Citrus Sinensis ID: 020356

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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-------240-------250-------260-------270-------280-------290-------300-------310-------320-------
Protein Sequence
MRNLQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIAKCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLDIHDMLGSEFYVLVAESEAERRSLSKRKR
Secondary Structure (PSIPRED)
cccccccccccccccHHHHHHHHHHcccccccccEEEcccccccccccccccccEEEcccEEEEEEEEEEEEEccEEEEEEcccccccccccEEEEEEEEEcccEEEEEEccccccEEccccccccccccccccHHHHHHHHcccccccEEEEEEEEEcccccEEEEEcccccccccccEEEEEcccccccccccccccccccEEEEEEEccEEEEEEcccccccccccccccHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccEccccccccccccHHHHHHHHHccccccccEEccccEEEcccccccccccEEEcccEEEEEEEEEEEEEcEEEEEEEcccccccccccEEEEEEEEEcccEEEEEccccccEEEEEHccccccccEEcccHHHHHHHHHHHHcccEEEEEEEEEcccccEEEEEEccccccccccEEEEEcccHEEcccccEEEccccccEEEEEcccEEEEEccccccHHHHccHHcccccccccHHHHcHHccccccccccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHccccHHHHccHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MRNLQLSFNQTQKVRLEKALERLEslssksnpnscvtvgdtipvyedgilkghgtsdqkgELAATVCGVVERINKLIYVRALRarykpetgdiVIGRVIEVVPKRWKLEINFTQDAILMLSsmnlpdgiQRRRTAVDElnmrsiftenDLVCAEVrssqgdgslQLQARNQKygklergqlltvdpylvKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKmvvdqgsnseQLIAKcdknsmdldeqdgtctpreARQNICRIANAIRVLSRLGFNITVEVILETVnlsnslnldihdMLGSEFYVLVAESEAERRSLSKRKR
Flexible Loop (DISEMBL)
mrnlqlsfnqtQKVRLEKALERleslssksnpnscvtvGDTIPVYEDGILKghgtsdqkGELAATVCGVVERINKLIYVRAlrarykpetgdivigrvievvpkrwKLEINFTQDAILMlssmnlpdgIQRRRTAVDELNMRSIFTENDLVCAEVRssqgdgslqLQARNqkygklergqlltvdpYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIAKCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLDIHDMLGSEFYVLVAeseaerrslskrkr
Low Complexity Region (SEG)
MRNLQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIAKCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLDIHDMLGSEFYVLVAESEAERRSLSKRKR
Disordered region (IsUnstruct)
**********************************CVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEV*****************YGKLERGQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMV*********************************RQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLDIHDMLGSEFYVLVA**************
Disordered Region (DISOPRED)
***********************************VTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEAR******************************TCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLDIHDMLGSEFYVLVAESE***********
Disordered Region (DISEMBL)
MRNLQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIAKCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLDIHDMLGSEFYVLVAES************
Disordered Region (DISPRO)
**********TQKVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHV*******************************DGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLDIHDMLGSEFYVLVAESEAERRSL*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRNLQxxxxxxxxxxxxxxxxxxxxxxxxSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIAKCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLDIHDMLGSEFYVLVAESEAERRSLSKRKR
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	327	2.2.26 [Sep-21-2011]
Q09704	329	Exosome complex component	yes	no	0.688	0.683	0.440	2e-48
Q8VBV3	293	Exosome complex component	yes	no	0.645	0.720	0.483	3e-48
Q2KID0	293	Exosome complex component	yes	no	0.617	0.689	0.485	1e-46
Q13868	293	Exosome complex component	yes	no	0.617	0.689	0.490	2e-46
P38792	359	Exosome complex component	yes	no	0.788	0.718	0.378	4e-41
Q5JIR5	257	Probable exosome complex	yes	no	0.547	0.696	0.256	5e-11
Q9V120	265	Probable exosome complex	yes	no	0.553	0.683	0.253	1e-09
O59221	265	Probable exosome complex	yes	no	0.553	0.683	0.248	7e-09
A1RXQ7	237	Probable exosome complex	yes	no	0.418	0.578	0.263	3e-08
Q8U0L8	264	Probable exosome complex	yes	no	0.525	0.651	0.237	4e-08

>sp|Q09704|RRP4_SCHPO Exosome complex component rrp4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rrp4 PE=3 SV=1

 Score =  192 bits (489), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 103/234 (44%), Positives = 142/234 (60%), Gaps = 9/234 (3%)

Query: 49  ILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKL 108
            ++GHGT  + G + A+V G V+R+NKLI V+ LR++Y PE GD++IG++ EV PKRWK+
Sbjct: 70  FMRGHGTYFEDGGIYASVAGSVQRVNKLISVKPLRSKYVPEIGDLIIGKIAEVQPKRWKV 129

Query: 109 EINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQA 168
           +I   Q+A+LMLSS+NLP GIQRR+   DEL MRS F E DL+ AEV+    DGS+ +  
Sbjct: 130 DIGAKQNAVLMLSSINLPGGIQRRKLETDELQMRSFFQEGDLLVAEVQQYFSDGSVSIHT 189

Query: 169 RNQKYGKLERGQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVV 228
           R+ KYGKL  G  L V P LV R K H + L   G+D+I+  NGY+W+ +H E +   V 
Sbjct: 190 RSLKYGKLRNGVFLKVPPALVVRSKSHAYALAG-GVDIILSVNGYVWVSKHNENQHSSVS 248

Query: 229 DQGSNSEQLIAKCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNIT 282
                 E   A     S + DE DG       R NI R++  I+ L+     +T
Sbjct: 249 ITRLEEE---ASESIYSNENDEIDGYT-----RLNISRVSICIKGLASRSLPLT 294

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. rrp4 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|Q8VBV3|EXOS2_MOUSE Exosome complex component RRP4 OS=Mus musculus GN=Exosc2 PE=2 SV=1

 Score =  192 bits (488), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 103/213 (48%), Positives = 138/213 (64%), Gaps = 2/213 (0%)

Query: 13  KVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVER 72
           ++RL KA + L     + +    V  GDTI   + G ++GHGT   + +L A+V G VER
Sbjct: 4   EMRLPKARKPLSESLGRDSKKHLVVPGDTITT-DTGFMRGHGTYMGEEKLIASVAGSVER 62

Query: 73  INKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRR 132
           +NKLI V+AL+ RY  E GDIV+GR+ EV  KRWK+E N   D++L+LSSMNLP G  RR
Sbjct: 63  VNKLICVKALKTRYNGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRR 122

Query: 133 RTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRR 192
           R+A DEL MR    E DL+ AEV++   DG++ L  R+ KYGKL +G L+ V P LVKR+
Sbjct: 123 RSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQ 182

Query: 193 KQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDK 225
           K HFH L   G  +I+G NG+IWI    E +D+
Sbjct: 183 KTHFHDL-PCGASVILGNNGFIWIYPTPEHKDE 214

Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and 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. EXOSC2 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC4 and EXOSC7.

Mus musculus (taxid: 10090)

>sp|Q2KID0|EXOS2_BOVIN Exosome complex component RRP4 OS=Bos taurus GN=EXOSC2 PE=2 SV=1

 Score =  187 bits (474), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 99/204 (48%), Positives = 133/204 (65%), Gaps = 2/204 (0%)

Query: 13  KVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVER 72
           ++RL  A + L     + +    V  GDTI   + G ++GHGT   + +L A+V G VER
Sbjct: 4   EMRLPVARKPLSESLGRESKKHLVVPGDTI-TTDTGFMRGHGTYMGEEKLIASVAGSVER 62

Query: 73  INKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRR 132
           +NKLI V+AL+ RY  E GDIV+GR+ EV  KRWK+E N   D++L+LSSMNLP G  RR
Sbjct: 63  VNKLICVKALKTRYNGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRR 122

Query: 133 RTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRR 192
           R+A DEL MR    E DL+ AEV++   DG++ L  R+ KYGKL +G L+ V P LVKR+
Sbjct: 123 RSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQ 182

Query: 193 KQHFHHLEEYGIDLIIGCNGYIWI 216
           K HFH L   G  +I+G NG+IW+
Sbjct: 183 KTHFHDL-PCGASVILGNNGFIWV 205

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. EXOSC2 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC4 and EXOSC7.

Bos taurus (taxid: 9913)

>sp|Q13868|EXOS2_HUMAN Exosome complex component RRP4 OS=Homo sapiens GN=EXOSC2 PE=1 SV=2

 Score =  186 bits (473), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 100/204 (49%), Positives = 132/204 (64%), Gaps = 2/204 (0%)

Query: 13  KVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVER 72
           ++RL  A + L     +      V  GDTI   + G ++GHGT   + +L A+V G VER
Sbjct: 4   EMRLPVARKPLSERLGRDTKKHLVVPGDTI-TTDTGFMRGHGTYMGEEKLIASVAGSVER 62

Query: 73  INKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRR 132
           +NKLI V+AL+ RY  E GDIV+GR+ EV  KRWK+E N   D++L+LSSMNLP G  RR
Sbjct: 63  VNKLICVKALKTRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRR 122

Query: 133 RTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRR 192
           R+A DEL MR    E DL+ AEV++   DG++ L  R+ KYGKL +G L+ V P LVKR+
Sbjct: 123 RSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQ 182

Query: 193 KQHFHHLEEYGIDLIIGCNGYIWI 216
           K HFH L   G  +I+G NG+IWI
Sbjct: 183 KTHFHDL-PCGASVILGNNGFIWI 205

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. EXOSC2 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC4 and EXOSC7.

Homo sapiens (taxid: 9606)

>sp|P38792|RRP4_YEAST Exosome complex component RRP4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RRP4 PE=1 SV=1

 Score =  169 bits (427), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 110/291 (37%), Positives = 154/291 (52%), Gaps = 33/291 (11%)

Query: 27  SSKSNPNS-CVTVGDTI---PVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRAL 82
           +SKS  +S  VT G+ +   P++    ++GHGT        ++V G V R+N+L+ V  L
Sbjct: 45  ASKSESDSQIVTPGELVTDDPIW----MRGHGTYFLDNMTYSSVAGTVSRVNRLLSVIPL 100

Query: 83  RARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMR 142
           + RY PETGD V+GR+ EV  KRWK++I   Q A+LML S+NLP GI RR++  DEL MR
Sbjct: 101 KGRYAPETGDHVVGRIAEVGNKRWKVDIGGKQHAVLMLGSVNLPGGILRRKSESDELQMR 160

Query: 143 SIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRRKQHFHHLEEY 202
           S   E DL+ AEV+S   DGS  L  R+ KYGKL  G    V   L+ R K H H+L   
Sbjct: 161 SFLKEGDLLNAEVQSLFQDGSASLHTRSLKYGKLRNGMFCQVPSSLIVRAKNHTHNLPG- 219

Query: 203 GIDLIIGCNGYIWIGEHVE---ARDKMVVDQGSNSEQLIAKCDKNSMDL----------- 248
            I +++G NGYIW+ +  +   ARD       +NS  + +     ++ L           
Sbjct: 220 NITVVLGVNGYIWLRKTSQMDLARD---TPSANNSSSIKSTGPTGAVSLNPSITRLEEES 276

Query: 249 ------DEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLS 293
                 DE D + +    RQ ICR AN I+ L+     IT + I+     S
Sbjct: 277 SWQIYSDENDPSIS-NNIRQAICRYANVIKALAFCEIGITQQRIVSAYEAS 326

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. RRP4 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|Q5JIR5|ECR1_PYRKO Probable exosome complex RNA-binding protein 1 OS=Pyrococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) GN=TK1635 PE=3 SV=1

 Score = 68.9 bits (167), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 52/203 (25%), Positives = 98/203 (48%), Gaps = 24/203 (11%)

Query: 52  GHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEIN 111
           G GT  +   + +TV G+VE    +I V  L   Y PE GD V+G++++V    W ++I 
Sbjct: 26  GRGTFREGNAIYSTVIGLVEIRGNVIRVIPLEGPYIPEVGDNVLGKIVDVKFSSWTVDIG 85

Query: 112 FTQDAILMLSSMNLPDGIQRRRTAVDEL--NMRSIFTENDLVCAEVRSSQGDGSLQLQAR 169
               A     S+ + D ++ R   +D L  ++R IF   D++ A+V++      + L  +
Sbjct: 86  APYQA-----SLRVQDAVEER---IDLLKTDLRKIFDIGDIIYAKVKAFNEVNQIDLTTK 137

Query: 170 NQKY--GKLERGQLLTVDPY----LVKRRKQHFHHLEEY-GIDLIIGCNGYIWIGEHVEA 222
              +  G L  GQL+T+ P     L+ +     + ++   G  +I+G NG++W+    + 
Sbjct: 138 GMPFKGGPLRGGQLVTITPSKVPRLIGKGGSMINMIKTLTGTRIIVGQNGWVWVSGKNDE 197

Query: 223 RDKMVVDQGSNSEQLIAKCDKNS 245
            +++ ++        I K D+ S
Sbjct: 198 LERLAIEA-------ILKVDRES 213

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

Pyrococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (taxid: 69014)

>sp|Q9V120|ECR1_PYRAB Probable exosome complex RNA-binding protein 1 OS=Pyrococcus abyssi (strain GE5 / Orsay) GN=PYRAB06090 PE=3 SV=1

 Score = 64.3 bits (155), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 51/201 (25%), Positives = 95/201 (47%), Gaps = 20/201 (9%)

Query: 52  GHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEIN 111
           G GT  +   + +TV G+V+     I V  L   Y PE GD VIG++++V    W ++I 
Sbjct: 26  GRGTFREGSRIYSTVIGLVDIKGNTIRVIPLEGPYIPEVGDNVIGKIVDVKFSSWVVDIG 85

Query: 112 FTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQ 171
               A L +      + I   RT     ++R  F   D++ A+V++     ++ L  +  
Sbjct: 86  APYPANLKIQDFT-DEKIDLLRT-----DLRKFFDIGDIIYAKVKAITEVNNIDLTTKGM 139

Query: 172 KY--GKLERGQLLTVDPY----LVKRRKQHFHHLEEYGID-LIIGCNGYIWIGEHVEARD 224
            +  G L+ GQ++ + P     ++ R     + +++  +  +I+G NG+IW+    +A +
Sbjct: 140 PFNGGPLKGGQIVKITPSRVPRVIGRGGSMINMIKKLTMTRIIVGQNGWIWVSGKNDALE 199

Query: 225 KMVVDQGSNSEQLIAKCDKNS 245
           K+ ++        I K DK S
Sbjct: 200 KLAIEA-------ILKIDKES 213

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

Pyrococcus abyssi (strain GE5 / Orsay) (taxid: 272844)

>sp|O59221|ECR1_PYRHO Probable exosome complex RNA-binding protein 1 OS=Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) GN=PH1551 PE=3 SV=1

 Score = 61.6 bits (148), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 50/201 (24%), Positives = 94/201 (46%), Gaps = 20/201 (9%)

Query: 52  GHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEIN 111
           G GT  +   + +TV G+V+     I V  L   Y PE GD VIG++++V    W ++I 
Sbjct: 26  GRGTFREGSRIYSTVIGLVDIKGNTIRVIPLEGPYIPEVGDNVIGKIVDVKFSSWVVDIG 85

Query: 112 FTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQ 171
               A L +      + I   RT     ++R  F   D++  +V++     ++ L  +  
Sbjct: 86  APYLANLKIQDFT-DEKIDLLRT-----DLRKFFDIGDIIYGKVKAITEVNNIDLTTKGM 139

Query: 172 KY--GKLERGQLLTVDPY----LVKRRKQHFHHLEEYGID-LIIGCNGYIWIGEHVEARD 224
            +  G L+ GQ++ + P     ++ R     + +++  +  +I+G NG+IW+    EA +
Sbjct: 140 PFNGGPLKGGQIVKITPSRVPRVIGRGGSMINMIKKLTMTRIIVGQNGWIWVNGKNEALE 199

Query: 225 KMVVDQGSNSEQLIAKCDKNS 245
           K+ ++        I K D+ S
Sbjct: 200 KLAIEA-------ILKIDRES 213

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

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (taxid: 70601)

>sp|A1RXQ7|ECR1_THEPD Probable exosome complex RNA-binding protein 1 OS=Thermofilum pendens (strain Hrk 5) GN=Tpen_0582 PE=3 SV=1

 Score = 59.7 bits (143), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 39/148 (26%), Positives = 72/148 (48%), Gaps = 11/148 (7%)

Query: 74  NKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRR 133
           N+++ V  L+ +Y P  G IV+G+V+++    W+++IN    A+L +S       +  R 
Sbjct: 55  NRVVKVIPLKGKYFPVEGHIVVGKVVDIGFTSWEVDINSPYVAVLPVSE------VTSRP 108

Query: 134 TAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPY----LV 189
             +    +  I    DL+ A++ S        L  +  + GK+ RG L+ + P     ++
Sbjct: 109 VTISRNELSRILDVGDLILAKIVSFDLSKDPVLTIKESRLGKIPRGTLVEIPPQKVPRVI 168

Query: 190 KRRKQHFHHLEE-YGIDLIIGCNGYIWI 216
            RR      +E+  G+ LI+G NG I +
Sbjct: 169 GRRGSMVSMIEDLLGVKLIVGQNGRIVV 196

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

Thermofilum pendens (strain Hrk 5) (taxid: 368408)

>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 = 59.3 bits (142), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 44/185 (23%), Positives = 86/185 (46%), Gaps = 13/185 (7%)

Query: 52  GHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEIN 111
           G GT  +   + +TV G+V+     I V  L   Y PE GD V+G++++V    W ++I 
Sbjct: 26  GRGTFKEGSRIYSTVIGLVDIKGNTIRVIPLEGPYIPEVGDNVLGKIVDVKFSSWTVDIG 85

Query: 112 FTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQ 171
               A L +      + I   RT     ++R  F   D++ A+V+      +++L  +  
Sbjct: 86  SPYSATLKIQDYT-DEKIDLLRT-----DLRKFFDIGDIIYAKVKGINEVNNIELTTKGM 139

Query: 172 KY--GKLERGQLLTVD----PYLVKRRKQHFHHLEEYGID-LIIGCNGYIWIGEHVEARD 224
            +  G L  GQ++ +     P ++ +     + +++     +I+G NG+IWI       +
Sbjct: 140 PFNGGPLRGGQIIKITSSKVPRVIGKGGSMINMIKKLTQSRIIVGQNGWIWISSKNPELE 199

Query: 225 KMVVD 229
           K+ ++
Sbjct: 200 KLAIE 204

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)

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	327
225436884	330	PREDICTED: exosome complex component rrp	1.0	0.990	0.720	1e-140
296086683	320	unnamed protein product [Vitis vinifera]	0.972	0.993	0.713	1e-137
449453800	327	PREDICTED: exosome complex component RRP	0.987	0.987	0.702	1e-129
224072941	320	predicted protein [Populus trichocarpa]	0.969	0.990	0.679	1e-128
356572158	327	PREDICTED: exosome complex component RRP	0.996	0.996	0.682	1e-128
255567640	322	rrp4, putative [Ricinus communis] gi|223	0.975	0.990	0.675	1e-127
357478895	327	Exosome complex exonuclease RRP4 [Medica	0.996	0.996	0.682	1e-127
15218790	322	exosome complex component RRP4 [Arabidop	0.975	0.990	0.669	1e-127
297843148	322	ATRRP4 [Arabidopsis lyrata subsp. lyrata	0.975	0.990	0.669	1e-125
222619320	428	hypothetical protein OsJ_03610 [Oryza sa	0.911	0.696	0.650	1e-117

>gi|225436884|ref|XP_002271258.1| PREDICTED: exosome complex component rrp4-like [Vitis vinifera]

 Score =  505 bits (1301), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 237/329 (72%), Positives = 283/329 (86%), Gaps = 2/329 (0%)

Query: 1   MRNLQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPV-YEDGILKGHGTSDQK 59
           MR  QLS NQTQK+RL++ALE+LESLSSKSN N+ V V DTIPV YEDG+LKGHGT D  
Sbjct: 1   MRGFQLSLNQTQKLRLQRALEQLESLSSKSNSNASVAVADTIPVNYEDGVLKGHGTLDLD 60

Query: 60  GELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILM 119
           GE+ AT+CGVVER+NKL+Y+R LRARYKPETGDI++GRV E+ PKRW+L+INF+QDA+LM
Sbjct: 61  GEVVATLCGVVERVNKLVYIRTLRARYKPETGDIIVGRVTEIAPKRWRLDINFSQDAVLM 120

Query: 120 LSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERG 179
           LSSMNLPDGIQRRRTAVDELNMRSIF END+VCAEVR  Q DGSL LQAR+QKYGKLERG
Sbjct: 121 LSSMNLPDGIQRRRTAVDELNMRSIFEENDIVCAEVRGFQHDGSLHLQARSQKYGKLERG 180

Query: 180 QLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIA 239
           Q+LT+ PYLVKRRKQH H+LEE+G+DLI+GCNG+IW+GEHVEA+  ++ DQ   +EQL  
Sbjct: 181 QVLTISPYLVKRRKQHLHYLEEFGVDLILGCNGFIWVGEHVEAKGILIEDQTDKAEQLNT 240

Query: 240 KCDKNS-MDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNL 298
           K   ++ M L+EQ+ T T  E RQNICRIANA+RVL+ LGF++TVEVI ETVNLS+SLNL
Sbjct: 241 KSSSSTFMSLEEQERTYTSLETRQNICRIANAVRVLANLGFSVTVEVIKETVNLSSSLNL 300

Query: 299 DIHDMLGSEFYVLVAESEAERRSLSKRKR 327
           DIH+MLGSEFYVLVAE EA R+S+  +K+
Sbjct: 301 DIHEMLGSEFYVLVAEGEATRKSMFTKKK 329

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296086683|emb|CBI32318.3| unnamed protein product [Vitis vinifera]

 Score =  494 bits (1272), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 234/328 (71%), Positives = 276/328 (84%), Gaps = 10/328 (3%)

Query: 1   MRNLQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPV-YEDGILKGHGTSDQK 59
           MR  QLS NQTQK+RL++ALE+LESLSSKSN N+ V V DTIPV YEDG+LKGHGT D  
Sbjct: 1   MRGFQLSLNQTQKLRLQRALEQLESLSSKSNSNASVAVADTIPVNYEDGVLKGHGTLDLD 60

Query: 60  GELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILM 119
           GE+ AT+CGVVER+NKL+Y+R LRARYKPETGDI++GRV E+ PKRW+L+INF+QDA+LM
Sbjct: 61  GEVVATLCGVVERVNKLVYIRTLRARYKPETGDIIVGRVTEIAPKRWRLDINFSQDAVLM 120

Query: 120 LSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERG 179
           LSSMNLPDGIQRRRTAVDELNMRSIF END+VCAEVR  Q DGSL LQAR+QKYGKLERG
Sbjct: 121 LSSMNLPDGIQRRRTAVDELNMRSIFEENDIVCAEVRGFQHDGSLHLQARSQKYGKLERG 180

Query: 180 QLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIA 239
           Q+LT+ PYLVKRRKQH H+LEE+G+DLI+GCNG+IW+GEHVEA+  ++ DQ   +EQL  
Sbjct: 181 QVLTISPYLVKRRKQHLHYLEEFGVDLILGCNGFIWVGEHVEAKGILIEDQTDKAEQLNT 240

Query: 240 KCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLD 299
           K  K          T T  E RQNICRIANA+RVL+ LGF++TVEVI ETVNLS+SLNLD
Sbjct: 241 KSSKR---------TYTSLETRQNICRIANAVRVLANLGFSVTVEVIKETVNLSSSLNLD 291

Query: 300 IHDMLGSEFYVLVAESEAERRSLSKRKR 327
           IH+MLGSEFYVLVAE EA R+S+  +K+
Sbjct: 292 IHEMLGSEFYVLVAEGEATRKSMFTKKK 319

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449453800|ref|XP_004144644.1| PREDICTED: exosome complex component RRP4-like [Cucumis sativus]

 Score =  467 bits (1202), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 231/329 (70%), Positives = 270/329 (82%), Gaps = 6/329 (1%)

Query: 1   MRNLQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPV-YEDGILKGHGTSDQK 59
           M+ LQLS N TQK+RLE+A ERL+SLSSK N ++ V V DTIP+ YEDG+LKGHGT D  
Sbjct: 1   MKGLQLSLNHTQKIRLERAQERLKSLSSKGNSDASVVVADTIPLNYEDGVLKGHGTLDLN 60

Query: 60  GELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILM 119
           GE+ A++CGVVER+NKLIYVRALRARYKPE GDIV+GRV EV PKRW+L+IN+ QDA+LM
Sbjct: 61  GEVVASICGVVERVNKLIYVRALRARYKPEVGDIVVGRVTEVAPKRWRLDINYCQDAVLM 120

Query: 120 LSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERG 179
           LSSMNLPDGIQRRRTAVDELNMRSIF END++CAEVR  Q DG L LQAR+QKYGKLERG
Sbjct: 121 LSSMNLPDGIQRRRTAVDELNMRSIFEENDVICAEVRGLQHDG-LHLQARSQKYGKLERG 179

Query: 180 QLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEAR--DKMVVDQGSNSEQL 237
           QLLTV PYL+KRRKQHFHHLE+YGIDLI+GCNG+IWIGEHV+ +  D M+ DQ    EQ 
Sbjct: 180 QLLTVSPYLIKRRKQHFHHLEQYGIDLILGCNGFIWIGEHVDPKVVDTMIEDQVDKPEQK 239

Query: 238 IAKCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLN 297
            +K +    +  ++    TP E RQNICR ANAIRVLS LGF +TVEVI+E VNLS SLN
Sbjct: 240 GSKFEGTFGNQVQE--VYTPLETRQNICRTANAIRVLSTLGFIMTVEVIMEIVNLSISLN 297

Query: 298 LDIHDMLGSEFYVLVAESEAERRSLSKRK 326
           +D+H+MLGSEF VL AE E ERRS SK++
Sbjct: 298 IDVHEMLGSEFCVLTAEKEVERRSSSKKR 326

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224072941|ref|XP_002303939.1| predicted protein [Populus trichocarpa] gi|222841371|gb|EEE78918.1| predicted protein [Populus trichocarpa]

 Score =  464 bits (1194), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 223/328 (67%), Positives = 276/328 (84%), Gaps = 11/328 (3%)

Query: 1   MRNLQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPVY-EDGILKGHGTSDQK 59
           MR +++S NQTQK+RL++AL++LESL  ++N N+ VTV DTIPV  ED ILKGHGTS++ 
Sbjct: 1   MRGIEISLNQTQKIRLQRALKQLESLYLRANFNASVTVADTIPVSNEDTILKGHGTSERD 60

Query: 60  GELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILM 119
           GE+ AT+CGVVER+NKL+YVR LRARYKPE GDI++GRV+EV  KRWKLEINF+QDA+LM
Sbjct: 61  GEVVATLCGVVERVNKLVYVRTLRARYKPEIGDIIVGRVVEVAQKRWKLEINFSQDAVLM 120

Query: 120 LSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERG 179
           LSSMNLPDG+QRRRTA+DELNMRSIF END+VC EVR+ Q DG +QLQAR+QKYGKLE+G
Sbjct: 121 LSSMNLPDGLQRRRTALDELNMRSIFEENDVVCGEVRNFQNDGGIQLQARSQKYGKLEKG 180

Query: 180 QLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIA 239
           QLLT+ PYLVKR+K HFHHLE+YG+DLI+GCNG+IW+GEHVEARD +V DQ +N+EQ   
Sbjct: 181 QLLTIPPYLVKRQKHHFHHLEQYGVDLILGCNGFIWVGEHVEARDCIVEDQLNNTEQQFT 240

Query: 240 KCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLD 299
           K +              P E R++IC+IANAIRVLS LGFN+T+EVILET++LS++LNL 
Sbjct: 241 KSNTTKE---------MPLETRRSICQIANAIRVLSILGFNVTLEVILETIDLSSTLNLG 291

Query: 300 IHDMLGSEFYVLVAESEAERR-SLSKRK 326
           I +MLG EF+VLVAE EAERR S++KRK
Sbjct: 292 IDEMLGPEFHVLVAEREAERRTSMTKRK 319

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356572158|ref|XP_003554237.1| PREDICTED: exosome complex component RRP4-like [Glycine max]

 Score =  462 bits (1190), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 224/328 (68%), Positives = 273/328 (83%), Gaps = 2/328 (0%)

Query: 1   MRNLQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPV-YEDGILKGHGTSDQK 59
           MR +QL  +QTQKVRL+KALE+LESLS+K N ++ V + D+I V +EDG+LKGHGT+D  
Sbjct: 1   MREIQLPLSQTQKVRLQKALEQLESLSTKVNSDASVIIADSIHVNHEDGVLKGHGTADLN 60

Query: 60  GELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILM 119
           GE+ AT+CGVVER+NKL+YVRALR+RYKPE GDIVIGRV+EV  KRW+LEIN+ QDA+L+
Sbjct: 61  GEVVATLCGVVERVNKLVYVRALRSRYKPEVGDIVIGRVVEVAQKRWRLEINYNQDAVLL 120

Query: 120 LSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERG 179
           LSSMN+PDG+QRRRTAVDELNMR IF END+VCAEVR  Q DG L LQAR++KYGKL RG
Sbjct: 121 LSSMNMPDGVQRRRTAVDELNMRCIFEENDVVCAEVRGFQHDG-LHLQARSRKYGKLNRG 179

Query: 180 QLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIA 239
           QLLTV PYLVKR+KQHFHHLEE+GIDLI+GCNG+IW+GEHVEA+D M+ DQ S S+  + 
Sbjct: 180 QLLTVPPYLVKRQKQHFHHLEEFGIDLILGCNGFIWVGEHVEAKDDMIEDQVSQSDSQVL 239

Query: 240 KCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLD 299
             +KN + L+EQ+   T  E R+ I R ANA+RVLS LGFNIT+E+I   ++LS S+NLD
Sbjct: 240 FPNKNCVSLEEQEKNYTILETRKYISRAANAVRVLSTLGFNITLEIIKGIIDLSLSMNLD 299

Query: 300 IHDMLGSEFYVLVAESEAERRSLSKRKR 327
           IHDMLGSEF VLVAE EAERRS  K++R
Sbjct: 300 IHDMLGSEFCVLVAEKEAERRSSMKKRR 327

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255567640|ref|XP_002524799.1| rrp4, putative [Ricinus communis] gi|223535983|gb|EEF37642.1| rrp4, putative [Ricinus communis]

 Score =  460 bits (1183), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 223/330 (67%), Positives = 276/330 (83%), Gaps = 11/330 (3%)

Query: 1   MRNLQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPV-YEDG-ILKGHGTSDQ 58
           MR +QL  NQTQK+RL++AL++LESL SK + ++ VTV DTIP+  EDG ILKGHGT+++
Sbjct: 1   MREIQLPLNQTQKIRLQRALQQLESLHSKVHSDASVTVADTIPISLEDGNILKGHGTAER 60

Query: 59  KGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAIL 118
            GE+ AT CGVVER+N L+YVR+LR+RYKPE GDI++GRVIEV  KRWKLEINF+QDA+L
Sbjct: 61  DGEVVATTCGVVERVNMLVYVRSLRSRYKPEVGDIIVGRVIEVAQKRWKLEINFSQDAVL 120

Query: 119 MLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLER 178
           MLSSMNLPDGIQRRRTA+DELNMR++F END+VCAEVR+ Q DGSLQLQAR+QKYGKLE+
Sbjct: 121 MLSSMNLPDGIQRRRTALDELNMRNVFEENDVVCAEVRNFQNDGSLQLQARSQKYGKLEK 180

Query: 179 GQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLI 238
           GQLLTV PYLVKR+KQHFHHL +Y +DLI+GCNG+IW+GEHV+ARD MV DQ + +E   
Sbjct: 181 GQLLTVSPYLVKRQKQHFHHLVQYDVDLILGCNGFIWVGEHVDARDSMVEDQVNETEDQD 240

Query: 239 AKCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNL 298
            K +K   ++        P E R+NICRIANA+RVLS LGF++T+EVILET +LS++LNL
Sbjct: 241 TKSNKTFEEV--------PLETRRNICRIANAVRVLSTLGFSLTLEVILETFSLSSTLNL 292

Query: 299 DIHDMLGSEFYVLVAESEAERR-SLSKRKR 327
            I +M G EF+VLVAE EAERR SL+K+KR
Sbjct: 293 GIDEMPGPEFHVLVAEKEAERRSSLTKKKR 322

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357478895|ref|XP_003609733.1| Exosome complex exonuclease RRP4 [Medicago truncatula] gi|217074186|gb|ACJ85453.1| unknown [Medicago truncatula] gi|355510788|gb|AES91930.1| Exosome complex exonuclease RRP4 [Medicago truncatula] gi|388516977|gb|AFK46550.1| unknown [Medicago truncatula]

 Score =  459 bits (1182), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 224/328 (68%), Positives = 269/328 (82%), Gaps = 2/328 (0%)

Query: 1   MRNLQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPV-YEDGILKGHGTSDQK 59
           MR + L  +QTQK+RL+KALE LESLSSK N +S VT+ D+IPV +EDG+LKGHGT+D  
Sbjct: 1   MRGIHLQLSQTQKLRLQKALEHLESLSSKVNSDSSVTIADSIPVNHEDGVLKGHGTADLD 60

Query: 60  GELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILM 119
           GE+ AT+CGVVER+NKL+YVRALR+RYKPE GDIVIGRVIEV  KRW+L+IN++Q+A LM
Sbjct: 61  GEVVATLCGVVERVNKLVYVRALRSRYKPEVGDIVIGRVIEVAQKRWRLDINYSQNAYLM 120

Query: 120 LSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERG 179
           LS+MN+PDG+QRRRTA+DELNMR IF E D++CAEVR  Q DG L LQAR+QKYGKL  G
Sbjct: 121 LSAMNMPDGVQRRRTALDELNMRCIFEEADVICAEVRGFQHDG-LHLQARSQKYGKLSTG 179

Query: 180 QLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIA 239
           QLLTV PYLVKR+KQHFHHLE+YGIDLIIGCNG+IW+GEHVE RD MV DQ + S+  + 
Sbjct: 180 QLLTVTPYLVKRQKQHFHHLEQYGIDLIIGCNGFIWVGEHVEVRDDMVEDQVNQSDPQVL 239

Query: 240 KCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLD 299
             +KNS+ L+EQ+   T  E R+ ICR ANA+R LS LGF IT E+I   ++LS S NLD
Sbjct: 240 TPNKNSVSLEEQEKKYTALETRKYICRAANAVRGLSTLGFIITSEIIKGVIDLSLSANLD 299

Query: 300 IHDMLGSEFYVLVAESEAERRSLSKRKR 327
           IHDMLGSEF VLVAE EAERRS +K+KR
Sbjct: 300 IHDMLGSEFCVLVAEKEAERRSSNKKKR 327

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15218790|ref|NP_171835.1| exosome complex component RRP4 [Arabidopsis thaliana] gi|3850568|gb|AAC72108.1| Similar to hypothetical protein SPAC2F7.14c gi|1052797 from Schizosaccharomyces pombe cosmid gb|Z50142 [Arabidopsis thaliana] gi|34365689|gb|AAQ65156.1| At1g03360 [Arabidopsis thaliana] gi|51970606|dbj|BAD43995.1| hypothetical protein [Arabidopsis thaliana] gi|332189442|gb|AEE27563.1| exosome complex component RRP4 [Arabidopsis thaliana]

 Score =  459 bits (1181), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 219/327 (66%), Positives = 267/327 (81%), Gaps = 8/327 (2%)

Query: 1   MRNLQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPV-YEDGILKGHGTSDQK 59
           MR LQL  +QTQKVR E+A+ERL+SLSS +N ++ V V D+IPV ++D  LKGHGTS+  
Sbjct: 3   MRKLQLPLSQTQKVRFERAIERLQSLSSSANSDASVIVTDSIPVNHDDAFLKGHGTSEVD 62

Query: 60  GELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILM 119
           GEL ATVCGVVER++KL+YVR LRARYKPE GDIV+GRVIEV  KRW++E+NF QD +LM
Sbjct: 63  GELLATVCGVVERVDKLVYVRTLRARYKPEVGDIVVGRVIEVAQKRWRVELNFNQDGVLM 122

Query: 120 LSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERG 179
           LSSMN+PDGIQRRRT+VDELNMR+IF E+D+VCAEVR+ Q DGSLQLQAR+QKYGKLE+G
Sbjct: 123 LSSMNMPDGIQRRRTSVDELNMRNIFVEHDVVCAEVRNFQHDGSLQLQARSQKYGKLEKG 182

Query: 180 QLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIA 239
           QLL VDPYLVKR K HFH++E  GIDLIIGCNG+IW+GEHVE RD M +D   + E++I+
Sbjct: 183 QLLKVDPYLVKRSKHHFHYVESLGIDLIIGCNGFIWVGEHVEVRDPMAIDDQKD-EEMIS 241

Query: 240 KCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLD 299
                      ++ +  P E RQ ICRI NAIRVLS LGF +T+EVI+ETVNLSNS N+D
Sbjct: 242 SSSTG------KEQSHIPLETRQTICRIGNAIRVLSNLGFTVTLEVIMETVNLSNSKNID 295

Query: 300 IHDMLGSEFYVLVAESEAERRSLSKRK 326
           IHDMLGSEF+V+VAE+EAERR   ++K
Sbjct: 296 IHDMLGSEFHVVVAENEAERRRTKRKK 322

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297843148|ref|XP_002889455.1| ATRRP4 [Arabidopsis lyrata subsp. lyrata] gi|297335297|gb|EFH65714.1| ATRRP4 [Arabidopsis lyrata subsp. lyrata]

 Score =  454 bits (1167), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 219/327 (66%), Positives = 265/327 (81%), Gaps = 8/327 (2%)

Query: 1   MRNLQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPV-YEDGILKGHGTSDQK 59
           +R LQL  +QTQKVR E+A+ERL+SLSS +N ++ V V D+IPV ++D  LKGHGTS+  
Sbjct: 3   LRKLQLPLSQTQKVRFERAIERLQSLSSTANSDASVIVTDSIPVNHDDAFLKGHGTSEVD 62

Query: 60  GELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILM 119
           GEL ATVCGVVER++KL+YVR LRARYKPE GDIV+GRVIEV  KRW++E+NFTQD +LM
Sbjct: 63  GELLATVCGVVERVDKLVYVRTLRARYKPEVGDIVVGRVIEVAQKRWRVELNFTQDGVLM 122

Query: 120 LSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERG 179
           LSSMN+PDGIQRRRT+VDELNMR+IF E+D+VCAEVR+ Q DGSLQLQAR+QKYGKLE+G
Sbjct: 123 LSSMNMPDGIQRRRTSVDELNMRNIFVEHDVVCAEVRNFQHDGSLQLQARSQKYGKLEKG 182

Query: 180 QLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIA 239
           QLL VDPYLVKR K HFH++E  GIDLIIGCNG+IW+GEHVE RD M +D   + E +  
Sbjct: 183 QLLKVDPYLVKRSKHHFHYVESLGIDLIIGCNGFIWVGEHVEVRDPMAIDDQKDEEMI-- 240

Query: 240 KCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLD 299
               +S    EQ+    P E RQ ICRI N IRVLS LGF +T+EVI+ETVNLSNS N+D
Sbjct: 241 ---SSSSTGKEQNH--IPPETRQTICRIGNVIRVLSNLGFTVTLEVIIETVNLSNSKNID 295

Query: 300 IHDMLGSEFYVLVAESEAERRSLSKRK 326
           I DMLGSEF+V+VAE+EAERR   ++K
Sbjct: 296 IQDMLGSEFHVVVAENEAERRRTKRKK 322

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222619320|gb|EEE55452.1| hypothetical protein OsJ_03610 [Oryza sativa Japonica Group]

 Score =  426 bits (1096), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 207/318 (65%), Positives = 253/318 (79%), Gaps = 20/318 (6%)

Query: 1   MRNLQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDG--ILKGHGTSDQ 58
           MR+LQLS NQTQ+VRLE AL  L++++    P + VTV +TIPV +DG  I KGHGTSDQ
Sbjct: 1   MRDLQLSLNQTQRVRLEAALHELQTVA----PGAAVTVAETIPV-KDGEKIFKGHGTSDQ 55

Query: 59  KGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAIL 118
            GE+ AT+CGVVER+NKL+YVR LRARYKPE GDI++GRVIE+ PKRW+LEINF+QDA+L
Sbjct: 56  DGEVVATLCGVVERVNKLVYVRTLRARYKPEVGDIIVGRVIEIAPKRWRLEINFSQDAVL 115

Query: 119 MLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLER 178
           MLSSMNLPDGIQRRRTAVDELNMR+IF END++CAEVR  Q DGSL LQAR+QKYGKLER
Sbjct: 116 MLSSMNLPDGIQRRRTAVDELNMRTIFEENDVICAEVRGFQHDGSLHLQARSQKYGKLER 175

Query: 179 GQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLI 238
           GQLL V  YLVKRRKQHFHHLE+Y +DLI+GCNG+IW+GEHV      VV + +N  +  
Sbjct: 176 GQLLVVPAYLVKRRKQHFHHLEQYDVDLILGCNGFIWVGEHV------VVGENANMME-- 227

Query: 239 AKCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNL 298
                N ++L  +    TP E R++ICR+ANA+RVLS LGF +TVE+I+ET   S S N+
Sbjct: 228 -----NKLNLSAEVENFTPLETRKHICRLANAVRVLSALGFTLTVELIIETAEASVSSNI 282

Query: 299 DIHDMLGSEFYVLVAESE 316
           +I++MLG+EFYV  AE E
Sbjct: 283 EINNMLGAEFYVQTAERE 300

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	327
TAIR|locus:2014535	322	RRP4 "AT1G03360" [Arabidopsis	0.975	0.990	0.679	2.4e-115
DICTYBASE|DDB_G0291310	380	DDB_G0291310 "Exosome complex	0.798	0.686	0.448	1.3e-54
MGI|MGI:2385133	293	Exosc2 "exosome component 2" [	0.645	0.720	0.483	3.8e-46
POMBASE|SPAC2F7.14c	329	SPAC2F7.14c "exosome subunit R	0.844	0.838	0.400	1.3e-45
UNIPROTKB|Q2KID0	293	EXOSC2 "Exosome complex compon	0.629	0.703	0.497	3.4e-45
UNIPROTKB|J9NXW2	293	EXOSC2 "Uncharacterized protei	0.633	0.706	0.485	5.6e-45
UNIPROTKB|Q13868	293	EXOSC2 "Exosome complex compon	0.633	0.706	0.485	1.2e-44
FB|FBgn0034879	298	Rrp4 "Rrp4" [Drosophila melano	0.608	0.667	0.460	2.3e-44
UNIPROTKB|F1NGC4	294	EXOSC2 "Uncharacterized protei	0.574	0.639	0.510	3.1e-44
UNIPROTKB|E2QU26	296	EXOSC2 "Uncharacterized protei	0.633	0.699	0.479	1.3e-43

TAIR|locus:2014535 RRP4 "AT1G03360" [Arabidopsis thaliana (taxid:3702)]

 Score = 1137 (405.3 bits), Expect = 2.4e-115, P = 2.4e-115
 Identities = 223/328 (67%), Positives = 267/328 (81%)

Query:     1 MRNLQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPV-YEDGILKGHGTSDQK 59
             MR LQL  +QTQKVR E+A+ERL+SLSS +N ++ V V D+IPV ++D  LKGHGTS+  
Sbjct:     3 MRKLQLPLSQTQKVRFERAIERLQSLSSSANSDASVIVTDSIPVNHDDAFLKGHGTSEVD 62

Query:    60 GELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILM 119
             GEL ATVCGVVER++KL+YVR LRARYKPE GDIV+GRVIEV  KRW++E+NF QD +LM
Sbjct:    63 GELLATVCGVVERVDKLVYVRTLRARYKPEVGDIVVGRVIEVAQKRWRVELNFNQDGVLM 122

Query:   120 LSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERG 179
             LSSMN+PDGIQRRRT+VDELNMR+IF E+D+VCAEVR+ Q DGSLQLQAR+QKYGKLE+G
Sbjct:   123 LSSMNMPDGIQRRRTSVDELNMRNIFVEHDVVCAEVRNFQHDGSLQLQARSQKYGKLEKG 182

Query:   180 QLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIA 239
             QLL VDPYLVKR K HFH++E  GIDLIIGCNG+IW+GEHVE RD M +D     E++I+
Sbjct:   183 QLLKVDPYLVKRSKHHFHYVESLGIDLIIGCNGFIWVGEHVEVRDPMAIDD-QKDEEMIS 241

Query:   240 KCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLD 299
                       EQ     P E RQ ICRI NAIRVLS LGF +T+EVI+ETVNLSNS N+D
Sbjct:   242 SSSTGK----EQSHI--PLETRQTICRIGNAIRVLSNLGFTVTLEVIMETVNLSNSKNID 295

Query:   300 IHDMLGSEFYVLVAESEAERRSLSKRKR 327
             IHDMLGSEF+V+VAE+EAERR  +KRK+
Sbjct:   296 IHDMLGSEFHVVVAENEAERRR-TKRKK 322

GO:0004527 "exonuclease activity" evidence=ISS

GO:0009561 "megagametogenesis" evidence=RCA

DICTYBASE|DDB_G0291310 DDB_G0291310 "Exosome complex exonuclease RRP4" [Dictyostelium discoideum (taxid:44689)]

 Score = 564 (203.6 bits), Expect = 1.3e-54, P = 1.3e-54
 Identities = 126/281 (44%), Positives = 175/281 (62%)

Query:    36 VTVGDTIPVYEDGILKGHGT-SDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIV 94
             V  G TI   E   LKGHGT +D  G L A+VCG ++++++L+ V+AL++RY  E GDI+
Sbjct:    89 VITGQTIS-REGEYLKGHGTFNDGSGSLVASVCGTLDKVDRLVSVKALKSRYHGEVGDII 147

Query:    95 IGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAE 154
             +GR+ E+  KRWK+++N   D ILMLS++NLP GIQRRRT+ DEL MRS F ENDLV AE
Sbjct:   148 VGRITEITSKRWKVDVNSRLDYILMLSAINLPGGIQRRRTSADELQMRSFFVENDLVYAE 207

Query:   155 VRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYI 214
             V+   GDGS+ +  RNQKYGKL+ G    V P L+KR KQHF++LE  G+D+I+G NGYI
Sbjct:   208 VQMVMGDGSVAIHTRNQKYGKLQNGHFTKVIPSLIKRSKQHFYNLE-CGVDVILGVNGYI 266

Query:   215 WIGEHVEARDKMVVDQGSNSEQLIAKCDKN-----SMDLDEQDGTC-TPREARQNICRIA 268
             WI +          +Q  N +Q I K +K      S+ L   D      +E+R  I R+ 
Sbjct:   267 WIADS---------EQQKNQQQFIQKHEKEPTFDPSIPLIIPDEIKQVSKESRDRIARVK 317

Query:   269 NAIRVLSRLGFN-ITVEVILETVNLSNSLNLDIHDMLGSEF 308
             N+I +L + GF  I  + I+    LS  + L   D+L  ++
Sbjct:   318 NSISLLEK-GFLLIHQKSIMNVYKLSLKMKLQSKDLLHPQY 357

GO:0003723 "RNA binding" evidence=IEA

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

MGI|MGI:2385133 Exosc2 "exosome component 2" [Mus musculus (taxid:10090)]

 Score = 484 (175.4 bits), Expect = 3.8e-46, P = 3.8e-46
 Identities = 103/213 (48%), Positives = 138/213 (64%)

Query:    13 KVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVER 72
             ++RL KA + L     + +    V  GDTI   + G ++GHGT   + +L A+V G VER
Sbjct:     4 EMRLPKARKPLSESLGRDSKKHLVVPGDTITT-DTGFMRGHGTYMGEEKLIASVAGSVER 62

Query:    73 INKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRR 132
             +NKLI V+AL+ RY  E GDIV+GR+ EV  KRWK+E N   D++L+LSSMNLP G  RR
Sbjct:    63 VNKLICVKALKTRYNGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRR 122

Query:   133 RTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRR 192
             R+A DEL MR    E DL+ AEV++   DG++ L  R+ KYGKL +G L+ V P LVKR+
Sbjct:   123 RSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQ 182

Query:   193 KQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDK 225
             K HFH L   G  +I+G NG+IWI    E +D+
Sbjct:   183 KTHFHDLP-CGASVILGNNGFIWIYPTPEHKDE 214

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

GO:0003674 "molecular_function" evidence=ND

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006364 "rRNA processing" evidence=IEA

GO:0030307 "positive regulation of cell growth" evidence=ISO

POMBASE|SPAC2F7.14c SPAC2F7.14c "exosome subunit Rrp4 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 479 (173.7 bits), Expect = 1.3e-45, P = 1.3e-45
 Identities = 113/282 (40%), Positives = 160/282 (56%)

Query:     1 MRNLQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKG 60
             M  ++    + +++ L    + LE    KS   + VT G  +   +   ++GHGT  + G
Sbjct:    24 MTEMEDEIMEDEQMGLVDGEDVLEEFD-KSIHQNLVTPGQLV-TDDPQFMRGHGTYFEDG 81

Query:    61 ELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILML 120
              + A+V G V+R+NKLI V+ LR++Y PE GD++IG++ EV PKRWK++I   Q+A+LML
Sbjct:    82 GIYASVAGSVQRVNKLISVKPLRSKYVPEIGDLIIGKIAEVQPKRWKVDIGAKQNAVLML 141

Query:   121 SSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQ 180
             SS+NLP GIQRR+   DEL MRS F E DL+ AEV+    DGS+ +  R+ KYGKL  G 
Sbjct:   142 SSINLPGGIQRRKLETDELQMRSFFQEGDLLVAEVQQYFSDGSVSIHTRSLKYGKLRNGV 201

Query:   181 LLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIAK 240
              L V P LV R K H + L   G+D+I+  NGY+W+ +H E +   V       E   A 
Sbjct:   202 FLKVPPALVVRSKSHAYALAG-GVDIILSVNGYVWVSKHNENQHSSVSITRLEEE---AS 257

Query:   241 CDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNIT 282
                 S + DE DG      +R +IC    A R L     +IT
Sbjct:   258 ESIYSNENDEIDGYTRLNISRVSICIKGLASRSLPLTQASIT 299

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

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

GO:0000467 "exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" evidence=ISO

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0034661 "ncRNA catabolic process" evidence=ISO

GO:0044732 "mitotic spindle pole body" evidence=IDA

GO:0070478 "nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay" evidence=ISO

GO:0070481 "nuclear-transcribed mRNA catabolic process, non-stop decay" evidence=ISO

GO:0070651 "nonfunctional rRNA decay" evidence=ISO

GO:0071035 "nuclear polyadenylation-dependent rRNA catabolic process" evidence=ISO

GO:0071038 "nuclear polyadenylation-dependent tRNA catabolic process" evidence=ISO

GO:0071042 "nuclear polyadenylation-dependent mRNA catabolic process" evidence=ISO

UNIPROTKB|Q2KID0 EXOSC2 "Exosome complex component RRP4" [Bos taurus (taxid:9913)]

 Score = 475 (172.3 bits), Expect = 3.4e-45, P = 3.4e-45
 Identities = 106/213 (49%), Positives = 140/213 (65%)

Query:    13 KVRLEKALERL-ESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVE 71
             ++RL  A + L ESL  +S  +  V  GDTI   + G ++GHGT   + +L A+V G VE
Sbjct:     4 EMRLPVARKPLSESLGRESKKH-LVVPGDTITT-DTGFMRGHGTYMGEEKLIASVAGSVE 61

Query:    72 RINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQR 131
             R+NKLI V+AL+ RY  E GDIV+GR+ EV  KRWK+E N   D++L+LSSMNLP G  R
Sbjct:    62 RVNKLICVKALKTRYNGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELR 121

Query:   132 RRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKR 191
             RR+A DEL MR    E DL+ AEV++   DG++ L  R+ KYGKL +G L+ V P LVKR
Sbjct:   122 RRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKR 181

Query:   192 RKQHFHHLEEYGIDLIIGCNGYIWI---GEHVE 221
             +K HFH L   G  +I+G NG+IW+    EH E
Sbjct:   182 QKTHFHDLP-CGASVILGNNGFIWVYPTPEHKE 213

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

GO:0005737 "cytoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0030307 "positive regulation of cell growth" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|J9NXW2 EXOSC2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 473 (171.6 bits), Expect = 5.6e-45, P = 5.6e-45
 Identities = 103/212 (48%), Positives = 135/212 (63%)

Query:    13 KVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVER 72
             ++RL  A + L     +      V  GDTI   + G ++GHGT   + +L A+V G VER
Sbjct:     4 EMRLPVARKPLSESVGRDTKKHLVVPGDTITT-DTGFMRGHGTYMGEEKLIASVAGSVER 62

Query:    73 INKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRR 132
             +NKLI V+AL+ RY  E GDIV+GR+ EV  KRWK+E N   D++L+LSSMNLP G  RR
Sbjct:    63 VNKLICVKALKTRYNGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRR 122

Query:   133 RTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRR 192
             R+A DEL MR    E DL+ AEV++   DG++ L  R+ KYGKL +G L+ V P LVKR+
Sbjct:   123 RSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQ 182

Query:   193 KQHFHHLEEYGIDLIIGCNGYIWI---GEHVE 221
             K HFH L   G  +I+G NG+IWI    EH E
Sbjct:   183 KTHFHDLP-CGASVILGNNGFIWIYPTPEHKE 213

GO:0003723 "RNA binding" evidence=IEA

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

UNIPROTKB|Q13868 EXOSC2 "Exosome complex component RRP4" [Homo sapiens (taxid:9606)]

 Score = 470 (170.5 bits), Expect = 1.2e-44, P = 1.2e-44
 Identities = 103/212 (48%), Positives = 135/212 (63%)

Query:    13 KVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVER 72
             ++RL  A + L     +      V  GDTI   + G ++GHGT   + +L A+V G VER
Sbjct:     4 EMRLPVARKPLSERLGRDTKKHLVVPGDTITT-DTGFMRGHGTYMGEEKLIASVAGSVER 62

Query:    73 INKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRR 132
             +NKLI V+AL+ RY  E GDIV+GR+ EV  KRWK+E N   D++L+LSSMNLP G  RR
Sbjct:    63 VNKLICVKALKTRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRR 122

Query:   133 RTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRR 192
             R+A DEL MR    E DL+ AEV++   DG++ L  R+ KYGKL +G L+ V P LVKR+
Sbjct:   123 RSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQ 182

Query:   193 KQHFHHLEEYGIDLIIGCNGYIWI---GEHVE 221
             K HFH L   G  +I+G NG+IWI    EH E
Sbjct:   183 KTHFHDLP-CGASVILGNNGFIWIYPTPEHKE 213

GO:0006364 "rRNA processing" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

GO:0004532 "exoribonuclease activity" evidence=IDA

GO:0030307 "positive regulation of cell growth" evidence=IMP

GO:0005737 "cytoplasm" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

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

GO:0008312 "7S RNA binding" evidence=TAS

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

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

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

GO:0005515 "protein binding" evidence=IPI

FB|FBgn0034879 Rrp4 "Rrp4" [Drosophila melanogaster (taxid:7227)]

 Score = 437 (158.9 bits), Expect = 2.3e-44, Sum P(2) = 2.3e-44
 Identities = 94/204 (46%), Positives = 137/204 (67%)

Query:    16 LEKALERLE--SLSSKSNPNSCV-TVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVER 72
             ++ AL+R++   L++++     V T G+ + + E G ++GHGT  +   + ++V GV+++
Sbjct:     7 IDLALDRVDWRDLAAQTEEQPRVYTPGEVL-MPEAGFMRGHGTFVEDENIKSSVAGVIQK 65

Query:    73 INKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRR 132
             +NKLI VR L++RY  E GD+V+ RV EV  KRW+++ N   D+IL+LSS+NLP G  RR
Sbjct:    66 VNKLISVRPLKSRYVGEIGDVVVARVSEVQQKRWRVDTNSRLDSILLLSSVNLPGGELRR 125

Query:   133 RTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRR 192
             R+A DE  MR    E DL+ AEV++   +GSL L  R+ KYGKL +G L+ V P LVKRR
Sbjct:   126 RSAEDEQMMRRYLDEGDLISAEVQNIFEEGSLSLYTRSLKYGKLSQGILVKVFPALVKRR 185

Query:   193 KQHFHHLEEYGIDLIIGCNGYIWI 216
             K HFH+L   G  +I+G NGYIWI
Sbjct:   186 KMHFHNLP-CGASVILGNNGYIWI 208

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

GO:0006397 "mRNA processing" evidence=ISS

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

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005652 "nuclear lamina" evidence=IDA

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

UNIPROTKB|F1NGC4 EXOSC2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 466 (169.1 bits), Expect = 3.1e-44, P = 3.1e-44
 Identities = 97/190 (51%), Positives = 126/190 (66%)

Query:    36 VTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVI 95
             V  GDTI   + G ++GHGT   + +L A+V G VER+NKL+ V  L+ RY  E GDIV+
Sbjct:    28 VVPGDTITT-DTGYMRGHGTYVDEEKLVASVAGAVERVNKLVCVTPLKTRYNGEVGDIVV 86

Query:    96 GRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEV 155
             GR+ EV  KRWK+E N   D++L+LSSMNLP G  RRR+A DEL MR    E DL+ AEV
Sbjct:    87 GRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRDYLQEGDLISAEV 146

Query:   156 RSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIW 215
             +S   DG++ L  R+ KYGKL +G L+ V P LVKR+K HFH L   G  +I+G NG+IW
Sbjct:   147 QSVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQKTHFHDLP-CGASVILGNNGFIW 205

Query:   216 IGEHVEARDK 225
             I    E +D+
Sbjct:   206 IYPTPEQKDE 215

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0030307 "positive regulation of cell growth" evidence=IEA

UNIPROTKB|E2QU26 EXOSC2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 103/215 (47%), Positives = 135/215 (62%)

Query:    13 KVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVER 72
             ++RL  A + L     +      V  GDTI   + G ++GHGT   + +L A+V G VER
Sbjct:     4 EMRLPVARKPLSESVGRDTKKHLVVPGDTITT-DTGFMRGHGTYMGEEKLIASVAGSVER 62

Query:    73 INKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRR 132
             +NKLI V+AL+ RY  E GDIV+GR+ EV  KRWK+E N   D++L+LSSMNLP G  RR
Sbjct:    63 VNKLICVKALKTRYNGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRR 122

Query:   133 RTAVDELNMRSIFTENDLVC---AEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLV 189
             R+A DEL MR    E DL+    AEV++   DG++ L  R+ KYGKL +G L+ V P LV
Sbjct:   123 RSAEDELAMRGFLQEGDLISSGQAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLV 182

Query:   190 KRRKQHFHHLEEYGIDLIIGCNGYIWI---GEHVE 221
             KR+K HFH L   G  +I+G NG+IWI    EH E
Sbjct:   183 KRQKTHFHDLP-CGASVILGNNGFIWIYPTPEHKE 216

GO:0003723 "RNA binding" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	327
COG1097	239	COG1097, RRP4, RNA-binding protein Rrp4 and relate	3e-44
cd05789	86	cd05789, S1_Rrp4, S1_Rrp4: Rrp4 S1-like RNA-bindin	7e-36
PRK04163	235	PRK04163, PRK04163, exosome complex RNA-binding pr	4e-20
cd04454	82	cd04454, S1_Rrp4_like, S1_Rrp4_like: Rrp4-like, S1	4e-14
PRK09521	189	PRK09521, PRK09521, exosome complex RNA-binding pr	6e-07
COG1096	188	COG1096, COG1096, Predicted RNA-binding protein (c	4e-05
cd05791	92	cd05791, S1_CSL4, S1_CSL4: CSL4, S1-like RNA-bindi	0.002

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

 Score =  151 bits (383), Expect = 3e-44
 Identities = 68/242 (28%), Positives = 115/242 (47%), Gaps = 28/242 (11%)

Query: 36  VTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVI 95
           V  GD +   E     GHGT  + G++ ++V G+++   KL+ V  L  RY PE GD+VI
Sbjct: 11  VLPGDLVLA-EGSYKLGHGTYFEGGKIYSSVVGLLDVKGKLVRVIPLEGRYIPEVGDVVI 69

Query: 96  GRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEV 155
           G++IEV P  WK++I     A+L LS         RR+    E ++R      DLV A+V
Sbjct: 70  GKIIEVGPSGWKVDIGSPYPALLSLSDF------LRRKFENAEKDLRPFLNVGDLVYAKV 123

Query: 156 RSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRRKQHFHHL-----EEYGIDLIIGC 210
                DG ++L  +++  GKL+ GQ++ + P  V R       +     E+ G ++I+G 
Sbjct: 124 VDVDRDGEVELTLKDEGLGKLKNGQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ 183

Query: 211 NGYIWIGEHVEARDKMVVDQGSNSEQLIAKCDKNSMDLDEQDGTCTPREARQNICRIANA 270
           NG IW+    E+ +++       + + I K ++ +          T     +    +   
Sbjct: 184 NGRIWVDGENESLEEL-------AIEAIRKIEREAH---------TSGLTDRIKEFLKKL 227

Query: 271 IR 272
           +R
Sbjct: 228 LR 229

Length = 239

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

 Score =  124 bits (314), Expect = 7e-36
 Identities = 53/92 (57%), Positives = 62/92 (67%), Gaps = 6/92 (6%)

Query: 85  RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSI 144
           RY PE GD+VIGRV EV  KRWK++IN   DA+L LS +NLP      RT  DELNMRS 
Sbjct: 1   RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLP------RTDEDELNMRSY 54

Query: 145 FTENDLVCAEVRSSQGDGSLQLQARNQKYGKL 176
             E DL+ AEV+S   DGS+ L  R+ KYGKL
Sbjct: 55  LDEGDLIVAEVQSVDSDGSVSLHTRSLKYGKL 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|235233 PRK04163, PRK04163, exosome complex RNA-binding protein Rrp4; Provisional

 Score = 87.3 bits (217), Expect = 4e-20
 Identities = 55/186 (29%), Positives = 92/186 (49%), Gaps = 13/186 (6%)

Query: 36  VTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVI 95
           V  GD   + E     G GT  + G++ +TV G+V+  +  + V  L  +Y P+ GD+VI
Sbjct: 11  VVPGD--LLAEGEFKAGRGTYKENGKIYSTVVGLVDIKDDKVRVIPLEGKYIPKVGDLVI 68

Query: 96  GRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEV 155
           G+V +V    W+++IN    A L +S   +      R   V+  ++R      D + A+V
Sbjct: 69  GKVTDVTFSGWEVDINSPYKAYLPVS--EVLG----RPVNVEGTDLRKYLDIGDYIIAKV 122

Query: 156 RSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKR---RKQHFHHL--EEYGIDLIIGC 210
           +       + L  + +  GK+E G ++ + P  V R   +K    ++  EE G D+I+G 
Sbjct: 123 KDVDRTRDVVLTLKGKGLGKIEGGTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ 182

Query: 211 NGYIWI 216
           NG IWI
Sbjct: 183 NGRIWI 188

Length = 235

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

 Score = 66.4 bits (162), Expect = 4e-14
 Identities = 29/92 (31%), Positives = 42/92 (45%), Gaps = 10/92 (10%)

Query: 85  RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSI 144
           RY P+ GDIVIG V EV  + WK++I     A L  SS              D+  +R  
Sbjct: 1   RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEK----------DKKEIRKS 50

Query: 145 FTENDLVCAEVRSSQGDGSLQLQARNQKYGKL 176
               DL+ A+V S   D ++ L   + + G +
Sbjct: 51  LQPGDLILAKVISLGDDMNVLLTTADNELGVI 82

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

 Score = 48.8 bits (117), Expect = 6e-07
 Identities = 28/75 (37%), Positives = 40/75 (53%), Gaps = 4/75 (5%)

Query: 39  GDTIPVYEDGILKGHGTSDQKGELAATVCGVVER--INKLIYVRALRAR-YKPETGDIVI 95
           GD + V E+  L G GT +  GE+ A+V G V    IN+ I V   +      + GDIV 
Sbjct: 11  GDYLAVIEE-YLPGEGTYEDNGEVYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVY 69

Query: 96  GRVIEVVPKRWKLEI 110
           GRV++V  +R  + I
Sbjct: 70  GRVVDVKEQRALVRI 84

Length = 189

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

 Score = 43.5 bits (103), Expect = 4e-05
 Identities = 30/78 (38%), Positives = 43/78 (55%), Gaps = 4/78 (5%)

Query: 36  VTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVER--INKLIYVR-ALRARYKPETGD 92
           V  GD + V E+  L G GT ++ GE+ A   GVV R   N++I V+   +    P+ GD
Sbjct: 8   VLPGDVLAVIEE-FLPGEGTYEEGGEIRAAATGVVRRDDKNRVISVKPGKKTPPLPKGGD 66

Query: 93  IVIGRVIEVVPKRWKLEI 110
           IV GRV +V  +R  + I
Sbjct: 67  IVYGRVTDVREQRALVRI 84

Length = 188

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 25/83 (30%), Positives = 37/83 (44%), Gaps = 15/83 (18%)

Query: 88  PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQR-------RRTAVDELN 140
           P+ G IVI RV  + P+  K++       IL +    L +  +        R T  D++ 
Sbjct: 4   PKVGSIVIARVTRINPRFAKVD-------ILCVGGRPLKESFRGVIRKEDIRATEKDKVE 56

Query: 141 MRSIFTENDLVCAEVRSSQGDGS 163
           M   F   D+V A+V  S GD S
Sbjct: 57  MYKCFRPGDIVRAKV-ISLGDAS 78

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure". Length = 92

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	327
KOG3013	301	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
COG1097	239	RRP4 RNA-binding protein Rrp4 and related proteins	100.0
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	100.0
KOG1004	230	consensus Exosomal 3'-5' exoribonuclease complex s	100.0
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	99.94
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	99.91
KOG3409	193	consensus Exosomal 3'-5' exoribonuclease complex,	99.85
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	99.85
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	99.81
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	99.7
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.59
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	99.38
PF14382	39	ECR1_N: Exosome complex exonuclease RRP4 N-termina	99.19
COG1098	129	VacB Predicted RNA binding protein (contains ribos	98.92
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	98.86
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	98.77
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	98.69
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	98.66
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	98.64
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	98.61
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	98.6
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	98.57
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	98.55
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	98.53
PRK08582	139	hypothetical protein; Provisional	98.53
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	98.51
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	98.49
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	98.48
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.44
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.42
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.41
PRK07252	120	hypothetical protein; Provisional	98.39
PRK08059	123	general stress protein 13; Validated	98.38
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	98.36
PRK05807	136	hypothetical protein; Provisional	98.36
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	98.34
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	98.34
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.31
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	98.3
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	98.25
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.23
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.22
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	98.21
PHA02945	88	interferon resistance protein; Provisional	98.2
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	98.18
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	98.18
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	98.17
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	98.15
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	98.13
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	97.99
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	97.93
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	97.92
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	97.91
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	97.87
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.85
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	97.84
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	97.81
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	97.81
PRK07400	318	30S ribosomal protein S1; Reviewed	97.8
PRK07400	318	30S ribosomal protein S1; Reviewed	97.79
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.79
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	97.7
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	97.65
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.62
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	97.58
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	97.56
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	97.55
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.53
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	97.46
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	97.46
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	97.44
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	97.38
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	97.36
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	97.33
COG2183	780	Tex Transcriptional accessory protein [Transcripti	97.29
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	97.27
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	97.24
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	97.23
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	97.18
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	97.17
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	97.17
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	97.14
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	97.05
TIGR01953	341	NusA transcription termination factor NusA. This m	97.02
PRK12327	362	nusA transcription elongation factor NusA; Provisi	96.97
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	96.81
PRK09202	470	nusA transcription elongation factor NusA; Validat	96.51
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	96.15
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.01
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	94.12
PRK12328	374	nusA transcription elongation factor NusA; Provisi	93.77
PRK12329	449	nusA transcription elongation factor NusA; Provisi	93.73
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	93.29
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	93.22
PRK10811	1068	rne ribonuclease E; Reviewed	93.22
PRK11642	813	exoribonuclease R; Provisional	92.67
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	91.74
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	91.7
KOG2916	304	consensus Translation initiation factor 2, alpha s	91.68
PRK11712	489	ribonuclease G; Provisional	91.66
KOG1856	1299	consensus Transcription elongation factor SPT6 [RN	89.95
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	84.86
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	84.57
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	84.21
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	82.61
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	81.76

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

Probab=100.00  E-value=1.2e-80  Score=572.74  Aligned_cols=300  Identities=46%  Similarity=0.757  Sum_probs=270.7

Q ss_pred             ccccchhhHHHHHHHHHHHHhhccCCCCCCceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEECcEEEEEecC
Q 020356            4 LQLSFNQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALR   83 (327)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~nk~v~V~pl~   83 (327)
                      ++++++|.++++.+++.+.. +++.+....++|+||+.++. +++||+|||||+.||.|+||++|.++++||+++|+|++
T Consensus         1 ~~~~~s~~~~v~~~~~~e~~-~a~~~~~~~~ivtPG~~V~~-d~~fmRGHGTy~~d~~i~ssvaG~v~rvNkLi~V~plk   78 (301)
T KOG3013|consen    1 LQFPLSQALKVNFERMSERE-SASDTSDHSTIVTPGELVTD-DPGFMRGHGTYVRDGEIYSSVAGVVQRVNKLISVKPLK   78 (301)
T ss_pred             CCccccCCccccchhcchhh-hhcccccCceeecCCccccC-chhhhhcccceecCCeEEEeecchhhhhcceEEEeehh
Confidence            47899999999999999987 33344556789999999975 44699999999999999999999999999999999999


Q ss_pred             CccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCc
Q 020356           84 ARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGS  163 (327)
Q Consensus        84 ~rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~  163 (327)
                      .||.|++||+|+|||++|++++|+||+|+.++|+|+||++|+|||++|||...||++||+||++||+|+||||+++.||+
T Consensus        79 ~rY~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs  158 (301)
T KOG3013|consen   79 SRYAPEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHDGS  158 (301)
T ss_pred             hhcCCccCCEEEEEeeeeecceeEEecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhccCCe
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEccCCCccCCCCeEEEeChhhhhhccccccccCccceEEEEeecceeeeccccccccccccccCCCchhhhhhccC
Q 020356          164 LQLQARNQKYGKLERGQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIAKCDK  243 (327)
Q Consensus       164 i~Lstr~~~lGkL~~G~lv~V~~~li~r~~~h~~~L~~~~~eiivG~NG~IWI~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (327)
                      +.||||+.+||||.+|++++|||.|++|.|.|||.|+ +|+++|+||||||||.+.....       .++ +...+++..
T Consensus       159 ~sLhTRS~KYGKL~~G~lvkVpp~Lvkr~K~hfh~lp-~g~~vIlG~NGyIWv~~s~~~~-------~ee-~~~~~~~~~  229 (301)
T KOG3013|consen  159 LSLHTRSLKYGKLGQGILVKVPPALVKRSKTHFHNLP-GGVDVILGCNGYIWVGPSIKDQ-------EEE-ESIGSYSSE  229 (301)
T ss_pred             EEEEecchhcccccCceEEEeCHHHhhhhhhhhccCC-CCeEEEEecCceEEecCCCCcc-------hhh-hcccccccC
Confidence            9999999999999999999999999999999999998 9999999999999999854311       111 111122211


Q ss_pred             CCCccccCCCCCCCHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHhhhhCCCCchhcccchHHHHHHHHHHHHhhhh
Q 020356          244 NSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLDIHDMLGSEFYVLVAESEAERRSLS  323 (327)
Q Consensus       244 ~~~~~~~~~~~~~~~~~r~~i~r~~n~i~~l~~~~~~i~~~~i~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  323 (327)
                              .++.||.++|++|||++|||++|+.++++||+++|+++||+|  +-++++|||.+++|..+|+.+++|+..+
T Consensus       230 --------~~~~v~~~~R~~i~Rl~n~i~~La~~~~~i~~~sI~~~ye~S--~~~~i~ell~~~~~~~ia~~~~~rl~~~  299 (301)
T KOG3013|consen  230 --------NDEHVSLNTRVNICRLANCIRALANCSIMITLTSITYCYEAS--LPYEIHELLEQEFMEVIAMEIAARLRTK  299 (301)
T ss_pred             --------cccCCCHHHHHHHHHHHHHHHHHHhcCeeeeHHHHHHHHHhc--CcchHHHHhhhhHHHHHHHHHHHHHHhh
Confidence                    124599999999999999999999999999999999999999  5569999999999999999999998765


Q ss_pred             h
Q 020356          324 K  324 (327)
Q Consensus       324 ~  324 (327)
                      .
T Consensus       300 ~  300 (301)
T KOG3013|consen  300 R  300 (301)
T ss_pred             c
Confidence            3

>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=1.6e-48  Score=359.07  Aligned_cols=225  Identities=29%  Similarity=0.462  Sum_probs=189.6

Q ss_pred             CCCceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEECcEEEEEecCCccCCCCCCEEEEEEEEEecceEEEEE
Q 020356           31 NPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEI  110 (327)
Q Consensus        31 ~~~~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~nk~v~V~pl~~rY~P~vGDiVIGrV~~V~~~~w~VDI  110 (327)
                      +..++|+|||.|.. ++.+++|||||..++++||+++|.+..+++.+.|+|++++|.|++||+|||+|+++.+++|+|||
T Consensus         6 ~~~~iV~PGd~vl~-~~~~~~G~Gty~~~~~iyssv~G~~~~~~~~v~VIpl~g~YiP~~gD~VIG~I~~v~~~~W~VDI   84 (239)
T COG1097           6 SMRKIVLPGDLVLA-EGSYKLGHGTYFEGGKIYSSVVGLLDVKGKLVRVIPLEGRYIPEVGDVVIGKIIEVGPSGWKVDI   84 (239)
T ss_pred             cccceecCCCccCC-CCCEecCCCcEecCCEEEEEEEeEEEEeCCEEEEEeCCCcccCCCCCEEEEEEEEEcccceEEEc
Confidence            44689999997754 44699999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccCCCccCCCCeEEEeChhhhh
Q 020356          111 NFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVK  190 (327)
Q Consensus       111 ~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~~lGkL~~G~lv~V~~~li~  190 (327)
                      ++++.|.||+|++      ++|+.+.++.+|+.+|++||+|+|||+++++++++.||||+.+||+|++|++++|+|++++
T Consensus        85 ~sp~~A~L~ls~~------~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p~kVp  158 (239)
T COG1097          85 GSPYPALLSLSDF------LRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPPSKVP  158 (239)
T ss_pred             CCccceEeehhhh------hcccccccccccccccccCCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEchhhcc
Confidence            9999999999976      3677777788999999999999999999999999999999999999999999999999999


Q ss_pred             hcccc----ccccC-ccceEEEEeecceeeeccccccccccccccCCCchhhhhhccCCCCccccCCCCCCCHHHHHHHH
Q 020356          191 RRKQH----FHHLE-EYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIAKCDKNSMDLDEQDGTCTPREARQNIC  265 (327)
Q Consensus       191 r~~~h----~~~L~-~~~~eiivG~NG~IWI~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~i~  265 (327)
                      |...|    +.+|+ +++|+|+||+||||||++..+......        ....+..+...        -++--|++.++
T Consensus       159 Rvig~~~sm~~~l~~~~~~~I~VG~NG~IWV~~~~~~~e~~~--------~~aI~~ie~ea--------~~~gltdr~~~  222 (239)
T COG1097         159 RVIGKKGSMLNMLKEKTGCEIIVGQNGRIWVDGENESLEELA--------IEAIRKIEREA--------HTSGLTDRIKE  222 (239)
T ss_pred             eEecCCCcHHHHhhhhcCeEEEEecCCEEEecCCCcchHHHH--------HHHHHHHhhhh--------hhhhHHHHHHH
Confidence            98644    55563 789999999999999999765321110        01111111101        16778899999


Q ss_pred             HHHHHHHHHHhCCC
Q 020356          266 RIANAIRVLSRLGF  279 (327)
Q Consensus       266 r~~n~i~~l~~~~~  279 (327)
                      ++.+++ .|++.+.
T Consensus       223 ~i~~~~-~~~~~~~  235 (239)
T COG1097         223 FLKKLL-RLKESKD  235 (239)
T ss_pred             HHHHHH-hcccccc
Confidence            999988 5554443

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=100.00  E-value=3.3e-42  Score=319.98  Aligned_cols=183  Identities=31%  Similarity=0.521  Sum_probs=165.7

Q ss_pred             CCCceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEECcEEEEEecCCccCCCCCCEEEEEEEEEecceEEEEE
Q 020356           31 NPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEI  110 (327)
Q Consensus        31 ~~~~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~nk~v~V~pl~~rY~P~vGDiVIGrV~~V~~~~w~VDI  110 (327)
                      ....+|+|||.|+  +++|++|+|||..+|+++||++|.+..+++.++|+|++++|.|++||+|+|+|+++++++|+|||
T Consensus         6 ~~~~~V~PGd~l~--~~~~~~G~Gty~~~g~i~As~~G~~~~~~~~i~V~p~~~~y~P~vGDiViG~V~~i~~~~~~vdI   83 (235)
T PRK04163          6 EDRKIVVPGDLLA--EGEFKAGRGTYKENGKIYSTVVGLVDIKDDKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEVDI   83 (235)
T ss_pred             eCCcEECCCCCcC--cCCeecCCceEEeCCEEEEEEeEEEEEECCEEEEEECCCcccCCCCCEEEEEEEEEeCceEEEEe
Confidence            3468999999996  34599999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccCCCccCCCCeEEEeChhhhh
Q 020356          111 NFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVK  190 (327)
Q Consensus       111 ~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~~lGkL~~G~lv~V~~~li~  190 (327)
                      ++++.|+||++++.      +++.+.|+.+|+++|++||+|+|+|+++++++.+.|||++.+||+|.+|++++|+|.+++
T Consensus        84 ~~~~~g~L~~s~i~------~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~~lG~L~~G~~~~V~~~~i~  157 (235)
T PRK04163         84 NSPYKAYLPVSEVL------GRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGKGLGKIEGGTIVEIKPVKVP  157 (235)
T ss_pred             CCCceeEEEHHHcC------CCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCCCCCccCCCEEEEECHHHHH
Confidence            99999999999874      344456778999999999999999999998888999999999999999999999999999


Q ss_pred             hcc----cccccc-CccceEEEEeecceeeeccccc
Q 020356          191 RRK----QHFHHL-EEYGIDLIIGCNGYIWIGEHVE  221 (327)
Q Consensus       191 r~~----~h~~~L-~~~~~eiivG~NG~IWI~~~~~  221 (327)
                      ++.    .++..| +.++|+|++|.||+|||.+++.
T Consensus       158 ~lig~~g~~i~~l~~~~~~~I~ig~NG~VwI~~~~~  193 (235)
T PRK04163        158 RVIGKKGSMINMLKEETGCDIIVGQNGRIWIKGPDE  193 (235)
T ss_pred             hhcCCCChhHhhhhhhhCcEEEEcCCcEEEEeeCCH
Confidence            983    345555 3689999999999999988654

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

Probab=100.00  E-value=1.3e-33  Score=254.94  Aligned_cols=177  Identities=26%  Similarity=0.412  Sum_probs=157.4

Q ss_pred             ceEecCCccCCCC-CceeecCCEEeeCCeEEEEEeeEEEEE--Cc----EEEEEecCCccCCCCCCEEEEEEEEEecceE
Q 020356           34 SCVTVGDTIPVYE-DGILKGHGTSDQKGELAATVCGVVERI--NK----LIYVRALRARYKPETGDIVIGRVIEVVPKRW  106 (327)
Q Consensus        34 ~iV~PGD~I~~~e-e~~~~G~Gty~~~g~i~Ssv~G~v~~~--nk----~v~V~pl~~rY~P~vGDiVIGrV~~V~~~~w  106 (327)
                      .+.+|||.++... ....+|+|.+..++.+..+.+|.+...  ++    ..||...++||+|.+||.|||+|+...++.|
T Consensus         2 ~~~~pg~~~~~~~~~sv~~G~g~~~~g~~~~~~~~G~~~~~~~gk~~~~v~~vds~~kRYiP~~~D~VIGiV~~~~gd~y   81 (230)
T KOG1004|consen    2 TFYFPGDSIPRPRLCSVVLGPGLRRRGQERLVTKCGRLRHKEPGKGGGGVYWVDSQQKRYIPVKGDHVIGIVTSKSGDIY   81 (230)
T ss_pred             ceecCCcccccCccCceeecCCccccCceEEeccccceeeccCCcccceeEEEecccceecCCCCCEEEEEEEeccCceE
Confidence            5789999997542 248899999999999999999977663  33    6799999999999999999999999999999


Q ss_pred             EEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccC-----CCccCCCCeE
Q 020356          107 KLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQ-----KYGKLERGQL  181 (327)
Q Consensus       107 ~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~-----~lGkL~~G~l  181 (327)
                      +|||+.++.|.  |+.++|+|+++|+||+         |+.||+|||+|...+++.+++|+|-+.     +||+|++|++
T Consensus        82 kVDigg~~~a~--L~~laFe~AtkrNrPn---------l~vGdliyakv~~a~~~~Epel~Cids~graaGfG~LkdG~i  150 (230)
T KOG1004|consen   82 KVDIGGSEPAS--LSYLAFEGATKRNRPN---------LQVGDLIYAKVVDANKDMEPELTCIDSTGRAAGFGVLKDGMI  150 (230)
T ss_pred             EEecCCCCeee--eeeccccCccccCCCc---------cccccEEEEEEEecCCCcCcceEEEcccCcccCcccccCceE
Confidence            99999999988  6889999999999998         899999999999999999999999555     9999999999


Q ss_pred             EEeChhhhhhccc-ccccc----CccceEEEEeecceeeeccccc
Q 020356          182 LTVDPYLVKRRKQ-HFHHL----EEYGIDLIIGCNGYIWIGEHVE  221 (327)
Q Consensus       182 v~V~~~li~r~~~-h~~~L----~~~~~eiivG~NG~IWI~~~~~  221 (327)
                      ++++++++|++.. -+..|    +.++|||++|+||+|||++.+.
T Consensus       151 f~vs~~~~R~Ll~p~~~iLq~vGk~~~FEia~GlNGriWV~ae~~  195 (230)
T KOG1004|consen  151 FKVSLGLCRKLLLPDCPILQTVGKKYPFEIAFGLNGRIWVKAETL  195 (230)
T ss_pred             EEecHHHHHHHHcCCCcHHHHhhcccceEEEEecCceEEEeccCc
Confidence            9999999999864 35555    4789999999999999988654

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=99.94  E-value=3.7e-26  Score=205.78  Aligned_cols=134  Identities=31%  Similarity=0.401  Sum_probs=117.7

Q ss_pred             CCCceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEE--CcEEEEEecCC-ccCCCCCCEEEEEEEEEecceEE
Q 020356           31 NPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERI--NKLIYVRALRA-RYKPETGDIVIGRVIEVVPKRWK  107 (327)
Q Consensus        31 ~~~~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~--nk~v~V~pl~~-rY~P~vGDiVIGrV~~V~~~~w~  107 (327)
                      +..++|+|||.|+..++ |++|+|||+++|.|+||++|.++.+  ++.++|.|++. .|.|++||+|+|+|+++.+++|+
T Consensus         3 ~~~~~V~PGe~l~~~~e-~~~G~Gty~~~~~i~as~~G~~~id~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~i~~~g~~   81 (189)
T PRK09521          3 KQGDLVLPGDYLAVIEE-YLPGEGTYEDNGEVYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVYGRVVDVKEQRAL   81 (189)
T ss_pred             ccCCEECCCCccccccc-eEcCCCEEeeCCEEEEEeeEEEEEcCCCCEEEEecCcCCCCCCCCCCEEEEEEEEEcCCeEE
Confidence            35689999999987666 9999999999999999999999874  56899999987 89999999999999999999999


Q ss_pred             EEEcC----------ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccCCCccCC
Q 020356          108 LEINF----------TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLE  177 (327)
Q Consensus       108 VDI~s----------~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~~lGkL~  177 (327)
                      |||.+          ...|++|.++++        ....+  +|+++|++||+|.|+|++++  +.+.||+++.+||+|.
T Consensus        82 V~I~~~~~~~~~l~~~~~G~l~~s~i~--------~~~~~--~~~~~~~~GD~V~akV~~i~--~~i~LS~k~~~lGvv~  149 (189)
T PRK09521         82 VRIVSIEGSERELATSKLAYIHISQVS--------DGYVE--SLTDAFKIGDIVRAKVISYT--DPLQLSTKGKDLGVIY  149 (189)
T ss_pred             EEEEEecccccccCCCceeeEEhhHcC--------hhhhh--hHHhccCCCCEEEEEEEecC--CcEEEEEecCCceEEE
Confidence            99964          467888887664        12222  78999999999999999998  7899999999999996

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

Probab=99.91  E-value=3.1e-24  Score=191.59  Aligned_cols=134  Identities=31%  Similarity=0.452  Sum_probs=117.7

Q ss_pred             CCCceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEE--ECcEEEEEecCC-ccCCCCCCEEEEEEEEEecceEE
Q 020356           31 NPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVER--INKLIYVRALRA-RYKPETGDIVIGRVIEVVPKRWK  107 (327)
Q Consensus        31 ~~~~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~--~nk~v~V~pl~~-rY~P~vGDiVIGrV~~V~~~~w~  107 (327)
                      ....+|+|||.|+..|| |++|.|||+++|.|+|+..|.+.+  .|..++|+|.++ ..+|+.||+|+|+|+++..+++.
T Consensus         3 ~~g~~v~PGd~~a~~EE-~~~G~gt~~~~g~i~Aa~~G~~~~d~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~~~~a~   81 (188)
T COG1096           3 KDGTFVLPGDVLAVIEE-FLPGEGTYEEGGEIRAAATGVVRRDDKNRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRAL   81 (188)
T ss_pred             ccCcEEcCcceeeeeee-eecCCCeEeECCEEEEeecccEEEcccceEEEeccCCCCCCCCCCCCEEEEEEeeccceEEE
Confidence            35789999999998888 999999999999999999999998  578999999998 78999999999999999999999


Q ss_pred             EEEcC----------ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccCCCccCC
Q 020356          108 LEINF----------TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLE  177 (327)
Q Consensus       108 VDI~s----------~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~~lGkL~  177 (327)
                      |.|-+          +..|.+|+|++.        ..+..  +++++|++||+|+|+|.+..  ..+.|||+++.||++.
T Consensus        82 V~i~~ve~~~r~~~~~~~~~ihvs~~~--------~~~~~--~~~d~f~~GDivrA~Vis~~--~~~~Lst~~~dlGVI~  149 (188)
T COG1096          82 VRIVGVEGKERELATSGAADIHVSQVR--------DGYVE--KLSDAFRIGDIVRARVISTG--DPIQLSTKGNDLGVIY  149 (188)
T ss_pred             EEEEEEecccccCCCCceeeEEEEecc--------ccccc--ccccccccccEEEEEEEecC--CCeEEEecCCcceEEE
Confidence            99854          356778888763        12222  56789999999999999987  5799999999999986

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

Probab=99.85  E-value=5.6e-21  Score=168.46  Aligned_cols=159  Identities=25%  Similarity=0.252  Sum_probs=129.7

Q ss_pred             CceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEE--CcEEEEEecC----CccCCCCCCEEEEEEEEEecceE
Q 020356           33 NSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERI--NKLIYVRALR----ARYKPETGDIVIGRVIEVVPKRW  106 (327)
Q Consensus        33 ~~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~--nk~v~V~pl~----~rY~P~vGDiVIGrV~~V~~~~w  106 (327)
                      ..+|+|||++|..++.+..|.|||+.+++|+||++|...+.  ++.+.|....    ..-+|.+||||..+|..++.+++
T Consensus         5 ~~~~lpG~~~c~~e~~~~~g~Gtye~~~yI~aS~ag~~~~~~~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~~i~~rfA   84 (193)
T KOG3409|consen    5 ETLVLPGEVVCRAEGEYRMGEGTYERNGYIFASVAGVNFRDNLVQKIEVVSVEKQLFNELLPFVGAIVTARVSRINLRFA   84 (193)
T ss_pred             eEEEcccceeeecccccccccceeecCCeEEeccccceeecCCccceeeeeecccchhhcCCccCcEEEEEEEeecccee
Confidence            57899999999887779999999999999999999955443  3455554433    35799999999999999999999


Q ss_pred             EEEEcCccceeeecccccCCCccc---ccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccCCCccC------C
Q 020356          107 KLEINFTQDAILMLSSMNLPDGIQ---RRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKL------E  177 (327)
Q Consensus       107 ~VDI~s~~~a~L~ls~v~fpg~i~---rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~~lGkL------~  177 (327)
                      +|+|-+..+-.|.-   .|.|.++   .|.++.|.+++.+.|+|||+|.|+|.+.+...++.|||.++.||++      .
T Consensus        85 kv~I~~V~d~~lk~---~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LTtAeneLGVV~a~as~~  161 (193)
T KOG3409|consen   85 KVDILSVGDKPLKK---SFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLTTAENELGVVFARASET  161 (193)
T ss_pred             eEEEEEEcCEEhhh---hhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCCcEEEEEecccceEEEEecccc
Confidence            99999876655321   3666555   4567788899999999999999999997766689999999999998      3


Q ss_pred             CCeEEEeChhhhhhccc
Q 020356          178 RGQLLTVDPYLVKRRKQ  194 (327)
Q Consensus       178 ~G~lv~V~~~li~r~~~  194 (327)
                      ++.|++|+...+.--+.
T Consensus       162 g~~M~pvdw~~mqsp~T  178 (193)
T KOG3409|consen  162 GEPMVPVDWQEMQSPKT  178 (193)
T ss_pred             CCceeeccceeEEcCcc
Confidence            78899988776554333

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

Probab=99.85  E-value=4.4e-21  Score=153.19  Aligned_cols=75  Identities=29%  Similarity=0.421  Sum_probs=68.5

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCce
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSL  164 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i  164 (327)
                      ||+|++||+|||+|+++..++|+|||++++.|.||+  .+|+|+++|+|+.         |++||+|+|||++++++.++
T Consensus         1 rY~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~--~~f~gatk~~rp~---------L~~GDlV~ArV~~~~~~~~~   69 (86)
T cd05790           1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSY--LAFEGATKRNRPN---------LNVGDLVYARVVKANRDMEP   69 (86)
T ss_pred             CCcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEech--HHccccccccccc---------CCCCCEEEEEEEecCCCCCe
Confidence            699999999999999999999999999999999877  4699997776544         89999999999999999999


Q ss_pred             EEEEcc
Q 020356          165 QLQARN  170 (327)
Q Consensus       165 ~Lstr~  170 (327)
                      +|+|.+
T Consensus        70 eLtc~~   75 (86)
T cd05790          70 ELSCVD   75 (86)
T ss_pred             EEEEeC
Confidence            999965

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".

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

Probab=99.81  E-value=1.1e-19  Score=146.54  Aligned_cols=83  Identities=28%  Similarity=0.396  Sum_probs=75.3

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEE--------cCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEe
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEI--------NFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRS  157 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI--------~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~s  157 (327)
                      |.|++||+|+|+|++++.++|.|||        ++++.|.||.+++        +..+.|+++|+++|++||+|+|||++
T Consensus         2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv--------~~~~~d~~~~~~~f~~GDiV~AkVis   73 (92)
T cd05791           2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDI--------RATEKDKVEMYKCFRPGDIVRAKVIS   73 (92)
T ss_pred             CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHc--------cccccchHHHHhhcCCCCEEEEEEEE
Confidence            8999999999999999999999999        7788888888765        34667888999999999999999999


Q ss_pred             cCCCCceEEEEccCCCccC
Q 020356          158 SQGDGSLQLQARNQKYGKL  176 (327)
Q Consensus       158 v~~~g~i~Lstr~~~lGkL  176 (327)
                      +++..++.|||++++||++
T Consensus        74 ~~~~~~~~Lst~~~~lGVv   92 (92)
T cd05791          74 LGDASSYYLSTAENELGVV   92 (92)
T ss_pred             cCCCCCcEEEecCCCCccC
Confidence            9877789999999999985

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=99.70  E-value=1.3e-16  Score=124.73  Aligned_cols=82  Identities=35%  Similarity=0.477  Sum_probs=73.9

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCce
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSL  164 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i  164 (327)
                      +|+|++||+|+|+|+++..+.|.|||++..+|++|+++++-+          ...+|++.|++||+|.|+|++++.++.+
T Consensus         1 ~y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~----------~~~~~~~~~~~GD~i~~~V~~~~~~~~i   70 (82)
T cd04454           1 RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEK----------DKKEIRKSLQPGDLILAKVISLGDDMNV   70 (82)
T ss_pred             CCCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCc----------chHHHHhcCCCCCEEEEEEEEeCCCCCE
Confidence            699999999999999999999999999999999999987521          1237888999999999999999877889


Q ss_pred             EEEEccCCCccC
Q 020356          165 QLQARNQKYGKL  176 (327)
Q Consensus       165 ~Lstr~~~lGkL  176 (327)
                      .||+++.+||+|
T Consensus        71 ~LS~~~~~~Gvi   82 (82)
T cd04454          71 LLTTADNELGVI   82 (82)
T ss_pred             EEEECCCCCccC
Confidence            999999999986

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=99.59  E-value=9.2e-15  Score=114.90  Aligned_cols=86  Identities=62%  Similarity=0.925  Sum_probs=74.7

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCce
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSL  164 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i  164 (327)
                      +|.|++||+|.|+|+++.+++|+|+|+....|+||++++.-+      +......++.+.|++||.|.|+|+++++++.+
T Consensus         1 ~y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~------~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~~i   74 (86)
T cd05789           1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLP------RTDEDELNMRSYLDEGDLIVAEVQSVDSDGSV   74 (86)
T ss_pred             CCcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCC------CCccchHHHHhhCCCCCEEEEEEEEECCCCCE
Confidence            699999999999999999999999999999999999987521      11112237788899999999999999888899


Q ss_pred             EEEEccCCCccC
Q 020356          165 QLQARNQKYGKL  176 (327)
Q Consensus       165 ~Lstr~~~lGkL  176 (327)
                      .||++..+||+|
T Consensus        75 ~LS~~~~~~g~~   86 (86)
T cd05789          75 SLHTRSLKYGKL   86 (86)
T ss_pred             EEEeCcccccCC
Confidence            999999999986

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=99.38  E-value=9.1e-13  Score=104.50  Aligned_cols=69  Identities=38%  Similarity=0.484  Sum_probs=44.0

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCc----------cceeeecccccCCCcccc---cccccchhhhhcccCCCCEEEE
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFT----------QDAILMLSSMNLPDGIQR---RRTAVDELNMRSIFTENDLVCA  153 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~----------~~a~L~ls~v~fpg~i~r---rr~~~de~~mr~~~~~GDlV~A  153 (327)
                      +|++||+|+|+|++++++++.|+|.+.          ....  +.+ .|.|.+++   |.++.|+++|.++|+|||+|+|
T Consensus         1 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~--l~~-~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA   77 (82)
T PF10447_consen    1 LPKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRP--LKE-PFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRA   77 (82)
T ss_dssp             ---TT-EEEEEEEEE-SSEEEEEEEES----------SSS-------SS-S-EEEEGGGT-SS----GGGT--SSSEEEE
T ss_pred             CCCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcc--ccc-ccEEEEEeeeecccccchhhHHhccCCCCEEEE
Confidence            599999999999999999999999876          2222  222 47777764   5678899999999999999999


Q ss_pred             EEEec
Q 020356          154 EVRSS  158 (327)
Q Consensus       154 eV~sv  158 (327)
                      +|.|+
T Consensus        78 ~ViSl   82 (82)
T PF10447_consen   78 RVISL   82 (82)
T ss_dssp             EEEEE
T ss_pred             EEeeC
Confidence            99984

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=99.19  E-value=1.4e-11  Score=84.79  Aligned_cols=39  Identities=36%  Similarity=0.525  Sum_probs=33.9

Q ss_pred             eEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEEC
Q 020356           35 CVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERIN   74 (327)
Q Consensus        35 iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~n   74 (327)
                      +|+|||.|+..++ |++|+|||+.+|+|+||++|.++++|
T Consensus         1 iV~PG~~l~~~~e-~~~G~GTY~~~g~I~asv~G~v~~~n   39 (39)
T PF14382_consen    1 IVVPGDRLGSSEE-YMPGHGTYVRDGNIYASVAGTVKIDN   39 (39)
T ss_dssp             EE-TT-EEEETTT-SEESTTEEEETTEEEESSSEEEEEET
T ss_pred             CCCCCCEeecCCC-EecCCCEEEeCCEEEEEeeEEEEEcC
Confidence            6999999998665 99999999999999999999998865

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

Probab=98.92  E-value=2.3e-09  Score=90.68  Aligned_cols=77  Identities=14%  Similarity=0.231  Sum_probs=69.1

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEE
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQL  166 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~L  166 (327)
                      .+++||+|-|+||++++.++||++.....+++|||+++        ..++.  ++.+++.+||-|.++|++++++|.+.|
T Consensus         2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa--------~~fVk--dI~d~L~vG~eV~vKVl~ide~GKisL   71 (129)
T COG1098           2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIA--------DGFVK--DIHDHLKVGQEVKVKVLDIDENGKISL   71 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEecCCCcceEEehHhh--------hhhHH--hHHHHhcCCCEEEEEEEeeccCCCcce
Confidence            46899999999999999999999999999999999985        23444  789999999999999999999999999


Q ss_pred             EEccCCC
Q 020356          167 QARNQKY  173 (327)
Q Consensus       167 str~~~l  173 (327)
                      |+|....
T Consensus        72 SIr~~~e   78 (129)
T COG1098          72 SIRKLEE   78 (129)
T ss_pred             ehHHhhh
Confidence            9997544

>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=98.86  E-value=1.2e-08  Score=78.24  Aligned_cols=70  Identities=21%  Similarity=0.398  Sum_probs=59.1

Q ss_pred             CCCCEEEEEEEEEec-ceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEE
Q 020356           89 ETGDIVIGRVIEVVP-KRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQ  167 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~-~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Ls  167 (327)
                      ++||+|.|+|+++.+ .+++|++....+|.+|+|+++      ..+  ..  ++.+.|++||.|.|+|.+++. +.+.||
T Consensus         2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s------~~~--~~--~~~~~~~~Gd~v~~kV~~~~~-~~i~LS   70 (72)
T cd05704           2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLS------DSY--TE--NPLEGFKPGKIVRCCILSKKD-GKYQLS   70 (72)
T ss_pred             CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhc------Ccc--cC--CHHHhCCCCCEEEEEEEEecC-CEEEEE
Confidence            589999999999986 799999999999999999875      111  11  446789999999999999975 789998


Q ss_pred             Ec
Q 020356          168 AR  169 (327)
Q Consensus       168 tr  169 (327)
                      +|
T Consensus        71 l~   72 (72)
T cd05704          71 LR   72 (72)
T ss_pred             eC
Confidence            75

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.

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

Probab=98.77  E-value=3.9e-08  Score=74.03  Aligned_cols=69  Identities=25%  Similarity=0.355  Sum_probs=57.5

Q ss_pred             CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEEEc
Q 020356           91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQAR  169 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Lstr  169 (327)
                      ||+|.|+|+++.+++|+|+++....|+||.+++.-+      +  .+  ++.++|++||.|.|+|.++++ .+.+.||.+
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~------~--~~--~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDD------P--IE--NGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCcc------c--cC--CHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence            899999999999999999999899999999987521      1  11  567889999999999999984 456877753

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

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

Probab=98.69  E-value=1.3e-07  Score=71.92  Aligned_cols=72  Identities=17%  Similarity=0.290  Sum_probs=59.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEcC--ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCce
Q 020356           88 PETGDIVIGRVIEVVPKRWKLEINF--TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSL  164 (327)
Q Consensus        88 P~vGDiVIGrV~~V~~~~w~VDI~s--~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i  164 (327)
                      |+.|++|.|+|+++...+|+|++..  ...|++|++++...      + . .  ++.+.|+.||.|.|+|.+++. .+.+
T Consensus         1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~------~-~-~--~~~~~~~~Gd~v~vkv~~~d~~~~~i   70 (76)
T cd04452           1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRR------R-I-R--SIRKLVKVGRKEVVKVIRVDKEKGYI   70 (76)
T ss_pred             CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCc------c-c-C--CHHHeeCCCCEEEEEEEEEECCCCEE
Confidence            7899999999999999999999974  37999999987511      1 1 1  457889999999999999986 4678


Q ss_pred             EEEEc
Q 020356          165 QLQAR  169 (327)
Q Consensus       165 ~Lstr  169 (327)
                      .|+++
T Consensus        71 ~ls~k   75 (76)
T cd04452          71 DLSKK   75 (76)
T ss_pred             EEEEc
Confidence            99886

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=98.66  E-value=2e-07  Score=68.59  Aligned_cols=69  Identities=23%  Similarity=0.386  Sum_probs=58.1

Q ss_pred             CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEc
Q 020356           91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQAR  169 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr  169 (327)
                      ||+|.|+|+++.+.+|+|+|.....|++|.+++.  +    .+  ..  ++.+.|++||.|.++|.+++..+.+.||++
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 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIA--H----KR--VK--DVKDVLKEGDKVKVKVLSIDARGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcC--C----cc--cC--CHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence            8999999999999999999999999999998764  1    11  11  445779999999999999987778999875

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=98.64  E-value=2e-07  Score=70.17  Aligned_cols=71  Identities=23%  Similarity=0.328  Sum_probs=59.7

Q ss_pred             CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEEEEc
Q 020356           91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQLQAR  169 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~Lstr  169 (327)
                      ||+|.|+|+++.+++|+|+|.....|++|.+++.-+      .  .+  ++.+.|++||.|.|+|.+++.. +.+.|+++
T Consensus         1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~------~--~~--~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k   70 (73)
T cd05691           1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRD------R--VE--DATERFKVGDEVEAKITNVDRKNRKISLSIK   70 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCc------c--cc--CHHHccCCCCEEEEEEEEEeCCCCEEEEEEE
Confidence            899999999999999999999889999999987511      1  11  4567799999999999999875 67999987


Q ss_pred             cC
Q 020356          170 NQ  171 (327)
Q Consensus       170 ~~  171 (327)
                      ..
T Consensus        71 ~~   72 (73)
T cd05691          71 AK   72 (73)
T ss_pred             Ec
Confidence            54

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=98.61  E-value=3e-07  Score=69.69  Aligned_cols=72  Identities=19%  Similarity=0.314  Sum_probs=60.9

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEE
Q 020356           88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQL  166 (327)
Q Consensus        88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~L  166 (327)
                      |++||+|-|+|+++..++++|+++....|++|+++++..      .  .+  +....|++||.|.|+|.+++.+ +.+.|
T Consensus         2 ~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~------~--~~--~~~~~~~~G~~v~v~v~~vd~~~~~i~l   71 (74)
T PF00575_consen    2 LKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDD------R--ID--DPSEVYKIGQTVRVKVIKVDKEKGRIRL   71 (74)
T ss_dssp             SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSS------E--ES--SSHGTCETTCEEEEEEEEEETTTTEEEE
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCc------c--cc--ccccccCCCCEEEEEEEEEECCCCeEEE
Confidence            689999999999999999999999999999999988621      1  11  4456799999999999999875 45888


Q ss_pred             EEc
Q 020356          167 QAR  169 (327)
Q Consensus       167 str  169 (327)
                      |+|
T Consensus        72 S~k   74 (74)
T PF00575_consen   72 SLK   74 (74)
T ss_dssp             EST
T ss_pred             EEC
Confidence            875

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 ....

>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=98.60  E-value=1.8e-07  Score=72.33  Aligned_cols=72  Identities=14%  Similarity=0.153  Sum_probs=57.6

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQLQ  167 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~Ls  167 (327)
                      ++||+|.|+|+++++.+++|+++....|.+|+++++...   ...+    -++.+.|++||.|.|+|.+++++ +.+.||
T Consensus         2 k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~---~~~~----~~~~~~~~~G~~v~~kVl~id~~~~~i~LS   74 (74)
T cd05705           2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYF---VSDP----SLYNKYLPEGKLLTAKVLSVNSEKNLVELS   74 (74)
T ss_pred             CCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCcc---ccCh----hhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence            589999999999999999999998899999999886221   0111    13568899999999999999864 456553

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.

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

Probab=98.57  E-value=4.3e-07  Score=66.49  Aligned_cols=71  Identities=23%  Similarity=0.332  Sum_probs=58.8

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQLQ  167 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~Ls  167 (327)
                      ++||+|.|+|+++...+|+|+++....|++|.+++.-+      .    ..++.+.|++||.|.|+|.+++.+ +.+.|+
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~------~----~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls   70 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDK------R----VKDPEEVLKVGDEVKVKVLSVDEEKGRIILS   70 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCcc------c----cCCHHHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence            47999999999999999999999889999999877511      1    114456799999999999999875 778887


Q ss_pred             Ec
Q 020356          168 AR  169 (327)
Q Consensus       168 tr  169 (327)
                      ++
T Consensus        71 ~~   72 (72)
T smart00316       71 LK   72 (72)
T ss_pred             eC
Confidence            64

>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=98.55  E-value=5.6e-07  Score=68.22  Aligned_cols=71  Identities=23%  Similarity=0.226  Sum_probs=59.1

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ  167 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls  167 (327)
                      ++|++|.|+|+++.+++++|++.....|++|+++++-      ..  .  .+..+.|++||.|.|+|.+++. .+.+.||
T Consensus         2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~------~~--~--~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls   71 (73)
T cd05706           2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALD------DY--S--EALPYKFKKNDIVRACVLSVDVPNKKIALS   71 (73)
T ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccC------cc--c--cccccccCCCCEEEEEEEEEeCCCCEEEEE
Confidence            5899999999999999999999999999999998741      11  1  1346779999999999999986 4688888


Q ss_pred             Ec
Q 020356          168 AR  169 (327)
Q Consensus       168 tr  169 (327)
                      +|
T Consensus        72 ~~   73 (73)
T cd05706          72 LR   73 (73)
T ss_pred             EC
Confidence            74

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.

>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=98.53  E-value=6.1e-07  Score=68.03  Aligned_cols=74  Identities=18%  Similarity=0.196  Sum_probs=60.8

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcC-ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINF-TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQL  166 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s-~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~L  166 (327)
                      ++|++|.|+|+++...+|+|++.. ...|++|++++. +.     + .   .++.+.|++||.|.|+|.+++. .+.+.|
T Consensus         1 ~~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~-~~-----~-~---~~~~~~~~~Gd~v~v~i~~vd~~~~~i~l   70 (77)
T cd05708           1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEIS-DN-----R-V---ADASKLFRVGDKVRAKVLKIDAEKKRISL   70 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCC-CC-----c-c---CCHhHeecCCCEEEEEEEEEeCCCCEEEE
Confidence            469999999999999999999984 789999999874 11     1 1   1356789999999999999987 578999


Q ss_pred             EEccCC
Q 020356          167 QARNQK  172 (327)
Q Consensus       167 str~~~  172 (327)
                      +++...
T Consensus        71 s~k~~~   76 (77)
T cd05708          71 GLKASY   76 (77)
T ss_pred             EEEeec
Confidence            987653

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=98.53  E-value=6.2e-07  Score=77.68  Aligned_cols=76  Identities=18%  Similarity=0.211  Sum_probs=64.2

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEE
Q 020356           88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQ  167 (327)
Q Consensus        88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Ls  167 (327)
                      .++|++|.|+|+++++.+++|+|.....|++|++++.-.      .  .  .++.+.|++||.|.|+|.+++.++.+.|+
T Consensus         3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~------~--v--~~~~~~l~vGD~VkvkV~~id~~gkI~LS   72 (139)
T PRK08582          3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADN------Y--V--KDINDHLKVGDEVEVKVLNVEDDGKIGLS   72 (139)
T ss_pred             CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcc------c--c--cccccccCCCCEEEEEEEEECCCCcEEEE
Confidence            468999999999999999999999989999999987511      1  1  14567899999999999999877899999


Q ss_pred             EccCCC
Q 020356          168 ARNQKY  173 (327)
Q Consensus       168 tr~~~l  173 (327)
                      ++....
T Consensus        73 lk~~~~   78 (139)
T PRK08582         73 IKKAKD   78 (139)
T ss_pred             EEeccc
Confidence            976533

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

Probab=98.51  E-value=9.3e-07  Score=67.67  Aligned_cols=71  Identities=20%  Similarity=0.197  Sum_probs=58.8

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEcC-ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEE
Q 020356           88 PETGDIVIGRVIEVVPKRWKLEINF-TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQL  166 (327)
Q Consensus        88 P~vGDiVIGrV~~V~~~~w~VDI~s-~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~L  166 (327)
                      |+.|+++-|+|+++.+.+++|++.. ...|++|++++.-      .+  .+  +..++|++||.|.++|.+++..+.+.|
T Consensus         1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~------~~--~~--~~~~~~~~Gd~v~vkv~~vd~~~ki~l   70 (73)
T cd05686           1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSS------CR--VD--DPSEVVDVGEKVWVKVIGREMKDKMKL   70 (73)
T ss_pred             CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCC------Cc--cc--CHhhEECCCCEEEEEEEEECCCCcEEE
Confidence            6899999999999999999999954 2689999998751      11  22  567789999999999999987667777


Q ss_pred             EE
Q 020356          167 QA  168 (327)
Q Consensus       167 st  168 (327)
                      |+
T Consensus        71 s~   72 (73)
T cd05686          71 SL   72 (73)
T ss_pred             Ee
Confidence            75

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.

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=98.49  E-value=4.3e-07  Score=88.48  Aligned_cols=74  Identities=15%  Similarity=0.290  Sum_probs=64.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEc--CccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCc
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEIN--FTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGS  163 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~--s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~  163 (327)
                      .|++||+|.|+|+.+...+++|+|.  ....|++|+|.++      +++..    ++++++++||.|.++|++++. .+.
T Consensus        14 ~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS------~~ri~----~i~d~vkvGd~v~vkVl~VD~ekg~   83 (319)
T PTZ00248         14 FPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELS------KRRIR----SINKLIRVGRHEVVVVLRVDKEKGY   83 (319)
T ss_pred             CCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhc------ccccC----CHHHhcCCCCEEEEEEEEEeCCCCE
Confidence            7999999999999999999999996  3589999999987      33332    788999999999999999975 578


Q ss_pred             eEEEEcc
Q 020356          164 LQLQARN  170 (327)
Q Consensus       164 i~Lstr~  170 (327)
                      +.||.|.
T Consensus        84 IdLS~K~   90 (319)
T PTZ00248         84 IDLSKKR   90 (319)
T ss_pred             EEEEeee
Confidence            9999875

>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=98.48  E-value=4.3e-07  Score=74.34  Aligned_cols=81  Identities=15%  Similarity=0.226  Sum_probs=63.1

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccc----------cccccchhhhhcccCCCCEEEEEEEec
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQR----------RRTAVDELNMRSIFTENDLVCAEVRSS  158 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~r----------rr~~~de~~mr~~~~~GDlV~AeV~sv  158 (327)
                      ++||+|.|+|+++.+.+.+|++.....|++|+++++- ..+++          ...+.+..++.+.|++||+|.|+|.++
T Consensus         2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~   80 (100)
T cd05693           2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISD-AYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL   80 (100)
T ss_pred             CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhH-HHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence            5899999999999999999999988999999998751 10011          011222346789999999999999999


Q ss_pred             CCC----CceEEEEcc
Q 020356          159 QGD----GSLQLQARN  170 (327)
Q Consensus       159 ~~~----g~i~Lstr~  170 (327)
                      +..    ..+.||.|.
T Consensus        81 d~~~~~~~~i~LSlr~   96 (100)
T cd05693          81 DKSKSGKKRIELSLEP   96 (100)
T ss_pred             cCCcCCCcEEEEEecH
Confidence            874    578888874

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.

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

Probab=98.44  E-value=9.6e-07  Score=79.10  Aligned_cols=89  Identities=27%  Similarity=0.388  Sum_probs=68.1

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccc---cccccchhhhhcccCCCCEEEEEEEecC---
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQR---RRTAVDELNMRSIFTENDLVCAEVRSSQ---  159 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~r---rr~~~de~~mr~~~~~GDlV~AeV~sv~---  159 (327)
                      |.|.+|+++.|+|++++..+++|+++ +.++++|.+++. |....-   +..-.. -+....|+.||.|+++|.+++   
T Consensus        77 f~p~~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~~l~-~~~~~~d~~~~~~~~-~~~~~~~~~Gd~VrvrV~~v~~~~  153 (179)
T TIGR00448        77 FKPELGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVSQVT-DDYCYYDPKESALIG-KETKKVLDEGDKVRARIVALSLKD  153 (179)
T ss_pred             EeccCCCEEEEEEEEEEeeEEEEEeC-CceEEEEcHHhC-CCceEEccccceEEE-ccCCeEEcCCCEEEEEEEEEEccC
Confidence            67899999999999999999999995 689999888764 321110   000000 023567999999999999986   


Q ss_pred             ---CCCceEEEEccCCCccCC
Q 020356          160 ---GDGSLQLQARNQKYGKLE  177 (327)
Q Consensus       160 ---~~g~i~Lstr~~~lGkL~  177 (327)
                         +...+.||+|+++||+++
T Consensus       154 ~~~~~~~I~lt~k~~~LG~~~  174 (179)
T TIGR00448       154 RRPEGSKIGLTMRQPLLGKLE  174 (179)
T ss_pred             CCCCcceEEEEeccCcCCccc
Confidence               235799999999999986

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

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

Probab=98.42  E-value=9.5e-07  Score=79.39  Aligned_cols=90  Identities=27%  Similarity=0.362  Sum_probs=67.8

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccc---cccccchhhhhcccCCCCEEEEEEEecCCC
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQR---RRTAVDELNMRSIFTENDLVCAEVRSSQGD  161 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~r---rr~~~de~~mr~~~~~GDlV~AeV~sv~~~  161 (327)
                      -|.|.+|++|.|+|+++...+|+|+++ +.+++++.+++. +....-   +..-.. .+...+++.||.|+++|.+++.+
T Consensus        76 vf~P~~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~-~~~~~~d~~~~~~~~-~~~~~~i~~Gd~VrvrV~~v~~~  152 (187)
T PRK08563         76 VFKPELQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIM-DDYISYDPKNGRLIG-KESKRVLKVGDVVRARIVAVSLK  152 (187)
T ss_pred             EEeccCCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcC-CCceEEccccceEEE-ccCCeEEcCCCEEEEEEEEEEcc
Confidence            356999999999999999999999998 688998887663 211110   000000 13467799999999999999753


Q ss_pred             ------CceEEEEccCCCccCC
Q 020356          162 ------GSLQLQARNQKYGKLE  177 (327)
Q Consensus       162 ------g~i~Lstr~~~lGkL~  177 (327)
                            ..+.||+++++||+++
T Consensus       153 ~~~~~~~~I~ls~~~~~LG~~~  174 (187)
T PRK08563        153 ERRPRGSKIGLTMRQPGLGKLE  174 (187)
T ss_pred             cCCCCCCEEEEEecCCCCCcHH
Confidence                  3689999999999985

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

Probab=98.41  E-value=1.1e-06  Score=83.61  Aligned_cols=76  Identities=21%  Similarity=0.298  Sum_probs=63.6

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcC--ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-C
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINF--TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-G  162 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s--~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g  162 (327)
                      -.|++||+|.|+|+++.+.+|+|++..  ...|++|+|+++      .++..    ++++.|++||.|.|+|.+++.. +
T Consensus         4 ~~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls------~~~i~----~i~~~~kvGd~V~vkVi~VD~~k~   73 (262)
T PRK03987          4 EWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVA------SGWVK----NIRDHVKEGQKVVCKVIRVDPRKG   73 (262)
T ss_pred             CCCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcC------ccccc----CHHHhCCCCCEEEEEEEEEecccC
Confidence            479999999999999999999999975  479999999875      11111    5678899999999999999864 6


Q ss_pred             ceEEEEccC
Q 020356          163 SLQLQARNQ  171 (327)
Q Consensus       163 ~i~Lstr~~  171 (327)
                      .+.||++..
T Consensus        74 ~I~LSlK~v   82 (262)
T PRK03987         74 HIDLSLKRV   82 (262)
T ss_pred             eEEEEEEec
Confidence            799999753

>PRK07252 hypothetical protein; Provisional

Probab=98.39  E-value=2e-06  Score=72.83  Aligned_cols=73  Identities=16%  Similarity=0.269  Sum_probs=60.9

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ  167 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls  167 (327)
                      ++||+|.|+|+++...+|+|+|.....|++|++++.-.      +  .+  +..+.|++||.|.|+|.+++. .+.+.|+
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~------~--~~--~~~~~~~vGD~V~VkI~~iD~~~~ri~lS   71 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTG------F--ID--NIHQLLKVGEEVLVQVVDFDEYTGKASLS   71 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCc------c--cc--ChhhccCCCCEEEEEEEEEeCCCCEEEEE
Confidence            47999999999999999999999889999999987411      1  11  345779999999999999987 5788898


Q ss_pred             EccC
Q 020356          168 ARNQ  171 (327)
Q Consensus       168 tr~~  171 (327)
                      ++..
T Consensus        72 lk~~   75 (120)
T PRK07252         72 LRTL   75 (120)
T ss_pred             Eeec
Confidence            8764

>PRK08059 general stress protein 13; Validated

Probab=98.38  E-value=2e-06  Score=72.69  Aligned_cols=76  Identities=20%  Similarity=0.291  Sum_probs=63.3

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEE
Q 020356           88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQL  166 (327)
Q Consensus        88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~L  166 (327)
                      .++|++|.|+|+++...+|+|+|.....|++|++++.-+      +  .  -++.+.|++||.|.|+|.+++. .+.+.|
T Consensus         5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~------~--~--~~~~~~~~vGD~I~vkI~~id~~~~~i~l   74 (123)
T PRK08059          5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHG------F--V--KDIHDFLSVGDEVKVKVLSVDEEKGKISL   74 (123)
T ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcc------c--c--cCHHHcCCCCCEEEEEEEEEECCCCeEEE
Confidence            468999999999999999999999999999999987411      1  1  1456789999999999999965 678999


Q ss_pred             EEccCCC
Q 020356          167 QARNQKY  173 (327)
Q Consensus       167 str~~~l  173 (327)
                      +++....
T Consensus        75 slk~~~~   81 (123)
T PRK08059         75 SIRATEE   81 (123)
T ss_pred             EEEEccc
Confidence            9987644

>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=98.36  E-value=1.6e-06  Score=64.99  Aligned_cols=67  Identities=19%  Similarity=0.282  Sum_probs=54.6

Q ss_pred             CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356           91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ  167 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls  167 (327)
                      |++|.|+|+++.+.+++|++.....|++|+++++-      ..  ..  +..+.|++||.|.|+|.++++ .+.+.||
T Consensus         1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~------~~--~~--~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls   68 (68)
T cd05707           1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSD------SY--LK--DWKKRFKVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCc------hh--hc--CHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence            89999999999999999999988999999998741      11  11  456779999999999999987 4455553

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.

>PRK05807 hypothetical protein; Provisional

Probab=98.36  E-value=2.5e-06  Score=73.59  Aligned_cols=72  Identities=21%  Similarity=0.358  Sum_probs=60.7

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQA  168 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lst  168 (327)
                      ++|++|.|+|+++++.+++|+|. ...|++|++.+. ++       ...  +..++|++||.|.++|.+++.++.+.||+
T Consensus         4 ~vG~vv~G~Vt~i~~~GafV~L~-~~~Glvhiseis-~~-------~v~--~~~~~~kvGd~V~VkV~~id~~gkI~LSl   72 (136)
T PRK05807          4 KAGSILEGTVVNITNFGAFVEVE-GKTGLVHISEVA-DT-------YVK--DIREHLKEQDKVKVKVISIDDNGKISLSI   72 (136)
T ss_pred             cCCCEEEEEEEEEECCeEEEEEC-CEEEEEEhhhcc-cc-------ccc--CccccCCCCCEEEEEEEEECCCCcEEEEE
Confidence            58999999999999999999995 568999999875 11       111  44677999999999999998888999999


Q ss_pred             ccC
Q 020356          169 RNQ  171 (327)
Q Consensus       169 r~~  171 (327)
                      +..
T Consensus        73 k~~   75 (136)
T PRK05807         73 KQA   75 (136)
T ss_pred             Eec
Confidence            864

>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=98.34  E-value=3.1e-06  Score=63.50  Aligned_cols=69  Identities=17%  Similarity=0.202  Sum_probs=57.4

Q ss_pred             CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEEEc
Q 020356           91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQAR  169 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Lstr  169 (327)
                      ||+|.|+|+++.+.+++|++.....|++|++++.-+      +  ..  +..+.|++||.|.++|.+++. .+.+.||++
T Consensus         1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~------~--~~--~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~k   70 (70)
T cd05698           1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEA------F--IK--DPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChh------h--cC--CHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            899999999999999999998779999999987511      1  11  345679999999999999987 567888874

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.

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

Probab=98.34  E-value=9.7e-07  Score=83.34  Aligned_cols=79  Identities=24%  Similarity=0.383  Sum_probs=66.3

Q ss_pred             cCCccCCCCCCEEEEEEEEEecceEEEEEcC--ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecC
Q 020356           82 LRARYKPETGDIVIGRVIEVVPKRWKLEINF--TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQ  159 (327)
Q Consensus        82 l~~rY~P~vGDiVIGrV~~V~~~~w~VDI~s--~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~  159 (327)
                      +..+-.|++||+|||+|.+|.+.+++|.+.-  ...|++|+|+++    ..|-|      ++|+++++|..+.|+|++++
T Consensus         3 ~~~~~~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEva----s~wVk------nIrd~vkegqkvV~kVlrVd   72 (269)
T COG1093           3 MKRREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVA----SGWVK------NIRDYVKEGQKVVAKVLRVD   72 (269)
T ss_pred             ccccCCCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHH----HHHHH------HHHHHhhcCCeEEEEEEEEc
Confidence            3445689999999999999999999999974  467999999996    12222      88999999999999999999


Q ss_pred             C-CCceEEEEcc
Q 020356          160 G-DGSLQLQARN  170 (327)
Q Consensus       160 ~-~g~i~Lstr~  170 (327)
                      + -|.+.||.|.
T Consensus        73 ~~rg~IDLSlkr   84 (269)
T COG1093          73 PKRGHIDLSLKR   84 (269)
T ss_pred             CCCCeEeeehhh
Confidence            7 4678998863

>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=98.31  E-value=2.7e-06  Score=64.37  Aligned_cols=64  Identities=20%  Similarity=0.194  Sum_probs=52.8

Q ss_pred             CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC
Q 020356           91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG  162 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g  162 (327)
                      ||+|.|+|+++..++++|++....+|.+|++++.-      +.  .+..++.+.|++||.|.|+|.+++...
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~------~~--~~~~~~~~~~~~Gd~i~~kVl~~d~~~   64 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFD------EW--PDGKNPLSKFKIGQKIKARVIGGHDAK   64 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhcc------cc--ccccChhHhCCCCCEEEEEEEEEeCcc
Confidence            89999999999999999999999999999998741      10  011256788999999999999997653

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.

>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=98.30  E-value=4.5e-06  Score=64.24  Aligned_cols=71  Identities=21%  Similarity=0.138  Sum_probs=58.1

Q ss_pred             CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEEEEc
Q 020356           91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQLQAR  169 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~Lstr  169 (327)
                      ||+|-|.|+++.+++++|.+...-.|.+|+++++-+.      ...  .+..+.|++||.|.|+|.+++.. ..+.||.+
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 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDV------SVL--EHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCcc------ccc--cCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            8999999999999999999988899999999885220      001  14567799999999999999864 57888875

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

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

Probab=98.25  E-value=5.5e-06  Score=64.67  Aligned_cols=73  Identities=19%  Similarity=0.087  Sum_probs=60.7

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCce
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSL  164 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i  164 (327)
                      ..+++|+++.|+|+++...+.+|++.....|++|++++.-.      +  .  .++.+.|++||.|.++|.+++. .+.+
T Consensus        10 ~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~------~--~--~~~~~~~~~Gd~v~vkV~~id~~~~~i   79 (83)
T cd04461          10 SDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDE------F--V--TDPSFGFKKGQSVTAKVTSVDEEKQRF   79 (83)
T ss_pred             HhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcc------c--c--cCHHHhcCCCCEEEEEEEEEcCCCCEE
Confidence            35789999999999999999999998889999999987521      1  1  1467889999999999999986 4677


Q ss_pred             EEEE
Q 020356          165 QLQA  168 (327)
Q Consensus       165 ~Lst  168 (327)
                      .||+
T Consensus        80 ~lsl   83 (83)
T cd04461          80 LLSL   83 (83)
T ss_pred             EEeC
Confidence            7764

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.

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

Probab=98.23  E-value=3.8e-06  Score=75.77  Aligned_cols=90  Identities=27%  Similarity=0.398  Sum_probs=69.5

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcc---cccccccchhhhhcccCCCCEEEEEEEecCCC
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGI---QRRRTAVDELNMRSIFTENDLVCAEVRSSQGD  161 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i---~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~  161 (327)
                      .|.|..|.+|-|.|+++...+++|.|+ |.++++|.|++. ++-.   .++.....+ .-...|+.||.|+|||.++..+
T Consensus        76 ~fkP~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~-dd~~~~d~~~~~~~g~-~tk~~i~~gd~VR~RIv~~s~~  152 (183)
T COG1095          76 VFKPFRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIM-DDYIDYDEKNKVLIGE-ETKRVLKVGDKVRARIVGVSLK  152 (183)
T ss_pred             EEEeccccEEEEEEEEEeecceEEEec-cccccccHhhcc-CcccccCcccceeeec-ccceEEecCCEEEEEEEEEecc
Confidence            478999999999999999999999999 999999999873 2211   111111111 2234699999999999987642


Q ss_pred             ------CceEEEEccCCCccCC
Q 020356          162 ------GSLQLQARNQKYGKLE  177 (327)
Q Consensus       162 ------g~i~Lstr~~~lGkL~  177 (327)
                            ..+.||+|++++|+++
T Consensus       153 ~~~~~~~~I~lTmrq~~LGkle  174 (183)
T COG1095         153 SRRPRESKIGLTMRQPGLGKLE  174 (183)
T ss_pred             cCccccceEEEEeccccCCcch
Confidence                  4589999999999996

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

Probab=98.22  E-value=8.4e-06  Score=65.20  Aligned_cols=74  Identities=20%  Similarity=0.321  Sum_probs=57.2

Q ss_pred             CCCCCEEEEEEEEEecc--eEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC-ce
Q 020356           88 PETGDIVIGRVIEVVPK--RWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG-SL  164 (327)
Q Consensus        88 P~vGDiVIGrV~~V~~~--~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g-~i  164 (327)
                      |++|+++.|+|+.+.+.  +++|||+....|+||+|+++...   .++.    .+..+.|++||.|.++|.....++ .+
T Consensus         5 ~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~---~~~v----~~~~~~~~~Gd~v~VqV~~~~~~~K~~   77 (88)
T cd04453           5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAY---FKKH----KKIAKLLKEGQEILVQVVKEPIGTKGP   77 (88)
T ss_pred             CCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchh---cccc----CCHHHcCCCCCEEEEEEEEecCCCCCc
Confidence            57999999999999996  99999998889999999885310   0111    144567999999999999976543 45


Q ss_pred             EEEE
Q 020356          165 QLQA  168 (327)
Q Consensus       165 ~Lst  168 (327)
                      .||+
T Consensus        78 ~lt~   81 (88)
T cd04453          78 RLTT   81 (88)
T ss_pred             eEEE
Confidence            5555

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

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

Probab=98.21  E-value=9.4e-06  Score=59.90  Aligned_cols=67  Identities=24%  Similarity=0.376  Sum_probs=54.7

Q ss_pred             CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEE
Q 020356           91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQ  167 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Ls  167 (327)
                      |+++.|+|+++...+|+|+|.....|++|++++.  .    .+  ..  ...+.|++||.|.++|.+++..+.+.||
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 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELS--D----ER--VE--KVEDVLKVGDEVKVKVIEVDDRGRISLS   67 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcC--C----cc--cc--CHHHccCCCCEEEEEEEEECCCCcEEee
Confidence            7899999999999999999998899999998764  1    11  11  3346799999999999999876677776

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.

>PHA02945 interferon resistance protein; Provisional

Probab=98.20  E-value=8.8e-06  Score=65.28  Aligned_cols=73  Identities=21%  Similarity=0.225  Sum_probs=59.1

Q ss_pred             cc-CCCCCCEEEEEEEEEecceEEEEEcC--ccceeeecccc--cCCCcccccccccchhhhhcccCCCCEEEEEEEecC
Q 020356           85 RY-KPETGDIVIGRVIEVVPKRWKLEINF--TQDAILMLSSM--NLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQ  159 (327)
Q Consensus        85 rY-~P~vGDiVIGrV~~V~~~~w~VDI~s--~~~a~L~ls~v--~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~  159 (327)
                      .| .|++||+|+|+|.. .+.+++|++.-  ...|++|+|.+  + +|   +-|      + |+++ +|..|.|+|+.++
T Consensus         5 cy~~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva-~~---wvK------~-rd~l-~GqkvV~KVirVd   71 (88)
T PHA02945          5 CYSLPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHM-NR---YFK------Y-RDKL-VGKTVKVKVIRVD   71 (88)
T ss_pred             eecCCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhc-cc---eEe------e-eeEe-cCCEEEEEEEEEC
Confidence            35 89999999999999 99999999974  57899999954  4 22   222      4 6788 9999999999999


Q ss_pred             CC-CceEEEEcc
Q 020356          160 GD-GSLQLQARN  170 (327)
Q Consensus       160 ~~-g~i~Lstr~  170 (327)
                      +. |.+-||.+.
T Consensus        72 ~~kg~IDlSlK~   83 (88)
T PHA02945         72 YTKGYIDVNYKR   83 (88)
T ss_pred             CCCCEEEeEeeE
Confidence            74 678888763

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

Probab=98.18  E-value=4.7e-06  Score=86.17  Aligned_cols=76  Identities=22%  Similarity=0.272  Sum_probs=65.9

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceE
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQ  165 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~  165 (327)
                      .-++||+|-|+|+++++.+++|||+. -+|.||+++++.      .+..    ...++|++||-|.++|++++. .+.++
T Consensus       189 ~l~~G~vV~G~V~~It~~GafVdigG-vdGLlHiseiS~------~rv~----~P~~vvkvGd~VkvkVi~~D~e~~RVs  257 (541)
T COG0539         189 KLEVGEVVEGVVKNITDYGAFVDIGG-VDGLLHISEISW------KRVD----HPSEVVKVGDEVKVKVISLDEERGRVS  257 (541)
T ss_pred             cCCCCceEEEEEEEeecCcEEEEecC-eeeEEehhhccc------cccC----CHHHhcccCCEEEEEEEEEccCCCeEE
Confidence            45899999999999999999999998 999999999973      3322    667889999999999999995 56899


Q ss_pred             EEEccCCC
Q 020356          166 LQARNQKY  173 (327)
Q Consensus       166 Lstr~~~l  173 (327)
                      ||++...-
T Consensus       258 LSlK~l~~  265 (541)
T COG0539         258 LSLKQLEE  265 (541)
T ss_pred             EEehhccc
Confidence            99987544

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

Probab=98.18  E-value=7.3e-06  Score=60.37  Aligned_cols=66  Identities=21%  Similarity=0.270  Sum_probs=52.6

Q ss_pred             CCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEE
Q 020356           90 TGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQL  166 (327)
Q Consensus        90 vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~L  166 (327)
                      +|++|.|+|+++...+|+|+++ ...|++|.+++...      +.    ..+.+.|++||.|.|+|.+++.. +.+.|
T Consensus         1 ~g~~~~g~V~~v~~~g~~v~l~-~~~g~l~~~e~~~~------~~----~~~~~~~~~Gd~v~v~i~~vd~~~~~i~l   67 (68)
T cd05688           1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWG------RV----KHPSEVVNVGDEVEVKVLKIDKERKRISL   67 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCCc------cc----cCHhHEECCCCEEEEEEEEEECCCCEEec
Confidence            5999999999999999999998 58899999887521      11    13457799999999999999763 44544

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.

>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=98.17  E-value=1.4e-05  Score=61.94  Aligned_cols=67  Identities=19%  Similarity=0.187  Sum_probs=56.6

Q ss_pred             CCCCEEEEEEEEEecceEEEEEc-CccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEIN-FTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQL  166 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~-s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~L  166 (327)
                      +.|++|.|.|.++.+.+++||++ ....|++|.++++      +.          +.|++||.+.|+|.++++. ..+.|
T Consensus         3 ~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~------~~----------~~~~~Gq~v~~~V~~vd~~~~~v~l   66 (74)
T cd05694           3 VEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAG------NF----------SKLKVGQLLLCVVEKVKDDGRVVSL   66 (74)
T ss_pred             CCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCC------cc----------cccCCCCEEEEEEEEEECCCCEEEE
Confidence            57999999999999999999997 4578999988775      11          4589999999999999864 57899


Q ss_pred             EEccC
Q 020356          167 QARNQ  171 (327)
Q Consensus       167 str~~  171 (327)
                      |++..
T Consensus        67 s~k~~   71 (74)
T cd05694          67 SADPS   71 (74)
T ss_pred             EEeec
Confidence            98764

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.

>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=98.15  E-value=8.5e-06  Score=59.78  Aligned_cols=67  Identities=24%  Similarity=0.310  Sum_probs=53.8

Q ss_pred             CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356           91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ  167 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls  167 (327)
                      |+++.|+|+++.+.+|+|+++....|++|.+++. ++   +    ..  ++.+.|++||.|.|+|.+++. .+.+.||
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~-~~---~----~~--~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMA-DR---F----VS--HPSDVVSVGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCC-Cc---c----cc--CHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence            7899999999999999999998889999998764 11   1    11  446779999999999999986 4555553

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.

>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=98.13  E-value=1.5e-05  Score=59.91  Aligned_cols=67  Identities=15%  Similarity=0.107  Sum_probs=54.7

Q ss_pred             CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356           91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ  167 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls  167 (327)
                      |++|.|+|+++...+++|++.....|++|.++++-.       ..   .+..+.|++||.|.++|.+++. .+.+.|+
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 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADV-------RL---KHPEKKFKPGLKVKCRVLSVEPERKRLVLT   68 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCc-------cc---cCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence            799999999999999999998779999999877411       11   1345679999999999999986 4567776

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.

>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=97.99  E-value=3.4e-05  Score=58.87  Aligned_cols=68  Identities=21%  Similarity=0.152  Sum_probs=55.0

Q ss_pred             CCEEE-EEEEEE-ecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356           91 GDIVI-GRVIEV-VPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ  167 (327)
Q Consensus        91 GDiVI-GrV~~V-~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls  167 (327)
                      |+++- |+|+++ .+.+++|++....+|++|.|+++-+      +  .+  +..+.|++||.+.|+|.++++ ++.+.||
T Consensus         1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~------~--~~--~~~~~~~vG~~v~~kV~~id~~~~~i~lS   70 (71)
T cd05696           1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDD------K--VP--SDTGPFKAGTTHKARIIGYSPMDGLLQLS   70 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcc------h--hc--CcccccCCCCEEEEEEEEEeCCCCEEEEe
Confidence            78888 999999 7999999998778999999987511      1  11  345679999999999999986 5578887


Q ss_pred             E
Q 020356          168 A  168 (327)
Q Consensus       168 t  168 (327)
                      +
T Consensus        71 ~   71 (71)
T cd05696          71 L   71 (71)
T ss_pred             C
Confidence            4

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.

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

Probab=97.93  E-value=3.3e-05  Score=55.35  Aligned_cols=63  Identities=17%  Similarity=0.237  Sum_probs=49.8

Q ss_pred             EEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEE
Q 020356           94 VIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQL  166 (327)
Q Consensus        94 VIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~L  166 (327)
                      |.|+|+++.+.+|+|++.....|++|.+++.-.      . .   .++.+.|++||.|.|+|.+++. ++.+.|
T Consensus         1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~------~-~---~~~~~~~~~G~~v~~~v~~~d~~~~~i~l   64 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDK------F-V---KDPSEVFKVGDEVEVKVLEVDPEKGRISL   64 (65)
T ss_pred             CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCc------c-c---cCHhhEeCCCCEEEEEEEEEcCCcCEEec
Confidence            479999999999999999889999999876411      1 1   1456779999999999999975 344544

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.

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

Probab=97.92  E-value=4.9e-05  Score=61.45  Aligned_cols=83  Identities=25%  Similarity=0.334  Sum_probs=60.8

Q ss_pred             CEEEEEEEEEecceEEEEEcCccceeeecccccCCCccccc--c-cccchhhhhcccCCCCEEEEEEEecCCC------C
Q 020356           92 DIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRR--R-TAVDELNMRSIFTENDLVCAEVRSSQGD------G  162 (327)
Q Consensus        92 DiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rr--r-~~~de~~mr~~~~~GDlV~AeV~sv~~~------g  162 (327)
                      ++|.|+|+++...+++|++. +..|++|++++. ++.....  . ...+ -.-.+.|++||.|.++|.+++..      .
T Consensus         1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~-~~~~~~~~~~~~~~~-~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~   77 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIM-DDYISYDPKNKRLIG-EETKRVLKVGDVVRARIVAVSLKERRPRES   77 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEcc-CCceEechhheeecc-cCcCCEECCCCEEEEEEEEEeHHHCcCCCc
Confidence            47899999999999999998 488999988764 1100000  0 0000 01235689999999999999853      5


Q ss_pred             ceEEEEccCCCccCC
Q 020356          163 SLQLQARNQKYGKLE  177 (327)
Q Consensus       163 ~i~Lstr~~~lGkL~  177 (327)
                      .+.||+++..+|++.
T Consensus        78 ~i~ls~k~~~~g~~~   92 (99)
T cd04460          78 KIGLTMRQPGLGKLE   92 (99)
T ss_pred             eEEEEEecCCCCcHH
Confidence            799999999999874

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.

>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=97.91  E-value=7.5e-05  Score=57.59  Aligned_cols=70  Identities=19%  Similarity=0.316  Sum_probs=57.5

Q ss_pred             CCEEEEEEEEEecceEEEEEc---CccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEE
Q 020356           91 GDIVIGRVIEVVPKRWKLEIN---FTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQ  167 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~---s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Ls  167 (327)
                      |+++-|+|+++.+.+++|+|.   ....|++|++++. ++   +  . .+  ++.+.|+.||.|.++|.+++ .+.+.|+
T Consensus         1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~-~~---~--~-~~--~~~~~~~~Gd~v~v~v~~vd-~~~i~~s   70 (79)
T cd05684           1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLS-FE---G--R-VA--NPSDVVKRGQKVKVKVISIQ-NGKISLS   70 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhcc-CC---C--C-cC--ChhheeCCCCEEEEEEEEEe-CCEEEEE
Confidence            789999999999999999998   3578999999875 11   1  1 12  45678999999999999998 7889998


Q ss_pred             Ecc
Q 020356          168 ARN  170 (327)
Q Consensus       168 tr~  170 (327)
                      ++.
T Consensus        71 ~k~   73 (79)
T cd05684          71 MKD   73 (79)
T ss_pred             EEe
Confidence            875

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.

>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=97.87  E-value=6.1e-05  Score=56.74  Aligned_cols=65  Identities=17%  Similarity=0.202  Sum_probs=52.1

Q ss_pred             CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEEE
Q 020356           91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQLQ  167 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~Ls  167 (327)
                      ||+|-|+|+++.+++.+|++....+|++|.++++-+    +.       . .+.|++||.|.|+|.++++. +.+.||
T Consensus         1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~----~~-------~-~~~~~~G~~i~~kVi~id~~~~~i~LS   66 (66)
T cd05695           1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPE----KS-------S-KSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCc----cC-------c-ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            899999999999999999997678999999877411    10       1 45699999999999999864 455553

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.

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.85  E-value=5.1e-05  Score=80.98  Aligned_cols=75  Identities=20%  Similarity=0.351  Sum_probs=61.5

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeeccccc-CCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCce
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMN-LPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSL  164 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~-fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i  164 (327)
                      +.|++|++|.|+|+++.+.+++|+|....+|++|+|++. +..   .++..    ++.+.|++||.|.++|.+++..+.+
T Consensus       643 ~~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~---~~rv~----~~~dv~kvGd~V~VKVl~ID~~gKI  715 (719)
T TIGR02696       643 TMPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAG---GKRVE----NVEDVLSVGQKIQVEIADIDDRGKL  715 (719)
T ss_pred             CcCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhcccccc---ccCcC----CHHHcCCCCCEEEEEEEEECCCCCe
Confidence            358999999999999999999999987789999999873 100   11111    6688899999999999999977778


Q ss_pred             EEE
Q 020356          165 QLQ  167 (327)
Q Consensus       165 ~Ls  167 (327)
                      .|+
T Consensus       716 ~L~  718 (719)
T TIGR02696       716 SLV  718 (719)
T ss_pred             eec
Confidence            774

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.

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=97.84  E-value=6.6e-05  Score=80.26  Aligned_cols=99  Identities=20%  Similarity=0.289  Sum_probs=76.9

Q ss_pred             eCCeEEEEEeeEEEEE--CcEEEEEecCCccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccc
Q 020356           58 QKGELAATVCGVVERI--NKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTA  135 (327)
Q Consensus        58 ~~g~i~Ssv~G~v~~~--nk~v~V~pl~~rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~  135 (327)
                      ++|.++++..|.....  ...+...+    ..|++|+++.|+|+++.+.+++|+|....+|++|+|++.      ..+. 
T Consensus       591 d~G~v~i~~~~~~~~~~a~~~I~~~~----~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels------~~~v-  659 (693)
T PRK11824        591 DDGTVKIAATDGEAAEAAKERIEGIT----AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIA------DERV-  659 (693)
T ss_pred             CCceEEEEcccHHHHHHHHHHHHHhc----ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeecc------Cccc-
Confidence            4778888777766542  22222222    247899999999999999999999998899999999875      1111 


Q ss_pred             cchhhhhcccCCCCEEEEEEEecCCCCceEEEEcc
Q 020356          136 VDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARN  170 (327)
Q Consensus       136 ~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~  170 (327)
                       .  +..+.|++||.|.++|.+++..+.+.||++.
T Consensus       660 -~--~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~  691 (693)
T PRK11824        660 -E--KVEDVLKEGDEVKVKVLEIDKRGRIRLSRKA  691 (693)
T ss_pred             -c--CccceeCCCCEEEEEEEEECCCCcEEEEEEe
Confidence             1  4567899999999999999877899999875

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

Probab=97.81  E-value=0.00026  Score=54.72  Aligned_cols=64  Identities=19%  Similarity=0.229  Sum_probs=55.1

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEE
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQL  166 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~L  166 (327)
                      -.++|+.+.|+|+++++.+++|++.....|.+|.+++.                  +.++.||.+.++|.++.+++.+.|
T Consensus        13 ~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~------------------~~~~iGd~v~v~I~~i~e~~~i~l   74 (77)
T cd04473          13 DLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL------------------RDYEVGDEVIVQVTDIPENGNIDL   74 (77)
T ss_pred             hCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc------------------CcCCCCCEEEEEEEEECCCCcEEE
Confidence            46799999999999999999999998899999887642                  338999999999999966777877


Q ss_pred             EE
Q 020356          167 QA  168 (327)
Q Consensus       167 st  168 (327)
                      +.
T Consensus        75 ~~   76 (77)
T cd04473          75 IP   76 (77)
T ss_pred             EE
Confidence            64

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.

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

Probab=97.81  E-value=0.00011  Score=55.32  Aligned_cols=56  Identities=23%  Similarity=0.225  Sum_probs=47.9

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD  161 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~  161 (327)
                      ..|++|-|+|..+..++++|||+. .+|+||.++.. |               .+.|++||-|.+.|.+++.+
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig~-~eg~lp~~e~~-~---------------~~~~~~Gd~v~v~v~~v~~~   57 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLGK-VEAILPKKEQI-P---------------GESYRPGDRIKAYVLEVRKT   57 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcCC-eEEEeeHHHCC-C---------------CCcCCCCCEEEEEEEEEecC
Confidence            579999999999999999999986 89999888764 1               23489999999999998753

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.

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=97.80  E-value=9.3e-05  Score=72.22  Aligned_cols=74  Identities=20%  Similarity=0.339  Sum_probs=61.7

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceE
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQ  165 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~  165 (327)
                      ..++||+|.|+|+.+.+.+++|+++ ...|++|++.++-      .+.    .+..+.|++||.|.|+|.+++. .+.+.
T Consensus       193 ~~k~G~vv~G~V~~I~~~G~fV~i~-gv~Gllhisels~------~~~----~~~~~~~~vGd~VkvkVl~iD~e~~rI~  261 (318)
T PRK07400        193 RLEVGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISH------EHI----ETPHSVFNVNDEMKVMIIDLDAERGRIS  261 (318)
T ss_pred             cCCCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHccc------ccc----cChhhccCCCCEEEEEEEEEeCCCCEEE
Confidence            4678999999999999999999997 4679999998862      111    1456889999999999999975 57899


Q ss_pred             EEEccC
Q 020356          166 LQARNQ  171 (327)
Q Consensus       166 Lstr~~  171 (327)
                      |+++..
T Consensus       262 LS~K~l  267 (318)
T PRK07400        262 LSTKQL  267 (318)
T ss_pred             EEEecc
Confidence            999864

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=97.79  E-value=8.1e-05  Score=72.64  Aligned_cols=76  Identities=25%  Similarity=0.396  Sum_probs=63.5

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCce
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSL  164 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i  164 (327)
                      |..++||+|-|+|+.+..++.+|||+....|+||++++...      +.  .  +..+.|++||.|.+.|.+++. ++.+
T Consensus        27 ~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~------~~--~--~~~~~~~~G~~v~~~Vi~~~~~~~~i   96 (318)
T PRK07400         27 YHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSIN------RV--E--GPEEVLQPNETREFFILSDENEDGQL   96 (318)
T ss_pred             hhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccc------cc--c--CHHHccCCCCEEEEEEEEEeCCCCeE
Confidence            45689999999999999999999999888999999988622      11  1  445779999999999999875 5689


Q ss_pred             EEEEccC
Q 020356          165 QLQARNQ  171 (327)
Q Consensus       165 ~Lstr~~  171 (327)
                      .||+|..
T Consensus        97 ~lS~k~~  103 (318)
T PRK07400         97 TLSIRRI  103 (318)
T ss_pred             EEehhhh
Confidence            9999864

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

Probab=97.79  E-value=0.00062  Score=61.28  Aligned_cols=90  Identities=11%  Similarity=0.070  Sum_probs=65.8

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeeccccc----CCCcccccccccchhhhhcccCCCCEEEEEEEecCC
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMN----LPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG  160 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~----fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~  160 (327)
                      -|.|..|.+|.|+|+++...+++|+++ +.+..+|.+++.    |....+.. ...++ +-...++.||.|++||.++.-
T Consensus        76 vFrPf~gEVv~g~V~~v~~~G~~v~~G-p~~ifI~~~~l~~~~~fd~~~~~~-~~~~~-~~~~~i~~g~~VR~rV~~v~~  152 (176)
T PTZ00162         76 VFKPFKDEVLDAIVTDVNKLGFFAQAG-PLKAFVSRSAIPPDFVYDSDSAYP-CYISS-DGQIQIKPNTEVRLRLQGVRY  152 (176)
T ss_pred             EEecCCCCEEEEEEEEEecceEEEEee-CeEEEEcHHHCCCccEECCCCCcc-eEecC-CCcEEECCCCEEEEEEEEEEe
Confidence            478999999999999999999999997 666888777662    21111100 00111 225679999999999988753


Q ss_pred             ---CCceEEEEccCCCccCC
Q 020356          161 ---DGSLQLQARNQKYGKLE  177 (327)
Q Consensus       161 ---~g~i~Lstr~~~lGkL~  177 (327)
                         +.....|+|++.||+++
T Consensus       153 ~~~~~~~i~T~~~~~LG~~~  172 (176)
T PTZ00162        153 DASNLFAIATINSDYLGPIE  172 (176)
T ss_pred             cCCCcEEEEEecCCCcCccc
Confidence               23577799999999995

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

Probab=97.70  E-value=0.00016  Score=53.74  Aligned_cols=67  Identities=16%  Similarity=0.241  Sum_probs=52.9

Q ss_pred             CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEE
Q 020356           91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQL  166 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~L  166 (327)
                      |+++-|+|+++.+.+++|++.....|++|.+++..+.   +  .    .+..+.|++||.|.|+|.+++.. +.+.|
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~---~--~----~~~~~~~~~G~~v~v~v~~id~~~~~i~l   68 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQ---R--V----RHPSEIYKKGQEVEAVVLNIDVERERISL   68 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCcc---c--c----CChhhEECCCCEEEEEEEEEECCcCEEeC
Confidence            7899999999999999999998899999999875211   1  0    13356799999999999999754 34444

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.

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

Probab=97.65  E-value=0.00032  Score=52.35  Aligned_cols=66  Identities=21%  Similarity=0.237  Sum_probs=51.8

Q ss_pred             CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEEEc
Q 020356           91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQAR  169 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Lstr  169 (327)
                      |++|.|+|+++...+++|++ ....|++|.+++..+      +..    +..+  .+||.+.|+|.+++. .+.+.||.|
T Consensus         1 G~iv~g~V~~v~~~G~~v~l-~g~~gfip~s~~~~~------~~~----~~~~--~vG~~i~~~i~~vd~~~~~i~lS~k   67 (67)
T cd04465           1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLR------PVE----DLDE--YVGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCCc------ccC----ChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence            79999999999999999999 468999999987521      110    1111  389999999999986 567888764

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.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.62  E-value=0.00014  Score=77.72  Aligned_cols=94  Identities=20%  Similarity=0.289  Sum_probs=69.0

Q ss_pred             eCCeEEEEEeeEEEEE--CcEEEEEecCCccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccc
Q 020356           58 QKGELAATVCGVVERI--NKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTA  135 (327)
Q Consensus        58 ~~g~i~Ssv~G~v~~~--nk~v~V~pl~~rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~  135 (327)
                      ++|.++....+.....  ...+....    ..|++|+++.|+|+++.+.+++|+|....+|+||+|++.      ..+. 
T Consensus       588 ddG~V~i~~~~~~~~~~a~~~I~~~~----~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~------~~~v-  656 (684)
T TIGR03591       588 DDGTVKIAASDGEAAEAAIKMIEGIT----AEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIA------NERV-  656 (684)
T ss_pred             cCeEEEEEECcHHHHHHHHHHHHhhh----cccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcC------CCcc-
Confidence            4666666665554332  22333322    258999999999999999999999998899999999885      1111 


Q ss_pred             cchhhhhcccCCCCEEEEEEEecCCCCceE
Q 020356          136 VDELNMRSIFTENDLVCAEVRSSQGDGSLQ  165 (327)
Q Consensus       136 ~de~~mr~~~~~GDlV~AeV~sv~~~g~i~  165 (327)
                       +  +..+.|++||.|.++|.+++..+.+.
T Consensus       657 -~--~~~~~~kvGD~V~VkVi~id~~gki~  683 (684)
T TIGR03591       657 -E--KVEDVLKEGDEVKVKVLEIDKQGRIK  683 (684)
T ss_pred             -c--ChhhccCCCCEEEEEEEEECCCCCcc
Confidence             1  56788999999999999998655443

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).

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.58  E-value=0.00027  Score=72.73  Aligned_cols=71  Identities=15%  Similarity=0.201  Sum_probs=60.0

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ  167 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls  167 (327)
                      ++||+|-|+|+++.+.+++|||+. ..|++|+|+++.      .+.  +  +..+.|++||.|.++|.+++. .+.+.||
T Consensus       207 k~G~iv~G~V~~i~~~G~FVdlgg-v~Glv~~Sels~------~~v--~--~~~~~~kvGd~V~vkVl~iD~e~~rI~LS  275 (486)
T PRK07899        207 QKGQVRKGVVSSIVNFGAFVDLGG-VDGLVHVSELSW------KHI--D--HPSEVVEVGQEVTVEVLDVDMDRERVSLS  275 (486)
T ss_pred             cCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHCCC------ccc--C--CHHHhcCCCCEEEEEEEEEECCCCEEEEE
Confidence            589999999999999999999974 889999998862      221  1  456789999999999999986 4789999


Q ss_pred             Ecc
Q 020356          168 ARN  170 (327)
Q Consensus       168 tr~  170 (327)
                      +|.
T Consensus       276 lK~  278 (486)
T PRK07899        276 LKA  278 (486)
T ss_pred             Eee
Confidence            875

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=97.56  E-value=0.00027  Score=72.71  Aligned_cols=75  Identities=19%  Similarity=0.272  Sum_probs=61.9

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC----
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG----  162 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g----  162 (327)
                      ..++||+|-|+|+++...+++|+|+....|++|+++++.      .+  .+  ++.++|++||.|.|+|.+++.+.    
T Consensus       199 ~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~------~~--~~--~~~~~~~vGd~i~vkVl~id~~~~~~~  268 (491)
T PRK13806        199 TVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSW------SR--VQ--KADEAVSVGDTVRVKVLGIERAKKGKG  268 (491)
T ss_pred             hCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCC------cc--cc--ChhHhcCCCCEEEEEEEEEecccCCcc
Confidence            468999999999999999999999877899999998862      11  11  45677999999999999998653    


Q ss_pred             -ceEEEEccC
Q 020356          163 -SLQLQARNQ  171 (327)
Q Consensus       163 -~i~Lstr~~  171 (327)
                       .+.||+|..
T Consensus       269 ~ri~lS~K~~  278 (491)
T PRK13806        269 LRISLSIKQA  278 (491)
T ss_pred             eEEEEEehhh
Confidence             588998653

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

Probab=97.55  E-value=0.00041  Score=52.26  Aligned_cols=64  Identities=14%  Similarity=0.236  Sum_probs=51.9

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD  161 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~  161 (327)
                      .+|+++.|+|+++...+++|++.....|++|++++.-++     +    ..+..+.|+.||.|.++|.+++..
T Consensus         2 ~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~-----~----~~~~~~~~~~Gd~v~v~v~~id~~   65 (72)
T cd05689           2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTN-----K----NIHPSKVVSLGDEVEVMVLDIDEE   65 (72)
T ss_pred             cCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcc-----c----ccCcccEeCCCCEEEEEEEEeeCC
Confidence            379999999999999999999987789999998774110     1    113457799999999999999764

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.53  E-value=0.00029  Score=76.90  Aligned_cols=75  Identities=20%  Similarity=0.276  Sum_probs=63.4

Q ss_pred             CCCCCCEEE-EEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceE
Q 020356           87 KPETGDIVI-GRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQ  165 (327)
Q Consensus        87 ~P~vGDiVI-GrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~  165 (327)
                      .|++|+++. |+|++|.+.+++|+|....+|++|+|++.      .++..    +..+.|++||.|.++|.+++..+.+.
T Consensus       750 ~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs------~~rv~----~~~dv~kvGD~V~VkVi~ID~~grI~  819 (891)
T PLN00207        750 VPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELS------SNWLA----KPEDAFKVGDRIDVKLIEVNDKGQLR  819 (891)
T ss_pred             CcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcC------Ccccc----CHHHhcCCCCEEEEEEEEECCCCcEE
Confidence            589999995 69999999999999987789999999885      22221    44578999999999999999878899


Q ss_pred             EEEccC
Q 020356          166 LQARNQ  171 (327)
Q Consensus       166 Lstr~~  171 (327)
                      |+++..
T Consensus       820 LSlK~l  825 (891)
T PLN00207        820 LSRRAL  825 (891)
T ss_pred             EEEecc
Confidence            998753

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.46  E-value=0.00059  Score=67.67  Aligned_cols=74  Identities=19%  Similarity=0.232  Sum_probs=61.1

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceE
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQ  165 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~  165 (327)
                      ..++||+|-|+|+++.+.+++|+++. ..|++|+++++..      +  .+  ++.+.|++||.|.|+|.+++. ++.+.
T Consensus       189 ~~~~G~~v~g~V~~v~~~G~fV~l~~-v~g~v~~sels~~------~--~~--~~~~~~~vGd~i~~~Vl~vd~~~~~i~  257 (390)
T PRK06676        189 SLKEGDVVEGTVARLTDFGAFVDIGG-VDGLVHISELSHE------R--VE--KPSEVVSVGQEVEVKVLSIDWETERIS  257 (390)
T ss_pred             hCCCCCEEEEEEEEEecceEEEEeCC-eEEEEEHHHcCcc------c--cC--CHHHhcCCCCEEEEEEEEEeCCCCEEE
Confidence            35799999999999999999999975 8899999987621      1  11  456779999999999999976 57899


Q ss_pred             EEEccC
Q 020356          166 LQARNQ  171 (327)
Q Consensus       166 Lstr~~  171 (327)
                      ||+|..
T Consensus       258 lS~k~~  263 (390)
T PRK06676        258 LSLKDT  263 (390)
T ss_pred             EEEeec
Confidence            998753

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.46  E-value=0.00045  Score=71.16  Aligned_cols=74  Identities=22%  Similarity=0.349  Sum_probs=61.2

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEE
Q 020356           88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQL  166 (327)
Q Consensus        88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~L  166 (327)
                      .+.||+|.|+|+.+..+.++|||+....|+||.++++..      +.    .+..+.|++||.|.|.|.++++ .+.+.|
T Consensus        33 ~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~~------~~----~~~~~~~~vGd~Ie~~V~~~~~~~g~liL  102 (486)
T PRK07899         33 FNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIK------HD----VDPNEVVEVGDEVEALVLQKEDKEGRLIL  102 (486)
T ss_pred             CCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhccc------cc----CChhhcCCCCCEEEEEEEEEECCCCeEEE
Confidence            579999999999999999999999888999999887621      11    1345669999999999999865 568999


Q ss_pred             EEccC
Q 020356          167 QARNQ  171 (327)
Q Consensus       167 str~~  171 (327)
                      |.+..
T Consensus       103 S~k~~  107 (486)
T PRK07899        103 SKKRA  107 (486)
T ss_pred             Eehhh
Confidence            99864

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.44  E-value=0.00057  Score=71.05  Aligned_cols=73  Identities=16%  Similarity=0.214  Sum_probs=61.5

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceE
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQ  165 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~  165 (327)
                      ..++|++|-|+|+.+...+++||++ ...|.+|+++++..      +.    .++.+.|++||-|.|+|.+++. ++.+.
T Consensus       198 ~l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~~------~~----~~~~~~~kvG~~v~v~V~~~d~~~~~i~  266 (565)
T PRK06299        198 NLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISWK------RV----NHPSEVVNVGDEVKVKVLKFDKEKKRVS  266 (565)
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhccc------cc----CCHhhcCCCCCEEEEEEEEEeCCCCeEE
Confidence            3579999999999999999999998 78999999988632      11    1556779999999999999986 57899


Q ss_pred             EEEcc
Q 020356          166 LQARN  170 (327)
Q Consensus       166 Lstr~  170 (327)
                      ||++.
T Consensus       267 lS~k~  271 (565)
T PRK06299        267 LGLKQ  271 (565)
T ss_pred             EEEEe
Confidence            99874

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.38  E-value=0.0016  Score=67.80  Aligned_cols=73  Identities=23%  Similarity=0.302  Sum_probs=61.0

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ  167 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls  167 (327)
                      ++||+|.|+|+.+.+.+.+|.+.....|++|.|+++-      .+  ..  +..+.|++||.|.|+|.+++. .+.+.||
T Consensus       459 ~~G~vV~G~V~~v~~~G~fV~l~~gi~g~i~~se~s~------~~--~~--~~~~~~~~Gd~v~~~V~~vd~~~~~i~LS  528 (565)
T PRK06299        459 KKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSR------DR--VE--DATEVLKVGDEVEAKVINIDRKNRRISLS  528 (565)
T ss_pred             CCCCEEEEEEEEEecCceEEecCCCcEEEEEHHHhcc------hh--cc--CccccCCCCCEEEEEEEEEccccCEEEEE
Confidence            6899999999999999999999877899999998751      11  11  456779999999999999986 5789999


Q ss_pred             EccC
Q 020356          168 ARNQ  171 (327)
Q Consensus       168 tr~~  171 (327)
                      ++..
T Consensus       529 ~k~~  532 (565)
T PRK06299        529 IKAL  532 (565)
T ss_pred             eeeh
Confidence            9753

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.36  E-value=0.00066  Score=67.33  Aligned_cols=74  Identities=22%  Similarity=0.376  Sum_probs=59.7

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEE-cCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-Cce
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEI-NFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSL  164 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI-~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i  164 (327)
                      ..++||+|.|+|+.+..+++.||| +....|+||.+++...      +..    +....|++||.|.|.|.+++.+ +.+
T Consensus        14 ~~~~G~iv~G~V~~i~~~g~~V~i~~~~~~g~lp~~e~~~~------~~~----~~~~~~~vGd~v~~~V~~v~~~~~~i   83 (390)
T PRK06676         14 EVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSND------HIE----DINDVVKVGDELEVYVLKVEDGEGNL   83 (390)
T ss_pred             cccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccc------ccc----CcccccCCCCEEEEEEEEEECCCCCE
Confidence            457999999999999999999999 7788999999887521      000    2345589999999999999864 469


Q ss_pred             EEEEcc
Q 020356          165 QLQARN  170 (327)
Q Consensus       165 ~Lstr~  170 (327)
                      .||.+.
T Consensus        84 ~lS~k~   89 (390)
T PRK06676         84 LLSKRR   89 (390)
T ss_pred             EEEHHH
Confidence            999875

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

Probab=97.33  E-value=0.0017  Score=49.81  Aligned_cols=72  Identities=18%  Similarity=0.218  Sum_probs=53.4

Q ss_pred             CCCEEEEEEEEEecceEEEEEcC-ccceeeecccccCCCcccccccccchh-------hhhcccCCCCEEEEEEEecCC-
Q 020356           90 TGDIVIGRVIEVVPKRWKLEINF-TQDAILMLSSMNLPDGIQRRRTAVDEL-------NMRSIFTENDLVCAEVRSSQG-  160 (327)
Q Consensus        90 vGDiVIGrV~~V~~~~w~VDI~s-~~~a~L~ls~v~fpg~i~rrr~~~de~-------~mr~~~~~GDlV~AeV~sv~~-  160 (327)
                      +|+++-|.|+.+.+.+++|++.. ...|.+|++++.  +.  +  -..|+.       .....|++||.|.++|.+++. 
T Consensus         1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~--~~--~--~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~   74 (83)
T cd04471           1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLG--DD--Y--YEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLD   74 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecC--CC--c--EEEcccceEEEeccCCCEEcCCCEEEEEEEEeccc
Confidence            48999999999999999999986 578899998764  11  0  001111       234679999999999999986 


Q ss_pred             CCceEEE
Q 020356          161 DGSLQLQ  167 (327)
Q Consensus       161 ~g~i~Ls  167 (327)
                      .+.+.|+
T Consensus        75 ~~~i~~~   81 (83)
T cd04471          75 RRKIDFE   81 (83)
T ss_pred             cCEEEEE
Confidence            3556654

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.

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=97.29  E-value=0.00054  Score=73.38  Aligned_cols=73  Identities=22%  Similarity=0.287  Sum_probs=62.1

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQLQ  167 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~Ls  167 (327)
                      ++|.++.|+|+.|...+++|||+..++|.+|+|.++      .+  .+.  +..+.++.||+|.++|..++.. ..+.||
T Consensus       657 k~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls------~~--fv~--~P~~vv~vGdiV~v~V~~vD~~r~rI~Ls  726 (780)
T COG2183         657 KPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLS------DK--FVK--DPNEVVKVGDIVKVKVIEVDTARKRIALS  726 (780)
T ss_pred             cCCCEEEEEEEEeeeccceEEeccccceeeeHHHhh------hh--hcC--ChHHhcccCCEEEEEEEEEecccCeeeeE
Confidence            789999999999999999999999999999999886      11  111  3367799999999999999864 579999


Q ss_pred             EccC
Q 020356          168 ARNQ  171 (327)
Q Consensus       168 tr~~  171 (327)
                      +|..
T Consensus       727 mr~~  730 (780)
T COG2183         727 MRLD  730 (780)
T ss_pred             eecc
Confidence            9864

>TIGR00717 rpsA ribosomal protein S1

Probab=97.27  E-value=0.0011  Score=67.96  Aligned_cols=73  Identities=18%  Similarity=0.226  Sum_probs=60.4

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceE
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQ  165 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~  165 (327)
                      ..++||+|-|.|+.+.+.+++||++. ..|++|.++++..      +..    +..+.|++||.|.|+|.+++. .+.+.
T Consensus       184 ~l~~G~~v~g~V~~i~~~G~~V~l~g-~~g~lp~~e~s~~------~~~----~~~~~~~vG~~v~v~Vl~~d~~~~~i~  252 (516)
T TIGR00717       184 NLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWK------RVK----HPSEYVKVGQEVKVKVIKFDKEKGRIS  252 (516)
T ss_pred             hccCCCEEEEEEEEEECCeEEEEECC-EEEEEEHHHcCCC------CCC----CHHHhccCCCEEEEEEEEEECCCCcEE
Confidence            56899999999999999999999975 7899999988631      111    455679999999999999986 46799


Q ss_pred             EEEcc
Q 020356          166 LQARN  170 (327)
Q Consensus       166 Lstr~  170 (327)
                      ||.+.
T Consensus       253 lS~k~  257 (516)
T TIGR00717       253 LSLKQ  257 (516)
T ss_pred             EEEEe
Confidence            99874

This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.

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

Probab=97.24  E-value=0.001  Score=70.63  Aligned_cols=72  Identities=19%  Similarity=0.244  Sum_probs=60.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEE
Q 020356           88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQL  166 (327)
Q Consensus        88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~L  166 (327)
                      .++||+|.|+|+++.+.+++|++ ....|++|+++++..      +.  .  ++.+.|++||.|.|+|.+++. ++.+.|
T Consensus       475 l~~G~iV~g~V~~v~~~G~fV~l-~gv~Gll~~sels~~------~~--~--~~~~~~~vGd~V~vkV~~id~~~~~I~l  543 (647)
T PRK00087        475 LEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWG------RV--E--KPSDVLKVGDEIKVYILDIDKENKKLSL  543 (647)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEHHHcCcc------cc--C--CHHHhcCCCCEEEEEEEEEECCCCEEEE
Confidence            46899999999999999999999 568899999987521      11  1  456779999999999999975 578999


Q ss_pred             EEcc
Q 020356          167 QARN  170 (327)
Q Consensus       167 str~  170 (327)
                      |+|.
T Consensus       544 S~K~  547 (647)
T PRK00087        544 SLKK  547 (647)
T ss_pred             Eeec
Confidence            9975

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

Probab=97.23  E-value=0.00092  Score=69.50  Aligned_cols=73  Identities=15%  Similarity=0.172  Sum_probs=62.8

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQLQ  167 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~Ls  167 (327)
                      .+||.+.|+|+.+++++++|+|.....|++|+|+++-      .+..    ...+.+++||.|.++|++++++ ..+.|+
T Consensus       276 ~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw------~~~~----~P~evv~~Gq~V~V~Vl~id~e~rRIsL~  345 (541)
T COG0539         276 PVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISW------TKKN----VPSEVVKVGQEVEVKVLDIDPERRRISLG  345 (541)
T ss_pred             CCCCEEEEEEEEeecCcEEEEecCCccceeechhhcc------cccC----CHHHhcccCCEEEEEEEeeCchhceEEee
Confidence            4899999999999999999999999999999999872      2211    2467899999999999999974 689999


Q ss_pred             EccC
Q 020356          168 ARNQ  171 (327)
Q Consensus       168 tr~~  171 (327)
                      ||..
T Consensus       346 iKq~  349 (541)
T COG0539         346 LKQL  349 (541)
T ss_pred             ehhh
Confidence            9864

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=97.18  E-value=0.0012  Score=67.84  Aligned_cols=73  Identities=14%  Similarity=0.076  Sum_probs=60.3

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQLQ  167 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~Ls  167 (327)
                      .+|++|-|+|+++.+.+++|++....+|++|.|+++-.    +  .    -+..+.|++||.|.|+|.+++.+ ..+.|+
T Consensus       378 ~vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~~----~--~----~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls  447 (491)
T PRK13806        378 APGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRA----G--K----PATYEKLKPGDSVTLVVEEIDTAKRKISLA  447 (491)
T ss_pred             CCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCcc----c--c----cchhhcCCCCCEEEEEEEEEeCCCCEEEEE
Confidence            47999999999999999999998789999999988621    1  1    13456689999999999999864 579999


Q ss_pred             EccC
Q 020356          168 ARNQ  171 (327)
Q Consensus       168 tr~~  171 (327)
                      ++..
T Consensus       448 ~~~~  451 (491)
T PRK13806        448 PAGA  451 (491)
T ss_pred             eehh
Confidence            8843

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=97.17  E-value=0.0039  Score=68.40  Aligned_cols=105  Identities=11%  Similarity=0.132  Sum_probs=73.2

Q ss_pred             eeCCeEEEEEeeEEEEECcEE--EEEecC-Cc---c--CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCc
Q 020356           57 DQKGELAATVCGVVERINKLI--YVRALR-AR---Y--KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDG  128 (327)
Q Consensus        57 ~~~g~i~Ssv~G~v~~~nk~v--~V~pl~-~r---Y--~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~  128 (327)
                      ..++++.+.+.+. ...++.+  +++-+. .+   +  .-.+|++|-|.|+.+++.+++|++...-.|++|.|+++..  
T Consensus       625 kvGd~V~vkVl~i-D~e~~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~sels~~--  701 (863)
T PRK12269        625 KIGDEVECMILGY-DIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWV--  701 (863)
T ss_pred             CCCCEEEEEEEEE-ecccCceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHHhhcc--
Confidence            3456677777665 3223333  333221 11   1  1147999999999999999999998888999999988621  


Q ss_pred             ccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEEEccC
Q 020356          129 IQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQARNQ  171 (327)
Q Consensus       129 i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Lstr~~  171 (327)
                        ++ ..    ...+.|++||.|.|+|.+++. ...+.||+|..
T Consensus       702 --~~-~~----~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~l  738 (863)
T PRK12269        702 --KR-TR----PADHELEVGKEIECMVIECDPQARRIRLGVKQL  738 (863)
T ss_pred             --cc-cc----chhhccCCCCEEEEEEEEEeccCCEEEEEeccc
Confidence              11 11    233569999999999999986 46899999853

>TIGR00717 rpsA ribosomal protein S1

Probab=97.17  E-value=0.0016  Score=66.71  Aligned_cols=73  Identities=18%  Similarity=0.219  Sum_probs=60.0

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ  167 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls  167 (327)
                      ++||++-|+|+++...+++|+++....|++|++++....     ..    .+..+.|++||.|.|+|.+++. .+.+.||
T Consensus       271 ~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~~-----~~----~~~~~~~~vG~~v~v~V~~id~~~~~i~lS  341 (516)
T TIGR00717       271 PVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVK-----KN----SHPSKVVKKGDEVEVMILDIDPERRRLSLG  341 (516)
T ss_pred             cCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCcc-----cc----CCHHHhccCCCEEEEEEEEEcCCCCEEEEE
Confidence            589999999999999999999988889999999875321     00    1234569999999999999986 4689999


Q ss_pred             Ecc
Q 020356          168 ARN  170 (327)
Q Consensus       168 tr~  170 (327)
                      ++.
T Consensus       342 ~k~  344 (516)
T TIGR00717       342 LKQ  344 (516)
T ss_pred             ehh
Confidence            875

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=97.14  E-value=0.0013  Score=71.92  Aligned_cols=74  Identities=16%  Similarity=0.169  Sum_probs=61.7

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEE
Q 020356           88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQL  166 (327)
Q Consensus        88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~L  166 (327)
                      ..+||+|-|+|+++.+.+++|++.....|++|+|+++..     ++.    .+..+.|++||.|.|+|.+++. .+.+.|
T Consensus       576 ~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~-----~~~----~~p~~~~kvGd~V~vkVl~iD~e~~rIsL  646 (863)
T PRK12269        576 FGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWV-----KKT----SKPSDMVKIGDEVECMILGYDIQAGRVSL  646 (863)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCc-----ccc----CCHHHcCCCCCEEEEEEEEEecccCceEE
Confidence            468999999999999999999998888999999998631     111    1456779999999999999985 568999


Q ss_pred             EEcc
Q 020356          167 QARN  170 (327)
Q Consensus       167 str~  170 (327)
                      |++.
T Consensus       647 S~K~  650 (863)
T PRK12269        647 GLKQ  650 (863)
T ss_pred             Eehh
Confidence            9875

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

Probab=97.05  E-value=0.0022  Score=68.12  Aligned_cols=77  Identities=18%  Similarity=0.329  Sum_probs=63.4

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecC-CCCce
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQ-GDGSL  164 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~-~~g~i  164 (327)
                      +..++|++|.|+|+++..++++||++....|+||.+++....          ..+..+.|++||.|.++|.+++ .++.+
T Consensus       298 ~~l~~G~iV~G~V~~v~~~gv~Vdig~~~~G~lp~~els~~~----------~~~~~~~~~vGd~V~v~V~~vd~~~g~i  367 (647)
T PRK00087        298 KQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDE----------ISSLKESVKVGDEIEVKVLKLEDEDGYV  367 (647)
T ss_pred             hhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcccc----------cCChhhccCCCCEEEEEEEEEECCCCcE
Confidence            467899999999999999999999998889999998875221          1134566999999999999986 46789


Q ss_pred             EEEEccCC
Q 020356          165 QLQARNQK  172 (327)
Q Consensus       165 ~Lstr~~~  172 (327)
                      .||.+...
T Consensus       368 ~LS~k~~~  375 (647)
T PRK00087        368 VLSKKEAD  375 (647)
T ss_pred             EEEeehhc
Confidence            99998653

>TIGR01953 NusA transcription termination factor NusA

Probab=97.02  E-value=0.0022  Score=63.35  Aligned_cols=113  Identities=16%  Similarity=0.186  Sum_probs=76.8

Q ss_pred             ccCCCCCCEEEEEEEEEecce-EEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC--
Q 020356           85 RYKPETGDIVIGRVIEVVPKR-WKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD--  161 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~-w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~--  161 (327)
                      .|..+.|++|.|+|.++..++ |.|||+ ...|+||.++.. |               .+.|++||-|.|.|.++..+  
T Consensus       126 ey~~k~GeiV~G~V~~v~~~g~v~VdiG-~~ea~LP~~E~i-p---------------~E~~~~Gd~ik~~V~~V~~~~k  188 (341)
T TIGR01953       126 EFSSKEGEIISGTVKRVNRRGNLYVELG-KTEGILPKKEQI-P---------------GEKFRIGDRIKAYVYEVRKTAK  188 (341)
T ss_pred             HHHhhcCCEEEEEEEEEecCCcEEEEEC-CeEEEecHHHcC-C---------------CcCCCCCCEEEEEEEEEEcCCC
Confidence            488899999999999999866 799997 578898877653 2               22389999999999999743  


Q ss_pred             -CceEEEEccCCC---------ccCCCCeEEEeChhhhhhcccccccc---C-ccceEEEEeeccee
Q 020356          162 -GSLQLQARNQKY---------GKLERGQLLTVDPYLVKRRKQHFHHL---E-EYGIDLIIGCNGYI  214 (327)
Q Consensus       162 -g~i~Lstr~~~l---------GkL~~G~lv~V~~~li~r~~~h~~~L---~-~~~~eiivG~NG~I  214 (327)
                       +.+.||.+.++|         -.+.+|.+-=...+-..=.++.+...   + --++-.|||.+|-=
T Consensus       189 g~qIivSRt~~~~v~~Lfe~EVPEI~dG~VeI~~iaR~pG~RtKvAV~s~~~~iDpvga~vG~~G~r  255 (341)
T TIGR01953       189 GPQIILSRTHPEFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVESNDENIDPVGACVGPKGSR  255 (341)
T ss_pred             CCeEEEEeCcHHHHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCcceeeECCCCch
Confidence             368888877554         45567766543332222112211111   1 12667788988853

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.

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=96.97  E-value=0.0022  Score=63.87  Aligned_cols=112  Identities=13%  Similarity=0.103  Sum_probs=74.9

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC---
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG---  162 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g---  162 (327)
                      |.+++|++|.|+|..+....|+|||+. ..|+||.++.. |               ++.|++||-|.|.|.++..+.   
T Consensus       130 f~~k~GeiV~G~V~~~~~~~~~Vdlg~-vEa~LP~~E~i-p---------------~e~~~~Gd~Ika~V~~V~~~~kgp  192 (362)
T PRK12327        130 FSEREGDIVTGVVQRRDNRFVYVNLGK-IEAVLPPAEQI-P---------------GETYKHGDRIKVYVVKVEKTTKGP  192 (362)
T ss_pred             HHHhcCCEEEEEEEEEeCCcEEEEeCC-eEEEecHHHcC-C---------------CCCCCCCCEEEEEEEEEecCCCCC
Confidence            899999999999999999999999986 78898866542 2               244899999999999998432   


Q ss_pred             ceEEEEccCCC---------ccCCCCeEEEeChhhhhhcccccccc---Cc-cceEEEEeeccee
Q 020356          163 SLQLQARNQKY---------GKLERGQLLTVDPYLVKRRKQHFHHL---EE-YGIDLIIGCNGYI  214 (327)
Q Consensus       163 ~i~Lstr~~~l---------GkL~~G~lv~V~~~li~r~~~h~~~L---~~-~~~eiivG~NG~I  214 (327)
                      .+.||-..++|         -.+.+|.+-=...+-.+=.++.+...   +. -++-.|||.+|-=
T Consensus       193 ~IivSRt~p~~v~~Lfe~EVPEI~~G~VeIk~iaR~pG~RtKVAV~s~~~~iDpvGa~iG~~G~r  257 (362)
T PRK12327        193 QIFVSRTHPGLVKRLFELEVPEIYDGTVEIKSIAREAGDRTKIAVRSNNPNVDAKGACVGPKGQR  257 (362)
T ss_pred             eEEEEeCCHHHHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCchheeECCCChh
Confidence            57777655443         34556765533322211111111111   11 2566688888853

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

Probab=96.81  E-value=0.01  Score=47.56  Aligned_cols=81  Identities=11%  Similarity=0.115  Sum_probs=51.7

Q ss_pred             CCCEEEEEEEEEecceEEEEEcCccceeeecccc----cCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-Cc-
Q 020356           90 TGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSM----NLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GS-  163 (327)
Q Consensus        90 vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v----~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~-  163 (327)
                      +|.+|.|+|+++...+++|+++ |.+++++-+.+    -|.+..+ .-...+  +-..+++.||.|++||.++.-+ .. 
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~G-pl~~f~~~~~ip~~~~~~~~~~-~~~~~~--~~~~~i~~g~~VR~rV~~v~~~~~~~   76 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVG-PLSIFISRHLIPSDMEFDPNAS-PPCFTS--NEDIVIKKDTEVRLKIIGTRVDATDI   76 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEc-CceEEEEeeecCccceECCcCC-CCeEeC--CCcEEECCCCEEEEEEEEEEEccCce
Confidence            5899999999999999999998 45555544433    1211000 001111  1256799999999999887532 11 


Q ss_pred             -eEEEEccCCCc
Q 020356          164 -LQLQARNQKYG  174 (327)
Q Consensus       164 -i~Lstr~~~lG  174 (327)
                       ..-|++++.||
T Consensus        77 ~~igt~~~~~LG   88 (88)
T cd04462          77 FAIGTIKDDYLG   88 (88)
T ss_pred             EEEEEccCCCCC
Confidence             22266777776

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.

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=96.51  E-value=0.0054  Score=63.08  Aligned_cols=72  Identities=25%  Similarity=0.350  Sum_probs=59.4

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC---
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD---  161 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~---  161 (327)
                      .|..++|++|.|+|.++...+++||++ ...|+||.+++. |               ++.|++||-|.|.|..++..   
T Consensus       129 eyk~~~GeIV~G~V~ri~~~giiVDLg-gvea~LP~sE~i-p---------------~E~~~~GdrIka~I~~Vd~~~kg  191 (470)
T PRK09202        129 EYKDRVGEIITGVVKRVERGNIIVDLG-RAEAILPRKEQI-P---------------RENFRPGDRVRAYVYEVRKEARG  191 (470)
T ss_pred             HHHhhcCCEEEEEEEEEecCCEEEEEC-CeEEEecHHHcC-C---------------CccCCCCCEEEEEEEEEecCCCC
Confidence            388899999999999999999999997 468898887763 2               34589999999999999763   


Q ss_pred             CceEEEEccCCC
Q 020356          162 GSLQLQARNQKY  173 (327)
Q Consensus       162 g~i~Lstr~~~l  173 (327)
                      ..+.||-+.+.|
T Consensus       192 ~qIilSRt~p~~  203 (470)
T PRK09202        192 PQIILSRTHPEF  203 (470)
T ss_pred             CeEEEEeCcHHH
Confidence            268888777554

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=96.15  E-value=0.042  Score=55.75  Aligned_cols=81  Identities=19%  Similarity=0.295  Sum_probs=57.7

Q ss_pred             cCCCCCCEEEEEEEEEecc--eEEEEEcCccceeeecccccCCCccc-----ccccccchhhhhcccCCCCEEEEEEEec
Q 020356           86 YKPETGDIVIGRVIEVVPK--RWKLEINFTQDAILMLSSMNLPDGIQ-----RRRTAVDELNMRSIFTENDLVCAEVRSS  158 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~--~w~VDI~s~~~a~L~ls~v~fpg~i~-----rrr~~~de~~mr~~~~~GDlV~AeV~sv  158 (327)
                      ..+.+|||..|+|..+.+.  .+||||+...+|+||++++. |+.-.     .++...  -++.+.+++||.|.+.|..-
T Consensus        21 ~~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~-~~~~~~~~~~~~~~~~--~~i~~~l~~G~~IlVQV~Ke   97 (414)
T TIGR00757        21 SRQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIG-PNYECLAPAEAKREAG--PSISELLRPGQSVLVQVVKE   97 (414)
T ss_pred             CcCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcC-chhhcccccccccccc--CCHHHhCcCCCEEEEEEeeC
Confidence            3445899999999999998  99999999999999999874 21000     000011  14566799999999999883


Q ss_pred             CC-CCceEEEEc
Q 020356          159 QG-DGSLQLQAR  169 (327)
Q Consensus       159 ~~-~g~i~Lstr  169 (327)
                      .. +..+.||+.
T Consensus        98 ~~~~Kgp~lT~~  109 (414)
T TIGR00757        98 PRGNKGARLTTD  109 (414)
T ss_pred             CcCCCCCeEEEE
Confidence            22 234666663

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.

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

Probab=96.01  E-value=0.015  Score=61.74  Aligned_cols=75  Identities=20%  Similarity=0.328  Sum_probs=64.8

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceE
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQ  165 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~  165 (327)
                      --|++|.+-.|+|+.+.+.+++|.+....++.+|+|.+.-.      |.  +  +..+.+++||.|+.+|..+++-|.+.
T Consensus       615 ~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~------rv--~--kv~dvlk~Gd~v~Vkv~~iD~~Gri~  684 (692)
T COG1185         615 REVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKE------RV--E--KVEDVLKEGDEVKVKVIEIDKQGRIR  684 (692)
T ss_pred             hhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhh------hh--h--cccceeecCceEEEEEeeecccCCcc
Confidence            36799999999999999999999999999999999988611      11  1  45588999999999999999989999


Q ss_pred             EEEcc
Q 020356          166 LQARN  170 (327)
Q Consensus       166 Lstr~  170 (327)
                      |+++.
T Consensus       685 ls~~~  689 (692)
T COG1185         685 LSIKA  689 (692)
T ss_pred             ceehh
Confidence            98864

>TIGR02063 RNase_R ribonuclease R

Probab=94.12  E-value=0.18  Score=54.22  Aligned_cols=81  Identities=16%  Similarity=0.165  Sum_probs=57.1

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcC-ccceeeecccccCCCccccc--ccccchhhhhcccCCCCEEEEEEEecCC-CC
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINF-TQDAILMLSSMNLPDGIQRR--RTAVDELNMRSIFTENDLVCAEVRSSQG-DG  162 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s-~~~a~L~ls~v~fpg~i~rr--r~~~de~~mr~~~~~GDlV~AeV~sv~~-~g  162 (327)
                      .+++|.++-|+|++++..+++|.+.. ...|.+|++++. .+.....  .....-......|++||.|.++|.+++. .+
T Consensus       624 ~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~-~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~  702 (709)
T TIGR02063       624 SEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLK-DDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTG  702 (709)
T ss_pred             hccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecC-CCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccC
Confidence            56889999999999999999999986 589999999874 1100000  0000000223569999999999999986 46


Q ss_pred             ceEEEE
Q 020356          163 SLQLQA  168 (327)
Q Consensus       163 ~i~Lst  168 (327)
                      .+.++.
T Consensus       703 ~I~~~l  708 (709)
T TIGR02063       703 KIDFEL  708 (709)
T ss_pred             eEEEEE
Confidence            666653

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.

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=93.77  E-value=0.14  Score=51.35  Aligned_cols=69  Identities=26%  Similarity=0.388  Sum_probs=51.7

Q ss_pred             ccCCCCCCEEEEEEEEEec-ceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC-
Q 020356           85 RYKPETGDIVIGRVIEVVP-KRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG-  162 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~-~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g-  162 (327)
                      .|.+++|++|-|+|..+.. ..+.||++ ...|+||-++. .|               ++.|++||-|.|-|..+..+. 
T Consensus       133 ey~~~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eq-ip---------------~E~~~~Gdrik~~i~~V~~~~k  195 (374)
T PRK12328        133 KYKKKVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNR-IK---------------GEKFKVGDVVKAVLKRVKIDKN  195 (374)
T ss_pred             HHHHhcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHc-CC---------------CCcCCCCCEEEEEEEEEecCCC
Confidence            4999999999999999986 46889998 46788765443 12               345999999999999997532 


Q ss_pred             ---ceEEEEcc
Q 020356          163 ---SLQLQARN  170 (327)
Q Consensus       163 ---~i~Lstr~  170 (327)
                         .+.||...
T Consensus       196 ~gp~IilSRt~  206 (374)
T PRK12328        196 NGILIELSRTS  206 (374)
T ss_pred             CCCEEEEEcCC
Confidence               34455443

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=93.73  E-value=0.14  Score=52.32  Aligned_cols=84  Identities=15%  Similarity=0.222  Sum_probs=61.3

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcC-----ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecC
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINF-----TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQ  159 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s-----~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~  159 (327)
                      .|.+++|++|.|+|..+....+.||+++     ...|+||-++. .|               ++.|++||.|+|-|..+.
T Consensus       147 ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eq-ip---------------~E~y~~Gdrika~i~~V~  210 (449)
T PRK12329        147 EFQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQ-LP---------------NDNYRANATFKVFLKEVS  210 (449)
T ss_pred             HHHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHc-CC---------------CCcCCCCCEEEEEEEEee
Confidence            3899999999999999999999999953     25677665443 22               345999999999999996


Q ss_pred             CC---C-ceEEEEccCCC---------ccCCCCeEEEe
Q 020356          160 GD---G-SLQLQARNQKY---------GKLERGQLLTV  184 (327)
Q Consensus       160 ~~---g-~i~Lstr~~~l---------GkL~~G~lv~V  184 (327)
                      .+   | .+.||-..++|         -.+.+|.+--.
T Consensus       211 ~~~~kGpqIilSRt~p~lv~~Lfe~EVPEI~dG~VeIk  248 (449)
T PRK12329        211 EGPRRGPQLFVSRANAGLVVYLFENEVPEIEEGVVRIV  248 (449)
T ss_pred             cCCCCCCEEEEEcCCHHHHHHHHHhhCcccccCeEEEE
Confidence            53   2 46777655443         45567766544

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=93.29  E-value=0.41  Score=38.44  Aligned_cols=71  Identities=11%  Similarity=0.242  Sum_probs=52.1

Q ss_pred             cc-CCCCCCEEEEEEEEEecceEEEEEcC-ccceeee-cccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC
Q 020356           85 RY-KPETGDIVIGRVIEVVPKRWKLEINF-TQDAILM-LSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD  161 (327)
Q Consensus        85 rY-~P~vGDiVIGrV~~V~~~~w~VDI~s-~~~a~L~-ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~  161 (327)
                      .| .|++||+|. .|+.++...+.|.+-. ...|.+. .++++      |+|..    .+++.+ +|-.+.+.|..++..
T Consensus        10 cy~~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~sels------r~rir----si~kll-VGk~e~v~ViRVDk~   77 (86)
T PHA02858         10 CYVFPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVN------ADRAE----KLKKKL-VGKTINVQVIRTDKL   77 (86)
T ss_pred             EEecCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHh------HHHHH----hhhhhh-cCCeeEEEEEEECCC
Confidence            45 899999999 7888999999998753 2455554 66664      44333    667778 999999999999865


Q ss_pred             -CceEEE
Q 020356          162 -GSLQLQ  167 (327)
Q Consensus       162 -g~i~Ls  167 (327)
                       |=+-|+
T Consensus        78 KGYIDLs   84 (86)
T PHA02858         78 KGYIDVR   84 (86)
T ss_pred             CCEEEeE
Confidence             334443

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=93.22  E-value=0.55  Score=34.89  Aligned_cols=61  Identities=18%  Similarity=0.141  Sum_probs=33.4

Q ss_pred             CCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEc
Q 020356           90 TGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQAR  169 (327)
Q Consensus        90 vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr  169 (327)
                      +|+++-.+|++++..+|++|.+...+-.||.+++.                  .-+++||-|.+-|-. +.++.+..||+
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~------------------~~~~~Gd~v~VFvY~-D~~~rl~AT~k   61 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVP------------------EPLKVGDEVEVFVYL-DKEGRLVATTK   61 (61)
T ss_dssp             --------EEEE-SSEEEEEETT-EEEEEEGGG------------------------TTSEEEEEEEE--TTS-EEEE--
T ss_pred             CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcC------------------CCCCCCCEEEEEEEE-CCCCCEEEecC
Confidence            58999999999999999999887777776665442                  227899999998866 34456766663

>PRK10811 rne ribonuclease E; Reviewed

Probab=93.22  E-value=0.56  Score=52.19  Aligned_cols=78  Identities=12%  Similarity=0.232  Sum_probs=54.5

Q ss_pred             CCCCCEEEEEEEEE--ecceEEEEEcCccceeeeccccc---CCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-
Q 020356           88 PETGDIVIGRVIEV--VPKRWKLEINFTQDAILMLSSMN---LPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-  161 (327)
Q Consensus        88 P~vGDiVIGrV~~V--~~~~w~VDI~s~~~a~L~ls~v~---fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-  161 (327)
                      +.+|+|-+|+|..|  +-+.+||||+....|+|+|+++.   |+....  ..  ..-++...+++||.|...|..-... 
T Consensus        36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~--~~--~~~~i~~~Lk~GqeILVQV~KEa~gt  111 (1068)
T PRK10811         36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYS--AH--GRPNIKDVLREGQEVIVQIDKEERGN  111 (1068)
T ss_pred             cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccc--cc--cccccccccCCCCEEEEEEeecccCC
Confidence            35899999999999  46789999999999999998874   221110  00  0013455689999999999874432 


Q ss_pred             CceEEEEc
Q 020356          162 GSLQLQAR  169 (327)
Q Consensus       162 g~i~Lstr  169 (327)
                      .-+.||++
T Consensus       112 KGp~LTt~  119 (1068)
T PRK10811        112 KGAALTTF  119 (1068)
T ss_pred             CCCceeee
Confidence            23555554

>PRK11642 exoribonuclease R; Provisional

Probab=92.67  E-value=0.47  Score=52.11  Aligned_cols=76  Identities=13%  Similarity=0.200  Sum_probs=56.7

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCc-cceeeecccccCCCcccccccccch-------hhhhcccCCCCEEEEEEEec
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFT-QDAILMLSSMNLPDGIQRRRTAVDE-------LNMRSIFTENDLVCAEVRSS  158 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~-~~a~L~ls~v~fpg~i~rrr~~~de-------~~mr~~~~~GDlV~AeV~sv  158 (327)
                      ...+|+++-|+|++|+..+++|.|... -.|++|++++.  +.    ....|+       ......|+.||.|.++|.++
T Consensus       640 ~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~--~d----~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~v  713 (813)
T PRK11642        640 LDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLD--ND----YYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAV  713 (813)
T ss_pred             hccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecC--Cc----ceEecchheEEecccCCcEECCCCEEEEEEEEe
Confidence            447999999999999999999999754 89999998764  10    000111       12346699999999999999


Q ss_pred             CC-CCceEEEE
Q 020356          159 QG-DGSLQLQA  168 (327)
Q Consensus       159 ~~-~g~i~Lst  168 (327)
                      +. .+.+.|+.
T Consensus       714 D~~~rkI~f~l  724 (813)
T PRK11642        714 NMDERKIDFSL  724 (813)
T ss_pred             ecCCCeEEEEE
Confidence            75 45677765

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

Probab=91.74  E-value=0.72  Score=49.40  Aligned_cols=75  Identities=12%  Similarity=0.190  Sum_probs=55.7

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEc-CccceeeecccccCCCcccccccccch-------hhhhcccCCCCEEEEEEEec
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEIN-FTQDAILMLSSMNLPDGIQRRRTAVDE-------LNMRSIFTENDLVCAEVRSS  158 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~-s~~~a~L~ls~v~fpg~i~rrr~~~de-------~~mr~~~~~GDlV~AeV~sv  158 (327)
                      ..++|+.+-|+|++++..+++|.|. ....|.+|++++.  +.    ....|+       ......|+.||.|..+|.++
T Consensus       569 ~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~--~d----~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~v  642 (654)
T TIGR00358       569 LDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLH--ND----YYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEV  642 (654)
T ss_pred             hhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCC--Cc----ceEEeccccEEEeccCCcEECCCCEEEEEEEEE
Confidence            4578999999999999999999997 5689999998764  21    011111       12236799999999999999


Q ss_pred             CC-CCceEEE
Q 020356          159 QG-DGSLQLQ  167 (327)
Q Consensus       159 ~~-~g~i~Ls  167 (327)
                      +. .+.+.++
T Consensus       643 d~~~~~I~f~  652 (654)
T TIGR00358       643 NMETRSIIFE  652 (654)
T ss_pred             ecccCeEEEE
Confidence            75 4455554

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=91.70  E-value=0.66  Score=53.23  Aligned_cols=73  Identities=25%  Similarity=0.296  Sum_probs=60.6

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC-ceEEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG-SLQLQ  167 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g-~i~Ls  167 (327)
                      ++||+|-|.|..+..++.++-+.....|.+++|... +-.         +..-+..|.+|++|.++|.+++++. .++|+
T Consensus      1161 k~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~-ds~---------~k~w~k~~~~gklv~~rv~~ve~~s~riel~ 1230 (1710)
T KOG1070|consen 1161 KIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLS-DSF---------EKEWEKHLPVGKLVTGRVLSVEEDSKRIELS 1230 (1710)
T ss_pred             ccCceeEEEEEEecCCcEEEEEccceEEEEEccccc-cch---------hhhhhccCCccceeeeEEEEeeccCceEEEE
Confidence            689999999999999999999999999999988763 211         1234567999999999999998764 78998


Q ss_pred             EccC
Q 020356          168 ARNQ  171 (327)
Q Consensus       168 tr~~  171 (327)
                      .+..
T Consensus      1231 Lk~s 1234 (1710)
T KOG1070|consen 1231 LKNS 1234 (1710)
T ss_pred             Eecc
Confidence            7653

>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

Probab=91.68  E-value=0.22  Score=47.78  Aligned_cols=74  Identities=19%  Similarity=0.271  Sum_probs=60.1

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcC--ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-C
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINF--TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-G  162 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s--~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g  162 (327)
                      -.|+++|+|++.|..++.-++.|.+--  ...|.+.||.++      |||..    .+....++|-.=.+-|+.++.. |
T Consensus        12 kyPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELS------rRRIR----SI~klirVGr~E~vvVlrVDkekG   81 (304)
T KOG2916|consen   12 KYPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELS------RRRIR----SIQKLIRVGRNEPVVVLRVDKEKG   81 (304)
T ss_pred             cCCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHH------HHHHH----HHHHHHhcCCcceEEEEEEcCCCC
Confidence            379999999999999999999999853  446677788876      55544    6677899999999999999864 5


Q ss_pred             ceEEEEc
Q 020356          163 SLQLQAR  169 (327)
Q Consensus       163 ~i~Lstr  169 (327)
                      =+.||.|
T Consensus        82 YIDLSkr   88 (304)
T KOG2916|consen   82 YIDLSKR   88 (304)
T ss_pred             ceechhc
Confidence            6888875

>PRK11712 ribonuclease G; Provisional

Probab=91.66  E-value=1.4  Score=45.73  Aligned_cols=95  Identities=16%  Similarity=0.171  Sum_probs=60.6

Q ss_pred             CcEEEEEecCCccCCCCCCEEEEEEEEEe--cceEEEEEcCccceeeecccccCCCccc-cc--ccccchhhhhcccCCC
Q 020356           74 NKLIYVRALRARYKPETGDIVIGRVIEVV--PKRWKLEINFTQDAILMLSSMNLPDGIQ-RR--RTAVDELNMRSIFTEN  148 (327)
Q Consensus        74 nk~v~V~pl~~rY~P~vGDiVIGrV~~V~--~~~w~VDI~s~~~a~L~ls~v~fpg~i~-rr--r~~~de~~mr~~~~~G  148 (327)
                      ++++.+.--+......+|+|-.|+|..|-  -+.+||||+...+|+||++++ +|..-. ..  +.......+.+.+++|
T Consensus        22 g~l~e~~iE~~~~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~-~~~~~~~~~~~~~~~~~~~i~~~l~~G  100 (489)
T PRK11712         22 GILQEIHIEREAKRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDI-VPHTECVAGEEQKQFVVRDISELVRQG  100 (489)
T ss_pred             CEEEEEEEecCCcccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhc-cchhhhcccccccccccccHHHhccCC
Confidence            34443333333345568999999999995  467999999999999999987 231000 00  0000011356679999


Q ss_pred             CEEEEEEEecCC-CCceEEEEc
Q 020356          149 DLVCAEVRSSQG-DGSLQLQAR  169 (327)
Q Consensus       149 DlV~AeV~sv~~-~g~i~Lstr  169 (327)
                      |.|...|..-.- ..-+.||+.
T Consensus       101 q~iLVQV~Ke~~~~KG~~lT~~  122 (489)
T PRK11712        101 QDIMVQVVKDPLGTKGARLTTD  122 (489)
T ss_pred             CEEEEEEEeCCcCCCCCeEEEE
Confidence            999999987432 234666663

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

Probab=89.95  E-value=0.41  Score=53.75  Aligned_cols=76  Identities=17%  Similarity=0.223  Sum_probs=58.8

Q ss_pred             CCCCEEEEEEEEEecce---EEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-Cce
Q 020356           89 ETGDIVIGRVIEVVPKR---WKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSL  164 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~---w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i  164 (327)
                      .+|-+|.++|++|+..+   .+|-+.+..+++++..+++  + -..+       +..+-+++|+.|+|+|.+++.. -++
T Consensus       984 ~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~S--d-~~v~-------~p~~~v~vgq~v~~kvi~id~e~f~v 1053 (1299)
T KOG1856|consen  984 YEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLS--D-RDVR-------RPENRVKVGQTVYCKVIKIDKERFSV 1053 (1299)
T ss_pred             ccCceEEEeeeEEEecccceeEEEecCCCceeeeccccC--h-hhcc-------CHHHhhccCceEEEEeeeeeHhhhhh
Confidence            47999999999999998   6668888889998877654  1 1112       3445588999999999999864 478


Q ss_pred             EEEEccCCCc
Q 020356          165 QLQARNQKYG  174 (327)
Q Consensus       165 ~Lstr~~~lG  174 (327)
                      .||||...|-
T Consensus      1054 ~Ls~r~sdlk 1063 (1299)
T KOG1856|consen 1054 ELSCRTSDLK 1063 (1299)
T ss_pred             hhhhhhHHhh
Confidence            9999876554

>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]

Probab=84.86  E-value=3  Score=40.32  Aligned_cols=64  Identities=16%  Similarity=0.037  Sum_probs=47.7

Q ss_pred             CCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEcc
Q 020356           91 GDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARN  170 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~  170 (327)
                      ++.|-|.|.+....+.+|=+...+-+++|-|++                  ....+.|+.+.|+|..+.+||++.||++-
T Consensus       156 nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr------------------~~~prlG~~l~~rVi~~reDg~lnLSl~p  217 (287)
T COG2996         156 NQEVDATVYRLLESGTFVITENGYLGFIHKSER------------------FAEPRLGERLTARVIGVREDGKLNLSLRP  217 (287)
T ss_pred             cCeeeeEEEEEeccceEEEEcCCeEEEEcchhh------------------cccccCCceEEEEEEEEccCCeeeccccc
Confidence            566666777776667776666666777665543                  23368999999999999999999999975


Q ss_pred             CC
Q 020356          171 QK  172 (327)
Q Consensus       171 ~~  172 (327)
                      ..
T Consensus       218 ~~  219 (287)
T COG2996         218 RA  219 (287)
T ss_pred             cc
Confidence            43

>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=84.57  E-value=5  Score=31.30  Aligned_cols=69  Identities=19%  Similarity=0.183  Sum_probs=46.2

Q ss_pred             CCEEEEEEEEEecceEEEEEcC-ccceeeecccccCCCcccccccccchhhhhcccCCCCEE-EEEEEecCCCCceEEEE
Q 020356           91 GDIVIGRVIEVVPKRWKLEINF-TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLV-CAEVRSSQGDGSLQLQA  168 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~s-~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV-~AeV~sv~~~g~i~Lst  168 (327)
                      |++|-|+|.+++.+...|++.. ...|+|+...++  .....++      .+-..+++||-+ .+-|.+. ....+.||.
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLs--D~~~k~~------~~~~klrvG~~L~~~lvL~~-~~r~i~lt~   71 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLS--DHVSNCP------LLWHCLQEGDTIPNLMCLSN-YKGRIILTK   71 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccC--CchhhCH------HHHhhhhcCCCccceEEEec-cccEEEEec
Confidence            7999999999999999999975 677887655443  1111222      345568999988 6666621 223455553

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.

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

Probab=84.21  E-value=1.6  Score=50.22  Aligned_cols=77  Identities=16%  Similarity=0.180  Sum_probs=59.9

Q ss_pred             cCCccCCCCCCEEEEEEEEEecceEEEEEcCccceeeeccccc--CCCcccccccccchhhhhcccCCCCEEEEEEEecC
Q 020356           82 LRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMN--LPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQ  159 (327)
Q Consensus        82 l~~rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~--fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~  159 (327)
                      ++..|.-.+|+||-|.|+++.++...|++.+...+-+|+|++-  ++..       .   +.-+-|+.||-|.|+|..-+
T Consensus       877 ~k~~~~~~igsiv~a~v~svKp~~L~v~l~~~~~gri~isev~d~~~ei-------t---Dp~~k~~vG~~I~vrviG~~  946 (1710)
T KOG1070|consen  877 IKSTEDLSIGSIVRAYVKSVKPDQLNVLLAANHHGRIHISEVLDNLHEI-------T---DPLDKFKVGDGIFVRVIGGH  946 (1710)
T ss_pred             cccccceeeeeEEEEEEeeecccceEEeccccccCceehHHhhcccccc-------C---ChhhhcccCCeEEEEEEcCC
Confidence            3456778899999999999999999999999999999999873  3321       1   24456999999999999875


Q ss_pred             CCCceEEEE
Q 020356          160 GDGSLQLQA  168 (327)
Q Consensus       160 ~~g~i~Lst  168 (327)
                      +-.++-.|+
T Consensus       947 D~k~lpith  955 (1710)
T KOG1070|consen  947 DVKDLPITH  955 (1710)
T ss_pred             ccccCcccc
Confidence            433444443

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

Probab=82.61  E-value=7.1  Score=35.10  Aligned_cols=88  Identities=14%  Similarity=0.138  Sum_probs=53.6

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceee---ecccccC-CCcccccccccchhhhhcccCCCCEEEEEEEecCC
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAIL---MLSSMNL-PDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG  160 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L---~ls~v~f-pg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~  160 (327)
                      .+.|-.|++|=|.|+.|...+++++++.-.-.++   .-+.+.| ||   -+.+.....++. .++.|+.|+-+|..+--
T Consensus        76 ~FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~---~n~P~f~~~d~s-~I~~~~~VR~kiigtr~  151 (170)
T KOG3298|consen   76 TFKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPG---ENPPNFQTEDES-VIQKGVEVRLKIIGTRV  151 (170)
T ss_pred             EEeecCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccCCC---CCCCcccccccc-eeeeCcEEEEEEEEEEE
Confidence            4788999999999999999999999985333331   1122222 22   111211111222 57899999999987643


Q ss_pred             CC--ceEE-EEccCCCccC
Q 020356          161 DG--SLQL-QARNQKYGKL  176 (327)
Q Consensus       161 ~g--~i~L-str~~~lGkL  176 (327)
                      +-  -+.| |+.++.||.+
T Consensus       152 ~~~~i~algtl~~D~LG~i  170 (170)
T KOG3298|consen  152 DETEIFALGTLKGDYLGPI  170 (170)
T ss_pred             eeeeEEEEEEecCcccccC
Confidence            22  1223 5567777753

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

Probab=81.76  E-value=6.6  Score=33.45  Aligned_cols=67  Identities=15%  Similarity=0.267  Sum_probs=42.4

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccc--------cccccchhhhhcccCCCCEEEEEEEecC
Q 020356           88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQR--------RRTAVDELNMRSIFTENDLVCAEVRSSQ  159 (327)
Q Consensus        88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~r--------rr~~~de~~mr~~~~~GDlV~AeV~sv~  159 (327)
                      |-+|.++.|+|.+...++.+|.++--.+-.  ++.-.||....-        -...   -+-.-+|..|+.|+=||.++.
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 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIF--IPPSLLPEPSRFDEEEQAWVWEYD---EEQELFFDIGEEIRFRVESEI   75 (122)
T ss_dssp             --TT-EEEEEEEEEETTEEEEEECCEEEEE--EECCCC-TTEEEECCCTEEEEEES---SSEEEEE-TT-EEEEEEEEEE
T ss_pred             CCCCCEEEEEEEecCCCcEEEEecccccEE--ECHHHCCCCCccCccCCEEEEECC---CCceeEccCCCEEEEEEeEEE
Confidence            789999999999999999999998766644  344444432210        0010   133456899999999998864

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	327
2nn6_H	308	Structure Of The Human Rna Exosome Composed Of Rrp4		1e-47
4ifd_H	361	Crystal Structure Of An 11-subunit Eukaryotic Exoso		3e-42
2ba0_A	229	Archaeal Exosome Core Length = 229		4e-08
2z0s_A	235	Crystal Structure Of Putative Exosome Complex Rna-B		6e-04

>pdb|2NN6|H Chain H, Structure Of The Human Rna Exosome Composed Of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40 Length = 308

Iteration: 1
 Score =  186 bits (473), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 100/208 (48%), Positives = 133/208 (63%), Gaps = 2/208 (0%)
Query: 9   NQTQKVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCG 68
           +   ++RL  A + L     +      V  GDTI   + G ++GHGT   + +L A+V G
Sbjct: 15  HMAMEMRLPVARKPLSERLGRDTKKHLVVPGDTI-TTDTGFMRGHGTYMGEEKLIASVAG 73
Query: 69  VVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDG 128
            VER+NKLI V+AL+ RY  E GDIV+GR+ EV  KRWK+E N   D++L+LSSMNLP G
Sbjct: 74  SVERVNKLICVKALKTRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGG 133
Query: 129 IQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYL 188
             RRR+A DEL MR    E DL+ AEV++   DG++ L  R+ KYGKL +G L+ V P L
Sbjct: 134 ELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSL 193
Query: 189 VKRRKQHFHHLEEYGIDLIIGCNGYIWI 216
           VKR+K HFH L   G  +I+G NG+IWI
Sbjct: 194 VKRQKTHFHDL-PCGASVILGNNGFIWI 220

>pdb|4IFD|H Chain H, Crystal Structure Of An 11-subunit Eukaryotic Exosome Complex Bound To Rna Length = 361

Iteration: 1
 Score =  169 bits (427), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 110/291 (37%), Positives = 154/291 (52%), Gaps = 33/291 (11%)
Query: 27  SSKSNPNS-CVTVGDTI---PVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRAL 82
           +SKS  +S  VT G+ +   P++    ++GHGT        ++V G V R+N+L+ V  L
Sbjct: 47  ASKSESDSQIVTPGELVTDDPIW----MRGHGTYFLDNMTYSSVAGTVSRVNRLLSVIPL 102
Query: 83  RARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMR 142
           + RY PETGD V+GR+ EV  KRWK++I   Q A+LML S+NLP GI RR++  DEL MR
Sbjct: 103 KGRYAPETGDHVVGRIAEVGNKRWKVDIGGKQHAVLMLGSVNLPGGILRRKSESDELQMR 162
Query: 143 SIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRRKQHFHHLEEY 202
           S   E DL+ AEV+S   DGS  L  R+ KYGKL  G    V   L+ R K H H+L   
Sbjct: 163 SFLKEGDLLNAEVQSLFQDGSASLHTRSLKYGKLRNGMFCQVPSSLIVRAKNHTHNLPG- 221
Query: 203 GIDLIIGCNGYIWIGEHVE---ARDKMVVDQGSNSEQLIAKCDKNSMDL----------- 248
            I +++G NGYIW+ +  +   ARD       +NS  + +     ++ L           
Sbjct: 222 NITVVLGVNGYIWLRKTSQMDLARD---TPSANNSSSIKSTGPTGAVSLNPSITRLEEES 278
Query: 249 ------DEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLS 293
                 DE D + +    RQ ICR AN I+ L+     IT + I+     S
Sbjct: 279 SWQIYSDENDPSIS-NNIRQAICRYANVIKALAFCEIGITQQRIVSAYEAS 328

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 43/183 (23%), Positives = 77/183 (42%), Gaps = 40/183 (21%)
Query: 52  GHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEIN 111
           G+GT  + G++ A + G+ ++    + V  L+ RY P  GD+VIG + EV    W ++I 
Sbjct: 19  GYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGRYTPSVGDVVIGIIREVAANGWAVDIY 78
Query: 112 FTQDAILMLSS-------------MNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSS 158
               A L +S              +++ D I  +   +D   M+   T  D +C  +R  
Sbjct: 79  SPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDP-KMKVTLTMKDRICRPIRF- 136
Query: 159 QGDGSLQLQARNQKYGKLERGQLLTVDPYLVKR---RKQHFHHL--EEYGIDLIIGCNGY 213
                               G+++ ++P  V R   +K     L   E  + +++G NG 
Sbjct: 137 --------------------GRIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQNGL 176
Query: 214 IWI 216
           IW+
Sbjct: 177 IWV 179

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 40/139 (28%), Positives = 68/139 (48%), Gaps = 12/139 (8%)
Query: 57  DQKGELAATVCGVVERINK---LIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFT 113
           D KG   ATV G++          +V+ L+  Y P+ GD+VIG +  V    W ++IN  
Sbjct: 31  DYKGVKRATVVGLLREKGDGGGRAFVK-LKEIYVPQAGDVVIGLIQSVGIMNWFVDINSP 89
Query: 114 QDAILMLSSMNLPDGIQRR-RTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQK 172
             A+L     ++ D + R    AVD  +M+S+    D + A+V +     S  L  + + 
Sbjct: 90  YVAVL-----SVQDFLGRPFNPAVD--DMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGEG 142
Query: 173 YGKLERGQLLTVDPYLVKR 191
            G++ RG+++ + P  V R
Sbjct: 143 LGRIVRGKIVEISPAKVPR 161

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	327
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	4e-82
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	3e-47
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	1e-45
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	4e-45
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	7e-42
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	6e-34
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	3e-29
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	2e-26
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-06

>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 =  250 bits (639), Expect = 4e-82
 Identities = 118/312 (37%), Positives = 162/312 (51%), Gaps = 23/312 (7%)

Query: 13  KVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVER 72
           ++RL  A + L     +      V  GDTI   + G ++GHGT   + +L A+V G VER
Sbjct: 19  EMRLPVARKPLSERLGRDTKKHLVVPGDTITT-DTGFMRGHGTYMGEEKLIASVAGSVER 77

Query: 73  INKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRR 132
           +NKLI V+AL+ RY  E GDIV+GR+ EV  KRWK+E N   D++L+LSSMNLP G  RR
Sbjct: 78  VNKLICVKALKTRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRR 137

Query: 133 RTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRR 192
           R+A DEL MR    E DL+ AEV++   DG++ L  R+ KYGKL +G L+ V P LVKR+
Sbjct: 138 RSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQ 197

Query: 193 KQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIAKCDKNSMDLDEQD 252
           K HFH L   G  +I+G NG+IWI    E +++      +N E +               
Sbjct: 198 KTHFHDL-PCGASVILGNNGFIWIYPTPEHKEEEAGGFIANLEPV--------------- 241

Query: 253 GTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLDIHDMLGSEFYVLV 312
                   R+ I R+ N I  L      +    IL       SL   I D+L  E    +
Sbjct: 242 ----SLADREVISRLRNCIISLVTQRMMLYDTSILYCYEA--SLPHQIKDILKPEIMEEI 295

Query: 313 AESEAERRSLSK 324
                +R    +
Sbjct: 296 VMETRQRLLEQE 307

>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 =  158 bits (400), Expect = 3e-47
 Identities = 41/197 (20%), Positives = 81/197 (41%), Gaps = 16/197 (8%)

Query: 36  VTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVI 95
           V  GD +    +    G+GT  + G++ A + G+ ++    + V  L+ RY P  GD+VI
Sbjct: 5   VLPGDLLS--TNPRAAGYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGRYTPSVGDVVI 62

Query: 96  GRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEV 155
           G + EV    W ++I     A L +S    P+    ++          +    D + A+V
Sbjct: 63  GIIREVAANGWAVDIYSPYQAFLPVSEN--PEMKPNKK-------PNEVLDIGDAIIAKV 113

Query: 156 RSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRRKQHFHHL-----EEYGIDLIIGC 210
            +      + L  +++    +  G+++ ++P  V R       +      E  + +++G 
Sbjct: 114 LNIDPKMKVTLTMKDRICRPIRFGRIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ 173

Query: 211 NGYIWIGEHVEARDKMV 227
           NG IW+           
Sbjct: 174 NGLIWVNGDRRKVSIAE 190

>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 =  154 bits (390), Expect = 1e-45
 Identities = 46/201 (22%), Positives = 80/201 (39%), Gaps = 15/201 (7%)

Query: 36  VTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKL--IYVRALRARYKPETGDI 93
           V  G+ +P  E+         D KG   ATV G++             L+  Y P+ GD+
Sbjct: 12  VVPGEPLP--EEVEASPPYVIDYKGVKRATVVGLLREKGDGGGRAFVKLKEIYVPQAGDV 69

Query: 94  VIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCA 153
           VIG +  V    W ++IN    A+L +           R       +M+S+    D + A
Sbjct: 70  VIGLIQSVGIMNWFVDINSPYVAVLSVQD------FLGRPFNPAVDDMQSLLKVGDYIKA 123

Query: 154 EVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKR----RKQHFHHL-EEYGIDLII 208
           +V +     S  L  + +  G++ RG+++ + P  V R    +      L E+    + +
Sbjct: 124 KVVAFDKTRSPLLTVQGEGLGRIVRGKIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFV 183

Query: 209 GCNGYIWIGEHVEARDKMVVD 229
             NG I +    E  + + V 
Sbjct: 184 ARNGRIHLECPNEDLEAIAVM 204

>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 =  153 bits (387), Expect = 4e-45
 Identities = 44/212 (20%), Positives = 77/212 (36%), Gaps = 13/212 (6%)

Query: 31  NPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRA-RYKPE 89
            P S V  G+ +   E  I           +  +TV G+ +  +    V  L    Y P+
Sbjct: 14  QPRSIVVPGELLAEGEFQIPWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEGSFYYPK 73

Query: 90  TGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTEND 149
             DIVIG V +V    W ++I     A L       P      R+     ++R      D
Sbjct: 74  INDIVIGLVEDVEIYGWVVDIKAPYKAYL-------PASNLLGRSINVGEDLRRYLDVGD 126

Query: 150 LVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKR----RKQHFHHL-EEYGI 204
            V A + +        L  + +  G++  G ++ + P  V R     K  +  L  + G 
Sbjct: 127 YVIARIENFDRSIDPVLSVKGKDLGRVSNGIVIDIMPVKVPRVIGKNKSMYETLTSKSGC 186

Query: 205 DLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQ 236
            + +  NG IW        ++++++     E 
Sbjct: 187 SIFVANNGRIWATCPSRFSEEILIEAIRKIEN 218

>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 =  146 bits (368), Expect = 7e-42
 Identities = 39/239 (16%), Positives = 79/239 (33%), Gaps = 29/239 (12%)

Query: 20  LERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVV-------ER 72
           L   E               +        ++ G G       L  T CG +         
Sbjct: 50  LPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGS 109

Query: 73  INKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRR 132
              + +V + + RY P  GD VIG V       +K+++  ++ A L    ++     +R 
Sbjct: 110 GGGVYWVDSQQKRYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSY--LSFEGATKR- 166

Query: 133 RTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQL-----QARNQKYGKLER-GQLLTVDP 186
                    R      DL+  +   +  D   ++       R    G + + G L  V  
Sbjct: 167 --------NRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVIGQDGLLFKVTL 218

Query: 187 YLVKRRKQHFHHL-----EEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIAK 240
            L+++       +     + Y ++++ G NG IW+      +  ++ +     E + + 
Sbjct: 219 GLIRKLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTIQQTLILANILEACEHMTSD 277

>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 =  122 bits (306), Expect = 6e-34
 Identities = 34/177 (19%), Positives = 66/177 (37%), Gaps = 28/177 (15%)

Query: 85  RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSI 144
           RY P   D VIG +I      +K+ +     ++  LS M  P+  ++          R  
Sbjct: 2   RYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVS-LSYMAFPNASKK---------NRPT 51

Query: 145 FTENDLVCAEVRSSQGDGSLQLQA------RNQKYGKLERGQLLTVDPYLVKRR--KQHF 196
               DLV A V +++ +   +++       R+  +G LE G ++ V+    ++      F
Sbjct: 52  LQVGDLVYARVCTAEKELEAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDF 111

Query: 197 HHLE----EYGIDLIIGCNGYIWIGEHVEARDKMV------VDQGSNSEQLIAKCDK 243
             L+        ++ IG NG IW+     +             Q +++        +
Sbjct: 112 PLLKVLAAHTKFEVAIGLNGKIWVKCEELSNTLACYRTIMECCQKNDTAAFKDIAKR 168

>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 =  109 bits (274), Expect = 3e-29
 Identities = 30/160 (18%), Positives = 64/160 (40%), Gaps = 10/160 (6%)

Query: 36  VTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVI 95
           V  GD I    +  +KG G  ++ GEL A V G +   +++  V ++    +   GD+V+
Sbjct: 4   VMPGDRIGS-AEEYVKGEGVYEEGGELFAAVAGKLIIKDRVAKVESISPIPEIVKGDVVL 62

Query: 96  GRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEV 155
           GRV+++      +E++  +      S+  +               +       D++ A V
Sbjct: 63  GRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARV 122

Query: 156 RSSQGDGSLQLQARNQKYGKLER-----GQLLTVDPYLVK 190
                  +L+L  + ++ G L          +  +  ++K
Sbjct: 123 I----GDNLRLSTKEEEMGVLRALCSNCKTEMVREGDILK 158

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

 Score =  102 bits (256), Expect = 2e-26
 Identities = 31/162 (19%), Positives = 62/162 (38%), Gaps = 8/162 (4%)

Query: 22  RLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINK-----L 76
              S    + P      G+ +   E+    G GT  + G + +++ G + + ++     +
Sbjct: 8   HHHSQDPMAPPVRYCIPGERLCNLEE-GSPGSGTYTRHGYIFSSLAGCLMKSSENGALPV 66

Query: 77  IYV-RALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTA 135
           + V R   ++  P+ G IV  +V  +  +  K+ I +     L  S          R T 
Sbjct: 67  VSVVRETESQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATE 126

Query: 136 VDELNMRSIFTENDLVCAEVRS-SQGDGSLQLQARNQKYGKL 176
            D++ +   F   D+V A+V S      +  L     + G +
Sbjct: 127 KDKVEIYKSFRPGDIVLAKVISLGDAQSNYLLTTAENELGVV 168

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 52.9 bits (126), Expect = 7e-08
 Identities = 41/291 (14%), Positives = 90/291 (30%), Gaps = 89/291 (30%)

Query: 70  VERINKLIYVR-ALRARYKPETGDIV-----IGR---VIEVVPKRWKLEINFTQDAILML 120
           V R+   + +R AL    +P    ++      G+    ++V    +K++           
Sbjct: 131 VSRLQPYLKLRQALL-ELRPAKNVLIDGVLGSGKTWVALDVC-LSYKVQCKM-------- 180

Query: 121 SSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQ 180
                   I         LN+++  +   ++       Q    L  Q       + +   
Sbjct: 181 -----DFKIFW-------LNLKNCNSPETVL----EMLQ---KLLYQIDPNWTSRSDHSS 221

Query: 181 LLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEA-----------RDKMVVD 229
            + +  + ++   +     + Y   L++  N  +   +   A           R K V D
Sbjct: 222 NIKLRIHSIQAELRRLLKSKPYENCLLVLLN--VQNAKAWNAFNLSCKILLTTRFKQVTD 279

Query: 230 QGSN-------------------SEQLIAKCDKNSMDLDEQDGTCTPREARQN----ICR 266
             S                     + L+ K     +D   QD    PRE        +  
Sbjct: 280 FLSAATTTHISLDHHSMTLTPDEVKSLLLKY----LDCRPQD---LPREVLTTNPRRLSI 332

Query: 267 IANAIRV-LSRLGF--NITVEVILETVNLSNSLN-LDIHDMLGSEFYVLVA 313
           IA +IR  L+      ++  + +     + +SLN L+  +    + +  ++
Sbjct: 333 IAESIRDGLATWDNWKHVNCDKLTTI--IESSLNVLEPAEY--RKMFDRLS 379

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 47.9 bits (113), Expect = 3e-06
 Identities = 43/360 (11%), Positives = 93/360 (25%), Gaps = 138/360 (38%)

Query: 6   LSFNQTQKVRLEKALERLESLSSKSNPNSCVTV--GDTIPVYEDGILKGHGTSDQKGELA 63
           L+            LE L+ L  + +PN          I                +    
Sbjct: 187 LNLKNCNSPETV--LEMLQKLLYQIDPNWTSRSDHSSNIK---------LRIHSIQ---- 231

Query: 64  ATVCGVVERINKLI----YVRALRARYKPETGDIVIGRVIEVVPKRWKLEI----NF--- 112
                    + +L+    Y   L          +V+  V          +     N    
Sbjct: 232 -------AELRRLLKSKPYENCL----------LVLLNV-------QNAKAWNAFNLSCK 267

Query: 113 ----TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQA 168
               T+         +          ++D        T ++                L  
Sbjct: 268 ILLTTRFK----QVTDFLSAATTTHISLDH--HSMTLTPDE-------------VKSLLL 308

Query: 169 R--NQKYGKLERGQLLTVDPYLV----KRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEA 222
           +  + +   L R ++LT +P  +    +  +      + +               +HV  
Sbjct: 309 KYLDCRPQDLPR-EVLTTNPRRLSIIAESIRDGLATWDNW---------------KHVN- 351

Query: 223 RDKMVVDQGSNSEQLIAKCDKNSMDLDEQDGTCTPREARQNICRIA----NA---IRVLS 275
            DK+          +I         L+  +    P E R+   R++    +A     +LS
Sbjct: 352 CDKL--------TTIIESS------LNVLE----PAEYRKMFDRLSVFPPSAHIPTILLS 393

Query: 276 RLGFNITVEVILETVN-LSNSLNLD---------IHDMLGSEFYVLVAESEAERRSLSKR 325
            + F++    ++  VN L     ++         I  +     Y+ +        +L + 
Sbjct: 394 LIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI-----YLELKVKLENEYALHRS 448

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	327
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	100.0
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
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	100.0
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	100.0
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	99.97
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	99.96
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	98.89
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	98.75
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	98.75
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	98.74
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	98.71
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	98.7
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	98.7
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	98.69
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	98.68
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	98.64
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	98.55
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.5
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	98.44
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	98.42
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	98.4
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.32
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.26
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.14
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.11
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	97.99
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.84
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	97.77
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	97.54
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	97.45
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	97.4
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	97.3
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	97.25
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	97.09
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.0
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	96.67
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	96.63
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	96.42
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	96.34
2bh8_A	101	1B11; transcription, molecular evolution, unique a	92.84
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	92.65
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	91.87
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	87.3
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	84.5

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

Probab=100.00  E-value=1.2e-66  Score=498.88  Aligned_cols=287  Identities=40%  Similarity=0.588  Sum_probs=229.1

Q ss_pred             HHHHHHHHHHHHhhccCCCCCCceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEECcEEEEEecCCccCCCCC
Q 020356           12 QKVRLEKALERLESLSSKSNPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETG   91 (327)
Q Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~nk~v~V~pl~~rY~P~vG   91 (327)
                      .+.|+.+|++++..+++...+..+|+|||.|+..++ |++|+|||..+|+|+||++|.+..+++++||+|++++|.|++|
T Consensus        18 ~~~~~~~~~~~~~~~~~~~~~~~iVlPGd~L~~~~~-~~~G~Gty~~~g~I~Asv~G~v~~~~~~vsV~p~~~rY~P~vG   96 (308)
T 2nn6_H           18 MEMRLPVARKPLSERLGRDTKKHLVVPGDTITTDTG-FMRGHGTYMGEEKLIASVAGSVERVNKLICVKALKTRYIGEVG   96 (308)
T ss_dssp             ----------------------CBCCTTCBCCCCTT-CCBCTTEEECSSSEEECSSEEEEEETTEEEEEESSCCCCCCSS
T ss_pred             ccccchhhhhccccccccCCCCcEEeCCCCCCCCCC-EeecCCeEEECCEEEEEEEEEEEecCCEEEEeeCCCccCCCCC
Confidence            488999999999999988899999999999986555 9999999999999999999999999999999999999999999


Q ss_pred             CEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccC
Q 020356           92 DIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQ  171 (327)
Q Consensus        92 DiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~  171 (327)
                      |+|+|+|+++++++|+|||+++.++.+|+|+++|||+++|++...|+.+|+++|++||+|+|||+++++++++.||||++
T Consensus        97 DvViG~Vt~V~~~~a~VdI~s~~~~~l~iS~v~f~gg~iR~~~~~D~~~m~~~l~vGDlV~ArVisv~~~~~i~LStr~~  176 (308)
T 2nn6_H           97 DIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSL  176 (308)
T ss_dssp             BCCCEEEEEEETTEEEEECSSSSCEEEESSCCC-------------CHHHHHHSCSSCEECCEEEEEETTTEEEEECCSS
T ss_pred             CEEEEEEEEEeCceEEEEECCCcCCceechhhccccceeecccchhhhhhhccCCCCCEEEEEEEEcCCCCCEEEEecCc
Confidence            99999999999999999999999999999999999999988888888999999999999999999999889999999999


Q ss_pred             CCccCCCCeEEEeChhhhhhccccccccCccceEEEEeecceeeeccccccccccccccCCCchhhhhhccCCCCccccC
Q 020356          172 KYGKLERGQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIAKCDKNSMDLDEQ  251 (327)
Q Consensus       172 ~lGkL~~G~lv~V~~~li~r~~~h~~~L~~~~~eiivG~NG~IWI~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  251 (327)
                      +||+|++|+++.|++.+++|+++|++.|. |+|+|++|+||||||++.....+       +..+   .++         +
T Consensus       177 ~LGkL~~G~v~~vs~~lv~r~~~~l~~l~-~g~eI~vG~NG~IWi~~~~~~~~-------~~~~---~~~---------~  236 (308)
T 2nn6_H          177 KYGKLGQGVLVQVSPSLVKRQKTHFHDLP-CGASVILGNNGFIWIYPTPEHKE-------EEAG---GFI---------A  236 (308)
T ss_dssp             TTCEECSSCEEECCTTSCCCSTTCSCCCB-TTBEEEEETTTEEEEECCCCC----------------CCG---------G
T ss_pred             CCcccCCeEEEEEChhheechhheEecCC-CCcEEEEeCCCEEEEcCCcchhh-------hhcc---ccc---------c
Confidence            99999999999999999999999999985 99999999999999997643211       0000   011         1


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHhhhhCCCCchhcccchHHHHHHHHHHHHhh
Q 020356          252 DGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLDIHDMLGSEFYVLVAESEAERRS  321 (327)
Q Consensus       252 ~~~~~~~~~r~~i~r~~n~i~~l~~~~~~i~~~~i~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~~~~  321 (327)
                      +.++++.++|++|||++|||++|++++++||+++|+++|++|+++  +++|||.||++..+++.+++|=.
T Consensus       237 ~~~~~~~~~r~~i~r~~n~i~~l~~~~~~i~~~~i~~~~~~s~~~--~~~~~l~~~~~~~~~~~~~~~~~  304 (308)
T 2nn6_H          237 NLEPVSLADREVISRLRNCIISLVTQRMMLYDTSILYCYEASLPH--QIKDILKPEIMEEIVMETRQRLL  304 (308)
T ss_dssp             GSSCCCHHHHHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHTHHHH--CCSSCCTTHHHHHHHHHHHHHHH
T ss_pred             cCCcCCHHHHHHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHhhC--CHHHhccHHHHHHHHHHHHHHHH
Confidence            124699999999999999999999999999999999999999655  99999999999999999998743

>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=1.6e-44  Score=342.97  Aligned_cols=182  Identities=21%  Similarity=0.352  Sum_probs=153.0

Q ss_pred             CCCCCCceEecCCccCCCC-C---------------------ceee--cCCEEeeCCeEEEEEeeEEEEECc-------E
Q 020356           28 SKSNPNSCVTVGDTIPVYE-D---------------------GILK--GHGTSDQKGELAATVCGVVERINK-------L   76 (327)
Q Consensus        28 ~~~~~~~iV~PGD~I~~~e-e---------------------~~~~--G~Gty~~~g~i~Ssv~G~v~~~nk-------~   76 (327)
                      |....+.+|+|||.|+..+ +                     .|++  |+|||..+++|+|+++|.++.+++       +
T Consensus        34 ~~~~~~~iVlPGD~L~~~~~~~~~~~g~~~~~~l~~~~~~~~~~~~~~G~Gty~~~~~I~as~aG~l~~~~~~~~~~~~~  113 (289)
T 2nn6_G           34 ARTVLGQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGV  113 (289)
T ss_dssp             CTGGGSSBCCSSEEECCSCSCCEECSSEEECC-----------------------CCCEEECSCCEEEEECCTTTSSCCE
T ss_pred             HhhcCCcEEeCCCCcCccccccccccccccccccccccccCcceEEccCCCeEEECCEEEEEEeEeEEeccCCccCccce
Confidence            4455678999999998654 0                     4888  999999999999999999998765       7


Q ss_pred             EEEEecCCccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEE
Q 020356           77 IYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVR  156 (327)
Q Consensus        77 v~V~pl~~rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~  156 (327)
                      +||+|++++|+|++||+|||+|+++++++|+|||++++.|.|++++  |||+++         +|+++|++||+|+|||+
T Consensus       114 v~V~~~~~rYiP~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~~--f~Gatk---------~~r~~f~~GDlV~ArV~  182 (289)
T 2nn6_G          114 YWVDSQQKRYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLS--FEGATK---------RNRPNVQVGDLIYGQFV  182 (289)
T ss_dssp             EEEECCCSSCCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCS--SSCCSS---------CSSSSSCTTCEEEEEEE
T ss_pred             EEEEecCCCCCCCCCCEEEEEEEEEeCcEEEEEECCCceeEEehhh--cCcchh---------hhhhhcCCCCEEEEEEE
Confidence            9999999999999999999999999999999999999999998874  888764         46788999999999999


Q ss_pred             ecCCCCceEEEE-----ccCCCccC-CCCeEEEeChhhhhhcccccc----ccC-ccceEEEEeecceeeecccc
Q 020356          157 SSQGDGSLQLQA-----RNQKYGKL-ERGQLLTVDPYLVKRRKQHFH----HLE-EYGIDLIIGCNGYIWIGEHV  220 (327)
Q Consensus       157 sv~~~g~i~Lst-----r~~~lGkL-~~G~lv~V~~~li~r~~~h~~----~L~-~~~~eiivG~NG~IWI~~~~  220 (327)
                      +++++++++|||     |+.+||+| .+|++++|+|++++|+..|.+    .|. .++|+|+||+||||||++.+
T Consensus       183 s~~~~~~~eLsc~~~~~k~~~lG~L~~~G~l~~Vs~~lvrrl~~~~~~~l~~L~~~~~~eI~vG~NG~IWI~~~~  257 (289)
T 2nn6_G          183 VANKDMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKT  257 (289)
T ss_dssp             ECCTTSCCEEECSBTTTTBCCCCSCCSSCEEECCCHHHHHHHHCTTCSHHHHTTCSSSCCCEEETTTEEEECCSS
T ss_pred             EcCCCCceEEEecccccccccCCEecCCeEEEEEChHHhhhhhcCchhHHHHhcccCCeEEEEECCcEEEEecCC
Confidence            999999999999     99999999 999999999999999987643    343 68999999999999998754

>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=8.3e-44  Score=328.21  Aligned_cols=177  Identities=23%  Similarity=0.405  Sum_probs=161.0

Q ss_pred             CceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEECcEEEEEecCCccCCCCCCEEEEEEEEEecceEEEEEcC
Q 020356           33 NSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRARYKPETGDIVIGRVIEVVPKRWKLEINF  112 (327)
Q Consensus        33 ~~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~nk~v~V~pl~~rY~P~vGDiVIGrV~~V~~~~w~VDI~s  112 (327)
                      ..+|+|||.|+ .+ .|++|+|||..+|+|+||++|.+..+++.++|+|++++|.|++||+|+|+|+++++++|+|||++
T Consensus         2 ~~iV~PGd~l~-~~-~~~~G~Gty~~~g~i~as~~G~v~~~~~~v~V~p~~~~y~p~~GDiV~G~V~~v~~~~a~V~I~~   79 (229)
T 2ba0_A            2 RKIVLPGDLLS-TN-PRAAGYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGRYTPSVGDVVIGIIREVAANGWAVDIYS   79 (229)
T ss_dssp             CCEECTTCEEE-SC-TTSBCTTEEEETTEEEECSSEEEEECSSCEEEEECSSSCCCCTTCEEEEEEEEECSSEEEEECSS
T ss_pred             CCEEcCCCCcc-cC-CeEecCCEEEeCCEEEEEEEEEEEEeCCEEEEEeCCCcccCCCCCEEEEEEEEEeCCeEEEEeCC
Confidence            36899999997 34 49999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccCCCccCCCCeEEEeChhhhhhc
Q 020356          113 TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLVKRR  192 (327)
Q Consensus       113 ~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~~lGkL~~G~lv~V~~~li~r~  192 (327)
                      +++|+||++++..       +.  +..+|+++|++||+|+|+|+++++++++.||||+.+||+|.+|++++++|.+++|+
T Consensus        80 ~~~g~l~isev~~-------~~--~~~~~~~~l~~GD~V~arVi~v~~~~~i~LS~r~~~lG~L~~G~v~~vs~~~v~rl  150 (229)
T 2ba0_A           80 PYQAFLPVSENPE-------MK--PNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDRICRPIRFGRIVAINPARVPRV  150 (229)
T ss_dssp             SSCEEEEGGGCTT-------CC--TTSCGGGTCCTTCEEEEEEEEECTTCCEEEECCSSSCEEESSSEEEECCGGGHHHH
T ss_pred             CeEEEEEHHHccc-------cc--cccchhcccCCCCEEEEEEEEECCCCcEEEEEccccCCcccCCEEEEECHHHhHHH
Confidence            9999999998861       11  12389999999999999999999999999999999999999999999999999997


Q ss_pred             c----ccccccC-ccceEEEEeecceeeecccc
Q 020356          193 K----QHFHHLE-EYGIDLIIGCNGYIWIGEHV  220 (327)
Q Consensus       193 ~----~h~~~L~-~~~~eiivG~NG~IWI~~~~  220 (327)
                      .    +|+++|. .++|+|++|+||+|||++.+
T Consensus       151 ~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~  183 (229)
T 2ba0_A          151 IGKKGSMIKLLKSELDVQIVVGQNGLIWVNGDR  183 (229)
T ss_dssp             HCGGGHHHHHHHHHHTCEEEECTTSEEEEESCH
T ss_pred             hcCCchHHHHhcccCCeEEEEECCcEEEEeCCc
Confidence            4    4677774 68999999999999999653

>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=2.2e-43  Score=326.19  Aligned_cols=181  Identities=24%  Similarity=0.311  Sum_probs=120.0

Q ss_pred             CCceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEECc--EEEEEecCCccCCCCCCEEEEEEEEEecceEEEE
Q 020356           32 PNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINK--LIYVRALRARYKPETGDIVIGRVIEVVPKRWKLE  109 (327)
Q Consensus        32 ~~~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~nk--~v~V~pl~~rY~P~vGDiVIGrV~~V~~~~w~VD  109 (327)
                      ...+|+|||.|+. ++ |++|+|||..+|+|+||++|.+...++  .+||+|++++|.|++||+|+|+|+++++++|+||
T Consensus         8 ~~~iV~PGd~l~~-~~-~~~G~Gty~~~~~I~Asv~G~v~~~~~~~~vsV~p~~~~y~p~~GDiV~G~V~~v~~~~~~V~   85 (235)
T 2z0s_A            8 AGRIVVPGEPLPE-EV-EASPPYVIDYKGVKRATVVGLLREKGDGGGRAFVKLKEIYVPQAGDVVIGLIQSVGIMNWFVD   85 (235)
T ss_dssp             ------------------------------------------------------CCCCCCTTCCEEEEEEEECSSEEEEE
T ss_pred             CCcEEeCCCCccc-Cc-eEcCCCEEEECCEEEEEEeEEEEEeCCccEEEEEeCCCccCCCCCCEEEEEEEEEeCCeEEEE
Confidence            3579999999973 43 999999999999999999999998776  8999999999999999999999999999999999


Q ss_pred             EcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccCCCccCCCCeEEEeChhhh
Q 020356          110 INFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPYLV  189 (327)
Q Consensus       110 I~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~~lGkL~~G~lv~V~~~li  189 (327)
                      |+++++|+||++++.  +    ++.+.+..+|+++|++||+|+|+|+++++++.+.||||+..||+|++|++++++|.++
T Consensus        86 I~~~~~g~l~isei~--~----~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~~~~i~LS~k~~~lG~l~gG~vv~vs~~~~  159 (235)
T 2z0s_A           86 INSPYVAVLSVQDFL--G----RPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGEGLGRIVRGKIVEISPAKV  159 (235)
T ss_dssp             CSSSSCEEEEHHHHH--T----SCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCSSSCEECCSSEEEECCGGGS
T ss_pred             eCCCeEEEEEHHHhC--C----CccccchhhHhhcCCCCCEEEEEEEEECCCCcEEEEEecccCccccCCEEEEECHHHh
Confidence            999999999999875  2    2334456699999999999999999999888999999999999999999999999999


Q ss_pred             hhcc----ccccccC-ccceEEEEeecceeeecccc
Q 020356          190 KRRK----QHFHHLE-EYGIDLIIGCNGYIWIGEHV  220 (327)
Q Consensus       190 ~r~~----~h~~~L~-~~~~eiivG~NG~IWI~~~~  220 (327)
                      +|+.    +|+++|. +++|++++|+||+|||++..
T Consensus       160 ~rl~~~~~~~l~~l~~~~~~~i~vG~NG~IWi~~~~  195 (235)
T 2z0s_A          160 PRVIGRKMSMLKTLEEKTECKIFVARNGRIHLECPN  195 (235)
T ss_dssp             GGGTCGGGHHHHHHHHHHCCEEEEETTTEEEEECSC
T ss_pred             HHHhcCcchHHHHhcccCCeEEEEeCCCEEEEecCC
Confidence            9986    4888885 68999999999999998753

>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=5.1e-43  Score=326.98  Aligned_cols=182  Identities=23%  Similarity=0.331  Sum_probs=158.7

Q ss_pred             CCCceEecCCccCCCCCceeecC--CEEeeCCeEEEEEeeEEEEECcEEEEEecCC-ccCCCCCCEEEEEEEEEecceEE
Q 020356           31 NPNSCVTVGDTIPVYEDGILKGH--GTSDQKGELAATVCGVVERINKLIYVRALRA-RYKPETGDIVIGRVIEVVPKRWK  107 (327)
Q Consensus        31 ~~~~iV~PGD~I~~~ee~~~~G~--Gty~~~g~i~Ssv~G~v~~~nk~v~V~pl~~-rY~P~vGDiVIGrV~~V~~~~w~  107 (327)
                      +...+|+|||.|+. ++ |++|+  |||..+|+|+||++|.+..+++.++|+|+++ +|.|++||+|+|+|+++++++|+
T Consensus        14 ~~~~iV~PGd~l~~-~~-~~~G~~~Gty~~~g~i~as~~G~v~~~~~~v~V~p~~~~~y~p~~GDiV~G~V~~v~~~ga~   91 (251)
T 2je6_I           14 QPRSIVVPGELLAE-GE-FQIPWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEGSFYYPKINDIVIGLVEDVEIYGWV   91 (251)
T ss_dssp             CSSCEECTTCEEEE-EC-CCCCCCTTEEEETTEEEECSSEEEEEETTEEEEEESCCSCCCCCTTCEEEEEEEEECSSEEE
T ss_pred             CCCcEEcCCCCCcc-CC-eeeCCCCCEEEECCEEEEEEEEEEEEeCCEEEEEECCCcccCCCCCCEEEEEEEEEeCceEE
Confidence            45789999999983 43 99999  9999999999999999999999999999998 99999999999999999999999


Q ss_pred             EEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccCCCccCCCCeEEEeChh
Q 020356          108 LEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLERGQLLTVDPY  187 (327)
Q Consensus       108 VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~~lGkL~~G~lv~V~~~  187 (327)
                      |||+++++|+||++++.  +  .+  ...| .+|+++|++||+|+|+|+++++++.+.||||+.+||+|.+|++++++|.
T Consensus        92 VdI~~~~~GlL~isei~--~--~~--~~~~-~~~~~~l~vGD~V~arVi~v~~~~~i~LS~r~~~lG~L~~G~v~~vs~~  164 (251)
T 2je6_I           92 VDIKAPYKAYLPASNLL--G--RS--INVG-EDLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRVSNGIVIDIMPV  164 (251)
T ss_dssp             EECSSSSCEEEEHHHHH--T--SC--CCTT-CCCSSSCCTTCEEEEEEEEEETTEEEEEECCSTTCEECCSSCEEECCGG
T ss_pred             EEcCCCeEEEEEHHHhc--C--Cc--cccc-cchhhcCCCCCEEEEEEEEECCCCcEEEEEccccCCcccCCEEEEECHH
Confidence            99999999999999875  2  12  2233 6999999999999999999998899999999999999999999999999


Q ss_pred             hhhhc----cccccccC-ccceEEEEeecceeeeccccc
Q 020356          188 LVKRR----KQHFHHLE-EYGIDLIIGCNGYIWIGEHVE  221 (327)
Q Consensus       188 li~r~----~~h~~~L~-~~~~eiivG~NG~IWI~~~~~  221 (327)
                      +++|+    .+|+++|. .++|+||||+||||||++.+.
T Consensus       165 ~v~rl~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~  203 (251)
T 2je6_I          165 KVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSR  203 (251)
T ss_dssp             GHHHHHCGGGHHHHHHHTTC---CEECTTSEEEC-----
T ss_pred             HhHHHhcCcchHHHHhcccCCeEEEEECCcEEEEeCCCH
Confidence            99997    35788884 789999999999999997643

>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=6e-34  Score=252.97  Aligned_cols=125  Identities=25%  Similarity=0.474  Sum_probs=114.1

Q ss_pred             CccCCCCCCEEEEEEEEEecceEEEEEcC-ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC
Q 020356           84 ARYKPETGDIVIGRVIEVVPKRWKLEINF-TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG  162 (327)
Q Consensus        84 ~rY~P~vGDiVIGrV~~V~~~~w~VDI~s-~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g  162 (327)
                      +||.|++||+|+|+|+++.+++|+|||++ +++|.||++  +|||+++         +|+.+|++||+|+|||++++.++
T Consensus         1 krY~P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s--~~~g~~k---------~~r~~l~~GDlV~ArV~~~~~~~   69 (175)
T 2ja9_A            1 KRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYM--AFPNASK---------KNRPTLQVGDLVYARVCTAEKEL   69 (175)
T ss_dssp             CCCCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETT--SSTTCCS---------SSCCCCCTTCEEEEEEEECCTTS
T ss_pred             CCccCCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHH--HCCchhh---------hhhccCCCCCEEEEEEEEecCCC
Confidence            58999999999999999999999999999 999999988  4777754         46777999999999999999999


Q ss_pred             ceEEE------EccCCCccCCCCeEEEeChhhhhhcc--ccccccC----ccceEEEEeecceeeeccc
Q 020356          163 SLQLQ------ARNQKYGKLERGQLLTVDPYLVKRRK--QHFHHLE----EYGIDLIIGCNGYIWIGEH  219 (327)
Q Consensus       163 ~i~Ls------tr~~~lGkL~~G~lv~V~~~li~r~~--~h~~~L~----~~~~eiivG~NG~IWI~~~  219 (327)
                      +++||      +|+++||+|++|++++|+|++++|+.  .|+++|+    .++|+|++|+||||||++.
T Consensus        70 ~~~Ltc~~~~~~r~~~lG~L~~G~l~~v~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~  138 (175)
T 2ja9_A           70 EAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWVKCE  138 (175)
T ss_dssp             CCEEESSCTTTCSCTTCEEECSCEEEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETTTEEEEECS
T ss_pred             ceEEEecccccccccCCcCcCCCEEEEEcHHHhhHHhcCCCcchHHhhhccCCeEEEEECCcEEEEecC
Confidence            99999      89999999999999999999999986  4776663    6899999999999999874

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

Probab=99.97  E-value=1.6e-30  Score=231.22  Aligned_cols=128  Identities=26%  Similarity=0.378  Sum_probs=117.7

Q ss_pred             ceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEECcEEEEEecCC-ccCCCCCCEEEEEEEEEecceEEEEEcC
Q 020356           34 SCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRA-RYKPETGDIVIGRVIEVVPKRWKLEINF  112 (327)
Q Consensus        34 ~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~nk~v~V~pl~~-rY~P~vGDiVIGrV~~V~~~~w~VDI~s  112 (327)
                      ++|+|||.|+..++ |++|||||..+|+|+||++|.++.+++++||+|+++ +|.|+ ||+|+|+|+++++++|+|||++
T Consensus         2 ~iV~PGd~l~~~~~-~~~G~Gty~~~~~i~as~~G~v~~~~~~v~V~~~~~~~y~p~-GdiV~G~V~~V~~~ga~V~I~~   79 (179)
T 3m7n_A            2 RFVMPGDRIGSAEE-YVKGEGVYEEGGELFAAVAGKLIIKDRVAKVESISPIPEIVK-GDVVLGRVVDLRNSIALIEVSS   79 (179)
T ss_dssp             CEECTTCEEEETTT-SEECTTEEEETTEEEESSSEEEEEETTEEEEEESSCCCCCCT-TCEEEEEEEEECSSEEEEEEEE
T ss_pred             eEEcCCCCCCCCCC-EeccCCEEEeCCEEEEEEEEEEEEeCCEEEEEECCCCcccCC-CCEEEEEEEEEeCCcEEEEEcc
Confidence            69999999987665 999999999999999999999999999999999966 69999 9999999999999999999998


Q ss_pred             ----------ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEEEccCCCccCC
Q 020356          113 ----------TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKLE  177 (327)
Q Consensus       113 ----------~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Lstr~~~lGkL~  177 (327)
                                +.+|+||+|++.      .  .+.+  +|+++|++||+|.|+|++    +.+.||||+++||+|.
T Consensus        80 v~~~~~~~~~~~~Gll~isei~------~--~~~~--~~~~~~~~GD~V~akVi~----~~i~LS~k~~~lGvv~  140 (179)
T 3m7n_A           80 KKGENRGPSNRGIGILHVSNVD------E--GYVK--EISEAVGYLDILKARVIG----DNLRLSTKEEEMGVLR  140 (179)
T ss_dssp             ETTCCSCCTTCEEEEEEGGGTT------S--SCCS--SGGGTCCTTCEEEEEEEE----TTTEEECCSTTCEEEE
T ss_pred             ccCcccccccCeeEEEEHHHcC------c--chhh--CHhhcCCCCCEEEEEEEC----CeEEEEEecCCCCEEE
Confidence                      899999999885      1  1223  899999999999999998    7899999999999995

>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=99.96  E-value=8.8e-30  Score=231.79  Aligned_cols=138  Identities=19%  Similarity=0.259  Sum_probs=115.7

Q ss_pred             CCCceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEE-----CcEEEEEecCC-ccCCCCCCEEEEEEEEEecc
Q 020356           31 NPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERI-----NKLIYVRALRA-RYKPETGDIVIGRVIEVVPK  104 (327)
Q Consensus        31 ~~~~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~-----nk~v~V~pl~~-rY~P~vGDiVIGrV~~V~~~  104 (327)
                      +...+|+|||.|+..++ |++|+|||+.+|+||||++|.+.++     +++++|+|+++ +|.|++||+|+|+|++++++
T Consensus        17 ~~~~iV~PGd~l~~~~~-~~~G~Gty~~~g~I~Asv~G~v~~~~~~~~~~vi~V~p~~~~~y~p~vGDvV~G~V~~v~~~   95 (209)
T 2nn6_I           17 PPVRYCIPGERLCNLEE-GSPGSGTYTRHGYIFSSLAGCLMKSSENGALPVVSVVRETESQLLPDVGAIVTCKVSSINSR   95 (209)
T ss_dssp             ---CCCCTTCEEEETTT-CCCSSSCEEETTEEECCSCSCBCCCBCTTSSBC-CBCCSCCCCCCCCTTCEEEEEEEEECSS
T ss_pred             CCCcEEcCCCCCCCCCC-eeecCCEEEECCEEEEEEEEEEEEeccCCcccEEEEecCCCCcCCCCCCCEEEEEEEEEECc
Confidence            44679999999986665 9999999999999999999999864     35789999987 59999999999999999999


Q ss_pred             eEEEEEcCc--------cceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC-ceEEEEccCCCcc
Q 020356          105 RWKLEINFT--------QDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG-SLQLQARNQKYGK  175 (327)
Q Consensus       105 ~w~VDI~s~--------~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g-~i~Lstr~~~lGk  175 (327)
                      +|+|||++.        ..|+||++++.        ....|+.+|+++|++||+|+|+|+++++++ .+.||||+++||+
T Consensus        96 ~a~V~I~~v~~~~L~~~~~GlIhisei~--------~~~~~~~~~~~~l~~GD~V~akVisi~~~~~~i~LS~k~~~lGV  167 (209)
T 2nn6_I           96 FAKVHILYVGSMPLKNSFRGTIRKEDVR--------ATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLLTTAENELGV  167 (209)
T ss_dssp             EEEEEEEESSSSCCCCSSCSCEEEEGGG--------TCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEEEECCSSSCEE
T ss_pred             eEEEEECccccccccCCceeEEEHHHcc--------cccccccchhhhcCCCCEEEEEEEEEeCCCCeEEEEEecCCCcE
Confidence            999999754        45555555542        345566799999999999999999998765 5999999999999


Q ss_pred             CC
Q 020356          176 LE  177 (327)
Q Consensus       176 L~  177 (327)
                      +.
T Consensus       168 v~  169 (209)
T 2nn6_I          168 VV  169 (209)
T ss_dssp             CC
T ss_pred             EE
Confidence            96

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

Probab=98.89  E-value=9.8e-09  Score=78.98  Aligned_cols=71  Identities=13%  Similarity=0.094  Sum_probs=61.5

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceE
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQ  165 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~  165 (327)
                      .|++||+|.|+|+++.+.+|+|+|+....|++|+|++.      ..+.        +.|++||.|.|+|.+++.+ +.+.
T Consensus         2 ~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gllh~sel~------~~~~--------~~~~~Gd~V~v~V~~vd~~~~~i~   67 (80)
T 2k52_A            2 DVEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMI------SLRL--------ENLNVGDEIIVQAIDVRPEKREID   67 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGGCS------SCCG--------GGCCTTCEEEEEEEEEETTTTEEE
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHCC------cccc--------eeeCCCCEEEEEEEEEECCCCEEE
Confidence            47899999999999999999999998899999999874      1111        5699999999999999986 8899


Q ss_pred             EEEccC
Q 020356          166 LQARNQ  171 (327)
Q Consensus       166 Lstr~~  171 (327)
                      |+.+..
T Consensus        68 lsl~~~   73 (80)
T 2k52_A           68 FKYIPL   73 (80)
T ss_dssp             EEECSC
T ss_pred             EEEeec
Confidence            998754

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

Probab=98.75  E-value=3.2e-08  Score=83.15  Aligned_cols=74  Identities=18%  Similarity=0.256  Sum_probs=63.7

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceE
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQ  165 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~  165 (327)
                      .+++||+|.|+|+++.+.+++|+|.....|++|+|++. .+     +  ..  ++.+.|++||.|.|+|.+++. ++.+.
T Consensus         4 ~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~-~~-----~--~~--~~~~~~~vGd~V~vkV~~vd~~~~kI~   73 (130)
T 2k4k_A            4 KFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVT-HG-----F--VK--DINEHLSVGDEVQVKVLAVDEEKGKIS   73 (130)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTS-SS-----C--CS--CGGGTCCTTCEEEEEEEEEETTTTEEE
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCC-cc-----c--cc--CccccCCCCCEEEEEEEEEeCCCCEEE
Confidence            46899999999999999999999988899999999885 11     1  11  567789999999999999987 78999


Q ss_pred             EEEcc
Q 020356          166 LQARN  170 (327)
Q Consensus       166 Lstr~  170 (327)
                      ||++.
T Consensus        74 LSlk~   78 (130)
T 2k4k_A           74 LSIRA   78 (130)
T ss_dssp             EESHH
T ss_pred             EEEee
Confidence            99875

>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=98.75  E-value=2.7e-08  Score=88.50  Aligned_cols=77  Identities=18%  Similarity=0.295  Sum_probs=58.8

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEE--cCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-C
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEI--NFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-D  161 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI--~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~  161 (327)
                      .+.|++||+|.|+|+++++.+++|+|  .....|++|+|+++-      .+  ..  ++++.|++||.|.++|.+++. .
T Consensus        10 ~~~p~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~------~~--v~--~~~~~~~vGd~V~VkVl~vD~~~   79 (182)
T 1kl9_A           10 HKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSR------RR--IR--SINKLIRIGRNECVVVIRVDKEK   79 (182)
T ss_dssp             SSSCCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC----------------------CTTCEEEEEEEEEETTT
T ss_pred             ccCCCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCC------cc--cC--CHHHhcCCCCEEEEEEEEEECCC
Confidence            34679999999999999999999999  467899999999861      11  11  567889999999999999986 5


Q ss_pred             CceEEEEccC
Q 020356          162 GSLQLQARNQ  171 (327)
Q Consensus       162 g~i~Lstr~~  171 (327)
                      +.+.||++..
T Consensus        80 ~rI~LSlk~~   89 (182)
T 1kl9_A           80 GYIDLSKRRV   89 (182)
T ss_dssp             TEEEEESTTC
T ss_pred             CEEEEEEeec
Confidence            7899999864

>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=98.74  E-value=4.1e-08  Score=79.19  Aligned_cols=76  Identities=20%  Similarity=0.303  Sum_probs=63.6

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcC---ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINF---TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD  161 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s---~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~  161 (327)
                      ...|++||++.|+|+++.+.+++|+|..   ...|++|+|++.-..   +    ..  ++.+.|++||.|.++|.+++. 
T Consensus         7 ~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~---~----~~--~~~~~~~~Gd~V~VkV~~vd~-   76 (103)
T 2eqs_A            7 GEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREG---R----VA--NVADVVSKGQRVKVKVLSFTG-   76 (103)
T ss_dssp             CSSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSS---C----CC--CHHHHCCTTCEEEEEEEEEET-
T ss_pred             cccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCc---c----cC--CcccEeCCCCEEEEEEEEEEC-
Confidence            3578999999999999999999999996   789999999873111   1    11  556789999999999999987 


Q ss_pred             CceEEEEcc
Q 020356          162 GSLQLQARN  170 (327)
Q Consensus       162 g~i~Lstr~  170 (327)
                      +.+.||++.
T Consensus        77 ~~i~LSlk~   85 (103)
T 2eqs_A           77 TKTSLSMKD   85 (103)
T ss_dssp             TEEEEESTT
T ss_pred             CeeEEEEee
Confidence            689999986

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

Probab=98.71  E-value=5.3e-08  Score=79.93  Aligned_cols=88  Identities=15%  Similarity=0.154  Sum_probs=67.7

Q ss_pred             cEEEEEecCC-ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEE
Q 020356           75 KLIYVRALRA-RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCA  153 (327)
Q Consensus        75 k~v~V~pl~~-rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~A  153 (327)
                      |.+.+.|... .+.|++||+|.|+|+++.+.+++|+|+....|++|+|++....   +.      .+..+.|++||.|.+
T Consensus        14 k~~~~~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~~~---~~------~~~~~~~~vGd~V~v   84 (115)
T 2khi_A           14 LVPRGSHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTN---KN------IHPSKVVNVGDVVEV   84 (115)
T ss_dssp             -------CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSCSS---TT------CSSTTTCCTTCEEEE
T ss_pred             hhcccCCHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCccc---cc------cCcccEECCCCEEEE
Confidence            3456677765 5789999999999999999999999998899999999885311   11      145667999999999


Q ss_pred             EEEecCC-CCceEEEEccC
Q 020356          154 EVRSSQG-DGSLQLQARNQ  171 (327)
Q Consensus       154 eV~sv~~-~g~i~Lstr~~  171 (327)
                      +|.+++. ++.+.|+++..
T Consensus        85 kV~~vd~~~~rI~lslk~~  103 (115)
T 2khi_A           85 MVLDIDEERRRISLGLKQC  103 (115)
T ss_dssp             EEEEEETTTTEEEECCCCC
T ss_pred             EEEEEECCCCEEEEEEEec
Confidence            9999987 57899998864

>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=98.70  E-value=3.6e-08  Score=87.06  Aligned_cols=85  Identities=24%  Similarity=0.339  Sum_probs=68.7

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccch-------hhhhcccCCCCEEEEEEEec
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDE-------LNMRSIFTENDLVCAEVRSS  158 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de-------~~mr~~~~~GDlV~AeV~sv  158 (327)
                      |.|++|+++.|+|+++.+.+++|+|+ +.+|++|+|++. ++     +...|+       .+..+.|++||.|.++|.++
T Consensus        77 ~~~~~Gev~~G~V~~v~~~G~fV~l~-~~eglvhis~l~-~~-----~~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~v  149 (187)
T 1go3_E           77 YIPEMYELIEGEVVDVVEFGSFVRLG-PLDGLIHVSQIM-DD-----YVSYDPKREAIIGKETGKVLEIGDYVRARIVAI  149 (187)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSC-SS-----CEEECCC--CEEETTTCCEECTTCEEEEEEEEE
T ss_pred             EccCCCCEEEEEEEEEeCcEEEEEEc-CccEEEEhHHhC-CC-----cceECCccceEEecCCCeEEcCCCEEEEEEEEE
Confidence            68999999999999999999999997 489999999874 21     111111       14567899999999999999


Q ss_pred             CC------CCceEEEEccCCCccCC
Q 020356          159 QG------DGSLQLQARNQKYGKLE  177 (327)
Q Consensus       159 ~~------~g~i~Lstr~~~lGkL~  177 (327)
                      +.      .+.+.||++.++||++.
T Consensus       150 d~~~~~p~~~~I~lS~k~~~LG~~~  174 (187)
T 1go3_E          150 SLKAERKRGSKIALTMRQPYLGKLE  174 (187)
T ss_dssp             ECCC-----CEEEEECCSTTCEEHH
T ss_pred             EcccCCCCccEEEEEEcCCCCCcHH
Confidence            86      34799999999999773

>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=98.70  E-value=3.7e-08  Score=81.65  Aligned_cols=77  Identities=18%  Similarity=0.120  Sum_probs=63.8

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcC-ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC--
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINF-TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD--  161 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s-~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~--  161 (327)
                      .+.|++||+|.|+|+++.+.+++|+|.. ...|++|++++.-.      +  .+  ++.+.|++||.|.|+|.+++..  
T Consensus        17 ~~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~------~--~~--~~~~~~~~Gd~V~VkV~~vd~~~~   86 (119)
T 2cqo_A           17 ENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSC------R--VD--KPSEIVDVGDKVWVKLIGREMKND   86 (119)
T ss_dssp             CCSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSS------C--CS--CHHHHCCTTCEEEEEEEEEEECSS
T ss_pred             hcccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCcc------c--cc--ChhhcCCCCCEEEEEEEEEecccc
Confidence            3789999999999999999999999965 37999999988511      1  11  5677899999999999999753  


Q ss_pred             -CceEEEEccC
Q 020356          162 -GSLQLQARNQ  171 (327)
Q Consensus       162 -g~i~Lstr~~  171 (327)
                       +.+.|+++..
T Consensus        87 ~~~i~LSlk~~   97 (119)
T 2cqo_A           87 RIKVSLSMKVV   97 (119)
T ss_dssp             CEEEEEESTTB
T ss_pred             CceEEEEEeec
Confidence             5899998864

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

Probab=98.69  E-value=5e-08  Score=79.20  Aligned_cols=77  Identities=22%  Similarity=0.256  Sum_probs=64.6

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC-c
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG-S  163 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g-~  163 (327)
                      .+.+++||+|.|+|+++.+.+++|+|+....|++|++++.-      .+  .+  ++.+.|++||.|.|+|.+++.++ .
T Consensus        26 ~~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~------~~--~~--~~~~~~~vGd~V~v~V~~vd~~~~k   95 (109)
T 2khj_A           26 VALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASR------DR--VE--DATLVLSVGDEVEAKFTGVDRKNRA   95 (109)
T ss_dssp             TTTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCS------SS--SS--SGGGSCCTTCEEEEEEEEEETTTTE
T ss_pred             hhcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCc------cc--cc--ChhhccCCCCEEEEEEEEEECCCCE
Confidence            35789999999999999999999999988999999998741      11  11  45678999999999999998764 7


Q ss_pred             eEEEEccC
Q 020356          164 LQLQARNQ  171 (327)
Q Consensus       164 i~Lstr~~  171 (327)
                      +.||++..
T Consensus        96 i~LS~k~~  103 (109)
T 2khj_A           96 ISLSVRAK  103 (109)
T ss_dssp             EEEETTSS
T ss_pred             EEEEEeec
Confidence            99998763

>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=98.68  E-value=6.3e-08  Score=85.54  Aligned_cols=77  Identities=19%  Similarity=0.257  Sum_probs=61.3

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEc--CccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-C
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEIN--FTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-D  161 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~--s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~  161 (327)
                      .+.|++||+|.|+|+++.+.+++|+|.  ....|++|+|+++-      .+.  .  ++++.|++||.|.|+|.+++. .
T Consensus        10 ~~~p~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~------~~v--~--~~~~~~~vGd~V~vkVl~vd~~~   79 (175)
T 2a19_A           10 NKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSR------RRI--R--SIQKLIRVGKNDVAVVLRVDKEK   79 (175)
T ss_dssp             SSSCCTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC------------------CCCCCCCTTSEEEEEEEEEETTT
T ss_pred             hcCCCCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCC------ccc--C--CHHHcCCCCCEEEEEEEEEECCC
Confidence            457899999999999999999999994  56899999999851      111  1  567789999999999999986 5


Q ss_pred             CceEEEEccC
Q 020356          162 GSLQLQARNQ  171 (327)
Q Consensus       162 g~i~Lstr~~  171 (327)
                      +.+.||++..
T Consensus        80 ~~I~LSlk~~   89 (175)
T 2a19_A           80 GYIDLSKRRV   89 (175)
T ss_dssp             TEEEEESTTC
T ss_pred             CeEEEEEEec
Confidence            7899999864

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

Probab=98.64  E-value=9.7e-08  Score=89.95  Aligned_cols=81  Identities=25%  Similarity=0.343  Sum_probs=65.5

Q ss_pred             ecCCccCCCCCCEEEEEEEEEecceEEEEEc--CccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEec
Q 020356           81 ALRARYKPETGDIVIGRVIEVVPKRWKLEIN--FTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSS  158 (327)
Q Consensus        81 pl~~rY~P~vGDiVIGrV~~V~~~~w~VDI~--s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv  158 (327)
                      |+...+.|++||+|.|+|+++.+.+++|+|.  ....|++|+|+++      ..+.  .  ++++.|++||.|.++|.++
T Consensus         2 ~~~~~~~p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels------~~~v--~--~~~~~~kvGd~V~vkVi~v   71 (275)
T 3aev_A            2 PRKAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVA------STWV--R--NIRDYLKEGQKVVAKVIRV   71 (275)
T ss_dssp             -----CCCCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSC------SSCC--S--CGGGTCCTTCEEEEEEEEE
T ss_pred             CcccccCCCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcC------cccc--c--CHHhccCCCCEEEEEEEEE
Confidence            4556678999999999999999999999998  4789999999985      1111  1  4677899999999999999


Q ss_pred             CC-CCceEEEEccC
Q 020356          159 QG-DGSLQLQARNQ  171 (327)
Q Consensus       159 ~~-~g~i~Lstr~~  171 (327)
                      +. .+.+.||++..
T Consensus        72 D~~~~~I~LSlk~~   85 (275)
T 3aev_A           72 DPRKGHIDLSLRRV   85 (275)
T ss_dssp             ETTTTEEEEESTTC
T ss_pred             ECCCCEEEEEEeec
Confidence            87 68899999874

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

Probab=98.55  E-value=2e-07  Score=73.39  Aligned_cols=74  Identities=23%  Similarity=0.267  Sum_probs=61.3

Q ss_pred             cc-CCCCCCEEEEEEEEEecceEEEEEcC--ccceeeecc-cccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC
Q 020356           85 RY-KPETGDIVIGRVIEVVPKRWKLEINF--TQDAILMLS-SMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG  160 (327)
Q Consensus        85 rY-~P~vGDiVIGrV~~V~~~~w~VDI~s--~~~a~L~ls-~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~  160 (327)
                      .| .|++|+++.|+|+ +++.+++|+|..  ...|.+|+| +++      ..+.    .+.++.| +||.|.++|.+++.
T Consensus         5 ~y~~~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~------~~~~----~~~~~~~-~Gd~V~VkV~~vd~   72 (88)
T 1luz_A            5 CYSLPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMH------MDRY----VEYRDKL-VGKTVKVKVIRVDY   72 (88)
T ss_dssp             CSCCCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCC------HHHH----HHHHHHH-TTCEEEEEEEEEET
T ss_pred             EecCCCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhC------cccc----cCHhHEe-CCCEEEEEEEEEEC
Confidence            45 5899999999999 999999999974  589999999 885      1111    1456778 99999999999986


Q ss_pred             -CCceEEEEcc
Q 020356          161 -DGSLQLQARN  170 (327)
Q Consensus       161 -~g~i~Lstr~  170 (327)
                       .+.+.|++|.
T Consensus        73 ~~~kI~lslk~   83 (88)
T 1luz_A           73 TKGYIDVNYKR   83 (88)
T ss_dssp             TTTEEEEEEEE
T ss_pred             CCCEEEEEEee
Confidence             5789999875

>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=98.50  E-value=3.7e-07  Score=80.12  Aligned_cols=90  Identities=23%  Similarity=0.323  Sum_probs=67.9

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCccc---ccccccchhhhhcccCCCCEEEEEEEecCC-
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQ---RRRTAVDELNMRSIFTENDLVCAEVRSSQG-  160 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~---rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-  160 (327)
                      .+.|.+|+++.|+|++++..+++|+++ +.++++|+|++. +....   .+..-.. .+-...|++||.|+++|.+++. 
T Consensus        76 v~~p~~Gev~~G~V~~v~~~G~fv~l~-~~~glvh~s~l~-~d~~~~d~~~~~~~g-~~~~~~~~~Gd~VrvkV~~v~~~  152 (180)
T 4ayb_E           76 TYVPVVQEVVEGEVLQVDNYGVFVNLG-PMDGLVHISQIT-DDTLKYDNVRGIIFG-EKSKKVIQKGDKVRARVISVAST  152 (180)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSC-SSCEEECSSSCCEEE-TTTCCCCCTTCEEEEEEEEECC-
T ss_pred             eeeccCCCEEEEEEeeeccceEEEEEC-CccceEEeeecC-CCccccchhcceEEE-eccCeEECCCCEEEEEEEEEeCC
Confidence            468999999999999999999999997 689999999874 21110   0000000 1335679999999999999974 


Q ss_pred             ----CCceEEEEccCCCccCC
Q 020356          161 ----DGSLQLQARNQKYGKLE  177 (327)
Q Consensus       161 ----~g~i~Lstr~~~lGkL~  177 (327)
                          .+.+.||+|+++||++.
T Consensus       153 ~~~~~~rI~ls~k~~gLG~~~  173 (180)
T 4ayb_E          153 VTGRLPRIALTMRQPYLGKLE  173 (180)
T ss_dssp             ------CEEEECCSTTCEEHH
T ss_pred             CCcccCcEEEEcCCCCCCCCh
Confidence                34799999999999863

>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=98.44  E-value=4.9e-07  Score=86.42  Aligned_cols=76  Identities=18%  Similarity=0.253  Sum_probs=64.6

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEc--CccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CC
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEIN--FTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DG  162 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~--s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g  162 (327)
                      ..|++||+|.|+|+++.+.+++|+|.  ....|++|+|+++.      .+.    .++.+.|++||.|.++|.+++. .+
T Consensus         9 ~~~~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~------~~i----~~~~~~~kvGd~V~VkVl~vD~~~~   78 (308)
T 1q8k_A            9 KFPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSR------RRI----RSINKLIRIGRNECVKVIRVDKEKG   78 (308)
T ss_dssp             CCCSSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSC------SSC----SCCTTTCSSSCEEEEEEEEEETTTT
T ss_pred             cCCCCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCc------ccc----cCHHHhcCCCCEEEEEEEEEeCCCC
Confidence            35789999999999999999999997  67899999999852      111    1567889999999999999987 57


Q ss_pred             ceEEEEccC
Q 020356          163 SLQLQARNQ  171 (327)
Q Consensus       163 ~i~Lstr~~  171 (327)
                      .+.||++..
T Consensus        79 rI~LSlK~~   87 (308)
T 1q8k_A           79 YIDLSKRRV   87 (308)
T ss_dssp             EEEEECSSC
T ss_pred             EEEEEEEec
Confidence            899999875

>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=98.42  E-value=3.3e-07  Score=85.85  Aligned_cols=80  Identities=21%  Similarity=0.295  Sum_probs=67.6

Q ss_pred             CCccCCCCCCEEEEEEEEEecceEEEEEc--CccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC
Q 020356           83 RARYKPETGDIVIGRVIEVVPKRWKLEIN--FTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG  160 (327)
Q Consensus        83 ~~rY~P~vGDiVIGrV~~V~~~~w~VDI~--s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~  160 (327)
                      ...+.|++||+|.|+|+++.+.+++|+|+  ....|++|+|++.-      .+  ..  ++++.|++||.|.++|.+++.
T Consensus         4 ~~~~~~~vG~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~------~~--v~--~~~~~~~vGd~V~VkVi~vd~   73 (266)
T 3cw2_C            4 SRSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSS------KW--VK--NIRDVLKENRKVIVKVIRVDR   73 (266)
T ss_dssp             CSSSSCCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSC------SS--CC--CHHHHSCTTCEEEEEECCCCS
T ss_pred             cccccCCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCc------cc--cc--CHHHhCcCCCEEEEEEEEEeC
Confidence            34678999999999999999999999997  67899999998851      11  11  567889999999999999986


Q ss_pred             -CCceEEEEccCC
Q 020356          161 -DGSLQLQARNQK  172 (327)
Q Consensus       161 -~g~i~Lstr~~~  172 (327)
                       ++.+.||++...
T Consensus        74 ~~g~I~LSlk~~~   86 (266)
T 3cw2_C           74 RKGTVDVSLKKVT   86 (266)
T ss_dssp             SSCCCBEESTTSC
T ss_pred             CCCEEEEEEEecc
Confidence             788999998754

>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=98.40  E-value=7.6e-07  Score=73.23  Aligned_cols=82  Identities=11%  Similarity=0.163  Sum_probs=61.6

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceE
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQ  165 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~  165 (327)
                      .+++||+|.|+|+++.+.+|+|+|+....+.+|.++.. .+   ..  ..+  +.++.|++||.|.|+|.+++.+ +.+.
T Consensus        18 ~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~-~~---~~--~~~--~~~~~~~~Gd~V~vkV~~vd~~~~~i~   89 (119)
T 1wi5_A           18 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKA-QE---YI--RQK--NKGAKLKVGQYLNCIVEKVKGNGGVVS   89 (119)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHH-HH---HH--HHH--SSSCCCCTTCEEEEEEEECCTTSCEEE
T ss_pred             cCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEecc-cc---cc--ccc--CccCEeCCCCEEEEEEEEEeCCCCEEE
Confidence            57899999999999999999999983233444444431 00   00  011  3467899999999999999874 6899


Q ss_pred             EEEccCCCccC
Q 020356          166 LQARNQKYGKL  176 (327)
Q Consensus       166 Lstr~~~lGkL  176 (327)
                      |+++...+|+-
T Consensus        90 Lslk~~~l~~~  100 (119)
T 1wi5_A           90 LSVGHSEVSTA  100 (119)
T ss_dssp             EECCCCCSCCC
T ss_pred             EEEchhhcccc
Confidence            99999988865

>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=98.32  E-value=1.2e-06  Score=76.47  Aligned_cols=89  Identities=12%  Similarity=0.132  Sum_probs=64.4

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccc-----cchhhhhcccCCCCEEEEEEEecC
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTA-----VDELNMRSIFTENDLVCAEVRSSQ  159 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~-----~de~~mr~~~~~GDlV~AeV~sv~  159 (327)
                      .+.|.+|+++.|+|+++++.+|+|+|+ +.++++|+|++.  .........     ..+ .-...|+.||.|.++|.+++
T Consensus        76 ~~~~~~Gev~~G~V~~v~~fG~fV~l~-~~~glvhis~l~--~~~~~d~~~~~~~~~~~-~~~~~~~~Gd~V~vkV~~vd  151 (172)
T 2c35_B           76 VFRPFKGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIP--SEMEFDPNSNPPCYKTM-DEDIVIQQDDEIRLKIVGTR  151 (172)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSC--TTEEEESSSSSCEEEET-TSCSEEETTCEEEEEEEEEE
T ss_pred             EeeCCCCCEEEEEEEEEeCCEEEEEEC-CEEEEEEHHHCC--CCcEECCCCCccEEEeC-CCCEEECCCCEEEEEEEEEE
Confidence            467999999999999999999999997 566999999763  211100000     000 12557999999999999997


Q ss_pred             CCC---ceEEEEccCCCccCC
Q 020356          160 GDG---SLQLQARNQKYGKLE  177 (327)
Q Consensus       160 ~~g---~i~Lstr~~~lGkL~  177 (327)
                      .+.   ...-|+++++||++.
T Consensus       152 ~~~~~~~~igsm~~~~LG~~~  172 (172)
T 2c35_B          152 VDKNDIFAIGSLMDDYLGLVS  172 (172)
T ss_dssp             EETTEEEEEEECCSTTCEEC-
T ss_pred             cCCCCcEEEEEecCCCCCCCC
Confidence            542   233389999999863

>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=98.26  E-value=1.9e-06  Score=75.16  Aligned_cols=82  Identities=11%  Similarity=0.265  Sum_probs=62.9

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhh-------hcccCCCCEEEEEEEec
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNM-------RSIFTENDLVCAEVRSS  158 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~m-------r~~~~~GDlV~AeV~sv  158 (327)
                      +.|.+|+++.|+|+++++.+++|+|+. .++++|+|++.  ....     .|+.+.       ++.|++||.|.++|.++
T Consensus        79 ~~~~~Gev~~G~V~~v~~fG~FV~l~~-~dglvhis~l~--~~~~-----~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~v  150 (171)
T 1y14_B           79 FKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMP--QDLT-----FNAGSNPPSYQSSEDVITIKSRIRVKIEGC  150 (171)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSC--TTCE-----ECC-----CEECSSCEECTTCEEEEEEEEE
T ss_pred             ccCCCCCEEEEEEEEEecCEEEEEecC-eEEEEEHHHCC--CCce-----ECcccCceEEeccceEECCCCEEEEEEEEE
Confidence            578999999999999999999999987 99999999773  2111     010000       15699999999999998


Q ss_pred             CCCC----ceEEEEccCCCccC
Q 020356          159 QGDG----SLQLQARNQKYGKL  176 (327)
Q Consensus       159 ~~~g----~i~Lstr~~~lGkL  176 (327)
                      +.+.    .+. |+++++||++
T Consensus       151 d~~~~~~~~ig-sm~~~~LG~~  171 (171)
T 1y14_B          151 ISQVSSIHAIG-SIKEDYLGAI  171 (171)
T ss_dssp             EEETTEEEEEE-ECCSTTCEEC
T ss_pred             EcCCCCcEEEE-EcCCCCCCCC
Confidence            7542    344 7899999864

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

Probab=98.14  E-value=1.4e-06  Score=76.31  Aligned_cols=86  Identities=12%  Similarity=0.169  Sum_probs=65.4

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCccccc----ccccchhhhhcccCCCCEEEEEEEecCC
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRR----RTAVDELNMRSIFTENDLVCAEVRSSQG  160 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rr----r~~~de~~mr~~~~~GDlV~AeV~sv~~  160 (327)
                      -+.|.+|+++.|+|+++++.+++|+++ +.++++|+|++.  ....-.    ....  .+....|++||.|+++|.+++.
T Consensus        79 vf~p~~Gev~~G~V~~v~~fG~FV~l~-~~~glVh~s~l~--~~~~~d~~~~~~~~--~~~~~~~~~Gd~VrvkV~~vd~  153 (172)
T 3h0g_G           79 LWRPFRGEVVDAIVTTVNKMGFFANIG-PLNVFVSSHLVP--PDMKFDPTANPPNY--SGEDQVIEKGSNVRLKIVGTRT  153 (172)
T ss_dssp             EECCCTTCEEECCCCEEETTEEECCBT-TBCCEEEGGGSC--TTCCCBSSSSSCBE--ESSSCEECSSCCEEEEEEEEEE
T ss_pred             eeccCCCCEEEEEEEEEEcceEEEEeC-CeEEEEEHHHCC--CccccCcccccceE--ecCCcEECCCCEEEEEEEEEEC
Confidence            368999999999999999999999998 566999999873  210000    0001  1234679999999999999986


Q ss_pred             CC----ceEEEEccCCCccC
Q 020356          161 DG----SLQLQARNQKYGKL  176 (327)
Q Consensus       161 ~g----~i~Lstr~~~lGkL  176 (327)
                      +.    .+. |+++++||+|
T Consensus       154 ~~~~~~~Ig-tm~~~~LG~~  172 (172)
T 3h0g_G          154 DATEIFAIA-TMKEDYLGVL  172 (172)
T ss_dssp             SSSCEEEEE-ECCSTTCEEC
T ss_pred             CCCCceEEE-EcCCCCCCCC
Confidence            43    566 8999999986

>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=98.11  E-value=4.2e-06  Score=76.12  Aligned_cols=85  Identities=11%  Similarity=0.255  Sum_probs=64.5

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCccc---cccc--ccchhhhhcccCCCCEEEEEEEecCC
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQ---RRRT--AVDELNMRSIFTENDLVCAEVRSSQG  160 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~---rrr~--~~de~~mr~~~~~GDlV~AeV~sv~~  160 (327)
                      +.|++|+++.|+|+++++.+++|+|+. .++++|+|.+.  ....   ...+  ...+   ++.+++||.|..+|.+++.
T Consensus        79 ~~p~vGev~~G~V~~vt~fG~FVelg~-~dGlVhiS~l~--d~~~~d~~~~~w~~~~~---~~~~~~Gd~VrVkV~~vd~  152 (215)
T 2b8k_G           79 FKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMP--QDLTFNAGSNPPSYQSS---EDVITIKSRIRVKIEGCIS  152 (215)
T ss_dssp             ECCCTTEEEEEEEEEEETTEEEEECTT-SEEEEEGGGSC--SSCCCBSSCSSCEEECS---SCEEETTCEEEEEEEEEEE
T ss_pred             eccCCCCEEEEEEEEEecceEEEEecC-cEEEEEHHHCC--ccceeccccccceeecc---ccEECCCCEEEEEEEEEEc
Confidence            578999999999999999999999986 99999999773  2100   0000  0000   1569999999999999975


Q ss_pred             CC----ceEEEEccCCCccCC
Q 020356          161 DG----SLQLQARNQKYGKLE  177 (327)
Q Consensus       161 ~g----~i~Lstr~~~lGkL~  177 (327)
                      +.    .+. |++++++|++.
T Consensus       153 ~~~~i~~Ig-Smk~~~LG~~~  172 (215)
T 2b8k_G          153 QVSSIHAIG-SIKEDYLGAIS  172 (215)
T ss_dssp             ETTEEEEEE-ECCSTTCEEC-
T ss_pred             CCCccEEEE-EcCCCCCCCcc
Confidence            42    455 88999999886

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

Probab=97.99  E-value=1.7e-05  Score=74.91  Aligned_cols=70  Identities=11%  Similarity=-0.041  Sum_probs=63.8

Q ss_pred             CCCCEEEEEEEEEecceEEE-EEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKL-EINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQL  166 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~V-DI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~L  166 (327)
                      ++||+|-|+|.++++.+++| +|+....|++|.|++.                  +.+++||-|.|+|.++++ ++.+.|
T Consensus       151 ~~G~~V~g~V~~i~~~G~fV~~i~~g~~Glih~SEl~------------------~~l~~Gd~v~~~V~~id~~d~kI~L  212 (285)
T 3go5_A          151 MQNQNWPAIVYRLKLSGTFVYLPENNMLGFIHPSERY------------------AEPRLGQVLDARVIGFREVDRTLNL  212 (285)
T ss_dssp             CTTCEEEEEEEEEETTEEEEEETTTTEEEEECGGGCS------------------SCCCTTCEEEEEEEEEETTTTEEEE
T ss_pred             CCCCEEEEEEEEEeCCcEEEEEeCCCeEEEEEHHHcc------------------ccCCCCCEEEEEEEEEECCCCeEEE
Confidence            57999999999999999999 9998999999999874                  238999999999999998 899999


Q ss_pred             EEccCCCccC
Q 020356          167 QARNQKYGKL  176 (327)
Q Consensus       167 str~~~lGkL  176 (327)
                      |++...|..+
T Consensus       213 Slk~~~~~~~  222 (285)
T 3go5_A          213 SLKPRSFEML  222 (285)
T ss_dssp             ECSCCCCCCC
T ss_pred             EeChhhhhcc
Confidence            9999888655

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

Probab=97.84  E-value=2.2e-06  Score=90.18  Aligned_cols=76  Identities=20%  Similarity=0.276  Sum_probs=0.0

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceE
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQ  165 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~  165 (327)
                      ..|++|+++.|+|+++.+.+++|+|....+|++|+|++.      ..+..    ++.+.|++||.|.++|.+++..+.+.
T Consensus       633 ~~~~vG~v~~G~V~~I~~fGaFVel~~g~eGLvHiSels------~~rv~----~~~d~~kvGD~V~VkVi~iD~~grI~  702 (726)
T 4aid_A          633 DEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQIS------NERVA----KPSDVLKEGQMVKVKLLGFDDRGKTK  702 (726)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhcCCcEEEEEEEEEeccEEEEEECCCcEEEEEHHHcC------ccccc----CccccCCCCCEEEEEEEEECCCCcEE
Confidence            368999999999999999999999998899999999985      12211    56788999999999999999888999


Q ss_pred             EEEccC
Q 020356          166 LQARNQ  171 (327)
Q Consensus       166 Lstr~~  171 (327)
                      ||+|..
T Consensus       703 LS~K~~  708 (726)
T 4aid_A          703 LSMKVV  708 (726)
T ss_dssp             ------
T ss_pred             EEEeec
Confidence            998863

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

Probab=97.77  E-value=7.8e-05  Score=66.91  Aligned_cols=90  Identities=16%  Similarity=0.189  Sum_probs=65.1

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCccc---ccccccc-------hhhhhcccCCCCEEEEEE
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQ---RRRTAVD-------ELNMRSIFTENDLVCAEV  155 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~---rrr~~~d-------e~~mr~~~~~GDlV~AeV  155 (327)
                      +.|.+|+++.|+|++++..+.+|+++ +.++++|++++. |....   .+..-..       ..+-+..|+.||.|+.+|
T Consensus        77 f~p~~GEv~~G~Vs~vt~~GifV~lg-~~eglv~~~~l~-~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~VrvrV  154 (203)
T 3ayh_B           77 FRPFRGEVMLGKIKSCSEEGIRVTIS-FFDDIFIPKDML-FDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQI  154 (203)
T ss_dssp             ECCCTTCEEEEEEEEEETTEEEEECS-SCCCEEEEGGGB-CTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEEEE
T ss_pred             EccCCCCEEEEEEEEEeccEEEEEEe-CceEEEEcHHhC-CCCceECccCceEEeecccccccccCCcEEcCCCEEEEEE
Confidence            57999999999999999999999996 778889888763 32110   0000000       012356799999999999


Q ss_pred             EecCCC------------------------CceEEEEccCCCccCC
Q 020356          156 RSSQGD------------------------GSLQLQARNQKYGKLE  177 (327)
Q Consensus       156 ~sv~~~------------------------g~i~Lstr~~~lGkL~  177 (327)
                      .+++-.                        ..+.+|+++++||.+.
T Consensus       155 ~~v~~~~~~p~~~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~~~  200 (203)
T 3ayh_B          155 ESEDFVDISPKRNKNATAITGTEALESVSPYTLIASCSRDGLGIPA  200 (203)
T ss_dssp             EEEEECC--------------------CCSEEEEEEBCSTTCBCGG
T ss_pred             EEEEccccCCCCccccccccccccccCCCCeEEEEEecCCCCceee
Confidence            997631                        1277789999999874

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

Probab=97.54  E-value=0.00011  Score=81.28  Aligned_cols=77  Identities=10%  Similarity=-0.026  Sum_probs=63.8

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCce
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSL  164 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i  164 (327)
                      -..++|++|-|+|++|+..+++|+|....+|++|+|+++  .    .+ ..  .+..+.|++||.|.|+|.+++. .+.+
T Consensus       898 ~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSels--d----~~-~v--~~p~~v~kvGd~V~vkVl~VD~~~~rI  968 (1219)
T 3psi_A          898 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHA--G----AQ-LR--RPANEIYEIGKTYPAKVIYIDYANITA  968 (1219)
T ss_dssp             TTSCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSS--S----TT-SC--SCSTTTSCTTCEEEEEEEEEEGGGTEE
T ss_pred             hhCCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcC--C----Cc-cc--CCHHHcCCCCCEEEEEEEEEECCCCEE
Confidence            466899999999999999999999998899999999885  1    11 01  1345779999999999999984 5789


Q ss_pred             EEEEccC
Q 020356          165 QLQARNQ  171 (327)
Q Consensus       165 ~Lstr~~  171 (327)
                      .||++..
T Consensus       969 ~LSlk~~  975 (1219)
T 3psi_A          969 EVSLLDH  975 (1219)
T ss_dssp             EEECCHH
T ss_pred             EEEecHH
Confidence            9999763

>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=97.45  E-value=6.4e-05  Score=79.84  Aligned_cols=76  Identities=18%  Similarity=0.250  Sum_probs=64.1

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceE
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQ  165 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~  165 (327)
                      ..++|++|-|+|++|+..+.+|+|+...+|++|+|++.  .    .+  ..  +..+.|++||.|.++|.+++. .+.+.
T Consensus       651 ~l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Ls--d----~~--v~--d~~~~~~vGd~V~VkVi~VD~~~~rI~  720 (785)
T 3bzc_A          651 DLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALS--E----KF--VK--DPYEVVKAGDIVKVKVMEVDIPRNRVG  720 (785)
T ss_dssp             TCCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSC--S----SC--CS--CHHHHCCTTCCCCCBEEEEETTTTEEE
T ss_pred             hcCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcC--c----cc--cC--ChhheeCCCCEEEEEEEEEECCCCEEE
Confidence            46899999999999999999999998889999999885  1    11  11  456789999999999999986 57899


Q ss_pred             EEEccCC
Q 020356          166 LQARNQK  172 (327)
Q Consensus       166 Lstr~~~  172 (327)
                      ||++...
T Consensus       721 LSlk~~~  727 (785)
T 3bzc_A          721 LSMRMSD  727 (785)
T ss_dssp             ECCSSCC
T ss_pred             EEEecCC
Confidence            9998654

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

Probab=97.40  E-value=2.3e-05  Score=82.63  Aligned_cols=76  Identities=16%  Similarity=0.244  Sum_probs=0.0

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceE
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQ  165 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~  165 (327)
                      ..|++|+++.|+|+++.+.++||+|....+|++|+|++.      ..+.    .+..+.|++||.|.++|.+++..+.+.
T Consensus       623 ~~~~vG~i~~G~V~~i~~fGaFVel~~g~eGLvHiSel~------~~~v----~~~~~~~~vGd~V~VkVi~vd~~grI~  692 (723)
T 3cdi_A          623 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIA------DKRV----EKVTDYLQMGQEVPVKVLEVDRQGRIR  692 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHHcC------Cccc----cCcccccCCCCEEEEEEEEECCCCcEE
Confidence            468999999999999999999999988899999999985      1111    155678999999999999998888999


Q ss_pred             EEEccC
Q 020356          166 LQARNQ  171 (327)
Q Consensus       166 Lstr~~  171 (327)
                      ||++..
T Consensus       693 LS~k~~  698 (723)
T 3cdi_A          693 LSIKEA  698 (723)
T ss_dssp             ------
T ss_pred             EEEEec
Confidence            998853

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

Probab=97.30  E-value=3.5e-05  Score=83.95  Aligned_cols=78  Identities=10%  Similarity=-0.023  Sum_probs=0.0

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceE
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQ  165 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~  165 (327)
                      ..++|++|-|+|++|+..+++|+|+...+|++|+|+++      ..+ ..  .+..+.|++||.|.|+|.+++. .+.+.
T Consensus       902 ~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSels------d~~-~v--~~~~~v~kvGd~V~vkVl~VD~~~~rI~  972 (1030)
T 3psf_A          902 TFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHA------GAQ-LR--RPANEIYEIGKTYPAKVIYIDYANITAE  972 (1030)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HhcCCCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHcC------CCc-cc--CCHHHcCCCCCEEEEEEEEEECCCCEEE
Confidence            45789999999999999999999998889999999885      111 01  1456789999999999999984 67899


Q ss_pred             EEEccCCC
Q 020356          166 LQARNQKY  173 (327)
Q Consensus       166 Lstr~~~l  173 (327)
                      ||+|...+
T Consensus       973 LSlk~~dl  980 (1030)
T 3psf_A          973 VSLLDHDV  980 (1030)
T ss_dssp             --------
T ss_pred             EEechHHh
Confidence            99987644

>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=97.25  E-value=2.7e-05  Score=82.44  Aligned_cols=76  Identities=21%  Similarity=0.325  Sum_probs=37.8

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccc----cCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSM----NLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD  161 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v----~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~  161 (327)
                      ..|++|+++.|+|+++.+.+++|+|....+|++|+|++    .      ..+  .  .+..+.|++||.|.++|.+++..
T Consensus       663 ~~~~vG~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSel~~~~s------~~r--v--~~~~~~~~vGd~V~VkVi~vd~~  732 (757)
T 1e3p_A          663 TSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAG------GKR--V--ENVEDVLGVGQKVQVEIAEIDSR  732 (757)
T ss_dssp             ----------CBEEECC-CSCEECCC---CCCCC-----------------------------CCSSCBCCCCCCCCCSS
T ss_pred             hhcccccEEEEEEEEccccEEEEEEcCCcEEEEEhHHhccccC------CCc--c--cCcccccCCCCEEEEEEEEECCC
Confidence            57899999999999999999999998789999999987    4      111  1  15567899999999999999888


Q ss_pred             CceEEEEccC
Q 020356          162 GSLQLQARNQ  171 (327)
Q Consensus       162 g~i~Lstr~~  171 (327)
                      +.+.||++..
T Consensus       733 grI~LS~k~~  742 (757)
T 1e3p_A          733 GKLSLIPVIE  742 (757)
T ss_dssp             CC--------
T ss_pred             CCEEEEEecC
Confidence            8999998764

>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=97.09  E-value=0.00087  Score=64.91  Aligned_cols=69  Identities=17%  Similarity=0.208  Sum_probs=56.9

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC---
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD---  161 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~---  161 (327)
                      .|..+.||+|-|+|..+..+.++||++ ...|+||.++.. |+               +.|++||-|.|.|.+++..   
T Consensus       129 e~~~~~GeIV~G~V~ri~~~~v~VDlG-k~EgiLp~sE~i-p~---------------E~~~vGD~Vkv~V~~V~~~~kg  191 (344)
T 1hh2_P          129 KYSELKGTVTTAEVIRVMGEWADIRIG-KLETRLPKKEWI-PG---------------EEIKAGDLVKVYIIDVVKTTKG  191 (344)
T ss_dssp             CTTCCTTCEEEEEEEEECSSEEEEEET-TEEEEEEGGGSC-TT---------------CCCCTTCEEEEEEEEEEEETTE
T ss_pred             HHhhcCCCEEEEEEEEEecCcEEEEeC-CeEEEEeHHHcC-CC---------------cCCCCCCEEEEEEEEEEcCCCC
Confidence            477889999999999999999999998 789999998763 32               3489999999999999743   


Q ss_pred             CceEEEEcc
Q 020356          162 GSLQLQARN  170 (327)
Q Consensus       162 g~i~Lstr~  170 (327)
                      +.+.||-..
T Consensus       192 ~~I~LSRt~  200 (344)
T 1hh2_P          192 PKILVSRRV  200 (344)
T ss_dssp             EEEEEESSS
T ss_pred             cEEEEEeec
Confidence            256666543

>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=97.00  E-value=0.00078  Score=62.57  Aligned_cols=71  Identities=11%  Similarity=0.180  Sum_probs=55.9

Q ss_pred             ccCCCCCCEEEEEEEE----EecceEEEEEcC---ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEe
Q 020356           85 RYKPETGDIVIGRVIE----VVPKRWKLEINF---TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRS  157 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~----V~~~~w~VDI~s---~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~s  157 (327)
                      .|..++||+|.|+|..    +..+.+.|||+.   ...|+||.++.. |               .+.|++||-|.|-|..
T Consensus         2 ~~~~r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eqi-p---------------~E~~~~GDrIkayV~~   65 (251)
T 2asb_A            2 EFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV-P---------------GESYEHGNRLRCYVVG   65 (251)
T ss_dssp             --CCCTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGSC-T---------------TCCCCTTCEEEEEEEE
T ss_pred             chhhcCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHcC-C---------------CccCCCCCEEEEEEEE
Confidence            4889999999999999    899999999986   478998877652 3               3459999999999999


Q ss_pred             cCCC---CceEEEEccC
Q 020356          158 SQGD---GSLQLQARNQ  171 (327)
Q Consensus       158 v~~~---g~i~Lstr~~  171 (327)
                      +...   +.+.||-..+
T Consensus        66 V~~~~~gpqIiLSRt~p   82 (251)
T 2asb_A           66 VTRGAREPLITLSRTHP   82 (251)
T ss_dssp             EECCSSSCEEEEESSCH
T ss_pred             EEcCCCCCEEEEEeccH
Confidence            9754   3566765443

>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=96.67  E-value=0.011  Score=59.92  Aligned_cols=83  Identities=12%  Similarity=0.206  Sum_probs=59.9

Q ss_pred             cCCCCCCEEEEEEEEEecc--eEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-C
Q 020356           86 YKPETGDIVIGRVIEVVPK--RWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-G  162 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~--~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g  162 (327)
                      -.+.+|+|..|+|+.+.+.  .+||||+...+|+||++++. +.-...........++.+.+++||-|..+|...... .
T Consensus        41 ~~~~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei~-~~~~~~~~~~~~~~~i~d~lk~Gq~VlVQV~Ke~~g~K  119 (517)
T 2bx2_L           41 HEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIA-REYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNK  119 (517)
T ss_dssp             SCCCTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSC-GGGCC-------CCCGGGTCCTTCEEEEEEEECCCTTC
T ss_pred             CcCCCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHcC-hhhhccccccccccchhhhccCCCEEEEEEEeeccccC
Confidence            3567999999999999999  99999999999999999984 110000000000124667899999999999997543 3


Q ss_pred             ceEEEEc
Q 020356          163 SLQLQAR  169 (327)
Q Consensus       163 ~i~Lstr  169 (327)
                      -+.||+.
T Consensus       120 Ga~lTt~  126 (517)
T 2bx2_L          120 GAALTTF  126 (517)
T ss_dssp             CCEEESS
T ss_pred             CceEEee
Confidence            4777774

>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=96.63  E-value=0.002  Score=62.78  Aligned_cols=69  Identities=12%  Similarity=0.196  Sum_probs=54.7

Q ss_pred             ccCCCCCCEEEEEEEE----EecceEEEEEcC---ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEe
Q 020356           85 RYKPETGDIVIGRVIE----VVPKRWKLEINF---TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRS  157 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~----V~~~~w~VDI~s---~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~s  157 (327)
                      .|..++||+|-|+|..    +..+.++|||+.   ...|+||.++.. |+               +.|++||-|.|.|..
T Consensus       125 ef~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~Eqi-P~---------------E~~~~GDrVkvyV~~  188 (366)
T 1k0r_A          125 EFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV-PG---------------ESYEHGNRLRCYVVG  188 (366)
T ss_dssp             --CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSC-TT---------------CCCCTTCEEEEEEEE
T ss_pred             HHHhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcC-CC---------------ccCCCCCEEEEEEEE
Confidence            4889999999999999    999999999986   478999887753 32               459999999999999


Q ss_pred             cCCCC---ceEEEEc
Q 020356          158 SQGDG---SLQLQAR  169 (327)
Q Consensus       158 v~~~g---~i~Lstr  169 (327)
                      +..+.   .+.||-.
T Consensus       189 V~~~~kgpqI~LSRT  203 (366)
T 1k0r_A          189 VTRGAREPLITLSRT  203 (366)
T ss_dssp             EECCSSSCEEEEESS
T ss_pred             EecCCCccEEEEEeC
Confidence            97642   3555543

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

Probab=96.42  E-value=0.0072  Score=54.80  Aligned_cols=75  Identities=17%  Similarity=0.198  Sum_probs=53.8

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCccc---ccccccc--hhhhhcccCCCCEEEEEEEecC
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQ---RRRTAVD--ELNMRSIFTENDLVCAEVRSSQ  159 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~---rrr~~~d--e~~mr~~~~~GDlV~AeV~sv~  159 (327)
                      -+.|.+|+++.|+|++++..+++|.+..+.++++|++++. |....   .+..-..  ...-...|+.||.|+.+|.+++
T Consensus        76 ~f~p~vGEv~~G~Is~Vt~fGifVeL~g~~eglv~~s~l~-~d~~~fd~~~~~~vg~~~e~t~~~~~~Gd~VrvrV~~v~  154 (218)
T 2ckz_B           76 VFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNML-FEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREV  154 (218)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECTTSCCCEEEETTTS-CTTCEEETTTTEEEEECC--CEEEECTTCEEEEEEEEEE
T ss_pred             EecCCCCCEEEEEEEEEccCcEEEEccCccceEEEcHHHC-CCCcEEcCcCceEEeeccccCCcEEcCCCEEEEEEEEEE
Confidence            3589999999999999999999999955788899988763 22111   0000000  0122567999999999999986


Q ss_pred             C
Q 020356          160 G  160 (327)
Q Consensus       160 ~  160 (327)
                      .
T Consensus       155 ~  155 (218)
T 2ckz_B          155 F  155 (218)
T ss_dssp             E
T ss_pred             c
Confidence            4

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

Probab=96.34  E-value=0.015  Score=54.76  Aligned_cols=67  Identities=10%  Similarity=0.044  Sum_probs=54.7

Q ss_pred             CCCCEEEEEEEEEe-cceEEEEEcCc-cceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEE
Q 020356           89 ETGDIVIGRVIEVV-PKRWKLEINFT-QDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQL  166 (327)
Q Consensus        89 ~vGDiVIGrV~~V~-~~~w~VDI~s~-~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~L  166 (327)
                      ++|+++.|+|++++ ..+++||++.+ .++++|+|+++.      .+        ...+++||-+.+. ..++..+.+.|
T Consensus        68 ~~G~~~~g~V~~v~~~~GaFVdiG~~~~d~lvp~sel~~------~~--------~~~~~~Gd~v~v~-l~iD~~~Ri~l  132 (285)
T 3go5_A           68 TQDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDILPE------LK--------ELWPKKGDQLYIR-LEVDKKDRIWG  132 (285)
T ss_dssp             CSSSCEEEEEEEEETTTEEEEECSCTTCCEEEEGGGSCS------SG--------GGSCCTTCEEEEE-EEECTTSCEEE
T ss_pred             cCCCEEEEEEEEEccCceEEEEECCCCcEEEEEHHHCCc------cc--------ccccCCCCEEEEE-EEECCCCcEEE
Confidence            68999999999999 79999999974 899999998752      11        1237999999765 57887788999


Q ss_pred             EEcc
Q 020356          167 QARN  170 (327)
Q Consensus       167 str~  170 (327)
                      |+|.
T Consensus       133 s~k~  136 (285)
T 3go5_A          133 LLAY  136 (285)
T ss_dssp             EECC
T ss_pred             Eehh
Confidence            9864

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

Probab=92.84  E-value=0.065  Score=42.60  Aligned_cols=38  Identities=21%  Similarity=0.357  Sum_probs=35.9

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCccceeeeccccc
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMN  124 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~  124 (327)
                      .|++|+.|-|.|+.+.+.+.+|+|....++++|+|+++
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            79999999999999999999999987899999999885

>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=92.65  E-value=0.87  Score=35.99  Aligned_cols=64  Identities=9%  Similarity=0.054  Sum_probs=47.4

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhh-hhcccCCCCEEEEE
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELN-MRSIFTENDLVCAE  154 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~-mr~~~~~GDlV~Ae  154 (327)
                      ..|..|+...+.|+++.++.+.|-+.....+.|+...+.+-.   +...  ..-. ..+.|++||+|+.+
T Consensus        29 ~~~~~~~~~~AvV~~v~~~~~~v~~~~g~~~~l~~~~~~WA~---~~~~--~~~~~~~~~l~~GdvI~V~   93 (106)
T 3d0f_A           29 DIGNSDDILAAVVLSATPGAVEAFRKNGETIRITGDGLKAAH---RFLS--NDPKIGEKRIRPGALIRVK   93 (106)
T ss_dssp             TSCTTTTCEEEEEEEEETTEEEEEETTSCEEEECGGGGSTTG---GGTT--TCTTTGGGSCCTTEEEEEE
T ss_pred             ccCccCCeEEEEEEEeCCCeEEEEEcCCCeEEEcHHHChhhh---hccc--ccccchhccCCCCCEEEEE
Confidence            367789999999999999999999977677777777765431   1000  1113 46779999999988

>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=91.87  E-value=0.37  Score=49.91  Aligned_cols=78  Identities=6%  Similarity=0.139  Sum_probs=57.0

Q ss_pred             CCCCCC--EEEEEEEEEecceEEEEEc-CccceeeecccccCCCcccccccccch----h--hhhcccCCCCEEEEEEEe
Q 020356           87 KPETGD--IVIGRVIEVVPKRWKLEIN-FTQDAILMLSSMNLPDGIQRRRTAVDE----L--NMRSIFTENDLVCAEVRS  157 (327)
Q Consensus        87 ~P~vGD--iVIGrV~~V~~~~w~VDI~-s~~~a~L~ls~v~fpg~i~rrr~~~de----~--~mr~~~~~GDlV~AeV~s  157 (327)
                      .+++|+  ..-|+|++|+..+++|.|. ....|.+|+|++.-.+.  .  ...|+    +  .....|++||.|..+|.+
T Consensus       555 ~~~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~~~~d--~--~~~d~~~~~l~~~~~~~~~lGD~V~VkV~~  630 (644)
T 2id0_A          555 KDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRD--E--LVCSQENGTVQIKGETVYKVTDVIDVTIAE  630 (644)
T ss_dssp             GGGTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGG--G--EEEETTTTEEEETTEEEEETTCEEEEEEEE
T ss_pred             hhccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhccCcCc--e--eEEcccccEEEecCCCEeCCCCEEEEEEEE
Confidence            678999  9999999999999999994 45789999998741000  0  00111    1  224569999999999999


Q ss_pred             cCC-CCceEEEE
Q 020356          158 SQG-DGSLQLQA  168 (327)
Q Consensus       158 v~~-~g~i~Lst  168 (327)
                      ++. .+.+.|+.
T Consensus       631 vd~~~~~I~~~l  642 (644)
T 2id0_A          631 VRMETRSIIARP  642 (644)
T ss_dssp             EETTTTEEEEEE
T ss_pred             EeCCCCEEEEEE
Confidence            986 46677664

>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16

Probab=87.30  E-value=0.83  Score=48.26  Aligned_cols=77  Identities=19%  Similarity=0.150  Sum_probs=49.4

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEcC-ccceeeecccccCCCcccccccccch----h---h----hhcccCCCCEEEEEE
Q 020356           88 PETGDIVIGRVIEVVPKRWKLEINF-TQDAILMLSSMNLPDGIQRRRTAVDE----L---N----MRSIFTENDLVCAEV  155 (327)
Q Consensus        88 P~vGDiVIGrV~~V~~~~w~VDI~s-~~~a~L~ls~v~fpg~i~rrr~~~de----~---~----mr~~~~~GDlV~AeV  155 (327)
                      .++ ...-|+|+++...+++|.|.. ...|.+|++++.-|+.  .  ...|+    +   .    ....|+.||.|.++|
T Consensus       668 ~~~-~~~~g~V~~V~~~G~fV~l~~~giEGlVhis~L~~~~d--~--~~fd~~~~~l~g~~~~~~~~~~~~lGD~V~VkV  742 (760)
T 2vnu_D          668 NNE-STETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPN--S--AAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQV  742 (760)
T ss_dssp             TCC-SEEEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSCGG--G--CEEETTTTEEEECCTTCSSCEEEETTCEEEEEE
T ss_pred             cCc-eEEEEEEEEEECCeEEEEEeCCCcEEEEEeccccCCCc--e--eEEcccccEEEEecCCCccCcEEecCCEEEEEE
Confidence            444 799999999999999999976 5789999998731110  0  00010    0   1    136799999999999


Q ss_pred             EecCCC----CceEEEEc
Q 020356          156 RSSQGD----GSLQLQAR  169 (327)
Q Consensus       156 ~sv~~~----g~i~Lstr  169 (327)
                      .+++..    +.+.|++|
T Consensus       743 ~~vd~~~~~~~kI~lslk  760 (760)
T 2vnu_D          743 RSVMDPITSKRKAELLLK  760 (760)
T ss_dssp             C--------CCEEEC---
T ss_pred             EEEECccccCCcEEEEeC
Confidence            999865    56766653

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=84.50  E-value=1.4  Score=47.89  Aligned_cols=81  Identities=14%  Similarity=0.028  Sum_probs=55.6

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEcC-ccceeeecccccCCCcc----cccccccchhh---hhcccCCCCEEEEEEEecC
Q 020356           88 PETGDIVIGRVIEVVPKRWKLEINF-TQDAILMLSSMNLPDGI----QRRRTAVDELN---MRSIFTENDLVCAEVRSSQ  159 (327)
Q Consensus        88 P~vGDiVIGrV~~V~~~~w~VDI~s-~~~a~L~ls~v~fpg~i----~rrr~~~de~~---mr~~~~~GDlV~AeV~sv~  159 (327)
                      ++ |...-|.|+++...+++|.|.. ...|.+|++++.-|+.-    .+...-..+-.   ....|+.||.|..+|.+++
T Consensus       885 ~~-ge~~~g~V~~V~~~G~fV~L~~~giEGlVhis~L~~~~d~y~fde~~~~L~g~~~~g~~~~~~~lGD~V~VkV~~vd  963 (977)
T 2wp8_J          885 NN-ESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVM  963 (977)
T ss_dssp             HT-TCEEEEEEEEECSSEEEEECTTTCCEEEEEGGGTCSCGGGCEEETTTTEEEECCTTCCSCEEEETTCEEEEEECCCC
T ss_pred             cc-ceEEEEEEEEEcCCeEEEEEcCCCeEEEEEeccccCCCceeEEcccccEEEeecCCCccCcEEccCCEEEEEEEEEc
Confidence            44 8999999999999999999976 57899999987411100    00000000000   2356999999999999987


Q ss_pred             CC----CceEEEEc
Q 020356          160 GD----GSLQLQAR  169 (327)
Q Consensus       160 ~~----g~i~Lstr  169 (327)
                      ..    +.+.|+++
T Consensus       964 ~~~~~~~kI~Lslk  977 (977)
T 2wp8_J          964 DPITSKRKAELLLK  977 (977)
T ss_dssp             CSSSCCCCCCEEEC
T ss_pred             CcccCCCceEEEeC
Confidence            52    56777764

---

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	327
d2nn6h3	126	d.51.1.1 (H:168-293) Ribosomal RNA-processing prot	2e-34
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	1e-26
d2nn6i1	125	b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {H	8e-18
d2ja9a1	90	b.40.4.5 (A:62-151) S1-domain of exosome component	8e-18
d2nn6g1	88	b.40.4.5 (G:107-194) S1-domain of exosome componen	2e-15
d2nn6h2	48	b.84.4.2 (H:25-72) Ribosomal RNA-processing protei	1e-13
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	2e-11
d2ba0a2	51	b.84.4.2 (A:2-52) Exosome complex RNA-binding prot	2e-10
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	2e-10
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	5e-08
d2je6i2	59	b.84.4.2 (I:7-65) Exosome complex RNA-binding prot	6e-08

>d2nn6h3 d.51.1.1 (H:168-293) Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 126

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]

 Score =  119 bits (301), Expect = 2e-34
 Identities = 39/143 (27%), Positives = 56/143 (39%), Gaps = 22/143 (15%)

Query: 178 RGQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQL 237
           +G L+ V P LVKR+K HFH L   G  +I+G NG+IWI    E +++      +N E +
Sbjct: 1   QGVLVQVSPSLVKRQKTHFHDLP-CGASVILGNNGFIWIYPTPEHKEEEAGGFIANLEPV 59

Query: 238 IAKCDKNSMDLDEQDGTCTPREARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLN 297
                                  R+ I R+ N I  L      +    IL       SL 
Sbjct: 60  -------------------SLADREVISRLRNCIISLVTQRMMLYDTSILYCYEA--SLP 98

Query: 298 LDIHDMLGSEFYVLVAESEAERR 320
             I D+L  E    +     +R 
Sbjct: 99  HQIKDILKPEIMEEIVMETRQRL 121

>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 = 98.9 bits (246), Expect = 1e-26
 Identities = 51/94 (54%), Positives = 65/94 (69%)

Query: 83  RARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMR 142
           + RY  E GDIV+GR+ EV  KRWK+E N   D++L+LSSMNLP G  RRR+A DEL MR
Sbjct: 1   KTRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMR 60

Query: 143 SIFTENDLVCAEVRSSQGDGSLQLQARNQKYGKL 176
               E DL+ AEV++   DG++ L  R+ KYGKL
Sbjct: 61  GFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKL 94

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

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

 Score = 76.1 bits (187), Expect = 8e-18
 Identities = 20/92 (21%), Positives = 35/92 (38%), Gaps = 1/92 (1%)

Query: 84  ARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRS 143
           ++  P+ G IV  +V  +  +  K+ I +     L  S          R T  D++ +  
Sbjct: 1   SQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYK 60

Query: 144 IFTENDLVCAEVRS-SQGDGSLQLQARNQKYG 174
            F   D+V A+V S      +  L     + G
Sbjct: 61  SFRPGDIVLAKVISLGDAQSNYLLTTAENELG 92

>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 = 74.8 bits (184), Expect = 8e-18
 Identities = 21/98 (21%), Positives = 40/98 (40%), Gaps = 11/98 (11%)

Query: 85  RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSI 144
           RY P   D VIG +I      +K+ +     ++ + S M  P+  ++          R  
Sbjct: 2   RYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSL-SYMAFPNASKK---------NRPT 51

Query: 145 FTENDLVCAEVRSSQGDGSLQLQARNQKYGKLER-GQL 181
               DLV A V +++ +   +++  +   G+    G L
Sbjct: 52  LQVGDLVYARVCTAEKELEAEIECFDSTTGRDAGFGIL 89

>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 = 68.3 bits (167), Expect = 2e-15
 Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 16/97 (16%)

Query: 85  RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSI 144
           RY P  GD VIG V       +K+++  ++ A   LS ++     +           R  
Sbjct: 1   RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPAS--LSYLSFEGATK---------RNRPN 49

Query: 145 FTENDLVCAEVRSSQGDGSLQL-----QARNQKYGKL 176
               DL+  +   +  D   ++       R    G +
Sbjct: 50  VQVGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVI 86

>d2nn6h2 b.84.4.2 (H:25-72) Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 48

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]

 Score = 62.0 bits (151), Expect = 1e-13
 Identities = 24/47 (51%), Positives = 32/47 (68%), Gaps = 1/47 (2%)

Query: 36 VTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRAL 82
          V  GDTI   + G ++GHGT   + +L A+V G VER+NKLI V+AL
Sbjct: 3  VVPGDTI-TTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKAL 48

>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 = 57.2 bits (138), Expect = 2e-11
 Identities = 22/91 (24%), Positives = 39/91 (42%), Gaps = 6/91 (6%)

Query: 86  YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIF 145
           Y P+ GD+VIG +  V    W ++IN    A+L +           R       +M+S+ 
Sbjct: 3   YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFL------GRPFNPAVDDMQSLL 56

Query: 146 TENDLVCAEVRSSQGDGSLQLQARNQKYGKL 176
              D + A+V +     S  L  + +  G++
Sbjct: 57  KVGDYIKAKVVAFDKTRSPLLTVQGEGLGRI 87

>d2ba0a2 b.84.4.2 (A:2-52) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 51

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]

 Score = 53.4 bits (129), Expect = 2e-10
 Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 36 VTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRAR 85
          V  GD +    +    G+GT  + G++ A + G+ ++    + V  L+ R
Sbjct: 4  VLPGDLL--STNPRAAGYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGR 51

>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 = 54.2 bits (130), Expect = 2e-10
 Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 7/92 (7%)

Query: 85  RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSI 144
            Y P+  DIVIG V +V    W ++I     A L  S++         R+     ++R  
Sbjct: 2   FYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNL-------LGRSINVGEDLRRY 54

Query: 145 FTENDLVCAEVRSSQGDGSLQLQARNQKYGKL 176
               D V A + +        L  + +  G++
Sbjct: 55  LDVGDYVIARIENFDRSIDPVLSVKGKDLGRV 86

>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 = 47.3 bits (112), Expect = 5e-08
 Identities = 18/91 (19%), Positives = 32/91 (35%), Gaps = 9/91 (9%)

Query: 86  YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIF 145
           Y P  GD+VIG + EV    W ++I     A L +S                      + 
Sbjct: 1   YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSEN---------PEMKPNKKPNEVL 51

Query: 146 TENDLVCAEVRSSQGDGSLQLQARNQKYGKL 176
              D + A+V +      + L  +++    +
Sbjct: 52  DIGDAIIAKVLNIDPKMKVTLTMKDRICRPI 82

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

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

 Score = 46.6 bits (111), Expect = 6e-08
 Identities = 11/53 (20%), Positives = 18/53 (33%)

Query: 31 NPNSCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALR 83
           P S V  G+ +   E  I           +  +TV G+ +  +    V  L 
Sbjct: 6  QPRSIVVPGELLAEGEFQIPWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLE 58

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	327
d2nn6h3	126	Ribosomal RNA-processing protein 4, RRP4 {Human (H	100.0
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.9
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	99.87
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	99.87
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	99.81
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.76
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.73
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.7
d2nn6h2	48	Ribosomal RNA-processing protein 4, RRP4 {Human (H	99.6
d2ba0a2	51	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.5
d2je6i2	59	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.33
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	98.99
d2nn6i2	55	Exosome component 1, EXOSC1 {Human (Homo sapiens)	98.97
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	98.94
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	98.93
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	98.77
d2nn6g3	80	Ribosomal RNA-processing protein 40, RRP40 {Human	98.7
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	98.62
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	98.62
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	98.37
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.24
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.04
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	97.7
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	97.63
d2nn6g2	91	Ribosomal RNA-processing protein 40, RRP40 {Human	96.73
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	96.43
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	96.32
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	96.18
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	95.32
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	95.04
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	92.68
d1v8qa_	66	Ribosomal protein L27 {Thermus thermophilus [TaxId	90.95
d2zjrt1	84	Ribosomal protein L27 {Deinococcus radiodurans [Ta	85.98

>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=100.00  E-value=5.4e-34  Score=238.70  Aligned_cols=122  Identities=30%  Similarity=0.403  Sum_probs=104.0

Q ss_pred             CCeEEEeChhhhhhccccccccCccceEEEEeecceeeeccccccccccccccCCCchhhhhhccCCCCccccCCCCCCC
Q 020356          178 RGQLLTVDPYLVKRRKQHFHHLEEYGIDLIIGCNGYIWIGEHVEARDKMVVDQGSNSEQLIAKCDKNSMDLDEQDGTCTP  257 (327)
Q Consensus       178 ~G~lv~V~~~li~r~~~h~~~L~~~~~eiivG~NG~IWI~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  257 (327)
                      .|+|++|+|+|++|+|+|||.|+ ||+++|+|+||||||+++.+..+.        .++  .++         ++++++|
T Consensus         1 ~G~lv~V~p~LVkR~K~Hf~~L~-~gv~vILG~NGyIWIs~~~~~~~~--------~~~--~~~---------~~~~~v~   60 (126)
T d2nn6h3           1 QGVLVQVSPSLVKRQKTHFHDLP-CGASVILGNNGFIWIYPTPEHKEE--------EAG--GFI---------ANLEPVS   60 (126)
T ss_dssp             SSCEEECCTTSCCCSTTCSCCCB-TTBEEEEETTTEEEEECCCCC----------------CCG---------GGSSCCC
T ss_pred             CCEEEEEChHHhhhhhhceEEcC-CCceEEEecCCEEEeeCCcccccc--------ccc--ccc---------cccCCCC
Confidence            49999999999999999999997 999999999999999987653221        000  011         1124699


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHhhhhCCCCchhcccchHHHHHHHHHHHHhh
Q 020356          258 REARQNICRIANAIRVLSRLGFNITVEVILETVNLSNSLNLDIHDMLGSEFYVLVAESEAERRS  321 (327)
Q Consensus       258 ~~~r~~i~r~~n~i~~l~~~~~~i~~~~i~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~~~~  321 (327)
                      +++|++|||+||||++|++++++||+++|+++|++|+  +++++|||.||++.++++.++.|..
T Consensus        61 ~~~R~~IaRvaNcI~~La~~~~~I~~~sI~~~yeaSl--~~~v~dlL~~e~~~~i~~~~~~rl~  122 (126)
T d2nn6h3          61 LADREVISRLRNCIISLVTQRMMLYDTSILYCYEASL--PHQIKDILKPEIMEEIVMETRQRLL  122 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHTHH--HHCCSSCCTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCcccHHHHHHHHHHHh--cCCHHHHhCHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999995  5689999999999999999998864

>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=99.90  E-value=5.4e-25  Score=175.09  Aligned_cols=94  Identities=54%  Similarity=0.873  Sum_probs=79.1

Q ss_pred             CCccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC
Q 020356           83 RARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG  162 (327)
Q Consensus        83 ~~rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g  162 (327)
                      +++|.|++||+|+|+|+++.+++|+|||++..+|+||+|++++|+++.||++..+..+|+++|++||.|.|+|.+++.++
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            46999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEccCCCccC
Q 020356          163 SLQLQARNQKYGKL  176 (327)
Q Consensus       163 ~i~Lstr~~~lGkL  176 (327)
                      .+.||||+.+||||
T Consensus        81 ~i~Ls~r~~~~gkl   94 (95)
T d2nn6h1          81 AVSLHTRSLKYGKL   94 (95)
T ss_dssp             EEEEECCSSTTCEE
T ss_pred             CEEEEeccccCCcC
Confidence            99999999999997

>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=99.87  E-value=9.4e-23  Score=160.34  Aligned_cols=82  Identities=24%  Similarity=0.337  Sum_probs=75.7

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCce
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSL  164 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i  164 (327)
                      ||+|++||+|||+|++++.++|+|||+++++|+||+++  |||+++++|+         +|++||+|+|||++++.++.+
T Consensus         1 rY~P~~GD~ViG~V~~~~~~~~~VdI~s~~~a~L~~~~--f~g~~k~~r~---------~l~~GD~V~arV~~v~~~~~~   69 (88)
T d2nn6g1           1 RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLS--FEGATKRNRP---------NVQVGDLIYGQFVVANKDMEP   69 (88)
T ss_dssp             SCCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCS--SSCCSSCSSS---------SSCTTCEEEEEEEECCTTSCC
T ss_pred             CCcCCCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHH--cCccccccCc---------ccCCCCEEEEEEEEeCCCCCE
Confidence            79999999999999999999999999999999999875  7998887654         489999999999999999999


Q ss_pred             EEEE-----ccCCCccCC
Q 020356          165 QLQA-----RNQKYGKLE  177 (327)
Q Consensus       165 ~Lst-----r~~~lGkL~  177 (327)
                      .|||     |+.+||+|.
T Consensus        70 ~Lscvd~~~k~~g~G~L~   87 (88)
T d2nn6g1          70 EMVCIDSCGRANGMGVIG   87 (88)
T ss_dssp             EEECSBTTTTBCCCCSCC
T ss_pred             EEEEEcccCcccCCcccC
Confidence            9999     889999985

>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=99.87  E-value=2.3e-22  Score=158.75  Aligned_cols=83  Identities=22%  Similarity=0.409  Sum_probs=74.7

Q ss_pred             CccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCc
Q 020356           84 ARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGS  163 (327)
Q Consensus        84 ~rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~  163 (327)
                      +||+|++||+|||+|+++++++|+|||+++++|+||. +.+|||++++++         .+|++||+|+|||++++.+++
T Consensus         1 krY~P~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~-~~~f~g~~k~~r---------~~l~~GDlV~arV~~v~~~~~   70 (90)
T d2ja9a1           1 KRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLS-YMAFPNASKKNR---------PTLQVGDLVYARVCTAEKELE   70 (90)
T ss_dssp             CCCCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEE-TTSSTTCCSSSC---------CCCCTTCEEEEEEEECCTTSC
T ss_pred             CCccCCCCCEEEEEEEEEeCCcEEEEcCCcchhhhhh-hhccCccccccC---------CccCCCCEEEEEEEEECCCCC
Confidence            5899999999999999999999999999999999864 467999887655         448999999999999999999


Q ss_pred             eEEEEccCCCccC
Q 020356          164 LQLQARNQKYGKL  176 (327)
Q Consensus       164 i~Lstr~~~lGkL  176 (327)
                      ++|||++..+||-
T Consensus        71 ~~Lsc~~~~~gK~   83 (90)
T d2ja9a1          71 AEIECFDSTTGRD   83 (90)
T ss_dssp             CEEESSCTTTCSC
T ss_pred             EEEEEeccccCcc
Confidence            9999988888773

>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=99.81  E-value=2.8e-20  Score=154.76  Aligned_cols=94  Identities=21%  Similarity=0.221  Sum_probs=80.0

Q ss_pred             CccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC-
Q 020356           84 ARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG-  162 (327)
Q Consensus        84 ~rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g-  162 (327)
                      ++|+|++||+|+|+|+++++++|+|+|.+..+..++.+..+++....+|.++.|+.+|+++|++||+|+|+|+++++.. 
T Consensus         1 s~~vP~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dvr~te~d~~~m~~~fr~GDiV~A~Vis~~~~~~   80 (125)
T d2nn6i1           1 SQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGDIVLAKVISLGDAQS   80 (125)
T ss_dssp             CCCCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCSSCCCCGGGTCCSSSEEEEEEEEEETTTT
T ss_pred             CCcCCCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHcccchhhhhhHHHhcCCCCEEEEEEEEccCCCc
Confidence            3799999999999999999999999999987777655433333333466788899999999999999999999998765 


Q ss_pred             ceEEEEccCCCccCC
Q 020356          163 SLQLQARNQKYGKLE  177 (327)
Q Consensus       163 ~i~Lstr~~~lGkL~  177 (327)
                      .++|||+++.||+|.
T Consensus        81 ~~~Lst~~~~LGVv~   95 (125)
T d2nn6i1          81 NYLLTTAENELGVVV   95 (125)
T ss_dssp             EEEEECCSSSCEECC
T ss_pred             cEEEEecCCCcEEEE
Confidence            599999999999996

>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=99.76  E-value=8.5e-19  Score=136.42  Aligned_cols=86  Identities=24%  Similarity=0.326  Sum_probs=76.6

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCce
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSL  164 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i  164 (327)
                      -|.|++||+|+|+|+++++++|+|||++...|+||+++++-.      +...+.-+++++|++||.|.|+|.++++++.+
T Consensus         2 ~Y~Pk~GdvV~G~V~~v~~~g~fV~i~~~~~g~l~~se~~~~------~~~~~~~~~~~~~~vGd~V~~kV~~vd~~~~i   75 (88)
T d2z0sa1           2 IYVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGR------PFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSP   75 (88)
T ss_dssp             CCCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTS------CCCTTTTCCTTSSCTTCEEEEEEEEECTTSCE
T ss_pred             CcCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCcc------cccccccchhhhcccCcEEEEEEEEECCCCCE
Confidence            599999999999999999999999999999999999988621      11223347899999999999999999999999


Q ss_pred             EEEEccCCCccC
Q 020356          165 QLQARNQKYGKL  176 (327)
Q Consensus       165 ~Lstr~~~lGkL  176 (327)
                      .||+|+.++|||
T Consensus        76 ~Ls~k~~~~gkl   87 (88)
T d2z0sa1          76 LLTVQGEGLGRI   87 (88)
T ss_dssp             EEECCSSSCEEC
T ss_pred             EEEEecCCCccc
Confidence            999999999997

>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=99.73  E-value=2.6e-18  Score=133.51  Aligned_cols=87  Identities=23%  Similarity=0.286  Sum_probs=76.3

Q ss_pred             CccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCc
Q 020356           84 ARYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGS  163 (327)
Q Consensus        84 ~rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~  163 (327)
                      +.|.|++||+|+|+|+++++++|+|||++..+|+||++++...      + ..+..+|+++|++||.|.|+|+++++++.
T Consensus         1 s~Y~Pk~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~~------~-~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~   73 (87)
T d2je6i1           1 SFYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGR------S-INVGEDLRRYLDVGDYVIARIENFDRSID   73 (87)
T ss_dssp             SCCCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHTS------C-CCTTCCCSSSCCTTCEEEEEEEEEETTEE
T ss_pred             CcccCCCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCCc------e-eccccccchhhcccceEEEEEEEECCCCC
Confidence            3699999999999999999999999999999999999988521      1 11223688999999999999999998899


Q ss_pred             eEEEEccCCCccCC
Q 020356          164 LQLQARNQKYGKLE  177 (327)
Q Consensus       164 i~Lstr~~~lGkL~  177 (327)
                      +.||+|+.+||+|.
T Consensus        74 i~LS~k~~~lgkl~   87 (87)
T d2je6i1          74 PVLSVKGKDLGRVS   87 (87)
T ss_dssp             EEEECCSTTCEECC
T ss_pred             EEEEEecCCCccCC
Confidence            99999999999984

>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=99.70  E-value=3.8e-17  Score=125.54  Aligned_cols=83  Identities=22%  Similarity=0.352  Sum_probs=74.0

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceE
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQ  165 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~  165 (327)
                      |.|++||+|.|+|+++++++|+|||++..+|+||++++..      .+   +..+++++|++||.|.|+|.++++++.+.
T Consensus         1 Y~Pk~Gd~V~G~V~~v~~~g~~V~i~~~~~g~l~~se~s~------~~---~~~~~~~~~~vGd~V~~kV~~vd~~~~i~   71 (83)
T d2ba0a1           1 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPE------MK---PNKKPNEVLDIGDAIIAKVLNIDPKMKVT   71 (83)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTT------CC---TTSCGGGTCCTTCEEEEEEEEECTTCCEE
T ss_pred             CcCCCCCEEEEEEEEEECCEEEEecCCCeeEEEecccccc------cc---cccChhhhcccccEEEEEEEEECCCCCEE
Confidence            8999999999999999999999999999999999998751      11   11267889999999999999999889999


Q ss_pred             EEEccCCCccCC
Q 020356          166 LQARNQKYGKLE  177 (327)
Q Consensus       166 Lstr~~~lGkL~  177 (327)
                      ||+|+.++|+|+
T Consensus        72 LS~k~~~~~k~r   83 (83)
T d2ba0a1          72 LTMKDRICRPIR   83 (83)
T ss_dssp             EECCSSSCEEES
T ss_pred             EEecCCCCCCCC
Confidence            999999999874

>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=99.60  E-value=2.8e-16  Score=109.18  Aligned_cols=48  Identities=50%  Similarity=0.760  Sum_probs=44.5

Q ss_pred             ceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEECcEEEEEec
Q 020356           34 SCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRAL   82 (327)
Q Consensus        34 ~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~nk~v~V~pl   82 (327)
                      ++|+|||.|.. +++||+|||||+++++++||++|+++++||+++|+|+
T Consensus         1 ~iv~PGe~It~-~~~~mrGHGTy~~~~~i~aSv~G~vervNKLvsV~pL   48 (48)
T d2nn6h2           1 HLVVPGDTITT-DTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKAL   48 (48)
T ss_dssp             CBCCTTCBCCC-CTTCCBCTTEEECSSSEEECSSEEEEEETTEEEEEES
T ss_pred             CEecCCcEeec-CCCeEcccccEecCCEEEEEEeeeEEEeccEEEEEcC
Confidence            58999999975 4569999999999999999999999999999999996

>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=99.50  E-value=6.9e-15  Score=103.95  Aligned_cols=50  Identities=24%  Similarity=0.366  Sum_probs=46.3

Q ss_pred             ceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEEECcEEEEEecCCc
Q 020356           34 SCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVERINKLIYVRALRAR   85 (327)
Q Consensus        34 ~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~~nk~v~V~pl~~r   85 (327)
                      ++|+|||.|+. + .|++|||||.++++|+|+++|.++++|++++|+|+++|
T Consensus         2 ~iV~PGe~i~~-~-~~~~G~Gty~~~~~i~ss~~G~v~~~n~~i~V~PL~gr   51 (51)
T d2ba0a2           2 KIVLPGDLLST-N-PRAAGYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGR   51 (51)
T ss_dssp             CEECTTCEEES-C-TTSBCTTEEEETTEEEECSSEEEEECSSCEEEEECSSS
T ss_pred             CEEcCCcEeec-C-CeeCCCCcEEECCEEEEEEEEEEEEECCEEEEEeCccC
Confidence            68999999963 3 59999999999999999999999999999999999875

>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=99.33  E-value=5.3e-13  Score=96.76  Aligned_cols=53  Identities=19%  Similarity=0.151  Sum_probs=47.4

Q ss_pred             CCCceEecCCccCCCCCcee-ecCCEEeeCCeEEEEEeeEEEEECcEEEEEecCC
Q 020356           31 NPNSCVTVGDTIPVYEDGIL-KGHGTSDQKGELAATVCGVVERINKLIYVRALRA   84 (327)
Q Consensus        31 ~~~~iV~PGD~I~~~ee~~~-~G~Gty~~~g~i~Ssv~G~v~~~nk~v~V~pl~~   84 (327)
                      ...++|+|||.|+..++ |+ .|||||.++++|+||++|+++++|++++|+|+++
T Consensus         6 ~~r~iV~PGdvi~~~~~-~~~~g~~ty~~~~ki~asv~G~v~~~nkli~ViPL~G   59 (59)
T d2je6i2           6 QPRSIVVPGELLAEGEF-QIPWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEG   59 (59)
T ss_dssp             CSSCEECTTCEEEEECC-CCCCCTTEEEETTEEEECSSEEEEEETTEEEEEESCC
T ss_pred             cCCeEECCCcEeeeCCc-cccCCCEEEecCCEEEEEEEEEEEEECCEEEEEECCC
Confidence            46789999999975454 77 6999999999999999999999999999999974

>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=98.99  E-value=9.1e-10  Score=82.58  Aligned_cols=73  Identities=16%  Similarity=0.267  Sum_probs=64.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCCceEEE
Q 020356           88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDGSLQLQ  167 (327)
Q Consensus        88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g~i~Ls  167 (327)
                      .++|++|-|+|+.+.+.+++|+++...+|++|+++++.      .+.  +  ++++.|++||.|.|+|.++++.+.+.||
T Consensus         3 ~kvG~iv~G~V~~v~~~G~fV~l~~~~~Glv~~sels~------~~~--~--~~~~~~~~G~~v~v~Vi~id~~~ri~LS   72 (76)
T d1sroa_           3 IEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIAD------KRV--E--KVTDYLQMGQEVPVKVLEVDRQGRIRLS   72 (76)
T ss_dssp             CCTTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSSCS------SCC--S--CHHHHCCTTCEEEEEEEECCTTCCCEEE
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHhCc------ccc--C--CHHHccCCCCEEEEEEEEECCCCCEEEE
Confidence            47999999999999999999999988999999999862      111  1  5678899999999999999888899999


Q ss_pred             Ecc
Q 020356          168 ARN  170 (327)
Q Consensus       168 tr~  170 (327)
                      +|.
T Consensus        73 ~k~   75 (76)
T d1sroa_          73 IKE   75 (76)
T ss_dssp             ECC
T ss_pred             EEc
Confidence            985

>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=98.97  E-value=1.2e-11  Score=88.22  Aligned_cols=48  Identities=19%  Similarity=0.276  Sum_probs=41.0

Q ss_pred             ceEecCCccCCCCCceeecCCEEeeCCeEEEEEeeEEEE--ECcEEEEEec
Q 020356           34 SCVTVGDTIPVYEDGILKGHGTSDQKGELAATVCGVVER--INKLIYVRAL   82 (327)
Q Consensus        34 ~iV~PGD~I~~~ee~~~~G~Gty~~~g~i~Ssv~G~v~~--~nk~v~V~pl   82 (327)
                      ++|+|||.|+..++ |++|+|||+.+|.|+||++|.+.+  .++.++|.+.
T Consensus         1 k~~lPGe~L~~~ee-y~~G~gTy~~~g~I~as~~G~v~id~~~~~isVisV   50 (55)
T d2nn6i2           1 RYCIPGERLCNLEE-GSPGSGTYTRHGYIFSSLAGCLMKSSENGALPVVSV   50 (55)
T ss_dssp             CCCCTTCEEEETTT-CCCSSSCEEETTEEECCSCSCBCCCBCTTSSBC-CB
T ss_pred             CcccCCcEEeehhe-ecCCCCeEEcCCEEEEEeeEEEEEecCCCEeeEEEE
Confidence            47899999998887 999999999999999999999987  4566666654

>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=98.94  E-value=1.6e-09  Score=82.84  Aligned_cols=74  Identities=19%  Similarity=0.274  Sum_probs=56.4

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcC--ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CC
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINF--TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DG  162 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s--~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g  162 (327)
                      ..|++||+|.|+|+++...+++|+|..  ...|++|+++++-      .+.    .++.+.|++||.|.|+|.+++. .+
T Consensus         9 ~~p~~G~iv~G~V~~i~~~G~fV~l~~~~~i~G~i~~sels~------~~~----~~~~~~~~~Gd~v~~kV~~vd~~~~   78 (86)
T d1kl9a2           9 KFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSR------RRI----RSINKLIRIGRNECVVVIRVDKEKG   78 (86)
T ss_dssp             SSCCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC----------------------CTTCEEEEEEEEEETTTT
T ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccc------ccc----ccceEEeecccEEEEEEEEEECCCC
Confidence            378999999999999999999999974  4789999999862      111    1567889999999999999975 57


Q ss_pred             ceEEEEc
Q 020356          163 SLQLQAR  169 (327)
Q Consensus       163 ~i~Lstr  169 (327)
                      .+.||.|
T Consensus        79 ki~LS~K   85 (86)
T d1kl9a2          79 YIDLSKR   85 (86)
T ss_dssp             EEEEEST
T ss_pred             EEEEEee
Confidence            8999986

>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=98.93  E-value=9.8e-10  Score=83.50  Aligned_cols=75  Identities=21%  Similarity=0.312  Sum_probs=62.0

Q ss_pred             cCCCCCCEEEEEEEEEecceEEEEEcC--ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CC
Q 020356           86 YKPETGDIVIGRVIEVVPKRWKLEINF--TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DG  162 (327)
Q Consensus        86 Y~P~vGDiVIGrV~~V~~~~w~VDI~s--~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g  162 (327)
                      -.|++||+|.|+|+++++.+++|++..  ...|++|+++++.      .+..    ++.+.|++||.|.|+|.+++. .+
T Consensus         7 ~~p~~G~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~------~~~~----~~~~~~~~G~~v~~kV~~vd~~~~   76 (84)
T d2ahob2           7 KLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSS------KWVK----NIRDVLKENRKVIVKVIRVDRRKG   76 (84)
T ss_dssp             SSCCTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC---------------CHHHHTCSSCEEECEEEEEETTTT
T ss_pred             cCCCCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEcccccc------cccc----ccceEeecccEEEEEEEEEECCCC
Confidence            389999999999999999999999974  4689999998862      1111    567889999999999999985 57


Q ss_pred             ceEEEEcc
Q 020356          163 SLQLQARN  170 (327)
Q Consensus       163 ~i~Lstr~  170 (327)
                      .+.||+|.
T Consensus        77 ~i~LS~Kq   84 (84)
T d2ahob2          77 TVDVSLKK   84 (84)
T ss_dssp             EEEEESSS
T ss_pred             EEEEEEcC
Confidence            89999873

>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=98.77  E-value=1.5e-09  Score=83.70  Aligned_cols=43  Identities=23%  Similarity=0.459  Sum_probs=36.0

Q ss_pred             CCeEEEeChhhhhhcc--cccccc----CccceEEEEeecceeeecccc
Q 020356          178 RGQLLTVDPYLVKRRK--QHFHHL----EEYGIDLIIGCNGYIWIGEHV  220 (327)
Q Consensus       178 ~G~lv~V~~~li~r~~--~h~~~L----~~~~~eiivG~NG~IWI~~~~  220 (327)
                      +|+++.|++++++|+.  .++.+|    +.++|+|+||+||+|||++.+
T Consensus         1 dG~v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~NGrIWi~~~~   49 (85)
T d2ja9a2           1 DGMIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWVKCEE   49 (85)
T ss_dssp             SCEEEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETTTEEEEECSS
T ss_pred             CCEEEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEecCcEEEEECCC
Confidence            6999999999999974  455444    378999999999999998853

>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=98.70  E-value=1.8e-09  Score=82.29  Aligned_cols=43  Identities=23%  Similarity=0.532  Sum_probs=36.4

Q ss_pred             CCeEEEeChhhhhhcc-cccccc----CccceEEEEeecceeeecccc
Q 020356          178 RGQLLTVDPYLVKRRK-QHFHHL----EEYGIDLIIGCNGYIWIGEHV  220 (327)
Q Consensus       178 ~G~lv~V~~~li~r~~-~h~~~L----~~~~~eiivG~NG~IWI~~~~  220 (327)
                      +|++++|+.+++|++. .++..|    +.++|||++|+||+|||++++
T Consensus         1 dG~~f~vsl~laR~Ll~~~~~vL~~Lgk~~~FEIavG~NGrVWvk~~~   48 (80)
T d2nn6g3           1 DGLLFKVTLGLIRKLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKT   48 (80)
T ss_dssp             SCEEECCCHHHHHHHHCTTCSHHHHTTCSSSCCCEEETTTEEEECCSS
T ss_pred             CCEEEEecHHHHHHHhcCCCHHHHHHhhhCCeEEEEecCCeEEEeCCC
Confidence            6999999999999985 445555    368999999999999998864

>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=98.62  E-value=6.9e-08  Score=74.75  Aligned_cols=73  Identities=18%  Similarity=0.226  Sum_probs=63.1

Q ss_pred             CCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQ  167 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Ls  167 (327)
                      ++|++|.|+|+.+...+.+|+++....|++|+++++-      .+.  +  ++++.|++||.|.|+|.+++. .+.+.||
T Consensus        17 k~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~------~~~--~--~~~~~~~vGq~v~~~V~~id~~~~~i~LS   86 (94)
T d3bzka4          17 KPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSE------KFV--K--DPYEVVKAGDIVKVKVMEVDIPRNRVGLS   86 (94)
T ss_dssp             CTTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCS------SCC--S--CHHHHCCTTCEEEEEEEEEETTTTEEEEE
T ss_pred             CCCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhc------ccc--c--ChhhhhccCcEEEEEEEEEECCCCEEEEE
Confidence            6799999999999999999999999999999998861      111  1  667889999999999999985 6789999


Q ss_pred             EccC
Q 020356          168 ARNQ  171 (327)
Q Consensus       168 tr~~  171 (327)
                      +|..
T Consensus        87 ~K~~   90 (94)
T d3bzka4          87 MRMS   90 (94)
T ss_dssp             SCTT
T ss_pred             Eecc
Confidence            9853

>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=98.62  E-value=7e-08  Score=76.51  Aligned_cols=82  Identities=21%  Similarity=0.271  Sum_probs=64.2

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccch-------hhhhcccCCCCEEEEEEEecCC
Q 020356           88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDE-------LNMRSIFTENDLVCAEVRSSQG  160 (327)
Q Consensus        88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de-------~~mr~~~~~GDlV~AeV~sv~~  160 (327)
                      |++||++-|+|++|+..+++|+|+ +.+|++|++++.-. .     ...|+       ....+.|++||.|.++|.+++.
T Consensus         1 p~~gei~~g~V~~v~~~G~FVel~-~ieGlv~~s~l~~~-~-----~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~   73 (106)
T d1go3e1           1 PEMYELIEGEVVDVVEFGSFVRLG-PLDGLIHVSQIMDD-Y-----VSYDPKREAIIGKETGKVLEIGDYVRARIVAISL   73 (106)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSCSS-C-----EEECCC--CEEETTTCCEECTTCEEEEEEEEEEC
T ss_pred             CCCCCEEEEEEEEEeeeEEEEEee-CeEEEEEeecccCc-e-----eeeccceeEEeecccccceeecceEEEEEEEEch
Confidence            899999999999999999999998 58999999988511 0     00111       1345779999999999999975


Q ss_pred             CC------ceEEEEccCCCccC
Q 020356          161 DG------SLQLQARNQKYGKL  176 (327)
Q Consensus       161 ~g------~i~Lstr~~~lGkL  176 (327)
                      +.      .+.||++....|..
T Consensus        74 ~~~~~~~~~i~ls~K~~~~~~~   95 (106)
T d1go3e1          74 KAERKRGSKIALTMRQPYLGKL   95 (106)
T ss_dssp             CC-----CEEEEECCSTTCEEH
T ss_pred             hhccccCceeecccccCCCCcc
Confidence            43      37889888877653

>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=98.37  E-value=3.9e-07  Score=73.40  Aligned_cols=76  Identities=16%  Similarity=0.225  Sum_probs=60.6

Q ss_pred             CCCCEEEEEEEEEecceEEEEEc-CccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCC-CceEE
Q 020356           89 ETGDIVIGRVIEVVPKRWKLEIN-FTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GSLQL  166 (327)
Q Consensus        89 ~vGDiVIGrV~~V~~~~w~VDI~-s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~i~L  166 (327)
                      ++|++|-|+|+++..++++|+|+ ....|++|++++.-      .   ...-+..+.|++||.|.|+|.+++.. +.+.|
T Consensus        20 ~~G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~------~---~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~L   90 (119)
T d1wi5a_          20 KPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQE------Y---IRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSL   90 (119)
T ss_dssp             CTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHH------H---HHHHSSSCCCCTTCEEEEEEEECCTTSCEEEE
T ss_pred             CCCCEEEEEEEEEeccEEEEEEeccccceEEeHHHhcc------c---cccCCHHHhcccceEEEEEEEEEeCCCCEEEE
Confidence            68999999999999999999996 56799999998750      0   00113456799999999999999864 56999


Q ss_pred             EEccCCC
Q 020356          167 QARNQKY  173 (327)
Q Consensus       167 str~~~l  173 (327)
                      |++....
T Consensus        91 S~k~~~~   97 (119)
T d1wi5a_          91 SVGHSEV   97 (119)
T ss_dssp             ECCCCCS
T ss_pred             EecHHHh
Confidence            9986533

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

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

Probab=98.24  E-value=1.9e-06  Score=65.74  Aligned_cols=85  Identities=11%  Similarity=0.221  Sum_probs=61.1

Q ss_pred             CCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccch---hhhhcccCCCCEEEEEEEecCCC-Cc
Q 020356           88 PETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDE---LNMRSIFTENDLVCAEVRSSQGD-GS  163 (327)
Q Consensus        88 P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de---~~mr~~~~~GDlV~AeV~sv~~~-g~  163 (327)
                      |.+|+++-|+|++++..+++|+|+ +.++++|.+++.  .... .......   .+-.+.|+.||.|+++|.+++.+ +.
T Consensus         1 Pf~Gev~~g~I~~v~~~G~fv~lg-~~eg~i~~~~l~--~~~~-~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~   76 (91)
T d1y14b1           1 PFKGEVVDGTVVSCSQHGFEVQVG-PMKVFVTKHLMP--QDLT-FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSS   76 (91)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSC--TTCE-ECC-----CEECSSCEECTTCEEEEEEEEEEEETTE
T ss_pred             CCCCCEEEEEEEEEEeeEEEEEEc-CeEEEEEhhhcC--cceE-EccccceeEecccCeEEeCCCEEEEEEEEEecccCc
Confidence            889999999999999999999997 568999998763  2111 0000000   12234699999999999998753 23


Q ss_pred             --eEEEEccCCCccC
Q 020356          164 --LQLQARNQKYGKL  176 (327)
Q Consensus       164 --i~Lstr~~~lGkL  176 (327)
                        ...|++++.||.+
T Consensus        77 i~~ig~~~~d~LG~i   91 (91)
T d1y14b1          77 IHAIGSIKEDYLGAI   91 (91)
T ss_dssp             EEEEEECCSTTCEEC
T ss_pred             cEEEEEccCCCCCcC
Confidence              3448888999875

>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=98.04  E-value=6.4e-06  Score=63.22  Aligned_cols=89  Identities=12%  Similarity=0.137  Sum_probs=62.4

Q ss_pred             CCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcc--cccccccchhhhhcccCCCCEEEEEEEecCCC-Cc
Q 020356           87 KPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGI--QRRRTAVDELNMRSIFTENDLVCAEVRSSQGD-GS  163 (327)
Q Consensus        87 ~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i--~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~-g~  163 (327)
                      .|.+|+++-|+|+++++.+++|+++ +.++++|.+++.-+-.-  ...+....-.+-...|+.||.|++||.+++.+ +.
T Consensus         1 rPf~Gev~~g~V~~v~~~G~fv~lg-~~~~~v~~~~l~~d~~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~~~   79 (94)
T d2c35b1           1 RPFKGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKND   79 (94)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEETTE
T ss_pred             CCCCCCEEEEEEEEEEeeEEEEEec-CceEEEEhhhcCcceeecccccceEEEcccceEEEeCCCEEEEEEEEEecCcCc
Confidence            3889999999999999999999997 57899999876411000  00000000013345699999999999988643 33


Q ss_pred             --eEEEEccCCCccC
Q 020356          164 --LQLQARNQKYGKL  176 (327)
Q Consensus       164 --i~Lstr~~~lGkL  176 (327)
                        +..+++++.||.+
T Consensus        80 I~~igt~~~d~LG~i   94 (94)
T d2c35b1          80 IFAIGSLMDDYLGLV   94 (94)
T ss_dssp             EEEEEECCSTTCEEC
T ss_pred             ceEEEEccCCCcccC
Confidence              3468899999864

>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=97.70  E-value=1.2e-06  Score=62.97  Aligned_cols=61  Identities=18%  Similarity=0.219  Sum_probs=35.5

Q ss_pred             EEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCCCC
Q 020356           96 GRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQGDG  162 (327)
Q Consensus        96 GrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~~g  162 (327)
                      |+|+.+.+.+++|+|....+|++|+|+++......+-      -++++.|++||.|.|+|.++++.+
T Consensus         1 G~V~~i~~fG~FV~l~~g~~Glihiseis~~~~~~~v------~~~~~~~~~G~~V~vkV~~iD~~~   61 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRV------ENVEDVLGVGQKVQVEIAEIDSRG   61 (62)
T ss_dssp             CBEEECC-CSCEECCC---CCCCC-------------------------CCSSCBCCCCCCCCCSSC
T ss_pred             CEEEEEEeceEEEEecCCceEEEEHHHcccccccccc------cCHHHhcCCCCEEEEEEEEEcCCC
Confidence            7899999999999999999999999998632111121      167788999999999999998653

>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=97.63  E-value=0.00013  Score=53.74  Aligned_cols=59  Identities=19%  Similarity=0.248  Sum_probs=50.2

Q ss_pred             ccCCCCCCEEEEEEEEEecceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC
Q 020356           85 RYKPETGDIVIGRVIEVVPKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG  160 (327)
Q Consensus        85 rY~P~vGDiVIGrV~~V~~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~  160 (327)
                      .|..++|++|.|+|..+..+.+.|||+ ...|+||-++. .|               .+.|++||-|.|-|..+..
T Consensus         3 ef~~~~geiv~G~V~r~~~~~~~Vdlg-~~eaiLp~~eq-ip---------------~E~~~~Gdrik~~i~~V~~   61 (72)
T d1hh2p1           3 KYSELKGTVTTAEVIRVMGEWADIRIG-KLETRLPKKEW-IP---------------GEEIKAGDLVKVYIIDVVK   61 (72)
T ss_dssp             CTTCCTTCEEEEEEEEECSSEEEEEET-TEEEEEEGGGS-CT---------------TCCCCTTCEEEEEEEEEEE
T ss_pred             hHhhccCcEEEEEEEEEcCCCEEEEEC-CcEEECCHHHc-CC---------------CCCCCCCCEEEEEEEEEEE
Confidence            588899999999999999999999998 57889877654 23               3559999999999998864

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

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

Probab=96.73  E-value=0.00027  Score=53.76  Aligned_cols=54  Identities=19%  Similarity=0.279  Sum_probs=32.7

Q ss_pred             CCCCceEecCCccCCCC------------------------CceeecCCEEeeCCeEEEEEeeEEEEEC-c------EEE
Q 020356           30 SNPNSCVTVGDTIPVYE------------------------DGILKGHGTSDQKGELAATVCGVVERIN-K------LIY   78 (327)
Q Consensus        30 ~~~~~iV~PGD~I~~~e------------------------e~~~~G~Gty~~~g~i~Ssv~G~v~~~n-k------~v~   78 (327)
                      ...+.+|+|||+|...+                        ...+.|+|...+++.|.++.||+++++. +      .+|
T Consensus         6 ~~~~qvVlPGD~l~lp~~~~~~g~~~~~~~~l~L~~~~~~~~~v~lGPGLRq~~d~v~atKaG~LR~k~P~~~~~~~~yW   85 (91)
T d2nn6g2           6 TVLGQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYW   85 (91)
T ss_dssp             GGGSSBCCSSEEECCSCSCCEECSSEEECC-----------------------CCCEEECSCCEEEEECCTTTSSCCEEE
T ss_pred             hhcCCEEeCCcEEEecccccccccCcCcccccccccccCCCceEEeCCccceeCCEEEEeecceeeecCCCCCCCcceEE
Confidence            44578999999994221                        1477899999999999999999999852 3      599


Q ss_pred             EEecC
Q 020356           79 VRALR   83 (327)
Q Consensus        79 V~pl~   83 (327)
                      |+...
T Consensus        86 VDs~Q   90 (91)
T d2nn6g2          86 VDSQQ   90 (91)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            98753

>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=96.43  E-value=0.0049  Score=46.48  Aligned_cols=77  Identities=12%  Similarity=0.150  Sum_probs=53.6

Q ss_pred             CEEEEEEEEEe--cceEEEEEcCccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC-CCceEEEE
Q 020356           92 DIVIGRVIEVV--PKRWKLEINFTQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG-DGSLQLQA  168 (327)
Q Consensus        92 DiVIGrV~~V~--~~~w~VDI~s~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~-~g~i~Lst  168 (327)
                      ||-.|+|..|.  -+.+||||+...+|+||++++..+.. ........+.++.+.+++||.|...|..=.. +.-+.||+
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~~di~~~~~-~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~~~~KGprlT~   80 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYF-PANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTT   80 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSSSCEEEEGGGSCGGGC-SSCCCSSSCCCGGGTCCTTCEEEEEEEECCBTTBCCEEES
T ss_pred             CcEEEEEEEecCCceEEEEEeCCCccceeEecccceeee-ccccccccccchhhhccCCCeEEEEEeecccCCCCceEEE
Confidence            67899999996  57899999999999999998752211 1111111223567889999999999987332 23466665


Q ss_pred             c
Q 020356          169 R  169 (327)
Q Consensus       169 r  169 (327)
                      .
T Consensus        81 ~   81 (87)
T d1smxa_          81 F   81 (87)
T ss_dssp             C
T ss_pred             E
Confidence            3

>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=96.32  E-value=0.00057  Score=51.96  Aligned_cols=42  Identities=21%  Similarity=0.343  Sum_probs=36.0

Q ss_pred             CeEEEeChhhhhhc----cccccccC-ccceEEEEeecceeeecccc
Q 020356          179 GQLLTVDPYLVKRR----KQHFHHLE-EYGIDLIIGCNGYIWIGEHV  220 (327)
Q Consensus       179 G~lv~V~~~li~r~----~~h~~~L~-~~~~eiivG~NG~IWI~~~~  220 (327)
                      |.+++|||.++++.    .+++..|. .+++.|.++.||+|||.+..
T Consensus         2 g~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~G~V~I~g~~   48 (87)
T d2z0sa2           2 GKIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARNGRIHLECPN   48 (87)
T ss_dssp             SEEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETTTEEEEECSC
T ss_pred             cEEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCCcEEEEEeCC
Confidence            78999999999986    36777774 68999999999999998754

>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=96.18  E-value=0.0059  Score=44.92  Aligned_cols=58  Identities=12%  Similarity=0.184  Sum_probs=44.3

Q ss_pred             CCCCCEEEEEEEEEecc----eEEEEEcC---ccceeeecccccCCCcccccccccchhhhhcccCCCCEEEEEEEecCC
Q 020356           88 PETGDIVIGRVIEVVPK----RWKLEINF---TQDAILMLSSMNLPDGIQRRRTAVDELNMRSIFTENDLVCAEVRSSQG  160 (327)
Q Consensus        88 P~vGDiVIGrV~~V~~~----~w~VDI~s---~~~a~L~ls~v~fpg~i~rrr~~~de~~mr~~~~~GDlV~AeV~sv~~  160 (327)
                      .++|++|.|.|..+..+    ...|||+.   ...|+||-++. .|               .+.|++||-|+|-|..+..
T Consensus         2 ~r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eq-ip---------------~E~y~~Gdrik~~i~~V~~   65 (76)
T d2asba1           2 TREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQ-VP---------------GESYEHGNRLRCYVVGVTR   65 (76)
T ss_dssp             CCTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGS-CT---------------TCCCCTTCEEEEEEEEEEC
T ss_pred             CccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHc-CC---------------CcccCCCCEEEEEEEEEEe
Confidence            36899999999998654    37999984   35678765443 23               4569999999999999875


Q ss_pred             C
Q 020356          161 D  161 (327)
Q Consensus       161 ~  161 (327)
                      +
T Consensus        66 ~   66 (76)
T d2asba1          66 G   66 (76)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=95.32  E-value=0.02  Score=42.74  Aligned_cols=65  Identities=5%  Similarity=0.103  Sum_probs=47.3

Q ss_pred             CCEEEEEEEEEecceEEEEEcC-ccceeeecccccCCCcccccccccch--------hhhhcccCCCCEEEEEEEecCCC
Q 020356           91 GDIVIGRVIEVVPKRWKLEINF-TQDAILMLSSMNLPDGIQRRRTAVDE--------LNMRSIFTENDLVCAEVRSSQGD  161 (327)
Q Consensus        91 GDiVIGrV~~V~~~~w~VDI~s-~~~a~L~ls~v~fpg~i~rrr~~~de--------~~mr~~~~~GDlV~AeV~sv~~~  161 (327)
                      |..--|.|++++..+.+|.|.. .-.|++|+|++.  +.    +.+.|+        .+-...|+.||-|.++|.+++..
T Consensus         4 ~~~F~g~Is~v~~~GifV~L~e~~~eGlI~~s~L~--~d----~y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~   77 (87)
T d2ix0a3           4 DTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLH--AV----RDELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRME   77 (87)
T ss_dssp             CCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTC--SC----GGGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETT
T ss_pred             CCEEEEEEEEEEcCeEEEEEecCCcEEEEEehhCC--Cc----eEEEeccceEEEEEEcccEEEECCCEEEEEEEEEecc
Confidence            3445699999999999999964 679999999873  21    111111        11235699999999999999864

>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=95.04  E-value=0.0028  Score=45.67  Aligned_cols=43  Identities=26%  Similarity=0.480  Sum_probs=30.4

Q ss_pred             CCeEEEeChhhhhhc----ccccccc-CccceEEEEeecceeeecccc
Q 020356          178 RGQLLTVDPYLVKRR----KQHFHHL-EEYGIDLIIGCNGYIWIGEHV  220 (327)
Q Consensus       178 ~G~lv~V~~~li~r~----~~h~~~L-~~~~~eiivG~NG~IWI~~~~  220 (327)
                      +|.+++|||.++++.    ++.+..| +.++++|.++.||.|||.+..
T Consensus         1 ~g~vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~g~v~I~g~~   48 (69)
T d2je6i3           1 NGIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPS   48 (69)
T ss_dssp             SSCEEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTTSEEEC----
T ss_pred             CCEEEEEChhhccceECCchhHHHHHHHHHCCEEEEcCCCEEEEEeCC
Confidence            489999999999886    3556666 378999999999999998753

>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=92.68  E-value=0.015  Score=43.22  Aligned_cols=43  Identities=26%  Similarity=0.628  Sum_probs=35.9

Q ss_pred             CeEEEeChhhhhhc----cccccccC-ccceEEEEeecceeeeccccc
Q 020356          179 GQLLTVDPYLVKRR----KQHFHHLE-EYGIDLIIGCNGYIWIGEHVE  221 (327)
Q Consensus       179 G~lv~V~~~li~r~----~~h~~~L~-~~~~eiivG~NG~IWI~~~~~  221 (327)
                      |.++.|||.++.+.    ++++..|. .+++.|.+..||.|||.+..+
T Consensus         2 g~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~~g~v~I~G~~e   49 (84)
T d2ba0a3           2 GRIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQNGLIWVNGDRR   49 (84)
T ss_dssp             SEEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECTTSEEEEESCHH
T ss_pred             cEEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECCCCEEEEEeCHH
Confidence            78999999988886    46677774 689999999999999987543

>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=90.95  E-value=0.18  Score=35.77  Aligned_cols=53  Identities=25%  Similarity=0.217  Sum_probs=41.9

Q ss_pred             CCCCceEecCCccCCC-CCceeecCCEEee-CCeEEEEEeeEEEEE-----CcEEEEEec
Q 020356           30 SNPNSCVTVGDTIPVY-EDGILKGHGTSDQ-KGELAATVCGVVERI-----NKLIYVRAL   82 (327)
Q Consensus        30 ~~~~~iV~PGD~I~~~-ee~~~~G~Gty~~-~g~i~Ssv~G~v~~~-----nk~v~V~pl   82 (327)
                      .....+|.||..|.-- ...|.+|.++..- |..|+|.+.|.|...     .+.|+|.|+
T Consensus         6 ~~~Gq~V~~G~IivRQRGtk~~pG~nVg~GkD~TLfAl~~G~V~F~~~~~~~~~VsV~P~   65 (66)
T d1v8qa_           6 RYEGQVVRAGNILVRQRGTRFKPGKNVGMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPL   65 (66)
T ss_dssp             SCTTCEECTTCEEEECSSCSSEECTTEEECTTCCEEESSSEEEEEEECGGGCEEEEEEEC
T ss_pred             EeCCEEEeCCeEEEEeccCeEeCCCCeeecCCCcEEEeeeeEEEEEEeCCCCeEEEEEEC
Confidence            3457899999988532 2369999999884 788999999999873     348899986

>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=85.98  E-value=0.48  Score=35.03  Aligned_cols=54  Identities=24%  Similarity=0.223  Sum_probs=41.9

Q ss_pred             CCCCCceEecCCccCCC-CCceeecCCEEee-CCeEEEEEeeEEEEEC-----cEEEEEec
Q 020356           29 KSNPNSCVTVGDTIPVY-EDGILKGHGTSDQ-KGELAATVCGVVERIN-----KLIYVRAL   82 (327)
Q Consensus        29 ~~~~~~iV~PGD~I~~~-ee~~~~G~Gty~~-~g~i~Ssv~G~v~~~n-----k~v~V~pl   82 (327)
                      ......+|.||+.|.-- ...|.+|.++..- |..|+|.+.|.|....     +.|+|.|.
T Consensus        23 K~~~Gq~V~~G~IivRQRGtk~hpG~nVg~GkD~TLfA~~~G~V~F~k~~~~rk~V~V~p~   83 (84)
T d2zjrt1          23 KKFGGEVVKAGNILVRQRGTKFKAGQGVGMGRDHTLFALSDGKVVFINKGKGARFISIEAA   83 (84)
T ss_dssp             SSCTTCEECSSCEEECCSSSSSEECTTEECCTTSCEEESSCEEEEEEEETTTEEEEEECCC
T ss_pred             EECCCEEEeCCcEEEEecCceEcCCCCccccCCCcEEEeeceEEEEEEcCCCCEEEEEEeC
Confidence            34567899999998533 2369999999884 7789999999998742     47788774