Citrus Sinensis ID: 026458

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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-------230-------24
Protein Sequence
MEAKPSTANLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK
Secondary Structure (PSIPRED)
cccccccccccccEEEcccccccccccccccEEEcccEEEEccEEEEEEEEEEEEccccEEEEEccccccccccccEEEEEEEEEcccEEEEEcccccEEEEEcccccccccccccccccccEEEEEEEEcccccccEEEEEcccccccccccccccEEEEEcccccccEEccccccHHHHHcccccEEEEEEEccEEEEEccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
cccccccccccccEEccccccccccccccccEEEcccEEEcccEEEEEEEEEEEEccccEEEEEcccccEEcccccEEEEEEEEccccEEEEEcccccccEEcHHcccccccccccccccccEEEEEEEEcccccccEEEEEcccccccccccccccEEEEEcHHHHHHHHcccccHHHHHHHHcccEEEEEEcccEEEEEcccHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
meakpstanlvdkivvpGDVVLDLSsmtnqtiklggglrqecdsvsvikagklrfskpnkywvessqkryvpcvedtVLGIVVDCkadnffvdirgptiaflpvlafeggtrrnipkfeigSLLYVRVVKanpgmnpelsctdasgkaaefgllkdgymfetstglsrmllssptcpvlEELGKQLSFEIAVGLNGrvwvnaespsTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK
Flexible Loop (DISEMBL)
meakpstanlvdkivvpGDVVLDLSSMTNQTiklggglrqecdsvsvikagklrfskpnkywvessqkryvPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNseslsavqqkimvdkllqrik
Low Complexity Region (SEG)
MEAKPSTANLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK
Disordered region (IsUnstruct)
*********LVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMN**********I**********
Disordered Region (DISOPRED)
*************IVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAF*****RN*PKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRI*
Disordered Region (DISEMBL)
********NLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK
Disordered Region (DISPRO)
*********LVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEAKPSTANLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK
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	238	2.2.26 [Sep-21-2011]
Q7KWX9	237	Putative exosome complex	yes	no	0.890	0.894	0.451	5e-46
Q3T0E1	275	Exosome complex component	yes	no	0.894	0.774	0.389	4e-39
Q7TQK4	274	Exosome complex component	yes	no	0.941	0.817	0.381	7e-39
Q9NQT5	275	Exosome complex component	yes	no	0.894	0.774	0.375	9e-38
O13903	240	Exosome complex component	yes	no	0.907	0.9	0.406	3e-37
Q08285	240	Exosome complex component	yes	no	0.768	0.762	0.311	1e-23
E3GZ90	222	Probable exosome complex	yes	no	0.554	0.594	0.280	4e-07
O29758	223	Probable exosome complex	yes	no	0.655	0.699	0.251	4e-07
Q8U0L8	264	Probable exosome complex	yes	no	0.634	0.571	0.290	5e-07
B1L6N8	228	Probable exosome complex	yes	no	0.617	0.644	0.273	9e-07

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

 Score =  184 bits (467), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 98/217 (45%), Positives = 134/217 (61%), Gaps = 5/217 (2%)

Query: 10  LVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNK-YWVESSQK 68
           L D+ VVPGDV+  +  +    +++G GL Q  D+V   KAG LR+SK ++ YW+E+ QK
Sbjct: 4   LKDQFVVPGDVIGKIGDLK---VRIGPGLLQTKDTVLATKAGVLRYSKFHRFYWIENEQK 60

Query: 69  RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRV 128
           RYVP VED V+G +++  A++F VDI     A L   +FEG T+ N P   +G+L+Y RV
Sbjct: 61  RYVPQVEDMVIGTIIEKHAESFKVDIGSSCSALLSAYSFEGATKSNKPLLNVGNLIYCRV 120

Query: 129 VKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSF 188
             AN  M PE+ C     KA  FG L  GYM   S GLS  LLS   C +L+ LGK + +
Sbjct: 121 TVANRDMEPEVVCLSQKQKAEGFGQLIGGYMLNCSLGLSHYLLSED-CFLLQILGKHIPY 179

Query: 189 EIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQ 225
           EIAVG+NGRVW+N+ S    ++VSN I NS+ +   Q
Sbjct: 180 EIAVGVNGRVWINSGSNHNTIVVSNTIYNSQYIQDDQ 216

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

 Score =  161 bits (408), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 86/221 (38%), Positives = 131/221 (59%), Gaps = 8/221 (3%)

Query: 22  LDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNK------YWVESSQKRYVPCVE 75
           L+ ++ +   +  G GLR+  D + V K G+LR  +P        YWV+S QKRYVP   
Sbjct: 55  LNAAARSRGRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPVKG 114

Query: 76  DTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGM 135
           D V+GIV     D F VD+ G   A L  LAFEG T+RN P  ++G L+Y + V AN  M
Sbjct: 115 DHVIGIVTAKSGDIFKVDVGGSEPASLSYLAFEGATKRNRPNVQVGDLIYGQFVVANKDM 174

Query: 136 NPELSCTDASGKAAEFGLL-KDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL 194
            PE+ C D+ G+A   G++ +DG +F+ + GL R LL +P C +L+E+GK    EI  G+
Sbjct: 175 EPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLL-APDCEILQEVGKLYPLEIVFGM 233

Query: 195 NGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQ 235
           NGR+WV A++    ++++N +   E ++A Q+K +  +L +
Sbjct: 234 NGRIWVKAKTIQQTLILANILEACEHMTADQRKQIFSRLAE 274

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

 Score =  160 bits (405), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 89/233 (38%), Positives = 138/233 (59%), Gaps = 9/233 (3%)

Query: 11  VDKIVVPGDVVLDLSSMTNQTIKL--GGGLRQECDSVSVIKAGKLRFSKPNK-----YWV 63
           VD +   G+  L L++     +++  G GLR+  D + V K G+LR  +P+      YWV
Sbjct: 42  VDGLGGAGEQPLRLNAGARPRLRVVCGPGLRRCGDRLLVTKCGRLRHKEPSGGGGGVYWV 101

Query: 64  ESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSL 123
           +S QKRYVP   D V+GIV+    D F VD+ G   A L  LAFEG T+RN P  ++G L
Sbjct: 102 DSQQKRYVPVKGDHVIGIVIAKSGDIFKVDVGGSEPASLSYLAFEGATKRNRPNVQVGDL 161

Query: 124 LYVRVVKANPGMNPELSCTDASGKAAEFGLL-KDGYMFETSTGLSRMLLSSPTCPVLEEL 182
           +Y + V AN  M PE+ C D+ G+A   G++ +DG +F+ + GL R LL +P C +++EL
Sbjct: 162 IYGQCVVANKDMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLL-APDCEIVQEL 220

Query: 183 GKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQ 235
           GK    EI  G+NGR+WV A++    ++++N +   E ++  Q+K +  +L +
Sbjct: 221 GKLYPLEIVFGMNGRIWVKAKTIQQTLILANVLEACEHMTTEQRKQIFARLAE 273

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

 Score =  157 bits (396), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 83/221 (37%), Positives = 130/221 (58%), Gaps = 8/221 (3%)

Query: 22  LDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNK------YWVESSQKRYVPCVE 75
           L+  + +   +  G GLR+  D + V K G+LR  +P        YWV+S QKRYVP   
Sbjct: 55  LNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPVKG 114

Query: 76  DTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGM 135
           D V+GIV     D F VD+ G   A L  L+FEG T+RN P  ++G L+Y + V AN  M
Sbjct: 115 DHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDM 174

Query: 136 NPELSCTDASGKAAEFGLL-KDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL 194
            PE+ C D+ G+A   G++ +DG +F+ + GL R LL +P C +++E+GK    EI  G+
Sbjct: 175 EPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLL-APDCEIIQEVGKLYPLEIVFGM 233

Query: 195 NGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQ 235
           NGR+WV A++    ++++N +   E +++ Q+K +  +L +
Sbjct: 234 NGRIWVKAKTIQQTLILANILEACEHMTSDQRKQIFSRLAE 274

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

 Score =  155 bits (391), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 94/231 (40%), Positives = 136/231 (58%), Gaps = 15/231 (6%)

Query: 17  PGDVVLDLSSMTNQTIKLGGGL----RQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVP 72
           PG+ + D     + +I+LG GL    +   + + V KAG+L  +  N   ++S  KRY+P
Sbjct: 15  PGERIPDSIISQDGSIRLGPGLVFQKKDREEEIVVSKAGRLHQTGKNAMLIDSRTKRYIP 74

Query: 73  CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKAN 132
              D V+G ++   A+ + VDI    IA L  LAFE  TR++ P   +GSL+Y RV  A+
Sbjct: 75  ATNDQVIGQIISRFAEGYRVDIGSAHIAQLNALAFENVTRKSRPNLNVGSLVYARVSLAD 134

Query: 133 PGMNPELSCTDA-SGKAAEFGLLKDGYMFETSTGLS-----RMLLSSPTCPVLEELGKQL 186
             M PEL C DA +GKAA +G LK+GYM    TGLS     +++L  P   +L+ LG  +
Sbjct: 135 RDMEPELECFDATTGKAAGYGELKNGYMI---TGLSLSHCRKLIL--PKNTLLQTLGSYI 189

Query: 187 SFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRI 237
            FEIAVG+NGRVWVN+E+ ST VL+  AI N E +S  +Q      L++++
Sbjct: 190 PFEIAVGMNGRVWVNSENLSTTVLICTAIRNCEFMSDEEQIKYCKDLIKKL 240

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

 Score =  109 bits (273), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 61/196 (31%), Positives = 106/196 (54%), Gaps = 13/196 (6%)

Query: 32  IKLGGGLRQECD----SVSVIKAGKLRFSKPNK-----YWVESSQKRYVPCVEDTVLGIV 82
           +KLG G+   CD     +  +  G L  S   K      +++ S KRY+P V D V+G++
Sbjct: 19  VKLGPGIY--CDPNTQEIRPVNTGVLHVSAKGKSGVQTAYIDYSSKRYIPSVNDFVIGVI 76

Query: 83  VDCKADNFFVDIRGPTIAF-LPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSC 141
           +   +D++ V ++  + +  L  +AF   +++N P  ++G L+Y RV  A   +  E+ C
Sbjct: 77  IGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIEC 136

Query: 142 TDAS-GKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWV 200
            D++ G+ A FG+L+DG + + +   +R LL +   P+L+ L     FE+A+GLNG++WV
Sbjct: 137 FDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWV 196

Query: 201 NAESPSTVVLVSNAIM 216
             E  S  +     IM
Sbjct: 197 KCEELSNTLACYRTIM 212

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|E3GZ90|ECR1_METFV Probable exosome complex RNA-binding protein 1 OS=Methanothermus fervidus (strain ATCC 43054 / DSM 2088 / JCM 10308 / V24 S) GN=Mfer_0823 PE=3 SV=1

 Score = 55.1 bits (131), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 39/139 (28%), Positives = 69/139 (49%), Gaps = 7/139 (5%)

Query: 67  QKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPK-FEIGSLLY 125
           Q +Y+P   D+V+G VVD K   + VDIR P  A LPV       ++N+ + F IG  L+
Sbjct: 55  QGKYIPKKNDSVIGKVVDVKFARWIVDIRSPYSAILPVSEVIDKGKKNLEEIFGIGDTLF 114

Query: 126 VRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQ 185
           +++++ +     +L   +      E G L     + T + + R++       +++ L K 
Sbjct: 115 LKIIEVDEVKKVKLGLHEGGPIKLEGGTL----AYITPSKVPRVI--GRKGSMIKMLKKL 168

Query: 186 LSFEIAVGLNGRVWVNAES 204
            + EI +G NG +WV  + 
Sbjct: 169 TNCEILLGQNGVIWVKGDK 187

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

Methanothermus fervidus (strain ATCC 43054 / DSM 2088 / JCM 10308 / V24 S) (taxid: 523846)

>sp|O29758|ECR1_ARCFU Probable exosome complex RNA-binding protein 1 OS=Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) GN=AF_0492 PE=1 SV=1

 Score = 55.1 bits (131), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 43/171 (25%), Positives = 76/171 (44%), Gaps = 15/171 (8%)

Query: 69  RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPK--FEIGSLLYV 126
           RY P V D V+GI+ +  A+ + VDI  P  AFLPV           P    +IG  +  
Sbjct: 52  RYTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIA 111

Query: 127 RVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQL 186
           +V+  +P M   L+  D   +   FG +    +      + R++    +  +++ L  +L
Sbjct: 112 KVLNIDPKMKVTLTMKDRICRPIRFGRI----VAINPARVPRVIGKKGS--MIKLLKSEL 165

Query: 187 SFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRI 237
             +I VG NG +WVN +     +         E++  ++Q+   + L  R+
Sbjct: 166 DVQIVVGQNGLIWVNGDRRKVSIA-------EEAIYLIEQEAHTEGLTDRV 209

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

Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (taxid: 224325)

>sp|Q8U0L8|ECR1_PYRFU Probable exosome complex RNA-binding protein 1 OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) GN=PF1569 PE=3 SV=1

 Score = 54.7 bits (130), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 47/162 (29%), Positives = 78/162 (48%), Gaps = 11/162 (6%)

Query: 70  YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGT----RRNIPK-FEIGSLL 124
           Y+P V D VLG +VD K  ++ VDI  P  A L +  +        R ++ K F+IG ++
Sbjct: 60  YIPEVGDNVLGKIVDVKFSSWTVDIGSPYSATLKIQDYTDEKIDLLRTDLRKFFDIGDII 119

Query: 125 YVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFE-TSTGLSRMLLSSPTCPVLEELG 183
           Y +V   N   N EL+     G     G L+ G + + TS+ + R++       ++  + 
Sbjct: 120 YAKVKGINEVNNIELTT---KGMPFNGGPLRGGQIIKITSSKVPRVI--GKGGSMINMIK 174

Query: 184 KQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQ 225
           K     I VG NG +W+++++P    L   AI+  E  S  +
Sbjct: 175 KLTQSRIIVGQNGWIWISSKNPELEKLAIEAILKIERESHTR 216

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

Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (taxid: 186497)

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

 Score = 53.9 bits (128), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 43/157 (27%), Positives = 71/157 (45%), Gaps = 10/157 (6%)

Query: 70  YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFE--IGSLLYVR 127
           Y+P  +D V+GIV     +   VDIR P    LP+       R ++ K++  IG ++  +
Sbjct: 63  YIPKEDDLVIGIVSKISGNTILVDIRSPYQGALPI--QRRAERVDLKKYDLKIGDVILAK 120

Query: 128 VVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLS 187
            V++  G +  +   DA G     G L+ GY+ E        ++      +L  L +   
Sbjct: 121 -VRSFDGASSLILTIDAEG----LGKLEGGYLLEVDPAKVPRVIGKRQS-MLSMLKEATR 174

Query: 188 FEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAV 224
            EI V  NGR+WV   S   ++++  A+   E  S V
Sbjct: 175 SEIIVANNGRIWVKPPSVKELIVLEKALKKIEEESHV 211

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)

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	238
225457023	237	PREDICTED: putative exosome complex comp	0.970	0.974	0.870	1e-115
224119330	242	predicted protein [Populus trichocarpa]	1.0	0.983	0.820	1e-114
356499851	240	PREDICTED: putative exosome complex comp	1.0	0.991	0.783	1e-110
449440676	243	PREDICTED: putative exosome complex comp	1.0	0.979	0.8	1e-109
357487343	240	Exosome complex exonuclease RRP40 [Medic	1.0	0.991	0.783	1e-109
255540683	234	Exosome complex exonuclease RRP40, putat	0.890	0.905	0.849	1e-105
242053885	239	hypothetical protein SORBIDRAFT_03g03023	0.983	0.979	0.777	1e-104
125528678	239	hypothetical protein OsI_04749 [Oryza sa	0.995	0.991	0.768	1e-104
57899790	239	ALM beta-like [Oryza sativa Japonica Gro	0.983	0.979	0.773	1e-104
115438997	239	Os01g0661400 [Oryza sativa Japonica Grou	0.983	0.979	0.764	1e-103

>gi|225457023|ref|XP_002282635.1| PREDICTED: putative exosome complex component rrp40 [Vitis vinifera] gi|297733775|emb|CBI15022.3| unnamed protein product [Vitis vinifera]

 Score =  420 bits (1080), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 201/231 (87%), Positives = 217/231 (93%)

Query: 8   ANLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQ 67
           A+ VD++VVPGDVVLDLS M NQTIKLGGGL Q+CD+++V KAG+LRFSKPNKYWVESSQ
Sbjct: 7   ASFVDQLVVPGDVVLDLSKMGNQTIKLGGGLHQDCDAITVTKAGRLRFSKPNKYWVESSQ 66

Query: 68  KRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVR 127
           KRYVPCVEDTVLGIVVD KADNF VDI+GP +AFLPVLAFEGGTRRNIPKFE G+LLYVR
Sbjct: 67  KRYVPCVEDTVLGIVVDSKADNFLVDIKGPALAFLPVLAFEGGTRRNIPKFEAGTLLYVR 126

Query: 128 VVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLS 187
           VVKAN GMNPELSCTDASGKAAEFG LKDGYMFE+STGLSRMLLSSPTCPVLE LGK+LS
Sbjct: 127 VVKANTGMNPELSCTDASGKAAEFGPLKDGYMFESSTGLSRMLLSSPTCPVLEALGKKLS 186

Query: 188 FEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK 238
           FEIAVGLNGRVWVNA SPSTV+LV+NAIMNSESLS VQQKIMVDKLLQRI+
Sbjct: 187 FEIAVGLNGRVWVNASSPSTVILVANAIMNSESLSVVQQKIMVDKLLQRIQ 237

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224119330|ref|XP_002318044.1| predicted protein [Populus trichocarpa] gi|118482713|gb|ABK93275.1| unknown [Populus trichocarpa] gi|222858717|gb|EEE96264.1| predicted protein [Populus trichocarpa]

 Score =  415 bits (1066), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 197/240 (82%), Positives = 220/240 (91%), Gaps = 2/240 (0%)

Query: 1   MEAKPS--TANLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKP 58
           ME+K S   A  +D +VVPGDVV+DLSSMTNQTIKLG GLRQ+CD++SV+KAGKLRFSKP
Sbjct: 1   MESKSSGSPATFIDNLVVPGDVVVDLSSMTNQTIKLGSGLRQDCDAISVMKAGKLRFSKP 60

Query: 59  NKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKF 118
           NKYWVE+SQKRYVPC ED+VLGIVVD K+DNF +DI+GP +AFLPVLAFEGGTRRNIPKF
Sbjct: 61  NKYWVETSQKRYVPCAEDSVLGIVVDSKSDNFLIDIKGPALAFLPVLAFEGGTRRNIPKF 120

Query: 119 EIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPV 178
           E G+LLYVRVVKANPGMNPELSCTDASGKAAEFG LKDGYMFE STGLSRMLLSSPTCPV
Sbjct: 121 EAGTLLYVRVVKANPGMNPELSCTDASGKAAEFGALKDGYMFECSTGLSRMLLSSPTCPV 180

Query: 179 LEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK 238
           LE LGK+LSFEIAVGLNGRVWVNA SPS V++V+NAIMNSE+LS VQQKIM +KLLQ+I+
Sbjct: 181 LEALGKKLSFEIAVGLNGRVWVNANSPSIVIIVANAIMNSETLSGVQQKIMAEKLLQKIQ 240

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356499851|ref|XP_003518749.1| PREDICTED: putative exosome complex component rrp40-like [Glycine max]

 Score =  403 bits (1035), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 188/240 (78%), Positives = 219/240 (91%), Gaps = 2/240 (0%)

Query: 1   MEAKPSTA--NLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKP 58
           ME K S++  NLVD+ V PGDV+LDLS+MTNQTIKLGGGLRQ+CD++SV+KAG+LRFSKP
Sbjct: 1   METKSSSSSTNLVDQSVCPGDVILDLSNMTNQTIKLGGGLRQDCDAISVMKAGRLRFSKP 60

Query: 59  NKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKF 118
           NKYWVE+SQKRYVP  ED+VLGIVVD ++DNF VDI+GP +AFLPVLAFEGGTRRNIP+F
Sbjct: 61  NKYWVENSQKRYVPHAEDSVLGIVVDSRSDNFLVDIKGPALAFLPVLAFEGGTRRNIPRF 120

Query: 119 EIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPV 178
           EIG+L+Y RVVKANPGMNPEL+CTDASGKAAEFG LKDGYMFE +TGLSRMLLSSPTCPV
Sbjct: 121 EIGTLIYARVVKANPGMNPELACTDASGKAAEFGALKDGYMFECTTGLSRMLLSSPTCPV 180

Query: 179 LEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK 238
           L+ LGK+LSFEIAVGLNGRVWV+A SP T ++V+NAIMNSE+LS  QQ+IMV+KLL+RI 
Sbjct: 181 LDALGKKLSFEIAVGLNGRVWVSAASPQTTIVVANAIMNSETLSGAQQRIMVEKLLERIH 240

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449440676|ref|XP_004138110.1| PREDICTED: putative exosome complex component rrp40-like [Cucumis sativus] gi|449477413|ref|XP_004155016.1| PREDICTED: putative exosome complex component rrp40-like [Cucumis sativus]

 Score =  400 bits (1028), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 192/240 (80%), Positives = 219/240 (91%), Gaps = 2/240 (0%)

Query: 1   MEAKPSTAN--LVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKP 58
           M  KPS+++  LVD+ VVPGDVVLDLS+M N+TIKLGGGLRQ+ D++SV K GKLRFSKP
Sbjct: 1   MVEKPSSSSSTLVDQPVVPGDVVLDLSNMANETIKLGGGLRQDQDAISVSKVGKLRFSKP 60

Query: 59  NKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKF 118
           NKYWVESSQKRYVPC ED VLGIV+D +ADNF VDI+GP++AFLPVLAFEGGTRRNIPKF
Sbjct: 61  NKYWVESSQKRYVPCAEDCVLGIVLDSRADNFLVDIKGPSLAFLPVLAFEGGTRRNIPKF 120

Query: 119 EIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPV 178
           E+G+LLYVRVVK NPGMNPEL+CTDASGKAA FGLLKDGYMFE STGLSRMLLSSP+CPV
Sbjct: 121 EMGALLYVRVVKVNPGMNPELACTDASGKAAGFGLLKDGYMFECSTGLSRMLLSSPSCPV 180

Query: 179 LEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK 238
           LE LGK+LSFE AVGLNGRVWVNA+SPST+++VSNAI+NSE+LS VQQ+IMVDKLL  +K
Sbjct: 181 LESLGKKLSFETAVGLNGRVWVNADSPSTIIVVSNAILNSETLSGVQQRIMVDKLLANLK 240

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357487343|ref|XP_003613959.1| Exosome complex exonuclease RRP40 [Medicago truncatula] gi|217074508|gb|ACJ85614.1| unknown [Medicago truncatula] gi|355515294|gb|AES96917.1| Exosome complex exonuclease RRP40 [Medicago truncatula] gi|388510130|gb|AFK43131.1| unknown [Medicago truncatula]

 Score =  399 bits (1024), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 188/240 (78%), Positives = 218/240 (90%), Gaps = 2/240 (0%)

Query: 1   MEAKP--STANLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKP 58
           ME+K   S+ N VD++V PGDVVLDLS+MTNQTIKLGGGLRQ+ D +SV+KAG+LRFSKP
Sbjct: 1   MESKSAGSSTNFVDQLVYPGDVVLDLSTMTNQTIKLGGGLRQDGDVISVMKAGRLRFSKP 60

Query: 59  NKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKF 118
           NKYWVESSQKRYVP  ED+VLGI+VD ++DNF VDI+GPT+AFLPVLAFEGGTRRNIPKF
Sbjct: 61  NKYWVESSQKRYVPHAEDSVLGIIVDSRSDNFLVDIKGPTLAFLPVLAFEGGTRRNIPKF 120

Query: 119 EIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPV 178
           E+G+L+YVRVVKA PGMNPELSCTDASGKA EFG LK+GYMFE STGLSRMLLS+PTCPV
Sbjct: 121 EVGALIYVRVVKAIPGMNPELSCTDASGKAGEFGALKEGYMFECSTGLSRMLLSTPTCPV 180

Query: 179 LEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK 238
           L+ LGK+LSFEIAVGLNGRVWVNA SPST ++V+NA++NSE LS VQQKIM +KLLQR++
Sbjct: 181 LDTLGKKLSFEIAVGLNGRVWVNASSPSTTIIVANALINSEVLSGVQQKIMAEKLLQRVQ 240

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255540683|ref|XP_002511406.1| Exosome complex exonuclease RRP40, putative [Ricinus communis] gi|223550521|gb|EEF52008.1| Exosome complex exonuclease RRP40, putative [Ricinus communis]

 Score =  387 bits (995), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 180/212 (84%), Positives = 200/212 (94%)

Query: 27  MTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCK 86
           MTNQTIKLGGGLRQ+CD+V+VIKAGKLRFSKPNKYWVESS KRY+PC ED+VLGIVVD K
Sbjct: 1   MTNQTIKLGGGLRQDCDAVTVIKAGKLRFSKPNKYWVESSHKRYMPCAEDSVLGIVVDSK 60

Query: 87  ADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASG 146
           A+NF VDI+GP +AFLPVLAFEGGTRRN+PKFE G+LLYVRVVKANPGMNPELSCTDASG
Sbjct: 61  AENFLVDIKGPAMAFLPVLAFEGGTRRNVPKFEAGTLLYVRVVKANPGMNPELSCTDASG 120

Query: 147 KAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPS 206
           KA EFG+LKDGYMFE STGLSRMLLSSPTCPVLE LGK+LSFEIAVG+NGRVWVNA SPS
Sbjct: 121 KAVEFGVLKDGYMFECSTGLSRMLLSSPTCPVLEALGKKLSFEIAVGINGRVWVNATSPS 180

Query: 207 TVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK 238
           T+++V+NAIMNSE+LSAVQQKIMVD LL +I+
Sbjct: 181 TIIVVANAIMNSETLSAVQQKIMVDNLLDKIR 212

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242053885|ref|XP_002456088.1| hypothetical protein SORBIDRAFT_03g030230 [Sorghum bicolor] gi|241928063|gb|EES01208.1| hypothetical protein SORBIDRAFT_03g030230 [Sorghum bicolor]

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 182/234 (77%), Positives = 204/234 (87%)

Query: 4   KPSTANLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWV 63
           KP+ + LVD  VVPGDVVLDLS M NQTIKLG GLRQECD++    AGKLR  KPNKYW+
Sbjct: 5   KPAPSPLVDNYVVPGDVVLDLSEMNNQTIKLGAGLRQECDTIQATSAGKLRLLKPNKYWI 64

Query: 64  ESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSL 123
           E+SQKRY+P VEDTVLGIVVD K DNF VDI+GP +AFLPVLAFEGGTRRNIPKFEIG+L
Sbjct: 65  ENSQKRYIPSVEDTVLGIVVDTKPDNFLVDIKGPNLAFLPVLAFEGGTRRNIPKFEIGTL 124

Query: 124 LYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELG 183
           +Y RVVKAN  MNPELSC DASGKAAEFG LKDGYMF+TSTG+SRMLLSSPTCPVLE LG
Sbjct: 125 IYARVVKANSIMNPELSCMDASGKAAEFGQLKDGYMFDTSTGMSRMLLSSPTCPVLEALG 184

Query: 184 KQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRI 237
           K+LSFEIAVGLNGRVWVNA + STV+LVSNAIM SESLS ++Q+ MV+ LL+R+
Sbjct: 185 KKLSFEIAVGLNGRVWVNAPAASTVILVSNAIMRSESLSGIKQRAMVENLLERL 238

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125528678|gb|EAY76792.1| hypothetical protein OsI_04749 [Oryza sativa Indica Group]

 Score =  382 bits (981), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 183/238 (76%), Positives = 207/238 (86%), Gaps = 1/238 (0%)

Query: 1   MEA-KPSTANLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPN 59
           ME+ KP  + LVD  VVPGDVVLDL+ MTNQTIKLG GLRQ+CD++    AG+LR SKPN
Sbjct: 1   MESRKPPPSALVDNHVVPGDVVLDLTEMTNQTIKLGAGLRQDCDTIQTTSAGRLRLSKPN 60

Query: 60  KYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFE 119
           KYWVESSQKRY+P VEDTVLG+VVD K DNF VDI+GP +AFLPVLAFEGGTRRNIPKFE
Sbjct: 61  KYWVESSQKRYIPSVEDTVLGVVVDTKPDNFLVDIKGPNLAFLPVLAFEGGTRRNIPKFE 120

Query: 120 IGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVL 179
           IG+L+Y RVVKAN  MNPELSC DA+GKAAEFG LKDGYMF+TSTGLSRMLLSSPTCPVL
Sbjct: 121 IGTLIYARVVKANSIMNPELSCMDATGKAAEFGQLKDGYMFDTSTGLSRMLLSSPTCPVL 180

Query: 180 EELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRI 237
           E LGK+LSFEIAVGLNGRVWVNA SPS V++VSNAI+ SESLS + Q+ MV+ LL+R+
Sbjct: 181 EALGKKLSFEIAVGLNGRVWVNAPSPSNVIVVSNAIIKSESLSGIGQRSMVESLLERL 238

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|57899790|dbj|BAD87535.1| ALM beta-like [Oryza sativa Japonica Group] gi|125572934|gb|EAZ14449.1| hypothetical protein OsJ_04370 [Oryza sativa Japonica Group] gi|215768884|dbj|BAH01113.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  382 bits (981), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 181/234 (77%), Positives = 204/234 (87%)

Query: 4   KPSTANLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWV 63
           KP  + LVD  VVPGDVVLDL+ MTNQTIKLG GLRQ+CD++    AG+LR SKPNKYWV
Sbjct: 5   KPPPSALVDNHVVPGDVVLDLTEMTNQTIKLGAGLRQDCDTIQATSAGRLRLSKPNKYWV 64

Query: 64  ESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSL 123
           ESSQKRY+P VEDTVLG+VVD K DNF VDI+GP +AFLPVLAFEGGTRRNIPKFEIG+L
Sbjct: 65  ESSQKRYIPSVEDTVLGVVVDTKPDNFLVDIKGPNLAFLPVLAFEGGTRRNIPKFEIGTL 124

Query: 124 LYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELG 183
           +Y RVVKAN  MNPELSC DA+GKAAEFG LKDGYMF+TSTGLSRMLLSSPTCPVLE LG
Sbjct: 125 IYARVVKANSIMNPELSCMDATGKAAEFGQLKDGYMFDTSTGLSRMLLSSPTCPVLEALG 184

Query: 184 KQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRI 237
           K+LSFEIAVGLNGRVWVNA SPS V++VSNAI+ SESLS + Q+ MV+ LL+R+
Sbjct: 185 KKLSFEIAVGLNGRVWVNAPSPSNVIVVSNAIIKSESLSGIGQRSMVESLLERL 238

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115438997|ref|NP_001043778.1| Os01g0661400 [Oryza sativa Japonica Group] gi|113533309|dbj|BAF05692.1| Os01g0661400 [Oryza sativa Japonica Group] gi|215706438|dbj|BAG93294.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  379 bits (974), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 179/234 (76%), Positives = 204/234 (87%)

Query: 4   KPSTANLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWV 63
           KP  + LVD  VVPGDVVLDL+ MTNQTIKLG GLRQ+CD++    AG+LR SKP+KYWV
Sbjct: 5   KPPPSALVDNHVVPGDVVLDLAEMTNQTIKLGAGLRQDCDTIQATSAGRLRLSKPSKYWV 64

Query: 64  ESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSL 123
           ESSQKRY+P VEDTVLG+VVD K DNF VDI+GP +AFLPVLAFEGGTRRNIPKFEIG+L
Sbjct: 65  ESSQKRYIPSVEDTVLGVVVDTKPDNFLVDIKGPNLAFLPVLAFEGGTRRNIPKFEIGTL 124

Query: 124 LYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELG 183
           +Y RVVKAN  MNPELSC DA+GKAAEFG LKDGYMF+TSTGLSRMLLSSPTCP+LE LG
Sbjct: 125 IYARVVKANSIMNPELSCMDATGKAAEFGQLKDGYMFDTSTGLSRMLLSSPTCPILEALG 184

Query: 184 KQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRI 237
           K+LSFEIAVGLNGRVWVNA SPS V++VSNAI+ SESLS + Q+ MV+ LL+R+
Sbjct: 185 KKLSFEIAVGLNGRVWVNAPSPSNVIVVSNAIIKSESLSGIGQRSMVESLLERL 238

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

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	238
TAIR|locus:505006271	241	AT2G25355 [Arabidopsis thalian	0.991	0.979	0.716	2.8e-89
TAIR|locus:504955555	241	AT4G32175 "AT4G32175" [Arabido	0.983	0.970	0.733	7.5e-89
DICTYBASE|DDB_G0276783	237	DDB_G0276783 "RRP40 family pro	0.928	0.932	0.442	2.8e-43
UNIPROTKB|E2RHV4	275	EXOSC3 "Uncharacterized protei	0.915	0.792	0.399	8.9e-38
RGD|1304739	273	Exosc3 "exosome component 3" [	0.915	0.798	0.392	8.9e-38
UNIPROTKB|F1NWK4	272	EXOSC3 "Uncharacterized protei	0.886	0.775	0.378	1.5e-37
FB|FBgn0260648	232	Rrp40 [Drosophila melanogaster	0.903	0.926	0.389	2.4e-37
MGI|MGI:1913612	274	Exosc3 "exosome component 3" [	0.941	0.817	0.381	3.9e-37
UNIPROTKB|Q3T0E1	275	EXOSC3 "Exosome complex compon	0.894	0.774	0.389	4.9e-37
UNIPROTKB|Q9NQT5	275	EXOSC3 "Exosome complex compon	0.915	0.792	0.376	3.5e-36

TAIR|locus:505006271 AT2G25355 [Arabidopsis thaliana (taxid:3702)]

 Score = 891 (318.7 bits), Expect = 2.8e-89, P = 2.8e-89
 Identities = 169/236 (71%), Positives = 200/236 (84%)

Query:     2 EAKPSTANLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKY 61
             E   S  +L+D+ VVPGDVVLDLS+MTNQTIKLG GLRQ+ + +SV++AGKLR+SKPNKY
Sbjct:     4 EVSTSPTSLIDQTVVPGDVVLDLSNMTNQTIKLGSGLRQDNEVISVMRAGKLRYSKPNKY 63

Query:    62 WVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIG 121
             WVESS KRYVP  ED VLGIVVDCK +N+++DI+GP +A LPVLAFEG  RRN PKFE+ 
Sbjct:    64 WVESSHKRYVPRPEDHVLGIVVDCKGENYWIDIKGPQLALLPVLAFEGANRRNYPKFEVS 123

Query:   122 SLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEE 181
             +LLY RVVK N GMNPELSC D SGKAA FG LKDG+MFETSTGLSRMLLSSPTCPVLE 
Sbjct:   124 TLLYTRVVKTNTGMNPELSCVDESGKAAGFGPLKDGFMFETSTGLSRMLLSSPTCPVLEA 183

Query:   182 LGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRI 237
             LGK+LSFE A GLNGR WV+A +P  V++V+NA+MNSE+LS  QQ+IMV+KLL++I
Sbjct:   184 LGKKLSFETAFGLNGRCWVHAAAPRIVIIVANALMNSETLSGTQQRIMVEKLLEKI 239

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:504955555 AT4G32175 "AT4G32175" [Arabidopsis thaliana (taxid:3702)]

 Score = 887 (317.3 bits), Expect = 7.5e-89, P = 7.5e-89
 Identities = 173/236 (73%), Positives = 207/236 (87%)

Query:     1 MEAKPSTA--NLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKP 58
             M AK S +  +L+++IVVPGDVVLDLS+M NQTIKLG GL Q+ D++S ++AGKL +SKP
Sbjct:     1 MAAKVSVSPTSLLNQIVVPGDVVLDLSNMNNQTIKLGSGLLQDNDAISAMRAGKLSYSKP 60

Query:    59 NKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKF 118
             NKYW+ESS KRY+P  +D VLGIVVD +ADNF+VDI+GP +A LPVLAFEGGTRRNIPKF
Sbjct:    61 NKYWLESSHKRYIPRPDDHVLGIVVDSRADNFWVDIKGPQLALLPVLAFEGGTRRNIPKF 120

Query:   119 EIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPV 178
             E+G+LLY+RVVK N GMNPELSCT+ASGKAA FG L+DG+MFETSTGLSRMLL+SPT PV
Sbjct:   121 EVGTLLYLRVVKTNIGMNPELSCTEASGKAALFGPLRDGFMFETSTGLSRMLLNSPTRPV 180

Query:   179 LEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLL 234
             +E LGK+LSFEIAVGLNGRVWVNA +P  V++V+NAIMNSESLS  QQ+IMV+KLL
Sbjct:   181 IEALGKKLSFEIAVGLNGRVWVNATAPRIVIIVANAIMNSESLSGTQQRIMVEKLL 236

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

DICTYBASE|DDB_G0276783 DDB_G0276783 "RRP40 family protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 457 (165.9 bits), Expect = 2.8e-43, P = 2.8e-43
 Identities = 100/226 (44%), Positives = 138/226 (61%)

Query:    10 LVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNK-YWVESSQK 68
             L D+ VVPGDV+  +  +    +++G GL Q  D+V   KAG LR+SK ++ YW+E+ QK
Sbjct:     4 LKDQFVVPGDVIGKIGDLK---VRIGPGLLQTKDTVLATKAGVLRYSKFHRFYWIENEQK 60

Query:    69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRV 128
             RYVP VED V+G +++  A++F VDI     A L   +FEG T+ N P   +G+L+Y RV
Sbjct:    61 RYVPQVEDMVIGTIIEKHAESFKVDIGSSCSALLSAYSFEGATKSNKPLLNVGNLIYCRV 120

Query:   129 VKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSF 188
               AN  M PE+ C     KA  FG L  GYM   S GLS  LLS   C +L+ LGK + +
Sbjct:   121 TVANRDMEPEVVCLSQKQKAEGFGQLIGGYMLNCSLGLSHYLLSED-CFLLQILGKHIPY 179

Query:   189 EIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLL 234
             EIAVG+NGRVW+N+ S    ++VSN I NS+ +   Q +  + K L
Sbjct:   180 EIAVGVNGRVWINSGSNHNTIVVSNTIYNSQYIQDDQIEPFILKSL 225

GO:0003723 "RNA binding" evidence=IEA

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

GO:0006364 "rRNA processing" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

 Score = 405 (147.6 bits), Expect = 8.9e-38, P = 8.9e-38
 Identities = 91/228 (39%), Positives = 135/228 (59%)

Query:    17 PGDVVLDLSSMTNQT--IKLGGGLRQECDSVSVIKAGKLRFSKPNK------YWVESSQK 68
             PG+  L L++ T     +  G GLR+  D + V K G+LR  +P        YWV+S QK
Sbjct:    48 PGERPLRLNAGTRSRGRVVCGPGLRRCGDRLLVTKCGRLRHKEPGGGSGGGVYWVDSQQK 107

Query:    69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRV 128
             RYVP   D V+GIV     D F VD+ G   A L  LAFEG T+RN P  +IG L+Y + 
Sbjct:   108 RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLAFEGATKRNRPNVQIGDLIYGQF 167

Query:   129 VKANPGMNPELSCTDASGKAAEFGLL-KDGYMFETSTGLSRMLLSSPTCPVLEELGKQLS 187
             V AN  M PE+ C D+ G+A+  G++ +DG +F+ + GL R LL+ P C +L+E+GK   
Sbjct:   168 VVANKDMEPEMVCIDSCGRASGMGVIGQDGLLFKVTLGLIRKLLA-PDCEILQEVGKLYP 226

Query:   188 FEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQ 235
              EI  G+NGR+WV A++    ++++N +   E ++A Q+K +  +L +
Sbjct:   227 LEIVFGMNGRIWVKAKTIQQTLILANILEACEHMTADQRKQIFSRLAE 274

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

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

 Score = 405 (147.6 bits), Expect = 8.9e-38, P = 8.9e-38
 Identities = 89/227 (39%), Positives = 136/227 (59%)

Query:    17 PGDVVLDLSSMTNQTIKL--GGGLRQECDSVSVIKAGKLRFSKPNK-----YWVESSQKR 69
             PG+  L L++     +++  G GLR+  D + V K G+LR  +P+      YWV+S QKR
Sbjct:    47 PGEQPLRLNAGARPRLRIVCGPGLRRCGDRLLVTKCGRLRHKEPSGGGGGVYWVDSQQKR 106

Query:    70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVV 129
             YVP   D V+GIVV    D F VD+ G   A L  LAFEG T+RN P  ++G L+Y + V
Sbjct:   107 YVPVKGDHVIGIVVAKSGDIFKVDVGGSEPASLSYLAFEGATKRNRPNVQVGDLIYGQCV 166

Query:   130 KANPGMNPELSCTDASGKAAEFGLL-KDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSF 188
              AN  M PE+ C D+ G+A   G++ +DG +F+ + GL R LL+ P C +++ELGK    
Sbjct:   167 VANKDMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLA-PDCEIVQELGKLYPL 225

Query:   189 EIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQ 235
             EI  G+NGR+WV A++    ++++N +   E ++  Q+K +  +L +
Sbjct:   226 EIVFGMNGRIWVKAKTIQQTLILANVLEACEHMTTEQRKQIFARLAE 272

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

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

 Score = 379 (138.5 bits), Expect = 1.5e-37, Sum P(2) = 1.5e-37
 Identities = 84/222 (37%), Positives = 128/222 (57%)

Query:    22 LDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNK---------YWVESSQKRYVP 72
             L  S+     +  G GLR+    + V K G LR  +            YWV+S QKRYVP
Sbjct:    49 LGTSAAPRGRLLCGPGLRRCAGGLLVTKCGLLRHRRAGDGAAAAAGGAYWVDSQQKRYVP 108

Query:    73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKAN 132
                D V+GIV     D F +D+ G   A L  LAFEG T+RN P  ++G L+Y + + AN
Sbjct:   109 VKGDHVIGIVTGKVGDVFRLDVGGSEQASLSYLAFEGATKRNRPNVQVGDLIYGQFLVAN 168

Query:   133 PGMNPELSCTDASGKAAEFGLL-KDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIA 191
               M PE+ C D+SG+A+  G++ +DG++F+ S GL R LL+ P C +++EL +   FE+ 
Sbjct:   169 KDMEPEMVCIDSSGRASGMGVIGQDGFLFKVSLGLIRKLLA-PKCEIIQELSQLYPFELV 227

Query:   192 VGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKL 233
             +G+NGR+WV A++    +++ N +   E ++A Q+K  + KL
Sbjct:   228 LGMNGRIWVKAKTVQQTLIIVNILEACEYMTAEQRKQALAKL 269

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 = 401 (146.2 bits), Expect = 2.4e-37, P = 2.4e-37
 Identities = 86/221 (38%), Positives = 130/221 (58%)

Query:    14 IVVPGDVVLDLSSMT-NQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVP 72
             IV+PG+ +  +  +  ++ + LG GLR+  D+V   KAG LR  +P  +WV++ Q+RY+P
Sbjct:     7 IVMPGERIAAIEELAKSKRVILGPGLRRLDDTVVASKAGPLRHKEPGTFWVDNYQRRYIP 66

Query:    73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKAN 132
                D +LGIV     D + VDI     A +  LAFE  +++N P    G L+Y RV+ A+
Sbjct:    67 ARGDLILGIVRAKAGDLYRVDIGATDTASISYLAFEAASKKNRPDLIPGDLIYARVLNAS 126

Query:   133 PGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAV 192
               + PEL C ++ GK+ + G+L DG+ F+ S  L RMLL    CPVL  L ++L +EIAV
Sbjct:   127 ADIEPELVCVNSVGKSGKLGVLTDGFFFKCSLNLGRMLLRE-NCPVLAALTRELPYEIAV 185

Query:   193 GLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKL 233
             G+NGR+W+ A S    V ++NAI   E     +    +DK+
Sbjct:   186 GVNGRIWLKAHSLKETVALANAISALEQSGCAE----IDKI 222

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

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

 Score = 399 (145.5 bits), Expect = 3.9e-37, P = 3.9e-37
 Identities = 89/233 (38%), Positives = 138/233 (59%)

Query:    11 VDKIVVPGDVVLDLSSMTNQTIKL--GGGLRQECDSVSVIKAGKLRFSKPNK-----YWV 63
             VD +   G+  L L++     +++  G GLR+  D + V K G+LR  +P+      YWV
Sbjct:    42 VDGLGGAGEQPLRLNAGARPRLRVVCGPGLRRCGDRLLVTKCGRLRHKEPSGGGGGVYWV 101

Query:    64 ESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSL 123
             +S QKRYVP   D V+GIV+    D F VD+ G   A L  LAFEG T+RN P  ++G L
Sbjct:   102 DSQQKRYVPVKGDHVIGIVIAKSGDIFKVDVGGSEPASLSYLAFEGATKRNRPNVQVGDL 161

Query:   124 LYVRVVKANPGMNPELSCTDASGKAAEFGLL-KDGYMFETSTGLSRMLLSSPTCPVLEEL 182
             +Y + V AN  M PE+ C D+ G+A   G++ +DG +F+ + GL R LL+ P C +++EL
Sbjct:   162 IYGQCVVANKDMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLA-PDCEIVQEL 220

Query:   183 GKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQ 235
             GK    EI  G+NGR+WV A++    ++++N +   E ++  Q+K +  +L +
Sbjct:   221 GKLYPLEIVFGMNGRIWVKAKTIQQTLILANVLEACEHMTTEQRKQIFARLAE 273

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 = 398 (145.2 bits), Expect = 4.9e-37, P = 4.9e-37
 Identities = 86/221 (38%), Positives = 131/221 (59%)

Query:    22 LDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNK------YWVESSQKRYVPCVE 75
             L+ ++ +   +  G GLR+  D + V K G+LR  +P        YWV+S QKRYVP   
Sbjct:    55 LNAAARSRGRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPVKG 114

Query:    76 DTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGM 135
             D V+GIV     D F VD+ G   A L  LAFEG T+RN P  ++G L+Y + V AN  M
Sbjct:   115 DHVIGIVTAKSGDIFKVDVGGSEPASLSYLAFEGATKRNRPNVQVGDLIYGQFVVANKDM 174

Query:   136 NPELSCTDASGKAAEFGLL-KDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL 194
              PE+ C D+ G+A   G++ +DG +F+ + GL R LL+ P C +L+E+GK    EI  G+
Sbjct:   175 EPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLA-PDCEILQEVGKLYPLEIVFGM 233

Query:   195 NGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQ 235
             NGR+WV A++    ++++N +   E ++A Q+K +  +L +
Sbjct:   234 NGRIWVKAKTIQQTLILANILEACEHMTADQRKQIFSRLAE 274

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 = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 87/231 (37%), Positives = 135/231 (58%)

Query:    17 PGDVV---LDLSSMTNQTIKL--GGGLRQECDSVSVIKAGKLRFSKPNK------YWVES 65
             PG  V   L L++     +++  G GLR+  D + V K G+LR  +P        YWV+S
Sbjct:    45 PGGAVERPLSLNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDS 104

Query:    66 SQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLY 125
              QKRYVP   D V+GIV     D F VD+ G   A L  L+FEG T+RN P  ++G L+Y
Sbjct:   105 QQKRYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIY 164

Query:   126 VRVVKANPGMNPELSCTDASGKAAEFGLL-KDGYMFETSTGLSRMLLSSPTCPVLEELGK 184
              + V AN  M PE+ C D+ G+A   G++ +DG +F+ + GL R LL+ P C +++E+GK
Sbjct:   165 GQFVVANKDMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLA-PDCEIIQEVGK 223

Query:   185 QLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQ 235
                 EI  G+NGR+WV A++    ++++N +   E +++ Q+K +  +L +
Sbjct:   224 LYPLEIVFGMNGRIWVKAKTIQQTLILANILEACEHMTSDQRKQIFSRLAE 274

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

---

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)
Q7KWX9	EXOS3_DICDI	No assigned EC number	0.4516	0.8907	0.8945	yes	no
O13903	RRP40_SCHPO	No assigned EC number	0.4069	0.9075	0.9	yes	no
Q7TQK4	EXOS3_MOUSE	3, ., 1, ., 1, 3, ., -	0.3819	0.9411	0.8175	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00016075001	SubName- Full=Chromosome chr17 scaffold_12, whole genome shotgun sequence; (237 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00026977001	SubName- Full=Putative uncharacterized protein (Chromosome chr15 scaffold_40, whole genome shot [...] (241 aa)	•		•	•	•	•	•		0.983
	GSVIVG00032741001	SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (287 aa)	•		•	•	•	•	•		0.982
	GSVIVG00023648001	SubName- Full=Chromosome chr7 scaffold_31, whole genome shotgun sequence; (320 aa)			•	•	•	•	•		0.977
	GSVIVG00026698001	SubName- Full=Chromosome chr4 scaffold_39, whole genome shotgun sequence; (200 aa)				•	•	•	•		0.948
	GSVIVG00031795001	SubName- Full=Chromosome chr18 scaffold_59, whole genome shotgun sequence; (431 aa)	•		•	•	•	•	•		0.925
	GSVIVG00032429001	SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (243 aa)	•		•	•	•	•	•		0.878
	GSVIVG00019329001	SubName- Full=Chromosome chr7 scaffold_20, whole genome shotgun sequence; (943 aa)				•	•	•	•		0.850
	GSVIVG00024558001	SubName- Full=Putative uncharacterized protein (Chromosome chr6 scaffold_3, whole genome shotgu [...] (254 aa)	•		•	•	•	•	•		0.841
	GSVIVG00005498001	SubName- Full=Putative uncharacterized protein (Chromosome chr13 scaffold_152, whole genome sho [...] (293 aa)				•					0.632
	GSVIVG00026600001	SubName- Full=Chromosome chr12 scaffold_38, whole genome shotgun sequence; (229 aa)				•					0.618

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	238
cd05790	86	cd05790, S1_Rrp40, S1_Rrp40: Rrp40 S1-like RNA-bin	2e-41
COG1097	239	COG1097, RRP4, RNA-binding protein Rrp4 and relate	5e-37
PRK04163	235	PRK04163, PRK04163, exosome complex RNA-binding pr	2e-15
cd04454	82	cd04454, S1_Rrp4_like, S1_Rrp4_like: Rrp4-like, S1	1e-11
cd05789	86	cd05789, S1_Rrp4, S1_Rrp4: Rrp4 S1-like RNA-bindin	2e-07
smart00316	72	smart00316, S1, Ribosomal protein S1-like RNA-bind	0.003

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

 Score =  136 bits (344), Expect = 2e-41
 Identities = 50/86 (58%), Positives = 55/86 (63%)

Query: 69  RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRV 128
           RYVP   D V+GIVV    D F VDI G   A L  LAFEG T+RN P   +G L+Y RV
Sbjct: 1   RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARV 60

Query: 129 VKANPGMNPELSCTDASGKAAEFGLL 154
           VKAN  M PELSC D+SGKA  FG 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 =  129 bits (327), Expect = 5e-37
 Identities = 66/231 (28%), Positives = 96/231 (41%), Gaps = 23/231 (9%)

Query: 13  KIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVP 72
           KIV+PGD+VL          KLG G   E   +     G L   K     V   + RY+P
Sbjct: 9   KIVLPGDLVLA----EGS-YKLGHGTYFEGGKIYSSVVGLLDV-KGKLVRVIPLEGRYIP 62

Query: 73  CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAF-----EGGTRRNIPKFEIGSLLYVR 127
            V D V+G +++     + VDI  P  A L +  F     E   +   P   +G L+Y +
Sbjct: 63  EVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAK 122

Query: 128 VVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLS 187
           VV  +     EL+      K    G LK+G + +        ++      +L  L ++  
Sbjct: 123 VVDVDRDGEVELTL-----KDEGLGKLKNGQIVKIPPSKVPRVIG-KKGSMLNMLKEKTG 176

Query: 188 FEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK 238
            EI VG NGR+WV+ E+ S   L   AI   E      ++     L  RIK
Sbjct: 177 CEIIVGQNGRIWVDGENESLEELAIEAIRKIE------REAHTSGLTDRIK 221

Length = 239

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

 Score = 72.6 bits (179), Expect = 2e-15
 Identities = 52/225 (23%), Positives = 83/225 (36%), Gaps = 52/225 (23%)

Query: 13  KIVVPGDVVLDLSSMT-NQTIKLGG-------GL-RQECDSVSVIKAGKLRFSKPNKYWV 63
           KIVVPGD++ +        T K  G       GL   + D V VI               
Sbjct: 9   KIVVPGDLLAEGEFKAGRGTYKENGKIYSTVVGLVDIKDDKVRVIPL------------- 55

Query: 64  ESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG----TRRNIPKF- 118
              + +Y+P V D V+G V D     + VDI  P  A+LPV    G        ++ K+ 
Sbjct: 56  ---EGKYIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYL 112

Query: 119 EIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCP- 177
           +IG  +  +V   +   +  L+           G ++ G + E         +     P 
Sbjct: 113 DIGDYIIAKVKDVDRTRDVVLTLKGKG-----LGKIEGGTIVE---------IKPVKVPR 158

Query: 178 -------VLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAI 215
                  ++  L ++   +I VG NGR+W+         +   AI
Sbjct: 159 VIGKKGSMINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIEAI 203

Length = 235

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

 Score = 58.7 bits (142), Expect = 1e-11
 Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 69  RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVR 127
           RY+P V D V+GIV +  +  + VDI     A L   +      +      + G L+  +
Sbjct: 1   RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAK 60

Query: 128 VVKANPGMNPELSCTD 143
           V+     MN  L+  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|240215 cd05789, S1_Rrp4, S1_Rrp4: Rrp4 S1-like RNA-binding domain

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 21/77 (27%), Positives = 31/77 (40%), Gaps = 5/77 (6%)

Query: 69  RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAF-EGGTR---RNIPK-FEIGSL 123
           RY+P V D V+G V +     + VDI  P  A LP+       T     N+    + G L
Sbjct: 1   RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDL 60

Query: 124 LYVRVVKANPGMNPELS 140
           +   V   +   +  L 
Sbjct: 61  IVAEVQSVDSDGSVSLH 77

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|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 74  VEDTVLGIVVDCKADNFFVDIRGPTIAFLPV-LAFEGGTRRNIPKFEIGSLLYVRVVKAN 132
           V D V G V +      FVD+       +P+    +   +      ++G  + V+V+  +
Sbjct: 2   VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVD 61

Query: 133 P 133
            
Sbjct: 62  E 62

Length = 72

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	238
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	100.0
KOG1004	230	consensus Exosomal 3'-5' exoribonuclease complex s	100.0
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	100.0
KOG3013	301	consensus Exosomal 3'-5' exoribonuclease complex,	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	99.94
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	99.93
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	99.88
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-	99.75
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.57
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	99.27
PF14382	39	ECR1_N: Exosome complex exonuclease RRP4 N-termina	99.13
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	98.71
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	98.69
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	98.65
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	98.61
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	98.6
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	98.6
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	98.53
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	98.51
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.46
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	98.4
PRK08582	139	hypothetical protein; Provisional	98.37
PRK07252	120	hypothetical protein; Provisional	98.37
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	98.34
PRK08059	123	general stress protein 13; Validated	98.31
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	98.29
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.29
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	98.26
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	98.22
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	98.18
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	98.16
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.15
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	98.15
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.13
PRK05807	136	hypothetical protein; Provisional	98.13
cd02393	61	PNPase_KH Polynucleotide phosphorylase (PNPase) K	98.13
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	98.11
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	98.1
COG1098	129	VacB Predicted RNA binding protein (contains ribos	98.09
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	98.04
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	98.02
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	98.02
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.0
PHA02945	88	interferon resistance protein; Provisional	98.0
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	97.99
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	97.93
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	97.91
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	97.88
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	97.75
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	97.72
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	97.7
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	97.65
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	97.63
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	97.62
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	97.59
PRK07400	318	30S ribosomal protein S1; Reviewed	97.57
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	97.54
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	97.48
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	97.4
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.38
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.36
PRK07400	318	30S ribosomal protein S1; Reviewed	97.36
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	97.33
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.22
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	97.07
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	97.05
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	97.04
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	97.04
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	97.02
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	97.01
cd02394	62	vigilin_like_KH K homology RNA-binding domain_vigi	96.98
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	96.98
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	96.91
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	96.91
PRK12327	362	nusA transcription elongation factor NusA; Provisi	96.82
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	96.82
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	96.8
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	96.66
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	96.59
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	96.55
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	96.45
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	96.41
COG2183	780	Tex Transcriptional accessory protein [Transcripti	96.39
PRK09202	470	nusA transcription elongation factor NusA; Validat	96.32
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	96.25
TIGR01953	341	NusA transcription termination factor NusA. This m	96.16
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	96.1
cd00105	64	KH-I K homology RNA-binding domain, type I. KH bin	95.77
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	95.74
PF00013	60	KH_1: KH domain syndrome, contains KH motifs.; Int	95.69
PRK12328	374	nusA transcription elongation factor NusA; Provisi	95.6
PRK12329	449	nusA transcription elongation factor NusA; Provisi	95.29
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	94.53
smart00322	69	KH K homology RNA-binding domain.	94.44
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	94.26
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	93.33
PRK11642	813	exoribonuclease R; Provisional	92.58
PRK13763	180	putative RNA-processing protein; Provisional	92.04
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	91.93
TIGR03665	172	arCOG04150 arCOG04150 universal archaeal KH domain	91.73
PRK10811	1068	rne ribonuclease E; Reviewed	91.22
cd02396	65	PCBP_like_KH K homology RNA-binding domain, PCBP_l	90.63
cd02395	120	SF1_like-KH Splicing factor 1 (SF1) K homology RNA	90.53
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	90.52
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	90.04
PRK11712	489	ribonuclease G; Provisional	89.42
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	89.37
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	88.1
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	87.77
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	85.56
PRK04012	100	translation initiation factor IF-1A; Provisional	83.86
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	83.79
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	83.65
smart00652	83	eIF1a eukaryotic translation initiation factor 1A.	83.55
PF01176	65	eIF-1a: Translation initiation factor 1A / IF-1; I	82.94
PRK13763	180	putative RNA-processing protein; Provisional	82.66
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	81.82
PLN00208	145	translation initiation factor (eIF); Provisional	81.14
cd04456	78	S1_IF1A_like S1_IF1A_like: Translation initiation	80.96

>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=8.1e-58  Score=394.00  Aligned_cols=215  Identities=31%  Similarity=0.454  Sum_probs=201.0

Q ss_pred             ccCCCCcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEecCCeEEEEccCCccCCCCCCEEEEEEEEec
Q 026458            7 TANLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCK   86 (238)
Q Consensus         7 ~~~~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~~~~i~V~~~~~~Y~P~vGDiVIG~V~~v~   86 (238)
                      .....+++|+|||.|....     .+..|||||.+++++||+++|.++.. ++.+.|+|++++|+|++||+|||+|+++.
T Consensus         3 ~~~~~~~iV~PGd~vl~~~-----~~~~G~Gty~~~~~iyssv~G~~~~~-~~~v~VIpl~g~YiP~~gD~VIG~I~~v~   76 (239)
T COG1097           3 LSVSMRKIVLPGDLVLAEG-----SYKLGHGTYFEGGKIYSSVVGLLDVK-GKLVRVIPLEGRYIPEVGDVVIGKIIEVG   76 (239)
T ss_pred             eeccccceecCCCccCCCC-----CEecCCCcEecCCEEEEEEEeEEEEe-CCEEEEEeCCCcccCCCCCEEEEEEEEEc
Confidence            4456789999999766554     79999999999999999999999996 88999999999999999999999999999


Q ss_pred             CceEEEEecCCeeeeecCccc-----CCcccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcccCCeeEEE
Q 026458           87 ADNFFVDIRGPTIAFLPVLAF-----EGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFE  161 (238)
Q Consensus        87 ~~~~~VdI~~~~~a~L~~~~f-----~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~~~~  161 (238)
                      ++.|+|||++++.|+|++++|     +.++++||++|++||+|+|||+.++++++++|+|++     .+||+|++|++++
T Consensus        77 ~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~-----~~~GkL~~G~iv~  151 (239)
T COG1097          77 PSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKD-----EGLGKLKNGQIVK  151 (239)
T ss_pred             ccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCceEEEeec-----CCCccccCCEEEE
Confidence            999999999999999999988     456899999999999999999999999999999988     9999999999999


Q ss_pred             echhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc------CCHHHHHHHHHHHH
Q 026458          162 TSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES------LSAVQQKIMVDKLL  234 (238)
Q Consensus       162 V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~------lt~~~~~~~~~~~~  234 (238)
                      |+|++++|++++.++ |+++|+++++|+|+||+||||||++++...+.++..||++||+      +| +++++++++.+
T Consensus       152 i~p~kVpRvig~~~s-m~~~l~~~~~~~I~VG~NG~IWV~~~~~~~e~~~~~aI~~ie~ea~~~glt-dr~~~~i~~~~  228 (239)
T COG1097         152 IPPSKVPRVIGKKGS-MLNMLKEKTGCEIIVGQNGRIWVDGENESLEELAIEAIRKIEREAHTSGLT-DRIKEFLKKLL  228 (239)
T ss_pred             EchhhcceEecCCCc-HHHHhhhhcCeEEEEecCCEEEecCCCcchHHHHHHHHHHHhhhhhhhhHH-HHHHHHHHHHH
Confidence            999999999999998 9999999999999999999999999998889999999999997      66 78888877654

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

Probab=100.00  E-value=3.7e-56  Score=374.65  Aligned_cols=221  Identities=47%  Similarity=0.833  Sum_probs=206.6

Q ss_pred             cEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEec-CC----eEEEEccCCccCCCCCCEEEEEEEEecC
Q 026458           13 KIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSK-PN----KYWVESSQKRYVPCVEDTVLGIVVDCKA   87 (238)
Q Consensus        13 ~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~-~~----~i~V~~~~~~Y~P~vGDiVIG~V~~v~~   87 (238)
                      .+.+|||.+.....   .+..+|+|++..++.+..+.+|.++... ++    ..||...++||+|++||.|||+|++..+
T Consensus         2 ~~~~pg~~~~~~~~---~sv~~G~g~~~~g~~~~~~~~G~~~~~~~gk~~~~v~~vds~~kRYiP~~~D~VIGiV~~~~g   78 (230)
T KOG1004|consen    2 TFYFPGDSIPRPRL---CSVVLGPGLRRRGQERLVTKCGRLRHKEPGKGGGGVYWVDSQQKRYIPVKGDHVIGIVTSKSG   78 (230)
T ss_pred             ceecCCcccccCcc---CceeecCCccccCceEEeccccceeeccCCcccceeEEEecccceecCCCCCEEEEEEEeccC
Confidence            46799999876532   2589999999999999999999887642 22    6799999999999999999999999999


Q ss_pred             ceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcccCCeeEEEechhhh
Q 026458           88 DNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLS  167 (238)
Q Consensus        88 ~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~~~~V~~~~v  167 (238)
                      |.|+|||+.+..|.|++++|+||||+|||+|+.||+|||||..++++++++|+|.+++||+.+||+|+||+||+++++++
T Consensus        79 d~ykVDigg~~~a~L~~laFe~AtkrNrPnl~vGdliyakv~~a~~~~Epel~Cids~graaGfG~LkdG~if~vs~~~~  158 (230)
T KOG1004|consen   79 DIYKVDIGGSEPASLSYLAFEGATKRNRPNLQVGDLIYAKVVDANKDMEPELTCIDSTGRAAGFGVLKDGMIFKVSLGLC  158 (230)
T ss_pred             ceEEEecCCCCeeeeeeccccCccccCCCccccccEEEEEEEecCCCcCcceEEEcccCcccCcccccCceEEEecHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhccCCHHHHHHHHHHHHhhc
Q 026458          168 RMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRI  237 (238)
Q Consensus       168 ~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~lt~~~~~~~~~~~~~~~  237 (238)
                      |+|+. +.|++|+.++++++|||++|+||||||++++..++++++++|.+||+||.+|...|+++.++++
T Consensus       159 R~Ll~-p~~~iLq~vGk~~~FEia~GlNGriWV~ae~~~~t~~i~~~l~~~e~~td~~q~~~~k~~~~~~  227 (230)
T KOG1004|consen  159 RKLLL-PDCPILQTVGKKYPFEIAFGLNGRIWVKAETLSDTLIIANILMNCEFMTDTQQRIMVKQLFKRL  227 (230)
T ss_pred             HHHHc-CCCcHHHHhhcccceEEEEecCceEEEeccCcchHHHHHHHHHHhhccCcHHHHHHHHHHHHHH
Confidence            99997 7788999999999999999999999999999999999999999999999999888888888765

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=100.00  E-value=9.1e-52  Score=361.52  Aligned_cols=211  Identities=25%  Similarity=0.383  Sum_probs=197.9

Q ss_pred             CCcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEecCCeEEEEccCCccCCCCCCEEEEEEEEecCceE
Q 026458           11 VDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKADNF   90 (238)
Q Consensus        11 ~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~~~~i~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~   90 (238)
                      .+++|+|||.|+. +     +|.+|+|||.++|+|+||++|.++.+ ++.++|.|.+++|+|++||+|+|+|+++.++.|
T Consensus         7 ~~~~V~PGd~l~~-~-----~~~~G~Gty~~~g~i~As~~G~~~~~-~~~i~V~p~~~~y~P~vGDiViG~V~~i~~~~~   79 (235)
T PRK04163          7 DRKIVVPGDLLAE-G-----EFKAGRGTYKENGKIYSTVVGLVDIK-DDKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGW   79 (235)
T ss_pred             CCcEECCCCCcCc-C-----CeecCCceEEeCCEEEEEEeEEEEEE-CCEEEEEECCCcccCCCCCEEEEEEEEEeCceE
Confidence            4589999999973 3     79999999999999999999999987 679999999989999999999999999999999


Q ss_pred             EEEecCCeeeeecCcccCCc-----ccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcccCCeeEEEechh
Q 026458           91 FVDIRGPTIAFLPVLAFEGG-----TRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTG  165 (238)
Q Consensus        91 ~VdI~~~~~a~L~~~~f~ga-----tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~~~~V~~~  165 (238)
                      +|||++++.|+||.+++.++     +++++++|++||+|+|||+++++++.++|||++     ++||+|.+|++++||+.
T Consensus        80 ~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~-----~~lG~L~~G~~~~V~~~  154 (235)
T PRK04163         80 EVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKG-----KGLGKIEGGTIVEIKPV  154 (235)
T ss_pred             EEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcC-----CCCCccCCCEEEEECHH
Confidence            99999999999999998764     488999999999999999999988889999988     89999999999999999


Q ss_pred             hhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc------CCHHHHHHHHHHHHh
Q 026458          166 LSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES------LSAVQQKIMVDKLLQ  235 (238)
Q Consensus       166 ~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~------lt~~~~~~~~~~~~~  235 (238)
                      ++++|+|+.+. +++.|.+.++|+|++|+||+|||.+++.+.+.++.++|+++|+      || +++++|+++..+
T Consensus       155 ~i~~lig~~g~-~i~~l~~~~~~~I~ig~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~~~l~-~~v~~~~~~~~~  228 (235)
T PRK04163        155 KVPRVIGKKGS-MINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIKKIEREAHTSGLT-DRIKEFLEEELG  228 (235)
T ss_pred             HHHhhcCCCCh-hHhhhhhhhCcEEEEcCCcEEEEeeCCHHHHHHHHHHHHHHHhhhhccChH-HHHHHHHHHhhh
Confidence            99999997765 9999999999999999999999999999999999999999997      99 999999986654

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

Probab=100.00  E-value=1.7e-40  Score=286.91  Aligned_cols=175  Identities=22%  Similarity=0.321  Sum_probs=159.1

Q ss_pred             CCCcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEecCCeEEEEccCCccCCCCCCEEEEEEEEecCce
Q 026458           10 LVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKADN   89 (238)
Q Consensus        10 ~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~~~~i~V~~~~~~Y~P~vGDiVIG~V~~v~~~~   89 (238)
                      -..++|+||+.+...+     .|..|||||+.|+.|+||++|.+++. +++++|+|++.||.|++||+|+|+|+++.+++
T Consensus        27 ~~~~ivtPG~~V~~d~-----~fmRGHGTy~~d~~i~ssvaG~v~rv-NkLi~V~plk~rY~pEvGDvVVgRV~eVq~KR  100 (301)
T KOG3013|consen   27 DHSTIVTPGELVTDDP-----GFMRGHGTYVRDGEIYSSVAGVVQRV-NKLISVKPLKSRYAPEVGDVVVGRVIEVQQKR  100 (301)
T ss_pred             cCceeecCCccccCch-----hhhhcccceecCCeEEEeecchhhhh-cceEEEeehhhhcCCccCCEEEEEeeeeecce
Confidence            3557999999999876     69999999999999999999999987 89999999999999999999999999999999


Q ss_pred             EEEEecCCeeeeecCcc--cCCc---------ccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcccCCee
Q 026458           90 FFVDIRGPTIAFLPVLA--FEGG---------TRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGY  158 (238)
Q Consensus        90 ~~VdI~~~~~a~L~~~~--f~ga---------tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~  158 (238)
                      |+||+++-.+|+|..++  .||.         +..||.+|+.||+|.|+|+.+..++...|+++.     ..||||..|+
T Consensus       101 Wkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs~sLhTRS-----~KYGKL~~G~  175 (301)
T KOG3013|consen  101 WKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHDGSLSLHTRS-----LKYGKLGQGI  175 (301)
T ss_pred             eEEecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhccCCeEEEEecc-----hhcccccCce
Confidence            99999999999998864  5764         446999999999999999999999999999988     9999999999


Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEec
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNA  202 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~  202 (238)
                      +++|||.+++|..  .++   ..+  .++.++|+|+||+|||..
T Consensus       176 lvkVpp~Lvkr~K--~hf---h~l--p~g~~vIlG~NGyIWv~~  212 (301)
T KOG3013|consen  176 LVKVPPALVKRSK--THF---HNL--PGGVDVILGCNGYIWVGP  212 (301)
T ss_pred             EEEeCHHHhhhhh--hhh---ccC--CCCeEEEEecCceEEecC
Confidence            9999999999975  332   223  479999999999999976

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

Probab=99.97  E-value=3e-30  Score=192.61  Aligned_cols=86  Identities=58%  Similarity=0.888  Sum_probs=84.3

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCcc
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKA  148 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~  148 (238)
                      ||+|++||+|||+|+++.+++|+|||++++.|+||.++|+|++++|||+|++||+|||||.+++++++++|||.+++||+
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 026458          149 AEFGLL  154 (238)
Q Consensus       149 ~~~G~L  154 (238)
                      .+||.|
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=99.94  E-value=3.6e-26  Score=193.90  Aligned_cols=134  Identities=22%  Similarity=0.284  Sum_probs=118.4

Q ss_pred             CCCcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEec-CCeEEEEccCC-ccCCCCCCEEEEEEEEecC
Q 026458           10 LVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSK-PNKYWVESSQK-RYVPCVEDTVLGIVVDCKA   87 (238)
Q Consensus        10 ~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~-~~~i~V~~~~~-~Y~P~vGDiVIG~V~~v~~   87 (238)
                      ..+++|+|||.|+..+     +|.+|+|||+++|+|+|+++|.++.++ ++.++|.|.+. .|.|++||+|+|+|+++..
T Consensus         3 ~~~~~V~PGe~l~~~~-----e~~~G~Gty~~~~~i~as~~G~~~id~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~i~~   77 (189)
T PRK09521          3 KQGDLVLPGDYLAVIE-----EYLPGEGTYEDNGEVYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVYGRVVDVKE   77 (189)
T ss_pred             ccCCEECCCCcccccc-----ceEcCCCEEeeCCEEEEEeeEEEEEcCCCCEEEEecCcCCCCCCCCCCEEEEEEEEEcC
Confidence            3568999999998866     799999999999999999999999864 45899999876 8999999999999999999


Q ss_pred             ceEEEEecC----------CeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcccC
Q 026458           88 DNFFVDIRG----------PTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLK  155 (238)
Q Consensus        88 ~~~~VdI~~----------~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~  155 (238)
                      +.|.|||.+          +..|+||.+++.. ..+++++.|++||+|+|||++++  +.++|||++     ..||+|.
T Consensus        78 ~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~--~~i~LS~k~-----~~lGvv~  149 (189)
T PRK09521         78 QRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT--DPLQLSTKG-----KDLGVIY  149 (189)
T ss_pred             CeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC--CcEEEEEec-----CCceEEE
Confidence            999999963          5789999887643 35567899999999999999998  789999998     8899993

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

Probab=99.93  E-value=3.1e-25  Score=185.13  Aligned_cols=134  Identities=24%  Similarity=0.326  Sum_probs=120.3

Q ss_pred             CCCCcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEec-CCeEEEEccCC-ccCCCCCCEEEEEEEEec
Q 026458            9 NLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSK-PNKYWVESSQK-RYVPCVEDTVLGIVVDCK   86 (238)
Q Consensus         9 ~~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~-~~~i~V~~~~~-~Y~P~vGDiVIG~V~~v~   86 (238)
                      ...+.+|+|||.|+..|     ||.+|.|||+++|.|+|+.+|.+.+|+ +..++|.|.++ ..+|+.||+|+|+|+++.
T Consensus         2 ~~~g~~v~PGd~~a~~E-----E~~~G~gt~~~~g~i~Aa~~G~~~~d~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~   76 (188)
T COG1096           2 VKDGTFVLPGDVLAVIE-----EFLPGEGTYEEGGEIRAAATGVVRRDDKNRVISVKPGKKTPPLPKGGDIVYGRVTDVR   76 (188)
T ss_pred             cccCcEEcCcceeeeee-----eeecCCCeEeECCEEEEeecccEEEcccceEEEeccCCCCCCCCCCCCEEEEEEeecc
Confidence            45679999999999988     899999999999999999999999874 46889999988 889999999999999999


Q ss_pred             CceEEEEecC----------CeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCccc
Q 026458           87 ADNFFVDIRG----------PTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLL  154 (238)
Q Consensus        87 ~~~~~VdI~~----------~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L  154 (238)
                      .+.|.|.|-+          +..|.+|+++.. +..++.+++|++||+|+|||++..  ..++||+.+     +.||++
T Consensus        77 ~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~--~~~~Lst~~-----~dlGVI  148 (188)
T COG1096          77 EQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG--DPIQLSTKG-----NDLGVI  148 (188)
T ss_pred             ceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC--CCeEEEecC-----CcceEE
Confidence            9999999843          567899998765 447778899999999999999987  679999998     899998

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

Probab=99.88  E-value=7e-22  Score=162.51  Aligned_cols=149  Identities=19%  Similarity=0.217  Sum_probs=120.3

Q ss_pred             CCcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEec-CCeEEEEcc----CCccCCCCCCEEEEEEEEe
Q 026458           11 VDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSK-PNKYWVESS----QKRYVPCVEDTVLGIVVDC   85 (238)
Q Consensus        11 ~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~-~~~i~V~~~----~~~Y~P~vGDiVIG~V~~v   85 (238)
                      ...+|+|||+++..+    .++..|.|||+.++.|+||.+|....+. .+...|...    ...-+|.+||||.++|+.+
T Consensus         4 a~~~~lpG~~~c~~e----~~~~~g~Gtye~~~yI~aS~ag~~~~~~~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~~i   79 (193)
T KOG3409|consen    4 AETLVLPGEVVCRAE----GEYRMGEGTYERNGYIFASVAGVNFRDNLVQKIEVVSVEKQLFNELLPFVGAIVTARVSRI   79 (193)
T ss_pred             ceEEEcccceeeecc----cccccccceeecCCeEEeccccceeecCCccceeeeeecccchhhcCCccCcEEEEEEEee
Confidence            347899999999887    5799999999999999999999665441 234444432    3457999999999999999


Q ss_pred             cCceEEEEecC--------CeeeeecCcccCCcccccc----cCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcc
Q 026458           86 KADNFFVDIRG--------PTIAFLPVLAFEGGTRRNI----PKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGL  153 (238)
Q Consensus        86 ~~~~~~VdI~~--------~~~a~L~~~~f~gatk~~r----~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~  153 (238)
                      +..+++|||.+        .+.|+|+...+. +|+++|    .+|+|||+|.|+|++.+...+|.||+..     +.||+
T Consensus        80 ~~rfAkv~I~~V~d~~lk~~FrglirkqdvR-~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LTtAe-----neLGV  153 (193)
T KOG3409|consen   80 NLRFAKVDILSVGDKPLKKSFRGLIRKQDVR-ATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLTTAE-----NELGV  153 (193)
T ss_pred             ccceeeEEEEEEcCEEhhhhhcceeehhhcc-ccccchhhhhhccCCCcEEEEEEeecCCCCcEEEEEec-----ccceE
Confidence            99999999976        456677665553 344444    4799999999999998888899999998     89998


Q ss_pred             c------CCeeEEEechhhhhh
Q 026458          154 L------KDGYMFETSTGLSRM  169 (238)
Q Consensus       154 L------~~G~~~~V~~~~v~r  169 (238)
                      +      .++.|+.|++.....
T Consensus       154 V~a~as~~g~~M~pvdw~~mqs  175 (193)
T KOG3409|consen  154 VFARASETGEPMVPVDWQEMQS  175 (193)
T ss_pred             EEEeccccCCceeeccceeEEc
Confidence            8      578899999987654

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

Probab=99.78  E-value=6e-19  Score=133.50  Aligned_cols=80  Identities=18%  Similarity=0.203  Sum_probs=71.8

Q ss_pred             cCCCCCCEEEEEEEEecCceEEEEe--------cCCeeeeecCcccCCc---ccccccCcCCCCEEEEEEEecCCCCcce
Q 026458           70 YVPCVEDTVLGIVVDCKADNFFVDI--------RGPTIAFLPVLAFEGG---TRRNIPKFEIGSLLYVRVVKANPGMNPE  138 (238)
Q Consensus        70 Y~P~vGDiVIG~V~~v~~~~~~VdI--------~~~~~a~L~~~~f~ga---tk~~r~~l~~GDlV~ArV~~~~~~~~~~  138 (238)
                      |.|++||+|+|+|++++.++|.|||        ++++.|+||.+++...   ..+|+.+|++||+|+|||++.++.+.++
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        7789999998876432   2268999999999999999999888999


Q ss_pred             EEEecCCCccCCCccc
Q 026458          139 LSCTDASGKAAEFGLL  154 (238)
Q Consensus       139 Ls~~~~~~~~~~~G~L  154 (238)
                      ||+.+     ++||++
T Consensus        82 Lst~~-----~~lGVv   92 (92)
T cd05791          82 LSTAE-----NELGVV   92 (92)
T ss_pred             EEecC-----CCCccC
Confidence            99998     888875

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=99.75  E-value=5.3e-18  Score=124.90  Aligned_cols=81  Identities=28%  Similarity=0.413  Sum_probs=75.4

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCc
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGK  147 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~  147 (238)
                      +|.|++||+|+|+|+++..+.|.|||++..+|+||.+++... .+++++.|++||+|.|+|+++++.+.+.|||.+    
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            699999999999999999999999999999999999998754 778889999999999999999887889999998    


Q ss_pred             cCCCccc
Q 026458          148 AAEFGLL  154 (238)
Q Consensus       148 ~~~~G~L  154 (238)
                       ++||+|
T Consensus        77 -~~~Gvi   82 (82)
T cd04454          77 -NELGVI   82 (82)
T ss_pred             -CCCccC
Confidence             888875

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=99.57  E-value=1.2e-14  Score=107.77  Aligned_cols=81  Identities=26%  Similarity=0.379  Sum_probs=72.9

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-----cccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-----GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD  143 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-----atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  143 (238)
                      +|.|++||+|.|+|+++.++.|.|+|+....|+||.+++..     ..+++++.|++||.|.|+|+++++++.+.||+..
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            69999999999999999999999999999999999998853     3456677899999999999999887889999988


Q ss_pred             CCCccCCCccc
Q 026458          144 ASGKAAEFGLL  154 (238)
Q Consensus       144 ~~~~~~~~G~L  154 (238)
                           .+||+|
T Consensus        81 -----~~~g~~   86 (86)
T cd05789          81 -----LKYGKL   86 (86)
T ss_pred             -----ccccCC
Confidence                 788876

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=99.27  E-value=8.6e-12  Score=92.39  Aligned_cols=61  Identities=18%  Similarity=0.196  Sum_probs=38.5

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecCC------------------eeeeecCcccCCc---ccccccCcCCCCEEEEEEE
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRGP------------------TIAFLPVLAFEGG---TRRNIPKFEIGSLLYVRVV  129 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~------------------~~a~L~~~~f~ga---tk~~r~~l~~GDlV~ArV~  129 (238)
                      +|++||+|+|+|++++..++.|+|.+.                  +.|+++.+.....   .-+|..+|+|||+|+|||+
T Consensus         1 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~Vi   80 (82)
T PF10447_consen    1 LPKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVI   80 (82)
T ss_dssp             ---TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEE
T ss_pred             CCCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEe
Confidence            599999999999999999999999765                  2344444333211   1146789999999999999


Q ss_pred             ec
Q 026458          130 KA  131 (238)
Q Consensus       130 ~~  131 (238)
                      |+
T Consensus        81 Sl   82 (82)
T PF10447_consen   81 SL   82 (82)
T ss_dssp             EE
T ss_pred             eC
Confidence            84

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=99.13  E-value=3.8e-11  Score=76.82  Aligned_cols=38  Identities=26%  Similarity=0.330  Sum_probs=33.6

Q ss_pred             EEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEe
Q 026458           14 IVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFS   56 (238)
Q Consensus        14 iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~   56 (238)
                      +|+|||.|+..+     +|.+|+|||+++|+|+||++|.++++
T Consensus         1 iV~PG~~l~~~~-----e~~~G~GTY~~~g~I~asv~G~v~~~   38 (39)
T PF14382_consen    1 IVVPGDRLGSSE-----EYMPGHGTYVRDGNIYASVAGTVKID   38 (39)
T ss_dssp             EE-TT-EEEETT-----TSEESTTEEEETTEEEESSSEEEEEE
T ss_pred             CCCCCCEeecCC-----CEecCCCEEEeCCEEEEEeeEEEEEc
Confidence            699999999876     89999999999999999999999875

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

Probab=98.71  E-value=6.4e-08  Score=68.57  Aligned_cols=67  Identities=25%  Similarity=0.324  Sum_probs=56.0

Q ss_pred             CCEEEEEEEEecCceEEEEecCCeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCC-CCcceEEE
Q 026458           75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANP-GMNPELSC  141 (238)
Q Consensus        75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~  141 (238)
                      ||+|.|+|+++..+.|.||+++...|+||.+++. ...++....|++||.+.|+|.++++ ...+.||.
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            8999999999999999999998999999998774 3344456679999999999999974 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=98.69  E-value=7.4e-08  Score=69.27  Aligned_cols=68  Identities=13%  Similarity=0.187  Sum_probs=58.2

Q ss_pred             CCCCEEEEEEEEecC-ceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCCcceEEE
Q 026458           73 CVEDTVLGIVVDCKA-DNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSC  141 (238)
Q Consensus        73 ~vGDiVIG~V~~v~~-~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~  141 (238)
                      ++||+|.|+|+++.+ ..+.|++.....|.+|++++.. ..++....|++||.|.|+|.++++ ..+.||+
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 5899999999999999998754 344455679999999999999975 7788886

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=98.65  E-value=1.3e-07  Score=65.67  Aligned_cols=69  Identities=20%  Similarity=0.260  Sum_probs=59.0

Q ss_pred             CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEE
Q 026458           73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSC  141 (238)
Q Consensus        73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~  141 (238)
                      ++||+|.|+|+++....|.|++++...|.+|.+.+... .++....|++||.|.|+|.+++.+ ..+.||+
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            46999999999999999999999889999998876543 444556799999999999999876 6777776

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

Probab=98.61  E-value=2.3e-07  Score=66.45  Aligned_cols=71  Identities=14%  Similarity=0.110  Sum_probs=59.8

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecC--CeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEEe
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRG--PTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCT  142 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~  142 (238)
                      |++|++|.|+|+++....+.|++..  ...|.||.+++... ..+....|++||.|.|+|.+++.. ..+.||++
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  37999999887543 445566799999999999999864 45788874

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=98.60  E-value=2.8e-07  Score=64.02  Aligned_cols=68  Identities=18%  Similarity=0.186  Sum_probs=57.6

Q ss_pred             CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCCCcceEEEe
Q 026458           75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPGMNPELSCT  142 (238)
Q Consensus        75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~  142 (238)
                      ||+|.|+|+++....|.|+|.....|.||.+++... .......|++||.|.++|.+++..+.+.||++
T Consensus         1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~~~~i~ls~k   69 (69)
T cd05692           1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence            799999999999999999999999999999877543 22334569999999999999987667888873

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.

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

Probab=98.60  E-value=2.5e-07  Score=65.56  Aligned_cols=69  Identities=16%  Similarity=0.234  Sum_probs=59.5

Q ss_pred             CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458           75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD  143 (238)
Q Consensus        75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  143 (238)
                      ||+|.|+|+++.+..|.|+|.....|.+|.+.+... .++....|++||.|.|+|.+++.. ..+.||++.
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            899999999999999999999989999999877532 445566799999999999999876 568899875

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.

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

Probab=98.53  E-value=5.2e-07  Score=64.36  Aligned_cols=70  Identities=23%  Similarity=0.305  Sum_probs=61.4

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCCCc-ceEEE
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPGMN-PELSC  141 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~~-~~Ls~  141 (238)
                      |++||+|-|+|+++....+.|+++....|++|.+++... .......|++||-|.|+|.+++.... +.||+
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            789999999999999999999999999999999988643 45566789999999999999987654 77775

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=98.51  E-value=9.4e-07  Score=63.02  Aligned_cols=69  Identities=14%  Similarity=0.071  Sum_probs=59.0

Q ss_pred             CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEE
Q 026458           73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSC  141 (238)
Q Consensus        73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~  141 (238)
                      ++||+|.|+|+++.+..+.|++.....|.+|.+.+... .++....|++||.|.|+|.+++.+ ..+.||+
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            58999999999999999999999999999999887532 334566799999999999999864 5778876

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=98.46  E-value=6.6e-07  Score=63.63  Aligned_cols=62  Identities=19%  Similarity=0.231  Sum_probs=53.4

Q ss_pred             CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc---ccccccCcCCCCEEEEEEEecCCCCc
Q 026458           75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG---TRRNIPKFEIGSLLYVRVVKANPGMN  136 (238)
Q Consensus        75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga---tk~~r~~l~~GDlV~ArV~~~~~~~~  136 (238)
                      ||+|.|+|+++....+.|++.+..+|.+|.+++...   ..++...|++||.|.|+|++++....
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~   65 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT   65 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence            899999999999999999999999999999877532   44556779999999999999876543

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=98.40  E-value=1.8e-06  Score=61.68  Aligned_cols=71  Identities=17%  Similarity=0.214  Sum_probs=59.3

Q ss_pred             CCCCEEEEEEEEecCceEEEEecC-CeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCC-CCcceEEEec
Q 026458           73 CVEDTVLGIVVDCKADNFFVDIRG-PTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTD  143 (238)
Q Consensus        73 ~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  143 (238)
                      ++|++|.|+|+++....+.|++.. ...|.+|.+.+.. ...+....|++||.|.|+|.+++. ...+.|+++.
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 7899999887753 233445679999999999999986 4678888875

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=98.37  E-value=3.1e-06  Score=68.69  Aligned_cols=72  Identities=14%  Similarity=0.137  Sum_probs=63.6

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD  143 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  143 (238)
                      .++|++|.|+|+++....++|+|.....|.+|++++.. ...+....|.+||.|.|+|.+++..+.+.||+..
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            46899999999999999999999999999999998753 3455567899999999999999877889999876

>PRK07252 hypothetical protein; Provisional

Probab=98.37  E-value=2.3e-06  Score=67.76  Aligned_cols=72  Identities=18%  Similarity=0.250  Sum_probs=61.5

Q ss_pred             CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCC-CCcceEEEecC
Q 026458           73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTDA  144 (238)
Q Consensus        73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~~  144 (238)
                      ++||+|.|+|+++....+.|+|.....|.+|.+++... .......|++||.|.++|.+++. .+.+.||++..
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk~~   75 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTL   75 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence            47999999999999999999999889999999887532 33445679999999999999987 56788999874

>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=98.34  E-value=1.8e-06  Score=60.87  Aligned_cols=65  Identities=22%  Similarity=0.321  Sum_probs=54.7

Q ss_pred             CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceE
Q 026458           75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPEL  139 (238)
Q Consensus        75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~L  139 (238)
                      ||+|.|+|+++....+.|++.....|.+|.+.+... .++....|++||.|.|+|.++++. +.+.|
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            799999999999999999999889999999887543 445566799999999999999863 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.

>PRK08059 general stress protein 13; Validated

Probab=98.31  E-value=3.2e-06  Score=67.04  Aligned_cols=73  Identities=18%  Similarity=0.185  Sum_probs=61.9

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCC-CCcceEEEecC
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTDA  144 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~~  144 (238)
                      .++||+|.|+|+++....|.|+|.....|.+|.+++... ..+....|++||.|.|+|.+++. .+.+.||++..
T Consensus         5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~   79 (123)
T PRK08059          5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT   79 (123)
T ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEc
Confidence            468999999999999999999999999999999887543 33335679999999999999965 56899999873

>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=98.29  E-value=2.8e-06  Score=61.48  Aligned_cols=62  Identities=13%  Similarity=0.109  Sum_probs=52.7

Q ss_pred             CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcc-cc---cccCcCCCCEEEEEEEecCCC
Q 026458           73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGT-RR---NIPKFEIGSLLYVRVVKANPG  134 (238)
Q Consensus        73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gat-k~---~r~~l~~GDlV~ArV~~~~~~  134 (238)
                      ++||+|.|+|+++.+..+.|+++..-.|.+|.++..... ++   ....|++||.|.|+|++++++
T Consensus         2 k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~   67 (74)
T cd05705           2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSE   67 (74)
T ss_pred             CCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECC
Confidence            689999999999999999999998899999987764332 22   346899999999999999764

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.

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

Probab=98.29  E-value=2.8e-06  Score=71.80  Aligned_cols=80  Identities=20%  Similarity=0.308  Sum_probs=65.1

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc------------ccccccCcCCCCEEEEEEEecCCC--
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG------------TRRNIPKFEIGSLLYVRVVKANPG--  134 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~--  134 (238)
                      .|.|.+|++|.|+|++++...+.|+++ +.+++++.++.+..            .++.+..++.||.|++||.+++.+  
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            467999999999999999999999998 68888887665432            123456799999999999998753  


Q ss_pred             ----CcceEEEecCCCccCCCccc
Q 026458          135 ----MNPELSCTDASGKAAEFGLL  154 (238)
Q Consensus       135 ----~~~~Ls~~~~~~~~~~~G~L  154 (238)
                          ..+.||+.+     ++||++
T Consensus       155 ~~~~~~I~ls~~~-----~~LG~~  173 (187)
T PRK08563        155 RPRGSKIGLTMRQ-----PGLGKL  173 (187)
T ss_pred             CCCCCEEEEEecC-----CCCCcH
Confidence                257789988     899987

>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=98.26  E-value=2.6e-06  Score=65.27  Aligned_cols=71  Identities=18%  Similarity=0.253  Sum_probs=58.4

Q ss_pred             CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc--------------------ccccccCcCCCCEEEEEEEecC
Q 026458           73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG--------------------TRRNIPKFEIGSLLYVRVVKAN  132 (238)
Q Consensus        73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga--------------------tk~~r~~l~~GDlV~ArV~~~~  132 (238)
                      ++||+|.|+|+++......|++.....|.+|++++...                    ..+....|++||+|.|+|++++
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            68999999999999999999998888999998766421                    1124567999999999999999


Q ss_pred             CC----CcceEEEec
Q 026458          133 PG----MNPELSCTD  143 (238)
Q Consensus       133 ~~----~~~~Ls~~~  143 (238)
                      +.    ..+.||.+.
T Consensus        82 ~~~~~~~~i~LSlr~   96 (100)
T cd05693          82 KSKSGKKRIELSLEP   96 (100)
T ss_pred             CCcCCCcEEEEEecH
Confidence            74    467888754

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.

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

Probab=98.22  E-value=1.1e-05  Score=57.90  Aligned_cols=70  Identities=17%  Similarity=0.221  Sum_probs=57.4

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecC-CeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCCCcceEEE
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRG-PTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPGMNPELSC  141 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~  141 (238)
                      |+.|+++-|+|+++.+-.++|++.. ...|.+|.+++... .++.+..|++||-|.++|.+++....+.||.
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 36899999887543 3344556999999999999998766566664

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.

>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=98.18  E-value=7.9e-06  Score=59.91  Aligned_cols=72  Identities=17%  Similarity=0.086  Sum_probs=60.5

Q ss_pred             cCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEE
Q 026458           70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSC  141 (238)
Q Consensus        70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~  141 (238)
                      ..+++|+++-|+|+++......|++...-.|.+|.+.+... ..+....|++||.|.++|.+++.. +.+.||+
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            34789999999999999999999999889999999877543 445566799999999999999864 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.

>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=98.16  E-value=1e-05  Score=56.99  Aligned_cols=67  Identities=22%  Similarity=0.401  Sum_probs=56.4

Q ss_pred             CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEE
Q 026458           75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSC  141 (238)
Q Consensus        75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~  141 (238)
                      ||+|.|+|+++....+.|++.....|.+|.+++... ..+.+..|++||.|.++|.++++. +.+.||+
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            899999999999999999998779999999887532 333445699999999999999874 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.

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

Probab=98.15  E-value=9.8e-06  Score=68.19  Aligned_cols=81  Identities=19%  Similarity=0.269  Sum_probs=65.1

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc------------ccccccCcCCCCEEEEEEEecC----
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG------------TRRNIPKFEIGSLLYVRVVKAN----  132 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~----  132 (238)
                      .|.|.+|+++.|+|++++...+.|+++ +..++++.++....            .++.+..++.||.|++||.+++    
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            467999999999999999999999995 68888887654311            1234567999999999999986    


Q ss_pred             --CCCcceEEEecCCCccCCCcccC
Q 026458          133 --PGMNPELSCTDASGKAAEFGLLK  155 (238)
Q Consensus       133 --~~~~~~Ls~~~~~~~~~~~G~L~  155 (238)
                        +...+.||++.     ++||+++
T Consensus       155 ~~~~~~I~lt~k~-----~~LG~~~  174 (179)
T TIGR00448       155 RPEGSKIGLTMRQ-----PLLGKLE  174 (179)
T ss_pred             CCCcceEEEEecc-----CcCCccc
Confidence              23568899988     8999984

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

>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=1.1e-05  Score=58.15  Aligned_cols=68  Identities=22%  Similarity=0.292  Sum_probs=56.9

Q ss_pred             CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc---ccccccCcCCCCEEEEEEEecCCC-CcceEEEe
Q 026458           75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG---TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCT  142 (238)
Q Consensus        75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga---tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~  142 (238)
                      ||+|-|+|+++.+..+.|++...-.|.+|.+++...   .++....|++||.|.|+|+++++. ..+.||.+
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            899999999999999999998889999999877532   334456799999999999999875 45778754

Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

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

Probab=98.13  E-value=1.1e-05  Score=72.09  Aligned_cols=74  Identities=19%  Similarity=0.253  Sum_probs=63.6

Q ss_pred             cCCCCCCEEEEEEEEecCceEEEEecC--CeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458           70 YVPCVEDTVLGIVVDCKADNFFVDIRG--PTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD  143 (238)
Q Consensus        70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  143 (238)
                      -.|++||+|.|+|+++....|.|++..  ...|.+|.+.+. +..+..+..|++||.|.|+|.+++.. +.+.||.+.
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  479999998774 34556677899999999999999875 468899975

>PRK05807 hypothetical protein; Provisional

Probab=98.13  E-value=2.2e-05  Score=63.49  Aligned_cols=70  Identities=13%  Similarity=0.126  Sum_probs=60.8

Q ss_pred             CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458           73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD  143 (238)
Q Consensus        73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  143 (238)
                      ++||+|.|+|+++....++|+| ....|.+|.+.+.. ..++....|++||.|.++|.+++.++.+.||++.
T Consensus         4 ~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~   74 (136)
T PRK05807          4 KAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQ   74 (136)
T ss_pred             cCCCEEEEEEEEEECCeEEEEE-CCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEEe
Confidence            5799999999999999999999 45789999988753 3555567899999999999999877889999876

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

Probab=98.13  E-value=4.3e-06  Score=58.36  Aligned_cols=54  Identities=9%  Similarity=0.175  Sum_probs=47.2

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSN  213 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~  213 (238)
                      .+.||+.++.+++|+.++ .++.|.+.+++.|-+..||.|||.+.+.+....+..
T Consensus         5 ~i~Ip~~~ig~iIGkgG~-~ik~I~~~tg~~I~i~~~g~v~I~G~~~~~v~~A~~   58 (61)
T cd02393           5 TMKIPPDKIRDVIGPGGK-TIKKIIEETGVKIDIEDDGTVYIAASDKEAAEKAKK   58 (61)
T ss_pred             EEEeChhheeeeECCCch-HHHHHHHHHCCEEEeCCCCEEEEEeCCHHHHHHHHH
Confidence            589999999999999998 999999999999999999999999977754444433

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.

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

Probab=98.11  E-value=9.9e-06  Score=56.23  Aligned_cols=60  Identities=20%  Similarity=0.212  Sum_probs=49.6

Q ss_pred             CCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCC
Q 026458           74 VEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPG  134 (238)
Q Consensus        74 vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~  134 (238)
                      +|++|.|+|+++....|.|+++ ...|.||.+.... .....+..|++||.|.++|.+++..
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            5999999999999999999998 5899999876642 2333445699999999999998754

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=98.10  E-value=1.9e-05  Score=54.80  Aligned_cols=66  Identities=18%  Similarity=0.190  Sum_probs=54.5

Q ss_pred             CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCCCcceEE
Q 026458           75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPGMNPELS  140 (238)
Q Consensus        75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls  140 (238)
                      |+++.|+|+++....+.|+|.....|.||.+.++.. .......|++||.|.++|.+++..+.+.||
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            789999999999999999999889999999887643 222234699999999999999875566665

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.

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

Probab=98.09  E-value=5.1e-06  Score=65.72  Aligned_cols=74  Identities=15%  Similarity=0.209  Sum_probs=68.4

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCCCcceEEEecC
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDA  144 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~  144 (238)
                      .+++||+|-|+|+++.+=.++|++....+|..|+|.+. |..++..+.|.+||-|.++|+++++++.+.||++..
T Consensus         2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~~   76 (129)
T COG1098           2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRKL   76 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHHh
Confidence            36899999999999999999999999999999999874 568899999999999999999999999999999873

>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=98.04  E-value=3.6e-05  Score=55.70  Aligned_cols=66  Identities=24%  Similarity=0.273  Sum_probs=56.0

Q ss_pred             CCCCEEEEEEEEecCceEEEEec-CCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458           73 CVEDTVLGIVVDCKADNFFVDIR-GPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD  143 (238)
Q Consensus        73 ~vGDiVIG~V~~v~~~~~~VdI~-~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  143 (238)
                      ..|++|-|.|.++.+..|.||++ ....|.||.++....     ..|++||.+.|+|.++++. ..+.||++.
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 467999998766421     7899999999999999865 457898865

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.

>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=98.02  E-value=2.8e-05  Score=54.87  Aligned_cols=66  Identities=18%  Similarity=0.304  Sum_probs=54.9

Q ss_pred             CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEE
Q 026458           75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELS  140 (238)
Q Consensus        75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls  140 (238)
                      |++|-|+|+++....+.|++...-.|.+|.+.+... .++....|++||.+.++|.+++.+ +.+.||
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            799999999999999999998779999998877543 333445799999999999999864 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.

>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=98.02  E-value=1.6e-05  Score=54.99  Aligned_cols=65  Identities=15%  Similarity=0.200  Sum_probs=52.5

Q ss_pred             CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceE
Q 026458           75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPEL  139 (238)
Q Consensus        75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~L  139 (238)
                      |+++.|+|+++.+..+.|+++....|.+|.+.+... ..+....|++||.|.|+|.+++.. +.+.|
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            789999999999999999999889999998776532 233445699999999999998763 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.

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

Probab=98.00  E-value=4.7e-05  Score=56.96  Aligned_cols=71  Identities=27%  Similarity=0.313  Sum_probs=57.0

Q ss_pred             CCCCCEEEEEEEEecCc--eEEEEecCCeeeeecCcccCC----cccccccCcCCCCEEEEEEEecCCC-CcceEEEe
Q 026458           72 PCVEDTVLGIVVDCKAD--NFFVDIRGPTIAFLPVLAFEG----GTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCT  142 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~--~~~VdI~~~~~a~L~~~~f~g----atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~  142 (238)
                      |++||++.|+|+++.+.  .++|||+....|+||.++...    ...+....|++||.|.++|...... ..+.||+.
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  999999988899999987642    2233456799999999999986543 45667764

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

>PHA02945 interferon resistance protein; Provisional

Probab=98.00  E-value=4.3e-05  Score=57.04  Aligned_cols=70  Identities=17%  Similarity=0.246  Sum_probs=58.9

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecC--CeeeeecCccc---CCcccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRG--PTIAFLPVLAF---EGGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD  143 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f---~gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  143 (238)
                      .|.+||+|+|+|+. .+..+.|++.-  .-.|.+|.+..   .|..|. |+.+ .|..|.|+|+.+++. +-+.||.+.
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  46899999854   344666 9999 999999999999876 456788765

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

Probab=97.99  E-value=1.7e-05  Score=53.77  Aligned_cols=56  Identities=20%  Similarity=0.362  Sum_probs=47.8

Q ss_pred             EEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCC
Q 026458           78 VLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANP  133 (238)
Q Consensus        78 VIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~  133 (238)
                      |.|+|+++....+.|++.....|.+|.+.+... ..+.+..|++||.|.|+|.+++.
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            479999999999999999889999998877543 33456779999999999999875

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.

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

Probab=97.93  E-value=6.2e-05  Score=53.15  Aligned_cols=56  Identities=21%  Similarity=0.206  Sum_probs=48.9

Q ss_pred             CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC
Q 026458           73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG  134 (238)
Q Consensus        73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~  134 (238)
                      ..|++|-|+|.++..+.+.|||+. ..|+||.+.+.     .+..|++||-|.+.|.+++++
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 89999987773     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.

>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=97.91  E-value=5.4e-05  Score=53.39  Aligned_cols=59  Identities=12%  Similarity=0.187  Sum_probs=50.1

Q ss_pred             CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC
Q 026458           75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG  134 (238)
Q Consensus        75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~  134 (238)
                      ||+|-|+|+++......|++.....|.+|.+.+...... ...|++||-|.|||+.+++.
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            899999999999999999997778999998877422222 66799999999999999864

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.

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=97.88  E-value=4.4e-05  Score=69.84  Aligned_cols=93  Identities=15%  Similarity=0.088  Sum_probs=72.9

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEec--CCeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCC-CcceEEEecCCC
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIR--GPTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDASG  146 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~--~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~~~  146 (238)
                      .|.+||+|.|+|+++....+.|+|.  ....|++|.+.+. +..++.+..|++||-|.++|+++++. +.+.||.+.-+.
T Consensus        14 ~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~   93 (319)
T PTZ00248         14 FPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSP   93 (319)
T ss_pred             CCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeeccc
Confidence            6999999999999999999999996  3579999998874 34666778899999999999999765 457899887431


Q ss_pred             c-----cCC--CcccCCeeEEEec
Q 026458          147 K-----AAE--FGLLKDGYMFETS  163 (238)
Q Consensus       147 ~-----~~~--~G~L~~G~~~~V~  163 (238)
                      .     ...  -|....|.+..+.
T Consensus        94 ~pw~~~~e~~~~g~~v~~~V~~ia  117 (319)
T PTZ00248         94 EDIEACEEKFSKSKKVHSIMRHIA  117 (319)
T ss_pred             chHHHHHHhCcCCCEEEEEEEEch
Confidence            1     122  3666667766663

>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=97.75  E-value=0.00021  Score=51.69  Aligned_cols=68  Identities=16%  Similarity=0.150  Sum_probs=58.3

Q ss_pred             CCEEEEEEEEecCceEEEEec---CCeeeeecCcccCCc-c-cccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458           75 EDTVLGIVVDCKADNFFVDIR---GPTIAFLPVLAFEGG-T-RRNIPKFEIGSLLYVRVVKANPGMNPELSCTD  143 (238)
Q Consensus        75 GDiVIG~V~~v~~~~~~VdI~---~~~~a~L~~~~f~ga-t-k~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  143 (238)
                      |+++-|+|+++.+..++|+|.   ....|.+|.+.++.. . ++.+..|++||.|.++|.+++ ...+.+|++.
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            789999999999999999998   357999999888654 2 455567999999999999998 7788899865

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=97.72  E-value=9.7e-05  Score=62.32  Aligned_cols=81  Identities=20%  Similarity=0.249  Sum_probs=64.5

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc------------ccccccCcCCCCEEEEEEEecCCCC-
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG------------TRRNIPKFEIGSLLYVRVVKANPGM-  135 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~~-  135 (238)
                      .|.|..|.+|-|.|+++..-.++|.|+ |.++.+|.++....            .+..+..|+.||.|+|||....... 
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            478999999999999999999999999 88899988765321            2334558999999999999875432 


Q ss_pred             -----cceEEEecCCCccCCCcccC
Q 026458          136 -----NPELSCTDASGKAAEFGLLK  155 (238)
Q Consensus       136 -----~~~Ls~~~~~~~~~~~G~L~  155 (238)
                           .+.||++.     .++|+++
T Consensus       155 ~~~~~~I~lTmrq-----~~LGkle  174 (183)
T COG1095         155 RPRESKIGLTMRQ-----PGLGKLE  174 (183)
T ss_pred             ccccceEEEEecc-----ccCCcch
Confidence                 34566666     8999984

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

Probab=97.70  E-value=0.00018  Score=54.54  Aligned_cols=73  Identities=21%  Similarity=0.283  Sum_probs=58.3

Q ss_pred             CEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-c-----------cccccCcCCCCEEEEEEEecCCC------Ccc
Q 026458           76 DTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-T-----------RRNIPKFEIGSLLYVRVVKANPG------MNP  137 (238)
Q Consensus        76 DiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-t-----------k~~r~~l~~GDlV~ArV~~~~~~------~~~  137 (238)
                      ++|.|+|+++....+.|++. +..|.+|.+.+... .           ++....|++||.|.++|.+++..      ..+
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 48899988766432 1           12245689999999999999754      468


Q ss_pred             eEEEecCCCccCCCccc
Q 026458          138 ELSCTDASGKAAEFGLL  154 (238)
Q Consensus       138 ~Ls~~~~~~~~~~~G~L  154 (238)
                      .||...     +++|++
T Consensus        80 ~ls~k~-----~~~g~~   91 (99)
T cd04460          80 GLTMRQ-----PGLGKL   91 (99)
T ss_pred             EEEEec-----CCCCcH
Confidence            899987     788887

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.

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

Probab=97.65  E-value=0.00027  Score=49.48  Aligned_cols=65  Identities=23%  Similarity=0.241  Sum_probs=50.4

Q ss_pred             CCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCC-CCcceEEE
Q 026458           75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANP-GMNPELSC  141 (238)
Q Consensus        75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~  141 (238)
                      |++|.|+|+++....+.|++ ....|.+|.++......+. +.-.+||.+.|+|.++++ ...+.||.
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 5689999988764221111 122489999999999986 45667764

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.

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

Probab=97.63  E-value=0.00021  Score=49.97  Aligned_cols=60  Identities=13%  Similarity=0.149  Sum_probs=51.2

Q ss_pred             CCEEEEEEEEecCceEEEEecCCeeeeecCcccCC--cccccccCcCCCCEEEEEEEecCCC
Q 026458           75 EDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG--GTRRNIPKFEIGSLLYVRVVKANPG  134 (238)
Q Consensus        75 GDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~~  134 (238)
                      |+++-|+|+++.+..++|++.....|.+|.+.++.  ..++.+..|++||.|.++|.+++..
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            78999999999999999999988999999988763  2334456799999999999998754

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.

>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=97.62  E-value=0.00031  Score=50.15  Aligned_cols=67  Identities=13%  Similarity=0.135  Sum_probs=54.2

Q ss_pred             CCEEE-EEEEEe-cCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCC-CcceEEE
Q 026458           75 EDTVL-GIVVDC-KADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPG-MNPELSC  141 (238)
Q Consensus        75 GDiVI-G~V~~v-~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~  141 (238)
                      |+++= |+|+++ ....+.|++....+|.+|.+.+.. ..++....|++||.+.|+|+++++. +.+.|||
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            67788 899998 688899999877899999988753 3444556799999999999999864 4566764

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.

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

Probab=97.59  E-value=9e-05  Score=65.59  Aligned_cols=147  Identities=18%  Similarity=0.278  Sum_probs=102.9

Q ss_pred             CCccCCCCCCEEEEEEEEecCceEEEEecC--CeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCCC-cceEEEe
Q 026458           67 QKRYVPCVEDTVLGIVVDCKADNFFVDIRG--PTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPGM-NPELSCT  142 (238)
Q Consensus        67 ~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~  142 (238)
                      ..+-.|.+||+|||+|.++.+-.+.|.+.-  .-.|++|+|.+. |..++.|+.+++|.-+.|+|+.+++.+ -+.||.+
T Consensus         4 ~~~~~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlk   83 (269)
T COG1093           4 KRREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLK   83 (269)
T ss_pred             cccCCCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehh
Confidence            345579999999999999999999999975  358999998874 568899999999999999999999864 5779997


Q ss_pred             cCCC--c---------------------------------------cCCCcccCCee---------EEEe-ch--hhhhh
Q 026458          143 DASG--K---------------------------------------AAEFGLLKDGY---------MFET-ST--GLSRM  169 (238)
Q Consensus       143 ~~~~--~---------------------------------------~~~~G~L~~G~---------~~~V-~~--~~v~r  169 (238)
                      .-+.  +                                       .+.||.+-++|         .+.- .+  ..+  
T Consensus        84 rV~~~q~~~k~~~wk~~qka~klle~aaekl~~~~ee~~~~vg~~L~e~fG~~y~aFE~aa~~g~~~l~~~~~~~~~~--  161 (269)
T COG1093          84 RVTEHQRRKKIQEWKKEQKADKLLELAAEKLGKDLEEAYEEVGWKLEEEFGSLYDAFEAAAKEGGEVLDDEGVPEEWK--  161 (269)
T ss_pred             hCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHhHHHHHHhCCHHHHHHHHHhcCCcccccCCCCHHHH--
Confidence            7541  1                                       03356653222         1110 00  000  


Q ss_pred             hcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhccCC
Q 026458          170 LLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLS  222 (238)
Q Consensus       170 l~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~lt  222 (238)
                            -.+++...+++.. =.|-.-|+|=+.|..+..+..|-.||...+...
T Consensus       162 ------~~l~e~a~e~i~~-~~VkI~g~vev~s~~~dGVe~IK~aL~~A~~~~  207 (269)
T COG1093         162 ------EVLKEIARENIEP-PTVKIRGYVEVTSPAPDGVEKIKKALKAAEDNG  207 (269)
T ss_pred             ------HHHHHHHHhcCCC-CceEEEEEEEEEecCCCcHHHHHHHHHHHHhcC
Confidence                  0133333322110 124556899999999999999999999987633

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=97.57  E-value=0.00022  Score=65.31  Aligned_cols=75  Identities=17%  Similarity=0.133  Sum_probs=63.9

Q ss_pred             cCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCC-CcceEEEecC
Q 026458           70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDA  144 (238)
Q Consensus        70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~  144 (238)
                      |..++||+|-|+|+.+..+...|||+....|+||.+.+.. ..++....|++||.|.+.|++.++. +.+.|||+..
T Consensus        27 ~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~  103 (318)
T PRK07400         27 YHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRI  103 (318)
T ss_pred             hhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhhh
Confidence            4579999999999999999999999988899999988753 3455567799999999999998654 5789999864

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

Probab=97.54  E-value=0.0012  Score=47.74  Aligned_cols=64  Identities=19%  Similarity=0.188  Sum_probs=55.0

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEE
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSC  141 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~  141 (238)
                      -.++|+.+.|+|+++....++|++.....|.+|.+.+       ...++.||.+.++|.++..++.+.|+.
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            3778999999999999999999999889999998765       346999999999999995556677664

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=97.48  E-value=0.00052  Score=69.01  Aligned_cols=99  Identities=14%  Similarity=0.072  Sum_probs=76.7

Q ss_pred             eCCEEEEEEeeEeEEecC-CeEEEEccCCccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCc
Q 026458           41 ECDSVSVIKAGKLRFSKP-NKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKF  118 (238)
Q Consensus        41 ~~g~i~as~~G~v~~~~~-~~i~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l  118 (238)
                      ++|.++++..+....++- ..+...+    ..|++|+++.|+|+++....++|+|....+|.+|++.+.. ..++....|
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            467777777777665321 1222221    2378999999999999999999999988999999998853 345556779


Q ss_pred             CCCCEEEEEEEecCCCCcceEEEec
Q 026458          119 EIGSLLYVRVVKANPGMNPELSCTD  143 (238)
Q Consensus       119 ~~GDlV~ArV~~~~~~~~~~Ls~~~  143 (238)
                      ++||.|.++|.+++..+.+.||++.
T Consensus       667 kvGD~V~VkV~~iD~~grI~LS~k~  691 (693)
T PRK11824        667 KEGDEVKVKVLEIDKRGRIRLSRKA  691 (693)
T ss_pred             CCCCEEEEEEEEECCCCcEEEEEEe
Confidence            9999999999999876888999864

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

Probab=97.40  E-value=0.00098  Score=47.10  Aligned_cols=62  Identities=13%  Similarity=0.140  Sum_probs=52.0

Q ss_pred             CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC--cccccccCcCCCCEEEEEEEecCCC
Q 026458           73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG--GTRRNIPKFEIGSLLYVRVVKANPG  134 (238)
Q Consensus        73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~~  134 (238)
                      .+|+++.|+|+++....++|++....+|.+|.+.++.  ...+....|++||.|.++|.+++..
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            3699999999999999999999888999999988753  2223445699999999999998754

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=97.38  E-value=0.00081  Score=56.66  Aligned_cols=81  Identities=15%  Similarity=0.210  Sum_probs=61.7

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC------c-------ccccccCcCCCCEEEEEEEecCC--
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG------G-------TRRNIPKFEIGSLLYVRVVKANP--  133 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g------a-------tk~~r~~l~~GDlV~ArV~~~~~--  133 (238)
                      -|.|-.|.+|.|+|++++...+.|+++ +.++.+|.++.+.      .       .++.+..++.||.|++||..+.-  
T Consensus        76 vFrPf~gEVv~g~V~~v~~~G~~v~~G-p~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~  154 (176)
T PTZ00162         76 VFKPFKDEVLDAIVTDVNKLGFFAQAG-PLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDA  154 (176)
T ss_pred             EEecCCCCEEEEEEEEEecceEEEEee-CeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecC
Confidence            588999999999999999999999997 5558887765442      1       12234579999999999987642  


Q ss_pred             -CCcceEEEecCCCccCCCcccC
Q 026458          134 -GMNPELSCTDASGKAAEFGLLK  155 (238)
Q Consensus       134 -~~~~~Ls~~~~~~~~~~~G~L~  155 (238)
                       +.....|+++     ++||+++
T Consensus       155 ~~~~~i~T~~~-----~~LG~~~  172 (176)
T PTZ00162        155 SNLFAIATINS-----DYLGPIE  172 (176)
T ss_pred             CCcEEEEEecC-----CCcCccc
Confidence             2335567766     8999983

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.36  E-value=0.00059  Score=68.43  Aligned_cols=70  Identities=19%  Similarity=0.213  Sum_probs=60.1

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccC-----CcccccccCcCCCCEEEEEEEecCCCCcceEE
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFE-----GGTRRNIPKFEIGSLLYVRVVKANPGMNPELS  140 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-----gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls  140 (238)
                      .|.+|++|.|+|+++.+-.++|+|....+|.||++++.     ...++.+..|++||.|.++|.++++.+.+.|+
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            58999999999999999999999987789999999773     34556677899999999999999865556554

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.

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=97.36  E-value=0.00089  Score=61.38  Aligned_cols=72  Identities=18%  Similarity=0.201  Sum_probs=60.6

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCC-CCcceEEEec
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTD  143 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  143 (238)
                      ..++||+|.|+|+++....++|+++ ...|.+|.+.+... ..+....|++||.|.|+|.+++. .+.+.||++.
T Consensus       193 ~~k~G~vv~G~V~~I~~~G~fV~i~-gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K~  266 (318)
T PRK07400        193 RLEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQ  266 (318)
T ss_pred             cCCCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEec
Confidence            4788999999999999999999996 46899999877543 44556779999999999999975 4678899876

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

Probab=97.33  E-value=0.00057  Score=66.49  Aligned_cols=72  Identities=21%  Similarity=0.233  Sum_probs=63.3

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD  143 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  143 (238)
                      .-++||+|-|+|+++++-.++|||+. ..|.||++... ++.+.....|++||-|.++|++++.. ..+.||++.
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            46899999999999999999999999 99999998775 34566677899999999999999965 568899976

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.22  E-value=0.0009  Score=67.22  Aligned_cols=92  Identities=13%  Similarity=0.036  Sum_probs=68.1

Q ss_pred             eCCEEEEEEeeEeEEec-CCeEEEEccCCccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCc
Q 026458           41 ECDSVSVIKAGKLRFSK-PNKYWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKF  118 (238)
Q Consensus        41 ~~g~i~as~~G~v~~~~-~~~i~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l  118 (238)
                      ++|.+++...+....++ ...+...    ...|++|+++.|+|+++....++|+|.....|.||+++... ..++....|
T Consensus       588 ddG~V~i~~~~~~~~~~a~~~I~~~----~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~~  663 (684)
T TIGR03591       588 DDGTVKIAASDGEAAEAAIKMIEGI----TAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVL  663 (684)
T ss_pred             cCeEEEEEECcHHHHHHHHHHHHhh----hcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhcc
Confidence            35666666655544331 1122222    12489999999999999999999999988999999998853 355667789


Q ss_pred             CCCCEEEEEEEecCCCCc
Q 026458          119 EIGSLLYVRVVKANPGMN  136 (238)
Q Consensus       119 ~~GDlV~ArV~~~~~~~~  136 (238)
                      ++||.|.++|.+++..+.
T Consensus       664 kvGD~V~VkVi~id~~gk  681 (684)
T TIGR03591       664 KEGDEVKVKVLEIDKQGR  681 (684)
T ss_pred             CCCCEEEEEEEEECCCCC
Confidence            999999999999876443

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).

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.07  E-value=0.0022  Score=59.84  Aligned_cols=73  Identities=25%  Similarity=0.248  Sum_probs=59.9

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEe-cCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDI-RGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD  143 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI-~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  143 (238)
                      -.++||+|.|+|+++..+.+.||| +....|.||...+... .+.....|++||-|.|+|.+++.+ ..+.||.+.
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            468999999999999999999999 7788999998877532 333445699999999999999765 357888775

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

Probab=97.05  E-value=0.0049  Score=44.33  Aligned_cols=67  Identities=18%  Similarity=0.315  Sum_probs=52.7

Q ss_pred             CCCEEEEEEEEecCceEEEEecC-CeeeeecCcccCCcc------------cccccCcCCCCEEEEEEEecCCC-CcceE
Q 026458           74 VEDTVLGIVVDCKADNFFVDIRG-PTIAFLPVLAFEGGT------------RRNIPKFEIGSLLYVRVVKANPG-MNPEL  139 (238)
Q Consensus        74 vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~gat------------k~~r~~l~~GDlV~ArV~~~~~~-~~~~L  139 (238)
                      +|+++-|.|++++...+.|++.. ...|.++.+++++..            ++....|++||.|.++|.+++.. ..+.+
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 578999988775321            12346799999999999999763 34454


Q ss_pred             E
Q 026458          140 S  140 (238)
Q Consensus       140 s  140 (238)
                      +
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.

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.04  E-value=0.0024  Score=59.66  Aligned_cols=72  Identities=21%  Similarity=0.192  Sum_probs=60.0

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCC-CCcceEEEecC
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTDA  144 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~~  144 (238)
                      .++||+|-|+|+++....+.|+++. ..|.+|.+.+... .++....|++||.|.|+|.++++ .+.+.||++..
T Consensus       190 ~~~G~~v~g~V~~v~~~G~fV~l~~-v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~~  263 (390)
T PRK06676        190 LKEGDVVEGTVARLTDFGAFVDIGG-VDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDT  263 (390)
T ss_pred             CCCCCEEEEEEEEEecceEEEEeCC-eEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence            5899999999999999999999974 8899999877532 34445679999999999999976 46788998753

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.04  E-value=0.0029  Score=61.93  Aligned_cols=72  Identities=17%  Similarity=0.158  Sum_probs=61.2

Q ss_pred             CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-c-cccccCcCCCCEEEEEEEecCCC-CcceEEEecC
Q 026458           73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-T-RRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDA  144 (238)
Q Consensus        73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-t-k~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~  144 (238)
                      .+||+|-|+|+++....++|+|+....|.+|.+.+... . ++....|++||.|.|+|.+++.. +.+.||++..
T Consensus       372 ~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~~  446 (565)
T PRK06299        372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQL  446 (565)
T ss_pred             CCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEehh
Confidence            57999999999999999999999889999999877532 2 45567799999999999999854 6789998764

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=97.02  E-value=0.0031  Score=61.02  Aligned_cols=74  Identities=16%  Similarity=0.150  Sum_probs=61.6

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCC-----cceEEEecC
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGM-----NPELSCTDA  144 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~-----~~~Ls~~~~  144 (238)
                      ..++||+|-|+|+++....++|||+....|.+|.+.+.. ...+....|++||.|.|+|.+++...     .+.||++..
T Consensus       199 ~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~  278 (491)
T PRK13806        199 TVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQA  278 (491)
T ss_pred             hCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhh
Confidence            478999999999999999999999877899999988754 23455667999999999999998753     477887653

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.01  E-value=0.007  Score=59.28  Aligned_cols=72  Identities=14%  Similarity=0.198  Sum_probs=61.8

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD  143 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  143 (238)
                      .++||+|.|+|+++....++|.+.....|.+|.++.. ...++....|++||.|.|+|.+++.+ ..+.||+..
T Consensus       458 ~~~G~vV~G~V~~v~~~G~fV~l~~gi~g~i~~se~s~~~~~~~~~~~~~Gd~v~~~V~~vd~~~~~i~LS~k~  531 (565)
T PRK06299        458 HKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKA  531 (565)
T ss_pred             cCCCCEEEEEEEEEecCceEEecCCCcEEEEEHHHhcchhccCccccCCCCCEEEEEEEEEccccCEEEEEeee
Confidence            3789999999999999999999987889999988764 23456677899999999999999864 678899976

>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like

Probab=96.98  E-value=0.0013  Score=45.31  Aligned_cols=52  Identities=10%  Similarity=0.140  Sum_probs=44.3

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEee----CCeEEEecCChhHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL----NGRVWVNAESPSTVVLVS  212 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~----NG~IWi~~~~~~~~~~i~  212 (238)
                      -+.||+.++++++|++++ .++.|.+.+++.|-+..    ++.|||.++ .+.+..+.
T Consensus         3 ~i~Vp~~~~~~iIG~~G~-~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~-~~~v~~A~   58 (62)
T cd02394           3 EVEIPKKLHRFIIGKKGS-NIRKIMEETGVKIRFPDPGSKSDTITITGP-KENVEKAK   58 (62)
T ss_pred             EEEeCHHHhhhccCCCCC-cHHHHHHHhCCEEEcCCCCCCCCEEEEEcC-HHHHHHHH
Confidence            478999999999999998 89999999999999999    899999996 44444333

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.

>TIGR00717 rpsA ribosomal protein S1

Probab=96.98  E-value=0.0023  Score=61.87  Aligned_cols=68  Identities=21%  Similarity=0.176  Sum_probs=59.5

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCC-CCcceEEEec
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTD  143 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  143 (238)
                      .++|++|-|.|+++..+.+.|||+....|++|..++..    ..+.|++||.|.++|.+.++ .+.+.||+..
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            58899999999999999999999999999999888753    23679999999999998865 4678999864

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.

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=96.91  E-value=0.0043  Score=60.06  Aligned_cols=72  Identities=18%  Similarity=0.145  Sum_probs=60.1

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEEecC
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDA  144 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~  144 (238)
                      -++||+|-|+|+++.+..++|||+. ..|.+|.+.+... .++....|++||.|.++|..++.. ..+.||++..
T Consensus       206 lk~G~iv~G~V~~i~~~G~FVdlgg-v~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~  279 (486)
T PRK07899        206 LQKGQVRKGVVSSIVNFGAFVDLGG-VDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKAT  279 (486)
T ss_pred             ccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeec
Confidence            4589999999999999999999974 8999999887642 344455799999999999999864 6788998753

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=96.91  E-value=0.0031  Score=61.04  Aligned_cols=73  Identities=22%  Similarity=0.130  Sum_probs=59.7

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEEecC
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDA  144 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~  144 (238)
                      .+.||+|.|+|+++..+.+.|||+....|+||.+.+... ..+....|.+||-|.|.|++.++. +.+.||.+..
T Consensus        33 ~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~~~~~~~~~~~vGd~Ie~~V~~~~~~~g~liLS~k~~  107 (486)
T PRK07899         33 FNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEVVEVGDEVEALVLQKEDKEGRLILSKKRA  107 (486)
T ss_pred             CCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcccccCChhhcCCCCCEEEEEEEEEECCCCeEEEEehhh
Confidence            689999999999999999999999888999998877532 223344699999999999998653 5688888753

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=96.82  E-value=0.0035  Score=58.50  Aligned_cols=69  Identities=22%  Similarity=0.187  Sum_probs=56.4

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCC---cceEEEec
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGM---NPELSCTD  143 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~---~~~Ls~~~  143 (238)
                      .|..+.|++|.|+|.++....|.|||+. ..|+||.....     .+..|++||-|.|.|.++....   .+.||-.+
T Consensus       129 ef~~k~GeiV~G~V~~~~~~~~~Vdlg~-vEa~LP~~E~i-----p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt~  200 (362)
T PRK12327        129 EFSEREGDIVTGVVQRRDNRFVYVNLGK-IEAVLPPAEQI-----PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRTH  200 (362)
T ss_pred             HHHHhcCCEEEEEEEEEeCCcEEEEeCC-eEEEecHHHcC-----CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeCC
Confidence            3899999999999999999999999987 79999964431     2567999999999999998543   35666555

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=96.82  E-value=0.0073  Score=58.47  Aligned_cols=74  Identities=22%  Similarity=0.179  Sum_probs=62.1

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC--cccccccCcCCCCEEEEEEEecCCC-CcceEEEecCC
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG--GTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDAS  145 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~~  145 (238)
                      -.+|++|-|+|+++....++|++.....|.+|.+.+..  ...+....|++||.|.++|.+++.. +.+.||++...
T Consensus       290 ~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~~~  366 (491)
T PRK13806        290 LKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAE  366 (491)
T ss_pred             CCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEeecc
Confidence            46899999999999999999999877899999987753  2344556899999999999999864 67889998643

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

Probab=96.80  E-value=0.0068  Score=60.57  Aligned_cols=75  Identities=21%  Similarity=0.207  Sum_probs=62.7

Q ss_pred             cCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCC-CCcceEEEecC
Q 026458           70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTDA  144 (238)
Q Consensus        70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~~  144 (238)
                      +..++|++|-|+|+++..+.+.||++....|.||.+.+.. ..+.....|++||.|.++|.++++ .+.+.||.+.+
T Consensus       298 ~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~LS~k~~  374 (647)
T PRK00087        298 KQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEA  374 (647)
T ss_pred             hhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEEEeehh
Confidence            5689999999999999999999999988899999877653 233445679999999999999864 46788998765

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

Probab=96.66  E-value=0.0058  Score=59.65  Aligned_cols=94  Identities=23%  Similarity=0.304  Sum_probs=74.2

Q ss_pred             CccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC-CcceEEEecCC-
Q 026458           68 KRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDAS-  145 (238)
Q Consensus        68 ~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~~-  145 (238)
                      ..+.+++||+|-|.|+++..++..|||+.-..|++|.++|.+.-...  .|++||.|-+.|...... +.+.||-.... 
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            45789999999999999999999999999999999999997543222  799999999999987654 35677754322 


Q ss_pred             Cc----------------cCCCcccCCeeEEEec
Q 026458          146 GK----------------AAEFGLLKDGYMFETS  163 (238)
Q Consensus       146 ~~----------------~~~~G~L~~G~~~~V~  163 (238)
                      -+                ..-.|+++||+++.+.
T Consensus        93 ~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~  126 (541)
T COG0539          93 ERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIE  126 (541)
T ss_pred             HHhHHHHHHHHhcCCeEEEEEEEEecCcEEEEEC
Confidence            00                1225778999999995

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

Probab=96.59  E-value=0.0098  Score=59.45  Aligned_cols=72  Identities=17%  Similarity=0.194  Sum_probs=61.6

Q ss_pred             CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCC-CCcceEEEecC
Q 026458           73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTDA  144 (238)
Q Consensus        73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~~  144 (238)
                      ++|++|-|.|+++....++|++.....|.+|.+.+.. ..++....|++||.|.|+|.+++. .+.+.||++..
T Consensus       561 ~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~  634 (647)
T PRK00087        561 PVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEV  634 (647)
T ss_pred             cCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence            5899999999999999999999888999999987753 244555679999999999999985 47788999874

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=96.55  E-value=0.0079  Score=61.84  Aligned_cols=73  Identities=18%  Similarity=0.187  Sum_probs=63.2

Q ss_pred             CCCCCCEEE-EEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458           71 VPCVEDTVL-GIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD  143 (238)
Q Consensus        71 ~P~vGDiVI-G~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  143 (238)
                      .|++|+++- |+|+++.+-.++|+|....+|.+|++.+.. ..++....|++||.|..+|.+++..+.+.||.+.
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 699999999999999877899999998854 3555667899999999999999877788999865

>TIGR00717 rpsA ribosomal protein S1

Probab=96.45  E-value=0.036  Score=53.62  Aligned_cols=69  Identities=19%  Similarity=0.243  Sum_probs=58.3

Q ss_pred             CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCC-CCcceEEE
Q 026458           73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANP-GMNPELSC  141 (238)
Q Consensus        73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~  141 (238)
                      .+||+|-|+|+++....++|.+.....|.+|.+.+.. ..++....|++||.|.++|.+++. ...+.||.
T Consensus       445 ~~G~~v~g~V~~v~~~G~fV~l~~~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~id~~~~~i~ls~  515 (516)
T TIGR00717       445 KVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSV  515 (516)
T ss_pred             CcceEEEEEEEEEecceEEEEcCCCeEEEEEHHHcCccccccccccCCCCCEEEEEEEEEeCCCCEEEEEE
Confidence            5799999999999999999999888999999987643 244567789999999999999975 35666764

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.

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=96.41  E-value=0.011  Score=61.00  Aligned_cols=64  Identities=36%  Similarity=0.444  Sum_probs=56.0

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD  143 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  143 (238)
                      ++.||+|-|+|+++..+...|||+.-.+|++|...|..       .+++||-|.|.|.+.+..+ +.||-..
T Consensus       319 ~~~G~iV~G~Vv~i~~~~v~VdiG~K~eGiI~~~E~~~-------~~kvGd~i~~~V~~~~~~~-~~LS~~~  382 (863)
T PRK12269        319 PEPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEFEA-------PPKAGDGVRVYVERVTPYG-PELSKTK  382 (863)
T ss_pred             CCCCCEEEEEEEEEECCEEEEEeCCCceEEeEHHHhcc-------CCCCCCEEEEEEEEEcCCc-eEEEehH
Confidence            89999999999999999999999999999999888831       2589999999999987654 7888654

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=96.39  E-value=0.0072  Score=60.90  Aligned_cols=74  Identities=15%  Similarity=0.130  Sum_probs=64.5

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCC-CcceEEEecCC
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDAS  145 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~~  145 (238)
                      -++|-++.|.|+.+.+-.++|||+....|.+|++...+. .+.-...+++||+|.++|.+++.. ..+.||++.+.
T Consensus       656 Lk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~  731 (780)
T COG2183         656 LKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDE  731 (780)
T ss_pred             ccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccC
Confidence            488999999999999999999999999999999887654 444567899999999999999865 46899999864

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=96.32  E-value=0.012  Score=56.84  Aligned_cols=70  Identities=23%  Similarity=0.239  Sum_probs=57.4

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCC---cceEEEecC
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGM---NPELSCTDA  144 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~---~~~Ls~~~~  144 (238)
                      .|..++|++|.|+|.++....+.||++ ...|+||.+..     -.+..|++||-|.|.|..+++..   .+.||-.+|
T Consensus       129 eyk~~~GeIV~G~V~ri~~~giiVDLg-gvea~LP~sE~-----ip~E~~~~GdrIka~I~~Vd~~~kg~qIilSRt~p  201 (470)
T PRK09202        129 EYKDRVGEIITGVVKRVERGNIIVDLG-RAEAILPRKEQ-----IPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHP  201 (470)
T ss_pred             HHHhhcCCEEEEEEEEEecCCEEEEEC-CeEEEecHHHc-----CCCccCCCCCEEEEEEEEEecCCCCCeEEEEeCcH
Confidence            488999999999999999999999996 47999997654     24567999999999999997642   456776553

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=96.25  E-value=0.066  Score=50.93  Aligned_cols=92  Identities=18%  Similarity=0.140  Sum_probs=64.5

Q ss_pred             EEEEccCCccCCCCCCEEEEEEEEecCc--eEEEEecCCeeeeecCcccCCc-------------ccccccCcCCCCEEE
Q 026458           61 YWVESSQKRYVPCVEDTVLGIVVDCKAD--NFFVDIRGPTIAFLPVLAFEGG-------------TRRNIPKFEIGSLLY  125 (238)
Q Consensus        61 i~V~~~~~~Y~P~vGDiVIG~V~~v~~~--~~~VdI~~~~~a~L~~~~f~ga-------------tk~~r~~l~~GDlV~  125 (238)
                      +++++...  .+.+||+..|+|.++.+.  .++|||+...+|+||+++....             .++....+.+||-|.
T Consensus        14 ~~ie~~~~--~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~Il   91 (414)
T TIGR00757        14 LIIERPKS--RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVL   91 (414)
T ss_pred             EEEecCcC--cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEE
Confidence            45554433  346899999999999887  9999999999999999875311             112233599999999


Q ss_pred             EEEEecCC-CCcceEEEecCCCccCCCcccCCeeEEEec
Q 026458          126 VRVVKANP-GMNPELSCTDASGKAAEFGLLKDGYMFETS  163 (238)
Q Consensus       126 ArV~~~~~-~~~~~Ls~~~~~~~~~~~G~L~~G~~~~V~  163 (238)
                      .+|..-.. ...+.||+.-         .|.|.+++-.|
T Consensus        92 VQV~Ke~~~~Kgp~lT~~I---------sl~GrylVl~P  121 (414)
T TIGR00757        92 VQVVKEPRGNKGARLTTDI---------SLPGRYLVLMP  121 (414)
T ss_pred             EEEeeCCcCCCCCeEEEEE---------EeccceEEEec
Confidence            99998432 3457777743         14555555554

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.

>TIGR01953 NusA transcription termination factor NusA

Probab=96.16  E-value=0.016  Score=53.78  Aligned_cols=120  Identities=19%  Similarity=0.144  Sum_probs=75.1

Q ss_pred             ccCCCCCCEEEEEEEEecCce-EEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC---CcceEEEecC
Q 026458           69 RYVPCVEDTVLGIVVDCKADN-FFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG---MNPELSCTDA  144 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~-~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~---~~~~Ls~~~~  144 (238)
                      .|..++|++|.|+|.++..+. |.|||+ ...|+||.+...     .+..|++||-|.|.|.++.+.   ..+.||-..|
T Consensus       126 ey~~k~GeiV~G~V~~v~~~g~v~VdiG-~~ea~LP~~E~i-----p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~  199 (341)
T TIGR01953       126 EFSSKEGEIISGTVKRVNRRGNLYVELG-KTEGILPKKEQI-----PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP  199 (341)
T ss_pred             HHHhhcCCEEEEEEEEEecCCcEEEEEC-CeEEEecHHHcC-----CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH
Confidence            488999999999999998854 799996 579999976542     233499999999999999754   3466776553


Q ss_pred             C-Cc---cCCCcccCCeeEEEechhhhhhhcCCCCc-hhhHhhccccceEEEEeeCCe
Q 026458          145 S-GK---AAEFGLLKDGYMFETSTGLSRMLLSSPTC-PVLEELGKQLSFEIAVGLNGR  197 (238)
Q Consensus       145 ~-~~---~~~~G~L~~G~~~~V~~~~v~rl~~~~~~-~~l~~l~~~~~~ei~vG~NG~  197 (238)
                      . -+   +..--.+.+|.+-=.+.+..+   |.+.- .+...=..-=|.-.|||++|.
T Consensus       200 ~~v~~Lfe~EVPEI~dG~VeI~~iaR~p---G~RtKvAV~s~~~~iDpvga~vG~~G~  254 (341)
T TIGR01953       200 EFVKELLKLEVPEIADGIIEIKKIAREP---GYRTKIAVESNDENIDPVGACVGPKGS  254 (341)
T ss_pred             HHHHHHHHHhCccccCCeEEEEEEeeCC---cceeEEEEEcCCCCCCcceeeECCCCc
Confidence            1 00   122244567776544433322   21111 011111111356678888773

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.

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=96.10  E-value=0.036  Score=57.22  Aligned_cols=72  Identities=19%  Similarity=0.203  Sum_probs=60.5

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCC-CCcceEEEecC
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTDA  144 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~~  144 (238)
                      .++||+|.|+|..+....++||++ ...|.+|.+.+.. ...+.+..|.+||-|.++|+++++ .+.+.||++..
T Consensus       491 l~~G~~V~G~Vk~i~~~G~fVdl~-Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l  564 (863)
T PRK12269        491 VHIEDSVSGVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHF  564 (863)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEEC-CEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEecc
Confidence            568999999999999999999996 4789999987752 345556779999999999999986 46789998753

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

Probab=95.77  E-value=0.017  Score=39.43  Aligned_cols=44  Identities=9%  Similarity=0.112  Sum_probs=39.4

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEee------CCeEEEecC
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL------NGRVWVNAE  203 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~------NG~IWi~~~  203 (238)
                      -+.||..++++++|++++ .++.|.+.+++.|.+..      +..|||.+.
T Consensus         3 ~i~ip~~~~~~vIG~~G~-~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~   52 (64)
T cd00105           3 RVLVPSSLVGRIIGKGGS-TIKEIREETGAKIKIPDSGSGSEERIVTITGT   52 (64)
T ss_pred             EEEEchhhcceeECCCCH-HHHHHHHHHCCEEEEcCCCCCCCceEEEEEcC
Confidence            478999999999999998 99999999999999987      467999985

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.

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

Probab=95.74  E-value=0.079  Score=39.54  Aligned_cols=59  Identities=14%  Similarity=0.242  Sum_probs=41.0

Q ss_pred             CCCEEEEEEEEecCceEEEEecC----CeeeeecCc-ccCC-c-----ccccccCcCCCCEEEEEEEecC
Q 026458           74 VEDTVLGIVVDCKADNFFVDIRG----PTIAFLPVL-AFEG-G-----TRRNIPKFEIGSLLYVRVVKAN  132 (238)
Q Consensus        74 vGDiVIG~V~~v~~~~~~VdI~~----~~~a~L~~~-~f~g-a-----tk~~r~~l~~GDlV~ArV~~~~  132 (238)
                      +|.+|.|+|++++...+.|+++.    -....+|.. .|.. .     ..+.+..+++||.|++||....
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    222222211 1211 1     1123567999999999998874

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.

>PF00013 KH_1: KH domain syndrome, contains KH motifs

Probab=95.69  E-value=0.016  Score=39.56  Aligned_cols=54  Identities=15%  Similarity=0.224  Sum_probs=45.8

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeC---CeEEEecCChhHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN---GRVWVNAESPSTVVLVSNA  214 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N---G~IWi~~~~~~~~~~i~~~  214 (238)
                      -+.||..++.+++|++++ .++.|.+.+++.|-+-.+   ..|.|.+ +++....+.+.
T Consensus         3 ~i~vp~~~~~~iIG~~G~-~i~~I~~~t~~~I~i~~~~~~~~v~I~G-~~~~v~~A~~~   59 (60)
T PF00013_consen    3 RIEVPSSLVGRIIGKKGS-NIKEIEEETGVKIQIPDDDERDIVTISG-SPEQVEKAKKM   59 (60)
T ss_dssp             EEEEEHHHHHHHHTGGGH-HHHHHHHHHTSEEEEESTTEEEEEEEEE-SHHHHHHHHHH
T ss_pred             EEEECHHHcCEEECCCCC-cHHHhhhhcCeEEEEcCCCCcEEEEEEe-CHHHHHHHHhh
Confidence            478999999999999998 999999999999999875   6899998 77665555543

; 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 ....

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=95.60  E-value=0.047  Score=51.12  Aligned_cols=69  Identities=28%  Similarity=0.353  Sum_probs=53.0

Q ss_pred             ccCCCCCCEEEEEEEEecC-ceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCC----cceEEEec
Q 026458           69 RYVPCVEDTVLGIVVDCKA-DNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGM----NPELSCTD  143 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~-~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~----~~~Ls~~~  143 (238)
                      .|.+++|++|.|+|.++.. ..+.||++ ...|+||...-     -.+..|++||-|.|-|..+.+..    .+.||..+
T Consensus       133 ey~~~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eq-----ip~E~~~~Gdrik~~i~~V~~~~k~gp~IilSRt~  206 (374)
T PRK12328        133 KYKKKVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNR-----IKGEKFKVGDVVKAVLKRVKIDKNNGILIELSRTS  206 (374)
T ss_pred             HHHHhcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHc-----CCCCcCCCCCEEEEEEEEEecCCCCCCEEEEEcCC
Confidence            4899999999999999985 56889998 48999996432     23456999999999999986543    23455444

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=95.29  E-value=0.076  Score=50.71  Aligned_cols=93  Identities=11%  Similarity=0.084  Sum_probs=64.0

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecC-----CeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC--C--cceE
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRG-----PTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG--M--NPEL  139 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~-----~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~--~--~~~L  139 (238)
                      .|.+++|++|.|+|.++..+.+.||+++     ...|+||...-     --+..|++||-|+|-|..+...  .  .+.|
T Consensus       147 ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eq-----ip~E~y~~Gdrika~i~~V~~~~~kGpqIil  221 (449)
T PRK12329        147 EFQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQ-----LPNDNYRANATFKVFLKEVSEGPRRGPQLFV  221 (449)
T ss_pred             HHHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHc-----CCCCcCCCCCEEEEEEEEeecCCCCCCEEEE
Confidence            3899999999999999999999999953     26899996432     1235699999999999999654  2  2445


Q ss_pred             EEecCC-Cc---cCCCcccCCeeEEEechhh
Q 026458          140 SCTDAS-GK---AAEFGLLKDGYMFETSTGL  166 (238)
Q Consensus       140 s~~~~~-~~---~~~~G~L~~G~~~~V~~~~  166 (238)
                      |-.+|. -+   ...--.+.+|.+-=...+.
T Consensus       222 SRt~p~lv~~Lfe~EVPEI~dG~VeIk~IAR  252 (449)
T PRK12329        222 SRANAGLVVYLFENEVPEIEEGVVRIVAVAR  252 (449)
T ss_pred             EcCCHHHHHHHHHhhCcccccCeEEEEEEEe
Confidence            543321 00   1223555778766555444

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=94.53  E-value=0.25  Score=52.99  Aligned_cols=74  Identities=20%  Similarity=0.327  Sum_probs=65.4

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCC-CcceEEEecCC
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTDAS  145 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~~~  145 (238)
                      -++||+|.|.|..+.....++-+.....|.++++.+- ...+.-++.|.+|++|-+||.+++.+ ..++|+..+..
T Consensus      1160 lk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~s~ 1235 (1710)
T KOG1070|consen 1160 LKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKNSD 1235 (1710)
T ss_pred             cccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEeccc
Confidence            4789999999999999999999999999999988764 34677888999999999999999866 47999998864

>smart00322 KH K homology RNA-binding domain

Probab=94.44  E-value=0.14  Score=34.35  Aligned_cols=58  Identities=9%  Similarity=0.165  Sum_probs=48.3

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeC----CeEEEecCChhHHHHHHHHHHH
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN----GRVWVNAESPSTVVLVSNAIMN  217 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N----G~IWi~~~~~~~~~~i~~~i~~  217 (238)
                      .-+.|+..+...++|++++ .++.|.+.+++.|.+..+    ..++|.++ ..+...+..+|..
T Consensus         5 ~~i~i~~~~~~~liG~~G~-~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~-~~~v~~a~~~i~~   66 (69)
T smart00322        5 IEVLIPADKVGLIIGKGGS-TIKKIEEETGVKIDIPEDGSEERVVEITGP-PENVEKAAELILE   66 (69)
T ss_pred             EEEEEcchhcceeECCCch-HHHHHHHHHCCEEEECCCCCCccEEEEEcC-HHHHHHHHHHHHH
Confidence            4578999999999999998 889999999999998885    78999985 6667777766654

>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]

Probab=94.26  E-value=0.058  Score=56.36  Aligned_cols=74  Identities=19%  Similarity=0.260  Sum_probs=60.9

Q ss_pred             CCCCCEEEEEEEEecCce---EEEEecCCeeeeecCcccCCc-ccccccCcCCCCEEEEEEEecCCCC-cceEEEecCC
Q 026458           72 PCVEDTVLGIVVDCKADN---FFVDIRGPTIAFLPVLAFEGG-TRRNIPKFEIGSLLYVRVVKANPGM-NPELSCTDAS  145 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~---~~VdI~~~~~a~L~~~~f~ga-tk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~~~  145 (238)
                      -.+|-+|.+.|+++....   ..|-..|..+++++..+..++ .++.-..+++|+.|+|||++++... ..+|||+++.
T Consensus       983 ~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~id~e~f~v~Ls~r~sd 1061 (1299)
T KOG1856|consen  983 FYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKERFSVELSCRTSD 1061 (1299)
T ss_pred             hccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhhhhhhhhhhhHH
Confidence            458999999999999999   555899999999998877663 4445556889999999999998764 6889998754

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=93.33  E-value=0.15  Score=51.40  Aligned_cols=59  Identities=14%  Similarity=0.134  Sum_probs=50.1

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHH
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMN  217 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~  217 (238)
                      ..++|+|.+++.+||+.+. +++.|.+++++.|-+-.+|.|+|.+.+......+.+.|+.
T Consensus       553 ~~~~I~~~kI~~vIG~gGk-~Ik~I~~~tg~~I~i~ddG~V~i~~~~~~~~~~a~~~I~~  611 (684)
T TIGR03591       553 ETIKINPDKIRDVIGPGGK-VIREITEETGAKIDIEDDGTVKIAASDGEAAEAAIKMIEG  611 (684)
T ss_pred             EEEecCHHHHHhhcCCCcH-HHHHHHHHHCCEEEEecCeEEEEEECcHHHHHHHHHHHHh
Confidence            4689999999999999987 9999999999999999999999999887555544444443

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).

>PRK11642 exoribonuclease R; Provisional

Probab=92.58  E-value=0.72  Score=47.56  Aligned_cols=83  Identities=16%  Similarity=0.228  Sum_probs=62.8

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCC-eeeeecCcccCCc------------ccccccCcCCCCEEEEEEEecCCC-Ccc
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGP-TIAFLPVLAFEGG------------TRRNIPKFEIGSLLYVRVVKANPG-MNP  137 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~-~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~-~~~  137 (238)
                      ..+|+.+-|+|+++....++|.|... -+|.+|++.+.+.            -++....|++||-|..+|.+++.. +.+
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 7899998766431            113346799999999999998754 568


Q ss_pred             eEEEecCCCccCCCccc
Q 026458          138 ELSCTDASGKAAEFGLL  154 (238)
Q Consensus       138 ~Ls~~~~~~~~~~~G~L  154 (238)
                      .++....+-+..+.|+-
T Consensus       721 ~f~l~~~~~~~~~~~~~  737 (813)
T PRK11642        721 DFSLISSERAPRNVGKT  737 (813)
T ss_pred             EEEEecccccCCCCCcc
Confidence            88876543344455543

>PRK13763 putative RNA-processing protein; Provisional

Probab=92.04  E-value=0.42  Score=40.28  Aligned_cols=62  Identities=11%  Similarity=0.198  Sum_probs=53.0

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeC-CeEEEe---cCChhHHHHHHHHHHHhcc
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN-GRVWVN---AESPSTVVLVSNAIMNSES  220 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N-G~IWi~---~~~~~~~~~i~~~i~~~e~  220 (238)
                      ..+.||+.++..++|+.+. .++.|.+.+++.|-+-.+ |.|-|.   +.|+.....+.+.|+.+-.
T Consensus         5 ~~i~IP~~kig~iIG~gGk-~Ik~I~e~tg~~I~i~~~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~   70 (180)
T PRK13763          5 EYVKIPKDRIGVLIGKKGE-TKKEIEERTGVKLEIDSETGEVIIEPTDGEDPLAVLKARDIVKAIGR   70 (180)
T ss_pred             EEEEcCHHHhhhHhccchh-HHHHHHHHHCcEEEEECCCCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence            3578999999999998887 999999999999999999 999999   7788777777777765443

>TIGR02063 RNase_R ribonuclease R

Probab=91.93  E-value=0.7  Score=46.79  Aligned_cols=70  Identities=17%  Similarity=0.302  Sum_probs=55.8

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecC-CeeeeecCcccCCc------------ccccccCcCCCCEEEEEEEecCCC-Cc
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRG-PTIAFLPVLAFEGG------------TRRNIPKFEIGSLLYVRVVKANPG-MN  136 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~-~~  136 (238)
                      .+.+|.++-|+|+++..-.++|++.. ...|.+|++++.+.            .++....|++||-|..+|.+++.. +.
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            47889999999999999999999986 58999999877532            122345799999999999999753 45


Q ss_pred             ceEE
Q 026458          137 PELS  140 (238)
Q Consensus       137 ~~Ls  140 (238)
                      +.++
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.

>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein

Probab=91.73  E-value=0.32  Score=40.66  Aligned_cols=60  Identities=12%  Similarity=0.196  Sum_probs=51.8

Q ss_pred             EEechhhhhhhcCCCCchhhHhhccccceEEEEeeC-CeEEE--ecCChhHHHHHHHHHHHhcc
Q 026458          160 FETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN-GRVWV--NAESPSTVVLVSNAIMNSES  220 (238)
Q Consensus       160 ~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N-G~IWi--~~~~~~~~~~i~~~i~~~e~  220 (238)
                      +.||+.++..++|+.+. .++.|.+.+++.|-+-.+ |.|-|  .+.|+.....+...|+.+-.
T Consensus         2 i~Ip~~kig~vIG~gG~-~Ik~I~~~tgv~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~~   64 (172)
T TIGR03665         2 VKIPKDRIGVLIGKGGE-TKKEIEERTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGR   64 (172)
T ss_pred             ccCCHHHhhhHhCCchh-HHHHHHHHhCcEEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHc
Confidence            67999999999999988 999999999999999999 99999  67888777777777766443

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=91.22  E-value=1.3  Score=46.31  Aligned_cols=81  Identities=16%  Similarity=0.137  Sum_probs=56.1

Q ss_pred             EEEEccCCccCCCCCCEEEEEEEEe--cCceEEEEecCCeeeeecCcccCCc----------ccccccCcCCCCEEEEEE
Q 026458           61 YWVESSQKRYVPCVEDTVLGIVVDC--KADNFFVDIRGPTIAFLPVLAFEGG----------TRRNIPKFEIGSLLYVRV  128 (238)
Q Consensus        61 i~V~~~~~~Y~P~vGDiVIG~V~~v--~~~~~~VdI~~~~~a~L~~~~f~ga----------tk~~r~~l~~GDlV~ArV  128 (238)
                      +.|++...  -+.+|+|-+|+|.++  +-+.++|||+....|+|++......          ..+....|++||-|.-.|
T Consensus        27 L~IEr~~~--e~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV  104 (1068)
T PRK10811         27 LDIESPGH--EQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQI  104 (1068)
T ss_pred             EEeccCcc--ccCccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEE
Confidence            45555333  235899999999998  4578999999999999997654210          012234599999999999


Q ss_pred             EecC-CCCcceEEEec
Q 026458          129 VKAN-PGMNPELSCTD  143 (238)
Q Consensus       129 ~~~~-~~~~~~Ls~~~  143 (238)
                      ..-. ...-+.||+.-
T Consensus       105 ~KEa~gtKGp~LTt~I  120 (1068)
T PRK10811        105 DKEERGNKGAALTTFI  120 (1068)
T ss_pred             eecccCCCCCceeeeE
Confidence            9733 23446666543

>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like

Probab=90.63  E-value=0.58  Score=32.45  Aligned_cols=36  Identities=8%  Similarity=0.142  Sum_probs=33.5

Q ss_pred             EEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC
Q 026458          160 FETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG  196 (238)
Q Consensus       160 ~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG  196 (238)
                      +.||..++.+++|++++ .++.|.+.+++.|-+..|.
T Consensus         4 ~~ip~~~vg~iIG~~G~-~i~~i~~~tga~I~i~~~~   39 (65)
T cd02396           4 LLVPSSQAGSIIGKGGS-TIKEIREETGAKIRVSKSV   39 (65)
T ss_pred             EEECHHHcCeeECCCcH-HHHHHHHHHCCEEEEcCCC
Confidence            67999999999999998 9999999999999999887

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

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

Probab=90.53  E-value=0.46  Score=37.57  Aligned_cols=55  Identities=18%  Similarity=0.197  Sum_probs=42.5

Q ss_pred             hhhhhhhcCCCCchhhHhhccccceEEEEeeC-----------------------CeEEEecCC--hhHHHHHHHHHHHh
Q 026458          164 TGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN-----------------------GRVWVNAES--PSTVVLVSNAIMNS  218 (238)
Q Consensus       164 ~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N-----------------------G~IWi~~~~--~~~~~~i~~~i~~~  218 (238)
                      -.++.++||.+++ -++.|.+.++|.|.|--.                       |.|.|.+.+  .+....+...|+.+
T Consensus        14 ~N~IG~IIGPgG~-tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~l   92 (120)
T cd02395          14 YNFVGLILGPRGN-TLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEEL   92 (120)
T ss_pred             CCeeEEEECCCCh-HHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHH
Confidence            3577888999988 899999999999998766                       899999988  55555555555444


Q ss_pred             c
Q 026458          219 E  219 (238)
Q Consensus       219 e  219 (238)
                      -
T Consensus        93 l   93 (120)
T cd02395          93 L   93 (120)
T ss_pred             h
Confidence            3

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=90.52  E-value=0.58  Score=47.46  Aligned_cols=60  Identities=10%  Similarity=0.153  Sum_probs=51.5

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHh
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNS  218 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~  218 (238)
                      ..++|+|.+++.+||..+. .++.|.+.++++|=+-.+|.|.|.+.+.+....+...|+.+
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 ITVKIPVDKIGEVIGPKGK-MINQIQDETGAEISIEDDGTVYIGAADGPSAEAARAMINAI  639 (719)
T ss_pred             EEEEeChHHhhheeCCCcH-hHHHHHHHHCCEEEEecCcEEEEEeCCHHHHHHHHHHHHHh
Confidence            5789999999999998887 99999999999999999999999999986665555555443

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.

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

Probab=90.04  E-value=0.79  Score=45.99  Aligned_cols=73  Identities=15%  Similarity=0.102  Sum_probs=64.4

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD  143 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  143 (238)
                      -|++|.+=.|+|+++..=.++|.+...-.|.+|++.... ...+-.+.++.||.|+.||..+++.+.+.||.+.
T Consensus       616 e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri~ls~~~  689 (692)
T COG1185         616 EVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRLSIKA  689 (692)
T ss_pred             hcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeecccCCccceehh
Confidence            589999999999999999999999999999999987642 3555668899999999999999998999998764

>PRK11712 ribonuclease G; Provisional

Probab=89.42  E-value=5.3  Score=38.94  Aligned_cols=80  Identities=23%  Similarity=0.163  Sum_probs=56.0

Q ss_pred             EEEEccCCccCCCCCCEEEEEEEEecC--ceEEEEecCCeeeeecCccc-CC------cc------cccccCcCCCCEEE
Q 026458           61 YWVESSQKRYVPCVEDTVLGIVVDCKA--DNFFVDIRGPTIAFLPVLAF-EG------GT------RRNIPKFEIGSLLY  125 (238)
Q Consensus        61 i~V~~~~~~Y~P~vGDiVIG~V~~v~~--~~~~VdI~~~~~a~L~~~~f-~g------at------k~~r~~l~~GDlV~  125 (238)
                      +++++..  ....+|+|-.|+|.++.+  +.++|||+..-.|+||+... +.      ..      ......+++||-|.
T Consensus        27 ~~iE~~~--~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iL  104 (489)
T PRK11712         27 IHIEREA--KRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIM  104 (489)
T ss_pred             EEEecCC--cccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEE
Confidence            3445433  345689999999999955  78999999999999998754 11      00      01123499999999


Q ss_pred             EEEEecCC-CCcceEEEe
Q 026458          126 VRVVKANP-GMNPELSCT  142 (238)
Q Consensus       126 ArV~~~~~-~~~~~Ls~~  142 (238)
                      .+|..-.. ...+.||+.
T Consensus       105 VQV~Ke~~~~KG~~lT~~  122 (489)
T PRK11712        105 VQVVKDPLGTKGARLTTD  122 (489)
T ss_pred             EEEEeCCcCCCCCeEEEE
Confidence            99997432 345677764

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=89.37  E-value=2.6  Score=29.03  Aligned_cols=60  Identities=17%  Similarity=0.105  Sum_probs=33.9

Q ss_pred             CCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEE
Q 026458           74 VEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSC  141 (238)
Q Consensus        74 vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~  141 (238)
                      +|+++-.+|++++...|.+|-+......||..+.+       ..+.+||-|..-|=. ++......||
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~-------~~~~~Gd~v~VFvY~-D~~~rl~AT~   60 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVP-------EPLKVGDEVEVFVYL-DKEGRLVATT   60 (61)
T ss_dssp             --------EEEE-SSEEEEEETT-EEEEEEGGG-------------TTSEEEEEEEE--TTS-EEEE-
T ss_pred             CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcC-------CCCCCCCEEEEEEEE-CCCCCEEEec
Confidence            58899999999999999999888899999976553       348899999988765 3334455554

>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=88.10  E-value=2.2  Score=30.86  Aligned_cols=65  Identities=17%  Similarity=0.108  Sum_probs=46.3

Q ss_pred             CCEEEEEEEEecCceEEEEecC-CeeeeecCcccCCcccccc---cCcCCCCEE-EEEEEecCCCCcceEE
Q 026458           75 EDTVLGIVVDCKADNFFVDIRG-PTIAFLPVLAFEGGTRRNI---PKFEIGSLL-YVRVVKANPGMNPELS  140 (238)
Q Consensus        75 GDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~gatk~~r---~~l~~GDlV-~ArV~~~~~~~~~~Ls  140 (238)
                      |++|-|+|.+++.|...|++.. .-.|+||.........+++   ..+++||-+ -+=|.. .....+.||
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD~~~k~~~~~~klrvG~~L~~~lvL~-~~~r~i~lt   70 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLS-NYKGRIILT   70 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCchhhCHHHHhhhhcCCCccceEEEe-ccccEEEEe
Confidence            7899999999999999999976 6689998765544322332   358999988 666662 223344454

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.

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

Probab=87.77  E-value=2.5  Score=42.56  Aligned_cols=70  Identities=11%  Similarity=0.157  Sum_probs=54.5

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEec-CCeeeeecCcccCCc------------ccccccCcCCCCEEEEEEEecCCC-Cc
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIR-GPTIAFLPVLAFEGG------------TRRNIPKFEIGSLLYVRVVKANPG-MN  136 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~-~~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~-~~  136 (238)
                      ...+|..+-|+|+++....++|+|. ...+|.+|++++++.            .++....|++||.|..+|.+++.. ..
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            3567999999999999999999997 568999999877542            122346799999999999999753 33


Q ss_pred             ceEE
Q 026458          137 PELS  140 (238)
Q Consensus       137 ~~Ls  140 (238)
                      +.++
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 rRNA processing protein Rrp5 [RNA processing and modification]

Probab=85.56  E-value=1.5  Score=47.35  Aligned_cols=70  Identities=17%  Similarity=0.187  Sum_probs=57.2

Q ss_pred             CCccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCccc----CCcccccccCcCCCCEEEEEEEecCCCCcc
Q 026458           67 QKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAF----EGGTRRNIPKFEIGSLLYVRVVKANPGMNP  137 (238)
Q Consensus        67 ~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f----~gatk~~r~~l~~GDlV~ArV~~~~~~~~~  137 (238)
                      +..|.-++|++|-+.|+++.++.-.|++.+...|-+|++..    +..+. .-..|+.||-|.|||+.-++..+.
T Consensus       878 k~~~~~~igsiv~a~v~svKp~~L~v~l~~~~~gri~isev~d~~~eitD-p~~k~~vG~~I~vrviG~~D~k~l  951 (1710)
T KOG1070|consen  878 KSTEDLSIGSIVRAYVKSVKPDQLNVLLAANHHGRIHISEVLDNLHEITD-PLDKFKVGDGIFVRVIGGHDVKDL  951 (1710)
T ss_pred             ccccceeeeeEEEEEEeeecccceEEeccccccCceehHHhhccccccCC-hhhhcccCCeEEEEEEcCCccccC
Confidence            45688899999999999999999999999999999998753    22233 445799999999999987654443

>PRK04012 translation initiation factor IF-1A; Provisional

Probab=83.86  E-value=6.7  Score=30.07  Aligned_cols=55  Identities=18%  Similarity=0.220  Sum_probs=39.2

Q ss_pred             CCCCCCEEEEEEEEe-cCceEEEEecCCe--eeeecCcccCCcccccccCcCCCCEEEEEEEecC
Q 026458           71 VPCVEDTVLGIVVDC-KADNFFVDIRGPT--IAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKAN  132 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v-~~~~~~VdI~~~~--~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~  132 (238)
                      .|. .+-++|+|+.. .++.|.|.+....  .|.+     +|.-++ +-.+++||.|..+....+
T Consensus        17 ~p~-e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i-----~GK~Rk-~IwI~~GD~VlVe~~~~~   74 (100)
T PRK04012         17 MPE-EGEVFGVVEQMLGANRVRVRCMDGVERMGRI-----PGKMKK-RMWIREGDVVIVAPWDFQ   74 (100)
T ss_pred             CCC-CCEEEEEEEEEcCCCEEEEEeCCCCEEEEEE-----chhhcc-cEEecCCCEEEEEecccC
Confidence            454 55699999997 5678888886533  3333     455455 778999999999986654

>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=83.79  E-value=5.3  Score=31.66  Aligned_cols=61  Identities=21%  Similarity=0.267  Sum_probs=41.5

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcc------cCCc-------c-cccccCcCCCCEEEEEEEecC
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLA------FEGG-------T-RRNIPKFEIGSLLYVRVVKAN  132 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~------f~ga-------t-k~~r~~l~~GDlV~ArV~~~~  132 (238)
                      |-+|.++.|+|.+.+.+..+|.++--.+-.+|...      |...       . ...+-+++.|+-|+=||.+..
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            67899999999999999999999764444444433      3211       2 455667999999999999753

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

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=83.65  E-value=3.5  Score=30.70  Aligned_cols=64  Identities=16%  Similarity=0.269  Sum_probs=46.4

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecC-Ceeee-ecCcccCC-cccccccCcCCCCEEEEEEEecCCCCc
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRG-PTIAF-LPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMN  136 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~-L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~  136 (238)
                      .|++||+|. .|..+....+.|.+-- ..+|. |+.++..- .-++.+..+ +|-.+.++|+.+++..-
T Consensus        13 ~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KG   79 (86)
T PHA02858         13 FPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKG   79 (86)
T ss_pred             cCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCC
Confidence            699999999 8888999999998853 24444 43655532 233445567 99999999999987643

>smart00652 eIF1a eukaryotic translation initiation factor 1A

Probab=83.55  E-value=6.7  Score=28.96  Aligned_cols=53  Identities=15%  Similarity=0.105  Sum_probs=36.9

Q ss_pred             CCCCCEEEEEEEEe-cCceEEEEecCCe--eeeecCcccCCcccccccCcCCCCEEEEEEEec
Q 026458           72 PCVEDTVLGIVVDC-KADNFFVDIRGPT--IAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKA  131 (238)
Q Consensus        72 P~vGDiVIG~V~~v-~~~~~~VdI~~~~--~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~  131 (238)
                      |. .+-++|+|+.. .++.|.|......  .|.+     +|.-++ +-.++.||+|..+....
T Consensus         2 p~-e~q~~g~V~~~lG~~~~~V~~~dG~~~la~i-----pgK~Rk-~iwI~~GD~VlVe~~~~   57 (83)
T smart00652        2 KE-DGQEIAQVVKMLGNGRLEVMCADGKERLARI-----PGKMRK-KVWIRRGDIVLVDPWDF   57 (83)
T ss_pred             CC-CCcEEEEEEEEcCCCEEEEEECCCCEEEEEE-----chhhcc-cEEEcCCCEEEEEecCC
Confidence            54 44589999997 5688888886533  3444     344443 67899999999987543

>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins

Probab=82.94  E-value=4.5  Score=28.23  Aligned_cols=51  Identities=22%  Similarity=0.283  Sum_probs=34.7

Q ss_pred             CEEEEEEEEe-cCceEEEEecCCe--eeeecCcccCCcccccccCcCCCCEEEEEEEecC
Q 026458           76 DTVLGIVVDC-KADNFFVDIRGPT--IAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKAN  132 (238)
Q Consensus        76 DiVIG~V~~v-~~~~~~VdI~~~~--~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~  132 (238)
                      +-++|+|+.. .++.|.|.+....  .+.+|     |. .+.+-.+++||.|...+...+
T Consensus         3 ~e~~~~V~~~lG~~~~~V~~~dg~~~l~~i~-----gK-~r~~iwI~~GD~V~V~~~~~d   56 (65)
T PF01176_consen    3 GEVIGRVTEMLGNNLFEVECEDGEERLARIP-----GK-FRKRIWIKRGDFVLVEPSPYD   56 (65)
T ss_dssp             TEEEEEEEEEESSSEEEEEETTSEEEEEEE------HH-HHTCC---TTEEEEEEESTTC
T ss_pred             cEEEEEEEEECCCCEEEEEeCCCCEEEEEec-----cc-eeeeEecCCCCEEEEEecccC
Confidence            5689999997 6688999886643  34443     55 577888999999999885443

It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.

>PRK13763 putative RNA-processing protein; Provisional

Probab=82.66  E-value=5.7  Score=33.42  Aligned_cols=69  Identities=10%  Similarity=0.055  Sum_probs=53.7

Q ss_pred             hhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc-CCHHHHHHHHHHHHhhc
Q 026458          166 LSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES-LSAVQQKIMVDKLLQRI  237 (238)
Q Consensus       166 ~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~-lt~~~~~~~~~~~~~~~  237 (238)
                      ...|++|+.+. .++.|.+.++|.|.|.-+ .|-|.+ +++....+.++|..+-. -..+.+-.+++...+++
T Consensus       105 ~~griIG~~G~-~~k~ie~~t~~~i~i~~~-~v~i~G-~~~~~~~A~~~I~~li~g~~~~~~~~~l~~~~~~~  174 (180)
T PRK13763        105 IKGRIIGEGGK-TRRIIEELTGVDISVYGK-TVAIIG-DPEQVEIAREAIEMLIEGAPHGTVYKFLERKKREL  174 (180)
T ss_pred             HhhheeCCCcH-HHHHHHHHHCcEEEEcCC-EEEEEe-CHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHH
Confidence            56788999987 999999999999999754 477775 99989998998887664 44466666677666554

>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]

Probab=81.82  E-value=9  Score=32.01  Aligned_cols=63  Identities=14%  Similarity=0.277  Sum_probs=46.3

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCc-----cc-CCcc-----cccccCcCCCCEEEEEEEec
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVL-----AF-EGGT-----RRNIPKFEIGSLLYVRVVKA  131 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~-----~f-~gat-----k~~r~~l~~GDlV~ArV~~~  131 (238)
                      .+.|-.|++|=|.|+.++...+.++++.-...+++.+     .| ||..     ..+-...+.|+-|+-+|+..
T Consensus        76 ~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigt  149 (170)
T KOG3298|consen   76 TFKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGT  149 (170)
T ss_pred             EEeecCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEE
Confidence            4789999999999999999999999998666665543     23 2321     11112578888899888875

>PLN00208 translation initiation factor (eIF); Provisional

Probab=81.14  E-value=7  Score=32.02  Aligned_cols=56  Identities=11%  Similarity=-0.005  Sum_probs=37.9

Q ss_pred             CCCCCCEEEEEEEEe-cCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEec
Q 026458           71 VPCVEDTVLGIVVDC-KADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKA  131 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~  131 (238)
                      .|..|. ++|+|+.. .+..+.|.......-.-+   ++|.-++ +-.+++||+|..+....
T Consensus        28 ~p~egq-~~g~V~~~lGn~~~~V~c~dG~~rLa~---IpGKmRK-rIWI~~GD~VlVel~~~   84 (145)
T PLN00208         28 FKEDGQ-EYAQVLRMLGNGRCEALCIDGTKRLCH---IRGKMRK-KVWIAAGDIILVGLRDY   84 (145)
T ss_pred             cCCCCc-EEEEEEEEcCCCEEEEEECCCCEEEEE---Eecccee-eEEecCCCEEEEEccCC
Confidence            466655 89999997 567888887653332222   2454444 67899999999996544

>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain

Probab=80.96  E-value=13  Score=27.17  Aligned_cols=50  Identities=16%  Similarity=0.191  Sum_probs=33.9

Q ss_pred             EEEEEEEe-cCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEec
Q 026458           78 VLGIVVDC-KADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKA  131 (238)
Q Consensus        78 VIG~V~~v-~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~  131 (238)
                      ++|+|++. .++.|.|.......-..+   ++|.-++. -.+++||.|..+....
T Consensus         2 ~i~~V~~~lG~~~~~V~~~dg~~~l~~---i~gK~Rk~-iwI~~GD~VlV~~~~~   52 (78)
T cd04456           2 QIVRVLRMLGNNRHEVECADGQRRLVS---IPGKLRKN-IWIKRGDFLIVDPIEE   52 (78)
T ss_pred             eEEEEEEECCCCEEEEEECCCCEEEEE---EchhhccC-EEEcCCCEEEEEeccc
Confidence            68999997 568889888653322222   23443333 6799999999987665

IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	238
2nn6_G	289	Structure Of The Human Rna Exosome Composed Of Rrp4		7e-39
4ifd_G	242	Crystal Structure Of An 11-subunit Eukaryotic Exoso		1e-24
2ja9_A	175	Structure Of The N-Terminal Deletion Of Yeast Exoso		3e-23
2ba0_A	229	Archaeal Exosome Core Length = 229		3e-08
2jeb_I	251	Structure Of A 9-Subunit Archaeal Exosome Bound To		4e-05
3l7z_C	249	Crystal Structure Of The S. Solfataricus Archaeal E		4e-05
2je6_I	251	Structure Of A 9-Subunit Archaeal Exosome Length =		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 =  156 bits (395), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 83/221 (37%), Positives = 130/221 (58%), Gaps = 8/221 (3%)
Query: 22  LDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNK------YWVESSQKRYVPCVE 75
           L+  + +   +  G GLR+  D + V K G+LR  +P        YWV+S QKRYVP   
Sbjct: 69  LNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPVKG 128
Query: 76  DTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGM 135
           D V+GIV     D F VD+ G   A L  L+FEG T+RN P  ++G L+Y + V AN  M
Sbjct: 129 DHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDM 188
Query: 136 NPELSCTDASGKAAEFGLL-KDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL 194
            PE+ C D+ G+A   G++ +DG +F+ + GL R LL +P C +++E+GK    EI  G+
Sbjct: 189 EPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLL-APDCEIIQEVGKLYPLEIVFGM 247
Query: 195 NGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQ 235
           NGR+WV A++    ++++N +   E +++ Q+K +  +L +
Sbjct: 248 NGRIWVKAKTIQQTLILANILEACEHMTSDQRKQIFSRLAE 288

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

Iteration: 1
 Score =  110 bits (274), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 61/196 (31%), Positives = 106/196 (54%), Gaps = 13/196 (6%)
Query: 32  IKLGGGLRQECD----SVSVIKAGKLRFSKPNK-----YWVESSQKRYVPCVEDTVLGIV 82
           +KLG G+   CD     +  +  G L  S   K      +++ S KRY+P V D V+G++
Sbjct: 21  VKLGPGIY--CDPNTQEIRPVNTGVLHVSAKGKSGVQTAYIDYSSKRYIPSVNDFVIGVI 78
Query: 83  VDCKADNFFVDIRGPTIAF-LPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSC 141
           +   +D++ V ++  + +  L  +AF   +++N P  ++G L+Y RV  A   +  E+ C
Sbjct: 79  IGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYARVCTAEKELEAEIEC 138
Query: 142 TDAS-GKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWV 200
            D++ G+ A FG+L+DG + + +   +R LL +   P+L+ L     FE+A+GLNG++WV
Sbjct: 139 FDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWV 198
Query: 201 NAESPSTVVLVSNAIM 216
             E  S  +     IM
Sbjct: 199 KCEELSNTLACYRTIM 214

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

Iteration: 1
 Score =  104 bits (260), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 50/151 (33%), Positives = 88/151 (58%), Gaps = 2/151 (1%)
Query: 68  KRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAF-LPVLAFEGGTRRNIPKFEIGSLLYV 126
           KRY+P V D V+G+++   +D++ V ++  + +  L  +AF   +++N P  ++G L+Y 
Sbjct: 1   KRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYA 60
Query: 127 RVVKANPGMNPELSCTDAS-GKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQ 185
           RV  A   +  E+ C D++ G+ A FG+L+DG + + +   +R LL +   P+L+ L   
Sbjct: 61  RVCTAEKELEAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAH 120
Query: 186 LSFEIAVGLNGRVWVNAESPSTVVLVSNAIM 216
             FE+A+GLNG++WV  E  S  +     IM
Sbjct: 121 TKFEVAIGLNGKIWVKCEELSNTLACYRTIM 151

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 43/171 (25%), Positives = 76/171 (44%), Gaps = 15/171 (8%)
Query: 69  RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPK--FEIGSLLYV 126
           RY P V D V+GI+ +  A+ + VDI  P  AFLPV           P    +IG  +  
Sbjct: 52  RYTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIA 111
Query: 127 RVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQL 186
           +V+  +P M   L+  D   +   FG +    +      + R++    +  +++ L  +L
Sbjct: 112 KVLNIDPKMKVTLTMKDRICRPIRFGRI----VAINPARVPRVIGKKGS--MIKLLKSEL 165
Query: 187 SFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRI 237
             +I VG NG +WVN +     +         E++  ++Q+   + L  R+
Sbjct: 166 DVQIVVGQNGLIWVNGDRRKVSIA-------EEAIYLIEQEAHTEGLTDRV 209

>pdb|2JEB|I Chain I, Structure Of A 9-Subunit Archaeal Exosome Bound To Mn Ions Length = 251

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 43/177 (24%), Positives = 81/177 (45%), Gaps = 20/177 (11%)
Query: 70  YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGT-------RRNIPKFEIGS 122
           Y P + D V+G+V D +   + VDI+ P  A+LP     G +       RR +   ++G 
Sbjct: 70  YYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYL---DVGD 126
Query: 123 LLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFET-STGLSRMLLSSPTCPVLEE 181
            +  R+   +  ++P LS      K  + G + +G + +     + R++  + +  + E 
Sbjct: 127 YVIARIENFDRSIDPVLSV-----KGKDLGRVSNGIVIDIMPVKVPRVIGKNKS--MYET 179
Query: 182 LGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK 238
           L  +    I V  NGR+W    S  +  ++  AI   E+ S +  K + D++ Q I+
Sbjct: 180 LTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHI--KGLTDRIKQFIE 234

>pdb|3L7Z|C Chain C, Crystal Structure Of The S. Solfataricus Archaeal Exosome Length = 249

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 43/177 (24%), Positives = 81/177 (45%), Gaps = 20/177 (11%)
Query: 70  YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGT-------RRNIPKFEIGS 122
           Y P + D V+G+V D +   + VDI+ P  A+LP     G +       RR +   ++G 
Sbjct: 68  YYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYL---DVGD 124
Query: 123 LLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFET-STGLSRMLLSSPTCPVLEE 181
            +  R+   +  ++P LS      K  + G + +G + +     + R++  + +  + E 
Sbjct: 125 YVIARIENFDRSIDPVLSV-----KGKDLGRVSNGIVIDIMPVKVPRVIGKNKS--MYET 177
Query: 182 LGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK 238
           L  +    I V  NGR+W    S  +  ++  AI   E+ S +  K + D++ Q I+
Sbjct: 178 LTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHI--KGLTDRIKQFIE 232

>pdb|2JE6|I Chain I, Structure Of A 9-Subunit Archaeal Exosome Length = 251

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 43/177 (24%), Positives = 81/177 (45%), Gaps = 20/177 (11%)
Query: 70  YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGT-------RRNIPKFEIGS 122
           Y P + D V+G+V D +   + VDI+ P  A+LP     G +       RR +   ++G 
Sbjct: 70  YYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYL---DVGD 126
Query: 123 LLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFET-STGLSRMLLSSPTCPVLEE 181
            +  R+   +  ++P LS      K  + G + +G + +     + R++  + +  + E 
Sbjct: 127 YVIARIENFDRSIDPVLSV-----KGKDLGRVSNGIVIDIMPVKVPRVIGKNKS--MYET 179
Query: 182 LGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK 238
           L  +    I V  NGR+W    S  +  ++  AI   E+ S +  K + D++ Q I+
Sbjct: 180 LTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHI--KGLTDRIKQFIE 234

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	238
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	9e-73
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	2e-52
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	6e-46
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	1e-45
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	4e-45
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	4e-33
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	2e-04

>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 =  222 bits (566), Expect = 9e-73
 Identities = 86/258 (33%), Positives = 140/258 (54%), Gaps = 28/258 (10%)

Query: 5   PSTANLVDKIVVPGDVV--------------------LDLSSMTNQTIKLGGGLRQECDS 44
            +   ++ ++V+PG+ +                    L+  + +   +  G GLR+  D 
Sbjct: 32  RAARTVLGQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCGDR 91

Query: 45  VSVIKAGKLRFSKPNK------YWVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPT 98
           + V K G+LR  +P        YWV+S QKRYVP   D V+GIV     D F VD+ G  
Sbjct: 92  LLVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPVKGDHVIGIVTAKSGDIFKVDVGGSE 151

Query: 99  IAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFG-LLKDG 157
            A L  L+FEG T+RN P  ++G L+Y + V AN  M PE+ C D+ G+A   G + +DG
Sbjct: 152 PASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVIGQDG 211

Query: 158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMN 217
            +F+ + GL R LL +P C +++E+GK    EI  G+NGR+WV A++    ++++N +  
Sbjct: 212 LLFKVTLGLIRKLL-APDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTIQQTLILANILEA 270

Query: 218 SESLSAVQQKIMVDKLLQ 235
            E +++ Q+K +  +L +
Sbjct: 271 CEHMTSDQRKQIFSRLAE 288

>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 =  167 bits (423), Expect = 2e-52
 Identities = 52/173 (30%), Positives = 93/173 (53%), Gaps = 3/173 (1%)

Query: 68  KRYVPCVEDTVLGIVVDCKADNFFVDIRGPT-IAFLPVLAFEGGTRRNIPKFEIGSLLYV 126
           KRY+P V D V+G+++   +D++ V ++  +    L  +AF   +++N P  ++G L+Y 
Sbjct: 1   KRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYA 60

Query: 127 RVVKANPGMNPELSCTDA-SGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQ 185
           RV  A   +  E+ C D+ +G+ A FG+L+DG + + +   +R LL +   P+L+ L   
Sbjct: 61  RVCTAEKELEAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAH 120

Query: 186 LSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAV-QQKIMVDKLLQRI 237
             FE+A+GLNG++WV  E  S  +     IM     +     K +  +  + I
Sbjct: 121 TKFEVAIGLNGKIWVKCEELSNTLACYRTIMECCQKNDTAAFKDIAKRQFKEI 173

>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 =  152 bits (385), Expect = 6e-46
 Identities = 46/230 (20%), Positives = 88/230 (38%), Gaps = 16/230 (6%)

Query: 13  KIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVP 72
            IVVPG+++ +        I     + +          G           +      Y P
Sbjct: 17  SIVVPGELLAEGEFQ----IPWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEGSFYYP 72

Query: 73  CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPK----FEIGSLLYVRV 128
            + D V+G+V D +   + VDI+ P  A+LP     G +           ++G  +  R+
Sbjct: 73  KINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARI 132

Query: 129 VKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSF 188
              +  ++P LS      K  + G + +G + +        ++      + E L  +   
Sbjct: 133 ENFDRSIDPVLSV-----KGKDLGRVSNGIVIDIMPVKVPRVIGKN-KSMYETLTSKSGC 186

Query: 189 EIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK 238
            I V  NGR+W    S  +  ++  AI   E+ S ++   + D++ Q I+
Sbjct: 187 SIFVANNGRIWATCPSRFSEEILIEAIRKIENESHIK--GLTDRIKQFIE 234

>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 =  151 bits (381), Expect = 1e-45
 Identities = 52/230 (22%), Positives = 90/230 (39%), Gaps = 15/230 (6%)

Query: 11  VDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRY 70
           + KIV+PGD++      +      G G   E   V     G    ++     V   + RY
Sbjct: 1   MRKIVLPGDLL------STNPRAAGYGTYVEGGKVYAKIIGLFDQTE-THVRVIPLKGRY 53

Query: 71  VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPK--FEIGSLLYVRV 128
            P V D V+GI+ +  A+ + VDI  P  AFLPV           P    +IG  +  +V
Sbjct: 54  TPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKV 113

Query: 129 VKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSF 188
           +  +P M   L+  D          ++ G +   +      ++      +++ L  +L  
Sbjct: 114 LNIDPKMKVTLTMKD-----RICRPIRFGRIVAINPARVPRVI-GKKGSMIKLLKSELDV 167

Query: 189 EIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK 238
           +I VG NG +WVN +     +      +  +          V + ++R K
Sbjct: 168 QIVVGQNGLIWVNGDRRKVSIAEEAIYLIEQEAHTEGLTDRVAEFIKRRK 217

>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 =  149 bits (378), Expect = 4e-45
 Identities = 45/235 (19%), Positives = 86/235 (36%), Gaps = 20/235 (8%)

Query: 10  LVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFS-KPNKYWVESSQK 68
           L  +IVVPG+ +        +       +            G LR             ++
Sbjct: 7   LAGRIVVPGEPL------PEEVEASPPYVIDYKGVKRATVVGLLREKGDGGGRAFVKLKE 60

Query: 69  RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-----TRRNIPKFEIGSL 123
            YVP   D V+G++      N+FVDI  P +A L V  F G              ++G  
Sbjct: 61  IYVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDY 120

Query: 124 LYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELG 183
           +  +VV  +   +P L+      +    G +  G + E S      ++      +L+ L 
Sbjct: 121 IKAKVVAFDKTRSPLLTV-----QGEGLGRIVRGKIVEISPAKVPRVI-GRKMSMLKTLE 174

Query: 184 KQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQRIK 238
           ++   +I V  NGR+ +   +     +   AI   +  +      +  ++++ I+
Sbjct: 175 EKTECKIFVARNGRIHLECPNEDLEAIAVMAIKIIDEEAYTSG--LTKRIIKFIE 227

>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 =  120 bits (302), Expect = 4e-33
 Identities = 39/228 (17%), Positives = 77/228 (33%), Gaps = 29/228 (12%)

Query: 13  KIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVP 72
            +VVPGD +      T+     G G     + +    AG +         V++ + RY+ 
Sbjct: 40  HLVVPGDTIT-----TDTGFMRGHGTYMGEEKLIASVAGSVER-VNKLICVKALKTRYIG 93

Query: 73  CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPV--LAFEGGTRRNIPK---------FEIG 121
            V D V+G + + +   + V+      + L +  +   GG  R              + G
Sbjct: 94  EVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEG 153

Query: 122 SLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEE 181
            L+   V          L       ++ ++G L  G + + S  L +   +         
Sbjct: 154 DLISAEVQAVFSDGAVSLHT-----RSLKYGKLGQGVLVQVSPSLVKRQKTHF------- 201

Query: 182 LGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIM 229
                   + +G NG +W+              I N E +S   ++++
Sbjct: 202 HDLPCGASVILGNNGFIWIYPTPEHKEEEAGGFIANLEPVSLADREVI 249

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

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 28/129 (21%), Positives = 47/129 (36%), Gaps = 17/129 (13%)

Query: 13  KIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVP 72
           + V+PGD +      + +    G G+ +E   +    AGKL         VES       
Sbjct: 2   RFVMPGDRI-----GSAEEYVKGEGVYEEGGELFAAVAGKLIIKDRVA-KVESISPIPEI 55

Query: 73  CVEDTVLGIVVDCKADNFFVDI-------RGPTIAFLPVLAFEGGTRRNIPK----FEIG 121
              D VLG VVD +     +++       RGP+   + +L         + +        
Sbjct: 56  VKGDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYL 115

Query: 122 SLLYVRVVK 130
            +L  RV+ 
Sbjct: 116 DILKARVIG 124

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	238
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
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	100.0
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	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,	99.96
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	99.94
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	98.72
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	98.6
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	98.56
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	98.55
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	98.46
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	98.42
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	98.38
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	98.37
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	98.36
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	98.29
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	98.15
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.12
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	98.12
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	98.1
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	98.08
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.06
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	97.6
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	97.59
2ctl_A	97	Vigilin; K homology type I domain, RNA-binding, ce	97.5
2opv_A	85	KHSRP protein; KH domain, RNA binding protein, KSR	97.47
1vig_A	71	Vigilin; RNA-binding protein, ribonucleoprotein; N	97.41
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	97.37
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	97.35
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	97.33
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.32
2ctk_A	104	Vigilin; K homology type I domain, RNA-binding, ce	97.27
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	97.23
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	97.19
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.19
1x4m_A	94	FAR upstream element binding protein 1; KH domain,	97.02
2ctm_A	95	Vigilin; K homology type I domain, RNA-binding, ce	96.97
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	96.93
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	96.73
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	96.6
1we8_A	104	Tudor and KH domain containing protein; structural	96.6
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	96.54
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	96.52
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	96.4
2hh3_A	106	KH-type splicing regulatory protein; KH-RNA bindin	96.23
2cpq_A	91	FragIle X mental retardation syndrome related prot	96.22
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	96.12
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	96.04
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	95.97
2ctj_A	95	Vigilin; K homology type I domain, RNA-binding, ce	95.25
2hh2_A	107	KH-type splicing regulatory protein; KH-RNA bindin	95.16
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	94.96
1dtj_A	76	RNA-binding neurooncological ventral antigen 2; KH	94.92
2yqr_A	119	KIAA0907 protein; structure genomics, KH domain, s	94.86
2p2r_A	76	Poly(RC)-binding protein 2; protein-DNA complex, R	94.67
1zzk_A	82	Heterogeneous nuclear ribonucleoprotein K; KH domi	94.47
1k1g_A	131	SF1-BO isoform; splicing, branch point sequence, p	94.28
2cte_A	94	Vigilin; K homology type I domain, RNA-binding, ce	94.24
2axy_A	73	Poly(RC)-binding protein 2; protein-DNA complex, D	94.06
1wvn_A	82	Poly(RC)-binding protein 1; KH domain, RNA binding	94.05
1x4n_A	92	FAR upstream element binding protein 1; KH domain,	93.9
1j5k_A	89	Heterogeneous nuclear ribonucleoprotein K; single-	93.84
1ec6_A	87	RNA-binding protein NOVA-2; KH domain, alpha-beta	93.73
2jvz_A	164	KH type-splicing, FAR upstream element-binding pro	93.7
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	93.27
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	93.17
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	89.43
2dgr_A	83	Ring finger and KH domain-containing protein 1; st	87.96
2bl5_A	140	MGC83862 protein, quaking protein; STAR proteins,	87.9
2e3u_A	219	PH-DIM2P, hypothetical protein PH1566; PRE-ribosom	87.87
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	87.74
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	86.8
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	86.37
2bh8_A	101	1B11; transcription, molecular evolution, unique a	86.35
2anr_A	178	Neuro-oncological ventral antigen 1; protein-RNA c	84.18
3krm_A	163	Insulin-like growth factor 2 mRNA-binding protein	82.96
1j4w_A	174	FUSE binding protein; single-stranded DNA binding	82.32
2jzx_A	160	Poly(RC)-binding protein 2; PCBP2, KH domains, RNA	81.97

>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=3.3e-62  Score=436.43  Aligned_cols=227  Identities=37%  Similarity=0.699  Sum_probs=200.3

Q ss_pred             cCCCCcEEecCCccCCCCCC------------------CCCceee--cCcEEEeCCEEEEEEeeEeEEecCC------eE
Q 026458            8 ANLVDKIVVPGDVVLDLSSM------------------TNQTIKL--GGGLRQECDSVSVIKAGKLRFSKPN------KY   61 (238)
Q Consensus         8 ~~~~~~iV~PGd~l~~~~~~------------------~~~~~~~--G~G~y~~~g~i~as~~G~v~~~~~~------~i   61 (238)
                      .++.+++|+|||.|+..+..                  ...+|++  |+|||.++++|+|+++|.++.++++      .+
T Consensus        35 ~~~~~~iVlPGD~L~~~~~~~~~~~g~~~~~~l~~~~~~~~~~~~~~G~Gty~~~~~I~as~aG~l~~~~~~~~~~~~~v  114 (289)
T 2nn6_G           35 RTVLGQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVY  114 (289)
T ss_dssp             TGGGSSBCCSSEEECCSCSCCEECSSEEECC-----------------------CCCEEECSCCEEEEECCTTTSSCCEE
T ss_pred             hhcCCcEEeCCCCcCccccccccccccccccccccccccCcceEEccCCCeEEECCEEEEEEeEeEEeccCCccCccceE
Confidence            35567899999999865410                  0126888  9999999999999999999987442      79


Q ss_pred             EEEccCCccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEE
Q 026458           62 WVESSQKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSC  141 (238)
Q Consensus        62 ~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~  141 (238)
                      ||+|.+++|+|++||+|||+|+++++++|+|||++++.|+|+.++|+|++++||++|++||+|||||++++++++++|||
T Consensus       115 ~V~~~~~rYiP~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~~f~Gatk~~r~~f~~GDlV~ArV~s~~~~~~~eLsc  194 (289)
T 2nn6_G          115 WVDSQQKRYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVC  194 (289)
T ss_dssp             EEECCCSSCCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSSSCCSSCSSSSSCTTCEEEEEEEECCTTSCCEEEC
T ss_pred             EEEecCCCCCCCCCCEEEEEEEEEeCcEEEEEECCCceeEEehhhcCcchhhhhhhcCCCCEEEEEEEEcCCCCceEEEe
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCccCCCccc-CCeeEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc
Q 026458          142 TDASGKAAEFGLL-KDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES  220 (238)
Q Consensus       142 ~~~~~~~~~~G~L-~~G~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~  220 (238)
                      .++++|+.+||+| .+|++|+|+|+++|||+++.++ ||++|++.++|||+||+||||||++.+++++++++|||++||+
T Consensus       195 ~~~~~k~~~lG~L~~~G~l~~Vs~~lvrrl~~~~~~-~l~~L~~~~~~eI~vG~NG~IWI~~~~~~~~~~i~~aI~~~e~  273 (289)
T 2nn6_G          195 IDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCE-IIQEVGKLYPLEIVFGMNGRIWVKAKTIQQTLILANILEACEH  273 (289)
T ss_dssp             SBTTTTBCCCCSCCSSCEEECCCHHHHHHHHCTTCS-HHHHTTCSSSCCCEEETTTEEEECCSSHHHHHHHHHHHHHTTS
T ss_pred             cccccccccCCEecCCeEEEEEChHHhhhhhcCchh-HHHHhcccCCeEEEEECCcEEEEecCChhHHHHHHHHHHHhhc
Confidence            9988999999999 9999999999999999987665 9999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHh
Q 026458          221 LSAVQQKIMVDKLLQ  235 (238)
Q Consensus       221 lt~~~~~~~~~~~~~  235 (238)
                      ||.+|+++|++++++
T Consensus       274 ~~~~q~~~~~~~~~~  288 (289)
T 2nn6_G          274 MTSDQRKQIFSRLAE  288 (289)
T ss_dssp             SCTTTHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhh
Confidence            999999999999876

>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=6.5e-54  Score=372.48  Aligned_cols=209  Identities=25%  Similarity=0.379  Sum_probs=192.7

Q ss_pred             CcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEecCCeEEEEccCCccCCCCCCEEEEEEEEecCceEE
Q 026458           12 DKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKADNFF   91 (238)
Q Consensus        12 ~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~~~~i~V~~~~~~Y~P~vGDiVIG~V~~v~~~~~~   91 (238)
                      +++|+|||.|+..      +|.+|+|||.++++|+|+++|.+..+ ++.+||.|.+++|.|++||+|+|+|+++.++.|+
T Consensus         2 ~~iV~PGd~l~~~------~~~~G~Gty~~~g~i~as~~G~v~~~-~~~v~V~p~~~~y~p~~GDiV~G~V~~v~~~~a~   74 (229)
T 2ba0_A            2 RKIVLPGDLLSTN------PRAAGYGTYVEGGKVYAKIIGLFDQT-ETHVRVIPLKGRYTPSVGDVVIGIIREVAANGWA   74 (229)
T ss_dssp             CCEECTTCEEESC------TTSBCTTEEEETTEEEECSSEEEEEC-SSCEEEEECSSSCCCCTTCEEEEEEEEECSSEEE
T ss_pred             CCEEcCCCCcccC------CeEecCCEEEeCCEEEEEEEEEEEEe-CCEEEEEeCCCcccCCCCCEEEEEEEEEeCCeEE
Confidence            5799999999842      68999999999999999999999986 6689999999999999999999999999999999


Q ss_pred             EEecCCeeeeecCcccC--CcccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcccCCeeEEEechhhhhh
Q 026458           92 VDIRGPTIAFLPVLAFE--GGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETSTGLSRM  169 (238)
Q Consensus        92 VdI~~~~~a~L~~~~f~--gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~~~~V~~~~v~r  169 (238)
                      |||++++.|+||.++|.  +.+++++++|++||+|+|||+++++++++.|||++     .+||+|.+|++++++|.+++|
T Consensus        75 V~I~~~~~g~l~isev~~~~~~~~~~~~l~~GD~V~arVi~v~~~~~i~LS~r~-----~~lG~L~~G~v~~vs~~~v~r  149 (229)
T 2ba0_A           75 VDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKD-----RICRPIRFGRIVAINPARVPR  149 (229)
T ss_dssp             EECSSSSCEEEEGGGCTTCCTTSCGGGTCCTTCEEEEEEEEECTTCCEEEECCS-----SSCEEESSSEEEECCGGGHHH
T ss_pred             EEeCCCeEEEEEHHHccccccccchhcccCCCCEEEEEEEEECCCCcEEEEEcc-----ccCCcccCCEEEEECHHHhHH
Confidence            99999999999999998  56889999999999999999999999999999987     899999999999999999999


Q ss_pred             hcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc------CCHHHHHHHHHHHHh
Q 026458          170 LLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES------LSAVQQKIMVDKLLQ  235 (238)
Q Consensus       170 l~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~------lt~~~~~~~~~~~~~  235 (238)
                      ++++.++ ||++|++.++||||+|+||||||++. ..+++++++||+++|.      || +++++|+++..+
T Consensus       150 l~~~~~~-~l~~l~~~~~~ei~vG~NG~IWi~~~-~~~~~~~~~ai~~~e~~~~~~~l~-~~v~~~l~~~~~  218 (229)
T 2ba0_A          150 VIGKKGS-MIKLLKSELDVQIVVGQNGLIWVNGD-RRKVSIAEEAIYLIEQEAHTEGLT-DRVAEFIKRRKA  218 (229)
T ss_dssp             HHCGGGH-HHHHHHHHHTCEEEECTTSEEEEESC-HHHHHHHHHHHHHHHHCSCCSSHH-HHHHHHHHHHHH
T ss_pred             HhcCCch-HHHHhcccCCeEEEEECCcEEEEeCC-chhHHHHHHHHHHHHhhhhhhhHH-HHHHHHHHHhcc
Confidence            9986655 99999999999999999999999975 4599999999999985      44 888888877654

>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=2e-53  Score=370.69  Aligned_cols=218  Identities=21%  Similarity=0.275  Sum_probs=150.5

Q ss_pred             CccCCCCcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEecC-CeEEEEccCCccCCCCCCEEEEEEEE
Q 026458            6 STANLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKP-NKYWVESSQKRYVPCVEDTVLGIVVD   84 (238)
Q Consensus         6 ~~~~~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~~-~~i~V~~~~~~Y~P~vGDiVIG~V~~   84 (238)
                      |++++.+++|+|||.|+..      +|.+|+|||.++++|+|+++|.+..+++ +.+||+|.+++|.|++||+|+|+|++
T Consensus         3 ~~~~~~~~iV~PGd~l~~~------~~~~G~Gty~~~~~I~Asv~G~v~~~~~~~~vsV~p~~~~y~p~~GDiV~G~V~~   76 (235)
T 2z0s_A            3 SERQLAGRIVVPGEPLPEE------VEASPPYVIDYKGVKRATVVGLLREKGDGGGRAFVKLKEIYVPQAGDVVIGLIQS   76 (235)
T ss_dssp             ---------------------------------------------------------------CCCCCCTTCCEEEEEEE
T ss_pred             CccccCCcEEeCCCCcccC------ceEcCCCEEEECCEEEEEEeEEEEEeCCccEEEEEeCCCccCCCCCCEEEEEEEE
Confidence            4555668899999999852      6999999999999999999999987622 37999999999999999999999999


Q ss_pred             ecCceEEEEecCCeeeeecCcccCC-----cccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcccCCeeE
Q 026458           85 CKADNFFVDIRGPTIAFLPVLAFEG-----GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYM  159 (238)
Q Consensus        85 v~~~~~~VdI~~~~~a~L~~~~f~g-----atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~~  159 (238)
                      +.++.|+|||++++.|+||.++|.+     ..++++++|++||+|+|||+++++++.+.|||+.     .+||+|++|++
T Consensus        77 v~~~~~~V~I~~~~~g~l~isei~~~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~~~~i~LS~k~-----~~lG~l~gG~v  151 (235)
T 2z0s_A           77 VGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQG-----EGLGRIVRGKI  151 (235)
T ss_dssp             ECSSEEEEECSSSSCEEEEHHHHHTSCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCS-----SSCEECCSSEE
T ss_pred             EeCCeEEEEeCCCeEEEEEHHHhCCCccccchhhHhhcCCCCCEEEEEEEEECCCCcEEEEEec-----ccCccccCCEE
Confidence            9999999999999999999999865     3567888999999999999999988899999987     89999999999


Q ss_pred             EEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc------CCHHHHHHHHHHH
Q 026458          160 FETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES------LSAVQQKIMVDKL  233 (238)
Q Consensus       160 ~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~------lt~~~~~~~~~~~  233 (238)
                      ++++|.+++|+++++++ ||++|+++++||||+|+||||||+++++++++++++||++||+      || +++++|+++.
T Consensus       152 v~vs~~~~~rl~~~~~~-~l~~l~~~~~~~i~vG~NG~IWi~~~~~~~~~~~~~ai~~~e~~~~~~~l~-~~v~~~l~~~  229 (235)
T 2z0s_A          152 VEISPAKVPRVIGRKMS-MLKTLEEKTECKIFVARNGRIHLECPNEDLEAIAVMAIKIIDEEAYTSGLT-KRIIKFIEEE  229 (235)
T ss_dssp             EECCGGGSGGGTCGGGH-HHHHHHHHHCCEEEEETTTEEEEECSCHHHHHHHHHHHHHHHHCSCCTTCH-HHHHHHHHHH
T ss_pred             EEECHHHhHHHhcCcch-HHHHhcccCCeEEEEeCCCEEEEecCCHHHHHHHHHHHHHHHhhhhhhhHH-HHHHHHHHHh
Confidence            99999999999986655 9999998999999999999999999999999999999999986      66 8888888876


Q ss_pred             Hhh
Q 026458          234 LQR  236 (238)
Q Consensus       234 ~~~  236 (238)
                      ++.
T Consensus       230 ~~~  232 (235)
T 2z0s_A          230 RRI  232 (235)
T ss_dssp             HHH
T ss_pred             hhc
Confidence            654

>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=3.8e-52  Score=347.70  Aligned_cols=170  Identities=31%  Similarity=0.642  Sum_probs=165.1

Q ss_pred             CccCCCCCCEEEEEEEEecCceEEEEecC-CeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEEecC-C
Q 026458           68 KRYVPCVEDTVLGIVVDCKADNFFVDIRG-PTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDA-S  145 (238)
Q Consensus        68 ~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~-~  145 (238)
                      +||+|++||+|+|+|+++.+++|+|||++ ++.|+||.++|+|++++||++|++||+|+|||++++.+++++|||.++ +
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 999999999999999999999999999999999999999999999997 4


Q ss_pred             CccCCCcccCCeeEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHH-hccCCHH
Q 026458          146 GKAAEFGLLKDGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMN-SESLSAV  224 (238)
Q Consensus       146 ~~~~~~G~L~~G~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~-~e~lt~~  224 (238)
                      +|+.+||+|++|++|+|||+++|||+++++++||++|+++++|||++|+||||||+++++++++++++||++ ||++|.+
T Consensus        81 ~r~~~lG~L~~G~l~~v~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~v~~aI~~~~~~~~~~  160 (175)
T 2ja9_A           81 GRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWVKCEELSNTLACYRTIMECCQKNDTA  160 (175)
T ss_dssp             CSCTTCEEECSCEEEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETTTEEEEECSSHHHHHHHHHHHHHHHHHCCGG
T ss_pred             ccccCCcCcCCCEEEEEcHHHhhHHhcCCCcchHHhhhccCCeEEEEECCcEEEEecCCHHHHHHHHHHHHHHhccCCHH
Confidence            899999999999999999999999999888889999999999999999999999999999999999999999 9999999


Q ss_pred             HHHHHHHHHHhhc
Q 026458          225 QQKIMVDKLLQRI  237 (238)
Q Consensus       225 ~~~~~~~~~~~~~  237 (238)
                      |+++|++++++++
T Consensus       161 ~~~~~~~~~~~~~  173 (175)
T 2ja9_A          161 AFKDIAKRQFKEI  173 (175)
T ss_dssp             GHHHHHHHHTTTS
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999999875

>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=1.5e-52  Score=368.24  Aligned_cols=212  Identities=21%  Similarity=0.339  Sum_probs=176.5

Q ss_pred             CCcEEecCCccCCCCCCCCCceeecC--cEEEeCCEEEEEEeeEeEEecCCeEEEEccCC-ccCCCCCCEEEEEEEEecC
Q 026458           11 VDKIVVPGDVVLDLSSMTNQTIKLGG--GLRQECDSVSVIKAGKLRFSKPNKYWVESSQK-RYVPCVEDTVLGIVVDCKA   87 (238)
Q Consensus        11 ~~~iV~PGd~l~~~~~~~~~~~~~G~--G~y~~~g~i~as~~G~v~~~~~~~i~V~~~~~-~Y~P~vGDiVIG~V~~v~~   87 (238)
                      .+++|+|||.|+..      +|.+|+  |||.++++|+|+++|.+..+ ++.++|.|+++ +|.|++||+|+|+|+++.+
T Consensus        15 ~~~iV~PGd~l~~~------~~~~G~~~Gty~~~g~i~as~~G~v~~~-~~~v~V~p~~~~~y~p~~GDiV~G~V~~v~~   87 (251)
T 2je6_I           15 PRSIVVPGELLAEG------EFQIPWSPYILKINSKYYSTVVGLFDVK-DTQFEVIPLEGSFYYPKINDIVIGLVEDVEI   87 (251)
T ss_dssp             SSCEECTTCEEEEE------CCCCCCCTTEEEETTEEEECSSEEEEEE-TTEEEEEESCCSCCCCCTTCEEEEEEEEECS
T ss_pred             CCcEEcCCCCCccC------CeeeCCCCCEEEECCEEEEEEEEEEEEe-CCEEEEEECCCcccCCCCCCEEEEEEEEEeC
Confidence            47899999999852      699999  99999999999999999986 67899999987 9999999999999999999


Q ss_pred             ceEEEEecCCeeeeecCcccCCc-c---cccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcccCCeeEEEec
Q 026458           88 DNFFVDIRGPTIAFLPVLAFEGG-T---RRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDGYMFETS  163 (238)
Q Consensus        88 ~~~~VdI~~~~~a~L~~~~f~ga-t---k~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G~~~~V~  163 (238)
                      +.|+|||++++.|+||.++|.+. .   ++++.+|++||+|+|||+++++++.+.|||++     .+||+|.+|++++++
T Consensus        88 ~ga~VdI~~~~~GlL~isei~~~~~~~~~~~~~~l~vGD~V~arVi~v~~~~~i~LS~r~-----~~lG~L~~G~v~~vs  162 (251)
T 2je6_I           88 YGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKG-----KDLGRVSNGIVIDIM  162 (251)
T ss_dssp             SEEEEECSSSSCEEEEHHHHHTSCCCTTCCCSSSCCTTCEEEEEEEEEETTEEEEEECCS-----TTCEECCSSCEEECC
T ss_pred             ceEEEEcCCCeEEEEEHHHhcCCccccccchhhcCCCCCEEEEEEEEECCCCcEEEEEcc-----ccCCcccCCEEEEEC
Confidence            99999999999999999998753 2   66788999999999999999988899999987     899999999999999


Q ss_pred             hhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc------CCHHHHHHHHHHHHhh
Q 026458          164 TGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES------LSAVQQKIMVDKLLQR  236 (238)
Q Consensus       164 ~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~------lt~~~~~~~~~~~~~~  236 (238)
                      |.++||+++++++ ||++|++.++||||||+||||||++.++++++++++||+++|+      +| +++++|+++.++.
T Consensus       163 ~~~v~rl~~~~~~-~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~~~~aI~~~e~~~~~~~l~-~~v~~~l~~~~~~  239 (251)
T 2je6_I          163 PVKVPRVIGKNKS-MYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHIKGLT-DRIKQFIEEKLGE  239 (251)
T ss_dssp             GGGHHHHHCGGGH-HHHHHHTTC---CEECTTSEEEC-----CTTCCTHHHHTTTTTTTTCC-----------------
T ss_pred             HHHhHHHhcCcch-HHHHhcccCCeEEEEECCcEEEEeCCCHHHHHHHHHHHHHHHhhhhhhhHH-HHHHHHHHHhhhh
Confidence            9999999987665 9999999999999999999999999999999999999999987      55 7888887766543

>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=2.9e-45  Score=329.84  Aligned_cols=178  Identities=19%  Similarity=0.291  Sum_probs=154.1

Q ss_pred             CCCCcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEecCCeEEEEccCCccCCCCCCEEEEEEEEecCc
Q 026458            9 NLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKRYVPCVEDTVLGIVVDCKAD   88 (238)
Q Consensus         9 ~~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~~~~i~V~~~~~~Y~P~vGDiVIG~V~~v~~~   88 (238)
                      +-.+++|+|||.|+..+     +|.+|+|||.++|+|+|+++|.++.. ++.+||+|.+++|.|++||+|+|+|+++.++
T Consensus        36 ~~~~~iVlPGd~L~~~~-----~~~~G~Gty~~~g~I~Asv~G~v~~~-~~~vsV~p~~~rY~P~vGDvViG~Vt~V~~~  109 (308)
T 2nn6_H           36 DTKKHLVVPGDTITTDT-----GFMRGHGTYMGEEKLIASVAGSVERV-NKLICVKALKTRYIGEVGDIVVGRITEVQQK  109 (308)
T ss_dssp             ----CBCCTTCBCCCCT-----TCCBCTTEEECSSSEEECSSEEEEEE-TTEEEEEESSCCCCCCSSBCCCEEEEEEETT
T ss_pred             CCCCcEEeCCCCCCCCC-----CEeecCCeEEECCEEEEEEEEEEEec-CCEEEEeeCCCccCCCCCCEEEEEEEEEeCc
Confidence            34568999999999765     79999999999999999999999875 7899999999999999999999999999999


Q ss_pred             eEEEEecCCeeeeecCcc--cCCccc---------ccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcccCCe
Q 026458           89 NFFVDIRGPTIAFLPVLA--FEGGTR---------RNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLKDG  157 (238)
Q Consensus        89 ~~~VdI~~~~~a~L~~~~--f~gatk---------~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~~G  157 (238)
                      +|+|||++++.+.++.++  |+++++         +++++|++||+|+|||+++++++++.|||++     ++||+|++|
T Consensus       110 ~a~VdI~s~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArVisv~~~~~i~LStr~-----~~LGkL~~G  184 (308)
T 2nn6_H          110 RWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRS-----LKYGKLGQG  184 (308)
T ss_dssp             EEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEETTTEEEEECCS-----STTCEECSS
T ss_pred             eEEEEECCCcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCCCCCEEEEecC-----cCCcccCCe
Confidence            999999999999888765  566543         5678999999999999999988999999987     899999999


Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCC
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAES  204 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~  204 (238)
                      +++.|++.++|++..     ++..+  .++|||++|+||||||++..
T Consensus       185 ~v~~vs~~lv~r~~~-----~l~~l--~~g~eI~vG~NG~IWi~~~~  224 (308)
T 2nn6_H          185 VLVQVSPSLVKRQKT-----HFHDL--PCGASVILGNNGFIWIYPTP  224 (308)
T ss_dssp             CEEECCTTSCCCSTT-----CSCCC--BTTBEEEEETTTEEEEECCC
T ss_pred             EEEEEChhheechhh-----eEecC--CCCcEEEEeCCCEEEEcCCc
Confidence            999999999998752     45555  48999999999999999864

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

Probab=99.96  E-value=6.6e-29  Score=207.87  Aligned_cols=135  Identities=25%  Similarity=0.291  Sum_probs=121.2

Q ss_pred             cEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEecCCeEEEEccCC-ccCCCCCCEEEEEEEEecCceEE
Q 026458           13 KIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQK-RYVPCVEDTVLGIVVDCKADNFF   91 (238)
Q Consensus        13 ~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~~~~i~V~~~~~-~Y~P~vGDiVIG~V~~v~~~~~~   91 (238)
                      ++|+|||.|+..+     +|.+|+|||.++|+|+|+++|.++.. ++.+||+|.+. +|.|+ ||+|+|+|+++.+..|+
T Consensus         2 ~iV~PGd~l~~~~-----~~~~G~Gty~~~~~i~as~~G~v~~~-~~~v~V~~~~~~~y~p~-GdiV~G~V~~V~~~ga~   74 (179)
T 3m7n_A            2 RFVMPGDRIGSAE-----EYVKGEGVYEEGGELFAAVAGKLIIK-DRVAKVESISPIPEIVK-GDVVLGRVVDLRNSIAL   74 (179)
T ss_dssp             CEECTTCEEEETT-----TSEECTTEEEETTEEEESSSEEEEEE-TTEEEEEESSCCCCCCT-TCEEEEEEEEECSSEEE
T ss_pred             eEEcCCCCCCCCC-----CEeccCCEEEeCCEEEEEEEEEEEEe-CCEEEEEECCCCcccCC-CCEEEEEEEEEeCCcEE
Confidence            6999999999876     79999999999999999999999985 88999999855 69999 99999999999999999


Q ss_pred             EEecC----------CeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCccCCCcccC-----
Q 026458           92 VDIRG----------PTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKAAEFGLLK-----  155 (238)
Q Consensus        92 VdI~~----------~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~~~~G~L~-----  155 (238)
                      |||.+          ++.|+||.+++.. ..+++++.|++||+|.|+|++    +.+.||+++     .+||+|.     
T Consensus        75 V~I~~v~~~~~~~~~~~~Gll~isei~~~~~~~~~~~~~~GD~V~akVi~----~~i~LS~k~-----~~lGvv~a~~~~  145 (179)
T 3m7n_A           75 IEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARVIG----DNLRLSTKE-----EEMGVLRALCSN  145 (179)
T ss_dssp             EEEEEETTCCSCCTTCEEEEEEGGGTTSSCCSSGGGTCCTTCEEEEEEEE----TTTEEECCS-----TTCEEEECBCTT
T ss_pred             EEEccccCcccccccCeeEEEEHHHcCcchhhCHhhcCCCCCEEEEEEEC----CeEEEEEec-----CCCCEEEecccc
Confidence            99998          8999999999864 356889999999999999998    679999988     8999983     


Q ss_pred             -CeeEEEec
Q 026458          156 -DGYMFETS  163 (238)
Q Consensus       156 -~G~~~~V~  163 (238)
                       +..|++++
T Consensus       146 ~g~~m~~~~  154 (179)
T 3m7n_A          146 CKTEMVREG  154 (179)
T ss_dssp             TCCBCEECS
T ss_pred             cCCceEECC
Confidence             45566655

>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=99.94  E-value=7.4e-28  Score=206.08  Aligned_cols=148  Identities=17%  Similarity=0.099  Sum_probs=120.3

Q ss_pred             CCCCcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEec----CCeEEEEccCC-ccCCCCCCEEEEEEE
Q 026458            9 NLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSK----PNKYWVESSQK-RYVPCVEDTVLGIVV   83 (238)
Q Consensus         9 ~~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~----~~~i~V~~~~~-~Y~P~vGDiVIG~V~   83 (238)
                      ...+++|+|||.|+..+     +|.+|+|||+++|+|||+++|.+..++    .++++|.|.++ +|.|++||+|+|+|+
T Consensus        16 ~~~~~iV~PGd~l~~~~-----~~~~G~Gty~~~g~I~Asv~G~v~~~~~~~~~~vi~V~p~~~~~y~p~vGDvV~G~V~   90 (209)
T 2nn6_I           16 APPVRYCIPGERLCNLE-----EGSPGSGTYTRHGYIFSSLAGCLMKSSENGALPVVSVVRETESQLLPDVGAIVTCKVS   90 (209)
T ss_dssp             ----CCCCTTCEEEETT-----TCCCSSSCEEETTEEECCSCSCBCCCBCTTSSBC-CBCCSCCCCCCCCTTCEEEEEEE
T ss_pred             cCCCcEEcCCCCCCCCC-----CeeecCCEEEECCEEEEEEEEEEEEeccCCcccEEEEecCCCCcCCCCCCCEEEEEEE
Confidence            44578999999999765     799999999999999999999997642    24688999876 599999999999999


Q ss_pred             EecCceEEEEecC--------CeeeeecCcccCC-ccc--ccccCcCCCCEEEEEEEecCCCC-cceEEEecCCCccCCC
Q 026458           84 DCKADNFFVDIRG--------PTIAFLPVLAFEG-GTR--RNIPKFEIGSLLYVRVVKANPGM-NPELSCTDASGKAAEF  151 (238)
Q Consensus        84 ~v~~~~~~VdI~~--------~~~a~L~~~~f~g-atk--~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~~~~~~~~~  151 (238)
                      ++.+..|+|||.+        .+.|+||.+++.. ..+  +++.+|++||+|+|+|+++++.. .+.||++.     .+|
T Consensus        91 ~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~~~~~~~~~~l~~GD~V~akVisi~~~~~~i~LS~k~-----~~l  165 (209)
T 2nn6_I           91 SINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLLTTAE-----NEL  165 (209)
T ss_dssp             EECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEEEECCS-----SSC
T ss_pred             EEECceEEEEECccccccccCCceeEEEHHHcccccccccchhhhcCCCCEEEEEEEEEeCCCCeEEEEEec-----CCC
Confidence            9999999999963        5678888776642 233  68889999999999999998765 49999988     899


Q ss_pred             cccC-----CeeEEEechhh
Q 026458          152 GLLK-----DGYMFETSTGL  166 (238)
Q Consensus       152 G~L~-----~G~~~~V~~~~  166 (238)
                      |++.     +..|++++...
T Consensus       166 GVv~A~c~~g~~m~~~~~~~  185 (209)
T 2nn6_I          166 GVVVAHSESGIQMVPISWCE  185 (209)
T ss_dssp             EECCCBCSSSCBCEEEETTE
T ss_pred             cEEEEEcCCCCEEEEccCCE
Confidence            9993     56677777543

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

Probab=98.72  E-value=8.3e-08  Score=69.22  Aligned_cols=70  Identities=10%  Similarity=0.125  Sum_probs=60.9

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD  143 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  143 (238)
                      .|++||+|.|+|+++.+..++|+|+....|.+|.+++....  . ..|++||.|.|+|.+++.+ +.+.||.+.
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 DVEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLR--L-ENLNVGDEIIVQAIDVRPEKREIDFKYIP   72 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGGCSSCC--G-GGCCTTCEEEEEEEEEETTTTEEEEEECS
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHCCccc--c-eeeCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            37899999999999999999999998999999998875321  1 5799999999999999876 788899875

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

Probab=98.60  E-value=1.9e-07  Score=71.93  Aligned_cols=84  Identities=12%  Similarity=0.027  Sum_probs=66.6

Q ss_pred             eEEEEccCC-ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC--cccccccCcCCCCEEEEEEEecCC-CC
Q 026458           60 KYWVESSQK-RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG--GTRRNIPKFEIGSLLYVRVVKANP-GM  135 (238)
Q Consensus        60 ~i~V~~~~~-~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g--atk~~r~~l~~GDlV~ArV~~~~~-~~  135 (238)
                      .+.+.|... .+.|++||+|.|+|+++.+..++|+|.....|.+|.+++..  ..++.+..|++||.|.++|.+++. .+
T Consensus        15 ~~~~~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~~~~~~~~~~~vGd~V~vkV~~vd~~~~   94 (115)
T 2khi_A           15 VPRGSHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERR   94 (115)
T ss_dssp             ------CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSSTTCSSTTTCCTTCEEEEEEEEEETTTT
T ss_pred             hcccCCHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccccccCcccEECCCCEEEEEEEEEECCCC
Confidence            445666544 57899999999999999999999999988999999988753  345566789999999999999986 46


Q ss_pred             cceEEEec
Q 026458          136 NPELSCTD  143 (238)
Q Consensus       136 ~~~Ls~~~  143 (238)
                      .+.||++.
T Consensus        95 rI~lslk~  102 (115)
T 2khi_A           95 RISLGLKQ  102 (115)
T ss_dssp             EEEECCCC
T ss_pred             EEEEEEEe
Confidence            78888765

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

Probab=98.56  E-value=1.7e-07  Score=71.41  Aligned_cols=74  Identities=12%  Similarity=0.070  Sum_probs=63.9

Q ss_pred             cCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCC-cceEEEec
Q 026458           70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGM-NPELSCTD  143 (238)
Q Consensus        70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~~~  143 (238)
                      ..+++||+|.|+|+++.+..++|+|+....|.||.+++.. ..++.+..|++||.|.|+|.+++... .+.||++.
T Consensus        27 ~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~~~~~~~~~~~~vGd~V~v~V~~vd~~~~ki~LS~k~  102 (109)
T 2khj_A           27 ALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEVEAKFTGVDRKNRAISLSVRA  102 (109)
T ss_dssp             TTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCSSSSSSGGGSCCTTCEEEEEEEEEETTTTEEEEETTS
T ss_pred             hcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCcccccChhhccCCCCEEEEEEEEEECCCCEEEEEEee
Confidence            5789999999999999999999999988999999988753 34556678999999999999998764 68888765

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

Probab=98.55  E-value=2.6e-07  Score=72.84  Aligned_cols=73  Identities=18%  Similarity=0.153  Sum_probs=64.3

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCC-CCcceEEEec
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTD  143 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  143 (238)
                      .+++||+|.|+|+++..-.++|+|.....|.+|.+++. +...+.+..|++||.|.++|.+++. .+.+.||++.
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            37899999999999999999999998999999998875 3455667789999999999999987 6789999875

>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=98.46  E-value=3.9e-07  Score=68.86  Aligned_cols=74  Identities=18%  Similarity=0.177  Sum_probs=62.4

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecC---CeeeeecCcccC-C-cccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRG---PTIAFLPVLAFE-G-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD  143 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~---~~~a~L~~~~f~-g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  143 (238)
                      ...|++||++.|+|+++..-.++|+|..   ...|.+|.+++. . ..++.+..|++||.|.++|.+++. ..+.||++.
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   789999999883 2 234455679999999999999986 577888765

>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=98.42  E-value=2.4e-07  Score=71.96  Aligned_cols=75  Identities=13%  Similarity=0.216  Sum_probs=62.6

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecC-CeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCC---CcceEEEec
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRG-PTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPG---MNPELSCTD  143 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~---~~~~Ls~~~  143 (238)
                      .+.|++||+|.|+|+++....++|+|.. ...|.||++++.. ..++....|++||.|.++|.+++..   +.+.||++.
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            4789999999999999999999999965 3799999988753 3445566799999999999999753   468888876

>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=98.38  E-value=8.8e-07  Score=73.79  Aligned_cols=75  Identities=19%  Similarity=0.135  Sum_probs=56.9

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEe--cCCeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDI--RGPTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD  143 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI--~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  143 (238)
                      .+.|++||+|.|+|+++.+-.++|+|  .....|.+|++++. +..++.+..|++||.|.++|.+++.. +.+.||++.
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            34589999999999999999999999  46789999999885 34566778899999999999999864 568888765

>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=98.37  E-value=9.7e-07  Score=73.23  Aligned_cols=80  Identities=21%  Similarity=0.243  Sum_probs=66.0

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cc-----------cccccCcCCCCEEEEEEEecCCC--
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GT-----------RRNIPKFEIGSLLYVRVVKANPG--  134 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-at-----------k~~r~~l~~GDlV~ArV~~~~~~--  134 (238)
                      .|.|.+|+++.|+|+++....++|+|+. ..|.+|.++... ..           ++.+..|++||.|.+||.+++..  
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 899999887642 21           24567899999999999999763  


Q ss_pred             ----CcceEEEecCCCccCCCccc
Q 026458          135 ----MNPELSCTDASGKAAEFGLL  154 (238)
Q Consensus       135 ----~~~~Ls~~~~~~~~~~~G~L  154 (238)
                          +.+.||+++     .+||.+
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                367788877     788876

>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=98.36  E-value=1.4e-06  Score=72.13  Aligned_cols=75  Identities=13%  Similarity=0.094  Sum_probs=59.9

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEec--CCeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIR--GPTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD  143 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~--~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  143 (238)
                      .+.|++||+|.|+|+++.+-.++|+|.  ....|.+|++++. +..++.+..|++||.|.++|.+++.. +.+.||++.
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  6689999999875 34566778899999999999999764 568888865

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

Probab=98.29  E-value=2.2e-06  Score=75.68  Aligned_cols=79  Identities=16%  Similarity=0.203  Sum_probs=65.1

Q ss_pred             cCCccCCCCCCEEEEEEEEecCceEEEEec--CCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCC-CCcceEEE
Q 026458           66 SQKRYVPCVEDTVLGIVVDCKADNFFVDIR--GPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANP-GMNPELSC  141 (238)
Q Consensus        66 ~~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~--~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~  141 (238)
                      ....+.|++||+|.|+|+++.+-.++|+|.  ....|.+|.+++.. .....+..|++||.|.++|.+++. .+.+.||+
T Consensus         3 ~~~~~~p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~v~~~~~~~kvGd~V~vkVi~vD~~~~~I~LSl   82 (275)
T 3aev_A            3 RKAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSL   82 (275)
T ss_dssp             ----CCCCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSCCSCGGGTCCTTCEEEEEEEEEETTTTEEEEES
T ss_pred             cccccCCCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCcccccCHHhccCCCCEEEEEEEEEECCCCEEEEEE
Confidence            344577999999999999999999999998  47899999998753 355566789999999999999986 57788998


Q ss_pred             ecC
Q 026458          142 TDA  144 (238)
Q Consensus       142 ~~~  144 (238)
                      +..
T Consensus        83 k~~   85 (275)
T 3aev_A           83 RRV   85 (275)
T ss_dssp             TTC
T ss_pred             eec
Confidence            763

>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=98.15  E-value=4.5e-06  Score=64.44  Aligned_cols=74  Identities=24%  Similarity=0.234  Sum_probs=57.4

Q ss_pred             cCCCCCCEEEEEEEEecCceEEEEec-CCeeeeecCcccCCc--ccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458           70 YVPCVEDTVLGIVVDCKADNFFVDIR-GPTIAFLPVLAFEGG--TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD  143 (238)
Q Consensus        70 Y~P~vGDiVIG~V~~v~~~~~~VdI~-~~~~a~L~~~~f~ga--tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  143 (238)
                      ..+++||+|.|+|+++..-.++|||+ ....++++.......  ..+.+..|++||.|.++|.+++.. ..+.||++.
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            35799999999999999999999998 345566664432111  123457899999999999999865 678899887

>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=98.12  E-value=1.1e-05  Score=66.51  Aligned_cols=80  Identities=20%  Similarity=0.338  Sum_probs=65.7

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc------------ccccccCcCCCCEEEEEEEecCCC--
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG------------TRRNIPKFEIGSLLYVRVVKANPG--  134 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~--  134 (238)
                      .+.|.+|+++-|+|++++...++|+++ +..+.+|.++....            .++....|++||-|+.||.+++.+  
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            478999999999999999999999997 58899998876532            145666899999999999999743  


Q ss_pred             ---CcceEEEecCCCccCCCccc
Q 026458          135 ---MNPELSCTDASGKAAEFGLL  154 (238)
Q Consensus       135 ---~~~~Ls~~~~~~~~~~~G~L  154 (238)
                         ..+.||++.     ++||.+
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               356788877     788876

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

Probab=98.12  E-value=4.6e-06  Score=61.34  Aligned_cols=71  Identities=15%  Similarity=0.161  Sum_probs=59.5

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecC--CeeeeecCc-ccCC-cccccccCcCCCCEEEEEEEecCC-CCcceEEEec
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRG--PTIAFLPVL-AFEG-GTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTD  143 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~-~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  143 (238)
                      .|++|+++-|+|+ +.+-.++|+|..  ...|.+|++ +... ..+..+..| +||.|.++|.+++. .+.+.||++.
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  479999999 8753 234455667 99999999999986 4678898875

>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=98.10  E-value=4.3e-06  Score=73.44  Aligned_cols=77  Identities=14%  Similarity=0.200  Sum_probs=66.1

Q ss_pred             CccCCCCCCEEEEEEEEecCceEEEEec--CCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCC-CCcceEEEec
Q 026458           68 KRYVPCVEDTVLGIVVDCKADNFFVDIR--GPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTD  143 (238)
Q Consensus        68 ~~Y~P~vGDiVIG~V~~v~~~~~~VdI~--~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  143 (238)
                      ..+.|++||+|.|+|+++.+..++|+|.  ....|.+|.+++.. ..++.+..|++||.|.++|.+++. .+.+.||++.
T Consensus         5 ~~~~~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~~~v~~~~~~~~vGd~V~VkVi~vd~~~g~I~LSlk~   84 (266)
T 3cw2_C            5 RSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIRVDRRKGTVDVSLKK   84 (266)
T ss_dssp             SSSSCCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSCSSCCCHHHHSCTTCEEEEEECCCCSSSCCCBEESTT
T ss_pred             ccccCCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCcccccCHHHhCcCCCEEEEEEEEEeCCCCEEEEEEEe
Confidence            4578999999999999999999999997  67899999998853 345556779999999999999986 5778999876


Q ss_pred             C
Q 026458          144 A  144 (238)
Q Consensus       144 ~  144 (238)
                      .
T Consensus        85 ~   85 (266)
T 3cw2_C           85 V   85 (266)
T ss_dssp             S
T ss_pred             c
Confidence            3

>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=98.08  E-value=9.1e-06  Score=72.82  Aligned_cols=74  Identities=19%  Similarity=0.176  Sum_probs=63.9

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEec--CCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCC-CCcceEEEecC
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIR--GPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTDA  144 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~--~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~~  144 (238)
                      .|++||+|.|+|+++.+-.++|+|.  ....|.+|.+.+.. ..++.+..|++||.|.++|.+++. .+.+.||.+..
T Consensus        10 ~~~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~~~i~~~~~~~kvGd~V~VkVl~vD~~~~rI~LSlK~~   87 (308)
T 1q8k_A           10 FPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYIDLSKRRV   87 (308)
T ss_dssp             CCSSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSCSSCSCCTTTCSSSCEEEEEEEEEETTTTEEEEECSSC
T ss_pred             CCCCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCcccccCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEEec
Confidence            5789999999999999999999998  67899999998853 356677889999999999999987 46788998763

>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=98.06  E-value=1e-05  Score=66.24  Aligned_cols=80  Identities=16%  Similarity=0.229  Sum_probs=62.1

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-----cc--------ccccCcCCCCEEEEEEEecCCCC
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-----TR--------RNIPKFEIGSLLYVRVVKANPGM  135 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-----tk--------~~r~~l~~GDlV~ArV~~~~~~~  135 (238)
                      .+.|.+|+++.|+|++++.-.++|+|+ +..|.+|.+..+..     ..        +.+..|++||.|..||.+++.+.
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            467999999999999999999999996 66799999876532     11        22557999999999999987543


Q ss_pred             c---ceEEEecCCCccCCCccc
Q 026458          136 N---PELSCTDASGKAAEFGLL  154 (238)
Q Consensus       136 ~---~~Ls~~~~~~~~~~~G~L  154 (238)
                      .   ..-|+++     ++||++
T Consensus       155 ~~~~~igsm~~-----~~LG~~  171 (172)
T 2c35_B          155 NDIFAIGSLMD-----DYLGLV  171 (172)
T ss_dssp             TEEEEEEECCS-----TTCEEC
T ss_pred             CCcEEEEEecC-----CCCCCC
Confidence            2   2234444     788876

>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=97.60  E-value=0.00017  Score=58.98  Aligned_cols=83  Identities=20%  Similarity=0.260  Sum_probs=60.3

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-c---ccc-------ccCcCCCCEEEEEEEecCCCCcc
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-T---RRN-------IPKFEIGSLLYVRVVKANPGMNP  137 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-t---k~~-------r~~l~~GDlV~ArV~~~~~~~~~  137 (238)
                      .+.|.+|+++-|+|++++.-.++|+|+. .+|.+|.+..+.. .   .++       +..|++||.|..||.+++.+.. 
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            3569999999999999999999999987 9999999877532 1   111       2569999999999999875432 


Q ss_pred             eEEEecCCCccCCCccc
Q 026458          138 ELSCTDASGKAAEFGLL  154 (238)
Q Consensus       138 ~Ls~~~~~~~~~~~G~L  154 (238)
                      ..+..+ +=+.++||.+
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            112222 1133788764

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

Probab=97.59  E-value=3.8e-05  Score=63.01  Aligned_cols=83  Identities=20%  Similarity=0.262  Sum_probs=62.1

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-----------ccccccCcCCCCEEEEEEEecCCCCcc
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-----------TRRNIPKFEIGSLLYVRVVKANPGMNP  137 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-----------tk~~r~~l~~GDlV~ArV~~~~~~~~~  137 (238)
                      .+.|.+|+++-|+|++++.-.++|+++ +.++.+|.++.+..           -++....+++||.|++||.+++.+.. 
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 LWRPFRGEVVDAIVTTVNKMGFFANIG-PLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRTDAT-  156 (172)
T ss_dssp             EECCCTTCEEECCCCEEETTEEECCBT-TBCCEEEGGGSCTTCCCBSSSSSCBEESSSCEECSSCCEEEEEEEEEESSS-
T ss_pred             eeccCCCCEEEEEEEEEEcceEEEEeC-CeEEEEEHHHCCCccccCcccccceEecCCcEECCCCEEEEEEEEEECCCC-
Confidence            478999999999999999999999997 46699998876432           12334579999999999999875431 


Q ss_pred             eEEEecCCCccCCCccc
Q 026458          138 ELSCTDASGKAAEFGLL  154 (238)
Q Consensus       138 ~Ls~~~~~~~~~~~G~L  154 (238)
                      ...+.. +=+.++||+|
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            122332 2244888876

>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=97.50  E-value=0.00013  Score=54.35  Aligned_cols=60  Identities=7%  Similarity=0.093  Sum_probs=49.8

Q ss_pred             eeEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC-------eEEEecCChhHHHHHHHHHHHh
Q 026458          157 GYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG-------RVWVNAESPSTVVLVSNAIMNS  218 (238)
Q Consensus       157 G~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG-------~IWi~~~~~~~~~~i~~~i~~~  218 (238)
                      =..+.||+.++++++|+.++ +++.|.+.+++.|-+..+|       .|||.+. .+....+...|..+
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 KLSVTVDPKYHPKIIGRKGA-VITQIRLEHDVNIQFPDKDDGNQPQDQITITGY-EKNTEAARDAILRI   84 (97)
T ss_dssp             EEEEECCTTTHHHHSCSSSC-HHHHHHHHHTCEEECCCTTTCSSCSSEEEEESC-HHHHHHHHHHHHHH
T ss_pred             eEEEEECHHHhhhcCCCCch-hHHHHHHHHCCEEEecCCCCCCCCccEEEEEeC-HHHHHHHHHHHHHH
Confidence            34689999999999999998 9999999999999999999       9999985 66555555444443

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

Probab=97.47  E-value=0.00017  Score=52.19  Aligned_cols=59  Identities=10%  Similarity=0.206  Sum_probs=51.6

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCe--------EEEecCChhHHHHHHHHHHHh
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGR--------VWVNAESPSTVVLVSNAIMNS  218 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~--------IWi~~~~~~~~~~i~~~i~~~  218 (238)
                      ..+.||+.++.+++|+.++ .++.|.+.+++.|-+..+|.        |||.+ +++.+..+...|+.+
T Consensus        16 ~~i~Ip~~~ig~IIGkgG~-~Ik~I~~~tga~I~i~~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~~i   82 (85)
T 2opv_A           16 QEIMIPAGKAGLVIGKGGE-TIKQLQERAGVKMILIQDGSQNTNVDKPLRIIG-DPYKVQQACEMVMDI   82 (85)
T ss_dssp             EEEEECTTTHHHHHTTTTH-HHHHHHHHHTCEEEECSSSCSSTTSCEEEEEEE-CHHHHHHHHHHHHHH
T ss_pred             EEEEeChhheeeeECCCCH-HHHHHHHHHCCEEEEcCCCCCCCCCceEEEEEe-CHHHHHHHHHHHHHH
Confidence            3688999999999999998 99999999999999999998        99999 887776666666543

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

Probab=97.41  E-value=0.00024  Score=49.78  Aligned_cols=56  Identities=9%  Similarity=0.227  Sum_probs=46.9

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC----eEEEecCChhHHHHHHHHH
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG----RVWVNAESPSTVVLVSNAI  215 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG----~IWi~~~~~~~~~~i~~~i  215 (238)
                      ..+.||+.++++++|+.+. .++.|.+++++.|-+..+|    .|||.+. .+....+...|
T Consensus         7 ~~i~I~~~~ig~iIG~gG~-~I~~I~e~tg~~I~i~~~g~~~~~V~I~G~-~~~v~~A~~~I   66 (71)
T 1vig_A            7 VEINIDHKFHRHLIGKSGA-NINRIKDQYKVSVRIPPDSEKSNLIRIEGD-PQGVQQAKREL   66 (71)
T ss_dssp             EEEEECSSHHHHHTCSSCC-HHHHHHHHTCCEEECCCCCSSSEEEEEEES-SHHHHHHHHHH
T ss_pred             EEEEECHHHhhhhcCCCCc-cHHHHHHHHCCEEEECCCCCcccEEEEEcC-HHHHHHHHHHH
Confidence            3589999999999999998 9999999999999999999    9999996 54444333333

>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=97.37  E-value=0.0003  Score=59.87  Aligned_cols=84  Identities=20%  Similarity=0.258  Sum_probs=61.7

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-c---ccc-------ccCcCCCCEEEEEEEecCCCCcc
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-T---RRN-------IPKFEIGSLLYVRVVKANPGMNP  137 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-t---k~~-------r~~l~~GDlV~ArV~~~~~~~~~  137 (238)
                      .+.|.+|+++-|+|+++..-.++|+|+. .+|.+|.+..+.. .   ...       +..|++||.|..||.+++.+.. 
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 9999999877532 0   111       2569999999999999875432 


Q ss_pred             eEEEecCCCccCCCcccC
Q 026458          138 ELSCTDASGKAAEFGLLK  155 (238)
Q Consensus       138 ~Ls~~~~~~~~~~~G~L~  155 (238)
                      .+.... +=+.+++|.+.
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            112222 12347888884

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

Probab=97.35  E-value=0.00037  Score=58.64  Aligned_cols=64  Identities=13%  Similarity=0.149  Sum_probs=50.7

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccC-Cc-------------c------cccccCcCCCCEEEEEE
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFE-GG-------------T------RRNIPKFEIGSLLYVRV  128 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-ga-------------t------k~~r~~l~~GDlV~ArV  128 (238)
                      .+.|.+|.++.|+|++++....+|+++ +.+++++.+... ..             .      ++.+..++.||.|+.||
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            467999999999999999999999995 667777665442 11             0      34456799999999999


Q ss_pred             EecCC
Q 026458          129 VKANP  133 (238)
Q Consensus       129 ~~~~~  133 (238)
                      .+++-
T Consensus       155 ~~v~~  159 (203)
T 3ayh_B          155 ESEDF  159 (203)
T ss_dssp             EEEEE
T ss_pred             EEEEc
Confidence            98753

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

Probab=97.33  E-value=0.00058  Score=60.39  Aligned_cols=65  Identities=18%  Similarity=0.131  Sum_probs=58.7

Q ss_pred             CCCCCEEEEEEEEecCceEEE-EecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCC-CCcceEEEec
Q 026458           72 PCVEDTVLGIVVDCKADNFFV-DIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTD  143 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~V-dI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  143 (238)
                      -.+||.|-|+|+++..-.++| +|+..+.|.+|.++..       ..|++||-|.|+|..+++ ++.+.||++.
T Consensus       150 ~~~G~~V~g~V~~i~~~G~fV~~i~~g~~Glih~SEl~-------~~l~~Gd~v~~~V~~id~~d~kI~LSlk~  216 (285)
T 3go5_A          150 NMQNQNWPAIVYRLKLSGTFVYLPENNMLGFIHPSERY-------AEPRLGQVLDARVIGFREVDRTLNLSLKP  216 (285)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEETTTTEEEEECGGGCS-------SCCCTTCEEEEEEEEEETTTTEEEEECSC
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEEeCCCeEEEEEHHHcc-------ccCCCCCEEEEEEEEEECCCCeEEEEeCh
Confidence            357999999999999999999 9999999999998764       369999999999999988 7889999876

>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=97.32  E-value=0.00056  Score=59.42  Aligned_cols=61  Identities=18%  Similarity=0.206  Sum_probs=51.2

Q ss_pred             ccCCCCCCEEEEEEEE----ecCceEEEEecC---CeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC
Q 026458           69 RYVPCVEDTVLGIVVD----CKADNFFVDIRG---PTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG  134 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~----v~~~~~~VdI~~---~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~  134 (238)
                      .|..++||+|.|+|.+    +..+.+.|||+.   ...|+||....-     .+..|++||-|.|-|..+.+.
T Consensus         2 ~~~~r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqi-----p~E~~~~GDrIkayV~~V~~~   69 (251)
T 2asb_A            2 EFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV-----PGESYEHGNRLRCYVVGVTRG   69 (251)
T ss_dssp             --CCCTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC-----TTCCCCTTCEEEEEEEEEECC
T ss_pred             chhhcCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcC-----CCccCCCCCEEEEEEEEEEcC
Confidence            4888999999999999    899999999986   489999976542     346899999999999998764

>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=97.27  E-value=0.00026  Score=53.48  Aligned_cols=75  Identities=12%  Similarity=0.064  Sum_probs=57.9

Q ss_pred             eeEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC----eEEEecCChhHHHHHHHHHHHhccCCHHHHHHHHHH
Q 026458          157 GYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG----RVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDK  232 (238)
Q Consensus       157 G~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG----~IWi~~~~~~~~~~i~~~i~~~e~lt~~~~~~~~~~  232 (238)
                      -..+.||+.++++++|+.+. .++.|.+.+++.|-+..+|    .|||.+. ++   .+.+|...++.+..+.-....++
T Consensus        18 ~~~i~Ip~~~ig~IIG~gG~-~Ir~I~eetg~~I~I~~~g~~~~~V~I~G~-~e---~v~~A~~~I~~i~~e~e~~~~d~   92 (104)
T 2ctk_A           18 TIEVEVPFDLHRYVIGQKGS-GIRKMMDEFEVNIHVPAPELQSDIIAITGL-AA---NLDRAKAGLLERVKELQAEQEDR   92 (104)
T ss_dssp             EEEEECCHHHHHHHHCSSSH-HHHHHHHHTCCEEECCCTTTTCCEEEEEEC-HH---HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEChHHccceeCCCch-HHHHHHHHHCCEEEecCCCCCcceEEEEcC-HH---HHHHHHHHHHHHHhhHHHhHHHH
Confidence            45689999999999999998 9999999999999999999    9999985 43   35666666666654444444454


Q ss_pred             HHhh
Q 026458          233 LLQR  236 (238)
Q Consensus       233 ~~~~  236 (238)
                      .++.
T Consensus        93 ~~~~   96 (104)
T 2ctk_A           93 ALRS   96 (104)
T ss_dssp             HHCC
T ss_pred             Hhcc
Confidence            5543

>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=97.23  E-value=0.00088  Score=60.75  Aligned_cols=67  Identities=13%  Similarity=0.140  Sum_probs=55.5

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCC-cceEEE
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGM-NPELSC  141 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~-~~~Ls~  141 (238)
                      .|..+.||+|.|+|.++..+.+.||++ ...|+||.+.+.     .+..|++||-|.|.|.++++.. .+.|..
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 789999988763     2458999999999999987542 344443

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

Probab=97.19  E-value=0.00066  Score=70.49  Aligned_cols=75  Identities=13%  Similarity=0.102  Sum_probs=64.8

Q ss_pred             cCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc--ccccccCcCCCCEEEEEEEecCC-CCcceEEEecC
Q 026458           70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG--TRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTDA  144 (238)
Q Consensus        70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga--tk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~~  144 (238)
                      -..++|++|-|+|+++....++|+|.+...|.+|++++...  .+..+..|++||.|.|+|++++. ...+.|||+.+
T Consensus       898 ~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd~~~v~~p~~v~kvGd~V~vkVl~VD~~~~rI~LSlk~~  975 (1219)
T 3psi_A          898 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLDH  975 (1219)
T ss_dssp             TTSCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSSSTTSCSCSTTTSCTTCEEEEEEEEEEGGGTEEEEECCHH
T ss_pred             hhCCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcCCCcccCCHHHcCCCCCEEEEEEEEEECCCCEEEEEecHH
Confidence            46789999999999999999999999888999999988654  35566789999999999999974 46789998763

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

Probab=97.19  E-value=5.5e-05  Score=74.75  Aligned_cols=74  Identities=16%  Similarity=0.122  Sum_probs=0.0

Q ss_pred             cCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458           70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD  143 (238)
Q Consensus        70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  143 (238)
                      ..|++|+++.|+|+++..-.++|+|.....|.+|++++.. ...+....|++||.|.++|.++++.+.+.||.+.
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            3689999999999999999999999988999999998864 4556677899999999999999877788899876

>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=97.02  E-value=0.00096  Score=49.19  Aligned_cols=59  Identities=7%  Similarity=0.173  Sum_probs=51.4

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCe--------EEEecCChhHHHHHHHHHHHh
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGR--------VWVNAESPSTVVLVSNAIMNS  218 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~--------IWi~~~~~~~~~~i~~~i~~~  218 (238)
                      ..+.||+.++.++||+.+. .++.|.+.+++.|-|..+|.        |||.+ +++.+..+...|+.+
T Consensus        17 ~~i~Ip~~~vG~IIGkgG~-~Ik~I~~~tga~I~I~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~   83 (94)
T 1x4m_A           17 QEIMIPASKAGLVIGKGGE-TIKQLQERAGVKMVMIQDGPQNTGADKPLRITG-DPYKVQQAKEMVLEL   83 (94)
T ss_dssp             EEEEECHHHHHHHSCSSSS-HHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEE-CTTTHHHHHHHHHHH
T ss_pred             EEEEEChhhcceEECCCCH-HHHHHHHHHCCeEEecCCCCCCCCCceEEEEEe-CHHHHHHHHHHHHHH
Confidence            4688999999999999998 99999999999999999987        99998 877777766666554

>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=96.97  E-value=0.001  Score=49.31  Aligned_cols=57  Identities=12%  Similarity=0.148  Sum_probs=47.4

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC-----eEEEecCChhHHHHHHHHHH
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG-----RVWVNAESPSTVVLVSNAIM  216 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG-----~IWi~~~~~~~~~~i~~~i~  216 (238)
                      ..+.||+.++++++|+.+. .++.|.+.+++.|-+-.+|     .|||.+. ++.+..+...|+
T Consensus        19 ~~i~Ip~~~ig~IIG~gG~-~Ir~I~e~tg~~I~i~~~g~~~~~~V~I~G~-~e~v~~A~~~I~   80 (95)
T 2ctm_A           19 EDVPLDHRVHARIIGARGK-AIRKIMDEFKVDIRFPQSGAPDPNCVTVTGL-PENVEEAIDHIL   80 (95)
T ss_dssp             EEEECCTTTHHHHHCSSSC-HHHHHHHHHTCEEECCCTTCSCTTEEEEESC-HHHHHHHHHHHH
T ss_pred             EEEEECHHHccccCCCCcc-hHHHHHHHHCCeEEecCCCCCCCcEEEEEcC-HHHHHHHHHHHH
Confidence            4589999999999999998 9999999999999999999     8999985 555444444333

>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=96.93  E-value=0.0021  Score=58.72  Aligned_cols=69  Identities=17%  Similarity=0.223  Sum_probs=55.4

Q ss_pred             ccCCCCCCEEEEEEEE----ecCceEEEEecC---CeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC-CcceEE
Q 026458           69 RYVPCVEDTVLGIVVD----CKADNFFVDIRG---PTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG-MNPELS  140 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~----v~~~~~~VdI~~---~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls  140 (238)
                      .|..++||+|.|+|.+    +....+.|||+.   ...|+||....-     .+..|++||-|.|-|.++.+. ..++|.
T Consensus       125 ef~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~Eqi-----P~E~~~~GDrVkvyV~~V~~~~kgpqI~  199 (366)
T 1k0r_A          125 EFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV-----PGESYEHGNRLRCYVVGVTRGAREPLIT  199 (366)
T ss_dssp             --CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSC-----TTCCCCTTCEEEEEEEEEECCSSSCEEE
T ss_pred             HHHhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcC-----CCccCCCCCEEEEEEEEEecCCCccEEE
Confidence            4789999999999999    999999999987   489999986542     246899999999999999765 245555


Q ss_pred             Ee
Q 026458          141 CT  142 (238)
Q Consensus       141 ~~  142 (238)
                      +.
T Consensus       200 LS  201 (366)
T 1k0r_A          200 LS  201 (366)
T ss_dssp             EE
T ss_pred             EE
Confidence            43

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

Probab=96.73  E-value=0.00069  Score=66.04  Aligned_cols=61  Identities=13%  Similarity=0.032  Sum_probs=50.8

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhccCC
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLS  222 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~lt  222 (238)
                      ..++|+|.+++.+||+.+. +++.|.++++++|-+..||+|||.+.|.+   .+..|+..++.++
T Consensus       569 ~~~~I~~~kI~~vIG~gG~-~Ik~I~e~tg~~I~I~d~G~V~I~~~~~~---~~~~A~~~I~~i~  629 (630)
T 3u1k_A          569 ETVQVPLSKRAKFVGPGGY-NLKKLQAETGVTISQVDEETFSVFAPTPS---AMHEARDFITEIC  629 (630)
T ss_dssp             EEEECCHHHHHHHHCGGGH-HHHHHHHHHCCEEEECSSSEEEEEESSHH---HHHHHHHHTTC--
T ss_pred             EEEEeChhHhheeECCCCh-hHHHHHHHHCCEEEEcCCcEEEEEeCCHH---HHHHHHHHHHHHh
Confidence            4789999999999999887 99999999999999999999999998875   4455555555543

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

Probab=96.60  E-value=0.00033  Score=71.63  Aligned_cols=74  Identities=14%  Similarity=0.107  Sum_probs=0.0

Q ss_pred             cCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc--ccccccCcCCCCEEEEEEEecCC-CCcceEEEec
Q 026458           70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG--TRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTD  143 (238)
Q Consensus        70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga--tk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  143 (238)
                      -..++|++|-|+|+++..-.++|+|.+...|.+|++++...  .++.+..|++||.|.|+|++++. ...+.||++.
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            35689999999999999999999998888999999988643  35556789999999999999984 4679999987

>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=96.60  E-value=0.0019  Score=48.42  Aligned_cols=60  Identities=7%  Similarity=-0.025  Sum_probs=48.8

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEee--------CCeEEEecCChhHHHHHHHHHHHhccCC
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL--------NGRVWVNAESPSTVVLVSNAIMNSESLS  222 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~--------NG~IWi~~~~~~~~~~i~~~i~~~e~lt  222 (238)
                      ..+.||+.++.++||+.+. .++.|.+.+++.|-|..        +|.|||.+ +.+.   +.+|...++.+.
T Consensus        17 ~~i~Ip~~~ig~IIGkgG~-~Ik~I~~~tga~I~I~~~~~~~~~~~~~V~I~G-~~~~---v~~A~~~I~~~i   84 (104)
T 1we8_A           17 EQLSVPQRSVGRIIGRGGE-TIRSICKASGAKITCDKESEGTLLLSRLIKISG-TQKE---VAAAKHLILEKV   84 (104)
T ss_dssp             EEEEEETTTHHHHHTTTSH-HHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEE-EHHH---HHHHHHHHHHHH
T ss_pred             EEEEEChhheeeeECCCCH-HHHHHHHHHCCEEEEecCCCCCCCCcceEEEEc-CHHH---HHHHHHHHHHHH
Confidence            4689999999999999998 99999999999999997        79999998 4443   455555555543

>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=96.54  E-value=0.00077  Score=67.21  Aligned_cols=73  Identities=16%  Similarity=0.112  Sum_probs=62.4

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCC-CCcceEEEec
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTD  143 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  143 (238)
                      ..++|++|-|+|+++..-.++|+|+...+|.+|++++.. ...+.+..|++||.|.++|.+++. ...+.||++.
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            478999999999999999999999888899999998753 233445679999999999999986 4678999876

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

Probab=96.52  E-value=0.0004  Score=68.66  Aligned_cols=74  Identities=16%  Similarity=0.136  Sum_probs=0.0

Q ss_pred             cCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458           70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD  143 (238)
Q Consensus        70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  143 (238)
                      ..|++|+++-|+|+++..-.++|+|.....|.+|++++.. ..++....|++||.|.+||.+++..+.+.||.+.
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            4689999999999999999999999888999999998853 4556667899999999999999877788898875

>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=96.40  E-value=0.00038  Score=69.12  Aligned_cols=74  Identities=16%  Similarity=0.140  Sum_probs=37.4

Q ss_pred             cCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCccc----C-CcccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458           70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAF----E-GGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD  143 (238)
Q Consensus        70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f----~-gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  143 (238)
                      ..|++|+++-|+|+++..-.++|+|.....|.+|++++    . ...++....|++||.|.++|.+++..+.+.||++.
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            56899999999999999999999998889999999998    4 34556677899999999999999877788899876

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

Probab=96.23  E-value=0.0071  Score=45.63  Aligned_cols=58  Identities=5%  Similarity=0.085  Sum_probs=47.1

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC------eEEEecCChhHHHHHHHHHHH
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG------RVWVNAESPSTVVLVSNAIMN  217 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG------~IWi~~~~~~~~~~i~~~i~~  217 (238)
                      +.+.||+.++.++||+.++ .++.|.+.+++.|-|-.++      .|+|.+ +++.+..+.+.|+.
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 IDVPVPRHSVGVVIGRSGE-MIKKIQNDAGVRIQFKQDDGTGPEKIAHIMG-PPDRCEHAARIIND   76 (106)
T ss_dssp             EEEEEETTTHHHHHTTTTH-HHHHHHHHHTCEEEECSSCSSSSEEEEEEES-SHHHHHHHHHHHHH
T ss_pred             EEEEECHHHcCccCCCCcH-HHHHHHHHHCcEEEEecCCCCCceeEEEEEe-CHHHHHHHHHHHHH
Confidence            4689999999999999998 9999999999999998766      799997 46555555444443

>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=96.22  E-value=0.009  Score=44.07  Aligned_cols=67  Identities=15%  Similarity=0.174  Sum_probs=54.7

Q ss_pred             ccCCeeE--EEechhhhhhhcCCCCchhhHhhccccceE-EEEee-CCeEEEecCChhHHHHHHHHHHHhcc
Q 026458          153 LLKDGYM--FETSTGLSRMLLSSPTCPVLEELGKQLSFE-IAVGL-NGRVWVNAESPSTVVLVSNAIMNSES  220 (238)
Q Consensus       153 ~L~~G~~--~~V~~~~v~rl~~~~~~~~l~~l~~~~~~e-i~vG~-NG~IWi~~~~~~~~~~i~~~i~~~e~  220 (238)
                      .+..+++  +.|+|.+++.++|+.+. .++.|.+.++.. |-+-- +|.|.|.+.+.+.+..+...|+.+|.
T Consensus        10 ~~~~~~i~~i~I~~dkIg~vIG~gGk-~Ik~I~e~tGv~~IdI~eddG~V~I~g~~~ea~~~A~~~I~~ie~   80 (91)
T 2cpq_A           10 QLAAAFHEEFVVREDLMGLAIGTHGS-NIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLEFVED   80 (91)
T ss_dssp             SSSCSEEEEEECCHHHHHHHHTTTTH-HHHHHHTSTTEEEEEEETTTTEEEEEESSHHHHHHHHHHHSCCCC
T ss_pred             hccCceEEEEEEChHHhhhhcCCCcH-HHHHHHHHhCCeEEEEEcCCCEEEEEECCHHHHHHHHHHHHhhhe
Confidence            3445543  77999999999999998 999999999997 99986 59999999888777666666666654

>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=96.12  E-value=0.054  Score=51.57  Aligned_cols=72  Identities=17%  Similarity=0.188  Sum_probs=57.2

Q ss_pred             CCCCCCEEEEEEEEecCc--eEEEEecCCeeeeecCcccCCc----------ccccccCcCCCCEEEEEEEecCCC-Ccc
Q 026458           71 VPCVEDTVLGIVVDCKAD--NFFVDIRGPTIAFLPVLAFEGG----------TRRNIPKFEIGSLLYVRVVKANPG-MNP  137 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~--~~~VdI~~~~~a~L~~~~f~ga----------tk~~r~~l~~GDlV~ArV~~~~~~-~~~  137 (238)
                      .+.+|++..|+|+++.+.  .++|||+....|+||++.....          ..+....+++||-|..+|...... .-+
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            467899999999999888  9999999999999999876311          123445699999999999996543 347


Q ss_pred             eEEEe
Q 026458          138 ELSCT  142 (238)
Q Consensus       138 ~Ls~~  142 (238)
                      .||+.
T Consensus       122 ~lTt~  126 (517)
T 2bx2_L          122 ALTTF  126 (517)
T ss_dssp             EEESS
T ss_pred             eEEee
Confidence            77764

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

Probab=96.04  E-value=0.055  Score=47.65  Aligned_cols=63  Identities=11%  Similarity=0.137  Sum_probs=51.3

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEEecCC
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDAS  145 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~  145 (238)
                      ..+|++|-|+|+++....+.||++ ...+.||.+..+.         .+||-|.+.|.. +......+|+..|.
T Consensus         4 ~~~G~~v~g~V~~~~~~G~fv~~~-g~egllp~se~~~---------~vGdevev~v~~-d~~~r~iat~~~p~   66 (285)
T 3go5_A            4 TNLASFIVGLIIDENDRFYFVQKD-GQTYALAKEEGQH---------TVGDTVKGFAYT-DMKQKLRLTTLEVT   66 (285)
T ss_dssp             TTTTEEEEEEEEEECSSEEEEEET-TEEEEEEGGGCCC---------CTTSEEEEEEEE-CTTSCEEEECSCCC
T ss_pred             ccCCCEEEEEEEEEECCEEEEEcC-CeEEEEEHHHCcc---------ccCCEEEEEEEE-CCCCCEEEeccccc
Confidence            357999999999999999999997 6799999988752         788988888874 55556777776653

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

Probab=95.97  E-value=0.06  Score=45.60  Aligned_cols=65  Identities=14%  Similarity=0.189  Sum_probs=51.3

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-------c-------c-cccccCcCCCCEEEEEEEecCC
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-------G-------T-RRNIPKFEIGSLLYVRVVKANP  133 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-------a-------t-k~~r~~l~~GDlV~ArV~~~~~  133 (238)
                      .+.|.+|.++-|+|++++....+|++..+.+++++.+....       .       . ++.+..|+.||.|+.||.+++.
T Consensus        76 ~f~p~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~~  155 (218)
T 2ckz_B           76 VFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVF  155 (218)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTSCTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEEE
T ss_pred             EecCCCCCEEEEEEEEEccCcEEEEccCccceEEEcHHHCCCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEEc
Confidence            46899999999999999999999999556777777665421       1       1 3446679999999999999864

>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=95.25  E-value=0.02  Score=42.30  Aligned_cols=59  Identities=15%  Similarity=0.156  Sum_probs=47.9

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhcccc-ceEEEEeeCC----eEEEecCChhHHHHHHHHHHHhccC
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQL-SFEIAVGLNG----RVWVNAESPSTVVLVSNAIMNSESL  221 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~-~~ei~vG~NG----~IWi~~~~~~~~~~i~~~i~~~e~l  221 (238)
                      ..+.||+.+.+.++|+.+. .++.|.+++ ++.|-+-..|    .|-|.+++.    .+..|.+.++.+
T Consensus        19 ~~i~Ip~~~i~~iIG~gGk-~Ir~I~eetggv~I~i~~~g~~~~~V~I~G~~~----~v~~A~~~I~~i   82 (95)
T 2ctj_A           19 VEVSIPAKLHNSLIGTKGR-LIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSS----DVEKAKKQLLHL   82 (95)
T ss_dssp             EEEECCHHHHHHHHCSSSH-HHHHHHHHHTSCEEECCCTTTTCCEEEEESCHH----HHHHHHHHHHHH
T ss_pred             EEEEECHHHHhhhCCCCch-hHHHHHHHcCCCEEEeCCCCCCcceEEEEcCHH----HHHHHHHHHHHH
Confidence            3589999999999999988 999998999 9999999999    999999654    444444444443

>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA binding protein; NMR {Homo sapiens}

Probab=95.16  E-value=0.045  Score=41.04  Aligned_cols=58  Identities=10%  Similarity=0.131  Sum_probs=48.4

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeC---------CeEEEecCChhHHHHHHHHHHHh
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN---------GRVWVNAESPSTVVLVSNAIMNS  218 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N---------G~IWi~~~~~~~~~~i~~~i~~~  218 (238)
                      -+.|+..++.++||+.++ .++.|.+.+++.|-|-.+         +.|.|.+ +++.+..+...|..+
T Consensus        10 ~i~IP~~~vG~IIGkgG~-~Ik~I~~~TGa~I~I~~~~~~~~~~~~r~V~I~G-~~e~v~~A~~~I~~~   76 (107)
T 2hh2_A           10 TFSIPTHKCGLVIGRGGE-NVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRG-SPQQIDHAKQLIEEK   76 (107)
T ss_dssp             EEEEEGGGTTTTSTTTTC-HHHHHHHHSSSEEEECCCCCTTCCTTEEEEEEES-CHHHHHHHHHHHHHH
T ss_pred             EEEECHHHcCccCCCCcH-HHHHHHHHhCCEEEEcCccCCCCCCCceEEEEEC-CHHHHHHHHHHHHHH
Confidence            578999999999999998 899999999999999886         6888988 876666666555543

>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=94.96  E-value=0.021  Score=45.29  Aligned_cols=57  Identities=5%  Similarity=0.059  Sum_probs=47.1

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEee------CCeEEEecCChhHHHHHHHHHH
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL------NGRVWVNAESPSTVVLVSNAIM  216 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~------NG~IWi~~~~~~~~~~i~~~i~  216 (238)
                      +-+.||+.++.+++|+.+. .++.|.+.+++.|-+..      ++.|+|.+ +++.+..+...|.
T Consensus        93 ~~i~vp~~~~g~iIGk~G~-~I~~i~~~tg~~I~i~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~  155 (164)
T 2jvz_A           93 IDVPVPRHSVGVVIGRSGE-MIKKIQNDAGVRIQFKQDDGTGPEKIAHIMG-PPDRCEHAARIIN  155 (164)
T ss_dssp             BCCEEETTTHHHHHCSSSH-HHHHHHHHTCCEEEECCCCTTSSEEEEEEES-CHHHHHHHHHHHH
T ss_pred             EEEEEChhhccccCCCCcH-hHHHHHHHHCCeEEEeCCCCCCCcEEEEEEc-CHHHHHHHHHHHH
Confidence            4578999999999999998 99999999999999987      68999998 4665555444443

>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=94.92  E-value=0.042  Score=38.22  Aligned_cols=56  Identities=18%  Similarity=0.167  Sum_probs=45.6

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeC---------CeEEEecCChhHHHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN---------GRVWVNAESPSTVVLVSNAIM  216 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N---------G~IWi~~~~~~~~~~i~~~i~  216 (238)
                      -+.||+.++.+++|+.++ .++.|.+.+++.|-|..+         +.|.|.+ +++.+..+...|.
T Consensus         6 ~i~Ip~~~vg~IIGkgG~-~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~   70 (76)
T 1dtj_A            6 EMAVPENLVGAILGKGGK-TLVEYQELTGARIQISKKGEFLPGTRNRRVTITG-SPAATQAAQYLIS   70 (76)
T ss_dssp             EEEEETTTHHHHHCSTTH-HHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEE-SHHHHHHHHHHHH
T ss_pred             EEEEChHHcceEECCCch-HHHHHHHHhCCEEEECcCCCCCCCCceeEEEEEe-CHHHHHHHHHHHH
Confidence            478999999999999998 899999999999999985         5899988 4655544444444

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

Probab=94.86  E-value=0.024  Score=43.69  Aligned_cols=77  Identities=8%  Similarity=0.100  Sum_probs=55.8

Q ss_pred             cCCeeEEEec---h--hhhhhhcCCCCchhhHhhccccceEEEEe----------------eCCeEEEecCChhHHHHHH
Q 026458          154 LKDGYMFETS---T--GLSRMLLSSPTCPVLEELGKQLSFEIAVG----------------LNGRVWVNAESPSTVVLVS  212 (238)
Q Consensus       154 L~~G~~~~V~---~--~~v~rl~~~~~~~~l~~l~~~~~~ei~vG----------------~NG~IWi~~~~~~~~~~i~  212 (238)
                      +..=+.+.+.   |  .++.++||..+. .++.|.++++|.|.+-                -.|.|.|.+.+.+   .+.
T Consensus        12 ~~~ki~ip~~~~~p~fn~ig~IIGpgG~-tiK~I~~eTG~kI~I~G~gS~~~e~~~~~e~~e~l~V~I~a~~~e---~i~   87 (119)
T 2yqr_A           12 VQDKLFVGLEHAVPTFNVKEKVEGPGCS-YLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPE---GLA   87 (119)
T ss_dssp             EEEEEECCCTTSCTTTCHHHHHSCGGGH-HHHHHHHHHCCEEEEESBTTTCCCTTTSSCCSSBCEEEEEESSHH---HHH
T ss_pred             EEEEEEcCCccCCCCCCeeeeEECCCCh-HHHHHHHHHCCEEEEecCCccccccccccccCCCcEEEEEeCCHH---HHH
Confidence            3444455554   2  589999998887 8999999999999995                4589999998875   456


Q ss_pred             HHHHHhccCCHHHHHHHHHHHHh
Q 026458          213 NAIMNSESLSAVQQKIMVDKLLQ  235 (238)
Q Consensus       213 ~~i~~~e~lt~~~~~~~~~~~~~  235 (238)
                      +|++.++.|. ..+.+-..++.+
T Consensus        88 ~A~~~Ie~Ll-~~v~~~~~~~~~  109 (119)
T 2yqr_A           88 AAKKLCENLL-QTVHAEYSRFVN  109 (119)
T ss_dssp             HHHHHHHHHH-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHh-hchHHHHHHHHH
Confidence            7777777766 445544455444

>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA binding protein/DNA complex; 1.60A {Homo sapiens}

Probab=94.67  E-value=0.032  Score=39.00  Aligned_cols=57  Identities=12%  Similarity=0.181  Sum_probs=47.0

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEee------CCeEEEecCChhHHHHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL------NGRVWVNAESPSTVVLVSNAIMN  217 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~------NG~IWi~~~~~~~~~~i~~~i~~  217 (238)
                      -+.||..++.+++|+.++ .++.|.+.+++.|-+..      ++.|.|.+ +++.+..+...|..
T Consensus         8 ~i~Ip~~~vg~iIGkgG~-~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~   70 (76)
T 2p2r_A            8 ELTIPNDLIGCIIGRQGA-KINEIRQMSGAQIKIANPVEGSTDRQVTITG-SAASISLAQYLINV   70 (76)
T ss_dssp             EEEEEHHHHHHHHCGGGH-HHHHHHHHHCCEEEECCCCTTCSEEEEEEEE-CHHHHHHHHHHHHH
T ss_pred             EEEEChHHcceEECCCCh-HHHHHHHHHCCEEEEcCCCCCCCeEEEEEEe-CHHHHHHHHHHHHH
Confidence            478999999999999998 99999999999999987      78999998 47655555554443

>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=94.47  E-value=0.055  Score=38.42  Aligned_cols=55  Identities=4%  Similarity=0.069  Sum_probs=44.4

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeC------CeEEEecCChhHHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN------GRVWVNAESPSTVVLVSNAI  215 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N------G~IWi~~~~~~~~~~i~~~i  215 (238)
                      -+.||+.++.+++|+.++ .++.|.+.+++.|-+-..      +.|.|.+ +++.+..+...|
T Consensus        10 ~i~Vp~~~vg~iIGkgG~-~Ik~I~~~tga~I~i~~~~~~~~~~~v~I~G-~~~~v~~A~~~I   70 (82)
T 1zzk_A           10 QVTIPKDLAGSIIGKGGQ-RIKQIRHESGASIKIDEPLEGSEDRIITITG-TQDQIQNAQYLL   70 (82)
T ss_dssp             EEEEETTTGGGGTCGGGH-HHHHHHHHHCCEEEECCTTSCSSEEEEEEEE-CHHHHHHHHHHH
T ss_pred             EEEEChHhcCeeECCCch-HHHHHHHHHCCEEEEcCCCCCCCceEEEEEe-CHHHHHHHHHHH
Confidence            478999999999999998 999999999999999875      5899998 565444444433

>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=94.28  E-value=0.073  Score=41.60  Aligned_cols=52  Identities=17%  Similarity=0.158  Sum_probs=41.4

Q ss_pred             hhhhhcCCCCchhhHhhccccceEEEEee----------------------CCeEEEecCChhHHHHHHHHHHHh
Q 026458          166 LSRMLLSSPTCPVLEELGKQLSFEIAVGL----------------------NGRVWVNAESPSTVVLVSNAIMNS  218 (238)
Q Consensus       166 ~v~rl~~~~~~~~l~~l~~~~~~ei~vG~----------------------NG~IWi~~~~~~~~~~i~~~i~~~  218 (238)
                      ++.+++|.++. .++.|.+.++|.|.|--                      .|.|+|.+.+.+....+...|+.+
T Consensus        23 ~iG~IIGP~G~-tiK~Iq~eTG~kI~IrgkgS~~~~~~~~~~~~~~~~~~e~lhV~I~a~~~e~~~~A~~~I~~l   96 (131)
T 1k1g_A           23 FVGLLIGPRGN-TLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKAVEQIRNI   96 (131)
T ss_dssp             HHHHHHCSSSH-HHHHHHHHSCCEEEEEESTTSSSSSSSSCCCCCSCCSSCCEEEEEEESSHHHHHHHHHHHHHH
T ss_pred             eeeeEECCCcH-HHHHHHHHHCCeEEecCCcccccccccccccccccccCCCeEEEEEECCHHHHHHHHHHHHHH
Confidence            88899999998 89999999999999943                      679999998886555444444443

>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=94.24  E-value=0.033  Score=40.80  Aligned_cols=54  Identities=7%  Similarity=0.107  Sum_probs=44.3

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEee----CCeEEEecCChhHHHHHHH
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL----NGRVWVNAESPSTVVLVSN  213 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~----NG~IWi~~~~~~~~~~i~~  213 (238)
                      .-+.||+.+++.++|+.+. .++.|.+.+++.|-+-.    +|.|.|.+. ++....+..
T Consensus        19 ~~i~Ip~~~ig~IIG~gG~-~Ik~I~~etg~~I~i~~~~~~~~~V~I~G~-~e~v~~A~~   76 (94)
T 2cte_A           19 ATVAIPKEHHRFVIGKNGE-KLQDLELKTATKIQIPRPDDPSNQIKITGT-KEGIEKARH   76 (94)
T ss_dssp             EEEECCTTTHHHHHCSSSC-HHHHHHHHTTCCCBCCCTTSSCCEEEEEEC-HHHHHHHHH
T ss_pred             EEEEEChHHeeeeECCCCh-hHHHHHHHHCCEEEeCCCCCCCCeEEEEEC-HHHHHHHHH
Confidence            4578999999999999998 99999999999999965    699999986 654444433

>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=94.06  E-value=0.074  Score=36.97  Aligned_cols=55  Identities=4%  Similarity=0.008  Sum_probs=45.2

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC----eEEEecCChhHHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG----RVWVNAESPSTVVLVSNAI  215 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG----~IWi~~~~~~~~~~i~~~i  215 (238)
                      -+.||+.++..++|+.++ .++.|.+.+++.|-+-.+|    .|-|.+. ++....+...|
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 RLLMHGKEVGSIIGKKGE-SVKKMREESGARINISEGNCPERIITLAGP-TNAIFKAFAMI   66 (73)
T ss_dssp             EEEEEHHHHHHHHCGGGH-HHHHHHHHHCCEEEECSSCCSEEEEEEEEC-HHHHHHHHHHH
T ss_pred             EEEEChhHeeeEECCCCH-HHHHHHHHHCCEEEEecCCCCcEEEEEEeC-HHHHHHHHHHH
Confidence            478999999999999998 9999999999999999998    5888885 65554444443

>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=94.05  E-value=0.057  Score=38.29  Aligned_cols=56  Identities=13%  Similarity=0.185  Sum_probs=44.7

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEee------CCeEEEecCChhHHHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL------NGRVWVNAESPSTVVLVSNAIM  216 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~------NG~IWi~~~~~~~~~~i~~~i~  216 (238)
                      -+.||..++..++|+.++ .++.|.+.+++.|-|-.      ++.|.|.+ +++.+..+...|.
T Consensus         9 ~i~Ip~~~vg~IIGkgG~-~Ik~I~~~sga~I~i~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~   70 (82)
T 1wvn_A            9 ELTIPNNLIGCIIGRQGA-NINEIRQMSGAQIKIANPVEGSSGRQVTITG-SAASISLAQYLIN   70 (82)
T ss_dssp             EEEEEGGGHHHHHCGGGH-HHHHHHHHHCCEEEECCCCTTCSEEEEEEEE-CHHHHHHHHHHHH
T ss_pred             EEEEchHhccceeCCCch-hHHHHHHHhCCEEEEecCCCCCCceEEEEEc-CHHHHHHHHHHHH
Confidence            478999999999999998 99999999999999987      56999997 5554444444333

>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=93.90  E-value=0.11  Score=37.82  Aligned_cols=57  Identities=7%  Similarity=0.203  Sum_probs=45.8

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeC------CeEEEecCChhHHHHHHHHHH
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN------GRVWVNAESPSTVVLVSNAIM  216 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N------G~IWi~~~~~~~~~~i~~~i~  216 (238)
                      .-+.||..++.++||+.+. .++.|.+.+++.|-|-.+      +.|.|.+ +++.+..+...|.
T Consensus        17 ~~i~Ip~~~vG~IIGkgG~-~Ik~I~~~tga~I~I~~~~~g~~~r~v~I~G-~~e~v~~A~~~I~   79 (92)
T 1x4n_A           17 EEYKVPDGMVGFIIGRGGE-QISRIQQESGCKIQIAPDSGGLPERSCMLTG-TPESVQSAKRLLD   79 (92)
T ss_dssp             EEEEEEHHHHHHHHCSSSH-HHHHHHHHSCCEEEECSCCTTCSEEEEEEEE-CHHHHHHHHHHHH
T ss_pred             EEEEEChHHcceeECCCch-HHHHHHHHhCCEEEEcCCCCCCCccEEEEEe-CHHHHHHHHHHHH
Confidence            3588999999999999998 899999999999999886      4899998 4655544444443

>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=93.84  E-value=0.052  Score=39.24  Aligned_cols=55  Identities=4%  Similarity=0.078  Sum_probs=44.5

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEee------CCeEEEecCChhHHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL------NGRVWVNAESPSTVVLVSNAI  215 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~------NG~IWi~~~~~~~~~~i~~~i  215 (238)
                      -+.||+.++.++||+.++ .++.|.+.+++.|-|-.      ++.|.|.+. ++.+..+.+.|
T Consensus        17 ~i~Ip~~~vg~IIGkgG~-~Ik~I~~~tga~I~I~~~~~~~~~~~v~I~G~-~e~v~~A~~~I   77 (89)
T 1j5k_A           17 QVTIPKDLAGSIIGKGGQ-RIKQIRHESGASIKIDEPLEGSEDRIITITGT-QDQIQNAQYLL   77 (89)
T ss_dssp             EEEEEHHHHHHHHCGGGH-HHHHHHHHTCCEEEECSCCSSSSEEEEEEEEE-HHHHHHHHHHH
T ss_pred             EEEEChhhcceeECCCCH-hHHHHHHHhCCeEEecCCCCCCCccEEEEEcC-HHHHHHHHHHH
Confidence            478999999999999998 89999999999999987      488999984 65444444433

>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=93.73  E-value=0.079  Score=37.97  Aligned_cols=57  Identities=18%  Similarity=0.154  Sum_probs=45.1

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeC---------CeEEEecCChhHHHHHHHHHH
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN---------GRVWVNAESPSTVVLVSNAIM  216 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N---------G~IWi~~~~~~~~~~i~~~i~  216 (238)
                      +-+.||+.++.+++|+.+. .++.|.+.+++.|-|..+         +.|.|.+ +++.+..+...|.
T Consensus         5 ~~i~IP~~~vG~IIGkgG~-~Ik~I~~~tga~I~I~~~~~~~~g~~~r~v~I~G-~~~~v~~A~~~I~   70 (87)
T 1ec6_A            5 VEIAVPENLVGAILGKGGK-TLVEYQELTGARIQISKKGEFLPGTRNRRVTITG-SPAATQAAQYLIS   70 (87)
T ss_dssp             EEEEEEHHHHHHHHCGGGH-HHHHHHHHHCCEEEECCTTCBSTTSCEEEEEEES-SHHHHHHHHHHHH
T ss_pred             EEEEEChHHcCeeECCCcH-hHHHHHHHhCCEEEEccCCCCCCCCCceEEEEEc-CHHHHHHHHHHHH
Confidence            3578999999999999998 899999999999999975         4899988 4654444444333

>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=93.70  E-value=0.12  Score=40.75  Aligned_cols=58  Identities=10%  Similarity=0.216  Sum_probs=47.8

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC--------eEEEecCChhHHHHHHHHHHHh
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG--------RVWVNAESPSTVVLVSNAIMNS  218 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG--------~IWi~~~~~~~~~~i~~~i~~~  218 (238)
                      -+.||+.++..++|+.++ .++.|.+.+++.|-+-.++        .|+|.+ +++.+..+..+|..+
T Consensus         5 ~~~Vp~~~~g~iIGk~G~-~Ik~i~~~tg~~I~i~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~i   70 (164)
T 2jvz_A            5 EIMIPAGKAGLVIGKGGE-TIKQLQERAGVKMILIQDGSQNTNVDKPLRIIG-DPYKVQQACEMVMDI   70 (164)
T ss_dssp             EEEECTTCHHHHTCTTTH-HHHHHHHTSCSEEEECCCTTSSSSSCEEEEEEE-CHHHHHHHHHHHHHH
T ss_pred             EEEechhheeEEECCChH-HHHHHHHHhCCeEEEecCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHH
Confidence            367999999999999998 9999999999999997765        799998 776666666655543

>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=93.27  E-value=0.061  Score=42.66  Aligned_cols=56  Identities=11%  Similarity=0.048  Sum_probs=46.4

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC--------eEEEecCChhHHHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG--------RVWVNAESPSTVVLVSNAIM  216 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG--------~IWi~~~~~~~~~~i~~~i~  216 (238)
                      -+.||+.++.+++|+.++ .++.|.+.+++.|-+-.+|        .|+|.+ +++.+..+...|.
T Consensus        88 ~i~vp~~~~g~iIGkgG~-~I~~i~~~tga~I~i~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~  151 (163)
T 3krm_A           88 HIRVPASAAGRVIGKGGK-TVNELQNLTAAEVVVPRDQTPDENDQVIVKIIG-HFYASQMAQRKIR  151 (163)
T ss_dssp             EEEEETTTHHHHHCGGGH-HHHHHHHHHCCEEECCTTCCCCTTSEEEEEEEE-CHHHHHHHHHHHH
T ss_pred             EEEcChhheeeEEcCCCh-HHHHHHHHhCCeEEECCCCCCCCCCceEEEEEe-CHHHHHHHHHHHH
Confidence            478999999999999998 8999999999999999888        799998 7765554444443

>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=93.17  E-value=0.36  Score=35.75  Aligned_cols=58  Identities=9%  Similarity=0.116  Sum_probs=45.6

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcc------cc-cccCcCCCCEEEEEE
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGT------RR-NIPKFEIGSLLYVRV  128 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gat------k~-~r~~l~~GDlV~ArV  128 (238)
                      .|..|+...+.|+++..+.+.|-+.....+.|+.....-+.      ++ ....|++||+|+.+-
T Consensus        30 ~~~~~~~~~AvV~~v~~~~~~v~~~~g~~~~l~~~~~~WA~~~~~~~~~~~~~~l~~GdvI~V~~   94 (106)
T 3d0f_A           30 IGNSDDILAAVVLSATPGAVEAFRKNGETIRITGDGLKAAHRFLSNDPKIGEKRIRPGALIRVKK   94 (106)
T ss_dssp             SCTTTTCEEEEEEEEETTEEEEEETTSCEEEECGGGGSTTGGGTTTCTTTGGGSCCTTEEEEEEE
T ss_pred             cCccCCeEEEEEEEeCCCeEEEEEcCCCeEEEcHHHChhhhhcccccccchhccCCCCCEEEEEE
Confidence            57789999999999999999999977777778875544331      22 345699999999983

>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=89.43  E-value=0.43  Score=38.13  Aligned_cols=57  Identities=14%  Similarity=0.216  Sum_probs=47.0

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeC---------CeEEEecCChhHHHHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN---------GRVWVNAESPSTVVLVSNAIMN  217 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N---------G~IWi~~~~~~~~~~i~~~i~~  217 (238)
                      -+.||..++.+++|+.+. .++.|.+.+++.|-|-.+         +.|.|.+ +++.+..+...|..
T Consensus       107 ~i~vp~~~~g~iIGkgG~-~Ik~I~~~tga~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~  172 (174)
T 1j4w_A          107 NFIVPTGKTGLIIGKGGE-TIKSISQQSGARIELQRNPPPNADPNMKLFTIRG-TPQQIDYARQLIEE  172 (174)
T ss_dssp             EEEEETTTHHHHHCGGGH-HHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEEC-CHHHHHHHHHHHHH
T ss_pred             EEEEChHHcCeeECCCch-HHHHHHHHHCCEEEECCCCCCCCCCCceEEEEEC-CHHHHHHHHHHHHH
Confidence            478999999999999998 899999999999999875         6899988 77666665555543

>2dgr_A Ring finger and KH domain-containing protein 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=87.96  E-value=0.5  Score=33.75  Aligned_cols=59  Identities=8%  Similarity=0.087  Sum_probs=46.1

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEee--CCeEEEecCChhHHHHHHHHHHHh
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL--NGRVWVNAESPSTVVLVSNAIMNS  218 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~--NG~IWi~~~~~~~~~~i~~~i~~~  218 (238)
                      -+.||..++..++|+.++ .++.|.+.+++.|-+-.  ++++..-..+++....+.+.|...
T Consensus        13 ~i~VP~~~vG~IIGkgG~-tIk~Iqe~Tga~I~I~~~~~~~~v~ItG~~e~v~~A~~~I~~~   73 (83)
T 2dgr_A           13 QVRVPYRVVGLVVGPKGA-TIKRIQQRTHTYIVTPGRDKEPVFAVTGMPENVDRAREEIEAH   73 (83)
T ss_dssp             EEECCHHHHHHHHTTTTS-SHHHHHHHTTCEEECCCSSSCCEEEEEECTTTHHHHHHHHHHH
T ss_pred             EEEeChHHeeeeECCCch-HHHHHHHHhCCeEEecCCCCCCeEEEEcCHHHHHHHHHHHHHH
Confidence            478999999999999998 89999999999999873  455444444777777777666654

>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1

Probab=87.90  E-value=0.33  Score=38.34  Aligned_cols=55  Identities=15%  Similarity=0.207  Sum_probs=43.4

Q ss_pred             hhhhhhcCCCCchhhHhhccccceEEEEeeCC------------------------eEEEecCChhHH--HHHHHHHHHh
Q 026458          165 GLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG------------------------RVWVNAESPSTV--VLVSNAIMNS  218 (238)
Q Consensus       165 ~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG------------------------~IWi~~~~~~~~--~~i~~~i~~~  218 (238)
                      .++.+++|.+++ -++.|.+.++|.|.|-=.|                        .|+|.+.+++..  ..+..|+..+
T Consensus        17 NfiG~IiGPrG~-t~K~ie~eTg~kI~IrGkGS~kd~~~e~~~~g~~~~~~~~epLHV~Isa~~~~~~~~~~l~~A~~~I   95 (140)
T 2bl5_A           17 NFVGRILGPRGL-TAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEV   95 (140)
T ss_dssp             CHHHHHTTTTHH-HHHHHHHHHSEEEEEESTTSSCCHHHHHTSTTSHHHHTTTSCCEEEEEECSCCHHHHHHHHHHHHHH
T ss_pred             CeeeEEECCCcc-hHHHHHHHHCCeEEEecCCCcccccccccccCCCCccccCCCcEEEEEecCchhhHHHHHHHHHHHH
Confidence            568899999888 8899999999999997666                        899999887532  3556666666


Q ss_pred             cc
Q 026458          219 ES  220 (238)
Q Consensus       219 e~  220 (238)
                      +.
T Consensus        96 ~~   97 (140)
T 2bl5_A           96 KK   97 (140)
T ss_dssp             HH
T ss_pred             HH
Confidence            65

>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing factor, RNA binding protein; 2.30A {Pyrococcus horikoshii} PDB: 3aev_B

Probab=87.87  E-value=0.63  Score=39.31  Aligned_cols=60  Identities=15%  Similarity=0.293  Sum_probs=50.6

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEe-eCCeEEEecCC----hhHHHHHHHHHHHhc
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVG-LNGRVWVNAES----PSTVVLVSNAIMNSE  219 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG-~NG~IWi~~~~----~~~~~~i~~~i~~~e  219 (238)
                      .+.||+.++..++|+.+. +++.|.+++++.|-+- .+|.|-|.+.+    +.....+...|+.+-
T Consensus        37 ~i~IP~~kig~lIG~gGk-~Ik~I~e~tgvkI~I~~~~g~V~I~~~~~t~d~~~i~kA~~~I~~i~  101 (219)
T 2e3u_A           37 YVKIPKDRIAVLIGKKGQ-TKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKARDIVLAIG  101 (219)
T ss_dssp             EEECCHHHHHHHHCGGGH-HHHHHHHHHTEEEEECTTTCEEEEEECTTCCSHHHHHHHHHHHHHHH
T ss_pred             EEEeCHHHhhhhhcccHH-HHHHHHHHHCcEEEEEcCCCEEEEecCCCCCCHHHHHHHHHHHHHHh
Confidence            689999999999998887 9999999999999998 89999999876    666666666665543

>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=87.74  E-value=0.67  Score=37.08  Aligned_cols=54  Identities=7%  Similarity=0.053  Sum_probs=43.5

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeC--------CeEEEecCChhHHHHHHH
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN--------GRVWVNAESPSTVVLVSN  213 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N--------G~IWi~~~~~~~~~~i~~  213 (238)
                      .-+.||..++.+++|+.++ .++.|.+.+++.|-+-.+        +.|.|.+ +++.+..+..
T Consensus       106 ~~i~Vp~~~vg~iIGkgG~-~Ik~i~~~tga~I~i~~~~~~~~~~~~~v~I~G-~~~~v~~A~~  167 (178)
T 2anr_A          106 VKIIVPNSTAGLIIGKGGA-TVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSG-EPEQNRKAVE  167 (178)
T ss_dssp             EEEEEEHHHHHHHHCGGGH-HHHHHHHHSSCEEEECCCC----CCEEEEEEES-SHHHHHHHHH
T ss_pred             EEEEEchhheeeeECCCcH-HHHHHHHHHCCEEEEeCCCCCCCCCceEEEEEc-CHHHHHHHHH
Confidence            3588999999999999998 899999999999999876        5899987 4544433333

>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=86.80  E-value=0.31  Score=38.32  Aligned_cols=55  Identities=11%  Similarity=0.236  Sum_probs=44.5

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEee-------CCeEEEecCChhHHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL-------NGRVWVNAESPSTVVLVSNAI  215 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~-------NG~IWi~~~~~~~~~~i~~~i  215 (238)
                      -+.||+.++.+++|+.++ .++.|.+.+++.|-+-.       ++.|.|.+ +++.+..+...|
T Consensus        92 ~i~vp~~~~g~iIGkgG~-~Ik~i~~~tga~I~i~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I  153 (160)
T 2jzx_A           92 RLVVPASQCGSLIGKGGC-KIKEIRESTGAQVQVAGDMLPNSTERAITIAG-IPQSIIECVKQI  153 (160)
T ss_dssp             EEEEEHHHHHHHHCGGGH-HHHHHHHHHSSEECCCCCCSTTCCEEEEEEEE-CHHHHHHHHHHH
T ss_pred             EEEEChhheeeEECCCCH-HHHHHHHHhCCeEEECCCCCCCCCceEEEEEc-CHHHHHHHHHHH
Confidence            478999999999999998 89999999999999875       48899998 665554444433

>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=86.37  E-value=1.4  Score=42.85  Aligned_cols=71  Identities=11%  Similarity=0.128  Sum_probs=55.4

Q ss_pred             CCCCCC--EEEEEEEEecCceEEEEec-CCeeeeecCcccCC---c------cc----ccccCcCCCCEEEEEEEecCCC
Q 026458           71 VPCVED--TVLGIVVDCKADNFFVDIR-GPTIAFLPVLAFEG---G------TR----RNIPKFEIGSLLYVRVVKANPG  134 (238)
Q Consensus        71 ~P~vGD--iVIG~V~~v~~~~~~VdI~-~~~~a~L~~~~f~g---a------tk----~~r~~l~~GDlV~ArV~~~~~~  134 (238)
                      .+++|+  ..-|+|+++....++|.|. ....|.+|.+.+..   .      +.    +....|++||-|..+|.+++..
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            578899  9999999999999999995 45789999877642   1      11    2345699999999999999864


Q ss_pred             -CcceEEE
Q 026458          135 -MNPELSC  141 (238)
Q Consensus       135 -~~~~Ls~  141 (238)
                       +.+.++.
T Consensus       635 ~~~I~~~l  642 (644)
T 2id0_A          635 TRSIIARP  642 (644)
T ss_dssp             TTEEEEEE
T ss_pred             CCEEEEEE
Confidence             5566654

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

Probab=86.35  E-value=2.5  Score=31.00  Aligned_cols=38  Identities=16%  Similarity=0.220  Sum_probs=35.0

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccC
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFE  108 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~  108 (238)
                      .|++|+.|-+.|+.+......|+|....+|.+|++++.
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            79999999999999999999999988889999998763

>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=84.18  E-value=1.3  Score=35.37  Aligned_cols=56  Identities=9%  Similarity=0.042  Sum_probs=44.6

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC---------eEEEecCChhHHHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG---------RVWVNAESPSTVVLVSNAIM  216 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG---------~IWi~~~~~~~~~~i~~~i~  216 (238)
                      -+.||..++.+++|+.++ .++.|.+.+++.|-+-..+         .|.|.+ +++....+...|.
T Consensus         9 ~i~vp~~~ig~iIGkgG~-~Ik~i~~~tg~~I~i~~~~~~~~~~~er~v~I~G-~~~~v~~A~~~I~   73 (178)
T 2anr_A            9 KVLIPSYAAGSIIGKGGQ-TIVQLQKETGATIKLSKSKDFYPGTTERVCLIQG-TIEALNAVHGFIA   73 (178)
T ss_dssp             EEEEEHHHHHHHHCGGGH-HHHHHHHHHCCEEEECCTTCBCTTSSEEEEEEEE-CHHHHHHHHHHHH
T ss_pred             EEEEChhHeeeeECCCcH-HHHHHHHHhCCeEEEecCCCCCCCCCCceEEEEe-CHHHHHHHHHHHH
Confidence            478999999999999998 9999999999999998765         577877 4655555544444

>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=82.96  E-value=1.5  Score=34.30  Aligned_cols=57  Identities=11%  Similarity=0.099  Sum_probs=45.9

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCe-------EEEecCChhHHHHHHHHHH
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGR-------VWVNAESPSTVVLVSNAIM  216 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~-------IWi~~~~~~~~~~i~~~i~  216 (238)
                      +-+.||..++..++|++++ .++.|.+.+++.|-+-.++.       |-|.+ +++.+..+...|.
T Consensus         5 ~~~~ip~~~~g~iIGk~G~-~Ik~i~~~tg~~I~i~~~~~~~~~~r~v~I~G-~~e~v~~A~~~I~   68 (163)
T 3krm_A            5 VQVFIPAQAVGAIIGKKGQ-HIKQLSRFASASIKIAPPETPDSKVRMVIITG-PPEAQFKAQGRIY   68 (163)
T ss_dssp             EEEEEEGGGHHHHHCGGGH-HHHHHHHHHTCEEEECCCSSTTCSEEEEEEEE-CHHHHHHHHHHHH
T ss_pred             EEEEechhhcceeECCCcH-HHHHHHHHHCCeEEEcCCCCCCCCceEEEEEc-CHHHHHHHHHHHH
Confidence            3478999999999999998 89999999999999988774       78887 6665555554443

>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=82.32  E-value=1.9  Score=34.25  Aligned_cols=56  Identities=5%  Similarity=0.059  Sum_probs=43.4

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEee-C-----CeEEEecCChhHHHHHHHHH
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGL-N-----GRVWVNAESPSTVVLVSNAI  215 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~-N-----G~IWi~~~~~~~~~~i~~~i  215 (238)
                      +-+.||..++.+++|+.++ .++.|.+.+++.|-|-. +     ..|.|.+. ++.+..+...|
T Consensus         5 ~~~~vp~~~vg~iIGkgG~-~Ik~i~~~tg~~I~i~~~~~~~~~r~v~I~G~-~~~v~~A~~~I   66 (174)
T 1j4w_A            5 IDVPIPRFAVGIVIGRNGE-MIKKIQNDAGVRIQFKPDDGTTPERIAQITGP-PDRAQHAAEII   66 (174)
T ss_dssp             EEEEEEHHHHHHHHCGGGH-HHHHHHHHHCCEEEEECCTTSCSEEEEEEEEC-HHHHHHHHHHH
T ss_pred             EEEEEChhheeeeecCCch-HHHHHHHHhCCEEEEecCCCCCCccEEEEEeC-HHHHHHHHHHH
Confidence            3578999999999999998 99999999999999974 3     36888874 55444444333

>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=81.97  E-value=1.6  Score=34.04  Aligned_cols=53  Identities=2%  Similarity=-0.012  Sum_probs=43.2

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC----eEEEecCChhHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG----RVWVNAESPSTVVLVSN  213 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG----~IWi~~~~~~~~~~i~~  213 (238)
                      -+.||+.++..++|+.+. .++.|.+.+++.|-+-.+|    .|-|.+. ++.+..+..
T Consensus         8 ~~~vp~~~~g~iIGkgG~-~Ik~i~~~tg~~I~i~~~~~~~r~v~I~G~-~~~v~~A~~   64 (160)
T 2jzx_A            8 RLLMHGKEVGSIIGKKGE-SVKKMREESGARINISEGNCPERIITLAGP-TNAIFKAFA   64 (160)
T ss_dssp             EEEEEHHHHHHHHCGGGH-HHHHHHHHHCSEEEEECCTTTEEEEEEEEE-HHHHHHHHH
T ss_pred             EEEEchhheeeeECCCcH-HHHHHHHHHCCEEEEcCCCCCceEEEEEeC-HHHHHHHHH
Confidence            478999999999999998 9999999999999999887    8888874 444433333

---

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	238
d2nn6g3	80	d.51.1.1 (G:195-274) Ribosomal RNA-processing prot	4e-33
d2nn6g1	88	b.40.4.5 (G:107-194) S1-domain of exosome componen	3e-31
d2ja9a1	90	b.40.4.5 (A:62-151) S1-domain of exosome component	1e-28
d2ja9a2	85	d.51.1.1 (A:152-236) Ribosomal RNA-processing prot	1e-25
d2nn6g2	91	b.84.4.2 (G:16-106) Ribosomal RNA-processing prote	1e-20
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	6e-08
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	3e-06
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	1e-05
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	5e-05

>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 =  112 bits (283), Expect = 4e-33
 Identities = 27/80 (33%), Positives = 51/80 (63%), Gaps = 1/80 (1%)

Query: 156 DGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAI 215
           DG +F+ + GL R LL+ P C +++E+GK    EI  G+NGR+WV A++    ++++N +
Sbjct: 1   DGLLFKVTLGLIRKLLA-PDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTIQQTLILANIL 59

Query: 216 MNSESLSAVQQKIMVDKLLQ 235
              E +++ Q+K +  +L +
Sbjct: 60  EACEHMTSDQRKQIFSRLAE 79

>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 =  108 bits (271), Expect = 3e-31
 Identities = 38/88 (43%), Positives = 51/88 (57%)

Query: 69  RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRV 128
           RYVP   D V+GIV     D F VD+ G   A L  L+FEG T+RN P  ++G L+Y + 
Sbjct: 1   RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQF 60

Query: 129 VKANPGMNPELSCTDASGKAAEFGLLKD 156
           V AN  M PE+ C D+ G+A   G++  
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 =  101 bits (254), Expect = 1e-28
 Identities = 28/90 (31%), Positives = 54/90 (60%), Gaps = 2/90 (2%)

Query: 68  KRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPV-LAFEGGTRRNIPKFEIGSLLYV 126
           KRY+P V D V+G+++   +D++ V ++  + +     +AF   +++N P  ++G L+Y 
Sbjct: 1   KRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYA 60

Query: 127 RVVKANPGMNPELSCTDA-SGKAAEFGLLK 155
           RV  A   +  E+ C D+ +G+ A FG+L+
Sbjct: 61  RVCTAEKELEAEIECFDSTTGRDAGFGILE 90

>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 = 93.6 bits (233), Expect = 1e-25
 Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 156 DGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAI 215
           DG + + +   +R LL +   P+L+ L     FE+A+GLNG++WV  E  S  +     I
Sbjct: 1   DGMIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWVKCEELSNTLACYRTI 60

Query: 216 MNSESLSAV-QQKIMVDKLLQRI 237
           M     +     K +  +  + I
Sbjct: 61  MECCQKNDTAAFKDIAKRQFKEI 83

>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 = 80.9 bits (199), Expect = 1e-20
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 26/86 (30%)

Query: 9  NLVDKIVVPGDVV--------------------LDLSSMTNQTIKLGGGLRQECDSVSVI 48
           ++ ++V+PG+ +                    L+  + +   +  G GLR+  D + V 
Sbjct: 6  TVLGQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCGDRLLVT 65

Query: 49 KAGKLRFSKPNK------YWVESSQK 68
          K G+LR  +P        YWV+S QK
Sbjct: 66 KCGRLRHKEPGSGSGGGVYWVDSQQK 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 = 47.2 bits (112), Expect = 6e-08
 Identities = 15/84 (17%), Positives = 27/84 (32%), Gaps = 11/84 (13%)

Query: 69  RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPV--LAFEGGTRRNIPK--------- 117
           RY+  V D V+G + + +   + V+      + L +  +   GG  R             
Sbjct: 3   RYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGF 62

Query: 118 FEIGSLLYVRVVKANPGMNPELSC 141
            + G L+   V          L  
Sbjct: 63  LQEGDLISAEVQAVFSDGAVSLHT 86

>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 = 42.2 bits (99), Expect = 3e-06
 Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 70  YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIP-----KFEIGSLL 124
           YVP   D V+G++      N+FVDI  P +A L V  F G              ++G  +
Sbjct: 3   YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYI 62

Query: 125 YVRVVKANPGMNPELSC 141
             +VV  +   +P L+ 
Sbjct: 63  KAKVVAFDKTRSPLLTV 79

>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 = 40.4 bits (94), Expect = 1e-05
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 4/77 (5%)

Query: 69  RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPK----FEIGSLL 124
            Y P + D V+G+V D +   + VDI+ P  A+LP     G +           ++G  +
Sbjct: 2   FYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYV 61

Query: 125 YVRVVKANPGMNPELSC 141
             R+   +  ++P LS 
Sbjct: 62  IARIENFDRSIDPVLSV 78

>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 = 38.8 bits (90), Expect = 5e-05
 Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 2/80 (2%)

Query: 70  YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPK--FEIGSLLYVR 127
           Y P V D V+GI+ +  A+ + VDI  P  AFLPV           P    +IG  +  +
Sbjct: 1   YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAK 60

Query: 128 VVKANPGMNPELSCTDASGK 147
           V+  +P M   L+  D   +
Sbjct: 61  VLNIDPKMKVTLTMKDRICR 80

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	238
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	99.9
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.78
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	99.73
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.71
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.69
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.66
d2ba0a2	51	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.36
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	99.31
d2nn6h2	48	Ribosomal RNA-processing protein 4, RRP4 {Human (H	99.31
d2je6i2	59	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.16
d2nn6i2	55	Exosome component 1, EXOSC1 {Human (Homo sapiens)	98.98
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	98.93
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	98.84
d2nn6h3	126	Ribosomal RNA-processing protein 4, RRP4 {Human (H	98.78
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	98.72
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	98.65
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	98.63
d2nn6g2	91	Ribosomal RNA-processing protein 40, RRP40 {Human	98.4
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	98.27
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	98.13
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	98.09
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	97.96
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	97.7
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	97.69
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	96.91
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	96.53
d2cpqa1	78	Fragile X mental retardation syndrome related prot	96.45
d2ctma1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	95.3
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	95.28
d1tuaa1	84	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	94.98
d1viga_	71	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	94.61
d1e3ha4	54	Polynucleotide phosphorylase/guanosine pentaphosph	94.45
d2ctla1	84	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	94.44
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	94.02
d1x4na1	79	Far upstream binding element, FBP {Mouse (Mus musc	93.34
d2ctka1	91	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	92.9
d1x4ma1	81	Far upstream binding element, FBP {Mouse (Mus musc	92.77
d1v8qa_	66	Ribosomal protein L27 {Thermus thermophilus [TaxId	92.09
d1zzka1	75	HnRNP K, KH3 {Human (Homo sapiens) [TaxId: 9606]}	92.05
d2ctfa1	90	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	90.56
d1j4wa2	71	Far upstream binding element, FBP {Human (Homo sap	90.2
d2ctja1	82	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	89.88
d1we8a_	104	Tudor and KH domain containing protein, Tdrkh {Mou	89.76
d2ctea1	81	Vigilin {Human (Homo sapiens) [TaxId: 9606]}	89.75
d2axya1	71	Poly(RC)-binding protein 2 {Human (Homo sapiens) [	89.22
d2zjrt1	84	Ribosomal protein L27 {Deinococcus radiodurans [Ta	88.91
d1j4wa1	74	Far upstream binding element, FBP {Human (Homo sap	88.86
d1dtja_	74	Neuro-oncological ventral antigen 2, nova-2, KH3 {	86.49
d1wvna1	70	Poly(RC)-binding protein 1 {Human (Homo sapiens) [	86.09
d1tuaa2	104	Hypothetical protein APE0754 {Aeropyrum pernix [Ta	85.89

>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=2.4e-29  Score=186.08  Aligned_cols=87  Identities=44%  Similarity=0.759  Sum_probs=85.5

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCcc
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGKA  148 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~~  148 (238)
                      ||+|++||+|||+|++++.+.|+|||+++++|+||+++|+|+++++|++|++||+|+|||++++++++++|||+++++|+
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 026458          149 AEFGLLK  155 (238)
Q Consensus       149 ~~~G~L~  155 (238)
                      .+||+|.
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=2.9e-28  Score=180.87  Aligned_cols=88  Identities=32%  Similarity=0.705  Sum_probs=83.3

Q ss_pred             CccCCCCCCEEEEEEEEecCceEEEEecCCeeeeec-CcccCCcccccccCcCCCCEEEEEEEecCCCCcceEEEecCC-
Q 026458           68 KRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLP-VLAFEGGTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDAS-  145 (238)
Q Consensus        68 ~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~-~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~-  145 (238)
                      +||+|++||+|||+|+++.++.|+|||++++.|.|+ .++|+|++++||++|++||+|+|||++++++++++|||+++. 
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            589999999999999999999999999999998876 568999999999999999999999999999999999999985 


Q ss_pred             CccCCCcccC
Q 026458          146 GKAAEFGLLK  155 (238)
Q Consensus       146 ~~~~~~G~L~  155 (238)
                      ||+.+||+|+
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=7.7e-26  Score=163.34  Aligned_cols=79  Identities=34%  Similarity=0.739  Sum_probs=76.0

Q ss_pred             CeeEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhccCCHHHHHHHHHHHHh
Q 026458          156 DGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSESLSAVQQKIMVDKLLQ  235 (238)
Q Consensus       156 ~G~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~lt~~~~~~~~~~~~~  235 (238)
                      ||++|+||.+++|+|+. ++|++|+.|+++++|||+||+||||||+++++++|++++|||+.||+++.+|+++|++++++
T Consensus         1 dG~~f~vsl~laR~Ll~-~~~~vL~~Lgk~~~FEIavG~NGrVWvk~~~~~~ti~i~~aI~~~e~~~~~q~~~lv~~l~~   79 (80)
T d2nn6g3           1 DGLLFKVTLGLIRKLLA-PDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTIQQTLILANILEACEHMTSDQRKQIFSRLAE   79 (80)
T ss_dssp             SCEEECCCHHHHHHHHC-TTCSHHHHTTCSSSCCCEEETTTEEEECCSSHHHHHHHHHHHHHTTSSCTTTHHHHHHHHHH
T ss_pred             CCEEEEecHHHHHHHhc-CCCHHHHHHhhhCCeEEEEecCCeEEEeCCCHHHHHHHHHHHHHhhcCCHHHHHHHHHHHhc
Confidence            79999999999999996 56789999999999999999999999999999999999999999999999999999999876

>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=99.90  E-value=1.9e-24  Score=158.23  Aligned_cols=82  Identities=28%  Similarity=0.519  Sum_probs=76.9

Q ss_pred             CeeEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc-CCHHHHHHHHHHHH
Q 026458          156 DGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES-LSAVQQKIMVDKLL  234 (238)
Q Consensus       156 ~G~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~-lt~~~~~~~~~~~~  234 (238)
                      +|++|+||++++|||+++++|+||++|+++++|||+||+||||||+++++++++++++||+++++ ...++++.++++++
T Consensus         1 dG~v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~NGrIWi~~~~~~~~i~i~~aI~~~e~~~~~~~~~~~vk~~l   80 (85)
T d2ja9a2           1 DGMIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWVKCEELSNTLACYRTIMECCQKNDTAAFKDIAKRQF   80 (85)
T ss_dssp             SCEEEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETTTEEEEECSSHHHHHHHHHHHHHHHHHCCGGGHHHHHHHHT
T ss_pred             CCEEEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEecCcEEEEECCCHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHH
Confidence            69999999999999999999899999999999999999999999999999999999999999864 66689999999998


Q ss_pred             hhc
Q 026458          235 QRI  237 (238)
Q Consensus       235 ~~~  237 (238)
                      +++
T Consensus        81 ~e~   83 (85)
T d2ja9a2          81 KEI   83 (85)
T ss_dssp             TTS
T ss_pred             HHH
Confidence            875

>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=99.78  E-value=3.7e-20  Score=137.93  Aligned_cols=83  Identities=19%  Similarity=0.271  Sum_probs=73.7

Q ss_pred             CCccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCccc--CCc---------ccccccCcCCCCEEEEEEEecCCCC
Q 026458           67 QKRYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAF--EGG---------TRRNIPKFEIGSLLYVRVVKANPGM  135 (238)
Q Consensus        67 ~~~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f--~ga---------tk~~r~~l~~GDlV~ArV~~~~~~~  135 (238)
                      +.+|.|++||+|+|+|+++.+..|+|||++.++|.||++++  ++.         ..++++.|++||.|.|+|.++++++
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            46899999999999999999999999999999999999865  222         3356788999999999999999999


Q ss_pred             cceEEEecCCCccCCCccc
Q 026458          136 NPELSCTDASGKAAEFGLL  154 (238)
Q Consensus       136 ~~~Ls~~~~~~~~~~~G~L  154 (238)
                      .+.|||++     .+||+|
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            99999987     899987

>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=99.73  E-value=3.6e-18  Score=133.13  Aligned_cols=93  Identities=15%  Similarity=0.078  Sum_probs=75.2

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecC--------CeeeeecCcccC---CcccccccCcCCCCEEEEEEEecCCCCc-
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRG--------PTIAFLPVLAFE---GGTRRNIPKFEIGSLLYVRVVKANPGMN-  136 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~--------~~~a~L~~~~f~---gatk~~r~~l~~GDlV~ArV~~~~~~~~-  136 (238)
                      +|+|++||+|+|+|++++.++|.|||.+        ++.|+++.++..   ....+|+.+|++||+|+|||+++++... 
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        455666665442   2345688999999999999999987654 


Q ss_pred             ceEEEecCCCccCCCcccC-----CeeEEEechhh
Q 026458          137 PELSCTDASGKAAEFGLLK-----DGYMFETSTGL  166 (238)
Q Consensus       137 ~~Ls~~~~~~~~~~~G~L~-----~G~~~~V~~~~  166 (238)
                      |+|||.+     +.||+|.     +..|+.++...
T Consensus        82 ~~Lst~~-----~~LGVv~A~c~~g~~m~~~~~~~  111 (125)
T d2nn6i1          82 YLLTTAE-----NELGVVVAHSESGIQMVPISWCE  111 (125)
T ss_dssp             EEEECCS-----SSCEECCCBCSSSCBCEEEETTE
T ss_pred             EEEEecC-----CCcEEEEEECCCCCEeEeecCCE
Confidence            8899998     8999993     55566665543

>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=99.71  E-value=8e-18  Score=123.09  Aligned_cols=81  Identities=28%  Similarity=0.487  Sum_probs=74.1

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-----ccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-----TRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD  143 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-----tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  143 (238)
                      .|.|++||+|+|+|++++...|+|||++...|.||.+++...     ..++++.|++||.|.|||.++++++.+.|||++
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            599999999999999999999999999999999999877432     346788999999999999999988999999988


Q ss_pred             CCCccCCCccc
Q 026458          144 ASGKAAEFGLL  154 (238)
Q Consensus       144 ~~~~~~~~G~L  154 (238)
                           .++|+|
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=99.69  E-value=1.4e-17  Score=121.55  Aligned_cols=82  Identities=26%  Similarity=0.491  Sum_probs=74.8

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc----ccccccCcCCCCEEEEEEEecCCCCcceEEEecC
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG----TRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDA  144 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga----tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~  144 (238)
                      .|+|++||+|+|+|+++.+..|+|||++..+|.||.+++..+    ..+++..|++||.|.|+|+++++++.+.||+++ 
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    346788999999999999999988899999988 


Q ss_pred             CCccCCCcccC
Q 026458          145 SGKAAEFGLLK  155 (238)
Q Consensus       145 ~~~~~~~G~L~  155 (238)
                          .++|+|+
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=99.66  E-value=2.3e-16  Score=113.91  Aligned_cols=80  Identities=30%  Similarity=0.499  Sum_probs=73.6

Q ss_pred             cCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc--ccccccCcCCCCEEEEEEEecCCCCcceEEEecCCCc
Q 026458           70 YVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG--TRRNIPKFEIGSLLYVRVVKANPGMNPELSCTDASGK  147 (238)
Q Consensus        70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga--tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~~~~~  147 (238)
                      |.|++||+|.|+|+++.+..|+|||++...|+||.+++..+  ..+++..|++||.|.|+|.++++++.+.||+++    
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            89999999999999999999999999999999999988754  467788999999999999999988899999988    


Q ss_pred             cCCCccc
Q 026458          148 AAEFGLL  154 (238)
Q Consensus       148 ~~~~G~L  154 (238)
                       .++|+|
T Consensus        77 -~~~~k~   82 (83)
T d2ba0a1          77 -RICRPI   82 (83)
T ss_dssp             -SSCEEE
T ss_pred             -CCCCCC
Confidence             777776

>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=99.36  E-value=2.8e-13  Score=89.05  Aligned_cols=51  Identities=25%  Similarity=0.235  Sum_probs=46.0

Q ss_pred             CcEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEecCCeEEEEccCCc
Q 026458           12 DKIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQKR   69 (238)
Q Consensus        12 ~~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~~~~i~V~~~~~~   69 (238)
                      +++|+|||.|+..      +|.+|+|||.++++|+|+++|.++.. ++.++|+|+++|
T Consensus         1 r~iV~PGe~i~~~------~~~~G~Gty~~~~~i~ss~~G~v~~~-n~~i~V~PL~gr   51 (51)
T d2ba0a2           1 RKIVLPGDLLSTN------PRAAGYGTYVEGGKVYAKIIGLFDQT-ETHVRVIPLKGR   51 (51)
T ss_dssp             CCEECTTCEEESC------TTSBCTTEEEETTEEEECSSEEEEEC-SSCEEEEECSSS
T ss_pred             CCEEcCCcEeecC------CeeCCCCcEEECCEEEEEEEEEEEEE-CCEEEEEeCccC
Confidence            4799999999752      69999999999999999999999986 889999999865

>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=99.31  E-value=1.5e-12  Score=94.57  Aligned_cols=79  Identities=16%  Similarity=0.207  Sum_probs=71.9

Q ss_pred             CeeEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc------CCHHHHHHH
Q 026458          156 DGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES------LSAVQQKIM  229 (238)
Q Consensus       156 ~G~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~------lt~~~~~~~  229 (238)
                      .|.+++|||.++++++|+.++ +++.|.+.++|.|.|+.||+|||.+++......+..+|+.+..      ++ +++.+|
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~~f   78 (87)
T d2z0sa2           1 RGKIVEISPAKVPRVIGRKMS-MLKTLEEKTECKIFVARNGRIHLECPNEDLEAIAVMAIKIIDEEAYTSGLT-KRIIKF   78 (87)
T ss_dssp             SSEEEECCGGGSGGGTCGGGH-HHHHHHHHHCCEEEEETTTEEEEECSCHHHHHHHHHHHHHHHHCSCCTTCH-HHHHHH
T ss_pred             CcEEEEEChhhcceeECCCCc-HHHHHHHHHCCEEEECCCcEEEEEeCCHHHHHHHHHHHHHHHHhchhccHH-HHHHHH
Confidence            378999999999999999998 9999999999999999999999999999999999999998854      77 799999


Q ss_pred             HHHHHhh
Q 026458          230 VDKLLQR  236 (238)
Q Consensus       230 ~~~~~~~  236 (238)
                      +++..+.
T Consensus        79 le~~~~~   85 (87)
T d2z0sa2          79 IEEERRI   85 (87)
T ss_dssp             HHHHHHH
T ss_pred             HHHhhhc
Confidence            9987653

>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=99.31  E-value=6e-13  Score=85.62  Aligned_cols=48  Identities=21%  Similarity=0.243  Sum_probs=44.4

Q ss_pred             cEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEecCCeEEEEcc
Q 026458           13 KIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPNKYWVESS   66 (238)
Q Consensus        13 ~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~~~~i~V~~~   66 (238)
                      ++|+|||.|...+     .|..|||||.++++++||++|++++. +++++|+|+
T Consensus         1 ~iv~PGe~It~~~-----~~mrGHGTy~~~~~i~aSv~G~verv-NKLvsV~pL   48 (48)
T d2nn6h2           1 HLVVPGDTITTDT-----GFMRGHGTYMGEEKLIASVAGSVERV-NKLICVKAL   48 (48)
T ss_dssp             CBCCTTCBCCCCT-----TCCBCTTEEECSSSEEECSSEEEEEE-TTEEEEEES
T ss_pred             CEecCCcEeecCC-----CeEcccccEecCCEEEEEEeeeEEEe-ccEEEEEcC
Confidence            5899999998765     79999999999999999999999987 999999985

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

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

Probab=99.16  E-value=1.3e-11  Score=83.22  Aligned_cols=52  Identities=13%  Similarity=0.096  Sum_probs=45.6

Q ss_pred             CCcEEecCCccCCCCCCCCCcee-ecCcEEEeCCEEEEEEeeEeEEecCCeEEEEccCC
Q 026458           11 VDKIVVPGDVVLDLSSMTNQTIK-LGGGLRQECDSVSVIKAGKLRFSKPNKYWVESSQK   68 (238)
Q Consensus        11 ~~~iV~PGd~l~~~~~~~~~~~~-~G~G~y~~~g~i~as~~G~v~~~~~~~i~V~~~~~   68 (238)
                      .+++|+|||+|+..+     .+. .|+|||.++++|+|+++|+++.. ++.++|+|+++
T Consensus         7 ~r~iV~PGdvi~~~~-----~~~~~g~~ty~~~~ki~asv~G~v~~~-nkli~ViPL~G   59 (59)
T d2je6i2           7 PRSIVVPGELLAEGE-----FQIPWSPYILKINSKYYSTVVGLFDVK-DTQFEVIPLEG   59 (59)
T ss_dssp             SSCEECTTCEEEEEC-----CCCCCCTTEEEETTEEEECSSEEEEEE-TTEEEEEESCC
T ss_pred             CCeEECCCcEeeeCC-----ccccCCCEEEecCCEEEEEEEEEEEEE-CCEEEEEECCC
Confidence            568999999998765     455 48999999999999999999997 88999999864

>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=98.98  E-value=1e-11  Score=82.35  Aligned_cols=48  Identities=23%  Similarity=0.199  Sum_probs=39.8

Q ss_pred             cEEecCCccCCCCCCCCCceeecCcEEEeCCEEEEEEeeEeEEec-CCeEEEEc
Q 026458           13 KIVVPGDVVLDLSSMTNQTIKLGGGLRQECDSVSVIKAGKLRFSK-PNKYWVES   65 (238)
Q Consensus        13 ~iV~PGd~l~~~~~~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~-~~~i~V~~   65 (238)
                      ++|+|||.|+..+     +|.+|+|||+++|.||||++|.+..++ ++.+.|.+
T Consensus         1 k~~lPGe~L~~~e-----ey~~G~gTy~~~g~I~as~~G~v~id~~~~~isVis   49 (55)
T d2nn6i2           1 RYCIPGERLCNLE-----EGSPGSGTYTRHGYIFSSLAGCLMKSSENGALPVVS   49 (55)
T ss_dssp             CCCCTTCEEEETT-----TCCCSSSCEEETTEEECCSCSCBCCCBCTTSSBC-C
T ss_pred             CcccCCcEEeehh-----eecCCCCeEEcCCEEEEEeeEEEEEecCCCEeeEEE
Confidence            4789999999987     899999999999999999999998764 34444443

>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=98.93  E-value=4.7e-10  Score=80.72  Aligned_cols=76  Identities=21%  Similarity=0.350  Sum_probs=66.9

Q ss_pred             eeEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc------CCHHHHHHHH
Q 026458          157 GYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES------LSAVQQKIMV  230 (238)
Q Consensus       157 G~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~------lt~~~~~~~~  230 (238)
                      |.++.||+.++++++|+.++ +++.|.+.+++.|-+..||+|||.+ +++.+..+.++|+.+..      ++ +++++|+
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~~~l   78 (84)
T d2ba0a3           2 GRIVAINPARVPRVIGKKGS-MIKLLKSELDVQIVVGQNGLIWVNG-DRRKVSIAEEAIYLIEQEAHTEGLT-DRVAEFI   78 (84)
T ss_dssp             SEEEECCGGGHHHHHCGGGH-HHHHHHHHHTCEEEECTTSEEEEES-CHHHHHHHHHHHHHHHHCSCCSSHH-HHHHHHH
T ss_pred             cEEEEEChhhcceeeCCcHH-HHHHHHHHHCCEEEECCCCEEEEEe-CHHHHHHHHHHHHHHHHhcccCcHH-HHHHHHH
Confidence            67899999999999999998 9999999999999999999999998 77888888888877654      55 8999998


Q ss_pred             HHHHh
Q 026458          231 DKLLQ  235 (238)
Q Consensus       231 ~~~~~  235 (238)
                      ++...
T Consensus        79 ~~~~~   83 (84)
T d2ba0a3          79 KRRKA   83 (84)
T ss_dssp             HHHHH
T ss_pred             HHhhC
Confidence            87653

>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=1.8e-10  Score=79.98  Aligned_cols=63  Identities=21%  Similarity=0.303  Sum_probs=49.4

Q ss_pred             CeeEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhc
Q 026458          156 DGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSE  219 (238)
Q Consensus       156 ~G~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e  219 (238)
                      +|.+++||+.++++++|+.++ +++.|.+.++|+|-++.||+|||.+.+++....+..+|+.+.
T Consensus         1 ~g~vi~Ip~~~ig~iIGkgG~-~Ik~i~~~tg~~I~i~~~g~v~I~g~~~~~v~~A~~~I~~i~   63 (69)
T d2je6i3           1 NGIVIDIMPVKVPRVIGKNKS-MYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIE   63 (69)
T ss_dssp             SSCEEECCGGGHHHHHCGGGH-HHHHHHTTC---CEECTTSEEEC-----CTTCCTHHHHTTTT
T ss_pred             CCEEEEEChhhccceECCchh-HHHHHHHHHCCEEEEcCCCEEEEEeCCHHHHHHHHHHHHHHH
Confidence            589999999999999999998 999999999999999999999999988877777777776554

>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=98.78  E-value=4.3e-09  Score=80.94  Aligned_cols=72  Identities=17%  Similarity=0.250  Sum_probs=53.2

Q ss_pred             CeeEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCC---------------------hhHHHHHHHH
Q 026458          156 DGYMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAES---------------------PSTVVLVSNA  214 (238)
Q Consensus       156 ~G~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~---------------------~~~~~~i~~~  214 (238)
                      .|++++|||++++|..  .+++-|     .+++++++|+||+|||....                     .+....++||
T Consensus         1 ~G~lv~V~p~LVkR~K--~Hf~~L-----~~gv~vILG~NGyIWIs~~~~~~~~~~~~~~~~~~~v~~~~R~~IaRvaNc   73 (126)
T d2nn6h3           1 QGVLVQVSPSLVKRQK--THFHDL-----PCGASVILGNNGFIWIYPTPEHKEEEAGGFIANLEPVSLADREVISRLRNC   73 (126)
T ss_dssp             SSCEEECCTTSCCCST--TCSCCC-----BTTBEEEEETTTEEEEECCCCC------CCGGGSSCCCHHHHHHHHHHHHH
T ss_pred             CCEEEEEChHHhhhhh--hceEEc-----CCCceEEEecCCEEEeeCCcccccccccccccccCCCCHHHHHHHHHHHHH
Confidence            3889999999999975  444333     58999999999999997632                     2457788888


Q ss_pred             HHHhcc----CCHHHHHHHHHHHH
Q 026458          215 IMNSES----LSAVQQKIMVDKLL  234 (238)
Q Consensus       215 i~~~e~----lt~~~~~~~~~~~~  234 (238)
                      |+....    ++++-+....+..+
T Consensus        74 I~~La~~~~~I~~~sI~~~yeaSl   97 (126)
T d2nn6h3          74 IISLVTQRMMLYDTSILYCYEASL   97 (126)
T ss_dssp             HHHHHHTTCCCCHHHHHHHHHTHH
T ss_pred             HHHHHHCCCcccHHHHHHHHHHHh
Confidence            877665    67666665555443

>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=98.72  E-value=2.5e-08  Score=69.86  Aligned_cols=72  Identities=17%  Similarity=0.158  Sum_probs=63.9

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCCCcceEEEec
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPGMNPELSCTD  143 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls~~~  143 (238)
                      .++|++|-|+|+++....++|+++....|.+|.+++.. ..++.+..|++||-|.|+|+++++.+.+.||++.
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            47999999999999999999999988899999988753 3556677899999999999999887889999875

>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=98.65  E-value=4.1e-08  Score=70.15  Aligned_cols=72  Identities=19%  Similarity=0.133  Sum_probs=53.7

Q ss_pred             cCCCCCCEEEEEEEEecCceEEEEecC--CeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCC-CcceEEE
Q 026458           70 YVPCVEDTVLGIVVDCKADNFFVDIRG--PTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPG-MNPELSC  141 (238)
Q Consensus        70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~  141 (238)
                      ..|++||+|.|+|+++....++|+|..  ...|.+|.+++.. ..++.+..|++||.|.|+|++++++ +.+.||.
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            368999999999999999999999974  4799999988743 3556677899999999999999754 5677775

>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=98.63  E-value=2e-08  Score=71.39  Aligned_cols=73  Identities=14%  Similarity=0.163  Sum_probs=59.7

Q ss_pred             cCCCCCCEEEEEEEEecCceEEEEecC--CeeeeecCcccCC-cccccccCcCCCCEEEEEEEecCCC-CcceEEEe
Q 026458           70 YVPCVEDTVLGIVVDCKADNFFVDIRG--PTIAFLPVLAFEG-GTRRNIPKFEIGSLLYVRVVKANPG-MNPELSCT  142 (238)
Q Consensus        70 Y~P~vGDiVIG~V~~v~~~~~~VdI~~--~~~a~L~~~~f~g-atk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~  142 (238)
                      -.|++||+|.|+|+++.+..++|+|..  ...|.+|.+++.. ..++.+..|++||.|.|+|++++.. +.+.||++
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  4699999988753 3455667799999999999999754 56778764

>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=98.40  E-value=4.1e-08  Score=70.08  Aligned_cols=62  Identities=34%  Similarity=0.632  Sum_probs=36.8

Q ss_pred             ccCCCCcEEecCCccCCCCC--------------------CCCCceeecCcEEEeCCEEEEEEeeEeEEecCC------e
Q 026458            7 TANLVDKIVVPGDVVLDLSS--------------------MTNQTIKLGGGLRQECDSVSVIKAGKLRFSKPN------K   60 (238)
Q Consensus         7 ~~~~~~~iV~PGd~l~~~~~--------------------~~~~~~~~G~G~y~~~g~i~as~~G~v~~~~~~------~   60 (238)
                      ..++..++|+|||.|...+.                    .+....++|||++.+++.|.++.+|+++..+++      .
T Consensus         4 ~~~~~~qvVlPGD~l~lp~~~~~~g~~~~~~~~l~L~~~~~~~~~v~lGPGLRq~~d~v~atKaG~LR~k~P~~~~~~~~   83 (91)
T d2nn6g2           4 ARTVLGQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGV   83 (91)
T ss_dssp             CTGGGSSBCCSSEEECCSCSCCEECSSEEECC-----------------------CCCEEECSCCEEEEECCTTTSSCCE
T ss_pred             hhhhcCCEEeCCcEEEecccccccccCcCcccccccccccCCCceEEeCCccceeCCEEEEeecceeeecCCCCCCCcce
Confidence            35678899999999942211                    113368899999999999999999999986555      5


Q ss_pred             EEEEccCC
Q 026458           61 YWVESSQK   68 (238)
Q Consensus        61 i~V~~~~~   68 (238)
                      +||+..++
T Consensus        84 yWVDs~QK   91 (91)
T d2nn6g2          84 YWVDSQQK   91 (91)
T ss_dssp             EEEECCCS
T ss_pred             EEeecccC
Confidence            99997653

>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=1.1e-06  Score=63.62  Aligned_cols=71  Identities=17%  Similarity=0.138  Sum_probs=61.9

Q ss_pred             CCCCEEEEEEEEecCceEEEEecCCeeeeecCcccC-CcccccccCcCCCCEEEEEEEecCC-CCcceEEEec
Q 026458           73 CVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFE-GGTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCTD  143 (238)
Q Consensus        73 ~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~-gatk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~~  143 (238)
                      ++|++|-|+|+++......|+++....|.+|.++.. ....+.+..|.+||.|.|+|.+++. .+.+.||++.
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            679999999999999999999999999999998774 3355666789999999999999975 5778999874

>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=98.13  E-value=5.3e-06  Score=61.22  Aligned_cols=62  Identities=23%  Similarity=0.275  Sum_probs=53.4

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc------------ccccccCcCCCCEEEEEEEecCCC
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG------------TRRNIPKFEIGSLLYVRVVKANPG  134 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga------------tk~~r~~l~~GDlV~ArV~~~~~~  134 (238)
                      |++||++-|+|++++.-.++|+|+ +-.|.+|.+.++..            .++....|++||-|.++|.+++.+
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 58999999887642            134457899999999999999754

>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=98.09  E-value=2.7e-06  Score=64.05  Aligned_cols=72  Identities=25%  Similarity=0.252  Sum_probs=60.0

Q ss_pred             CCCCCEEEEEEEEecCceEEEEec-CCeeeeecCcccCCc--ccccccCcCCCCEEEEEEEecCCC-CcceEEEec
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIR-GPTIAFLPVLAFEGG--TRRNIPKFEIGSLLYVRVVKANPG-MNPELSCTD  143 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~-~~~~a~L~~~~f~ga--tk~~r~~l~~GDlV~ArV~~~~~~-~~~~Ls~~~  143 (238)
                      -++|++|-|+|+++....++|+|+ ....|++|.+.+...  .++....|++||.|.|+|.++++. +.+.||++.
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            578999999999999999999997 567999999876432  334456899999999999999865 558999875

>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=97.96  E-value=1.3e-05  Score=57.14  Aligned_cols=80  Identities=20%  Similarity=0.282  Sum_probs=59.2

Q ss_pred             CCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-----------ccccccCcCCCCEEEEEEEecCCCCcceEE
Q 026458           72 PCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-----------TRRNIPKFEIGSLLYVRVVKANPGMNPELS  140 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-----------tk~~r~~l~~GDlV~ArV~~~~~~~~~~Ls  140 (238)
                      |-+|+++-|+|++++...+.|+|+ +.++.+|.++.+..           -++....|+.||.|++||.+++.+.. .+.
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 56899998876532           13345579999999999999864321 233


Q ss_pred             EecCCCccCCCccc
Q 026458          141 CTDASGKAAEFGLL  154 (238)
Q Consensus       141 ~~~~~~~~~~~G~L  154 (238)
                      |.. +=+.++||.|
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            332 2233677764

>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=97.70  E-value=5.6e-05  Score=54.14  Aligned_cols=81  Identities=15%  Similarity=0.208  Sum_probs=59.3

Q ss_pred             CCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCc-------------ccccccCcCCCCEEEEEEEecCCCCcc
Q 026458           71 VPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGG-------------TRRNIPKFEIGSLLYVRVVKANPGMNP  137 (238)
Q Consensus        71 ~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~ga-------------tk~~r~~l~~GDlV~ArV~~~~~~~~~  137 (238)
                      .|-+|.++-|+|++++...+.|+++ +.++.+|.+..+..             .++.+..|+.||.|++||.+++.+ .-
T Consensus         1 rPf~Gev~~g~V~~v~~~G~fv~lg-~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~-~~   78 (94)
T d2c35b1           1 RPFKGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVD-KN   78 (94)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEE-TT
T ss_pred             CCCCCCEEEEEEEEEEeeEEEEEec-CceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecC-cC
Confidence            3888999999999999999999997 57899998766532             234455799999999999987643 12


Q ss_pred             eEEEecCCCccCCCccc
Q 026458          138 ELSCTDASGKAAEFGLL  154 (238)
Q Consensus       138 ~Ls~~~~~~~~~~~G~L  154 (238)
                      .+++.. +-+.++||.+
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            334332 2234777754

>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=97.69  E-value=0.00012  Score=50.15  Aligned_cols=59  Identities=14%  Similarity=0.111  Sum_probs=50.5

Q ss_pred             ccCCCCCCEEEEEEEEecCceEEEEecCCeeeeecCcccCCcccccccCcCCCCEEEEEEEecCC
Q 026458           69 RYVPCVEDTVLGIVVDCKADNFFVDIRGPTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANP  133 (238)
Q Consensus        69 ~Y~P~vGDiVIG~V~~v~~~~~~VdI~~~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~  133 (238)
                      .|..++|++|.|+|.++..+.+.|||+. ..|+||.++-     -....|++||-|+|-|..+.+
T Consensus         3 ef~~~~geiv~G~V~r~~~~~~~Vdlg~-~eaiLp~~eq-----ip~E~~~~Gdrik~~i~~V~~   61 (72)
T d1hh2p1           3 KYSELKGTVTTAEVIRVMGEWADIRIGK-LETRLPKKEW-----IPGEEIKAGDLVKVYIIDVVK   61 (72)
T ss_dssp             CTTCCTTCEEEEEEEEECSSEEEEEETT-EEEEEEGGGS-----CTTCCCCTTCEEEEEEEEEEE
T ss_pred             hHhhccCcEEEEEEEEEcCCCEEEEECC-cEEECCHHHc-----CCCCCCCCCCEEEEEEEEEEE
Confidence            4888999999999999999999999984 8999997542     235689999999999998754

>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=96.91  E-value=4e-05  Score=51.02  Aligned_cols=55  Identities=15%  Similarity=0.169  Sum_probs=34.7

Q ss_pred             EEEEEecCceEEEEecCCeeeeecCcccCC-----cccccccCcCCCCEEEEEEEecCCC
Q 026458           80 GIVVDCKADNFFVDIRGPTIAFLPVLAFEG-----GTRRNIPKFEIGSLLYVRVVKANPG  134 (238)
Q Consensus        80 G~V~~v~~~~~~VdI~~~~~a~L~~~~f~g-----atk~~r~~l~~GDlV~ArV~~~~~~  134 (238)
                      |+|+++.+-.++|+|.....|.+|.+++..     ..++.+..|++||-|.++|+++++.
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            789999999999999999999999998852     2456677899999999999999864

>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=96.53  E-value=0.0026  Score=43.67  Aligned_cols=58  Identities=19%  Similarity=0.183  Sum_probs=45.7

Q ss_pred             CCCCCEEEEEEEEecCc----eEEEEecC---CeeeeecCcccCCcccccccCcCCCCEEEEEEEecCCC
Q 026458           72 PCVEDTVLGIVVDCKAD----NFFVDIRG---PTIAFLPVLAFEGGTRRNIPKFEIGSLLYVRVVKANPG  134 (238)
Q Consensus        72 P~vGDiVIG~V~~v~~~----~~~VdI~~---~~~a~L~~~~f~gatk~~r~~l~~GDlV~ArV~~~~~~  134 (238)
                      -++|++|.|.|.++..+    ...|||+.   ..+|+||..+-     -....|++||-|+|-|..+.+.
T Consensus         2 ~r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eq-----ip~E~y~~Gdrik~~i~~V~~~   66 (76)
T d2asba1           2 TREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQ-----VPGESYEHGNRLRCYVVGVTRG   66 (76)
T ss_dssp             CCTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGS-----CTTCCCCTTCEEEEEEEEEECC
T ss_pred             CccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHc-----CCCcccCCCCEEEEEEEEEEec
Confidence            37899999999998654    47999985   47899996432     2346899999999999988654

>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=96.45  E-value=0.0018  Score=44.61  Aligned_cols=59  Identities=15%  Similarity=0.099  Sum_probs=48.0

Q ss_pred             EEechhhhhhhcCCCCchhhHhhccccceEEEE--eeCCeEEEecCChhHHHHHHHHHHHhccCC
Q 026458          160 FETSTGLSRMLLSSPTCPVLEELGKQLSFEIAV--GLNGRVWVNAESPSTVVLVSNAIMNSESLS  222 (238)
Q Consensus       160 ~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~v--G~NG~IWi~~~~~~~~~~i~~~i~~~e~lt  222 (238)
                      |.||+.++..+||++++ .++.|.+.+++.+.+  ..+|.|-|.+.|++.+   .+|-+.+|.+.
T Consensus        12 i~Ip~~~ig~vIG~gG~-~I~~I~~~tGa~i~i~~~~~g~v~I~g~~~eav---~~A~~~Ie~~~   72 (78)
T d2cpqa1          12 FVVREDLMGLAIGTHGS-NIQQARKVPGVTAIELDEDTGTFRIYGESADAV---KKARGFLEFVE   72 (78)
T ss_dssp             EECCHHHHHHHHTTTTH-HHHHHHTSTTEEEEEEETTTTEEEEEESSHHHH---HHHHHHHSCCC
T ss_pred             EEECHHHHHHHcCCChH-HHHHHHHhcCcEEEEecCCCceEEEEECCHHHH---HHHHHHHHHhh
Confidence            89999999999999998 999999999999887  4469999999887544   44444555543

>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=95.30  E-value=0.011  Score=40.47  Aligned_cols=56  Identities=13%  Similarity=0.170  Sum_probs=45.0

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC-----eEEEecCChhHHHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG-----RVWVNAESPSTVVLVSNAIM  216 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG-----~IWi~~~~~~~~~~i~~~i~  216 (238)
                      -+.||+.+.++++|++++ .++.|.+.+++.|-+..++     .|+|.+ +++.+..+.+.|.
T Consensus        13 ~i~Vp~~~~~~iIG~~G~-~i~~I~~~tg~~I~~p~~~~~~~~~v~I~G-~~~~V~~A~~~I~   73 (81)
T d2ctma1          13 DVPLDHRVHARIIGARGK-AIRKIMDEFKVDIRFPQSGAPDPNCVTVTG-LPENVEEAIDHIL   73 (81)
T ss_dssp             EEECCTTTHHHHHCSSSC-HHHHHHHHHTCEEECCCTTCSCTTEEEEES-CHHHHHHHHHHHH
T ss_pred             EEEECHHHHhhccCCCCc-cHHHHHHHhCCEEEeCCccCCCCCEEEEeC-CHHHHHHHHHHHH
Confidence            489999999999999998 8999999999999996654     699997 6655555444443

>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=0.029  Score=39.14  Aligned_cols=67  Identities=18%  Similarity=0.251  Sum_probs=50.1

Q ss_pred             CEEEEEEEEecC--ceEEEEecCCeeeeecCcccCC----------cccccccCcCCCCEEEEEEEecCC-CCcceEEEe
Q 026458           76 DTVLGIVVDCKA--DNFFVDIRGPTIAFLPVLAFEG----------GTRRNIPKFEIGSLLYVRVVKANP-GMNPELSCT  142 (238)
Q Consensus        76 DiVIG~V~~v~~--~~~~VdI~~~~~a~L~~~~f~g----------atk~~r~~l~~GDlV~ArV~~~~~-~~~~~Ls~~  142 (238)
                      ||-.|+|.++.+  +.++|||+....|+||+.+..-          ..++....+++||-|...|..=.. ..-+.||+.
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~~di~~~~~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~~~~KGprlT~~   81 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTF   81 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSSSCEEEEGGGSCGGGCSSCCCSSSCCCGGGTCCTTCEEEEEEEECCBTTBCCEEESC
T ss_pred             CcEEEEEEEecCCceEEEEEeCCCccceeEecccceeeeccccccccccchhhhccCCCeEEEEEeecccCCCCceEEEE
Confidence            678999999954  8899999999999999865321          123455679999999999987432 234667753

>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=94.98  E-value=0.0091  Score=41.56  Aligned_cols=61  Identities=15%  Similarity=0.140  Sum_probs=49.3

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEe-eCCeEEEecCC----hhHHHHHHHHHHHhcc
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVG-LNGRVWVNAES----PSTVVLVSNAIMNSES  220 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG-~NG~IWi~~~~----~~~~~~i~~~i~~~e~  220 (238)
                      .++||+.++..++|+.++ .++.|.+.+++.|-|- .+|.+.+.+.+    +.....+...|+.+..
T Consensus         6 ~i~ip~~~ig~vIG~gG~-~Ik~i~~~tg~~I~Id~d~g~v~i~~~~~~~~~~a~~~a~~iI~aI~r   71 (84)
T d1tuaa1           6 YVKVKPERLGAVIGPRGE-VKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVVKAISL   71 (84)
T ss_dssp             EEECCGGGHHHHHCGGGH-HHHHHHHHHTEEEEEETTTTEEEEEESSTTSCHHHHHHHHHHHHHHHH
T ss_pred             EEEeCHHHcCeeecCCch-hHHHHHHHHCCEEEEEcCCCeEEEecCCccccHHHHHHHHHHHHHHhC
Confidence            479999999999999998 9999999999999995 88999998754    3444455556666553

>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=94.61  E-value=0.022  Score=37.84  Aligned_cols=56  Identities=9%  Similarity=0.255  Sum_probs=45.0

Q ss_pred             EEechhhhhhhcCCCCchhhHhhccccceEEEEeeC----CeEEEecCChhHHHHHHHHHHH
Q 026458          160 FETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN----GRVWVNAESPSTVVLVSNAIMN  217 (238)
Q Consensus       160 ~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N----G~IWi~~~~~~~~~~i~~~i~~  217 (238)
                      +.||+.+.++++|++++ .++.|.+.+++.|-+-..    ..|.|.+ +++.+..+.+.|..
T Consensus         9 i~V~~~~~~~iIG~~G~-~i~~I~~~tg~~I~i~~~~~~~~~v~I~G-~~~~v~~A~~~I~~   68 (71)
T d1viga_           9 INIDHKFHRHLIGKSGA-NINRIKDQYKVSVRIPPDSEKSNLIRIEG-DPQGVQQAKRELLE   68 (71)
T ss_dssp             EEECSSHHHHHTCSSCC-HHHHHHHHTCCEEECCCCCSSSEEEEEEE-SSHHHHHHHHHHHH
T ss_pred             EEECHHHhcccCCCCCc-hHHHHHHHhCCEEEeCCCCCCCCEEEEEC-CHHHHHHHHHHHHH
Confidence            78999999999999998 899999999999998543    3589998 66666666555554

>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=94.45  E-value=0.0012  Score=42.60  Aligned_cols=46  Identities=9%  Similarity=0.224  Sum_probs=15.2

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCCeEEEecCCh
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESP  205 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~  205 (238)
                      .++||+.++..++|+.+. .++.|.++++++|-+..+|.|+|.+.|.
T Consensus         6 ~i~Ip~~kig~vIG~GG~-~Ik~I~~~tga~I~i~ddg~v~I~a~~~   51 (54)
T d1e3ha4           6 TVKIPVDKIGEVIGPKRQ-MINQIQEDTGAEITIEDDGTIYIGAADG   51 (54)
T ss_dssp             ----------------------CHHHHSCCCC--------CCCCBSS
T ss_pred             EEEeCHHHeeEEECCccH-HHHHHHHHHCCEEEEeCCeEEEEEecCc
Confidence            478999999999999998 9999999999999999999999998764

>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=94.44  E-value=0.026  Score=38.57  Aligned_cols=52  Identities=4%  Similarity=0.058  Sum_probs=41.6

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC-------eEEEecCChhHHHHH
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG-------RVWVNAESPSTVVLV  211 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG-------~IWi~~~~~~~~~~i  211 (238)
                      .-+.||..++++++|++++ .++.|.+.+++.|-+-..+       .|+|.+ +.+.+..+
T Consensus        12 ~~i~Vp~~~~~~iIG~~G~-~i~~I~~~t~~~I~~~~~~~~~~~~~~i~I~G-~~e~v~~A   70 (84)
T d2ctla1          12 LSVTVDPKYHPKIIGRKGA-VITQIRLEHDVNIQFPDKDDGNQPQDQITITG-YEKNTEAA   70 (84)
T ss_dssp             EEEECCTTTHHHHSCSSSC-HHHHHHHHHTCEEECCCTTTCSSCSSEEEEES-CHHHHHHH
T ss_pred             EEEEECHHHHhhhcCCCch-hHHHHHHHhCCEEEECCCCCCCCCcceEEEEC-CHHHHHHH
Confidence            3588999999999999998 9999999999999984332       699997 45544333

>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=94.02  E-value=0.061  Score=37.29  Aligned_cols=57  Identities=14%  Similarity=0.229  Sum_probs=45.8

Q ss_pred             EEEEEEEecCceEEEEecC-CeeeeecCcccCCc-------------ccccccCcCCCCEEEEEEEecCCC
Q 026458           78 VLGIVVDCKADNFFVDIRG-PTIAFLPVLAFEGG-------------TRRNIPKFEIGSLLYVRVVKANPG  134 (238)
Q Consensus        78 VIG~V~~v~~~~~~VdI~~-~~~a~L~~~~f~ga-------------tk~~r~~l~~GDlV~ArV~~~~~~  134 (238)
                      -=|.|++++....+|.|.- ...|.+|.+.++..             .++.+..|+.||-|.++|.+++..
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            4589999999999999964 68999999877642             122345699999999999999764

>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=93.34  E-value=0.06  Score=36.17  Aligned_cols=55  Identities=7%  Similarity=0.247  Sum_probs=43.4

Q ss_pred             EEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC------eEEEecCChhHHHHHHHHHH
Q 026458          160 FETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG------RVWVNAESPSTVVLVSNAIM  216 (238)
Q Consensus       160 ~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG------~IWi~~~~~~~~~~i~~~i~  216 (238)
                      +.||..++..++|+++. .++.|.+.+++.|-+-.+.      .|+|.+ +++.+..+...|.
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 YKVPDGMVGFIIGRGGE-QISRIQQESGCKIQIAPDSGGLPERSCMLTG-TPESVQSAKRLLD   72 (79)
T ss_dssp             EEEEHHHHHHHHCSSSH-HHHHHHHHSCCEEEECSCCTTCSEEEEEEEE-CHHHHHHHHHHHH
T ss_pred             EEEChHhhcceECCCch-hHHHHHHHhCCEEEEcCCCCCCCceEEEEEe-CHHHHHHHHHHHH
Confidence            78999999999999998 9999999999999986533      399998 6655544444443

>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=92.90  E-value=0.042  Score=38.08  Aligned_cols=57  Identities=9%  Similarity=0.135  Sum_probs=43.8

Q ss_pred             eEEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC----eEEEecCChhHHHHHHHHHH
Q 026458          158 YMFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG----RVWVNAESPSTVVLVSNAIM  216 (238)
Q Consensus       158 ~~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG----~IWi~~~~~~~~~~i~~~i~  216 (238)
                      .-+.||+.+.++++|++++ .++.|.+.+++.|.+-.-|    .|-|.+ +.+.+..+...|.
T Consensus        12 ~~i~Vp~~~~~~iIG~~G~-~i~~I~~~tg~~I~~p~~~~~~~~v~I~G-~~~~V~~A~~~I~   72 (91)
T d2ctka1          12 IEVEVPFDLHRYVIGQKGS-GIRKMMDEFEVNIHVPAPELQSDIIAITG-LAANLDRAKAGLL   72 (91)
T ss_dssp             EEEECCHHHHHHHHCSSSH-HHHHHHHHTCCEEECCCTTTTCCEEEEEE-CHHHHHHHHHHHH
T ss_pred             EEEEECHHHHhHhcCCCch-hHHHHHHHhCCEEEECCCCCCcceEEEEC-CHHHHHHHHHHHH
Confidence            4588999999999999998 9999999999999995433    577776 5655544444443

>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=92.77  E-value=0.08  Score=35.76  Aligned_cols=55  Identities=7%  Similarity=0.215  Sum_probs=42.9

Q ss_pred             EEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC--------eEEEecCChhHHHHHHHHHH
Q 026458          160 FETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG--------RVWVNAESPSTVVLVSNAIM  216 (238)
Q Consensus       160 ~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG--------~IWi~~~~~~~~~~i~~~i~  216 (238)
                      +.||..++.+++|+.++ .++.|.+.+++.|.|-.+.        .|-|.+ +++.+..+...|.
T Consensus        12 i~Vp~~~~g~iIGk~G~-~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~   74 (81)
T d1x4ma1          12 IMIPASKAGLVIGKGGE-TIKQLQERAGVKMVMIQDGPQNTGADKPLRITG-DPYKVQQAKEMVL   74 (81)
T ss_dssp             EEECHHHHHHHSCSSSS-HHHHHHHHHTSEEEECCSCCCSSCSCEEEEEEE-CTTTHHHHHHHHH
T ss_pred             EEECHHHcCeeECCCCc-hHHHHHHHhCCeEEEccCCCCCCCCceEEEEEe-CHHHHHHHHHHHH
Confidence            57999999999999998 9999999999999996554        266776 5655555555444

>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=92.09  E-value=0.1  Score=34.39  Aligned_cols=54  Identities=13%  Similarity=0.196  Sum_probs=41.3

Q ss_pred             CCCcEEecCCccCCCCCCCCCceeecCcEEE-eCCEEEEEEeeEeEEec----CCeEEEEcc
Q 026458           10 LVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQ-ECDSVSVIKAGKLRFSK----PNKYWVESS   66 (238)
Q Consensus        10 ~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~-~~g~i~as~~G~v~~~~----~~~i~V~~~   66 (238)
                      +..+.|.||..|.---   +..+.+|.++.. .|..|+|.+.|.|+..+    .+.++|.|.
T Consensus         7 ~~Gq~V~~G~IivRQR---Gtk~~pG~nVg~GkD~TLfAl~~G~V~F~~~~~~~~~VsV~P~   65 (66)
T d1v8qa_           7 YEGQVVRAGNILVRQR---GTRFKPGKNVGMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPL   65 (66)
T ss_dssp             CTTCEECTTCEEEECS---SCSSEECTTEEECTTCCEEESSSEEEEEEECGGGCEEEEEEEC
T ss_pred             eCCEEEeCCeEEEEec---cCeEeCCCCeeecCCCcEEEeeeeEEEEEEeCCCCeEEEEEEC
Confidence            4678999999885321   126899999987 58999999999998752    236788875

>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=92.05  E-value=0.11  Score=34.33  Aligned_cols=54  Identities=4%  Similarity=0.056  Sum_probs=42.2

Q ss_pred             EEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC------eEEEecCChhHHHHHHHHH
Q 026458          160 FETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG------RVWVNAESPSTVVLVSNAI  215 (238)
Q Consensus       160 ~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG------~IWi~~~~~~~~~~i~~~i  215 (238)
                      +.||..++.+++|++++ -++.|.+.+++.|-+-.+.      .|.|.+ +++.+..+...|
T Consensus         8 i~VP~~~vg~iIG~~G~-~I~~I~~~sga~I~i~~~~~~~~~r~i~I~G-~~~~v~~A~~~I   67 (75)
T d1zzka1           8 VTIPKDLAGSIIGKGGQ-RIKQIRHESGASIKIDEPLEGSEDRIITITG-TQDQIQNAQYLL   67 (75)
T ss_dssp             EEEETTTGGGGTCGGGH-HHHHHHHHHCCEEEECCTTSCSSEEEEEEEE-CHHHHHHHHHHH
T ss_pred             EEEChHhcCeeECCCCc-hHHHHHhhcCCeEEEccCCCCCCceEEEEEe-CHHHHHHHHHHH
Confidence            67999999999999998 8999999999999995432      588887 666554444433

>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=90.56  E-value=0.17  Score=34.96  Aligned_cols=56  Identities=13%  Similarity=0.143  Sum_probs=42.2

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhcccc-ceEEEEeeCCeEEEecCChhHHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQL-SFEIAVGLNGRVWVNAESPSTVVLVSNAI  215 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~-~~ei~vG~NG~IWi~~~~~~~~~~i~~~i  215 (238)
                      -+.||..+.+.++|++++ .++.|.+.+ ++.|-+..+..+..=..+++.+..+.+.|
T Consensus        24 ~v~VP~~~h~~iIG~~G~-~I~~i~~~~~~v~I~~~~~~~~v~i~G~~~~ve~Ak~~I   80 (90)
T d2ctfa1          24 SVAAPSWLHRFIIGKKGQ-NLAKITQQMPKVHIEFTEGEDKITLEGPTEDVSVAQEQI   80 (90)
T ss_dssp             EEECCSTTHHHHHTTTTC-HHHHHHHHCSSSEEEECSSSCEEEEEECHHHHHHHHHHH
T ss_pred             EEEcCHHHHhhcCCCCch-hHHHHHHHcCCcEEeeCCCCceEEEeCCHHHHHHHHHHH
Confidence            378899999999999998 888887775 79999997776655445776555544433

>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=90.20  E-value=0.25  Score=32.27  Aligned_cols=56  Identities=14%  Similarity=0.211  Sum_probs=43.6

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC---------eEEEecCChhHHHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG---------RVWVNAESPSTVVLVSNAIM  216 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG---------~IWi~~~~~~~~~~i~~~i~  216 (238)
                      -+.||..++.+++|++++ .++.|.+.+++.|-+-.+.         .|-|.+ +++.+..+...|.
T Consensus         4 ~~~IP~~~vg~IIGk~G~-~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~   68 (71)
T d1j4wa2           4 NFIVPTGKTGLIIGKGGE-TIKSISQQSGARIELQRNPPPNADPNMKLFTIRG-TPQQIDYARQLIE   68 (71)
T ss_dssp             EEEEETTTHHHHHCGGGH-HHHHHHHHHCCEEEEECCCTTTSCTTEEEEEEEC-CHHHHHHHHHHHH
T ss_pred             EEEEChHhcceEECCCCc-ChHHHHhhcCcEEEEeecCCCCCCCCeEEEEEEe-CHHHHHHHHHHHH
Confidence            477999999999999998 9999999999999986432         456776 7766665555554

>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=89.88  E-value=0.24  Score=33.25  Aligned_cols=55  Identities=13%  Similarity=0.187  Sum_probs=41.9

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccc-cceEEEEeeCC----eEEEecCChhHHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQ-LSFEIAVGLNG----RVWVNAESPSTVVLVSNAI  215 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~-~~~ei~vG~NG----~IWi~~~~~~~~~~i~~~i  215 (238)
                      -+.||..++++++|++++ .++.|.+. +++.|-+...|    .|-|.+ +++.+..+.+.|
T Consensus        13 ~i~Vp~~~~~~iIGk~G~-~I~~I~~~~~~~~I~~~~~~~~~~~v~I~G-~~~~v~~A~~~I   72 (82)
T d2ctja1          13 EVSIPAKLHNSLIGTKGR-LIRSIMEECGGVHIHFPVEGSGSDTVVIRG-PSSDVEKAKKQL   72 (82)
T ss_dssp             EEECCHHHHHHHHCSSSH-HHHHHHHHHTSCEEECCCTTTTCCEEEEES-CHHHHHHHHHHH
T ss_pred             EEEECHHHHhhcCCCCCc-cHHHHHHHcCCcEEEEeCCCCCCceEEEeC-CHHHHHHHHHHH
Confidence            478999999999999998 88888655 68999987666    588887 665554444433

>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=89.76  E-value=0.2  Score=35.29  Aligned_cols=55  Identities=7%  Similarity=0.081  Sum_probs=42.4

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC--------eEEEecCChhHHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG--------RVWVNAESPSTVVLVSNAI  215 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG--------~IWi~~~~~~~~~~i~~~i  215 (238)
                      -+.||..++.+++|++++ .++.|.+.+++.|-|-.++        .|-|.+ +++.+..+...|
T Consensus        18 ~i~IP~~~vg~vIGk~G~-~Ik~I~~~tga~I~i~~~~~~~~~~~r~v~I~G-~~~~v~~A~~~I   80 (104)
T d1we8a_          18 QLSVPQRSVGRIIGRGGE-TIRSICKASGAKITCDKESEGTLLLSRLIKISG-TQKEVAAAKHLI   80 (104)
T ss_dssp             EEEEETTTHHHHHTTTSH-HHHHHHHHHCCEEEECCSSCCSSSSEEEEEEEE-EHHHHHHHHHHH
T ss_pred             EEEECHHHhcceECCCCc-chHHHHHHcCCEEEECCCCCCCCCCccEEEEEe-CHHHHHHHHHHH
Confidence            378999999999999998 9999999999999995543        466776 665544444444

>d2ctea1 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=89.75  E-value=0.11  Score=35.00  Aligned_cols=56  Identities=7%  Similarity=0.170  Sum_probs=42.4

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEE----eeCCeEEEecCChhHHHHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAV----GLNGRVWVNAESPSTVVLVSNAIM  216 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~v----G~NG~IWi~~~~~~~~~~i~~~i~  216 (238)
                      -+.||..++++++|+++. .++.|.+.+++.|-+    ..+-.|-|.+ +++.+..+.+.|+
T Consensus        13 ~i~Ip~~~~~~iIG~~G~-~i~~I~~~tg~~I~~p~~~~~~~~v~I~G-~~~~v~~A~~~I~   72 (81)
T d2ctea1          13 TVAIPKEHHRFVIGKNGE-KLQDLELKTATKIQIPRPDDPSNQIKITG-TKEGIEKARHEVL   72 (81)
T ss_dssp             EEECCTTTHHHHHCSSSC-HHHHHHHHTTCCCBCCCTTSSCCEEEEEE-CHHHHHHHHHHHH
T ss_pred             EEEECHHHHhhccCCCCh-hHHHHHHHhCCEEEECCCCCCCCEEEEEe-CHHHHHHHHHHHH
Confidence            478999999999999998 899999999999987    3345566776 6655555544443

>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=89.22  E-value=0.23  Score=32.52  Aligned_cols=55  Identities=4%  Similarity=0.039  Sum_probs=44.1

Q ss_pred             EEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC----eEEEecCChhHHHHHHHHHH
Q 026458          160 FETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG----RVWVNAESPSTVVLVSNAIM  216 (238)
Q Consensus       160 ~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG----~IWi~~~~~~~~~~i~~~i~  216 (238)
                      +.||..++..++|++++ .++.|.+.+++.|-+-.++    .|-|.+ +++.+..+.+.|.
T Consensus         8 i~vp~~~~g~IIGk~G~-~I~~I~~~tga~I~i~~~~~~er~v~I~G-~~~~v~~A~~~I~   66 (71)
T d2axya1           8 LLMHGKEVGSIIGKKGE-SVKKMREESGARINISEGNCPERIITLAG-PTNAIFKAFAMII   66 (71)
T ss_dssp             EEEEHHHHHHHHCGGGH-HHHHHHHHHCCEEEECSSCCSEEEEEEEE-CHHHHHHHHHHHH
T ss_pred             EEECHHHcCeEECCCCh-hHHHHHHHhCCEEEEcCCCCCcceEEEEE-CHHHHHHHHHHHH
Confidence            67999999999999998 9999999999999998887    455776 6766555555443

>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=88.91  E-value=0.18  Score=34.70  Aligned_cols=55  Identities=16%  Similarity=0.320  Sum_probs=41.1

Q ss_pred             CCCCcEEecCCccCCCCCCCCCceeecCcEEE-eCCEEEEEEeeEeEEecC----CeEEEEcc
Q 026458            9 NLVDKIVVPGDVVLDLSSMTNQTIKLGGGLRQ-ECDSVSVIKAGKLRFSKP----NKYWVESS   66 (238)
Q Consensus         9 ~~~~~iV~PGd~l~~~~~~~~~~~~~G~G~y~-~~g~i~as~~G~v~~~~~----~~i~V~~~   66 (238)
                      -+..+.|.||+.|.---   +-.|.+|.++.. .|..|+|.+.|.|..++.    +.++|.|.
T Consensus        24 ~~~Gq~V~~G~IivRQR---Gtk~hpG~nVg~GkD~TLfA~~~G~V~F~k~~~~rk~V~V~p~   83 (84)
T d2zjrt1          24 KFGGEVVKAGNILVRQR---GTKFKAGQGVGMGRDHTLFALSDGKVVFINKGKGARFISIEAA   83 (84)
T ss_dssp             SCTTCEECSSCEEECCS---SSSSEECTTEECCTTSCEEESSCEEEEEEEETTTEEEEEECCC
T ss_pred             ECCCEEEeCCcEEEEec---CceEcCCCCccccCCCcEEEeeceEEEEEEcCCCCEEEEEEeC
Confidence            35678999999886421   126899999986 588999999999987531    36777764

>d1j4wa1 d.51.1.1 (A:1-74) 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=88.86  E-value=0.29  Score=32.05  Aligned_cols=52  Identities=4%  Similarity=0.080  Sum_probs=40.2

Q ss_pred             EEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC------eEEEecCChhHHHHHHH
Q 026458          160 FETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG------RVWVNAESPSTVVLVSN  213 (238)
Q Consensus       160 ~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG------~IWi~~~~~~~~~~i~~  213 (238)
                      +.||..++..++|++++ .++.|.+.+++.|-+-.+.      .+-|.+ +++.+..+.+
T Consensus         7 i~VP~~~vg~iIGk~G~-~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G-~~~~v~~A~~   64 (74)
T d1j4wa1           7 VPIPRFAVGIVIGRNGE-MIKKIQNDAGVRIQFKPDDGTTPERIAQITG-PPDRAQHAAE   64 (74)
T ss_dssp             EEEEHHHHHHHHCGGGH-HHHHHHHHHCCEEEEECCTTSCSEEEEEEEE-CHHHHHHHHH
T ss_pred             EEeCHHHCCeeECCCCc-HHHHHHHHcCCEEEeccCCCCCCeeEEEEEe-CHHHHHHHHH
Confidence            67899999999999998 9999999999999886443      477776 5654444433

>d1dtja_ d.51.1.1 (A:) Neuro-oncological ventral antigen 2, nova-2, 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: Neuro-oncological ventral antigen 2, nova-2, KH3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.49  E-value=0.57  Score=30.64  Aligned_cols=53  Identities=19%  Similarity=0.215  Sum_probs=41.3

Q ss_pred             EEEechhhhhhhcCCCCchhhHhhccccceEEEEeeCC---------eEEEecCChhHHHHHHH
Q 026458          159 MFETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLNG---------RVWVNAESPSTVVLVSN  213 (238)
Q Consensus       159 ~~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG---------~IWi~~~~~~~~~~i~~  213 (238)
                      =+.||..++..++|++++ .++.|.+.+++.|-+-.++         .|-|.+ +++.+..+..
T Consensus         6 ~i~VP~~~vg~iIGk~G~-~Ik~I~~~sga~I~i~~~~~~~~~~~~r~v~I~G-~~~~v~~A~~   67 (74)
T d1dtja_           6 EMAVPENLVGAILGKGGK-TLVEYQELTGARIQISKKGEFLPGTRNRRVTITG-SPAATQAAQY   67 (74)
T ss_dssp             EEEEETTTHHHHHCSTTH-HHHHHHHHHCCEEEECCTTCCSTTCCEEEEEEEE-SHHHHHHHHH
T ss_pred             EEEeCHHHcceeECCCCh-hHHHHHHHcCCEEEEccCCCCCCCCCceEEEEEe-CHHHHHHHHH
Confidence            367999999999999998 9999999999999987655         367776 5654444333

>d1wvna1 d.51.1.1 (A:5-74) Poly(RC)-binding protein 1 {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 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.09  E-value=0.52  Score=30.56  Aligned_cols=54  Identities=15%  Similarity=0.257  Sum_probs=40.7

Q ss_pred             EEechhhhhhhcCCCCchhhHhhccccceEEEEeeC-----C-eEEEecCChhHHHHHHHHH
Q 026458          160 FETSTGLSRMLLSSPTCPVLEELGKQLSFEIAVGLN-----G-RVWVNAESPSTVVLVSNAI  215 (238)
Q Consensus       160 ~~V~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~N-----G-~IWi~~~~~~~~~~i~~~i  215 (238)
                      +.||..++..++|++++ .++.|.+.+++.|-+-.+     - .|-|.+ +++....+...|
T Consensus         6 i~VP~~~vg~iIGk~G~-~I~~I~~~tga~I~i~~~~~~~~~r~v~I~G-~~~~v~~A~~~I   65 (70)
T d1wvna1           6 LTIPNNLIGCIIGRQGA-NINEIRQMSGAQIKIANPVEGSSGRQVTITG-SAASISLAQYLI   65 (70)
T ss_dssp             EEEEGGGHHHHHCGGGH-HHHHHHHHHCCEEEECCCCTTCSEEEEEEEE-CHHHHHHHHHHH
T ss_pred             EEEChHhcceeECCCCh-HHHHHHHHcCcEEEEcCCCCCCCcEEEEEEe-CHHHHHHHHHHH
Confidence            68999999999999998 999999999999998442     2 366666 565544444433

>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=85.89  E-value=0.45  Score=33.84  Aligned_cols=62  Identities=8%  Similarity=-0.002  Sum_probs=43.7

Q ss_pred             hhcCCCCchhhHhhccccceEEEEeeCCeEEEecCChhHHHHHHHHHHHhcc-CCHHHHHHHHHHH
Q 026458          169 MLLSSPTCPVLEELGKQLSFEIAVGLNGRVWVNAESPSTVVLVSNAIMNSES-LSAVQQKIMVDKL  233 (238)
Q Consensus       169 rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~~~~~i~~~i~~~e~-lt~~~~~~~~~~~  233 (238)
                      |++|+.+. .++.|.+.++|+|.|.-++..-+.  +++....+-.+|..+-. -..-.+-.++++.
T Consensus        26 rIIG~gGk-tik~Ie~~Tg~~I~I~d~~v~iig--~~e~i~~A~~~Ie~li~~~e~g~VY~~le~~   88 (104)
T d1tuaa2          26 RIIGEGGR-ARRTIEEMTDTYINVGEYEVAIIG--DYERAMAAKQAIEMLAEGRMHSTVYRHLERI   88 (104)
T ss_dssp             HHHCGGGH-HHHHHHHHHTCEEEECSSEEEEEE--EHHHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             ceeCCCcH-HHHHHHHHHCCeEEEeCCeEEEEE--CchhHHHHHHHHHHHHcCCCccHHHHHHHHH
Confidence            48898887 999999999999999999877664  56666777777766554 2223344444443