Citrus Sinensis ID: 022140

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300--
Protein Sequence
MGLPNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGMEID
Secondary Structure (PSIPRED)
cccccccccccccccHHHHHcccHHHHHHHHHHcccccccccccccccEEEEEcccccccEEEEEEEccEEEEEEEEEEEEccccccccccEEEEEEEcccccccccccccccccHHHHHHHHHHHHccccccccccccccccEEEEEEEEEEEEEcccccHHHHHHHHHHHHHHHccccEEEEcccEEEEcccccccccccccccccccccccccccEEEEEEEEEccEEEEcccHHHHHccccEEEEEEcccccEEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
cccccccccccHHHcHHHHcccccHHHHHHHHHccccccccccHcccEEEEEEEEEEccccEEEEEEcccEEEEEEEEEEccccccccccEEEEEEEcccccccccccccccccHHHHHHHHHHHHHHccccEcHHHEEEEcccEEEEEEEEEEEEcccccHHHHHHHHHHHHHHHccccEEEEcccEEEEEEcccccEEEEEcccccccccccccccEEEEEEEEEccEEEEccccHHHHHcccEEEEEEccccEEEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
mglpnasedlssEMEVDAFRRLFPLRYFERHLAesirpdarsLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEvmtpslespdegcvsidfhmppicsplvrpgrpaeaaPVVAKQLSdtisssgminlkelSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSnlqiptvslddgkivmlpeeqkeensekepvnkekrkltlggipfsltcilhknyiladptseeeSIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGMEID
Flexible Loop (DISEMBL)
mglpnasedlssemEVDAFRRLFPLRYFERhlaesirpdarslSRARNTTISMgavasadgsaLAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLpeeqkeensekepvnkekrkltlggipfsLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGMEID
Low Complexity Region (SEG)
MGLPNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCldadgalfdaallSAVAAFSNLQIPTVSLDDGKIVMLPeeqkeensekePVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGMEID
Disordered region (IsUnstruct)
****************DAFRRLFPLRYFERHLA******************************LAKIGSTTMLAAIKMEVM*********GCVSIDFHMPPICSPLV*******************I*SSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVM*********************LTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILE*********
Disordered Region (DISOPRED)
*******************RRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPP*****************VAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAIS*****
Disordered Region (DISEMBL)
************EMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEE**************KRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGMEID
Disordered Region (DISPRO)
*************MEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISG****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGLPNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGMEID
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	302	2.2.26 [Sep-21-2011]
Q96B26	276	Exosome complex component	yes	no	0.894	0.978	0.348	2e-49
Q9D753	276	Exosome complex component	yes	no	0.890	0.974	0.353	1e-48
Q2KHU3	276	Exosome complex component	yes	no	0.894	0.978	0.345	2e-47
Q10205	270	Exosome complex component	yes	no	0.831	0.929	0.302	3e-35
Q8TYC2	267	Probable exosome complex	yes	no	0.788	0.891	0.305	2e-31
Q8U0M0	277	Probable exosome complex	yes	no	0.841	0.916	0.301	8e-30
C5A2B8	273	Probable exosome complex	yes	no	0.827	0.915	0.309	2e-29
O59224	274	Probable exosome complex	yes	no	0.834	0.919	0.308	1e-28
Q9YC05	276	Probable exosome complex	yes	no	0.834	0.913	0.284	2e-27
Q0W2Y7	260	Probable exosome complex	yes	no	0.847	0.984	0.271	6e-27

>sp|Q96B26|EXOS8_HUMAN Exosome complex component RRP43 OS=Homo sapiens GN=EXOSC8 PE=1 SV=1

 Score =  196 bits (497), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 99/284 (34%), Positives = 166/284 (58%), Gaps = 14/284 (4%)

Query: 18  AFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK 77
            F+ + PL Y+ R L E+ RPD R L   R TT+++G++++ADGSAL K+G+TT++  +K
Sbjct: 4   GFKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVK 63

Query: 78  MEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKE 137
            E   PS ++PD+G V  +  +PP+CS   R G P E A V ++ ++D I +S +I  ++
Sbjct: 64  AEFAAPSTDAPDKGYVVPNVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKED 123

Query: 138 LSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQK 197
           L +  GK  W++Y D+ CLD DG + DA   + +AA  N+Q+P V+++            
Sbjct: 124 LCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTIN------------ 171

Query: 198 EENSEKEPVNKEKRKLTLGGIPFSLT-CILHKNYILADPTSEEESIMETLVTVVLDSSNQ 256
           EE +  E   K+K  L +   P + +  +     ++ DPT EEE +    +T+V+D   +
Sbjct: 172 EETALAEVNLKKKSYLNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGK 231

Query: 257 LVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME 300
           L  L+KPGG+ L   + +QDC++    R KE+ ++++E I  M+
Sbjct: 232 LCCLHKPGGSGLT-GAKLQDCMSRAVTRHKEVKKLMDEVIKSMK 274

Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. EXOSC8 binds to ARE-containing RNAs.
Homo sapiens (taxid: 9606)

>sp|Q9D753|EXOS8_MOUSE Exosome complex component RRP43 OS=Mus musculus GN=Exosc8 PE=2 SV=1

 Score =  193 bits (491), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 100/283 (35%), Positives = 164/283 (57%), Gaps = 14/283 (4%)

Query: 18  AFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK 77
            F+ + PL Y+ R L E+ RPD R L   R TT+++G++++ADGSAL K+G+TT++  +K
Sbjct: 4   GFKTVEPLEYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVK 63

Query: 78  MEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKE 137
            E   P +++PD G V  +  +PP+CS   R G P E A V ++ ++D + +S +I  ++
Sbjct: 64  AEFAAPPVDAPDRGYVVPNVDLPPLCSSRFRTGPPGEEAQVTSQFIADVVDNSQVIKKED 123

Query: 138 LSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQK 197
           L +  GK AW++Y D+ CLD DG + DA   + +AA  N+Q+P V+++            
Sbjct: 124 LCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTIN------------ 171

Query: 198 EENSEKEPVNKEKRKLTLGGIPFSLT-CILHKNYILADPTSEEESIMETLVTVVLDSSNQ 256
           EE +  E   K+K  L +   P + +  +     ++ DPT EEE +    +TVV D   +
Sbjct: 172 EETALAEVNLKKKSYLNVRTNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTDEDGK 231

Query: 257 LVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM 299
           L  L+KPGG+ L   + +QDC++    R KE+ ++L+E I  M
Sbjct: 232 LCCLHKPGGSGLT-GAKLQDCMSRAVTRHKEVSKLLDEVIQSM 273

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

Mus musculus (taxid: 10090)

>sp|Q2KHU3|EXOS8_BOVIN Exosome complex component RRP43 OS=Bos taurus GN=EXOSC8 PE=2 SV=1

 Score =  189 bits (481), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 98/284 (34%), Positives = 163/284 (57%), Gaps = 14/284 (4%)

Query: 18  AFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK 77
            F+ + PL Y+ R L E+ RPD R L   R TT+++G++ +ADGSAL K+G+TT++  IK
Sbjct: 4   GFKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNVGSIGTADGSALVKLGNTTVICGIK 63

Query: 78  MEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKE 137
            E   P  ++PD+G V  +  + P+CS   R G P E A V ++ ++D I +S +I  ++
Sbjct: 64  AEFGAPPTDAPDKGYVVPNVDLSPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKED 123

Query: 138 LSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQK 197
           L +  GK AW++Y D+ CL+ DG + DA   + +AA  N+Q+P V+++            
Sbjct: 124 LCISSGKLAWVLYCDLICLNHDGNILDACTFALLAALKNVQLPEVTIN------------ 171

Query: 198 EENSEKEPVNKEKRKLTLGGIPFSLT-CILHKNYILADPTSEEESIMETLVTVVLDSSNQ 256
           EE +  E   K+K  L +   P + +  +     ++ DPT EEE +    +TVV+D   +
Sbjct: 172 EETALAEVNLKKKSCLNIRTHPVATSFAVFDDTLLIVDPTEEEEHLATGTLTVVMDEEGR 231

Query: 257 LVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME 300
           L  L+KPGG+ L   + +QDC++    R KE+ ++++E    M+
Sbjct: 232 LCCLHKPGGSGLT-GAKLQDCMSRAVTRHKEVKKLMDEVFKSMK 274

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

Bos taurus (taxid: 9913)

>sp|Q10205|RRP43_SCHPO Exosome complex component rrp43 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rrp43 PE=3 SV=1

 Score =  149 bits (375), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 81/268 (30%), Positives = 142/268 (52%), Gaps = 17/268 (6%)

Query: 19  FRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKM 78
           F+++ P +Y    L + +R D RS+S  R   I+   +++A+GSA+ + G    +  IK 
Sbjct: 17  FKKITPEQYLSHLLNQDVRSDGRSVSEFREIVINDNCISTANGSAIIRAGENVFVCGIKA 76

Query: 79  EVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKEL 138
           E+  P   SP+EG +  +  + P+CS   +PG P++ A VV+++L  T+  S +INL+ L
Sbjct: 77  EIAEPFENSPNEGWIVPNLELSPLCSSKFKPGPPSDLAQVVSQELHQTLQQSNLINLQSL 136

Query: 139 SLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDG--KIVMLPEEQ 196
            +   KAAW++Y DI CL+ DG+ FD A  +  AA   +++PT   D+   +++      
Sbjct: 137 CIFEKKAAWVLYADIICLNYDGSAFDYAWAALFAALKTVKLPTAVWDEDLERVIC----- 191

Query: 197 KEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQ 256
                     +   R + L     S +  +  + +LADPT EEE +    +T++L+SS  
Sbjct: 192 ---------ASTLTRPVQLSTEVRSFSWSVFDDKLLADPTDEEEDLSTEFLTIMLNSSKN 242

Query: 257 LVSLYKPGGAVLAYTSAVQDCIALTRQR 284
           +V + K GG  +     ++ CI + R +
Sbjct: 243 IVKIIKLGGTHIQ-PLLLKKCIEVARSK 269

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. ski6 is part of the hexameric ring of RNase PH domain-containing subunits proposed to form a central channel which threads RNA substrates for degradation.

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

>sp|Q8TYC2|ECX2_METKA Probable exosome complex exonuclease 2 OS=Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938) GN=MK0380 PE=3 SV=1

 Score =  136 bits (342), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 78/255 (30%), Positives = 140/255 (54%), Gaps = 17/255 (6%)

Query: 37  RPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSID 96
           R D R     R   +  G ++ A+GSAL ++G+T ++  +K+EV  P  +SP+EG ++++
Sbjct: 23  RIDGRDFEEFRPIEVRAGVISKANGSALVRLGNTQLVVGVKLEVGRPYPDSPNEGALAVN 82

Query: 97  FHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCL 156
             + P+  P   PG P E A  +++ +   I  S MI+L+EL +  G+  W+ ++DI+ L
Sbjct: 83  AELVPLADPSFEPGPPDENAIELSRVVDRGIRESEMIDLEELCIEEGEHCWVTFVDIHVL 142

Query: 157 DADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLG 216
           D DG LFDA+++ +V+A S  ++P   + D ++     E  EE++E          L + 
Sbjct: 143 DHDGNLFDASMIGSVSALSITEVPKAEVVDDEV-----EVMEEDTE---------PLAIN 188

Query: 217 GIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSA-VQ 275
             P S+T      Y+L DP  EEE IM+T +TV +  S ++ ++ K  G +  +    ++
Sbjct: 189 DFPISVTIAKVGEYLLVDPCLEEEVIMDTRLTVTVTESGEVCAVQK--GELGDFPEHLLE 246

Query: 276 DCIALTRQRVKELHQ 290
           D I L  ++ +E+ +
Sbjct: 247 DAIDLATKKAEEVRR 261

Probably involved in the 3'->5' degradation of a variety of RNA species.

Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938) (taxid: 190192)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|Q8U0M0|ECX2_PYRFU Probable exosome complex exonuclease 2 OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) GN=PF1567 PE=3 SV=1

 Score =  130 bits (328), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 82/272 (30%), Positives = 139/272 (51%), Gaps = 18/272 (6%)

Query: 27  YFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLE 86
           Y    L E  R D R     R   + +G +  A+GSAL K+G+T +L  IK  +  P  +
Sbjct: 14  YILNLLKEKKRIDDRGFEDYRPIEVEVGVIEKAEGSALVKLGNTQVLVGIKATLGEPFPD 73

Query: 87  SPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAA 146
           +P+ G ++ +  + P+ SP   PG P E A  +A+ +   I  S  +NL+++ +  GK  
Sbjct: 74  TPNMGVMTTNVELVPLASPTFEPGPPDERAIELARVIDRGIRESRALNLEKMVIAPGKIV 133

Query: 147 WMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDD--GKIVMLPEEQKEENSEKE 204
            +V++D++ LD DG L DA  + A+AA  N ++P V  ++  G++ +L         EKE
Sbjct: 134 RVVFIDVHVLDHDGNLMDAIGIGAIAALLNARVPKVLYNEETGEVEIL--------EEKE 185

Query: 205 PVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPG 264
           P+  EK       IP S+T     NY++ DPT EEE IM+  +T+  D +  + ++ K  
Sbjct: 186 PLPVEK-------IPISVTFAKIGNYLVVDPTLEEEQIMDGRLTITTDETGHISAVQKSE 238

Query: 265 GAVLAYTSAVQDCIALTRQRVKELHQILEEAI 296
           G        V   +    ++ +E+ +I+  A+
Sbjct: 239 GGAFKL-EEVMYAVETAFKKAEEIRKIILNAL 269

Probably involved in the 3'->5' degradation of a variety of RNA species.

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

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|C5A2B8|ECX2_THEGJ Probable exosome complex exonuclease 2 OS=Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3) GN=TGAM_2035 PE=3 SV=1

 Score =  129 bits (324), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 83/268 (30%), Positives = 136/268 (50%), Gaps = 18/268 (6%)

Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEG 91
           L E  R D RS    R+  I  G +  A+GSA  ++G T +L  IK++V  P  + PD G
Sbjct: 19  LKEGKRIDGRSFEEYRDIEIKTGFIEKAEGSAWVRLGGTRVLVGIKVDVGEPFPDLPDRG 78

Query: 92  CVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYL 151
            ++ +  + P+ SP   PG P E A  +A+ +   I  S  + L++L +V GK   +V++
Sbjct: 79  VMTTNVELVPLASPTFEPGPPDERAIELARVIDRGIRESQAVELEKLVIVPGKLVRVVFI 138

Query: 152 DIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDD--GKIVMLPEEQKEENSEKEPVNKE 209
           D++ LD DG LFDA  L+A+AA    +IP V  ++  G+I+ L         E EP    
Sbjct: 139 DVHVLDHDGNLFDATGLAAMAALMTTKIPKVEYNEETGEIIKL--------DEYEP---- 186

Query: 210 KRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLA 269
              L +  +P  +T     + I+ DP  +EE++M++ +T+  D +  + ++ K  G    
Sbjct: 187 ---LPVKHVPIPVTFAKIGSSIIVDPNLDEETVMDSRLTITTDETGHISAVQKGEGGSFK 243

Query: 270 YTSAVQDCIALTRQRVKELHQILEEAIS 297
               V   I    ++  EL +IL EA+ 
Sbjct: 244 L-EEVMYAIDTALKKADELRKILLEAVG 270

Probably involved in the 3'->5' degradation of a variety of RNA species.

Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3) (taxid: 593117)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|O59224|ECX2_PYRHO Probable exosome complex exonuclease 2 OS=Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) GN=PH1548 PE=3 SV=1

 Score =  127 bits (318), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 82/266 (30%), Positives = 135/266 (50%), Gaps = 14/266 (5%)

Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEG 91
           L E  R D R     R   I +G +  A+GSAL K+GST +L  IK  +  P  ++P+ G
Sbjct: 19  LKEGKRIDDRGFEDYRPIEIEVGIIEKAEGSALVKLGSTQVLVGIKTTLGEPFPDTPNMG 78

Query: 92  CVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYL 151
            ++ +  + P+ SP   PG P E A  +A+     I  S  +NL+++ +V GK   +V++
Sbjct: 79  VMTTNVELVPLASPTFEPGPPDERAIELARVTDRGIRESRALNLEKMVIVPGKIVRVVFI 138

Query: 152 DIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKR 211
           D++ LD DG L DA  ++++AA  N ++P V            E  EE  E E + +EK 
Sbjct: 139 DVHVLDHDGNLMDAIGIASIAALLNAKVPKV------------EYNEETGEVE-ILEEKE 185

Query: 212 KLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYT 271
            L +  IP  +T     N ++ DP+ EEE +M+  +TV  D +  + ++ K  G      
Sbjct: 186 PLPVERIPIPVTFAKIGNILVVDPSLEEELVMDGRLTVTTDETGHISAVQKGEGGAFKL- 244

Query: 272 SAVQDCIALTRQRVKELHQILEEAIS 297
             V   +    ++ +E+ +I+ EAI 
Sbjct: 245 EEVMYAVETAFKKAEEIRKIVLEAIK 270

Probably involved in the 3'->5' degradation of a variety of RNA species.

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

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|Q9YC05|ECX2_AERPE Probable exosome complex exonuclease 2 OS=Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) GN=APE_1445 PE=3 SV=1

 Score =  122 bits (307), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 76/267 (28%), Positives = 137/267 (51%), Gaps = 15/267 (5%)

Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEG 91
           L +  RP  R L   RN  I  G +  A+GSAL K+G T ++A +K  V  P  ++P++G
Sbjct: 23  LRKGWRPGDRDLKTPRNVKIETGIIEKAEGSALVKLGKTQVIAGVKAGVGAPFKDTPNQG 82

Query: 92  CVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYL 151
            +++     P+ SP+  PG P E A  +A+ +  ++   G ++L+ L +  G+  W++++
Sbjct: 83  VLTVHAEFVPLASPVFEPGPPDENAIELARVVDRSLREVGAVDLESLVIRPGEKVWVLWV 142

Query: 152 DIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDD-GKIVMLPEEQKEENSEKEPVNKEK 210
           D+Y +D DG LFDA++L+ +A     ++P     + G+I++  E + EE           
Sbjct: 143 DLYIIDHDGNLFDASMLATMAVLLTARLPRYEESETGEIIISKEGEGEE----------- 191

Query: 211 RKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAY 270
             L +     ++T      YI+ DP  EEE++ +  +   +D + ++V L K G   L  
Sbjct: 192 --LKVKTRVVTVTTAKIDRYIVVDPNIEEEAVSDVRLVTAVDENGRIVGLQKTGMGSLT- 248

Query: 271 TSAVQDCIALTRQRVKELHQILEEAIS 297
            + ++  I  + +  K   + LEEAI 
Sbjct: 249 EADIETMIGYSLEASKVYFKALEEAIK 275

Probably involved in the 3'->5' degradation of a variety of RNA species.

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

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|Q0W2Y7|ECX2_UNCMA Probable exosome complex exonuclease 2 OS=Uncultured methanogenic archaeon RC-I GN=UNCMA_09920 PE=3 SV=1

 Score =  121 bits (304), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 78/287 (27%), Positives = 131/287 (45%), Gaps = 31/287 (10%)

Query: 7   SEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAK 66
           SED+ +E++ D         Y      +  R D R     R  ++  G +  A+GSA  K
Sbjct: 2   SEDVIAEIKRD---------YIYSLANQGDRADGRKFDEFRAISVETGVINKAEGSARVK 52

Query: 67  IGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDT 126
           IG + ++  +K++   P  ++PD G +  +  + P+ SP    G P E A  +A+ +   
Sbjct: 53  IGDSQVVVGVKIQPGEPFPDTPDSGVIITNLELVPLASPTFESGPPREDAIELARVVDRG 112

Query: 127 ISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDD 186
           +  SG I+L +L +  G+  WMV++D++ LD DG L DAA L A+AA    +IP      
Sbjct: 113 VRESGAIDLSKLCIESGQKVWMVFIDVHVLDHDGNLMDAASLGAIAALKATKIPNSKFGL 172

Query: 187 GKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETL 246
           G+ V LP                     L  +P  +T +     I+ DP+ +EES+    
Sbjct: 173 GEDVKLP---------------------LNDVPIGVTAVNIGGAIMLDPSLDEESVAPCK 211

Query: 247 VTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILE 293
           +TV+ +    +  + K G   L     +   I L +++   L + LE
Sbjct: 212 LTVITNKEGAISGMQKSGVGTLT-PDQINHIIRLAKEKANVLREKLE 257

Probably involved in the 3'->5' degradation of a variety of RNA species.

Uncultured methanogenic archaeon RC-I (taxid: 351160)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

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	302
255582593	303	exosome complex exonuclease rrp43, putat	1.0	0.996	0.811	1e-142
224138050	439	predicted protein [Populus trichocarpa]	0.986	0.678	0.789	1e-141
224090167	318	predicted protein [Populus trichocarpa]	1.0	0.949	0.795	1e-140
356526509	302	PREDICTED: exosome complex component RRP	0.996	0.996	0.808	1e-139
356552650	299	PREDICTED: exosome complex component RRP	0.980	0.989	0.791	1e-135
449463354	304	PREDICTED: exosome complex component RRP	1.0	0.993	0.805	1e-133
83283957	314	3'-5'-exoribonuclease/RNA binding protei	0.996	0.958	0.761	1e-130
356568754	301	PREDICTED: exosome complex component RRP	0.993	0.996	0.774	1e-129
83283987	303	3'-5'-exoribonuclease/RNA binding-like p	1.0	0.996	0.739	1e-128
225441838	303	PREDICTED: exosome complex component RRP	0.986	0.983	0.809	1e-127

>gi|255582593|ref|XP_002532079.1| exosome complex exonuclease rrp43, putative [Ricinus communis] gi|223528261|gb|EEF30313.1| exosome complex exonuclease rrp43, putative [Ricinus communis]

 Score =  508 bits (1309), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 246/303 (81%), Positives = 273/303 (90%), Gaps = 1/303 (0%)

Query: 1   MGLPNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASAD 60
           MGLPN S DLS+EME DAFRRLFPL + ERHLAESIRPD RSL RAR+TT+++GAV SAD
Sbjct: 1   MGLPNVSGDLSTEMEADAFRRLFPLLFHERHLAESIRPDGRSLGRARDTTLALGAVVSAD 60

Query: 61  GSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVA 120
           GSA+AKIGSTTM+AAIKMEVMTPS ESPDEGC++IDFHMPPICSPLVRPGRPAEAAPVV+
Sbjct: 61  GSAIAKIGSTTMMAAIKMEVMTPSSESPDEGCIAIDFHMPPICSPLVRPGRPAEAAPVVS 120

Query: 121 KQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP 180
           KQLSDTI SS MI+LKELSLV GKAAWM YLDIYCLDADG+LFDAAL SAVAAF+NLQIP
Sbjct: 121 KQLSDTIMSSAMIDLKELSLVSGKAAWMAYLDIYCLDADGSLFDAALFSAVAAFTNLQIP 180

Query: 181 TVSL-DDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEE 239
            VSL DDGK+V++ +E +    EKE VNKEKRKLTL  +PFSLTC+LHKNYILADPT+EE
Sbjct: 181 IVSLNDDGKVVVVSDENEGGKREKEAVNKEKRKLTLRSLPFSLTCVLHKNYILADPTAEE 240

Query: 240 ESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM 299
           ESIMETLVTVVLDSS +LVS YKPGG VLAYTSAVQDC+ALTRQRVKEL  IL+EA+SGM
Sbjct: 241 ESIMETLVTVVLDSSARLVSFYKPGGPVLAYTSAVQDCVALTRQRVKELQNILDEALSGM 300

Query: 300 EID 302
           +ID
Sbjct: 301 QID 303

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224138050|ref|XP_002322717.1| predicted protein [Populus trichocarpa] gi|222867347|gb|EEF04478.1| predicted protein [Populus trichocarpa]

 Score =  506 bits (1304), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 252/319 (78%), Positives = 275/319 (86%), Gaps = 21/319 (6%)

Query: 1   MGLPNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASAD 60
           MG+P+AS DLSSEMEVDAFR LFPLRYFERHL+ESIRPDAR L RAR+TT+++GAVASA 
Sbjct: 1   MGVPDASGDLSSEMEVDAFRHLFPLRYFERHLSESIRPDARPLGRARDTTLALGAVASAH 60

Query: 61  GSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVA 120
           GSALAKIGSTTMLAAIKMEVMTPS ESPDEGC++IDFHMPPICSP+VRPGRPAEAAPV++
Sbjct: 61  GSALAKIGSTTMLAAIKMEVMTPSTESPDEGCIAIDFHMPPICSPIVRPGRPAEAAPVIS 120

Query: 121 KQLSDTISS--------------------SGMINLKELSLVGGKAAWMVYLDIYCLDADG 160
           KQLSDTIS                     SGMINLKELSLV GKAAWM YLDIYCLDADG
Sbjct: 121 KQLSDTISRQVKFSASIDSPQRLILHAEISGMINLKELSLVSGKAAWMAYLDIYCLDADG 180

Query: 161 ALFDAALLSAVAAFSNLQIPTVSL-DDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIP 219
           ALFDAALLSAVAAFS+LQIP VSL DDGKIV++ EE +    EKEPVNKEKRKLTL  IP
Sbjct: 181 ALFDAALLSAVAAFSHLQIPIVSLNDDGKIVLVSEEDEGAKLEKEPVNKEKRKLTLSSIP 240

Query: 220 FSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIA 279
           FSLTCILHKNYILADPT+EEESIMETLVTVVLDSS +LVS YKPGG+V AYTSAV+DC+A
Sbjct: 241 FSLTCILHKNYILADPTAEEESIMETLVTVVLDSSARLVSFYKPGGSVFAYTSAVKDCVA 300

Query: 280 LTRQRVKELHQILEEAISG 298
           LTRQRVKEL +IL+EAIS 
Sbjct: 301 LTRQRVKELQEILDEAISA 319

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224090167|ref|XP_002308947.1| predicted protein [Populus trichocarpa] gi|222854923|gb|EEE92470.1| predicted protein [Populus trichocarpa]

 Score =  502 bits (1293), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 253/318 (79%), Positives = 277/318 (87%), Gaps = 16/318 (5%)

Query: 1   MGLPNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASAD 60
           MG+P+AS DLSSEMEVDAFRRLFPLRYFERHL+ESIRPDAR L RAR+TT+++GAVASA 
Sbjct: 1   MGVPDASGDLSSEMEVDAFRRLFPLRYFERHLSESIRPDARPLGRARDTTLALGAVASAH 60

Query: 61  GSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVA 120
           GSALAKIGSTTMLAAIKMEVMTPS ESP+EG ++IDFHMPPICSP+VRPGRPAEAAPV++
Sbjct: 61  GSALAKIGSTTMLAAIKMEVMTPSTESPEEGSIAIDFHMPPICSPIVRPGRPAEAAPVIS 120

Query: 121 KQLSDTIS---SSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSN- 176
           KQLSDTIS   +SGMINLKELSLV GKAAWM YLDIYCLDADGALFDAALLSAV AFS+ 
Sbjct: 121 KQLSDTISRQVNSGMINLKELSLVSGKAAWMAYLDIYCLDADGALFDAALLSAVGAFSHS 180

Query: 177 -----------LQIPTVSL-DDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTC 224
                      +QIP VSL DDGKIV++ EE      E+EPVNKEKRKLTL  IPFSLTC
Sbjct: 181 AFIYYRSLICAVQIPIVSLNDDGKIVLVSEEDDGTKLEEEPVNKEKRKLTLSSIPFSLTC 240

Query: 225 ILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQR 284
           ILHKNYILADPT+EEESIMETLVTVVLDSS++LVS YKPGG VLA TSAVQDC+ALTRQR
Sbjct: 241 ILHKNYILADPTAEEESIMETLVTVVLDSSSRLVSFYKPGGPVLAQTSAVQDCVALTRQR 300

Query: 285 VKELHQILEEAISGMEID 302
           VKEL  IL+E ISGMEID
Sbjct: 301 VKELQDILDETISGMEID 318

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356526509|ref|XP_003531860.1| PREDICTED: exosome complex component RRP43-like [Glycine max]

 Score =  501 bits (1290), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 245/303 (80%), Positives = 273/303 (90%), Gaps = 2/303 (0%)

Query: 1   MGLPNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASAD 60
           MGLPN SEDLSSEMEVDAFRRLFPLRYFERHLAESIRPD R L +AR T+I +GAVASA+
Sbjct: 1   MGLPNVSEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDGRPLGKARETSIFLGAVASAN 60

Query: 61  GSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVA 120
           GSAL KIGSTT+L AIKMEVMTPSLESPDEGC++IDFHMPPICSP+VRPGRPAEA+PVV+
Sbjct: 61  GSALVKIGSTTILTAIKMEVMTPSLESPDEGCLAIDFHMPPICSPIVRPGRPAEASPVVS 120

Query: 121 KQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP 180
           KQLSDTISSS MI+LKELSLV GKAAWM YLDIYCLDADGALFDAALLSAVA+ S+LQIP
Sbjct: 121 KQLSDTISSSKMIDLKELSLVSGKAAWMAYLDIYCLDADGALFDAALLSAVASLSHLQIP 180

Query: 181 TVSL-DDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEE 239
            V++ DDGKIV++ EE  ++  E+EPVNKEKRKLTL  IPFSLTCILHKNYILADPT+EE
Sbjct: 181 VVAMNDDGKIVLVSEEDGQKR-EQEPVNKEKRKLTLRSIPFSLTCILHKNYILADPTAEE 239

Query: 240 ESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM 299
           ESIMET VTVVLD+S QL+SLYKPGG VLAYTSA+QDC ALTRQRVKEL   L++A S M
Sbjct: 240 ESIMETHVTVVLDTSGQLISLYKPGGPVLAYTSAIQDCAALTRQRVKELKSFLDKANSAM 299

Query: 300 EID 302
           E++
Sbjct: 300 EVE 302

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356552650|ref|XP_003544676.1| PREDICTED: exosome complex component RRP43-like [Glycine max]

 Score =  486 bits (1252), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 239/302 (79%), Positives = 266/302 (88%), Gaps = 6/302 (1%)

Query: 1   MGLPNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASAD 60
           MGL NASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPD R L +AR T+I +GAVASA+
Sbjct: 1   MGLSNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDGRPLGKARETSIFLGAVASAN 60

Query: 61  GSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVA 120
           GSAL KIGSTTML AIKMEVMTPSLESPDEGC++IDFHMPPICSP+VRPGRPAEA+PVV+
Sbjct: 61  GSALVKIGSTTMLTAIKMEVMTPSLESPDEGCLAIDFHMPPICSPIVRPGRPAEASPVVS 120

Query: 121 KQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP 180
           KQLSDTISSS MI+LKELSLVGGKAAWM YLDIYCLDADGALFDAAL+SAVAA S+LQIP
Sbjct: 121 KQLSDTISSSRMIDLKELSLVGGKAAWMAYLDIYCLDADGALFDAALISAVAALSHLQIP 180

Query: 181 TVSL-DDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEE 239
            V++ DDGKIV++  E  +     +PVNKEKRKLTL  IPFSLTCILHKNYILADPT+EE
Sbjct: 181 AVAMNDDGKIVLVSGEDGQ-----KPVNKEKRKLTLRSIPFSLTCILHKNYILADPTAEE 235

Query: 240 ESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM 299
           ESIMET VT+VLD+S QL+SLYKPGG  LAYTSA+QDC+ LT QRVKEL   L++  S M
Sbjct: 236 ESIMETHVTIVLDTSGQLISLYKPGGPALAYTSAIQDCVGLTGQRVKELKSYLDKENSAM 295

Query: 300 EI 301
           E+
Sbjct: 296 EV 297

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463354|ref|XP_004149399.1| PREDICTED: exosome complex component RRP43-like [Cucumis sativus] gi|449503802|ref|XP_004162184.1| PREDICTED: exosome complex component RRP43-like [Cucumis sativus]

 Score =  479 bits (1234), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 245/304 (80%), Positives = 278/304 (91%), Gaps = 2/304 (0%)

Query: 1   MGLPNA-SEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASA 59
           MGLPNA S DLSS+MEVDAFRRLFP++++ERHL ESIRPD RSL +AR+TTI++G V+SA
Sbjct: 1   MGLPNAASGDLSSQMEVDAFRRLFPIQFYERHLTESIRPDGRSLGKARDTTIALGPVSSA 60

Query: 60  DGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVV 119
           +GSALAKIGSTTMLAAIKMEVMTPS+ESPDEGC+++DFHMPP+CSP+VRPGRPAEAAPV+
Sbjct: 61  NGSALAKIGSTTMLAAIKMEVMTPSVESPDEGCIALDFHMPPVCSPIVRPGRPAEAAPVI 120

Query: 120 AKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQI 179
           +KQLSDTISSSGMI+L+ELSLV GKAAWM YLDIYCLDADG+LFDAALLSA AAFS+LQI
Sbjct: 121 SKQLSDTISSSGMIDLRELSLVKGKAAWMAYLDIYCLDADGSLFDAALLSAAAAFSHLQI 180

Query: 180 PTVSL-DDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSE 238
           P V+L DDGK+V + EE+  EN EKEPVNKE RKL L  IPFSLTC+LHK YILADPT+E
Sbjct: 181 PVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKYILADPTAE 240

Query: 239 EESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISG 298
           EES+MET+VTVVLDSS QLVS YKPGG+VLAYTSAVQDCIALTRQR KEL  IL+EAISG
Sbjct: 241 EESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQDCIALTRQRSKELQIILDEAISG 300

Query: 299 MEID 302
           MEID
Sbjct: 301 MEID 304

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|83283957|gb|ABC01886.1| 3'-5'-exoribonuclease/RNA binding protein-like protein [Solanum tuberosum]

 Score =  471 bits (1212), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 230/302 (76%), Positives = 259/302 (85%), Gaps = 1/302 (0%)

Query: 1   MGLPNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASAD 60
           M   N S DLSSEMEVDAFRRLFPLRY E HL +S+RPDAR L  AR+TT+++GAVASAD
Sbjct: 1   MAAANGSSDLSSEMEVDAFRRLFPLRYHEHHLLKSVRPDARKLGSARDTTLALGAVASAD 60

Query: 61  GSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVA 120
           GSALAKIGSTTMLAAIKMEVMTP++E PDEG ++I+FHMPPICSPLVRPGRPAEAA V++
Sbjct: 61  GSALAKIGSTTMLAAIKMEVMTPTVECPDEGSIAIEFHMPPICSPLVRPGRPAEAASVIS 120

Query: 121 KQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP 180
           KQLSDTI SSGMI+LKEL LVGGKAAWM YLDIYCLDADGALFD ALLSAVAAFS+L IP
Sbjct: 121 KQLSDTILSSGMIDLKELCLVGGKAAWMAYLDIYCLDADGALFDTALLSAVAAFSHLNIP 180

Query: 181 TVSL-DDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEE 239
            VSL DDG+IV++ E+      EKEPVN EKRKL L  +PFSLTCILHKNYILADPT+EE
Sbjct: 181 VVSLNDDGRIVLVSEDTVRLKLEKEPVNTEKRKLKLNSLPFSLTCILHKNYILADPTAEE 240

Query: 240 ESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM 299
           E IMET+VTVVLDSS+QLVSL KPGG VL++TS +QDCI L R+R KEL  +L EAIS M
Sbjct: 241 EPIMETIVTVVLDSSHQLVSLNKPGGPVLSHTSVIQDCIGLARRRAKELQSVLNEAISDM 300

Query: 300 EI 301
           E+
Sbjct: 301 EV 302

Source: Solanum tuberosum

Species: Solanum tuberosum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356568754|ref|XP_003552575.1| PREDICTED: exosome complex component RRP43-like [Glycine max]

 Score =  466 bits (1199), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 234/302 (77%), Positives = 271/302 (89%), Gaps = 2/302 (0%)

Query: 1   MGLPNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASAD 60
           MGLPN SEDLSSE+EVDAF+R+FPLRYFERHLAESIR D R L +AR T+I +GAVA A+
Sbjct: 1   MGLPNVSEDLSSEVEVDAFKRIFPLRYFERHLAESIRADGRPLGKARETSIFLGAVAFAN 60

Query: 61  GSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVA 120
           GSAL KIGSTTML AIKME+MTPSLESPDEGC++IDFHMPPICSP+VRPGRPAEA+P+V+
Sbjct: 61  GSALVKIGSTTMLTAIKMEIMTPSLESPDEGCLAIDFHMPPICSPIVRPGRPAEASPMVS 120

Query: 121 KQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP 180
           KQLS+TISSS M +LKELSLV GKAAWM YLDIYCLDADGALFDAALLSA+AA S+LQIP
Sbjct: 121 KQLSNTISSSRMTDLKELSLVSGKAAWMAYLDIYCLDADGALFDAALLSAIAALSHLQIP 180

Query: 181 TVSL-DDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEE 239
           ++++ DDGKIV++ +E  ++ ++ EPVNKEKRKLTL  IPFSLTCILHKNYILADPT+EE
Sbjct: 181 SIAMNDDGKIVLVSDEDGQKRAQ-EPVNKEKRKLTLRSIPFSLTCILHKNYILADPTAEE 239

Query: 240 ESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM 299
           ESIMET VTVVLD+S QL+SLYKPGG VLAYTSA+QDC ALTRQRVKEL+  L++A S M
Sbjct: 240 ESIMETHVTVVLDTSGQLISLYKPGGPVLAYTSAIQDCAALTRQRVKELNNFLDKANSAM 299

Query: 300 EI 301
           E+
Sbjct: 300 EV 301

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|83283987|gb|ABC01901.1| 3'-5'-exoribonuclease/RNA binding-like protein [Solanum tuberosum]

 Score =  463 bits (1192), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 224/303 (73%), Positives = 260/303 (85%), Gaps = 1/303 (0%)

Query: 1   MGLPNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASAD 60
           M   N S DL SEMEVDAFRRLFPLRY E+HL +S+RPDAR L  AR+TT+++GAVASA+
Sbjct: 1   MAAANGSSDLYSEMEVDAFRRLFPLRYHEQHLLKSVRPDARKLGSARDTTLALGAVASAE 60

Query: 61  GSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVA 120
           GSALAKIGSTTMLAAIKME+MTP++E PDEG ++I+FHMPPICSPLVRPGRPAE A V++
Sbjct: 61  GSALAKIGSTTMLAAIKMEIMTPTVECPDEGSIAIEFHMPPICSPLVRPGRPAEVASVIS 120

Query: 121 KQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP 180
           KQLSDTI SSGMI+LKEL LVGGKAAWM YLDIYCLDADG+LFDAALLS VAAFS+L IP
Sbjct: 121 KQLSDTILSSGMIDLKELCLVGGKAAWMAYLDIYCLDADGSLFDAALLSTVAAFSHLNIP 180

Query: 181 TVSLD-DGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEE 239
            VSL+ DG+IV++ E+  +   EK+PVN EKRKL L   PFSLTC+LHKNYILADPT+EE
Sbjct: 181 VVSLNEDGRIVLVSEDNIQLKLEKQPVNTEKRKLKLNSPPFSLTCLLHKNYILADPTAEE 240

Query: 240 ESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM 299
           ESIMET VTVVLDSS QLVSLYKPGG V A+TS +QDC+AL ++RVKEL  +L EAIS M
Sbjct: 241 ESIMETAVTVVLDSSYQLVSLYKPGGPVHAHTSVIQDCVALAKRRVKELQSVLNEAISDM 300

Query: 300 EID 302
           E++
Sbjct: 301 EVE 303

Source: Solanum tuberosum

Species: Solanum tuberosum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225441838|ref|XP_002284088.1| PREDICTED: exosome complex component RRP43-like [Vitis vinifera]

 Score =  461 bits (1187), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 242/299 (80%), Positives = 268/299 (89%), Gaps = 1/299 (0%)

Query: 5   NASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSAL 64
           N S DLSSEMEVDAFRRLFPLRY ER L +SIRPDAR L RAR+T++++GAVASADGSAL
Sbjct: 5   NVSGDLSSEMEVDAFRRLFPLRYHERFLLDSIRPDARPLGRARDTSLALGAVASADGSAL 64

Query: 65  AKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLS 124
           AKIG TTMLAA+KMEVMTP  ESPDEG ++I+F+MPPICSPLVRPGRPAE APVV+KQLS
Sbjct: 65  AKIGCTTMLAAVKMEVMTPPKESPDEGSIAIEFYMPPICSPLVRPGRPAEEAPVVSKQLS 124

Query: 125 DTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSL 184
           DTI SSGMINLKELSLV GKAAWM YLDIYCLDADG+LFDAALL+AVAAFS+L+IP VSL
Sbjct: 125 DTILSSGMINLKELSLVSGKAAWMAYLDIYCLDADGSLFDAALLAAVAAFSHLRIPVVSL 184

Query: 185 D-DGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIM 243
           + +G++V++ EE +E  SEKEPVNK KRKLTL  +PFSLTCILHKNYILADPT+EEESIM
Sbjct: 185 NEEGRVVVVSEENEEGKSEKEPVNKGKRKLTLSSLPFSLTCILHKNYILADPTAEEESIM 244

Query: 244 ETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGMEID 302
           ETLVTVVLDSS QLVSLYKPGG VLAY SAVQDCIALTRQRVKEL  IL EAIS ME+D
Sbjct: 245 ETLVTVVLDSSGQLVSLYKPGGPVLAYASAVQDCIALTRQRVKELKSILNEAISDMEVD 303

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	302
TAIR|locus:2202705	302	AT1G60080 "AT1G60080" [Arabido	0.986	0.986	0.679	2.2e-105
RGD|1306169	276	Exosc8 "exosome component 8" [	0.887	0.971	0.330	2.2e-41
UNIPROTKB|Q96B26	276	EXOSC8 "Exosome complex compon	0.887	0.971	0.323	5.9e-41
UNIPROTKB|E2R7U8	276	EXOSC8 "Uncharacterized protei	0.887	0.971	0.330	1.2e-40
MGI|MGI:1916889	276	Exosc8 "exosome component 8" [	0.884	0.967	0.328	2e-40
UNIPROTKB|E1BUV1	277	LOC100858560 "Uncharacterized	0.890	0.971	0.321	2.6e-40
UNIPROTKB|Q2KHU3	276	EXOSC8 "Exosome complex compon	0.887	0.971	0.323	1.4e-39
POMBASE|SPBC17D1.03c	270	SPBC17D1.03c "exosome subunit	0.837	0.937	0.293	1e-29
TAIR|locus:2089215	307	RRP45a "AT3G12990" [Arabidopsi	0.850	0.837	0.247	9.2e-20
UNIPROTKB|F1RSQ6	113	EXOSC8 "Uncharacterized protei	0.360	0.964	0.394	1.9e-19

TAIR|locus:2202705 AT1G60080 "AT1G60080" [Arabidopsis thaliana (taxid:3702)]

 Score = 1043 (372.2 bits), Expect = 2.2e-105, P = 2.2e-105
 Identities = 208/306 (67%), Positives = 248/306 (81%)

Query:     1 MGLPNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASAD 60
             MG+P+A++DLS+EMEVDAFRR+FPLR+FERHL+ES+RPD R L +AR+T +++G V++AD
Sbjct:     1 MGIPDAAQDLSTEMEVDAFRRIFPLRFFERHLSESLRPDGRQLGKARDTIVNLGLVSTAD 60

Query:    61 GSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVA 120
             GSALAKIGSTTMLAAI+MEVMTPS +SPDEGC++I+FHMPPICSP VRPGRPAEAAPV++
Sbjct:    61 GSALAKIGSTTMLAAIRMEVMTPSTDSPDEGCIAIEFHMPPICSPTVRPGRPAEAAPVIS 120

Query:   121 KQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIP 180
             K+LSDTI SSGMI+LKEL LV GKAAWM YLDIYC             +AVAAFSNLQIP
Sbjct:   121 KRLSDTILSSGMIDLKELCLVSGKAAWMGYLDIYCLDADGALFDAALLAAVAAFSNLQIP 180

Query:   181 TVSLDD-GKIVMLPXXXXXXXXXXXP---VNKEKRKLTLGGIPFSLTCILHKNYILADPT 236
              V+L+D G+IV +                VNKEKRKLTL  IPFSLTCILHKNYILADPT
Sbjct:   181 IVALNDNGRIVAVTGEKDQDNALITEKEAVNKEKRKLTLKNIPFSLTCILHKNYILADPT 240

Query:   237 SEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAI 296
             +EEESIM+TLVTVVLDSS+Q+VS YK GGA LAY+SA++ C+ L R+R KEL QIL E  
Sbjct:   241 TEEESIMDTLVTVVLDSSDQMVSFYKSGGAALAYSSAIKSCVELARKRAKELKQILGE-- 298

Query:   297 SGMEID 302
               M+ID
Sbjct:   299 --MDID 302

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

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0006396 "RNA processing" evidence=IEA;ISS

GO:0005829 "cytosol" evidence=IDA

GO:0042991 "transcription factor import into nucleus" evidence=RCA

RGD|1306169 Exosc8 "exosome component 8" [Rattus norvegicus (taxid:10116)]

 Score = 439 (159.6 bits), Expect = 2.2e-41, P = 2.2e-41
 Identities = 94/284 (33%), Positives = 158/284 (55%)

Query:    19 FRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKM 78
             F+ + PL Y+ R L E+ RPD R L   R TT+++G++++ADGSAL K+G+TT++  +K 
Sbjct:     5 FKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKA 64

Query:    79 EVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKEL 138
             E   P +++PD G V  +  +PP+CS   R G P E A V ++ ++D I +S +I  ++L
Sbjct:    65 EFAAPPVDAPDRGYVVPNVDLPPLCSSRFRTGPPGEEAQVTSQFIADVIENSQIIKKEDL 124

Query:   139 SLVGGKAAWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXX 198
              +  GK AW++Y D+ C             + +AA  N+Q+P V++++            
Sbjct:   125 CISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINE------------ 172

Query:   199 XXXXXXPVN-KEKRKLTLGGIPFSLT-CILHKNYILADPTSEEESIMETLVTVVLDSSNQ 256
                    VN K+K  L +   P + +  +     ++ DPT EEE +    +TVV+D   +
Sbjct:   173 -ETALAEVNLKKKSYLNVRANPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVMDEEGK 231

Query:   257 LVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME 300
             L  L+KPGG+ L   + +QDC++    R KE+ ++L+E I  M+
Sbjct:   232 LCCLHKPGGSGLT-GAKLQDCMSRAVTRHKEVSKLLDEVIQSMK 274

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

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0017091 "AU-rich element binding" evidence=ISO

GO:0004532 "exoribonuclease activity" evidence=ISO

UNIPROTKB|Q96B26 EXOSC8 "Exosome complex component RRP43" [Homo sapiens (taxid:9606)]

 Score = 435 (158.2 bits), Expect = 5.9e-41, P = 5.9e-41
 Identities = 92/284 (32%), Positives = 158/284 (55%)

Query:    19 FRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKM 78
             F+ + PL Y+ R L E+ RPD R L   R TT+++G++++ADGSAL K+G+TT++  +K 
Sbjct:     5 FKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKA 64

Query:    79 EVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKEL 138
             E   PS ++PD+G V  +  +PP+CS   R G P E A V ++ ++D I +S +I  ++L
Sbjct:    65 EFAAPSTDAPDKGYVVPNVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDL 124

Query:   139 SLVGGKAAWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXX 198
              +  GK  W++Y D+ C             + +AA  N+Q+P V++++            
Sbjct:   125 CISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINE------------ 172

Query:   199 XXXXXXPVN-KEKRKLTLGGIPFSLT-CILHKNYILADPTSEEESIMETLVTVVLDSSNQ 256
                    VN K+K  L +   P + +  +     ++ DPT EEE +    +T+V+D   +
Sbjct:   173 -ETALAEVNLKKKSYLNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGK 231

Query:   257 LVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME 300
             L  L+KPGG+ L   + +QDC++    R KE+ ++++E I  M+
Sbjct:   232 LCCLHKPGGSGLT-GAKLQDCMSRAVTRHKEVKKLMDEVIKSMK 274

GO:0006364 "rRNA processing" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0008150 "biological_process" evidence=ND

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

GO:0017091 "AU-rich element binding" evidence=IDA

GO:0004532 "exoribonuclease activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

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

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|E2R7U8 EXOSC8 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 432 (157.1 bits), Expect = 1.2e-40, P = 1.2e-40
 Identities = 94/284 (33%), Positives = 157/284 (55%)

Query:    19 FRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKM 78
             F+ + PL Y+ R L E+ RPD R L   R TT+++G++++ADGSAL K+G+TT++  IK 
Sbjct:     5 FKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGIKA 64

Query:    79 EVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKEL 138
             E   P  ++PD+G V  +  +PP+CS   R G P E A V ++ ++D I +S +I  ++L
Sbjct:    65 EFAAPPTDAPDKGYVVPNVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDL 124

Query:   139 SLVGGKAAWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXX 198
              +  GK +W++Y DI C             + +AA  N Q+P V++++            
Sbjct:   125 CISPGKLSWVLYCDIICLDYDGNILDACTFALLAALKNAQLPEVTINE------------ 172

Query:   199 XXXXXXPVN-KEKRKLTLGGIPFSLT-CILHKNYILADPTSEEESIMETLVTVVLDSSNQ 256
                    VN K+K  L +   P + +  +     ++ DPT EEE +    +TVV+D   +
Sbjct:   173 -ETGLAEVNLKKKSYLNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTVVMDEEGK 231

Query:   257 LVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME 300
             L  L+KPGG+ L   + +QDC++    R KE+ ++++E I  M+
Sbjct:   232 LCCLHKPGGSGLT-GAKLQDCMSRAVTRHKEVKKLMDEVIKSMK 274

GO:0017091 "AU-rich element binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

MGI|MGI:1916889 Exosc8 "exosome component 8" [Mus musculus (taxid:10090)]

 Score = 430 (156.4 bits), Expect = 2.0e-40, P = 2.0e-40
 Identities = 93/283 (32%), Positives = 156/283 (55%)

Query:    19 FRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKM 78
             F+ + PL Y+ R L E+ RPD R L   R TT+++G++++ADGSAL K+G+TT++  +K 
Sbjct:     5 FKTVEPLEYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKA 64

Query:    79 EVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKEL 138
             E   P +++PD G V  +  +PP+CS   R G P E A V ++ ++D + +S +I  ++L
Sbjct:    65 EFAAPPVDAPDRGYVVPNVDLPPLCSSRFRTGPPGEEAQVTSQFIADVVDNSQVIKKEDL 124

Query:   139 SLVGGKAAWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXX 198
              +  GK AW++Y D+ C             + +AA  N+Q+P V++++            
Sbjct:   125 CISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINE------------ 172

Query:   199 XXXXXXPVN-KEKRKLTLGGIPFSLT-CILHKNYILADPTSEEESIMETLVTVVLDSSNQ 256
                    VN K+K  L +   P + +  +     ++ DPT EEE +    +TVV D   +
Sbjct:   173 -ETALAEVNLKKKSYLNVRTNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTDEDGK 231

Query:   257 LVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM 299
             L  L+KPGG+ L   + +QDC++    R KE+ ++L+E I  M
Sbjct:   232 LCCLHKPGGSGLT-GAKLQDCMSRAVTRHKEVSKLLDEVIQSM 273

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006364 "rRNA processing" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0017091 "AU-rich element binding" evidence=ISO

UNIPROTKB|E1BUV1 LOC100858560 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 429 (156.1 bits), Expect = 2.6e-40, P = 2.6e-40
 Identities = 92/286 (32%), Positives = 161/286 (56%)

Query:    18 AFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK 77
             AF+ + PL Y+ R L E+ RPD R L   R TT+++G++ +ADGSAL K+G+TT++  +K
Sbjct:     4 AFKTVEPLEYYRRFLKENCRPDGRELGEFRATTVNIGSITTADGSALVKLGNTTVICGVK 63

Query:    78 MEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKE 137
              E+  P+L+S ++G +  +  +P +CS   R G P E A   ++ ++D I +S +I  ++
Sbjct:    64 AELAAPALDSANKGYIVPNVELPSLCSTRFRSGPPGEEAQAASQFIADVIENSQVIAKED 123

Query:   138 LSLVGGKAAWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXX 197
             L +  GK AW++Y DI C             + +AA  N+Q+P+V++++           
Sbjct:   124 LCIADGKLAWVLYCDIICLDYDGNILDASTFALLAALKNVQLPSVTINE----------- 172

Query:   198 XXXXXXXPVN-KEKRKLTLGGIPFSLTCIL--HKNYILADPTSEEESIMETLVTVVLDSS 254
                     VN K+K  L +   P + +  +      ++ DPT+EEE +    VTVV D  
Sbjct:   173 --ETGLSEVNLKQKNPLVIRKHPVATSFAIFDESTLLIVDPTAEEEDLATGTVTVVTDED 230

Query:   255 NQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME 300
             ++L S++KPGG+ L   + +QDCI+    R KE+ +++++ I  ++
Sbjct:   231 DRLCSVHKPGGSPLT-GAKLQDCISRAITRHKEVKKLIDKVIKSIK 275

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

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0017091 "AU-rich element binding" evidence=IEA

UNIPROTKB|Q2KHU3 EXOSC8 "Exosome complex component RRP43" [Bos taurus (taxid:9913)]

 Score = 422 (153.6 bits), Expect = 1.4e-39, P = 1.4e-39
 Identities = 92/284 (32%), Positives = 155/284 (54%)

Query:    19 FRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKM 78
             F+ + PL Y+ R L E+ RPD R L   R TT+++G++ +ADGSAL K+G+TT++  IK 
Sbjct:     5 FKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNVGSIGTADGSALVKLGNTTVICGIKA 64

Query:    79 EVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKEL 138
             E   P  ++PD+G V  +  + P+CS   R G P E A V ++ ++D I +S +I  ++L
Sbjct:    65 EFGAPPTDAPDKGYVVPNVDLSPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDL 124

Query:   139 SLVGGKAAWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXX 198
              +  GK AW++Y D+ C             + +AA  N+Q+P V++++            
Sbjct:   125 CISSGKLAWVLYCDLICLNHDGNILDACTFALLAALKNVQLPEVTINE------------ 172

Query:   199 XXXXXXPVN-KEKRKLTLGGIPFSLT-CILHKNYILADPTSEEESIMETLVTVVLDSSNQ 256
                    VN K+K  L +   P + +  +     ++ DPT EEE +    +TVV+D   +
Sbjct:   173 -ETALAEVNLKKKSCLNIRTHPVATSFAVFDDTLLIVDPTEEEEHLATGTLTVVMDEEGR 231

Query:   257 LVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME 300
             L  L+KPGG+ L   + +QDC++    R KE+ ++++E    M+
Sbjct:   232 LCCLHKPGGSGLT-GAKLQDCMSRAVTRHKEVKKLMDEVFKSMK 274

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

GO:0005737 "cytoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0017091 "AU-rich element binding" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

POMBASE|SPBC17D1.03c SPBC17D1.03c "exosome subunit Rrp43 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 329 (120.9 bits), Expect = 1.0e-29, P = 1.0e-29
 Identities = 78/266 (29%), Positives = 134/266 (50%)

Query:    19 FRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKM 78
             F+++ P +Y    L + +R D RS+S  R   I+   +++A+GSA+ + G    +  IK 
Sbjct:    17 FKKITPEQYLSHLLNQDVRSDGRSVSEFREIVINDNCISTANGSAIIRAGENVFVCGIKA 76

Query:    79 EVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKEL 138
             E+  P   SP+EG +  +  + P+CS   +PG P++ A VV+++L  T+  S +INL+ L
Sbjct:    77 EIAEPFENSPNEGWIVPNLELSPLCSSKFKPGPPSDLAQVVSQELHQTLQQSNLINLQSL 136

Query:   139 SLVGGKAAWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXX 198
              +   KAAW++Y DI C             +  AA   +++PT   D+    ++      
Sbjct:   137 CIFEKKAAWVLYADIICLNYDGSAFDYAWAALFAALKTVKLPTAVWDEDLERVI-----C 191

Query:   199 XXXXXXPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLV 258
                   PV     +L+     FS +    K  +LADPT EEE +    +T++L+SS  +V
Sbjct:   192 ASTLTRPV-----QLSTEVRSFSWSVFDDK--LLADPTDEEEDLSTEFLTIMLNSSKNIV 244

Query:   259 SLYKPGGAVLAYTSAVQDCIALTRQR 284
              + K GG  +     ++ CI + R +
Sbjct:   245 KIIKLGGTHIQ-PLLLKKCIEVARSK 269

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

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

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

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0034661 "ncRNA catabolic process" evidence=ISO

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

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

GO:0070651 "nonfunctional rRNA decay" evidence=ISO

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

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

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

TAIR|locus:2089215 RRP45a "AT3G12990" [Arabidopsis thaliana (taxid:3702)]

 Score = 235 (87.8 bits), Expect = 9.2e-20, P = 9.2e-20
 Identities = 68/275 (24%), Positives = 124/275 (45%)

Query:    26 RYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSL 85
             ++ E  L   +R D R L   R  TI  G      GS+  ++G T ++A +  +++ P  
Sbjct:    17 KFVESALQSELRVDGRGLYDYRKLTIKFG---KEYGSSQVQLGQTHVMAFVTAQLVQPYK 73

Query:    86 ESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKA 145
             + P EG  SI     P+  P   PG P E+A  + + +   +  S  ++ + L ++ GK 
Sbjct:    74 DRPSEGSFSIFTEFSPMADPSFEPGHPGESAVELGRIIDRALRESRAVDTESLCVLAGKL 133

Query:   146 AWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIP--TVSLDDGKIVMLPXXXXXXXXXX 203
              W V +D++              +A+AA    + P  TV  D+ + V++           
Sbjct:   134 VWSVRIDLHILDNGGNLVDAANVAALAALMTFRRPDCTVGGDNSQDVII----------H 183

Query:   204 XPVNKEKRKLTLGGIPFSLTC-ILHKNYILA-DPTSEEESIMETLVTVVLDSSNQLVSLY 261
              P  +E   L +  +P + T    +K  IL  DPT  EE++M   +TV ++++  + ++ 
Sbjct:   184 PPEEREPLPLIIHHLPIAFTFGFFNKGSILVMDPTYVEEAVMCGRMTVTVNANGDICAIQ 243

Query:   262 KPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAI 296
             KPG   +   S +  C+ L   R     +I+ +A+
Sbjct:   244 KPGEEGVNQ-SVILHCLRLASSRASATTKIIRDAV 277

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

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0005737 "cytoplasm" evidence=ISM;IDA

GO:0006396 "RNA processing" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=IDA

GO:0010025 "wax biosynthetic process" evidence=IGI

UNIPROTKB|F1RSQ6 EXOSC8 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 43/109 (39%), Positives = 69/109 (63%)

Query:    19 FRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKM 78
             F+ + PL Y+ R L E+ RPD R L   R TT+++G++ +ADGS+L K+G+TT++  IK 
Sbjct:     5 FKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNVGSIGTADGSSLVKLGNTTVICGIKA 64

Query:    79 EVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTI 127
             E   P  ++PD+G +  +  + P+CS   R G P E A V ++ ++D I
Sbjct:    65 EFGAPPTDAPDKGYIVPNVDLSPLCSWRFRSGPPGEEAQVASQFIADVI 113

GO:0017091 "AU-rich element binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" 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)
Q2KHU3	EXOS8_BOVIN	No assigned EC number	0.3450	0.8940	0.9782	yes	no
Q8U0M0	ECX2_PYRFU	3, ., 1, ., 1, 3, ., -	0.3014	0.8410	0.9169	yes	no
Q9D753	EXOS8_MOUSE	No assigned EC number	0.3533	0.8907	0.9746	yes	no
Q10205	RRP43_SCHPO	No assigned EC number	0.3022	0.8311	0.9296	yes	no
O59224	ECX2_PYRHO	3, ., 1, ., 1, 3, ., -	0.3082	0.8344	0.9197	yes	no
Q96B26	EXOS8_HUMAN	No assigned EC number	0.3485	0.8940	0.9782	yes	no
C5A2B8	ECX2_THEGJ	3, ., 1, ., 1, 3, ., -	0.3097	0.8278	0.9157	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.13	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	eugene3.00160490	hypothetical protein (439 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.IX.3663.1	hypothetical protein (741 aa)			•						0.499
	gw1.IV.2852.1	SubName- Full=Putative uncharacterized protein; (422 aa)			•						0.498
	estExt_fgenesh4_pm.C_LG_XI0237	hypothetical protein (421 aa)			•						0.497
	gw1.I.795.1	annotation not avaliable (261 aa)			•						0.493
	gw1.XV.2421.1	annotation not avaliable (269 aa)			•						0.419
	estExt_fgenesh4_pg.C_LG_VI0825	SubName- Full=Putative uncharacterized protein; (372 aa)			•						0.419
	estExt_Genewise1_v1.C_LG_XVI3731	chlorophyll synthetase (EC-2.5.1.62) (329 aa)			•						0.416

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	302
cd11369	261	cd11369, RNase_PH_RRP43, RRP43 subunit of eukaryot	1e-122
cd11365	256	cd11365, RNase_PH_archRRP42, RRP42 subunit of arch	7e-53
PRK04282	271	PRK04282, PRK04282, exosome complex RNA-binding pr	2e-52
COG2123	272	COG2123, COG2123, RNase PH-related exoribonuclease	3e-51
cd11368	259	cd11368, RNase_PH_RRP45, RRP45 subunit of eukaryot	6e-40
cd11367	272	cd11367, RNase_PH_RRP42, RRP42 subunit of eukaryot	2e-38
cd11358	218	cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucl	2e-33
pfam01138	129	pfam01138, RNase_PH, 3' exoribonuclease family, do	4e-26
TIGR02065	230	TIGR02065, ECX1, archaeal exosome-like complex exo	8e-07
PRK03983	244	PRK03983, PRK03983, exosome complex exonuclease Rr	3e-06
pfam03725	68	pfam03725, RNase_PH_C, 3' exoribonuclease family,	4e-06
COG0689	230	COG0689, Rph, RNase PH [Translation, ribosomal str	2e-04
cd11366	214	cd11366, RNase_PH_archRRP41, RRP41 subunit of arch	3e-04
cd11370	226	cd11370, RNase_PH_RRP41, RRP41 subunit of eukaryot	0.003

>gnl|CDD|206774 cd11369, RNase_PH_RRP43, RRP43 subunit of eukaryotic exosome

 Score =  350 bits (900), Expect = e-122
 Identities = 118/274 (43%), Positives = 184/274 (67%), Gaps = 14/274 (5%)

Query: 20  RRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKME 79
           ++L PL Y+ R LAE++RPD R L   R T++++G++++ADGSAL K+G+TT+L  IK E
Sbjct: 1   KKLHPLEYYRRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAE 60

Query: 80  VMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELS 139
           V TP+ ++PDEG +  +  +PP+CS   RPG P+E A V++  L+D + +S +++L++L 
Sbjct: 61  VATPAADTPDEGYLVPNVDLPPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLC 120

Query: 140 LVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEE 199
           +V GK AW++Y D+YCLD DG L DAALL+ VAA  NL++P V++D            EE
Sbjct: 121 IVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRLPAVTID------------EE 168

Query: 200 NSEKEPVNKEKRKLTLGGIPFSLTC-ILHKNYILADPTSEEESIMETLVTVVLDSSNQLV 258
                   +E+R L L  +P S T  +    ++LADPT+EEE +   LVTVV+D + +L 
Sbjct: 169 TELVVVNPEERRPLNLKNLPVSTTFAVFDDKHLLADPTAEEELLASGLVTVVVDENGELC 228

Query: 259 SLYKPGGAVLAYTSAVQDCIALTRQRVKELHQIL 292
           S++KPGG+ L+  + +Q+CI L ++R KEL +++
Sbjct: 229 SVHKPGGSPLS-QAQLQECIELAKKRAKELQKLI 261

The RRP43 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Length = 261

>gnl|CDD|206770 cd11365, RNase_PH_archRRP42, RRP42 subunit of archaeal exosome

 Score =  173 bits (440), Expect = 7e-53
 Identities = 91/261 (34%), Positives = 142/261 (54%), Gaps = 17/261 (6%)

Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEG 91
           L +  R D R L   R+  I  G +  A+GSAL K+G+T +LA +K+EV  P  ++P+EG
Sbjct: 12  LEKGKRIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGVKLEVGEPFPDTPNEG 71

Query: 92  CVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYL 151
            + ++  + P+ SP   PG P E A  +A+ +   I  S  I+L++L +  GK  W+V++
Sbjct: 72  VLIVNAELLPLASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFI 131

Query: 152 DIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKR 211
           DIY LD DG LFDA+ L+AVAA  N               +PE + +EN E   V  E+ 
Sbjct: 132 DIYVLDYDGNLFDASALAAVAALLN-------------TKVPEYEVDEN-EVIEVLGEEL 177

Query: 212 KLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYT 271
            L +  +P S+T      YI+ DPT EEE +M+  +T+ +D    +V+L K GG   ++T
Sbjct: 178 PLPVNTLPVSVTVAKIGGYIVVDPTLEEELVMDARITITIDEDGNIVALQKGGGG--SFT 235

Query: 272 SA-VQDCIALTRQRVKELHQI 291
              +   I +  ++  EL + 
Sbjct: 236 EDEIDKAIDIALEKAAELREK 256

The RRP42 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 pocket at the interface between Rrp42 and Rrp41. The ring is capped by three copies of Rrp4 and/or Csl4 which contain putative RNA interaction domains. The archaeal exosome degrades single-stranded RNA (ssRNA) in the 3'-5' direction, but also can catalyze the reverse reaction of adding nucleoside diphosphates to the 3'-end of RNA which has been shown to lead to the formation of poly-A-rich tails on RNA. It is required for 3' processing of the 5.8S rRNA. Length = 256

>gnl|CDD|235268 PRK04282, PRK04282, exosome complex RNA-binding protein Rrp42; Provisional

 Score =  172 bits (439), Expect = 2e-52
 Identities = 90/270 (33%), Positives = 142/270 (52%), Gaps = 15/270 (5%)

Query: 27  YFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLE 86
           Y    L +  R D R L   R   I  G +  A+GSAL K+G+T +LA +K+E+  P  +
Sbjct: 15  YILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPD 74

Query: 87  SPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAA 146
           +P+EG + ++  + P+ SP   PG P E A  +A+ +   I  S  I+L++L +  GK  
Sbjct: 75  TPNEGVLIVNAELLPLASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKV 134

Query: 147 WMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPV 206
           W+V++D+Y LD DG L DA++L+AVAA  N ++P V   +  +V      K       PV
Sbjct: 135 WVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEGEDGVV-----DKLGEDFPLPV 189

Query: 207 NKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGA 266
           N           P ++T     NY++ DPT EEES+M+  +T+  D    +V++ K G  
Sbjct: 190 ND---------KPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIG 240

Query: 267 VLAYTSAVQDCIALTRQRVKELHQILEEAI 296
                  V   I +  ++ KEL + L+EA+
Sbjct: 241 SFTE-EEVDKAIDIALEKAKELREKLKEAL 269

Length = 271

>gnl|CDD|225034 COG2123, COG2123, RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]

 Score =  169 bits (430), Expect = 3e-51
 Identities = 77/266 (28%), Positives = 139/266 (52%), Gaps = 13/266 (4%)

Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEG 91
           L + IR D RS    R   I  G +  A+GSAL K+G+T ++  +K E+  P  ++P+EG
Sbjct: 19  LKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIGEPFPDTPNEG 78

Query: 92  CVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYL 151
            + ++  + P+ SP   PG P E A  +++ +   +  S  I+L++L +  GK  W+V++
Sbjct: 79  VLVVNVELSPLASPSFEPGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFV 138

Query: 152 DIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKR 211
           D++ LD DG L DAA L+AVAA  N ++P               +  +      V +E  
Sbjct: 139 DVHVLDYDGNLIDAASLAAVAALLNTRVPKA------------VEVGDGEIVIEVEEEPV 186

Query: 212 KLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYT 271
            L +   P S+T     N ++ DP+ EEE + +  +T+ ++   ++V++ K GG  +   
Sbjct: 187 PLPVSNPPISVTFAKIGNVLVVDPSLEEELVADGRLTITVNEDGEIVAIQKVGGGSIT-E 245

Query: 272 SAVQDCIALTRQRVKELHQILEEAIS 297
           S ++  +     + ++L + L+EA+ 
Sbjct: 246 SDLEKALKTALSKAEKLREALKEALK 271

Length = 272

>gnl|CDD|206773 cd11368, RNase_PH_RRP45, RRP45 subunit of eukaryotic exosome

 Score =  139 bits (354), Expect = 6e-40
 Identities = 76/262 (29%), Positives = 135/262 (51%), Gaps = 17/262 (6%)

Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEG 91
           L E +R D R L   R   I+ G      G     +G T +LA +  E++ P  + P+EG
Sbjct: 13  LKEGLRLDGRGLDEFRPIKITFG---LEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEG 69

Query: 92  CVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYL 151
            + I+  + P+ SP   PGRP+E    +++ L   +  S  ++ + L ++ G+  W + +
Sbjct: 70  ILFINVELSPMASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRV 129

Query: 152 DIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKR 211
           D++ L+ DG L DAA L+A+AA  + + P V++D  ++ +   E      E+EPV     
Sbjct: 130 DVHVLNHDGNLIDAASLAAIAALMHFRRPDVTVDGEEVTVHSPE------EREPV----- 178

Query: 212 KLTLGGIPFSLT-CILHKN-YILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLA 269
            L++  IP  +T         ++ DPT  EE++ +  +TV L+   ++ +L K GGA L+
Sbjct: 179 PLSIHHIPICVTFAFFDDGEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPLS 238

Query: 270 YTSAVQDCIALTRQRVKELHQI 291
             S +  C+ +   + KEL ++
Sbjct: 239 -PSQILRCVKIAAAKAKELTEL 259

The RRP45 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Length = 259

>gnl|CDD|206772 cd11367, RNase_PH_RRP42, RRP42 subunit of eukaryotic exosome

 Score =  136 bits (344), Expect = 2e-38
 Identities = 74/272 (27%), Positives = 136/272 (50%), Gaps = 20/272 (7%)

Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEG 91
           + ++IR D RS    R   +  G +++ +GSA  ++G+T +L  +K EV +P  E+P++G
Sbjct: 14  VEQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKG 73

Query: 92  --CVSIDFHMPPICSPLVRP---GRPAEA-APVVAKQLSDTISSSGMINLKELSLVGGKA 145
                +D      CSP   P   GR  E  A  ++  L   + S   I+L +L +V GK 
Sbjct: 74  RLEFFVD------CSPNASPEFEGRGGEELATELSSALERALKSGSAIDLSKLCIVPGKQ 127

Query: 146 AWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEP 205
            W++Y+D+  L++ G L DA  ++  AA  N +IP V + +       E  KE     +P
Sbjct: 128 CWVLYVDVLVLESGGNLLDAISIAVKAALFNTRIPKVEVSEDD-----EGTKEIELSDDP 182

Query: 206 VNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGG 265
            + +  +L +  +P  +T     N  + D T+EEE+     + V +++  ++  + K GG
Sbjct: 183 YDVK--RLDVSNVPLIVTLSKIGNRHIVDATAEEEACSSARLLVAVNAKGRICGVQKSGG 240

Query: 266 AVLAYTSAVQDCIALTRQRVKELHQILEEAIS 297
             L    ++ + I   ++  K+L+  L++A+ 
Sbjct: 241 GSL-EPESIIEMIETAKEVGKKLNAALDKALK 271

The RRP42 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Length = 272

>gnl|CDD|206766 cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucleases

 Score =  122 bits (307), Expect = 2e-33
 Identities = 68/243 (27%), Positives = 113/243 (46%), Gaps = 27/243 (11%)

Query: 47  RNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTP-SLESPDEGCVSIDFHMPPICSP 105
           R   I  G +  ADGSAL K+G+T ++ A+   ++ P  LE PD+G + ++  + P    
Sbjct: 2   RPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLERPDKGTLYVNVEISPGAVG 61

Query: 106 LVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDA 165
             R G P +    +++ L  TI +S +++            W++Y+DI  L  DG L DA
Sbjct: 62  ERRQGPPGDEEMEISRLLERTIEASVILDKSTRKPS-----WVLYVDIQVLSRDGGLLDA 116

Query: 166 ALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCI 225
              +A+AA  +  IP V +D+    +L  +                      I       
Sbjct: 117 CWNAAIAALKDAGIPRVFVDERSPPLLLMK--------------------DLIVAVSVGG 156

Query: 226 LHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRV 285
           +    +L DPT EEE + ++ +TV +D S +L  L K GG  L  T  +++C+ L ++R 
Sbjct: 157 ISDGVLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLD-TEEIKECLELAKKRS 215

Query: 286 KEL 288
             L
Sbjct: 216 LHL 218

RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites. Length = 218

>gnl|CDD|216323 pfam01138, RNase_PH, 3' exoribonuclease family, domain 1

 Score = 99.6 bits (249), Expect = 4e-26
 Identities = 37/135 (27%), Positives = 64/135 (47%), Gaps = 9/135 (6%)

Query: 47  RNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDE-GCVSIDFHMPPICSP 105
           R   I  G ++ ADGSAL ++G T +LA +   +  P  E     G +++++   P  S 
Sbjct: 3   RPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPPQKERDFFPGELTVEYEESPFASG 62

Query: 106 LVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDA 165
               GRP+E    +++ +   +  S  +         G   W + +D+  L  DG+L DA
Sbjct: 63  ERPEGRPSEREIELSRLIDRALRPSIPL--------EGYPRWEIRIDVTVLSDDGSLLDA 114

Query: 166 ALLSAVAAFSNLQIP 180
           A+ +A  A ++  IP
Sbjct: 115 AINAASLALADAGIP 129

This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria. Length = 129

>gnl|CDD|131120 TIGR02065, ECX1, archaeal exosome-like complex exonuclease 1

 Score = 49.0 bits (117), Expect = 8e-07
 Identities = 46/182 (25%), Positives = 82/182 (45%), Gaps = 20/182 (10%)

Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAI--KMEVMTPSLESPD 89
           L + +R D R     R   I  G + +ADGSA  + G T +LAA+    E     L+ PD
Sbjct: 4   LEDGVRLDGRKPDELRPIKIEAGVLKNADGSAYLEFGGTKILAAVYGPREAHPRHLQLPD 63

Query: 90  EGCVSIDFHMPPICS-PLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWM 148
              + + +HM P  +    RPG P+     ++K + + +  + ++     +++       
Sbjct: 64  RAVLRVRYHMAPFSTDERKRPG-PSRREIEISKVIREALEPAILLEQFPRTVID------ 116

Query: 149 VYLDIYCLDADGALFDAALLSAVAAFSNLQIP--------TVSLDDGKIVMLPEEQKEEN 200
           V++++  L ADG    A L +A  A ++  IP         V   DG +V+   E+++  
Sbjct: 117 VFIEV--LQADGGTRCAGLTAASLALADAGIPMRDLVVGVAVGKVDGVVVLDLSEEEDMY 174

Query: 201 SE 202
            E
Sbjct: 175 GE 176

This family contains the archaeal protein orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in Sulfolobus solfataricus, so members of this family are designated exosome complex exonuclease 1, after usage in SwissProt [Transcription, Degradation of RNA]. Length = 230

>gnl|CDD|235187 PRK03983, PRK03983, exosome complex exonuclease Rrp41; Provisional

 Score = 47.3 bits (113), Expect = 3e-06
 Identities = 46/181 (25%), Positives = 79/181 (43%), Gaps = 27/181 (14%)

Query: 34  ESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAI--KMEVMTPSLESPDEG 91
           + +R D R     R   I +G + +ADGSA  + G+  ++AA+    E+    L+ PD  
Sbjct: 12  DGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRA 71

Query: 92  CVSIDFHMPPIC-SPLVRPG---RPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAW 147
            + + ++M P       RPG   R  E + V+ + L   I       + EL     +   
Sbjct: 72  VLRVRYNMAPFSVDERKRPGPDRRSIEISKVIREALEPAI-------MLELF---PRTVI 121

Query: 148 MVYLDIYCLDADGALFDAALLSAVAAFSNLQIP--------TVSLDDGKIVMLPEEQKEE 199
            V++++  L AD     A + +A  A ++  IP         V   DG IV+   ++ E+
Sbjct: 122 DVFIEV--LQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKVDGVIVLDLNKE-ED 178

Query: 200 N 200
           N
Sbjct: 179 N 179

Length = 244

>gnl|CDD|217696 pfam03725, RNase_PH_C, 3' exoribonuclease family, domain 2

 Score = 43.3 bits (103), Expect = 4e-06
 Identities = 17/68 (25%), Positives = 35/68 (51%)

Query: 217 GIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQD 276
           G   ++T       ++ DPT EEES+ ++ +T+V+  + ++V+L K GG        + +
Sbjct: 1   GPVAAVTVGKIDGELVLDPTLEEESLADSDLTIVVAGTGEIVALMKEGGGAELTEEELLE 60

Query: 277 CIALTRQR 284
            + L  + 
Sbjct: 61  ALELAHEG 68

This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria. Length = 68

>gnl|CDD|223761 COG0689, Rph, RNase PH [Translation, ribosomal structure and biogenesis]

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 47/234 (20%), Positives = 90/234 (38%), Gaps = 53/234 (22%)

Query: 34  ESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKM--EVMTPSLESPDEG 91
           + +RPD R     R   I+ G +  A+GS+L + G+T ++  +    E +   L    +G
Sbjct: 6   DGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKG 65

Query: 92  CVSIDFHMPPICS-----PLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAA 146
            ++ ++ M P  +          GR  E + ++ + L        +I+L+ L     ++ 
Sbjct: 66  WLTAEYGMLPRSTDERKKREADRGRTKEISRLIGRALRA------VIDLELL----PEST 115

Query: 147 WMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPV 206
             + +D   L ADG    A++  A  A ++  IP   L     V                
Sbjct: 116 --IDIDCDVLQADGGTRTASITGASLALADAGIPLRDL-----VA--------------- 153

Query: 207 NKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSL 260
                         +++  +    I+ D   EE+S  E  + VV+  +  LV +
Sbjct: 154 --------------AISVGIVDGVIVLDLDYEEDSAAEADMNVVMTGNGGLVEI 193

Length = 230

>gnl|CDD|206771 cd11366, RNase_PH_archRRP41, RRP41 subunit of archaeal exosome

 Score = 41.2 bits (97), Expect = 3e-04
 Identities = 47/172 (27%), Positives = 75/172 (43%), Gaps = 28/172 (16%)

Query: 47  RNTTISMGAVASADGSALAKIGSTTMLAAI--KMEVMTPSLESPDEGCVSIDFHMPPICS 104
           R   I +G + +ADGSA  + G+  ++AA+    EV    L+ PD   + + ++M P   
Sbjct: 3   RPIKIEVGVLKNADGSAYVEWGNNKIIAAVYGPREVHPRHLQLPDRAVIRVRYNMAPFSV 62

Query: 105 P-LVRPG---RPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADG 160
               RPG   R  E + V+ + L   I       + E      + A  V++++  L AD 
Sbjct: 63  DERKRPGPDRREIEISKVIKEALEPAI-------ILEEF---PRTAIDVFVEV--LQADA 110

Query: 161 ALFDAALLSAVAAFSNLQIP--------TVSLDDGKIVMLPEEQKEENSEKE 204
               A L +A  A ++  IP             DGKIV+     KEE++  E
Sbjct: 111 GTRVAGLNAASLALADAGIPMRDLVAACAAGKVDGKIVLDLN--KEEDNYGE 160

The RRP41 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 pocket at the interface between Rrp42 and Rrp41. The ring is capped by three copies of Rrp4 and/or Csl4 which contain putative RNA interaction domains. The archaeal exosome degrades single-stranded RNA (ssRNA) in the 3'-5' direction, but also can catalyze the reverse reaction of adding nucleoside diphosphates to the 3'-end of RNA which has been shown to lead to the formation of poly-A-rich tails on RNA. Length = 214

>gnl|CDD|206775 cd11370, RNase_PH_RRP41, RRP41 subunit of eukaryotic exosome

 Score = 37.9 bits (89), Expect = 0.003
 Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 37  RPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK--MEVMTPSLESPDEGCVS 94
           R D R  +  R     +G  +SADGSA  + G+T +LAA+    E    S    D   V+
Sbjct: 3   RLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNRSQALHDRAVVN 62

Query: 95  IDFHMPP 101
            ++ M  
Sbjct: 63  CEYSMAT 69

The RRP41 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Length = 226

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	302
COG2123	272	RNase PH-related exoribonuclease [Translation, rib	100.0
PRK04282	271	exosome complex RNA-binding protein Rrp42; Provisi	100.0
KOG1614	291	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
KOG1613	298	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
KOG1612	288	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
PRK00173	238	rph ribonuclease PH; Reviewed	100.0
TIGR01966	236	RNasePH ribonuclease PH. This bacterial enzyme, ri	100.0
PRK03983	244	exosome complex exonuclease Rrp41; Provisional	100.0
TIGR02065	230	ECX1 archaeal exosome-like complex exonuclease 1.	100.0
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	100.0
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	100.0
COG0689	230	Rph RNase PH [Translation, ribosomal structure and	100.0
KOG1068	245	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	100.0
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.97
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	99.97
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	99.97
KOG1069	217	consensus Exosomal 3'-5' exoribonuclease complex,	99.96
PF01138	132	RNase_PH: 3' exoribonuclease family, domain 1 This	99.96
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.9
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	99.86
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.8
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.68
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.65
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	99.47
PF03725	68	RNase_PH_C: 3' exoribonuclease family, domain 2 Th	99.43
PF03726	83	PNPase: Polyribonucleotide nucleotidyltransferase,	86.49

>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.2e-61  Score=420.72  Aligned_cols=266  Identities=30%  Similarity=0.532  Sum_probs=249.3

Q ss_pred             HhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEe
Q 022140           19 FRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFH   98 (302)
Q Consensus        19 ~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~   98 (302)
                      +-...++.|+.+.+++++|+|||+++|||++.|++|++++|+|||+|++|+|+|+|+||.++++|.+++|++|.+.+|++
T Consensus         6 ~~~~~~~~~i~~ll~~g~R~DGR~~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK~eig~Pf~DtP~eG~~~~n~E   85 (272)
T COG2123           6 IISEIKREYILNLLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIGEPFPDTPNEGVLVVNVE   85 (272)
T ss_pred             hhhhhHHHHHHHHhccCcccCCCCcccccceEEEeCceecCCCcEEEEecCeEEEEEEEcccCCCCCCCCCCceEEeeee
Confidence            44556779999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCC
Q 022140           99 MPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQ  178 (302)
Q Consensus        99 ~~~~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~  178 (302)
                      +.|.+++.|++|++++.+.++++++++.++.++.+|+++|||.+|+++|.+++|++||++|||++||+++|+++||++++
T Consensus        86 l~Plas~~fE~Gppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~Da~~lA~~aAL~~t~  165 (272)
T COG2123          86 LSPLASPSFEPGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAAVAALLNTR  165 (272)
T ss_pred             eeccccccccCCCCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHhcC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcEEe-cCCceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcE
Q 022140          179 IPTVSL-DDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQL  257 (302)
Q Consensus       179 iP~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i  257 (302)
                      +|+... +++..+.             ..+.++.++.+.++|+++|++++++.+++|||.+||..+++.++|.++++|++
T Consensus       166 vP~~~~~~~~~~v~-------------~~~~~~~pl~~~~~pi~vt~a~ig~~lvvDPsleEe~v~d~~ltit~~~~~~I  232 (272)
T COG2123         166 VPKAVEVGDGEIVI-------------EVEEEPVPLPVSNPPISVTFAKIGNVLVVDPSLEEELVADGRLTITVNEDGEI  232 (272)
T ss_pred             CCceeecCCcceee-------------cccCCCcccccCCCceEEEEEEECCEEEeCCCcchhhhcCceEEEEECCCCcE
Confidence            997766 4443222             12236777999999999999999999999999999999999999999999999


Q ss_pred             EEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022140          258 VSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISG  298 (302)
Q Consensus       258 ~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~  298 (302)
                      ++++|.|+.+++.+. +.+|++.|.+.+.++.+.+.++|+.
T Consensus       233 v~iqK~g~~~~~~~~-~~~~~~~A~~~~~kl~~~~~~~L~~  272 (272)
T COG2123         233 VAIQKVGGGSITESD-LEKALKTALSKAEKLREALKEALKE  272 (272)
T ss_pred             EEEEEcCCCcCCHHH-HHHHHHHHHHHHHHHHHHHHHhhcC
Confidence            999999999999995 9999999999999999999998863

>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional

Probab=100.00  E-value=1.9e-58  Score=416.39  Aligned_cols=260  Identities=34%  Similarity=0.568  Sum_probs=244.5

Q ss_pred             ChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCC
Q 022140           23 FPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPI  102 (302)
Q Consensus        23 ~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~  102 (302)
                      .+++|+++++++++|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|++++..|..++|++|.+.++|+++|+
T Consensus        11 ~e~~~i~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~vl~~V~~~~~~p~~~~~~~g~i~~~v~~~~~   90 (271)
T PRK04282         11 IKKDYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPL   90 (271)
T ss_pred             HHHHHHHHHHhcCCCCCCCCCccccCeEEEeCCccCCCcEEEEEECCCEEEEEEEEEEecCCCCCCCCCEEEEEEEECCC
Confidence            45799999999999999999999999999999999999999999999999999999999888889999999999999999


Q ss_pred             CCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcE
Q 022140          103 CSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTV  182 (302)
Q Consensus       103 ~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~  182 (302)
                      +.+.|+.|++++.++.++++|+++|+++..+|+++|||.||+++|.|+|+++||++|||++||+++|+++||+|+++|.+
T Consensus        91 a~~~~~~~~~~~~~~~l~~~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG~~~daa~~Aa~aAL~~~~iP~~  170 (271)
T PRK04282         91 ASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAV  170 (271)
T ss_pred             cCccccCCCCCHHHHHHHHHHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhCCCCcE
Confidence            99888888888899999999999999989999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEc
Q 022140          183 SLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYK  262 (302)
Q Consensus       183 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~  262 (302)
                      .+.++...              .++.+..++.++++|+++||+++++.+|+|||.+||+++++.++|+++++|+++++++
T Consensus       171 ~~~~~~~~--------------~~~~~~~~l~~~~~p~~vt~~~~~~~~v~Dpt~~Ee~~~~~~l~va~~~~g~i~~l~~  236 (271)
T PRK04282        171 EEGEDGVV--------------DKLGEDFPLPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQK  236 (271)
T ss_pred             EEcCCcee--------------ccCCCcccCCCCCeeEEEEEEEECCEEEECCCHHHHhhcCceEEEEECCCCcEEEEEc
Confidence            99443321              1245677899999999999999999999999999999999999999999999999999


Q ss_pred             cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022140          263 PGGAVLAYTSAVQDCIALTRQRVKELHQILEEAIS  297 (302)
Q Consensus       263 ~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~  297 (302)
                      .|+.+++.++ +.+|+++|.+++++++++++++|+
T Consensus       237 ~g~~~~~~~~-l~~~i~~A~~~~~~l~~~~~~~l~  270 (271)
T PRK04282        237 SGIGSFTEEE-VDKAIDIALEKAKELREKLKEALG  270 (271)
T ss_pred             CCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHhc
Confidence            9988999996 999999999999999999999984

>KOG1614 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=5.5e-59  Score=394.26  Aligned_cols=266  Identities=26%  Similarity=0.514  Sum_probs=253.2

Q ss_pred             hhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecC
Q 022140           21 RLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMP  100 (302)
Q Consensus        21 ~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~  100 (302)
                      .+++..|+.++|+.|.|.|||+++|||.+.|++|.   ..||+.|++|+|+|+|.|++++.+|..++|.+|.+.+.++++
T Consensus         7 t~~e~~fvl~alk~g~R~DgR~l~efR~lei~fGk---e~gs~~vt~G~Tkvm~~vt~~ia~Py~dRP~eG~~~I~tels   83 (291)
T KOG1614|consen    7 TVNESKFVLNALKAGLRFDGRSLEEFRDLEIEFGK---EYGSVLVTMGNTKVMARVTAQIAQPYIDRPHEGSFSIFTELS   83 (291)
T ss_pred             ccchHHHHHHHHHhcccccccchhhhhceEEEecc---ccccEEEEecCeeEEEEeehhhcCcccCCCCCCeeeeeeccc
Confidence            45789999999999999999999999999999995   899999999999999999999999999999999999999999


Q ss_pred             CCCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCC
Q 022140          101 PICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP  180 (302)
Q Consensus       101 ~~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP  180 (302)
                      |++++.|++|+.++.+..++++|++.++.+++||+|+|||..|+++|.|++|+++|+.|||++||+++|+.+||++.|.|
T Consensus        84 PmA~~sfE~Gr~~~~~v~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlvDaA~iAviaaL~hFrrP  163 (291)
T KOG1614|consen   84 PMASPSFEPGRKGESEVELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLVDAACIAVIAALMHFRRP  163 (291)
T ss_pred             cccccccCCCCccchHHHHHHHHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCeehhHHHHHHHHHHhcCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEEC--CEEEECCChHHHhcCCceEEEEEcCCCcEE
Q 022140          181 TVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHK--NYILADPTSEEESIMETLVTVVLDSSNQLV  258 (302)
Q Consensus       181 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~--~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~  258 (302)
                      .+++....+..++           +.++++.||+|+|+|+|+||++++  +..++|||..||.+.++.++|++++++++|
T Consensus       164 dvTv~g~ev~ihp-----------~eEr~PvPL~I~HmPIC~tf~ffnkG~ivviDpt~~Ee~~~dGs~vVt~Nk~rEVc  232 (291)
T KOG1614|consen  164 DVTVGGEEVIIHP-----------VEEREPVPLSIHHMPICFTFGFFNKGEIVVIDPTEKEEAVMDGSMVVTMNKNREVC  232 (291)
T ss_pred             CcccccceeEecC-----------hhccCCcceeeeeccceEEEEEecCceEEEeCCcHHHHhccCceEEEEEcCCccEE
Confidence            9999665666554           346889999999999999999998  689999999999999999999999999999


Q ss_pred             EEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcccC
Q 022140          259 SLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGMEI  301 (302)
Q Consensus       259 ~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~~~  301 (302)
                      .++|.||..+...+ +..|.+.|..++.++...+.++|++.++
T Consensus       233 ~i~k~G~~~~~~~~-i~~C~k~A~~~a~~vt~ii~e~l~~d~~  274 (291)
T KOG1614|consen  233 AIQKSGGEILDESV-IERCYKLAKDRAVEVTGIILEALEEDQR  274 (291)
T ss_pred             EEecCCCccccHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999996 9999999999999999999999998764

>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.4e-59  Score=397.04  Aligned_cols=291  Identities=37%  Similarity=0.619  Sum_probs=255.4

Q ss_pred             CCCCCCCccccccccHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeee
Q 022140            1 MGLPNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEV   80 (302)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v   80 (302)
                      ||.|.+....+.+|++++|+|+.|..|++++|++++|+|||++.+||.+.|+.|.++++|||+.++.|+|.|+|+|++++
T Consensus         1 ~~~~~aa~~~~~~f~p~~fkrI~Pe~~l~rhLse~~RpdgR~lgefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~ei   80 (298)
T KOG1613|consen    1 STTLEAAGIHPITFPPEVFKRISPELYLQRHLSEGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKAEI   80 (298)
T ss_pred             CcccccccccccccCHHHHhhcCHHHHHHHHhhcccCcchhhhhHHhhhheecCceeccCcHHHHhcCCcEEEEEeeeee
Confidence            68899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCCcceEEEEEecCCCCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCC
Q 022140           81 MTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADG  160 (302)
Q Consensus        81 ~~p~~~~p~~g~l~v~V~~~~~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG  160 (302)
                      .+|..+.|++|.+..++.++|.|++.||+|+++++++.+|+.|.+.+.++++|+++.|||.+||++|.+|.|+.||++||
T Consensus        81 ~epstdapdeg~Iv~n~~lpplcs~r~RpG~p~dea~viSq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG  160 (298)
T KOG1613|consen   81 AEPSTDAPDEGDIVPNYALPPLCSSRFRPGPPTDEAQVISQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDG  160 (298)
T ss_pred             cccccCCCCCcceeecccCCcccccCCCCCCCchHHHHHHHHHHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHhhCCCCcEEecC-CceeecCcccccccc---CcCccccccccccCCCccEEEEEEEECC-EEEECC
Q 022140          161 ALFDAALLSAVAAFSNLQIPTVSLDD-GKIVMLPEEQKEENS---EKEPVNKEKRKLTLGGIPFSLTCILHKN-YILADP  235 (302)
Q Consensus       161 ~l~da~~~A~~~AL~~~~iP~~~~~~-~~~~~~~~~~~~~~~---~~~~~~~~~~~l~i~~~p~~vt~~~~~~-~~l~DP  235 (302)
                      ++||+|++|+++||++.++|.+.+++ +...........-+.   .....+.+.+++..++.+.+.+. ++++ .++.||
T Consensus       161 ~~fDa~w~al~aAlknvklP~a~ide~~~~~~~t~e~~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~-vl~~~li~adp  239 (298)
T KOG1613|consen  161 PVFDACWNALMAALKNVKLPRAFIDERASDLRMTIEEIICDQTLTVPLMLNAENRAFASQNSDFSEEE-VLDDVLIAADP  239 (298)
T ss_pred             cHHHHHHHHHHHHHhcCCCceeeecccchhhhhhHHHHHHhhhhcchhhhccccccccccCCCccHHH-hhcceeEecCC
Confidence            99999999999999999999999943 322211100000000   00112445556666666666554 4455 455999


Q ss_pred             ChHHHhcCCceEEEEEcCCCcEEEEEccCCcccCh-HHHHHHHHHHHHHHHHHHHHHHH
Q 022140          236 TSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAY-TSAVQDCIALTRQRVKELHQILE  293 (302)
Q Consensus       236 t~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~-~~~l~~~i~~A~~~~~~l~~~l~  293 (302)
                      |.+||..+.+.++|+++++|+++.+.|.||..+.. + .+++|+++|+.+++++.+.+.
T Consensus       240 T~eEE~l~~~~lTIvldss~n~v~l~k~GG~al~~~~-~iK~c~elar~Rakelk~~~~  297 (298)
T KOG1613|consen  240 TEEEETLITSTLTIVLDSSGNYVQLTKVGGGALITPE-MIKRCLELARVRAKELKTRFN  297 (298)
T ss_pred             CchhhhhhhceEEEEEcCCCCEEEEEecCcccccCHH-HHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999999999988755 6 799999999999999988764

>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=6.5e-48  Score=328.80  Aligned_cols=264  Identities=26%  Similarity=0.402  Sum_probs=234.7

Q ss_pred             hHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCC-eEEEEEEEeeeccCCCCCCCcceEEEEEecCCC
Q 022140           24 PLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGS-TTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPI  102 (302)
Q Consensus        24 p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~-T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~  102 (302)
                      +.-|+..+.++.+|+|||+++|||++.+++++++++||||+|++|. |.|+++||+|++.|+.+.|++|.+.+.|+++|.
T Consensus         9 e~~~~i~g~e~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVKaEvg~~~~~~p~egk~~~~VD~S~s   88 (288)
T KOG1612|consen    9 EKLYIITGSEPDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKAEVGSPDDETPVEGKYLFFVDCSPS   88 (288)
T ss_pred             ceeEEecccCcccccCCcCccccceEEEEeccccCCCCcEEEEecCCceEEEEEeeeccCccccCCCCCeEEEEEEecCC
Confidence            4467778889999999999999999999999999999999999998 899999999999999999999999999999999


Q ss_pred             CCCCccCCCC-CCcHHHHHHHHHHHhhcCCC-cccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCC
Q 022140          103 CSPLVRPGRP-AEAAPVVAKQLSDTISSSGM-INLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP  180 (302)
Q Consensus       103 ~~~~~~~g~~-~~~~~~ls~~l~~~l~~~~~-i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP  180 (302)
                      ++++|. ||. ++...+|+..|+++|..-.. +|+..|++-|| ++|.||||+.|++.|||++||..+|+++||.++++|
T Consensus        89 asp~f~-gRggde~~~eltsaLq~~l~~~~sgv~ls~L~lt~~-~~W~i~VDvlVi~s~gn~~dAiS~Ai~~AL~~T~lP  166 (288)
T KOG1612|consen   89 ASPQFQ-GRGGDELVEELTSALQRVLNSLGSGVDLSKLQLTPG-YCWKIYVDVLVISSDGNLLDAISIAIYAALNNTRLP  166 (288)
T ss_pred             cCcccc-CCChhhHHHHHHHHHHHHHhCcCcccchhheeccCC-eeEEEEEeEEEEecCCCHHHHHHHHHHHHHhcccCC
Confidence            999985 554 46788999999999987444 99999999998 799999999999999999999999999999999999


Q ss_pred             cEEe--c-CCceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcE
Q 022140          181 TVSL--D-DGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQL  257 (302)
Q Consensus       181 ~~~~--~-~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i  257 (302)
                      ++.+  + ++++.....++          ..+-..+....+|+.+|++.++..+++|||.+||.++.+.+.|.+++.|-+
T Consensus       167 kv~v~~dd~~~~~i~~s~~----------~Yd~~~~~~~~~P~ivtlskIG~~~lVD~T~eEe~~a~s~l~Isv~a~giv  236 (288)
T KOG1612|consen  167 KVIVAFDDDGEVEILLSDE----------EYDLMVKLVENVPLIVTLSKIGTNMLVDPTAEEESVANSGLLISVSAGGIV  236 (288)
T ss_pred             ccccccccCCceeeccCcc----------cchhhhhhcccCCEEEEEEeecceEEccCCccHHHhhhcceEEEEecCcce
Confidence            9998  3 44444322211          122233456789999999999999999999999999999999999999988


Q ss_pred             EEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 022140          258 VSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME  300 (302)
Q Consensus       258 ~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~~  300 (302)
                      .++++.|++.+.++. +.+|++.+++..+.++..+.+.|+++|
T Consensus       237 s~~r~VG~G~l~~s~-i~~mle~~~~~~e~l~~~l~k~L~~~e  278 (288)
T KOG1612|consen  237 SCTRSVGLGDLDPSS-IPEMLEQGKAVVETLAPDLVKSLENEE  278 (288)
T ss_pred             EEEEEecCCCCChhh-HHHHHHHHHHHHHhhhHHHHHHhhhhh
Confidence            889999987799995 999999999999999999999998876

>PRK00173 rph ribonuclease PH; Reviewed

Probab=100.00  E-value=4.2e-46  Score=329.63  Aligned_cols=231  Identities=22%  Similarity=0.340  Sum_probs=203.6

Q ss_pred             CCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCC-CCCCcceEEEEEecCCCCCCCcc-----C
Q 022140           36 IRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSL-ESPDEGCVSIDFHMPPICSPLVR-----P  109 (302)
Q Consensus        36 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~-~~p~~g~l~v~V~~~~~~~~~~~-----~  109 (302)
                      +|+|||+++++|++.+++|++++++|||+|++|+|+|+|+|++++..|.. ..|++|.++++++++|++++.++     .
T Consensus         1 ~R~DGR~~~e~R~i~~~~g~~~~a~GSa~v~~G~T~Vla~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~~~~~~~~~~   80 (238)
T PRK00173          1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGMLPRATHTRNDREAAK   80 (238)
T ss_pred             CCCCCCCcccccCeEEEeCCCCCCCeeEEEEecCcEEEEEEEcCCCCCCccCCCCcEEEEEEEecCCCCCcccccccccC
Confidence            59999999999999999999999999999999999999999999988854 45788999999999999988762     4


Q ss_pred             CCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCce
Q 022140          110 GRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKI  189 (302)
Q Consensus       110 g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~  189 (302)
                      |++++.+.+++++|++.|++  .+|++.|    ++.  .++|+++||++|||++||+++|+++||+|++++..  +.   
T Consensus        81 g~~~~~~~~~sr~i~r~lr~--~i~l~~l----~~~--~i~v~v~VL~~DG~~~~aai~Aa~~AL~da~~~~~--~~---  147 (238)
T PRK00173         81 GKQGGRTQEIQRLIGRSLRA--VVDLKAL----GER--TITIDCDVIQADGGTRTASITGAYVALADALNKLV--AR---  147 (238)
T ss_pred             CCCCccHHHHHHHHHHHHHH--hcCHHHc----CCe--EEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhhh--cc---
Confidence            66778899999999999996  8999887    343  46667778999999999999999999999985411  11   


Q ss_pred             eecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccC-Cccc
Q 022140          190 VMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPG-GAVL  268 (302)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G-~~~~  268 (302)
                                        .+..++.++++|+++|++++++.+|+|||.+||+++++.++|++++.|+||++++.| |..+
T Consensus       148 ------------------~~~~~ip~~~~~~~vt~~~~~~~~lvDpt~~Ee~~~~~~l~v~~~~~~~i~~v~~~g~g~~~  209 (238)
T PRK00173        148 ------------------GKLKKNPLKDQVAAVSVGIVDGEPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTAEGAPF  209 (238)
T ss_pred             ------------------CcccCCcccCceeEEEEEEECCEEEECCCHHHHhcCCceEEEEECCCCCEEEEEccCCCCCc
Confidence                              122346689999999999999999999999999999999999999999999999965 5689


Q ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022140          269 AYTSAVQDCIALTRQRVKELHQILEEAISG  298 (302)
Q Consensus       269 ~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~  298 (302)
                      +.++ +.+|+++|.+.+++|+++++++|++
T Consensus       210 ~~e~-l~~~i~~A~~~~~~l~~~~~~~l~~  238 (238)
T PRK00173        210 SREE-LDALLDLAEKGIAELVALQKAALAD  238 (238)
T ss_pred             CHHH-HHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            9996 9999999999999999999999864

>TIGR01966 RNasePH ribonuclease PH

Probab=100.00  E-value=1.6e-44  Score=319.21  Aligned_cols=228  Identities=18%  Similarity=0.326  Sum_probs=200.0

Q ss_pred             CCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCC-CCcceEEEEEecCCCCCCCc---c--CC
Q 022140           37 RPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLES-PDEGCVSIDFHMPPICSPLV---R--PG  110 (302)
Q Consensus        37 R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~-p~~g~l~v~V~~~~~~~~~~---~--~g  110 (302)
                      |+|||+++|+|++++++|++++|+|||+|++|+|+|+|+|+++...|...+ |++|.+.+++++.|++++.+   .  .|
T Consensus         1 R~DGR~~~e~R~i~i~~G~~~~A~GSa~v~~G~T~Vla~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~~~~~r~~~~g   80 (236)
T TIGR01966         1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQTRNRRESAKG   80 (236)
T ss_pred             CCCCCCCCCccCeEEEeCCcCCCCceEEEEecCCEEEEEEEccCccCCcccCCCcEEEEEEEecCCCCCCCCccccccCC
Confidence            899999999999999999999999999999999999999999887776554 57899999999999998755   1  35


Q ss_pred             CCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCcee
Q 022140          111 RPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIV  190 (302)
Q Consensus       111 ~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~~  190 (302)
                      ++++.+.++++++++.+++  .|+++.|    ++  +.|+|+++||++|||++|||++|+++||+|++++....      
T Consensus        81 ~~~~~~~e~~~~i~r~lr~--~i~l~~l----~~--~~i~I~v~VL~~DG~~~~aai~Aa~aAL~da~~~~~~~------  146 (236)
T TIGR01966        81 KQSGRTQEIQRLIGRALRA--VVDLEAL----GE--RTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKR------  146 (236)
T ss_pred             CCCccHHHHHHHHHHHHHH--hcCHhhc----CC--eEEEEEEEEEeCCCCHHHHHHHHHHHHHHHHHHhhhhc------
Confidence            6666788999999999996  7998877    23  36788888999999999999999999999996642100      


Q ss_pred             ecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccC-CcccC
Q 022140          191 MLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPG-GAVLA  269 (302)
Q Consensus       191 ~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G-~~~~~  269 (302)
                                       .....+.|+++|+++|++++++.+|+|||.+||+++++.++++++.+++||++++.| +..++
T Consensus       147 -----------------~~~~~ip~~~~~~~vt~~~~~~~~v~Dpt~~Ee~~~~~~l~l~~~~~~~i~~i~~~g~~~~~~  209 (236)
T TIGR01966       147 -----------------GILKESPIRDFVAAVSVGIVDGEPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFS  209 (236)
T ss_pred             -----------------CcccCCCccCceeEEEEEEECCEEEECCChhHHhccCceEEEEEcCCCCEEEEEecCCCCCcC
Confidence                             011236689999999999999999999999999999999999999999999999965 56899


Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022140          270 YTSAVQDCIALTRQRVKELHQILEEAI  296 (302)
Q Consensus       270 ~~~~l~~~i~~A~~~~~~l~~~l~~~l  296 (302)
                      .++ +.+|+++|.+++++++++++++|
T Consensus       210 ~~~-l~~~i~~a~~~~~~l~~~~~~~l  235 (236)
T TIGR01966       210 RDE-LNKLLDLAKKGIRELIELQKQAL  235 (236)
T ss_pred             HHH-HHHHHHHHHHHHHHHHHHHHHHh
Confidence            996 99999999999999999999987

This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and modification of tRNA precursors. This model is restricted absolutely to bacteria. Related families outside the model include proteins described as probable exosome complex exonucleases (rRNA processing) and polyribonucleotide nucleotidyltransferases (mRNA degradation). The most divergent member within the family is RNase PH from Deinococcus radiodurans.

>PRK03983 exosome complex exonuclease Rrp41; Provisional

Probab=100.00  E-value=3.6e-44  Score=318.64  Aligned_cols=224  Identities=21%  Similarity=0.290  Sum_probs=199.9

Q ss_pred             HHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeee--ccCCCCCCCcceEEEEEecCCCCCCCcc
Q 022140           31 HLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEV--MTPSLESPDEGCVSIDFHMPPICSPLVR  108 (302)
Q Consensus        31 ~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v--~~p~~~~p~~g~l~v~V~~~~~~~~~~~  108 (302)
                      ++++++|+|||+++++|++++++|++++++|||++++|+|+|+|+|+|+.  ..|....|++|.+.++++++|+++..++
T Consensus         9 ~~~~~~R~DGR~~~~~R~i~i~~G~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~p~~~~~~~   88 (244)
T PRK03983          9 ILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSVDERK   88 (244)
T ss_pred             hccCCCCCCCCCcCcccceEEEeCCCCCCCeEEEEEECCeEEEEEEecCCccccccccCCCcEEEEEEEEcCCCcccccc
Confidence            46889999999999999999999999999999999999999999999854  4455667899999999999999886544


Q ss_pred             CCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCc
Q 022140          109 PGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGK  188 (302)
Q Consensus       109 ~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~  188 (302)
                      .+.+++++.+++++|++.|++.  +.++.   +|   .|.|+|.++||++|||+++|+++|+++||.|+++|        
T Consensus        89 ~~~~~~~~~~~s~~l~~~l~~~--i~~~~---~p---~~~I~I~i~VL~~DG~~~~aai~Aa~lAL~dagIp--------  152 (244)
T PRK03983         89 RPGPDRRSIEISKVIREALEPA--IMLEL---FP---RTVIDVFIEVLQADAGTRVAGITAASLALADAGIP--------  152 (244)
T ss_pred             CCCCChhHHHHHHHHHHHHHHh--ccHHh---CC---CeEEEEEEEEEECCCCHHHHHHHHHHHHHHhcCCc--------
Confidence            4456778899999999999975  33332   34   47899999999999999999999999999999998        


Q ss_pred             eeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEc-CCCcEEEEEccCCcc
Q 022140          189 IVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLD-SSNQLVSLYKPGGAV  267 (302)
Q Consensus       189 ~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~-~~g~i~~i~~~G~~~  267 (302)
                                                ++++|.++|++++++.+++|||.+||+++++.++|+++ ..|+|+++++.|  .
T Consensus       153 --------------------------~~~~v~avtv~~~~~~~i~DPt~~Ee~~~~~~l~va~~~~~~~I~~l~~~G--~  204 (244)
T PRK03983        153 --------------------------MRDLVAGCAVGKVDGVIVLDLNKEEDNYGEADMPVAIMPRLGEITLLQLDG--N  204 (244)
T ss_pred             --------------------------cccceeEEEEEEECCEEEECCCHHHhccCCceEEEEEECCCCCEEEEEEec--C
Confidence                                      57899999999999999999999999999999999998 578999999988  6


Q ss_pred             cChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          268 LAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       268 ~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      ++.++ +.+|+++|.+.+++|+++|+++|+++
T Consensus       205 ~~~~~-~~~~i~~A~~~~~~i~~~i~~~l~~~  235 (244)
T PRK03983        205 LTREE-FLEALELAKKGIKRIYQLQREALKSK  235 (244)
T ss_pred             cCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            78886 99999999999999999999999864

>TIGR02065 ECX1 archaeal exosome-like complex exonuclease 1

Probab=100.00  E-value=1.5e-43  Score=312.10  Aligned_cols=223  Identities=22%  Similarity=0.305  Sum_probs=198.0

Q ss_pred             HhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeee--ccCCCCCCCcceEEEEEecCCCCCCCccC
Q 022140           32 LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEV--MTPSLESPDEGCVSIDFHMPPICSPLVRP  109 (302)
Q Consensus        32 l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v--~~p~~~~p~~g~l~v~V~~~~~~~~~~~~  109 (302)
                      +.+++|+|||+++|+|++.+++|++++++|||++++|+|+|+|+|+|+.  ..+....|++|.+.++++++|+++..++.
T Consensus         4 ~~~~~R~DGR~~~e~R~~~~~~g~~~~a~GSa~~~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~~~a~~~~~~   83 (230)
T TIGR02065         4 LEDGVRLDGRKPDELRPIKIEAGVLKNADGSAYVEFGGTKIIAAVYGPREMHPRHLQLPDRAVLRVRYHMAPFSTDERKR   83 (230)
T ss_pred             cCCCcCCCCCCcccccCeEEEECCCCCCCeEEEEEECCcEEEEEEeCCCccccccccCCCceEEEEEEEeCCcccCCccC
Confidence            5789999999999999999999999999999999999999999999954  34445668899999999999998865544


Q ss_pred             CCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCce
Q 022140          110 GRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKI  189 (302)
Q Consensus       110 g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~  189 (302)
                      +.+++++.+++++|++.+++.  +.++.   +|+   +.|+|.++||++||++++|+++|+++||.|++||         
T Consensus        84 ~~~~~~~~~~s~~l~~~l~~~--i~~~~---~p~---~~i~i~v~vl~~DG~~~~aai~aa~lAL~dagIp---------  146 (230)
T TIGR02065        84 PGPSRREIEISKVIREALEPA--ILLEQ---FPR---TAIDVFIEVLQADAGTRCAGLTAASLALADAGIP---------  146 (230)
T ss_pred             CCCCccHHHHHHHHHHHHHHH--hChhh---cCC---eEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCCc---------
Confidence            557788999999999999974  44442   342   5677788899999999999999999999999998         


Q ss_pred             eecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEc-CCCcEEEEEccCCccc
Q 022140          190 VMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLD-SSNQLVSLYKPGGAVL  268 (302)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~-~~g~i~~i~~~G~~~~  268 (302)
                                               |++++.++|++++++.+++|||.+||+.+.+.++|++. ..++++++++.|  .+
T Consensus       147 -------------------------~~~~v~avtv~~~~~~~v~Dpt~~Ee~~~~~~l~va~~~~~~~i~~i~~~g--~~  199 (230)
T TIGR02065       147 -------------------------MRDLVVGVAVGKVDGVVVLDLNEEEDMYGEADMPVAMMPKLGEITLLQLDG--DM  199 (230)
T ss_pred             -------------------------cccceeeEEEEEECCeEEECCCHHHhhcCCCceEEEEeCCCCCEEEEEEec--Cc
Confidence                                     57899999999999999999999999999999999985 478999999988  68


Q ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          269 AYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       269 ~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      ++++ +.+|++.|.+++++++++++++|+++
T Consensus       200 ~~e~-~~~~l~~a~~~~~~l~~~~~~~l~~~  229 (230)
T TIGR02065       200 TPDE-FRQALDLAVKGIKIIYQIQREALKNK  229 (230)
T ss_pred             CHHH-HHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            8886 99999999999999999999999875

This family contains the archaeal protein orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in Sulfolobus solfataricus, so members of this family are designated exosome complex exonuclease 1, after usage in SwissProt.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=100.00  E-value=9.4e-37  Score=304.26  Aligned_cols=242  Identities=17%  Similarity=0.181  Sum_probs=206.2

Q ss_pred             cHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEE-eeeccCCC----CCCC
Q 022140           15 EVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK-MEVMTPSL----ESPD   89 (302)
Q Consensus        15 ~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-~~v~~p~~----~~p~   89 (302)
                      -.++|..+.-..+-+-.+.+++|+|||+++|+|++.+++|.+++++|||+++.|+|+|+|+|+ |+......    ....
T Consensus       289 ~~~~~~~~~~~~~r~~il~~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSa~~~~G~Tqvl~~vt~g~~~~~~~~~~~~~~~  368 (684)
T TIGR03591       289 IKEAFKDLEKKIVRERILKEGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQIIDDLEGEY  368 (684)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCcCceEEEeCCCCCCCceEEEEeCCeEEEEEEecCCcccccCCcccCCCc
Confidence            445666666666666667899999999999999999999999999999999999999999997 43211100    1124


Q ss_pred             cceEEEEEecCCCCCCCcc-CCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHH
Q 022140           90 EGCVSIDFHMPPICSPLVR-PGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALL  168 (302)
Q Consensus        90 ~g~l~v~V~~~~~~~~~~~-~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~  168 (302)
                      .|.+.++++++||+++.++ .|++++++..+++++++.|++  .+++      .+.+.|+|+|+++||++|||..+|+++
T Consensus       369 ~~~~~~~y~~~pfs~~e~~~~g~~~rrei~~~~l~~ral~~--~i~~------~~~~p~tI~v~~~VLesdGs~~~Aai~  440 (684)
T TIGR03591       369 RKRFMLHYNFPPYSVGEVGRVGGPGRREIGHGALAERALKA--VLPS------EEEFPYTIRVVSEILESNGSSSMASVC  440 (684)
T ss_pred             cEEEEEEEEcCCCCCCCcCCCCCCChHHHHHHHHHHHHHHH--hcCc------cccCCeEEEEEEEEEeCCCChHHHHHH
Confidence            6899999999999988765 567788999999999999987  4542      245679999999999999999999999


Q ss_pred             HHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEEC-C----EEEECCChHHHhcC
Q 022140          169 SAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHK-N----YILADPTSEEESIM  243 (302)
Q Consensus       169 A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~-~----~~l~DPt~~Ee~~~  243 (302)
                      |+++||+|+++|                                  +.+++.++|+|+++ +    .+++||+.+|+..+
T Consensus       441 aaslAL~dAgvP----------------------------------~~~~Vagvs~gli~~~~~~~~il~D~~~~Ed~~~  486 (684)
T TIGR03591       441 GGSLALMDAGVP----------------------------------IKAPVAGIAMGLIKEGDERFAVLSDILGDEDHLG  486 (684)
T ss_pred             HHHHHHHhcCCC----------------------------------CcCCEEEEEEEEEcCCCcceEEEeCCChHHHhcC
Confidence            999999999999                                  45678999999985 1    59999999999999


Q ss_pred             CceEEEEEcCCCcEEEEEccC-CcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 022140          244 ETLVTVVLDSSNQLVSLYKPG-GAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME  300 (302)
Q Consensus       244 ~~~l~i~~~~~g~i~~i~~~G-~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~~  300 (302)
                      +..++|+.+.+| |+++++.+ +..++.+. |.+|++.|.+++++|++.|++++.++-
T Consensus       487 d~d~~va~t~~g-I~~lq~d~k~~~i~~~~-l~~al~~a~~~~~~I~~~m~~~l~~~~  542 (684)
T TIGR03591       487 DMDFKVAGTRDG-ITALQMDIKIDGITREI-MEQALEQAKEGRLHILGEMNKVISEPR  542 (684)
T ss_pred             CceEEEEEcCCc-eEEEEEEcCcCCcCHHH-HHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            999999999887 99999954 35689995 999999999999999999999998763

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).

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=100.00  E-value=2.5e-36  Score=301.86  Aligned_cols=238  Identities=18%  Similarity=0.216  Sum_probs=201.6

Q ss_pred             cHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCC-------C
Q 022140           15 EVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLE-------S   87 (302)
Q Consensus        15 ~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~-------~   87 (302)
                      -.++|..+.-..+-+..+.+++|+|||+++|+|++.+++|.+++++|||+++.|+|+|+|+|+.  ++|...       .
T Consensus       293 ~~~~~~~~~~~~~r~~il~~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSal~~~G~T~Vl~~vt~--g~~~~~~~~~~~~~  370 (693)
T PRK11824        293 IKEAFKKLEKKIVRRRILEEGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATL--GTLRDEQIIDGLEG  370 (693)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCCCCCcCcccceEEEeCCCCCCCceEEEEECCeEEEEEEec--CCCcccccccccCC
Confidence            3445666655555555568899999999999999999999999999999999999999999972  222221       1


Q ss_pred             CCcceEEEEEecCCCCCCCc-cCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHH
Q 022140           88 PDEGCVSIDFHMPPICSPLV-RPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAA  166 (302)
Q Consensus        88 p~~g~l~v~V~~~~~~~~~~-~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~  166 (302)
                      .++|.+.++++++|+++..+ +.|++++++..+++++++.|++  ++++      ++++.|+|+|+++||++|||..+|+
T Consensus       371 ~~~~~~~~~y~~~pfs~~e~~~~~~~~rre~~~~~li~ral~~--vi~~------~~~~p~~I~v~~~VLe~dGs~~~Aa  442 (693)
T PRK11824        371 EYKKRFMLHYNFPPYSVGETGRVGSPGRREIGHGALAERALEP--VLPS------EEEFPYTIRVVSEILESNGSSSMAS  442 (693)
T ss_pred             CCcEEEEEEEEcCCCCCCCcCCCCCCChhHHHHHHHHHHHHHH--hcCc------ccCCCEEEEEEEEEEecCCCHHHHH
Confidence            26799999999999998766 3566788999999999999987  4443      2456799999999999999999999


Q ss_pred             HHHHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEECC----EEEECCChHHHhc
Q 022140          167 LLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKN----YILADPTSEEESI  242 (302)
Q Consensus       167 ~~A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~----~~l~DPt~~Ee~~  242 (302)
                      ++|+++||+|+++|                                  +.+++.++++|++++    .+++||+..|+..
T Consensus       443 i~aaslAL~dAgvP----------------------------------~~~~Va~vs~gli~~~~~~~il~D~~~~Ed~~  488 (693)
T PRK11824        443 VCGSSLALMDAGVP----------------------------------IKAPVAGIAMGLIKEGDKYAVLTDILGDEDHL  488 (693)
T ss_pred             HHHHHHHHHhcCCC----------------------------------ccCceeEEEEEEEcCCCceEEEcCCChhhHhh
Confidence            99999999999999                                  467889999999853    4899999999999


Q ss_pred             CCceEEEEEcCCCcEEEEEccCC-cccChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022140          243 METLVTVVLDSSNQLVSLYKPGG-AVLAYTSAVQDCIALTRQRVKELHQILEEAISG  298 (302)
Q Consensus       243 ~~~~l~i~~~~~g~i~~i~~~G~-~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~  298 (302)
                      ++..++|+.+.+| |++++..|. ..++.+. |.+|++.|.+.+++|++.|++++..
T Consensus       489 ~d~d~~va~t~~g-i~~lq~d~k~~~i~~~~-l~~al~~a~~g~~~I~~~M~~aI~~  543 (693)
T PRK11824        489 GDMDFKVAGTRDG-ITALQMDIKIDGITREI-LEEALEQAKEGRLHILGKMNEAISE  543 (693)
T ss_pred             CCceEEEEecCCc-eEEEEEecccCCcCHHH-HHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            9999999999887 999995432 1578885 9999999999999999999999864

>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=3.1e-35  Score=253.48  Aligned_cols=220  Identities=21%  Similarity=0.348  Sum_probs=189.6

Q ss_pred             hcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeecc-C-CCCCCCcceEEEEEecCCCCCCCccCC
Q 022140           33 AESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMT-P-SLESPDEGCVSIDFHMPPICSPLVRPG  110 (302)
Q Consensus        33 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~-p-~~~~p~~g~l~v~V~~~~~~~~~~~~g  110 (302)
                      ..+.|+|||+++|.|++.++.|++++++||+++++|+|+|+|+|+|+... | ....+.+|++++.+.+.|+++......
T Consensus         5 ~~~~R~dgR~~delR~i~~~~~~~~~a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~ey~m~p~sT~~R~~~   84 (230)
T COG0689           5 EDGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLPRSTDERKKR   84 (230)
T ss_pred             ccCcCCCCCCcccccceEEEeccccCCCccEEEEeCCeEEEEEEecCCCCCChhhcCCCceEEEEEEecccccccccccc
Confidence            45899999999999999999999999999999999999999999986532 2 234456799999999999987332111


Q ss_pred             CCCC-cHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCce
Q 022140          111 RPAE-AAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKI  189 (302)
Q Consensus       111 ~~~~-~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~  189 (302)
                      .+.+ +.++++++|.++|++  +++++.   +|.   -+|+|++.|+++||+...|+++|+..||.|+++|         
T Consensus        85 ~~~~gR~~eisrli~~al~~--~i~L~~---~p~---~~I~i~~dVlqaDggTrta~It~A~lAL~DAgip---------  147 (230)
T COG0689          85 EADRGRTKEISRLIGRALRA--VIDLEL---LPE---STIDIDCDVLQADGGTRTASITGASLALADAGIP---------  147 (230)
T ss_pred             cccccchhHHHHHHHHHHHH--Hhhhhh---cCc---cEEEEEEEEEECCCCeeeehhhHHHHHHHHcCCc---------
Confidence            1223 689999999999986  677754   454   4899999999999999999999999999999988         


Q ss_pred             eecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCc---EEEEEccCCc
Q 022140          190 VMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQ---LVSLYKPGGA  266 (302)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~---i~~i~~~G~~  266 (302)
                                               +.++..++|+|++++.+++|++.+|++.+.+.++|++..+|+   |.+++..|  
T Consensus       148 -------------------------l~~~vaaiSvgi~~~~~~lDl~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~~--  200 (230)
T COG0689         148 -------------------------LRDLVAAISVGIVDGVIVLDLDYEEDSAAEADMNVVMTGNGGLVEIQGLAEDG--  200 (230)
T ss_pred             -------------------------hhhheeEeEEEEECCceEecCcchhhcccccCceEEEEecCCeEEEEEEeccC--
Confidence                                     456788999999999999999999999999999999988775   77777766  


Q ss_pred             ccChHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022140          267 VLAYTSAVQDCIALTRQRVKELHQILEEAIS  297 (302)
Q Consensus       267 ~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~  297 (302)
                      +++.++ +.+++++|.+.++++++.++++|.
T Consensus       201 ~~~~de-l~~lL~la~~g~~~~~~~~~~al~  230 (230)
T COG0689         201 PFTEDE-LLELLDLAIKGCNELRELQREALA  230 (230)
T ss_pred             CcCHHH-HHHHHHHHHHHHHHHHHHHHHHhC
Confidence            789998 999999999999999999999873

>KOG1068 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=3.9e-33  Score=239.32  Aligned_cols=222  Identities=21%  Similarity=0.221  Sum_probs=189.0

Q ss_pred             hcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCC--CCCCCcceEEEEEecCCCCCCCccC-
Q 022140           33 AESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPS--LESPDEGCVSIDFHMPPICSPLVRP-  109 (302)
Q Consensus        33 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~--~~~p~~g~l~v~V~~~~~~~~~~~~-  109 (302)
                      .++.|.|||.+++.|++....|++.+++|||+++.|||+|+|.|+||-....  ..+|+.+.++|.+.+.+|....++. 
T Consensus        10 eeg~r~dgRr~~elR~i~~~~g~~~~a~GSay~E~GnTKVl~aV~GPre~~~~~~~~~~~a~lnc~~~~a~Fst~~r~~~   89 (245)
T KOG1068|consen   10 EEGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCEVSSAQFSTGDRKKR   89 (245)
T ss_pred             ccccccCCCChhHhhhhhhhcCccccCCccchhhcCCeEEEEEEeCCcccccccccccccceEEEEEeeeccccchhccC
Confidence            5799999999999999999999999999999999999999999999754321  2357889999999998887655432 


Q ss_pred             CCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCce
Q 022140          110 GRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKI  189 (302)
Q Consensus       110 g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~  189 (302)
                      -+.+.++.+++.+|++++.+  +|.++   ++|.   .+|+|.|+||++||+.+.+|+||+.+||.|++||         
T Consensus        90 ~~~~rr~~e~s~~L~~afe~--~I~~~---lyPr---sqIDI~v~VleddG~~laa~inaatlAL~daGI~---------  152 (245)
T KOG1068|consen   90 PKGDRREKELSLMLQQAFEP--VILLE---LYPR---SQIDIYVQVLEDDGSNLAAAINAATLALADAGIP---------  152 (245)
T ss_pred             CCccHHHHHHHHHHHHHHHH--HHHhh---hCcc---ccceEEEEEEECCCccHHHHHHHHHHHHHHcCCC---------
Confidence            12346788999999999986  45443   4674   5999999999999999999999999999999998         


Q ss_pred             eecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCC-CcEEEEEccCCccc
Q 022140          190 VMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSS-NQLVSLYKPGGAVL  268 (302)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~-g~i~~i~~~G~~~~  268 (302)
                                               |.++..++|.++.++.+++||+..||......++|++-.+ +++..+++.+  .+
T Consensus       153 -------------------------m~D~i~~~t~~l~~~~~l~Dl~~~eesa~~~~ltVa~l~~~~~i~~l~~~~--~~  205 (245)
T KOG1068|consen  153 -------------------------MYDLITACTAGLADGTPLLDLTSLEESARAPGLTVAALPNREEIALLQLDE--RL  205 (245)
T ss_pred             -------------------------hhhhhhhceeeecCCccccccccchhhccCCceEEEEecCcceEEEEEecC--CC
Confidence                                     5788889999999999999999999999988999987654 4688888887  45


Q ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          269 AYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       269 ~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      +.+. |...++.|...|+++++.++..+.++
T Consensus       206 ~~d~-l~~vl~~a~~~c~~v~~~l~~~l~~~  235 (245)
T KOG1068|consen  206 HCDH-LETVLELAIAGCKRVYERLRLVLREH  235 (245)
T ss_pred             CHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6774 99999999999999999888877653

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=100.00  E-value=3.1e-31  Score=265.49  Aligned_cols=236  Identities=15%  Similarity=0.190  Sum_probs=195.3

Q ss_pred             HHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEE-eeeccC-CCC----CCCc
Q 022140           17 DAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK-MEVMTP-SLE----SPDE   90 (302)
Q Consensus        17 ~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-~~v~~p-~~~----~p~~   90 (302)
                      .+|..+.-..+.+..+.++.|+|||++++.|++.+++|.+++++|||+++.|+|+|+|+|+ |+...+ ..+    .+..
T Consensus       419 ~~~~~~~k~~~R~~i~~~g~R~DGR~~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVLatVtlGp~~~~q~~d~l~~~~~~  498 (891)
T PLN00207        419 LVFKEVTSKFLRRRIVEGGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEV  498 (891)
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCCCcCccceEEEEeCCcCCCCceEEEEECCeEEEEEEEecCccccccccccccccce
Confidence            4556665555555567889999999999999999999999999999999999999999997 442111 111    2456


Q ss_pred             ceEEEEEecCCCCCCCc-cCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCe--eeEEEEEEEEEecCCCCHHHHHH
Q 022140           91 GCVSIDFHMPPICSPLV-RPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGK--AAWMVYLDIYCLDADGALFDAAL  167 (302)
Q Consensus        91 g~l~v~V~~~~~~~~~~-~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~--~~w~i~v~v~Vl~~dG~l~da~~  167 (302)
                      +.+.+++.++|++.... +.|++++++..+++++++.|++  .        +|++  +.|.|+|+++||++||+...|++
T Consensus       499 ~~f~~~y~fPPfs~ge~~r~g~psrREi~hg~L~eRALrp--v--------ip~~~~fP~tIrV~~~VLesDGSssmAaV  568 (891)
T PLN00207        499 KRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERALEP--I--------LPSEDDFPYTIRVESTITESNGSSSMASV  568 (891)
T ss_pred             eeEEEEEEcCCCCCccccCCCCCCHHHHHHHHHHHHHHHH--h--------CCcccCCCEEEEEEEEEEeCCCChHHHHH
Confidence            88999999999986543 4567788899999999999997  2        3433  67999999999999999999999


Q ss_pred             HHHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEE-C--------CE-EEECCCh
Q 022140          168 LSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILH-K--------NY-ILADPTS  237 (302)
Q Consensus       168 ~A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~-~--------~~-~l~DPt~  237 (302)
                      +|+++||+|+++|                                  |+++..++++|++ +        .. +++||+.
T Consensus       569 ~aaSLALmDAGIP----------------------------------mk~~VAGvsvGli~d~~~~~~~g~~~IL~Dp~g  614 (891)
T PLN00207        569 CGGCLALQDAGVP----------------------------------VKCPIAGIAMGMVLDTEEFGGDGSPLILSDITG  614 (891)
T ss_pred             HHHHHHHHhcCCC----------------------------------ccCceeEEEEEEEecccccCCCCcEEEEeCCCH
Confidence            9999999999999                                  5677889999998 2        23 5679999


Q ss_pred             HHHhcCCceEEEEEcCCCcEEEEEccCCc-ccChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022140          238 EEESIMETLVTVVLDSSNQLVSLYKPGGA-VLAYTSAVQDCIALTRQRVKELHQILEEAISG  298 (302)
Q Consensus       238 ~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~-~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~  298 (302)
                      .|+..++..+.|+.+.+ .|++++..+.. .++.+. |.+++++|.+.+..|++.|++++..
T Consensus       615 ~Ed~~gdmDfkVAgT~~-gIt~iqmd~k~~gis~e~-l~eAL~~A~~g~~~Il~~M~~~i~~  674 (891)
T PLN00207        615 SEDASGDMDFKVAGNED-GITAFQMDIKVGGITLPI-MERALLQAKDGRKHILAEMSKCSPP  674 (891)
T ss_pred             HHHhcCCceEEEEeccc-ceEEEEEecccCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            99999999999997764 58898875532 478885 9999999999999999999999864

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.97  E-value=2.3e-29  Score=247.46  Aligned_cols=240  Identities=16%  Similarity=0.183  Sum_probs=198.9

Q ss_pred             cHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEe-eecc-CCC---CCCC
Q 022140           15 EVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKM-EVMT-PSL---ESPD   89 (302)
Q Consensus        15 ~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~-~v~~-p~~---~~p~   89 (302)
                      -..+|..+....+.+..++++.|+|||+++++|++.+++|.+++++|||+++.|+|+|+|.+++ +... ...   ...+
T Consensus       314 i~~~~~~~~k~~~r~~il~~g~R~DGR~~~eiR~i~~~~g~l~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~  393 (719)
T TIGR02696       314 ISAAYRAVTKKLVRERVLTEGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPET  393 (719)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCCCCCccccccceeecCCCCCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccc
Confidence            3456777888888888889999999999999999999999999999999999999999998774 1100 001   1245


Q ss_pred             cceEEEEEecCCCCCCCcc-CCCCCCcHHHHHHHHHHHhhcCCCcc-cccceeecCeeeEEEEEEEEEecCCCCHHHHHH
Q 022140           90 EGCVSIDFHMPPICSPLVR-PGRPAEAAPVVAKQLSDTISSSGMIN-LKELSLVGGKAAWMVYLDIYCLDADGALFDAAL  167 (302)
Q Consensus        90 ~g~l~v~V~~~~~~~~~~~-~g~~~~~~~~ls~~l~~~l~~~~~i~-~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~  167 (302)
                      .+.+.+++.|+||+....+ .+.++.++..++++++++|++  +++ ++.   +|    .+|.+...||++||+...|++
T Consensus       394 ~~~~~~~YnfpPFSt~er~~~~~~~RReighg~La~rALe~--vI~~~e~---fP----~TIrvvseVLeSdGSss~AsI  464 (719)
T TIGR02696       394 SKRYMHHYNFPPYSTGETGRVGSPKRREIGHGALAERALVP--VLPSREE---FP----YAIRQVSEALGSNGSTSMGSV  464 (719)
T ss_pred             cceEEEEEeCCCCcccCCCCCCCCCccHHHHHHHHHHHHHH--hhCcHhh---CC----CEEEEEEEeeccCCcHHHHHH
Confidence            6889999999999876543 344567889999999999986  454 333   44    358888899999999999999


Q ss_pred             HHHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEECC--------EEEECCChHH
Q 022140          168 LSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKN--------YILADPTSEE  239 (302)
Q Consensus       168 ~A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~--------~~l~DPt~~E  239 (302)
                      +|+++||+|+++|                                  |+++..++++|++++        .+|+||+..|
T Consensus       465 caasLALmDAGVP----------------------------------mkd~VAgis~Gli~e~~~~~~~~~iL~Di~g~E  510 (719)
T TIGR02696       465 CASTLSLLNAGVP----------------------------------LKAPVAGIAMGLISDEVDGETRYVALTDILGAE  510 (719)
T ss_pred             HHHHHHHHHcCcc----------------------------------hhheeeEEEEEEeccccCCCcceeEEeCCCchh
Confidence            9999999999999                                  578888999999843        2899999999


Q ss_pred             HhcCCceEEEEEcCCCcEEEEEccCCc-ccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          240 ESIMETLVTVVLDSSNQLVSLYKPGGA-VLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       240 e~~~~~~l~i~~~~~g~i~~i~~~G~~-~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      +...+..+.++.+. +.+++++..|.. .++.+. +.+++++|.+.+..|++.|+++|..-
T Consensus       511 D~~Gdmdfkvagt~-~gIt~lQmd~ki~gi~~e~-l~~aL~~A~~g~~~Il~~m~~al~~p  569 (719)
T TIGR02696       511 DAFGDMDFKVAGTS-EFVTALQLDTKLDGIPASV-LASALKQARDARLAILDVMAEAIDTP  569 (719)
T ss_pred             hhcCCceEEEEecC-CCEEEEEEEeeECCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence            99999999997665 569999987743 368885 99999999999999999999998753

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=99.97  E-value=1.4e-29  Score=253.36  Aligned_cols=202  Identities=20%  Similarity=0.233  Sum_probs=174.9

Q ss_pred             cceEEEeCCcc-CCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCCC--C----Cc--cCCCCCCcHH
Q 022140           47 RNTTISMGAVA-SADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICS--P----LV--RPGRPAEAAP  117 (302)
Q Consensus        47 R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~~--~----~~--~~g~~~~~~~  117 (302)
                      |++.+++|.++ +|+|||+|++|+|+|+|+|+++.. |   ++..+++.++|+|.+.+.  .    .|  +.|++++.+.
T Consensus        14 r~i~~e~G~ia~qAdGSa~v~~G~T~VlatV~~~~~-~---~~~~df~pL~v~y~e~~~A~gkiP~~f~kreg~pse~ei   89 (693)
T PRK11824         14 RTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKE-P---KEGQDFFPLTVDYEEKTYAAGKIPGGFFKREGRPSEKET   89 (693)
T ss_pred             ccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCC-C---CCCCCeeeeEEEEEehhhhccCCCcccccCCCCCChHHH
Confidence            79999999996 699999999999999999999765 3   355788889999876542  2    23  5688999999


Q ss_pred             HHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCH-HH-HHHHHHHHHHhhCCCCcEEecCCceeecCcc
Q 022140          118 VVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGAL-FD-AALLSAVAAFSNLQIPTVSLDDGKIVMLPEE  195 (302)
Q Consensus       118 ~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l-~d-a~~~A~~~AL~~~~iP~~~~~~~~~~~~~~~  195 (302)
                      .+++++++.|++          ++|+.++|.++|+++||++||+. .| ||++|+++||.++++|               
T Consensus        90 l~srlIdR~lrp----------lfp~~~~~~i~I~~~VL~~Dg~~~~d~aai~aAsaAL~~s~IP---------------  144 (693)
T PRK11824         90 LTSRLIDRPIRP----------LFPKGFRNEVQVVATVLSVDPENDPDILAMIGASAALSISGIP---------------  144 (693)
T ss_pred             HHHHHHhhhHHH----------hCCCCCCeEEEEEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCC---------------
Confidence            999999999997          27888899999999999999965 67 7999999999999999               


Q ss_pred             ccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHH
Q 022140          196 QKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQ  275 (302)
Q Consensus       196 ~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~  275 (302)
                                         +.+++.++++|++++.+++|||.+|++.++..++|+.+.+ .++.++ .|+..++.++ +.
T Consensus       145 -------------------~~~~v~av~vg~i~g~~ivdPt~~E~~~s~~~l~va~t~~-~i~mie-~~~~~l~e~~-l~  202 (693)
T PRK11824        145 -------------------FNGPIAAVRVGYIDGEFVLNPTVEELEESDLDLVVAGTKD-AVLMVE-SEAKELSEEV-ML  202 (693)
T ss_pred             -------------------cCCCeEEEEEEEECCEEEEcCCHHHHhhCcceEEEEEccC-ceEEEE-CCCCCCCHHH-HH
Confidence                               3567889999999999999999999999999999998765 455554 5656799996 99


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          276 DCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       276 ~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      +|+++|++.++++++++++.+++.
T Consensus       203 ~al~~a~~~~~~i~~~~~~~~~~~  226 (693)
T PRK11824        203 EAIEFGHEAIQELIDAQEELAAEA  226 (693)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999999988754

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=99.97  E-value=1.8e-29  Score=252.13  Aligned_cols=202  Identities=17%  Similarity=0.212  Sum_probs=172.8

Q ss_pred             cceEEEeCCc-cCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCCC--C----Cc--cCCCCCCcHH
Q 022140           47 RNTTISMGAV-ASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICS--P----LV--RPGRPAEAAP  117 (302)
Q Consensus        47 R~i~i~~g~l-~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~~--~----~~--~~g~~~~~~~  117 (302)
                      |++.+++|.+ ++|+|||++++|+|+|+|+|+++.. |   ++..+++.++|+|.+.++  .    .|  +.|++++.+.
T Consensus         5 R~i~ie~G~la~~AdGSa~v~~G~T~VlatV~~~~~-~---~~~~df~pL~vey~e~~~A~gkipg~f~kReg~p~~~ei   80 (684)
T TIGR03591         5 RTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKE-A---KEGQDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSEKET   80 (684)
T ss_pred             ccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCC-C---CCCCceEeEEEEEEehhhhccCCCCCcccCCCCCCHHHH
Confidence            7999999999 4799999999999999999999753 2   344678888888876442  2    22  5688999999


Q ss_pred             HHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHH-H-HHHHHHHHHHhhCCCCcEEecCCceeecCcc
Q 022140          118 VVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALF-D-AALLSAVAAFSNLQIPTVSLDDGKIVMLPEE  195 (302)
Q Consensus       118 ~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~-d-a~~~A~~~AL~~~~iP~~~~~~~~~~~~~~~  195 (302)
                      .+++++++.+++          .+|++++|.|+|+++||++||+.. | ||++|+++||.++++|               
T Consensus        81 l~srlIdR~lrp----------lfp~~~~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL~~s~IP---------------  135 (684)
T TIGR03591        81 LTSRLIDRPIRP----------LFPKGFRNEVQVVATVLSYDPENDPDILAIIGASAALAISGIP---------------  135 (684)
T ss_pred             HHHHHHhhHHHH----------hcCCCCCceEEEEEEEEecCcCCchHHHHHHHHHHHHHhcCCC---------------
Confidence            999999999986          388889999999999999999974 6 9999999999999999               


Q ss_pred             ccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHH
Q 022140          196 QKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQ  275 (302)
Q Consensus       196 ~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~  275 (302)
                                         +++++.+++++++++.+++|||.+|++.++..++++.+.+ .++.+ +.|+..++.++ +.
T Consensus       136 -------------------~~~~v~av~vg~idg~~ildPt~~E~~~s~~~l~va~t~~-~i~mi-e~~~~~i~e~~-l~  193 (684)
T TIGR03591       136 -------------------FNGPIAAVRVGYIDGQYVLNPTVDELEKSDLDLVVAGTKD-AVLMV-ESEAKELSEEV-ML  193 (684)
T ss_pred             -------------------cCCCeEEEEEEEECCEEEEcCCHHHHhhCCceEEEEccCC-cEEEE-EcCCCCCCHHH-HH
Confidence                               4678899999999999999999999999999998875432 35444 55666799996 99


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          276 DCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       276 ~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      +|+++|++.+++++++++++++++
T Consensus       194 ~al~~a~~~~~~i~~~~~~~~~~~  217 (684)
T TIGR03591       194 GAIEFGHEEIQPVIEAIEELAEEA  217 (684)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999988764

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).

>KOG1069 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]

Probab=99.96  E-value=2.8e-28  Score=202.14  Aligned_cols=201  Identities=19%  Similarity=0.344  Sum_probs=169.0

Q ss_pred             CCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeecc-CCCCCCCcceEEEEEecCCCCCCCccCCCCCCcHHHHHHHH
Q 022140           45 RARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMT-PSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQL  123 (302)
Q Consensus        45 e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~-p~~~~p~~g~l~v~V~~~~~~~~~~~~g~~~~~~~~ls~~l  123 (302)
                      +.|++.++.|.|+++|||+.+++|+|+|+|+|+||... .+.+.|++..+++.+  .|.+      |.....++.++++|
T Consensus         4 ~lr~~~cei~iLsr~dGSs~fsqgdT~V~c~V~GP~dvk~r~E~~~katleVi~--rp~~------G~~~~~eK~~e~iI   75 (217)
T KOG1069|consen    4 RLRGIACEISILSRPDGSSEFSQGDTKVICSVYGPIDVKARQEDPEKATLEVIW--RPKS------GVNGTVEKVLERII   75 (217)
T ss_pred             hhhhhhhhhceecCCCCccceecCCcEEEEEeeCCcchhhcccCchhceEEEEE--eccc------CcchHHHHHHHHHH
Confidence            68999999999999999999999999999999998753 335566666666655  4543      44455678999999


Q ss_pred             HHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCceeecCccccccccCc
Q 022140          124 SDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEK  203 (302)
Q Consensus       124 ~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~  203 (302)
                      .++|.+  +|.+   -++|.+   .|.|.++|+++||+.+.+|+||+++||.|+|+|                       
T Consensus        76 ~~tl~~--~I~l---~l~Prt---~iqVsiqvv~ddgs~LacaINaAclALvDaGIp-----------------------  124 (217)
T KOG1069|consen   76 RKTLSK--AIIL---ELYPRT---TIQVSIQVVEDDGSTLACAINAACLALVDAGIP-----------------------  124 (217)
T ss_pred             HHHHHH--hhee---eecCCc---eEEEEEEEEecCCcchHHHHHHHHHHHHhcCCc-----------------------
Confidence            999975  4443   246754   799999999999999999999999999999999                       


Q ss_pred             CccccccccccCCCccEEEEEEEECC-EEEECCChHHHhcCCceEEEEEc----CCCcEEEEEccCCcccChHHHHHHHH
Q 022140          204 EPVNKEKRKLTLGGIPFSLTCILHKN-YILADPTSEEESIMETLVTVVLD----SSNQLVSLYKPGGAVLAYTSAVQDCI  278 (302)
Q Consensus       204 ~~~~~~~~~l~i~~~p~~vt~~~~~~-~~l~DPt~~Ee~~~~~~l~i~~~----~~g~i~~i~~~G~~~~~~~~~l~~~i  278 (302)
                                 ++++++++.+++.++ .+++|||..+|+.+.+..++++-    ..-+++.+...|  .++.+| |..++
T Consensus       125 -----------l~~mfcai~~~~~~d~~lv~Dpt~~qek~~~~~~~lsf~~~~~~~~~vi~s~t~G--~~~~d~-lf~~l  190 (217)
T KOG1069|consen  125 -----------LRSMFCAISCALHEDGVLVLDPTAKQEKISTARATLSFEGGSLGEPKVIISETNG--EKSEDQ-LFYVL  190 (217)
T ss_pred             -----------hHHhhhhceEEEecCccEEECCcHHhhhhhhceEEEEEecCCCCCcceEEEeccC--CCCHHH-HHHHH
Confidence                       578999999998875 89999999999988888777763    234799999988  668887 99999


Q ss_pred             HHHHHHHHHHHHHHHHHhhc
Q 022140          279 ALTRQRVKELHQILEEAISG  298 (302)
Q Consensus       279 ~~A~~~~~~l~~~l~~~l~~  298 (302)
                      +.|...+++++.++++.+++
T Consensus       191 e~a~~~~~~~f~f~r~~~q~  210 (217)
T KOG1069|consen  191 ELAQAAAQSLFPFYREVLQR  210 (217)
T ss_pred             HhhHHHHHHHHHHHHHHHHh
Confidence            99999999999999999875

>PF01138 RNase_PH: 3' exoribonuclease family, domain 1 This Prosite family only includes Ribonuclease PH; InterPro: IPR001247 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function

Probab=99.96  E-value=8.2e-28  Score=194.12  Aligned_cols=128  Identities=32%  Similarity=0.544  Sum_probs=113.3

Q ss_pred             CCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeecc-CCCCCC-CcceEEEEEecCCCCCCCccC-CCCCCcHHHHHH
Q 022140           45 RARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMT-PSLESP-DEGCVSIDFHMPPICSPLVRP-GRPAEAAPVVAK  121 (302)
Q Consensus        45 e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~-p~~~~p-~~g~l~v~V~~~~~~~~~~~~-g~~~~~~~~ls~  121 (302)
                      |+|++.+++|.+++++|||+|++|+|+|+|+|++++.. |..+++ .+|.+.++|+++|++...++. +.+++.+..+++
T Consensus         1 e~R~i~i~~~~~~~a~GSa~v~~G~T~V~~~V~~~~~~~~~~~~~~~~g~~~v~v~~~~~~~~~~~~~~~~~~~~~~l~~   80 (132)
T PF01138_consen    1 ELRPISIETGVLPRADGSARVSLGNTKVICSVKGPIEPPPSNERDDAEGRLTVEVEFSPFASPSFRRGGRPDEEERELSS   80 (132)
T ss_dssp             CBEEEEEEESSSSSSSEEEEEEETTEEEEEEEEEEEEGCSCSTTSSSSEEEEEEEEECCCGSTSSSSSSSTHHHHHHHHH
T ss_pred             CCccEEEEeCCCCCCCeEEEEEECCeEEEEEEEecccccchhcccCCCceEEEEEEeccccccccccccccchhHHHHHH
Confidence            79999999999999999999999999999999999987 555434 358999999999999877653 556678889999


Q ss_pred             HHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCC-CHHHHHHHHHHHHHhhCCCC
Q 022140          122 QLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADG-ALFDAALLSAVAAFSNLQIP  180 (302)
Q Consensus       122 ~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG-~l~da~~~A~~~AL~~~~iP  180 (302)
                      +|+++|++...        .+++++|+|+|+++||++|| |++||+++|+++||+|+++|
T Consensus        81 ~l~~~l~~~~~--------~~~~~~~~i~v~v~vl~~dG~~~~~a~~~A~~~AL~~~~iP  132 (132)
T PF01138_consen   81 LLERALRSSIL--------LEGYPRWQIHVDVQVLSDDGGNLLDAAINAACLALLDAGIP  132 (132)
T ss_dssp             HHHHHHHHTBS--------TTTTSSEEEEEEEEEEECSSSSHHHHHHHHHHHHHHHHTCS
T ss_pred             HHhhhcccccc--------ccccCceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCC
Confidence            99999987432        36777899999999999999 99999999999999999998

An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 1, which has a core 2-layer alpha/beta structure with a left-handed crossover, similar to that found in ribosomal protein S5. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; PDB: 2C38_G 2BR2_O 2C37_M 3L7Z_A 2JEB_A 2C39_A 2JEA_A 2JE6_A 3U1K_A 4AM3_B ....

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.90  E-value=3.4e-22  Score=200.76  Aligned_cols=202  Identities=15%  Similarity=0.166  Sum_probs=168.4

Q ss_pred             cceEEEeCCcc-CCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCCCC------Cc--cCCCCCCcHH
Q 022140           47 RNTTISMGAVA-SADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSP------LV--RPGRPAEAAP  117 (302)
Q Consensus        47 R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~~~------~~--~~g~~~~~~~  117 (302)
                      |++.+++|.+. +|+||+.++.|+|.|+|+|...- .|   ++..+++.+.|+|....+.      .|  |.|++++.+.
T Consensus        89 ~~~~~etG~~a~qA~gav~v~~g~t~vl~t~~~~~-~~---~~~~dF~PLtV~y~Ek~~AaGkipggf~kREgrp~d~ei  164 (891)
T PLN00207         89 RHILVETGHIGRQASGSVTVTDGETIVYTSVCLAD-VP---SEPSDFFPLSVHYQERFSAAGRTSGGFFKREGRTKDHEV  164 (891)
T ss_pred             EEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEecc-CC---CCCCCccceeEeeeeehhhcCccCCceeccCCCCChHHH
Confidence            47999999998 59999999999999999998632 22   2345789999999754332      12  4688999999


Q ss_pred             HHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCC--HHHHHHHHHHHHHhhCCCCcEEecCCceeecCcc
Q 022140          118 VVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGA--LFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEE  195 (302)
Q Consensus       118 ~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~--l~da~~~A~~~AL~~~~iP~~~~~~~~~~~~~~~  195 (302)
                      .+++++++.|++  .        +|..++....|.++||++||+  ...+|++|+++||.+++||               
T Consensus       165 L~sRlIdR~lRP--l--------fp~~~~~etQI~i~VLsaDg~~~pd~~AInAASaAL~~SgIP---------------  219 (891)
T PLN00207        165 LICRLIDRPLRP--T--------MPKGFYHETQILSWVLSYDGLHSPDSLAVTAAGIAVALSEVP---------------  219 (891)
T ss_pred             HHHHHHCccchh--h--------ccccCCCCcEEEEEEEeeCCCCChhhHHHHHHHHHHHhhCCC---------------
Confidence            999999999997  2        444444567778899999998  5678999999999999999               


Q ss_pred             ccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHH
Q 022140          196 QKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQ  275 (302)
Q Consensus       196 ~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~  275 (302)
                                         ++++..+|++|.+++.+++|||.+|++.++..|.|+.+.+ .|++++..| ..++.++ +.
T Consensus       220 -------------------~~gpVaAVrVG~idg~~VlnPt~~E~~~s~ldLvvagt~~-~IvMIE~~a-~e~see~-l~  277 (891)
T PLN00207        220 -------------------NLKAIAGVRVGLIGGKFIVNPTTKEMEESELDLIMAGTDS-AILMIEGYC-NFLPEEK-LL  277 (891)
T ss_pred             -------------------ccCceEEEEEEEECCEEEECCCHHHHhcCCeeEEEEEcCC-eEEEEEcCC-CCCCHHH-HH
Confidence                               5677889999999999999999999999999998887754 588887654 4578886 99


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          276 DCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       276 ~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      +++++|++.++.+.+++++.++++
T Consensus       278 ~Al~~a~~aik~i~~~~~el~~~~  301 (891)
T PLN00207        278 EAVEVGQDAVRAICKEIEVLVKKC  301 (891)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999988764

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]

Probab=99.86  E-value=1.4e-20  Score=176.54  Aligned_cols=233  Identities=18%  Similarity=0.257  Sum_probs=186.4

Q ss_pred             ccHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccC-----CCCCC
Q 022140           14 MEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTP-----SLESP   88 (302)
Q Consensus        14 ~~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p-----~~~~p   88 (302)
                      --.+.|..+.-+.|-...++.+.|.|||.+++.|+|.++.+.++..+||++++-|.|+|+|+|+..-.+.     +...|
T Consensus       336 ~i~~~fn~vskkv~Rs~i~~~gkR~DGR~ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~  415 (760)
T KOG1067|consen  336 EIIESFNTVSKKVFRSRILEEGKRCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGP  415 (760)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcccccCCcchhhhcccceecCccccccchhhhhcCceeEEEEEEcCCHHHhhhhhhhccC
Confidence            3456788888999999999999999999999999999999999999999999999999999999731110     01133


Q ss_pred             Cc-ceEEEEEecCCCCCCCc-cCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHH
Q 022140           89 DE-GCVSIDFHMPPICSPLV-RPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAA  166 (302)
Q Consensus        89 ~~-g~l~v~V~~~~~~~~~~-~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~  166 (302)
                      ++ +.+.++++|+|.+...- +-|..+.++.--..+-++.|.+          ++|..+.|+|+|.-.||+.+|+--.|.
T Consensus       416 ~~~~~FmLhY~FPPyat~Evgkig~~nRRE~GhgaLAEkaL~~----------vlP~dfPftIRv~SeVleSnGSsSMAS  485 (760)
T KOG1067|consen  416 DNGINFMLHYEFPPYATNEVGKIGGLNRRELGHGALAEKALLP----------VLPEDFPFTIRVTSEVLESNGSSSMAS  485 (760)
T ss_pred             ccCceEEEEeccCCccccccccccCCcccccCchhHhhhhhhc----------cCcccCceEEEEeeeeeecCCcchHHh
Confidence            44 49999999999987643 2244455555566677777754          467778899999999999999999999


Q ss_pred             HHHHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEE-----------CCEEEECC
Q 022140          167 LLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILH-----------KNYILADP  235 (302)
Q Consensus       167 ~~A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~-----------~~~~l~DP  235 (302)
                      ..+-++||+|+++|.-....                                  .|.+|+.           +..++.|.
T Consensus       486 vCGGslALmDaGvPv~a~vA----------------------------------GvaiGlvt~td~e~g~i~dyriltDI  531 (760)
T KOG1067|consen  486 VCGGSLALMDAGVPVSAHVA----------------------------------GVAIGLVTKTDPEKGEIEDYRILTDI  531 (760)
T ss_pred             hhcchhhhhhcCCccccccc----------------------------------eeEEEeEeccCcccCCcccceeehhh
Confidence            99999999999999432211                                  2222322           23689999


Q ss_pred             ChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022140          236 TSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISG  298 (302)
Q Consensus       236 t~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~  298 (302)
                      ...|....+..+.|+-++.| ++.+   |   ++.+ +++++++.|..+..+|.+.|.+.+..
T Consensus       532 lGiEd~~GDMDFKiAGt~dG-vTA~---g---i~l~-Iv~eal~~a~~ar~~Il~~m~k~i~~  586 (760)
T KOG1067|consen  532 LGIEDYNGDMDFKIAGTNDG-VTAL---G---IPLK-IVMEALQKAREARLQILDIMEKNINS  586 (760)
T ss_pred             cchhhhcCCcceeeccccCc-ceec---C---CcHH-HHHHHHHhhhHHHHHHHHHHHhhcCC
Confidence            99999999999999998887 6666   3   4567 69999999999999999999987653

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.80  E-value=8.1e-18  Score=166.21  Aligned_cols=203  Identities=17%  Similarity=0.167  Sum_probs=168.8

Q ss_pred             cceEEEeCCcc-CCCeeEEEEe-CCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCCCC------Cc--cCCCCCCcH
Q 022140           47 RNTTISMGAVA-SADGSALAKI-GSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSP------LV--RPGRPAEAA  116 (302)
Q Consensus        47 R~i~i~~g~l~-~a~GSa~v~~-G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~~~------~~--~~g~~~~~~  116 (302)
                      |++.+++|.+. +|+||+.+++ |+|.|+|++...- +|   ++..+++.+.|+|....+.      .|  |.|+|++.+
T Consensus        17 ~~~~~etG~~A~qA~Gav~v~~~G~t~vl~t~~~~~-~~---~~~~dF~PLtV~y~Ek~yA~GkiPggf~kREgrps~~e   92 (719)
T TIGR02696        17 RTIRFETGRLARQAAGSVVAYLDDETMLLSATTASK-QP---KDQFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDA   92 (719)
T ss_pred             EEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecC-CC---CCCCCCcceeEeeeehhhhcCccCCceeccCCCCChhh
Confidence            47999999998 5999999999 9999999998631 22   2346789999999765432      12  468899999


Q ss_pred             HHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCC-HHH-HHHHHHHHHHhhCCCCcEEecCCceeecCc
Q 022140          117 PVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGA-LFD-AALLSAVAAFSNLQIPTVSLDDGKIVMLPE  194 (302)
Q Consensus       117 ~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~-l~d-a~~~A~~~AL~~~~iP~~~~~~~~~~~~~~  194 (302)
                      ...+++++|.+|+          ++|..++..++|.++||++|+. ..| .+++|+++||.-+.||              
T Consensus        93 iL~sRliDR~iRP----------LFp~~~~~e~qi~~~vls~D~~~~pdvla~~~ASaAl~iSdiP--------------  148 (719)
T TIGR02696        93 ILTCRLIDRPLRP----------SFVKGLRNEVQVVVTVLSLNPDHLYDVVAINAASASTQLAGLP--------------  148 (719)
T ss_pred             hHHHHhhCCCCcc----------CCCCCCCcceEEEEEEEEcCCCCChHHHHHHHHHHHHHhcCCC--------------
Confidence            9999999999997          4888888899999999999985 345 5789999999999998              


Q ss_pred             cccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcC----CCcEEEEEcc-------
Q 022140          195 EQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDS----SNQLVSLYKP-------  263 (302)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~----~g~i~~i~~~-------  263 (302)
                                          ++....+|.+|.+++.+++.||.+|-+.++-.|+|+-++    ++.+++++..       
T Consensus       149 --------------------f~gPv~~vrVg~i~g~~viNPt~~~~~~s~ldLvvagt~~~~~~~~i~MiE~~a~~~~~~  208 (719)
T TIGR02696       149 --------------------FSGPIGGVRVALIDGQWVAFPTHEQLEGAVFDMVVAGRVLENGDVAIMMVEAEATEKTWD  208 (719)
T ss_pred             --------------------CCCceEEEEEEEECCEEEECcCHHHHhhCeeeEEEEeeecCCCCccEEEEecCCcccccc
Confidence                                355567899999999999999999999988889998876    4478888852       


Q ss_pred             ----CCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022140          264 ----GGAVLAYTSAVQDCIALTRQRVKELHQILEEAISG  298 (302)
Q Consensus       264 ----G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~  298 (302)
                          |+..++.++ |.++|.+|++..+.+.+++++..+.
T Consensus       209 ~~~~~a~e~~e~~-~~~Ai~~a~~~i~~~~~~~~~l~~~  246 (719)
T TIGR02696       209 LVKGGAEAPTEEV-VAEGLEAAKPFIKVLCRAQADLAEK  246 (719)
T ss_pred             ccccCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                556788886 9999999999999999998886543

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

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

Probab=99.68  E-value=8.7e-16  Score=148.84  Aligned_cols=236  Identities=17%  Similarity=0.179  Sum_probs=183.7

Q ss_pred             HHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCC-------CCC
Q 022140           16 VDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSL-------ESP   88 (302)
Q Consensus        16 ~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~-------~~p   88 (302)
                      .+.|..+.+..-.+..++.++|+|||..++.|++.++.|.+++++||+++..|.|+.++.++.  +.+..       ..+
T Consensus       292 ~~~~~~l~~~~vR~~Il~~~vR~DGR~~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TL--G~~~d~Qvid~l~~e  369 (692)
T COG1185         292 KAILEKLEKKPVRRLILEGKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTL--GTPRDAQVIDILEGE  369 (692)
T ss_pred             HHHHHHHhHHHHHHHHhcCCcccCCCCcceeeeeeEEecCCCCccchhhhccCCCcceEEEEc--CCcchhhhhhhccch
Confidence            456888888888888889999999999999999999999999999999999999999988886  22221       122


Q ss_pred             CcceEEEEEecCCCCCCC-ccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHH
Q 022140           89 DEGCVSIDFHMPPICSPL-VRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAAL  167 (302)
Q Consensus        89 ~~g~l~v~V~~~~~~~~~-~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~  167 (302)
                      ...++..++.|+|++... .+-|.|+.++.--.++-++++.+  .++.      ..++.++|++--.|++.+|+--.|.+
T Consensus       370 ~~krfm~hYNFPp~SvGE~g~~g~p~RREiGHG~LA~Ral~~--vlp~------~e~fpytiRvVsEi~eSNGSsSmaSV  441 (692)
T COG1185         370 YKKRFLLHYNFPPFSVGETGRMGSPGRREIGHGALAERALAP--VLPS------EEEFPYTIRVVSEILESNGSSSMASV  441 (692)
T ss_pred             hhhheeeeccCCCCCccccCCCCCCCcccccCchhhHHHHhh--hCCc------hhcCCceeeeeehhhcccCcccchhh
Confidence            346789999999998533 23355555666666667777764  2221      12456899999999999999999999


Q ss_pred             HHHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEEC----CEEEECCChHHHhcC
Q 022140          168 LSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHK----NYILADPTSEEESIM  243 (302)
Q Consensus       168 ~A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~----~~~l~DPt~~Ee~~~  243 (302)
                      ++..+||+++++|.-                                  .....+..|++.    ..++.|....|....
T Consensus       442 Cg~sLaLmdAGVPIk----------------------------------~pVAGIAMGLI~eg~~~~vLsDI~G~EDhlG  487 (692)
T COG1185         442 CGGSLALMDAGVPIK----------------------------------APVAGIAMGLIKEGDKYAVLSDILGDEDHLG  487 (692)
T ss_pred             hhhHHHHHhCCCccc----------------------------------ccccchhccceecCCceEeeccccccccccC
Confidence            999999999999942                                  222223344432    257899999999999


Q ss_pred             CceEEEEEcCCCcEEEEEc---cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          244 ETLVTVVLDSSNQLVSLYK---PGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       244 ~~~l~i~~~~~g~i~~i~~---~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      +..+-|+-+..| ++.++.   ..  .++.+ +|.+++..|+.+..++...|.+++...
T Consensus       488 DMDFKVAGT~~G-iTAlQMDiKi~--Git~e-im~~AL~QAk~aRlhIL~~M~~ai~~p  542 (692)
T COG1185         488 DMDFKVAGTDDG-ITALQMDIKIK--GITKE-IMKKALEQAKGARLHILIVMNEAISEP  542 (692)
T ss_pred             CceeEEecCCCc-ceeeeeeeeec--CCCHH-HHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            999999998888 666653   33  35777 699999999999999999999998764

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

Probab=99.65  E-value=8e-15  Score=142.22  Aligned_cols=200  Identities=20%  Similarity=0.195  Sum_probs=164.2

Q ss_pred             cceEEEeCCcc-CCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCCCC------Cc--cCCCCCCcHH
Q 022140           47 RNTTISMGAVA-SADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSP------LV--RPGRPAEAAP  117 (302)
Q Consensus        47 R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~~~------~~--~~g~~~~~~~  117 (302)
                      |++.+++|.+. +|+|++.+++|+|.|++++.+.-  +   ++..+++.+.|+|.-....      .|  |.|+|++.+.
T Consensus        14 ~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~--~---~~~~dF~PLtV~y~Ek~yaaGkiPGgf~kREGrpse~e~   88 (692)
T COG1185          14 RTLTLETGKIARQANGAVLVRYGDTVVLATVVASK--P---KEGQDFFPLTVNYEEKTYAAGKIPGGFFKREGRPSEKEI   88 (692)
T ss_pred             eeEEEEcchhhhhcCccEEEEECCeEEEEEEeecC--C---CCCCCccceeEeeeeehhccCcCCCcccccCCCCCccch
Confidence            79999999998 69999999999999999999853  2   2356788888888643221      12  5799999999


Q ss_pred             HHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHH-H-HHHHHHHHHHhhCCCCcEEecCCceeecCcc
Q 022140          118 VVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALF-D-AALLSAVAAFSNLQIPTVSLDDGKIVMLPEE  195 (302)
Q Consensus       118 ~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~-d-a~~~A~~~AL~~~~iP~~~~~~~~~~~~~~~  195 (302)
                      ..++++++-+++          ++|..+..-++|..+|+++|+... | .+++|+++||.-+++|.              
T Consensus        89 L~sRLIDRpiRP----------lFp~g~~~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iPf--------------  144 (692)
T COG1185          89 LTSRLIDRPIRP----------LFPKGFRNEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPF--------------  144 (692)
T ss_pred             hhhhhccccccc----------ccchhhccceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCc--------------
Confidence            999999998886          477667778999999999998653 3 67899999999999884              


Q ss_pred             ccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHH
Q 022140          196 QKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQ  275 (302)
Q Consensus       196 ~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~  275 (302)
                                          .....++++|++++.+++.||.+|-+.++-.++|+-+++ .|.+++. |...++.++ +.
T Consensus       145 --------------------~gpi~~vrvg~idg~~vlNPt~~e~~~s~lDlvVAGT~~-aV~MVE~-~a~~l~E~~-ml  201 (692)
T COG1185         145 --------------------LGPIGAVRVGYIDGIFVLNPTLEELEESKLDLVVAGTKD-AVNMVES-EADELDEEV-ML  201 (692)
T ss_pred             --------------------cCccceEEEEEECCEEEECCChHHhhhcceeeEecCChh-hhheeec-ccccCCHHH-HH
Confidence                                455568999999999999999999998888888876665 4666654 556788775 99


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhc
Q 022140          276 DCIALTRQRVKELHQILEEAISG  298 (302)
Q Consensus       276 ~~i~~A~~~~~~l~~~l~~~l~~  298 (302)
                      +++..+++..+.+.+++++....
T Consensus       202 ~Av~fg~~~~~~~~~~qe~l~~~  224 (692)
T COG1185         202 EAVEFGHEAIQSVINAQEELALE  224 (692)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999998887654

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]

Probab=99.47  E-value=4.8e-13  Score=126.38  Aligned_cols=203  Identities=19%  Similarity=0.225  Sum_probs=155.2

Q ss_pred             CCcceEEEeCCccC-CCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCCCC------Cc--cCCCCCCc
Q 022140           45 RARNTTISMGAVAS-ADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSP------LV--RPGRPAEA  115 (302)
Q Consensus        45 e~R~i~i~~g~l~~-a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~~~------~~--~~g~~~~~  115 (302)
                      --|.+.+++|.+.+ |+||+.++.|+|.|+++|.+.- .|.   |.+ ++.+.|+|.-..+.      .|  |.|++++.
T Consensus        54 GnR~i~~etGklaRfAngsvvv~~GeT~Vm~Tv~~a~-~PS---p~q-FlPL~VdYqeK~aAvGRip~~fmRREg~tkdk  128 (760)
T KOG1067|consen   54 GNREILFETGKLARFANGSVVVQMGETAVMTTVVLAD-KPS---PPQ-FLPLVVDYQEKFAAVGRIPGNFMRREGRTKDK  128 (760)
T ss_pred             CCeEEEEecchhhhhcCCcEEEccCCeEEEEEEEecC-CCC---ccc-cceEEEehhhhhhhhccCCCcccccccCCcch
Confidence            46899999999996 9999999999999999998742 232   223 88889988754321      11  45777888


Q ss_pred             HHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCH-HH-HHHHHHHHHHhhCCCCcEEecCCceeecC
Q 022140          116 APVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGAL-FD-AALLSAVAAFSNLQIPTVSLDDGKIVMLP  193 (302)
Q Consensus       116 ~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l-~d-a~~~A~~~AL~~~~iP~~~~~~~~~~~~~  193 (302)
                      +....+++.+.+++          .+|.-++....+-..+|..||-. -| .+++|+.+||.-..+|             
T Consensus       129 EiL~~rLidrsirp----------lfp~g~~~etqi~~n~Ls~dG~~~pdvlainaas~Al~lsdvp-------------  185 (760)
T KOG1067|consen  129 EILTGRLIDRPIRP----------LFPKGFYHETQILCNVLSSDGVHDPDVLAINAASAALSLSDVP-------------  185 (760)
T ss_pred             hheeeecccccccc----------CCcccchhHHHHHhhheecccccCchHHHHhHHHHHhhhccCC-------------
Confidence            88888989888876          24444444455556677888843 23 4789999999998888             


Q ss_pred             ccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHH
Q 022140          194 EEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSA  273 (302)
Q Consensus       194 ~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~  273 (302)
                                           ++....++.+|++++.++++||..|.+.++-.+.++.+ ..+++.++..+. .+..++ 
T Consensus       186 ---------------------w~gpig~vRigLi~Ge~vVNPT~kEmssS~Lnlvvagt-~~~~vmle~~s~-~i~qqd-  241 (760)
T KOG1067|consen  186 ---------------------WNGPIGAVRIGLIDGEFVVNPTRKEMSSSQLNLVVAGT-KSQTVMLEGSSN-NILQQD-  241 (760)
T ss_pred             ---------------------CCCceeeeEeeeecceEEeCcchhhhhhccceeEEEec-cceEEEEEcccc-cccHHH-
Confidence                                 23444578999999999999999999998888888877 557888876654 456665 


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          274 VQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       274 l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      +.++++.+...++++..-+....+++
T Consensus       242 l~~Aikvg~~~~q~~i~~i~~L~k~~  267 (760)
T KOG1067|consen  242 LLHAIKVGVKEAQQIIQGIERLAKKY  267 (760)
T ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHh
Confidence            99999999999999988877766553

>PF03725 RNase_PH_C: 3' exoribonuclease family, domain 2 This Prosite family only includes Ribonuclease PH; InterPro: IPR015847 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function

Probab=99.43  E-value=6.6e-13  Score=94.54  Aligned_cols=67  Identities=27%  Similarity=0.509  Sum_probs=60.6

Q ss_pred             CccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcc-cChHHHHHHHHHHHHHH
Q 022140          217 GIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAV-LAYTSAVQDCIALTRQR  284 (302)
Q Consensus       217 ~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~-~~~~~~l~~~i~~A~~~  284 (302)
                      ++|+++|++++++.+++|||.+||+++++.++++++++++++.+.+.|+.. +++++ +.+|+++|+++
T Consensus         1 ~~~~avt~~~i~~~~v~Dpt~~Ee~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~-l~~~i~~A~~~   68 (68)
T PF03725_consen    1 DPPVAVTVGIIDGELVVDPTAEEESLSDSSLTLAVDGTGNICTLQKSGGGSELSEDQ-LEEAIELAKKA   68 (68)
T ss_dssp             SEEEEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSSEEEEEEEEESSEEEHHH-HHHHHHHHHHH
T ss_pred             CCeEEEEEEEECCEEEECCCHHHHhhcCCcEEEEEECCCCEEEEEEcCCCCCCCHHH-HHHHHHHHhcC
Confidence            579999999999999999999999999999999999999999999998876 99996 99999999864

An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents the phosphorolytic (PH) domain 2, which has a core 3-layer alpha/beta/alpha structure. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes []. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 2NN6_E 2WNR_A 3U1K_B 2BA0_H 2BA1_H 3M85_G 3M7N_H 3H1C_K ....

>PF03726 PNPase: Polyribonucleotide nucleotidyltransferase, RNA binding domain; InterPro: IPR015848 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function

Probab=86.49  E-value=0.46  Score=34.69  Aligned_cols=29  Identities=34%  Similarity=0.243  Sum_probs=20.8

Q ss_pred             ccHHHHhhhChHHHHHHHHhcCCCCCCCC
Q 022140           14 MEVDAFRRLFPLRYFERHLAESIRPDARS   42 (302)
Q Consensus        14 ~~~~~~~~~~p~~f~~~~l~~~~R~DGR~   42 (302)
                      .-..+|..+.-...-...|..++|+|||+
T Consensus        55 ~i~~~~~~l~k~~vR~~Il~~~~R~DGR~   83 (83)
T PF03726_consen   55 EIKEAFEELEKKIVREMILEEGIRIDGRK   83 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTSBTTTS-B
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Confidence            34456777777777777788899999995

An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents an RNA-binding phosphorolytic (PH) domain found in bacterial and organelle PNPases, but not in exosomes. It usually occurs in combination with PH domain 1 (IPR001247 from INTERPRO) and PH domain 2 (IPR015847 from INTERPRO), both of which are found in PNPases and exosomes. The core structure of the RNA-binding PH domain consists of a DNA/RNA-binding 3-helical bundle. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0000175 3'-5'-exoribonuclease activity, 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 3U1K_B 3GCM_A 3GLL_A 3GME_A 4AM3_B 4AID_C 4AIM_A 1WHU_A ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	302
2nn6_C	278	Structure Of The Human Rna Exosome Composed Of Rrp4		4e-44
3m85_G	259	Archaeoglobus Fulgidus Exosome Y70a With Rna Bound		2e-23
2ba0_I	259	Archaeal Exosome Core Length = 259		3e-23
2wnr_A	271	The Structure Of Methanothermobacter Thermautotroph		1e-21
2je6_A	277	Structure Of A 9-Subunit Archaeal Exosome Length =		7e-20
2br2_A	275	Rnase Ph Core Of The Archaeal Exosome Length = 275		8e-20
3l7z_A	271	Crystal Structure Of The S. Solfataricus Archaeal E		2e-19
2pnz_B	277	Crystal Structure Of The P. Abyssi Exosome Rnase Ph		2e-19
2nn6_A	358	Structure Of The Human Rna Exosome Composed Of Rrp4		3e-16
2nn6_E	305	Structure Of The Human Rna Exosome Composed Of Rrp4		4e-10
2wp8_A	305	Yeast Rrp44 Nuclease Length = 305		1e-08
4ifd_A	304	Crystal Structure Of An 11-subunit Eukaryotic Exoso		1e-08
2br2_B	248	Rnase Ph Core Of The Archaeal Exosome Length = 248		3e-05
3l7z_B	245	Crystal Structure Of The S. Solfataricus Archaeal E		3e-05
2je6_B	250	Structure Of A 9-Subunit Archaeal Exosome Length =		3e-05

>pdb|2NN6|C Chain C, Structure Of The Human Rna Exosome Composed Of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40 Length = 278

Iteration: 1
 Score =  174 bits (442), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 92/285 (32%), Positives = 158/285 (55%), Gaps = 16/285 (5%)
Query: 18  AFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK 77
            F+ + PL Y+ R L E+ RPD R L   R TT+++G++++ADGSAL K+G+TT++  +K
Sbjct: 6   GFKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVK 65
Query: 78  MEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKE 137
            E   PS ++PD+G V  +  +PP+CS   R G P E A V ++ ++D I +S +I  ++
Sbjct: 66  AEFAAPSTDAPDKGYVVPNVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKED 125
Query: 138 LSLVGGKAAWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXX 197
           L +  GK  W++Y D+ C             + +AA  N+Q+P V++++           
Sbjct: 126 LCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINE----------- 174
Query: 198 XXXXXXXPVN-KEKRKLTLGGIPFSLT-CILHKNYILADPTSEEESIMETLVTVVLDSSN 255
                   VN K+K  L +   P + +  +     ++ DPT EEE +    +T+V+D   
Sbjct: 175 --ETALAEVNLKKKSYLNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEG 232
Query: 256 QLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME 300
           +L  L+KPGG+ L   + +QDC++    R KE+ ++++E I  M+
Sbjct: 233 KLCCLHKPGGSGLT-GAKLQDCMSRAVTRHKEVKKLMDEVIKSMK 276

>pdb|3M85|G Chain G, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The Active Site Length = 259

Iteration: 1
 Score =  106 bits (264), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 69/268 (25%), Positives = 124/268 (46%), Gaps = 27/268 (10%)
Query: 27  YFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLE 86
           Y    L ++ R D R     R   I    +  A+GSAL K+G T ++  +KM+   P+ +
Sbjct: 13  YVLSKLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPAPD 72
Query: 87  SPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAA 146
           +PD G + ++  + P+ SP   PG P E +  +A+ +   I  S  ++L +L +  G+  
Sbjct: 73  TPDRGVIIVNAELVPLASPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKV 132
Query: 147 WMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXXXXXXXXPV 206
           W+V++DI+              +A+AA  N ++P    D G+  +LP             
Sbjct: 133 WIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLP------------- 179
Query: 207 NKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGA 266
                   +  +P S+T ++  N  L DP+ EE S+ +T +T+  D  + +V++ K GG 
Sbjct: 180 --------VRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITTDKDDNVVAMQKSGGY 231
Query: 267 VL------AYTSAVQDCIALTRQRVKEL 288
           +L             +C    R++ KE+
Sbjct: 232 LLDEKLFDELLDVSINCARKLREKFKEI 259

>pdb|2BA0|I Chain I, Archaeal Exosome Core Length = 259

Iteration: 1
 Score =  105 bits (262), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 69/268 (25%), Positives = 123/268 (45%), Gaps = 27/268 (10%)
Query: 27  YFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLE 86
           Y    L ++ R D R     R   I    +  A+GSAL K+G T ++  +KM+   P  +
Sbjct: 13  YVLSKLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYPD 72
Query: 87  SPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAA 146
           +PD G + ++  + P+ SP   PG P E +  +A+ +   I  S  ++L +L +  G+  
Sbjct: 73  TPDRGVIIVNAELVPLASPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKV 132
Query: 147 WMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXXXXXXXXPV 206
           W+V++DI+              +A+AA  N ++P    D G+  +LP             
Sbjct: 133 WIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLP------------- 179
Query: 207 NKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGA 266
                   +  +P S+T ++  N  L DP+ EE S+ +T +T+  D  + +V++ K GG 
Sbjct: 180 --------VRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITTDKDDNVVAMQKSGGY 231
Query: 267 VL------AYTSAVQDCIALTRQRVKEL 288
           +L             +C    R++ KE+
Sbjct: 232 LLDEKLFDELLDVSINCARKLREKFKEI 259

>pdb|2WNR|A Chain A, The Structure Of Methanothermobacter Thermautotrophicus Exosome Core Assembly Length = 271

Iteration: 1
 Score =  100 bits (248), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 64/263 (24%), Positives = 133/263 (50%), Gaps = 19/263 (7%)
Query: 37  RPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSID 96
           R D RSL   R+ +I  G ++ A+GS+  K+G+T ++  +K ++  P  ++P+ G +  +
Sbjct: 25  RIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKPQIGEPFPDTPEMGVILTN 84
Query: 97  FHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCX 156
             + P+ SP   PG P E +  +++ +   I  S MI+L++L ++ G   WM++LD++  
Sbjct: 85  SELLPMASPTFEPGPPDERSVELSRVVDRCIRESRMIDLEKLCIIEGSKVWMLFLDLHII 144
Query: 157 XXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXXXXXXXXPVNKEKRKLTLG 216
                       + VAA  + +IP   ++DG++V+             PVN++       
Sbjct: 145 DYDGNLFDAAVLATVAALLDTRIPAAEVEDGEVVI-----NREKMQPLPVNRK------- 192
Query: 217 GIPFSLTCILHK--NYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAV 274
               +L C   K  N I+ DP+ EEE I+   +++ +     + ++ K G   L     +
Sbjct: 193 ----ALMCTFAKIGNEIVLDPSLEEEDILTARISIGVTEEGSICAMQKGGEGPLTRDDVL 248
Query: 275 QDCIALTRQRVKELHQILEEAIS 297
           +  +++  ++V +L + L+++++
Sbjct: 249 K-AVSIAVEKVPQLIEYLDKSMT 270

>pdb|2JE6|A Chain A, Structure Of A 9-Subunit Archaeal Exosome Length = 277

Iteration: 1
 Score = 94.4 bits (233), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 65/239 (27%), Positives = 113/239 (47%), Gaps = 21/239 (8%)
Query: 28  FERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLES 87
           FE+     IR D R L+  R  +I++     ADGSAL K+G+T +LA  K+E+  P  ++
Sbjct: 25  FEK----GIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDT 80
Query: 88  PDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAW 147
           P++G + ++  + P+      PG P E A  +A+ +  ++  S  ++L +L +  GK+ W
Sbjct: 81  PNQGNLIVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVW 140
Query: 148 MVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXXXXXXXXPVN 207
            V+LD+Y              ++VAA  N ++  V      I                VN
Sbjct: 141 TVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGI---------------SVN 185
Query: 208 KEK--RKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPG 264
           K +   KL L     +++      Y++ DP  +EESIM+  ++       ++V + K G
Sbjct: 186 KNEVVGKLPLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSG 244

>pdb|2BR2|A Chain A, Rnase Ph Core Of The Archaeal Exosome Length = 275

Iteration: 1
 Score = 94.0 bits (232), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 65/239 (27%), Positives = 113/239 (47%), Gaps = 21/239 (8%)
Query: 28  FERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLES 87
           FE+     IR D R L+  R  +I++     ADGSAL K+G+T +LA  K+E+  P  ++
Sbjct: 23  FEK----GIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDT 78
Query: 88  PDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAW 147
           P++G + ++  + P+      PG P E A  +A+ +  ++  S  ++L +L +  GK+ W
Sbjct: 79  PNQGNLIVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVW 138
Query: 148 MVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXXXXXXXXPVN 207
            V+LD+Y              ++VAA  N ++  V      I                VN
Sbjct: 139 TVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGI---------------SVN 183
Query: 208 KEK--RKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPG 264
           K +   KL L     +++      Y++ DP  +EESIM+  ++       ++V + K G
Sbjct: 184 KNEVVGKLPLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSG 242

>pdb|3L7Z|A Chain A, Crystal Structure Of The S. Solfataricus Archaeal Exosome Length = 271

Iteration: 1
 Score = 93.2 bits (230), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 112/239 (46%), Gaps = 25/239 (10%)
Query: 28  FERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLES 87
           FE+     IR D R L+  R  +I++     ADGSAL K+G+T +LA  K+E+  P  ++
Sbjct: 23  FEK----GIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDT 78
Query: 88  PDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAW 147
           P++G + ++  + P+      PG P E A  +A+ +  ++  S  ++L +L +  GK+ W
Sbjct: 79  PNQGNLIVNVELLPLAYTTFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVW 138
Query: 148 MVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXXXXXXXXPVN 207
            V+LD+Y              ++VAA  N ++  V                       VN
Sbjct: 139 TVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVE-------------------QISVN 179
Query: 208 KEK--RKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPG 264
           K +   KL L     +++      Y++ DP  +EESIM+  ++       ++V + K G
Sbjct: 180 KNEVVGKLPLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSG 238

>pdb|2PNZ|B Chain B, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring Complexed With Udp And Gmp Length = 277

Iteration: 1
 Score = 92.8 bits (229), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 68/268 (25%), Positives = 126/268 (47%), Gaps = 18/268 (6%)
Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEG 91
           L E  R D R     R   I +G +  A+GSAL K+GST +L  IK  +  P  ++P+ G
Sbjct: 22  LKEGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLGEPFPDTPNMG 81
Query: 92  CVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYL 151
            ++ +  + P+ SP   PG P E A  +A+ +   I  S  +NL+++ +V GK   +V++
Sbjct: 82  VMTTNVELVPLASPTFEPGPPDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVFI 141
Query: 152 DIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDD--GKIVMLPXXXXXXXXXXXPVNKE 209
           D++              +A+AA  N ++P V  ++  G++  L                E
Sbjct: 142 DVHVLDHDGNLMDAIGIAAIAALLNARVPKVRYNEETGEVETL---------------DE 186
Query: 210 KRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLA 269
              L +  IP  +T     N ++ DP+ +EE +M+  +T+  D +  + ++ K  G    
Sbjct: 187 TEPLPVEKIPVPVTFAKIGNILVVDPSLDEELVMDGKITITTDETGHISAVQKSEGGAFK 246
Query: 270 YTSAVQDCIALTRQRVKELHQILEEAIS 297
               V   +    ++ +E+ +++ EA+ 
Sbjct: 247 L-EEVMYAVETAFKKAEEIRKLILEAVE 273

>pdb|2NN6|A Chain A, Structure Of The Human Rna Exosome Composed Of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40 Length = 358

Iteration: 1
 Score = 82.4 bits (202), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 55/275 (20%), Positives = 121/275 (44%), Gaps = 17/275 (6%)
Query: 26  RYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSL 85
           R+  R + E  R D R     RN  IS G   +  G  + ++G T +L  +  E+++P L
Sbjct: 29  RFLLRAIEEKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSPKL 85
Query: 86  ESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKA 145
               EG +  +  +  + +P   PGR ++    + + +   + +S  I+ + L +V G+ 
Sbjct: 86  NRATEGILFFNLELSQMAAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEK 145
Query: 146 AWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXXXXXXXXP 205
            W + +D++              +A+ A  + + P VS+   ++ +             P
Sbjct: 146 VWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLY-----------TP 194
Query: 206 VNKEKRKLTLGGIPF--SLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKP 263
             ++   L++  +P   S        Y+L DP   EE +M+ L+ + ++   ++ ++   
Sbjct: 195 EERDPVPLSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSS 254
Query: 264 GGAVLAYTSAVQDCIALTRQRVKELHQILEEAISG 298
           GG +L     ++ C  +   +V E+ +++ +A+  
Sbjct: 255 GGIMLLKDQVLR-CSKIAGVKVAEITELILKALEN 288

>pdb|2NN6|E Chain E, Structure Of The Human Rna Exosome Composed Of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40 Length = 305

Iteration: 1
 Score = 62.0 bits (149), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 40/162 (24%), Positives = 72/162 (44%), Gaps = 8/162 (4%)
Query: 27  YFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLE 86
           Y    + E +R D R     R   +    V++  GSA  K+G T +L  +K E+ TP LE
Sbjct: 27  YIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLE 86
Query: 87  SPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTI----SSSGMINLKELSLVG 142
            P+EG   ++F +   CS    P         +  ++++T+    ++   ++LK L +  
Sbjct: 87  KPNEG--YLEFFVD--CSASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISP 142
Query: 143 GKAAWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSL 184
            +  W++Y+D+               +  AA  N +IP V +
Sbjct: 143 REHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRV 184

>pdb|2WP8|A Chain A, Yeast Rrp44 Nuclease Length = 305

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 60/305 (19%), Positives = 124/305 (40%), Gaps = 40/305 (13%)
Query: 10  LSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGS 69
           ++ ++E+ A    F L      L ++ R D RS  + R+  I+ G      G    K+G+
Sbjct: 1   MAKDIEISASESKFILEA----LRQNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGN 53
Query: 70  TTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGR-PAEAAPVVAKQLSDTIS 128
           T +   I  ++  P  + P EG   I   + P+       G    E   + ++ +  ++ 
Sbjct: 54  TKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQFENGNITGEDEVLCSRIIEKSVR 113
Query: 129 SSGMINLKELSLVGGKAAWMVYLDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGK 188
            SG ++++ L +V G   W V  D++              + +A   + + P +++   +
Sbjct: 114 RSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQ 173
Query: 189 IVMLPXXXXXXXXXXXPVNKEKRKLTLG--GIPFSLTCIL--------------HKNYIL 232
           I++             PVN E+  + LG   IP  +T                 +    +
Sbjct: 174 IIV------------HPVN-EREPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISI 220
Query: 233 ADPTSEEESIMETLVTVVLDSSNQLVSLYKPGG---AVLAYTSAVQDCIALTRQRVKELH 289
            D T +EE + + ++TV L+ + ++V + K GG     L       +  ++  +   ++ 
Sbjct: 221 IDATLKEELLRDGVLTVTLNKNREVVQVSKAGGLPMDALTLMKCCHEAYSIIEKITDQIL 280
Query: 290 QILEE 294
           Q+L+E
Sbjct: 281 QLLKE 285

>pdb|4IFD|A Chain A, Crystal Structure Of An 11-subunit Eukaryotic Exosome Complex Bound To Rna Length = 304

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/283 (19%), Positives = 115/283 (40%), Gaps = 36/283 (12%)
Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEG 91
           L ++ R D RS  + R+  I+ G      G    K+G+T +   I  ++  P  + P EG
Sbjct: 18  LRQNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEG 74
Query: 92  CVSIDFHMPPICSPLVRPGR-PAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVY 150
              I   + P+       G    E   + ++ +  ++  SG ++++ L +V G   W V 
Sbjct: 75  LFVISTEISPMAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVR 134
Query: 151 LDIYCXXXXXXXXXXXXXSAVAAFSNLQIPTVSLDDGKIVMLPXXXXXXXXXXXPVNKEK 210
            D++              + +A   + + P +++   +I++             PVN E+
Sbjct: 135 ADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQIIV------------HPVN-ER 181
Query: 211 RKLTLG--GIPFSLTCIL--------------HKNYILADPTSEEESIMETLVTVVLDSS 254
             + LG   IP  +T                 +    + D T +EE + + ++TV L+ +
Sbjct: 182 EPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLNKN 241
Query: 255 NQLVSLYKPGG---AVLAYTSAVQDCIALTRQRVKELHQILEE 294
            ++V + K GG     L       +  ++  +   ++ Q+L+E
Sbjct: 242 REVVQVSKAGGLPMDALTLMKCCHEAYSIIEKITDQILQLLKE 284

>pdb|2BR2|B Chain B, Rnase Ph Core Of The Archaeal Exosome Length = 248

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/106 (25%), Positives = 53/106 (50%), Gaps = 2/106 (1%)
Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK--MEVMTPSLESPD 89
           L +  R D R     R+  I +G + +ADGSA+ ++G+T  +AA+    E+    L  PD
Sbjct: 14  LDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPD 73
Query: 90  EGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINL 135
              + + +HM P  +   +   P+     ++K + + + S+ ++ L
Sbjct: 74  RAVLRVRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVEL 119

>pdb|3L7Z|B Chain B, Crystal Structure Of The S. Solfataricus Archaeal Exosome Length = 245

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/106 (25%), Positives = 53/106 (50%), Gaps = 2/106 (1%)
Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK--MEVMTPSLESPD 89
           L +  R D R     R+  I +G + +ADGSA+ ++G+T  +AA+    E+    L  PD
Sbjct: 11  LDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPD 70
Query: 90  EGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINL 135
              + + +HM P  +   +   P+     ++K + + + S+ ++ L
Sbjct: 71  RAVLRVRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVEL 116

>pdb|2JE6|B Chain B, Structure Of A 9-Subunit Archaeal Exosome Length = 250

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/106 (25%), Positives = 53/106 (50%), Gaps = 2/106 (1%)
Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK--MEVMTPSLESPD 89
           L +  R D R     R+  I +G + +ADGSA+ ++G+T  +AA+    E+    L  PD
Sbjct: 16  LDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPD 75
Query: 90  EGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINL 135
              + + +HM P  +   +   P+     ++K + + + S+ ++ L
Sbjct: 76  RAVLRVRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVEL 121

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	302
2wnr_A	271	Probable exosome complex exonuclease 2; phosphate	7e-81
2je6_A	277	RRP42, exosome complex exonuclease 2; nuclease, hy	3e-79
2po1_B	277	Probable exosome complex exonuclease 2; RNAse PH,	4e-79
3m7n_G	259	Probable exosome complex exonuclease 2; exosome, R	3e-76
2nn6_C	278	Exosome complex exonuclease RRP43; RNA, exosome, P	3e-75
2nn6_A	358	Polymyositis/scleroderma autoantigen 1; RNA, exoso	2e-74
2nn6_E	305	Exosome complex exonuclease RRP42; RNA, exosome, P	3e-70
2wp8_A	305	Exosome complex component RRP45; nucleus, hydrolas	1e-61
3b4t_A	262	Ribonuclease PH; RNAse, tRNA nucleotidyltransferas	1e-18
1r6l_A	239	Ribonuclease PH; beta-alpha-beta-alpha fold, hexam	1e-17
1udn_A	255	Ribonuclease PH, RNAse PH; transferase, riken stru	1e-17
2wp8_B	246	Exosome complex component SKI6; nucleus, hydrolase	9e-10
2nn6_F	272	MTR3, exosome component 6; RNA, exosome, PM/SCL, p	5e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-08
3krn_A	222	Protein C14A4.5, confirmed by transcript evidence;	2e-07
2po1_A	249	Probable exosome complex exonuclease 1; RNAse PH,	9e-07
2je6_B	250	RRP41, exosome complex exonuclease 1; nuclease, hy	2e-06
3m7n_D	258	Probable exosome complex exonuclease 1; exosome, R	3e-06
3dd6_A	255	Ribonuclease PH; exoribonuclease, tRNA maturation,	3e-06
2wnr_B	240	Probable exosome complex exonuclease 1; phosphate	5e-06
1oys_A	245	Ribonuclease PH; transferase, tRNA processing; 2.4	1e-05
2nn6_B	249	Exosome complex exonuclease RRP41; RNA, exosome, P	2e-05
3hkm_A	246	OS03G0854200 protein; RNAse PH domain, phosphoryla	7e-04

>2wnr_A Probable exosome complex exonuclease 2; phosphate binding, 3'-5' exoribonuclease, hydrolase; 2.65A {Methanothermobacter thermautotrophicusorganism_taxid} Length = 271

 Score =  244 bits (626), Expect = 7e-81
 Identities = 71/271 (26%), Positives = 141/271 (52%), Gaps = 15/271 (5%)

Query: 27  YFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLE 86
                +    R D RSL   R+ +I  G ++ A+GS+  K+G+T ++  +K ++  P  +
Sbjct: 15  SITDLINNKERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKPQIGEPFPD 74

Query: 87  SPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAA 146
           +P+ G +  +  + P+ SP   PG P E +  +++ +   I  S MI+L++L ++ G   
Sbjct: 75  TPEMGVILTNSELLPMASPTFEPGPPDERSVELSRVVDRCIRESRMIDLEKLCIIEGSKV 134

Query: 147 WMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPV 206
           WM++LD++ +D DG LFDAA+L+ VAA  + +IP   ++DG++V+  E            
Sbjct: 135 WMLFLDLHIIDYDGNLFDAAVLATVAALLDTRIPAAEVEDGEVVINRE------------ 182

Query: 207 NKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGA 266
             + + L +       T     N I+ DP+ EEE I+   +++ +     + ++ K G  
Sbjct: 183 --KMQPLPVNRKALMCTFAKIGNEIVLDPSLEEEDILTARISIGVTEEGSICAMQKGGEG 240

Query: 267 VLAYTSAVQDCIALTRQRVKELHQILEEAIS 297
            L     V   +++  ++V +L + L+++++
Sbjct: 241 PLTRDD-VLKAVSIAVEKVPQLIEYLDKSMT 270

>2je6_A RRP42, exosome complex exonuclease 2; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_A* 2jeb_A* 2br2_A 2c37_A* 2c38_A* 2c39_A* 3l7z_A Length = 277

 Score =  241 bits (616), Expect = 3e-79
 Identities = 71/296 (23%), Positives = 136/296 (45%), Gaps = 23/296 (7%)

Query: 1   MGLPNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASAD 60
           M    +++++   ++ +                + IR D R L+  R  +I++     AD
Sbjct: 3   MSSTPSNQNIIPIIKKE---------SIVSLFEKGIRQDGRKLTDYRPLSITLDYAKKAD 53

Query: 61  GSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVA 120
           GSAL K+G+T +LA  K+E+  P  ++P++G + ++  + P+      PG P E A  +A
Sbjct: 54  GSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNLIVNVELLPLAYETFEPGPPDENAIELA 113

Query: 121 KQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP 180
           + +  ++  S  ++L +L +  GK+ W V+LD+Y LD  G + DA  L++VAA  N ++ 
Sbjct: 114 RVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVY 173

Query: 181 TVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEE 240
            V      I +   E                KL L     +++      Y++ DP  +EE
Sbjct: 174 KVEQHSNGISVNKNE-------------VVGKLPLNYPVVTISVAKVDKYLVVDPDLDEE 220

Query: 241 SIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAI 296
           SIM+  ++       ++V + K G   ++    +       R    +L + L++ +
Sbjct: 221 SIMDAKISFSYTPDLKIVGIQKSGKGSMS-LQDIDQAENTARSTAVKLLEELKKHL 275

>2po1_B Probable exosome complex exonuclease 2; RNAse PH, hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus abyssi} PDB: 2po0_B* 2pnz_B 2po2_B* Length = 277

 Score =  240 bits (615), Expect = 4e-79
 Identities = 76/293 (25%), Positives = 137/293 (46%), Gaps = 18/293 (6%)

Query: 8   EDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKI 67
             +S    V    R          L E  R D R     R   I +G +  A+GSAL K+
Sbjct: 2   SHMSDNEIVAGIMRDH----IINLLKEGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKL 57

Query: 68  GSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTI 127
           GST +L  IK  +  P  ++P+ G ++ +  + P+ SP   PG P E A  +A+ +   I
Sbjct: 58  GSTQVLVGIKTSLGEPFPDTPNMGVMTTNVELVPLASPTFEPGPPDERAIELARVIDRGI 117

Query: 128 SSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDG 187
             S  +NL+++ +V GK   +V++D++ LD DG L DA  ++A+AA  N ++P V  ++ 
Sbjct: 118 RESKALNLEKMVIVPGKIVRVVFIDVHVLDHDGNLMDAIGIAAIAALLNARVPKVRYNEE 177

Query: 188 KIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLV 247
              +   +             E   L +  IP  +T     N ++ DP+ +EE +M+  +
Sbjct: 178 TGEVETLD-------------ETEPLPVEKIPVPVTFAKIGNILVVDPSLDEELVMDGKI 224

Query: 248 TVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME 300
           T+  D +  + ++ K  G        V   +    ++ +E+ +++ EA+   +
Sbjct: 225 TITTDETGHISAVQKSEGGAFK-LEEVMYAVETAFKKAEEIRKLILEAVEKAK 276

>3m7n_G Probable exosome complex exonuclease 2; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_H 2ba0_I 3m85_G Length = 259

 Score =  232 bits (594), Expect = 3e-76
 Identities = 78/288 (27%), Positives = 141/288 (48%), Gaps = 31/288 (10%)

Query: 7   SEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAK 66
            ED+  +++ D         Y    L ++ R D R     R   I    +  A+GSAL K
Sbjct: 2   PEDILVDIKRD---------YVLSKLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVK 52

Query: 67  IGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDT 126
           +G T ++  +KM+   P  ++PD G + ++  + P+ SP   PG P E +  +A+ +   
Sbjct: 53  LGDTQVVVGVKMQPGEPYPDTPDRGVIIVNAELVPLASPTFEPGPPDENSIELARVVDRG 112

Query: 127 ISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDD 186
           I  S  ++L +L +  G+  W+V++DI+ LD DG L DA+ L+A+AA  N ++P    D 
Sbjct: 113 IRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDL 172

Query: 187 GKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETL 246
           G+  +LP                     +  +P S+T ++  N  L DP+ EE S+ +T 
Sbjct: 173 GEDYLLP---------------------VRDLPVSVTSLIVGNKYLVDPSREEMSVGDTT 211

Query: 247 VTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEE 294
           +T+  D  + +V++ K GG +L       + + ++    ++L +  +E
Sbjct: 212 LTITTDKDDNVVAMQKSGGYLLD-EKLFDELLDVSINCARKLREKFKE 258

>2nn6_C Exosome complex exonuclease RRP43; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1 Length = 278

 Score =  231 bits (589), Expect = 3e-75
 Identities = 96/285 (33%), Positives = 164/285 (57%), Gaps = 14/285 (4%)

Query: 17  DAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAI 76
             F+ + PL Y+ R L E+ RPD R L   R TT+++G++++ADGSAL K+G+TT++  +
Sbjct: 5   AGFKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGV 64

Query: 77  KMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLK 136
           K E   PS ++PD+G V  +  +PP+CS   R G P E A V ++ ++D I +S +I  +
Sbjct: 65  KAEFAAPSTDAPDKGYVVPNVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKE 124

Query: 137 ELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQ 196
           +L +  GK  W++Y D+ CLD DG + DA   + +AA  N+Q+P V++++   +      
Sbjct: 125 DLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETALAEVNL- 183

Query: 197 KEENSEKEPVNKEKRKLTLGGIPFSLT-CILHKNYILADPTSEEESIMETLVTVVLDSSN 255
                      K+K  L +   P + +  +     ++ DPT EEE +    +T+V+D   
Sbjct: 184 -----------KKKSYLNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEG 232

Query: 256 QLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME 300
           +L  L+KPGG+ L   + +QDC++    R KE+ ++++E I  M+
Sbjct: 233 KLCCLHKPGGSGLT-GAKLQDCMSRAVTRHKEVKKLMDEVIKSMK 276

>2nn6_A Polymyositis/scleroderma autoantigen 1; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1 Length = 358

 Score =  231 bits (590), Expect = 2e-74
 Identities = 67/299 (22%), Positives = 140/299 (46%), Gaps = 24/299 (8%)

Query: 7   SEDLSSEM---EVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSA 63
           S+D +S M    +    R    R+  R + E  R D R     RN  IS G   +  G  
Sbjct: 11  SQDPNSHMKETPLSNCER----RFLLRAIEEKKRLDGRQTYDYRNIRISFG---TDYGCC 63

Query: 64  LAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQL 123
           + ++G T +L  +  E+++P L    EG +  +  +  + +P   PGR ++    + + +
Sbjct: 64  IVELGKTRVLGQVSCELVSPKLNRATEGILFFNLELSQMAAPAFEPGRQSDLLVKLNRLM 123

Query: 124 SDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVS 183
              + +S  I+ + L +V G+  W + +D++ L+ DG + DAA ++A+ A  + + P VS
Sbjct: 124 ERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVS 183

Query: 184 LDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHK--NYILADPTSEEES 241
           +             +E +   P  ++   L++  +P  ++    +   Y+L DP   EE 
Sbjct: 184 VQG-----------DEVTLYTPEERDPVPLSIHHMPICVSFAFFQQGTYLLVDPNEREER 232

Query: 242 IMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME 300
           +M+ L+ + ++   ++ ++   GG +L     V  C  +   +V E+ +++ +A+   +
Sbjct: 233 VMDGLLVIAMNKHREICTIQSSGGIMLL-KDQVLRCSKIAGVKVAEITELILKALENDQ 290

>2nn6_E Exosome complex exonuclease RRP42; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1 Length = 305

 Score =  219 bits (558), Expect = 3e-70
 Identities = 63/274 (22%), Positives = 117/274 (42%), Gaps = 8/274 (2%)

Query: 27  YFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLE 86
           Y    + E +R D R     R   +    V++  GSA  K+G T +L  +K E+ TP LE
Sbjct: 27  YIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLE 86

Query: 87  SPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAA 146
            P+EG +          +P        +    +A  L    ++   ++LK L +   +  
Sbjct: 87  KPNEGYLEFFVDCSASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHC 146

Query: 147 WMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPV 206
           W++Y+D+  L+  G LFDA  ++  AA  N +IP V + +        E+  ++ E    
Sbjct: 147 WVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLED-------EEGSKDIELSDD 199

Query: 207 NKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGA 266
             +  +L++  +P  +T        + D T +EE+     + V + S   +  + K G  
Sbjct: 200 PYDCIRLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKG 259

Query: 267 VLAYTSAVQDCIALTRQRVKELHQILEEAISGME 300
            L    ++ + +   ++  K LH  L+  +   E
Sbjct: 260 SLD-PESIFEMMETGKRVGKVLHASLQSVVHKEE 292

>2wp8_A Exosome complex component RRP45; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} Length = 305

 Score =  196 bits (500), Expect = 1e-61
 Identities = 55/291 (18%), Positives = 126/291 (43%), Gaps = 12/291 (4%)

Query: 10  LSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGS 69
           ++ ++E+ A       ++    L ++ R D RS  + R+  I+ G      G    K+G+
Sbjct: 1   MAKDIEISASES----KFILEALRQNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGN 53

Query: 70  TTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPA-EAAPVVAKQLSDTIS 128
           T +   I  ++  P  + P EG   I   + P+       G    E   + ++ +  ++ 
Sbjct: 54  TKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQFENGNITGEDEVLCSRIIEKSVR 113

Query: 129 SSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGK 188
            SG ++++ L +V G   W V  D++ LD DG   DA+ ++ +A   + + P +++   +
Sbjct: 114 RSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQ 173

Query: 189 IVMLPEEQKEENS---EKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMET 245
           I++ P  ++E         P+              ++    +    + D T +EE + + 
Sbjct: 174 IIVHPVNEREPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDG 233

Query: 246 LVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAI 296
           ++TV L+ + ++V + K GG  +     +  C       ++++   + + +
Sbjct: 234 VLTVTLNKNREVVQVSKAGGLPMD-ALTLMKCCHEAYSIIEKITDQILQLL 283

>3b4t_A Ribonuclease PH; RNAse, tRNA nucleotidyltransferase, RPHA, STRU genomics, TBSGC; 2.10A {Mycobacterium tuberculosis} Length = 262

 Score = 82.6 bits (204), Expect = 1e-18
 Identities = 48/266 (18%), Positives = 90/266 (33%), Gaps = 30/266 (11%)

Query: 35  SIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTP-SLESPDEGCV 93
           S R D R     R   I+ G   +  GS L + G T +L    +    P   ++   G +
Sbjct: 5   SKREDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWL 64

Query: 94  SIDFHMPPICSPLVRPGRPAEAAPV--VAKQLSDTISSSGMINLKELSLVGGKAAWMVYL 151
           + ++ M P  +   R  R +    +    +++S  I  S    L+    +       + +
Sbjct: 65  TAEYAMLPS-ATHSRSDRESVRGRLSGRTQEISRLIGRS----LRACIDLAALGENTIAI 119

Query: 152 DIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKR 211
           D   L ADG    AA+  A  A ++                      + S+  P++    
Sbjct: 120 DCDVLQADGGTRTAAITGAYVALADAVTYLS-------------AAGKLSDPRPLS---- 162

Query: 212 KLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYT 271
                    +++  +    I  D   EE+S  E  + VV   +  LV +   G       
Sbjct: 163 -----CAIAAVSVGVVDGRIRVDLPYEEDSRAEVDMNVVATDTGTLVEIQGTGEGATFAR 217

Query: 272 SAVQDCIALTRQRVKELHQILEEAIS 297
           S +   + +       L     +A++
Sbjct: 218 STLDKLLDMALGACDTLFAAQRDALA 243

>1r6l_A Ribonuclease PH; beta-alpha-beta-alpha fold, hexamer, phosphate bound, transf; HET: NHE; 1.90A {Pseudomonas aeruginosa} SCOP: d.14.1.4 d.101.1.1 PDB: 1r6m_A Length = 239

 Score = 79.4 bits (196), Expect = 1e-17
 Identities = 48/264 (18%), Positives = 98/264 (37%), Gaps = 29/264 (10%)

Query: 36  IRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTP-SLESPDEGCVS 94
            RP  R+  + R   I+      A+GS L + G T ++  +  E   P  L+   +G ++
Sbjct: 2   NRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLT 61

Query: 95  IDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIY 154
            ++ M P  +        +             +    +    +LS +G      +Y+D  
Sbjct: 62  AEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGE---NTLYIDCD 118

Query: 155 CLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLT 214
            + ADG    A++  A  A          L D   V+      + N  K+ V        
Sbjct: 119 VIQADGGTRTASITGATVA----------LIDALAVLKKRGALKGNPLKQMV-------- 160

Query: 215 LGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPG-GAVLAYTSA 273
              +    +  +++   + D    E+S  ET + VV+  +   + +     GA     + 
Sbjct: 161 -AAV----SVGIYQGVPVLDLDYLEDSAAETDLNVVMTDAGGFIEVQGTAEGAPFRP-AE 214

Query: 274 VQDCIALTRQRVKELHQILEEAIS 297
           +   + L +Q ++EL ++   A++
Sbjct: 215 LNAMLELAQQGMQELFELQRAALA 238

>1udn_A Ribonuclease PH, RNAse PH; transferase, riken structural genomics/proteomics initiative structural genomics; 2.30A {Aquifex aeolicus} SCOP: d.14.1.4 d.101.1.1 PDB: 1udq_A 1uds_A 1udo_A Length = 255

 Score = 79.8 bits (197), Expect = 1e-17
 Identities = 46/266 (17%), Positives = 95/266 (35%), Gaps = 33/266 (12%)

Query: 36  IRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTP-SLESPDEGCVS 94
           +R D R   + R  +I    +   +GS L   G T ++    +    P  L+   +G ++
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWIT 60

Query: 95  IDFHMPPICSPLVRPGRPAEAAPV-VAKQLSDTISSS--GMINLKELSLVGGKAAWMVYL 151
            ++ M P  +         +        ++   I  +    + L ++          +++
Sbjct: 61  AEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIG------ERTIWV 114

Query: 152 DIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKR 211
           D   + ADG    AA+  A  A          + D  I +  E   EE   K+ V     
Sbjct: 115 DCDVIQADGGTRTAAITGAFVA----------VADAIIKLHKEGIIEETPIKDFV----- 159

Query: 212 KLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYT 271
                 +    +  +  + IL D   EE+S  +  + VV   S +L  ++  G       
Sbjct: 160 ----AAV----SVGIVNDRILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTK 211

Query: 272 SAVQDCIALTRQRVKELHQILEEAIS 297
             +   + L ++ + EL ++ ++   
Sbjct: 212 DELIKMLDLAQKGINELIELQKKLYV 237

>2wp8_B Exosome complex component SKI6; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} Length = 246

 Score = 56.9 bits (138), Expect = 9e-10
 Identities = 42/269 (15%), Positives = 88/269 (32%), Gaps = 46/269 (17%)

Query: 32  LAESIRPDARSLSRARNTTISMGAVA-SADGSALAKIGSTTMLAAI--KMEVMTPSLESP 88
             E +R D R  +  R    S+     +ADGS+  + G+  ++  +    E    S    
Sbjct: 8   SPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDT 67

Query: 89  DEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWM 148
            +  +++  ++                  V+  Q S        + L        +    
Sbjct: 68  SKALLNVSVNINKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIY----PRTVID 123

Query: 149 VYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNK 208
           + + +  L+ DG +  + +             T++L D  I M            + +  
Sbjct: 124 IEIHV--LEQDGGIMGSLINGI----------TLALIDAGISM-----------FDYI-- 158

Query: 209 EKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVL 268
                   GI    +  L+    L D  S EE+ M T+   V+  S +L  L       L
Sbjct: 159 -------SGI----SVGLYDTTPLLDTNSLEENAMSTVTLGVVGKSEKLSLLLVEDKIPL 207

Query: 269 AYTSAVQDCIALTRQRVKELHQILEEAIS 297
                +++ +A+       +  +++E + 
Sbjct: 208 ---DRLENVLAIGIAGAHRVRDLMDEELR 233

>2nn6_F MTR3, exosome component 6; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1 Length = 272

 Score = 54.9 bits (132), Expect = 5e-09
 Identities = 55/300 (18%), Positives = 91/300 (30%), Gaps = 58/300 (19%)

Query: 14  MEVDAFRRLFPLRYFERHLA---ESIRPDARSLSRARNTTISMGAVASADGSALAKIGST 70
           M  D  R   P       L    E   P  R  +R R      G ++ A GSA  + G T
Sbjct: 1   MPGDHRRIRGPEESQPPQLYAADEEEAPGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGT 60

Query: 71  TMLAAI-------------KMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAP 117
            +L A+                       +   G +  DF   P      R         
Sbjct: 61  KVLCAVSGPRQAEGGERGGGPAGAGGEAPAALRGRLLCDFRRAPFAGRRRRAPPGGCEER 120

Query: 118 VVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNL 177
            +A  L + +     + L        +A   V   +  L+  G+   AAL +A  A ++ 
Sbjct: 121 ELALALQEALEP--AVRLGRY----PRAQLEVSALL--LEDGGSALAAALTAAALALADA 172

Query: 178 QIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTS 237
            +    L  G  + L                                       L DPT 
Sbjct: 173 GVEMYDLVVGCGLSLAPG-------------------------------PAPTWLLDPTR 201

Query: 238 EEESIMETLVTV-VLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAI 296
            EE      +TV ++   NQ+  L   G      T +  + + L  +  + L+ +L++++
Sbjct: 202 LEEERAAAGLTVALMPVLNQVAGLLGSGE--GGLTESWAEAVRLGLEGCQRLYPVLQQSL 259

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

 Score = 52.9 bits (126), Expect = 7e-08
 Identities = 37/292 (12%), Positives = 80/292 (27%), Gaps = 83/292 (28%)

Query: 3   LPNASEDLSSEMEV--DAFRRLFPLRYFERHL--------AESIRP-DARSLSRARNTTI 51
             + S ++   +       RRL   + +E  L        A++    +           +
Sbjct: 216 RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSC------KIL 269

Query: 52  SMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEG------CVSIDFH-MPP-IC 103
               + +        + + T    I ++  + +L  PDE        +      +P  + 
Sbjct: 270 ----LTTRFKQVTDFLSAATT-THISLDHHSMTLT-PDEVKSLLLKYLDCRPQDLPREVL 323

Query: 104 --SPLV----------RPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYL 151
             +P                      V   +L+  I SS    L  L     +    ++ 
Sbjct: 324 TTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESS----LNVLEPAEYRK---MFD 376

Query: 152 DIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKR 211
            +       ++F            +  IPT+ L      ++  +  + +     VNK  +
Sbjct: 377 RL-------SVFP----------PSAHIPTILL-----SLIWFDVIKSDVMVV-VNKLHK 413

Query: 212 KLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKP 263
              +   P   T  +   Y+      E E  +             +V  Y  
Sbjct: 414 YSLVEKQPKESTISIPSIYLELKVKLENEYALH----------RSIVDHYNI 455

>3krn_A Protein C14A4.5, confirmed by transcript evidence; RNAse PH domain, homodimer, exosome, cell-death-related DNAS hydrolase; 3.92A {Caenorhabditis elegans} Length = 222

 Score = 49.7 bits (119), Expect = 2e-07
 Identities = 36/255 (14%), Positives = 78/255 (30%), Gaps = 60/255 (23%)

Query: 47  RNTTISMGAVASADGSALAKIGSTTMLAAI--KMEVMTPSLESPDEGCVSIDFHMPPICS 104
           R     +  + +ADGSA    G+T + A+     +V   S  S +   + I +       
Sbjct: 6   REMRCELSFLKNADGSACFSQGATCIWASCSGPGDV-HASKASDEAMTLDISYRA----- 59

Query: 105 PLVRPGRPAEAAPVVAKQLSDTISSS--GMINLKELSLVGGKAAWMVYLDIYCLDADGAL 162
                G            L++ I S+    INL+            + + ++ +  DG++
Sbjct: 60  ---NCGDNKF------NVLNNIIHSTLSNAINLELF----PHT--TISVTVHGIQDDGSM 104

Query: 163 FDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSL 222
              A+  A  A          L D  +                            +   +
Sbjct: 105 GAVAINGACFA----------LLDNGMPFE------------------------TVFCGV 130

Query: 223 TCILHKNYILADPTSEEESIMETLVT-VVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALT 281
             +  K+ ++ DPT+++E+     V   V   S+    +             ++   +L 
Sbjct: 131 LIVRVKDELIIDPTAKQEAASTGRVLFSVCKGSDGHPEVCAMDAIGHWDFIQLEAAWSLA 190

Query: 282 RQRVKELHQILEEAI 296
           +     +    +  +
Sbjct: 191 QPSASAIFDFYKTVM 205

>2po1_A Probable exosome complex exonuclease 1; RNAse PH, hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus abyssi} PDB: 2po0_A* 2pnz_A 2po2_A* Length = 249

 Score = 48.0 bits (115), Expect = 9e-07
 Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 5/85 (5%)

Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAI--KMEVMTPSLESPD 89
                R D R     R   + +G + +A+GSA  + G   ++AA+    E+    L+ PD
Sbjct: 12  DENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPD 71

Query: 90  EGCVSIDFHMPPICS---PLVRPGR 111
              + + ++M P          P R
Sbjct: 72  RAILRVRYNMAPFSVEERKKPGPDR 96

>2je6_B RRP41, exosome complex exonuclease 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_B* 2jeb_B* 2br2_B 2c37_B* 2c38_B* 2c39_B* 3l7z_B Length = 250

 Score = 46.9 bits (112), Expect = 2e-06
 Identities = 27/102 (26%), Positives = 45/102 (44%), Gaps = 10/102 (9%)

Query: 13  EMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTM 72
           EM      +L         L +  R D R     R+  I +G + +ADGSA+ ++G+T  
Sbjct: 5   EMLQVERPKLI--------LDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKA 56

Query: 73  LAAI--KMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRP 112
           +AA+    E+    L  PD   + + +HM P  +   +   P
Sbjct: 57  IAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDERKNPAP 98

>3m7n_D Probable exosome complex exonuclease 1; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 3m85_D 2ba0_F 2ba1_E Length = 258

 Score = 46.9 bits (112), Expect = 3e-06
 Identities = 20/85 (23%), Positives = 34/85 (40%), Gaps = 5/85 (5%)

Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAI--KMEVMTPSLESPD 89
           + + +R D R     R   I    +  ADGS   ++G   ++AA+    EV    L+ P 
Sbjct: 12  IVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPS 71

Query: 90  EGCVSIDFHMPPIC---SPLVRPGR 111
           +  +   ++M P          P R
Sbjct: 72  KAIIRYRYNMAPFSVEERKRPGPDR 96

>3dd6_A Ribonuclease PH; exoribonuclease, tRNA maturation, RNAse PH., transferase; 1.70A {Bacillus anthracis} Length = 255

 Score = 46.6 bits (111), Expect = 3e-06
 Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 29  ERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTP-SLES 87
             H    +R D R  +  R+  I    +   +GS L ++G T ++ +  +E   P  +  
Sbjct: 4   SHHHHHHMRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVPPFMRG 63

Query: 88  PDEGCVSIDFHMPP 101
             +G V+ ++ M P
Sbjct: 64  EGKGWVTAEYAMIP 77

>2wnr_B Probable exosome complex exonuclease 1; phosphate binding, 3'-5' exoribonuclease, hydrolase; 2.65A {Methanothermobacter thermautotrophicusorganism_taxid} Length = 240

 Score = 46.0 bits (110), Expect = 5e-06
 Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 2/70 (2%)

Query: 34  ESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK--MEVMTPSLESPDEG 91
            S+R D R+    R   I  G +  ADGS+  + G   +L A+    E     L+ PD  
Sbjct: 14  PSVREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRA 73

Query: 92  CVSIDFHMPP 101
            +   ++M P
Sbjct: 74  VIRCRYNMAP 83

>1oys_A Ribonuclease PH; transferase, tRNA processing; 2.40A {Bacillus subtilis} SCOP: d.14.1.4 d.101.1.1 PDB: 1oyp_A 1oyr_A Length = 245

 Score = 44.6 bits (106), Expect = 1e-05
 Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 1/67 (1%)

Query: 36  IRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPS-LESPDEGCVS 94
           +R D R     R  T  +  ++  +GS L   G+T ++    +E   P  L    +G ++
Sbjct: 1   MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWIT 60

Query: 95  IDFHMPP 101
            ++ M P
Sbjct: 61  AEYSMLP 67

>2nn6_B Exosome complex exonuclease RRP41; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1 Length = 249

 Score = 44.2 bits (105), Expect = 2e-05
 Identities = 21/87 (24%), Positives = 30/87 (34%), Gaps = 7/87 (8%)

Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAI--KMEVMTP-SLESP 88
             +  R D R     R     MG  A ADGSA  + G+T  LA +    E+    +   P
Sbjct: 12  SDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALP 71

Query: 89  DEGCVSIDFHMPPICS----PLVRPGR 111
           D   V+  +      +          R
Sbjct: 72  DRALVNCQYSSATFSTGERKRRPHGDR 98

>3hkm_A OS03G0854200 protein; RNAse PH domain, phosphorylase, hydrolase; 1.98A {Oryza sativa japonica group} Length = 246

 Score = 39.4 bits (92), Expect = 7e-04
 Identities = 41/267 (15%), Positives = 85/267 (31%), Gaps = 52/267 (19%)

Query: 34  ESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK--MEVMTPSLESPDEG 91
           E  R D R+ ++ R  + +   +  A GSA    G T +LAA+       T   E+P++ 
Sbjct: 2   EESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPG-TRKGENPEKA 60

Query: 92  CVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYL 151
            + + +            G+  +        L  T+ S  ++ +   +         V L
Sbjct: 61  SIEVVWKP--------MTGQIGKQEKEYEMTLKRTLQSICLLTVHPNTTT------SVIL 106

Query: 152 DIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKR 211
            +  +  DG+L   A+ +             +L    I +           K        
Sbjct: 107 QV--VGNDGSLLPCAINAC----------CAALVFAGIPL-----------KHLA----- 138

Query: 212 KLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYT 271
                 I   +   L    ++ D    EE  +++   +V  +S +  S  +P        
Sbjct: 139 ----VAIGCGV---LEDGEVILDTNKAEEQQLKSFAHLVFPNSRKSASSKEPNQKEEDSE 191

Query: 272 SAVQDCIALTRQRVKELHQILEEAISG 298
             +   I       ++    +E  ++ 
Sbjct: 192 RGLITSITHGVMSEEDYFSCIERGLAA 218

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	302
2po1_B	277	Probable exosome complex exonuclease 2; RNAse PH,	100.0
2nn6_C	278	Exosome complex exonuclease RRP43; RNA, exosome, P	100.0
2je6_A	277	RRP42, exosome complex exonuclease 2; nuclease, hy	100.0
2wnr_A	271	Probable exosome complex exonuclease 2; phosphate	100.0
3m7n_G	259	Probable exosome complex exonuclease 2; exosome, R	100.0
2wp8_A	305	Exosome complex component RRP45; nucleus, hydrolas	100.0
2nn6_A	358	Polymyositis/scleroderma autoantigen 1; RNA, exoso	100.0
2nn6_E	305	Exosome complex exonuclease RRP42; RNA, exosome, P	100.0
2wnr_B	240	Probable exosome complex exonuclease 1; phosphate	100.0
2nn6_B	249	Exosome complex exonuclease RRP41; RNA, exosome, P	100.0
2po1_A	249	Probable exosome complex exonuclease 1; RNAse PH,	100.0
3b4t_A	262	Ribonuclease PH; RNAse, tRNA nucleotidyltransferas	100.0
2je6_B	250	RRP41, exosome complex exonuclease 1; nuclease, hy	100.0
3m7n_D	258	Probable exosome complex exonuclease 1; exosome, R	100.0
1r6l_A	239	Ribonuclease PH; beta-alpha-beta-alpha fold, hexam	100.0
1udn_A	255	Ribonuclease PH, RNAse PH; transferase, riken stru	100.0
1oys_A	245	Ribonuclease PH; transferase, tRNA processing; 2.4	100.0
2wp8_B	246	Exosome complex component SKI6; nucleus, hydrolase	100.0
3dd6_A	255	Ribonuclease PH; exoribonuclease, tRNA maturation,	100.0
2nn6_D	237	Exosome complex exonuclease RRP46; RNA, exosome, P	100.0
3hkm_A	246	OS03G0854200 protein; RNAse PH domain, phosphoryla	100.0
2nn6_F	272	MTR3, exosome component 6; RNA, exosome, PM/SCL, p	100.0
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	100.0
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	100.0
3gme_A	549	Polyribonucleotide nucleotidyltransferase; protein	100.0
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	100.0
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	100.0
3krn_A	222	Protein C14A4.5, confirmed by transcript evidence;	100.0
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	99.97
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.96
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.94
3gme_A	549	Polyribonucleotide nucleotidyltransferase; protein	99.94
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.92
1whu_A	104	Polynucleotide phosphorylase; 3'-5' RNA exonucleas	94.44

>2po1_B Probable exosome complex exonuclease 2; RNAse PH, hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus abyssi} PDB: 2po0_B* 2pnz_B 2po2_B*

Probab=100.00  E-value=2.9e-58  Score=415.37  Aligned_cols=273  Identities=27%  Similarity=0.436  Sum_probs=247.1

Q ss_pred             cccHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcce
Q 022140           13 EMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGC   92 (302)
Q Consensus        13 ~~~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~   92 (302)
                      ++..+.|.+..|++|+++++++++|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|++++..|..+.|++|.
T Consensus         3 ~~~~~~~~s~~~~~~i~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~g~   82 (277)
T 2po1_B            3 HMSDNEIVAGIMRDHIINLLKEGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLGEPFPDTPNMGV   82 (277)
T ss_dssp             --------CCHHHHHHHHHHHTTCCTTSCCTTCCCCEEEEECCSTTSSEEEEEEETTEEEEEEEEEEEECCCTTCTTSCE
T ss_pred             CcccccccCccHHHHHHHHHhcCCCCCCCCCCCcCCeEEEeCCcCCCCeEEEEEECCeEEEEEEEecccCCCCCCCCceE
Confidence            34455688999999999999999999999999999999999999999999999999999999999888888888899999


Q ss_pred             EEEEEecCCCCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHH
Q 022140           93 VSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVA  172 (302)
Q Consensus        93 l~v~V~~~~~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~  172 (302)
                      +.++|+++|++++.++.|++++++++++++|++.|+++++||+++|||+||+++|.|+|+++||++|||++||+++|+++
T Consensus        83 l~~~~~~~p~a~~~~~~g~~~~~~~~l~~li~r~l~~s~~idl~~L~i~pg~~~w~i~id~~VL~~dG~~~~a~i~aa~~  162 (277)
T 2po1_B           83 MTTNVELVPLASPTFEPGPPDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVFIDVHVLDHDGNLMDAIGIAAIA  162 (277)
T ss_dssp             EEEEEEECGGGCTTCCSSSCCHHHHHHHHHHHHHHHTTTSBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHH
T ss_pred             EEEEEEeCCCccccccCCCCChHHHHHHHHHHHHHhhcccccHHHccccCCcEEEEEEEEEEEECCCCCHHHHHHHHHHH
Confidence            99999999999998888888999999999999999998899999999999999999999999999999999999999999


Q ss_pred             HHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEc
Q 022140          173 AFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLD  252 (302)
Q Consensus       173 AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~  252 (302)
                      ||+|+++|.+.++++....+             ...+..++.|+++|+++||+++++.+++|||.+||+.+++.++|+++
T Consensus       163 AL~da~~p~~~~~~~~~~~~-------------~~~~~~~ipl~~~~~avs~g~~~~~~l~Dp~~~Ee~~~~~~~~v~~~  229 (277)
T 2po1_B          163 ALLNARVPKVRYNEETGEVE-------------TLDETEPLPVEKIPVPVTFAKIGNILVVDPSLDEELVMDGKITITTD  229 (277)
T ss_dssp             HHHHCEEEEEEECTTTCCEE-------------EEEEEEECCBCCCCEEEEEEEETTEEEESCCHHHHHHCSEEEEEEEC
T ss_pred             HHHhcCCCcEEEeCCCceee-------------cccccccccccCceEEEEEEEECCEEEeCCCHHHHhhCCCcEEEEEc
Confidence            99999999998833211111             13456678899999999999999999999999999999999999999


Q ss_pred             CCCcEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          253 SSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       253 ~~g~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      ++|+++.+++.|+.+++.++ |.+|+++|.+++++|+++++++|++.
T Consensus       230 ~~g~i~~lq~~g~~~~~~~~-l~~~l~~A~~~~~~l~~~~~~~l~~~  275 (277)
T 2po1_B          230 ETGHISAVQKSEGGAFKLEE-VMYAVETAFKKAEEIRKLILEAVEKA  275 (277)
T ss_dssp             TTSCEEEEEEESSCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEccCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            99999999999888899996 99999999999999999999999864

>2nn6_C Exosome complex exonuclease RRP43; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=1e-58  Score=418.70  Aligned_cols=271  Identities=36%  Similarity=0.683  Sum_probs=249.5

Q ss_pred             HHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEE
Q 022140           16 VDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSI   95 (302)
Q Consensus        16 ~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v   95 (302)
                      +++|+++.|++|++++|++++|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|++++..|...+|++|.+.+
T Consensus         4 ~~~~~~~~~~~~~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~g~l~v   83 (278)
T 2nn6_C            4 AAGFKTVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVP   83 (278)
T ss_dssp             -----CCSTHHHHHHHHHTSCCTTSCCSCCCCSCCEEETCCSSSSEEEEEEETTEEEEEEEEEEECCCCSSSTTCCCCEE
T ss_pred             hhhhhhhCHHHHHHHHHhcCCCCCCCCcccccCeEEEeCCccCCCceEEEEeCCeEEEEEEEEEeecCCCCCCCccEEEE
Confidence            56899999999999999999999999999999999999999999999999999999999999999888888899999999


Q ss_pred             EEecCCCCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHh
Q 022140           96 DFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFS  175 (302)
Q Consensus        96 ~V~~~~~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~  175 (302)
                      +|+++|++++.|++|+++++++.++++|++.|+++.++|+++|||.||+++|.|+|+++||++|||+++|+++|+++||+
T Consensus        84 ~~~~~p~a~~~~~~g~~~~~~~~~s~li~r~l~~s~~i~l~~L~i~pg~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~  163 (278)
T 2nn6_C           84 NVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALK  163 (278)
T ss_dssp             EEECCSSSCTTSCSSSCCHHHHHHHHHHHHHHHHHCCSCHHHHCSSBTTBCEEEEEEEEESSCCSCTTHHHHHHHHHHHH
T ss_pred             EEEeCCccCccccCCCCcHHHHHHHHHHHHHHhccCCCCHHHCEEeCCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHH
Confidence            99999999999988999999999999999999987899999999999999999999999999999999999999999999


Q ss_pred             hCCCCcEEecC-CceeecCccccccccCcCccccccccccCCCccEEEEEEEECC-EEEECCChHHHhcCCceEEEEEcC
Q 022140          176 NLQIPTVSLDD-GKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKN-YILADPTSEEESIMETLVTVVLDS  253 (302)
Q Consensus       176 ~~~iP~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~-~~l~DPt~~Ee~~~~~~l~i~~~~  253 (302)
                      ++++|.+.+.. +.+.             ..++.+..++.++++|+++|||++++ .+++|||.+||+.+++.++|++++
T Consensus       164 ~a~iP~v~~~~~~~~~-------------~~~~~~~~~lp~~~~~~avs~g~~~~~~~l~Dpt~~Ee~~~~~~l~va~~~  230 (278)
T 2nn6_C          164 NVQLPEVTINEETALA-------------EVNLKKKSYLNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDE  230 (278)
T ss_dssp             TCCCCCCCBCSSSBCC-------------CTTSCCCSCSCCSCCCEEEEEEECTTTCCEESCCTTTTTSCSEEEEEEECT
T ss_pred             hCCCCeEEEeCCCcce-------------ecCcccccccccCCceEEEEEEEECCceEEECCCHHHHhhcCceEEEEEcC
Confidence            99999988832 2211             12345778899999999999999999 999999999999999999999999


Q ss_pred             CCcEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 022140          254 SNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME  300 (302)
Q Consensus       254 ~g~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~~  300 (302)
                      +|+|+++++.|+..++.++ |.+|+++|.+++++|++++++++++++
T Consensus       231 ~g~i~~v~~~g~~~~~~~~-l~~~l~~a~~~~~~i~~~~~~~l~~~~  276 (278)
T 2nn6_C          231 EGKLCCLHKPGGSGLTGAK-LQDCMSRAVTRHKEVKKLMDEVIKSMK  276 (278)
T ss_dssp             TCCEEEEEESCCSCCCHHH-HHHHHHHHHHHHHHHHHHHHTTTTTTC
T ss_pred             CCcEEEEEccCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            9999999999977899996 999999999999999999999998865

>2je6_A RRP42, exosome complex exonuclease 2; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_A* 2jeb_A* 2br2_A 2c37_A* 2c38_A* 2c39_A* 3l7z_A

Probab=100.00  E-value=3.1e-58  Score=415.33  Aligned_cols=274  Identities=26%  Similarity=0.438  Sum_probs=254.0

Q ss_pred             ccccccHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCC
Q 022140           10 LSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPD   89 (302)
Q Consensus        10 ~~~~~~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~   89 (302)
                      -+.+|..+.|.+..|++|+++++++++|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+++...|..+.|+
T Consensus         3 ~~~~~~~~~~~s~~~~~~i~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~   82 (277)
T 2je6_A            3 MSSTPSNQNIIPIIKKESIVSLFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPN   82 (277)
T ss_dssp             CEECCCCSSCCCHHHHHHHTTTGGGTBCTTSCBTTCCCCEEEEETCSTTSSEEEEEEETTEEEEEEEEEEEECCCTTCTT
T ss_pred             ccccccccccccccHHHHHHHHHhcCCCCCCCCcCcccCeEEEeCCcCCCCeEEEEEECCeEEEEEEEeeeeCCCCCCCC
Confidence            36788999999999999999999999999999999999999999999999999999999999999999988888877899


Q ss_pred             cceEEEEEecCCCCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHH
Q 022140           90 EGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLS  169 (302)
Q Consensus        90 ~g~l~v~V~~~~~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A  169 (302)
                      +|.+.++|+++|++++.++.|+++++++.++++|++.|+++++++++.|||.||+++|.|+|+++||++|||+++|+++|
T Consensus        83 ~g~l~v~~~~~p~a~~~~~~g~~~~~~~~is~li~r~lr~~~~i~~~~l~i~~g~~~~~i~i~~~VL~~DG~~~~aai~a  162 (277)
T 2je6_A           83 QGNLIVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLA  162 (277)
T ss_dssp             CCEEEEEEEECTTSCTTCCCSSCCHHHHHHHHHHHHHHHHTTCSCGGGGEEETTTEEEEEEEEEEEEECCSCHHHHHHHH
T ss_pred             ccEEEEEEEeCCccCcccccCCCChHHHHHHHHHHHHHhccCCcCHHHceeecCceEEEEEEEEEEECCCCCHHHHHHHH
Confidence            99999999999999998888999999999999999999998899999999999999999999999999999999999999


Q ss_pred             HHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEE
Q 022140          170 AVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTV  249 (302)
Q Consensus       170 ~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i  249 (302)
                      +++||+++++|.+.++++.+..++             ..+..++.++++|+++|||++++.+++|||.+||+.+++.++|
T Consensus       163 a~~AL~~a~~p~v~~~~~~~~~~~-------------~~~~~~ip~~~~~~avsvg~~~~~~l~Dpt~~Ee~~~~~~l~v  229 (277)
T 2je6_A          163 SVAALYNTKVYKVEQHSNGISVNK-------------NEVVGKLPLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISF  229 (277)
T ss_dssp             HHHHHHTCEEEEEECC---CEEEE-------------EEEEEECCCSCCCEEEEEEEETTEEEESCCHHHHHHCSEEEEE
T ss_pred             HHHHHHhcCCCeEEecCCcceEec-------------cCccccccccCCeEEEEEEEECCEEecCCCHHHHhcCCCcEEE
Confidence            999999999999988544333221             2356678899999999999999999999999999999999999


Q ss_pred             EEcCCCcEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022140          250 VLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAIS  297 (302)
Q Consensus       250 ~~~~~g~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~  297 (302)
                      +++++|+++++++.|+..++.++ +.+|+++|.+++++|+++++++++
T Consensus       230 a~~~~g~i~~v~~~g~~~~~~~~-l~~~l~~A~~~~~~i~~~~~~~l~  276 (277)
T 2je6_A          230 SYTPDLKIVGIQKSGKGSMSLQD-IDQAENTARSTAVKLLEELKKHLG  276 (277)
T ss_dssp             EECTTCCEEEEEEESSSCEEHHH-HHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             EEeCCCCEEEEECCCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999877899996 999999999999999999999875

>2wnr_A Probable exosome complex exonuclease 2; phosphate binding, 3'-5' exoribonuclease, hydrolase; 2.65A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=100.00  E-value=6.3e-57  Score=405.52  Aligned_cols=267  Identities=26%  Similarity=0.485  Sum_probs=244.7

Q ss_pred             HHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEE
Q 022140           16 VDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSI   95 (302)
Q Consensus        16 ~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v   95 (302)
                      ...|.+..|++|+++++++++|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+++..+|..+.|++|.+.+
T Consensus         4 ~~~~~s~~~~~~~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~g~l~v   83 (271)
T 2wnr_A            4 KMDIIPEITRKSITDLINNKERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKPQIGEPFPDTPEMGVILT   83 (271)
T ss_dssp             -----CCHHHHHHHHHHHTTCCTTCCCTTCCCCEEEEESCSTTSSEEEEEEETTEEEEEEEEEEEECCCTTCTTCCEEEE
T ss_pred             ccccccccHHHHHHHHHhcCCCCCCCCcccccCeEEEeCccCCCCeEEEEEECCeEEEEEEEeeeecCCCCCCCceEEEE
Confidence            45689999999999999999999999999999999999999999999999999999999999888788878899999999


Q ss_pred             EEecCCCCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHh
Q 022140           96 DFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFS  175 (302)
Q Consensus        96 ~V~~~~~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~  175 (302)
                      +|+++|++++.++.|+++++++.++++|++.|++++++|++.|||.||+++|.|+|+++||++|||++||+++|+++||+
T Consensus        84 ~~~~~p~a~~~~~~g~~~~~~~~~s~li~r~lr~s~~i~l~~l~i~pg~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~  163 (271)
T 2wnr_A           84 NSELLPMASPTFEPGPPDERSVELSRVVDRCIRESRMIDLEKLCIIEGSKVWMLFLDLHIIDYDGNLFDAAVLATVAALL  163 (271)
T ss_dssp             EEEECGGGCTTCCCSSCCHHHHHHHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHH
T ss_pred             EEEeCCcccccccCCCCchHHHHHHHHHHHHHhccCCccHHHccccCCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHH
Confidence            99999999998888999999999999999999998899999999999999999999999999999999999999999999


Q ss_pred             hCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCC
Q 022140          176 NLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSN  255 (302)
Q Consensus       176 ~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g  255 (302)
                      ++++|.+.++++... +             +..+..++.++++|+++|||++++.+++|||.+||+.+++.++|+++++|
T Consensus       164 ~a~~p~~~~~~~~~~-~-------------~~~~~~~ip~~~~~~avt~g~~~~~~l~Dpt~~Ee~~~~~~l~va~~~~~  229 (271)
T 2wnr_A          164 DTRIPAAEVEDGEVV-I-------------NREKMQPLPVNRKALMCTFAKIGNEIVLDPSLEEEDILTARISIGVTEEG  229 (271)
T ss_dssp             HCEEEEEEEETTEEE-E-------------EEEEEEECCBCCCEEEEEEEEETTEEEESCCHHHHTTCSEEEEEEEETTS
T ss_pred             hcCCCeEEecCCcee-e-------------ccCcccccCccCCeEEEEEEEECCEEEeCCCHHHHhcCCCcEEEEEeCCC
Confidence            999999998443221 1             13456678899999999999999999999999999999999999999999


Q ss_pred             cEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022140          256 QLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAIS  297 (302)
Q Consensus       256 ~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~  297 (302)
                      +++++++.|+..++.++ +.+|+++|.+++++|+++++++++
T Consensus       230 ~i~~i~~~g~~~~~~~~-l~~~l~~a~~~~~~i~~~~~~~l~  270 (271)
T 2wnr_A          230 SICAMQKGGEGPLTRDD-VLKAVSIAVEKVPQLIEYLDKSMT  270 (271)
T ss_dssp             CEEEEEEESSSCBCHHH-HHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             CEEEEECCCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHhC
Confidence            99999999877899996 999999999999999999999875

>3m7n_G Probable exosome complex exonuclease 2; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_H 2ba0_I 3m85_G

Probab=100.00  E-value=4.8e-57  Score=403.56  Aligned_cols=251  Identities=30%  Similarity=0.523  Sum_probs=236.7

Q ss_pred             hChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCC
Q 022140           22 LFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPP  101 (302)
Q Consensus        22 ~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~  101 (302)
                      ..+++|++++|++++|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|++++..|..++|++|.+.++|+++|
T Consensus         8 ~~e~~~i~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~g~l~v~~~~~p   87 (259)
T 3m7n_G            8 DIKRDYVLSKLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYPDTPDRGVIIVNAELVP   87 (259)
T ss_dssp             HHHHHHHHHHHHTTCCTTCCCTTCCCCEEEEETSSTTSSEEEEEEETTEEEEEEEEEEEECCCSSCTTSCEEEEEEECCT
T ss_pred             HHHHHHHHHHHhcCCCCCCCCCccccCeEEEeCCcCCCCceEEEEECCcEEEEEEEecccCCCCCCCCceEEEEEEEeCC
Confidence            46789999999999999999999999999999999999999999999999999999998888888899999999999999


Q ss_pred             CCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCc
Q 022140          102 ICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPT  181 (302)
Q Consensus       102 ~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~  181 (302)
                      ++++.|++|+++++++.++++|++.|++++++|+++|||+||+++|.|+|+++||++|||++||+++|+++||+++++|.
T Consensus        88 ~a~~~~~~g~~~~~~~~~srli~r~lr~s~~i~l~~L~i~pg~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~iP~  167 (259)
T 3m7n_G           88 LASPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPA  167 (259)
T ss_dssp             TSCTTCCSSSSCHHHHHHHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHTCEECT
T ss_pred             cccccccCCCCChHHHHHHHHHHHHHhhcCCccHHHhcccCCcEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHhCCCCe
Confidence            99999988999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             EEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEE
Q 022140          182 VSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLY  261 (302)
Q Consensus       182 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~  261 (302)
                      +.++++                     +..++.++++|+++|||++++.+++|||.+||+.+++.++|+++++|+++.++
T Consensus       168 ~~~~~~---------------------~~~~lp~~~~~~avtvg~~~~~~l~Dpt~~Ee~~~~~~l~va~~~~g~i~~i~  226 (259)
T 3m7n_G          168 ERFDLG---------------------EDYLLPVRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITTDKDDNVVAMQ  226 (259)
T ss_dssp             GGGTSS---------------------SCEECCBCCCCEEEEEEEETTEEEESCCTTGGGGCSCEEEEEECTTSCEEEEE
T ss_pred             EEecCC---------------------ceecccccCceeEEEEEEECCEEEECCCHHHHhhCCCcEEEEEeCCCcEEEEE
Confidence            766332                     34568899999999999999999999999999999999999999999999999


Q ss_pred             ccCCcccChHHHHHHHHHHHHHHHHHHHHHHHH
Q 022140          262 KPGGAVLAYTSAVQDCIALTRQRVKELHQILEE  294 (302)
Q Consensus       262 ~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~  294 (302)
                      +.|+..++.++ +.+|+++|.+++++|+++|++
T Consensus       227 ~~g~~~~~~~~-l~~~l~~a~~~~~~l~~~~~~  258 (259)
T 3m7n_G          227 KSGGYLLDEKL-FDELLDVSINCARKLREKFKE  258 (259)
T ss_dssp             EESSCCBCHHH-HHHHHHHHHHHHHHHHHTTC-
T ss_pred             CCCCCCcCHHH-HHHHHHHHHHHHHHHHHHHhh
Confidence            99888999996 999999999999999998765

>2wp8_A Exosome complex component RRP45; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.8e-57  Score=414.23  Aligned_cols=271  Identities=21%  Similarity=0.393  Sum_probs=226.1

Q ss_pred             ccHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceE
Q 022140           14 MEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCV   93 (302)
Q Consensus        14 ~~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l   93 (302)
                      |..+++....|++|++++|++++|+|||+++|+|++.+++|   +++|||+|++|+|+|+|+|++++..|..++|++|.+
T Consensus         1 m~~~~~~s~~e~~~i~~~l~~~~R~DGR~~~e~R~i~i~~g---~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~g~~   77 (305)
T 2wp8_A            1 MAKDIEISASESKFILEALRQNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLF   77 (305)
T ss_dssp             ------CCHHHHHHHHHHHTTTCCTTSCCTTCCCCEEEEEC---SSTTEEEEEETTEEEEEEEEEEEC-CCSSCTTCCEE
T ss_pred             CCCccccCcCHHHHHHHHHhhCCCCCCCCCcccCCeEEEEc---CCCcEEEEEECCeEEEEEEeccccCCcccCCCCcEE
Confidence            55667788899999999999999999999999999999999   799999999999999999999998888888999999


Q ss_pred             EEEEecCCCCCCCccCCCCC-CcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHH
Q 022140           94 SIDFHMPPICSPLVRPGRPA-EAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVA  172 (302)
Q Consensus        94 ~v~V~~~~~~~~~~~~g~~~-~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~  172 (302)
                      .++|+|+|++++.|++|+++ ++++.++++|++.|+++.+||+++|||+||+++|.|+|+++||++|||++||+++|+++
T Consensus        78 ~~~ve~~~~~~~~~~~g~~~~~~~~~is~li~r~l~~s~~idl~~L~i~pg~~~w~I~id~~VL~~DG~~~dAai~aa~~  157 (305)
T 2wp8_A           78 VISTEISPMAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMA  157 (305)
T ss_dssp             EEEECCC----------------------CHHHHHHHTTSBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHH
T ss_pred             EEEEEECCCCCccccCCCCChhHHHHHHHHHHHHHhhccCcCHHHccccCCcEEEEEEEEEEEEcCCCCHHHHHHHHHHH
Confidence            99999999999988888888 89999999999999988899999999999999999999999999999999999999999


Q ss_pred             HHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEEC--------------CEEEECCChH
Q 022140          173 AFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHK--------------NYILADPTSE  238 (302)
Q Consensus       173 AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~--------------~~~l~DPt~~  238 (302)
                      ||+++++|.+.+++|.+....           ++.+++.++.++++|+++|||+++              +.+|+|||.+
T Consensus       158 AL~~a~iP~~~~~~~~~~i~~-----------~~~~~~~~l~~~~~pvavs~g~i~~~~~~~~~~~~~~~~~~l~Dpt~~  226 (305)
T 2wp8_A          158 GLMHFKKPDITVHGEQIIVHP-----------VNEREPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLK  226 (305)
T ss_dssp             HHHHCEECCCBCTTSSCCBCC-----------SSSSCCEECCBSCCCEEEEEEECC---------------CEEESCCHH
T ss_pred             HHHHhCCCeEEecCCceEecc-----------cccccccccccccCeEEEEEEEEccccccccccccccCCeEEeCCCHH
Confidence            999999999888555433211           235677889999999999999997              7899999999


Q ss_pred             HHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          239 EESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       239 Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      ||+.+++.++|+++++|+++.+++.|+.+++.++ |.+|+++|.+++++|++++++++++.
T Consensus       227 Ee~~~~~~l~Va~~~~g~i~~l~~~g~~~~~~~~-l~~~l~~A~~~~~~i~~~~~~~l~~~  286 (305)
T 2wp8_A          227 EELLRDGVLTVTLNKNREVVQVSKAGGLPMDALT-LMKCCHEAYSIIEKITDQILQLLKED  286 (305)
T ss_dssp             HHHHCSEEEEEEECTTSEEEEEEEEEEEEECHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhccCCcEEEEEcCCCcEEEEEecCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999988899996 99999999999999999999999864

>2nn6_A Polymyositis/scleroderma autoantigen 1; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=1.1e-56  Score=416.18  Aligned_cols=274  Identities=22%  Similarity=0.474  Sum_probs=251.8

Q ss_pred             cccccHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCc
Q 022140           11 SSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDE   90 (302)
Q Consensus        11 ~~~~~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~   90 (302)
                      .+.|..+......|++|++++|++++|+|||+++|+|++.+++|   +++|||+|++|+|+|+|+|++++..|..++|++
T Consensus        14 ~~~~~~~~~~s~~e~~~i~~~L~~g~R~DGR~~~e~R~i~ie~g---~A~GSa~v~~G~T~VL~tV~~e~~~p~~~~~~~   90 (358)
T 2nn6_A           14 PNSHMKETPLSNCERRFLLRAIEEKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSPKLNRATE   90 (358)
T ss_dssp             ----CCCCCCCHHHHHHHHHHHHTTCCTTSCCTTCCCCCEEEEC---SSTTEEEEESSSCEEEEEECCEEECCCSTTTTS
T ss_pred             cccccccccccHhHHHHHHHHHhcCCCCCCCCccccCCeEEEEe---cCCcEEEEEECCcEEEEEEEecccCCcccCCCC
Confidence            35677777888899999999999999999999999999999999   899999999999999999999998888888999


Q ss_pred             ceEEEEEecCCCCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHH
Q 022140           91 GCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSA  170 (302)
Q Consensus        91 g~l~v~V~~~~~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~  170 (302)
                      |.+.++|+++|++++.+++|++++++++++++|++.|+++.++|+++|||+||+++|.|+|+++||++|||++||+++|+
T Consensus        91 g~l~~~v~~~p~a~~~~~~g~~s~~e~eisrli~r~Lr~s~~idl~~LcI~pg~~~w~I~Vdv~VL~~DGn~~dAai~Aa  170 (358)
T 2nn6_A           91 GILFFNLELSQMAAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAA  170 (358)
T ss_dssp             CCEEEEEEECTTTCSSCCSSSTHHHHTHHHHHHHHHHHHHTCBCSSSSCSBTTTBEEEEEEEEEECSCCSCCHHHHHHHH
T ss_pred             cEEEEEEEecCCccccccCCCCCHHHHHHHHHHHHHhhhccccchHhhcccCCCccEEEEEEEEEEeCCCCHHHHHHHHH
Confidence            99999999999999988889888999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEE--CCEEEECCChHHHhcCCceEE
Q 022140          171 VAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILH--KNYILADPTSEEESIMETLVT  248 (302)
Q Consensus       171 ~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~--~~~~l~DPt~~Ee~~~~~~l~  248 (302)
                      ++||+++++|.+.+.++.+...+           ++++++.++.++++|+++|||++  ++.+|+|||.+||+.+++.++
T Consensus       171 ~aAL~da~iP~v~~~~~~v~i~~-----------~~~~~~~~l~i~~~p~avsvgl~~~~~~illDPt~~Ee~~~~~~l~  239 (358)
T 2nn6_A          171 IVALCHFRRPDVSVQGDEVTLYT-----------PEERDPVPLSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLV  239 (358)
T ss_dssp             HHHHHHCCCCCCBCCTTCCBCCH-----------HHHTSCCCCCBCCCEEEEEEEECTTTSSEEESCCHHHHHHCSCEEE
T ss_pred             HHHHHHhCcCcEEeeCCeeEecc-----------cccccccccCccCCEEEEEEEEEeeCCEEEECCCHHHHhhcCccEE
Confidence            99999999999888655433211           23567788999999999999988  789999999999999999999


Q ss_pred             EEEcCCCcEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          249 VVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       249 i~~~~~g~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      |+++++|+|+.+++.|+.+++.++ +.+|+++|.+++++|++++++++++.
T Consensus       240 Va~t~~g~I~~lqk~G~~~ls~~~-l~~~l~~A~~~~~~i~~~~~~~l~~~  289 (358)
T 2nn6_A          240 IAMNKHREICTIQSSGGIMLLKDQ-VLRCSKIAGVKVAEITELILKALEND  289 (358)
T ss_dssp             EEEETTTEEEEEEEESCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEcCCCeEEEEEeCCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            999999999999999998899996 99999999999999999999999864

>2nn6_E Exosome complex exonuclease RRP42; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=4.5e-57  Score=412.60  Aligned_cols=272  Identities=23%  Similarity=0.308  Sum_probs=246.1

Q ss_pred             HhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEe
Q 022140           19 FRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFH   98 (302)
Q Consensus        19 ~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~   98 (302)
                      +-...|++|++++|++++|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|++++..|..++|++|++.++|+
T Consensus        19 ~~s~~e~~~i~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~e~~~p~~~~~~~g~l~~~v~   98 (305)
T 2nn6_E           19 TLSEAEKVYIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVD   98 (305)
T ss_dssp             CCCHHHHHHHHHHHHTTCCSSSCCSSCCCCCEEEECCCTTSSSEEEEEETTEEEEEECCCCCSCCCSSSCSSCCEEEECC
T ss_pred             ccChhHHHHHHHHHhcCCCCCCCCCcCccCeEEEeCcccCCCcEEEEEECCeEEEEEEEEEeeCCCcCCCCceEEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999888888899999999999


Q ss_pred             cCCCCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCC
Q 022140           99 MPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQ  178 (302)
Q Consensus        99 ~~~~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~  178 (302)
                      ++|++++.|+.+.++++++.++++|++.|+++++||+++||++||+++|.|+|+++||++|||++||+++|+++||++++
T Consensus        99 ~~p~a~~~~~~r~~~~~~~~isrli~r~lr~s~~idl~~L~i~p~~~~w~i~idv~VL~~DG~~~daai~aa~~AL~~a~  178 (305)
T 2nn6_E           99 CSASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTR  178 (305)
T ss_dssp             CCTTTCSSCCTTSTHHHHHHHHHHHHHHHHHSCCSCSSSSCSSTTTCCCCEEEEEEECCCCSSHHHHHHHHHHHTTTTCC
T ss_pred             eCCCcCccccCCCCchHHHHHHHHHHHHHhhcCcccHHHheeccCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcC
Confidence            99999988754444578999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcEEec--CCceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCc
Q 022140          179 IPTVSLD--DGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQ  256 (302)
Q Consensus       179 iP~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~  256 (302)
                      +|.+.+.  ++....         +.+..++.+..++.++++|+++|||++++.+|+|||.+||+.+++.++|+++++|+
T Consensus       179 iP~~~~~~~~~~~~~---------i~~~~d~~~~~~l~l~~~p~avt~g~i~~~~l~Dpt~~Ee~~~~~~l~Va~~~~g~  249 (305)
T 2nn6_E          179 IPRVRVLEDEEGSKD---------IELSDDPYDCIRLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGV  249 (305)
T ss_dssp             CCEEEEECC---------------EEEEESSCCCSCCCCTTCCCCEEEEESSSSEESSCCHHHHTSCSEEEEECCCSSSC
T ss_pred             CCeEEEecCCCCcee---------eeccCcccccccccccCceEEEEEEEECCEEEECCCHHHHhhcCCcEEEEEcCCCC
Confidence            9998872  222111         11223456788899999999999999999999999999999999999999999999


Q ss_pred             EEEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 022140          257 LVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGME  300 (302)
Q Consensus       257 i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~~  300 (302)
                      |+++++.|+..++.++ |.+|+++|.+++++|++++++++++++
T Consensus       250 i~~i~~~g~~~l~~~~-l~~~l~~A~~~~~~i~~~~~~~l~~~~  292 (305)
T 2nn6_E          250 VTCMRKVGKGSLDPES-IFEMMETGKRVGKVLHASLQSVVHKEE  292 (305)
T ss_dssp             CCEEEEEESSCBCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEccCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999988899996 999999999999999999999998764

>2wnr_B Probable exosome complex exonuclease 1; phosphate binding, 3'-5' exoribonuclease, hydrolase; 2.65A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=100.00  E-value=1.2e-48  Score=345.57  Aligned_cols=232  Identities=19%  Similarity=0.279  Sum_probs=203.2

Q ss_pred             ChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeee--ccCCCCCCCcceEEEEEecC
Q 022140           23 FPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEV--MTPSLESPDEGCVSIDFHMP  100 (302)
Q Consensus        23 ~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v--~~p~~~~p~~g~l~v~V~~~  100 (302)
                      .+..|.+..+++++|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+|+.  .+|..+.|++|.+.++|+++
T Consensus         3 ~~~~~~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~g~l~~~~~~~   82 (240)
T 2wnr_B            3 TIITQDQLKTSPSVREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIRCRYNMA   82 (240)
T ss_dssp             ------------CCCTTSCCTTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECCSSSSCCSSSCEEEEEEEEC
T ss_pred             ceEeeeEeecccCccCCCCCcCCccCeEEEeCCCCCCCEEEEEEECCeEEEEEEEcCCCCCcccccCCCcEEEEEEEEeC
Confidence            4567888889999999999999999999999999999999999999999999999954  33455789999999999999


Q ss_pred             CCCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCC
Q 022140          101 PICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP  180 (302)
Q Consensus       101 ~~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP  180 (302)
                      |++++.++.+++++++++++++|++.|++  .++++.|   |+   |+|+|+++||++|||++||+++|+++||+|+++|
T Consensus        83 p~a~~~~~~~~~~~~~~~l~~ll~r~l~~--~i~l~~~---p~---~~I~i~~~VL~~dG~~~~a~i~aa~~AL~da~iP  154 (240)
T 2wnr_B           83 PFSVEERKRPGPDRRSVEISKITAEALRP--ALILEKF---PR---SVIDVFIEVLEAEGGTRCAGITAASVALADAGIP  154 (240)
T ss_dssp             TTSSSSCCCSSCCHHHHHHHHHHHHHHGG--GBCGGGS---TT---EEEEEEEEEEECCSCHHHHHHHHHHHHHHHTTCC
T ss_pred             CCCcCCccCCCCChhHHHHHHHHHHHHHH--hcCHHHC---CC---cEEEEEEEEEeCCCCHHHHHHHHHHHHHHHcCCc
Confidence            99998887777889999999999999987  5777654   53   9999999999999999999999999999999998


Q ss_pred             cEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEE-cCCCcEEE
Q 022140          181 TVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVL-DSSNQLVS  259 (302)
Q Consensus       181 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~-~~~g~i~~  259 (302)
                                                        ++++|+++|++++++.+++|||.+||+.+++.++|++ +.+|+++.
T Consensus       155 ----------------------------------~~~~v~avs~g~~~~~~l~Dp~~~Ee~~~~~~~~v~~~~~~~~i~~  200 (240)
T 2wnr_B          155 ----------------------------------MRDMVVACAAGKVGDQVVLDLSEEEDKEGQADVPVAILPRTREITL  200 (240)
T ss_dssp             ----------------------------------BSSCCEEEEEEESSSSEEESCCSHHHHSCSEEEEEEEETTTTEEEE
T ss_pred             ----------------------------------cccceeeEEEEEECCEEEeCCCHHHhccCCceEEEEEECCCCCEEE
Confidence                                              5789999999999999999999999999999999998 67899999


Q ss_pred             EEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          260 LYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       260 i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      +++.|+  ++.++ +.+|+++|.+++++|++.++++|+++
T Consensus       201 lq~~g~--~~~~~-l~~~l~~A~~~~~~i~~~~~~~l~~~  237 (240)
T 2wnr_B          201 LQSDGN--LTPEE-FERALDLAVEGCLRIHEVQKEALRKR  237 (240)
T ss_dssp             EEEEEC--BCHHH-HHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             EEEEcc--cCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999985  78886 99999999999999999999999875

>2nn6_B Exosome complex exonuclease RRP41; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=5.2e-48  Score=343.17  Aligned_cols=232  Identities=20%  Similarity=0.216  Sum_probs=206.4

Q ss_pred             ChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCC---CCCCcceEEEEEec
Q 022140           23 FPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSL---ESPDEGCVSIDFHM   99 (302)
Q Consensus        23 ~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~---~~p~~g~l~v~V~~   99 (302)
                      +|..+++-.+++++|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+++...|..   +.|++|.+.+++++
T Consensus         3 ~~~~~~~~i~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~g~~~~~~~~~~~~~~~g~l~~~~~~   82 (249)
T 2nn6_B            3 DPMAGLELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSS   82 (249)
T ss_dssp             --------CCBTTBCSSSSCTTSCCCEEEEESCSSSSSEEEEEEESSCEEEEEEEEEEECCSSSCCCCCSSCCEEEEEEE
T ss_pred             ChhhhhhhcccCCcCCCCCCcCCcCCeEEEeCCCCCCCeEEEEEECCeEEEEEEEccCCccccccccCCCcEEEEEEEEc
Confidence            456666555688999999999999999999999999999999999999999999999876553   57899999999999


Q ss_pred             CCCCCCCcc-CCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCC
Q 022140          100 PPICSPLVR-PGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQ  178 (302)
Q Consensus       100 ~~~~~~~~~-~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~  178 (302)
                      +|++++.++ .+++++++++++++|++.|++  .++++.|   |   .|.|+|+++||++|||+++|+++|+++||+|++
T Consensus        83 ~p~a~~~~~~~~~~~~~~~~~~~ll~r~l~~--~i~~~~~---p---~~~I~i~~~VL~~dG~~~~A~i~aa~~AL~da~  154 (249)
T 2nn6_B           83 ATFSTGERKRRPHGDRKSCEMGLQLRQTFEA--AILTQLH---P---RSQIDIYVQVLQADGGTYAACVNAATLAVLDAG  154 (249)
T ss_dssp             CTTTSSSCCCTTTSTHHHHHHHHHHHHHHHH--TTCGGGC---T---TEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCcccccccCCCCCHhHHHHHHHHHHHHHH--hcCHHHC---C---CcEEEEEEEEEeCCCCHHHHHHHHHHHHHHhcC
Confidence            999987764 567788999999999999986  6888765   4   399999999999999999999999999999999


Q ss_pred             CCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEc-CCCcE
Q 022140          179 IPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLD-SSNQL  257 (302)
Q Consensus       179 iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~-~~g~i  257 (302)
                      +|                                  ++++|.++|++++++.+|+|||.+||+.+++.++|+++ ..|+|
T Consensus       155 iP----------------------------------l~~~v~avs~g~~~~~~l~Dp~~~Ee~~~~~~~~v~~~~~~~~i  200 (249)
T 2nn6_B          155 IP----------------------------------MRDFVCACSAGFVDGTALADLSHVEEAAGGPQLALALLPASGQI  200 (249)
T ss_dssp             CC----------------------------------CSSCCEEEEEEEETTEEEESCCHHHHTSSCCCEEEEEETTTTEE
T ss_pred             Cc----------------------------------ccCCeeeEEEEEECCeEEECCChHHhccCCcEEEEEEECCCCCE
Confidence            98                                  67999999999999999999999999999999999995 77899


Q ss_pred             EEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          258 VSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       258 ~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      +.+++.|  .++.++ +.+|+++|.+++++|+++++++|++.
T Consensus       201 ~~lq~~g--~~~~~~-l~~~l~~A~~~~~~i~~~~~~~l~~~  239 (249)
T 2nn6_B          201 ALLEMDA--RLHEDH-LERVLEAAAQAARDVHTLLDRVVRQH  239 (249)
T ss_dssp             EEEEECS--CCBTTS-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEC--CcCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999997  578886 99999999999999999999999764

>2po1_A Probable exosome complex exonuclease 1; RNAse PH, hydrolase/hydrolase/RNA complex; 1.94A {Pyrococcus abyssi} PDB: 2po0_A* 2pnz_A 2po2_A*

Probab=100.00  E-value=4.5e-47  Score=337.14  Aligned_cols=226  Identities=20%  Similarity=0.248  Sum_probs=206.5

Q ss_pred             HHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEe--eeccCCCCCCCcceEEEEEecCCCCCCC
Q 022140           29 ERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKM--EVMTPSLESPDEGCVSIDFHMPPICSPL  106 (302)
Q Consensus        29 ~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~--~v~~p~~~~p~~g~l~v~V~~~~~~~~~  106 (302)
                      +.++++++|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+|  +...|..+.|++|.+.++|+++|++++.
T Consensus         9 ~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~g~l~v~~~~~p~a~~~   88 (249)
T 2po1_A            9 KLIDENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILRVRYNMAPFSVEE   88 (249)
T ss_dssp             CCSBCSSCBTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEEECSSGGGCCSSSCEEEEEEEECGGGSSS
T ss_pred             EEecccCccCCCCCcccccCEEEEeCCcCCCCEEEEEEECCcEEEEEEEcCcccCcccccCCCceEEEEEEEeCCccccc
Confidence            44578899999999999999999999999999999999999999999999  5444456788999999999999999987


Q ss_pred             ccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecC
Q 022140          107 VRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDD  186 (302)
Q Consensus       107 ~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~  186 (302)
                      ++.+.++++++.++++|++.|++  +++++.|   |+   |.|+|+++||++|||+++|+++|+++||+|+++|      
T Consensus        89 ~~~~~~~~~~~~~s~li~r~l~~--~i~l~~~---p~---~~i~I~~~VL~~dG~~~~aai~aa~~AL~da~iP------  154 (249)
T 2po1_A           89 RKKPGPDRRSIEISKVIKGALEP--ALILEMF---PR---TAIDVFIEVLQADAGTRVAGITAASLALADAGIP------  154 (249)
T ss_dssp             CCCSSCCHHHHHHHHHHHHHHGG--GBCGGGS---TT---EEEEEEEEEEECCSCHHHHHHHHHHHHHHHTTCC------
T ss_pred             ccCCCCCHHHHHHHHHHHHHHHh--hccHHHC---CC---CEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCC------
Confidence            76666788999999999999987  6887654   64   9999999999999999999999999999999998      


Q ss_pred             CceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEE-cCCCcEEEEEccCC
Q 022140          187 GKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVL-DSSNQLVSLYKPGG  265 (302)
Q Consensus       187 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~-~~~g~i~~i~~~G~  265 (302)
                                                  ++++|+++|+|++++.+++|||.+||+.+++.++|++ +..|+|+.+++.| 
T Consensus       155 ----------------------------~~~~v~avs~g~~~~~~l~Dp~~~Ee~~~~~~l~va~~~~~~~i~~~~~~g-  205 (249)
T 2po1_A          155 ----------------------------MRDLVAACAAGKIEGEIVLDLNKEEDNYGEADVPVAIMPLKNDITLLQMDG-  205 (249)
T ss_dssp             ----------------------------BSSCCEEEEEEEETTEEEESCCHHHHHTCSEEEEEEEEGGGTEEEEECCEE-
T ss_pred             ----------------------------ccCceEEEEEEEECCEEEecCcHHHhccCCceEEEEEECCCCCEEEEEEEc-
Confidence                                        5788999999999999999999999999999999998 6788999999988 


Q ss_pred             cccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          266 AVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       266 ~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                       .++.++ +.+|+++|.+++++|++++++++++.
T Consensus       206 -~~~~~~-l~~~l~~A~~~~~~i~~~~~~~l~~~  237 (249)
T 2po1_A          206 -YLTKDE-FIEAVKLAIKGAKAVYQKQREALKEK  237 (249)
T ss_dssp             -CCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -ccCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             478886 99999999999999999999999764

>3b4t_A Ribonuclease PH; RNAse, tRNA nucleotidyltransferase, RPHA, STRU genomics, TBSGC; 2.10A {Mycobacterium tuberculosis}

Probab=100.00  E-value=5.8e-46  Score=332.33  Aligned_cols=235  Identities=21%  Similarity=0.255  Sum_probs=206.4

Q ss_pred             hcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCC-CCCcceEEEEEecCCCCCCCcc---
Q 022140           33 AESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLE-SPDEGCVSIDFHMPPICSPLVR---  108 (302)
Q Consensus        33 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~-~p~~g~l~v~V~~~~~~~~~~~---  108 (302)
                      ..++|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+++...|... .|++|++.+++++.|++++.|.   
T Consensus         3 ~~g~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~~~~~Re   82 (262)
T 3b4t_A            3 HVSKREDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTAEYAMLPSATHSRSDRE   82 (262)
T ss_dssp             --CCSTTSCCTTCCCCEEEEETSSSSSSEEEEEEETTEEEEEEEEEEESCC----CCSCCEEEEEEEECGGGSSSCCCCH
T ss_pred             CCCcCCCCCCCcCcCCeEEEeCCcCCCCeEEEEEECCCEEEEEEEecCcCCCccCCCCceEEEEEEEeCCCccccccccc
Confidence            357999999999999999999999999999999999999999999999877543 3789999999999999987763   


Q ss_pred             --CCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecC
Q 022140          109 --PGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDD  186 (302)
Q Consensus       109 --~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~  186 (302)
                        +|++++++++++++|++.|++  +||++.|   + +  |+|+|+++||++|||+++|+++|+++||++++.|.  +++
T Consensus        83 ~~~G~~~~~~~~isrli~r~lr~--~i~~~~l---~-~--~~I~i~~~VL~~DG~~~~aai~aa~~AL~~a~~~~--~~~  152 (262)
T 3b4t_A           83 SVRGRLSGRTQEISRLIGRSLRA--CIDLAAL---G-E--NTIAIDCDVLQADGGTRTAAITGAYVALADAVTYL--SAA  152 (262)
T ss_dssp             HHHTSCCHHHHHHHHHHHHHHHT--TBCHHHH---C-S--EEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHH--HHT
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHH--hcCHhHC---C-C--eEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhh--ccC
Confidence              377889999999999999996  8898877   3 3  99999999999999999999999999999996432  111


Q ss_pred             CceeecCccccccccCcCccccccc-cccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCC
Q 022140          187 GKIVMLPEEQKEENSEKEPVNKEKR-KLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGG  265 (302)
Q Consensus       187 ~~~~~~~~~~~~~~~~~~~~~~~~~-~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~  265 (302)
                      |.                     .. ++.++++|+++||+++++.+|+|||.+||+.+++.++|+++++|+|+++++.|+
T Consensus       153 ~~---------------------~~~~ip~~~~v~avsvg~~~g~~l~Dpt~~Ee~~~~~~l~va~~~~g~i~~i~~~g~  211 (262)
T 3b4t_A          153 GK---------------------LSDPRPLSCAIAAVSVGVVDGRIRVDLPYEEDSRAEVDMNVVATDTGTLVEIQGTGE  211 (262)
T ss_dssp             TC---------------------CSSSCCBCSCEEEEEEEEETTEEEESCCHHHHTTCSEEEEEEEETTSCEEEEEECSS
T ss_pred             Cc---------------------cccCCcccCceeEEEEEEECCEEEECCCHHHHhccCceEEEEEcCCCCEEEEEeeCC
Confidence            11                     11 355899999999999999999999999999999999999999999999999885


Q ss_pred             -cccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          266 -AVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       266 -~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                       ..++.++ |.+|+++|.+.+++|++++++++++.
T Consensus       212 ~~~~~~~~-l~~~l~~A~~~~~~i~~~~~~~l~~~  245 (262)
T 3b4t_A          212 GATFARST-LDKLLDMALGACDTLFAAQRDALALP  245 (262)
T ss_dssp             CCCBCHHH-HHHHHHHHHHHHHHHHHHHHHHHTSC
T ss_pred             CCCcCHHH-HHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence             6799996 99999999999999999999999864

>2je6_B RRP41, exosome complex exonuclease 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_B* 2jeb_B* 2br2_B 2c37_B* 2c38_B* 2c39_B* 3l7z_B

Probab=100.00  E-value=9e-46  Score=329.03  Aligned_cols=223  Identities=20%  Similarity=0.274  Sum_probs=204.5

Q ss_pred             HhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeec--cCCCCCCCcceEEEEEecCCCCCCCccC
Q 022140           32 LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVM--TPSLESPDEGCVSIDFHMPPICSPLVRP  109 (302)
Q Consensus        32 l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~--~p~~~~p~~g~l~v~V~~~~~~~~~~~~  109 (302)
                      +++++|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+++..  +|..+.|++|.+.++|+++|++++.++.
T Consensus        16 l~~~~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~g~~e~~~~~~~~~~~g~l~v~~~~~p~a~~~~~~   95 (250)
T 2je6_B           16 LDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDERKN   95 (250)
T ss_dssp             CTTSCBTTSCCTTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECSSGGGSCSSSCEEEEEEEECTTSSSSCCC
T ss_pred             cCCCccCCCCCccCcCCeEEEeCCCCCCCeEEEEEECCcEEEEEEEcccccccccccCCCcEEEEEEEEeCCCccCCccC
Confidence            68899999999999999999999999999999999999999999999653  3345678999999999999999988877


Q ss_pred             CCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCce
Q 022140          110 GRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKI  189 (302)
Q Consensus       110 g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~  189 (302)
                      |+++++++.++++|++.|++  .++++.+   |   .|.|+|+++||++|||+++|+++|+++||+++++|         
T Consensus        96 g~~~~~e~~~s~li~r~l~~--~i~~~~~---p---~~~i~I~~~VL~~DG~~~~aai~aa~~AL~~a~iP---------  158 (250)
T 2je6_B           96 PAPSRREIELSKVIREALES--AVLVELF---P---RTAIDVFTEILQADAGSRLVSLMAASLALADAGIP---------  158 (250)
T ss_dssp             SSCCHHHHHHHHHHHHHHHT--TBCGGGS---T---TEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCC---------
T ss_pred             CCCChhHHHHHHHHHHHHHh--hcCHhhC---C---CcEEEEEEEEEeCCCCHHHHHHHHHHHHHHhcCCC---------
Confidence            78889999999999999997  4776543   4   49999999999999999999999999999999998         


Q ss_pred             eecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEE-cCCCcEEEEEccCCccc
Q 022140          190 VMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVL-DSSNQLVSLYKPGGAVL  268 (302)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~-~~~g~i~~i~~~G~~~~  268 (302)
                                               ++++|.++|++++++.+|+|||.+||+.+++.++|++ +..++|+++++.|  .+
T Consensus       159 -------------------------~~~~v~avsvg~~~~~~l~Dpt~~Ee~~~~~~l~va~~~~~~~i~~v~~~g--~~  211 (250)
T 2je6_B          159 -------------------------MRDLIAGVAVGKADGVIILDLNETEAMWGEADMPIAMMPSLNQVTLFQLNG--SM  211 (250)
T ss_dssp             -------------------------BSSCCEEEEEEEETTEEEESCCHHHHHHSSEEEEEEEEGGGTEEEEEEEEE--CB
T ss_pred             -------------------------ccCceEEEEEEEECCEEEeCCCHHHHhcCCceEEEEEECCCCCEEEEEEEc--cc
Confidence                                     5788999999999999999999999999999999999 5678999999988  57


Q ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          269 AYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       269 ~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      +.++ +.+|+++|.+.+++|++++++++++.
T Consensus       212 ~~~~-l~~~l~~A~~~~~~i~~~~~~~l~~~  241 (250)
T 2je6_B          212 TPDE-FRQAFDLAVKGINIIYNLEREALKSK  241 (250)
T ss_dssp             CHHH-HHHHHHHHHHHHHHHHHHHHHHHHGG
T ss_pred             CHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8886 99999999999999999999999875

>3m7n_D Probable exosome complex exonuclease 1; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 3m85_D 2ba0_F 2ba1_E

Probab=100.00  E-value=3.4e-46  Score=332.26  Aligned_cols=224  Identities=19%  Similarity=0.281  Sum_probs=205.5

Q ss_pred             HHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeec--cCCCCCCCcceEEEEEecCCCCCCCc
Q 022140           30 RHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVM--TPSLESPDEGCVSIDFHMPPICSPLV  107 (302)
Q Consensus        30 ~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~--~p~~~~p~~g~l~v~V~~~~~~~~~~  107 (302)
                      +++.+++|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+|+..  .+....|++|.+.++++++|++++.+
T Consensus        10 ~~i~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~g~l~~~~~~~P~s~~~r   89 (258)
T 3m7n_D           10 KLIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKAIIRYRYNMAPFSVEER   89 (258)
T ss_dssp             CSEETTEETTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEEECSSSTTCCSSSCEEEEEEEECGGGSSSC
T ss_pred             HHHhcCCCCCCCCcCCccCeEEEECCCCCCCceEEEEECCeEEEEEEEcccCCCCccccCCCceEEEEEEEeCCcccccc
Confidence            3456899999999999999999999999999999999999999999998543  23346789999999999999999887


Q ss_pred             cCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCC
Q 022140          108 RPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDG  187 (302)
Q Consensus       108 ~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~  187 (302)
                      +.+++++++++++++|++.|++  .|+++.|   |   +|.|+|+++||++|||+++|+++|+++||+|+++|       
T Consensus        90 ~~~~~~~re~ei~~li~r~l~~--~i~~~~~---p---~~~I~V~~~VL~~DG~~~~Aai~aa~lAL~dagiP-------  154 (258)
T 3m7n_D           90 KRPGPDRRSIEISKVSKEAFEA--VIMKELF---P---RSAIDIFVEVLQADAGSRTACLNAASVALVDAGVP-------  154 (258)
T ss_dssp             CCSSCCHHHHHHHHHHHHHHHT--TBCGGGS---T---TEEEEEEEEEEECCTTHHHHHHHHHHHHHHHTTCC-------
T ss_pred             cCCCCCHHHHHHHHHHHHHHHh--hcCHHhC---C---ceEEEEEEEEEEcCCCHHHHHHHHHHHHHHhcCCC-------
Confidence            7788889999999999999997  6787765   4   59999999999999999999999999999999998       


Q ss_pred             ceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEE-cCC---CcEEEEEcc
Q 022140          188 KIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVL-DSS---NQLVSLYKP  263 (302)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~-~~~---g~i~~i~~~  263 (302)
                                                 ++++|.++|+|++++.+|+|||.+||+.+++.++|++ +..   |+|+.+++.
T Consensus       155 ---------------------------~~~~v~avsvg~i~~~~llDpt~~Ee~~~~~d~~va~~~~~~~~~~I~~lq~~  207 (258)
T 3m7n_D          155 ---------------------------MKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMD  207 (258)
T ss_dssp             ---------------------------BSSEEEEEEEEEETTEEEESCCHHHHHHSSEEEEEEEEEETTEEEEEEEEEEE
T ss_pred             ---------------------------CCCceEEEEEEEECCEEEECCCHHHHhccCceEEEEEEcCCCCCCCEEEEEec
Confidence                                       5789999999999999999999999999999999999 677   899999998


Q ss_pred             CCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022140          264 GGAVLAYTSAVQDCIALTRQRVKELHQILEEAISG  298 (302)
Q Consensus       264 G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~  298 (302)
                      |  .++.++ +.+|+++|.+.+++|++++++++++
T Consensus       208 g--~~~~~~-l~~~l~~A~~~~~~i~~~~~~~l~~  239 (258)
T 3m7n_D          208 G--RMTRDE-VKQAIELAKKGALQIYEMQREAILR  239 (258)
T ss_dssp             E--EECHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             C--CcCHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7  789996 9999999999999999999999875

>1r6l_A Ribonuclease PH; beta-alpha-beta-alpha fold, hexamer, phosphate bound, transf; HET: NHE; 1.90A {Pseudomonas aeruginosa} SCOP: d.14.1.4 d.101.1.1 PDB: 1r6m_A

Probab=100.00  E-value=1.9e-45  Score=324.92  Aligned_cols=231  Identities=19%  Similarity=0.305  Sum_probs=203.2

Q ss_pred             CCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCC-CCCcceEEEEEecCCCCCCCcc-----C
Q 022140           36 IRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLE-SPDEGCVSIDFHMPPICSPLVR-----P  109 (302)
Q Consensus        36 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~-~p~~g~l~v~V~~~~~~~~~~~-----~  109 (302)
                      .|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+++...|... .|++|.+.+++++.|++++.+.     +
T Consensus         2 ~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~v~~~~~p~~~~~r~~Re~~~   81 (239)
T 1r6l_A            2 NRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTAEYGMLPRSTGERNQREASR   81 (239)
T ss_dssp             CCTTCCCTTCCCCEEEESSCSSSSSEEEEEEETTEEEEEEEEEEESCSSCCC---CCEEEEEEEECTTSSSSCCCCHHHH
T ss_pred             cCCCCCCCCCcCCeEEEeCCcCCCCeEEEEEECCEEEEEEEEccCccCCccCCCCcEEEEEEEEeCCCccccccccccCC
Confidence            499999999999999999999999999999999999999999999877543 4789999999999999987652     3


Q ss_pred             CCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCce
Q 022140          110 GRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKI  189 (302)
Q Consensus       110 g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~  189 (302)
                      |++++.+++++++|++.|++  ++|++.|    ++  |.|+|+++||++|||+++|+++|+++||+|++.|..  ++|  
T Consensus        82 G~~~~~~~~isrli~r~l~~--~i~~~~l----~~--~~i~I~~~VL~~DG~~~~aai~aa~~AL~da~~~~~--~~~--  149 (239)
T 1r6l_A           82 GKQGGRTLEIQRLIGRSLRA--ALDLSKL----GE--NTLYIDCDVIQADGGTRTASITGATVALIDALAVLK--KRG--  149 (239)
T ss_dssp             TSCCHHHHHHHHHHHHHHHH--TBCGGGT----CS--EEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHH--HTT--
T ss_pred             CCCcHHHHHHHHHHHHHHHH--hcCHHHc----CC--eEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhcchhc--ccC--
Confidence            77889999999999999996  8998887    23  889999999999999999999999999999984421  111  


Q ss_pred             eecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccC-Cccc
Q 022140          190 VMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPG-GAVL  268 (302)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G-~~~~  268 (302)
                                         +..++.++++|+++||+++++.+++|||.+||+.+++.++|+++++|+++.+++.| +..+
T Consensus       150 -------------------~~~~ip~~~~~~avs~g~~~~~~l~Dpt~~Ee~~~~~~l~va~~~~g~i~~~~~~g~~~~~  210 (239)
T 1r6l_A          150 -------------------ALKGNPLKQMVAAVSVGIYQGVPVLDLDYLEDSAAETDLNVVMTDAGGFIEVQGTAEGAPF  210 (239)
T ss_dssp             -------------------CCSSCCBCCCEEEEEEEEETTEEEESCCHHHHHHCSEEEEEEEETTSCEEEEEEEESSSCC
T ss_pred             -------------------cccccCccCceeEEEEEEECCEEEECCCHHHHhcCCceEEEEEeCCCCEEEEEEeCCCCCc
Confidence                               11235689999999999999999999999999999999999999999999999987 4679


Q ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022140          269 AYTSAVQDCIALTRQRVKELHQILEEAISG  298 (302)
Q Consensus       269 ~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~  298 (302)
                      +.++ +.+|+++|.+.+++|++++++++++
T Consensus       211 ~~~~-l~~~l~~a~~~~~~i~~~~~~~l~~  239 (239)
T 1r6l_A          211 RPAE-LNAMLELAQQGMQELFELQRAALAE  239 (239)
T ss_dssp             CHHH-HHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CHHH-HHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            9996 9999999999999999999999864

>1udn_A Ribonuclease PH, RNAse PH; transferase, riken structural genomics/proteomics initiative structural genomics; 2.30A {Aquifex aeolicus} SCOP: d.14.1.4 d.101.1.1 PDB: 1udq_A 1uds_A 1udo_A

Probab=100.00  E-value=9.9e-46  Score=329.51  Aligned_cols=231  Identities=18%  Similarity=0.286  Sum_probs=205.8

Q ss_pred             CCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCC-CCCCcceEEEEEecCCCCCCCc-----cC
Q 022140           36 IRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSL-ESPDEGCVSIDFHMPPICSPLV-----RP  109 (302)
Q Consensus        36 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~-~~p~~g~l~v~V~~~~~~~~~~-----~~  109 (302)
                      +|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+++...|+. ..|++|++.+++++.|++++.+     .+
T Consensus         1 ~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~~~~~~~P~a~~~r~~Re~~~   80 (255)
T 1udn_A            1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITAEYSMLPRATQQRTIRESVQ   80 (255)
T ss_dssp             -CTTSCCTTCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEESCCCGGGTTSSCCEEEEEEEECSCCTTSCCCCSSTT
T ss_pred             CCCCCCCCCCccCeEEEECCCCCCCEEEEEEECCEEEEEEEEcCCcCCCCCCCCCceEEEEEEEcCCCccccccccccCC
Confidence            59999999999999999999999999999999999999999999877643 4578999999999999998765     24


Q ss_pred             CCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCce
Q 022140          110 GRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKI  189 (302)
Q Consensus       110 g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~  189 (302)
                      |++++++++++++|++.|++  +||++.|    ++  |.|+|+++||++|||+++|+++|+++||+|++.|.+  +.|  
T Consensus        81 G~~~~~~~eisrli~r~lr~--~i~~~~l----~~--~~i~I~~~VL~~DG~~~~aai~aa~~AL~da~~~~~--~~~--  148 (255)
T 1udn_A           81 GRIGGRTHEIQRMIGRAMRT--AVELTKI----GE--RTIWVDCDVIQADGGTRTAAITGAFVAVADAIIKLH--KEG--  148 (255)
T ss_dssp             CSCCHHHHHHHHHHHHHHHH--HBCGGGG----CS--CEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHH--HTT--
T ss_pred             CCCCHHHHHHHHHHHHHHHH--hcCHHHc----CC--eEEEEEEEEEeCCCCHHHHHHHHHHHHHHhhcchhc--ccC--
Confidence            77889999999999999996  8998887    23  999999999999999999999999999999995421  111  


Q ss_pred             eecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCC-ccc
Q 022140          190 VMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGG-AVL  268 (302)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~-~~~  268 (302)
                                         +..++.++++|+++|++++++.+|+|||.+||+.+++.++|+++++|+++.+++.|+ ..+
T Consensus       149 -------------------~~~~ipl~~~v~avsvg~~~g~~llDpt~~Ee~~~~~~l~va~~~~g~i~~~q~~g~~~~~  209 (255)
T 1udn_A          149 -------------------IIEETPIKDFVAAVSVGIVNDRILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYSF  209 (255)
T ss_dssp             -------------------SSSSCCBCCCEEEEEEEEETTEEEESCCHHHHHTCSEEEEEEEETTSCEEEEEEEESSCCC
T ss_pred             -------------------cccCCCccCceeEEEEEEECCEEEECCCHHHHhhCCCCEEEEEeCCCCEEEEEEeCCCCCc
Confidence                               123466899999999999999999999999999999999999999999999999873 679


Q ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 022140          269 AYTSAVQDCIALTRQRVKELHQILEEAISG  298 (302)
Q Consensus       269 ~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~  298 (302)
                      +.++ |.+|+++|.+.+++|++++++++++
T Consensus       210 ~~~~-l~~~l~~A~~~~~~i~~~~~~~l~~  238 (255)
T 1udn_A          210 TKDE-LIKMLDLAQKGINELIELQKKLYVI  238 (255)
T ss_dssp             CHHH-HHHHHHHHHHHHHHHHHHHHTTEEE
T ss_pred             CHHH-HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            9996 9999999999999999999999875

>1oys_A Ribonuclease PH; transferase, tRNA processing; 2.40A {Bacillus subtilis} SCOP: d.14.1.4 d.101.1.1 PDB: 1oyp_A 1oyr_A

Probab=100.00  E-value=6.3e-46  Score=329.08  Aligned_cols=232  Identities=19%  Similarity=0.315  Sum_probs=190.1

Q ss_pred             CCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCC-CCCCCcceEEEEEecCCCCCCCc-----cC
Q 022140           36 IRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPS-LESPDEGCVSIDFHMPPICSPLV-----RP  109 (302)
Q Consensus        36 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~-~~~p~~g~l~v~V~~~~~~~~~~-----~~  109 (302)
                      +|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+++...|. ...|++|.+.++++++|++++.+     .+
T Consensus         1 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~~~~~~~p~a~~~~~~Re~~~   80 (245)
T 1oys_A            1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPQATNQQTIQESSK   80 (245)
T ss_dssp             CCTTSCCTTCCCCEEEECC-----CCCEEEEETTEEEEEEEEEESCCCGGGTTSCCCEEEEEEEC---------------
T ss_pred             CCCCCCCCCCcCCeEEEeCCCCCCCEEEEEEECCeEEEEEEEeccccCCccCCCCceEEEEEEEeCCCcCcccccccccC
Confidence            4999999999999999999999999999999999999999999988774 35689999999999999998765     24


Q ss_pred             CCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCce
Q 022140          110 GRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKI  189 (302)
Q Consensus       110 g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~  189 (302)
                      |++++++++++++|++.|++  +||++.|   + +  |.|+|+++||++|||+++|+++|+++||+|++.|.+  +.   
T Consensus        81 G~~~~~~~eis~li~r~l~~--~i~~~~l---~-~--~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~~~~~--~~---  147 (245)
T 1oys_A           81 GKISGRTMEIQRLIGRALRA--VVDLEKL---G-E--RTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLI--KA---  147 (245)
T ss_dssp             ----CHHHHHHHHHHHHHHH--TBCHHHH---C-S--CEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHH--HT---
T ss_pred             CCCchHHHHHHHHHHHHHHH--hcCHhHC---C-C--EEEEEEEEEEeCCCCHHHHHHHHHHHHHHhccchhc--cc---
Confidence            67889999999999999996  8898887   2 3  688899999999999999999999999999997642  11   


Q ss_pred             eecCccccccccCcCccccccccccCCCccEEEEEEEECCEEE-ECCChHHHhcCCceEEEEEcCCCcEEEEEccCC-cc
Q 022140          190 VMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYIL-ADPTSEEESIMETLVTVVLDSSNQLVSLYKPGG-AV  267 (302)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l-~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~-~~  267 (302)
                                        .+..++.|+++|.++|+|++++.++ +|||.+||+.+++.++|+++++|+++.+++.|+ ..
T Consensus       148 ------------------~~~~~ipl~~~v~avs~g~~~g~~vl~Dp~~~Ee~~~~~~~~v~~~~~g~i~~iq~~g~~~~  209 (245)
T 1oys_A          148 ------------------GTIKTNPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEAT  209 (245)
T ss_dssp             ------------------TSSSSCCBCSCEEEEEEEEETTTEEEESCCHHHHHHEEEEEEEEEETTSCEEEEEEEESSCC
T ss_pred             ------------------CcccccCCCCceeEEEEEEECCEEEEecCCHHHHhcCCCcEEEEEcCCCcEEEEEEeCCCCC
Confidence                              1234577899999999999998777 999999999999999999999999999999874 67


Q ss_pred             cChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          268 LAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       268 ~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      ++.++ |.+|+++|.+++++|+++++++++++
T Consensus       210 ~~~~~-l~~~l~~A~~~~~~i~~~~~~~l~~~  240 (245)
T 1oys_A          210 FSRED-LNGLLGLAEKGIQELIDKQKEVLGDS  240 (245)
T ss_dssp             CCHHH-HHHHHHHHHHHHHHHHHHHHHHC---
T ss_pred             cCHHH-HHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            99996 99999999999999999999999864

>2wp8_B Exosome complex component SKI6; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.7e-45  Score=326.58  Aligned_cols=222  Identities=15%  Similarity=0.186  Sum_probs=191.2

Q ss_pred             HhcCCCCCCCCCCCCcceEEEeCCccCC-CeeEEEEeCCeEEEEEEEeeecc--CCCCCCCcceEEEEEecCCCCCCCcc
Q 022140           32 LAESIRPDARSLSRARNTTISMGAVASA-DGSALAKIGSTTMLAAIKMEVMT--PSLESPDEGCVSIDFHMPPICSPLVR  108 (302)
Q Consensus        32 l~~~~R~DGR~~~e~R~i~i~~g~l~~a-~GSa~v~~G~T~Vi~~V~~~v~~--p~~~~p~~g~l~v~V~~~~~~~~~~~  108 (302)
                      +++++|+|||+++|+|++.+++|.++++ +|||+|++|+|+|+|+|+++...  |..+.|++|.+.++++++|++++.+.
T Consensus         8 ~~~~~R~DGR~~~e~R~i~i~~g~l~~aa~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~~g~l~v~~~~~p~a~~~~~   87 (246)
T 2wp8_B            8 SPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNINKFSKFERS   87 (246)
T ss_dssp             CTTSCCTTSCCTTCCCCEEEEECSCTTTCSEEEEEEETTEEEEEEEEEEEC------CCSSSEEEEEEEEEC--------
T ss_pred             cccCccCCCCCcCCccCeEEEeCCCCCCCCceEEEEECCeEEEEEEEecCCcccccccCCCcEEEEEEEEeCCccccccc
Confidence            4789999999999999999999999999 99999999999999999998862  34567899999999999999988765


Q ss_pred             C--CCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecC
Q 022140          109 P--GRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDD  186 (302)
Q Consensus       109 ~--g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~  186 (302)
                      +  |+++++++.++++|++.|++  .++++.|   |   +|.|+|+++||++|||+++|+++|+++||+|+++|      
T Consensus        88 ~r~g~~~~~~~~~s~li~r~l~~--~i~~~~~---p---~~~I~i~~~VL~~dG~~~~aai~aa~~AL~~a~iP------  153 (246)
T 2wp8_B           88 KSSHKNERRVLEIQTSLVRMFEK--NVMLNIY---P---RTVIDIEIHVLEQDGGIMGSLINGITLALIDAGIS------  153 (246)
T ss_dssp             ------CHHHHHHHHHHHHHHHH--HBCTTTS---C---SEEEEEEEEEEECCSCHHHHHHHHHHHHHHHHTCC------
T ss_pred             ccCCCCChhHHHHHHHHHHHHHH--hhhHHHC---C---CeEEEEEEEEEECCCCHHHHHHHHHHHHHHHcCCc------
Confidence            4  56678999999999999987  5676654   3   69999999999999999999999999999999998      


Q ss_pred             CceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEE-cCCCcEEEEEccCC
Q 022140          187 GKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVL-DSSNQLVSLYKPGG  265 (302)
Q Consensus       187 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~-~~~g~i~~i~~~G~  265 (302)
                                                  ++++|.++|+|++++.+++|||.+|| .+++.++|++ +..++|+.+++.| 
T Consensus       154 ----------------------------~~~~v~avs~g~~~~~~l~Dp~~~Ee-~~~~~l~v~~~~~~~~i~~i~~~g-  203 (246)
T 2wp8_B          154 ----------------------------MFDYISGISVGLYDTTPLLDTNSLEE-NAMSTVTLGVVGKSEKLSLLLVED-  203 (246)
T ss_dssp             ----------------------------BSSCEEEEEEEEETTEEESSCCHHHH-HHSEEEEEEEETTSSCEEEEEECS-
T ss_pred             ----------------------------ccCceeEEEEEEECCEEEECCCchhh-ccCceEEEEEeCCCCCEEEEEecC-
Confidence                                        57899999999999999999999999 9999999999 5788999999855 


Q ss_pred             cccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          266 AVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       266 ~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                       .++.++ +.+|+++|.+.+++|++++++++++.
T Consensus       204 -~~~~~~-l~~~l~~A~~~~~~i~~~~~~~l~~~  235 (246)
T 2wp8_B          204 -KIPLDR-LENVLAIGIAGAHRVRDLMDEELRKH  235 (246)
T ss_dssp             -CEEHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -CcCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             678886 99999999999999999999998764

>3dd6_A Ribonuclease PH; exoribonuclease, tRNA maturation, RNAse PH., transferase; 1.70A {Bacillus anthracis}

Probab=100.00  E-value=2.3e-45  Score=326.54  Aligned_cols=235  Identities=18%  Similarity=0.294  Sum_probs=209.0

Q ss_pred             hcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccC-CCCCCCcceEEEEEecCCCCCCCcc---
Q 022140           33 AESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTP-SLESPDEGCVSIDFHMPPICSPLVR---  108 (302)
Q Consensus        33 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p-~~~~p~~g~l~v~V~~~~~~~~~~~---  108 (302)
                      ....|.|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+++...| ....|++|++.++++++|++++.++   
T Consensus         8 ~~~~~~~~R~~~e~R~i~i~~g~~~~A~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~v~~~~~P~a~~~~~~Re   87 (255)
T 3dd6_A            8 HHHMRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVPPFMRGEGKGWVTAEYAMIPRATEQRTIRE   87 (255)
T ss_dssp             ---CCCCSCCTTCCCCEEEEESCSSSSSEEEEEEETTEEEEEEEEEESCCCGGGTTSSCCEEEEEEEECTTSSSSCCCCC
T ss_pred             ccccccCCCCcCCCCCEEEEECCCCCCCeEEEEEECCeEEEEEEEecCCCCCCCCCCCceEEEEEEEECCCccccccccc
Confidence            346899999999999999999999999999999999999999999988654 4567899999999999999988763   


Q ss_pred             --CCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecC
Q 022140          109 --PGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDD  186 (302)
Q Consensus       109 --~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~  186 (302)
                        +|++++++++++++|++.|++  +||++.|   + +  |+|+|+++||++|||+++|+++|+++||+++++|.+  .+
T Consensus        88 ~~~g~~~~~~~eisrli~r~lr~--~i~~~~l---~-~--~~I~V~~~VL~~DG~~~~aai~aa~~AL~~a~~p~~--~~  157 (255)
T 3dd6_A           88 SSKGKVTGRTMEIQRLIGRALRA--VVDLEAL---G-E--RTVWIDCDVIQADGGTRTASITGAYVAMVLAFEKLL--QA  157 (255)
T ss_dssp             CC-CCCCHHHHHHHHHHHHHHHH--HBCHHHH---C-S--CEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHH--HT
T ss_pred             ccCCCCCHHHHHHHHHHHHHHHH--hcChhhc---C-C--eEEEEEEEEEECCCCHHHHHHHHHHHHHHHhhhhhh--hc
Confidence              277889999999999999997  7888876   2 3  999999999999999999999999999999998853  11


Q ss_pred             CceeecCccccccccCcCccccccccccCCCccEEEEEEEECCEEE-ECCChHHHhcCCceEEEEEcCCCcEEEEEccC-
Q 022140          187 GKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYIL-ADPTSEEESIMETLVTVVLDSSNQLVSLYKPG-  264 (302)
Q Consensus       187 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l-~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G-  264 (302)
                      |                     +..++.++++|.++|+|++++.++ +|||.+||+.++..++|+++++|+|+.+++.| 
T Consensus       158 g---------------------~~~~iPl~~~v~avsvg~i~g~~vllDpt~~Ee~~~~~~l~Va~~~~g~i~~vq~~g~  216 (255)
T 3dd6_A          158 E---------------------KVSKIPVKDYLAATSVGIVEEQGVVLDLNYAEDSKADVDMNVIMTGKGQFVEVQGTGE  216 (255)
T ss_dssp             T---------------------SSSSCCBSSCEEEEEEEEETTTEEEESCCHHHHHTEEEEEEEEEETTSCEEEEEEEES
T ss_pred             C---------------------cccCCCccCceeEEEEEEECCEEEEeCCCHHHHhhcCceEEEEEcCCCcEEEEEecCC
Confidence            1                     122356899999999999999888 99999999999999999999999999999987 


Q ss_pred             CcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          265 GAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       265 ~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      +..++.++ +.+|+++|.+.+++|++++++++++.
T Consensus       217 ~~~~~~~~-l~~~l~~A~~~~~~i~~~~~~~l~~~  250 (255)
T 3dd6_A          217 EATFSRAQ-LNELLDAAEQGIFQLIDIQKEALGDI  250 (255)
T ss_dssp             SSCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHGGG
T ss_pred             CCCcCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67899996 99999999999999999999999864

>2nn6_D Exosome complex exonuclease RRP46; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=1.2e-44  Score=319.31  Aligned_cols=218  Identities=19%  Similarity=0.267  Sum_probs=177.4

Q ss_pred             HHHHhcCCCCCCCCCC----CCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeec-cCCCCCCCcceEEEEEecCCCC
Q 022140           29 ERHLAESIRPDARSLS----RARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVM-TPSLESPDEGCVSIDFHMPPIC  103 (302)
Q Consensus        29 ~~~l~~~~R~DGR~~~----e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~-~p~~~~p~~g~l~v~V~~~~~~  103 (302)
                      .+...+++|+|||+++    |+|++.+++|.+++++|||+|++|+|+|+|+|+++.. .|..+.|++|.+.+  +|+|+ 
T Consensus         9 ~~~~~~~~R~DGR~~~~~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~g~~~~~~~~~~~~~g~l~~--~~~p~-   85 (237)
T 2nn6_D            9 TDAKIRAENGTGSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEV--ILRPK-   85 (237)
T ss_dssp             ------------------CCCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECC------CCEEEEE--EEECS-
T ss_pred             CCCCccCccCCCCCCCCccccccceEEEeCCCCCCCEEEEEEECCcEEEEEEeCCCcccccccCCCcEEEEE--EecCC-
Confidence            3456778999999999    9999999999999999999999999999999999987 45566778886665  45664 


Q ss_pred             CCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEE
Q 022140          104 SPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVS  183 (302)
Q Consensus       104 ~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~  183 (302)
                           .|++++++++++++|++.|++        +|+.+++.+|.|+|+++||++|||+++|+++|+++||+|+++|   
T Consensus        86 -----~g~~~~~e~~~~~li~r~l~~--------~i~~~~~p~~~I~I~~~VL~~dG~~~~aai~aa~~AL~da~iP---  149 (237)
T 2nn6_D           86 -----IGLPGVAEKSRERLIRNTCEA--------VVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVP---  149 (237)
T ss_dssp             -----SSCCCHHHHHHHHHHHHHHHH--------HCGGGCSSSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCC---
T ss_pred             -----CCCCCccHHHHHHHHHHHHHH--------HhchhcCCceEEEEEEEEEECCCcHHHHHHHHHHHHHHHcCCC---
Confidence                 366778899999999999864        3555667789999999999999999999999999999999998   


Q ss_pred             ecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEE-CCEEEECCChHHHhcCCceEEEEEcCCC-cEEEEE
Q 022140          184 LDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILH-KNYILADPTSEEESIMETLVTVVLDSSN-QLVSLY  261 (302)
Q Consensus       184 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~-~~~~l~DPt~~Ee~~~~~~l~i~~~~~g-~i~~i~  261 (302)
                                                     ++++|.++|+|++ ++.+++||+.+||+.+.+.++|+++.++ +|+.++
T Consensus       150 -------------------------------~~~~v~avs~g~~~~~~~llDp~~~Ee~~~~~~~~v~~~~~~~~i~~lq  198 (237)
T 2nn6_D          150 -------------------------------MRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFALDSVERKLLMSS  198 (237)
T ss_dssp             -------------------------------CSSCEEEEEEEECTTCCEEESCCHHHHHHCSEEEEEEEETTTCCCCEEE
T ss_pred             -------------------------------cccCeeeEEEEEecCCcEEeCCCHHHHhccCCceEEEEcCCCCCEEEEE
Confidence                                           5799999999999 7899999999999999999999999876 899999


Q ss_pred             ccCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          262 KPGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       262 ~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      +.|  .++.++ +.+|+++|.+++++|+++++++++++
T Consensus       199 ~~g--~~~~~~-l~~~l~~A~~~~~~i~~~~~~~l~~~  233 (237)
T 2nn6_D          199 TKG--LYSDTE-LQQCLAAAQAASQHVFRFYRESLQRR  233 (237)
T ss_dssp             EEE--SCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EeC--CcCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            987  578886 99999999999999999999999864

>3hkm_A OS03G0854200 protein; RNAse PH domain, phosphorylase, hydrolase; 1.98A {Oryza sativa japonica group}

Probab=100.00  E-value=2.9e-43  Score=311.26  Aligned_cols=214  Identities=20%  Similarity=0.269  Sum_probs=178.3

Q ss_pred             cCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeec-cCCCCCCCcceEEEEEecCCCCCCCccCCCC
Q 022140           34 ESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVM-TPSLESPDEGCVSIDFHMPPICSPLVRPGRP  112 (302)
Q Consensus        34 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~-~p~~~~p~~g~l~v~V~~~~~~~~~~~~g~~  112 (302)
                      +++|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|+|+.. .|..+.|+++.+  +|.|+|.      .|++
T Consensus         2 eg~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~g~~~~~~~~~~~~~~~~--~~~~~P~------~g~~   73 (246)
T 3hkm_A            2 EESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKASI--EVVWKPM------TGQI   73 (246)
T ss_dssp             ---CTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEECCCEECCCTTSCSSSCEE--EEEEECS------SSCC
T ss_pred             CCcCCCCCCCCCcCCeEEEECCCCCCCeEEEEEECCeEEEEEEecCcCCCcccCCCccEEE--EEEeCCC------CCCC
Confidence            589999999999999999999999999999999999999999999763 455566766665  4556673      3667


Q ss_pred             CCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCceeec
Q 022140          113 AEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVML  192 (302)
Q Consensus       113 ~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~~~~  192 (302)
                      ++.+.+++++|++.|++        +|+.+++.+|.|+|+++||++|||+++|+++|+++||+++++|            
T Consensus        74 ~~~~~e~~~li~r~l~~--------l~~~~~~~~~~I~v~~~VL~~dG~~~~aai~aa~~AL~dagiP------------  133 (246)
T 3hkm_A           74 GKQEKEYEMTLKRTLQS--------ICLLTVHPNTTTSVILQVVGNDGSLLPCAINACCAALVFAGIP------------  133 (246)
T ss_dssp             CTTHHHHHHHHHHHHHH--------HBCTTSSCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHTCC------------
T ss_pred             ChhHHHHHHHHHHHHHH--------hcCccCCCcEEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCC------------
Confidence            77889999999999865        4556677789999999999999999999999999999999998            


Q ss_pred             CccccccccCcCccccccccccCCCccEEEEEEEE-CCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccC-------
Q 022140          193 PEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILH-KNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPG-------  264 (302)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~-~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G-------  264 (302)
                                            ++++|.++|++++ ++.+|+|||.+||+.+++.++|++++++ +|.+++.|       
T Consensus       134 ----------------------~~~~v~avs~g~~~~g~~llDpt~~Ee~~~~~~~~va~~~~~-i~~lq~~g~~~~~~~  190 (246)
T 3hkm_A          134 ----------------------LKHLAVAIGCGVLEDGEVILDTNKAEEQQLKSFAHLVFPNSR-KSASSKEPNQKEEDS  190 (246)
T ss_dssp             ----------------------BSSCEEEEEEEECTTSCEEESCCHHHHTTCSEEEEEEEEC------------------
T ss_pred             ----------------------CCCceEEEEEEEEECCEEEECCCHHHHhcCCeeEEEEEeCCc-eEEEeeccccccccc
Confidence                                  5789999999998 7899999999999999999999999884 88888866       


Q ss_pred             ---------CcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          265 ---------GAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       265 ---------~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                               +..++.++ +.+|+++|.+.+++|+++++++|++.
T Consensus       191 ~~~~i~~~~~g~~~~~~-l~~~l~~A~~~~~~i~~~~~~~l~~~  233 (246)
T 3hkm_A          191 ERGLITSITHGVMSEED-YFSCIERGLAASSRISDFMRTTLQKQ  233 (246)
T ss_dssp             ---CCCEEEEECEEHHH-HHHHHHHHHHHHHHHHHHHHTTTC--
T ss_pred             ccceeeeeccCCcCHHH-HHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence                     45789886 99999999999999999999999864

>2nn6_F MTR3, exosome component 6; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: d.14.1.4 d.101.1.1

Probab=100.00  E-value=7.2e-44  Score=320.45  Aligned_cols=230  Identities=21%  Similarity=0.230  Sum_probs=193.2

Q ss_pred             hChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCC-C------------CC
Q 022140           22 LFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSL-E------------SP   88 (302)
Q Consensus        22 ~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~-~------------~p   88 (302)
                      ..|..|+.   ++++|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+++...+.. +            .+
T Consensus        15 ~~~~~~~~---~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~~~~~~~~~~~   91 (272)
T 2nn6_F           15 QPPQLYAA---DEEEAPGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAA   91 (272)
T ss_dssp             -----------------CCCCSSCCCCCCCCCSCCSSSSEEECCCSSSCEEEEEEEEEECC-------------------
T ss_pred             cCCccccc---ccCccCCCCCccccCCeEEEeCCCCCCCeEEEEEeCCeEEEEEEECCCcccccccccccccccccccCC
Confidence            34556654   77899999999999999999999999999999999999999999998876542 2            56


Q ss_pred             CcceEEEEEecCCCCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHH
Q 022140           89 DEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALL  168 (302)
Q Consensus        89 ~~g~l~v~V~~~~~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~  168 (302)
                      ++|.+.++|++.|+++..++.+++++.++.++++|++.|++  .++++.   +|   .|.|+|+++||++|||+++|+++
T Consensus        92 ~~g~l~v~~~~~p~a~~~~~~~~~~~~e~~~s~li~r~l~~--~i~~~~---~p---~~~I~I~~~VL~~DG~~~~aai~  163 (272)
T 2nn6_F           92 LRGRLLCDFRRAPFAGRRRRAPPGGCEERELALALQEALEP--AVRLGR---YP---RAQLEVSALLLEDGGSALAAALT  163 (272)
T ss_dssp             CBCEEEEEEEECTTSSSSCCCSCCHHHHHHHHHHHHHHHTT--TBCSTT---SB---TCEEEEEEEEEECCSSHHHHHHH
T ss_pred             CceEEEEEEEecCCCcCCccCCCCCHHHHHHHHHHHHHHHH--hccHHH---CC---ceEEEEEEEEEeCCCCHHHHHHH
Confidence            78999999999999998888888889999999999999987  466543   34   39999999999999999999999


Q ss_pred             HHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEE---ECCEEEECCChHHHhcCCc
Q 022140          169 SAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCIL---HKNYILADPTSEEESIMET  245 (302)
Q Consensus       169 A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~---~~~~~l~DPt~~Ee~~~~~  245 (302)
                      |+++||+++++|                                  +++++.++|+++   .++.+|+|||.+||+.+++
T Consensus       164 aa~~AL~da~iP----------------------------------~~~~v~avsvg~~~~~~~~~llDpt~~Ee~~~~~  209 (272)
T 2nn6_F          164 AAALALADAGVE----------------------------------MYDLVVGCGLSLAPGPAPTWLLDPTRLEEERAAA  209 (272)
T ss_dssp             HHHHHHHHHCCC----------------------------------BSSCCEEEECCCCSCSSCCCCSSCCTTTGGGCSS
T ss_pred             HHHHHHHHcCCc----------------------------------ccCcEEEEEEEEeeccCCeEEeCCCHHHhccCCc
Confidence            999999999998                                  468889999999   8889999999999999999


Q ss_pred             eEEEEE-cCCCcEEEEEccCCcccCh-HHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          246 LVTVVL-DSSNQLVSLYKPGGAVLAY-TSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       246 ~l~i~~-~~~g~i~~i~~~G~~~~~~-~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      .++|++ +..++|+++++.|  .++. ++ |.+|+++|.+.+++|++++++++++.
T Consensus       210 ~l~va~~~~~~~I~~i~~~g--~~~~~~~-l~~~l~~A~~~~~~i~~~~~~~l~~~  262 (272)
T 2nn6_F          210 GLTVALMPVLNQVAGLLGSG--EGGLTES-WAEAVRLGLEGCQRLYPVLQQSLVRA  262 (272)
T ss_dssp             EEEEEEETTTTEEEEEEEEC--CSSCTTT-THHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCEEEEEEec--CCCHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999997 5678999999988  4677 85 99999999999999999999998764

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

Probab=100.00  E-value=4e-39  Score=316.25  Aligned_cols=240  Identities=15%  Similarity=0.183  Sum_probs=215.0

Q ss_pred             ccHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCC--C-----
Q 022140           14 MEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSL--E-----   86 (302)
Q Consensus        14 ~~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~--~-----   86 (302)
                      .-.++|..+.+..+.+..+++++|+|||+++|+|++.+++|++++++|||++++|+|+|+|+|+++...|..  +     
T Consensus       296 ~~~~~~~~~~~~~~r~~il~~g~R~DGR~~~elRpi~i~~g~l~~a~GSal~~~G~T~Vl~~Vt~~~~~~~~~~d~~~~~  375 (630)
T 3u1k_A          296 EIIESFNVVAKEVFRSIVLNEYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITA  375 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSCCTTSCCTTCCCCEEEEECCSTTSSEEEEEEETTEEEEEEEEEECGGGGSCSSHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCCCCCCccccceEEEECCCCCCCceEEEEECCeEEEEEEEcCCCCchhcccccccc
Confidence            345779999999999999999999999999999999999999999999999999999999999997655432  1     


Q ss_pred             --CCCcceEEEEEecCCCCCCCc-cCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHH
Q 022140           87 --SPDEGCVSIDFHMPPICSPLV-RPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALF  163 (302)
Q Consensus        87 --~p~~g~l~v~V~~~~~~~~~~-~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~  163 (302)
                        .+++|++.++++++|+++..+ +.|+++.++..+++++++.|++  +++.        ++.|+|+|+++||++|||.+
T Consensus       376 l~~~~~g~~~~~y~~~P~st~e~~~~g~~~rREi~~~~Li~raLr~--vi~~--------~~p~tI~V~~~VLesDGs~~  445 (630)
T 3u1k_A          376 INGIKDKNFMLHYEFPPYATNEIGKVTGLNRRELGHGALAEKALYP--VIPR--------DFPFTIRVTSEVLESNGSSS  445 (630)
T ss_dssp             HHCCCGGGEEEEEECCGGGGTCCCCCSSCCHHHHHHHHHHHHHHGG--GSCT--------TCSSEEEEEEEEEECSSCHH
T ss_pred             cCCCCceEEEEEEEecCCcccccccCCCCChHHHHHHHHHHHHHHh--hCcc--------cCCeEEEEEEEEEEcCCCHH
Confidence              367899999999999998764 3466788899999999999985  4542        35689999999999999999


Q ss_pred             HHHHHHHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEEC------C-----EEE
Q 022140          164 DAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHK------N-----YIL  232 (302)
Q Consensus       164 da~~~A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~------~-----~~l  232 (302)
                      +|+++|+++||+|+++|                                  |++++.++|+|+++      +     .+|
T Consensus       446 ~AsI~aa~lAL~dAGIP----------------------------------l~~~Vaavs~gli~~~~~~~g~~~~~~iL  491 (630)
T 3u1k_A          446 MASACGGSLALMDSGVP----------------------------------ISSAVAGVAIGLVTKTDPEKGEIEDYRLL  491 (630)
T ss_dssp             HHHHHHHHHHHHHTTCC----------------------------------CSSCCEEEEEEEEEEECSSSSCEEEEEEE
T ss_pred             HHHHHHHHHHHHhCCCC----------------------------------cccceEEEEEEEecCCCcccccccCceEE
Confidence            99999999999999998                                  57889999999987      3     799


Q ss_pred             ECCChHHHhcCCceEEEEEcCCCcEEEEEccCCc-ccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          233 ADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGA-VLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       233 ~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~-~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      +||+..|+..++..+.|+.+.+| |+.+++.|.. +++.++ |.+|+++|.+.+++|++.|++++++.
T Consensus       492 lD~~~~Ed~~~d~d~~Va~t~~g-It~lQ~~~k~~~~s~~~-l~~aL~~A~~g~~~I~~~m~~al~~~  557 (630)
T 3u1k_A          492 TDILGIEDYNGDMDFKIAGTNKG-ITALQADIKLPGIPIKI-VMEAIQQASVAKKEILQIMNKTISKP  557 (630)
T ss_dssp             ESCCHHHHHTSSEEEEEEECSSC-EEEEEEEECSSCBCHHH-HHHHHHHHHHHHHHHHHHHHHHCSSC
T ss_pred             ecCCHHHHhhCcceEEEEecCCc-eEEEEecCCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999888 9999998864 789996 99999999999999999999999865

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

Probab=100.00  E-value=2.1e-38  Score=315.37  Aligned_cols=239  Identities=16%  Similarity=0.165  Sum_probs=196.7

Q ss_pred             HHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeecc--CCC---CCCCcc
Q 022140           17 DAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMT--PSL---ESPDEG   91 (302)
Q Consensus        17 ~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~--p~~---~~p~~g   91 (302)
                      ++|.++.+..+.+..+++++|+|||+++|+|++.+++|.+++++|||++++|+|+|+|+|+....+  +.+   ..+++|
T Consensus       301 ~~~~~~~k~~vr~~i~~~g~R~DGR~~~elRpI~ie~gvl~~a~GSAl~~~G~TqVL~~Vt~gp~e~~~~~d~l~~~~~g  380 (723)
T 3cdi_A          301 EILHAIEKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTD  380 (723)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCCTTSCCTTCCCCEEEEESCSTTSSEEEEEEETTEEEEEEEEECC-------------CTT
T ss_pred             HHHHHHHHHHHHHHHhccCcCCCCCCccccccceEEeCCCCCCCeEEEEEECCcEEEEEEEecCcccccCCcccCCCCce
Confidence            455555444444444458999999999999999999999999999999999999999999754322  222   235789


Q ss_pred             eEEEEEecCCCCCCCc-cCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHH
Q 022140           92 CVSIDFHMPPICSPLV-RPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSA  170 (302)
Q Consensus        92 ~l~v~V~~~~~~~~~~-~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~  170 (302)
                      ++.++++++|++++.+ +.|.+++++..++++++++|++  +++++.      .+.|+|+|+++||++|||+++|+++|+
T Consensus       381 ~~~~~y~~~P~st~e~~r~g~p~~REi~~~~li~raL~~--vI~~~~------~~p~tI~Vd~~VLesdGs~~~Asi~aa  452 (723)
T 3cdi_A          381 TFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLA--VMPDMD------KFPYTVRVVSEITESNGSSSMASVCGA  452 (723)
T ss_dssp             SEEEEEECCGGGGTCCCCC-----CTTHHHHHHHHHHHT--TSCCSS------SSCSCEEEEEEEEECSSCHHHHHHHHH
T ss_pred             EEEEEEecCCCCccccccCCCCCHHHHHHHHHHHHHHHH--hcCccc------CCCEEEEEEEEEEeCCCCHHHHHHHHH
Confidence            9999999999998765 3455677888899999999986  566543      356999999999999999999999999


Q ss_pred             HHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEEC-C---EEEECCChHHHhcCCce
Q 022140          171 VAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHK-N---YILADPTSEEESIMETL  246 (302)
Q Consensus       171 ~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~-~---~~l~DPt~~Ee~~~~~~  246 (302)
                      ++||+|+++|                                  +.+++.++|+|+++ +   .+|+||+.+||..+++.
T Consensus       453 ~lAL~dAgVP----------------------------------l~~~vaavs~gli~~g~~~~iL~Dp~~~Ed~~~d~d  498 (723)
T 3cdi_A          453 SLALMDAGVP----------------------------------IKAAVAGIAMGLVKEGDNYVVLSDILGDEDHLGDMD  498 (723)
T ss_dssp             HHHHHHTTCC----------------------------------CSSCCEEEEEEEEEETTEEEEESSCCGGGGGGCSEE
T ss_pred             HHHHhcCCCC----------------------------------cccceeeEEEEEEcCCCceEEEECCChHHhhhccce
Confidence            9999999999                                  46788999999996 3   59999999999999999


Q ss_pred             EEEEEcCCCcEEEEEccCC-cccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          247 VTVVLDSSNQLVSLYKPGG-AVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       247 l~i~~~~~g~i~~i~~~G~-~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      ++|+.+.+| |+.+++.|+ .+++.++ |.+|+++|.+.+++|++.|+++|++.
T Consensus       499 ~~Va~t~~g-I~~lq~~gk~~~is~e~-l~~~l~~A~~~~~~I~~~m~~al~~~  550 (723)
T 3cdi_A          499 FKVAGSRDG-ISALQMDIKIEGITKEI-MQVALNQAKGARLHILGVMEQAINAP  550 (723)
T ss_dssp             EEEEECSSC-EEEEEEEECSSCCCHHH-HHHHHHHHHHHHHHHHHHHHHHCC--
T ss_pred             eeecccCCc-eEEEEeCCccCCcCHHH-HHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            999999888 999999875 5789996 99999999999999999999999765

>3gme_A Polyribonucleotide nucleotidyltransferase; protein-RNA complex, cytoplasm, nucleotidyltransferase, RNA- binding, transferase, hydrolase; 2.40A {Escherichia coli E24377A} PDB: 3gll_A 3gcm_A 3h1c_A 3cdj_A

Probab=100.00  E-value=5.2e-38  Score=302.69  Aligned_cols=242  Identities=15%  Similarity=0.135  Sum_probs=202.1

Q ss_pred             ccHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEE-eeecc---CC-CCCC
Q 022140           14 MEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK-MEVMT---PS-LESP   88 (302)
Q Consensus        14 ~~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-~~v~~---p~-~~~p   88 (302)
                      .-.++|..+.+..+.+..+++++|+|||+++|+|++.+++|++++++|||++++|+|+|+|+|+ |+...   |. ...+
T Consensus       292 ~~~~~~~~~~~~~~R~~il~~g~R~DGR~~~elRpi~i~~g~l~~a~GSal~~~G~T~Vl~~Vt~gp~~~~~~~~~l~~~  371 (549)
T 3gme_A          292 ELGEILHAIEKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGE  371 (549)
T ss_dssp             -----CCHHHHHHHHHHHHHTCCCTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEC-------------
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCccceEEEECCCCCCCceEEEEECCeEEEEEEEecCcccccCccccCCC
Confidence            3556788888999999999999999999999999999999999999999999999999999996 54321   11 1234


Q ss_pred             CcceEEEEEecCCCCCCCc-cCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHH
Q 022140           89 DEGCVSIDFHMPPICSPLV-RPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAAL  167 (302)
Q Consensus        89 ~~g~l~v~V~~~~~~~~~~-~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~  167 (302)
                      ++|++.+++.++|+++... +.|+++.++..+++++++.|++  +|+++.+      +.|+|+|++.||++|||.++|++
T Consensus       372 ~~g~~~~~y~~~P~st~e~~~~g~~~~Reie~~~li~raL~~--vI~~~~~------~P~tI~V~~~VLesDGs~~~AsI  443 (549)
T 3gme_A          372 RTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLA--VMPDMDK------FPYTVRVVSEITESNGSSSMASV  443 (549)
T ss_dssp             --CCEEEEEECCGGGTTCCCCSSCCCSSHHHHHHHHHHHHTT--TCCCTTT------CCCEEEEEEEEEECSSCHHHHHH
T ss_pred             CceEEEEEEEeCCCCcCCcccCCCCChhHHHHHHHHHHHHHH--hcCcccc------CCeEEEEEEEEEECCCCHHHHHH
Confidence            7899999999999998754 3466788999999999999986  6765433      45899999999999999999999


Q ss_pred             HHHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEECC----EEEECCChHHHhcC
Q 022140          168 LSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKN----YILADPTSEEESIM  243 (302)
Q Consensus       168 ~A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~----~~l~DPt~~Ee~~~  243 (302)
                      +|+++||+|+++|                                  |++++.++++|++++    .+++||+..|+..+
T Consensus       444 ~aa~lAL~DAGvP----------------------------------m~~~Vaavs~Gli~~g~~~~iL~D~~~~Ed~~~  489 (549)
T 3gme_A          444 CGASLALMDAGVP----------------------------------IKAAVAGIAMGLVKEGDNYVVLSDILGDEDHLG  489 (549)
T ss_dssp             HHHHHHHHHHTCC----------------------------------CSSCCEEEEEEEEEETTEEEEEESCCHHHHHHS
T ss_pred             HHHHHHHHhCCCC----------------------------------cccceeEEEEEEEcCCCceEEEecCChHHHccC
Confidence            9999999999998                                  578899999999976    78999999999999


Q ss_pred             CceEEEEEcCCCcEEEEEccCC-cccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          244 ETLVTVVLDSSNQLVSLYKPGG-AVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       244 ~~~l~i~~~~~g~i~~i~~~G~-~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      +..+.|+.+.+| ++.++..+. ..++.++ |.+|+++|.+.+++|++.++++|.+.
T Consensus       490 d~d~~Va~t~~g-italqmd~ki~G~s~~~-l~~~L~~A~~g~~~I~~~m~~al~~p  544 (549)
T 3gme_A          490 DMDFKVAGSRDG-ISALQMDIKIEGITKEI-MQVALNQAKGARLHILGVMEQAINAP  544 (549)
T ss_dssp             SEEEEEEECSSC-EEEEEEEECCSCCCHHH-HHHHHHHHHHHHHHHHHHHHHHCCSC
T ss_pred             CceEEEEecCCC-eEEEEEccccCCcCHHH-HHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            999999988876 777765432 1378896 99999999999999999999999763

>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=100.00  E-value=1.1e-37  Score=311.20  Aligned_cols=241  Identities=17%  Similarity=0.162  Sum_probs=208.4

Q ss_pred             cHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEE-eeeccCC-C---CCCC
Q 022140           15 EVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK-MEVMTPS-L---ESPD   89 (302)
Q Consensus        15 ~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-~~v~~p~-~---~~p~   89 (302)
                      -.++|.++.+..+.+..+++++|+|||+++|+|++.+++|.+++++|||++++|+|+|+|+|+ |+...+. .   ..++
T Consensus       334 ~~~~~~~~~k~~~r~~i~~~g~R~DGR~~~elRpI~ie~gvl~~a~GSAl~~~G~TqVL~~Vt~Gp~~~~~~~d~l~~~~  413 (757)
T 1e3p_A          334 ISAAYRALTKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVT  413 (757)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCBCTTSCBTTCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEEEGGGSEECCSSSSCC
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCCCCCcccccceeEEeCCCCCCCEEEEEEECCcEEEEEEEecCCCccccccccCCCC
Confidence            346788888877777777899999999999999999999999999999999999999999997 5543221 1   2567


Q ss_pred             cceEEEEEecCCCCCCCcc-CCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHH
Q 022140           90 EGCVSIDFHMPPICSPLVR-PGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALL  168 (302)
Q Consensus        90 ~g~l~v~V~~~~~~~~~~~-~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~  168 (302)
                      +|++.++++++|+++..++ .|.++.++..+++++++.|++.  ++.      .+++.|+|+|+++||++|||.++|+++
T Consensus       414 ~g~~~~~y~f~P~st~e~~~~g~~~~reie~~~li~raL~~v--I~~------~~~~P~tI~V~~~VLesDGs~~~Asi~  485 (757)
T 1e3p_A          414 RKRYMHNYNFPPYSVGETGRVGSPKRREIGHGALAERAIVPV--LPT------REEFPYAIRQVSEALGSNGSTSMGSVC  485 (757)
T ss_dssp             EESEEEEEECCGGGGTCCCCCSSCCHHHHHHHHHHHHHHGGG--CCC------TTTSCEEEEEEEEEEECSSCHHHHHHH
T ss_pred             ceEEEEEEEeCCcccccccCCCCCchhHHHHHHHHHHHHHHh--ccc------cccCCEEEEEEEEEEECCCCHHHHHHH
Confidence            8999999999999987653 4567889999999999999863  331      235679999999999999999999999


Q ss_pred             HHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEE----CC----EEEECCChHHH
Q 022140          169 SAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILH----KN----YILADPTSEEE  240 (302)
Q Consensus       169 A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~----~~----~~l~DPt~~Ee  240 (302)
                      |+++||+|+++|                                  +++++.++|+|++    ++    .+|+||+..|+
T Consensus       486 aa~lAL~dAgIP----------------------------------~k~~Vaavs~gli~eg~dg~~~~~iLlDp~~~Ed  531 (757)
T 1e3p_A          486 ASTMSLLNAGVP----------------------------------LKAPVAGIAMGLISQEINGETHYVALTDILGAED  531 (757)
T ss_dssp             HHHHHHHHHTCC----------------------------------CSSCCEEEEEEEEEEESSSCEEEEEEESCCHHHH
T ss_pred             HHHHHHHHcCCC----------------------------------cccceEEEEEEEEecCCCCccceeEEeCCCHHHH
Confidence            999999999998                                  5677899999999    44    79999999999


Q ss_pred             hcCCceEEEEEcCCCcEEEEEccCC-cccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          241 SIMETLVTVVLDSSNQLVSLYKPGG-AVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       241 ~~~~~~l~i~~~~~g~i~~i~~~G~-~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      ..+++.++|+.+. ++|+.+++.|. ..++.++ |.+|+++|.+.+++|++.|+++|.+.
T Consensus       532 ~~gd~d~~Va~t~-~~It~lQ~~gk~~gi~~e~-l~~aL~~A~~~~~~I~~~m~~al~~~  589 (757)
T 1e3p_A          532 AFGDMDFKVAGTK-EFVTALQLDTKLDGIPASV-LAAALKQARDARLHILDVMMEAIDTP  589 (757)
T ss_dssp             HHCSEEEEEEECS-SSEEEEEEEECSSCCCHHH-HHHHHHHHHHHHHHHHHHHHHHCSSC
T ss_pred             hccCceEEEEecC-CeEEEEEEcCCccccCHHH-HHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            9999999999655 67999998886 4689995 99999999999999999999999764

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

Probab=100.00  E-value=3.2e-37  Score=305.47  Aligned_cols=244  Identities=16%  Similarity=0.137  Sum_probs=211.8

Q ss_pred             ccccHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEE-eeeccCC----CC
Q 022140           12 SEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK-MEVMTPS----LE   86 (302)
Q Consensus        12 ~~~~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-~~v~~p~----~~   86 (302)
                      ...-..+|..+.+..+.+..+++++|+|||+++|+|++.+++|++++++|||++++|+|+|+|+|+ |+...+.    ..
T Consensus       306 ~~~~~~~~~~~~~~~~r~~il~~g~R~DGR~~~elRpI~ie~gvl~~a~GSAl~~~G~TkVl~~Vt~Gp~~~~~~~d~l~  385 (726)
T 4aid_A          306 PLKLGAIFKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALE  385 (726)
T ss_dssp             SSSHHHHHHHHHHHHHHHHHHSSSBCTTSCBTTCCCCEEEEECSSTTSSEEEEEEETTEEEEEEEEEECGGGSEEEEETT
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCccceEEEECCCCCCCceEEEEeCCeEEEEEEEeCCCCccccccccc
Confidence            345678899999999999999999999999999999999999999999999999999999999996 5443221    12


Q ss_pred             CCCcceEEEEEecCCCCCCCcc-CCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHH
Q 022140           87 SPDEGCVSIDFHMPPICSPLVR-PGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDA  165 (302)
Q Consensus        87 ~p~~g~l~v~V~~~~~~~~~~~-~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da  165 (302)
                      .+++|++.+++.++|+++...+ .|+++.++..+++++++.|++  +++.      .+.+.|+|+|++.||++|||.++|
T Consensus       386 ~~~~g~~~~~y~~~P~st~er~~~g~~~~Reie~~~li~raL~~--vI~~------~~~~P~tI~V~~~VLesDGs~~~A  457 (726)
T 4aid_A          386 GTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRP--MLPT------KEDFPYTIRLVSEITESNGSSSMA  457 (726)
T ss_dssp             EEEEECEEEEEECCGGGGTCCCCCSSCCHHHHHHHHHHHHHHGG--GSCC------TTTCCCEEEEEEEEEECSSCHHHH
T ss_pred             CCCceEEEEEEEeCCCcccccccCCCcchhhHHHHHHHHHHHHH--hcCc------cccCCeEEEEEEEEEEcCCcHHHH
Confidence            3568999999999999876543 456778899999999999986  4442      234668999999999999999999


Q ss_pred             HHHHHHHHHhhCCCCcEEecCCceeecCccccccccCcCccccccccccCCCccEEEEEEEECC----EEEECCChHHHh
Q 022140          166 ALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKN----YILADPTSEEES  241 (302)
Q Consensus       166 ~~~A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~----~~l~DPt~~Ee~  241 (302)
                      +++|+++||+|+++|                                  |++++.++++|++++    .+++||+..|+.
T Consensus       458 sI~aa~lAL~DAGIP----------------------------------m~~~VaavsvGli~~g~~~~iLlD~~~~Ed~  503 (726)
T 4aid_A          458 TVCGSSLAMMDAGVP----------------------------------LVRPVSGIAMGLILEQDGFAVLSDILGDEDH  503 (726)
T ss_dssp             HHHHHHHHHHHTTCC----------------------------------CSSCCEEEEEEEEECSSCEEEEESCCTTGGG
T ss_pred             HHHHHHHHHHhcCCc----------------------------------cccCeeEEEEEEEcCCCceEEEecCChhHHh
Confidence            999999999999998                                  578899999999864    578999999999


Q ss_pred             cCCceEEEEEcCCCcEEEEEccCC-cccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          242 IMETLVTVVLDSSNQLVSLYKPGG-AVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       242 ~~~~~l~i~~~~~g~i~~i~~~G~-~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      .++..+.|+.+.+| ++.++..|. ..|+.++ |.+|+++|.+.+++|++.|+++|.+.
T Consensus       504 ~gd~d~~Va~t~~g-It~lQ~d~k~~~~s~e~-l~~aL~~A~~g~~~I~~~m~~al~~~  560 (726)
T 4aid_A          504 LGDMDFKVAGTSEG-LTSLQMDIKIAGITPAI-MEQALAQAKEGRAHILGEMNKAMDAP  560 (726)
T ss_dssp             GSSEEEEEEEETTE-EEEEEEEECSSCCCHHH-HHHHHHHHHHHHHHHHHHHHTTCSSC
T ss_pred             cCCceEEEEecCCc-eEEEEecCCcCCcCHHH-HHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            99999999987765 999998884 3789996 99999999999999999999999864

>3krn_A Protein C14A4.5, confirmed by transcript evidence; RNAse PH domain, homodimer, exosome, cell-death-related DNAS hydrolase; 3.92A {Caenorhabditis elegans}

Probab=100.00  E-value=3.5e-37  Score=268.78  Aligned_cols=201  Identities=17%  Similarity=0.239  Sum_probs=158.1

Q ss_pred             CCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccC-CCCCCCcceEEEEEecCCCCCCCccCCCCCCcHHHHHH
Q 022140           43 LSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTP-SLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAK  121 (302)
Q Consensus        43 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p-~~~~p~~g~l~v~V~~~~~~~~~~~~g~~~~~~~~ls~  121 (302)
                      .+|+|++.+++|.+++++|||+|++|+|+|+|+|+++...+ ..+.|+++  .++|+|+|+.      |++++.  ++++
T Consensus         2 ~~e~R~i~ie~g~l~~A~GSa~v~~G~T~Vl~~V~~~~e~~~~~~~~~~~--~l~v~~~p~~------G~~~~~--e~~~   71 (222)
T 3krn_A            2 AGRLREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASKASDEAM--TLDISYRANC------GDNKFN--VLNN   71 (222)
T ss_dssp             -CCCCCBCCBSCCC----CCCBCCBTTCEEECCCCSSCC---------------CCCSSCCC------C--CCS--SCTT
T ss_pred             CCcccceEEEECCCCCCCeEEEEEECCcEEEEEEECCCCCcccccCCceE--EEEEEEcCCC------CCCCHH--HHHH
Confidence            47899999999999999999999999999999999986432 23344444  4577888863      444444  7899


Q ss_pred             HHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEEecCCceeecCcccccccc
Q 022140          122 QLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENS  201 (302)
Q Consensus       122 ~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~~~~~~~~~~~~~~~~~~~  201 (302)
                      +|++.|++  .++++.   +|   .|.|+|+++||++||++++|+++|+++||+++++|                     
T Consensus        72 li~r~l~~--~i~~~~---~p---~~~I~I~~~VL~~DG~~~~aai~aa~~AL~dagiP---------------------  122 (222)
T 3krn_A           72 IIHSTLSN--AINLEL---FP---HTTISVTVHGIQDDGSMGAVAINGACFALLDNGMP---------------------  122 (222)
T ss_dssp             HHHHC--C--CSCC-----------CCCCCCCEEEECCSCHHHHHHHGGGTTTTTTTCC---------------------
T ss_pred             HHHHHHHH--hccHHh---CC---CcEEEEEEEEEECCCChHHHHHHHHHHHHHHCCCC---------------------
Confidence            99999987  455532   45   48999999999999999999999999999999998                     


Q ss_pred             CcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEE---cC-CCcEEEEEccCCcccChHHHHHHH
Q 022140          202 EKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVL---DS-SNQLVSLYKPGGAVLAYTSAVQDC  277 (302)
Q Consensus       202 ~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~---~~-~g~i~~i~~~G~~~~~~~~~l~~~  277 (302)
                                   +++++.++|+|++++.+++|||.+|++.+++.++|++   +. .++|+.+++.|  .++.++ +.+|
T Consensus       123 -------------~~~~v~avsvg~~~g~~llDpt~~Ee~~~~~~l~va~~~~~~~~~~i~~vq~~g--~~~~~~-l~~~  186 (222)
T 3krn_A          123 -------------FETVFCGVLIVRVKDELIIDPTAKQEAASTGRVLFSVCKGSDGHPEVCAMDAIG--HWDFIQ-LEAA  186 (222)
T ss_dssp             -------------TTSCCCCCCCEECSSSEESSCCTTTTTSCC-CCCCEECCCSSSSCCEEEECCBS--SCTTHH-HHTH
T ss_pred             -------------ccCcEEEEEEEEECCEEEeCCCHHHHhccCccEEEEEEccCCCCCCEEEEEEeC--CcCHHH-HHHH
Confidence                         5788999999999999999999999999999999999   75 68999999877  588886 9999


Q ss_pred             HHHHHHHHHHHHHHHHHHhhc
Q 022140          278 IALTRQRVKELHQILEEAISG  298 (302)
Q Consensus       278 i~~A~~~~~~l~~~l~~~l~~  298 (302)
                      +++|.+.+++|++++++++++
T Consensus       187 l~~a~~~~~~i~~~~~~~l~~  207 (222)
T 3krn_A          187 WSLAQPSASAIFDFYKTVMKR  207 (222)
T ss_dssp             HHHTTHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999875

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

Probab=99.97  E-value=3.2e-29  Score=246.16  Aligned_cols=205  Identities=17%  Similarity=0.147  Sum_probs=172.2

Q ss_pred             CcceEEEeCCccC-CCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCCCC----Cc--cCCCCCCcHHH
Q 022140           46 ARNTTISMGAVAS-ADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSP----LV--RPGRPAEAAPV  118 (302)
Q Consensus        46 ~R~i~i~~g~l~~-a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~~~----~~--~~g~~~~~~~~  118 (302)
                      -|++.+++|.+++ |+|||+|++|+|+|+|+|+++...+ +.  +...+.|+++..+++..    .|  |.|++++.+.+
T Consensus        14 ~R~i~ietG~~a~qA~GSa~v~~G~T~VL~tv~~~~~~~-~~--df~pL~v~y~~~~~a~g~iPg~f~kRegrps~~e~l   90 (630)
T 3u1k_A           14 NRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKPS-PS--QFMPLVVDYRQKAAAAGRIPTNYLRREVGTSDKEIL   90 (630)
T ss_dssp             SSEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCC-SS--SSCCEEEEEECSEETTTTEECTTC-----CCHHHHH
T ss_pred             CEEEEEEeCCccccCCeeEEEEECCeEEEEEEEecCCCC-CC--CeeEEEEEEEecccccCCCCccccccCCCCCHHHHH
Confidence            4799999999996 9999999999999999999986533 21  33446777776666652    12  35778899999


Q ss_pred             HHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCH--HHHHHHHHHHHHhhCCCCcEEecCCceeecCccc
Q 022140          119 VAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGAL--FDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQ  196 (302)
Q Consensus       119 ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l--~da~~~A~~~AL~~~~iP~~~~~~~~~~~~~~~~  196 (302)
                      ++++|.+.|++.  +        +..++|.++|+++||++||+.  ..|+++|+++||.++++|                
T Consensus        91 isRlIdR~lRp~--~--------~~~~~~~~qI~~~VLs~Dg~~~~~~aai~aAs~AL~~s~iP----------------  144 (630)
T 3u1k_A           91 TSRIIDRSIRPL--F--------PAGYFYDTQVLCNLLAVDGVNEPDVLAINGASVALSLSDIP----------------  144 (630)
T ss_dssp             HHHHHHHHHGGG--S--------CTTCCCCEEEEEEEEECCSSSCHHHHHHHHHHHHHHHSSSC----------------
T ss_pred             HHHHHhHHhhhc--c--------cccCCCceEEEEEEEECCCCCCHHHHHHHHHHHHHhccCCC----------------
Confidence            999999999973  3        334578899999999999997  668999999999999998                


Q ss_pred             cccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHHH
Q 022140          197 KEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQD  276 (302)
Q Consensus       197 ~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~~  276 (302)
                                        +++++.++++|++++.+++|||.+|++.++..++|+++.+|+|++++..| ..++.++ |.+
T Consensus       145 ------------------~~~~vaav~vg~i~g~~vldPt~~E~~~s~~dl~Va~t~~~~i~mve~~~-~~~se~~-~~~  204 (630)
T 3u1k_A          145 ------------------WNGPVGAVRIGIIDGEYVVNPTRKEMSSSTLNLVVAGAPKSQIVMLEASA-ENILQQD-FCH  204 (630)
T ss_dssp             ------------------CCCCCEEEEEEEETTEEEESCCHHHHHTEEEEEEEEEETTTEEEEEEEEE-EEECHHH-HHH
T ss_pred             ------------------cCCCeEEEEEEEECCEEEECCCHHHHhhCCceEEEEEccCCcEEEEECCC-ccCCHHH-HHH
Confidence                              56788899999999999999999999999999999999888999998754 4588886 999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcc
Q 022140          277 CIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       277 ~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      |+++|++.++++++++++++++.
T Consensus       205 al~~a~~~~~~l~~~~~~~~~~~  227 (630)
T 3u1k_A          205 AIKVGVKYTQQIIQGIQQLVKET  227 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999988764

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

Probab=99.96  E-value=6.1e-28  Score=240.25  Aligned_cols=202  Identities=15%  Similarity=0.206  Sum_probs=171.5

Q ss_pred             cceEEEeCCcc-CCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCCCC--C----c--cCCCCCCcHH
Q 022140           47 RNTTISMGAVA-SADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSP--L----V--RPGRPAEAAP  117 (302)
Q Consensus        47 R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~~~--~----~--~~g~~~~~~~  117 (302)
                      |++.+++|.+. +|+||++|++|+|+|+|+|+++. +|.   |..+++.++|+|.+....  .    |  |.|+|++.+.
T Consensus        20 r~i~ietg~ia~qA~GSv~v~~G~T~Vl~tv~~~~-~~~---~~~~f~pltv~y~ek~~a~g~ipg~f~kReGrpse~e~   95 (723)
T 3cdi_A           20 HTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQK-KAK---PGQDFFPLTVNYQERTYAAGRIPGSFFRREGRPSEGET   95 (723)
T ss_dssp             EEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECS-SCC---SSCCSCCEEEEEEECGGGGTCCCC-------CCCHHHH
T ss_pred             EEEEEEeCccccCCCeeEEEEECCEEEEEEEEecC-CCC---CCCCeeeEEEEEeEeccccccCCCccccCCCCCChHHh
Confidence            49999999985 79999999999999999999973 343   345788899999876322  1    2  5799999999


Q ss_pred             HHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCH-HH-HHHHHHHHHHhhCCCCcEEecCCceeecCcc
Q 022140          118 VVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGAL-FD-AALLSAVAAFSNLQIPTVSLDDGKIVMLPEE  195 (302)
Q Consensus       118 ~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l-~d-a~~~A~~~AL~~~~iP~~~~~~~~~~~~~~~  195 (302)
                      .+++++.|.||+          ++|..++|.++|+++||++||+. .| +|++|+++||..+++|               
T Consensus        96 l~sRlIdR~lRp----------lfp~~~~~~vqv~~~vls~Dg~~~~d~~ai~aAsaAL~~s~iP---------------  150 (723)
T 3cdi_A           96 LIARLIDRPIRP----------LFPEGFVNEVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIP---------------  150 (723)
T ss_dssp             HHHHHHHHHHGG----------GSCTTCCSCEEEEEEEEECCTTSCHHHHHHHHHHHHHHHHTSS---------------
T ss_pred             HHHHHhCccchh----------cccccCcceEEEEEEEEEcCCCCCHHHHHHHHHHHHHHhcCCC---------------
Confidence            999999999997          37778889999999999999995 56 9999999999999998               


Q ss_pred             ccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHH
Q 022140          196 QKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQ  275 (302)
Q Consensus       196 ~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~  275 (302)
                                         ++..+.+|++|++++.+++|||.+|++.++..++|+.+.++ ++.++ .|+..++.++ |.
T Consensus       151 -------------------~~~pv~av~vg~i~g~~v~nPt~~e~~~s~~~lvvagt~~~-i~mve-~~~~~~se~~-~~  208 (723)
T 3cdi_A          151 -------------------FNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVAGTEAA-VLMVE-SEAQLLSEDQ-ML  208 (723)
T ss_dssp             -------------------CCCCCCCEEEEEETTEEEESCCTTGGGGCSEEEEEEECSSC-EEEEE-EEEEEECHHH-HH
T ss_pred             -------------------CCCCeEEEEEEEECCEEEECcCHHHHHhCCceEEEEccCCE-EEEEe-CCCCCCCHHH-HH
Confidence                               45667899999999999999999999999999999976654 66655 5666799997 99


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          276 DCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       276 ~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      +|+++|++.++++.+++++++++.
T Consensus       209 ~al~~a~~~~~~l~~~~~~~~~~~  232 (723)
T 3cdi_A          209 GAVVFGHEQQQVVIQNINELVKEA  232 (723)
T ss_dssp             HHHHHHHHHTHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999998764

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

Probab=99.94  E-value=1.3e-25  Score=222.52  Aligned_cols=202  Identities=18%  Similarity=0.174  Sum_probs=169.2

Q ss_pred             CcceEEEeCCcc-CCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecC---------CCCCCCccCCCCCCc
Q 022140           46 ARNTTISMGAVA-SADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMP---------PICSPLVRPGRPAEA  115 (302)
Q Consensus        46 ~R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~---------~~~~~~~~~g~~~~~  115 (302)
                      -|++.+++|.+. +|+||+++++|+|+|+|+|+++...|    +..+++.+.|+|.         |.... .|.|+++++
T Consensus        27 ~R~i~ietg~~ak~A~GSvlv~~GdT~VL~tv~~~~~~~----~g~df~pltveY~ek~~a~G~iPg~~~-~REGrps~~  101 (726)
T 4aid_A           27 GKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQK----PGQDFFPLTVNYQEKTFAAGKIPGGFF-KREGRPSEK  101 (726)
T ss_dssp             TEEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCC----TTCCSCCEEEEEEECGGGGTCCCCSTT-CSCCSCCHH
T ss_pred             CeeEEEEECCccCCCCeeEEEEECCeEEEEEEEecCCCC----CCCCCcCceeeeeeehhhcccCCCccc-CCCCCCCch
Confidence            479999999887 59999999999999999999975322    2345666677664         22211 235899999


Q ss_pred             HHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCC-HHH-HHHHHHHHHHhhCCCCcEEecCCceeecC
Q 022140          116 APVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGA-LFD-AALLSAVAAFSNLQIPTVSLDDGKIVMLP  193 (302)
Q Consensus       116 ~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~-l~d-a~~~A~~~AL~~~~iP~~~~~~~~~~~~~  193 (302)
                      +.+++++|.|.||+.          +|..+.|.++|+++||++||+ ..| ++++|+++||..+++|             
T Consensus       102 ~~li~RlIdR~lRpl----------f~~~~~~evqI~~~Vls~Dg~~~~d~~ai~gAs~AL~~s~iP-------------  158 (726)
T 4aid_A          102 ETLVSRLIDRPIRPL----------FVKGFKNEVQVVVTVLQHDLENDPDILGMVAASAALCLSGAP-------------  158 (726)
T ss_dssp             HHHHHHHHHHHHGGG----------BCTTCCSCEEEEEEEEECCSSSCHHHHHHHHHHHHHHHHTCS-------------
T ss_pred             hhhHHHHhCCccccc----------cccCCccceEEEEEEEecCCCCChhHHHHHHHHHHHHhcCCC-------------
Confidence            999999999999972          455556889999999999986 445 5889999999999988             


Q ss_pred             ccccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHH
Q 022140          194 EEQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSA  273 (302)
Q Consensus       194 ~~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~  273 (302)
                                           +++.+.+|++|++++.+++|||.+|++.++..++|+.+.++ ++.++. ++..++.++ 
T Consensus       159 ---------------------~~~~vaaV~Vg~i~g~~vldPt~~E~~~s~~dl~va~t~~~-i~mve~-~~~~~se~~-  214 (726)
T 4aid_A          159 ---------------------FMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADA-VMMVES-EIQELSEEI-  214 (726)
T ss_dssp             ---------------------BCCCCEEEEEEEETTEEEESCCHHHHHTCSEEEEEEECSSC-EEEEEE-EESSBCHHH-
T ss_pred             ---------------------cCCCeEEEEEEEECCEEEECCCHHHHhhCceeEEEEEeCCe-EEEEEc-cCCCCCHHH-
Confidence                                 46778899999999999999999999999999999998887 888874 445799997 


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          274 VQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       274 l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      |.+++++|.+.+++|++++++++++.
T Consensus       215 ~~~al~~a~~~i~~l~~~q~~~~~~~  240 (726)
T 4aid_A          215 VLGGVNFAHQQMQAVIDAIIDLAEHA  240 (726)
T ss_dssp             HHHHHHHHHHHTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999988764

>3gme_A Polyribonucleotide nucleotidyltransferase; protein-RNA complex, cytoplasm, nucleotidyltransferase, RNA- binding, transferase, hydrolase; 2.40A {Escherichia coli E24377A} PDB: 3gll_A 3gcm_A 3h1c_A 3cdj_A

Probab=99.94  E-value=8.5e-26  Score=217.77  Aligned_cols=203  Identities=15%  Similarity=0.197  Sum_probs=167.0

Q ss_pred             CcceEEEeCCcc-CCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCCC-------CC-ccCCCCCCcH
Q 022140           46 ARNTTISMGAVA-SADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICS-------PL-VRPGRPAEAA  116 (302)
Q Consensus        46 ~R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~~-------~~-~~~g~~~~~~  116 (302)
                      -|++.+++|.+. +|+||+++++|+|+|+|+++++-..|    +..+++.+.|+|.....       .. .|.|++++.+
T Consensus        13 ~R~i~ietg~~ak~A~GSvlv~~GdT~Vl~tv~~~~~~~----~g~df~Pltv~Y~e~~~a~G~iPg~~~~REGrps~~~   88 (549)
T 3gme_A           13 QHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAK----PGQDFFPLTVNYQERTYAAGRIPGSFFRREGRPSEGE   88 (549)
T ss_dssp             TEEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCC----TTCCSCCEEEEEEECGGGTTCCCSCC-----CCCHHH
T ss_pred             CEEEEEEECCccCCCCeEEEEEECCEEEEEEEEecCCCC----CCCCCccceeeeeeehhhcccCCCcCcCcCCCCChhh
Confidence            479999999887 59999999999999999999964322    23567777777743211       11 1358899999


Q ss_pred             HHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCC-HHH-HHHHHHHHHHhhCCCCcEEecCCceeecCc
Q 022140          117 PVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGA-LFD-AALLSAVAAFSNLQIPTVSLDDGKIVMLPE  194 (302)
Q Consensus       117 ~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~-l~d-a~~~A~~~AL~~~~iP~~~~~~~~~~~~~~  194 (302)
                      .+++++|.+.||+          ++|..+.+.++|+++||++||+ ..| ++++|+++||..+++|              
T Consensus        89 ~l~~RlIdR~lRp----------lfp~~~~~evqI~~~Vls~D~~~~pd~~ai~gAs~AL~~s~iP--------------  144 (549)
T 3gme_A           89 TLIARLIDRPIRP----------LFPEGFVNEVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIP--------------  144 (549)
T ss_dssp             HHHHHHHHHHHGG----------GSCTTCCSCEEEEEEEEECCSSSCHHHHHHHHHHHHHHHHCSC--------------
T ss_pred             hHHHHHhCCcccc----------ccccCCcccEEEEEEEEecCCCCcHHHHHHHHHHHHHhccCCC--------------
Confidence            9999999999997          2555566789999999999985 445 6689999999999988              


Q ss_pred             cccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHH
Q 022140          195 EQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAV  274 (302)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l  274 (302)
                                          +++...+|++|++++.+++|||.+|++.++..++|+.+.++ ++.++. ++..++.++ +
T Consensus       145 --------------------~~gpvaaV~Vg~i~g~~vlnPt~~e~~~s~~dl~va~t~~~-i~mve~-e~~~~se~~-~  201 (549)
T 3gme_A          145 --------------------FNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVAGTEAA-VLMVES-EAELLSEDQ-M  201 (549)
T ss_dssp             --------------------CCCCCEEEEEEEETTEEEESCCTTTTTTCSBCEEEEECSSC-EEEEEE-EEEEECHHH-H
T ss_pred             --------------------cCCCeeEEEEEEECCEEEECCCHHHHhhCceEEEEEecCCe-EEEEEc-cCCCCCHHH-H
Confidence                                46778899999999999999999999999999999988876 888874 445799997 9


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          275 QDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       275 ~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                      .+++++|++.+++|++++++++++.
T Consensus       202 ~~al~~a~~~i~~l~~~q~~~~~~~  226 (549)
T 3gme_A          202 LGAVVFGHEQQQVVIQNINELVKEA  226 (549)
T ss_dssp             HHHHHHHHHHTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999988764

>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=99.92  E-value=1.8e-23  Score=208.90  Aligned_cols=204  Identities=16%  Similarity=0.118  Sum_probs=168.3

Q ss_pred             cceEEEeCCcc-CCCeeEEEEe-CCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCC-------CC-CccCCCCCCcH
Q 022140           47 RNTTISMGAVA-SADGSALAKI-GSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPIC-------SP-LVRPGRPAEAA  116 (302)
Q Consensus        47 R~i~i~~g~l~-~a~GSa~v~~-G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~-------~~-~~~~g~~~~~~  116 (302)
                      |++.+++|.+. +|+||+++++ |+|+|+|+++++-.. +   |...++.+.|+|....       .. ..|.|++++.+
T Consensus        37 r~i~~etg~la~qA~GSv~v~~~G~T~Vl~tv~~~~~~-~---~~~df~pLtv~y~ek~~a~g~iPg~f~~REGrps~~e  112 (757)
T 1e3p_A           37 RTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNP-K---DQLDFFPLTVDVEERMYAAGKIPGSFFRREGRPSEDA  112 (757)
T ss_dssp             EEEEEEESSSCTTSSEEEEEEETTTEEEEEEEEEEEEE-C---TTCSSCCEEEEEEECGGGGTCCCCSTTSSCCSCCHHH
T ss_pred             EeEEEEECccccCCCeEEEEEECCCeEEEEEEEecCCC-C---CCCCCccEEEEEEecccccccCCCcccccCcCCChHH
Confidence            69999999985 7999999999 999999999997542 1   2234555677764221       01 12468899999


Q ss_pred             HHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCH--HHHHHHHHHHHHhhCCCCcEEecCCceeecCc
Q 022140          117 PVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGAL--FDAALLSAVAAFSNLQIPTVSLDDGKIVMLPE  194 (302)
Q Consensus       117 ~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l--~da~~~A~~~AL~~~~iP~~~~~~~~~~~~~~  194 (302)
                      ..++++|.|.||+          ++|..+.-.++|+++||++||.-  .-++++|+++||.++++|              
T Consensus       113 ~l~~RlIdR~LRp----------lfp~~~~~evqv~~~Vls~D~~~~~~~~ai~gAs~AL~~s~iP--------------  168 (757)
T 1e3p_A          113 ILTCRLIDRPLRP----------SFKKGLRNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLP--------------  168 (757)
T ss_dssp             HHHHHHHHHHHGG----------GBCTTBCEEEEEEEEEEECCTTSCCHHHHHHHHHHHHHHTTSS--------------
T ss_pred             HHHHHHHCCcchh----------ccccCCCCceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCC--------------
Confidence            9999999999997          25555556799999999999864  788999999999999998              


Q ss_pred             cccccccCcCccccccccccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcC----CCcEEEEEc--------
Q 022140          195 EQKEENSEKEPVNKEKRKLTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDS----SNQLVSLYK--------  262 (302)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~----~g~i~~i~~--------  262 (302)
                                          +++...++++|++++.+++|||.+|++.++..++|+.+.    .+.+..++.        
T Consensus       169 --------------------~~~~vaav~vg~~~g~~vlnPt~~e~~~s~~dl~va~t~~~~~~~~i~mvE~q~t~~~~~  228 (757)
T 1e3p_A          169 --------------------FSGPIGGVRVALIRGQWVAFPTHTELEDAVFDMVVAGRVLEDGDVAIMMVEAEATEKTIQ  228 (757)
T ss_dssp             --------------------BCCCCEEEEEEEETTEEEESCCHHHHTTEEEEEEEEEEECTTSCEEEEEEEEEECSSHHH
T ss_pred             --------------------CCCceEEEEEEEECCEEEECCCHHHHhcCceeEEEEeccccCCCCcEEEEEEeccccccc
Confidence                                467778999999999999999999999999999999884    456777776        


Q ss_pred             ---cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 022140          263 ---PGGAVLAYTSAVQDCIALTRQRVKELHQILEEAISGM  299 (302)
Q Consensus       263 ---~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~~l~~~  299 (302)
                         .++..++.++ |.+++++|++.+++|.+++++++++.
T Consensus       229 ~~~~~~~~~se~~-l~~al~~a~~~i~~l~~~q~~~~~~~  267 (757)
T 1e3p_A          229 LVKDGAEAPTEEV-VAAGLDAAKPFIKVLCKAQADLAAKA  267 (757)
T ss_dssp             HHHTTCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence               2456899996 99999999999999999999988753

>1whu_A Polynucleotide phosphorylase; 3'-5' RNA exonuclease; pnpase, alpha-helical domain, structural genomics; NMR {Mus musculus} SCOP: a.4.9.1

Probab=94.44  E-value=0.025  Score=42.35  Aligned_cols=32  Identities=19%  Similarity=0.179  Sum_probs=26.1

Q ss_pred             HHHHhhhChHHHHHHHHhcCCCCCCCCCCCCc
Q 022140           16 VDAFRRLFPLRYFERHLAESIRPDARSLSRAR   47 (302)
Q Consensus        16 ~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R   47 (302)
                      ..+|..+.-...-...|+.++|+|||.+++.|
T Consensus        72 ~~~~~~lek~~vR~~IL~e~~RiDGR~~deIr  103 (104)
T 1whu_A           72 IESFNIVAKEVFRSIILNEYKRCDGRDSGPSS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHTTSSCSCCCCCSSCSC
T ss_pred             HHHHHHHHHHHHHHHHHCCCcCCCCCCccccc
Confidence            35677777767777778899999999999988

---

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	302
d2nn6e1	187	d.14.1.4 (E:5-191) Exosome complex exonuclease RRP	4e-34
d2nn6c1	181	d.14.1.4 (C:7-187) Exosome complex exonuclease RRP	8e-34
d2ba0g1	176	d.14.1.4 (G:3-178) Exosome complex exonuclease 2,E	1e-32
d2nn6a1	184	d.14.1.4 (A:1-184) Exosome complex exonuclease RRP	2e-31
d2je6a1	191	d.14.1.4 (A:1-191) Exosome complex exonuclease 2,E	6e-26
d2nn6c2	89	d.101.1.1 (C:188-276) Exosome complex exonuclease	1e-15
d2nn6a2	118	d.101.1.1 (A:185-302) Exosome complex exonuclease	3e-13
d2je6b1	148	d.14.1.4 (B:8-155) Exosome complex exonuclease 1,	9e-13
d1r6la1	151	d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Pseu	1e-11
d2ba0d1	144	d.14.1.4 (D:10-153) Exosome complex exonuclease 1,	1e-11
d2nn6e2	94	d.101.1.1 (E:192-285) Exosome complex exonuclease	2e-11
d2ba0g2	79	d.101.1.1 (G:179-257) Exosome complex exonuclease	2e-11
d1udsa1	149	d.14.1.4 (A:2-150) Ribonuclease PH, domain 1 {Aqui	5e-11
d2nn6f1	147	d.14.1.4 (F:29-175) Exosome complex exonuclease MT	7e-11
d1e3ha3	137	d.14.1.4 (A:346-482) Polynucleotide phosphorylase/	3e-10
d1oysa1	151	d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Baci	1e-09
d2nn6b1	145	d.14.1.4 (B:6-150) Exosome complex exonuclease RRP	1e-08
d2je6a2	84	d.101.1.1 (A:192-275) Exosome complex exonuclease	8e-06
d2nn6d1	122	d.14.1.4 (D:25-146) Exosome complex exonuclease RR	9e-06
d1e3ha2	149	d.14.1.4 (A:3-151) Polynucleotide phosphorylase/gu	4e-05

>d2nn6e1 d.14.1.4 (E:5-191) Exosome complex exonuclease RRP42 {Human (Homo sapiens) [TaxId: 9606]} Length = 187

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP42
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  120 bits (303), Expect = 4e-34
 Identities = 47/184 (25%), Positives = 82/184 (44%), Gaps = 5/184 (2%)

Query: 27  YFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLE 86
           Y    + E +R D R     R   +    V++  GSA  K+G T +L  +K E+ TP LE
Sbjct: 9   YIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLE 68

Query: 87  SPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAA 146
            P+EG +          +P        +    +A  L    ++   ++LK L +   +  
Sbjct: 69  KPNEGYLEFFVDCSASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHC 128

Query: 147 WMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEPV 206
           W++Y+D+  L+  G LFDA  ++  AA  N +IP V + + +     E  K+     +P 
Sbjct: 129 WVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLEDE-----EGSKDIELSDDPY 183

Query: 207 NKEK 210
           +  +
Sbjct: 184 DCIR 187

>d2nn6c1 d.14.1.4 (C:7-187) Exosome complex exonuclease RRP43 {Human (Homo sapiens) [TaxId: 9606]} Length = 181

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP43
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  119 bits (300), Expect = 8e-34
 Identities = 67/176 (38%), Positives = 111/176 (63%)

Query: 24  PLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTP 83
           PL Y+ R L E+ RPD R L   R TT+++G++++ADGSAL K+G+TT++  +K E   P
Sbjct: 4   PLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAP 63

Query: 84  SLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGG 143
           S ++PD+G V  +  +PP+CS   R G P E A V ++ ++D I +S +I  ++L +  G
Sbjct: 64  STDAPDKGYVVPNVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPG 123

Query: 144 KAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEE 199
           K  W++Y D+ CLD DG + DA   + +AA  N+Q+P V++++   +     +K+ 
Sbjct: 124 KLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETALAEVNLKKKS 179

>d2ba0g1 d.14.1.4 (G:3-178) Exosome complex exonuclease 2,ECX2 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 176

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 2,ECX2
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score =  116 bits (292), Expect = 1e-32
 Identities = 57/185 (30%), Positives = 97/185 (52%), Gaps = 9/185 (4%)

Query: 8   EDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKI 67
           ED+  +++ D         Y    L ++ R D R     R   I    +  A+GSAL K+
Sbjct: 1   EDILVDIKRD---------YVLSKLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKL 51

Query: 68  GSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTI 127
           G T ++  +KM+   P  ++PD G + ++  + P+ SP   PG P E +  +A+ +   I
Sbjct: 52  GDTQVVVGVKMQPGEPYPDTPDRGVIIVNAELVPLASPTFEPGPPDENSIELARVVDRGI 111

Query: 128 SSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDG 187
             S  ++L +L +  G+  W+V++DI+ LD DG L DA+ L+A+AA  N ++P    D G
Sbjct: 112 RESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLG 171

Query: 188 KIVML 192
           +  +L
Sbjct: 172 EDYLL 176

>d2nn6a1 d.14.1.4 (A:1-184) Exosome complex exonuclease RRP45 {Human (Homo sapiens) [TaxId: 9606]} Length = 184

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP45
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  113 bits (284), Expect = 2e-31
 Identities = 46/181 (25%), Positives = 90/181 (49%), Gaps = 9/181 (4%)

Query: 26  RYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSL 85
           R+  R + E  R D R     RN  IS G   +  G  + ++G T +L  +  E+++P L
Sbjct: 12  RFLLRAIEEKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSPKL 68

Query: 86  ESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKA 145
               EG +  +  +  + +P   PGR ++    + + +   + +S  I+ + L +V G+ 
Sbjct: 69  NRATEGILFFNLELSQMAAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEK 128

Query: 146 AWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVSLDDGKIVMLPEEQKEENSEKEP 205
            W + +D++ L+ DG + DAA ++A+ A  + + P VS+   ++ +   E      E++P
Sbjct: 129 VWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPE------ERDP 182

Query: 206 V 206
           V
Sbjct: 183 V 183

>d2je6a1 d.14.1.4 (A:1-191) Exosome complex exonuclease 2,ECX2 {Sulfolobus solfataricus [TaxId: 2287]} Length = 191

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 2,ECX2
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 99.5 bits (247), Expect = 6e-26
 Identities = 54/191 (28%), Positives = 100/191 (52%), Gaps = 9/191 (4%)

Query: 1   MGLPNASEDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASAD 60
           M    +++++   ++ ++   L           + IR D R L+  R  +I++     AD
Sbjct: 1   MSSTPSNQNIIPIIKKESIVSL---------FEKGIRQDGRKLTDYRPLSITLDYAKKAD 51

Query: 61  GSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVA 120
           GSAL K+G+T +LA  K+E+  P  ++P++G + ++  + P+      PG P E A  +A
Sbjct: 52  GSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNLIVNVELLPLAYETFEPGPPDENAIELA 111

Query: 121 KQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP 180
           + +  ++  S  ++L +L +  GK+ W V+LD+Y LD  G + DA  L++VAA  N ++ 
Sbjct: 112 RVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVY 171

Query: 181 TVSLDDGKIVM 191
            V      I +
Sbjct: 172 KVEQHSNGISV 182

>d2nn6c2 d.101.1.1 (C:188-276) Exosome complex exonuclease RRP43 {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.7 bits (168), Expect = 1e-15
 Identities = 26/85 (30%), Positives = 48/85 (56%), Gaps = 2/85 (2%)

Query: 217 GIPFSLTC-ILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQ 275
             P + +  +     ++ DPT EEE +    +T+V+D   +L  L+KPGG+ L   + +Q
Sbjct: 4   THPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTG-AKLQ 62

Query: 276 DCIALTRQRVKELHQILEEAISGME 300
           DC++    R KE+ ++++E I  M+
Sbjct: 63  DCMSRAVTRHKEVKKLMDEVIKSMK 87

>d2nn6a2 d.101.1.1 (A:185-302) Exosome complex exonuclease RRP45 {Human (Homo sapiens) [TaxId: 9606]} Length = 118

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP45
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.0 bits (153), Expect = 3e-13
 Identities = 18/86 (20%), Positives = 44/86 (51%), Gaps = 3/86 (3%)

Query: 213 LTLGGIPFSLTCILHK--NYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAY 270
           L++  +P  ++    +   Y+L DP   EE +M+ L+ + ++   ++ ++   GG +L  
Sbjct: 1   LSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGIMLL- 59

Query: 271 TSAVQDCIALTRQRVKELHQILEEAI 296
              V  C  +   +V E+ +++ +A+
Sbjct: 60  KDQVLRCSKIAGVKVAEITELILKAL 85

>d2je6b1 d.14.1.4 (B:8-155) Exosome complex exonuclease 1, ECX1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 148

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 1, ECX1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 62.5 bits (151), Expect = 9e-13
 Identities = 34/144 (23%), Positives = 66/144 (45%), Gaps = 10/144 (6%)

Query: 32  LAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKME--VMTPSLESPD 89
           L +  R D R     R+  I +G + +ADGSA+ ++G+T  +AA+     +    L  PD
Sbjct: 7   LDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPD 66

Query: 90  EGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMV 149
              + + +HM P  +   +   P+     ++K + + + S   + ++       + A  V
Sbjct: 67  RAVLRVRYHMTPFSTDERKNPAPSRREIELSKVIREALES--AVLVELF----PRTAIDV 120

Query: 150 YLDIYCLDADGALFDAALLSAVAA 173
           + +I  L AD      +L++A  A
Sbjct: 121 FTEI--LQADAGSRLVSLMAASLA 142

>d1r6la1 d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Pseudomonas aeruginosa [TaxId: 287]} Length = 151

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Pseudomonas aeruginosa [TaxId: 287]

 Score = 59.5 bits (143), Expect = 1e-11
 Identities = 26/145 (17%), Positives = 53/145 (36%), Gaps = 4/145 (2%)

Query: 37  RPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK-MEVMTPSLESPDEGCVSI 95
           RP  R+  + R   I+      A+GS L + G T ++  +     +   L+   +G ++ 
Sbjct: 3   RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTA 62

Query: 96  DFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYC 155
           ++ M P  +        +             +    +    +LS +G      +Y+D   
Sbjct: 63  EYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGE---NTLYIDCDV 119

Query: 156 LDADGALFDAALLSAVAAFSNLQIP 180
           + ADG    A++  A  A  +    
Sbjct: 120 IQADGGTRTASITGATVALIDALAV 144

>d2ba0d1 d.14.1.4 (D:10-153) Exosome complex exonuclease 1, ECX1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 144

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 1, ECX1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 59.1 bits (142), Expect = 1e-11
 Identities = 29/146 (19%), Positives = 54/146 (36%), Gaps = 10/146 (6%)

Query: 30  RHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAI--KMEVMTPSLES 87
           + + + +R D R     R   I    +  ADGS   ++G   ++AA+    EV    L+ 
Sbjct: 1   KLIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQD 60

Query: 88  PDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAW 147
           P +  +   ++M P      +   P   +  ++K   +   +  M  L            
Sbjct: 61  PSKAIIRYRYNMAPFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFP--------RS 112

Query: 148 MVYLDIYCLDADGALFDAALLSAVAA 173
            + + +  L AD     A L +A  A
Sbjct: 113 AIDIFVEVLQADAGSRTACLNAASVA 138

>d2nn6e2 d.101.1.1 (E:192-285) Exosome complex exonuclease RRP42 {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP42
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.6 bits (139), Expect = 2e-11
 Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 1/88 (1%)

Query: 213 LTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTS 272
           L++  +P  +T        + D T +EE+     + V + S   +  + K G   L   S
Sbjct: 1   LSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPES 60

Query: 273 AVQDCIALTRQRVKELHQILEEAISGME 300
            + + +   ++  K LH  L+  +   E
Sbjct: 61  -IFEMMETGKRVGKVLHASLQSVVHKEE 87

>d2ba0g2 d.101.1.1 (G:179-257) Exosome complex exonuclease 2, ECX2 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 2, ECX2
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 56.7 bits (137), Expect = 2e-11
 Identities = 19/77 (24%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 217 GIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQD 276
            +P S+T ++  N  L DP+ EE S+ +T +T+  D  + +V++ K GG +L       +
Sbjct: 4   DLPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITTDKDDNVVAMQKSGGYLLD-EKLFDE 62

Query: 277 CIALTRQRVKELHQILE 293
            + ++    ++L +  +
Sbjct: 63  LLDVSINCARKLREKFK 79

>d1udsa1 d.14.1.4 (A:2-150) Ribonuclease PH, domain 1 {Aquifex aeolicus [TaxId: 63363]} Length = 149

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Aquifex aeolicus [TaxId: 63363]

 Score = 57.6 bits (138), Expect = 5e-11
 Identities = 28/145 (19%), Positives = 54/145 (37%), Gaps = 4/145 (2%)

Query: 37  RPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPS-LESPDEGCVSI 95
           R D R   + R  +I    +   +GS L   G T ++    +    P+ L+   +G ++ 
Sbjct: 1   RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITA 60

Query: 96  DFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYC 155
           ++ M P  +         +            +    M    EL+ +G      +++D   
Sbjct: 61  EYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGE---RTIWVDCDV 117

Query: 156 LDADGALFDAALLSAVAAFSNLQIP 180
           + ADG    AA+  A  A ++  I 
Sbjct: 118 IQADGGTATAAITGAFVAVADAIIK 142

>d2nn6f1 d.14.1.4 (F:29-175) Exosome complex exonuclease MTR3 {Human (Homo sapiens) [TaxId: 9606]} Length = 147

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease MTR3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.2 bits (137), Expect = 7e-11
 Identities = 26/146 (17%), Positives = 44/146 (30%), Gaps = 21/146 (14%)

Query: 41  RSLSRARNTTISMGAVASADGSALAKIGSTTMLAAI-------------KMEVMTPSLES 87
           R  +R R      G ++ A GSA  + G T +L A+                       +
Sbjct: 3   RDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPA 62

Query: 88  PDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAW 147
              G +  DF   P      R          +A  L + +  +  +              
Sbjct: 63  ALRGRLLCDFRRAPFAGRRRRAPPGGCEERELALALQEALEPAVRLGR--------YPRA 114

Query: 148 MVYLDIYCLDADGALFDAALLSAVAA 173
            + +    L+  G+   AAL +A  A
Sbjct: 115 QLEVSALLLEDGGSALAAALTAAALA 140

>d1e3ha3 d.14.1.4 (A:346-482) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 {Streptomyces antibioticus [TaxId: 1890]} Length = 137

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 55.2 bits (132), Expect = 3e-10
 Identities = 17/134 (12%), Positives = 43/134 (32%), Gaps = 2/134 (1%)

Query: 47  RNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPL 106
           R     + A+    GSAL + G T +L    + ++    +      V+   +M     P 
Sbjct: 4   RTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPP 63

Query: 107 VRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAA 166
              G          +       +     +  +     +  + +      L ++G+    +
Sbjct: 64  YSVGETGRVGSPKRR--EIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGS 121

Query: 167 LLSAVAAFSNLQIP 180
           + ++  +  N  +P
Sbjct: 122 VCASTMSLLNAGVP 135

>d1oysa1 d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Bacillus subtilis [TaxId: 1423]} Length = 151

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Bacillus subtilis [TaxId: 1423]

 Score = 54.1 bits (129), Expect = 1e-09
 Identities = 25/139 (17%), Positives = 53/139 (38%), Gaps = 4/139 (2%)

Query: 36  IRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIK-MEVMTPSLESPDEGCVS 94
           +R D R     R  T  +  ++  +GS L   G+T ++      + + P L    +G ++
Sbjct: 1   MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWIT 60

Query: 95  IDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIY 154
            ++ M P  +        ++            +    +  + +L  +G +  W+   D  
Sbjct: 61  AEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWI---DCD 117

Query: 155 CLDADGALFDAALLSAVAA 173
            + ADG    A++  A  A
Sbjct: 118 VIQADGGTRTASITGAFLA 136

>d2nn6b1 d.14.1.4 (B:6-150) Exosome complex exonuclease RRP41 {Human (Homo sapiens) [TaxId: 9606]} Length = 145

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.0 bits (121), Expect = 1e-08
 Identities = 30/144 (20%), Positives = 50/144 (34%), Gaps = 12/144 (8%)

Query: 34  ESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTP---SLESPDE 90
           +  R D R     R     MG  A ADGSA  + G+T  LA +          +   PD 
Sbjct: 4   QGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDR 63

Query: 91  GCVSIDFHMPPICSPLVR-PGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMV 149
             V+  +      +   +        +  +  QL  T  ++ +  L             +
Sbjct: 64  ALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPR--------SQI 115

Query: 150 YLDIYCLDADGALFDAALLSAVAA 173
            + +  L ADG  + A + +A  A
Sbjct: 116 DIYVQVLQADGGTYAACVNAATLA 139

>d2je6a2 d.101.1.1 (A:192-275) Exosome complex exonuclease 2, ECX2 {Sulfolobus solfataricus [TaxId: 2287]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 2, ECX2
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 41.1 bits (96), Expect = 8e-06
 Identities = 14/80 (17%), Positives = 34/80 (42%), Gaps = 1/80 (1%)

Query: 217 GIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQD 276
               +++      Y++ DP  +EESIM+  ++       ++V + K G   ++    +  
Sbjct: 4   YPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSGKGSMS-LQDIDQ 62

Query: 277 CIALTRQRVKELHQILEEAI 296
                R    +L + L++ +
Sbjct: 63  AENTARSTAVKLLEELKKHL 82

>d2nn6d1 d.14.1.4 (D:25-146) Exosome complex exonuclease RRP46 {Human (Homo sapiens) [TaxId: 9606]} Length = 122

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP46
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 9e-06
 Identities = 21/128 (16%), Positives = 43/128 (33%), Gaps = 17/128 (13%)

Query: 47  RNTTISMGAVASADGSALAKIGSTTMLAAIK-MEVMTPSLESPDEGCVSIDFHMPPICSP 105
           R+       ++  DGSA    G T++LA +     +  S E  ++  + +          
Sbjct: 5   RHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPK----- 59

Query: 106 LVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDA 165
               G P  A     + + +T  +  +  L             + + +  +   G+L   
Sbjct: 60  ---IGLPGVAEKSRERLIRNTCEAVVLGTL--------HPRTSITVVLQVVSDAGSLLAC 108

Query: 166 ALLSAVAA 173
            L +A  A
Sbjct: 109 CLNAACMA 116

>d1e3ha2 d.14.1.4 (A:3-151) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 {Streptomyces antibioticus [TaxId: 1890]} Length = 149

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 40.9 bits (95), Expect = 4e-05
 Identities = 30/154 (19%), Positives = 48/154 (31%), Gaps = 8/154 (5%)

Query: 29  ERHLAESIRPDARSLSRARNTTISMGAVA-SADGSALAKIGSTTMLAAIKMEVMTPSLES 87
           E H AE++  D  +    R      G +A  A GSA+A +   TM+ +       P  + 
Sbjct: 2   ETHYAEAVI-DNGAFG-TRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQL 59

Query: 88  PDEG-CVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAA 146
                 V ++  M           R        A              L+     G +  
Sbjct: 60  DFFPLTVDVEERMYAAGKIPGSFFRREGRPSEDAIL----TCRLIDRPLRPSFKKGLRNE 115

Query: 147 WMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP 180
             V   I  L+ D      A+ +A A+     +P
Sbjct: 116 IQVVATIMALNPDHLYDVVAINAASASTQLAGLP 149

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	302
d2ba0g1	176	Exosome complex exonuclease 2,ECX2 {Archaeoglobus	100.0
d2nn6e1	187	Exosome complex exonuclease RRP42 {Human (Homo sap	100.0
d2nn6a1	184	Exosome complex exonuclease RRP45 {Human (Homo sap	100.0
d2je6a1	191	Exosome complex exonuclease 2,ECX2 {Sulfolobus sol	100.0
d2nn6c1	181	Exosome complex exonuclease RRP43 {Human (Homo sap	100.0
d2ba0d1	144	Exosome complex exonuclease 1, ECX1 {Archaeoglobus	99.98
d2je6b1	148	Exosome complex exonuclease 1, ECX1 {Sulfolobus so	99.98
d1udsa1	149	Ribonuclease PH, domain 1 {Aquifex aeolicus [TaxId	99.97
d2nn6b1	145	Exosome complex exonuclease RRP41 {Human (Homo sap	99.97
d1r6la1	151	Ribonuclease PH, domain 1 {Pseudomonas aeruginosa	99.97
d1oysa1	151	Ribonuclease PH, domain 1 {Bacillus subtilis [TaxI	99.96
d2nn6f1	147	Exosome complex exonuclease MTR3 {Human (Homo sapi	99.93
d1e3ha3	137	Polynucleotide phosphorylase/guanosine pentaphosph	99.92
d2nn6d1	122	Exosome complex exonuclease RRP46 {Human (Homo sap	99.9
d2nn6e2	94	Exosome complex exonuclease RRP42 {Human (Homo sap	99.81
d2nn6c2	89	Exosome complex exonuclease RRP43 {Human (Homo sap	99.8
d2nn6a2	118	Exosome complex exonuclease RRP45 {Human (Homo sap	99.79
d2je6a2	84	Exosome complex exonuclease 2, ECX2 {Sulfolobus so	99.77
d1e3ha2	149	Polynucleotide phosphorylase/guanosine pentaphosph	99.77
d2ba0g2	79	Exosome complex exonuclease 2, ECX2 {Archaeoglobus	99.76
d2nn6d2	89	Exosome complex exonuclease RRP46 {Human (Homo sap	99.46
d2nn6b2	90	Exosome complex exonuclease RRP41 {Human (Homo sap	99.45
d2je6b2	86	Exosome complex exonuclease 1, ECX1 {Sulfolobus so	99.42
d1r6la2	88	Ribonuclease PH, domain 2 {Pseudomonas aeruginosa	99.36
d1oysa2	86	Ribonuclease PH, domain 2 {Bacillus subtilis [TaxI	99.14
d1udsa2	105	Ribonuclease PH, domain 2 {Aquifex aeolicus [TaxId	99.11
d2ba0d2	99	Exosome complex exonuclease 1, ECX1 {Archaeoglobus	99.11
d2nn6f2	95	Exosome complex exonuclease MTR3 {Human (Homo sapi	99.01
d1e3ha5	111	Polynucleotide phosphorylase/guanosine pentaphosph	97.52
d1e3ha6	96	Polynucleotide phosphorylase/guanosine pentaphosph	96.59
d1e3ha1	83	Polynucleotide phosphorylase/guanosine pentaphosph	90.92
d1whua_	104	Polynucleotide phosphorylase/guanosine pentaphosph	81.11

>d2ba0g1 d.14.1.4 (G:3-178) Exosome complex exonuclease 2,ECX2 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 2,ECX2
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=100.00  E-value=2.2e-41  Score=283.52  Aligned_cols=164  Identities=32%  Similarity=0.581  Sum_probs=156.6

Q ss_pred             hHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCC
Q 022140           24 PLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPIC  103 (302)
Q Consensus        24 p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~  103 (302)
                      +++|+.++|++++|+|||+++|+|++++++|.+++++|||+|++|+|+|+|+|++++..|.+.+|++|.+.++|+++|++
T Consensus         8 e~~~i~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~~~~~p~~~~~~~g~~~~~v~~~~~~   87 (176)
T d2ba0g1           8 KRDYVLSKLRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYPDTPDRGVIIVNAELVPLA   87 (176)
T ss_dssp             HHHHHHHHHTTTCCTTCCCTTCCCCEEEEECCCTTSSEEEEEEETTEEEEEEEEEEEECCCTTCTTCCEEEEEEECCTTT
T ss_pred             HHHHHHHHHHhCCCCCCCCCCCccCeEEEeCccCCCCeEEEEEeCCcEEEEEEeccccccccccCCCceeeeeeEecccc
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcEE
Q 022140          104 SPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTVS  183 (302)
Q Consensus       104 ~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~~  183 (302)
                      .+.++.+++++....+++++++.+.++.++|+++||+.+|+++|+|+|+|+||++|||++||+++|+++||+|+++|.++
T Consensus        88 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~e~L~i~~~~~~~~i~i~v~VL~~DG~l~dA~~~A~~~AL~da~iP~~~  167 (176)
T d2ba0g1          88 SPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAER  167 (176)
T ss_dssp             CTTSCSSSCCHHHHHHHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHTTCEECTGG
T ss_pred             CccccCCCCCchhHHHHHHHHHhhccccccchhhccCCCCCceEEEEEEEEEEeCCCCHHHHHHHHHHHHHHHcCCCcEE
Confidence            98887777788889999999999999899999999999999999999999999999999999999999999999999987


Q ss_pred             ecCC
Q 022140          184 LDDG  187 (302)
Q Consensus       184 ~~~~  187 (302)
                      ++.|
T Consensus       168 ~~~g  171 (176)
T d2ba0g1         168 FDLG  171 (176)
T ss_dssp             GTSS
T ss_pred             ecCC
Confidence            7443

>d2nn6e1 d.14.1.4 (E:5-191) Exosome complex exonuclease RRP42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3e-41  Score=285.37  Aligned_cols=162  Identities=27%  Similarity=0.452  Sum_probs=154.8

Q ss_pred             ChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCC
Q 022140           23 FPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPI  102 (302)
Q Consensus        23 ~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~  102 (302)
                      .|+.|++++|++|+|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|++++..|...+|++|.+.++|+++|+
T Consensus         5 ~E~~~i~~~l~~~iR~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~~~~~~~~~~~~~g~~~~~v~~~~~   84 (187)
T d2nn6e1           5 AEKVYIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDCSAS   84 (187)
T ss_dssp             HHHHHHHHHHHTTCCSSSCCSSCCCCCEEEECCCTTSSSEEEEEETTEEEEEECCCCCSCCCSSSCSSCCEEEECCCCTT
T ss_pred             HHHHHHHHHHhhCCCCCCcCCCCccCeEEEeCccCCCCceEEEEeCCceEEEEEEeccccccccccccceeeeeeeeccc
Confidence            46899999999999999999999999999999999999999999999999999999999998889999999999999999


Q ss_pred             CCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcE
Q 022140          103 CSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTV  182 (302)
Q Consensus       103 ~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~  182 (302)
                      +.+.+..+.+++....+++++++.|+++..+|+++||+.+|+++|.|+|+|+||++|||++||+++|+++||+|+++|.+
T Consensus        85 ~~~~~~~~~~~~~~~~ls~~l~~~l~~~~~~d~~~L~i~~~~~~w~i~v~v~vL~~DG~~~da~~~A~~~AL~d~~iP~v  164 (187)
T d2nn6e1          85 ATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRV  164 (187)
T ss_dssp             TCSSCCTTSTHHHHHHHHHHHHHHHHHSCCSCSSSSCSSTTTCCCCEEEEEEECCCCSSHHHHHHHHHHHTTTTCCCCEE
T ss_pred             cccCcCCCCcchHHHHHHHHHHHHhccccccchhhheecCCCccEEEEEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCEE
Confidence            98877666667788899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Ee
Q 022140          183 SL  184 (302)
Q Consensus       183 ~~  184 (302)
                      .+
T Consensus       165 ~v  166 (187)
T d2nn6e1         165 RV  166 (187)
T ss_dssp             EE
T ss_pred             EE
Confidence            88

>d2nn6a1 d.14.1.4 (A:1-184) Exosome complex exonuclease RRP45 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP45
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.3e-40  Score=279.23  Aligned_cols=162  Identities=26%  Similarity=0.514  Sum_probs=153.5

Q ss_pred             ChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCC
Q 022140           23 FPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPI  102 (302)
Q Consensus        23 ~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~  102 (302)
                      .|++|++++|++++|+|||+++|+|++.+++|.   ++|||+|++|+|+|+|+|++++..|...+|++|.+.++|+++++
T Consensus         9 ~e~~fi~~~l~~~~R~DGR~~~e~R~~~i~~g~---a~GSa~v~~G~T~V~~~V~~~~~~p~~~~~~~g~~~~~v~~~~~   85 (184)
T d2nn6a1           9 CERRFLLRAIEEKKRLDGRQTYDYRNIRISFGT---DYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLELSQM   85 (184)
T ss_dssp             HHHHHHHHHHHTTCCTTSCCTTCCCCCEEEECS---STTEEEEESSSCEEEEEECCEEECCCSTTTTSCCEEEEEEECTT
T ss_pred             HHHHHHHHHHhhCcCCCCCCCCCcCCeEEEecC---CCCEEEEEeCCCEEEEEEEeccccccccCCCccceeEEEEeccc
Confidence            388999999999999999999999999999984   89999999999999999999999999999999999999999999


Q ss_pred             CCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcE
Q 022140          103 CSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTV  182 (302)
Q Consensus       103 ~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~  182 (302)
                      +++.++.+.+++.+..++++|++.++.+.++|+++|||.+|+++|.|+|+++||++|||++||+++|+++||+|+++|.+
T Consensus        86 ~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~d~~~L~i~~~~~~w~i~i~v~VL~~DG~~~da~~~a~~~AL~~~~iP~v  165 (184)
T d2nn6a1          86 AAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDV  165 (184)
T ss_dssp             TCSSCCSSSTHHHHTHHHHHHHHHHHHHTCBCSSSSCSBTTTBEEEEEEEEEECSCCSCCHHHHHHHHHHHHHHCCCCCC
T ss_pred             cCcccccCCCCchhHHHHHHHHhhhhhhhhhhhhhhccccccCcEEEEEEEEEECCCCCHHHHHHHHHHHHHHhhCCCeE
Confidence            98887777777788899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCC
Q 022140          183 SLDDG  187 (302)
Q Consensus       183 ~~~~~  187 (302)
                      .++++
T Consensus       166 ~v~~~  170 (184)
T d2nn6a1         166 SVQGD  170 (184)
T ss_dssp             BCCTT
T ss_pred             EEeCC
Confidence            88443

>d2je6a1 d.14.1.4 (A:1-191) Exosome complex exonuclease 2,ECX2 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 2,ECX2
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=100.00  E-value=1.4e-39  Score=275.94  Aligned_cols=172  Identities=30%  Similarity=0.492  Sum_probs=159.0

Q ss_pred             ccccccccHHHHhhhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCC
Q 022140            8 EDLSSEMEVDAFRRLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLES   87 (302)
Q Consensus         8 ~~~~~~~~~~~~~~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~   87 (302)
                      +|+...+.+...     ++|++++|++|+|+|||+++|+|++++++|.+++++|||+|++|+|+|+|+|++++..|....
T Consensus         4 ~~~~~~~~~~~~-----~~~~~~~l~~giR~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~a~V~~~~~~~~~~~   78 (191)
T d2je6a1           4 TPSNQNIIPIIK-----KESIVSLFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDT   78 (191)
T ss_dssp             CCCCSSCCCHHH-----HHHHTTTGGGTBCTTSCBTTCCCCEEEEETCSTTSSEEEEEEETTEEEEEEEEEEEECCCTTC
T ss_pred             CcccchHHHHHH-----HHHHHHHHhcCCCCCCcCCCCccCeEEEECCccCcCceEEEEcCCceEEEEEEecccCchhcc
Confidence            445555555554     599999999999999999999999999999999999999999999999999999999998889


Q ss_pred             CCcceEEEEEecCCCCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHH
Q 022140           88 PDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAAL  167 (302)
Q Consensus        88 p~~g~l~v~V~~~~~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~  167 (302)
                      |+++.+.+++++++++...+..+...+....++++|++.+.++..+|+++||+.+++++|.|+|+++||++|||++||++
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~id~~~l~i~~~~~~w~I~v~v~VL~~DG~l~dA~~  158 (191)
T d2je6a1          79 PNQGNLIVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACT  158 (191)
T ss_dssp             TTCCEEEEEEEECTTSCTTCCCSSCCHHHHHHHHHHHHHHHHTTCSCGGGGEEETTTEEEEEEEEEEEEECCSCHHHHHH
T ss_pred             CccCccccccccccccccccccccCCcchhHHHHHHHHhhcchhhcccccccccCccccEEEEEEEEEEcCCCCHHHHHH
Confidence            99999999999999887766666677788899999999999889999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhCCCCcEEe
Q 022140          168 LSAVAAFSNLQIPTVSL  184 (302)
Q Consensus       168 ~A~~~AL~~~~iP~~~~  184 (302)
                      +|+++||+|+++|++.+
T Consensus       159 ~A~~~AL~da~iP~v~~  175 (191)
T d2je6a1         159 LASVAALYNTKVYKVEQ  175 (191)
T ss_dssp             HHHHHHHHTCEEEEEEC
T ss_pred             HHHHHHHHHcCCCeEEe
Confidence            99999999999999887

>d2nn6c1 d.14.1.4 (C:7-187) Exosome complex exonuclease RRP43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.1e-39  Score=273.96  Aligned_cols=164  Identities=40%  Similarity=0.783  Sum_probs=155.8

Q ss_pred             hhChHHHHHHHHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecC
Q 022140           21 RLFPLRYFERHLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMP  100 (302)
Q Consensus        21 ~~~p~~f~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~  100 (302)
                      .+.|.+|++++|++|+|+|||+++|+|++++++|++++++|||+|++|+|+|+|+|++++..|....++++.+.+++++.
T Consensus         1 ~~~p~~y~~~~l~~giR~DGR~~~e~R~~~i~~g~l~~a~GSa~v~~G~T~v~~~v~~~~~~~~~~~~~~~~~~~~~~~~   80 (181)
T d2nn6c1           1 TVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLP   80 (181)
T ss_dssp             CCSTHHHHHHHHHTSCCTTSCCSCCCCSCCEEETCCSSSSEEEEEEETTEEEEEEEEEEECCCCSSSTTCCCCEEEEECC
T ss_pred             CCCHHHHHHHHHhcCCCCCCcCCCCccCeEEEeCCcCCCCeEEEEEeCCcEEEEEEeccccccccccCCCceeeeeeeee
Confidence            36899999999999999999999999999999999999999999999999999999999998888889999999999999


Q ss_pred             CCCCCCccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCC
Q 022140          101 PICSPLVRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP  180 (302)
Q Consensus       101 ~~~~~~~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP  180 (302)
                      +++.+.+..+.+.+....+++++++.++++..+++++||+.+++++|+|+|+++||++|||++||+++|+++||+|+++|
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~~~~~~i~i~v~vl~~DG~l~da~~~A~~~AL~d~~iP  160 (181)
T d2nn6c1          81 PLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLP  160 (181)
T ss_dssp             SSSCTTSCSSSCCHHHHHHHHHHHHHHHHHCCSCHHHHCSSBTTBCEEEEEEEEESSCCSCTTHHHHHHHHHHHHTCCCC
T ss_pred             ccccccccccCCCchhhhhHHHHHHHHHhhhhhhhhhccccCCcceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCC
Confidence            99887776666777888999999999998889999999999999999999999999999999999999999999999999


Q ss_pred             cEEe
Q 022140          181 TVSL  184 (302)
Q Consensus       181 ~~~~  184 (302)
                      ++.+
T Consensus       161 ~v~v  164 (181)
T d2nn6c1         161 EVTI  164 (181)
T ss_dssp             CCCB
T ss_pred             eEEE
Confidence            9888

>d2ba0d1 d.14.1.4 (D:10-153) Exosome complex exonuclease 1, ECX1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 1, ECX1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.98  E-value=2.9e-32  Score=220.37  Aligned_cols=141  Identities=18%  Similarity=0.273  Sum_probs=124.5

Q ss_pred             HHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccC--CCCCCCcceEEEEEecCCCCCCCcc
Q 022140           31 HLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTP--SLESPDEGCVSIDFHMPPICSPLVR  108 (302)
Q Consensus        31 ~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p--~~~~p~~g~l~v~V~~~~~~~~~~~  108 (302)
                      ++++|+|+|||.++|+|++++++|++++++|||+|++|+|+|+|+|+++...+  ....|+++.+.+++++.|++...+.
T Consensus         2 ~~~~g~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~   81 (144)
T d2ba0d1           2 LIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKAIIRYRYNMAPFSVEERK   81 (144)
T ss_dssp             CBCSSCBTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEEECCSGGGCCSSSCEEEEEEEECTTSSSSCC
T ss_pred             cccCCcCCCCCCCCCccCeEEEECCCCCCCceEEEEEcccceEEEEeccchhhhhhcccccceEEEEEEecCCccccccc
Confidence            46789999999999999999999999999999999999999999999986543  3456788999999999999887765


Q ss_pred             CCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCC
Q 022140          109 PGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQI  179 (302)
Q Consensus       109 ~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~i  179 (302)
                      .+.+.+.+.+++++|++.+++  .++++.+      ..|.|+|+++||++|||+++||++|+++||+|++|
T Consensus        82 ~~~~~~~~~~l~~~l~~~l~~--~i~~~~~------~~~~i~v~v~VL~~DG~~~~a~i~aa~lAL~daGI  144 (144)
T d2ba0d1          82 RPGPDRRSIEISKVSKEAFEA--VIMKELF------PRSAIDIFVEVLQADAGSRTACLNAASVALVDAGV  144 (144)
T ss_dssp             CSSCCHHHHHHHHHHHHHHHT--TBCGGGC------TTEEEEEEEEEEECCTTHHHHHHHHHHHHHHHHTC
T ss_pred             ccCCCchhhhhhhhhhhhhcc--ccchhhc------CCeEEEEEEEEEccCCCHHHHHHHHHHHHHHHcCC
Confidence            566677888999999999986  5666554      25999999999999999999999999999999985

>d2je6b1 d.14.1.4 (B:8-155) Exosome complex exonuclease 1, ECX1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 1, ECX1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.98  E-value=1.1e-31  Score=218.08  Aligned_cols=141  Identities=23%  Similarity=0.336  Sum_probs=123.6

Q ss_pred             HHhcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeee--ccCCCCCCCcceEEEEEecCCCCCCCcc
Q 022140           31 HLAESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEV--MTPSLESPDEGCVSIDFHMPPICSPLVR  108 (302)
Q Consensus        31 ~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v--~~p~~~~p~~g~l~v~V~~~~~~~~~~~  108 (302)
                      .+++|+|+|||.++|+|++++++|++++++|||++++|+|+|+|+|+||.  ..+..+.|+++.+.++++++|+++..++
T Consensus         6 i~~~g~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~~~v~~~~~~~~~~~~~   85 (148)
T d2je6b1           6 ILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDERK   85 (148)
T ss_dssp             BCTTSCBTTSCCTTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECSSGGGSCSSSCEEEEEEEECTTSSSSCC
T ss_pred             ecCCCccCCCCCCCCccCeEEEECCCCCCCEEEEEEcCCccEEeecccCccccchhhcCCcceEEEEEEEeccccccccc
Confidence            36789999999999999999999999999999999999999999999964  4445677899999999999999987776


Q ss_pred             CCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCC
Q 022140          109 PGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQI  179 (302)
Q Consensus       109 ~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~i  179 (302)
                      .+.++..+.+++++|++.|.+  .++++.+   | +  +.|.|+++||++|||+++||++|+++||+|++|
T Consensus        86 ~~~~~~~~~el~~~l~~~l~~--~i~~~~~---p-~--~~i~v~v~VL~~DG~~~~a~i~aa~~AL~daGI  148 (148)
T d2je6b1          86 NPAPSRREIELSKVIREALES--AVLVELF---P-R--TAIDVFTEILQADAGSRLVSLMAASLALADAGI  148 (148)
T ss_dssp             CSSCCHHHHHHHHHHHHHHHT--TBCGGGS---T-T--EEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTC
T ss_pred             cccccchhHHHHHHHHHHhhc--cccHHHc---C-C--EEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCC
Confidence            666677888999999999986  6777654   4 2  356677889999999999999999999999986

>d1udsa1 d.14.1.4 (A:2-150) Ribonuclease PH, domain 1 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.97  E-value=1.2e-31  Score=218.06  Aligned_cols=138  Identities=19%  Similarity=0.301  Sum_probs=117.9

Q ss_pred             CCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCC-CCCCCcceEEEEEecCCCCCCCccC-----C
Q 022140           37 RPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPS-LESPDEGCVSIDFHMPPICSPLVRP-----G  110 (302)
Q Consensus        37 R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~-~~~p~~g~l~v~V~~~~~~~~~~~~-----g  110 (302)
                      |+|||+++|+|++++++|++++++|||+|++|+|+|+|+|+++...|. ...+++|.+.++++++|++...+..     +
T Consensus         1 R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~   80 (149)
T d1udsa1           1 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITAEYSMLPRATQQRTIRESVQG   80 (149)
T ss_dssp             CTTSCCTTCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEESCCCGGGTTSSCCEEEEEEEECSEETTEECCCSSSSC
T ss_pred             CCCCCCCCCccCeEEEeCCCCCCCEEEEEEECCCEEEEEEEeeccccccccCCCceeEEeeecchhhccccccccccccc
Confidence            899999999999999999999999999999999999999999987764 4678899999999999987654322     3


Q ss_pred             CCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCcE
Q 022140          111 RPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPTV  182 (302)
Q Consensus       111 ~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~~  182 (302)
                      ++......+++++.+.+.+  .      ++..+...|.|+|+|+||++|||++||+++|+++||.|+++|+.
T Consensus        81 ~~~~~~~~~~~~l~~~l~~--~------i~l~~~~~~~i~v~v~VL~~DG~l~da~~~A~~~AL~dagipm~  144 (149)
T d1udsa1          81 RIGGRTHEIQRMIGRAMRT--A------VELTKIGERTIWVDCDVIQADGGTATAAITGAFVAVADAIIKLH  144 (149)
T ss_dssp             CCCHHHHHHHHHHHHHHHH--H------BCGGGSCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccchhHHHHHHHhhhhh--e------ehhhhcCCceEEEEEEEEccCCCHHHHHHHHHHHHHHHhChHHH
Confidence            3445667788888887764  2      33444557999999999999999999999999999999999963

>d2nn6b1 d.14.1.4 (B:6-150) Exosome complex exonuclease RRP41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=8.9e-31  Score=211.85  Aligned_cols=139  Identities=22%  Similarity=0.230  Sum_probs=118.6

Q ss_pred             hcCCCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCC---CCCCCcceEEEEEecCCCCCCCccC
Q 022140           33 AESIRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPS---LESPDEGCVSIDFHMPPICSPLVRP  109 (302)
Q Consensus        33 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~---~~~p~~g~l~v~V~~~~~~~~~~~~  109 (302)
                      ++|+|+|||+++|+|++++++|++++++|||+|++|+|+|+|+|++|...+.   ...|+++.+.+++.+.|++...+..
T Consensus         3 e~g~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~~v~v~~~~~~~~~~~~~~   82 (145)
T d2nn6b1           3 DQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATFSTGERKR   82 (145)
T ss_dssp             BTTBCSSSSCTTSCCCEEEEESCSSSSSEEEEEEESSCEEEEEEEEEEECCSSSCCCCCSSCCEEEEEEECTTTSSSCCC
T ss_pred             CCCccCCCCCCCCccCeEEEECCCCCCCceEEEEeCCceEEEEEEeccccccchhhccccceeEEEEeeecCcccccccc
Confidence            5799999999999999999999999999999999999999999999876532   2347789999999999998765433


Q ss_pred             -CCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCC
Q 022140          110 -GRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQI  179 (302)
Q Consensus       110 -g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~i  179 (302)
                       +..+.++.+++++|++.|++  .+.++.   +|   .|.|+|+++||++|||++|||++|+++||+|++|
T Consensus        83 ~~~~~~~~~~l~~~l~~~l~~--~i~~~~---~~---~~~I~v~v~VL~~DG~l~~a~i~aa~lAL~daGI  145 (145)
T d2nn6b1          83 RPHGDRKSCEMGLQLRQTFEA--AILTQL---HP---RSQIDIYVQVLQADGGTYAACVNAATLAVLDAGI  145 (145)
T ss_dssp             TTTSTHHHHHHHHHHHHHHHH--TTCGGG---CT---TEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTCC
T ss_pred             cCCCCchhhhHHHHHHHhhhc--ccchHh---hC---ceeeEEEEEEEeCCCCHHHHHHHHHHHHHHHcCC
Confidence             23445788899999999986  444443   33   3789999999999999999999999999999986

>d1r6la1 d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.97  E-value=7.3e-30  Score=207.73  Aligned_cols=138  Identities=21%  Similarity=0.361  Sum_probs=114.4

Q ss_pred             CCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCC-CCCCCcceEEEEEecCCCCCCCccC-----
Q 022140           36 IRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPS-LESPDEGCVSIDFHMPPICSPLVRP-----  109 (302)
Q Consensus        36 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~-~~~p~~g~l~v~V~~~~~~~~~~~~-----  109 (302)
                      .|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|+++...|. .+.|++|.+.++++++|++...+..     
T Consensus         2 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~   81 (151)
T d1r6la1           2 NRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTAEYGMLPRSTGERNQREASR   81 (151)
T ss_dssp             CCTTCCCTTCCCCEEEESSCSSSSSEEEEEEETTEEEEEEEEEEESCSSCCC---CCEEEEEEEECTTSSSSCCCCHHHH
T ss_pred             CCCCCCCCCCccCeEEEeCCCCCCCEEEEEEeCCCEEEEEEEecccccccccCCCceeEEEEEEecCccccccccccCCC
Confidence            4999999999999999999999999999999999999999999988764 4567899999999999998765432     


Q ss_pred             CCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCc
Q 022140          110 GRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPT  181 (302)
Q Consensus       110 g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~  181 (302)
                      +...+....+.+.+.+.+.+  .+++   +++|   .|+|+|+++||++|||++||+++|+++||+|+++|+
T Consensus        82 ~~~~~~~~~~~~~l~~~~~~--~~~l---~~~~---~~~i~v~v~VL~~DG~~~da~~~Aa~~AL~dagip~  145 (151)
T d1r6la1          82 GKQGGRTLEIQRLIGRSLRA--ALDL---SKLG---ENTLYIDCDVIQADGGTRTASITGATVALIDALAVL  145 (151)
T ss_dssp             TSCCHHHHHHHHHHHHHHHH--TBCG---GGTC---SEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccchhHHHHHHhhhhh--ccch---hhhC---ceEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhcHHH
Confidence            22334566777888888875  3333   3455   378899999999999999999999999999999996

>d1oysa1 d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Bacillus subtilis [TaxId: 1423]

Probab=99.96  E-value=9.1e-30  Score=207.16  Aligned_cols=137  Identities=19%  Similarity=0.353  Sum_probs=103.5

Q ss_pred             CCCCCCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeecc-CCCCCCCcceEEEEEecCCCCCCCcc-----C
Q 022140           36 IRPDARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMT-PSLESPDEGCVSIDFHMPPICSPLVR-----P  109 (302)
Q Consensus        36 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~-p~~~~p~~g~l~v~V~~~~~~~~~~~-----~  109 (302)
                      +|+|||+++|+|++++++|++++++|||+|++|+|+|+|+|+++... +..+.|++|.+++++++.|++.+.+.     .
T Consensus         1 lR~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~   80 (151)
T d1oysa1           1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPQATNQQTIQESSK   80 (151)
T ss_dssp             CCTTSCCTTCCCCEEEECC-----CCCEEEEETTEEEEEEEEEESCCCGGGTTSCCCEEEEEEEC---------------
T ss_pred             CCCCCCCCCCccCeEEEeCCCCCCCEEEEEEEcCCEEEEEEEecccccccccccccceeeeeeeeccccccccccccccC
Confidence            69999999999999999999999999999999999999999976544 45567889999999999998865432     2


Q ss_pred             CCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCC
Q 022140          110 GRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP  180 (302)
Q Consensus       110 g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP  180 (302)
                      +.+.+....+++++++.+.+  .++++.   +|   .|.|+|+|+||++|||++||+++|+++||+|+..|
T Consensus        81 ~~~~~~~~~~~~~l~~~l~~--~i~l~~---~~---~~~i~v~v~VL~~DG~l~~a~i~Aa~~AL~dA~~~  143 (151)
T d1oysa1          81 GKISGRTMEIQRLIGRALRA--VVDLEK---LG---ERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGK  143 (151)
T ss_dssp             ----CHHHHHHHHHHHHHHH--TBCHHH---HC---SCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CcccchhhHHhHHHHHHhhh--hhhhhh---hc---cceEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHH
Confidence            33466788999999999875  454433   33   58999999999999999999999999999998654

>d2nn6f1 d.14.1.4 (F:29-175) Exosome complex exonuclease MTR3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease MTR3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=2.4e-26  Score=185.61  Aligned_cols=132  Identities=21%  Similarity=0.264  Sum_probs=110.0

Q ss_pred             CCCCCCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCC-------------CCCcceEEEEEecCCCCCCC
Q 022140           40 ARSLSRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLE-------------SPDEGCVSIDFHMPPICSPL  106 (302)
Q Consensus        40 GR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~-------------~p~~g~l~v~V~~~~~~~~~  106 (302)
                      .|+++|+|++++++|++++++|||+|++|+|+|+|+|+++...+...             .+..+.+.+++++.|+++..
T Consensus         2 ~R~~~e~R~i~i~~gvi~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (147)
T d2nn6f1           2 TRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAALRGRLLCDFRRAPFAGRR   81 (147)
T ss_dssp             CCCSSCCCCCCCCCSCCSSSSEEECCCSSSCEEEEEEEEEECC-------------------CBCEEEEEEEECTTSSSS
T ss_pred             CCCCCCccceEEEeCCCCCCCEEEEEEECCeEEEEEEeccccccccccCCccccccccccccccceeEEEEEecCCcccc
Confidence            59999999999999999999999999999999999999987543221             23458899999999998776


Q ss_pred             ccCCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCC
Q 022140          107 VRPGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQI  179 (302)
Q Consensus       107 ~~~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~i  179 (302)
                      ++.+...+.+..++..+...+.+.  +      +......|.|+|+++||++|||++|||++|+++||+|++|
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~l~~~--~------~~~~~~~~~i~v~v~Vl~~DG~l~~a~i~A~~~AL~daGI  146 (147)
T d2nn6f1          82 RRAPPGGCEERELALALQEALEPA--V------RLGRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGV  146 (147)
T ss_dssp             CCCSCCHHHHHHHHHHHHHHHTTT--B------CSTTSBTCEEEEEEEEEECCSSHHHHHHHHHHHHHHHHCC
T ss_pred             ccccCCccchhhhhhhhhhccccc--c------cccccCCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHhCC
Confidence            655555667888999999988753  2      2334557999999999999999999999999999999987

>d1e3ha3 d.14.1.4 (A:346-482) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4
species: Streptomyces antibioticus [TaxId: 1890]

Probab=99.92  E-value=8.3e-25  Score=174.73  Aligned_cols=130  Identities=15%  Similarity=0.216  Sum_probs=105.8

Q ss_pred             CCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCC-----cceEEEEEecCCCCCCCc-cCCCCCCcHH
Q 022140           44 SRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPD-----EGCVSIDFHMPPICSPLV-RPGRPAEAAP  117 (302)
Q Consensus        44 ~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~-----~g~l~v~V~~~~~~~~~~-~~g~~~~~~~  117 (302)
                      .|+|++++++|++++++|||++++|+|+|+|+|+++...|....++     .+.+.+++.+.|+.+... +.+.++..+.
T Consensus         1 tE~R~i~~~~gv~~~adGSa~~~~G~T~Vl~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (137)
T d1e3ha3           1 TDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPPYSVGETGRVGSPKRREI   80 (137)
T ss_dssp             TCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEEEGGGSEECCSSSSCCEESEEEEEECCGGGGTCCCCCSSCCHHHH
T ss_pred             CCcceEEEEeCCCCCCCeeEEEEECCeEEEEEEccCccCccccccccCcceeeeeeeecccccccccccccccccccccc
Confidence            4899999999999999999999999999999999988765433322     245777777777755432 2344567888


Q ss_pred             HHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCCc
Q 022140          118 VVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIPT  181 (302)
Q Consensus       118 ~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP~  181 (302)
                      .+++.+.+.+++  .+.      ......|+|+|+++||++|||+++|+++|+++||.|++||+
T Consensus        81 ~~~~~i~~~l~~--~i~------~~~~~~~~I~v~v~vl~~DG~~~~aainAa~lAL~dAGIpm  136 (137)
T d1e3ha3          81 GHGALAERAIVP--VLP------TREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPL  136 (137)
T ss_dssp             HHHHHHHHHHGG--GCC------CTTTSCEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCC
T ss_pred             ccchHHHHHHHh--ccc------hhhcCcEEEEEEEEEecCCCCHHHHHHHHHHHHHHHcCCcc
Confidence            999999999976  333      33445799999999999999999999999999999999995

>d2nn6d1 d.14.1.4 (D:25-146) Exosome complex exonuclease RRP46 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP46
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=2.2e-23  Score=163.06  Aligned_cols=121  Identities=16%  Similarity=0.152  Sum_probs=95.7

Q ss_pred             CCCcceEEEeCCccCCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEEecCCCCCCCccCCCCCCcHHHHHHHH
Q 022140           44 SRARNTTISMGAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPAEAAPVVAKQL  123 (302)
Q Consensus        44 ~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V~~~~~~~~~~~~g~~~~~~~~ls~~l  123 (302)
                      .|+|++.+++|+++++||||++++|+|+|+|+|+||...+. .....+...++|++.|.      .+.++..++.++++|
T Consensus         2 ~elR~i~~~~gvl~~adGSa~~~~G~T~Vi~~V~gP~e~~~-~~~~~~~~~~~v~~~~~------~~~~~~~~~~~~~~l   74 (122)
T d2nn6d1           2 CSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKV-SKEIFNKATLEVILRPK------IGLPGVAEKSRERLI   74 (122)
T ss_dssp             CCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECC-------CCEEEEEEEECS------SSCCCHHHHHHHHHH
T ss_pred             CccceEEEEECCCCCCCeEEEEEECCcEEEEEEEecccccc-hhhCcCCCceEEEeeee------cCCCCchhhHHHHHH
Confidence            48999999999999999999999999999999999875322 22223445555555443      244566788999999


Q ss_pred             HHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCC
Q 022140          124 SDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQI  179 (302)
Q Consensus       124 ~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~i  179 (302)
                      ++.|++  .++++.+   |   .|+|+|+++|+++|||+++|+++|+++||.|++|
T Consensus        75 ~~~l~~--~i~~~~~---p---~~~i~i~v~Vl~~DG~~~~a~ina~~lAL~dagI  122 (122)
T d2nn6d1          75 RNTCEA--VVLGTLH---P---RTSITVVLQVVSDAGSLLACCLNAACMALVDAGV  122 (122)
T ss_dssp             HHHHHH--HCGGGCS---S---SEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTC
T ss_pred             Hhhhhc--ccchhhc---C---CeEEEEEEEEEcCCCChhHHHHHHHHHHHHHcCC
Confidence            999986  5655543   3   5999999999999999999999999999999985

>d2nn6e2 d.101.1.1 (E:192-285) Exosome complex exonuclease RRP42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=1.5e-20  Score=139.79  Aligned_cols=87  Identities=21%  Similarity=0.210  Sum_probs=83.3

Q ss_pred             ccCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHH
Q 022140          213 LTLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQIL  292 (302)
Q Consensus       213 l~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l  292 (302)
                      |+++++|+++||+++++.+|+|||.+||+++++.++|+++++|+||++++.|+.++++++ +.+|+++|.+++++|++.+
T Consensus         1 L~i~~~Pv~vT~~~i~~~~lvDpt~~EE~~~~~~l~v~~~~~g~i~~l~k~G~~~l~~~~-i~~~i~~A~~~~~el~~~l   79 (94)
T d2nn6e2           1 LSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPES-IFEMMETGKRVGKVLHASL   79 (94)
T ss_dssp             CCCTTCCCCEEEEESSSSEESSCCHHHHTSCSEEEEECCCSSSCCCEEEEEESSCBCHHH-HHHHHHHHHHHHHHHHHHH
T ss_pred             CCcCceEEEEEEEEECCEEEECCCHHHHhccCceEEEEEcCCCcEEEEEecCCCccCHHH-HHHHHHHHHHHHHHHHHHH
Confidence            468899999999999999999999999999999999999999999999999999999996 9999999999999999999


Q ss_pred             HHHhhccc
Q 022140          293 EEAISGME  300 (302)
Q Consensus       293 ~~~l~~~~  300 (302)
                      +++|++++
T Consensus        80 ~~~L~~~e   87 (94)
T d2nn6e2          80 QSVVHKEE   87 (94)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            99998764

>d2nn6c2 d.101.1.1 (C:188-276) Exosome complex exonuclease RRP43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=6.9e-20  Score=134.88  Aligned_cols=86  Identities=30%  Similarity=0.573  Sum_probs=81.3

Q ss_pred             cCCCccEEEEEEEECC-EEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHH
Q 022140          214 TLGGIPFSLTCILHKN-YILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQIL  292 (302)
Q Consensus       214 ~i~~~p~~vt~~~~~~-~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l  292 (302)
                      +++++|+++||+++++ ++|+|||.+||+++++.++|+++++|++|++++.||.++++++ +.+|+++|.+++++|++++
T Consensus         1 ni~~~Pi~vT~~~~~~~~~lvDpt~~EE~~~~~~lti~~~~~g~i~~l~k~G~~~l~~~~-l~~~~~~A~~~~~~l~~~l   79 (89)
T d2nn6c2           1 NIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAK-LQDCMSRAVTRHKEVKKLM   79 (89)
T ss_dssp             CCSCCCEEEEEEECTTTCCEESCCTTTTTSCSEEEEEEECTTCCEEEEEESCCSCCCHHH-HHHHHHHHHHHHHHHHHHH
T ss_pred             CccCCEEEEEEEEECCEEEEEcCCHHHHhcCCceEEEEEcCCCCEEEEEecCCcccCHHH-HHHHHHHHHHHHHHHHHHH
Confidence            3789999999999976 5789999999999999999999999999999999999999996 9999999999999999999


Q ss_pred             HHHhhccc
Q 022140          293 EEAISGME  300 (302)
Q Consensus       293 ~~~l~~~~  300 (302)
                      +++|++.+
T Consensus        80 ~~al~~~~   87 (89)
T d2nn6c2          80 DEVIKSMK   87 (89)
T ss_dssp             HTTTTTTC
T ss_pred             HHHHHhcc
Confidence            99999875

>d2nn6a2 d.101.1.1 (A:185-302) Exosome complex exonuclease RRP45 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP45
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.9e-19  Score=139.25  Aligned_cols=87  Identities=21%  Similarity=0.525  Sum_probs=82.0

Q ss_pred             ccCCCccEEEEEEEEC--CEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHH
Q 022140          213 LTLGGIPFSLTCILHK--NYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQ  290 (302)
Q Consensus       213 l~i~~~p~~vt~~~~~--~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~  290 (302)
                      |+++++|+++||++++  +.+|+|||.+||.++++.++|+++++|+||++++.||.+++.++ +.+|++.|..++++|++
T Consensus         1 L~i~h~Pi~vT~~~~~~g~~~lvDPt~~EE~~~~~~ltv~~n~~gei~~l~k~Gg~~l~~~~-l~~~~~~A~~~~~el~~   79 (118)
T d2nn6a2           1 LSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGIMLLKDQ-VLRCSKIAGVKVAEITE   79 (118)
T ss_dssp             CCBCCCEEEEEEEECTTTSSEEESCCHHHHHHCSCEEEEEEETTTEEEEEEEESCCCCCHHH-HHHHHHHHHHHHHHHHH
T ss_pred             CCcCceEEEEEEEEEecCCeEEECCCHHHHhCCCCcEEEEEeCCCcEEEEEecCCcccCHHH-HHHHHHHHHHHHHHHHH
Confidence            4689999999999986  57999999999999999999999999999999999999999997 99999999999999999


Q ss_pred             HHHHHhhccc
Q 022140          291 ILEEAISGME  300 (302)
Q Consensus       291 ~l~~~l~~~~  300 (302)
                      +++++|+++.
T Consensus        80 ~i~~aLk~~~   89 (118)
T d2nn6a2          80 LILKALENDQ   89 (118)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999998753

>d2je6a2 d.101.1.1 (A:192-275) Exosome complex exonuclease 2, ECX2 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 2, ECX2
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.77  E-value=1.6e-18  Score=126.07  Aligned_cols=82  Identities=18%  Similarity=0.336  Sum_probs=79.1

Q ss_pred             CCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHHH
Q 022140          215 LGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILEE  294 (302)
Q Consensus       215 i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~~  294 (302)
                      ++++|+++||+++++.+|+|||.+||+++++.++|+++++|++|.+++.|+.+++.++ +.+|+++|.+++++|++.+++
T Consensus         2 ~~~~~~~vt~~~i~~~~lvDpt~~EE~~~~~~l~v~~~~~g~i~~~~k~g~~~~~~~~-i~~~i~~A~~~~~~l~~~l~~   80 (84)
T d2je6a2           2 LNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSGKGSMSLQD-IDQAENTARSTAVKLLEELKK   80 (84)
T ss_dssp             CSCCCEEEEEEEETTEEEESCCHHHHHHCSEEEEEEECTTCCEEEEEEESSSCEEHHH-HHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEEEEECCEEEecCCHHHHHhcCCceeeeecCCCceeeEEeccCCcCCHHH-HHHHHHHHHHHHHHHHHHHHH
Confidence            6799999999999999999999999999999999999999999999999999999996 999999999999999999999


Q ss_pred             Hhh
Q 022140          295 AIS  297 (302)
Q Consensus       295 ~l~  297 (302)
                      +|.
T Consensus        81 ~l~   83 (84)
T d2je6a2          81 HLG   83 (84)
T ss_dssp             HHT
T ss_pred             HhC
Confidence            874

>d1e3ha2 d.14.1.4 (A:3-151) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4
species: Streptomyces antibioticus [TaxId: 1890]

Probab=99.77  E-value=2e-18  Score=138.84  Aligned_cols=135  Identities=21%  Similarity=0.229  Sum_probs=99.6

Q ss_pred             CCCCCCCCCCCcceEEEeCCcc-CCCeeEEEEeCCeEEEEEEEeeeccCCCCCCCcceEEEEE--ecCCCC---CCC-cc
Q 022140           36 IRPDARSLSRARNTTISMGAVA-SADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDF--HMPPIC---SPL-VR  108 (302)
Q Consensus        36 ~R~DGR~~~e~R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~~~v~~p~~~~p~~g~l~v~V--~~~~~~---~~~-~~  108 (302)
                      .+.|+|.+.+ |++++++|+++ +|+|||++++|+|+|+|++++.-..|.... +...+.+..  .+.+..   +.. .+
T Consensus         8 ~~~~~~~~~~-R~i~ie~G~lakqA~GSalv~~G~T~vl~ta~~~~~~~~~~~-~~~~~~v~~~~~~~~~~~~~~~~~rr   85 (149)
T d1e3ha2           8 AVIDNGAFGT-RTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQL-DFFPLTVDVEERMYAAGKIPGSFFRR   85 (149)
T ss_dssp             EEEECGGGCE-EEEEEEESSSCTTSSEEEEEEETTTEEEEEEEEECSSCCTTC-SSCCEEEEEEECGGGGTCCCCSTTSS
T ss_pred             EEEeCCcCCC-cEEEEEeCcccccCCceEEEEECCcEEEEEeeeccccccccc-ccCCceeEEEEecccccccccccccc
Confidence            4678888777 99999999996 699999999999999999998655444322 122233333  222211   111 13


Q ss_pred             CCCCCCcHHHHHHHHHHHhhcCCCcccccceeecCeeeEEEEEEEEEecCCCCHHHHHHHHHHHHHhhCCCC
Q 022140          109 PGRPAEAAPVVAKQLSDTISSSGMINLKELSLVGGKAAWMVYLDIYCLDADGALFDAALLSAVAAFSNLQIP  180 (302)
Q Consensus       109 ~g~~~~~~~~ls~~l~~~l~~~~~i~~~~L~i~~g~~~w~i~v~v~Vl~~dG~l~da~~~A~~~AL~~~~iP  180 (302)
                      .+++++.+..+++++++.|++  .++.+.   .   .-.+|.+++.+++.||+...|+++|+++||++++||
T Consensus        86 e~~~~~reil~~rlidR~Lrp--l~p~~~---~---~~~qI~~~vl~~d~d~~~~~aai~aAs~AL~~agIP  149 (149)
T d1e3ha2          86 EGRPSEDAILTCRLIDRPLRP--SFKKGL---R---NEIQVVATIMALNPDHLYDVVAINAASASTQLAGLP  149 (149)
T ss_dssp             CCSCCHHHHHHHHHHHHHHHH--HBCTTB---C---SCEEEEEEEEECCTTSCCHHHHHHHHHHHHHHTTCS
T ss_pred             ccccchHHHHHHHHHHHHHHh--hccccC---C---CceEEEEEEEEeCCCCChHHHHHHHHHHHHHhcCCC
Confidence            467788999999999999997  344321   1   124788888888889999999999999999999998

>d2ba0g2 d.101.1.1 (G:179-257) Exosome complex exonuclease 2, ECX2 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 2, ECX2
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.76  E-value=8.5e-19  Score=125.97  Aligned_cols=77  Identities=25%  Similarity=0.440  Sum_probs=73.4

Q ss_pred             CCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHH
Q 022140          215 LGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQIL  292 (302)
Q Consensus       215 i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l  292 (302)
                      ++++|+++||+++++.+|+|||.+||+++++.++|+++++|++|++++.|+.+++.++ +.+|+++|.+++++|.+.+
T Consensus         2 v~~~Pv~vT~~~~~~~~lvDpt~eEE~~~~~~iti~~~~~g~i~~~~k~G~~~~~~~~-i~~~i~~A~~~~~~l~e~l   78 (79)
T d2ba0g2           2 VRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITTDKDDNVVAMQKSGGYLLDEKL-FDELLDVSINCARKLREKF   78 (79)
T ss_dssp             BCCCCEEEEEEEETTEEEESCCTTGGGGCSCEEEEEECTTSCEEEEEEESSCCBCHHH-HHHHHHHHHHHHHHHTTTT
T ss_pred             CCCceEEEEEEEECCEEEECCCHHHHhcCCceEEEEEcCCCCEEEEEccCCCCcCHHH-HHHHHHHHHHHHHHHHHHh
Confidence            6899999999999999999999999999999999999999999999999999999996 9999999999999997654

>d2nn6d2 d.101.1.1 (D:147-235) Exosome complex exonuclease RRP46 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP46
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=1.6e-13  Score=100.09  Aligned_cols=82  Identities=21%  Similarity=0.408  Sum_probs=74.7

Q ss_pred             CCCccEEEEEEEE-CCEEEECCChHHHhcCCceEEEEEc-CCCcEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHH
Q 022140          215 LGGIPFSLTCILH-KNYILADPTSEEESIMETLVTVVLD-SSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQIL  292 (302)
Q Consensus       215 i~~~p~~vt~~~~-~~~~l~DPt~~Ee~~~~~~l~i~~~-~~g~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l  292 (302)
                      |++++.++|+|+. ++.+++|||.+||+.+++.+++++. .+++++.++..|  .+++++ +.+++++|.+.+++|++++
T Consensus         2 m~~~v~av~~~~~~dg~~vlDpt~~Ee~~~~~~~~~a~~~~~~~i~~~~~~g--~~s~~~-~~~~l~~a~~~~~~I~~~~   78 (89)
T d2nn6d2           2 MRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFALDSVERKLLMSSTKG--LYSDTE-LQQCLAAAQAASQHVFRFY   78 (89)
T ss_dssp             CSSCEEEEEEEECTTCCEEESCCHHHHHHCSEEEEEEEETTTCCCCEEEEEE--SCCHHH-HHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEeEEEEEEEcCCceeeCCCHHHHhhcceEEEEEEEcCCCeEEEEeecC--CcCHHH-HHHHHHHHHHHHHHHHHHH
Confidence            7899999999998 5789999999999999999999986 467899998877  689997 9999999999999999999


Q ss_pred             HHHhhcc
Q 022140          293 EEAISGM  299 (302)
Q Consensus       293 ~~~l~~~  299 (302)
                      +++|+++
T Consensus        79 r~~l~k~   85 (89)
T d2nn6d2          79 RESLQRR   85 (89)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999864

>d2nn6b2 d.101.1.1 (B:151-240) Exosome complex exonuclease RRP41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=3e-13  Score=98.93  Aligned_cols=82  Identities=16%  Similarity=0.201  Sum_probs=75.7

Q ss_pred             CCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEE-cCCCcEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHH
Q 022140          215 LGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVL-DSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILE  293 (302)
Q Consensus       215 i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~-~~~g~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~  293 (302)
                      |++++.++|+|++++.+++|||.+|++.+++.++|++ ...++|+.++..|  .++.++ +.+++++|.+.+++|+++++
T Consensus         2 m~d~V~avs~g~~~~~~llDp~~~E~~~~~~~l~va~~~~~~~I~~~~~~g--~~~~~~-~~~~l~~a~~~~~~i~~~~~   78 (90)
T d2nn6b2           2 MRDFVCACSAGFVDGTALADLSHVEEAAGGPQLALALLPASGQIALLEMDA--RLHEDH-LERVLEAAAQAARDVHTLLD   78 (90)
T ss_dssp             CSSCCEEEEEEEETTEEEESCCHHHHTSSCCCEEEEEETTTTEEEEEEECS--CCBTTS-HHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEEEEECCEEeeCCccccccccccceEEEEEecCCCEEEEEEec--ccCHHH-HHHHHHHHHHHHHHHHHHHH
Confidence            7899999999999999999999999999999999976 6678999999877  578887 99999999999999999999


Q ss_pred             HHhhcc
Q 022140          294 EAISGM  299 (302)
Q Consensus       294 ~~l~~~  299 (302)
                      ++++++
T Consensus        79 ~~l~~~   84 (90)
T d2nn6b2          79 RVVRQH   84 (90)
T ss_dssp             HHHHHH
T ss_pred             HHHHhh
Confidence            999764

>d2je6b2 d.101.1.1 (B:156-241) Exosome complex exonuclease 1, ECX1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 1, ECX1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.42  E-value=7.3e-13  Score=95.98  Aligned_cols=81  Identities=12%  Similarity=0.135  Sum_probs=74.9

Q ss_pred             CCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcC-CCcEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHHHHH
Q 022140          215 LGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDS-SNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQILE  293 (302)
Q Consensus       215 i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~-~g~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~~l~  293 (302)
                      |+++..++|+|++++.+++|||.+|++.++..++|++.+ .++|+.++..|  .++.++ +.+++++|.+.+++|+++++
T Consensus         2 m~d~V~avsvg~~d~~~llDp~~~E~~~~~~~l~va~~~~~~~i~~~~~~g--~~~~~~-~~~~l~~a~~~~~~I~~~~~   78 (86)
T d2je6b2           2 MRDLIAGVAVGKADGVIILDLNETEAMWGEADMPIAMMPSLNQVTLFQLNG--SMTPDE-FRQAFDLAVKGINIIYNLER   78 (86)
T ss_dssp             BSSCCEEEEEEEETTEEEESCCHHHHHHSSEEEEEEEEGGGTEEEEEEEEE--CBCHHH-HHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEEEEECCEEEEecchhhhhcCceeEEEEEeCCCCeEEEEeecC--CCCHHH-HHHHHHHHHHHHHHHHHHHH
Confidence            688999999999999999999999999999999999864 57899999877  688897 99999999999999999999


Q ss_pred             HHhhc
Q 022140          294 EAISG  298 (302)
Q Consensus       294 ~~l~~  298 (302)
                      ++|++
T Consensus        79 e~l~~   83 (86)
T d2je6b2          79 EALKS   83 (86)
T ss_dssp             HHHHG
T ss_pred             HHHHh
Confidence            99985

>d1r6la2 d.101.1.1 (A:152-239) Ribonuclease PH, domain 2 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.36  E-value=5.1e-12  Score=91.74  Aligned_cols=84  Identities=17%  Similarity=0.218  Sum_probs=77.2

Q ss_pred             cCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCC-cccChHHHHHHHHHHHHHHHHHHHHHH
Q 022140          214 TLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGG-AVLAYTSAVQDCIALTRQRVKELHQIL  292 (302)
Q Consensus       214 ~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~-~~~~~~~~l~~~i~~A~~~~~~l~~~l  292 (302)
                      +++++..+|++|++++.+++|||.+|+..++..+.++++++|+++.++..|. ..++.++ +.+++++|++.+++|++++
T Consensus         4 P~~~~VaavsvG~idg~~vld~~~~E~~~~~~Dl~va~t~~g~i~~iq~~ge~~~~sed~-~~~al~~A~~~i~~i~~~Q   82 (88)
T d1r6la2           4 PLKQMVAAVSVGIYQGVPVLDLDYLEDSAAETDLNVVMTDAGGFIEVQGTAEGAPFRPAE-LNAMLELAQQGMQELFELQ   82 (88)
T ss_dssp             CBCCCEEEEEEEEETTEEEESCCHHHHHHCSEEEEEEEETTSCEEEEEEEESSSCCCHHH-HHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCccEEEEEEECCEEEecCcHHhhccCceeEEEEEeCCCCEEeehhhcccCCCCHHH-HHHHHHHHHHHHHHHHHHH
Confidence            4678889999999999999999999999999999999999999998887764 4789997 9999999999999999999


Q ss_pred             HHHhhc
Q 022140          293 EEAISG  298 (302)
Q Consensus       293 ~~~l~~  298 (302)
                      +++|++
T Consensus        83 keal~e   88 (88)
T d1r6la2          83 RAALAE   88 (88)
T ss_dssp             HHHHTC
T ss_pred             HHHhcC
Confidence            999864

>d1oysa2 d.101.1.1 (A:152-237) Ribonuclease PH, domain 2 {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Bacillus subtilis [TaxId: 1423]

Probab=99.14  E-value=1.6e-10  Score=83.25  Aligned_cols=81  Identities=22%  Similarity=0.327  Sum_probs=72.6

Q ss_pred             CCCccEEEEEEEECCE-EEECCChHHHhcCCceEEEEEcCCCcEEEEEccCC-cccChHHHHHHHHHHHHHHHHHHHHHH
Q 022140          215 LGGIPFSLTCILHKNY-ILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGG-AVLAYTSAVQDCIALTRQRVKELHQIL  292 (302)
Q Consensus       215 i~~~p~~vt~~~~~~~-~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~-~~~~~~~~l~~~i~~A~~~~~~l~~~l  292 (302)
                      |++...++++|++++. +++||+.+|++.++..+.|+++++|+++.++..|. ..++.++ +.+++++|++.+++|++++
T Consensus         4 ~~~~VaavsvG~i~~~~vlldl~~~Ed~~~~~D~~va~t~~g~i~~iq~~ge~~~~s~d~-~~~al~lA~~gi~~I~~~Q   82 (86)
T d1oysa2           4 ITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSRED-LNGLLGLAEKGIQELIDKQ   82 (86)
T ss_dssp             BCSCEEEEEEEEETTTEEEESCCHHHHHHEEEEEEEEEETTSCEEEEEEEESSCCCCHHH-HHHHHHHHHHHHHHHHHHH
T ss_pred             ccCcccEEEEEEEcCCcEECCCHHHHhcCCCcceEEEEeCCCCEEEEEEeeccCcccHHH-HHHHHHHHHHHHHHHHHHH
Confidence            6788899999999875 67899999999999999999999999887777663 4689997 9999999999999999999


Q ss_pred             HHHh
Q 022140          293 EEAI  296 (302)
Q Consensus       293 ~~~l  296 (302)
                      +++|
T Consensus        83 keal   86 (86)
T d1oysa2          83 KEVL   86 (86)
T ss_dssp             HHHC
T ss_pred             HHhC
Confidence            9886

>d1udsa2 d.101.1.1 (A:151-255) Ribonuclease PH, domain 2 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.11  E-value=3.2e-10  Score=84.68  Aligned_cols=83  Identities=17%  Similarity=0.199  Sum_probs=73.8

Q ss_pred             cCCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCCcEEEEEccCC-cccChHHHHHHHHHHHHHHHHHHHHHH
Q 022140          214 TLGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSNQLVSLYKPGG-AVLAYTSAVQDCIALTRQRVKELHQIL  292 (302)
Q Consensus       214 ~i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~~G~-~~~~~~~~l~~~i~~A~~~~~~l~~~l  292 (302)
                      +|+++..+|++|++++.+++|||.+|.+.++..+.++++++|++..++..|. ..++.++ +.+++++|++.+++|++++
T Consensus         4 P~~~~VaAVsvG~idg~~vldp~~~Ed~~~~~dl~va~t~~g~~~ei~~~~e~~~~see~-~~eal~~a~~~i~~i~~~Q   82 (105)
T d1udsa2           4 PIKDFVAAVSVGIVNDRILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTKDE-LIKMLDLAQKGINELIELQ   82 (105)
T ss_dssp             CBCCCEEEEEEEEETTEEEESCCHHHHHTCSEEEEEEEETTSCEEEEEEEESSCCCCHHH-HHHHHHHHHHHHHHHHHHH
T ss_pred             CccCCceEEEEEEECCEEeecCCHHHHhcCccceeEEEecCCcchhhhhhhccccccHHH-HHHHHHHHHHHHHHHHHHH
Confidence            3678889999999999999999999999999999999999998766665542 3689997 9999999999999999999


Q ss_pred             HHHhh
Q 022140          293 EEAIS  297 (302)
Q Consensus       293 ~~~l~  297 (302)
                      +++|.
T Consensus        83 ke~l~   87 (105)
T d1udsa2          83 KKLYV   87 (105)
T ss_dssp             HTTEE
T ss_pred             HHHHh
Confidence            99875

>d2ba0d2 d.101.1.1 (D:154-252) Exosome complex exonuclease 1, ECX1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 1, ECX1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.11  E-value=2.3e-10  Score=84.69  Aligned_cols=83  Identities=17%  Similarity=0.219  Sum_probs=69.8

Q ss_pred             CCCccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcC-CCcEEEEEccC-CcccChHHHHHHHHHHHHHHHHHHHHHH
Q 022140          215 LGGIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDS-SNQLVSLYKPG-GAVLAYTSAVQDCIALTRQRVKELHQIL  292 (302)
Q Consensus       215 i~~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~-~g~i~~i~~~G-~~~~~~~~~l~~~i~~A~~~~~~l~~~l  292 (302)
                      |+++..++|+|++++.+++|||..|++.++..+++++.+ .+++..+...+ .+.++.++ +.+++++|...+++|++++
T Consensus         2 m~~~V~avsvG~~d~~~llDp~~~E~~~~~~~l~va~~~~~~~~~ei~~~~~~~~~~~~~-~~~~l~~a~~~~~~I~~~~   80 (99)
T d2ba0d2           2 MKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMDGRMTRDE-VKQAIELAKKGALQIYEMQ   80 (99)
T ss_dssp             BSSEEEEEEEEEETTEEEESCCHHHHHHSSEEEEEEEEEETTEEEEEEEEEEEEEECHHH-HHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcEEEEEEEEECCEEEEcCCcchhhcccCceEEEEecCcceEEEEEEEeccccchHHH-HHHHHHHHHHHHHHHHHHH
Confidence            678889999999999999999999999999999998654 45554443332 12688886 9999999999999999999


Q ss_pred             HHHhhc
Q 022140          293 EEAISG  298 (302)
Q Consensus       293 ~~~l~~  298 (302)
                      ++++++
T Consensus        81 ~~alk~   86 (99)
T d2ba0d2          81 REAILR   86 (99)
T ss_dssp             HHHHHH
T ss_pred             HHHHhh
Confidence            999985

>d2nn6f2 d.101.1.1 (F:176-270) Exosome complex exonuclease MTR3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease MTR3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.01  E-value=2e-10  Score=84.39  Aligned_cols=83  Identities=22%  Similarity=0.195  Sum_probs=71.7

Q ss_pred             CCCccEEEEEEEEC---CEEEECCChHHHhcCCceEEEEE-cCCCcEEEEEccCCcccChHHHHHHHHHHHHHHHHHHHH
Q 022140          215 LGGIPFSLTCILHK---NYILADPTSEEESIMETLVTVVL-DSSNQLVSLYKPGGAVLAYTSAVQDCIALTRQRVKELHQ  290 (302)
Q Consensus       215 i~~~p~~vt~~~~~---~~~l~DPt~~Ee~~~~~~l~i~~-~~~g~i~~i~~~G~~~~~~~~~l~~~i~~A~~~~~~l~~  290 (302)
                      |+++..++|+++.+   +.+|+|||..||..+.+.++|++ .+.++|+.++..|.. ++.++ +.+++++|.+.+++|++
T Consensus         1 M~D~V~acs~~~~~~~~~~~llD~~~~Ee~~~~~~~~va~~p~~~~i~~~~~~G~~-~~~d~-l~~~lela~~g~~~I~~   78 (95)
T d2nn6f2           1 MYDLVVGCGLSLAPGPAPTWLLDPTRLEEERAAAGLTVALMPVLNQVAGLLGSGEG-GLTES-WAEAVRLGLEGCQRLYP   78 (95)
T ss_dssp             BSSCCEEEECCCCSCSSCCCCSSCCTTTGGGCSSEEEEEEETTTTEEEEEEEECCS-SCTTT-THHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEEEeecCCCCcEEECCCHHHhcCCCCcEEEEEcCCCceeEEEEEeccc-chHHH-HHHHHHHHHHHHHHHHH
Confidence            56888999999975   56899999999999999999976 567889999999842 34565 99999999999999999


Q ss_pred             HHHHHhhcc
Q 022140          291 ILEEAISGM  299 (302)
Q Consensus       291 ~l~~~l~~~  299 (302)
                      +++++|.+.
T Consensus        79 i~~~aL~~~   87 (95)
T d2nn6f2          79 VLQQSLVRA   87 (95)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999998753

>d1e3ha5 d.101.1.1 (A:152-262) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
species: Streptomyces antibioticus [TaxId: 1890]

Probab=97.52  E-value=0.00054  Score=50.41  Aligned_cols=81  Identities=14%  Similarity=0.030  Sum_probs=64.1

Q ss_pred             CccEEEEEEEECCEEEECCChHHHhcCCceEEEEEcCCC----cEEEEEcc-----------CCcccChHHHHHHHHHHH
Q 022140          217 GIPFSLTCILHKNYILADPTSEEESIMETLVTVVLDSSN----QLVSLYKP-----------GGAVLAYTSAVQDCIALT  281 (302)
Q Consensus       217 ~~p~~vt~~~~~~~~l~DPt~~Ee~~~~~~l~i~~~~~g----~i~~i~~~-----------G~~~~~~~~~l~~~i~~A  281 (302)
                      ....+|.+|.+++.+++.||.+|-+.++-.|.|+-++++    .+..+...           |...++.+. +.++++.|
T Consensus         3 GPvgaVRVg~idge~viNPt~~el~~S~ldLvVaGt~~~~~~~~v~mie~~~~e~~~~mie~~a~e~~E~~-~~~ai~~a   81 (111)
T d1e3ha5           3 GPIGGVRVALIRGQWVAFPTHTELEDAVFDMVVAGRVLEDGDVAIMMVEAEATEKTIQLVKDGAEAPTEEV-VAAGLDAA   81 (111)
T ss_dssp             CCCEEEEEEEETTEEEESCCHHHHTTEEEEEEEEEEECTTSCEEEEEEEEEECTTHHHHHHTTCCCCCHHH-HHHHHHHH
T ss_pred             CCEEEEEEEEECCEEEECCCHHHHhcCceEEEEeecccccchHHHHHHHhcchhHHHHHHHhccccccHHH-HHHHHHHH
Confidence            445689999999999999999999998888888876543    35555432           223467775 99999999


Q ss_pred             HHHHHHHHHHHHHHhhc
Q 022140          282 RQRVKELHQILEEAISG  298 (302)
Q Consensus       282 ~~~~~~l~~~l~~~l~~  298 (302)
                      ++..+.+.+++++..+.
T Consensus        82 ~~~i~~~i~~q~el~~~   98 (111)
T d1e3ha5          82 KPFIKVLCKAQADLAAK   98 (111)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999988887764

>d1e3ha6 d.101.1.1 (A:483-578) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
species: Streptomyces antibioticus [TaxId: 1890]

Probab=96.59  E-value=0.013  Score=41.01  Aligned_cols=74  Identities=14%  Similarity=0.101  Sum_probs=62.5

Q ss_pred             EEEEEEEC--------CEEEECCChHHHhcCCceEEEEEcCCCcEEEEEc---cCCcccChHHHHHHHHHHHHHHHHHHH
Q 022140          221 SLTCILHK--------NYILADPTSEEESIMETLVTVVLDSSNQLVSLYK---PGGAVLAYTSAVQDCIALTRQRVKELH  289 (302)
Q Consensus       221 ~vt~~~~~--------~~~l~DPt~~Ee~~~~~~l~i~~~~~g~i~~i~~---~G~~~~~~~~~l~~~i~~A~~~~~~l~  289 (302)
                      .+++|++.        ..++.|....|....+..+-|+-+++| |++++.   ..  .++.+ ++.++++.|++...+|.
T Consensus         5 GIamGLi~~~~~~~~~~~iLtDI~G~ED~~GDMDFKVAGT~~G-ITa~QmDiKi~--Gi~~~-il~~Al~qAk~gR~~IL   80 (96)
T d1e3ha6           5 GIAMGLISQEINGETHYVALTDILGAEDAFGDMDFKVAGTKEF-VTALQLDTKLD--GIPAS-VLAAALKQARDARLHIL   80 (96)
T ss_dssp             EEEEEEEEEEETTEEEEEEESSCCSHHHHHCSEEEEEEECSSC-EEEEEEEECCS--CCCHH-HHHHHHHHHHHHHHHHH
T ss_pred             eeeeeeeeccCCCCccEEEEeeccCchhhccCcccccccCccc-ceeeeeeeccc--CCCHH-HHHHHHHHHHHHHHHHH
Confidence            45666652        257999999999999999999999999 888874   35  36778 69999999999999999


Q ss_pred             HHHHHHhhc
Q 022140          290 QILEEAISG  298 (302)
Q Consensus       290 ~~l~~~l~~  298 (302)
                      +.|.+++..
T Consensus        81 ~~M~~~i~~   89 (96)
T d1e3ha6          81 DVMMEAIDT   89 (96)
T ss_dssp             HHHHHHCSS
T ss_pred             HHHHHHhcc
Confidence            999998864

>d1e3ha1 a.4.9.1 (A:263-345) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 {Streptomyces antibioticus [TaxId: 1890]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
family: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
species: Streptomyces antibioticus [TaxId: 1890]

Probab=90.92  E-value=0.053  Score=37.01  Aligned_cols=30  Identities=33%  Similarity=0.285  Sum_probs=23.8

Q ss_pred             ccHHHHhhhChHHHHHHHHhcCCCCCCCCC
Q 022140           14 MEVDAFRRLFPLRYFERHLAESIRPDARSL   43 (302)
Q Consensus        14 ~~~~~~~~~~p~~f~~~~l~~~~R~DGR~~   43 (302)
                      .-.++|..+....+-...|..+.|+|||++
T Consensus        54 ~i~~~~~~l~k~~vR~~Il~~~~RiDGR~L   83 (83)
T d1e3ha1          54 EISAAYRALTKSLVRERVIAEKKRIDGRGV   83 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCBCTTSCBT
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCCCCCCCC
Confidence            345568888777777778899999999974

>d1whua_ a.4.9.1 (A:) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
family: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.11  E-value=0.53  Score=33.20  Aligned_cols=30  Identities=20%  Similarity=0.134  Sum_probs=24.4

Q ss_pred             ccHHHHhhhChHHHHHHHHhcCCCCCCCCC
Q 022140           14 MEVDAFRRLFPLRYFERHLAESIRPDARSL   43 (302)
Q Consensus        14 ~~~~~~~~~~p~~f~~~~l~~~~R~DGR~~   43 (302)
                      .-..+|..+.-..+-...|..++|+|||..
T Consensus        70 ~i~~af~~v~k~ivR~~IL~~~~RiDGRd~   99 (104)
T d1whua_          70 EIIESFNIVAKEVFRSIILNEYKRCDGRDS   99 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTSSCSCCCCCS
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCcCCCCCC
Confidence            445578888888888888999999999953