Citrus Sinensis ID: 032397

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-
Protein Sequence
MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYIELLMHLLYGYLGSCKMQLNYSL
Secondary Structure (PSIPRED)
cccccccccEEEccccccccccccccccEEEEEcccEEEEEEEEEEEEccccccccccccEEEEEcccccccccccccEEEEEEEEEEccEEEEEEEEEccEEccccEEEEEEEHHHHHHHHHHHccccccEEEEEEEEcc
Secondary Structure Prediction (SSPRO)
cccccccEEEEEcccccccHHHccccccEEEEccccEEEEEEEEEEEEEcccccccccccEEEEEcccccccccccccEEEEEEEEEcccEEEEEEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHccccEEEEccc
Coil and Loop (DISEMBL)
MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGllrtlspppdspdqrptvevtghkahgpvpepgSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYIELLMHLLYGYLGSckmqlnysl
Flexible Loop (DISEMBL)
mvvkeeemvlvtpgevlgkateVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGhkahgpvpepgsvVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYIELLMHLLYGYLGSCKMQLNYSL
Low Complexity Region (SEG)
MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYIELLMHLLYGYLGSCKMQLNYSL
Disordered region (IsUnstruct)
********VLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLR******************************SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYIELLMHLLYGYLGSCKMQL****
Disordered Region (DISOPRED)
******E***VTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLR***********************GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYIELLMHLLYGYLGSCKMQLNYS*
Disordered Region (DISEMBL)
********VLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSP*************TGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYIELLMHLLYGYLGSCKMQLNYSL
Disordered Region (DISPRO)
*****EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYIELLMHLLYGYLGSCKMQLNYSL
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYIELLMHLLYGYLGSCKMQLNYSL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	141	2.2.26 [Sep-21-2011]
Q9DAA6	195	Exosome complex component	yes	no	0.673	0.487	0.306	0.0002
Q9Y3B2	195	Exosome complex component	yes	no	0.673	0.487	0.297	0.0002

>sp|Q9DAA6|EXOS1_MOUSE Exosome complex component CSL4 OS=Mus musculus GN=Exosc1 PE=2 SV=1

 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 31/101 (30%), Positives = 46/101 (45%), Gaps = 6/101 (5%)

Query: 13  PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
           PGE L    E   G G Y    +G +++SL G L   S         P V V        
Sbjct: 10  PGERLCNLEEGSPGSGTYT--RHGYIFSSLAGCLMKTS----ENGAVPVVSVMRETESQL 63

Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
           +P+ G+VV  +V+ + +R A   I+ VG+  ++  F G IR
Sbjct: 64  LPDVGAVVTCKVSSINSRFAKVHILYVGSTPLKNAFRGTIR 104

Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. EXOSC1 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC6 and EXOSC8.
Mus musculus (taxid: 10090)

>sp|Q9Y3B2|EXOS1_HUMAN Exosome complex component CSL4 OS=Homo sapiens GN=EXOSC1 PE=1 SV=1

 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/101 (29%), Positives = 46/101 (45%), Gaps = 6/101 (5%)

Query: 13  PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
           PGE L    E   G G Y    +G +++SL G L   S         P V V        
Sbjct: 10  PGERLCNLEEGSPGSGTYT--RHGYIFSSLAGCLMKSS----ENGALPVVSVVRETESQL 63

Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
           +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR
Sbjct: 64  LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIR 104

Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. EXOSC1 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC6 and EXOSC8.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	141
255634132	189	unknown [Glycine max]	0.780	0.582	0.763	1e-41
363814479	197	uncharacterized protein LOC100796154 [Gl	0.780	0.558	0.754	9e-41
357441291	1109	Ammonium transporter [Medicago truncatul	0.773	0.098	0.724	1e-40
224125764	199	predicted protein [Populus trichocarpa]	0.773	0.547	0.752	1e-40
255562013	593	conserved hypothetical protein [Ricinus	0.765	0.182	0.745	2e-40
224105431	119	predicted protein [Populus trichocarpa]	0.765	0.907	0.741	3e-39
225430615	200	PREDICTED: exosome complex component CSL	0.801	0.565	0.716	2e-38
297805862	191	hypothetical protein ARALYDRAFT_494089 [	0.723	0.534	0.721	4e-36
9758066	145	unnamed protein product [Arabidopsis tha	0.723	0.703	0.711	9e-36
42568189	191	exosome complex component CSL4 [Arabidop	0.723	0.534	0.711	1e-35

>gi|255634132|gb|ACU17429.1| unknown [Glycine max]

 Score =  174 bits (441), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 84/110 (76%), Positives = 94/110 (85%)

Query: 4   KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVE 63
           +E+E V+VTPGEVLG+ ++VKAG+GAY A HN  VYASLTG   T+ P PDS D RPTVE
Sbjct: 3   EEKEAVMVTPGEVLGRTSDVKAGRGAYAALHNNTVYASLTGFRHTVPPAPDSSDLRPTVE 62

Query: 64  VTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
           VTGHKAHGPVP+PGSVVIARVTKVM R ASADIMCVG KSVREKF+GIIR
Sbjct: 63  VTGHKAHGPVPQPGSVVIARVTKVMARSASADIMCVGPKSVREKFTGIIR 112

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363814479|ref|NP_001242874.1| uncharacterized protein LOC100796154 [Glycine max] gi|255640712|gb|ACU20640.1| unknown [Glycine max]

 Score =  171 bits (433), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 83/110 (75%), Positives = 93/110 (84%)

Query: 4   KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVE 63
           +E+E V+VTPGEVLG+ ++VKAG+GAY A HN  VYASLTG   T+ P PDS D RPTVE
Sbjct: 3   EEKEAVMVTPGEVLGRTSDVKAGRGAYAALHNNTVYASLTGFRHTVPPAPDSSDLRPTVE 62

Query: 64  VTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
           VTGHKAHGPVP+PGSVVIARVTKVM R ASADIMCVG KSVR KF+GIIR
Sbjct: 63  VTGHKAHGPVPQPGSVVIARVTKVMARSASADIMCVGPKSVRGKFTGIIR 112

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357441291|ref|XP_003590923.1| Ammonium transporter [Medicago truncatula] gi|355479971|gb|AES61174.1| Ammonium transporter [Medicago truncatula]

 Score =  171 bits (432), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 79/109 (72%), Positives = 89/109 (81%)

Query: 5   EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEV 64
           E E  +VTPGEV+GK  +VKAG+G Y + HN  VYASLTG   T+ P  DSPDQRP VEV
Sbjct: 2   EAERDMVTPGEVIGKTHDVKAGRGTYTSTHNNTVYASLTGFRHTIPPASDSPDQRPIVEV 61

Query: 65  TGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
           TGHKAHGPVPEPGSVVI RVTKVMT++A ADIMCVG KSVREKF+G+IR
Sbjct: 62  TGHKAHGPVPEPGSVVIVRVTKVMTKIAEADIMCVGQKSVREKFTGVIR 110

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224125764|ref|XP_002319669.1| predicted protein [Populus trichocarpa] gi|118483759|gb|ABK93772.1| unknown [Populus trichocarpa] gi|222858045|gb|EEE95592.1| predicted protein [Populus trichocarpa]

 Score =  171 bits (432), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 85/113 (75%), Positives = 95/113 (84%), Gaps = 4/113 (3%)

Query: 5   EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGL----VYASLTGLLRTLSPPPDSPDQRP 60
           +EE  + TPGEVLGKATE+KAGKGAY+  +       V++SLTGL RTLSP PDSPDQRP
Sbjct: 2   QEEGEMATPGEVLGKATELKAGKGAYIGSYRDTDIQYVFSSLTGLRRTLSPSPDSPDQRP 61

Query: 61  TVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
           TVEVTGHKAHG VPEPGSVVIARVTKVM + ASADIMCVG KSV+EKF+GIIR
Sbjct: 62  TVEVTGHKAHGAVPEPGSVVIARVTKVMAKTASADIMCVGPKSVQEKFTGIIR 114

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255562013|ref|XP_002522015.1| conserved hypothetical protein [Ricinus communis] gi|223538819|gb|EEF40419.1| conserved hypothetical protein [Ricinus communis]

 Score =  170 bits (430), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 85/114 (74%), Positives = 96/114 (84%), Gaps = 6/114 (5%)

Query: 4   KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNG----LVYASLTGLLRTLSPPPDSPDQR 59
           ++EEMV  TPGEVLGKA+E+KAGKGAYVA +       VY+SL+G LRTL+P PDSPDQR
Sbjct: 397 EKEEMV--TPGEVLGKASELKAGKGAYVAPYRNTDIFYVYSSLSGFLRTLAPTPDSPDQR 454

Query: 60  PTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
           PTVEVTG KA G VPE GSVVIARVTKVM +MASADIMCVG KSVREKF+G+IR
Sbjct: 455 PTVEVTGLKARGAVPEAGSVVIARVTKVMAKMASADIMCVGPKSVREKFTGLIR 508

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224105431|ref|XP_002333818.1| predicted protein [Populus trichocarpa] gi|222838632|gb|EEE76997.1| predicted protein [Populus trichocarpa]

 Score =  166 bits (420), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 83/112 (74%), Positives = 94/112 (83%), Gaps = 4/112 (3%)

Query: 5   EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGL----VYASLTGLLRTLSPPPDSPDQRP 60
           +EE  + TPGEVLGKATE+KAGKGAY+  +       V++SLTGL RTLSP PDSPDQRP
Sbjct: 2   QEEGEMATPGEVLGKATELKAGKGAYIGSYRDTDIQYVFSSLTGLRRTLSPSPDSPDQRP 61

Query: 61  TVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGII 112
           TVEVTGHKAHG VPEPGSVVIARVTKVM + ASADIMCVG KSV+EKF+GI+
Sbjct: 62  TVEVTGHKAHGAVPEPGSVVIARVTKVMAKTASADIMCVGPKSVQEKFTGIM 113

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225430615|ref|XP_002266663.1| PREDICTED: exosome complex component CSL4 [Vitis vinifera] gi|296085148|emb|CBI28643.3| unnamed protein product [Vitis vinifera]

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 81/113 (71%), Positives = 90/113 (79%)

Query: 1   MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRP 60
           M  +EE   LVTPGEVLGK +++KAG+GAY    NG VYASLTG    + P P S DQRP
Sbjct: 1   MQEREEAEELVTPGEVLGKGSQLKAGRGAYFLPQNGTVYASLTGRRSLIPPSPLSSDQRP 60

Query: 61  TVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
           TVEVTGH AHG +PEPGS+VIARVTKVM RMASADIMCVG KSVREKF+GIIR
Sbjct: 61  TVEVTGHSAHGAIPEPGSIVIARVTKVMARMASADIMCVGPKSVREKFTGIIR 113

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297805862|ref|XP_002870815.1| hypothetical protein ARALYDRAFT_494089 [Arabidopsis lyrata subsp. lyrata] gi|297316651|gb|EFH47074.1| hypothetical protein ARALYDRAFT_494089 [Arabidopsis lyrata subsp. lyrata]

 Score =  155 bits (393), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 75/104 (72%), Positives = 89/104 (85%), Gaps = 2/104 (1%)

Query: 10  LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
           LVTPG+V+GKATE KAGKGAYV  ++  +YASLTG  R +SP P+S DQR  VEVTGHKA
Sbjct: 5   LVTPGDVIGKATEFKAGKGAYV--NDTTIYASLTGTRRIVSPLPESLDQRAVVEVTGHKA 62

Query: 70  HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
           HGP+PEPGSVVIARVTKVM RMA+ DI+CVG+K+VRE F+G+IR
Sbjct: 63  HGPIPEPGSVVIARVTKVMARMAAVDILCVGSKAVRENFAGVIR 106

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|9758066|dbj|BAB08645.1| unnamed protein product [Arabidopsis thaliana]

 Score =  154 bits (390), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 74/104 (71%), Positives = 89/104 (85%), Gaps = 2/104 (1%)

Query: 10  LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
           LVTPG+V+GKATE KAGKGAYV  ++  +YASLTG  R +SP P+S DQR  VEVTGHKA
Sbjct: 5   LVTPGDVIGKATEFKAGKGAYV--NDATIYASLTGTCRIVSPLPESIDQRAIVEVTGHKA 62

Query: 70  HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
           HGP+PE GSVVIARVTKVMT+MA+ DI+CVG+K+VRE F+G+IR
Sbjct: 63  HGPIPETGSVVIARVTKVMTKMAAVDILCVGSKAVRENFAGVIR 106

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42568189|ref|NP_568559.2| exosome complex component CSL4 [Arabidopsis thaliana] gi|124301132|gb|ABN04818.1| At5g38890 [Arabidopsis thaliana] gi|222423301|dbj|BAH19626.1| AT5G38890 [Arabidopsis thaliana] gi|332006986|gb|AED94369.1| exosome complex component CSL4 [Arabidopsis thaliana]

 Score =  154 bits (390), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 74/104 (71%), Positives = 89/104 (85%), Gaps = 2/104 (1%)

Query: 10  LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
           LVTPG+V+GKATE KAGKGAYV  ++  +YASLTG  R +SP P+S DQR  VEVTGHKA
Sbjct: 5   LVTPGDVIGKATEFKAGKGAYV--NDATIYASLTGTCRIVSPLPESIDQRAIVEVTGHKA 62

Query: 70  HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
           HGP+PE GSVVIARVTKVMT+MA+ DI+CVG+K+VRE F+G+IR
Sbjct: 63  HGPIPETGSVVIARVTKVMTKMAAVDILCVGSKAVRENFAGVIR 106

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	141
TAIR|locus:2152297	191	AT5G38890 [Arabidopsis thalian	0.723	0.534	0.711	3.1e-35
DICTYBASE|DDB_G0285377	156	DDB_G0285377 "3'-5' exoribonuc	0.723	0.653	0.302	5.2e-10
ZFIN|ZDB-GENE-080926-3	194	exosc1 "exosome component 1" [	0.702	0.510	0.308	5.3e-08
UNIPROTKB|G4ML19	213	MGG_08628 "3'-5' exoribonuclea	0.347	0.230	0.346	1e-07
FB|FBgn0032346	204	Csl4 "Csl4" [Drosophila melano	0.758	0.524	0.307	1.3e-07
UNIPROTKB|B1AMU4	178	EXOSC1 "Exosome complex compon	0.673	0.533	0.306	1e-06
UNIPROTKB|Q9Y3B2	195	EXOSC1 "Exosome complex compon	0.673	0.487	0.306	1.3e-06
UNIPROTKB|Q5E9E9	195	EXOSC1 "Uncharacterized protei	0.673	0.487	0.297	1.7e-06
MGI|MGI:1913833	195	Exosc1 "exosome component 1" [	0.673	0.487	0.316	1.7e-06
UNIPROTKB|E2RT56	207	EXOSC1 "Uncharacterized protei	0.673	0.458	0.297	2.8e-06

TAIR|locus:2152297 AT5G38890 [Arabidopsis thaliana (taxid:3702)]

 Score = 381 (139.2 bits), Expect = 3.1e-35, P = 3.1e-35
 Identities = 74/104 (71%), Positives = 89/104 (85%)

Query:    10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
             LVTPG+V+GKATE KAGKGAYV  ++  +YASLTG  R +SP P+S DQR  VEVTGHKA
Sbjct:     5 LVTPGDVIGKATEFKAGKGAYV--NDATIYASLTGTCRIVSPLPESIDQRAIVEVTGHKA 62

Query:    70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
             HGP+PE GSVVIARVTKVMT+MA+ DI+CVG+K+VRE F+G+IR
Sbjct:    63 HGPIPETGSVVIARVTKVMTKMAAVDILCVGSKAVRENFAGVIR 106

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0006626 "protein targeting to mitochondrion" evidence=RCA

DICTYBASE|DDB_G0285377 DDB_G0285377 "3'-5' exoribonuclease CSL4 homolog" [Dictyostelium discoideum (taxid:44689)]

 Score = 143 (55.4 bits), Expect = 5.2e-10, P = 5.2e-10
 Identities = 36/119 (30%), Positives = 63/119 (52%)

Query:    10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQ----------- 58
             ++TPG+ L K ++  + +G YV  H G +Y+S+ G    +    D+ ++           
Sbjct:     9 IITPGQRLCKESDFISSEGTYV--HKGYIYSSVLGFKHVIKRNIDTTNENNVNNSNNSNE 66

Query:    59 ----RPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
                 +  + V   K    VPE GS+V  +V ++  ++AS  I+CVG K+++E F+GIIR
Sbjct:    67 IENNKDYIVVLKEKEPSVVPEIGSIVTVQVLRINPKLASVAILCVGTKALKETFNGIIR 125

GO:0003723 "RNA binding" evidence=IEA

GO:0000178 "exosome (RNase complex)" evidence=IEA

ZFIN|ZDB-GENE-080926-3 exosc1 "exosome component 1" [Danio rerio (taxid:7955)]

 Score = 124 (48.7 bits), Expect = 5.3e-08, P = 5.3e-08
 Identities = 33/107 (30%), Positives = 55/107 (51%)

Query:     8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTG-LLRTLSPPPDSPDQRPTVEVTG 66
             M L  PGE L    +   G G Y+ +H G ++ASL G +LR      +  ++ P + V  
Sbjct:     4 MKLCVPGERLCSTEDCIPGTGTYL-RH-GYIFASLAGYVLRK-----NEGEELPVISVVR 56

Query:    67 HKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
                   +P+ G++V  +VT +  R A   I+ VG+  ++++F G IR
Sbjct:    57 ETEAQLLPDVGAIVTCKVTSINPRFAKVHILYVGSTPLKDRFRGTIR 103

GO:0000178 "exosome (RNase complex)" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=ISS

UNIPROTKB|G4ML19 MGG_08628 "3'-5' exoribonuclease CSL4" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 85 (35.0 bits), Expect = 1.0e-07, Sum P(2) = 1.0e-07
 Identities = 18/52 (34%), Positives = 29/52 (55%)

Query:    10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPP-PDSPDQRP 60
             L  PG++LG ++  +AG G ++  H   +Y+SL G +    P  P  P +RP
Sbjct:     9 LALPGQLLGPSSRYRAGPGTHI--HEANLYSSLLGAVSITQPAKPAGPTKRP 58

GO:0005575 "cellular_component" evidence=ND

GO:0009405 "pathogenesis" evidence=IMP

FB|FBgn0032346 Csl4 "Csl4" [Drosophila melanogaster (taxid:7227)]

 Score = 121 (47.7 bits), Expect = 1.3e-07, P = 1.3e-07
 Identities = 35/114 (30%), Positives = 54/114 (47%)

Query:     1 MVVKEEEMVLVTPGEVLGKATE-VKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQR 59
             M  +++E V+  PGE L +  + +  G G Y  + NG +YAS +G++       DS D+ 
Sbjct:     1 MSEQQDETVVCLPGERLCRTEDSIVLGIGTY--EQNGYIYASKSGIVNI----EDSGDKC 54

Query:    60 PTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
               V V     H  +P  G VV ARV     + A   I CV    +   + G++R
Sbjct:    55 QVVSVHKPGFHLTIPATGDVVTARVLVTTPKFAKCAIFCVRNVLLESSYRGLLR 108

GO:0006397 "mRNA processing" evidence=ISS

GO:0000177 "cytoplasmic exosome (RNase complex)" evidence=ISS

GO:0000175 "3'-5'-exoribonuclease activity" evidence=ISS

GO:0000176 "nuclear exosome (RNase complex)" evidence=ISS;IDA

GO:0035327 "transcriptionally active chromatin" evidence=IDA

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0010468 "regulation of gene expression" evidence=IMP

UNIPROTKB|B1AMU4 EXOSC1 "Exosome complex component CSL4" [Homo sapiens (taxid:9606)]

 Score = 112 (44.5 bits), Expect = 1.0e-06, P = 1.0e-06
 Identities = 31/101 (30%), Positives = 47/101 (46%)

Query:    13 PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
             PGE L    E   G G Y  +H G +++SL G L   S         P V V        
Sbjct:    10 PGERLCNLEEGSPGSGTYT-RH-GYIFSSLAGCLMKSS----ENGALPVVSVVRETESQL 63

Query:    73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
             +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR
Sbjct:    64 LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIR 104

GO:0000178 "exosome (RNase complex)" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

UNIPROTKB|Q9Y3B2 EXOSC1 "Exosome complex component CSL4" [Homo sapiens (taxid:9606)]

 Score = 112 (44.5 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 31/101 (30%), Positives = 47/101 (46%)

Query:    13 PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
             PGE L    E   G G Y  +H G +++SL G L   S         P V V        
Sbjct:    10 PGERLCNLEEGSPGSGTYT-RH-GYIFSSLAGCLMKSS----ENGALPVVSVVRETESQL 63

Query:    73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
             +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR
Sbjct:    64 LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIR 104

GO:0006364 "rRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

GO:0005730 "nucleolus" evidence=IDA

GO:0000178 "exosome (RNase complex)" evidence=IDA;NAS

GO:0004532 "exoribonuclease activity" evidence=IDA

GO:0000288 "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0043928 "exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

UNIPROTKB|Q5E9E9 EXOSC1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 111 (44.1 bits), Expect = 1.7e-06, P = 1.7e-06
 Identities = 30/101 (29%), Positives = 47/101 (46%)

Query:    13 PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
             PGE L    E   G G Y  +H G +++SL G L   S         P + V        
Sbjct:    10 PGERLCNLEEGSPGSGTYT-RH-GYIFSSLAGCLTKTS----ENGALPVISVMRETESQL 63

Query:    73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
             +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR
Sbjct:    64 LPDVGAIVTCKVSSINSRFAKVHILYVGSTPLKNSFRGTIR 104

GO:0005730 "nucleolus" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0000178 "exosome (RNase complex)" evidence=IEA

MGI|MGI:1913833 Exosc1 "exosome component 1" [Mus musculus (taxid:10090)]

 Score = 111 (44.1 bits), Expect = 1.7e-06, P = 1.7e-06
 Identities = 32/101 (31%), Positives = 47/101 (46%)

Query:    13 PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
             PGE L    E   G G Y  +H G +++SL G L   S         P V V        
Sbjct:    10 PGERLCNLEEGSPGSGTYT-RH-GYIFSSLAGCLMKTS----ENGAVPVVSVMRETESQL 63

Query:    73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
             +P+ G+VV  +V+ + +R A   I+ VG+  ++  F G IR
Sbjct:    64 LPDVGAVVTCKVSSINSRFAKVHILYVGSTPLKNAFRGTIR 104

GO:0000178 "exosome (RNase complex)" evidence=ISO

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0006396 "RNA processing" evidence=ISO

UNIPROTKB|E2RT56 EXOSC1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 110 (43.8 bits), Expect = 2.8e-06, P = 2.8e-06
 Identities = 30/101 (29%), Positives = 47/101 (46%)

Query:    13 PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
             PGE L    E   G G Y  +H G +++SL G L   S         P + V        
Sbjct:    22 PGERLCNLEEGSPGSGTYT-RH-GYIFSSLAGCLTKSS----ENGALPVISVMRETESQL 75

Query:    73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
             +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR
Sbjct:    76 LPDVGTIVTCKVSSINSRFAKVHILYVGSTPLKNSFRGTIR 116

GO:0003723 "RNA binding" evidence=IEA

GO:0000178 "exosome (RNase complex)" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	grail3.0016041401	SubName- Full=Putative uncharacterized protein; (199 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	estExt_fgenesh4_pm.C_LG_XIV0164	hypothetical protein (241 aa)			•	•	•	•	•		0.950
	eugene3.00031704	hypothetical protein (320 aa)			•	•	•	•	•		0.926
	estExt_Genewise1_v1.C_LG_XII0359	SubName- Full=Putative uncharacterized protein; (242 aa)				•	•	•	•		0.901
	estExt_fgenesh4_pm.C_LG_XIV0472	hypothetical protein (288 aa)			•	•	•	•	•		0.882
	estExt_fgenesh4_pg.C_LG_III0702	hypothetical protein (935 aa)				•	•	•	•		0.793
	gw1.I.838.1	hypothetical protein (302 aa)			•	•	•	•	•		0.735
	gw1.IX.3706.1	annotation not avaliable (298 aa)			•	•	•	•	•		0.730
	gw1.XVIII.1197.1	hypothetical protein (232 aa)				•	•	•	•		0.671
	eugene3.00060466	hypothetical protein (318 aa)			•	•	•	•	•		0.644
	estExt_Genewise1_v1.C_LG_XVIII2468	hypothetical protein (213 aa)	•								0.638

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	141
pfam10447	72	pfam10447, EXOSC1, Exosome component EXOSC1/CSL4	1e-12
cd05791	92	cd05791, S1_CSL4, S1_CSL4: CSL4, S1-like RNA-bindi	2e-10
pfam14382	39	pfam14382, ECR1_N, Exosome complex exonuclease RRP	4e-09
COG1096	188	COG1096, COG1096, Predicted RNA-binding protein (c	8e-08
PRK09521	189	PRK09521, PRK09521, exosome complex RNA-binding pr	9e-06
PRK04163	235	PRK04163, PRK04163, exosome complex RNA-binding pr	0.002

>gnl|CDD|192591 pfam10447, EXOSC1, Exosome component EXOSC1/CSL4

 Score = 58.3 bits (142), Expect = 1e-12
 Identities = 19/41 (46%), Positives = 29/41 (70%)

Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
           +P+ G +V+ARVT+V  R A  +I+ VG  +++E F GIIR
Sbjct: 1   LPKVGDIVLARVTRVTPRQAYCEILAVGGTALKETFKGIIR 41

This family of proteins are components of the exosome 3'->5' exoribonuclease complex. The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions. Length = 72

>gnl|CDD|240217 cd05791, S1_CSL4, S1_CSL4: CSL4, S1-like RNA-binding domain

 Score = 53.8 bits (130), Expect = 2e-10
 Identities = 21/42 (50%), Positives = 31/42 (73%)

Query: 72  PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
            +P+ GS+VIARVT++  R A  DI+CVG + ++E F G+IR
Sbjct: 2   VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIR 43

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 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 S. 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". Length = 92

>gnl|CDD|206550 pfam14382, ECR1_N, Exosome complex exonuclease RRP4 N-terminal region

 Score = 48.5 bits (117), Expect = 4e-09
 Identities = 17/39 (43%), Positives = 24/39 (61%), Gaps = 2/39 (5%)

Query: 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRT 48
          +V PGE LG A+E   G G YV   +G +YAS+ G++  
Sbjct: 1  IVVPGERLGTASEYMPGHGTYV--EDGNIYASVAGVVSI 37

ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology. Length = 39

>gnl|CDD|224021 COG1096, COG1096, Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]

 Score = 48.5 bits (116), Expect = 8e-08
 Identities = 29/96 (30%), Positives = 44/96 (45%), Gaps = 9/96 (9%)

Query: 4  KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVE 63
            ++   V PG+VL    E   G+G Y     G + A+ TG++R      D  D+   + 
Sbjct: 1  MVKDGTFVLPGDVLAVIEEFLPGEGTYE--EGGEIRAAATGVVR-----RD--DKNRVIS 51

Query: 64 VTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCV 99
          V   K   P+P+ G +V  RVT V  + A   I+ V
Sbjct: 52 VKPGKKTPPLPKGGDIVYGRVTDVREQRALVRIVGV 87

Length = 188

>gnl|CDD|236547 PRK09521, PRK09521, exosome complex RNA-binding protein Csl4; Provisional

 Score = 43.0 bits (102), Expect = 9e-06
 Identities = 25/84 (29%), Positives = 35/84 (41%), Gaps = 9/84 (10%)

Query: 4  KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVE 63
            ++  LV PG+ L    E   G+G Y    NG VYAS+ G +          D    + 
Sbjct: 1  MVKQGDLVLPGDYLAVIEEYLPGEGTYE--DNGEVYASVVGKVFI-------DDINRKIS 51

Query: 64 VTGHKAHGPVPEPGSVVIARVTKV 87
          V   K   P+ + G +V  RV  V
Sbjct: 52 VIPFKKTPPLLKKGDIVYGRVVDV 75

Length = 189

>gnl|CDD|235233 PRK04163, PRK04163, exosome complex RNA-binding protein Rrp4; Provisional

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 29/102 (28%), Positives = 46/102 (45%), Gaps = 25/102 (24%)

Query: 1  MVVKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRP 60
          M +  E+  +V PG++L +  E KAG+G Y    NG +Y+++ GL               
Sbjct: 1  MKIFVEDRKIVVPGDLLAEG-EFKAGRGTYKE--NGKIYSTVVGL--------------- 42

Query: 61 TVEVTGHKA-----HGP-VPEPGSVVIARVTKVMTRMASADI 96
           V++   K       G  +P+ G +VI +VT V       DI
Sbjct: 43 -VDIKDDKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEVDI 83

Length = 235

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	141
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	99.95
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	99.94
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	99.91
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	99.87
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	99.84
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	99.84
KOG3013	301	consensus Exosomal 3'-5' exoribonuclease complex,	99.78
PF14382	39	ECR1_N: Exosome complex exonuclease RRP4 N-termina	99.5
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	98.85
KOG1004	230	consensus Exosomal 3'-5' exoribonuclease complex s	98.68
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	98.66
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	98.43
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	97.64
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	97.56
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	97.23
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	97.2
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	97.08
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	97.04
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	96.93
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	96.84
COG1098	129	VacB Predicted RNA binding protein (contains ribos	96.71
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	96.68
PRK07252	120	hypothetical protein; Provisional	96.68
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	96.65
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	96.63
PRK08582	139	hypothetical protein; Provisional	96.6
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	96.57
PRK08059	123	general stress protein 13; Validated	96.56
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	96.54
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	96.51
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	96.45
PRK03987	262	translation initiation factor IF-2 subunit alpha;	96.41
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	96.29
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	96.19
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	96.16
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	96.04
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	95.71
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	95.67
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	95.5
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	95.45
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	95.44
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	95.36
PRK05807	136	hypothetical protein; Provisional	95.28
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	95.18
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	95.0
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	94.92
PHA02945	88	interferon resistance protein; Provisional	94.82
PF01016	81	Ribosomal_L27: Ribosomal L27 protein; InterPro: IP	94.17
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	94.15
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	94.03
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	93.96
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	93.93
PRK05435	82	rpmA 50S ribosomal protein L27; Validated	93.88
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	93.63
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	93.36
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	93.34
CHL00121	86	rpl27 ribosomal protein L27; Reviewed	93.07
PRK07400	318	30S ribosomal protein S1; Reviewed	92.6
PRK07400	318	30S ribosomal protein S1; Reviewed	92.39
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	91.99
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	91.91
TIGR00062	83	L27 ribosomal protein L27. Eubacterial, chloroplas	91.14
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	90.78
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	90.43
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	90.38
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	90.36
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	89.68
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	89.6
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	89.45
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	89.41
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	88.57
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	87.89
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	87.3
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	86.86
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	86.43
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	85.52
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	85.47
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	83.97
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	83.97
KOG4600	144	consensus Mitochondrial ribosomal protein MRP7 (L2	82.41
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	80.96
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	80.7
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	80.2
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	80.17
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	80.1
PF01959	354	DHQS: 3-dehydroquinate synthase (EC 4.6.1.3); Inte	80.01

>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=6e-33  Score=210.54  Aligned_cols=129  Identities=29%  Similarity=0.402  Sum_probs=113.0

Q ss_pred             CCcEEecCCccCCCCC-eeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 032397            7 EMVLVTPGEVLGKATE-VKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT   85 (141)
Q Consensus         7 ~~~iVlPGd~L~~~~e-~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V~   85 (141)
                      ...+|+|||+++..++ |..|.|||+++  |+|+||..|...++    +.....++.+++.......+|.+||||++||+
T Consensus         4 a~~~~lpG~~~c~~e~~~~~g~Gtye~~--~yI~aS~ag~~~~~----~~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~   77 (193)
T KOG3409|consen    4 AETLVLPGEVVCRAEGEYRMGEGTYERN--GYIFASVAGVNFRD----NLVQKIEVVSVEKQLFNELLPFVGAIVTARVS   77 (193)
T ss_pred             ceEEEcccceeeecccccccccceeecC--CeEEeccccceeec----CCccceeeeeecccchhhcCCccCcEEEEEEE
Confidence            4568999999987765 99999999999  99999999955441    11233456666665556899999999999999


Q ss_pred             EeccceEEEEEEEecCeecccceeEEEeccccch----hhhHHHHhh-------hhccccccceeeC
Q 032397           86 KVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI----ELLMHLLYG-------YLGSCKMQLNYSL  141 (141)
Q Consensus        86 ~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~----~v~~~~~f~-------~vis~gd~~~y~l  141 (141)
                      +++.+||+|+|++|++++|++.|+|+||+||||+    ++++++|||       +|||+||++||||
T Consensus        78 ~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~L  144 (193)
T KOG3409|consen   78 RINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLL  144 (193)
T ss_pred             eeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEEE
Confidence            9999999999999999999999999999999997    799999995       9999999999997

>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]

Probab=99.95  E-value=8.7e-28  Score=184.52  Aligned_cols=122  Identities=25%  Similarity=0.301  Sum_probs=113.0

Q ss_pred             ccCCcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEE
Q 032397            5 EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARV   84 (141)
Q Consensus         5 ~~~~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V   84 (141)
                      ..++.+|+|||.|+.+|||.+|+|||+.+  |+|+|+.+|.+..       |+++..++|.|.+..+.+|+.||+|+|+|
T Consensus         2 ~~~g~~v~PGd~~a~~EE~~~G~gt~~~~--g~i~Aa~~G~~~~-------d~~n~~~~V~p~~~~~~~~K~GdiV~grV   72 (188)
T COG1096           2 VKDGTFVLPGDVLAVIEEFLPGEGTYEEG--GEIRAAATGVVRR-------DDKNRVISVKPGKKTPPLPKGGDIVYGRV   72 (188)
T ss_pred             cccCcEEcCcceeeeeeeeecCCCeEeEC--CEEEEeecccEEE-------cccceEEEeccCCCCCCCCCCCCEEEEEE
Confidence            45788999999999999999999999999  9999999999998       67889999999997799999999999999


Q ss_pred             EEeccceEEEEEEEecCe--ecccceeEEEeccccch--hhhHHHHhh-------hhccccc
Q 032397           85 TKVMTRMASADIMCVGAK--SVREKFSGIIRFFIFYI--ELLMHLLYG-------YLGSCKM  135 (141)
Q Consensus        85 ~~v~~~~a~v~I~~v~~~--~l~~~~~G~Ir~~dvr~--~v~~~~~f~-------~vis~gd  135 (141)
                      +++..++|.|+|..|.++  .+.+++.|.||.|++++  .-++.++|+       +|||+||
T Consensus        73 ~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~~  134 (188)
T COG1096          73 TDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTGD  134 (188)
T ss_pred             eeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecCC
Confidence            999999999999999994  59999999999999998  456668885       9999994

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=99.94  E-value=7.2e-26  Score=174.87  Aligned_cols=121  Identities=23%  Similarity=0.266  Sum_probs=108.6

Q ss_pred             ccCCcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEE
Q 032397            5 EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARV   84 (141)
Q Consensus         5 ~~~~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V   84 (141)
                      ++++.+|+|||+|+..++|.+|+|||+++  |.||||++|.+++       |..++.|+|.|.+...+.|++||+|+|+|
T Consensus         2 ~~~~~~V~PGe~l~~~~e~~~G~Gty~~~--~~i~as~~G~~~i-------d~~~~~Isv~P~~~~~~~~~~GdiV~GkV   72 (189)
T PRK09521          2 VKQGDLVLPGDYLAVIEEYLPGEGTYEDN--GEVYASVVGKVFI-------DDINRKISVIPFKKTPPLLKKGDIVYGRV   72 (189)
T ss_pred             cccCCEECCCCccccccceEcCCCEEeeC--CEEEEEeeEEEEE-------cCCCCEEEEecCcCCCCCCCCCCEEEEEE
Confidence            34778999999999989999999999999  9999999999998       44578999999886689999999999999


Q ss_pred             EEeccceEEEEEEEec--CeecccceeEEEeccccch--hhhHHHHhh-------hhcccc
Q 032397           85 TKVMTRMASADIMCVG--AKSVREKFSGIIRFFIFYI--ELLMHLLYG-------YLGSCK  134 (141)
Q Consensus        85 ~~v~~~~a~v~I~~v~--~~~l~~~~~G~Ir~~dvr~--~v~~~~~f~-------~vis~g  134 (141)
                      +++.++.|.|+|.+++  ++++..++.|+||.++++.  ..+|.++|+       ++++++
T Consensus        73 ~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~  133 (189)
T PRK09521         73 VDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT  133 (189)
T ss_pred             EEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC
Confidence            9999999999999988  7888899999999999986  356778884       777776

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=99.91  E-value=1.8e-23  Score=166.69  Aligned_cols=116  Identities=23%  Similarity=0.351  Sum_probs=101.7

Q ss_pred             ccCCcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEE
Q 032397            5 EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARV   84 (141)
Q Consensus         5 ~~~~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V   84 (141)
                      ..++.+|+|||.|+ +++|.+|+|||+++  |.|+||++|.+...         +..++|.|.+. .|+|++||+|+|+|
T Consensus         5 ~~~~~~V~PGd~l~-~~~~~~G~Gty~~~--g~i~As~~G~~~~~---------~~~i~V~p~~~-~y~P~vGDiViG~V   71 (235)
T PRK04163          5 VEDRKIVVPGDLLA-EGEFKAGRGTYKEN--GKIYSTVVGLVDIK---------DDKVRVIPLEG-KYIPKVGDLVIGKV   71 (235)
T ss_pred             eeCCcEECCCCCcC-cCCeecCCceEEeC--CEEEEEEeEEEEEE---------CCEEEEEECCC-cccCCCCCEEEEEE
Confidence            34568999999997 57899999999999  99999999999983         35999999986 59999999999999


Q ss_pred             EEeccceEEEEEEEecCeecccceeEEEeccccch-h-----hhHHHHhh-------hhccccccceeeC
Q 032397           85 TKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-E-----LLMHLLYG-------YLGSCKMQLNYSL  141 (141)
Q Consensus        85 ~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~-----v~~~~~f~-------~vis~gd~~~y~l  141 (141)
                      ++++++.|.|+|        .+++.|+||.++++. +     .+|.++|+       +|+++++...+.|
T Consensus        72 ~~i~~~~~~vdI--------~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~L  133 (235)
T PRK04163         72 TDVTFSGWEVDI--------NSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVL  133 (235)
T ss_pred             EEEeCceEEEEe--------CCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEE
Confidence            999999999999        788999999999986 3     78999994       8888877655543

>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

Probab=99.87  E-value=1.3e-21  Score=155.53  Aligned_cols=114  Identities=22%  Similarity=0.290  Sum_probs=100.0

Q ss_pred             ccccCCcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEE
Q 032397            3 VKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIA   82 (141)
Q Consensus         3 ~~~~~~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig   82 (141)
                      ......++|+|||.|.....+..|+|||..+  +.|||+++|.++++         ++.+.|+|.++ +|+|++||+|||
T Consensus         3 ~~~~~~~iV~PGd~vl~~~~~~~G~Gty~~~--~~iyssv~G~~~~~---------~~~v~VIpl~g-~YiP~~gD~VIG   70 (239)
T COG1097           3 LSVSMRKIVLPGDLVLAEGSYKLGHGTYFEG--GKIYSSVVGLLDVK---------GKLVRVIPLEG-RYIPEVGDVVIG   70 (239)
T ss_pred             eeccccceecCCCccCCCCCEecCCCcEecC--CEEEEEEEeEEEEe---------CCEEEEEeCCC-cccCCCCCEEEE
Confidence            4456788999999887778899999999999  99999999999994         57899999996 999999999999


Q ss_pred             EEEEeccceEEEEEEEecCeecccceeEEEeccccch-hhh-HHHHhhhhcccccc
Q 032397           83 RVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-ELL-MHLLYGYLGSCKMQ  136 (141)
Q Consensus        83 ~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~v~-~~~~f~~vis~gd~  136 (141)
                      +|+.+.+..|+|||        .++|.++|+.+++-. +.+ .....|.+++.||.
T Consensus        71 ~I~~v~~~~W~VDI--------~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~  118 (239)
T COG1097          71 KIIEVGPSGWKVDI--------GSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDL  118 (239)
T ss_pred             EEEEEcccceEEEc--------CCccceEeehhhhhcccccccccccccccccCCE
Confidence            99999999999999        999999999999954 333 23556788888875

>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain

Probab=99.84  E-value=2.6e-21  Score=134.27  Aligned_cols=71  Identities=35%  Similarity=0.508  Sum_probs=67.4

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch----hhhHHHHhh-------hhcccccccee
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI----ELLMHLLYG-------YLGSCKMQLNY  139 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~----~v~~~~~f~-------~vis~gd~~~y  139 (141)
                      .|+|++||+|+|+|++++.++|.|+|+++++++++++|+|+||+||+|+    +++|++||+       +++|+||+.+|
T Consensus         1 ~~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~   80 (92)
T cd05791           1 LVLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSY   80 (92)
T ss_pred             CCCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCc
Confidence            3789999999999999999999999999999999999999999999997    678999995       99999999999


Q ss_pred             eC
Q 032397          140 SL  141 (141)
Q Consensus       140 ~l  141 (141)
                      ||
T Consensus        81 ~L   82 (92)
T cd05791          81 YL   82 (92)
T ss_pred             EE
Confidence            86

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 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 S. 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".

>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []

Probab=99.84  E-value=8.5e-22  Score=134.33  Aligned_cols=61  Identities=38%  Similarity=0.564  Sum_probs=43.0

Q ss_pred             CCCCCCEEEEEEEEeccceEEEEEEEe----------cCeecccceeEEEeccccch----hhhHHHHhh-------hhc
Q 032397           73 VPEPGSVVIARVTKVMTRMASADIMCV----------GAKSVREKFSGIIRFFIFYI----ELLMHLLYG-------YLG  131 (141)
Q Consensus        73 ~P~~GdiVig~V~~v~~~~a~v~I~~v----------~~~~l~~~~~G~Ir~~dvr~----~v~~~~~f~-------~vi  131 (141)
                      +|++||+|+|||+++++++|+|+|+|+          ++.+|.++|+|+||+||||+    +++|++|||       +||
T Consensus         1 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~Vi   80 (82)
T PF10447_consen    1 LPKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVI   80 (82)
T ss_dssp             ---TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEE
T ss_pred             CCCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEe
Confidence            699999999999999999999999999          88899999999999999997    799999996       888


Q ss_pred             cc
Q 032397          132 SC  133 (141)
Q Consensus       132 s~  133 (141)
                      |+
T Consensus        81 Sl   82 (82)
T PF10447_consen   81 SL   82 (82)
T ss_dssp             EE
T ss_pred             eC
Confidence            75

The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.

>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]

Probab=99.78  E-value=2.3e-19  Score=143.86  Aligned_cols=117  Identities=26%  Similarity=0.347  Sum_probs=100.2

Q ss_pred             cCCcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 032397            6 EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT   85 (141)
Q Consensus         6 ~~~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V~   85 (141)
                      ....+|+||+.+.....|..|+|||..+  |.|+||++|.++..         ++.|+|+|.+ .+|.|++||+|.|||+
T Consensus        27 ~~~~ivtPG~~V~~d~~fmRGHGTy~~d--~~i~ssvaG~v~rv---------NkLi~V~plk-~rY~pEvGDvVVgRV~   94 (301)
T KOG3013|consen   27 DHSTIVTPGELVTDDPGFMRGHGTYVRD--GEIYSSVAGVVQRV---------NKLISVKPLK-SRYAPEVGDVVVGRVI   94 (301)
T ss_pred             cCceeecCCccccCchhhhhcccceecC--CeEEEeecchhhhh---------cceEEEeehh-hhcCCccCCEEEEEee
Confidence            4557999999999988899999999999  99999999999874         7999999999 6999999999999999


Q ss_pred             EeccceEEEEEEEecCeecc--c--ceeEEEeccccchhhhHHHHhh--hhcccc
Q 032397           86 KVMTRMASADIMCVGAKSVR--E--KFSGIIRFFIFYIELLMHLLYG--YLGSCK  134 (141)
Q Consensus        86 ~v~~~~a~v~I~~v~~~~l~--~--~~~G~Ir~~dvr~~v~~~~~f~--~vis~g  134 (141)
                      .|.+++|+|++.+-.+..|-  +  =.-|++|+.+..++..|.+-|.  .+|+..
T Consensus        95 eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AE  149 (301)
T KOG3013|consen   95 EVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAE  149 (301)
T ss_pred             eeecceeEEecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHH
Confidence            99999999999877766653  2  2567888888888899987774  444433

>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C

Probab=99.50  E-value=1.3e-14  Score=86.02  Aligned_cols=37  Identities=41%  Similarity=0.814  Sum_probs=33.8

Q ss_pred             EEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEe
Q 032397           10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRT   48 (141)
Q Consensus        10 iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~   48 (141)
                      +|+|||+|+.+++|.+|+|||+++  |+||||++|.+++
T Consensus         1 iV~PG~~l~~~~e~~~G~GTY~~~--g~I~asv~G~v~~   37 (39)
T PF14382_consen    1 IVVPGDRLGSSEEYMPGHGTYVRD--GNIYASVAGTVKI   37 (39)
T ss_dssp             EE-TT-EEEETTTSEESTTEEEET--TEEEESSSEEEEE
T ss_pred             CCCCCCEeecCCCEecCCCEEEeC--CEEEEEeeEEEEE
Confidence            699999999999999999999999  9999999999987

>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain

Probab=98.85  E-value=8.3e-09  Score=69.14  Aligned_cols=58  Identities=19%  Similarity=0.074  Sum_probs=48.5

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch--hhhHHHHhh-------hhcccccc
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI--ELLMHLLYG-------YLGSCKMQ  136 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~--~v~~~~~f~-------~vis~gd~  136 (141)
                      .|+|++||+|+|+|+++..+.|.|+|        .+.+.|+|+.+++..  .-+|.+.|+       +++++.+.
T Consensus         1 ~y~p~~GdiV~G~V~~v~~~~~~V~i--------~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~   67 (82)
T cd04454           1 RYLPDVGDIVIGIVTEVNSRFWKVDI--------LSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD   67 (82)
T ss_pred             CCCCCCCCEEEEEEEEEcCCEEEEEe--------CCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC
Confidence            48999999999999999999999999        677999999999975  455666663       66666553

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits 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".

>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]

Probab=98.68  E-value=8.4e-08  Score=75.59  Aligned_cols=101  Identities=21%  Similarity=0.195  Sum_probs=74.5

Q ss_pred             cEEecCCccCC--CCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEE
Q 032397            9 VLVTPGEVLGK--ATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTK   86 (141)
Q Consensus         9 ~iVlPGd~L~~--~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V~~   86 (141)
                      .+.+|||.+..  ..+..+|+|.+.++  +.+..+..|.+....+.   .......+|.... .+|+|.+||.|||+|+.
T Consensus         2 ~~~~pg~~~~~~~~~sv~~G~g~~~~g--~~~~~~~~G~~~~~~~g---k~~~~v~~vds~~-kRYiP~~~D~VIGiV~~   75 (230)
T KOG1004|consen    2 TFYFPGDSIPRPRLCSVVLGPGLRRRG--QERLVTKCGRLRHKEPG---KGGGGVYWVDSQQ-KRYIPVKGDHVIGIVTS   75 (230)
T ss_pred             ceecCCcccccCccCceeecCCccccC--ceEEeccccceeeccCC---cccceeEEEeccc-ceecCCCCCEEEEEEEe
Confidence            46789998753  24589999999988  99999999988774200   0011356777766 69999999999999999


Q ss_pred             eccceEEEEEEEecCeecc-cceeEEEecc
Q 032397           87 VMTRMASADIMCVGAKSVR-EKFSGIIRFF  115 (141)
Q Consensus        87 v~~~~a~v~I~~v~~~~l~-~~~~G~Ir~~  115 (141)
                      -+++..+|||-.-.-..|+ ..|.|.-+++
T Consensus        76 ~~gd~ykVDigg~~~a~L~~laFe~AtkrN  105 (230)
T KOG1004|consen   76 KSGDIYKVDIGGSEPASLSYLAFEGATKRN  105 (230)
T ss_pred             ccCceEEEecCCCCeeeeeeccccCccccC
Confidence            9999999999332222233 2688877665

>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain

Probab=98.66  E-value=3.5e-08  Score=67.85  Aligned_cols=39  Identities=23%  Similarity=0.290  Sum_probs=34.8

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEecccc
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIF  117 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dv  117 (141)
                      +|+|++||+|||+|++++.+.|+|+|        ++++.|+|+..+.
T Consensus         1 rY~P~~gD~VIG~V~~~~~~~~~VdI--------~s~~~a~L~~~~f   39 (86)
T cd05790           1 RYVPAKGDHVIGIVVAKAGDFFKVDI--------GGSEPASLSYLAF   39 (86)
T ss_pred             CCcCCCCCEEEEEEEEEcCCeEEEEc--------CCCcceEechHHc
Confidence            48999999999999999999999999        7777777777665

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".

>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain

Probab=98.43  E-value=7e-07  Score=60.07  Aligned_cols=40  Identities=30%  Similarity=0.408  Sum_probs=37.6

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY  118 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr  118 (141)
                      .|.|++||+|.|+|+++.+..|.|+|        ...+.|+|+.+++.
T Consensus         1 ~y~p~~GdiV~g~V~~i~~~g~~v~i--------~~~~~G~l~~se~~   40 (86)
T cd05789           1 RYIPEVGDVVIGRVTEVGFKRWKVDI--------NSPYDAVLPLSEVN   40 (86)
T ss_pred             CCcCCCCCEEEEEEEEECCCEEEEEC--------CCCeEEEEEHHHcc
Confidence            47899999999999999999999999        77899999999996

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".

>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=97.64  E-value=0.00011  Score=47.51  Aligned_cols=55  Identities=13%  Similarity=0.051  Sum_probs=45.3

Q ss_pred             CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch----hhhHHHHhh-------hhcccccccee
Q 032397           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI----ELLMHLLYG-------YLGSCKMQLNY  139 (141)
Q Consensus        77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~----~v~~~~~f~-------~vis~gd~~~y  139 (141)
                      |++|.|+|+++....+.|++        ...+.|.|+.++++.    ...+.++|+       +++++.+...+
T Consensus         1 G~iV~g~V~~i~~~gi~v~l--------~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~~   66 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQL--------ADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTH   66 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEe--------CCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcccc
Confidence            89999999999999999999        678999999999974    234567774       78888776654

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=97.56  E-value=0.00019  Score=47.49  Aligned_cols=37  Identities=14%  Similarity=0.125  Sum_probs=34.6

Q ss_pred             CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ++||+|.|+|+++++..++|++        .....|.||.+|+..
T Consensus         2 k~G~~V~g~V~~i~~~G~fV~l--------~~~v~G~v~~~~ls~   38 (74)
T cd05705           2 KEGQLLRGYVSSVTKQGVFFRL--------SSSIVGRVLFQNVTK   38 (74)
T ss_pred             CCCCEEEEEEEEEeCCcEEEEe--------CCCCEEEEEHHHccC
Confidence            6899999999999999999999        778999999999986

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 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=97.23  E-value=0.00077  Score=47.19  Aligned_cols=37  Identities=11%  Similarity=0.174  Sum_probs=34.2

Q ss_pred             CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ++|++|.|+|+++.+..+.+++        .....|+++.+|+.+
T Consensus         2 ~~G~vV~G~V~~v~~~gl~v~L--------~~g~~G~v~~seis~   38 (100)
T cd05693           2 SEGMLVLGQVKEITKLDLVISL--------PNGLTGYVPITNISD   38 (100)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEC--------CCCcEEEEEHHHhhH
Confidence            6899999999999999999988        778999999999975

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 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain

Probab=97.20  E-value=0.00078  Score=43.19  Aligned_cols=44  Identities=25%  Similarity=0.072  Sum_probs=36.4

Q ss_pred             CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch-h-hhHHHHhh
Q 032397           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-E-LLMHLLYG  128 (141)
Q Consensus        77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~-v~~~~~f~  128 (141)
                      ||+|.|+|+++.+..|.|++        ...+.|+|+.+++.. + ..+.++|+
T Consensus         1 G~iv~g~V~~i~~~~~~v~l--------~~~~~g~l~~~e~~~~~~~~~~~~~~   46 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDI--------GYKSEGIIPISEFSDDPIENGEDEVK   46 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEe--------CCCceEEEEHHHhCccccCCHhHcCC
Confidence            89999999999999999999        556899999999975 3 34555553

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.

>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain

Probab=97.08  E-value=0.0013  Score=42.56  Aligned_cols=40  Identities=20%  Similarity=0.296  Sum_probs=34.4

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |++|++|.|+|+++....|.+++...      ....|+||.++++.
T Consensus         1 ~~~G~~~~g~V~~v~~~g~~v~l~~~------~~~~gll~~s~l~~   40 (76)
T cd04452           1 PEEGELVVVTVKSIADMGAYVSLLEY------GNIEGMILLSELSR   40 (76)
T ss_pred             CCCCCEEEEEEEEEEccEEEEEEcCC------CCeEEEEEhHHcCC
Confidence            68999999999999999999999321      13899999999976

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 c

>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=97.04  E-value=0.0016  Score=42.61  Aligned_cols=37  Identities=24%  Similarity=0.344  Sum_probs=33.0

Q ss_pred             CCCCEEEEEEEEecc-ceEEEEEEEecCeecccceeEEEeccccch
Q 032397           75 EPGSVVIARVTKVMT-RMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        75 ~~GdiVig~V~~v~~-~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ++|++|.|+|+++.+ ..+.+++        .....|++|.+++..
T Consensus         2 ~~G~iv~G~V~~i~~~~g~~v~l--------~~~~~Glvhis~~s~   39 (72)
T cd05704           2 EEGAVTLGMVTKVIPHSGLTVQL--------PFGKTGLVSIFHLSD   39 (72)
T ss_pred             CCCCEEEEEEEEeeCCcEEEEEC--------CCCCEEEEEHHHhcC
Confidence            689999999999987 4688887        888999999999976

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.

>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=96.93  E-value=0.0033  Score=40.50  Aligned_cols=38  Identities=21%  Similarity=0.183  Sum_probs=35.6

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |++|++|.|+|+++.+..+.++|        .....|+|+.+++..
T Consensus         2 ~~~G~iv~g~V~~v~~~g~~V~l--------~~~~~g~ip~~~l~~   39 (74)
T PF00575_consen    2 LKEGDIVEGKVTSVEDFGVFVDL--------GNGIEGFIPISELSD   39 (74)
T ss_dssp             SSTTSEEEEEEEEEETTEEEEEE--------STSSEEEEEGGGSSS
T ss_pred             CCCCCEEEEEEEEEECCEEEEEE--------CCcEEEEEEeehhcC
Confidence            68999999999999999999999        788999999999974

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....

>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=96.84  E-value=0.0034  Score=40.51  Aligned_cols=37  Identities=24%  Similarity=0.211  Sum_probs=34.5

Q ss_pred             CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ++|++|.|+|+++....+.|++        ....+|++|.+++..
T Consensus         2 ~~G~iv~g~V~~v~~~gi~v~l--------~~~~~g~v~~s~l~~   38 (73)
T cd05706           2 KVGDILPGRVTKVNDRYVLVQL--------GNKVTGPSFITDALD   38 (73)
T ss_pred             CCCCEEEEEEEEEeCCeEEEEe--------CCCcEEEEEhhhccC
Confidence            5899999999999999999998        778999999999986

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.

>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]

Probab=96.71  E-value=0.0031  Score=46.20  Aligned_cols=55  Identities=9%  Similarity=-0.074  Sum_probs=44.9

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch-hhhHHHHh--------hhhcccccc
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-ELLMHLLY--------GYLGSCKMQ  136 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~v~~~~~f--------~~vis~gd~  136 (141)
                      +++||++.|+||.|++=-|+|++        ...-+|++|++.|.. .|+-.+.+        .+||++.+.
T Consensus         3 ~kvG~~l~GkItgI~~yGAFV~l--------~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~   66 (129)
T COG1098           3 MKVGSKLKGKITGITPYGAFVEL--------EGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDEN   66 (129)
T ss_pred             ccccceEEEEEEeeEecceEEEe--------cCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccC
Confidence            68999999999999999999999        777889999999997 65544333        277777663

>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain

Probab=96.68  E-value=0.0044  Score=39.58  Aligned_cols=35  Identities=26%  Similarity=0.372  Sum_probs=32.4

Q ss_pred             CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |++|.|+|+++....|.|+|        .....|+++.+++..
T Consensus         1 G~~v~g~V~~v~~~g~~v~l--------~~~~~g~i~~~~~~~   35 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKL--------GDGVEGFLRAAELSR   35 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEe--------CCCCEEEEEHHHCCC
Confidence            89999999999999999999        567999999999876

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.

>PRK07252 hypothetical protein; Provisional

Probab=96.68  E-value=0.0043  Score=44.87  Aligned_cols=37  Identities=14%  Similarity=0.133  Sum_probs=34.0

Q ss_pred             CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ++|++|.|+|++|....|.|+|        .....|+|+.++++.
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei--------~~~~~GllhiseLs~   38 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVAL--------ENGTTGLIHISEIKT   38 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEE--------CCCCEEEEEHHHcCC
Confidence            5799999999999999999999        667899999999975

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=96.65  E-value=0.0035  Score=52.51  Aligned_cols=41  Identities=17%  Similarity=0.284  Sum_probs=36.6

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecc--cceeEEEeccccch
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRFFIFYI  119 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~--~~~~G~Ir~~dvr~  119 (141)
                      .-.|++||+|.|+|++|..-.|.|+|        .  ....|+||.+++..
T Consensus        12 ~~~P~~GdvV~g~V~~I~d~GafV~L--------~EY~gvEGlIhiSElS~   54 (319)
T PTZ00248         12 QKFPEEDDLVMVKVVRITEMGAYVSL--------LEYDDIEGMILMSELSK   54 (319)
T ss_pred             hhCCCCCCEEEEEEEEEeCCeEEEEe--------cCCCCcEEEEEHHHhcc
Confidence            45699999999999999999999999        4  35899999999965

>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=96.63  E-value=0.0061  Score=38.86  Aligned_cols=35  Identities=14%  Similarity=0.085  Sum_probs=32.4

Q ss_pred             CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |++|.|+|+++.+..+.|++        ...+.|++|.+++..
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l--------~~~~~G~v~~s~l~~   35 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTL--------GRGVDARVRVSELSD   35 (68)
T ss_pred             CCEEEEEEEEEECccEEEEe--------CCCCEEEEEHHHCCc
Confidence            79999999999999999999        567999999999975

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.

>PRK08582 hypothetical protein; Provisional

Probab=96.60  E-value=0.0057  Score=45.31  Aligned_cols=38  Identities=21%  Similarity=0.162  Sum_probs=35.0

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .++|++|.|+|+.|++..|.|+|        .....|+||.+++..
T Consensus         3 ~kvG~iv~G~V~~I~~fG~fV~L--------~~~~~GlVhiSels~   40 (139)
T PRK08582          3 IEVGSKLQGKVTGITNFGAFVEL--------PEGKTGLVHISEVAD   40 (139)
T ss_pred             CcCCCEEEEEEEEEECCeEEEEE--------CCCCEEEEEeeccCc
Confidence            57899999999999999999999        667999999999975

>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=96.57  E-value=0.0057  Score=39.38  Aligned_cols=37  Identities=19%  Similarity=0.087  Sum_probs=33.1

Q ss_pred             CCCCEEEEEEEEeccceEEEEEEEecCeecc-cceeEEEeccccch
Q 032397           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRFFIFYI  119 (141)
Q Consensus        75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~-~~~~G~Ir~~dvr~  119 (141)
                      ++|++|.|+|+++.+..|.|++        . ....|+++.+++..
T Consensus         1 ~~g~~v~g~V~~i~~~g~~v~l--------~~~~~~g~i~~~~l~~   38 (77)
T cd05708           1 KVGQKIDGTVRRVEDYGVFIDI--------DGTNVSGLCHKSEISD   38 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEE--------CCCCeEEEEEHHHCCC
Confidence            4699999999999999999999        4 36899999999986

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.

>PRK08059 general stress protein 13; Validated

Probab=96.56  E-value=0.0056  Score=44.15  Aligned_cols=38  Identities=26%  Similarity=0.254  Sum_probs=34.9

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .++|++|.|+|+++.+..|.|+|        ...+.|+|+.++++.
T Consensus         5 ~k~G~iv~G~V~~i~~~G~fV~i--------~~~~~Gli~~sel~~   42 (123)
T PRK08059          5 YEVGSVVTGKVTGIQPYGAFVAL--------DEETQGLVHISEITH   42 (123)
T ss_pred             CCCCCEEEEEEEEEecceEEEEE--------CCCCEEEEEHHHCCc
Confidence            57899999999999999999999        667999999999975

>smart00316 S1 Ribosomal protein S1-like RNA-binding domain

Probab=96.54  E-value=0.0065  Score=37.67  Aligned_cols=37  Identities=27%  Similarity=0.244  Sum_probs=33.7

Q ss_pred             CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ++|++|.|+|++++...+.|+|        ...+.|+++.+++..
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i--------~~~~~g~l~~~~~~~   37 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDL--------GNGVEGLIPISELSD   37 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEe--------CCCCEEEEEHHHCCc
Confidence            4699999999999999999999        657999999999986

>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain

Probab=96.51  E-value=0.0086  Score=38.98  Aligned_cols=39  Identities=15%  Similarity=0.067  Sum_probs=33.3

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |+.|+++.|+|+++.+..+.+++   ++.    ...|++|.+++..
T Consensus         1 ~~~g~~~~g~V~~i~~fG~fv~l---~~~----~~eGlvh~sel~~   39 (73)
T cd05686           1 PALYQIFKGEVASVTEYGAFVKI---PGC----RKQGLVHKSHMSS   39 (73)
T ss_pred             CcCCCEEEEEEEEEEeeeEEEEE---CCC----CeEEEEEchhhCC
Confidence            67999999999999999999999   111    2589999999976

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.

>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=96.45  E-value=0.0069  Score=39.70  Aligned_cols=35  Identities=20%  Similarity=0.166  Sum_probs=32.6

Q ss_pred             CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ||+|.|+|+++.+..++|++        .....|.|+.+|+..
T Consensus         1 G~~V~g~V~~i~~~g~~V~l--------~~~i~G~i~~~~ls~   35 (73)
T cd05703           1 GQEVTGFVNNVSKEFVWLTI--------SPDVKGRIPLLDLSD   35 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEe--------CCCcEEEEEHHHcCC
Confidence            89999999999999999999        778999999999964

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 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PRK03987 translation initiation factor IF-2 subunit alpha; Validated

Probab=96.41  E-value=0.0081  Score=48.95  Aligned_cols=43  Identities=21%  Similarity=0.129  Sum_probs=36.5

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .-+|++||+|.|+|+++.+..|.|++...      ....|+||.+++..
T Consensus         3 ~~~P~~GdiV~G~V~~I~~~G~fV~L~e~------~gieGlI~iSEls~   45 (262)
T PRK03987          3 KEWPEEGELVVGTVKEVKDFGAFVTLDEY------PGKEGFIHISEVAS   45 (262)
T ss_pred             CCCCCCCCEEEEEEEEEECCEEEEEECCC------CCcEEEEEHHHcCc
Confidence            45799999999999999999999999321      14799999999875

>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain

Probab=96.29  E-value=0.01  Score=36.98  Aligned_cols=35  Identities=26%  Similarity=0.260  Sum_probs=32.4

Q ss_pred             CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |++|.|+|+++.+..|.|+|        ...+.|+|+.++++.
T Consensus         1 G~~~~g~V~~i~~~g~~v~i--------~~~~~g~l~~~~l~~   35 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVEL--------GGGISGLVHISQIAH   35 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEE--------CCCCEEEEEhHHcCC
Confidence            79999999999999999999        667999999999875

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.

>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=96.19  E-value=0.013  Score=37.45  Aligned_cols=35  Identities=14%  Similarity=0.208  Sum_probs=32.4

Q ss_pred             CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |++|.|+|+++....+.|++        .....|++|.+++..
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l--------~~~v~g~i~~~~l~~   35 (69)
T cd05697           1 GQVVKGTIRKLRPSGIFVKL--------SDHIKGLVPPMHLAD   35 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEe--------cCCcEEEEEHHHCCC
Confidence            79999999999999999999        667999999999975

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.

>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=96.16  E-value=0.014  Score=37.19  Aligned_cols=35  Identities=11%  Similarity=0.046  Sum_probs=32.1

Q ss_pred             CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |+++.|+|+++.+..+.|++        .....|+||.+++..
T Consensus         1 g~~~~g~V~~v~~~G~~V~l--------~~~~~gli~~s~l~~   35 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSF--------YNNVKGFLPKSELSE   35 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEE--------CCCCEEEEEHHHcCh
Confidence            89999999999999999999        556899999999975

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.

>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain

Probab=96.04  E-value=0.017  Score=39.38  Aligned_cols=37  Identities=24%  Similarity=0.352  Sum_probs=33.0

Q ss_pred             CCCCCEEEEEEEEeccc--eEEEEEEEecCeecccceeEEEeccccc
Q 032397           74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRFFIFY  118 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~--~a~v~I~~v~~~~l~~~~~G~Ir~~dvr  118 (141)
                      |++|+++.|+|+++.+.  .|.|+|        .....|+||.+++.
T Consensus         5 ~~~G~iy~g~V~~i~~~~~GaFV~l--------~~g~~Gllh~seis   43 (88)
T cd04453           5 PIVGNIYLGRVKKIVPGLQAAFVDI--------GLGKNGFLHLSDIL   43 (88)
T ss_pred             CCCCCEEEEEEEEeccCCcEEEEEe--------CCCCEEEEEhHHcC
Confidence            68999999999999996  899999        55678999999884

RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th

>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa

Probab=95.71  E-value=0.025  Score=35.08  Aligned_cols=35  Identities=31%  Similarity=0.205  Sum_probs=31.9

Q ss_pred             CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |+++.|+|+++++..|.+++        .....|+++.++++.
T Consensus         1 g~~~~g~V~~i~~~G~fv~l--------~~~~~g~~~~~~l~~   35 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDI--------GVKQDGLIHISKMAD   35 (68)
T ss_pred             CCEEEEEEEEEecccEEEEc--------CCCCEEEEEHHHCCC
Confidence            78999999999999999999        556899999999976

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.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=95.67  E-value=0.0049  Score=56.28  Aligned_cols=64  Identities=17%  Similarity=0.134  Sum_probs=48.7

Q ss_pred             CeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEecc
Q 032397           36 GLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFF  115 (141)
Q Consensus        36 g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~  115 (141)
                      |.++++..+....       +.....|....     ..|++|+++.|+|+++.+..+.|+|        .....|+||++
T Consensus       590 G~V~i~~~~~~~~-------~~a~~~I~~~~-----~~~~~G~i~~G~V~~I~~~GafVei--------~~g~~GllHiS  649 (684)
T TIGR03591       590 GTVKIAASDGEAA-------EAAIKMIEGIT-----AEPEVGKIYEGKVVRIMDFGAFVEI--------LPGKDGLVHIS  649 (684)
T ss_pred             eEEEEEECcHHHH-------HHHHHHHHhhh-----cccccCcEEEEEEEEEeCCEEEEEE--------CCCcEEEEEHH
Confidence            7888777776555       11223444432     2489999999999999999999999        44689999999


Q ss_pred             ccch
Q 032397          116 IFYI  119 (141)
Q Consensus       116 dvr~  119 (141)
                      ++..
T Consensus       650 ei~~  653 (684)
T TIGR03591       650 EIAN  653 (684)
T ss_pred             HcCC
Confidence            9975

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).

>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=95.50  E-value=0.037  Score=35.45  Aligned_cols=35  Identities=31%  Similarity=0.441  Sum_probs=31.5

Q ss_pred             CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ||+|.|+|+++.+..+.+++        ...+.|+++..++..
T Consensus         1 G~~V~g~V~~i~~~G~~v~l--------~~~v~g~v~~~~l~~   35 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDF--------LSSFTGTVDFLHLDP   35 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEE--------cCCceEEEEHHHcCC
Confidence            89999999999999999999        566999999988864

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 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain

Probab=95.45  E-value=0.041  Score=34.34  Aligned_cols=35  Identities=17%  Similarity=0.150  Sum_probs=31.9

Q ss_pred             CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |+++.|+|+++.+..|.++|        .....|+++.++++.
T Consensus         1 g~~~~g~V~~v~~~G~~v~l--------~~~~~g~l~~~~l~~   35 (68)
T cd04472           1 GKIYEGKVVKIKDFGAFVEI--------LPGKDGLVHISELSD   35 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEe--------CCCCEEEEEhHHcCC
Confidence            78999999999999999999        556899999999976

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.

>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains

Probab=95.44  E-value=0.042  Score=36.41  Aligned_cols=38  Identities=16%  Similarity=0.116  Sum_probs=34.9

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      +++|+++.|+|+++....+.|++        .....|++|.+++..
T Consensus        12 ~~~G~i~~g~V~~v~~~G~fv~l--------~~~~~g~v~~~el~~   49 (83)
T cd04461          12 LKPGMVVHGYVRNITPYGVFVEF--------LGGLTGLAPKSYISD   49 (83)
T ss_pred             CCCCCEEEEEEEEEeeceEEEEc--------CCCCEEEEEHHHCCc
Confidence            68999999999999999999999        556899999999975

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.

>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain

Probab=95.36  E-value=0.043  Score=34.15  Aligned_cols=35  Identities=20%  Similarity=0.204  Sum_probs=30.9

Q ss_pred             CCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           76 PGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        76 ~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      +|+++.|+|+++....|.++|        . ...|+|+.+++..
T Consensus         1 ~g~~~~g~V~~v~~~g~~v~l--------~-~~~g~l~~~e~~~   35 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDL--------G-GVDGLLHISDMSW   35 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEE--------C-CeEEEEEhHHCCC
Confidence            599999999999999999998        3 4789999999864

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.

>PRK05807 hypothetical protein; Provisional

Probab=95.28  E-value=0.049  Score=40.12  Aligned_cols=37  Identities=14%  Similarity=0.156  Sum_probs=32.4

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .++|++|.|+|+.+++..|.|++   ++      ..|+||.+++..
T Consensus         3 ~~vG~vv~G~Vt~i~~~GafV~L---~~------~~Glvhiseis~   39 (136)
T PRK05807          3 LKAGSILEGTVVNITNFGAFVEV---EG------KTGLVHISEVAD   39 (136)
T ss_pred             ccCCCEEEEEEEEEECCeEEEEE---CC------EEEEEEhhhccc
Confidence            36899999999999999999999   22      489999999975

>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=95.18  E-value=0.056  Score=35.59  Aligned_cols=37  Identities=19%  Similarity=-0.014  Sum_probs=33.1

Q ss_pred             CCCCEEEEEEEEeccceEEEEEEEecCeecc-cceeEEEeccccch
Q 032397           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRFFIFYI  119 (141)
Q Consensus        75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~-~~~~G~Ir~~dvr~  119 (141)
                      +.|++|.|.|.++.+..+.+++        . ..+.|+|+++++..
T Consensus         3 ~~G~~v~g~V~si~d~G~~v~~--------g~~gv~Gfl~~~~~~~   40 (74)
T cd05694           3 VEGMVLSGCVSSVEDHGYILDI--------GIPGTTGFLPKKDAGN   40 (74)
T ss_pred             CCCCEEEEEEEEEeCCEEEEEe--------CCCCcEEEEEHHHCCc
Confidence            6899999999999999999998        4 46899999999864

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

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=95.00  E-value=0.01  Score=54.35  Aligned_cols=64  Identities=17%  Similarity=0.144  Sum_probs=49.3

Q ss_pred             CeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEecc
Q 032397           36 GLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFF  115 (141)
Q Consensus        36 g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~  115 (141)
                      |.++++..+...+       +..+..|+....     .|++|+++.|+|+++.+..+.|+|        .....|++|.+
T Consensus       593 G~v~i~~~~~~~~-------~~a~~~I~~~~~-----~~~vG~v~~G~V~~I~~fGafVei--------~~~~~GllhiS  652 (693)
T PRK11824        593 GTVKIAATDGEAA-------EAAKERIEGITA-----EPEVGEIYEGKVVRIVDFGAFVEI--------LPGKDGLVHIS  652 (693)
T ss_pred             ceEEEEcccHHHH-------HHHHHHHHHhcc-----cCcCCeEEEEEEEEEECCeEEEEE--------CCCCEEEEEee
Confidence            8888887777665       222334444332     379999999999999999999999        45689999999


Q ss_pred             ccch
Q 032397          116 IFYI  119 (141)
Q Consensus       116 dvr~  119 (141)
                      ++..
T Consensus       653 els~  656 (693)
T PRK11824        653 EIAD  656 (693)
T ss_pred             eccC
Confidence            9975

>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain

Probab=94.92  E-value=0.066  Score=34.26  Aligned_cols=35  Identities=17%  Similarity=0.136  Sum_probs=30.8

Q ss_pred             CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY  118 (141)
Q Consensus        75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr  118 (141)
                      +.|++|.|+|.++....+.++|        .. ..|+|+.++..
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdi--------g~-~eg~lp~~e~~   36 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDL--------GK-VEAILPKKEQI   36 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEc--------CC-eEEEeeHHHCC
Confidence            5799999999999999999999        44 78899988875

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.

>PHA02945 interferon resistance protein; Provisional

Probab=94.82  E-value=0.087  Score=36.39  Aligned_cols=40  Identities=15%  Similarity=0.120  Sum_probs=32.0

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEecccc
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIF  117 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dv  117 (141)
                      --+|++|++|+|+|+. ....|.+++.--      ...+|+|+.+.+
T Consensus         6 y~~P~~GelvigtV~~-~d~ga~v~L~EY------~g~eg~i~~sev   45 (88)
T PHA02945          6 YSLPNVGDVLKGKVYE-NGYALYIDLFDY------PHSEAILAESVQ   45 (88)
T ss_pred             ecCCCCCcEEEEEEEe-cCceEEEEeccc------CCcEEEEEeehh
Confidence            3579999999999999 888899999321      147888888855

>PF01016 Ribosomal_L27: Ribosomal L27 protein; InterPro: IPR001684 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=94.17  E-value=0.06  Score=36.66  Aligned_cols=47  Identities=17%  Similarity=0.316  Sum_probs=39.4

Q ss_pred             ccccCCcEEecCCccCCC--CCeeecCcEEEeCCCCeEEEEEeeEEEeeC
Q 032397            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTLS   50 (141)
Q Consensus         3 ~~~~~~~iVlPGd~L~~~--~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~   50 (141)
                      +|..+++.|.||+.|...  ..|-||.++..-. |..|+|..-|.+.++.
T Consensus        22 vK~~~G~~V~~G~IivRQRgtk~hPG~NVg~Gr-D~TLfAl~~G~V~f~~   70 (81)
T PF01016_consen   22 VKKFGGQFVKAGNIIVRQRGTKFHPGENVGMGR-DHTLFALVDGRVKFTK   70 (81)
T ss_dssp             ESSSTTCEESSTSEEEEBSSSSSEEBTTEEEET-TSEEEESSSCEEEEEE
T ss_pred             EEEeCCEEEcCCCEEEEeCCCcCcCCCCEEECC-CCcEEEecCEEEEEEE
Confidence            577889999999999643  4599999998773 4899999999999963

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. L27 is a protein from the large (50S) subunit; it is essential for ribosome function, but its exact role is unclear. It belongs to a family of ribosomal proteins, examples of which are found in bacteria, chloroplasts of plants and red algae and the mitochondria of fungi (e.g. MRP7 from yeast mitochondria). The schematic relationship between these groups of proteins is shown below. Bacterial L27 Nxxxxxxxxx Algal L27 Nxxxxxxxxx Plant L27 tttttNxxxxxxxxxxxxx Yeast MRP7 tttNxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 't': transit peptide. 'N': N-terminal of mature protein. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZJQ_T 2ZJP_T 3PIP_T 3DLL_T 3PIO_T 1Y69_U 3CF5_T 2ZJR_T 1VSA_U 3PYT_W ....

>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease

Probab=94.15  E-value=0.26  Score=32.26  Aligned_cols=38  Identities=18%  Similarity=0.190  Sum_probs=33.9

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .++|+++.|+|+++++..+.+++        .....|+++.+++..
T Consensus        14 ~~~G~~~~g~V~~i~~~G~fV~l--------~~~~~Glv~~se~~~   51 (77)
T cd04473          14 LEVGKLYKGKVNGVAKYGVFVDL--------NDHVRGLIHRSNLLR   51 (77)
T ss_pred             CCCCCEEEEEEEeEecceEEEEE--------CCCcEEEEEchhccC
Confidence            68999999999999999999999        557999999998653

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.

>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain

Probab=94.03  E-value=0.12  Score=32.45  Aligned_cols=34  Identities=12%  Similarity=0.205  Sum_probs=31.0

Q ss_pred             CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY  118 (141)
Q Consensus        77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr  118 (141)
                      |+++.|+|+++++..+.|++        .....|++|.+++.
T Consensus         1 G~~~~g~V~~i~~~G~fv~l--------~~~~~Glv~~~~l~   34 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGL--------DGGIDGLVHISDIS   34 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEe--------CCCCEEEEEHHHCC
Confidence            78999999999999999999        45689999999986

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.

>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain

Probab=93.96  E-value=0.17  Score=32.30  Aligned_cols=36  Identities=14%  Similarity=0.249  Sum_probs=32.5

Q ss_pred             CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY  118 (141)
Q Consensus        75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr  118 (141)
                      .+|+++.|+|+++++..+.|++        .....|++|.+++.
T Consensus         2 ~~g~~~~g~V~~i~~~G~fv~l--------~~~~~Gl~~~~~l~   37 (72)
T cd05689           2 PEGTRLFGKVTNLTDYGCFVEL--------EEGVEGLVHVSEMD   37 (72)
T ss_pred             cCCCEEEEEEEEEEeeEEEEEc--------CCCCEEEEEEEecc
Confidence            4799999999999999999999        55689999999986

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.

>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

Probab=93.93  E-value=0.13  Score=42.13  Aligned_cols=43  Identities=21%  Similarity=0.198  Sum_probs=36.5

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .-.|.+|++|+|+|.+|..-.|.+.+.--      ...+|+||.+.|..
T Consensus         6 ~~~PeeGEiVv~tV~~V~~~GAyv~L~EY------~g~Eg~ihiSEvas   48 (269)
T COG1093           6 REYPEEGEIVVGTVKQVADYGAYVELDEY------PGKEGFIHISEVAS   48 (269)
T ss_pred             cCCCCCCcEEEEEEEEeeccccEEEeecc------CCeeeeEEHHHHHH
Confidence            56799999999999999999999999321      13789999999976

>PRK05435 rpmA 50S ribosomal protein L27; Validated

Probab=93.88  E-value=0.18  Score=34.37  Aligned_cols=46  Identities=20%  Similarity=0.291  Sum_probs=38.1

Q ss_pred             ccccCCcEEecCCccCCC--CCeeecCcEEEeCCCCeEEEEEeeEEEee
Q 032397            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTL   49 (141)
Q Consensus         3 ~~~~~~~iVlPGd~L~~~--~e~~~G~GtY~~~~~g~I~Asv~G~~~~~   49 (141)
                      +|......|.||+.|...  ..|-||.++-.-. |..|+|.+.|.+++.
T Consensus        23 vK~~~g~~V~~G~IivRQRGtk~~PG~nVg~Gr-D~TlfA~~~G~V~f~   70 (82)
T PRK05435         23 VKRFGGQFVKAGNIIVRQRGTKFHPGVNVGRGK-DHTLFALVDGVVKFE   70 (82)
T ss_pred             eEecCCEEEcCCcEEEEeCCCeECCCCCEeecC-CceEEEecceEEEEE
Confidence            577788999999998644  3499999987653 489999999999995

>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional

Probab=93.63  E-value=0.15  Score=38.94  Aligned_cols=39  Identities=23%  Similarity=0.164  Sum_probs=34.6

Q ss_pred             CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      +-|.+|++|.|+|++++...+.+++        . ++.|+++.+++..
T Consensus        77 f~P~~GEVv~g~V~~v~~~Gi~V~l--------g-~~~g~v~~~~l~~  115 (187)
T PRK08563         77 FKPELQEVVEGEVVEVVEFGAFVRI--------G-PVDGLLHISQIMD  115 (187)
T ss_pred             EeccCCCEEEEEEEEEEccEEEEEE--------e-CceEEEEcHHcCC
Confidence            4599999999999999999999999        3 5889999988865

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=93.36  E-value=0.12  Score=47.57  Aligned_cols=38  Identities=18%  Similarity=0.209  Sum_probs=34.4

Q ss_pred             CCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY  118 (141)
Q Consensus        73 ~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr  118 (141)
                      .|++|+++.|+|+++.+-.|.|+|        .....|++|++++.
T Consensus       644 ~~~vG~i~~GkV~~I~dfGaFVel--------~~G~eGLvHISeis  681 (719)
T TIGR02696       644 MPEVGERFLGTVVKTTAFGAFVSL--------LPGKDGLLHISQIR  681 (719)
T ss_pred             cCCCCCEEEEEEEEEECceEEEEe--------cCCceEEEEhhhcc
Confidence            489999999999999999999999        45689999999774

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

Probab=93.34  E-value=0.14  Score=45.74  Aligned_cols=46  Identities=20%  Similarity=0.084  Sum_probs=38.3

Q ss_pred             CCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch-h-hhHHHHh
Q 032397           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-E-LLMHLLY  127 (141)
Q Consensus        73 ~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~-v~~~~~f  127 (141)
                      -.++|++|.|.|+++++-.|.|+|        .. +.|++|++++.- + ..+.+-|
T Consensus       189 ~l~~G~vV~G~V~~It~~GafVdi--------gG-vdGLlHiseiS~~rv~~P~~vv  236 (541)
T COG0539         189 KLEVGEVVEGVVKNITDYGAFVDI--------GG-VDGLLHISEISWKRVDHPSEVV  236 (541)
T ss_pred             cCCCCceEEEEEEEeecCcEEEEe--------cC-eeeEEehhhccccccCCHHHhc
Confidence            368999999999999999999999        44 999999999985 2 4455544

>CHL00121 rpl27 ribosomal protein L27; Reviewed

Probab=93.07  E-value=0.22  Score=34.25  Aligned_cols=60  Identities=20%  Similarity=0.268  Sum_probs=43.5

Q ss_pred             ccccCCcEEecCCccCCC--CCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecC
Q 032397            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (141)
Q Consensus         3 ~~~~~~~iVlPGd~L~~~--~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~   67 (141)
                      +|......|.||+.|...  ..|-||.++=.- +|..|+|...|.++++.    ...++..|+|.|.
T Consensus        23 vK~~~gq~V~~G~IivRQRGtk~hPG~NVg~G-rD~TlfAl~~G~V~f~~----~~~~~~~vsv~~~   84 (86)
T CHL00121         23 VKRFGGEKVSAGNILIRQRGTKFKPGLNVGCG-KDFTLYALIDGFVKFKK----KNKKQKSINVINI   84 (86)
T ss_pred             eEEcCCEEEcCCcEEEEcCCCeECCCCccccc-CCceEEEccceEEEEEE----eCCCCEEEEEeec
Confidence            567788999999998654  348888887554 24899999999999952    1123457777653

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=92.60  E-value=0.26  Score=41.06  Aligned_cols=38  Identities=26%  Similarity=0.267  Sum_probs=34.4

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .++|++|.|+|+++....+.|+|        .....|+|+.+++..
T Consensus        29 ~~~G~iv~G~V~~i~~~g~~Vdi--------g~k~~g~lp~sEis~   66 (318)
T PRK07400         29 FKPGDIVNGTVFSLEPRGALIDI--------GAKTAAFMPIQEMSI   66 (318)
T ss_pred             cCCCCEEEEEEEEEECCEEEEEE--------CCCeEEEEEHHHhcc
Confidence            69999999999999999999999        666789999999875

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=92.39  E-value=0.3  Score=40.70  Aligned_cols=38  Identities=26%  Similarity=0.208  Sum_probs=33.4

Q ss_pred             CCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        73 ~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      -.++|++|.|+|+++++..+.|++.         ...|++|.+++..
T Consensus       193 ~~k~G~vv~G~V~~I~~~G~fV~i~---------gv~Gllhisels~  230 (318)
T PRK07400        193 RLEVGEVVVGTVRGIKPYGAFIDIG---------GVSGLLHISEISH  230 (318)
T ss_pred             cCCCCCEEEEEEEEEECCeEEEEEC---------CEEEEEEHHHccc
Confidence            3688999999999999999999982         3579999999986

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=91.99  E-value=0.25  Score=43.68  Aligned_cols=38  Identities=29%  Similarity=0.206  Sum_probs=34.6

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .++||+|.|+|+++....+.|+|        .....|+|+..++..
T Consensus        33 ~~~GdiV~G~V~~v~~~gv~VdI--------g~k~eG~Ip~~Els~   70 (486)
T PRK07899         33 FNDGDIVEGTVVKVDRDEVLLDI--------GYKTEGVIPSRELSI   70 (486)
T ss_pred             CCCCCEEEEEEEEEECCcEEEEE--------CCCcEEEEEHHHhcc
Confidence            68999999999999999999999        667899999998864

>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide

Probab=91.91  E-value=0.38  Score=31.33  Aligned_cols=38  Identities=13%  Similarity=0.246  Sum_probs=30.9

Q ss_pred             CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |+++.|+|+++.+..+.++|.-.     ..+..|+++.+++..
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~-----~~~~~gll~~s~l~~   38 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGL-----KGRKEGLVHISQLSF   38 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCC-----CCCcEEEEEhHhccC
Confidence            78999999999999999999210     035789999999875

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.

>TIGR00062 L27 ribosomal protein L27

Probab=91.14  E-value=0.48  Score=32.37  Aligned_cols=46  Identities=20%  Similarity=0.328  Sum_probs=37.6

Q ss_pred             ccccCCcEEecCCccCCC--CCeeecCcEEEeCCCCeEEEEEeeEEEee
Q 032397            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTL   49 (141)
Q Consensus         3 ~~~~~~~iVlPGd~L~~~--~e~~~G~GtY~~~~~g~I~Asv~G~~~~~   49 (141)
                      +|......|.||+.|-..  ..|-||.++-.-. |..|+|.+.|.++++
T Consensus        23 vK~~~gq~V~~G~IivRQRGtk~hPG~nVg~Gr-D~TlfAl~~G~V~f~   70 (83)
T TIGR00062        23 VKRAGGQFVRAGSIIVRQRGTKFHPGNNVGMGK-DHTLFALSDGVVKFE   70 (83)
T ss_pred             eEecCCEEEcCCcEEEEcCCceECCCCcccccC-CCeEEEecceEEEEE
Confidence            577788999999998654  3489999887652 489999999999995

Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.

>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=90.78  E-value=0.6  Score=30.08  Aligned_cols=35  Identities=26%  Similarity=0.290  Sum_probs=30.4

Q ss_pred             CCEEE-EEEEEe-ccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           77 GSVVI-ARVTKV-MTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        77 GdiVi-g~V~~v-~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |+++- |+|+++ ....|.|++        .....|+||.+++..
T Consensus         1 G~v~~~g~V~~v~~~~G~~V~l--------~~gv~G~i~~s~l~~   37 (71)
T cd05696           1 GAVVDSVKVTKVEPDLGAVFEL--------KDGLLGFVHISHLSD   37 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEe--------CCCCEEEEEHHHCCc
Confidence            67888 999999 578899999        667999999999964

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 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form

Probab=90.43  E-value=0.58  Score=35.65  Aligned_cols=39  Identities=21%  Similarity=0.228  Sum_probs=34.7

Q ss_pred             CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      +-|.+|+++.|+|++++...+.+++        . ++.|+++.++...
T Consensus        77 f~p~~gEvv~G~V~~v~~~GifV~l--------g-~~~gi~~~~~l~~  115 (179)
T TIGR00448        77 FKPELGEIVEGEVIEIVEFGAFVSL--------G-PFDGLFHVSQVTD  115 (179)
T ss_pred             EeccCCCEEEEEEEEEEeeEEEEEe--------C-CceEEEEcHHhCC
Confidence            4588999999999999999999998        3 5899999998874

This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.

>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

Probab=90.38  E-value=0.45  Score=42.66  Aligned_cols=41  Identities=29%  Similarity=0.280  Sum_probs=33.3

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ..-+++||+|.|.|+.+..++|.|+|        ..--.|+|+.+.+..
T Consensus        16 ~~~~~~G~vV~G~Vv~i~~~~v~Vdi--------g~Kseg~ip~~E~~~   56 (541)
T COG0539          16 DEEFEPGDVVKGTVVSIEKDGVLVDI--------GGKSEGVIPISEFSN   56 (541)
T ss_pred             hhccCCCCEEEEEEEEEeCCeEEEEe--------cCccccEeEHHHhcc
Confidence            45689999999999999999999999        444567777766654

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=90.36  E-value=0.46  Score=41.81  Aligned_cols=37  Identities=16%  Similarity=0.204  Sum_probs=33.5

Q ss_pred             CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ++|++|.|+|+++++..+.|++        .....|++|.+++..
T Consensus       378 ~vG~~v~G~V~~i~~~G~FV~l--------~~gv~Gli~~se~s~  414 (491)
T PRK13806        378 APGTTVTGTVEKRAQFGLFVNL--------APGVTGLLPASVISR  414 (491)
T ss_pred             CCCCEEEEEEEEEecCceEEEc--------CCCcEEEEEHHHcCc
Confidence            4799999999999999999999        667999999998874

>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain

Probab=89.68  E-value=1  Score=28.27  Aligned_cols=34  Identities=18%  Similarity=0.177  Sum_probs=29.7

Q ss_pred             CCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           77 GSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        77 GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |++|.|+|+++....+.+++        . ...|.|+.+++..
T Consensus         1 G~iv~g~V~~v~~~G~~v~l--------~-g~~gfip~s~~~~   34 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDI--------E-GVRAFLPASQVDL   34 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE--------C-CEEEEEEHHHCCC
Confidence            78999999999999999998        3 4899999988864

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.

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=89.60  E-value=0.63  Score=40.92  Aligned_cols=46  Identities=15%  Similarity=0.109  Sum_probs=37.7

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch-h-hhHHHHh
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-E-LLMHLLY  127 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~-v~~~~~f  127 (141)
                      .++|++|.|+|+++.+..+.|+|        .....|+||.+++.. + ..+.+.|
T Consensus       200 l~~G~iv~G~V~~v~~~G~fV~l--------~~gv~g~v~~sels~~~~~~~~~~~  247 (491)
T PRK13806        200 VKEGDVVEGTVTRLAPFGAFVEL--------APGVEGMVHISELSWSRVQKADEAV  247 (491)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEc--------CCCcEEEEEHHHCCCccccChhHhc
Confidence            68999999999999999999998        556889999999975 3 3344444

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=89.45  E-value=0.6  Score=44.01  Aligned_cols=55  Identities=13%  Similarity=-0.106  Sum_probs=41.3

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch-hhh-HHHHhhhhccccccc
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-ELL-MHLLYGYLGSCKMQL  137 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~v~-~~~~f~~vis~gd~~  137 (141)
                      .++||+|.|+|+++++..++|++        .....|+++.+++.. +.+ ..+. .+.++.||..
T Consensus       750 ~~vG~iV~GkV~~v~~~GvFVeL--------~~gVeGlI~~s~lsdd~~~~~~~~-~~~f~vGD~V  806 (863)
T PRK12269        750 YGVGSTVEGEVSSVTDFGIFVRV--------PGGVEGLVRKQHLVENRDGDPGEA-LRKYAVGDRV  806 (863)
T ss_pred             CCCCCEEEEEEEEEecCeEEEEc--------CCCeEEEEEHHHcCCcccccchhh-ccccCCCCEE
Confidence            46899999999999999999999        667999999999875 322 2222 3345556543

>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain

Probab=89.41  E-value=1.2  Score=28.70  Aligned_cols=36  Identities=8%  Similarity=0.054  Sum_probs=31.3

Q ss_pred             CCCEEEEEEEEeccceEEEEEEEecCeeccc-ceeEEEeccccch
Q 032397           76 PGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRFFIFYI  119 (141)
Q Consensus        76 ~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~-~~~G~Ir~~dvr~  119 (141)
                      +|+++-|.|++++...+.+++        .. ...|+++.+++..
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l--------~~~~~~G~v~~~~l~~   37 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVEL--------DNLTVEGLVHVSTLGD   37 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEe--------cCCCEEEEEEEEecCC
Confidence            489999999999999999999        43 5889999998864

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.

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=88.57  E-value=0.81  Score=39.66  Aligned_cols=37  Identities=22%  Similarity=0.229  Sum_probs=33.6

Q ss_pred             CCCCCEEEEEEEEeccc--eEEEEEEEecCeecccceeEEEeccccc
Q 032397           74 PEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRFFIFY  118 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~--~a~v~I~~v~~~~l~~~~~G~Ir~~dvr  118 (141)
                      +.+|+|..|+|+++.+.  .|+|+|        ...-.|+||.+|+.
T Consensus        23 ~~vGnIY~GrV~~i~p~l~aAFVdi--------G~~k~gfL~~~d~~   61 (414)
T TIGR00757        23 QLKGNIYKGRVTRILPSLQAAFVDI--------GLEKNGFLHASDIG   61 (414)
T ss_pred             CCCCCEEEEEEeeecCCCceEEEEc--------CCCceEEEEHHHcC
Confidence            46899999999999999  799999        77788999999985

The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.

>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain

Probab=87.89  E-value=1.1  Score=30.54  Aligned_cols=33  Identities=21%  Similarity=0.170  Sum_probs=28.6

Q ss_pred             CEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           78 SVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        78 diVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      +++.|+|+++....+.|++        . +..|++|.++++.
T Consensus         1 ~vv~g~V~~i~~~GifV~l--------~-~v~G~v~~~~l~~   33 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRI--------G-PVDGLLHISQIMD   33 (99)
T ss_pred             CEEEEEEEEEEeccEEEEE--------c-CeEEEEEEEEccC
Confidence            4789999999999999999        2 3689999999875

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.

>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain

Probab=87.30  E-value=0.97  Score=26.99  Aligned_cols=32  Identities=9%  Similarity=0.163  Sum_probs=28.2

Q ss_pred             EEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           80 VIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        80 Vig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |.|+|+++....|.|++        .....|+++.+++..
T Consensus         1 v~g~V~~v~~~g~~v~l--------~~~~~g~~~~~~~~~   32 (65)
T cd00164           1 VTGKVVSITKFGVFVEL--------EDGVEGLVHISELSD   32 (65)
T ss_pred             CEEEEEEEEeeeEEEEe--------cCCCEEEEEHHHCCC
Confidence            57999999999999999        567899999999875

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.

>TIGR00717 rpsA ribosomal protein S1

Probab=86.86  E-value=1.4  Score=38.57  Aligned_cols=38  Identities=26%  Similarity=0.241  Sum_probs=33.9

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .++|++|.|.|+++.++.+.|+|        .....|+|+.+++..
T Consensus        16 ~~~G~~v~g~V~~i~~~~~~v~~--------g~k~~g~i~~~E~~~   53 (516)
T TIGR00717        16 TRPGSIVKGTVVAINKDTVFVDV--------GLKSEGRIPKEEFLD   53 (516)
T ss_pred             CCCCCEEEEEEEEEECCEEEEEc--------CCCcEEEEEHHHhcC
Confidence            58899999999999999999999        666899999888863

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=86.43  E-value=1.2  Score=42.31  Aligned_cols=39  Identities=15%  Similarity=0.182  Sum_probs=34.5

Q ss_pred             CCCCCCEEE-EEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           73 VPEPGSVVI-ARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        73 ~P~~GdiVi-g~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .|++|+++. |+|++|.+-.++|+|        .....|++|++++..
T Consensus       750 ~~~vG~iy~~g~V~~I~~FGaFVeL--------~~g~EGLVHISeLs~  789 (891)
T PLN00207        750 VPTVGDIYRNCEIKSIAPYGAFVEI--------APGREGLCHISELSS  789 (891)
T ss_pred             CcCCCcEEECcEEEEEeccEEEEEe--------CCCCEEEEEhhhcCC
Confidence            489999995 699999999999999        555799999999975

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=85.52  E-value=1.4  Score=41.67  Aligned_cols=36  Identities=36%  Similarity=0.452  Sum_probs=28.9

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEecccc
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIF  117 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dv  117 (141)
                      +++|++|.|+|++++.+.+.|+|        ..-..|+|..+++
T Consensus       319 ~~~G~iV~G~Vv~i~~~~v~Vdi--------G~K~eGiI~~~E~  354 (863)
T PRK12269        319 PEPGSVRMGTVVQVNAGTVFVDI--------GGKSEGRVPVEEF  354 (863)
T ss_pred             CCCCCEEEEEEEEEECCEEEEEe--------CCCceEEeEHHHh
Confidence            68999999999999999999999        4444555555544

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=85.47  E-value=1.3  Score=39.17  Aligned_cols=37  Identities=16%  Similarity=0.187  Sum_probs=33.6

Q ss_pred             CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ++|++|.|+|++++...+.|+|        .....|+||.+|+..
T Consensus       372 ~~G~~v~g~V~~v~~~G~fV~l--------~~~v~g~i~~s~l~~  408 (565)
T PRK06299        372 PVGDVVEGKVKNITDFGAFVGL--------EGGIDGLVHLSDISW  408 (565)
T ss_pred             CCCCEEEEEEEEEecceEEEEC--------CCCCEEEEEHHHcCc
Confidence            6899999999999999999999        667889999999874

>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain

Probab=83.97  E-value=2.2  Score=29.16  Aligned_cols=30  Identities=33%  Similarity=0.544  Sum_probs=22.8

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecC
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGA  101 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~  101 (141)
                      ++..++||+|+|||..+...+ ..++-|++.
T Consensus        47 rp~L~~GDlV~ArV~~~~~~~-~~eLtc~~~   76 (86)
T cd05790          47 RPNLNVGDLVYARVVKANRDM-EPELSCVDS   76 (86)
T ss_pred             cccCCCCCEEEEEEEecCCCC-CeEEEEeCC
Confidence            455699999999999998764 456666653

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".

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=83.97  E-value=1.9  Score=38.23  Aligned_cols=37  Identities=22%  Similarity=0.267  Sum_probs=33.3

Q ss_pred             CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ++|++|.|+|+++.+..+.|++        .....|++|.+++..
T Consensus       292 ~vG~vv~G~V~~I~~fGvFVeL--------~~gieGLvh~SeLs~  328 (486)
T PRK07899        292 AIGQIVPGKVTKLVPFGAFVRV--------EEGIEGLVHISELAE  328 (486)
T ss_pred             CCCCEEEEEEEEEeccEEEEEe--------CCCcEEEEEHHHcCc
Confidence            5799999999999999999999        557899999998875

>KOG4600 consensus Mitochondrial ribosomal protein MRP7 (L2) [Translation, ribosomal structure and biogenesis]

Probab=82.41  E-value=4.1  Score=30.41  Aligned_cols=69  Identities=22%  Similarity=0.293  Sum_probs=47.2

Q ss_pred             ccccCCcEEecCCccCCCCC--eeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCC
Q 032397            3 VKEEEMVLVTPGEVLGKATE--VKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPE   75 (141)
Q Consensus         3 ~~~~~~~iVlPGd~L~~~~e--~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~   75 (141)
                      +|..++..|.||+.|...-.  |-||..+=+-. |-.|||-.-|.++..+.....  .++.|.|.+... ..+|.
T Consensus        50 vKk~egq~V~~G~IIvrQRgtkfHPG~nVGiGK-DhtifaL~eG~Vrf~k~~~~~--~Rk~i~V~~~~~-~~l~~  120 (144)
T KOG4600|consen   50 VKKYEGQSVIPGNIIVRQRGTKFHPGDNVGIGK-DHTIFALEEGRVRFEKSKITP--PRKWIGVDPRGG-LPLPP  120 (144)
T ss_pred             ceecCCeeeecccEEEEecccccCCCcccccCC-cceEEEeeccEEEEEEccCCC--CcceEEEeecCC-ccCCC
Confidence            56678889999999976543  66666554332 367999999999996532222  367899998763 33343

>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

Probab=80.96  E-value=2.8  Score=38.15  Aligned_cols=40  Identities=20%  Similarity=0.197  Sum_probs=33.8

Q ss_pred             CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .-.++|++|.|+|+++..+.+.|++        .....|+|+..++..
T Consensus       298 ~~l~~G~iV~G~V~~v~~~gv~Vdi--------g~~~~G~lp~~els~  337 (647)
T PRK00087        298 KQIRRGDIVKGTVVSVNENEVFVDV--------GYKSEGVIPLRELTL  337 (647)
T ss_pred             hhccCCCEEEEEEEEEECCEEEEEE--------CCCeEEEEEHHHhcc
Confidence            3469999999999999999999998        556788888887763

>TIGR00717 rpsA ribosomal protein S1

Probab=80.70  E-value=2.9  Score=36.52  Aligned_cols=37  Identities=19%  Similarity=0.229  Sum_probs=31.9

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY  118 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr  118 (141)
                      -++|+++.|+|+++.+..+.|++        .....|+++.+++.
T Consensus       270 ~~~G~i~~g~V~~v~~~G~fV~l--------~~~v~g~v~~sels  306 (516)
T TIGR00717       270 FPVGDKITGRVTNLTDYGVFVEI--------EEGIEGLVHVSEMS  306 (516)
T ss_pred             ccCCCEEEEEEEEeeCCcEEEEe--------CCCCEEEEEHHHcC
Confidence            36899999999999999999998        55678888887764

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.

>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

Probab=80.20  E-value=3.3  Score=37.71  Aligned_cols=37  Identities=16%  Similarity=0.292  Sum_probs=33.7

Q ss_pred             CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ++|++|.|+|+++++..+.|++        .....|+++.+++..
T Consensus       561 ~~G~~v~g~V~~i~~~G~fV~l--------~~~i~Gli~~sel~~  597 (647)
T PRK00087        561 PVGSIVLGKVVRIAPFGAFVEL--------EPGVDGLVHISQISW  597 (647)
T ss_pred             cCCeEEEEEEEEEECCeEEEEE--------CCCCEEEEEhhhcCc
Confidence            6899999999999999999998        567999999999876

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=80.17  E-value=4  Score=34.41  Aligned_cols=37  Identities=22%  Similarity=0.222  Sum_probs=32.1

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .++|++|.|+|+++.+..+.|++        . ...|+||.+++..
T Consensus       190 ~~~G~~v~g~V~~v~~~G~fV~l--------~-~v~g~v~~sels~  226 (390)
T PRK06676        190 LKEGDVVEGTVARLTDFGAFVDI--------G-GVDGLVHISELSH  226 (390)
T ss_pred             CCCCCEEEEEEEEEecceEEEEe--------C-CeEEEEEHHHcCc
Confidence            58999999999999999999998        2 3679999988864

>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional

Probab=80.10  E-value=3.8  Score=31.36  Aligned_cols=40  Identities=18%  Similarity=-0.089  Sum_probs=34.3

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ..-|-.|.+|.|+|++++...+.+++         .+|.+.|+.+.+.+
T Consensus        76 vFrPf~gEVv~g~V~~v~~~G~~v~~---------Gp~~ifI~~~~l~~  115 (176)
T PTZ00162         76 VFKPFKDEVLDAIVTDVNKLGFFAQA---------GPLKAFVSRSAIPP  115 (176)
T ss_pred             EEecCCCCEEEEEEEEEecceEEEEe---------eCeEEEEcHHHCCC
Confidence            35599999999999999999999999         36778888887764

>PF01959 DHQS: 3-dehydroquinate synthase (EC 4

Probab=80.01  E-value=9.8  Score=32.54  Aligned_cols=40  Identities=18%  Similarity=0.370  Sum_probs=34.3

Q ss_pred             EEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEee
Q 032397           10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTL   49 (141)
Q Consensus        10 iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~   49 (141)
                      +.+||++=.--+|..+|.-+.+-+.+|.-+..++|++++.
T Consensus       246 v~~pg~kT~YLSEL~sG~~VlvVd~~G~tR~~~VGRvKIE  285 (354)
T PF01959_consen  246 VLMPGGKTRYLSELRSGDEVLVVDADGRTRTAIVGRVKIE  285 (354)
T ss_pred             EEcCCCceeehhhhcCCCEEEEEeCCCCEEEEEeeEEEEe
Confidence            4678988776678999999887777799999999999995

6.1.3); InterPro: IPR002812 3-Dehydroquinate synthase (4.2.3.4 from EC) is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyses the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid []. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	141
2nn6_I	209	Structure Of The Human Rna Exosome Composed Of Rrp4		3e-05

>pdb|2NN6|I Chain I, Structure Of The Human Rna Exosome Composed Of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40 Length = 209

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 30/101 (29%), Positives = 46/101 (45%), Gaps = 6/101 (5%)
Query: 13  PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
           PGE L    E   G G Y    +G +++SL G L   S         P V V        
Sbjct: 24  PGERLCNLEEGSPGSGTYT--RHGYIFSSLAGCLMKSS----ENGALPVVSVVRETESQL 77
Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
           +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR
Sbjct: 78  LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIR 118

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	141
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	9e-21
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	2e-14
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	4e-14
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	9e-11
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	3e-09
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	1e-07

>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 Length = 209

 Score = 82.8 bits (204), Expect = 9e-21
 Identities = 29/104 (27%), Positives = 45/104 (43%), Gaps = 6/104 (5%)

Query: 10  LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
              PGE L    E   G G Y    +G +++SL G L             P V V     
Sbjct: 21  YCIPGERLCNLEEGSPGSGTYT--RHGYIFSSLAGCLMK----SSENGALPVVSVVRETE 74

Query: 70  HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
              +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR
Sbjct: 75  SQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIR 118

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A Length = 179

 Score = 65.8 bits (160), Expect = 2e-14
 Identities = 24/108 (22%), Positives = 39/108 (36%), Gaps = 14/108 (12%)

Query: 8   MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH 67
           M  V PG+ +G A E   G+G Y     G ++A++ G L             P       
Sbjct: 1   MRFVMPGDRIGSAEEYVKGEGVYE--EGGELFAAVAGKLIIKDRVAKVESISPI------ 52

Query: 68  KAHGPVPEPGSVVIARVTKVMTRMASADIMCV--GAKSVREKFSGIIR 113
               P    G VV+ RV  +   +A  ++       +    +  GI+ 
Sbjct: 53  ----PEIVKGDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILH 96

>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 PDB: 2jea_I* 2jeb_I* 3l7z_C Length = 251

 Score = 65.9 bits (160), Expect = 4e-14
 Identities = 21/96 (21%), Positives = 34/96 (35%), Gaps = 10/96 (10%)

Query: 3  VKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTV 62
          +  +   +V PGE+L    E +     Y+ K N   Y+++ GL            +    
Sbjct: 11 IVLQPRSIVVPGELLA-EGEFQIPWSPYILKINSKYYSTVVGLFD---------VKDTQF 60

Query: 63 EVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMC 98
          EV   +     P+   +VI  V  V       DI  
Sbjct: 61 EVIPLEGSFYYPKINDIVIGLVEDVEIYGWVVDIKA 96

>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 Length = 308

 Score = 57.1 bits (137), Expect = 9e-11
 Identities = 19/97 (19%), Positives = 36/97 (37%), Gaps = 12/97 (12%)

Query: 4   KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVE 63
           ++ +  LV PG+ +   T    G G Y+      + AS+ G +               + 
Sbjct: 35  RDTKKHLVVPGDTITTDTGFMRGHGTYM--GEEKLIASVAGSVE---------RVNKLIC 83

Query: 64  VTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVG 100
           V   K    + E G +V+ R+T+V  +    +     
Sbjct: 84  VKALKTR-YIGEVGDIVVGRITEVQQKRWKVETNSRL 119

>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1 Length = 235

 Score = 52.4 bits (125), Expect = 3e-09
 Identities = 24/95 (25%), Positives = 34/95 (35%), Gaps = 11/95 (11%)

Query: 4  KEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVE 63
          ++    +V PGE L +  E       YV  + G+  A++ GLLR                
Sbjct: 5  RQLAGRIVVPGEPLPEEVEAS---PPYVIDYKGVKRATVVGLLRE-------KGDGGGRA 54

Query: 64 VTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMC 98
              K    VP+ G VVI  +  V       DI  
Sbjct: 55 FVKLKEI-YVPQAGDVVIGLIQSVGIMNWFVDINS 88

>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 Length = 229

 Score = 47.8 bits (113), Expect = 1e-07
 Identities = 26/89 (29%), Positives = 33/89 (37%), Gaps = 13/89 (14%)

Query: 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA 69
          +V PG++L       AG G YV    G VYA + GL                V V   K 
Sbjct: 4  IVLPGDLLSTN-PRAAGYGTYV--EGGKVYAKIIGLFDQ---------TETHVRVIPLKG 51

Query: 70 HGPVPEPGSVVIARVTKVMTRMASADIMC 98
              P  G VVI  + +V     + DI  
Sbjct: 52 R-YTPSVGDVVIGIIREVAANGWAVDIYS 79

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	141
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	99.95
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	99.95
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	99.9
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	99.9
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	99.89
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	99.87
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	99.87
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	98.58
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	97.69
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	97.23
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	97.12
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	97.03
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	96.95
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	96.95
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	96.88
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	96.8
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	96.59
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	96.55
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	96.33
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	96.18
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	94.78
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	94.78
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	94.24
2bh8_A	101	1B11; transcription, molecular evolution, unique a	93.45
3v2d_0	85	50S ribosomal protein L27; ribosome associated inh	93.12
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	93.12
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	92.47
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	92.43
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	92.27
3r8s_W	76	50S ribosomal protein L27; protein biosynthesis, R	91.55
2zjr_T	91	50S ribosomal protein L27; ribosome, large ribosom	91.06
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	89.68
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	89.53
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	88.92
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	88.53
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	87.21
2ftc_O	69	L27MT, MRP-L27, mitochondrial 39S ribosomal protei	87.13
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	86.78
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	86.4
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	86.28
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	85.4
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	85.29
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	85.28
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	83.46
1y71_A	130	Kinase-associated protein B; structural genomics,	81.41

>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2

Probab=99.95  E-value=5.7e-29  Score=194.20  Aligned_cols=130  Identities=26%  Similarity=0.394  Sum_probs=111.0

Q ss_pred             cCCcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEE
Q 032397            6 EEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVT   85 (141)
Q Consensus         6 ~~~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V~   85 (141)
                      +++.+|+|||+|+..++|.+|+|||+++  |+||||++|.+....    .++..++|+|.|.+...|.|++||+|+|+|+
T Consensus        17 ~~~~iV~PGd~l~~~~~~~~G~Gty~~~--g~I~Asv~G~v~~~~----~~~~~~vi~V~p~~~~~y~p~vGDvV~G~V~   90 (209)
T 2nn6_I           17 PPVRYCIPGERLCNLEEGSPGSGTYTRH--GYIFSSLAGCLMKSS----ENGALPVVSVVRETESQLLPDVGAIVTCKVS   90 (209)
T ss_dssp             ---CCCCTTCEEEETTTCCCSSSCEEET--TEEECCSCSCBCCCB----CTTSSBC-CBCCSCCCCCCCCTTCEEEEEEE
T ss_pred             CCCcEEcCCCCCCCCCCeeecCCEEEEC--CEEEEEEEEEEEEec----cCCcccEEEEecCCCCcCCCCCCCEEEEEEE
Confidence            3567999999999888999999999999  999999999987521    1223567899998766799999999999999


Q ss_pred             EeccceEEEEEEEecCeecccceeEEEeccccch----hhhHHHHhh-------hhccccccc-eeeC
Q 032397           86 KVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI----ELLMHLLYG-------YLGSCKMQL-NYSL  141 (141)
Q Consensus        86 ~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~----~v~~~~~f~-------~vis~gd~~-~y~l  141 (141)
                      ++++.+|+|+|.++++++|..+|.|+||++|++.    +++|.++|+       +|+|++|.. .|+|
T Consensus        91 ~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akVisi~~~~~~i~L  158 (209)
T 2nn6_I           91 SINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLL  158 (209)
T ss_dssp             EECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEEE
T ss_pred             EEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEEEEEeCCCCeEEE
Confidence            9999999999999999999999999999999996    358999995       899999875 4665

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A

Probab=99.95  E-value=9.6e-28  Score=183.04  Aligned_cols=109  Identities=22%  Similarity=0.312  Sum_probs=99.9

Q ss_pred             CcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEe
Q 032397            8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKV   87 (141)
Q Consensus         8 ~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V~~v   87 (141)
                      |++|+|||+|+.+++|.+|+|||.++  |+|+||++|.+++.         ++.++|.|.+..+|+|+ ||+|+|+|++|
T Consensus         1 m~iV~PGd~l~~~~~~~~G~Gty~~~--~~i~as~~G~v~~~---------~~~v~V~~~~~~~y~p~-GdiV~G~V~~V   68 (179)
T 3m7n_A            1 MRFVMPGDRIGSAEEYVKGEGVYEEG--GELFAAVAGKLIIK---------DRVAKVESISPIPEIVK-GDVVLGRVVDL   68 (179)
T ss_dssp             CCEECTTCEEEETTTSEECTTEEEET--TEEEESSSEEEEEE---------TTEEEEEESSCCCCCCT-TCEEEEEEEEE
T ss_pred             CeEEcCCCCCCCCCCEeccCCEEEeC--CEEEEEEEEEEEEe---------CCEEEEEECCCCcccCC-CCEEEEEEEEE
Confidence            57999999999989999999999999  99999999999983         57999999876789999 99999999999


Q ss_pred             ccceEEEEEEEe--cCeecccceeEEEeccccch--hhhHHHHhh
Q 032397           88 MTRMASADIMCV--GAKSVREKFSGIIRFFIFYI--ELLMHLLYG  128 (141)
Q Consensus        88 ~~~~a~v~I~~v--~~~~l~~~~~G~Ir~~dvr~--~v~~~~~f~  128 (141)
                      .+..|+|+|.++  +++++..++.|+||++|++.  ..+|.++|+
T Consensus        69 ~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~~  113 (179)
T 3m7n_A           69 RNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVG  113 (179)
T ss_dssp             CSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTCC
T ss_pred             eCCcEEEEEccccCcccccccCeeEEEEHHHcCcchhhCHhhcCC
Confidence            999999999999  66788899999999999997  357778874

>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=99.90  E-value=1.1e-24  Score=178.60  Aligned_cols=125  Identities=21%  Similarity=0.241  Sum_probs=95.8

Q ss_pred             ccCCcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEE
Q 032397            5 EEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARV   84 (141)
Q Consensus         5 ~~~~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V   84 (141)
                      ..++.+|+|||+|+..++|.+|+|||.++  |+||||++|.+...         ++.++|.|.+ .+|+|++||+|+|+|
T Consensus        36 ~~~~~iVlPGd~L~~~~~~~~G~Gty~~~--g~I~Asv~G~v~~~---------~~~vsV~p~~-~rY~P~vGDvViG~V  103 (308)
T 2nn6_H           36 DTKKHLVVPGDTITTDTGFMRGHGTYMGE--EKLIASVAGSVERV---------NKLICVKALK-TRYIGEVGDIVVGRI  103 (308)
T ss_dssp             ----CBCCTTCBCCCCTTCCBCTTEEECS--SSEEECSSEEEEEE---------TTEEEEEESS-CCCCCCSSBCCCEEE
T ss_pred             CCCCcEEeCCCCCCCCCCEeecCCeEEEC--CEEEEEEEEEEEec---------CCEEEEeeCC-CccCCCCCCEEEEEE
Confidence            34567999999999888999999999999  99999999998873         5799999988 479999999999999


Q ss_pred             EEeccceEEEEEEEecCeecc-c--ce-eEEEeccccchhhhHHHHhh-------hhccccccceeeC
Q 032397           85 TKVMTRMASADIMCVGAKSVR-E--KF-SGIIRFFIFYIELLMHLLYG-------YLGSCKMQLNYSL  141 (141)
Q Consensus        85 ~~v~~~~a~v~I~~v~~~~l~-~--~~-~G~Ir~~dvr~~v~~~~~f~-------~vis~gd~~~y~l  141 (141)
                      +++++++|+|+|.+..+..+. +  .| .|++|+++++++.+|+++|+       +|+|+++...|+|
T Consensus       104 t~V~~~~a~VdI~s~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArVisv~~~~~i~L  171 (308)
T 2nn6_H          104 TEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSL  171 (308)
T ss_dssp             EEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEETTTEEEE
T ss_pred             EEEeCceEEEEECCCcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCCCCCEEE
Confidence            999999999999876555432 2  35 58889999988889999994       9999998777765

>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=99.90  E-value=1.4e-23  Score=165.66  Aligned_cols=113  Identities=24%  Similarity=0.299  Sum_probs=100.1

Q ss_pred             CcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEe
Q 032397            8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKV   87 (141)
Q Consensus         8 ~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V~~v   87 (141)
                      +++|+|||.|+. ++|.+|+|||.++  |+||||++|.+...         ++.++|.|.+ .+|.|++||+|+|+|+++
T Consensus         2 ~~iV~PGd~l~~-~~~~~G~Gty~~~--g~i~as~~G~v~~~---------~~~v~V~p~~-~~y~p~~GDiV~G~V~~v   68 (229)
T 2ba0_A            2 RKIVLPGDLLST-NPRAAGYGTYVEG--GKVYAKIIGLFDQT---------ETHVRVIPLK-GRYTPSVGDVVIGIIREV   68 (229)
T ss_dssp             CCEECTTCEEES-CTTSBCTTEEEET--TEEEECSSEEEEEC---------SSCEEEEECS-SSCCCCTTCEEEEEEEEE
T ss_pred             CCEEcCCCCccc-CCeEecCCEEEeC--CEEEEEEEEEEEEe---------CCEEEEEeCC-CcccCCCCCEEEEEEEEE
Confidence            469999999985 6799999999999  99999999999873         3579999988 479999999999999999


Q ss_pred             ccceEEEEEEEecCeecccceeEEEeccccch---hhhHHHHhh-------hhccccccceeeC
Q 032397           88 MTRMASADIMCVGAKSVREKFSGIIRFFIFYI---ELLMHLLYG-------YLGSCKMQLNYSL  141 (141)
Q Consensus        88 ~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~---~v~~~~~f~-------~vis~gd~~~y~l  141 (141)
                      .++.|+|+|        .+++.|+||.++++.   ..+|.++|+       +|+++++..++.|
T Consensus        69 ~~~~a~V~I--------~~~~~g~l~isev~~~~~~~~~~~~l~~GD~V~arVi~v~~~~~i~L  124 (229)
T 2ba0_A           69 AANGWAVDI--------YSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTL  124 (229)
T ss_dssp             CSSEEEEEC--------SSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECTTCCEEE
T ss_pred             eCCeEEEEe--------CCCeEEEEEHHHccccccccchhcccCCCCEEEEEEEEECCCCcEEE
Confidence            999999999        788999999999994   567888884       8999988766654

>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 PDB: 2jea_I* 2jeb_I* 3l7z_C

Probab=99.89  E-value=7.5e-24  Score=169.25  Aligned_cols=117  Identities=16%  Similarity=0.139  Sum_probs=102.7

Q ss_pred             ccCCcEEecCCccCCCCCeeecC--cEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEE
Q 032397            5 EEEMVLVTPGEVLGKATEVKAGK--GAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIA   82 (141)
Q Consensus         5 ~~~~~iVlPGd~L~~~~e~~~G~--GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig   82 (141)
                      +++..+|+|||.|+. ++|.+|+  |||.++  |+||||++|.+...         ++.++|.|.+..+|.|++||+|+|
T Consensus        13 ~~~~~iV~PGd~l~~-~~~~~G~~~Gty~~~--g~i~as~~G~v~~~---------~~~v~V~p~~~~~y~p~~GDiV~G   80 (251)
T 2je6_I           13 LQPRSIVVPGELLAE-GEFQIPWSPYILKIN--SKYYSTVVGLFDVK---------DTQFEVIPLEGSFYYPKINDIVIG   80 (251)
T ss_dssp             CCSSCEECTTCEEEE-ECCCCCCCTTEEEET--TEEEECSSEEEEEE---------TTEEEEEESCCSCCCCCTTCEEEE
T ss_pred             cCCCcEEcCCCCCcc-CCeeeCCCCCEEEEC--CEEEEEEEEEEEEe---------CCEEEEEECCCcccCCCCCCEEEE
Confidence            456789999999996 6799999  999999  99999999999883         368999999866899999999999


Q ss_pred             EEEEeccceEEEEEEEecCeecccceeEEEeccccch----h-hhHHHHhh-------hhccccccceeeC
Q 032397           83 RVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI----E-LLMHLLYG-------YLGSCKMQLNYSL  141 (141)
Q Consensus        83 ~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~----~-v~~~~~f~-------~vis~gd~~~y~l  141 (141)
                      +|+++++..|+|+|        .+++.|+||.++++.    + .+|.++|+       +|+++++...+.|
T Consensus        81 ~V~~v~~~ga~VdI--------~~~~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~~~~~i~L  143 (251)
T 2je6_I           81 LVEDVEIYGWVVDI--------KAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVL  143 (251)
T ss_dssp             EEEEECSSEEEEEC--------SSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETTEEEEE
T ss_pred             EEEEEeCceEEEEc--------CCCeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECCCCcEEE
Confidence            99999999999998        889999999999986    2 66777874       8899887666654

>2nn6_G Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=99.87  E-value=3.5e-23  Score=168.37  Aligned_cols=122  Identities=18%  Similarity=0.135  Sum_probs=91.0

Q ss_pred             CCcEEecCCccCCCC-----------------------Ceee--cCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCe
Q 032397            7 EMVLVTPGEVLGKAT-----------------------EVKA--GKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPT   61 (141)
Q Consensus         7 ~~~iVlPGd~L~~~~-----------------------e~~~--G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~   61 (141)
                      -+.+|+|||.|+..+                       +|.+  |+|||..+  |.||||++|.++...+..  ....+.
T Consensus        38 ~~~iVlPGD~L~~~~~~~~~~~g~~~~~~l~~~~~~~~~~~~~~G~Gty~~~--~~I~as~aG~l~~~~~~~--~~~~~~  113 (289)
T 2nn6_G           38 LGQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCG--DRLLVTKCGRLRHKEPGS--GSGGGV  113 (289)
T ss_dssp             GSSBCCSSEEECCSCSCCEECSSEEECC-----------------------C--CCEEECSCCEEEEECCTT--TSSCCE
T ss_pred             CCcEEeCCCCcCccccccccccccccccccccccccCcceEEccCCCeEEEC--CEEEEEEeEeEEeccCCc--cCccce
Confidence            356899999998765                       7889  99999999  999999999998842000  001148


Q ss_pred             EEEecCCCCCCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch-hhhHHHHhh-------hhccc
Q 032397           62 VEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-ELLMHLLYG-------YLGSC  133 (141)
Q Consensus        62 i~V~~~~~~~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~v~~~~~f~-------~vis~  133 (141)
                      +||.|.+ .+|+|++||+|+|+|+++++++|+|+|        ..++.|+|+.++++. ..+|+++|+       +|+|+
T Consensus       114 v~V~~~~-~rYiP~vGDiVIG~Vt~v~~~~~~VdI--------~s~~~a~L~~~~f~Gatk~~r~~f~~GDlV~ArV~s~  184 (289)
T 2nn6_G          114 YWVDSQQ-KRYVPVKGDHVIGIVTAKSGDIFKVDV--------GGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVA  184 (289)
T ss_dssp             EEEECCC-SSCCCCSSEEEEEEEEEEETTEEEEEC--------SSSSCCCEESCSSSCCSSCSSSSSCTTCEEEEEEEEC
T ss_pred             EEEEecC-CCCCCCCCCEEEEEEEEEeCcEEEEEE--------CCCceeEEehhhcCcchhhhhhhcCCCCEEEEEEEEc
Confidence            8999988 479999999999999999999999999        678999999999984 456888884       89999


Q ss_pred             cccceeeC
Q 032397          134 KMQLNYSL  141 (141)
Q Consensus       134 gd~~~y~l  141 (141)
                      ++...+.|
T Consensus       185 ~~~~~~eL  192 (289)
T 2nn6_G          185 NKDMEPEM  192 (289)
T ss_dssp             CTTSCCEE
T ss_pred             CCCCceEE
Confidence            88766654

>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1

Probab=99.87  E-value=2.9e-23  Score=164.18  Aligned_cols=115  Identities=23%  Similarity=0.152  Sum_probs=55.3

Q ss_pred             CcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCCCCCCCCCCCEEEEEEEEe
Q 032397            8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGPVPEPGSVVIARVTKV   87 (141)
Q Consensus         8 ~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~~~~~P~~GdiVig~V~~v   87 (141)
                      +.+|+|||.|+. ++|.+|+|||.++  |.|||+++|.+..       ++++..++|.|.+. +|.|++||+|+|+|+++
T Consensus         9 ~~iV~PGd~l~~-~~~~~G~Gty~~~--~~I~Asv~G~v~~-------~~~~~~vsV~p~~~-~y~p~~GDiV~G~V~~v   77 (235)
T 2z0s_A            9 GRIVVPGEPLPE-EVEASPPYVIDYK--GVKRATVVGLLRE-------KGDGGGRAFVKLKE-IYVPQAGDVVIGLIQSV   77 (235)
T ss_dssp             -------------------------------------------------------------C-CCCCCTTCCEEEEEEEE
T ss_pred             CcEEeCCCCccc-CceEcCCCEEEEC--CEEEEEEeEEEEE-------eCCccEEEEEeCCC-ccCCCCCCEEEEEEEEE
Confidence            479999999986 6699999999999  9999999998876       23345899999884 79999999999999999


Q ss_pred             ccceEEEEEEEecCeecccceeEEEeccccch------hhhHHHHhh-------hhccccccceeeC
Q 032397           88 MTRMASADIMCVGAKSVREKFSGIIRFFIFYI------ELLMHLLYG-------YLGSCKMQLNYSL  141 (141)
Q Consensus        88 ~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~------~v~~~~~f~-------~vis~gd~~~y~l  141 (141)
                      +++.|+|+|        .+++.|+||.+++..      ..+|.++|+       +|+++++...++|
T Consensus        78 ~~~~~~V~I--------~~~~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~~~~i~L  136 (235)
T 2z0s_A           78 GIMNWFVDI--------NSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLL  136 (235)
T ss_dssp             CSSEEEEEC--------SSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEE
T ss_pred             eCCeEEEEe--------CCCeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECCCCcEEE
Confidence            999999999        889999999999964      367778884       8999988666654

>2ja9_A Exosome complex exonuclease RRP40; RNA-binding protein, RNA, S1 domain, KH domain, hydrolase, RNA-binding, nuclear protein; 2.20A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.51.1.1

Probab=98.58  E-value=2.6e-08  Score=75.49  Aligned_cols=49  Identities=10%  Similarity=0.092  Sum_probs=41.9

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeeccc-ceeEEEeccccch-hhhHHHHh
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRFFIFYI-ELLMHLLY  127 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~-~~~G~Ir~~dvr~-~v~~~~~f  127 (141)
                      +|+|++||+|+|+|+.+.++.|+|+|        .. ++.|+|+.+++.. .-+|...|
T Consensus         2 rY~P~~gDvViG~V~~v~~~~~~VdI--------~~~~~~a~L~~s~~~g~~k~~r~~l   52 (175)
T 2ja9_A            2 RYIPSVNDFVIGVIIGTFSDSYKVSL--------QNFSSSVSLSYMAFPNASKKNRPTL   52 (175)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEES--------STTSCCEEEETTSSTTCCSSSCCCC
T ss_pred             CccCCCcCEEEEEEEEEECcEEEEEE--------CCCCccEEEEHHHCCchhhhhhccC
Confidence            69999999999999999999999999        77 8999999999874 33344444

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii}

Probab=97.69  E-value=0.0001  Score=48.12  Aligned_cols=38  Identities=24%  Similarity=0.267  Sum_probs=35.1

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |++|+++.|+|+++++..|.|+|        .....|+|+.+++..
T Consensus         3 ~~~G~iv~G~V~~v~~~G~fV~l--------~~~~~Gllh~sel~~   40 (80)
T 2k52_A            3 VEPGKFYKGVVTRIEKYGAFINL--------NEQVRGLLRPRDMIS   40 (80)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEE--------ETTEEEEECGGGCSS
T ss_pred             CCCCCEEEEEEEEEeCCEEEEEE--------CCCCEEEEEHHHCCc
Confidence            78999999999999999999999        667999999999865

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis}

Probab=97.23  E-value=0.00069  Score=48.28  Aligned_cols=38  Identities=24%  Similarity=0.194  Sum_probs=35.3

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      +++|++|.|+|++|++..|.|+|        .....|+||.+++..
T Consensus         5 ~~vG~iv~G~V~~i~~~G~FV~l--------~~~~~Glihisel~~   42 (130)
T 2k4k_A            5 FEVGSVYTGKVTGLQAYGAFVAL--------DEETQGLVHISEVTH   42 (130)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEE--------ETTEEEEEEGGGTSS
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEE--------CCCcEEEEEHHHCCc
Confidence            78999999999999999999999        667999999999975

>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5

Probab=97.12  E-value=0.0011  Score=50.01  Aligned_cols=41  Identities=20%  Similarity=0.221  Sum_probs=35.1

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecc--cceeEEEeccccch
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRFFIFYI  119 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~--~~~~G~Ir~~dvr~  119 (141)
                      ...|++|++|.|+|++|++-.|.|+|        .  ....|+||++++..
T Consensus        10 ~~~p~~G~iv~G~V~~I~~fGaFV~L--------~e~~g~eGLvhiSels~   52 (182)
T 1kl9_A           10 HKFPEVEDVVMVNVRSIAEMGAYVSL--------LEYNNIEGMILLSELSR   52 (182)
T ss_dssp             SSSCCTTCEEEEEEEEECSSEEEEEE--------TTTTTEEEEEEGGGC--
T ss_pred             ccCCCCCCEEEEEEEEEeccEEEEEE--------ccCCCcEEEEEHHHCCC
Confidence            35689999999999999999999999        4  35899999999964

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=97.03  E-value=0.00048  Score=47.42  Aligned_cols=40  Identities=20%  Similarity=0.286  Sum_probs=36.1

Q ss_pred             CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .-+++|++|.|+|+++.+..|.|+|        .....|+|+.+++..
T Consensus        27 ~~~~~G~iv~G~V~~v~~~G~fV~l--------~~~~~Gll~~sel~~   66 (109)
T 2khj_A           27 ALNKKGAIVTGKVTAVDAKGATVEL--------ADGVEGYLRASEASR   66 (109)
T ss_dssp             TTCCSSSEEEEEEEEECSSCEEEEC--------STTCBCCBCTTCCCS
T ss_pred             hcCCCCCEEEEEEEEEECCeEEEEE--------CCCCEEEEEHHHcCc
Confidence            4589999999999999999999999        667999999999864

>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.95  E-value=0.0011  Score=46.65  Aligned_cols=49  Identities=12%  Similarity=0.005  Sum_probs=39.4

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeeccc-ceeEEEeccccch-h-hhHHHHh
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE-KFSGIIRFFIFYI-E-LLMHLLY  127 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~-~~~G~Ir~~dvr~-~-v~~~~~f  127 (141)
                      .+.|++|++|.|+|++|++..|+|+|        .. ...|+||.+++.. + -.+.+.|
T Consensus        17 ~~~~~vG~iv~G~V~~I~~fGaFV~l--------~g~~~~Glvhisel~~~~~~~~~~~~   68 (119)
T 2cqo_A           17 ENLPALYTIFQGEVAMVTDYGAFIKI--------PGCRKQGLVHRTHMSSCRVDKPSEIV   68 (119)
T ss_dssp             CCSCCTTCEEEEEEEEEETTEEEEEC--------TTCSSCEEEEHHHHCSSCCSCHHHHC
T ss_pred             hcccCCCCEEEEEEEEEeCceEEEEE--------CCCcEEEEEEHHHCCcccccChhhcC
Confidence            46789999999999999999999999        33 3789999999975 3 3344444

>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A

Probab=96.95  E-value=0.0015  Score=49.08  Aligned_cols=41  Identities=17%  Similarity=0.252  Sum_probs=33.3

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecc--cceeEEEeccccch
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRFFIFYI  119 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~--~~~~G~Ir~~dvr~  119 (141)
                      ...|++||+|.|+|+++++-.|.|+|        .  ....|+||.+++..
T Consensus        10 ~~~p~~G~iv~G~V~~i~~fGaFV~L--------~e~~gveGLvhiSels~   52 (175)
T 2a19_A           10 NKYPEIDDIVMVNVQQIAEMGAYVKL--------LEYDNIEGMILLSELSR   52 (175)
T ss_dssp             SSSCCTTCEEEEEEEEEETTEEEEEE--------TTTTTCEEEEECC----
T ss_pred             hcCCCCCCEEEEEEEEEecceEEEEE--------cCCCCcEEEEEHHHcCC
Confidence            45689999999999999999999999        4  45899999999864

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=96.88  E-value=0.0022  Score=44.52  Aligned_cols=51  Identities=16%  Similarity=0.095  Sum_probs=38.7

Q ss_pred             CeEEEecCCCCCCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397           60 PTVEVTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY  118 (141)
Q Consensus        60 ~~i~V~~~~~~~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr  118 (141)
                      +.+.+.|......-|++|+++.|+|+++++..|.|+|        .....|+|+.+++.
T Consensus        14 k~~~~~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l--------~~~~~Glvhisel~   64 (115)
T 2khi_A           14 LVPRGSHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEI--------EEGVEGLVHVSEMD   64 (115)
T ss_dssp             -------CCCSSCSSCSSCEEEEEEEEEETTEEEEEC--------STTCEEEEETTSSS
T ss_pred             hhcccCCHHHHhhcCCCCCEEEEEEEEEECCEEEEEE--------CCCCEEEEEHHHCC
Confidence            4556666654456789999999999999999999999        66799999999985

>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.80  E-value=0.0025  Score=43.51  Aligned_cols=40  Identities=18%  Similarity=0.349  Sum_probs=35.5

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeeccc---ceeEEEeccccc
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE---KFSGIIRFFIFY  118 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~---~~~G~Ir~~dvr  118 (141)
                      ...|++|+++.|+|++|.+..|.|+|        ..   ...|+||.+++.
T Consensus         7 ~~~~~vG~i~~G~V~~v~~fG~FV~l--------~~~~~~~~Glvhisel~   49 (103)
T 2eqs_A            7 GEEPTIGDIYNGKVTSIMQFGCFVQL--------EGLRKRWEGLVHISELR   49 (103)
T ss_dssp             CSSCCTTCEEEEEEEEECSSCEEEEE--------CSSSSCCEEEECGGGTS
T ss_pred             cccCCCCCEEEEEEEEEeccEEEEEE--------cCCCCCeEEEEEHHHCC
Confidence            34589999999999999999999999        54   789999999994

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A

Probab=96.59  E-value=0.0043  Score=49.65  Aligned_cols=41  Identities=17%  Similarity=0.181  Sum_probs=36.3

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecc--cceeEEEeccccch
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRFFIFYI  119 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~--~~~~G~Ir~~dvr~  119 (141)
                      ...|++||+|.|+|+++.+..|.|+|        .  ....|+||.+++..
T Consensus         6 ~~~p~~Gdiv~G~V~~I~~fGaFV~L--------~e~~gieGlIhiSels~   48 (275)
T 3aev_A            6 REYPEEGEFVVATVKRIHNYGAFLEL--------DEYPGKEAFMHISEVAS   48 (275)
T ss_dssp             -CCCCTTCEEEEEEEEEETTEEEEEE--------TTSTTCEEEEEGGGSCS
T ss_pred             ccCCCCCCEEEEEEEEEECcEEEEEE--------CCCCCeEEEEEHHHcCc
Confidence            45689999999999999999999999        6  36899999999964

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5

Probab=96.55  E-value=0.0071  Score=40.23  Aligned_cols=39  Identities=18%  Similarity=0.229  Sum_probs=34.8

Q ss_pred             CCCCCCCEEEEEEEEeccceEEEEEEEecCeeccc--ceeEEEecc-ccch
Q 032397           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE--KFSGIIRFF-IFYI  119 (141)
Q Consensus        72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~--~~~G~Ir~~-dvr~  119 (141)
                      -.|++|+++.|+|+ +++-.|.|+|        .+  ...|++|.+ ++..
T Consensus         7 ~~~~vG~~~~G~V~-v~~fG~FVel--------~~~~~~eGLvhis~el~~   48 (88)
T 1luz_A            7 SLPNAGDVIKGRVY-EKDYALYIYL--------FDYPHFEAILAESVKMHM   48 (88)
T ss_dssp             CCCCTTCEEEEEEE-EETTEEEEEE--------TTCTTSEEEEGGGSSCCH
T ss_pred             cCCCCCCEEEEEEE-EEccEEEEEE--------CCCCCeEEEEEeeHHhCc
Confidence            45899999999999 9999999999        54  489999999 9865

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B*

Probab=96.33  E-value=0.0031  Score=50.17  Aligned_cols=41  Identities=15%  Similarity=0.262  Sum_probs=37.0

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecc--cceeEEEeccccch
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRFFIFYI  119 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~--~~~~G~Ir~~dvr~  119 (141)
                      .+.|++|++|.|+|+++.+..|.|+|        .  ....|+||.+++..
T Consensus         6 ~~~~~vG~iv~G~V~~I~~~GaFV~l--------~e~~~~~GlihiSels~   48 (266)
T 3cw2_C            6 SKLPSEGEILIATVKQVFDYGSYVSL--------DEYGGLQAFLPWSEVSS   48 (266)
T ss_dssp             SSSCCTTCEEEEEEEECCSSSBEEEE--------TTTTSEECBBCGGGSSC
T ss_pred             cccCCCCCEEEEEEEEEeccEEEEEE--------cCCCCeEEEEEhHHcCc
Confidence            56799999999999999999999999        6  56899999999964

>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1

Probab=96.18  E-value=0.0042  Score=50.53  Aligned_cols=40  Identities=20%  Similarity=0.259  Sum_probs=35.6

Q ss_pred             CCCCCCCEEEEEEEEeccceEEEEEEEecCeecc--cceeEEEeccccch
Q 032397           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRFFIFYI  119 (141)
Q Consensus        72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~--~~~~G~Ir~~dvr~  119 (141)
                      ..|++||+|.|+|++|++..|.|+|        .  ....|+||.+++..
T Consensus         9 ~~~~vG~iv~G~V~~I~~fGaFV~L--------~ey~gveGLvhiSels~   50 (308)
T 1q8k_A            9 KFPEVEDVVMVNVRSIQEMGAYVSL--------LEYNNIEGMIHLSELSR   50 (308)
T ss_dssp             CCCSSCCEEEEEEEEEETTEEEEES--------CTTTSCCEEECGGGTSC
T ss_pred             cCCCCCCEEEEEEEEEeCcEEEEEE--------CCCCCeEEEEEhHHcCc
Confidence            4588999999999999999999999        5  46889999999964

>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1

Probab=94.78  E-value=0.064  Score=39.38  Aligned_cols=40  Identities=28%  Similarity=0.058  Sum_probs=35.3

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ..-|.+|+++.|+|++++.-.|.|+|        . +++|++|.+++.+
T Consensus        76 ~~~~~~Gev~~G~V~~v~~fG~fV~l--------~-~~~glvhis~l~~  115 (172)
T 2c35_B           76 VFRPFKGEVVDAVVTQVNKVGLFTEI--------G-PMSCFISRHSIPS  115 (172)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEEE--------T-TEEEEEEGGGSCT
T ss_pred             EeeCCCCCEEEEEEEEEeCCEEEEEE--------C-CEEEEEEHHHCCC
Confidence            34589999999999999999999999        3 6889999998854

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1

Probab=94.78  E-value=0.045  Score=40.64  Aligned_cols=39  Identities=15%  Similarity=0.159  Sum_probs=34.7

Q ss_pred             CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      +-|++|+++.|+|+++++..|.|+|        . ++.|++|.+++..
T Consensus        77 ~~~~~Gev~~G~V~~v~~~G~fV~l--------~-~~eglvhis~l~~  115 (187)
T 1go3_E           77 YIPEMYELIEGEVVDVVEFGSFVRL--------G-PLDGLIHVSQIMD  115 (187)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEC--------S-SSEEEEEGGGSCS
T ss_pred             EccCCCCEEEEEEEEEeCcEEEEEE--------c-CccEEEEhHHhCC
Confidence            4599999999999999999999999        2 3899999998864

>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=94.24  E-value=0.068  Score=36.94  Aligned_cols=37  Identities=14%  Similarity=0.206  Sum_probs=29.7

Q ss_pred             CCCCCCEEEEEEEEeccceEEEEEEEecCeecc-cceeEEEecccc
Q 032397           73 VPEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRFFIF  117 (141)
Q Consensus        73 ~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~-~~~~G~Ir~~dv  117 (141)
                      -+++|+++.|+|++|....|.|+|        . ....|+++.++.
T Consensus        18 ~l~~G~i~~G~V~~v~~fG~fV~l--------~~~~~~~l~~~~~~   55 (119)
T 1wi5_A           18 ALKPGMLLTGTVSSLEDHGYLVDI--------GVDGTRAFLPLLKA   55 (119)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEEC--------CCSSCEEEEEHHHH
T ss_pred             cCCCCCEEEEEEEEEeCceEEEEE--------CCCCeEEEEEEecc
Confidence            379999999999999999999999        3 235566666654

>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli}

Probab=93.45  E-value=0.08  Score=35.90  Aligned_cols=40  Identities=10%  Similarity=0.144  Sum_probs=35.5

Q ss_pred             CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      --|++|++|.+.|+++.+.-+.++|        .....|++|++++..
T Consensus        57 ~~l~~Ge~V~g~V~~i~~fG~fv~l--------~~~~eGlvhis~i~~   96 (101)
T 2bh8_A           57 GNPQQGDRVEGKIKSITDFGIFIGL--------DGGIDGLVHLSDISW   96 (101)
T ss_dssp             CCCCTTCEEEEEEEECCSEEEEECT--------TSCEEEEEEEEEEEE
T ss_pred             cCCCCCCEEEEEEEEeCCcEEEEEc--------CCCceEEEEHHHCcc
Confidence            3689999999999999999999998        567899999999853

>3v2d_0 50S ribosomal protein L27; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2hgj_Z 2hgq_Z 2hgu_Z 2j01_0 2j03_0 2jl6_0 2jl8_0 2wdi_0 2wdj_0 2wdl_0 2wdn_0 2wh2_0 2wh4_0 2wrj_0 2wrl_0 2wro_0 2wrr_0 2x9s_0 2x9u_0 2xg0_0 ...

Probab=93.12  E-value=0.12  Score=34.41  Aligned_cols=60  Identities=23%  Similarity=0.262  Sum_probs=46.3

Q ss_pred             ccccCCcEEecCCccCCC--CCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecC
Q 032397            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (141)
Q Consensus         3 ~~~~~~~iVlPGd~L~~~--~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~   67 (141)
                      +|...++.|.||..|...  ..+-||.++-.-. |..|||.+-|.+++...    ..+++.|+|.|.
T Consensus        23 vK~~~Gq~V~aG~IivRQRGtk~hPG~NVg~Gk-D~TLfAl~~G~V~f~~~----~~~r~~VsV~p~   84 (85)
T 3v2d_0           23 VKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGR-DFTLFALVDGVVEFQDR----GRLGRYVHVRPL   84 (85)
T ss_dssp             ESSCTTCEECTTCEEEECSSCSEEECTTEEECT-TCCEEESSSEEEEEEEC----GGGCEEEEEEEC
T ss_pred             eEecCCeEEcCCeEEEecCCccCcCCCCEeEcC-CCeEEEecCEEEEEEEc----CCCCEEEEEEEC
Confidence            677889999999999654  3499999987663 48999999999999530    134578888763

>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ...

Probab=93.12  E-value=0.21  Score=36.59  Aligned_cols=58  Identities=12%  Similarity=0.042  Sum_probs=42.6

Q ss_pred             CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccchh--hh-HHH--Hh---hhhccccccce
Q 032397           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYIE--LL-MHL--LY---GYLGSCKMQLN  138 (141)
Q Consensus        72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~~--v~-~~~--~f---~~vis~gd~~~  138 (141)
                      .-|.+|+++.|+|++++.-.|.|+|        .. ..|++|.+++..+  .+ -..  ++   +++++.||.-.
T Consensus        79 ~~~~~Gev~~G~V~~v~~fG~FV~l--------~~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~  144 (171)
T 1y14_B           79 FKPFKGEVVDGTVVSCSQHGFEVQV--------GP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIR  144 (171)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEE--------TT-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEE
T ss_pred             ccCCCCCEEEEEEEEEecCEEEEEe--------cC-eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEE
Confidence            3489999999999999999999999        54 8999999988541  11 111  22   26688887643

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=92.47  E-value=0.023  Score=51.08  Aligned_cols=40  Identities=18%  Similarity=0.110  Sum_probs=0.0

Q ss_pred             CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .-|++|+++.|+|++|.+-.|+|+|        .....|+||++++..
T Consensus       633 ~~~~vG~v~~G~V~~I~~fGaFVel--------~~g~eGLvHiSels~  672 (726)
T 4aid_A          633 DEAEVGKIYDGKVVKVVDFGAFVNF--------FGAKDGLVHVSQISN  672 (726)
T ss_dssp             ------------------------------------------------
T ss_pred             hhhcCCcEEEEEEEEEeccEEEEEE--------CCCcEEEEEHHHcCc
Confidence            4589999999999999999999999        456999999999975

>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E

Probab=92.43  E-value=0.21  Score=36.77  Aligned_cols=39  Identities=18%  Similarity=0.132  Sum_probs=34.9

Q ss_pred             CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .-|.+|+++.|+|++++.-.+.|++        . ++.|++|.+++..
T Consensus        77 ~~p~~Gev~~G~V~~v~~~G~fv~l--------~-~~~glvh~s~l~~  115 (180)
T 4ayb_E           77 YVPVVQEVVEGEVLQVDNYGVFVNL--------G-PMDGLVHISQITD  115 (180)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEC--------S-SSEEEEEGGGSCS
T ss_pred             eeccCCCEEEEEEeeeccceEEEEE--------C-CccceEEeeecCC
Confidence            4599999999999999999999997        3 5899999999975

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}

Probab=92.27  E-value=0.16  Score=40.53  Aligned_cols=38  Identities=13%  Similarity=-0.091  Sum_probs=34.4

Q ss_pred             CCCCCEEEEEEEEeccceEEE-EEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASA-DIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v-~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      -++||+|.|+|+++++--|+| .|        ...+.|+||.+++..
T Consensus       150 ~~~G~~V~g~V~~i~~~G~fV~~i--------~~g~~Glih~SEl~~  188 (285)
T 3go5_A          150 NMQNQNWPAIVYRLKLSGTFVYLP--------ENNMLGFIHPSERYA  188 (285)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEET--------TTTEEEEECGGGCSS
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEEe--------CCCeEEEEEHHHccc
Confidence            367999999999999999999 88        778999999999874

>3r8s_W 50S ribosomal protein L27; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 3j19_W 2qam_W* 1p85_U 1p86_U 2awb_W 2gya_U 2gyc_U 2aw4_W 2i2v_W 2j28_W 2i2t_W* 2qao_W* 2qba_W* 2qbc_W* 2qbe_W 2qbg_W 2qbi_W* 2qbk_W* 2qov_W 2qox_W ...

Probab=91.55  E-value=0.2  Score=32.79  Aligned_cols=60  Identities=18%  Similarity=0.284  Sum_probs=45.4

Q ss_pred             ccccCCcEEecCCccCCC--CCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEec
Q 032397            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTG   66 (141)
Q Consensus         3 ~~~~~~~iVlPGd~L~~~--~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~   66 (141)
                      +|...++.|.||..|...  ..+-||.++-.-. |..++|.+-|.++...   ....+++.|+|.|
T Consensus        14 vK~~~Gq~V~aG~IivRQRGtk~hPG~NVG~Gk-D~TLfAl~~G~V~f~~---~~~~~r~~VsV~p   75 (76)
T 3r8s_W           14 VKRFGGESVLAGSIIVRQRGTKFHAGANVGCGR-DHTLFAKADGKVKFEV---KGPKNRKFISIEA   75 (76)
T ss_dssp             ESSCTTCEECTTCEEEECSSCSSEECTTEEECT-TSCEEESSSEEEEEEE---ETTTTEEEEEEEC
T ss_pred             EEecCCeEEecCcEEEeccCccCcCCCCeeecC-CCeEEEccCEEEEEEE---eCCCCCEEEEEEe
Confidence            677889999999999654  3499999987663 4899999999999852   0112356788875

>2zjr_T 50S ribosomal protein L27; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.84.4.1 PDB: 1nwx_U* 1nwy_U* 1sm1_U* 1xbp_U* 1y69_U 1yl3_3 2b66_0 2b9n_0 2b9p_0 2zjp_T* 2zjq_T 1nkw_U 3cf5_T* 3dll_T* 3pio_T* 3pip_T* 1pnu_U 1pny_U 1vor_X 1vou_X ...

Probab=91.06  E-value=0.21  Score=33.65  Aligned_cols=60  Identities=20%  Similarity=0.291  Sum_probs=46.2

Q ss_pred             ccccCCcEEecCCccCCC--CCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecC
Q 032397            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (141)
Q Consensus         3 ~~~~~~~iVlPGd~L~~~--~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~   67 (141)
                      +|...+..|.||..|...  ..+-||.++-.-. |..|+|.+-|.+++...    ..+++.|+|.|.
T Consensus        23 vK~~gGq~V~aG~IivRQRGtk~hPG~NVg~Gk-D~TLfAl~~G~V~f~~~----~~~r~~V~V~p~   84 (91)
T 2zjr_T           23 VKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGR-DHTLFALSDGKVVFINK----GKGARFISIEAA   84 (91)
T ss_dssp             CSSCTTCEECSSCEEECCSSSSSEECTTEECCT-TSCEEESSCEEEEEEEE----TTTEEEEEECCC
T ss_pred             EEecCCeEEcCCeEEEecCCCEEcCCCCEEEcC-CCcEEeccceEEEEEEc----CCCcEEEEEEeC
Confidence            677889999999999654  3499999987652 48999999999999520    134578888874

>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1

Probab=89.68  E-value=0.42  Score=36.64  Aligned_cols=39  Identities=13%  Similarity=0.051  Sum_probs=34.5

Q ss_pred             CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .-|++|+++.|+|++++.-.+.|+|        .. ..|++|++.+.+
T Consensus        79 ~~p~vGev~~G~V~~vt~fG~FVel--------g~-~dGlVhiS~l~d  117 (215)
T 2b8k_G           79 FKPFKGEVVDGTVVSCSQHGFEVQV--------GP-MKVFVTKHLMPQ  117 (215)
T ss_dssp             ECCCTTEEEEEEEEEEETTEEEEEC--------TT-SEEEEEGGGSCS
T ss_pred             eccCCCCEEEEEEEEEecceEEEEe--------cC-cEEEEEHHHCCc
Confidence            4489999999999999999999999        44 789999998854

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=89.53  E-value=0.77  Score=37.73  Aligned_cols=39  Identities=23%  Similarity=0.158  Sum_probs=33.1

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY  118 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr  118 (141)
                      .|..+.|++|.|+|.++....+.|+|        . ...|+|++++..
T Consensus       129 e~~~~~GeIV~G~V~ri~~~~v~VDl--------G-k~EgiLp~sE~i  167 (344)
T 1hh2_P          129 KYSELKGTVTTAEVIRVMGEWADIRI--------G-KLETRLPKKEWI  167 (344)
T ss_dssp             CTTCCTTCEEEEEEEEECSSEEEEEE--------T-TEEEEEEGGGSC
T ss_pred             HHhhcCCCEEEEEEEEEecCcEEEEe--------C-CeEEEEeHHHcC
Confidence            45677999999999999999999999        3 478888888774

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=88.92  E-value=0.14  Score=37.74  Aligned_cols=58  Identities=17%  Similarity=-0.084  Sum_probs=42.8

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccchh--hhHH------HHhhhhccccccc
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYIE--LLMH------LLYGYLGSCKMQL  137 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~~--v~~~------~~f~~vis~gd~~  137 (141)
                      ..-|.+|+++.|+|+++++-.+.|++        . ++.|++|.+++.+.  .+..      +.-.+++.+||.-
T Consensus        79 vf~p~~Gev~~G~V~~v~~fG~FV~l--------~-~~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V  144 (172)
T 3h0g_G           79 LWRPFRGEVVDAIVTTVNKMGFFANI--------G-PLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNV  144 (172)
T ss_dssp             EECCCTTCEEECCCCEEETTEEECCB--------T-TBCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCE
T ss_pred             eeccCCCCEEEEEEEEEEcceEEEEe--------C-CeEEEEEHHHCCCccccCcccccceEecCCcEECCCCEE
Confidence            34599999999999999999999998        3 68899999998541  1110      1123577777754

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=88.53  E-value=0.086  Score=47.35  Aligned_cols=40  Identities=20%  Similarity=0.146  Sum_probs=0.0

Q ss_pred             CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .-|++|+++.|+|+++.+-.|+|+|        .....|+||++++..
T Consensus       623 ~~~~vG~i~~G~V~~i~~fGaFVel--------~~g~eGLvHiSel~~  662 (723)
T 3cdi_A          623 AEIEVGRVYTGKVTRIVDFGAFVAI--------GGGKEGLVHISQIAD  662 (723)
T ss_dssp             ------------------------------------------------
T ss_pred             hhhhcCcEEEEEEEEEecceEEEEe--------CCCceEEEEHHHcCC
Confidence            4589999999999999999999999        456889999999864

>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A

Probab=87.21  E-value=0.69  Score=39.99  Aligned_cols=38  Identities=11%  Similarity=0.146  Sum_probs=34.4

Q ss_pred             CCCCCCEEEEEEEEeccc--eEEEEEEEecCeecccceeEEEeccccc
Q 032397           73 VPEPGSVVIARVTKVMTR--MASADIMCVGAKSVREKFSGIIRFFIFY  118 (141)
Q Consensus        73 ~P~~GdiVig~V~~v~~~--~a~v~I~~v~~~~l~~~~~G~Ir~~dvr  118 (141)
                      -+.+|+|..|+|+++.+.  .|+|+|        ...-.|+||.+|+.
T Consensus        42 ~~~vGnIY~GkV~rv~p~~~aAFVdi--------G~gk~gfLhisei~   81 (517)
T 2bx2_L           42 EQKKANIYKGKITRIEPSLEAAFVDY--------GAERHGFLPLKEIA   81 (517)
T ss_dssp             CCCTTCEEEEEEEEEETTTTEEEEES--------SSSSCEEEEGGGSC
T ss_pred             cCCCCCEEEEEEEEeccCCceEEEEe--------CCCcEEEEEHHHcC
Confidence            368999999999999999  899999        77788999999985

>2ftc_O L27MT, MRP-L27, mitochondrial 39S ribosomal protein L27; mitochondrial ribosome, large ribosomal subunit, ribosomal R ribosome; 12.10A {Bos taurus} PDB: 3iy9_O

Probab=87.13  E-value=0.64  Score=29.76  Aligned_cols=44  Identities=27%  Similarity=0.391  Sum_probs=35.4

Q ss_pred             ccccCCcEEecCCccCCCC--CeeecCcEEEeCCCCeEEEEEeeEEE
Q 032397            3 VKEEEMVLVTPGEVLGKAT--EVKAGKGAYVAKHNGLVYASLTGLLR   47 (141)
Q Consensus         3 ~~~~~~~iVlPGd~L~~~~--e~~~G~GtY~~~~~g~I~Asv~G~~~   47 (141)
                      +|......|.||..|...-  .+-||.++-.-. |..|+|.+.|.++
T Consensus        23 vK~~~Gq~V~aG~IivrQRgtk~hPG~nVg~Gk-D~TLfAl~~G~V~   68 (69)
T 2ftc_O           23 IKKMEGHYVHAGNIIATQRHFRWHPGAHVGVGK-NKCLYALEEGIVR   68 (69)
T ss_pred             EEecCCeEecCCeEEEecCCCeEcCCCCeeecC-CCcEEEccceEEe
Confidence            5778889999999997543  488898886652 4899999999885

>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A

Probab=86.78  E-value=0.39  Score=43.54  Aligned_cols=38  Identities=26%  Similarity=0.246  Sum_probs=34.3

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .++|++|.|+|++|+.-.++|+|        .....|+||++++..
T Consensus       652 l~vG~iv~G~V~~V~~fGaFV~l--------~~~~eGLVhiS~Lsd  689 (785)
T 3bzc_A          652 LKPGMVLEGVVTNVTNFGAFVDI--------GVHQDGLVHISALSE  689 (785)
T ss_dssp             CCTTCBCCCEEEEEETTEEEEEC--------SSSSEEEEETTTSCS
T ss_pred             cCCCCEEEEEEEEEecCCeEEEe--------CCCcEEEEEHHHcCc
Confidence            68999999999999999999998        445789999999975

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=86.40  E-value=0.91  Score=34.82  Aligned_cols=41  Identities=15%  Similarity=0.084  Sum_probs=36.3

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ..-|.+|.++.|+|+.++...+.|++        ..++.|+++.++..+
T Consensus        76 ~f~p~vGEv~~G~Is~Vt~fGifVeL--------~g~~eglv~~s~l~~  116 (218)
T 2ckz_B           76 VFKPFLGEIVTGWISKCTAEGIKVSL--------LGIFDDIFIPQNMLF  116 (218)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEEC--------TTSCCCEEEETTTSC
T ss_pred             EecCCCCCEEEEEEEEEccCcEEEEc--------cCccceEEEcHHHCC
Confidence            35589999999999999999999999        667899999998864

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=86.28  E-value=0.11  Score=46.83  Aligned_cols=38  Identities=21%  Similarity=0.246  Sum_probs=19.0

Q ss_pred             CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEecccc
Q 032397           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIF  117 (141)
Q Consensus        72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dv  117 (141)
                      .-|++|+++.|+|+++.+-.|+|+|        .....|+||++++
T Consensus       663 ~~~~vG~i~~G~V~~i~~fGaFV~l--------~~g~eGLvHiSel  700 (757)
T 1e3p_A          663 TSPEVGERILGSVVKTTTFGAFVSL--------LPGKDGLLHISQI  700 (757)
T ss_dssp             ----------CBEEECC-CSCEECC--------C---CCCCC----
T ss_pred             hhcccccEEEEEEEEccccEEEEEE--------cCCcEEEEEhHHh
Confidence            4589999999999999999999999        5568999999999

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=85.40  E-value=0.97  Score=35.66  Aligned_cols=39  Identities=13%  Similarity=0.099  Sum_probs=30.9

Q ss_pred             CCCCCCCEEEEEEEE----eccceEEEEEEEecCeeccc---ceeEEEeccccc
Q 032397           72 PVPEPGSVVIARVTK----VMTRMASADIMCVGAKSVRE---KFSGIIRFFIFY  118 (141)
Q Consensus        72 ~~P~~GdiVig~V~~----v~~~~a~v~I~~v~~~~l~~---~~~G~Ir~~dvr  118 (141)
                      |..++|++|.|.|.+    +....+.|+|        ..   ...|+|.+++.-
T Consensus         3 ~~~r~GeIVtG~V~r~~~~v~~~~ViVdl--------G~~~~k~EgiLP~~Eqi   48 (251)
T 2asb_A            3 FSTREGEIVAGVIQRDSRANARGLVVVRI--------GTETKASEGVIPAAEQV   48 (251)
T ss_dssp             -CCCTTCEEEEEEECCHHHHHTTCEEEEE--------CSSSSCEEEEECGGGSC
T ss_pred             hhhcCCCEEEEEEEEccccccCCeEEEEe--------CCCCcceEEEEcHHHcC
Confidence            567899999999999    8999999999        33   367777777654

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae}

Probab=85.29  E-value=0.92  Score=43.01  Aligned_cols=41  Identities=10%  Similarity=-0.003  Sum_probs=36.2

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .--+++|++|.|+|++|+.-.|.|+|        .....|+||++++..
T Consensus       897 ~~~l~~G~iv~G~V~~V~~fGaFV~L--------~~gveGLVHiSelsd  937 (1219)
T 3psi_A          897 EKTFFKGSIIPVRVERFWHNDIICTT--------NSEVECVVNAQRHAG  937 (1219)
T ss_dssp             TTTSCTTCEEEEEEEEECSSCEEEEC--------TTSCEEEECTTSSSS
T ss_pred             HhhCCCCCEEEEEEEEEecceEEEEe--------CCCceEEEEHHHcCC
Confidence            34578999999999999999999999        566899999999875

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=85.28  E-value=1.1  Score=33.69  Aligned_cols=39  Identities=15%  Similarity=0.130  Sum_probs=34.2

Q ss_pred             CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .-|.+|.++.|+|++++...+.|++        . ++.|+++.++...
T Consensus        77 f~p~~GEv~~G~Vs~vt~~GifV~l--------g-~~eglv~~~~l~~  115 (203)
T 3ayh_B           77 FRPFRGEVMLGKIKSCSEEGIRVTI--------S-FFDDIFIPKDMLF  115 (203)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEC--------S-SCCCEEEEGGGBC
T ss_pred             EccCCCCEEEEEEEEEeccEEEEEE--------e-CceEEEEcHHhCC
Confidence            4489999999999999999999998        3 6889999988864

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=83.46  E-value=1.2  Score=36.88  Aligned_cols=40  Identities=13%  Similarity=0.090  Sum_probs=32.1

Q ss_pred             CCCCCCCCEEEEEEEE----eccceEEEEEEEecCeeccc---ceeEEEeccccc
Q 032397           71 GPVPEPGSVVIARVTK----VMTRMASADIMCVGAKSVRE---KFSGIIRFFIFY  118 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~----v~~~~a~v~I~~v~~~~l~~---~~~G~Ir~~dvr  118 (141)
                      .|..++|++|.|.|.+    +....+.|+|        ..   ...|+|++++.-
T Consensus       125 ef~~r~GeIVtG~V~r~~~~v~~~~v~VdL--------G~~~~k~EgiLP~~Eqi  171 (366)
T 1k0r_A          125 EFSTREGEIVAGVIQRDSRANARGLVVVRI--------GTETKASEGVIPAAEQV  171 (366)
T ss_dssp             --CCCTTCEEEEEEECCHHHHHTTCEEEEE--------CCSSSCEEEEECGGGSC
T ss_pred             HHHhcCCCEEEEEEEEccccccCCeEEEEe--------CCCccceEEEEcHHHcC
Confidence            4668999999999999    9999999999        33   367888877764

>1y71_A Kinase-associated protein B; structural genomics, midwest CE structural genomics, MCSG, protein structure initiative, PS unknown function; 1.95A {Bacillus cereus} SCOP: b.34.16.1

Probab=81.41  E-value=2.7  Score=29.92  Aligned_cols=46  Identities=17%  Similarity=0.080  Sum_probs=37.2

Q ss_pred             CCCCCEE---------EEEEEEeccceEEEEEEEecC---------------------eecccceeEEEeccccch
Q 032397           74 PEPGSVV---------IARVTKVMTRMASADIMCVGA---------------------KSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiV---------ig~V~~v~~~~a~v~I~~v~~---------------------~~l~~~~~G~Ir~~dvr~  119 (141)
                      .++||+|         +|.|+..+++.+.|.|++|--                     +.|+..-+..+..+.+++
T Consensus         8 ~~~g~~v~~~yKTG~YigeI~e~~~~~~lVkVlaVlKHP~QGDLHnP~q~dvpfFHERkALs~~Ek~~ip~~~vk~   83 (130)
T 1y71_A            8 FEIGEIVTGIYKTGKYIGEVTNSRPGSYVVKVLAVLKHPVQGDLHNVKQANVPFFHERRALAFREQTNIPEQMVKK   83 (130)
T ss_dssp             CCTTCEEEEEETTEEEEEEEEEEETTEEEEEEEEEEECCCC---------------CCCCCCTTCEEEEEGGGEEE
T ss_pred             CCccceeEEEEecceeEEEEEeecCCeEEEEEEEEecCCCccCCCCCCcCCCcceeehhhccHHHHhcCCHHhccc
Confidence            5889999         899999999999999999822                     455666677778888875

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	141
d2nn6i1	125	b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {H	4e-09
d2nn6i2	55	b.84.4.2 (I:6-60) Exosome component 1, EXOSC1 {Hum	1e-05
d2je6i2	59	b.84.4.2 (I:7-65) Exosome complex RNA-binding prot	0.004

>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]} Length = 125

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.5 bits (118), Expect = 4e-09
 Identities = 13/43 (30%), Positives = 25/43 (58%)

Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFF 115
           +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR  
Sbjct: 4   LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKE 46

>d2nn6i2 b.84.4.2 (I:6-60) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]} Length = 55

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: ECR1 N-terminal domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (90), Expect = 1e-05
 Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 2/35 (5%)

Query: 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTG 44
             PGE L    E   G G Y    +G +++SL G
Sbjct: 2  YCIPGERLCNLEEGSPGSGTYT--RHGYIFSSLAG 34

>d2je6i2 b.84.4.2 (I:7-65) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 59

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: ECR1 N-terminal domain-like
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 31.6 bits (72), Expect = 0.004
 Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 1/36 (2%)

Query: 10 LVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGL 45
          +V PGE+L +    +     Y+ K N   Y+++ GL
Sbjct: 10 IVVPGELLAEGEF-QIPWSPYILKINSKYYSTVVGL 44

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	141
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	99.8
d2nn6i2	55	Exosome component 1, EXOSC1 {Human (Homo sapiens)	99.52
d2ba0a2	51	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.42
d2nn6h2	48	Ribosomal RNA-processing protein 4, RRP4 {Human (H	99.32
d2je6i2	59	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.3
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	98.89
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	98.79
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	98.7
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	98.7
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	98.69
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	98.55
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	97.72
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	97.63
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	96.97
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	96.92
d2nn6g2	91	Ribosomal RNA-processing protein 40, RRP40 {Human	96.79
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	96.6
d1v8qa_	66	Ribosomal protein L27 {Thermus thermophilus [TaxId	96.31
d2zjrt1	84	Ribosomal protein L27 {Deinococcus radiodurans [Ta	95.86
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	95.22
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	94.74
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	94.69
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	93.16
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	89.31
d1uwva1	60	rRNA (Uracil-5-)-methyltransferase RumA, N-termina	85.34
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	84.97
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	83.96
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	80.28

>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=8.1e-21  Score=135.87  Aligned_cols=71  Identities=24%  Similarity=0.350  Sum_probs=66.9

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch----hhhHHHHhh-------hhccccccc-e
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI----ELLMHLLYG-------YLGSCKMQL-N  138 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~----~v~~~~~f~-------~vis~gd~~-~  138 (141)
                      .++|++||+|+|+|+++++++|.|+|++++++++..+|.|+||.||+|.    +++|++||+       +++|+||.+ +
T Consensus         2 ~~vP~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~~~~~~   81 (125)
T d2nn6i1           2 QLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSN   81 (125)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTE
T ss_pred             CcCCCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEccCCCcc
Confidence            6899999999999999999999999999999999999999999999986    689999995       999999986 5


Q ss_pred             eeC
Q 032397          139 YSL  141 (141)
Q Consensus       139 y~l  141 (141)
                      |||
T Consensus        82 ~~L   84 (125)
T d2nn6i1          82 YLL   84 (125)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            886

>d2nn6i2 b.84.4.2 (I:6-60) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: ECR1 N-terminal domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=2.2e-16  Score=97.56  Aligned_cols=38  Identities=34%  Similarity=0.591  Sum_probs=36.5

Q ss_pred             cEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEe
Q 032397            9 VLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRT   48 (141)
Q Consensus         9 ~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~   48 (141)
                      ++|+|||+|+.++||.||+|||+++  |+||||++|.+.+
T Consensus         1 k~~lPGe~L~~~eey~~G~gTy~~~--g~I~as~~G~v~i   38 (55)
T d2nn6i2           1 RYCIPGERLCNLEEGSPGSGTYTRH--GYIFSSLAGCLMK   38 (55)
T ss_dssp             CCCCTTCEEEETTTCCCSSSCEEET--TEEECCSCSCBCC
T ss_pred             CcccCCcEEeehheecCCCCeEEcC--CEEEEEeeEEEEE
Confidence            4799999999999999999999999  9999999999988

>d2ba0a2 b.84.4.2 (A:2-52) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: ECR1 N-terminal domain-like
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.42  E-value=8.6e-14  Score=84.65  Aligned_cols=50  Identities=36%  Similarity=0.567  Sum_probs=45.0

Q ss_pred             CcEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCCC
Q 032397            8 MVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKA   69 (141)
Q Consensus         8 ~~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~~   69 (141)
                      +++|+|||.|++ ++|.+|+|||.++  |+|+|+++|.++..         ++.|+|+|+++
T Consensus         1 r~iV~PGe~i~~-~~~~~G~Gty~~~--~~i~ss~~G~v~~~---------n~~i~V~PL~g   50 (51)
T d2ba0a2           1 RKIVLPGDLLST-NPRAAGYGTYVEG--GKVYAKIIGLFDQT---------ETHVRVIPLKG   50 (51)
T ss_dssp             CCEECTTCEEES-CTTSBCTTEEEET--TEEEECSSEEEEEC---------SSCEEEEECSS
T ss_pred             CCEEcCCcEeec-CCeeCCCCcEEEC--CEEEEEEEEEEEEE---------CCEEEEEeCcc
Confidence            369999999986 5799999999999  99999999999883         78999999874

>d2nn6h2 b.84.4.2 (H:25-72) Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: ECR1 N-terminal domain-like
domain: Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=6.5e-13  Score=79.36  Aligned_cols=48  Identities=25%  Similarity=0.440  Sum_probs=44.1

Q ss_pred             cEEecCCccCCCCCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecC
Q 032397            9 VLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (141)
Q Consensus         9 ~iVlPGd~L~~~~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~   67 (141)
                      .+|+|||.|...+.|..|+|||+++  ++++||++|.++..         ++.++|+|.
T Consensus         1 ~iv~PGe~It~~~~~mrGHGTy~~~--~~i~aSv~G~verv---------NKLvsV~pL   48 (48)
T d2nn6h2           1 HLVVPGDTITTDTGFMRGHGTYMGE--EKLIASVAGSVERV---------NKLICVKAL   48 (48)
T ss_dssp             CBCCTTCBCCCCTTCCBCTTEEECS--SSEEECSSEEEEEE---------TTEEEEEES
T ss_pred             CEecCCcEeecCCCeEcccccEecC--CEEEEEEeeeEEEe---------ccEEEEEcC
Confidence            3799999999988899999999999  99999999999885         799999974

>d2je6i2 b.84.4.2 (I:7-65) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: ECR1 N-terminal domain-like
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.30  E-value=1.2e-12  Score=81.65  Aligned_cols=53  Identities=19%  Similarity=0.236  Sum_probs=47.4

Q ss_pred             ccCCcEEecCCccCCCCCeee-cCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecCC
Q 032397            5 EEEMVLVTPGEVLGKATEVKA-GKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHK   68 (141)
Q Consensus         5 ~~~~~iVlPGd~L~~~~e~~~-G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~~   68 (141)
                      .+++++|+|||.|+...++.+ |.|||..+  ++||||++|.+++.         ++.|+|+|++
T Consensus         5 v~~r~iV~PGdvi~~~~~~~~~g~~ty~~~--~ki~asv~G~v~~~---------nkli~ViPL~   58 (59)
T d2je6i2           5 LQPRSIVVPGELLAEGEFQIPWSPYILKIN--SKYYSTVVGLFDVK---------DTQFEVIPLE   58 (59)
T ss_dssp             CCSSCEECTTCEEEEECCCCCCCTTEEEET--TEEEECSSEEEEEE---------TTEEEEEESC
T ss_pred             EcCCeEECCCcEeeeCCccccCCCEEEecC--CEEEEEEEEEEEEE---------CCEEEEEECC
Confidence            467889999999998777874 99999999  99999999999984         6899999976

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.89  E-value=6.4e-10  Score=74.66  Aligned_cols=60  Identities=15%  Similarity=0.189  Sum_probs=48.1

Q ss_pred             CCCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc--------h----hhhHHHHhh-------hh
Q 032397           70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY--------I----ELLMHLLYG-------YL  130 (141)
Q Consensus        70 ~~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr--------~----~v~~~~~f~-------~v  130 (141)
                      ..|.|++||+|+|+|+++++..|.|+|        ...+.|+||.+++.        .    ..+|.+.|+       ++
T Consensus         2 ~~Y~P~vGdiV~G~V~~v~~~g~~V~I--------~~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV   73 (95)
T d2nn6h1           2 TRYIGEVGDIVVGRITEVQQKRWKVET--------NSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEV   73 (95)
T ss_dssp             CCCCCCSSBCCCEEEEEEETTEEEEEC--------SSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEE
T ss_pred             CcccCCCCCEEEEEEEEEecCcEEEEe--------CCCceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEE
Confidence            479999999999999999999999999        77789999998872        1    356777774       66


Q ss_pred             ccccccc
Q 032397          131 GSCKMQL  137 (141)
Q Consensus       131 is~gd~~  137 (141)
                      +++....
T Consensus        74 ~~v~~dg   80 (95)
T d2nn6h1          74 QAVFSDG   80 (95)
T ss_dssp             EEEETTT
T ss_pred             EEECCCC
Confidence            6664433

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.79  E-value=1.2e-09  Score=71.85  Aligned_cols=41  Identities=17%  Similarity=0.072  Sum_probs=38.8

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .|.|++||+|+|+|++++...|.|+|        ...+.|+||.+++..
T Consensus         2 ~Y~Pk~Gdiv~G~V~~i~~~g~fV~i--------~~~~~gll~~s~~~~   42 (87)
T d2je6i1           2 FYYPKINDIVIGLVEDVEIYGWVVDI--------KAPYKAYLPASNLLG   42 (87)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEEC--------SSSSCEEEEHHHHHT
T ss_pred             cccCCCCCEEEEEEEEEECCEEEEEe--------CCCEEEEEehHHhCC
Confidence            69999999999999999999999999        888999999999965

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.70  E-value=4.7e-09  Score=69.72  Aligned_cols=40  Identities=23%  Similarity=0.251  Sum_probs=37.5

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY  118 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr  118 (141)
                      +|+|++||+|+|+|++++...|+|+|        .+++.|+|+.+++.
T Consensus         1 rY~P~~GD~ViG~V~~~~~~~~~VdI--------~s~~~a~L~~~~f~   40 (88)
T d2nn6g1           1 RYVPVKGDHVIGIVTAKSGDIFKVDV--------GGSEPASLSYLSFE   40 (88)
T ss_dssp             SCCCCSSEEEEEEEEEEETTEEEEEC--------SSSSCCCEESCSSS
T ss_pred             CCcCCCCCEEEEEEEEEeCCeEEEEc--------CCCeeEEEeHHHcC
Confidence            58999999999999999999999999        88999999998874

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=98.70  E-value=6.4e-09  Score=69.30  Aligned_cols=41  Identities=10%  Similarity=0.156  Sum_probs=36.2

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      +|+|++||+|+|+|++++...|.|+|        .+++.|+|+.+...+
T Consensus         2 rY~P~~gD~ViG~V~~~~~~~~~vdI--------~~~~~~~L~~~~~f~   42 (90)
T d2ja9a1           2 RYIPSVNDFVIGVIIGTFSDSYKVSL--------QNFSSSVSLSYMAFP   42 (90)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEES--------STTSCCEEEETTSST
T ss_pred             CccCCCCCEEEEEEEEEeCCcEEEEc--------CCcchhhhhhhhccC
Confidence            79999999999999999999999999        777888887666554

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.69  E-value=3.7e-09  Score=69.51  Aligned_cols=41  Identities=24%  Similarity=0.237  Sum_probs=38.6

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      .|.|++||+|+|+|+++++..|.|+|        ...+.|+||.+++..
T Consensus         2 ~Y~Pk~GdvV~G~V~~v~~~g~fV~i--------~~~~~g~l~~se~~~   42 (88)
T d2z0sa1           2 IYVPQAGDVVIGLIQSVGIMNWFVDI--------NSPYVAVLSVQDFLG   42 (88)
T ss_dssp             CCCCCTTCCEEEEEEEECSSEEEEEC--------SSSSCEEEEHHHHHT
T ss_pred             CcCCCCCCEEEEEEEEEECCeEEEEe--------CCCeEEEEehHHhCc
Confidence            58999999999999999999999999        888999999999965

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.55  E-value=4e-08  Score=63.66  Aligned_cols=48  Identities=17%  Similarity=0.114  Sum_probs=41.3

Q ss_pred             CCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch---hhhHHHHh
Q 032397           72 PVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI---ELLMHLLY  127 (141)
Q Consensus        72 ~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~---~v~~~~~f  127 (141)
                      |.|++||+|+|+|+++.+..|.|+|        ...+.|+||.+++..   .-++.+.|
T Consensus         1 Y~Pk~Gd~V~G~V~~v~~~g~~V~i--------~~~~~g~l~~se~s~~~~~~~~~~~~   51 (83)
T d2ba0a1           1 YTPSVGDVVIGIIREVAANGWAVDI--------YSPYQAFLPVSENPEMKPNKKPNEVL   51 (83)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEEC--------SSSSCEEEEGGGCTTCCTTSCGGGTC
T ss_pred             CcCCCCCEEEEEEEEEECCEEEEec--------CCCeeEEEecccccccccccChhhhc
Confidence            7899999999999999999999999        888999999999964   23455555

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.72  E-value=4.6e-05  Score=49.03  Aligned_cols=41  Identities=20%  Similarity=0.221  Sum_probs=35.1

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecc--cceeEEEeccccch
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVR--EKFSGIIRFFIFYI  119 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~--~~~~G~Ir~~dvr~  119 (141)
                      ...|++||+|.|+|++++...+.|+|        .  ....|+||.+++..
T Consensus         8 ~~~p~~G~iv~G~V~~i~~~G~fV~l--------~~~~~i~G~i~~sels~   50 (86)
T d1kl9a2           8 HKFPEVEDVVMVNVRSIAEMGAYVSL--------LEYNNIEGMILLSELSR   50 (86)
T ss_dssp             SSSCCTTCEEEEEEEEECSSEEEEEE--------TTTTTEEEEEEGGGC--
T ss_pred             hcCCCCCCEEEEEEEEEeCCeEEEEE--------ecCCCEEEEEEeeeccc
Confidence            35699999999999999999999999        4  35899999999975

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=97.63  E-value=4.9e-05  Score=48.53  Aligned_cols=42  Identities=17%  Similarity=0.295  Sum_probs=36.9

Q ss_pred             CCCCCCCCCEEEEEEEEeccceEEEEEEEecCeeccc--ceeEEEeccccch
Q 032397           70 HGPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVRE--KFSGIIRFFIFYI  119 (141)
Q Consensus        70 ~~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~--~~~G~Ir~~dvr~  119 (141)
                      ...+|++|++|.|+|+++++..+.|++        ..  ...|+||.+++..
T Consensus         5 ~~~~p~~G~iv~G~V~~v~~~G~fV~l--------~~~~gi~Gli~~sels~   48 (84)
T d2ahob2           5 RSKLPSEGEILIATVKQVFDYGSYVSL--------DEYGGLQAFLPWSEVSS   48 (84)
T ss_dssp             SSSSCCTTCCCEEEEEEEETTEEEEEE--------TTTTTEEEEECGGGCC-
T ss_pred             cccCCCCCCEEEEEEEEEECCEEEEEE--------CCcCCEEEEEEcccccc
Confidence            356799999999999999999999999        53  5899999999986

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=96.97  E-value=0.00034  Score=46.64  Aligned_cols=37  Identities=16%  Similarity=0.168  Sum_probs=34.1

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |++|+++-|+|++|++..+.|+|        . +..|++|.+++..
T Consensus         1 p~~gei~~g~V~~v~~~G~FVel--------~-~ieGlv~~s~l~~   37 (106)
T d1go3e1           1 PEMYELIEGEVVDVVEFGSFVRL--------G-PLDGLIHVSQIMD   37 (106)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEC--------S-SSEEEEEGGGSCS
T ss_pred             CCCCCEEEEEEEEEeeeEEEEEe--------e-CeEEEEEeecccC
Confidence            89999999999999999999998        3 4789999999975

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Escherichia coli [TaxId: 562]

Probab=96.92  E-value=0.00034  Score=43.83  Aligned_cols=46  Identities=17%  Similarity=0.087  Sum_probs=38.6

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch-h-hhHHHHh
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI-E-LLMHLLY  127 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~-~-v~~~~~f  127 (141)
                      .++|++|.|+|+++.+..|.|++        .....|+||.+++.. + ..+.+-|
T Consensus         3 ~kvG~iv~G~V~~v~~~G~fV~l--------~~~~~Glv~~sels~~~~~~~~~~~   50 (76)
T d1sroa_           3 IEVGRVYTGKVTRIVDFGAFVAI--------GGGKEGLVHISQIADKRVEKVTDYL   50 (76)
T ss_dssp             CCTTSEEEEEEEEEETTEEEEEC--------SSSCCCBCCTTSSCSSCCSCHHHHC
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEe--------CCCCEEEEEhHHhCccccCCHHHcc
Confidence            58999999999999999999999        667899999999976 3 3444444

>d2nn6g2 b.84.4.2 (G:16-106) Ribosomal RNA-processing protein 40, RRP40 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: ECR1 N-terminal domain-like
domain: Ribosomal RNA-processing protein 40, RRP40
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.79  E-value=0.00062  Score=44.38  Aligned_cols=56  Identities=23%  Similarity=0.199  Sum_probs=31.9

Q ss_pred             CcEEecCCccCCC-------------------------CCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeE
Q 032397            8 MVLVTPGEVLGKA-------------------------TEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTV   62 (141)
Q Consensus         8 ~~iVlPGd~L~~~-------------------------~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i   62 (141)
                      ..+|+|||.|...                         ...+.|+|...++  +.|.|+.+|.+++.+|+.  .......
T Consensus         9 ~qvVlPGD~l~lp~~~~~~g~~~~~~~~l~L~~~~~~~~~v~lGPGLRq~~--d~v~atKaG~LR~k~P~~--~~~~~~y   84 (91)
T d2nn6g2           9 GQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCG--DRLLVTKCGRLRHKEPGS--GSGGGVY   84 (91)
T ss_dssp             SSBCCSSEEECCSCSCCEECSSEEECC-----------------------C--CCEEECSCCEEEEECCTT--TSSCCEE
T ss_pred             CCEEeCCcEEEecccccccccCcCcccccccccccCCCceEEeCCccceeC--CEEEEeecceeeecCCCC--CCCcceE
Confidence            5789999999411                         1378899999999  999999999999965321  1123578


Q ss_pred             EEecC
Q 032397           63 EVTGH   67 (141)
Q Consensus        63 ~V~~~   67 (141)
                      ||...
T Consensus        85 WVDs~   89 (91)
T d2nn6g2          85 WVDSQ   89 (91)
T ss_dssp             EEECC
T ss_pred             Eeecc
Confidence            88764

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Tex S1-domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=96.60  E-value=0.0016  Score=42.11  Aligned_cols=37  Identities=27%  Similarity=0.274  Sum_probs=34.9

Q ss_pred             CCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           75 EPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        75 ~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ++|++|.|+|++++...+.|++        .....|+||.+++..
T Consensus        17 k~G~iv~g~V~~v~~~G~~V~l--------~~~i~G~i~~~~ls~   53 (94)
T d3bzka4          17 KPGMVLEGVVTNVTNFGAFVDI--------GVHQDGLVHISALSE   53 (94)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEC--------SSSSCEEEEGGGGCS
T ss_pred             CCCCEEEEEEEEEECcEEEEEe--------CCCceEEeehhhhhc
Confidence            7899999999999999999999        778999999999975

>d1v8qa_ b.84.4.1 (A:) Ribosomal protein L27 {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: Ribosomal L27 protein
domain: Ribosomal protein L27
species: Thermus thermophilus [TaxId: 274]

Probab=96.31  E-value=0.0021  Score=39.66  Aligned_cols=60  Identities=23%  Similarity=0.262  Sum_probs=47.5

Q ss_pred             ccccCCcEEecCCccCCC--CCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecC
Q 032397            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (141)
Q Consensus         3 ~~~~~~~iVlPGd~L~~~--~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~   67 (141)
                      +|...+++|.||+.|...  ..|.||.++..-. |..|+|..-|.++..+.    ..+++.|+|.|.
T Consensus         4 vK~~~Gq~V~~G~IivRQRGtk~~pG~nVg~Gk-D~TLfAl~~G~V~F~~~----~~~~~~VsV~P~   65 (66)
T d1v8qa_           4 VKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGR-DFTLFALVDGVVEFQDR----GRLGRYVHVRPL   65 (66)
T ss_dssp             ECSCTTCEECTTCEEEECSSCSSEECTTEEECT-TCCEEESSSEEEEEEEC----GGGCEEEEEEEC
T ss_pred             cEEeCCEEEeCCeEEEEeccCeEeCCCCeeecC-CCcEEEeeeeEEEEEEe----CCCCeEEEEEEC
Confidence            577889999999999654  3599999999873 58999999999998531    123578999875

>d2zjrt1 b.84.4.1 (T:2-85) Ribosomal protein L27 {Deinococcus radiodurans [TaxId: 1299]}

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: Ribosomal L27 protein
domain: Ribosomal protein L27
species: Deinococcus radiodurans [TaxId: 1299]

Probab=95.86  E-value=0.0037  Score=40.20  Aligned_cols=60  Identities=20%  Similarity=0.295  Sum_probs=46.8

Q ss_pred             ccccCCcEEecCCccCCC--CCeeecCcEEEeCCCCeEEEEEeeEEEeeCCCCCCCCCCCeEEEecC
Q 032397            3 VKEEEMVLVTPGEVLGKA--TEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGH   67 (141)
Q Consensus         3 ~~~~~~~iVlPGd~L~~~--~e~~~G~GtY~~~~~g~I~Asv~G~~~~~~~~~~~~~~~~~i~V~~~   67 (141)
                      +|....++|.||+.|...  ..|.||.++..-. |..|+|.+-|.+++..    ...+++.|+|.|.
T Consensus        22 vK~~~Gq~V~~G~IivRQRGtk~hpG~nVg~Gk-D~TLfA~~~G~V~F~k----~~~~rk~V~V~p~   83 (84)
T d2zjrt1          22 VKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGR-DHTLFALSDGKVVFIN----KGKGARFISIEAA   83 (84)
T ss_dssp             CSSCTTCEECSSCEEECCSSSSSEECTTEECCT-TSCEEESSCEEEEEEE----ETTTEEEEEECCC
T ss_pred             EEECCCEEEeCCcEEEEecCceEcCCCCccccC-CCcEEEeeceEEEEEE----cCCCCEEEEEEeC
Confidence            577788999999999654  3599999999863 5899999999999952    0123468888874

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of RRP5 protein homolog (PDCD11, KIAA0185)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.22  E-value=0.011  Score=39.69  Aligned_cols=38  Identities=13%  Similarity=0.162  Sum_probs=34.2

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecc-cceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVR-EKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~-~~~~G~Ir~~dvr~  119 (141)
                      .++|++|.|+|++|....+.|+|        . ..+.|+|+.+++.+
T Consensus        19 l~~G~iv~G~V~~i~~~G~~V~l--------g~~~~~G~l~~~els~   57 (119)
T d1wi5a_          19 LKPGMLLTGTVSSLEDHGYLVDI--------GVDGTRAFLPLLKAQE   57 (119)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEEC--------CCSSCEEEEEHHHHHH
T ss_pred             cCCCCEEEEEEEEEeccEEEEEE--------eccccceEEeHHHhcc
Confidence            58899999999999999999998        5 56899999999864

>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.74  E-value=0.04  Score=34.77  Aligned_cols=37  Identities=14%  Similarity=0.102  Sum_probs=33.6

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |-+|+++-|+|++++..-+.|+|        . ++.|+|+++.+.+
T Consensus         1 Pf~Gev~~g~I~~v~~~G~fv~l--------g-~~eg~i~~~~l~~   37 (91)
T d1y14b1           1 PFKGEVVDGTVVSCSQHGFEVQV--------G-PMKVFVTKHLMPQ   37 (91)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEE--------T-TEEEEEEGGGSCT
T ss_pred             CCCCCEEEEEEEEEEeeEEEEEE--------c-CeEEEEEhhhcCc
Confidence            77899999999999999999999        3 5799999998875

>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 domain of NusA
species: Thermotoga maritima [TaxId: 2336]

Probab=94.69  E-value=0.054  Score=33.30  Aligned_cols=39  Identities=23%  Similarity=0.158  Sum_probs=32.4

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccc
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY  118 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr  118 (141)
                      .|..++|++|.|.|.++..+.+.|+|        . ...|+|.+++--
T Consensus         3 ef~~~~geiv~G~V~r~~~~~~~Vdl--------g-~~eaiLp~~eqi   41 (72)
T d1hh2p1           3 KYSELKGTVTTAEVIRVMGEWADIRI--------G-KLETRLPKKEWI   41 (72)
T ss_dssp             CTTCCTTCEEEEEEEEECSSEEEEEE--------T-TEEEEEEGGGSC
T ss_pred             hHhhccCcEEEEEEEEEcCCCEEEEE--------C-CcEEECCHHHcC
Confidence            35678999999999999999999998        3 477888877653

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.16  E-value=0.13  Score=32.53  Aligned_cols=37  Identities=30%  Similarity=0.144  Sum_probs=33.9

Q ss_pred             CCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           74 PEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        74 P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |-.|.++.|+|++++..-+.|++        . ++.|+++++++..
T Consensus         2 Pf~Gev~~g~V~~v~~~G~fv~l--------g-~~~~~v~~~~l~~   38 (94)
T d2c35b1           2 PFKGEVVDAVVTQVNKVGLFTEI--------G-PMSCFISRHSIPS   38 (94)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEE--------T-TEEEEEEGGGSCT
T ss_pred             CCCCCEEEEEEEEEEeeEEEEEe--------c-CceEEEEhhhcCc
Confidence            77899999999999999999999        3 6899999999875

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Streptomyces antibioticus [TaxId: 1890]

Probab=89.31  E-value=0.025  Score=33.74  Aligned_cols=30  Identities=17%  Similarity=0.054  Sum_probs=18.6

Q ss_pred             EEEEEeccceEEEEEEEecCeecccceeEEEeccccch
Q 032397           82 ARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        82 g~V~~v~~~~a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      |+|++|.+--|.|+|        .....|+||++++..
T Consensus         1 G~V~~i~~fG~FV~l--------~~g~~Glihiseis~   30 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSL--------LPGKDGLLHISQIRK   30 (62)
T ss_dssp             CBEEECC-CSCEECC--------C---CCCCC------
T ss_pred             CEEEEEEeceEEEEe--------cCCceEEEEHHHccc
Confidence            689999999999999        678999999999963

>d1uwva1 b.40.4.12 (A:15-74) rRNA (Uracil-5-)-methyltransferase RumA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: TRAM domain
domain: rRNA (Uracil-5-)-methyltransferase RumA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=85.34  E-value=0.83  Score=26.34  Aligned_cols=25  Identities=20%  Similarity=0.100  Sum_probs=22.7

Q ss_pred             CCCEEEEEEEEeccceEEEEEEEec
Q 032397           76 PGSVVIARVTKVMTRMASADIMCVG  100 (141)
Q Consensus        76 ~GdiVig~V~~v~~~~a~v~I~~v~  100 (141)
                      +||.|..+|++...++|..+++.+-
T Consensus        32 PGE~V~v~i~~~~~~~~~a~~~eil   56 (60)
T d1uwva1          32 PQENAEVTVTEDKKQYARAKVVRRL   56 (60)
T ss_dssp             TTCEEEEEEEEECSSEEEEEEEEEC
T ss_pred             CCCEEEEEEEEecCCeEEEEEEEEe
Confidence            6999999999999999999997653

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=84.97  E-value=0.39  Score=30.29  Aligned_cols=41  Identities=29%  Similarity=0.473  Sum_probs=25.3

Q ss_pred             CCCCCCCCEEEEEEEEeccceEEEEEEEecCeecccceeEEE
Q 032397           71 GPVPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGII  112 (141)
Q Consensus        71 ~~~P~~GdiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~G~I  112 (141)
                      ...-++||+|+|||.++..+. .+++-|++...=++...|.|
T Consensus        49 r~~l~~GDlV~arV~~v~~~~-~~~Lsc~~~~~gK~~g~G~L   89 (90)
T d2ja9a1          49 RPTLQVGDLVYARVCTAEKEL-EAEIECFDSTTGRDAGFGIL   89 (90)
T ss_dssp             CCCCCTTCEEEEEEEECCTTS-CCEEESSCTTTCSCTTCEEE
T ss_pred             CCccCCCCEEEEEEEEECCCC-CEEEEEeccccCcccccccc
Confidence            344599999999999998775 23334444322233444443

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribonuclease E
species: Escherichia coli [TaxId: 562]

Probab=83.96  E-value=0.52  Score=29.64  Aligned_cols=34  Identities=12%  Similarity=0.183  Sum_probs=30.0

Q ss_pred             CEEEEEEEEeccce--EEEEEEEecCeecccceeEEEeccccch
Q 032397           78 SVVIARVTKVMTRM--ASADIMCVGAKSVREKFSGIIRFFIFYI  119 (141)
Q Consensus        78 diVig~V~~v~~~~--a~v~I~~v~~~~l~~~~~G~Ir~~dvr~  119 (141)
                      ||-+|+|++|.+..  |+|||        ...-.|.|+..|+..
T Consensus         2 NIY~G~V~~V~pgl~AAFVDi--------G~~k~gFL~~~di~~   37 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDY--------GAERHGFLPLKEIAR   37 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEES--------SSSSCEEEEGGGSCG
T ss_pred             CcEEEEEEEecCCceEEEEEe--------CCCccceeEecccce
Confidence            67899999997765  99999        888899999999874

>d2asba1 b.40.4.5 (A:108-183) S1 domain of NusA {Mycobacterium tuberculosis [TaxId: 1773]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 domain of NusA
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=80.28  E-value=0.86  Score=27.85  Aligned_cols=38  Identities=13%  Similarity=0.110  Sum_probs=25.7

Q ss_pred             CCCCEEEEEEEEeccc----eEEEEEEEecCeecccceeEEEecccc
Q 032397           75 EPGSVVIARVTKVMTR----MASADIMCVGAKSVREKFSGIIRFFIF  117 (141)
Q Consensus        75 ~~GdiVig~V~~v~~~----~a~v~I~~v~~~~l~~~~~G~Ir~~dv  117 (141)
                      ++|++|.|.|.++..+    .+.+++-.-     .....|+|.+++-
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~-----~~~~EaiLp~~eq   44 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTE-----TKASEGVIPAAEQ   44 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSS-----SSCEEEEECGGGS
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCC-----CCCEEEECCHHHc
Confidence            7899999999999754    377887110     0235677766554