Psyllid ID: psy10116

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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-------30
Protein Sequence
MAEEKDKPVIEIMLASDRIDPLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWVSAIDENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTLGLAD
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccEEEccccccccccEEccccEEccccEEEEEEEEEEEEEccEEEEEEcccccccccccEEEEEEEEEEccEEEEEEccccccEEccccccccccccccccHHHHHHHHcccccccEEEEEEEEEcccccEEEEEccccccccccEEEEEEccccccccccccccccccEEEEEEEccEEEEEEcccccccccHHccccccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccHHcccccEEEHHHHHccccHHHcccccccEEccccEEEccccccccccEEEcccEEEEEEEEEEEEEcEEEEEEEcccccccccccEEEEEEEEEcccEEEEEccccccEEEEEHccccccccEccccHHHHHHHHHHHHcccEEEEEEEEEcccccEEEEEcccccccccccEEEEEcccccEcccccEEccccccEEEEEcccEEEEEccccccccccEcccccccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccHHHHccHHHHHHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
maeekdkpVIEIMLAsdridplieiheftdpiltpgetvEYLEgymtghgtfpddeeikaSVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTglqsqkwvvdtNSILESALhltsvnlpggeqrrrsVQDEEMMREFLKEGDLISAEIHQIstegsltlhtrslkygklgqgilltvppslirrskshfcnlacgaqviLGCNGYVWVSAIdenksggfiqnmevvklsDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLKystydllkpeskldLVLCTAQKLQTLGLAD
Flexible Loop (DISEMBL)
MAEEKDKPVIEIMLAsdridplieiheftdpiltPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESalhltsvnlpggeqrrRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWVSAIDENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTLGLAD
Low Complexity Region (SEG)
MAEEKDKPVIEIMLASDRIDPLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYigeigevvvgRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWVSAIDENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTLGLAD
Disordered region (IsUnstruct)
********VIEIMLASDRIDPLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSV************************GDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWVSAIDENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQT*****
Disordered Region (DISOPRED)
********************************LTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRR*VQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWVSAIDENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQK*Q******
Disordered Region (DISEMBL)
********VIEIMLASDRIDPLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWVSAIDENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTLGLAD
Disordered Region (DISPRO)
*****DKPVIEIMLASDRIDPLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWVSAIDENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTL****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAEEKDKPVIEIMLASDRIDPLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWVSAIDENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTLGLAD
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	298	2.2.26 [Sep-21-2011]
Q13868	293	Exosome complex component	yes	N/A	0.872	0.887	0.536	8e-81
Q2KID0	293	Exosome complex component	yes	N/A	0.872	0.887	0.539	9e-81
Q8VBV3	293	Exosome complex component	yes	N/A	0.872	0.887	0.536	3e-80
Q09704	329	Exosome complex component	yes	N/A	0.855	0.775	0.397	9e-53
P38792	359	Exosome complex component	yes	N/A	0.885	0.735	0.377	6e-45
Q9V120	265	Probable exosome complex	yes	N/A	0.647	0.728	0.260	4e-12
Q5JIR5	257	Probable exosome complex	yes	N/A	0.546	0.634	0.265	5e-12
Q6L222	230	Probable exosome complex	yes	N/A	0.583	0.756	0.257	1e-11
O59221	265	Probable exosome complex	yes	N/A	0.647	0.728	0.255	8e-11
Q8U0L8	264	Probable exosome complex	yes	N/A	0.624	0.704	0.247	2e-10

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

 Score =  300 bits (768), Expect = 8e-81,   Method: Compositional matrix adjust.
 Identities = 141/263 (53%), Positives = 200/263 (76%), Gaps = 3/263 (1%)

Query: 32  ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVV 91
           ++ PG+T+    G+M GHGT+  +E++ ASV G VE+VN+L+ V+A+ +RYIGE+G++VV
Sbjct: 26  LVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKALKTRYIGEVGDIVV 85

Query: 92  GRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
           GR+T +Q ++W V+TNS L+S L L+S+NLPGGE RRRS +DE  MR FL+EGDLISAE+
Sbjct: 86  GRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEV 145

Query: 152 HQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWV 211
             + ++G+++LHTRSLKYGKLGQG+L+ V PSL++R K+HF +L CGA VILG NG++W+
Sbjct: 146 QAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWI 205

Query: 212 SAIDENK---SGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLK 268
               E+K   +GGFI N+E V L+DRE I+RL N I +L   ++ML+DTSI Y YE SL 
Sbjct: 206 YPTPEHKEEEAGGFIANLEPVSLADREVISRLRNCIISLVTQRMMLYDTSILYCYEASLP 265

Query: 269 YSTYDLLKPESKLDLVLCTAQKL 291
           +   D+LKPE   ++V+ T Q+L
Sbjct: 266 HQIKDILKPEIMEEIVMETRQRL 288

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

 Score =  300 bits (768), Expect = 9e-81,   Method: Compositional matrix adjust.
 Identities = 142/263 (53%), Positives = 200/263 (76%), Gaps = 3/263 (1%)

Query: 32  ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVV 91
           ++ PG+T+    G+M GHGT+  +E++ ASV G VE+VN+L+ V+A+ +RY GE+G++VV
Sbjct: 26  LVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKALKTRYNGEVGDIVV 85

Query: 92  GRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
           GR+T +Q ++W V+TNS L+S L L+S+NLPGGE RRRS +DE  MR FL+EGDLISAE+
Sbjct: 86  GRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEV 145

Query: 152 HQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWV 211
             + ++G+++LHTRSLKYGKLGQG+L+ V PSL++R K+HF +L CGA VILG NG++WV
Sbjct: 146 QAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWV 205

Query: 212 SAIDENK---SGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLK 268
               E+K   +GGFI N+E V L+DRE I+RL N I +LA  ++ML+DTSI Y YE SL 
Sbjct: 206 YPTPEHKEDDAGGFIANLEPVSLTDREVISRLRNCIVSLATQRMMLYDTSILYCYEASLP 265

Query: 269 YSTYDLLKPESKLDLVLCTAQKL 291
           +   D+LKPE   ++V+ T Q+L
Sbjct: 266 HQIKDILKPEIMEEIVMETRQRL 288

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

 Score =  298 bits (763), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 141/263 (53%), Positives = 198/263 (75%), Gaps = 3/263 (1%)

Query: 32  ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVV 91
           ++ PG+T+    G+M GHGT+  +E++ ASV G VE+VN+L+ V+A+ +RY GE+G++VV
Sbjct: 26  LVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKALKTRYNGEVGDIVV 85

Query: 92  GRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
           GR+T +Q ++W V+TNS L+S L L+S+NLPGGE RRRS +DE  MR FL+EGDLISAE+
Sbjct: 86  GRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEV 145

Query: 152 HQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWV 211
             + ++G+++LHTRSLKYGKLGQG+L+ V PSL++R K+HF +L CGA VILG NG++W+
Sbjct: 146 QAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWI 205

Query: 212 SAIDENK---SGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLK 268
               E+K   +GGFI N+E V LSDRE I+RL N +  L   ++MLFDTSI Y YE SL 
Sbjct: 206 YPTPEHKDEDAGGFIANLEPVALSDREVISRLRNCVVLLVTQRMMLFDTSILYCYEASLA 265

Query: 269 YSTYDLLKPESKLDLVLCTAQKL 291
           +   D+LKPE   +++L T Q+L
Sbjct: 266 HQIKDILKPEVMEEIMLETRQRL 288

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

 Score =  207 bits (526), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 110/277 (39%), Positives = 165/277 (59%), Gaps = 22/277 (7%)

Query: 32  ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVV 91
           ++TPG+ V     +M GHGT+ +D  I ASV G V++VN+L+SV+ + S+Y+ EIG++++
Sbjct: 57  LVTPGQLVTDDPQFMRGHGTYFEDGGIYASVAGSVQRVNKLISVKPLRSKYVPEIGDLII 116

Query: 92  GRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
           G++  +Q ++W VD  +   + L L+S+NLPGG QRR+   DE  MR F +EGDL+ AE+
Sbjct: 117 GKIAEVQPKRWKVDIGAKQNAVLMLSSINLPGGIQRRKLETDELQMRSFFQEGDLLVAEV 176

Query: 152 HQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWV 211
            Q  ++GS+++HTRSLKYGKL  G+ L VPP+L+ RSKSH   LA G  +IL  NGYVWV
Sbjct: 177 QQYFSDGSVSIHTRSLKYGKLRNGVFLKVPPALVVRSKSHAYALAGGVDIILSVNGYVWV 236

Query: 212 SAIDENKSGGFIQNMEVVKLSD------------------RETITRLNNVIKALAESKVM 253
           S  +EN+      ++ + +L +                  R  I+R++  IK LA   + 
Sbjct: 237 SKHNENQHS----SVSITRLEEEASESIYSNENDEIDGYTRLNISRVSICIKGLASRSLP 292

Query: 254 LFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQK 290
           L   SI   YE SL +S    L     +D +   A +
Sbjct: 293 LTQASITNFYESSLVFSNLQDLTVPKNMDQIAMEAMQ 329

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

 Score =  181 bits (459), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 115/305 (37%), Positives = 162/305 (53%), Gaps = 41/305 (13%)

Query: 32  ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVV 91
           I+TPGE V     +M GHGT+  D    +SV G V +VN+L+SV  +  RY  E G+ VV
Sbjct: 54  IVTPGELVTDDPIWMRGHGTYFLDNMTYSSVAGTVSRVNRLLSVIPLKGRYAPETGDHVV 113

Query: 92  GRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
           GR+  + +++W VD      + L L SVNLPGG  RR+S  DE  MR FLKEGDL++AE+
Sbjct: 114 GRIAEVGNKRWKVDIGGKQHAVLMLGSVNLPGGILRRKSESDELQMRSFLKEGDLLNAEV 173

Query: 152 HQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWV 211
             +  +GS +LHTRSLKYGKL  G+   VP SLI R+K+H  NL     V+LG NGY+W+
Sbjct: 174 QSLFQDGSASLHTRSLKYGKLRNGMFCQVPSSLIVRAKNHTHNLPGNITVVLGVNGYIWL 233

Query: 212 ------------------SAIDENKSGGFIQ-NMEVVKLSD------------------- 233
                             S+I      G +  N  + +L +                   
Sbjct: 234 RKTSQMDLARDTPSANNSSSIKSTGPTGAVSLNPSITRLEEESSWQIYSDENDPSISNNI 293

Query: 234 RETITRLNNVIKALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLV---LCTAQK 290
           R+ I R  NVIKALA  ++ +    I  AYE S+ YS    L  ++ ++ +   + TA+K
Sbjct: 294 RQAICRYANVIKALAFCEIGITQQRIVSAYEASMVYSNVGELIEKNVMESIGSDILTAEK 353

Query: 291 LQTLG 295
           ++  G
Sbjct: 354 MRGNG 358

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

 Score = 72.4 bits (176), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 58/223 (26%), Positives = 110/223 (49%), Gaps = 30/223 (13%)

Query: 45  YMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVV 104
           Y  G GTF +   I ++V G+V+     + V  +   YI E+G+ V+G++  ++   WVV
Sbjct: 23  YKNGRGTFREGSRIYSTVIGLVDIKGNTIRVIPLEGPYIPEVGDNVIGKIVDVKFSSWVV 82

Query: 105 DTNSILESALHLTSVNLPGGEQRRRSVQDEEM------MREFLKEGDLISAEIHQISTEG 158
           D  +   + L +            +   DE++      +R+F   GD+I A++  I+   
Sbjct: 83  DIGAPYPANLKI------------QDFTDEKIDLLRTDLRKFFDIGDIIYAKVKAITEVN 130

Query: 159 SLTLHTRSLKY--GKLGQGILLTVPPSLIRR------SKSHFCNLACGAQVILGCNGYVW 210
           ++ L T+ + +  G L  G ++ + PS + R      S  +        ++I+G NG++W
Sbjct: 131 NIDLTTKGMPFNGGPLKGGQIVKITPSRVPRVIGRGGSMINMIKKLTMTRIIVGQNGWIW 190

Query: 211 VSAIDENKSGGFIQNMEVVKLSDRETITR-LNNVIKALAESKV 252
           VS  ++      I+   ++K+ D+E+ TR L + IKAL  S++
Sbjct: 191 VSGKNDALEKLAIE--AILKI-DKESHTRGLTDRIKALLLSRL 230

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|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 = 72.0 bits (175), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 47/177 (26%), Positives = 89/177 (50%), Gaps = 14/177 (7%)

Query: 45  YMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVV 104
           +  G GTF +   I ++V G+VE    ++ V  +   YI E+G+ V+G++  ++   W V
Sbjct: 23  FKNGRGTFREGNAIYSTVIGLVEIRGNVIRVIPLEGPYIPEVGDNVLGKIVDVKFSSWTV 82

Query: 105 DTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHT 164
           D  +  +++L +        E+R   ++ +  +R+    GD+I A++   +    + L T
Sbjct: 83  DIGAPYQASLRVQDAV----EERIDLLKTD--LRKIFDIGDIIYAKVKAFNEVNQIDLTT 136

Query: 165 RSLKY--GKLGQGILLTVPPSLIRR------SKSHFCNLACGAQVILGCNGYVWVSA 213
           + + +  G L  G L+T+ PS + R      S  +      G ++I+G NG+VWVS 
Sbjct: 137 KGMPFKGGPLRGGQLVTITPSKVPRLIGKGGSMINMIKTLTGTRIIVGQNGWVWVSG 193

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|Q6L222|ECR1_PICTO Probable exosome complex RNA-binding protein 1 OS=Picrophilus torridus (strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828) GN=PTO0395 PE=3 SV=1

 Score = 70.5 bits (171), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 50/194 (25%), Positives = 97/194 (50%), Gaps = 20/194 (10%)

Query: 32  ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVV 91
           I+ PGE ++ LEG    +G + +++E  +   GVV+K ++ + +   N  Y+  I + V+
Sbjct: 6   IVYPGEKID-LEGQKPRNGLYEENDEYYSEYFGVVQKSDKFIDIVPFNGPYMPRINDKVI 64

Query: 92  GRVTGLQSQKWVVDTNSILESALHL--TSVNLPGGEQRRRSVQDEEMMREFLKEGDLISA 149
           G+V  + +  W VD NS   S +H+  T  ++  G+           +R++L  GD I A
Sbjct: 65  GKVIDVSATMWTVDINSPYFSLMHMNDTPWHVTSGD-----------LRKYLNVGDYIYA 113

Query: 150 EIHQIS--TEGSLTLHTRSLKYGKLGQGILLTVP--PSLIRRSKS--HFCNLACGAQVIL 203
           ++  ++   E  L+L   +L+  + G  I +  P  P +I ++ +  +        ++I+
Sbjct: 114 KVSILNEIKESWLSLKDVNLRKLEEGSIIYIKAPKVPRVIGKAGNMINMIKSETNTKIIV 173

Query: 204 GCNGYVWVSAIDEN 217
           G NG +W+    EN
Sbjct: 174 GQNGLIWIDGEPEN 187

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

Picrophilus torridus (strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828) (taxid: 263820)

>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 = 67.8 bits (164), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 57/223 (25%), Positives = 111/223 (49%), Gaps = 30/223 (13%)

Query: 45  YMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVV 104
           Y  G GTF +   I ++V G+V+     + V  +   YI E+G+ V+G++  ++   WVV
Sbjct: 23  YKNGRGTFREGSRIYSTVIGLVDIKGNTIRVIPLEGPYIPEVGDNVIGKIVDVKFSSWVV 82

Query: 105 DTNSILESALHLTSVNLPGGEQRRRSVQDEEM------MREFLKEGDLISAEIHQISTEG 158
           D       A +L ++ +       +   DE++      +R+F   GD+I  ++  I+   
Sbjct: 83  DI-----GAPYLANLKI-------QDFTDEKIDLLRTDLRKFFDIGDIIYGKVKAITEVN 130

Query: 159 SLTLHTRSLKY--GKLGQGILLTVPPSLIRR------SKSHFCNLACGAQVILGCNGYVW 210
           ++ L T+ + +  G L  G ++ + PS + R      S  +        ++I+G NG++W
Sbjct: 131 NIDLTTKGMPFNGGPLKGGQIVKITPSRVPRVIGRGGSMINMIKKLTMTRIIVGQNGWIW 190

Query: 211 VSAIDENKSGGFIQNMEVVKLSDRETITR-LNNVIKALAESKV 252
           V+  +E      I+   ++K+ DRE+ T+ L + IK+L  S++
Sbjct: 191 VNGKNEALEKLAIE--AILKI-DRESHTKGLTDRIKSLLLSRL 230

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|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 = 66.6 bits (161), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 57/230 (24%), Positives = 108/230 (46%), Gaps = 44/230 (19%)

Query: 45  YMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVV 104
           Y  G GTF +   I ++V G+V+     + V  +   YI E+G+ V+G++  ++   W V
Sbjct: 23  YKNGRGTFKEGSRIYSTVIGLVDIKGNTIRVIPLEGPYIPEVGDNVLGKIVDVKFSSWTV 82

Query: 105 DTNSILESALHLTSVNLPGGEQRRRSVQDEEM------MREFLKEGDLISAEIHQISTEG 158
           D  S   + L +            +   DE++      +R+F   GD+I A++  I+   
Sbjct: 83  DIGSPYSATLKI------------QDYTDEKIDLLRTDLRKFFDIGDIIYAKVKGINEVN 130

Query: 159 SLTLHTRSLKY--GKLGQGILLTVPPSLIRR------SKSHFCNLACGAQVILGCNGYVW 210
           ++ L T+ + +  G L  G ++ +  S + R      S  +       +++I+G NG++W
Sbjct: 131 NIELTTKGMPFNGGPLRGGQIIKITSSKVPRVIGKGGSMINMIKKLTQSRIIVGQNGWIW 190

Query: 211 VSAIDENKSGGFIQNMEVVKLS-------DRETITR-LNNVIKALAESKV 252
           +S+          +N E+ KL+       +RE+ TR L + IK +  SK+
Sbjct: 191 ISS----------KNPELEKLAIEAILKIERESHTRGLTDRIKNMLLSKL 230

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	298
312373972	296	hypothetical protein AND_16688 [Anophele	0.956	0.962	0.555	2e-87
242013476	296	Exosome complex exonuclease RRP4, putati	0.949	0.956	0.564	1e-86
170065837	294	exosome complex exonuclease RRP4 [Culex	0.942	0.955	0.550	1e-86
91078208	296	PREDICTED: similar to AGAP011211-PA [Tri	0.956	0.962	0.546	3e-85
170065835	296	exosome complex exonuclease RRP4 [Culex	0.942	0.949	0.540	1e-84
170045026	296	exosome complex exonuclease RRP4 [Culex	0.942	0.949	0.540	1e-84
158287391	296	AGAP011211-PA [Anopheles gambiae str. PE	0.956	0.962	0.541	2e-84
195026059	300	GH20673 [Drosophila grimshawi] gi|193902	0.956	0.95	0.568	5e-84
195455765	300	GK22923 [Drosophila willistoni] gi|19417	0.953	0.946	0.563	2e-83
125809363	298	GA17783 [Drosophila pseudoobscura pseudo	0.942	0.942	0.565	2e-83

>gi|312373972|gb|EFR21633.1| hypothetical protein AND_16688 [Anopheles darlingi]

 Score =  328 bits (841), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 161/290 (55%), Positives = 216/290 (74%), Gaps = 5/290 (1%)

Query: 10  IEIMLASDRID-PLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEK 68
           ++I LA+DR+D PL+   +    + TPGE V   +G+M GHGT+ +D+ IK+SV GV+ +
Sbjct: 5   VKIGLAADRVDIPLLNTEDKNRRLFTPGEIVTSQQGFMRGHGTYMEDDSIKSSVAGVMVQ 64

Query: 69  VNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRR 128
           VN+L++V+A+  RY+GEIG+VVV RVT +Q ++W VDTNS L+S L L+SVNLPGGE RR
Sbjct: 65  VNKLITVKALKGRYVGEIGDVVVARVTEVQEKRWKVDTNSRLDSVLLLSSVNLPGGELRR 124

Query: 129 RSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRS 188
           R  +DE+ MR++L+EGDLISAE+  + ++G L+LHTRSLKYGKL QGIL+ V PSLIRR 
Sbjct: 125 RGAEDEKQMRKYLQEGDLISAEVQNVHSDGVLSLHTRSLKYGKLAQGILVKVFPSLIRRR 184

Query: 189 KSHFCNLACGAQVILGCNGYVWVSAI---DENKSGGFIQNM-EVVKLSDRETITRLNNVI 244
           K+HF NL CGA +ILG NG++W+S I   +  +SGGF QN+ +VV   DRET+ RL N I
Sbjct: 185 KTHFHNLPCGASIILGNNGFIWISPILNSEGEESGGFTQNLGDVVTQEDRETVARLKNCI 244

Query: 245 KALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTL 294
             LA  K+ML+DTSI YAYEES+KY   +LL+PES   +   T Q+LQ L
Sbjct: 245 LGLAHCKMMLYDTSILYAYEESMKYEVQELLQPESMAIVAFNTQQRLQLL 294

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242013476|ref|XP_002427432.1| Exosome complex exonuclease RRP4, putative [Pediculus humanus corporis] gi|212511812|gb|EEB14694.1| Exosome complex exonuclease RRP4, putative [Pediculus humanus corporis]

 Score =  326 bits (835), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 162/287 (56%), Positives = 218/287 (75%), Gaps = 4/287 (1%)

Query: 12  IMLASDRIDPLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEE--IKASVGGVVEKV 69
           I L + RI+P+I+ +  T  I TPGET+    G+M GHGT+ DD+   +KASV G VE+V
Sbjct: 7   IRLGALRINPIIDNNNDTSNIYTPGETITCQTGFMRGHGTYVDDDNNALKASVAGSVEQV 66

Query: 70  NQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRR 129
           N+L+S+R + SRY GEIG+V+VGR+T +Q ++W VDTNS L+S L L+SVNLPGGE RRR
Sbjct: 67  NKLISMRPLKSRYFGEIGDVIVGRITEVQQKRWKVDTNSRLDSILSLSSVNLPGGELRRR 126

Query: 130 SVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSK 189
           SV+DE+MMR++L+EGDLISAEI  I ++G+L L+TRSLKYGKL QGILL V PSL+RRSK
Sbjct: 127 SVEDEQMMRKYLQEGDLISAEIQNILSDGTLQLYTRSLKYGKLSQGILLKVFPSLVRRSK 186

Query: 190 SHFCNLACGAQVILGCNGYVWVS-AIDENKSGGFIQNMEV-VKLSDRETITRLNNVIKAL 247
           +HF +L CGA +ILG NG++W++ A  E+K GGF Q+++  V  +DR  ++RL N I AL
Sbjct: 187 THFHSLPCGANIILGNNGFIWITPAALEDKKGGFTQDLKYKVSKTDRIVLSRLRNCILAL 246

Query: 248 AESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTL 294
           A SK+ L+DTS+ YAYEES KY+  +LL PE  LD+ + T  +LQ +
Sbjct: 247 ANSKMPLYDTSVMYAYEESQKYTVSELLAPEPMLDVAVLTTLRLQMI 293

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170065837|ref|XP_001868042.1| exosome complex exonuclease RRP4 [Culex quinquefasciatus] gi|167862584|gb|EDS25967.1| exosome complex exonuclease RRP4 [Culex quinquefasciatus]

 Score =  325 bits (834), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 157/285 (55%), Positives = 212/285 (74%), Gaps = 4/285 (1%)

Query: 12  IMLASDRIDPLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQ 71
           I LASDR++P +   +    + TPGE +   +G+M GHGT+ +DE+IK+SV GV+ +VN+
Sbjct: 7   IKLASDRVNPSLLSGDSNPRLFTPGEVITSQQGFMRGHGTYMEDEDIKSSVAGVMVQVNK 66

Query: 72  LVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSV 131
           L++V+A+  RY+GEIG+VVV RVT +Q ++W VDTNS L+S L L+SVNLPGGE RRR V
Sbjct: 67  LITVKALKGRYVGEIGDVVVARVTDVQQKRWKVDTNSRLDSILLLSSVNLPGGELRRRGV 126

Query: 132 QDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSH 191
           +DE+ MR++L+EGDLISAE+  + ++G L+LHTRSLKYGKLGQGIL+ V PSLI+R K+H
Sbjct: 127 EDEQQMRKYLQEGDLISAEVQNVHSDGVLSLHTRSLKYGKLGQGILVKVFPSLIKRRKTH 186

Query: 192 FCNLACGAQVILGCNGYVWVSAI---DENKSGGFIQNM-EVVKLSDRETITRLNNVIKAL 247
           F NL CGA +ILG NG++W+S +   +    GGF QN+ E V   DRE I+RL N I AL
Sbjct: 187 FHNLPCGASIILGNNGFIWISPVVNTEGEDGGGFTQNLDEAVSKQDREVISRLRNSILAL 246

Query: 248 AESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQ 292
           A  K++L+DTSI YAYEESLKY  ++LL  E+  D+   T  KL+
Sbjct: 247 AHCKMLLYDTSILYAYEESLKYDVHELLHQEAMFDIAFLTQHKLR 291

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91078208|ref|XP_968880.1| PREDICTED: similar to AGAP011211-PA [Tribolium castaneum] gi|270002359|gb|EEZ98806.1| hypothetical protein TcasGA2_TC001377 [Tribolium castaneum]

 Score =  320 bits (821), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 158/289 (54%), Positives = 212/289 (73%), Gaps = 4/289 (1%)

Query: 10  IEIMLASDRIDPLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKV 69
           I I LA+ RI+P I ++     I TPG+ +     +M GHGT+ ++  +K+SV GV E+V
Sbjct: 5   IHIRLAAHRINPSIAVNRRVPKIFTPGQVITEQNEFMRGHGTYEEEGFLKSSVAGVKEQV 64

Query: 70  NQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRR 129
           N L+S+R + SRY GE+G+VVVGRVT +Q ++W VDTNS L+S L L+SVNLPGGE RRR
Sbjct: 65  NNLISIRPLKSRYNGEVGDVVVGRVTEVQQKRWKVDTNSRLDSVLLLSSVNLPGGELRRR 124

Query: 130 SVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSK 189
           S +DE MMR++L+EGDLISAE+  + ++GSL+LHTRSLKYGKL QGIL+ V PSLI+RSK
Sbjct: 125 SAEDEHMMRQYLQEGDLISAEVQSVYSDGSLSLHTRSLKYGKLSQGILVKVFPSLIKRSK 184

Query: 190 SHFCNLACGAQVILGCNGYVWVSAI---DENKSGGFIQNME-VVKLSDRETITRLNNVIK 245
           +HF N   GA +ILG NG++W+       E+ +GGF+QN+E VV   +RETI RL N I 
Sbjct: 185 THFHNFYVGASIILGNNGFIWIYPTVSNAEDNAGGFVQNLEQVVSRPERETIGRLRNCIL 244

Query: 246 ALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTL 294
           AL +SK+ML+DTSI YA+EES KYS  +LL PE+ +D+ + T  +L  L
Sbjct: 245 ALIQSKMMLYDTSILYAFEESQKYSVAELLIPEAMVDVAILTQDRLSML 293

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170065835|ref|XP_001868041.1| exosome complex exonuclease RRP4 [Culex quinquefasciatus] gi|167862583|gb|EDS25966.1| exosome complex exonuclease RRP4 [Culex quinquefasciatus]

 Score =  318 bits (816), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 154/285 (54%), Positives = 209/285 (73%), Gaps = 4/285 (1%)

Query: 12  IMLASDRIDPLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQ 71
           I   SDR++P +   +    + TPGE +   +G+M GHGT+ +DE+IK+SV GV+ +VN+
Sbjct: 9   ITRKSDRVNPSLLSGDSNPRLFTPGEVITSQQGFMRGHGTYMEDEDIKSSVAGVMVQVNK 68

Query: 72  LVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSV 131
           L++V+A+  RY+GEIG+VVV RVT +Q ++W VDTNS L+S L L+SVNLPGGE RRR V
Sbjct: 69  LITVKALKGRYVGEIGDVVVARVTDVQQKRWKVDTNSRLDSILLLSSVNLPGGELRRRGV 128

Query: 132 QDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSH 191
           +DE+ MR++L+EGDLISAE+  + ++G L+LHTRSLKYGKLGQGIL+ V PSLI+R K+H
Sbjct: 129 EDEQQMRKYLQEGDLISAEVQNVHSDGVLSLHTRSLKYGKLGQGILVKVFPSLIKRRKTH 188

Query: 192 FCNLACGAQVILGCNGYVWVSAI---DENKSGGFIQNM-EVVKLSDRETITRLNNVIKAL 247
           F NL CGA +ILG NG++W+S +   +    GGF QN+ E V   DRE I+RL N I AL
Sbjct: 189 FHNLPCGASIILGNNGFIWISPVVNTEGEDGGGFTQNLDEAVSKQDREVISRLRNCILAL 248

Query: 248 AESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQ 292
           A  K++L+DTSI YAYEESLKY  ++LL   +  D+   T  KL+
Sbjct: 249 AHCKMLLYDTSILYAYEESLKYDVHELLHQGAMFDIAFLTQHKLR 293

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170045026|ref|XP_001850125.1| exosome complex exonuclease RRP4 [Culex quinquefasciatus] gi|167868077|gb|EDS31460.1| exosome complex exonuclease RRP4 [Culex quinquefasciatus]

 Score =  318 bits (816), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 154/285 (54%), Positives = 209/285 (73%), Gaps = 4/285 (1%)

Query: 12  IMLASDRIDPLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQ 71
           I   SDR++P +   +    + TPGE +   +G+M GHGT+ +DE+IK+SV GV+ +VN+
Sbjct: 9   ITRKSDRVNPSLLSGDSNPRLFTPGEVITSQQGFMRGHGTYMEDEDIKSSVAGVMVQVNK 68

Query: 72  LVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSV 131
           L++V+A+  RY+GEIG+VVV RVT +Q ++W VDTNS L+S L L+SVNLPGGE RRR V
Sbjct: 69  LITVKALKGRYVGEIGDVVVARVTDVQQKRWKVDTNSRLDSILLLSSVNLPGGELRRRGV 128

Query: 132 QDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSH 191
           +DE+ MR++L+EGDLISAE+  + ++G L+LHTRSLKYGKLGQGIL+ V PSLI+R K+H
Sbjct: 129 EDEQQMRKYLQEGDLISAEVQNVHSDGVLSLHTRSLKYGKLGQGILVKVFPSLIKRRKTH 188

Query: 192 FCNLACGAQVILGCNGYVWVSAI---DENKSGGFIQNM-EVVKLSDRETITRLNNVIKAL 247
           F NL CGA +ILG NG++W+S +   +    GGF QN+ E V   DRE I+RL N I AL
Sbjct: 189 FHNLPCGASIILGNNGFIWISPVVNAEGEDGGGFTQNLDEAVSKQDREVISRLRNCILAL 248

Query: 248 AESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQ 292
           A  K++L+DTSI YAYEESLKY  ++LL   +  D+   T  KL+
Sbjct: 249 AHCKMLLYDTSILYAYEESLKYDVHELLHQGAMFDIAFLTQHKLR 293

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158287391|ref|XP_309432.3| AGAP011211-PA [Anopheles gambiae str. PEST] gi|157019628|gb|EAA05284.3| AGAP011211-PA [Anopheles gambiae str. PEST]

 Score =  318 bits (814), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 157/290 (54%), Positives = 212/290 (73%), Gaps = 5/290 (1%)

Query: 10  IEIMLASDRID-PLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEK 68
           + I LA DR++ PLI     +  + TPGE V   +G+M GHGT+ +D+ IK+SV GV+ +
Sbjct: 5   VSIRLACDRVNIPLISDESKSQRLFTPGEVVTSQQGFMRGHGTYMEDDTIKSSVAGVMVQ 64

Query: 69  VNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRR 128
           VN+L++V+A+  RY+GEIG+VVV RVT +Q ++W VDTNS L+S L L+SVNLPGGE RR
Sbjct: 65  VNKLITVKALKGRYVGEIGDVVVARVTEVQEKRWKVDTNSRLDSMLLLSSVNLPGGELRR 124

Query: 129 RSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRS 188
           R V+DE+ MR++L+EGDLISAE+  + ++G+L+LHTRSLKYGKL QGIL+ V PSLI+R 
Sbjct: 125 RGVEDEKQMRKYLQEGDLISAEVQNVHSDGTLSLHTRSLKYGKLAQGILVKVFPSLIQRR 184

Query: 189 KSHFCNLACGAQVILGCNGYVWVSAI---DENKSGGFIQNM-EVVKLSDRETITRLNNVI 244
           K+HF NL CGA +ILG NG++W+S +   +  + GGF QN+ +VV   DR+TI RL N I
Sbjct: 185 KTHFHNLPCGASIILGNNGFIWISPMMNSEGGEGGGFTQNLDDVVTKEDRQTIARLRNCI 244

Query: 245 KALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTL 294
            ALA  K+ML+DTSI YAYEES KY   +LL  E   D+   T  +L+ L
Sbjct: 245 LALAHCKMMLYDTSILYAYEESQKYEVSELLHQECMTDIAFLTQHRLRVL 294

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195026059|ref|XP_001986172.1| GH20673 [Drosophila grimshawi] gi|193902172|gb|EDW01039.1| GH20673 [Drosophila grimshawi]

 Score =  317 bits (812), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 166/292 (56%), Positives = 208/292 (71%), Gaps = 7/292 (2%)

Query: 14  LASDRID--PLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQ 71
           LA DR+D   L E  E    I TPGE +    G+M GHGTF +DE+IKASV GV++KVN+
Sbjct: 9   LAIDRVDWNALAENQEQLPRIYTPGEVLMPEAGFMRGHGTFVEDEDIKASVAGVIQKVNK 68

Query: 72  LVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSV 131
           L+SVR + SRY+GEIG+VVV RV  +  ++W VDTNS L+S L L+SVNLPGGE RRRS 
Sbjct: 69  LISVRPLKSRYVGEIGDVVVARVLEVGQKRWRVDTNSRLDSVLLLSSVNLPGGELRRRSA 128

Query: 132 QDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSH 191
           +DE+MMR +L EGDLISAE+  +  E +L+L+TRSLKYGKL QGIL+ V P+L++R K H
Sbjct: 129 EDEQMMRRYLDEGDLISAEVQNVFEESTLSLYTRSLKYGKLSQGILVKVFPALVKRRKMH 188

Query: 192 FCNLACGAQVILGCNGYVWVSAI----DENKSGGFIQNM-EVVKLSDRETITRLNNVIKA 246
           F NLACGA VILG NGY+W+S       E   GGF QN+ EVV  ++RE I RL N I A
Sbjct: 189 FHNLACGASVILGNNGYIWISPTKSDEQEGGEGGFAQNLSEVVPRNEREIIARLRNCILA 248

Query: 247 LAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTLGLAD 298
           LA+ K+MLFDTSIQYAYEESLKY   +LL+     D+   T  +L+ + L D
Sbjct: 249 LAKCKLMLFDTSIQYAYEESLKYEPRELLQQHVIFDIGEQTQARLRDVDLLD 300

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195455765|ref|XP_002074857.1| GK22923 [Drosophila willistoni] gi|194170942|gb|EDW85843.1| GK22923 [Drosophila willistoni]

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 164/291 (56%), Positives = 207/291 (71%), Gaps = 7/291 (2%)

Query: 12  IMLASDRID--PLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKV 69
           I LA DR+D   L E  +    I TPGE +    GYM GHGTF ++E IKASV GV+EKV
Sbjct: 7   IGLALDRVDWNDLAEHQDRLPRIYTPGEILMPEAGYMRGHGTFVEEENIKASVAGVIEKV 66

Query: 70  NQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRR 129
           N+L+SVR + SRY+GEIG+VVV RV  +Q ++W VDTNS L+S L L+SVNLPGGE RRR
Sbjct: 67  NKLISVRPLKSRYVGEIGDVVVARVIDVQQKRWRVDTNSRLDSVLLLSSVNLPGGELRRR 126

Query: 130 SVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSK 189
           S +DE+MMR +L EGDLISAE+  I  EG+L+L+TRSLKYGKL QGIL+ V P+L++R K
Sbjct: 127 SAEDEQMMRRYLDEGDLISAEVQNIFEEGTLSLYTRSLKYGKLSQGILVKVFPALVKRRK 186

Query: 190 SHFCNLACGAQVILGCNGYVWVSAI----DENKSGGFIQNM-EVVKLSDRETITRLNNVI 244
            HF NL CGA +ILG NGY+W++       E   GGF QN+ EVV   +RE I RL N I
Sbjct: 187 MHFHNLPCGASIILGNNGYIWIAPTKAENQEGGEGGFAQNLSEVVPRPEREVIARLRNCI 246

Query: 245 KALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTLG 295
            ALA+ K+ML+DTSIQYA++ESLKY  Y+LL+     D+   T  +L+  G
Sbjct: 247 LALAKCKLMLYDTSIQYAFDESLKYEAYELLQQNVIHDIGEQTQARLRDAG 297

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|125809363|ref|XP_001361091.1| GA17783 [Drosophila pseudoobscura pseudoobscura] gi|195154659|ref|XP_002018239.1| GL17601 [Drosophila persimilis] gi|54636264|gb|EAL25667.1| GA17783 [Drosophila pseudoobscura pseudoobscura] gi|194114035|gb|EDW36078.1| GL17601 [Drosophila persimilis]

 Score =  315 bits (806), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 163/288 (56%), Positives = 206/288 (71%), Gaps = 7/288 (2%)

Query: 12  IMLASDRID--PLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKV 69
           I LA DR+D   L E  +    + TPGE V    G+M GHGTF +DE IKASV GV+EKV
Sbjct: 7   IELALDRVDWCALAERQDVLPRVYTPGEVVMPEAGFMRGHGTFVEDENIKASVAGVIEKV 66

Query: 70  NQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRR 129
           N+L+SVR + SRY+GEIG+VVV RV  +Q ++W VDTNS L+S L L+SVNLPGGE RRR
Sbjct: 67  NKLISVRPLKSRYVGEIGDVVVARVIEVQQKRWRVDTNSRLDSILLLSSVNLPGGELRRR 126

Query: 130 SVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSK 189
           S +DE+MMR +L EGDLISAE+  I  EG+L+L+TRSLKYGKL QG+L+ V P+L++R K
Sbjct: 127 SAEDEQMMRRYLDEGDLISAEVQNIFEEGTLSLYTRSLKYGKLSQGVLVKVFPALVKRRK 186

Query: 190 SHFCNLACGAQVILGCNGYVWVSAI----DENKSGGFIQNM-EVVKLSDRETITRLNNVI 244
            HF NL CGA VILG NGY+W+S       E   GGF QN+ E V  ++RE I RL N I
Sbjct: 187 MHFHNLPCGASVILGNNGYIWISPPKSQDQEGGEGGFAQNLGEAVPRNEREVIARLRNCI 246

Query: 245 KALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQ 292
            ALA+ K+ML+DTSIQYAY+ESLKY  ++LL+     D+   T  +L+
Sbjct: 247 LALAKCKLMLYDTSIQYAYDESLKYEAHELLQQNVIYDIGEQTQARLR 294

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	298
FB|FBgn0034879	298	Rrp4 "Rrp4" [Drosophila melano	0.942	0.942	0.538	3.2e-72
ZFIN|ZDB-GENE-050417-27	295	exosc2 "exosome component 2" [	0.872	0.881	0.528	2.3e-71
UNIPROTKB|F1NGC4	294	EXOSC2 "Uncharacterized protei	0.882	0.894	0.526	2.1e-70
UNIPROTKB|Q2KID0	293	EXOSC2 "Exosome complex compon	0.942	0.959	0.498	4.9e-69
MGI|MGI:2385133	293	Exosc2 "exosome component 2" [	0.872	0.887	0.513	1.7e-68
UNIPROTKB|Q13868	293	EXOSC2 "Exosome complex compon	0.956	0.972	0.486	2.1e-68
UNIPROTKB|J9NXW2	293	EXOSC2 "Uncharacterized protei	0.872	0.887	0.501	2.4e-67
UNIPROTKB|Q5ZHN8	254	EXOSC2 "Uncharacterized protei	0.835	0.980	0.535	4e-67
UNIPROTKB|F1S0X6	299	EXOSC2 "Uncharacterized protei	0.872	0.869	0.501	1.1e-66
UNIPROTKB|E2QU26	296	EXOSC2 "Uncharacterized protei	0.872	0.878	0.496	5.8e-66

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

 Score = 730 (262.0 bits), Expect = 3.2e-72, P = 3.2e-72
 Identities = 155/288 (53%), Positives = 199/288 (69%)

Query:    12 IMLASDRID--PLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKV 69
             I LA DR+D   L    E    + TPGE +    G+M GHGTF +DE IK+SV GV++KV
Sbjct:     7 IDLALDRVDWRDLAAQTEEQPRVYTPGEVLMPEAGFMRGHGTFVEDENIKSSVAGVIQKV 66

Query:    70 NQLVSVRAMNSRYXXXXXXXXXXRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRR 129
             N+L+SVR + SRY          RV+ +Q ++W VDTNS L+S L L+SVNLPGGE RRR
Sbjct:    67 NKLISVRPLKSRYVGEIGDVVVARVSEVQQKRWRVDTNSRLDSILLLSSVNLPGGELRRR 126

Query:   130 SVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSK 189
             S +DE+MMR +L EGDLISAE+  I  EGSL+L+TRSLKYGKL QGIL+ V P+L++R K
Sbjct:   127 SAEDEQMMRRYLDEGDLISAEVQNIFEEGSLSLYTRSLKYGKLSQGILVKVFPALVKRRK 186

Query:   190 SHFCNLACGAQVILGCNGYVWVSAI----DENKSGGFIQNM-EVVKLSDRETITRLNNVI 244
              HF NL CGA VILG NGY+W+S      +E   GGF QN+ E V  +DRE I RL N I
Sbjct:   187 MHFHNLPCGASVILGNNGYIWISPTKGQEEEGGEGGFAQNLNEHVPRADREVIARLRNSI 246

Query:   245 KALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQ 292
              ALA+ K+M++DTSIQYAYEESL+Y  ++LL+  +  D+   T  +L+
Sbjct:   247 LALAKCKLMIYDTSIQYAYEESLRYEAHELLQQNAIYDIGQQTQGRLR 294

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

ZFIN|ZDB-GENE-050417-27 exosc2 "exosome component 2" [Danio rerio (taxid:7955)]

 Score = 722 (259.2 bits), Expect = 2.3e-71, P = 2.3e-71
 Identities = 139/263 (52%), Positives = 192/263 (73%)

Query:    32 ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYXXXXXXXXX 91
             ++ PG+ +    G+M GHGT+ D++ + ASV G VE+VN+L+ V+ + +RY         
Sbjct:    28 LVVPGDVITSDTGFMRGHGTYMDEDRLTASVAGQVERVNKLICVKPLKTRYNGEVGDVVV 87

Query:    92 XRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
              R+T +Q ++W V+TNS L+S L L++VNLPGGE RRRS QDE  MR++L+EGDLISAE+
Sbjct:    88 GRITEVQQKRWKVETNSRLDSVLLLSAVNLPGGELRRRSTQDELAMRDYLQEGDLISAEV 147

Query:   152 HQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWV 211
               I ++G+L+LHTRSLKYGKLGQG+L+ V PSL++R K+HF NL CGA +ILG NGYVW+
Sbjct:   148 QSIFSDGALSLHTRSLKYGKLGQGVLVYVSPSLVKRQKTHFHNLPCGASLILGNNGYVWL 207

Query:   212 S---AIDENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLK 268
             S   A+ E ++GGF  +ME V LSDRE ++RL N + ALA  KV+LFDTS+ Y YE SL+
Sbjct:   208 SPTPALQEEQAGGFYTSMEPVSLSDREVVSRLRNCLLALANQKVLLFDTSVLYCYEASLQ 267

Query:   269 YSTYDLLKPESKLDLVLCTAQKL 291
             +   D+LKPE   ++VL T Q+L
Sbjct:   268 HQIKDILKPEIMEEIVLETRQRL 290

GO:0003723 "RNA binding" evidence=IEA

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

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

 Score = 713 (256.0 bits), Expect = 2.1e-70, P = 2.1e-70
 Identities = 140/266 (52%), Positives = 189/266 (71%)

Query:    32 ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYXXXXXXXXX 91
             ++ PG+T+    GYM GHGT+ D+E++ ASV G VE+VN+LV V  + +RY         
Sbjct:    27 LVVPGDTITTDTGYMRGHGTYVDEEKLVASVAGAVERVNKLVCVTPLKTRYNGEVGDIVV 86

Query:    92 XRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
              R+T +Q ++W V+TNS L+S L L+S+NLPGGE RRRS +DE  MR++L+EGDLISAE+
Sbjct:    87 GRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRDYLQEGDLISAEV 146

Query:   152 HQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWV 211
               + ++G+++LHTRSLKYGKLGQG+L+ V PSL++R K+HF +L CGA VILG NG++W+
Sbjct:   147 QSVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWI 206

Query:   212 SAIDENK---SGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLK 268
                 E K   +GGF  N+E V LSDRE I+RL N + AL   K+MLFDTSI Y YE SL 
Sbjct:   207 YPTPEQKDEEAGGFTTNLEPVPLSDREVISRLRNCVVALVTQKLMLFDTSILYCYEASLP 266

Query:   269 YSTYDLLKPESKLDLVLCTAQKLQTL 294
             +   D+LKPE   ++VL T QKL  L
Sbjct:   267 HQIKDILKPEVMEEIVLETRQKLLDL 292

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

 Score = 700 (251.5 bits), Expect = 4.9e-69, P = 4.9e-69
 Identities = 143/287 (49%), Positives = 200/287 (69%)

Query:    10 IEIMLASDRIDPLIEI--HEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVE 67
             +E+ L   R  PL E    E    ++ PG+T+    G+M GHGT+  +E++ ASV G VE
Sbjct:     3 LEMRLPVAR-KPLSESLGRESKKHLVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVE 61

Query:    68 KVNQLVSVRAMNSRYXXXXXXXXXXRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQR 127
             +VN+L+ V+A+ +RY          R+T +Q ++W V+TNS L+S L L+S+NLPGGE R
Sbjct:    62 RVNKLICVKALKTRYNGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELR 121

Query:   128 RRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRR 187
             RRS +DE  MR FL+EGDLISAE+  + ++G+++LHTRSLKYGKLGQG+L+ V PSL++R
Sbjct:   122 RRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKR 181

Query:   188 SKSHFCNLACGAQVILGCNGYVWVSAIDENK---SGGFIQNMEVVKLSDRETITRLNNVI 244
              K+HF +L CGA VILG NG++WV    E+K   +GGFI N+E V L+DRE I+RL N I
Sbjct:   182 QKTHFHDLPCGASVILGNNGFIWVYPTPEHKEDDAGGFIANLEPVSLTDREVISRLRNCI 241

Query:   245 KALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKL 291
              +LA  ++ML+DTSI Y YE SL +   D+LKPE   ++V+ T Q+L
Sbjct:   242 VSLATQRMMLYDTSILYCYEASLPHQIKDILKPEIMEEIVMETRQRL 288

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

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

 Score = 695 (249.7 bits), Expect = 1.7e-68, P = 1.7e-68
 Identities = 135/263 (51%), Positives = 189/263 (71%)

Query:    32 ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYXXXXXXXXX 91
             ++ PG+T+    G+M GHGT+  +E++ ASV G VE+VN+L+ V+A+ +RY         
Sbjct:    26 LVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKALKTRYNGEVGDIVV 85

Query:    92 XRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
              R+T +Q ++W V+TNS L+S L L+S+NLPGGE RRRS +DE  MR FL+EGDLISAE+
Sbjct:    86 GRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEV 145

Query:   152 HQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWV 211
               + ++G+++LHTRSLKYGKLGQG+L+ V PSL++R K+HF +L CGA VILG NG++W+
Sbjct:   146 QAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWI 205

Query:   212 SAIDENK---SGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLK 268
                 E+K   +GGFI N+E V LSDRE I+RL N +  L   ++MLFDTSI Y YE SL 
Sbjct:   206 YPTPEHKDEDAGGFIANLEPVALSDREVISRLRNCVVLLVTQRMMLFDTSILYCYEASLA 265

Query:   269 YSTYDLLKPESKLDLVLCTAQKL 291
             +   D+LKPE   +++L T Q+L
Sbjct:   266 HQIKDILKPEVMEEIMLETRQRL 288

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

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

 Score = 694 (249.4 bits), Expect = 2.1e-68, P = 2.1e-68
 Identities = 143/294 (48%), Positives = 202/294 (68%)

Query:     1 MAEEKDKPVIEIMLASDRIDPLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKA 60
             MA E   PV    L S+R+    + H     ++ PG+T+    G+M GHGT+  +E++ A
Sbjct:     1 MAMEMRLPVARKPL-SERLGRDTKKH-----LVVPGDTITTDTGFMRGHGTYMGEEKLIA 54

Query:    61 SVGGVVEKVNQLVSVRAMNSRYXXXXXXXXXXRVTGLQSQKWVVDTNSILESALHLTSVN 120
             SV G VE+VN+L+ V+A+ +RY          R+T +Q ++W V+TNS L+S L L+S+N
Sbjct:    55 SVAGSVERVNKLICVKALKTRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMN 114

Query:   121 LPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTV 180
             LPGGE RRRS +DE  MR FL+EGDLISAE+  + ++G+++LHTRSLKYGKLGQG+L+ V
Sbjct:   115 LPGGELRRRSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQV 174

Query:   181 PPSLIRRSKSHFCNLACGAQVILGCNGYVWVSAIDENK---SGGFIQNMEVVKLSDRETI 237
              PSL++R K+HF +L CGA VILG NG++W+    E+K   +GGFI N+E V L+DRE I
Sbjct:   175 SPSLVKRQKTHFHDLPCGASVILGNNGFIWIYPTPEHKEEEAGGFIANLEPVSLADREVI 234

Query:   238 TRLNNVIKALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKL 291
             +RL N I +L   ++ML+DTSI Y YE SL +   D+LKPE   ++V+ T Q+L
Sbjct:   235 SRLRNCIISLVTQRMMLYDTSILYCYEASLPHQIKDILKPEIMEEIVMETRQRL 288

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

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

 Score = 684 (245.8 bits), Expect = 2.4e-67, P = 2.4e-67
 Identities = 132/263 (50%), Positives = 189/263 (71%)

Query:    32 ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYXXXXXXXXX 91
             ++ PG+T+    G+M GHGT+  +E++ ASV G VE+VN+L+ V+A+ +RY         
Sbjct:    26 LVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKALKTRYNGEVGDIVV 85

Query:    92 XRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
              R+T +Q ++W V+TNS L+S L L+S+NLPGGE RRRS +DE  MR FL+EGDLISAE+
Sbjct:    86 GRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEV 145

Query:   152 HQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWV 211
               + ++G+++LHTRSLKYGKLGQG+L+ V PSL++R K+HF +L CGA VILG NG++W+
Sbjct:   146 QAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWI 205

Query:   212 SAIDENK---SGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLK 268
                 E+K   +GGF  ++E + L+DRE I+RL N I +L   ++ML+DTSI Y YE SL 
Sbjct:   206 YPTPEHKEEDTGGFTAHLEPISLADREVISRLRNCIVSLVTQRMMLYDTSILYCYEASLP 265

Query:   269 YSTYDLLKPESKLDLVLCTAQKL 291
             +   DLLKPE   ++V+ T Q+L
Sbjct:   266 HQIKDLLKPEIMEEVVMETRQRL 288

GO:0003723 "RNA binding" evidence=IEA

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

UNIPROTKB|Q5ZHN8 EXOSC2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 682 (245.1 bits), Expect = 4.0e-67, P = 4.0e-67
 Identities = 135/252 (53%), Positives = 180/252 (71%)

Query:    46 MTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYXXXXXXXXXXRVTGLQSQKWVVD 105
             M GHGT+ D+E++ ASV G VE+VN+LV V  + +RY          R+T +Q ++W V+
Sbjct:     1 MRGHGTYVDEEKLVASVAGAVERVNKLVCVTPLKTRYNGEVGDIVVGRITEVQQKRWKVE 60

Query:   106 TNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTR 165
             TNS L+S L L+S+NLPGGE RRRS +DE  MR++L+EGDLISAE+  + ++G+++LHTR
Sbjct:    61 TNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRDYLQEGDLISAEVQSVFSDGAVSLHTR 120

Query:   166 SLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWVSAIDENK---SGGF 222
             SLKYGKLGQG+L+ V PSL++R K+HF +L CGA VILG NG++W+    E K   +GGF
Sbjct:   121 SLKYGKLGQGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWIYPTPEQKDEEAGGF 180

Query:   223 IQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLD 282
               N+E V LSDRE I+RL N + AL   K+MLFDTSI Y YE SL +   D+LKPE   +
Sbjct:   181 TTNLEPVPLSDREVISRLRNCVVALVTQKLMLFDTSILYCYEASLPHQIKDILKPEVMEE 240

Query:   283 LVLCTAQKLQTL 294
             +VL T QKL  L
Sbjct:   241 IVLETRQKLLDL 252

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|F1S0X6 EXOSC2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 678 (243.7 bits), Expect = 1.1e-66, P = 1.1e-66
 Identities = 135/269 (50%), Positives = 190/269 (70%)

Query:    32 ILTPGETVEYLEGYMT------GHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYXXX 85
             ++ PG+T+    G+M       GHGT+  +E++ ASV G VE+VN+L+ V+A+ +RY   
Sbjct:    26 LVVPGDTITTDTGFMRSSCCHRGHGTYMGEEKLIASVAGSVERVNKLICVKALKTRYNGE 85

Query:    86 XXXXXXXRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGD 145
                    R+T +Q ++W V+TNS L+S L L+S+NLPGGE RRRS +DE  MR FL+EGD
Sbjct:    86 VGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGD 145

Query:   146 LISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGC 205
             LISAE+  + ++G+++LHTRSLKYGKLGQG+L+ V PSL++R K+HF +L CGA VILG 
Sbjct:   146 LISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQKTHFHDLPCGASVILGN 205

Query:   206 NGYVWVSAIDENK---SGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYA 262
             NG++W+    E+K   +GGFI N+E V L+DRE I+RL N I +L   +VML+DTSI Y 
Sbjct:   206 NGFIWIYPTPEHKEEEAGGFIANLEPVSLADREVISRLRNCIVSLVTQRVMLYDTSILYC 265

Query:   263 YEESLKYSTYDLLKPESKLDLVLCTAQKL 291
             YE SL +   D+LKPE   ++V+ T Q+L
Sbjct:   266 YEASLPHQIKDILKPEVMEEIVMETRQRL 294

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

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

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

 Score = 671 (241.3 bits), Expect = 5.8e-66, P = 5.8e-66
 Identities = 132/266 (49%), Positives = 189/266 (71%)

Query:    32 ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYXXXXXXXXX 91
             ++ PG+T+    G+M GHGT+  +E++ ASV G VE+VN+L+ V+A+ +RY         
Sbjct:    26 LVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKALKTRYNGEVGDIVV 85

Query:    92 XRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLIS--- 148
              R+T +Q ++W V+TNS L+S L L+S+NLPGGE RRRS +DE  MR FL+EGDLIS   
Sbjct:    86 GRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISSGQ 145

Query:   149 AEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGY 208
             AE+  + ++G+++LHTRSLKYGKLGQG+L+ V PSL++R K+HF +L CGA VILG NG+
Sbjct:   146 AEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGF 205

Query:   209 VWVSAIDENK---SGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEE 265
             +W+    E+K   +GGF  ++E + L+DRE I+RL N I +L   ++ML+DTSI Y YE 
Sbjct:   206 IWIYPTPEHKEEDTGGFTAHLEPISLADREVISRLRNCIVSLVTQRMMLYDTSILYCYEA 265

Query:   266 SLKYSTYDLLKPESKLDLVLCTAQKL 291
             SL +   DLLKPE   ++V+ T Q+L
Sbjct:   266 SLPHQIKDLLKPEIMEEVVMETRQRL 291

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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q2KID0	EXOS2_BOVIN	No assigned EC number	0.5399	0.8724	0.8873	yes	N/A
Q13868	EXOS2_HUMAN	No assigned EC number	0.5361	0.8724	0.8873	yes	N/A
P38792	RRP4_YEAST	No assigned EC number	0.3770	0.8859	0.7353	yes	N/A
Q8VBV3	EXOS2_MOUSE	No assigned EC number	0.5361	0.8724	0.8873	yes	N/A
Q09704	RRP4_SCHPO	No assigned EC number	0.3971	0.8557	0.7750	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	298
COG1097	239	COG1097, RRP4, RNA-binding protein Rrp4 and relate	2e-45
cd05789	86	cd05789, S1_Rrp4, S1_Rrp4: Rrp4 S1-like RNA-bindin	2e-32
PRK04163	235	PRK04163, PRK04163, exosome complex RNA-binding pr	1e-20
cd04454	82	cd04454, S1_Rrp4_like, S1_Rrp4_like: Rrp4-like, S1	5e-16
PRK09521	189	PRK09521, PRK09521, exosome complex RNA-binding pr	2e-08
COG1096	188	COG1096, COG1096, Predicted RNA-binding protein (c	3e-07
pfam14382	39	pfam14382, ECR1_N, Exosome complex exonuclease RRP	2e-06

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

 Score =  153 bits (389), Expect = 2e-45
 Identities = 58/191 (30%), Positives = 98/191 (51%), Gaps = 12/191 (6%)

Query: 32  ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVV 91
           I+ PG+ V     Y  GHGT+ +  +I +SV G+++   +LV V  +  RYI E+G+VV+
Sbjct: 10  IVLPGDLVLAEGSYKLGHGTYFEGGKIYSSVVGLLDVKGKLVRVIPLEGRYIPEVGDVVI 69

Query: 92  GRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
           G++  +    W VD  S   + L L+         RR+    E+ +R FL  GDL+ A++
Sbjct: 70  GKIIEVGPSGWKVDIGSPYPALLSLSDF------LRRKFENAEKDLRPFLNVGDLVYAKV 123

Query: 152 HQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLA------CGAQVILGC 205
             +  +G + L  +    GKL  G ++ +PPS + R      ++        G ++I+G 
Sbjct: 124 VDVDRDGEVELTLKDEGLGKLKNGQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ 183

Query: 206 NGYVWVSAIDE 216
           NG +WV   +E
Sbjct: 184 NGRIWVDGENE 194

Length = 239

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

 Score =  114 bits (288), Expect = 2e-32
 Identities = 48/92 (52%), Positives = 66/92 (71%), Gaps = 6/92 (6%)

Query: 81  RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREF 140
           RYI E+G+VV+GRVT +  ++W VD NS  ++ L L+ VNLP      R+ +DE  MR +
Sbjct: 1   RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLP------RTDEDELNMRSY 54

Query: 141 LKEGDLISAEIHQISTEGSLTLHTRSLKYGKL 172
           L EGDLI AE+  + ++GS++LHTRSLKYGKL
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 = 88.0 bits (219), Expect = 1e-20
 Identities = 62/231 (26%), Positives = 114/231 (49%), Gaps = 25/231 (10%)

Query: 32  ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVV 91
           I+ PG+ +     +  G GT+ ++ +I ++V G+V+  +  V V  +  +YI ++G++V+
Sbjct: 10  IVVPGDLLAE-GEFKAGRGTYKENGKIYSTVVGLVDIKDDKVRVIPLEGKYIPKVGDLVI 68

Query: 92  GRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
           G+VT +    W VD NS  ++ L ++ V   G    R    +   +R++L  GD I A++
Sbjct: 69  GKVTDVTFSGWEVDINSPYKAYLPVSEV--LG----RPVNVEGTDLRKYLDIGDYIIAKV 122

Query: 152 HQI--STEGSLTLHTRSLKYGKLGQGILLTVPPS----LIRRSKSHFCNL--ACGAQVIL 203
             +  + +  LTL  + L  GK+  G ++ + P     +I +  S    L    G  +I+
Sbjct: 123 KDVDRTRDVVLTLKGKGL--GKIEGGTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIV 180

Query: 204 GCNGYVWVSAIDENKSGGFIQNM--EVVKLSDRETITR-LNNVIKALAESK 251
           G NG +W+   DE       + +  E +K  +RE  T  L + IK   E +
Sbjct: 181 GQNGRIWIKGPDEED-----EEIAIEAIKKIEREAHTSGLTDRIKEFLEEE 226

Length = 235

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

 Score = 71.4 bits (175), Expect = 5e-16
 Identities = 25/92 (27%), Positives = 48/92 (52%), Gaps = 10/92 (10%)

Query: 81  RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREF 140
           RY+ ++G++V+G VT + S+ W VD  S   + L  +S              D++ +R+ 
Sbjct: 1   RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEK----------DKKEIRKS 50

Query: 141 LKEGDLISAEIHQISTEGSLTLHTRSLKYGKL 172
           L+ GDLI A++  +  + ++ L T   + 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 = 52.7 bits (127), Expect = 2e-08
 Identities = 38/142 (26%), Positives = 67/142 (47%), Gaps = 11/142 (7%)

Query: 35  PGETVEYLEGYMTGHGTFPDDEEIKASVGGVVE--KVNQLVSVRAMNSR-YIGEIGEVVV 91
           PG+ +  +E Y+ G GT+ D+ E+ ASV G V    +N+ +SV        + + G++V 
Sbjct: 10  PGDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVY 69

Query: 92  GRVTGLQSQKWVVDTNSILESALHLTSVNLPGG---EQRRRSVQDEEMMREFLKEGDLIS 148
           GRV  ++ Q+ +V   SI E +    + +        Q      +   + +  K GD++ 
Sbjct: 70  GRVVDVKEQRALVRIVSI-EGSERELATSKLAYIHISQVSDGYVES--LTDAFKIGDIVR 126

Query: 149 AEIHQISTEGSLTLHTRSLKYG 170
           A++  IS    L L T+    G
Sbjct: 127 AKV--ISYTDPLQLSTKGKDLG 146

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 = 49.6 bits (119), Expect = 3e-07
 Identities = 34/142 (23%), Positives = 69/142 (48%), Gaps = 5/142 (3%)

Query: 32  ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVV--EKVNQLVSVR-AMNSRYIGEIGE 88
            + PG+ +  +E ++ G GT+ +  EI+A+  GVV  +  N+++SV+    +  + + G+
Sbjct: 7   FVLPGDVLAVIEEFLPGEGTYEEGGEIRAAATGVVRRDDKNRVISVKPGKKTPPLPKGGD 66

Query: 89  VVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLIS 148
           +V GRVT ++ Q+ +V    +      L +         +      E + +  + GD++ 
Sbjct: 67  IVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVR 126

Query: 149 AEIHQISTEGSLTLHTRSLKYG 170
           A +  IST   + L T+    G
Sbjct: 127 ARV--ISTGDPIQLSTKGNDLG 146

Length = 188

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

 Score = 43.5 bits (104), Expect = 2e-06
 Identities = 20/39 (51%), Positives = 24/39 (61%)

Query: 32 ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVN 70
          I+ PGE +     YM GHGT+ +D  I ASV GVV  VN
Sbjct: 1  IVVPGERLGTASEYMPGHGTYVEDGNIYASVAGVVSIVN 39

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	298
KOG3013|consensus	301		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|consensus	230		100.0
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	99.96
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	99.94
cd05790	86	S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai	99.85
KOG3409|consensus	193		99.83
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-	99.76
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	99.65
PF10447	82	EXOSC1: Exosome component EXOSC1/CSL4; InterPro: I	99.41
PF14382	39	ECR1_N: Exosome complex exonuclease RRP4 N-termina	99.3
COG1098	129	VacB Predicted RNA binding protein (contains ribos	99.05
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	99.01
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	98.94
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	98.83
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	98.83
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	98.81
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	98.79
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	98.79
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	98.76
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	98.74
PRK08582	139	hypothetical protein; Provisional	98.72
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	98.69
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	98.65
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	98.64
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	98.59
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	98.59
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	98.59
PRK07252	120	hypothetical protein; Provisional	98.57
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	98.57
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	98.56
PRK08059	123	general stress protein 13; Validated	98.56
PRK05807	136	hypothetical protein; Provisional	98.55
PRK03987	262	translation initiation factor IF-2 subunit alpha;	98.55
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.52
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	98.51
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	98.5
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	98.48
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	98.47
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.43
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	98.43
PHA02945	88	interferon resistance protein; Provisional	98.43
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	98.42
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	98.42
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	98.4
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	98.39
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	98.38
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	98.31
PRK07400	318	30S ribosomal protein S1; Reviewed	98.31
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	98.3
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	98.24
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	98.19
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	98.18
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	98.17
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	98.16
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.12
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.09
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	98.08
PRK07400	318	30S ribosomal protein S1; Reviewed	98.05
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	98.04
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	98.02
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	98.01
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	98.0
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	97.98
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	97.95
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	97.92
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	97.9
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	97.89
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.83
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	97.78
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	97.76
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	97.75
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	97.73
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.73
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	97.71
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	97.69
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	97.65
COG2183	780	Tex Transcriptional accessory protein [Transcripti	97.64
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	97.61
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	97.57
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.52
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	97.41
TIGR01953	341	NusA transcription termination factor NusA. This m	97.37
PRK12327	362	nusA transcription elongation factor NusA; Provisi	97.35
PRK09202	470	nusA transcription elongation factor NusA; Validat	97.35
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	96.88
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.36
PRK12328	374	nusA transcription elongation factor NusA; Provisi	96.28
PRK12329	449	nusA transcription elongation factor NusA; Provisi	96.11
KOG1070|consensus	1710		96.06
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	95.75
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	94.99
PF13509	61	S1_2: S1 domain; PDB: 3GO5_A.	94.85
PRK11712	489	ribonuclease G; Provisional	94.64
PRK11642	813	exoribonuclease R; Provisional	94.39
KOG2916|consensus	304		94.02
PRK10811	1068	rne ribonuclease E; Reviewed	93.97
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	93.58
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	92.85
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	92.57
KOG1856|consensus	1299		92.35
COG2088	95	SpoVG Uncharacterized protein, involved in the reg	88.91
KOG1070|consensus	1710		88.12
PF10246	104	MRP-S35: Mitochondrial ribosomal protein MRP-S35;	85.41
KOG3298|consensus	170		85.38
KOG1067|consensus	760		85.26
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	84.77
CHL00121	86	rpl27 ribosomal protein L27; Reviewed	83.01
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	81.94
PF04026	84	SpoVG: SpoVG; InterPro: IPR007170 This is a stage	80.84

>KOG3013|consensus

Probab=100.00  E-value=7.9e-81  Score=566.44  Aligned_cols=271  Identities=51%  Similarity=0.808  Sum_probs=259.3

Q ss_pred             ccccCCCeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEeCcEEEEEecCccccccCCCEEEEEEEEEecceEEE
Q psy10116         25 IHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVV  104 (298)
Q Consensus        25 ~~~~~~~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~nk~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~V  104 (298)
                      .......+|+||+.++.++.||+|||||+.|+.|+||++|.++++||+++|+|++.||.|++||+|+|||++|++++|+|
T Consensus        24 ~~~~~~~ivtPG~~V~~d~~fmRGHGTy~~d~~i~ssvaG~v~rvNkLi~V~plk~rY~pEvGDvVVgRV~eVq~KRWkv  103 (301)
T KOG3013|consen   24 DTSDHSTIVTPGELVTDDPGFMRGHGTYVRDGEIYSSVAGVVQRVNKLISVKPLKSRYAPEVGDVVVGRVIEVQQKRWKV  103 (301)
T ss_pred             ccccCceeecCCccccCchhhhhcccceecCCeEEEeecchhhhhcceEEEeehhhhcCCccCCEEEEEeeeeecceeEE
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccCCCccCCCceEEEeCchh
Q psy10116        105 DTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSL  184 (298)
Q Consensus       105 DI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL~~G~lv~v~~~l  184 (298)
                      |+|+.++|+|++|++|+|||++|||+++||.+||+||++||+|.|+||+++.||+++||||+.+||||.+|++++|||+|
T Consensus       104 d~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs~sLhTRS~KYGKL~~G~lvkVpp~L  183 (301)
T KOG3013|consen  104 DLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHDGSLSLHTRSLKYGKLGQGILVKVPPAL  183 (301)
T ss_pred             ecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhccCCeEEEEecchhcccccCceEEEeCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccCcceeccccEEEEEeeCceEEEecCCCC-----CCCcccccc-ccCCHHHHHHHHHHHHHHHHHhhCCcccCHHH
Q psy10116        185 IRRSKSHFCNLACGAQVILGCNGYVWVSAIDEN-----KSGGFIQNM-EVVKLSDRETITRLNNVIKALAESKVMLFDTS  258 (298)
Q Consensus       185 i~r~~~~~~~l~~~~eiivG~NG~IWI~~~~~~-----~~~~~~~~~-~~i~~~~r~~i~rv~n~i~~l~~~~~~i~~~~  258 (298)
                      ++|+|+|||.++||+++|+|+|||||+.+.++.     ..++|++.+ +.+|.++|++|||++|||++|+.++++||+++
T Consensus       184 vkr~K~hfh~lp~g~~vIlG~NGyIWv~~s~~~~~ee~~~~~~~~~~~~~v~~~~R~~i~Rl~n~i~~La~~~~~i~~~s  263 (301)
T KOG3013|consen  184 VKRSKTHFHNLPGGVDVILGCNGYIWVGPSIKDQEEEESIGSYSSENDEHVSLNTRVNICRLANCIRALANCSIMITLTS  263 (301)
T ss_pred             hhhhhhhhccCCCCeEEEEecCceEEecCCCCcchhhhcccccccCcccCCCHHHHHHHHHHHHHHHHHHhcCeeeeHHH
Confidence            999999999999999999999999999997662     134566666 67999999999999999999999999999999


Q ss_pred             HHHHHHHHhCCCCcccCChhHHHHHHHHHHHHHHHcc
Q psy10116        259 IQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTLG  295 (298)
Q Consensus       259 i~~~~~~s~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  295 (298)
                      |+++||+|+.|+++||+.|++|+.+|+++++||.++.
T Consensus       264 I~~~ye~S~~~~i~ell~~~~~~~ia~~~~~rl~~~~  300 (301)
T KOG3013|consen  264 ITYCYEASLPYEIHELLEQEFMEVIAMEIAARLRTKR  300 (301)
T ss_pred             HHHHHHhcCcchHHHHhhhhHHHHHHHHHHHHHHhhc
Confidence            9999999999999999999999999999999998763

>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=6.4e-50  Score=363.36  Aligned_cols=216  Identities=29%  Similarity=0.481  Sum_probs=190.9

Q ss_pred             cCCCeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEeCcEEEEEecCccccccCCCEEEEEEEEEecceEEEEeC
Q psy10116         28 FTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTN  107 (298)
Q Consensus        28 ~~~~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~nk~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~  107 (298)
                      ..+++|+|||.+...+++++|||||.+++++|||++|.++.+++.+.|+|++++|.|++||+|||+|+++..++|+|||+
T Consensus         6 ~~~~iV~PGd~vl~~~~~~~G~Gty~~~~~iyssv~G~~~~~~~~v~VIpl~g~YiP~~gD~VIG~I~~v~~~~W~VDI~   85 (239)
T COG1097           6 SMRKIVLPGDLVLAEGSYKLGHGTYFEGGKIYSSVVGLLDVKGKLVRVIPLEGRYIPEVGDVVIGKIIEVGPSGWKVDIG   85 (239)
T ss_pred             cccceecCCCccCCCCCEecCCCcEecCCEEEEEEEeEEEEeCCEEEEEeCCCcccCCCCCEEEEEEEEEcccceEEEcC
Confidence            35789999998888889999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccCCCccCCCceEEEeCchhhcc
Q psy10116        108 SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRR  187 (298)
Q Consensus       108 s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL~~G~lv~v~~~li~r  187 (298)
                      |++.|.||+|++      +||+.+.++.+||++|++||+|+|||++++.+++++||||+.+||+|++|+++.++|+++.|
T Consensus        86 sp~~A~L~ls~~------~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~~~L~~k~~~~GkL~~G~iv~i~p~kVpR  159 (239)
T COG1097          86 SPYPALLSLSDF------LRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGEVELTLKDEGLGKLKNGQIVKIPPSKVPR  159 (239)
T ss_pred             CccceEeehhhh------hcccccccccccccccccCCEEEEEEEEccCCCceEEEeecCCCccccCCEEEEEchhhcce
Confidence            999999999997      48988999999999999999999999999999999999999999999999999999999988


Q ss_pred             ccCcceec------cccEEEEEeeCceEEEecCCCCC-CCcc----cccc-ccCCHHHHHHHHHHHHHHHHHhhC
Q psy10116        188 SKSHFCNL------ACGAQVILGCNGYVWVSAIDENK-SGGF----IQNM-EVVKLSDRETITRLNNVIKALAES  250 (298)
Q Consensus       188 ~~~~~~~l------~~~~eiivG~NG~IWI~~~~~~~-~~~~----~~~~-~~i~~~~r~~i~rv~n~i~~l~~~  250 (298)
                      ..+|...+      .++|+|++|+|||||+++++... +...    .-.. .+++--+++.++++.+++ .+++.
T Consensus       160 vig~~~sm~~~l~~~~~~~I~VG~NG~IWV~~~~~~~e~~~~~aI~~ie~ea~~~gltdr~~~~i~~~~-~~~~~  233 (239)
T COG1097         160 VIGKKGSMLNMLKEKTGCEIIVGQNGRIWVDGENESLEELAIEAIRKIEREAHTSGLTDRIKEFLKKLL-RLKES  233 (239)
T ss_pred             EecCCCcHHHHhhhhcCeEEEEecCCEEEecCCCcchHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHH-hcccc
Confidence            87766653      38999999999999999998732 1111    1112 246667778888877777 44443

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=100.00  E-value=7.6e-44  Score=326.30  Aligned_cols=200  Identities=26%  Similarity=0.468  Sum_probs=177.9

Q ss_pred             cCCCeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEeCcEEEEEecCccccccCCCEEEEEEEEEecceEEEEeC
Q psy10116         28 FTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTN  107 (298)
Q Consensus        28 ~~~~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~nk~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~  107 (298)
                      .++.+|+|||.|+. ++|++|+|||.++|+++||++|.+...++.++|+|++++|.|++||+|+|+|+++.+++|+|||+
T Consensus         6 ~~~~~V~PGd~l~~-~~~~~G~Gty~~~g~i~As~~G~~~~~~~~i~V~p~~~~y~P~vGDiViG~V~~i~~~~~~vdI~   84 (235)
T PRK04163          6 EDRKIVVPGDLLAE-GEFKAGRGTYKENGKIYSTVVGLVDIKDDKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEVDIN   84 (235)
T ss_pred             eCCcEECCCCCcCc-CCeecCCceEEeCCEEEEEEeEEEEEECCEEEEEECCCcccCCCCCEEEEEEEEEeCceEEEEeC
Confidence            35689999999974 68999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccCCCccCCCceEEEeCchhhcc
Q psy10116        108 SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRR  187 (298)
Q Consensus       108 s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL~~G~lv~v~~~li~r  187 (298)
                      ++++|+||++++.      +++.+.|+.+|+++|++||+|+|||++++.++.+.|||++.+||+|.+|++++|+|.+++|
T Consensus        85 ~~~~g~L~~s~i~------~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~k~~~lG~L~~G~~~~V~~~~i~~  158 (235)
T PRK04163         85 SPYKAYLPVSEVL------GRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGKGLGKIEGGTIVEIKPVKVPR  158 (235)
T ss_pred             CCceeEEEHHHcC------CCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEEcCCCCCccCCCEEEEECHHHHHh
Confidence            9999999999984      3445568899999999999999999999988889999999999999999999999999988


Q ss_pred             ccC----cceec--cccEEEEEeeCceEEEecCCCCCCCccccccccCCHHHHHHHHHHHHHHHHHhhCCc
Q psy10116        188 SKS----HFCNL--ACGAQVILGCNGYVWVSAIDENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKV  252 (298)
Q Consensus       188 ~~~----~~~~l--~~~~eiivG~NG~IWI~~~~~~~~~~~~~~~~~i~~~~r~~i~rv~n~i~~l~~~~~  252 (298)
                      +..    ++..|  .++|+|++|+||+|||++++.                  +.+....++|+.+++..-
T Consensus       159 lig~~g~~i~~l~~~~~~~I~ig~NG~VwI~~~~~------------------~~~~~a~~~I~~~e~~~~  211 (235)
T PRK04163        159 VIGKKGSMINMLKEETGCDIIVGQNGRIWIKGPDE------------------EDEEIAIEAIKKIEREAH  211 (235)
T ss_pred             hcCCCChhHhhhhhhhCcEEEEcCCcEEEEeeCCH------------------HHHHHHHHHHHHHHhhhh
Confidence            843    33334  489999999999999999875                  455566777777665543

>KOG1004|consensus

Probab=100.00  E-value=1.4e-32  Score=244.80  Aligned_cols=175  Identities=24%  Similarity=0.365  Sum_probs=156.0

Q ss_pred             CeEecCCccCCC--CCeeccCCeEecCCeEEEEEeeEEEEe--Cc----EEEEEecCccccccCCCEEEEEEEEEecceE
Q psy10116         31 PILTPGETVEYL--EGYMTGHGTFPDDEEIKASVGGVVEKV--NQ----LVSVRAMNSRYIGEIGEVVVGRVTGLQSQKW  102 (298)
Q Consensus        31 ~iV~PGD~I~~~--~~~~~G~Gty~~~g~i~Asv~G~v~~~--nk----~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~  102 (298)
                      ...+|||.+...  .+..+|+|.+..++.+..+.+|.+...  ++    ..||...++||+|.+||.|||+|++..++.|
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            467899988763  357799999999999999999977753  33    5799999999999999999999999999999


Q ss_pred             EEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEe-----ccCCCccCCCceE
Q psy10116        103 VVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHT-----RSLKYGKLGQGIL  177 (298)
Q Consensus       103 ~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lst-----r~~~lGkL~~G~l  177 (298)
                      +|||+++..|.|+..+  |||+++|+         ||.|++||+|||+|...++|.+++|++     |..+||+|++|++
T Consensus        82 kVDigg~~~a~L~~la--Fe~AtkrN---------rPnl~vGdliyakv~~a~~~~Epel~Cids~graaGfG~LkdG~i  150 (230)
T KOG1004|consen   82 KVDIGGSEPASLSYLA--FEGATKRN---------RPNLQVGDLIYAKVVDANKDMEPELTCIDSTGRAAGFGVLKDGMI  150 (230)
T ss_pred             EEecCCCCeeeeeecc--ccCccccC---------CCccccccEEEEEEEecCCCcCcceEEEcccCcccCcccccCceE
Confidence            9999999999998666  58999888         799999999999999999999999996     5569999999999


Q ss_pred             EEeCchhhccccCcceec------cccEEEEEeeCceEEEecCCC
Q psy10116        178 LTVPPSLIRRSKSHFCNL------ACGAQVILGCNGYVWVSAIDE  216 (298)
Q Consensus       178 v~v~~~li~r~~~~~~~l------~~~~eiivG~NG~IWI~~~~~  216 (298)
                      ++++++++|++..+-+.+      .++|||++|+||||||++...
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            999999999998866653      389999999999999999875

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=99.96  E-value=3.2e-28  Score=216.08  Aligned_cols=137  Identities=26%  Similarity=0.403  Sum_probs=122.9

Q ss_pred             CCCeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEe--CcEEEEEecCc-cccccCCCEEEEEEEEEecceEEEE
Q psy10116         29 TDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKV--NQLVSVRAMNS-RYIGEIGEVVVGRVTGLQSQKWVVD  105 (298)
Q Consensus        29 ~~~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~--nk~v~V~p~~~-rY~P~vGDiVIG~V~~V~~~~~~VD  105 (298)
                      ++++|+|||.|++.++|++|+|||+++|+|+||++|.++..  ++.++|.|.+. .|.|++||+|+|+|+++.+++|+||
T Consensus         4 ~~~~V~PGe~l~~~~e~~~G~Gty~~~~~i~as~~G~~~id~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~   83 (189)
T PRK09521          4 QGDLVLPGDYLAVIEEYLPGEGTYEDNGEVYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVYGRVVDVKEQRALVR   83 (189)
T ss_pred             cCCEECCCCccccccceEcCCCEEeeCCEEEEEeeEEEEEcCCCCEEEEecCcCCCCCCCCCCEEEEEEEEEcCCeEEEE
Confidence            56899999999998899999999999999999999999964  66899999987 9999999999999999999999999


Q ss_pred             eC----------CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccCCCccCCCc
Q psy10116        106 TN----------SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQG  175 (298)
Q Consensus       106 I~----------s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL~~G  175 (298)
                      |.          ++.+|+||.++++          +....+|+++|++||+|.|+|++++  +.+.||+++.+||+    
T Consensus        84 I~~~~~~~~~l~~~~~G~l~~s~i~----------~~~~~~~~~~~~~GD~V~akV~~i~--~~i~LS~k~~~lGv----  147 (189)
T PRK09521         84 IVSIEGSERELATSKLAYIHISQVS----------DGYVESLTDAFKIGDIVRAKVISYT--DPLQLSTKGKDLGV----  147 (189)
T ss_pred             EEEecccccccCCCceeeEEhhHcC----------hhhhhhHHhccCCCCEEEEEEEecC--CcEEEEEecCCceE----
Confidence            95          3678999999874          2234578999999999999999997  78999999999999    


Q ss_pred             eEEEeCc
Q psy10116        176 ILLTVPP  182 (298)
Q Consensus       176 ~lv~v~~  182 (298)
                       +++.|+
T Consensus       148 -v~a~~~  153 (189)
T PRK09521        148 -IYAMCS  153 (189)
T ss_pred             -EEEEcc
Confidence             677664

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

Probab=99.94  E-value=5.3e-26  Score=200.11  Aligned_cols=157  Identities=22%  Similarity=0.405  Sum_probs=137.8

Q ss_pred             cCCCeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEE--eCcEEEEEecCc-cccccCCCEEEEEEEEEecceEEE
Q psy10116         28 FTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEK--VNQLVSVRAMNS-RYIGEIGEVVVGRVTGLQSQKWVV  104 (298)
Q Consensus        28 ~~~~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~--~nk~v~V~p~~~-rY~P~vGDiVIG~V~~V~~~~~~V  104 (298)
                      ..+.+|+|||.|+..|+|++|.|||+++|+|+|+.+|.+..  +|..++|+|.+. ..+|+.||+|+|+|+++..+.+.|
T Consensus         3 ~~g~~v~PGd~~a~~EE~~~G~gt~~~~g~i~Aa~~G~~~~d~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~~~~a~V   82 (188)
T COG1096           3 KDGTFVLPGDVLAVIEEFLPGEGTYEEGGEIRAAATGVVRRDDKNRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRALV   82 (188)
T ss_pred             ccCcEEcCcceeeeeeeeecCCCeEeECCEEEEeecccEEEcccceEEEeccCCCCCCCCCCCCEEEEEEeeccceEEEE
Confidence            35789999999999999999999999999999999999997  578999999998 899999999999999999999999


Q ss_pred             Ee----------CCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccCCCccCCC
Q psy10116        105 DT----------NSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQ  174 (298)
Q Consensus       105 DI----------~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL~~  174 (298)
                      .|          .++..|.+|+|++.          +....+.+++|++||+|+|+|++..  ..+.|||+.+.||+   
T Consensus        83 ~i~~ve~~~r~~~~~~~~~ihvs~~~----------~~~~~~~~d~f~~GDivrA~Vis~~--~~~~Lst~~~dlGV---  147 (188)
T COG1096          83 RIVGVEGKERELATSGAADIHVSQVR----------DGYVEKLSDAFRIGDIVRARVISTG--DPIQLSTKGNDLGV---  147 (188)
T ss_pred             EEEEEecccccCCCCceeeEEEEecc----------cccccccccccccccEEEEEEEecC--CCeEEEecCCcceE---
Confidence            88          23578999999983          3344567899999999999999986  67999999999999   


Q ss_pred             ceEEEeCchhhccccCcceeccccEEEEEeeCceEEEecCCC
Q psy10116        175 GILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWVSAIDE  216 (298)
Q Consensus       175 G~lv~v~~~li~r~~~~~~~l~~~~eiivG~NG~IWI~~~~~  216 (298)
                        +++.|+             .|+..+..  -|+..-|+.|.
T Consensus       148 --I~A~Cs-------------rC~~~L~~--~~~~l~Cp~Cg  172 (188)
T COG1096         148 --IYARCS-------------RCRAPLVK--KGNMLKCPNCG  172 (188)
T ss_pred             --EEEEcc-------------CCCcceEE--cCcEEECCCCC
Confidence              899884             57777776  56677777775

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

Probab=99.85  E-value=3.2e-21  Score=151.84  Aligned_cols=75  Identities=24%  Similarity=0.337  Sum_probs=68.9

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcE
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSL  160 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~  160 (298)
                      ||+|++||+|||+|+++..+.|+|||++++.|+||.++|  ||+++|         +|++|++||+|+|||++++.++++
T Consensus         1 rY~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f--~gatk~---------~rp~L~~GDlV~ArV~~~~~~~~~   69 (86)
T cd05790           1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAF--EGATKR---------NRPNLNVGDLVYARVVKANRDMEP   69 (86)
T ss_pred             CCcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHc--cccccc---------ccccCCCCCEEEEEEEecCCCCCe
Confidence            699999999999999999999999999999999998774  788654         389999999999999999999999


Q ss_pred             EEEecc
Q psy10116        161 TLHTRS  166 (298)
Q Consensus       161 ~Lstr~  166 (298)
                      +|++..
T Consensus        70 eLtc~~   75 (86)
T cd05790          70 ELSCVD   75 (86)
T ss_pred             EEEEeC
Confidence            999854

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".

>KOG3409|consensus

Probab=99.83  E-value=7.6e-20  Score=159.11  Aligned_cols=136  Identities=24%  Similarity=0.342  Sum_probs=114.5

Q ss_pred             CCCeEecCCccCCCC-CeeccCCeEecCCeEEEEEeeEEEEe--CcEEEEEec----CccccccCCCEEEEEEEEEecce
Q psy10116         29 TDPILTPGETVEYLE-GYMTGHGTFPDDEEIKASVGGVVEKV--NQLVSVRAM----NSRYIGEIGEVVVGRVTGLQSQK  101 (298)
Q Consensus        29 ~~~iV~PGD~I~~~~-~~~~G~Gty~~~g~i~Asv~G~v~~~--nk~v~V~p~----~~rY~P~vGDiVIG~V~~V~~~~  101 (298)
                      ...+++|||.++..+ ++..|.|||..++.|+||.+|+..+.  ++.+.|...    ...-+|.+||||..+|..++..+
T Consensus         4 a~~~~lpG~~~c~~e~~~~~g~Gtye~~~yI~aS~ag~~~~~~~~~~~~v~~~~~~~~~~~LP~~G~IVtarV~~i~~rf   83 (193)
T KOG3409|consen    4 AETLVLPGEVVCRAEGEYRMGEGTYERNGYIFASVAGVNFRDNLVQKIEVVSVEKQLFNELLPFVGAIVTARVSRINLRF   83 (193)
T ss_pred             ceEEEcccceeeecccccccccceeecCCeEEeccccceeecCCccceeeeeecccchhhcCCccCcEEEEEEEeeccce
Confidence            346899999999864 48899999999999999999955443  344444333    34688999999999999999999


Q ss_pred             EEEEe--------CCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccCCCccC
Q psy10116        102 WVVDT--------NSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKL  172 (298)
Q Consensus       102 ~~VDI--------~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL  172 (298)
                      ++|||        ...+.|+|+..++        |.++.|..+...+|+|||+|+|+|++.+...++.|||.++.||++
T Consensus        84 Akv~I~~V~d~~lk~~Frglirkqdv--------R~tEkdrv~v~ksFrPgDiVlAkVis~~~~~~y~LTtAeneLGVV  154 (193)
T KOG3409|consen   84 AKVDILSVGDKPLKKSFRGLIRKQDV--------RATEKDRVKVYKSFRPGDIVLAKVISLGDGSNYLLTTAENELGVV  154 (193)
T ss_pred             eeEEEEEEcCEEhhhhhcceeehhhc--------cccccchhhhhhccCCCcEEEEEEeecCCCCcEEEEEecccceEE
Confidence            99999        3467888888777        678899999999999999999999997655679999999999993

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

Probab=99.81  E-value=8.6e-20  Score=145.10  Aligned_cols=83  Identities=20%  Similarity=0.374  Sum_probs=76.6

Q ss_pred             ccccCCCEEEEEEEEEecceEEEEe--------CCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEE
Q psy10116         82 YIGEIGEVVVGRVTGLQSQKWVVDT--------NSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQ  153 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~~~~~~VDI--------~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~s  153 (298)
                      |.|++||+|+|+|+++..++|.|||        ++++.|+||.+++        |.++.|+.+|+++|++||+|+|||++
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        8899999999997        34567788999999999999999999


Q ss_pred             eCCCCcEEEEeccCCCccC
Q psy10116        154 ISTEGSLTLHTRSLKYGKL  172 (298)
Q Consensus       154 v~~dg~~~Lstr~~~lGkL  172 (298)
                      ++....+.|||++++||++
T Consensus        74 ~~~~~~~~Lst~~~~lGVv   92 (92)
T cd05791          74 LGDASSYYLSTAENELGVV   92 (92)
T ss_pred             cCCCCCcEEEecCCCCccC
Confidence            9766789999999999984

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=99.76  E-value=6.4e-18  Score=130.23  Aligned_cols=82  Identities=30%  Similarity=0.490  Sum_probs=75.4

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcE
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSL  160 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~  160 (298)
                      +|.|++||+|+|+|+++.++.|+|||++..+|+||.++++.          .+..++++.|++||+|.|+|++++.++.+
T Consensus         1 ~y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~----------~~~~~~~~~~~~GD~i~~~V~~~~~~~~i   70 (82)
T cd04454           1 RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATE----------KDKKEIRKSLQPGDLILAKVISLGDDMNV   70 (82)
T ss_pred             CCCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccC----------cchHHHHhcCCCCCEEEEEEEEeCCCCCE
Confidence            69999999999999999999999999999999999999852          23567899999999999999999877889


Q ss_pred             EEEeccCCCccC
Q psy10116        161 TLHTRSLKYGKL  172 (298)
Q Consensus       161 ~Lstr~~~lGkL  172 (298)
                      .||+++.+||+|
T Consensus        71 ~LS~~~~~~Gvi   82 (82)
T cd04454          71 LLTTADNELGVI   82 (82)
T ss_pred             EEEECCCCCccC
Confidence            999999999985

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=99.65  E-value=1e-15  Score=118.61  Aligned_cols=86  Identities=55%  Similarity=0.903  Sum_probs=76.4

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcE
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSL  160 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~  160 (298)
                      +|.|++||+|.|+|+++.+++|+|+|++..+|+||++++..      .+++....++.+.|++||.|.|+|+++++++.+
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 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNL------PRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSV   74 (86)
T ss_pred             CCcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccC------CCCccchHHHHhhCCCCCEEEEEEEEECCCCCE
Confidence            69999999999999999999999999999999999999841      112334567889999999999999999878899


Q ss_pred             EEEeccCCCccC
Q psy10116        161 TLHTRSLKYGKL  172 (298)
Q Consensus       161 ~Lstr~~~lGkL  172 (298)
                      .||++..+||+|
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=99.41  E-value=4.2e-13  Score=104.94  Aligned_cols=64  Identities=20%  Similarity=0.437  Sum_probs=43.6

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeCC------------------CceeeEecccccCCCCcccccchhhhhhhhcccCCC
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTNS------------------ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEG  144 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~s------------------~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~G  144 (298)
                      +|++||+|+|+|+++++++++|+|-+                  ++.|+|+.+++        |.++.|+.+|.++|+||
T Consensus         1 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DV--------R~te~Dkv~~~~~FrpG   72 (82)
T PF10447_consen    1 LPKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDV--------RATEKDKVKMYDCFRPG   72 (82)
T ss_dssp             ---TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGG--------GT-SS----GGGT--SS
T ss_pred             CCCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeee--------cccccchhhHHhccCCC
Confidence            59999999999999999999999832                  45667776666        67889999999999999


Q ss_pred             CEEEEEEEEe
Q psy10116        145 DLISAEIHQI  154 (298)
Q Consensus       145 DlV~A~V~sv  154 (298)
                      |+|+|+|+|+
T Consensus        73 DIVrA~ViSl   82 (82)
T PF10447_consen   73 DIVRARVISL   82 (82)
T ss_dssp             SEEEEEEEEE
T ss_pred             CEEEEEEeeC
Confidence            9999999984

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=99.30  E-value=1.9e-12  Score=87.80  Aligned_cols=39  Identities=46%  Similarity=0.721  Sum_probs=35.1

Q ss_pred             eEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEeC
Q psy10116         32 ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVN   70 (298)
Q Consensus        32 iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~n   70 (298)
                      +|+|||.|+..++|++|+|||+++|+|+||++|.+++.|
T Consensus         1 iV~PG~~l~~~~e~~~G~GTY~~~g~I~asv~G~v~~~n   39 (39)
T PF14382_consen    1 IVVPGDRLGSSEEYMPGHGTYVRDGNIYASVAGTVKIDN   39 (39)
T ss_dssp             EE-TT-EEEETTTSEESTTEEEETTEEEESSSEEEEEET
T ss_pred             CCCCCCEeecCCCEecCCCEEEeCCEEEEEeeEEEEEcC
Confidence            699999999999999999999999999999999998765

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

Probab=99.05  E-value=4.3e-10  Score=93.74  Aligned_cols=76  Identities=18%  Similarity=0.335  Sum_probs=70.6

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEE
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTL  162 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~L  162 (298)
                      .+++||+|-|+|+++++.++||++....+|++|+|++.          +....++.++|++||.|.++|++++.+|.++|
T Consensus         2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa----------~~fVkdI~d~L~vG~eV~vKVl~ide~GKisL   71 (129)
T COG1098           2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIA----------DGFVKDIHDHLKVGQEVKVKVLDIDENGKISL   71 (129)
T ss_pred             CccccceEEEEEEeeEecceEEEecCCCcceEEehHhh----------hhhHHhHHHHhcCCCEEEEEEEeeccCCCcce
Confidence            36899999999999999999999998899999999994          66789999999999999999999999999999


Q ss_pred             EeccCC
Q psy10116        163 HTRSLK  168 (298)
Q Consensus       163 str~~~  168 (298)
                      |.|...
T Consensus        72 SIr~~~   77 (129)
T COG1098          72 SIRKLE   77 (129)
T ss_pred             ehHHhh
Confidence            998754

>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=99.01  E-value=1.7e-09  Score=81.76  Aligned_cols=70  Identities=21%  Similarity=0.170  Sum_probs=59.9

Q ss_pred             cCCCEEEEEEEEEec-ceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEE
Q psy10116         85 EIGEVVVGRVTGLQS-QKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLH  163 (298)
Q Consensus        85 ~vGDiVIG~V~~V~~-~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Ls  163 (298)
                      ++||+|.|+|+++.+ .+++|++....+|++|+|++.-          ....+..+.|++||.|.|+|.+++. +.+.||
T Consensus         2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~----------~~~~~~~~~~~~Gd~v~~kV~~~~~-~~i~LS   70 (72)
T cd05704           2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSD----------SYTENPLEGFKPGKIVRCCILSKKD-GKYQLS   70 (72)
T ss_pred             CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcC----------cccCCHHHhCCCCCEEEEEEEEecC-CEEEEE
Confidence            589999999999986 6999999999999999999851          1233456889999999999999975 889998


Q ss_pred             ec
Q psy10116        164 TR  165 (298)
Q Consensus       164 tr  165 (298)
                      +|
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=98.94  E-value=4.7e-09  Score=77.96  Aligned_cols=69  Identities=22%  Similarity=0.338  Sum_probs=58.0

Q ss_pred             CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCCcEEEEec
Q psy10116         87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEGSLTLHTR  165 (298)
Q Consensus        87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg~~~Lstr  165 (298)
                      ||+|.|+|+++.+++|+||+++..+|+||.+++..+          ...++.+.|++||.+.|+|.+++ .++.+.||.+
T Consensus         1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~----------~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~~   70 (70)
T cd05687           1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDD----------PIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR   70 (70)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCcc----------ccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEeC
Confidence            899999999999999999999899999999988421          12346788999999999999998 4466777753

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.

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

Probab=98.83  E-value=2.5e-08  Score=74.07  Aligned_cols=71  Identities=23%  Similarity=0.332  Sum_probs=60.0

Q ss_pred             CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcEEEEec
Q psy10116         87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSLTLHTR  165 (298)
Q Consensus        87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~~Lstr  165 (298)
                      ||+|.|+|+++.+++|+|++....+|++|.+++..          ....+..+.|++||.|.|+|.+++.. +.+.|+.+
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 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSR----------DRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK   70 (73)
T ss_pred             CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCC----------ccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEE
Confidence            89999999999999999999989999999998741          11234578899999999999999854 67899887


Q ss_pred             cC
Q psy10116        166 SL  167 (298)
Q Consensus       166 ~~  167 (298)
                      ..
T Consensus        71 ~~   72 (73)
T cd05691          71 AK   72 (73)
T ss_pred             Ec
Confidence            53

RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

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

Probab=98.83  E-value=2.6e-08  Score=74.74  Aligned_cols=72  Identities=19%  Similarity=0.276  Sum_probs=60.1

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCC--CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNS--ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSL  160 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s--~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~  160 (298)
                      |+.|++|.|+|+++...+|+|++..  ..+|++|.+++..          ....++.+.|++||.|.|+|.+++. .+.+
T Consensus         1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~----------~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i   70 (76)
T cd04452           1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSR----------RRIRSIRKLVKVGRKEVVKVIRVDKEKGYI   70 (76)
T ss_pred             CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCC----------cccCCHHHeeCCCCEEEEEEEEEECCCCEE
Confidence            6899999999999999999999974  3799999999741          1123457889999999999999985 4678


Q ss_pred             EEEec
Q psy10116        161 TLHTR  165 (298)
Q Consensus       161 ~Lstr  165 (298)
                      .|+++
T Consensus        71 ~ls~k   75 (76)
T cd04452          71 DLSKK   75 (76)
T ss_pred             EEEEc
Confidence            88876

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=98.81  E-value=3.4e-08  Score=71.70  Aligned_cols=69  Identities=26%  Similarity=0.472  Sum_probs=58.4

Q ss_pred             CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEec
Q psy10116         87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTR  165 (298)
Q Consensus        87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr  165 (298)
                      ||+|.|+|+++.+.+|+|+|+...+|+||.+++.  .   ++     ..+..+.|++||.|.++|.+++.++.+.||++
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-----VKDVKDVLKEGDKVKVKVLSIDARGRISLSIK   69 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcC--C---cc-----cCCHHHccCCCCEEEEEEEEECCCCcEEEEEC
Confidence            8999999999999999999999999999999873  1   11     12345789999999999999987778888874

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.

>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=98.79  E-value=4.7e-08  Score=73.13  Aligned_cols=71  Identities=18%  Similarity=0.306  Sum_probs=59.9

Q ss_pred             cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116         85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH  163 (298)
Q Consensus        85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls  163 (298)
                      ++|++|.|+|+++.+++++|++.+..+|++|++++.-          ....+..+.|++||.|.|+|.+++. .+.+.||
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----------DYSEALPYKFKKNDIVRACVLSVDVPNKKIALS   71 (73)
T ss_pred             CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccC----------ccccccccccCCCCEEEEEEEEEeCCCCEEEEE
Confidence            5899999999999999999999999999999998741          1122346889999999999999985 4678888


Q ss_pred             ec
Q psy10116        164 TR  165 (298)
Q Consensus       164 tr  165 (298)
                      +|
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.

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

Probab=98.79  E-value=3.5e-08  Score=73.76  Aligned_cols=72  Identities=19%  Similarity=0.308  Sum_probs=61.5

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcEEE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSLTL  162 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~~L  162 (298)
                      |++||+|-|+|+++.+++++||++...+|++|.+++...          ........|++||.|.|+|.+++.+ +.+.|
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----------RIDDPSEVYKIGQTVRVKVIKVDKEKGRIRL   71 (74)
T ss_dssp             SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSS----------EESSSHGTCETTCEEEEEEEEEETTTTEEEE
T ss_pred             CCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCc----------cccccccccCCCCEEEEEEEEEECCCCeEEE
Confidence            689999999999999999999999999999999998521          1234478999999999999999955 45888


Q ss_pred             Eec
Q psy10116        163 HTR  165 (298)
Q Consensus       163 str  165 (298)
                      |.|
T Consensus        72 S~k   74 (74)
T PF00575_consen   72 SLK   74 (74)
T ss_dssp             EST
T ss_pred             EEC
Confidence            865

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=98.76  E-value=3.8e-08  Score=75.04  Aligned_cols=72  Identities=19%  Similarity=0.347  Sum_probs=58.3

Q ss_pred             cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116         85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH  163 (298)
Q Consensus        85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls  163 (298)
                      ++||+|.|+|+++++.+++|+++...+|.+|+++++.     ++  -.+..++.+.|++||.|.|+|++++. ++.+.||
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 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTK-----YF--VSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS   74 (74)
T ss_pred             CCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccC-----cc--ccChhhHhcccCCCCEEEEEEEEEECCCCEEecC
Confidence            6899999999999999999999989999999999852     11  01123467899999999999999985 3556654

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=98.74  E-value=7.1e-08  Score=69.71  Aligned_cols=71  Identities=25%  Similarity=0.373  Sum_probs=59.3

Q ss_pred             cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcEEEE
Q psy10116         85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSLTLH  163 (298)
Q Consensus        85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~~Ls  163 (298)
                      ++|++|.|+|+++.+.+|+|+++....|++|.+++..+          ...+....|++||.|.|+|.+++.+ +.+.|+
T Consensus         1 ~~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~----------~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls   70 (72)
T smart00316        1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDK----------RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS   70 (72)
T ss_pred             CCCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCcc----------ccCCHHHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence            47999999999999999999999889999999987421          0233457799999999999999865 778887


Q ss_pred             ec
Q psy10116        164 TR  165 (298)
Q Consensus       164 tr  165 (298)
                      ++
T Consensus        71 ~~   72 (72)
T smart00316       71 LK   72 (72)
T ss_pred             eC
Confidence            64

>PRK08582 hypothetical protein; Provisional

Probab=98.72  E-value=8.2e-08  Score=81.92  Aligned_cols=75  Identities=21%  Similarity=0.340  Sum_probs=64.6

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLH  163 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Ls  163 (298)
                      .++|++|.|+|+++.+.+++|+|+...+|++|++++..          ....++.+.|++||.|.|+|++++.++.+.|+
T Consensus         3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~----------~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LS   72 (139)
T PRK08582          3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVAD----------NYVKDINDHLKVGDEVEVKVLNVEDDGKIGLS   72 (139)
T ss_pred             CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCc----------ccccccccccCCCCEEEEEEEEECCCCcEEEE
Confidence            47899999999999999999999999999999999841          11234568899999999999999877899999


Q ss_pred             eccCC
Q psy10116        164 TRSLK  168 (298)
Q Consensus       164 tr~~~  168 (298)
                      ++...
T Consensus        73 lk~~~   77 (139)
T PRK08582         73 IKKAK   77 (139)
T ss_pred             EEecc
Confidence            87654

>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=98.69  E-value=1.2e-07  Score=70.97  Aligned_cols=74  Identities=15%  Similarity=0.293  Sum_probs=61.0

Q ss_pred             cCCCEEEEEEEEEecceEEEEeCC-CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116         85 EIGEVVVGRVTGLQSQKWVVDTNS-ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL  162 (298)
Q Consensus        85 ~vGDiVIG~V~~V~~~~~~VDI~s-~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L  162 (298)
                      ++|++|.|+|+++.+.+|+|++.. ..+|++|.+++.. .    +     ..++.+.|++||.|.|+|.+++. .+.+.|
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 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISD-N----R-----VADASKLFRVGDKVRAKVLKIDAEKKRISL   70 (77)
T ss_pred             CCCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCC-C----c-----cCCHhHeecCCCEEEEEEEEEeCCCCEEEE
Confidence            469999999999999999999984 7899999998741 1    1     12356889999999999999985 578999


Q ss_pred             EeccCC
Q psy10116        163 HTRSLK  168 (298)
Q Consensus       163 str~~~  168 (298)
                      +.|...
T Consensus        71 s~k~~~   76 (77)
T cd05708          71 GLKASY   76 (77)
T ss_pred             EEEeec
Confidence            887653

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.

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

Probab=98.65  E-value=2.2e-07  Score=70.12  Aligned_cols=71  Identities=10%  Similarity=0.111  Sum_probs=58.7

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCC-CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNS-ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTL  162 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s-~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~L  162 (298)
                      |+.|+++.|+|+++.+.+++|++.. ..+|++|++++.-     .     ...+..+.|++||.|.++|.+++..+.+.|
T Consensus         1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~-----~-----~~~~~~~~~~~Gd~v~vkv~~vd~~~ki~l   70 (73)
T cd05686           1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSS-----C-----RVDDPSEVVDVGEKVWVKVIGREMKDKMKL   70 (73)
T ss_pred             CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCC-----C-----cccCHhhEECCCCEEEEEEEEECCCCcEEE
Confidence            6799999999999999999999954 3699999999841     1     123557889999999999999987667777


Q ss_pred             Ee
Q psy10116        163 HT  164 (298)
Q Consensus       163 st  164 (298)
                      |+
T Consensus        71 s~   72 (73)
T cd05686          71 SL   72 (73)
T ss_pred             Ee
Confidence            64

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.

>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=98.64  E-value=1.5e-07  Score=69.69  Aligned_cols=67  Identities=18%  Similarity=0.310  Sum_probs=55.8

Q ss_pred             CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116         87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH  163 (298)
Q Consensus        87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls  163 (298)
                      |++|.|+|+++.+++++|++....+|++|++++.          +....+..+.|++||.|.|+|.+++. .+.+.||
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 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELS----------DSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT   68 (68)
T ss_pred             CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCC----------chhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence            7999999999999999999998899999999874          11233557889999999999999985 4556553

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.

>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=98.59  E-value=3.3e-07  Score=67.84  Aligned_cols=69  Identities=12%  Similarity=0.170  Sum_probs=57.7

Q ss_pred             CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEEec
Q psy10116         87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLHTR  165 (298)
Q Consensus        87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Lstr  165 (298)
                      ||++.|+|+++.+.+++|++....+|++|.+++.-          ....+....|++||.|.++|.+++. .+.+.||.+
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 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSE----------AFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK   70 (70)
T ss_pred             CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcCh----------hhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEeC
Confidence            89999999999999999999878999999999841          1122346789999999999999985 567888864

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=98.59  E-value=1.4e-07  Score=87.77  Aligned_cols=78  Identities=26%  Similarity=0.401  Sum_probs=67.6

Q ss_pred             cCccccccCCCEEEEEEEEEecceEEEEeCC--CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC
Q psy10116         78 MNSRYIGEIGEVVVGRVTGLQSQKWVVDTNS--ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS  155 (298)
Q Consensus        78 ~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~s--~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~  155 (298)
                      +..+-.|++||+|+|+|.+|.+.+++|.+.-  ...|++|+|++.          ..+..++|+++++|..+.|+|++++
T Consensus         3 ~~~~~~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEva----------s~wVknIrd~vkegqkvV~kVlrVd   72 (269)
T COG1093           3 MKRREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVA----------SGWVKNIRDYVKEGQKVVAKVLRVD   72 (269)
T ss_pred             ccccCCCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHH----------HHHHHHHHHHhhcCCeEEEEEEEEc
Confidence            3456679999999999999999999999953  368999999994          4568999999999999999999999


Q ss_pred             C-CCcEEEEec
Q psy10116        156 T-EGSLTLHTR  165 (298)
Q Consensus       156 ~-dg~~~Lstr  165 (298)
                      + .|.+.||.|
T Consensus        73 ~~rg~IDLSlk   83 (269)
T COG1093          73 PKRGHIDLSLK   83 (269)
T ss_pred             CCCCeEeeehh
Confidence            4 577889864

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=98.59  E-value=1.7e-07  Score=89.95  Aligned_cols=75  Identities=13%  Similarity=0.244  Sum_probs=64.2

Q ss_pred             ccccCCCEEEEEEEEEecceEEEEeC--CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCC
Q psy10116         82 YIGEIGEVVVGRVTGLQSQKWVVDTN--SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEG  158 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~~~~~~VDI~--s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg  158 (298)
                      -.|++||+|.|+|+.+.+.+++|+|.  ...+|++|+|+++      +++    ..++++.|++||.|.++|++++ ..+
T Consensus        13 ~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS------~~r----i~~i~d~vkvGd~v~vkVl~VD~ekg   82 (319)
T PTZ00248         13 KFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELS------KRR----IRSINKLIRVGRHEVVVVLRVDKEKG   82 (319)
T ss_pred             hCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhc------ccc----cCCHHHhcCCCCEEEEEEEEEeCCCC
Confidence            45899999999999999999999995  3689999999985      222    3567999999999999999998 457


Q ss_pred             cEEEEecc
Q psy10116        159 SLTLHTRS  166 (298)
Q Consensus       159 ~~~Lstr~  166 (298)
                      .+.||.|.
T Consensus        83 ~IdLS~K~   90 (319)
T PTZ00248         83 YIDLSKKR   90 (319)
T ss_pred             EEEEEeee
Confidence            79999764

>PRK07252 hypothetical protein; Provisional

Probab=98.57  E-value=3.7e-07  Score=76.12  Aligned_cols=73  Identities=19%  Similarity=0.370  Sum_probs=61.0

Q ss_pred             cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116         85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH  163 (298)
Q Consensus        85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls  163 (298)
                      ++||+|.|+|+++.+.+|+|+|.....|++|++++..     .+     ..+..+.|++||.|.++|.+++. .+.+.|+
T Consensus         2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~-----~~-----~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lS   71 (120)
T PRK07252          2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKT-----GF-----IDNIHQLLKVGEEVLVQVVDFDEYTGKASLS   71 (120)
T ss_pred             CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCC-----cc-----ccChhhccCCCCEEEEEEEEEeCCCCEEEEE
Confidence            5799999999999999999999988999999998741     11     12346789999999999999985 6778888


Q ss_pred             eccC
Q psy10116        164 TRSL  167 (298)
Q Consensus       164 tr~~  167 (298)
                      ++..
T Consensus        72 lk~~   75 (120)
T PRK07252         72 LRTL   75 (120)
T ss_pred             Eeec
Confidence            7654

>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=98.57  E-value=3.3e-07  Score=73.96  Aligned_cols=81  Identities=14%  Similarity=0.267  Sum_probs=63.2

Q ss_pred             cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCccc----------ccchhhhhhhhcccCCCCEEEEEEEEe
Q psy10116         85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQR----------RRSVQDEEMMREFLKEGDLISAEIHQI  154 (298)
Q Consensus        85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~R----------r~~~~d~~~mr~~~~~GDlV~A~V~sv  154 (298)
                      ++|++|.|+|+++.+...+|++.....|++|++++.-. .+.+          +..+.+..++.+.|++||+|.|+|+++
T Consensus         2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~   80 (100)
T cd05693           2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDA-YTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSL   80 (100)
T ss_pred             CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHH-HHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEc
Confidence            68999999999999999999999889999999998410 0000          012223345789999999999999999


Q ss_pred             CCC----CcEEEEecc
Q psy10116        155 STE----GSLTLHTRS  166 (298)
Q Consensus       155 ~~d----g~~~Lstr~  166 (298)
                      +..    ..+.||.|.
T Consensus        81 d~~~~~~~~i~LSlr~   96 (100)
T cd05693          81 DKSKSGKKRIELSLEP   96 (100)
T ss_pred             cCCcCCCcEEEEEecH
Confidence            864    578888764

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.

>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=98.56  E-value=2.7e-07  Score=68.89  Aligned_cols=63  Identities=17%  Similarity=0.188  Sum_probs=53.1

Q ss_pred             CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC
Q psy10116         87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE  157 (298)
Q Consensus        87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d  157 (298)
                      ||+|.|+|+++.+++++|++.+..+|.+|++++.-.        .....++.+.|++||.|.|+|++++..
T Consensus         1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~--------~~~~~~~~~~~~~Gd~i~~kVl~~d~~   63 (70)
T cd05702           1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDE--------WPDGKNPLSKFKIGQKIKARVIGGHDA   63 (70)
T ss_pred             CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccc--------cccccChhHhCCCCCEEEEEEEEEeCc
Confidence            899999999999999999999999999999998410        002345678899999999999999754

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.

>PRK08059 general stress protein 13; Validated

Probab=98.56  E-value=4e-07  Score=75.86  Aligned_cols=75  Identities=24%  Similarity=0.441  Sum_probs=63.2

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCCcEEE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEGSLTL  162 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg~~~L  162 (298)
                      .++|++|.|+|+++.+.+|+|+|....+|++|.+++..     ++     ..+..+.|++||.|.|+|.+++ .++.+.|
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 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITH-----GF-----VKDIHDFLSVGDEVKVKVLSVDEEKGKISL   74 (123)
T ss_pred             CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCc-----cc-----ccCHHHcCCCCCEEEEEEEEEECCCCeEEE
Confidence            46899999999999999999999999999999998741     11     2344678999999999999997 4678999


Q ss_pred             EeccCC
Q psy10116        163 HTRSLK  168 (298)
Q Consensus       163 str~~~  168 (298)
                      +++...
T Consensus        75 slk~~~   80 (123)
T PRK08059         75 SIRATE   80 (123)
T ss_pred             EEEEcc
Confidence            987764

>PRK05807 hypothetical protein; Provisional

Probab=98.55  E-value=4.4e-07  Score=77.17  Aligned_cols=72  Identities=21%  Similarity=0.332  Sum_probs=61.4

Q ss_pred             cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEe
Q psy10116         85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHT  164 (298)
Q Consensus        85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lst  164 (298)
                      ++|++|.|+|+++++.+++|++. ...|++|++++..          ....+...+|++||.|.++|.+++.++.+.||+
T Consensus         4 ~vG~vv~G~Vt~i~~~GafV~L~-~~~Glvhiseis~----------~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSl   72 (136)
T PRK05807          4 KAGSILEGTVVNITNFGAFVEVE-GKTGLVHISEVAD----------TYVKDIREHLKEQDKVKVKVISIDDNGKISLSI   72 (136)
T ss_pred             cCCCEEEEEEEEEECCeEEEEEC-CEEEEEEhhhccc----------ccccCccccCCCCCEEEEEEEEECCCCcEEEEE
Confidence            58999999999999999999994 5789999999841          122345678999999999999998888999998


Q ss_pred             ccC
Q psy10116        165 RSL  167 (298)
Q Consensus       165 r~~  167 (298)
                      +..
T Consensus        73 k~~   75 (136)
T PRK05807         73 KQA   75 (136)
T ss_pred             Eec
Confidence            764

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

Probab=98.55  E-value=2.9e-07  Score=86.22  Aligned_cols=77  Identities=22%  Similarity=0.338  Sum_probs=63.9

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCC--CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-C
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNS--ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-E  157 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s--~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-d  157 (298)
                      .-.|++||+|.|+|+++.+.+|+|++..  ..+|+||+|++.-      +    ...++++.|++||.|.|+|.+++. .
T Consensus         3 ~~~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~------~----~i~~i~~~~kvGd~V~vkVi~VD~~k   72 (262)
T PRK03987          3 KEWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVAS------G----WVKNIRDHVKEGQKVVCKVIRVDPRK   72 (262)
T ss_pred             CCCCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCc------c----cccCHHHhCCCCCEEEEEEEEEeccc
Confidence            3469999999999999999999999975  5799999999841      1    123567899999999999999985 4


Q ss_pred             CcEEEEeccC
Q psy10116        158 GSLTLHTRSL  167 (298)
Q Consensus       158 g~~~Lstr~~  167 (298)
                      +.+.||.+..
T Consensus        73 ~~I~LSlK~v   82 (262)
T PRK03987         73 GHIDLSLKRV   82 (262)
T ss_pred             CeEEEEEEec
Confidence            6799997643

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

Probab=98.52  E-value=1.3e-06  Score=77.13  Aligned_cols=86  Identities=26%  Similarity=0.341  Sum_probs=69.1

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhh-------hhhhcccCCCCEEEEEEEE
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDE-------EMMREFLKEGDLISAEIHQ  153 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~-------~~mr~~~~~GDlV~A~V~s  153 (298)
                      -|.|.+|+++.|+|+++++.+++|+++ +.+|+++.+++. |...     ..|+       .+....|+.||.|+++|.+
T Consensus        76 ~f~p~~gEvv~G~V~~v~~~GifV~lg-~~~gi~~~~~l~-~~~~-----~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~  148 (179)
T TIGR00448        76 VFKPELGEIVEGEVIEIVEFGAFVSLG-PFDGLFHVSQVT-DDYC-----YYDPKESALIGKETKKVLDEGDKVRARIVA  148 (179)
T ss_pred             EEeccCCCEEEEEEEEEEeeEEEEEeC-CceEEEEcHHhC-CCce-----EEccccceEEEccCCeEEcCCCEEEEEEEE
Confidence            367999999999999999999999996 799999999873 2211     1111       1335789999999999999


Q ss_pred             eC------CCCcEEEEeccCCCccCC
Q psy10116        154 IS------TEGSLTLHTRSLKYGKLG  173 (298)
Q Consensus       154 v~------~dg~~~Lstr~~~lGkL~  173 (298)
                      ++      ....+.||+|++.||+++
T Consensus       149 v~~~~~~~~~~~I~lt~k~~~LG~~~  174 (179)
T TIGR00448       149 LSLKDRRPEGSKIGLTMRQPLLGKLE  174 (179)
T ss_pred             EEccCCCCCcceEEEEeccCcCCccc
Confidence            96      235699999999999974

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

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

Probab=98.51  E-value=7.2e-07  Score=67.66  Aligned_cols=71  Identities=15%  Similarity=0.152  Sum_probs=58.6

Q ss_pred             CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEEec
Q psy10116         87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLHTR  165 (298)
Q Consensus        87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Lstr  165 (298)
                      ||+|.|+|+++.+++++|.+....+|.+|+++++...        ....+....|++||.|.|+|++++. ...+.||.+
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--------SVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSAR   72 (73)
T ss_pred             CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCcc--------ccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEec
Confidence            8999999999999999999988899999999984210        1123457889999999999999985 456888864

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.

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

Probab=98.50  E-value=4.5e-07  Score=80.33  Aligned_cols=88  Identities=24%  Similarity=0.286  Sum_probs=68.6

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhh-----hhhhhcccCCCCEEEEEEEEeC
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQD-----EEMMREFLKEGDLISAEIHQIS  155 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d-----~~~mr~~~~~GDlV~A~V~sv~  155 (298)
                      -|.|.+|++|.|+|+++...+|+|+++ +.+++++.+++. +....   .+..     ..+....++.||.|+++|.+++
T Consensus        76 vf~P~~GEVv~g~V~~v~~~Gi~V~lg-~~~g~v~~~~l~-~~~~~---~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~  150 (187)
T PRK08563         76 VFKPELQEVVEGEVVEVVEFGAFVRIG-PVDGLLHISQIM-DDYIS---YDPKNGRLIGKESKRVLKVGDVVRARIVAVS  150 (187)
T ss_pred             EEeccCCCEEEEEEEEEEccEEEEEEe-CceEEEEcHHcC-CCceE---EccccceEEEccCCeEEcCCCEEEEEEEEEE
Confidence            467999999999999999999999998 799999998873 21100   0000     0234678999999999999998


Q ss_pred             CC------CcEEEEeccCCCccCC
Q psy10116        156 TE------GSLTLHTRSLKYGKLG  173 (298)
Q Consensus       156 ~d------g~~~Lstr~~~lGkL~  173 (298)
                      .+      ..+.||+++++||+++
T Consensus       151 ~~~~~~~~~~I~ls~~~~~LG~~~  174 (187)
T PRK08563        151 LKERRPRGSKIGLTMRQPGLGKLE  174 (187)
T ss_pred             cccCCCCCCEEEEEecCCCCCcHH
Confidence            43      3688999999999863

>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=98.48  E-value=8.1e-07  Score=68.38  Aligned_cols=73  Identities=15%  Similarity=0.046  Sum_probs=61.2

Q ss_pred             ccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcE
Q psy10116         82 YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSL  160 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~  160 (298)
                      ..+++|+++.|+|+.+.+.+.+|+++...+|++|.+++..     ++     ..++.+.|++||.|.++|.+++. .+.+
T Consensus        10 ~~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~-----~~-----~~~~~~~~~~Gd~v~vkV~~id~~~~~i   79 (83)
T cd04461          10 SDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISD-----EF-----VTDPSFGFKKGQSVTAKVTSVDEEKQRF   79 (83)
T ss_pred             HhCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCc-----cc-----ccCHHHhcCCCCEEEEEEEEEcCCCCEE
Confidence            3478999999999999999999999888999999999842     11     23457899999999999999985 4677


Q ss_pred             EEEe
Q psy10116        161 TLHT  164 (298)
Q Consensus       161 ~Lst  164 (298)
                      .||+
T Consensus        80 ~lsl   83 (83)
T cd04461          80 LLSL   83 (83)
T ss_pred             EEeC
Confidence            7763

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.

>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=98.47  E-value=1.3e-06  Score=66.71  Aligned_cols=67  Identities=16%  Similarity=0.238  Sum_probs=57.3

Q ss_pred             cCCCEEEEEEEEEecceEEEEeC-CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcEEE
Q psy10116         85 EIGEVVVGRVTGLQSQKWVVDTN-SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSLTL  162 (298)
Q Consensus        85 ~vGDiVIG~V~~V~~~~~~VDI~-s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~~L  162 (298)
                      +.|++|.|.|.++.+.+++||++ ...+|+||.++++.                ...|++||.+.|+|.+++.. ..+.|
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 VEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGN----------------FSKLKVGQLLLCVVEKVKDDGRVVSL   66 (74)
T ss_pred             CCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCc----------------ccccCCCCEEEEEEEEEECCCCEEEE
Confidence            58999999999999999999997 46899999998741                17899999999999999844 56888


Q ss_pred             EeccC
Q psy10116        163 HTRSL  167 (298)
Q Consensus       163 str~~  167 (298)
                      |.+..
T Consensus        67 s~k~~   71 (74)
T cd05694          67 SADPS   71 (74)
T ss_pred             EEeec
Confidence            88754

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.

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

Probab=98.43  E-value=6.8e-07  Score=79.42  Aligned_cols=91  Identities=25%  Similarity=0.302  Sum_probs=70.4

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCC--CCcccccchhhhhhhhcccCCCCEEEEEEEEeCC--
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLP--GGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST--  156 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~p--gg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~--  156 (298)
                      -|.|..|++|-|.|+++...+++|.|+ |.+|++|.+++..+  ....++..=. ...-...|++||.|+|||.+++.  
T Consensus        76 ~fkP~~gEVV~GeVv~~~~~G~fV~ig-p~dglvh~sqi~dd~~~~d~~~~~~~-g~~tk~~i~~gd~VR~RIv~~s~~~  153 (183)
T COG1095          76 VFKPFRGEVVEGEVVEVVEFGAFVRIG-PLDGLVHVSQIMDDYIDYDEKNKVLI-GEETKRVLKVGDKVRARIVGVSLKS  153 (183)
T ss_pred             EEEeccccEEEEEEEEEeecceEEEec-cccccccHhhccCcccccCcccceee-ecccceEEecCCEEEEEEEEEeccc
Confidence            578999999999999999999999999 99999999998532  0001111000 12235589999999999999882  


Q ss_pred             ----CCcEEEEeccCCCccCC
Q psy10116        157 ----EGSLTLHTRSLKYGKLG  173 (298)
Q Consensus       157 ----dg~~~Lstr~~~lGkL~  173 (298)
                          +..+.||+|++.||+++
T Consensus       154 ~~~~~~~I~lTmrq~~LGkle  174 (183)
T COG1095         154 RRPRESKIGLTMRQPGLGKLE  174 (183)
T ss_pred             CccccceEEEEeccccCCcch
Confidence                24588999999999975

>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=98.43  E-value=9.4e-07  Score=63.99  Aligned_cols=67  Identities=21%  Similarity=0.336  Sum_probs=54.6

Q ss_pred             CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116         87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH  163 (298)
Q Consensus        87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls  163 (298)
                      |+++.|+|+++.+.+|+|+++....|++|.+++..     .+     ..+....|++||.|.|+|.+++. ++.+.||
T Consensus         1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~-----~~-----~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls   68 (68)
T cd05685           1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMAD-----RF-----VSHPSDVVSVGDIVEVKVISIDEERGRISLS   68 (68)
T ss_pred             CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCC-----cc-----ccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence            78999999999999999999988999999998741     11     12346789999999999999985 4566553

The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.

>PHA02945 interferon resistance protein; Provisional

Probab=98.43  E-value=1.2e-06  Score=69.25  Aligned_cols=72  Identities=15%  Similarity=0.230  Sum_probs=58.8

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeCC--CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCc
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTNS--ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGS  159 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~s--~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~  159 (298)
                      .|++||+|+|+|.+ .+.+++|++..  ..+|++|+|.+..        ++.+.++ |+++ +|..|.|+|+.+++ .|.
T Consensus         8 ~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~sevev--------a~~wvK~-rd~l-~GqkvV~KVirVd~~kg~   76 (88)
T PHA02945          8 LPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMH--------MNRYFKY-RDKL-VGKTVKVKVIRVDYTKGY   76 (88)
T ss_pred             CCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhh--------ccceEee-eeEe-cCCEEEEEEEEECCCCCE
Confidence            59999999999999 99999999953  4789999995510        1234456 9999 99999999999994 467


Q ss_pred             EEEEec
Q psy10116        160 LTLHTR  165 (298)
Q Consensus       160 ~~Lstr  165 (298)
                      +-||.+
T Consensus        77 IDlSlK   82 (88)
T PHA02945         77 IDVNYK   82 (88)
T ss_pred             EEeEee
Confidence            888765

>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=98.42  E-value=1.6e-06  Score=64.29  Aligned_cols=67  Identities=15%  Similarity=0.185  Sum_probs=55.5

Q ss_pred             CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116         87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH  163 (298)
Q Consensus        87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls  163 (298)
                      |++|.|+|+++.+.+++|++....+|++|.++++..          ...+..+.|++||.+.++|.+++. .+.+.|+
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----------RLKHPEKKFKPGLKVKCRVLSVEPERKRLVLT   68 (69)
T ss_pred             CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCc----------cccCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence            799999999999999999998789999999987411          112346789999999999999985 4667776

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.

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

Probab=98.42  E-value=1.9e-06  Score=62.77  Aligned_cols=67  Identities=19%  Similarity=0.379  Sum_probs=55.2

Q ss_pred             CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEE
Q psy10116         87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLH  163 (298)
Q Consensus        87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Ls  163 (298)
                      |+++.|+|+++.+.+|+|+|+....|+||++++..     ++     .......|++||.|.++|.+++..+.+.||
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 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSD-----ER-----VEKVEDVLKVGDEVKVKVIEVDDRGRISLS   67 (68)
T ss_pred             CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCC-----cc-----ccCHHHccCCCCEEEEEEEEECCCCcEEee
Confidence            78999999999999999999988999999998741     11     112346899999999999999876677776

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.

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

Probab=98.40  E-value=1.7e-06  Score=68.17  Aligned_cols=74  Identities=22%  Similarity=0.260  Sum_probs=57.5

Q ss_pred             ccCCCEEEEEEEEEecc--eEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCc-E
Q psy10116         84 GEIGEVVVGRVTGLQSQ--KWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGS-L  160 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~--~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~-~  160 (298)
                      |++|+++.|+|+++.+.  .++||++...+|+||++++.-.   .++    ...+..+.|++||.|.++|.....+++ +
T Consensus         5 ~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~---~~~----~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~   77 (88)
T cd04453           5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPA---YFK----KHKKIAKLLKEGQEILVQVVKEPIGTKGP   77 (88)
T ss_pred             CCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCch---hcc----ccCCHHHcCCCCCEEEEEEEEecCCCCCc
Confidence            57999999999999996  9999999889999999998420   001    123446789999999999999874433 5


Q ss_pred             EEEe
Q psy10116        161 TLHT  164 (298)
Q Consensus       161 ~Lst  164 (298)
                      .||+
T Consensus        78 ~lt~   81 (88)
T cd04453          78 RLTT   81 (88)
T ss_pred             eEEE
Confidence            5654

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

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

Probab=98.39  E-value=1.4e-06  Score=63.25  Aligned_cols=66  Identities=23%  Similarity=0.366  Sum_probs=53.2

Q ss_pred             CCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116         86 IGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL  162 (298)
Q Consensus        86 vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L  162 (298)
                      +|++|.|+|+++.+.+|+|+++ ..+|+||.+++..     ++     ...+...|++||.|.|+|.+++. .+.+.|
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-GVDGLLHISDMSW-----GR-----VKHPSEVVNVGDEVEVKVLKIDKERKRISL   67 (68)
T ss_pred             CCCEEEEEEEEEEeeeEEEEEC-CeEEEEEhHHCCC-----cc-----ccCHhHEECCCCEEEEEEEEEECCCCEEec
Confidence            5999999999999999999998 5899999998741     11     12346789999999999999985 345554

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.

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

Probab=98.38  E-value=1.4e-06  Score=88.70  Aligned_cols=74  Identities=24%  Similarity=0.432  Sum_probs=64.5

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCCcEEE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEGSLTL  162 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg~~~L  162 (298)
                      .++||+|.|+|+++++.+++|||+. .+|+||+++++.          .......++|++||-|.++|++++ ..+.++|
T Consensus       190 l~~G~vV~G~V~~It~~GafVdigG-vdGLlHiseiS~----------~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsL  258 (541)
T COG0539         190 LEVGEVVEGVVKNITDYGAFVDIGG-VDGLLHISEISW----------KRVDHPSEVVKVGDEVKVKVISLDEERGRVSL  258 (541)
T ss_pred             CCCCceEEEEEEEeecCcEEEEecC-eeeEEehhhccc----------cccCCHHHhcccCCEEEEEEEEEccCCCeEEE
Confidence            5899999999999999999999997 999999999963          113455899999999999999999 4567999


Q ss_pred             EeccCC
Q psy10116        163 HTRSLK  168 (298)
Q Consensus       163 str~~~  168 (298)
                      |++...
T Consensus       259 SlK~l~  264 (541)
T COG0539         259 SLKQLE  264 (541)
T ss_pred             Eehhcc
Confidence            998754

>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=98.31  E-value=3.6e-06  Score=63.35  Aligned_cols=68  Identities=24%  Similarity=0.194  Sum_probs=55.5

Q ss_pred             CCEEE-EEEEEE-ecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116         87 GEVVV-GRVTGL-QSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH  163 (298)
Q Consensus        87 GDiVI-G~V~~V-~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls  163 (298)
                      |+++- |+|+++ .+.+++|++....+|++|.|++.-          ....+..+.|++||.+.|+|+++++ ++.+.||
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 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSD----------DKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLS   70 (71)
T ss_pred             CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCc----------chhcCcccccCCCCEEEEEEEEEeCCCCEEEEe
Confidence            78888 999999 699999999878999999999841          1123346789999999999999984 5578777


Q ss_pred             e
Q psy10116        164 T  164 (298)
Q Consensus       164 t  164 (298)
                      +
T Consensus        71 ~   71 (71)
T cd05696          71 L   71 (71)
T ss_pred             C
Confidence            3

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.

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=98.31  E-value=3.9e-06  Score=80.61  Aligned_cols=76  Identities=21%  Similarity=0.281  Sum_probs=64.2

Q ss_pred             ccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcE
Q psy10116         82 YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSL  160 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~  160 (298)
                      |..++||+|-|+|+.+..++.+|||+....|+||++++..          ....+..+.|++||.|.+.|++++. ++.+
T Consensus        27 ~~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~----------~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i   96 (318)
T PRK07400         27 YHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSI----------NRVEGPEEVLQPNETREFFILSDENEDGQL   96 (318)
T ss_pred             hhcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhcc----------ccccCHHHccCCCCEEEEEEEEEeCCCCeE
Confidence            4579999999999999999999999988999999999852          1123446789999999999999874 5789


Q ss_pred             EEEeccC
Q psy10116        161 TLHTRSL  167 (298)
Q Consensus       161 ~Lstr~~  167 (298)
                      .||.|..
T Consensus        97 ~lS~k~~  103 (318)
T PRK07400         97 TLSIRRI  103 (318)
T ss_pred             EEehhhh
Confidence            9998754

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

Probab=98.30  E-value=4.5e-06  Score=62.04  Aligned_cols=55  Identities=27%  Similarity=0.378  Sum_probs=48.9

Q ss_pred             cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC
Q psy10116         85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST  156 (298)
Q Consensus        85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~  156 (298)
                      ..|++|.|+|.++..+.++|||+. .+|+||.+++. |               .+.|++||.|.+.|.+++.
T Consensus         2 ~~g~iV~G~V~~~~~~~~~vdig~-~eg~lp~~e~~-~---------------~~~~~~Gd~v~v~v~~v~~   56 (67)
T cd04455           2 REGEIVTGIVKRVDRGNVIVDLGK-VEAILPKKEQI-P---------------GESYRPGDRIKAYVLEVRK   56 (67)
T ss_pred             CCCCEEEEEEEEEcCCCEEEEcCC-eEEEeeHHHCC-C---------------CCcCCCCCEEEEEEEEEec
Confidence            579999999999999999999986 89999998874 2               3568999999999999974

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.

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

Probab=98.24  E-value=3.8e-06  Score=59.45  Aligned_cols=64  Identities=19%  Similarity=0.339  Sum_probs=51.1

Q ss_pred             EEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116         90 VVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH  163 (298)
Q Consensus        90 VIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls  163 (298)
                      |.|+|+++.+.+|+|+++...+|++|.+++..      +    ...+++..|++||.|.|+|.+++. ++.+.||
T Consensus         1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~------~----~~~~~~~~~~~G~~v~~~v~~~d~~~~~i~ls   65 (65)
T cd00164           1 VTGKVVSITKFGVFVELEDGVEGLVHISELSD------K----FVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS   65 (65)
T ss_pred             CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCC------c----cccCHhhEeCCCCEEEEEEEEEcCCcCEEecC
Confidence            47999999999999999988999999998741      1    113457889999999999999974 4555543

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.

>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=98.19  E-value=7.1e-06  Score=60.95  Aligned_cols=65  Identities=20%  Similarity=0.275  Sum_probs=52.8

Q ss_pred             CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcEEEE
Q psy10116         87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSLTLH  163 (298)
Q Consensus        87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~~Ls  163 (298)
                      ||+|-|+|+++.+++++|++....+|++|.+++..+           ... .+.|++||.|.|+|++++++ ..+.||
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-----------KSS-KSTYKEGQKVRARILYVDPSTKVVGLS   66 (66)
T ss_pred             CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCc-----------cCc-ccCcCCCCEEEEEEEEEeCCCCEEecC
Confidence            899999999999999999997679999999987411           011 56799999999999999853 445553

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.

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=98.18  E-value=9.3e-06  Score=82.22  Aligned_cols=74  Identities=20%  Similarity=0.285  Sum_probs=61.9

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCCcEEE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEGSLTL  162 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg~~~L  162 (298)
                      .+.||+|.|+|+.+..+.++|||+...+|+||.+++..          ....+....|++||.|.|.|++++ ..+.+.|
T Consensus        33 ~~~GdiV~G~V~~v~~~gv~VdIg~k~eG~Ip~~Els~----------~~~~~~~~~~~vGd~Ie~~V~~~~~~~g~liL  102 (486)
T PRK07899         33 FNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSI----------KHDVDPNEVVEVGDEVEALVLQKEDKEGRLIL  102 (486)
T ss_pred             CCCCCEEEEEEEEEECCcEEEEECCCcEEEEEHHHhcc----------cccCChhhcCCCCCEEEEEEEEEECCCCeEEE
Confidence            58999999999999999999999988999999998852          111234567999999999999987 4567999


Q ss_pred             EeccC
Q psy10116        163 HTRSL  167 (298)
Q Consensus       163 str~~  167 (298)
                      |.|..
T Consensus       103 S~k~~  107 (486)
T PRK07899        103 SKKRA  107 (486)
T ss_pred             Eehhh
Confidence            98754

>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=98.17  E-value=1.3e-05  Score=60.93  Aligned_cols=70  Identities=19%  Similarity=0.377  Sum_probs=57.6

Q ss_pred             CCEEEEEEEEEecceEEEEeC---CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEE
Q psy10116         87 GEVVVGRVTGLQSQKWVVDTN---SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLH  163 (298)
Q Consensus        87 GDiVIG~V~~V~~~~~~VDI~---s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Ls  163 (298)
                      |+++.|+|+++.+.+++|+|.   ...+|++|++++.. .    +.    ..+....|++||.|.++|.+++ .+.+.|+
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 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSF-E----GR----VANPSDVVKRGQKVKVKVISIQ-NGKISLS   70 (79)
T ss_pred             CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccC-C----CC----cCChhheeCCCCEEEEEEEEEe-CCEEEEE
Confidence            789999999999999999998   45899999999841 1    10    1244678999999999999998 7888888


Q ss_pred             ecc
Q psy10116        164 TRS  166 (298)
Q Consensus       164 tr~  166 (298)
                      .+.
T Consensus        71 ~k~   73 (79)
T cd05684          71 MKD   73 (79)
T ss_pred             EEe
Confidence            765

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.

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

Probab=98.16  E-value=1.5e-05  Score=70.58  Aligned_cols=91  Identities=11%  Similarity=0.032  Sum_probs=68.5

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCccc-ccch--hh-hhhhhcccCCCCEEEEEEEEeC-
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQR-RRSV--QD-EEMMREFLKEGDLISAEIHQIS-  155 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~R-r~~~--~d-~~~mr~~~~~GDlV~A~V~sv~-  155 (298)
                      -|.|-.|++|.|+|+++...+++|++| +.++++|.+++  |....= ....  .+ ..+-+..++.||.|++||.++. 
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-PLKAFVSRSAI--PPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRY  152 (176)
T ss_pred             EEecCCCCEEEEEEEEEecceEEEEee-CeEEEEcHHHC--CCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEe
Confidence            588999999999999999999999997 78899998887  322110 0000  00 1122678999999999999887 


Q ss_pred             --CCCcEEEEeccCCCccCCC
Q psy10116        156 --TEGSLTLHTRSLKYGKLGQ  174 (298)
Q Consensus       156 --~dg~~~Lstr~~~lGkL~~  174 (298)
                        .+.....|+|++.||+++.
T Consensus       153 ~~~~~~~i~T~~~~~LG~~~~  173 (176)
T PTZ00162        153 DASNLFAIATINSDYLGPIES  173 (176)
T ss_pred             cCCCcEEEEEecCCCcCcccc
Confidence              3345677899999999843

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

Probab=98.12  E-value=1.1e-05  Score=64.28  Aligned_cols=83  Identities=25%  Similarity=0.282  Sum_probs=60.9

Q ss_pred             CEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCccc--ccchhhhhhhhcccCCCCEEEEEEEEeCCC------Cc
Q psy10116         88 EVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQR--RRSVQDEEMMREFLKEGDLISAEIHQISTE------GS  159 (298)
Q Consensus        88 DiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~R--r~~~~d~~~mr~~~~~GDlV~A~V~sv~~d------g~  159 (298)
                      ++|.|+|+++...+++|++. +.+|++|++++.- .-...  +............|++||.|.++|.+++.+      ..
T Consensus         1 ~vv~g~V~~i~~~GifV~l~-~v~G~v~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~   78 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIG-PVDGLLHISQIMD-DYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESK   78 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEc-CeEEEEEEEEccC-CceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCce
Confidence            47899999999999999998 5899999988731 10000  000000011246799999999999999843      57


Q ss_pred             EEEEeccCCCccC
Q psy10116        160 LTLHTRSLKYGKL  172 (298)
Q Consensus       160 ~~Lstr~~~lGkL  172 (298)
                      +.||+++..+|.+
T Consensus        79 i~ls~k~~~~g~~   91 (99)
T cd04460          79 IGLTMRQPGLGKL   91 (99)
T ss_pred             EEEEEecCCCCcH
Confidence            9999999999986

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.

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

Probab=98.09  E-value=3.4e-05  Score=58.88  Aligned_cols=64  Identities=22%  Similarity=0.343  Sum_probs=56.0

Q ss_pred             ccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEE
Q psy10116         82 YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLT  161 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~  161 (298)
                      --.++|+.+.|+|+++++.+++|++....+|++|.+++                  .+.++.||.+.++|.++..++.+.
T Consensus        12 ~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~------------------~~~~~iGd~v~v~I~~i~e~~~i~   73 (77)
T cd04473          12 EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNL------------------LRDYEVGDEVIVQVTDIPENGNID   73 (77)
T ss_pred             hhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhc------------------cCcCCCCCEEEEEEEEECCCCcEE
Confidence            33689999999999999999999999889999998875                  245999999999999996667777


Q ss_pred             EE
Q psy10116        162 LH  163 (298)
Q Consensus       162 Ls  163 (298)
                      |+
T Consensus        74 l~   75 (77)
T cd04473          74 LI   75 (77)
T ss_pred             EE
Confidence            76

The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.

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

Probab=98.08  E-value=1.5e-05  Score=58.51  Aligned_cols=67  Identities=22%  Similarity=0.404  Sum_probs=53.3

Q ss_pred             CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcEEE
Q psy10116         87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSLTL  162 (298)
Q Consensus        87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~~L  162 (298)
                      |+++.|+|+++.+.+++|++....+|++|.+++..+   .+      ..+.++.|++||.|.|+|.+++.+ +.+.|
T Consensus         1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~---~~------~~~~~~~~~~G~~v~v~v~~id~~~~~i~l   68 (69)
T cd05690           1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWT---QR------VRHPSEIYKKGQEVEAVVLNIDVERERISL   68 (69)
T ss_pred             CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCc---cc------cCChhhEECCCCEEEEEEEEEECCcCEEeC
Confidence            789999999999999999999889999999987411   01      123357899999999999999743 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 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.

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=98.05  E-value=2e-05  Score=75.78  Aligned_cols=74  Identities=26%  Similarity=0.408  Sum_probs=62.1

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEE
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLT  161 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~  161 (298)
                      ..++|++|.|+|+.+.+.+++|+++ ...|++|++++..     .+     ..+..+.|++||.|.|+|.+++. .+.+.
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-----EH-----IETPHSVFNVNDEMKVMIIDLDAERGRIS  261 (318)
T ss_pred             cCCCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHccc-----cc-----ccChhhccCCCCEEEEEEEEEeCCCCEEE
Confidence            3688999999999999999999996 5789999999852     11     23457889999999999999984 57899


Q ss_pred             EEeccC
Q psy10116        162 LHTRSL  167 (298)
Q Consensus       162 Lstr~~  167 (298)
                      |+++..
T Consensus       262 LS~K~l  267 (318)
T PRK07400        262 LSTKQL  267 (318)
T ss_pred             EEEecc
Confidence            998764

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=98.04  E-value=1.4e-05  Score=84.00  Aligned_cols=75  Identities=27%  Similarity=0.376  Sum_probs=61.6

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEE
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTL  162 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~L  162 (298)
                      .|++|++|.|+|+++.+.+++|+|....+|++|+|++.-=.. .+|     ..+.++.|++||.|.++|++++..+.+.|
T Consensus       644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~-~~r-----v~~~~dv~kvGd~V~VKVl~ID~~gKI~L  717 (719)
T TIGR02696       644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAG-GKR-----VENVEDVLSVGQKIQVEIADIDDRGKLSL  717 (719)
T ss_pred             cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhcccccc-ccC-----cCCHHHcCCCCCEEEEEEEEECCCCCeee
Confidence            589999999999999999999999878999999998730000 011     24668999999999999999997778877


Q ss_pred             E
Q psy10116        163 H  163 (298)
Q Consensus       163 s  163 (298)
                      +
T Consensus       718 ~  718 (719)
T TIGR02696       718 V  718 (719)
T ss_pred             c
Confidence            5

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=98.02  E-value=2e-05  Score=82.95  Aligned_cols=99  Identities=20%  Similarity=0.308  Sum_probs=77.5

Q ss_pred             cCCeEEEEEeeEEEEe--CcEEEEEecCccccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccch
Q psy10116         54 DDEEIKASVGGVVEKV--NQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSV  131 (298)
Q Consensus        54 ~~g~i~Asv~G~v~~~--nk~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~  131 (298)
                      ++|.++++..|.....  +..+...+.    .|++|+++.|+|+++.+.+++|+|....+|++|+|++.-     +|   
T Consensus       591 d~G~v~i~~~~~~~~~~a~~~I~~~~~----~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~-----~~---  658 (693)
T PRK11824        591 DDGTVKIAATDGEAAEAAKERIEGITA----EPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIAD-----ER---  658 (693)
T ss_pred             CCceEEEEcccHHHHHHHHHHHHHhcc----cCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccC-----cc---
Confidence            4688888888776642  222332222    378999999999999999999999988999999999741     11   


Q ss_pred             hhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEecc
Q psy10116        132 QDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRS  166 (298)
Q Consensus       132 ~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~  166 (298)
                        ..+..+.|++||.|.++|.+++..+.+.||+|.
T Consensus       659 --v~~~~~v~kvGD~V~VkV~~iD~~grI~LS~k~  691 (693)
T PRK11824        659 --VEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKA  691 (693)
T ss_pred             --ccCccceeCCCCEEEEEEEEECCCCcEEEEEEe
Confidence              234568899999999999999876899999875

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=98.01  E-value=3.1e-05  Score=78.43  Aligned_cols=75  Identities=20%  Similarity=0.276  Sum_probs=62.1

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCC----
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEG----  158 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg----  158 (298)
                      ..++|++|.|+|+++.+.+++|||+...+|++|++++..          ....++...|++||.|.|+|.+++.+.    
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----------SRVQKADEAVSVGDTVRVKVLGIERAKKGKG  268 (491)
T ss_pred             hCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCC----------ccccChhHhcCCCCEEEEEEEEEecccCCcc
Confidence            368999999999999999999999878999999999852          112345678999999999999998543    


Q ss_pred             -cEEEEeccC
Q psy10116        159 -SLTLHTRSL  167 (298)
Q Consensus       159 -~~~Lstr~~  167 (298)
                       .+.||.|..
T Consensus       269 ~ri~lS~K~~  278 (491)
T PRK13806        269 LRISLSIKQA  278 (491)
T ss_pred             eEEEEEehhh
Confidence             588887643

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=98.00  E-value=3.4e-05  Score=75.38  Aligned_cols=74  Identities=22%  Similarity=0.368  Sum_probs=60.8

Q ss_pred             cccCCCEEEEEEEEEecceEEEEe-CCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcE
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDT-NSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSL  160 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI-~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~  160 (298)
                      -.++||+|.|+|+.+.++++.||| +...+|+||.+++...          ...+....|++||.|.|+|.+++.+ +.+
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----------HIEDINDVVKVGDELEVYVLKVEDGEGNL   83 (390)
T ss_pred             cccCCCEEEEEEEEEECCeEEEEEecCCcEEEEEHHHhccc----------cccCcccccCCCCEEEEEEEEEECCCCCE
Confidence            468999999999999999999999 8789999999988421          1123356799999999999999844 469


Q ss_pred             EEEecc
Q psy10116        161 TLHTRS  166 (298)
Q Consensus       161 ~Lstr~  166 (298)
                      .||.+.
T Consensus        84 ~lS~k~   89 (390)
T PRK06676         84 LLSKRR   89 (390)
T ss_pred             EEEHHH
Confidence            999875

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

Probab=97.98  E-value=4.5e-05  Score=56.20  Aligned_cols=66  Identities=29%  Similarity=0.377  Sum_probs=51.6

Q ss_pred             CCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEEec
Q psy10116         87 GEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLHTR  165 (298)
Q Consensus        87 GDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Lstr  165 (298)
                      |++|.|+|+++.+.+++|++ ....|++|.+++..     ++.     .+..+  .+||.+.|+|.+++. .+.+.||.|
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-EGVRAFLPASQVDL-----RPV-----EDLDE--YVGKELKFKIIEIDRERNNIVLSRR   67 (67)
T ss_pred             CCEEEEEEEEEECCeEEEEE-CCEEEEEEHHHCCC-----ccc-----CChHH--hCCCEEEEEEEEEeCCCCEEEEEcC
Confidence            78999999999999999999 57999999998842     110     11111  389999999999995 567888753

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.

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.95  E-value=4.3e-05  Score=77.43  Aligned_cols=72  Identities=15%  Similarity=0.275  Sum_probs=60.2

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL  162 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L  162 (298)
                      -++||+|-|+|+++.+.+++|||+ ..+|++|++++..     ++     ..+..+.|++||.|.++|++++. ++.+.|
T Consensus       206 lk~G~iv~G~V~~i~~~G~FVdlg-gv~Glv~~Sels~-----~~-----v~~~~~~~kvGd~V~vkVl~iD~e~~rI~L  274 (486)
T PRK07899        206 LQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSW-----KH-----IDHPSEVVEVGQEVTVEVLDVDMDRERVSL  274 (486)
T ss_pred             ccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHCCC-----cc-----cCCHHHhcCCCCEEEEEEEEEECCCCEEEE
Confidence            469999999999999999999997 5899999999852     11     23456789999999999999985 477899


Q ss_pred             Eecc
Q psy10116        163 HTRS  166 (298)
Q Consensus       163 str~  166 (298)
                      |.|.
T Consensus       275 SlK~  278 (486)
T PRK07899        275 SLKA  278 (486)
T ss_pred             EEee
Confidence            9764

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.92  E-value=5.8e-05  Score=77.23  Aligned_cols=72  Identities=21%  Similarity=0.308  Sum_probs=61.4

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL  162 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L  162 (298)
                      .++|++|-|+|+.+.+.+++||++ ..+|++|++++..          ....+..+.|++||.|.|+|.+++. ++.+.|
T Consensus       199 l~~G~iv~g~V~~v~~~G~~V~i~-g~~glv~~se~s~----------~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~l  267 (565)
T PRK06299        199 LEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDISW----------KRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSL  267 (565)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEEC-CEEEEEEHHHhcc----------cccCCHhhcCCCCCEEEEEEEEEeCCCCeEEE
Confidence            579999999999999999999998 8999999999852          1123457789999999999999985 578999


Q ss_pred             Eecc
Q psy10116        163 HTRS  166 (298)
Q Consensus       163 str~  166 (298)
                      |.+.
T Consensus       268 S~k~  271 (565)
T PRK06299        268 GLKQ  271 (565)
T ss_pred             EEEe
Confidence            9874

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

Probab=97.90  E-value=6.6e-05  Score=55.80  Aligned_cols=64  Identities=19%  Similarity=0.303  Sum_probs=52.2

Q ss_pred             cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC
Q psy10116         85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE  157 (298)
Q Consensus        85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d  157 (298)
                      .+|+++.|+|+++.+.+++|++....+|++|.+++.-+    ++     ..+....|+.||.|.++|.+++.+
T Consensus         2 ~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~----~~-----~~~~~~~~~~Gd~v~v~v~~id~~   65 (72)
T cd05689           2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWT----NK-----NIHPSKVVSLGDEVEVMVLDIDEE   65 (72)
T ss_pred             cCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCc----cc-----ccCcccEeCCCCEEEEEEEEeeCC
Confidence            37999999999999999999998889999999987311    01     123457899999999999999743

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.

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.89  E-value=8.5e-05  Score=72.54  Aligned_cols=72  Identities=19%  Similarity=0.267  Sum_probs=60.5

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL  162 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L  162 (298)
                      .++||+|.|+|+++.+.+++|+++ ..+|++|.+++..     +     ...++.+.|++||.|.|+|.+++. ++.+.|
T Consensus       190 ~~~G~~v~g~V~~v~~~G~fV~l~-~v~g~v~~sels~-----~-----~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~l  258 (390)
T PRK06676        190 LKEGDVVEGTVARLTDFGAFVDIG-GVDGLVHISELSH-----E-----RVEKPSEVVSVGQEVEVKVLSIDWETERISL  258 (390)
T ss_pred             CCCCCEEEEEEEEEecceEEEEeC-CeEEEEEHHHcCc-----c-----ccCCHHHhcCCCCEEEEEEEEEeCCCCEEEE
Confidence            589999999999999999999997 4899999999852     1     123456789999999999999984 577999


Q ss_pred             Eecc
Q psy10116        163 HTRS  166 (298)
Q Consensus       163 str~  166 (298)
                      |.|.
T Consensus       259 S~k~  262 (390)
T PRK06676        259 SLKD  262 (390)
T ss_pred             EEee
Confidence            9874

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.83  E-value=3.8e-05  Score=80.77  Aligned_cols=94  Identities=18%  Similarity=0.287  Sum_probs=69.7

Q ss_pred             cCCeEEEEEeeEEEEe--CcEEEEEecCccccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccch
Q psy10116         54 DDEEIKASVGGVVEKV--NQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSV  131 (298)
Q Consensus        54 ~~g~i~Asv~G~v~~~--nk~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~  131 (298)
                      ++|.++....+.....  ...+....    ..|++|+++.|+|+++.+.+++|+|....+|+||+|++.-     +    
T Consensus       588 ddG~V~i~~~~~~~~~~a~~~I~~~~----~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~-----~----  654 (684)
T TIGR03591       588 DDGTVKIAASDGEAAEAAIKMIEGIT----AEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIAN-----E----  654 (684)
T ss_pred             cCeEEEEEECcHHHHHHHHHHHHhhh----cccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCC-----C----
Confidence            3677776666654422  22333322    2489999999999999999999999888999999999841     1    


Q ss_pred             hhhhhhhcccCCCCEEEEEEEEeCCCCcEE
Q psy10116        132 QDEEMMREFLKEGDLISAEIHQISTEGSLT  161 (298)
Q Consensus       132 ~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~  161 (298)
                       ...+..+.|++||.|.++|.+++..+.+.
T Consensus       655 -~v~~~~~~~kvGD~V~VkVi~id~~gki~  683 (684)
T TIGR03591       655 -RVEKVEDVLKEGDEVKVKVLEIDKQGRIK  683 (684)
T ss_pred             -cccChhhccCCCCEEEEEEEEECCCCCcc
Confidence             12356789999999999999998655544

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).

>TIGR00717 rpsA ribosomal protein S1

Probab=97.78  E-value=0.00034  Score=70.66  Aligned_cols=74  Identities=22%  Similarity=0.354  Sum_probs=60.4

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL  162 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L  162 (298)
                      -++|+++.|+|+++.+.+++|+++....|++|++++...    +     ...+..+.|++||.|.|+|.+++. ++.+.|
T Consensus       270 ~~~G~i~~g~V~~v~~~G~fV~l~~~v~g~v~~sels~~----~-----~~~~~~~~~~vG~~v~v~V~~id~~~~~i~l  340 (516)
T TIGR00717       270 FPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWV----K-----KNSHPSKVVKKGDEVEVMILDIDPERRRLSL  340 (516)
T ss_pred             ccCCCEEEEEEEEeeCCcEEEEeCCCCEEEEEHHHcCCc----c-----ccCCHHHhccCCCEEEEEEEEEcCCCCEEEE
Confidence            368999999999999999999999889999999987421    0     112234679999999999999985 467999


Q ss_pred             Eecc
Q psy10116        163 HTRS  166 (298)
Q Consensus       163 str~  166 (298)
                      |+|.
T Consensus       341 S~k~  344 (516)
T TIGR00717       341 GLKQ  344 (516)
T ss_pred             Eehh
Confidence            9875

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=97.76  E-value=0.00042  Score=74.71  Aligned_cols=104  Identities=13%  Similarity=0.191  Sum_probs=72.6

Q ss_pred             ecCCeEEEEEeeEEEEeCcEEE--EEecCc-c---cc--ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCC
Q psy10116         53 PDDEEIKASVGGVVEKVNQLVS--VRAMNS-R---YI--GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGG  124 (298)
Q Consensus        53 ~~~g~i~Asv~G~v~~~nk~v~--V~p~~~-r---Y~--P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg  124 (298)
                      ..++++.+.+.+. ...++.++  ++-+.. +   +.  -.+|++|.|+|+.+.+.+++|++....+|+||.++++..  
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            3455666666665 22233333  332221 1   11  257999999999999999999998889999999987521  


Q ss_pred             cccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEEecc
Q psy10116        125 EQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLHTRS  166 (298)
Q Consensus       125 ~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Lstr~  166 (298)
                        ++     .......|++||.|.|+|++++. ...+.||.|.
T Consensus       702 --~~-----~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~K~  737 (863)
T PRK12269        702 --KR-----TRPADHELEVGKEIECMVIECDPQARRIRLGVKQ  737 (863)
T ss_pred             --cc-----ccchhhccCCCCEEEEEEEEEeccCCEEEEEecc
Confidence              11     12234579999999999999985 4679999874

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.75  E-value=0.00029  Score=72.16  Aligned_cols=73  Identities=23%  Similarity=0.363  Sum_probs=62.2

Q ss_pred             cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116         85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH  163 (298)
Q Consensus        85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls  163 (298)
                      ++||+|.|+|+++.+.+++|.+.....|++|.+++.          .....+..+.|++||.|.|+|++++. ++.+.||
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 KKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELS----------RDRVEDATEVLKVGDEVEAKVINIDRKNRRISLS  528 (565)
T ss_pred             CCCCEEEEEEEEEecCceEEecCCCcEEEEEHHHhc----------chhccCccccCCCCCEEEEEEEEEccccCEEEEE
Confidence            689999999999999999999987899999999874          11234567889999999999999985 5789999


Q ss_pred             eccC
Q psy10116        164 TRSL  167 (298)
Q Consensus       164 tr~~  167 (298)
                      ++..
T Consensus       529 ~k~~  532 (565)
T PRK06299        529 IKAL  532 (565)
T ss_pred             eeeh
Confidence            8643

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=97.73  E-value=0.00016  Score=77.82  Aligned_cols=74  Identities=19%  Similarity=0.276  Sum_probs=61.7

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL  162 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L  162 (298)
                      ..+||+|-|+|+++.+.+++|+++...+|++|+|++...    +     ...+..+.|++||.|.|+|++++. .+.++|
T Consensus       576 ~~vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~----~-----~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsL  646 (863)
T PRK12269        576 FGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWV----K-----KTSKPSDMVKIGDEVECMILGYDIQAGRVSL  646 (863)
T ss_pred             CCCCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCc----c-----ccCCHHHcCCCCCEEEEEEEEEecccCceEE
Confidence            469999999999999999999999889999999998521    1     123446789999999999999984 467899


Q ss_pred             Eecc
Q psy10116        163 HTRS  166 (298)
Q Consensus       163 str~  166 (298)
                      |.+.
T Consensus       647 S~K~  650 (863)
T PRK12269        647 GLKQ  650 (863)
T ss_pred             Eehh
Confidence            9764

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.73  E-value=9.7e-05  Score=79.30  Aligned_cols=75  Identities=17%  Similarity=0.297  Sum_probs=63.2

Q ss_pred             cccCCCEEE-EEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEE
Q psy10116         83 IGEIGEVVV-GRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLT  161 (298)
Q Consensus        83 ~P~vGDiVI-G~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~  161 (298)
                      .|++|+++. |+|++|.+.+++|+|....+|++|+|++.-     +|     ..+..+.|++||.|.++|.+++..+.+.
T Consensus       750 ~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~-----~r-----v~~~~dv~kvGD~V~VkVi~ID~~grI~  819 (891)
T PLN00207        750 VPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSS-----NW-----LAKPEDAFKVGDRIDVKLIEVNDKGQLR  819 (891)
T ss_pred             CcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCC-----cc-----ccCHHHhcCCCCEEEEEEEEECCCCcEE
Confidence            389999995 699999999999999877999999999841     11     2334688999999999999999778899


Q ss_pred             EEeccC
Q psy10116        162 LHTRSL  167 (298)
Q Consensus       162 Lstr~~  167 (298)
                      |+.+..
T Consensus       820 LSlK~l  825 (891)
T PLN00207        820 LSRRAL  825 (891)
T ss_pred             EEEecc
Confidence            998753

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

Probab=97.71  E-value=0.00018  Score=75.25  Aligned_cols=72  Identities=31%  Similarity=0.365  Sum_probs=60.1

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL  162 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L  162 (298)
                      .++||+|.|+|+++.+.+++|++ ...+|++|.+++...     +     ..++.+.|++||.|.|+|.+++. ++.+.|
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-----R-----VEKPSDVLKVGDEIKVYILDIDKENKKLSL  543 (647)
T ss_pred             CCCCCEEEEEEEEEeCCcEEEEE-CCEEEEEEHHHcCcc-----c-----cCCHHHhcCCCCEEEEEEEEEECCCCEEEE
Confidence            46899999999999999999999 578999999987521     1     12356789999999999999974 578999


Q ss_pred             Eecc
Q psy10116        163 HTRS  166 (298)
Q Consensus       163 str~  166 (298)
                      |+|.
T Consensus       544 S~K~  547 (647)
T PRK00087        544 SLKK  547 (647)
T ss_pred             Eeec
Confidence            9874

>TIGR00717 rpsA ribosomal protein S1

Probab=97.69  E-value=0.00025  Score=71.66  Aligned_cols=73  Identities=21%  Similarity=0.326  Sum_probs=60.3

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEE
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLT  161 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~  161 (298)
                      ..++||+|.|+|+++.+.+++||++ ..+|++|.++++..          ...+..+.|++||.|.|+|.+++. ++.+.
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 NLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWK----------RVKHPSEYVKVGQEVKVKVIKFDKEKGRIS  252 (516)
T ss_pred             hccCCCEEEEEEEEEECCeEEEEEC-CEEEEEEHHHcCCC----------CCCCHHHhccCCCEEEEEEEEEECCCCcEE
Confidence            4689999999999999999999997 48999999998521          113346789999999999999985 46799


Q ss_pred             EEecc
Q psy10116        162 LHTRS  166 (298)
Q Consensus       162 Lstr~  166 (298)
                      ||.|.
T Consensus       253 lS~k~  257 (516)
T TIGR00717       253 LSLKQ  257 (516)
T ss_pred             EEEEe
Confidence            98774

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=97.65  E-value=0.00028  Score=73.75  Aligned_cols=77  Identities=21%  Similarity=0.334  Sum_probs=64.5

Q ss_pred             ccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCCcE
Q psy10116         82 YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEGSL  160 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg~~  160 (298)
                      +..++|++|.|+|+++..++++||++...+|+||.+++...          ...+....|++||.|.++|.+++ .++.+
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 KQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLD----------EISSLKESVKVGDEIEVKVLKLEDEDGYV  367 (647)
T ss_pred             hhccCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccc----------ccCChhhccCCCCEEEEEEEEEECCCCcE
Confidence            45799999999999999999999999889999999988521          12344678999999999999996 56789


Q ss_pred             EEEeccCC
Q psy10116        161 TLHTRSLK  168 (298)
Q Consensus       161 ~Lstr~~~  168 (298)
                      .||.+...
T Consensus       368 ~LS~k~~~  375 (647)
T PRK00087        368 VLSKKEAD  375 (647)
T ss_pred             EEEeehhc
Confidence            99987653

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=97.64  E-value=0.00011  Score=77.32  Aligned_cols=76  Identities=16%  Similarity=0.211  Sum_probs=65.5

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCCcEE
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEGSLT  161 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg~~~  161 (298)
                      -.++|.++.|+|+.|...+++||||..++|.+|+|+.+          +....+..+.+++||+|.++|.+++ ....+.
T Consensus       655 dLk~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls----------~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~  724 (780)
T COG2183         655 DLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLS----------DKFVKDPNEVVKVGDIVKVKVIEVDTARKRIA  724 (780)
T ss_pred             hccCCCEEEEEEEEeeeccceEEeccccceeeeHHHhh----------hhhcCChHHhcccCCEEEEEEEEEecccCeee
Confidence            35899999999999999999999999999999999974          3334445899999999999999999 456799


Q ss_pred             EEeccCC
Q psy10116        162 LHTRSLK  168 (298)
Q Consensus       162 Lstr~~~  168 (298)
                      ||+|...
T Consensus       725 Lsmr~~~  731 (780)
T COG2183         725 LSMRLDE  731 (780)
T ss_pred             eEeeccC
Confidence            9987643

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=97.61  E-value=0.00067  Score=68.81  Aligned_cols=73  Identities=19%  Similarity=0.211  Sum_probs=60.9

Q ss_pred             cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcEEEE
Q psy10116         85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSLTLH  163 (298)
Q Consensus        85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~~Ls  163 (298)
                      .+|++|.|+|+++.+.+++|++....+|++|.+++..    .|      ..+..+.|++||.|.|+|++++.+ ..++|+
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 APGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISR----AG------KPATYEKLKPGDSVTLVVEEIDTAKRKISLA  447 (491)
T ss_pred             CCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCc----cc------ccchhhcCCCCCEEEEEEEEEeCCCCEEEEE
Confidence            4799999999999999999999888999999999842    11      134467899999999999999854 569999


Q ss_pred             eccC
Q psy10116        164 TRSL  167 (298)
Q Consensus       164 tr~~  167 (298)
                      .+..
T Consensus       448 ~~~~  451 (491)
T PRK13806        448 PAGA  451 (491)
T ss_pred             eehh
Confidence            8743

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

Probab=97.57  E-value=0.00055  Score=51.73  Aligned_cols=72  Identities=18%  Similarity=0.354  Sum_probs=54.3

Q ss_pred             CCCEEEEEEEEEecceEEEEeCC-CceeeEecccccCCCCcccccchhhh-------hhhhcccCCCCEEEEEEEEeCC-
Q psy10116         86 IGEVVVGRVTGLQSQKWVVDTNS-ILESALHLTSVNLPGGEQRRRSVQDE-------EMMREFLKEGDLISAEIHQIST-  156 (298)
Q Consensus        86 vGDiVIG~V~~V~~~~~~VDI~s-~~~a~L~~s~v~~pgg~~Rr~~~~d~-------~~mr~~~~~GDlV~A~V~sv~~-  156 (298)
                      +|+++.|.|+++.+.+++|++.. ..+|++|++++.  ...    ...|+       ......|++||.|.++|.+++. 
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--DDY----YEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLD   74 (83)
T ss_pred             CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecC--CCc----EEEcccceEEEeccCCCEEcCCCEEEEEEEEeccc
Confidence            48999999999999999999986 589999999863  111    01111       1235789999999999999985 


Q ss_pred             CCcEEEE
Q psy10116        157 EGSLTLH  163 (298)
Q Consensus       157 dg~~~Ls  163 (298)
                      .+.+.|+
T Consensus        75 ~~~i~~~   81 (83)
T cd04471          75 RRKIDFE   81 (83)
T ss_pred             cCEEEEE
Confidence            3556554

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.

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

Probab=97.52  E-value=0.00075  Score=53.29  Aligned_cols=82  Identities=13%  Similarity=0.053  Sum_probs=55.2

Q ss_pred             CCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCccccc-ch--hhhhhhhcccCCCCEEEEEEEEeCCC---Cc
Q psy10116         86 IGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRR-SV--QDEEMMREFLKEGDLISAEIHQISTE---GS  159 (298)
Q Consensus        86 vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~-~~--~d~~~mr~~~~~GDlV~A~V~sv~~d---g~  159 (298)
                      +|++|.|+|+++...+++|+++ |.+++++.+.+  |...+-.. ..  .+..+-..+++.||.|++||.++.-+   ..
T Consensus         1 kgEVi~g~V~~v~~~G~~v~~G-pl~~f~~~~~i--p~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~   77 (88)
T cd04462           1 KGEVVDAIVTSVNKTGFFAEVG-PLSIFISRHLI--PSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDATDIF   77 (88)
T ss_pred             CCcEEEEEEEEEeccEEEEEEc-CceEEEEeeec--CccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEccCceE
Confidence            5899999999999999999997 77788876665  32211110 00  11112367899999999999998622   11


Q ss_pred             EEEEeccCCCc
Q psy10116        160 LTLHTRSLKYG  170 (298)
Q Consensus       160 ~~Lstr~~~lG  170 (298)
                      ..-|.+++.||
T Consensus        78 ~igt~~~~~LG   88 (88)
T cd04462          78 AIGTIKDDYLG   88 (88)
T ss_pred             EEEEccCCCCC
Confidence            22255777766

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.

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

Probab=97.41  E-value=0.00039  Score=71.14  Aligned_cols=73  Identities=21%  Similarity=0.389  Sum_probs=62.3

Q ss_pred             cCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEEE
Q psy10116         85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTLH  163 (298)
Q Consensus        85 ~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~Ls  163 (298)
                      .+||.+.|+|+.+.+.+++|+|....+|++|+|+++-     .+     ....++.+++||.|.++|++++. +..++|+
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-----TK-----KNVPSEVVKVGQEVEVKVLDIDPERRRISLG  345 (541)
T ss_pred             CCCCEEEEEEEEeecCcEEEEecCCccceeechhhcc-----cc-----cCCHHHhcccCCEEEEEEEeeCchhceEEee
Confidence            5899999999999999999999999999999999862     11     11257899999999999999995 4679999


Q ss_pred             eccC
Q psy10116        164 TRSL  167 (298)
Q Consensus       164 tr~~  167 (298)
                      +|..
T Consensus       346 iKq~  349 (541)
T COG0539         346 LKQL  349 (541)
T ss_pred             ehhh
Confidence            8753

>TIGR01953 NusA transcription termination factor NusA

Probab=97.37  E-value=0.00048  Score=67.01  Aligned_cols=71  Identities=20%  Similarity=0.282  Sum_probs=58.5

Q ss_pred             cccccCCCEEEEEEEEEecce-EEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC--
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQK-WVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE--  157 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~-~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d--  157 (298)
                      .|..+.|++|.|+|.++..++ |+|||+ ..+|+||.++.. |               ++.|++||.|.|.|.++..+  
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 689999988763 3               35599999999999999833  


Q ss_pred             -CcEEEEeccCC
Q psy10116        158 -GSLTLHTRSLK  168 (298)
Q Consensus       158 -g~~~Lstr~~~  168 (298)
                       +.+.||.+.++
T Consensus       189 g~qIivSRt~~~  200 (341)
T TIGR01953       189 GPQIILSRTHPE  200 (341)
T ss_pred             CCeEEEEeCcHH
Confidence             45788866544

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=97.35  E-value=0.00052  Score=67.28  Aligned_cols=70  Identities=19%  Similarity=0.254  Sum_probs=57.9

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC---
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE---  157 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d---  157 (298)
                      .|..+.|++|.|+|.++..+.|+||++. .+|+||.++.. |               ++.|++||.|.|.|.++..+   
T Consensus       129 ef~~k~GeiV~G~V~~~~~~~~~Vdlg~-vEa~LP~~E~i-p---------------~e~~~~Gd~Ika~V~~V~~~~kg  191 (362)
T PRK12327        129 EFSEREGDIVTGVVQRRDNRFVYVNLGK-IEAVLPPAEQI-P---------------GETYKHGDRIKVYVVKVEKTTKG  191 (362)
T ss_pred             HHHHhcCCEEEEEEEEEeCCcEEEEeCC-eEEEecHHHcC-C---------------CCCCCCCCEEEEEEEEEecCCCC
Confidence            3999999999999999999999999986 89999977652 3               56799999999999999833   


Q ss_pred             CcEEEEeccC
Q psy10116        158 GSLTLHTRSL  167 (298)
Q Consensus       158 g~~~Lstr~~  167 (298)
                      ..+.||..++
T Consensus       192 p~IivSRt~p  201 (362)
T PRK12327        192 PQIFVSRTHP  201 (362)
T ss_pred             CeEEEEeCCH
Confidence            2477774443

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=97.35  E-value=0.00051  Score=69.48  Aligned_cols=71  Identities=24%  Similarity=0.389  Sum_probs=60.2

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC---
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE---  157 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d---  157 (298)
                      .|..+.|++|.|+|..+...+++||++ ..+|+||.++.. |               ++.|++||.|.|.|..++..   
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            488899999999999999999999996 579999988873 3               57899999999999999853   


Q ss_pred             CcEEEEeccCC
Q psy10116        158 GSLTLHTRSLK  168 (298)
Q Consensus       158 g~~~Lstr~~~  168 (298)
                      ..+.||-+++.
T Consensus       192 ~qIilSRt~p~  202 (470)
T PRK09202        192 PQIILSRTHPE  202 (470)
T ss_pred             CeEEEEeCcHH
Confidence            35888865544

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=96.88  E-value=0.0072  Score=60.31  Aligned_cols=88  Identities=20%  Similarity=0.260  Sum_probs=61.2

Q ss_pred             EEEEecCccccccCCCEEEEEEEEEecc--eEEEEeCCCceeeEecccccCCCCcc-----cccchhhhhhhhcccCCCC
Q psy10116         73 VSVRAMNSRYIGEIGEVVVGRVTGLQSQ--KWVVDTNSILESALHLTSVNLPGGEQ-----RRRSVQDEEMMREFLKEGD  145 (298)
Q Consensus        73 v~V~p~~~rY~P~vGDiVIG~V~~V~~~--~~~VDI~s~~~a~L~~s~v~~pgg~~-----Rr~~~~d~~~mr~~~~~GD  145 (298)
                      +.+++...  .+.+|++..|+|+.+.+.  .+||||+....|+||++++. |....     .++  ....+..+.+++||
T Consensus        14 ~~ie~~~~--~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~-~~~~~~~~~~~~~--~~~~~i~~~l~~G~   88 (414)
T TIGR00757        14 LIIERPKS--RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIG-PNYECLAPAEAKR--EAGPSISELLRPGQ   88 (414)
T ss_pred             EEEecCcC--cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcC-chhhccccccccc--cccCCHHHhCcCCC
Confidence            34444433  345899999999999998  99999999999999999973 21100     000  00124566899999


Q ss_pred             EEEEEEEEeC-CCCcEEEEec
Q psy10116        146 LISAEIHQIS-TEGSLTLHTR  165 (298)
Q Consensus       146 lV~A~V~sv~-~dg~~~Lstr  165 (298)
                      .|.++|..-. ....+.||+.
T Consensus        89 ~IlVQV~Ke~~~~Kgp~lT~~  109 (414)
T TIGR00757        89 SVLVQVVKEPRGNKGARLTTD  109 (414)
T ss_pred             EEEEEEeeCCcCCCCCeEEEE
Confidence            9999999843 2234667763

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=96.36  E-value=0.0095  Score=62.34  Aligned_cols=74  Identities=24%  Similarity=0.395  Sum_probs=64.5

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEE
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTL  162 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~L  162 (298)
                      -+++|.+-.|+|+.+.+.+++|.+-...+|.+|+|++.    .+|      ..+..+.+++||.|+.||..+++.|.+.|
T Consensus       616 e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~----~~r------v~kv~dvlk~Gd~v~Vkv~~iD~~Gri~l  685 (692)
T COG1185         616 EVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLA----KER------VEKVEDVLKEGDEVKVKVIEIDKQGRIRL  685 (692)
T ss_pred             hcccccEEEEEEEEEeecceEEEecCCcceeEEehhhh----hhh------hhcccceeecCceEEEEEeeecccCCccc
Confidence            47999999999999999999999999999999999974    122      24456999999999999999999899999


Q ss_pred             Eecc
Q psy10116        163 HTRS  166 (298)
Q Consensus       163 str~  166 (298)
                      +.+.
T Consensus       686 s~~~  689 (692)
T COG1185         686 SIKA  689 (692)
T ss_pred             eehh
Confidence            8754

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=96.28  E-value=0.011  Score=58.25  Aligned_cols=59  Identities=19%  Similarity=0.455  Sum_probs=50.6

Q ss_pred             cccccCCCEEEEEEEEEec-ceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC
Q psy10116         81 RYIGEIGEVVVGRVTGLQS-QKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST  156 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~-~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~  156 (298)
                      .|.+++|++|.|+|..+.. ..+.||++ ...|+||..+. .|               ++.|++||.|.|-|..+..
T Consensus       133 ey~~~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eq-ip---------------~E~~~~Gdrik~~i~~V~~  192 (374)
T PRK12328        133 KYKKKVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNR-IK---------------GEKFKVGDVVKAVLKRVKI  192 (374)
T ss_pred             HHHHhcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHc-CC---------------CCcCCCCCEEEEEEEEEec
Confidence            5999999999999999986 46889998 57899997765 23               5779999999999999973

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=96.11  E-value=0.015  Score=58.49  Aligned_cols=70  Identities=16%  Similarity=0.220  Sum_probs=56.6

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCC-----CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNS-----ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS  155 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s-----~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~  155 (298)
                      .|.+++|++|.|+|..+..+.+.||+++     ...|+||..+. +|               ++.|++||.|+|-|..+.
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            4999999999999999999999999943     27899997765 34               577999999999999996


Q ss_pred             CC----CcEEEEecc
Q psy10116        156 TE----GSLTLHTRS  166 (298)
Q Consensus       156 ~d----g~~~Lstr~  166 (298)
                      .+    ..+.||-..
T Consensus       211 ~~~~kGpqIilSRt~  225 (449)
T PRK12329        211 EGPRRGPQLFVSRAN  225 (449)
T ss_pred             cCCCCCCEEEEEcCC
Confidence            43    246777443

>KOG1070|consensus

Probab=96.06  E-value=0.019  Score=64.13  Aligned_cols=75  Identities=15%  Similarity=0.304  Sum_probs=65.3

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCC-cEEE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEG-SLTL  162 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg-~~~L  162 (298)
                      -+.||+|-|+|..+..++.++-++...+|++++++..          +..+..-++.|.+|++|.++|.+++.+. .++|
T Consensus      1160 lk~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~----------ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel 1229 (1710)
T KOG1070|consen 1160 LKIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLS----------DSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIEL 1229 (1710)
T ss_pred             cccCceeEEEEEEecCCcEEEEEccceEEEEEccccc----------cchhhhhhccCCccceeeeEEEEeeccCceEEE
Confidence            4789999999999999999999999999999999873          4556777899999999999999999664 6888


Q ss_pred             EeccCC
Q psy10116        163 HTRSLK  168 (298)
Q Consensus       163 str~~~  168 (298)
                      +.+..+
T Consensus      1230 ~Lk~s~ 1235 (1710)
T KOG1070|consen 1230 SLKNSD 1235 (1710)
T ss_pred             EEeccc
Confidence            876544

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=95.75  E-value=0.061  Score=42.48  Aligned_cols=69  Identities=20%  Similarity=0.268  Sum_probs=53.5

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeC-CCceeeEe-cccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-Cc
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTN-SILESALH-LTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GS  159 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~-s~~~a~L~-~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~  159 (298)
                      .|++||+|. .|+.+++..+.|.+- ...+|.+. .++++      ||+    -.+++..+ +|-.+.++|+.++.+ |-
T Consensus        13 ~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~sels------r~r----irsi~kll-VGk~e~v~ViRVDk~KGY   80 (86)
T PHA02858         13 FPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVN------ADR----AEKLKKKL-VGKTINVQVIRTDKLKGY   80 (86)
T ss_pred             cCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHh------HHH----HHhhhhhh-cCCeeEEEEEEECCCCCE
Confidence            499999999 788899999999873 33667666 88875      333    35567788 999999999999854 55


Q ss_pred             EEEE
Q psy10116        160 LTLH  163 (298)
Q Consensus       160 ~~Ls  163 (298)
                      +-||
T Consensus        81 IDLs   84 (86)
T PHA02858         81 IDVR   84 (86)
T ss_pred             EEeE
Confidence            6665

>TIGR02063 RNase_R ribonuclease R

Probab=94.99  E-value=0.087  Score=55.84  Aligned_cols=74  Identities=22%  Similarity=0.398  Sum_probs=56.5

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCC-CceeeEecccccCCCCcccccchhhh-------hhhhcccCCCCEEEEEEEEeC
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNS-ILESALHLTSVNLPGGEQRRRSVQDE-------EMMREFLKEGDLISAEIHQIS  155 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s-~~~a~L~~s~v~~pgg~~Rr~~~~d~-------~~mr~~~~~GDlV~A~V~sv~  155 (298)
                      .++|+++-|+|+++.+.+++|++.. ..+|++|++++.  +..    ...|+       ......|++||.|.++|.+++
T Consensus       625 ~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~--~d~----~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd  698 (709)
T TIGR02063       625 EKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLK--DDY----YVFDEKGLALVGERTGKVFRLGDRVKVRVVKAD  698 (709)
T ss_pred             ccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecC--CCc----EEEcccceEEEeccCCcEECCCCEEEEEEEEEe
Confidence            6889999999999999999999976 689999999873  110    00011       112467999999999999998


Q ss_pred             C-CCcEEEE
Q psy10116        156 T-EGSLTLH  163 (298)
Q Consensus       156 ~-dg~~~Ls  163 (298)
                      . .+.+.++
T Consensus       699 ~~~~~I~~~  707 (709)
T TIGR02063       699 LDTGKIDFE  707 (709)
T ss_pred             cccCeEEEE
Confidence            4 4666665

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.

>PF13509 S1_2: S1 domain; PDB: 3GO5_A

Probab=94.85  E-value=0.19  Score=36.78  Aligned_cols=60  Identities=27%  Similarity=0.275  Sum_probs=34.9

Q ss_pred             CCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEe
Q psy10116         86 IGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHT  164 (298)
Q Consensus        86 vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lst  164 (298)
                      +|+++..+|+++...+|++|.+...+-.||.+++                  ...+++||.|.+-|=. +.++.+..||
T Consensus         1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~------------------~~~~~~Gd~v~VFvY~-D~~~rl~AT~   60 (61)
T PF13509_consen    1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEV------------------PEPLKVGDEVEVFVYL-DKEGRLVATT   60 (61)
T ss_dssp             --------EEEE-SSEEEEEETT-EEEEEEGGG------------------------TTSEEEEEEEE--TTS-EEEE-
T ss_pred             CCCCcceEEEEEeCCEEEEECCCCCEEEechHHc------------------CCCCCCCCEEEEEEEE-CCCCCEEEec
Confidence            5899999999999999999998888889997775                  2448999999988865 3455666665

>PRK11712 ribonuclease G; Provisional

Probab=94.64  E-value=0.22  Score=50.95  Aligned_cols=83  Identities=20%  Similarity=0.227  Sum_probs=56.9

Q ss_pred             ccccCCCEEEEEEEEEe--cceEEEEeCCCceeeEecccccCCCCcc-cc--cchhhhhhhhcccCCCCEEEEEEEEeC-
Q psy10116         82 YIGEIGEVVVGRVTGLQ--SQKWVVDTNSILESALHLTSVNLPGGEQ-RR--RSVQDEEMMREFLKEGDLISAEIHQIS-  155 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~--~~~~~VDI~s~~~a~L~~s~v~~pgg~~-Rr--~~~~d~~~mr~~~~~GDlV~A~V~sv~-  155 (298)
                      ....+|+|-.|+|..|.  -+.+|||||....|+||++++ .|.... +.  +.......+.+.+++||.|...|..-. 
T Consensus        34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~-~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~  112 (489)
T PRK11712         34 KRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDI-VPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPL  112 (489)
T ss_pred             cccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhc-cchhhhcccccccccccccHHHhccCCCEEEEEEEeCCc
Confidence            34569999999999995  467999999999999999987 231100 00  000001134567999999999999854 


Q ss_pred             CCCcEEEEec
Q psy10116        156 TEGSLTLHTR  165 (298)
Q Consensus       156 ~dg~~~Lstr  165 (298)
                      ....+.||+.
T Consensus       113 ~~KG~~lT~~  122 (489)
T PRK11712        113 GTKGARLTTD  122 (489)
T ss_pred             CCCCCeEEEE
Confidence            2234667663

>PRK11642 exoribonuclease R; Provisional

Probab=94.39  E-value=0.18  Score=54.42  Aligned_cols=75  Identities=15%  Similarity=0.351  Sum_probs=56.3

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCC-ceeeEecccccCCCCcccccchhhh-------hhhhcccCCCCEEEEEEEEeC
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSI-LESALHLTSVNLPGGEQRRRSVQDE-------EMMREFLKEGDLISAEIHQIS  155 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~-~~a~L~~s~v~~pgg~~Rr~~~~d~-------~~mr~~~~~GDlV~A~V~sv~  155 (298)
                      .++|+++-|+|++|.+.+++|.+... .+|++|++++.  ..    ....|+       ......|+.||.|.++|.+++
T Consensus       641 ~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~--~d----~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD  714 (813)
T PRK11642        641 DQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLD--ND----YYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVN  714 (813)
T ss_pred             ccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecC--Cc----ceEecchheEEecccCCcEECCCCEEEEEEEEee
Confidence            47999999999999999999999754 89999999863  11    000111       123477999999999999998


Q ss_pred             C-CCcEEEEe
Q psy10116        156 T-EGSLTLHT  164 (298)
Q Consensus       156 ~-dg~~~Lst  164 (298)
                      . .+.+.++.
T Consensus       715 ~~~rkI~f~l  724 (813)
T PRK11642        715 MDERKIDFSL  724 (813)
T ss_pred             cCCCeEEEEE
Confidence            3 45666653

>KOG2916|consensus

Probab=94.02  E-value=0.077  Score=50.08  Aligned_cols=74  Identities=19%  Similarity=0.300  Sum_probs=61.4

Q ss_pred             ccccCCCEEEEEEEEEecceEEEEeCC--CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CC
Q psy10116         82 YIGEIGEVVVGRVTGLQSQKWVVDTNS--ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EG  158 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s--~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg  158 (298)
                      -.|+++|+|++.|..+..-++.|.+--  ...|.+.+|+.+      |||    ...+...+++|-.=.+-|+.++. .|
T Consensus        12 kyPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELS------rRR----IRSI~klirVGr~E~vvVlrVDkekG   81 (304)
T KOG2916|consen   12 KYPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELS------RRR----IRSIQKLIRVGRNEPVVVLRVDKEKG   81 (304)
T ss_pred             cCCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHH------HHH----HHHHHHHHhcCCcceEEEEEEcCCCC
Confidence            359999999999999999999998842  456888888875      554    35668889999999999999994 57


Q ss_pred             cEEEEec
Q psy10116        159 SLTLHTR  165 (298)
Q Consensus       159 ~~~Lstr  165 (298)
                      -+-||.|
T Consensus        82 YIDLSkr   88 (304)
T KOG2916|consen   82 YIDLSKR   88 (304)
T ss_pred             ceechhc
Confidence            7889975

>PRK10811 rne ribonuclease E; Reviewed

Probab=93.97  E-value=0.28  Score=53.66  Aligned_cols=81  Identities=16%  Similarity=0.171  Sum_probs=55.2

Q ss_pred             ccCCCEEEEEEEEE--ecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcE
Q psy10116         84 GEIGEVVVGRVTGL--QSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSL  160 (298)
Q Consensus        84 P~vGDiVIG~V~~V--~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~  160 (298)
                      +.+|+|-+|+|..|  +-+.+|||||....|+|+++++.-|.-.... ......+....+++||.|...|..-... ...
T Consensus        36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~-~~~~~~~i~~~Lk~GqeILVQV~KEa~gtKGp  114 (1068)
T PRK10811         36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANY-SAHGRPNIKDVLREGQEVIVQIDKEERGNKGA  114 (1068)
T ss_pred             cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhcccccccccc-ccccccccccccCCCCEEEEEEeecccCCCCC
Confidence            35899999999999  4678999999999999999987411100000 0000113456799999999999985422 235


Q ss_pred             EEEec
Q psy10116        161 TLHTR  165 (298)
Q Consensus       161 ~Lstr  165 (298)
                      .||++
T Consensus       115 ~LTt~  119 (1068)
T PRK10811        115 ALTTF  119 (1068)
T ss_pred             ceeee
Confidence            66654

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

Probab=93.58  E-value=0.3  Score=51.51  Aligned_cols=74  Identities=12%  Similarity=0.317  Sum_probs=55.6

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeC-CCceeeEecccccCCCCcccccchhhh-------hhhhcccCCCCEEEEEEEEeC
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTN-SILESALHLTSVNLPGGEQRRRSVQDE-------EMMREFLKEGDLISAEIHQIS  155 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~-s~~~a~L~~s~v~~pgg~~Rr~~~~d~-------~~mr~~~~~GDlV~A~V~sv~  155 (298)
                      .++|+.+-|+|+++...+++|.+. ...+|++|++++.  +.    ....|+       ......|++||.|..+|.+++
T Consensus       570 ~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~--~d----~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd  643 (654)
T TIGR00358       570 DKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLH--ND----YYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVN  643 (654)
T ss_pred             hCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCC--Cc----ceEEeccccEEEeccCCcEECCCCEEEEEEEEEe
Confidence            478999999999999999999997 5689999999873  21    011111       122467999999999999998


Q ss_pred             -CCCcEEEE
Q psy10116        156 -TEGSLTLH  163 (298)
Q Consensus       156 -~dg~~~Ls  163 (298)
                       ..+.+.++
T Consensus       644 ~~~~~I~f~  652 (654)
T TIGR00358       644 METRSIIFE  652 (654)
T ss_pred             cccCeEEEE
Confidence             34455554

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.

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

Probab=92.85  E-value=0.39  Score=45.64  Aligned_cols=65  Identities=18%  Similarity=0.131  Sum_probs=55.9

Q ss_pred             CCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEec
Q psy10116         86 IGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTR  165 (298)
Q Consensus        86 vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr  165 (298)
                      .++.|-|+|.+....+.+|=+...+-|++|-|+.                  ....+.|+.+.|+|+.+..||++-||++
T Consensus       155 ~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr------------------~~~prlG~~l~~rVi~~reDg~lnLSl~  216 (287)
T COG2996         155 KNQEVDATVYRLLESGTFVITENGYLGFIHKSER------------------FAEPRLGERLTARVIGVREDGKLNLSLR  216 (287)
T ss_pred             hcCeeeeEEEEEeccceEEEEcCCeEEEEcchhh------------------cccccCCceEEEEEEEEccCCeeecccc
Confidence            3788889999999999999888899999998875                  3557899999999999999999999987


Q ss_pred             cCC
Q psy10116        166 SLK  168 (298)
Q Consensus       166 ~~~  168 (298)
                      ...
T Consensus       217 p~~  219 (287)
T COG2996         217 PRA  219 (287)
T ss_pred             ccc
Confidence            543

>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=92.57  E-value=0.73  Score=35.40  Aligned_cols=68  Identities=19%  Similarity=0.157  Sum_probs=49.1

Q ss_pred             CCEEEEEEEEEecceEEEEeCC-CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEE-EEEEEEeCCCCcEEEE
Q psy10116         87 GEVVVGRVTGLQSQKWVVDTNS-ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLI-SAEIHQISTEGSLTLH  163 (298)
Q Consensus        87 GDiVIG~V~~V~~~~~~VDI~s-~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV-~A~V~sv~~dg~~~Ls  163 (298)
                      |++|-|+|.+...+...|++.. ...|+|+...... ...+.       ..+...+++||.+ .+-|.+. ....+.||
T Consensus         1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD-~~~k~-------~~~~~klrvG~~L~~~lvL~~-~~r~i~lt   70 (72)
T cd05699           1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD-HVSNC-------PLLWHCLQEGDTIPNLMCLSN-YKGRIILT   70 (72)
T ss_pred             CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC-chhhC-------HHHHhhhhcCCCccceEEEec-cccEEEEe
Confidence            7899999999999999999965 7789998777642 22222       3346789999999 7777722 23344454

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.

>KOG1856|consensus

Probab=92.35  E-value=0.19  Score=55.47  Aligned_cols=77  Identities=17%  Similarity=0.135  Sum_probs=61.1

Q ss_pred             cccCCCEEEEEEEEEecce---EEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-C
Q psy10116         83 IGEIGEVVVGRVTGLQSQK---WVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-G  158 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~---~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g  158 (298)
                      +-.+|-+|.++|++|+..+   ..|-..+..+|+++..+++          +.+.....+-+++|+.|+|+|++++.. =
T Consensus       982 t~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~S----------d~~v~~p~~~v~vgq~v~~kvi~id~e~f 1051 (1299)
T KOG1856|consen  982 TFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLS----------DRDVRRPENRVKVGQTVYCKVIKIDKERF 1051 (1299)
T ss_pred             HhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccC----------hhhccCHHHhhccCceEEEEeeeeeHhhh
Confidence            3468999999999999998   6668999999999988774          233444567789999999999999843 3


Q ss_pred             cEEEEeccCCC
Q psy10116        159 SLTLHTRSLKY  169 (298)
Q Consensus       159 ~~~Lstr~~~l  169 (298)
                      .+.||+|...|
T Consensus      1052 ~v~Ls~r~sdl 1062 (1299)
T KOG1856|consen 1052 SVELSCRTSDL 1062 (1299)
T ss_pred             hhhhhhhhHHh
Confidence            57788876543

>COG2088 SpoVG Uncharacterized protein, involved in the regulation of septum location [Cell envelope biogenesis, outer membrane]

Probab=88.91  E-value=1.3  Score=35.41  Aligned_cols=41  Identities=27%  Similarity=0.392  Sum_probs=34.3

Q ss_pred             ccEEEEEeeCceEEEecCCCC-CCCccccccccCCHHHHHHHH
Q psy10116        197 CGAQVILGCNGYVWVSAIDEN-KSGGFIQNMEVVKLSDRETIT  238 (298)
Q Consensus       197 ~~~eiivG~NG~IWI~~~~~~-~~~~~~~~~~~i~~~~r~~i~  238 (298)
                      -+..++=|.|| +||..++.. .++.|-+...||+.++|+.|.
T Consensus        32 hdirVi~G~~G-lfVAMPSrrt~dgEFrDI~HPI~~~~R~kIq   73 (95)
T COG2088          32 HDIRVIEGNNG-LFVAMPSRRTPDGEFRDIAHPINSDTREKIQ   73 (95)
T ss_pred             eccEEEeCCcc-eEEEccCccCCCcchhhccCcCCHHHHHHHH
Confidence            47899999999 999988873 356677778899999999994

>KOG1070|consensus

Probab=88.12  E-value=0.65  Score=52.53  Aligned_cols=69  Identities=17%  Similarity=0.090  Sum_probs=56.7

Q ss_pred             CccccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC
Q psy10116         79 NSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS  155 (298)
Q Consensus        79 ~~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~  155 (298)
                      ++.|.-++|++|-+.|+++.++...|+..+...|-+|+|++..-        .....+.-..|++||-|.|+|+.-.
T Consensus       878 k~~~~~~igsiv~a~v~svKp~~L~v~l~~~~~gri~isev~d~--------~~eitDp~~k~~vG~~I~vrviG~~  946 (1710)
T KOG1070|consen  878 KSTEDLSIGSIVRAYVKSVKPDQLNVLLAANHHGRIHISEVLDN--------LHEITDPLDKFKVGDGIFVRVIGGH  946 (1710)
T ss_pred             ccccceeeeeEEEEEEeeecccceEEeccccccCceehHHhhcc--------ccccCChhhhcccCCeEEEEEEcCC
Confidence            34688899999999999999999999999999999999987421        0111225678999999999999864

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

Probab=85.41  E-value=4.2  Score=33.37  Aligned_cols=54  Identities=15%  Similarity=0.297  Sum_probs=45.0

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEe
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQI  154 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv  154 (298)
                      +-.|-+|+|+|..+-++-.++|.|..+.++.+-.+.+                 .+.+..|+.|+.++...
T Consensus        21 ~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~~-----------------~~~y~~G~rV~lrLkdl   74 (104)
T PF10246_consen   21 DPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAVN-----------------GEKYVRGSRVRLRLKDL   74 (104)
T ss_pred             CccCCEEEEEEEEEecCceEEEeCCceeEEEeccccc-----------------ccccccCCEEEEEECCH
Confidence            3478899999999999999999999999998755543                 34588899999998753

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].

>KOG3298|consensus

Probab=85.38  E-value=6.7  Score=34.71  Aligned_cols=87  Identities=16%  Similarity=0.124  Sum_probs=52.9

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEec---cccc-CCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHL---TSVN-LPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST  156 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~---s~v~-~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~  156 (298)
                      -+.|-.||+|=|.|+.+...++++++|--.-.+++-   .++. .||.-.-.   -...++. .++.|+.|+.+|+..--
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 TFKPFKGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPN---FQTEDES-VIQKGVEVRLKIIGTRV  151 (170)
T ss_pred             EEeecCCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccCCCCCCCc---ccccccc-eeeeCcEEEEEEEEEEE
Confidence            578999999999999999999999998432222221   1111 13211000   0011222 68999999999998752


Q ss_pred             C--CcEEE-EeccCCCcc
Q psy10116        157 E--GSLTL-HTRSLKYGK  171 (298)
Q Consensus       157 d--g~~~L-str~~~lGk  171 (298)
                      |  .-+.| |..++.||.
T Consensus       152 ~~~~i~algtl~~D~LG~  169 (170)
T KOG3298|consen  152 DETEIFALGTLKGDYLGP  169 (170)
T ss_pred             eeeeEEEEEEecCccccc
Confidence            2  12334 346667775

>KOG1067|consensus

Probab=85.26  E-value=1.6  Score=45.49  Aligned_cols=76  Identities=16%  Similarity=0.281  Sum_probs=61.9

Q ss_pred             ccccCCCEEE-----EEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC
Q psy10116         82 YIGEIGEVVV-----GRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST  156 (298)
Q Consensus        82 Y~P~vGDiVI-----G~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~  156 (298)
                      -.|+++|++.     ++|+++.+.+++|.+-....|.||.|+..     +|     ...+..+.+++||.|..+-...+.
T Consensus       659 ~~~~~~~l~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~-----~e-----~iakpsd~levGq~I~vk~ie~d~  728 (760)
T KOG1067|consen  659 KDDQVQDLEFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLD-----QE-----KIAKPSDLLEVGQEIQVKYIERDP  728 (760)
T ss_pred             cCccccceEeeeEEEEEEeeecccceEEEecCCchhhccchhcc-----cc-----cccChHHHHhhcceeEEEEEeecC
Confidence            3477888876     78999999999999988889999999974     22     234446779999999999999998


Q ss_pred             CCcEEEEeccC
Q psy10116        157 EGSLTLHTRSL  167 (298)
Q Consensus       157 dg~~~Lstr~~  167 (298)
                      .+.+.|+.|..
T Consensus       729 ~g~~~ls~ral  739 (760)
T KOG1067|consen  729 RGGIMLSSRAL  739 (760)
T ss_pred             ccceeehhhhh
Confidence            88888887653

>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=84.77  E-value=3.7  Score=34.47  Aligned_cols=70  Identities=14%  Similarity=0.171  Sum_probs=44.1

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCccc-ccch----hhhhhhhcccCCCCEEEEEEEEeC
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQR-RRSV----QDEEMMREFLKEGDLISAEIHQIS  155 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~R-r~~~----~d~~~mr~~~~~GDlV~A~V~sv~  155 (298)
                      |-+|+++.|+|.+-..++.+|.++--.+-++|.+.+  |....- ....    ......+-++..|+.|+-||.++.
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 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLL--PEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEI   75 (122)
T ss_dssp             --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC---TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEE
T ss_pred             CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHC--CCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEE
Confidence            678999999999999999999997656666665543  322110 0000    001344678999999999999975

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

>CHL00121 rpl27 ribosomal protein L27; Reviewed

Probab=83.01  E-value=2.5  Score=33.53  Aligned_cols=52  Identities=15%  Similarity=0.184  Sum_probs=39.4

Q ss_pred             ccCCCeEecCCccCCC--CCeeccCCeEe-cCCeEEEEEeeEEEEe-----CcEEEEEec
Q psy10116         27 EFTDPILTPGETVEYL--EGYMTGHGTFP-DDEEIKASVGGVVEKV-----NQLVSVRAM   78 (298)
Q Consensus        27 ~~~~~iV~PGD~I~~~--~~~~~G~Gty~-~~g~i~Asv~G~v~~~-----nk~v~V~p~   78 (298)
                      ....+.|.||+.|.-.  ..|-||.++-. .|..|+|.+.|.|...     .+.|+|.|.
T Consensus        25 ~~~gq~V~~G~IivRQRGtk~hPG~NVg~GrD~TlfAl~~G~V~f~~~~~~~~~vsv~~~   84 (86)
T CHL00121         25 RFGGEKVSAGNILIRQRGTKFKPGLNVGCGKDFTLYALIDGFVKFKKKNKKQKSINVINI   84 (86)
T ss_pred             EcCCEEEcCCcEEEEcCCCeECCCCcccccCCceEEEccceEEEEEEeCCCCEEEEEeec
Confidence            3466899999999764  35778887655 4899999999999963     245777664

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

Probab=81.94  E-value=31  Score=33.06  Aligned_cols=64  Identities=14%  Similarity=0.147  Sum_probs=49.2

Q ss_pred             cccCCCEEEEEEEEEe-cceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEE
Q psy10116         83 IGEIGEVVVGRVTGLQ-SQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLT  161 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~-~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~  161 (298)
                      .-.+|+.=-++|+++. .-+++||.|=+.+.++|+++.  |-            .-+-..++||-+++.+-- ++.+-+.
T Consensus        70 ~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~el--p~------------~~~~wpq~Gd~l~v~l~~-Dkk~Ri~  134 (287)
T COG2996          70 KATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDEL--PT------------LKSLWPQKGDKLLVYLYV-DKKGRIW  134 (287)
T ss_pred             eEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhc--cc------------ccccCCCCCCEEEEEEEE-ccCCcEE
Confidence            3489999999999999 999999999999999998875  20            003458999999988764 3333343

>PF04026 SpoVG: SpoVG; InterPro: IPR007170 This is a stage V sporulation protein G

Probab=80.84  E-value=3.5  Score=32.42  Aligned_cols=41  Identities=24%  Similarity=0.333  Sum_probs=31.7

Q ss_pred             ccEEEEEeeCceEEEecCCC-CCCCccccccccCCHHHHHHHH
Q psy10116        197 CGAQVILGCNGYVWVSAIDE-NKSGGFIQNMEVVKLSDRETIT  238 (298)
Q Consensus       197 ~~~eiivG~NG~IWI~~~~~-~~~~~~~~~~~~i~~~~r~~i~  238 (298)
                      -++.|+=|.|| .||.-++. ..++.|.+...|++.+.|+.|.
T Consensus        32 ~~ikVieg~~G-lFVaMPs~k~~~g~y~Di~~Pitke~Re~i~   73 (84)
T PF04026_consen   32 HDIKVIEGEKG-LFVAMPSRKSKDGEYKDICHPITKEFREQIE   73 (84)
T ss_dssp             EEEEEEEETTE-EEEE--EEE-TTS-EEESEEESSHHHHHHHH
T ss_pred             EeEEEEECCCC-cEEECCCcCCCCCCEEEEEEECCHHHHHHHH
Confidence            47899999999 99998876 3456777888999999999985

It is essential for sporulation and specific to stage V sporulation in Bacillus megaterium and Bacillus subtilis []. In B. subtilis, expression decreases after 30-60 minutes of cold shock [].; GO: 0030435 sporulation resulting in formation of a cellular spore; PDB: 2IA9_F 2I9X_B 2I9Z_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	298
2nn6_H	308	Structure Of The Human Rna Exosome Composed Of Rrp4		9e-76
4ifd_H	361	Crystal Structure Of An 11-subunit Eukaryotic Exoso		1e-42
3l7z_C	249	Crystal Structure Of The S. Solfataricus Archaeal E		2e-04
2jeb_I	251	Structure Of A 9-Subunit Archaeal Exosome Bound To		2e-04
2je6_I	251	Structure Of A 9-Subunit Archaeal Exosome Length =		2e-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 =  280 bits (715), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 134/263 (50%), Positives = 190/263 (72%), Gaps = 3/263 (1%)
Query: 32  ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYXXXXXXXXX 91
           ++ PG+T+    G+M GHGT+  +E++ ASV G VE+VN+L+ V+A+ +RY         
Sbjct: 41  LVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKALKTRYIGEVGDIVV 100
Query: 92  XRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
            R+T +Q ++W V+TNS L+S L L+S+NLPGGE RRRS +DE  MR FL+EGDLISAE+
Sbjct: 101 GRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEV 160
Query: 152 HQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWV 211
             + ++G+++LHTRSLKYGKLGQG+L+ V PSL++R K+HF +L CGA VILG NG++W+
Sbjct: 161 QAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWI 220
Query: 212 SAIDENK---SGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLK 268
               E+K   +GGFI N+E V L+DRE I+RL N I +L   ++ML+DTSI Y YE SL 
Sbjct: 221 YPTPEHKEEEAGGFIANLEPVSLADREVISRLRNCIISLVTQRMMLYDTSILYCYEASLP 280
Query: 269 YSTYDLLKPESKLDLVLCTAQKL 291
           +   D+LKPE   ++V+ T Q+L
Sbjct: 281 HQIKDILKPEIMEEIVMETRQRL 303

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

Iteration: 1
 Score =  169 bits (429), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 110/305 (36%), Positives = 156/305 (51%), Gaps = 41/305 (13%)
Query: 32  ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYXXXXXXXXX 91
           I+TPGE V     +M GHGT+  D    +SV G V +VN+L+SV  +  RY         
Sbjct: 56  IVTPGELVTDDPIWMRGHGTYFLDNMTYSSVAGTVSRVNRLLSVIPLKGRYAPETGDHVV 115
Query: 92  XRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
            R+  + +++W VD      + L L SVNLPGG  RR+S  DE  MR FLKEGDL++AE+
Sbjct: 116 GRIAEVGNKRWKVDIGGKQHAVLMLGSVNLPGGILRRKSESDELQMRSFLKEGDLLNAEV 175
Query: 152 HQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWV 211
             +  +GS +LHTRSLKYGKL  G+   VP SLI R+K+H  NL     V+LG NGY+W+
Sbjct: 176 QSLFQDGSASLHTRSLKYGKLRNGMFCQVPSSLIVRAKNHTHNLPGNITVVLGVNGYIWL 235
Query: 212 ------------------SAIDENKSGGFIQ-NMEVVKLSD------------------- 233
                             S+I      G +  N  + +L +                   
Sbjct: 236 RKTSQMDLARDTPSANNSSSIKSTGPTGAVSLNPSITRLEEESSWQIYSDENDPSISNNI 295
Query: 234 RETITRLNNVIKALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLV---LCTAQK 290
           R+ I R  NVIKALA  ++ +    I  AYE S+ YS    L  ++ ++ +   + TA+K
Sbjct: 296 RQAICRYANVIKALAFCEIGITQQRIVSAYEASMVYSNVGELIEKNVMESIGSDILTAEK 355
Query: 291 LQTLG 295
           ++  G
Sbjct: 356 MRGNG 360

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/157 (24%), Positives = 67/157 (42%), Gaps = 15/157 (9%)
Query: 102 WVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLT 161
           WVVD  +  ++  +L + NL G     RS+   E +R +L  GD + A I          
Sbjct: 88  WVVDIKAPYKA--YLPASNLLG-----RSINVGEDLRRYLDVGDYVIARIENFDRSIDPV 140
Query: 162 LHTRSLKYGKLGQGILLTV----PPSLIRRSKSHFCNLA--CGAQVILGCNGYVWVSAID 215
           L  +    G++  GI++ +     P +I ++KS +  L    G  + +  NG +W +   
Sbjct: 141 LSVKGKDLGRVSNGIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPS 200
Query: 216 ENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKV 252
                  I+ +   K+ +   I  L + IK   E K+
Sbjct: 201 RFSEEILIEAIR--KIENESHIKGLTDRIKQFIEEKL 235

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/157 (24%), Positives = 67/157 (42%), Gaps = 15/157 (9%)
Query: 102 WVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLT 161
           WVVD  +  ++  +L + NL G     RS+   E +R +L  GD + A I          
Sbjct: 90  WVVDIKAPYKA--YLPASNLLG-----RSINVGEDLRRYLDVGDYVIARIENFDRSIDPV 142
Query: 162 LHTRSLKYGKLGQGILLTV----PPSLIRRSKSHFCNLA--CGAQVILGCNGYVWVSAID 215
           L  +    G++  GI++ +     P +I ++KS +  L    G  + +  NG +W +   
Sbjct: 143 LSVKGKDLGRVSNGIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPS 202
Query: 216 ENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKV 252
                  I+ +   K+ +   I  L + IK   E K+
Sbjct: 203 RFSEEILIEAIR--KIENESHIKGLTDRIKQFIEEKL 237

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/157 (24%), Positives = 67/157 (42%), Gaps = 15/157 (9%)
Query: 102 WVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLT 161
           WVVD  +  ++  +L + NL G     RS+   E +R +L  GD + A I          
Sbjct: 90  WVVDIKAPYKA--YLPASNLLG-----RSINVGEDLRRYLDVGDYVIARIENFDRSIDPV 142
Query: 162 LHTRSLKYGKLGQGILLTV----PPSLIRRSKSHFCNLA--CGAQVILGCNGYVWVSAID 215
           L  +    G++  GI++ +     P +I ++KS +  L    G  + +  NG +W +   
Sbjct: 143 LSVKGKDLGRVSNGIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPS 202
Query: 216 ENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKV 252
                  I+ +   K+ +   I  L + IK   E K+
Sbjct: 203 RFSEEILIEAIR--KIENESHIKGLTDRIKQFIEEKL 237

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	298
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	1e-88
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	1e-46
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	5e-44
2nn6_G	289	Exosome complex exonuclease RRP40; RNA, exosome, P	2e-43
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	2e-42
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	7e-33
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	6e-31
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	2e-29
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-04

>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 =  266 bits (680), Expect = 1e-88
 Identities = 145/289 (50%), Positives = 207/289 (71%), Gaps = 4/289 (1%)

Query: 10  IEIMLASDRIDPLIEIHEFTDP-ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEK 68
           +E+ L   R      +   T   ++ PG+T+    G+M GHGT+  +E++ ASV G VE+
Sbjct: 18  MEMRLPVARKPLSERLGRDTKKHLVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVER 77

Query: 69  VNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRR 128
           VN+L+ V+A+ +RYIGE+G++VVGR+T +Q ++W V+TNS L+S L L+S+NLPGGE RR
Sbjct: 78  VNKLICVKALKTRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRR 137

Query: 129 RSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRS 188
           RS +DE  MR FL+EGDLISAE+  + ++G+++LHTRSLKYGKLGQG+L+ V PSL++R 
Sbjct: 138 RSAEDELAMRGFLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQ 197

Query: 189 KSHFCNLACGAQVILGCNGYVWVSAIDENK---SGGFIQNMEVVKLSDRETITRLNNVIK 245
           K+HF +L CGA VILG NG++W+    E+K   +GGFI N+E V L+DRE I+RL N I 
Sbjct: 198 KTHFHDLPCGASVILGNNGFIWIYPTPEHKEEEAGGFIANLEPVSLADREVISRLRNCII 257

Query: 246 ALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTL 294
           +L   ++ML+DTSI Y YE SL +   D+LKPE   ++V+ T Q+L   
Sbjct: 258 SLVTQRMMLYDTSILYCYEASLPHQIKDILKPEIMEEIVMETRQRLLEQ 306

>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 =  155 bits (393), Expect = 1e-46
 Identities = 41/194 (21%), Positives = 83/194 (42%), Gaps = 16/194 (8%)

Query: 32  ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVV 91
           I+ PG+ +        G+GT+ +  ++ A + G+ ++    V V  +  RY   +G+VV+
Sbjct: 4   IVLPGDLLST-NPRAAGYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGRYTPSVGDVVI 62

Query: 92  GRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
           G +  + +  W VD  S  ++ L ++    P  +  ++         E L  GD I A++
Sbjct: 63  GIIREVAANGWAVDIYSPYQAFLPVSEN--PEMKPNKK-------PNEVLDIGDAIIAKV 113

Query: 152 HQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFC------NLACGAQVILGC 205
             I  +  +TL  +      +  G ++ + P+ + R                  Q+++G 
Sbjct: 114 LNIDPKMKVTLTMKDRICRPIRFGRIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQ 173

Query: 206 NGYVWVSAIDENKS 219
           NG +WV+      S
Sbjct: 174 NGLIWVNGDRRKVS 187

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

 Score =  149 bits (377), Expect = 5e-44
 Identities = 42/235 (17%), Positives = 88/235 (37%), Gaps = 19/235 (8%)

Query: 26  HEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQL--VSVRAMNSRYI 83
            +    I+ PGE +   E   +           +A+V G++ +       +   +   Y+
Sbjct: 5   RQLAGRIVVPGEPLPE-EVEASPPYVIDYKGVKRATVVGLLREKGDGGGRAFVKLKEIYV 63

Query: 84  GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKE 143
            + G+VV+G +  +    W VD NS   + L +           R      + M+  LK 
Sbjct: 64  PQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDF------LGRPFNPAVDDMQSLLKV 117

Query: 144 GDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNL------AC 197
           GD I A++       S  L  +    G++ +G ++ + P+ + R      ++        
Sbjct: 118 GDYIKAKVVAFDKTRSPLLTVQGEGLGRIVRGKIVEISPAKVPRVIGRKMSMLKTLEEKT 177

Query: 198 GAQVILGCNGYVWVSAIDENKSGGFIQNMEVVKLSDRE-TITRLNNVIKALAESK 251
             ++ +  NG + +   +E+        +  +K+ D E   + L   I    E +
Sbjct: 178 ECKIFVARNGRIHLECPNEDLE---AIAVMAIKIIDEEAYTSGLTKRIIKFIEEE 229

>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 =  149 bits (377), Expect = 2e-43
 Identities = 45/256 (17%), Positives = 89/256 (34%), Gaps = 33/256 (12%)

Query: 14  LASDRIDPLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVV------- 66
           L     +         +  L+           + G G     + +  +  G +       
Sbjct: 48  LLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGS 107

Query: 67  EKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQ 126
                +  V +   RY+   G+ V+G VT      + VD      ++L    ++  G  +
Sbjct: 108 GSGGGVYWVDSQQKRYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSY--LSFEGATK 165

Query: 127 RRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTL-----HTRSLKYGKLGQ-GILLTV 180
           R          R  ++ GDLI  +    + +    +       R+   G +GQ G+L  V
Sbjct: 166 R---------NRPNVQVGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVIGQDGLLFKV 216

Query: 181 PPSLIRRSKSHFCNL------ACGAQVILGCNGYVWVSAIDENKSGGFIQNMEVVKLSDR 234
              LIR+  +  C +          +++ G NG +WV A    ++   +    +++  + 
Sbjct: 217 TLGLIRKLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTIQQT---LILANILEACEH 273

Query: 235 ETITRLNNVIKALAES 250
            T  +   +   LAES
Sbjct: 274 MTSDQRKQIFSRLAES 289

>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 =  145 bits (366), Expect = 2e-42
 Identities = 50/230 (21%), Positives = 93/230 (40%), Gaps = 21/230 (9%)

Query: 32  ILTPGETVEYLEGYMTGHGTF--PDDEEIKASVGGVVEKVNQLVSVRAMN-SRYIGEIGE 88
           I+ PGE +   E +      +    + +  ++V G+ +  +    V  +  S Y  +I +
Sbjct: 18  IVVPGELLAEGE-FQIPWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEGSFYYPKIND 76

Query: 89  VVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLIS 148
           +V+G V  ++   WVVD  +  ++        LP      RS+   E +R +L  GD + 
Sbjct: 77  IVIGLVEDVEIYGWVVDIKAPYKA-------YLPASNLLGRSINVGEDLRRYLDVGDYVI 129

Query: 149 AEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRR----SKSHFCNL--ACGAQVI 202
           A I          L  +    G++  GI++ + P  + R    +KS +  L    G  + 
Sbjct: 130 ARIENFDRSIDPVLSVKGKDLGRVSNGIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIF 189

Query: 203 LGCNGYVWVSAIDENKSGGFIQNMEVVKLSDRE-TITRLNNVIKALAESK 251
           +  NG +W +             +E ++  + E  I  L + IK   E K
Sbjct: 190 VANNGRIWATCPSRFSE---EILIEAIRKIENESHIKGLTDRIKQFIEEK 236

>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 =  118 bits (297), Expect = 7e-33
 Identities = 27/143 (18%), Positives = 62/143 (43%), Gaps = 4/143 (2%)

Query: 32  ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVV 91
            + PG+ +   E Y+ G G + +  E+ A+V G +   +++  V +++       G+VV+
Sbjct: 3   FVMPGDRIGSAEEYVKGEGVYEEGGELFAAVAGKLIIKDRVAKVESISPIPEIVKGDVVL 62

Query: 92  GRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
           GRV  L++   +++ +S        ++  +             + + E +   D++ A +
Sbjct: 63  GRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKARV 122

Query: 152 HQISTEGSLTLHTRSLKYGKLGQ 174
                  +L L T+  + G L  
Sbjct: 123 I----GDNLRLSTKEEEMGVLRA 141

>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 =  113 bits (283), Expect = 6e-31
 Identities = 32/146 (21%), Positives = 55/146 (37%), Gaps = 23/146 (15%)

Query: 81  RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREF 140
           RYI  + + V+G + G  S  + V   +   S   L+ +  P   ++          R  
Sbjct: 2   RYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVS-LSYMAFPNASKK---------NRPT 51

Query: 141 LKEGDLISAEIHQISTEGSLT------LHTRSLKYGKLGQGILLTVPPSLIRR--SKSHF 192
           L+ GDL+ A +     E             R   +G L  G+++ V  +  R+    + F
Sbjct: 52  LQVGDLVYARVCTAEKELEAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDF 111

Query: 193 CNLA-----CGAQVILGCNGYVWVSA 213
             L         +V +G NG +WV  
Sbjct: 112 PLLKVLAAHTKFEVAIGLNGKIWVKC 137

>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 =  110 bits (275), Expect = 2e-29
 Identities = 33/148 (22%), Positives = 64/148 (43%), Gaps = 7/148 (4%)

Query: 32  ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVN-----QLVSV-RAMNSRYIGE 85
              PGE +  LE    G GT+     I +S+ G + K +      +VSV R   S+ + +
Sbjct: 21  YCIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSSENGALPVVSVVRETESQLLPD 80

Query: 86  IGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGD 145
           +G +V  +V+ + S+   V    +    L  +       E  R + +D+  + +  + GD
Sbjct: 81  VGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYKSFRPGD 140

Query: 146 LISAEIHQISTEGS-LTLHTRSLKYGKL 172
           ++ A++  +    S   L T   + G +
Sbjct: 141 IVLAKVISLGDAQSNYLLTTAENELGVV 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 = 40.6 bits (94), Expect = 6e-04
 Identities = 36/332 (10%), Positives = 90/332 (27%), Gaps = 111/332 (33%)

Query: 24  EIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEE-IKASVGGVVEKVNQLVSVRAMNSRY 82
           ++ +    IL+  E    +           D           ++ K  ++V       ++
Sbjct: 37  DVQDMPKSILSKEEIDHIIMS--------KDAVSGTLRLFWTLLSKQEEMVQ------KF 82

Query: 83  IGEIGEVVVGRVTGLQSQ-KWVVDT------NSILESALHLTSVN-LPGGEQ--RRRSVQ 132
           + E+          L+   K+++           + + +++   + L    Q   + +V 
Sbjct: 83  VEEV----------LRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVS 132

Query: 133 DEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHF 192
             +   + L++       + ++    ++ +       G LG G             K+  
Sbjct: 133 RLQPYLK-LRQA------LLELRPAKNVLID------GVLGSG-------------KTWV 166

Query: 193 CNLACGAQVILGC--NGYVWVSAIDENKSGGFIQNM------------------------ 226
               C +  +         W++  + N     ++ +                        
Sbjct: 167 ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLR 226

Query: 227 -EVVKLSDRETITR---------LNNV-----IKALA-ESKVMLF--DTSI------QYA 262
              ++   R  +           L NV       A     K++L      +         
Sbjct: 227 IHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATT 286

Query: 263 YEESLKYSTYDLLKPESKLDLVLCTAQKLQTL 294
              SL + +  L   E K  L+     + Q L
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKYLDCRPQDL 318

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	298
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,	99.98
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	99.97
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	98.97
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	98.89
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	98.87
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	98.87
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	98.85
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	98.83
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	98.8
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	98.8
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	98.76
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	98.74
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	98.73
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.61
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	98.58
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	98.54
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	98.5
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.47
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.36
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	98.34
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.32
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.2
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	98.01
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	97.95
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	97.83
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	97.82
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	97.8
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	97.74
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	97.67
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	97.62
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	97.6
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	97.48
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	97.25
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	97.2
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	97.01
2bh8_A	101	1B11; transcription, molecular evolution, unique a	94.25
3d0f_A	106	Penicillin-binding 1 transmembrane protein MRCA; B	94.21
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	93.85
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	89.89
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	86.88
2i9x_A	87	Putative septation protein spovg; APC86317.1, stap	85.87
2ia9_A	100	Putative septation protein spovg; APC85465, bacill	83.83
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	82.79
3v2d_0	85	50S ribosomal protein L27; ribosome associated inh	80.88
2i9z_A	105	Putative septation protein spovg; APC86317, staphy	80.27

>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=1.1e-70  Score=519.31  Aligned_cols=287  Identities=49%  Similarity=0.858  Sum_probs=242.0

Q ss_pred             CceeeeccccCCCccccccccCCCeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEeCcEEEEEecCccccccCC
Q psy10116          8 PVIEIMLASDRIDPLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIG   87 (298)
Q Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~nk~v~V~p~~~rY~P~vG   87 (298)
                      |.++++++.+++++... .+..+++|+|||.|+..++|++|+|||.++|+|+||++|.+...++++||+|++++|.|++|
T Consensus        18 ~~~~~~~~~~~~~~~~~-~~~~~~iVlPGd~L~~~~~~~~G~Gty~~~g~I~Asv~G~v~~~~~~vsV~p~~~rY~P~vG   96 (308)
T 2nn6_H           18 MEMRLPVARKPLSERLG-RDTKKHLVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKALKTRYIGEVG   96 (308)
T ss_dssp             -----------------------CBCCTTCBCCCCTTCCBCTTEEECSSSEEECSSEEEEEETTEEEEEESSCCCCCCSS
T ss_pred             ccccchhhhhccccccc-cCCCCcEEeCCCCCCCCCCEeecCCeEEECCEEEEEEEEEEEecCCEEEEeeCCCccCCCCC
Confidence            56889999999987443 45567899999999988899999999999999999999999999999999999999999999


Q ss_pred             CEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccC
Q psy10116         88 EVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSL  167 (298)
Q Consensus        88 DiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~  167 (298)
                      |+|+|+|+++++++|+|||++++++.+++|+++||||++|++...|+.+|+++|++||+|+|||++++.++++.||||++
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            99999999999999999999999999999999999999999888889999999999999999999999889999999999


Q ss_pred             CCccCCCceEEEeCchhhccccCcceeccccEEEEEeeCceEEEecCCCC---CCCccccccccCCHHHHHHHHHHHHHH
Q psy10116        168 KYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWVSAIDEN---KSGGFIQNMEVVKLSDRETITRLNNVI  244 (298)
Q Consensus       168 ~lGkL~~G~lv~v~~~li~r~~~~~~~l~~~~eiivG~NG~IWI~~~~~~---~~~~~~~~~~~i~~~~r~~i~rv~n~i  244 (298)
                      +||+|++|+++++++.|++|+++|++++.|+|+|++|+||||||++...+   ...+|.+++++++.++|+.|||++|||
T Consensus       177 ~LGkL~~G~v~~vs~~lv~r~~~~l~~l~~g~eI~vG~NG~IWi~~~~~~~~~~~~~~~~~~~~~~~~~r~~i~r~~n~i  256 (308)
T 2nn6_H          177 KYGKLGQGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWIYPTPEHKEEEAGGFIANLEPVSLADREVISRLRNCI  256 (308)
T ss_dssp             TTCEECSSCEEECCTTSCCCSTTCSCCCBTTBEEEEETTTEEEEECCCCC------CCGGGSSCCCHHHHHHHHHHHHHH
T ss_pred             CCcccCCeEEEEEChhheechhheEecCCCCcEEEEeCCCEEEEcCCcchhhhhcccccccCCcCCHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999987642   234688888999999999999999999


Q ss_pred             HHHhhCCcccCHHHHHHHHHHHhCCCCcccCChhHHHHHHHHHHHHHHHcc
Q psy10116        245 KALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTLG  295 (298)
Q Consensus       245 ~~l~~~~~~i~~~~i~~~~~~s~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  295 (298)
                      ++|++++++||+++|+++|++|++++++|||.||+++++++++++||++++
T Consensus       257 ~~l~~~~~~i~~~~i~~~~~~s~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  307 (308)
T 2nn6_H          257 ISLVTQRMMLYDTSILYCYEASLPHQIKDILKPEIMEEIVMETRQRLLEQE  307 (308)
T ss_dssp             HHHHHTTCCCCHHHHHHHHHTHHHHCCSSCCTTHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHcCCccCHHHHHHHHHHHhhCCHHHhccHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999999999999999999999999999999999999875

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

Probab=100.00  E-value=2.4e-46  Score=350.51  Aligned_cols=192  Identities=23%  Similarity=0.352  Sum_probs=162.2

Q ss_pred             cCCCeEecCCccCCCC-----------------------Ceec--cCCeEecCCeEEEEEeeEEEEeCc-------EEEE
Q psy10116         28 FTDPILTPGETVEYLE-----------------------GYMT--GHGTFPDDEEIKASVGGVVEKVNQ-------LVSV   75 (298)
Q Consensus        28 ~~~~iV~PGD~I~~~~-----------------------~~~~--G~Gty~~~g~i~Asv~G~v~~~nk-------~v~V   75 (298)
                      ..+.+|+|||.|+..+                       +|++  |+|||.++++++||++|.++.+++       ++||
T Consensus        37 ~~~~iVlPGD~L~~~~~~~~~~~g~~~~~~l~~~~~~~~~~~~~~G~Gty~~~~~I~as~aG~l~~~~~~~~~~~~~v~V  116 (289)
T 2nn6_G           37 VLGQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWV  116 (289)
T ss_dssp             GGSSBCCSSEEECCSCSCCEECSSEEECC-----------------------CCCEEECSCCEEEEECCTTTSSCCEEEE
T ss_pred             cCCcEEeCCCCcCccccccccccccccccccccccccCcceEEccCCCeEEECCEEEEEEeEeEEeccCCccCccceEEE
Confidence            4568999999998765                       7888  999999999999999999998865       7999


Q ss_pred             EecCccccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC
Q psy10116         76 RAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS  155 (298)
Q Consensus        76 ~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~  155 (298)
                      +|++++|+|++||+|+|+|+++.+++|+|||++++.|+|++++|  ||+++         +||++|++||+|+|||++++
T Consensus       117 ~~~~~rYiP~vGDiVIG~Vt~v~~~~~~VdI~s~~~a~L~~~~f--~Gatk---------~~r~~f~~GDlV~ArV~s~~  185 (289)
T 2nn6_G          117 DSQQKRYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSF--EGATK---------RNRPNVQVGDLIYGQFVVAN  185 (289)
T ss_dssp             ECCCSSCCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSS--SCCSS---------CSSSSSCTTCEEEEEEEECC
T ss_pred             EecCCCCCCCCCCEEEEEEEEEeCcEEEEEECCCceeEEehhhc--Ccchh---------hhhhhcCCCCEEEEEEEEcC
Confidence            99999999999999999999999999999999999999999985  68764         46999999999999999999


Q ss_pred             CCCcEEEEe-----ccCCCccC-CCceEEEeCchhhccccCccee----c--cccEEEEEeeCceEEEecCCCCCCCccc
Q psy10116        156 TEGSLTLHT-----RSLKYGKL-GQGILLTVPPSLIRRSKSHFCN----L--ACGAQVILGCNGYVWVSAIDENKSGGFI  223 (298)
Q Consensus       156 ~dg~~~Lst-----r~~~lGkL-~~G~lv~v~~~li~r~~~~~~~----l--~~~~eiivG~NG~IWI~~~~~~~~~~~~  223 (298)
                      .+++++|||     |+.+||+| ++|++|+|+|++++|+++|.+.    |  .++|||++|+||||||++.+.       
T Consensus       186 ~~~~~eLsc~~~~~k~~~lG~L~~~G~l~~Vs~~lvrrl~~~~~~~l~~L~~~~~~eI~vG~NG~IWI~~~~~-------  258 (289)
T 2nn6_G          186 KDMEPEMVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTI-------  258 (289)
T ss_dssp             TTSCCEEECSBTTTTBCCCCSCCSSCEEECCCHHHHHHHHCTTCSHHHHTTCSSSCCCEEETTTEEEECCSSH-------
T ss_pred             CCCceEEEecccccccccCCEecCCeEEEEEChHHhhhhhcCchhHHHHhcccCCeEEEEECCcEEEEecCCh-------
Confidence            999999999     99999999 9999999999999999988765    3  489999999999999998653       


Q ss_pred             cccccCCHHHHHHHHHHHHHHHHHh
Q psy10116        224 QNMEVVKLSDRETITRLNNVIKALA  248 (298)
Q Consensus       224 ~~~~~i~~~~r~~i~rv~n~i~~l~  248 (298)
                                ++++ .+.|||+..+
T Consensus       259 ----------~~~~-~i~~aI~~~e  272 (289)
T 2nn6_G          259 ----------QQTL-ILANILEACE  272 (289)
T ss_dssp             ----------HHHH-HHHHHHHHTT
T ss_pred             ----------hHHH-HHHHHHHHhh
Confidence                      3344 4777877763

>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=7.1e-46  Score=337.22  Aligned_cols=207  Identities=20%  Similarity=0.349  Sum_probs=179.8

Q ss_pred             CCeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEeCcEEEEEecCccccccCCCEEEEEEEEEecceEEEEeCCC
Q psy10116         30 DPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTNSI  109 (298)
Q Consensus        30 ~~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~nk~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~  109 (298)
                      +++|+|||.|+. ++|++|+|||.++|+++||++|.+...++.+||+|++++|.|++||+|+|+|+++.+++|+|||+++
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~~~   80 (229)
T 2ba0_A            2 RKIVLPGDLLST-NPRAAGYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGRYTPSVGDVVIGIIREVAANGWAVDIYSP   80 (229)
T ss_dssp             CCEECTTCEEES-CTTSBCTTEEEETTEEEECSSEEEEECSSCEEEEECSSSCCCCTTCEEEEEEEEECSSEEEEECSSS
T ss_pred             CCEEcCCCCccc-CCeEecCCEEEeCCEEEEEEEEEEEEeCCEEEEEeCCCcccCCCCCEEEEEEEEEeCCeEEEEeCCC
Confidence            579999999986 5799999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccCCCccCCCceEEEeCchhhcccc
Q psy10116        110 LESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSK  189 (298)
Q Consensus       110 ~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL~~G~lv~v~~~li~r~~  189 (298)
                      ++|+||+++++.         ..+..+|+++|++||+|+|+|++++.++.+.||||+.+||+|++|++++++|++++|+.
T Consensus        81 ~~g~l~isev~~---------~~~~~~~~~~l~~GD~V~arVi~v~~~~~i~LS~r~~~lG~L~~G~v~~vs~~~v~rl~  151 (229)
T 2ba0_A           81 YQAFLPVSENPE---------MKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKDRICRPIRFGRIVAINPARVPRVI  151 (229)
T ss_dssp             SCEEEEGGGCTT---------CCTTSCGGGTCCTTCEEEEEEEEECTTCCEEEECCSSSCEEESSSEEEECCGGGHHHHH
T ss_pred             eEEEEEHHHccc---------cccccchhcccCCCCEEEEEEEEECCCCcEEEEEccccCCcccCCEEEEECHHHhHHHh
Confidence            999999999851         12457899999999999999999998899999999999999999999999999999975


Q ss_pred             C----cceec--cccEEEEEeeCceEEEecCCCCCCCccccccccCCHHHHHHHHHHHHHHHHHhhCCcc-cCHHHHHHH
Q psy10116        190 S----HFCNL--ACGAQVILGCNGYVWVSAIDENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKVM-LFDTSIQYA  262 (298)
Q Consensus       190 ~----~~~~l--~~~~eiivG~NG~IWI~~~~~~~~~~~~~~~~~i~~~~r~~i~rv~n~i~~l~~~~~~-i~~~~i~~~  262 (298)
                      +    |+++|  .|+|+|++|+||||||++..                   +....+.|||+..++.... --.+.|...
T Consensus       152 ~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~-------------------~~~~~~~~ai~~~e~~~~~~~l~~~v~~~  212 (229)
T 2ba0_A          152 GKKGSMIKLLKSELDVQIVVGQNGLIWVNGDR-------------------RKVSIAEEAIYLIEQEAHTEGLTDRVAEF  212 (229)
T ss_dssp             CGGGHHHHHHHHHHTCEEEECTTSEEEEESCH-------------------HHHHHHHHHHHHHHHCSCCSSHHHHHHHH
T ss_pred             cCCchHHHHhcccCCeEEEEECCcEEEEeCCc-------------------hhHHHHHHHHHHHHhhhhhhhHHHHHHHH
Confidence            4    55556  58999999999999999643                   2344588999988766652 224555554


Q ss_pred             HHH
Q psy10116        263 YEE  265 (298)
Q Consensus       263 ~~~  265 (298)
                      .+.
T Consensus       213 l~~  215 (229)
T 2ba0_A          213 IKR  215 (229)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>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=3.5e-45  Score=333.57  Aligned_cols=198  Identities=21%  Similarity=0.303  Sum_probs=134.7

Q ss_pred             CCeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEeCc--EEEEEecCccccccCCCEEEEEEEEEecceEEEEeC
Q psy10116         30 DPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQ--LVSVRAMNSRYIGEIGEVVVGRVTGLQSQKWVVDTN  107 (298)
Q Consensus        30 ~~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~nk--~v~V~p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~  107 (298)
                      +.+|+|||.|+. ++|++|||||.++++++||++|.+...++  .+||+|.+++|.|++||+|+|+|+++.+++|+|||+
T Consensus         9 ~~iV~PGd~l~~-~~~~~G~Gty~~~~~I~Asv~G~v~~~~~~~~vsV~p~~~~y~p~~GDiV~G~V~~v~~~~~~V~I~   87 (235)
T 2z0s_A            9 GRIVVPGEPLPE-EVEASPPYVIDYKGVKRATVVGLLREKGDGGGRAFVKLKEIYVPQAGDVVIGLIQSVGIMNWFVDIN   87 (235)
T ss_dssp             ----------------------------------------------------CCCCCCTTCCEEEEEEEECSSEEEEECS
T ss_pred             CcEEeCCCCccc-CceEcCCCEEEECCEEEEEEeEEEEEeCCccEEEEEeCCCccCCCCCCEEEEEEEEEeCCeEEEEeC
Confidence            579999999987 56999999999999999999999998876  899999999999999999999999999999999999


Q ss_pred             CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccCCCccCCCceEEEeCchhhcc
Q psy10116        108 SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRR  187 (298)
Q Consensus       108 s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL~~G~lv~v~~~li~r  187 (298)
                      ++++|+||+++++  +    ++++.+..+|+++|++||+|+|+|++++.++.+.||||+..||+|++|++++++|.+++|
T Consensus        88 ~~~~g~l~isei~--~----~~~~~~~~~~~~~l~~GD~V~a~Vi~v~~~~~i~LS~k~~~lG~l~gG~vv~vs~~~~~r  161 (235)
T 2z0s_A           88 SPYVAVLSVQDFL--G----RPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSPLLTVQGEGLGRIVRGKIVEISPAKVPR  161 (235)
T ss_dssp             SSSCEEEEHHHHH--T----SCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCEEEECCSSSCEECCSSEEEECCGGGSGG
T ss_pred             CCeEEEEEHHHhC--C----CccccchhhHhhcCCCCCEEEEEEEEECCCCcEEEEEecccCccccCCEEEEECHHHhHH
Confidence            9999999999996  2    345678899999999999999999999988899999999999999999999999999999


Q ss_pred             ccC----cceecc--ccEEEEEeeCceEEEecCCCCCCCccccccccCCHHHHHHHHHHHHHHHHHhhCCc
Q psy10116        188 SKS----HFCNLA--CGAQVILGCNGYVWVSAIDENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKV  252 (298)
Q Consensus       188 ~~~----~~~~l~--~~~eiivG~NG~IWI~~~~~~~~~~~~~~~~~i~~~~r~~i~rv~n~i~~l~~~~~  252 (298)
                      +..    |+++|.  ++|++++|+||+|||++...                  +....+.|||+..++...
T Consensus       162 l~~~~~~~l~~l~~~~~~~i~vG~NG~IWi~~~~~------------------~~~~~~~~ai~~~e~~~~  214 (235)
T 2z0s_A          162 VIGRKMSMLKTLEEKTECKIFVARNGRIHLECPNE------------------DLEAIAVMAIKIIDEEAY  214 (235)
T ss_dssp             GTCGGGHHHHHHHHHHCCEEEEETTTEEEEECSCH------------------HHHHHHHHHHHHHHHCSC
T ss_pred             HhcCcchHHHHhcccCCeEEEEeCCCEEEEecCCH------------------HHHHHHHHHHHHHHhhhh
Confidence            985    777774  89999999999999999753                  344468999998876654

>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=3e-44  Score=330.65  Aligned_cols=181  Identities=21%  Similarity=0.384  Sum_probs=159.4

Q ss_pred             CCCeEecCCccCCCCCeeccC--CeEecCCeEEEEEeeEEEEeCcEEEEEecCc-cccccCCCEEEEEEEEEecceEEEE
Q psy10116         29 TDPILTPGETVEYLEGYMTGH--GTFPDDEEIKASVGGVVEKVNQLVSVRAMNS-RYIGEIGEVVVGRVTGLQSQKWVVD  105 (298)
Q Consensus        29 ~~~iV~PGD~I~~~~~~~~G~--Gty~~~g~i~Asv~G~v~~~nk~v~V~p~~~-rY~P~vGDiVIG~V~~V~~~~~~VD  105 (298)
                      ++++|+|||.|+. ++|++||  |||.++|+|+||++|.+...++.++|+|+++ +|.|++||+|+|+|+++.+++|+||
T Consensus        15 ~~~iV~PGd~l~~-~~~~~G~~~Gty~~~g~i~as~~G~v~~~~~~v~V~p~~~~~y~p~~GDiV~G~V~~v~~~ga~Vd   93 (251)
T 2je6_I           15 PRSIVVPGELLAE-GEFQIPWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEGSFYYPKINDIVIGLVEDVEIYGWVVD   93 (251)
T ss_dssp             SSCEECTTCEEEE-ECCCCCCCTTEEEETTEEEECSSEEEEEETTEEEEEESCCSCCCCCTTCEEEEEEEEECSSEEEEE
T ss_pred             CCcEEcCCCCCcc-CCeeeCCCCCEEEECCEEEEEEEEEEEEeCCEEEEEECCCcccCCCCCCEEEEEEEEEeCceEEEE
Confidence            4689999999996 5699999  9999999999999999999999999999998 9999999999999999999999999


Q ss_pred             eCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccCCCccCCCceEEEeCchhh
Q psy10116        106 TNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLI  185 (298)
Q Consensus       106 I~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL~~G~lv~v~~~li  185 (298)
                      |+++++|+||++++.  +    ++.+.+ .+|+++|++||+|+|+|++++.++.+.||||+.+||+|++|++++++|.++
T Consensus        94 I~~~~~GlL~isei~--~----~~~~~~-~~~~~~l~vGD~V~arVi~v~~~~~i~LS~r~~~lG~L~~G~v~~vs~~~v  166 (251)
T 2je6_I           94 IKAPYKAYLPASNLL--G----RSINVG-EDLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRVSNGIVIDIMPVKV  166 (251)
T ss_dssp             CSSSSCEEEEHHHHH--T----SCCCTT-CCCSSSCCTTCEEEEEEEEEETTEEEEEECCSTTCEECCSSCEEECCGGGH
T ss_pred             cCCCeEEEEEHHHhc--C----Cccccc-cchhhcCCCCCEEEEEEEEECCCCcEEEEEccccCCcccCCEEEEECHHHh
Confidence            999999999999985  2    223445 889999999999999999999889999999999999999999999999999


Q ss_pred             cccc----Ccceec--cccEEEEEeeCceEEEecCCCC
Q psy10116        186 RRSK----SHFCNL--ACGAQVILGCNGYVWVSAIDEN  217 (298)
Q Consensus       186 ~r~~----~~~~~l--~~~~eiivG~NG~IWI~~~~~~  217 (298)
                      +|+.    +|+++|  .|+|+|++|+||||||++.+..
T Consensus       167 ~rl~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~~  204 (251)
T 2je6_I          167 PRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRF  204 (251)
T ss_dssp             HHHHCGGGHHHHHHHTTC---CEECTTSEEEC-----C
T ss_pred             HHHhcCcchHHHHhcccCCeEEEEECCcEEEEeCCCHH
Confidence            8863    477777  6999999999999999987653

>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=1.6e-35  Score=259.46  Aligned_cols=138  Identities=24%  Similarity=0.386  Sum_probs=123.7

Q ss_pred             ccccccCCCEEEEEEEEEecceEEEEeCC-CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCC
Q psy10116         80 SRYIGEIGEVVVGRVTGLQSQKWVVDTNS-ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEG  158 (298)
Q Consensus        80 ~rY~P~vGDiVIG~V~~V~~~~~~VDI~s-~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg  158 (298)
                      +||.|++||+|+|+|+++.+++|+|||++ +++|+||++++  ||+++         +||++|++||+|+|||++++.++
T Consensus         1 krY~P~~gDvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~--~g~~k---------~~r~~l~~GDlV~ArV~~~~~~~   69 (175)
T 2ja9_A            1 KRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAF--PNASK---------KNRPTLQVGDLVYARVCTAEKEL   69 (175)
T ss_dssp             CCCCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETTSS--TTCCS---------SSCCCCCTTCEEEEEEEECCTTS
T ss_pred             CCccCCCcCEEEEEEEEEECcEEEEEECCCCccEEEEHHHC--Cchhh---------hhhccCCCCCEEEEEEEEecCCC
Confidence            48999999999999999999999999999 99999999986  57653         46999999999999999999999


Q ss_pred             cEEEE------eccCCCccCCCceEEEeCchhhccccC--cceec-----cccEEEEEeeCceEEEecCCCCCCCccccc
Q psy10116        159 SLTLH------TRSLKYGKLGQGILLTVPPSLIRRSKS--HFCNL-----ACGAQVILGCNGYVWVSAIDENKSGGFIQN  225 (298)
Q Consensus       159 ~~~Ls------tr~~~lGkL~~G~lv~v~~~li~r~~~--~~~~l-----~~~~eiivG~NG~IWI~~~~~~~~~~~~~~  225 (298)
                      +++||      +|+.+||+|++|++++|+|++++|+++  |++.|     .++|||++|+||||||++.+.         
T Consensus        70 ~~~Ltc~~~~~~r~~~lG~L~~G~l~~v~~~~v~rl~~~~~~~~l~~l~~~~~~ei~vG~NG~IWi~~~~~---------  140 (175)
T 2ja9_A           70 EAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWVKCEEL---------  140 (175)
T ss_dssp             CCEEESSCTTTCSCTTCEEECSCEEEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETTTEEEEECSSH---------
T ss_pred             ceEEEecccccccccCCcCcCCCEEEEEcHHHhhHHhcCCCcchHHhhhccCCeEEEEECCcEEEEecCCH---------
Confidence            99999      999999999999999999999999974  66555     389999999999999998652         


Q ss_pred             cccCCHHHHHHHHHHHHHHHH
Q psy10116        226 MEVVKLSDRETITRLNNVIKA  246 (298)
Q Consensus       226 ~~~i~~~~r~~i~rv~n~i~~  246 (298)
                              ++++ .+.|||+.
T Consensus       141 --------~~~~-~v~~aI~~  152 (175)
T 2ja9_A          141 --------SNTL-ACYRTIME  152 (175)
T ss_dssp             --------HHHH-HHHHHHHH
T ss_pred             --------HHHH-HHHHHHHH
Confidence                    3444 58899998

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

Probab=99.98  E-value=2e-32  Score=240.05  Aligned_cols=132  Identities=23%  Similarity=0.375  Sum_probs=121.4

Q ss_pred             CeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEeCcEEEEEecCc-cccccCCCEEEEEEEEEecceEEEEeCC-
Q psy10116         31 PILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNS-RYIGEIGEVVVGRVTGLQSQKWVVDTNS-  108 (298)
Q Consensus        31 ~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~nk~v~V~p~~~-rY~P~vGDiVIG~V~~V~~~~~~VDI~s-  108 (298)
                      ++|+|||.|+..++|++|||||.++|+|+||++|.++.+++++||+|+++ +|.|+ ||+|+|+|+++.+++|+|||++ 
T Consensus         2 ~iV~PGd~l~~~~~~~~G~Gty~~~~~i~as~~G~v~~~~~~v~V~~~~~~~y~p~-GdiV~G~V~~V~~~ga~V~I~~v   80 (179)
T 3m7n_A            2 RFVMPGDRIGSAEEYVKGEGVYEEGGELFAAVAGKLIIKDRVAKVESISPIPEIVK-GDVVLGRVVDLRNSIALIEVSSK   80 (179)
T ss_dssp             CEECTTCEEEETTTSEECTTEEEETTEEEESSSEEEEEETTEEEEEESSCCCCCCT-TCEEEEEEEEECSSEEEEEEEEE
T ss_pred             eEEcCCCCCCCCCCEeccCCEEEeCCEEEEEEEEEEEEeCCEEEEEECCCCcccCC-CCEEEEEEEEEeCCcEEEEEccc
Confidence            69999999998889999999999999999999999999999999999976 69999 9999999999999999999988 


Q ss_pred             ---------CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEEeccCCCccCCCceEEE
Q psy10116        109 ---------ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLGQGILLT  179 (298)
Q Consensus       109 ---------~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Lstr~~~lGkL~~G~lv~  179 (298)
                               +++|+||+|++.          +....+|+++|++||+|.|+|++    +.+.||||+++||+     +.+
T Consensus        81 ~~~~~~~~~~~~Gll~isei~----------~~~~~~~~~~~~~GD~V~akVi~----~~i~LS~k~~~lGv-----v~a  141 (179)
T 3m7n_A           81 KGENRGPSNRGIGILHVSNVD----------EGYVKEISEAVGYLDILKARVIG----DNLRLSTKEEEMGV-----LRA  141 (179)
T ss_dssp             TTCCSCCTTCEEEEEEGGGTT----------SSCCSSGGGTCCTTCEEEEEEEE----TTTEEECCSTTCEE-----EEC
T ss_pred             cCcccccccCeeEEEEHHHcC----------cchhhCHhhcCCCCCEEEEEEEC----CeEEEEEecCCCCE-----EEe
Confidence                     899999999984          11235899999999999999998    78999999999999     666


Q ss_pred             eCc
Q psy10116        180 VPP  182 (298)
Q Consensus       180 v~~  182 (298)
                      .|+
T Consensus       142 ~~~  144 (179)
T 3m7n_A          142 LCS  144 (179)
T ss_dssp             BCT
T ss_pred             ccc
Confidence            663

>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=99.97  E-value=1.9e-31  Score=239.31  Aligned_cols=142  Identities=20%  Similarity=0.271  Sum_probs=121.1

Q ss_pred             cCCCeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEe-----CcEEEEEecCc-cccccCCCEEEEEEEEEecce
Q psy10116         28 FTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKV-----NQLVSVRAMNS-RYIGEIGEVVVGRVTGLQSQK  101 (298)
Q Consensus        28 ~~~~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~-----nk~v~V~p~~~-rY~P~vGDiVIG~V~~V~~~~  101 (298)
                      ..+.+|+|||.|+..++|++|+|||.++|+||||++|.+...     +++++|.|+++ +|.|++||+|+|+|+++++++
T Consensus        17 ~~~~iV~PGd~l~~~~~~~~G~Gty~~~g~I~Asv~G~v~~~~~~~~~~vi~V~p~~~~~y~p~vGDvV~G~V~~v~~~~   96 (209)
T 2nn6_I           17 PPVRYCIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSSENGALPVVSVVRETESQLLPDVGAIVTCKVSSINSRF   96 (209)
T ss_dssp             ---CCCCTTCEEEETTTCCCSSSCEEETTEEECCSCSCBCCCBCTTSSBC-CBCCSCCCCCCCCTTCEEEEEEEEECSSE
T ss_pred             CCCcEEcCCCCCCCCCCeeecCCEEEECCEEEEEEEEEEEEeccCCcccEEEEecCCCCcCCCCCCCEEEEEEEEEECce
Confidence            346799999999988899999999999999999999999864     35689999987 599999999999999999999


Q ss_pred             EEEEeC--------CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCC-cEEEEeccCCCccC
Q psy10116        102 WVVDTN--------SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEG-SLTLHTRSLKYGKL  172 (298)
Q Consensus       102 ~~VDI~--------s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg-~~~Lstr~~~lGkL  172 (298)
                      |+|||+        .+++|+||++++.        .+..++.+|+++|++||+|+|+|++++.++ .+.||||+++||++
T Consensus        97 a~V~I~~v~~~~L~~~~~GlIhisei~--------~~~~~~~~~~~~l~~GD~V~akVisi~~~~~~i~LS~k~~~lGVv  168 (209)
T 2nn6_I           97 AKVHILYVGSMPLKNSFRGTIRKEDVR--------ATEKDKVEIYKSFRPGDIVLAKVISLGDAQSNYLLTTAENELGVV  168 (209)
T ss_dssp             EEEEEEESSSSCCCCSSCSCEEEEGGG--------TCSSCCCCGGGTCCSSSEEEEEEEEEETTTTEEEEECCSSSCEEC
T ss_pred             EEEEECccccccccCCceeEEEHHHcc--------cccccccchhhhcCCCCEEEEEEEEEeCCCCeEEEEEecCCCcEE
Confidence            999985        4678999999873        234455689999999999999999998654 59999999999994


Q ss_pred             CCceEEEeCc
Q psy10116        173 GQGILLTVPP  182 (298)
Q Consensus       173 ~~G~lv~v~~  182 (298)
                           ++.|+
T Consensus       169 -----~A~c~  173 (209)
T 2nn6_I          169 -----VAHSE  173 (209)
T ss_dssp             -----CCBCS
T ss_pred             -----EEEcC
Confidence                 55564

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

Probab=98.97  E-value=3.6e-09  Score=80.26  Aligned_cols=71  Identities=21%  Similarity=0.186  Sum_probs=61.7

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcEE
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSLT  161 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~~  161 (298)
                      .|++||+|.|+|+++.+.+|+|+|+...+|++|+|++..     ++ .        +.|++||.|.|+|.+++.+ +.+.
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 DVEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMIS-----LR-L--------ENLNVGDEIIVQAIDVRPEKREID   67 (80)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEECGGGCSS-----CC-G--------GGCCTTCEEEEEEEEEETTTTEEE
T ss_pred             CCCCCCEEEEEEEEEeCCEEEEEECCCCEEEEEHHHCCc-----cc-c--------eeeCCCCEEEEEEEEEECCCCEEE
Confidence            378999999999999999999999989999999999741     11 0        6799999999999999976 8899


Q ss_pred             EEeccC
Q psy10116        162 LHTRSL  167 (298)
Q Consensus       162 Lstr~~  167 (298)
                      ||.+..
T Consensus        68 lsl~~~   73 (80)
T 2k52_A           68 FKYIPL   73 (80)
T ss_dssp             EEECSC
T ss_pred             EEEeec
Confidence            998754

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

Probab=98.89  E-value=7.1e-09  Score=83.95  Aligned_cols=88  Identities=15%  Similarity=0.200  Sum_probs=68.1

Q ss_pred             cEEEEEecCc-cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEE
Q psy10116         71 QLVSVRAMNS-RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISA  149 (298)
Q Consensus        71 k~v~V~p~~~-rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A  149 (298)
                      |.+.+.|... .+.|++||++.|+|+++.+.+++|+|+...+|++|+|++..   ..+      ..+....|++||.|.+
T Consensus        14 k~~~~~p~~~~~~~~~~G~~~~G~V~~v~~~G~FV~l~~~~~Glvhisel~~---~~~------~~~~~~~~~vGd~V~v   84 (115)
T 2khi_A           14 LVPRGSHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDW---TNK------NIHPSKVVNVGDVVEV   84 (115)
T ss_dssp             -------CCCSSCSSCSSCEEEEEEEEEETTEEEEECSTTCEEEEETTSSSC---SST------TCSSTTTCCTTCEEEE
T ss_pred             hhcccCCHHHHhhcCCCCCEEEEEEEEEECCEEEEEECCCCEEEEEHHHCCc---ccc------ccCcccEECCCCEEEE
Confidence            3456777776 57899999999999999999999999988999999999842   001      1244678999999999


Q ss_pred             EEEEeCC-CCcEEEEeccC
Q psy10116        150 EIHQIST-EGSLTLHTRSL  167 (298)
Q Consensus       150 ~V~sv~~-dg~~~Lstr~~  167 (298)
                      +|.+++. ++.+.|+.+..
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            9999986 67899998764

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

Probab=98.87  E-value=6e-09  Score=86.34  Aligned_cols=74  Identities=27%  Similarity=0.420  Sum_probs=63.8

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEE
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLT  161 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~  161 (298)
                      .+++||+|.|+|+++.+.+++|+|....+|+||+|++.. +         ...++.+.|++||.|.|+|++++. ++.+.
T Consensus         4 ~~~vG~iv~G~V~~i~~~G~FV~l~~~~~Glihisel~~-~---------~~~~~~~~~~vGd~V~vkV~~vd~~~~kI~   73 (130)
T 2k4k_A            4 KFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTH-G---------FVKDINEHLSVGDEVQVKVLAVDEEKGKIS   73 (130)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEEETTEEEEEEGGGTSS-S---------CCSCGGGTCCTTCEEEEEEEEEETTTTEEE
T ss_pred             cCCCCCEEEEEEEEEeCCeEEEEECCCcEEEEEHHHCCc-c---------cccCccccCCCCCEEEEEEEEEeCCCCEEE
Confidence            368999999999999999999999888999999999841 1         123457899999999999999986 78999


Q ss_pred             EEecc
Q psy10116        162 LHTRS  166 (298)
Q Consensus       162 Lstr~  166 (298)
                      ||++.
T Consensus        74 LSlk~   78 (130)
T 2k4k_A           74 LSIRA   78 (130)
T ss_dssp             EESHH
T ss_pred             EEEee
Confidence            99864

>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=98.87  E-value=8e-09  Score=90.58  Aligned_cols=77  Identities=14%  Similarity=0.236  Sum_probs=58.7

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEe--CCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-C
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDT--NSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-E  157 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI--~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-d  157 (298)
                      .+.|++||+|.|+|+++.+.+++|+|  ....+|++|+|++.-          ....+.++.|++||.|.++|++++. .
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----------RRIRSINKLIRIGRNECVVVIRVDKEK   79 (182)
T ss_dssp             SSSCCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC----------------------CTTCEEEEEEEEEETTT
T ss_pred             ccCCCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCC----------cccCCHHHhcCCCCEEEEEEEEEECCC
Confidence            35579999999999999999999999  567999999999841          1134568999999999999999985 5


Q ss_pred             CcEEEEeccC
Q psy10116        158 GSLTLHTRSL  167 (298)
Q Consensus       158 g~~~Lstr~~  167 (298)
                      +.+.||.|..
T Consensus        80 ~rI~LSlk~~   89 (182)
T 1kl9_A           80 GYIDLSKRRV   89 (182)
T ss_dssp             TEEEEESTTC
T ss_pred             CEEEEEEeec
Confidence            7899998764

>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=98.85  E-value=8.8e-09  Score=81.95  Aligned_cols=77  Identities=14%  Similarity=0.261  Sum_probs=63.9

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCC---CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNS---ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE  157 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s---~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d  157 (298)
                      ...|++||++.|+|+++.+.+++|+|+.   ..+|++|+|++.- .  .|      ..+.++.|++||.|.++|.+++. 
T Consensus         7 ~~~~~vG~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~-~--~~------~~~~~~~~~~Gd~V~VkV~~vd~-   76 (103)
T 2eqs_A            7 GEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRR-E--GR------VANVADVVSKGQRVKVKVLSFTG-   76 (103)
T ss_dssp             CSSCCTTCEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSS-S--SC------CCCHHHHCCTTCEEEEEEEEEET-
T ss_pred             cccCCCCCEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCC-C--cc------cCCcccEeCCCCEEEEEEEEEEC-
Confidence            4568999999999999999999999986   7899999999821 1  11      13456789999999999999986 


Q ss_pred             CcEEEEeccC
Q psy10116        158 GSLTLHTRSL  167 (298)
Q Consensus       158 g~~~Lstr~~  167 (298)
                      +.+.||.+..
T Consensus        77 ~~i~LSlk~~   86 (103)
T 2eqs_A           77 TKTSLSMKDV   86 (103)
T ss_dssp             TEEEEESTTB
T ss_pred             CeeEEEEeec
Confidence            6899998763

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

Probab=98.83  E-value=8.4e-09  Score=82.62  Aligned_cols=83  Identities=20%  Similarity=0.304  Sum_probs=66.6

Q ss_pred             EEecCc-cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEE
Q psy10116         75 VRAMNS-RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQ  153 (298)
Q Consensus        75 V~p~~~-rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~s  153 (298)
                      -.|... ...+++||+|.|+|+++.+.+++|+|+...+|+||++++..     .+     ..++.+.|++||.|.|+|.+
T Consensus        19 ~~p~~~~~~~~~~G~iv~G~V~~v~~~G~fV~l~~~~~Gll~~sel~~-----~~-----~~~~~~~~~vGd~V~v~V~~   88 (109)
T 2khj_A           19 SHMFNNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASR-----DR-----VEDATLVLSVGDEVEAKFTG   88 (109)
T ss_dssp             --CHHHHTTTCCSSSEEEEEEEEECSSCEEEECSTTCBCCBCTTCCCS-----SS-----SSSGGGSCCTTCEEEEEEEE
T ss_pred             cCHHHHHhhcCCCCCEEEEEEEEEECCeEEEEECCCCEEEEEHHHcCc-----cc-----ccChhhccCCCCEEEEEEEE
Confidence            344433 45689999999999999999999999988999999999741     11     13457789999999999999


Q ss_pred             eCCCC-cEEEEeccC
Q psy10116        154 ISTEG-SLTLHTRSL  167 (298)
Q Consensus       154 v~~dg-~~~Lstr~~  167 (298)
                      ++.++ .+.||.+..
T Consensus        89 vd~~~~ki~LS~k~~  103 (109)
T 2khj_A           89 VDRKNRAISLSVRAK  103 (109)
T ss_dssp             EETTTTEEEEETTSS
T ss_pred             EECCCCEEEEEEeec
Confidence            98664 799998764

>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=98.80  E-value=8.6e-09  Score=84.29  Aligned_cols=77  Identities=12%  Similarity=0.126  Sum_probs=63.9

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCC-CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC---
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNS-ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST---  156 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s-~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~---  156 (298)
                      .+.|++||+|.|+|+++.+.+++|+|.. ..+|+||++++..     .+     ..+..+.|++||.|.++|.+++.   
T Consensus        17 ~~~~~vG~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~-----~~-----~~~~~~~~~~Gd~V~VkV~~vd~~~~   86 (119)
T 2cqo_A           17 ENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSS-----CR-----VDKPSEIVDVGDKVWVKLIGREMKND   86 (119)
T ss_dssp             CCSCCTTCEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCS-----SC-----CSCHHHHCCTTCEEEEEEEEEEECSS
T ss_pred             hcccCCCCEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCc-----cc-----ccChhhcCCCCCEEEEEEEEEecccc
Confidence            4779999999999999999999999955 4799999999841     11     13457789999999999999984   


Q ss_pred             CCcEEEEeccC
Q psy10116        157 EGSLTLHTRSL  167 (298)
Q Consensus       157 dg~~~Lstr~~  167 (298)
                      ++.+.|+++..
T Consensus        87 ~~~i~LSlk~~   97 (119)
T 2cqo_A           87 RIKVSLSMKVV   97 (119)
T ss_dssp             CEEEEEESTTB
T ss_pred             CceEEEEEeec
Confidence            36899998764

>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=98.80  E-value=1.9e-08  Score=87.55  Aligned_cols=77  Identities=16%  Similarity=0.234  Sum_probs=61.3

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeC--CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-C
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTN--SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-E  157 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~--s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-d  157 (298)
                      .+.|++||+|.|+|+++.+.+++|+|.  ...+|++|+|++..          ....+.++.|++||.|.++|++++. .
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----------RRIRSIQKLIRVGKNDVAVVLRVDKEK   79 (175)
T ss_dssp             SSSCCTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC------------------CCCCCCCTTSEEEEEEEEEETTT
T ss_pred             hcCCCCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCC----------cccCCHHHcCCCCCEEEEEEEEEECCC
Confidence            456889999999999999999999994  67899999999841          1124567899999999999999985 5


Q ss_pred             CcEEEEeccC
Q psy10116        158 GSLTLHTRSL  167 (298)
Q Consensus       158 g~~~Lstr~~  167 (298)
                      +.+.||.|..
T Consensus        80 ~~I~LSlk~~   89 (175)
T 2a19_A           80 GYIDLSKRRV   89 (175)
T ss_dssp             TEEEEESTTC
T ss_pred             CeEEEEEEec
Confidence            7899998764

>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=98.76  E-value=1.9e-08  Score=87.55  Aligned_cols=85  Identities=26%  Similarity=0.328  Sum_probs=68.8

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhh-------hhhhcccCCCCEEEEEEEE
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDE-------EMMREFLKEGDLISAEIHQ  153 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~-------~~mr~~~~~GDlV~A~V~s  153 (298)
                      -|.|++|+++.|+|+++.+.+++|+++ +.+|++|+|++. +.   |  ...|+       .+..+.|++||.|+++|.+
T Consensus        76 ~~~~~~Gev~~G~V~~v~~~G~fV~l~-~~eglvhis~l~-~~---~--~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~  148 (187)
T 1go3_E           76 VYIPEMYELIEGEVVDVVEFGSFVRLG-PLDGLIHVSQIM-DD---Y--VSYDPKREAIIGKETGKVLEIGDYVRARIVA  148 (187)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSC-SS---C--EEECCC--CEEETTTCCEECTTCEEEEEEEE
T ss_pred             EEccCCCCEEEEEEEEEeCcEEEEEEc-CccEEEEhHHhC-CC---c--ceECCccceEEecCCCeEEcCCCEEEEEEEE
Confidence            367999999999999999999999997 599999999974 21   1  11111       1457889999999999999


Q ss_pred             eCC------CCcEEEEeccCCCccC
Q psy10116        154 IST------EGSLTLHTRSLKYGKL  172 (298)
Q Consensus       154 v~~------dg~~~Lstr~~~lGkL  172 (298)
                      ++.      .+.+.||.+.++||++
T Consensus       149 vd~~~~~p~~~~I~lS~k~~~LG~~  173 (187)
T 1go3_E          149 ISLKAERKRGSKIALTMRQPYLGKL  173 (187)
T ss_dssp             EECCC-----CEEEEECCSTTCEEH
T ss_pred             EEcccCCCCccEEEEEEcCCCCCcH
Confidence            985      3479999999999975

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

Probab=98.74  E-value=4.5e-08  Score=75.98  Aligned_cols=71  Identities=15%  Similarity=0.255  Sum_probs=60.2

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCC--CceeeEecc-cccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCc
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNS--ILESALHLT-SVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGS  159 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s--~~~a~L~~s-~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~  159 (298)
                      |++|+++.|+|+ +.+.+++|+|..  ..+|++|+| ++.          .....+.++.| +||.|.++|.+++. .+.
T Consensus         9 ~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~----------~~~~~~~~~~~-~Gd~V~VkV~~vd~~~~k   76 (88)
T 1luz_A            9 PNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMH----------MDRYVEYRDKL-VGKTVKVKVIRVDYTKGY   76 (88)
T ss_dssp             CCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCC----------HHHHHHHHHHH-TTCEEEEEEEEEETTTTE
T ss_pred             CCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhC----------cccccCHhHEe-CCCEEEEEEEEEECCCCE
Confidence            899999999999 999999999974  589999999 984          12234556778 99999999999985 578


Q ss_pred             EEEEecc
Q psy10116        160 LTLHTRS  166 (298)
Q Consensus       160 ~~Lstr~  166 (298)
                      +.||.|.
T Consensus        77 I~lslk~   83 (88)
T 1luz_A           77 IDVNYKR   83 (88)
T ss_dssp             EEEEEEE
T ss_pred             EEEEEee
Confidence            9999875

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

Probab=98.73  E-value=3.2e-08  Score=91.89  Aligned_cols=81  Identities=23%  Similarity=0.381  Sum_probs=65.4

Q ss_pred             ecCccccccCCCEEEEEEEEEecceEEEEeC--CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEe
Q psy10116         77 AMNSRYIGEIGEVVVGRVTGLQSQKWVVDTN--SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQI  154 (298)
Q Consensus        77 p~~~rY~P~vGDiVIG~V~~V~~~~~~VDI~--s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv  154 (298)
                      |+...+.|++||+|.|+|+++.+.+++|+|+  ...+|++|+|++..     +|     ..+.++.|++||.|.++|.++
T Consensus         2 ~~~~~~~p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~-----~~-----v~~~~~~~kvGd~V~vkVi~v   71 (275)
T 3aev_A            2 PRKAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVAS-----TW-----VRNIRDYLKEGQKVVAKVIRV   71 (275)
T ss_dssp             -----CCCCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCS-----SC-----CSCGGGTCCTTCEEEEEEEEE
T ss_pred             CcccccCCCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCc-----cc-----ccCHHhccCCCCEEEEEEEEE
Confidence            4555678999999999999999999999998  47899999999841     11     234578999999999999999


Q ss_pred             CC-CCcEEEEeccC
Q psy10116        155 ST-EGSLTLHTRSL  167 (298)
Q Consensus       155 ~~-dg~~~Lstr~~  167 (298)
                      +. ++.+.||.+..
T Consensus        72 D~~~~~I~LSlk~~   85 (275)
T 3aev_A           72 DPRKGHIDLSLRRV   85 (275)
T ss_dssp             ETTTTEEEEESTTC
T ss_pred             ECCCCEEEEEEeec
Confidence            85 68899998764

>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=98.61  E-value=1e-07  Score=82.44  Aligned_cols=90  Identities=20%  Similarity=0.338  Sum_probs=68.1

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcc-c-ccchhhhhhhhcccCCCCEEEEEEEEeCC--
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQ-R-RRSVQDEEMMREFLKEGDLISAEIHQIST--  156 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~-R-r~~~~d~~~mr~~~~~GDlV~A~V~sv~~--  156 (298)
                      .+.|.+|+++.|+|+++++.+++|+++ +.+|++|+|++. +.-.. - ......-.+....|++||.|++||.+++.  
T Consensus        76 v~~p~~Gev~~G~V~~v~~~G~fv~l~-~~~glvh~s~l~-~d~~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~~v~~~~  153 (180)
T 4ayb_E           76 TYVPVVQEVVEGEVLQVDNYGVFVNLG-PMDGLVHISQIT-DDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTV  153 (180)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSC-SSCEEECSSSCCEEETTTCCCCCTTCEEEEEEEEECC--
T ss_pred             eeeccCCCEEEEEEeeeccceEEEEEC-CccceEEeeecC-CCccccchhcceEEEeccCeEECCCCEEEEEEEEEeCCC
Confidence            478999999999999999999999997 689999999974 11100 0 00000002346789999999999999983  


Q ss_pred             ---CCcEEEEeccCCCccC
Q psy10116        157 ---EGSLTLHTRSLKYGKL  172 (298)
Q Consensus       157 ---dg~~~Lstr~~~lGkL  172 (298)
                         .+.+.||+|+++||++
T Consensus       154 ~~~~~rI~ls~k~~gLG~~  172 (180)
T 4ayb_E          154 TGRLPRIALTMRQPYLGKL  172 (180)
T ss_dssp             -----CEEEECCSTTCEEH
T ss_pred             CcccCcEEEEcCCCCCCCC
Confidence               3468999999999985

>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=98.58  E-value=2.1e-07  Score=75.56  Aligned_cols=81  Identities=16%  Similarity=0.236  Sum_probs=61.9

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeC-CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC-CcE
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTN-SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE-GSL  160 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~-s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d-g~~  160 (298)
                      .+++||++.|+|+++.+.+|+|||+ ....++++.+...         ......+.++.|++||.|.++|.+++.+ +.+
T Consensus        18 ~l~~G~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~~---------~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~i   88 (119)
T 1wi5_A           18 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQ---------EYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVV   88 (119)
T ss_dssp             TCCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHH---------HHHHHHSSSCCCCTTCEEEEEEEECCTTSCEE
T ss_pred             cCCCCCEEEEEEEEEeCceEEEEECCCCeEEEEEEeccc---------ccccccCccCEeCCCCEEEEEEEEEeCCCCEE
Confidence            4789999999999999999999998 3444554433321         0001123468999999999999999854 689


Q ss_pred             EEEeccCCCccC
Q psy10116        161 TLHTRSLKYGKL  172 (298)
Q Consensus       161 ~Lstr~~~lGkL  172 (298)
                      .|+.+...+|+-
T Consensus        89 ~Lslk~~~l~~~  100 (119)
T 1wi5_A           89 SLSVGHSEVSTA  100 (119)
T ss_dssp             EEECCCCCSCCC
T ss_pred             EEEEchhhcccc
Confidence            999999999873

>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=98.54  E-value=1.8e-07  Score=88.13  Aligned_cols=76  Identities=20%  Similarity=0.326  Sum_probs=64.4

Q ss_pred             ccccCCCEEEEEEEEEecceEEEEeC--CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CC
Q psy10116         82 YIGEIGEVVVGRVTGLQSQKWVVDTN--SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EG  158 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~~~~~~VDI~--s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg  158 (298)
                      ..|++||+|.|+|+++.+.+|+|+|+  ...+|++|+|++..     +|     ..+.++.|++||.|.++|++++. .+
T Consensus         9 ~~~~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~-----~~-----i~~~~~~~kvGd~V~VkVl~vD~~~~   78 (308)
T 1q8k_A            9 KFPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSR-----RR-----IRSINKLIRIGRNECVKVIRVDKEKG   78 (308)
T ss_dssp             CCCSSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSC-----SS-----CSCCTTTCSSSCEEEEEEEEEETTTT
T ss_pred             cCCCCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCc-----cc-----ccCHHHhcCCCCEEEEEEEEEeCCCC
Confidence            34789999999999999999999997  67999999999841     11     23467899999999999999985 57


Q ss_pred             cEEEEeccC
Q psy10116        159 SLTLHTRSL  167 (298)
Q Consensus       159 ~~~Lstr~~  167 (298)
                      .+.||.|..
T Consensus        79 rI~LSlK~~   87 (308)
T 1q8k_A           79 YIDLSKRRV   87 (308)
T ss_dssp             EEEEECSSC
T ss_pred             EEEEEEEec
Confidence            899998764

>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=98.50  E-value=8.3e-08  Score=88.62  Aligned_cols=80  Identities=15%  Similarity=0.266  Sum_probs=67.3

Q ss_pred             CccccccCCCEEEEEEEEEecceEEEEeC--CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC
Q psy10116         79 NSRYIGEIGEVVVGRVTGLQSQKWVVDTN--SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST  156 (298)
Q Consensus        79 ~~rY~P~vGDiVIG~V~~V~~~~~~VDI~--s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~  156 (298)
                      ...+.|++||+|.|+|+++.+.+++|+|+  ...+|+||+|++..     ++     ..+.++.|++||.|.++|.+++.
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-----VKNIRDVLKENRKVIVKVIRVDR   73 (266)
T ss_dssp             CSSSSCCTTCEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSC-----SS-----CCCHHHHSCTTCEEEEEECCCCS
T ss_pred             cccccCCCCCEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCc-----cc-----ccCHHHhCcCCCEEEEEEEEEeC
Confidence            34678999999999999999999999997  67999999999841     11     23457889999999999999985


Q ss_pred             -CCcEEEEeccCC
Q psy10116        157 -EGSLTLHTRSLK  168 (298)
Q Consensus       157 -dg~~~Lstr~~~  168 (298)
                       ++.+.||.|...
T Consensus        74 ~~g~I~LSlk~~~   86 (266)
T 3cw2_C           74 RKGTVDVSLKKVT   86 (266)
T ss_dssp             SSCCCBEESTTSC
T ss_pred             CCCEEEEEEEecc
Confidence             688999987653

>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=98.47  E-value=7.7e-07  Score=76.48  Aligned_cols=86  Identities=13%  Similarity=-0.003  Sum_probs=64.4

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhh-------hhhhcccCCCCEEEEEEEE
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDE-------EMMREFLKEGDLISAEIHQ  153 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~-------~~mr~~~~~GDlV~A~V~s  153 (298)
                      .+.|++|+++.|+|+++++.+|+|+|+ +.+|++|+|++.  ..-  + .+..+       ...+..|++||.|+++|.+
T Consensus        76 ~~~~~~Gev~~G~V~~v~~fG~fV~l~-~~~glvhis~l~--~~~--~-~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~~  149 (172)
T 2c35_B           76 VFRPFKGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIP--SEM--E-FDPNSNPPCYKTMDEDIVIQQDDEIRLKIVG  149 (172)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSC--TTE--E-EESSSSSCEEEETTSCSEEETTCEEEEEEEE
T ss_pred             EeeCCCCCEEEEEEEEEeCCEEEEEEC-CEEEEEEHHHCC--CCc--E-ECCCCCccEEEeCCCCEEECCCCEEEEEEEE
Confidence            466999999999999999999999996 677999999863  210  0 00000       1225689999999999999


Q ss_pred             eCCC---CcEEEEeccCCCccC
Q psy10116        154 ISTE---GSLTLHTRSLKYGKL  172 (298)
Q Consensus       154 v~~d---g~~~Lstr~~~lGkL  172 (298)
                      ++.+   ....-|+++++||++
T Consensus       150 vd~~~~~~~~igsm~~~~LG~~  171 (172)
T 2c35_B          150 TRVDKNDIFAIGSLMDDYLGLV  171 (172)
T ss_dssp             EEEETTEEEEEEECCSTTCEEC
T ss_pred             EEcCCCCcEEEEEecCCCCCCC
Confidence            9843   223337899999986

>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=98.36  E-value=9e-07  Score=76.14  Aligned_cols=85  Identities=12%  Similarity=0.101  Sum_probs=62.7

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhh-----hhhcccCCCCEEEEEEEEeC
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEE-----MMREFLKEGDLISAEIHQIS  155 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~-----~mr~~~~~GDlV~A~V~sv~  155 (298)
                      -+.|.+|+++.|+|+++.+.+++|+++. .+|++|+|++.  ..-  + .+....     .-++.|++||.|+++|.+++
T Consensus        78 ~~~~~~Gev~~G~V~~v~~fG~FV~l~~-~dglvhis~l~--~~~--~-~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd  151 (171)
T 1y14_B           78 VFKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMP--QDL--T-FNAGSNPPSYQSSEDVITIKSRIRVKIEGCI  151 (171)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEEETT-EEEEEEGGGSC--TTC--E-ECC-----CEECSSCEECTTCEEEEEEEEEE
T ss_pred             EccCCCCCEEEEEEEEEecCEEEEEecC-eEEEEEHHHCC--CCc--e-ECcccCceEEeccceEECCCCEEEEEEEEEE
Confidence            3568999999999999999999999986 99999999873  210  1 000000     00267999999999999998


Q ss_pred             CCC----cEEEEeccCCCccC
Q psy10116        156 TEG----SLTLHTRSLKYGKL  172 (298)
Q Consensus       156 ~dg----~~~Lstr~~~lGkL  172 (298)
                      .+.    .+. |+++++||++
T Consensus       152 ~~~~~~~~ig-sm~~~~LG~~  171 (171)
T 1y14_B          152 SQVSSIHAIG-SIKEDYLGAI  171 (171)
T ss_dssp             EETTEEEEEE-ECCSTTCEEC
T ss_pred             cCCCCcEEEE-EcCCCCCCCC
Confidence            432    234 6788899863

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

Probab=98.34  E-value=1.7e-06  Score=80.59  Aligned_cols=70  Identities=13%  Similarity=0.090  Sum_probs=63.7

Q ss_pred             cCCCEEEEEEEEEecceEEE-EeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEEE
Q psy10116         85 EIGEVVVGRVTGLQSQKWVV-DTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLTL  162 (298)
Q Consensus        85 ~vGDiVIG~V~~V~~~~~~V-DI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~L  162 (298)
                      ++||+|-|+|.++++.+++| +++..++|++|.|++.                  ..+++||.|.|+|++++. ++.+.|
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            68999999999999999999 9999999999999973                  459999999999999997 899999


Q ss_pred             EeccCCCccC
Q psy10116        163 HTRSLKYGKL  172 (298)
Q Consensus       163 str~~~lGkL  172 (298)
                      |.|...+..+
T Consensus       213 Slk~~~~~~~  222 (285)
T 3go5_A          213 SLKPRSFEML  222 (285)
T ss_dssp             ECSCCCCCCC
T ss_pred             EeChhhhhcc
Confidence            9998877543

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

Probab=98.32  E-value=3.2e-07  Score=79.26  Aligned_cols=85  Identities=15%  Similarity=0.111  Sum_probs=65.6

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhh-----hhhhhcccCCCCEEEEEEEEeC
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQD-----EEMMREFLKEGDLISAEIHQIS  155 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d-----~~~mr~~~~~GDlV~A~V~sv~  155 (298)
                      -+.|.+|+++.|+|+++++.+++|+++ +.+|++|+|++.  ..-   ..+.+     -.+....+++||.|+++|.+++
T Consensus        79 vf~p~~Gev~~G~V~~v~~fG~FV~l~-~~~glVh~s~l~--~~~---~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~vd  152 (172)
T 3h0g_G           79 LWRPFRGEVVDAIVTTVNKMGFFANIG-PLNVFVSSHLVP--PDM---KFDPTANPPNYSGEDQVIEKGSNVRLKIVGTR  152 (172)
T ss_dssp             EECCCTTCEEECCCCEEETTEEECCBT-TBCCEEEGGGSC--TTC---CCBSSSSSCBEESSSCEECSSCCEEEEEEEEE
T ss_pred             eeccCCCCEEEEEEEEEEcceEEEEeC-CeEEEEEHHHCC--Ccc---ccCcccccceEecCCcEECCCCEEEEEEEEEE
Confidence            467999999999999999999999997 677999999873  210   00000     0223578999999999999998


Q ss_pred             CCC----cEEEEeccCCCccC
Q psy10116        156 TEG----SLTLHTRSLKYGKL  172 (298)
Q Consensus       156 ~dg----~~~Lstr~~~lGkL  172 (298)
                      .+.    .+. |+|+++||+|
T Consensus       153 ~~~~~~~~Ig-tm~~~~LG~~  172 (172)
T 3h0g_G          153 TDATEIFAIA-TMKEDYLGVL  172 (172)
T ss_dssp             ESSSCEEEEE-ECCSTTCEEC
T ss_pred             CCCCCceEEE-EcCCCCCCCC
Confidence            432    455 7899999985

>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=98.20  E-value=2.1e-06  Score=76.93  Aligned_cols=84  Identities=12%  Similarity=0.111  Sum_probs=64.2

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhh-------hcccCCCCEEEEEEEE
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMM-------REFLKEGDLISAEIHQ  153 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~m-------r~~~~~GDlV~A~V~s  153 (298)
                      -+.|++|+++.|+|+++.+.+++|+|+. .+|++|+|++.  ..-  +   .|+.+.       ++.+++||.|..+|.+
T Consensus        78 ~~~p~vGev~~G~V~~vt~fG~FVelg~-~dGlVhiS~l~--d~~--~---~d~~~~~w~~~~~~~~~~~Gd~VrVkV~~  149 (215)
T 2b8k_G           78 VFKPFKGEVVDGTVVSCSQHGFEVQVGP-MKVFVTKHLMP--QDL--T---FNAGSNPPSYQSSEDVITIKSRIRVKIEG  149 (215)
T ss_dssp             EECCCTTEEEEEEEEEEETTEEEEECTT-SEEEEEGGGSC--SSC--C---CBSSCSSCEEECSSCEEETTCEEEEEEEE
T ss_pred             eeccCCCCEEEEEEEEEecceEEEEecC-cEEEEEHHHCC--ccc--e---eccccccceeeccccEECCCCEEEEEEEE
Confidence            3568999999999999999999999986 99999999873  110  0   011000       1679999999999999


Q ss_pred             eCCCC----cEEEEeccCCCccCC
Q psy10116        154 ISTEG----SLTLHTRSLKYGKLG  173 (298)
Q Consensus       154 v~~dg----~~~Lstr~~~lGkL~  173 (298)
                      ++.+.    .+. |+++++||.++
T Consensus       150 vd~~~~~i~~Ig-Smk~~~LG~~~  172 (215)
T 2b8k_G          150 CISQVSSIHAIG-SIKEDYLGAIS  172 (215)
T ss_dssp             EEEETTEEEEEE-ECCSTTCEEC-
T ss_pred             EEcCCCccEEEE-EcCCCCCCCcc
Confidence            98432    355 78999999864

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

Probab=98.01  E-value=7.5e-07  Score=92.39  Aligned_cols=76  Identities=16%  Similarity=0.281  Sum_probs=0.0

Q ss_pred             ccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEE
Q psy10116         82 YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLT  161 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~  161 (298)
                      ..|++|+++.|+|+++.+.+++|+|....+|++|+|++.-          ....+..+.|++||.|.++|.+++.++.+.
T Consensus       633 ~~~~vG~v~~G~V~~I~~fGaFVel~~g~eGLvHiSels~----------~rv~~~~d~~kvGD~V~VkVi~iD~~grI~  702 (726)
T 4aid_A          633 DEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISN----------ERVAKPSDVLKEGQMVKVKLLGFDDRGKTK  702 (726)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhcCCcEEEEEEEEEeccEEEEEECCCcEEEEEHHHcCc----------ccccCccccCCCCCEEEEEEEEECCCCcEE
Confidence            3589999999999999999999999888999999999841          123466889999999999999999888999


Q ss_pred             EEeccC
Q psy10116        162 LHTRSL  167 (298)
Q Consensus       162 Lstr~~  167 (298)
                      ||.|..
T Consensus       703 LS~K~~  708 (726)
T 4aid_A          703 LSMKVV  708 (726)
T ss_dssp             ------
T ss_pred             EEEeec
Confidence            998763

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

Probab=97.95  E-value=0.0002  Score=63.30  Aligned_cols=90  Identities=13%  Similarity=0.086  Sum_probs=65.7

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcc-c--cc-------chhhhhhhhcccCCCCEEEEE
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQ-R--RR-------SVQDEEMMREFLKEGDLISAE  150 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~-R--r~-------~~~d~~~mr~~~~~GDlV~A~  150 (298)
                      -+.|.+|+++.|+|+++++.+++|+++ +.++++|.++.. |.... .  +.       .+.+...-+..|+.||.|+.|
T Consensus        76 ~f~p~~GEv~~G~Vs~vt~~GifV~lg-~~eglv~~~~l~-~d~~~fd~~~~~~v~~~~~~~~~~~~~~~~~~Gd~Vrvr  153 (203)
T 3ayh_B           76 IFRPFRGEVMLGKIKSCSEEGIRVTIS-FFDDIFIPKDML-FDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQ  153 (203)
T ss_dssp             EECCCTTCEEEEEEEEEETTEEEEECS-SCCCEEEEGGGB-CTTEEEEGGGTEEEEEECCCTTSCCEEEECCTTCEEEEE
T ss_pred             EEccCCCCEEEEEEEEEeccEEEEEEe-CceEEEEcHHhC-CCCceECccCceEEeecccccccccCCcEEcCCCEEEEE
Confidence            466999999999999999999999996 789999999873 32110 0  00       000002236789999999999


Q ss_pred             EEEeCCC------------------------CcEEEEeccCCCccC
Q psy10116        151 IHQISTE------------------------GSLTLHTRSLKYGKL  172 (298)
Q Consensus       151 V~sv~~d------------------------g~~~Lstr~~~lGkL  172 (298)
                      |.+++-+                        ..+..|+++++||.+
T Consensus       154 V~~v~~~~~~p~~~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~~  199 (203)
T 3ayh_B          154 IESEDFVDISPKRNKNATAITGTEALESVSPYTLIASCSRDGLGIP  199 (203)
T ss_dssp             EEEEEECC--------------------CCSEEEEEEBCSTTCBCG
T ss_pred             EEEEEccccCCCCccccccccccccccCCCCeEEEEEecCCCCcee
Confidence            9998731                        126778899999986

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

Probab=97.83  E-value=2.3e-05  Score=85.36  Aligned_cols=77  Identities=14%  Similarity=0.061  Sum_probs=64.3

Q ss_pred             ccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCCcE
Q psy10116         82 YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEGSL  160 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg~~  160 (298)
                      -..++|++|-|+|+.|.+.+++|+|+...+|++|+|++.-     ++    ...+.++.|++||.|.|+|++++ ..+.+
T Consensus       898 ~~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd-----~~----~v~~p~~v~kvGd~V~vkVl~VD~~~~rI  968 (1219)
T 3psi_A          898 KTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAG-----AQ----LRRPANEIYEIGKTYPAKVIYIDYANITA  968 (1219)
T ss_dssp             TTSCTTCEEEEEEEEECSSCEEEECTTSCEEEECTTSSSS-----TT----SCSCSTTTSCTTCEEEEEEEEEEGGGTEE
T ss_pred             hhCCCCCEEEEEEEEEecceEEEEeCCCceEEEEHHHcCC-----Cc----ccCCHHHcCCCCCEEEEEEEEEECCCCEE
Confidence            4578999999999999999999999989999999999851     11    02344688999999999999998 45789


Q ss_pred             EEEeccC
Q psy10116        161 TLHTRSL  167 (298)
Q Consensus       161 ~Lstr~~  167 (298)
                      .||+|..
T Consensus       969 ~LSlk~~  975 (1219)
T 3psi_A          969 EVSLLDH  975 (1219)
T ss_dssp             EEECCHH
T ss_pred             EEEecHH
Confidence            9998753

>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=97.82  E-value=2.5e-05  Score=71.51  Aligned_cols=69  Identities=17%  Similarity=0.243  Sum_probs=57.2

Q ss_pred             cccccCCCEEEEEEEE----EecceEEEEeCC---CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEE
Q psy10116         81 RYIGEIGEVVVGRVTG----LQSQKWVVDTNS---ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQ  153 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~----V~~~~~~VDI~s---~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~s  153 (298)
                      .|..++||+|.|+|..    +..+.+.|||+.   ..+|+||.++. .|               ++.|++||.|.|.|..
T Consensus         2 ~~~~r~GeIVtG~V~r~~~~v~~~~ViVdlG~~~~k~EgiLP~~Eq-ip---------------~E~~~~GDrIkayV~~   65 (251)
T 2asb_A            2 EFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQ-VP---------------GESYEHGNRLRCYVVG   65 (251)
T ss_dssp             --CCCTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGS-CT---------------TCCCCTTCEEEEEEEE
T ss_pred             chhhcCCCEEEEEEEEccccccCCeEEEEeCCCCcceEEEEcHHHc-CC---------------CccCCCCCEEEEEEEE
Confidence            4888999999999999    899999999997   58999998876 34               5789999999999999


Q ss_pred             eCCC---CcEEEEec
Q psy10116        154 ISTE---GSLTLHTR  165 (298)
Q Consensus       154 v~~d---g~~~Lstr  165 (298)
                      +...   +.+.||-.
T Consensus        66 V~~~~~gpqIiLSRt   80 (251)
T 2asb_A           66 VTRGAREPLITLSRT   80 (251)
T ss_dssp             EECCSSSCEEEEESS
T ss_pred             EEcCCCCCEEEEEec
Confidence            9743   45777743

>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=97.80  E-value=3.7e-05  Score=73.40  Aligned_cols=68  Identities=22%  Similarity=0.258  Sum_probs=58.1

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC---
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE---  157 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d---  157 (298)
                      .|..+.||+|.|+|..+..+.++||+| ..+|+||.+++. |               ++.|++||.|.|.|.+++.+   
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-P---------------GEEIKAGDLVKVYIIDVVKTTKG  191 (344)
T ss_dssp             CTTCCTTCEEEEEEEEECSSEEEEEET-TEEEEEEGGGSC-T---------------TCCCCTTCEEEEEEEEEEEETTE
T ss_pred             HHhhcCCCEEEEEEEEEecCcEEEEeC-CeEEEEeHHHcC-C---------------CcCCCCCCEEEEEEEEEEcCCCC
Confidence            477889999999999999999999998 789999999873 4               46899999999999999732   


Q ss_pred             CcEEEEec
Q psy10116        158 GSLTLHTR  165 (298)
Q Consensus       158 g~~~Lstr  165 (298)
                      +.+.||-+
T Consensus       192 ~~I~LSRt  199 (344)
T 1hh2_P          192 PKILVSRR  199 (344)
T ss_dssp             EEEEEESS
T ss_pred             cEEEEEee
Confidence            35777744

>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=97.74  E-value=1.3e-05  Score=83.84  Aligned_cols=76  Identities=18%  Similarity=0.235  Sum_probs=64.5

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEE
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLT  161 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~  161 (298)
                      ..++|++|-|+|++|.+.+++|+|+...+|++|+|++..     +     ...+.++.|++||.|.++|.+++. .+.+.
T Consensus       651 ~l~vG~iv~G~V~~V~~fGaFV~l~~~~eGLVhiS~Lsd-----~-----~v~d~~~~~~vGd~V~VkVi~VD~~~~rI~  720 (785)
T 3bzc_A          651 DLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSE-----K-----FVKDPYEVVKAGDIVKVKVMEVDIPRNRVG  720 (785)
T ss_dssp             TCCTTCBCCCEEEEEETTEEEEECSSSSEEEEETTTSCS-----S-----CCSCHHHHCCTTCCCCCBEEEEETTTTEEE
T ss_pred             hcCCCCEEEEEEEEEecCCeEEEeCCCcEEEEEHHHcCc-----c-----ccCChhheeCCCCEEEEEEEEEECCCCEEE
Confidence            468999999999999999999999988899999999841     1     122357889999999999999985 57899


Q ss_pred             EEeccCC
Q psy10116        162 LHTRSLK  168 (298)
Q Consensus       162 Lstr~~~  168 (298)
                      ||++...
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=97.67  E-value=6e-06  Score=85.73  Aligned_cols=76  Identities=18%  Similarity=0.316  Sum_probs=0.0

Q ss_pred             ccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEE
Q psy10116         82 YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLT  161 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~  161 (298)
                      ..|++|+++.|+|+++.+.+++|+|....+|++|+|++.-          ....+..+.|++||.|.++|.+++.++.+.
T Consensus       623 ~~~~vG~i~~G~V~~i~~fGaFVel~~g~eGLvHiSel~~----------~~v~~~~~~~~vGd~V~VkVi~vd~~grI~  692 (723)
T 3cdi_A          623 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIAD----------KRVEKVTDYLQMGQEVPVKVLEVDRQGRIR  692 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhhcCcEEEEEEEEEecceEEEEeCCCceEEEEHHHcCC----------ccccCcccccCCCCEEEEEEEEECCCCcEE
Confidence            4589999999999999999999999888999999999841          113456788999999999999998788899


Q ss_pred             EEeccC
Q psy10116        162 LHTRSL  167 (298)
Q Consensus       162 Lstr~~  167 (298)
                      ||.+..
T Consensus       693 LS~k~~  698 (723)
T 3cdi_A          693 LSIKEA  698 (723)
T ss_dssp             ------
T ss_pred             EEEEec
Confidence            998753

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

Probab=97.62  E-value=7.7e-06  Score=87.70  Aligned_cols=78  Identities=14%  Similarity=0.067  Sum_probs=0.0

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCCcEE
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEGSLT  161 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg~~~  161 (298)
                      ..++|++|-|+|+.|.+.+++|+|+...+|++|+|++.-     ++    ...+..+.|++||.|.|+|++++ ..+.+.
T Consensus       902 ~l~~G~iv~G~V~~V~~fGaFV~L~~gveGLVHiSelsd-----~~----~v~~~~~v~kvGd~V~vkVl~VD~~~~rI~  972 (1030)
T 3psf_A          902 TFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAG-----AQ----LRRPANEIYEIGKTYPAKVIYIDYANITAE  972 (1030)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HhcCCCEEEEEEEEEccCeEEEEeCCCcEEEEEHHHcCC-----Cc----ccCCHHHcCCCCCEEEEEEEEEECCCCEEE
Confidence            468999999999999999999999988999999999841     00    12445788999999999999998 567899


Q ss_pred             EEeccCCC
Q psy10116        162 LHTRSLKY  169 (298)
Q Consensus       162 Lstr~~~l  169 (298)
                      ||+|...+
T Consensus       973 LSlk~~dl  980 (1030)
T 3psf_A          973 VSLLDHDV  980 (1030)
T ss_dssp             --------
T ss_pred             EEechHHh
Confidence            99887654

>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=97.60  E-value=7.7e-05  Score=71.71  Aligned_cols=67  Identities=18%  Similarity=0.233  Sum_probs=56.1

Q ss_pred             cccccCCCEEEEEEEE----EecceEEEEeCC---CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEE
Q psy10116         81 RYIGEIGEVVVGRVTG----LQSQKWVVDTNS---ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQ  153 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~----V~~~~~~VDI~s---~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~s  153 (298)
                      .|..++||+|.|+|..    +..+.++||||.   ..+|+||.++.. |               ++.|++||.|.|.|.+
T Consensus       125 ef~~r~GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~Eqi-P---------------~E~~~~GDrVkvyV~~  188 (366)
T 1k0r_A          125 EFSTREGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV-P---------------GESYEHGNRLRCYVVG  188 (366)
T ss_dssp             --CCCTTCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSC-T---------------TCCCCTTCEEEEEEEE
T ss_pred             HHHhcCCCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcC-C---------------CccCCCCCEEEEEEEE
Confidence            5889999999999999    999999999997   589999998863 4               4789999999999999


Q ss_pred             eCCC---CcEEEE
Q psy10116        154 ISTE---GSLTLH  163 (298)
Q Consensus       154 v~~d---g~~~Ls  163 (298)
                      +..+   +.+.||
T Consensus       189 V~~~~kgpqI~LS  201 (366)
T 1k0r_A          189 VTRGAREPLITLS  201 (366)
T ss_dssp             EECCSSSCEEEEE
T ss_pred             EecCCCccEEEEE
Confidence            9853   346666

>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=97.48  E-value=8.4e-06  Score=85.00  Aligned_cols=76  Identities=22%  Similarity=0.277  Sum_probs=37.9

Q ss_pred             ccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccc----cCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCC
Q psy10116         82 YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSV----NLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTE  157 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v----~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~d  157 (298)
                      ..|++|+++.|+|+++.+.+++|+|....+|++|+|++    .-          ....+..+.|++||.|.++|.+++.+
T Consensus       663 ~~~~vG~i~~G~V~~i~~fGaFV~l~~g~eGLvHiSel~~~~s~----------~rv~~~~~~~~vGd~V~VkVi~vd~~  732 (757)
T 1e3p_A          663 TSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGG----------KRVENVEDVLGVGQKVQVEIAEIDSR  732 (757)
T ss_dssp             ----------CBEEECC-CSCEECCC---CCCCC-----------------------------CCSSCBCCCCCCCCCSS
T ss_pred             hhcccccEEEEEEEEccccEEEEEEcCCcEEEEEhHHhccccCC----------CcccCcccccCCCCEEEEEEEEECCC
Confidence            56899999999999999999999998789999999998    31          11245678999999999999999888


Q ss_pred             CcEEEEeccC
Q psy10116        158 GSLTLHTRSL  167 (298)
Q Consensus       158 g~~~Lstr~~  167 (298)
                      +.+.||.+..
T Consensus       733 grI~LS~k~~  742 (757)
T 1e3p_A          733 GKLSLIPVIE  742 (757)
T ss_dssp             CC--------
T ss_pred             CCEEEEEecC
Confidence            8899998754

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

Probab=97.25  E-value=0.00092  Score=62.10  Aligned_cols=67  Identities=18%  Similarity=0.132  Sum_probs=54.8

Q ss_pred             ccCCCEEEEEEEEEe-cceEEEEeCC-CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEE
Q psy10116         84 GEIGEVVVGRVTGLQ-SQKWVVDTNS-ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLT  161 (298)
Q Consensus        84 P~vGDiVIG~V~~V~-~~~~~VDI~s-~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~  161 (298)
                      -++|+++.|+|++++ +.+++||++- ..++++|+|++..     .+         ...+++||.+.+. +.++..+.+.
T Consensus        67 ~~~G~~~~g~V~~v~~~~GaFVdiG~~~~d~lvp~sel~~-----~~---------~~~~~~Gd~v~v~-l~iD~~~Ri~  131 (285)
T 3go5_A           67 ATQDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLDILPE-----LK---------ELWPKKGDQLYIR-LEVDKKDRIW  131 (285)
T ss_dssp             SCSSSCEEEEEEEEETTTEEEEECSCTTCCEEEEGGGSCS-----SG---------GGSCCTTCEEEEE-EEECTTSCEE
T ss_pred             ccCCCEEEEEEEEEccCceEEEEECCCCcEEEEEHHHCCc-----cc---------ccccCCCCEEEEE-EEECCCCcEE
Confidence            379999999999999 7999999997 4899999998731     11         2357999999765 5788777899


Q ss_pred             EEec
Q psy10116        162 LHTR  165 (298)
Q Consensus       162 Lstr  165 (298)
                      ||+|
T Consensus       132 ls~k  135 (285)
T 3go5_A          132 GLLA  135 (285)
T ss_dssp             EEEC
T ss_pred             EEeh
Confidence            9985

>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=97.20  E-value=0.0021  Score=64.35  Aligned_cols=87  Identities=14%  Similarity=0.189  Sum_probs=62.8

Q ss_pred             EEEEecCccccccCCCEEEEEEEEEecc--eEEEEeCCCceeeEecccccCCCCcccccch---hhhhhhhcccCCCCEE
Q psy10116         73 VSVRAMNSRYIGEIGEVVVGRVTGLQSQ--KWVVDTNSILESALHLTSVNLPGGEQRRRSV---QDEEMMREFLKEGDLI  147 (298)
Q Consensus        73 v~V~p~~~rY~P~vGDiVIG~V~~V~~~--~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~---~d~~~mr~~~~~GDlV  147 (298)
                      +.+++...  .+.+|++..|+|+.+.+.  .+||||+...+|+||++++. |.   +-...   ....++.+.+++||.|
T Consensus        34 l~iE~~~~--~~~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei~-~~---~~~~~~~~~~~~~i~d~lk~Gq~V  107 (517)
T 2bx2_L           34 LDIESPGH--EQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIA-RE---YFPANYSAHGRPNIKDVLREGQEV  107 (517)
T ss_dssp             EEEECSSS--CCCTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSC-GG---GCC-------CCCGGGTCCTTCEE
T ss_pred             EEEecCCC--cCCCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHcC-hh---hhccccccccccchhhhccCCCEE
Confidence            34444333  457999999999999999  99999999999999999984 11   10000   0122466889999999


Q ss_pred             EEEEEEeCCC-CcEEEEec
Q psy10116        148 SAEIHQISTE-GSLTLHTR  165 (298)
Q Consensus       148 ~A~V~sv~~d-g~~~Lstr  165 (298)
                      ..+|...... ..+.|||.
T Consensus       108 lVQV~Ke~~g~KGa~lTt~  126 (517)
T 2bx2_L          108 IVQIDKEERGNKGAALTTF  126 (517)
T ss_dssp             EEEEEECCCTTCCCEEESS
T ss_pred             EEEEEeeccccCCceEEee
Confidence            9999997632 34778764

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

Probab=97.01  E-value=0.011  Score=52.88  Aligned_cols=74  Identities=14%  Similarity=0.131  Sum_probs=54.5

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcc-c--ccchhh--hhhhhcccCCCCEEEEEEEEeC
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQ-R--RRSVQD--EEMMREFLKEGDLISAEIHQIS  155 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~-R--r~~~~d--~~~mr~~~~~GDlV~A~V~sv~  155 (298)
                      -+.|.+|+++.|+|++++..+++|.+..+.+|+++++++. |..-. .  +..-..  ...-+..|+.||.|+.||.+++
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            4679999999999999999999999954789999999873 32210 0  000000  0223678999999999999987

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

Probab=94.25  E-value=0.036  Score=43.43  Aligned_cols=38  Identities=13%  Similarity=0.330  Sum_probs=35.9

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeCCCceeeEeccccc
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVN  120 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~  120 (298)
                      .|++|+.|.|.|+.+.+.+++|+|....+|++|+|++.
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            79999999999999999999999987899999999984

>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=94.21  E-value=0.33  Score=37.88  Aligned_cols=63  Identities=11%  Similarity=0.119  Sum_probs=48.7

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhh-hhcccCCCCEEEEE
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEM-MREFLKEGDLISAE  150 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~-mr~~~~~GDlV~A~  150 (298)
                      .|..|+...+.|+++.++.+.|-+.....+.|+..++..-    |+ ......+ ..+.|++||+|+.+
T Consensus        30 ~~~~~~~~~AvV~~v~~~~~~v~~~~g~~~~l~~~~~~WA----~~-~~~~~~~~~~~~l~~GdvI~V~   93 (106)
T 3d0f_A           30 IGNSDDILAAVVLSATPGAVEAFRKNGETIRITGDGLKAA----HR-FLSNDPKIGEKRIRPGALIRVK   93 (106)
T ss_dssp             SCTTTTCEEEEEEEEETTEEEEEETTSCEEEECGGGGSTT----GG-GTTTCTTTGGGSCCTTEEEEEE
T ss_pred             cCccCCeEEEEEEEeCCCeEEEEEcCCCeEEEcHHHChhh----hh-cccccccchhccCCCCCEEEEE
Confidence            5778999999999999999999997777788888877531    22 1112234 57889999999998

>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=93.85  E-value=0.13  Score=52.51  Aligned_cols=80  Identities=10%  Similarity=0.045  Sum_probs=57.4

Q ss_pred             cccCCC--EEEEEEEEEecceEEEEeC-CCceeeEecccccCCCCcccccchhhhh----hhhcccCCCCEEEEEEEEeC
Q psy10116         83 IGEIGE--VVVGRVTGLQSQKWVVDTN-SILESALHLTSVNLPGGEQRRRSVQDEE----MMREFLKEGDLISAEIHQIS  155 (298)
Q Consensus        83 ~P~vGD--iVIG~V~~V~~~~~~VDI~-s~~~a~L~~s~v~~pgg~~Rr~~~~d~~----~mr~~~~~GDlV~A~V~sv~  155 (298)
                      .+++|+  ..-|+|+++...+++|.|. ...+|++|+|++.....  .-..+....    .....|++||.|..+|.+++
T Consensus       555 ~~~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~~~~d--~~~~d~~~~~l~~~~~~~~~lGD~V~VkV~~vd  632 (644)
T 2id0_A          555 KDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRD--ELVCSQENGTVQIKGETVYKVTDVIDVTIAEVR  632 (644)
T ss_dssp             GGGTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGG--GEEEETTTTEEEETTEEEEETTCEEEEEEEEEE
T ss_pred             hhccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhccCcCc--eeEEcccccEEEecCCCEeCCCCEEEEEEEEEe
Confidence            478999  9999999999999999994 56899999998731000  000000011    22467999999999999998


Q ss_pred             C-CCcEEEEe
Q psy10116        156 T-EGSLTLHT  164 (298)
Q Consensus       156 ~-dg~~~Lst  164 (298)
                      . .+.+.++.
T Consensus       633 ~~~~~I~~~l  642 (644)
T 2id0_A          633 METRSIIARP  642 (644)
T ss_dssp             TTTTEEEEEE
T ss_pred             CCCCEEEEEE
Confidence            5 46676653

>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=89.89  E-value=0.33  Score=50.56  Aligned_cols=79  Identities=13%  Similarity=0.038  Sum_probs=51.1

Q ss_pred             ccccCCCEEEEEEEEEecceEEEEeCC-CceeeEecccccCCCCcccccchhhh-------hh----hhcccCCCCEEEE
Q psy10116         82 YIGEIGEVVVGRVTGLQSQKWVVDTNS-ILESALHLTSVNLPGGEQRRRSVQDE-------EM----MREFLKEGDLISA  149 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s-~~~a~L~~s~v~~pgg~~Rr~~~~d~-------~~----mr~~~~~GDlV~A  149 (298)
                      |+=...+..-|+|+++...+++|.|.. ..+|.+|++++.-|..  .  ...|+       ..    ....|++||.|.+
T Consensus       665 ~l~~~~~~~~g~V~~V~~~G~fV~l~~~giEGlVhis~L~~~~d--~--~~fd~~~~~l~g~~~~~~~~~~~~lGD~V~V  740 (760)
T 2vnu_D          665 VMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPN--S--AAFDEVEYKLTFVPTNSDKPRDVYVFDKVEV  740 (760)
T ss_dssp             HHHTCCSEEEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSCGG--G--CEEETTTTEEEECCTTCSSCEEEETTCEEEE
T ss_pred             HhhcCceEEEEEEEEEECCeEEEEEeCCCcEEEEEeccccCCCc--e--eEEcccccEEEEecCCCccCcEEecCCEEEE
Confidence            443333899999999999999999976 6899999998731110  0  00010       01    1478999999999


Q ss_pred             EEEEeCCC----CcEEEEe
Q psy10116        150 EIHQISTE----GSLTLHT  164 (298)
Q Consensus       150 ~V~sv~~d----g~~~Lst  164 (298)
                      +|.+++.+    +.+.|+.
T Consensus       741 kV~~vd~~~~~~~kI~lsl  759 (760)
T 2vnu_D          741 QVRSVMDPITSKRKAELLL  759 (760)
T ss_dssp             EEC--------CCEEEC--
T ss_pred             EEEEEECccccCCcEEEEe
Confidence            99999854    5666654

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=86.88  E-value=0.99  Score=48.34  Aligned_cols=80  Identities=13%  Similarity=0.045  Sum_probs=56.9

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCC-CceeeEecccccCCCCcccccchhhh-------hh----hhcccCCCCEEE
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNS-ILESALHLTSVNLPGGEQRRRSVQDE-------EM----MREFLKEGDLIS  148 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s-~~~a~L~~s~v~~pgg~~Rr~~~~d~-------~~----mr~~~~~GDlV~  148 (298)
                      .|+-..|...-|+|+++...+++|.|.. ..+|.+|++++.-|...    ...|+       ..    ....|+.||.|.
T Consensus       881 ~~l~~~ge~~~g~V~~V~~~G~fV~L~~~giEGlVhis~L~~~~d~----y~fde~~~~L~g~~~~g~~~~~~~lGD~V~  956 (977)
T 2wp8_J          881 QVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNS----AAFDEVEYKLTFVPTNSDKPRDVYVFDKVE  956 (977)
T ss_dssp             HHHHHTTCEEEEEEEEECSSEEEEECTTTCCEEEEEGGGTCSCGGG----CEEETTTTEEEECCTTCCSCEEEETTCEEE
T ss_pred             hhhcccceEEEEEEEEEcCCeEEEEEcCCCeEEEEEeccccCCCce----eEEcccccEEEeecCCCccCcEEccCCEEE
Confidence            3543339999999999999999999976 68999999987411100    00011       00    246899999999


Q ss_pred             EEEEEeCCC----CcEEEEe
Q psy10116        149 AEIHQISTE----GSLTLHT  164 (298)
Q Consensus       149 A~V~sv~~d----g~~~Lst  164 (298)
                      .+|.+++..    +.+.|+.
T Consensus       957 VkV~~vd~~~~~~~kI~Lsl  976 (977)
T 2wp8_J          957 VQVRSVMDPITSKRKAELLL  976 (977)
T ss_dssp             EEECCCCCSSSCCCCCCEEE
T ss_pred             EEEEEEcCcccCCCceEEEe
Confidence            999998752    5676665

>2i9x_A Putative septation protein spovg; APC86317.1, staphylococcus epidermidis ATCC 12228, ST genomics, PSI-2, protein structure initiative; 1.80A {Staphylococcus epidermidis} SCOP: d.366.1.1

Probab=85.87  E-value=1.2  Score=34.25  Aligned_cols=41  Identities=22%  Similarity=0.332  Sum_probs=34.6

Q ss_pred             ccEEEEEeeCceEEEecCCC-CCCCccccccccCCHHHHHHHH
Q psy10116        197 CGAQVILGCNGYVWVSAIDE-NKSGGFIQNMEVVKLSDRETIT  238 (298)
Q Consensus       197 ~~~eiivG~NG~IWI~~~~~-~~~~~~~~~~~~i~~~~r~~i~  238 (298)
                      -++.|+=|.|| +||.-++. ..++.|.+...|++.+.|+.|.
T Consensus        35 ~~ikVieg~~G-lFVaMPs~k~~~g~y~Di~hPit~e~Re~i~   76 (87)
T 2i9x_A           35 HDLRVIEGNSG-LFVAMPSKRTPDGEFRDIAHPINSDMRQEIQ   76 (87)
T ss_dssp             EEEEEEEETTE-EEEECCEEECTTSCEEECEEECSHHHHHHHH
T ss_pred             eeEEEEECCCc-eEEECCCcCCCCCCEEEEEEECCHHHHHHHH
Confidence            47999999999 99998876 3456787888999999999985

>2ia9_A Putative septation protein spovg; APC85465, bacillus subtilis subsp. subtilis STR. 168, structural genomics, PSI-2; 3.00A {Bacillus subtilis} SCOP: d.366.1.1

Probab=83.83  E-value=2  Score=33.80  Aligned_cols=52  Identities=23%  Similarity=0.313  Sum_probs=42.4

Q ss_pred             ccEEEEEeeCceEEEecCCC-CCCCccccccccCCHHHHHHHHHHHHHHHHHhhCCcccCHHHHHHHHHHHh
Q psy10116        197 CGAQVILGCNGYVWVSAIDE-NKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESL  267 (298)
Q Consensus       197 ~~~eiivG~NG~IWI~~~~~-~~~~~~~~~~~~i~~~~r~~i~rv~n~i~~l~~~~~~i~~~~i~~~~~~s~  267 (298)
                      -++.|+=|.|| +||.-++. ..++.|.+...|++.+.|+.|.                  +.|+.+|+.++
T Consensus        35 ~dIkVieg~~G-lFVaMPSrk~~~Gey~DI~hPit~e~Re~i~------------------~aVl~aY~~~~   87 (100)
T 2ia9_A           35 HDIRVIDGNNG-LFVAMPSKRTPDGEFRDITHPINSSTRGKIQ------------------DAVLNEYHRLG   87 (100)
T ss_dssp             EEEEEEEETTE-EEEECCEEECTTSCEEESEEESSHHHHHHHH------------------HHHHHHHHHHH
T ss_pred             eeEEEEECCCc-eEEECCCcCCCCCCEEEEEEECCHHHHHHHH------------------HHHHHHHHHHH
Confidence            48999999999 99998876 3456687888999999999995                  56777887764

>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA, DNA-binding, phosphorylation, POL I, POLI, rpoli, nuclear protein; 3.10A {Saccharomyces cerevisiae}

Probab=82.79  E-value=2.9  Score=36.81  Aligned_cols=74  Identities=8%  Similarity=0.074  Sum_probs=49.2

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccch------hhhhhhhcccCCCCEEEEEEEEe
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSV------QDEEMMREFLKEGDLISAEIHQI  154 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~------~d~~~mr~~~~~GDlV~A~V~sv  154 (298)
                      -+.|.+|+++.|+|+.+..+...+-+-..+++.++...+  |..-+-...+      .+..  .+--++|+.|+-+|.++
T Consensus       124 VFrPf~GevL~G~V~~~s~~~Ig~~~~G~Fn~~Ip~~~i--p~~~~f~~~~~~~~~~~wv~--~~~~~ig~~IRFrV~~~  199 (214)
T 2rf4_A          124 VWQPQVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNI--PVDWTFVHNDGNRSLGHWVD--SNGEPIDGKLRFTVRNV  199 (214)
T ss_dssp             EECCCTTCEEEEEECCCCSSCEEEEETTTEEEEECSTTS--CSSCBCCCCSCC-CCCCCBC--SSCCBCCSEEEEEEEEE
T ss_pred             EEecCCCCEEEEEEEEECCCcEEEEEeCCEEEEEcHHHC--CCcccccccccccCCCceEc--CCCCCCCCEEEEEEEEE
Confidence            578999999999999999998888665688888886664  3221110000      0000  01112599999999998


Q ss_pred             CCCC
Q psy10116        155 STEG  158 (298)
Q Consensus       155 ~~dg  158 (298)
                      ..++
T Consensus       200 ~~~~  203 (214)
T 2rf4_A          200 HTTG  203 (214)
T ss_dssp             ECCS
T ss_pred             EecC
Confidence            7544

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

Probab=80.88  E-value=2.9  Score=32.01  Aligned_cols=52  Identities=23%  Similarity=0.313  Sum_probs=41.3

Q ss_pred             ccCCCeEecCCccCCC--CCeeccCCeEe-cCCeEEEEEeeEEEEe-----CcEEEEEec
Q psy10116         27 EFTDPILTPGETVEYL--EGYMTGHGTFP-DDEEIKASVGGVVEKV-----NQLVSVRAM   78 (298)
Q Consensus        27 ~~~~~iV~PGD~I~~~--~~~~~G~Gty~-~~g~i~Asv~G~v~~~-----nk~v~V~p~   78 (298)
                      .+..+.|.||..|.-.  ..|-||.++-. .|..|+|.+.|.|+..     .+.|+|.|.
T Consensus        25 ~~~Gq~V~aG~IivRQRGtk~hPG~NVg~GkD~TLfAl~~G~V~f~~~~~~r~~VsV~p~   84 (85)
T 3v2d_0           25 RYEGQVVRAGNILVRQRGTRFKPGKNVGMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPL   84 (85)
T ss_dssp             SCTTCEECTTCEEEECSSCSEEECTTEEECTTCCEEESSSEEEEEEECGGGCEEEEEEEC
T ss_pred             ecCCeEEcCCeEEEecCCccCcCCCCEeEcCCCeEEEecCEEEEEEEcCCCCEEEEEEEC
Confidence            4567899999999764  35889998876 4899999999999964     246888774

>2i9z_A Putative septation protein spovg; APC86317, staphylococcus epidermidis ATCC 12228, STRU genomics, PSI-2, protein structure initiative; 2.30A {Staphylococcus epidermidis} SCOP: d.366.1.1

Probab=80.27  E-value=2.3  Score=33.77  Aligned_cols=52  Identities=21%  Similarity=0.344  Sum_probs=42.3

Q ss_pred             ccEEEEEeeCceEEEecCCC-CCCCccccccccCCHHHHHHHHHHHHHHHHHhhCCcccCHHHHHHHHHHHh
Q psy10116        197 CGAQVILGCNGYVWVSAIDE-NKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESL  267 (298)
Q Consensus       197 ~~~eiivG~NG~IWI~~~~~-~~~~~~~~~~~~i~~~~r~~i~rv~n~i~~l~~~~~~i~~~~i~~~~~~s~  267 (298)
                      -++.|+=|.|| +||.-++. ..++.|.+...|++.+.|+.|.                  +.|+.+|+..+
T Consensus        35 ~dIKViEg~~G-lFVaMPSrk~~~GeyrDI~hPIt~e~Re~i~------------------~aVl~aY~~~~   87 (105)
T 2i9z_A           35 HDLRVIEGNSG-LFVAMPSKRTPDGEFRDIAHPINSDMRQEIQ------------------DAVMKVYDETD   87 (105)
T ss_dssp             EEEEEEEETTE-EEEECCEEECTTSCEEECEEESSHHHHHHHH------------------HHHHHHHHTST
T ss_pred             eeEEEEECCCc-eEEECCCcCCCCCCEEEEEEECCHHHHHHHH------------------HHHHHHHHHHH
Confidence            47999999999 99998875 3456787888999999999995                  56777887764

---

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	298
d2nn6h3	126	d.51.1.1 (H:168-293) Ribosomal RNA-processing prot	2e-46
d2nn6h1	95	b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-pro	9e-27
d2nn6i1	125	b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {H	2e-18
d2ja9a1	90	b.40.4.5 (A:62-151) S1-domain of exosome component	1e-16
d2nn6h2	48	b.84.4.2 (H:25-72) Ribosomal RNA-processing protei	4e-16
d2nn6g1	88	b.40.4.5 (G:107-194) S1-domain of exosome componen	6e-15
d2ba0a2	51	b.84.4.2 (A:2-52) Exosome complex RNA-binding prot	2e-11
d2je6i1	87	b.40.4.5 (I:66-152) S1-domain of exosome complex R	2e-11
d2z0sa1	88	b.40.4.5 (A:60-147) S1-domain of exosome complex R	3e-11
d2je6i2	59	b.84.4.2 (I:7-65) Exosome complex RNA-binding prot	9e-08
d2ba0a1	83	b.40.4.5 (A:53-135) S1-domain of exosome complex R	3e-07
d2nn6i2	55	b.84.4.2 (I:6-60) Exosome component 1, EXOSC1 {Hum	2e-05
d1sroa_	76	b.40.4.5 (A:) S1 RNA-binding domain of polyribonuc	0.003

>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 =  150 bits (380), Expect = 2e-46
 Identities = 60/124 (48%), Positives = 84/124 (67%), Gaps = 3/124 (2%)

Query: 174 QGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWVSAI---DENKSGGFIQNMEVVK 230
           QG+L+ V PSL++R K+HF +L CGA VILG NG++W+       E ++GGFI N+E V 
Sbjct: 1   QGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWIYPTPEHKEEEAGGFIANLEPVS 60

Query: 231 LSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQK 290
           L+DRE I+RL N I +L   ++ML+DTSI Y YE SL +   D+LKPE   ++V+ T Q+
Sbjct: 61  LADREVISRLRNCIISLVTQRMMLYDTSILYCYEASLPHQIKDILKPEIMEEIVMETRQR 120

Query: 291 LQTL 294
           L   
Sbjct: 121 LLEQ 124

>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 = 98.5 bits (245), Expect = 9e-27
 Identities = 59/94 (62%), Positives = 80/94 (85%)

Query: 80  SRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMRE 139
           +RYIGE+G++VVGR+T +Q ++W V+TNS L+S L L+S+NLPGGE RRRS +DE  MR 
Sbjct: 2   TRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRG 61

Query: 140 FLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLG 173
           FL+EGDLISAE+  + ++G+++LHTRSLKYGKLG
Sbjct: 62  FLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLG 95

>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 = 77.2 bits (190), Expect = 2e-18
 Identities = 16/92 (17%), Positives = 41/92 (44%), Gaps = 1/92 (1%)

Query: 80  SRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMRE 139
           S+ + ++G +V  +V+ + S+   V    +    L  +       E  R + +D+  + +
Sbjct: 1   SQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYK 60

Query: 140 FLKEGDLISAEIHQIS-TEGSLTLHTRSLKYG 170
             + GD++ A++  +   + +  L T   + 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 = 71.8 bits (176), Expect = 1e-16
 Identities = 22/98 (22%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 81  RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREF 140
           RYI  + + V+G + G  S  + V   +   S      +  P   ++          R  
Sbjct: 2   RYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLS-YMAFPNASKK---------NRPT 51

Query: 141 LKEGDLISAEIHQISTEGSLTLHTRSLKYGK-LGQGIL 177
           L+ GDL+ A +     E    +       G+  G GIL
Sbjct: 52  LQVGDLVYARVCTAEKELEAEIECFDSTTGRDAGFGIL 89

>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 = 68.5 bits (168), Expect = 4e-16
 Identities = 21/47 (44%), Positives = 35/47 (74%)

Query: 32 ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAM 78
          ++ PG+T+    G+M GHGT+  +E++ ASV G VE+VN+L+ V+A+
Sbjct: 2  LVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKAL 48

>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 = 66.8 bits (163), Expect = 6e-15
 Identities = 21/99 (21%), Positives = 38/99 (38%), Gaps = 16/99 (16%)

Query: 81  RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREF 140
           RY+   G+ V+G VT      + VD      ++L    ++  G  +R          R  
Sbjct: 1   RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSY--LSFEGATKR---------NRPN 49

Query: 141 LKEGDLISAEIHQISTEGSLTL-----HTRSLKYGKLGQ 174
           ++ GDLI  +    + +    +       R+   G +GQ
Sbjct: 50  VQVGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVIGQ 88

>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 = 56.1 bits (136), Expect = 2e-11
 Identities = 11/50 (22%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 32 ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSR 81
          I+ PG+ +        G+GT+ +  ++ A + G+ ++    V V  +  R
Sbjct: 3  IVLPGDLLS-TNPRAAGYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGR 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 = 57.3 bits (138), Expect = 2e-11
 Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 7/93 (7%)

Query: 80  SRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMRE 139
           S Y  +I ++V+G V  ++   WVVD  +  ++ L  +           RS+   E +R 
Sbjct: 1   SFYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPAS-------NLLGRSINVGEDLRR 53

Query: 140 FLKEGDLISAEIHQISTEGSLTLHTRSLKYGKL 172
           +L  GD + A I          L  +    G++
Sbjct: 54  YLDVGDYVIARIENFDRSIDPVLSVKGKDLGRV 86

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Length = 88

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

 Score = 56.4 bits (136), Expect = 3e-11
 Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 6/91 (6%)

Query: 82  YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFL 141
           Y+ + G+VV+G +  +    W VD NS   + L +           R      + M+  L
Sbjct: 3   YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFL------GRPFNPAVDDMQSLL 56

Query: 142 KEGDLISAEIHQISTEGSLTLHTRSLKYGKL 172
           K GD I A++       S  L  +    G++
Sbjct: 57  KVGDYIKAKVVAFDKTRSPLLTVQGEGLGRI 87

>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 = 45.8 bits (109), Expect = 9e-08
 Identities = 8/48 (16%), Positives = 19/48 (39%), Gaps = 1/48 (2%)

Query: 32 ILTPGETVEYLEGYMT-GHGTFPDDEEIKASVGGVVEKVNQLVSVRAM 78
          I+ PGE +   E  +         + +  ++V G+ +  +    V  +
Sbjct: 10 IVVPGELLAEGEFQIPWSPYILKINSKYYSTVVGLFDVKDTQFEVIPL 57

>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 = 45.4 bits (107), Expect = 3e-07
 Identities = 19/91 (20%), Positives = 37/91 (40%), Gaps = 9/91 (9%)

Query: 82  YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFL 141
           Y   +G+VV+G +  + +  W VD  S  ++ L +              ++  +   E L
Sbjct: 1   YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPV---------SENPEMKPNKKPNEVL 51

Query: 142 KEGDLISAEIHQISTEGSLTLHTRSLKYGKL 172
             GD I A++  I  +  +TL  +      +
Sbjct: 52  DIGDAIIAKVLNIDPKMKVTLTMKDRICRPI 82

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

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

 Score = 39.3 bits (92), Expect = 2e-05
 Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 2/43 (4%)

Query: 35 PGETVEYLEGYMTGHGTFPDDEEIKASVGGVV--EKVNQLVSV 75
          PGE +  LE    G GT+     I +S+ G +     N  + V
Sbjct: 5  PGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSSENGALPV 47

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} Length = 76

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]

 Score = 33.6 bits (77), Expect = 0.003
 Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 13/84 (15%)

Query: 85  EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEG 144
           E+G V  G+VT +      V      E  +H            + + +  E + ++L+ G
Sbjct: 4   EVGRVYTGKVTRIVDFGAFVAIGGGKEGLVH----------ISQIADKRVEKVTDYLQMG 53

Query: 145 DLISAEIHQISTEGSLTLHTRSLK 168
             +  ++ ++  +G + L   S+K
Sbjct: 54  QEVPVKVLEVDRQGRIRL---SIK 74

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	298
d2nn6h3	126	Ribosomal RNA-processing protein 4, RRP4 {Human (H	100.0
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	99.92
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	99.89
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	99.87
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	99.78
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	99.78
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	99.76
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	99.72
d2nn6h2	48	Ribosomal RNA-processing protein 4, RRP4 {Human (H	99.68
d2ba0a2	51	Exosome complex RNA-binding protein 1, ECR1 {Archa	99.58
d2je6i2	59	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	99.45
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.09
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	99.09
d2nn6g3	80	Ribosomal RNA-processing protein 40, RRP40 {Human	99.07
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	99.06
d2nn6i2	55	Exosome component 1, EXOSC1 {Human (Homo sapiens)	99.03
d2ja9a2	85	Ribosomal RNA-processing protein 40, RRP40 {Saccha	98.94
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	98.8
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	98.69
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	98.63
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.39
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.23
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	98.19
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	97.87
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	97.4
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	97.07
d2nn6g2	91	Ribosomal RNA-processing protein 40, RRP40 {Human	96.98
d2z0sa2	87	Exosome complex RNA-binding protein 1, ECR1 {Aerop	96.88
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	95.67
d2je6i3	69	Exosome complex RNA-binding protein 1, ECR1 {Sulfo	94.9
d2ba0a3	84	Exosome complex RNA-binding protein 1, ECR1 {Archa	94.71
d1v8qa_	66	Ribosomal protein L27 {Thermus thermophilus [TaxId	94.04
d2zjrt1	84	Ribosomal protein L27 {Deinococcus radiodurans [Ta	91.34

>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=1.2e-37  Score=257.29  Aligned_cols=122  Identities=49%  Similarity=0.851  Sum_probs=114.1

Q ss_pred             CceEEEeCchhhccccCcceeccccEEEEEeeCceEEEecCCC---CCCCccccccccCCHHHHHHHHHHHHHHHHHhhC
Q psy10116        174 QGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWVSAIDE---NKSGGFIQNMEVVKLSDRETITRLNNVIKALAES  250 (298)
Q Consensus       174 ~G~lv~v~~~li~r~~~~~~~l~~~~eiivG~NG~IWI~~~~~---~~~~~~~~~~~~i~~~~r~~i~rv~n~i~~l~~~  250 (298)
                      .|++++|+|+||+|+|+|||+|+||+++|+|+||||||+++.+   +++.+|+++++++|.++|++|||++|||++|+++
T Consensus         1 ~G~lv~V~p~LVkR~K~Hf~~L~~gv~vILG~NGyIWIs~~~~~~~~~~~~~~~~~~~v~~~~R~~IaRvaNcI~~La~~   80 (126)
T d2nn6h3           1 QGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWIYPTPEHKEEEAGGFIANLEPVSLADREVISRLRNCIISLVTQ   80 (126)
T ss_dssp             SSCEEECCTTSCCCSTTCSCCCBTTBEEEEETTTEEEEECCCCC------CCGGGSSCCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEChHHhhhhhhceEEcCCCceEEEecCCEEEeeCCcccccccccccccccCCCCHHHHHHHHHHHHHHHHHHHC
Confidence            4889999999999999999999999999999999999999866   3456788889999999999999999999999999


Q ss_pred             CcccCHHHHHHHHHHHhCCCCcccCChhHHHHHHHHHHHHHHHcc
Q psy10116        251 KVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQKLQTLG  295 (298)
Q Consensus       251 ~~~i~~~~i~~~~~~s~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  295 (298)
                      +++||+++|+++||+|++++++|||.|++++++++.+++||++++
T Consensus        81 ~~~I~~~sI~~~yeaSl~~~v~dlL~~e~~~~i~~~~~~rl~~~~  125 (126)
T d2nn6h3          81 RMMLYDTSILYCYEASLPHQIKDILKPEIMEEIVMETRQRLLEQE  125 (126)
T ss_dssp             TCCCCHHHHHHHHHTHHHHCCSSCCTTHHHHHHHHHHHHHHHTTT
T ss_pred             CCcccHHHHHHHHHHHhcCCHHHHhCHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999999999999999999999999999875

>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=99.92  E-value=9.6e-26  Score=176.98  Aligned_cols=94  Identities=62%  Similarity=1.043  Sum_probs=79.1

Q ss_pred             CccccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCC
Q psy10116         79 NSRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEG  158 (298)
Q Consensus        79 ~~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg  158 (298)
                      +++|.|++||+|+|+|+++.+++|+|||++.++|+||+|++++|++.+||+++.+..+|+++|++||.|.|+|++++.++
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 psy10116        159 SLTLHTRSLKYGKL  172 (298)
Q Consensus       159 ~~~Lstr~~~lGkL  172 (298)
                      .+.||||+.+||||
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=99.89  E-value=2.5e-23  Score=161.42  Aligned_cols=82  Identities=26%  Similarity=0.368  Sum_probs=76.9

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcE
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSL  160 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~  160 (298)
                      ||+|++||+|+|+|++++.+.|+|||+++++|+||++++  ||+++|+         |++|++||+|+|||++++.++.+
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 RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSYLSF--EGATKRN---------RPNVQVGDLIYGQFVVANKDMEP   69 (88)
T ss_dssp             SCCCCSSEEEEEEEEEEETTEEEEECSSSSCCCEESCSS--SCCSSCS---------SSSSCTTCEEEEEEEECCTTSCC
T ss_pred             CCcCCCCCEEEEEEEEEeCCeEEEEcCCCeeEEEeHHHc--Ccccccc---------CcccCCCCEEEEEEEEeCCCCCE
Confidence            799999999999999999999999999999999999985  7888765         79999999999999999999999


Q ss_pred             EEEe-----ccCCCccCC
Q psy10116        161 TLHT-----RSLKYGKLG  173 (298)
Q Consensus       161 ~Lst-----r~~~lGkL~  173 (298)
                      +||+     |+.+||+|.
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            9997     888999985

>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=1.4e-22  Score=157.75  Aligned_cols=82  Identities=22%  Similarity=0.334  Sum_probs=74.6

Q ss_pred             ccccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCc
Q psy10116         80 SRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGS  159 (298)
Q Consensus        80 ~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~  159 (298)
                      +||+|++||+|||+|+++..++|+|||+++++|+||.+. +|||+++|         |+++|++||+|+|||++++.+++
T Consensus         1 krY~P~~gD~ViG~V~~~~~~~~~vdI~~~~~~~L~~~~-~f~g~~k~---------~r~~l~~GDlV~arV~~v~~~~~   70 (90)
T d2ja9a1           1 KRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYM-AFPNASKK---------NRPTLQVGDLVYARVCTAEKELE   70 (90)
T ss_dssp             CCCCCCTTCEEEEEEEEECSSEEEEESSTTSCCEEEETT-SSTTCCSS---------SCCCCCTTCEEEEEEEECCTTSC
T ss_pred             CCccCCCCCEEEEEEEEEeCCcEEEEcCCcchhhhhhhh-ccCccccc---------cCCccCCCCEEEEEEEEECCCCC
Confidence            489999999999999999999999999999999998654 47888765         48999999999999999999999


Q ss_pred             EEEEeccCCCcc
Q psy10116        160 LTLHTRSLKYGK  171 (298)
Q Consensus       160 ~~Lstr~~~lGk  171 (298)
                      ++|||++..+||
T Consensus        71 ~~Lsc~~~~~gK   82 (90)
T d2ja9a1          71 AEIECFDSTTGR   82 (90)
T ss_dssp             CEEESSCTTTCS
T ss_pred             EEEEEeccccCc
Confidence            999998777777

>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=99.78  E-value=5.2e-20  Score=150.99  Aligned_cols=90  Identities=17%  Similarity=0.285  Sum_probs=76.8

Q ss_pred             ccccccCCCEEEEEEEEEecceEEEEeCC--------CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEE
Q psy10116         80 SRYIGEIGEVVVGRVTGLQSQKWVVDTNS--------ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI  151 (298)
Q Consensus        80 ~rY~P~vGDiVIG~V~~V~~~~~~VDI~s--------~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V  151 (298)
                      ++|+|++||+|+|+|+++++++|+|||.+        ++.|+++.+++        |.++.|..+|+++|++||+|+|+|
T Consensus         1 s~~vP~vGDiVig~V~~v~~~~a~v~I~~v~~~~l~~~~~g~i~~~dv--------r~te~d~~~m~~~fr~GDiV~A~V   72 (125)
T d2nn6i1           1 SQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDV--------RATEKDKVEIYKSFRPGDIVLAKV   72 (125)
T ss_dssp             CCCCCCTTCEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGG--------GTCSSCCCCGGGTCCSSSEEEEEE
T ss_pred             CCcCCCCCCEEEEEEEEecCCEEEEEEeEecCcccccCccccccHHHc--------ccchhhhhhHHHhcCCCCEEEEEE
Confidence            47999999999999999999999999965        45566665554        678899999999999999999999


Q ss_pred             EEeCCCC-cEEEEeccCCCccCCCceEEEeCc
Q psy10116        152 HQISTEG-SLTLHTRSLKYGKLGQGILLTVPP  182 (298)
Q Consensus       152 ~sv~~dg-~~~Lstr~~~lGkL~~G~lv~v~~  182 (298)
                      ++++... .+.|||+++.||+     +++.|+
T Consensus        73 is~~~~~~~~~Lst~~~~LGV-----v~A~c~   99 (125)
T d2nn6i1          73 ISLGDAQSNYLLTTAENELGV-----VVAHSE   99 (125)
T ss_dssp             EEEETTTTEEEEECCSSSCEE-----CCCBCS
T ss_pred             EEccCCCccEEEEecCCCcEE-----EEEECC
Confidence            9997544 5999999999999     555553

>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=99.78  E-value=1.9e-19  Score=138.28  Aligned_cols=86  Identities=26%  Similarity=0.386  Sum_probs=78.0

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcE
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSL  160 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~  160 (298)
                      .|.|++||+|+|+|+++++++|+|||++..+|+||+++++.      .....+..+++++|++||.|.|+|+++++++.+
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 IYVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLG------RPFNPAVDDMQSLLKVGDYIKAKVVAFDKTRSP   75 (88)
T ss_dssp             CCCCCTTCCEEEEEEEECSSEEEEECSSSSCEEEEHHHHHT------SCCCTTTTCCTTSSCTTCEEEEEEEEECTTSCE
T ss_pred             CcCCCCCCEEEEEEEEEECCeEEEEeCCCeEEEEehHHhCc------ccccccccchhhhcccCcEEEEEEEEECCCCCE
Confidence            59999999999999999999999999999999999999862      223345568899999999999999999999999


Q ss_pred             EEEeccCCCccC
Q psy10116        161 TLHTRSLKYGKL  172 (298)
Q Consensus       161 ~Lstr~~~lGkL  172 (298)
                      .||+|+.++|||
T Consensus        76 ~Ls~k~~~~gkl   87 (88)
T d2z0sa1          76 LLTVQGEGLGRI   87 (88)
T ss_dssp             EEECCSSSCEEC
T ss_pred             EEEEecCCCccc
Confidence            999999999996

>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=99.76  E-value=5.6e-19  Score=135.38  Aligned_cols=87  Identities=25%  Similarity=0.414  Sum_probs=77.1

Q ss_pred             ccccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCc
Q psy10116         80 SRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGS  159 (298)
Q Consensus        80 ~rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~  159 (298)
                      +.|+|++||+|+|+|+++.+++|+|||++..+|+||++++..       .......++++.|++||.|.|+|+++++++.
T Consensus         1 s~Y~Pk~Gdiv~G~V~~i~~~g~fV~i~~~~~gll~~s~~~~-------~~~~~~~~~~~~~~~Gd~v~~kV~~vd~~~~   73 (87)
T d2je6i1           1 SFYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLG-------RSINVGEDLRRYLDVGDYVIARIENFDRSID   73 (87)
T ss_dssp             SCCCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEHHHHHT-------SCCCTTCCCSSSCCTTCEEEEEEEEEETTEE
T ss_pred             CcccCCCCCEEEEEEEEEECCEEEEEeCCCEEEEEehHHhCC-------ceeccccccchhhcccceEEEEEEEECCCCC
Confidence            369999999999999999999999999999999999999852       1122335688999999999999999998899


Q ss_pred             EEEEeccCCCccCC
Q psy10116        160 LTLHTRSLKYGKLG  173 (298)
Q Consensus       160 ~~Lstr~~~lGkL~  173 (298)
                      +.||+|+.+||+|.
T Consensus        74 i~LS~k~~~lgkl~   87 (87)
T d2je6i1          74 PVLSVKGKDLGRVS   87 (87)
T ss_dssp             EEEECCSTTCEECC
T ss_pred             EEEEEecCCCccCC
Confidence            99999999999974

>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=99.72  E-value=8.9e-18  Score=127.30  Aligned_cols=83  Identities=23%  Similarity=0.364  Sum_probs=74.7

Q ss_pred             ccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEE
Q psy10116         82 YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLT  161 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~  161 (298)
                      |.|++||+|.|+|+++.+++|+|||++..+|+||++++..         ..+..++++.|++||.|.|+|+++++++.+.
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---------MKPNKKPNEVLDIGDAIIAKVLNIDPKMKVT   71 (83)
T ss_dssp             CCCCTTCEEEEEEEEECSSEEEEECSSSSCEEEEGGGCTT---------CCTTSCGGGTCCTTCEEEEEEEEECTTCCEE
T ss_pred             CcCCCCCEEEEEEEEEECCEEEEecCCCeeEEEecccccc---------cccccChhhhcccccEEEEEEEEECCCCCEE
Confidence            8999999999999999999999999999999999999741         1223567899999999999999999889999


Q ss_pred             EEeccCCCccCC
Q psy10116        162 LHTRSLKYGKLG  173 (298)
Q Consensus       162 Lstr~~~lGkL~  173 (298)
                      ||+|+.++|+|+
T Consensus        72 LS~k~~~~~k~r   83 (83)
T d2ba0a1          72 LTMKDRICRPIR   83 (83)
T ss_dssp             EECCSSSCEEES
T ss_pred             EEecCCCCCCCC
Confidence            999999999863

>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=99.68  E-value=1.3e-17  Score=114.36  Aligned_cols=48  Identities=44%  Similarity=0.829  Sum_probs=46.4

Q ss_pred             CeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEeCcEEEEEec
Q psy10116         31 PILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAM   78 (298)
Q Consensus        31 ~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~nk~v~V~p~   78 (298)
                      +||+|||.|+++++||+|||||.++++++||++|+++++||+++|+|+
T Consensus         1 ~iv~PGe~It~~~~~mrGHGTy~~~~~i~aSv~G~vervNKLvsV~pL   48 (48)
T d2nn6h2           1 HLVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKAL   48 (48)
T ss_dssp             CBCCTTCBCCCCTTCCBCTTEEECSSSEEECSSEEEEEETTEEEEEES
T ss_pred             CEecCCcEeecCCCeEcccccEecCCEEEEEEeeeEEEeccEEEEEcC
Confidence            489999999999999999999999999999999999999999999996

>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=99.58  E-value=6.1e-16  Score=107.90  Aligned_cols=51  Identities=22%  Similarity=0.417  Sum_probs=47.9

Q ss_pred             CCeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEEeCcEEEEEecCcc
Q psy10116         30 DPILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSR   81 (298)
Q Consensus        30 ~~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~~nk~v~V~p~~~r   81 (298)
                      +++|+|||.|++ ++|++|||||.++++|+||++|.++..|++|+|+|+++|
T Consensus         1 r~iV~PGe~i~~-~~~~~G~Gty~~~~~i~ss~~G~v~~~n~~i~V~PL~gr   51 (51)
T d2ba0a2           1 RKIVLPGDLLST-NPRAAGYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGR   51 (51)
T ss_dssp             CCEECTTCEEES-CTTSBCTTEEEETTEEEECSSEEEEECSSCEEEEECSSS
T ss_pred             CCEEcCCcEeec-CCeeCCCCcEEECCEEEEEEEEEEEEECCEEEEEeCccC
Confidence            479999999987 479999999999999999999999999999999999875

>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=99.45  E-value=3e-14  Score=101.99  Aligned_cols=53  Identities=15%  Similarity=0.129  Sum_probs=49.4

Q ss_pred             cCCCeEecCCccCCCCCee-ccCCeEecCCeEEEEEeeEEEEeCcEEEEEecCc
Q psy10116         28 FTDPILTPGETVEYLEGYM-TGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNS   80 (298)
Q Consensus        28 ~~~~iV~PGD~I~~~~~~~-~G~Gty~~~g~i~Asv~G~v~~~nk~v~V~p~~~   80 (298)
                      .++++|+|||+|++.+.|+ .|||||.++++|+||++|.++.+|++++|+|+++
T Consensus         6 ~~r~iV~PGdvi~~~~~~~~~g~~ty~~~~ki~asv~G~v~~~nkli~ViPL~G   59 (59)
T d2je6i2           6 QPRSIVVPGELLAEGEFQIPWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEG   59 (59)
T ss_dssp             CSSCEECTTCEEEEECCCCCCCTTEEEETTEEEECSSEEEEEETTEEEEEESCC
T ss_pred             cCCeEECCCcEeeeCCccccCCCEEEecCCEEEEEEEEEEEEECCEEEEEECCC
Confidence            3679999999999988888 5999999999999999999999999999999975

>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=99.09  E-value=2.2e-10  Score=86.49  Aligned_cols=75  Identities=15%  Similarity=0.222  Sum_probs=56.9

Q ss_pred             ccccCCCEEEEEEEEEecceEEEEeCC--CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCC
Q psy10116         82 YIGEIGEVVVGRVTGLQSQKWVVDTNS--ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEG  158 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s--~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg  158 (298)
                      ..|++||+|.|+|+++.+.+++|+|..  ..+|++|+++++          .....+..+.|++||.|.|+|++++ ..+
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 KFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELS----------RRRIRSINKLIRIGRNECVVVIRVDKEKG   78 (86)
T ss_dssp             SSCCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC----------------------CTTCEEEEEEEEEETTTT
T ss_pred             cCCCCCCEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeecc----------ccccccceEEeecccEEEEEEEEEECCCC
Confidence            468999999999999999999999973  579999999985          2233566889999999999999998 467


Q ss_pred             cEEEEecc
Q psy10116        159 SLTLHTRS  166 (298)
Q Consensus       159 ~~~Lstr~  166 (298)
                      .+.||.|.
T Consensus        79 ki~LS~Kq   86 (86)
T d1kl9a2          79 YIDLSKRR   86 (86)
T ss_dssp             EEEEESTT
T ss_pred             EEEEEeeC
Confidence            89999863

>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=99.09  E-value=1.2e-10  Score=86.25  Aligned_cols=73  Identities=19%  Similarity=0.356  Sum_probs=64.3

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCCcEEEE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLH  163 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg~~~Ls  163 (298)
                      .++|++|.|+|+.+.+.+++|+++...+|++|++++..          ....++++.|++||.|.|+|+++++++.+.||
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----------KRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLS   72 (76)
T ss_dssp             CCTTSEEEEEEEEEETTEEEEECSSSCCCBCCTTSSCS----------SCCSCHHHHCCTTCEEEEEEEECCTTCCCEEE
T ss_pred             CCCCCEEEEEEEEEeCcEEEEEeCCCCEEEEEhHHhCc----------cccCCHHHccCCCCEEEEEEEEECCCCCEEEE
Confidence            47999999999999999999999988999999999852          11245688899999999999999988899999


Q ss_pred             ecc
Q psy10116        164 TRS  166 (298)
Q Consensus       164 tr~  166 (298)
                      +|.
T Consensus        73 ~k~   75 (76)
T d1sroa_          73 IKE   75 (76)
T ss_dssp             ECC
T ss_pred             EEc
Confidence            886

>d2nn6g3 d.51.1.1 (G:195-274) Ribosomal RNA-processing protein 40, RRP40 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Eukaryotic type KH-domain (KH-domain type I)
superfamily: Eukaryotic type KH-domain (KH-domain type I)
family: Eukaryotic type KH-domain (KH-domain type I)
domain: Ribosomal RNA-processing protein 40, RRP40
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.07  E-value=5.5e-11  Score=89.62  Aligned_cols=58  Identities=29%  Similarity=0.586  Sum_probs=48.0

Q ss_pred             CceEEEeCchhhccccCcceec------cccEEEEEeeCceEEEecCCCCCCCccccccccCCHHHHHHHHHHHHHHHHH
Q psy10116        174 QGILLTVPPSLIRRSKSHFCNL------ACGAQVILGCNGYVWVSAIDENKSGGFIQNMEVVKLSDRETITRLNNVIKAL  247 (298)
Q Consensus       174 ~G~lv~v~~~li~r~~~~~~~l------~~~~eiivG~NG~IWI~~~~~~~~~~~~~~~~~i~~~~r~~i~rv~n~i~~l  247 (298)
                      +|++|+||.++++|+.+.-+.+      .++|||++|+||+|||++++.                 +++|+ ++|||+..
T Consensus         1 dG~~f~vsl~laR~Ll~~~~~vL~~Lgk~~~FEIavG~NGrVWvk~~~~-----------------~~ti~-i~~aI~~~   62 (80)
T d2nn6g3           1 DGLLFKVTLGLIRKLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTI-----------------QQTLI-LANILEAC   62 (80)
T ss_dssp             SCEEECCCHHHHHHHHCTTCSHHHHTTCSSSCCCEEETTTEEEECCSSH-----------------HHHHH-HHHHHHHT
T ss_pred             CCEEEEecHHHHHHHhcCCCHHHHHHhhhCCeEEEEecCCeEEEeCCCH-----------------HHHHH-HHHHHHHh
Confidence            6999999999999998765543      389999999999999999763                 45665 88888887


Q ss_pred             hh
Q psy10116        248 AE  249 (298)
Q Consensus       248 ~~  249 (298)
                      +.
T Consensus        63 e~   64 (80)
T d2nn6g3          63 EH   64 (80)
T ss_dssp             TS
T ss_pred             hc
Confidence            64

>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=99.06  E-value=1.8e-10  Score=86.47  Aligned_cols=75  Identities=16%  Similarity=0.251  Sum_probs=62.3

Q ss_pred             ccccCCCEEEEEEEEEecceEEEEeCC--CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCC
Q psy10116         82 YIGEIGEVVVGRVTGLQSQKWVVDTNS--ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEG  158 (298)
Q Consensus        82 Y~P~vGDiVIG~V~~V~~~~~~VDI~s--~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg  158 (298)
                      -.|++||+|.|+|+++.+.+++|++..  ..+|++|.++++.          ....+.++.|++||.|.|+|++++ .++
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----------KWVKNIRDVLKENRKVIVKVIRVDRRKG   76 (84)
T ss_dssp             SSCCTTCCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC---------------CHHHHTCSSCEEECEEEEEETTTT
T ss_pred             cCCCCCCEEEEEEEEEECCEEEEEECCcCCEEEEEEcccccc----------ccccccceEeecccEEEEEEEEEECCCC
Confidence            468999999999999999999999974  5799999999852          223456788999999999999998 457


Q ss_pred             cEEEEecc
Q psy10116        159 SLTLHTRS  166 (298)
Q Consensus       159 ~~~Lstr~  166 (298)
                      .+.||.|+
T Consensus        77 ~i~LS~Kq   84 (84)
T d2ahob2          77 TVDVSLKK   84 (84)
T ss_dssp             EEEEESSS
T ss_pred             EEEEEEcC
Confidence            89999864

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

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

Probab=99.03  E-value=7.2e-12  Score=88.10  Aligned_cols=49  Identities=29%  Similarity=0.340  Sum_probs=41.9

Q ss_pred             CeEecCCccCCCCCeeccCCeEecCCeEEEEEeeEEEE--eCcEEEEEecC
Q psy10116         31 PILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEK--VNQLVSVRAMN   79 (298)
Q Consensus        31 ~iV~PGD~I~~~~~~~~G~Gty~~~g~i~Asv~G~v~~--~nk~v~V~p~~   79 (298)
                      ++++|||.|+..++|++|+|||+++|.||||++|.+..  .++.++|.+..
T Consensus         1 k~~lPGe~L~~~eey~~G~gTy~~~g~I~as~~G~v~id~~~~~isVisV~   51 (55)
T d2nn6i2           1 RYCIPGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSSENGALPVVSVV   51 (55)
T ss_dssp             CCCCTTCEEEETTTCCCSSSCEEETTEEECCSCSCBCCCBCTTSSBC-CBC
T ss_pred             CcccCCcEEeehheecCCCCeEEcCCEEEEEeeEEEEEecCCCEeeEEEEE
Confidence            47899999999999999999999999999999999985  45666666543

>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=98.94  E-value=3.7e-10  Score=85.96  Aligned_cols=72  Identities=18%  Similarity=0.315  Sum_probs=52.0

Q ss_pred             CceEEEeCchhhcccc-C-cceec-----cccEEEEEeeCceEEEecCCCCCCCccccccccCCHHHHHHHHHHHHHHHH
Q psy10116        174 QGILLTVPPSLIRRSK-S-HFCNL-----ACGAQVILGCNGYVWVSAIDENKSGGFIQNMEVVKLSDRETITRLNNVIKA  246 (298)
Q Consensus       174 ~G~lv~v~~~li~r~~-~-~~~~l-----~~~~eiivG~NG~IWI~~~~~~~~~~~~~~~~~i~~~~r~~i~rv~n~i~~  246 (298)
                      +|++++|++++++|+. + +...|     .++|+|+||+||+|||++++.                  +.+..+++||+.
T Consensus         1 dG~v~~vs~~~~rrll~~~~~~ml~~l~~~~~~eI~VG~NGrIWi~~~~~------------------~~~i~i~~aI~~   62 (85)
T d2ja9a2           1 DGMIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWVKCEEL------------------SNTLACYRTIME   62 (85)
T ss_dssp             SCEEEECCHHHHHHHHHCTTCCHHHHHHTTCCCEEEEETTTEEEEECSSH------------------HHHHHHHHHHHH
T ss_pred             CCEEEEecHHHHHHHHcCCCChHHHHHHhhcCceEEEecCcEEEEECCCH------------------HHHHHHHHHHHH
Confidence            6999999999999985 2 22233     499999999999999999763                  344458899977


Q ss_pred             Hh-hCCcccCHHHHHHHH
Q psy10116        247 LA-ESKVMLFDTSIQYAY  263 (298)
Q Consensus       247 l~-~~~~~i~~~~i~~~~  263 (298)
                      .+ +.+..-..+.|.+.+
T Consensus        63 ~e~~~~~~~~~~~vk~~l   80 (85)
T d2ja9a2          63 CCQKNDTAAFKDIAKRQF   80 (85)
T ss_dssp             HHHHCCGGGHHHHHHHHT
T ss_pred             HHHhCCHhHHHHHHHHHH
Confidence            75 444444555555443

>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=98.80  E-value=8.4e-09  Score=78.93  Aligned_cols=74  Identities=19%  Similarity=0.254  Sum_probs=64.2

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCCcEEE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEGSLTL  162 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg~~~L  162 (298)
                      -++|++|.|+|+.+...+.+|+++...+|++|++++..          ....++++.|++||.|.|+|.+++ .++.+.|
T Consensus        16 ~k~G~iv~g~V~~v~~~G~~V~l~~~i~G~i~~~~ls~----------~~~~~~~~~~~vGq~v~~~V~~id~~~~~i~L   85 (94)
T d3bzka4          16 LKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSE----------KFVKDPYEVVKAGDIVKVKVMEVDIPRNRVGL   85 (94)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECSSSSCEEEEGGGGCS----------SCCSCHHHHCCTTCEEEEEEEEEETTTTEEEE
T ss_pred             CCCCCEEEEEEEEEECcEEEEEeCCCceEEeehhhhhc----------ccccChhhhhccCcEEEEEEEEEECCCCEEEE
Confidence            36899999999999999999999999999999999852          123456789999999999999998 4788999


Q ss_pred             EeccC
Q psy10116        163 HTRSL  167 (298)
Q Consensus       163 str~~  167 (298)
                      |.|..
T Consensus        86 S~K~~   90 (94)
T d3bzka4          86 SMRMS   90 (94)
T ss_dssp             ESCTT
T ss_pred             EEecc
Confidence            98753

>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=98.69  E-value=3.5e-08  Score=77.20  Aligned_cols=81  Identities=23%  Similarity=0.300  Sum_probs=63.8

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhh-------hhhhcccCCCCEEEEEEEEeCC
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDE-------EMMREFLKEGDLISAEIHQIST  156 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~-------~~mr~~~~~GDlV~A~V~sv~~  156 (298)
                      |++||++-|+|++|.+.+++|+|+ +.+|++|++++.  ..  +  ...++       .+....|++||.|.++|.+++.
T Consensus         1 p~~gei~~g~V~~v~~~G~FVel~-~ieGlv~~s~l~--~~--~--~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~   73 (106)
T d1go3e1           1 PEMYELIEGEVVDVVEFGSFVRLG-PLDGLIHVSQIM--DD--Y--VSYDPKREAIIGKETGKVLEIGDYVRARIVAISL   73 (106)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEECS-SSEEEEEGGGSC--SS--C--EEECCC--CEEETTTCCEECTTCEEEEEEEEEEC
T ss_pred             CCCCCEEEEEEEEEeeeEEEEEee-CeEEEEEeeccc--Cc--e--eeeccceeEEeecccccceeecceEEEEEEEEch
Confidence            899999999999999999999997 689999999974  11  1  01111       2346899999999999999984


Q ss_pred             CC------cEEEEeccCCCcc
Q psy10116        157 EG------SLTLHTRSLKYGK  171 (298)
Q Consensus       157 dg------~~~Lstr~~~lGk  171 (298)
                      +.      .+.||.+....|.
T Consensus        74 ~~~~~~~~~i~ls~K~~~~~~   94 (106)
T d1go3e1          74 KAERKRGSKIALTMRQPYLGK   94 (106)
T ss_dssp             CC-----CEEEEECCSTTCEE
T ss_pred             hhccccCceeecccccCCCCc
Confidence            32      3778888877765

>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=98.63  E-value=4.8e-08  Score=77.80  Aligned_cols=77  Identities=17%  Similarity=0.234  Sum_probs=62.9

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeC-CCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC-CCcEE
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTN-SILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST-EGSLT  161 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~-s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~-dg~~~  161 (298)
                      .++|++|.|+|+++.+++++|+++ ...+|++|++++..         .....+..+.|++||.|.|+|++++. .+.+.
T Consensus        19 l~~G~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~---------~~~~~~~~~~~~vGq~v~~~V~~vd~~~~~i~   89 (119)
T d1wi5a_          19 LKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQE---------YIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVS   89 (119)
T ss_dssp             CCTTCEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHH---------HHHHHSSSCCCCTTCEEEEEEEECCTTSCEEE
T ss_pred             cCCCCEEEEEEEEEeccEEEEEEeccccceEEeHHHhcc---------ccccCCHHHhcccceEEEEEEEEEeCCCCEEE
Confidence            479999999999999999999997 66799999998741         11133456789999999999999985 45699


Q ss_pred             EEeccCCC
Q psy10116        162 LHTRSLKY  169 (298)
Q Consensus       162 Lstr~~~l  169 (298)
                      ||+|....
T Consensus        90 LS~k~~~~   97 (119)
T d1wi5a_          90 LSVGHSEV   97 (119)
T ss_dssp             EECCCCCS
T ss_pred             EEecHHHh
Confidence            99886543

>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=98.39  E-value=6e-07  Score=67.69  Aligned_cols=83  Identities=13%  Similarity=0.079  Sum_probs=62.0

Q ss_pred             ccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhh-----hhhhcccCCCCEEEEEEEEeCCC-
Q psy10116         84 GEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDE-----EMMREFLKEGDLISAEIHQISTE-  157 (298)
Q Consensus        84 P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~-----~~mr~~~~~GDlV~A~V~sv~~d-  157 (298)
                      |-+|+++-|+|+++.+.+++|+++ +.++++|.+++.  ..-.   .+.+.     .+....|+.||.|+++|.+++.+ 
T Consensus         1 Pf~Gev~~g~I~~v~~~G~fv~lg-~~eg~i~~~~l~--~~~~---~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~~   74 (91)
T d1y14b1           1 PFKGEVVDGTVVSCSQHGFEVQVG-PMKVFVTKHLMP--QDLT---FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQV   74 (91)
T ss_dssp             CCTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSC--TTCE---ECC-----CEECSSCEECTTCEEEEEEEEEEEET
T ss_pred             CCCCCEEEEEEEEEEeeEEEEEEc-CeEEEEEhhhcC--cceE---EccccceeEecccCeEEeCCCEEEEEEEEEeccc
Confidence            779999999999999999999997 679999999873  2211   00000     12346799999999999999832 


Q ss_pred             Cc--EEEEeccCCCccC
Q psy10116        158 GS--LTLHTRSLKYGKL  172 (298)
Q Consensus       158 g~--~~Lstr~~~lGkL  172 (298)
                      +.  ..-+++++.||.+
T Consensus        75 ~~i~~ig~~~~d~LG~i   91 (91)
T d1y14b1          75 SSIHAIGSIKEDYLGAI   91 (91)
T ss_dssp             TEEEEEEECCSTTCEEC
T ss_pred             CccEEEEEccCCCCCcC
Confidence            33  3446788888874

>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=98.23  E-value=1.8e-06  Score=65.43  Aligned_cols=84  Identities=13%  Similarity=0.011  Sum_probs=63.3

Q ss_pred             cccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhh-------hhhhcccCCCCEEEEEEEEeC
Q psy10116         83 IGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDE-------EMMREFLKEGDLISAEIHQIS  155 (298)
Q Consensus        83 ~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~-------~~mr~~~~~GDlV~A~V~sv~  155 (298)
                      .|-+|+++.|+|+++.+.+++|+++ +.++++|.+++.  ..-   ..+.++       .+-+..|+.||.|++||.+++
T Consensus         1 rPf~Gev~~g~V~~v~~~G~fv~lg-~~~~~v~~~~l~--~d~---~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~   74 (94)
T d2c35b1           1 RPFKGEVVDAVVTQVNKVGLFTEIG-PMSCFISRHSIP--SEM---EFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTR   74 (94)
T ss_dssp             CCCTTCEEEEEEEEEETTEEEEEET-TEEEEEEGGGSC--TTE---EEESSSSSCEEEETTSCSEEETTCEEEEEEEEEE
T ss_pred             CCCCCCEEEEEEEEEEeeEEEEEec-CceEEEEhhhcC--cce---eecccccceEEEcccceEEEeCCCEEEEEEEEEe
Confidence            3789999999999999999999997 689999999864  210   001111       233567999999999999987


Q ss_pred             C-CCc--EEEEeccCCCccC
Q psy10116        156 T-EGS--LTLHTRSLKYGKL  172 (298)
Q Consensus       156 ~-dg~--~~Lstr~~~lGkL  172 (298)
                      . .+.  +..+++++.||.+
T Consensus        75 ~~~~~I~~igt~~~d~LG~i   94 (94)
T d2c35b1          75 VDKNDIFAIGSLMDDYLGLV   94 (94)
T ss_dssp             EETTEEEEEEECCSTTCEEC
T ss_pred             cCcCcceEEEEccCCCcccC
Confidence            2 333  3467899999864

>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=98.19  E-value=4e-06  Score=61.18  Aligned_cols=58  Identities=24%  Similarity=0.299  Sum_probs=52.2

Q ss_pred             cccccCCCEEEEEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC
Q psy10116         81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS  155 (298)
Q Consensus        81 rY~P~vGDiVIG~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~  155 (298)
                      .|..++|++|.|+|..+..+.+.||++ ..+|+||.++. .|               .+.|++||-|+|-|..+.
T Consensus         3 ef~~~~geiv~G~V~r~~~~~~~Vdlg-~~eaiLp~~eq-ip---------------~E~~~~Gdrik~~i~~V~   60 (72)
T d1hh2p1           3 KYSELKGTVTTAEVIRVMGEWADIRIG-KLETRLPKKEW-IP---------------GEEIKAGDLVKVYIIDVV   60 (72)
T ss_dssp             CTTCCTTCEEEEEEEEECSSEEEEEET-TEEEEEEGGGS-CT---------------TCCCCTTCEEEEEEEEEE
T ss_pred             hHhhccCcEEEEEEEEEcCCCEEEEEC-CcEEECCHHHc-CC---------------CCCCCCCCEEEEEEEEEE
Confidence            478899999999999999999999998 68999998875 34               588999999999999986

>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=97.87  E-value=3.6e-07  Score=64.83  Aligned_cols=61  Identities=21%  Similarity=0.295  Sum_probs=35.5

Q ss_pred             EEEEEEecceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCCCC
Q psy10116         92 GRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEG  158 (298)
Q Consensus        92 G~V~~V~~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~dg  158 (298)
                      |+|+.+.+.+++|+|....+|++|+|++......      ....++++.|++||.|.|+|+++++++
T Consensus         1 G~V~~i~~fG~FV~l~~g~~Glihiseis~~~~~------~~v~~~~~~~~~G~~V~vkV~~iD~~~   61 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGG------KRVENVEDVLGVGQKVQVEIAEIDSRG   61 (62)
T ss_dssp             CBEEECC-CSCEECCC---CCCCC-------------------------CCSSCBCCCCCCCCCSSC
T ss_pred             CEEEEEEeceEEEEecCCceEEEEHHHccccccc------ccccCHHHhcCCCCEEEEEEEEEcCCC
Confidence            7899999999999999999999999998521111      123467899999999999999998654

>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=97.40  E-value=0.00021  Score=52.26  Aligned_cols=56  Identities=18%  Similarity=0.260  Sum_probs=46.9

Q ss_pred             cCCCEEEEEEEEEecc----eEEEEeCC---CceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeCC
Q psy10116         85 EIGEVVVGRVTGLQSQ----KWVVDTNS---ILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIST  156 (298)
Q Consensus        85 ~vGDiVIG~V~~V~~~----~~~VDI~s---~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~~  156 (298)
                      ++|++|.|.|..+..+    .+.||++.   ..+|+||.++- .|               .+.|++||-|+|-|..+..
T Consensus         3 r~geiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eq-ip---------------~E~y~~Gdrik~~i~~V~~   65 (76)
T d2asba1           3 REGEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQ-VP---------------GESYEHGNRLRCYVVGVTR   65 (76)
T ss_dssp             CTTCEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGS-CT---------------TCCCCTTCEEEEEEEEEEC
T ss_pred             ccceEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHc-CC---------------CcccCCCCEEEEEEEEEEe
Confidence            6899999999998654    37999984   57899998765 34               5889999999999999974

>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=97.07  E-value=0.00094  Score=49.85  Aligned_cols=77  Identities=17%  Similarity=0.201  Sum_probs=54.0

Q ss_pred             CEEEEEEEEEe--cceEEEEeCCCceeeEecccccCCCCcccccchhhhhhhhcccCCCCEEEEEEEEeC-CCCcEEEEe
Q psy10116         88 EVVVGRVTGLQ--SQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQIS-TEGSLTLHT  164 (298)
Q Consensus        88 DiVIG~V~~V~--~~~~~VDI~s~~~a~L~~s~v~~pgg~~Rr~~~~d~~~mr~~~~~GDlV~A~V~sv~-~dg~~~Lst  164 (298)
                      ||-.|+|..|.  -+.+||||+...+|+||++++..+- ...........++.+.+++||.|...|..=. ....+.|||
T Consensus         2 NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~~di~~~~-~~~~~~~~~~~~i~~~l~~G~~ilVQV~Ke~~~~KGprlT~   80 (87)
T d1smxa_           2 NIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREY-FPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTT   80 (87)
T ss_dssp             CCEEEEEEEEEGGGTEEEEESSSSSCEEEEGGGSCGGG-CSSCCCSSSCCCGGGTCCTTCEEEEEEEECCBTTBCCEEES
T ss_pred             CcEEEEEEEecCCceEEEEEeCCCccceeEecccceee-eccccccccccchhhhccCCCeEEEEEeecccCCCCceEEE
Confidence            57789999996  4689999999999999998864211 0000111122456788999999999999854 233477776


Q ss_pred             c
Q psy10116        165 R  165 (298)
Q Consensus       165 r  165 (298)
                      .
T Consensus        81 ~   81 (87)
T d1smxa_          81 F   81 (87)
T ss_dssp             C
T ss_pred             E
Confidence            4

>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=96.98  E-value=0.00023  Score=53.35  Aligned_cols=53  Identities=13%  Similarity=0.165  Sum_probs=32.5

Q ss_pred             ccCCCeEecCCccCCC-------------------------CCeeccCCeEecCCeEEEEEeeEEEEeC-c------EEE
Q psy10116         27 EFTDPILTPGETVEYL-------------------------EGYMTGHGTFPDDEEIKASVGGVVEKVN-Q------LVS   74 (298)
Q Consensus        27 ~~~~~iV~PGD~I~~~-------------------------~~~~~G~Gty~~~g~i~Asv~G~v~~~n-k------~v~   74 (298)
                      +.-.++|+|||.|...                         ...+.|+|.+.+++.|.++.+|+++++. +      .+|
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            3456899999999421                         1356799999999999999999999763 2      599


Q ss_pred             EEecC
Q psy10116         75 VRAMN   79 (298)
Q Consensus        75 V~p~~   79 (298)
                      |+..+
T Consensus        86 VDs~Q   90 (91)
T d2nn6g2          86 VDSQQ   90 (91)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            98754

>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=96.88  E-value=0.0011  Score=49.60  Aligned_cols=42  Identities=19%  Similarity=0.392  Sum_probs=34.2

Q ss_pred             ceEEEeCchhhccc----cCcceec--cccEEEEEeeCceEEEecCCC
Q psy10116        175 GILLTVPPSLIRRS----KSHFCNL--ACGAQVILGCNGYVWVSAIDE  216 (298)
Q Consensus       175 G~lv~v~~~li~r~----~~~~~~l--~~~~eiivG~NG~IWI~~~~~  216 (298)
                      |.+++|+|..++|.    ++++..|  .+++.|.++.||+|||.+.+.
T Consensus         2 g~vi~I~~~ki~~vIG~gG~~ik~i~~~t~~~I~I~d~G~V~I~g~~~   49 (87)
T d2z0sa2           2 GKIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARNGRIHLECPNE   49 (87)
T ss_dssp             SEEEECCGGGSGGGTCGGGHHHHHHHHHHCCEEEEETTTEEEEECSCH
T ss_pred             cEEEEEChhhcceeECCCCcHHHHHHHHHCCEEEECCCcEEEEEeCCH
Confidence            77999999966655    4556556  489999999999999999764

>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=95.67  E-value=0.013  Score=43.13  Aligned_cols=67  Identities=10%  Similarity=0.027  Sum_probs=47.9

Q ss_pred             CCEEEEEEEEEecceEEEEeCC-CceeeEecccccCCCCcccccchhhh------hhhhcccCCCCEEEEEEEEeCCC
Q psy10116         87 GEVVVGRVTGLQSQKWVVDTNS-ILESALHLTSVNLPGGEQRRRSVQDE------EMMREFLKEGDLISAEIHQISTE  157 (298)
Q Consensus        87 GDiVIG~V~~V~~~~~~VDI~s-~~~a~L~~s~v~~pgg~~Rr~~~~d~------~~mr~~~~~GDlV~A~V~sv~~d  157 (298)
                      |..--|.|+++...+.+|.|.. ..+|++|++++.  ...  ...+...      .+-+..|+.||.|.++|.+++.+
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--AVR--DELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRME   77 (87)
T ss_dssp             CCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTC--SCG--GGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETT
T ss_pred             CCEEEEEEEEEEcCeEEEEEecCCcEEEEEehhCC--Cce--EEEeccceEEEEEEcccEEEECCCEEEEEEEEEecc
Confidence            3445699999999999999954 689999999873  211  1111111      12245799999999999999843

>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=94.90  E-value=0.0029  Score=44.94  Aligned_cols=43  Identities=26%  Similarity=0.587  Sum_probs=27.6

Q ss_pred             CceEEEeCchhhccc----cCcceec--cccEEEEEeeCceEEEecCCC
Q psy10116        174 QGILLTVPPSLIRRS----KSHFCNL--ACGAQVILGCNGYVWVSAIDE  216 (298)
Q Consensus       174 ~G~lv~v~~~li~r~----~~~~~~l--~~~~eiivG~NG~IWI~~~~~  216 (298)
                      +|.++.|||..+++.    ++.+..|  .+|++|.++.||.|||.+.++
T Consensus         1 ~g~vi~Ip~~~ig~iIGkgG~~Ik~i~~~tg~~I~i~~~g~v~I~g~~~   49 (69)
T d2je6i3           1 NGIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSR   49 (69)
T ss_dssp             SSCEEECCGGGHHHHHCGGGHHHHHHHTTC---CEECTTSEEEC-----
T ss_pred             CCEEEEEChhhccceECCchhHHHHHHHHHCCEEEEcCCCEEEEEeCCH
Confidence            488999999965544    4555555  599999999999999999754

>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=94.71  E-value=0.013  Score=42.88  Aligned_cols=41  Identities=27%  Similarity=0.528  Sum_probs=32.8

Q ss_pred             ceEEEeCchh----hccccCcceec--cccEEEEEeeCceEEEecCC
Q psy10116        175 GILLTVPPSL----IRRSKSHFCNL--ACGAQVILGCNGYVWVSAID  215 (298)
Q Consensus       175 G~lv~v~~~l----i~r~~~~~~~l--~~~~eiivG~NG~IWI~~~~  215 (298)
                      |.++.|||++    |++.++.+..|  .+|+.|.+..||.|||.++.
T Consensus         2 g~vi~Ip~~~ig~IIG~gG~~I~~I~~~tg~~I~i~~~g~v~I~G~~   48 (84)
T d2ba0a3           2 GRIVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQNGLIWVNGDR   48 (84)
T ss_dssp             SEEEECCGGGHHHHHCGGGHHHHHHHHHHTCEEEECTTSEEEEESCH
T ss_pred             cEEEEEChhhcceeeCCcHHHHHHHHHHHCCEEEECCCCEEEEEeCH
Confidence            5599999995    55555666666  49999999999999999854

>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=94.04  E-value=0.034  Score=39.14  Aligned_cols=51  Identities=24%  Similarity=0.319  Sum_probs=42.1

Q ss_pred             cCCCeEecCCccCCC--CCeeccCCeEec-CCeEEEEEeeEEEEe-----CcEEEEEec
Q psy10116         28 FTDPILTPGETVEYL--EGYMTGHGTFPD-DEEIKASVGGVVEKV-----NQLVSVRAM   78 (298)
Q Consensus        28 ~~~~iV~PGD~I~~~--~~~~~G~Gty~~-~g~i~Asv~G~v~~~-----nk~v~V~p~   78 (298)
                      ...+.|.||..|.-.  ..|.||.++..- |..|+|.+.|.|...     .+.|+|.|.
T Consensus         7 ~~Gq~V~~G~IivRQRGtk~~pG~nVg~GkD~TLfAl~~G~V~F~~~~~~~~~VsV~P~   65 (66)
T d1v8qa_           7 YEGQVVRAGNILVRQRGTRFKPGKNVGMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPL   65 (66)
T ss_dssp             CTTCEECTTCEEEECSSCSSEECTTEEECTTCCEEESSSEEEEEEECGGGCEEEEEEEC
T ss_pred             eCCEEEeCCeEEEEeccCeEeCCCCeeecCCCcEEEeeeeEEEEEEeCCCCeEEEEEEC
Confidence            457899999999764  368899999885 899999999999863     347899886

>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=91.34  E-value=0.1  Score=38.18  Aligned_cols=52  Identities=21%  Similarity=0.343  Sum_probs=42.0

Q ss_pred             ccCCCeEecCCccCCC--CCeeccCCeEec-CCeEEEEEeeEEEEeC-----cEEEEEec
Q psy10116         27 EFTDPILTPGETVEYL--EGYMTGHGTFPD-DEEIKASVGGVVEKVN-----QLVSVRAM   78 (298)
Q Consensus        27 ~~~~~iV~PGD~I~~~--~~~~~G~Gty~~-~g~i~Asv~G~v~~~n-----k~v~V~p~   78 (298)
                      ....+.|.||+.|.-.  ..|-||.++..- |..|+|.+.|.|....     +.|+|.|.
T Consensus        24 ~~~Gq~V~~G~IivRQRGtk~hpG~nVg~GkD~TLfA~~~G~V~F~k~~~~rk~V~V~p~   83 (84)
T d2zjrt1          24 KFGGEVVKAGNILVRQRGTKFKAGQGVGMGRDHTLFALSDGKVVFINKGKGARFISIEAA   83 (84)
T ss_dssp             SCTTCEECSSCEEECCSSSSSEECTTEECCTTSCEEESSCEEEEEEEETTTEEEEEECCC
T ss_pred             ECCCEEEeCCcEEEEecCceEcCCCCccccCCCcEEEeeceEEEEEEcCCCCEEEEEEeC
Confidence            3567899999999874  368899999885 8899999999999642     46788774