Citrus Sinensis ID: 026141

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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---
Protein Sequence
MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDLSKAE
Secondary Structure (PSIPRED)
ccccccccccccccccEEEEEccccccccEEEEEEccEEEEEEEEccccccccccccccEEEEEEEcccccccccHHHHHHHHHHHHHHHHHccccccccEEEEEEEEEEccccHHHHHHHHHHHHHHHcccccccccEEEEEEEEcccEEEEcccHHHHHccccccEEEccccccccccccccccccccccccHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccEEEEEEEEccccccccEEEEEEcccEEEEEEEcccccccccccccccEEEEccccccccccccEHHHHHHHHHHHHHHccHHHccccEEEEEEEEEEccccccHHHHHHHHHHHHHccccccccEEEEEEEEEEccEEEEcccccHHcccccccEEEEcccccEEEEEEcccccccHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHcc
Coil and Loop (DISEMBL)
mevdradgrnpnqlrplacscsilhrahgsaswsqgDTKVLAAvygpkagtkknenpekasieviwkprtgqigkpeKEYEIILKRTLQSICIltinpnttTSVIIQVvhddgallPCAINAACAALVDAGIPMKHLAVAICCcsaesgycildptklEEQKMKGFaylvfpnsilsvlpegsslvqgepmehgiitsvthgamsvddyFHCLERGRAASAKLSDFLRRSLQsklpgdlskae
Flexible Loop (DISEMBL)
mevdradgrnpnqlrPLACSCSILHRAHgsaswsqgdTKVLAAVYGpkagtkknenpekasieviwkprtgqigkpEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLrrslqsklpgdlskae
Low Complexity Region (SEG)
MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDLSKAE
Disordered region (IsUnstruct)
****************LACSCSILHRAHGSASWSQGDTKVLAAVYG***************IEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRA*************************
Disordered Region (DISOPRED)
*EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVY****************IEVI*****************ILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSL************
Disordered Region (DISEMBL)
*********NPNQLRPLACSCSILHR*********GDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQS**********
Disordered Region (DISPRO)
********RNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLP*******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDLSKAE
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	243	2.2.26 [Sep-21-2011]
Q84T68	238	Exosome complex exonuclea	yes	no	0.979	1.0	0.673	3e-90
Q9NQT4	235	Exosome complex component	yes	no	0.662	0.685	0.432	3e-31
Q9CRA8	235	Exosome complex component	yes	no	0.641	0.663	0.430	2e-30
O29757	258	Probable exosome complex	yes	no	0.711	0.670	0.301	1e-17
Q7YRA3	245	Exosome complex component	no	no	0.629	0.624	0.301	2e-17
Q9NPD3	245	Exosome complex component	no	no	0.629	0.624	0.301	2e-17
Q975G8	243	Probable exosome complex	yes	no	0.613	0.613	0.314	3e-17
Q921I9	245	Exosome complex component	no	no	0.629	0.624	0.301	3e-17
A2BKC0	255	Probable exosome complex	yes	no	0.872	0.831	0.271	4e-17
O59223	249	Probable exosome complex	yes	no	0.637	0.622	0.345	5e-17

>sp|Q84T68|EXOS5_ORYSJ Exosome complex exonuclease RRP46 homolog OS=Oryza sativa subsp. japonica GN=RRP46 PE=1 SV=2

 Score =  331 bits (848), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 161/239 (67%), Positives = 192/239 (80%), Gaps = 1/239 (0%)

Query: 1   MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60
           ME  RADGRNPNQLRP +C+ + L RAHGSA W+QGDT VLAAVYGPK GT+K ENPEKA
Sbjct: 1   MEESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKA 60

Query: 61  SIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 120
           SIEV+WKP TGQIGK EKEYE+ LKRTLQSIC+LT++PNTTTSVI+QVV +DG+LLPCAI
Sbjct: 61  SIEVVWKPMTGQIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLLPCAI 120

Query: 121 NAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLP 180
           NA CAALV AGIP+KHLAVAI C   E G  ILD  K EEQ++K FA+LVFPNS  S   
Sbjct: 121 NACCAALVFAGIPLKHLAVAIGCGVLEDGEVILDTNKAEEQQLKSFAHLVFPNSRKSASS 180

Query: 181 EGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDL 239
           +  +  + E  E G+ITS+THG MS +DYF C+ERG AAS+++SDF+R +LQ + PGD+
Sbjct: 181 KEPNQKE-EDSERGLITSITHGVMSEEDYFSCIERGLAASSRISDFMRTTLQKQAPGDV 238

Probable component of the exosome 3'->5' exoribonuclease complex, a complex that degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3'-untranslated regions. May form a homodimer separately from exosome complexes and function in DNA cleavage process. Binds double-stranded DNA (dsDNA) and single-stranded RNA (ssRNA), and possesses hydrolytic DNase and phosphorolytic RNase activities in vitro.
Oryza sativa subsp. japonica (taxid: 39947)
EC: 3EC: .EC: 1EC: .EC: 1EC: 3EC: .EC: -

>sp|Q9NQT4|EXOS5_HUMAN Exosome complex component RRP46 OS=Homo sapiens GN=EXOSC5 PE=1 SV=1

 Score =  135 bits (340), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 71/164 (43%), Positives = 101/164 (61%), Gaps = 3/164 (1%)

Query: 9   RNPN-QLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWK 67
           R P   LR  AC  ++L R  GSAS+ QGDT VLA VYGP       E   KA++EVI +
Sbjct: 22  RGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILR 81

Query: 68  PRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAAL 127
           P+ G  G  EK  E +++ T +++ + T++P T+ +V++QVV D G+LL C +NAAC AL
Sbjct: 82  PKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMAL 141

Query: 128 VDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVF 171
           VDAG+PM+ L   + C     G  +LDPT  +E++ +  A L F
Sbjct: 142 VDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEAR--AVLTF 183

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.

Homo sapiens (taxid: 9606)

>sp|Q9CRA8|EXOS5_MOUSE Exosome complex component RRP46 OS=Mus musculus GN=Exosc5 PE=1 SV=1

 Score =  132 bits (332), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 68/158 (43%), Positives = 98/158 (62%), Gaps = 2/158 (1%)

Query: 14  LRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQI 73
           LR  AC  ++L R  GSAS+ QGDT VLA VYGP       E   KA++EVI +P+ G  
Sbjct: 28  LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLP 87

Query: 74  GKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIP 133
           G  EK  E +++ T +++ +  ++P T+ +V++QVV D G+LL C +NAAC ALVDAG+P
Sbjct: 88  GVAEKSRERLVRNTCEAVVLGALHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVP 147

Query: 134 MKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVF 171
           M+ L   + C     G  +LDPT  +E++ +  A L F
Sbjct: 148 MRALFCGVTCALDSDGNLVLDPTTKQEKEAR--AILTF 183

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.

Mus musculus (taxid: 10090)

>sp|O29757|ECX1_ARCFU Probable exosome complex exonuclease 1 OS=Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) GN=AF_0493 PE=1 SV=1

 Score = 90.5 bits (223), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 56/186 (30%), Positives = 93/186 (50%), Gaps = 13/186 (6%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN-ENPEKASIE 63
           R DGR  ++LRP+    S+L RA GS     G  KV+AAV+GP+    ++ ++P KA I 
Sbjct: 17  RLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKAIIR 76

Query: 64  VIWK------PRTGQIGKPEKEYEI--ILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
             +           + G   +  EI  + K   +++ +  + P +   + ++V+  D   
Sbjct: 77  YRYNMAPFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGS 136

Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKG---FAYLVFP 172
               +NAA  ALVDAG+PMK +  ++    A+ G  +LDP K E+   +    FA+L+  
Sbjct: 137 RTACLNAASVALVDAGVPMKGMITSVAVGKAD-GQLVLDPMKEEDNFGEADMPFAFLIRN 195

Query: 173 NSILSV 178
             I S+
Sbjct: 196 GKIESI 201

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

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

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|Q7YRA3|EXOS4_BOVIN Exosome complex component RRP41 OS=Bos taurus GN=EXOSC4 PE=2 SV=3

 Score = 89.4 bits (220), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 51/169 (30%), Positives = 85/169 (50%), Gaps = 16/169 (9%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKA--GTKKNENPEKASI 62
           R DGR   +LR +     +  +A GSA   QG+TK LA VYGP    G++    P++A +
Sbjct: 13  RVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALV 72

Query: 63  EVIWKPRTGQIGKPEK---------EYEIILKRTLQSICILTINPNTTTSVIIQVVHDDG 113
              +   T   G+ ++         E  + L++T ++  +  ++P +   + +QV+  DG
Sbjct: 73  NCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADG 132

Query: 114 ALLPCAINAACAALVDAGIPMKHLAVAICCCSAE--SGYCILDPTKLEE 160
                 +NAA  A++DAGIPM+     +C CSA    G  + D + +EE
Sbjct: 133 GTYAACVNAATLAVLDAGIPMRDF---VCACSAGFVDGTALADLSHVEE 178

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. EXOSC4 binds to ARE-containing RNAs.

Bos taurus (taxid: 9913)

>sp|Q9NPD3|EXOS4_HUMAN Exosome complex component RRP41 OS=Homo sapiens GN=EXOSC4 PE=1 SV=3

 Score = 89.0 bits (219), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 51/169 (30%), Positives = 85/169 (50%), Gaps = 16/169 (9%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKA--GTKKNENPEKASI 62
           R DGR   +LR +     +  +A GSA   QG+TK LA VYGP    G++    P++A +
Sbjct: 13  RVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALV 72

Query: 63  EVIWKPRTGQIGKPEK---------EYEIILKRTLQSICILTINPNTTTSVIIQVVHDDG 113
              +   T   G+ ++         E  + L++T ++  +  ++P +   + +QV+  DG
Sbjct: 73  NCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADG 132

Query: 114 ALLPCAINAACAALVDAGIPMKHLAVAICCCSAE--SGYCILDPTKLEE 160
                 +NAA  A++DAGIPM+     +C CSA    G  + D + +EE
Sbjct: 133 GTYAACVNAATLAVLDAGIPMRDF---VCACSAGFVDGTALADLSHVEE 178

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. EXOSC4 binds to ARE-containing RNAs.

Homo sapiens (taxid: 9606)

>sp|Q975G8|ECX1_SULTO Probable exosome complex exonuclease 1 OS=Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) GN=STK_04430 PE=3 SV=2

 Score = 89.0 bits (219), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 50/159 (31%), Positives = 83/159 (52%), Gaps = 10/159 (6%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN-ENPEKASIE 63
           R DGR P+++RP+     +L  A GSA +  G+TKV+AAVYGPK    ++   P++A + 
Sbjct: 16  RLDGRKPDEMRPIKIELGVLKNADGSAIFEMGNTKVIAAVYGPKEMHPRHLALPDRAVLR 75

Query: 64  VIW--------KPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
           V +        + +     + E E   +++  L+S  ++ + P T   V ++V+  D   
Sbjct: 76  VRYHMTPFSTDERKNPAPSRREIELSKVIREALESTILVELFPRTVIDVFMEVLQADAGT 135

Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILD 154
              ++ AA  AL DAGIPM+ L   +    A+ G  +LD
Sbjct: 136 RLVSLMAASMALADAGIPMRDLIAGVAVGKAD-GVLVLD 173

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

Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (taxid: 273063)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|Q921I9|EXOS4_MOUSE Exosome complex component RRP41 OS=Mus musculus GN=Exosc4 PE=2 SV=3

 Score = 89.0 bits (219), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 51/169 (30%), Positives = 85/169 (50%), Gaps = 16/169 (9%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKA--GTKKNENPEKASI 62
           R DGR   +LR +     +  +A GSA   QG+TK LA VYGP    G++    P++A +
Sbjct: 13  RIDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRSRALPDRALV 72

Query: 63  EVIWKPRTGQIGKPEK---------EYEIILKRTLQSICILTINPNTTTSVIIQVVHDDG 113
              +   T   G+ ++         E  + L++T ++  +  ++P +   + +QV+  DG
Sbjct: 73  NCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADG 132

Query: 114 ALLPCAINAACAALVDAGIPMKHLAVAICCCSAE--SGYCILDPTKLEE 160
                 +NAA  A++DAGIPM+     +C CSA    G  + D + +EE
Sbjct: 133 GTYAACVNAATLAVMDAGIPMRDF---VCACSAGFVDGTALADLSHVEE 178

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. EXOSC4 binds to ARE-containing RNAs.

Mus musculus (taxid: 10090)

>sp|A2BKC0|ECX1_HYPBU Probable exosome complex exonuclease 1 OS=Hyperthermus butylicus (strain DSM 5456 / JCM 9403) GN=Hbut_0571 PE=3 SV=1

 Score = 88.6 bits (218), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 65/239 (27%), Positives = 109/239 (45%), Gaps = 27/239 (11%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNEN-PEKASIE 63
           R DGR P QLRP+     +L  A GSA    G T+V+AAVYGP+    ++   P++A I 
Sbjct: 25  RHDGRLPEQLRPIRMEVGVLSNADGSALVEYGGTRVIAAVYGPREAHPRHVALPDRAIIR 84

Query: 64  VIW--------KPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
             +        + +T    + E E   +++  L+++ I  + P T   V ++V+  DG  
Sbjct: 85  CRYHMAPFSTAERKTPAPTRREVELSKVIREALEAVVISELYPRTAIDVYMEVLQSDGGT 144

Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI 175
              AI AA  AL DAGI M+ L   +     + G  +LD  ++E+   +    +    S+
Sbjct: 145 RTAAITAASLALADAGIAMRDLVAGVAVGKVD-GVLVLDIDEIEDNYAEADMPVAMAPSL 203

Query: 176 LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSK 234
             VL     L+Q             +G ++ D++   LE  R     + +  + +L+ K
Sbjct: 204 DKVL-----LLQ------------LNGVLTHDEFVKALELARKGIQVIYNLQKEALRKK 245

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

Hyperthermus butylicus (strain DSM 5456 / JCM 9403) (taxid: 415426)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|O59223|ECX1_PYRHO Probable exosome complex exonuclease 1 OS=Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) GN=PH1549 PE=3 SV=1

 Score = 88.2 bits (217), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 57/165 (34%), Positives = 82/165 (49%), Gaps = 10/165 (6%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKA-GTKKNENPEKASIE 63
           R DGR   +LRP+     +L  A+GSA    G  K++AAVYGP+   +K  + P++A + 
Sbjct: 17  RIDGRKKYELRPIKMKVGVLKNANGSAYIEWGRNKIIAAVYGPRELHSKHLQRPDRAILR 76

Query: 64  VIWK------PRTGQIGKPEKEYEI--ILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
           V +           + G   +  EI  ++K  L+   IL + P T+  V I+V+  D   
Sbjct: 77  VRYNMAPFSVEERKKPGPDRRSIEISKVIKGALEPALILEMFPRTSIDVFIEVLQADAGT 136

Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEE 160
               I AA  AL DAGIPM+ L VA C      G  +LD  K E+
Sbjct: 137 RVAGITAASLALADAGIPMRDL-VAACAAGKIEGEIVLDLNKEED 180

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: -

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	243
224141741	243	predicted protein [Populus trichocarpa]	0.995	0.995	0.847	1e-119
449511723	243	PREDICTED: exosome complex exonuclease R	0.995	0.995	0.805	1e-113
449465139	243	PREDICTED: exosome complex exonuclease R	0.995	0.995	0.801	1e-113
297819162	242	hypothetical protein ARALYDRAFT_485002 [	0.991	0.995	0.797	1e-112
15231368	239	exosome complex component RRP46 [Arabido	0.954	0.970	0.814	1e-112
224089018	243	predicted protein [Populus trichocarpa]	0.942	0.942	0.829	1e-110
225429944	245	PREDICTED: exosome complex exonuclease R	0.995	0.987	0.822	1e-109
296081851	243	unnamed protein product [Vitis vinifera]	0.995	0.995	0.822	1e-109
356568370	243	PREDICTED: exosome complex exonuclease R	0.995	0.995	0.785	1e-109
356532014	243	PREDICTED: exosome complex exonuclease R	0.995	0.995	0.793	1e-108

>gi|224141741|ref|XP_002324223.1| predicted protein [Populus trichocarpa] gi|222865657|gb|EEF02788.1| predicted protein [Populus trichocarpa]

 Score =  433 bits (1113), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 205/242 (84%), Positives = 225/242 (92%)

Query: 1   MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60
           ME DR DGR+P+QLRPL+C+ ++LHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA
Sbjct: 1   MESDRDDGRSPSQLRPLSCARNVLHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60

Query: 61  SIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 120
            IEVIWKP+TGQIGK EKE+E+ILKRTLQSICILT+NPNTTTS+I+QVV+DDGALL CAI
Sbjct: 61  CIEVIWKPKTGQIGKLEKEFEMILKRTLQSICILTLNPNTTTSIIVQVVNDDGALLVCAI 120

Query: 121 NAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLP 180
           NAACAALVDAGIPMKHLAVAICCC AE GY ILDPTKLEEQKM+GF YLVFPNS++SVLP
Sbjct: 121 NAACAALVDAGIPMKHLAVAICCCLAEGGYVILDPTKLEEQKMRGFTYLVFPNSVVSVLP 180

Query: 181 EGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDLS 240
           EGSS V+GEPMEHGIITSVTHG MSV++Y  CLERGRAAS KLSDFLRRSLQS+LP D S
Sbjct: 181 EGSSHVEGEPMEHGIITSVTHGVMSVEEYLKCLERGRAASTKLSDFLRRSLQSQLPSDSS 240

Query: 241 KA 242
           KA
Sbjct: 241 KA 242

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449511723|ref|XP_004164036.1| PREDICTED: exosome complex exonuclease RRP46 homolog [Cucumis sativus]

 Score =  413 bits (1062), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 195/242 (80%), Positives = 220/242 (90%)

Query: 1   MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60
           ME+DR DGR PNQLRPLACSC++L+RAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA
Sbjct: 1   MEIDRDDGRTPNQLRPLACSCNVLNRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60

Query: 61  SIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 120
           SIEVIWKP+TGQIGK E+E E+ILKRTLQSICILT NPNTTTS+I+QV+HDDGALLPCAI
Sbjct: 61  SIEVIWKPKTGQIGKLERECEMILKRTLQSICILTTNPNTTTSIIVQVIHDDGALLPCAI 120

Query: 121 NAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLP 180
           NA+CAALVDAGIP+KHLAVAI CC +E+GY ILDPTK+EE+KMK   +LVFPN+ +SV+P
Sbjct: 121 NASCAALVDAGIPLKHLAVAISCCLSENGYVILDPTKIEEEKMKASVHLVFPNAPVSVVP 180

Query: 181 EGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDLS 240
           EGS+   GEP+EHGIITSVT GAMSVDDY HCLERGRAA+ K+S FLRRSLQ +LP D S
Sbjct: 181 EGSTQGVGEPLEHGIITSVTQGAMSVDDYIHCLERGRAATTKMSAFLRRSLQPQLPMDSS 240

Query: 241 KA 242
           KA
Sbjct: 241 KA 242

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449465139|ref|XP_004150286.1| PREDICTED: exosome complex exonuclease RRP46 homolog [Cucumis sativus]

 Score =  411 bits (1057), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 194/242 (80%), Positives = 220/242 (90%)

Query: 1   MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60
           ME+DR DGR PNQLRPLACSC++L+RAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA
Sbjct: 1   MEIDRDDGRTPNQLRPLACSCNVLNRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60

Query: 61  SIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 120
           SIEVIWKP+TGQIGK E+E E+ILKRTLQSICILT NPNTTTS+I+QV+HDDGALLPCAI
Sbjct: 61  SIEVIWKPKTGQIGKLERECEMILKRTLQSICILTTNPNTTTSIIVQVIHDDGALLPCAI 120

Query: 121 NAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLP 180
           NA+CAALVDAGIP+KHLAVAI CC +E+GY ILDPTK+EE+KMK   +LVFPN+ +SV+P
Sbjct: 121 NASCAALVDAGIPLKHLAVAISCCLSENGYVILDPTKIEEEKMKASVHLVFPNAPVSVVP 180

Query: 181 EGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDLS 240
           EGS+   GEP+EHGIITSVT GAMSVDDY HCLERGRAA+ K+S FLRRSLQ +LP + S
Sbjct: 181 EGSTQGVGEPLEHGIITSVTQGAMSVDDYIHCLERGRAATTKMSAFLRRSLQPQLPMNSS 240

Query: 241 KA 242
           KA
Sbjct: 241 KA 242

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297819162|ref|XP_002877464.1| hypothetical protein ARALYDRAFT_485002 [Arabidopsis lyrata subsp. lyrata] gi|297323302|gb|EFH53723.1| hypothetical protein ARALYDRAFT_485002 [Arabidopsis lyrata subsp. lyrata]

 Score =  409 bits (1051), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 193/242 (79%), Positives = 214/242 (88%), Gaps = 1/242 (0%)

Query: 1   MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60
           ME+DR DGR PNQLRPLACS +ILHR HGSASWSQGDTKVLAAVYGPKAGTKKNEN EKA
Sbjct: 1   MEIDREDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVLAAVYGPKAGTKKNENAEKA 60

Query: 61  SIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 120
             EVIWKP+TGQIGK EKEYE+I+KRT+QSIC+LT+NPNTTTSVIIQVVHDDG+LLPCAI
Sbjct: 61  CFEVIWKPKTGQIGKVEKEYEMIMKRTIQSICVLTVNPNTTTSVIIQVVHDDGSLLPCAI 120

Query: 121 NAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLP 180
           NAACAALVDAGIPMKHLAVAICCC A++GY +LDP KLEE+KM  FAYLVFPN+ LSVLP
Sbjct: 121 NAACAALVDAGIPMKHLAVAICCCLADNGYLVLDPNKLEEKKMTAFAYLVFPNTTLSVLP 180

Query: 181 EGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDLS 240
           EGSS+ +GEP+EHGIITSVTHG MSVDDYF C+E GRAA+A LS F R++ Q     D S
Sbjct: 181 EGSSVAEGEPVEHGIITSVTHGVMSVDDYFLCVENGRAATASLSAFFRKNFQQS-QKDSS 239

Query: 241 KA 242
           KA
Sbjct: 240 KA 241

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15231368|ref|NP_190207.1| exosome complex component RRP46 [Arabidopsis thaliana] gi|79314404|ref|NP_001030817.1| exosome complex component RRP46 [Arabidopsis thaliana] gi|79314427|ref|NP_001030818.1| exosome complex component RRP46 [Arabidopsis thaliana] gi|79314448|ref|NP_001030819.1| exosome complex component RRP46 [Arabidopsis thaliana] gi|145332769|ref|NP_001078250.1| exosome complex component RRP46 [Arabidopsis thaliana] gi|334185757|ref|NP_001190019.1| exosome complex component RRP46 [Arabidopsis thaliana] gi|7799009|emb|CAB90948.1| putative protein [Arabidopsis thaliana] gi|27808554|gb|AAO24557.1| At3g46210 [Arabidopsis thaliana] gi|110736314|dbj|BAF00127.1| hypothetical protein [Arabidopsis thaliana] gi|222423954|dbj|BAH19939.1| AT3G46210 [Arabidopsis thaliana] gi|222424492|dbj|BAH20201.1| AT3G46210 [Arabidopsis thaliana] gi|332644608|gb|AEE78129.1| exosome complex component RRP46 [Arabidopsis thaliana] gi|332644609|gb|AEE78130.1| exosome complex component RRP46 [Arabidopsis thaliana] gi|332644610|gb|AEE78131.1| exosome complex component RRP46 [Arabidopsis thaliana] gi|332644611|gb|AEE78132.1| exosome complex component RRP46 [Arabidopsis thaliana] gi|332644612|gb|AEE78133.1| exosome complex component RRP46 [Arabidopsis thaliana] gi|332644613|gb|AEE78134.1| exosome complex component RRP46 [Arabidopsis thaliana]

 Score =  409 bits (1050), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 189/232 (81%), Positives = 210/232 (90%)

Query: 1   MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60
           ME+DR DGR PNQLRPLACS +ILHR HGSASWSQGDTKVLAAVYGPKAGTKKNEN EKA
Sbjct: 1   MEIDREDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVLAAVYGPKAGTKKNENAEKA 60

Query: 61  SIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 120
             EVIWKP++GQIGK EKEYE+ILKRT+QSIC+LT+NPNTTTSVIIQVVHDDG+LLPCAI
Sbjct: 61  CFEVIWKPKSGQIGKVEKEYEMILKRTIQSICVLTVNPNTTTSVIIQVVHDDGSLLPCAI 120

Query: 121 NAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLP 180
           NAACAALVDAGIPMKHLAVAICCC AE+GY +LDP KLEE+KM  FAYLVFPN+ LSVLP
Sbjct: 121 NAACAALVDAGIPMKHLAVAICCCLAENGYLVLDPNKLEEKKMTAFAYLVFPNTTLSVLP 180

Query: 181 EGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQ 232
           EGSS+ +GEP+EHGIITS+THG MSVDDYF C+E GRAA+A LS F R++ Q
Sbjct: 181 EGSSVAEGEPVEHGIITSITHGVMSVDDYFLCVENGRAATASLSAFFRKNFQ 232

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224089018|ref|XP_002308603.1| predicted protein [Populus trichocarpa] gi|222854579|gb|EEE92126.1| predicted protein [Populus trichocarpa]

 Score =  402 bits (1034), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 190/229 (82%), Positives = 211/229 (92%)

Query: 1   MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60
           ME+DR DGR+P+QLRPL+CS ++LHRAHGSASWSQGDTKV AAVYGPKAGTKKNENPEKA
Sbjct: 1   MEIDRDDGRSPSQLRPLSCSHNVLHRAHGSASWSQGDTKVSAAVYGPKAGTKKNENPEKA 60

Query: 61  SIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 120
            +EVIWKP+TGQIGK E+EYE+ILKRTLQSICILT+NPNTTTS+I+Q V+DDGALL CAI
Sbjct: 61  CVEVIWKPKTGQIGKLEREYEMILKRTLQSICILTLNPNTTTSIIVQFVNDDGALLVCAI 120

Query: 121 NAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLP 180
           NAACAALVDA IPMKHLAVAICCC A+ GY ILDPTKLEEQKMKGFAYLVFPNS+LSVL 
Sbjct: 121 NAACAALVDARIPMKHLAVAICCCLADVGYVILDPTKLEEQKMKGFAYLVFPNSVLSVLL 180

Query: 181 EGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRR 229
           EGSSLV+GE  EHGIITSVTHG M V++Y  C+ERGRAASAKLSDFLR+
Sbjct: 181 EGSSLVEGESTEHGIITSVTHGVMPVEEYLKCVERGRAASAKLSDFLRK 229

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225429944|ref|XP_002281273.1| PREDICTED: exosome complex exonuclease RRP46 homolog [Vitis vinifera]

 Score =  401 bits (1031), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 199/242 (82%), Positives = 219/242 (90%)

Query: 1   MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60
           ME+ R DGR  NQLRPLACS +IL+RAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA
Sbjct: 3   MEIGRDDGRTANQLRPLACSRNILNRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 62

Query: 61  SIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 120
            IEV+WKP+TGQIGKPEKEYE+ILKRTL+SIC+L INPNTTTS+IIQVV DDGALLPCAI
Sbjct: 63  CIEVVWKPKTGQIGKPEKEYEVILKRTLKSICLLNINPNTTTSIIIQVVSDDGALLPCAI 122

Query: 121 NAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLP 180
           NAACAALVDA IP+KHLAVAICCC  ESGY ILDPTK+EEQKMK FAYLVFPNS +S++P
Sbjct: 123 NAACAALVDAAIPLKHLAVAICCCLTESGYVILDPTKVEEQKMKAFAYLVFPNSAISIIP 182

Query: 181 EGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDLS 240
           EGSS ++GE MEHGIITSVTHG MSVDDY HCLERG+AAS K+S FLRRSLQS+ P D S
Sbjct: 183 EGSSHMEGELMEHGIITSVTHGVMSVDDYLHCLERGQAASTKMSAFLRRSLQSQAPNDSS 242

Query: 241 KA 242
           +A
Sbjct: 243 RA 244

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296081851|emb|CBI20856.3| unnamed protein product [Vitis vinifera]

 Score =  400 bits (1029), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 199/242 (82%), Positives = 219/242 (90%)

Query: 1   MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60
           ME+ R DGR  NQLRPLACS +IL+RAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA
Sbjct: 1   MEIGRDDGRTANQLRPLACSRNILNRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60

Query: 61  SIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 120
            IEV+WKP+TGQIGKPEKEYE+ILKRTL+SIC+L INPNTTTS+IIQVV DDGALLPCAI
Sbjct: 61  CIEVVWKPKTGQIGKPEKEYEVILKRTLKSICLLNINPNTTTSIIIQVVSDDGALLPCAI 120

Query: 121 NAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLP 180
           NAACAALVDA IP+KHLAVAICCC  ESGY ILDPTK+EEQKMK FAYLVFPNS +S++P
Sbjct: 121 NAACAALVDAAIPLKHLAVAICCCLTESGYVILDPTKVEEQKMKAFAYLVFPNSAISIIP 180

Query: 181 EGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDLS 240
           EGSS ++GE MEHGIITSVTHG MSVDDY HCLERG+AAS K+S FLRRSLQS+ P D S
Sbjct: 181 EGSSHMEGELMEHGIITSVTHGVMSVDDYLHCLERGQAASTKMSAFLRRSLQSQAPNDSS 240

Query: 241 KA 242
           +A
Sbjct: 241 RA 242

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356568370|ref|XP_003552384.1| PREDICTED: exosome complex exonuclease RRP46 homolog [Glycine max]

 Score =  399 bits (1024), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 190/242 (78%), Positives = 213/242 (88%)

Query: 1   MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60
           ME DR DGR PNQLRPL CSCSILHR+HGSASW+QG+TKVLAAVYGPKAGTKK+ENPEKA
Sbjct: 1   METDRPDGRTPNQLRPLVCSCSILHRSHGSASWAQGETKVLAAVYGPKAGTKKSENPEKA 60

Query: 61  SIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 120
           SIEVIWKP+TGQIGK EKEYE+ILKRTL+SICI TI PNTTTSVI+QVVHDDGALLPCAI
Sbjct: 61  SIEVIWKPKTGQIGKVEKEYEMILKRTLESICIRTIYPNTTTSVIVQVVHDDGALLPCAI 120

Query: 121 NAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLP 180
           NAACAALVDAGIP+KHLAVAICC   +SG  ILDPTK EE+KMK F  LVFPN+I+SVLP
Sbjct: 121 NAACAALVDAGIPLKHLAVAICCSVTDSGCIILDPTKDEEEKMKAFINLVFPNTIVSVLP 180

Query: 181 EGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDLS 240
           EGS     EPM HGI+TS+T GAMSVDDY HCLERGRAASA+LS+F+R++++ K   + S
Sbjct: 181 EGSLQAGSEPMAHGIMTSITQGAMSVDDYLHCLERGRAASARLSEFVRKNIELKSTSEAS 240

Query: 241 KA 242
           KA
Sbjct: 241 KA 242

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356532014|ref|XP_003534569.1| PREDICTED: exosome complex exonuclease RRP46 homolog [Glycine max]

 Score =  398 bits (1022), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 192/242 (79%), Positives = 213/242 (88%)

Query: 1   MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60
           ME DR DGR PNQLRPLACSCSILHRAHGSASW+QG+TKVLAAVYGPKAGTKKNENPEKA
Sbjct: 1   METDRPDGRTPNQLRPLACSCSILHRAHGSASWAQGETKVLAAVYGPKAGTKKNENPEKA 60

Query: 61  SIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 120
           SIEVIWKP+TGQIGK EKEYE+ILKRTL+SICI TI PNTTTSVI+QVVHDDGALLPCAI
Sbjct: 61  SIEVIWKPKTGQIGKLEKEYEMILKRTLESICIRTIYPNTTTSVIVQVVHDDGALLPCAI 120

Query: 121 NAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLP 180
           NAAC ALVDAGIP+KHLAVAICC   +SG  ILDPTK EE+KMK +  LVFPN+I+SVLP
Sbjct: 121 NAACTALVDAGIPLKHLAVAICCSVTDSGCIILDPTKEEEEKMKAYINLVFPNTIVSVLP 180

Query: 181 EGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDLS 240
           E SS V  EPM HGI+TSVT GAMSVDDY HCL+RGRAASA+LS+F+R+++  K   + S
Sbjct: 181 ERSSQVGSEPMAHGIMTSVTQGAMSVDDYLHCLDRGRAASARLSEFVRKNIGPKSTCEAS 240

Query: 241 KA 242
           KA
Sbjct: 241 KA 242

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	243
TAIR|locus:2075351	239	AT3G46210 "AT3G46210" [Arabido	0.954	0.970	0.814	6e-103
UNIPROTKB|Q84T68	238	RRP46 "Exosome complex exonucl	0.979	1.0	0.673	6.4e-83
UNIPROTKB|Q9NQT4	235	EXOSC5 "Exosome complex compon	0.662	0.685	0.432	3.9e-35
UNIPROTKB|E1BAG2	235	EXOSC5 "Uncharacterized protei	0.641	0.663	0.436	2.7e-34
RGD|1307861	235	Exosc5 "exosome component 5" [	0.662	0.685	0.426	3.4e-34
MGI|MGI:107889	235	Exosc5 "exosome component 5" [	0.662	0.685	0.426	4.4e-34
ZFIN|ZDB-GENE-060503-675	243	exosc5 "exosome component 5" [	0.716	0.716	0.372	2.1e-32
TAIR|locus:2060111	150	AT2G07110 "AT2G07110" [Arabido	0.181	0.293	0.727	1.4e-22
TAIR|locus:2076710	241	RRP41 "AT3G61620" [Arabidopsis	0.600	0.605	0.369	2.2e-18
FB|FBgn0032487	246	Ski6 "Ski6" [Drosophila melano	0.641	0.634	0.314	2.5e-17

TAIR|locus:2075351 AT3G46210 "AT3G46210" [Arabidopsis thaliana (taxid:3702)]

 Score = 1020 (364.1 bits), Expect = 6.0e-103, P = 6.0e-103
 Identities = 189/232 (81%), Positives = 210/232 (90%)

Query:     1 MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60
             ME+DR DGR PNQLRPLACS +ILHR HGSASWSQGDTKVLAAVYGPKAGTKKNEN EKA
Sbjct:     1 MEIDREDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVLAAVYGPKAGTKKNENAEKA 60

Query:    61 SIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 120
               EVIWKP++GQIGK EKEYE+ILKRT+QSIC+LT+NPNTTTSVIIQVVHDDG+LLPCAI
Sbjct:    61 CFEVIWKPKSGQIGKVEKEYEMILKRTIQSICVLTVNPNTTTSVIIQVVHDDGSLLPCAI 120

Query:   121 NAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLP 180
             NAACAALVDAGIPMKHLAVAICCC AE+GY +LDP KLEE+KM  FAYLVFPN+ LSVLP
Sbjct:   121 NAACAALVDAGIPMKHLAVAICCCLAENGYLVLDPNKLEEKKMTAFAYLVFPNTTLSVLP 180

Query:   181 EGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQ 232
             EGSS+ +GEP+EHGIITS+THG MSVDDYF C+E GRAA+A LS F R++ Q
Sbjct:   181 EGSSVAEGEPVEHGIITSITHGVMSVDDYFLCVENGRAATASLSAFFRKNFQ 232

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

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0006396 "RNA processing" evidence=ISS

GO:0000398 "mRNA splicing, via spliceosome" evidence=RCA

GO:0001510 "RNA methylation" evidence=RCA

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

GO:0051604 "protein maturation" evidence=RCA

UNIPROTKB|Q84T68 RRP46 "Exosome complex exonuclease RRP46 homolog" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 831 (297.6 bits), Expect = 6.4e-83, P = 6.4e-83
 Identities = 161/239 (67%), Positives = 192/239 (80%)

Query:     1 MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60
             ME  RADGRNPNQLRP +C+ + L RAHGSA W+QGDT VLAAVYGPK GT+K ENPEKA
Sbjct:     1 MEESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKA 60

Query:    61 SIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 120
             SIEV+WKP TGQIGK EKEYE+ LKRTLQSIC+LT++PNTTTSVI+QVV +DG+LLPCAI
Sbjct:    61 SIEVVWKPMTGQIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLLPCAI 120

Query:   121 NAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLP 180
             NA CAALV AGIP+KHLAVAI C   E G  ILD  K EEQ++K FA+LVFPNS  S   
Sbjct:   121 NACCAALVFAGIPLKHLAVAIGCGVLEDGEVILDTNKAEEQQLKSFAHLVFPNSRKSASS 180

Query:   181 EGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDL 239
             +  +  + E  E G+ITS+THG MS +DYF C+ERG AAS+++SDF+R +LQ + PGD+
Sbjct:   181 KEPNQKE-EDSERGLITSITHGVMSEEDYFSCIERGLAASSRISDFMRTTLQKQAPGDV 238

GO:0003690 "double-stranded DNA binding" evidence=IDA

GO:0003727 "single-stranded RNA binding" evidence=IDA

GO:0004536 "deoxyribonuclease activity" evidence=IDA

GO:0004540 "ribonuclease activity" evidence=IDA

GO:0042802 "identical protein binding" evidence=IPI

UNIPROTKB|Q9NQT4 EXOSC5 "Exosome complex component RRP46" [Homo sapiens (taxid:9606)]

 Score = 337 (123.7 bits), Expect = 3.9e-35, Sum P(2) = 3.9e-35
 Identities = 71/164 (43%), Positives = 101/164 (61%)

Query:     9 RNPN-QLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWK 67
             R P   LR  AC  ++L R  GSAS+ QGDT VLA VYGP       E   KA++EVI +
Sbjct:    22 RGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILR 81

Query:    68 PRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAAL 127
             P+ G  G  EK  E +++ T +++ + T++P T+ +V++QVV D G+LL C +NAAC AL
Sbjct:    82 PKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMAL 141

Query:   128 VDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVF 171
             VDAG+PM+ L   + C     G  +LDPT  +E++ +  A L F
Sbjct:   142 VDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEAR--AVLTF 183

GO:0003723 "RNA binding" evidence=IEA

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

GO:0006364 "rRNA processing" evidence=NAS

GO:0005737 "cytoplasm" evidence=NAS

GO:0005730 "nucleolus" evidence=NAS

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

GO:0005515 "protein binding" evidence=IPI

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

GO:0045006 "DNA deamination" evidence=IDA

GO:0035327 "transcriptionally active chromatin" evidence=IMP

GO:0004532 "exoribonuclease activity" evidence=IDA

GO:0051607 "defense response to virus" evidence=IMP

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

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

UNIPROTKB|E1BAG2 EXOSC5 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 330 (121.2 bits), Expect = 2.7e-34, Sum P(2) = 2.7e-34
 Identities = 69/158 (43%), Positives = 99/158 (62%)

Query:    14 LRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQI 73
             LR  AC  ++L R  GSAS+ QGDT VLA VYGP       E   KA++EVI +P+TG  
Sbjct:    28 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKISKEIFNKATLEVILRPKTGLP 87

Query:    74 GKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIP 133
             G  EK  E +++ T +++ +  ++P T+ +V++QVV D G+LL C +NAAC ALVDAG+P
Sbjct:    88 GVAEKSRERLIRNTCEAVVLGALHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVP 147

Query:   134 MKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVF 171
             M+ L   + C     G  +LDPT  +E++ +  A L F
Sbjct:   148 MRALFCGVTCALDSDGTLMLDPTAKQEKEAR--AVLTF 183

GO:0051607 "defense response to virus" evidence=IEA

GO:0045006 "DNA deamination" evidence=IEA

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

GO:0035327 "transcriptionally active chromatin" evidence=IEA

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

RGD|1307861 Exosc5 "exosome component 5" [Rattus norvegicus (taxid:10116)]

 Score = 328 (120.5 bits), Expect = 3.4e-34, Sum P(2) = 3.4e-34
 Identities = 70/164 (42%), Positives = 101/164 (61%)

Query:     9 RNPN-QLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWK 67
             R+P   LR  AC  ++L R  GSAS+ QGDT VLA VYGP       E   KA++EVI +
Sbjct:    22 RSPVCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILR 81

Query:    68 PRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAAL 127
             P+ G  G  EK  E +++ T +++ +  ++P T+ +V++QVV D G+LL C +NAAC AL
Sbjct:    82 PKIGLPGVAEKSRERLIRNTCEAVVLGALHPRTSITVVLQVVSDTGSLLACCLNAACMAL 141

Query:   128 VDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVF 171
             VDAG+PM+ L   + C     G  +LDPT  +E++ +  A L F
Sbjct:   142 VDAGVPMRALFCGVTCALDPDGNLVLDPTTKQEKEAR--AILTF 183

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

GO:0006401 "RNA catabolic process" evidence=ISO

GO:0035327 "transcriptionally active chromatin" evidence=IEA;ISO

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

GO:0045006 "DNA deamination" evidence=IEA;ISO

GO:0051607 "defense response to virus" evidence=IEA;ISO

GO:0004532 "exoribonuclease activity" evidence=ISO

MGI|MGI:107889 Exosc5 "exosome component 5" [Mus musculus (taxid:10090)]

 Score = 327 (120.2 bits), Expect = 4.4e-34, Sum P(2) = 4.4e-34
 Identities = 70/164 (42%), Positives = 101/164 (61%)

Query:     9 RNPN-QLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWK 67
             R+P   LR  AC  ++L R  GSAS+ QGDT VLA VYGP       E   KA++EVI +
Sbjct:    22 RSPVCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILR 81

Query:    68 PRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAAL 127
             P+ G  G  EK  E +++ T +++ +  ++P T+ +V++QVV D G+LL C +NAAC AL
Sbjct:    82 PKIGLPGVAEKSRERLVRNTCEAVVLGALHPRTSITVVLQVVSDAGSLLACCLNAACMAL 141

Query:   128 VDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVF 171
             VDAG+PM+ L   + C     G  +LDPT  +E++ +  A L F
Sbjct:   142 VDAGVPMRALFCGVTCALDSDGNLVLDPTTKQEKEAR--AILTF 183

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

GO:0003674 "molecular_function" evidence=ND

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0006401 "RNA catabolic process" evidence=IMP

GO:0035327 "transcriptionally active chromatin" evidence=ISO

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

GO:0045006 "DNA deamination" evidence=ISO

GO:0051607 "defense response to virus" evidence=ISO

ZFIN|ZDB-GENE-060503-675 exosc5 "exosome component 5" [Danio rerio (taxid:7955)]

 Score = 313 (115.2 bits), Expect = 2.1e-32, Sum P(2) = 2.1e-32
 Identities = 66/177 (37%), Positives = 106/177 (59%)

Query:    14 LRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQI 73
             LR      S+L R  GS+++ QGDT +LA VYGP       E  ++A++EV+ +P+ G  
Sbjct:    35 LREYGSEQSLLSRPDGSSTFVQGDTSILAGVYGPAEVKVSKEIYDRATVEVLIQPKMGLP 94

Query:    74 GKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIP 133
                E+  E  ++ T ++  +LT++P ++ +VI+QVVHDDG+LL C +NAAC AL+DAG+P
Sbjct:    95 SVRERAREQCVRETCEAALLLTLHPRSSLTVILQVVHDDGSLLSCCLNAACMALMDAGLP 154

Query:   134 MKHLAVAICCCSAESGYCILDPTKLEEQKMKGF-AYLVFPN--SILSVLPEGSSLVQ 187
             M  L  ++ C  ++ G  I DPT  +E++ +    + +  N  ++L     GS  VQ
Sbjct:   155 MSRLFCSVTCAISKEGQIITDPTARQEKESRALLTFAIDSNERNVLMSSTTGSFSVQ 211

GO:0005575 "cellular_component" evidence=ND

TAIR|locus:2060111 AT2G07110 "AT2G07110" [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 1.4e-22, Sum P(2) = 1.4e-22
 Identities = 32/44 (72%), Positives = 38/44 (86%)

Query:    72 QIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
             ++ K EKEYE ILKRTLQSIC+L + PNTTTSVIIQVVHD G++
Sbjct:    76 RLRKVEKEYETILKRTLQSICVLRVVPNTTTSVIIQVVHDGGSV 119

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2076710 RRP41 "AT3G61620" [Arabidopsis thaliana (taxid:3702)]

 Score = 222 (83.2 bits), Expect = 2.2e-18, P = 2.2e-18
 Identities = 61/165 (36%), Positives = 93/165 (56%)

Query:     5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGP-----KAGTKKNENP-- 57
             R DGR  N++R +     ++ +A GSA +  G+TKV+AAVYGP     K+  KKN++   
Sbjct:    10 RLDGRRFNEMRQIVAEVGVVSKADGSAVFEMGNTKVIAAVYGPREIQNKSQQKKNDHAVV 69

Query:    58 --EKASIEVIWKPRTGQ-IGKPEKEYEIILKRTLQSICILT-INPNTTTSVIIQVVHDDG 113
               E +  +     R  Q   +   E  +++++T+++ CILT + P++   + +QV+  DG
Sbjct:    70 LCEYSMAQFSTGDRRRQKFDRRSTELSLVIRQTMEA-CILTELMPHSQIDIFLQVLQADG 128

Query:   114 ALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKL 158
                   INAA  AL DAGIPM+ LAV+   CSA  GY  L+ T L
Sbjct:   129 GTRSACINAATLALADAGIPMRDLAVS---CSA--GY--LNSTPL 166

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

FB|FBgn0032487 Ski6 "Ski6" [Drosophila melanogaster (taxid:7227)]

 Score = 212 (79.7 bits), Expect = 2.5e-17, P = 2.5e-17
 Identities = 51/162 (31%), Positives = 85/162 (52%)

Query:     5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGP-KAGTKKNENP-----E 58
             R DGR P++LR + C   +  +  GSA   QG+TKVLAAVYGP +A   + E+       
Sbjct:    14 RLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAVYGPHQAKGNQTESVINCQYS 73

Query:    59 KASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPC 118
             +A+     +    +  +   E+++ L++ L +     + P +   + ++V+ DDGA    
Sbjct:    74 QATFSTAERKNRPRGDRKSLEFKLYLQQALSAAIKSELYPRSQIDIYVEVLQDDGANYAV 133

Query:   119 AINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEE 160
             A+NAA  AL+DAGI +    VA     ++S   + D ++ EE
Sbjct:   134 ALNAATLALIDAGICLNEFIVACTASLSKSNIPLTDISQFEE 175

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

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

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

GO:0035327 "transcriptionally active chromatin" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005652 "nuclear lamina" evidence=IDA

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

---

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)
Q84T68	EXOS5_ORYSJ	3, ., 1, ., 1, 3, ., -	0.6736	0.9794	1.0	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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	243
cd11372	199	cd11372, RNase_PH_RRP46, RRP46 subunit of eukaryot	7e-82
cd11358	218	cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucl	1e-39
cd11370	226	cd11370, RNase_PH_RRP41, RRP41 subunit of eukaryot	3e-38
COG0689	230	COG0689, Rph, RNase PH [Translation, ribosomal str	1e-34
pfam01138	129	pfam01138, RNase_PH, 3' exoribonuclease family, do	3e-30
cd11371	210	cd11371, RNase_PH_MTR3, MTR3 subunit of eukaryotic	1e-27
PRK03983	244	PRK03983, PRK03983, exosome complex exonuclease Rr	2e-27
TIGR02065	230	TIGR02065, ECX1, archaeal exosome-like complex exo	1e-25
cd11366	214	cd11366, RNase_PH_archRRP41, RRP41 subunit of arch	3e-21
PLN00207	891	PLN00207, PLN00207, polyribonucleotide nucleotidyl	8e-12
COG2123	272	COG2123, COG2123, RNase PH-related exoribonuclease	5e-07
cd11367	272	cd11367, RNase_PH_RRP42, RRP42 subunit of eukaryot	1e-06
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	2e-06
cd11368	259	cd11368, RNase_PH_RRP45, RRP45 subunit of eukaryot	3e-06
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	4e-06
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	6e-05
PRK04282	271	PRK04282, PRK04282, exosome complex RNA-binding pr	6e-05
cd11369	261	cd11369, RNase_PH_RRP43, RRP43 subunit of eukaryot	1e-04
TIGR02696	719	TIGR02696, pppGpp_PNP, guanosine pentaphosphate sy	4e-04
cd08887	185	cd08887, RHO_alpha_C_3, C-terminal catalytic domai	5e-04
cd11365	256	cd11365, RNase_PH_archRRP42, RRP42 subunit of arch	5e-04
PRK00173	238	PRK00173, rph, ribonuclease PH; Reviewed	9e-04
cd11364	223	cd11364, RNase_PH_PNPase_2, Polyribonucleotide nuc	0.001
TIGR01966	236	TIGR01966, RNasePH, ribonuclease PH	0.003

>gnl|CDD|206777 cd11372, RNase_PH_RRP46, RRP46 subunit of eukaryotic exosome

 Score =  243 bits (622), Expect = 7e-82
 Identities = 95/215 (44%), Positives = 132/215 (61%), Gaps = 16/215 (7%)

Query: 14  LRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQI 73
           LRPL+C   +L RA GSA +SQGDT VLAAVYGP     + E P++A++EVI +P++G  
Sbjct: 1   LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLP 60

Query: 74  GKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIP 133
           G  EK  E++L+ TL+ I +L ++P T  SV++QV+ DDG+LL CAINAAC AL+DAG+P
Sbjct: 61  GVKEKLLELLLRSTLEPIILLHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVP 120

Query: 134 MKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEH 193
           MK L  A+ C   E G  ILDPT  EE++ K  A   F +                    
Sbjct: 121 MKGLFAAVTCAITEDGEIILDPTAEEEKEAKAVATFAFDSGEEK---------------- 164

Query: 194 GIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLR 228
            ++ S + G+ + ++ F CLE  +AASA + DF R
Sbjct: 165 NLVLSESEGSFTEEELFACLELAQAASAAIFDFYR 199

The RRP46 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 = 199

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

 Score =  135 bits (343), Expect = 1e-39
 Identities = 70/236 (29%), Positives = 95/236 (40%), Gaps = 44/236 (18%)

Query: 14  LRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQ- 72
            RP+     +L++A GSA    G+TKV+ AV GP     K E P+K ++ V  +   G  
Sbjct: 1   FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLERPDKGTLYVNVEISPGAV 60

Query: 73  -------IGKPEKEYEIILKRTLQSICILTIN---PNTTTSVIIQVVHDDGALLPCAINA 122
                   G  E E   +L+RT+++  IL  +   P+    V IQV+  DG LL    NA
Sbjct: 61  GERRQGPPGDEEMEISRLLERTIEASVILDKSTRKPSWVLYVDIQVLSRDGGLLDACWNA 120

Query: 123 ACAALVDAGIP-------------MKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYL 169
           A AAL DAGIP             MK L VA+       G  +LDPT  EE+       +
Sbjct: 121 AIAALKDAGIPRVFVDERSPPLLLMKDLIVAVSVGGISDGVLLLDPTGEEEELADSTLTV 180

Query: 170 VFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDD--YFHCLERGRAASAKL 223
               S                    +      G  S+D      CLE  +  S  L
Sbjct: 181 AVDKS------------------GKLCLLSKVGGGSLDTEEIKECLELAKKRSLHL 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|206775 cd11370, RNase_PH_RRP41, RRP41 subunit of eukaryotic exosome

 Score =  132 bits (335), Expect = 3e-38
 Identities = 68/210 (32%), Positives = 104/210 (49%), Gaps = 35/210 (16%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNE-NPEKASIE 63
           R DGR PN+LR + C   +   A GSA   QG+TKVLAAVYGP     +++   ++A + 
Sbjct: 3   RLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNRSQALHDRAVVN 62

Query: 64  VIW----------KPRTGQIGKPEK---EYEIILKRTLQSICILTINPNTTTSVIIQVVH 110
             +          K R    GK ++   E  + +++T +++ +  + P +   + +QV+ 
Sbjct: 63  CEYSMATFSTGERKRR----GKGDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQ 118

Query: 111 DDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAE--SGYCILDPTKLEEQKMKGFAY 168
            DG LL   INAA  AL+DAGIPMK     +C CSA       +LD   LEE        
Sbjct: 119 ADGGLLAACINAATLALIDAGIPMKDY---VCACSAGYLDSTPLLDLNYLEES------- 168

Query: 169 LVFPNSILSVLP--EGSSLVQGE---PMEH 193
              P+  ++VLP  +   L+Q E    ++ 
Sbjct: 169 GDLPDLTVAVLPKSDKVVLLQMESRLHLDR 198

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

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

 Score =  123 bits (311), Expect = 1e-34
 Identities = 58/239 (24%), Positives = 97/239 (40%), Gaps = 28/239 (11%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
           R DGR P++LRP+  +  +L  A GS+    G+TKV+  V GP+    +           
Sbjct: 9   RPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLT 68

Query: 65  IW---KPR-TGQIGKPE------KEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGA 114
                 PR T +  K E      KE   ++ R L+++  L + P +T  +   V+  DG 
Sbjct: 69  AEYGMLPRSTDERKKREADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADGG 128

Query: 115 LLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNS 174
               +I  A  AL DAGIP++ L  AI     +    +LD    E+   +        + 
Sbjct: 129 TRTASITGASLALADAGIPLRDLVAAISVGIVDGVI-VLDLDYEEDSAAE-------ADM 180

Query: 175 ILSVLPEGSSL-VQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQ 232
            + +   G  + +QG   +         G  + D+    L+       +L +  R +L 
Sbjct: 181 NVVMTGNGGLVEIQGLAED---------GPFTEDELLELLDLAIKGCNELRELQREALA 230

Length = 230

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

 Score =  108 bits (273), Expect = 3e-30
 Identities = 45/129 (34%), Positives = 63/129 (48%), Gaps = 8/129 (6%)

Query: 13  QLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKP---- 68
           +LRP+     +L +A GSA    GDTKVLA V GP    +K  +     + V ++     
Sbjct: 1   ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPPQKERDFFPGELTVEYEESPFA 60

Query: 69  ----RTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAAC 124
                 G+  + E E   ++ R L+    L   P     + + V+ DDG+LL  AINAA 
Sbjct: 61  SGERPEGRPSEREIELSRLIDRALRPSIPLEGYPRWEIRIDVTVLSDDGSLLDAAINAAS 120

Query: 125 AALVDAGIP 133
            AL DAGIP
Sbjct: 121 LALADAGIP 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|206776 cd11371, RNase_PH_MTR3, MTR3 subunit of eukaryotic exosome

 Score =  104 bits (261), Expect = 1e-27
 Identities = 62/229 (27%), Positives = 101/229 (44%), Gaps = 28/229 (12%)

Query: 14  LRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASI--EVIWKP--- 68
           +RP+     ++ +A GSA    G+TKV+ +VYGP+    + E  ++  +  EV + P   
Sbjct: 1   IRPIFLKTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFSDRGRLNCEVKFAPFAT 60

Query: 69  ---RTGQIGKPEKEYEIILKRTLQ-SICILTINPNTTTSVIIQVVHDDGALLPCAINAAC 124
              R       E+E   +L + L+ ++  L   P +   V + V+  DG++L  AI AA 
Sbjct: 61  PGRRRHGQDSEERELSSLLHQALEPAVR-LEKYPKSQIDVFVTVLESDGSVLAAAITAAS 119

Query: 125 AALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSS 184
            AL DAGI M  L  A C  +      +LDPT+ EE+   G   L    + +  L + + 
Sbjct: 120 LALADAGIEMYDLVTA-CSAALIGDELLLDPTREEEEASSGGVML----AYMPSLNQVTQ 174

Query: 185 LVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQS 233
           L Q              G M VD     L+       ++   +R++L  
Sbjct: 175 LWQ-------------SGEMDVDQLEEALDLCIDGCNRIHPVVRQALLE 210

The MTR3 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 = 210

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

 Score =  104 bits (262), Expect = 2e-27
 Identities = 54/171 (31%), Positives = 81/171 (47%), Gaps = 20/171 (11%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPK-AGTKKNENPEKASIE 63
           R DGR P++LRP+     +L  A GSA    G+ K++AAVYGP+    +  + P++A + 
Sbjct: 15  RLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLR 74

Query: 64  VIW-----------KPRTGQIGKPEKEYEI--ILKRTLQSICILTINPNTTTSVIIQVVH 110
           V +           +P     G   +  EI  +++  L+   +L + P T   V I+V+ 
Sbjct: 75  VRYNMAPFSVDERKRP-----GPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQ 129

Query: 111 DDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQ 161
            D       I AA  AL DAGIPM+ L    C      G  +LD  K E+ 
Sbjct: 130 ADAGTRVAGITAASLALADAGIPMRDLVAG-CAVGKVDGVIVLDLNKEEDN 179

Length = 244

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

 Score = 99.8 bits (249), Expect = 1e-25
 Identities = 57/171 (33%), Positives = 84/171 (49%), Gaps = 20/171 (11%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPK-AGTKKNENPEKASIE 63
           R DGR P++LRP+     +L  A GSA    G TK+LAAVYGP+ A  +  + P++A + 
Sbjct: 9   RLDGRKPDELRPIKIEAGVLKNADGSAYLEFGGTKILAAVYGPREAHPRHLQLPDRAVLR 68

Query: 64  VIW-----------KPRTGQIGKPEKEYEI--ILKRTLQSICILTINPNTTTSVIIQVVH 110
           V +           +P     G   +E EI  +++  L+   +L   P T   V I+V+ 
Sbjct: 69  VRYHMAPFSTDERKRP-----GPSRREIEISKVIREALEPAILLEQFPRTVIDVFIEVLQ 123

Query: 111 DDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQ 161
            DG      + AA  AL DAGIPM+ L V         G  +LD ++ E+ 
Sbjct: 124 ADGGTRCAGLTAASLALADAGIPMRDLVVG-VAVGKVDGVVVLDLSEEEDM 173

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|206771 cd11366, RNase_PH_archRRP41, RRP41 subunit of archaeal exosome

 Score = 88.2 bits (219), Expect = 3e-21
 Identities = 53/158 (33%), Positives = 77/158 (48%), Gaps = 10/158 (6%)

Query: 13  QLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPK-AGTKKNENPEKASIEVIWK---- 67
           +LRP+     +L  A GSA    G+ K++AAVYGP+    +  + P++A I V +     
Sbjct: 1   ELRPIKIEVGVLKNADGSAYVEWGNNKIIAAVYGPREVHPRHLQLPDRAVIRVRYNMAPF 60

Query: 68  --PRTGQIGKPEKEYEI--ILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAA 123
                 + G   +E EI  ++K  L+   IL   P T   V ++V+  D       +NAA
Sbjct: 61  SVDERKRPGPDRREIEISKVIKEALEPAIILEEFPRTAIDVFVEVLQADAGTRVAGLNAA 120

Query: 124 CAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQ 161
             AL DAGIPM+ L VA C      G  +LD  K E+ 
Sbjct: 121 SLALADAGIPMRDL-VAACAAGKVDGKIVLDLNKEEDN 157

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|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase; Provisional

 Score = 64.1 bits (156), Expect = 8e-12
 Identities = 46/146 (31%), Positives = 76/146 (52%), Gaps = 16/146 (10%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV-YGPKAGTKKNENPEKAS-- 61
           R+DGR P+++RP+  SC +L RAHGSA +++G+T+ LA V  G K   ++ +N   A   
Sbjct: 439 RSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEV 498

Query: 62  ----IEVIWKP----RTGQIGKPEKEYEI----ILKRTLQSICILTINPNTTTSVIIQVV 109
               ++  + P      G+IG P +  EI    + +R L+ I     +   T  V   + 
Sbjct: 499 KRFYLQYSFPPSCVGEVGRIGAPSRR-EIGHGMLAERALEPILPSEDDFPYTIRVESTIT 557

Query: 110 HDDGALLPCAINAACAALVDAGIPMK 135
             +G+    ++   C AL DAG+P+K
Sbjct: 558 ESNGSSSMASVCGGCLALQDAGVPVK 583

Length = 891

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

 Score = 48.9 bits (117), Expect = 5e-07
 Identities = 54/267 (20%), Positives = 98/267 (36%), Gaps = 60/267 (22%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKK------NENPE 58
           R DGR+ ++ RPL     ++ +A+GSA    G+T+V+  V   KA   +      NE   
Sbjct: 24  RIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGV---KAEIGEPFPDTPNEGVL 80

Query: 59  KASIE----VIWKPRTGQIGKPEKEYEIILKRTLQS-----ICILTINPNTTTSVI---I 106
             ++E           G   +   E   ++ R L+      +  L I       V+   +
Sbjct: 81  VVNVELSPLASPSFEPGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDV 140

Query: 107 QVVHDDGALLPCAINAACAALVDAGIP----------------------MKHLAVAICCC 144
            V+  DG L+  A  AA AAL++  +P                      + +  +++   
Sbjct: 141 HVLDYDGNLIDAASLAAVAALLNTRVPKAVEVGDGEIVIEVEEEPVPLPVSNPPISVTFA 200

Query: 145 SAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAM 204
                  ++DP+  EE    G         +   + E   +V  + +  G IT       
Sbjct: 201 KI-GNVLVVDPSLEEELVADG--------RLTITVNEDGEIVAIQKVGGGSIT------- 244

Query: 205 SVDDYFHCLERGRAASAKLSDFLRRSL 231
              D    L+   + + KL + L+ +L
Sbjct: 245 -ESDLEKALKTALSKAEKLREALKEAL 270

Length = 272

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

 Score = 48.0 bits (115), Expect = 1e-06
 Identities = 56/266 (21%), Positives = 83/266 (31%), Gaps = 69/266 (25%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKA--GTKKNENPEKASI 62
           R DGR+    RP+     +L   +GSA    G+T VL  V   KA  G+   E P K  +
Sbjct: 19  RNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGV---KAEVGSPDPETPNKGRL 75

Query: 63  EV---IWKPRTGQI-GKPEKEYEIILKRTLQSICI---------LTINPNTTTSVI---I 106
           E         + +  G+  +E    L   L+             L I P     V+   +
Sbjct: 76  EFFVDCSPNASPEFEGRGGEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDV 135

Query: 107 QVVHDDGALLPCAINAACAALVDAGIP-----------------------MKHLAVAICC 143
            V+   G LL     A  AAL +  IP                        +     +  
Sbjct: 136 LVLESGGNLLDAISIAVKAALFNTRIPKVEVSEDDEGTKEIELSDDPYDVKRLDVSNVPL 195

Query: 144 C---SAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVT 200
               S      I+D T  EE            ++ L V       V  +    G I  V 
Sbjct: 196 IVTLSKIGNRHIVDATAEEEACS---------SARLLV------AVNAK----GRICGVQ 236

Query: 201 H---GAMSVDDYFHCLERGRAASAKL 223
               G++  +     +E  +    KL
Sbjct: 237 KSGGGSLEPESIIEMIETAKEVGKKL 262

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|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 48.3 bits (116), Expect = 2e-06
 Identities = 15/40 (37%), Positives = 26/40 (65%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV 44
           R DGR+ + +RP++    +L R HGSA +++G+T+ L   
Sbjct: 311 RIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVT 350

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) [Transcription, Degradation of RNA]. Length = 684

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

 Score = 46.8 bits (112), Expect = 3e-06
 Identities = 48/209 (22%), Positives = 76/209 (36%), Gaps = 60/209 (28%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
           R DGR  ++ RP+  +       +G    S G T+VLA V   +    K + P +  + +
Sbjct: 18  RLDGRGLDEFRPIKIT---FGLEYGCVEVSLGKTRVLAQVSC-EIVEPKPDRPNEGILFI 73

Query: 65  IWKPRTGQIGKPE------KEYEIILKRTLQ------------SICILT------INPNT 100
                   +  P        E E+ L R L+            S+CI+       I    
Sbjct: 74  --NVELSPMASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSI---- 127

Query: 101 TTSVIIQVVHDDGALLPCAINAACAAL---------VDAG------------IP--MKHL 137
              V + V++ DG L+  A  AA AAL         VD              +P  + H+
Sbjct: 128 --RVDVHVLNHDGNLIDAASLAAIAALMHFRRPDVTVDGEEVTVHSPEEREPVPLSIHHI 185

Query: 138 AVAICCCS-AESGYCILDPTKLEEQKMKG 165
            + +      +    ++DPT LEE    G
Sbjct: 186 PICVTFAFFDDGEIVVVDPTLLEEAVADG 214

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|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 47.0 bits (113), Expect = 4e-06
 Identities = 15/40 (37%), Positives = 26/40 (65%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV 44
           R DGR  +++RP++    +L R HGSA +++G+T+ L   
Sbjct: 315 RIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVA 354

Length = 693

>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

 Score = 43.3 bits (103), Expect = 6e-05
 Identities = 17/44 (38%), Positives = 27/44 (61%), Gaps = 1/44 (2%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV-YGP 47
           R DGR  +++RP+     +L R HGSA +++G+T+ L  V  G 
Sbjct: 313 RIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGT 356

Length = 692

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

 Score = 42.6 bits (101), Expect = 6e-05
 Identities = 53/204 (25%), Positives = 80/204 (39%), Gaps = 50/204 (24%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
           R DGR  ++ RP+     ++ +A GSA    G+T+VLA V   + G    + P +  + V
Sbjct: 25  RIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGV-KLEIGEPFPDTPNEGVLIV 83

Query: 65  ------IWKPRTGQIGKPEKEYEIILKRT------------LQSICILTINPNTTTSVI- 105
                 +  P T + G P  E  I L R             L+ + I    P     V+ 
Sbjct: 84  NAELLPLASP-TFEPGPP-DENAIELARVVDRGIRESKAIDLEKLVIE---PGKKVWVVF 138

Query: 106 --IQVVHDDGALLPCAINAACAALVDAGIP--------------------MKHLAVAICC 143
             + V+  DG LL  ++ AA AAL++  +P                    +    V    
Sbjct: 139 IDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEGEDGVVDKLGEDFPLPVNDKPVT--V 196

Query: 144 CSAESG-YCILDPTKLEEQKMKGF 166
             A+ G Y I+DPT  EE  M   
Sbjct: 197 TFAKIGNYLIVDPTLEEESVMDAR 220

Length = 271

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

 Score = 41.8 bits (99), Expect = 1e-04
 Identities = 45/198 (22%), Positives = 76/198 (38%), Gaps = 45/198 (22%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKA--GTKKNENPEKASI 62
           R DGR  ++ RP + +   +  A GSA    G+T VL  +   KA   T   + P++  +
Sbjct: 18  RPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGI---KAEVATPAADTPDEGYL 74

Query: 63  EV------IWKPRTGQIGKPEKEYEIILKRT----LQSICI----LTINPNTTTSVI--- 105
                   +   +  + G P +E +++        L S  +    L I P     V+   
Sbjct: 75  VPNVDLPPLCSSKF-RPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCD 133

Query: 106 IQVVHDDGALLPCAINAACAALVDAGIP----------------------MKHLAVAICC 143
           +  +  DG LL  A+ A  AAL +  +P                      +K+L V+   
Sbjct: 134 VYCLDYDGNLLDAALLALVAALKNLRLPAVTIDEETELVVVNPEERRPLNLKNLPVSTTF 193

Query: 144 CSAESGYCILDPTKLEEQ 161
              +  + + DPT  EE 
Sbjct: 194 AVFDDKHLLADPTAEEEL 211

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|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

 Score = 40.6 bits (95), Expect = 4e-04
 Identities = 15/37 (40%), Positives = 23/37 (62%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVL 41
           R DGR    +RPL     ++ R HGSA + +G+T++L
Sbjct: 336 RIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQIL 372

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. Length = 719

>gnl|CDD|176896 cd08887, RHO_alpha_C_3, C-terminal catalytic domain of the oxygenase alpha subunit of an uncharacterized subgroup of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases

 Score = 39.6 bits (93), Expect = 5e-04
 Identities = 20/78 (25%), Positives = 29/78 (37%), Gaps = 7/78 (8%)

Query: 153 LDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHG--IITSVTHGAMSVDDYF 210
           L   + + ++     Y +FPN  L V P+   ++Q EP       +T         D   
Sbjct: 66  LPEDEWDLRRHLTVIYTLFPNVSLLVQPDHLEIIQIEPGSPDRTRVTVYLLIPPPPDT-- 123

Query: 211 HCLERGRAASAKLSDFLR 228
              E  RA   K  DFL 
Sbjct: 124 ---EEARAYWDKNWDFLM 138

C-terminal catalytic domain of the oxygenase alpha subunit of a functionally uncharacterized subgroup of the Rieske-type non-heme iron aromatic ring-hydroxylating oxygenase (RHO) family. RHOs, also known as aromatic ring hydroxylating dioxygenases, utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC) and an oxygenase. The ETC transfers reducing equivalents from the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and a C-terminal domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. This group contains a putative Parvibaculum lavamentivorans (T) DS-1 oxygenase; this organism catabolizes commercial linear alkylbenzenesulfonate surfactant (LAS) and other surfactants, by a pathway involving an undefined 'omega-oxygenation' and beta-oxidation of the LAS side chain. The nature of the LAS-oxygenase is unknown but is likely a multicomponent system. This subfamily belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Length = 185

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

 Score = 39.9 bits (94), Expect = 5e-04
 Identities = 15/40 (37%), Positives = 23/40 (57%)

Query: 5  RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV 44
          R DGR  ++ R +     ++ +A GSA    G+T+VLA V
Sbjct: 17 RIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGV 56

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|178914 PRK00173, rph, ribonuclease PH; Reviewed

 Score = 38.9 bits (92), Expect = 9e-04
 Identities = 17/37 (45%), Positives = 21/37 (56%)

Query: 5  RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVL 41
          R DGR  +QLRP+  + +    A GS     GDTKVL
Sbjct: 2  RPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVL 38

Length = 238

>gnl|CDD|206769 cd11364, RNase_PH_PNPase_2, Polyribonucleotide nucleotidyltransferase, repeat 2

 Score = 38.7 bits (91), Expect = 0.001
 Identities = 14/32 (43%), Positives = 24/32 (75%)

Query: 13 QLRPLACSCSILHRAHGSASWSQGDTKVLAAV 44
          ++RP++C   +L R HGSA +++G+T+VL  V
Sbjct: 1  EIRPISCEVGLLPRTHGSALFTRGETQVLCTV 32

Polyribonucleotide nucleotidyltransferase (PNPase) 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. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction and in quality control of ribosomal RNA precursors, with the second repeat containing the active site. PNPase is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E. Length = 223

>gnl|CDD|131021 TIGR01966, RNasePH, ribonuclease PH

 Score = 37.3 bits (87), Expect = 0.003
 Identities = 38/139 (27%), Positives = 57/139 (41%), Gaps = 13/139 (9%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVL--AAVYGPKAGTKKNENPEKASI 62
           R DGR P+QLRP++ +   L  A GS     G+TKVL  A+V        +       + 
Sbjct: 1   RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITA 60

Query: 63  EVIWKPR-----------TGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
           E    PR            G+     +E + ++ R L+++  L      T  +   V+  
Sbjct: 61  EYGMLPRATQTRNRRESAKGKQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQA 120

Query: 112 DGALLPCAINAACAALVDA 130
           DG     +I  A  AL DA
Sbjct: 121 DGGTRTASITGAFVALADA 139

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 [Transcription, RNA processing]. Length = 236

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	243
TIGR02065	230	ECX1 archaeal exosome-like complex exonuclease 1.	100.0
PRK03983	244	exosome complex exonuclease Rrp41; Provisional	100.0
PRK00173	238	rph ribonuclease PH; Reviewed	100.0
TIGR01966	236	RNasePH ribonuclease PH. This bacterial enzyme, ri	100.0
PRK04282	271	exosome complex RNA-binding protein Rrp42; Provisi	100.0
KOG1069	217	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
COG2123	272	RNase PH-related exoribonuclease [Translation, rib	100.0
KOG1068	245	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
COG0689	230	Rph RNase PH [Translation, ribosomal structure and	100.0
KOG1614	291	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	100.0
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	100.0
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	100.0
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	100.0
KOG1612	288	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	100.0
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	100.0
KOG1613	298	consensus Exosomal 3'-5' exoribonuclease complex,	99.97
PF01138	132	RNase_PH: 3' exoribonuclease family, domain 1 This	99.96
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.95
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.88
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	99.86
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.84
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.79
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	99.73
PF03725	68	RNase_PH_C: 3' exoribonuclease family, domain 2 Th	99.22

>TIGR02065 ECX1 archaeal exosome-like complex exonuclease 1

Probab=100.00  E-value=1.5e-47  Score=324.09  Aligned_cols=215  Identities=28%  Similarity=0.422  Sum_probs=191.6

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCC-CCCCCCCceEEEEEec--CCCC------C
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGT-KKNENPEKASIEVIWK--PRTG------Q   72 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~-~~~~~~~~~~l~v~~~--p~~~------~   72 (243)
                      +|+|+|||+++|+|++.+++|.++++||||++++|+|+|+|+|+||++.+ +..+.|+++.|+|+|.  |++.      .
T Consensus         6 ~~~R~DGR~~~e~R~~~~~~g~~~~a~GSa~~~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~~~a~~~~~~~~   85 (230)
T TIGR02065         6 DGVRLDGRKPDELRPIKIEAGVLKNADGSAYVEFGGTKIIAAVYGPREMHPRHLQLPDRAVLRVRYHMAPFSTDERKRPG   85 (230)
T ss_pred             CCcCCCCCCcccccCeEEEECCCCCCCeEEEEEECCcEEEEEEeCCCccccccccCCCceEEEEEEEeCCcccCCccCCC
Confidence            68999999999999999999999999999999999999999999998764 3456789999987764  5422      2


Q ss_pred             CCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEE
Q 026141           73 IGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCI  152 (243)
Q Consensus        73 ~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~l  152 (243)
                      +++++.+++++|+++|++++.++.||++.|+|.++||++||++++|++||+++||.|+||||++++++++++++ ++.+|
T Consensus        86 ~~~~~~~~s~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~DG~~~~aai~aa~lAL~dagIp~~~~v~avtv~~~-~~~~v  164 (230)
T TIGR02065        86 PSRREIEISKVIREALEPAILLEQFPRTAIDVFIEVLQADAGTRCAGLTAASLALADAGIPMRDLVVGVAVGKV-DGVVV  164 (230)
T ss_pred             CCccHHHHHHHHHHHHHHHhChhhcCCeEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCCccccceeeEEEEEE-CCeEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999997 88999


Q ss_pred             eCCCHHHHhhccccEEEEeeC-CccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          153 LDPTKLEEQKMKGFAYLVFPN-SILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSL  231 (243)
Q Consensus       153 vDPt~~Ee~~~~~~~~v~~~~-~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l  231 (243)
                      +|||.+|++.+.+.+++++.. .+                  ++..++..|.++++++.+|++.|.++|+.++++|++++
T Consensus       165 ~Dpt~~Ee~~~~~~l~va~~~~~~------------------~i~~i~~~g~~~~e~~~~~l~~a~~~~~~l~~~~~~~l  226 (230)
T TIGR02065       165 LDLNEEEDMYGEADMPVAMMPKLG------------------EITLLQLDGDMTPDEFRQALDLAVKGIKIIYQIQREAL  226 (230)
T ss_pred             ECCCHHHhhcCCCceEEEEeCCCC------------------CEEEEEEecCcCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999998743 22                  22233457899999999999999999999999999999


Q ss_pred             Hhhc
Q 026141          232 QSKL  235 (243)
Q Consensus       232 ~~~~  235 (243)
                      ++|.
T Consensus       227 ~~~~  230 (230)
T TIGR02065       227 KNKY  230 (230)
T ss_pred             HhhC
Confidence            8874

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.

>PRK03983 exosome complex exonuclease Rrp41; Provisional

Probab=100.00  E-value=3.8e-47  Score=324.22  Aligned_cols=218  Identities=27%  Similarity=0.418  Sum_probs=194.4

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCC-CCCCCCCceEEEEEe--cCCCC------C
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGT-KKNENPEKASIEVIW--KPRTG------Q   72 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~-~~~~~~~~~~l~v~~--~p~~~------~   72 (243)
                      +|+|.|||+++++|++++++|.+++++|||++++|+|+|+|+|+||.+.. +..+.|+++.++|++  .|++.      .
T Consensus        12 ~~~R~DGR~~~~~R~i~i~~G~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~p~~~~~~~~~~   91 (244)
T PRK03983         12 DGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSVDERKRPG   91 (244)
T ss_pred             CCCCCCCCCcCcccceEEEeCCCCCCCeEEEEEECCeEEEEEEecCCccccccccCCCcEEEEEEEEcCCCccccccCCC
Confidence            78999999999999999999999999999999999999999999998764 445689999998775  46432      2


Q ss_pred             CCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEE
Q 026141           73 IGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCI  152 (243)
Q Consensus        73 ~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~l  152 (243)
                      +++++.+++++|+++|++++.++.||++.|+|.++||++|||+++|++||+++||+|+||||++++++++++++ ++.+|
T Consensus        92 ~~~~~~~~s~~l~~~l~~~i~~~~~p~~~I~I~i~VL~~DG~~~~aai~Aa~lAL~dagIp~~~~v~avtv~~~-~~~~i  170 (244)
T PRK03983         92 PDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKV-DGVIV  170 (244)
T ss_pred             CChhHHHHHHHHHHHHHHhccHHhCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHhcCCccccceeEEEEEEE-CCEEE
Confidence            34456799999999999999999999999999999999999999999999999999999999999999999997 88999


Q ss_pred             eCCCHHHHhhccccEEEEeeC-CccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          153 LDPTKLEEQKMKGFAYLVFPN-SILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSL  231 (243)
Q Consensus       153 vDPt~~Ee~~~~~~~~v~~~~-~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l  231 (243)
                      +|||..||+.+++.+++++++ .+                  .++.++..|.++.+++.+|+++|.++|++++++|+++|
T Consensus       171 ~DPt~~Ee~~~~~~l~va~~~~~~------------------~I~~l~~~G~~~~~~~~~~i~~A~~~~~~i~~~i~~~l  232 (244)
T PRK03983        171 LDLNKEEDNYGEADMPVAIMPRLG------------------EITLLQLDGNLTREEFLEALELAKKGIKRIYQLQREAL  232 (244)
T ss_pred             ECCCHHHhccCCceEEEEEECCCC------------------CEEEEEEecCcCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999874 33                  12233357899999999999999999999999999999


Q ss_pred             Hhhcccc
Q 026141          232 QSKLPGD  238 (243)
Q Consensus       232 ~~~~~~~  238 (243)
                      +++..+.
T Consensus       233 ~~~~~~~  239 (244)
T PRK03983        233 KSKYGEI  239 (244)
T ss_pred             HHHHHhh
Confidence            9887754

>PRK00173 rph ribonuclease PH; Reviewed

Probab=100.00  E-value=3.7e-45  Score=310.72  Aligned_cols=213  Identities=23%  Similarity=0.292  Sum_probs=185.9

Q ss_pred             CCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEec--CCC-----------
Q 026141            4 DRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWK--PRT-----------   70 (243)
Q Consensus         4 ~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~--p~~-----------   70 (243)
                      +|+|||+++|+|++++++|++++++|||+|++|+|+|+|+|++|...++....+++|.|.|+|.  |++           
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            5999999999999999999999999999999999999999998654332335678899887764  532           


Q ss_pred             CCCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHc-----------CCCCCCcee
Q 026141           71 GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDA-----------GIPMKHLAV  139 (243)
Q Consensus        71 ~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a-----------~ip~~~~~~  139 (243)
                      +.+++++.+++++|+++|++++.++.++++.++|+++||++|||+++|++||+++||+|+           ++||+++|+
T Consensus        81 g~~~~~~~~~sr~i~r~lr~~i~l~~l~~~~i~v~v~VL~~DG~~~~aai~Aa~~AL~da~~~~~~~~~~~~ip~~~~~~  160 (238)
T PRK00173         81 GKQGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLKDQVA  160 (238)
T ss_pred             CCCCccHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhhhccCcccCCcccCcee
Confidence            223445689999999999999988999999999999999999999999999999999999           999999999


Q ss_pred             EEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHH
Q 026141          140 AICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRA  218 (243)
Q Consensus       140 avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~  218 (243)
                      ++|++++ ++.+|+|||.+||+.+++.+++++++.+ +|.+++.+                +.+.++++++.+|++.|.+
T Consensus       161 ~vt~~~~-~~~~lvDpt~~Ee~~~~~~l~v~~~~~~~i~~v~~~g----------------~g~~~~~e~l~~~i~~A~~  223 (238)
T PRK00173        161 AVSVGIV-DGEPVLDLDYEEDSAAETDMNVVMTGSGGFVEVQGTA----------------EGAPFSREELDALLDLAEK  223 (238)
T ss_pred             EEEEEEE-CCEEEECCCHHHHhcCCceEEEEECCCCCEEEEEccC----------------CCCCcCHHHHHHHHHHHHH
Confidence            9999998 8899999999999999999999998764 66555420                1238999999999999999


Q ss_pred             HHHHHHHHHHHHHHh
Q 026141          219 ASAKLSDFLRRSLQS  233 (243)
Q Consensus       219 ~~~~l~~~i~~~l~~  233 (243)
                      .+++++++++++|++
T Consensus       224 ~~~~l~~~~~~~l~~  238 (238)
T PRK00173        224 GIAELVALQKAALAD  238 (238)
T ss_pred             HHHHHHHHHHHHhcC
Confidence            999999999998863

>TIGR01966 RNasePH ribonuclease PH

Probab=100.00  E-value=2e-44  Score=305.92  Aligned_cols=209  Identities=23%  Similarity=0.312  Sum_probs=181.7

Q ss_pred             CCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCC-CCCceEEEEEe--cCCCC----------
Q 026141            5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNE-NPEKASIEVIW--KPRTG----------   71 (243)
Q Consensus         5 R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~-~~~~~~l~v~~--~p~~~----------   71 (243)
                      |+|||+++|+|++++++|++++++|||+|++|+|+|+|+|+++. .+|... .+++|.+.|++  .|++.          
T Consensus         1 R~DGR~~~e~R~i~i~~G~~~~A~GSa~v~~G~T~Vla~V~~~~-~~p~~~~~~~~g~l~v~~~~~p~a~~~~~~r~~~~   79 (236)
T TIGR01966         1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEE-KVPPFLRGSGEGWITAEYGMLPRATQTRNRRESAK   79 (236)
T ss_pred             CCCCCCCCCccCeEEEeCCcCCCCceEEEEecCCEEEEEEEccC-ccCCcccCCCcEEEEEEEecCCCCCCCCccccccC
Confidence            89999999999999999999999999999999999999999744 344433 46788887765  46321          


Q ss_pred             -CCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHc-----------CCCCCCcee
Q 026141           72 -QIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDA-----------GIPMKHLAV  139 (243)
Q Consensus        72 -~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a-----------~ip~~~~~~  139 (243)
                       .+++++.+++++|+|+|++++.++.|+++.|+|+++||++|||+++|++||+++||+|+           ++||+++|+
T Consensus        80 g~~~~~~~e~~~~i~r~lr~~i~l~~l~~~~i~I~v~VL~~DG~~~~aai~Aa~aAL~da~~~~~~~~~~~~ip~~~~~~  159 (236)
T TIGR01966        80 GKQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVA  159 (236)
T ss_pred             CCCCccHHHHHHHHHHHHHHhcCHhhcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHHHHhhhhcCcccCCCccCcee
Confidence             22224678999999999999999999999999999999999999999999999999999           999999999


Q ss_pred             EEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHH
Q 026141          140 AICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRA  218 (243)
Q Consensus       140 avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~  218 (243)
                      ++|++++ ++.+|+|||.+||+.+++.+++++++++ +|.+++.+                +.+.++++++.+|+++|.+
T Consensus       160 ~vt~~~~-~~~~v~Dpt~~Ee~~~~~~l~l~~~~~~~i~~i~~~g----------------~~~~~~~~~l~~~i~~a~~  222 (236)
T TIGR01966       160 AVSVGIV-DGEPVLDLDYEEDSAADVDMNVVMTGSGGFVEVQGTA----------------EEGPFSRDELNKLLDLAKK  222 (236)
T ss_pred             EEEEEEE-CCEEEECCChhHHhccCceEEEEEcCCCCEEEEEecC----------------CCCCcCHHHHHHHHHHHHH
Confidence            9999998 7899999999999999999999998764 45544310                1358999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 026141          219 ASAKLSDFLRRSL  231 (243)
Q Consensus       219 ~~~~l~~~i~~~l  231 (243)
                      ++++++++|+++|
T Consensus       223 ~~~~l~~~~~~~l  235 (236)
T TIGR01966       223 GIRELIELQKQAL  235 (236)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999999986

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.

>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional

Probab=100.00  E-value=7.3e-44  Score=308.41  Aligned_cols=212  Identities=23%  Similarity=0.332  Sum_probs=186.4

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cCCC------CCC
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KPRT------GQI   73 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p~~------~~~   73 (243)
                      +|+|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|++ +...|..+.|++|.+.|++  .|++      +.+
T Consensus        22 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~vl~~V~~-~~~~p~~~~~~~g~i~~~v~~~~~a~~~~~~~~~  100 (271)
T PRK04282         22 KGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKL-EIGEPFPDTPNEGVLIVNAELLPLASPTFEPGPP  100 (271)
T ss_pred             cCCCCCCCCCccccCeEEEeCCccCCCcEEEEEECCCEEEEEEEE-EEecCCCCCCCCCEEEEEEEECCCcCccccCCCC
Confidence            689999999999999999999999999999999999999999996 4556777789999887765  4542      233


Q ss_pred             CCchHHHHHHHHHHHHh--------hhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCC------------
Q 026141           74 GKPEKEYEIILKRTLQS--------ICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIP------------  133 (243)
Q Consensus        74 ~~~~~~l~~~l~~~l~~--------~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip------------  133 (243)
                      ++.+.+++++|+++|++        +|+.++..+|.|+|+++||++|||++||+++|+++||+|+++|            
T Consensus       101 ~~~~~~l~~~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG~~~daa~~Aa~aAL~~~~iP~~~~~~~~~~~~  180 (271)
T PRK04282        101 DENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEGEDGVVDK  180 (271)
T ss_pred             CHHHHHHHHHHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhCCCCcEEEcCCceecc
Confidence            44567899999998754        5667777799999999999999999999999999999999995            


Q ss_pred             --------CCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEeecCCC
Q 026141          134 --------MKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVTHGAM  204 (243)
Q Consensus       134 --------~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~~  204 (243)
                              |+++|+++|++++ ++.+|+|||..||+.+++.+++++++++ +|.+.|.                 +.|.+
T Consensus       181 ~~~~~~l~~~~~p~~vt~~~~-~~~~v~Dpt~~Ee~~~~~~l~va~~~~g~i~~l~~~-----------------g~~~~  242 (271)
T PRK04282        181 LGEDFPLPVNDKPVTVTFAKI-GNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKS-----------------GIGSF  242 (271)
T ss_pred             CCCcccCCCCCeeEEEEEEEE-CCEEEECCCHHHHhhcCceEEEEECCCCcEEEEEcC-----------------CCCCC
Confidence                    9999999999998 8899999999999999999999998874 5555542                 24689


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          205 SVDDYFHCLERGRAASAKLSDFLRRSLQ  232 (243)
Q Consensus       205 ~~~~l~~~l~~a~~~~~~l~~~i~~~l~  232 (243)
                      +.+++.+|++.|.+.+++++++++++++
T Consensus       243 ~~~~l~~~i~~A~~~~~~l~~~~~~~l~  270 (271)
T PRK04282        243 TEEEVDKAIDIALEKAKELREKLKEALG  270 (271)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999999999884

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

Probab=100.00  E-value=2.2e-44  Score=287.68  Aligned_cols=212  Identities=47%  Similarity=0.704  Sum_probs=199.6

Q ss_pred             CCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEecCCCCCCCCchHHHHHHHHHHHHhhh
Q 026141           13 QLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSIC   92 (243)
Q Consensus        13 e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~p~~~~~~~~~~~l~~~l~~~l~~~~   92 (243)
                      .+|++.++.|+++++|||+.|++|+|+|+|+|+||.+++.+.+.|++..|+|.++|..|.+++.|+.+++.|+++|+++|
T Consensus         4 ~lr~~~cei~iLsr~dGSs~fsqgdT~V~c~V~GP~dvk~r~E~~~katleVi~rp~~G~~~~~eK~~e~iI~~tl~~~I   83 (217)
T KOG1069|consen    4 RLRGIACEISILSRPDGSSEFSQGDTKVICSVYGPIDVKARQEDPEKATLEVIWRPKSGVNGTVEKVLERIIRKTLSKAI   83 (217)
T ss_pred             hhhhhhhhhceecCCCCccceecCCcEEEEEeeCCcchhhcccCchhceEEEEEecccCcchHHHHHHHHHHHHHHHHhh
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEee
Q 026141           93 ILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFP  172 (243)
Q Consensus        93 ~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~  172 (243)
                      .++.||+..|+|.++|+++||+.+++++|||++||.|+||||+++++++.+++.+++.+++|||..++..+.+..++.+.
T Consensus        84 ~l~l~Prt~iqVsiqvv~ddgs~LacaINaAclALvDaGIpl~~mfcai~~~~~~d~~lv~Dpt~~qek~~~~~~~lsf~  163 (217)
T KOG1069|consen   84 ILELYPRTTIQVSIQVVEDDGSTLACAINAACLALVDAGIPLRSMFCAISCALHEDGVLVLDPTAKQEKISTARATLSFE  163 (217)
T ss_pred             eeeecCCceEEEEEEEEecCCcchHHHHHHHHHHHHhcCCchHHhhhhceEEEecCccEEECCcHHhhhhhhceEEEEEe
Confidence            99999999999999999999999999999999999999999999999999999988899999999999998888887775


Q ss_pred             CCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Q 026141          173 NSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGD  238 (243)
Q Consensus       173 ~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~~~~~  238 (243)
                      ...           .   .+++++.+..+|.++.++|..+++.|..++++++.++++.++++.+++
T Consensus       164 ~~~-----------~---~~~~vi~s~t~G~~~~d~lf~~le~a~~~~~~~f~f~r~~~q~~~s~~  215 (217)
T KOG1069|consen  164 GGS-----------L---GEPKVIISETNGEKSEDQLFYVLELAQAAAQSLFPFYREVLQRKYSKS  215 (217)
T ss_pred             cCC-----------C---CCcceEEEeccCCCCHHHHHHHHHhhHHHHHHHHHHHHHHHHhhcCcc
Confidence            421           0   145788888999999999999999999999999999999999987765

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

Probab=100.00  E-value=1.5e-43  Score=296.77  Aligned_cols=212  Identities=24%  Similarity=0.355  Sum_probs=192.5

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEE--ecCC---CCCCCCc
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVI--WKPR---TGQIGKP   76 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~--~~p~---~~~~~~~   76 (243)
                      +|+|+|||.++|+|++++++|++++++|||+|++|+|+|+|+|+. +..+|+++.|++|.+.+|  +.|.   .+++|++
T Consensus        21 ~g~R~DGR~~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK~-eig~Pf~DtP~eG~~~~n~El~Plas~~fE~Gpp   99 (272)
T COG2123          21 KGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKA-EIGEPFPDTPNEGVLVVNVELSPLASPSFEPGPP   99 (272)
T ss_pred             cCcccCCCCcccccceEEEeCceecCCCcEEEEecCeEEEEEEEc-ccCCCCCCCCCCceEEeeeeeeccccccccCCCC
Confidence            589999999999999999999999999999999999999999997 789999999999987655  5562   3455554


Q ss_pred             ---hHHHHHHHHHHH--------HhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCC------------
Q 026141           77 ---EKEYEIILKRTL--------QSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIP------------  133 (243)
Q Consensus        77 ---~~~l~~~l~~~l--------~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip------------  133 (243)
                         ..+++++++|.+        +++|+..+..+|.+++|++||++|||++||++.|+++||+++++|            
T Consensus       100 de~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~Da~~lA~~aAL~~t~vP~~~~~~~~~~v~  179 (272)
T COG2123         100 DELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAAVAALLNTRVPKAVEVGDGEIVI  179 (272)
T ss_pred             chhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHhcCCCceeecCCcceee
Confidence               478999999986        467998899999999999999999999999999999999999988            


Q ss_pred             ----------CCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEeecC
Q 026141          134 ----------MKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVTHG  202 (243)
Q Consensus       134 ----------~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g  202 (243)
                                +.++|.++|++++ ++.+++|||.+||..+++.+++.+++++ ++.++|.                 +.|
T Consensus       180 ~~~~~~~pl~~~~~pi~vt~a~i-g~~lvvDPsleEe~v~d~~ltit~~~~~~Iv~iqK~-----------------g~~  241 (272)
T COG2123         180 EVEEEPVPLPVSNPPISVTFAKI-GNVLVVDPSLEEELVADGRLTITVNEDGEIVAIQKV-----------------GGG  241 (272)
T ss_pred             cccCCCcccccCCCceEEEEEEE-CCEEEeCCCcchhhhcCceEEEEECCCCcEEEEEEc-----------------CCC
Confidence                      5688999999998 8999999999999999999999999885 8888775                 367


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          203 AMSVDDYFHCLERGRAASAKLSDFLRRSLQ  232 (243)
Q Consensus       203 ~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~  232 (243)
                      .++++.+.+|++.|.+.+.++.+.+.+.|+
T Consensus       242 ~~~~~~~~~~~~~A~~~~~kl~~~~~~~L~  271 (272)
T COG2123         242 SITESDLEKALKTALSKAEKLREALKEALK  271 (272)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999999999999886

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

Probab=100.00  E-value=1.4e-43  Score=292.90  Aligned_cols=223  Identities=33%  Similarity=0.420  Sum_probs=196.8

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCC-CCCceEEEEEec--CCC-------C
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNE-NPEKASIEVIWK--PRT-------G   71 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~-~~~~~~l~v~~~--p~~-------~   71 (243)
                      ||+|.|||.++|+|++..+.|++.+++|||++++|||+|+|.|+||++.+.+.. +|+++.+++.|.  ++.       .
T Consensus        11 eg~r~dgRr~~elR~i~~~~g~~~~a~GSay~E~GnTKVl~aV~GPre~~~~~~~~~~~a~lnc~~~~a~Fst~~r~~~~   90 (245)
T KOG1068|consen   11 EGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCEVSSAQFSTGDRKKRP   90 (245)
T ss_pred             cccccCCCChhHhhhhhhhcCccccCCccchhhcCCeEEEEEEeCCcccccccccccccceEEEEEeeeccccchhccCC
Confidence            689999999999999999999999999999999999999999999998765433 688888887653  321       2


Q ss_pred             CCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeE
Q 026141           72 QIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYC  151 (243)
Q Consensus        72 ~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~  151 (243)
                      ..++++++++.+|+++|++.+.++.||+.+|+|+|+||++||+.+++++||+++||.|+||||+|+++++|+++. ++.+
T Consensus        91 ~~~rr~~e~s~~L~~afe~~I~~~lyPrsqIDI~v~VleddG~~laa~inaatlAL~daGI~m~D~i~~~t~~l~-~~~~  169 (245)
T KOG1068|consen   91 KGDRREKELSLMLQQAFEPVILLELYPRSQIDIYVQVLEDDGSNLAAAINAATLALADAGIPMYDLITACTAGLA-DGTP  169 (245)
T ss_pred             CccHHHHHHHHHHHHHHHHHHHhhhCccccceEEEEEEECCCccHHHHHHHHHHHHHHcCCChhhhhhhceeeec-CCcc
Confidence            345578999999999999999999999999999999999999999999999999999999999999999999997 7799


Q ss_pred             EeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          152 ILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSL  231 (243)
Q Consensus       152 lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l  231 (243)
                      ++||+..||......++|++-.+.                 .....++..+.++.+.|...++.+..+|+++++.++.++
T Consensus       170 l~Dl~~~eesa~~~~ltVa~l~~~-----------------~~i~~l~~~~~~~~d~l~~vl~~a~~~c~~v~~~l~~~l  232 (245)
T KOG1068|consen  170 LLDLTSLEESARAPGLTVAALPNR-----------------EEIALLQLDERLHCDHLETVLELAIAGCKRVYERLRLVL  232 (245)
T ss_pred             ccccccchhhccCCceEEEEecCc-----------------ceEEEEEecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999998888888764331                 113334457899999999999999999999999999999


Q ss_pred             HhhcccccccC
Q 026141          232 QSKLPGDLSKA  242 (243)
Q Consensus       232 ~~~~~~~~~~~  242 (243)
                      .+++.+...++
T Consensus       233 ~~~l~~~~~~~  243 (245)
T KOG1068|consen  233 REHLKNAESAL  243 (245)
T ss_pred             HHHHHHhhhhc
Confidence            99998877664

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

Probab=100.00  E-value=7.5e-42  Score=283.74  Aligned_cols=214  Identities=26%  Similarity=0.401  Sum_probs=189.7

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCC-CCCCceEEEEEe--cCCCC----CC-
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN-ENPEKASIEVIW--KPRTG----QI-   73 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~-~~~~~~~l~v~~--~p~~~----~~-   73 (243)
                      +++|+|||.++|.|+++++.|++++++||+++++|+|+|+|+|+||++..|+. ..+++|++++.|  .|++.    .+ 
T Consensus         6 ~~~R~dgR~~delR~i~~~~~~~~~a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~ey~m~p~sT~~R~~~~   85 (230)
T COG0689           6 DGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLPRSTDERKKRE   85 (230)
T ss_pred             cCcCCCCCCcccccceEEEeccccCCCccEEEEeCCeEEEEEEecCCCCCChhhcCCCceEEEEEEeccccccccccccc
Confidence            68999999999999999999999999999999999999999999999877664 457789888776  46543    11 


Q ss_pred             -CC-chHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeE
Q 026141           74 -GK-PEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYC  151 (243)
Q Consensus        74 -~~-~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~  151 (243)
                       .+ ++++++++|.++|++.+.++.||+..|+|++.|+++||+.+.|++||+++||+|||+||+++++|+++|++ ++.+
T Consensus        86 ~~~gR~~eisrli~~al~~~i~L~~~p~~~I~i~~dVlqaDggTrta~It~A~lAL~DAgipl~~~vaaiSvgi~-~~~~  164 (230)
T COG0689          86 ADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVGIV-DGVI  164 (230)
T ss_pred             ccccchhHHHHHHHHHHHHHhhhhhcCccEEEEEEEEEECCCCeeeehhhHHHHHHHHcCCchhhheeEeEEEEE-CCce
Confidence             12 57899999999999999999999999999999999999999999999999999999999999999999998 7779


Q ss_pred             EeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEE-EeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          152 ILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIIT-SVTHGAMSVDDYFHCLERGRAASAKLSDFLRRS  230 (243)
Q Consensus       152 lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~-~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~  230 (243)
                      ++||+..|++.+...++|++..++..                ..|+ ....|++++++|.+++++|.++|+++++.++++
T Consensus       165 ~lDl~~~Eds~~~~d~~v~~~~~~~~----------------~ei~~~~~~~~~~~del~~lL~la~~g~~~~~~~~~~a  228 (230)
T COG0689         165 VLDLDYEEDSAAEADMNVVMTGNGGL----------------VEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQREA  228 (230)
T ss_pred             EecCcchhhcccccCceEEEEecCCe----------------EEEEEEeccCCcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999998765321                1233 234789999999999999999999999999998


Q ss_pred             HH
Q 026141          231 LQ  232 (243)
Q Consensus       231 l~  232 (243)
                      |.
T Consensus       229 l~  230 (230)
T COG0689         229 LA  230 (230)
T ss_pred             hC
Confidence            73

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

Probab=100.00  E-value=5.2e-41  Score=275.28  Aligned_cols=215  Identities=20%  Similarity=0.316  Sum_probs=192.7

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEE--EecCC---CCCCCCc
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV--IWKPR---TGQIGKP   76 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v--~~~p~---~~~~~~~   76 (243)
                      .|.|.|||++.|+|.+.+++|.   ..||+.+++|+|+|+|.|+. +..+|+.++|.+|.+.+  +++|.   ++++|+.
T Consensus        20 ~g~R~DgR~l~efR~lei~fGk---e~gs~~vt~G~Tkvm~~vt~-~ia~Py~dRP~eG~~~I~telsPmA~~sfE~Gr~   95 (291)
T KOG1614|consen   20 AGLRFDGRSLEEFRDLEIEFGK---EYGSVLVTMGNTKVMARVTA-QIAQPYIDRPHEGSFSIFTELSPMASPSFEPGRK   95 (291)
T ss_pred             hcccccccchhhhhceEEEecc---ccccEEEEecCeeEEEEeeh-hhcCcccCCCCCCeeeeeeccccccccccCCCCc
Confidence            5899999999999999999994   88999999999999999998 78999999999998765  56774   3445543


Q ss_pred             ---hHHHHHHHHHHH--------HhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCC------------
Q 026141           77 ---EKEYEIILKRTL--------QSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIP------------  133 (243)
Q Consensus        77 ---~~~l~~~l~~~l--------~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip------------  133 (243)
                         +.++.++|++++        +++|+..+..+|.|++|+++|+.|||++||++.|+++||++++.|            
T Consensus        96 ~~~~v~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlvDaA~iAviaaL~hFrrPdvTv~g~ev~ih  175 (291)
T KOG1614|consen   96 GESEVELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLVDAACIAVIAALMHFRRPDVTVGGEEVIIH  175 (291)
T ss_pred             cchHHHHHHHHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCeehhHHHHHHHHHHhcCCCCcccccceeEec
Confidence               578999999886        579999999999999999999999999999999999999999955            


Q ss_pred             -----------CCCceeEEEEEEecC-CeEEeCCCHHHHhhccccEEEEeeCC-ccccccCCCcccCCCCcccceEEEee
Q 026141          134 -----------MKHLAVAICCCSAES-GYCILDPTKLEEQKMKGFAYLVFPNS-ILSVLPEGSSLVQGEPMEHGIITSVT  200 (243)
Q Consensus       134 -----------~~~~~~avt~~~~~~-~~~lvDPt~~Ee~~~~~~~~v~~~~~-~~~~~~k~~~~~~~~~~~~~~i~~~~  200 (243)
                                 |+|+|.|+||+++.+ +.+++|||..||..++|.++|.+|++ ++|.++|+                  
T Consensus       176 p~eEr~PvPL~I~HmPIC~tf~ffnkG~ivviDpt~~Ee~~~dGs~vVt~Nk~rEVc~i~k~------------------  237 (291)
T KOG1614|consen  176 PVEEREPVPLSIHHMPICFTFGFFNKGEIVVIDPTEKEEAVMDGSMVVTMNKNREVCAIQKS------------------  237 (291)
T ss_pred             ChhccCCcceeeeeccceEEEEEecCceEEEeCCcHHHHhccCceEEEEEcCCccEEEEecC------------------
Confidence                       799999999999954 57899999999999999999999988 48888775                  


Q ss_pred             cC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Q 026141          201 HG-AMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGD  238 (243)
Q Consensus       201 ~g-~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~~~~~  238 (243)
                      .| .++..++..|.+.|.+.+.++...+.++|+++..++
T Consensus       238 G~~~~~~~~i~~C~k~A~~~a~~vt~ii~e~l~~d~~~r  276 (291)
T KOG1614|consen  238 GGEILDESVIERCYKLAKDRAVEVTGIILEALEEDQRER  276 (291)
T ss_pred             CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33 789999999999999999999999999999887665

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=100.00  E-value=6.5e-38  Score=299.73  Aligned_cols=218  Identities=19%  Similarity=0.277  Sum_probs=184.8

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEE-cCccCCCCC---CCCCceEE--EEEecCCC-----
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVY-GPKAGTKKN---ENPEKASI--EVIWKPRT-----   70 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~-gp~~~~~~~---~~~~~~~l--~v~~~p~~-----   70 (243)
                      +|+|+|||+++|+||+.+++|++++++|||+|++|+|+|+|+|+ ||.+.....   ...+++.+  +++|.|++     
T Consensus       308 ~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSa~~~~G~Tqvl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~  387 (684)
T TIGR03591       308 EGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQIIDDLEGEYRKRFMLHYNFPPYSVGEVG  387 (684)
T ss_pred             CCCCCCCCCCCCcCceEEEeCCCCCCCceEEEEeCCeEEEEEEecCCcccccCCcccCCCccEEEEEEEEcCCCCCCCcC
Confidence            68999999999999999999999999999999999999999994 876432111   11234554  56667742     


Q ss_pred             --CCCCCchHHHHHHHHHHHHhhhhc-CCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEec
Q 026141           71 --GQIGKPEKEYEIILKRTLQSICIL-TINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAE  147 (243)
Q Consensus        71 --~~~~~~~~~l~~~l~~~l~~~~~~-~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~  147 (243)
                        +.+++++.+++++++|+|++++.. +.|| |.|+|+++||++|||..+|+++|+++||+||||||+++|+++++|++.
T Consensus       388 ~~g~~~rrei~~~~l~~ral~~~i~~~~~~p-~tI~v~~~VLesdGs~~~Aai~aaslAL~dAgvP~~~~Vagvs~gli~  466 (684)
T TIGR03591       388 RVGGPGRREIGHGALAERALKAVLPSEEEFP-YTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIK  466 (684)
T ss_pred             CCCCCChHHHHHHHHHHHHHHHhcCccccCC-eEEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCCcCCEEEEEEEEEc
Confidence              235667888999999999998885 5676 889999999999999999999999999999999999999999999985


Q ss_pred             CC----eEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHH
Q 026141          148 SG----YCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKL  223 (243)
Q Consensus       148 ~~----~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l  223 (243)
                      ++    .+++||+..|+..++..++++.+.++++.+++..                ..+.++.+.|.+|+++|.+++++|
T Consensus       467 ~~~~~~~il~D~~~~Ed~~~d~d~~va~t~~gI~~lq~d~----------------k~~~i~~~~l~~al~~a~~~~~~I  530 (684)
T TIGR03591       467 EGDERFAVLSDILGDEDHLGDMDFKVAGTRDGITALQMDI----------------KIDGITREIMEQALEQAKEGRLHI  530 (684)
T ss_pred             CCCcceEEEeCCChHHHhcCCceEEEEEcCCceEEEEEEc----------------CcCCcCHHHHHHHHHHHHHHHHHH
Confidence            32    5999999999999999999998877776665420                123689999999999999999999


Q ss_pred             HHHHHHHHHhhcc
Q 026141          224 SDFLRRSLQSKLP  236 (243)
Q Consensus       224 ~~~i~~~l~~~~~  236 (243)
                      ++.|++++.++..
T Consensus       531 ~~~m~~~l~~~~~  543 (684)
T TIGR03591       531 LGEMNKVISEPRA  543 (684)
T ss_pred             HHHHHHHHhhhhc
Confidence            9999999998754

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=3e-37  Score=295.76  Aligned_cols=216  Identities=20%  Similarity=0.276  Sum_probs=182.3

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEE-cCcc-CCCCC--CCCCceEE--EEEecCCC-----
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVY-GPKA-GTKKN--ENPEKASI--EVIWKPRT-----   70 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~-gp~~-~~~~~--~~~~~~~l--~v~~~p~~-----   70 (243)
                      +|+|+|||+++|+||+.+++|++++++|||+|++|+|+|+|+|+ ||.. ..+.+  ...+++.+  +++|.|++     
T Consensus       312 ~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSal~~~G~T~Vl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~  391 (693)
T PRK11824        312 EGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLRDEQIIDGLEGEYKKRFMLHYNFPPYSVGETG  391 (693)
T ss_pred             CCCCCCCCCcCcccceEEEeCCCCCCCceEEEEECCeEEEEEEecCCCcccccccccCCCCcEEEEEEEEcCCCCCCCcC
Confidence            68999999999999999999999999999999999999999995 7632 22211  11255655  45567742     


Q ss_pred             --CCCCCchHHHHHHHHHHHHhhhhc-CCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEec
Q 026141           71 --GQIGKPEKEYEIILKRTLQSICIL-TINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAE  147 (243)
Q Consensus        71 --~~~~~~~~~l~~~l~~~l~~~~~~-~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~  147 (243)
                        +.+++++.+++++++|+|++++.. +.|| |.|+|+++||++|||..+|+++|+++||+||||||+++++++++|++.
T Consensus       392 ~~~~~~rre~~~~~li~ral~~vi~~~~~~p-~~I~v~~~VLe~dGs~~~Aai~aaslAL~dAgvP~~~~Va~vs~gli~  470 (693)
T PRK11824        392 RVGSPGRREIGHGALAERALEPVLPSEEEFP-YTIRVVSEILESNGSSSMASVCGSSLALMDAGVPIKAPVAGIAMGLIK  470 (693)
T ss_pred             CCCCCChhHHHHHHHHHHHHHHhcCcccCCC-EEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCccCceeEEEEEEEc
Confidence              224667888999999999999987 5666 899999999999999999999999999999999999999999999985


Q ss_pred             CC---eEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHH
Q 026141          148 SG---YCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLS  224 (243)
Q Consensus       148 ~~---~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~  224 (243)
                      ++   .+++||+..|+..++..++++++.++++.++...                ..|.++.+.+.+++++|.+++++|+
T Consensus       471 ~~~~~~il~D~~~~Ed~~~d~d~~va~t~~gi~~lq~d~----------------k~~~i~~~~l~~al~~a~~g~~~I~  534 (693)
T PRK11824        471 EGDKYAVLTDILGDEDHLGDMDFKVAGTRDGITALQMDI----------------KIDGITREILEEALEQAKEGRLHIL  534 (693)
T ss_pred             CCCceEEEcCCChhhHhhCCceEEEEecCCceEEEEEec----------------ccCCcCHHHHHHHHHHHHHHHHHHH
Confidence            43   4899999999999999999998877766655210                1346899999999999999999999


Q ss_pred             HHHHHHHHhh
Q 026141          225 DFLRRSLQSK  234 (243)
Q Consensus       225 ~~i~~~l~~~  234 (243)
                      +.|++++...
T Consensus       535 ~~M~~aI~~~  544 (693)
T PRK11824        535 GKMNEAISEP  544 (693)
T ss_pred             HHHHHHhcCC
Confidence            9999998754

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=100.00  E-value=4.7e-35  Score=276.22  Aligned_cols=217  Identities=18%  Similarity=0.256  Sum_probs=181.6

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEE-cCccCCCCC-----CCCCceEEEEEecCCC-----
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVY-GPKAGTKKN-----ENPEKASIEVIWKPRT-----   70 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~-gp~~~~~~~-----~~~~~~~l~v~~~p~~-----   70 (243)
                      +|+|+|||.++++|++.+++|++++++|||+|+.|+|+|+|.+. ||.......     +......++++|.|++     
T Consensus       333 ~g~R~DGR~~~eiR~i~~~~g~l~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~~~~~~~~YnfpPFSt~er~  412 (719)
T TIGR02696       333 EGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPPYSTGETG  412 (719)
T ss_pred             CCCCCCCCCccccccceeecCCCCCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccccceEEEEEeCCCCcccCCC
Confidence            57899999999999999999999999999999999999999876 333222211     1223445677788863     


Q ss_pred             --CCCCCchHHHHHHHHHHHHhhhh-cCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEec
Q 026141           71 --GQIGKPEKEYEIILKRTLQSICI-LTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAE  147 (243)
Q Consensus        71 --~~~~~~~~~l~~~l~~~l~~~~~-~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~  147 (243)
                        +.+++++.+++++++|+|++++. .+.||++ |.+..+||++||+...|++||+++||+||||||++++++|++|++.
T Consensus       413 ~~~~~~RReighg~La~rALe~vI~~~e~fP~T-IrvvseVLeSdGSss~AsIcaasLALmDAGVPmkd~VAgis~Gli~  491 (719)
T TIGR02696       413 RVGSPKRREIGHGALAERALVPVLPSREEFPYA-IRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAGIAMGLIS  491 (719)
T ss_pred             CCCCCCccHHHHHHHHHHHHHHhhCcHhhCCCE-EEEEEEeeccCCcHHHHHHHHHHHHHHHcCcchhheeeEEEEEEec
Confidence              23467899999999999999998 6999976 8888899999999999999999999999999999999999999984


Q ss_pred             C---Ce----EEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCC---CCHHHHHHHHHHHH
Q 026141          148 S---GY----CILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGA---MSVDDYFHCLERGR  217 (243)
Q Consensus       148 ~---~~----~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~---~~~~~l~~~l~~a~  217 (243)
                      +   +.    +++||+..|+..++..+.++.+.+++..++                   ..|.   ++.+.|.+++++|.
T Consensus       492 e~~~~~~~~~iL~Di~g~ED~~Gdmdfkvagt~~gIt~lQ-------------------md~ki~gi~~e~l~~aL~~A~  552 (719)
T TIGR02696       492 DEVDGETRYVALTDILGAEDAFGDMDFKVAGTSEFVTALQ-------------------LDTKLDGIPASVLASALKQAR  552 (719)
T ss_pred             cccCCCcceeEEeCCCchhhhcCCceEEEEecCCCEEEEE-------------------EEeeECCCCHHHHHHHHHHHH
Confidence            4   33    899999999999988888876655444432                   3443   69999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhcccccc
Q 026141          218 AASAKLSDFLRRSLQSKLPGDLS  240 (243)
Q Consensus       218 ~~~~~l~~~i~~~l~~~~~~~~~  240 (243)
                      ++|.+|++.|++++...  .+++
T Consensus       553 ~g~~~Il~~m~~al~~p--~~~s  573 (719)
T TIGR02696       553 DARLAILDVMAEAIDTP--DEMS  573 (719)
T ss_pred             HHHHHHHHHHHHHHhCc--cccc
Confidence            99999999999999987  4444

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.

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=100.00  E-value=1.3e-34  Score=278.23  Aligned_cols=216  Identities=22%  Similarity=0.316  Sum_probs=179.8

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEE-cCccCCCCCC------CCCceEEEEEecCCC----
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVY-GPKAGTKKNE------NPEKASIEVIWKPRT----   70 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~-gp~~~~~~~~------~~~~~~l~v~~~p~~----   70 (243)
                      +|+|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+ ||.+.....+      ...+..++++|.|+.    
T Consensus       436 ~g~R~DGR~~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVLatVtlGp~~~~q~~d~l~~~~~~~~f~~~y~fPPfs~ge~  515 (891)
T PLN00207        436 GGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEVKRFYLQYSFPPSCVGEV  515 (891)
T ss_pred             CCCCCCCCCcCccceEEEEeCCcCCCCceEEEEECCeEEEEEEEecCccccccccccccccceeeEEEEEEcCCCCCccc
Confidence            68999999999999999999999999999999999999999996 8765432211      123345677888853    


Q ss_pred             ---CCCCCchHHHHHHHHHHHHhhhhcC-CCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEe
Q 026141           71 ---GQIGKPEKEYEIILKRTLQSICILT-INPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSA  146 (243)
Q Consensus        71 ---~~~~~~~~~l~~~l~~~l~~~~~~~-~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~  146 (243)
                         +.+++++.+++++++|+|++++..+ .|| |.|+|+++||++||+...|++||+++||+||||||++++++|++|++
T Consensus       516 ~r~g~psrREi~hg~L~eRALrpvip~~~~fP-~tIrV~~~VLesDGSssmAaV~aaSLALmDAGIPmk~~VAGvsvGli  594 (891)
T PLN00207        516 GRIGAPSRREIGHGMLAERALEPILPSEDDFP-YTIRVESTITESNGSSSMASVCGGCLALQDAGVPVKCPIAGIAMGMV  594 (891)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhCCcccCCC-EEEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCccCceeEEEEEEE
Confidence               2245667889999999999999885 677 89999999999999999999999999999999999999999999998


Q ss_pred             cC-------Ce--EEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHH
Q 026141          147 ES-------GY--CILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGR  217 (243)
Q Consensus       147 ~~-------~~--~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~  217 (243)
                      .+       +.  +++||+..|+..++..+.++.+.+++..++-.     +           ..+.++.+.|.++++.|.
T Consensus       595 ~d~~~~~~~g~~~IL~Dp~g~Ed~~gdmDfkVAgT~~gIt~iqmd-----~-----------k~~gis~e~l~eAL~~A~  658 (891)
T PLN00207        595 LDTEEFGGDGSPLILSDITGSEDASGDMDFKVAGNEDGITAFQMD-----I-----------KVGGITLPIMERALLQAK  658 (891)
T ss_pred             ecccccCCCCcEEEEeCCCHHHHhcCCceEEEEecccceEEEEEe-----c-----------ccCCCCHHHHHHHHHHHH
Confidence            32       23  56799999999999999888765554433210     0           123579999999999999


Q ss_pred             HHHHHHHHHHHHHHHhh
Q 026141          218 AASAKLSDFLRRSLQSK  234 (243)
Q Consensus       218 ~~~~~l~~~i~~~l~~~  234 (243)
                      +++..|++.|++++...
T Consensus       659 ~g~~~Il~~M~~~i~~p  675 (891)
T PLN00207        659 DGRKHILAEMSKCSPPP  675 (891)
T ss_pred             HHHHHHHHHHHHHHhhh
Confidence            99999999999998764

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

Probab=100.00  E-value=2.5e-33  Score=231.33  Aligned_cols=216  Identities=25%  Similarity=0.313  Sum_probs=180.7

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCC-eEEEEEEEcCccCCCCCCCCCceEE--EEEecCCC-----CCC
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGD-TKVLAAVYGPKAGTKKNENPEKASI--EVIWKPRT-----GQI   73 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~-T~Vi~~V~gp~~~~~~~~~~~~~~l--~v~~~p~~-----~~~   73 (243)
                      +.+|.|||++++|||+.++++++++++|||+|++|+ |.|+++|++ +...|..+.|+++.+  .|+++|.+     |+.
T Consensus        19 ~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVKa-Evg~~~~~~p~egk~~~~VD~S~sasp~f~gRg   97 (288)
T KOG1612|consen   19 PDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKA-EVGSPDDETPVEGKYLFFVDCSPSASPQFQGRG   97 (288)
T ss_pred             cccccCCcCccccceEEEEeccccCCCCcEEEEecCCceEEEEEee-eccCccccCCCCCeEEEEEEecCCcCccccCCC
Confidence            468999999999999999999999999999999998 999999998 778899999999975  45666643     232


Q ss_pred             CCc-hHHHHHHHHHHHHh---------hhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCC---------
Q 026141           74 GKP-EKEYEIILKRTLQS---------ICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPM---------  134 (243)
Q Consensus        74 ~~~-~~~l~~~l~~~l~~---------~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~---------  134 (243)
                      +.. ..++...++++|.+         +++.++| +|.|+||+.|++.|||++||...|+.+||.++.+|-         
T Consensus        98 gde~~~eltsaLq~~l~~~~sgv~ls~L~lt~~~-~W~i~VDvlVi~s~gn~~dAiS~Ai~~AL~~T~lPkv~v~~dd~~  176 (288)
T KOG1612|consen   98 GDELVEELTSALQRVLNSLGSGVDLSKLQLTPGY-CWKIYVDVLVISSDGNLLDAISIAIYAALNNTRLPKVIVAFDDDG  176 (288)
T ss_pred             hhhHHHHHHHHHHHHHhCcCcccchhheeccCCe-eEEEEEeEEEEecCCCHHHHHHHHHHHHHhcccCCccccccccCC
Confidence            222 35777778887765         4566675 899999999999999999999999999999999981         


Q ss_pred             ------------------CCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceE
Q 026141          135 ------------------KHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGII  196 (243)
Q Consensus       135 ------------------~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i  196 (243)
                                        -.+|+-++++.+ +..++||||.+||+++.+.+.|.+++.+++...+.              
T Consensus       177 ~~~i~~s~~~Yd~~~~~~~~~P~ivtlskI-G~~~lVD~T~eEe~~a~s~l~Isv~a~givs~~r~--------------  241 (288)
T KOG1612|consen  177 EVEILLSDEEYDLMVKLVENVPLIVTLSKI-GTNMLVDPTAEEESVANSGLLISVSAGGIVSCTRS--------------  241 (288)
T ss_pred             ceeeccCcccchhhhhhcccCCEEEEEEee-cceEEccCCccHHHhhhcceEEEEecCcceEEEEE--------------
Confidence                              235666788886 88999999999999999999999888765544332              


Q ss_pred             EEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 026141          197 TSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLP  236 (243)
Q Consensus       197 ~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~~~  236 (243)
                        .+.|.+.++.+.+|++.+.+..+.++..+.+.|.+...
T Consensus       242 --VG~G~l~~s~i~~mle~~~~~~e~l~~~l~k~L~~~e~  279 (288)
T KOG1612|consen  242 --VGLGDLDPSSIPEMLEQGKAVVETLAPDLVKSLENEED  279 (288)
T ss_pred             --ecCCCCChhhHHHHHHHHHHHHHhhhHHHHHHhhhhhh
Confidence              24567999999999999999999999999998877544

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=100.00  E-value=3e-31  Score=253.96  Aligned_cols=199  Identities=19%  Similarity=0.188  Sum_probs=167.0

Q ss_pred             CCceEEeCCC-CCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEecCC--------------CCCCCCchHH
Q 026141           15 RPLACSCSIL-HRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPR--------------TGQIGKPEKE   79 (243)
Q Consensus        15 R~i~i~~~~l-~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~p~--------------~~~~~~~~~~   79 (243)
                      |++.+++|.+ .+|||||++++|+|+|+|+|++|.+.++.   .+.+.|+|+|.+.              .|.+++++.+
T Consensus         5 R~i~ie~G~la~~AdGSa~v~~G~T~VlatV~~~~~~~~~---~df~pL~vey~e~~~A~gkipg~f~kReg~p~~~eil   81 (684)
T TIGR03591         5 RTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKEG---QDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSEKETL   81 (684)
T ss_pred             ccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCCC---CceEeEEEEEEehhhhccCCCCCcccCCCCCCHHHHH
Confidence            7999999999 57999999999999999999998764332   3567888888641              1334556788


Q ss_pred             HHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChH-H-HHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEEeCCCH
Q 026141           80 YEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALL-P-CAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTK  157 (243)
Q Consensus        80 l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~-~-a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~lvDPt~  157 (243)
                      ++++|+|+|++++.. +| .|.|+|+++||++||+.. + +++||+++||++++|||+++++||+++++ +|.+++|||.
T Consensus        82 ~srlIdR~lrplfp~-~~-~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~i-dg~~ildPt~  158 (684)
T TIGR03591        82 TSRLIDRPIRPLFPK-GF-RNEVQVVATVLSYDPENDPDILAIIGASAALAISGIPFNGPIAAVRVGYI-DGQYVLNPTV  158 (684)
T ss_pred             HHHHHhhHHHHhcCC-CC-CceEEEEEEEEecCcCCchHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEE-CCEEEEcCCH
Confidence            999999999998653 33 499999999999999974 4 99999999999999999999999999997 8899999999


Q ss_pred             HHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 026141          158 LEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPG  237 (243)
Q Consensus       158 ~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~~~~  237 (243)
                      .|++.++..++++.+.+ .+.|.++                 ..+.++.+++.++++.|.+++++++++++++++++...
T Consensus       159 ~E~~~s~~~l~va~t~~-~i~mie~-----------------~~~~i~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~~~  220 (684)
T TIGR03591       159 DELEKSDLDLVVAGTKD-AVLMVES-----------------EAKELSEEVMLGAIEFGHEEIQPVIEAIEELAEEAGKE  220 (684)
T ss_pred             HHHhhCCceEEEEccCC-cEEEEEc-----------------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence            99999999988875432 3444432                 12369999999999999999999999999999887754

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=3.7e-31  Score=253.85  Aligned_cols=198  Identities=20%  Similarity=0.189  Sum_probs=168.0

Q ss_pred             CCCceEEeCCCC-CCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEecCC--------------CCCCCCchH
Q 026141           14 LRPLACSCSILH-RAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPR--------------TGQIGKPEK   78 (243)
Q Consensus        14 ~R~i~i~~~~l~-~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~p~--------------~~~~~~~~~   78 (243)
                      -|++.+++|.+. +|||||++++|+|+|+|+|++|.+.++   ..+.+.|+|+|.+.              .|.+++++.
T Consensus        13 ~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         13 GRTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPKE---GQDFFPLTVDYEEKTYAAGKIPGGFFKREGRPSEKET   89 (693)
T ss_pred             CccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCC---CCCeeeeEEEEEehhhhccCCCcccccCCCCCChHHH
Confidence            379999999996 699999999999999999999876322   24567788887641              133455678


Q ss_pred             HHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCCh-HH-HHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEEeCCC
Q 026141           79 EYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL-LP-CAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPT  156 (243)
Q Consensus        79 ~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~-~~-a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~lvDPt  156 (243)
                      +++++|+|+|++++.  +.++|.|+|+++||++||+. .+ +++||+++||.+++|||+++++||+++++ +|.+|+|||
T Consensus        90 l~srlIdR~lrplfp--~~~~~~i~I~~~VL~~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~i-~g~~ivdPt  166 (693)
T PRK11824         90 LTSRLIDRPIRPLFP--KGFRNEVQVVATVLSVDPENDPDILAMIGASAALSISGIPFNGPIAAVRVGYI-DGEFVLNPT  166 (693)
T ss_pred             HHHHHHhhhHHHhCC--CCCCeEEEEEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEE-CCEEEEcCC
Confidence            899999999999865  33579999999999999976 45 89999999999999999999999999997 889999999


Q ss_pred             HHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 026141          157 KLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKL  235 (243)
Q Consensus       157 ~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~~  235 (243)
                      .+|++.++..++++.+.+ .+.|.+.                 +.+.++.+++.++++.|.++++++++++++.+++..
T Consensus       167 ~~E~~~s~~~l~va~t~~-~i~mie~-----------------~~~~l~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~  227 (693)
T PRK11824        167 VEELEESDLDLVVAGTKD-AVLMVES-----------------EAKELSEEVMLEAIEFGHEAIQELIDAQEELAAEAG  227 (693)
T ss_pred             HHHHhhCcceEEEEEccC-ceEEEEC-----------------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            999999999998887654 4445442                 134699999999999999999999999999998877

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

Probab=99.97  E-value=1.9e-31  Score=218.71  Aligned_cols=210  Identities=22%  Similarity=0.269  Sum_probs=170.3

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cC---CCCCCCCc
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KP---RTGQIGKP   76 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p---~~~~~~~~   76 (243)
                      +|+|+|||+..|+|.+.++.|.++.+|||+.++.|+|.|+|++++ +...|..+.|++|.+-.||  +|   ..+++|++
T Consensus        34 e~~RpdgR~lgefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~-ei~epstdapdeg~Iv~n~~lpplcs~r~RpG~p  112 (298)
T KOG1613|consen   34 EGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKA-EIAEPSTDAPDEGDIVPNYALPPLCSSRFRPGPP  112 (298)
T ss_pred             cccCcchhhhhHHhhhheecCceeccCcHHHHhcCCcEEEEEeee-eecccccCCCCCcceeecccCCcccccCCCCCCC
Confidence            689999999999999999999999999999999999999999999 7889999999999987665  44   34556654


Q ss_pred             ---hHHHHHHHHHHH--------HhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCC----------
Q 026141           77 ---EKEYEIILKRTL--------QSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMK----------  135 (243)
Q Consensus        77 ---~~~l~~~l~~~l--------~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~----------  135 (243)
                         +.-+++.|..++        +.+|+..++..|.++.++.+|++||+++|+|.+|.++||.+-.+|..          
T Consensus       113 ~dea~viSq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG~~fDa~w~al~aAlknvklP~a~ide~~~~~~  192 (298)
T KOG1613|consen  113 TDEAQVISQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDGPVFDACWNALMAALKNVKLPRAFIDERASDLR  192 (298)
T ss_pred             chHHHHHHHHHHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCCcHHHHHHHHHHHHHhcCCCceeeecccchhhh
Confidence               345666665543        56899999999999999999999999999999999999999999921          


Q ss_pred             ---------------------Ccee-----EEEEE-EecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccC
Q 026141          136 ---------------------HLAV-----AICCC-SAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQ  187 (243)
Q Consensus       136 ---------------------~~~~-----avt~~-~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~  187 (243)
                                           ..+.     ..+.. ++.+..++.|||.+||..+++.++|++++++ .+.+.|.+    
T Consensus       193 ~t~e~~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~vl~~~li~adpT~eEE~l~~~~lTIvldss~n~v~l~k~G----  268 (298)
T KOG1613|consen  193 MTIEEIICDQTLTVPLMLNAENRAFASQNSDFSEEEVLDDVLIAADPTEEEETLITSTLTIVLDSSGNYVQLTKVG----  268 (298)
T ss_pred             hhHHHHHHhhhhcchhhhccccccccccCCCccHHHhhcceeEecCCCchhhhhhhceEEEEEcCCCCEEEEEecC----
Confidence                                 0000     11222 3434556699999999999999999998875 44444431    


Q ss_pred             CCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          188 GEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLR  228 (243)
Q Consensus       188 ~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~  228 (243)
                                  +.+..+++.++.|+++|..+++++.+.+.
T Consensus       269 ------------G~al~~~~~iK~c~elar~Rakelk~~~~  297 (298)
T KOG1613|consen  269 ------------GGALITPEMIKRCLELARVRAKELKTRFN  297 (298)
T ss_pred             ------------cccccCHHHHHHHHHHHHHHHHHHHHHhc
Confidence                        13367789999999999999999987764

>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=2.3e-28  Score=189.54  Aligned_cols=121  Identities=42%  Similarity=0.627  Sum_probs=105.4

Q ss_pred             CCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCC-CceEEEE--EecCCC-------CCCCCchHHHHH
Q 026141           13 QLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENP-EKASIEV--IWKPRT-------GQIGKPEKEYEI   82 (243)
Q Consensus        13 e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~-~~~~l~v--~~~p~~-------~~~~~~~~~l~~   82 (243)
                      |+|++.+++|++++++|||+|++|+|+|+|+|++|.+.+|+.+.+ .+|.+.|  ++.|..       +.++..++++++
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            799999999999999999999999999999999988776766633 3565554  556643       223334689999


Q ss_pred             HHHHHHHhhhhcCCCCceEEEEEEEEEeCCC-ChHHHHHHHHHHHHHHcCCC
Q 026141           83 ILKRTLQSICILTINPNTTTSVIIQVVHDDG-ALLPCAINAACAALVDAGIP  133 (243)
Q Consensus        83 ~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG-~~~~a~~~a~~~AL~~a~ip  133 (243)
                      +|+++|++.+.+++||+|.|+|+++||++|| |++++++||+++||+|+|||
T Consensus        81 ~l~~~l~~~~~~~~~~~~~i~v~v~vl~~dG~~~~~a~~~A~~~AL~~~~iP  132 (132)
T PF01138_consen   81 LLERALRSSILLEGYPRWQIHVDVQVLSDDGGNLLDAAINAACLALLDAGIP  132 (132)
T ss_dssp             HHHHHHHHTBSTTTTSSEEEEEEEEEEECSSSSHHHHHHHHHHHHHHHHTCS
T ss_pred             HHhhhccccccccccCceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCC
Confidence            9999999999999999999999999999999 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=99.95  E-value=1.9e-26  Score=222.18  Aligned_cols=199  Identities=17%  Similarity=0.159  Sum_probs=166.1

Q ss_pred             CCceEEeCCCC-CCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEecC--------------CCCCCCCchHH
Q 026141           15 RPLACSCSILH-RAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKP--------------RTGQIGKPEKE   79 (243)
Q Consensus        15 R~i~i~~~~l~-~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~p--------------~~~~~~~~~~~   79 (243)
                      |++.+++|.+. +|+||+.+++|+|.|+|+|..-+.  | .+..+...|.|+|.-              +.|+++..|..
T Consensus        89 ~~~~~etG~~a~qA~gav~v~~g~t~vl~t~~~~~~--~-~~~~dF~PLtV~y~Ek~~AaGkipggf~kREgrp~d~eiL  165 (891)
T PLN00207         89 RHILVETGHIGRQASGSVTVTDGETIVYTSVCLADV--P-SEPSDFFPLSVHYQERFSAAGRTSGGFFKREGRTKDHEVL  165 (891)
T ss_pred             EEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEeccC--C-CCCCCccceeEeeeeehhhcCccCCceeccCCCCChHHHH
Confidence            47899999886 599999999999999999986232  2 223456788998852              13445556789


Q ss_pred             HHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCC--hHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEEeCCCH
Q 026141           80 YEIILKRTLQSICILTINPNTTTSVIIQVVHDDGA--LLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTK  157 (243)
Q Consensus        80 l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~--~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~lvDPt~  157 (243)
                      ++++|+|+|++++....|+..+|  .++||++||+  ...+++|||++||+++||||+++++||++|++ +|.+|+|||.
T Consensus       166 ~sRlIdR~lRPlfp~~~~~etQI--~i~VLsaDg~~~pd~~AInAASaAL~~SgIP~~gpVaAVrVG~i-dg~~VlnPt~  242 (891)
T PLN00207        166 ICRLIDRPLRPTMPKGFYHETQI--LSWVLSYDGLHSPDSLAVTAAGIAVALSEVPNLKAIAGVRVGLI-GGKFIVNPTT  242 (891)
T ss_pred             HHHHHCccchhhccccCCCCcEE--EEEEEeeCCCCChhhHHHHHHHHHHHhhCCCccCceEEEEEEEE-CCEEEECCCH
Confidence            99999999999999988876555  5599999998  77999999999999999999999999999997 8999999999


Q ss_pred             HHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 026141          158 LEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHG-AMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLP  236 (243)
Q Consensus       158 ~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g-~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~~~  236 (243)
                      .|++.++..++++...+                   +++.+++.| .++.+++.++++.|.++++.+++++++.++++..
T Consensus       243 ~E~~~s~ldLvvagt~~-------------------~IvMIE~~a~e~see~l~~Al~~a~~aik~i~~~~~el~~~~gk  303 (891)
T PLN00207        243 KEMEESELDLIMAGTDS-------------------AILMIEGYCNFLPEEKLLEAVEVGQDAVRAICKEIEVLVKKCGK  303 (891)
T ss_pred             HHHhcCCeeEEEEEcCC-------------------eEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            99999998887776543                   233344455 5699999999999999999999999999988876


Q ss_pred             cc
Q 026141          237 GD  238 (243)
Q Consensus       237 ~~  238 (243)
                      ..
T Consensus       304 ~k  305 (891)
T PLN00207        304 PK  305 (891)
T ss_pred             CC
Confidence            53

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.88  E-value=5e-21  Score=181.45  Aligned_cols=210  Identities=16%  Similarity=0.075  Sum_probs=166.0

Q ss_pred             CCceEEeCCCC-CCCceEEEEe-CCeEEEEEEEcCccCCCCCCCCCceEEEEEec---------C-----CCCCCCCchH
Q 026141           15 RPLACSCSILH-RAHGSASWSQ-GDTKVLAAVYGPKAGTKKNENPEKASIEVIWK---------P-----RTGQIGKPEK   78 (243)
Q Consensus        15 R~i~i~~~~l~-~a~GSa~v~~-G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~---------p-----~~~~~~~~~~   78 (243)
                      |++.+++|.+. +||||+.+++ |+|.|+|++..-+.  + .+.-+...|.|+|.         |     +.|+++..+.
T Consensus        17 ~~~~~etG~~A~qA~Gav~v~~~G~t~vl~t~~~~~~--~-~~~~dF~PLtV~y~Ek~yA~GkiPggf~kREgrps~~ei   93 (719)
T TIGR02696        17 RTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQ--P-KDQFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAI   93 (719)
T ss_pred             EEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecCC--C-CCCCCCcceeEeeeehhhhcCccCCceeccCCCCChhhh
Confidence            47999999997 5999999999 99999999985232  2 22345678899885         2     1344555678


Q ss_pred             HHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCC--hHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEEeCCC
Q 026141           79 EYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGA--LLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPT  156 (243)
Q Consensus        79 ~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~--~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~lvDPt  156 (243)
                      ..+|+|+|.|+|++.. +| +..+||.++||+.|+.  .--.++||+++||.-++||+..++++|.+|.+ +|.+|++||
T Consensus        94 L~sRliDR~iRPLFp~-~~-~~e~qi~~~vls~D~~~~pdvla~~~ASaAl~iSdiPf~gPv~~vrVg~i-~g~~viNPt  170 (719)
T TIGR02696        94 LTCRLIDRPLRPSFVK-GL-RNEVQVVVTVLSLNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALI-DGQWVAFPT  170 (719)
T ss_pred             HHHHhhCCCCccCCCC-CC-CcceEEEEEEEEcCCCCChHHHHHHHHHHHHHhcCCCCCCceEEEEEEEE-CCEEEECcC
Confidence            9999999999999984 66 4789999999999984  57789999999999999999999999999997 999999999


Q ss_pred             HHHHhhccccEEEEeeC----CccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          157 KLEEQKMKGFAYLVFPN----SILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQ  232 (243)
Q Consensus       157 ~~Ee~~~~~~~~v~~~~----~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~  232 (243)
                      ..|.+.++..++++.+.    ++...|.++++....|     .........++++++.++|+.|.+.++.+++++++..+
T Consensus       171 ~~~~~~s~ldLvvagt~~~~~~~~i~MiE~~a~~~~~-----~~~~~~a~e~~e~~~~~Ai~~a~~~i~~~~~~~~~l~~  245 (719)
T TIGR02696       171 HEQLEGAVFDMVVAGRVLENGDVAIMMVEAEATEKTW-----DLVKGGAEAPTEEVVAEGLEAAKPFIKVLCRAQADLAE  245 (719)
T ss_pred             HHHHhhCeeeEEEEeeecCCCCccEEEEecCCccccc-----cccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999998875    2245555532111000     00001123799999999999999999999999999665


Q ss_pred             hhc
Q 026141          233 SKL  235 (243)
Q Consensus       233 ~~~  235 (243)
                      +..
T Consensus       246 ~~g  248 (719)
T TIGR02696       246 KAA  248 (719)
T ss_pred             HhC
Confidence            544

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.

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

Probab=99.86  E-value=3.8e-21  Score=174.08  Aligned_cols=208  Identities=21%  Similarity=0.312  Sum_probs=170.3

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEc--CccCCCCC--CCC---CceEEEEEecCCC----
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYG--PKAGTKKN--ENP---EKASIEVIWKPRT----   70 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~g--p~~~~~~~--~~~---~~~~l~v~~~p~~----   70 (243)
                      +|+|.|||..++.|+|.|+.+.++..+||+.|+-|+|+|+|+|+-  ++.....+  ..+   -++.|++.|.|.+    
T Consensus       356 ~gkR~DGR~ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~~~~~~FmLhY~FPPyat~Ev  435 (760)
T KOG1067|consen  356 EGKRCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNGINFMLHYEFPPYATNEV  435 (760)
T ss_pred             cccccCCcchhhhcccceecCccccccchhhhhcCceeEEEEEEcCCHHHhhhhhhhccCccCceEEEEeccCCcccccc
Confidence            589999999999999999999999999999999999999999984  11111111  122   2567888888852    


Q ss_pred             ---CCCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEec
Q 026141           71 ---GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAE  147 (243)
Q Consensus        71 ---~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~  147 (243)
                         +..+|+|.....+-+++|.+++. +.|| +.|+|.-.||+.||+.-.|++++-++||+|+|+|++..+++|++|+..
T Consensus       436 gkig~~nRRE~GhgaLAEkaL~~vlP-~dfP-ftIRv~SeVleSnGSsSMASvCGGslALmDaGvPv~a~vAGvaiGlvt  513 (760)
T KOG1067|consen  436 GKIGGLNRRELGHGALAEKALLPVLP-EDFP-FTIRVTSEVLESNGSSSMASVCGGSLALMDAGVPVSAHVAGVAIGLVT  513 (760)
T ss_pred             ccccCCcccccCchhHhhhhhhccCc-ccCc-eEEEEeeeeeecCCcchHHhhhcchhhhhhcCCccccccceeEEEeEe
Confidence               33456777777888999999988 6787 899999999999999999999999999999999999999999999963


Q ss_pred             C----------CeEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHH
Q 026141          148 S----------GYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGR  217 (243)
Q Consensus       148 ~----------~~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~  217 (243)
                      +          -.++-|-.-.|....+-.+-|+.+++|+.+                    .   .++++..+++++.|.
T Consensus       514 ~td~e~g~i~dyriltDIlGiEd~~GDMDFKiAGt~dGvTA--------------------~---gi~l~Iv~eal~~a~  570 (760)
T KOG1067|consen  514 KTDPEKGEIEDYRILTDILGIEDYNGDMDFKIAGTNDGVTA--------------------L---GIPLKIVMEALQKAR  570 (760)
T ss_pred             ccCcccCCcccceeehhhcchhhhcCCcceeeccccCccee--------------------c---CCcHHHHHHHHHhhh
Confidence            2          157777778888777777777766654321                    1   789999999999999


Q ss_pred             HHHHHHHHHHHHHHHhh
Q 026141          218 AASAKLSDFLRRSLQSK  234 (243)
Q Consensus       218 ~~~~~l~~~i~~~l~~~  234 (243)
                      .+-.+|.+.|.+.+...
T Consensus       571 ~ar~~Il~~m~k~i~~P  587 (760)
T KOG1067|consen  571 EARLQILDIMEKNINSP  587 (760)
T ss_pred             HHHHHHHHHHHhhcCCc
Confidence            99999999999877543

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

Probab=99.84  E-value=4.5e-20  Score=171.68  Aligned_cols=222  Identities=19%  Similarity=0.265  Sum_probs=185.4

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEE-cC-ccCCC----CCCCCCceEEEEEecCCC-----
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVY-GP-KAGTK----KNENPEKASIEVIWKPRT-----   70 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~-gp-~~~~~----~~~~~~~~~l~v~~~p~~-----   70 (243)
                      .++|+|||..++.||+.++.|++++.+||+.|..|.|+.++.++ |+ ....-    ..+...++.+..||.|++     
T Consensus       310 ~~vR~DGR~~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TLG~~~d~Qvid~l~~e~~krfm~hYNFPp~SvGE~g  389 (692)
T COG1185         310 GKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLHYNFPPFSVGETG  389 (692)
T ss_pred             CCcccCCCCcceeeeeeEEecCCCCccchhhhccCCCcceEEEEcCCcchhhhhhhccchhhhheeeeccCCCCCccccC
Confidence            47899999999999999999999999999999999999999987 32 11111    113456778899999964     


Q ss_pred             --CCCCCchHHHHHHHHHHHHhhhh-cCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEec
Q 026141           71 --GQIGKPEKEYEIILKRTLQSICI-LTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAE  147 (243)
Q Consensus        71 --~~~~~~~~~l~~~l~~~l~~~~~-~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~  147 (243)
                        +.++|+|.-..++-+|++.+.+. .+.|| +.|++.-.|++.+|+--.|.+++.++||+++|+|++.+++++..|++.
T Consensus       390 ~~g~p~RREiGHG~LA~Ral~~vlp~~e~fp-ytiRvVsEi~eSNGSsSmaSVCg~sLaLmdAGVPIk~pVAGIAMGLI~  468 (692)
T COG1185         390 RMGSPGRREIGHGALAERALAPVLPSEEEFP-YTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIK  468 (692)
T ss_pred             CCCCCCcccccCchhhHHHHhhhCCchhcCC-ceeeeeehhhcccCcccchhhhhhHHHHHhCCCcccccccchhcccee
Confidence              33567888888999999999988 45666 899999999999999999999999999999999999999999999986


Q ss_pred             CC---eEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHH
Q 026141          148 SG---YCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLS  224 (243)
Q Consensus       148 ~~---~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~  224 (243)
                      ++   .++-|-...|....+-.+-|+.+.+|+.+++..                ..-..++.+.+.+++..|..+..++.
T Consensus       469 eg~~~~vLsDI~G~EDhlGDMDFKVAGT~~GiTAlQMD----------------iKi~Git~eim~~AL~QAk~aRlhIL  532 (692)
T COG1185         469 EGDKYAVLSDILGDEDHLGDMDFKVAGTDDGITALQMD----------------IKIKGITKEIMKKALEQAKGARLHIL  532 (692)
T ss_pred             cCCceEeeccccccccccCCceeEEecCCCcceeeeee----------------eeecCCCHHHHHHHHHHHHHHHHHHH
Confidence            54   578888888888888888888877777666542                12357999999999999999999999


Q ss_pred             HHHHHHHHhhcccccc
Q 026141          225 DFLRRSLQSKLPGDLS  240 (243)
Q Consensus       225 ~~i~~~l~~~~~~~~~  240 (243)
                      ..|.+++.+...+--.
T Consensus       533 ~~M~~ai~~pr~els~  548 (692)
T COG1185         533 IVMNEAISEPRKELSP  548 (692)
T ss_pred             HHHHHHHhhhhhhhhc
Confidence            9999999887544433

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

Probab=99.79  E-value=9.9e-18  Score=156.15  Aligned_cols=197  Identities=20%  Similarity=0.172  Sum_probs=164.2

Q ss_pred             CCCceEEeCCCC-CCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEec---------C-----CCCCCCCchH
Q 026141           14 LRPLACSCSILH-RAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWK---------P-----RTGQIGKPEK   78 (243)
Q Consensus        14 ~R~i~i~~~~l~-~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~---------p-----~~~~~~~~~~   78 (243)
                      -|++.+++|.+. +|+|++.+++|+|.|++++.+..   + .+.-|.+.|.|+|.         |     +.|+|...+.
T Consensus        13 ~~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~---~-~~~~dF~PLtV~y~Ek~yaaGkiPGgf~kREGrpse~e~   88 (692)
T COG1185          13 GRTLTLETGKIARQANGAVLVRYGDTVVLATVVASK---P-KEGQDFFPLTVNYEEKTYAAGKIPGGFFKREGRPSEKEI   88 (692)
T ss_pred             CeeEEEEcchhhhhcCccEEEEECCeEEEEEEeecC---C-CCCCCccceeEeeeeehhccCcCCCcccccCCCCCccch
Confidence            388999999997 59999999999999999999733   2 33457788888874         3     2355556678


Q ss_pred             HHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCC--hHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEEeCCC
Q 026141           79 EYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGA--LLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPT  156 (243)
Q Consensus        79 ~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~--~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~lvDPt  156 (243)
                      ..+|+|+|.+++++.. +| +..++|..+|++.|+.  ..-.+++++++||.-++||+..+++++++|++ +|.++++||
T Consensus        89 L~sRLIDRpiRPlFp~-g~-~~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iPf~gpi~~vrvg~i-dg~~vlNPt  165 (692)
T COG1185          89 LTSRLIDRPIRPLFPK-GF-RNEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYI-DGIFVLNPT  165 (692)
T ss_pred             hhhhhcccccccccch-hh-ccceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCccCccceEEEEEE-CCEEEECCC
Confidence            9999999999999885 55 4789999999999986  46788999999999999999999999999997 999999999


Q ss_pred             HHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 026141          157 KLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKL  235 (243)
Q Consensus       157 ~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~~  235 (243)
                      .+|.+.++..++++.+.+. ..|.++                 ..-.++.+.+.+++..+.+..+.+++++++......
T Consensus       166 ~~e~~~s~lDlvVAGT~~a-V~MVE~-----------------~a~~l~E~~ml~Av~fg~~~~~~~~~~qe~l~~~~g  226 (692)
T COG1185         166 LEELEESKLDLVVAGTKDA-VNMVES-----------------EADELDEEVMLEAVEFGHEAIQSVINAQEELALEVG  226 (692)
T ss_pred             hHHhhhcceeeEecCChhh-hheeec-----------------ccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            9999999998888866542 222221                 123788999999999999999999999999877655

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

Probab=99.73  E-value=4.9e-17  Score=147.64  Aligned_cols=199  Identities=21%  Similarity=0.203  Sum_probs=161.0

Q ss_pred             CCCCceEEeCCCCC-CCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEec---------C-----CCCCCCCch
Q 026141           13 QLRPLACSCSILHR-AHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWK---------P-----RTGQIGKPE   77 (243)
Q Consensus        13 e~R~i~i~~~~l~~-a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~---------p-----~~~~~~~~~   77 (243)
                      -.|.+.+++|.+.+ |+||+.++.|+|.|+++|..  -.+|++  |+...|.|+|.         |     +.+.+..+|
T Consensus        54 GnR~i~~etGklaRfAngsvvv~~GeT~Vm~Tv~~--a~~PSp--~qFlPL~VdYqeK~aAvGRip~~fmRREg~tkdkE  129 (760)
T KOG1067|consen   54 GNREILFETGKLARFANGSVVVQMGETAVMTTVVL--ADKPSP--PQFLPLVVDYQEKFAAVGRIPGNFMRREGRTKDKE  129 (760)
T ss_pred             CCeEEEEecchhhhhcCCcEEEccCCeEEEEEEEe--cCCCCc--cccceEEEehhhhhhhhccCCCcccccccCCcchh
Confidence            46999999999986 99999999999999999986  233432  44567888874         2     123334456


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCC--hHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEEeCC
Q 026141           78 KEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGA--LLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDP  155 (243)
Q Consensus        78 ~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~--~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~lvDP  155 (243)
                      ....++|+|.+++++.. +| .+..++-..+|..||-  .-..++|++++||.-+.+|+...+.++.+|++ +|.++|+|
T Consensus       130 iL~~rLidrsirplfp~-g~-~~etqi~~n~Ls~dG~~~pdvlainaas~Al~lsdvpw~gpig~vRigLi-~Ge~vVNP  206 (760)
T KOG1067|consen  130 ILTGRLIDRPIRPLFPK-GF-YHETQILCNVLSSDGVHDPDVLAINAASAALSLSDVPWNGPIGAVRIGLI-DGEFVVNP  206 (760)
T ss_pred             heeeeccccccccCCcc-cc-hhHHHHHhhheecccccCchHHHHhHHHHHhhhccCCCCCceeeeEeeee-cceEEeCc
Confidence            67789999999999875 44 3677788888999984  56778999999999999999999999999997 99999999


Q ss_pred             CHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026141          156 TKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHG-AMSVDDYFHCLERGRAASAKLSDFLRRSLQSK  234 (243)
Q Consensus       156 t~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g-~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~  234 (243)
                      |.+|.+.++..++++...+ .                  +++++..+ .+..++|.++++.+.+.++++..-|.+..++.
T Consensus       207 T~kEmssS~Lnlvvagt~~-~------------------~vmle~~s~~i~qqdl~~Aikvg~~~~q~~i~~i~~L~k~~  267 (760)
T KOG1067|consen  207 TRKEMSSSQLNLVVAGTKS-Q------------------TVMLEGSSNNILQQDLLHAIKVGVKEAQQIIQGIERLAKKY  267 (760)
T ss_pred             chhhhhhccceeEEEeccc-e------------------EEEEEcccccccHHHHHHHHHhccHHHHHHHHHHHHHHHHh
Confidence            9999999999888886632 2                  33444444 78999999999999999999999999988876


Q ss_pred             ccc
Q 026141          235 LPG  237 (243)
Q Consensus       235 ~~~  237 (243)
                      ...
T Consensus       268 Gk~  270 (760)
T KOG1067|consen  268 GKQ  270 (760)
T ss_pred             Ccc
Confidence            554

>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=99.22  E-value=3.4e-11  Score=82.55  Aligned_cols=66  Identities=23%  Similarity=0.254  Sum_probs=53.4

Q ss_pred             CceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEeecCC-CCHHHHHHHH
Q 026141          136 HLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVTHGA-MSVDDYFHCL  213 (243)
Q Consensus       136 ~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~-~~~~~l~~~l  213 (243)
                      |+|+++|++++ ++.+|+|||.+||..+++.++++++.++ .|.+++.                 +.+. ++++++.+|+
T Consensus         1 ~~~~avt~~~i-~~~~v~Dpt~~Ee~~~~~~l~~~~~~~~~~~~~~~~-----------------~g~~~~~~~~l~~~i   62 (68)
T PF03725_consen    1 DPPVAVTVGII-DGELVVDPTAEEESLSDSSLTLAVDGTGNICTLQKS-----------------GGGSELSEDQLEEAI   62 (68)
T ss_dssp             SEEEEEEEEEE-TTEEEES--HHHHHHSSEEEEEEEETTSSEEEEEEE-----------------EESSEEEHHHHHHHH
T ss_pred             CCeEEEEEEEE-CCEEEECCCHHHHhhcCCcEEEEEECCCCEEEEEEc-----------------CCCCCCCHHHHHHHH
Confidence            57999999998 8899999999999999999999998765 4455442                 2333 9999999999


Q ss_pred             HHHHHH
Q 026141          214 ERGRAA  219 (243)
Q Consensus       214 ~~a~~~  219 (243)
                      ++|.++
T Consensus        63 ~~A~~~   68 (68)
T PF03725_consen   63 ELAKKA   68 (68)
T ss_dssp             HHHHHH
T ss_pred             HHHhcC
Confidence            999874

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 ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	243
3hkm_A	246	Crystal Structure Of Rice(Oryza Sativa) Rrp46 Lengt		3e-91
2nn6_D	237	Structure Of The Human Rna Exosome Composed Of Rrp4		2e-32
2ba0_F	258	Archaeal Exosome Core Length = 258		8e-19
3m7n_D	258	Archaeoglobus Fulgidus Exosome With Rna Bound To Th		1e-18
2nn6_B	249	Structure Of The Human Rna Exosome Composed Of Rrp4		2e-18
2pnz_A	249	Crystal Structure Of The P. Abyssi Exosome Rnase Ph		8e-18
2br2_B	248	Rnase Ph Core Of The Archaeal Exosome Length = 248		3e-17
3l7z_B	245	Crystal Structure Of The S. Solfataricus Archaeal E		3e-17
2je6_B	250	Structure Of A 9-Subunit Archaeal Exosome Length =		5e-17
2wnr_B	240	The Structure Of Methanothermobacter Thermautotroph		1e-16
3krn_A	222	Crystal Structure Of C. Elegans Cell-Death-Related		1e-13
4ifd_D	245	Crystal Structure Of An 11-subunit Eukaryotic Exoso		4e-12
4ifd_B	248	Crystal Structure Of An 11-subunit Eukaryotic Exoso		4e-12
2wp8_B	246	Yeast Rrp44 Nuclease Length = 246		6e-12
3cdj_A	559	Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCA		4e-07
3cdi_A	723	Crystal Structure Of E. Coli Pnpase Length = 723		4e-07
3gcm_A	549	Crystal Structure Of E. Coli Polynucleotide Phospho		5e-07
3h1c_A	549	Crystal Structure Of Polynucleotide Phosphorylase (		5e-07
2nn6_F	272	Structure Of The Human Rna Exosome Composed Of Rrp4		2e-05
1r6m_A	239	Crystal Structure Of The Trna Processing Enzyme Rna		4e-05
4am3_A	717	Crystal Structure Of C. Crescentus Pnpase Bound To		5e-05
4aid_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		5e-05
4aim_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		5e-05
1udo_A	255	Crystal Structure Of The Trna Processing Enzyme Rna		6e-05
1uds_A	255	Crystal Structure Of The Trna Processing Enzyme Rna		7e-05
1udn_A	255	Crystal Structure Of The Trna Processing Enzyme Rna		7e-05
1udq_A	255	Crystal Structure Of The Trna Processing Enzyme Rna		8e-05
1r6l_A	239	Crystal Structure Of The Trna Processing Enzyme Rna		2e-04

>pdb|3HKM|A Chain A, Crystal Structure Of Rice(Oryza Sativa) Rrp46 Length = 246

Iteration: 1
 Score =  331 bits (848), Expect = 3e-91,   Method: Compositional matrix adjust.
 Identities = 161/239 (67%), Positives = 192/239 (80%), Gaps = 1/239 (0%)
Query: 1   MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60
           ME  RADGRNPNQLRP +C+ + L RAHGSA W+QGDT VLAAVYGPK GT+K ENPEKA
Sbjct: 1   MEESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKA 60
Query: 61  SIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 120
           SIEV+WKP TGQIGK EKEYE+ LKRTLQSIC+LT++PNTTTSVI+QVV +DG+LLPCAI
Sbjct: 61  SIEVVWKPMTGQIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLLPCAI 120
Query: 121 NAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLP 180
           NA CAALV AGIP+KHLAVAI C   E G  ILD  K EEQ++K FA+LVFPNS  S   
Sbjct: 121 NACCAALVFAGIPLKHLAVAIGCGVLEDGEVILDTNKAEEQQLKSFAHLVFPNSRKSASS 180
Query: 181 EGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDL 239
           +  +  + E  E G+ITS+THG MS +DYF C+ERG AAS+++SDF+R +LQ + PGD+
Sbjct: 181 KEPNQKE-EDSERGLITSITHGVMSEEDYFSCIERGLAASSRISDFMRTTLQKQAPGDV 238

>pdb|2NN6|D Chain D, Structure Of The Human Rna Exosome Composed Of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40 Length = 237

Iteration: 1
 Score =  135 bits (340), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 71/164 (43%), Positives = 101/164 (61%), Gaps = 3/164 (1%)
Query: 9   RNPN-QLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWK 67
           R P   LR  AC  ++L R  GSAS+ QGDT VLA VYGP       E   KA++EVI +
Sbjct: 24  RGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILR 83
Query: 68  PRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAAL 127
           P+ G  G  EK  E +++ T +++ + T++P T+ +V++QVV D G+LL C +NAAC AL
Sbjct: 84  PKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMAL 143
Query: 128 VDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVF 171
           VDAG+PM+ L   + C     G  +LDPT  +E++ +  A L F
Sbjct: 144 VDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEAR--AVLTF 185

>pdb|2BA0|F Chain F, Archaeal Exosome Core Length = 258

Iteration: 1
 Score = 90.5 bits (223), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 56/186 (30%), Positives = 93/186 (50%), Gaps = 13/186 (6%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN-ENPEKASIE 63
           R DGR  ++LRP+    S+L RA GS     G  KV+AAV+GP+    ++ ++P KA I 
Sbjct: 17  RLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKAIIR 76
Query: 64  VIWK------PRTGQIGKPEKEYEI--ILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
             +           + G   +  EI  + K   +++ +  + P +   + ++V+  D   
Sbjct: 77  YRYNMAPFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGS 136
Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKG---FAYLVFP 172
               +NAA  ALVDAG+PMK +  ++    A+ G  +LDP K E+   +    FA+L+  
Sbjct: 137 RTACLNAASVALVDAGVPMKGMITSVAVGKAD-GQLVLDPMKEEDNFGEADMPFAFLIRN 195
Query: 173 NSILSV 178
             I S+
Sbjct: 196 GKIESI 201

>pdb|3M7N|D Chain D, Archaeoglobus Fulgidus Exosome With Rna Bound To The Active Site Length = 258

Iteration: 1
 Score = 89.7 bits (221), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 56/186 (30%), Positives = 93/186 (50%), Gaps = 13/186 (6%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN-ENPEKASIE 63
           R DGR  ++LRP+    S+L RA GS     G  KV+AAV+GP+    ++ ++P KA I 
Sbjct: 17  RLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKAIIR 76
Query: 64  VIWK------PRTGQIGKPEKEYEI--ILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
             +           + G   +  EI  + K   +++ +  + P +   + ++V+  D   
Sbjct: 77  YRYNMAPFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGS 136
Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKG---FAYLVFP 172
               +NAA  ALVDAG+PMK +  ++    A+ G  +LDP K E+   +    FA+L+  
Sbjct: 137 RTACLNAASVALVDAGVPMKGMITSVAVGKAD-GQLVLDPMKEEDNFGEADMPFAFLIRN 195
Query: 173 NSILSV 178
             I S+
Sbjct: 196 GKIESI 201

>pdb|2NN6|B Chain B, Structure Of The Human Rna Exosome Composed Of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40 Length = 249

Iteration: 1
 Score = 89.0 bits (219), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 51/169 (30%), Positives = 85/169 (50%), Gaps = 16/169 (9%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKA--GTKKNENPEKASI 62
           R DGR   +LR +     +  +A GSA   QG+TK LA VYGP    G++    P++A +
Sbjct: 17  RVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALV 76
Query: 63  EVIWKPRTGQIGKPEK---------EYEIILKRTLQSICILTINPNTTTSVIIQVVHDDG 113
              +   T   G+ ++         E  + L++T ++  +  ++P +   + +QV+  DG
Sbjct: 77  NCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADG 136
Query: 114 ALLPCAINAACAALVDAGIPMKHLAVAICCCSAE--SGYCILDPTKLEE 160
                 +NAA  A++DAGIPM+     +C CSA    G  + D + +EE
Sbjct: 137 GTYAACVNAATLAVLDAGIPMRDF---VCACSAGFVDGTALADLSHVEE 182

>pdb|2PNZ|A Chain A, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring Complexed With Udp And Gmp Length = 249

Iteration: 1
 Score = 87.0 bits (214), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 57/165 (34%), Positives = 81/165 (49%), Gaps = 10/165 (6%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN-ENPEKASIE 63
           R DGR   +LRP+     +L  A+GSA    G  K++AAVYGP+    K+ + P++A + 
Sbjct: 17  RIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILR 76
Query: 64  VIWK------PRTGQIGKPEKEYEI--ILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
           V +           + G   +  EI  ++K  L+   IL + P T   V I+V+  D   
Sbjct: 77  VRYNMAPFSVEERKKPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQADAGT 136
Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEE 160
               I AA  AL DAGIPM+ L VA C      G  +LD  K E+
Sbjct: 137 RVAGITAASLALADAGIPMRDL-VAACAAGKIEGEIVLDLNKEED 180

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

Iteration: 1
 Score = 85.1 bits (209), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 50/165 (30%), Positives = 84/165 (50%), Gaps = 10/165 (6%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNEN-PEKASIE 63
           R DGR P++LR +     +L  A GSA +  G+TK +AAVYGPK    ++ + P++A + 
Sbjct: 19  RTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLR 78
Query: 64  VIW--------KPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
           V +        + +     + E E   +++  L+S  ++ + P T   V  +++  D   
Sbjct: 79  VRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGS 138
Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEE 160
              ++ AA  AL DAGIPM+ L   +    A+ G  ILD  + E+
Sbjct: 139 RLVSLMAASLALADAGIPMRDLIAGVAVGKAD-GVIILDLNETED 182

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

Iteration: 1
 Score = 85.1 bits (209), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 50/165 (30%), Positives = 84/165 (50%), Gaps = 10/165 (6%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNEN-PEKASIE 63
           R DGR P++LR +     +L  A GSA +  G+TK +AAVYGPK    ++ + P++A + 
Sbjct: 16  RTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLR 75
Query: 64  VIW--------KPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
           V +        + +     + E E   +++  L+S  ++ + P T   V  +++  D   
Sbjct: 76  VRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGS 135
Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEE 160
              ++ AA  AL DAGIPM+ L   +    A+ G  ILD  + E+
Sbjct: 136 RLVSLMAASLALADAGIPMRDLIAGVAVGKAD-GVIILDLNETED 179

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

Iteration: 1
 Score = 84.3 bits (207), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 50/164 (30%), Positives = 83/164 (50%), Gaps = 10/164 (6%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNEN-PEKASIE 63
           R DGR P++LR +     +L  A GSA +  G+TK +AAVYGPK    ++ + P++A + 
Sbjct: 21  RTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLR 80
Query: 64  VIW--------KPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
           V +        + +     + E E   +++  L+S  ++ + P T   V  +++  D   
Sbjct: 81  VRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGS 140
Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLE 159
              ++ AA  AL DAGIPM+ L   +    A+ G  ILD  + E
Sbjct: 141 RLVSLMAASLALADAGIPMRDLIAGVAVGKAD-GVIILDLNETE 183

>pdb|2WNR|B Chain B, The Structure Of Methanothermobacter Thermautotrophicus Exosome Core Assembly Length = 240

Iteration: 1
 Score = 83.2 bits (204), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 56/167 (33%), Positives = 81/167 (48%), Gaps = 10/167 (5%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPK-AGTKKNENPEKASIE 63
           R DGR  ++LRPL     IL RA GS+    G  K+L AVYGP+ A  +K + P++A I 
Sbjct: 17  REDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIR 76
Query: 64  VIWK------PRTGQIGKPEKEYEI--ILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
             +           + G   +  EI  I    L+   IL   P +   V I+V+  +G  
Sbjct: 77  CRYNMAPFSVEERKRPGPDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEGGT 136
Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQK 162
               I AA  AL DAGIPM+ + VA C         +LD ++ E+++
Sbjct: 137 RCAGITAASVALADAGIPMRDMVVA-CAAGKVGDQVVLDLSEEEDKE 182

>pdb|3KRN|A Chain A, Crystal Structure Of C. Elegans Cell-Death-Related Nuclease 5(Crn-5) Length = 222

Iteration: 1
 Score = 73.2 bits (178), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/156 (29%), Positives = 78/156 (50%), Gaps = 9/156 (5%)
Query: 13  QLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQ 72
           +LR + C  S L  A GSA +SQG T + A+  GP        + E  ++++ ++   G 
Sbjct: 4   RLREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISYRANCG- 62
Query: 73  IGKPEKEYEI---ILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVD 129
               + ++ +   I+  TL +   L + P+TT SV +  + DDG++   AIN AC AL+D
Sbjct: 63  ----DNKFNVLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAVAINGACFALLD 118
Query: 130 AGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKG 165
            G+P + +   +     +    I+DPT  +E    G
Sbjct: 119 NGMPFETVFCGVLIVRVKDEL-IIDPTAKQEAASTG 153

>pdb|4IFD|D Chain D, Crystal Structure Of An 11-subunit Eukaryotic Exosome Complex Bound To Rna Length = 245

Iteration: 1
 Score = 68.2 bits (165), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 99/240 (41%), Gaps = 20/240 (8%)
Query: 4   DRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIE 63
           +R D     +   +     IL    GS+ +   DTKV+ +V GP     + E P + ++E
Sbjct: 12  NRLDSAEKKKKMSVQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALE 71
Query: 64  VIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVV---HDDGAL----L 116
           +I +P  G     EK  E  L+  L  +      P     +  Q++    D+       L
Sbjct: 72  IIVRPAKGVATTREKVLEDKLRAVLTPLITRHCYPRQLCQITCQILESGEDEAEFSLREL 131
Query: 117 PCAINAACAALVDAGIPMKHLAVAI-CCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI 175
            C INAA  ALVDAGI +  +  +I      ++   I+DPT  E+ K+            
Sbjct: 132 SCCINAAFLALVDAGIALNSMCASIPIAIIKDTSDIIVDPTA-EQLKIS----------- 179
Query: 176 LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKL 235
           LSV       V G  +   ++   ++G  + D  F  LE G     +L   +RR +Q  +
Sbjct: 180 LSVHTLALEFVNGGKVVKNVLLLDSNGDFNEDQLFSLLELGEQKCQELVTNIRRIIQDNI 239

>pdb|4IFD|B Chain B, Crystal Structure Of An 11-subunit Eukaryotic Exosome Complex Bound To Rna Length = 248

Iteration: 1
 Score = 68.2 bits (165), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 55/171 (32%), Positives = 78/171 (45%), Gaps = 13/171 (7%)
Query: 5   RADGRNPNQLRPLACSCSIL-HRAHGSASWSQGDTKVLAAVYGPKAGTKKNE-NPEKASI 62
           R DGR  N+LR    S +   H A GS+   QG+ K++  V GPK    K++ +  KA +
Sbjct: 15  RLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALL 74
Query: 63  EV---IWK----PRTGQIGKPEK---EYEIILKRTLQSICILTINPNTTTSVIIQVVHDD 112
            V   I K     R+    K E+   E +  L R  +   +L I P T   + I V+  D
Sbjct: 75  NVSVNITKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQD 134
Query: 113 GALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKM 163
           G ++   IN    AL+DAGI M      I     ++   +LD   LEE  M
Sbjct: 135 GGIMGSLINGITLALIDAGISMFDYISGISVGLYDT-TPLLDTNSLEENAM 184

>pdb|2WP8|B Chain B, Yeast Rrp44 Nuclease Length = 246

Iteration: 1
 Score = 67.8 bits (164), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 55/171 (32%), Positives = 78/171 (45%), Gaps = 13/171 (7%)
Query: 5   RADGRNPNQLRPLACSCSIL-HRAHGSASWSQGDTKVLAAVYGPKAGTKKNE-NPEKASI 62
           R DGR  N+LR    S +   H A GS+   QG+ K++  V GPK    K++ +  KA +
Sbjct: 13  RLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALL 72
Query: 63  EV---IWK----PRTGQIGKPEK---EYEIILKRTLQSICILTINPNTTTSVIIQVVHDD 112
            V   I K     R+    K E+   E +  L R  +   +L I P T   + I V+  D
Sbjct: 73  NVSVNINKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQD 132
Query: 113 GALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKM 163
           G ++   IN    AL+DAGI M      I     ++   +LD   LEE  M
Sbjct: 133 GGIMGSLINGITLALIDAGISMFDYISGISVGLYDT-TPLLDTNSLEENAM 182

>pdb|3CDJ|A Chain A, Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCATED Pnpase Length = 559

Iteration: 1
 Score = 51.6 bits (122), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 45/169 (26%), Positives = 73/169 (43%), Gaps = 25/169 (14%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN---------E 55
           R DGR  + +R L     +L R HGSA +++G+T+ L        GT ++         E
Sbjct: 321 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTA---TLGTARDAQVLDELMGE 377
Query: 56  NPEKASIEVIWKP----RTGQIGKPEKEYEIILKRTLQSICILTINPNT-----TTSVII 106
             +       + P     TG +G P K  EI   R L    +L + P+      T  V+ 
Sbjct: 378 RTDTFLFHYNFPPYSVGETGMVGSP-KRREIGHGR-LAKRGVLAVMPDMDKFPYTVRVVS 435
Query: 107 QVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESG--YCIL 153
           ++   +G+    ++  A  AL+DAG+P+K     I     + G  Y +L
Sbjct: 436 EITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVL 484

>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase Length = 723

Iteration: 1
 Score = 51.6 bits (122), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 45/169 (26%), Positives = 73/169 (43%), Gaps = 25/169 (14%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN---------E 55
           R DGR  + +R L     +L R HGSA +++G+T+ L        GT ++         E
Sbjct: 321 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTA---TLGTARDAQVLDELMGE 377
Query: 56  NPEKASIEVIWKP----RTGQIGKPEKEYEIILKRTLQSICILTINPNT-----TTSVII 106
             +       + P     TG +G P K  EI   R L    +L + P+      T  V+ 
Sbjct: 378 RTDTFLFHYNFPPYSVGETGMVGSP-KRREIGHGR-LAKRGVLAVMPDMDKFPYTVRVVS 435
Query: 107 QVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESG--YCIL 153
           ++   +G+    ++  A  AL+DAG+P+K     I     + G  Y +L
Sbjct: 436 EITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVL 484

>pdb|3GCM|A Chain A, Crystal Structure Of E. Coli Polynucleotide Phosphorylase Bound To Rna And Rnase E Length = 549

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 45/169 (26%), Positives = 73/169 (43%), Gaps = 25/169 (14%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN---------E 55
           R DGR  + +R L     +L R HGSA +++G+T+ L        GT ++         E
Sbjct: 315 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTA---TLGTARDAQVLDELMGE 371
Query: 56  NPEKASIEVIWKP----RTGQIGKPEKEYEIILKRTLQSICILTINPNT-----TTSVII 106
             +       + P     TG +G P K  EI   R L    +L + P+      T  V+ 
Sbjct: 372 RTDTFLFHYNFPPYSVGETGMVGSP-KRREIGHGR-LAKRGVLAVMPDMDKFPYTVRVVS 429
Query: 107 QVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESG--YCIL 153
           ++   +G+    ++  A  AL+DAG+P+K     I     + G  Y +L
Sbjct: 430 EITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVL 478

>pdb|3H1C|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase) Core Bound To Rnase E And Tungstate Length = 549

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 45/169 (26%), Positives = 73/169 (43%), Gaps = 25/169 (14%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN---------E 55
           R DGR  + +R L     +L R HGSA +++G+T+ L        GT ++         E
Sbjct: 315 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTA---TLGTARDAQVLDELMGE 371
Query: 56  NPEKASIEVIWKP----RTGQIGKPEKEYEIILKRTLQSICILTINPNT-----TTSVII 106
             +       + P     TG +G P K  EI   R L    +L + P+      T  V+ 
Sbjct: 372 RTDTFLFHYNFPPYSVGETGMVGSP-KRREIGHGR-LAKRGVLAVMPDMDKFPYTVRVVS 429
Query: 107 QVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESG--YCIL 153
           ++   +G+    ++  A  AL+DAG+P+K     I     + G  Y +L
Sbjct: 430 EITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVL 478

>pdb|2NN6|F Chain F, Structure Of The Human Rna Exosome Composed Of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40 Length = 272

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 54/177 (30%), Positives = 75/177 (42%), Gaps = 24/177 (13%)
Query: 9   RNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASI------ 62
           R+P +LRP+     +L +A GSA    G TKVL AV GP+           A        
Sbjct: 31  RDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPA 90
Query: 63  --------EVIWKPRTGQI------GKPEKEYEIILKRTLQSICILTINPNTTTSVIIQV 108
                   +    P  G+       G  E+E  + L+  L+    L   P     V   +
Sbjct: 91  ALRGRLLCDFRRAPFAGRRRRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALL 150
Query: 109 VHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYC---ILDPTKLEEQK 162
           + D G+ L  A+ AA  AL DAG+ M  L V  C  S   G     +LDPT+LEE++
Sbjct: 151 LEDGGSALAAALTAAALALADAGVEMYDLVVG-CGLSLAPGPAPTWLLDPTRLEEER 206

>pdb|1R6M|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph From Pseudomonas Aeruginosa In Complex With Phosphate Length = 239

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 46/182 (25%), Positives = 72/182 (39%), Gaps = 25/182 (13%)
Query: 3   VDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTK--KNENPEKA 60
           ++R  GR  +QLRP+  +      A GS     GDTKV+  V       +  K +     
Sbjct: 1   MNRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWL 60
Query: 61  SIEVIWKPRT-----------GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVV 109
           + E    PR+           G+ G    E + ++ R+L++   L+     T  +   V+
Sbjct: 61  TAEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVI 120
Query: 110 HDDGALLPCAINAACAALVDA-----------GIPMKHLAVAICCCSAESGYCILDPTKL 158
             DG     +I  A  AL+DA           G P+K + VA        G  +LD   L
Sbjct: 121 QADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQM-VAAVSVGIYQGVPVLDLDYL 179
Query: 159 EE 160
           E+
Sbjct: 180 ED 181

>pdb|4AM3|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rna Length = 717

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 39/168 (23%), Positives = 75/168 (44%), Gaps = 23/168 (13%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
           R DGR+   +RP+     IL R HGSA +++G+T+   A+     GT  +E    A +E 
Sbjct: 322 RIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQ---AIVVATLGTGDDEQFIDA-LEG 377
Query: 65  IWKP--------------RTGQIGKP---EKEYEIILKRTLQSICILTINPNTTTSVIIQ 107
            +K                TG++G P   E  +  +  R L+ +     +   T  ++ +
Sbjct: 378 TYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSE 437
Query: 108 VVHDDGALLPCAINAACAALVDAGIPMKH--LAVAICCCSAESGYCIL 153
           +   +G+     +  +  A++DAG+P+      +A+     + G+ +L
Sbjct: 438 ITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVL 485

>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E Recognition Peptide Length = 726

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 39/168 (23%), Positives = 75/168 (44%), Gaps = 23/168 (13%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
           R DGR+   +RP+     IL R HGSA +++G+T+   A+     GT  +E    A +E 
Sbjct: 331 RIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQ---AIVVATLGTGDDEQFIDA-LEG 386
Query: 65  IWKP--------------RTGQIGKP---EKEYEIILKRTLQSICILTINPNTTTSVIIQ 107
            +K                TG++G P   E  +  +  R L+ +     +   T  ++ +
Sbjct: 387 TYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSE 446
Query: 108 VVHDDGALLPCAINAACAALVDAGIPMKH--LAVAICCCSAESGYCIL 153
           +   +G+     +  +  A++DAG+P+      +A+     + G+ +L
Sbjct: 447 ITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVL 494

>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E Recognition Peptide Length = 726

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 39/168 (23%), Positives = 75/168 (44%), Gaps = 23/168 (13%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
           R DGR+   +RP+     IL R HGSA +++G+T+   A+     GT  +E    A +E 
Sbjct: 331 RIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQ---AIVVATLGTGDDEQFIDA-LEG 386
Query: 65  IWKP--------------RTGQIGKP---EKEYEIILKRTLQSICILTINPNTTTSVIIQ 107
            +K                TG++G P   E  +  +  R L+ +     +   T  ++ +
Sbjct: 387 TYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSE 446
Query: 108 VVHDDGALLPCAINAACAALVDAGIPMKH--LAVAICCCSAESGYCIL 153
           +   +G+     +  +  A++DAG+P+      +A+     + G+ +L
Sbjct: 447 ITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVL 494

>pdb|1UDO|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph R86a Mutant From Aquifex Aeolicus Length = 255

Iteration: 1
 Score = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 42/143 (29%), Positives = 59/143 (41%), Gaps = 13/143 (9%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVL--AAVY--------GPKAGTKKN 54
           R+DGR  +QLRP++     L    GS   S G TKV+  A+V         G   G    
Sbjct: 2   RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITA 61
Query: 55  EN---PEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
           E    P       I +   G+IG    E + ++ R +++   LT     T  V   V+  
Sbjct: 62  EYSMLPRATQQRTIRESVQGRIGGATHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQA 121
Query: 112 DGALLPCAINAACAALVDAGIPM 134
           DG     AI  A  A+ DA I +
Sbjct: 122 DGGTRTAAITGAFVAVADAIIKL 144

>pdb|1UDS|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph R126a Mutant From Aquifex Aeolicus Length = 255

Iteration: 1
 Score = 44.3 bits (103), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 42/143 (29%), Positives = 59/143 (41%), Gaps = 13/143 (9%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVL--AAVY--------GPKAGTKKN 54
           R+DGR  +QLRP++     L    GS   S G TKV+  A+V         G   G    
Sbjct: 2   RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITA 61
Query: 55  EN---PEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
           E    P       I +   G+IG    E + ++ R +++   LT     T  V   V+  
Sbjct: 62  EYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQA 121
Query: 112 DGALLPCAINAACAALVDAGIPM 134
           DG     AI  A  A+ DA I +
Sbjct: 122 DGGTATAAITGAFVAVADAIIKL 144

>pdb|1UDN|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph From Aquifex Aeolicus Length = 255

Iteration: 1
 Score = 43.9 bits (102), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 42/143 (29%), Positives = 59/143 (41%), Gaps = 13/143 (9%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVL--AAVY--------GPKAGTKKN 54
           R+DGR  +QLRP++     L    GS   S G TKV+  A+V         G   G    
Sbjct: 2   RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITA 61
Query: 55  EN---PEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
           E    P       I +   G+IG    E + ++ R +++   LT     T  V   V+  
Sbjct: 62  EYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQA 121
Query: 112 DGALLPCAINAACAALVDAGIPM 134
           DG     AI  A  A+ DA I +
Sbjct: 122 DGGTRTAAITGAFVAVADAIIKL 144

>pdb|1UDQ|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph T125a Mutant From Aquifex Aeolicus Length = 255

Iteration: 1
 Score = 43.9 bits (102), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 42/143 (29%), Positives = 59/143 (41%), Gaps = 13/143 (9%)
Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVL--AAVY--------GPKAGTKKN 54
           R+DGR  +QLRP++     L    GS   S G TKV+  A+V         G   G    
Sbjct: 2   RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITA 61
Query: 55  EN---PEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
           E    P       I +   G+IG    E + ++ R +++   LT     T  V   V+  
Sbjct: 62  EYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQA 121
Query: 112 DGALLPCAINAACAALVDAGIPM 134
           DG     AI  A  A+ DA I +
Sbjct: 122 DGGARTAAITGAFVAVADAIIKL 144

>pdb|1R6L|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph From Pseudomonas Aeruginosa Length = 239

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 48/189 (25%), Positives = 69/189 (36%), Gaps = 41/189 (21%)
Query: 4   DRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKV---------------------LA 42
           +R  GR  +QLRP+  +      A GS     GDTKV                     L 
Sbjct: 2   NRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLT 61
Query: 43  AVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTT 102
           A YG    +    N  +AS         G+ G    E + ++ R+L++   L+     T 
Sbjct: 62  AEYGXLPRSTGERNQREAS--------RGKQGGRTLEIQRLIGRSLRAALDLSKLGENTL 113
Query: 103 SVIIQVVHDDGALLPCAINAACAALVDA-----------GIPMKHLAVAICCCSAESGYC 151
            +   V+  DG     +I  A  AL+DA           G P+K   VA        G  
Sbjct: 114 YIDCDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQ-XVAAVSVGIYQGVP 172
Query: 152 ILDPTKLEE 160
           +LD   LE+
Sbjct: 173 VLDLDYLED 181

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	243
3hkm_A	246	OS03G0854200 protein; RNAse PH domain, phosphoryla	7e-75
2nn6_D	237	Exosome complex exonuclease RRP46; RNA, exosome, P	3e-66
3krn_A	222	Protein C14A4.5, confirmed by transcript evidence;	5e-61
2nn6_F	272	MTR3, exosome component 6; RNA, exosome, PM/SCL, p	5e-46
2wp8_B	246	Exosome complex component SKI6; nucleus, hydrolase	8e-39
2nn6_B	249	Exosome complex exonuclease RRP41; RNA, exosome, P	6e-30
2wnr_B	240	Probable exosome complex exonuclease 1; phosphate	1e-28
3b4t_A	262	Ribonuclease PH; RNAse, tRNA nucleotidyltransferas	4e-28
2po1_A	249	Probable exosome complex exonuclease 1; RNAse PH,	3e-26
1udn_A	255	Ribonuclease PH, RNAse PH; transferase, riken stru	5e-26
1r6l_A	239	Ribonuclease PH; beta-alpha-beta-alpha fold, hexam	6e-25
3dd6_A	255	Ribonuclease PH; exoribonuclease, tRNA maturation,	5e-24
2je6_B	250	RRP41, exosome complex exonuclease 1; nuclease, hy	1e-23
3m7n_D	258	Probable exosome complex exonuclease 1; exosome, R	4e-23
2nn6_C	278	Exosome complex exonuclease RRP43; RNA, exosome, P	4e-22
2wnr_A	271	Probable exosome complex exonuclease 2; phosphate	5e-22
2nn6_E	305	Exosome complex exonuclease RRP42; RNA, exosome, P	2e-21
2po1_B	277	Probable exosome complex exonuclease 2; RNAse PH,	4e-21
2je6_A	277	RRP42, exosome complex exonuclease 2; nuclease, hy	2e-20
2nn6_A	358	Polymyositis/scleroderma autoantigen 1; RNA, exoso	8e-20
3m7n_G	259	Probable exosome complex exonuclease 2; exosome, R	1e-19
1oys_A	245	Ribonuclease PH; transferase, tRNA processing; 2.4	1e-16
2wp8_A	305	Exosome complex component RRP45; nucleus, hydrolas	4e-15
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	5e-07
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	6e-07
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	8e-07
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	9e-07
3gme_A	549	Polyribonucleotide nucleotidyltransferase; protein	1e-06

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

 Score =  226 bits (578), Expect = 7e-75
 Identities = 161/242 (66%), Positives = 193/242 (79%), Gaps = 1/242 (0%)

Query: 1   MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKA 60
           ME  RADGRNPNQLRP +C+ + L RAHGSA W+QGDT VLAAVYGPK GT+K ENPEKA
Sbjct: 1   MEESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKA 60

Query: 61  SIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAI 120
           SIEV+WKP TGQIGK EKEYE+ LKRTLQSIC+LT++PNTTTSVI+QVV +DG+LLPCAI
Sbjct: 61  SIEVVWKPMTGQIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLLPCAI 120

Query: 121 NAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLP 180
           NA CAALV AGIP+KHLAVAI C   E G  ILD  K EEQ++K FA+LVFPNS  S   
Sbjct: 121 NACCAALVFAGIPLKHLAVAIGCGVLEDGEVILDTNKAEEQQLKSFAHLVFPNSRKSASS 180

Query: 181 EGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDLS 240
           +  +  + E  E G+ITS+THG MS +DYF C+ERG AAS+++SDF+R +LQ + PGD+ 
Sbjct: 181 KEPN-QKEEDSERGLITSITHGVMSEEDYFSCIERGLAASSRISDFMRTTLQKQAPGDVL 239

Query: 241 KA 242
           + 
Sbjct: 240 EH 241

>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 Length = 237

 Score =  204 bits (520), Expect = 3e-66
 Identities = 83/232 (35%), Positives = 122/232 (52%), Gaps = 18/232 (7%)

Query: 5   RADGRNPN-QLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIE 63
            +  R P   LR  AC  ++L R  GSAS+ QGDT VLA VYGP       E   KA++E
Sbjct: 20  GSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLE 79

Query: 64  VIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAA 123
           VI +P+ G  G  EK  E +++ T +++ + T++P T+ +V++QVV D G+LL C +NAA
Sbjct: 80  VILRPKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAA 139

Query: 124 CAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGS 183
           C ALVDAG+PM+ L   + C     G  +LDPT  +E++ +                   
Sbjct: 140 CMALVDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFAL------------ 187

Query: 184 SLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKL 235
                + +E  ++ S T G  S  +   CL   +AAS  +  F R SLQ + 
Sbjct: 188 -----DSVERKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYRESLQRRY 234

>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 =  190 bits (484), Expect = 5e-61
 Identities = 52/229 (22%), Positives = 90/229 (39%), Gaps = 17/229 (7%)

Query: 11  PNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRT 70
             +LR + C  S L  A GSA +SQG T + A+  GP        + E  ++++ ++   
Sbjct: 2   AGRLREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISYRANC 61

Query: 71  GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDA 130
           G           I+  TL +   L + P+TT SV +  + DDG++   AIN AC AL+D 
Sbjct: 62  G--DNKFNVLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAVAINGACFALLDN 119

Query: 131 GIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEP 190
           G+P + +   +     +    I+DPT  +E    G                     +   
Sbjct: 120 GMPFETVFCGVLIVRVK-DELIIDPTAKQEAASTGRVLFSV-------CKGSDGHPE--- 168

Query: 191 MEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDL 239
               +      G              + +++ + DF +  ++ KL  D 
Sbjct: 169 ----VCAMDAIGHWDFIQLEAAWSLAQPSASAIFDFYKTVMKRKLSVDE 213

>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 =  153 bits (389), Expect = 5e-46
 Identities = 56/254 (22%), Positives = 92/254 (36%), Gaps = 40/254 (15%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGT------------K 52
               R+P +LRP+     +L +A GSA    G TKVL AV GP+                
Sbjct: 27  APGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGG 86

Query: 53  KNENPEKASIEVIWK--------PRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSV 104
           +     +  +   ++         R    G  E+E  + L+  L+    L   P     V
Sbjct: 87  EAPAALRGRLLCDFRRAPFAGRRRRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEV 146

Query: 105 IIQVVHDDGALLPCAINAACAALVDAGIPMKHL--AVAICCCSAESGYCILDPTKLEEQK 162
              ++ D G+ L  A+ AA  AL DAG+ M  L     +      +   +LDPT+LEE+ 
Sbjct: 147 SALLLEDGGSALAAALTAAALALADAGVEMYDLVVGCGLSLAPGPAPTWLLDPTRLEEE- 205

Query: 163 MKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYF-HCLERGRAASA 221
                                  V   P+ + +   +  G   + + +   +  G     
Sbjct: 206 ----------------RAAAGLTVALMPVLNQVAGLLGSGEGGLTESWAEAVRLGLEGCQ 249

Query: 222 KLSDFLRRSLQSKL 235
           +L   L++SL    
Sbjct: 250 RLYPVLQQSLVRAA 263

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

 Score =  133 bits (338), Expect = 8e-39
 Identities = 59/251 (23%), Positives = 96/251 (38%), Gaps = 31/251 (12%)

Query: 5   RADGRNPNQLRPLACSCSIL-HRAHGSASWSQGDTKVLAAVYGPKAGTKKNE-NPEKASI 62
           R DGR  N+LR    S +   H A GS+   QG+ K++  V GPK    K++ +  KA +
Sbjct: 13  RLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALL 72

Query: 63  EV----------IWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDD 112
            V               + +  +   E +  L R  +   +L I P T   + I V+  D
Sbjct: 73  NVSVNINKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQD 132

Query: 113 GALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFP 172
           G ++   IN    AL+DAGI M    ++           +LD   LEE  M         
Sbjct: 133 GGIMGSLINGITLALIDAGISMFDY-ISGISVGLYDTTPLLDTNSLEENAM--------S 183

Query: 173 NSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQ 232
              L V+ +             +   +    + +D   + L  G A + ++ D +   L+
Sbjct: 184 TVTLGVVGKS----------EKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELR 233

Query: 233 SKLPGDLSKAE 243
                 +S A 
Sbjct: 234 KHAQKRVSNAS 244

>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 =  111 bits (279), Expect = 6e-30
 Identities = 50/170 (29%), Positives = 80/170 (47%), Gaps = 18/170 (10%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKA--GTKKNENPEKASI 62
           R DGR   +LR +     +  +A GSA   QG+TK LA VYGP    G++    P++A +
Sbjct: 17  RVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALV 76

Query: 63  ------------EVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVH 110
                       E   K R     +   E  + L++T ++  +  ++P +   + +QV+ 
Sbjct: 77  NCQYSSATFSTGER--KRRPHG-DRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQ 133

Query: 111 DDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEE 160
            DG      +NAA  A++DAGIPM+   V  C      G  + D + +EE
Sbjct: 134 ADGGTYAACVNAATLAVLDAGIPMRDF-VCACSAGFVDGTALADLSHVEE 182

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

 Score =  107 bits (270), Expect = 1e-28
 Identities = 55/165 (33%), Positives = 78/165 (47%), Gaps = 10/165 (6%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGT-KKNENPEKASI- 62
           R DGR  ++LRPL     IL RA GS+    G  K+L AVYGP+    +K + P++A I 
Sbjct: 17  REDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIR 76

Query: 63  -EVIWKPR-TGQIGKPE---KEYEI--ILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
                 P    +  +P    +  EI  I    L+   IL   P +   V I+V+  +G  
Sbjct: 77  CRYNMAPFSVEERKRPGPDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEGGT 136

Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEE 160
               I AA  AL DAGIPM+ + V  C         +LD ++ E+
Sbjct: 137 RCAGITAASVALADAGIPMRDM-VVACAAGKVGDQVVLDLSEEED 180

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

 Score =  106 bits (266), Expect = 4e-28
 Identities = 49/263 (18%), Positives = 82/263 (31%), Gaps = 41/263 (15%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
           R DGR  ++LRP+  +        GS     G TKVL      +   +  +      +  
Sbjct: 7   REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTA 66

Query: 65  ----------IWKPRTGQIGKP---EKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
                         R    G+     +E   ++ R+L++   L      T ++   V+  
Sbjct: 67  EYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQA 126

Query: 112 DGALLPCAINAACAALVDAGIPMKH------LAVAICCCSAES-----GYCILDPTKLEE 160
           DG     AI  A  AL DA   +             C  +A S     G   +D    E+
Sbjct: 127 DGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVVDGRIRVDLPYEED 186

Query: 161 QKMKGFAYLVFPNSILSVLPEGS-SLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAA 219
            + +    +V  ++       G+   +QG                +       L+    A
Sbjct: 187 SRAEVDMNVVATDT-------GTLVEIQGTGEGATF---------ARSTLDKLLDMALGA 230

Query: 220 SAKLSDFLRRSLQSKLPGDLSKA 242
              L    R +L    PG L + 
Sbjct: 231 CDTLFAAQRDALALPYPGVLPQG 253

>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 =  101 bits (253), Expect = 3e-26
 Identities = 59/165 (35%), Positives = 83/165 (50%), Gaps = 10/165 (6%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN-ENPEKASIE 63
           R DGR   +LRP+     +L  A+GSA    G  K++AAVYGP+    K+ + P++A + 
Sbjct: 17  RIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILR 76

Query: 64  VIWK--PR-TGQIGKPE---KEYEI--ILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
           V +   P    +  KP    +  EI  ++K  L+   IL + P T   V I+V+  D   
Sbjct: 77  VRYNMAPFSVEERKKPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQADAGT 136

Query: 116 LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEE 160
               I AA  AL DAGIPM+ L VA C      G  +LD  K E+
Sbjct: 137 RVAGITAASLALADAGIPMRDL-VAACAAGKIEGEIVLDLNKEED 180

>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 =  100 bits (252), Expect = 5e-26
 Identities = 52/256 (20%), Positives = 87/256 (33%), Gaps = 40/256 (15%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
           R+DGR  +QLRP++     L    GS   S G TKV+      +      +   +  I  
Sbjct: 2   RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITA 61

Query: 65  IW----------KPRTGQIGKP-EKEYEI--ILKRTLQSICILTINPNTTTSVIIQVVHD 111
            +            R    G+   + +EI  ++ R +++   LT     T  V   V+  
Sbjct: 62  EYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQA 121

Query: 112 DGALLPCAINAACAALVDAGI-----------PMKHLAVAICCCSAESGYCILDPTKLEE 160
           DG     AI  A  A+ DA I           P+K   VA       +   +LD    E+
Sbjct: 122 DGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDF-VAAVSVGIVNDRILLDLNFEED 180

Query: 161 QKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAAS 220
              +    +V   S    L E    V     E+           + D+    L+  +   
Sbjct: 181 SAAQVDMNVVGTGS--GRLSE----VHTMGEEYSF---------TKDELIKMLDLAQKGI 225

Query: 221 AKLSDFLRRSLQSKLP 236
            +L +  ++    +  
Sbjct: 226 NELIELQKKLYVIQDG 241

>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 = 97.9 bits (244), Expect = 6e-25
 Identities = 43/185 (23%), Positives = 68/185 (36%), Gaps = 29/185 (15%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
           R  GR  +QLRP+  +      A GS     GDTKV+  V       +  +   +  +  
Sbjct: 3   RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTA 62

Query: 65  IW----------KPRTGQIGKP---EKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
            +            R    GK      E + ++ R+L++   L+     T  +   V+  
Sbjct: 63  EYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQA 122

Query: 112 DGALLPCAINAACAALVDA-----------GIPMKHLAVAICCCSAE--SGYCILDPTKL 158
           DG     +I  A  AL+DA           G P+K +  A+   S     G  +LD   L
Sbjct: 123 DGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAV---SVGIYQGVPVLDLDYL 179

Query: 159 EEQKM 163
           E+   
Sbjct: 180 EDSAA 184

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

 Score = 95.5 bits (238), Expect = 5e-24
 Identities = 39/182 (21%), Positives = 61/182 (33%), Gaps = 28/182 (15%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASI-- 62
           R DGR   +LR +    + L    GS     GDTKV+ +    +          K  +  
Sbjct: 12  RVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVPPFMRGEGKGWVTA 71

Query: 63  ----------EVIWKPRTGQIGKP-EKEYEI--ILKRTLQSICILTINPNTTTSVIIQVV 109
                     +     R    GK   +  EI  ++ R L+++  L      T  +   V+
Sbjct: 72  EYAMIPRATEQR--TIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWIDCDVI 129

Query: 110 HDDGALLPCAINAACAALVD-----------AGIPMKHLAVAICCCSAESGYCILDPTKL 158
             DG     +I  A  A+V            + IP+K    A      E    +LD    
Sbjct: 130 QADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEEQGVVLDLNYA 189

Query: 159 EE 160
           E+
Sbjct: 190 ED 191

>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 = 94.6 bits (236), Expect = 1e-23
 Identities = 45/150 (30%), Positives = 72/150 (48%), Gaps = 17/150 (11%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN-ENPEKASI- 62
           R DGR P++LR +     +L  A GSA +  G+TK +AAVYGPK    ++   P++A + 
Sbjct: 21  RTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLR 80

Query: 63  -----------EVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
                      E   K       + E E   +++  L+S  ++ + P T   V  +++  
Sbjct: 81  VRYHMTPFSTDER--KNPAP--SRREIELSKVIREALESAVLVELFPRTAIDVFTEILQA 136

Query: 112 DGALLPCAINAACAALVDAGIPMKHLAVAI 141
           D      ++ AA  AL DAGIPM+ L   +
Sbjct: 137 DAGSRLVSLMAASLALADAGIPMRDLIAGV 166

>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 = 93.1 bits (232), Expect = 4e-23
 Identities = 44/150 (29%), Positives = 73/150 (48%), Gaps = 17/150 (11%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKN-ENPEKASIE 63
           R DGR  ++LRP+    S+L RA GS     G  KV+AAV+GP+    ++ ++P KA I 
Sbjct: 17  RLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKAIIR 76

Query: 64  VIWKPR-------TGQIGKP-----EKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
                R         +  +P       E   + K   +++ +  + P +   + ++V+  
Sbjct: 77  Y----RYNMAPFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQA 132

Query: 112 DGALLPCAINAACAALVDAGIPMKHLAVAI 141
           D       +NAA  ALVDAG+PMK +  ++
Sbjct: 133 DAGSRTACLNAASVALVDAGVPMKGMITSV 162

>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 = 91.2 bits (226), Expect = 4e-22
 Identities = 46/270 (17%), Positives = 84/270 (31%), Gaps = 61/270 (22%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
           R DGR   + R    +   +  A GSA    G+T V+  V   +      + P+K  +  
Sbjct: 25  RPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKA-EFAAPSTDAPDKGYVVP 83

Query: 65  IWKP--------RTGQIGKPEKEYEIILKRTLQSICI-----LTINPNTTTSVI---IQV 108
                       R+G  G+  +     +   +++  I     L I+P     V+   +  
Sbjct: 84  NVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLIC 143

Query: 109 VHDDGALLPCAINAACAALVDAGIP----------------------MKHLAVAICCCSA 146
           +  DG +L     A  AAL +  +P                      ++   VA      
Sbjct: 144 LDYDGNILDACTFALLAALKNVQLPEVTINEETALAEVNLKKKSYLNIRTHPVATSFAVF 203

Query: 147 ESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTH---GA 203
           +    I+DPT  EE    G   +V                     E G +  +       
Sbjct: 204 DDTLLIVDPTGEEEHLATGTLTIVM-------------------DEEGKLCCLHKPGGSG 244

Query: 204 MSVDDYFHCLERGRAASAKLSDFLRRSLQS 233
           ++      C+ R      ++   +   ++S
Sbjct: 245 LTGAKLQDCMSRAVTRHKEVKKLMDEVIKS 274

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

 Score = 90.5 bits (225), Expect = 5e-22
 Identities = 51/266 (19%), Positives = 97/266 (36%), Gaps = 60/266 (22%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASI-- 62
           R DGR+ ++ R ++    ++ +A GS+    G+T+++  V   + G    + PE   I  
Sbjct: 25  RIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKP-QIGEPFPDTPEMGVILT 83

Query: 63  EVIWKPRTG---QIGKP-EKEYEI--ILKRTL-QSICI----LTINPNTTTSVI---IQV 108
                P      + G P E+  E+  ++ R + +S  I    L I   +   ++   + +
Sbjct: 84  NSELLPMASPTFEPGPPDERSVELSRVVDRCIRESRMIDLEKLCIIEGSKVWMLFLDLHI 143

Query: 109 VHDDGALLPCAINAACAALVDAGIP--------------------MKHLAVAICCCSAES 148
           +  DG L   A+ A  AAL+D  IP                    +   A+         
Sbjct: 144 IDYDGNLFDAAVLATVAALLDTRIPAAEVEDGEVVINREKMQPLPVNRKALMCTFAKIG- 202

Query: 149 GYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTH---GAMS 205
              +LDP+  EE  +     +                      E G I ++     G ++
Sbjct: 203 NEIVLDPSLEEEDILTARISIGV-------------------TEEGSICAMQKGGEGPLT 243

Query: 206 VDDYFHCLERGRAASAKLSDFLRRSL 231
            DD    +        +L ++L +S+
Sbjct: 244 RDDVLKAVSIAVEKVPQLIEYLDKSM 269

>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 = 90.1 bits (223), Expect = 2e-21
 Identities = 44/273 (16%), Positives = 77/273 (28%), Gaps = 65/273 (23%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVY---GPKAGTKKNENPEKAS 61
           R DGR     R +     ++    GSA    G T +L  V    G     K NE   +  
Sbjct: 37  RVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFF 96

Query: 62  IEVI----WKPRTGQIGKPEKEYEIILKRTLQSICI-----LTINPNTTTSVI---IQVV 109
           ++       +           E    L R   +        L I+P     V+   + ++
Sbjct: 97  VDCSASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLL 156

Query: 110 HDDGALLPCAINAACAALVDAGIP---------------------------MKHLAVAIC 142
              G L      A  AAL +  IP                           ++++   + 
Sbjct: 157 ECGGNLFDAISIAVKAALFNTRIPRVRVLEDEEGSKDIELSDDPYDCIRLSVENVPCIVT 216

Query: 143 CCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVT-- 200
            C       ++D T  EE        +                        G++T +   
Sbjct: 217 LCKIG-YRHVVDATLQEEACSLASLLVSV-------------------TSKGVVTCMRKV 256

Query: 201 -HGAMSVDDYFHCLERGRAASAKLSDFLRRSLQ 232
             G++  +  F  +E G+     L   L+  + 
Sbjct: 257 GKGSLDPESIFEMMETGKRVGKVLHASLQSVVH 289

>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 = 88.2 bits (219), Expect = 4e-21
 Identities = 51/269 (18%), Positives = 96/269 (35%), Gaps = 61/269 (22%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASI-- 62
           R D R     RP+     ++ +A GSA    G T+VL  +     G    + P    +  
Sbjct: 27  RIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKT-SLGEPFPDTPNMGVMTT 85

Query: 63  EVIWKPRTGQI---GKP-EKEYEI--ILKRTL-QSICI----LTINPNTTTSVI---IQV 108
            V   P        G P E+  E+  ++ R + +S  +    + I P     V+   + V
Sbjct: 86  NVELVPLASPTFEPGPPDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVFIDVHV 145

Query: 109 VHDDGALLPCAINAACAALVDAGIP---------------------MKHLAVAICCCSAE 147
           +  DG L+     AA AAL++A +P                     ++ + V +      
Sbjct: 146 LDHDGNLMDAIGIAAIAALLNARVPKVRYNEETGEVETLDETEPLPVEKIPVPVTFAKIG 205

Query: 148 SGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVT---HGAM 204
               ++DP+  EE  M G   +                      E G I++V     GA 
Sbjct: 206 -NILVVDPSLDEELVMDGKITITT-------------------DETGHISAVQKSEGGAF 245

Query: 205 SVDDYFHCLERGRAASAKLSDFLRRSLQS 233
            +++  + +E     + ++   +  +++ 
Sbjct: 246 KLEEVMYAVETAFKKAEEIRKLILEAVEK 274

>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 = 86.3 bits (214), Expect = 2e-20
 Identities = 55/269 (20%), Positives = 90/269 (33%), Gaps = 65/269 (24%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKA--GTKKNENPEKASI 62
           R DGR     RPL+ +     +A GSA    G T VLA     K        + P + ++
Sbjct: 30  RQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGT---KLEIDKPYEDTPNQGNL 86

Query: 63  --EVIWKPRTGQI---GKP-EKEYEI--ILKRTL-QSICI----LTINPNTTTSVI---I 106
              V   P   +    G P E   E+  ++ R+L  S  +    L I P  +   +   +
Sbjct: 87  IVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDV 146

Query: 107 QVVHDDGALLPCAINAACAALVDAGIP---------------------MKHLAVAICCCS 145
            V+   G +L     A+ AAL +  +                      + +  V I    
Sbjct: 147 YVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVVTISVAK 206

Query: 146 AESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVT---HG 202
            +  Y ++DP   EE  M       +                        I  +     G
Sbjct: 207 VD-KYLVVDPDLDEESIMDAKISFSY-------------------TPDLKIVGIQKSGKG 246

Query: 203 AMSVDDYFHCLERGRAASAKLSDFLRRSL 231
           +MS+ D        R+ + KL + L++ L
Sbjct: 247 SMSLQDIDQAENTARSTAVKLLEELKKHL 275

>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 = 85.8 bits (212), Expect = 8e-20
 Identities = 41/271 (15%), Positives = 84/271 (30%), Gaps = 64/271 (23%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVY---GPKAGTKKNENPEKAS 61
           R DGR     R +  S       +G      G T+VL  V          +  E     +
Sbjct: 40  RLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFN 96

Query: 62  IEVIWKPRTGQIGKPEKEYEIILKRTLQSICI---------LTINPNTTTSVI---IQVV 109
           +E+            + +  + L R ++             L +        I   + ++
Sbjct: 97  LELSQMAAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLL 156

Query: 110 HDDGALLPCAINAACAALVDAGIP-----------------------MKHLAVAICCCSA 146
           + DG ++  A  AA  AL     P                       + H+ + +     
Sbjct: 157 NHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDPVPLSIHHMPICVSFAFF 216

Query: 147 ESG-YCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVT---HG 202
           + G Y ++DP + EE+ M G   +                      +H  I ++      
Sbjct: 217 QQGTYLLVDPNEREERVMDGLLVIAM-------------------NKHREICTIQSSGGI 257

Query: 203 AMSVDDYFHCLERGRAASAKLSDFLRRSLQS 233
            +  D    C +      A++++ + ++L++
Sbjct: 258 MLLKDQVLRCSKIAGVKVAEITELILKALEN 288

>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 = 84.0 bits (208), Expect = 1e-19
 Identities = 46/258 (17%), Positives = 92/258 (35%), Gaps = 57/258 (22%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKA--GTKKNENPEKA-- 60
           R DGR  ++ R +    +++ +A GSA    GDT+V+  V   K   G    + P++   
Sbjct: 23  RIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGV---KMQPGEPYPDTPDRGVI 79

Query: 61  SIEVIWKPRTG---QIGKP-EKEYEI--ILKRTL-QSICI----LTINPNTTTSVI---I 106
            +     P      + G P E   E+  ++ R + +S  +    L I       ++   I
Sbjct: 80  IVNAELVPLASPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDI 139

Query: 107 QVVHDDGALLPCAINAACAALVDAGIP-------------MKHLAVAICCCSAESGYCIL 153
             + DDG LL  +  AA AAL++  +P             ++ L V++          ++
Sbjct: 140 HALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLPVRDLPVSVTSLIVG-NKYLV 198

Query: 154 DPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGA---MSVDDYF 210
           DP++ E         +                      +   + ++       +    + 
Sbjct: 199 DPSREEMSVGDTTLTITT-------------------DKDDNVVAMQKSGGYLLDEKLFD 239

Query: 211 HCLERGRAASAKLSDFLR 228
             L+     + KL +  +
Sbjct: 240 ELLDVSINCARKLREKFK 257

>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 = 75.4 bits (186), Expect = 1e-16
 Identities = 34/161 (21%), Positives = 55/161 (34%), Gaps = 24/161 (14%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKA--GTKKNENPEKASI 62
           R DGR  ++LRP+      +    GS   + G+TKV+             +       + 
Sbjct: 2   RHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITA 61

Query: 63  EVIWKPR-TGQIGKPE--------KEYEI--ILKRTLQSICILTINPNTTTSVIIQVVHD 111
           E    P+ T Q    E        +  EI  ++ R L+++  L      T  +   V+  
Sbjct: 62  EYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQA 121

Query: 112 DGALLPCAINAACAALVDA-----------GIPMKHLAVAI 141
           DG     +I  A  A+  A             P+     AI
Sbjct: 122 DGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAI 162

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

 Score = 72.0 bits (176), Expect = 4e-15
 Identities = 41/284 (14%), Positives = 79/284 (27%), Gaps = 79/284 (27%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASI-- 62
           R DGR+ +Q R +  +     +  G  S   G+TKV   +   +      + P +     
Sbjct: 24  RLDGRSFDQFRDVEITFG---KEFGDVSVKMGNTKVHCRISC-QIAQPYEDRPFEGLFVI 79

Query: 63  EVIWKPRTG---QIGKPEKEYEIILKRTLQSICI---------LTINPNTTTSVI---IQ 107
                P  G   + G    E E++  R ++             L I   +    +   + 
Sbjct: 80  STEISPMAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVH 139

Query: 108 VVHDDGALLPCAINAACAALVDAGIP-----------------------MKHLAVAICCC 144
            +  DG  +  +  A  A L+    P                       + H+ + +   
Sbjct: 140 FLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQIIVHPVNEREPVPLGILHIPICVTFS 199

Query: 145 -------------SAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPM 191
                           S   I+D T  EE    G   +                      
Sbjct: 200 FFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTL-------------------N 240

Query: 192 EHGIITSVTH---GAMSVDDYFHCLERGRAASAKLSDFLRRSLQ 232
           ++  +  V+      M       C     +   K++D + + L+
Sbjct: 241 KNREVVQVSKAGGLPMDALTLMKCCHEAYSIIEKITDQILQLLK 284

>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens} Length = 630

 Score = 49.1 bits (118), Expect = 5e-07
 Identities = 16/40 (40%), Positives = 23/40 (57%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV 44
           R DGR+   LR ++C   +    HGSA + +G T+VL  V
Sbjct: 319 RCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTV 358

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Length = 726

 Score = 49.0 bits (118), Expect = 6e-07
 Identities = 15/40 (37%), Positives = 24/40 (60%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV 44
           R DGR+   +RP+     IL R HGSA +++G+T+ +   
Sbjct: 331 RIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVA 370

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723

 Score = 48.6 bits (117), Expect = 8e-07
 Identities = 15/40 (37%), Positives = 23/40 (57%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV 44
           R DGR  + +R L     +L R HGSA +++G+T+ L   
Sbjct: 321 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTA 360

>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 Length = 757

 Score = 48.4 bits (116), Expect = 9e-07
 Identities = 15/40 (37%), Positives = 22/40 (55%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV 44
           R DGR    +R LA     + R HGSA + +G+T++L   
Sbjct: 356 RIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVT 395

>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 Length = 549

 Score = 48.3 bits (116), Expect = 1e-06
 Identities = 15/40 (37%), Positives = 23/40 (57%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV 44
           R DGR  + +R L     +L R HGSA +++G+T+ L   
Sbjct: 315 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTA 354

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	243
3hkm_A	246	OS03G0854200 protein; RNAse PH domain, phosphoryla	100.0
2nn6_D	237	Exosome complex exonuclease RRP46; RNA, exosome, P	100.0
2wnr_B	240	Probable exosome complex exonuclease 1; phosphate	100.0
2po1_A	249	Probable exosome complex exonuclease 1; RNAse PH,	100.0
3m7n_D	258	Probable exosome complex exonuclease 1; exosome, R	100.0
2je6_B	250	RRP41, exosome complex exonuclease 1; nuclease, hy	100.0
2wp8_B	246	Exosome complex component SKI6; nucleus, hydrolase	100.0
2nn6_B	249	Exosome complex exonuclease RRP41; RNA, exosome, P	100.0
3dd6_A	255	Ribonuclease PH; exoribonuclease, tRNA maturation,	100.0
3b4t_A	262	Ribonuclease PH; RNAse, tRNA nucleotidyltransferas	100.0
2nn6_F	272	MTR3, exosome component 6; RNA, exosome, PM/SCL, p	100.0
1oys_A	245	Ribonuclease PH; transferase, tRNA processing; 2.4	100.0
1r6l_A	239	Ribonuclease PH; beta-alpha-beta-alpha fold, hexam	100.0
2po1_B	277	Probable exosome complex exonuclease 2; RNAse PH,	100.0
1udn_A	255	Ribonuclease PH, RNAse PH; transferase, riken stru	100.0
3m7n_G	259	Probable exosome complex exonuclease 2; exosome, R	100.0
2wnr_A	271	Probable exosome complex exonuclease 2; phosphate	100.0
2je6_A	277	RRP42, exosome complex exonuclease 2; nuclease, hy	100.0
2nn6_C	278	Exosome complex exonuclease RRP43; RNA, exosome, P	100.0
2nn6_A	358	Polymyositis/scleroderma autoantigen 1; RNA, exoso	100.0
2wp8_A	305	Exosome complex component RRP45; nucleus, hydrolas	100.0
3krn_A	222	Protein C14A4.5, confirmed by transcript evidence;	100.0
2nn6_E	305	Exosome complex exonuclease RRP42; RNA, exosome, P	100.0
3gme_A	549	Polyribonucleotide nucleotidyltransferase; protein	100.0
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	100.0
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	100.0
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	100.0
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	100.0
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	100.0
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.97
3gme_A	549	Polyribonucleotide nucleotidyltransferase; protein	99.96
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.96
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.96

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

Probab=100.00  E-value=4.7e-56  Score=377.66  Aligned_cols=239  Identities=67%  Similarity=1.051  Sum_probs=200.7

Q ss_pred             CCCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEecCCCCCCCCchHHH
Q 026141            1 MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEY   80 (243)
Q Consensus         1 ~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~p~~~~~~~~~~~l   80 (243)
                      |+|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|+||.+.+|+.+.|+++.++|+|+|+.|+++++++++
T Consensus         1 meg~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~g~~~~~~~~~~~~~~~~~~~~~P~~g~~~~~~~e~   80 (246)
T 3hkm_A            1 MEESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKASIEVVWKPMTGQIGKQEKEY   80 (246)
T ss_dssp             ----CTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEECCCEECCCTTSCSSSCEEEEEEECSSSCCCTTHHHH
T ss_pred             CCCcCCCCCCCCCcCCeEEEECCCCCCCeEEEEEECCeEEEEEEecCcCCCcccCCCccEEEEEEeCCCCCCCChhHHHH
Confidence            99999999999999999999999999999999999999999999999888888889999999999999889899999999


Q ss_pred             HHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEEeCCCHHHH
Q 026141           81 EIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEE  160 (243)
Q Consensus        81 ~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~lvDPt~~Ee  160 (243)
                      +++|+|+|+++|+.++||+|.|+|+++||++|||+++|++||+++||+++||||+++|+|++++++.++.+|+|||..|+
T Consensus        81 ~~li~r~l~~l~~~~~~~~~~I~v~~~VL~~dG~~~~aai~aa~~AL~dagiP~~~~v~avs~g~~~~g~~llDpt~~Ee  160 (246)
T 3hkm_A           81 EMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLEDGEVILDTNKAEE  160 (246)
T ss_dssp             HHHHHHHHHHHBCTTSSCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCBSSCEEEEEEEECTTSCEEESCCHHHH
T ss_pred             HHHHHHHHHHhcCccCCCcEEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCCCCceEEEEEEEEECCEEEECCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999878899999999999


Q ss_pred             hhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc
Q 026141          161 QKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDLS  240 (243)
Q Consensus       161 ~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~~~~~~~  240 (243)
                      ..+++.++++++.+++|.++|.+....+.| ..+.|++...|.++.+++.+|+++|.+++++|.++++++|+++..+++.
T Consensus       161 ~~~~~~~~va~~~~~i~~lq~~g~~~~~~~-~~~~i~~~~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~~~~  239 (246)
T 3hkm_A          161 QQLKSFAHLVFPNSRKSASSKEPNQKEEDS-ERGLITSITHGVMSEEDYFSCIERGLAASSRISDFMRTTLQKQAPGDVL  239 (246)
T ss_dssp             TTCSEEEEEEEEC---------------------CCCEEEEECEEHHHHHHHHHHHHHHHHHHHHHHHTTTC--------
T ss_pred             hcCCeeEEEEEeCCceEEEeeccccccccc-ccceeeeeccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhchhh
Confidence            999999999999889999988532222222 4567777778899999999999999999999999999999999988864

>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=4e-52  Score=352.34  Aligned_cols=219  Identities=37%  Similarity=0.629  Sum_probs=188.3

Q ss_pred             CCCCCCCCCCCC----CCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEecCCCCCCCCc
Q 026141            1 MEVDRADGRNPN----QLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKP   76 (243)
Q Consensus         1 ~~~~R~DGR~~~----e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~p~~~~~~~~   76 (243)
                      ++|+|+|||+++    |+|++.+++|++++++|||+|++|+|+|+|+|+||.+.+|+.+.|++|+|+++|.|+.|.++++
T Consensus        13 ~~~~R~DGR~~~~~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~g~~~~~~~~~~~~~g~l~~~~~p~~g~~~~~   92 (237)
T 2nn6_D           13 IRAENGTGSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVA   92 (237)
T ss_dssp             --------------CCCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECC------CCEEEEEEEECSSSCCCHH
T ss_pred             ccCccCCCCCCCCccccccceEEEeCCCCCCCEEEEEEECCcEEEEEEeCCCcccccccCCCcEEEEEEecCCCCCCCcc
Confidence            468999999999    9999999999999999999999999999999999988788888999999999999998888888


Q ss_pred             hHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEEeCCC
Q 026141           77 EKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPT  156 (243)
Q Consensus        77 ~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~lvDPt  156 (243)
                      +++++++|+++|+++|+.++||+|.|+|+++||++|||+++|++||+++||+|+||||+++|++++++++.++.+|+||+
T Consensus        93 e~~~~~li~r~l~~~i~~~~~p~~~I~I~~~VL~~dG~~~~aai~aa~~AL~da~iP~~~~v~avs~g~~~~~~~llDp~  172 (237)
T 2nn6_D           93 EKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACALDSDGTLVLDPT  172 (237)
T ss_dssp             HHHHHHHHHHHHHHHCGGGCSSSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCEEEEEEEECTTCCEEESCC
T ss_pred             HHHHHHHHHHHHHHHhchhcCCceEEEEEEEEEECCCcHHHHHHHHHHHHHHHcCCCcccCeeeEEEEEecCCcEEeCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999986789999999


Q ss_pred             HHHHhhccccEEEEeeCCc--cccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026141          157 KLEEQKMKGFAYLVFPNSI--LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSK  234 (243)
Q Consensus       157 ~~Ee~~~~~~~~v~~~~~~--~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~  234 (243)
                      ..||+.+.+.++++++.++  ++.+                   ...|.++.++|.+|+++|.+++++|+++++++++++
T Consensus       173 ~~Ee~~~~~~~~v~~~~~~~~i~~l-------------------q~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~  233 (237)
T 2nn6_D          173 SKQEKEARAVLTFALDSVERKLLMS-------------------STKGLYSDTELQQCLAAAQAASQHVFRFYRESLQRR  233 (237)
T ss_dssp             HHHHHHCSEEEEEEEETTTCCCCEE-------------------EEEESCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhccCCceEEEEcCCCCCEEEE-------------------EEeCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999998653  3332                   346789999999999999999999999999999998


Q ss_pred             cccc
Q 026141          235 LPGD  238 (243)
Q Consensus       235 ~~~~  238 (243)
                      .+++
T Consensus       234 ~~~~  237 (237)
T 2nn6_D          234 YSKS  237 (237)
T ss_dssp             TCC-
T ss_pred             ccCC
Confidence            7653

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

Probab=100.00  E-value=7.6e-49  Score=332.82  Aligned_cols=216  Identities=27%  Similarity=0.442  Sum_probs=190.7

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCC-CCCCCCceEEEEEe--cCCC------CC
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTK-KNENPEKASIEVIW--KPRT------GQ   72 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~-~~~~~~~~~l~v~~--~p~~------~~   72 (243)
                      +|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|+||.+..| ..+.|++|.|.++|  .|++      +.
T Consensus        14 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~g~l~~~~~~~p~a~~~~~~~~   93 (240)
T 2wnr_B           14 PSVREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIRCRYNMAPFSVEERKRPG   93 (240)
T ss_dssp             -CCCTTSCCTTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECCSSSSCCSSSCEEEEEEEECTTSSSSCCCSS
T ss_pred             cCccCCCCCcCCccCeEEEeCCCCCCCEEEEEEECCeEEEEEEEcCCCCCcccccCCCcEEEEEEEEeCCCCcCCccCCC
Confidence            589999999999999999999999999999999999999999999887655 45789999987765  4753      23


Q ss_pred             CCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEE
Q 026141           73 IGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCI  152 (243)
Q Consensus        73 ~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~l  152 (243)
                      +++++++++++|+++|++.+.++.||+|.|+|+++||++|||+++|++||+++||+|+|+||+++|+++|++++ ++.++
T Consensus        94 ~~~~~~~l~~ll~r~l~~~i~l~~~p~~~I~i~~~VL~~dG~~~~a~i~aa~~AL~da~iP~~~~v~avs~g~~-~~~~l  172 (240)
T 2wnr_B           94 PDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEGGTRCAGITAASVALADAGIPMRDMVVACAAGKV-GDQVV  172 (240)
T ss_dssp             CCHHHHHHHHHHHHHHGGGBCGGGSTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTTCCBSSCCEEEEEEES-SSSEE
T ss_pred             CChhHHHHHHHHHHHHHHhcCHHHCCCcEEEEEEEEEeCCCCHHHHHHHHHHHHHHHcCCccccceeeEEEEEE-CCEEE
Confidence            45568899999999999999899999999999999999999999999999999999999999999999999998 77999


Q ss_pred             eCCCHHHHhhccccEEEEe-eCCc-cccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          153 LDPTKLEEQKMKGFAYLVF-PNSI-LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRS  230 (243)
Q Consensus       153 vDPt~~Ee~~~~~~~~v~~-~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~  230 (243)
                      +|||..||..+++.++|++ +..+ ++.+                   ...|.++.+++.+|+++|.+++++|++.++++
T Consensus       173 ~Dp~~~Ee~~~~~~~~v~~~~~~~~i~~l-------------------q~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~  233 (240)
T 2wnr_B          173 LDLSEEEDKEGQADVPVAILPRTREITLL-------------------QSDGNLTPEEFERALDLAVEGCLRIHEVQKEA  233 (240)
T ss_dssp             ESCCSHHHHSCSEEEEEEEETTTTEEEEE-------------------EEEECBCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eCCCHHHhccCCceEEEEEECCCCCEEEE-------------------EEEcccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999998 4333 3333                   34678999999999999999999999999999


Q ss_pred             HHhhccc
Q 026141          231 LQSKLPG  237 (243)
Q Consensus       231 l~~~~~~  237 (243)
                      ++++.++
T Consensus       234 l~~~~~~  240 (240)
T 2wnr_B          234 LRKRYGE  240 (240)
T ss_dssp             HHC----
T ss_pred             HHHhhcC
Confidence            9987653

>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=9.4e-49  Score=333.90  Aligned_cols=220  Identities=27%  Similarity=0.408  Sum_probs=197.1

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCC-CCCCCCceEEEEEec--CCC------CC
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTK-KNENPEKASIEVIWK--PRT------GQ   72 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~-~~~~~~~~~l~v~~~--p~~------~~   72 (243)
                      +|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|+||.+..| ..+.|++|.|.++|.  |++      +.
T Consensus        14 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~g~l~v~~~~~p~a~~~~~~~~   93 (249)
T 2po1_A           14 NGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILRVRYNMAPFSVEERKKPG   93 (249)
T ss_dssp             SSCBTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEEECSSGGGCCSSSCEEEEEEEECGGGSSSCCCSS
T ss_pred             cCccCCCCCcccccCEEEEeCCcCCCCEEEEEEECCcEEEEEEEcCcccCcccccCCCceEEEEEEEeCCcccccccCCC
Confidence            589999999999999999999999999999999999999999999887665 567899999887764  532      22


Q ss_pred             CCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEE
Q 026141           73 IGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCI  152 (243)
Q Consensus        73 ~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~l  152 (243)
                      +++++.+++++|+++|++.+.++.||+|.|+|+++||++|||+++|+++|+++||+|+||||+++|+++|++++ ++.++
T Consensus        94 ~~~~~~~~s~li~r~l~~~i~l~~~p~~~i~I~~~VL~~dG~~~~aai~aa~~AL~da~iP~~~~v~avs~g~~-~~~~l  172 (249)
T 2po1_A           94 PDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKI-EGEIV  172 (249)
T ss_dssp             CCHHHHHHHHHHHHHHGGGBCGGGSTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTTCCBSSCCEEEEEEEE-TTEEE
T ss_pred             CCHHHHHHHHHHHHHHHhhccHHHCCCCEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCccCceEEEEEEEE-CCEEE
Confidence            45567899999999999999889999999999999999999999999999999999999999999999999998 88999


Q ss_pred             eCCCHHHHhhccccEEEEe-eCCc-cccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          153 LDPTKLEEQKMKGFAYLVF-PNSI-LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRS  230 (243)
Q Consensus       153 vDPt~~Ee~~~~~~~~v~~-~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~  230 (243)
                      +|||..||..+++.++|++ +..+ ++.++                   ..|.++.+++.+|+++|.+++++++++++++
T Consensus       173 ~Dp~~~Ee~~~~~~l~va~~~~~~~i~~~~-------------------~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~  233 (249)
T 2po1_A          173 LDLNKEEDNYGEADVPVAIMPLKNDITLLQ-------------------MDGYLTKDEFIEAVKLAIKGAKAVYQKQREA  233 (249)
T ss_dssp             ESCCHHHHHTCSEEEEEEEEGGGTEEEEEC-------------------CEECCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ecCcHHHhccCCceEEEEEECCCCCEEEEE-------------------EEcccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999998 4433 44433                   3568999999999999999999999999999


Q ss_pred             HHhhccccccc
Q 026141          231 LQSKLPGDLSK  241 (243)
Q Consensus       231 l~~~~~~~~~~  241 (243)
                      ++++..++..+
T Consensus       234 l~~~~~~~~~~  244 (249)
T 2po1_A          234 LKEKYLKIAQE  244 (249)
T ss_dssp             HHHHHHHHTCC
T ss_pred             HHHHHHhhhhh
Confidence            99988776654

>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=1.7e-48  Score=333.32  Aligned_cols=219  Identities=26%  Similarity=0.408  Sum_probs=193.2

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCC-CCCCCceEEEEEe--cCCC------CC
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKK-NENPEKASIEVIW--KPRT------GQ   72 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~-~~~~~~~~l~v~~--~p~~------~~   72 (243)
                      +|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|+||.+..|. .+.|++|+|.++|  .|++      +.
T Consensus        14 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~g~l~~~~~~~P~s~~~r~~~~   93 (258)
T 3m7n_D           14 DGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKAIIRYRYNMAPFSVEERKRPG   93 (258)
T ss_dssp             TTEETTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEEECSSSTTCCSSSCEEEEEEEECGGGSSSCCCSS
T ss_pred             cCCCCCCCCcCCccCeEEEECCCCCCCceEEEEECCeEEEEEEEcccCCCCccccCCCceEEEEEEEeCCcccccccCCC
Confidence            5899999999999999999999999999999999999999999999876654 4789999988765  4532      23


Q ss_pred             CCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEE
Q 026141           73 IGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCI  152 (243)
Q Consensus        73 ~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~l  152 (243)
                      +++++.+++++|+|+|++++.++.||+|.|+|+++||++|||+++|++||+++||+|+||||+++|++++++++ ++.+|
T Consensus        94 ~~~re~ei~~li~r~l~~~i~~~~~p~~~I~V~~~VL~~DG~~~~Aai~aa~lAL~dagiP~~~~v~avsvg~i-~~~~l  172 (258)
T 3m7n_D           94 PDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKA-DGQLV  172 (258)
T ss_dssp             CCHHHHHHHHHHHHHHHTTBCGGGSTTEEEEEEEEEEECCTTHHHHHHHHHHHHHHHTTCCBSSEEEEEEEEEE-TTEEE
T ss_pred             CCHHHHHHHHHHHHHHHhhcCHHhCCceEEEEEEEEEEcCCCHHHHHHHHHHHHHHhcCCCCCCceEEEEEEEE-CCEEE
Confidence            45567899999999999999889999999999999999999999999999999999999999999999999998 88999


Q ss_pred             eCCCHHHHhhccccEEEEe-eCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          153 LDPTKLEEQKMKGFAYLVF-PNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSL  231 (243)
Q Consensus       153 vDPt~~Ee~~~~~~~~v~~-~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l  231 (243)
                      +|||..|+..+++.++|++ +..+.               ..+.+.++..|.++.+++.+|+++|.+++++|++++++++
T Consensus       173 lDpt~~Ee~~~~~d~~va~~~~~~~---------------~~~I~~lq~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l  237 (258)
T 3m7n_D          173 LDPMKEEDNFGEADMPFAFLIRNGK---------------IESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAI  237 (258)
T ss_dssp             ESCCHHHHHHSSEEEEEEEEEETTE---------------EEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ECCCHHHHhccCceEEEEEEcCCCC---------------CCCEEEEEecCCcCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999998 54300               0122223346799999999999999999999999999999


Q ss_pred             Hhhcc
Q 026141          232 QSKLP  236 (243)
Q Consensus       232 ~~~~~  236 (243)
                      +++..
T Consensus       238 ~~~~~  242 (258)
T 3m7n_D          238 LRRYI  242 (258)
T ss_dssp             HHHHH
T ss_pred             HHHhh
Confidence            98654

>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=6.9e-48  Score=328.78  Aligned_cols=218  Identities=27%  Similarity=0.406  Sum_probs=193.2

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCC-CCCCCCceEEEEEe--cCCC------CC
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTK-KNENPEKASIEVIW--KPRT------GQ   72 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~-~~~~~~~~~l~v~~--~p~~------~~   72 (243)
                      +|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|+||.+..| ..+.|+++.|.|+|  .|++      +.
T Consensus        18 ~~~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~g~~e~~~~~~~~~~~g~l~v~~~~~p~a~~~~~~g~   97 (250)
T 2je6_B           18 DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDERKNPA   97 (250)
T ss_dssp             TSCBTTSCCTTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECSSGGGSCSSSCEEEEEEEECTTSSSSCCCSS
T ss_pred             CCccCCCCCccCcCCeEEEeCCCCCCCeEEEEEECCcEEEEEEEcccccccccccCCCcEEEEEEEEeCCCccCCccCCC
Confidence            589999999999999999999999999999999999999999999887554 55678999988776  4542      23


Q ss_pred             CCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEE
Q 026141           73 IGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCI  152 (243)
Q Consensus        73 ~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~l  152 (243)
                      +++++++++++|+++|++++.++.||+|.|+|+++||++|||+++|+++|+++||+++||||+++|++++++++ ++.+|
T Consensus        98 ~~~~e~~~s~li~r~l~~~i~~~~~p~~~i~I~~~VL~~DG~~~~aai~aa~~AL~~a~iP~~~~v~avsvg~~-~~~~l  176 (250)
T 2je6_B           98 PSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKA-DGVII  176 (250)
T ss_dssp             CCHHHHHHHHHHHHHHHTTBCGGGSTTEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCBSSCCEEEEEEEE-TTEEE
T ss_pred             CChhHHHHHHHHHHHHHhhcCHhhCCCcEEEEEEEEEeCCCCHHHHHHHHHHHHHHhcCCCccCceEEEEEEEE-CCEEE
Confidence            45567899999999999999999999999999999999999999999999999999999999999999999997 88999


Q ss_pred             eCCCHHHHhhccccEEEEee-CCc-cccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          153 LDPTKLEEQKMKGFAYLVFP-NSI-LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRS  230 (243)
Q Consensus       153 vDPt~~Ee~~~~~~~~v~~~-~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~  230 (243)
                      +|||..|+..+++.++|++. ..+ ++.                   ++..|.++.+++.+|+++|.+++++++++++++
T Consensus       177 ~Dpt~~Ee~~~~~~l~va~~~~~~~i~~-------------------v~~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~  237 (250)
T 2je6_B          177 LDLNETEAMWGEADMPIAMMPSLNQVTL-------------------FQLNGSMTPDEFRQAFDLAVKGINIIYNLEREA  237 (250)
T ss_dssp             ESCCHHHHHHSSEEEEEEEEGGGTEEEE-------------------EEEEECBCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eCCCHHHHhcCCceEEEEEECCCCCEEE-------------------EEEEcccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999984 333 332                   334678999999999999999999999999999


Q ss_pred             HHhhccccc
Q 026141          231 LQSKLPGDL  239 (243)
Q Consensus       231 l~~~~~~~~  239 (243)
                      ++++..++.
T Consensus       238 l~~~~~~~~  246 (250)
T 2je6_B          238 LKSKYVEFK  246 (250)
T ss_dssp             HHGGGC---
T ss_pred             HHHHHhhhh
Confidence            999877653

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

Probab=100.00  E-value=6.5e-48  Score=328.22  Aligned_cols=220  Identities=26%  Similarity=0.321  Sum_probs=189.0

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCC-CceEEEEeCCeEEEEEEEcCccC-CCCCCCCCceEEEEEe--cCCC-------
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRA-HGSASWSQGDTKVLAAVYGPKAG-TKKNENPEKASIEVIW--KPRT-------   70 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a-~GSa~v~~G~T~Vi~~V~gp~~~-~~~~~~~~~~~l~v~~--~p~~-------   70 (243)
                      +|+|+|||+++|+|++.+++|.++++ +|||+|++|+|+|+|+|+||.+. +|..+.|+++.|.|+|  .|++       
T Consensus        10 ~~~R~DGR~~~e~R~i~i~~g~l~~aa~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~~g~l~v~~~~~p~a~~~~~~r   89 (246)
T 2wp8_B           10 EGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNINKFSKFERSKS   89 (246)
T ss_dssp             TSCCTTSCCTTCCCCEEEEECSCTTTCSEEEEEEETTEEEEEEEEEEEC------CCSSSEEEEEEEEEC----------
T ss_pred             cCccCCCCCcCCccCeEEEeCCCCCCCCceEEEEECCeEEEEEEEecCCcccccccCCCcEEEEEEEEeCCccccccccc
Confidence            68999999999999999999999999 99999999999999999998774 3456789999998776  4532       


Q ss_pred             -CCCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCC
Q 026141           71 -GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESG  149 (243)
Q Consensus        71 -~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~  149 (243)
                       +.+++++.+++++|+++|++++.++.||+|.|+|+++||++|||+++|++||+++||+++||||+++|+++++|++ ++
T Consensus        90 ~g~~~~~~~~~s~li~r~l~~~i~~~~~p~~~I~i~~~VL~~dG~~~~aai~aa~~AL~~a~iP~~~~v~avs~g~~-~~  168 (246)
T 2wp8_B           90 SHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLY-DT  168 (246)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHBCTTTSCSEEEEEEEEEEECCSCHHHHHHHHHHHHHHHHTCCBSSCEEEEEEEEE-TT
T ss_pred             CCCCChhHHHHHHHHHHHHHHhhhHHHCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHHcCCcccCceeEEEEEEE-CC
Confidence             2234567899999999999999999999999999999999999999999999999999999999999999999998 88


Q ss_pred             eEEeCCCHHHHhhccccEEEEee-CCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          150 YCILDPTKLEEQKMKGFAYLVFP-NSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLR  228 (243)
Q Consensus       150 ~~lvDPt~~Ee~~~~~~~~v~~~-~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~  228 (243)
                      .+++|||..|+ .+++.++|++. ..+                  +.+.++..|.++.+++.+|+++|.+++++|+++++
T Consensus       169 ~~l~Dp~~~Ee-~~~~~l~v~~~~~~~------------------~i~~i~~~g~~~~~~l~~~l~~A~~~~~~i~~~~~  229 (246)
T 2wp8_B          169 TPLLDTNSLEE-NAMSTVTLGVVGKSE------------------KLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMD  229 (246)
T ss_dssp             EEESSCCHHHH-HHSEEEEEEEETTSS------------------CEEEEEECSCEEHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEECCCchhh-ccCceEEEEEeCCCC------------------CEEEEEecCCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999 99999999985 333                  12223346799999999999999999999999999


Q ss_pred             HHHHhhccccccc
Q 026141          229 RSLQSKLPGDLSK  241 (243)
Q Consensus       229 ~~l~~~~~~~~~~  241 (243)
                      ++++++..+++..
T Consensus       230 ~~l~~~~~~~~~~  242 (246)
T 2wp8_B          230 EELRKHAQKRVSN  242 (246)
T ss_dssp             HHHHHHHHCC---
T ss_pred             HHHHHHHHhhhhh
Confidence            9999998877654

>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=9.9e-48  Score=327.59  Aligned_cols=218  Identities=24%  Similarity=0.371  Sum_probs=192.6

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCC--CCCCCceEEEEEe--cCCC-------
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKK--NENPEKASIEVIW--KPRT-------   70 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~--~~~~~~~~l~v~~--~p~~-------   70 (243)
                      +|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|+||.+.+..  .+.|++++|.++|  .|++       
T Consensus        14 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~g~~~~~~~~~~~~~~~g~l~~~~~~~p~a~~~~~~~   93 (249)
T 2nn6_B           14 QGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATFSTGERKRR   93 (249)
T ss_dssp             TTBCSSSSCTTSCCCEEEEESCSSSSSEEEEEEESSCEEEEEEEEEEECCSSSCCCCCSSCCEEEEEEECTTTSSSCCCT
T ss_pred             CCcCCCCCCcCCcCCeEEEeCCCCCCCeEEEEEECCeEEEEEEEccCCccccccccCCCcEEEEEEEEcCCCcccccccC
Confidence            5899999999999999999999999999999999999999999998664322  3578999887765  4632       


Q ss_pred             CCCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCe
Q 026141           71 GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGY  150 (243)
Q Consensus        71 ~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~  150 (243)
                      +.+++++.+++++|+++|++++.++.||+|.|+|+++||++|||+++|++||+++||+|+||||+++|+++|++++ ++.
T Consensus        94 ~~~~~~~~~~~~ll~r~l~~~i~~~~~p~~~I~i~~~VL~~dG~~~~A~i~aa~~AL~da~iPl~~~v~avs~g~~-~~~  172 (249)
T 2nn6_B           94 PHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFV-DGT  172 (249)
T ss_dssp             TTSTHHHHHHHHHHHHHHHHTTCGGGCTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTCCCCSSCCEEEEEEEE-TTE
T ss_pred             CCCCHhHHHHHHHHHHHHHHhcCHHHCCCcEEEEEEEEEeCCCCHHHHHHHHHHHHHHhcCCcccCCeeeEEEEEE-CCe
Confidence            2234567899999999999999999999999999999999999999999999999999999999999999999998 889


Q ss_pred             EEeCCCHHHHhhccccEEEEee-CCc-cccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          151 CILDPTKLEEQKMKGFAYLVFP-NSI-LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLR  228 (243)
Q Consensus       151 ~lvDPt~~Ee~~~~~~~~v~~~-~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~  228 (243)
                      +|+|||..||..+++.++|+++ ..+ ++.                   +...|.++.+++.+|+++|.+++++|+++++
T Consensus       173 ~l~Dp~~~Ee~~~~~~~~v~~~~~~~~i~~-------------------lq~~g~~~~~~l~~~l~~A~~~~~~i~~~~~  233 (249)
T 2nn6_B          173 ALADLSHVEEAAGGPQLALALLPASGQIAL-------------------LEMDARLHEDHLERVLEAAAQAARDVHTLLD  233 (249)
T ss_dssp             EEESCCHHHHTSSCCCEEEEEETTTTEEEE-------------------EEECSCCBTTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEECCChHHhccCCcEEEEEEECCCCCEEE-------------------EEEECCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999986 433 333                   3346899999999999999999999999999


Q ss_pred             HHHHhhccccc
Q 026141          229 RSLQSKLPGDL  239 (243)
Q Consensus       229 ~~l~~~~~~~~  239 (243)
                      ++++++..+..
T Consensus       234 ~~l~~~~~~~~  244 (249)
T 2nn6_B          234 RVVRQHVREAS  244 (249)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHhhh
Confidence            99998876543

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

Probab=100.00  E-value=3.3e-46  Score=318.78  Aligned_cols=216  Identities=20%  Similarity=0.229  Sum_probs=190.6

Q ss_pred             CCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cCCC----------
Q 026141            3 VDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KPRT----------   70 (243)
Q Consensus         3 ~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p~~----------   70 (243)
                      .+|.|||+++|+|++.+++|++++++|||+|++|+|+|+|+|++|...+++...|++|+|.|+|  .|++          
T Consensus        10 ~~~~~~R~~~e~R~i~i~~g~~~~A~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~v~~~~~P~a~~~~~~Re~~   89 (255)
T 3dd6_A           10 HMRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVPPFMRGEGKGWVTAEYAMIPRATEQRTIRESS   89 (255)
T ss_dssp             -CCCCSCCTTCCCCEEEEESCSSSSSEEEEEEETTEEEEEEEEEESCCCGGGTTSSCCEEEEEEEECTTSSSSCCCCCCC
T ss_pred             ccccCCCCcCCCCCEEEEECCCCCCCeEEEEEECCeEEEEEEEecCCCCCCCCCCCceEEEEEEEECCCccccccccccc
Confidence            5799999999999999999999999999999999999999999976654566789999988776  4632          


Q ss_pred             -CCCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHc-----------CCCCCCce
Q 026141           71 -GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDA-----------GIPMKHLA  138 (243)
Q Consensus        71 -~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a-----------~ip~~~~~  138 (243)
                       |.+++++.+++++|+|+|++++.++.+|+|.|+|+++||++|||+++|++||+++||+++           +|||+++|
T Consensus        90 ~g~~~~~~~eisrli~r~lr~~i~~~~l~~~~I~V~~~VL~~DG~~~~aai~aa~~AL~~a~~p~~~~g~~~~iPl~~~v  169 (255)
T 3dd6_A           90 KGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWIDCDVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYL  169 (255)
T ss_dssp             -CCCCHHHHHHHHHHHHHHHHHBCHHHHCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTSSSSCCBSSCE
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhcChhhcCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHHhhhhhhhcCcccCCCccCce
Confidence             334455789999999999999998888999999999999999999999999999999999           99999999


Q ss_pred             eEEEEEEecCCeEE-eCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEee-cCCCCHHHHHHHHHH
Q 026141          139 VAICCCSAESGYCI-LDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVT-HGAMSVDDYFHCLER  215 (243)
Q Consensus       139 ~avt~~~~~~~~~l-vDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~-~g~~~~~~l~~~l~~  215 (243)
                      ++++++++ ++.++ +|||..|+..++..++|+++.++ +|.+++.                 + .+.++.+++.+|+++
T Consensus       170 ~avsvg~i-~g~~vllDpt~~Ee~~~~~~l~Va~~~~g~i~~vq~~-----------------g~~~~~~~~~l~~~l~~  231 (255)
T 3dd6_A          170 AATSVGIV-EEQGVVLDLNYAEDSKADVDMNVIMTGKGQFVEVQGT-----------------GEEATFSRAQLNELLDA  231 (255)
T ss_dssp             EEEEEEEE-TTTEEEESCCHHHHHTEEEEEEEEEETTSCEEEEEEE-----------------ESSSCCCHHHHHHHHHH
T ss_pred             eEEEEEEE-CCEEEEeCCCHHHHhhcCceEEEEEcCCCcEEEEEec-----------------CCCCCcCHHHHHHHHHH
Confidence            99999998 66677 99999999999999999998876 5544321                 2 358999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhhcc
Q 026141          216 GRAASAKLSDFLRRSLQSKLP  236 (243)
Q Consensus       216 a~~~~~~l~~~i~~~l~~~~~  236 (243)
                      |.+++++|++++++++++-..
T Consensus       232 A~~~~~~i~~~~~~~l~~~~~  252 (255)
T 3dd6_A          232 AEQGIFQLIDIQKEALGDIVS  252 (255)
T ss_dssp             HHHHHHHHHHHHHHHHGGGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999987654

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

Probab=100.00  E-value=6.6e-46  Score=318.52  Aligned_cols=221  Identities=21%  Similarity=0.230  Sum_probs=191.6

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cCCC---------
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KPRT---------   70 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p~~---------   70 (243)
                      .|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|++|...++....++++.|.|+|  .|++         
T Consensus         4 ~g~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~~~~~Re~   83 (262)
T 3b4t_A            4 VSKREDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTAEYAMLPSATHSRSDRES   83 (262)
T ss_dssp             -CCSTTSCCTTCCCCEEEEETSSSSSSEEEEEEETTEEEEEEEEEEESCC----CCSCCEEEEEEEECGGGSSSCCCCHH
T ss_pred             CCcCCCCCCCcCcCCeEEEeCCcCCCCeEEEEEECCCEEEEEEEecCcCCCccCCCCceEEEEEEEeCCCcccccccccc
Confidence            47899999999999999999999999999999999999999999966543333447889888776  4531         


Q ss_pred             --CCCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHc------------CCCCCC
Q 026141           71 --GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDA------------GIPMKH  136 (243)
Q Consensus        71 --~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a------------~ip~~~  136 (243)
                        |.+++++++++++|+|+|++++.++.+|+|.|+|+++||++|||+++|++||+++||+++            +|||++
T Consensus        84 ~~G~~~~~~~~isrli~r~lr~~i~~~~l~~~~I~i~~~VL~~DG~~~~aai~aa~~AL~~a~~~~~~~~~~~~~ip~~~  163 (262)
T 3b4t_A           84 VRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSC  163 (262)
T ss_dssp             HHTSCCHHHHHHHHHHHHHHHTTBCHHHHCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTCCSSSCCBCS
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHhcCHhHCCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhhccCCccccCCcccC
Confidence              234556789999999999999998889999999999999999999999999999999999            999999


Q ss_pred             ceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEeec-CCCCHHHHHHHHH
Q 026141          137 LAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVTH-GAMSVDDYFHCLE  214 (243)
Q Consensus       137 ~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~-g~~~~~~l~~~l~  214 (243)
                      +|++++++++ ++.+|+|||.+|+..+++.++|+++.++ +|.+++.                 +. +.++.++|.+|++
T Consensus       164 ~v~avsvg~~-~g~~l~Dpt~~Ee~~~~~~l~va~~~~g~i~~i~~~-----------------g~~~~~~~~~l~~~l~  225 (262)
T 3b4t_A          164 AIAAVSVGVV-DGRIRVDLPYEEDSRAEVDMNVVATDTGTLVEIQGT-----------------GEGATFARSTLDKLLD  225 (262)
T ss_dssp             CEEEEEEEEE-TTEEEESCCHHHHTTCSEEEEEEEETTSCEEEEEEC-----------------SSCCCBCHHHHHHHHH
T ss_pred             ceeEEEEEEE-CCEEEECCCHHHHhccCceEEEEEcCCCCEEEEEee-----------------CCCCCcCHHHHHHHHH
Confidence            9999999998 8899999999999999999999998764 4444331                 11 4899999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhhcccccc
Q 026141          215 RGRAASAKLSDFLRRSLQSKLPGDLS  240 (243)
Q Consensus       215 ~a~~~~~~l~~~i~~~l~~~~~~~~~  240 (243)
                      +|.+++++|+++++++++++..+...
T Consensus       226 ~A~~~~~~i~~~~~~~l~~~~~~~~~  251 (262)
T 3b4t_A          226 MALGACDTLFAAQRDALALPYPGVLP  251 (262)
T ss_dssp             HHHHHHHHHHHHHHHHHTSCCSSCCC
T ss_pred             HHHHHHHHHHHHHHHHHhcchhccCc
Confidence            99999999999999999988776543

>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=3.3e-47  Score=328.30  Aligned_cols=223  Identities=26%  Similarity=0.353  Sum_probs=187.9

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCC------------CCCceEEEEE--ec
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNE------------NPEKASIEVI--WK   67 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~------------~~~~~~l~v~--~~   67 (243)
                      +++|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+||.+.++..+            .++++.+.|+  +.
T Consensus        24 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~g~l~v~~~~~  103 (272)
T 2nn6_F           24 EEEAPGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAALRGRLLCDFRRA  103 (272)
T ss_dssp             -----CCCCSSCCCCCCCCCSCCSSSSEEECCCSSSCEEEEEEEEEECC-------------------CBCEEEEEEEEC
T ss_pred             cCccCCCCCccccCCeEEEeCCCCCCCeEEEEEeCCeEEEEEEECCCcccccccccccccccccccCCCceEEEEEEEec
Confidence            579999999999999999999999999999999999999999999887666544            5677877665  46


Q ss_pred             CCCC------CCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEE
Q 026141           68 PRTG------QIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAI  141 (243)
Q Consensus        68 p~~~------~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~av  141 (243)
                      |++.      .+++++++++++|+|+|++++.++.||+|.|+|+++||++||++++|++||+++||+++||||+++++++
T Consensus       104 p~a~~~~~~~~~~~~e~~~s~li~r~l~~~i~~~~~p~~~I~I~~~VL~~DG~~~~aai~aa~~AL~da~iP~~~~v~av  183 (272)
T 2nn6_F          104 PFAGRRRRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVEMYDLVVGC  183 (272)
T ss_dssp             TTSSSSCCCSCCHHHHHHHHHHHHHHHTTTBCSTTSBTCEEEEEEEEEECCSSHHHHHHHHHHHHHHHHCCCBSSCCEEE
T ss_pred             CCCcCCccCCCCCHHHHHHHHHHHHHHHHhccHHHCCceEEEEEEEEEeCCCCHHHHHHHHHHHHHHHcCCcccCcEEEE
Confidence            7532      2344578999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEe--cCCeEEeCCCHHHHhhccccEEEEeeC-CccccccCCCcccCCCCcccceEEEeecCCCCH-HHHHHHHHHHH
Q 026141          142 CCCSA--ESGYCILDPTKLEEQKMKGFAYLVFPN-SILSVLPEGSSLVQGEPMEHGIITSVTHGAMSV-DDYFHCLERGR  217 (243)
Q Consensus       142 t~~~~--~~~~~lvDPt~~Ee~~~~~~~~v~~~~-~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~-~~l~~~l~~a~  217 (243)
                      +++++  .++.+|+|||..|+..+++.++|++.. .+                  +++.++..|.++. ++|.+|+++|.
T Consensus       184 svg~~~~~~~~~llDpt~~Ee~~~~~~l~va~~~~~~------------------~I~~i~~~g~~~~~~~l~~~l~~A~  245 (272)
T 2nn6_F          184 GLSLAPGPAPTWLLDPTRLEEERAAAGLTVALMPVLN------------------QVAGLLGSGEGGLTESWAEAVRLGL  245 (272)
T ss_dssp             ECCCCSCSSCCCCSSCCTTTGGGCSSEEEEEEETTTT------------------EEEEEEEECCSSCTTTTHHHHHHHH
T ss_pred             EEEEeeccCCeEEeCCCHHHhccCCceEEEEEeCCCC------------------CEEEEEEecCCCHHHHHHHHHHHHH
Confidence            99994  488999999999999999999999643 22                  1222334678999 99999999999


Q ss_pred             HHHHHHHHHHHHHHHhhcccccccC
Q 026141          218 AASAKLSDFLRRSLQSKLPGDLSKA  242 (243)
Q Consensus       218 ~~~~~l~~~i~~~l~~~~~~~~~~~  242 (243)
                      +++++|+++++++++++.++++..+
T Consensus       246 ~~~~~i~~~~~~~l~~~~~~~~~~~  270 (272)
T 2nn6_F          246 EGCQRLYPVLQQSLVRAARRRGAAA  270 (272)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHhhcccC
Confidence            9999999999999999998887655

>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=3.8e-46  Score=317.15  Aligned_cols=216  Identities=22%  Similarity=0.234  Sum_probs=177.4

Q ss_pred             CCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cCCC-----------
Q 026141            4 DRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KPRT-----------   70 (243)
Q Consensus         4 ~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p~~-----------   70 (243)
                      +|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|++|...++....+++|+|.++|  .|++           
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            499999999999999999999999999999999999999999976544445678899887765  4532           


Q ss_pred             CCCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcC-----------CCCCCcee
Q 026141           71 GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAG-----------IPMKHLAV  139 (243)
Q Consensus        71 ~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~-----------ip~~~~~~  139 (243)
                      |.++.++++++++|+++|++++.++.+|+|.|+|+++||++|||+++|++||+++||+|++           +||+++|+
T Consensus        81 G~~~~~~~eis~li~r~l~~~i~~~~l~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~~~~~~~~~~~~ipl~~~v~  160 (245)
T 1oys_A           81 GKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLA  160 (245)
T ss_dssp             ----CHHHHHHHHHHHHHHHTBCHHHHCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTSSSSCCBCSCEE
T ss_pred             CCCchHHHHHHHHHHHHHHHhcCHhHCCCEEEEEEEEEEeCCCCHHHHHHHHHHHHHHhccchhcccCcccccCCCCcee
Confidence            2345567899999999999999888889999999999999999999999999999999999           99999999


Q ss_pred             EEEEEEecCCeEE-eCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEee-cCCCCHHHHHHHHHHH
Q 026141          140 AICCCSAESGYCI-LDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVT-HGAMSVDDYFHCLERG  216 (243)
Q Consensus       140 avt~~~~~~~~~l-vDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~-~g~~~~~~l~~~l~~a  216 (243)
                      ++|++++ ++.++ +|||..||..+++.++|+++.++ +|.+++.                 + .+.++.+++.+|+++|
T Consensus       161 avs~g~~-~g~~vl~Dp~~~Ee~~~~~~~~v~~~~~g~i~~iq~~-----------------g~~~~~~~~~l~~~l~~A  222 (245)
T 1oys_A          161 AISVGID-KEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGT-----------------GEEATFSREDLNGLLGLA  222 (245)
T ss_dssp             EEEEEEE-TTTEEEESCCHHHHHHEEEEEEEEEETTSCEEEEEEE-----------------ESSCCCCHHHHHHHHHHH
T ss_pred             EEEEEEE-CCEEEEecCCHHHHhcCCCcEEEEEcCCCcEEEEEEe-----------------CCCCCcCHHHHHHHHHHH
Confidence            9999998 56666 99999999999999999998765 5544331                 1 2589999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhhccc
Q 026141          217 RAASAKLSDFLRRSLQSKLPG  237 (243)
Q Consensus       217 ~~~~~~l~~~i~~~l~~~~~~  237 (243)
                      .+++++|+++++++++++..+
T Consensus       223 ~~~~~~i~~~~~~~l~~~~~~  243 (245)
T 1oys_A          223 EKGIQELIDKQKEVLGDSLPE  243 (245)
T ss_dssp             HHHHHHHHHHHHHHC------
T ss_pred             HHHHHHHHHHHHHHHhhhhhh
Confidence            999999999999999887543

>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=2.3e-45  Score=311.29  Aligned_cols=212  Identities=23%  Similarity=0.292  Sum_probs=184.2

Q ss_pred             CCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cCCC-----------
Q 026141            4 DRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KPRT-----------   70 (243)
Q Consensus         4 ~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p~~-----------   70 (243)
                      .|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|++|...++....|++|+|.|+|  .|++           
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            399999999999999999999999999999999999999999976543333457888887765  5642           


Q ss_pred             CCCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcC-----------CCCCCcee
Q 026141           71 GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAG-----------IPMKHLAV  139 (243)
Q Consensus        71 ~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~-----------ip~~~~~~  139 (243)
                      |.++.++++++++|+++|++++.++.+|+|.|+|+++||++|||+++|++||+++||++++           +||+++|+
T Consensus        82 G~~~~~~~~isrli~r~l~~~i~~~~l~~~~i~I~~~VL~~DG~~~~aai~aa~~AL~da~~~~~~~~~~~~ip~~~~~~  161 (239)
T 1r6l_A           82 GKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVA  161 (239)
T ss_dssp             TSCCHHHHHHHHHHHHHHHHTBCGGGTCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCBCCCEE
T ss_pred             CCCcHHHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhcchhcccCcccccCccCcee
Confidence            2344457899999999999999999999999999999999999999999999999999999           99999999


Q ss_pred             EEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEee-cCCCCHHHHHHHHHHHH
Q 026141          140 AICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVT-HGAMSVDDYFHCLERGR  217 (243)
Q Consensus       140 avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~-~g~~~~~~l~~~l~~a~  217 (243)
                      ++|++++ ++.+|+|||.+|+..+++.++|++++++ +|.+++.                 + .+.++.+++.+|+++|.
T Consensus       162 avs~g~~-~~~~l~Dpt~~Ee~~~~~~l~va~~~~g~i~~~~~~-----------------g~~~~~~~~~l~~~l~~a~  223 (239)
T 1r6l_A          162 AVSVGIY-QGVPVLDLDYLEDSAAETDLNVVMTDAGGFIEVQGT-----------------AEGAPFRPAELNAMLELAQ  223 (239)
T ss_dssp             EEEEEEE-TTEEEESCCHHHHHHCSEEEEEEEETTSCEEEEEEE-----------------ESSSCCCHHHHHHHHHHHH
T ss_pred             EEEEEEE-CCEEEECCCHHHHhcCCceEEEEEeCCCCEEEEEEe-----------------CCCCCcCHHHHHHHHHHHH
Confidence            9999998 8899999999999999999999998765 4433321                 2 35899999999999999


Q ss_pred             HHHHHHHHHHHHHHHh
Q 026141          218 AASAKLSDFLRRSLQS  233 (243)
Q Consensus       218 ~~~~~l~~~i~~~l~~  233 (243)
                      +++++|++++++++++
T Consensus       224 ~~~~~i~~~~~~~l~~  239 (239)
T 1r6l_A          224 QGMQELFELQRAALAE  239 (239)
T ss_dssp             HHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHhC
Confidence            9999999999999863

>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=2.6e-45  Score=317.23  Aligned_cols=214  Identities=20%  Similarity=0.299  Sum_probs=187.3

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEE-cCccCCCCCCCCCceEEEEEe--cCCC------CC
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVY-GPKAGTKKNENPEKASIEVIW--KPRT------GQ   72 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~-gp~~~~~~~~~~~~~~l~v~~--~p~~------~~   72 (243)
                      +|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|+ +|.  .|+.+.|++|.|.++|  .|++      +.
T Consensus        24 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~--~p~~~~~~~g~l~~~~~~~p~a~~~~~~g~  101 (277)
T 2po1_B           24 EGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLG--EPFPDTPNMGVMTTNVELVPLASPTFEPGP  101 (277)
T ss_dssp             TTCCTTSCCTTCCCCEEEEECCSTTSSEEEEEEETTEEEEEEEEEEEE--CCCTTCTTSCEEEEEEEECGGGCTTCCSSS
T ss_pred             cCCCCCCCCCCCcCCeEEEeCCcCCCCeEEEEEECCeEEEEEEEeccc--CCCCCCCCceEEEEEEEeCCCccccccCCC
Confidence            58999999999999999999999999999999999999999999 543  4566789999887765  4532      33


Q ss_pred             CCCchHHHHHHHHHHHHhh--------hhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcC-------------
Q 026141           73 IGKPEKEYEIILKRTLQSI--------CILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAG-------------  131 (243)
Q Consensus        73 ~~~~~~~l~~~l~~~l~~~--------~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~-------------  131 (243)
                      +++++.+++++|+++|++.        |+.++..+|.|+|+++||++|||+++|+++|+++||+|++             
T Consensus       102 ~~~~~~~l~~li~r~l~~s~~idl~~L~i~pg~~~w~i~id~~VL~~dG~~~~a~i~aa~~AL~da~~p~~~~~~~~~~~  181 (277)
T 2po1_B          102 PDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVFIDVHVLDHDGNLMDAIGIAAIAALLNARVPKVRYNEETGEV  181 (277)
T ss_dssp             CCHHHHHHHHHHHHHHHTTTSBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHHCEEEEEEECTTTCCE
T ss_pred             CChHHHHHHHHHHHHHhhcccccHHHccccCCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcCCCcEEEeCCCcee
Confidence            4556789999999999872        4455667899999999999999999999999999999999             


Q ss_pred             --------CCCCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEeecC
Q 026141          132 --------IPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVTHG  202 (243)
Q Consensus       132 --------ip~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g  202 (243)
                              +||+++|+++|++++ ++.+++|||..||..+++.++|+++.++ ++.+++.                 +.|
T Consensus       182 ~~~~~~~~ipl~~~~~avs~g~~-~~~~l~Dp~~~Ee~~~~~~~~v~~~~~g~i~~lq~~-----------------g~~  243 (277)
T 2po1_B          182 ETLDETEPLPVEKIPVPVTFAKI-GNILVVDPSLDEELVMDGKITITTDETGHISAVQKS-----------------EGG  243 (277)
T ss_dssp             EEEEEEEECCBCCCCEEEEEEEE-TTEEEESCCHHHHHHCSEEEEEEECTTSCEEEEEEE-----------------SSC
T ss_pred             ecccccccccccCceEEEEEEEE-CCEEEeCCCHHHHhhCCCcEEEEEcCCCCEEEEEcc-----------------CCC
Confidence                    899999999999998 7799999999999999999999998765 5554431                 236


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 026141          203 AMSVDDYFHCLERGRAASAKLSDFLRRSLQSKL  235 (243)
Q Consensus       203 ~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~~  235 (243)
                      .++.+++.+|+++|.+++++|+++++++|++..
T Consensus       244 ~~~~~~l~~~l~~A~~~~~~l~~~~~~~l~~~~  276 (277)
T 2po1_B          244 AFKLEEVMYAVETAFKKAEEIRKLILEAVEKAK  276 (277)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            899999999999999999999999999998754

>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=1.1e-45  Score=315.84  Aligned_cols=212  Identities=24%  Similarity=0.260  Sum_probs=186.6

Q ss_pred             CCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cCCC-----------
Q 026141            4 DRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KPRT-----------   70 (243)
Q Consensus         4 ~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p~~-----------   70 (243)
                      +|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|++|...++....|++|+|.++|  .|++           
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            499999999999999999999999999999999999999999976553344558888887765  4632           


Q ss_pred             CCCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcC-----------CCCCCcee
Q 026141           71 GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAG-----------IPMKHLAV  139 (243)
Q Consensus        71 ~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~-----------ip~~~~~~  139 (243)
                      |.++.++++++++|+++|++++.++.+|+|.|+|+++||++|||+++|++||+++||+|++           +||+++|+
T Consensus        81 G~~~~~~~eisrli~r~lr~~i~~~~l~~~~i~I~~~VL~~DG~~~~aai~aa~~AL~da~~~~~~~~~~~~ipl~~~v~  160 (255)
T 1udn_A           81 GRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVA  160 (255)
T ss_dssp             CSCCHHHHHHHHHHHHHHHHHBCGGGGCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTSSSSCCBCCCEE
T ss_pred             CCCCHHHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHhhcchhcccCcccCCCccCcee
Confidence            2234457899999999999999999999999999999999999999999999999999999           99999999


Q ss_pred             EEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEee-cCCCCHHHHHHHHHHHH
Q 026141          140 AICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVT-HGAMSVDDYFHCLERGR  217 (243)
Q Consensus       140 avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~-~g~~~~~~l~~~l~~a~  217 (243)
                      +++++++ ++.+|+|||.+||..+++.++|+++.++ +|.+++.                 + .+.++.++|.+|+++|.
T Consensus       161 avsvg~~-~g~~llDpt~~Ee~~~~~~l~va~~~~g~i~~~q~~-----------------g~~~~~~~~~l~~~l~~A~  222 (255)
T 1udn_A          161 AVSVGIV-NDRILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTM-----------------GEEYSFTKDELIKMLDLAQ  222 (255)
T ss_dssp             EEEEEEE-TTEEEESCCHHHHHTCSEEEEEEEETTSCEEEEEEE-----------------ESSCCCCHHHHHHHHHHHH
T ss_pred             EEEEEEE-CCEEEECCCHHHHhhCCCCEEEEEeCCCCEEEEEEe-----------------CCCCCcCHHHHHHHHHHHH
Confidence            9999998 8899999999999999999999998765 4433321                 1 25899999999999999


Q ss_pred             HHHHHHHHHHHHHHHh
Q 026141          218 AASAKLSDFLRRSLQS  233 (243)
Q Consensus       218 ~~~~~l~~~i~~~l~~  233 (243)
                      +++++|++++++++++
T Consensus       223 ~~~~~i~~~~~~~l~~  238 (255)
T 1udn_A          223 KGINELIELQKKLYVI  238 (255)
T ss_dssp             HHHHHHHHHHHTTEEE
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            9999999999999876

>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=3.9e-45  Score=313.26  Aligned_cols=209  Identities=21%  Similarity=0.271  Sum_probs=180.2

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cCCC------CCC
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KPRT------GQI   73 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p~~------~~~   73 (243)
                      +|+|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+++ ...|+.+.|++|.|.++|  .|++      |.+
T Consensus        20 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~-~~~p~~~~~~~g~l~v~~~~~p~a~~~~~~g~~   98 (259)
T 3m7n_G           20 DNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQ-PGEPYPDTPDRGVIIVNAELVPLASPTFEPGPP   98 (259)
T ss_dssp             TTCCTTCCCTTCCCCEEEEETSSTTSSEEEEEEETTEEEEEEEEEE-EECCCSSCTTSCEEEEEEECCTTSCTTCCSSSS
T ss_pred             cCCCCCCCCCccccCeEEEeCCcCCCCceEEEEECCcEEEEEEEec-ccCCCCCCCCceEEEEEEEeCCcccccccCCCC
Confidence            6899999999999999999999999999999999999999999962 334566778899887765  4642      334


Q ss_pred             CCchHHHHHHHHHHHHh--hh------hcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCC-------------
Q 026141           74 GKPEKEYEIILKRTLQS--IC------ILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGI-------------  132 (243)
Q Consensus        74 ~~~~~~l~~~l~~~l~~--~~------~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~i-------------  132 (243)
                      ++++.+++++|+|+|++  ++      +.++..+|.|+|+++||++|||+++|+++|+++||.++++             
T Consensus        99 ~~~~~~~srli~r~lr~s~~i~l~~L~i~pg~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~iP~~~~~~~~~~~l  178 (259)
T 3m7n_G           99 DENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLL  178 (259)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHTCEECTGGGTSSSCEEC
T ss_pred             ChHHHHHHHHHHHHHhhcCCccHHHhcccCCcEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHhCCCCeEEecCCceecc
Confidence            45678999999999998  33      3344456999999999999999999999999999999999             


Q ss_pred             CCCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEeecCCCCHHHHHH
Q 026141          133 PMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFH  211 (243)
Q Consensus       133 p~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~  211 (243)
                      ||+++|+++|++++ ++.+++|||..||..+++.++|+++.++ ++.+++.                 +.+.++.+++.+
T Consensus       179 p~~~~~~avtvg~~-~~~~l~Dpt~~Ee~~~~~~l~va~~~~g~i~~i~~~-----------------g~~~~~~~~l~~  240 (259)
T 3m7n_G          179 PVRDLPVSVTSLIV-GNKYLVDPSREEMSVGDTTLTITTDKDDNVVAMQKS-----------------GGYLLDEKLFDE  240 (259)
T ss_dssp             CBCCCCEEEEEEEE-TTEEEESCCTTGGGGCSCEEEEEECTTSCEEEEEEE-----------------SSCCBCHHHHHH
T ss_pred             cccCceeEEEEEEE-CCEEEECCCHHHHhhCCCcEEEEEeCCCcEEEEECC-----------------CCCCcCHHHHHH
Confidence            79999999999998 8899999999999999999999998764 5544431                 236999999999


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 026141          212 CLERGRAASAKLSDFLRR  229 (243)
Q Consensus       212 ~l~~a~~~~~~l~~~i~~  229 (243)
                      |+++|.+++++|+++|++
T Consensus       241 ~l~~a~~~~~~l~~~~~~  258 (259)
T 3m7n_G          241 LLDVSINCARKLREKFKE  258 (259)
T ss_dssp             HHHHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHHHHHHhh
Confidence            999999999999998865

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

Probab=100.00  E-value=2.7e-44  Score=310.01  Aligned_cols=211  Identities=20%  Similarity=0.314  Sum_probs=182.3

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEE-cCccCCCCCCCCCceEEEEEe--cCC------CCC
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVY-GPKAGTKKNENPEKASIEVIW--KPR------TGQ   72 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~-gp~~~~~~~~~~~~~~l~v~~--~p~------~~~   72 (243)
                      +|+|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+ +|.  .|+.+.|++|.|.|+|  .|+      .+.
T Consensus        22 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~--~p~~~~~~~g~l~v~~~~~p~a~~~~~~g~   99 (271)
T 2wnr_A           22 NKERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKPQIG--EPFPDTPEMGVILTNSELLPMASPTFEPGP   99 (271)
T ss_dssp             TTCCTTCCCTTCCCCEEEEESCSTTSSEEEEEEETTEEEEEEEEEEEE--CCCTTCTTCCEEEEEEEECGGGCTTCCCSS
T ss_pred             cCCCCCCCCcccccCeEEEeCccCCCCeEEEEEECCeEEEEEEEeeee--cCCCCCCCceEEEEEEEeCCcccccccCCC
Confidence            58999999999999999999999999999999999999999999 443  4556778999988776  453      233


Q ss_pred             CCCchHHHHHHHHHHHHh--hhhcC------CCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcC-------------
Q 026141           73 IGKPEKEYEIILKRTLQS--ICILT------INPNTTTSVIIQVVHDDGALLPCAINAACAALVDAG-------------  131 (243)
Q Consensus        73 ~~~~~~~l~~~l~~~l~~--~~~~~------~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~-------------  131 (243)
                      +++++.+++++|+|+|++  ++.++      ++.+|.|+|+++||++|||+++|+++|+++||++++             
T Consensus       100 ~~~~~~~~s~li~r~lr~s~~i~l~~l~i~pg~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~~p~~~~~~~~~~~  179 (271)
T 2wnr_A          100 PDERSVELSRVVDRCIRESRMIDLEKLCIIEGSKVWMLFLDLHIIDYDGNLFDAAVLATVAALLDTRIPAAEVEDGEVVI  179 (271)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHHCEEEEEEEETTEEEE
T ss_pred             CchHHHHHHHHHHHHHhccCCccHHHccccCCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcCCCeEEecCCceee
Confidence            455678999999999988  44433      445799999999999999999999999999999999             


Q ss_pred             -------CCCCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEeecCC
Q 026141          132 -------IPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVTHGA  203 (243)
Q Consensus       132 -------ip~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~  203 (243)
                             +||+++|+++|++++ ++.+++|||.+||..+++.++|+++.++ ++.+++.                 +.|.
T Consensus       180 ~~~~~~~ip~~~~~~avt~g~~-~~~~l~Dpt~~Ee~~~~~~l~va~~~~~~i~~i~~~-----------------g~~~  241 (271)
T 2wnr_A          180 NREKMQPLPVNRKALMCTFAKI-GNEIVLDPSLEEEDILTARISIGVTEEGSICAMQKG-----------------GEGP  241 (271)
T ss_dssp             EEEEEEECCBCCCEEEEEEEEE-TTEEEESCCHHHHTTCSEEEEEEEETTSCEEEEEEE-----------------SSSC
T ss_pred             ccCcccccCccCCeEEEEEEEE-CCEEEeCCCHHHHhcCCCcEEEEEeCCCCEEEEECC-----------------CCCC
Confidence                   999999999999998 8899999999999999999999998754 4443321                 1368


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          204 MSVDDYFHCLERGRAASAKLSDFLRRSLQ  232 (243)
Q Consensus       204 ~~~~~l~~~l~~a~~~~~~l~~~i~~~l~  232 (243)
                      ++.+++.+|+++|.+++++|+++++++++
T Consensus       242 ~~~~~l~~~l~~a~~~~~~i~~~~~~~l~  270 (271)
T 2wnr_A          242 LTRDDVLKAVSIAVEKVPQLIEYLDKSMT  270 (271)
T ss_dssp             BCHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            99999999999999999999999998864

>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=2.6e-44  Score=311.03  Aligned_cols=212  Identities=24%  Similarity=0.302  Sum_probs=183.2

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cCCC------CCC
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KPRT------GQI   73 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p~~------~~~   73 (243)
                      +|+|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|++ ....|+.+.|++|.|.++|  .|++      +.+
T Consensus        27 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~-~~~~p~~~~~~~g~l~v~~~~~p~a~~~~~~g~~  105 (277)
T 2je6_A           27 KGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKL-EIDKPYEDTPNQGNLIVNVELLPLAYETFEPGPP  105 (277)
T ss_dssp             GTBCTTSCBTTCCCCEEEEETCSTTSSEEEEEEETTEEEEEEEEE-EEECCCTTCTTCCEEEEEEEECTTSCTTCCCSSC
T ss_pred             cCCCCCCCCcCcccCeEEEeCCcCCCCeEEEEEECCeEEEEEEEe-eeeCCCCCCCCccEEEEEEEeCCccCcccccCCC
Confidence            589999999999999999999999999999999999999999995 2234566788999987765  4642      334


Q ss_pred             CCchHHHHHHHHHHHHhh--h------hcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcC--------------
Q 026141           74 GKPEKEYEIILKRTLQSI--C------ILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAG--------------  131 (243)
Q Consensus        74 ~~~~~~l~~~l~~~l~~~--~------~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~--------------  131 (243)
                      ++++.+++++|+|+|++.  +      +.+++++|.|+|+++||++|||+++|+++|+++||++++              
T Consensus       106 ~~~~~~is~li~r~lr~~~~i~~~~l~i~~g~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~~p~v~~~~~~~~~~  185 (277)
T 2je6_A          106 DENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVN  185 (277)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCSCGGGGEEETTTEEEEEEEEEEEEECCSCHHHHHHHHHHHHHHTCEEEEEECC---CEEE
T ss_pred             ChHHHHHHHHHHHHHhccCCcCHHHceeecCceEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcCCCeEEecCCcceEe
Confidence            455789999999999983  3      344557899999999999999999999999999999999              


Q ss_pred             -------CCCCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEeecCC
Q 026141          132 -------IPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVTHGA  203 (243)
Q Consensus       132 -------ip~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~  203 (243)
                             +||+++|+++|++++ ++.+++|||.+||..+++.++|+++.++ ++.+++.                 +.+.
T Consensus       186 ~~~~~~~ip~~~~~~avsvg~~-~~~~l~Dpt~~Ee~~~~~~l~va~~~~g~i~~v~~~-----------------g~~~  247 (277)
T 2je6_A          186 KNEVVGKLPLNYPVVTISVAKV-DKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKS-----------------GKGS  247 (277)
T ss_dssp             EEEEEEECCCSCCCEEEEEEEE-TTEEEESCCHHHHHHCSEEEEEEECTTCCEEEEEEE-----------------SSSC
T ss_pred             ccCccccccccCCeEEEEEEEE-CCEEecCCCHHHHhcCCCcEEEEEeCCCCEEEEECC-----------------CCCC
Confidence                   999999999999998 8899999999999999999999998754 4443321                 1358


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          204 MSVDDYFHCLERGRAASAKLSDFLRRSLQ  232 (243)
Q Consensus       204 ~~~~~l~~~l~~a~~~~~~l~~~i~~~l~  232 (243)
                      ++.+++.+|+++|.+++++++++++++++
T Consensus       248 ~~~~~l~~~l~~A~~~~~~i~~~~~~~l~  276 (277)
T 2je6_A          248 MSLQDIDQAENTARSTAVKLLEELKKHLG  276 (277)
T ss_dssp             EEHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999999874

>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=6.8e-44  Score=308.50  Aligned_cols=215  Identities=20%  Similarity=0.259  Sum_probs=185.8

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cCCC------CCC
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KPRT------GQI   73 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p~~------~~~   73 (243)
                      +|+|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+++. ..|+.+.|++|.|.++|  .|++      |.+
T Consensus        22 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~-~~p~~~~~~~g~l~v~~~~~p~a~~~~~~g~~  100 (278)
T 2nn6_C           22 ENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEF-AAPSTDAPDKGYVVPNVDLPPLCSSRFRSGPP  100 (278)
T ss_dssp             TSCCTTSCCSCCCCSCCEEETCCSSSSEEEEEEETTEEEEEEEEEEE-CCCCSSSTTCCCCEEEEECCSSSCTTSCSSSC
T ss_pred             cCCCCCCCCcccccCeEEEeCCccCCCceEEEEeCCeEEEEEEEEEe-ecCCCCCCCccEEEEEEEeCCccCccccCCCC
Confidence            58999999999999999999999999999999999999999999954 45666778999887766  4542      334


Q ss_pred             CCchHHHHHHHHHHHHh--------hhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCC-------------
Q 026141           74 GKPEKEYEIILKRTLQS--------ICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGI-------------  132 (243)
Q Consensus        74 ~~~~~~l~~~l~~~l~~--------~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~i-------------  132 (243)
                      ++++.+++++|+|+|++        +|+.+++++|.|+|+++||++|||+++|+++|+++||+++||             
T Consensus       101 ~~~~~~~s~li~r~l~~s~~i~l~~L~i~pg~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~iP~v~~~~~~~~~~  180 (278)
T 2nn6_C          101 GEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETALAE  180 (278)
T ss_dssp             CHHHHHHHHHHHHHHHHHCCSCHHHHCSSBTTBCEEEEEEEEESSCCSCTTHHHHHHHHHHHHTCCCCCCCBCSSSBCCC
T ss_pred             cHHHHHHHHHHHHHHhccCCCCHHHCEEeCCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhCCCCeEEEeCCCccee
Confidence            45678999999999984        344567789999999999999999999999999999999996             


Q ss_pred             ---------CCCCceeEEEEEEecCC-eEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEeec
Q 026141          133 ---------PMKHLAVAICCCSAESG-YCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVTH  201 (243)
Q Consensus       133 ---------p~~~~~~avt~~~~~~~-~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~  201 (243)
                               ||+++|+++|++++ ++ .+|+|||.+||..+++.++|+++.++ ++.+++.                 +.
T Consensus       181 ~~~~~~~~lp~~~~~~avs~g~~-~~~~~l~Dpt~~Ee~~~~~~l~va~~~~g~i~~v~~~-----------------g~  242 (278)
T 2nn6_C          181 VNLKKKSYLNIRTHPVATSFAVF-DDTLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKP-----------------GG  242 (278)
T ss_dssp             TTSCCCSCSCCSCCCEEEEEEEC-TTTCCEESCCTTTTTSCSEEEEEEECTTCCEEEEEES-----------------CC
T ss_pred             cCcccccccccCCceEEEEEEEE-CCceEEECCCHHHHhhcCceEEEEEcCCCcEEEEEcc-----------------CC
Confidence                     79999999999998 66 99999999999999999999998764 4444321                 12


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 026141          202 GAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKL  235 (243)
Q Consensus       202 g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~~  235 (243)
                      +.++.+++.+|+++|.+++++|++++++++++..
T Consensus       243 ~~~~~~~l~~~l~~a~~~~~~i~~~~~~~l~~~~  276 (278)
T 2nn6_C          243 SGLTGAKLQDCMSRAVTRHKEVKKLMDEVIKSMK  276 (278)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHHHHHHHHTTTTTTC
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            3899999999999999999999999999988754

>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=1.7e-43  Score=314.78  Aligned_cols=217  Identities=18%  Similarity=0.283  Sum_probs=186.8

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEE--ecCCC------CCC
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVI--WKPRT------GQI   73 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~--~~p~~------~~~   73 (243)
                      +|+|+|||+++|+|++.+++|   +++|||+|++|+|+|+|+|++|.. .|+.+.|++|.|.++  +.|.+      +.+
T Consensus        37 ~g~R~DGR~~~e~R~i~ie~g---~A~GSa~v~~G~T~VL~tV~~e~~-~p~~~~~~~g~l~~~v~~~p~a~~~~~~g~~  112 (358)
T 2nn6_A           37 EKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELV-SPKLNRATEGILFFNLELSQMAAPAFEPGRQ  112 (358)
T ss_dssp             TTCCTTSCCTTCCCCCEEEEC---SSTTEEEEESSSCEEEEEECCEEE-CCCSTTTTSCCEEEEEEECTTTCSSCCSSST
T ss_pred             cCCCCCCCCccccCCeEEEEe---cCCcEEEEEECCcEEEEEEEeccc-CCcccCCCCcEEEEEEEecCCccccccCCCC
Confidence            589999999999999999999   899999999999999999999653 456667888877654  55743      223


Q ss_pred             CCchHHHHHHHHHHHHhh--------hhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCC------------
Q 026141           74 GKPEKEYEIILKRTLQSI--------CILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIP------------  133 (243)
Q Consensus        74 ~~~~~~l~~~l~~~l~~~--------~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip------------  133 (243)
                      ++++.+++++|+|+|++.        |+.+++++|.|+|+++||++|||+++|+++|+++||+++++|            
T Consensus       113 s~~e~eisrli~r~Lr~s~~idl~~LcI~pg~~~w~I~Vdv~VL~~DGn~~dAai~Aa~aAL~da~iP~v~~~~~~v~i~  192 (358)
T 2nn6_A          113 SDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLY  192 (358)
T ss_dssp             HHHHTHHHHHHHHHHHHHTCBCSSSSCSBTTTBEEEEEEEEEECSCCSCCHHHHHHHHHHHHHHCCCCCCBCCTTCCBCC
T ss_pred             CHHHHHHHHHHHHHhhhccccchHhhcccCCCccEEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhCcCcEEeeCCeeEec
Confidence            345689999999999874        556677999999999999999999999999999999999999            


Q ss_pred             -----------CCCceeEEEEEEec-CCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEee
Q 026141          134 -----------MKHLAVAICCCSAE-SGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVT  200 (243)
Q Consensus       134 -----------~~~~~~avt~~~~~-~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~  200 (243)
                                 |+++|+++|+|++. ++.+|+|||..||..+++.++|+++.++ +|.+++.                 +
T Consensus       193 ~~~~~~~~~l~i~~~p~avsvgl~~~~~~illDPt~~Ee~~~~~~l~Va~t~~g~I~~lqk~-----------------G  255 (358)
T 2nn6_A          193 TPEERDPVPLSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSS-----------------G  255 (358)
T ss_dssp             HHHHTSCCCCCBCCCEEEEEEEECTTTSSEEESCCHHHHHHCSCEEEEEEETTTEEEEEEEE-----------------S
T ss_pred             ccccccccccCccCCEEEEEEEEEeeCCEEEECCCHHHHhhcCccEEEEEcCCCeEEEEEeC-----------------C
Confidence                       89999999999863 5799999999999999999999998875 5555432                 1


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccc
Q 026141          201 HGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDL  239 (243)
Q Consensus       201 ~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~~~~~~  239 (243)
                      .+.++.+++.+|+++|.+++++|.++++++++++..++.
T Consensus       256 ~~~ls~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~r~  294 (358)
T 2nn6_A          256 GIMLLKDQVLRCSKIAGVKVAEITELILKALENDQKVRK  294 (358)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHhhh
Confidence            236899999999999999999999999999998776553

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

Probab=100.00  E-value=2.9e-43  Score=308.24  Aligned_cols=218  Identities=17%  Similarity=0.243  Sum_probs=175.2

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEE--EEecCC------CCCC
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIE--VIWKPR------TGQI   73 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~--v~~~p~------~~~~   73 (243)
                      +|+|+|||+++|+|++.+++|   +++|||+|++|+|+|+|+|++|. ..|..+.|+++.+.  |+|.|.      .|.+
T Consensus        21 ~~~R~DGR~~~e~R~i~i~~g---~a~GSa~v~~G~T~Vl~~V~~~~-~~p~~~~~~~g~~~~~ve~~~~~~~~~~~g~~   96 (305)
T 2wp8_A           21 QNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGNTKVHCRISCQI-AQPYEDRPFEGLFVISTEISPMAGSQFENGNI   96 (305)
T ss_dssp             TTCCTTSCCTTCCCCEEEEEC---SSTTEEEEEETTEEEEEEEEEEE-C-CCSSCTTCCEEEEEECCC------------
T ss_pred             hCCCCCCCCCcccCCeEEEEc---CCCcEEEEEECCeEEEEEEeccc-cCCcccCCCCcEEEEEEEECCCCCccccCCCC
Confidence            589999999999999999999   79999999999999999999954 45666677777665  456663      2445


Q ss_pred             C-CchHHHHHHHHHHHHh--------hhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCC-----------
Q 026141           74 G-KPEKEYEIILKRTLQS--------ICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIP-----------  133 (243)
Q Consensus        74 ~-~~~~~l~~~l~~~l~~--------~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip-----------  133 (243)
                      + +++.+++++|+++|++        +|+.+++..|.|+|+++||++|||+++|+++|+++||+++++|           
T Consensus        97 ~~~~~~~is~li~r~l~~s~~idl~~L~i~pg~~~w~I~id~~VL~~DG~~~dAai~aa~~AL~~a~iP~~~~~~~~~~i  176 (305)
T 2wp8_A           97 TGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQIIV  176 (305)
T ss_dssp             ----------CHHHHHHHTTSBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHHCEECCCBCTTSSCCB
T ss_pred             ChhHHHHHHHHHHHHHhhccCcCHHHccccCCcEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHHhCCCeEEecCCceEe
Confidence            5 6778999999999984        3555677789999999999999999999999999999999999           


Q ss_pred             ------------CCCceeEEEEEEec---------C----CeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccC
Q 026141          134 ------------MKHLAVAICCCSAE---------S----GYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQ  187 (243)
Q Consensus       134 ------------~~~~~~avt~~~~~---------~----~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~  187 (243)
                                  |++.|+++|+|++.         +    +.+|+|||..||..+++.++|+++.++ +|.+++.     
T Consensus       177 ~~~~~~~~~~l~~~~~pvavs~g~i~~~~~~~~~~~~~~~~~~l~Dpt~~Ee~~~~~~l~Va~~~~g~i~~l~~~-----  251 (305)
T 2wp8_A          177 HPVNEREPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLNKNREVVQVSKA-----  251 (305)
T ss_dssp             CCSSSSCCEECCBSCCCEEEEEEECC---------------CEEESCCHHHHHHCSEEEEEEECTTSEEEEEEEE-----
T ss_pred             cccccccccccccccCeEEEEEEEEccccccccccccccCCeEEeCCCHHHHhccCCcEEEEEcCCCcEEEEEec-----
Confidence                        67899999999983         1    789999999999999999999998765 5555432     


Q ss_pred             CCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc
Q 026141          188 GEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDLS  240 (243)
Q Consensus       188 ~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~~~~~~~  240 (243)
                                  +.+.++.+++.+|+++|.+++++|+++++++++++..++.+
T Consensus       252 ------------g~~~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~r~~  292 (305)
T 2wp8_A          252 ------------GGLPMDALTLMKCCHEAYSIIEKITDQILQLLKEDSEKRNK  292 (305)
T ss_dssp             ------------EEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             ------------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence                        22379999999999999999999999999999998877744

>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=2e-46  Score=314.22  Aligned_cols=208  Identities=25%  Similarity=0.382  Sum_probs=164.7

Q ss_pred             CCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEecCCCCCCCCchHHHHHHHHHHHHh
Q 026141           11 PNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQS   90 (243)
Q Consensus        11 ~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~p~~~~~~~~~~~l~~~l~~~l~~   90 (243)
                      ++|+|++.+++|.+++++|||+|++|+|+|+|+|+||.+.+++.+.+++++|+|+|.|+.|.++++  +++++|+|+|++
T Consensus         2 ~~e~R~i~ie~g~l~~A~GSa~v~~G~T~Vl~~V~~~~e~~~~~~~~~~~~l~v~~~p~~G~~~~~--e~~~li~r~l~~   79 (222)
T 3krn_A            2 AGRLREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISYRANCGDNKFN--VLNNIIHSTLSN   79 (222)
T ss_dssp             -CCCCCBCCBSCCC----CCCBCCBTTCEEECCCCSSCC-------------CCCSSCCCC--CCS--SCTTHHHHC--C
T ss_pred             CCcccceEEEECCCCCCCeEEEEEECCcEEEEEEECCCCCcccccCCceEEEEEEEcCCCCCCCHH--HHHHHHHHHHHH
Confidence            579999999999999999999999999999999999988777778899999999999988876655  899999999999


Q ss_pred             hhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEE
Q 026141           91 ICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLV  170 (243)
Q Consensus        91 ~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~  170 (243)
                      ++.++.||+|.|+|+++||++||++++|++||+++||+++||||+++++|++++++ ++.+++|||..|+..+++.++|+
T Consensus        80 ~i~~~~~p~~~I~I~~~VL~~DG~~~~aai~aa~~AL~dagiP~~~~v~avsvg~~-~g~~llDpt~~Ee~~~~~~l~va  158 (222)
T 3krn_A           80 AINLELFPHTTISVTVHGIQDDGSMGAVAINGACFALLDNGMPFETVFCGVLIVRV-KDELIIDPTAKQEAASTGRVLFS  158 (222)
T ss_dssp             CSCC-----CCCCCCCEEEECCSCHHHHHHHGGGTTTTTTTCCTTSCCCCCCCEEC-SSSEESSCCTTTTTSCC-CCCCE
T ss_pred             hccHHhCCCcEEEEEEEEEECCCChHHHHHHHHHHHHHHCCCCccCcEEEEEEEEE-CCEEEeCCCHHHHhccCccEEEE
Confidence            99999999999999999999999999999999999999999999999999999995 88999999999999999999999


Q ss_pred             e---eC-Cc-cccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc
Q 026141          171 F---PN-SI-LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDLS  240 (243)
Q Consensus       171 ~---~~-~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~~~~~~~  240 (243)
                      +   ++ .+ ++.                   ++..|.++.+++.+|+++|.+++++|.++++++++++..+++.
T Consensus       159 ~~~~~~~~~~i~~-------------------vq~~g~~~~~~l~~~l~~a~~~~~~i~~~~~~~l~~~~~~~~~  214 (222)
T 3krn_A          159 VCKGSDGHPEVCA-------------------MDAIGHWDFIQLEAAWSLAQPSASAIFDFYKTVMKRKLSVDEQ  214 (222)
T ss_dssp             ECCCSSSSCCEEE-------------------ECCBSSCTTHHHHTHHHHTTHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             EEccCCCCCCEEE-------------------EEEeCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhh
Confidence            8   54 22 333                   2346799999999999999999999999999999998887653

>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=3.1e-43  Score=307.97  Aligned_cols=219  Identities=20%  Similarity=0.243  Sum_probs=185.9

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cCCCC-----CC-
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KPRTG-----QI-   73 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p~~~-----~~-   73 (243)
                      +|+|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|+++ ...|..+.|++|.+.++|  .|++.     .+ 
T Consensus        34 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~e-~~~p~~~~~~~g~l~~~v~~~p~a~~~~~~r~~  112 (305)
T 2nn6_E           34 EDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAE-MGTPKLEKPNEGYLEFFVDCSASATPEFEGRGG  112 (305)
T ss_dssp             TTCCSSSCCSSCCCCCEEEECCCTTSSSEEEEEETTEEEEEECCCC-CSCCCSSSCSSCCEEEECCCCTTTCSSCCTTST
T ss_pred             cCCCCCCCCCcCccCeEEEeCcccCCCcEEEEEECCeEEEEEEEEE-eeCCCcCCCCceEEEEEEEeCCCcCccccCCCC
Confidence            5899999999999999999999999999999999999999999994 445777788888877654  57531     11 


Q ss_pred             CCchHHHHHHHHHHHHh--------hhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCC----------
Q 026141           74 GKPEKEYEIILKRTLQS--------ICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMK----------  135 (243)
Q Consensus        74 ~~~~~~l~~~l~~~l~~--------~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~----------  135 (243)
                      ++++.+++++|+|+|++        +|+.++..+|.|+|+++||++|||+++|+++|+++||+++++|+.          
T Consensus       113 ~~~~~~isrli~r~lr~s~~idl~~L~i~p~~~~w~i~idv~VL~~DG~~~daai~aa~~AL~~a~iP~~~~~~~~~~~~  192 (305)
T 2nn6_E          113 DDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLEDEEGSK  192 (305)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCSCSSSSCSSTTTCCCCEEEEEEECCCCSSHHHHHHHHHHHTTTTCCCCEEEEECC-----
T ss_pred             chHHHHHHHHHHHHHhhcCcccHHHheeccCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcCCCeEEEecCCCCce
Confidence            13467899999999987        334456667999999999999999999999999999999999954          


Q ss_pred             -----------------CceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEE
Q 026141          136 -----------------HLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIIT  197 (243)
Q Consensus       136 -----------------~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~  197 (243)
                                       ++|+++|++++ ++.+|+|||.+||..+++.++|+++.++ ++.+++.               
T Consensus       193 ~i~~~~d~~~~~~l~l~~~p~avt~g~i-~~~~l~Dpt~~Ee~~~~~~l~Va~~~~g~i~~i~~~---------------  256 (305)
T 2nn6_E          193 DIELSDDPYDCIRLSVENVPCIVTLCKI-GYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKV---------------  256 (305)
T ss_dssp             -EEEEESSCCCSCCCCTTCCCCEEEEES-SSSEESSCCHHHHTSCSEEEEECCCSSSCCCEEEEE---------------
T ss_pred             eeeccCcccccccccccCceEEEEEEEE-CCEEEECCCHHHHhhcCCcEEEEEcCCCCEEEEEcc---------------
Confidence                             35789999997 8899999999999999999999998765 5544431               


Q ss_pred             EeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccc
Q 026141          198 SVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLPGDL  239 (243)
Q Consensus       198 ~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~~~~~~  239 (243)
                        +.+.++.+++.+|+++|.+++++|+++++++++++...+-
T Consensus       257 --g~~~l~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~~~  296 (305)
T 2nn6_E          257 --GKGSLDPESIFEMMETGKRVGKVLHASLQSVVHKEESLGP  296 (305)
T ss_dssp             --ESSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CC
T ss_pred             --CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence              2348999999999999999999999999999998776443

>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=3.3e-40  Score=305.30  Aligned_cols=216  Identities=19%  Similarity=0.268  Sum_probs=179.1

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEE-EcCccCCCCC---CCCCceEE--EEEecCCC-----
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV-YGPKAGTKKN---ENPEKASI--EVIWKPRT-----   70 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V-~gp~~~~~~~---~~~~~~~l--~v~~~p~~-----   70 (243)
                      +|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+| .||.+..+..   ..++++++  +++|.|++     
T Consensus       312 ~g~R~DGR~~~elRpi~i~~g~l~~a~GSal~~~G~T~Vl~~Vt~gp~~~~~~~~~l~~~~~g~~~~~y~~~P~st~e~~  391 (549)
T 3gme_A          312 GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETG  391 (549)
T ss_dssp             TCCCTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEC---------------CCEEEEEECCGGGTTCCC
T ss_pred             CCCCCCCCCCCCccceEEEECCCCCCCceEEEEECCeEEEEEEEecCcccccCccccCCCCceEEEEEEEeCCCCcCCcc
Confidence            6899999999999999999999999999999999999999999 5886543322   12355555  56667742     


Q ss_pred             --CCCCCchHHHHHHHHHHHHhhhh-cCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEec
Q 026141           71 --GQIGKPEKEYEIILKRTLQSICI-LTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAE  147 (243)
Q Consensus        71 --~~~~~~~~~l~~~l~~~l~~~~~-~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~  147 (243)
                        +.+++++.+++++++|+|++++. .+.|| |.|+|+++||++|||.++|++||+++||+||||||+++++++++|++.
T Consensus       392 ~~g~~~~Reie~~~li~raL~~vI~~~~~~P-~tI~V~~~VLesDGs~~~AsI~aa~lAL~DAGvPm~~~Vaavs~Gli~  470 (549)
T 3gme_A          392 MVGSPKRREIGHGRLAKRGVLAVMPDMDKFP-YTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVK  470 (549)
T ss_dssp             CSSCCCSSHHHHHHHHHHHHTTTCCCTTTCC-CEEEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCCSSCCEEEEEEEEE
T ss_pred             cCCCCChhHHHHHHHHHHHHHHhcCccccCC-eEEEEEEEEEECCCCHHHHHHHHHHHHHHhCCCCcccceeEEEEEEEc
Confidence              23567889999999999999988 56777 679999999999999999999999999999999999999999999985


Q ss_pred             CC---eEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHH
Q 026141          148 SG---YCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLS  224 (243)
Q Consensus       148 ~~---~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~  224 (243)
                      ++   .+++||+..|+..++..+.|+++.+++++++..                ..-+.++.++|.+|+++|.+++++|+
T Consensus       471 ~g~~~~iL~D~~~~Ed~~~d~d~~Va~t~~gitalqmd----------------~ki~G~s~~~l~~~L~~A~~g~~~I~  534 (549)
T 3gme_A          471 EGDNYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMD----------------IKIEGITKEIMQVALNQAKGARLHIL  534 (549)
T ss_dssp             ETTEEEEEESCCHHHHHHSSEEEEEEECSSCEEEEEEE----------------ECCSCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCceEEEecCChHHHccCCceEEEEecCCCeEEEEEc----------------cccCCcCHHHHHHHHHHHHHHHHHHH
Confidence            53   789999999999999999999877766554421                01234899999999999999999999


Q ss_pred             HHHHHHHHhh
Q 026141          225 DFLRRSLQSK  234 (243)
Q Consensus       225 ~~i~~~l~~~  234 (243)
                      +.|++++.+.
T Consensus       535 ~~m~~al~~p  544 (549)
T 3gme_A          535 GVMEQAINAP  544 (549)
T ss_dssp             HHHHHHCCSC
T ss_pred             HHHHHHHHhh
Confidence            9999999764

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

Probab=100.00  E-value=1e-39  Score=307.43  Aligned_cols=214  Identities=17%  Similarity=0.277  Sum_probs=182.0

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCC-CCC-------CCCceE--EEEEecCCC-
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTK-KNE-------NPEKAS--IEVIWKPRT-   70 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~-~~~-------~~~~~~--l~v~~~p~~-   70 (243)
                      +|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|++|...+. +.+       .+++++  ++++|.|++ 
T Consensus       316 ~g~R~DGR~~~elRpi~i~~g~l~~a~GSal~~~G~T~Vl~~Vt~~~~~~~~~~d~~~~~l~~~~~g~~~~~y~~~P~st  395 (630)
T 3u1k_A          316 EYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITAINGIKDKNFMLHYEFPPYAT  395 (630)
T ss_dssp             HSCCTTSCCTTCCCCEEEEECCSTTSSEEEEEEETTEEEEEEEEEECGGGGSCSSHHHHHHHCCCGGGEEEEEECCGGGG
T ss_pred             CCCCCCCCCCccccceEEEECCCCCCCceEEEEECCeEEEEEEEcCCCCchhcccccccccCCCCceEEEEEEEecCCcc
Confidence            589999999999999999999999999999999999999999998432221 111       245554  566677753 


Q ss_pred             ------CCCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEE
Q 026141           71 ------GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCC  144 (243)
Q Consensus        71 ------~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~  144 (243)
                            +.+++++.+++++++|+|++++. ..|| |.|+|+++||++|||.++|++||+++||+||||||+++++++++|
T Consensus       396 ~e~~~~g~~~rREi~~~~Li~raLr~vi~-~~~p-~tI~V~~~VLesDGs~~~AsI~aa~lAL~dAGIPl~~~Vaavs~g  473 (630)
T 3u1k_A          396 NEIGKVTGLNRRELGHGALAEKALYPVIP-RDFP-FTIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIG  473 (630)
T ss_dssp             TCCCCCSSCCHHHHHHHHHHHHHHGGGSC-TTCS-SEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCCEEEEEE
T ss_pred             cccccCCCCChHHHHHHHHHHHHHHhhCc-ccCC-eEEEEEEEEEEcCCCHHHHHHHHHHHHHHhCCCCcccceEEEEEE
Confidence                  33456788999999999999887 4676 779999999999999999999999999999999999999999999


Q ss_pred             EecC-----C-----eEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecC-CCCHHHHHHHH
Q 026141          145 SAES-----G-----YCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHG-AMSVDDYFHCL  213 (243)
Q Consensus       145 ~~~~-----~-----~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g-~~~~~~l~~~l  213 (243)
                      ++.+     +     .+++||+..|+..++..+.|+++.++++.+++.                 +.+ .++.++|.+|+
T Consensus       474 li~~~~~~~g~~~~~~iLlD~~~~Ed~~~d~d~~Va~t~~gIt~lQ~~-----------------~k~~~~s~~~l~~aL  536 (630)
T 3u1k_A          474 LVTKTDPEKGEIEDYRLLTDILGIEDYNGDMDFKIAGTNKGITALQAD-----------------IKLPGIPIKIVMEAI  536 (630)
T ss_dssp             EEEEECSSSSCEEEEEEEESCCHHHHHTSSEEEEEEECSSCEEEEEEE-----------------ECSSCBCHHHHHHHH
T ss_pred             EecCCCcccccccCceEEecCCHHHHhhCcceEEEEecCCceEEEEec-----------------CCCCCCCHHHHHHHH
Confidence            9862     3     799999999999999999999887766555431                 222 78999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhh
Q 026141          214 ERGRAASAKLSDFLRRSLQSK  234 (243)
Q Consensus       214 ~~a~~~~~~l~~~i~~~l~~~  234 (243)
                      ++|.+++++|++.|++++.+.
T Consensus       537 ~~A~~g~~~I~~~m~~al~~~  557 (630)
T 3u1k_A          537 QQASVAKKEILQIMNKTISKP  557 (630)
T ss_dssp             HHHHHHHHHHHHHHHHHCSSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999875

>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-39  Score=312.30  Aligned_cols=216  Identities=17%  Similarity=0.235  Sum_probs=185.6

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEE-cCccCCCCCC---CCCceE--EEEEecCCC-----
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVY-GPKAGTKKNE---NPEKAS--IEVIWKPRT-----   70 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~-gp~~~~~~~~---~~~~~~--l~v~~~p~~-----   70 (243)
                      +|+|+|||.++|+|++.+++|++++++|||+|++|+|+|+|+|+ ||.+..++.+   .+++++  ++++|.|++     
T Consensus       353 ~g~R~DGR~~~elRpI~ie~gvl~~a~GSAl~~~G~TqVL~~Vt~Gp~~~~~~~d~l~~~~~g~~~~~y~f~P~st~e~~  432 (757)
T 1e3p_A          353 EKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPPYSVGETG  432 (757)
T ss_dssp             TCBCTTSCBTTCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEEEGGGSEECCSSSSCCEESEEEEEECCGGGGTCCC
T ss_pred             CCCCCCCCCcccccceeEEeCCCCCCCEEEEEEECCcEEEEEEEecCCCccccccccCCCCceEEEEEEEeCCccccccc
Confidence            68999999999999999999999999999999999999999994 8876554322   456666  566677742     


Q ss_pred             --CCCCCchHHHHHHHHHHHHhhhh-cCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEec
Q 026141           71 --GQIGKPEKEYEIILKRTLQSICI-LTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAE  147 (243)
Q Consensus        71 --~~~~~~~~~l~~~l~~~l~~~~~-~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~  147 (243)
                        +.+++++.+++++++|+|+++++ .+.|| |.|+|+++||++|||+++|+++|+++||+|||+||++++++++++++.
T Consensus       433 ~~g~~~~reie~~~li~raL~~vI~~~~~~P-~tI~V~~~VLesDGs~~~Asi~aa~lAL~dAgIP~k~~Vaavs~gli~  511 (757)
T 1e3p_A          433 RVGSPKRREIGHGALAERAIVPVLPTREEFP-YAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIAMGLIS  511 (757)
T ss_dssp             CCSSCCHHHHHHHHHHHHHHGGGCCCTTTSC-EEEEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCCSSCCEEEEEEEEE
T ss_pred             CCCCCchhHHHHHHHHHHHHHHhccccccCC-EEEEEEEEEEECCCCHHHHHHHHHHHHHHHcCCCcccceEEEEEEEEe
Confidence              23556789999999999999988 56676 779999999999999999999999999999999999999999999984


Q ss_pred             C---C----eEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHH
Q 026141          148 S---G----YCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAAS  220 (243)
Q Consensus       148 ~---~----~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~  220 (243)
                      +   +    .+|+||+..|+..++..++|+.+..+++.+++.+                ..+.++.+++.+|+++|.+++
T Consensus       512 eg~dg~~~~~iLlDp~~~Ed~~gd~d~~Va~t~~~It~lQ~~g----------------k~~gi~~e~l~~aL~~A~~~~  575 (757)
T 1e3p_A          512 QEINGETHYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDT----------------KLDGIPASVLAAALKQARDAR  575 (757)
T ss_dssp             EESSSCEEEEEEESCCHHHHHHCSEEEEEEECSSSEEEEEEEE----------------CSSCCCHHHHHHHHHHHHHHH
T ss_pred             cCCCCccceeEEeCCCHHHHhccCceEEEEecCCeEEEEEEcC----------------CccccCHHHHHHHHHHHHHHH
Confidence            3   2    7999999999999999999987665566554320                125689999999999999999


Q ss_pred             HHHHHHHHHHHHhh
Q 026141          221 AKLSDFLRRSLQSK  234 (243)
Q Consensus       221 ~~l~~~i~~~l~~~  234 (243)
                      ++|++.|+++|.++
T Consensus       576 ~~I~~~m~~al~~~  589 (757)
T 1e3p_A          576 LHILDVMMEAIDTP  589 (757)
T ss_dssp             HHHHHHHHHHCSSC
T ss_pred             HHHHHHHHHHhccc
Confidence            99999999999887

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

Probab=100.00  E-value=1.6e-39  Score=310.13  Aligned_cols=217  Identities=19%  Similarity=0.249  Sum_probs=178.6

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEE-EcCccCCCCCC-----CCCceEEEEEecCCC-----
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV-YGPKAGTKKNE-----NPEKASIEVIWKPRT-----   70 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V-~gp~~~~~~~~-----~~~~~~l~v~~~p~~-----   70 (243)
                      +|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+| .||.+..+..+     ......++++|.|++     
T Consensus       318 ~g~R~DGR~~~elRpI~ie~gvl~~a~GSAl~~~G~TqVL~~Vt~gp~e~~~~~d~l~~~~~g~~~~~y~~~P~st~e~~  397 (723)
T 3cdi_A          318 GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETG  397 (723)
T ss_dssp             TCCCTTSCCTTCCCCEEEEESCSTTSSEEEEEEETTEEEEEEEEECC-------------CTTSEEEEEECCGGGGTCCC
T ss_pred             cCcCCCCCCccccccceEEeCCCCCCCeEEEEEECCcEEEEEEEecCcccccCCcccCCCCceEEEEEEecCCCCccccc
Confidence            6899999999999999999999999999999999999999999 58876544322     233445667777752     


Q ss_pred             --CCCCCchHHHHHHHHHHHHhhhhc-CCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEec
Q 026141           71 --GQIGKPEKEYEIILKRTLQSICIL-TINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAE  147 (243)
Q Consensus        71 --~~~~~~~~~l~~~l~~~l~~~~~~-~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~  147 (243)
                        +.+++++..++++++|+|++++.. +.|| |.|+|+++||++|||+++|+++|+++||+|+||||++++++++++++.
T Consensus       398 r~g~p~~REi~~~~li~raL~~vI~~~~~~p-~tI~Vd~~VLesdGs~~~Asi~aa~lAL~dAgVPl~~~vaavs~gli~  476 (723)
T 3cdi_A          398 MVGSPKRREIGHGRLAKRGVLAVMPDMDKFP-YTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVK  476 (723)
T ss_dssp             CC-----CTTHHHHHHHHHHHTTSCCSSSSC-SCEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCCEEEEEEEEE
T ss_pred             cCCCCCHHHHHHHHHHHHHHHHhcCcccCCC-EEEEEEEEEEeCCCCHHHHHHHHHHHHHhcCCCCcccceeeEEEEEEc
Confidence              223567889999999999999885 5565 789999999999999999999999999999999999999999999986


Q ss_pred             CC---eEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHH
Q 026141          148 SG---YCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLS  224 (243)
Q Consensus       148 ~~---~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~  224 (243)
                      +|   .+|+||+..|+..++..++|+++.+++|.+++..                ..+.++.++|.+|+++|.+++++|+
T Consensus       477 ~g~~~~iL~Dp~~~Ed~~~d~d~~Va~t~~gI~~lq~~g----------------k~~~is~e~l~~~l~~A~~~~~~I~  540 (723)
T 3cdi_A          477 EGDNYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMDI----------------KIEGITKEIMQVALNQAKGARLHIL  540 (723)
T ss_dssp             ETTEEEEESSCCGGGGGGCSEEEEEEECSSCEEEEEEEE----------------CSSCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCceEEEECCChHHhhhccceeeecccCCceEEEEeCC----------------ccCCcCHHHHHHHHHHHHHHHHHHH
Confidence            44   4999999999999999999998887766655420                1257999999999999999999999


Q ss_pred             HHHHHHHHhhc
Q 026141          225 DFLRRSLQSKL  235 (243)
Q Consensus       225 ~~i~~~l~~~~  235 (243)
                      +.|+++|.++.
T Consensus       541 ~~m~~al~~~~  551 (723)
T 3cdi_A          541 GVMEQAINAPR  551 (723)
T ss_dssp             HHHHHHCC---
T ss_pred             HHHHHHhhhcc
Confidence            99999998763

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

Probab=100.00  E-value=2.9e-39  Score=307.24  Aligned_cols=216  Identities=19%  Similarity=0.221  Sum_probs=183.8

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEE-EcCccCCCCC---CCCCceEEE--EEecCCC-----
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAV-YGPKAGTKKN---ENPEKASIE--VIWKPRT-----   70 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V-~gp~~~~~~~---~~~~~~~l~--v~~~p~~-----   70 (243)
                      +|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+| .||.+..++.   ..++++++.  ++|.|++     
T Consensus       328 ~g~R~DGR~~~elRpI~ie~gvl~~a~GSAl~~~G~TkVl~~Vt~Gp~~~~~~~d~l~~~~~g~~~~~y~~~P~st~er~  407 (726)
T 4aid_A          328 TGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETG  407 (726)
T ss_dssp             SSBCTTSCBTTCCCCEEEEECSSTTSSEEEEEEETTEEEEEEEEEECGGGSEEEEETTEEEEECEEEEEECCGGGGTCCC
T ss_pred             CCCCCCCCCCCCccceEEEECCCCCCCceEEEEeCCeEEEEEEEeCCCCcccccccccCCCceEEEEEEEeCCCcccccc
Confidence            6899999999999999999999999999999999999999999 6887665432   234666654  5566742     


Q ss_pred             --CCCCCchHHHHHHHHHHHHhhhh-cCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCceeEEEEEEec
Q 026141           71 --GQIGKPEKEYEIILKRTLQSICI-LTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLAVAICCCSAE  147 (243)
Q Consensus        71 --~~~~~~~~~l~~~l~~~l~~~~~-~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~  147 (243)
                        +.+++++.+++++++|+|++++. .+.|| |.|+|+++||++|||.++|++||+++||+||||||+++++++++|++.
T Consensus       408 ~~g~~~~Reie~~~li~raL~~vI~~~~~~P-~tI~V~~~VLesDGs~~~AsI~aa~lAL~DAGIPm~~~VaavsvGli~  486 (726)
T 4aid_A          408 RMGSPGRREIGHGKLAWRALRPMLPTKEDFP-YTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLIL  486 (726)
T ss_dssp             CCSSCCHHHHHHHHHHHHHHGGGSCCTTTCC-CEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCCEEEEEEEEE
T ss_pred             cCCCcchhhHHHHHHHHHHHHHhcCccccCC-eEEEEEEEEEEcCCcHHHHHHHHHHHHHHhcCCccccCeeEEEEEEEc
Confidence              33556788999999999999998 56776 679999999999999999999999999999999999999999999986


Q ss_pred             CC---eEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHH
Q 026141          148 SG---YCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLS  224 (243)
Q Consensus       148 ~~---~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~  224 (243)
                      ++   .+++||+..|+..++..+.++.+.++++.++...                ..+.++.++|.+|+++|.+++.+|+
T Consensus       487 ~g~~~~iLlD~~~~Ed~~gd~d~~Va~t~~gIt~lQ~d~----------------k~~~~s~e~l~~aL~~A~~g~~~I~  550 (726)
T 4aid_A          487 EQDGFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDI----------------KIAGITPAIMEQALAQAKEGRAHIL  550 (726)
T ss_dssp             CSSCEEEEESCCTTGGGGSSEEEEEEEETTEEEEEEEEE----------------CSSCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCceEEEecCChhHHhcCCceEEEEecCCceEEEEecC----------------CcCCcCHHHHHHHHHHHHHHHHHHH
Confidence            53   5789999999999998898887766555444210                1247899999999999999999999


Q ss_pred             HHHHHHHHhh
Q 026141          225 DFLRRSLQSK  234 (243)
Q Consensus       225 ~~i~~~l~~~  234 (243)
                      +.|++++.++
T Consensus       551 ~~m~~al~~~  560 (726)
T 4aid_A          551 GEMNKAMDAP  560 (726)
T ss_dssp             HHHHTTCSSC
T ss_pred             HHHHHHHHhh
Confidence            9999999864

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

Probab=100.00  E-value=2.6e-32  Score=257.19  Aligned_cols=200  Identities=19%  Similarity=0.165  Sum_probs=169.2

Q ss_pred             CCCCceEEeCCCCC-CCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEecC--CC------------CCCCCch
Q 026141           13 QLRPLACSCSILHR-AHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKP--RT------------GQIGKPE   77 (243)
Q Consensus        13 e~R~i~i~~~~l~~-a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~p--~~------------~~~~~~~   77 (243)
                      .-|++.+++|.+.+ |+|||++++|+|+|+|+|++|...++.    +.+.|.|+|..  ++            +.++.++
T Consensus        13 ~~R~i~ietG~~a~qA~GSa~v~~G~T~VL~tv~~~~~~~~~----df~pL~v~y~~~~~a~g~iPg~f~kRegrps~~e   88 (630)
T 3u1k_A           13 GNRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKPSPS----QFMPLVVDYRQKAAAAGRIPTNYLRREVGTSDKE   88 (630)
T ss_dssp             SSSEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCCSS----SSCCEEEEEECSEETTTTEECTTC-----CCHHH
T ss_pred             CCEEEEEEeCCccccCCeeEEEEECCeEEEEEEEecCCCCCC----CeeEEEEEEEecccccCCCCccccccCCCCCHHH
Confidence            36899999999986 999999999999999999998765432    56668887753  11            2234457


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCCh--HHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEEeCC
Q 026141           78 KEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL--LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDP  155 (243)
Q Consensus        78 ~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~--~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~lvDP  155 (243)
                      .+++++|+|+|++++....  .|.++|+++||++||+.  ..+++||+++||.+++|||++++++|+++++ +|.+|+||
T Consensus        89 ~lisRlIdR~lRp~~~~~~--~~~~qI~~~VLs~Dg~~~~~~aai~aAs~AL~~s~iP~~~~vaav~vg~i-~g~~vldP  165 (630)
T 3u1k_A           89 ILTSRIIDRSIRPLFPAGY--FYDTQVLCNLLAVDGVNEPDVLAINGASVALSLSDIPWNGPVGAVRIGII-DGEYVVNP  165 (630)
T ss_dssp             HHHHHHHHHHHGGGSCTTC--CCCEEEEEEEEECCSSSCHHHHHHHHHHHHHHHSSSCCCCCCEEEEEEEE-TTEEEESC
T ss_pred             HHHHHHHhHHhhhcccccC--CCceEEEEEEEECCCCCCHHHHHHHHHHHHHhccCCCcCCCeEEEEEEEE-CCEEEECC
Confidence            8899999999999998644  47788999999999997  8899999999999999999999999999997 89999999


Q ss_pred             CHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026141          156 TKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHG-AMSVDDYFHCLERGRAASAKLSDFLRRSLQSK  234 (243)
Q Consensus       156 t~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g-~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~  234 (243)
                      |..|++.++..++|+++.++...+                  .++.| .++.+++.+++++|.++++.+++++++.+++.
T Consensus       166 t~~E~~~s~~dl~Va~t~~~~i~m------------------ve~~~~~~se~~~~~al~~a~~~~~~l~~~~~~~~~~~  227 (630)
T 3u1k_A          166 TRKEMSSSTLNLVVAGAPKSQIVM------------------LEASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKET  227 (630)
T ss_dssp             CHHHHHTEEEEEEEEEETTTEEEE------------------EEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHhhCCceEEEEEccCCcEEE------------------EECCCccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999986542222                  22344 48999999999999999999999999999876


Q ss_pred             ccc
Q 026141          235 LPG  237 (243)
Q Consensus       235 ~~~  237 (243)
                      ...
T Consensus       228 ~~~  230 (630)
T 3u1k_A          228 GVT  230 (630)
T ss_dssp             TCC
T ss_pred             CCC
Confidence            543

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

Probab=99.97  E-value=4.6e-29  Score=238.17  Aligned_cols=198  Identities=18%  Similarity=0.166  Sum_probs=165.7

Q ss_pred             CCceEEeCCCC-CCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEecCC--------------CCCCCCchHH
Q 026141           15 RPLACSCSILH-RAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPR--------------TGQIGKPEKE   79 (243)
Q Consensus        15 R~i~i~~~~l~-~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~p~--------------~~~~~~~~~~   79 (243)
                      |++.+++|.+. +|+||+++++|+|+|+|+|+++..  |++ .-+...|+|+|.|.              .|+++.++.+
T Consensus        20 r~i~ietg~ia~qA~GSv~v~~G~T~Vl~tv~~~~~--~~~-~~~f~pltv~y~ek~~a~g~ipg~f~kReGrpse~e~l   96 (723)
T 3cdi_A           20 HTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKK--AKP-GQDFFPLTVNYQERTYAAGRIPGSFFRREGRPSEGETL   96 (723)
T ss_dssp             EEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSS--CCS-SCCSCCEEEEEEECGGGGTCCCC-------CCCHHHHH
T ss_pred             EEEEEEeCccccCCCeeEEEEECCEEEEEEEEecCC--CCC-CCCeeeEEEEEeEeccccccCCCccccCCCCCChHHhH
Confidence            69999999885 799999999999999999998643  321 12445688888753              2334445789


Q ss_pred             HHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCCh--HHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEEeCCCH
Q 026141           80 YEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL--LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDPTK  157 (243)
Q Consensus        80 l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~--~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~lvDPt~  157 (243)
                      ++|+|+|.|++++.. +| +|.++|+++||++||+.  ..+++||+++||..+++|+.+++++|++|++ +|.+|+|||.
T Consensus        97 ~sRlIdR~lRplfp~-~~-~~~vqv~~~vls~Dg~~~~d~~ai~aAsaAL~~s~iP~~~pv~av~vg~i-~g~~v~nPt~  173 (723)
T 3cdi_A           97 IARLIDRPIRPLFPE-GF-VNEVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYI-NDQYVLNPTQ  173 (723)
T ss_dssp             HHHHHHHHHGGGSCT-TC-CSCEEEEEEEEECCTTSCHHHHHHHHHHHHHHHHTSSCCCCCCCEEEEEE-TTEEEESCCT
T ss_pred             HHHHhCccchhcccc-cC-cceEEEEEEEEEcCCCCCHHHHHHHHHHHHHHhcCCCCCCCeEEEEEEEE-CCEEEECcCH
Confidence            999999999999775 34 69999999999999986  5599999999999999999999999999997 8899999999


Q ss_pred             HHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 026141          158 LEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHG-AMSVDDYFHCLERGRAASAKLSDFLRRSLQSKLP  236 (243)
Q Consensus       158 ~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g-~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~~~  236 (243)
                      +|++.++..++++.+.+. +.|.+                  +.| .++.+++.++++.|.+.++++++++++++++...
T Consensus       174 ~e~~~s~~~lvvagt~~~-i~mve------------------~~~~~~se~~~~~al~~a~~~~~~l~~~~~~~~~~~~~  234 (723)
T 3cdi_A          174 DELKESKLDLVVAGTEAA-VLMVE------------------SEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGK  234 (723)
T ss_dssp             TGGGGCSEEEEEEECSSC-EEEEE------------------EEEEEECHHHHHHHHHHHHHHTHHHHHHHHHHHHHTCC
T ss_pred             HHHHhCCceEEEEccCCE-EEEEe------------------CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            999999999999865533 33433                  333 7999999999999999999999999999987655


Q ss_pred             c
Q 026141          237 G  237 (243)
Q Consensus       237 ~  237 (243)
                      .
T Consensus       235 ~  235 (723)
T 3cdi_A          235 P  235 (723)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.96  E-value=1e-28  Score=228.68  Aligned_cols=200  Identities=17%  Similarity=0.146  Sum_probs=165.5

Q ss_pred             CCCCceEEeCCCC-CCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEecC---------C-----CCCCCCch
Q 026141           13 QLRPLACSCSILH-RAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKP---------R-----TGQIGKPE   77 (243)
Q Consensus        13 e~R~i~i~~~~l~-~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~p---------~-----~~~~~~~~   77 (243)
                      .-|++.+++|.+. +|+||+++++|+|+|+|+|+++...++   .-+...|+|+|.+         .     .|+++.++
T Consensus        12 ~~R~i~ietg~~ak~A~GSvlv~~GdT~Vl~tv~~~~~~~~---g~df~Pltv~Y~e~~~a~G~iPg~~~~REGrps~~~   88 (549)
T 3gme_A           12 GQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKP---GQDFFPLTVNYQERTYAAGRIPGSFFRREGRPSEGE   88 (549)
T ss_dssp             TTEEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCCT---TCCSCCEEEEEEECGGGTTCCCSCC-----CCCHHH
T ss_pred             CCEEEEEEECCccCCCCeEEEEEECCEEEEEEEEecCCCCC---CCCCccceeeeeeehhhcccCCCcCcCcCCCCChhh
Confidence            3589999999886 599999999999999999998654321   1233458888752         1     24455567


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCCh--HHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEEeCC
Q 026141           78 KEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL--LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDP  155 (243)
Q Consensus        78 ~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~--~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~lvDP  155 (243)
                      .+++|+|+|.|++++....  .+.++|+++||+.||+.  ..+++||+++||..++||+++++++|++|++ +|.+|+||
T Consensus        89 ~l~~RlIdR~lRplfp~~~--~~evqI~~~Vls~D~~~~pd~~ai~gAs~AL~~s~iP~~gpvaaV~Vg~i-~g~~vlnP  165 (549)
T 3gme_A           89 TLIARLIDRPIRPLFPEGF--VNEVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYI-NDQYVLNP  165 (549)
T ss_dssp             HHHHHHHHHHHGGGSCTTC--CSCEEEEEEEEECCSSSCHHHHHHHHHHHHHHHHCSCCCCCCEEEEEEEE-TTEEEESC
T ss_pred             hHHHHHhCCccccccccCC--cccEEEEEEEEecCCCCcHHHHHHHHHHHHHhccCCCcCCCeeEEEEEEE-CCEEEECC
Confidence            8999999999999988643  46899999999999865  4688999999999999999999999999996 99999999


Q ss_pred             CHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeec-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026141          156 TKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTH-GAMSVDDYFHCLERGRAASAKLSDFLRRSLQSK  234 (243)
Q Consensus       156 t~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~-g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~  234 (243)
                      |.+|++.++..++++++.++ .                  +..++. +.++.+++.+++++|.+.++++++++++++++.
T Consensus       166 t~~e~~~s~~dl~va~t~~~-i------------------~mve~e~~~~se~~~~~al~~a~~~i~~l~~~q~~~~~~~  226 (549)
T 3gme_A          166 TQDELKESKLDLVVAGTEAA-V------------------LMVESEAELLSEDQMLGAVVFGHEQQQVVIQNINELVKEA  226 (549)
T ss_dssp             CTTTTTTCSBCEEEEECSSC-E------------------EEEEEEEEEECHHHHHHHHHHHHHHTHHHHHHHHHHHHHH
T ss_pred             CHHHHhhCceEEEEEecCCe-E------------------EEEEccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999987654 2                  223334 489999999999999999999999999999876


Q ss_pred             ccc
Q 026141          235 LPG  237 (243)
Q Consensus       235 ~~~  237 (243)
                      ...
T Consensus       227 ~~~  229 (549)
T 3gme_A          227 GKP  229 (549)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

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

Probab=99.96  E-value=1.8e-28  Score=233.25  Aligned_cols=200  Identities=17%  Similarity=0.152  Sum_probs=167.5

Q ss_pred             CCCCceEEeCCCC-CCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEec---------C-----CCCCCCCch
Q 026141           13 QLRPLACSCSILH-RAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWK---------P-----RTGQIGKPE   77 (243)
Q Consensus        13 e~R~i~i~~~~l~-~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~---------p-----~~~~~~~~~   77 (243)
                      .-|++.+++|.+. +|+||+++++|+|+|+|+|+++...++   ..+..+|+++|.         |     +.|+++.++
T Consensus        26 ~~R~i~ietg~~ak~A~GSvlv~~GdT~VL~tv~~~~~~~~---g~df~pltveY~ek~~a~G~iPg~~~~REGrps~~~  102 (726)
T 4aid_A           26 GGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKP---GQDFFPLTVNYQEKTFAAGKIPGGFFKREGRPSEKE  102 (726)
T ss_dssp             TTEEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCCT---TCCSCCEEEEEEECGGGGTCCCCSTTCSCCSCCHHH
T ss_pred             CCeeEEEEECCccCCCCeeEEEEECCeEEEEEEEecCCCCC---CCCCcCceeeeeeehhhcccCCCcccCCCCCCCchh
Confidence            4689999999886 599999999999999999998654322   123456888875         2     124455567


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCCh--HHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEEeCC
Q 026141           78 KEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL--LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDP  155 (243)
Q Consensus        78 ~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~--~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~lvDP  155 (243)
                      .+++|+|+|.|++++....  .+.++|+++||+.||+.  ..+++||+++||..+++|+++++++|++|++ +|.+++||
T Consensus       103 ~li~RlIdR~lRplf~~~~--~~evqI~~~Vls~Dg~~~~d~~ai~gAs~AL~~s~iP~~~~vaaV~Vg~i-~g~~vldP  179 (726)
T 4aid_A          103 TLVSRLIDRPIRPLFVKGF--KNEVQVVVTVLQHDLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWV-DGAYVLNP  179 (726)
T ss_dssp             HHHHHHHHHHHGGGBCTTC--CSCEEEEEEEEECCSSSCHHHHHHHHHHHHHHHHTCSBCCCCEEEEEEEE-TTEEEESC
T ss_pred             hhHHHHhCCccccccccCC--ccceEEEEEEEecCCCCChhHHHHHHHHHHHHhcCCCcCCCeEEEEEEEE-CCEEEECC
Confidence            8999999999999988643  47899999999999874  4679999999999999999999999999996 89999999


Q ss_pred             CHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeec-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026141          156 TKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTH-GAMSVDDYFHCLERGRAASAKLSDFLRRSLQSK  234 (243)
Q Consensus       156 t~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~-g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l~~~  234 (243)
                      |.+|++.++..++++++.++ ..|.                  ++. +.++.+++.+++++|.++++++++++++++++.
T Consensus       180 t~~E~~~s~~dl~va~t~~~-i~mv------------------e~~~~~~se~~~~~al~~a~~~i~~l~~~q~~~~~~~  240 (726)
T 4aid_A          180 TLDEMKESKMDLVVAGTADA-VMMV------------------ESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHA  240 (726)
T ss_dssp             CHHHHHTCSEEEEEEECSSC-EEEE------------------EEEESSBCHHHHHHHHHHHHHHTHHHHHHHHHHHHHH
T ss_pred             CHHHHhhCceeEEEEEeCCe-EEEE------------------EccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999987654 2332                  233 489999999999999999999999999999876


Q ss_pred             ccc
Q 026141          235 LPG  237 (243)
Q Consensus       235 ~~~  237 (243)
                      ...
T Consensus       241 g~~  243 (726)
T 4aid_A          241 AKE  243 (726)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.96  E-value=2.9e-27  Score=226.52  Aligned_cols=212  Identities=17%  Similarity=0.064  Sum_probs=168.5

Q ss_pred             CCCceEEeCCCC-CCCceEEEEe-CCeEEEEEEEcCccCCCCCCCCCceEEEEEec---------C-----CCCCCCCch
Q 026141           14 LRPLACSCSILH-RAHGSASWSQ-GDTKVLAAVYGPKAGTKKNENPEKASIEVIWK---------P-----RTGQIGKPE   77 (243)
Q Consensus        14 ~R~i~i~~~~l~-~a~GSa~v~~-G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~---------p-----~~~~~~~~~   77 (243)
                      -|++.+++|.+. +|+||+++++ |+|+|+|+|++|...+|.   .+...|+|+|.         |     +.|+++.++
T Consensus        36 ~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           36 TRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQ---LDFFPLTVDVEERMYAAGKIPGSFFRREGRPSEDA  112 (757)
T ss_dssp             EEEEEEEESSSCTTSSEEEEEEETTTEEEEEEEEEEEEECTT---CSSCCEEEEEEECGGGGTCCCCSTTSSCCSCCHHH
T ss_pred             CEeEEEEECccccCCCeEEEEEECCCeEEEEEEEecCCCCCC---CCCccEEEEEEecccccccCCCcccccCcCCChHH
Confidence            489999999974 7999999999 999999999997665442   23455888884         2     134455568


Q ss_pred             HHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCCh--HHHHHHHHHHHHHHcCCCCCCceeEEEEEEecCCeEEeCC
Q 026141           78 KEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL--LPCAINAACAALVDAGIPMKHLAVAICCCSAESGYCILDP  155 (243)
Q Consensus        78 ~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~--~~a~~~a~~~AL~~a~ip~~~~~~avt~~~~~~~~~lvDP  155 (243)
                      ++++++|+|.|++++.. +| +..++|+++||++||+.  ..+++||+++||.+++|||+++++||++|++ +|.+++||
T Consensus       113 ~l~~RlIdR~LRplfp~-~~-~~evqv~~~Vls~D~~~~~~~~ai~gAs~AL~~s~iP~~~~vaav~vg~~-~g~~vlnP  189 (757)
T 1e3p_A          113 ILTCRLIDRPLRPSFKK-GL-RNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALI-RGQWVAFP  189 (757)
T ss_dssp             HHHHHHHHHHHGGGBCT-TB-CEEEEEEEEEEECCTTSCCHHHHHHHHHHHHHHTTSSBCCCCEEEEEEEE-TTEEEESC
T ss_pred             HHHHHHHCCcchhcccc-CC-CCceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCCCCceEEEEEEEE-CCEEEECC
Confidence            89999999999999875 33 46899999999999865  9999999999999999999999999999997 89999999


Q ss_pred             CHHHHhhccccEEEEeeC----CccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026141          156 TKLEEQKMKGFAYLVFPN----SILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSL  231 (243)
Q Consensus       156 t~~Ee~~~~~~~~v~~~~----~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~a~~~~~~l~~~i~~~l  231 (243)
                      |..|++.++..++++++.    .+...|.+..++++.     ..+.....+.++.+++.+++++|.++++++++++++++
T Consensus       190 t~~e~~~s~~dl~va~t~~~~~~~~i~mvE~q~t~~~-----~~~~~~~~~~~se~~l~~al~~a~~~i~~l~~~q~~~~  264 (757)
T 1e3p_A          190 THTELEDAVFDMVVAGRVLEDGDVAIMMVEAEATEKT-----IQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLA  264 (757)
T ss_dssp             CHHHHTTEEEEEEEEEEECTTSCEEEEEEEEEECSSH-----HHHHHTTCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHhcCceeEEEEeccccCCCCcEEEEEEeccccc-----ccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999873    222233332100000     00000014589999999999999999999999999998


Q ss_pred             Hhhcc
Q 026141          232 QSKLP  236 (243)
Q Consensus       232 ~~~~~  236 (243)
                      ++...
T Consensus       265 ~~~~~  269 (757)
T 1e3p_A          265 AKAAK  269 (757)
T ss_dssp             HHHCC
T ss_pred             HhcCC
Confidence            87654

---

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	243
d2nn6d1	122	d.14.1.4 (D:25-146) Exosome complex exonuclease RR	5e-27
d1r6la1	151	d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Pseu	1e-25
d1udsa1	149	d.14.1.4 (A:2-150) Ribonuclease PH, domain 1 {Aqui	1e-23
d2nn6b1	145	d.14.1.4 (B:6-150) Exosome complex exonuclease RRP	2e-22
d2je6b1	148	d.14.1.4 (B:8-155) Exosome complex exonuclease 1,	3e-22
d2ba0g1	176	d.14.1.4 (G:3-178) Exosome complex exonuclease 2,E	1e-21
d2nn6c1	181	d.14.1.4 (C:7-187) Exosome complex exonuclease RRP	1e-21
d2ba0d1	144	d.14.1.4 (D:10-153) Exosome complex exonuclease 1,	2e-21
d1oysa1	151	d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Baci	4e-21
d2nn6f1	147	d.14.1.4 (F:29-175) Exosome complex exonuclease MT	1e-20
d1e3ha3	137	d.14.1.4 (A:346-482) Polynucleotide phosphorylase/	2e-20
d2nn6e1	187	d.14.1.4 (E:5-191) Exosome complex exonuclease RRP	1e-19
d2je6a1	191	d.14.1.4 (A:1-191) Exosome complex exonuclease 2,E	1e-17
d2nn6a1	184	d.14.1.4 (A:1-184) Exosome complex exonuclease RRP	2e-16
d1e3ha2	149	d.14.1.4 (A:3-151) Polynucleotide phosphorylase/gu	4e-08
d2nn6d2	89	d.101.1.1 (D:147-235) Exosome complex exonuclease	5e-08
d2nn6a2	118	d.101.1.1 (A:185-302) Exosome complex exonuclease	0.004

>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 = 98.6 bits (245), Expect = 5e-27
 Identities = 56/120 (46%), Positives = 79/120 (65%)

Query: 13  QLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQ 72
            LR  AC  ++L R  GSAS+ QGDT VLA VYGP       E   KA++EVI +P+ G 
Sbjct: 3   SLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGL 62

Query: 73  IGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGI 132
            G  EK  E +++ T +++ + T++P T+ +V++QVV D G+LL C +NAAC ALVDAG+
Sbjct: 63  PGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGV 122

>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 = 96.1 bits (238), Expect = 1e-25
 Identities = 33/144 (22%), Positives = 55/144 (38%), Gaps = 13/144 (9%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
           R  GR  +QLRP+  +      A GS     GDTKV+  V       +  +   +  +  
Sbjct: 3   RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTA 62

Query: 65  I-------------WKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
                          +   G+ G    E + ++ R+L++   L+     T  +   V+  
Sbjct: 63  EYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQA 122

Query: 112 DGALLPCAINAACAALVDAGIPMK 135
           DG     +I  A  AL+DA   +K
Sbjct: 123 DGGTRTASITGATVALIDALAVLK 146

>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 = 91.1 bits (225), Expect = 1e-23
 Identities = 36/144 (25%), Positives = 55/144 (38%), Gaps = 13/144 (9%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
           R+DGR  +QLRP++     L    GS   S G TKV+      +      +   +  I  
Sbjct: 1   RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITA 60

Query: 65  I-------------WKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
                          +   G+IG    E + ++ R +++   LT     T  V   V+  
Sbjct: 61  EYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQA 120

Query: 112 DGALLPCAINAACAALVDAGIPMK 135
           DG     AI  A  A+ DA I + 
Sbjct: 121 DGGTATAAITGAFVAVADAIIKLH 144

>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 = 87.6 bits (216), Expect = 2e-22
 Identities = 41/139 (29%), Positives = 68/139 (48%), Gaps = 11/139 (7%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKA--GTKKNENPEKASI 62
           R DGR   +LR +     +  +A GSA   QG+TK LA VYGP    G++    P++A +
Sbjct: 7   RVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALV 66

Query: 63  EVIWKPRTGQIGK---------PEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDG 113
              +   T   G+            E  + L++T ++  +  ++P +   + +QV+  DG
Sbjct: 67  NCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADG 126

Query: 114 ALLPCAINAACAALVDAGI 132
                 +NAA  A++DAGI
Sbjct: 127 GTYAACVNAATLAVLDAGI 145

>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 = 87.2 bits (215), Expect = 3e-22
 Identities = 39/137 (28%), Positives = 62/137 (45%), Gaps = 9/137 (6%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPK---AGTKKNENPEKAS 61
           R DGR P++LR +     +L  A GSA +  G+TK +AAVYGPK          +     
Sbjct: 12  RTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLR 71

Query: 62  IEVIWKPRT------GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
           +     P +          + E E   +++  L+S  ++ + P T   V  +++  D   
Sbjct: 72  VRYHMTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGS 131

Query: 116 LPCAINAACAALVDAGI 132
              ++ AA  AL DAGI
Sbjct: 132 RLVSLMAASLALADAGI 148

>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 = 86.3 bits (213), Expect = 1e-21
 Identities = 34/146 (23%), Positives = 56/146 (38%), Gaps = 15/146 (10%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKA-----GTKKNENPEK 59
           R DGR  ++ R +    +++ +A GSA    GDT+V+  V             +      
Sbjct: 21  RIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYPDTPDRGVIIVN 80

Query: 60  ASIEVIWKP--RTGQIGKPEKEYEIILKRT--------LQSICILTINPNTTTSVIIQVV 109
           A +  +  P    G   +   E   ++ R         L  + I          V I  +
Sbjct: 81  AELVPLASPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHAL 140

Query: 110 HDDGALLPCAINAACAALVDAGIPMK 135
            DDG LL  +  AA AAL++  +P +
Sbjct: 141 DDDGNLLDASALAAIAALMNTKVPAE 166

>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 = 86.4 bits (213), Expect = 1e-21
 Identities = 27/145 (18%), Positives = 42/145 (28%), Gaps = 15/145 (10%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKA-GTKKNENPEKASIE 63
           R DGR   + R    +   +  A GSA    G+T V+  V    A  +    +       
Sbjct: 17  RPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPN 76

Query: 64  VIWKPRTGQIGKP--------------EKEYEIILKRTLQSICILTINPNTTTSVIIQVV 109
           V   P      +                   E       + +CI            +  +
Sbjct: 77  VDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICL 136

Query: 110 HDDGALLPCAINAACAALVDAGIPM 134
             DG +L     A  AAL +  +P 
Sbjct: 137 DYDGNILDACTFALLAALKNVQLPE 161

>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 = 84.9 bits (209), Expect = 2e-21
 Identities = 35/137 (25%), Positives = 62/137 (45%), Gaps = 9/137 (6%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPE------ 58
           R DGR  ++LRP+    S+L RA GS     G  KV+AAV+GP+    ++          
Sbjct: 8   RLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKAIIR 67

Query: 59  ---KASIEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGAL 115
                +   + + +     +   E   + K   +++ +  + P +   + ++V+  D   
Sbjct: 68  YRYNMAPFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGS 127

Query: 116 LPCAINAACAALVDAGI 132
               +NAA  ALVDAG+
Sbjct: 128 RTACLNAASVALVDAGV 144

>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 = 84.2 bits (207), Expect = 4e-21
 Identities = 29/144 (20%), Positives = 49/144 (34%), Gaps = 13/144 (9%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV 64
           R DGR  ++LRP+      +    GS   + G+TKV+                 K  I  
Sbjct: 2   RHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITA 61

Query: 65  I-------------WKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHD 111
                          +   G+I     E + ++ R L+++  L      T  +   V+  
Sbjct: 62  EYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQA 121

Query: 112 DGALLPCAINAACAALVDAGIPMK 135
           DG     +I  A  A+  A   + 
Sbjct: 122 DGGTRTASITGAFLAMAIAIGKLI 145

>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 = 82.6 bits (203), Expect = 1e-20
 Identities = 37/145 (25%), Positives = 54/145 (37%), Gaps = 20/145 (13%)

Query: 8   GRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTK--------------K 53
            R+P +LRP+     +L +A GSA    G TKVL AV GP+                   
Sbjct: 2   TRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAP 61

Query: 54  NENPEKASIEVIWKPRTGQIGKPEKEYEI------ILKRTLQSICILTINPNTTTSVIIQ 107
                +   +    P  G+  +              L+  L+    L   P     V   
Sbjct: 62  AALRGRLLCDFRRAPFAGRRRRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSAL 121

Query: 108 VVHDDGALLPCAINAACAALVDAGI 132
           ++ D G+ L  A+ AA  AL DAG+
Sbjct: 122 LLEDGGSALAAALTAAALALADAGV 146

>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 = 81.8 bits (201), Expect = 2e-20
 Identities = 24/136 (17%), Positives = 53/136 (38%), Gaps = 13/136 (9%)

Query: 13  QLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAG------TKKNENPEKASIEVIW 66
            +R LA     + R HGSA + +G+T++L               T      ++      +
Sbjct: 2   DIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNF 61

Query: 67  KP-------RTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCA 119
            P       R G   + E  +  + +R +  +             + + +  +G+    +
Sbjct: 62  PPYSVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGS 121

Query: 120 INAACAALVDAGIPMK 135
           + A+  +L++AG+P+K
Sbjct: 122 VCASTMSLLNAGVPLK 137

>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 = 81.3 bits (200), Expect = 1e-19
 Identities = 28/144 (19%), Positives = 44/144 (30%), Gaps = 15/144 (10%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEK---AS 61
           R DGR     R +     ++    GSA    G T +L  V       K  +  E      
Sbjct: 19  RVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFF 78

Query: 62  IEVIWKPRTGQIGKPEKEYEIILKRTLQ------------SICILTINPNTTTSVIIQVV 109
           ++          G+   +    +  TL             ++CI          V + ++
Sbjct: 79  VDCSASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLL 138

Query: 110 HDDGALLPCAINAACAALVDAGIP 133
              G L      A  AAL +  IP
Sbjct: 139 ECGGNLFDAISIAVKAALFNTRIP 162

>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 = 76.0 bits (186), Expect = 1e-17
 Identities = 29/151 (19%), Positives = 46/151 (30%), Gaps = 15/151 (9%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKA-------GTKKNENP 57
           R DGR     RPL+ +     +A GSA    G T VLA                      
Sbjct: 28  RQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNLIVN 87

Query: 58  EKASIEVIWKPRTGQIGKPEKEYEIILKRTLQS--------ICILTINPNTTTSVIIQVV 109
            +           G   +   E   ++ R+L+         + I       T  + + V+
Sbjct: 88  VELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVL 147

Query: 110 HDDGALLPCAINAACAALVDAGIPMKHLAVA 140
              G +L     A+ AAL +  +        
Sbjct: 148 DYGGNVLDACTLASVAALYNTKVYKVEQHSN 178

>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 = 72.5 bits (177), Expect = 2e-16
 Identities = 26/145 (17%), Positives = 46/145 (31%), Gaps = 18/145 (12%)

Query: 5   RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVY---GPKAGTKKNENPEKAS 61
           R DGR     R +  S       +G      G T+VL  V          +  E     +
Sbjct: 23  RLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFN 79

Query: 62  IEVIWKPRTGQIGKPEKEYEIILKRTLQSI------------CILTINPNTTTSVIIQVV 109
           +E+            + +  + L R ++              C++         V + ++
Sbjct: 80  LELSQMAAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLL 139

Query: 110 HDDGALLPCAINAACAALVDAGIPM 134
           + DG ++  A  AA  AL     P 
Sbjct: 140 NHDGNIIDAASIAAIVALCHFRRPD 164

>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 = 49.0 bits (116), Expect = 4e-08
 Identities = 25/132 (18%), Positives = 41/132 (31%), Gaps = 13/132 (9%)

Query: 15  RPLACSCSILHR-AHGSASWSQGDTKVLAAVYG------------PKAGTKKNENPEKAS 61
           R +      L R A GSA     D  ++ +               P     +        
Sbjct: 18  RTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDVEERMYAAGK 77

Query: 62  IEVIWKPRTGQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAIN 121
           I   +  R G+  +       ++ R L+      +         I  ++ D      AIN
Sbjct: 78  IPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVVAIN 137

Query: 122 AACAALVDAGIP 133
           AA A+   AG+P
Sbjct: 138 AASASTQLAGLP 149

>d2nn6d2 d.101.1.1 (D:147-235) Exosome complex exonuclease RRP46 {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 RRP46
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 5e-08
 Identities = 25/103 (24%), Positives = 39/103 (37%), Gaps = 17/103 (16%)

Query: 133 PMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPME 192
           PM+ L   + C     G  +LDPT  +E++ +        +                  E
Sbjct: 1   PMRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFALDSV-----------------E 43

Query: 193 HGIITSVTHGAMSVDDYFHCLERGRAASAKLSDFLRRSLQSKL 235
             ++ S T G  S  +   CL   +AAS  +  F R SLQ + 
Sbjct: 44  RKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYRESLQRRY 86

>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 = 34.1 bits (78), Expect = 0.004
 Identities = 15/104 (14%), Positives = 38/104 (36%), Gaps = 23/104 (22%)

Query: 133 PMKHLAVAICCCSAESG-YCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPM 191
            + H+ + +     + G Y ++DP + EE+ M G   +                      
Sbjct: 2   SIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAM-------------------N 42

Query: 192 EHGIITSVTH---GAMSVDDYFHCLERGRAASAKLSDFLRRSLQ 232
           +H  I ++       +  D    C +      A++++ + ++L+
Sbjct: 43  KHREICTIQSSGGIMLLKDQVLRCSKIAGVKVAEITELILKALE 86

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	243
d2ba0d1	144	Exosome complex exonuclease 1, ECX1 {Archaeoglobus	100.0
d2nn6b1	145	Exosome complex exonuclease RRP41 {Human (Homo sap	100.0
d1udsa1	149	Ribonuclease PH, domain 1 {Aquifex aeolicus [TaxId	100.0
d2je6b1	148	Exosome complex exonuclease 1, ECX1 {Sulfolobus so	100.0
d1oysa1	151	Ribonuclease PH, domain 1 {Bacillus subtilis [TaxI	99.98
d1r6la1	151	Ribonuclease PH, domain 1 {Pseudomonas aeruginosa	99.98
d2nn6d1	122	Exosome complex exonuclease RRP46 {Human (Homo sap	99.98
d2ba0g1	176	Exosome complex exonuclease 2,ECX2 {Archaeoglobus	99.97
d2je6a1	191	Exosome complex exonuclease 2,ECX2 {Sulfolobus sol	99.97
d2nn6c1	181	Exosome complex exonuclease RRP43 {Human (Homo sap	99.97
d2nn6e1	187	Exosome complex exonuclease RRP42 {Human (Homo sap	99.96
d1e3ha3	137	Polynucleotide phosphorylase/guanosine pentaphosph	99.96
d2nn6a1	184	Exosome complex exonuclease RRP45 {Human (Homo sap	99.96
d2nn6f1	147	Exosome complex exonuclease MTR3 {Human (Homo sapi	99.95
d1e3ha2	149	Polynucleotide phosphorylase/guanosine pentaphosph	99.88
d2nn6d2	89	Exosome complex exonuclease RRP46 {Human (Homo sap	99.69
d2nn6a2	118	Exosome complex exonuclease RRP45 {Human (Homo sap	99.69
d2je6a2	84	Exosome complex exonuclease 2, ECX2 {Sulfolobus so	99.68
d2nn6e2	94	Exosome complex exonuclease RRP42 {Human (Homo sap	99.66
d2nn6c2	89	Exosome complex exonuclease RRP43 {Human (Homo sap	99.65
d2nn6b2	90	Exosome complex exonuclease RRP41 {Human (Homo sap	99.61
d2ba0g2	79	Exosome complex exonuclease 2, ECX2 {Archaeoglobus	99.6
d2je6b2	86	Exosome complex exonuclease 1, ECX1 {Sulfolobus so	99.6
d1r6la2	88	Ribonuclease PH, domain 2 {Pseudomonas aeruginosa	99.51
d2ba0d2	99	Exosome complex exonuclease 1, ECX1 {Archaeoglobus	99.41
d2nn6f2	95	Exosome complex exonuclease MTR3 {Human (Homo sapi	99.37
d1oysa2	86	Ribonuclease PH, domain 2 {Bacillus subtilis [TaxI	99.32
d1udsa2	105	Ribonuclease PH, domain 2 {Aquifex aeolicus [TaxId	99.24
d1e3ha5	111	Polynucleotide phosphorylase/guanosine pentaphosph	98.32
d1e3ha6	96	Polynucleotide phosphorylase/guanosine pentaphosph	96.59

>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=100.00  E-value=6.7e-35  Score=226.77  Aligned_cols=132  Identities=30%  Similarity=0.502  Sum_probs=117.1

Q ss_pred             CCCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCC-CCCCCCceEEEEEec--CCCC------
Q 026141            1 MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTK-KNENPEKASIEVIWK--PRTG------   71 (243)
Q Consensus         1 ~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~-~~~~~~~~~l~v~~~--p~~~------   71 (243)
                      .+|+|+|||+++|+|++++++|++++++|||+|++|+|+|+|+|+||.+... ..+.++++.+++++.  |++.      
T Consensus         4 ~~g~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~   83 (144)
T d2ba0d1           4 VDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKAIIRYRYNMAPFSVEERKRP   83 (144)
T ss_dssp             CSSCBTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEEECCSGGGCCSSSCEEEEEEEECTTSSSSCCCS
T ss_pred             cCCcCCCCCCCCCccCeEEEECCCCCCCceEEEEEcccceEEEEeccchhhhhhcccccceEEEEEEecCCccccccccc
Confidence            4799999999999999999999999999999999999999999999987543 446788999887764  4321      


Q ss_pred             CCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCC
Q 026141           72 QIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGI  132 (243)
Q Consensus        72 ~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~i  132 (243)
                      .+.+.+.+++++|+++|++++.++.||+|.|+|+++||++|||+++|++||+++||+||||
T Consensus        84 ~~~~~~~~l~~~l~~~l~~~i~~~~~~~~~i~v~v~VL~~DG~~~~a~i~aa~lAL~daGI  144 (144)
T d2ba0d1          84 GPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACLNAASVALVDAGV  144 (144)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTBCGGGCTTEEEEEEEEEEECCTTHHHHHHHHHHHHHHHHTC
T ss_pred             CCCchhhhhhhhhhhhhccccchhhcCCeEEEEEEEEEccCCCHHHHHHHHHHHHHHHcCC
Confidence            1223467899999999999999999999999999999999999999999999999999997

>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=100.00  E-value=1e-34  Score=226.07  Aligned_cols=131  Identities=29%  Similarity=0.489  Sum_probs=116.3

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCC--CCCCCceEEEEEec--CCC-------
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKK--NENPEKASIEVIWK--PRT-------   70 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~--~~~~~~~~l~v~~~--p~~-------   70 (243)
                      +|+|+|||+++|+|++++++|++++++|||+|++|+|+|+|+|+||.+.++.  .+.++++.++|+|.  |++       
T Consensus         4 ~g~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~~v~v~~~~~~~~~~~~~~~   83 (145)
T d2nn6b1           4 QGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATFSTGERKRR   83 (145)
T ss_dssp             TTBCSSSSCTTSCCCEEEEESCSSSSSEEEEEEESSCEEEEEEEEEEECCSSSCCCCCSSCCEEEEEEECTTTSSSCCCT
T ss_pred             CCccCCCCCCCCccCeEEEECCCCCCCceEEEEeCCceEEEEEEeccccccchhhccccceeEEEEeeecCccccccccc
Confidence            6999999999999999999999999999999999999999999998866443  45688999888765  322       


Q ss_pred             CCCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCC
Q 026141           71 GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGI  132 (243)
Q Consensus        71 ~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~i  132 (243)
                      +..++++.+++++|+++|++.++.+.||+|.|+|+++||++|||+++|++||+++||+|+||
T Consensus        84 ~~~~~~~~~l~~~l~~~l~~~i~~~~~~~~~I~v~v~VL~~DG~l~~a~i~aa~lAL~daGI  145 (145)
T d2nn6b1          84 PHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGI  145 (145)
T ss_dssp             TTSTHHHHHHHHHHHHHHHHTTCGGGCTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCchhhhHHHHHHHhhhcccchHhhCceeeEEEEEEEeCCCCHHHHHHHHHHHHHHHcCC
Confidence            11233467899999999999999999999999999999999999999999999999999997

>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=100.00  E-value=2.1e-34  Score=225.19  Aligned_cols=131  Identities=28%  Similarity=0.344  Sum_probs=115.1

Q ss_pred             CCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cCCCC-----------
Q 026141            5 RADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KPRTG-----------   71 (243)
Q Consensus         5 R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p~~~-----------   71 (243)
                      |+|||+++|+|++++++|++++++|||+|++|+|+|+|+|++|...++....++++.+.+++  .|...           
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            89999999999999999999999999999999999999999987655555778888877654  45311           


Q ss_pred             CCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCC
Q 026141           72 QIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMK  135 (243)
Q Consensus        72 ~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~  135 (243)
                      .....+.+++++++++++++|.++.||+|.|+|+++||++|||+++|++||+++||+|+||||+
T Consensus        81 ~~~~~~~~~~~~l~~~l~~~i~l~~~~~~~i~v~v~VL~~DG~l~da~~~A~~~AL~dagipm~  144 (149)
T d1udsa1          81 RIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGGTATAAITGAFVAVADAIIKLH  144 (149)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHBCGGGSCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccchhHHHHHHHhhhhheehhhhcCCceEEEEEEEEccCCCHHHHHHHHHHHHHHHhChHHH
Confidence            1122346889999999999999999999999999999999999999999999999999999986

>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=100.00  E-value=1.3e-33  Score=220.48  Aligned_cols=131  Identities=32%  Similarity=0.540  Sum_probs=116.8

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCC-CCCCCCCceEEEEEe--cCCC------CC
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGT-KKNENPEKASIEVIW--KPRT------GQ   72 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~-~~~~~~~~~~l~v~~--~p~~------~~   72 (243)
                      +|+|+|||.++|+|++.+++|+++++||||+|++|+|+|+|+|+||.+.. +..+.++++.++|++  .|+.      +.
T Consensus         9 ~g~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~   88 (148)
T d2je6b1           9 DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDERKNPA   88 (148)
T ss_dssp             TSCBTTSCCTTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECSSGGGSCSSSCEEEEEEEECTTSSSSCCCSS
T ss_pred             CCccCCCCCCCCccCeEEEECCCCCCCEEEEEEcCCccEEeecccCccccchhhcCCcceEEEEEEEecccccccccccc
Confidence            68999999999999999999999999999999999999999999997653 445678999888765  4542      22


Q ss_pred             CCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCC
Q 026141           73 IGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGI  132 (243)
Q Consensus        73 ~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~i  132 (243)
                      +.+++.+++++|+++|++++.++.||++.|+|+++||++||++++|++||+++||+|+||
T Consensus        89 ~~~~~~el~~~l~~~l~~~i~~~~~p~~~i~v~v~VL~~DG~~~~a~i~aa~~AL~daGI  148 (148)
T d2je6b1          89 PSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGI  148 (148)
T ss_dssp             CCHHHHHHHHHHHHHHHTTBCGGGSTTEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTC
T ss_pred             ccchhHHHHHHHHHHhhccccHHHcCCEEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCC
Confidence            334568899999999999999999999999999999999999999999999999999997

>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=99.98  E-value=3.5e-33  Score=218.55  Aligned_cols=130  Identities=22%  Similarity=0.255  Sum_probs=108.1

Q ss_pred             CCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cCCCC----------
Q 026141            4 DRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KPRTG----------   71 (243)
Q Consensus         4 ~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p~~~----------   71 (243)
                      +|+|||+++|+|++++++|++++++|||+|++|+|+|+|+|++|...++..+.+++|.+.++|  .|...          
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            699999999999999999999999999999999999999999877777778889999887765  34211          


Q ss_pred             -CCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCC
Q 026141           72 -QIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIP  133 (243)
Q Consensus        72 -~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip  133 (243)
                       .....+.+++++++++|++++.++.||+|.|+|+++||++|||+++|++||+++||+||.++
T Consensus        81 ~~~~~~~~~~~~~l~~~l~~~i~l~~~~~~~i~v~v~VL~~DG~l~~a~i~Aa~~AL~dA~~~  143 (151)
T d1oysa1          81 GKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGK  143 (151)
T ss_dssp             ----CHHHHHHHHHHHHHHHTBCHHHHCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CcccchhhHHhHHHHHHhhhhhhhhhhccceEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHH
Confidence             12234678999999999999999999999999999999999999999999999999998554

>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=99.98  E-value=1.4e-32  Score=215.17  Aligned_cols=132  Identities=26%  Similarity=0.326  Sum_probs=112.5

Q ss_pred             CCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cCCCCCC--------
Q 026141            4 DRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KPRTGQI--------   73 (243)
Q Consensus         4 ~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p~~~~~--------   73 (243)
                      .|+|||+++|+|++.+++|+++++||||+|++|+|+|+|+|++|...++..+.++++.+.+++  .|+....        
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            499999999999999999999999999999999999999999987766666778888887665  4543211        


Q ss_pred             ---CCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCC
Q 026141           74 ---GKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMK  135 (243)
Q Consensus        74 ---~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~  135 (243)
                         ...+.++++.+.+++++++.+..+|+|.|+|+++||++|||+++|+++|+++||+|+||||+
T Consensus        82 ~~~~~~~~~~~~~l~~~~~~~~~l~~~~~~~i~v~v~VL~~DG~~~da~~~Aa~~AL~dagip~~  146 (151)
T d1r6la1          82 GKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADGGTRTASITGATVALIDALAVLK  146 (151)
T ss_dssp             TSCCHHHHHHHHHHHHHHHHTBCGGGTCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccchhHHHHHHhhhhhccchhhhCceEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhcHHHH
Confidence               11234778889999999999999999999999999999999999999999999999999985

>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=99.98  E-value=4.4e-32  Score=205.09  Aligned_cols=121  Identities=46%  Similarity=0.752  Sum_probs=111.1

Q ss_pred             CCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEecCCCCCCCCchHHHHHHHHHHHHhh
Q 026141           12 NQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWKPRTGQIGKPEKEYEIILKRTLQSI   91 (243)
Q Consensus        12 ~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~p~~~~~~~~~~~l~~~l~~~l~~~   91 (243)
                      .|+|++.+++|+++++||||+|++|+|+|+|+|+||.+.+++.+.++++.++|+++|..+.+++.+++++++|+++|+++
T Consensus         2 ~elR~i~~~~gvl~~adGSa~~~~G~T~Vi~~V~gP~e~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~l~~~l~~~   81 (122)
T d2nn6d1           2 CSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAV   81 (122)
T ss_dssp             CCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECC------CCEEEEEEEECSSSCCCHHHHHHHHHHHHHHHHH
T ss_pred             CccceEEEEECCCCCCCeEEEEEECCcEEEEEEEecccccchhhCcCCCceEEEeeeecCCCCchhhHHHHHHHhhhhcc
Confidence            48999999999999999999999999999999999998888888899999999999988888888899999999999999


Q ss_pred             hhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCC
Q 026141           92 CILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGI  132 (243)
Q Consensus        92 ~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~i  132 (243)
                      |+++.||+|.|+|+++|+++||++++|++||+++||+|+||
T Consensus        82 i~~~~~p~~~i~i~v~Vl~~DG~~~~a~ina~~lAL~dagI  122 (122)
T d2nn6d1          82 VLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGV  122 (122)
T ss_dssp             CGGGCSSSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTC
T ss_pred             cchhhcCCeEEEEEEEEEcCCCChhHHHHHHHHHHHHHcCC
Confidence            99999999999999999999999999999999999999997

>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=99.97  E-value=1.1e-31  Score=215.19  Aligned_cols=137  Identities=26%  Similarity=0.351  Sum_probs=116.9

Q ss_pred             CCCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEE--ecCCCC------C
Q 026141            1 MEVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVI--WKPRTG------Q   72 (243)
Q Consensus         1 ~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~--~~p~~~------~   72 (243)
                      .+|+|+|||+++|+|++.+++|.+++++|||+|++|+|+|+|+|++ ....|....|++|.+.++  +.|+..      .
T Consensus        17 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~-~~~~p~~~~~~~g~~~~~v~~~~~~~~~~~~~~   95 (176)
T d2ba0g1          17 RDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKM-QPGEPYPDTPDRGVIIVNAELVPLASPTFEPGP   95 (176)
T ss_dssp             TTTCCTTCCCTTCCCCEEEEECCCTTSSEEEEEEETTEEEEEEEEE-EEECCCTTCTTCCEEEEEEECCTTTCTTSCSSS
T ss_pred             HhCCCCCCCCCCCccCeEEEeCccCCCCeEEEEEeCCcEEEEEEec-cccccccccCCCceeeeeeEeccccCccccCCC
Confidence            4799999999999999999999999999999999999999999997 455677788998887655  455322      1


Q ss_pred             CCCchHHHHHHHHHHH--------HhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCCce
Q 026141           73 IGKPEKEYEIILKRTL--------QSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKHLA  138 (243)
Q Consensus        73 ~~~~~~~l~~~l~~~l--------~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~~~  138 (243)
                      .+..+..+++++++++        +++|+.+++++|.|+|+++||++|||+++|+++|+++||+|+|||+..+.
T Consensus        96 ~~~~~~~~~~~l~~~~~~~~~i~~e~L~i~~~~~~~~i~i~v~VL~~DG~l~dA~~~A~~~AL~da~iP~~~~~  169 (176)
T d2ba0g1          96 PDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFD  169 (176)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHTTCEECTGGGT
T ss_pred             CCchhHHHHHHHHHhhccccccchhhccCCCCCceEEEEEEEEEEeCCCCHHHHHHHHHHHHHHHcCCCcEEec
Confidence            2233567888888875        45788889999999999999999999999999999999999999987653

>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=99.97  E-value=3.4e-30  Score=208.98  Aligned_cols=134  Identities=23%  Similarity=0.222  Sum_probs=113.0

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cCCCC------CC
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KPRTG------QI   73 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p~~~------~~   73 (243)
                      +|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|++|. ..|....|+++.+.+++  .+...      ..
T Consensus        25 ~giR~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~a~V~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (191)
T d2je6a1          25 KGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEI-DKPYEDTPNQGNLIVNVELLPLAYETFEPGPP  103 (191)
T ss_dssp             GTBCTTSCBTTCCCCEEEEETCSTTSSEEEEEEETTEEEEEEEEEEE-ECCCTTCTTCCEEEEEEEECTTSCTTCCCSSC
T ss_pred             cCCCCCCcCCCCccCeEEEECCccCcCceEEEEcCCceEEEEEEecc-cCchhccCccCccccccccccccccccccccC
Confidence            79999999999999999999999999999999999999999999965 45556788888876654  34321      12


Q ss_pred             CCchHHHHHHHHHHH--------HhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCC
Q 026141           74 GKPEKEYEIILKRTL--------QSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKH  136 (243)
Q Consensus        74 ~~~~~~l~~~l~~~l--------~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~  136 (243)
                      .+.+..+++.|++.+        +++|+.+++++|.|+|+++||++|||+++|+++|+++||+|++||+..
T Consensus       104 ~~~~~~l~~~l~~~~~~~~~id~~~l~i~~~~~~w~I~v~v~VL~~DG~l~dA~~~A~~~AL~da~iP~v~  174 (191)
T d2je6a1         104 DENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVE  174 (191)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCSCGGGGEEETTTEEEEEEEEEEEEECCSCHHHHHHHHHHHHHHTCEEEEEE
T ss_pred             CcchhHHHHHHHHhhcchhhcccccccccCccccEEEEEEEEEEcCCCCHHHHHHHHHHHHHHHcCCCeEE
Confidence            223567788888775        457788899999999999999999999999999999999999999643

>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=99.97  E-value=6.2e-30  Score=205.20  Aligned_cols=133  Identities=21%  Similarity=0.255  Sum_probs=110.7

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cCCCC------CC
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KPRTG------QI   73 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p~~~------~~   73 (243)
                      +|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|++|. ..+....++++.+.+++  .+...      ..
T Consensus        14 ~giR~DGR~~~e~R~~~i~~g~l~~a~GSa~v~~G~T~v~~~v~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   92 (181)
T d2nn6c1          14 ENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEF-AAPSTDAPDKGYVVPNVDLPPLCSSRFRSGPP   92 (181)
T ss_dssp             TSCCTTSCCSCCCCSCCEEETCCSSSSEEEEEEETTEEEEEEEEEEE-CCCCSSSTTCCCCEEEEECCSSSCTTSCSSSC
T ss_pred             cCCCCCCcCCCCccCeEEEeCCcCCCCeEEEEEeCCcEEEEEEeccc-cccccccCCCceeeeeeeeeccccccccccCC
Confidence            68999999999999999999999999999999999999999999954 45556677777766654  33221      11


Q ss_pred             CCchHHHHHHHHHHH--------HhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCC
Q 026141           74 GKPEKEYEIILKRTL--------QSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMK  135 (243)
Q Consensus        74 ~~~~~~l~~~l~~~l--------~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~  135 (243)
                      ......+.+.+++.+        +++|+.+++++|.|+|+++||++|||++||+++|+++||+|++||+.
T Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~~~~~~i~i~v~vl~~DG~l~da~~~A~~~AL~d~~iP~v  162 (181)
T d2nn6c1          93 GEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEV  162 (181)
T ss_dssp             CHHHHHHHHHHHHHHHHHCCSCHHHHCSSBTTBCEEEEEEEEESSCCSCTTHHHHHHHHHHHHTCCCCCC
T ss_pred             CchhhhhHHHHHHHHHhhhhhhhhhccccCCcceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCCeE
Confidence            223456677777664        66788899999999999999999999999999999999999999973

>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=99.96  E-value=3e-30  Score=208.66  Aligned_cols=132  Identities=25%  Similarity=0.287  Sum_probs=113.0

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEe--cCCCCC---C---
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIW--KPRTGQ---I---   73 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~--~p~~~~---~---   73 (243)
                      +|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|++| ...|....|++|.+.+++  .|..+.   +   
T Consensus        16 ~~iR~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~~-~~~~~~~~~~~g~~~~~v~~~~~~~~~~~~~~~   94 (187)
T d2nn6e1          16 EDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAE-MGTPKLEKPNEGYLEFFVDCSASATPEFEGRGG   94 (187)
T ss_dssp             TTCCSSSCCSSCCCCCEEEECCCTTSSSEEEEEETTEEEEEECCCC-CSCCCSSSCSSCCEEEECCCCTTTCSSCCTTST
T ss_pred             hCCCCCCcCCCCccCeEEEeCccCCCCceEEEEeCCceEEEEEEec-cccccccccccceeeeeeeeccccccCcCCCCc
Confidence            6899999999999999999999999999999999999999999995 456667788888877665  443221   1   


Q ss_pred             CCchHHHHHHHHHHHHh--------hhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCC
Q 026141           74 GKPEKEYEIILKRTLQS--------ICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPM  134 (243)
Q Consensus        74 ~~~~~~l~~~l~~~l~~--------~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~  134 (243)
                      +..+.++++++++.|++        +|+.+++++|.|+|+++||++|||+++|+++|+++||+|+++|.
T Consensus        95 ~~~~~~ls~~l~~~l~~~~~~d~~~L~i~~~~~~w~i~v~v~vL~~DG~~~da~~~A~~~AL~d~~iP~  163 (187)
T d2nn6e1          95 DDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPR  163 (187)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCSCSSSSCSSTTTCCCCEEEEEEECCCCSSHHHHHHHHHHHTTTTCCCCE
T ss_pred             chHHHHHHHHHHHHhccccccchhhheecCCCccEEEEEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCE
Confidence            12245788888888854        56778899999999999999999999999999999999999994

>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=99.96  E-value=2.7e-29  Score=193.31  Aligned_cols=124  Identities=18%  Similarity=0.266  Sum_probs=102.0

Q ss_pred             CCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCC----CCCceEEEEEe--cCC-------CCCCCCchH
Q 026141           12 NQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNE----NPEKASIEVIW--KPR-------TGQIGKPEK   78 (243)
Q Consensus        12 ~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~----~~~~~~l~v~~--~p~-------~~~~~~~~~   78 (243)
                      .|+|++++++|+++++||||+|++|+|+|+|+|++|...+....    .-....+.+++  .|+       .+.++++++
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            48999999999999999999999999999999998765432211    11222333333  332       122345578


Q ss_pred             HHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCC
Q 026141           79 EYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMK  135 (243)
Q Consensus        79 ~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~  135 (243)
                      ++++.++++|+++|.++.||+|.|+|+++||++|||+++|++||+++||+|+||||+
T Consensus        81 ~~~~~i~~~l~~~i~~~~~~~~~I~v~v~vl~~DG~~~~aainAa~lAL~dAGIpmk  137 (137)
T d1e3ha3          81 GHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLK  137 (137)
T ss_dssp             HHHHHHHHHHGGGCCCTTTSCEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCCS
T ss_pred             ccchHHHHHHHhccchhhcCcEEEEEEEEEecCCCCHHHHHHHHHHHHHHHcCCccC
Confidence            999999999999999999999999999999999999999999999999999999996

>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=99.96  E-value=1.3e-28  Score=198.42  Aligned_cols=131  Identities=21%  Similarity=0.246  Sum_probs=109.6

Q ss_pred             CCCCCCCCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEE--EecCCCC---CCC--
Q 026141            2 EVDRADGRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEV--IWKPRTG---QIG--   74 (243)
Q Consensus         2 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v--~~~p~~~---~~~--   74 (243)
                      +|+|+|||+++|+|++.+++|   .++|||+|++|+|+|+|+|++|. ..|....|++|.+.+  ++.|..+   ..+  
T Consensus        20 ~~~R~DGR~~~e~R~~~i~~g---~a~GSa~v~~G~T~V~~~V~~~~-~~p~~~~~~~g~~~~~v~~~~~~~~~~~~~~~   95 (184)
T d2nn6a1          20 EKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCEL-VSPKLNRATEGILFFNLELSQMAAPAFEPGRQ   95 (184)
T ss_dssp             TTCCTTSCCTTCCCCCEEEEC---SSTTEEEEESSSCEEEEEECCEE-ECCCSTTTTSCCEEEEEEECTTTCSSCCSSST
T ss_pred             hCcCCCCCCCCCcCCeEEEec---CCCCEEEEEeCCCEEEEEEEecc-ccccccCCCccceeEEEEeccccCcccccCCC
Confidence            789999999999999999998   48999999999999999999954 456677888887655  4555432   122  


Q ss_pred             -CchHHHHHHHHHHHH--------hhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCCCCC
Q 026141           75 -KPEKEYEIILKRTLQ--------SICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIPMKH  136 (243)
Q Consensus        75 -~~~~~l~~~l~~~l~--------~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip~~~  136 (243)
                       ..+.++++.|++.+.        ++|+++++++|.|+|+++||++|||++||+++|+++||+|+++|...
T Consensus        96 ~~~~~~l~~~l~~~~~~~~~~d~~~L~i~~~~~~w~i~i~v~VL~~DG~~~da~~~a~~~AL~~~~iP~v~  166 (184)
T d2nn6a1          96 SDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVS  166 (184)
T ss_dssp             HHHHTHHHHHHHHHHHHHTCBCSSSSCSBTTTBEEEEEEEEEECSCCSCCHHHHHHHHHHHHHHCCCCCCB
T ss_pred             CchhHHHHHHHHhhhhhhhhhhhhhhccccccCcEEEEEEEEEECCCCCHHHHHHHHHHHHHHhhCCCeEE
Confidence             224677788887754        46888999999999999999999999999999999999999999654

>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=99.95  E-value=2.2e-28  Score=189.88  Aligned_cols=126  Identities=32%  Similarity=0.497  Sum_probs=103.7

Q ss_pred             CCCCCCCCCceEEeCCCCCCCceEEEEeCCeEEEEEEEcCccCCCCCC------------CCCceEE--EEEecCCCCCC
Q 026141            8 GRNPNQLRPLACSCSILHRAHGSASWSQGDTKVLAAVYGPKAGTKKNE------------NPEKASI--EVIWKPRTGQI   73 (243)
Q Consensus         8 GR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~------------~~~~~~l--~v~~~p~~~~~   73 (243)
                      .|+++|+|++.+++|++++++|||+|++|+|+|+|+|+||.+.++...            .+..+.+  ++++.|+.+..
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            589999999999999999999999999999999999999987655432            1233444  44556653321


Q ss_pred             ------CCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCC
Q 026141           74 ------GKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIP  133 (243)
Q Consensus        74 ------~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip  133 (243)
                            ...+.+++..+.+.++++++++.||+|.|+|+++||++|||+++|++||+++||+|+||.
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~i~v~v~Vl~~DG~l~~a~i~A~~~AL~daGIe  147 (147)
T d2nn6f1          82 RRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVE  147 (147)
T ss_dssp             CCCSCCHHHHHHHHHHHHHHHTTTBCSTTSBTCEEEEEEEEEECCSSHHHHHHHHHHHHHHHHCCC
T ss_pred             ccccCCccchhhhhhhhhhcccccccccccCCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHhCCC
Confidence                  123578999999999999999999999999999999999999999999999999999984

>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=99.88  E-value=2.2e-22  Score=156.18  Aligned_cols=129  Identities=20%  Similarity=0.173  Sum_probs=103.0

Q ss_pred             CCCCCCCCCCCCCceEEeCCCC-CCCceEEEEeCCeEEEEEEEcCccCCCCCCCCCceEEEEEec-------C-----CC
Q 026141            4 DRADGRNPNQLRPLACSCSILH-RAHGSASWSQGDTKVLAAVYGPKAGTKKNENPEKASIEVIWK-------P-----RT   70 (243)
Q Consensus         4 ~R~DGR~~~e~R~i~i~~~~l~-~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~l~v~~~-------p-----~~   70 (243)
                      .+.|+|.+.+ |+|++++|.++ +|||||+|++|+|+|+|+++++....+....+..+.+.....       |     ..
T Consensus         8 ~~~~~~~~~~-R~i~ie~G~lakqA~GSalv~~G~T~vl~ta~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~rre   86 (149)
T d1e3ha2           8 AVIDNGAFGT-RTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDVEERMYAAGKIPGSFFRRE   86 (149)
T ss_dssp             EEEECGGGCE-EEEEEEESSSCTTSSEEEEEEETTTEEEEEEEEECSSCCTTCSSCCEEEEEEECGGGGTCCCCSTTSSC
T ss_pred             EEEeCCcCCC-cEEEEEeCcccccCCceEEEEECCcEEEEEeeecccccccccccCCceeEEEEeccccccccccccccc
Confidence            4678887766 99999999996 699999999999999999987544333333344444444321       1     12


Q ss_pred             CCCCCchHHHHHHHHHHHHhhhhcCCCCceEEEEEEEEEeCCCChHHHHHHHHHHHHHHcCCC
Q 026141           71 GQIGKPEKEYEIILKRTLQSICILTINPNTTTSVIIQVVHDDGALLPCAINAACAALVDAGIP  133 (243)
Q Consensus        71 ~~~~~~~~~l~~~l~~~l~~~~~~~~~~~~~i~i~v~vl~~dG~~~~a~~~a~~~AL~~a~ip  133 (243)
                      +.+++++.+++++|+|+|++++....++..+|.+++.+++.||+...|++||+++||+++|||
T Consensus        87 ~~~~~reil~~rlidR~Lrpl~p~~~~~~~qI~~~vl~~d~d~~~~~aai~aAs~AL~~agIP  149 (149)
T d1e3ha2          87 GRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLP  149 (149)
T ss_dssp             CSCCHHHHHHHHHHHHHHHHHBCTTBCSCEEEEEEEEECCTTSCCHHHHHHHHHHHHHHTTCS
T ss_pred             cccchHHHHHHHHHHHHHHhhccccCCCceEEEEEEEEeCCCCChHHHHHHHHHHHHHhcCCC
Confidence            334556789999999999999998878888888888889999999999999999999999998

>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=99.69  E-value=1.2e-16  Score=112.84  Aligned_cols=88  Identities=27%  Similarity=0.461  Sum_probs=77.2

Q ss_pred             CCCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHH
Q 026141          133 PMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHC  212 (243)
Q Consensus       133 p~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~  212 (243)
                      ||+++++||++|++.+|.+|+|||..||+.+.+.+++++.+..                 ...+.+...|.++.+++.++
T Consensus         1 Pm~~~v~av~~~~~~dg~~vlDpt~~Ee~~~~~~~~~a~~~~~-----------------~~i~~~~~~g~~s~~~~~~~   63 (89)
T d2nn6d2           1 PMRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFALDSVE-----------------RKLLMSSTKGLYSDTELQQC   63 (89)
T ss_dssp             CCSSCEEEEEEEECTTCCEEESCCHHHHHHCSEEEEEEEETTT-----------------CCCCEEEEEESCCHHHHHHH
T ss_pred             CCCCCEeEEEEEEEcCCceeeCCCHHHHhhcceEEEEEEEcCC-----------------CeEEEEeecCCcCHHHHHHH
Confidence            8999999999999878899999999999999999999986542                 12333446789999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhccc
Q 026141          213 LERGRAASAKLSDFLRRSLQSKLPG  237 (243)
Q Consensus       213 l~~a~~~~~~l~~~i~~~l~~~~~~  237 (243)
                      +++|.++|++|+++++++|+++..+
T Consensus        64 l~~a~~~~~~I~~~~r~~l~k~~~k   88 (89)
T d2nn6d2          64 LAAAQAASQHVFRFYRESLQRRYSK   88 (89)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            9999999999999999999988765

>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=99.69  E-value=4.1e-17  Score=121.26  Aligned_cols=93  Identities=13%  Similarity=0.311  Sum_probs=82.6

Q ss_pred             CCCCCceeEEEEEEecC-CeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEeecCCCCHHHH
Q 026141          132 IPMKHLAVAICCCSAES-GYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDY  209 (243)
Q Consensus       132 ip~~~~~~avt~~~~~~-~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l  209 (243)
                      ++++|+|+++||++++. +.+|+|||..||.++++.++++++.++ +|.++|+                 +.+.++.+++
T Consensus         1 L~i~h~Pi~vT~~~~~~g~~~lvDPt~~EE~~~~~~ltv~~n~~gei~~l~k~-----------------Gg~~l~~~~l   63 (118)
T d2nn6a2           1 LSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSS-----------------GGIMLLKDQV   63 (118)
T ss_dssp             CCBCCCEEEEEEEECTTTSSEEESCCHHHHHHCSCEEEEEEETTTEEEEEEEE-----------------SCCCCCHHHH
T ss_pred             CCcCceEEEEEEEEEecCCeEEECCCHHHHhCCCCcEEEEEeCCCcEEEEEec-----------------CCcccCHHHH
Confidence            47899999999999854 579999999999999999999999885 8887764                 2458999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhccccccc
Q 026141          210 FHCLERGRAASAKLSDFLRRSLQSKLPGDLSK  241 (243)
Q Consensus       210 ~~~l~~a~~~~~~l~~~i~~~l~~~~~~~~~~  241 (243)
                      .+|++.|...+++|+++++++|+++..+|..+
T Consensus        64 ~~~~~~A~~~~~el~~~i~~aLk~~~~~R~~~   95 (118)
T d2nn6a2          64 LRCSKIAGVKVAEITELILKALENDQKVRKEG   95 (118)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            99999999999999999999999888777644

>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=99.68  E-value=9.2e-17  Score=112.28  Aligned_cols=82  Identities=22%  Similarity=0.359  Sum_probs=74.4

Q ss_pred             CCCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEeecCCCCHHHHHH
Q 026141          133 PMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFH  211 (243)
Q Consensus       133 p~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~  211 (243)
                      |++++|++||++++ ++.+|+|||.+||.++++.+++++++++ +|.++|.                 +.+.++++++.+
T Consensus         1 P~~~~~~~vt~~~i-~~~~lvDpt~~EE~~~~~~l~v~~~~~g~i~~~~k~-----------------g~~~~~~~~i~~   62 (84)
T d2je6a2           1 PLNYPVVTISVAKV-DKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKS-----------------GKGSMSLQDIDQ   62 (84)
T ss_dssp             CCSCCCEEEEEEEE-TTEEEESCCHHHHHHCSEEEEEEECTTCCEEEEEEE-----------------SSSCEEHHHHHH
T ss_pred             CCCCCeEEEEEEEE-CCEEEecCCHHHHHhcCCceeeeecCCCceeeEEec-----------------cCCcCCHHHHHH
Confidence            89999999999998 8899999999999999999999999875 6666653                 245899999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 026141          212 CLERGRAASAKLSDFLRRSLQ  232 (243)
Q Consensus       212 ~l~~a~~~~~~l~~~i~~~l~  232 (243)
                      |+++|.+.++++++.++++|.
T Consensus        63 ~i~~A~~~~~~l~~~l~~~l~   83 (84)
T d2je6a2          63 AENTARSTAVKLLEELKKHLG   83 (84)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHhC
Confidence            999999999999999999874

>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=99.66  E-value=1.2e-16  Score=113.95  Aligned_cols=89  Identities=12%  Similarity=0.203  Sum_probs=79.3

Q ss_pred             CCCCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEeecCCCCHHHHH
Q 026141          132 IPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYF  210 (243)
Q Consensus       132 ip~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~  210 (243)
                      +|++++|+++||+++ ++.+|+|||..||.++++.++|++++++ +|.++|.                 +.+.++++++.
T Consensus         1 L~i~~~Pv~vT~~~i-~~~~lvDpt~~EE~~~~~~l~v~~~~~g~i~~l~k~-----------------G~~~l~~~~i~   62 (94)
T d2nn6e2           1 LSVENVPCIVTLCKI-GYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKV-----------------GKGSLDPESIF   62 (94)
T ss_dssp             CCCTTCCCCEEEEES-SSSEESSCCHHHHTSCSEEEEECCCSSSCCCEEEEE-----------------ESSCBCHHHHH
T ss_pred             CCcCceEEEEEEEEE-CCEEEECCCHHHHhccCceEEEEEcCCCcEEEEEec-----------------CCCccCHHHHH
Confidence            478999999999998 8899999999999999999999998875 7777663                 34589999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcccc
Q 026141          211 HCLERGRAASAKLSDFLRRSLQSKLPGD  238 (243)
Q Consensus       211 ~~l~~a~~~~~~l~~~i~~~l~~~~~~~  238 (243)
                      +|+++|.+.+++|++.++++|+++.+.+
T Consensus        63 ~~i~~A~~~~~el~~~l~~~L~~~e~~~   90 (94)
T d2nn6e2          63 EMMETGKRVGKVLHASLQSVVHKEESLG   90 (94)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHC-C
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            9999999999999999999998877654

>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=99.65  E-value=9.5e-17  Score=113.43  Aligned_cols=86  Identities=19%  Similarity=0.281  Sum_probs=76.1

Q ss_pred             CCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEeecCCCCHHHHHHH
Q 026141          134 MKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHC  212 (243)
Q Consensus       134 ~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~  212 (243)
                      ++++|+++|++++.++.+|+|||.+||..+++.++|++++++ +|.++|.                 +.+.++++++.+|
T Consensus         2 i~~~Pi~vT~~~~~~~~~lvDpt~~EE~~~~~~lti~~~~~g~i~~l~k~-----------------G~~~l~~~~l~~~   64 (89)
T d2nn6c2           2 IRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKP-----------------GGSGLTGAKLQDC   64 (89)
T ss_dssp             CSCCCEEEEEEECTTTCCEESCCTTTTTSCSEEEEEEECTTCCEEEEEES-----------------CCSCCCHHHHHHH
T ss_pred             ccCCEEEEEEEEECCEEEEEcCCHHHHhcCCceEEEEEcCCCCEEEEEec-----------------CCcccCHHHHHHH
Confidence            689999999999966678999999999999999999999885 7777664                 2458999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcc
Q 026141          213 LERGRAASAKLSDFLRRSLQSKLP  236 (243)
Q Consensus       213 l~~a~~~~~~l~~~i~~~l~~~~~  236 (243)
                      +++|..++++|+++++++|++...
T Consensus        65 ~~~A~~~~~~l~~~l~~al~~~~~   88 (89)
T d2nn6c2          65 MSRAVTRHKEVKKLMDEVIKSMKP   88 (89)
T ss_dssp             HHHHHHHHHHHHHHHHTTTTTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccC
Confidence            999999999999999999987543

>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=99.61  E-value=2.5e-15  Score=106.20  Aligned_cols=87  Identities=17%  Similarity=0.184  Sum_probs=76.1

Q ss_pred             CCCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHH
Q 026141          133 PMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHC  212 (243)
Q Consensus       133 p~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~  212 (243)
                      ||+++++||++|++ ++.+++|||..|++.+++.+++++.++.                 .+++.+...|.+++++|.++
T Consensus         1 Pm~d~V~avs~g~~-~~~~llDp~~~E~~~~~~~l~va~~~~~-----------------~~I~~~~~~g~~~~~~~~~~   62 (90)
T d2nn6b2           1 PMRDFVCACSAGFV-DGTALADLSHVEEAAGGPQLALALLPAS-----------------GQIALLEMDARLHEDHLERV   62 (90)
T ss_dssp             CCSSCCEEEEEEEE-TTEEEESCCHHHHTSSCCCEEEEEETTT-----------------TEEEEEEECSCCBTTSHHHH
T ss_pred             CCCCCeEEEEEEEE-CCEEeeCCccccccccccceEEEEEecC-----------------CCEEEEEEecccCHHHHHHH
Confidence            89999999999997 9999999999999999999999864431                 12334446789999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhccc
Q 026141          213 LERGRAASAKLSDFLRRSLQSKLPG  237 (243)
Q Consensus       213 l~~a~~~~~~l~~~i~~~l~~~~~~  237 (243)
                      +++|.++|++|+++++++++++.++
T Consensus        63 l~~a~~~~~~i~~~~~~~l~~~~~e   87 (90)
T d2nn6b2          63 LEAAAQAARDVHTLLDRVVRQHVRE   87 (90)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            9999999999999999999998764

>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=99.60  E-value=4.1e-16  Score=107.65  Aligned_cols=77  Identities=12%  Similarity=0.140  Sum_probs=69.2

Q ss_pred             CCCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCc-cccccCCCcccCCCCcccceEEEeecCCCCHHHHHH
Q 026141          133 PMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSI-LSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFH  211 (243)
Q Consensus       133 p~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~-~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~  211 (243)
                      |++++|+++|++++ ++.+|+|||.+||..+++.+++++++++ +|.++|.                 +.|.++.+++.+
T Consensus         1 Pv~~~Pv~vT~~~~-~~~~lvDpt~eEE~~~~~~iti~~~~~g~i~~~~k~-----------------G~~~~~~~~i~~   62 (79)
T d2ba0g2           1 PVRDLPVSVTSLIV-GNKYLVDPSREEMSVGDTTLTITTDKDDNVVAMQKS-----------------GGYLLDEKLFDE   62 (79)
T ss_dssp             CBCCCCEEEEEEEE-TTEEEESCCTTGGGGCSCEEEEEECTTSCEEEEEEE-----------------SSCCBCHHHHHH
T ss_pred             CCCCceEEEEEEEE-CCEEEECCCHHHHhcCCceEEEEEcCCCCEEEEEcc-----------------CCCCcCHHHHHH
Confidence            89999999999998 8899999999999999999999999885 7777764                 245899999999


Q ss_pred             HHHHHHHHHHHHHHHH
Q 026141          212 CLERGRAASAKLSDFL  227 (243)
Q Consensus       212 ~l~~a~~~~~~l~~~i  227 (243)
                      |++.|.+.+++|.+.+
T Consensus        63 ~i~~A~~~~~~l~e~l   78 (79)
T d2ba0g2          63 LLDVSINCARKLREKF   78 (79)
T ss_dssp             HHHHHHHHHHHHTTTT
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            9999999999987654

>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=99.60  E-value=6.1e-15  Score=103.26  Aligned_cols=84  Identities=20%  Similarity=0.279  Sum_probs=73.7

Q ss_pred             CCCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHHHHH
Q 026141          133 PMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDYFHC  212 (243)
Q Consensus       133 p~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l~~~  212 (243)
                      ||+++++||++|++ ++.+|+|||..|++.+++.+++++.++.                 ...+.+...|.+++++|.++
T Consensus         1 Pm~d~V~avsvg~~-d~~~llDp~~~E~~~~~~~l~va~~~~~-----------------~~i~~~~~~g~~~~~~~~~~   62 (86)
T d2je6b2           1 PMRDLIAGVAVGKA-DGVIILDLNETEAMWGEADMPIAMMPSL-----------------NQVTLFQLNGSMTPDEFRQA   62 (86)
T ss_dssp             CBSSCCEEEEEEEE-TTEEEESCCHHHHHHSSEEEEEEEEGGG-----------------TEEEEEEEEECBCHHHHHHH
T ss_pred             CCCCCeEEEEEEEE-CCEEEEecchhhhhcCceeEEEEEeCCC-----------------CeEEEEeecCCCCHHHHHHH
Confidence            89999999999997 9999999999999999999999875431                 12333446789999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhh
Q 026141          213 LERGRAASAKLSDFLRRSLQSK  234 (243)
Q Consensus       213 l~~a~~~~~~l~~~i~~~l~~~  234 (243)
                      +++|.++|++|+++++++|+++
T Consensus        63 l~~a~~~~~~I~~~~~e~l~~r   84 (86)
T d2je6b2          63 FDLAVKGINIIYNLEREALKSK   84 (86)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999974

>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=99.51  E-value=1.4e-13  Score=96.61  Aligned_cols=86  Identities=17%  Similarity=0.211  Sum_probs=73.5

Q ss_pred             CCCCCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEee-cCCCCHHHH
Q 026141          131 GIPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVT-HGAMSVDDY  209 (243)
Q Consensus       131 ~ip~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~-~g~~~~~~l  209 (243)
                      |+||+++++||++|++ +|.+++|||.+|+..++..+.++++.++....                +...+ ...++.+++
T Consensus         2 g~P~~~~VaavsvG~i-dg~~vld~~~~E~~~~~~Dl~va~t~~g~i~~----------------iq~~ge~~~~sed~~   64 (88)
T d1r6la2           2 GNPLKQMVAAVSVGIY-QGVPVLDLDYLEDSAAETDLNVVMTDAGGFIE----------------VQGTAEGAPFRPAEL   64 (88)
T ss_dssp             SCCBCCCEEEEEEEEE-TTEEEESCCHHHHHHCSEEEEEEEETTSCEEE----------------EEEEESSSCCCHHHH
T ss_pred             CCCcCCCccEEEEEEE-CCEEEecCcHHhhccCceeEEEEEeCCCCEEe----------------ehhhcccCCCCHHHH
Confidence            8999999999999997 99999999999999999999999987652211                11222 347999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Q 026141          210 FHCLERGRAASAKLSDFLRRSLQS  233 (243)
Q Consensus       210 ~~~l~~a~~~~~~l~~~i~~~l~~  233 (243)
                      .+++++|.+++++++++++++|++
T Consensus        65 ~~al~~A~~~i~~i~~~Qkeal~e   88 (88)
T d1r6la2          65 NAMLELAQQGMQELFELQRAALAE   88 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcC
Confidence            999999999999999999999863

>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=99.41  E-value=1e-12  Score=94.05  Aligned_cols=87  Identities=20%  Similarity=0.253  Sum_probs=73.2

Q ss_pred             CCCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCC-ccccccCCCcccCCCCcccceEEE-eecCCCCHHHHH
Q 026141          133 PMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNS-ILSVLPEGSSLVQGEPMEHGIITS-VTHGAMSVDDYF  210 (243)
Q Consensus       133 p~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~-~~~~~~k~~~~~~~~~~~~~~i~~-~~~g~~~~~~l~  210 (243)
                      ||+++++||++|++ ++.+++|||..|+..++..+++++... +..                ..++. ...|.++.++|.
T Consensus         1 Pm~~~V~avsvG~~-d~~~llDp~~~E~~~~~~~l~va~~~~~~~~----------------~ei~~~~~~~~~~~~~~~   63 (99)
T d2ba0d2           1 PMKGMITSVAVGKA-DGQLVLDPMKEEDNFGEADMPFAFLIRNGKI----------------ESIALLQMDGRMTRDEVK   63 (99)
T ss_dssp             CBSSEEEEEEEEEE-TTEEEESCCHHHHHHSSEEEEEEEEEETTEE----------------EEEEEEEEEEEECHHHHH
T ss_pred             CCCCcEEEEEEEEE-CCEEEEcCCcchhhcccCceEEEEecCcceE----------------EEEEEEeccccchHHHHH
Confidence            89999999999997 999999999999999999999986432 211                11222 246899999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcc
Q 026141          211 HCLERGRAASAKLSDFLRRSLQSKLP  236 (243)
Q Consensus       211 ~~l~~a~~~~~~l~~~i~~~l~~~~~  236 (243)
                      +++++|.++|++|+++++++++++..
T Consensus        64 ~~l~~a~~~~~~I~~~~~~alk~~~~   89 (99)
T d2ba0d2          64 QAIELAKKGALQIYEMQREAILRRYI   89 (99)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            99999999999999999999988643

>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=99.37  E-value=3.5e-13  Score=95.84  Aligned_cols=92  Identities=20%  Similarity=0.212  Sum_probs=75.8

Q ss_pred             CCCceeEEEEEEec--CCeEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCC-CHHHHH
Q 026141          134 MKHLAVAICCCSAE--SGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAM-SVDDYF  210 (243)
Q Consensus       134 ~~~~~~avt~~~~~--~~~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~-~~~~l~  210 (243)
                      |++++++||+++..  ++.+|+|||..||..+.+.+++++....                 ...+.+...|.+ +.++|.
T Consensus         1 M~D~V~acs~~~~~~~~~~~llD~~~~Ee~~~~~~~~va~~p~~-----------------~~i~~~~~~G~~~~~d~l~   63 (95)
T d2nn6f2           1 MYDLVVGCGLSLAPGPAPTWLLDPTRLEEERAAAGLTVALMPVL-----------------NQVAGLLGSGEGGLTESWA   63 (95)
T ss_dssp             BSSCCEEEECCCCSCSSCCCCSSCCTTTGGGCSSEEEEEEETTT-----------------TEEEEEEEECCSSCTTTTH
T ss_pred             CCcEEEEEEEEeecCCCCcEEECCCHHHhcCCCCcEEEEEcCCC-----------------ceeEEEEEecccchHHHHH
Confidence            78999999999863  3689999999999999999999874421                 122333457865 778999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcccccccC
Q 026141          211 HCLERGRAASAKLSDFLRRSLQSKLPGDLSKA  242 (243)
Q Consensus       211 ~~l~~a~~~~~~l~~~i~~~l~~~~~~~~~~~  242 (243)
                      +++++|.++|++|++.++++|.++.+++.+.|
T Consensus        64 ~~lela~~g~~~I~~i~~~aL~~~~~k~~~~~   95 (95)
T d2nn6f2          64 EAVRLGLEGCQRLYPVLQQSLVRAARRRGAAA   95 (95)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Confidence            99999999999999999999999999887654

>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=99.32  E-value=9.3e-12  Score=86.64  Aligned_cols=84  Identities=17%  Similarity=0.101  Sum_probs=70.3

Q ss_pred             CCCCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEee-cCCCCHHHHH
Q 026141          132 IPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVT-HGAMSVDDYF  210 (243)
Q Consensus       132 ip~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~-~g~~~~~~l~  210 (243)
                      .||+++++||++|++.++.+++||+.+|+..++..+.++++.++...                .|...+ .+.++.++|.
T Consensus         2 ~P~~~~VaavsvG~i~~~~vlldl~~~Ed~~~~~D~~va~t~~g~i~----------------~iq~~ge~~~~s~d~~~   65 (86)
T d1oysa2           2 NPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFV----------------ELQGTGEEATFSREDLN   65 (86)
T ss_dssp             CCBCSCEEEEEEEEETTTEEEESCCHHHHHHEEEEEEEEEETTSCEE----------------EEEEEESSCCCCHHHHH
T ss_pred             CCccCcccEEEEEEEcCCcEECCCHHHHhcCCCcceEEEEeCCCCEE----------------EEEEeeccCcccHHHHH
Confidence            59999999999999855567899999999999999999998765321                123333 3479999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 026141          211 HCLERGRAASAKLSDFLRRSL  231 (243)
Q Consensus       211 ~~l~~a~~~~~~l~~~i~~~l  231 (243)
                      +++++|.+++++|+++++++|
T Consensus        66 ~al~lA~~gi~~I~~~Qkeal   86 (86)
T d1oysa2          66 GLLGLAEKGIQELIDKQKEVL   86 (86)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHhC
Confidence            999999999999999999875

>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=99.24  E-value=3.4e-11  Score=86.77  Aligned_cols=85  Identities=13%  Similarity=0.115  Sum_probs=72.5

Q ss_pred             CCCCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEee-cCCCCHHHHH
Q 026141          132 IPMKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVT-HGAMSVDDYF  210 (243)
Q Consensus       132 ip~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~-~g~~~~~~l~  210 (243)
                      .||+++++||++|++ +|.+|+|||..|.+.++..+.+++..++...                .|.... .+.++.++|.
T Consensus         3 ~P~~~~VaAVsvG~i-dg~~vldp~~~Ed~~~~~dl~va~t~~g~~~----------------ei~~~~e~~~~see~~~   65 (105)
T d1udsa2           3 TPIKDFVAAVSVGIV-NDRILLDLNFEEDSAAQVDMNVVGTGSGRLS----------------EVHTMGEEYSFTKDELI   65 (105)
T ss_dssp             CCBCCCEEEEEEEEE-TTEEEESCCHHHHHTCSEEEEEEEETTSCEE----------------EEEEEESSCCCCHHHHH
T ss_pred             CCccCCceEEEEEEE-CCEEeecCCHHHHhcCccceeEEEecCCcch----------------hhhhhhccccccHHHHH
Confidence            699999999999997 8999999999999999999999998764211                222322 4689999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHh
Q 026141          211 HCLERGRAASAKLSDFLRRSLQS  233 (243)
Q Consensus       211 ~~l~~a~~~~~~l~~~i~~~l~~  233 (243)
                      +++++|.+++++|+++++++|..
T Consensus        66 eal~~a~~~i~~i~~~Qke~l~~   88 (105)
T d1udsa2          66 KMLDLAQKGINELIELQKKLYVI   88 (105)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999998643

>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=98.32  E-value=5.1e-06  Score=59.48  Aligned_cols=97  Identities=10%  Similarity=-0.097  Sum_probs=69.2

Q ss_pred             CCCceeEEEEEEecCCeEEeCCCHHHHhhccccEEEEeeCCcc----ccccCCCcccCCCCcccceEEEee-cCCCCHHH
Q 026141          134 MKHLAVAICCCSAESGYCILDPTKLEEQKMKGFAYLVFPNSIL----SVLPEGSSLVQGEPMEHGIITSVT-HGAMSVDD  208 (243)
Q Consensus       134 ~~~~~~avt~~~~~~~~~lvDPt~~Ee~~~~~~~~v~~~~~~~----~~~~k~~~~~~~~~~~~~~i~~~~-~g~~~~~~  208 (243)
                      +++++.||.+|.+ +|.+|++||.+|.+.++..++++.+.++.    ..+.++..+      +........ .-.++.+.
T Consensus         1 f~GPvgaVRVg~i-dge~viNPt~~el~~S~ldLvVaGt~~~~~~~~v~mie~~~~------e~~~~mie~~a~e~~E~~   73 (111)
T d1e3ha5           1 FSGPIGGVRVALI-RGQWVAFPTHTELEDAVFDMVVAGRVLEDGDVAIMMVEAEAT------EKTIQLVKDGAEAPTEEV   73 (111)
T ss_dssp             BCCCCEEEEEEEE-TTEEEESCCHHHHTTEEEEEEEEEEECTTSCEEEEEEEEEEC------TTHHHHHHTTCCCCCHHH
T ss_pred             CCCCEEEEEEEEE-CCEEEECCCHHHHhcCceEEEEeecccccchHHHHHHHhcch------hHHHHHHHhccccccHHH
Confidence            4678999999997 89999999999999999999998765321    111111000      000000001 12589999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 026141          209 YFHCLERGRAASAKLSDFLRRSLQSKLPG  237 (243)
Q Consensus       209 l~~~l~~a~~~~~~l~~~i~~~l~~~~~~  237 (243)
                      +.++++.|.+..+.+.+++++..++..+.
T Consensus        74 ~~~ai~~a~~~i~~~i~~q~el~~~~gk~  102 (111)
T d1e3ha5          74 VAAGLDAAKPFIKVLCKAQADLAAKAAKP  102 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence            99999999999999999999998775543

>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=0.0048  Score=41.83  Aligned_cols=82  Identities=10%  Similarity=0.041  Sum_probs=67.8

Q ss_pred             ceeEEEEEEecCC-------eEEeCCCHHHHhhccccEEEEeeCCccccccCCCcccCCCCcccceEEEeecCCCCHHHH
Q 026141          137 LAVAICCCSAESG-------YCILDPTKLEEQKMKGFAYLVFPNSILSVLPEGSSLVQGEPMEHGIITSVTHGAMSVDDY  209 (243)
Q Consensus       137 ~~~avt~~~~~~~-------~~lvDPt~~Ee~~~~~~~~v~~~~~~~~~~~k~~~~~~~~~~~~~~i~~~~~g~~~~~~l  209 (243)
                      +++++++|++.++       .++.|-.-.|.-..+-.+-|+.+.+|+.+++-.                ..-..++.+.+
T Consensus         2 PVAGIamGLi~~~~~~~~~~~iLtDI~G~ED~~GDMDFKVAGT~~GITa~QmD----------------iKi~Gi~~~il   65 (96)
T d1e3ha6           2 PVAGIAMGLISQEINGETHYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLD----------------TKLDGIPASVL   65 (96)
T ss_dssp             CCEEEEEEEEEEEETTEEEEEEESSCCSHHHHHCSEEEEEEECSSCEEEEEEE----------------ECCSCCCHHHH
T ss_pred             CcceeeeeeeeccCCCCccEEEEeeccCchhhccCcccccccCcccceeeeee----------------ecccCCCHHHH
Confidence            5788999998531       579999999999999999999888776655421                02368999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhh
Q 026141          210 FHCLERGRAASAKLSDFLRRSLQSK  234 (243)
Q Consensus       210 ~~~l~~a~~~~~~l~~~i~~~l~~~  234 (243)
                      .++++.|.++..+|.+.|.+++...
T Consensus        66 ~~Al~qAk~gR~~IL~~M~~~i~~p   90 (96)
T d1e3ha6          66 AAALKQARDARLHILDVMMEAIDTP   90 (96)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCSSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhccc
Confidence            9999999999999999999998654