Psyllid ID: psy15057

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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-
Protein Sequence
MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN
Secondary Structure (PSIPRED)
cccccccEEEEcccccccEEEEEEEccEEEEEEEEcccccccccccccccEEEEEEEEcccccccHHHHHHHHHHHHHHHHHccccccccEEEEEEEEEEccccHHHHHHHHHHHHHHHccccccccEEEEEEEEEccccEEEcccccccc
Secondary Structure Prediction (SSPRO)
cccccEEEEEEcEEEccccEEEEEEcccEEEEEEEcccccccccccccccEEEEEEcHccccccccHHHHHHHHHHHHHHHHHHHHccccEEEEEEEEEEcccccHHHHHHHHHHHHHHccccHHHHEEEEEEEEccccEEEEEccccccc
Coil and Loop (DISEMBL)
MDSLRELKSQLNILSrsdgsvifsQGQTVVVASMYGPVEAKIQKTIIDKASvevifrpksglsfVQDRLKESVIKSTCESALLtmlhprtsVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIIndknevildanqiqsn
Flexible Loop (DISEMBL)
MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIfrpksglsfvqdrLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN
Low Complexity Region (SEG)
MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN
Disordered region (IsUnstruct)
******************GSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILD*******
Disordered Region (DISOPRED)
MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPV*************VEV********************KSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVIL*AN*****
Disordered Region (DISEMBL)
MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN
Disordered Region (DISPRO)
MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQ****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN
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	151	2.2.26 [Sep-21-2011]
Q9NQT4	235	Exosome complex component	yes	N/A	0.973	0.625	0.462	2e-37
Q9CRA8	235	Exosome complex component	yes	N/A	0.973	0.625	0.455	2e-37
Q84T68	238	Exosome complex exonuclea	yes	N/A	0.980	0.621	0.358	4e-24
O42894	226	Exosome complex component	yes	N/A	0.860	0.575	0.366	8e-19
Q921I9	245	Exosome complex component	no	N/A	0.887	0.546	0.310	2e-14
Q7YRA3	245	Exosome complex component	no	N/A	0.867	0.534	0.304	2e-14
Q9NPD3	245	Exosome complex component	no	N/A	0.887	0.546	0.310	3e-14
Q9UXC2	248	Probable exosome complex	yes	N/A	0.947	0.576	0.347	5e-14
P53256	223	Exosome complex component	yes	N/A	0.947	0.641	0.298	6e-14
A2BKC0	255	Probable exosome complex	yes	N/A	0.986	0.584	0.295	1e-13

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

 Score =  154 bits (389), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 68/147 (46%), Positives = 101/147 (68%)

Query: 3   SLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGL 62
           SLR    + N+LSR DGS  F QG T V+A +YGP E K+ K I +KA++EVI RPK GL
Sbjct: 27  SLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGL 86

Query: 63  SFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGI 122
             V ++ +E +I++TCE+ +L  LHPRTS+ + +Q + D GSLL+CC+NAAC+AL+++G+
Sbjct: 87  PGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGV 146

Query: 123 SMRYILAAVSCIINDKNEVILDANQIQ 149
            MR +   V+C ++    ++LD    Q
Sbjct: 147 PMRALFCGVACALDSDGTLVLDPTSKQ 173

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 =  154 bits (388), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 67/147 (45%), Positives = 101/147 (68%)

Query: 3   SLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGL 62
           SLR    + N+LSR DGS  F QG T V+A +YGP E K+ K I +KA++EVI RPK GL
Sbjct: 27  SLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGL 86

Query: 63  SFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGI 122
             V ++ +E ++++TCE+ +L  LHPRTS+ + +Q + D GSLL+CC+NAAC+AL+++G+
Sbjct: 87  PGVAEKSRERLVRNTCEAVVLGALHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGV 146

Query: 123 SMRYILAAVSCIINDKNEVILDANQIQ 149
            MR +   V+C ++    ++LD    Q
Sbjct: 147 PMRALFCGVTCALDSDGNLVLDPTTKQ 173

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

 Score =  110 bits (274), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 53/148 (35%), Positives = 89/148 (60%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSG 61
           + LR      N L R+ GS  ++QG T+V+A++YGP     +    +KAS+EV+++P +G
Sbjct: 12  NQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKASIEVVWKPMTG 71

Query: 62  LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG 121
               Q++  E  +K T +S  L  +HP T+  + +Q + + GSLL C INA C AL+ +G
Sbjct: 72  QIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLLPCAINACCAALVFAG 131

Query: 122 ISMRYILAAVSCIINDKNEVILDANQIQ 149
           I ++++  A+ C + +  EVILD N+ +
Sbjct: 132 IPLKHLAVAIGCGVLEDGEVILDTNKAE 159

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: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|O42894|RRP46_SCHPO Exosome complex component rrp46 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rrp46 PE=3 SV=1

 Score = 92.4 bits (228), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 48/131 (36%), Positives = 85/131 (64%), Gaps = 1/131 (0%)

Query: 9   SQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQDR 68
           +++ ILSRSDGS  + QG   V+  + GP++ KI+   ++KA+VEV+ +P SG++   ++
Sbjct: 2   NRIGILSRSDGSSEWKQGSARVICGVNGPIDVKIRDERLNKATVEVLVQPVSGVAETLEK 61

Query: 69  LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGS-LLSCCINAACLALINSGISMRYI 127
           +  S I    E A+    +PRT + ++IQ +++ G+  L+  IN A LAL+++GIS++YI
Sbjct: 62  MISSRIVGILEDAIFLNTYPRTLIQVSIQIIEEDGTDTLAAVINGAVLALLDAGISLKYI 121

Query: 128 LAAVSCIINDK 138
             A++C   +K
Sbjct: 122 PCAINCHWKNK 132

Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and in RNA surveillance pathways, preventing translation of aberrant mRNAs. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. ski6 is part of the hexameric ring of RNase PH domain-containing subunits proposed to form a central channel which threads RNA substrates for degradation.

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

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

 Score = 78.2 bits (191), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 45/145 (31%), Positives = 79/145 (54%), Gaps = 11/145 (7%)

Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKT--IIDKASVEVIFRPKSG 61
           LR++++++ + +++DGS    QG T  +A +YGP E +  ++  + D+A V   +   + 
Sbjct: 22  LRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRSRALPDRALVNCQYSSATF 81

Query: 62  LSFVQDRLKESVIKS---------TCESALLTMLHPRTSVILTIQELQDQGSLLSCCINA 112
            +  + R      KS         T E+A+LT LHPR+ + + +Q LQ  G   + C+NA
Sbjct: 82  STGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNA 141

Query: 113 ACLALINSGISMRYILAAVSCIIND 137
           A LA++++GI MR  + A S    D
Sbjct: 142 ATLAVMDAGIPMRDFVCACSAGFVD 166

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

 Score = 77.8 bits (190), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 45/148 (30%), Positives = 78/148 (52%), Gaps = 17/148 (11%)

Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVE--AKIQKTIIDKASVEVIF----- 56
           LR++++++ + +++DGS    QG T  +A +YGP E      + + D+A V   +     
Sbjct: 22  LRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATF 81

Query: 57  -------RPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCC 109
                  RP       +  L+   ++ T E+A+LT LHPR+ + + +Q LQ  G   + C
Sbjct: 82  STGERKRRPHGDRKSCEMGLQ---LRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAAC 138

Query: 110 INAACLALINSGISMRYILAAVSCIIND 137
           +NAA LA++++GI MR  + A S    D
Sbjct: 139 VNAATLAVLDAGIPMRDFVCACSAGFVD 166

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 = 77.4 bits (189), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 45/145 (31%), Positives = 78/145 (53%), Gaps = 11/145 (7%)

Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKT--IIDKASVEVIFRPKSG 61
           LR++++++ + +++DGS    QG T  +A +YGP E +  +   + D+A V   +   + 
Sbjct: 22  LRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATF 81

Query: 62  LSFVQDRLKESVIKS---------TCESALLTMLHPRTSVILTIQELQDQGSLLSCCINA 112
            +  + R      KS         T E+A+LT LHPR+ + + +Q LQ  G   + C+NA
Sbjct: 82  STGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNA 141

Query: 113 ACLALINSGISMRYILAAVSCIIND 137
           A LA++++GI MR  + A S    D
Sbjct: 142 ATLAVLDAGIPMRDFVCACSAGFVD 166

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|Q9UXC2|ECX1_SULSO Probable exosome complex exonuclease 1 OS=Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) GN=SSO0735 PE=1 SV=1

 Score = 76.6 bits (187), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 56/161 (34%), Positives = 84/161 (52%), Gaps = 18/161 (11%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKASVEVIFRPKS 60
           D LR +K +L +L  +DGS IF  G T  +A++YGP E   +  ++ D+A + V +    
Sbjct: 26  DELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYH--- 82

Query: 61  GLSFVQDRLKES-----------VIKSTCESALLTMLHPRTSVILTIQELQ-DQGSLLSC 108
              F  D  K             VI+   ESA+L  L PRT++ +  + LQ D GS L  
Sbjct: 83  MTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRL-V 141

Query: 109 CINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQ 149
            + AA LAL ++GI MR ++A V+    D   +ILD N+ +
Sbjct: 142 SLMAASLALADAGIPMRDLIAGVAVGKAD-GVIILDLNETE 181

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

Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (taxid: 273057)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|P53256|RRP46_YEAST Exosome complex component RRP46 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RRP46 PE=1 SV=2

 Score = 76.6 bits (187), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 45/151 (29%), Positives = 86/151 (56%), Gaps = 8/151 (5%)

Query: 7   LKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQ 66
           +++++ IL   DGS  F    T V+ S+ GP+E K ++ +  + ++E+I RP  G++  +
Sbjct: 3   VQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEIIVRPAKGVATTR 62

Query: 67  DRLKESVIKSTCESALLTMLHPRTSVILTIQEL---QDQGSL----LSCCINAACLALIN 119
           +++ E  +++     +    +PR    +T Q L   +D+       LSCCINAA LAL++
Sbjct: 63  EKVLEDKLRAVLTPLITRHCYPRQLCQITCQILESGEDEAEFSLRELSCCINAAFLALVD 122

Query: 120 SGISMRYILAAVS-CIINDKNEVILDANQIQ 149
           +GI++  + A++   II D +++I+D    Q
Sbjct: 123 AGIALNSMCASIPIAIIKDTSDIIVDPTAEQ 153

Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and in RNA surveillance pathways, preventing translation of aberrant mRNAs. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. RRP46 is part of the hexameric ring of RNase PH domain-containing subunits proposed to form a central channel which threads RNA substrates for degradation.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>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 = 75.5 bits (184), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 47/159 (29%), Positives = 89/159 (55%), Gaps = 10/159 (6%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTII-DKASVEVIFR--P 58
           + LR ++ ++ +LS +DGS +   G T V+A++YGP EA  +   + D+A +   +   P
Sbjct: 32  EQLRPIRMEVGVLSNADGSALVEYGGTRVIAAVYGPREAHPRHVALPDRAIIRCRYHMAP 91

Query: 59  ------KSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINA 112
                 K+     ++     VI+   E+ +++ L+PRT++ + ++ LQ  G   +  I A
Sbjct: 92  FSTAERKTPAPTRREVELSKVIREALEAVVISELYPRTAIDVYMEVLQSDGGTRTAAITA 151

Query: 113 ACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN 151
           A LAL ++GI+MR ++A V+    D   ++LD ++I+ N
Sbjct: 152 ASLALADAGIAMRDLVAGVAVGKVD-GVLVLDIDEIEDN 189

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: -

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	151
170067650	217	exosome complex exonuclease RRP46 [Culex	0.986	0.686	0.523	1e-41
405978848	215	Exosome complex exonuclease RRP46 [Crass	0.966	0.679	0.513	1e-41
157114354	217	hypothetical protein AaeL_AAEL006819 [Ae	0.986	0.686	0.496	2e-41
289742861	245	exosomal 3'-5' exoribonuclease complex s	0.973	0.6	0.510	5e-41
321475274	218	hypothetical protein DAPPUDRAFT_193332 [	0.947	0.655	0.524	9e-40
357620682	205	exosome complex exonuclease RRP46 [Danau	0.953	0.702	0.527	4e-38
350422333	220	PREDICTED: exosome complex component RRP	0.966	0.663	0.517	8e-38
332020128	220	Exosome complex exonuclease RRP46 [Acrom	0.966	0.663	0.510	1e-37
340714151	220	PREDICTED: exosome complex component RRP	0.966	0.663	0.510	2e-37
380026087	223	PREDICTED: exosome complex component RRP	0.966	0.654	0.503	2e-37

>gi|170067650|ref|XP_001868566.1| exosome complex exonuclease RRP46 [Culex quinquefasciatus] gi|167863769|gb|EDS27152.1| exosome complex exonuclease RRP46 [Culex quinquefasciatus]

 Score =  174 bits (441), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 78/149 (52%), Positives = 117/149 (78%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSG 61
           DSLR +  +LNIL+RSDGS + +QG+T V AS+ GPVE K+Q   ++K+ VE+ FRP+SG
Sbjct: 8   DSLRPMFCELNILTRSDGSAMLTQGETAVTASVNGPVEVKLQHMNVEKSYVEIHFRPRSG 67

Query: 62  LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG 121
           +  V DRL E++I++T ESALLT LHPRT+V + IQE+QD+G L++C INA CLALI+SG
Sbjct: 68  MGSVNDRLLENLIRNTYESALLTALHPRTAVSIQIQEMQDRGGLVACAINAVCLALIDSG 127

Query: 122 ISMRYILAAVSCIINDKNEVILDANQIQS 150
           I M+Y++AAV  +++++  + LD +++++
Sbjct: 128 IEMKYLVAAVHSVLDEEGGITLDPDELRA 156

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|405978848|gb|EKC43209.1| Exosome complex exonuclease RRP46 [Crassostrea gigas]

 Score =  174 bits (440), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 75/146 (51%), Positives = 112/146 (76%)

Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
           LR+L S L  LSR DG    SQG T V +++YGP E K+ K ++DKA+++V+++PKSGL 
Sbjct: 8   LRQLSSTLGDLSRPDGDATVSQGDTCVTSAVYGPGEVKVTKELLDKATIDVVYKPKSGLP 67

Query: 64  FVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS 123
              ++L E  I+++CE+ +L  LHPR+S+ +T+QE+Q++GSLLSCCIN+ C+AL++SG+S
Sbjct: 68  GCAEKLLERTIRNSCETVILGNLHPRSSISITVQEIQNRGSLLSCCINSTCMALLDSGVS 127

Query: 124 MRYILAAVSCIINDKNEVILDANQIQ 149
           MRY++AAVSC IND   +I+D N +Q
Sbjct: 128 MRYLMAAVSCAINDNGSIIMDPNTLQ 153

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|157114354|ref|XP_001658056.1| hypothetical protein AaeL_AAEL006819 [Aedes aegypti] gi|108877318|gb|EAT41543.1| AAEL006819-PA [Aedes aegypti]

 Score =  173 bits (439), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 74/149 (49%), Positives = 117/149 (78%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSG 61
           +SLR +  +LN+L+RSDGS + +QG+T VVAS+ GP+E K+Q   ++K+ +++ F+P+SG
Sbjct: 8   NSLRPMHCELNLLTRSDGSAMLTQGETAVVASVNGPIEVKLQHMNVEKSHIDIYFKPRSG 67

Query: 62  LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG 121
           +  V DRL ES+IK+T ESA+LT LHPRT++ + +QE+QDQG L++C INA CLAL+NSG
Sbjct: 68  MGSVNDRLLESLIKNTYESAILTGLHPRTAISIQLQEMQDQGGLVACAINAVCLALMNSG 127

Query: 122 ISMRYILAAVSCIINDKNEVILDANQIQS 150
           I M++++AAV  ++ +  +++LD + +QS
Sbjct: 128 IEMKFLVAAVHSVLREDGDIVLDPDALQS 156

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|289742861|gb|ADD20178.1| exosomal 3'-5' exoribonuclease complex subunit Rrp46 [Glossina morsitans morsitans]

 Score =  172 bits (436), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 75/147 (51%), Positives = 112/147 (76%)

Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
           LR L  +LN L+R+DGS +F QG T V+ASM GPVE K+Q   IDKA V+ I+RPK+GL 
Sbjct: 20  LRTLNCELNPLTRTDGSTLFIQGATCVLASMLGPVEVKLQNLKIDKAHVDCIYRPKAGLP 79

Query: 64  FVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS 123
            ++D+++E++IK TCE+ALL+ LHPRT + + +QEL D+G L +C INAAC+AL+  G+ 
Sbjct: 80  TIRDKIRETMIKDTCEAALLSALHPRTLISIQLQELDDRGGLDACAINAACMALLIGGVP 139

Query: 124 MRYILAAVSCIINDKNEVILDANQIQS 150
           M++ +AAV C+++   E++LD +Q+Q+
Sbjct: 140 MKFTVAAVHCVVDKNGEIVLDPDQLQA 166

Source: Glossina morsitans morsitans

Species: Glossina morsitans

Genus: Glossina

Family: Glossinidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321475274|gb|EFX86237.1| hypothetical protein DAPPUDRAFT_193332 [Daphnia pulex]

 Score =  168 bits (425), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 75/143 (52%), Positives = 116/143 (81%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSG 61
           +S+R LK + ++LSR+DGSV+FSQG TVV+AS+YGP+EAKIQK + D+  +E+ ++PK+G
Sbjct: 6   NSIRALKCEQSVLSRADGSVMFSQGNTVVMASVYGPLEAKIQKELSDRMYIELNYKPKTG 65

Query: 62  LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG 121
           +  V +R KE +IK+TC   +LT LHPRT+V +T+QE+QD G+LL+  INA CLAL++SG
Sbjct: 66  MPGVAERGKEKLIKTTCNHIILTNLHPRTAVCITVQEMQDGGTLLAASINAVCLALLDSG 125

Query: 122 ISMRYILAAVSCIINDKNEVILD 144
           + ++ ++AAV+C+++ K+ +ILD
Sbjct: 126 LPLQCLVAAVTCLVDKKDRIILD 148

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357620682|gb|EHJ72793.1| exosome complex exonuclease RRP46 [Danaus plexippus]

 Score =  162 bits (410), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 77/146 (52%), Positives = 109/146 (74%), Gaps = 2/146 (1%)

Query: 7   LKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQ 66
           +K +LN LSRSDGS I SQG+TVV  S+ GP++ K     I+KA++E++F  K G   V 
Sbjct: 1   MKCELNFLSRSDGSAILSQGETVVTVSVNGPLDIKTTSQSIEKATLEILFSSKGGKPSVA 60

Query: 67  DRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRY 126
           DR KE+VI+ TCE+A+L  L+PRT + +TIQEL+D G LLSC IN ACLAL+NSGIS+ +
Sbjct: 61  DRFKENVIRQTCETAILGCLYPRTGITITIQELEDYGGLLSCAINCACLALLNSGISLHH 120

Query: 127 ILAAVSCIINDKNEVILDAN--QIQS 150
           ++AAVSCI+++   ++L+ +  Q+QS
Sbjct: 121 VVAAVSCIVDETGNIVLEPSYQQVQS 146

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350422333|ref|XP_003493132.1| PREDICTED: exosome complex component RRP46-like [Bombus impatiens]

 Score =  161 bits (408), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 76/147 (51%), Positives = 103/147 (70%), Gaps = 1/147 (0%)

Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
           LR +  +LN LS  DGS +  QG T VVA +YGP+EAK QK I DKASVEV + P  G +
Sbjct: 12  LRPMNCELNQLSMPDGSAMLMQGNTAVVAGIYGPIEAKPQKMIYDKASVEVSYSPIKGPA 71

Query: 64  FVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS 123
            V DR+ E  IK TCE+A++   HP T++ + IQEL+D G +L+C INAACLALIN+GI 
Sbjct: 72  KVDDRMTEMYIKETCEAAIIVTFHPATAICINIQELEDSGGILACTINAACLALINAGIP 131

Query: 124 MRYILAAVSCIINDKNE-VILDANQIQ 149
           M++ +AAV+C+I +  E ++LD +  Q
Sbjct: 132 MKFTIAAVNCMIQEGTENIVLDPDTTQ 158

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332020128|gb|EGI60572.1| Exosome complex exonuclease RRP46 [Acromyrmex echinatior]

 Score =  160 bits (405), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 75/147 (51%), Positives = 105/147 (71%), Gaps = 1/147 (0%)

Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
           LR +  ++N+LSRSDGS +F QG T ++A + GP+EAK QK   D+ S+EV + P  G +
Sbjct: 12  LRPINCEINLLSRSDGSTMFMQGDTTIIAGVNGPLEAKSQKMAYDRVSIEVTYTPLKGPA 71

Query: 64  FVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS 123
            V DRL E+ IK TCESA+L   HP T V + +QE+QD G LL+C INA+CLALINSG+S
Sbjct: 72  KVDDRLIETYIKETCESAILVSFHPNTMVCINLQEMQDSGGLLACAINASCLALINSGLS 131

Query: 124 MRYILAAVSCII-NDKNEVILDANQIQ 149
           MR+ +AA+SC+I  +  ++I+D +  Q
Sbjct: 132 MRFTVAAISCMIEKETGDIIMDPDSSQ 158

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340714151|ref|XP_003395595.1| PREDICTED: exosome complex component RRP46-like [Bombus terrestris]

 Score =  160 bits (404), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 75/147 (51%), Positives = 103/147 (70%), Gaps = 1/147 (0%)

Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
           LR +  +LN LS  DGS +  QG T VVA +YGP+EAK QK I DKASVEV + P  G +
Sbjct: 12  LRPMNCELNQLSMPDGSAMLMQGNTTVVAGIYGPIEAKPQKMIYDKASVEVSYSPIKGPA 71

Query: 64  FVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS 123
            V DR+ E  IK TCE+A++   HP T++ + +QEL+D G +L+C INAACLALIN+GI 
Sbjct: 72  KVDDRMTEMYIKETCEAAIIVTFHPATAICINVQELEDSGGILACTINAACLALINAGIP 131

Query: 124 MRYILAAVSCIINDKNE-VILDANQIQ 149
           M++ +AAV+C+I +  E +I+D +  Q
Sbjct: 132 MKFTIAAVNCMIQEGTENIIVDPDTTQ 158

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380026087|ref|XP_003696793.1| PREDICTED: exosome complex component RRP46-like [Apis florea]

 Score =  159 bits (403), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 74/147 (50%), Positives = 103/147 (70%), Gaps = 1/147 (0%)

Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
           LR +  +LN LS  DGS +  QG T VVA +YGP+EAK QK I DKAS+EV + P  G +
Sbjct: 15  LRPMNCELNQLSMPDGSAMLMQGNTAVVAGIYGPIEAKPQKMIYDKASIEVSYIPVKGPA 74

Query: 64  FVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS 123
            + DR+ E  IK TCE+A++   HP T++ + IQE++D G +L+C INAACLALIN+GI 
Sbjct: 75  KIDDRMTEMYIKETCEAAIIVTFHPATAICINIQEMEDSGGMLACTINAACLALINAGIP 134

Query: 124 MRYILAAVSCIIND-KNEVILDANQIQ 149
           M++ +AAV+C+I +  N +ILD +  Q
Sbjct: 135 MKFTIAAVNCMIQEGTNNIILDPDSTQ 161

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	151
UNIPROTKB|E1BAG2	235	EXOSC5 "Uncharacterized protei	0.940	0.604	0.478	2.2e-34
UNIPROTKB|Q9NQT4	235	EXOSC5 "Exosome complex compon	0.973	0.625	0.462	2.8e-34
ZFIN|ZDB-GENE-060503-675	243	exosc5 "exosome component 5" [	0.933	0.580	0.475	2.8e-34
MGI|MGI:107889	235	Exosc5 "exosome component 5" [	0.940	0.604	0.464	3.6e-34
RGD|1307861	235	Exosc5 "exosome component 5" [	0.940	0.604	0.471	3.6e-34
FB|FBgn0037815	233	Rrp46 "Rrp46" [Drosophila mela	0.986	0.639	0.436	1.3e-31
TAIR|locus:2075351	239	AT3G46210 "AT3G46210" [Arabido	0.980	0.619	0.378	4.2e-24
UNIPROTKB|Q84T68	238	RRP46 "Exosome complex exonucl	0.980	0.621	0.358	7.8e-23
POMBASE|SPBC115.01c	226	rrp46 "exosome subunit Rrp46 (	0.887	0.592	0.364	1.5e-19
WB|WBGene00000798	214	crn-5 [Caenorhabditis elegans	0.913	0.644	0.319	6.7e-17

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

 Score = 373 (136.4 bits), Expect = 2.2e-34, P = 2.2e-34
 Identities = 68/142 (47%), Positives = 101/142 (71%)

Query:     3 SLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGL 62
             SLR    + N+LSR DGS  F QG T V+A +YGP E KI K I +KA++EVI RPK+GL
Sbjct:    27 SLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKISKEIFNKATLEVILRPKTGL 86

Query:    63 SFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGI 122
               V ++ +E +I++TCE+ +L  LHPRTS+ + +Q + D GSLL+CC+NAAC+AL+++G+
Sbjct:    87 PGVAEKSRERLIRNTCEAVVLGALHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGV 146

Query:   123 SMRYILAAVSCIINDKNEVILD 144
              MR +   V+C ++    ++LD
Sbjct:   147 PMRALFCGVTCALDSDGTLMLD 168

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

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

 Score = 372 (136.0 bits), Expect = 2.8e-34, P = 2.8e-34
 Identities = 68/147 (46%), Positives = 101/147 (68%)

Query:     3 SLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGL 62
             SLR    + N+LSR DGS  F QG T V+A +YGP E K+ K I +KA++EVI RPK GL
Sbjct:    27 SLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGL 86

Query:    63 SFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGI 122
               V ++ +E +I++TCE+ +L  LHPRTS+ + +Q + D GSLL+CC+NAAC+AL+++G+
Sbjct:    87 PGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGV 146

Query:   123 SMRYILAAVSCIINDKNEVILDANQIQ 149
              MR +   V+C ++    ++LD    Q
Sbjct:   147 PMRALFCGVACALDSDGTLVLDPTSKQ 173

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

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

 Score = 372 (136.0 bits), Expect = 2.8e-34, P = 2.8e-34
 Identities = 67/141 (47%), Positives = 102/141 (72%)

Query:     4 LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
             LRE  S+ ++LSR DGS  F QG T ++A +YGP E K+ K I D+A+VEV+ +PK GL 
Sbjct:    35 LREYGSEQSLLSRPDGSSTFVQGDTSILAGVYGPAEVKVSKEIYDRATVEVLIQPKMGLP 94

Query:    64 FVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS 123
              V++R +E  ++ TCE+ALL  LHPR+S+ + +Q + D GSLLSCC+NAAC+AL+++G+ 
Sbjct:    95 SVRERAREQCVRETCEAALLLTLHPRSSLTVILQVVHDDGSLLSCCLNAACMALMDAGLP 154

Query:   124 MRYILAAVSCIINDKNEVILD 144
             M  +  +V+C I+ + ++I D
Sbjct:   155 MSRLFCSVTCAISKEGQIITD 175

GO:0005575 "cellular_component" evidence=ND

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

 Score = 371 (135.7 bits), Expect = 3.6e-34, P = 3.6e-34
 Identities = 66/142 (46%), Positives = 100/142 (70%)

Query:     3 SLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGL 62
             SLR    + N+LSR DGS  F QG T V+A +YGP E K+ K I +KA++EVI RPK GL
Sbjct:    27 SLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGL 86

Query:    63 SFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGI 122
               V ++ +E ++++TCE+ +L  LHPRTS+ + +Q + D GSLL+CC+NAAC+AL+++G+
Sbjct:    87 PGVAEKSRERLVRNTCEAVVLGALHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGV 146

Query:   123 SMRYILAAVSCIINDKNEVILD 144
              MR +   V+C ++    ++LD
Sbjct:   147 PMRALFCGVTCALDSDGNLVLD 168

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

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

 Score = 371 (135.7 bits), Expect = 3.6e-34, P = 3.6e-34
 Identities = 67/142 (47%), Positives = 100/142 (70%)

Query:     3 SLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGL 62
             SLR    + N+LSR DGS  F QG T V+A +YGP E K+ K I +KA++EVI RPK GL
Sbjct:    27 SLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGL 86

Query:    63 SFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGI 122
               V ++ +E +I++TCE+ +L  LHPRTS+ + +Q + D GSLL+CC+NAAC+AL+++G+
Sbjct:    87 PGVAEKSRERLIRNTCEAVVLGALHPRTSITVVLQVVSDTGSLLACCLNAACMALVDAGV 146

Query:   123 SMRYILAAVSCIINDKNEVILD 144
              MR +   V+C ++    ++LD
Sbjct:   147 PMRALFCGVTCALDPDGNLVLD 168

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

FB|FBgn0037815 Rrp46 "Rrp46" [Drosophila melanogaster (taxid:7227)]

 Score = 347 (127.2 bits), Expect = 1.3e-31, P = 1.3e-31
 Identities = 65/149 (43%), Positives = 103/149 (69%)

Query:     2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSG 61
             D LR++  + N LSR DGSV++SQG T ++ ++ GP+E K Q   ID + +E  +RPK+G
Sbjct:    12 DKLRQMHCEFNPLSRCDGSVMYSQGATGLIGAVLGPIEVKTQNLSIDGSYLECNYRPKAG 71

Query:    62 LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG 121
             L  V DR++E+ I+   E ALL+  HPR+ + + IQEL+D+GS+ +C +N ACLA++  G
Sbjct:    72 LPQVTDRIREAAIRDVLELALLSEAHPRSKMSVQIQELEDRGSIDACAVNCACLAMLIGG 131

Query:   122 ISMRYILAAVSCIINDKNEVILDANQIQS 150
             + ++Y  AAV  IIN++ E +LD +Q ++
Sbjct:   132 LPLKYSFAAVHAIINEQGEYVLDPDQSET 160

GO:0006397 "mRNA processing" evidence=ISS

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:0005737 "cytoplasm" evidence=IDA

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

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

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 56/148 (37%), Positives = 90/148 (60%)

Query:     2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSG 61
             + LR L    NIL R  GS  +SQG T V+A++YGP     +    +KA  EVI++PKSG
Sbjct:    12 NQLRPLACSRNILHRPHGSASWSQGDTKVLAAVYGPKAGTKKNENAEKACFEVIWKPKSG 71

Query:    62 LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG 121
                  ++  E ++K T +S  +  ++P T+  + IQ + D GSLL C INAAC AL+++G
Sbjct:    72 QIGKVEKEYEMILKRTIQSICVLTVNPNTTTSVIIQVVHDDGSLLPCAINAACAALVDAG 131

Query:   122 ISMRYILAAVSCIINDKNEVILDANQIQ 149
             I M+++  A+ C + +   ++LD N+++
Sbjct:   132 IPMKHLAVAICCCLAENGYLVLDPNKLE 159

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 = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 53/148 (35%), Positives = 89/148 (60%)

Query:     2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSG 61
             + LR      N L R+ GS  ++QG T+V+A++YGP     +    +KAS+EV+++P +G
Sbjct:    12 NQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKASIEVVWKPMTG 71

Query:    62 LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG 121
                 Q++  E  +K T +S  L  +HP T+  + +Q + + GSLL C INA C AL+ +G
Sbjct:    72 QIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLLPCAINACCAALVFAG 131

Query:   122 ISMRYILAAVSCIINDKNEVILDANQIQ 149
             I ++++  A+ C + +  EVILD N+ +
Sbjct:   132 IPLKHLAVAIGCGVLEDGEVILDTNKAE 159

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

POMBASE|SPBC115.01c rrp46 "exosome subunit Rrp46 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 233 (87.1 bits), Expect = 1.5e-19, P = 1.5e-19
 Identities = 50/137 (36%), Positives = 89/137 (64%)

Query:     9 SQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQDR 68
             +++ ILSRSDGS  + QG   V+  + GP++ KI+   ++KA+VEV+ +P SG++   ++
Sbjct:     2 NRIGILSRSDGSSEWKQGSARVICGVNGPIDVKIRDERLNKATVEVLVQPVSGVAETLEK 61

Query:    69 LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGS-LLSCCINAACLALINSGISMRYI 127
             +  S I    E A+    +PRT + ++IQ +++ G+  L+  IN A LAL+++GIS++YI
Sbjct:    62 MISSRIVGILEDAIFLNTYPRTLIQVSIQIIEEDGTDTLAAVINGAVLALLDAGISLKYI 121

Query:   128 LAAVSCIINDKNEVILD 144
               A++C  + KN++  D
Sbjct:   122 PCAINC--HWKNKITQD 136

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

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

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

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

GO:0003723 "RNA binding" evidence=ISM

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IEA

GO:0005829 "cytosol" evidence=IDA

GO:0034661 "ncRNA catabolic process" evidence=ISO

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

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

GO:0070651 "nonfunctional rRNA decay" evidence=ISO

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

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

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

WB|WBGene00000798 crn-5 [Caenorhabditis elegans (taxid:6239)]

 Score = 208 (78.3 bits), Expect = 6.7e-17, P = 6.7e-17
 Identities = 45/141 (31%), Positives = 81/141 (57%)

Query:     4 LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
             LRE++ +L+ L  +DGS  FSQG T + AS  GP +    K   +  ++++ +R   G +
Sbjct:     5 LREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISYRANCGDN 64

Query:    64 FVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS 123
               +  +  ++I ST  +A+   L P T++ +T+  +QD GS+ +  IN AC AL+++G+ 
Sbjct:    65 --KFNVLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAVAINGACFALLDNGMP 122

Query:   124 MRYILAAVSCIINDKNEVILD 144
                +   V  I+  K+E+I+D
Sbjct:   123 FETVFCGV-LIVRVKDELIID 142

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0008340 "determination of adult lifespan" evidence=IMP

GO:0006915 "apoptotic process" evidence=IMP

GO:0006309 "apoptotic DNA fragmentation" evidence=IMP

GO:0006396 "RNA processing" evidence=IMP

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

GO:0008408 "3'-5' exonuclease activity" evidence=ISS

GO:0019899 "enzyme binding" evidence=IPI

GO:0032077 "positive regulation of deoxyribonuclease activity" evidence=IDA

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

---

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)
Q9CRA8	EXOS5_MOUSE	No assigned EC number	0.4557	0.9735	0.6255	yes	N/A
Q9NQT4	EXOS5_HUMAN	No assigned EC number	0.4625	0.9735	0.6255	yes	N/A
Q84T68	EXOS5_ORYSJ	3, ., 1, ., 1, 3, ., -	0.3581	0.9801	0.6218	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	151
cd11372	199	cd11372, RNase_PH_RRP46, RRP46 subunit of eukaryot	3e-68
cd11370	226	cd11370, RNase_PH_RRP41, RRP41 subunit of eukaryot	4e-31
pfam01138	129	pfam01138, RNase_PH, 3' exoribonuclease family, do	2e-23
COG0689	230	COG0689, Rph, RNase PH [Translation, ribosomal str	9e-23
PRK03983	244	PRK03983, PRK03983, exosome complex exonuclease Rr	2e-19
TIGR02065	230	TIGR02065, ECX1, archaeal exosome-like complex exo	1e-18
cd11358	218	cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucl	7e-18
cd11366	214	cd11366, RNase_PH_archRRP41, RRP41 subunit of arch	4e-16
cd11371	210	cd11371, RNase_PH_MTR3, MTR3 subunit of eukaryotic	2e-11

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

 Score =  204 bits (522), Expect = 3e-68
 Identities = 74/146 (50%), Positives = 108/146 (73%)

Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
           LR L  +L +LSR+DGS  FSQG T V+A++YGP+E K++K + D+A++EVI RPKSGL 
Sbjct: 1   LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLP 60

Query: 64  FVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS 123
            V+++L E +++ST E  +L  LHPRT + + +Q LQD GSLL+C INAACLAL+++G+ 
Sbjct: 61  GVKEKLLELLLRSTLEPIILLHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVP 120

Query: 124 MRYILAAVSCIINDKNEVILDANQIQ 149
           M+ + AAV+C I +  E+ILD    +
Sbjct: 121 MKGLFAAVTCAITEDGEIILDPTAEE 146

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|206775 cd11370, RNase_PH_RRP41, RRP41 subunit of eukaryotic exosome

 Score =  110 bits (278), Expect = 4e-31
 Identities = 54/162 (33%), Positives = 85/162 (52%), Gaps = 25/162 (15%)

Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKI-QKTIIDKASVEVIF------ 56
           LR ++ ++ + S +DGS    QG T V+A++YGP E +   + + D+A V   +      
Sbjct: 12  LRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNRSQALHDRAVVNCEYSMATFS 71

Query: 57  ------RPKSGLSFVQD-RLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLS 107
                 R K       D R  E    I+ T E+ +LT L+PR+ + + +Q LQ  G LL+
Sbjct: 72  TGERKRRGKG------DRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLA 125

Query: 108 CCINAACLALINSGISMRYILAAVSC-IINDKNEVILDANQI 148
            CINAA LALI++GI M+  + A S   ++     +LD N +
Sbjct: 126 ACINAATLALIDAGIPMKDYVCACSAGYLDSTP--LLDLNYL 165

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|216323 pfam01138, RNase_PH, 3' exoribonuclease family, domain 1

 Score = 88.4 bits (220), Expect = 2e-23
 Identities = 34/127 (26%), Positives = 60/127 (47%), Gaps = 8/127 (6%)

Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
           LR ++ +  +LS++DGS +   G T V+A++ GP+E   ++       + V +      S
Sbjct: 2   LRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPPQKERDFFPGELTVEYEESPFAS 61

Query: 64  F--------VQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACL 115
                     ++     +I      ++    +PR  + + +  L D GSLL   INAA L
Sbjct: 62  GERPEGRPSEREIELSRLIDRALRPSIPLEGYPRWEIRIDVTVLSDDGSLLDAAINAASL 121

Query: 116 ALINSGI 122
           AL ++GI
Sbjct: 122 ALADAGI 128

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

 Score = 89.3 bits (222), Expect = 9e-23
 Identities = 40/151 (26%), Positives = 66/151 (43%), Gaps = 10/151 (6%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKI-QKTIIDKA--SVEVIFRP 58
           D LR +K    +L  ++GS +   G T V+ ++ GP E          K   + E    P
Sbjct: 16  DELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLP 75

Query: 59  KSGLS-----FVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCIN 111
           +S          + R KE   +I     + +   L P +++ +    LQ  G   +  I 
Sbjct: 76  RSTDERKKREADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTRTASIT 135

Query: 112 AACLALINSGISMRYILAAVSCIINDKNEVI 142
            A LAL ++GI +R ++AA+S  I D   V+
Sbjct: 136 GASLALADAGIPLRDLVAAISVGIVDGVIVL 166

Length = 230

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

 Score = 81.2 bits (201), Expect = 2e-19
 Identities = 48/163 (29%), Positives = 79/163 (48%), Gaps = 18/163 (11%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKASVEVIFR--P 58
           D LR +K ++ +L  +DGS     G   ++A++YGP E   +   + D+A + V +   P
Sbjct: 22  DELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAP 81

Query: 59  KSGLSFVQDRLK----------ESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSC 108
            S    V +R +            VI+   E A++  L PRT + + I+ LQ        
Sbjct: 82  FS----VDERKRPGPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVA 137

Query: 109 CINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN 151
            I AA LAL ++GI MR ++A  +    D   ++LD N+ + N
Sbjct: 138 GITAASLALADAGIPMRDLVAGCAVGKVD-GVIVLDLNKEEDN 179

Length = 244

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

 Score = 78.3 bits (193), Expect = 1e-18
 Identities = 48/160 (30%), Positives = 80/160 (50%), Gaps = 12/160 (7%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKASVEVIF---- 56
           D LR +K +  +L  +DGS     G T ++A++YGP EA  +   + D+A + V +    
Sbjct: 16  DELRPIKIEAGVLKNADGSAYLEFGGTKILAAVYGPREAHPRHLQLPDRAVLRVRYHMAP 75

Query: 57  -----RPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCIN 111
                R + G S  +  + + VI+   E A+L    PRT + + I+ LQ  G      + 
Sbjct: 76  FSTDERKRPGPSRREIEISK-VIREALEPAILLEQFPRTVIDVFIEVLQADGGTRCAGLT 134

Query: 112 AACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN 151
           AA LAL ++GI MR ++  V+    D   V+LD ++ +  
Sbjct: 135 AASLALADAGIPMRDLVVGVAVGKVD-GVVVLDLSEEEDM 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|206766 cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucleases

 Score = 76.2 bits (188), Expect = 7e-18
 Identities = 39/168 (23%), Positives = 70/168 (41%), Gaps = 24/168 (14%)

Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
            R ++ +  +L+++DGS +   G T V+ ++ GP+    +    DK ++ V      G  
Sbjct: 1   FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLERPDKGTLYVNVEISPGAV 60

Query: 64  FVQ------DRLKE--SVIKSTCESA---LLTMLHPRTSVILTIQELQDQGSLLSCCINA 112
             +      D   E   +++ T E++     +   P   + + IQ L   G LL  C NA
Sbjct: 61  GERRQGPPGDEEMEISRLLERTIEASVILDKSTRKPSWVLYVDIQVLSRDGGLLDACWNA 120

Query: 113 ACLALINSGI-------------SMRYILAAVSCIINDKNEVILDANQ 147
           A  AL ++GI              M+ ++ AVS        ++LD   
Sbjct: 121 AIAALKDAGIPRVFVDERSPPLLLMKDLIVAVSVGGISDGVLLLDPTG 168

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|206771 cd11366, RNase_PH_archRRP41, RRP41 subunit of archaeal exosome

 Score = 71.6 bits (176), Expect = 4e-16
 Identities = 46/157 (29%), Positives = 79/157 (50%), Gaps = 20/157 (12%)

Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKASVEVIFR--PKS 60
           LR +K ++ +L  +DGS     G   ++A++YGP E   +   + D+A + V +   P S
Sbjct: 2   LRPIKIEVGVLKNADGSAYVEWGNNKIIAAVYGPREVHPRHLQLPDRAVIRVRYNMAPFS 61

Query: 61  GLSFVQDRLK----------ESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCI 110
               V +R +            VIK   E A++    PRT++ + ++ LQ         +
Sbjct: 62  ----VDERKRPGPDRREIEISKVIKEALEPAIILEEFPRTAIDVFVEVLQADAGTRVAGL 117

Query: 111 NAACLALINSGISMRYILAAVSC-IINDKNEVILDAN 146
           NAA LAL ++GI MR ++AA +   ++ K  ++LD N
Sbjct: 118 NAASLALADAGIPMRDLVAACAAGKVDGK--IVLDLN 152

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|206776 cd11371, RNase_PH_MTR3, MTR3 subunit of eukaryotic exosome

 Score = 59.1 bits (144), Expect = 2e-11
 Identities = 38/143 (26%), Positives = 71/143 (49%), Gaps = 9/143 (6%)

Query: 10  QLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKA--SVEVIFRP------KSG 61
           +  ++S++ GS     G T V+ S+YGP     +    D+   + EV F P      +  
Sbjct: 7   KTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFSDRGRLNCEVKFAPFATPGRRRH 66

Query: 62  LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG 121
               ++R   S++    E A+    +P++ + + +  L+  GS+L+  I AA LAL ++G
Sbjct: 67  GQDSEERELSSLLHQALEPAVRLEKYPKSQIDVFVTVLESDGSVLAAAITAASLALADAG 126

Query: 122 ISMRYILAAVSCIINDKNEVILD 144
           I M  ++ A S  +   +E++LD
Sbjct: 127 IEMYDLVTACSAALIG-DELLLD 148

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	151
KOG1069|consensus	217		100.0
TIGR02065	230	ECX1 archaeal exosome-like complex exonuclease 1.	100.0
KOG1068|consensus	245		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
COG0689	230	Rph RNase PH [Translation, ribosomal structure and	100.0
PF01138	132	RNase_PH: 3' exoribonuclease family, domain 1 This	100.0
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	100.0
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	99.98
PRK04282	271	exosome complex RNA-binding protein Rrp42; Provisi	99.98
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.97
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.97
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	99.96
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	99.96
COG2123	272	RNase PH-related exoribonuclease [Translation, rib	99.96
KOG1614|consensus	291		99.94
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.91
KOG1612|consensus	288		99.88
KOG1067|consensus	760		99.75
KOG1613|consensus	298		99.74
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.72
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.64
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.62
KOG1067|consensus	760		99.39
PF03725	68	RNase_PH_C: 3' exoribonuclease family, domain 2 Th	97.51

>KOG1069|consensus

Probab=100.00  E-value=3.4e-45  Score=269.25  Aligned_cols=149  Identities=42%  Similarity=0.745  Sum_probs=145.1

Q ss_pred             CccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcCCCCCCcchhhHHHHHHHHHHHHhh
Q psy15057          3 SLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQDRLKESVIKSTCESAL   82 (151)
Q Consensus         3 e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p~~g~~~~~~~~~~~~l~~~l~~~i   82 (151)
                      .+|++.++.|+++++|||+.|++|+|+|+|+|+||.+++.+++.+++++++|.++|..|..+..||.+++.|+++|+++|
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            57999999999999999999999999999999999999999999999999999999999988889999999999999999


Q ss_pred             cccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057         83 LTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus        83 ~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                      .++.||++.|+|.+||+++||+++++|+|||++||+|+||||+++++|+++++.+++.+++|||..+|+
T Consensus        84 ~l~l~Prt~iqVsiqvv~ddgs~LacaINaAclALvDaGIpl~~mfcai~~~~~~d~~lv~Dpt~~qek  152 (217)
T KOG1069|consen   84 ILELYPRTTIQVSIQVVEDDGSTLACAINAACLALVDAGIPLRSMFCAISCALHEDGVLVLDPTAKQEK  152 (217)
T ss_pred             eeeecCCceEEEEEEEEecCCcchHHHHHHHHHHHHhcCCchHHhhhhceEEEecCccEEECCcHHhhh
Confidence            999999999999999999999999999999999999999999999999999999888999999999874

>TIGR02065 ECX1 archaeal exosome-like complex exonuclease 1

Probab=100.00  E-value=5.2e-40  Score=252.30  Aligned_cols=150  Identities=30%  Similarity=0.399  Sum_probs=134.5

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccc-cCCCCeeEEEEEEc--CCCC------CCcchhhHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKASVEVIFR--PKSG------LSFVQDRLKE   71 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~-~~~~~~~~v~v~~~--p~~g------~~~~~~~~~~   71 (151)
                      ++|+|++++++|+++++||||++++|+|+|+|+|+||.+.+++ .+.++++.++|++.  |+++      .+...+++++
T Consensus        15 ~~e~R~~~~~~g~~~~a~GSa~~~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~~~a~~~~~~~~~~~~~~~~s   94 (230)
T TIGR02065        15 PDELRPIKIEAGVLKNADGSAYVEFGGTKIIAAVYGPREMHPRHLQLPDRAVLRVRYHMAPFSTDERKRPGPSRREIEIS   94 (230)
T ss_pred             cccccCeEEEECCCCCCCeEEEEEECCcEEEEEEeCCCccccccccCCCceEEEEEEEeCCcccCCccCCCCCccHHHHH
Confidence            4799999999999999999999999999999999999976543 45688888887775  5433      2345567889


Q ss_pred             HHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057         72 SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus        72 ~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                      ++|+++|++++.++.||++.|+|+++||++||++++|++||+++||+|+||||+++++|++++++ ++++++|||.+||+
T Consensus        95 ~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~DG~~~~aai~aa~lAL~dagIp~~~~v~avtv~~~-~~~~v~Dpt~~Ee~  173 (230)
T TIGR02065        95 KVIREALEPAILLEQFPRTAIDVFIEVLQADAGTRCAGLTAASLALADAGIPMRDLVVGVAVGKV-DGVVVLDLNEEEDM  173 (230)
T ss_pred             HHHHHHHHHHhChhhcCCeEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCCccccceeeEEEEEE-CCeEEECCCHHHhh
Confidence            99999999999999999999999999999999999999999999999999999999999999998 58999999999984

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.

>KOG1068|consensus

Probab=100.00  E-value=7.6e-41  Score=253.74  Aligned_cols=150  Identities=29%  Similarity=0.457  Sum_probs=135.5

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccc-cCCCCeeEEEEEEcC--CC-C------CCcchhhHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKASVEVIFRP--KS-G------LSFVQDRLK   70 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~-~~~~~~~~v~v~~~p--~~-g------~~~~~~~~~   70 (151)
                      +||+|++..++|++.+++||||+++|||||+|.|+||++++.. ...++++.++|.+..  +. |      ..+.+++++
T Consensus        20 ~~elR~i~~~~g~~~~a~GSay~E~GnTKVl~aV~GPre~~~~~~~~~~~a~lnc~~~~a~Fst~~r~~~~~~~rr~~e~   99 (245)
T KOG1068|consen   20 PNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCEVSSAQFSTGDRKKRPKGDRREKEL   99 (245)
T ss_pred             hhHhhhhhhhcCccccCCccchhhcCCeEEEEEEeCCcccccccccccccceEEEEEeeeccccchhccCCCccHHHHHH
Confidence            5899999999999999999999999999999999999998764 336888999888853  21 1      123467889


Q ss_pred             HHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCcccc
Q psy15057         71 ESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQS  150 (151)
Q Consensus        71 ~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee  150 (151)
                      +.+|+++|+++|.++.||+++|+|+|+|+++||+.+++|+||+.+||.|+||||+|+++|+|+++.+ +..++||++.||
T Consensus       100 s~~L~~afe~~I~~~lyPrsqIDI~v~VleddG~~laa~inaatlAL~daGI~m~D~i~~~t~~l~~-~~~l~Dl~~~ee  178 (245)
T KOG1068|consen  100 SLMLQQAFEPVILLELYPRSQIDIYVQVLEDDGSNLAAAINAATLALADAGIPMYDLITACTAGLAD-GTPLLDLTSLEE  178 (245)
T ss_pred             HHHHHHHHHHHHHhhhCccccceEEEEEEECCCccHHHHHHHHHHHHHHcCCChhhhhhhceeeecC-Cccccccccchh
Confidence            9999999999999999999999999999999999999999999999999999999999999999995 799999999998


Q ss_pred             C
Q psy15057        151 N  151 (151)
Q Consensus       151 ~  151 (151)
                      .
T Consensus       179 s  179 (245)
T KOG1068|consen  179 S  179 (245)
T ss_pred             h
Confidence            4

>PRK03983 exosome complex exonuclease Rrp41; Provisional

Probab=100.00  E-value=3.8e-39  Score=249.45  Aligned_cols=150  Identities=30%  Similarity=0.410  Sum_probs=134.1

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccc-cCCCCeeEEEEEEc--CCCC------CCcchhhHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKASVEVIFR--PKSG------LSFVQDRLKE   71 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~-~~~~~~~~v~v~~~--p~~g------~~~~~~~~~~   71 (151)
                      .+|+|++++++|++++++|||++++|+|+|+|+|+||.+.+++ .+.++++.+++++.  |+++      .+..++.+++
T Consensus        21 ~~~~R~i~i~~G~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~p~~~~~~~~~~~~~~~~~~s  100 (244)
T PRK03983         21 PDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSVDERKRPGPDRRSIEIS  100 (244)
T ss_pred             cCcccceEEEeCCCCCCCeEEEEEECCeEEEEEEecCCccccccccCCCcEEEEEEEEcCCCccccccCCCCChhHHHHH
Confidence            4799999999999999999999999999999999999986543 45688888877765  5443      1234556789


Q ss_pred             HHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057         72 SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus        72 ~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                      ++|+++|++++.++.||++.|+|+++||++|||+++|++||+++||+|+||||++++++++++++ ++++++|||..||+
T Consensus       101 ~~l~~~l~~~i~~~~~p~~~I~I~i~VL~~DG~~~~aai~Aa~lAL~dagIp~~~~v~avtv~~~-~~~~i~DPt~~Ee~  179 (244)
T PRK03983        101 KVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKV-DGVIVLDLNKEEDN  179 (244)
T ss_pred             HHHHHHHHHhccHHhCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHhcCCccccceeEEEEEEE-CCEEEECCCHHHhc
Confidence            99999999999999999999999999999999999999999999999999999999999999998 58999999999985

>PRK00173 rph ribonuclease PH; Reviewed

Probab=100.00  E-value=1.3e-37  Score=240.05  Aligned_cols=150  Identities=19%  Similarity=0.193  Sum_probs=131.9

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEc--CCC-----------CCCcchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFR--PKS-----------GLSFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~--p~~-----------g~~~~~~   67 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|++|.+.+.....++++.++|+|.  |++           |.++.++
T Consensus         8 ~~e~R~i~~~~g~~~~a~GSa~v~~G~T~Vla~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~~~~~~~~~~g~~~~~~   87 (238)
T PRK00173          8 ADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGWVTAEYGMLPRATHTRNDREAAKGKQGGRT   87 (238)
T ss_pred             cccccCeEEEeCCCCCCCeeEEEEecCcEEEEEEEcCCCCCCccCCCCcEEEEEEEecCCCCCcccccccccCCCCCccH
Confidence            589999999999999999999999999999999999886432224467788777775  532           2233456


Q ss_pred             hHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhc-----------CccccceeeEEEEEEe
Q psy15057         68 RLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINS-----------GISMRYILAAVSCIIN  136 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~a-----------gip~~~~~~avtv~~~  136 (151)
                      ++++++|+++|+++++++.||++.|+|+++||++|||+++|++||+++||+|+           |+||+++|+++|++++
T Consensus        88 ~~~sr~i~r~lr~~i~l~~l~~~~i~v~v~VL~~DG~~~~aai~Aa~~AL~da~~~~~~~~~~~~ip~~~~~~~vt~~~~  167 (238)
T PRK00173         88 QEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLKDQVAAVSVGIV  167 (238)
T ss_pred             HHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhhhccCcccCCcccCceeEEEEEEE
Confidence            78899999999999999999999999999999999999999999999999999           9999999999999999


Q ss_pred             cCCeEEeCCCccccC
Q psy15057        137 DKNEVILDANQIQSN  151 (151)
Q Consensus       137 ~~~~~lvDpt~~Ee~  151 (151)
                       ++++|+|||.+||+
T Consensus       168 -~~~~lvDpt~~Ee~  181 (238)
T PRK00173        168 -DGEPVLDLDYEEDS  181 (238)
T ss_pred             -CCEEEECCCHHHHh
Confidence             58899999999984

>TIGR01966 RNasePH ribonuclease PH

Probab=100.00  E-value=2.6e-37  Score=238.18  Aligned_cols=150  Identities=18%  Similarity=0.193  Sum_probs=129.3

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEE--cCCCC-----------CCcchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIF--RPKSG-----------LSFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~--~p~~g-----------~~~~~~   67 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|+++.+.+.....++++.++|++  .|++.           .+..++
T Consensus         7 ~~e~R~i~i~~G~~~~A~GSa~v~~G~T~Vla~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~~~~~r~~~~g~~~~~~   86 (236)
T TIGR01966         7 PDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRATQTRNRRESAKGKQSGRT   86 (236)
T ss_pred             CCCccCeEEEeCCcCCCCceEEEEecCCEEEEEEEccCccCCcccCCCcEEEEEEEecCCCCCCCCccccccCCCCCccH
Confidence            57999999999999999999999999999999999877532222335667766655  45422           222356


Q ss_pred             hHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhc-----------CccccceeeEEEEEEe
Q psy15057         68 RLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINS-----------GISMRYILAAVSCIIN  136 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~a-----------gip~~~~~~avtv~~~  136 (151)
                      ++++++|+++|+++|+++.||++.|+|+++||++|||+++|++||+++||+|+           ||||+++++++|++++
T Consensus        87 ~e~~~~i~r~lr~~i~l~~l~~~~i~I~v~VL~~DG~~~~aai~Aa~aAL~da~~~~~~~~~~~~ip~~~~~~~vt~~~~  166 (236)
T TIGR01966        87 QEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAAVSVGIV  166 (236)
T ss_pred             HHHHHHHHHHHHHhcCHhhcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHHHHhhhhcCcccCCCccCceeEEEEEEE
Confidence            68899999999999999999999999999999999999999999999999999           9999999999999999


Q ss_pred             cCCeEEeCCCccccC
Q psy15057        137 DKNEVILDANQIQSN  151 (151)
Q Consensus       137 ~~~~~lvDpt~~Ee~  151 (151)
                       ++.+++|||.+||+
T Consensus       167 -~~~~v~Dpt~~Ee~  180 (236)
T TIGR01966       167 -DGEPVLDLDYEEDS  180 (236)
T ss_pred             -CCEEEECCChhHHh
Confidence             48899999999984

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.

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

Probab=100.00  E-value=3.8e-36  Score=228.48  Aligned_cols=150  Identities=25%  Similarity=0.343  Sum_probs=133.8

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCccccccc-CCCCeeEEEEEEc--CCCCC----Ccc---hhhHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKASVEVIFR--PKSGL----SFV---QDRLK   70 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~-~~~~~~~v~v~~~--p~~g~----~~~---~~~~~   70 (151)
                      +||+|+++++.|++++++||+++++|+|||+|+|+||.++.++. ..++++.+.++|.  |++..    +..   +.+++
T Consensus        15 ~delR~i~~~~~~~~~a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~ey~m~p~sT~~R~~~~~~~gR~~ei   94 (230)
T COG0689          15 PDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLPRSTDERKKREADRGRTKEI   94 (230)
T ss_pred             cccccceEEEeccccCCCccEEEEeCCeEEEEEEecCCCCCChhhcCCCceEEEEEEecccccccccccccccccchhHH
Confidence            58999999999999999999999999999999999999887753 4466788877775  44431    111   35788


Q ss_pred             HHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCcccc
Q psy15057         71 ESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQS  150 (151)
Q Consensus        71 ~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee  150 (151)
                      +++|.++|+++++++.||++.|+|+++|+++||+.+.|++||+++||+|||+||+++++|+|+|+++ +.+++|+++.|+
T Consensus        95 srli~~al~~~i~L~~~p~~~I~i~~dVlqaDggTrta~It~A~lAL~DAgipl~~~vaaiSvgi~~-~~~~lDl~~~Ed  173 (230)
T COG0689          95 SRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVGIVD-GVIVLDLDYEED  173 (230)
T ss_pred             HHHHHHHHHHHhhhhhcCccEEEEEEEEEECCCCeeeehhhHHHHHHHHcCCchhhheeEeEEEEEC-CceEecCcchhh
Confidence            9999999999999999999999999999999999999999999999999999999999999999995 779999999987


Q ss_pred             C
Q psy15057        151 N  151 (151)
Q Consensus       151 ~  151 (151)
                      +
T Consensus       174 s  174 (230)
T COG0689         174 S  174 (230)
T ss_pred             c
Confidence            4

>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=100.00  E-value=2.1e-32  Score=193.11  Aligned_cols=121  Identities=36%  Similarity=0.525  Sum_probs=106.0

Q ss_pred             CccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCC-CCe--eEEEEEEcCCC-------CCCcchhhHHHH
Q psy15057          3 SLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTI-IDK--ASVEVIFRPKS-------GLSFVQDRLKES   72 (151)
Q Consensus         3 e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~-~~~--~~v~v~~~p~~-------g~~~~~~~~~~~   72 (151)
                      |+|++.+++|++++++|||+|++|+|+|+|+|+||.+.+++.+. ...  ..++|++.|.+       |.+...+++++.
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            79999999999999999999999999999999999987555442 223  55666667754       234456778999


Q ss_pred             HHHHHHHHhhcccCCCCcEEEEEEEEEeCCC-ChhHHHHHHHHHHHHhcCcc
Q psy15057         73 VIKSTCESALLTMLHPRTSVILTIQELQDQG-SLLSCCINAACLALINSGIS  123 (151)
Q Consensus        73 ~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG-~~l~a~inaa~lAL~~agip  123 (151)
                      +|+++|++.+.++.||+|.|+|+++||++|| |++++++||+++||+|+|||
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 ....

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=100.00  E-value=1.5e-31  Score=231.88  Aligned_cols=150  Identities=18%  Similarity=0.300  Sum_probs=124.3

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEE-cCc-cccccc----CCCCeeEEEEEEcCCCC-------CCcchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMY-GPV-EAKIQK----TIIDKASVEVIFRPKSG-------LSFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~-gp~-~~~~~~----~~~~~~~v~v~~~p~~g-------~~~~~~   67 (151)
                      +||+|++++++|+++++||||+|++|+|+|+|+|+ ||. +.++.+    +...+..++++|.|++.       .++.++
T Consensus       321 ~~e~Rpi~~~~g~l~~a~GSal~~~G~T~Vl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~~~~~~~rre  400 (693)
T PRK11824        321 LDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLRDEQIIDGLEGEYKKRFMLHYNFPPYSVGETGRVGSPGRRE  400 (693)
T ss_pred             cCcccceEEEeCCCCCCCceEEEEECCeEEEEEEecCCCcccccccccCCCCcEEEEEEEEcCCCCCCCcCCCCCCChhH
Confidence            58999999999999999999999999999999995 885 322211    12234456777777532       133444


Q ss_pred             hHHHHHHHHHHHHhhcc-cCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCC---eEEe
Q psy15057         68 RLKESVIKSTCESALLT-MLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKN---EVIL  143 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~~-~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~---~~lv  143 (151)
                      ...+++++|+|++++++ +.|| |.|+|+++||++|||.++|++||+++||+||||||+++++|+++|+++++   .+++
T Consensus       401 ~~~~~li~ral~~vi~~~~~~p-~~I~v~~~VLe~dGs~~~Aai~aaslAL~dAgvP~~~~Va~vs~gli~~~~~~~il~  479 (693)
T PRK11824        401 IGHGALAERALEPVLPSEEEFP-YTIRVVSEILESNGSSSMASVCGSSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLT  479 (693)
T ss_pred             HHHHHHHHHHHHHhcCcccCCC-EEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCccCceeEEEEEEEcCCCceEEEc
Confidence            45679999999999998 7899 58999999999999999999999999999999999999999999999644   3899


Q ss_pred             CCCccccC
Q psy15057        144 DANQIQSN  151 (151)
Q Consensus       144 Dpt~~Ee~  151 (151)
                      ||+..||.
T Consensus       480 D~~~~Ed~  487 (693)
T PRK11824        480 DILGDEDH  487 (693)
T ss_pred             CCChhhHh
Confidence            99999974

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=99.98  E-value=1.9e-31  Score=230.93  Aligned_cols=150  Identities=17%  Similarity=0.257  Sum_probs=125.0

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEE-cCccccccc-----CCCCeeEEEEEEcCCCC-------CCcchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMY-GPVEAKIQK-----TIIDKASVEVIFRPKSG-------LSFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~-gp~~~~~~~-----~~~~~~~v~v~~~p~~g-------~~~~~~   67 (151)
                      +||+|++++++|+++++||||+|++|+|+|+|+|+ ||.+.....     +...+..++++|.|++.       .++.++
T Consensus       317 ~~e~Rpi~~~~g~l~~a~GSa~~~~G~Tqvl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs~~e~~~~g~~~rre  396 (684)
T TIGR03591       317 LDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQIIDDLEGEYRKRFMLHYNFPPYSVGEVGRVGGPGRRE  396 (684)
T ss_pred             CCCcCceEEEeCCCCCCCceEEEEeCCeEEEEEEecCCcccccCCcccCCCccEEEEEEEEcCCCCCCCcCCCCCCChHH
Confidence            58999999999999999999999999999999994 887542211     11224556777777532       233444


Q ss_pred             hHHHHHHHHHHHHhhcc-cCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCC----eEE
Q psy15057         68 RLKESVIKSTCESALLT-MLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKN----EVI  142 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~~-~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~----~~l  142 (151)
                      ...+++++++|+++|+. +.||+ .|+|+++||++|||.++|++||+++||+||||||++.++|+++|++.++    .++
T Consensus       397 i~~~~l~~ral~~~i~~~~~~p~-tI~v~~~VLesdGs~~~Aai~aaslAL~dAgvP~~~~Vagvs~gli~~~~~~~~il  475 (684)
T TIGR03591       397 IGHGALAERALKAVLPSEEEFPY-TIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDERFAVL  475 (684)
T ss_pred             HHHHHHHHHHHHHhcCccccCCe-EEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCCcCCEEEEEEEEEcCCCcceEEE
Confidence            55679999999999986 78995 5999999999999999999999999999999999999999999999533    499


Q ss_pred             eCCCccccC
Q psy15057        143 LDANQIQSN  151 (151)
Q Consensus       143 vDpt~~Ee~  151 (151)
                      +||+..||.
T Consensus       476 ~D~~~~Ed~  484 (684)
T TIGR03591       476 SDILGDEDH  484 (684)
T ss_pred             eCCChHHHh
Confidence            999999974

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).

>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional

Probab=99.98  E-value=2.5e-31  Score=208.55  Aligned_cols=149  Identities=17%  Similarity=0.212  Sum_probs=122.3

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEE--EEEcCCC------CCCcchhhHHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVE--VIFRPKS------GLSFVQDRLKES   72 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~--v~~~p~~------g~~~~~~~~~~~   72 (151)
                      ++|+|++++++|++++++|||++++|+|+|+|+|+++.. .+..+.+++|.++  +++.|++      |.++..+.++++
T Consensus        31 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~vl~~V~~~~~-~p~~~~~~~g~i~~~v~~~~~a~~~~~~~~~~~~~~~l~~  109 (271)
T PRK04282         31 LDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIG-EPFPDTPNEGVLIVNAELLPLASPTFEPGPPDENAIELAR  109 (271)
T ss_pred             CccccCeEEEeCCccCCCcEEEEEECCCEEEEEEEEEEe-cCCCCCCCCCEEEEEEEECCCcCccccCCCCCHHHHHHHH
Confidence            479999999999999999999999999999999996542 2233456666655  4555643      334455667889


Q ss_pred             HHHHHHHHh--hcccCC---C---CcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCcc--------------------c
Q psy15057         73 VIKSTCESA--LLTMLH---P---RTSVILTIQELQDQGSLLSCCINAACLALINSGIS--------------------M  124 (151)
Q Consensus        73 ~l~~~l~~~--i~~~~~---p---~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip--------------------~  124 (151)
                      +|+++|++.  ++++.+   |   .|.|+|+++||++|||+++|+++|+++||.|+++|                    |
T Consensus       110 ~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG~~~daa~~Aa~aAL~~~~iP~~~~~~~~~~~~~~~~~~l~~  189 (271)
T PRK04282        110 VVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEGEDGVVDKLGEDFPLPV  189 (271)
T ss_pred             HHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhCCCCcEEEcCCceeccCCCcccCCC
Confidence            999998875  333322   3   58999999999999999999999999999999995                    9


Q ss_pred             cceeeEEEEEEecCCeEEeCCCccccC
Q psy15057        125 RYILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus       125 ~~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                      +++|+++|++++ ++.+|+|||..||+
T Consensus       190 ~~~p~~vt~~~~-~~~~v~Dpt~~Ee~  215 (271)
T PRK04282        190 NDKPVTVTFAKI-GNYLIVDPTLEEES  215 (271)
T ss_pred             CCeeEEEEEEEE-CCEEEECCCHHHHh
Confidence            999999999999 58899999999984

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.97  E-value=3.2e-30  Score=221.51  Aligned_cols=150  Identities=17%  Similarity=0.241  Sum_probs=124.9

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEE-cCccccccc-----CCCCeeEEEEEEcCCCC----C---Ccchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMY-GPVEAKIQK-----TIIDKASVEVIFRPKSG----L---SFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~-gp~~~~~~~-----~~~~~~~v~v~~~p~~g----~---~~~~~   67 (151)
                      ++|+|++.+++|+++++||||+|+.|+|+|+|++. ||.+.....     +...+..++++|.|++.    +   ++.++
T Consensus       342 ~~eiR~i~~~~g~l~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~~~~~~~~YnfpPFSt~er~~~~~~~RRe  421 (719)
T TIGR02696       342 VTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPPYSTGETGRVGSPKRRE  421 (719)
T ss_pred             ccccccceeecCCCCCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccccceEEEEEeCCCCcccCCCCCCCCCccH
Confidence            48999999999999999999999999999999987 454322211     11234557788888642    1   23455


Q ss_pred             hHHHHHHHHHHHHhhc-ccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecC---Ce---
Q psy15057         68 RLKESVIKSTCESALL-TMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDK---NE---  140 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~-~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~---~~---  140 (151)
                      .+.+.+++++|+++|+ ++.||++ |+++.+||++||+..+|++||++|||+||||||+++++|+++|++.+   +.   
T Consensus       422 ighg~La~rALe~vI~~~e~fP~T-IrvvseVLeSdGSss~AsIcaasLALmDAGVPmkd~VAgis~Gli~e~~~~~~~~  500 (719)
T TIGR02696       422 IGHGALAERALVPVLPSREEFPYA-IRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAGIAMGLISDEVDGETRY  500 (719)
T ss_pred             HHHHHHHHHHHHHhhCcHhhCCCE-EEEEEEeeccCCcHHHHHHHHHHHHHHHcCcchhheeeEEEEEEeccccCCCcce
Confidence            5678999999999998 6999998 88999999999999999999999999999999999999999999954   33   


Q ss_pred             -EEeCCCccccC
Q psy15057        141 -VILDANQIQSN  151 (151)
Q Consensus       141 -~lvDpt~~Ee~  151 (151)
                       +++||+..|+.
T Consensus       501 ~iL~Di~g~ED~  512 (719)
T TIGR02696       501 VALTDILGAEDA  512 (719)
T ss_pred             eEEeCCCchhhh
Confidence             89999999973

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=99.97  E-value=2e-29  Score=220.39  Aligned_cols=150  Identities=18%  Similarity=0.294  Sum_probs=125.1

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEE-cCccccccc------CCCCeeEEEEEEcCCC----CC---Ccch
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMY-GPVEAKIQK------TIIDKASVEVIFRPKS----GL---SFVQ   66 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~-gp~~~~~~~------~~~~~~~v~v~~~p~~----g~---~~~~   66 (151)
                      ++|+|++.+++|.++++||||+|++|+|+|+|+|+ ||.+.....      +...+..++++|.|++    ++   ++.+
T Consensus       445 ~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVLatVtlGp~~~~q~~d~l~~~~~~~~f~~~y~fPPfs~ge~~r~g~psrR  524 (891)
T PLN00207        445 PDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEVKRFYLQYSFPPSCVGEVGRIGAPSRR  524 (891)
T ss_pred             cCccceEEEEeCCcCCCCceEEEEECCeEEEEEEEecCccccccccccccccceeeEEEEEEcCCCCCccccCCCCCCHH
Confidence            48999999999999999999999999999999996 887543221      1223456888888864    22   2334


Q ss_pred             hhHHHHHHHHHHHHhhccc-CCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecC-------
Q psy15057         67 DRLKESVIKSTCESALLTM-LHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDK-------  138 (151)
Q Consensus        67 ~~~~~~~l~~~l~~~i~~~-~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~-------  138 (151)
                      +...+++++|+|++++..+ .|| |.|+|+++||++||+..+|++||+++||+||||||+++++|+++|++.+       
T Consensus       525 Ei~hg~L~eRALrpvip~~~~fP-~tIrV~~~VLesDGSssmAaV~aaSLALmDAGIPmk~~VAGvsvGli~d~~~~~~~  603 (891)
T PLN00207        525 EIGHGMLAERALEPILPSEDDFP-YTIRVESTITESNGSSSMASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGGD  603 (891)
T ss_pred             HHHHHHHHHHHHHHhCCcccCCC-EEEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCccCceeEEEEEEEecccccCCC
Confidence            4456899999999999985 899 5899999999999999999999999999999999999999999999932       


Q ss_pred             Ce--EEeCCCccccC
Q psy15057        139 NE--VILDANQIQSN  151 (151)
Q Consensus       139 ~~--~lvDpt~~Ee~  151 (151)
                      +.  +++||+..|+.
T Consensus       604 g~~~IL~Dp~g~Ed~  618 (891)
T PLN00207        604 GSPLILSDITGSEDA  618 (891)
T ss_pred             CcEEEEeCCCHHHHh
Confidence            24  56799999873

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=99.96  E-value=8.7e-29  Score=214.42  Aligned_cols=138  Identities=23%  Similarity=0.247  Sum_probs=118.5

Q ss_pred             cceEEEecCC-CCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcCC--------------CCCCcchhhH
Q psy15057          5 RELKSQLNIL-SRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPK--------------SGLSFVQDRL   69 (151)
Q Consensus         5 R~i~i~~g~~-~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p~--------------~g~~~~~~~~   69 (151)
                      |++.+++|.+ ++|||||++++|+|+|+|+|+||.++++.   .+...++|+|.+.              .|+++.++.+
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 57999999999999999999999875432   3567788888642              1234455666


Q ss_pred             HHHHHHHHHHHhhcccCCCC---cEEEEEEEEEeCCCChh--HHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeC
Q psy15057         70 KESVIKSTCESALLTMLHPR---TSVILTIQELQDQGSLL--SCCINAACLALINSGISMRYILAAVSCIINDKNEVILD  144 (151)
Q Consensus        70 ~~~~l~~~l~~~i~~~~~p~---~~i~i~v~vl~~dG~~l--~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvD  144 (151)
                      ++++|+|+|+++     ||+   |.++|+++||++||+.+  .|++||+++||+++||||+++++|+++|++ +|++++|
T Consensus        82 ~srlIdR~lrpl-----fp~~~~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~i-dg~~ild  155 (684)
T TIGR03591        82 TSRLIDRPIRPL-----FPKGFRNEVQVVATVLSYDPENDPDILAIIGASAALAISGIPFNGPIAAVRVGYI-DGQYVLN  155 (684)
T ss_pred             HHHHHhhHHHHh-----cCCCCCceEEEEEEEEecCcCCchHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEE-CCEEEEc
Confidence            899999999985     665   89999999999999974  399999999999999999999999999999 5899999


Q ss_pred             CCccccC
Q psy15057        145 ANQIQSN  151 (151)
Q Consensus       145 pt~~Ee~  151 (151)
                      ||..||+
T Consensus       156 Pt~~E~~  162 (684)
T TIGR03591       156 PTVDELE  162 (684)
T ss_pred             CCHHHHh
Confidence            9999874

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=99.96  E-value=2.8e-28  Score=211.57  Aligned_cols=142  Identities=22%  Similarity=0.196  Sum_probs=119.6

Q ss_pred             ccceEEEecCCC-CCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcCC---C-----------CCCcchhh
Q psy15057          4 LRELKSQLNILS-RSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPK---S-----------GLSFVQDR   68 (151)
Q Consensus         4 ~R~i~i~~g~~~-~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p~---~-----------g~~~~~~~   68 (151)
                      -|++.+++|.++ +|||||++++|+|+|+|+|++|.++++   ..+...++|+|.+.   +           |+++.++.
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 699999999999999999999997532   24567788888652   1           23445566


Q ss_pred             HHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCCh-hH-HHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCC
Q psy15057         69 LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSL-LS-CCINAACLALINSGISMRYILAAVSCIINDKNEVILDAN  146 (151)
Q Consensus        69 ~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~-l~-a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt  146 (151)
                      +++++++|+|++++.  ..++|.++|+++||++||+. .+ +++||+++||+++||||+++++|+++|++ +|++++|||
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            679999999999643  23479999999999999976 44 89999999999999999999999999999 589999999


Q ss_pred             ccccC
Q psy15057        147 QIQSN  151 (151)
Q Consensus       147 ~~Ee~  151 (151)
                      ..||+
T Consensus       167 ~~E~~  171 (693)
T PRK11824        167 VEELE  171 (693)
T ss_pred             HHHHh
Confidence            99974

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

Probab=99.96  E-value=5.4e-28  Score=186.15  Aligned_cols=149  Identities=18%  Similarity=0.205  Sum_probs=125.7

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeE--EEEEEcCC------CCCCcchhhHHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKAS--VEVIFRPK------SGLSFVQDRLKES   72 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~--v~v~~~p~------~g~~~~~~~~~~~   72 (151)
                      ++|+|++++++|+++.++|||+|++|+|+|+|+|+.... +|-.+.|++|.  +++++.|.      +|++...+-++++
T Consensus        30 ~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK~eig-~Pf~DtP~eG~~~~n~El~Plas~~fE~Gppde~aielsr  108 (272)
T COG2123          30 FDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIG-EPFPDTPNEGVLVVNVELSPLASPSFEPGPPDELAIELSR  108 (272)
T ss_pred             cccccceEEEeCceecCCCcEEEEecCeEEEEEEEcccC-CCCCCCCCCceEEeeeeeeccccccccCCCCchhHHHHHH
Confidence            479999999999999999999999999999999998773 44567788874  57777774      4555545556889


Q ss_pred             HHHHHHHH--hhcc------cCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCcc---------------------
Q psy15057         73 VIKSTCES--ALLT------MLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS---------------------  123 (151)
Q Consensus        73 ~l~~~l~~--~i~~------~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip---------------------  123 (151)
                      .++|.++.  .+++      ++...|.+.++++||++|||++||+..|+++||+++++|                     
T Consensus       109 vvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~Da~~lA~~aAL~~t~vP~~~~~~~~~~v~~~~~~~~pl  188 (272)
T COG2123         109 VVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAAVAALLNTRVPKAVEVGDGEIVIEVEEEPVPL  188 (272)
T ss_pred             HHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHhcCCCceeecCCcceeecccCCCccc
Confidence            99998864  3333      345679999999999999999999999999999999877                     


Q ss_pred             -ccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057        124 -MRYILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus       124 -~~~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                       +.+.+.++|++++ ++.+++|||.+||.
T Consensus       189 ~~~~~pi~vt~a~i-g~~lvvDPsleEe~  216 (272)
T COG2123         189 PVSNPPISVTFAKI-GNVLVVDPSLEEEL  216 (272)
T ss_pred             ccCCCceEEEEEEE-CCEEEeCCCcchhh
Confidence             5788999999999 58999999999983

>KOG1614|consensus

Probab=99.94  E-value=5.3e-26  Score=172.27  Aligned_cols=147  Identities=16%  Similarity=0.205  Sum_probs=123.9

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeE--EEEEEcCCCC------CCcchhhHHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKAS--VEVIFRPKSG------LSFVQDRLKES   72 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~--v~v~~~p~~g------~~~~~~~~~~~   72 (151)
                      ++|+|++++++|   .-.||+.+++|+|+|+|.|+... .+|..++|.+|.  +..+++|.++      +.+..+-++.+
T Consensus        29 l~efR~lei~fG---ke~gs~~vt~G~Tkvm~~vt~~i-a~Py~dRP~eG~~~I~telsPmA~~sfE~Gr~~~~~v~l~R  104 (291)
T KOG1614|consen   29 LEEFRDLEIEFG---KEYGSVLVTMGNTKVMARVTAQI-AQPYIDRPHEGSFSIFTELSPMASPSFEPGRKGESEVELSR  104 (291)
T ss_pred             hhhhhceEEEec---cccccEEEEecCeeEEEEeehhh-cCcccCCCCCCeeeeeeccccccccccCCCCccchHHHHHH
Confidence            468999999999   67899999999999999999887 456677888885  5567788644      34445667789


Q ss_pred             HHHHHHH--------HhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcC-----------------------
Q psy15057         73 VIKSTCE--------SALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG-----------------------  121 (151)
Q Consensus        73 ~l~~~l~--------~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~ag-----------------------  121 (151)
                      +|+++++        +++.......|.|++++++|+.|||+.||++.|+++||++.+                       
T Consensus       105 liek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlvDaA~iAviaaL~hFrrPdvTv~g~ev~ihp~eEr~PvP  184 (291)
T KOG1614|consen  105 LIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLVDAACIAVIAALMHFRRPDVTVGGEEVIIHPVEEREPVP  184 (291)
T ss_pred             HHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCeehhHHHHHHHHHHhcCCCCcccccceeEecChhccCCcc
Confidence            9999874        445555667899999999999999999999999999999999                       


Q ss_pred             ccccceeeEEEEEEecCC-eEEeCCCccccC
Q psy15057        122 ISMRYILAAVSCIINDKN-EVILDANQIQSN  151 (151)
Q Consensus       122 ip~~~~~~avtv~~~~~~-~~lvDpt~~Ee~  151 (151)
                      +.|+++|+++|++++.+| .+++|||..||.
T Consensus       185 L~I~HmPIC~tf~ffnkG~ivviDpt~~Ee~  215 (291)
T KOG1614|consen  185 LSIHHMPICFTFGFFNKGEIVVIDPTEKEEA  215 (291)
T ss_pred             eeeeeccceEEEEEecCceEEEeCCcHHHHh
Confidence            558999999999999755 489999999984

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.91  E-value=6.6e-24  Score=185.98  Aligned_cols=141  Identities=17%  Similarity=0.160  Sum_probs=118.5

Q ss_pred             cceEEEecCCC-CCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcC---CCC-----------CCcchhhH
Q psy15057          5 RELKSQLNILS-RSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRP---KSG-----------LSFVQDRL   69 (151)
Q Consensus         5 R~i~i~~g~~~-~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p---~~g-----------~~~~~~~~   69 (151)
                      |.+.+++|.+. +|+||+.+++|+|.|+|+|..-.+++   +..+...+.|+|..   .+|           +++.+|-.
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 RHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPS---EPSDFFPLSVHYQERFSAAGRTSGGFFKREGRTKDHEVL  165 (891)
T ss_pred             EEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEeccCCC---CCCCccceeEeeeeehhhcCccCCceeccCCCCChHHHH
Confidence            47999999998 69999999999999999999755433   22345566777653   122           34555656


Q ss_pred             HHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCC--hhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCc
Q psy15057         70 KESVIKSTCESALLTMLHPRTSVILTIQELQDQGS--LLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQ  147 (151)
Q Consensus        70 ~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~--~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~  147 (151)
                      ++++|+|.|+++++.+.||.++|.+  +||++||+  ...+++|||++||+++||||+++++||++|++ +|++|+|||.
T Consensus       166 ~sRlIdR~lRPlfp~~~~~etQI~i--~VLsaDg~~~pd~~AInAASaAL~~SgIP~~gpVaAVrVG~i-dg~~VlnPt~  242 (891)
T PLN00207        166 ICRLIDRPLRPTMPKGFYHETQILS--WVLSYDGLHSPDSLAVTAAGIAVALSEVPNLKAIAGVRVGLI-GGKFIVNPTT  242 (891)
T ss_pred             HHHHHCccchhhccccCCCCcEEEE--EEEeeCCCCChhhHHHHHHHHHHHhhCCCccCceEEEEEEEE-CCEEEECCCH
Confidence            7999999999999999999987755  99999998  67999999999999999999999999999999 6999999999


Q ss_pred             cccC
Q psy15057        148 IQSN  151 (151)
Q Consensus       148 ~Ee~  151 (151)
                      .|++
T Consensus       243 ~E~~  246 (891)
T PLN00207        243 KEME  246 (891)
T ss_pred             HHHh
Confidence            9863

>KOG1612|consensus

Probab=99.88  E-value=4.4e-21  Score=146.25  Aligned_cols=147  Identities=14%  Similarity=0.132  Sum_probs=113.2

Q ss_pred             CCccceEEEecCCCCCCeeEEEEeCC-eEEEEEEEcCcccccccCCCCeeE--EEEEEcCCC-----CCCcch-hhHHHH
Q psy15057          2 DSLRELKSQLNILSRSDGSVIFSQGQ-TVVVASMYGPVEAKIQKTIIDKAS--VEVIFRPKS-----GLSFVQ-DRLKES   72 (151)
Q Consensus         2 ~e~R~i~i~~g~~~~a~GSa~v~~G~-T~V~~~V~gp~~~~~~~~~~~~~~--v~v~~~p~~-----g~~~~~-~~~~~~   72 (151)
                      +++|++.++++++++++|||+|++|+ |.|+++|+.... ++..+.|.++.  +.|++.|.+     |+.+.+ -.++..
T Consensus        29 ~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVKaEvg-~~~~~~p~egk~~~~VD~S~sasp~f~gRggde~~~elts  107 (288)
T KOG1612|consen   29 HQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKAEVG-SPDDETPVEGKYLFFVDCSPSASPQFQGRGGDELVEELTS  107 (288)
T ss_pred             cccceEEEEeccccCCCCcEEEEecCCceEEEEEeeecc-CccccCCCCCeEEEEEEecCCcCccccCCChhhHHHHHHH
Confidence            58999999999999999999999999 999999999885 45667777665  566666643     232211 123455


Q ss_pred             HHHHHHHH---hhcc------cCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccc-------------------
Q psy15057         73 VIKSTCES---ALLT------MLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISM-------------------  124 (151)
Q Consensus        73 ~l~~~l~~---~i~~------~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~-------------------  124 (151)
                      .|+++|.+   -+++      +. -+|.|+|++.|++.|||+++|+..|+.+||.+..+|-                   
T Consensus       108 aLq~~l~~~~sgv~ls~L~lt~~-~~W~i~VDvlVi~s~gn~~dAiS~Ai~~AL~~T~lPkv~v~~dd~~~~~i~~s~~~  186 (288)
T KOG1612|consen  108 ALQRVLNSLGSGVDLSKLQLTPG-YCWKIYVDVLVISSDGNLLDAISIAIYAALNNTRLPKVIVAFDDDGEVEILLSDEE  186 (288)
T ss_pred             HHHHHHhCcCcccchhheeccCC-eeEEEEEeEEEEecCCCHHHHHHHHHHHHHhcccCCccccccccCCceeeccCccc
Confidence            55666554   1111      22 3799999999999999999999999999999998883                   


Q ss_pred             --------cceeeEEEEEEecCCeEEeCCCccccC
Q psy15057        125 --------RYILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus       125 --------~~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                              ..+|.=+++..+ +..++||||.+||.
T Consensus       187 Yd~~~~~~~~~P~ivtlskI-G~~~lVD~T~eEe~  220 (288)
T KOG1612|consen  187 YDLMVKLVENVPLIVTLSKI-GTNMLVDPTAEEES  220 (288)
T ss_pred             chhhhhhcccCCEEEEEEee-cceEEccCCccHHH
Confidence                    235667788888 57899999999984

>KOG1067|consensus

Probab=99.75  E-value=5.8e-18  Score=140.97  Aligned_cols=135  Identities=21%  Similarity=0.303  Sum_probs=112.8

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEc-Ccccccc-c--CCCC---eeEEEEEEcCCC----CC-Ccchhh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYG-PVEAKIQ-K--TIID---KASVEVIFRPKS----GL-SFVQDR   68 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~g-p~~~~~~-~--~~~~---~~~v~v~~~p~~----g~-~~~~~~   68 (151)
                      +||+|+|.|+.+.++..|||++|+.|+|+|+|+|+- ..+...+ +  ..++   +..++++|.|.+    |+ .+..+|
T Consensus       365 ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~~~~~~FmLhY~FPPyat~Evgkig~~nRR  444 (760)
T KOG1067|consen  365 LDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNGINFMLHYEFPPYATNEVGKIGGLNRR  444 (760)
T ss_pred             hhhhcccceecCccccccchhhhhcCceeEEEEEEcCCHHHhhhhhhhccCccCceEEEEeccCCccccccccccCCccc
Confidence            589999999999999999999999999999999984 3333222 1  1222   457899998853    33 234566


Q ss_pred             HH--HHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEec
Q psy15057         69 LK--ESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIIND  137 (151)
Q Consensus        69 ~~--~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~  137 (151)
                      ++  ..+-+++|.+++. +.||. .|++.-.|+++||+--.|.++.-++||+|||+|++.-++++++|++.
T Consensus       445 E~GhgaLAEkaL~~vlP-~dfPf-tIRv~SeVleSnGSsSMASvCGGslALmDaGvPv~a~vAGvaiGlvt  513 (760)
T KOG1067|consen  445 ELGHGALAEKALLPVLP-EDFPF-TIRVTSEVLESNGSSSMASVCGGSLALMDAGVPVSAHVAGVAIGLVT  513 (760)
T ss_pred             ccCchhHhhhhhhccCc-ccCce-EEEEeeeeeecCCcchHHhhhcchhhhhhcCCccccccceeEEEeEe
Confidence            76  5888999999998 78996 69999999999999999999999999999999999999999999985

>KOG1613|consensus

Probab=99.74  E-value=9.6e-18  Score=127.36  Aligned_cols=121  Identities=17%  Similarity=0.250  Sum_probs=97.8

Q ss_pred             CCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEE--cC------CCCCCcchhhHHHHH
Q psy15057          2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIF--RP------KSGLSFVQDRLKESV   73 (151)
Q Consensus         2 ~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~--~p------~~g~~~~~~~~~~~~   73 (151)
                      .|+|.+.++.|.++.+|||+.++.|+|.|+|++++..- .|....|+++.|-.+|  .|      ..|+++..+..+++.
T Consensus        44 gefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~ei~-epstdapdeg~Iv~n~~lpplcs~r~RpG~p~dea~viSq~  122 (298)
T KOG1613|consen   44 GEFRDTAINAGNISTANGSALLKSGKTTVICGIKAEIA-EPSTDAPDEGDIVPNYALPPLCSSRFRPGPPTDEAQVISQK  122 (298)
T ss_pred             hHHhhhheecCceeccCcHHHHhcCCcEEEEEeeeeec-ccccCCCCCcceeecccCCcccccCCCCCCCchHHHHHHHH
Confidence            47899999999999999999999999999999999883 4556778888775555  34      256666677777877


Q ss_pred             HHHHHHH--hhcc------cCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCcc
Q psy15057         74 IKSTCES--ALLT------MLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS  123 (151)
Q Consensus        74 l~~~l~~--~i~~------~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip  123 (151)
                      |..++.+  +|++      ...-.|.++.++.+|+.||+++|+|.||.++||.+-.+|
T Consensus       123 LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG~~fDa~w~al~aAlknvklP  180 (298)
T KOG1613|consen  123 LHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDGPVFDACWNALMAALKNVKLP  180 (298)
T ss_pred             HHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCCcHHHHHHHHHHHHHhcCCCc
Confidence            7776654  3333      233358899999999999999999999999999988777

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.72  E-value=1e-16  Score=138.56  Aligned_cols=140  Identities=16%  Similarity=0.168  Sum_probs=112.1

Q ss_pred             cceEEEecCCC-CCCeeEEEEe-CCeEEEEEEEcCcccccccCCCCeeEEEEEEcC---CC-----------CCCcchhh
Q psy15057          5 RELKSQLNILS-RSDGSVIFSQ-GQTVVVASMYGPVEAKIQKTIIDKASVEVIFRP---KS-----------GLSFVQDR   68 (151)
Q Consensus         5 R~i~i~~g~~~-~a~GSa~v~~-G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p---~~-----------g~~~~~~~   68 (151)
                      |.+.+++|.+. +|+||+.+++ |+|.|+|++..-.+++   +..+...+.|+|+.   .+           |+|+.+|-
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 RTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPK---DQFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAI   93 (719)
T ss_pred             EEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecCCCC---CCCCCcceeEeeeehhhhcCccCCceeccCCCCChhhh
Confidence            37999999998 6999999999 9999999999655433   22345566777753   12           23455555


Q ss_pred             HHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCC--hhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCC
Q psy15057         69 LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGS--LLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDAN  146 (151)
Q Consensus        69 ~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~--~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt  146 (151)
                      ..+++++|.++|++....  +..++|.++||+.|+.  .--.++|||++||.-++||+.+.++||.+|.+ +|+++++||
T Consensus        94 L~sRliDR~iRPLFp~~~--~~e~qi~~~vls~D~~~~pdvla~~~ASaAl~iSdiPf~gPv~~vrVg~i-~g~~viNPt  170 (719)
T TIGR02696        94 LTCRLIDRPLRPSFVKGL--RNEVQVVVTVLSLNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALI-DGQWVAFPT  170 (719)
T ss_pred             HHHHhhCCCCccCCCCCC--CcceEEEEEEEEcCCCCChHHHHHHHHHHHHHhcCCCCCCceEEEEEEEE-CCEEEECcC
Confidence            669999999998776543  3468888999998875  56778999999999999999999999999999 599999999


Q ss_pred             cccc
Q psy15057        147 QIQS  150 (151)
Q Consensus       147 ~~Ee  150 (151)
                      ..|-
T Consensus       171 ~~~~  174 (719)
T TIGR02696       171 HEQL  174 (719)
T ss_pred             HHHH
Confidence            8763

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

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

Probab=99.64  E-value=4.2e-16  Score=132.74  Aligned_cols=148  Identities=19%  Similarity=0.291  Sum_probs=120.5

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEE-cCc-cccccc----CCCCeeEEEEEEcCCC-C---C-CcchhhH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMY-GPV-EAKIQK----TIIDKASVEVIFRPKS-G---L-SFVQDRL   69 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~-gp~-~~~~~~----~~~~~~~v~v~~~p~~-g---~-~~~~~~~   69 (151)
                      .++.|++.++.|+++++|||++|..|+|+.++.++ |+. +.+.-+    +...+..++++|.|++ |   + ..+.+|+
T Consensus       319 ~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TLG~~~d~Qvid~l~~e~~krfm~hYNFPp~SvGE~g~~g~p~RRE  398 (692)
T COG1185         319 GDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLHYNFPPFSVGETGRMGSPGRRE  398 (692)
T ss_pred             cceeeeeeEEecCCCCccchhhhccCCCcceEEEEcCCcchhhhhhhccchhhhheeeeccCCCCCccccCCCCCCCccc
Confidence            37899999999999999999999999999999997 543 333222    2234567899999975 3   2 2344556


Q ss_pred             H--HHHHHHHHHHhhc-ccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCC---eEEe
Q psy15057         70 K--ESVIKSTCESALL-TMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKN---EVIL  143 (151)
Q Consensus        70 ~--~~~l~~~l~~~i~-~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~---~~lv  143 (151)
                      +  ..+-+|++.+++. .+.||. .|++.-.|++++|+--.|.+++.+|||+|||+|++..++++..|++.++   .++-
T Consensus       399 iGHG~LA~Ral~~vlp~~e~fpy-tiRvVsEi~eSNGSsSmaSVCg~sLaLmdAGVPIk~pVAGIAMGLI~eg~~~~vLs  477 (692)
T COG1185         399 IGHGALAERALAPVLPSEEEFPY-TIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLS  477 (692)
T ss_pred             ccCchhhHHHHhhhCCchhcCCc-eeeeeehhhcccCcccchhhhhhHHHHHhCCCcccccccchhccceecCCceEeec
Confidence            5  6888999999998 578997 6999999999999999999999999999999999999999999999653   2666


Q ss_pred             CCCccc
Q psy15057        144 DANQIQ  149 (151)
Q Consensus       144 Dpt~~E  149 (151)
                      |-...|
T Consensus       478 DI~G~E  483 (692)
T COG1185         478 DILGDE  483 (692)
T ss_pred             cccccc
Confidence            666555

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

Probab=99.62  E-value=6.9e-15  Score=125.39  Aligned_cols=139  Identities=19%  Similarity=0.173  Sum_probs=112.7

Q ss_pred             cceEEEecCCC-CCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcC---C-----------CCCCcchhhH
Q psy15057          5 RELKSQLNILS-RSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRP---K-----------SGLSFVQDRL   69 (151)
Q Consensus         5 R~i~i~~g~~~-~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p---~-----------~g~~~~~~~~   69 (151)
                      |.+.+++|.+. +|+|++++++|+|.|++++.+.. ++   +..+...+.|+|.-   .           -|+|+.++..
T Consensus        14 ~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~-~~---~~~dF~PLtV~y~Ek~yaaGkiPGgf~kREGrpse~e~L   89 (692)
T COG1185          14 RTLTLETGKIARQANGAVLVRYGDTVVLATVVASK-PK---EGQDFFPLTVNYEEKTYAAGKIPGGFFKREGRPSEKEIL   89 (692)
T ss_pred             eeEEEEcchhhhhcCccEEEEECCeEEEEEEeecC-CC---CCCCccceeEeeeeehhccCcCCCcccccCCCCCccchh
Confidence            89999999998 79999999999999999999876 32   22344555565542   1           2345556666


Q ss_pred             HHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCCh--hHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCc
Q psy15057         70 KESVIKSTCESALLTMLHPRTSVILTIQELQDQGSL--LSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQ  147 (151)
Q Consensus        70 ~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~--l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~  147 (151)
                      .+++++|-+++++....  +..++|..+|++.|+..  .-.+++++++||.-++||+...++++.+|++ ||+++++||.
T Consensus        90 ~sRLIDRpiRPlFp~g~--~~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iPf~gpi~~vrvg~i-dg~~vlNPt~  166 (692)
T COG1185          90 TSRLIDRPIRPLFPKGF--RNEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYI-DGIFVLNPTL  166 (692)
T ss_pred             hhhhcccccccccchhh--ccceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCccCccceEEEEEE-CCEEEECCCh
Confidence            79999999998665432  45689999999999864  5678999999999999999999999999999 6999999998


Q ss_pred             ccc
Q psy15057        148 IQS  150 (151)
Q Consensus       148 ~Ee  150 (151)
                      .|.
T Consensus       167 ~e~  169 (692)
T COG1185         167 EEL  169 (692)
T ss_pred             HHh
Confidence            764

>KOG1067|consensus

Probab=99.39  E-value=3.8e-13  Score=112.56  Aligned_cols=140  Identities=19%  Similarity=0.177  Sum_probs=108.4

Q ss_pred             ccceEEEecCCCC-CCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcC---CCCC---------CcchhhHH
Q psy15057          4 LRELKSQLNILSR-SDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRP---KSGL---------SFVQDRLK   70 (151)
Q Consensus         4 ~R~i~i~~g~~~~-a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p---~~g~---------~~~~~~~~   70 (151)
                      -|.+.+++|.+.+ |+||+.+..|+|.|+++|..-..+.+.    +...+.|.|.-   ..|+         .+.++|++
T Consensus        55 nR~i~~etGklaRfAngsvvv~~GeT~Vm~Tv~~a~~PSp~----qFlPL~VdYqeK~aAvGRip~~fmRREg~tkdkEi  130 (760)
T KOG1067|consen   55 NREILFETGKLARFANGSVVVQMGETAVMTTVVLADKPSPP----QFLPLVVDYQEKFAAVGRIPGNFMRREGRTKDKEI  130 (760)
T ss_pred             CeEEEEecchhhhhcCCcEEEccCCeEEEEEEEecCCCCcc----ccceEEEehhhhhhhhccCCCcccccccCCcchhh
Confidence            4899999999995 999999999999999999875543332    34556666653   2232         12334443


Q ss_pred             --HHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCC--hhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCC
Q psy15057         71 --ESVIKSTCESALLTMLHPRTSVILTIQELQDQGS--LLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDAN  146 (151)
Q Consensus        71 --~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~--~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt  146 (151)
                        .+++++.+++......|  +..++-..+|..||-  .-.-++|++++||.-+.|||...+.++.+|++ +|+++|+||
T Consensus       131 L~~rLidrsirplfp~g~~--~etqi~~n~Ls~dG~~~pdvlainaas~Al~lsdvpw~gpig~vRigLi-~Ge~vVNPT  207 (760)
T KOG1067|consen  131 LTGRLIDRPIRPLFPKGFY--HETQILCNVLSSDGVHDPDVLAINAASAALSLSDVPWNGPIGAVRIGLI-DGEFVVNPT  207 (760)
T ss_pred             eeeeccccccccCCcccch--hHHHHHhhheecccccCchHHHHhHHHHHhhhccCCCCCceeeeEeeee-cceEEeCcc
Confidence              78888888876655443  455677888999984  34567899999999999999999999999999 699999999


Q ss_pred             cccc
Q psy15057        147 QIQS  150 (151)
Q Consensus       147 ~~Ee  150 (151)
                      .+|.
T Consensus       208 ~kEm  211 (760)
T KOG1067|consen  208 RKEM  211 (760)
T ss_pred             hhhh
Confidence            9985

>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=97.51  E-value=8.4e-05  Score=46.23  Aligned_cols=25  Identities=20%  Similarity=0.175  Sum_probs=20.3

Q ss_pred             ceeeEEEEEEecCCeEEeCCCccccC
Q psy15057        126 YILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus       126 ~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                      ++|+++|++++ ++++++|||.+||+
T Consensus         1 ~~~~avt~~~i-~~~~v~Dpt~~Ee~   25 (68)
T PF03725_consen    1 DPPVAVTVGII-DGELVVDPTAEEES   25 (68)
T ss_dssp             SEEEEEEEEEE-TTEEEES--HHHHH
T ss_pred             CCeEEEEEEEE-CCEEEECCCHHHHh
Confidence            57899999999 58899999999973

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	151
2nn6_D	237	Structure Of The Human Rna Exosome Composed Of Rrp4		2e-38
3hkm_A	246	Crystal Structure Of Rice(Oryza Sativa) Rrp46 Lengt		3e-25
3krn_A	222	Crystal Structure Of C. Elegans Cell-Death-Related		2e-17
2nn6_B	249	Structure Of The Human Rna Exosome Composed Of Rrp4		2e-15
2je6_B	250	Structure Of A 9-Subunit Archaeal Exosome Length =		4e-15
2br2_B	248	Rnase Ph Core Of The Archaeal Exosome Length = 248		5e-15
3l7z_B	245	Crystal Structure Of The S. Solfataricus Archaeal E		5e-15
4ifd_D	245	Crystal Structure Of An 11-subunit Eukaryotic Exoso		5e-15
2pnz_A	249	Crystal Structure Of The P. Abyssi Exosome Rnase Ph		2e-12
2ba0_F	258	Archaeal Exosome Core Length = 258		2e-12
3m7n_D	258	Archaeoglobus Fulgidus Exosome With Rna Bound To Th		2e-12
2wnr_B	240	The Structure Of Methanothermobacter Thermautotroph		1e-10
4ifd_B	248	Crystal Structure Of An 11-subunit Eukaryotic Exoso		7e-08
2wp8_B	246	Yeast Rrp44 Nuclease Length = 246		8e-08

>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 =  154 bits (389), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 68/147 (46%), Positives = 101/147 (68%)
Query: 3   SLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGL 62
           SLR    + N+LSR DGS  F QG T V+A +YGP E K+ K I +KA++EVI RPK GL
Sbjct: 29  SLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGL 88
Query: 63  SFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGI 122
             V ++ +E +I++TCE+ +L  LHPRTS+ + +Q + D GSLL+CC+NAAC+AL+++G+
Sbjct: 89  PGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGV 148
Query: 123 SMRYILAAVSCIINDKNEVILDANQIQ 149
            MR +   V+C ++    ++LD    Q
Sbjct: 149 PMRALFCGVACALDSDGTLVLDPTSKQ 175

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

Iteration: 1
 Score =  110 bits (275), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 53/148 (35%), Positives = 89/148 (60%)
Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSG 61
           + LR      N L R+ GS  ++QG T+V+A++YGP     +    +KAS+EV+++P +G
Sbjct: 12  NQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKASIEVVWKPMTG 71
Query: 62  LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG 121
               Q++  E  +K T +S  L  +HP T+  + +Q + + GSLL C INA C AL+ +G
Sbjct: 72  QIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLLPCAINACCAALVFAG 131
Query: 122 ISMRYILAAVSCIINDKNEVILDANQIQ 149
           I ++++  A+ C + +  EVILD N+ +
Sbjct: 132 IPLKHLAVAIGCGVLEDGEVILDTNKAE 159

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

Iteration: 1
 Score = 84.7 bits (208), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 46/146 (31%), Positives = 82/146 (56%), Gaps = 3/146 (2%)
Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
           LRE++ +L+ L  +DGS  FSQG T + AS  GP +    K   +  ++++ +R   G +
Sbjct: 5   LREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISYRANCGDN 64
Query: 64  FVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS 123
             +  +  ++I ST  +A+   L P T++ +T+  +QD GS+ +  IN AC AL+++G+ 
Sbjct: 65  --KFNVLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAVAINGACFALLDNGMP 122
Query: 124 MRYILAAVSCIINDKNEVILDANQIQ 149
              +   V  I+  K+E+I+D    Q
Sbjct: 123 FETVFCGV-LIVRVKDELIIDPTAKQ 147

>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 = 77.8 bits (190), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 45/145 (31%), Positives = 77/145 (53%), Gaps = 11/145 (7%)
Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVE--AKIQKTIIDKASVEVIFRPKSG 61
           LR++++++ + +++DGS    QG T  +A +YGP E      + + D+A V   +   + 
Sbjct: 26  LRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATF 85
Query: 62  LSFVQDRLKESVIKS---------TCESALLTMLHPRTSVILTIQELQDQGSLLSCCINA 112
            +  + R      KS         T E+A+LT LHPR+ + + +Q LQ  G   + C+NA
Sbjct: 86  STGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNA 145
Query: 113 ACLALINSGISMRYILAAVSCIIND 137
           A LA++++GI MR  + A S    D
Sbjct: 146 ATLAVLDAGIPMRDFVCACSAGFVD 170

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

Iteration: 1
 Score = 77.0 bits (188), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 56/162 (34%), Positives = 85/162 (52%), Gaps = 18/162 (11%)
Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKASVEVIFRPKS 60
           D LR +K +L +L  +DGS IF  G T  +A++YGP E   +  ++ D+A + V +    
Sbjct: 28  DELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYH--- 84
Query: 61  GLSFVQDRLKES-----------VIKSTCESALLTMLHPRTSVILTIQELQ-DQGSLLSC 108
              F  D  K             VI+   ESA+L  L PRT++ +  + LQ D GS L  
Sbjct: 85  MTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRL-V 143
Query: 109 CINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQS 150
            + AA LAL ++GI MR ++A V+    D   +ILD N+ ++
Sbjct: 144 SLMAASLALADAGIPMRDLIAGVAVGKAD-GVIILDLNETEA 184

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

Iteration: 1
 Score = 76.6 bits (187), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 56/161 (34%), Positives = 84/161 (52%), Gaps = 18/161 (11%)
Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKASVEVIFRPKS 60
           D LR +K +L +L  +DGS IF  G T  +A++YGP E   +  ++ D+A + V +    
Sbjct: 26  DELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYH--- 82
Query: 61  GLSFVQDRLKES-----------VIKSTCESALLTMLHPRTSVILTIQELQ-DQGSLLSC 108
              F  D  K             VI+   ESA+L  L PRT++ +  + LQ D GS L  
Sbjct: 83  MTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRL-V 141
Query: 109 CINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQ 149
            + AA LAL ++GI MR ++A V+    D   +ILD N+ +
Sbjct: 142 SLMAASLALADAGIPMRDLIAGVAVGKAD-GVIILDLNETE 181

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

Iteration: 1
 Score = 76.6 bits (187), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 56/161 (34%), Positives = 84/161 (52%), Gaps = 18/161 (11%)
Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKASVEVIFRPKS 60
           D LR +K +L +L  +DGS IF  G T  +A++YGP E   +  ++ D+A + V +    
Sbjct: 23  DELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYH--- 79
Query: 61  GLSFVQDRLKES-----------VIKSTCESALLTMLHPRTSVILTIQELQ-DQGSLLSC 108
              F  D  K             VI+   ESA+L  L PRT++ +  + LQ D GS L  
Sbjct: 80  MTPFSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRL-V 138
Query: 109 CINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQ 149
            + AA LAL ++GI MR ++A V+    D   +ILD N+ +
Sbjct: 139 SLMAASLALADAGIPMRDLIAGVAVGKAD-GVIILDLNETE 178

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

Iteration: 1
 Score = 76.6 bits (187), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 45/151 (29%), Positives = 86/151 (56%), Gaps = 8/151 (5%)
Query: 7   LKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQ 66
           +++++ IL   DGS  F    T V+ S+ GP+E K ++ +  + ++E+I RP  G++  +
Sbjct: 25  VQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEIIVRPAKGVATTR 84
Query: 67  DRLKESVIKSTCESALLTMLHPRTSVILTIQEL---QDQGSL----LSCCINAACLALIN 119
           +++ E  +++     +    +PR    +T Q L   +D+       LSCCINAA LAL++
Sbjct: 85  EKVLEDKLRAVLTPLITRHCYPRQLCQITCQILESGEDEAEFSLRELSCCINAAFLALVD 144
Query: 120 SGISMRYILAAVS-CIINDKNEVILDANQIQ 149
           +GI++  + A++   II D +++I+D    Q
Sbjct: 145 AGIALNSMCASIPIAIIKDTSDIIVDPTAEQ 175

>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 = 68.2 bits (165), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 51/165 (30%), Positives = 84/165 (50%), Gaps = 24/165 (14%)
Query: 3   SLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVE---AKIQKTIIDKASVEVIFR-- 57
            LR +K ++ +L  ++GS     G+  ++A++YGP E     +Q+   D+A + V +   
Sbjct: 25  ELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRP--DRAILRVRYNMA 82
Query: 58  PKSGLSFVQDRLKES----------VIKSTCESALLTMLHPRTSVILTIQELQDQGSLLS 107
           P S    V++R K            VIK   E AL+  + PRT++ + I+ LQ       
Sbjct: 83  PFS----VEERKKPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQADAGTRV 138
Query: 108 CCINAACLALINSGISMRYILAAVSCIIND-KNEVILDANQIQSN 151
             I AA LAL ++GI MR ++AA  C     + E++LD N+ + N
Sbjct: 139 AGITAASLALADAGIPMRDLVAA--CAAGKIEGEIVLDLNKEEDN 181

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 40/161 (24%), Positives = 84/161 (52%), Gaps = 12/161 (7%)
Query: 1   MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKS 60
            D LR +K + ++L R+DGS     G+  V+A+++GP E    + + D +   + +R   
Sbjct: 23  FDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVH-PRHLQDPSKAIIRYRYNM 81
Query: 61  GLSFVQDRLKES----------VIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCI 110
               V++R +            V K   E+ ++  L PR+++ + ++ LQ      + C+
Sbjct: 82  APFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACL 141
Query: 111 NAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN 151
           NAA +AL+++G+ M+ ++ +V+    D  +++LD  + + N
Sbjct: 142 NAASVALVDAGVPMKGMITSVAVGKAD-GQLVLDPMKEEDN 181

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

Iteration: 1
 Score = 67.8 bits (164), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 40/161 (24%), Positives = 84/161 (52%), Gaps = 12/161 (7%)
Query: 1   MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKS 60
            D LR +K + ++L R+DGS     G+  V+A+++GP E   +  + D +   + +R   
Sbjct: 23  FDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEH-LQDPSKAIIRYRYNM 81
Query: 61  GLSFVQDRLKES----------VIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCI 110
               V++R +            V K   E+ ++  L PR+++ + ++ LQ      + C+
Sbjct: 82  APFSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACL 141
Query: 111 NAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN 151
           NAA +AL+++G+ M+ ++ +V+    D  +++LD  + + N
Sbjct: 142 NAASVALVDAGVPMKGMITSVAVGKAD-GQLVLDPMKEEDN 181

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 52/163 (31%), Positives = 81/163 (49%), Gaps = 24/163 (14%)
Query: 1   MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-TIIDKA--------- 50
            D LR LK +  IL R+DGS     G   ++ ++YGP EA+I+K    D+A         
Sbjct: 23  FDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIRCRYNMA 82
Query: 51  --SVEVIFRPKSGLSFVQDRLKESVIKSTCES---ALLTMLHPRTSVILTIQELQDQGSL 105
             SVE   RP        DR    + K T E+   AL+    PR+ + + I+ L+ +G  
Sbjct: 83  PFSVEERKRPGP------DRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEGGT 136
Query: 106 LSCCINAACLALINSGISMRYILAAVSCIIND-KNEVILDANQ 147
               I AA +AL ++GI MR ++  V+C      ++V+LD ++
Sbjct: 137 RCAGITAASVALADAGIPMRDMV--VACAAGKVGDQVVLDLSE 177

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 44/166 (26%), Positives = 81/166 (48%), Gaps = 19/166 (11%)
Query: 1   MDSLRELKSQLNILSRS-DGSVIFSQGQTVVVASMYGPVEAKIQKTI-IDKASVEV---- 54
            + LR  +S +N    + DGS    QG   ++  + GP E +++  +   KA + V    
Sbjct: 21  WNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNI 80
Query: 55  -----IFRPKSGLSFVQDR----LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSL 105
                  R KS  S   +R    ++ S+++   ++ +L  ++PRT + + I  L+  G +
Sbjct: 81  TKFSKFERSKS--SHKNERRVLEIQTSLVRMFEKNVMLN-IYPRTVIDIEIHVLEQDGGI 137
Query: 106 LSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN 151
           +   IN   LALI++GISM   ++ +S  + D    +LD N ++ N
Sbjct: 138 MGSLINGITLALIDAGISMFDYISGISVGLYDTTP-LLDTNSLEEN 182

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 44/166 (26%), Positives = 81/166 (48%), Gaps = 19/166 (11%)
Query: 1   MDSLRELKSQLNILSRS-DGSVIFSQGQTVVVASMYGPVEAKIQKTI-IDKASVEV---- 54
            + LR  +S +N    + DGS    QG   ++  + GP E +++  +   KA + V    
Sbjct: 19  WNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNI 78
Query: 55  -----IFRPKSGLSFVQDR----LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSL 105
                  R KS  S   +R    ++ S+++   ++ +L  ++PRT + + I  L+  G +
Sbjct: 79  NKFSKFERSKS--SHKNERRVLEIQTSLVRMFEKNVMLN-IYPRTVIDIEIHVLEQDGGI 135
Query: 106 LSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN 151
           +   IN   LALI++GISM   ++ +S  + D    +LD N ++ N
Sbjct: 136 MGSLINGITLALIDAGISMFDYISGISVGLYDTTP-LLDTNSLEEN 180

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	151
2nn6_D	237	Exosome complex exonuclease RRP46; RNA, exosome, P	2e-46
3hkm_A	246	OS03G0854200 protein; RNAse PH domain, phosphoryla	2e-46
3krn_A	222	Protein C14A4.5, confirmed by transcript evidence;	5e-43
2nn6_F	272	MTR3, exosome component 6; RNA, exosome, PM/SCL, p	2e-27
2nn6_B	249	Exosome complex exonuclease RRP41; RNA, exosome, P	1e-22
2wp8_B	246	Exosome complex component SKI6; nucleus, hydrolase	2e-22
2po1_A	249	Probable exosome complex exonuclease 1; RNAse PH,	1e-18
2wnr_B	240	Probable exosome complex exonuclease 1; phosphate	1e-18
3b4t_A	262	Ribonuclease PH; RNAse, tRNA nucleotidyltransferas	3e-17
2je6_B	250	RRP41, exosome complex exonuclease 1; nuclease, hy	3e-15
3m7n_D	258	Probable exosome complex exonuclease 1; exosome, R	4e-15
1r6l_A	239	Ribonuclease PH; beta-alpha-beta-alpha fold, hexam	9e-14
1udn_A	255	Ribonuclease PH, RNAse PH; transferase, riken stru	2e-13
3dd6_A	255	Ribonuclease PH; exoribonuclease, tRNA maturation,	4e-13
1oys_A	245	Ribonuclease PH; transferase, tRNA processing; 2.4	3e-07
2nn6_C	278	Exosome complex exonuclease RRP43; RNA, exosome, P	8e-06
3m7n_G	259	Probable exosome complex exonuclease 2; exosome, R	1e-05
2wnr_A	271	Probable exosome complex exonuclease 2; phosphate	7e-05
2po1_B	277	Probable exosome complex exonuclease 2; RNAse PH,	7e-05
2je6_A	277	RRP42, exosome complex exonuclease 2; nuclease, hy	4e-04
2nn6_E	305	Exosome complex exonuclease RRP42; RNA, exosome, P	6e-04

>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 =  150 bits (380), Expect = 2e-46
 Identities = 68/150 (45%), Positives = 101/150 (67%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSG 61
            SLR    + N+LSR DGS  F QG T V+A +YGP E K+ K I +KA++EVI RPK G
Sbjct: 28  CSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIG 87

Query: 62  LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG 121
           L  V ++ +E +I++TCE+ +L  LHPRTS+ + +Q + D GSLL+CC+NAAC+AL+++G
Sbjct: 88  LPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAG 147

Query: 122 ISMRYILAAVSCIINDKNEVILDANQIQSN 151
           + MR +   V+C ++    ++LD    Q  
Sbjct: 148 VPMRALFCGVACALDSDGTLVLDPTSKQEK 177

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

 Score =  150 bits (380), Expect = 2e-46
 Identities = 53/150 (35%), Positives = 89/150 (59%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSG 61
           + LR      N L R+ GS  ++QG T+V+A++YGP     +    +KAS+EV+++P +G
Sbjct: 12  NQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKASIEVVWKPMTG 71

Query: 62  LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG 121
               Q++  E  +K T +S  L  +HP T+  + +Q + + GSLL C INA C AL+ +G
Sbjct: 72  QIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLLPCAINACCAALVFAG 131

Query: 122 ISMRYILAAVSCIINDKNEVILDANQIQSN 151
           I ++++  A+ C + +  EVILD N+ +  
Sbjct: 132 IPLKHLAVAIGCGVLEDGEVILDTNKAEEQ 161

>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 =  140 bits (355), Expect = 5e-43
 Identities = 44/148 (29%), Positives = 80/148 (54%), Gaps = 3/148 (2%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSG 61
             LRE++ +L+ L  +DGS  FSQG T + AS  GP +    K   +  ++++ +R   G
Sbjct: 3   GRLREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISYRANCG 62

Query: 62  LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG 121
            +  +  +  ++I ST  +A+   L P T++ +T+  +QD GS+ +  IN AC AL+++G
Sbjct: 63  DN--KFNVLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAVAINGACFALLDNG 120

Query: 122 ISMRYILAAVSCIINDKNEVILDANQIQ 149
           +    +   V  +    +E+I+D    Q
Sbjct: 121 MPFETVFCGVLIVRVK-DELIIDPTAKQ 147

>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 =  102 bits (255), Expect = 2e-27
 Identities = 33/167 (19%), Positives = 67/167 (40%), Gaps = 22/167 (13%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK------------TIIDK 49
             LR + ++  +LS++ GS     G T V+ ++ GP +A+  +                +
Sbjct: 34  TRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAALR 93

Query: 50  ASVEVIF--------RPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQD 101
             +   F        R ++     ++R     ++   E A+    +PR  + ++   L+D
Sbjct: 94  GRLLCDFRRAPFAGRRRRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLED 153

Query: 102 QGSLLSCCINAACLALINSGISMRYILAAVSC--IINDKNEVILDAN 146
            GS L+  + AA LAL ++G+ M  ++               +LD  
Sbjct: 154 GGSALAAALTAAALALADAGVEMYDLVVGCGLSLAPGPAPTWLLDPT 200

>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 = 88.9 bits (221), Expect = 1e-22
 Identities = 46/164 (28%), Positives = 83/164 (50%), Gaps = 24/164 (14%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK--TIIDKASV------- 52
             LR++++++ + +++DGS    QG T  +A +YGP E +  +   + D+A V       
Sbjct: 24  GELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSA 83

Query: 53  -----EVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSL 105
                E   RP         +  E    ++ T E+A+LT LHPR+ + + +Q LQ  G  
Sbjct: 84  TFSTGERKRRPHGD-----RKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGT 138

Query: 106 LSCCINAACLALINSGISMRYILAAVSC-IINDKNEVILDANQI 148
            + C+NAA LA++++GI MR  + A S   ++     + D + +
Sbjct: 139 YAACVNAATLAVLDAGIPMRDFVCACSAGFVDG--TALADLSHV 180

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

 Score = 88.1 bits (219), Expect = 2e-22
 Identities = 38/159 (23%), Positives = 69/159 (43%), Gaps = 15/159 (9%)

Query: 2   DSLRELKSQLNILSRS-DGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKASV--EVIFR 57
           + LR  +S +N    + DGS    QG   ++  + GP E +++ +    KA +   V   
Sbjct: 20  NELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNIN 79

Query: 58  PKSGLSFVQDRLKES--------VIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCC 109
             S     +   K           +    E  ++  ++PRT + + I  L+  G ++   
Sbjct: 80  KFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSL 139

Query: 110 INAACLALINSGISMRYILAAVSC-IINDKNEVILDANQ 147
           IN   LALI++GISM   ++ +S  + +     +LD N 
Sbjct: 140 INGITLALIDAGISMFDYISGISVGLYDT--TPLLDTNS 176

>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 = 78.1 bits (193), Expect = 1e-18
 Identities = 49/160 (30%), Positives = 76/160 (47%), Gaps = 22/160 (13%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKA---------- 50
             LR +K ++ +L  ++GS     G+  ++A++YGP E   +     D+A          
Sbjct: 24  YELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILRVRYNMAP 83

Query: 51  -SVEVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLS 107
            SVE   +P         R  E   VIK   E AL+  + PRT++ + I+ LQ       
Sbjct: 84  FSVEERKKPGPD-----RRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQADAGTRV 138

Query: 108 CCINAACLALINSGISMRYILAAVSC-IINDKNEVILDAN 146
             I AA LAL ++GI MR ++AA +   I    E++LD N
Sbjct: 139 AGITAASLALADAGIPMRDLVAACAAGKIEG--EIVLDLN 176

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

 Score = 78.0 bits (193), Expect = 1e-18
 Identities = 48/158 (30%), Positives = 74/158 (46%), Gaps = 22/158 (13%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKA---------- 50
           D LR LK +  IL R+DGS     G   ++ ++YGP EA+I+     D+A          
Sbjct: 24  DELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIRCRYNMAP 83

Query: 51  -SVEVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLS 107
            SVE   RP         R  E   +       AL+    PR+ + + I+ L+ +G    
Sbjct: 84  FSVEERKRPGPD-----RRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEGGTRC 138

Query: 108 CCINAACLALINSGISMRYILAAVSC-IINDKNEVILD 144
             I AA +AL ++GI MR ++ A +   + D  +V+LD
Sbjct: 139 AGITAASVALADAGIPMRDMVVACAAGKVGD--QVVLD 174

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

 Score = 74.9 bits (184), Expect = 3e-17
 Identities = 25/170 (14%), Positives = 48/170 (28%), Gaps = 26/170 (15%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKA--SVEVIFRPK 59
             LR +           GSV+   G T V+ +          +        + E    P 
Sbjct: 14  HELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTAEYAMLPS 73

Query: 60  SGLSFV--------QDRL---KESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSC 108
           +  S                    +I  +  + +        ++ +    LQ  G   + 
Sbjct: 74  ATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQADGGTRTA 133

Query: 109 CINAACLALINSGISM------------RYILAAVSCIINDKNEVILDAN 146
            I  A +AL ++   +               +AAVS  + D   + +D  
Sbjct: 134 AITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVVD-GRIRVDLP 182

>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 = 69.2 bits (170), Expect = 3e-15
 Identities = 47/145 (32%), Positives = 71/145 (48%), Gaps = 19/145 (13%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKA---------- 50
           D LR +K +L +L  +DGS IF  G T  +A++YGP E   +  ++ D+A          
Sbjct: 28  DELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTP 87

Query: 51  -SVEVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLS 107
            S +    P         R  E   VI+   ESA+L  L PRT++ +  + LQ       
Sbjct: 88  FSTDERKNPAPS-----RREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRL 142

Query: 108 CCINAACLALINSGISMRYILAAVS 132
             + AA LAL ++GI MR ++A V+
Sbjct: 143 VSLMAASLALADAGIPMRDLIAGVA 167

>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 = 69.2 bits (170), Expect = 4e-15
 Identities = 44/159 (27%), Positives = 77/159 (48%), Gaps = 24/159 (15%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKA---------- 50
           D LR +K + ++L R+DGS     G+  V+A+++GP E   +      KA          
Sbjct: 24  DELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKAIIRYRYNMAP 83

Query: 51  -SVEVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLS 107
            SVE   RP         R  E   V K   E+ ++  L PR+++ + ++ LQ      +
Sbjct: 84  FSVEERKRPGPD-----RRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRT 138

Query: 108 CCINAACLALINSGISMRYILA--AVSCIINDKNEVILD 144
            C+NAA +AL+++G+ M+ ++   AV        +++LD
Sbjct: 139 ACLNAASVALVDAGVPMKGMITSVAVGKA---DGQLVLD 174

>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 = 65.1 bits (159), Expect = 9e-14
 Identities = 30/170 (17%), Positives = 59/170 (34%), Gaps = 27/170 (15%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKA----------- 50
           D LR ++   +    ++GSV+   G T V+ ++              +            
Sbjct: 10  DQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTAEYGMLPR 69

Query: 51  SVEVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSC 108
           S     + ++       R  E   +I  +  +AL        ++ +    +Q  G   + 
Sbjct: 70  STGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADGGTRTA 129

Query: 109 CINAACLALIN-----------SGISMRYILAAVSC-IINDKNEVILDAN 146
            I  A +ALI+            G  ++ ++AAVS  I       +LD +
Sbjct: 130 SITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIYQG--VPVLDLD 177

>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 = 64.4 bits (157), Expect = 2e-13
 Identities = 31/168 (18%), Positives = 61/168 (36%), Gaps = 27/168 (16%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKA----------- 50
           D LR +  Q + L   +GS + S G+T V+ +               +            
Sbjct: 9   DQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITAEYSMLPR 68

Query: 51  SVEVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSC 108
           + +     +S    +  R  E   +I     +A+        ++ +    +Q  G   + 
Sbjct: 69  ATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGGTRTA 128

Query: 109 CINAACLALINSGIS-----------MRYILAAVSC-IINDKNEVILD 144
            I  A +A+ ++ I            ++  +AAVS  I+ND   ++LD
Sbjct: 129 AITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND--RILLD 174

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

 Score = 63.5 bits (155), Expect = 4e-13
 Identities = 35/169 (20%), Positives = 56/169 (33%), Gaps = 24/169 (14%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKA----------- 50
             LR +    N L   +GSV+   G T V+ S               K            
Sbjct: 19  TELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVPPFMRGEGKGWVTAEYAMIPR 78

Query: 51  SVEVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSC 108
           + E     +S    V  R  E   +I     + +        +V +    +Q  G   + 
Sbjct: 79  ATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWIDCDVIQADGGTRTA 138

Query: 109 CINAACLALIN-----------SGISMRYILAAVSCIINDKNEVILDAN 146
            I  A +A++            S I ++  LAA S  I ++  V+LD N
Sbjct: 139 SITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEEQGVVLDLN 187

>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 = 46.9 bits (112), Expect = 3e-07
 Identities = 30/169 (17%), Positives = 59/169 (34%), Gaps = 28/169 (16%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDK------------ 49
           D LR +   L+ +S  +GSV+ + G T V+ +    VE ++   +               
Sbjct: 9   DELRPITFDLDFISHPEGSVLITAGNTKVICNAS--VEDRVPPFLRGGGKGWITAEYSML 66

Query: 50  -ASVEVIFRPKSGLSFVQDRLKE--SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLL 106
             +       +S    +  R  E   +I     + +        ++ +    +Q  G   
Sbjct: 67  PQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTR 126

Query: 107 SCCINAACLAL-----------INSGISMRYILAAVSCIINDKNEVILD 144
           +  I  A LA+                 +   LAA+S  I+ +  ++LD
Sbjct: 127 TASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLD 175

>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 = 43.0 bits (101), Expect = 8e-06
 Identities = 28/182 (15%), Positives = 49/182 (26%), Gaps = 37/182 (20%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEA-----------KIQKTIIDKA 50
              R     +  +S +DGS +   G T V+  +     A                +    
Sbjct: 32  GEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLC 91

Query: 51  SVEVIFRPKSG----LSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLL 106
           S      P        S     + E+      E   ++       +   +  L   G++L
Sbjct: 92  SSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNIL 151

Query: 107 SCCINAACLALINSGI----------------------SMRYILAAVSCIINDKNEVILD 144
             C  A   AL N  +                      ++R    A S  + D   +I+D
Sbjct: 152 DACTFALLAALKNVQLPEVTINEETALAEVNLKKKSYLNIRTHPVATSFAVFDDTLLIVD 211

Query: 145 AN 146
             
Sbjct: 212 PT 213

>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 = 42.7 bits (101), Expect = 1e-05
 Identities = 34/173 (19%), Positives = 65/173 (37%), Gaps = 29/173 (16%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVA---------SMYGPVEAKIQKT--IIDKA 50
           D  R+++   N++ +++GS +   G T VV              P    I     ++  A
Sbjct: 30  DEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYPDTPDRGVIIVNAELVPLA 89

Query: 51  SVEVIFRPKSGLSFVQDRLKESVIKSTC----ESALLTMLHPRTSVILTIQELQDQGSLL 106
           S      P    S    R+ +  I+ +        ++        V + I  L D G+LL
Sbjct: 90  SPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLL 149

Query: 107 SCCINAACLALINSGI-------------SMRYILAAVSCIINDKNEVILDAN 146
                AA  AL+N+ +              +R +  +V+ +I   N+ ++D +
Sbjct: 150 DASALAAIAALMNTKVPAERFDLGEDYLLPVRDLPVSVTSLIVG-NKYLVDPS 201

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

 Score = 40.4 bits (95), Expect = 7e-05
 Identities = 26/180 (14%), Positives = 55/180 (30%), Gaps = 36/180 (20%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVAS---------MYGPVEAKIQKTI--IDKA 50
              R++  +  ++S+++GS     G T ++              P    I      +  A
Sbjct: 32  HEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKPQIGEPFPDTPEMGVILTNSELLPMA 91

Query: 51  SVEVIFRPKSGLSFVQDRLKESVIKSTC----ESALLTMLHPRTSVILTIQELQDQGSLL 106
           S      P    S    R+ +  I+ +     E   +        + L +  +   G+L 
Sbjct: 92  SPTFEPGPPDERSVELSRVVDRCIRESRMIDLEKLCIIEGSKVWMLFLDLHIIDYDGNLF 151

Query: 107 SCCINAACLALINSGI--------------------SMRYILAAVSCIINDKNEVILDAN 146
              + A   AL+++ I                     +       +      NE++LD +
Sbjct: 152 DAAVLATVAALLDTRIPAAEVEDGEVVINREKMQPLPVNRKALMCTFAKIG-NEIVLDPS 210

>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 = 40.5 bits (95), Expect = 7e-05
 Identities = 26/181 (14%), Positives = 61/181 (33%), Gaps = 37/181 (20%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVAS---------MYGPVEAKIQKTI--IDKA 50
           +  R ++ ++ ++ +++GS +   G T V+              P    +   +  +  A
Sbjct: 34  EDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLGEPFPDTPNMGVMTTNVELVPLA 93

Query: 51  SVEVIFRPKSGLSFVQDRLKESVIKSTC----ESALLTMLHPRTSVILTIQELQDQGSLL 106
           S      P    +    R+ +  I+ +     E  ++        V + +  L   G+L+
Sbjct: 94  SPTFEPGPPDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVFIDVHVLDHDGNLM 153

Query: 107 SCCINAACLALINSGI---------------------SMRYILAAVSCIINDKNEVILDA 145
                AA  AL+N+ +                      +  I   V+      N +++D 
Sbjct: 154 DAIGIAAIAALLNARVPKVRYNEETGEVETLDETEPLPVEKIPVPVTFAKIG-NILVVDP 212

Query: 146 N 146
           +
Sbjct: 213 S 213

>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 = 38.5 bits (90), Expect = 4e-04
 Identities = 29/183 (15%), Positives = 62/183 (33%), Gaps = 41/183 (22%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVAS---------MYGPVEAKIQKT--IIDKA 50
              R L   L+   ++DGS +   G T+V+A             P +  +     ++  A
Sbjct: 37  TDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNLIVNVELLPLA 96

Query: 51  SVEVIFRPKSGLSFVQDRLKESVIKSTC----ESALLTMLHPRT--SVILTIQELQDQGS 104
                  P    +    R+ +  ++ +         L +   ++  +V L +  L   G+
Sbjct: 97  YETFEPGPPDENAIELARVVDRSLRDSKALDLTK--LVIEPGKSVWTVWLDVYVLDYGGN 154

Query: 105 LLSCCINAACLALINSGI---------------------SMRYILAAVSCIINDKNEVIL 143
           +L  C  A+  AL N+ +                      + Y +  +S    D   +++
Sbjct: 155 VLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVVTISVAKVD-KYLVV 213

Query: 144 DAN 146
           D +
Sbjct: 214 DPD 216

>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 = 37.7 bits (87), Expect = 6e-04
 Identities = 18/136 (13%), Positives = 44/136 (32%), Gaps = 15/136 (11%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKT-----------IIDKA 50
           +  R ++ + +++S + GS     G T ++  +   +     +                A
Sbjct: 44  EDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDCSASA 103

Query: 51  SVEVIFRPKSGLSFVQDRLKESVIKSTC----ESALLTMLHPRTSVILTIQELQDQGSLL 106
           + E   R    L          +  +      ++  ++       + + +  L+  G+L 
Sbjct: 104 TPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLF 163

Query: 107 SCCINAACLALINSGI 122
                A   AL N+ I
Sbjct: 164 DAISIAVKAALFNTRI 179

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	151
3hkm_A	246	OS03G0854200 protein; RNAse PH domain, phosphoryla	100.0
2nn6_D	237	Exosome complex exonuclease RRP46; RNA, exosome, P	100.0
3m7n_D	258	Probable exosome complex exonuclease 1; exosome, R	100.0
2wnr_B	240	Probable exosome complex exonuclease 1; phosphate	100.0
2nn6_B	249	Exosome complex exonuclease RRP41; RNA, exosome, P	100.0
2po1_A	249	Probable exosome complex exonuclease 1; RNAse PH,	100.0
3krn_A	222	Protein C14A4.5, confirmed by transcript evidence;	100.0
2wp8_B	246	Exosome complex component SKI6; nucleus, hydrolase	100.0
2je6_B	250	RRP41, exosome complex exonuclease 1; nuclease, hy	100.0
3dd6_A	255	Ribonuclease PH; exoribonuclease, tRNA maturation,	100.0
1udn_A	255	Ribonuclease PH, RNAse PH; transferase, riken stru	100.0
1r6l_A	239	Ribonuclease PH; beta-alpha-beta-alpha fold, hexam	100.0
2nn6_F	272	MTR3, exosome component 6; RNA, exosome, PM/SCL, p	100.0
3b4t_A	262	Ribonuclease PH; RNAse, tRNA nucleotidyltransferas	100.0
1oys_A	245	Ribonuclease PH; transferase, tRNA processing; 2.4	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
2po1_B	277	Probable exosome complex exonuclease 2; RNAse PH,	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
3gme_A	549	Polyribonucleotide nucleotidyltransferase; protein	100.0
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	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
2nn6_A	358	Polymyositis/scleroderma autoantigen 1; RNA, exoso	100.0
2nn6_E	305	Exosome complex exonuclease RRP42; RNA, exosome, P	100.0
2wp8_A	305	Exosome complex component RRP45; nucleus, hydrolas	99.98
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	99.97
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.94
3gme_A	549	Polyribonucleotide nucleotidyltransferase; protein	99.93
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.93
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.93

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

Probab=100.00  E-value=2.7e-43  Score=271.77  Aligned_cols=151  Identities=35%  Similarity=0.584  Sum_probs=143.9

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcCCCCCCcchhhHHHHHHHHHHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQDRLKESVIKSTCES   80 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p~~g~~~~~~~~~~~~l~~~l~~   80 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|+||.+.+++.+.++++.++++|.|..|+++.++++++++|+++|++
T Consensus        11 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~g~~~~~~~~~~~~~~~~~~~~~P~~g~~~~~~~e~~~li~r~l~~   90 (246)
T 3hkm_A           11 PNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKASIEVVWKPMTGQIGKQEKEYEMTLKRTLQS   90 (246)
T ss_dssp             TTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEECCCEECCCTTSCSSSCEEEEEEECSSSCCCTTHHHHHHHHHHHHHH
T ss_pred             CCCcCCeEEEECCCCCCCeEEEEEECCeEEEEEEecCcCCCcccCCCccEEEEEEeCCCCCCCChhHHHHHHHHHHHHHH
Confidence            58999999999999999999999999999999999998766667788999999999999898888899999999999999


Q ss_pred             hhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057         81 ALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus        81 ~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                      +++++.||+|.|+|+++||++||++++|++||+++||+|+||||+++++|+++|++.++++++||+..||+
T Consensus        91 l~~~~~~~~~~I~v~~~VL~~dG~~~~aai~aa~~AL~dagiP~~~~v~avs~g~~~~g~~llDpt~~Ee~  161 (246)
T 3hkm_A           91 ICLLTVHPNTTTSVILQVVGNDGSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLEDGEVILDTNKAEEQ  161 (246)
T ss_dssp             HBCTTSSCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCBSSCEEEEEEEECTTSCEEESCCHHHHT
T ss_pred             hcCccCCCcEEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCCCCceEEEEEEEEECCEEEECCCHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999668999999999984

>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=5.2e-43  Score=268.85  Aligned_cols=149  Identities=46%  Similarity=0.848  Sum_probs=138.0

Q ss_pred             CccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcCCCCCCcchhhHHHHHHHHHHHHhh
Q psy15057          3 SLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQDRLKESVIKSTCESAL   82 (151)
Q Consensus         3 e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p~~g~~~~~~~~~~~~l~~~l~~~i   82 (151)
                      |+|++++++|++++++|||+|++|+|+|+|+|+||.+.++..+.++++.++++|+|+.|.++.++++++++|+++|++++
T Consensus        29 e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~g~~~~~~~~~~~~~g~l~~~~~p~~g~~~~~e~~~~~li~r~l~~~i  108 (237)
T 2nn6_D           29 SLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVV  108 (237)
T ss_dssp             CCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECC------CCEEEEEEEECSSSCCCHHHHHHHHHHHHHHHHHC
T ss_pred             cccceEEEeCCCCCCCEEEEEEECCcEEEEEEeCCCcccccccCCCcEEEEEEecCCCCCCCccHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999986666677899999999999999888889999999999999999


Q ss_pred             cccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057         83 LTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus        83 ~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                      +++.||+|.|+|+++||++|||+++|++||+++||+|+||||+++++|+++|++.++.+++||+..||.
T Consensus       109 ~~~~~p~~~I~I~~~VL~~dG~~~~aai~aa~~AL~da~iP~~~~v~avs~g~~~~~~~llDp~~~Ee~  177 (237)
T 2nn6_D          109 LGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACALDSDGTLVLDPTSKQEK  177 (237)
T ss_dssp             GGGCSSSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCEEEEEEEECTTCCEEESCCHHHHH
T ss_pred             chhcCCceEEEEEEEEEECCCcHHHHHHHHHHHHHHHcCCCcccCeeeEEEEEecCCcEEeCCCHHHHh
Confidence            999999999999999999999999999999999999999999999999999999668999999999983

>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=2.5e-40  Score=256.78  Aligned_cols=149  Identities=26%  Similarity=0.423  Sum_probs=134.1

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccc-cCCCCeeEEEEEEc--CCC------CCCcchhhHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKASVEVIFR--PKS------GLSFVQDRLKE   71 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~-~~~~~~~~v~v~~~--p~~------g~~~~~~~~~~   71 (151)
                      +||+|++++++|++++++|||+|++|+|+|+|+|+||.++++. .+.++++.++++|.  |++      +.++.++.+++
T Consensus        23 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~g~l~~~~~~~P~s~~~r~~~~~~~re~ei~  102 (258)
T 3m7n_D           23 FDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKAIIRYRYNMAPFSVEERKRPGPDRRSIEIS  102 (258)
T ss_dssp             TTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEEECSSSTTCCSSSCEEEEEEEECGGGSSSCCCSSCCHHHHHHH
T ss_pred             cCCccCeEEEECCCCCCCceEEEEECCeEEEEEEEcccCCCCccccCCCceEEEEEEEeCCcccccccCCCCCHHHHHHH
Confidence            5899999999999999999999999999999999999987654 35688888776654  532      23455677889


Q ss_pred             HHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCcccc
Q psy15057         72 SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQS  150 (151)
Q Consensus        72 ~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee  150 (151)
                      ++|+++|+++|+++.||+|.|+|+++||++||++++|++||+++||+||||||+++++|+++|++ ++.+++||+..||
T Consensus       103 ~li~r~l~~~i~~~~~p~~~I~V~~~VL~~DG~~~~Aai~aa~lAL~dagiP~~~~v~avsvg~i-~~~~llDpt~~Ee  180 (258)
T 3m7n_D          103 KVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKA-DGQLVLDPMKEED  180 (258)
T ss_dssp             HHHHHHHHTTBCGGGSTTEEEEEEEEEEECCTTHHHHHHHHHHHHHHHTTCCBSSEEEEEEEEEE-TTEEEESCCHHHH
T ss_pred             HHHHHHHHhhcCHHhCCceEEEEEEEEEEcCCCHHHHHHHHHHHHHHhcCCCCCCceEEEEEEEE-CCEEEECCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999 5899999999997

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

Probab=100.00  E-value=4e-40  Score=253.17  Aligned_cols=150  Identities=28%  Similarity=0.394  Sum_probs=134.4

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccc-cCCCCeeEEEEEEc--CCC------CCCcchhhHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKASVEVIFR--PKS------GLSFVQDRLKE   71 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~-~~~~~~~~v~v~~~--p~~------g~~~~~~~~~~   71 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|+||.+..++ .+.++++.++++|.  |++      |.++.++++++
T Consensus        23 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~g~l~~~~~~~p~a~~~~~~~~~~~~~~~l~  102 (240)
T 2wnr_B           23 FDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIRCRYNMAPFSVEERKRPGPDRRSVEIS  102 (240)
T ss_dssp             TTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECCSSSSCCSSSCEEEEEEEECTTSSSSCCCSSCCHHHHHHH
T ss_pred             cCCccCeEEEeCCCCCCCEEEEEEECCeEEEEEEEcCCCCCcccccCCCcEEEEEEEEeCCCCcCCccCCCCChhHHHHH
Confidence            4799999999999999999999999999999999999876553 35678887766655  653      23456677889


Q ss_pred             HHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057         72 SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus        72 ~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                      ++|+++|+++++++.||+|.|+|+++||++|||+++|++||+++||+|+|+||+++++++|+|++ ++.+++||+..||.
T Consensus       103 ~ll~r~l~~~i~l~~~p~~~I~i~~~VL~~dG~~~~a~i~aa~~AL~da~iP~~~~v~avs~g~~-~~~~l~Dp~~~Ee~  181 (240)
T 2wnr_B          103 KITAEALRPALILEKFPRSVIDVFIEVLEAEGGTRCAGITAASVALADAGIPMRDMVVACAAGKV-GDQVVLDLSEEEDK  181 (240)
T ss_dssp             HHHHHHHGGGBCGGGSTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTTCCBSSCCEEEEEEES-SSSEEESCCSHHHH
T ss_pred             HHHHHHHHHhcCHHHCCCcEEEEEEEEEeCCCCHHHHHHHHHHHHHHHcCCccccceeeEEEEEE-CCEEEeCCCHHHhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999 47899999999973

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

Probab=100.00  E-value=5.6e-40  Score=253.60  Aligned_cols=150  Identities=29%  Similarity=0.475  Sum_probs=132.6

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccc--cCCCCeeEEEEEE--cCCC-------CCCcchhhH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ--KTIIDKASVEVIF--RPKS-------GLSFVQDRL   69 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~--~~~~~~~~v~v~~--~p~~-------g~~~~~~~~   69 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|+||.+++..  .+.++++.+.++|  .|++       |.++.++.+
T Consensus        23 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~g~~~~~~~~~~~~~~~g~l~~~~~~~p~a~~~~~~~~~~~~~~~~  102 (249)
T 2nn6_B           23 AGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATFSTGERKRRPHGDRKSCE  102 (249)
T ss_dssp             TTSCCCEEEEESCSSSSSEEEEEEESSCEEEEEEEEEEECCSSSCCCCCSSCCEEEEEEECTTTSSSCCCTTTSTHHHHH
T ss_pred             cCCcCCeEEEeCCCCCCCeEEEEEECCeEEEEEEEccCCccccccccCCCcEEEEEEEEcCCCcccccccCCCCCHhHHH
Confidence            5899999999999999999999999999999999999875432  2467777666555  4542       224456678


Q ss_pred             HHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCccc
Q psy15057         70 KESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQ  149 (151)
Q Consensus        70 ~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~E  149 (151)
                      ++++|+++|+++|+++.||+|.|+|+++||++|||+++|++||+++||+|+||||+++++|+|+|++ ++.+++||+..|
T Consensus       103 ~~~ll~r~l~~~i~~~~~p~~~I~i~~~VL~~dG~~~~A~i~aa~~AL~da~iPl~~~v~avs~g~~-~~~~l~Dp~~~E  181 (249)
T 2nn6_B          103 MGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFV-DGTALADLSHVE  181 (249)
T ss_dssp             HHHHHHHHHHHTTCGGGCTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTCCCCSSCCEEEEEEEE-TTEEEESCCHHH
T ss_pred             HHHHHHHHHHHhcCHHHCCCcEEEEEEEEEeCCCCHHHHHHHHHHHHHHhcCCcccCCeeeEEEEEE-CCeEEECCChHH
Confidence            8999999999999999999999999999999999999999999999999999999999999999999 589999999999


Q ss_pred             cC
Q psy15057        150 SN  151 (151)
Q Consensus       150 e~  151 (151)
                      |.
T Consensus       182 e~  183 (249)
T 2nn6_B          182 EA  183 (249)
T ss_dssp             HT
T ss_pred             hc
Confidence            84

>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=1.6e-39  Score=251.01  Aligned_cols=149  Identities=30%  Similarity=0.394  Sum_probs=133.5

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCccccc-ccCCCCeeEEEEEEc--CCCC------CCcchhhHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKI-QKTIIDKASVEVIFR--PKSG------LSFVQDRLKE   71 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~-~~~~~~~~~v~v~~~--p~~g------~~~~~~~~~~   71 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|+||.+..+ ..+.++++.+.++|.  |++.      .++.++.+++
T Consensus        23 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~g~l~v~~~~~p~a~~~~~~~~~~~~~~~~s  102 (249)
T 2po1_A           23 KYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILRVRYNMAPFSVEERKKPGPDRRSIEIS  102 (249)
T ss_dssp             TTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEEECSSGGGCCSSSCEEEEEEEECGGGSSSCCCSSCCHHHHHHH
T ss_pred             cccccCEEEEeCCcCCCCEEEEEEECCcEEEEEEEcCcccCcccccCCCceEEEEEEEeCCcccccccCCCCCHHHHHHH
Confidence            589999999999999999999999999999999999887655 355678887766664  4322      2445677889


Q ss_pred             HHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCcccc
Q psy15057         72 SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQS  150 (151)
Q Consensus        72 ~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee  150 (151)
                      ++|+++|+++|+++.||+|.|+|+++||++||++++|++||+++||+|+||||+++++++++|++ ++.+++||+..||
T Consensus       103 ~li~r~l~~~i~l~~~p~~~i~I~~~VL~~dG~~~~aai~aa~~AL~da~iP~~~~v~avs~g~~-~~~~l~Dp~~~Ee  180 (249)
T 2po1_A          103 KVIKGALEPALILEMFPRTAIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKI-EGEIVLDLNKEED  180 (249)
T ss_dssp             HHHHHHHGGGBCGGGSTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTTCCBSSCCEEEEEEEE-TTEEEESCCHHHH
T ss_pred             HHHHHHHHhhccHHHCCCCEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCccCceEEEEEEEE-CCEEEecCcHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999 5899999999997

>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=1.8e-43  Score=269.14  Aligned_cols=147  Identities=31%  Similarity=0.525  Sum_probs=115.9

Q ss_pred             CCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcCCCCCCcchhhHHHHHHHHHHHHh
Q psy15057          2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQDRLKESVIKSTCESA   81 (151)
Q Consensus         2 ~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p~~g~~~~~~~~~~~~l~~~l~~~   81 (151)
                      ||+|++++++|++++++|||+|++|+|+|+|+|+||.+++++.+.++++.++|+|+|++|+++.+  +++++|+|+|+++
T Consensus         3 ~e~R~i~ie~g~l~~A~GSa~v~~G~T~Vl~~V~~~~e~~~~~~~~~~~~l~v~~~p~~G~~~~~--e~~~li~r~l~~~   80 (222)
T 3krn_A            3 GRLREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASKASDEAMTLDISYRANCGDNKFN--VLNNIIHSTLSNA   80 (222)
T ss_dssp             CCCCCBCCBSCCC----CCCBCCBTTCEEECCCCSSCC-------------CCCSSCCCC--CCS--SCTTHHHHC--CC
T ss_pred             CcccceEEEECCCCCCCeEEEEEECCcEEEEEEECCCCCcccccCCceEEEEEEEcCCCCCCCHH--HHHHHHHHHHHHh
Confidence            89999999999999999999999999999999999998776667789999999999999876433  8899999999999


Q ss_pred             hcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057         82 LLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus        82 i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                      ++++.||+|.|+|+++||++||++++|++||+++||+|+||||+++++|+++|++ +|++++|||..||+
T Consensus        81 i~~~~~p~~~I~I~~~VL~~DG~~~~aai~aa~~AL~dagiP~~~~v~avsvg~~-~g~~llDpt~~Ee~  149 (222)
T 3krn_A           81 INLELFPHTTISVTVHGIQDDGSMGAVAINGACFALLDNGMPFETVFCGVLIVRV-KDELIIDPTAKQEA  149 (222)
T ss_dssp             SCC-----CCCCCCCEEEECCSCHHHHHHHGGGTTTTTTTCCTTSCCCCCCCEEC-SSSEESSCCTTTTT
T ss_pred             ccHHhCCCcEEEEEEEEEECCCChHHHHHHHHHHHHHHCCCCccCcEEEEEEEEE-CCEEEeCCCHHHHh
Confidence            9999999999999999999999999999999999999999999999999999997 58999999999984

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

Probab=100.00  E-value=2.4e-39  Score=249.63  Aligned_cols=149  Identities=25%  Similarity=0.368  Sum_probs=128.8

Q ss_pred             CCCccceEEEecCCCCC-CeeEEEEeCCeEEEEEEEcCccccc-ccCCCCeeEEEEEEc--CCC--------CCCcchhh
Q psy15057          1 MDSLRELKSQLNILSRS-DGSVIFSQGQTVVVASMYGPVEAKI-QKTIIDKASVEVIFR--PKS--------GLSFVQDR   68 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a-~GSa~v~~G~T~V~~~V~gp~~~~~-~~~~~~~~~v~v~~~--p~~--------g~~~~~~~   68 (151)
                      ++|+|++++++|+++++ +|||+|++|+|+|+|+|+||.++.+ ..+.++++.+.++|.  |++        |+++.++.
T Consensus        19 ~~e~R~i~i~~g~l~~aa~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~~g~l~v~~~~~p~a~~~~~~r~g~~~~~~~   98 (246)
T 2wp8_B           19 WNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNINKFSKFERSKSSHKNERRVL   98 (246)
T ss_dssp             TTCCCCEEEEECSCTTTCSEEEEEEETTEEEEEEEEEEEC------CCSSSEEEEEEEEEC--------------CHHHH
T ss_pred             cCCccCeEEEeCCCCCCCCceEEEEECCeEEEEEEEecCCcccccccCCCcEEEEEEEEeCCcccccccccCCCCChhHH
Confidence            47999999999999999 9999999999999999999997544 345688887766664  432        22345677


Q ss_pred             HHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCcc
Q psy15057         69 LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQI  148 (151)
Q Consensus        69 ~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~  148 (151)
                      +++++|+++|+++++++.||+|.|+|+++||++||++++|++||+++||+|+||||+++++++++|++ ++.+++||+..
T Consensus        99 ~~s~li~r~l~~~i~~~~~p~~~I~i~~~VL~~dG~~~~aai~aa~~AL~~a~iP~~~~v~avs~g~~-~~~~l~Dp~~~  177 (246)
T 2wp8_B           99 EIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLY-DTTPLLDTNSL  177 (246)
T ss_dssp             HHHHHHHHHHHHHBCTTTSCSEEEEEEEEEEECCSCHHHHHHHHHHHHHHHHTCCBSSCEEEEEEEEE-TTEEESSCCHH
T ss_pred             HHHHHHHHHHHHhhhHHHCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHHcCCcccCceeEEEEEEE-CCEEEECCCch
Confidence            88999999999999999999999999999999999999999999999999999999999999999999 58999999999


Q ss_pred             cc
Q psy15057        149 QS  150 (151)
Q Consensus       149 Ee  150 (151)
                      ||
T Consensus       178 Ee  179 (246)
T 2wp8_B          178 EE  179 (246)
T ss_dssp             HH
T ss_pred             hh
Confidence            86

>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=3.1e-39  Score=249.49  Aligned_cols=149  Identities=34%  Similarity=0.469  Sum_probs=133.4

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCccccc-ccCCCCeeEEEEEE--cCCC------CCCcchhhHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKI-QKTIIDKASVEVIF--RPKS------GLSFVQDRLKE   71 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~-~~~~~~~~~v~v~~--~p~~------g~~~~~~~~~~   71 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|+||.+..+ ..+.++++.+.++|  .|++      |.++.++++++
T Consensus        27 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~g~~e~~~~~~~~~~~g~l~v~~~~~p~a~~~~~~g~~~~~e~~~s  106 (250)
T 2je6_B           27 PDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDERKNPAPSRREIELS  106 (250)
T ss_dssp             TTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECSSGGGSCSSSCEEEEEEEECTTSSSSCCCSSCCHHHHHHH
T ss_pred             ccCcCCeEEEeCCCCCCCeEEEEEECCcEEEEEEEcccccccccccCCCcEEEEEEEEeCCCccCCccCCCCChhHHHHH
Confidence            479999999999999999999999999999999999987554 34567777766655  4542      23456777889


Q ss_pred             HHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCCcccc
Q psy15057         72 SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDANQIQS  150 (151)
Q Consensus        72 ~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt~~Ee  150 (151)
                      ++|+++|+++++++.||+|.|+|+++||++||++++|++||+++||+|+||||+++++++++|++ ++.+++|||..||
T Consensus       107 ~li~r~l~~~i~~~~~p~~~i~I~~~VL~~DG~~~~aai~aa~~AL~~a~iP~~~~v~avsvg~~-~~~~l~Dpt~~Ee  184 (250)
T 2je6_B          107 KVIREALESAVLVELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKA-DGVIILDLNETEA  184 (250)
T ss_dssp             HHHHHHHHTTBCGGGSTTEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCBSSCCEEEEEEEE-TTEEEESCCHHHH
T ss_pred             HHHHHHHHhhcCHhhCCCcEEEEEEEEEeCCCCHHHHHHHHHHHHHHhcCCCccCceEEEEEEEE-CCEEEeCCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999 5899999999997

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

Probab=100.00  E-value=4.3e-38  Score=243.87  Aligned_cols=149  Identities=21%  Similarity=0.210  Sum_probs=131.3

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEE--cCCC-----------CCCcchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIF--RPKS-----------GLSFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~--~p~~-----------g~~~~~~   67 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|++|.+.++....++++.+.++|  .|++           |+++.++
T Consensus        18 ~~e~R~i~i~~g~~~~A~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~v~~~~~P~a~~~~~~Re~~~g~~~~~~   97 (255)
T 3dd6_A           18 KTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVPPFMRGEGKGWVTAEYAMIPRATEQRTIRESSKGKVTGRT   97 (255)
T ss_dssp             TTCCCCEEEEESCSSSSSEEEEEEETTEEEEEEEEEESCCCGGGTTSSCCEEEEEEEECTTSSSSCCCCCCC-CCCCHHH
T ss_pred             cCCCCCEEEEECCCCCCCeEEEEEECCeEEEEEEEecCCCCCCCCCCCceEEEEEEEECCCcccccccccccCCCCCHHH
Confidence            58999999999999999999999999999999999987533334557777766655  4532           4445566


Q ss_pred             hHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhc-----------CccccceeeEEEEEEe
Q psy15057         68 RLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINS-----------GISMRYILAAVSCIIN  136 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~a-----------gip~~~~~~avtv~~~  136 (151)
                      .+++++|+|+|+++++++.||+|.|+|+++||++||++++|++||+++||+|+           ||||+++++|+++|++
T Consensus        98 ~eisrli~r~lr~~i~~~~l~~~~I~V~~~VL~~DG~~~~aai~aa~~AL~~a~~p~~~~g~~~~iPl~~~v~avsvg~i  177 (255)
T 3dd6_A           98 MEIQRLIGRALRAVVDLEALGERTVWIDCDVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIV  177 (255)
T ss_dssp             HHHHHHHHHHHHHHBCHHHHCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTSSSSCCBSSCEEEEEEEEE
T ss_pred             HHHHHHHHHHHHHhcChhhcCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHHhhhhhhhcCcccCCCccCceeEEEEEEE
Confidence            77899999999999999999999999999999999999999999999999999           9999999999999999


Q ss_pred             cCCeEE-eCCCcccc
Q psy15057        137 DKNEVI-LDANQIQS  150 (151)
Q Consensus       137 ~~~~~l-vDpt~~Ee  150 (151)
                      + ++++ +|||..||
T Consensus       178 ~-g~~vllDpt~~Ee  191 (255)
T 3dd6_A          178 E-EQGVVLDLNYAED  191 (255)
T ss_dssp             T-TTEEEESCCHHHH
T ss_pred             C-CEEEEeCCCHHHH
Confidence            5 7777 99999997

>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=1.3e-37  Score=241.14  Aligned_cols=149  Identities=19%  Similarity=0.197  Sum_probs=131.3

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEE--cCCC-----------CCCcchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIF--RPKS-----------GLSFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~--~p~~-----------g~~~~~~   67 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|++|.+.+.....++++.+.++|  .|++           |+++.++
T Consensus         8 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~~~~~~~P~a~~~r~~Re~~~G~~~~~~   87 (255)
T 1udn_A            8 EDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITAEYSMLPRATQQRTIRESVQGRIGGRT   87 (255)
T ss_dssp             TTCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEESCCCGGGTTSSCCEEEEEEEECSCCTTSCCCCSSTTCSCCHHH
T ss_pred             CCCccCeEEEECCCCCCCEEEEEEECCEEEEEEEEcCCcCCCCCCCCCceEEEEEEEcCCCccccccccccCCCCCCHHH
Confidence            48999999999999999999999999999999999988643223346676665544  4532           3345667


Q ss_pred             hHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcC-----------ccccceeeEEEEEEe
Q psy15057         68 RLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG-----------ISMRYILAAVSCIIN  136 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~ag-----------ip~~~~~~avtv~~~  136 (151)
                      ++++++|+++|+++|+++.||+|.|+|+++||++||++++|++||+++||+|+|           |||+++++++++|++
T Consensus        88 ~eisrli~r~lr~~i~~~~l~~~~i~I~~~VL~~DG~~~~aai~aa~~AL~da~~~~~~~~~~~~ipl~~~v~avsvg~~  167 (255)
T 1udn_A           88 HEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIV  167 (255)
T ss_dssp             HHHHHHHHHHHHHHBCGGGGCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTSSSSCCBCCCEEEEEEEEE
T ss_pred             HHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHhhcchhcccCcccCCCccCceeEEEEEEE
Confidence            789999999999999999999999999999999999999999999999999999           999999999999999


Q ss_pred             cCCeEEeCCCcccc
Q psy15057        137 DKNEVILDANQIQS  150 (151)
Q Consensus       137 ~~~~~lvDpt~~Ee  150 (151)
                       ++++++||+..||
T Consensus       168 -~g~~llDpt~~Ee  180 (255)
T 1udn_A          168 -NDRILLDLNFEED  180 (255)
T ss_dssp             -TTEEEESCCHHHH
T ss_pred             -CCEEEECCCHHHH
Confidence             5899999999997

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

Probab=100.00  E-value=1.3e-37  Score=238.92  Aligned_cols=149  Identities=19%  Similarity=0.215  Sum_probs=129.3

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEE--EcCCC-----------CCCcchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVI--FRPKS-----------GLSFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~--~~p~~-----------g~~~~~~   67 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|++|.+.+.....++++.+.++  +.|.+           |+++.++
T Consensus         9 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~v~~~~~p~~~~~r~~Re~~~G~~~~~~   88 (239)
T 1r6l_A            9 ADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTAEYGMLPRSTGERNQREASRGKQGGRT   88 (239)
T ss_dssp             TTCCCCEEEESSCSSSSSEEEEEEETTEEEEEEEEEEESCSSCCC---CCEEEEEEEECTTSSSSCCCCHHHHTSCCHHH
T ss_pred             CCCcCCeEEEeCCcCCCCeEEEEEECCEEEEEEEEccCccCCccCCCCcEEEEEEEEeCCCccccccccccCCCCCcHHH
Confidence            4799999999999999999999999999999999998854322233566666555  55643           3345667


Q ss_pred             hHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcC-----------ccccceeeEEEEEEe
Q psy15057         68 RLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG-----------ISMRYILAAVSCIIN  136 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~ag-----------ip~~~~~~avtv~~~  136 (151)
                      ++++++|+++|+++++++.||+|.|+|+++||++||++++|++||+++||+|||           |||+++++++++|++
T Consensus        89 ~~isrli~r~l~~~i~~~~l~~~~i~I~~~VL~~DG~~~~aai~aa~~AL~da~~~~~~~~~~~~ip~~~~~~avs~g~~  168 (239)
T 1r6l_A           89 LEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIY  168 (239)
T ss_dssp             HHHHHHHHHHHHHTBCGGGTCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCBCCCEEEEEEEEE
T ss_pred             HHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhcchhcccCcccccCccCceeEEEEEEE
Confidence            788999999999999999999999999999999999999999999999999999           999999999999999


Q ss_pred             cCCeEEeCCCcccc
Q psy15057        137 DKNEVILDANQIQS  150 (151)
Q Consensus       137 ~~~~~lvDpt~~Ee  150 (151)
                       ++++++|||..||
T Consensus       169 -~~~~l~Dpt~~Ee  181 (239)
T 1r6l_A          169 -QGVPVLDLDYLED  181 (239)
T ss_dssp             -TTEEEESCCHHHH
T ss_pred             -CCEEEECCCHHHH
Confidence             5899999999997

>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=1e-38  Score=249.33  Aligned_cols=151  Identities=22%  Similarity=0.305  Sum_probs=129.9

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccC------------CCCe--eEEEEEEcCCCCC----
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKT------------IIDK--ASVEVIFRPKSGL----   62 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~------------~~~~--~~v~v~~~p~~g~----   62 (151)
                      ++|+|++++++|+++++||||+|++|+|+|+|+|+||.+.++..+            .+++  .++++++.|++..    
T Consensus        33 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~g~l~v~~~~~p~a~~~~~~  112 (272)
T 2nn6_F           33 PTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAALRGRLLCDFRRAPFAGRRRRA  112 (272)
T ss_dssp             SSCCCCCCCCCSCCSSSSEEECCCSSSCEEEEEEEEEECC-------------------CBCEEEEEEEECTTSSSSCCC
T ss_pred             ccccCCeEEEeCCCCCCCeEEEEEeCCeEEEEEEECCCcccccccccccccccccccCCCceEEEEEEEecCCCcCCccC
Confidence            489999999999999999999999999999999999997655433            3444  4566677776432    


Q ss_pred             --CcchhhHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEe--cC
Q psy15057         63 --SFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIIN--DK  138 (151)
Q Consensus        63 --~~~~~~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~--~~  138 (151)
                        ++.++++++++|+++|+++++++.||+|.|+|+++||++||++++|++||+++||+|+||||+++++|+++|++  .+
T Consensus       113 ~~~~~~e~~~s~li~r~l~~~i~~~~~p~~~I~I~~~VL~~DG~~~~aai~aa~~AL~da~iP~~~~v~avsvg~~~~~~  192 (272)
T 2nn6_F          113 PPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVEMYDLVVGCGLSLAPGPA  192 (272)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTTBCSTTSBTCEEEEEEEEEECCSSHHHHHHHHHHHHHHHHCCCBSSCCEEEECCCCSCSS
T ss_pred             CCCCHHHHHHHHHHHHHHHHhccHHHCCceEEEEEEEEEeCCCCHHHHHHHHHHHHHHHcCCcccCcEEEEEEEEeeccC
Confidence              34567788999999999999999999999999999999999999999999999999999999999999999993  26


Q ss_pred             CeEEeCCCccccC
Q psy15057        139 NEVILDANQIQSN  151 (151)
Q Consensus       139 ~~~lvDpt~~Ee~  151 (151)
                      +.+|+|||..||.
T Consensus       193 ~~~llDpt~~Ee~  205 (272)
T 2nn6_F          193 PTWLLDPTRLEEE  205 (272)
T ss_dssp             CCCCSSCCTTTGG
T ss_pred             CeEEeCCCHHHhc
Confidence            8999999999984

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

Probab=100.00  E-value=1.3e-37  Score=241.86  Aligned_cols=150  Identities=15%  Similarity=0.150  Sum_probs=130.7

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEE--cCCC-----------CCCcchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIF--RPKS-----------GLSFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~--~p~~-----------g~~~~~~   67 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|++|.+.++....++++.+.++|  .|++           |+++.++
T Consensus        13 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~v~~~~~p~a~~~~~~Re~~~G~~~~~~   92 (262)
T 3b4t_A           13 DHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRWRKATGLGWLTAEYAMLPSATHSRSDRESVRGRLSGRT   92 (262)
T ss_dssp             TTCCCCEEEEETSSSSSSEEEEEEETTEEEEEEEEEEESCC----CCSCCEEEEEEEECGGGSSSCCCCHHHHTSCCHHH
T ss_pred             CcCcCCeEEEeCCcCCCCeEEEEEECCCEEEEEEEecCcCCCccCCCCceEEEEEEEeCCCccccccccccCCCCCCHHH
Confidence            47999999999999999999999999999999999988643222335666666655  5532           3455667


Q ss_pred             hHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhc------------CccccceeeEEEEEE
Q psy15057         68 RLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINS------------GISMRYILAAVSCII  135 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~a------------gip~~~~~~avtv~~  135 (151)
                      .+++++|+++|+++|+++.||+|+|+|+++||++||++++|++||+++||+|+            +|||+++++++++|+
T Consensus        93 ~~isrli~r~lr~~i~~~~l~~~~I~i~~~VL~~DG~~~~aai~aa~~AL~~a~~~~~~~~~~~~~ip~~~~v~avsvg~  172 (262)
T 3b4t_A           93 QEISRLIGRSLRACIDLAALGENTIAIDCDVLQADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGV  172 (262)
T ss_dssp             HHHHHHHHHHHHTTBCHHHHCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTCCSSSCCBCSCEEEEEEEE
T ss_pred             HHHHHHHHHHHHHhcCHhHCCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhhccCCccccCCcccCceeEEEEEE
Confidence            78899999999999999999999999999999999999999999999999999            999999999999999


Q ss_pred             ecCCeEEeCCCccccC
Q psy15057        136 NDKNEVILDANQIQSN  151 (151)
Q Consensus       136 ~~~~~~lvDpt~~Ee~  151 (151)
                      + ++++++|||..||.
T Consensus       173 ~-~g~~l~Dpt~~Ee~  187 (262)
T 3b4t_A          173 V-DGRIRVDLPYEEDS  187 (262)
T ss_dssp             E-TTEEEESCCHHHHT
T ss_pred             E-CCEEEECCCHHHHh
Confidence            9 58999999999984

>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=9.6e-38  Score=240.54  Aligned_cols=150  Identities=20%  Similarity=0.200  Sum_probs=123.2

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEE--cCCC-----------CCCcchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIF--RPKS-----------GLSFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~--~p~~-----------g~~~~~~   67 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|++|...++....++++.+.++|  .|++           |.++.++
T Consensus         8 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~~~~~~~g~l~~~~~~~p~a~~~~~~Re~~~G~~~~~~   87 (245)
T 1oys_A            8 HDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPQATNQQTIQESSKGKISGRT   87 (245)
T ss_dssp             TTCCCCEEEECC-----CCCEEEEETTEEEEEEEEEESCCCGGGTTSCCCEEEEEEEC-------------------CHH
T ss_pred             CCCcCCeEEEeCCCCCCCEEEEEEECCeEEEEEEEeccccCCccCCCCceEEEEEEEeCCCcCcccccccccCCCCchHH
Confidence            58999999999999999999999999999999999988643333456777766655  4532           3355677


Q ss_pred             hHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcC-----------ccccceeeEEEEEEe
Q psy15057         68 RLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSG-----------ISMRYILAAVSCIIN  136 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~ag-----------ip~~~~~~avtv~~~  136 (151)
                      ++++++|+++|+++|+++.||++.|+|+++||++|||+++|++||+++||+|+|           +||+++++|+|+|++
T Consensus        88 ~eis~li~r~l~~~i~~~~l~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~~~~~~~~~~~~ipl~~~v~avs~g~~  167 (245)
T 1oys_A           88 MEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGID  167 (245)
T ss_dssp             HHHHHHHHHHHHHTBCHHHHCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTSSSSCCBCSCEEEEEEEEE
T ss_pred             HHHHHHHHHHHHHhcCHhHCCCEEEEEEEEEEeCCCCHHHHHHHHHHHHHHhccchhcccCcccccCCCCceeEEEEEEE
Confidence            789999999999999999999999999999999999999999999999999999           999999999999999


Q ss_pred             cCCeEE-eCCCccccC
Q psy15057        137 DKNEVI-LDANQIQSN  151 (151)
Q Consensus       137 ~~~~~l-vDpt~~Ee~  151 (151)
                      + +.++ +||+..||.
T Consensus       168 ~-g~~vl~Dp~~~Ee~  182 (245)
T 1oys_A          168 K-EQGILLDLNYEEDS  182 (245)
T ss_dssp             T-TTEEEESCCHHHHH
T ss_pred             C-CEEEEecCCHHHHh
Confidence            5 6666 999999973

>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=3.4e-35  Score=227.99  Aligned_cols=149  Identities=21%  Similarity=0.267  Sum_probs=127.6

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEE--EcCC------CCCCcchhhHHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVI--FRPK------SGLSFVQDRLKES   72 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~--~~p~------~g~~~~~~~~~~~   72 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|+++... +..+.++++.+.++  +.|+      .|+++.++.++++
T Consensus        29 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~-p~~~~~~~g~l~v~~~~~p~a~~~~~~g~~~~~~~~~sr  107 (259)
T 3m7n_G           29 FDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGE-PYPDTPDRGVIIVNAELVPLASPTFEPGPPDENSIELAR  107 (259)
T ss_dssp             TTCCCCEEEEETSSTTSSEEEEEEETTEEEEEEEEEEEEC-CCSSCTTSCEEEEEEECCTTSCTTCCSSSSCHHHHHHHH
T ss_pred             CccccCeEEEeCCcCCCCceEEEEECCcEEEEEEEecccC-CCCCCCCceEEEEEEEeCCcccccccCCCCChHHHHHHH
Confidence            5899999999999999999999999999999999965421 23344666665554  5564      3445567778899


Q ss_pred             HHHHHHHH--hhcccCC---CC---cEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCc-------------cccceeeEE
Q psy15057         73 VIKSTCES--ALLTMLH---PR---TSVILTIQELQDQGSLLSCCINAACLALINSGI-------------SMRYILAAV  131 (151)
Q Consensus        73 ~l~~~l~~--~i~~~~~---p~---~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agi-------------p~~~~~~av  131 (151)
                      +|+++|++  +++++.|   |+   |.|+|+++||++||++++|++||+++||.|+||             ||+++++++
T Consensus       108 li~r~lr~s~~i~l~~L~i~pg~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~iP~~~~~~~~~~~lp~~~~~~av  187 (259)
T 3m7n_G          108 VVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLPVRDLPVSV  187 (259)
T ss_dssp             HHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHTCEECTGGGTSSSCEECCBCCCCEEE
T ss_pred             HHHHHHhhcCCccHHHhcccCCcEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHhCCCCeEEecCCceecccccCceeEE
Confidence            99999999  8888775   73   999999999999999999999999999999999             799999999


Q ss_pred             EEEEecCCeEEeCCCccccC
Q psy15057        132 SCIINDKNEVILDANQIQSN  151 (151)
Q Consensus       132 tv~~~~~~~~lvDpt~~Ee~  151 (151)
                      |+|++ ++.+++|||..||.
T Consensus       188 tvg~~-~~~~l~Dpt~~Ee~  206 (259)
T 3m7n_G          188 TSLIV-GNKYLVDPSREEMS  206 (259)
T ss_dssp             EEEEE-TTEEEESCCTTGGG
T ss_pred             EEEEE-CCEEEECCCHHHHh
Confidence            99999 58999999999984

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

Probab=100.00  E-value=7.5e-35  Score=227.18  Aligned_cols=148  Identities=14%  Similarity=0.169  Sum_probs=128.5

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEE-cCcccccccCCCCeeEEEEEE--cCC------CCCCcchhhHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMY-GPVEAKIQKTIIDKASVEVIF--RPK------SGLSFVQDRLKE   71 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~-gp~~~~~~~~~~~~~~v~v~~--~p~------~g~~~~~~~~~~   71 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|+ +|.+++  .+.++++.+.++|  .|+      .|.++.++.+++
T Consensus        31 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~--~~~~~~g~l~v~~~~~p~a~~~~~~g~~~~~~~~~s  108 (271)
T 2wnr_A           31 LHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKPQIGEPF--PDTPEMGVILTNSELLPMASPTFEPGPPDERSVELS  108 (271)
T ss_dssp             TTCCCCEEEEESCSTTSSEEEEEEETTEEEEEEEEEEEECCC--TTCTTCCEEEEEEEECGGGCTTCCCSSCCHHHHHHH
T ss_pred             cccccCeEEEeCccCCCCeEEEEEECCeEEEEEEEeeeecCC--CCCCCceEEEEEEEeCCcccccccCCCCchHHHHHH
Confidence            47999999999999999999999999999999999 676543  3456777665555  453      244556777889


Q ss_pred             HHHHHHHHH--hhcccCC---C---CcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcC--------------------cc
Q psy15057         72 SVIKSTCES--ALLTMLH---P---RTSVILTIQELQDQGSLLSCCINAACLALINSG--------------------IS  123 (151)
Q Consensus        72 ~~l~~~l~~--~i~~~~~---p---~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~ag--------------------ip  123 (151)
                      ++|+++|++  +++++.|   |   .|.|+|+++||++|||+++|++||+++||+|+|                    +|
T Consensus       109 ~li~r~lr~s~~i~l~~l~i~pg~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~~p~~~~~~~~~~~~~~~~~~ip  188 (271)
T 2wnr_A          109 RVVDRCIRESRMIDLEKLCIIEGSKVWMLFLDLHIIDYDGNLFDAAVLATVAALLDTRIPAAEVEDGEVVINREKMQPLP  188 (271)
T ss_dssp             HHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHHCEEEEEEEETTEEEEEEEEEEECC
T ss_pred             HHHHHHHhccCCccHHHccccCCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcCCCeEEecCCceeeccCcccccC
Confidence            999999999  6887776   4   589999999999999999999999999999999                    99


Q ss_pred             ccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057        124 MRYILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus       124 ~~~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                      |+++++++|+|++ ++.+++|||..||.
T Consensus       189 ~~~~~~avt~g~~-~~~~l~Dpt~~Ee~  215 (271)
T 2wnr_A          189 VNRKALMCTFAKI-GNEIVLDPSLEEED  215 (271)
T ss_dssp             BCCCEEEEEEEEE-TTEEEESCCHHHHT
T ss_pred             ccCCeEEEEEEEE-CCEEEeCCCHHHHh
Confidence            9999999999999 58999999999984

>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=5.5e-35  Score=228.72  Aligned_cols=148  Identities=18%  Similarity=0.216  Sum_probs=128.0

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEE-cCcccccccCCCCeeEEEEEE--cCC------CCCCcchhhHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMY-GPVEAKIQKTIIDKASVEVIF--RPK------SGLSFVQDRLKE   71 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~-gp~~~~~~~~~~~~~~v~v~~--~p~------~g~~~~~~~~~~   71 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|+ +|.++.  .+.++++.+.++|  .|+      .|.++.++.+++
T Consensus        33 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~--~~~~~~g~l~~~~~~~p~a~~~~~~g~~~~~~~~l~  110 (277)
T 2po1_B           33 FEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLGEPF--PDTPNMGVMTTNVELVPLASPTFEPGPPDERAIELA  110 (277)
T ss_dssp             TTCCCCEEEEECCSTTSSEEEEEEETTEEEEEEEEEEEECCC--TTCTTSCEEEEEEEECGGGCTTCCSSSCCHHHHHHH
T ss_pred             CCCcCCeEEEeCCcCCCCeEEEEEECCeEEEEEEEecccCCC--CCCCCceEEEEEEEeCCCccccccCCCCChHHHHHH
Confidence            47999999999999999999999999999999999 777653  3557777665555  554      244556777889


Q ss_pred             HHHHHHHHH--hhcccCC---C---CcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcC---------------------c
Q psy15057         72 SVIKSTCES--ALLTMLH---P---RTSVILTIQELQDQGSLLSCCINAACLALINSG---------------------I  122 (151)
Q Consensus        72 ~~l~~~l~~--~i~~~~~---p---~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~ag---------------------i  122 (151)
                      ++|+++|++  +|+++.|   |   .|.|+|+++||++|||+++|++||+++||+|+|                     +
T Consensus       111 ~li~r~l~~s~~idl~~L~i~pg~~~w~i~id~~VL~~dG~~~~a~i~aa~~AL~da~~p~~~~~~~~~~~~~~~~~~~i  190 (277)
T 2po1_B          111 RVIDRGIRESKALNLEKMVIVPGKIVRVVFIDVHVLDHDGNLMDAIGIAAIAALLNARVPKVRYNEETGEVETLDETEPL  190 (277)
T ss_dssp             HHHHHHHHTTTSBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHHCEEEEEEECTTTCCEEEEEEEEEC
T ss_pred             HHHHHHHhhcccccHHHccccCCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcCCCcEEEeCCCceeecccccccc
Confidence            999999998  6887765   4   479999999999999999999999999999999                     8


Q ss_pred             cccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057        123 SMRYILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus       123 p~~~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                      ||+++|+++|+|+++ +.+++||+..||.
T Consensus       191 pl~~~~~avs~g~~~-~~~l~Dp~~~Ee~  218 (277)
T 2po1_B          191 PVEKIPVPVTFAKIG-NILVVDPSLDEEL  218 (277)
T ss_dssp             CBCCCCEEEEEEEET-TEEEESCCHHHHH
T ss_pred             cccCceEEEEEEEEC-CEEEeCCCHHHHh
Confidence            999999999999994 7999999999973

>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=1e-34  Score=227.12  Aligned_cols=148  Identities=20%  Similarity=0.245  Sum_probs=127.9

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEE-cCcccccccCCCCeeEEEEE--EcCCC------CCCcchhhHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMY-GPVEAKIQKTIIDKASVEVI--FRPKS------GLSFVQDRLKE   71 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~-gp~~~~~~~~~~~~~~v~v~--~~p~~------g~~~~~~~~~~   71 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|+ +|.++  ..+.++++.+.++  +.|++      |+++.++.+++
T Consensus        36 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p--~~~~~~~g~l~v~~~~~p~a~~~~~~g~~~~~~~~is  113 (277)
T 2je6_A           36 LTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKP--YEDTPNQGNLIVNVELLPLAYETFEPGPPDENAIELA  113 (277)
T ss_dssp             TTCCCCEEEEETCSTTSSEEEEEEETTEEEEEEEEEEEECC--CTTCTTCCEEEEEEEECTTSCTTCCCSSCCHHHHHHH
T ss_pred             cCcccCeEEEeCCcCCCCeEEEEEECCeEEEEEEEeeeeCC--CCCCCCccEEEEEEEeCCccCcccccCCCChHHHHHH
Confidence            47999999999999999999999999999999999 55554  3345677766554  45643      34456677889


Q ss_pred             HHHHHHHHH--hhcccCC------CCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcC---------------------c
Q psy15057         72 SVIKSTCES--ALLTMLH------PRTSVILTIQELQDQGSLLSCCINAACLALINSG---------------------I  122 (151)
Q Consensus        72 ~~l~~~l~~--~i~~~~~------p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~ag---------------------i  122 (151)
                      ++|+++|++  +++++.|      ++|.|+|+++||++|||+++|++||+++||+|+|                     +
T Consensus       114 ~li~r~lr~~~~i~~~~l~i~~g~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~~p~v~~~~~~~~~~~~~~~~~i  193 (277)
T 2je6_A          114 RVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKL  193 (277)
T ss_dssp             HHHHHHHHHTTCSCGGGGEEETTTEEEEEEEEEEEEECCSCHHHHHHHHHHHHHHTCEEEEEECC---CEEEEEEEEEEC
T ss_pred             HHHHHHHhccCCcCHHHceeecCceEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcCCCeEEecCCcceEeccCccccc
Confidence            999999999  5888877      4799999999999999999999999999999999                     9


Q ss_pred             cccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057        123 SMRYILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus       123 p~~~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                      ||+++|+++|+|++ ++.+++|||..||.
T Consensus       194 p~~~~~~avsvg~~-~~~~l~Dpt~~Ee~  221 (277)
T 2je6_A          194 PLNYPVVTISVAKV-DKYLVVDPDLDEES  221 (277)
T ss_dssp             CCSCCCEEEEEEEE-TTEEEESCCHHHHH
T ss_pred             cccCCeEEEEEEEE-CCEEecCCCHHHHh
Confidence            99999999999999 58999999999973

>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=1.1e-34  Score=226.86  Aligned_cols=150  Identities=20%  Similarity=0.223  Sum_probs=127.2

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEE--cCCC------CCCcchhhHHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIF--RPKS------GLSFVQDRLKES   72 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~--~p~~------g~~~~~~~~~~~   72 (151)
                      ++|+|++.+++|++++++|||+|++|+|+|+|+|+++... +....++++.+.++|  .|++      |+++.++.++++
T Consensus        31 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~-p~~~~~~~g~l~v~~~~~p~a~~~~~~g~~~~~~~~~s~  109 (278)
T 2nn6_C           31 LGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAA-PSTDAPDKGYVVPNVDLPPLCSSRFRSGPPGEEAQVASQ  109 (278)
T ss_dssp             SCCCCSCCEEETCCSSSSEEEEEEETTEEEEEEEEEEECC-CCSSSTTCCCCEEEEECCSSSCTTSCSSSCCHHHHHHHH
T ss_pred             cccccCeEEEeCCccCCCceEEEEeCCeEEEEEEEEEeec-CCCCCCCccEEEEEEEeCCccCccccCCCCcHHHHHHHH
Confidence            4799999999999999999999999999999999998752 344456777655555  4542      445566778899


Q ss_pred             HHHHHHHH--hhcccC------CCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCc----------------------
Q psy15057         73 VIKSTCES--ALLTML------HPRTSVILTIQELQDQGSLLSCCINAACLALINSGI----------------------  122 (151)
Q Consensus        73 ~l~~~l~~--~i~~~~------~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agi----------------------  122 (151)
                      +|+++|++  +++++.      .++|.|+|+++||++||++++|++||+++||+|+||                      
T Consensus       110 li~r~l~~s~~i~l~~L~i~pg~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~iP~v~~~~~~~~~~~~~~~~~~l  189 (278)
T 2nn6_C          110 FIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETALAEVNLKKKSYL  189 (278)
T ss_dssp             HHHHHHHHHCCSCHHHHCSSBTTBCEEEEEEEEESSCCSCTTHHHHHHHHHHHHTCCCCCCCBCSSSBCCCTTSCCCSCS
T ss_pred             HHHHHHhccCCCCHHHCEEeCCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhCCCCeEEEeCCCcceecCccccccc
Confidence            99999995  676654      368999999999999999999999999999999996                      


Q ss_pred             cccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057        123 SMRYILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus       123 p~~~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                      ||+++++++|+|+++++.+++|||..||.
T Consensus       190 p~~~~~~avs~g~~~~~~~l~Dpt~~Ee~  218 (278)
T 2nn6_C          190 NIRTHPVATSFAVFDDTLLIVDPTGEEEH  218 (278)
T ss_dssp             CCSCCCEEEEEEECTTTCCEESCCTTTTT
T ss_pred             ccCCceEEEEEEEECCceEEECCCHHHHh
Confidence            79999999999999533999999999984

>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=4.5e-34  Score=239.94  Aligned_cols=149  Identities=20%  Similarity=0.259  Sum_probs=124.2

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEE-EcCcccccccC-----CCCeeEEEEEEcCCC-------CCCcchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASM-YGPVEAKIQKT-----IIDKASVEVIFRPKS-------GLSFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V-~gp~~~~~~~~-----~~~~~~v~v~~~p~~-------g~~~~~~   67 (151)
                      +||+|++++++|+++++||||+|++|+|+|+|+| .||.+..+..+     ...+..+++++.|++       |.++.++
T Consensus       321 ~~elRpi~i~~g~l~~a~GSal~~~G~T~Vl~~Vt~gp~~~~~~~~~l~~~~~g~~~~~y~~~P~st~e~~~~g~~~~Re  400 (549)
T 3gme_A          321 KDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRRE  400 (549)
T ss_dssp             TTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEC---------------CCEEEEEECCGGGTTCCCCSSCCCSSH
T ss_pred             CCCccceEEEECCCCCCCceEEEEECCeEEEEEEEecCcccccCccccCCCCceEEEEEEEeCCCCcCCcccCCCCChhH
Confidence            5899999999999999999999999999999999 69976543211     223456677777852       2244566


Q ss_pred             hHHHHHHHHHHHHhhc-ccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCC---eEEe
Q psy15057         68 RLKESVIKSTCESALL-TMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKN---EVIL  143 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~-~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~---~~lv  143 (151)
                      .+++++++++|+++|+ .++||++ |+|+++||++|||.++|++||+++||+||||||+++++|+++|+++++   .+++
T Consensus       401 ie~~~li~raL~~vI~~~~~~P~t-I~V~~~VLesDGs~~~AsI~aa~lAL~DAGvPm~~~Vaavs~Gli~~g~~~~iL~  479 (549)
T 3gme_A          401 IGHGRLAKRGVLAVMPDMDKFPYT-VRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLS  479 (549)
T ss_dssp             HHHHHHHHHHHTTTCCCTTTCCCE-EEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCCSSCCEEEEEEEEEETTEEEEEE
T ss_pred             HHHHHHHHHHHHHhcCccccCCeE-EEEEEEEEECCCCHHHHHHHHHHHHHHhCCCCcccceeEEEEEEEcCCCceEEEe
Confidence            7789999999999999 6899986 999999999999999999999999999999999999999999999643   6899


Q ss_pred             CCCcccc
Q psy15057        144 DANQIQS  150 (151)
Q Consensus       144 Dpt~~Ee  150 (151)
                      ||+..||
T Consensus       480 D~~~~Ed  486 (549)
T 3gme_A          480 DILGDED  486 (549)
T ss_dssp             SCCHHHH
T ss_pred             cCChHHH
Confidence            9999997

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

Probab=100.00  E-value=3.5e-33  Score=240.64  Aligned_cols=150  Identities=17%  Similarity=0.220  Sum_probs=128.1

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEE-EcCcccccccC---CCCee--EEEEEEcCCC-------CCCcchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASM-YGPVEAKIQKT---IIDKA--SVEVIFRPKS-------GLSFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V-~gp~~~~~~~~---~~~~~--~v~v~~~p~~-------g~~~~~~   67 (151)
                      +||+|++++++|+++++||||+|++|+|+|+|+| .||.++.++.+   .++++  .+++++.|++       |.++.++
T Consensus       337 ~~elRpI~ie~gvl~~a~GSAl~~~G~TkVl~~Vt~Gp~~~~~~~d~l~~~~~g~~~~~y~~~P~st~er~~~g~~~~Re  416 (726)
T 4aid_A          337 VKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRRE  416 (726)
T ss_dssp             TTCCCCEEEEECSSTTSSEEEEEEETTEEEEEEEEEECGGGSEEEEETTEEEEECEEEEEECCGGGGTCCCCCSSCCHHH
T ss_pred             CCCccceEEEECCCCCCCceEEEEeCCeEEEEEEEeCCCCcccccccccCCCceEEEEEEEeCCCcccccccCCCcchhh
Confidence            5899999999999999999999999999999999 69997654321   23444  5566677742       2244556


Q ss_pred             hHHHHHHHHHHHHhhc-ccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCC---eEEe
Q psy15057         68 RLKESVIKSTCESALL-TMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKN---EVIL  143 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~-~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~---~~lv  143 (151)
                      .+++++++++|+++|+ .++||++ |+|+++||++|||+++|++||+++||+||||||+++++|+++|+++++   .+++
T Consensus       417 ie~~~li~raL~~vI~~~~~~P~t-I~V~~~VLesDGs~~~AsI~aa~lAL~DAGIPm~~~VaavsvGli~~g~~~~iLl  495 (726)
T 4aid_A          417 IGHGKLAWRALRPMLPTKEDFPYT-IRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLS  495 (726)
T ss_dssp             HHHHHHHHHHHGGGSCCTTTCCCE-EEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCCEEEEEEEEECSSCEEEEE
T ss_pred             HHHHHHHHHHHHHhcCccccCCeE-EEEEEEEEEcCCcHHHHHHHHHHHHHHhcCCccccCeeEEEEEEEcCCCceEEEe
Confidence            6788999999999999 6899996 999999999999999999999999999999999999999999999753   4888


Q ss_pred             CCCccccC
Q psy15057        144 DANQIQSN  151 (151)
Q Consensus       144 Dpt~~Ee~  151 (151)
                      ||+..||.
T Consensus       496 D~~~~Ed~  503 (726)
T 4aid_A          496 DILGDEDH  503 (726)
T ss_dssp             SCCTTGGG
T ss_pred             cCChhHHh
Confidence            99999973

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

Probab=100.00  E-value=6.4e-33  Score=236.66  Aligned_cols=148  Identities=20%  Similarity=0.251  Sum_probs=125.3

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCc-cccccc---------CCCCeeEEEEEEcCCC-------CCC
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPV-EAKIQK---------TIIDKASVEVIFRPKS-------GLS   63 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~-~~~~~~---------~~~~~~~v~v~~~p~~-------g~~   63 (151)
                      +||+|++++++|+++++||||+|++|+|+|+|+|++|. .+..+.         ....+..+++++.|++       |.+
T Consensus       325 ~~elRpi~i~~g~l~~a~GSal~~~G~T~Vl~~Vt~~~~~~~~~~d~~~~~l~~~~~g~~~~~y~~~P~st~e~~~~g~~  404 (630)
T 3u1k_A          325 LTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITAINGIKDKNFMLHYEFPPYATNEIGKVTGL  404 (630)
T ss_dssp             TTCCCCEEEEECCSTTSSEEEEEEETTEEEEEEEEEECGGGGSCSSHHHHHHHCCCGGGEEEEEECCGGGGTCCCCCSSC
T ss_pred             CccccceEEEECCCCCCCceEEEEECCeEEEEEEEcCCCCchhcccccccccCCCCceEEEEEEEecCCcccccccCCCC
Confidence            58999999999999999999999999999999999854 322211         1223456788888864       233


Q ss_pred             cchhhHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecC-----
Q psy15057         64 FVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDK-----  138 (151)
Q Consensus        64 ~~~~~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~-----  138 (151)
                      +.++.+++++++++|+++++ ..||++ |+|+++||++|||.++|++||+++||+||||||+++++|+++|++++     
T Consensus       405 ~rREi~~~~Li~raLr~vi~-~~~p~t-I~V~~~VLesDGs~~~AsI~aa~lAL~dAGIPl~~~Vaavs~gli~~~~~~~  482 (630)
T 3u1k_A          405 NRRELGHGALAEKALYPVIP-RDFPFT-IRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEK  482 (630)
T ss_dssp             CHHHHHHHHHHHHHHGGGSC-TTCSSE-EEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCCEEEEEEEEEEECSSS
T ss_pred             ChHHHHHHHHHHHHHHhhCc-ccCCeE-EEEEEEEEEcCCCHHHHHHHHHHHHHHhCCCCcccceEEEEEEEecCCCccc
Confidence            45566678999999999998 569975 99999999999999999999999999999999999999999999972     


Q ss_pred             C-----eEEeCCCcccc
Q psy15057        139 N-----EVILDANQIQS  150 (151)
Q Consensus       139 ~-----~~lvDpt~~Ee  150 (151)
                      +     .+|+||+..||
T Consensus       483 g~~~~~~iLlD~~~~Ed  499 (630)
T 3u1k_A          483 GEIEDYRLLTDILGIED  499 (630)
T ss_dssp             SCEEEEEEEESCCHHHH
T ss_pred             ccccCceEEecCCHHHH
Confidence            3     69999999997

>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=6.7e-33  Score=240.29  Aligned_cols=149  Identities=16%  Similarity=0.248  Sum_probs=128.7

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEE-cCcccccccC---CCCee--EEEEEEcCCC-------CCCcchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMY-GPVEAKIQKT---IIDKA--SVEVIFRPKS-------GLSFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~-gp~~~~~~~~---~~~~~--~v~v~~~p~~-------g~~~~~~   67 (151)
                      ++|+|++++++|+++++||||+|++|+|+|+|+|+ ||.++.++.+   .++++  .+++++.|++       |.++.++
T Consensus       362 ~~elRpI~ie~gvl~~a~GSAl~~~G~TqVL~~Vt~Gp~~~~~~~d~l~~~~~g~~~~~y~f~P~st~e~~~~g~~~~re  441 (757)
T 1e3p_A          362 VTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPPYSVGETGRVGSPKRRE  441 (757)
T ss_dssp             TTCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEEEGGGSEECCSSSSCCEESEEEEEECCGGGGTCCCCCSSCCHHH
T ss_pred             cccccceeEEeCCCCCCCEEEEEEECCcEEEEEEEecCCCccccccccCCCCceEEEEEEEeCCcccccccCCCCCchhH
Confidence            58999999999999999999999999999999995 9987654322   34544  5777887842       2244566


Q ss_pred             hHHHHHHHHHHHHhhc-ccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecC---C----
Q psy15057         68 RLKESVIKSTCESALL-TMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDK---N----  139 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~-~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~---~----  139 (151)
                      .+++++++++|+++|+ .+.||++ |+|+++||++|||+++|++||+++||+||||||+++++|+++|++++   +    
T Consensus       442 ie~~~li~raL~~vI~~~~~~P~t-I~V~~~VLesDGs~~~Asi~aa~lAL~dAgIP~k~~Vaavs~gli~eg~dg~~~~  520 (757)
T 1e3p_A          442 IGHGALAERAIVPVLPTREEFPYA-IRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIAMGLISQEINGETHY  520 (757)
T ss_dssp             HHHHHHHHHHHGGGCCCTTTSCEE-EEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCCSSCCEEEEEEEEEEESSSCEEE
T ss_pred             HHHHHHHHHHHHHhccccccCCEE-EEEEEEEEECCCCHHHHHHHHHHHHHHHcCCCcccceEEEEEEEEecCCCCccce
Confidence            7789999999999999 6899976 99999999999999999999999999999999999999999999942   2    


Q ss_pred             eEEeCCCcccc
Q psy15057        140 EVILDANQIQS  150 (151)
Q Consensus       140 ~~lvDpt~~Ee  150 (151)
                      .+|+||+..||
T Consensus       521 ~iLlDp~~~Ed  531 (757)
T 1e3p_A          521 VALTDILGAED  531 (757)
T ss_dssp             EEEESCCHHHH
T ss_pred             eEEeCCCHHHH
Confidence            79999999997

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

Probab=100.00  E-value=1.9e-32  Score=236.61  Aligned_cols=150  Identities=19%  Similarity=0.240  Sum_probs=124.0

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEE-EcCccccccc-----CCCCeeEEEEEEcCCCC-------CCcchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASM-YGPVEAKIQK-----TIIDKASVEVIFRPKSG-------LSFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V-~gp~~~~~~~-----~~~~~~~v~v~~~p~~g-------~~~~~~   67 (151)
                      ++|+|++++++|+++++||||+|++|+|+|+|+| .||.+.++..     +...+..+++++.|++.       .++.++
T Consensus       327 ~~elRpI~ie~gvl~~a~GSAl~~~G~TqVL~~Vt~gp~e~~~~~d~l~~~~~g~~~~~y~~~P~st~e~~r~g~p~~RE  406 (723)
T 3cdi_A          327 KDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRRE  406 (723)
T ss_dssp             TTCCCCEEEEESCSTTSSEEEEEEETTEEEEEEEEECC-------------CTTSEEEEEECCGGGGTCCCCC-----CT
T ss_pred             ccccccceEEeCCCCCCCeEEEEEECCcEEEEEEEecCcccccCCcccCCCCceEEEEEEecCCCCccccccCCCCCHHH
Confidence            5899999999999999999999999999999999 5998643321     23456678888888632       223455


Q ss_pred             hHHHHHHHHHHHHhhcc-cCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccceeeEEEEEEecCC---eEEe
Q psy15057         68 RLKESVIKSTCESALLT-MLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYILAAVSCIINDKN---EVIL  143 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~~-~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~---~~lv  143 (151)
                      ...+.+++++|+++|++ ++||++ |+|+++||++|||+++|++||+++||+||||||+++++|+++|++++|   .+|+
T Consensus       407 i~~~~li~raL~~vI~~~~~~p~t-I~Vd~~VLesdGs~~~Asi~aa~lAL~dAgVPl~~~vaavs~gli~~g~~~~iL~  485 (723)
T 3cdi_A          407 IGHGRLAKRGVLAVMPDMDKFPYT-VRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLS  485 (723)
T ss_dssp             THHHHHHHHHHHTTSCCSSSSCSC-EEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCCEEEEEEEEEETTEEEEES
T ss_pred             HHHHHHHHHHHHHhcCcccCCCEE-EEEEEEEEeCCCCHHHHHHHHHHHHHhcCCCCcccceeeEEEEEEcCCCceEEEE
Confidence            56789999999999996 789976 999999999999999999999999999999999999999999999644   4999


Q ss_pred             CCCccccC
Q psy15057        144 DANQIQSN  151 (151)
Q Consensus       144 Dpt~~Ee~  151 (151)
                      ||+..||.
T Consensus       486 Dp~~~Ed~  493 (723)
T 3cdi_A          486 DILGDEDH  493 (723)
T ss_dssp             SCCGGGGG
T ss_pred             CCChHHhh
Confidence            99999984

>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=1.9e-32  Score=220.95  Aligned_cols=146  Identities=12%  Similarity=0.100  Sum_probs=123.2

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeE--EEEEEcCCC------CCCcchhhHHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKAS--VEVIFRPKS------GLSFVQDRLKES   72 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~--v~v~~~p~~------g~~~~~~~~~~~   72 (151)
                      ++|+|++.+++|   +++|||+|++|+|+|+|+|++|... +..+.++++.  ++|++.|.+      |+++.++.++++
T Consensus        46 ~~e~R~i~ie~g---~A~GSa~v~~G~T~VL~tV~~e~~~-p~~~~~~~g~l~~~v~~~p~a~~~~~~g~~s~~e~eisr  121 (358)
T 2nn6_A           46 TYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVS-PKLNRATEGILFFNLELSQMAAPAFEPGRQSDLLVKLNR  121 (358)
T ss_dssp             TTCCCCCEEEEC---SSTTEEEEESSSCEEEEEECCEEEC-CCSTTTTSCCEEEEEEECTTTCSSCCSSSTHHHHTHHHH
T ss_pred             ccccCCeEEEEe---cCCcEEEEEECCcEEEEEEEecccC-CcccCCCCcEEEEEEEecCCccccccCCCCCHHHHHHHH
Confidence            479999999999   9999999999999999999999843 3334456555  556666753      444556778899


Q ss_pred             HHHHHHHHhhccc--------CCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCcc---------------------
Q psy15057         73 VIKSTCESALLTM--------LHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS---------------------  123 (151)
Q Consensus        73 ~l~~~l~~~i~~~--------~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip---------------------  123 (151)
                      +|+++|++...++        ..|+|.|+|+++||++|||+++|+++|+++||+|+|+|                     
T Consensus       122 li~r~Lr~s~~idl~~LcI~pg~~~w~I~Vdv~VL~~DGn~~dAai~Aa~aAL~da~iP~v~~~~~~v~i~~~~~~~~~~  201 (358)
T 2nn6_A          122 LMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDPVP  201 (358)
T ss_dssp             HHHHHHHHHTCBCSSSSCSBTTTBEEEEEEEEEECSCCSCCHHHHHHHHHHHHHHCCCCCCBCCTTCCBCCHHHHTSCCC
T ss_pred             HHHHHhhhccccchHhhcccCCCccEEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhCcCcEEeeCCeeEecccccccccc
Confidence            9999999954433        34789999999999999999999999999999999999                     


Q ss_pred             --ccceeeEEEEEEec-CCeEEeCCCcccc
Q psy15057        124 --MRYILAAVSCIIND-KNEVILDANQIQS  150 (151)
Q Consensus       124 --~~~~~~avtv~~~~-~~~~lvDpt~~Ee  150 (151)
                        |+++|+++|+|++. ++.+|+|||..||
T Consensus       202 l~i~~~p~avsvgl~~~~~~illDPt~~Ee  231 (358)
T 2nn6_A          202 LSIHHMPICVSFAFFQQGTYLLVDPNEREE  231 (358)
T ss_dssp             CCBCCCEEEEEEEECTTTSSEEESCCHHHH
T ss_pred             cCccCCEEEEEEEEEeeCCEEEECCCHHHH
Confidence              89999999999884 4689999999987

>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=7.5e-33  Score=219.29  Aligned_cols=149  Identities=13%  Similarity=0.098  Sum_probs=124.7

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEE--EEcCCCC-----CC-cchhhHHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEV--IFRPKSG-----LS-FVQDRLKES   72 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v--~~~p~~g-----~~-~~~~~~~~~   72 (151)
                      ++|+|++.+++|++++++|||+|++|+|+|+|+|+++... +..+.++++.+.+  ++.|++.     ++ +.++.++++
T Consensus        43 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~e~~~-p~~~~~~~g~l~~~v~~~p~a~~~~~~r~~~~~~~~isr  121 (305)
T 2nn6_E           43 CEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGT-PKLEKPNEGYLEFFVDCSASATPEFEGRGGDDLGTEIAN  121 (305)
T ss_dssp             SSCCCCCEEEECCCTTSSSEEEEEETTEEEEEECCCCCSC-CCSSSCSSCCEEEECCCCTTTCSSCCTTSTHHHHHHHHH
T ss_pred             CcCccCeEEEeCcccCCCcEEEEEECCeEEEEEEEEEeeC-CCcCCCCceEEEEEEEeCCCcCccccCCCCchHHHHHHH
Confidence            4799999999999999999999999999999999998752 3444566665555  5556532     22 245667899


Q ss_pred             HHHHHHHH--hhccc---CCC---CcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccce-----------------
Q psy15057         73 VIKSTCES--ALLTM---LHP---RTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYI-----------------  127 (151)
Q Consensus        73 ~l~~~l~~--~i~~~---~~p---~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~-----------------  127 (151)
                      +|+++|++  +|+++   .||   .|.|+|+++||++|||+++|++||+++||.|+++|+.++                 
T Consensus       122 li~r~lr~s~~idl~~L~i~p~~~~w~i~idv~VL~~DG~~~daai~aa~~AL~~a~iP~~~~~~~~~~~~~i~~~~d~~  201 (305)
T 2nn6_E          122 TLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLEDEEGSKDIELSDDPY  201 (305)
T ss_dssp             HHHHHHHHSCCSCSSSSCSSTTTCCCCEEEEEEECCCCSSHHHHHHHHHHHTTTTCCCCEEEEECC------EEEEESSC
T ss_pred             HHHHHHhhcCcccHHHheeccCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcCCCeEEEecCCCCceeeeccCccc
Confidence            99999999  78777   677   477999999999999999999999999999999997654                 


Q ss_pred             ----------eeEEEEEEecCCeEEeCCCccccC
Q psy15057        128 ----------LAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus       128 ----------~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                                |+++|+|++ ++.+|+|||..||.
T Consensus       202 ~~~~l~l~~~p~avt~g~i-~~~~l~Dpt~~Ee~  234 (305)
T 2nn6_E          202 DCIRLSVENVPCIVTLCKI-GYRHVVDATLQEEA  234 (305)
T ss_dssp             CCSCCCCTTCCCCEEEEES-SSSEESSCCHHHHT
T ss_pred             ccccccccCceEEEEEEEE-CCEEEECCCHHHHh
Confidence                      679999999 58999999999984

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

Probab=99.98  E-value=2.2e-32  Score=216.49  Aligned_cols=146  Identities=16%  Similarity=0.133  Sum_probs=111.4

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCe--eEEEEEEcCCC------CCCc-chhhHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDK--ASVEVIFRPKS------GLSF-VQDRLKE   71 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~--~~v~v~~~p~~------g~~~-~~~~~~~   71 (151)
                      ++|+|++++++|   +++|||+|++|+|+|+|+|++|... +..+.+++  ..++++|.|.+      |+++ .++.+++
T Consensus        30 ~~e~R~i~i~~g---~a~GSa~v~~G~T~Vl~~V~~~~~~-p~~~~~~~g~~~~~ve~~~~~~~~~~~g~~~~~~~~~is  105 (305)
T 2wp8_A           30 FDQFRDVEITFG---KEFGDVSVKMGNTKVHCRISCQIAQ-PYEDRPFEGLFVISTEISPMAGSQFENGNITGEDEVLCS  105 (305)
T ss_dssp             TTCCCCEEEEEC---SSTTEEEEEETTEEEEEEEEEEEC--CCSSCTTCCEEEEEECCC---------------------
T ss_pred             CcccCCeEEEEc---CCCcEEEEEECCeEEEEEEeccccC-CcccCCCCcEEEEEEEECCCCCccccCCCCChhHHHHHH
Confidence            479999999999   8999999999999999999998743 33334554  45666766642      4455 6667789


Q ss_pred             HHHHHHHH--HhhcccCC---C---CcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCcc--------------------
Q psy15057         72 SVIKSTCE--SALLTMLH---P---RTSVILTIQELQDQGSLLSCCINAACLALINSGIS--------------------  123 (151)
Q Consensus        72 ~~l~~~l~--~~i~~~~~---p---~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip--------------------  123 (151)
                      ++|+++|+  ++|+++.+   |   .|.|+|+++||++|||+++|+++|+++||+|+|+|                    
T Consensus       106 ~li~r~l~~s~~idl~~L~i~pg~~~w~I~id~~VL~~DG~~~dAai~aa~~AL~~a~iP~~~~~~~~~~i~~~~~~~~~  185 (305)
T 2wp8_A          106 RIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQIIVHPVNEREPV  185 (305)
T ss_dssp             -CHHHHHHHTTSBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHHCEECCCBCTTSSCCBCCSSSSCCE
T ss_pred             HHHHHHHhhccCcCHHHccccCCcEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHHhCCCeEEecCCceEeccccccccc
Confidence            99999999  57777644   4   38899999999999999999999999999999999                    


Q ss_pred             ---ccceeeEEEEEEec---------C----CeEEeCCCcccc
Q psy15057        124 ---MRYILAAVSCIIND---------K----NEVILDANQIQS  150 (151)
Q Consensus       124 ---~~~~~~avtv~~~~---------~----~~~lvDpt~~Ee  150 (151)
                         |++.|+++|+|+++         +    +.+|+||+..||
T Consensus       186 ~l~~~~~pvavs~g~i~~~~~~~~~~~~~~~~~~l~Dpt~~Ee  228 (305)
T 2wp8_A          186 PLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLKEE  228 (305)
T ss_dssp             ECCBSCCCEEEEEEECC---------------CEEESCCHHHH
T ss_pred             ccccccCeEEEEEEEEccccccccccccccCCeEEeCCCHHHH
Confidence               77899999999994         2    689999999997

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

Probab=99.97  E-value=2.3e-29  Score=214.77  Aligned_cols=140  Identities=20%  Similarity=0.172  Sum_probs=119.6

Q ss_pred             ccceEEEecCCCC-CCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEc--CC-C-----------CCCcchhh
Q psy15057          4 LRELKSQLNILSR-SDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFR--PK-S-----------GLSFVQDR   68 (151)
Q Consensus         4 ~R~i~i~~g~~~~-a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~--p~-~-----------g~~~~~~~   68 (151)
                      -|++++++|.+++ |+|||++++|+|+|+|+|+||.++++.    +...+.|+|+  ++ +           |+++.++.
T Consensus        14 ~R~i~ietG~~a~qA~GSa~v~~G~T~VL~tv~~~~~~~~~----df~pL~v~y~~~~~a~g~iPg~f~kRegrps~~e~   89 (630)
T 3u1k_A           14 NRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKPSPS----QFMPLVVDYRQKAAAAGRIPTNYLRREVGTSDKEI   89 (630)
T ss_dssp             SSEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCCSS----SSCCEEEEEECSEETTTTEECTTC-----CCHHHH
T ss_pred             CEEEEEEeCCccccCCeeEEEEECCeEEEEEEEecCCCCCC----CeeEEEEEEEecccccCCCCccccccCCCCCHHHH
Confidence            5999999999996 999999999999999999999976543    3444556554  32 2           23445566


Q ss_pred             HHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCCh--hHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCC
Q psy15057         69 LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSL--LSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDAN  146 (151)
Q Consensus        69 ~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~--l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt  146 (151)
                      +++++|+|.|++++++..||..  +|+++||+.||+.  ..+++||+++||.++||||+++++||++|++ +|++++|||
T Consensus        90 lisRlIdR~lRp~~~~~~~~~~--qI~~~VLs~Dg~~~~~~aai~aAs~AL~~s~iP~~~~vaav~vg~i-~g~~vldPt  166 (630)
T 3u1k_A           90 LTSRIIDRSIRPLFPAGYFYDT--QVLCNLLAVDGVNEPDVLAINGASVALSLSDIPWNGPVGAVRIGII-DGEYVVNPT  166 (630)
T ss_dssp             HHHHHHHHHHGGGSCTTCCCCE--EEEEEEEECCSSSCHHHHHHHHHHHHHHHSSSCCCCCCEEEEEEEE-TTEEEESCC
T ss_pred             HHHHHHhHHhhhcccccCCCce--EEEEEEEECCCCCCHHHHHHHHHHHHHhccCCCcCCCeEEEEEEEE-CCEEEECCC
Confidence            7899999999999999888774  5799999999998  8899999999999999999999999999999 599999999


Q ss_pred             cccc
Q psy15057        147 QIQS  150 (151)
Q Consensus       147 ~~Ee  150 (151)
                      ..|+
T Consensus       167 ~~E~  170 (630)
T 3u1k_A          167 RKEM  170 (630)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9986

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

Probab=99.94  E-value=9.2e-26  Score=195.07  Aligned_cols=142  Identities=15%  Similarity=0.155  Sum_probs=120.2

Q ss_pred             ccceEEEecCCC-CCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcCC--------------CCCCcchhh
Q psy15057          4 LRELKSQLNILS-RSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPK--------------SGLSFVQDR   68 (151)
Q Consensus         4 ~R~i~i~~g~~~-~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p~--------------~g~~~~~~~   68 (151)
                      -|++.+++|.+. +|+||+++++|+|+|+|+|+++.++++.   .+...++|+|.+.              .|+|+.++.
T Consensus        19 ~r~i~ietg~ia~qA~GSv~v~~G~T~Vl~tv~~~~~~~~~---~~f~pltv~y~ek~~a~g~ipg~f~kReGrpse~e~   95 (723)
T 3cdi_A           19 QHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPG---QDFFPLTVNYQERTYAAGRIPGSFFRREGRPSEGET   95 (723)
T ss_dssp             TEEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCCSS---CCSCCEEEEEEECGGGGTCCCC-------CCCHHHH
T ss_pred             CEEEEEEeCccccCCCeeEEEEECCEEEEEEEEecCCCCCC---CCeeeEEEEEeEeccccccCCCccccCCCCCChHHh
Confidence            389999999885 8999999999999999999999765432   1333477777643              345666777


Q ss_pred             HHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCCh--hHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCC
Q psy15057         69 LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSL--LSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDAN  146 (151)
Q Consensus        69 ~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~--l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt  146 (151)
                      +++++|+|.|++++....  +|.++|+++||+.||+.  ..+++|||++||..++||+++.++||++|++ +|++++|||
T Consensus        96 l~sRlIdR~lRplfp~~~--~~~vqv~~~vls~Dg~~~~d~~ai~aAsaAL~~s~iP~~~pv~av~vg~i-~g~~v~nPt  172 (723)
T 3cdi_A           96 LIARLIDRPIRPLFPEGF--VNEVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYI-NDQYVLNPT  172 (723)
T ss_dssp             HHHHHHHHHHGGGSCTTC--CSCEEEEEEEEECCTTSCHHHHHHHHHHHHHHHHTSSCCCCCCCEEEEEE-TTEEEESCC
T ss_pred             HHHHHhCccchhcccccC--cceEEEEEEEEEcCCCCCHHHHHHHHHHHHHHhcCCCCCCCeEEEEEEEE-CCEEEECcC
Confidence            889999999999887664  68899999999999996  5699999999999999999999999999999 589999999


Q ss_pred             ccccC
Q psy15057        147 QIQSN  151 (151)
Q Consensus       147 ~~Ee~  151 (151)
                      ..|++
T Consensus       173 ~~e~~  177 (723)
T 3cdi_A          173 QDELK  177 (723)
T ss_dssp             TTGGG
T ss_pred             HHHHH
Confidence            99873

>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=99.93  E-value=2.1e-25  Score=187.48  Aligned_cols=142  Identities=15%  Similarity=0.155  Sum_probs=117.0

Q ss_pred             ccceEEEecCCC-CCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcC--------------CCCCCcchhh
Q psy15057          4 LRELKSQLNILS-RSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRP--------------KSGLSFVQDR   68 (151)
Q Consensus         4 ~R~i~i~~g~~~-~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p--------------~~g~~~~~~~   68 (151)
                      -|++++++|.+. +|+||+++++|+|+|+|+|+++.+++..   .+...+.++|..              ..|+++.++.
T Consensus        13 ~R~i~ietg~~ak~A~GSvlv~~GdT~Vl~tv~~~~~~~~g---~df~Pltv~Y~e~~~a~G~iPg~~~~REGrps~~~~   89 (549)
T 3gme_A           13 QHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPG---QDFFPLTVNYQERTYAAGRIPGSFFRREGRPSEGET   89 (549)
T ss_dssp             TEEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCCTT---CCSCCEEEEEEECGGGTTCCCSCC-----CCCHHHH
T ss_pred             CEEEEEEECCccCCCCeEEEEEECCEEEEEEEEecCCCCCC---CCCccceeeeeeehhhcccCCCcCcCcCCCCChhhh
Confidence            489999999887 5999999999999999999999865422   223336666642              1245666777


Q ss_pred             HHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCCh--hHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCC
Q psy15057         69 LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSL--LSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDAN  146 (151)
Q Consensus        69 ~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~--l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt  146 (151)
                      +++++|+|.|+++++...+  ..++|+++||+.||+.  ..+++||+++||..++||+++.++||++|++ +|++++|||
T Consensus        90 l~~RlIdR~lRplfp~~~~--~evqI~~~Vls~D~~~~pd~~ai~gAs~AL~~s~iP~~gpvaaV~Vg~i-~g~~vlnPt  166 (549)
T 3gme_A           90 LIARLIDRPIRPLFPEGFV--NEVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYI-NDQYVLNPT  166 (549)
T ss_dssp             HHHHHHHHHHGGGSCTTCC--SCEEEEEEEEECCSSSCHHHHHHHHHHHHHHHHCSCCCCCCEEEEEEEE-TTEEEESCC
T ss_pred             HHHHHhCCccccccccCCc--ccEEEEEEEEecCCCCcHHHHHHHHHHHHHhccCCCcCCCeeEEEEEEE-CCEEEECCC
Confidence            8899999999998877653  4689999999999865  3788999999999999999999999999998 599999999


Q ss_pred             ccccC
Q psy15057        147 QIQSN  151 (151)
Q Consensus       147 ~~Ee~  151 (151)
                      ..|++
T Consensus       167 ~~e~~  171 (549)
T 3gme_A          167 QDELK  171 (549)
T ss_dssp             TTTTT
T ss_pred             HHHHh
Confidence            99864

>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=99.93  E-value=2e-25  Score=193.66  Aligned_cols=142  Identities=15%  Similarity=0.142  Sum_probs=120.2

Q ss_pred             ccceEEEecCCC-CCCeeEEEEe-CCeEEEEEEEcCcccccccCCCCeeEEEEEEcCC--------------CCCCcchh
Q psy15057          4 LRELKSQLNILS-RSDGSVIFSQ-GQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPK--------------SGLSFVQD   67 (151)
Q Consensus         4 ~R~i~i~~g~~~-~a~GSa~v~~-G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p~--------------~g~~~~~~   67 (151)
                      -|++++++|.+. +|+||+++++ |+|+|+|+|++|.++++.   .+...|.|+|+..              .|+++.++
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            489999999975 7999999999 999999999999876443   1233377777421              24566778


Q ss_pred             hHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCCh--hHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCC
Q psy15057         68 RLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSL--LSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDA  145 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~--l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDp  145 (151)
                      ++++++|+|.|+++++...  +..++|+++||+.||+.  ..+++|||++||.++||||++.++||++|++ +|++++||
T Consensus       113 ~l~~RlIdR~LRplfp~~~--~~evqv~~~Vls~D~~~~~~~~ai~gAs~AL~~s~iP~~~~vaav~vg~~-~g~~vlnP  189 (757)
T 1e3p_A          113 ILTCRLIDRPLRPSFKKGL--RNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALI-RGQWVAFP  189 (757)
T ss_dssp             HHHHHHHHHHHGGGBCTTB--CEEEEEEEEEEECCTTSCCHHHHHHHHHHHHHHTTSSBCCCCEEEEEEEE-TTEEEESC
T ss_pred             HHHHHHHCCcchhccccCC--CCceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCCCCceEEEEEEEE-CCEEEECC
Confidence            8899999999999876654  45799999999999865  9999999999999999999999999999999 59999999


Q ss_pred             CccccC
Q psy15057        146 NQIQSN  151 (151)
Q Consensus       146 t~~Ee~  151 (151)
                      |..|++
T Consensus       190 t~~e~~  195 (757)
T 1e3p_A          190 THTELE  195 (757)
T ss_dssp             CHHHHT
T ss_pred             CHHHHh
Confidence            998863

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

Probab=99.93  E-value=6.5e-25  Score=189.35  Aligned_cols=141  Identities=18%  Similarity=0.154  Sum_probs=118.6

Q ss_pred             ccceEEEecCCC-CCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcC--------------CCCCCcchhh
Q psy15057          4 LRELKSQLNILS-RSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRP--------------KSGLSFVQDR   68 (151)
Q Consensus         4 ~R~i~i~~g~~~-~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p--------------~~g~~~~~~~   68 (151)
                      -|++++++|.+. +|+||+++++|+|+|+|+|+++.++++.   .+...+.++|.+              ..|+++.++.
T Consensus        27 ~R~i~ietg~~ak~A~GSvlv~~GdT~VL~tv~~~~~~~~g---~df~pltveY~ek~~a~G~iPg~~~~REGrps~~~~  103 (726)
T 4aid_A           27 GKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPG---QDFFPLTVNYQEKTFAAGKIPGGFFKREGRPSEKET  103 (726)
T ss_dssp             TEEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCCTT---CCSCCEEEEEEECGGGGTCCCCSTTCSCCSCCHHHH
T ss_pred             CeeEEEEECCccCCCCeeEEEEECCeEEEEEEEecCCCCCC---CCCcCceeeeeeehhhcccCCCcccCCCCCCCchhh
Confidence            589999999887 5999999999999999999999865432   233346666642              1255666777


Q ss_pred             HHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCCh--hHHHHHHHHHHHHhcCccccceeeEEEEEEecCCeEEeCCC
Q psy15057         69 LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSL--LSCCINAACLALINSGISMRYILAAVSCIINDKNEVILDAN  146 (151)
Q Consensus        69 ~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~--l~a~inaa~lAL~~agip~~~~~~avtv~~~~~~~~lvDpt  146 (151)
                      +++++|.|.|+++++...+  +.++|+++||+.||+.  ..+++|||++||.+++||+++.++||++|++ +|++++|||
T Consensus       104 li~RlIdR~lRplf~~~~~--~evqI~~~Vls~Dg~~~~d~~ai~gAs~AL~~s~iP~~~~vaaV~Vg~i-~g~~vldPt  180 (726)
T 4aid_A          104 LVSRLIDRPIRPLFVKGFK--NEVQVVVTVLQHDLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWV-DGAYVLNPT  180 (726)
T ss_dssp             HHHHHHHHHHGGGBCTTCC--SCEEEEEEEEECCSSSCHHHHHHHHHHHHHHHHTCSBCCCCEEEEEEEE-TTEEEESCC
T ss_pred             hHHHHhCCccccccccCCc--cceEEEEEEEecCCCCChhHHHHHHHHHHHHhcCCCcCCCeEEEEEEEE-CCEEEECCC
Confidence            8999999999999887653  5699999999999875  4789999999999999999999999999998 599999999


Q ss_pred             cccc
Q psy15057        147 QIQS  150 (151)
Q Consensus       147 ~~Ee  150 (151)
                      ..|+
T Consensus       181 ~~E~  184 (726)
T 4aid_A          181 LDEM  184 (726)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9886

---

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	151
d2nn6d1	122	d.14.1.4 (D:25-146) Exosome complex exonuclease RR	2e-22
d2je6b1	148	d.14.1.4 (B:8-155) Exosome complex exonuclease 1,	3e-17
d2nn6f1	147	d.14.1.4 (F:29-175) Exosome complex exonuclease MT	2e-16
d1e3ha3	137	d.14.1.4 (A:346-482) Polynucleotide phosphorylase/	4e-14
d1r6la1	151	d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Pseu	7e-14
d2ba0d1	144	d.14.1.4 (D:10-153) Exosome complex exonuclease 1,	7e-14
d2nn6b1	145	d.14.1.4 (B:6-150) Exosome complex exonuclease RRP	4e-13
d1udsa1	149	d.14.1.4 (A:2-150) Ribonuclease PH, domain 1 {Aqui	8e-13
d2nn6c1	181	d.14.1.4 (C:7-187) Exosome complex exonuclease RRP	4e-12
d2ba0g1	176	d.14.1.4 (G:3-178) Exosome complex exonuclease 2,E	2e-11
d2nn6e1	187	d.14.1.4 (E:5-191) Exosome complex exonuclease RRP	2e-11
d2je6a1	191	d.14.1.4 (A:1-191) Exosome complex exonuclease 2,E	1e-10
d1oysa1	151	d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Baci	1e-08
d2nn6a1	184	d.14.1.4 (A:1-184) Exosome complex exonuclease RRP	1e-05
d1e3ha2	149	d.14.1.4 (A:3-151) Polynucleotide phosphorylase/gu	2e-05

>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 = 84.4 bits (208), Expect = 2e-22
 Identities = 60/119 (50%), Positives = 87/119 (73%)

Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
           LR    + N+LSR DGS  F QG T V+A +YGP E K+ K I +KA++EVI RPK GL 
Sbjct: 4   LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLP 63

Query: 64  FVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGI 122
            V ++ +E +I++TCE+ +L  LHPRTS+ + +Q + D GSLL+CC+NAAC+AL+++G+
Sbjct: 64  GVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGV 122

>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 = 71.4 bits (174), Expect = 3e-17
 Identities = 40/130 (30%), Positives = 60/130 (46%), Gaps = 9/130 (6%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIID---KASVEVIFRP 58
           D LR +K +L +L  +DGS IF  G T  +A++YGP E   +   +       V     P
Sbjct: 19  DELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTP 78

Query: 59  KS------GLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINA 112
            S           ++     VI+   ESA+L  L PRT++ +  + LQ         + A
Sbjct: 79  FSTDERKNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRLVSLMA 138

Query: 113 ACLALINSGI 122
           A LAL ++GI
Sbjct: 139 ASLALADAGI 148

>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 = 69.5 bits (169), Expect = 2e-16
 Identities = 29/141 (20%), Positives = 58/141 (41%), Gaps = 20/141 (14%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK--------------TII 47
             LR + ++  +LS++ GS     G T V+ ++ GP +A+  +               + 
Sbjct: 6   TRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAALR 65

Query: 48  DKASVEVIFRPKSGLSFVQDRLKE------SVIKSTCESALLTMLHPRTSVILTIQELQD 101
            +   +    P +G                  ++   E A+    +PR  + ++   L+D
Sbjct: 66  GRLLCDFRRAPFAGRRRRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLED 125

Query: 102 QGSLLSCCINAACLALINSGI 122
            GS L+  + AA LAL ++G+
Sbjct: 126 GGSALAAALTAAALALADAGV 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 = 63.3 bits (153), Expect = 4e-14
 Identities = 19/135 (14%), Positives = 49/135 (36%), Gaps = 13/135 (9%)

Query: 4   LRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-----------KTIIDKASV 52
           +R L +++  + R  GS +F +G+T ++      +    Q           + + +    
Sbjct: 3   IRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFP 62

Query: 53  EVIFRPKSGLSFVQDRLKES--VIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCI 110
                    +   + R      + +      L T      ++    + L   GS     +
Sbjct: 63  PYSVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSV 122

Query: 111 NAACLALINSGISMR 125
            A+ ++L+N+G+ ++
Sbjct: 123 CASTMSLLNAGVPLK 137

>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 = 62.6 bits (151), Expect = 7e-14
 Identities = 20/137 (14%), Positives = 47/137 (34%), Gaps = 13/137 (9%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIF----- 56
           D LR ++   +    ++GSV+   G T V+ ++              +  +   +     
Sbjct: 10  DQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTAEYGMLPR 69

Query: 57  --------RPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSC 108
                       G    +    + +I  +  +AL        ++ +    +Q  G   + 
Sbjct: 70  STGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADGGTRTA 129

Query: 109 CINAACLALINSGISMR 125
            I  A +ALI++   ++
Sbjct: 130 SITGATVALIDALAVLK 146

>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 = 62.6 bits (151), Expect = 7e-14
 Identities = 32/130 (24%), Positives = 61/130 (46%), Gaps = 9/130 (6%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKAS---VEVIFRP 58
           D LR +K + ++L R+DGS     G+  V+A+++GP E   +       +         P
Sbjct: 15  DELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKAIIRYRYNMAP 74

Query: 59  KSGLSFVQDRLKES------VIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINA 112
            S     +            V K   E+ ++  L PR+++ + ++ LQ      + C+NA
Sbjct: 75  FSVEERKRPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACLNA 134

Query: 113 ACLALINSGI 122
           A +AL+++G+
Sbjct: 135 ASVALVDAGV 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 = 60.7 bits (146), Expect = 4e-13
 Identities = 38/132 (28%), Positives = 72/132 (54%), Gaps = 11/132 (8%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK--TIIDKASVEVIFRPK 59
             LR++++++ + +++DGS    QG T  +A +YGP E +  +   + D+A V   +   
Sbjct: 14  GELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSA 73

Query: 60  SGLSFVQDRLKES---------VIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCI 110
           +  +  + R              ++ T E+A+LT LHPR+ + + +Q LQ  G   + C+
Sbjct: 74  TFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACV 133

Query: 111 NAACLALINSGI 122
           NAA LA++++GI
Sbjct: 134 NAATLAVLDAGI 145

>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 = 59.9 bits (144), Expect = 8e-13
 Identities = 20/137 (14%), Positives = 45/137 (32%), Gaps = 13/137 (9%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIF----- 56
           D LR +  Q + L   +GS + S G+T V+ +               +  +   +     
Sbjct: 8   DQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITAEYSMLPR 67

Query: 57  --------RPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSC 108
                       G    +    + +I     +A+        ++ +    +Q  G   + 
Sbjct: 68  ATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGGTATA 127

Query: 109 CINAACLALINSGISMR 125
            I  A +A+ ++ I + 
Sbjct: 128 AITGAFVAVADAIIKLH 144

>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 = 58.7 bits (141), Expect = 4e-12
 Identities = 24/156 (15%), Positives = 42/156 (26%), Gaps = 18/156 (11%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIF----- 56
              R     +  +S +DGS +   G T V+  +     A           V  +      
Sbjct: 24  GEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLC 83

Query: 57  ----------RPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLL 106
                           S     + E+      E   ++       +   +  L   G++L
Sbjct: 84  SSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNIL 143

Query: 107 SCCINAACLALINSGISMRYI---LAAVSCIINDKN 139
             C  A   AL N  +    I    A     +  K+
Sbjct: 144 DACTFALLAALKNVQLPEVTINEETALAEVNLKKKS 179

>d2ba0g1 d.14.1.4 (G:3-178) Exosome complex exonuclease 2,ECX2 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 176

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 2,ECX2
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 56.6 bits (136), Expect = 2e-11
 Identities = 31/139 (22%), Positives = 51/139 (36%), Gaps = 15/139 (10%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVAS-MYGPVEAKIQKTIIDKASVEVIFRPKS 60
           D  R+++   N++ +++GS +   G T VV      P E            V     P +
Sbjct: 28  DEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYPDTPDRGVIIVNAELVPLA 87

Query: 61  GLSFVQDRLKESVIKST---------CESALLTMLHPR-----TSVILTIQELQDQGSLL 106
             +F      E+ I+            E+  L+ L          V + I  L D G+LL
Sbjct: 88  SPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLL 147

Query: 107 SCCINAACLALINSGISMR 125
                AA  AL+N+ +   
Sbjct: 148 DASALAAIAALMNTKVPAE 166

>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 = 56.6 bits (136), Expect = 2e-11
 Identities = 18/136 (13%), Positives = 44/136 (32%), Gaps = 15/136 (11%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQK-----------TIIDKA 50
           +  R ++ + +++S + GS     G T ++  +   +     +                A
Sbjct: 26  EDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDCSASA 85

Query: 51  SVEVIFRPKSGLSFVQDRLKESVIKST----CESALLTMLHPRTSVILTIQELQDQGSLL 106
           + E   R    L          +  +      ++  ++       + + +  L+  G+L 
Sbjct: 86  TPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLF 145

Query: 107 SCCINAACLALINSGI 122
                A   AL N+ I
Sbjct: 146 DAISIAVKAALFNTRI 161

>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 = 54.8 bits (131), Expect = 1e-10
 Identities = 30/156 (19%), Positives = 55/156 (35%), Gaps = 17/156 (10%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIF----- 56
              R L   L+   ++DGS +   G T+V+A     ++   + T      +  +      
Sbjct: 35  TDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNLIVNVELLPLA 94

Query: 57  ----------RPKSGLSFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLL 106
                          L+ V DR             ++       +V L +  L   G++L
Sbjct: 95  YETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVL 154

Query: 107 SCCINAACLALINSGISMRYILAAVSCIINDKNEVI 142
             C  A+  AL N+ +    +    + I  +KNEV+
Sbjct: 155 DACTLASVAALYNTKVYK--VEQHSNGISVNKNEVV 188

>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 = 49.1 bits (116), Expect = 1e-08
 Identities = 21/136 (15%), Positives = 44/136 (32%), Gaps = 13/136 (9%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSG 61
           D LR +   L+ +S  +GSV+ + G T V+ +               K  +   +     
Sbjct: 9   DELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPQ 68

Query: 62  LSFVQDRLKES-------------VIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSC 108
            +  Q   + S             +I     + +        ++ +    +Q  G   + 
Sbjct: 69  ATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTA 128

Query: 109 CINAACLALINSGISM 124
            I  A LA+  +   +
Sbjct: 129 SITGAFLAMAIAIGKL 144

>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 = 40.5 bits (94), Expect = 1e-05
 Identities = 18/136 (13%), Positives = 43/136 (31%), Gaps = 18/136 (13%)

Query: 2   DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKT-----------IIDKA 50
              R ++          G  I   G+T V+  +   + +                +   A
Sbjct: 30  YDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLELSQMA 86

Query: 51  SVEVIFRPKSGLSFVQDRLKESVIKSTCESALLTMLH----PRTSVILTIQELQDQGSLL 106
           +       +S L    +RL E  ++++      ++          + + +  L   G+++
Sbjct: 87  APAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNII 146

Query: 107 SCCINAACLALINSGI 122
                AA +AL +   
Sbjct: 147 DAASIAAIVALCHFRR 162

>d1e3ha2 d.14.1.4 (A:3-151) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 {Streptomyces antibioticus [TaxId: 1890]} Length = 149

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 40.1 bits (93), Expect = 2e-05
 Identities = 20/131 (15%), Positives = 39/131 (29%), Gaps = 13/131 (9%)

Query: 5   RELKSQLNILSR-SDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLS 63
           R ++ +   L+R + GS +       +V S     +    +      +V+V  R  +   
Sbjct: 18  RTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDVEERMYAAGK 77

Query: 64  FV--------QDRLKESVIKSTCESALLTML----HPRTSVILTIQELQDQGSLLSCCIN 111
                     +      +     +  L             V+ TI  L          IN
Sbjct: 78  IPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVVAIN 137

Query: 112 AACLALINSGI 122
           AA  +   +G+
Sbjct: 138 AASASTQLAGL 148

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	151
d2nn6d1	122	Exosome complex exonuclease RRP46 {Human (Homo sap	100.0
d2nn6b1	145	Exosome complex exonuclease RRP41 {Human (Homo sap	100.0
d1e3ha3	137	Polynucleotide phosphorylase/guanosine pentaphosph	100.0
d2ba0d1	144	Exosome complex exonuclease 1, ECX1 {Archaeoglobus	100.0
d1udsa1	149	Ribonuclease PH, domain 1 {Aquifex aeolicus [TaxId	100.0
d2je6b1	148	Exosome complex exonuclease 1, ECX1 {Sulfolobus so	100.0
d1r6la1	151	Ribonuclease PH, domain 1 {Pseudomonas aeruginosa	100.0
d2nn6f1	147	Exosome complex exonuclease MTR3 {Human (Homo sapi	99.97
d1oysa1	151	Ribonuclease PH, domain 1 {Bacillus subtilis [TaxI	99.97
d2ba0g1	176	Exosome complex exonuclease 2,ECX2 {Archaeoglobus	99.95
d2nn6c1	181	Exosome complex exonuclease RRP43 {Human (Homo sap	99.95
d2je6a1	191	Exosome complex exonuclease 2,ECX2 {Sulfolobus sol	99.94
d2nn6e1	187	Exosome complex exonuclease RRP42 {Human (Homo sap	99.94
d2nn6a1	184	Exosome complex exonuclease RRP45 {Human (Homo sap	99.92
d1e3ha2	149	Polynucleotide phosphorylase/guanosine pentaphosph	99.92
d1r6la2	88	Ribonuclease PH, domain 2 {Pseudomonas aeruginosa	98.12
d2ba0g2	79	Exosome complex exonuclease 2, ECX2 {Archaeoglobus	98.06
d2je6a2	84	Exosome complex exonuclease 2, ECX2 {Sulfolobus so	97.95
d1oysa2	86	Ribonuclease PH, domain 2 {Bacillus subtilis [TaxI	97.26
d2je6b2	86	Exosome complex exonuclease 1, ECX1 {Sulfolobus so	87.96

>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=100.00  E-value=2.1e-38  Score=219.06  Aligned_cols=121  Identities=50%  Similarity=0.895  Sum_probs=111.4

Q ss_pred             CCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcCCCCCCcchhhHHHHHHHHHHHHh
Q psy15057          2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRPKSGLSFVQDRLKESVIKSTCESA   81 (151)
Q Consensus         2 ~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p~~g~~~~~~~~~~~~l~~~l~~~   81 (151)
                      -|+|++++++|+++++||||+|++|+|+|+|+|+||.+.+++++.++++.++|+++|..+.++.++++++++|+++|+++
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            48999999999999999999999999999999999998877777889999999999998888888999999999999999


Q ss_pred             hcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCc
Q psy15057         82 LLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGI  122 (151)
Q Consensus        82 i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agi  122 (151)
                      |+++.||+|+|+|+++|+++||++++|++||+++||+||||
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

>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=1.5e-34  Score=204.84  Aligned_cols=122  Identities=30%  Similarity=0.521  Sum_probs=107.1

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccc--cCCCCeeEEEEEEcCCCC---------CCcchhhH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ--KTIIDKASVEVIFRPKSG---------LSFVQDRL   69 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~--~~~~~~~~v~v~~~p~~g---------~~~~~~~~   69 (151)
                      ++|+|++++++|+++++||||+|++|+|+|+|+|+||.+.++.  ++.++++.++|+++...+         .+..++++
T Consensus        13 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~~v~v~~~~~~~~~~~~~~~~~~~~~~~~   92 (145)
T d2nn6b1          13 AGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATFSTGERKRRPHGDRKSCE   92 (145)
T ss_dssp             TTSCCCEEEEESCSSSSSEEEEEEESSCEEEEEEEEEEECCSSSCCCCCSSCCEEEEEEECTTTSSSCCCTTTSTHHHHH
T ss_pred             CCCccCeEEEECCCCCCCceEEEEeCCceEEEEEEeccccccchhhccccceeEEEEeeecCcccccccccCCCCchhhh
Confidence            4799999999999999999999999999999999999866443  455788888887764221         12345667


Q ss_pred             HHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCc
Q psy15057         70 KESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGI  122 (151)
Q Consensus        70 ~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agi  122 (151)
                      ++.+|+++|+++++++.||++.|+|+++||++|||+++|++||+++||+||||
T Consensus        93 l~~~l~~~l~~~i~~~~~~~~~I~v~v~VL~~DG~l~~a~i~aa~lAL~daGI  145 (145)
T d2nn6b1          93 MGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGI  145 (145)
T ss_dssp             HHHHHHHHHHHTTCGGGCTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHhhhcccchHhhCceeeEEEEEEEeCCCCHHHHHHHHHHHHHHHcCC
Confidence            89999999999999999999999999999999999999999999999999997

>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=100.00  E-value=2.9e-34  Score=201.65  Aligned_cols=124  Identities=16%  Similarity=0.209  Sum_probs=103.2

Q ss_pred             CCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccC----CCCeeEEEEEE--cCCCC-------CCcchhh
Q psy15057          2 DSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKT----IIDKASVEVIF--RPKSG-------LSFVQDR   68 (151)
Q Consensus         2 ~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~----~~~~~~v~v~~--~p~~g-------~~~~~~~   68 (151)
                      .|+|++++++|+++++||||+|++|+|+|+|+|+||.+......    ......+.+.+  .|+.+       .++..++
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            58999999999999999999999999999999999885433211    11223344444  33221       2345677


Q ss_pred             HHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCcccc
Q psy15057         69 LKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMR  125 (151)
Q Consensus        69 ~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~  125 (151)
                      +++..++++|++++.++.||+|+|+|+++||++||++++|++||+++||+||||||+
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            889999999999999999999999999999999999999999999999999999996

>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=2.8e-34  Score=202.99  Aligned_cols=122  Identities=28%  Similarity=0.447  Sum_probs=106.8

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccc-cCCCCeeEEEEEEc--CCCC------CCcchhhHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKASVEVIFR--PKSG------LSFVQDRLKE   71 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~-~~~~~~~~v~v~~~--p~~g------~~~~~~~~~~   71 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|+||.+...+ .+.++++.+++++.  |++.      .+..++++++
T Consensus        14 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~l~   93 (144)
T d2ba0d1          14 FDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKAIIRYRYNMAPFSVEERKRPGPDRRSIEIS   93 (144)
T ss_dssp             TTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEEECCSGGGCCSSSCEEEEEEEECTTSSSSCCCSSCCHHHHHHH
T ss_pred             CCCccCeEEEECCCCCCCceEEEEEcccceEEEEeccchhhhhhcccccceEEEEEEecCCcccccccccCCCchhhhhh
Confidence            5899999999999999999999999999999999999976543 45677888777765  3322      1234566789


Q ss_pred             HHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCc
Q psy15057         72 SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGI  122 (151)
Q Consensus        72 ~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agi  122 (151)
                      .+|+++|+++++++.||+|.|+|+++||++||++++||+||+++||+||||
T Consensus        94 ~~l~~~l~~~i~~~~~~~~~i~v~v~VL~~DG~~~~a~i~aa~lAL~daGI  144 (144)
T d2ba0d1          94 KVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACLNAASVALVDAGV  144 (144)
T ss_dssp             HHHHHHHHTTBCGGGCTTEEEEEEEEEEECCTTHHHHHHHHHHHHHHHHTC
T ss_pred             hhhhhhhccccchhhcCCeEEEEEEEEEccCCCHHHHHHHHHHHHHHHcCC
Confidence            999999999999999999999999999999999999999999999999997

>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=2e-34  Score=204.80  Aligned_cols=125  Identities=16%  Similarity=0.150  Sum_probs=107.5

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEE--EEcCCCC-----------CCcchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEV--IFRPKSG-----------LSFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v--~~~p~~g-----------~~~~~~   67 (151)
                      ++|+|++++++|+++++||||+|++|+|+|+|+|++|.+.+.....++++.+.+  ++.|.++           .....+
T Consensus         7 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (149)
T d1udsa1           7 EDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITAEYSMLPRATQQRTIRESVQGRIGGRT   86 (149)
T ss_dssp             TTCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEESCCCGGGTTSSCCEEEEEEEECSEETTEECCCSSSSCCCCHHH
T ss_pred             CCCccCeEEEeCCCCCCCEEEEEEECCCEEEEEEEeeccccccccCCCceeEEeeecchhhcccccccccccccccccch
Confidence            489999999999999999999999999999999999986544455567766555  4455322           122345


Q ss_pred             hHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCcccc
Q psy15057         68 RLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMR  125 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~  125 (151)
                      ++++.++++++++++.++.||+|.|+|+++||++|||+++|++||+++||+|+||||+
T Consensus        87 ~~~~~~l~~~l~~~i~l~~~~~~~i~v~v~VL~~DG~l~da~~~A~~~AL~dagipm~  144 (149)
T d1udsa1          87 HEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGGTATAAITGAFVAVADAIIKLH  144 (149)
T ss_dssp             HHHHHHHHHHHHHHBCGGGSCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHhhhhheehhhhcCCceEEEEEEEEccCCCHHHHHHHHHHHHHHHhChHHH
Confidence            5678999999999999999999999999999999999999999999999999999998

>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=1.2e-33  Score=200.83  Aligned_cols=122  Identities=34%  Similarity=0.484  Sum_probs=106.5

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccc-cCCCCeeEEEEEEc--CCCC------CCcchhhHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQ-KTIIDKASVEVIFR--PKSG------LSFVQDRLKE   71 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~-~~~~~~~~v~v~~~--p~~g------~~~~~~~~~~   71 (151)
                      ++|+|++++++|+++++||||+|++|+|+|+|+|+||.+.... .+.++++.+++++.  |++.      .+...+++++
T Consensus        18 ~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~el~   97 (148)
T d2je6b1          18 PDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDERKNPAPSRREIELS   97 (148)
T ss_dssp             TTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECSSGGGSCSSSCEEEEEEEECTTSSSSCCCSSCCHHHHHHH
T ss_pred             CCCccCeEEEECCCCCCCEEEEEEcCCccEEeecccCccccchhhcCCcceEEEEEEEeccccccccccccccchhHHHH
Confidence            4799999999999999999999999999999999999876443 45678887766664  4322      2334566789


Q ss_pred             HHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCc
Q psy15057         72 SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGI  122 (151)
Q Consensus        72 ~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agi  122 (151)
                      .+|+++|+++++++.||++.|+|+++||++||++++|++||+++||+||||
T Consensus        98 ~~l~~~l~~~i~~~~~p~~~i~v~v~VL~~DG~~~~a~i~aa~~AL~daGI  148 (148)
T d2je6b1          98 KVIREALESAVLVELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGI  148 (148)
T ss_dssp             HHHHHHHHTTBCGGGSTTEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhhccccHHHcCCEEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCC
Confidence            999999999999999999999999999999999999999999999999997

>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=100.00  E-value=5e-33  Score=197.87  Aligned_cols=126  Identities=17%  Similarity=0.166  Sum_probs=104.6

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEE--cCCCCC-----------Ccchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIF--RPKSGL-----------SFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~--~p~~g~-----------~~~~~   67 (151)
                      ++|+|++++++|+++++||||+|++|+|+|+|+|+||.+.+...+.++++.+.+++  .|++..           ....+
T Consensus         9 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (151)
T d1r6la1           9 ADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQGWLTAEYGMLPRSTGERNQREASRGKQGGRT   88 (151)
T ss_dssp             TTCCCCEEEESSCSSSSSEEEEEEETTEEEEEEEEEEESCSSCCC---CCEEEEEEEECTTSSSSCCCCHHHHTSCCHHH
T ss_pred             CCCccCeEEEeCCCCCCCEEEEEEeCCCEEEEEEEecccccccccCCCceeEEEEEEecCccccccccccCCCccccccc
Confidence            48999999999999999999999999999999999998655445556777665555  454321           11123


Q ss_pred             hHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccc
Q psy15057         68 RLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRY  126 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~  126 (151)
                      .+++..+++.+++.++++.||++.|+|+++||++|||+++|++||+++||+|+||||+.
T Consensus        89 ~~~~~~l~~~~~~~~~l~~~~~~~i~v~v~VL~~DG~~~da~~~Aa~~AL~dagip~~~  147 (151)
T d1r6la1          89 LEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADGGTRTASITGATVALIDALAVLKK  147 (151)
T ss_dssp             HHHHHHHHHHHHHTBCGGGTCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHhhhhhccchhhhCceEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhcHHHHH
Confidence            35678999999999999999999999999999999999999999999999999999964

>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=99.97  E-value=1.7e-32  Score=193.75  Aligned_cols=123  Identities=24%  Similarity=0.311  Sum_probs=102.2

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCC------------CC--eeEEEEEEcCCCCC----
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTI------------ID--KASVEVIFRPKSGL----   62 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~------------~~--~~~v~v~~~p~~g~----   62 (151)
                      .+|+|++++++|++++++|||+|++|+|+|+|+|+||.+.++....            ..  +..+++++.|+.+.    
T Consensus         5 ~~e~R~i~i~~gvi~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (147)
T d2nn6f1           5 PTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAALRGRLLCDFRRAPFAGRRRRA   84 (147)
T ss_dssp             SSCCCCCCCCCSCCSSSSEEECCCSSSCEEEEEEEEEECC-------------------CBCEEEEEEEECTTSSSSCCC
T ss_pred             CCCccceEEEeCCCCCCCEEEEEEECCeEEEEEEeccccccccccCCccccccccccccccceeEEEEEecCCccccccc
Confidence            4899999999999999999999999999999999999876543211            12  23456666665432    


Q ss_pred             --CcchhhHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCcc
Q psy15057         63 --SFVQDRLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS  123 (151)
Q Consensus        63 --~~~~~~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip  123 (151)
                        ....+++++..+.+.|+++++++.||+|.|+|+++||++|||+++|++||+++||+||||+
T Consensus        85 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~i~v~v~Vl~~DG~l~~a~i~A~~~AL~daGIe  147 (147)
T d2nn6f1          85 PPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVE  147 (147)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTTBCSTTSBTCEEEEEEEEEECCSSHHHHHHHHHHHHHHHHCCC
T ss_pred             cCCccchhhhhhhhhhcccccccccccCCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHhCCC
Confidence              2245667899999999999999999999999999999999999999999999999999985

>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=99.97  E-value=2.7e-32  Score=194.00  Aligned_cols=124  Identities=16%  Similarity=0.147  Sum_probs=99.2

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEc--CCCC-----------CCcchh
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFR--PKSG-----------LSFVQD   67 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~--p~~g-----------~~~~~~   67 (151)
                      ++|+|++++++|+++++||||+|++|+|+|+|+|++|.+.++..+.++++.++++|.  |.+.           .....+
T Consensus         8 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (151)
T d1oysa1           8 HDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPQATNQQTIQESSKGKISGRT   87 (151)
T ss_dssp             TTCCCCEEEECC-----CCCEEEEETTEEEEEEEEEESCCCGGGTTSCCCEEEEEEEC-------------------CHH
T ss_pred             CCCccCeEEEeCCCCCCCEEEEEEEcCCEEEEEEEecccccccccccccceeeeeeeeccccccccccccccCCcccchh
Confidence            589999999999999999999999999999999998876665666677887766653  4321           122345


Q ss_pred             hHHHHHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccc
Q psy15057         68 RLKESVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISM  124 (151)
Q Consensus        68 ~~~~~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~  124 (151)
                      +.++.+++++|++++.++.||+|.|+|+++||++|||+++|++||+++||+||.+++
T Consensus        88 ~~~~~~l~~~l~~~i~l~~~~~~~i~v~v~VL~~DG~l~~a~i~Aa~~AL~dA~~~~  144 (151)
T d1oysa1          88 MEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKL  144 (151)
T ss_dssp             HHHHHHHHHHHHHTBCHHHHCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHhHHHHHHhhhhhhhhhhccceEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            577899999999999999999999999999999999999999999999999996554

>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=99.95  E-value=5.2e-28  Score=175.93  Aligned_cols=127  Identities=19%  Similarity=0.220  Sum_probs=100.2

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEE--EEEEcCCCCC------CcchhhHHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASV--EVIFRPKSGL------SFVQDRLKES   72 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v--~v~~~p~~g~------~~~~~~~~~~   72 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|+++... +....++++.+  ++++.|.+..      +...+..+++
T Consensus        27 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~~~~~-p~~~~~~~g~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~  105 (176)
T d2ba0g1          27 FDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGE-PYPDTPDRGVIIVNAELVPLASPTFEPGPPDENSIELAR  105 (176)
T ss_dssp             TTCCCCEEEEECCCTTSSEEEEEEETTEEEEEEEEEEEEC-CCTTCTTCCEEEEEEECCTTTCTTSCSSSCCHHHHHHHH
T ss_pred             CCCccCeEEEeCccCCCCeEEEEEeCCcEEEEEEeccccc-cccccCCCceeeeeeEeccccCccccCCCCCchhHHHHH
Confidence            4899999999999999999999999999999999976632 33445666655  5555664332      2234456778


Q ss_pred             HHHHHHHH--------hhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCcccccee
Q psy15057         73 VIKSTCES--------ALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYIL  128 (151)
Q Consensus        73 ~l~~~l~~--------~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~~  128 (151)
                      ++++++.+        ++..+.++.|.|+++++||++|||+++|++||+++||+|+|||+..+.
T Consensus       106 ~l~~~~~~~~~i~~e~L~i~~~~~~~~i~i~v~VL~~DG~l~dA~~~A~~~AL~da~iP~~~~~  169 (176)
T d2ba0g1         106 VVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFD  169 (176)
T ss_dssp             HHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHTTCEECTGGGT
T ss_pred             HHHHhhccccccchhhccCCCCCceEEEEEEEEEEeCCCCHHHHHHHHHHHHHHHcCCCcEEec
Confidence            88888754        333345667999999999999999999999999999999999998863

>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=99.95  E-value=5.8e-27  Score=170.06  Aligned_cols=125  Identities=18%  Similarity=0.198  Sum_probs=99.1

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeE--EEEEEcCCCCC------CcchhhHHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKAS--VEVIFRPKSGL------SFVQDRLKES   72 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~--v~v~~~p~~g~------~~~~~~~~~~   72 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|++|...+ ....++++.  +++.+.+....      +....+.+++
T Consensus        23 ~~e~R~~~i~~g~l~~a~GSa~v~~G~T~v~~~v~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (181)
T d2nn6c1          23 LGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAP-STDAPDKGYVVPNVDLPPLCSSRFRSGPPGEEAQVASQ  101 (181)
T ss_dssp             SCCCCSCCEEETCCSSSSEEEEEEETTEEEEEEEEEEECCC-CSSSTTCCCCEEEEECCSSSCTTSCSSSCCHHHHHHHH
T ss_pred             CCCccCeEEEeCCcCCCCeEEEEEeCCcEEEEEEecccccc-ccccCCCceeeeeeeeeccccccccccCCCchhhhhHH
Confidence            48999999999999999999999999999999999987543 333344444  45555543221      2334445667


Q ss_pred             HHHHHH--------HHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccc
Q psy15057         73 VIKSTC--------ESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRY  126 (151)
Q Consensus        73 ~l~~~l--------~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~  126 (151)
                      .+++.+        ++++..+.+|+|.|+|+++||++|||+++|+++|+++||.|++||+..
T Consensus       102 ~~~~~~~~~~~~~~~~l~i~~~~~~~~i~i~v~vl~~DG~l~da~~~A~~~AL~d~~iP~v~  163 (181)
T d2nn6c1         102 FIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVT  163 (181)
T ss_dssp             HHHHHHHHHCCSCHHHHCSSBTTBCEEEEEEEEESSCCSCTTHHHHHHHHHHHHTCCCCCCC
T ss_pred             HHHHHHHhhhhhhhhhccccCCcceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCCeEE
Confidence            776664        556667889999999999999999999999999999999999999743

>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=99.94  E-value=8.5e-27  Score=171.31  Aligned_cols=133  Identities=18%  Similarity=0.179  Sum_probs=101.4

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEE--EEcCCCC------CCcchhhHHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEV--IFRPKSG------LSFVQDRLKES   72 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v--~~~p~~g------~~~~~~~~~~~   72 (151)
                      .+|+|++++++|++++++|||+|++|+|+|+|+|++|... +....++++.+.+  .+.+.+.      .....++.+++
T Consensus        34 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~a~V~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  112 (191)
T d2je6a1          34 LTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDK-PYEDTPNQGNLIVNVELLPLAYETFEPGPPDENAIELAR  112 (191)
T ss_dssp             TTCCCCEEEEETCSTTSSEEEEEEETTEEEEEEEEEEEEC-CCTTCTTCCEEEEEEEECTTSCTTCCCSSCCHHHHHHHH
T ss_pred             CCCccCeEEEECCccCcCceEEEEcCCceEEEEEEecccC-chhccCccCccccccccccccccccccccCCcchhHHHH
Confidence            4799999999999999999999999999999999999854 3345566665544  4444322      12344556778


Q ss_pred             HHHHHHHH--------hhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccce-eeEEEEE
Q psy15057         73 VIKSTCES--------ALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYI-LAAVSCI  134 (151)
Q Consensus        73 ~l~~~l~~--------~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~-~~avtv~  134 (151)
                      .|++.+.+        ++..+.++.|.|+|+++||++|||+++|+++|+++||+|+|||+..+ ..++.+.
T Consensus       113 ~l~~~~~~~~~id~~~l~i~~~~~~w~I~v~v~VL~~DG~l~dA~~~A~~~AL~da~iP~v~~~~~~~~v~  183 (191)
T d2je6a1         113 VVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVN  183 (191)
T ss_dssp             HHHHHHHHTTCSCGGGGEEETTTEEEEEEEEEEEEECCSCHHHHHHHHHHHHHHTCEEEEEECC---CEEE
T ss_pred             HHHHhhcchhhcccccccccCccccEEEEEEEEEEcCCCCHHHHHHHHHHHHHHHcCCCeEEeecCceeec
Confidence            88887764        33345677899999999999999999999999999999999997543 3343433

>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=99.94  E-value=9.6e-27  Score=170.49  Aligned_cols=124  Identities=12%  Similarity=0.084  Sum_probs=99.4

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEE--EEcCCCCC------CcchhhHHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEV--IFRPKSGL------SFVQDRLKES   72 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v--~~~p~~g~------~~~~~~~~~~   72 (151)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|++|... +....++++.+.+  ++.|.++.      ++..+.++++
T Consensus        25 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~~~~~-~~~~~~~~g~~~~~v~~~~~~~~~~~~~~~~~~~~~ls~  103 (187)
T d2nn6e1          25 CEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGT-PKLEKPNEGYLEFFVDCSASATPEFEGRGGDDLGTEIAN  103 (187)
T ss_dssp             SSCCCCCEEEECCCTTSSSEEEEEETTEEEEEECCCCCSC-CCSSSCSSCCEEEECCCCTTTCSSCCTTSTHHHHHHHHH
T ss_pred             CCCccCeEEEeCccCCCCceEEEEeCCceEEEEEEecccc-ccccccccceeeeeeeeccccccCcCCCCcchHHHHHHH
Confidence            4899999999999999999999999999999999999854 3345566665555  44454322      2233446778


Q ss_pred             HHHHHHHHhh--------cccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCcccc
Q psy15057         73 VIKSTCESAL--------LTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMR  125 (151)
Q Consensus        73 ~l~~~l~~~i--------~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~  125 (151)
                      ++++.|++..        ..+.++.|.|+|+++||++||++++|+++|+++||+|++||..
T Consensus       104 ~l~~~l~~~~~~d~~~L~i~~~~~~w~i~v~v~vL~~DG~~~da~~~A~~~AL~d~~iP~v  164 (187)
T d2nn6e1         104 TLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRV  164 (187)
T ss_dssp             HHHHHHHHSCCSCSSSSCSSTTTCCCCEEEEEEECCCCSSHHHHHHHHHHHTTTTCCCCEE
T ss_pred             HHHHHhccccccchhhheecCCCccEEEEEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCEE
Confidence            8888887643        2345789999999999999999999999999999999999953

>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=99.92  E-value=1.3e-24  Score=158.73  Aligned_cols=123  Identities=10%  Similarity=0.062  Sum_probs=97.1

Q ss_pred             CCCccceEEEecCCCCCCeeEEEEeCCeEEEEEEEcCcccccccCCCCee--EEEEEEcCCCCC------CcchhhHHHH
Q psy15057          1 MDSLRELKSQLNILSRSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKA--SVEVIFRPKSGL------SFVQDRLKES   72 (151)
Q Consensus         1 ~~e~R~i~i~~g~~~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~--~v~v~~~p~~g~------~~~~~~~~~~   72 (151)
                      ++|+|++.+++|   .++|||+|++|+|+|+|+|++|... +....++++  .+++++.+.++.      +...+..+++
T Consensus        29 ~~e~R~~~i~~g---~a~GSa~v~~G~T~V~~~V~~~~~~-p~~~~~~~g~~~~~v~~~~~~~~~~~~~~~~~~~~~l~~  104 (184)
T d2nn6a1          29 TYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVS-PKLNRATEGILFFNLELSQMAAPAFEPGRQSDLLVKLNR  104 (184)
T ss_dssp             TTCCCCCEEEEC---SSTTEEEEESSSCEEEEEECCEEEC-CCSTTTTSCCEEEEEEECTTTCSSCCSSSTHHHHTHHHH
T ss_pred             CCCcCCeEEEec---CCCCEEEEEeCCCEEEEEEEecccc-ccccCCCccceeEEEEeccccCcccccCCCCchhHHHHH
Confidence            589999999999   5899999999999999999998743 334445555  556676765432      2233445678


Q ss_pred             HHHHHHHHh--------hcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCccccce
Q psy15057         73 VIKSTCESA--------LLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGISMRYI  127 (151)
Q Consensus        73 ~l~~~l~~~--------i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip~~~~  127 (151)
                      .|++.+...        +.++.++.|.|+|+++||++|||+++|+++|+++||+|++||...+
T Consensus       105 ~l~~~~~~~~~~d~~~L~i~~~~~~w~i~i~v~VL~~DG~~~da~~~a~~~AL~~~~iP~v~v  167 (184)
T d2nn6a1         105 LMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSV  167 (184)
T ss_dssp             HHHHHHHHHTCBCSSSSCSBTTTBEEEEEEEEEECSCCSCCHHHHHHHHHHHHHHCCCCCCBC
T ss_pred             HHHhhhhhhhhhhhhhhccccccCcEEEEEEEEEECCCCCHHHHHHHHHHHHHHhhCCCeEEE
Confidence            888777653        3345667899999999999999999999999999999999997654

>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=99.92  E-value=3.4e-24  Score=152.02  Aligned_cols=119  Identities=18%  Similarity=0.141  Sum_probs=96.2

Q ss_pred             cceEEEecCCC-CCCeeEEEEeCCeEEEEEEEcCcccccccCCCCeeEEEEEEcC-C-----------CCCCcchhhHHH
Q psy15057          5 RELKSQLNILS-RSDGSVIFSQGQTVVVASMYGPVEAKIQKTIIDKASVEVIFRP-K-----------SGLSFVQDRLKE   71 (151)
Q Consensus         5 R~i~i~~g~~~-~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~v~v~~~p-~-----------~g~~~~~~~~~~   71 (151)
                      |+|++++|+++ +|||||+|++|+|+|+|+++++.+..........+.++...+. .           .|.++.++.+.+
T Consensus        18 R~i~ie~G~lakqA~GSalv~~G~T~vl~ta~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~rre~~~~~reil~~   97 (149)
T d1e3ha2          18 RTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDVEERMYAAGKIPGSFFRREGRPSEDAILTC   97 (149)
T ss_dssp             EEEEEEESSSCTTSSEEEEEEETTTEEEEEEEEECSSCCTTCSSCCEEEEEEECGGGGTCCCCSTTSSCCSCCHHHHHHH
T ss_pred             cEEEEEeCcccccCCceEEEEECCcEEEEEeeecccccccccccCCceeEEEEeccccccccccccccccccchHHHHHH
Confidence            99999999996 7999999999999999999876543222333445555554432 1           112344556678


Q ss_pred             HHHHHHHHHhhcccCCCCcEEEEEEEEEeCCCChhHHHHHHHHHHHHhcCcc
Q psy15057         72 SVIKSTCESALLTMLHPRTSVILTIQELQDQGSLLSCCINAACLALINSGIS  123 (151)
Q Consensus        72 ~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~dG~~l~a~inaa~lAL~~agip  123 (151)
                      ++++|.|+++++.+.++..+|.+++.+++.||+...+++||+++||++||||
T Consensus        98 rlidR~Lrpl~p~~~~~~~qI~~~vl~~d~d~~~~~aai~aAs~AL~~agIP  149 (149)
T d1e3ha2          98 RLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLP  149 (149)
T ss_dssp             HHHHHHHHHHBCTTBCSCEEEEEEEEECCTTSCCHHHHHHHHHHHHHHTTCS
T ss_pred             HHHHHHHHhhccccCCCceEEEEEEEEeCCCCChHHHHHHHHHHHHHhcCCC
Confidence            9999999999999999999999999999999999999999999999999998

>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=98.12  E-value=8e-07  Score=56.06  Aligned_cols=29  Identities=28%  Similarity=0.405  Sum_probs=27.3

Q ss_pred             CccccceeeEEEEEEecCCeEEeCCCcccc
Q psy15057        121 GISMRYILAAVSCIINDKNEVILDANQIQS  150 (151)
Q Consensus       121 gip~~~~~~avtv~~~~~~~~lvDpt~~Ee  150 (151)
                      |+||++.++||++|++ ||++++|||..|+
T Consensus         2 g~P~~~~VaavsvG~i-dg~~vld~~~~E~   30 (88)
T d1r6la2           2 GNPLKQMVAAVSVGIY-QGVPVLDLDYLED   30 (88)
T ss_dssp             SCCBCCCEEEEEEEEE-TTEEEESCCHHHH
T ss_pred             CCCcCCCccEEEEEEE-CCEEEecCcHHhh
Confidence            8999999999999999 5999999999886

>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=98.06  E-value=1.5e-06  Score=53.64  Aligned_cols=28  Identities=18%  Similarity=0.341  Sum_probs=26.1

Q ss_pred             cccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057        123 SMRYILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus       123 p~~~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                      |++++|+++|++++ ++++|+|||.+||.
T Consensus         1 Pv~~~Pv~vT~~~~-~~~~lvDpt~eEE~   28 (79)
T d2ba0g2           1 PVRDLPVSVTSLIV-GNKYLVDPSREEMS   28 (79)
T ss_dssp             CBCCCCEEEEEEEE-TTEEEESCCTTGGG
T ss_pred             CCCCceEEEEEEEE-CCEEEECCCHHHHh
Confidence            78999999999999 58999999999984

>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=97.95  E-value=2.2e-06  Score=53.28  Aligned_cols=28  Identities=11%  Similarity=0.255  Sum_probs=25.9

Q ss_pred             cccceeeEEEEEEecCCeEEeCCCccccC
Q psy15057        123 SMRYILAAVSCIINDKNEVILDANQIQSN  151 (151)
Q Consensus       123 p~~~~~~avtv~~~~~~~~lvDpt~~Ee~  151 (151)
                      |+++.|+++|+|++ ++.+|+|||.+||.
T Consensus         1 P~~~~~~~vt~~~i-~~~~lvDpt~~EE~   28 (84)
T d2je6a2           1 PLNYPVVTISVAKV-DKYLVVDPDLDEES   28 (84)
T ss_dssp             CCSCCCEEEEEEEE-TTEEEESCCHHHHH
T ss_pred             CCCCCeEEEEEEEE-CCEEEecCCHHHHH
Confidence            89999999999999 58999999999983

>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=97.26  E-value=9.4e-05  Score=45.96  Aligned_cols=29  Identities=28%  Similarity=0.352  Sum_probs=24.9

Q ss_pred             ccccceeeEEEEEEecCCeEEeCCCcccc
Q psy15057        122 ISMRYILAAVSCIINDKNEVILDANQIQS  150 (151)
Q Consensus       122 ip~~~~~~avtv~~~~~~~~lvDpt~~Ee  150 (151)
                      .||++.++||++|+++++.+++||++.|+
T Consensus         2 ~P~~~~VaavsvG~i~~~~vlldl~~~Ed   30 (86)
T d1oysa2           2 NPITDFLAAISVGIDKEQGILLDLNYEED   30 (86)
T ss_dssp             CCBCSCEEEEEEEEETTTEEEESCCHHHH
T ss_pred             CCccCcccEEEEEEEcCCcEECCCHHHHh
Confidence            59999999999999964457889999886

>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=87.96  E-value=0.16  Score=30.34  Aligned_cols=15  Identities=33%  Similarity=0.388  Sum_probs=14.1

Q ss_pred             cccceeeEEEEEEec
Q psy15057        123 SMRYILAAVSCIIND  137 (151)
Q Consensus       123 p~~~~~~avtv~~~~  137 (151)
                      ||+++++||++|+++
T Consensus         1 Pm~d~V~avsvg~~d   15 (86)
T d2je6b2           1 PMRDLIAGVAVGKAD   15 (86)
T ss_dssp             CBSSCCEEEEEEEET
T ss_pred             CCCCCeEEEEEEEEC
Confidence            899999999999994