSKTELEDLYLPYKPKRRTRGQIAIEAGLEPLADLLWSDPSHTPEVAAAQYVDADKGVADTKAALDG 161
Cdd:COG2183    81 KLTPELKAKIEAADTKQELEDLYLPYKPKRRTKATIAREKGLEPLADLLLAQPTGDPEAEAAKYINEEKGVADVEAALDG 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 162 ARYILMERFAEDAALLAKVRDYLWKNAHLVSTVVSGKEEEGAKFRDYFDHHEPLSTVPSHRALAMFRGRNEGVLQLSLNA 241
Cdd:COG2183   161 ARDILAERISEDAELRGKLRELLWKEGVLVSKVKKGKEEEGAKFRDYFDYSEPLKKIPSHRILALNRGEKEGVLKVKLEP 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 242 DPQFdeppkesyCEQIIMDHLgLRLNNAPADSWRKGVVSWTWRIKVLMHLETELMGTVRERAEDEAINVFARNLHDLLMA 321
Cdd:COG2183   241 DEEE--------AEAYIARRF-IKDQGRPADEWLKEAVRDAYKRLLAPSLERELRNELKEKAEEEAIKVFAENLRDLLLA 311

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 322 APAGLRATMGLDPGLRTGVKVAVVDATGKLVATDTIYPHTGQAAKAAMTV--AALCEKHNVELVAIGNGTASRETERFYL 399
Cdd:COG2183   312 APAGGKVVLGLDPGFRTGCKVAVVDETGKLLDTATIYPHPPQNKWEEAAKtlAALIKKYKVELIAIGNGTASRETEQFVA 391

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 400 DVQKQFPKvTAQKVIVSEAGASVYSASELAAQEFPDLDVSLRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVSQTQL 479
Cdd:COG2183   392 ELIKELDL-KVQYVIVSEAGASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAELVKIDPKSIGVGQYQHDVNQKKL 470

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 480 ARKLDAVVEDCVNAVGVDLNTASVPLLTRVAGLTRMMAQNIVAWRDENGQFQNRQQLLKVSRLGPKAFEQCAGFLRINHG 559
Cdd:COG2183   471 KRSLDAVVEDCVNAVGVDLNTASAPLLSYVSGLNPTLAKNIVAYRDENGAFKSRKELLKVPRLGPKAFEQAAGFLRIRDG 550

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 560 DNPLDASTVHPEAYPVVERILAATQQALKDLMGNSSELRNLKASDFTDEKFGVPTVTDIIKELEKPGRDPRPEFKTAQFA 639
Cdd:COG2183   551 DNPLDNSAVHPESYPVVEKILKDLGVSVKDLIGNKELLKKLDPEKYADELFGLPTLRDILKELEKPGRDPRPEFKTPTFR 630

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 640 DGVETMNDLQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTM 719
Cdd:COG2183   631 EGVLKIEDLKPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSM 710


                  ....*...
gi 2786195043 720 RLDEQPGE 727
Cdd:COG2183   711 KLDDEAGA 718

Tex_N

pfam09371

Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...

10-194

2.76e-105

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: 320.12 E-value: 2.76e-105

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043  10 IAGEIQARPEQVDAAVRLLDEGNTVPFIARYRKEITGGLDDTQLRNLETRLSYLRELEERRQAILKSISEQGKLTDDLAK 89
Cdd:pfam09371   1 IAEELGLKPKQVEATVKLLDEGNTVPFIARYRKEATGGLDEVQLREIEERLEYLRELEKRKETILKSIEEQGKLTDELKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043  90 AINATLSKTELEDLYLPYKPKRRTRGQIAIEAGLEPLADLLWSDPShtPEVAAAQYVDADKGVADTKAALDGARYILMER 169
Cdd:pfam09371  81 AIEAADTLTELEDLYLPYKPKRRTKATIAREKGLEPLADAILAQPD--PEEEAAKYINPEKGVADVEEALAGARDIIAER 158

                         170       180
                  ....*....|....*....|....*
gi 2786195043 170 FAEDAALLAKVRDYLWKNAHLVSTV 194
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 ...

328-451

1.39e-69

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: 224.20 E-value: 1.39e-69

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 328 ATMGLDPGLRTGVKVAVVDATGKLVATDTIYPHTGQAAKAAMTV--AALCEKHNVELVAIGNGTASRETERFYLDVQKQF 405
Cdd:pfam16921   1 VVLGLDPGYRTGCKLAVVDETGKVLDTAVIYPHPPQNKVEEAKKklKKLIKKYGVELIAIGNGTASRETEQFVAELIKEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2786195043 406 PKvTAQKVIVSEAGASVYSASELAAQEFPDLDVSLRGAVSIARRLQ 451
Cdd:pfam16921  81 PL-KVKYVIVSEAGASVYSASELAREEFPDLDVSLRGAVSIARRLQ 125

S1_Tex

cd05685

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...

651-718

2.46e-35

Pssm-ID: 240190 [Multi-domain] Cd Length: 68 Bit Score: 128.12 E-value: 2.46e-35

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2786195043 651 GMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALT 718
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68

HHH_3

pfam12836

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

493-554

8.88e-31

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

Pssm-ID: 463723 [Multi-domain] Cd Length: 62 Bit Score: 114.89 E-value: 8.88e-31

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2786195043 493 AVGVDLNTASVPLLTRVAGLTRMMAQNIVAWRDENGQFQNRQQLLKVSRLGPKAFEQCAGFL 554
Cdd:pfam12836   1 AVGVDINTASAELLSRVPGLGPKLAKNIVEYREENGPFRSREDLLKVKGLGPKTFEQLAGFL 62

HHH_9

pfam17674

HHH domain;

561-630

1.40e-29

HHH domain;

Pssm-ID: 465451 [Multi-domain] Cd Length: 70 Bit Score: 111.86 E-value: 1.40e-29

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 561 NPLDASTVHPEAYPVVERILAATQQALKDLMGNSSELRNLKASDFTDEKFGVPTVTDIIKELEKPGRDPR 630
Cdd:pfam17674   1 NPLDNTAIHPESYPLAEKILKDLGLDLKDLIGNSALLKKLDPKKLAEEEVGLPTLKDILEELAKPGRDPR 70

RpsA

COG0539

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...

643-732

7.35e-25

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

Pssm-ID: 440305 [Multi-domain] Cd Length: 348 Bit Score: 106.67 E-value: 7.35e-25

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 643 ETMNDLQPGMILEGAVTNVTNFGAFVDI-GVhqDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR- 720
Cdd:COG0539   182 ELLEKLEEGDVVEGTVKNITDFGAFVDLgGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKq 259

                          90
                  ....*....|..
gi 2786195043 721 LDEQPGETNARR 732
Cdd:COG0539   260 LQPDPWENIAEK 271

YabR

COG1098

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...

647-742

7.66e-25

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

Pssm-ID: 440715 [Multi-domain] Cd Length: 130 Bit Score: 100.25 E-value: 7.66e-25

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 647 DLQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDlQRKRIALTMR-LDEQP 725
Cdd:COG1098     2 SIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSID-EDGKISLSIKqAEEKP 80

                          90
                  ....*....|....*..
gi 2786195043 726 GETNARRGGGNERPQNN 742
Cdd:COG1098    81 KRPPRPRRNSRPKAGFE 97

smart00316

Ribosomal protein S1-like RNA-binding domain;

649-720

5.60e-24

Ribosomal protein S1-like RNA-binding domain;

Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 95.75 E-value: 5.60e-24

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2786195043  649 QPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72

pfam00575

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...

648-719

1.41e-23

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: 94.66 E-value: 1.41e-23

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2786195043 648 LQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTM 719
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72

YqgFc

smart00732

Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...

327-424

8.39e-23

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: 93.40 E-value: 8.39e-23

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043  327 RATMGLDPGlRTGVKVAVVDATGKLVATDTIYPHTgQAAKAAMTVAALCEKHNVELVAIG-----NGTASRETERFYLDV 401
Cdd:smart00732   1 KRVLGLDPG-RKGIGVAVVDETGKLADPLEVIPRT-NKEADAARLKKLIKKYQPDLIVIGlplnmNGTASRETEEAFAEL 78

                           90       100
                   ....*....|....*....|...
gi 2786195043  402 QKQFPKVtaQKVIVSEAGASVYS 424
Cdd:smart00732  79 LKERFNL--PVVLVDERLATVYA 99

S1_RPS1_repeat_hs4

cd05692

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...

651-720

1.26e-22

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

Pssm-ID: 240197 [Multi-domain] Cd Length: 69 Bit Score: 91.96 E-value: 1.26e-22

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 651 GMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDlQRKRIALTMR 720
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID-ARGRISLSIK 69

rpsA

30S ribosomal protein S1; Reviewed

643-726

1.54e-22

30S ribosomal protein S1; Reviewed

Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 100.72 E-value: 1.54e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 643 ETMNDLQPGMILEGAVTNVTNFGAFVDIG-VhqDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMRl 721
Cdd:PRK06676  185 ELLSSLKEGDVVEGTVARLTDFGAFVDIGgV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLK- 261


                  ....*
gi 2786195043 722 DEQPG 726
Cdd:PRK06676  262 DTLPG 266

S1_dom_CvfD

NF040579

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...

651-732

6.18e-22

Pssm-ID: 468553 [Multi-domain] Cd Length: 113 Bit Score: 91.33 E-value: 6.18e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 651 GMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR-LDEQPGETN 729
Cdd:NF040579    4 GDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSLRaLEEAPEKHR 83


                  ...
gi 2786195043 730 ARR 732
Cdd:NF040579   84 KRR 86

S1_RPS1_repeat_ec3

cd05688

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...

650-717

7.19e-22

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

Pssm-ID: 240193 [Multi-domain] Cd Length: 68 Bit Score: 89.61 E-value: 7.19e-22

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2786195043 650 PGMILEGAVTNVTNFGAFVDIGVhQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIAL 717
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDLGG-VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISL 67

RpsA

COG0539

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...

648-720

8.23e-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: 97.42 E-value: 8.23e-22

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2786195043 648 LQPGMILEGAVTNVTNFGAFVDI--GVhqDGLVHISSLS-NKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:COG0539   272 YPVGDVVKGKVTRLTDFGAFVELepGV--EGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345

rpsA

30S ribosomal protein S1; Reviewed

640-727

4.74e-21

30S ribosomal protein S1; Reviewed

Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 96.10 E-value: 4.74e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 640 DGVEtmNDLQPGMILEGAVTNVTNFGAFVDI--GVhqDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIAL 717
Cdd:PRK06676  269 EGVE--EKLPEGDVIEGTVKRLTDFGAFVEVlpGV--EGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISL 344

                          90
                  ....*....|.
gi 2786195043 718 TMR-LDEQPGE 727
Cdd:PRK06676  345 SIKaLEEAPAE 355

Pnp

COG1185

Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...

647-720

3.60e-19

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

Pssm-ID: 440798 [Multi-domain] Cd Length: 686 Bit Score: 92.38 E-value: 3.60e-19

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2786195043 647 DLQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDlQRKRIALTMR 720
Cdd:COG1185   613 EPEVGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEID-DQGRIKLSRK 685

rpsA

30S ribosomal protein S1; Reviewed

643-719

4.08e-19

30S ribosomal protein S1; Reviewed

Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 91.76 E-value: 4.08e-19

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2786195043 643 ETMNDLQPGMILEGAVTNVTNFGAFVDIGVhQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTM 719
Cdd:PRK06299  194 ELLENLEEGQVVEGVVKNITDYGAFVDLGG-VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGL 269

PRK08059

general stress protein 13; Validated

645-744

6.26e-19

general stress protein 13; Validated

Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 83.17 E-value: 6.26e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 645 MNDLQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMRlDEQ 724
Cdd:PRK08059    2 MSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR-ATE 80

                          90       100
                  ....*....|....*....|
gi 2786195043 725 PGETNARRGGGNERPQNNRP 744
Cdd:PRK08059   81 EAPEAKRKKGKILIPNPSEQ 100

PRK08582

RNA-binding protein S1;

654-747

1.47e-18

RNA-binding protein S1;

Pssm-ID: 236305 [Multi-domain] Cd Length: 139 Bit Score: 82.77 E-value: 1.47e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 654 LEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDlQRKRIALTMR--LDEQPGETNAR 731
Cdd:PRK08582    9 LQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE-DDGKIGLSIKkaKDRPKRQHDRP 87

                          90
                  ....*....|....*.
gi 2786195043 732 RGGGNERPQNNRPAAK 747
Cdd:PRK08582   88 RHEDNRGGGNDVAPKE 103

PRK11824

polynucleotide phosphorylase/polyadenylase; Provisional

646-720

1.53e-18

polynucleotide phosphorylase/polyadenylase; Provisional

Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 90.49 E-value: 1.53e-18

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2786195043 646 NDLQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDlQRKRIALTMR 720
Cdd:PRK11824  617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSRK 690

rpsA

PRK07899

30S ribosomal protein S1; Reviewed

643-731

2.15e-18

30S ribosomal protein S1; Reviewed

Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 88.95 E-value: 2.15e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 643 ETMNDLQPGMILEGAVTNVTNFGAFVDIGvHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR-L 721
Cdd:PRK07899  201 EFLNQLQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKaT 279

                          90
                  ....*....|
gi 2786195043 722 DEQPGETNAR 731
Cdd:PRK07899  280 QEDPWQQFAR 289

PRK00087

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

643-728

2.85e-18

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

Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 89.24 E-value: 2.85e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 643 ETMNDLQPGMILEGAVTNVTNFGAFVDI-GVhqDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR- 720
Cdd:PRK00087  470 ETWNSLEEGDVVEGEVKRLTDFGAFVDIgGV--DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKk 547


                  ....*...
gi 2786195043 721 LDEQPGET 728
Cdd:PRK00087  548 LLPDPWEN 555

S1_PNPase

cd04472

S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...

651-719

3.09e-18

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: 79.12 E-value: 3.09e-18

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2786195043 651 GMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDlQRKRIALTM 719
Cdd:cd04472     1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD-DRGRISLSR 68

S1_like

cd00164

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...

654-718

3.31e-18

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

Pssm-ID: 238094 [Multi-domain] Cd Length: 65 Bit Score: 78.96 E-value: 3.31e-18

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2786195043 654 LEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALT 718
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65

PRK00087

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

651-728

7.34e-18

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

Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 88.08 E-value: 7.34e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 651 GMILEGAVTNVTNFGAFVDI--GVhqDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR-LDEQPGE 727
Cdd:PRK00087  563 GSIVLGKVVRIAPFGAFVELepGV--DGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKeVEEEPGD 640


                  .
gi 2786195043 728 T 728
Cdd:PRK00087  641 I 641

PRK05807

RNA-binding protein S1;

648-746

8.90e-17

RNA-binding protein S1;

Pssm-ID: 235614 [Multi-domain] Cd Length: 136 Bit Score: 77.48 E-value: 8.90e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 648 LQPGMILEGAVTNVTNFGAFVDI-GvhQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDlQRKRIALTMRLDEQPG 726
Cdd:PRK05807    3 LKAGSILEGTVVNITNFGAFVEVeG--KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISLSIKQAMKQK 79

                          90       100
                  ....*....|....*....|
gi 2786195043 727 ETNARRGGGNERPQNNRPAA 746
Cdd:PRK05807   80 KSVKPAEIDWQKEKNKNNNG 99

rpsA

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...

643-727

1.16e-16

Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 83.63 E-value: 1.16e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 643 ETMNDLQPGMILEGAVTNVTNFGAFVDIGVhQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR-L 721
Cdd:TIGR00717 180 ELLENLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKqL 258


                  ....*.
gi 2786195043 722 DEQPGE 727
Cdd:TIGR00717 259 GEDPWE 264

rpsA

30S ribosomal protein S1; Reviewed

649-725

6.19e-16

30S ribosomal protein S1; Reviewed

Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 81.75 E-value: 6.19e-16

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2786195043 649 QPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLS-NKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTM-RLDEQP 725
Cdd:PRK06299  372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIkQLEEDP 450

S1_DHX8_helicase

cd05684

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...

651-720

6.67e-16

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

Pssm-ID: 240189 [Multi-domain] Cd Length: 79 Bit Score: 73.04 E-value: 6.67e-16

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2786195043 651 GMILEGAVTNVTNFGAFVDI---GVHQDGLVHISSLS-NKFVEDPHTVVKAGDIVKVKVLEVdlQRKRIALTMR 720
Cdd:cd05684     1 GKIYKGKVTSIMDFGCFVQLeglKGRKEGLVHISQLSfEGRVANPSDVVKRGQKVKVKVISI--QNGKISLSMK 72

rpsA

PRK07899

30S ribosomal protein S1; Reviewed

649-720

2.23e-15

30S ribosomal protein S1; Reviewed

Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 79.70 E-value: 2.23e-15

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2786195043 649 QPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:PRK07899  292 AIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLK 363

rpsA

30S ribosomal protein S1; Reviewed

648-720

1.70e-14

30S ribosomal protein S1; Reviewed

Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 77.13 E-value: 1.70e-14

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2786195043 648 LQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLS-NKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:PRK06299  284 YPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLK 357

rpsA

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...

642-720

6.13e-14

Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 75.16 E-value: 6.13e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 642 VETMNDLQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLS-NKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:TIGR00717 264 EAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343

S1_RPS1_repeat_ec5

cd05690

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...

651-717

1.20e-13

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: 66.36 E-value: 1.20e-13

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2786195043 651 GMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLS-NKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIAL 717
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68

PRK07400

30S ribosomal protein S1; Reviewed

645-727

1.80e-13

30S ribosomal protein S1; Reviewed

Pssm-ID: 180960 [Multi-domain] Cd Length: 318 Bit Score: 72.14 E-value: 1.80e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 645 MNDLQPGMILEGAVTNVTNFGAFVDIGvHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIAL-TMRLDE 723
Cdd:PRK07400  191 MNRLEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLsTKQLEP 269


                  ....
gi 2786195043 724 QPGE 727
Cdd:PRK07400  270 EPGD 273

rpsA

PRK13806

30S ribosomal protein S1; Provisional

645-732

2.58e-13

30S ribosomal protein S1; Provisional

Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 73.22 E-value: 2.58e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 645 MNDLQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRK----RIALTMR 720
Cdd:PRK13806  197 METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIK 276

                          90
                  ....*....|...
gi 2786195043 721 -LDEQPGETNARR 732
Cdd:PRK13806  277 qAGGDPWDTVGDR 289

rpsA

PRK13806

30S ribosomal protein S1; Provisional

634-720

2.81e-13

30S ribosomal protein S1; Provisional

Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 72.83 E-value: 2.81e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 634 KTAQfADGVETMND-LQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLS-NKFVEDPHTVVKAGDIVKVKVLEVDLQ 711
Cdd:PRK13806  276 KQAG-GDPWDTVGDrLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPA 354


                  ....*....
gi 2786195043 712 RKRIALTMR 720
Cdd:PRK13806  355 KRRISLSLR 363

S1_Rrp5_repeat_sc12

cd05708

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...

651-720

4.90e-13

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

Pssm-ID: 240213 [Multi-domain] Cd Length: 77 Bit Score: 64.66 E-value: 4.90e-13

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2786195043 651 GMILEGAVTNVTNFGAFVDI-GVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:cd05708     3 GQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73

PRK08563

DNA-directed RNA polymerase subunit E'; Provisional

653-726

1.76e-12

DNA-directed RNA polymerase subunit E'; Provisional

Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 66.77 E-value: 1.76e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 653 ILEGAVTNVTNFGAFVDIGVhQDGLVHISSLSNKFV-----------EDPHTVVKAGDIVKVKVLEVDL-----QRKRIA 716
Cdd:PRK08563   84 VVEGEVVEVVEFGAFVRIGP-VDGLLHISQIMDDYIsydpkngrligKESKRVLKVGDVVRARIVAVSLkerrpRGSKIG 162

                          90
                  ....*....|
gi 2786195043 717 LTMRldeQPG 726
Cdd:PRK08563  163 LTMR---QPG 169

S1_Rrp5_repeat_hs8_sc7

cd04461

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...

644-719

2.05e-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: 2.05e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2786195043 644 TMNDLQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTM 719
Cdd:cd04461     8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83

rpsA

30S ribosomal protein S1; Reviewed

619-724

2.70e-12

30S ribosomal protein S1; Reviewed

Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 70.19 E-value: 2.70e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 619 IKELEKpgrDPRPEFktaqfadgvetMNDLQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAG 698
Cdd:PRK06299  443 IKQLEE---DPFEEF-----------AKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVG 508

                          90       100
                  ....*....|....*....|....*..
gi 2786195043 699 DIVKVKVLEVDLQRKRIALTMR-LDEQ 724
Cdd:PRK06299  509 DEVEAKVINIDRKNRRISLSIKaLDEA 535

ComEA

COG1555

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

496-549

2.72e-12

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

Pssm-ID: 441164 [Multi-domain] Cd Length: 72 Bit Score: 62.57 E-value: 2.72e-12

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2786195043 496 VDLNTASVPLLTRVAGLTRMMAQNIVAWRDENGQFQNRQQLLKVSRLGPKAFEQ 549
Cdd:COG1555    13 VDINTATAEELQTLPGIGPKLAQRIVEYREKNGPFKSVEDLLEVKGIGPKTLEK 66

S1_RPS1_repeat_ec4

cd05689

S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...

651-717

5.49e-12

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

Pssm-ID: 240194 [Multi-domain] Cd Length: 72 Bit Score: 61.82 E-value: 5.49e-12

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2786195043 651 GMILEGAVTNVTNFGAFVDIGVHQDGLVHISSL--SNKFVEdPHTVVKAGDIVKVKVLEVDLQRKRIAL 717
Cdd:cd05689     4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMdwTNKNIH-PSKVVSLGDEVEVMVLDIDEERRRISL 71

S1_RNase_R

cd04471

S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...

651-719

1.17e-11

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: 61.26 E-value: 1.17e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 651 GMILEGAVTNVTNFGAFV---DIGVhqDGLVHISSLSN---KFVEDPHTVV--------KAGDIVKVKVLEVDLQRKRIA 716
Cdd:cd04471     2 GEEFDGVISGVTSFGLFVeldNLTV--EGLVHVSTLGDdyyEFDEENHALVgertgkvfRLGDKVKVRVVRVDLDRRKID 79


                  ...
gi 2786195043 717 LTM 719
Cdd:cd04471    80 FEL 82

S1_pNO40

cd05686

S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...

653-719

1.53e-11

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: 60.57 E-value: 1.53e-11

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2786195043 653 ILEGAVTNVTNFGAFVDI-GVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKrIALTM 719
Cdd:cd05686     6 IFKGEVASVTEYGAFVKIpGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDK-MKLSL 72

S1_RpoE

cd04460

S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...

653-726

2.03e-11

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: 61.15 E-value: 2.03e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 653 ILEGAVTNVTNFGAFVDIGvHQDGLVHISSLSNKFVE-DPHT----------VVKAGDIVKVKVLEVDL-----QRKRIA 716
Cdd:cd04460     2 VVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISyDPKNkrligeetkrVLKVGDVVRARIVAVSLkerrpRESKIG 80

                          90
                  ....*....|
gi 2786195043 717 LTMRldeQPG 726
Cdd:cd04460    81 LTMR---QPG 87

rpsA

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...

651-727

2.64e-11

Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 66.68 E-value: 2.64e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2786195043 651 GMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLS-NKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR-LDEQPGE 727
Cdd:TIGR00717 360 GDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKqLTENPWE 438

S1_Rrp5_repeat_sc10

cd05706

S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...

648-720

6.75e-11

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: 58.80 E-value: 6.75e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2786195043 648 LQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:cd05706     1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73

VacB

COG0557

Exoribonuclease R [Transcription];

651-719

1.24e-10

Exoribonuclease R [Transcription];

Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 65.13 E-value: 1.24e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 651 GMILEGAVTNVTNFGAFV---DIGVhqDGLVHISSLSN---KFVEDPHTVV--------KAGDIVKVKVLEVDLQRKRIA 716
Cdd:COG0557   623 GEEFEGVISGVTSFGLFVeldELGV--EGLVHVSSLGDdyyEYDERRQALVgertgkryRLGDRVEVRVVRVDLDRRQID 700


                  ...
gi 2786195043 717 LTM 719
Cdd:COG0557   701 FEL 703

S1_Rrp5_repeat_sc11

cd05707

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...

651-718

1.67e-09

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: 54.61 E-value: 1.67e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2786195043 651 GMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALT 718
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68

HHH_7

pfam14635

Helix-hairpin-helix motif;

461-556

2.40e-09

Helix-hairpin-helix motif;

Pssm-ID: 291309 Cd Length: 104 Bit Score: 55.24 E-value: 2.40e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 461 DPKSIGVGQYQHDVSQTQLARKLDAVVEDCVNAVGVDLNTA-----SVPLLTRVAGLTRMMAQNIV-AWRDENGQFQNRQ 534
Cdd:pfam14635   2 DILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAiankyEAAILPYIAGLGPRKADHLLkILAANNGRLDNRS 81

                          90       100
                  ....*....|....*....|..
gi 2786195043 535 QLLKVSRLGPKAFEQCAGFLRI 556
Cdd:pfam14635  82 QLITKCIMGPKVFMNCAGFLII 103

rpsA

30S ribosomal protein S1; Reviewed

637-721

2.73e-09

30S ribosomal protein S1; Reviewed

Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 59.89 E-value: 2.73e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 637 QFADGVETMNDLQPGMILEGAVTNVTNFGAFVDI-GVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRI 715
Cdd:PRK06676    4 EFEESLNSVKEVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNL 83


                  ....*.
gi 2786195043 716 ALTMRL 721
Cdd:PRK06676   84 LLSKRR 89

S1_Rrp5_repeat_hs5

cd05697

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...

651-718

4.10e-09

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

Pssm-ID: 240202 [Multi-domain] Cd Length: 69 Bit Score: 53.40 E-value: 4.10e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2786195043 651 GMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALT 718
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLT 68

PRK07252

S1 RNA-binding domain-containing protein;

654-738

4.11e-09

S1 RNA-binding domain-containing protein;

Pssm-ID: 180908 [Multi-domain] Cd Length: 120 Bit Score: 55.09 E-value: 4.11e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 654 LEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR-LDEQPGETNARR 732
Cdd:PRK07252    7 LKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRtLEEEKQHFPHRH 86


                  ....*.
gi 2786195043 733 GGGNER 738
Cdd:PRK07252   87 RFSNSR 92

S1_Rrp5_repeat_hs6_sc5

cd05698

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...

651-720

1.93e-08

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: 51.46 E-value: 1.93e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 651 GMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70

S1_RecJ_like

cd04473

S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...

644-700

2.38e-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: 51.45 E-value: 2.38e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2786195043 644 TMNDLQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDI 700
Cdd:cd04473    10 TMEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDYEVGDEVIVQVTDI 66

S1_RPS1_repeat_ec1_hs1

cd05687

S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...

651-709

8.38e-08

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

Pssm-ID: 240192 [Multi-domain] Cd Length: 70 Bit Score: 49.84 E-value: 8.38e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2786195043 651 GMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVD 709
Cdd:cd05687     1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVE 59

rpsA

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...

651-720

8.69e-08

Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 55.51 E-value: 8.69e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 651 GMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:TIGR00717 447 GSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516

PRK12269

bifunctional cytidylate kinase/ribosomal protein S1; Provisional

620-720

9.46e-08

bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 55.87 E-value: 9.46e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 620 KELEKPGRDPRPEF-KTAQFADGVEtmndlqpgmileGAVTNVTNFGAFVDIGVHqDGLVHISSLSNKFVEDPHTVVKAG 698
Cdd:PRK12269  474 RYLEERARQAREEFfNSVHIEDSVS------------GVVKSFTSFGAFIDLGGF-DGLLHVNDMSWGHVARPREFVKKG 540

                          90       100
                  ....*....|....*....|..
gi 2786195043 699 DIVKVKVLEVDLQRKRIALTMR 720
Cdd:PRK12269  541 QTIELKVIRLDQAEKRINLSLK 562

RpsA

COG0539

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...

643-709

2.41e-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: 53.51 E-value: 2.41e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2786195043 643 ETMNDLQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNkfvEDPHTVVKAGDIVKVKVLEVD 709
Cdd:COG0539    11 ESLKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSD---EPGELEVKVGDEVEVYVEKVE 74

S1_IF2_alpha

cd04452

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...

651-720

2.54e-07

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

Pssm-ID: 239899 [Multi-domain] Cd Length: 76 Bit Score: 48.73 E-value: 2.54e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2786195043 651 GMILEGAVTNVTNFGAFVDIGVHQD--GLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:cd04452     4 GELVVVTVKSIADMGAYVSLLEYGNieGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75

PRK03987

translation initiation factor IF-2 subunit alpha; Validated

650-720

3.76e-07

translation initiation factor IF-2 subunit alpha; Validated

Pssm-ID: 235188 [Multi-domain] Cd Length: 262 Bit Score: 52.13 E-value: 3.76e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2786195043 650 PGMILEGAVTNVTNFGAFVDI----GVhqDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:PRK03987    8 EGELVVGTVKEVKDFGAFVTLdeypGK--EGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80

YqgF

pfam14639

Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...

384-456

1.55e-06

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: 48.32 E-value: 1.55e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 384 AIGNGTASRETERFYLDVQKQFPKVTAQK-------VIVSEAGASVYSASELAAQEFPDLDVSLRGAVSIARRLQDPLAE 456
Cdd:pfam14639  66 VIGVSGENRDAQKFYEDVQRVLHELEQDSrlhtigvILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLE 145

PRK00087

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

618-715

2.47e-06

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

Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 51.10 E-value: 2.47e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 618 IIKE----LEKPGRDPRPEFKTAQFADGVEtMNDLQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHT 693
Cdd:PRK00087  267 IIEEvikkMSELDNMEEVEENEQLEYMNEL-EKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKE 345

                          90       100
                  ....*....|....*....|....*....
gi 2786195043 694 VVKAGDIVKVKVLEVD-------LQRKRI 715
Cdd:PRK00087  346 SVKVGDEIEVKVLKLEdedgyvvLSKKEA 374

COG1107

Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...

644-708

2.65e-06

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

Pssm-ID: 440724 [Multi-domain] Cd Length: 626 Bit Score: 50.99 E-value: 2.65e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2786195043 644 TMNDLQPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFvedphtvvKAGDIVKVKVLEV 708
Cdd:COG1107    33 TPDDLEPGRYYRGTVDGVADFGVFVDLNDHVTGLLHRSELDQDW--------EVGDEVFVQVKEV 89

TIGR00426

competence protein ComEA helix-hairpin-helix repeat region; Members of the subfamily ...

496-549

3.59e-06

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

Pssm-ID: 129520 [Multi-domain] Cd Length: 69 Bit Score: 45.31 E-value: 3.59e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2786195043 496 VDLNTASVPLLTR-VAGLTRMMAQNIVAWRDENGQFQNRQQLLKVSRLGPKAFEQ 549
Cdd:TIGR00426   8 VNINTATAEELQRaMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSLVEK 62

PLN00207

polyribonucleotide nucleotidyltransferase; Provisional

658-759

4.74e-06

polyribonucleotide nucleotidyltransferase; Provisional

Pssm-ID: 215104 [Multi-domain] Cd Length: 891 Bit Score: 50.28 E-value: 4.74e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 658 VTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVD----LQRKRIALtmrLDEQPGETNARRG 733
Cdd:PLN00207  762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNdkgqLRLSRRAL---LPEANSEKSSQKQ 838

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2786195043 734 GGNERPQNNRP------AAKPRgREAQPAGNS 759
Cdd:PLN00207  839 QGGSTKDKAPQkkyvntSSRPR-RAAQAEKNS 869

PRK11642

ribonuclease R;

645-756

6.24e-06

ribonuclease R;

Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 49.74 E-value: 6.24e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 645 MNDlQPGMILEGAVTNVTNFGAFVDIG-VHQDGLVHISSLSNKFV-----------EDPHTVVKAGDIVKVKVLEVDLQR 712
Cdd:PRK11642  639 MLD-QVGNVFKGVISSVTGFGFFVRLDdLFIDGLVHVSSLDNDYYrfdqvgqrligESSGQTYRLGDRVEVRVEAVNMDE 717

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2786195043 713 KRIALTM----RLDEQPGET---NARRGGGNERPQNNRPAAKPRGREAQPA 756
Cdd:PRK11642  718 RKIDFSLisseRAPRNVGKTareKAKKGDAGKKGGKRRQVGKKVNFEPDSA 768

PRK12269

bifunctional cytidylate kinase/ribosomal protein S1; Provisional

653-720

6.58e-06

bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 49.71 E-value: 6.58e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2786195043 653 ILEGAVTNVTNFGAFVDIGVHQDGLVHISSLS-NKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:PRK12269  581 VVKGRVTKIADFGAFIELAEGIEGLAHISEFSwVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLK 649

S1_RPS1_repeat_ec6

cd05691

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...

651-720

1.26e-05

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: 43.80 E-value: 1.26e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 651 GMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70

Csl4

COG1096

Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular ...

643-709

2.93e-05

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

Pssm-ID: 440713 [Multi-domain] Cd Length: 191 Bit Score: 45.66 E-value: 2.93e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2786195043 643 ETMNDLQPGMILEGAVTNVTNFGAFVDI----------GVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVD 709
Cdd:COG1096    58 KPPPVPKKGDIVIGEVVDVRESMALVKIyaiegnerelPSSFSGIIHISQVSDSYVKDLSDEFRVGDIVRAKVISTL 134

rpsA

PRK13806

30S ribosomal protein S1; Provisional

650-757

4.66e-05

30S ribosomal protein S1; Provisional

Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 46.64 E-value: 4.66e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2786195043 650 PGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTmrldeqPGETN 729
Cdd:PRK13806  379 PGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLA------PAGAA 452

                          90       100
                  ....*....|....*....|....*...
gi 2786195043 730 ARRGGGNERPQnnrpaAKPRGREAQPAG 757
Cdd:PRK13806  453 GSGADDDDWKQ-----FAPKKSAPASGG 475

S1_Rrp5_repeat_hs13

cd05704

S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...

648-707

2.51e-04

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: 40.03 E-value: 2.51e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2786195043 648 LQPGMILEGAVTNVT-NFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLE 707
Cdd:cd05704     1 LEEGAVTLGMVTKVIpHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILS 61

S1_RPS1_repeat_ec2_hs2

cd04465

S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...

651-720

2.93e-04

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

Pssm-ID: 239911 [Multi-domain] Cd Length: 67 Bit Score: 39.75 E-value: 2.93e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2786195043 651 GMILEGAVTNVTNFGAFVDI-GVhqDGLVHISSLSNKFVEDPHTVVkaGDIVKVKVLEVDLQRKRIALTMR 720
Cdd:cd04465     1 GEIVEGKVTEKVKGGLIVDIeGV--RAFLPASQVDLRPVEDLDEYV--GKELKFKIIEIDRERNNIVLSRR 67

S1_Rrp4

cd05789

S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...

649-720

5.20e-04

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

Pssm-ID: 240215 [Multi-domain] Cd Length: 86 Bit Score: 39.45 E-value: 5.20e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2786195043 649 QPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSL----SNKFVEDPHTVVKAGDIVKVKVLEVDLQRKrIALTMR 720
Cdd:cd05789     5 EVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVnlprTDEDELNMRSYLDEGDLIVAEVQSVDSDGS-VSLHTR 79

rpsA