Psyllid ID: psy230

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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-------150-------160-------170-------180-------190-------200-------210-------220--
Protein Sequence
MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFLQ
Secondary Structure (PSIPRED)
ccccEEcccccccEEEcccEEEEccEEEEEEEEEEEEEcccEEEEEccccccccccccEEEEEEEEEEccEEEEEccccccEEEEcccccccccccccccccccEEEEEEEEEcccccEEEEEEccccccccEEEcccEEEEEEccHHHHHHccccccHHHHHHHcccccEEEEEEEccEEEEEcccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccccccEEEccccEccccEEEEEEEEEEEEccccEEEEEccccEEEcccccEEEEEEEEccccEEEEEcccccccEccHHcccccccccccccccEccccccEcEccHHHcHHHHEEcccccccccccccccEEEEEcHHHHHHHHccccHHHHHHHHHccccEEEEEEcccEEEEEcccHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
magdtlslnaeprlilgpglrressAILVSQsgilrhakpftyYVDYIQrryvptrgdlVIGVVTsrvgdnyrvdigshdpAVLSYLAfegatkknppkvetgdvVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKllnpkcplLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFLQ
Flexible Loop (DISEMBL)
magdtlslnaeprlilgpglrreSSAILVsqsgilrhakpFTYYVDYIQRryvptrgdlVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEgatkknppkvetgdvVAGKLltankdmeseMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFLQ
Low Complexity Region (SEG)
MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFLQ
Disordered region (IsUnstruct)
**************ILG**L***SSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGAT*********GDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRF**
Disordered Region (DISOPRED)
MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE***KKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFL*
Disordered Region (DISEMBL)
MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFLQ
Disordered Region (DISPRO)
***DTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRF**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFLQ
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	222	2.2.26 [Sep-21-2011]
Q3T0E1	275	Exosome complex component	yes	N/A	0.905	0.730	0.443	8e-49
Q9NQT5	275	Exosome complex component	yes	N/A	0.905	0.730	0.439	1e-48
Q7TQK4	274	Exosome complex component	yes	N/A	0.905	0.733	0.450	1e-48
Q7KWX9	237	Putative exosome complex	yes	N/A	0.923	0.864	0.350	5e-33
Q08285	240	Exosome complex component	yes	N/A	0.896	0.829	0.369	8e-33
O13903	240	Exosome complex component	yes	N/A	0.896	0.829	0.386	8e-33
E0SQX5	253	Probable exosome complex	yes	N/A	0.576	0.505	0.3	6e-07
B1L6N8	228	Probable exosome complex	yes	N/A	0.603	0.587	0.255	4e-05
Q9YC02	235	Probable exosome complex	yes	N/A	0.572	0.540	0.287	0.0002
D5U396	247	Probable exosome complex	yes	N/A	0.639	0.574	0.262	0.0002

>sp|Q3T0E1|EXOS3_BOVIN Exosome complex component RRP40 OS=Bos taurus GN=EXOSC3 PE=2 SV=1

 Score =  193 bits (490), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 95/214 (44%), Positives = 144/214 (67%), Gaps = 13/214 (6%)

Query: 6   LSLNAEPR----LILGPGLRRESSAILVSQSGILRHAKPFT------YYVDYIQRRYVPT 55
           L LNA  R    ++ GPGLRR    +LV++ G LRH +P +      Y+VD  Q+RYVP 
Sbjct: 53  LRLNAAARSRGRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPV 112

Query: 56  RGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANK 115
           +GD VIG+VT++ GD ++VD+G  +PA LSYLAFEGATK+N P V+ GD++ G+ + ANK
Sbjct: 113 KGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLAFEGATKRNRPNVQVGDLIYGQFVVANK 172

Query: 116 DMESEMVCVDSRGKEFIMGIL-NDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELS 174
           DME EMVC+DS G+   MG++  DG L   ++ L RKLL P C +L+++ K     +E+ 
Sbjct: 173 DMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEILQEVGK--LYPLEIV 230

Query: 175 IGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEE 208
            GMNG+IW++ ++   T+ + N++ +CE ++ ++
Sbjct: 231 FGMNGRIWVKAKTIQQTLILANILEACEHMTADQ 264

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. EXOSC3 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC9 and EXOSC5.
Bos taurus (taxid: 9913)

>sp|Q9NQT5|EXOS3_HUMAN Exosome complex component RRP40 OS=Homo sapiens GN=EXOSC3 PE=1 SV=3

 Score =  193 bits (490), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 94/214 (43%), Positives = 145/214 (67%), Gaps = 13/214 (6%)

Query: 6   LSLNAEP----RLILGPGLRRESSAILVSQSGILRHAKPFT------YYVDYIQRRYVPT 55
           LSLNA      R++ GPGLRR    +LV++ G LRH +P +      Y+VD  Q+RYVP 
Sbjct: 53  LSLNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPV 112

Query: 56  RGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANK 115
           +GD VIG+VT++ GD ++VD+G  +PA LSYL+FEGATK+N P V+ GD++ G+ + ANK
Sbjct: 113 KGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANK 172

Query: 116 DMESEMVCVDSRGKEFIMGIL-NDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELS 174
           DME EMVC+DS G+   MG++  DG L   ++ L RKLL P C +++++ K     +E+ 
Sbjct: 173 DMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIIQEVGK--LYPLEIV 230

Query: 175 IGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEE 208
            GMNG+IW++ ++   T+ + N++ +CE ++ ++
Sbjct: 231 FGMNGRIWVKAKTIQQTLILANILEACEHMTSDQ 264

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. EXOSC3 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC9 and EXOSC5.

Homo sapiens (taxid: 9606)

>sp|Q7TQK4|EXOS3_MOUSE Exosome complex component RRP40 OS=Mus musculus GN=Exosc3 PE=1 SV=3

 Score =  192 bits (489), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 95/211 (45%), Positives = 142/211 (67%), Gaps = 10/211 (4%)

Query: 6   LSLNAEPRL--ILGPGLRRESSAILVSQSGILRHAKPF-----TYYVDYIQRRYVPTRGD 58
           L+  A PRL  + GPGLRR    +LV++ G LRH +P       Y+VD  Q+RYVP +GD
Sbjct: 55  LNAGARPRLRVVCGPGLRRCGDRLLVTKCGRLRHKEPSGGGGGVYWVDSQQKRYVPVKGD 114

Query: 59  LVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDME 118
            VIG+V ++ GD ++VD+G  +PA LSYLAFEGATK+N P V+ GD++ G+ + ANKDME
Sbjct: 115 HVIGIVIAKSGDIFKVDVGGSEPASLSYLAFEGATKRNRPNVQVGDLIYGQCVVANKDME 174

Query: 119 SEMVCVDSRGKEFIMGIL-NDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM 177
            EMVC+DS G+   MG++  DG L   ++ L RKLL P C ++++L K     +E+  GM
Sbjct: 175 PEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIVQELGKLY--PLEIVFGM 232

Query: 178 NGKIWIRCESFSDTVRVGNLIMSCELLSYEE 208
           NG+IW++ ++   T+ + N++ +CE ++ E+
Sbjct: 233 NGRIWVKAKTIQQTLILANVLEACEHMTTEQ 263

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. EXOSC3 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC9 and EXOSC5.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|Q7KWX9|EXOS3_DICDI Putative exosome complex component rrp40 OS=Dictyostelium discoideum GN=exosc3 PE=3 SV=1

 Score =  140 bits (354), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 73/208 (35%), Positives = 127/208 (61%), Gaps = 3/208 (1%)

Query: 3   GDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYY-VDYIQRRYVPTRGDLVI 61
           GD +    + ++ +GPGL +    +L +++G+LR++K   +Y ++  Q+RYVP   D+VI
Sbjct: 12  GDVIGKIGDLKVRIGPGLLQTKDTVLATKAGVLRYSKFHRFYWIENEQKRYVPQVEDMVI 71

Query: 62  GVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEM 121
           G +  +  ++++VDIGS   A+LS  +FEGATK N P +  G+++  ++  AN+DME E+
Sbjct: 72  GTIIEKHAESFKVDIGSSCSALLSAYSFEGATKSNKPLLNVGNLIYCRVTVANRDMEPEV 131

Query: 122 VCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKI 181
           VC+  + K    G L  GY+L+ S+ L   LL+  C LL+ L K      E+++G+NG++
Sbjct: 132 VCLSQKQKAEGFGQLIGGYMLNCSLGLSHYLLSEDCFLLQILGKHI--PYEIAVGVNGRV 189

Query: 182 WIRCESFSDTVRVGNLIMSCELLSYEEI 209
           WI   S  +T+ V N I + + +  ++I
Sbjct: 190 WINSGSNHNTIVVSNTIYNSQYIQDDQI 217

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.

Dictyostelium discoideum (taxid: 44689)

>sp|Q08285|RRP40_YEAST Exosome complex component RRP40 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RRP40 PE=1 SV=2

 Score =  140 bits (352), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 78/211 (36%), Positives = 125/211 (59%), Gaps = 12/211 (5%)

Query: 1   MAGDTLSLNAEPRLILGPGLRRE--SSAILVSQSGILRHAKP-----FTYYVDYIQRRYV 53
             GD+  ++    + LGPG+  +  +  I    +G+L  +        T Y+DY  +RY+
Sbjct: 6   FPGDSFPVDPTTPVKLGPGIYCDPNTQEIRPVNTGVLHVSAKGKSGVQTAYIDYSSKRYI 65

Query: 54  PTRGDLVIGVVTSRVGDNYRVDIGSHDPAV-LSYLAFEGATKKNPPKVETGDVVAGKLLT 112
           P+  D VIGV+     D+Y+V + +   +V LSY+AF  A+KKN P ++ GD+V  ++ T
Sbjct: 66  PSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCT 125

Query: 113 ANKDMESEMVCVDS-RGKEFIMGILNDGYLLHTSISLCRKLL-NPKCPLLKQLAKRSRQK 170
           A K++E+E+ C DS  G++   GIL DG ++  +++  R+LL N   PLLK LA  +  K
Sbjct: 126 AEKELEAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAHT--K 183

Query: 171 MELSIGMNGKIWIRCESFSDTVRVGNLIMSC 201
            E++IG+NGKIW++CE  S+T+     IM C
Sbjct: 184 FEVAIGLNGKIWVKCEELSNTLACYRTIMEC 214

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 cryptic unstable transcripts (CUTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and in RNA surveillance pathways, preventing translation of aberrant mRNAs. 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. RRP40 as peripheral part of the Exo-9 complex is thought to stabilize the hexameric ring of RNase PH-domain subunits.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|O13903|RRP40_SCHPO Exosome complex component rrp40 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rrp40 PE=3 SV=1

 Score =  140 bits (352), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 80/207 (38%), Positives = 119/207 (57%), Gaps = 8/207 (3%)

Query: 16  LGPGL----RRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDN 71
           LGPGL    +     I+VS++G L         +D   +RY+P   D VIG + SR  + 
Sbjct: 32  LGPGLVFQKKDREEEIVVSKAGRLHQTGKNAMLIDSRTKRYIPATNDQVIGQIISRFAEG 91

Query: 72  YRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD-SRGKE 130
           YRVDIGS   A L+ LAFE  T+K+ P +  G +V  ++  A++DME E+ C D + GK 
Sbjct: 92  YRVDIGSAHIAQLNALAFENVTRKSRPNLNVGSLVYARVSLADRDMEPELECFDATTGKA 151

Query: 131 FIMGILNDGYLLH-TSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFS 189
              G L +GY++   S+S CRKL+ PK  LL+ L   S    E+++GMNG++W+  E+ S
Sbjct: 152 AGYGELKNGYMITGLSLSHCRKLILPKNTLLQTLG--SYIPFEIAVGMNGRVWVNSENLS 209

Query: 190 DTVRVGNLIMSCELLSYEEILNLCESI 216
            TV +   I +CE +S EE +  C+ +
Sbjct: 210 TTVLICTAIRNCEFMSDEEQIKYCKDL 236

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 cryptic unstable transcripts (CUTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and in RNA surveillance pathways, preventing translation of aberrant mRNAs. 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. rrp40 as peripheral part of the Exo-9 complex is thought to stabilize the hexameric ring of RNase PH-domain subunits.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|E0SQX5|ECR1_IGNAA Probable exosome complex RNA-binding protein 1 OS=Ignisphaera aggregans (strain DSM 17230 / JCM 13409 / AQ1.S1) GN=Igag_1503 PE=3 SV=1

 Score = 54.3 bits (129), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 42/140 (30%), Positives = 73/140 (52%), Gaps = 12/140 (8%)

Query: 51  RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLS---YL--AFEGATKKNPPKVETGDV 105
           RY+P  GD+VIG+V      ++ +DI S   +VL+   YL  +F   T      +E GDV
Sbjct: 74  RYIPREGDIVIGIVVDVTLSSWIIDINSPYLSVLNASDYLGRSFNPLTDNIRKYLEIGDV 133

Query: 106 VAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAK 165
           V GK+ T ++     ++ V  +G    +G + DG L+        +++  K  +L  L +
Sbjct: 134 VVGKIATFDRS-RGPILTVQDKG----LGKVVDGSLIEIEPIKVARVIGKKKSMLNMLIE 188

Query: 166 RSRQKMELSIGMNGKIWIRC 185
           ++  K ++ +G NG+I +RC
Sbjct: 189 QT--KCDILVGNNGRIILRC 206

Probably involved in degradation of a variety of RNA species; could act a RNA-binding component of the exosome.

Ignisphaera aggregans (strain DSM 17230 / JCM 13409 / AQ1.S1) (taxid: 583356)

>sp|B1L6N8|ECR1_KORCO Probable exosome complex RNA-binding protein 1 OS=Korarchaeum cryptofilum (strain OPF8) GN=Kcr_1371 PE=3 SV=1

 Score = 48.5 bits (114), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 36/141 (25%), Positives = 66/141 (46%), Gaps = 7/141 (4%)

Query: 52  YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLL 111
           Y+P   DLVIG+V+   G+   VDI S     L               ++ GDV+  K+ 
Sbjct: 63  YIPKEDDLVIGIVSKISGNTILVDIRSPYQGALPIQRRAERVDLKKYDLKIGDVILAKVR 122

Query: 112 TANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKM 171
           + +    S ++ +D+ G    +G L  GYLL    +   +++  +  +L  L + +R   
Sbjct: 123 SFD-GASSLILTIDAEG----LGKLEGGYLLEVDPAKVPRVIGKRQSMLSMLKEATRS-- 175

Query: 172 ELSIGMNGKIWIRCESFSDTV 192
           E+ +  NG+IW++  S  + +
Sbjct: 176 EIIVANNGRIWVKPPSVKELI 196

Probably involved in degradation of a variety of RNA species; could act a RNA-binding component of the exosome.

Korarchaeum cryptofilum (strain OPF8) (taxid: 374847)

>sp|Q9YC02|ECR1_AERPE Probable exosome complex RNA-binding protein 1 OS=Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) GN=APE_1448 PE=1 SV=1

 Score = 46.2 bits (108), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 40/139 (28%), Positives = 68/139 (48%), Gaps = 12/139 (8%)

Query: 52  YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-----ATKKNPPKVETGDVV 106
           YVP  GD+VIG++ S    N+ VDI S   AVLS   F G     A       ++ GD +
Sbjct: 62  YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYI 121

Query: 107 AGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKR 166
             K++  +K   S ++ V   G    +G +  G ++  S +   +++  K  +LK L ++
Sbjct: 122 KAKVVAFDK-TRSPLLTVQGEG----LGRIVRGKIVEISPAKVPRVIGRKMSMLKTLEEK 176

Query: 167 SRQKMELSIGMNGKIWIRC 185
           +  K  + +  NG+I + C
Sbjct: 177 TECK--IFVARNGRIHLEC 193

Probably involved in degradation of a variety of RNA species; could act a RNA-binding component of the exosome.

Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) (taxid: 272557)

>sp|D5U396|ECR1_THEAM Probable exosome complex RNA-binding protein 1 OS=Thermosphaera aggregans (strain DSM 11486 / M11TL) GN=Tagg_1335 PE=3 SV=1

 Score = 45.8 bits (107), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 42/160 (26%), Positives = 76/160 (47%), Gaps = 18/160 (11%)

Query: 52  YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNP------PKVETGDV 105
           Y+P + DLVIG+V +     + +DI S  P VL+  A E     NP        ++TGD 
Sbjct: 70  YIPRKDDLVIGIVENVGVTAWTLDIRSPYPGVLN--ASEVIEGFNPLIHNLRNYLDTGDF 127

Query: 106 VAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAK 165
           V G++   ++  +  ++ V  +G    +G + +G ++    S   +L+  +  +   L  
Sbjct: 128 VIGRIALFDRTRDP-VITVKGKG----LGKITEGVVVDVKPSKIPRLIGKRGSMYNLLT- 181

Query: 166 RSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLS 205
            S    E++I  NG +W++C    D  R   LI + +L+ 
Sbjct: 182 -SMSGCEITIAQNGFVWLKCH---DENRAKVLIQAIKLIE 217

Probably involved in degradation of a variety of RNA species; could act a RNA-binding component of the exosome.

Thermosphaera aggregans (strain DSM 11486 / M11TL) (taxid: 633148)

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	222
322797836	240	hypothetical protein SINV_05937 [Solenop	0.986	0.912	0.519	1e-58
383865315	241	PREDICTED: exosome complex component RRP	0.986	0.908	0.495	5e-58
332025490	241	Exosome complex exonuclease RRP40 [Acrom	0.950	0.875	0.530	6e-58
170063463	238	exosome complex exonuclease RRP40 [Culex	0.909	0.848	0.517	3e-57
307206972	236	Exosome complex exonuclease RRP40 [Harpe	0.932	0.877	0.509	1e-56
157134439	237	hypothetical protein AaeL_AAEL013103 [Ae	0.909	0.852	0.502	4e-56
157105451	237	hypothetical protein AaeL_AAEL014498 [Ae	0.909	0.852	0.502	4e-56
237648986	236	exosome complex exonuclease Rrp40 [Bomby	0.918	0.864	0.490	3e-55
119114696	238	AGAP010247-PA [Anopheles gambiae str. PE	0.963	0.899	0.484	8e-55
312385541	234	hypothetical protein AND_00665 [Anophele	0.963	0.914	0.484	2e-54

>gi|322797836|gb|EFZ19744.1| hypothetical protein SINV_05937 [Solenopsis invicta]

 Score =  232 bits (591), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 120/231 (51%), Positives = 154/231 (66%), Gaps = 12/231 (5%)

Query: 1   MAGDTLSL---------NAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRR 51
           M GD LS+         N +  +ILGPGLRRE   +LV ++G+LR  +P  YYVD  Q+R
Sbjct: 10  MPGDKLSIVVPVKKERGNEKEVVILGPGLRREGDTVLVCKAGVLRKREPAVYYVDCYQKR 69

Query: 52  YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLL 111
           Y+P RG+ VIG+VT + GD Y+VDIG+ D A LSYLAFEGATKKN P V+ GD+V  KLL
Sbjct: 70  YIPNRGENVIGIVTQKSGDIYKVDIGASDQATLSYLAFEGATKKNRPDVQVGDLVYAKLL 129

Query: 112 TANKDMESEMVCVDSRGKEFIMGIL-NDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQK 170
            A+KDME E+VCVDS GKE  +G+L +DG +   S+SL RKLLNP+CPL K L +   Q 
Sbjct: 130 VASKDMEPELVCVDSHGKENDLGVLSSDGMMFTCSLSLVRKLLNPECPLFKLLGQ--NQM 187

Query: 171 MELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFL 221
            EL+ GMNG+IWI+  S  +T+ V N I++ E     E+  LC  I   FL
Sbjct: 188 YELAAGMNGRIWIKARSVQETIAVANAILAAEYTIPSEMQKLCTKIEKIFL 238

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383865315|ref|XP_003708120.1| PREDICTED: exosome complex component RRP40-like [Megachile rotundata]

 Score =  229 bits (585), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 112/226 (49%), Positives = 154/226 (68%), Gaps = 7/226 (3%)

Query: 1   MAGDTL----SLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTR 56
           M GDT+    ++N +  +ILGPGLRRE+  +   ++GIL+ A+P  YYVD  Q+RY+P R
Sbjct: 10  MPGDTVKDITTVNKKETIILGPGLRREADTVFAYKAGILKKAEPAVYYVDTYQKRYIPNR 69

Query: 57  GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD 116
           G+ V+G+VT + GD ++VDIG+ D A LSYLAFEGATKKN P ++ GD+V  KLL A+KD
Sbjct: 70  GENVVGIVTQKGGDIFKVDIGASDQASLSYLAFEGATKKNRPDIQVGDLVYAKLLVASKD 129

Query: 117 MESEMVCVDSRGKEFIMGIL-NDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSI 175
           MESE+VCVDS GKE  +G+L NDG L   S+SL RK+LN K PL K LA  + Q  E++ 
Sbjct: 130 MESELVCVDSHGKEKNLGVLSNDGMLFTCSLSLIRKILNQKSPLFKTLA--NSQAFEVAA 187

Query: 176 GMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFL 221
           GMNG++W++  +  +T+ V N I++ E  +   I  LC  I    L
Sbjct: 188 GMNGRVWVKARTIHETIAVANAILAAEYATPNYIKKLCSDIEKTLL 233

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332025490|gb|EGI65653.1| Exosome complex exonuclease RRP40 [Acromyrmex echinatior]

 Score =  229 bits (584), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 114/215 (53%), Positives = 151/215 (70%), Gaps = 4/215 (1%)

Query: 9   NAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRV 68
           N +  +ILGPGLRRE  A+L+ ++G+LR  +P  YYVD  Q+RY+P+RG+ V+G+VT + 
Sbjct: 27  NEKEIVILGPGLRREDDAVLICKAGVLRKREPAVYYVDSYQKRYIPSRGENVVGIVTQKS 86

Query: 69  GDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRG 128
           GD Y+VDIG  + A LSYLAFEGATKKN P V+ GD+V GKLL A+KDME E+VCVDS G
Sbjct: 87  GDIYKVDIGGSEQATLSYLAFEGATKKNRPDVQIGDLVYGKLLVASKDMEPELVCVDSHG 146

Query: 129 KEFIMGIL-NDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCES 187
           KE  +G+L +DG +   S+SL RKLLNP+CPL + L +   Q  EL+ GMNG+IWI+  S
Sbjct: 147 KENELGMLSSDGMMFICSLSLVRKLLNPECPLFRLLGR--NQAYELAAGMNGRIWIKARS 204

Query: 188 FSDTVRVGNLIMSCELLSYEEILNLCESIH-IRFL 221
             +T+ V N I++ E     E+  LC  I  I FL
Sbjct: 205 VQETIAVANAILAAEFTVSSEMQKLCSKIEKILFL 239

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170063463|ref|XP_001867115.1| exosome complex exonuclease RRP40 [Culex quinquefasciatus] gi|167881089|gb|EDS44472.1| exosome complex exonuclease RRP40 [Culex quinquefasciatus]

 Score =  227 bits (578), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 106/205 (51%), Positives = 150/205 (73%), Gaps = 3/205 (1%)

Query: 13  RLILGPGLRRE-SSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDN 71
           ++ILGPGLR++    +LV +SG+LR   P T++VD  Q+RYVP RG++VIG+VT + GD 
Sbjct: 27  KVILGPGLRQDRDDLVLVCKSGVLRKKPPNTFWVDCHQKRYVPNRGEIVIGIVTQKAGDI 86

Query: 72  YRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEF 131
           +RVDIG+ +PA LSY+AFEGATKKN P V  G+V+  +LL ANKD+E E++CVDS GK+ 
Sbjct: 87  FRVDIGASEPASLSYMAFEGATKKNRPDVNVGEVICARLLIANKDLEPELICVDSHGKKG 146

Query: 132 IMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDT 191
            +G L DG++ + SI+L RK+LNPKCP L  LAK      E++ GMNG+IW++ ++  +T
Sbjct: 147 KLGALQDGFVFNCSINLVRKILNPKCPFLDLLAK--ELAFEMAAGMNGRIWVKGKTVKET 204

Query: 192 VRVGNLIMSCELLSYEEILNLCESI 216
           + VGN I++ E  S EE+  LC+ I
Sbjct: 205 IAVGNAILAVEFKSNEELRELCDDI 229

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307206972|gb|EFN84811.1| Exosome complex exonuclease RRP40 [Harpegnathos saltator]

 Score =  225 bits (573), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 107/210 (50%), Positives = 148/210 (70%), Gaps = 3/210 (1%)

Query: 9   NAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRV 68
           N +  +ILGPGLRR++ AI + ++GIL+  +P  YYVD  Q+RY+P+RG+ ++G++T + 
Sbjct: 22  NEKEVVILGPGLRRDNDAIFICKAGILKKREPAVYYVDGYQKRYIPSRGENIVGIITQKA 81

Query: 69  GDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRG 128
           GD Y+VDIG+ + A LSYLAFEGA+KKN P ++ GDVV  KLL A+KDME E+VCVDS+G
Sbjct: 82  GDIYKVDIGASEQASLSYLAFEGASKKNRPDIQIGDVVFAKLLIASKDMEPELVCVDSQG 141

Query: 129 KEFIMGIL-NDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCES 187
           KE  +G+L  DG +   S+SL RK+LNP CPL K L K   Q  E+++GMNGKIWI+  S
Sbjct: 142 KENDLGVLGTDGMMFTCSLSLVRKILNPDCPLFKLLGK--NQAYEIAVGMNGKIWIKARS 199

Query: 188 FSDTVRVGNLIMSCELLSYEEILNLCESIH 217
             +T+ V N I++ E     E+  LC  I 
Sbjct: 200 VQETIAVANAILAAEYTVPAEMNKLCAKIE 229

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157134439|ref|XP_001663303.1| hypothetical protein AaeL_AAEL013103 [Aedes aegypti] gi|108870467|gb|EAT34692.1| AAEL013103-PA [Aedes aegypti] gi|122937754|gb|ABM68596.1| AAEL013103-PA [Aedes aegypti]

 Score =  223 bits (568), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 103/205 (50%), Positives = 148/205 (72%), Gaps = 3/205 (1%)

Query: 13  RLILGPGLRRE-SSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDN 71
           +++LGPGLR++   A+LV +SG+LR   P T++VD  Q+RYVP R ++V+G+VT + GD 
Sbjct: 27  KVVLGPGLRQDRDDAVLVCKSGVLRKKTPNTFWVDCYQKRYVPNRSEIVVGIVTQKAGDI 86

Query: 72  YRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEF 131
           +RVDIG  +PA LSYLAFEGATKKN P V  GD +  +LL AN+D+E E++CVDS GK+ 
Sbjct: 87  FRVDIGGSEPASLSYLAFEGATKKNRPDVNVGDAICARLLIANRDLEPELICVDSHGKKG 146

Query: 132 IMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDT 191
            +G+L DG++ + SI+L RK+LNPKC  L  LAK      E++ GMNG+IWI+ ++  +T
Sbjct: 147 KLGVLQDGFVFNCSINLVRKILNPKCVFLDLLAK--EMAFEMAAGMNGRIWIKGKTVKET 204

Query: 192 VRVGNLIMSCELLSYEEILNLCESI 216
           + VGN I++ E  S +E+  LC+ I
Sbjct: 205 IAVGNAILAVEFKSNDELKELCDDI 229

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157105451|ref|XP_001648874.1| hypothetical protein AaeL_AAEL014498 [Aedes aegypti] gi|108869016|gb|EAT33241.1| AAEL014498-PA [Aedes aegypti]

 Score =  223 bits (568), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 103/205 (50%), Positives = 148/205 (72%), Gaps = 3/205 (1%)

Query: 13  RLILGPGLRRE-SSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDN 71
           +++LGPGLR++   A+LV +SG+LR   P T++VD  Q+RYVP R ++V+G+VT + GD 
Sbjct: 27  KVVLGPGLRQDKDDAVLVCKSGVLRKKTPNTFWVDCYQKRYVPNRSEIVVGIVTQKAGDI 86

Query: 72  YRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEF 131
           +RVDIG  +PA LSYLAFEGATKKN P V  GD +  +LL AN+D+E E++CVDS GK+ 
Sbjct: 87  FRVDIGGSEPASLSYLAFEGATKKNRPDVNVGDAICARLLIANRDLEPELICVDSHGKKG 146

Query: 132 IMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDT 191
            +G+L DG++ + SI+L RK+LNPKC  L  LAK      E++ GMNG+IWI+ ++  +T
Sbjct: 147 KLGVLQDGFVFNCSINLVRKILNPKCVFLDLLAK--EMAFEIAAGMNGRIWIKGKTVKET 204

Query: 192 VRVGNLIMSCELLSYEEILNLCESI 216
           + VGN I++ E  S +E+  LC+ I
Sbjct: 205 IAVGNAILAVEFKSNDELKELCDDI 229

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|237648986|ref|NP_001153670.1| exosome complex exonuclease Rrp40 [Bombyx mori] gi|224814347|gb|ACN65392.1| exosome complex exonuclease [Bombyx mori]

 Score =  220 bits (560), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 101/206 (49%), Positives = 149/206 (72%), Gaps = 2/206 (0%)

Query: 13  RLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNY 72
           +++LGPGLR+E + + +++ G+LR   P TY+VD  Q+RYVP+RG+ VIG V  + GD +
Sbjct: 26  KVLLGPGLRKEINGVFITKPGVLRKRTPNTYWVDNYQKRYVPSRGENVIGTVVQKAGDIF 85

Query: 73  RVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFI 132
           RVD+G    A LSYL+FEGATKKN P ++TGDVV  K+L A+KDME E+VCVDS GK+  
Sbjct: 86  RVDVGGSCAASLSYLSFEGATKKNRPAIKTGDVVYAKMLNASKDMEPELVCVDSHGKKGR 145

Query: 133 MGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTV 192
           +G+L +G++   S++L RK+LNP CPLL  L  ++    EL+ GMNG+IWI+  +  +T+
Sbjct: 146 LGVLEEGFVFKCSLNLIRKILNPHCPLLNSL--KNEWPFELAAGMNGRIWIKANTMRETL 203

Query: 193 RVGNLIMSCELLSYEEILNLCESIHI 218
            +GN I+  E LS +EI ++C++I +
Sbjct: 204 ALGNAILGSEYLSNDEIKSMCKNIAV 229

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|119114696|ref|XP_319438.3| AGAP010247-PA [Anopheles gambiae str. PEST] gi|116118540|gb|EAA43646.3| AGAP010247-PA [Anopheles gambiae str. PEST]

 Score =  219 bits (557), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 107/221 (48%), Positives = 151/221 (68%), Gaps = 7/221 (3%)

Query: 1   MAGDTLS-----LNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPT 55
           +AGD +S     + A  ++ILGPG+R E   +  S+ G+L+   P T++VD  QRRYVP 
Sbjct: 11  LAGDIISEPMEMMKANKKVILGPGIRVEKETVRASKCGMLKMKPPNTFWVDAYQRRYVPN 70

Query: 56  RGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANK 115
           RG+LVIGVV ++ GD +R+DIG  + A LSY+AFEGATKKN P V  GD+V  +LL A+ 
Sbjct: 71  RGELVIGVVMAKTGDTFRLDIGGSETASLSYMAFEGATKKNRPDVNVGDIVYARLLIAHP 130

Query: 116 DMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSI 175
           D+E E+VCVDS GK+  +G+L+DG+++  S++L RK+LNPK   L QLAK      E++ 
Sbjct: 131 DVEPELVCVDSHGKKGKLGVLHDGFMISCSLNLVRKILNPKSNFLSQLAK--ELPFEIAA 188

Query: 176 GMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESI 216
           GMNG+IWIR  +  +T+ VGN I++ E L  + I  LC+ I
Sbjct: 189 GMNGRIWIRGRTIKETIAVGNAILALEYLPNDRIRELCDDI 229

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312385541|gb|EFR30016.1| hypothetical protein AND_00665 [Anopheles darlingi]

 Score =  218 bits (554), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 107/221 (48%), Positives = 152/221 (68%), Gaps = 7/221 (3%)

Query: 1   MAGDTL-----SLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPT 55
           +AGD +      +    ++ILGPGLR +   +  S+ G L+   P T++VD  Q+RYVPT
Sbjct: 7   LAGDVIIEPMEMIKTSKKVILGPGLRMDQDVVRASKCGQLKTKPPNTFWVDAHQKRYVPT 66

Query: 56  RGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANK 115
           RG+LV+GVV ++ GD +RVDIGS + A LSY+AFEGATKKN P V  GD+V  +LL A+ 
Sbjct: 67  RGELVVGVVMAKAGDIFRVDIGSSETASLSYVAFEGATKKNRPDVNIGDIVYARLLIAHP 126

Query: 116 DMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSI 175
           D+E E+VCVDS GK+  +GIL+DG+LL  S++L RK+LNPKC  L  L+K    K EL+ 
Sbjct: 127 DVEPELVCVDSHGKKGKLGILHDGFLLSCSLNLIRKILNPKCTFLSLLSK--ELKFELAA 184

Query: 176 GMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESI 216
           GMNG++WIR ++  +T+ +GN I++ E +  ++I  LC  I
Sbjct: 185 GMNGRLWIRGKTVKETIAIGNAILALEFVPSDQIRELCNDI 225

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

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	222
UNIPROTKB|F1NWK4	272	EXOSC3 "Uncharacterized protei	0.905	0.738	0.460	3.3e-47
FB|FBgn0260648	232	Rrp40 [Drosophila melanogaster	0.932	0.892	0.447	3.8e-46
RGD|1304739	273	Exosc3 "exosome component 3" [	0.905	0.736	0.450	7.9e-46
MGI|MGI:1913612	274	Exosc3 "exosome component 3" [	0.905	0.733	0.450	1e-45
UNIPROTKB|Q3T0E1	275	EXOSC3 "Exosome complex compon	0.923	0.745	0.442	1.6e-45
UNIPROTKB|Q9NQT5	275	EXOSC3 "Exosome complex compon	0.905	0.730	0.439	2.1e-45
UNIPROTKB|E2RHV4	275	EXOSC3 "Uncharacterized protei	0.873	0.705	0.448	3.4e-45
ZFIN|ZDB-GENE-050706-140	247	exosc3 "exosome component 3" [	0.900	0.809	0.463	7.1e-45
UNIPROTKB|F1ST67	275	EXOSC3 "Uncharacterized protei	0.905	0.730	0.438	1.2e-44
WB|WBGene00010325	226	exos-3 [Caenorhabditis elegans	0.972	0.955	0.321	4.1e-33

UNIPROTKB|F1NWK4 EXOSC3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 494 (179.0 bits), Expect = 3.3e-47, P = 3.3e-47
 Identities = 99/215 (46%), Positives = 146/215 (67%)

Query:     6 LSLNAEPR--LILGPGLRRESSAILVSQSGILRH---------AKPFTYYVDYIQRRYVP 54
             L  +A PR  L+ GPGLRR +  +LV++ G+LRH         A    Y+VD  Q+RYVP
Sbjct:    49 LGTSAAPRGRLLCGPGLRRCAGGLLVTKCGLLRHRRAGDGAAAAAGGAYWVDSQQKRYVP 108

Query:    55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTAN 114
              +GD VIG+VT +VGD +R+D+G  + A LSYLAFEGATK+N P V+ GD++ G+ L AN
Sbjct:   109 VKGDHVIGIVTGKVGDVFRLDVGGSEQASLSYLAFEGATKRNRPNVQVGDLIYGQFLVAN 168

Query:   115 KDMESEMVCVDSRGKEFIMGILN-DGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMEL 173
             KDME EMVC+DS G+   MG++  DG+L   S+ L RKLL PKC ++++L++      EL
Sbjct:   169 KDMEPEMVCIDSSGRASGMGVIGQDGFLFKVSLGLIRKLLAPKCEIIQELSQL--YPFEL 226

Query:   174 SIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEE 208
              +GMNG+IW++ ++   T+ + N++ +CE ++ E+
Sbjct:   227 VLGMNGRIWVKAKTVQQTLIIVNILEACEYMTAEQ 261

GO:0003723 "RNA binding" evidence=IEA

GO:0000176 "nuclear exosome (RNase complex)" evidence=IEA

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

GO:0005730 "nucleolus" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0035327 "transcriptionally active chromatin" evidence=IEA

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

GO:0045006 "DNA deamination" evidence=IEA

GO:0045190 "isotype switching" evidence=IEA

GO:0071034 "CUT catabolic process" evidence=IEA

FB|FBgn0260648 Rrp40 [Drosophila melanogaster (taxid:7227)]

 Score = 484 (175.4 bits), Expect = 3.8e-46, P = 3.8e-46
 Identities = 94/210 (44%), Positives = 140/210 (66%)

Query:    13 RLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNY 72
             R+ILGPGLRR    ++ S++G LRH +P T++VD  QRRY+P RGDL++G+V ++ GD Y
Sbjct:    25 RVILGPGLRRLDDTVVASKAGPLRHKEPGTFWVDNYQRRYIPARGDLILGIVRAKAGDLY 84

Query:    73 RVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFI 132
             RVDIG+ D A +SYLAFE A+KKN P +  GD++  ++L A+ D+E E+VCV+S GK   
Sbjct:    85 RVDIGATDTASISYLAFEAASKKNRPDLIPGDLIYARVLNASADIEPELVCVNSVGKSGK 144

Query:   133 MGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTV 192
             +G+L DG+    S++L R LL   CP+L  L +      E+++G+NG+IW++  S  +TV
Sbjct:   145 LGVLTDGFFFKCSLNLGRMLLRENCPVLAALTREL--PYEIAVGVNGRIWLKAHSLKETV 202

Query:   193 RVGNLIMSCELLSYEEILNLCESIHIRFLQ 222
              + N I + E     EI  +C ++   FLQ
Sbjct:   203 ALANAISALEQSGCAEIDKICGNLG-DFLQ 231

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

GO:0006364 "rRNA processing" evidence=ISS

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

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

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

RGD|1304739 Exosc3 "exosome component 3" [Rattus norvegicus (taxid:10116)]

 Score = 481 (174.4 bits), Expect = 7.9e-46, P = 7.9e-46
 Identities = 95/211 (45%), Positives = 142/211 (67%)

Query:     6 LSLNAEPRL--ILGPGLRRESSAILVSQSGILRHAKPF-----TYYVDYIQRRYVPTRGD 58
             L+  A PRL  + GPGLRR    +LV++ G LRH +P       Y+VD  Q+RYVP +GD
Sbjct:    54 LNAGARPRLRIVCGPGLRRCGDRLLVTKCGRLRHKEPSGGGGGVYWVDSQQKRYVPVKGD 113

Query:    59 LVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDME 118
              VIG+V ++ GD ++VD+G  +PA LSYLAFEGATK+N P V+ GD++ G+ + ANKDME
Sbjct:   114 HVIGIVVAKSGDIFKVDVGGSEPASLSYLAFEGATKRNRPNVQVGDLIYGQCVVANKDME 173

Query:   119 SEMVCVDSRGKEFIMGILN-DGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM 177
              EMVC+DS G+   MG++  DG L   ++ L RKLL P C ++++L K     +E+  GM
Sbjct:   174 PEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIVQELGKL--YPLEIVFGM 231

Query:   178 NGKIWIRCESFSDTVRVGNLIMSCELLSYEE 208
             NG+IW++ ++   T+ + N++ +CE ++ E+
Sbjct:   232 NGRIWVKAKTIQQTLILANVLEACEHMTTEQ 262

GO:0000176 "nuclear exosome (RNase complex)" evidence=ISO

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

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006364 "rRNA processing" evidence=ISO

GO:0035327 "transcriptionally active chromatin" evidence=ISO

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

GO:0045006 "DNA deamination" evidence=ISO

GO:0045190 "isotype switching" evidence=ISO

GO:0045830 "positive regulation of isotype switching" evidence=ISO

GO:0071034 "CUT catabolic process" evidence=ISO

GO:0004532 "exoribonuclease activity" evidence=ISO

MGI|MGI:1913612 Exosc3 "exosome component 3" [Mus musculus (taxid:10090)]

 Score = 480 (174.0 bits), Expect = 1.0e-45, P = 1.0e-45
 Identities = 95/211 (45%), Positives = 142/211 (67%)

Query:     6 LSLNAEPRL--ILGPGLRRESSAILVSQSGILRHAKPF-----TYYVDYIQRRYVPTRGD 58
             L+  A PRL  + GPGLRR    +LV++ G LRH +P       Y+VD  Q+RYVP +GD
Sbjct:    55 LNAGARPRLRVVCGPGLRRCGDRLLVTKCGRLRHKEPSGGGGGVYWVDSQQKRYVPVKGD 114

Query:    59 LVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDME 118
              VIG+V ++ GD ++VD+G  +PA LSYLAFEGATK+N P V+ GD++ G+ + ANKDME
Sbjct:   115 HVIGIVIAKSGDIFKVDVGGSEPASLSYLAFEGATKRNRPNVQVGDLIYGQCVVANKDME 174

Query:   119 SEMVCVDSRGKEFIMGILN-DGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM 177
              EMVC+DS G+   MG++  DG L   ++ L RKLL P C ++++L K     +E+  GM
Sbjct:   175 PEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIVQELGKL--YPLEIVFGM 232

Query:   178 NGKIWIRCESFSDTVRVGNLIMSCELLSYEE 208
             NG+IW++ ++   T+ + N++ +CE ++ E+
Sbjct:   233 NGRIWVKAKTIQQTLILANVLEACEHMTTEQ 263

GO:0000176 "nuclear exosome (RNase complex)" evidence=ISO

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

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

GO:0003674 "molecular_function" evidence=ND

GO:0003723 "RNA binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0004527 "exonuclease activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006364 "rRNA processing" evidence=ISO

GO:0016787 "hydrolase activity" evidence=IEA

GO:0035327 "transcriptionally active chromatin" evidence=ISO

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

GO:0045006 "DNA deamination" evidence=ISO

GO:0045190 "isotype switching" evidence=IMP

GO:0045830 "positive regulation of isotype switching" evidence=IMP

GO:0071034 "CUT catabolic process" evidence=ISO

UNIPROTKB|Q3T0E1 EXOSC3 "Exosome complex component RRP40" [Bos taurus (taxid:9913)]

 Score = 478 (173.3 bits), Expect = 1.6e-45, P = 1.6e-45
 Identities = 97/219 (44%), Positives = 147/219 (67%)

Query:     2 AGDT-LSLNAEPR----LILGPGLRRESSAILVSQSGILRHAKPFT------YYVDYIQR 50
             AG+  L LNA  R    ++ GPGLRR    +LV++ G LRH +P +      Y+VD  Q+
Sbjct:    48 AGERPLRLNAAARSRGRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQK 107

Query:    51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKL 110
             RYVP +GD VIG+VT++ GD ++VD+G  +PA LSYLAFEGATK+N P V+ GD++ G+ 
Sbjct:   108 RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLAFEGATKRNRPNVQVGDLIYGQF 167

Query:   111 LTANKDMESEMVCVDSRGKEFIMGILN-DGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQ 169
             + ANKDME EMVC+DS G+   MG++  DG L   ++ L RKLL P C +L+++ K    
Sbjct:   168 VVANKDMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEILQEVGKL--Y 225

Query:   170 KMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEE 208
              +E+  GMNG+IW++ ++   T+ + N++ +CE ++ ++
Sbjct:   226 PLEIVFGMNGRIWVKAKTIQQTLILANILEACEHMTADQ 264

GO:0005730 "nucleolus" evidence=ISS

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

GO:0071034 "CUT catabolic process" evidence=IEA

GO:0045190 "isotype switching" evidence=IEA

GO:0045006 "DNA deamination" evidence=IEA

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

GO:0035327 "transcriptionally active chromatin" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

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

GO:0000176 "nuclear exosome (RNase complex)" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q9NQT5 EXOSC3 "Exosome complex component RRP40" [Homo sapiens (taxid:9606)]

 Score = 477 (173.0 bits), Expect = 2.1e-45, P = 2.1e-45
 Identities = 94/214 (43%), Positives = 145/214 (67%)

Query:     6 LSLNAEP----RLILGPGLRRESSAILVSQSGILRHAKPFT------YYVDYIQRRYVPT 55
             LSLNA      R++ GPGLRR    +LV++ G LRH +P +      Y+VD  Q+RYVP 
Sbjct:    53 LSLNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPV 112

Query:    56 RGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANK 115
             +GD VIG+VT++ GD ++VD+G  +PA LSYL+FEGATK+N P V+ GD++ G+ + ANK
Sbjct:   113 KGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANK 172

Query:   116 DMESEMVCVDSRGKEFIMGILN-DGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELS 174
             DME EMVC+DS G+   MG++  DG L   ++ L RKLL P C +++++ K     +E+ 
Sbjct:   173 DMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIIQEVGKL--YPLEIV 230

Query:   175 IGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEE 208
              GMNG+IW++ ++   T+ + N++ +CE ++ ++
Sbjct:   231 FGMNGRIWVKAKTIQQTLILANILEACEHMTSDQ 264

GO:0003723 "RNA binding" evidence=IEA

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

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

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

GO:0006364 "rRNA processing" evidence=IDA

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

GO:0005730 "nucleolus" evidence=IDA

GO:0071034 "CUT catabolic process" evidence=IMP

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

GO:0045190 "isotype switching" evidence=ISS

GO:0045006 "DNA deamination" evidence=IDA

GO:0035327 "transcriptionally active chromatin" evidence=IMP

GO:0004532 "exoribonuclease activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

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

UNIPROTKB|E2RHV4 EXOSC3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 475 (172.3 bits), Expect = 3.4e-45, P = 3.4e-45
 Identities = 91/203 (44%), Positives = 139/203 (68%)

Query:    13 RLILGPGLRRESSAILVSQSGILRHAKPF------TYYVDYIQRRYVPTRGDLVIGVVTS 66
             R++ GPGLRR    +LV++ G LRH +P        Y+VD  Q+RYVP +GD VIG+VT+
Sbjct:    64 RVVCGPGLRRCGDRLLVTKCGRLRHKEPGGGSGGGVYWVDSQQKRYVPVKGDHVIGIVTA 123

Query:    67 RVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDS 126
             + GD ++VD+G  +PA LSYLAFEGATK+N P V+ GD++ G+ + ANKDME EMVC+DS
Sbjct:   124 KSGDIFKVDVGGSEPASLSYLAFEGATKRNRPNVQIGDLIYGQFVVANKDMEPEMVCIDS 183

Query:   127 RGKEFIMGILN-DGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRC 185
              G+   MG++  DG L   ++ L RKLL P C +L+++ K     +E+  GMNG+IW++ 
Sbjct:   184 CGRASGMGVIGQDGLLFKVTLGLIRKLLAPDCEILQEVGKL--YPLEIVFGMNGRIWVKA 241

Query:   186 ESFSDTVRVGNLIMSCELLSYEE 208
             ++   T+ + N++ +CE ++ ++
Sbjct:   242 KTIQQTLILANILEACEHMTADQ 264

GO:0071034 "CUT catabolic process" evidence=IEA

GO:0045190 "isotype switching" evidence=IEA

GO:0045006 "DNA deamination" evidence=IEA

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

GO:0035327 "transcriptionally active chromatin" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

GO:0000176 "nuclear exosome (RNase complex)" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

ZFIN|ZDB-GENE-050706-140 exosc3 "exosome component 3" [Danio rerio (taxid:7955)]

 Score = 472 (171.2 bits), Expect = 7.1e-45, P = 7.1e-45
 Identities = 95/205 (46%), Positives = 138/205 (67%)

Query:     2 AGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVI 61
             AGD  +  A+ RLI GPGLRR  + I V ++G+L+H +P  Y+V+  QRRYVP +G+ VI
Sbjct:    31 AGDA-NPKAD-RLICGPGLRRSGAEIRVCRAGVLKHKQPNMYWVNCQQRRYVPAKGESVI 88

Query:    62 GVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEM 121
             G+VT++ GD ++VD+G  + A LSYLAFEGATK+N P V+ GD+V G+   ANKDME E+
Sbjct:    89 GIVTAKSGDVFKVDVGGSEQASLSYLAFEGATKRNRPNVQVGDLVFGQFTIANKDMEPEL 148

Query:   122 VCVDSRGKEFIMGILN-DGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGK 180
             VC+DS G+   MG+   DG L   S+ L R+LL P+  L+  L K      E+ +GMNG+
Sbjct:   149 VCIDSCGRANGMGVFGGDGLLFKVSLGLVRRLLAPQSDLVSDLEKMF--PCEMVVGMNGR 206

Query:   181 IWIRCESFSDTVRVGNLIMSCELLS 205
             +W++  +   T+ + NL+ +CE +S
Sbjct:   207 VWVKARTVQHTLILSNLLEACENMS 231

GO:0003723 "RNA binding" evidence=IEA

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

GO:0009790 "embryo development" evidence=IMP

GO:0007420 "brain development" evidence=IMP

UNIPROTKB|F1ST67 EXOSC3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 470 (170.5 bits), Expect = 1.2e-44, P = 1.2e-44
 Identities = 93/212 (43%), Positives = 142/212 (66%)

Query:     6 LSLNAEPRL--ILGPGLRRESSAILVSQSGILRHAKPF------TYYVDYIQRRYVPTRG 57
             L+  A PR+  + GPGLRR    +LV++ G LRH +         Y+VD  Q+RYVP +G
Sbjct:    55 LNAGARPRVRVVCGPGLRRCGDRLLVTKCGRLRHKEAGGGGGSGVYWVDSQQKRYVPVKG 114

Query:    58 DLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDM 117
             D VIG+VT++ GD ++VD+G  +PA LSYLAFEGATK+N P V+ GD++ G+ + ANKDM
Sbjct:   115 DHVIGIVTAKSGDIFKVDVGGSEPASLSYLAFEGATKRNRPNVQIGDLIYGQFVVANKDM 174

Query:   118 ESEMVCVDSRGKEFIMGILN-DGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIG 176
             E EMVC+DS G+   MG++  DG L   ++ L RKLL P C +L+++ K     +E+  G
Sbjct:   175 EPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLVRKLLAPNCEILQEVGKL--YPLEIVFG 232

Query:   177 MNGKIWIRCESFSDTVRVGNLIMSCELLSYEE 208
             MNG+IW++ ++   T+ + N++ +CE ++ ++
Sbjct:   233 MNGRIWVKAKTIQQTLILANVLEACEHMTADQ 264

GO:0071034 "CUT catabolic process" evidence=IEA

GO:0045190 "isotype switching" evidence=IEA

GO:0045006 "DNA deamination" evidence=IEA

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

GO:0035327 "transcriptionally active chromatin" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

GO:0000176 "nuclear exosome (RNase complex)" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

WB|WBGene00010325 exos-3 [Caenorhabditis elegans (taxid:6239)]

 Score = 361 (132.1 bits), Expect = 4.1e-33, P = 4.1e-33
 Identities = 71/221 (32%), Positives = 130/221 (58%)

Query:     1 MAGDTLSL-NAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDL 59
             + GD ++  ++    I+G G+       + +Q G   H      +++   +RY+P  GD 
Sbjct:     5 LPGDVINEPSSSDSSIIGYGISVRGQTRIATQPGAF-HNDDGKVWLNVHSKRYIPQEGDR 63

Query:    60 VIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMES 119
             VI +VTS+ GD +R+DIG+ + A++++  FEGATK+N P ++TGD++   +       E+
Sbjct:    64 VIAIVTSKTGDFFRLDIGTAEYAMINFTNFEGATKRNRPNLKTGDIIYATVFDTTPRTEA 123

Query:   120 EMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG 179
             E+ CVD   +   MG LN G++   S++ CR+L+NP C +L+ + K    K E+++GMNG
Sbjct:   124 ELTCVDDEKRARGMGQLNGGFMFKVSLNHCRRLINPSCKILQTVGKFF--KFEITVGMNG 181

Query:   180 KIWIRCESFSDTVRVGNLIMSCELLSYE-EILNLCESIHIR 219
             +IWI   +  D +++ ++I   E ++ E E++ L ++ + R
Sbjct:   182 RIWISASTSDDIIKIHDIINKSEFITDEDELITLVQNNYTR 222

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

GO:0003723 "RNA binding" evidence=IEA

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0005737 "cytoplasm" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q08285	RRP40_YEAST	No assigned EC number	0.3696	0.8963	0.8291	yes	N/A
Q7KWX9	EXOS3_DICDI	No assigned EC number	0.3509	0.9234	0.8649	yes	N/A
O13903	RRP40_SCHPO	No assigned EC number	0.3864	0.8963	0.8291	yes	N/A
Q7TQK4	EXOS3_MOUSE	3, ., 1, ., 1, 3, ., -	0.4502	0.9054	0.7335	yes	N/A
Q3T0E1	EXOS3_BOVIN	No assigned EC number	0.4439	0.9054	0.7309	yes	N/A
Q9NQT5	EXOS3_HUMAN	No assigned EC number	0.4392	0.9054	0.7309	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	222
cd05790	86	cd05790, S1_Rrp40, S1_Rrp40: Rrp40 S1-like RNA-bin	2e-40
COG1097	239	COG1097, RRP4, RNA-binding protein Rrp4 and relate	2e-29
cd04454	82	cd04454, S1_Rrp4_like, S1_Rrp4_like: Rrp4-like, S1	3e-17
PRK04163	235	PRK04163, PRK04163, exosome complex RNA-binding pr	2e-07
cd05789	86	cd05789, S1_Rrp4, S1_Rrp4: Rrp4 S1-like RNA-bindin	7e-06

>gnl|CDD|240216 cd05790, S1_Rrp40, S1_Rrp40: Rrp40 S1-like RNA-binding domain

 Score =  132 bits (335), Expect = 2e-40
 Identities = 48/86 (55%), Positives = 63/86 (73%)

Query: 51  RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKL 110
           RYVP +GD VIG+V ++ GD ++VDIG  +PA LSYLAFEGATK+N P +  GD+V  ++
Sbjct: 1   RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARV 60

Query: 111 LTANKDMESEMVCVDSRGKEFIMGIL 136
           + AN+DME E+ CVDS GK    G L
Sbjct: 61  VKANRDMEPELSCVDSSGKADGFGPL 86

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". Length = 86

>gnl|CDD|224022 COG1097, RRP4, RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]

 Score =  109 bits (274), Expect = 2e-29
 Identities = 59/211 (27%), Positives = 95/211 (45%), Gaps = 15/211 (7%)

Query: 3   GDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIG 62
           GD +   AE    LG G   E   I  S  G+L         +   + RY+P  GD+VIG
Sbjct: 14  GDLVL--AEGSYKLGHGTYFEGGKIYSSVVGLLDVKGKLVRVIPL-EGRYIPEVGDVVIG 70

Query: 63  VVTSRVGDNYRVDIGSHDPAVLSYLAF-----EGATKKNPPKVETGDVVAGKLLTANKDM 117
            +       ++VDIGS  PA+LS   F     E A K   P +  GD+V  K++  ++D 
Sbjct: 71  KIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDG 130

Query: 118 ESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM 177
           E E+       K+  +G L +G ++    S   +++  K  +L  L +++    E+ +G 
Sbjct: 131 EVELTL-----KDEGLGKLKNGQIVKIPPSKVPRVIGKKGSMLNMLKEKTG--CEIIVGQ 183

Query: 178 NGKIWIRCESFSDTVRVGNLIMSCELLSYEE 208
           NG+IW+  E+ S        I   E  ++  
Sbjct: 184 NGRIWVDGENESLEELAIEAIRKIEREAHTS 214

Length = 239

>gnl|CDD|239901 cd04454, S1_Rrp4_like, S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain

 Score = 73.4 bits (180), Expect = 3e-17
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 51  RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA-TKKNPPKVETGDVVAGK 109
           RY+P  GD+VIG+VT      ++VDI S   A L   +      K+    ++ GD++  K
Sbjct: 1   RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAK 60

Query: 110 LLTANKDMESEMVCVD 125
           +++   DM   +   D
Sbjct: 61  VISLGDDMNVLLTTAD 76

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". Length = 82

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

 Score = 49.5 bits (119), Expect = 2e-07
 Identities = 34/153 (22%), Positives = 63/153 (41%), Gaps = 12/153 (7%)

Query: 51  RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG----ATKKNPPKV-ETGDV 105
           +Y+P  GDLVIG VT      + VDI S   A L      G        +  K  + GD 
Sbjct: 58  KYIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDY 117

Query: 106 VAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAK 165
           +  K+   ++  +  +  +  +G    +G +  G ++        +++  K  ++  L +
Sbjct: 118 IIAKVKDVDRTRDVVLT-LKGKG----LGKIEGGTIVEIKPVKVPRVIGKKGSMINMLKE 172

Query: 166 RSRQKMELSIGMNGKIWIRCESFSDTVRVGNLI 198
            +    ++ +G NG+IWI+     D       I
Sbjct: 173 ETG--CDIIVGQNGRIWIKGPDEEDEEIAIEAI 203

Length = 235

>gnl|CDD|240215 cd05789, S1_Rrp4, S1_Rrp4: Rrp4 S1-like RNA-binding domain

 Score = 42.5 bits (101), Expect = 7e-06
 Identities = 17/35 (48%), Positives = 21/35 (60%)

Query: 51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLS 85
          RY+P  GD+VIG VT      ++VDI S   AVL 
Sbjct: 1  RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLP 35

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". Length = 86

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	222
KOG1004|consensus	230		100.0
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	100.0
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	100.0
KOG3013|consensus	301		100.0
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	99.97
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	99.93
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	99.91
KOG3409|consensus	193		99.84
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	99.78
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	99.77
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.58
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	99.3
PF14382	39	ECR1_N: Exosome complex exonuclease RRP4 N-termina	98.96
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	98.72
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	98.67
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	98.63
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	98.6
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	98.58
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	98.56
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	98.47
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	98.46
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.43
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	98.36
PRK08582	139	hypothetical protein; Provisional	98.34
PRK07252	120	hypothetical protein; Provisional	98.34
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	98.33
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.29
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	98.28
PRK08059	123	general stress protein 13; Validated	98.28
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	98.23
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	98.17
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.17
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	98.17
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	98.15
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	98.15
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.11
COG1098	129	VacB Predicted RNA binding protein (contains ribos	98.1
PRK05807	136	hypothetical protein; Provisional	98.09
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	98.08
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	98.07
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	98.04
PHA02945	88	interferon resistance protein; Provisional	98.01
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	98.01
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	97.99
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	97.97
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	97.96
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	97.96
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	97.93
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	97.92
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	97.89
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	97.76
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	97.69
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	97.66
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	97.64
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	97.6
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	97.59
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	97.55
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	97.55
PRK07400	318	30S ribosomal protein S1; Reviewed	97.54
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	97.46
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	97.4
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.37
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.37
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	97.36
PRK07400	318	30S ribosomal protein S1; Reviewed	97.25
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.23
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	97.1
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	97.07
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	97.01
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	97.01
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	97.0
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	96.95
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	96.93
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	96.89
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	96.86
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	96.83
PRK12327	362	nusA transcription elongation factor NusA; Provisi	96.82
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	96.74
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	96.73
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	96.71
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	96.69
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	96.67
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.45
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	96.38
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	96.13
PRK09202	470	nusA transcription elongation factor NusA; Validat	96.11
TIGR01953	341	NusA transcription termination factor NusA. This m	96.06
COG2183	780	Tex Transcriptional accessory protein [Transcripti	96.01
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	95.99
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	95.79
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	95.47
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.38
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	95.12
PRK12329	449	nusA transcription elongation factor NusA; Provisi	94.51
KOG1070|consensus	1710		93.49
smart00322	69	KH K homology RNA-binding domain.	93.26
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	92.59
KOG1856|consensus	1299		92.42
PRK11642	813	exoribonuclease R; Provisional	92.2
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	91.75
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	91.3
PRK13763	180	putative RNA-processing protein; Provisional	90.56
PRK11712	489	ribonuclease G; Provisional	90.38
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	90.19
PRK10811	1068	rne ribonuclease E; Reviewed	90.07
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	89.5
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	88.88
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	87.71
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	86.98
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	86.19
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	85.72
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	85.21
KOG1070|consensus	1710		84.7
cd03524	75	RPA2_OBF_family RPA2_OBF_family: A family of oligo	84.52
KOG3298|consensus	170		82.5
PRK04012	100	translation initiation factor IF-1A; Provisional	81.98
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	81.19
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	80.96
PF01336	75	tRNA_anti-codon: OB-fold nucleic acid binding doma	80.93
KOG3297|consensus	202		80.09

>KOG1004|consensus

Probab=100.00  E-value=6e-59  Score=385.92  Aligned_cols=219  Identities=44%  Similarity=0.864  Sum_probs=207.1

Q ss_pred             CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEec-Cc----EEEEEccccccCCCCCCEEEEEEEEEecceEEEE
Q psy230            1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAK-PF----TYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVD   75 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~-~~----~v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~Vd   75 (222)
                      +|||.+......+..+|+|++..++.+.++.+|.++... ++    .+||...++||+|.+||.|||+|++..+|.|+||
T Consensus         5 ~pg~~~~~~~~~sv~~G~g~~~~g~~~~~~~~G~~~~~~~gk~~~~v~~vds~~kRYiP~~~D~VIGiV~~~~gd~ykVD   84 (230)
T KOG1004|consen    5 FPGDSIPRPRLCSVVLGPGLRRRGQERLVTKCGRLRHKEPGKGGGGVYWVDSQQKRYIPVKGDHVIGIVTSKSGDIYKVD   84 (230)
T ss_pred             cCCcccccCccCceeecCCccccCceEEeccccceeeccCCcccceeEEEecccceecCCCCCEEEEEEEeccCceEEEe
Confidence            699999854434588999999999999999999877653 22    7899999999999999999999999999999999


Q ss_pred             ECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCcccCCceEEEechhhhhhccCC
Q psy230           76 IGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNP  155 (222)
Q Consensus        76 I~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~l~~v~~~~~~rl~~~  155 (222)
                      |++++.|.||+++||||||||||+|+.||+|||||..+++++|++|+|+|++||+.+||+|++|+||++|++++|+|+.+
T Consensus        85 igg~~~a~L~~laFe~AtkrNrPnl~vGdliyakv~~a~~~~Epel~Cids~graaGfG~LkdG~if~vs~~~~R~Ll~p  164 (230)
T KOG1004|consen   85 IGGSEPASLSYLAFEGATKRNRPNLQVGDLIYAKVVDANKDMEPELTCIDSTGRAAGFGVLKDGMIFKVSLGLCRKLLLP  164 (230)
T ss_pred             cCCCCeeeeeeccccCccccCCCccccccEEEEEEEecCCCcCcceEEEcccCcccCcccccCceEEEecHHHHHHHHcC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHhc
Q psy230          156 KCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFL  221 (222)
Q Consensus       156 ~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~~l~  221 (222)
                      .|.+|+.+++  +++|||++|+||||||++++..++++++++|.+||.|+.+|...|++++.+.+.
T Consensus       165 ~~~iLq~vGk--~~~FEia~GlNGriWV~ae~~~~t~~i~~~l~~~e~~td~~q~~~~k~~~~~~~  228 (230)
T KOG1004|consen  165 DCPILQTVGK--KYPFEIAFGLNGRIWVKAETLSDTLIIANILMNCEFMTDTQQRIMVKQLFKRLA  228 (230)
T ss_pred             CCcHHHHhhc--ccceEEEEecCceEEEeccCcchHHHHHHHHHHhhccCcHHHHHHHHHHHHHHh
Confidence            9999999999  999999999999999999999999999999999999999998899999888764

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

Probab=100.00  E-value=3.6e-58  Score=390.45  Aligned_cols=209  Identities=29%  Similarity=0.383  Sum_probs=199.2

Q ss_pred             CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEecCcEEEEEccccccCCCCCCEEEEEEEEEecceEEEEECCCC
Q psy230            1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHD   80 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~~~~v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~   80 (222)
                      +|||.+...  .++..|||||.+++++||+++|.++.++ +.+.|.|++++|+|++||+|||+|+++.++.|+|||++++
T Consensus        12 ~PGd~vl~~--~~~~~G~Gty~~~~~iyssv~G~~~~~~-~~v~VIpl~g~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~   88 (239)
T COG1097          12 LPGDLVLAE--GSYKLGHGTYFEGGKIYSSVVGLLDVKG-KLVRVIPLEGRYIPEVGDVVIGKIIEVGPSGWKVDIGSPY   88 (239)
T ss_pred             cCCCccCCC--CCEecCCCcEecCCEEEEEEEeEEEEeC-CEEEEEeCCCcccCCCCCEEEEEEEEEcccceEEEcCCcc
Confidence            699976655  4699999999999999999999999995 7789999999999999999999999999999999999999


Q ss_pred             Ceeeecccc-----ccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCcccCCceEEEechhhhhhccCC
Q psy230           81 PAVLSYLAF-----EGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNP  155 (222)
Q Consensus        81 ~a~L~~~~f-----~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~l~~v~~~~~~rl~~~  155 (222)
                      .|.||+++|     +.++++||++|++||+|+|||+.++++++++|+|++     .+||+|++|++++|+|++++|++++
T Consensus        89 ~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~-----~~~GkL~~G~iv~i~p~kVpRvig~  163 (239)
T COG1097          89 PALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKD-----EGLGKLKNGQIVKIPPSKVPRVIGK  163 (239)
T ss_pred             ceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeec-----CCCccccCCEEEEEchhhcceEecC
Confidence            999999887     567899999999999999999999999999999966     9999999999999999999999999


Q ss_pred             ChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHhc
Q psy230          156 KCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFL  221 (222)
Q Consensus       156 ~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~~l~  221 (222)
                      +.+|+++|++  +++|||+||+||||||++++...+.++..||.+||.  ++|+.+++++++++|.
T Consensus       164 ~~sm~~~l~~--~~~~~I~VG~NG~IWV~~~~~~~e~~~~~aI~~ie~--ea~~~gltdr~~~~i~  225 (239)
T COG1097         164 KGSMLNMLKE--KTGCEIIVGQNGRIWVDGENESLEELAIEAIRKIER--EAHTSGLTDRIKEFLK  225 (239)
T ss_pred             CCcHHHHhhh--hcCeEEEEecCCEEEecCCCcchHHHHHHHHHHHhh--hhhhhhHHHHHHHHHH
Confidence            9999999999  999999999999999999999889999999999999  9999999999998874

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=100.00  E-value=2e-51  Score=354.21  Aligned_cols=208  Identities=21%  Similarity=0.291  Sum_probs=197.9

Q ss_pred             CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEecCcEEEEEccccccCCCCCCEEEEEEEEEecceEEEEECCCC
Q psy230            1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHD   80 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~~~~v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~   80 (222)
                      +|||.|+.   ++|.+|+|||.++|.|+||++|.++.++ +.++|.|.+++|+|++||+|+|+|++++++.|+|||++++
T Consensus        12 ~PGd~l~~---~~~~~G~Gty~~~g~i~As~~G~~~~~~-~~i~V~p~~~~y~P~vGDiViG~V~~i~~~~~~vdI~~~~   87 (235)
T PRK04163         12 VPGDLLAE---GEFKAGRGTYKENGKIYSTVVGLVDIKD-DKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEVDINSPY   87 (235)
T ss_pred             CCCCCcCc---CCeecCCceEEeCCEEEEEEeEEEEEEC-CEEEEEECCCcccCCCCCEEEEEEEEEeCceEEEEeCCCc
Confidence            69999973   4799999999999999999999999885 7999999999999999999999999999999999999999


Q ss_pred             Ceeeeccccccc-----cccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCcccCCceEEEechhhhhhccCC
Q psy230           81 PAVLSYLAFEGA-----TKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNP  155 (222)
Q Consensus        81 ~a~L~~~~f~ga-----tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~l~~v~~~~~~rl~~~  155 (222)
                      .|+||.++|.++     +++|+++|++||+|+|||+++++++.++|||++     ++||+|.+|++++|++.++++|+++
T Consensus        88 ~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~-----~~lG~L~~G~~~~V~~~~i~~lig~  162 (235)
T PRK04163         88 KAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKG-----KGLGKIEGGTIVEIKPVKVPRVIGK  162 (235)
T ss_pred             eeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcC-----CCCCccCCCEEEEECHHHHHhhcCC
Confidence            999999988764     489999999999999999999988889999965     8999999999999999999999999


Q ss_pred             ChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHhc
Q psy230          156 KCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFL  221 (222)
Q Consensus       156 ~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~~l~  221 (222)
                      ++++++.|.+  .++|+|++|.||+|||.+++.+.+..+.++|+++|+  ++|..+|+++++++|.
T Consensus       163 ~g~~i~~l~~--~~~~~I~ig~NG~VwI~~~~~~~~~~a~~~I~~~e~--~~~~~~l~~~v~~~~~  224 (235)
T PRK04163        163 KGSMINMLKE--ETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIKKIER--EAHTSGLTDRIKEFLE  224 (235)
T ss_pred             CChhHhhhhh--hhCcEEEEcCCcEEEEeeCCHHHHHHHHHHHHHHHh--hhhccChHHHHHHHHH
Confidence            9999999999  999999999999999999999999999999999999  9999999999999984

>KOG3013|consensus

Probab=100.00  E-value=1.2e-39  Score=277.63  Aligned_cols=169  Identities=22%  Similarity=0.387  Sum_probs=153.4

Q ss_pred             CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEecCcEEEEEccccccCCCCCCEEEEEEEEEecceEEEEECCCC
Q psy230            1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHD   80 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~~~~v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~   80 (222)
                      +||+.+...  ..|..|||||..++.|+||++|.++.. |++++|+|++.||.|++||+|+|+|+++.+++|+||+|+..
T Consensus        33 tPG~~V~~d--~~fmRGHGTy~~d~~i~ssvaG~v~rv-NkLi~V~plk~rY~pEvGDvVVgRV~eVq~KRWkvd~nsk~  109 (301)
T KOG3013|consen   33 TPGELVTDD--PGFMRGHGTYVRDGEIYSSVAGVVQRV-NKLISVKPLKSRYAPEVGDVVVGRVIEVQQKRWKVDLNSKQ  109 (301)
T ss_pred             cCCccccCc--hhhhhcccceecCCeEEEeecchhhhh-cceEEEeehhhhcCCccCCEEEEEeeeeecceeEEeccccc
Confidence            599999876  469999999999999999999999988 59999999999999999999999999999999999999999


Q ss_pred             Ceeeeccc--ccccc---------ccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCcccCCceEEEechhhh
Q psy230           81 PAVLSYLA--FEGAT---------KKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLC  149 (222)
Q Consensus        81 ~a~L~~~~--f~gat---------k~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~l~~v~~~~~  149 (222)
                      +|+|.+++  +||..         ..||.+|+.||+|.|+|+.+..++...|+|+     +..||||..|++++|+|.++
T Consensus       110 d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs~sLhTR-----S~KYGKL~~G~lvkVpp~Lv  184 (301)
T KOG3013|consen  110 DAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHDGSLSLHTR-----SLKYGKLGQGILVKVPPALV  184 (301)
T ss_pred             ceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhccCCeEEEEec-----chhcccccCceEEEeCHHHh
Confidence            99999865  67743         2699999999999999999999999999995     49999999999999999999


Q ss_pred             hhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEee
Q psy230          150 RKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRC  185 (222)
Q Consensus       150 ~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~  185 (222)
                      +|...   +++ .+    .++.++|+|+||+|||..
T Consensus       185 kr~K~---hfh-~l----p~g~~vIlG~NGyIWv~~  212 (301)
T KOG3013|consen  185 KRSKT---HFH-NL----PGGVDVILGCNGYIWVGP  212 (301)
T ss_pred             hhhhh---hhc-cC----CCCeEEEEecCceEEecC
Confidence            98764   333 23    689999999999999986

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

Probab=99.97  E-value=1.8e-31  Score=196.27  Aligned_cols=86  Identities=56%  Similarity=0.969  Sum_probs=84.3

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCcc
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKE  130 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~  130 (222)
                      ||+|++||+|||+|+++.+++|+|||++++.|+||.++|+|++|+|||+|++||+|||||.+++++++++|||++++||+
T Consensus         1 rY~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~gatk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~~~~k~   80 (86)
T cd05790           1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCVDSSGKA   80 (86)
T ss_pred             CCcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccccccccccCCCCCEEEEEEEecCCCCCeEEEEeCCCCcc
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCccc
Q psy230          131 FIMGIL  136 (222)
Q Consensus       131 ~~~G~L  136 (222)
                      .+||.|
T Consensus        81 ~g~G~L   86 (86)
T cd05790          81 DGFGPL   86 (86)
T ss_pred             cccccC
Confidence            999986

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".

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=99.93  E-value=6.6e-25  Score=183.49  Aligned_cols=139  Identities=17%  Similarity=0.192  Sum_probs=118.8

Q ss_pred             CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEec-CcEEEEEcccc-ccCCCCCCEEEEEEEEEecceEEEEECC
Q psy230            1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAK-PFTYYVDYIQR-RYVPTRGDLVIGVVTSRVGDNYRVDIGS   78 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~-~~~v~V~~~~~-~Y~P~vGDiVIG~V~~v~~~~~~VdI~~   78 (222)
                      +|||.|+..  ++|.+|+|||.+++.|+||++|.++.+. ++.++|.|.+. .|.|++||+|+|+|+++..+.|.|||++
T Consensus         9 ~PGe~l~~~--~e~~~G~Gty~~~~~i~as~~G~~~id~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~   86 (189)
T PRK09521          9 LPGDYLAVI--EEYLPGEGTYEDNGEVYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVS   86 (189)
T ss_pred             CCCCccccc--cceEcCCCEEeeCCEEEEEeeEEEEEcCCCCEEEEecCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEE
Confidence            699999875  4799999999999999999999999864 56899999876 8999999999999999999999999963


Q ss_pred             ----------CCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCcccC------CceE
Q psy230           79 ----------HDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILN------DGYL  141 (222)
Q Consensus        79 ----------~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~------~G~l  141 (222)
                                +..|+||.+.+. ...+++++.|++||+|+|||++++  ..++|||++     +.||+|.      ++.|
T Consensus        87 ~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~--~~i~LS~k~-----~~lGvv~a~~~~~g~~~  159 (189)
T PRK09521         87 IEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT--DPLQLSTKG-----KDLGVIYAMCSRCRTPL  159 (189)
T ss_pred             ecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC--CcEEEEEec-----CCceEEEEEccccCCce
Confidence                      567888877653 345678999999999999999998  689999965     8999993      4556


Q ss_pred             EEechhh
Q psy230          142 LHTSISL  148 (222)
Q Consensus       142 ~~v~~~~  148 (222)
                      +++++..
T Consensus       160 ~~~~~~~  166 (189)
T PRK09521        160 VKKGENE  166 (189)
T ss_pred             EECCCCE
Confidence            6666544

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

Probab=99.91  E-value=7.2e-24  Score=174.40  Aligned_cols=127  Identities=20%  Similarity=0.310  Sum_probs=114.6

Q ss_pred             CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEec-CcEEEEEcccc-ccCCCCCCEEEEEEEEEecceEEEEECC
Q psy230            1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAK-PFTYYVDYIQR-RYVPTRGDLVIGVVTSRVGDNYRVDIGS   78 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~-~~~v~V~~~~~-~Y~P~vGDiVIG~V~~v~~~~~~VdI~~   78 (222)
                      +|||.|+..  +||++|.|||+++|.|+|+.+|.+..++ +.+++|+|.++ ..+|+.||+|+|+|+++..+.+.|.|-+
T Consensus         9 ~PGd~~a~~--EE~~~G~gt~~~~g~i~Aa~~G~~~~d~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~~~~a~V~i~~   86 (188)
T COG1096           9 LPGDVLAVI--EEFLPGEGTYEEGGEIRAAATGVVRRDDKNRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRALVRIVG   86 (188)
T ss_pred             cCcceeeee--eeeecCCCeEeECCEEEEeecccEEEcccceEEEeccCCCCCCCCCCCCEEEEEEeeccceEEEEEEEE
Confidence            799999987  6899999999999999999999998874 57799999888 7999999999999999999999999843


Q ss_pred             ----------CCCeeeecccc-ccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCccc
Q psy230           79 ----------HDPAVLSYLAF-EGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGIL  136 (222)
Q Consensus        79 ----------~~~a~L~~~~f-~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L  136 (222)
                                +..|.+|+++. .+..++.+++|++||+|+|||+|..  ..++|||.+     +.||++
T Consensus        87 ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~--~~~~Lst~~-----~dlGVI  148 (188)
T COG1096          87 VEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG--DPIQLSTKG-----NDLGVI  148 (188)
T ss_pred             EecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC--CCeEEEecC-----CcceEE
Confidence                      56789998764 5677899999999999999999998  579999976     999999

>KOG3409|consensus

Probab=99.84  E-value=1.7e-20  Score=152.18  Aligned_cols=144  Identities=16%  Similarity=0.175  Sum_probs=113.3

Q ss_pred             CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEec-CcEEEEE----ccccccCCCCCCEEEEEEEEEecceEEEE
Q psy230            1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAK-PFTYYVD----YIQRRYVPTRGDLVIGVVTSRVGDNYRVD   75 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~-~~~v~V~----~~~~~Y~P~vGDiVIG~V~~v~~~~~~Vd   75 (222)
                      +|||+++... +++..|.|||+.++.|+||.+|....++ .....|.    +....-+|.+||+|.++|+.++..+++||
T Consensus         9 lpG~~~c~~e-~~~~~g~Gtye~~~yI~aS~ag~~~~~~~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~~i~~rfAkv~   87 (193)
T KOG3409|consen    9 LPGEVVCRAE-GEYRMGEGTYERNGYIFASVAGVNFRDNLVQKIEVVSVEKQLFNELLPFVGAIVTARVSRINLRFAKVD   87 (193)
T ss_pred             cccceeeecc-cccccccceeecCCeEEeccccceeecCCccceeeeeecccchhhcCCccCcEEEEEEEeeccceeeEE
Confidence            6999999754 4689999999999999999999654442 1222333    23346899999999999999999999999


Q ss_pred             ECC--------CCCeeeeccccccccc----cCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCccc------C
Q psy230           76 IGS--------HDPAVLSYLAFEGATK----KNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGIL------N  137 (222)
Q Consensus        76 I~~--------~~~a~L~~~~f~gatk----~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L------~  137 (222)
                      |.+        ++.|+|+..... +|+    +...+|+|||+|.|+|+|.+...++.||+.+     +.||++      .
T Consensus        88 I~~V~d~~lk~~FrglirkqdvR-~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LTtAe-----neLGVV~a~as~~  161 (193)
T KOG3409|consen   88 ILSVGDKPLKKSFRGLIRKQDVR-ATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLTTAE-----NELGVVFARASET  161 (193)
T ss_pred             EEEEcCEEhhhhhcceeehhhcc-ccccchhhhhhccCCCcEEEEEEeecCCCCcEEEEEec-----ccceEEEEecccc
Confidence            976        344555432221 232    4568999999999999998888899999987     999998      5


Q ss_pred             CceEEEechhhhhh
Q psy230          138 DGYLLHTSISLCRK  151 (222)
Q Consensus       138 ~G~l~~v~~~~~~r  151 (222)
                      ++.|++|+++.+..
T Consensus       162 g~~M~pvdw~~mqs  175 (193)
T KOG3409|consen  162 GEPMVPVDWQEMQS  175 (193)
T ss_pred             CCceeeccceeEEc
Confidence            78999999988764

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

Probab=99.78  E-value=5.8e-19  Score=131.70  Aligned_cols=80  Identities=19%  Similarity=0.222  Sum_probs=71.4

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEE--------CCCCCeeeeccccc-cccc--cCCcCCCCCCEEEEEEEecCCCCeeE
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDI--------GSHDPAVLSYLAFE-GATK--KNPPKVETGDVVAGKLLTANKDMESE  120 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI--------~~~~~a~L~~~~f~-gatk--~~r~~l~~GDlV~ArV~~~~~~~~~~  120 (222)
                      |.|++||+|+|+|++++.++|.|||        ++++.|+|+.+.+. ...+  +|+.+|++||+|+|||++.++.++++
T Consensus         2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~~~   81 (92)
T cd05791           2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASSYY   81 (92)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCCcE
Confidence            8999999999999999999999999        78999999987653 3333  79999999999999999999888999


Q ss_pred             EEEecCCCccccCccc
Q psy230          121 MVCVDSRGKEFIMGIL  136 (222)
Q Consensus       121 Ls~~~~~~~~~~~G~L  136 (222)
                      ||+.+     ++||++
T Consensus        82 Lst~~-----~~lGVv   92 (92)
T cd05791          82 LSTAE-----NELGVV   92 (92)
T ss_pred             EEecC-----CCCccC
Confidence            99976     889975

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".

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

Probab=99.77  E-value=2.2e-18  Score=125.23  Aligned_cols=81  Identities=30%  Similarity=0.478  Sum_probs=75.2

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCc
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGK  129 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~  129 (222)
                      +|+|++||+|+|+|+++..+.|.|||++...|+||.++|.. ..+++++.|++||+|.|+|+++++.+.+.|||.+    
T Consensus         1 ~y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~~~i~LS~~~----   76 (82)
T cd04454           1 RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMNVLLTTAD----   76 (82)
T ss_pred             CCCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCCCCEEEEECC----
Confidence            69999999999999999999999999999999999999875 4788999999999999999999887889999966    


Q ss_pred             cccCccc
Q psy230          130 EFIMGIL  136 (222)
Q Consensus       130 ~~~~G~L  136 (222)
                       ++||+|
T Consensus        77 -~~~Gvi   82 (82)
T cd04454          77 -NELGVI   82 (82)
T ss_pred             -CCCccC
Confidence             889985

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".

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

Probab=99.58  E-value=7.6e-15  Score=107.25  Aligned_cols=81  Identities=27%  Similarity=0.379  Sum_probs=72.8

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-----ccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-----ATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD  125 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-----atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  125 (222)
                      +|.|++||+|.|+|+++.++.|.|+|++...|+||.+.+..     ..+++.+.|++||.|.|+|+++++++.+.||+..
T Consensus         1 ~y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~~i~LS~~~   80 (86)
T cd05789           1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRS   80 (86)
T ss_pred             CCcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCCCEEEEeCc
Confidence            69999999999999999999999999999999999988752     3456778899999999999999887889999965


Q ss_pred             CCCccccCccc
Q psy230          126 SRGKEFIMGIL  136 (222)
Q Consensus       126 ~~~~~~~~G~L  136 (222)
                           .+||+|
T Consensus        81 -----~~~g~~   86 (86)
T cd05789          81 -----LKYGKL   86 (86)
T ss_pred             -----ccccCC
Confidence                 888876

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".

>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=99.30  E-value=4.6e-12  Score=92.50  Aligned_cols=60  Identities=28%  Similarity=0.386  Sum_probs=38.0

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCC----------CCeeeeccccccc--------cc----cCCcCCCCCCEEEEEE
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGSH----------DPAVLSYLAFEGA--------TK----KNPPKVETGDVVAGKL  110 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~----------~~a~L~~~~f~ga--------tk----~~r~~l~~GDlV~ArV  110 (222)
                      +|++||+|+|+|+++++.++.|+|.+-          ....|. ..|.|.        |+    +|..+|+|||+|+|||
T Consensus         1 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~-~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~V   79 (82)
T PF10447_consen    1 LPKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLK-EPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARV   79 (82)
T ss_dssp             ---TT-EEEEEEEEE-SSEEEEEEEES----------SSS-----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEE
T ss_pred             CCCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccc-cccEEEEEeeeecccccchhhHHhccCCCCEEEEEE
Confidence            599999999999999999999999765          222222 245542        21    5899999999999999


Q ss_pred             Eec
Q psy230          111 LTA  113 (222)
Q Consensus       111 ~~~  113 (222)
                      +|.
T Consensus        80 iSl   82 (82)
T PF10447_consen   80 ISL   82 (82)
T ss_dssp             EEE
T ss_pred             eeC
Confidence            984

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.

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

Probab=98.96  E-value=6.2e-10  Score=70.17  Aligned_cols=36  Identities=22%  Similarity=0.355  Sum_probs=31.6

Q ss_pred             CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEe
Q psy230            1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHA   38 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~   38 (222)
                      +|||.|+..  ++|.+|+|||+++++|+||++|.++.+
T Consensus         3 ~PG~~l~~~--~e~~~G~GTY~~~g~I~asv~G~v~~~   38 (39)
T PF14382_consen    3 VPGDRLGSS--EEYMPGHGTYVRDGNIYASVAGTVKID   38 (39)
T ss_dssp             -TT-EEEET--TTSEESTTEEEETTEEEESSSEEEEEE
T ss_pred             CCCCEeecC--CCEecCCCEEEeCCEEEEEeeEEEEEc
Confidence            699999986  579999999999999999999999875

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

Probab=98.72  E-value=8.6e-08  Score=66.93  Aligned_cols=67  Identities=25%  Similarity=0.356  Sum_probs=56.7

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCC-CCeeEEEE
Q psy230           57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANK-DMESEMVC  123 (222)
Q Consensus        57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~  123 (222)
                      ||+|.|+|+++.++.+.||+++...|.||.+.+. ...++....|++||.+.|+|.++++ ...+.||.
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~   69 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSK   69 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEe
Confidence            8999999999999999999998899999987764 3445667789999999999999974 34566664

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.

>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=98.67  E-value=1.1e-07  Score=67.32  Aligned_cols=68  Identities=15%  Similarity=0.252  Sum_probs=58.8

Q ss_pred             CCCCEEEEEEEEEec-ceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCCeeEEEE
Q psy230           55 TRGDLVIGVVTSRVG-DNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDMESEMVC  123 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~-~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~  123 (222)
                      ++||+|.|+|+++.+ ..+.|++.....|.+|.+.+. ...++..+.|++||.|.|+|.++++ ..+.||+
T Consensus         2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~-~~i~LSl   71 (72)
T cd05704           2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD-GKYQLSL   71 (72)
T ss_pred             CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC-CEEEEEe
Confidence            589999999999986 589999999999999998774 3455556789999999999999976 6788886

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.

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

Probab=98.63  E-value=1.8e-07  Score=64.01  Aligned_cols=69  Identities=22%  Similarity=0.247  Sum_probs=59.0

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc-cccCCcCCCCCCEEEEEEEecCCC-CeeEEEE
Q psy230           55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA-TKKNPPKVETGDVVAGKLLTANKD-MESEMVC  123 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~  123 (222)
                      ++||+|.|+|+++....|.|++++...|.+|.+.+... .+++...|++||.|.|+|.+++.+ ..+.||+
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~   71 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL   71 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEe
Confidence            46999999999999999999999889999998766533 455567799999999999999876 6788876

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

Probab=98.60  E-value=3.3e-07  Score=64.09  Aligned_cols=69  Identities=17%  Similarity=0.263  Sum_probs=59.9

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230           57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD  125 (222)
Q Consensus        57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  125 (222)
                      ||+|.|+|+++.+..+.|++.+...|.+|.+.+.. ..++....|++||.|.|+|.+++.. ..+.||++.
T Consensus         1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k~   71 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKA   71 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEEE
Confidence            79999999999999999999998999999887643 3456678899999999999999876 568999854

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.

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

Probab=98.58  E-value=3.7e-07  Score=64.49  Aligned_cols=71  Identities=15%  Similarity=0.142  Sum_probs=60.0

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECC--CCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEe
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGS--HDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEMVCV  124 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~  124 (222)
                      |++|++|.|+|+++....+.|++..  ...|.+|.+.+.. ..++....|++||.|.|+|.+++.. ..+.||++
T Consensus         1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~k   75 (76)
T cd04452           1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK   75 (76)
T ss_pred             CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEEc
Confidence            7899999999999999999999975  3789999887753 3456677899999999999999864 56888874

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

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

Probab=98.56  E-value=4.8e-07  Score=61.96  Aligned_cols=67  Identities=19%  Similarity=0.181  Sum_probs=57.3

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeeeeccccccc-cccCCcCCCCCCEEEEEEEecCCCCeeEEEE
Q psy230           57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA-TKKNPPKVETGDVVAGKLLTANKDMESEMVC  123 (222)
Q Consensus        57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~  123 (222)
                      ||+|.|+|+++....|.|+|.....|.||.+.+... .+.....|++||.|.++|.+++..+.+.||+
T Consensus         1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~~~~i~ls~   68 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSI   68 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECCCCcEEEEE
Confidence            799999999999999999999999999998776532 3344467999999999999998766788887

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.

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

Probab=98.47  E-value=9.6e-07  Score=62.08  Aligned_cols=70  Identities=20%  Similarity=0.228  Sum_probs=61.5

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCCC-eeEEEE
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDM-ESEMVC  123 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~  123 (222)
                      |++||+|-|+|+++....+.||++....|.+|...+.. ........+++||-|.|+|.+++.+. .+.||+
T Consensus         2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~   73 (74)
T PF00575_consen    2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSL   73 (74)
T ss_dssp             SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEES
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEE
Confidence            78999999999999999999999999999999988764 34567789999999999999998764 477775

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=98.46  E-value=1.8e-06  Score=60.62  Aligned_cols=69  Identities=17%  Similarity=0.158  Sum_probs=59.3

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEE
Q psy230           55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEMVC  123 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~  123 (222)
                      ++||+|-|+|+++.+..+.|++.....|.+|.+.+.. ..++....|++||.|.|+|.+++.+ ..+.||+
T Consensus         2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~   72 (73)
T cd05706           2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSL   72 (73)
T ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEE
Confidence            5799999999999999999999999999999887653 3345677899999999999999864 5788886

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.

>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=98.43  E-value=1e-06  Score=61.82  Aligned_cols=61  Identities=16%  Similarity=0.197  Sum_probs=53.4

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeeeecccccc---ccccCCcCCCCCCEEEEEEEecCCCC
Q psy230           57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG---ATKKNPPKVETGDVVAGKLLTANKDM  117 (222)
Q Consensus        57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g---atk~~r~~l~~GDlV~ArV~~~~~~~  117 (222)
                      ||+|.|+|+++....+.|++.+...|.+|...+..   ..+++...|++||.|.|+|++++...
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~   64 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAK   64 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcc
Confidence            89999999999999999999999999999877642   25567788999999999999997654

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.

>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=98.36  E-value=3.1e-06  Score=59.60  Aligned_cols=71  Identities=14%  Similarity=0.119  Sum_probs=59.3

Q ss_pred             CCCCEEEEEEEEEecceEEEEECC-CCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           55 TRGDLVIGVVTSRVGDNYRVDIGS-HDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      ++|++|.|+|+++....+.|++.. ...|.+|.+.+.. ...+....|++||.|.|+|.+++. ...+.|+++.
T Consensus         1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k~   74 (77)
T cd05708           1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKA   74 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence            469999999999999999999985 7899999877643 334556789999999999999986 4678888864

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.

>PRK08582 hypothetical protein; Provisional

Probab=98.34  E-value=4.6e-06  Score=66.69  Aligned_cols=72  Identities=17%  Similarity=0.135  Sum_probs=63.9

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD  125 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  125 (222)
                      .++|++|.|+|++++...+.|+|.....|++|++.+. ...++....|++||.|.|+|++++.+..+.||+..
T Consensus         3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk~   75 (139)
T PRK08582          3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKK   75 (139)
T ss_pred             CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEEe
Confidence            4689999999999999999999999999999998774 34566678899999999999999877889999875

>PRK07252 hypothetical protein; Provisional

Probab=98.34  E-value=4.1e-06  Score=65.40  Aligned_cols=71  Identities=10%  Similarity=0.090  Sum_probs=61.3

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      ++||+|.|+|+++....+.|+|.....|.+|.+.+.. ..+.....|++||.|.++|.+++. ...+.|+++.
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~   74 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRT   74 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEee
Confidence            4799999999999999999999988999999887643 334556789999999999999986 5678999986

>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=98.33  E-value=2.6e-06  Score=59.19  Aligned_cols=65  Identities=25%  Similarity=0.342  Sum_probs=55.3

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEE
Q psy230           57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEM  121 (222)
Q Consensus        57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~L  121 (222)
                      ||+|.|+|+++.+..+.|++.....|.+|.+.+.. ..++....|++||.|.|+|.++++. ..+.|
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~l   67 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEM   67 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEec
Confidence            79999999999999999999988999999987753 4556678899999999999999863 34444

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.

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

Probab=98.29  E-value=3.7e-06  Score=70.06  Aligned_cols=80  Identities=20%  Similarity=0.216  Sum_probs=64.6

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc------------cccCCcCCCCCCEEEEEEEecCCC--
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA------------TKKNPPKVETGDVVAGKLLTANKD--  116 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~--  116 (222)
                      .|.|.+|++|.|+|++++...+.|+++ +..++++..+.+..            .++....++.||.|++||.+++.+  
T Consensus        76 vf~P~~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~  154 (187)
T PRK08563         76 VFKPELQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKER  154 (187)
T ss_pred             EEeccCCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccC
Confidence            367999999999999999999999998 58888887654321            134567899999999999998743  


Q ss_pred             ----CeeEEEEecCCCccccCccc
Q psy230          117 ----MESEMVCVDSRGKEFIMGIL  136 (222)
Q Consensus       117 ----~~~~Ls~~~~~~~~~~~G~L  136 (222)
                          ..+.||+.+     ++||++
T Consensus       155 ~~~~~~I~ls~~~-----~~LG~~  173 (187)
T PRK08563        155 RPRGSKIGLTMRQ-----PGLGKL  173 (187)
T ss_pred             CCCCCEEEEEecC-----CCCCcH
Confidence                357888865     899987

>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=98.28  E-value=4.6e-06  Score=59.49  Aligned_cols=67  Identities=16%  Similarity=0.189  Sum_probs=54.6

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeeeecccccccc-c---cCCcCCCCCCEEEEEEEecCCCC-eeEE
Q psy230           55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGAT-K---KNPPKVETGDVVAGKLLTANKDM-ESEM  121 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gat-k---~~r~~l~~GDlV~ArV~~~~~~~-~~~L  121 (222)
                      ++||+|.|+|+++++..+.|+++..-.|.+|++...... +   .....|++||.|.|+|++++++. .+.|
T Consensus         2 k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~L   73 (74)
T cd05705           2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVEL   73 (74)
T ss_pred             CCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEec
Confidence            589999999999999999999998899999987654321 2   24578999999999999998653 3444

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.

>PRK08059 general stress protein 13; Validated

Probab=98.28  E-value=5.3e-06  Score=64.84  Aligned_cols=72  Identities=17%  Similarity=0.118  Sum_probs=61.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      .++||+|.|+|+++....+.|+|.....|.+|.+.++. ..++....|++||.|.|+|.+++. ...+.||++.
T Consensus         5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~   78 (123)
T PRK08059          5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRA   78 (123)
T ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEE
Confidence            46799999999999999999999999999999887653 333446679999999999999964 5689999976

>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=98.23  E-value=3.8e-06  Score=63.49  Aligned_cols=70  Identities=16%  Similarity=0.167  Sum_probs=58.1

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-cc-------------------ccCCcCCCCCCEEEEEEEecC
Q psy230           55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-AT-------------------KKNPPKVETGDVVAGKLLTAN  114 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-at-------------------k~~r~~l~~GDlV~ArV~~~~  114 (222)
                      ++||+|.|+|+++......|++.....|++|++.+.. .+                   .+....|++||+|.|+|++++
T Consensus         2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~d   81 (100)
T cd05693           2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLD   81 (100)
T ss_pred             CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEcc
Confidence            5899999999999999999999888899999865531 11                   235688999999999999999


Q ss_pred             CC----CeeEEEEe
Q psy230          115 KD----MESEMVCV  124 (222)
Q Consensus       115 ~~----~~~~Ls~~  124 (222)
                      +.    ..+.||.+
T Consensus        82 ~~~~~~~~i~LSlr   95 (100)
T cd05693          82 KSKSGKKRIELSLE   95 (100)
T ss_pred             CCcCCCcEEEEEec
Confidence            75    46788875

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.

>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=98.17  E-value=1.3e-05  Score=55.64  Aligned_cols=67  Identities=16%  Similarity=0.190  Sum_probs=56.7

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEE
Q psy230           57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEMVC  123 (222)
Q Consensus        57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~  123 (222)
                      ||++.|+|+++.+..+.|++...-.|.+|.+.+.. ...+....|++||.|.++|.++++. ..+.||+
T Consensus         1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~   69 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSC   69 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEe
Confidence            89999999999999999999877899999887642 3334456799999999999999874 5788886

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.

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

Probab=98.17  E-value=9.9e-06  Score=71.24  Aligned_cols=74  Identities=18%  Similarity=0.206  Sum_probs=63.9

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECC--CCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGS--HDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD  125 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  125 (222)
                      -.|++||+|.|+|+++....|.|++..  ...|.+|.+.+. +..+.++..|++||.|.|+|.+++.. ..+.||.+.
T Consensus         4 ~~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSlK~   81 (262)
T PRK03987          4 EWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKR   81 (262)
T ss_pred             CCCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEEEe
Confidence            469999999999999999999999976  478999988764 45567788999999999999999875 468999975

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

Probab=98.17  E-value=1.6e-05  Score=56.27  Aligned_cols=70  Identities=14%  Similarity=0.121  Sum_probs=57.8

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECC-CCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCCCeeEEEE
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGS-HDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDMESEMVC  123 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~  123 (222)
                      |+.|+++-|+|+++.+..+.|++.. ...|.+|.+.+.. ..++.+..|++||-|.++|.+++....+.||.
T Consensus         1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~ki~ls~   72 (73)
T cd05686           1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL   72 (73)
T ss_pred             CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCCcEEEEe
Confidence            6899999999999999999999954 3589999887643 33456677999999999999998765666664

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=98.15  E-value=1.5e-05  Score=56.59  Aligned_cols=68  Identities=15%  Similarity=0.204  Sum_probs=57.5

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeeeeccccccc---cccCCcCCCCCCEEEEEEEecCCC-CeeEEEEe
Q psy230           57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA---TKKNPPKVETGDVVAGKLLTANKD-MESEMVCV  124 (222)
Q Consensus        57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga---tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~  124 (222)
                      ||+|-|+|+++.+..+.|++...-.|.+|.+.+...   .++....|++||.|.|+|+++++. ..+.||.+
T Consensus         1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~k   72 (73)
T cd05703           1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            899999999999999999998889999998876422   445667899999999999999865 46788763

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.

>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=98.15  E-value=1.3e-05  Score=57.86  Aligned_cols=72  Identities=11%  Similarity=0.015  Sum_probs=61.0

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEE
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEMVC  123 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~  123 (222)
                      ..+++|+++-|+|+++......|++...-.|.+|.+.+.. ...+....|++||.|.++|.+++.. ..+.||+
T Consensus        10 ~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~lsl   83 (83)
T cd04461          10 SDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL   83 (83)
T ss_pred             HhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEeC
Confidence            4578999999999999999999999988999999877643 3456778899999999999999864 5677764

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.

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

Probab=98.11  E-value=1.8e-05  Score=65.69  Aligned_cols=81  Identities=17%  Similarity=0.255  Sum_probs=64.6

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-------c-----cccCCcCCCCCCEEEEEEEecC----
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-------A-----TKKNPPKVETGDVVAGKLLTAN----  114 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-------a-----tk~~r~~l~~GDlV~ArV~~~~----  114 (222)
                      .|.|.+|+++-|+|++++...+.|+++ +..++++..++..       .     -++....++.||.|++||.+++    
T Consensus        76 ~f~p~~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~  154 (179)
T TIGR00448        76 VFKPELGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDR  154 (179)
T ss_pred             EEeccCCCEEEEEEEEEEeeEEEEEeC-CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCC
Confidence            378999999999999999999999995 6888888654321       1     1245578999999999999986    


Q ss_pred             --CCCeeEEEEecCCCccccCcccC
Q psy230          115 --KDMESEMVCVDSRGKEFIMGILN  137 (222)
Q Consensus       115 --~~~~~~Ls~~~~~~~~~~~G~L~  137 (222)
                        +...+.||+++     +++|+++
T Consensus       155 ~~~~~~I~lt~k~-----~~LG~~~  174 (179)
T TIGR00448       155 RPEGSKIGLTMRQ-----PLLGKLE  174 (179)
T ss_pred             CCCcceEEEEecc-----CcCCccc
Confidence              23468889865     8999984

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

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

Probab=98.10  E-value=5.1e-06  Score=64.73  Aligned_cols=73  Identities=14%  Similarity=0.150  Sum_probs=68.4

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccc-ccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAF-EGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD  125 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f-~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  125 (222)
                      .+++||+|-|+||.+++-.++|++.....++.|++.. .|..+++.+.|.+||-|.++|+++++++.+.||++.
T Consensus         2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~   75 (129)
T COG1098           2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRK   75 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHH
Confidence            3689999999999999999999999999999999876 578899999999999999999999999999999976

>PRK05807 hypothetical protein; Provisional

Probab=98.09  E-value=2.9e-05  Score=61.88  Aligned_cols=70  Identities=11%  Similarity=0.133  Sum_probs=61.0

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230           55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD  125 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  125 (222)
                      ++||+|.|+|+++.+..+.|++. ...|++|.+.+. +..++....|++||.|.++|.+++.++.+.||+..
T Consensus         4 ~vG~vv~G~Vt~i~~~GafV~L~-~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~   74 (136)
T PRK05807          4 KAGSILEGTVVNITNFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQ   74 (136)
T ss_pred             cCCCEEEEEEEEEECCeEEEEEC-CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEEe
Confidence            57999999999999999999994 468999988764 45566678899999999999999877789999865

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

Probab=98.08  E-value=1.4e-05  Score=54.60  Aligned_cols=60  Identities=32%  Similarity=0.386  Sum_probs=49.9

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC
Q psy230           56 RGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD  116 (222)
Q Consensus        56 vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~  116 (222)
                      +|++|.|+|+++....|.|+++ ...|.||...+. ...+..+..|++||.|.|+|.+++.+
T Consensus         1 ~g~~~~g~V~~v~~~g~~v~l~-~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~   61 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKE   61 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECC
Confidence            4899999999999999999998 588999986653 23344556799999999999999764

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.

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

Probab=98.07  E-value=2.8e-05  Score=53.20  Aligned_cols=66  Identities=15%  Similarity=0.141  Sum_probs=54.5

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeeeeccccccc-cccCCcCCCCCCEEEEEEEecCCCCeeEEE
Q psy230           57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA-TKKNPPKVETGDVVAGKLLTANKDMESEMV  122 (222)
Q Consensus        57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls  122 (222)
                      |+++.|+|+++....+.|+|.....|.||...++.. .......|++||.|.++|.+++....+.||
T Consensus         1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~~~~i~ls   67 (68)
T cd04472           1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLS   67 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECCCCcEEee
Confidence            789999999999999999999889999998877543 223345799999999999999875566665

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.

>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=98.04  E-value=1.8e-05  Score=53.95  Aligned_cols=65  Identities=22%  Similarity=0.300  Sum_probs=52.8

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEE
Q psy230           57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEM  121 (222)
Q Consensus        57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~L  121 (222)
                      |+++.|+|+++.+..+.|+++....|.+|...+.. ...+....|++||.|.|+|.+++.. ..+.|
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~l   67 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISL   67 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEec
Confidence            78999999999999999999988899999876543 2334556799999999999999863 34444

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.

>PHA02945 interferon resistance protein; Provisional

Probab=98.01  E-value=4.5e-05  Score=56.09  Aligned_cols=70  Identities=21%  Similarity=0.241  Sum_probs=59.0

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECC--CCCeeeecccc---ccccccCCcCCCCCCEEEEEEEecCCCC-eeEEEEec
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGS--HDPAVLSYLAF---EGATKKNPPKVETGDVVAGKLLTANKDM-ESEMVCVD  125 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f---~gatk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~  125 (222)
                      .|.+||+|+|+|+. .+..+.|++.-  .-.|.+|.+..   +|..|. |+.+ .|..|.|+|+.+++.. -+.||.+.
T Consensus         8 ~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSlK~   83 (88)
T PHA02945          8 LPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNYKR   83 (88)
T ss_pred             CCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEeeE
Confidence            69999999999999 99999999975  45799998744   355566 9999 9999999999999763 57888765

>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=98.01  E-value=3.8e-05  Score=53.38  Aligned_cols=66  Identities=15%  Similarity=0.221  Sum_probs=55.0

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEEE
Q psy230           57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEMV  122 (222)
Q Consensus        57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls  122 (222)
                      |++|-|+|+++....+.|++...-.|.+|.+.+.. ..++....|++||.+.++|.+++.+ ..+.||
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls   68 (69)
T cd05697           1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLT   68 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence            78999999999999999999877899999877653 2344556799999999999999864 566665

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.

>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=97.99  E-value=7.3e-05  Score=53.33  Aligned_cols=66  Identities=18%  Similarity=0.234  Sum_probs=54.8

Q ss_pred             CCCCEEEEEEEEEecceEEEEEC-CCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230           55 TRGDLVIGVVTSRVGDNYRVDIG-SHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD  125 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~~~~~VdI~-~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  125 (222)
                      +.|++|-|.|.++.+..|.||++ ....|+||.......     ..|++||.+.|+|.++++. ..+.||+..
T Consensus         3 ~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~-----~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~   70 (74)
T cd05694           3 VEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-----SKLKVGQLLLCVVEKVKDDGRVVSLSADP   70 (74)
T ss_pred             CCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc-----cccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            57999999999999999999997 456899997554311     7899999999999999865 457888864

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.

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

Probab=97.97  E-value=2.7e-05  Score=52.01  Aligned_cols=56  Identities=20%  Similarity=0.173  Sum_probs=47.8

Q ss_pred             EEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCC
Q psy230           60 VIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANK  115 (222)
Q Consensus        60 VIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~  115 (222)
                      |.|+|+++....+.|++.....|.+|.+.+.. ..++++..|++||.|.|+|.+++.
T Consensus         1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~   57 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDP   57 (65)
T ss_pred             CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcC
Confidence            47999999999999999988999999877653 234567789999999999999875

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.

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

Probab=97.96  E-value=5.3e-05  Score=55.85  Aligned_cols=71  Identities=18%  Similarity=0.200  Sum_probs=56.6

Q ss_pred             CCCCCEEEEEEEEEecc--eEEEEECCCCCeeeecccccc----ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEe
Q psy230           54 PTRGDLVIGVVTSRVGD--NYRVDIGSHDPAVLSYLAFEG----ATKKNPPKVETGDVVAGKLLTANKD-MESEMVCV  124 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~--~~~VdI~~~~~a~L~~~~f~g----atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~  124 (222)
                      |++||++.|+|+++.+.  .+.|||+....|+||.+....    ..++....|++||.|.++|...... ..+.||+.
T Consensus         5 ~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~~   82 (88)
T cd04453           5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTN   82 (88)
T ss_pred             CCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEEEE
Confidence            57999999999999985  999999988899999877632    2234466899999999999986533 34666653

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

>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH)

Probab=97.96  E-value=1.4e-05  Score=55.02  Aligned_cols=47  Identities=13%  Similarity=0.309  Sum_probs=44.2

Q ss_pred             EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCch
Q psy230          141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFS  189 (222)
Q Consensus       141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~  189 (222)
                      .+.|++.++.+++|++++.++.|.+  .+++.|-+..||.|||.+.+..
T Consensus         5 ~i~Ip~~~ig~iIGkgG~~ik~I~~--~tg~~I~i~~~g~v~I~G~~~~   51 (61)
T cd02393           5 TMKIPPDKIRDVIGPGGKTIKKIIE--ETGVKIDIEDDGTVYIAASDKE   51 (61)
T ss_pred             EEEeChhheeeeECCCchHHHHHHH--HHCCEEEeCCCCEEEEEeCCHH
Confidence            5889999999999999999999999  9999999999999999998765

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>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=97.93  E-value=6.8e-05  Score=52.10  Aligned_cols=59  Identities=17%  Similarity=0.254  Sum_probs=50.2

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC
Q psy230           57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD  116 (222)
Q Consensus        57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~  116 (222)
                      ||+|-|+|+++.+....|++.....|.+|.+.+...... ...|++||-|.|||+.+++.
T Consensus         1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~~-~~~~~~G~~i~~kVi~id~~   59 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSS-KSTYKEGQKVRARILYVDPS   59 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc-ccCcCCCCEEEEEEEEEeCC
Confidence            899999999999999999997778999998776422222 67799999999999999864

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.

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

Probab=97.92  E-value=8.8e-05  Score=51.60  Aligned_cols=56  Identities=25%  Similarity=0.319  Sum_probs=48.5

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC
Q psy230           55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD  116 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~  116 (222)
                      ..|++|-|+|.++..+.+.|||+. ..|+||...+.     .++.|++||-|.+.|.+++++
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig~-~eg~lp~~e~~-----~~~~~~~Gd~v~v~v~~v~~~   57 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLGK-VEAILPKKEQI-----PGESYRPGDRIKAYVLEVRKT   57 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcCC-eEEEeeHHHCC-----CCCcCCCCCEEEEEEEEEecC
Confidence            579999999999999999999987 89999977663     234689999999999998754

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.

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=97.89  E-value=5.1e-05  Score=68.37  Aligned_cols=94  Identities=12%  Similarity=0.028  Sum_probs=73.4

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEC--CCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEecCC
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIG--SHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVDSR  127 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~--~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~~  127 (222)
                      -.|.+||+|.|+|+++....+.|+|.  ....|++|.+.+. +..++.+..+++||-|.++|+++++. +.+.||.+..+
T Consensus        13 ~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~   92 (319)
T PTZ00248         13 KFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVS   92 (319)
T ss_pred             hCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeecc
Confidence            36899999999999999999999996  3579999998764 46678889999999999999999754 45899988632


Q ss_pred             Cc-----ccc--CcccCCceEEEec
Q psy230          128 GK-----EFI--MGILNDGYLLHTS  145 (222)
Q Consensus       128 ~~-----~~~--~G~L~~G~l~~v~  145 (222)
                      ..     ...  -|..-.|.+..+.
T Consensus        93 ~~pw~~~~e~~~~g~~v~~~V~~ia  117 (319)
T PTZ00248         93 PEDIEACEEKFSKSKKVHSIMRHIA  117 (319)
T ss_pred             cchHHHHHHhCcCCCEEEEEEEEch
Confidence            11     111  2666666666663

>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=97.76  E-value=0.00024  Score=50.70  Aligned_cols=68  Identities=16%  Similarity=0.174  Sum_probs=58.5

Q ss_pred             CCEEEEEEEEEecceEEEEEC---CCCCeeeeccccccc-c-ccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230           57 GDLVIGVVTSRVGDNYRVDIG---SHDPAVLSYLAFEGA-T-KKNPPKVETGDVVAGKLLTANKDMESEMVCVD  125 (222)
Q Consensus        57 GDiVIG~V~~v~~~~~~VdI~---~~~~a~L~~~~f~ga-t-k~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  125 (222)
                      |+++-|+|+++.+..+.|+|.   ....|.+|.+.++.. . ++.+..|++||.|.++|.+++ ...+.|+++.
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd-~~~i~~s~k~   73 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ-NGKISLSMKD   73 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe-CCEEEEEEEe
Confidence            688999999999999999998   357899999887543 2 566778999999999999998 7789999865

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.

>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]

Probab=97.69  E-value=0.00015  Score=60.27  Aligned_cols=81  Identities=19%  Similarity=0.238  Sum_probs=64.0

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc------------cccCCcCCCCCCEEEEEEEecCCCC-
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA------------TKKNPPKVETGDVVAGKLLTANKDM-  117 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~~-  117 (222)
                      .|.|..|.+|-|.|+++....++|.|+ |.++.+|.++....            .+..+..|+.||.|+|||.+.+... 
T Consensus        76 ~fkP~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~  154 (183)
T COG1095          76 VFKPFRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSR  154 (183)
T ss_pred             EEEeccccEEEEEEEEEeecceEEEec-cccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccC
Confidence            489999999999999999999999999 78999998764311            1345568999999999999876432 


Q ss_pred             -----eeEEEEecCCCccccCcccC
Q psy230          118 -----ESEMVCVDSRGKEFIMGILN  137 (222)
Q Consensus       118 -----~~~Ls~~~~~~~~~~~G~L~  137 (222)
                           .+.||.     |.+++|+++
T Consensus       155 ~~~~~~I~lTm-----rq~~LGkle  174 (183)
T COG1095         155 RPRESKIGLTM-----RQPGLGKLE  174 (183)
T ss_pred             ccccceEEEEe-----ccccCCcch
Confidence                 244554     559999984

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

Probab=97.66  E-value=0.0002  Score=49.30  Aligned_cols=60  Identities=13%  Similarity=0.142  Sum_probs=51.7

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeeeecccccc--ccccCCcCCCCCCEEEEEEEecCCC
Q psy230           57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG--ATKKNPPKVETGDVVAGKLLTANKD  116 (222)
Q Consensus        57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~~  116 (222)
                      |+++-|+|+++.+..+.|++.....|.+|.+.++.  ..++.+..|++||.|.|+|.+++..
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~   62 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVE   62 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECC
Confidence            78999999999999999999988899999887753  3345567899999999999998754

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.

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

Probab=97.64  E-value=7.6e-05  Score=65.08  Aligned_cols=149  Identities=17%  Similarity=0.211  Sum_probs=104.1

Q ss_pred             cccCCCCCCEEEEEEEEEecceEEEEECC--CCCeeeecccc-ccccccCCcCCCCCCEEEEEEEecCCCC-eeEEEEec
Q psy230           50 RRYVPTRGDLVIGVVTSRVGDNYRVDIGS--HDPAVLSYLAF-EGATKKNPPKVETGDVVAGKLLTANKDM-ESEMVCVD  125 (222)
Q Consensus        50 ~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f-~gatk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~  125 (222)
                      .+-.|..||+|||+|.++.+-.+.|.+.-  .-.|.+|++.. .|..|..|+.+++|.-+.|+|+.+++.+ -+.||.+.
T Consensus         5 ~~~~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkr   84 (269)
T COG1093           5 RREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKR   84 (269)
T ss_pred             ccCCCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhh
Confidence            44579999999999999999999999975  35799998875 5788999999999999999999999764 58999987


Q ss_pred             CCC--c---------------------------------------cccCcccCCceEEEechhhhh----hcc--CCC--
Q psy230          126 SRG--K---------------------------------------EFIMGILNDGYLLHTSISLCR----KLL--NPK--  156 (222)
Q Consensus       126 ~~~--~---------------------------------------~~~~G~L~~G~l~~v~~~~~~----rl~--~~~--  156 (222)
                      .+.  +                                       ...||.+-.+|=     ..+.    -|.  +..  
T Consensus        85 V~~~q~~~k~~~wk~~qka~klle~aaekl~~~~ee~~~~vg~~L~e~fG~~y~aFE-----~aa~~g~~~l~~~~~~~~  159 (269)
T COG1093          85 VTEHQRRKKIQEWKKEQKADKLLELAAEKLGKDLEEAYEEVGWKLEEEFGSLYDAFE-----AAAKEGGEVLDDEGVPEE  159 (269)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHhHHHHHHhCCHHHHHH-----HHHhcCCcccccCCCCHH
Confidence            431  0                                       122555522211     0000    000  011  


Q ss_pred             --hhHHHHhhhcCCCcEEE-EEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHH
Q psy230          157 --CPLLKQLAKRSRQKMEL-SIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYE  207 (222)
Q Consensus       157 --~~~l~~l~~~~~~~~ei-~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~  207 (222)
                        ..+++..++    .++. .|-.-|+|=+.|..+.-+..|-.||...+...+.
T Consensus       160 ~~~~l~e~a~e----~i~~~~VkI~g~vev~s~~~dGVe~IK~aL~~A~~~~~~  209 (269)
T COG1093         160 WKEVLKEIARE----NIEPPTVKIRGYVEVTSPAPDGVEKIKKALKAAEDNGEE  209 (269)
T ss_pred             HHHHHHHHHHh----cCCCCceEEEEEEEEEecCCCcHHHHHHHHHHHHhcCcc
Confidence              134444443    2222 4556789999999999899999999988765433

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

Probab=97.60  E-value=0.0011  Score=47.34  Aligned_cols=64  Identities=17%  Similarity=0.159  Sum_probs=54.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEE
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVC  123 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~  123 (222)
                      -.++|+.+.|+|+++++..+.|++.....|.+|.+.+       ...++.||.+.++|.++..++.+.|+.
T Consensus        13 ~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~-------~~~~~iGd~v~v~I~~i~e~~~i~l~~   76 (77)
T cd04473          13 DLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNL-------LRDYEVGDEVIVQVTDIPENGNIDLIP   76 (77)
T ss_pred             hCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhc-------cCcCCCCCEEEEEEEEECCCCcEEEEE
Confidence            4789999999999999999999999889999997654       356999999999999995556677664

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.

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

Probab=97.59  E-value=0.00034  Score=52.22  Aligned_cols=73  Identities=19%  Similarity=0.206  Sum_probs=57.6

Q ss_pred             CEEEEEEEEEecceEEEEECCCCCeeeeccccccc-c-----------ccCCcCCCCCCEEEEEEEecCCC------Cee
Q psy230           58 DLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA-T-----------KKNPPKVETGDVVAGKLLTANKD------MES  119 (222)
Q Consensus        58 DiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-t-----------k~~r~~l~~GDlV~ArV~~~~~~------~~~  119 (222)
                      ++|.|+|+++....+.|++. +..|.+|...+... .           ++....|++||.|.++|.+++..      ..+
T Consensus         1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i   79 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI   79 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceE
Confidence            47899999999999999998 47888887665321 1           12346789999999999999854      468


Q ss_pred             EEEEecCCCccccCccc
Q psy230          120 EMVCVDSRGKEFIMGIL  136 (222)
Q Consensus       120 ~Ls~~~~~~~~~~~G~L  136 (222)
                      .||..+     +.+|.+
T Consensus        80 ~ls~k~-----~~~g~~   91 (99)
T cd04460          80 GLTMRQ-----PGLGKL   91 (99)
T ss_pred             EEEEec-----CCCCcH
Confidence            899865     888887

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.

>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=97.55  E-value=0.0006  Score=47.92  Aligned_cols=67  Identities=7%  Similarity=-0.012  Sum_probs=54.3

Q ss_pred             CCEEE-EEEEEE-ecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC-CeeEEEE
Q psy230           57 GDLVI-GVVTSR-VGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD-MESEMVC  123 (222)
Q Consensus        57 GDiVI-G~V~~v-~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~  123 (222)
                      |+++= |+|+++ ....+.|++.....|.+|.+.+. ...++....|++||.+.|+|+++++. ..+.||+
T Consensus         1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS~   71 (71)
T cd05696           1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL   71 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEeC
Confidence            66777 899998 68889999987789999998775 34455667799999999999999854 4567764

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.

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

Probab=97.55  E-value=0.00052  Score=47.36  Aligned_cols=65  Identities=20%  Similarity=0.197  Sum_probs=49.9

Q ss_pred             CCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCC-CCeeEEEE
Q psy230           57 GDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANK-DMESEMVC  123 (222)
Q Consensus        57 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~  123 (222)
                      |++|-|+|+++....+.|++ ....|.+|.+.......+. +.-.+||.+.|+|.++++ ...+.||.
T Consensus         1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~~~~~~-~~~~vG~~i~~~i~~vd~~~~~i~lS~   66 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVED-LDEYVGKELKFKIIEIDRERNNIVLSR   66 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCcccCC-hHHhCCCEEEEEEEEEeCCCCEEEEEc
Confidence            78999999999999999999 4589999987654221111 112489999999999986 45677774

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.

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=97.54  E-value=0.00031  Score=63.40  Aligned_cols=74  Identities=16%  Similarity=0.186  Sum_probs=63.6

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD  125 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  125 (222)
                      |..++||+|-|+|+++..+...|||+....|.||.+.+. ...++....|++||.|.+.|++.++. ..+.|||+.
T Consensus        27 ~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~  102 (318)
T PRK07400         27 YHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRR  102 (318)
T ss_pred             hhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhh
Confidence            557999999999999999999999998889999988764 34456677899999999999998653 578999975

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=97.46  E-value=0.00064  Score=67.39  Aligned_cols=98  Identities=14%  Similarity=0.061  Sum_probs=76.1

Q ss_pred             eCCEEEEEEeeEEEEec-CcEEEEEccccccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCC
Q psy230           23 ESSAILVSQSGILRHAK-PFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKV  100 (222)
Q Consensus        23 ~~~~i~as~~G~l~~~~-~~~v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l  100 (222)
                      ++|.++++..+....+. +..+...+    ..|++|+++.|+|+++....++|+|.....|.+|++.+. ...++....|
T Consensus       591 d~G~v~i~~~~~~~~~~a~~~I~~~~----~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~  666 (693)
T PRK11824        591 DDGTVKIAATDGEAAEAAKERIEGIT----AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVL  666 (693)
T ss_pred             CCceEEEEcccHHHHHHHHHHHHHhc----ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCcccee
Confidence            46777777777655432 11222222    247899999999999999999999998899999998875 3456677889


Q ss_pred             CCCCEEEEEEEecCCCCeeEEEEe
Q psy230          101 ETGDVVAGKLLTANKDMESEMVCV  124 (222)
Q Consensus       101 ~~GDlV~ArV~~~~~~~~~~Ls~~  124 (222)
                      ++||.|.++|.+++....+.||++
T Consensus       667 kvGD~V~VkV~~iD~~grI~LS~k  690 (693)
T PRK11824        667 KEGDEVKVKVLEIDKRGRIRLSRK  690 (693)
T ss_pred             CCCCEEEEEEEEECCCCcEEEEEE
Confidence            999999999999987678999985

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

Probab=97.40  E-value=0.0011  Score=46.17  Aligned_cols=62  Identities=16%  Similarity=0.179  Sum_probs=52.3

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc--ccccCCcCCCCCCEEEEEEEecCCC
Q psy230           55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG--ATKKNPPKVETGDVVAGKLLTANKD  116 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~~  116 (222)
                      .+|+.+-|+|+++....+.|++.....|.+|.+.++.  ...+....|++||.|.++|.+++.+
T Consensus         2 ~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~   65 (72)
T cd05689           2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEE   65 (72)
T ss_pred             cCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCC
Confidence            3699999999999999999999887899999887752  2234456799999999999998754

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.

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

Probab=97.37  E-value=0.00098  Score=55.35  Aligned_cols=81  Identities=12%  Similarity=0.134  Sum_probs=61.0

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc------cc-------cccCCcCCCCCCEEEEEEEecCC--
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE------GA-------TKKNPPKVETGDVVAGKLLTANK--  115 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~------ga-------tk~~r~~l~~GDlV~ArV~~~~~--  115 (222)
                      .|.|-+|.+|.|+|++++...+.|+++. ..+.+|.++.+      ..       .++.+..++.||.|++||..+.-  
T Consensus        76 vFrPf~gEVv~g~V~~v~~~G~~v~~Gp-~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~  154 (176)
T PTZ00162         76 VFKPFKDEVLDAIVTDVNKLGFFAQAGP-LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDA  154 (176)
T ss_pred             EEecCCCCEEEEEEEEEecceEEEEeeC-eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecC
Confidence            5899999999999999999999999975 44888765433      21       12335689999999999987742  


Q ss_pred             -CCeeEEEEecCCCccccCcccC
Q psy230          116 -DMESEMVCVDSRGKEFIMGILN  137 (222)
Q Consensus       116 -~~~~~Ls~~~~~~~~~~~G~L~  137 (222)
                       +.....|+     |.++||++.
T Consensus       155 ~~~~~i~T~-----~~~~LG~~~  172 (176)
T PTZ00162        155 SNLFAIATI-----NSDYLGPIE  172 (176)
T ss_pred             CCcEEEEEe-----cCCCcCccc
Confidence             22345555     459999983

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.37  E-value=0.00063  Score=67.23  Aligned_cols=70  Identities=11%  Similarity=0.157  Sum_probs=60.4

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-----cccccCCcCCCCCCEEEEEEEecCCCCeeEEE
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-----GATKKNPPKVETGDVVAGKLLTANKDMESEMV  122 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-----gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls  122 (222)
                      .|++|++|.|+|+++.+-.++|+|.....|++|++.+.     ...++.++.|++||.|.++|+++++...+.|+
T Consensus       644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~~gKI~L~  718 (719)
T TIGR02696       644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRGKLSLV  718 (719)
T ss_pred             cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECCCCCeeec
Confidence            58999999999999999999999987789999998763     35567788999999999999999865555554

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=97.36  E-value=0.00051  Score=65.87  Aligned_cols=72  Identities=21%  Similarity=0.234  Sum_probs=63.9

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD  125 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  125 (222)
                      .-++||+|-|+|+++++-.++|||++ -.|.||.+... ++.+.-...|++||-|.++|++++.+ .-+.||++.
T Consensus       189 ~l~~G~vV~G~V~~It~~GafVdigG-vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~  262 (541)
T COG0539         189 KLEVGEVVEGVVKNITDYGAFVDIGG-VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQ  262 (541)
T ss_pred             cCCCCceEEEEEEEeecCcEEEEecC-eeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehh
Confidence            45899999999999999999999999 99999998765 46677888999999999999999965 458999975

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=97.25  E-value=0.0015  Score=58.96  Aligned_cols=73  Identities=12%  Similarity=0.116  Sum_probs=61.0

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      ...++||+|.|+|+++....+.|++++ ..|++|.+.+.. ...+....|++||.|.|+|.+++. ...+.||++.
T Consensus       192 ~~~k~G~vv~G~V~~I~~~G~fV~i~g-v~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~  266 (318)
T PRK07400        192 NRLEVGEVVVGTVRGIKPYGAFIDIGG-VSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQ  266 (318)
T ss_pred             ccCCCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEec
Confidence            346889999999999999999999964 679999877653 345667889999999999999975 4678999864

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.23  E-value=0.00089  Score=66.28  Aligned_cols=65  Identities=20%  Similarity=0.181  Sum_probs=57.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCC
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDM  117 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~  117 (222)
                      .|++|+++.|+|+++....+.|+|.....|.||.+... ...++....|++||.|.++|.+++..+
T Consensus       615 ~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~~g  680 (684)
T TIGR03591       615 EPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDKQG  680 (684)
T ss_pred             ccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECCCC
Confidence            58999999999999999999999998899999998874 346677888999999999999998643

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).

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.10  E-value=0.003  Score=60.89  Aligned_cols=71  Identities=14%  Similarity=0.090  Sum_probs=61.1

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-cc-ccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-AT-KKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-at-k~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      .+||+|-|+|++++...+.|+|+....|.+|.+.+.. .. ++....|++||.|.|+|.+++. ...+.||++.
T Consensus       372 ~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~  445 (565)
T PRK06299        372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQ  445 (565)
T ss_pred             CCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEeh
Confidence            5799999999999999999999988999999877653 33 5666889999999999999985 4679999876

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=97.07  E-value=0.003  Score=60.18  Aligned_cols=73  Identities=19%  Similarity=0.185  Sum_probs=61.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCCC-----eeEEEEec
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDM-----ESEMVCVD  125 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~-----~~~Ls~~~  125 (222)
                      ..++||+|-|+|+++....+.|||+....|.+|.+.+.. ...+....|++||.|.|+|.+++.+.     .+.||++.
T Consensus       199 ~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~  277 (491)
T PRK13806        199 TVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQ  277 (491)
T ss_pred             hCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehh
Confidence            468999999999999999999999877899999887653 44566778999999999999998753     47788765

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

Probab=97.01  E-value=0.0063  Score=43.12  Aligned_cols=67  Identities=12%  Similarity=0.169  Sum_probs=52.7

Q ss_pred             CCCEEEEEEEEEecceEEEEECC-CCCeeeecccccccc------------ccCCcCCCCCCEEEEEEEecCCC-CeeEE
Q psy230           56 RGDLVIGVVTSRVGDNYRVDIGS-HDPAVLSYLAFEGAT------------KKNPPKVETGDVVAGKLLTANKD-MESEM  121 (222)
Q Consensus        56 vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~gat------------k~~r~~l~~GDlV~ArV~~~~~~-~~~~L  121 (222)
                      +|+++-|.|++++...+.|++.. .-.|.+|.+.++...            ++....|++||.|.++|.+++.. ..+.+
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~   80 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF   80 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEE
Confidence            48899999999999999999987 478899987765311            13457899999999999999863 44555


Q ss_pred             E
Q psy230          122 V  122 (222)
Q Consensus       122 s  122 (222)
                      +
T Consensus        81 ~   81 (83)
T cd04471          81 E   81 (83)
T ss_pred             E
Confidence            4

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.

>TIGR00717 rpsA ribosomal protein S1

Probab=97.01  E-value=0.0027  Score=60.49  Aligned_cols=68  Identities=22%  Similarity=0.232  Sum_probs=59.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      .++|++|-|+|+++..+.+.||++....|.+|...+..    ..+.|++||.|.++|.+.++ .+.+.||+..
T Consensus        16 ~~~G~~v~g~V~~i~~~~~~v~~g~k~~g~i~~~E~~~----~~~~~~vGd~i~~~V~~~~~~~g~i~lS~~~   84 (516)
T TIGR00717        16 TRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLD----APLEIQVGDEVEVYLDRVEDRFGETVLSREK   84 (516)
T ss_pred             CCCCCEEEEEEEEEECCEEEEEcCCCcEEEEEHHHhcC----CccCCCCCCEEEEEEEEEeCCCCcEEEEHHH
Confidence            58899999999999999999999999999999877753    23679999999999998865 4678999863

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.

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.00  E-value=0.0037  Score=57.55  Aligned_cols=73  Identities=18%  Similarity=0.145  Sum_probs=59.9

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEE-CCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCCC-eeEEEEec
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDI-GSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDM-ESEMVCVD  125 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI-~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~  125 (222)
                      ..++||+|.|+|+++..+.+.||| +....|.||...+.. ..+.....|++||-|.|+|.+++++. .+.||.+.
T Consensus        14 ~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~~~vGd~v~~~V~~v~~~~~~i~lS~k~   89 (390)
T PRK06676         14 EVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRR   89 (390)
T ss_pred             cccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccccccCcccccCCCCEEEEEEEEEECCCCCEEEEHHH
Confidence            468899999999999999999999 777899999876643 33445567999999999999997653 47888764

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=96.95  E-value=0.0036  Score=59.64  Aligned_cols=72  Identities=22%  Similarity=0.198  Sum_probs=59.3

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD  125 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  125 (222)
                      .+.||+|-|+|+++..+...|||+....|.||...+.. ...+....|++||-|.|.|++.++. +.+.||.+.
T Consensus        33 ~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~~~~~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~  106 (486)
T PRK07899         33 FNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEVVEVGDEVEALVLQKEDKEGRLILSKKR  106 (486)
T ss_pred             CCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcccccCChhhcCCCCCEEEEEEEEEECCCCeEEEEehh
Confidence            68999999999999999999999988899999876643 2233455699999999999998643 568888864

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=96.93  E-value=0.0037  Score=57.56  Aligned_cols=72  Identities=22%  Similarity=0.215  Sum_probs=60.1

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      ..++||+|-|+|+++.+..+.|+++. ..|.+|.+.+.. ..++....|++||.|.|+|.++++ ...+.||++.
T Consensus       189 ~~~~G~~v~g~V~~v~~~G~fV~l~~-v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~  262 (390)
T PRK06676        189 SLKEGDVVEGTVARLTDFGAFVDIGG-VDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKD  262 (390)
T ss_pred             hCCCCCEEEEEEEEEecceEEEEeCC-eEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEee
Confidence            35899999999999999999999975 789999877643 344556779999999999999975 4678999875

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=96.89  E-value=0.0049  Score=58.76  Aligned_cols=71  Identities=21%  Similarity=0.221  Sum_probs=59.7

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD  125 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  125 (222)
                      -++||+|-|+|+++.+....|||+. -.|.+|.+.+.. ..++....|++||.|.++|..++.. ..+.||++.
T Consensus       206 lk~G~iv~G~V~~i~~~G~FVdlgg-v~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~  278 (486)
T PRK07899        206 LQKGQVRKGVVSSIVNFGAFVDLGG-VDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKA  278 (486)
T ss_pred             ccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            3589999999999999999999975 789999887653 3345556899999999999999864 678899875

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=96.86  E-value=0.0048  Score=59.55  Aligned_cols=71  Identities=14%  Similarity=0.239  Sum_probs=61.6

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230           55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD  125 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  125 (222)
                      ++||+|.|+|+++......|.+.....|++|.+... ...++....|++||.|.|+|++++.+ ..+.||+..
T Consensus       459 ~~G~vV~G~V~~v~~~G~fV~l~~gi~g~i~~se~s~~~~~~~~~~~~~Gd~v~~~V~~vd~~~~~i~LS~k~  531 (565)
T PRK06299        459 KKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKA  531 (565)
T ss_pred             CCCCEEEEEEEEEecCceEEecCCCcEEEEEHHHhcchhccCccccCCCCCEEEEEEEEEccccCEEEEEeee
Confidence            689999999999999999999987789999987653 34567788999999999999999864 678999975

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=96.83  E-value=0.0088  Score=57.04  Aligned_cols=72  Identities=21%  Similarity=0.116  Sum_probs=61.3

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc--ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG--ATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD  125 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  125 (222)
                      -.+|++|-|+|+++.+..+.|++...-.|.+|.+.+..  ...+....|++||.|.++|.+++.. ..+.||++.
T Consensus       290 ~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~  364 (491)
T PRK13806        290 LKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRD  364 (491)
T ss_pred             CCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEee
Confidence            36899999999999999999999877899999887653  3345567899999999999999764 578999986

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=96.82  E-value=0.0037  Score=57.52  Aligned_cols=69  Identities=22%  Similarity=0.233  Sum_probs=56.2

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCC---eeEEEEec
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDM---ESEMVCVD  125 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~---~~~Ls~~~  125 (222)
                      .|.++.|++|.|+|.++....|.|||+. ..|+||....     --+..|++||-|.|-|..+..+.   .+.||-.+
T Consensus       129 ef~~k~GeiV~G~V~~~~~~~~~Vdlg~-vEa~LP~~E~-----ip~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~  200 (362)
T PRK12327        129 EFSEREGDIVTGVVQRRDNRFVYVNLGK-IEAVLPPAEQ-----IPGETYKHGDRIKVYVVKVEKTTKGPQIFVSRTH  200 (362)
T ss_pred             HHHHhcCCEEEEEEEEEeCCcEEEEeCC-eEEEecHHHc-----CCCCCCCCCCEEEEEEEEEecCCCCCeEEEEeCC
Confidence            5899999999999999999999999987 7999996432     12566999999999999998443   46666543

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

Probab=96.74  E-value=0.0064  Score=58.46  Aligned_cols=95  Identities=24%  Similarity=0.277  Sum_probs=74.8

Q ss_pred             cccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCC-eeEEEEecCC-
Q psy230           50 RRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDM-ESEMVCVDSR-  127 (222)
Q Consensus        50 ~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~~~-  127 (222)
                      ..+.+++||+|-|.|+++..++..|||+.-..+.+|...|.+.-...  .|++||.|-+.|....+.. .+.||-.... 
T Consensus        15 ~~~~~~~G~vV~G~Vv~i~~~~v~Vdig~Kseg~ip~~E~~~~~~~~--~~~~gd~v~v~v~~~e~~~g~~~lS~~k~~~   92 (541)
T COG0539          15 SDEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPVED--VVQVGDEVEVLVLRVEDGEGELVLSRRKAER   92 (541)
T ss_pred             chhccCCCCEEEEEEEEEeCCeEEEEecCccccEeEHHHhccccccc--eecCCCEEEEEEEEEecCCceEEeeHHHHHH
Confidence            45789999999999999999999999999999999998887543322  7999999999999886553 5777754310 


Q ss_pred             -------------C---ccccCcccCCceEEEech
Q psy230          128 -------------G---KEFIMGILNDGYLLHTSI  146 (222)
Q Consensus       128 -------------~---~~~~~G~L~~G~l~~v~~  146 (222)
                                   +   ++.-.|++.+|+++.+..
T Consensus        93 ~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~g  127 (541)
T COG0539          93 ERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIEG  127 (541)
T ss_pred             HHhHHHHHHHHhcCCeEEEEEEEEecCcEEEEECC
Confidence                         0   122367889999999853

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

Probab=96.73  E-value=0.0071  Score=59.53  Aligned_cols=71  Identities=21%  Similarity=0.225  Sum_probs=59.2

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      .++||+|-|+|+++....+.|++ ....|.+|.+.+. ...++....|++||.|.|+|.++++ ...+.||++.
T Consensus       475 l~~G~iV~g~V~~v~~~G~fV~l-~gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~  547 (647)
T PRK00087        475 LEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKK  547 (647)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeec
Confidence            46899999999999999999999 5678999987654 3345566789999999999999975 4678999875

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

Probab=96.71  E-value=0.0096  Score=58.63  Aligned_cols=75  Identities=23%  Similarity=0.239  Sum_probs=62.3

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      .+..++|++|-|+|+++..+.+.||++....|.||...+.. ..+.....|++||.|.++|.++++ ++.+.||...
T Consensus       297 ~~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~  373 (647)
T PRK00087        297 EKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKE  373 (647)
T ss_pred             HhhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEEEeeh
Confidence            35689999999999999999999999988899999876542 334556679999999999999863 4568888875

>TIGR00717 rpsA ribosomal protein S1

Probab=96.69  E-value=0.027  Score=53.62  Aligned_cols=72  Identities=17%  Similarity=0.125  Sum_probs=58.3

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc--cccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA--TKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD  125 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga--tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  125 (222)
                      -++||++-|+|+++....+.|+++....|.+|.+.+...  ..+....|++||.|.|+|.+++.+ ..+.||++.
T Consensus       270 ~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k~  344 (516)
T TIGR00717       270 FPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQ  344 (516)
T ss_pred             ccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEehh
Confidence            357999999999999999999999888999998766422  222234599999999999999864 568888764

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.

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=96.67  E-value=0.0031  Score=42.78  Aligned_cols=44  Identities=11%  Similarity=0.151  Sum_probs=41.4

Q ss_pred             EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEe----CCeEEEeeC
Q psy230          141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM----NGKIWIRCE  186 (222)
Q Consensus       141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~----NG~iWi~~~  186 (222)
                      -+.|+..++++++|+++..++.|.+  .+++.|.+..    ++.|||.++
T Consensus         3 ~i~Vp~~~~~~iIG~~G~~i~~i~~--~~g~~I~i~~~~~~~~~v~I~G~   50 (62)
T cd02394           3 EVEIPKKLHRFIIGKKGSNIRKIME--ETGVKIRFPDPGSKSDTITITGP   50 (62)
T ss_pred             EEEeCHHHhhhccCCCCCcHHHHHH--HhCCEEEcCCCCCCCCEEEEEcC
Confidence            4789999999999999999999999  9999999999    899999998

The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.45  E-value=0.01  Score=60.09  Aligned_cols=73  Identities=19%  Similarity=0.163  Sum_probs=63.4

Q ss_pred             CCCCCCEEE-EEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230           53 VPTRGDLVI-GVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD  125 (222)
Q Consensus        53 ~P~vGDiVI-G~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  125 (222)
                      .|++|+++- |+|+++.+-.++|+|.....+.+|++.+.. ..++....|++||.|..+|.+++..+.+.|+.+.
T Consensus       750 ~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~~grI~LSlK~  824 (891)
T PLN00207        750 VPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQLRLSRRA  824 (891)
T ss_pred             CcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECCCCcEEEEEec
Confidence            489999995 699999999999999877899999988753 4566678899999999999999976788999864

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=96.38  E-value=0.015  Score=59.01  Aligned_cols=63  Identities=22%  Similarity=0.249  Sum_probs=55.4

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEe
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCV  124 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~  124 (222)
                      +++||+|-|+|+++..+...|||+.-..|++|...|..       .+++||-|.|.|.+.+.+. +.||-.
T Consensus       319 ~~~G~iV~G~Vv~i~~~~v~VdiG~K~eGiI~~~E~~~-------~~kvGd~i~~~V~~~~~~~-~~LS~~  381 (863)
T PRK12269        319 PEPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEFEA-------PPKAGDGVRVYVERVTPYG-PELSKT  381 (863)
T ss_pred             CCCCCEEEEEEEEEECCEEEEEeCCCceEEeEHHHhcc-------CCCCCCEEEEEEEEEcCCc-eEEEeh
Confidence            89999999999999999999999999999999877731       2589999999999987654 788865

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=96.13  E-value=0.052  Score=50.83  Aligned_cols=71  Identities=17%  Similarity=0.171  Sum_probs=54.1

Q ss_pred             CCCCCCEEEEEEEEEecc--eEEEEECCCCCeeeecccccc-------------ccccCCcCCCCCCEEEEEEEecC-CC
Q psy230           53 VPTRGDLVIGVVTSRVGD--NYRVDIGSHDPAVLSYLAFEG-------------ATKKNPPKVETGDVVAGKLLTAN-KD  116 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~--~~~VdI~~~~~a~L~~~~f~g-------------atk~~r~~l~~GDlV~ArV~~~~-~~  116 (222)
                      .+.+||+..|+|+++.+.  .++|||+....|+||+.....             ..++....+++||-|..+|..-. ..
T Consensus        22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~  101 (414)
T TIGR00757        22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGN  101 (414)
T ss_pred             cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCC
Confidence            456899999999999887  999999999999999876421             11223446999999999998732 23


Q ss_pred             CeeEEEE
Q psy230          117 MESEMVC  123 (222)
Q Consensus       117 ~~~~Ls~  123 (222)
                      ..+.||+
T Consensus       102 Kgp~lT~  108 (414)
T TIGR00757       102 KGARLTT  108 (414)
T ss_pred             CCCeEEE
Confidence            3466666

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=96.11  E-value=0.017  Score=54.91  Aligned_cols=69  Identities=22%  Similarity=0.280  Sum_probs=56.4

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC---CeeEEEEec
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD---MESEMVCVD  125 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~---~~~~Ls~~~  125 (222)
                      .|..+.|++|.|+|.++....+.||++. ..|+||.+..     --+..|++||-|.|.|..+.+.   ..+.||-..
T Consensus       129 eyk~~~GeIV~G~V~ri~~~giiVDLgg-vea~LP~sE~-----ip~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~  200 (470)
T PRK09202        129 EYKDRVGEIITGVVKRVERGNIIVDLGR-AEAILPRKEQ-----IPRENFRPGDRVRAYVYEVRKEARGPQIILSRTH  200 (470)
T ss_pred             HHHhhcCCEEEEEEEEEecCCEEEEECC-eEEEecHHHc-----CCCccCCCCCEEEEEEEEEecCCCCCeEEEEeCc
Confidence            5888999999999999999999999964 6999996542     2456799999999999999764   246666543

>TIGR01953 NusA transcription termination factor NusA

Probab=96.06  E-value=0.02  Score=52.33  Aligned_cols=70  Identities=14%  Similarity=0.222  Sum_probs=54.8

Q ss_pred             cccCCCCCCEEEEEEEEEecce-EEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC---CeeEEEEec
Q psy230           50 RRYVPTRGDLVIGVVTSRVGDN-YRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD---MESEMVCVD  125 (222)
Q Consensus        50 ~~Y~P~vGDiVIG~V~~v~~~~-~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~---~~~~Ls~~~  125 (222)
                      ..|..+.|++|-|+|.++..+. |.|||+ ...|+||.....     .+..|++||-|.|-|.++.++   ..+.||-..
T Consensus       125 ~ey~~k~GeiV~G~V~~v~~~g~v~VdiG-~~ea~LP~~E~i-----p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~  198 (341)
T TIGR01953       125 DEFSSKEGEIISGTVKRVNRRGNLYVELG-KTEGILPKKEQI-----PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTH  198 (341)
T ss_pred             HHHHhhcCCEEEEEEEEEecCCcEEEEEC-CeEEEecHHHcC-----CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCc
Confidence            3588899999999999998855 799996 578999965432     233499999999999999754   346777543

This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=96.01  E-value=0.02  Score=56.95  Aligned_cols=73  Identities=21%  Similarity=0.242  Sum_probs=63.3

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc-cccCCcCCCCCCEEEEEEEecCCC-CeeEEEEecC
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA-TKKNPPKVETGDVVAGKLLTANKD-MESEMVCVDS  126 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~  126 (222)
                      -++|-++.|.|.++..-...|||+...++.+|++..... .+.-...+++||+|.++|.+++-. ..+.||++..
T Consensus       656 Lk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~  730 (780)
T COG2183         656 LKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLD  730 (780)
T ss_pred             ccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeecc
Confidence            388999999999999999999999999999999876543 455578999999999999999754 4689999863

>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain

Probab=95.99  E-value=0.034  Score=40.88  Aligned_cols=59  Identities=17%  Similarity=0.308  Sum_probs=41.4

Q ss_pred             CCCEEEEEEEEEecceEEEEECC----CCCeeeec-cccccc------cccCCcCCCCCCEEEEEEEecC
Q psy230           56 RGDLVIGVVTSRVGDNYRVDIGS----HDPAVLSY-LAFEGA------TKKNPPKVETGDVVAGKLLTAN  114 (222)
Q Consensus        56 vGDiVIG~V~~v~~~~~~VdI~~----~~~a~L~~-~~f~ga------tk~~r~~l~~GDlV~ArV~~~~  114 (222)
                      +|.+|.|+|++++...+.|+++.    -....+|. ..|++.      ..+.+..++.||.|++||.++.
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~   70 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTR   70 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEE
Confidence            48899999999999999999984    22222221 112221      1124677999999999998875

RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=95.79  E-value=0.031  Score=56.84  Aligned_cols=72  Identities=18%  Similarity=0.091  Sum_probs=60.4

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc--ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG--ATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD  125 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  125 (222)
                      ..+||+|-|+|+++.+..+.|++.....|.+|.+.+..  ...+....|++||-|.|+|++++.. ..+.||.+.
T Consensus       576 ~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~  650 (863)
T PRK12269        576 FGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQ  650 (863)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehh
Confidence            46899999999999999999999988899999987753  2345566799999999999999754 467888875

>cd00105 KH-I K homology RNA-binding domain, type I

Probab=95.47  E-value=0.038  Score=37.08  Aligned_cols=44  Identities=11%  Similarity=0.138  Sum_probs=39.2

Q ss_pred             EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEe------CCeEEEeeC
Q psy230          141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM------NGKIWIRCE  186 (222)
Q Consensus       141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~------NG~iWi~~~  186 (222)
                      -+.|+..++++++|+++..++.|.+  .+++.|.+..      +..|||.+.
T Consensus         3 ~i~ip~~~~~~vIG~~G~~i~~I~~--~s~~~I~i~~~~~~~~~~~v~i~G~   52 (64)
T cd00105           3 RVLVPSSLVGRIIGKGGSTIKEIRE--ETGAKIKIPDSGSGSEERIVTITGT   52 (64)
T ss_pred             EEEEchhhcceeECCCCHHHHHHHH--HHCCEEEEcCCCCCCCceEEEEEcC
Confidence            4789999999999999999999999  8888898877      467999987

KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.38  E-value=0.059  Score=49.75  Aligned_cols=60  Identities=28%  Similarity=0.367  Sum_probs=48.8

Q ss_pred             ccCCCCCCEEEEEEEEEec-ceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC
Q psy230           51 RYVPTRGDLVIGVVTSRVG-DNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD  116 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~-~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~  116 (222)
                      .|.+++|++|.|+|.++.. ..+.||++. ..|+||...     .--+..|++||-|.|-|..+..+
T Consensus       133 ey~~~~Geiv~g~V~r~~~~~~i~vdlg~-~ea~LP~~e-----qip~E~~~~Gdrik~~i~~V~~~  193 (374)
T PRK12328        133 KYKKKVGKIVFGTVVRVDNEENTFIEIDE-IRAVLPMKN-----RIKGEKFKVGDVVKAVLKRVKID  193 (374)
T ss_pred             HHHHhcCcEEEEEEEEEecCCCEEEEcCC-eEEEeCHHH-----cCCCCcCCCCCEEEEEEEEEecC
Confidence            5999999999999999986 568899984 799999532     12345699999999999988654

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=95.12  E-value=0.042  Score=36.84  Aligned_cols=51  Identities=14%  Similarity=0.196  Sum_probs=42.8

Q ss_pred             EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC---CeEEEeeCCchhHHHH
Q psy230          141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN---GKIWIRCESFSDTVRV  194 (222)
Q Consensus       141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N---G~iWi~~~~~~~~~~i  194 (222)
                      -+.|+..++.+++|+++..++.|.+  .+++.|-+-.+   ..|.|.+ +++....+
T Consensus         3 ~i~vp~~~~~~iIG~~G~~i~~I~~--~t~~~I~i~~~~~~~~v~I~G-~~~~v~~A   56 (60)
T PF00013_consen    3 RIEVPSSLVGRIIGKKGSNIKEIEE--ETGVKIQIPDDDERDIVTISG-SPEQVEKA   56 (60)
T ss_dssp             EEEEEHHHHHHHHTGGGHHHHHHHH--HHTSEEEEESTTEEEEEEEEE-SHHHHHHH
T ss_pred             EEEECHHHcCEEECCCCCcHHHhhh--hcCeEEEEcCCCCcEEEEEEe-CHHHHHHH
Confidence            4789999999999999999999999  89999999875   6899999 55533333

; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=94.51  E-value=0.15  Score=48.06  Aligned_cols=61  Identities=8%  Similarity=-0.011  Sum_probs=49.7

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECC-----CCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGS-----HDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD  116 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~-----~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~  116 (222)
                      .|.+++|++|.|+|.++..+.+.||+++     ...|+||...     .--+..|++||-|.|-|..+...
T Consensus       147 ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~E-----qip~E~y~~Gdrika~i~~V~~~  212 (449)
T PRK12329        147 EFQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKRE-----QLPNDNYRANATFKVFLKEVSEG  212 (449)
T ss_pred             HHHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHH-----cCCCCcCCCCCEEEEEEEEeecC
Confidence            5999999999999999999999999953     2678999532     12345699999999999999654

>KOG1070|consensus

Probab=93.49  E-value=0.47  Score=50.23  Aligned_cols=71  Identities=18%  Similarity=0.303  Sum_probs=63.4

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeeeecccc-ccccccCCcCCCCCCEEEEEEEecCCCC-eeEEEEec
Q psy230           55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAF-EGATKKNPPKVETGDVVAGKLLTANKDM-ESEMVCVD  125 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f-~gatk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~  125 (222)
                      +.||+|-|.|..+.....++-++....|.++++.+ +-..+.-++.|.+|++|-+||.+++.+. .++|+...
T Consensus      1161 k~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~ 1233 (1710)
T KOG1070|consen 1161 KIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKN 1233 (1710)
T ss_pred             ccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEec
Confidence            78999999999999999999999999999998775 4455788899999999999999998664 78999986

>smart00322 KH K homology RNA-binding domain

Probab=93.26  E-value=0.3  Score=32.19  Aligned_cols=58  Identities=9%  Similarity=0.122  Sum_probs=46.1

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC----CeEEEeeCCchhHHHHHHHHHH
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN----GKIWIRCESFSDTVRVGNLIMS  200 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N----G~iWi~~~~~~~~~~i~~~i~~  200 (222)
                      .-+.|+..+..+++|+++..++.|.+  .+++.|.+..+    ..++|.++ ..+...+..+|..
T Consensus         5 ~~i~i~~~~~~~liG~~G~~i~~i~~--~~~~~i~~~~~~~~~~~v~i~g~-~~~v~~a~~~i~~   66 (69)
T smart00322        5 IEVLIPADKVGLIIGKGGSTIKKIEE--ETGVKIDIPEDGSEERVVEITGP-PENVEKAAELILE   66 (69)
T ss_pred             EEEEEcchhcceeECCCchHHHHHHH--HHCCEEEECCCCCCccEEEEEcC-HHHHHHHHHHHHH
Confidence            45788999999999999999999999  88888888774    78999987 4445555555543

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=92.59  E-value=0.28  Score=48.87  Aligned_cols=58  Identities=10%  Similarity=0.189  Sum_probs=49.3

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHH
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIM  199 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~  199 (222)
                      ..++|+|.+++.++|+++.+++.|.+  .+++.|-|-.+|.|+|.+.+......+.+.|+
T Consensus       553 ~~~~I~~~kI~~vIG~gGk~Ik~I~~--~tg~~I~i~ddG~V~i~~~~~~~~~~a~~~I~  610 (684)
T TIGR03591       553 ETIKINPDKIRDVIGPGGKVIREITE--ETGAKIDIEDDGTVKIAASDGEAAEAAIKMIE  610 (684)
T ss_pred             EEEecCHHHHHhhcCCCcHHHHHHHH--HHCCEEEEecCeEEEEEECcHHHHHHHHHHHH
Confidence            56899999999999999999999999  99999999999999999988764444333333

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).

>KOG1856|consensus

Probab=92.42  E-value=0.18  Score=52.18  Aligned_cols=72  Identities=19%  Similarity=0.274  Sum_probs=59.3

Q ss_pred             CCCCEEEEEEEEEecce---EEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCCC-eeEEEEecC
Q psy230           55 TRGDLVIGVVTSRVGDN---YRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDM-ESEMVCVDS  126 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~~~---~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~~  126 (222)
                      .+|-+|.+.|++++...   .+|-..|.-+++++.....+ ..++.-..+++|+.|+|||+++.... .++|||+++
T Consensus       984 ~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~s 1060 (1299)
T KOG1856|consen  984 YEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTS 1060 (1299)
T ss_pred             ccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhH
Confidence            57999999999999999   55588999999999766554 44566667889999999999998664 589999873

>PRK11642 exoribonuclease R; Provisional

Probab=92.20  E-value=0.94  Score=46.03  Aligned_cols=83  Identities=16%  Similarity=0.205  Sum_probs=63.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCC-CCeeeeccccccc------------cccCCcCCCCCCEEEEEEEecCCC-Cee
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSH-DPAVLSYLAFEGA------------TKKNPPKVETGDVVAGKLLTANKD-MES  119 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~-~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~-~~~  119 (222)
                      ..+|+.+-|+|++++...+.|.+... -.|.+|++.+...            -++....|++||-|..+|.+++.. ..+
T Consensus       641 ~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI  720 (813)
T PRK11642        641 DQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKI  720 (813)
T ss_pred             ccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeE
Confidence            47899999999999999999999764 7899998765421            024457899999999999998753 568


Q ss_pred             EEEEecCCCccccCccc
Q psy230          120 EMVCVDSRGKEFIMGIL  136 (222)
Q Consensus       120 ~Ls~~~~~~~~~~~G~L  136 (222)
                      .++....+.+..+.|+-
T Consensus       721 ~f~l~~~~~~~~~~~~~  737 (813)
T PRK11642        721 DFSLISSERAPRNVGKT  737 (813)
T ss_pred             EEEEecccccCCCCCcc
Confidence            88877644444455543

>TIGR02063 RNase_R ribonuclease R

Probab=91.75  E-value=0.81  Score=45.66  Aligned_cols=70  Identities=13%  Similarity=0.168  Sum_probs=55.7

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECC-CCCeeeeccccccc------------cccCCcCCCCCCEEEEEEEecCCC-Ce
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGS-HDPAVLSYLAFEGA------------TKKNPPKVETGDVVAGKLLTANKD-ME  118 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~-~~  118 (222)
                      .+.+|..+-|+|+++..-.+.|++.. ...|.+|++.+.+.            .++....|++||-|..+|.+++.. ..
T Consensus       624 ~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~  703 (709)
T TIGR02063       624 SEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGK  703 (709)
T ss_pred             hccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCe
Confidence            46789999999999999999999986 57899998776521            023356799999999999999853 45


Q ss_pred             eEEE
Q psy230          119 SEMV  122 (222)
Q Consensus       119 ~~Ls  122 (222)
                      +.++
T Consensus       704 I~~~  707 (709)
T TIGR02063       704 IDFE  707 (709)
T ss_pred             EEEE
Confidence            5554

This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.

>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

Probab=91.30  E-value=0.6  Score=46.12  Aligned_cols=74  Identities=15%  Similarity=0.113  Sum_probs=65.3

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD  125 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  125 (222)
                      --|++|.+=.|+|+++..-.++|.+.....+.+|.+... ....+-.+.+++||.|+.||..+++.+.+.|+.+.
T Consensus       615 ~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri~ls~~~  689 (692)
T COG1185         615 REVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRLSIKA  689 (692)
T ss_pred             hhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecccCCccceehh
Confidence            358999999999999999999999999999999988753 34567778999999999999999998888888753

>PRK13763 putative RNA-processing protein; Provisional

Probab=90.56  E-value=0.86  Score=37.81  Aligned_cols=61  Identities=15%  Similarity=0.208  Sum_probs=50.2

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC-CeEEEe---eCCchhHHHHHHHHHHhh
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN-GKIWIR---CESFSDTVRVGNLIMSCE  202 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N-G~iWi~---~~~~~~~~~i~~~i~~~e  202 (222)
                      ..+.||+.++..++|+++..++.|.+  .+++.|-+-.+ |.|-|.   +.++.....+...|+.+-
T Consensus         5 ~~i~IP~~kig~iIG~gGk~Ik~I~e--~tg~~I~i~~~~g~V~I~~~~~~d~~~i~kA~~~I~ai~   69 (180)
T PRK13763          5 EYVKIPKDRIGVLIGKKGETKKEIEE--RTGVKLEIDSETGEVIIEPTDGEDPLAVLKARDIVKAIG   69 (180)
T ss_pred             EEEEcCHHHhhhHhccchhHHHHHHH--HHCcEEEEECCCCeEEEEeCCCCCHHHHHHHHHHHHHHh
Confidence            35789999999999999999999999  88888888888 999999   667765555555555443

>PRK11712 ribonuclease G; Provisional

Probab=90.38  E-value=2.6  Score=40.41  Aligned_cols=72  Identities=15%  Similarity=0.148  Sum_probs=52.4

Q ss_pred             cCCCCCCEEEEEEEEEec--ceEEEEECCCCCeeeecccc-cc------c------cccCCcCCCCCCEEEEEEEecC-C
Q psy230           52 YVPTRGDLVIGVVTSRVG--DNYRVDIGSHDPAVLSYLAF-EG------A------TKKNPPKVETGDVVAGKLLTAN-K  115 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~--~~~~VdI~~~~~a~L~~~~f-~g------a------tk~~r~~l~~GDlV~ArV~~~~-~  115 (222)
                      ....+|++-.|+|.++.+  +.++|||+..-.|+||+... +.      .      .......+++||-|...|..-. .
T Consensus        34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~  113 (489)
T PRK11712         34 KRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLG  113 (489)
T ss_pred             cccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcC
Confidence            445689999999999965  78999999999999998653 11      0      0112344999999999998642 2


Q ss_pred             CCeeEEEE
Q psy230          116 DMESEMVC  123 (222)
Q Consensus       116 ~~~~~Ls~  123 (222)
                      ...+.||+
T Consensus       114 ~KG~~lT~  121 (489)
T PRK11712        114 TKGARLTT  121 (489)
T ss_pred             CCCCeEEE
Confidence            33466665

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=90.19  E-value=0.68  Score=38.13  Aligned_cols=59  Identities=14%  Similarity=0.178  Sum_probs=49.0

Q ss_pred             EEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC-CeEEE--eeCCchhHHHHHHHHHHhh
Q psy230          142 LHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN-GKIWI--RCESFSDTVRVGNLIMSCE  202 (222)
Q Consensus       142 ~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N-G~iWi--~~~~~~~~~~i~~~i~~~e  202 (222)
                      +.||+.++..++|+++..++.|.+  .+++.|-+-.+ |.|-|  .+.++.....+...|+.+-
T Consensus         2 i~Ip~~kig~vIG~gG~~Ik~I~~--~tgv~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~   63 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGETKKEIEE--RTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIG   63 (172)
T ss_pred             ccCCHHHhhhHhCCchhHHHHHHH--HhCcEEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHH
Confidence            679999999999999999999999  89999988888 99999  6777765566655555543

This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.

>PRK10811 rne ribonuclease E; Reviewed

Probab=90.07  E-value=2.7  Score=43.39  Aligned_cols=70  Identities=11%  Similarity=0.126  Sum_probs=50.7

Q ss_pred             CCCCCEEEEEEEEEe--cceEEEEECCCCCeeeecccc-----ccc-----cccCCcCCCCCCEEEEEEEecC-CCCeeE
Q psy230           54 PTRGDLVIGVVTSRV--GDNYRVDIGSHDPAVLSYLAF-----EGA-----TKKNPPKVETGDVVAGKLLTAN-KDMESE  120 (222)
Q Consensus        54 P~vGDiVIG~V~~v~--~~~~~VdI~~~~~a~L~~~~f-----~ga-----tk~~r~~l~~GDlV~ArV~~~~-~~~~~~  120 (222)
                      +.+|+|-+|+|.++-  -+.++|||+....|+|++...     ...     ..+....|++||-|.-.|..-. +..-+.
T Consensus        36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~gtKGp~  115 (1068)
T PRK10811         36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAA  115 (1068)
T ss_pred             cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeecccCCCCCc
Confidence            468999999999994  478999999999999997543     111     0123456999999999998632 333355


Q ss_pred             EEE
Q psy230          121 MVC  123 (222)
Q Consensus       121 Ls~  123 (222)
                      ||+
T Consensus       116 LTt  118 (1068)
T PRK10811        116 LTT  118 (1068)
T ss_pred             eee
Confidence            554

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=89.50  E-value=0.89  Score=45.48  Aligned_cols=60  Identities=15%  Similarity=0.284  Sum_probs=51.1

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHh
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSC  201 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~  201 (222)
                      ..++|+|.+++.++|+++.+++.|.+  .++++|=+-.+|.|.|.+.+......+...|+.+
T Consensus       580 ~~~~I~~~ki~~vIG~gGk~I~~i~~--~tg~~Idi~d~G~V~I~a~d~~~~~~A~~~I~~i  639 (719)
T TIGR02696       580 ITVKIPVDKIGEVIGPKGKMINQIQD--ETGAEISIEDDGTVYIGAADGPSAEAARAMINAI  639 (719)
T ss_pred             EEEEeChHHhhheeCCCcHhHHHHHH--HHCCEEEEecCcEEEEEeCCHHHHHHHHHHHHHh
Confidence            67899999999999999999999999  9999999999999999998876554444444443

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.

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=88.88  E-value=1.7  Score=31.86  Aligned_cols=63  Identities=13%  Similarity=0.203  Sum_probs=47.1

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCC-CCe-eeecccccc-ccccCCcCCCCCCEEEEEEEecCCCC
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGSH-DPA-VLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDM  117 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~-~~a-~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~  117 (222)
                      .|++||+|. .|..+....+.|.+--. ..| +|+++...- ..++++..+ +|-.+.++|+.+++..
T Consensus        13 ~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~K   78 (86)
T PHA02858         13 FPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLK   78 (86)
T ss_pred             cCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCC
Confidence            699999999 78888998899988542 334 343555432 345667778 9999999999998763

>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=87.71  E-value=2.7  Score=29.93  Aligned_cols=66  Identities=17%  Similarity=0.064  Sum_probs=46.4

Q ss_pred             CCEEEEEEEEEecceEEEEECC-CCCeeeeccccccccc---cCCcCCCCCCEE-EEEEEecCCCCeeEEEE
Q psy230           57 GDLVIGVVTSRVGDNYRVDIGS-HDPAVLSYLAFEGATK---KNPPKVETGDVV-AGKLLTANKDMESEMVC  123 (222)
Q Consensus        57 GDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~gatk---~~r~~l~~GDlV-~ArV~~~~~~~~~~Ls~  123 (222)
                      |++|=|+|.+++.|...|++.. .-.|.||.........   .....+++||-+ -+-|.+. ....+.||+
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL~~-~~r~i~lt~   71 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSN-YKGRIILTK   71 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEEec-cccEEEEec
Confidence            7899999999999999999987 6689998754432222   345678899988 6666622 223444543

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 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH)

Probab=86.98  E-value=1.4  Score=34.28  Aligned_cols=52  Identities=23%  Similarity=0.255  Sum_probs=40.1

Q ss_pred             hhhhhccCCChhHHHHhhhcCCCcEEEEEEeC-----------------------CeEEEeeCC--chhHHHHHHHHHH
Q psy230          147 SLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN-----------------------GKIWIRCES--FSDTVRVGNLIMS  200 (222)
Q Consensus       147 ~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N-----------------------G~iWi~~~~--~~~~~~i~~~i~~  200 (222)
                      +++.+++|+++..++.|.+  .++|.|.|--.                       |.|.|.+.+  ......+...|+.
T Consensus        15 N~IG~IIGPgG~tiK~i~~--eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~   91 (120)
T cd02395          15 NFVGLILGPRGNTLKQLEK--ETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEE   91 (120)
T ss_pred             CeeEEEECCCChHHHHHHH--HHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHH
Confidence            6778889999999999999  99999977655                       899999988  4434444444443

Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=86.19  E-value=4.4  Score=27.45  Aligned_cols=60  Identities=18%  Similarity=0.165  Sum_probs=32.6

Q ss_pred             CCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEE
Q psy230           56 RGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVC  123 (222)
Q Consensus        56 vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~  123 (222)
                      +|+++-.+|++++...|.+|-+......||....       ...+++||-|..-|=. +++.....||
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~-------~~~~~~Gd~v~VFvY~-D~~~rl~AT~   60 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEV-------PEPLKVGDEVEVFVYL-DKEGRLVATT   60 (61)
T ss_dssp             --------EEEE-SSEEEEEETT-EEEEEEGGG-------------TTSEEEEEEEE--TTS-EEEE-
T ss_pred             CCCCcceEEEEEeCCEEEEECCCCCEEEechHHc-------CCCCCCCCEEEEEEEE-CCCCCEEEec
Confidence            5889999999999999999998889999996433       3458899999888743 3333444444

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=85.72  E-value=2.1  Score=29.08  Aligned_cols=37  Identities=8%  Similarity=0.123  Sum_probs=34.0

Q ss_pred             EEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCe
Q psy230          142 LHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGK  180 (222)
Q Consensus       142 ~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~  180 (222)
                      +.||..++.+++|+++..++.|.+  .+++.|-+..|..
T Consensus         4 ~~ip~~~vg~iIG~~G~~i~~i~~--~tga~I~i~~~~~   40 (65)
T cd02396           4 LLVPSSQAGSIIGKGGSTIKEIRE--ETGAKIRVSKSVL   40 (65)
T ss_pred             EEECHHHcCeeECCCcHHHHHHHH--HHCCEEEEcCCCC
Confidence            678999999999999999999999  8999999988873

Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran

>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases

Probab=85.21  E-value=3  Score=41.36  Aligned_cols=70  Identities=16%  Similarity=0.091  Sum_probs=54.4

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEC-CCCCeeeecccccccc------------ccCCcCCCCCCEEEEEEEecCCC-Ce
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIG-SHDPAVLSYLAFEGAT------------KKNPPKVETGDVVAGKLLTANKD-ME  118 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~-~~~~a~L~~~~f~gat------------k~~r~~l~~GDlV~ArV~~~~~~-~~  118 (222)
                      ...+|..+-|+|++++...+.|+|. ....|.+|++.+++..            ++....|++||.|..+|.+++.. ..
T Consensus       569 ~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~  648 (654)
T TIGR00358       569 LDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRS  648 (654)
T ss_pred             hhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCe
Confidence            3467999999999999999999997 4588999987765321            23457899999999999999753 34


Q ss_pred             eEEE
Q psy230          119 SEMV  122 (222)
Q Consensus       119 ~~Ls  122 (222)
                      +.++
T Consensus       649 I~f~  652 (654)
T TIGR00358       649 IIFE  652 (654)
T ss_pred             EEEE
Confidence            4443

This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.

>KOG1070|consensus

Probab=84.70  E-value=1.7  Score=46.31  Aligned_cols=69  Identities=14%  Similarity=0.148  Sum_probs=56.9

Q ss_pred             ccccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccc-cc---cccccCCcCCCCCCEEEEEEEecCCCCe
Q psy230           49 QRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLA-FE---GATKKNPPKVETGDVVAGKLLTANKDME  118 (222)
Q Consensus        49 ~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~-f~---gatk~~r~~l~~GDlV~ArV~~~~~~~~  118 (222)
                      +..|.-++|++|-|.|+++.++.-.|+..+...+-+|++. |.   ..+. .-..|++||-|.|||+.-++..+
T Consensus       878 k~~~~~~igsiv~a~v~svKp~~L~v~l~~~~~gri~isev~d~~~eitD-p~~k~~vG~~I~vrviG~~D~k~  950 (1710)
T KOG1070|consen  878 KSTEDLSIGSIVRAYVKSVKPDQLNVLLAANHHGRIHISEVLDNLHEITD-PLDKFKVGDGIFVRVIGGHDVKD  950 (1710)
T ss_pred             ccccceeeeeEEEEEEeeecccceEEeccccccCceehHHhhccccccCC-hhhhcccCCeEEEEEEcCCcccc
Confidence            4578889999999999999999999999999999999864 33   2333 56679999999999997654433

>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32)

Probab=84.52  E-value=5.5  Score=25.98  Aligned_cols=64  Identities=11%  Similarity=0.093  Sum_probs=41.8

Q ss_pred             EEEEEEEEec-----ceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEE
Q psy230           60 VIGVVTSRVG-----DNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVC  123 (222)
Q Consensus        60 VIG~V~~v~~-----~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~  123 (222)
                      |.|+|.++..     .++.+.|.....+.+++..|+....+....+.+|+.++.+..--.....+.|.+
T Consensus         2 v~g~v~~~~~~~~~~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~g~v~~~~~~~~l~~   70 (75)
T cd03524           2 IVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIKGKVKKFRGRLQLIV   70 (75)
T ss_pred             eEEEEEeecccccCCeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEEEEEEecCCeEEEEe
Confidence            5677777764     457777776554777777776554556678999999887743222233456655

RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco

>KOG3298|consensus

Probab=82.50  E-value=11  Score=30.96  Aligned_cols=65  Identities=23%  Similarity=0.285  Sum_probs=46.6

Q ss_pred             cccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecc-----cc-cccc-----ccCCcCCCCCCEEEEEEEecC
Q psy230           50 RRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYL-----AF-EGAT-----KKNPPKVETGDVVAGKLLTAN  114 (222)
Q Consensus        50 ~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~-----~f-~gat-----k~~r~~l~~GDlV~ArV~~~~  114 (222)
                      -.+.|-.|++|=|.|+.++...+.++++.-...+++.+     .| +|..     ...-..++.|+-|+-+|+...
T Consensus        75 v~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr  150 (170)
T KOG3298|consen   75 VTFKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTR  150 (170)
T ss_pred             EEEeecCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEE
Confidence            35889999999999999999999999998665555532     23 2211     111225778888888888653

>PRK04012 translation initiation factor IF-1A; Provisional

Probab=81.98  E-value=8.2  Score=29.14  Aligned_cols=57  Identities=25%  Similarity=0.227  Sum_probs=39.1

Q ss_pred             CCCCCCEEEEEEEEE-ecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecC
Q psy230           53 VPTRGDLVIGVVTSR-VGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTAN  114 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~  114 (222)
                      .| ..+-++|+|+.. .++.|.|....-.. .|-  .++|..++ +-.+++||.|..+....+
T Consensus        17 ~p-~e~e~~g~V~~~lG~~~~~V~~~dG~~-~la--~i~GK~Rk-~IwI~~GD~VlVe~~~~~   74 (100)
T PRK04012         17 MP-EEGEVFGVVEQMLGANRVRVRCMDGVE-RMG--RIPGKMKK-RMWIREGDVVIVAPWDFQ   74 (100)
T ss_pred             CC-CCCEEEEEEEEEcCCCEEEEEeCCCCE-EEE--EEchhhcc-cEEecCCCEEEEEecccC
Confidence            44 456699999998 45788888864322 111  23454455 778999999999986665

>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit

Probab=81.19  E-value=4.6  Score=31.52  Aligned_cols=61  Identities=16%  Similarity=0.316  Sum_probs=41.8

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeecc------cccccc--------ccCCcCCCCCCEEEEEEEecC
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYL------AFEGAT--------KKNPPKVETGDVVAGKLLTAN  114 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~------~f~gat--------k~~r~~l~~GDlV~ArV~~~~  114 (222)
                      |-+|.++.|+|.+.+.+..+|.++--.+-.+|..      .|....        ...+-+++.|+-|+=||.+..
T Consensus         1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~   75 (122)
T PF08292_consen    1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEI   75 (122)
T ss_dssp             --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEE
T ss_pred             CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEE
Confidence            6789999999999999999999976444444433      333211        455667899999999998764

Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.

>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=80.96  E-value=7.2  Score=29.66  Aligned_cols=53  Identities=28%  Similarity=0.310  Sum_probs=42.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEe
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLT  112 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~  112 (222)
                      |..|-+|+|+|..+..+---+|.|.-+.++.+--+      .+...|..|+-|.-|+..
T Consensus        21 ~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~------~~~~~y~~G~rV~lrLkd   73 (104)
T PF10246_consen   21 DPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPA------VNGEKYVRGSRVRLRLKD   73 (104)
T ss_pred             CccCCEEEEEEEEEecCceEEEeCCceeEEEeccc------ccccccccCCEEEEEECC
Confidence            45799999999999999999999998888887322      334568899999999753

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 [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].

>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands

Probab=80.93  E-value=4.4  Score=27.37  Aligned_cols=62  Identities=23%  Similarity=0.248  Sum_probs=42.4

Q ss_pred             EEEEEEEE---ecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEE--EEecCCCCeeEEEE
Q psy230           60 VIGVVTSR---VGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGK--LLTANKDMESEMVC  123 (222)
Q Consensus        60 VIG~V~~v---~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~Ar--V~~~~~~~~~~Ls~  123 (222)
                      |.|+|+++   ......++|.... +.+.+..|.....+..+.+++||.|..+  |.... ..+++|++
T Consensus         3 v~G~V~~~~~~~~~~~~~~l~D~t-g~i~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~~~-~~~~~l~~   69 (75)
T PF01336_consen    3 VEGRVTSIRRSGGKIVFFTLEDGT-GSIQVVFFNEEYERFREKLKEGDIVRVRGKVKRYN-GGELELIV   69 (75)
T ss_dssp             EEEEEEEEEEEETTEEEEEEEETT-EEEEEEEETHHHHHHHHTS-TTSEEEEEEEEEEET-TSSEEEEE
T ss_pred             EEEEEEEEEcCCCCEEEEEEEECC-ccEEEEEccHHhhHHhhcCCCCeEEEEEEEEEEEC-CccEEEEE
Confidence            67888877   5677888887654 7777767765556777789999998655  55443 23477766

The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....

>KOG3297|consensus

Probab=80.09  E-value=8.3  Score=32.40  Aligned_cols=62  Identities=16%  Similarity=0.296  Sum_probs=45.4

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccc------cccc---------c---ccCCcCCCCCCEEEEEEEec
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLA------FEGA---------T---KKNPPKVETGDVVAGKLLTA  113 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~------f~ga---------t---k~~r~~l~~GDlV~ArV~~~  113 (222)
                      +.|-+|.++.|+|.+-..+..+|.|+--.+=..|...      |+-+         .   ...+-+|++|.-|+=||.+.
T Consensus        77 FrPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e  156 (202)
T KOG3297|consen   77 FRPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDE  156 (202)
T ss_pred             EecccceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeee
Confidence            6799999999999999999999998753333333322      2211         1   14566899999999999875

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	222
2nn6_G	289	Structure Of The Human Rna Exosome Composed Of Rrp4		8e-50
4ifd_G	242	Crystal Structure Of An 11-subunit Eukaryotic Exoso		7e-34
2ja9_A	175	Structure Of The N-Terminal Deletion Of Yeast Exoso		1e-30
2z0s_A	235	Crystal Structure Of Putative Exosome Complex Rna-B		1e-05
2ba0_A	229	Archaeal Exosome Core Length = 229		4e-05

>pdb|2NN6|G Chain G, Structure Of The Human Rna Exosome Composed Of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40 Length = 289

Iteration: 1
 Score =  192 bits (489), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 94/214 (43%), Positives = 145/214 (67%), Gaps = 13/214 (6%)
Query: 6   LSLNAEP----RLILGPGLRRESSAILVSQSGILRHAKPFT------YYVDYIQRRYVPT 55
           LSLNA      R++ GPGLRR    +LV++ G LRH +P +      Y+VD  Q+RYVP 
Sbjct: 67  LSLNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPV 126
Query: 56  RGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANK 115
           +GD VIG+VT++ GD ++VD+G  +PA LSYL+FEGATK+N P V+ GD++ G+ + ANK
Sbjct: 127 KGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANK 186
Query: 116 DMESEMVCVDSRGKEFIMGIL-NDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELS 174
           DME EMVC+DS G+   MG++  DG L   ++ L RKLL P C +++++ K     +E+ 
Sbjct: 187 DMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIIQEVGK--LYPLEIV 244
Query: 175 IGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEE 208
            GMNG+IW++ ++   T+ + N++ +CE ++ ++
Sbjct: 245 FGMNGRIWVKAKTIQQTLILANILEACEHMTSDQ 278

>pdb|4IFD|G Chain G, Crystal Structure Of An 11-subunit Eukaryotic Exosome Complex Bound To Rna Length = 242

Iteration: 1
 Score =  140 bits (352), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 78/211 (36%), Positives = 125/211 (59%), Gaps = 12/211 (5%)
Query: 1   MAGDTLSLNAEPRLILGPGLRRE--SSAILVSQSGILR-----HAKPFTYYVDYIQRRYV 53
             GD+  ++    + LGPG+  +  +  I    +G+L       +   T Y+DY  +RY+
Sbjct: 8   FPGDSFPVDPTTPVKLGPGIYCDPNTQEIRPVNTGVLHVSAKGKSGVQTAYIDYSSKRYI 67
Query: 54  PTRGDLVIGVVTSRVGDNYRVDIGSHDPAV-LSYLAFEGATKKNPPKVETGDVVAGKLLT 112
           P+  D VIGV+     D+Y+V + +   +V LSY+AF  A+KKN P ++ GD+V  ++ T
Sbjct: 68  PSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCT 127
Query: 113 ANKDMESEMVCVDS-RGKEFIMGILNDGYLLHTSISLCRKLL-NPKCPLLKQLAKRSRQK 170
           A K++E+E+ C DS  G++   GIL DG ++  +++  R+LL N   PLLK LA  +  K
Sbjct: 128 AEKELEAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAHT--K 185
Query: 171 MELSIGMNGKIWIRCESFSDTVRVGNLIMSC 201
            E++IG+NGKIW++CE  S+T+     IM C
Sbjct: 186 FEVAIGLNGKIWVKCEELSNTLACYRTIMEC 216

>pdb|2JA9|A Chain A, Structure Of The N-Terminal Deletion Of Yeast Exosome Component Rrp40 Length = 175

Iteration: 1
 Score =  129 bits (324), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 65/155 (41%), Positives = 101/155 (65%), Gaps = 5/155 (3%)
Query: 50  RRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAV-LSYLAFEGATKKNPPKVETGDVVAG 108
           +RY+P+  D VIGV+     D+Y+V + +   +V LSY+AF  A+KKN P ++ GD+V  
Sbjct: 1   KRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYA 60
Query: 109 KLLTANKDMESEMVCVDS-RGKEFIMGILNDGYLLHTSISLCRKLL-NPKCPLLKQLAKR 166
           ++ TA K++E+E+ C DS  G++   GIL DG ++  +++  R+LL N   PLLK LA  
Sbjct: 61  RVCTAEKELEAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAH 120
Query: 167 SRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSC 201
           +  K E++IG+NGKIW++CE  S+T+     IM C
Sbjct: 121 T--KFEVAIGLNGKIWVKCEELSNTLACYRTIMEC 153

>pdb|2Z0S|A Chain A, Crystal Structure Of Putative Exosome Complex Rna-Binding Protein Length = 235

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 40/139 (28%), Positives = 68/139 (48%), Gaps = 12/139 (8%)
Query: 52  YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-----ATKKNPPKVETGDVV 106
           YVP  GD+VIG++ S    N+ VDI S   AVLS   F G     A       ++ GD +
Sbjct: 62  YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYI 121
Query: 107 AGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKR 166
             K++  +K   S ++ V   G    +G +  G ++  S +   +++  K  +LK L ++
Sbjct: 122 KAKVVAFDK-TRSPLLTVQGEG----LGRIVRGKIVEISPAKVPRVIGRKMSMLKTLEEK 176
Query: 167 SRQKMELSIGMNGKIWIRC 185
           +  K  + +  NG+I + C
Sbjct: 177 TECK--IFVARNGRIHLEC 193

>pdb|2BA0|A Chain A, Archaeal Exosome Core Length = 229

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 47/191 (24%), Positives = 84/191 (43%), Gaps = 25/191 (13%)
Query: 1   MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLV 60
           + GD LS N  PR   G G   E   +     G+    +     +  ++ RY P+ GD+V
Sbjct: 6   LPGDLLSTN--PRA-AGYGTYVEGGKVYAKIIGLFDQTETHVRVIP-LKGRYTPSVGDVV 61
Query: 61  IGVVTSRVGDNYRVDIGSHDPAVLSYLAF-------EGATKKNPPKV-ETGDVVAGKLLT 112
           IG++     + + VDI S       Y AF       E    K P +V + GD +  K+L 
Sbjct: 62  IGIIREVAANGWAVDIYS------PYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLN 115
Query: 113 ANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKME 172
            +  M+  +       K+ I   +  G ++  + +   +++  K  ++K L  +S   ++
Sbjct: 116 IDPKMKVTLTM-----KDRICRPIRFGRIVAINPARVPRVIGKKGSMIKLL--KSELDVQ 168
Query: 173 LSIGMNGKIWI 183
           + +G NG IW+
Sbjct: 169 IVVGQNGLIWV 179

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	222
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	1e-62
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	2e-44
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	1e-38
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	7e-37
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	8e-36
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	2e-29

>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 Length = 289

 Score =  195 bits (497), Expect = 1e-62
 Identities = 89/217 (41%), Positives = 142/217 (65%), Gaps = 9/217 (4%)

Query: 7   SLNAEPRLILGPGLRRESSAILVSQSGILRHAKPF------TYYVDYIQRRYVPTRGDLV 60
              +  R++ GPGLRR    +LV++ G LRH +P        Y+VD  Q+RYVP +GD V
Sbjct: 72  RACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPVKGDHV 131

Query: 61  IGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESE 120
           IG+VT++ GD ++VD+G  +PA LSYL+FEGATK+N P V+ GD++ G+ + ANKDME E
Sbjct: 132 IGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPE 191

Query: 121 MVCVDSRGKEFIMGIL-NDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG 179
           MVC+DS G+   MG++  DG L   ++ L RKLL P C +++++ K     +E+  GMNG
Sbjct: 192 MVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIIQEVGKLY--PLEIVFGMNG 249

Query: 180 KIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESI 216
           +IW++ ++   T+ + N++ +CE ++ ++   +   +
Sbjct: 250 RIWVKAKTIQQTLILANILEACEHMTSDQRKQIFSRL 286

>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 Length = 175

 Score =  145 bits (368), Expect = 2e-44
 Identities = 62/164 (37%), Positives = 98/164 (59%), Gaps = 5/164 (3%)

Query: 50  RRYVPTRGDLVIGVVTSRVGDNYRVDIGSH-DPAVLSYLAFEGATKKNPPKVETGDVVAG 108
           +RY+P+  D VIGV+     D+Y+V + +      LSY+AF  A+KKN P ++ GD+V  
Sbjct: 1   KRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYA 60

Query: 109 KLLTANKDMESEMVCVDSR-GKEFIMGILNDGYLLHTSISLC-RKLLNPKCPLLKQLAKR 166
           ++ TA K++E+E+ C DS  G++   GIL DG ++  +++   + L N   PLLK LA  
Sbjct: 61  RVCTAEKELEAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAH 120

Query: 167 SRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEIL 210
           +  K E++IG+NGKIW++CE  S+T+     IM C   +     
Sbjct: 121 T--KFEVAIGLNGKIWVKCEELSNTLACYRTIMECCQKNDTAAF 162

>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 =  133 bits (335), Expect = 1e-38
 Identities = 36/213 (16%), Positives = 78/213 (36%), Gaps = 12/213 (5%)

Query: 3   GDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIG 62
           G+ L+   E ++   P + + +S    +  G+          +      Y P   D+VIG
Sbjct: 22  GELLA-EGEFQIPWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEGSFYYPKINDIVIG 80

Query: 63  VVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKV----ETGDVVAGKLLTANKDME 118
           +V       + VDI +   A L      G +      +    + GD V  ++   ++ ++
Sbjct: 81  LVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSID 140

Query: 119 SEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN 178
             +           +G +++G ++        +++     + + L  +S     + +  N
Sbjct: 141 PVLSVKGKD-----LGRVSNGIVIDIMPVKVPRVIGKNKSMYETLTSKS--GCSIFVANN 193

Query: 179 GKIWIRCESFSDTVRVGNLIMSCELLSYEEILN 211
           G+IW  C S      +   I   E  S+ + L 
Sbjct: 194 GRIWATCPSRFSEEILIEAIRKIENESHIKGLT 226

>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 =  127 bits (321), Expect = 7e-37
 Identities = 41/209 (19%), Positives = 81/209 (38%), Gaps = 13/209 (6%)

Query: 3   GDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIG 62
           GD LS N       G G   E   +     G+    +     V  ++ RY P+ GD+VIG
Sbjct: 8   GDLLSTNP---RAAGYGTYVEGGKVYAKIIGLFDQTET-HVRVIPLKGRYTPSVGDVVIG 63

Query: 63  VVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPK--VETGDVVAGKLLTANKDMESE 120
           ++     + + VDI S   A L             P   ++ GD +  K+L  +  M+  
Sbjct: 64  IIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVT 123

Query: 121 MVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGK 180
           +   D          +  G ++  + +   +++  K  ++K L       +++ +G NG 
Sbjct: 124 LTMKDRIC-----RPIRFGRIVAINPARVPRVIGKKGSMIKLLKSEL--DVQIVVGQNGL 176

Query: 181 IWIRCESFSDTVRVGNLIMSCELLSYEEI 209
           IW+  +    ++    + +  +    E +
Sbjct: 177 IWVNGDRRKVSIAEEAIYLIEQEAHTEGL 205

>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 =  125 bits (315), Expect = 8e-36
 Identities = 46/220 (20%), Positives = 84/220 (38%), Gaps = 18/220 (8%)

Query: 3   GDTLSLNAEPRLILGPGLRRESSAILVSQSGILRH-AKPFTYYVDYIQRRYVPTRGDLVI 61
           G+ L    E      P +         +  G+LR            ++  YVP  GD+VI
Sbjct: 15  GEPLPEEVE---ASPPYVIDYKGVKRATVVGLLREKGDGGGRAFVKLKEIYVPQAGDVVI 71

Query: 62  GVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-----ATKKNPPKVETGDVVAGKLLTANKD 116
           G++ S    N+ VDI S   AVLS   F G     A       ++ GD +  K++  +K 
Sbjct: 72  GLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKT 131

Query: 117 MESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIG 176
               +           +G +  G ++  S +   +++  K  +LK L +++  + ++ + 
Sbjct: 132 RSPLLTVQGEG-----LGRIVRGKIVEISPAKVPRVIGRKMSMLKTLEEKT--ECKIFVA 184

Query: 177 MNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESI 216
            NG+I + C +          I   +         L + I
Sbjct: 185 RNGRIHLECPNEDLEAIAVMAIKIID--EEAYTSGLTKRI 222

>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 =  110 bits (277), Expect = 2e-29
 Identities = 42/222 (18%), Positives = 79/222 (35%), Gaps = 27/222 (12%)

Query: 3   GDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIG 62
           GDT++   +   + G G       ++ S +G +         V  ++ RY+   GD+V+G
Sbjct: 45  GDTIT--TDTGFMRGHGTYMGEEKLIASVAGSVERVNK-LICVKALKTRYIGEVGDIVVG 101

Query: 63  VVTSRVGDNYRVDIGSHDPAVL--SYLAFEGATKKNPPKVET---------GDVVAGKLL 111
            +T      ++V+  S   +VL  S +   G   +     +          GD+++ ++ 
Sbjct: 102 RITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQ 161

Query: 112 TANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKM 171
               D    +     +      G L  G L+  S SL ++         K          
Sbjct: 162 AVFSDGAVSLHTRSLK-----YGKLGQGVLVQVSPSLVKR--------QKTHFHDLPCGA 208

Query: 172 ELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLC 213
            + +G NG IWI           G  I + E +S  +   + 
Sbjct: 209 SVILGNNGFIWIYPTPEHKEEEAGGFIANLEPVSLADREVIS 250

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	222
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	100.0
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	100.0
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	100.0
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	100.0
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	100.0
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	100.0
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	99.95
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	99.93
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	98.67
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	98.57
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	98.54
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	98.49
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	98.45
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	98.43
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	98.4
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	98.39
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	98.38
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	98.31
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	98.2
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	98.14
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.1
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	98.08
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	98.0
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	97.98
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	97.75
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	97.67
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	97.47
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	97.46
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	97.26
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	97.19
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.18
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	97.16
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	97.15
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.14
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	97.13
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	97.13
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	97.07
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	96.76
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	96.72
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	96.5
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	96.42
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	96.39
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	96.35
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	96.34
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	96.33
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	96.29
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	96.13
1we8_A	104	Tudor and KH domain containing protein; structural	96.0
2cpq_A	91	FragIle X mental retardation syndrome related prot	95.67
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	95.44
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	94.29
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	94.2
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	93.98
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	93.82
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	93.76
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	93.68
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	93.62
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	93.59
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	93.56
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	93.26
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	92.74
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	92.73
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	92.38
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	92.34
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	92.28
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	92.25
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	91.83
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	91.68
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	89.78
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	85.8
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	85.76
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	85.37
2bh8_A	101	1B11; transcription, molecular evolution, unique a	83.78
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	82.83
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	81.52

>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=100.00  E-value=2.5e-62  Score=430.88  Aligned_cols=216  Identities=43%  Similarity=0.841  Sum_probs=195.9

Q ss_pred             CCCCeecCCCC---------------------CCeee--CCCeEEeCCEEEEEEeeEEEEecCc------EEEEEccccc
Q psy230            1 MAGDTLSLNAE---------------------PRLIL--GPGLRRESSAILVSQSGILRHAKPF------TYYVDYIQRR   51 (222)
Q Consensus         1 ~PGd~l~~~~~---------------------~~~~~--G~G~y~~~~~i~as~~G~l~~~~~~------~v~V~~~~~~   51 (222)
                      +|||.|+....                     .+|++  |+|||.++++|+|+++|.++.++++      ++||+|.+++
T Consensus        43 lPGD~L~~~~~~~~~~~g~~~~~~l~~~~~~~~~~~~~~G~Gty~~~~~I~as~aG~l~~~~~~~~~~~~~v~V~~~~~r  122 (289)
T 2nn6_G           43 LPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQKR  122 (289)
T ss_dssp             CSSEEECCSCSCCEECSSEEECC-----------------------CCCEEECSCCEEEEECCTTTSSCCEEEEECCCSS
T ss_pred             eCCCCcCccccccccccccccccccccccccCcceEEccCCCeEEECCEEEEEEeEeEEeccCCccCccceEEEEecCCC
Confidence            69999986421                     16888  9999999999999999999988643      8999999999


Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccc
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEF  131 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~  131 (222)
                      |+|++||+|||+|+++++++|+|||++++.|+|+.++|+|+|++||++|++||+|||||++++++++++|||+++++|++
T Consensus       123 YiP~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~~f~Gatk~~r~~f~~GDlV~ArV~s~~~~~~~eLsc~~~~~k~~  202 (289)
T 2nn6_G          123 YVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCGRAN  202 (289)
T ss_dssp             CCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSCCSSCSSSSSCTTCEEEEEEEECCTTSCCEEECSBTTTTBC
T ss_pred             CCCCCCCEEEEEEEEEeCcEEEEEECCCceeEEehhhcCcchhhhhhhcCCCCEEEEEEEEcCCCCceEEEecccccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCccc-CCceEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHH
Q psy230          132 IMGIL-NDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEIL  210 (222)
Q Consensus       132 ~~G~L-~~G~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~  210 (222)
                      +||+| ++|++|+|+++++|||++++++||++|++  +++|||+||+||||||++++++++++++|||++||.++.+|++
T Consensus       203 ~lG~L~~~G~l~~Vs~~lvrrl~~~~~~~l~~L~~--~~~~eI~vG~NG~IWI~~~~~~~~~~i~~aI~~~e~~~~~q~~  280 (289)
T 2nn6_G          203 GMGVIGQDGLLFKVTLGLIRKLLAPDCEIIQEVGK--LYPLEIVFGMNGRIWVKAKTIQQTLILANILEACEHMTSDQRK  280 (289)
T ss_dssp             CCCSCCSSCEEECCCHHHHHHHHCTTCSHHHHTTC--SSSCCCEEETTTEEEECCSSHHHHHHHHHHHHHTTSSCTTTHH
T ss_pred             cCCEecCCeEEEEEChHHhhhhhcCchhHHHHhcc--cCCeEEEEECCcEEEEecCChhHHHHHHHHHHHhhcCCHHHHH
Confidence            99999 99999999999999999999999999999  9999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHH
Q psy230          211 NLCESIHI  218 (222)
Q Consensus       211 ~~~~~~~~  218 (222)
                      +|++++++
T Consensus       281 ~~~~~~~~  288 (289)
T 2nn6_G          281 QIFSRLAE  288 (289)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHhh
Confidence            99999975

>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=100.00  E-value=1.2e-53  Score=365.50  Aligned_cols=205  Identities=21%  Similarity=0.309  Sum_probs=186.2

Q ss_pred             CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEecCcEEEEEccccccCCCCCCEEEEEEEEEecceEEEEECCCC
Q psy230            1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHD   80 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~~~~v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~   80 (222)
                      +|||.|+.   ++|.+|+|||.++++|+||++|.++.++ +.+||.|.+++|.|++||+|+|+|+++.++.|+|||++++
T Consensus         6 ~PGd~l~~---~~~~~G~Gty~~~g~i~as~~G~v~~~~-~~v~V~p~~~~y~p~~GDiV~G~V~~v~~~~a~V~I~~~~   81 (229)
T 2ba0_A            6 LPGDLLST---NPRAAGYGTYVEGGKVYAKIIGLFDQTE-THVRVIPLKGRYTPSVGDVVIGIIREVAANGWAVDIYSPY   81 (229)
T ss_dssp             CTTCEEES---CTTSBCTTEEEETTEEEECSSEEEEECS-SCEEEEECSSSCCCCTTCEEEEEEEEECSSEEEEECSSSS
T ss_pred             cCCCCccc---CCeEecCCEEEeCCEEEEEEEEEEEEeC-CEEEEEeCCCcccCCCCCEEEEEEEEEeCCeEEEEeCCCe
Confidence            69999984   3589999999999999999999999885 6789999999999999999999999999999999999999


Q ss_pred             Ceeeeccccc--cccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCcccCCceEEEechhhhhhccCCChh
Q psy230           81 PAVLSYLAFE--GATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCP  158 (222)
Q Consensus        81 ~a~L~~~~f~--gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~l~~v~~~~~~rl~~~~~~  158 (222)
                      .|+||.++|.  +++++++++|++||+|+|||+++++++++.|||++     ++||+|++|++++++|.+++|+++++++
T Consensus        82 ~g~l~isev~~~~~~~~~~~~l~~GD~V~arVi~v~~~~~i~LS~r~-----~~lG~L~~G~v~~vs~~~v~rl~~~~~~  156 (229)
T 2ba0_A           82 QAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKD-----RICRPIRFGRIVAINPARVPRVIGKKGS  156 (229)
T ss_dssp             CEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECTTCCEEEECCS-----SSCEEESSSEEEECCGGGHHHHHCGGGH
T ss_pred             EEEEEHHHccccccccchhcccCCCCEEEEEEEEECCCCcEEEEEcc-----ccCCcccCCEEEEECHHHhHHHhcCCch
Confidence            9999999987  57889999999999999999999999999999965     8999999999999999999999999999


Q ss_pred             HHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHHHH
Q psy230          159 LLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIR  219 (222)
Q Consensus       159 ~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~~  219 (222)
                      |+++|++  +++||||+|+||||||++++. +++++++||+++|..+  +..++.+++.++
T Consensus       157 ~l~~l~~--~~~~ei~vG~NG~IWi~~~~~-~~~~~~~ai~~~e~~~--~~~~l~~~v~~~  212 (229)
T 2ba0_A          157 MIKLLKS--ELDVQIVVGQNGLIWVNGDRR-KVSIAEEAIYLIEQEA--HTEGLTDRVAEF  212 (229)
T ss_dssp             HHHHHHH--HHTCEEEECTTSEEEEESCHH-HHHHHHHHHHHHHHCS--CCSSHHHHHHHH
T ss_pred             HHHHhcc--cCCeEEEEECCcEEEEeCCch-hHHHHHHHHHHHHhhh--hhhhHHHHHHHH
Confidence            9999999  999999999999999997665 8999999999999733  233344444333

>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=100.00  E-value=5.1e-52  Score=341.94  Aligned_cols=169  Identities=37%  Similarity=0.723  Sum_probs=162.7

Q ss_pred             cccCCCCCCEEEEEEEEEecceEEEEECC-CCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecC-C
Q psy230           50 RRYVPTRGDLVIGVVTSRVGDNYRVDIGS-HDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDS-R  127 (222)
Q Consensus        50 ~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~-~  127 (222)
                      +||+|++||+|||+|+++.+++|+|||++ ++.|.||.++|+|++++||++|++||+|+|||++++.+++++|||+|+ +
T Consensus         1 krY~P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~~g~~k~~r~~l~~GDlV~ArV~~~~~~~~~~Ltc~~~~~   80 (175)
T 2ja9_A            1 KRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDSTT   80 (175)
T ss_dssp             CCCCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCTTSCCEEESSCTTT
T ss_pred             CCccCCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHHHCCchhhhhhccCCCCCEEEEEEEEecCCCceEEEeccccc
Confidence            58999999999999999999999999999 999999999999999999999999999999999999999999999995 7


Q ss_pred             CccccCcccCCceEEEechhhhhhccCC-ChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHH-hhcCC
Q psy230          128 GKEFIMGILNDGYLLHTSISLCRKLLNP-KCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMS-CELLS  205 (222)
Q Consensus       128 ~~~~~~G~L~~G~l~~v~~~~~~rl~~~-~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~-~e~~~  205 (222)
                      +|+++||+|++|++|+|||+++|||+++ +++||++|++  +++|||++|+||||||+++++++++++++||++ ||.++
T Consensus        81 ~r~~~lG~L~~G~l~~v~~~~v~rl~~~~~~~~l~~l~~--~~~~ei~vG~NG~IWi~~~~~~~~~~v~~aI~~~~~~~~  158 (175)
T 2ja9_A           81 GRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAA--HTKFEVAIGLNGKIWVKCEELSNTLACYRTIMECCQKND  158 (175)
T ss_dssp             CSCTTCEEECSCEEEECCHHHHHHHHHCTTCCHHHHHHT--TCCCEEEEETTTEEEEECSSHHHHHHHHHHHHHHHHHCC
T ss_pred             ccccCCcCcCCCEEEEEcHHHhhHHhcCCCcchHHhhhc--cCCeEEEEECCcEEEEecCCHHHHHHHHHHHHHHhccCC
Confidence            8999999999999999999999999984 6679999999  999999999999999999999999999999999 99999


Q ss_pred             HHHHHHHHHHHHHHh
Q psy230          206 YEEILNLCESIHIRF  220 (222)
Q Consensus       206 ~~~~~~~~~~~~~~l  220 (222)
                      .+|+++|++++.+.+
T Consensus       159 ~~~~~~~~~~~~~~~  173 (175)
T 2ja9_A          159 TAAFKDIAKRQFKEI  173 (175)
T ss_dssp             GGGHHHHHHHHTTTS
T ss_pred             HHHHHHHHHHHHHHh
Confidence            999999999998765

>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=100.00  E-value=4.5e-52  Score=356.98  Aligned_cols=208  Identities=22%  Similarity=0.234  Sum_probs=148.6

Q ss_pred             CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEecC-cEEEEEccccccCCCCCCEEEEEEEEEecceEEEEECCC
Q psy230            1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKP-FTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSH   79 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~~-~~v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~   79 (222)
                      +|||.|+..   +|.+|+|||.+++.|+||++|.+..+++ +.+||+|.+++|.|++||+|+|+|+++.++.|+|||+++
T Consensus        13 ~PGd~l~~~---~~~~G~Gty~~~~~I~Asv~G~v~~~~~~~~vsV~p~~~~y~p~~GDiV~G~V~~v~~~~~~V~I~~~   89 (235)
T 2z0s_A           13 VPGEPLPEE---VEASPPYVIDYKGVKRATVVGLLREKGDGGGRAFVKLKEIYVPQAGDVVIGLIQSVGIMNWFVDINSP   89 (235)
T ss_dssp             --------------------------------------------------CCCCCCTTCCEEEEEEEECSSEEEEECSSS
T ss_pred             eCCCCcccC---ceEcCCCEEEECCEEEEEEeEEEEEeCCccEEEEEeCCCccCCCCCCEEEEEEEEEeCCeEEEEeCCC
Confidence            699999853   5999999999999999999999987753 378999999999999999999999999999999999999


Q ss_pred             CCeeeecccccc-----ccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCcccCCceEEEechhhhhhccC
Q psy230           80 DPAVLSYLAFEG-----ATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLN  154 (222)
Q Consensus        80 ~~a~L~~~~f~g-----atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~l~~v~~~~~~rl~~  154 (222)
                      +.|+||.++|.+     ..++++++|++||+|+|||+++++++++.|||+.     ++||+|++|++++++|.+++|+++
T Consensus        90 ~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~~~~i~LS~k~-----~~lG~l~gG~vv~vs~~~~~rl~~  164 (235)
T 2z0s_A           90 YVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQG-----EGLGRIVRGKIVEISPAKVPRVIG  164 (235)
T ss_dssp             SCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCS-----SSCEECCSSEEEECCGGGSGGGTC
T ss_pred             eEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECCCCcEEEEEec-----ccCccccCCEEEEECHHHhHHHhc
Confidence            999999999875     4578899999999999999999988899999955     899999999999999999999999


Q ss_pred             CChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHh
Q psy230          155 PKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRF  220 (222)
Q Consensus       155 ~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~~l  220 (222)
                      ++++||++|++  +++||||+|+||+|||+++++++++++++||++||..  ++..++.+++.++|
T Consensus       165 ~~~~~l~~l~~--~~~~~i~vG~NG~IWi~~~~~~~~~~~~~ai~~~e~~--~~~~~l~~~v~~~l  226 (235)
T 2z0s_A          165 RKMSMLKTLEE--KTECKIFVARNGRIHLECPNEDLEAIAVMAIKIIDEE--AYTSGLTKRIIKFI  226 (235)
T ss_dssp             GGGHHHHHHHH--HHCCEEEEETTTEEEEECSCHHHHHHHHHHHHHHHHC--SCCTTCHHHHHHHH
T ss_pred             CcchHHHHhcc--cCCeEEEEeCCCEEEEecCCHHHHHHHHHHHHHHHhh--hhhhhHHHHHHHHH
Confidence            99999999998  8999999999999999999999999999999999983  44555555555544

>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=100.00  E-value=1.1e-51  Score=357.52  Aligned_cols=208  Identities=17%  Similarity=0.228  Sum_probs=175.8

Q ss_pred             CCCCeecCCCCCCeeeCC--CeEEeCCEEEEEEeeEEEEecCcEEEEEcccc-ccCCCCCCEEEEEEEEEecceEEEEEC
Q psy230            1 MAGDTLSLNAEPRLILGP--GLRRESSAILVSQSGILRHAKPFTYYVDYIQR-RYVPTRGDLVIGVVTSRVGDNYRVDIG   77 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~--G~y~~~~~i~as~~G~l~~~~~~~v~V~~~~~-~Y~P~vGDiVIG~V~~v~~~~~~VdI~   77 (222)
                      +|||.|+..   +|.+|+  |||.++++|+||++|.++.++ +.++|.|.++ +|.|++||+|+|+|+++.++.|+|||+
T Consensus        20 ~PGd~l~~~---~~~~G~~~Gty~~~g~i~as~~G~v~~~~-~~v~V~p~~~~~y~p~~GDiV~G~V~~v~~~ga~VdI~   95 (251)
T 2je6_I           20 VPGELLAEG---EFQIPWSPYILKINSKYYSTVVGLFDVKD-TQFEVIPLEGSFYYPKINDIVIGLVEDVEIYGWVVDIK   95 (251)
T ss_dssp             CTTCEEEEE---CCCCCCCTTEEEETTEEEECSSEEEEEET-TEEEEEESCCSCCCCCTTCEEEEEEEEECSSEEEEECS
T ss_pred             cCCCCCccC---CeeeCCCCCEEEECCEEEEEEEEEEEEeC-CEEEEEECCCcccCCCCCCEEEEEEEEEeCceEEEEcC
Confidence            699999853   589999  999999999999999999885 7889999887 899999999999999999999999999


Q ss_pred             CCCCeeeecccccc-cc---ccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCcccCCceEEEechhhhhhcc
Q psy230           78 SHDPAVLSYLAFEG-AT---KKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLL  153 (222)
Q Consensus        78 ~~~~a~L~~~~f~g-at---k~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~l~~v~~~~~~rl~  153 (222)
                      +++.|+||.++|.+ ..   ++++++|++||+|+|||+++++++++.|||++     .+||+|++|+++++++.+++|++
T Consensus        96 ~~~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~~~~~i~LS~r~-----~~lG~L~~G~v~~vs~~~v~rl~  170 (251)
T 2je6_I           96 APYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKG-----KDLGRVSNGIVIDIMPVKVPRVI  170 (251)
T ss_dssp             SSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETTEEEEEECCS-----TTCEECCSSCEEECCGGGHHHHH
T ss_pred             CCeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECCCCcEEEEEcc-----ccCCcccCCEEEEECHHHhHHHh
Confidence            99999999998874 23   67888999999999999999998999999965     89999999999999999999999


Q ss_pred             CCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHHHHhc
Q psy230          154 NPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIRFL  221 (222)
Q Consensus       154 ~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~~l~  221 (222)
                      +++++||++|++  +++||||||+||||||+++++++++++++||++||.  ++|..++.+++.++|.
T Consensus       171 ~~~~~~l~~l~~--~~~~ei~vG~NG~IWi~~~~~~~~~~~~~aI~~~e~--~~~~~~l~~~v~~~l~  234 (251)
T 2je6_I          171 GKNKSMYETLTS--KSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIEN--ESHIKGLTDRIKQFIE  234 (251)
T ss_dssp             CGGGHHHHHHHT--TC---CEECTTSEEEC-----CTTCCTHHHHTTTTT--TTTCC-----------
T ss_pred             cCcchHHHHhcc--cCCeEEEEECCcEEEEeCCCHHHHHHHHHHHHHHHh--hhhhhhHHHHHHHHHH
Confidence            999999999999  999999999999999999999999999999999998  4446666666666553

>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=100.00  E-value=1.7e-44  Score=320.12  Aligned_cols=202  Identities=20%  Similarity=0.316  Sum_probs=163.7

Q ss_pred             CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEecCcEEEEEccccccCCCCCCEEEEEEEEEecceEEEEECCCC
Q psy230            1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHD   80 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~~~~v~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~   80 (222)
                      +|||.|+..  ++|.+|+|||.++++|+||++|.++.+ ++++||+|.+++|.|++||+|+|+|+++++++|+|||+++.
T Consensus        43 lPGd~L~~~--~~~~~G~Gty~~~g~I~Asv~G~v~~~-~~~vsV~p~~~rY~P~vGDvViG~Vt~V~~~~a~VdI~s~~  119 (308)
T 2nn6_H           43 VPGDTITTD--TGFMRGHGTYMGEEKLIASVAGSVERV-NKLICVKALKTRYIGEVGDIVVGRITEVQQKRWKVETNSRL  119 (308)
T ss_dssp             CTTCBCCCC--TTCCBCTTEEECSSSEEECSSEEEEEE-TTEEEEEESSCCCCCCSSBCCCEEEEEEETTEEEEECSSSS
T ss_pred             eCCCCCCCC--CCEeecCCeEEECCEEEEEEEEEEEec-CCEEEEeeCCCccCCCCCCEEEEEEEEEeCceEEEEECCCc
Confidence            699999965  479999999999999999999999877 58999999999999999999999999999999999999999


Q ss_pred             Ceeeeccc--cccccc---------cCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCcccCCceEEEechhhh
Q psy230           81 PAVLSYLA--FEGATK---------KNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLC  149 (222)
Q Consensus        81 ~a~L~~~~--f~gatk---------~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~l~~v~~~~~  149 (222)
                      .+.++.++  |+++++         +|+++|++||+|+|||+++++++++.|||++     ++||+|++|+++.|++.++
T Consensus       120 ~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArVisv~~~~~i~LStr~-----~~LGkL~~G~v~~vs~~lv  194 (308)
T 2nn6_H          120 DSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRS-----LKYGKLGQGVLVQVSPSLV  194 (308)
T ss_dssp             CEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEETTTEEEEECCS-----STTCEECSSCEEECCTTSC
T ss_pred             CCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCCCCCEEEEecC-----cCCcccCCeEEEEEChhhe
Confidence            99888754  677653         4669999999999999999988999999965     9999999999999999999


Q ss_pred             hhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHHHH
Q psy230          150 RKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHIR  219 (222)
Q Consensus       150 ~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~~  219 (222)
                      |++..    ++..+    .++|||++|+||||||++...+......+...+++.++.++. ..+.|+.+.
T Consensus       195 ~r~~~----~l~~l----~~g~eI~vG~NG~IWi~~~~~~~~~~~~~~~~~~~~~~~~~r-~~i~r~~n~  255 (308)
T 2nn6_H          195 KRQKT----HFHDL----PCGASVILGNNGFIWIYPTPEHKEEEAGGFIANLEPVSLADR-EVISRLRNC  255 (308)
T ss_dssp             CCSTT----CSCCC----BTTBEEEEETTTEEEEECCCCC------CCGGGSSCCCHHHH-HHHHHHHHH
T ss_pred             echhh----eEecC----CCCcEEEEeCCCEEEEcCCcchhhhhcccccccCCcCCHHHH-HHHHHHHHH
Confidence            98754    45445    579999999999999998754433333345566666666555 445555443

>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=1.2e-27  Score=197.44  Aligned_cols=132  Identities=17%  Similarity=0.248  Sum_probs=117.5

Q ss_pred             CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEecCcEEEEEcccc-ccCCCCCCEEEEEEEEEecceEEEEECC-
Q psy230            1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQR-RYVPTRGDLVIGVVTSRVGDNYRVDIGS-   78 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~~~~v~V~~~~~-~Y~P~vGDiVIG~V~~v~~~~~~VdI~~-   78 (222)
                      +|||.|+..  ++|.+|+|||.++++|+||++|.++.+ ++++||+|.+. +|.|+ ||+|+|+|+++.+..|+|||++ 
T Consensus         5 ~PGd~l~~~--~~~~~G~Gty~~~~~i~as~~G~v~~~-~~~v~V~~~~~~~y~p~-GdiV~G~V~~V~~~ga~V~I~~v   80 (179)
T 3m7n_A            5 MPGDRIGSA--EEYVKGEGVYEEGGELFAAVAGKLIIK-DRVAKVESISPIPEIVK-GDVVLGRVVDLRNSIALIEVSSK   80 (179)
T ss_dssp             CTTCEEEET--TTSEECTTEEEETTEEEESSSEEEEEE-TTEEEEEESSCCCCCCT-TCEEEEEEEEECSSEEEEEEEEE
T ss_pred             cCCCCCCCC--CCEeccCCEEEeCCEEEEEEEEEEEEe-CCEEEEEECCCCcccCC-CCEEEEEEEEEeCCcEEEEEccc
Confidence            699999976  479999999999999999999999997 48999999855 69999 9999999999999999999998 


Q ss_pred             ---------CCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCccccCcccC------CceEE
Q psy230           79 ---------HDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIMGILN------DGYLL  142 (222)
Q Consensus        79 ---------~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~------~G~l~  142 (222)
                               +..|+||.+++.. ..+++++.|++||+|.|+|++    ..+.||+++     ++||+|.      +..|+
T Consensus        81 ~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~~~GD~V~akVi~----~~i~LS~k~-----~~lGvv~a~~~~~g~~m~  151 (179)
T 3m7n_A           81 KGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIG----DNLRLSTKE-----EEMGVLRALCSNCKTEMV  151 (179)
T ss_dssp             TTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTCCTTCEEEEEEEE----TTTEEECCS-----TTCEEEECBCTTTCCBCE
T ss_pred             cCcccccccCeeEEEEHHHcCcchhhCHhhcCCCCCEEEEEEEC----CeEEEEEec-----CCCCEEEecccccCCceE
Confidence                     8899999988754 457899999999999999998    579999965     9999992      45677


Q ss_pred             Eec
Q psy230          143 HTS  145 (222)
Q Consensus       143 ~v~  145 (222)
                      +++
T Consensus       152 ~~~  154 (179)
T 3m7n_A          152 REG  154 (179)
T ss_dssp             ECS
T ss_pred             ECC
Confidence            766

>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=99.93  E-value=9e-27  Score=196.50  Aligned_cols=142  Identities=15%  Similarity=0.117  Sum_probs=117.7

Q ss_pred             CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEec----CcEEEEEcccc-ccCCCCCCEEEEEEEEEecceEEEE
Q psy230            1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAK----PFTYYVDYIQR-RYVPTRGDLVIGVVTSRVGDNYRVD   75 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~----~~~v~V~~~~~-~Y~P~vGDiVIG~V~~v~~~~~~Vd   75 (222)
                      +|||.|+..  ++|++|+|||.++++|+|+++|.++.+.    .++++|.|.++ +|.|++||+|+|+|+++++..|+||
T Consensus        23 ~PGd~l~~~--~~~~~G~Gty~~~g~I~Asv~G~v~~~~~~~~~~vi~V~p~~~~~y~p~vGDvV~G~V~~v~~~~a~V~  100 (209)
T 2nn6_I           23 IPGERLCNL--EEGSPGSGTYTRHGYIFSSLAGCLMKSSENGALPVVSVVRETESQLLPDVGAIVTCKVSSINSRFAKVH  100 (209)
T ss_dssp             CTTCEEEET--TTCCCSSSCEEETTEEECCSCSCBCCCBCTTSSBC-CBCCSCCCCCCCCTTCEEEEEEEEECSSEEEEE
T ss_pred             cCCCCCCCC--CCeeecCCEEEECCEEEEEEEEEEEEeccCCcccEEEEecCCCCcCCCCCCCEEEEEEEEEECceEEEE
Confidence            699999865  4699999999999999999999987652    25688999876 5999999999999999999999999


Q ss_pred             ECC--------CCCeeeeccccc-cccc--cCCcCCCCCCEEEEEEEecCCCC-eeEEEEecCCCccccCccc-----CC
Q psy230           76 IGS--------HDPAVLSYLAFE-GATK--KNPPKVETGDVVAGKLLTANKDM-ESEMVCVDSRGKEFIMGIL-----ND  138 (222)
Q Consensus        76 I~~--------~~~a~L~~~~f~-gatk--~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~~~~~~~~~G~L-----~~  138 (222)
                      |++        ++.|+||.+++. ...+  +++.+|++||+|+|+|++++++. .+.||++.     .+||++     .+
T Consensus       101 I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akVisi~~~~~~i~LS~k~-----~~lGVv~A~c~~g  175 (209)
T 2nn6_I          101 ILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLLTTAE-----NELGVVVAHSESG  175 (209)
T ss_dssp             EEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEEEECCS-----SSCEECCCBCSSS
T ss_pred             ECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEEEEEeCCCCeEEEEEec-----CCCcEEEEEcCCC
Confidence            963        456777766553 2334  78899999999999999998765 59999965     999999     35


Q ss_pred             ceEEEechhhh
Q psy230          139 GYLLHTSISLC  149 (222)
Q Consensus       139 G~l~~v~~~~~  149 (222)
                      ..|+++++...
T Consensus       176 ~~m~~~~~~~m  186 (209)
T 2nn6_I          176 IQMVPISWCEM  186 (209)
T ss_dssp             CBCEEEETTEE
T ss_pred             CEEEEccCCEE
Confidence            78888887544

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

Probab=98.67  E-value=1.3e-07  Score=67.19  Aligned_cols=70  Identities=13%  Similarity=0.139  Sum_probs=60.4

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD  125 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  125 (222)
                      .|++||+|.|+|+++.+..+.|+|+....|.+|.+.+...  +. ..|++||.|.|+|.+++.+ +.+.||.+.
T Consensus         2 ~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gllh~sel~~~--~~-~~~~~Gd~V~v~V~~vd~~~~~i~lsl~~   72 (80)
T 2k52_A            2 DVEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISL--RL-ENLNVGDEIIVQAIDVRPEKREIDFKYIP   72 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGGCSSC--CG-GGCCTTCEEEEEEEEEETTTTEEEEEECS
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHCCcc--cc-eeeCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            4789999999999999999999999889999998876421  11 5799999999999999876 789999865

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

Probab=98.57  E-value=2.8e-07  Score=69.95  Aligned_cols=83  Identities=14%  Similarity=0.040  Sum_probs=66.9

Q ss_pred             EEEEcccc-ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc--ccccCCcCCCCCCEEEEEEEecCC-CCe
Q psy230           43 YYVDYIQR-RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG--ATKKNPPKVETGDVVAGKLLTANK-DME  118 (222)
Q Consensus        43 v~V~~~~~-~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~-~~~  118 (222)
                      ..+.|... .+.|++||+|.|+|+++.+..+.|+|+....|.+|.+.+..  ..++.+..|++||.|.++|.+++. ...
T Consensus        16 ~~~~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~r   95 (115)
T 2khi_A           16 PRGSHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERRR   95 (115)
T ss_dssp             -----CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEETTTTE
T ss_pred             cccCCHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEECCCCE
Confidence            34556544 47899999999999999999999999988999999987643  445677899999999999999986 467


Q ss_pred             eEEEEec
Q psy230          119 SEMVCVD  125 (222)
Q Consensus       119 ~~Ls~~~  125 (222)
                      +.||++.
T Consensus        96 I~lslk~  102 (115)
T 2khi_A           96 ISLGLKQ  102 (115)
T ss_dssp             EEECCCC
T ss_pred             EEEEEEe
Confidence            8888864

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

Probab=98.54  E-value=2.2e-07  Score=69.78  Aligned_cols=75  Identities=15%  Similarity=0.160  Sum_probs=64.5

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCC-eeEEEEec
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDM-ESEMVCVD  125 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~  125 (222)
                      .+.+++||+|.|+|+++.+..+.|+|+....|+||.+.+. ...++.+..|++||.|.|+|.+++.+. .+.||++.
T Consensus        26 ~~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~vd~~~~ki~LS~k~  102 (109)
T 2khj_A           26 VALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVDRKNRAISLSVRA  102 (109)
T ss_dssp             TTTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEEETTTTEEEEETTS
T ss_pred             hhcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCcccccChhhccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            3578999999999999999999999998899999988764 345566778999999999999998764 68888754

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

Probab=98.49  E-value=4.1e-07  Score=70.63  Aligned_cols=73  Identities=16%  Similarity=0.144  Sum_probs=64.7

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      .+++||+|.|+|+++.+..+.|+|.....|++|.+.+. +...+.+..|++||.|.|+|++++. ...+.||++.
T Consensus         4 ~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~kI~LSlk~   78 (130)
T 2k4k_A            4 KFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDEEKGKISLSIRA   78 (130)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEESHH
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCcccccCccccCCCCCEEEEEEEEEeCCCCEEEEEEee
Confidence            47899999999999999999999988899999998764 4556677899999999999999987 6789999875

>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=98.45  E-value=2.7e-07  Score=70.66  Aligned_cols=75  Identities=15%  Similarity=0.127  Sum_probs=63.1

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECC-CCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC---CeeEEEEec
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGS-HDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD---MESEMVCVD  125 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~---~~~~Ls~~~  125 (222)
                      .+.|++||+|.|+|+++.+..++|+|.. ...|+||++.+. ...++....|++||.|.++|++++..   ..+.||++.
T Consensus        17 ~~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~~~~~~~~~~~Gd~V~VkV~~vd~~~~~~~i~LSlk~   96 (119)
T 2cqo_A           17 ENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKV   96 (119)
T ss_dssp             CCSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSCCSCHHHHCCTTCEEEEEEEEEEECSSCEEEEEESTT
T ss_pred             hcccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcccccChhhcCCCCCEEEEEEEEEeccccCceEEEEEee
Confidence            3789999999999999999999999965 379999998764 34455667899999999999999753   478899865

>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=98.43  E-value=4.4e-07  Score=67.61  Aligned_cols=74  Identities=22%  Similarity=0.207  Sum_probs=62.8

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECC---CCCeeeeccccc--cccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGS---HDPAVLSYLAFE--GATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD  125 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~---~~~a~L~~~~f~--gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  125 (222)
                      ...|++||++.|+|+++.+..++|+|..   ...|.+|.+.+.  ...++.+..|++||.|.++|.+++. ..+.||++.
T Consensus         7 ~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~~~~~~~~~~~~Gd~V~VkV~~vd~-~~i~LSlk~   85 (103)
T 2eqs_A            7 GEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTG-TKTSLSMKD   85 (103)
T ss_dssp             CSSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSSCCCCHHHHCCTTCEEEEEEEEEET-TEEEEESTT
T ss_pred             cccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCcccCCcccEeCCCCEEEEEEEEEEC-CeeEEEEee
Confidence            3568999999999999999999999996   689999998873  2344556779999999999999987 578888865

>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=98.40  E-value=1e-06  Score=72.10  Aligned_cols=80  Identities=19%  Similarity=0.234  Sum_probs=66.0

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-ccc-----------ccCCcCCCCCCEEEEEEEecCCC--
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GAT-----------KKNPPKVETGDVVAGKLLTANKD--  116 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gat-----------k~~r~~l~~GDlV~ArV~~~~~~--  116 (222)
                      .|.|.+|+++.|+|+++.+..+.|+|+. ..+++|.+.+. ...           ++....|++||.|.+||.+++..  
T Consensus        76 ~~~~~~Gev~~G~V~~v~~~G~fV~l~~-~eglvhis~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~  154 (187)
T 1go3_E           76 VYIPEMYELIEGEVVDVVEFGSFVRLGP-LDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAE  154 (187)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECSS-SEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC-
T ss_pred             EEccCCCCEEEEEEEEEeCcEEEEEEcC-ccEEEEhHHhCCCcceECCccceEEecCCCeEEcCCCEEEEEEEEEEcccC
Confidence            3789999999999999999999999975 89999987653 222           25678899999999999999753  


Q ss_pred             ----CeeEEEEecCCCccccCccc
Q psy230          117 ----MESEMVCVDSRGKEFIMGIL  136 (222)
Q Consensus       117 ----~~~~Ls~~~~~~~~~~~G~L  136 (222)
                          +.+.||+++     ++||++
T Consensus       155 ~p~~~~I~lS~k~-----~~LG~~  173 (187)
T 1go3_E          155 RKRGSKIALTMRQ-----PYLGKL  173 (187)
T ss_dssp             ----CEEEEECCS-----TTCEEH
T ss_pred             CCCccEEEEEEcC-----CCCCcH
Confidence                367888855     888876

>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=98.39  E-value=8.5e-07  Score=72.81  Aligned_cols=75  Identities=11%  Similarity=0.038  Sum_probs=56.5

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEE--CCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDI--GSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD  125 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI--~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  125 (222)
                      .+.|++||+|.|+|+++.+-.++|+|  .....|.+|++.+. +..++.+..|++||.|.++|++++.. ..+.||++.
T Consensus        10 ~~~p~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~~~v~~~~~~~~vGd~V~VkVl~vD~~~~rI~LSlk~   88 (182)
T 1kl9_A           10 HKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRR   88 (182)
T ss_dssp             SSSCCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEESTT
T ss_pred             ccCCCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            35689999999999999999999999  46689999998874 45677889999999999999999864 578898864

>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=98.38  E-value=1.4e-06  Score=71.04  Aligned_cols=75  Identities=11%  Similarity=0.052  Sum_probs=60.3

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEC--CCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIG--SHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD  125 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~--~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  125 (222)
                      .+.|++||+|.|+|+++.+-.+.|+|.  ....|.+|++.+. +..++.+..|++||.|.++|++++.. ..+.||++.
T Consensus        10 ~~~p~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~v~~~~~~~~vGd~V~vkVl~vd~~~~~I~LSlk~   88 (175)
T 2a19_A           10 NKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRR   88 (175)
T ss_dssp             SSSCCTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC--------CCCCCCCTTSEEEEEEEEEETTTTEEEEESTT
T ss_pred             hcCCCCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCcccCCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEe
Confidence            356899999999999999999999994  5689999998874 45677888999999999999999764 578899864

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

Probab=98.31  E-value=2e-06  Score=74.80  Aligned_cols=79  Identities=11%  Similarity=0.143  Sum_probs=65.0

Q ss_pred             ccccccCCCCCCEEEEEEEEEecceEEEEEC--CCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCC-CCeeEEE
Q psy230           47 YIQRRYVPTRGDLVIGVVTSRVGDNYRVDIG--SHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANK-DMESEMV  122 (222)
Q Consensus        47 ~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~--~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls  122 (222)
                      |+...+.|++||+|.|+|+++.+..+.|+|.  ....|.+|.+.+. +..+..+..|++||.|.++|.+++. .+.+.||
T Consensus         2 ~~~~~~~p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~LS   81 (275)
T 3aev_A            2 PRKAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLS   81 (275)
T ss_dssp             -----CCCCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEE
T ss_pred             CcccccCCCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEEE
Confidence            3345578999999999999999999999998  4689999998874 4456677889999999999999986 5789999


Q ss_pred             Eec
Q psy230          123 CVD  125 (222)
Q Consensus       123 ~~~  125 (222)
                      ++.
T Consensus        82 lk~   84 (275)
T 3aev_A           82 LRR   84 (275)
T ss_dssp             STT
T ss_pred             Eee
Confidence            865

>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=98.20  E-value=5.6e-06  Score=62.98  Aligned_cols=74  Identities=22%  Similarity=0.222  Sum_probs=56.8

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECC-CCCeeeeccccccc--cccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGS-HDPAVLSYLAFEGA--TKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD  125 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~ga--tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  125 (222)
                      ..+++||+|.|+|+++....+.|||+. ...++++.......  ..+.+..|++||.|.++|.+++.. ..+.|+++.
T Consensus        17 ~~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~i~Lslk~   94 (119)
T 1wi5_A           17 EALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGH   94 (119)
T ss_dssp             TTCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECCC
T ss_pred             hcCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecccccccccCccCEeCCCCEEEEEEEEEeCCCCEEEEEEch
Confidence            457999999999999999999999983 34455543322211  224577899999999999999864 578999865

>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=98.14  E-value=8.6e-06  Score=71.92  Aligned_cols=74  Identities=12%  Similarity=0.048  Sum_probs=64.6

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEC--CCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIG--SHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~--~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      ..|++||+|.|+|+++.+..++|+|.  ....|.+|++.+. +..++.+..|++||.|.++|+++++ ...+.||.+.
T Consensus         9 ~~~~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~~~i~~~~~~~kvGd~V~VkVl~vD~~~~rI~LSlK~   86 (308)
T 1q8k_A            9 KFPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYIDLSKRR   86 (308)
T ss_dssp             CCCSSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEEETTTTEEEEECSS
T ss_pred             cCCCCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCcccccCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence            35789999999999999999999998  6789999998875 4557788899999999999999986 4678999875

>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=98.10  E-value=1.7e-05  Score=64.33  Aligned_cols=80  Identities=18%  Similarity=0.252  Sum_probs=65.2

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc------------cccCCcCCCCCCEEEEEEEecCCC--
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA------------TKKNPPKVETGDVVAGKLLTANKD--  116 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~--  116 (222)
                      .+.|.+|+++-|+|++++...+.|+++ +..+.+|.+.+...            .++....|+.||-|+.||.+++.+  
T Consensus        76 v~~p~~Gev~~G~V~~v~~~G~fv~l~-~~~glvh~s~l~~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~~v~~~~~  154 (180)
T 4ayb_E           76 TYVPVVQEVVEGEVLQVDNYGVFVNLG-PMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTVT  154 (180)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSCSSCEEECSSSCCEEETTTCCCCCTTCEEEEEEEEECC---
T ss_pred             eeeccCCCEEEEEEeeeccceEEEEEC-CccceEEeeecCCCccccchhcceEEEeccCeEECCCCEEEEEEEEEeCCCC
Confidence            578999999999999999999999997 57899998765421            146677899999999999999753  


Q ss_pred             ---CeeEEEEecCCCccccCccc
Q psy230          117 ---MESEMVCVDSRGKEFIMGIL  136 (222)
Q Consensus       117 ---~~~~Ls~~~~~~~~~~~G~L  136 (222)
                         ..+.||+++     ++||.+
T Consensus       155 ~~~~rI~ls~k~-----~gLG~~  172 (180)
T 4ayb_E          155 GRLPRIALTMRQ-----PYLGKL  172 (180)
T ss_dssp             ----CEEEECCS-----TTCEEH
T ss_pred             cccCcEEEEcCC-----CCCCCC
Confidence               246788754     899986

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

Probab=98.08  E-value=6.5e-06  Score=59.65  Aligned_cols=71  Identities=17%  Similarity=0.171  Sum_probs=59.5

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECC--CCCeeeecc-ccc-cccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGS--HDPAVLSYL-AFE-GATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~-~f~-gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      .|++|+++-|+|+ +.+-.+.|+|..  ...|.+|++ .+. +..+..+..+ +||.|.++|++++. .+.+.||++.
T Consensus         8 ~~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~~~~~~~~~~-~Gd~V~VkV~~vd~~~~kI~lslk~   83 (88)
T 1luz_A            8 LPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDRYVEYRDKL-VGKTVKVKVIRVDYTKGYIDVNYKR   83 (88)
T ss_dssp             CCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHHHHHHHHHH-TTCEEEEEEEEEETTTTEEEEEEEE
T ss_pred             CCCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCcccccCHhHEe-CCCEEEEEEEEEECCCCEEEEEEee
Confidence            4899999999999 999999999974  479999998 774 3344555677 99999999999986 4678999865

>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=98.00  E-value=4.1e-06  Score=72.52  Aligned_cols=77  Identities=14%  Similarity=0.183  Sum_probs=65.9

Q ss_pred             ccccCCCCCCEEEEEEEEEecceEEEEEC--CCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEe
Q psy230           49 QRRYVPTRGDLVIGVVTSRVGDNYRVDIG--SHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANK-DMESEMVCV  124 (222)
Q Consensus        49 ~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~--~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~  124 (222)
                      ...+.|++||+|.|+|+++.+..++|+|+  ....|.+|.+.+. +..++.+..|++||.|.++|++++. .+.+.||.+
T Consensus         4 ~~~~~~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~~~v~~~~~~~~vGd~V~VkVi~vd~~~g~I~LSlk   83 (266)
T 3cw2_C            4 SRSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLK   83 (266)
T ss_dssp             CSSSSCCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSCSSCCCHHHHSCTTCEEEEEECCCCSSSCCCBEEST
T ss_pred             cccccCCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCcccccCHHHhCcCCCEEEEEEEEEeCCCCEEEEEEE
Confidence            34578999999999999999999999997  6789999998874 3455666789999999999999986 567889986


Q ss_pred             c
Q psy230          125 D  125 (222)
Q Consensus       125 ~  125 (222)
                      .
T Consensus        84 ~   84 (266)
T 3cw2_C           84 K   84 (266)
T ss_dssp             T
T ss_pred             e
Confidence            5

>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=97.98  E-value=1.5e-05  Score=64.32  Aligned_cols=83  Identities=16%  Similarity=0.233  Sum_probs=61.9

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc-----cc--------cCCcCCCCCCEEEEEEEecCCCC
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA-----TK--------KNPPKVETGDVVAGKLLTANKDM  117 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-----tk--------~~r~~l~~GDlV~ArV~~~~~~~  117 (222)
                      .+.|.+|+++-|+|+++++..+.|+|+ +..+.+|.+.++..     ..        +.+..|++||.|..||.+++.+.
T Consensus        76 ~~~~~~Gev~~G~V~~v~~fG~fV~l~-~~~glvhis~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~  154 (172)
T 2c35_B           76 VFRPFKGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDK  154 (172)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEET
T ss_pred             EeeCCCCCEEEEEEEEEeCCEEEEEEC-CEEEEEEHHHCCCCcEECCCCCccEEEeCCCCEEECCCCEEEEEEEEEEcCC
Confidence            578999999999999999999999996 55699999865431     11        23567999999999999987542


Q ss_pred             eeEEEEecCCCccccCccc
Q psy230          118 ESEMVCVDSRGKEFIMGIL  136 (222)
Q Consensus       118 ~~~Ls~~~~~~~~~~~G~L  136 (222)
                      .. .+.+. +-+.++||++
T Consensus       155 ~~-~~~ig-sm~~~~LG~~  171 (172)
T 2c35_B          155 ND-IFAIG-SLMDDYLGLV  171 (172)
T ss_dssp             TE-EEEEE-ECCSTTCEEC
T ss_pred             CC-cEEEE-EecCCCCCCC
Confidence            21 12222 2255889976

>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=97.75  E-value=8.3e-05  Score=59.92  Aligned_cols=83  Identities=16%  Similarity=0.228  Sum_probs=61.9

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccccc----ccC-------CcCCCCCCEEEEEEEecCCCCee
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGAT----KKN-------PPKVETGDVVAGKLLTANKDMES  119 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gat----k~~-------r~~l~~GDlV~ArV~~~~~~~~~  119 (222)
                      .+.|.+|+++-|+|++++.-.++|+++. .++.+|.+.++...    .++       +..+++||.|..||.+++.+.. 
T Consensus        78 ~~~~~~Gev~~G~V~~v~~fG~FV~l~~-~dglvhis~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~-  155 (171)
T 1y14_B           78 VFKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVS-  155 (171)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETT-
T ss_pred             EccCCCCCEEEEEEEEEecCEEEEEecC-eEEEEEHHHCCCCceECcccCceEEeccceEECCCCEEEEEEEEEEcCCC-
Confidence            3679999999999999999999999987 89999998765321    111       2569999999999999875432 


Q ss_pred             EEEEecCCCccccCccc
Q psy230          120 EMVCVDSRGKEFIMGIL  136 (222)
Q Consensus       120 ~Ls~~~~~~~~~~~G~L  136 (222)
                      ....+. +-+.++||.+
T Consensus       156 ~~~~ig-sm~~~~LG~~  171 (171)
T 1y14_B          156 SIHAIG-SIKEDYLGAI  171 (171)
T ss_dssp             EEEEEE-ECCSTTCEEC
T ss_pred             CcEEEE-EcCCCCCCCC
Confidence            123333 3366888864

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

Probab=97.67  E-value=3.4e-05  Score=62.39  Aligned_cols=83  Identities=23%  Similarity=0.291  Sum_probs=64.3

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-----------ccccCCcCCCCCCEEEEEEEecCCCCee
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-----------ATKKNPPKVETGDVVAGKLLTANKDMES  119 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-----------atk~~r~~l~~GDlV~ArV~~~~~~~~~  119 (222)
                      .+.|.+|+++-|+|+++++..+.|+++. ..+.+|.+..+.           ..++....+++||.|.+||.+++.+.. 
T Consensus        79 vf~p~~Gev~~G~V~~v~~fG~FV~l~~-~~glVh~s~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~vd~~~~-  156 (172)
T 3h0g_G           79 LWRPFRGEVVDAIVTTVNKMGFFANIGP-LNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRTDAT-  156 (172)
T ss_dssp             EECCCTTCEEECCCCEEETTEEECCBTT-BCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEEEEESSS-
T ss_pred             eeccCCCCEEEEEEEEEEcceEEEEeCC-eEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEEEECCCC-
Confidence            4789999999999999999999999975 569999876542           123456789999999999999875431 


Q ss_pred             EEEEecCCCccccCccc
Q psy230          120 EMVCVDSRGKEFIMGIL  136 (222)
Q Consensus       120 ~Ls~~~~~~~~~~~G~L  136 (222)
                      ...++. +-|.++||+|
T Consensus       157 ~~~~Ig-tm~~~~LG~~  172 (172)
T 3h0g_G          157 EIFAIA-TMKEDYLGVL  172 (172)
T ss_dssp             CEEEEE-ECCSTTCEEC
T ss_pred             CceEEE-EcCCCCCCCC
Confidence            223443 4467899986

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

Probab=97.47  E-value=0.002  Score=53.32  Aligned_cols=64  Identities=13%  Similarity=0.185  Sum_probs=50.6

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccc-ccc-------------c------ccCCcCCCCCCEEEEEE
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAF-EGA-------------T------KKNPPKVETGDVVAGKL  110 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f-~ga-------------t------k~~r~~l~~GDlV~ArV  110 (222)
                      -+.|.+|.++-|+|++++.....|+++ +..++++.+.. +..             .      ++.+..++.||.|+.||
T Consensus        76 ~f~p~~GEv~~G~Vs~vt~~GifV~lg-~~eglv~~~~l~~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~VrvrV  154 (203)
T 3ayh_B           76 IFRPFRGEVMLGKIKSCSEEGIRVTIS-FFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQI  154 (203)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECS-SCCCEEEEGGGBCTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEEEE
T ss_pred             EEccCCCCEEEEEEEEEeccEEEEEEe-CceEEEEcHHhCCCCceECccCceEEeecccccccccCCcEEcCCCEEEEEE
Confidence            478999999999999999999999995 66777776543 110             0      34456799999999999


Q ss_pred             EecCC
Q psy230          111 LTANK  115 (222)
Q Consensus       111 ~~~~~  115 (222)
                      .+++-
T Consensus       155 ~~v~~  159 (203)
T 3ayh_B          155 ESEDF  159 (203)
T ss_dssp             EEEEE
T ss_pred             EEEEc
Confidence            98753

>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=97.46  E-value=0.00031  Score=58.89  Aligned_cols=84  Identities=15%  Similarity=0.229  Sum_probs=63.2

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccccc----ccC-------CcCCCCCCEEEEEEEecCCCCee
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGAT----KKN-------PPKVETGDVVAGKLLTANKDMES  119 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gat----k~~-------r~~l~~GDlV~ArV~~~~~~~~~  119 (222)
                      .+.|.+|+++-|+|++++.-.+.|+|+. .++.+|.+..+...    .+.       +..+++||.|..||.+++.+.. 
T Consensus        78 ~~~p~vGev~~G~V~~vt~fG~FVelg~-~dGlVhiS~l~d~~~~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~vd~~~~-  155 (215)
T 2b8k_G           78 VFKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVS-  155 (215)
T ss_dssp             EECCCTTEEEEEEEEEEETTEEEEECTT-SEEEEEGGGSCSSCCCBSSCSSCEEECSSCEEETTCEEEEEEEEEEEETT-
T ss_pred             eeccCCCCEEEEEEEEEecceEEEEecC-cEEEEEHHHCCccceeccccccceeeccccEECCCCEEEEEEEEEEcCCC-
Confidence            4679999999999999999999999987 89999998765321    111       2569999999999999875421 


Q ss_pred             EEEEecCCCccccCcccC
Q psy230          120 EMVCVDSRGKEFIMGILN  137 (222)
Q Consensus       120 ~Ls~~~~~~~~~~~G~L~  137 (222)
                      .+..+. +-+.+++|.+.
T Consensus       156 ~i~~Ig-Smk~~~LG~~~  172 (215)
T 2b8k_G          156 SIHAIG-SIKEDYLGAIS  172 (215)
T ss_dssp             EEEEEE-ECCSTTCEEC-
T ss_pred             ccEEEE-EcCCCCCCCcc
Confidence            123333 33668999884

>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=97.26  E-value=0.00026  Score=52.69  Aligned_cols=75  Identities=8%  Similarity=-0.012  Sum_probs=59.4

Q ss_pred             ceEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC----eEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHH
Q psy230          139 GYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG----KIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCE  214 (222)
Q Consensus       139 G~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG----~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~  214 (222)
                      -..+.|++.++++++|+++..++.|.+  .+++.|-+..+|    .|||.+.+ .   .+..|...++.+..+......+
T Consensus        18 ~~~i~Ip~~~ig~IIG~gG~~Ir~I~e--etg~~I~I~~~g~~~~~V~I~G~~-e---~v~~A~~~I~~i~~e~e~~~~d   91 (104)
T 2ctk_A           18 TIEVEVPFDLHRYVIGQKGSGIRKMMD--EFEVNIHVPAPELQSDIIAITGLA-A---NLDRAKAGLLERVKELQAEQED   91 (104)
T ss_dssp             EEEEECCHHHHHHHHCSSSHHHHHHHH--HTCCEEECCCTTTTCCEEEEEECH-H---HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEChHHccceeCCCchHHHHHHH--HHCCEEEecCCCCCcceEEEEcCH-H---HHHHHHHHHHHHHhhHHHhHHH
Confidence            456899999999999999999999999  999999999999    99999974 3   4566666666655555555556


Q ss_pred             HHHHH
Q psy230          215 SIHIR  219 (222)
Q Consensus       215 ~~~~~  219 (222)
                      +.++.
T Consensus        92 ~~~~~   96 (104)
T 2ctk_A           92 RALRS   96 (104)
T ss_dssp             HHHCC
T ss_pred             HHhcc
Confidence            55543

>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo sapiens}

Probab=97.19  E-value=0.00051  Score=48.96  Aligned_cols=58  Identities=12%  Similarity=0.141  Sum_probs=49.4

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCe--------EEEeeCCchhHHHHHHHHHH
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGK--------IWIRCESFSDTVRVGNLIMS  200 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~--------iWi~~~~~~~~~~i~~~i~~  200 (222)
                      ..+.|++.++.+++|+++..++.|.+  .+++.|-+..+|.        |||.+ ++.....+..+|..
T Consensus        16 ~~i~Ip~~~ig~IIGkgG~~Ik~I~~--~tga~I~i~~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~~   81 (85)
T 2opv_A           16 QEIMIPAGKAGLVIGKGGETIKQLQE--RAGVKMILIQDGSQNTNVDKPLRIIG-DPYKVQQACEMVMD   81 (85)
T ss_dssp             EEEEECTTTHHHHHTTTTHHHHHHHH--HHTCEEEECSSSCSSTTSCEEEEEEE-CHHHHHHHHHHHHH
T ss_pred             EEEEeChhheeeeECCCCHHHHHHHH--HHCCEEEEcCCCCCCCCCceEEEEEe-CHHHHHHHHHHHHH
Confidence            46889999999999999999999999  9999999999998        99999 66655555555544

>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=97.18  E-value=0.00093  Score=57.16  Aligned_cols=68  Identities=15%  Similarity=0.204  Sum_probs=54.0

Q ss_pred             ccCCCCCCEEEEEEEE----EecceEEEEECC---CCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC---CeeE
Q psy230           51 RYVPTRGDLVIGVVTS----RVGDNYRVDIGS---HDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD---MESE  120 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~----v~~~~~~VdI~~---~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~---~~~~  120 (222)
                      .|..+.||+|.|+|.+    +..+.+.|||+.   ...|+||....     -.+..|++||-|.|-|..+.+.   ..+.
T Consensus         2 ~~~~r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eq-----ip~E~~~~GDrIkayV~~V~~~~~gpqIi   76 (251)
T 2asb_A            2 EFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQ-----VPGESYEHGNRLRCYVVGVTRGAREPLIT   76 (251)
T ss_dssp             --CCCTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGS-----CTTCCCCTTCEEEEEEEEEECCSSSCEEE
T ss_pred             chhhcCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHc-----CCCccCCCCCEEEEEEEEEEcCCCCCEEE
Confidence            4888999999999999    899999999986   47999996542     1356899999999999999765   3455


Q ss_pred             EEE
Q psy230          121 MVC  123 (222)
Q Consensus       121 Ls~  123 (222)
                      ||-
T Consensus        77 LSR   79 (251)
T 2asb_A           77 LSR   79 (251)
T ss_dssp             EES
T ss_pred             EEe
Confidence            553

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

Probab=97.16  E-value=0.0012  Score=57.62  Aligned_cols=64  Identities=8%  Similarity=-0.060  Sum_probs=57.5

Q ss_pred             CCCCEEEEEEEEEecceEEE-EECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           55 TRGDLVIGVVTSRVGDNYRV-DIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~~~~~V-dI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      .+||.|-|+|+++++-.++| +|+..+.|.+|.+...       ..+++||-|.|+|+.+++ +..+.||++.
T Consensus       151 ~~G~~V~g~V~~i~~~G~fV~~i~~g~~Glih~SEl~-------~~l~~Gd~v~~~V~~id~~d~kI~LSlk~  216 (285)
T 3go5_A          151 MQNQNWPAIVYRLKLSGTFVYLPENNMLGFIHPSERY-------AEPRLGQVLDARVIGFREVDRTLNLSLKP  216 (285)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTTTEEEEECGGGCS-------SCCCTTCEEEEEEEEEETTTTEEEEECSC
T ss_pred             CCCCEEEEEEEEEeCCcEEEEEeCCCeEEEEEHHHcc-------ccCCCCCEEEEEEEEEECCCCeEEEEeCh
Confidence            57999999999999999999 9999999999976643       469999999999999998 7889999964

>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=97.15  E-value=0.0014  Score=58.55  Aligned_cols=67  Identities=16%  Similarity=0.278  Sum_probs=54.9

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC-CeeEEEE
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD-MESEMVC  123 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~  123 (222)
                      .|..+.||+|-|+|.++..+.+.||++ -..|+||.+.+.     .+..|++||-|.|.|.++.++ ..+.|..
T Consensus       129 e~~~~~GeIV~G~V~ri~~~~v~VDlG-k~EgiLp~sE~i-----p~E~~~vGD~Vkv~V~~V~~~~kg~~I~L  196 (344)
T 1hh2_P          129 KYSELKGTVTTAEVIRVMGEWADIRIG-KLETRLPKKEWI-----PGEEIKAGDLVKVYIIDVVKTTKGPKILV  196 (344)
T ss_dssp             CTTCCTTCEEEEEEEEECSSEEEEEET-TEEEEEEGGGSC-----TTCCCCTTCEEEEEEEEEEEETTEEEEEE
T ss_pred             HHhhcCCCEEEEEEEEEecCcEEEEeC-CeEEEEeHHHcC-----CCcCCCCCCEEEEEEEEEEcCCCCcEEEE
Confidence            477889999999999999999999998 679999987653     245899999999999999754 2344443

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

Probab=97.14  E-value=6.5e-05  Score=73.16  Aligned_cols=74  Identities=15%  Similarity=0.086  Sum_probs=0.0

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD  125 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  125 (222)
                      ..|++|+++.|+|+++.+-.++|+|.....|.+|++.+. ...++....|++||.|.++|.++++.+.+.||.+.
T Consensus       633 ~~~~vG~v~~G~V~~I~~fGaFVel~~g~eGLvHiSels~~rv~~~~d~~kvGD~V~VkVi~iD~~grI~LS~K~  707 (726)
T 4aid_A          633 DEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSMKV  707 (726)
T ss_dssp             ---------------------------------------------------------------------------
T ss_pred             hhhcCCcEEEEEEEEEeccEEEEEECCCcEEEEEHHHcCcccccCccccCCCCCEEEEEEEEECCCCcEEEEEee
Confidence            468999999999999999999999998899999998875 35667788999999999999999877788899865

>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1vih_A

Probab=97.13  E-value=0.00078  Score=46.46  Aligned_cols=58  Identities=12%  Similarity=0.088  Sum_probs=48.8

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC----eEEEeeCCchhHHHHHHHHHHhhc
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG----KIWIRCESFSDTVRVGNLIMSCEL  203 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG----~iWi~~~~~~~~~~i~~~i~~~e~  203 (222)
                      ..+.|++.++++++|+++..++.|.+  .+++.|-+..+|    .|||.+. .+   .+..|...++.
T Consensus         7 ~~i~I~~~~ig~iIG~gG~~I~~I~e--~tg~~I~i~~~g~~~~~V~I~G~-~~---~v~~A~~~I~~   68 (71)
T 1vig_A            7 VEINIDHKFHRHLIGKSGANINRIKD--QYKVSVRIPPDSEKSNLIRIEGD-PQ---GVQQAKRELLE   68 (71)
T ss_dssp             EEEEECSSHHHHHTCSSCCHHHHHHH--HTCCEEECCCCCSSSEEEEEEES-SH---HHHHHHHHHHH
T ss_pred             EEEEECHHHhhhhcCCCCccHHHHHH--HHCCEEEECCCCCcccEEEEEcC-HH---HHHHHHHHHHH
Confidence            45899999999999999999999999  999999999999    9999998 44   34555555443

>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=97.13  E-value=0.00045  Score=50.68  Aligned_cols=60  Identities=12%  Similarity=0.121  Sum_probs=49.5

Q ss_pred             ceEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC-------eEEEeeCCchhHHHHHHHHHHh
Q psy230          139 GYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG-------KIWIRCESFSDTVRVGNLIMSC  201 (222)
Q Consensus       139 G~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG-------~iWi~~~~~~~~~~i~~~i~~~  201 (222)
                      -..+.|++.++++++|+++.+++.|.+  .+++.|-|..+|       .|||.+. ......+...|..+
T Consensus        18 ~~~i~Ip~~~ig~IIGkgG~~Ik~I~~--etg~~I~i~~~g~~~~~~~~V~I~G~-~e~v~~A~~~I~~i   84 (97)
T 2ctl_A           18 KLSVTVDPKYHPKIIGRKGAVITQIRL--EHDVNIQFPDKDDGNQPQDQITITGY-EKNTEAARDAILRI   84 (97)
T ss_dssp             EEEEECCTTTHHHHSCSSSCHHHHHHH--HHTCEEECCCTTTCSSCSSEEEEESC-HHHHHHHHHHHHHH
T ss_pred             eEEEEECHHHhhhcCCCCchhHHHHHH--HHCCEEEecCCCCCCCCccEEEEEeC-HHHHHHHHHHHHHH
Confidence            456899999999999999999999999  999999999999       9999996 54444444444443

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

Probab=97.07  E-value=0.001  Score=68.05  Aligned_cols=74  Identities=15%  Similarity=0.155  Sum_probs=64.5

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc--cccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA--TKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga--tk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      -..++|++|-|+|+++.....+|+|.+...|.+|++.+...  .+..+..|++||.|.|+|++++. ...+.||++.
T Consensus       898 ~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~p~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~  974 (1219)
T 3psi_A          898 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLD  974 (1219)
T ss_dssp             TTSCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSSSTTSCSCSTTTSCTTCEEEEEEEEEEGGGTEEEEECCH
T ss_pred             hhCCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEecH
Confidence            46789999999999999999999999888999999887643  45667889999999999999974 4679999976

>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=96.76  E-value=0.0032  Score=56.61  Aligned_cols=69  Identities=16%  Similarity=0.238  Sum_probs=54.2

Q ss_pred             cccCCCCCCEEEEEEEE----EecceEEEEECC---CCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCC-eeEE
Q psy230           50 RRYVPTRGDLVIGVVTS----RVGDNYRVDIGS---HDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDM-ESEM  121 (222)
Q Consensus        50 ~~Y~P~vGDiVIG~V~~----v~~~~~~VdI~~---~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~-~~~L  121 (222)
                      ..|..++||+|.|+|.+    +....+.|||+.   ...|+||....-     .+..|++||-|.|-|..+.++. .+.|
T Consensus       124 ~ef~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~Eqi-----P~E~~~~GDrVkvyV~~V~~~~kgpqI  198 (366)
T 1k0r_A          124 GEFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV-----PGESYEHGNRLRCYVVGVTRGAREPLI  198 (366)
T ss_dssp             ---CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSC-----TTCCCCTTCEEEEEEEEEECCSSSCEE
T ss_pred             HHHHhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcC-----CCccCCCCCEEEEEEEEEecCCCccEE
Confidence            35889999999999999    999999999986   479999975421     2468999999999999998652 3455


Q ss_pred             EE
Q psy230          122 VC  123 (222)
Q Consensus       122 s~  123 (222)
                      ..
T Consensus       199 ~L  200 (366)
T 1k0r_A          199 TL  200 (366)
T ss_dssp             EE
T ss_pred             EE
Confidence            54

>1x4m_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1

Probab=96.72  E-value=0.0028  Score=45.94  Aligned_cols=61  Identities=11%  Similarity=0.109  Sum_probs=51.2

Q ss_pred             ceEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCe--------EEEeeCCchhHHHHHHHHHHhh
Q psy230          139 GYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGK--------IWIRCESFSDTVRVGNLIMSCE  202 (222)
Q Consensus       139 G~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~--------iWi~~~~~~~~~~i~~~i~~~e  202 (222)
                      =..+.|++.++.+++|+++..++.|.+  .+.+.|-|..+|.        |||.+ +++.+..+...|..+-
T Consensus        16 ~~~i~Ip~~~vG~IIGkgG~~Ik~I~~--~tga~I~I~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i   84 (94)
T 1x4m_A           16 VQEIMIPASKAGLVIGKGGETIKQLQE--RAGVKMVMIQDGPQNTGADKPLRITG-DPYKVQQAKEMVLELI   84 (94)
T ss_dssp             EEEEEECHHHHHHHSCSSSSHHHHHHH--HHTSEEEECCSCCCSSCSCEEEEEEE-CTTTHHHHHHHHHHHH
T ss_pred             EEEEEEChhhcceEECCCCHHHHHHHH--HHCCeEEecCCCCCCCCCceEEEEEe-CHHHHHHHHHHHHHHH
Confidence            356889999999999999999999999  9999999999987        99999 6665666666665543

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}

Probab=96.50  E-value=0.0014  Score=62.96  Aligned_cols=60  Identities=13%  Similarity=0.017  Sum_probs=51.8

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcC
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELL  204 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~  204 (222)
                      ..++|++.+++.++|+++.+++.|.+  .++++|-|..||.|||.+.+..   .+.+|+..++.+
T Consensus       569 ~~~~I~~~kI~~vIG~gG~~Ik~I~e--~tg~~I~I~d~G~V~I~~~~~~---~~~~A~~~I~~i  628 (630)
T 3u1k_A          569 ETVQVPLSKRAKFVGPGGYNLKKLQA--ETGVTISQVDEETFSVFAPTPS---AMHEARDFITEI  628 (630)
T ss_dssp             EEEECCHHHHHHHHCGGGHHHHHHHH--HHCCEEEECSSSEEEEEESSHH---HHHHHHHHTTC-
T ss_pred             EEEEeChhHhheeECCCChhHHHHHH--HHCCEEEEcCCcEEEEEeCCHH---HHHHHHHHHHHH
Confidence            67899999999999999999999999  9999999999999999998765   456666666553

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

Probab=96.42  E-value=0.0005  Score=67.01  Aligned_cols=74  Identities=18%  Similarity=0.151  Sum_probs=0.0

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD  125 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  125 (222)
                      ..|++|+++-|+|+++.+-.++|+|.....|.+|.+.+. ...++....|++||.|.++|.+++..+.+.||.+.
T Consensus       623 ~~~~vG~i~~G~V~~i~~fGaFVel~~g~eGLvHiSel~~~~v~~~~~~~~vGd~V~VkVi~vd~~grI~LS~k~  697 (723)
T 3cdi_A          623 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSIKE  697 (723)
T ss_dssp             ---------------------------------------------------------------------------
T ss_pred             hhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCccccCcccccCCCCEEEEEEEEECCCCcEEEEEEe
Confidence            568999999999999999999999988899999998875 35677788999999999999999876778888864

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae}

Probab=96.39  E-value=0.00054  Score=69.07  Aligned_cols=74  Identities=15%  Similarity=0.155  Sum_probs=0.0

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc--cccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA--TKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga--tk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      -..++|++|-|+|+++.....+|+|.....|.+|++.+...  .++....|++||.|.|+|++++. ...+.||++.
T Consensus       901 ~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~~~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~  977 (1030)
T 3psf_A          901 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLD  977 (1030)
T ss_dssp             -----------------------------------------------------------------------------
T ss_pred             HHhcCCCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEech
Confidence            35689999999999999999999998888999999887543  46667889999999999999984 4678999975

>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=96.35  E-value=0.0033  Score=45.84  Aligned_cols=58  Identities=5%  Similarity=0.103  Sum_probs=47.6

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC-----eEEEeeCCchhHHHHHHHHHH
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG-----KIWIRCESFSDTVRVGNLIMS  200 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG-----~iWi~~~~~~~~~~i~~~i~~  200 (222)
                      ..+.|++.++++++|+++..++.|.+  .+++.|-+-.+|     .|||.+. ++....+..+|+.
T Consensus        19 ~~i~Ip~~~ig~IIG~gG~~Ir~I~e--~tg~~I~i~~~g~~~~~~V~I~G~-~e~v~~A~~~I~~   81 (95)
T 2ctm_A           19 EDVPLDHRVHARIIGARGKAIRKIMD--EFKVDIRFPQSGAPDPNCVTVTGL-PENVEEAIDHILN   81 (95)
T ss_dssp             EEEECCTTTHHHHHCSSSCHHHHHHH--HHTCEEECCCTTCSCTTEEEEESC-HHHHHHHHHHHHH
T ss_pred             EEEEECHHHccccCCCCcchHHHHHH--HHCCeEEecCCCCCCCcEEEEEcC-HHHHHHHHHHHHH
Confidence            56899999999999999999999999  899999999999     8999997 3434444444433

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

Probab=96.34  E-value=0.049  Score=45.49  Aligned_cols=66  Identities=8%  Similarity=0.081  Sum_probs=51.6

Q ss_pred             cccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccc-cc------c-------c-ccCCcCCCCCCEEEEEEEecC
Q psy230           50 RRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAF-EG------A-------T-KKNPPKVETGDVVAGKLLTAN  114 (222)
Q Consensus        50 ~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f-~g------a-------t-k~~r~~l~~GDlV~ArV~~~~  114 (222)
                      -.+.|.+|.++-|+|++++...+.|++..+..++++.+.+ +.      .       . ++.+..|+.||.|+.||.+++
T Consensus        75 ~~f~p~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~  154 (218)
T 2ckz_B           75 VVFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREV  154 (218)
T ss_dssp             EEECCCTTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEE
T ss_pred             EEecCCCCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEE
Confidence            3578999999999999999999999995567777776543 11      1       1 345678999999999999886


Q ss_pred             C
Q psy230          115 K  115 (222)
Q Consensus       115 ~  115 (222)
                      .
T Consensus       155 ~  155 (218)
T 2ckz_B          155 F  155 (218)
T ss_dssp             E
T ss_pred             c
Confidence            4

>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=96.33  E-value=0.00042  Score=67.84  Aligned_cols=74  Identities=12%  Similarity=0.103  Sum_probs=37.3

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccc----c-cccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAF----E-GATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD  125 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f----~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  125 (222)
                      ..|++|+++-|+|+++.+-.++|+|.....|.+|++.+    . ...++....|++||.|.++|.++++.+.+.||++.
T Consensus       663 ~~~~vG~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSel~~~~s~~rv~~~~~~~~vGd~V~VkVi~vd~~grI~LS~k~  741 (757)
T 1e3p_A          663 TSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGKLSLIPVI  741 (757)
T ss_dssp             ----------CBEEECC-CSCEECCC---CCCCC-------------------CCSSCBCCCCCCCCCSSCC-------
T ss_pred             hhcccccEEEEEEEEccccEEEEEEcCCcEEEEEhHHhccccCCCcccCcccccCCCCEEEEEEEEECCCCCEEEEEec
Confidence            56899999999999999999999998889999999987    3 35667788999999999999999877778888865

>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=96.29  E-value=0.0012  Score=64.80  Aligned_cols=73  Identities=23%  Similarity=0.218  Sum_probs=62.2

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccc-ccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-ATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      ..++|++|-|+|+++..-..+|+|+....|.+|++.+.. ...+....|++||.|.++|++++. ...+.||++.
T Consensus       651 ~l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Lsd~~v~d~~~~~~vGd~V~VkVi~VD~~~~rI~LSlk~  725 (785)
T 3bzc_A          651 DLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRM  725 (785)
T ss_dssp             TCCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSCSSCCSCHHHHCCTTCCCCCBEEEEETTTTEEEECCSS
T ss_pred             hcCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcCccccCChhheeCCCCEEEEEEEEEECCCCEEEEEEec
Confidence            468999999999999999999999888899999987653 334445679999999999999986 4679999875

>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=96.13  E-value=0.047  Score=51.19  Aligned_cols=71  Identities=11%  Similarity=0.113  Sum_probs=56.3

Q ss_pred             CCCCCCEEEEEEEEEecc--eEEEEECCCCCeeeecccccc-c---------cccCCcCCCCCCEEEEEEEecCCC-Cee
Q psy230           53 VPTRGDLVIGVVTSRVGD--NYRVDIGSHDPAVLSYLAFEG-A---------TKKNPPKVETGDVVAGKLLTANKD-MES  119 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~--~~~VdI~~~~~a~L~~~~f~g-a---------tk~~r~~l~~GDlV~ArV~~~~~~-~~~  119 (222)
                      .+.+|++..|+|+++.+.  .++|||+..-.|+||++.... .         ..+..+.+++||-|..+|...... .-+
T Consensus        42 ~~~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei~~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke~~g~KGa  121 (517)
T 2bx2_L           42 EQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGA  121 (517)
T ss_dssp             CCCTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSCGGGCC-------CCCGGGTCCTTCEEEEEEEECCCTTCCC
T ss_pred             cCCCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHcChhhhccccccccccchhhhccCCCEEEEEEEeeccccCCc
Confidence            467999999999999998  999999999999999876521 1         123456799999999999986533 336


Q ss_pred             EEEE
Q psy230          120 EMVC  123 (222)
Q Consensus       120 ~Ls~  123 (222)
                      .||+
T Consensus       122 ~lTt  125 (517)
T 2bx2_L          122 ALTT  125 (517)
T ss_dssp             EEES
T ss_pred             eEEe
Confidence            6666

>1we8_A Tudor and KH domain containing protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.51.1.1

Probab=96.00  E-value=0.0047  Score=45.55  Aligned_cols=58  Identities=9%  Similarity=-0.008  Sum_probs=48.2

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEe--------CCeEEEeeCCchhHHHHHHHHHHhhc
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM--------NGKIWIRCESFSDTVRVGNLIMSCEL  203 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~--------NG~iWi~~~~~~~~~~i~~~i~~~e~  203 (222)
                      ..+.|++.++.+++|+++..++.|.+  .+++.|-|..        ++.|||.+.+.    .+.+|...++.
T Consensus        17 ~~i~Ip~~~ig~IIGkgG~~Ik~I~~--~tga~I~I~~~~~~~~~~~~~V~I~G~~~----~v~~A~~~I~~   82 (104)
T 1we8_A           17 EQLSVPQRSVGRIIGRGGETIRSICK--ASGAKITCDKESEGTLLLSRLIKISGTQK----EVAAAKHLILE   82 (104)
T ss_dssp             EEEEEETTTHHHHHTTTSHHHHHHHH--HHCCEEEECCSSCCSSSSEEEEEEEEEHH----HHHHHHHHHHH
T ss_pred             EEEEEChhheeeeECCCCHHHHHHHH--HHCCEEEEecCCCCCCCCcceEEEEcCHH----HHHHHHHHHHH
Confidence            56889999999999999999999999  8999999986        79999998654    34555555554

>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform B'; KH domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=95.67  E-value=0.025  Score=40.99  Aligned_cols=66  Identities=14%  Similarity=0.133  Sum_probs=51.6

Q ss_pred             ccCCceE--EEechhhhhhccCCChhHHHHhhhcCCCcEE-EEEEe-CCeEEEeeCCchhHHHHHHHHHHhh
Q psy230          135 ILNDGYL--LHTSISLCRKLLNPKCPLLKQLAKRSRQKME-LSIGM-NGKIWIRCESFSDTVRVGNLIMSCE  202 (222)
Q Consensus       135 ~L~~G~l--~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~e-i~vG~-NG~iWi~~~~~~~~~~i~~~i~~~e  202 (222)
                      .+..+++  +.|++.+++.++|+++..++.|.+  .++.. |-+-- +|.|-|.+.+......+...|+.+|
T Consensus        10 ~~~~~~i~~i~I~~dkIg~vIG~gGk~Ik~I~e--~tGv~~IdI~eddG~V~I~g~~~ea~~~A~~~I~~ie   79 (91)
T 2cpq_A           10 QLAAAFHEEFVVREDLMGLAIGTHGSNIQQARK--VPGVTAIELDEDTGTFRIYGESADAVKKARGFLEFVE   79 (91)
T ss_dssp             SSSCSEEEEEECCHHHHHHHHTTTTHHHHHHHT--STTEEEEEEETTTTEEEEEESSHHHHHHHHHHHSCCC
T ss_pred             hccCceEEEEEEChHHhhhhcCCCcHHHHHHHH--HhCCeEEEEEcCCCEEEEEECCHHHHHHHHHHHHhhh
Confidence            4444544  679999999999999999999999  99997 98886 5999999988775544444444444

>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=95.44  E-value=0.021  Score=42.33  Aligned_cols=58  Identities=5%  Similarity=0.035  Sum_probs=46.2

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC------eEEEeeCCchhHHHHHHHHHH
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG------KIWIRCESFSDTVRVGNLIMS  200 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG------~iWi~~~~~~~~~~i~~~i~~  200 (222)
                      ..+.|++.++.+++++....++.|.+  .+.+.|-|-.++      .|+|.+. ++.+..+...|+.
T Consensus        13 ~~i~Ip~~~iG~IIGkgG~~Ik~I~~--~TGakI~I~~~~~~~~er~V~I~G~-~e~v~~A~~~I~~   76 (106)
T 2hh3_A           13 IDVPVPRHSVGVVIGRSGEMIKKIQN--DAGVRIQFKQDDGTGPEKIAHIMGP-PDRCEHAARIIND   76 (106)
T ss_dssp             EEEEEETTTHHHHHTTTTHHHHHHHH--HHTCEEEECSSCSSSSEEEEEEESS-HHHHHHHHHHHHH
T ss_pred             EEEEECHHHcCccCCCCcHHHHHHHH--HHCcEEEEecCCCCCceeEEEEEeC-HHHHHHHHHHHHH
Confidence            57899999999999999999999999  999999998765      7999986 4434444444433

>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=94.29  E-value=0.044  Score=39.84  Aligned_cols=58  Identities=16%  Similarity=0.169  Sum_probs=48.5

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCC-cEEEEEEeCC----eEEEeeCCchhHHHHHHHHHHhhc
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQ-KMELSIGMNG----KIWIRCESFSDTVRVGNLIMSCEL  203 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~-~~ei~vG~NG----~iWi~~~~~~~~~~i~~~i~~~e~  203 (222)
                      ..+.|++.+.+.++|+++..++.|.+  .+ ++.|-+-..|    .|-|.+++.    .+..|...++.
T Consensus        19 ~~i~Ip~~~i~~iIG~gGk~Ir~I~e--etggv~I~i~~~g~~~~~V~I~G~~~----~v~~A~~~I~~   81 (95)
T 2ctj_A           19 VEVSIPAKLHNSLIGTKGRLIRSIME--ECGGVHIHFPVEGSGSDTVVIRGPSS----DVEKAKKQLLH   81 (95)
T ss_dssp             EEEECCHHHHHHHHCSSSHHHHHHHH--HHTSCEEECCCTTTTCCEEEEESCHH----HHHHHHHHHHH
T ss_pred             EEEEECHHHHhhhCCCCchhHHHHHH--HcCCCEEEeCCCCCCcceEEEEcCHH----HHHHHHHHHHH
Confidence            45889999999999999999999988  88 8999999999    999999754    44555555544

>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.20  E-value=0.08  Score=40.13  Aligned_cols=70  Identities=16%  Similarity=0.158  Sum_probs=52.2

Q ss_pred             ccCcccCCceEEEec---h--hhhhhccCCChhHHHHhhhcCCCcEEEEEE----------------eCCeEEEeeCCch
Q psy230          131 FIMGILNDGYLLHTS---I--SLCRKLLNPKCPLLKQLAKRSRQKMELSIG----------------MNGKIWIRCESFS  189 (222)
Q Consensus       131 ~~~G~L~~G~l~~v~---~--~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG----------------~NG~iWi~~~~~~  189 (222)
                      .++-.+..=+.+.+.   |  .++.+++|+++..++.|.+  .++|.|.|-                -.|.|.|.+.+..
T Consensus         7 ~~~~~~~~ki~ip~~~~~p~fn~ig~IIGpgG~tiK~I~~--eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e   84 (119)
T 2yqr_A            7 GGMHYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQI--ETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPE   84 (119)
T ss_dssp             SCCSCEEEEEECCCTTSCTTTCHHHHHSCGGGHHHHHHHH--HHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHH
T ss_pred             CCeeEEEEEEEcCCccCCCCCCeeeeEECCCChHHHHHHH--HHCCEEEEecCCccccccccccccCCCcEEEEEeCCHH
Confidence            334334445555554   2  5999999999999999999  999999985                4589999998876


Q ss_pred             hHHHHHHHHHHhhcCC
Q psy230          190 DTVRVGNLIMSCELLS  205 (222)
Q Consensus       190 ~~~~i~~~i~~~e~~~  205 (222)
                         .+.+|...|+.+.
T Consensus        85 ---~i~~A~~~Ie~Ll   97 (119)
T 2yqr_A           85 ---GLAAAKKLCENLL   97 (119)
T ss_dssp             ---HHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHHHh
Confidence               5566666666653

>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA recognition, complex E, KH domain, QUA2 homology; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=93.98  E-value=0.093  Score=40.38  Aligned_cols=51  Identities=14%  Similarity=0.220  Sum_probs=40.8

Q ss_pred             hhhhhccCCChhHHHHhhhcCCCcEEEEEEe----------------------CCeEEEeeCCchhHHHHHHHHHHhh
Q psy230          147 SLCRKLLNPKCPLLKQLAKRSRQKMELSIGM----------------------NGKIWIRCESFSDTVRVGNLIMSCE  202 (222)
Q Consensus       147 ~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~----------------------NG~iWi~~~~~~~~~~i~~~i~~~e  202 (222)
                      .++.+++|+++..++.|.+  .++|.|.|--                      .|.|+|.+.+...   +..|+..|+
T Consensus        22 n~iG~IIGP~G~tiK~Iq~--eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e~---~~~A~~~I~   94 (131)
T 1k1g_A           22 NFVGLLIGPRGNTLKNIEK--ECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN---VKKAVEQIR   94 (131)
T ss_dssp             HHHHHHHCSSSHHHHHHHH--HSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHH---HHHHHHHHH
T ss_pred             ceeeeEECCCcHHHHHHHH--HHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHHH---HHHHHHHHH
Confidence            3889999999999999999  9999998843                      6799999988764   444444444

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}

Probab=93.82  E-value=0.048  Score=42.49  Aligned_cols=56  Identities=5%  Similarity=0.032  Sum_probs=45.6

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEe------CCeEEEeeCCchhHHHHHHHH
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM------NGKIWIRCESFSDTVRVGNLI  198 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~------NG~iWi~~~~~~~~~~i~~~i  198 (222)
                      .-+.|++.++.+++|+++..++.|.+  .+++.|-+..      ++.|+|.+. +..+..+..+|
T Consensus        93 ~~i~vp~~~~g~iIGk~G~~I~~i~~--~tg~~I~i~~~~~~~~~~~v~I~G~-~~~v~~A~~~I  154 (164)
T 2jvz_A           93 IDVPVPRHSVGVVIGRSGEMIKKIQN--DAGVRIQFKQDDGTGPEKIAHIMGP-PDRCEHAARII  154 (164)
T ss_dssp             BCCEEETTTHHHHHCSSSHHHHHHHH--HTCCEEEECCCCTTSSEEEEEEESC-HHHHHHHHHHH
T ss_pred             EEEEEChhhccccCCCCcHhHHHHHH--HHCCeEEEeCCCCCCCcEEEEEEcC-HHHHHHHHHHH
Confidence            56789999999999999999999999  8999999987      689999996 44343333333

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

Probab=93.76  E-value=0.31  Score=42.11  Aligned_cols=61  Identities=15%  Similarity=0.215  Sum_probs=45.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD  125 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  125 (222)
                      ..+|++|-|+|++++...+.||++ ...+.||.+..+.         .+||-|.+.|.. +......+|+..
T Consensus         4 ~~~G~~v~g~V~~~~~~G~fv~~~-g~egllp~se~~~---------~vGdevev~v~~-d~~~r~iat~~~   64 (285)
T 3go5_A            4 TNLASFIVGLIIDENDRFYFVQKD-GQTYALAKEEGQH---------TVGDTVKGFAYT-DMKQKLRLTTLE   64 (285)
T ss_dssp             TTTTEEEEEEEEEECSSEEEEEET-TEEEEEEGGGCCC---------CTTSEEEEEEEE-CTTSCEEEECSC
T ss_pred             ccCCCEEEEEEEEEECCEEEEEcC-CeEEEEEHHHCcc---------ccCCEEEEEEEE-CCCCCEEEeccc
Confidence            358999999999999999999997 5789999876542         677777777653 333445555543

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=93.68  E-value=0.092  Score=36.05  Aligned_cols=55  Identities=11%  Similarity=0.114  Sum_probs=44.5

Q ss_pred             EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEe------CCeEEEeeCCchhHHHHHHHH
Q psy230          141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM------NGKIWIRCESFSDTVRVGNLI  198 (222)
Q Consensus       141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~------NG~iWi~~~~~~~~~~i~~~i  198 (222)
                      -+.|+..++.+++|+++..++.|.+  .+++.|-+..      ++.|.|.+. +..+..+...|
T Consensus         8 ~i~Ip~~~vg~iIGkgG~~Ik~I~~--~tga~I~i~~~~~~~~~~~v~I~G~-~~~v~~A~~~I   68 (76)
T 2p2r_A            8 ELTIPNDLIGCIIGRQGAKINEIRQ--MSGAQIKIANPVEGSTDRQVTITGS-AASISLAQYLI   68 (76)
T ss_dssp             EEEEEHHHHHHHHCGGGHHHHHHHH--HHCCEEEECCCCTTCSEEEEEEEEC-HHHHHHHHHHH
T ss_pred             EEEEChHHcceEECCCChHHHHHHH--HHCCEEEEcCCCCCCCeEEEEEEeC-HHHHHHHHHHH
Confidence            4789999999999999999999999  8899998887      789999986 44343333333

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=93.62  E-value=0.13  Score=37.99  Aligned_cols=58  Identities=14%  Similarity=0.107  Sum_probs=45.7

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC---------CeEEEeeCCchhHHHHHHHHHH
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN---------GKIWIRCESFSDTVRVGNLIMS  200 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N---------G~iWi~~~~~~~~~~i~~~i~~  200 (222)
                      .-+.|+..++.+++|+++..++.|.+  .+.+.|-|-.+         +.|.|.+ +.+.+..+...|..
T Consensus         9 ~~i~IP~~~vG~IIGkgG~~Ik~I~~--~TGa~I~I~~~~~~~~~~~~r~V~I~G-~~e~v~~A~~~I~~   75 (107)
T 2hh2_A            9 MTFSIPTHKCGLVIGRGGENVKAINQ--QTGAFVEISRQLPPNGDPNFKLFIIRG-SPQQIDHAKQLIEE   75 (107)
T ss_dssp             EEEEEEGGGTTTTSTTTTCHHHHHHH--HSSSEEEECCCCCTTCCTTEEEEEEES-CHHHHHHHHHHHHH
T ss_pred             EEEEECHHHcCccCCCCcHHHHHHHH--HhCCEEEEcCccCCCCCCCceEEEEEC-CHHHHHHHHHHHHH
Confidence            45789999999999999999999999  88889988876         6888988 55544444444443

>3d0f_A Penicillin-binding 1 transmembrane protein MRCA; BIG_1156.2, STR genomics, PSI-2, protein structure initiative; 1.64A {Nitrosomonas europaea atcc 19718}

Probab=93.59  E-value=0.25  Score=36.12  Aligned_cols=58  Identities=14%  Similarity=0.149  Sum_probs=45.1

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccccccc------cc-CCcCCCCCCEEEEE
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGAT------KK-NPPKVETGDVVAGK  109 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gat------k~-~r~~l~~GDlV~Ar  109 (222)
                      ..|..|+...+.|+++.++...|-+.....+.|+.....-|-      ++ ....|++||+|+.+
T Consensus        29 ~~~~~~~~~~AvV~~v~~~~~~v~~~~g~~~~l~~~~~~WA~~~~~~~~~~~~~~l~~GdvI~V~   93 (106)
T 3d0f_A           29 DIGNSDDILAAVVLSATPGAVEAFRKNGETIRITGDGLKAAHRFLSNDPKIGEKRIRPGALIRVK   93 (106)
T ss_dssp             TSCTTTTCEEEEEEEEETTEEEEEETTSCEEEECGGGGSTTGGGTTTCTTTGGGSCCTTEEEEEE
T ss_pred             ccCccCCeEEEEEEEeCCCeEEEEEcCCCeEEEcHHHChhhhhcccccccchhccCCCCCEEEEE
Confidence            357789999999999999999999977677778764433221      22 44669999999998

>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain, alpha-beta fold RNA-binding motif, immune system; 2.00A {Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A

Probab=93.56  E-value=0.12  Score=35.40  Aligned_cols=57  Identities=9%  Similarity=0.011  Sum_probs=45.3

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC---------CeEEEeeCCchhHHHHHHHHHHhh
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN---------GKIWIRCESFSDTVRVGNLIMSCE  202 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N---------G~iWi~~~~~~~~~~i~~~i~~~e  202 (222)
                      .-+.||..++.+++|+++..++.|.+  .+++.|-|..+         +.|.|.+. +.   .+..|...++
T Consensus         5 ~~i~Ip~~~vg~IIGkgG~~Ik~I~~--~tga~I~i~~~~~~~~~~~~~~v~I~G~-~~---~v~~A~~~I~   70 (76)
T 1dtj_A            5 VEMAVPENLVGAILGKGGKTLVEYQE--LTGARIQISKKGEFLPGTRNRRVTITGS-PA---ATQAAQYLIS   70 (76)
T ss_dssp             EEEEEETTTHHHHHCSTTHHHHHHHH--HHCCEEEECCTTCCSTTCCEEEEEEEES-HH---HHHHHHHHHH
T ss_pred             EEEEEChHHcceEECCCchHHHHHHH--HhCCEEEECcCCCCCCCCceeEEEEEeC-HH---HHHHHHHHHH
Confidence            34789999999999999999999999  89999999875         58999885 44   4444444444

>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta fold, DNA binding protein; 0.95A {Homo sapiens} SCOP: d.51.1.1 PDB: 1zzj_A 1zzi_A

Probab=93.26  E-value=0.15  Score=35.49  Aligned_cols=56  Identities=13%  Similarity=0.094  Sum_probs=43.9

Q ss_pred             EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC------CeEEEeeCCchhHHHHHHHHHHhh
Q psy230          141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN------GKIWIRCESFSDTVRVGNLIMSCE  202 (222)
Q Consensus       141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N------G~iWi~~~~~~~~~~i~~~i~~~e  202 (222)
                      -+.|++.++.+++|+++..++.|.+  .+++.|-+-..      +.|.|.+. ++   .+.+|...++
T Consensus        10 ~i~Vp~~~vg~iIGkgG~~Ik~I~~--~tga~I~i~~~~~~~~~~~v~I~G~-~~---~v~~A~~~I~   71 (82)
T 1zzk_A           10 QVTIPKDLAGSIIGKGGQRIKQIRH--ESGASIKIDEPLEGSEDRIITITGT-QD---QIQNAQYLLQ   71 (82)
T ss_dssp             EEEEETTTGGGGTCGGGHHHHHHHH--HHCCEEEECCTTSCSSEEEEEEEEC-HH---HHHHHHHHHH
T ss_pred             EEEEChHhcCeeECCCchHHHHHHH--HHCCEEEEcCCCCCCCceEEEEEeC-HH---HHHHHHHHHH
Confidence            4789999999999999999999999  88888888764      58999984 44   3444444443

>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1 PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*

Probab=92.74  E-value=0.22  Score=34.01  Aligned_cols=55  Identities=9%  Similarity=0.018  Sum_probs=44.5

Q ss_pred             EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC----eEEEeeCCchhHHHHHHHHHHh
Q psy230          141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG----KIWIRCESFSDTVRVGNLIMSC  201 (222)
Q Consensus       141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG----~iWi~~~~~~~~~~i~~~i~~~  201 (222)
                      -+.|++.++..++|+++..++.|.+  .+++.|-+..+|    .|-|.+. +.   .+.+|...+
T Consensus         8 ~i~ip~~~ig~iIGkgG~~Ik~I~~--~tga~I~i~~~~~~er~v~I~G~-~~---~v~~A~~~I   66 (73)
T 2axy_A            8 RLLMHGKEVGSIIGKKGESVKKMRE--ESGARINISEGNCPERIITLAGP-TN---AIFKAFAMI   66 (73)
T ss_dssp             EEEEEHHHHHHHHCGGGHHHHHHHH--HHCCEEEECSSCCSEEEEEEEEC-HH---HHHHHHHHH
T ss_pred             EEEEChhHeeeEECCCCHHHHHHHH--HHCCEEEEecCCCCcEEEEEEeC-HH---HHHHHHHHH
Confidence            4689999999999999999999999  899999999888    5888886 44   334444443

>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA binding protein, transcription factor, hnRNP K, CT element, C-MYC oncogene; NMR {Homo sapiens} SCOP: d.51.1.1 PDB: 1khm_A

Probab=92.73  E-value=0.15  Score=36.20  Aligned_cols=57  Identities=12%  Similarity=0.099  Sum_probs=44.8

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEe------CCeEEEeeCCchhHHHHHHHHHHhh
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM------NGKIWIRCESFSDTVRVGNLIMSCE  202 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~------NG~iWi~~~~~~~~~~i~~~i~~~e  202 (222)
                      .-+.|+..++.+++|+++..++.|.+  .+++.|-|-.      ++.|.|.+. ++   .+.+|...++
T Consensus        16 ~~i~Ip~~~vg~IIGkgG~~Ik~I~~--~tga~I~I~~~~~~~~~~~v~I~G~-~e---~v~~A~~~I~   78 (89)
T 1j5k_A           16 TQVTIPKDLAGSIIGKGGQRIKQIRH--ESGASIKIDEPLEGSEDRIITITGT-QD---QIQNAQYLLQ   78 (89)
T ss_dssp             EEEEEEHHHHHHHHCGGGHHHHHHHH--HTCCEEEECSCCSSSSEEEEEEEEE-HH---HHHHHHHHHH
T ss_pred             EEEEEChhhcceeECCCCHhHHHHHH--HhCCeEEecCCCCCCCccEEEEEcC-HH---HHHHHHHHHH
Confidence            34789999999999999999999999  8888888876      488999986 43   3344444443

>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA binding protein, KH domain, KSRP, posttranscriptional regulation, mRNA decay; NMR {Homo sapiens}

Probab=92.38  E-value=0.28  Score=38.05  Aligned_cols=57  Identities=12%  Similarity=0.149  Sum_probs=45.2

Q ss_pred             EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC--------eEEEeeCCchhHHHHHHHHHH
Q psy230          141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG--------KIWIRCESFSDTVRVGNLIMS  200 (222)
Q Consensus       141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG--------~iWi~~~~~~~~~~i~~~i~~  200 (222)
                      -+.|++.++..++|+++..++.|.+  .+++.|-+-.++        .|+|.+ ++..+..+..+|..
T Consensus         5 ~~~Vp~~~~g~iIGk~G~~Ik~i~~--~tg~~I~i~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~   69 (164)
T 2jvz_A            5 EIMIPAGKAGLVIGKGGETIKQLQE--RAGVKMILIQDGSQNTNVDKPLRIIG-DPYKVQQACEMVMD   69 (164)
T ss_dssp             EEEECTTCHHHHTCTTTHHHHHHHH--TSCSEEEECCCTTSSSSSCEEEEEEE-CHHHHHHHHHHHHH
T ss_pred             EEEechhheeEEECCChHHHHHHHH--HhCCeEEEecCCCCCCCCceEEEEEc-CHHHHHHHHHHHHH
Confidence            3679999999999999999999999  999999887765        799998 44444444444443

>1x4n_A FAR upstream element binding protein 1; KH domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.51.1.1 PDB: 2opu_A

Probab=92.34  E-value=0.28  Score=35.02  Aligned_cols=51  Identities=2%  Similarity=-0.005  Sum_probs=42.3

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC------CeEEEeeCCchhHHH
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN------GKIWIRCESFSDTVR  193 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N------G~iWi~~~~~~~~~~  193 (222)
                      .-+.|+..++.+++|+++..++.|.+  .+++.|-|-.+      +.|.|.+. ++.+..
T Consensus        17 ~~i~Ip~~~vG~IIGkgG~~Ik~I~~--~tga~I~I~~~~~g~~~r~v~I~G~-~e~v~~   73 (92)
T 1x4n_A           17 EEYKVPDGMVGFIIGRGGEQISRIQQ--ESGCKIQIAPDSGGLPERSCMLTGT-PESVQS   73 (92)
T ss_dssp             EEEEEEHHHHHHHHCSSSHHHHHHHH--HSCCEEEECSCCTTCSEEEEEEEEC-HHHHHH
T ss_pred             EEEEEChHHcceeECCCchHHHHHHH--HhCCEEEEcCCCCCCCccEEEEEeC-HHHHHH
Confidence            45789999999999999999999999  89999988876      48999986 443333

>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding motif, protein/RNA structure, RNA binding protein/RNA complex; 2.40A {Homo sapiens} SCOP: d.51.1.1

Probab=92.28  E-value=0.21  Score=35.17  Aligned_cols=58  Identities=9%  Similarity=0.002  Sum_probs=46.0

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC---------CeEEEeeCCchhHHHHHHHHHHhhc
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN---------GKIWIRCESFSDTVRVGNLIMSCEL  203 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N---------G~iWi~~~~~~~~~~i~~~i~~~e~  203 (222)
                      .-+.||..++.+++|+++..++.|.+  .+++.|-|..+         +.|.|.+. +.   .+..|...++.
T Consensus         5 ~~i~IP~~~vG~IIGkgG~~Ik~I~~--~tga~I~I~~~~~~~~g~~~r~v~I~G~-~~---~v~~A~~~I~~   71 (87)
T 1ec6_A            5 VEIAVPENLVGAILGKGGKTLVEYQE--LTGARIQISKKGEFLPGTRNRRVTITGS-PA---ATQAAQYLISQ   71 (87)
T ss_dssp             EEEEEEHHHHHHHHCGGGHHHHHHHH--HHCCEEEECCTTCBSTTSCEEEEEEESS-HH---HHHHHHHHHHH
T ss_pred             EEEEEChHHcCeeECCCcHhHHHHHH--HhCCEEEEccCCCCCCCCCceEEEEEcC-HH---HHHHHHHHHHH
Confidence            45789999999999999999999999  89999999875         48999885 44   44445444444

>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1

Probab=92.25  E-value=0.16  Score=35.36  Aligned_cols=58  Identities=7%  Similarity=0.051  Sum_probs=45.6

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEe------CCeEEEeeCCchhHHHHHHHHHHhhc
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM------NGKIWIRCESFSDTVRVGNLIMSCEL  203 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~------NG~iWi~~~~~~~~~~i~~~i~~~e~  203 (222)
                      .-+.|+..++..++|+++..++.|.+  .+++.|-|-.      ++.|.|.+.. .   .+..|...++.
T Consensus         8 ~~i~Ip~~~vg~IIGkgG~~Ik~I~~--~sga~I~i~~~~~~~~~r~v~I~G~~-~---~v~~A~~~I~~   71 (82)
T 1wvn_A            8 HELTIPNNLIGCIIGRQGANINEIRQ--MSGAQIKIANPVEGSSGRQVTITGSA-A---SISLAQYLINA   71 (82)
T ss_dssp             EEEEEEGGGHHHHHCGGGHHHHHHHH--HHCCEEEECCCCTTCSEEEEEEEECH-H---HHHHHHHHHHH
T ss_pred             EEEEEchHhccceeCCCchhHHHHHH--HhCCEEEEecCCCCCCceEEEEEcCH-H---HHHHHHHHHHH
Confidence            34789999999999999999999999  8888888876      5699999854 3   34445554443

>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol metabolism, beta-alpha-alpha-beta-BETA-alpha structure, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.51.1.1

Probab=91.83  E-value=0.092  Score=37.78  Aligned_cols=58  Identities=12%  Similarity=0.058  Sum_probs=45.8

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEe----CCeEEEeeCCchhHHHHHHHHHHhhc
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM----NGKIWIRCESFSDTVRVGNLIMSCEL  203 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~----NG~iWi~~~~~~~~~~i~~~i~~~e~  203 (222)
                      .-+.|++.+++.++|+++..++.|.+  .+++.|-+-.    +|.|.|.+. +.   .+.+|...++.
T Consensus        19 ~~i~Ip~~~ig~IIG~gG~~Ik~I~~--etg~~I~i~~~~~~~~~V~I~G~-~e---~v~~A~~~I~~   80 (94)
T 2cte_A           19 ATVAIPKEHHRFVIGKNGEKLQDLEL--KTATKIQIPRPDDPSNQIKITGT-KE---GIEKARHEVLL   80 (94)
T ss_dssp             EEEECCTTTHHHHHCSSSCHHHHHHH--HTTCCCBCCCTTSSCCEEEEEEC-HH---HHHHHHHHHHH
T ss_pred             EEEEEChHHeeeeECCCChhHHHHHH--HHCCEEEeCCCCCCCCeEEEEEC-HH---HHHHHHHHHHH
Confidence            45789999999999999999999999  8888888865    589999997 44   34445544444

>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain, cell projection, cytoplasm, nucleus, phosphoprotein, translation regulation; 2.75A {Homo sapiens}

Probab=91.68  E-value=0.14  Score=39.84  Aligned_cols=51  Identities=10%  Similarity=0.099  Sum_probs=42.9

Q ss_pred             EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC--------eEEEeeCCchhHHHH
Q psy230          141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG--------KIWIRCESFSDTVRV  194 (222)
Q Consensus       141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG--------~iWi~~~~~~~~~~i  194 (222)
                      -+.|++.++.+++|+++..++.|.+  .+++.|-+-.+|        .|+|.+ ++..+..+
T Consensus        88 ~i~vp~~~~g~iIGkgG~~I~~i~~--~tga~I~i~~~~~~~~~~~~~v~I~G-~~~~v~~A  146 (163)
T 3krm_A           88 HIRVPASAAGRVIGKGGKTVNELQN--LTAAEVVVPRDQTPDENDQVIVKIIG-HFYASQMA  146 (163)
T ss_dssp             EEEEETTTHHHHHCGGGHHHHHHHH--HHCCEEECCTTCCCCTTSEEEEEEEE-CHHHHHHH
T ss_pred             EEEcChhheeeEEcCCChHHHHHHH--HhCCeEEECCCCCCCCCCceEEEEEe-CHHHHHHH
Confidence            4789999999999999999999998  889999998888        799999 45433333

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=89.78  E-value=0.46  Score=36.96  Aligned_cols=55  Identities=15%  Similarity=0.288  Sum_probs=43.5

Q ss_pred             hhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC------------------------eEEEeeCCchhH--HHHHHHHHH
Q psy230          147 SLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG------------------------KIWIRCESFSDT--VRVGNLIMS  200 (222)
Q Consensus       147 ~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG------------------------~iWi~~~~~~~~--~~i~~~i~~  200 (222)
                      +++.+++|+++..++.|.+  .++|.|.|-=.|                        .|+|.+.+....  ..+..|+..
T Consensus        17 NfiG~IiGPrG~t~K~ie~--eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~~~~~~~l~~A~~~   94 (140)
T 2bl5_A           17 NFVGRILGPRGLTAKQLEA--ETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEE   94 (140)
T ss_dssp             CHHHHHTTTTHHHHHHHHH--HHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHHHHHHHHHHHHH
T ss_pred             CeeeEEECCCcchHHHHHH--HHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCchhhHHHHHHHHHHH
Confidence            5688999999999999999  999999887666                        899999877421  255666666


Q ss_pred             hhc
Q psy230          201 CEL  203 (222)
Q Consensus       201 ~e~  203 (222)
                      |+.
T Consensus        95 I~~   97 (140)
T 2bl5_A           95 VKK   97 (140)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1

Probab=85.80  E-value=1  Score=35.27  Aligned_cols=56  Identities=11%  Similarity=0.109  Sum_probs=43.6

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC---------CeEEEeeCCchhHHHHHHHH
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN---------GKIWIRCESFSDTVRVGNLI  198 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N---------G~iWi~~~~~~~~~~i~~~i  198 (222)
                      +-+.|+..++.+++|+++..++.|.+  .+++.|-|-.+         +.|.|.+ ++..+..+...|
T Consensus       106 ~~i~vp~~~~g~iIGkgG~~Ik~I~~--~tga~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I  170 (174)
T 1j4w_A          106 FNFIVPTGKTGLIIGKGGETIKSISQ--QSGARIELQRNPPPNADPNMKLFTIRG-TPQQIDYARQLI  170 (174)
T ss_dssp             EEEEEETTTHHHHHCGGGHHHHHHHH--HHCCEEEEECCCTTTSCTTEEEEEEEC-CHHHHHHHHHHH
T ss_pred             EEEEEChHHcCeeECCCchHHHHHHH--HHCCEEEECCCCCCCCCCCceEEEEEC-CHHHHHHHHHHH
Confidence            35788999999999999999999999  88889988765         6899988 444333333333

>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A

Probab=85.76  E-value=1.9  Score=41.25  Aligned_cols=71  Identities=10%  Similarity=0.019  Sum_probs=55.1

Q ss_pred             CCCCCC--EEEEEEEEEecceEEEEEC-CCCCeeeecccccc---c------cc----cCCcCCCCCCEEEEEEEecCCC
Q psy230           53 VPTRGD--LVIGVVTSRVGDNYRVDIG-SHDPAVLSYLAFEG---A------TK----KNPPKVETGDVVAGKLLTANKD  116 (222)
Q Consensus        53 ~P~vGD--iVIG~V~~v~~~~~~VdI~-~~~~a~L~~~~f~g---a------tk----~~r~~l~~GDlV~ArV~~~~~~  116 (222)
                      .+++|+  ..-|+|++++...+.|.|. ....+.+|++.+..   .      ..    +....|++||-|..+|.+++..
T Consensus       555 ~~~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~~~~d~~~~d~~~~~l~~~~~~~~~lGD~V~VkV~~vd~~  634 (644)
T 2id0_A          555 KDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRME  634 (644)
T ss_dssp             GGGTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETT
T ss_pred             hhccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhccCcCceeEEcccccEEEecCCCEeCCCCEEEEEEEEEeCC
Confidence            567899  9999999999999999995 45689999866531   1      11    3345799999999999999864


Q ss_pred             -CeeEEEE
Q psy230          117 -MESEMVC  123 (222)
Q Consensus       117 -~~~~Ls~  123 (222)
                       ..+.++.
T Consensus       635 ~~~I~~~l  642 (644)
T 2id0_A          635 TRSIIARP  642 (644)
T ss_dssp             TTEEEEEE
T ss_pred             CCEEEEEE
Confidence             5666665

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=85.37  E-value=1.3  Score=36.81  Aligned_cols=60  Identities=17%  Similarity=0.311  Sum_probs=48.3

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEE-eCCeEEEeeCC----chhHHHHHHHHHHh
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIG-MNGKIWIRCES----FSDTVRVGNLIMSC  201 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG-~NG~iWi~~~~----~~~~~~i~~~i~~~  201 (222)
                      ..+.||+.++..++|+.+.+++.|.+  ++++.|-+- .+|.|-|.+.+    +.....+...|+.+
T Consensus        36 ~~i~IP~~kig~lIG~gGk~Ik~I~e--~tgvkI~I~~~~g~V~I~~~~~t~d~~~i~kA~~~I~~i  100 (219)
T 2e3u_A           36 EYVKIPKDRIAVLIGKKGQTKKEIEK--RTKTKITIDSETGEVWITSTKETEDPLAVWKARDIVLAI  100 (219)
T ss_dssp             EEEECCHHHHHHHHCGGGHHHHHHHH--HHTEEEEECTTTCEEEEEECTTCCSHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHhhhhhcccHHHHHHHHH--HHCcEEEEEcCCCEEEEecCCCCCCHHHHHHHHHHHHHH
Confidence            36899999999999999999999999  889998888 88999999876    44444444444443

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

Probab=83.78  E-value=3  Score=30.13  Aligned_cols=38  Identities=16%  Similarity=0.177  Sum_probs=34.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE   90 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~   90 (222)
                      .|++|+.|-+.|+.+.+....|+|.....+.+|++.+.
T Consensus        58 ~l~~Ge~V~g~V~~i~~fG~fv~l~~~~eGlvhis~i~   95 (101)
T 2bh8_A           58 NPQQGDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDIS   95 (101)
T ss_dssp             CCCTTCEEEEEEEECCSEEEEECTTSCEEEEEEEEEEE
T ss_pred             CCCCCCEEEEEEEEeCCcEEEEEcCCCceEEEEHHHCc
Confidence            79999999999999999999999987789999987653

>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding, DNA-binding, nucleus, phosph ribonucleoprotein, RNA-binding, RNA binding protein; NMR {Homo sapiens}

Probab=82.83  E-value=0.77  Score=35.46  Aligned_cols=57  Identities=12%  Similarity=0.081  Sum_probs=44.1

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEe-------CCeEEEeeCCchhHHHHHHHHHHhh
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM-------NGKIWIRCESFSDTVRVGNLIMSCE  202 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~-------NG~iWi~~~~~~~~~~i~~~i~~~e  202 (222)
                      .-+.|+..++.+++|+++..++.|.+  .+++.|-+-.       .+.|.|.+ ++.   .+.+|...+.
T Consensus        91 ~~i~vp~~~~g~iIGkgG~~Ik~i~~--~tga~I~i~~~~~~~~~~~~v~I~G-~~~---~v~~A~~~I~  154 (160)
T 2jzx_A           91 LRLVVPASQCGSLIGKGGCKIKEIRE--STGAQVQVAGDMLPNSTERAITIAG-IPQ---SIIECVKQIC  154 (160)
T ss_dssp             EEEEEEHHHHHHHHCGGGHHHHHHHH--HHSSEECCCCCCSTTCCEEEEEEEE-CHH---HHHHHHHHHH
T ss_pred             EEEEEChhheeeEECCCCHHHHHHHH--HhCCeEEECCCCCCCCCceEEEEEc-CHH---HHHHHHHHHH
Confidence            34788999999999999999999999  8888888865       48899999 444   3444444443

>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH domain, hairpin, RNA-binding protein complex; HET: 5BU; 1.94A {Homo sapiens} PDB: 2ann_A*

Probab=81.52  E-value=2  Score=33.70  Aligned_cols=57  Identities=5%  Similarity=-0.007  Sum_probs=44.9

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC--------CeEEEeeCCchhHHHHHHHHHHhh
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN--------GKIWIRCESFSDTVRVGNLIMSCE  202 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N--------G~iWi~~~~~~~~~~i~~~i~~~e  202 (222)
                      .-+.|+..++.+++|+++..++.|.+  .+++.|-+-.+        +.|.|.+.. .   .+.+|+..+.
T Consensus       106 ~~i~Vp~~~vg~iIGkgG~~Ik~i~~--~tga~I~i~~~~~~~~~~~~~v~I~G~~-~---~v~~A~~~I~  170 (178)
T 2anr_A          106 VKIIVPNSTAGLIIGKGGATVKAIME--QSGAWVQLSQKPDGINLQNRVVTVSGEP-E---QNRKAVELII  170 (178)
T ss_dssp             EEEEEEHHHHHHHHCGGGHHHHHHHH--HSSCEEEECCCC----CCEEEEEEESSH-H---HHHHHHHHHH
T ss_pred             EEEEEchhheeeeECCCcHHHHHHHH--HHCCEEEEeCCCCCCCCCceEEEEEcCH-H---HHHHHHHHHH
Confidence            46889999999999999999999999  88888888766        588898864 2   4444444443

---

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	222
d2nn6g1	88	b.40.4.5 (G:107-194) S1-domain of exosome componen	4e-28
d2ja9a1	90	b.40.4.5 (A:62-151) S1-domain of exosome component	5e-26
d2nn6g3	80	d.51.1.1 (G:195-274) Ribosomal RNA-processing prot	2e-25
d2ja9a2	85	d.51.1.1 (A:152-236) Ribosomal RNA-processing prot	2e-13
d2nn6g2	91	b.84.4.2 (G:16-106) Ribosomal RNA-processing prote	8e-09
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	3e-08
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	9e-06
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	2e-04
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	0.004

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]} Length = 88

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]

 Score =   99 bits (249), Expect = 4e-28
 Identities = 49/88 (55%), Positives = 68/88 (77%)

Query: 51  RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKL 110
           RYVP +GD VIG+VT++ GD ++VD+G  +PA LSYL+FEGATK+N P V+ GD++ G+ 
Sbjct: 1   RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQF 60

Query: 111 LTANKDMESEMVCVDSRGKEFIMGILND 138
           + ANKDME EMVC+DS G+   MG++  
Sbjct: 61  VVANKDMEPEMVCIDSCGRANGMGVIGQ 88

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]} Length = 90

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]

 Score = 94.5 bits (235), Expect = 5e-26
 Identities = 36/89 (40%), Positives = 57/89 (64%), Gaps = 2/89 (2%)

Query: 50  RRYVPTRGDLVIGVVTSRVGDNYRVDIGSH-DPAVLSYLAFEGATKKNPPKVETGDVVAG 108
           +RY+P+  D VIGV+     D+Y+V + +      LSY+AF  A+KKN P ++ GD+V  
Sbjct: 1   KRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYA 60

Query: 109 KLLTANKDMESEMVCVDSR-GKEFIMGIL 136
           ++ TA K++E+E+ C DS  G++   GIL
Sbjct: 61  RVCTAEKELEAEIECFDSTTGRDAGFGIL 89

>d2nn6g3 d.51.1.1 (G:195-274) Ribosomal RNA-processing protein 40, RRP40 {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Ribosomal RNA-processing protein 40, RRP40
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 92.4 bits (230), Expect = 2e-25
 Identities = 22/79 (27%), Positives = 47/79 (59%), Gaps = 2/79 (2%)

Query: 138 DGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNL 197
           DG L   ++ L RKLL P C +++++ K     +E+  GMNG+IW++ ++   T+ + N+
Sbjct: 1   DGLLFKVTLGLIRKLLAPDCEIIQEVGKLY--PLEIVFGMNGRIWVKAKTIQQTLILANI 58

Query: 198 IMSCELLSYEEILNLCESI 216
           + +CE ++ ++   +   +
Sbjct: 59  LEACEHMTSDQRKQIFSRL 77

>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Ribosomal RNA-processing protein 40, RRP40
species: Saccharomyces cerevisiae [TaxId: 4932]

 Score = 61.7 bits (150), Expect = 2e-13
 Identities = 28/66 (42%), Positives = 42/66 (63%), Gaps = 3/66 (4%)

Query: 138 DGYLLHTSISLCRKLL-NPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGN 196
           DG ++  +++  R+LL N   PLLK LA  +  K E++IG+NGKIW++CE  S+T+    
Sbjct: 1   DGMIIDVNLNFARQLLFNNDFPLLKVLAAHT--KFEVAIGLNGKIWVKCEELSNTLACYR 58

Query: 197 LIMSCE 202
            IM C 
Sbjct: 59  TIMECC 64

>d2nn6g2 b.84.4.2 (G:16-106) Ribosomal RNA-processing protein 40, RRP40 {Human (Homo sapiens) [TaxId: 9606]} Length = 91

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]

 Score = 49.3 bits (117), Expect = 8e-09
 Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 8/53 (15%)

Query: 6  LSLNAEP--RLILGPGLRRESSAILVSQSGILRHAKPFT------YYVDYIQR 50
          L+  A    R++ GPGLRR    +LV++ G LRH +P +      Y+VD  Q+
Sbjct: 39 LNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQK 91

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

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]

 Score = 47.6 bits (113), Expect = 3e-08
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 4/81 (4%)

Query: 51  RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVL--SYLAFEGATKKNPPKVETGDVVAG 108
           RY+   GD+V+G +T      ++V+  S   +VL  S +   G   +     +   +   
Sbjct: 3   RYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMR-- 60

Query: 109 KLLTANKDMESEMVCVDSRGK 129
             L     + +E+  V S G 
Sbjct: 61  GFLQEGDLISAEVQAVFSDGA 81

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 88

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]

 Score = 40.6 bits (95), Expect = 9e-06
 Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 52  YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPP-----KVETGDVV 106
           YVP  GD+VIG++ S    N+ VDI S   AVLS   F G             ++ GD +
Sbjct: 3   YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYI 62

Query: 107 AGKLLTANKDME 118
             K++  +K   
Sbjct: 63  KAKVVAFDKTRS 74

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 87

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]

 Score = 36.9 bits (85), Expect = 2e-04
 Identities = 16/72 (22%), Positives = 28/72 (38%), Gaps = 4/72 (5%)

Query: 51  RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVET----GDVV 106
            Y P   D+VIG+V       + VDI +   A L      G +      +      GD V
Sbjct: 2   FYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYV 61

Query: 107 AGKLLTANKDME 118
             ++   ++ ++
Sbjct: 62  IARIENFDRSID 73

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 83

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]

 Score = 33.1 bits (75), Expect = 0.004
 Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 2/68 (2%)

Query: 52  YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPK--VETGDVVAGK 109
           Y P+ GD+VIG++     + + VDI S   A L             P   ++ GD +  K
Sbjct: 1   YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAK 60

Query: 110 LLTANKDM 117
           +L  +  M
Sbjct: 61  VLNIDPKM 68

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	222
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	99.96
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	99.95
d2nn6g3	80	Ribosomal RNA-processing protein 40, RRP40 {Human	99.92
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	99.88
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.79
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	99.74
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.73
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.71
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.67
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	99.35
d2ba0a2	51	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.2
d2nn6h2	48	Ribosomal RNA-processing protein 4, RRP4 {Human (H	99.19
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.95
d2je6i2	59	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.92
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.84
d2nn6i2	55	Exosome component 1, EXOSC1 {Human (Homo sapiens)	98.82
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	98.66
d2nn6h3	126	Ribosomal RNA-processing protein 4, RRP4 {Human (H	98.64
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	98.61
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	98.55
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	98.27
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	98.12
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	98.12
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.06
d2nn6g2	91	Ribosomal RNA-processing protein 40, RRP40 {Human	97.93
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	97.8
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	97.68
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	96.97
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	96.26
d2cpqa1	78	Fragile X mental retardation syndrome related prot	96.13
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	95.28
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	94.53
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	93.83
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	93.7
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	92.55
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	92.01
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	91.23
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	90.06
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	88.77
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	88.39
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	87.53
d1v8qa_	66	Ribosomal protein L27 {Thermus thermophilus [TaxId	86.96
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	84.8
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	84.05
d2zjrt1	84	Ribosomal protein L27 {Deinococcus radiodurans [Ta	83.9
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	83.51
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	83.39
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	82.06
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	82.0

>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=99.96  E-value=2.1e-30  Score=189.11  Aligned_cols=87  Identities=56%  Similarity=1.029  Sum_probs=85.5

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCcc
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKE  130 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~  130 (222)
                      ||+|++||+|||+|++++.+.|+|||++++.|+||+++|+|+++++||+|++||+|+|||++++++++++|||+++++|+
T Consensus         1 rY~P~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~f~g~~k~~r~~l~~GD~V~arV~~v~~~~~~~Lscvd~~~k~   80 (88)
T d2nn6g1           1 RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCGRA   80 (88)
T ss_dssp             SCCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSCCSSCSSSSSCTTCEEEEEEEECCTTSCCEEECSBTTTTB
T ss_pred             CCcCCCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHcCccccccCcccCCCCEEEEEEEEeCCCCCEEEEEEcccCcc
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCcccC
Q psy230          131 FIMGILN  137 (222)
Q Consensus       131 ~~~G~L~  137 (222)
                      .+||+|.
T Consensus        81 ~g~G~L~   87 (88)
T d2nn6g1          81 NGMGVIG   87 (88)
T ss_dssp             CCCCSCC
T ss_pred             cCCcccC
Confidence            9999995

>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=99.95  E-value=5.3e-29  Score=182.31  Aligned_cols=88  Identities=39%  Similarity=0.732  Sum_probs=83.1

Q ss_pred             cccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeec-cccccccccCCcCCCCCCEEEEEEEecCCCCeeEEEEecC-C
Q psy230           50 RRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSY-LAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDS-R  127 (222)
Q Consensus        50 ~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~-~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~-~  127 (222)
                      +||+|++||+|||+|+++.++.|+|||++++.|.||. ++|+|++++|||+|++||+|+|||++++++++++|||+++ +
T Consensus         1 krY~P~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~~f~g~~k~~r~~l~~GDlV~arV~~v~~~~~~~Lsc~~~~~   80 (90)
T d2ja9a1           1 KRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIECFDSTT   80 (90)
T ss_dssp             CCCCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCCSSSCCCCCTTCEEEEEEEECCTTSCCEEESSCTTT
T ss_pred             CCccCCCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhhccCccccccCCccCCCCEEEEEEEEECCCCCEEEEEecccc
Confidence            5899999999999999999999999999999988774 6899999999999999999999999999999999999995 6


Q ss_pred             CccccCcccC
Q psy230          128 GKEFIMGILN  137 (222)
Q Consensus       128 ~~~~~~G~L~  137 (222)
                      ||+.+||+|+
T Consensus        81 gK~~g~G~L~   90 (90)
T d2ja9a1          81 GRDAGFGILE   90 (90)
T ss_dssp             CSCTTCEEEC
T ss_pred             CccccccccC
Confidence            8999999984

>d2nn6g3 d.51.1.1 (G:195-274) Ribosomal RNA-processing protein 40, RRP40 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Ribosomal RNA-processing protein 40, RRP40
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=1.5e-26  Score=164.65  Aligned_cols=79  Identities=28%  Similarity=0.687  Sum_probs=77.4

Q ss_pred             CceEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHH
Q psy230          138 DGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIH  217 (222)
Q Consensus       138 ~G~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~  217 (222)
                      +|++|+||++++|||++++|.+|+.|++  +++|||+||+||||||++++.++|++++|||+.||+++.+|+++|++++.
T Consensus         1 dG~~f~vsl~laR~Ll~~~~~vL~~Lgk--~~~FEIavG~NGrVWvk~~~~~~ti~i~~aI~~~e~~~~~q~~~lv~~l~   78 (80)
T d2nn6g3           1 DGLLFKVTLGLIRKLLAPDCEIIQEVGK--LYPLEIVFGMNGRIWVKAKTIQQTLILANILEACEHMTSDQRKQIFSRLA   78 (80)
T ss_dssp             SCEEECCCHHHHHHHHCTTCSHHHHTTC--SSSCCCEEETTTEEEECCSSHHHHHHHHHHHHHTTSSCTTTHHHHHHHHH
T ss_pred             CCEEEEecHHHHHHHhcCCCHHHHHHhh--hCCeEEEEecCCeEEEeCCCHHHHHHHHHHHHHhhcCCHHHHHHHHHHHh
Confidence            6999999999999999999999999999  99999999999999999999999999999999999999999999999987


Q ss_pred             H
Q psy230          218 I  218 (222)
Q Consensus       218 ~  218 (222)
                      +
T Consensus        79 ~   79 (80)
T d2nn6g3          79 E   79 (80)
T ss_dssp             H
T ss_pred             c
Confidence            5

>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40, RRP40 {Saccharomyces cerevisiae [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Ribosomal RNA-processing protein 40, RRP40
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=99.88  E-value=1.4e-23  Score=151.44  Aligned_cols=81  Identities=33%  Similarity=0.627  Sum_probs=69.2

Q ss_pred             CceEEEechhhhhhccCCCh-hHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhc-CCHHHHHHHHHH
Q psy230          138 DGYLLHTSISLCRKLLNPKC-PLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCEL-LSYEEILNLCES  215 (222)
Q Consensus       138 ~G~l~~v~~~~~~rl~~~~~-~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~-~~~~~~~~~~~~  215 (222)
                      +|++|+||++++|||+++++ .|+++|++  .++|||+||+||||||+++++++++++++||++|+. .+.++...++++
T Consensus         1 dG~v~~vs~~~~rrll~~~~~~ml~~l~~--~~~~eI~VG~NGrIWi~~~~~~~~i~i~~aI~~~e~~~~~~~~~~~vk~   78 (85)
T d2ja9a2           1 DGMIIDVNLNFARQLLFNNDFPLLKVLAA--HTKFEVAIGLNGKIWVKCEELSNTLACYRTIMECCQKNDTAAFKDIAKR   78 (85)
T ss_dssp             SCEEEECCHHHHHHHHHCTTCCHHHHHHT--TCCCEEEEETTTEEEEECSSHHHHHHHHHHHHHHHHHCCGGGHHHHHHH
T ss_pred             CCEEEEecHHHHHHHHcCCCChHHHHHHh--hcCceEEEecCcEEEEECCCHHHHHHHHHHHHHHHHhCCHhHHHHHHHH
Confidence            69999999999999997654 69999999  999999999999999999999999999999999975 445555555555


Q ss_pred             HHHHh
Q psy230          216 IHIRF  220 (222)
Q Consensus       216 ~~~~l  220 (222)
                      +.+.+
T Consensus        79 ~l~e~   83 (85)
T d2ja9a2          79 QFKEI   83 (85)
T ss_dssp             HTTTS
T ss_pred             HHHHH
Confidence            55443

>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=99.79  E-value=1.7e-20  Score=137.81  Aligned_cols=83  Identities=20%  Similarity=0.331  Sum_probs=72.9

Q ss_pred             ccccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeecccc--ccc---------cccCCcCCCCCCEEEEEEEecCCCC
Q psy230           49 QRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAF--EGA---------TKKNPPKVETGDVVAGKLLTANKDM  117 (222)
Q Consensus        49 ~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f--~ga---------tk~~r~~l~~GDlV~ArV~~~~~~~  117 (222)
                      +.+|+|++||+|+|+|+++.+..|+|||++.+.|.||++++  ++.         ..++++.|++||.|.|+|+++++++
T Consensus         1 k~~Y~P~vGdiV~G~V~~v~~~g~~V~I~~~~~g~l~is~i~~~~~~~rr~~~~~~~~~~~~~~~Gd~V~~kV~~v~~dg   80 (95)
T d2nn6h1           1 KTRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDG   80 (95)
T ss_dssp             SCCCCCCSSBCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEETTT
T ss_pred             CCcccCCCCCEEEEEEEEEecCcEEEEeCCCceEEEEHHHccccccccccccchhhhhhhhhcccccEEEEEEEEECCCC
Confidence            46899999999999999999999999999999999998764  332         2357788999999999999999999


Q ss_pred             eeEEEEecCCCccccCccc
Q psy230          118 ESEMVCVDSRGKEFIMGIL  136 (222)
Q Consensus       118 ~~~Ls~~~~~~~~~~~G~L  136 (222)
                      .+.|||++     .+||+|
T Consensus        81 ~i~Ls~r~-----~~~gkl   94 (95)
T d2nn6h1          81 AVSLHTRS-----LKYGKL   94 (95)
T ss_dssp             EEEEECCS-----STTCEE
T ss_pred             CEEEEecc-----ccCCcC
Confidence            99999955     899998

>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=99.74  E-value=2e-18  Score=132.68  Aligned_cols=94  Identities=15%  Similarity=0.130  Sum_probs=76.2

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECC--------CCCeeeecccc---ccccccCCcCCCCCCEEEEEEEecCCCC-e
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGS--------HDPAVLSYLAF---EGATKKNPPKVETGDVVAGKLLTANKDM-E  118 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~--------~~~a~L~~~~f---~gatk~~r~~l~~GDlV~ArV~~~~~~~-~  118 (222)
                      +|+|++||+|+|+|+++++++|.|||.+        ++.|+++....   +....+|+++|++||+|.|||+|+++.. .
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            6999999999999999999999999976        45566665432   2233479999999999999999998765 5


Q ss_pred             eEEEEecCCCccccCccc-----CCceEEEechhhh
Q psy230          119 SEMVCVDSRGKEFIMGIL-----NDGYLLHTSISLC  149 (222)
Q Consensus       119 ~~Ls~~~~~~~~~~~G~L-----~~G~l~~v~~~~~  149 (222)
                      ++|||.+     +.||+|     .+..|+++++..+
T Consensus        82 ~~Lst~~-----~~LGVv~A~c~~g~~m~~~~~~~m  112 (125)
T d2nn6i1          82 YLLTTAE-----NELGVVVAHSESGIQMVPISWCEM  112 (125)
T ss_dssp             EEEECCS-----SSCEECCCBCSSSCBCEEEETTEE
T ss_pred             EEEEecC-----CCcEEEEEECCCCCEeEeecCCEE
Confidence            8999966     899999     4567777777644

>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=99.73  E-value=6.6e-18  Score=121.82  Aligned_cols=81  Identities=31%  Similarity=0.383  Sum_probs=73.9

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc-----cccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA-----TKKNPPKVETGDVVAGKLLTANKDMESEMVCVD  125 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-----tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  125 (222)
                      .|.|++||+|+|+|+++++..|.|||++...|.||.+.+...     ..++++.|++||.|.|||.++++++.+.|||++
T Consensus         2 ~Y~Pk~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se~~~~~~~~~~~~~~~~~~vGd~V~~kV~~vd~~~~i~Ls~k~   81 (88)
T d2z0sa1           2 IYVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQG   81 (88)
T ss_dssp             CCCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCS
T ss_pred             CcCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCcccccccccchhhhcccCcEEEEEEEEECCCCCEEEEEec
Confidence            599999999999999999999999999999999999876542     347889999999999999999998999999966


Q ss_pred             CCCccccCccc
Q psy230          126 SRGKEFIMGIL  136 (222)
Q Consensus       126 ~~~~~~~~G~L  136 (222)
                           .++|+|
T Consensus        82 -----~~~gkl   87 (88)
T d2z0sa1          82 -----EGLGRI   87 (88)
T ss_dssp             -----SSCEEC
T ss_pred             -----CCCccc
Confidence                 899987

>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=99.71  E-value=1.5e-17  Score=119.76  Aligned_cols=82  Identities=21%  Similarity=0.269  Sum_probs=74.6

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc----cccCCcCCCCCCEEEEEEEecCCCCeeEEEEecC
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA----TKKNPPKVETGDVVAGKLLTANKDMESEMVCVDS  126 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga----tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~  126 (222)
                      .|+|++||+|+|+|+++++..|+|||++...|.||.+.+..+    .+++++.|++||.|.|+|+++++++.+.||+++ 
T Consensus         2 ~Y~Pk~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~~~~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~i~LS~k~-   80 (87)
T d2je6i1           2 FYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKG-   80 (87)
T ss_dssp             CCCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETTEEEEEECCS-
T ss_pred             cccCCCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCceeccccccchhhcccceEEEEEEEECCCCCEEEEEec-
Confidence            699999999999999999999999999999999999887543    346889999999999999999988999999965 


Q ss_pred             CCccccCcccC
Q psy230          127 RGKEFIMGILN  137 (222)
Q Consensus       127 ~~~~~~~G~L~  137 (222)
                          .++|+|+
T Consensus        81 ----~~lgkl~   87 (87)
T d2je6i1          81 ----KDLGRVS   87 (87)
T ss_dssp             ----TTCEECC
T ss_pred             ----CCCccCC
Confidence                8999984

>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=99.67  E-value=1.8e-16  Score=112.81  Aligned_cols=80  Identities=28%  Similarity=0.409  Sum_probs=73.2

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc--cccCCcCCCCCCEEEEEEEecCCCCeeEEEEecCCCc
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA--TKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGK  129 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga--tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~  129 (222)
                      |.|++||+|.|+|+++.+..|.|||++...|+||.+.++..  .+++++.|++||.|.|+|.++++++.+.||+++    
T Consensus         1 Y~Pk~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~s~~~~~~~~~~~~~vGd~V~~kV~~vd~~~~i~LS~k~----   76 (83)
T d2ba0a1           1 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKD----   76 (83)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECTTCCEEEECCS----
T ss_pred             CcCCCCCEEEEEEEEEECCEEEEecCCCeeEEEecccccccccccChhhhcccccEEEEEEEEECCCCCEEEEecC----
Confidence            89999999999999999999999999999999999887653  467889999999999999999988899999966    


Q ss_pred             cccCccc
Q psy230          130 EFIMGIL  136 (222)
Q Consensus       130 ~~~~G~L  136 (222)
                       .++|+|
T Consensus        77 -~~~~k~   82 (83)
T d2ba0a1          77 -RICRPI   82 (83)
T ss_dssp             -SSCEEE
T ss_pred             -CCCCCC
Confidence             788876

>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.35  E-value=1.3e-13  Score=98.95  Aligned_cols=80  Identities=16%  Similarity=0.182  Sum_probs=73.1

Q ss_pred             CceEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHH
Q psy230          138 DGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIH  217 (222)
Q Consensus       138 ~G~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~  217 (222)
                      .|.+++|++.++++++|+++++++.|.+  .++|.|.|+.||+|||.+++......+..+|+.+..  ++|+.++++++.
T Consensus         1 ~g~vi~I~~~ki~~vIG~gG~~ik~i~~--~t~~~I~I~d~G~V~I~g~~~~~~~~A~~~I~~I~~--ea~v~gl~~rI~   76 (87)
T d2z0sa2           1 RGKIVEISPAKVPRVIGRKMSMLKTLEE--KTECKIFVARNGRIHLECPNEDLEAIAVMAIKIIDE--EAYTSGLTKRII   76 (87)
T ss_dssp             SSEEEECCGGGSGGGTCGGGHHHHHHHH--HHCCEEEEETTTEEEEECSCHHHHHHHHHHHHHHHH--CSCCTTCHHHHH
T ss_pred             CcEEEEEChhhcceeECCCCcHHHHHHH--HHCCEEEECCCcEEEEEeCCHHHHHHHHHHHHHHHH--hchhccHHHHHH
Confidence            3789999999999999999999999999  999999999999999999999888889999999987  677788888888


Q ss_pred             HHhc
Q psy230          218 IRFL  221 (222)
Q Consensus       218 ~~l~  221 (222)
                      ++|.
T Consensus        77 ~fle   80 (87)
T d2z0sa2          77 KFIE   80 (87)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8774

>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=99.20  E-value=7.5e-12  Score=80.87  Aligned_cols=47  Identities=23%  Similarity=0.263  Sum_probs=42.2

Q ss_pred             CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEecCcEEEEEccccc
Q psy230            1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRR   51 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~~~~v~V~~~~~~   51 (222)
                      +|||.|++.   +|++|+|||.++++|+|+++|.++.. +++++|.|+++|
T Consensus         5 ~PGe~i~~~---~~~~G~Gty~~~~~i~ss~~G~v~~~-n~~i~V~PL~gr   51 (51)
T d2ba0a2           5 LPGDLLSTN---PRAAGYGTYVEGGKVYAKIIGLFDQT-ETHVRVIPLKGR   51 (51)
T ss_dssp             CTTCEEESC---TTSBCTTEEEETTEEEECSSEEEEEC-SSCEEEEECSSS
T ss_pred             cCCcEeecC---CeeCCCCcEEECCEEEEEEEEEEEEE-CCEEEEEeCccC
Confidence            699999864   58999999999999999999999988 589999998764

>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=99.19  E-value=9.4e-12  Score=78.76  Aligned_cols=45  Identities=18%  Similarity=0.311  Sum_probs=41.2

Q ss_pred             CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEecCcEEEEEcc
Q psy230            1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYI   48 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~~~~v~V~~~   48 (222)
                      +|||.|...  +.|+.|||||.++++++||++|.++.. |++++|+|+
T Consensus         4 ~PGe~It~~--~~~mrGHGTy~~~~~i~aSv~G~verv-NKLvsV~pL   48 (48)
T d2nn6h2           4 VPGDTITTD--TGFMRGHGTYMGEEKLIASVAGSVERV-NKLICVKAL   48 (48)
T ss_dssp             CTTCBCCCC--TTCCBCTTEEECSSSEEECSSEEEEEE-TTEEEEEES
T ss_pred             cCCcEeecC--CCeEcccccEecCCEEEEEEeeeEEEe-ccEEEEEcC
Confidence            599999876  579999999999999999999999998 599999984

>d2ba0a3 d.51.1.1 (A:136-219) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.95  E-value=9.7e-11  Score=83.17  Aligned_cols=78  Identities=15%  Similarity=0.253  Sum_probs=67.9

Q ss_pred             ceEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcCCHHHHHHHHHHHHH
Q psy230          139 GYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESIHI  218 (222)
Q Consensus       139 G~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~~~~~~~~~~~~~~~  218 (222)
                      |.++.||+.++++++|+++++++.|.+  .+++.|-+..||+|||.++ +.....+..+|+.+..  +++..++++++.+
T Consensus         2 g~vi~Ip~~~ig~IIG~gG~~I~~I~~--~tg~~I~i~~~g~v~I~G~-~e~v~~A~~~I~~i~~--ea~~~g~~~~I~~   76 (84)
T d2ba0a3           2 GRIVAINPARVPRVIGKKGSMIKLLKS--ELDVQIVVGQNGLIWVNGD-RRKVSIAEEAIYLIEQ--EAHTEGLTDRVAE   76 (84)
T ss_dssp             SEEEECCGGGHHHHHCGGGHHHHHHHH--HHTCEEEECTTSEEEEESC-HHHHHHHHHHHHHHHH--CSCCSSHHHHHHH
T ss_pred             cEEEEEChhhcceeeCCcHHHHHHHHH--HHCCEEEECCCCEEEEEeC-HHHHHHHHHHHHHHHH--hcccCcHHHHHHH
Confidence            678999999999999999999999999  9999999999999999985 5567777777777766  6677788888888


Q ss_pred             Hhc
Q psy230          219 RFL  221 (222)
Q Consensus       219 ~l~  221 (222)
                      +|.
T Consensus        77 ~l~   79 (84)
T d2ba0a3          77 FIK   79 (84)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            775

>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=98.92  E-value=4.8e-10  Score=74.24  Aligned_cols=47  Identities=15%  Similarity=0.168  Sum_probs=40.7

Q ss_pred             CCCCeecCCCCCCee-eCCCeEEeCCEEEEEEeeEEEEecCcEEEEEcccc
Q psy230            1 MAGDTLSLNAEPRLI-LGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQR   50 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~-~G~G~y~~~~~i~as~~G~l~~~~~~~v~V~~~~~   50 (222)
                      +|||+|++.  ..+. .|+|||.++++|+||++|.++.. +++++|.|+++
T Consensus        12 ~PGdvi~~~--~~~~~~g~~ty~~~~ki~asv~G~v~~~-nkli~ViPL~G   59 (59)
T d2je6i2          12 VPGELLAEG--EFQIPWSPYILKINSKYYSTVVGLFDVK-DTQFEVIPLEG   59 (59)
T ss_dssp             CTTCEEEEE--CCCCCCCTTEEEETTEEEECSSEEEEEE-TTEEEEEESCC
T ss_pred             CCCcEeeeC--CccccCCCEEEecCCEEEEEEEEEEEEE-CCEEEEEECCC
Confidence            699999875  3455 49999999999999999999998 58999999864

>d2je6i3 d.51.1.1 (I:153-221) Exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.84  E-value=1.2e-10  Score=79.76  Aligned_cols=64  Identities=16%  Similarity=0.281  Sum_probs=51.2

Q ss_pred             CceEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhc
Q psy230          138 DGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCEL  203 (222)
Q Consensus       138 ~G~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~  203 (222)
                      +|.+++||+.++++++|+++.+++.|.+  .++++|-++.||+|||.+.+......+..+|+.+..
T Consensus         1 ~g~vi~Ip~~~ig~iIGkgG~~Ik~i~~--~tg~~I~i~~~g~v~I~g~~~~~v~~A~~~I~~i~~   64 (69)
T d2je6i3           1 NGIVIDIMPVKVPRVIGKNKSMYETLTS--KSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIEN   64 (69)
T ss_dssp             SSCEEECCGGGHHHHHCGGGHHHHHHHT--TC---CEECTTSEEEC-----CTTCCTHHHHTTTTT
T ss_pred             CCEEEEEChhhccceECCchhHHHHHHH--HHCCEEEEcCCCEEEEEeCCHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999  999999999999999999888777778888877765

>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=98.82  E-value=1.5e-10  Score=75.51  Aligned_cols=45  Identities=20%  Similarity=0.124  Sum_probs=36.7

Q ss_pred             CCCCeecCCCCCCeeeCCCeEEeCCEEEEEEeeEEEEec-CcEEEEEc
Q psy230            1 MAGDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAK-PFTYYVDY   47 (222)
Q Consensus         1 ~PGd~l~~~~~~~~~~G~G~y~~~~~i~as~~G~l~~~~-~~~v~V~~   47 (222)
                      +|||.|+..  ++|.+|+|||+++|.|+||++|.+..++ ++.++|.+
T Consensus         4 lPGe~L~~~--eey~~G~gTy~~~g~I~as~~G~v~id~~~~~isVis   49 (55)
T d2nn6i2           4 IPGERLCNL--EEGSPGSGTYTRHGYIFSSLAGCLMKSSENGALPVVS   49 (55)
T ss_dssp             CTTCEEEET--TTCCCSSSCEEETTEEECCSCSCBCCCBCTTSSBC-C
T ss_pred             cCCcEEeeh--heecCCCCeEEcCCEEEEEeeEEEEEecCCCEeeEEE
Confidence            699999987  5799999999999999999999998753 33344443

>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=98.66  E-value=3.3e-08  Score=68.18  Aligned_cols=72  Identities=18%  Similarity=0.174  Sum_probs=63.7

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCCCeeEEEEec
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD  125 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  125 (222)
                      .++|++|-|+|+++.+..+.|+++....|.+|.+.+. ...++.+..|++||-|.|+|+++++...+.||+++
T Consensus         3 ~kvG~iv~G~V~~v~~~G~fV~l~~~~~Glv~~sels~~~~~~~~~~~~~G~~v~v~Vi~id~~~ri~LS~k~   75 (76)
T d1sroa_           3 IEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSIKE   75 (76)
T ss_dssp             CCTTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSSCSSCCSCHHHHCCTTCEEEEEEEECCTTCCCEEEECC
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHhCccccCCHHHccCCCCEEEEEEEEECCCCCEEEEEEc
Confidence            4799999999999999999999998889999998764 34566778899999999999999887789999864

>d2nn6h3 d.51.1.1 (H:168-293) Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.64  E-value=5e-09  Score=79.40  Aligned_cols=41  Identities=29%  Similarity=0.385  Sum_probs=33.9

Q ss_pred             CceEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeC
Q psy230          138 DGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCE  186 (222)
Q Consensus       138 ~G~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~  186 (222)
                      .|++++|+|++++|...+..    .|    .+++++++|+||+|||+..
T Consensus         1 ~G~lv~V~p~LVkR~K~Hf~----~L----~~gv~vILG~NGyIWIs~~   41 (126)
T d2nn6h3           1 QGVLVQVSPSLVKRQKTHFH----DL----PCGASVILGNNGFIWIYPT   41 (126)
T ss_dssp             SSCEEECCTTSCCCSTTCSC----CC----BTTBEEEEETTTEEEEECC
T ss_pred             CCEEEEEChHHhhhhhhceE----Ec----CCCceEEEecCCEEEeeCC
Confidence            38999999999999875322    23    6899999999999999765

>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=98.61  E-value=1.2e-07  Score=66.66  Aligned_cols=72  Identities=11%  Similarity=0.033  Sum_probs=53.3

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECC--CCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCC-CCeeEEEE
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGS--HDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANK-DMESEMVC  123 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~  123 (222)
                      ..|++||+|.|+|+++....+.|+|..  .-.|.+|.+.+. ...++....|++||.|.|+|+++++ ...+.||.
T Consensus         9 ~~p~~G~iv~G~V~~i~~~G~fV~l~~~~~i~G~i~~sels~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~ki~LS~   84 (86)
T d1kl9a2           9 KFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSK   84 (86)
T ss_dssp             SSCCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC------------CTTCEEEEEEEEEETTTTEEEEES
T ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccccccccceEEeecccEEEEEEEEEECCCCEEEEEe
Confidence            368999999999999999999999975  468999988764 4556778889999999999999975 45677775

>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=98.55  E-value=3.7e-08  Score=69.00  Aligned_cols=73  Identities=14%  Similarity=0.165  Sum_probs=59.4

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEECC--CCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEe
Q psy230           52 YVPTRGDLVIGVVTSRVGDNYRVDIGS--HDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANKD-MESEMVCV  124 (222)
Q Consensus        52 Y~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~  124 (222)
                      -.|++||+|-|+|+++.+..+.|++..  ...|.+|.+.+. ...++.+..|++||.|.|+|+++++. ..+.||++
T Consensus         7 ~~p~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~~~~~~~~~~~~~G~~v~~kV~~vd~~~~~i~LS~K   83 (84)
T d2ahob2           7 KLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLK   83 (84)
T ss_dssp             SSCCTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC-----CHHHHTCSSCEEECEEEEEETTTTEEEEESS
T ss_pred             cCCCCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEccccccccccccceEeecccEEEEEEEEEECCCCEEEEEEc
Confidence            479999999999999999999999985  358999988765 34456677899999999999999754 56888863

>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=98.27  E-value=1.3e-06  Score=62.24  Aligned_cols=71  Identities=24%  Similarity=0.247  Sum_probs=61.9

Q ss_pred             CCCCEEEEEEEEEecceEEEEECCCCCeeeeccccc-cccccCCcCCCCCCEEEEEEEecCC-CCeeEEEEec
Q psy230           55 TRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFE-GATKKNPPKVETGDVVAGKLLTANK-DMESEMVCVD  125 (222)
Q Consensus        55 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  125 (222)
                      ++|++|-|+|+++......|+++....|.+|.+... ....+.+..|++||.|.|+|.+++. .+.+.||++.
T Consensus        17 k~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~vGq~v~~~V~~id~~~~~i~LS~K~   89 (94)
T d3bzka4          17 KPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGLSMRM   89 (94)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCSSCCSCHHHHCCTTCEEEEEEEEEETTTTEEEEESCT
T ss_pred             CCCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhcccccChhhhhccCcEEEEEEEEEECCCCEEEEEEec
Confidence            679999999999999999999999999999987763 4456677789999999999999975 5779999863

>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=98.12  E-value=6.8e-06  Score=59.71  Aligned_cols=62  Identities=19%  Similarity=0.220  Sum_probs=53.3

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc------------cccCCcCCCCCCEEEEEEEecCCC
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA------------TKKNPPKVETGDVVAGKLLTANKD  116 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~  116 (222)
                      |++||++=|+|++++.-.++|+|+ +-.|.+|.+.++..            .++....|++||-|.++|.+++.+
T Consensus         1 p~~gei~~g~V~~v~~~G~FVel~-~ieGlv~~s~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~   74 (106)
T d1go3e1           1 PEMYELIEGEVVDVVEFGSFVRLG-PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLK   74 (106)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSCSSCEEECCC--CEEETTTCCEECTTCEEEEEEEEEECC
T ss_pred             CCCCCEEEEEEEEEeeeEEEEEee-CeEEEEEeecccCceeeeccceeEEeecccccceeecceEEEEEEEEchh
Confidence            899999999999999999999997 47899998876531            135668999999999999999754

>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=98.12  E-value=3.8e-06  Score=62.29  Aligned_cols=72  Identities=22%  Similarity=0.254  Sum_probs=60.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEC-CCCCeeeecccccc--ccccCCcCCCCCCEEEEEEEecCCC-CeeEEEEec
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIG-SHDPAVLSYLAFEG--ATKKNPPKVETGDVVAGKLLTANKD-MESEMVCVD  125 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~-~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  125 (222)
                      -++|++|-|+|+++....+.|+|+ ....|++|...+..  ..+.....|++||.|.|+|.++++. ..+.||++.
T Consensus        19 l~~G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~~~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~LS~k~   94 (119)
T d1wi5a_          19 LKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGH   94 (119)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHHHHHHSSSCCCCTTCEEEEEEEECCTTSCEEEEECCC
T ss_pred             cCCCCEEEEEEEEEeccEEEEEEeccccceEEeHHHhccccccCCHHHhcccceEEEEEEEEEeCCCCEEEEEecH
Confidence            478999999999999999999997 56689999877543  2345567899999999999999865 459999864

>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=98.06  E-value=8.7e-06  Score=57.30  Aligned_cols=80  Identities=15%  Similarity=0.221  Sum_probs=60.5

Q ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc-----------cccCCcCCCCCCEEEEEEEecCCCCeeEEE
Q psy230           54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA-----------TKKNPPKVETGDVVAGKLLTANKDMESEMV  122 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-----------tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls  122 (222)
                      |-+|+++-|+|++++...+.|+|+ +..+.+|.+..+..           -++....++.||.|.+||.+++.+.. .+.
T Consensus         1 Pf~Gev~~g~I~~v~~~G~fv~lg-~~eg~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~-~i~   78 (91)
T d1y14b1           1 PFKGEVVDGTVVSCSQHGFEVQVG-PMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVS-SIH   78 (91)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCTTCEECC-----CEECSSCEECTTCEEEEEEEEEEEETT-EEE
T ss_pred             CCCCCEEEEEEEEEEeeEEEEEEc-CeEEEEEhhhcCcceEEccccceeEecccCeEEeCCCEEEEEEEEEecccC-ccE
Confidence            789999999999999999999997 46899998765421           13556789999999999999874322 234


Q ss_pred             EecCCCccccCccc
Q psy230          123 CVDSRGKEFIMGIL  136 (222)
Q Consensus       123 ~~~~~~~~~~~G~L  136 (222)
                      |.. +-++++||.+
T Consensus        79 ~ig-~~~~d~LG~i   91 (91)
T d1y14b1          79 AIG-SIKEDYLGAI   91 (91)
T ss_dssp             EEE-ECCSTTCEEC
T ss_pred             EEE-EccCCCCCcC
Confidence            433 3355788864

>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=97.93  E-value=2.2e-06  Score=60.06  Aligned_cols=38  Identities=47%  Similarity=0.847  Sum_probs=23.1

Q ss_pred             CeeeCCCeEEeCCEEEEEEeeEEEEecCc------EEEEEcccc
Q psy230           13 RLILGPGLRRESSAILVSQSGILRHAKPF------TYYVDYIQR   50 (222)
Q Consensus        13 ~~~~G~G~y~~~~~i~as~~G~l~~~~~~------~v~V~~~~~   50 (222)
                      ..+.|||++.+++.|.++.+|.|++++++      +|||+..++
T Consensus        48 ~v~lGPGLRq~~d~v~atKaG~LR~k~P~~~~~~~~yWVDs~QK   91 (91)
T d2nn6g2          48 RVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQK   91 (91)
T ss_dssp             -----------CCCEEECSCCEEEEECCTTTSSCCEEEEECCCS
T ss_pred             eEEeCCccceeCCEEEEeecceeeecCCCCCCCcceEEeecccC
Confidence            57889999999999999999999988655      599998653

>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=97.80  E-value=3.2e-05  Score=54.65  Aligned_cols=81  Identities=17%  Similarity=0.237  Sum_probs=60.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccc-------------cccCCcCCCCCCEEEEEEEecCCCCee
Q psy230           53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA-------------TKKNPPKVETGDVVAGKLLTANKDMES  119 (222)
Q Consensus        53 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-------------tk~~r~~l~~GDlV~ArV~~~~~~~~~  119 (222)
                      .|-+|.++-|+|++++...+.|+++ +..+.+|.+.++..             .++.+..++.||.|++||.+++.+. -
T Consensus         1 rPf~Gev~~g~V~~v~~~G~fv~lg-~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~-~   78 (94)
T d2c35b1           1 RPFKGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDK-N   78 (94)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEET-T
T ss_pred             CCCCCCEEEEEEEEEEeeEEEEEec-CceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCc-C
Confidence            3889999999999999999999997 56899987665421             1355678999999999999876432 2


Q ss_pred             EEEEecCCCccccCccc
Q psy230          120 EMVCVDSRGKEFIMGIL  136 (222)
Q Consensus       120 ~Ls~~~~~~~~~~~G~L  136 (222)
                      .++++. +-++++||.+
T Consensus        79 ~I~~ig-t~~~d~LG~i   94 (94)
T d2c35b1          79 DIFAIG-SLMDDYLGLV   94 (94)
T ss_dssp             EEEEEE-ECCSTTCEEC
T ss_pred             cceEEE-EccCCCcccC
Confidence            334442 3356888864

>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=97.68  E-value=0.00013  Score=49.30  Aligned_cols=59  Identities=19%  Similarity=0.255  Sum_probs=50.1

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEECCCCCeeeeccccccccccCCcCCCCCCEEEEEEEecCC
Q psy230           51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANK  115 (222)
Q Consensus        51 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~  115 (222)
                      .|..++|++|.|+|.++..+.+.|||+. ..|+||...     .-....|++||-|.|-|..+.+
T Consensus         3 ef~~~~geiv~G~V~r~~~~~~~Vdlg~-~eaiLp~~e-----qip~E~~~~Gdrik~~i~~V~~   61 (72)
T d1hh2p1           3 KYSELKGTVTTAEVIRVMGEWADIRIGK-LETRLPKKE-----WIPGEEIKAGDLVKVYIIDVVK   61 (72)
T ss_dssp             CTTCCTTCEEEEEEEEECSSEEEEEETT-EEEEEEGGG-----SCTTCCCCTTCEEEEEEEEEEE
T ss_pred             hHhhccCcEEEEEEEEEcCCCEEEEECC-cEEECCHHH-----cCCCCCCCCCCEEEEEEEEEEE
Confidence            4788999999999999999999999985 889999543     2235689999999999998754

>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=96.97  E-value=3.3e-05  Score=50.72  Aligned_cols=55  Identities=11%  Similarity=0.061  Sum_probs=34.7

Q ss_pred             EEEEEEecceEEEEECCCCCeeeecccccc-----ccccCCcCCCCCCEEEEEEEecCCC
Q psy230           62 GVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-----ATKKNPPKVETGDVVAGKLLTANKD  116 (222)
Q Consensus        62 G~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-----atk~~r~~l~~GDlV~ArV~~~~~~  116 (222)
                      |+|+++.+-.++|+|.....|.+|.+.+..     ..++.+..|++||.|.|+|+++++.
T Consensus         1 G~V~~i~~fG~FV~l~~g~~Glihiseis~~~~~~~v~~~~~~~~~G~~V~vkV~~iD~~   60 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSR   60 (62)
T ss_dssp             CBEEECC-CSCEECCC---CCCCC-------------------CCSSCBCCCCCCCCCSS
T ss_pred             CEEEEEEeceEEEEecCCceEEEEHHHcccccccccccCHHHhcCCCCEEEEEEEEEcCC
Confidence            789999999999999999999999988742     3457788999999999999999864

>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=96.26  E-value=0.0041  Score=42.01  Aligned_cols=58  Identities=17%  Similarity=0.267  Sum_probs=45.2

Q ss_pred             CCCCCEEEEEEEEEecc----eEEEEECC---CCCeeeeccccccccccCCcCCCCCCEEEEEEEecCCC
Q psy230           54 PTRGDLVIGVVTSRVGD----NYRVDIGS---HDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKD  116 (222)
Q Consensus        54 P~vGDiVIG~V~~v~~~----~~~VdI~~---~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~  116 (222)
                      -++|++|.|+|..+..+    ...||++.   ...|+||...     +--...|++||-|+|-|..+.++
T Consensus         2 ~r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~e-----qip~E~y~~Gdrik~~i~~V~~~   66 (76)
T d2asba1           2 TREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAE-----QVPGESYEHGNRLRCYVVGVTRG   66 (76)
T ss_dssp             CCTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGG-----SCTTCCCCTTCEEEEEEEEEECC
T ss_pred             CccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHH-----cCCCcccCCCCEEEEEEEEEEec
Confidence            36899999999998654    47899985   4679999532     23356799999999999988654

>d2cpqa1 d.51.1.1 (A:212-289) Fragile X mental retardation syndrome related protein 1, FXR1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Fragile X mental retardation syndrome related protein 1, FXR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.13  E-value=0.0062  Score=41.15  Aligned_cols=57  Identities=16%  Similarity=0.004  Sum_probs=47.3

Q ss_pred             EEechhhhhhccCCChhHHHHhhhcCCCcEEEEE--EeCCeEEEeeCCchhHHHHHHHHHHhhc
Q psy230          142 LHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSI--GMNGKIWIRCESFSDTVRVGNLIMSCEL  203 (222)
Q Consensus       142 ~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~v--G~NG~iWi~~~~~~~~~~i~~~i~~~e~  203 (222)
                      |.|++.++..++|+++..++.|.+  .+++.+.+  ..+|.|-|.+.++.   .+.+|-+.+|.
T Consensus        12 i~Ip~~~ig~vIG~gG~~I~~I~~--~tGa~i~i~~~~~g~v~I~g~~~e---av~~A~~~Ie~   70 (78)
T d2cpqa1          12 FVVREDLMGLAIGTHGSNIQQARK--VPGVTAIELDEDTGTFRIYGESAD---AVKKARGFLEF   70 (78)
T ss_dssp             EECCHHHHHHHHTTTTHHHHHHHT--STTEEEEEEETTTTEEEEEESSHH---HHHHHHHHHSC
T ss_pred             EEECHHHHHHHcCCChHHHHHHHH--hcCcEEEEecCCCceEEEEECCHH---HHHHHHHHHHH
Confidence            889999999999999999999999  99998887  44699999998776   45555555554

>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=95.28  E-value=0.037  Score=37.96  Aligned_cols=66  Identities=12%  Similarity=0.131  Sum_probs=49.7

Q ss_pred             CEEEEEEEEEec--ceEEEEECCCCCeeeecccccc----------ccccCCcCCCCCCEEEEEEEecC-CCCeeEEEE
Q psy230           58 DLVIGVVTSRVG--DNYRVDIGSHDPAVLSYLAFEG----------ATKKNPPKVETGDVVAGKLLTAN-KDMESEMVC  123 (222)
Q Consensus        58 DiVIG~V~~v~~--~~~~VdI~~~~~a~L~~~~f~g----------atk~~r~~l~~GDlV~ArV~~~~-~~~~~~Ls~  123 (222)
                      |+-.|+|.++.+  +.++|||+..-.|+||+.....          ..++....+++||-|...|..=. ...-+.||+
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~~~~KGprlT~   80 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTT   80 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSSSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEECCBTTBCCEEES
T ss_pred             CcEEEEEEEecCCceEEEEEeCCCccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeecccCCCCceEEE
Confidence            678999999965  8899999999999999854210          12356678999999999998643 223466665

>d1tuaa1 d.51.1.1 (A:1-84) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=94.53  E-value=0.021  Score=39.01  Aligned_cols=61  Identities=7%  Similarity=0.196  Sum_probs=47.9

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEE-eCCeEEEeeCCch----hHHHHHHHHHHhh
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIG-MNGKIWIRCESFS----DTVRVGNLIMSCE  202 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG-~NG~iWi~~~~~~----~~~~i~~~i~~~e  202 (222)
                      +.++|++.++..++|+++..++.|.+  .+++.|-|- .+|.+.+.+.+..    ....+...|+.+.
T Consensus         5 i~i~ip~~~ig~vIG~gG~~Ik~i~~--~tg~~I~Id~d~g~v~i~~~~~~~~~~a~~~a~~iI~aI~   70 (84)
T d1tuaa1           5 IYVKVKPERLGAVIGPRGEVKAEIMR--RTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVVKAIS   70 (84)
T ss_dssp             EEEECCGGGHHHHHCGGGHHHHHHHH--HHTEEEEEETTTTEEEEEESSTTSCHHHHHHHHHHHHHHH
T ss_pred             EEEEeCHHHcCeeecCCchhHHHHHH--HHCCEEEEEcCCCeEEEecCCccccHHHHHHHHHHHHHHh
Confidence            35799999999999999999999999  999999885 8899999986532    2334444555444

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=93.83  E-value=0.066  Score=36.51  Aligned_cols=57  Identities=11%  Similarity=0.073  Sum_probs=45.7

Q ss_pred             EEEEEEEEecceEEEEECC-CCCeeeeccccccc-------------cccCCcCCCCCCEEEEEEEecCCC
Q psy230           60 VIGVVTSRVGDNYRVDIGS-HDPAVLSYLAFEGA-------------TKKNPPKVETGDVVAGKLLTANKD  116 (222)
Q Consensus        60 VIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~ga-------------tk~~r~~l~~GDlV~ArV~~~~~~  116 (222)
                      -=|.|++++.....|.|.. ...|.+|++.++..             -++.+..|+.||-|.++|..++..
T Consensus         7 F~g~Is~v~~~GifV~L~e~~~eGlI~~s~L~~d~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~   77 (87)
T d2ix0a3           7 FAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRME   77 (87)
T ss_dssp             EEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETT
T ss_pred             EEEEEEEEEcCeEEEEEecCCcEEEEEehhCCCceEEEeccceEEEEEEcccEEEECCCEEEEEEEEEecc
Confidence            3489999999999999965 67999998776531             123456799999999999999765

>d1e3ha4 d.52.3.1 (A:579-632) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6
species: Streptomyces antibioticus [TaxId: 1890]

Probab=93.70  E-value=0.0022  Score=40.65  Aligned_cols=47  Identities=17%  Similarity=0.356  Sum_probs=15.5

Q ss_pred             EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCch
Q psy230          141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFS  189 (222)
Q Consensus       141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~  189 (222)
                      .++|++.++..++|+++..++.|.+  .++++|-+..+|.|+|.+.|..
T Consensus         6 ~i~Ip~~kig~vIG~GG~~Ik~I~~--~tga~I~i~ddg~v~I~a~~~~   52 (54)
T d1e3ha4           6 TVKIPVDKIGEVIGPKRQMINQIQE--DTGAEITIEDDGTIYIGAADGP   52 (54)
T ss_dssp             ---------------------CHHH--HSCCCC--------CCCCBSSC
T ss_pred             EEEeCHHHeeEEECCccHHHHHHHH--HHCCEEEEeCCeEEEEEecCcc
Confidence            4789999999999999999999999  8999999999999999987753

>d2ctma1 d.51.1.1 (A:8-88) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.55  E-value=0.052  Score=36.25  Aligned_cols=57  Identities=7%  Similarity=0.075  Sum_probs=44.1

Q ss_pred             EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC-----eEEEeeCCchhHHHHHHHHHHhhc
Q psy230          141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG-----KIWIRCESFSDTVRVGNLIMSCEL  203 (222)
Q Consensus       141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG-----~iWi~~~~~~~~~~i~~~i~~~e~  203 (222)
                      -+.|++.+.++++|++++.++.|.+  .+++.|-+..++     .|+|.++ +.   .+.+|.+.++.
T Consensus        13 ~i~Vp~~~~~~iIG~~G~~i~~I~~--~tg~~I~~p~~~~~~~~~v~I~G~-~~---~V~~A~~~I~~   74 (81)
T d2ctma1          13 DVPLDHRVHARIIGARGKAIRKIMD--EFKVDIRFPQSGAPDPNCVTVTGL-PE---NVEEAIDHILN   74 (81)
T ss_dssp             EEECCTTTHHHHHCSSSCHHHHHHH--HHTCEEECCCTTCSCTTEEEEESC-HH---HHHHHHHHHHH
T ss_pred             EEEECHHHHhhccCCCCccHHHHHH--HhCCEEEeCCccCCCCCEEEEeCC-HH---HHHHHHHHHHH
Confidence            4889999999999999999999999  899999886644     6899884 33   34444444443

>d1viga_ d.51.1.1 (A:) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.01  E-value=0.11  Score=33.68  Aligned_cols=55  Identities=11%  Similarity=0.189  Sum_probs=41.6

Q ss_pred             EEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeC----CeEEEeeCCchhHHHHHHHHH
Q psy230          142 LHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN----GKIWIRCESFSDTVRVGNLIM  199 (222)
Q Consensus       142 ~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~N----G~iWi~~~~~~~~~~i~~~i~  199 (222)
                      +.|++.+.++++|+++..++.|.+  .+++.|-+-..    ..|.|.+. +..+..+.+.|.
T Consensus         9 i~V~~~~~~~iIG~~G~~i~~I~~--~tg~~I~i~~~~~~~~~v~I~G~-~~~v~~A~~~I~   67 (71)
T d1viga_           9 INIDHKFHRHLIGKSGANINRIKD--QYKVSVRIPPDSEKSNLIRIEGD-PQGVQQAKRELL   67 (71)
T ss_dssp             EEECSSHHHHHTCSSCCHHHHHHH--HTCCEEECCCCCSSSEEEEEEES-SHHHHHHHHHHH
T ss_pred             EEECHHHhcccCCCCCchHHHHHH--HhCCEEEeCCCCCCCCEEEEECC-HHHHHHHHHHHH
Confidence            789999999999999999999999  88888888543    35889885 333444444333

>d1x4na1 d.51.1.1 (A:8-86) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.23  E-value=0.18  Score=33.15  Aligned_cols=55  Identities=4%  Similarity=0.027  Sum_probs=42.1

Q ss_pred             EEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC------eEEEeeCCchhHHHHHHHHHHhh
Q psy230          142 LHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG------KIWIRCESFSDTVRVGNLIMSCE  202 (222)
Q Consensus       142 ~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG------~iWi~~~~~~~~~~i~~~i~~~e  202 (222)
                      +.||..++..++|+++..++.|.+  .+++.|-|-.+.      .|+|.+. +.   .+.+|...++
T Consensus        12 i~IP~~~~g~iIG~~G~~i~~I~~--~tg~~I~i~~~~~~~~~r~v~I~G~-~~---~v~~A~~~I~   72 (79)
T d1x4na1          12 YKVPDGMVGFIIGRGGEQISRIQQ--ESGCKIQIAPDSGGLPERSCMLTGT-PE---SVQSAKRLLD   72 (79)
T ss_dssp             EEEEHHHHHHHHCSSSHHHHHHHH--HSCCEEEECSCCTTCSEEEEEEEEC-HH---HHHHHHHHHH
T ss_pred             EEEChHhhcceECCCchhHHHHHH--HhCCEEEEcCCCCCCCceEEEEEeC-HH---HHHHHHHHHH
Confidence            789999999999999999999999  899999886532      3889984 33   3444444443

>d2ctla1 d.51.1.1 (A:8-91) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.06  E-value=0.15  Score=33.94  Aligned_cols=45  Identities=11%  Similarity=0.139  Sum_probs=38.3

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC-------eEEEeeC
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG-------KIWIRCE  186 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG-------~iWi~~~  186 (222)
                      .-+.|+..++++++|++++.++.|.+  .+++.|-+-..+       .|+|.+.
T Consensus        12 ~~i~Vp~~~~~~iIG~~G~~i~~I~~--~t~~~I~~~~~~~~~~~~~~i~I~G~   63 (84)
T d2ctla1          12 LSVTVDPKYHPKIIGRKGAVITQIRL--EHDVNIQFPDKDDGNQPQDQITITGY   63 (84)
T ss_dssp             EEEECCTTTHHHHSCSSSCHHHHHHH--HHTCEEECCCTTTCSSCSSEEEEESC
T ss_pred             EEEEECHHHHhhhcCCCchhHHHHHH--HhCCEEEECCCCCCCCCcceEEEECC
Confidence            45789999999999999999999999  899999884332       5899885

>d1zzka1 d.51.1.1 (A:11-85) HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: HnRNP K, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.77  E-value=0.38  Score=30.97  Aligned_cols=43  Identities=14%  Similarity=0.107  Sum_probs=36.2

Q ss_pred             EEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC------eEEEeeC
Q psy230          142 LHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG------KIWIRCE  186 (222)
Q Consensus       142 ~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG------~iWi~~~  186 (222)
                      +.||..++.+++|+++..++.|.+  .+++.|-+-.+.      .|.|.+.
T Consensus         8 i~VP~~~vg~iIG~~G~~I~~I~~--~sga~I~i~~~~~~~~~r~i~I~G~   56 (75)
T d1zzka1           8 VTIPKDLAGSIIGKGGQRIKQIRH--ESGASIKIDEPLEGSEDRIITITGT   56 (75)
T ss_dssp             EEEETTTGGGGTCGGGHHHHHHHH--HHCCEEEECCTTSCSSEEEEEEEEC
T ss_pred             EEEChHhcCeeECCCCchHHHHHh--hcCCeEEEccCCCCCCceEEEEEeC
Confidence            678999999999999999999999  888888885432      5888884

>d2ctka1 d.51.1.1 (A:8-98) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.39  E-value=0.29  Score=33.04  Aligned_cols=58  Identities=9%  Similarity=0.052  Sum_probs=43.6

Q ss_pred             eEEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC----eEEEeeCCchhHHHHHHHHHHhhc
Q psy230          140 YLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG----KIWIRCESFSDTVRVGNLIMSCEL  203 (222)
Q Consensus       140 ~l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG----~iWi~~~~~~~~~~i~~~i~~~e~  203 (222)
                      .-+.|++.+.++++|+++..++.|.+  .+++.|.+-.-|    .|-|.++ ..   .+.+|...++.
T Consensus        12 ~~i~Vp~~~~~~iIG~~G~~i~~I~~--~tg~~I~~p~~~~~~~~v~I~G~-~~---~V~~A~~~I~~   73 (91)
T d2ctka1          12 IEVEVPFDLHRYVIGQKGSGIRKMMD--EFEVNIHVPAPELQSDIIAITGL-AA---NLDRAKAGLLE   73 (91)
T ss_dssp             EEEECCHHHHHHHHCSSSHHHHHHHH--HTCCEEECCCTTTTCCEEEEEEC-HH---HHHHHHHHHHH
T ss_pred             EEEEECHHHHhHhcCCCchhHHHHHH--HhCCEEEECCCCCCcceEEEECC-HH---HHHHHHHHHHH
Confidence            45889999999999999999999999  899999985433    4777774 33   34444444443

>d1x4ma1 d.51.1.1 (A:8-88) Far upstream binding element, FBP {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.53  E-value=0.51  Score=30.96  Aligned_cols=54  Identities=13%  Similarity=0.217  Sum_probs=40.1

Q ss_pred             EEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC--------eEEEeeCCchhHHHHHHHH
Q psy230          142 LHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG--------KIWIRCESFSDTVRVGNLI  198 (222)
Q Consensus       142 ~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG--------~iWi~~~~~~~~~~i~~~i  198 (222)
                      +.||..++.+++|+++..++.|.+  .+++.|.|-.+.        .|-|.+.. ..+..+...|
T Consensus        12 i~Vp~~~~g~iIGk~G~~Ik~I~~--~tga~I~i~~~~~~~~~~~r~v~I~G~~-~~v~~A~~~I   73 (81)
T d1x4ma1          12 IMIPASKAGLVIGKGGETIKQLQE--RAGVKMVMIQDGPQNTGADKPLRITGDP-YKVQQAKEMV   73 (81)
T ss_dssp             EEECHHHHHHHSCSSSSHHHHHHH--HHTSEEEECCSCCCSSCSCEEEEEEECT-TTHHHHHHHH
T ss_pred             EEECHHHcCeeECCCCchHHHHHH--HhCCeEEEccCCCCCCCCceEEEEEeCH-HHHHHHHHHH
Confidence            569999999999999999999999  889999886554        26677643 3333333333

>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=86.96  E-value=0.51  Score=30.42  Aligned_cols=47  Identities=15%  Similarity=0.172  Sum_probs=34.3

Q ss_pred             CCCeecCCCCCCeeeCCCeEE-eCCEEEEEEeeEEEEec----CcEEEEEcc
Q psy230            2 AGDTLSLNAEPRLILGPGLRR-ESSAILVSQSGILRHAK----PFTYYVDYI   48 (222)
Q Consensus         2 PGd~l~~~~~~~~~~G~G~y~-~~~~i~as~~G~l~~~~----~~~v~V~~~   48 (222)
                      ||..|..--...|.+|.++.. .|..++|...|.++.+.    .+.++|.|.
T Consensus        14 ~G~IivRQRGtk~~pG~nVg~GkD~TLfAl~~G~V~F~~~~~~~~~VsV~P~   65 (66)
T d1v8qa_          14 AGNILVRQRGTRFKPGKNVGMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPL   65 (66)
T ss_dssp             TTCEEEECSSCSSEECTTEEECTTCCEEESSSEEEEEEECGGGCEEEEEEEC
T ss_pred             CCeEEEEeccCeEeCCCCeeecCCCcEEEeeeeEEEEEEeCCCCeEEEEEEC
Confidence            666665321236889999987 47899999999998742    456888874

>d2ctfa1 d.51.1.1 (A:7-96) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.80  E-value=0.5  Score=31.89  Aligned_cols=52  Identities=12%  Similarity=0.058  Sum_probs=37.4

Q ss_pred             EEEechhhhhhccCCChhHHHHhhhcCCC-cEEEEEEeCCeEEEeeCCchhHHHH
Q psy230          141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQ-KMELSIGMNGKIWIRCESFSDTVRV  194 (222)
Q Consensus       141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~-~~ei~vG~NG~iWi~~~~~~~~~~i  194 (222)
                      -+.||..+.+.++|+++..++.|.+  .+ ++.|-+..+..+..=..++..+..+
T Consensus        24 ~v~VP~~~h~~iIG~~G~~I~~i~~--~~~~v~I~~~~~~~~v~i~G~~~~ve~A   76 (90)
T d2ctfa1          24 SVAAPSWLHRFIIGKKGQNLAKITQ--QMPKVHIEFTEGEDKITLEGPTEDVSVA   76 (90)
T ss_dssp             EEECCSTTHHHHHTTTTCHHHHHHH--HCSSSEEEECSSSCEEEEEECHHHHHHH
T ss_pred             EEEcCHHHHhhcCCCCchhHHHHHH--HcCCcEEeeCCCCceEEEeCCHHHHHHH
Confidence            3678899999999999999999987  54 6888888666554433344433333

>d1we8a_ d.51.1.1 (A:) Tudor and KH domain containing protein, Tdrkh {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Tudor and KH domain containing protein, Tdrkh
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.05  E-value=0.59  Score=32.16  Aligned_cols=56  Identities=9%  Similarity=0.060  Sum_probs=42.1

Q ss_pred             EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC--------eEEEeeCCchhHHHHHHHHHHhh
Q psy230          141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG--------KIWIRCESFSDTVRVGNLIMSCE  202 (222)
Q Consensus       141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG--------~iWi~~~~~~~~~~i~~~i~~~e  202 (222)
                      -+.||..++.+++|+++..++.|.+  .+++.|-|-.++        .|=|.+ ++..   +.+|...++
T Consensus        18 ~i~IP~~~vg~vIGk~G~~Ik~I~~--~tga~I~i~~~~~~~~~~~r~v~I~G-~~~~---v~~A~~~I~   81 (104)
T d1we8a_          18 QLSVPQRSVGRIIGRGGETIRSICK--ASGAKITCDKESEGTLLLSRLIKISG-TQKE---VAAAKHLIL   81 (104)
T ss_dssp             EEEEETTTHHHHHTTTSHHHHHHHH--HHCCEEEECCSSCCSSSSEEEEEEEE-EHHH---HHHHHHHHH
T ss_pred             EEEECHHHhcceECCCCcchHHHHH--HcCCEEEECCCCCCCCCCccEEEEEe-CHHH---HHHHHHHHH
Confidence            3779999999999999999999999  899999885543        366776 4443   444444444

>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=83.90  E-value=0.57  Score=31.55  Aligned_cols=47  Identities=13%  Similarity=0.203  Sum_probs=34.3

Q ss_pred             CCCeecCCCCCCeeeCCCeEE-eCCEEEEEEeeEEEEec----CcEEEEEcc
Q psy230            2 AGDTLSLNAEPRLILGPGLRR-ESSAILVSQSGILRHAK----PFTYYVDYI   48 (222)
Q Consensus         2 PGd~l~~~~~~~~~~G~G~y~-~~~~i~as~~G~l~~~~----~~~v~V~~~   48 (222)
                      ||+.|..--...|.+|.++.. .|..|+|.+-|.|+.+.    .+.++|.|.
T Consensus        32 ~G~IivRQRGtk~hpG~nVg~GkD~TLfA~~~G~V~F~k~~~~rk~V~V~p~   83 (84)
T d2zjrt1          32 AGNILVRQRGTKFKAGQGVGMGRDHTLFALSDGKVVFINKGKGARFISIEAA   83 (84)
T ss_dssp             SSCEEECCSSSSSEECTTEECCTTSCEEESSCEEEEEEEETTTEEEEEECCC
T ss_pred             CCcEEEEecCceEcCCCCccccCCCcEEEeeceEEEEEEcCCCCEEEEEEeC
Confidence            677776322246889999986 47789999999998852    246778774

>d2axya1 d.51.1.1 (A:11-81) Poly(RC)-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Poly(RC)-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.51  E-value=0.93  Score=28.86  Aligned_cols=42  Identities=12%  Similarity=0.096  Sum_probs=35.3

Q ss_pred             EEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEeCC----eEEEee
Q psy230          142 LHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG----KIWIRC  185 (222)
Q Consensus       142 ~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~NG----~iWi~~  185 (222)
                      +.|+..++..++|+++..++.|.+  .+++.|-+..++    .+-|.+
T Consensus         8 i~vp~~~~g~IIGk~G~~I~~I~~--~tga~I~i~~~~~~er~v~I~G   53 (71)
T d2axya1           8 LLMHGKEVGSIIGKKGESVKKMRE--ESGARINISEGNCPERIITLAG   53 (71)
T ss_dssp             EEEEHHHHHHHHCGGGHHHHHHHH--HHCCEEEECSSCCSEEEEEEEE
T ss_pred             EEECHHHcCeEECCCChhHHHHHH--HhCCEEEEcCCCCCcceEEEEE
Confidence            678999999999999999999999  888888887766    344655

>d1j4wa2 d.51.1.1 (A:104-174) Far upstream binding element, FBP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Far upstream binding element, FBP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.39  E-value=1.2  Score=28.32  Aligned_cols=35  Identities=3%  Similarity=0.067  Sum_probs=31.2

Q ss_pred             EEEechhhhhhccCCChhHHHHhhhcCCCcEEEEEEe
Q psy230          141 LLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM  177 (222)
Q Consensus       141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~~~~ei~vG~  177 (222)
                      -+.||..++.+++|+++..++.|.+  .+++.|-+-.
T Consensus         4 ~~~IP~~~vg~IIGk~G~~Ik~I~~--~sga~I~i~~   38 (71)
T d1j4wa2           4 NFIVPTGKTGLIIGKGGETIKSISQ--QSGARIELQR   38 (71)
T ss_dssp             EEEEETTTHHHHHCGGGHHHHHHHH--HHCCEEEEEC
T ss_pred             EEEEChHhcceEECCCCcChHHHHh--hcCcEEEEee
Confidence            4679999999999999999999999  8888888854

>d1tuaa2 d.51.1.1 (A:85-188) Hypothetical protein APE0754 {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Hypothetical protein APE0754
species: Aeropyrum pernix [TaxId: 56636]

Probab=82.06  E-value=0.7  Score=32.31  Aligned_cols=66  Identities=8%  Similarity=0.053  Sum_probs=45.2

Q ss_pred             hccCCChhHHHHhhhcCCCcEEEEEEeCCeEEEeeCCchhHHHHHHHHHHhhcC-CHHHHHHHHHHHHHHh
Q psy230          151 KLLNPKCPLLKQLAKRSRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELL-SYEEILNLCESIHIRF  220 (222)
Q Consensus       151 rl~~~~~~~l~~l~~~~~~~~ei~vG~NG~iWi~~~~~~~~~~i~~~i~~~e~~-~~~~~~~~~~~~~~~l  220 (222)
                      |++|+++..++.|.+  .++++|.|.-++-.-+.  ++.....+-.+|..+-.- ....+-..+++.++.|
T Consensus        26 rIIG~gGktik~Ie~--~Tg~~I~I~d~~v~iig--~~e~i~~A~~~Ie~li~~~e~g~VY~~le~~~~el   92 (104)
T d1tuaa2          26 RIIGEGGRARRTIEE--MTDTYINVGEYEVAIIG--DYERAMAAKQAIEMLAEGRMHSTVYRHLERIMREI   92 (104)
T ss_dssp             HHHCGGGHHHHHHHH--HHTCEEEECSSEEEEEE--EHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             ceeCCCcHHHHHHHH--HHCCeEEEeCCeEEEEE--CchhHHHHHHHHHHHHcCCCccHHHHHHHHHHHHH
Confidence            588999999999999  99999999999876664  344456666666665532 2334445555544443

>d2ctja1 d.51.1.1 (A:8-89) Vigilin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Vigilin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.00  E-value=1  Score=29.44  Aligned_cols=44  Identities=16%  Similarity=0.303  Sum_probs=35.9

Q ss_pred             EEEechhhhhhccCCChhHHHHhhhcCC-CcEEEEEEeCC----eEEEeeC
Q psy230          141 LLHTSISLCRKLLNPKCPLLKQLAKRSR-QKMELSIGMNG----KIWIRCE  186 (222)
Q Consensus       141 l~~v~~~~~~rl~~~~~~~l~~l~~~~~-~~~ei~vG~NG----~iWi~~~  186 (222)
                      -+.||..++++++|+++..++.|.+  . +.+.|-+...|    .|-|.+.
T Consensus        13 ~i~Vp~~~~~~iIGk~G~~I~~I~~--~~~~~~I~~~~~~~~~~~v~I~G~   61 (82)
T d2ctja1          13 EVSIPAKLHNSLIGTKGRLIRSIME--ECGGVHIHFPVEGSGSDTVVIRGP   61 (82)
T ss_dssp             EEECCHHHHHHHHCSSSHHHHHHHH--HHTSCEEECCCTTTTCCEEEEESC
T ss_pred             EEEECHHHHhhcCCCCCccHHHHHH--HcCCcEEEEeCCCCCCceEEEeCC
Confidence            4789999999999999999999965  4 57888886665    5777774