Citrus Sinensis ID: 026213

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-
Protein Sequence
MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRRGL
Secondary Structure (PSIPRED)
ccccccccccccccccccccEEEEEEccccccccEEEEEEccEEEEEEEEcccccccccccccccEEEEEEEEEccccccccccccccccHHHHHHHHHHHHHHHHHccccccccEEEEEEEEEEccccHHHHHHHHHHHHHHHcccccccEEEEEEEEEEccEEEEEccccccccccccEEEEEEcccccEEEEEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccEEEcccccccccccccEEEEEEEEcEccccccEEEEEEccEEEEEEEEcccccccccccccccEEEEEEEcccccccccccccccccHHHHHHHHHHHcccccccccccccccEEEEEEEEEcccccccHHHHHHHHHHHHHccccccccEEEEEEEEEccEEEEcccccHHHcccccccEEEEcccccEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccc
Coil and Loop (DISEMBL)
mefvspeglrldgrrptEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAvygprevqnksqqmSDQALVRCEYSmanfstgdrmrkpkgdrrsTEISLVIRQTMEACIlthlmprsQIDIFVQVLqadggtrsACINAATLAlqdagipmrdivtscsagylnstplldlnyvedsaggpdvtvgilptlDKVTLLQmdaklptntfEDVMQLAIEGCKAVANYIREVLLENTkqlecrrgl
Flexible Loop (DISEMBL)
mefvspeglrldgrrpteMRQLRAEIGnvakadgsavFEMGNTKVIAAVYgprevqnksqqmsdqALVRCEYSManfstgdrmrkpkgdrrsTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLlentkqlecrrgl
Low Complexity Region (SEG)
MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRRGL
Disordered region (IsUnstruct)
********************************DGSAVFEMGNTKVIAAVYG*****************RC************************ISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENT*********
Disordered Region (DISOPRED)
MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYG***************LVRCEYSMA**********************VIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLE*RRG*
Disordered Region (DISEMBL)
MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPRE*********DQALVRCEYSMANFSTG*************EISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRRGL
Disordered Region (DISPRO)
*EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLEN**********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRRGL
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	241	2.2.26 [Sep-21-2011]
Q921I9	245	Exosome complex component	yes	no	0.970	0.955	0.510	3e-69
Q9NPD3	245	Exosome complex component	yes	no	0.970	0.955	0.510	5e-69
Q7YRA3	245	Exosome complex component	yes	no	0.970	0.955	0.510	1e-68
Q5JIR6	249	Probable exosome complex	yes	no	0.954	0.923	0.489	1e-59
Q8U0L9	250	Probable exosome complex	yes	no	0.954	0.92	0.489	2e-58
B6YSI2	249	Probable exosome complex	yes	no	0.954	0.923	0.489	2e-58
C5A2B9	249	Probable exosome complex	yes	no	0.954	0.923	0.480	4e-58
Q9V119	249	Probable exosome complex	yes	no	0.954	0.923	0.480	9e-58
O59223	249	Probable exosome complex	yes	no	0.954	0.923	0.476	2e-57
Q8TYC1	239	Probable exosome complex	yes	no	0.946	0.953	0.484	4e-57

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

 Score =  261 bits (667), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 120/235 (51%), Positives = 175/235 (74%), Gaps = 1/235 (0%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQ-NKS 59
           +E +S +G R+DGRR  E+R+++A +G  A+ADGSA  E GNTK +A VYGP E++ ++S
Sbjct: 4   LELLSDQGYRIDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRS 63

Query: 60  QQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDI 119
           + + D+ALV C+YS A FSTG+R R+P GDR+S E+ L +RQT EA ILT L PRSQIDI
Sbjct: 64  RALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDI 123

Query: 120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGP 179
           +VQVLQADGGT +AC+NAATLA+ DAGIPMRD V +CSAG+++ T L DL++VE++AGGP
Sbjct: 124 YVQVLQADGGTYAACVNAATLAVMDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAGGP 183

Query: 180 DVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ 234
            + + +LP   ++ LL+MD++L  +  E V++ A +  + V   +  V+ ++ ++
Sbjct: 184 QLALALLPASGQIALLEMDSRLHEDHLEQVLEAAAQAARGVHTLLDLVVRQHVQE 238

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

 Score =  260 bits (665), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 120/235 (51%), Positives = 175/235 (74%), Gaps = 1/235 (0%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQ-NKS 59
           +E +S +G R+DGRR  E+R+++A +G  A+ADGSA  E GNTK +A VYGP E++ +++
Sbjct: 4   LELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRA 63

Query: 60  QQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDI 119
           + + D+ALV C+YS A FSTG+R R+P GDR+S E+ L +RQT EA ILT L PRSQIDI
Sbjct: 64  RALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDI 123

Query: 120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGP 179
           +VQVLQADGGT +AC+NAATLA+ DAGIPMRD V +CSAG+++ T L DL++VE++AGGP
Sbjct: 124 YVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAGGP 183

Query: 180 DVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ 234
            + + +LP   ++ LL+MDA+L  +  E V++ A +  + V   +  V+ ++ ++
Sbjct: 184 QLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVRE 238

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

 Score =  259 bits (662), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 120/235 (51%), Positives = 174/235 (74%), Gaps = 1/235 (0%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQ-NKS 59
           +E +S +G R+DGRR  E+R+++A +G  A+ADGSA  E GNTK +A VYGP E++ +++
Sbjct: 4   LELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRA 63

Query: 60  QQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDI 119
           + + D+ALV C+YS A FSTG+R R+P GDR+S E+ L +RQT EA ILT L PRSQIDI
Sbjct: 64  RALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDI 123

Query: 120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGP 179
           +VQVLQADGGT +AC+NAATLA+ DAGIPMRD V +CSAG+++ T L DL++VE++AGGP
Sbjct: 124 YVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAGGP 183

Query: 180 DVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ 234
            + + +LP   ++ LL+MDA+L  +  E V++ A    + V   +  V+ ++ ++
Sbjct: 184 QLALALLPASGQIALLEMDARLHEDHLEQVLEAAARASRDVHTVLDRVVRQHVQE 238

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|Q5JIR6|ECX1_PYRKO Probable exosome complex exonuclease 1 OS=Pyrococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) GN=TK1634 PE=3 SV=1

 Score =  229 bits (585), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 113/231 (48%), Positives = 156/231 (67%), Gaps = 1/231 (0%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
           ++ +   G R+DGR+  E+R ++ E+G +  ADGSA  E G  KV+AAVYGPRE+  K  
Sbjct: 8   LKLIDENGKRIDGRKKYELRPIKMEVGVLKNADGSAYVEWGKNKVLAAVYGPREIHPKHL 67

Query: 61  QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
           Q  D+A++R  Y+MA FS  +R +KP  DRRS EIS VIR  +E  +L H+ PR+ ID+F
Sbjct: 68  QRPDRAILRVRYNMAPFSVEER-KKPGPDRRSVEISKVIRGALEPALLLHMFPRTAIDVF 126

Query: 121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180
           +++LQAD GTR A I AA+LAL DAGIPM+D+V +C+AG ++   +LDLN  ED+ G  D
Sbjct: 127 IEILQADAGTRVAGITAASLALADAGIPMKDLVAACAAGKIDGEIVLDLNKEEDNYGEAD 186

Query: 181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLEN 231
           V V I+P  + +TLLQMD  L  + F + ++LAI+G KAV    RE L E 
Sbjct: 187 VPVAIMPLKNDITLLQMDGYLTKDEFLEAVRLAIKGAKAVYQKQREALKEK 237

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

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

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|Q8U0L9|ECX1_PYRFU Probable exosome complex exonuclease 1 OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) GN=PF1568 PE=3 SV=1

 Score =  225 bits (574), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 113/231 (48%), Positives = 153/231 (66%), Gaps = 1/231 (0%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
           ++ +   G RLDGR+  E+R ++ ++G +  A+GSA  E G  K+IAAVYGPRE+  K  
Sbjct: 8   LKLIDENGRRLDGRKKYELRPIKMKVGVLKNANGSAYIEWGKNKIIAAVYGPREIHPKHL 67

Query: 61  QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
           Q  D+A++R  Y+MA FS  +R +KP  DRRS EIS VIR  +E  ++  + PR+ ID+F
Sbjct: 68  QRPDRAILRVRYNMAPFSVEER-KKPGPDRRSIEISKVIRGALEPALILEMFPRTAIDVF 126

Query: 121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180
           ++VLQAD GTR A I AA+LAL DAGIPMRD+V +CSAG +    +LDLN  ED+ G  D
Sbjct: 127 IEVLQADAGTRVAGITAASLALADAGIPMRDLVAACSAGKIEGEIVLDLNKEEDNYGEAD 186

Query: 181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLEN 231
           V V I+P  + +TLLQMD  L    F + ++LAI+G KAV    RE L E 
Sbjct: 187 VPVAIMPIKNDITLLQMDGYLTKEEFIEAVKLAIKGAKAVYQKQREALKEK 237

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

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

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|B6YSI2|ECX1_THEON Probable exosome complex exonuclease 1 OS=Thermococcus onnurineus (strain NA1) GN=TON_0030 PE=3 SV=1

 Score =  225 bits (574), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 113/231 (48%), Positives = 154/231 (66%), Gaps = 1/231 (0%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
           ++ +   G R+DGR+  E+R ++ E+G +  ADGSA  E G  K++AAVYGPRE+  K  
Sbjct: 8   LKLIDENGRRIDGRKKYELRPIKMEVGVLKNADGSAYVEWGKNKILAAVYGPREIHPKHL 67

Query: 61  QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
           Q  D+A++R  Y+MA FS  +R +KP  DRRS EIS VIR  +E  ++  + PR+ IDIF
Sbjct: 68  QRPDRAILRVRYNMAPFSVEER-KKPGPDRRSVEISKVIRGALEPALILEMFPRTAIDIF 126

Query: 121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180
           ++VLQAD GTR A I AA+LAL DAGIPMRD+V +C+AG +    +LDLN  ED+ G  D
Sbjct: 127 IEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKIEGEIVLDLNKEEDNYGEAD 186

Query: 181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLEN 231
           V V I+P  + +TLLQMD  L  + F + ++LAI+G KAV    RE L E 
Sbjct: 187 VPVAIMPLKNDITLLQMDGYLTRDEFIEAVRLAIKGAKAVYQKQREALKEK 237

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

Thermococcus onnurineus (strain NA1) (taxid: 523850)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|C5A2B9|ECX1_THEGJ Probable exosome complex exonuclease 1 OS=Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3) GN=TGAM_2036 PE=3 SV=1

 Score =  224 bits (571), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 111/231 (48%), Positives = 153/231 (66%), Gaps = 1/231 (0%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
           ++ +   G R+DGRR  E+R++  E+G +  ADGSA  E G  K++AAVYGPRE+  K  
Sbjct: 8   LKLIDENGRRIDGRRKYELRKIHMEVGVLKNADGSAYIEWGKNKILAAVYGPREIHPKHL 67

Query: 61  QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
           Q  D A++R  Y+MA FS  +R +KP  DRRS EIS VIR  +E  ++  + PR+ +D+F
Sbjct: 68  QRPDTAVLRVRYNMAPFSVEER-KKPGPDRRSVEISKVIRGALEPALILEMFPRTVVDVF 126

Query: 121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180
           ++VLQAD GTR A I AA+LAL DAG+PMRD+V +C+AG ++   +LDLN  ED+ G  D
Sbjct: 127 IEVLQADAGTRVAGITAASLALADAGVPMRDLVAACAAGKIDGEIVLDLNKDEDNYGEAD 186

Query: 181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLEN 231
           V V I+P  + +TLLQMD  L    F + ++LAI+G KAV    RE L E 
Sbjct: 187 VPVAIMPLKNDITLLQMDGYLTKEEFIEAVKLAIKGAKAVYQKQREALKEK 237

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

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

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|Q9V119|ECX1_PYRAB Probable exosome complex exonuclease 1 OS=Pyrococcus abyssi (strain GE5 / Orsay) GN=PYRAB06100 PE=1 SV=1

 Score =  223 bits (568), Expect = 9e-58,   Method: Compositional matrix adjust.
 Identities = 111/231 (48%), Positives = 154/231 (66%), Gaps = 1/231 (0%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
           ++ +   G R+DGR+  E+R ++ E+G +  A+GSA  E G  K+IAAVYGPRE+  K  
Sbjct: 8   LKLIDENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHL 67

Query: 61  QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
           Q  D+A++R  Y+MA FS  +R +KP  DRRS EIS VI+  +E  ++  + PR+ ID+F
Sbjct: 68  QRPDRAILRVRYNMAPFSVEER-KKPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVF 126

Query: 121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180
           ++VLQAD GTR A I AA+LAL DAGIPMRD+V +C+AG +    +LDLN  ED+ G  D
Sbjct: 127 IEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKIEGEIVLDLNKEEDNYGEAD 186

Query: 181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLEN 231
           V V I+P  + +TLLQMD  L  + F + ++LAI+G KAV    RE L E 
Sbjct: 187 VPVAIMPLKNDITLLQMDGYLTKDEFIEAVKLAIKGAKAVYQKQREALKEK 237

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

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

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

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

 Score =  222 bits (565), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 110/231 (47%), Positives = 154/231 (66%), Gaps = 1/231 (0%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
           ++ +   G R+DGR+  E+R ++ ++G +  A+GSA  E G  K+IAAVYGPRE+ +K  
Sbjct: 8   LKLIDENGRRIDGRKKYELRPIKMKVGVLKNANGSAYIEWGRNKIIAAVYGPRELHSKHL 67

Query: 61  QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
           Q  D+A++R  Y+MA FS  +R +KP  DRRS EIS VI+  +E  ++  + PR+ ID+F
Sbjct: 68  QRPDRAILRVRYNMAPFSVEER-KKPGPDRRSIEISKVIKGALEPALILEMFPRTSIDVF 126

Query: 121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180
           ++VLQAD GTR A I AA+LAL DAGIPMRD+V +C+AG +    +LDLN  ED+ G  D
Sbjct: 127 IEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKIEGEIVLDLNKEEDNYGEAD 186

Query: 181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLEN 231
           V V I+P  + +TLLQMD  L    F + ++LAI+G KAV    RE L E 
Sbjct: 187 VPVAIMPLKNDITLLQMDGYLTKEEFIEAVRLAIKGAKAVYQKQREALKEK 237

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

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

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|Q8TYC1|ECX1_METKA Probable exosome complex exonuclease 1 OS=Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938) GN=MK0381 PE=3 SV=1

 Score =  221 bits (562), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 111/229 (48%), Positives = 151/229 (65%), Gaps = 1/229 (0%)

Query: 3   FVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQM 62
            +S +GLRLDGR+P EMR L+ + G + +ADGSA  E+G  K++AAVYGPRE+  + +Q 
Sbjct: 8   LISEDGLRLDGRKPDEMRPLKIQAGVLKRADGSAYLELGANKIVAAVYGPRELHPRHKQK 67

Query: 63  SDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQ 122
            D+A+VR  Y+MA FS  +R R P  DRRS EIS + ++ +E  I T   PR+ IDIFV+
Sbjct: 68  PDRAVVRFRYNMAPFSVDERKR-PGPDRRSIEISKLSKEALEPAIFTEYYPRTAIDIFVE 126

Query: 123 VLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVT 182
           VLQAD GTR A I+AA++AL DAGI MRD+V +C+AG +    +LD  Y ED  G  DV 
Sbjct: 127 VLQADAGTRCAGISAASVALADAGIEMRDLVAACAAGKVEGKVVLDPMYYEDGYGEADVP 186

Query: 183 VGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLEN 231
           + ++P   K+TLLQMD  +    F+  ++LA +GCK V    R  L E 
Sbjct: 187 LAMMPKEGKITLLQMDGDMTPGEFKQAVKLAKKGCKIVYKEQRRALKEK 235

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

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

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

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	241
225454436	241	PREDICTED: exosome complex component RRP	0.995	0.995	0.925	1e-127
255579328	241	Exosome complex exonuclease RRP41, putat	1.0	1.0	0.912	1e-127
224130470	241	predicted protein [Populus trichocarpa]	1.0	1.0	0.908	1e-125
356562860	241	PREDICTED: exosome complex component RRP	1.0	1.0	0.892	1e-125
357512489	241	Exosome complex exonuclease RRP41 [Medic	0.995	0.995	0.895	1e-124
356573193	241	PREDICTED: exosome complex component RRP	1.0	1.0	0.879	1e-123
449451735	241	PREDICTED: exosome complex component RRP	0.991	0.991	0.878	1e-121
218201746	242	hypothetical protein OsI_30553 [Oryza sa	0.995	0.991	0.838	1e-113
242088177	242	hypothetical protein SORBIDRAFT_09g02255	0.995	0.991	0.838	1e-113
357132600	242	PREDICTED: exosome complex component RRP	0.995	0.991	0.834	1e-113

>gi|225454436|ref|XP_002280302.1| PREDICTED: exosome complex component RRP41 [Vitis vinifera] gi|147867252|emb|CAN81194.1| hypothetical protein VITISV_022853 [Vitis vinifera] gi|297745390|emb|CBI40470.3| unnamed protein product [Vitis vinifera]

 Score =  460 bits (1184), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 222/240 (92%), Positives = 231/240 (96%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
           MEFVSPEGLRLDGRRP EMRQ+R EIG VAKADGSA FEMGNTKVIAAVYGPREV+N+SQ
Sbjct: 1   MEFVSPEGLRLDGRRPMEMRQIRGEIGAVAKADGSAFFEMGNTKVIAAVYGPREVENRSQ 60

Query: 61  QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
           Q+SDQALVRCEY+MANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF
Sbjct: 61  QISDQALVRCEYTMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120

Query: 121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180
           VQVLQADGGTRSACINAATLAL DAGIPMRD+VTSCSAGYLNSTPLLDLNYVEDSAGGPD
Sbjct: 121 VQVLQADGGTRSACINAATLALADAGIPMRDLVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180

Query: 181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRRG 240
           VTVGILP LDKVTLLQMDAKLP + FE+VMQLAIEGCKA+ANYIREVLLENTKQLE RRG
Sbjct: 181 VTVGILPKLDKVTLLQMDAKLPMDIFENVMQLAIEGCKAIANYIREVLLENTKQLEYRRG 240

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255579328|ref|XP_002530509.1| Exosome complex exonuclease RRP41, putative [Ricinus communis] gi|223529966|gb|EEF31893.1| Exosome complex exonuclease RRP41, putative [Ricinus communis]

 Score =  460 bits (1183), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 220/241 (91%), Positives = 233/241 (96%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
           ME+VSPEGLRLDGRRP EMRQLRA+IG V+KADGSAVFEMGNTKVIAAVYGPREVQN+SQ
Sbjct: 1   MEYVSPEGLRLDGRRPMEMRQLRAQIGAVSKADGSAVFEMGNTKVIAAVYGPREVQNRSQ 60

Query: 61  QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
           Q+ DQALVRCEY+MANFSTGDRMRKPKGDRRSTEISLVIRQTME CILTHLMPRSQIDI+
Sbjct: 61  QIIDQALVRCEYTMANFSTGDRMRKPKGDRRSTEISLVIRQTMEECILTHLMPRSQIDIY 120

Query: 121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180
           VQVLQADGGTRSACINAATLAL DAGIPMRD+VTSCSAGYLNSTPLLDLNYVEDSAGGPD
Sbjct: 121 VQVLQADGGTRSACINAATLALADAGIPMRDLVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180

Query: 181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRRG 240
           VTVGILP LDKVTLLQMDAKLP +TFE+VMQLA+EGCKA+ANYIRE+LLENTKQLE RRG
Sbjct: 181 VTVGILPKLDKVTLLQMDAKLPIDTFENVMQLAVEGCKAIANYIREILLENTKQLEYRRG 240

Query: 241 L 241
           L
Sbjct: 241 L 241

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224130470|ref|XP_002320845.1| predicted protein [Populus trichocarpa] gi|118489833|gb|ABK96716.1| unknown [Populus trichocarpa x Populus deltoides] gi|222861618|gb|EEE99160.1| predicted protein [Populus trichocarpa]

 Score =  454 bits (1168), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 219/241 (90%), Positives = 232/241 (96%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
           MEFV+PEGLRLDGRRP EMRQLRA+IG VAKADGSAVFEMGNTKVIAAVYGPREVQN+SQ
Sbjct: 1   MEFVNPEGLRLDGRRPMEMRQLRAQIGAVAKADGSAVFEMGNTKVIAAVYGPREVQNRSQ 60

Query: 61  QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
           Q++DQALVRCEYSMANFSTGDR RKPKGDRRSTEISLVIRQ ME CILT+LMPRSQIDI+
Sbjct: 61  QINDQALVRCEYSMANFSTGDRRRKPKGDRRSTEISLVIRQAMEECILTNLMPRSQIDIY 120

Query: 121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180
           VQVLQADGGTRSACINAATLAL DAGIPMRD+VTSCSAG+LNSTPLLDLNYVEDSAGGPD
Sbjct: 121 VQVLQADGGTRSACINAATLALADAGIPMRDLVTSCSAGFLNSTPLLDLNYVEDSAGGPD 180

Query: 181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRRG 240
           VTVGILP LDKVTLLQMDAKLP +TFE+VMQLA+EGCKA+ANYIREVLLENTKQLE RRG
Sbjct: 181 VTVGILPKLDKVTLLQMDAKLPIDTFENVMQLAVEGCKAIANYIREVLLENTKQLEYRRG 240

Query: 241 L 241
           L
Sbjct: 241 L 241

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356562860|ref|XP_003549686.1| PREDICTED: exosome complex component RRP41-like [Glycine max]

 Score =  452 bits (1163), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 215/241 (89%), Positives = 231/241 (95%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
           ME+VSPEGLRLDGRRP EMRQ+RAEIG V+KADGSA+FEMGNTKVIAAVYGPREVQN++Q
Sbjct: 1   MEYVSPEGLRLDGRRPMEMRQIRAEIGAVSKADGSAIFEMGNTKVIAAVYGPREVQNRNQ 60

Query: 61  QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
           Q+S  ALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHL+PRSQIDI+
Sbjct: 61  QISSHALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLLPRSQIDIY 120

Query: 121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180
           VQVLQADGGTRSACINAATLAL DAGIPMRD+VTSCSAGYLNSTPLLDLNYVEDSAGGPD
Sbjct: 121 VQVLQADGGTRSACINAATLALADAGIPMRDLVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180

Query: 181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRRG 240
           VT+GILP LDKVTLLQMD+KLP +  E+VMQLAIEGCKA+ANYIREVLLENTKQLE RRG
Sbjct: 181 VTLGILPKLDKVTLLQMDSKLPIDILENVMQLAIEGCKAIANYIREVLLENTKQLEYRRG 240

Query: 241 L 241
           +
Sbjct: 241 V 241

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357512489|ref|XP_003626533.1| Exosome complex exonuclease RRP41 [Medicago truncatula] gi|355501548|gb|AES82751.1| Exosome complex exonuclease RRP41 [Medicago truncatula]

 Score =  450 bits (1157), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 215/240 (89%), Positives = 228/240 (95%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
           ME+VSPEGLR DGRRP EMRQ+RAEIG V+KADGSA+FEMGNTKVIAAVYGPREVQN+SQ
Sbjct: 1   MEYVSPEGLRSDGRRPMEMRQIRAEIGAVSKADGSAIFEMGNTKVIAAVYGPREVQNRSQ 60

Query: 61  QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
           QMSD+ALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTME CILTHLMPRSQIDI+
Sbjct: 61  QMSDKALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEECILTHLMPRSQIDIY 120

Query: 121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180
           VQVLQADGGTRSACINAATLAL DAGIPM D+VTSCSAGYLNSTPLLDLNYVEDSAGGPD
Sbjct: 121 VQVLQADGGTRSACINAATLALADAGIPMLDLVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180

Query: 181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRRG 240
           VTVGILP LDKVTLLQMD+KLP +  E+VMQLA EGCKA+ANYIRE+LLENTKQLE RRG
Sbjct: 181 VTVGILPKLDKVTLLQMDSKLPIDILENVMQLATEGCKAIANYIREILLENTKQLEYRRG 240

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356573193|ref|XP_003554748.1| PREDICTED: exosome complex component RRP41-like [Glycine max]

 Score =  446 bits (1146), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 212/241 (87%), Positives = 228/241 (94%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
           ME+VSPEGLRLDGRRP EMRQ+RAEIG V+KADGSA+FEMGNTKVIAAVYGPREVQN+SQ
Sbjct: 1   MEYVSPEGLRLDGRRPMEMRQIRAEIGAVSKADGSAIFEMGNTKVIAAVYGPREVQNRSQ 60

Query: 61  QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
           Q+S  ALVRCEY MANFSTGDRMRK KGDRRSTEISLVIRQTMEACILTHL+PRSQIDI+
Sbjct: 61  QISSHALVRCEYCMANFSTGDRMRKSKGDRRSTEISLVIRQTMEACILTHLLPRSQIDIY 120

Query: 121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180
           VQVLQADGGTRSACINAATLAL DAGIPMRD+VTSCSAGYLNSTPLLDLNYVEDSAGGPD
Sbjct: 121 VQVLQADGGTRSACINAATLALADAGIPMRDLVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180

Query: 181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRRG 240
           VT+GILP LDKVTLLQMD+KLP +  E+VMQLAIEGCKA+ANYIRE+LL NTKQLE RRG
Sbjct: 181 VTLGILPKLDKVTLLQMDSKLPIDILENVMQLAIEGCKAIANYIREILLANTKQLEYRRG 240

Query: 241 L 241
           +
Sbjct: 241 V 241

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449451735|ref|XP_004143616.1| PREDICTED: exosome complex component RRP41-like [Cucumis sativus] gi|449516461|ref|XP_004165265.1| PREDICTED: exosome complex component RRP41-like [Cucumis sativus]

 Score =  438 bits (1127), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 210/239 (87%), Positives = 224/239 (93%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
           MEFV+PEGLR DGRRP E+R++RAEIG V+KA+GSAVFEMGNTKV+AAVYGPREVQNKSQ
Sbjct: 1   MEFVTPEGLRQDGRRPRELREMRAEIGAVSKANGSAVFEMGNTKVLAAVYGPREVQNKSQ 60

Query: 61  QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
           QMS+QALVRCEY+MANFSTGDRMRKPKGDRRSTEISLVIRQTME CILTHLMPRSQIDIF
Sbjct: 61  QMSNQALVRCEYTMANFSTGDRMRKPKGDRRSTEISLVIRQTMEECILTHLMPRSQIDIF 120

Query: 121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180
           VQVLQADGGTRSACINAATLAL DAGIPMRDIVTSCSAGYLNS  LLDLNYVEDSAGGPD
Sbjct: 121 VQVLQADGGTRSACINAATLALADAGIPMRDIVTSCSAGYLNSNALLDLNYVEDSAGGPD 180

Query: 181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRR 239
           VTVG LP LDKVTLLQMDAKLP + FEDVM+LAIEGCKA+A YIR V+LE+TKQLE  R
Sbjct: 181 VTVGFLPKLDKVTLLQMDAKLPIDVFEDVMELAIEGCKAIATYIRNVMLEHTKQLEYHR 239

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218201746|gb|EEC84173.1| hypothetical protein OsI_30553 [Oryza sativa Indica Group] gi|222641142|gb|EEE69274.1| hypothetical protein OsJ_28540 [Oryza sativa Japonica Group]

 Score =  414 bits (1065), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 203/242 (83%), Positives = 221/242 (91%), Gaps = 2/242 (0%)

Query: 1   MEFVSP-EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKS 59
           ME+V+P  G R+DGRRP EMRQL+ E+G VA+ADGSA+FEMGNT+VIAAVYGPREVQNK 
Sbjct: 1   MEYVNPLTGFRVDGRRPNEMRQLKGEVGVVARADGSALFEMGNTRVIAAVYGPREVQNKG 60

Query: 60  QQM-SDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQID 118
           QQ+ S  ALVRCEY MA+FSTGDR RKPKGDRRSTEISLVIRQTMEA ILTHLMPRSQID
Sbjct: 61  QQVNSKDALVRCEYRMADFSTGDRRRKPKGDRRSTEISLVIRQTMEASILTHLMPRSQID 120

Query: 119 IFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGG 178
           IFVQVLQADGGTR+ACINAATLAL DAGIPMRDIVTSCSAGYL STPLLDLNY+EDSAGG
Sbjct: 121 IFVQVLQADGGTRAACINAATLALADAGIPMRDIVTSCSAGYLCSTPLLDLNYIEDSAGG 180

Query: 179 PDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECR 238
           PDVTVG L  +DKVTLLQMDAKLP +TFE VM LAIEGCKA+ANYIREVLLENT++LEC+
Sbjct: 181 PDVTVGFLTKMDKVTLLQMDAKLPMDTFETVMDLAIEGCKAIANYIREVLLENTRRLECQ 240

Query: 239 RG 240
           RG
Sbjct: 241 RG 242

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242088177|ref|XP_002439921.1| hypothetical protein SORBIDRAFT_09g022550 [Sorghum bicolor] gi|241945206|gb|EES18351.1| hypothetical protein SORBIDRAFT_09g022550 [Sorghum bicolor]

 Score =  414 bits (1065), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 203/242 (83%), Positives = 222/242 (91%), Gaps = 2/242 (0%)

Query: 1   MEFVSP-EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKS 59
           ME+V+P  G R+DGRRP EMRQL+ E+G VA+ADGSA+FEMGNT+VIAAVYGPREVQNK 
Sbjct: 1   MEYVNPLTGFRVDGRRPNEMRQLKGEVGVVARADGSALFEMGNTRVIAAVYGPREVQNKG 60

Query: 60  QQM-SDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQID 118
           QQ+ S++ALVRCEY MA FSTGDR RKPKGDRRSTEISLVIRQTMEA ILTHLMPRSQID
Sbjct: 61  QQVNSNEALVRCEYRMAEFSTGDRRRKPKGDRRSTEISLVIRQTMEASILTHLMPRSQID 120

Query: 119 IFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGG 178
           I+VQVLQADGGTRSACINAATLAL DAGIPMRDIVTSCSAGYL STPLLDLNY+EDSAGG
Sbjct: 121 IYVQVLQADGGTRSACINAATLALADAGIPMRDIVTSCSAGYLCSTPLLDLNYLEDSAGG 180

Query: 179 PDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECR 238
            DVTVGIL  +DKVTLLQMDAKLP +TFE+VM LAIEGCKA+A YIREVLLENTK+LEC+
Sbjct: 181 SDVTVGILAKMDKVTLLQMDAKLPMDTFENVMGLAIEGCKAIATYIREVLLENTKKLECQ 240

Query: 239 RG 240
           RG
Sbjct: 241 RG 242

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357132600|ref|XP_003567917.1| PREDICTED: exosome complex component RRP41-like [Brachypodium distachyon]

 Score =  414 bits (1065), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 202/242 (83%), Positives = 221/242 (91%), Gaps = 2/242 (0%)

Query: 1   MEFVSP-EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKS 59
           ME+V+P  G R+DGRRP EMRQL+ E+G V++ADGSA+FEMGNT+VIAAVYGPREVQN+S
Sbjct: 1   MEYVNPLTGFRVDGRRPNEMRQLKGEVGVVSRADGSALFEMGNTRVIAAVYGPREVQNRS 60

Query: 60  QQM-SDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQID 118
           QQ+ S +ALVRCEY MA FSTGDR RKPKGDRRSTEISLVIRQTMEA ILTHLMP SQID
Sbjct: 61  QQVNSKEALVRCEYRMAEFSTGDRRRKPKGDRRSTEISLVIRQTMEASILTHLMPHSQID 120

Query: 119 IFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGG 178
           IFVQVLQADGGTRSACINAATLAL DAGIPMRDIVTSCSAGYL S+PLLDLNY+EDSAGG
Sbjct: 121 IFVQVLQADGGTRSACINAATLALADAGIPMRDIVTSCSAGYLCSSPLLDLNYIEDSAGG 180

Query: 179 PDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECR 238
           PDVTVGIL  +DKVTLLQMDAKLP +TFE VM+LAIEGCKA+A YIRE+LLENTKQLE R
Sbjct: 181 PDVTVGILAKMDKVTLLQMDAKLPMDTFETVMELAIEGCKAIATYIREILLENTKQLEYR 240

Query: 239 RG 240
           RG
Sbjct: 241 RG 242

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	241
TAIR|locus:2076710	241	RRP41 "AT3G61620" [Arabidopsis	0.987	0.987	0.820	2e-97
MGI|MGI:1923576	245	Exosc4 "exosome component 4" [	0.995	0.979	0.502	6.9e-63
RGD|1310986	245	Exosc4 "exosome component 4" [	0.970	0.955	0.510	6.9e-63
UNIPROTKB|E2RIM3	245	EXOSC4 "Uncharacterized protei	0.970	0.955	0.510	1.8e-62
UNIPROTKB|Q9NPD3	245	EXOSC4 "Exosome complex compon	0.970	0.955	0.510	1.8e-62
UNIPROTKB|Q7YRA3	245	EXOSC4 "Exosome complex compon	0.970	0.955	0.510	3e-62
ZFIN|ZDB-GENE-040426-1702	245	exosc4 "exosome component 4" [	0.975	0.959	0.495	7.9e-62
UNIPROTKB|F1RSL0	245	EXOSC4 "Uncharacterized protei	0.970	0.955	0.502	2.1e-61
FB|FBgn0032487	246	Ski6 "Ski6" [Drosophila melano	0.937	0.918	0.424	2.3e-48
WB|WBGene00007201	240	exos-4.1 [Caenorhabditis elega	0.962	0.966	0.386	8.4e-42

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

 Score = 968 (345.8 bits), Expect = 2.0e-97, P = 2.0e-97
 Identities = 197/240 (82%), Positives = 211/240 (87%)

Query:     1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
             ME+V+PEGLRLDGRR  EMRQ+ AE+G V+KADGSAVFEMGNTKVIAAVYGPRE+QNKSQ
Sbjct:     1 MEYVNPEGLRLDGRRFNEMRQIVAEVGVVSKADGSAVFEMGNTKVIAAVYGPREIQNKSQ 60

Query:    61 QM-SDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDI 119
             Q  +D A+V CEYSMA FSTGDR R+ K DRRSTE+SLVIRQTMEACILT LMP SQIDI
Sbjct:    61 QKKNDHAVVLCEYSMAQFSTGDR-RRQKFDRRSTELSLVIRQTMEACILTELMPHSQIDI 119

Query:   120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGP 179
             F+QVLQADGGTRSACINAATLAL DAGIPMRD+  SCSAGYLNSTPLLDLNYVEDSAGG 
Sbjct:   120 FLQVLQADGGTRSACINAATLALADAGIPMRDLAVSCSAGYLNSTPLLDLNYVEDSAGGA 179

Query:   180 DVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRR 239
             DVTVGILP LDKV+LLQMDAKLP  TFE V  LA EGCKA+A  IREVL ENTKQLE RR
Sbjct:   180 DVTVGILPKLDKVSLLQMDAKLPMETFETVFALASEGCKAIAERIREVLQENTKQLEYRR 239

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

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

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0005829 "cytosol" evidence=IDA

MGI|MGI:1923576 Exosc4 "exosome component 4" [Mus musculus (taxid:10090)]

 Score = 642 (231.1 bits), Expect = 6.9e-63, P = 6.9e-63
 Identities = 121/241 (50%), Positives = 176/241 (73%)

Query:     1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQ-NKS 59
             +E +S +G R+DGRR  E+R+++A +G  A+ADGSA  E GNTK +A VYGP E++ ++S
Sbjct:     4 LELLSDQGYRIDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRS 63

Query:    60 QQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDI 119
             + + D+ALV C+YS A FSTG+R R+P GDR+S E+ L +RQT EA ILT L PRSQIDI
Sbjct:    64 RALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDI 123

Query:   120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGP 179
             +VQVLQADGGT +AC+NAATLA+ DAGIPMRD V +CSAG+++ T L DL++VE++AGGP
Sbjct:   124 YVQVLQADGGTYAACVNAATLAVMDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAGGP 183

Query:   180 DVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRR 239
              + + +LP   ++ LL+MD++L  +  E V++ A +  + V   +  V+ ++ ++     
Sbjct:   184 QLALALLPASGQIALLEMDSRLHEDHLEQVLEAAAQAARGVHTLLDLVVRQHVQEASVSL 243

Query:   240 G 240
             G
Sbjct:   244 G 244

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

GO:0000460 "maturation of 5.8S rRNA" evidence=ISO

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=ISO

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006364 "rRNA processing" evidence=IEA

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

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

GO:0035327 "transcriptionally active chromatin" evidence=ISO

GO:0045006 "DNA deamination" evidence=ISO

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

GO:0071028 "nuclear mRNA surveillance" evidence=ISO

GO:0071044 "histone mRNA catabolic process" evidence=ISO

RGD|1310986 Exosc4 "exosome component 4" [Rattus norvegicus (taxid:10116)]

 Score = 642 (231.1 bits), Expect = 6.9e-63, P = 6.9e-63
 Identities = 120/235 (51%), Positives = 175/235 (74%)

Query:     1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQ-NKS 59
             +E +S +G R+DGRR  E+R+++A +G  A+ADGSA  E GNTK +A VYGP E++ ++S
Sbjct:     4 LELLSDQGYRIDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRS 63

Query:    60 QQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDI 119
             + + D+ALV C+YS A FSTG+R R+P GDR+S E+ L +RQT EA ILT L PRSQIDI
Sbjct:    64 RALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDI 123

Query:   120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGP 179
             +VQVLQADGGT +AC+NAATLA+ DAGIPMRD V +CSAG+++ T L DL++VE++AGGP
Sbjct:   124 YVQVLQADGGTYAACVNAATLAVMDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAGGP 183

Query:   180 DVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ 234
              + + +LP   ++ LL+MD++L  +  E V++ A +  + V   +  V+ ++ ++
Sbjct:   184 QLALALLPASGQIALLEMDSRLHEDHLEQVLEAAAQAARDVHTLLDRVVRQHVQE 238

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

GO:0000460 "maturation of 5.8S rRNA" evidence=IEA;ISO

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=ISO

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=ISO

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

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

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

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

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

GO:0071028 "nuclear mRNA surveillance" evidence=IEA;ISO

GO:0071044 "histone mRNA catabolic process" evidence=IEA;ISO

GO:0004532 "exoribonuclease activity" evidence=ISO

UNIPROTKB|E2RIM3 EXOSC4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 638 (229.6 bits), Expect = 1.8e-62, P = 1.8e-62
 Identities = 120/235 (51%), Positives = 175/235 (74%)

Query:     1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQ-NKS 59
             +E +S +G R+DGRR  E+R+++A +G  A+ADGSA  E GNTK +A VYGP E++ +++
Sbjct:     4 LELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRA 63

Query:    60 QQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDI 119
             + + D+ALV C+YS A FSTG+R R+P GDR+S E+ L +RQT EA ILT L PRSQIDI
Sbjct:    64 RALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLHLRQTFEAAILTQLHPRSQIDI 123

Query:   120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGP 179
             +VQVLQADGGT +AC+NAATLA+ DAGIPMRD V +CSAG++++T L DL++VE++AGGP
Sbjct:   124 YVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDNTALADLSHVEEAAGGP 183

Query:   180 DVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ 234
              + + +LP   ++ LL+MDA+L  +  E V++ A    + V   +  V+ ++ ++
Sbjct:   184 QLALALLPASGQIALLEMDARLHEDHLEQVLEAAARAARDVHTVLDRVVRQHVRE 238

GO:0071044 "histone mRNA catabolic process" evidence=IEA

GO:0071028 "nuclear mRNA surveillance" evidence=IEA

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

GO:0045006 "DNA deamination" evidence=IEA

GO:0035327 "transcriptionally active chromatin" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0000460 "maturation of 5.8S rRNA" evidence=IEA

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

UNIPROTKB|Q9NPD3 EXOSC4 "Exosome complex component RRP41" [Homo sapiens (taxid:9606)]

 Score = 638 (229.6 bits), Expect = 1.8e-62, P = 1.8e-62
 Identities = 120/235 (51%), Positives = 175/235 (74%)

Query:     1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQ-NKS 59
             +E +S +G R+DGRR  E+R+++A +G  A+ADGSA  E GNTK +A VYGP E++ +++
Sbjct:     4 LELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRA 63

Query:    60 QQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDI 119
             + + D+ALV C+YS A FSTG+R R+P GDR+S E+ L +RQT EA ILT L PRSQIDI
Sbjct:    64 RALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDI 123

Query:   120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGP 179
             +VQVLQADGGT +AC+NAATLA+ DAGIPMRD V +CSAG+++ T L DL++VE++AGGP
Sbjct:   124 YVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAGGP 183

Query:   180 DVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ 234
              + + +LP   ++ LL+MDA+L  +  E V++ A +  + V   +  V+ ++ ++
Sbjct:   184 QLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVRE 238

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

GO:0005730 "nucleolus" evidence=NAS

GO:0005737 "cytoplasm" evidence=IDA;NAS

GO:0006364 "rRNA processing" evidence=NAS

GO:0071044 "histone mRNA catabolic process" evidence=IMP

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

GO:0005515 "protein binding" evidence=IPI

GO:0000460 "maturation of 5.8S rRNA" evidence=IMP

GO:0045006 "DNA deamination" evidence=IDA

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

GO:0035327 "transcriptionally active chromatin" evidence=IMP

GO:0004532 "exoribonuclease activity" evidence=IDA

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=IMP

GO:0071028 "nuclear mRNA surveillance" evidence=IMP

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

GO:0005634 "nucleus" 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

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

UNIPROTKB|Q7YRA3 EXOSC4 "Exosome complex component RRP41" [Bos taurus (taxid:9913)]

 Score = 636 (228.9 bits), Expect = 3.0e-62, P = 3.0e-62
 Identities = 120/235 (51%), Positives = 174/235 (74%)

Query:     1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQ-NKS 59
             +E +S +G R+DGRR  E+R+++A +G  A+ADGSA  E GNTK +A VYGP E++ +++
Sbjct:     4 LELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRA 63

Query:    60 QQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDI 119
             + + D+ALV C+YS A FSTG+R R+P GDR+S E+ L +RQT EA ILT L PRSQIDI
Sbjct:    64 RALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDI 123

Query:   120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGP 179
             +VQVLQADGGT +AC+NAATLA+ DAGIPMRD V +CSAG+++ T L DL++VE++AGGP
Sbjct:   124 YVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAGGP 183

Query:   180 DVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ 234
              + + +LP   ++ LL+MDA+L  +  E V++ A    + V   +  V+ ++ ++
Sbjct:   184 QLALALLPASGQIALLEMDARLHEDHLEQVLEAAARASRDVHTVLDRVVRQHVQE 238

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

GO:0071044 "histone mRNA catabolic process" evidence=ISS

GO:0005737 "cytoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0071028 "nuclear mRNA surveillance" evidence=IEA

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

GO:0045006 "DNA deamination" evidence=IEA

GO:0035327 "transcriptionally active chromatin" evidence=IEA

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

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

GO:0000460 "maturation of 5.8S rRNA" evidence=IEA

GO:0004527 "exonuclease activity" evidence=IEA

ZFIN|ZDB-GENE-040426-1702 exosc4 "exosome component 4" [Danio rerio (taxid:7955)]

 Score = 632 (227.5 bits), Expect = 7.9e-62, P = 7.9e-62
 Identities = 117/236 (49%), Positives = 173/236 (73%)

Query:     1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQ-NKS 59
             +E +S +G RLDGR+ TE+R+++A +   A+ADGSA  E GNTK +A VYGP E++ ++S
Sbjct:     4 LELLSDQGYRLDGRKATELRKVQARMSVFAQADGSAYLEQGNTKALAVVYGPHEIRGSRS 63

Query:    60 QQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDI 119
             + + D+A++ C+YSMA FST +R R+P GDR+S+E+SL ++QT EA +LT L PRSQIDI
Sbjct:    64 KSLHDRAIINCQYSMATFSTAERKRRPHGDRKSSEMSLHLKQTFEAAVLTELYPRSQIDI 123

Query:   120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGP 179
             +V++LQADGG  SAC+NAATLAL DAGIPMRD V +CSAG++  TPL DL + E+S GG 
Sbjct:   124 YVKILQADGGNYSACVNAATLALVDAGIPMRDYVCACSAGFVEDTPLADLCHAEESGGGT 183

Query:   180 DVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQL 235
              + + +LP    + LLQMDA+L  +  + +M+ A+  CK  +  +  V+ ++ +++
Sbjct:   184 ALALALLPRSGNIALLQMDARLHQDHLDTLMEAAMTACKEFSKVLDSVVRQHLEEV 239

GO:0004527 "exonuclease activity" evidence=IEA

UNIPROTKB|F1RSL0 EXOSC4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 628 (226.1 bits), Expect = 2.1e-61, P = 2.1e-61
 Identities = 118/235 (50%), Positives = 172/235 (73%)

Query:     1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQ-NKS 59
             +E +S +G R+DGRR  E+R+++A +G  A+ADGSA  E GNTK +A VYGP E++ ++S
Sbjct:     4 LELLSDQGYRVDGRRARELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRS 63

Query:    60 QQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDI 119
             + + D+ALV C+YS A FSTG+R R+P GDR+S E+ L +RQ  EA ILT L PRSQIDI
Sbjct:    64 RALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQAFEAAILTQLHPRSQIDI 123

Query:   120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGP 179
             +VQVLQADGG  +AC+N ATLA+ DAGIPMRD V +CSAG+++ T L DL++VE++AGGP
Sbjct:   124 YVQVLQADGGIYAACVNVATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAGGP 183

Query:   180 DVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ 234
              + + +LP   ++ LL+MDA+L  +  E V++ A +  + V   +  V+ ++ ++
Sbjct:   184 QLALALLPASGQIALLEMDARLHEDHLEQVLEAAAQAARDVHTVLDRVVRQHVQE 238

GO:0071044 "histone mRNA catabolic process" evidence=IEA

GO:0071028 "nuclear mRNA surveillance" evidence=IEA

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

GO:0045006 "DNA deamination" evidence=IEA

GO:0035327 "transcriptionally active chromatin" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0000460 "maturation of 5.8S rRNA" evidence=IEA

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

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

 Score = 505 (182.8 bits), Expect = 2.3e-48, P = 2.3e-48
 Identities = 98/231 (42%), Positives = 150/231 (64%)

Query:     2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQ 61
             + +S +GLRLDGRRP E+R+++ ++G   + DGSA  E GNTKV+AAVYGP   Q K  Q
Sbjct:     6 DLLSEQGLRLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAVYGPH--QAKGNQ 63

Query:    62 MSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFV 121
                ++++ C+YS A FST +R  +P+GDR+S E  L ++Q + A I + L PRSQIDI+V
Sbjct:    64 T--ESVINCQYSQATFSTAERKNRPRGDRKSLEFKLYLQQALSAAIKSELYPRSQIDIYV 121

Query:   122 QVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNST-PLLDLNYVEDSAGGPD 180
             +VLQ DG   +  +NAATLAL DAGI + + + +C+A    S  PL D++  E+ +GGP 
Sbjct:   122 EVLQDDGANYAVALNAATLALIDAGICLNEFIVACTASLSKSNIPLTDISQFEEVSGGPK 181

Query:   181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLEN 231
             +TV  LPT +K+  L+M  +   +    V++ A+ GC+ + + +   + E+
Sbjct:   182 LTVAALPTAEKIAFLEMSERFHIDHLGTVIETAMAGCREIRDILEAAVKEH 232

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

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

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

GO:0035327 "transcriptionally active chromatin" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005652 "nuclear lamina" evidence=IDA

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

WB|WBGene00007201 exos-4.1 [Caenorhabditis elegans (taxid:6239)]

 Score = 443 (161.0 bits), Expect = 8.4e-42, P = 8.4e-42
 Identities = 90/233 (38%), Positives = 141/233 (60%)

Query:     1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
             M  +S  G R+DGRRP ++R +   +G    A+GS   E GNTKV+ AVYGP E ++ S+
Sbjct:     1 MNIISEHGFRIDGRRPAQIRNINTRLGLNRNAEGSCYLEHGNTKVLCAVYGPYEGKS-SK 59

Query:    61 QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
             ++ D+  + C+YS   FS  +R  + +GDR+STEIS ++ +  E+ ILT   PRSQ+DIF
Sbjct:    60 RIEDKCAIVCQYSATKFSGLERKNRTRGDRKSTEISRLLEKAFESVILTEAFPRSQLDIF 119

Query:   121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180
              +V+Q DG   +AC+NA +LAL DAGIPM+ I ++ + G ++  P++DL   E++   P 
Sbjct:   120 CEVIQGDGSNLAACVNATSLALADAGIPMKGIASAATCGVVDGKPIVDLTSREETDLLPR 179

Query:   181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTK 233
             VT+  +   D+V L+++  +L  +    VM  A   C  V   +  V  ++ K
Sbjct:   180 VTLATICGRDEVILVELQNRLHIDHLSTVMDAAKATCADVYECLAVVAQQHLK 232

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

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

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0008406 "gonad development" evidence=IMP

GO:0010171 "body morphogenesis" evidence=IMP

GO:0040018 "positive regulation of multicellular organism growth" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O26779	ECX1_METTH	3, ., 1, ., 1, 3, ., -	0.4636	0.9087	0.9125	yes	no
Q5JIR6	ECX1_PYRKO	3, ., 1, ., 1, 3, ., -	0.4891	0.9543	0.9236	yes	no
Q8TYC1	ECX1_METKA	3, ., 1, ., 1, 3, ., -	0.4847	0.9460	0.9539	yes	no
B6YSI2	ECX1_THEON	3, ., 1, ., 1, 3, ., -	0.4891	0.9543	0.9236	yes	no
Q82XJ4	RNPH_NITEU	2, ., 7, ., 7, ., 5, 6	0.3220	0.9045	0.9045	yes	no
Q9UXC2	ECX1_SULSO	3, ., 1, ., 1, 3, ., -	0.4267	0.9502	0.9233	yes	no
A0RXU1	ECX1_CENSY	3, ., 1, ., 1, 3, ., -	0.4253	0.9128	0.9053	yes	no
B1Y978	ECX1_PYRNV	3, ., 1, ., 1, 3, ., -	0.4298	0.9170	0.8983	yes	no
P46948	RRP41_YEAST	No assigned EC number	0.3771	0.9668	0.9471	yes	no
B8I1A8	RNPH_CLOCE	2, ., 7, ., 7, ., 5, 6	0.3045	0.9087	0.9125	yes	no
Q6A759	RNPH_PROAC	2, ., 7, ., 7, ., 5, 6	0.3151	0.8962	0.8852	yes	no
O29757	ECX1_ARCFU	3, ., 1, ., 1, 3, ., -	0.4380	0.9211	0.8604	yes	no
O42872	RRP41_SCHPO	No assigned EC number	0.4206	0.9626	0.9586	yes	no
B5YFY8	RNPH_THEYD	2, ., 7, ., 7, ., 5, 6	0.3106	0.8796	0.8983	yes	no
Q97BZ5	ECX1_THEVO	3, ., 1, ., 1, 3, ., -	0.4206	0.9626	0.9354	yes	no
A5G3S1	RNPH_GEOUR	2, ., 7, ., 7, ., 5, 6	0.3305	0.8879	0.8991	yes	no
Q9YC03	ECX1_AERPE	3, ., 1, ., 1, 3, ., -	0.4054	0.9170	0.8983	yes	no
Q9HIP2	ECX1_THEAC	3, ., 1, ., 1, 3, ., -	0.3991	0.9626	0.9354	yes	no
Q8E9L4	RNPH_SHEON	2, ., 7, ., 7, ., 5, 6	0.3096	0.8713	0.8860	yes	no
A1RST0	ECX1_PYRIL	3, ., 1, ., 1, 3, ., -	0.4298	0.9170	0.8983	yes	no
B9M3E3	RNPH_GEOSF	2, ., 7, ., 7, ., 5, 6	0.3264	0.8879	0.8991	yes	no
A3MUP1	ECX1_PYRCJ	3, ., 1, ., 1, 3, ., -	0.4524	0.9170	0.8983	yes	no
A2BKC0	ECX1_HYPBU	3, ., 1, ., 1, 3, ., -	0.4291	0.9626	0.9098	yes	no
Q975G8	ECX1_SULTO	3, ., 1, ., 1, 3, ., -	0.4454	0.9460	0.9382	yes	no
Q4JB27	ECX1_SULAC	3, ., 1, ., 1, 3, ., -	0.4458	0.9460	0.9382	yes	no
A9A5C9	ECX1_NITMS	3, ., 1, ., 1, 3, ., -	0.4078	0.9419	0.9303	yes	no
A4WM67	ECX1_PYRAR	3, ., 1, ., 1, 3, ., -	0.4298	0.9170	0.8983	yes	no
O59223	ECX1_PYRHO	3, ., 1, ., 1, 3, ., -	0.4761	0.9543	0.9236	yes	no
Q9S2H7	RNPH_STRCO	2, ., 7, ., 7, ., 5, 6	0.3112	0.8921	0.8775	yes	no
Q8ZVM9	ECX1_PYRAE	3, ., 1, ., 1, 3, ., -	0.4389	0.9170	0.8983	yes	no
Q9NPD3	EXOS4_HUMAN	No assigned EC number	0.5106	0.9709	0.9551	yes	no
Q9V119	ECX1_PYRAB	3, ., 1, ., 1, 3, ., -	0.4805	0.9543	0.9236	yes	no
Q8U0L9	ECX1_PYRFU	3, ., 1, ., 1, 3, ., -	0.4891	0.9543	0.92	yes	no
C1DCK5	RNPH_LARHH	2, ., 7, ., 7, ., 5, 6	0.3217	0.8713	0.8823	yes	no
Q7YRA3	EXOS4_BOVIN	No assigned EC number	0.5106	0.9709	0.9551	yes	no
Q921I9	EXOS4_MOUSE	No assigned EC number	0.5106	0.9709	0.9551	yes	no
C5A2B9	ECX1_THEGJ	3, ., 1, ., 1, 3, ., -	0.4805	0.9543	0.9236	yes	no
Q17533	EXOS4_CAEEL	No assigned EC number	0.4	0.9087	0.9125	yes	no
Q11B42	RNPH_MESSB	2, ., 7, ., 7, ., 5, 6	0.3039	0.8547	0.8655	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.13	LOW CONFIDENCE prediction!
3rd Layer	2.7.7	0.766

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	241
cd11370	226	cd11370, RNase_PH_RRP41, RRP41 subunit of eukaryot	1e-142
PRK03983	244	PRK03983, PRK03983, exosome complex exonuclease Rr	6e-94
cd11366	214	cd11366, RNase_PH_archRRP41, RRP41 subunit of arch	2e-87
TIGR02065	230	TIGR02065, ECX1, archaeal exosome-like complex exo	8e-84
COG0689	230	COG0689, Rph, RNase PH [Translation, ribosomal str	6e-83
cd11371	210	cd11371, RNase_PH_MTR3, MTR3 subunit of eukaryotic	2e-65
cd11358	218	cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucl	1e-46
pfam01138	129	pfam01138, RNase_PH, 3' exoribonuclease family, do	1e-44
cd11372	199	cd11372, RNase_PH_RRP46, RRP46 subunit of eukaryot	2e-42
cd11362	227	cd11362, RNase_PH_bact, Ribonuclease PH	6e-28
PRK00173	238	PRK00173, rph, ribonuclease PH; Reviewed	2e-27
TIGR01966	236	TIGR01966, RNasePH, ribonuclease PH	3e-26
TIGR02696	719	TIGR02696, pppGpp_PNP, guanosine pentaphosphate sy	2e-13
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	3e-13
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	1e-11
cd11364	223	cd11364, RNase_PH_PNPase_2, Polyribonucleotide nuc	3e-11
PLN00207	891	PLN00207, PLN00207, polyribonucleotide nucleotidyl	3e-11
cd11365	256	cd11365, RNase_PH_archRRP42, RRP42 subunit of arch	8e-10
pfam03725	68	pfam03725, RNase_PH_C, 3' exoribonuclease family,	1e-08
PRK11824	693	PRK11824, PRK11824, polynucleotide phosphorylase/p	3e-08
PRK04282	271	PRK04282, PRK04282, exosome complex RNA-binding pr	4e-08
COG2123	272	COG2123, COG2123, RNase PH-related exoribonuclease	2e-07
cd11368	259	cd11368, RNase_PH_RRP45, RRP45 subunit of eukaryot	2e-06
cd11369	261	cd11369, RNase_PH_RRP43, RRP43 subunit of eukaryot	5e-06
cd11367	272	cd11367, RNase_PH_RRP42, RRP42 subunit of eukaryot	4e-04

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

 Score =  397 bits (1023), Expect = e-142
 Identities = 150/226 (66%), Positives = 182/226 (80%)

Query: 8   GLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQAL 67
           GLRLDGRRP E+R++R  IG  + ADGSA  E GNTKV+AAVYGP E +N+SQ + D+A+
Sbjct: 1   GLRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNRSQALHDRAV 60

Query: 68  VRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQAD 127
           V CEYSMA FSTG+R R+ KGDRRSTE+SL IRQT EA ILTHL PRSQIDI+VQVLQAD
Sbjct: 61  VNCEYSMATFSTGERKRRGKGDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQAD 120

Query: 128 GGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILP 187
           GG  +ACINAATLAL DAGIPM+D V +CSAGYL+STPLLDLNY+E+S   PD+TV +LP
Sbjct: 121 GGLLAACINAATLALIDAGIPMKDYVCACSAGYLDSTPLLDLNYLEESGDLPDLTVAVLP 180

Query: 188 TLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTK 233
             DKV LLQM+++L  +  E V++LAIEGCK +   + EV+ E+TK
Sbjct: 181 KSDKVVLLQMESRLHLDRLEKVLELAIEGCKVIREIMDEVVREHTK 226

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|235187 PRK03983, PRK03983, exosome complex exonuclease Rrp41; Provisional

 Score =  275 bits (705), Expect = 6e-94
 Identities = 111/224 (49%), Positives = 153/224 (68%), Gaps = 1/224 (0%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           +GLRLDGR+P E+R ++ E+G +  ADGSA  E GN K+IAAVYGPRE+  +  Q+ D+A
Sbjct: 12  DGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRA 71

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
           ++R  Y+MA FS  +R ++P  DRRS EIS VIR+ +E  I+  L PR+ ID+F++VLQA
Sbjct: 72  VLRVRYNMAPFSVDER-KRPGPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQA 130

Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGIL 186
           D GTR A I AA+LAL DAGIPMRD+V  C+ G ++   +LDLN  ED+ G  D+ V I+
Sbjct: 131 DAGTRVAGITAASLALADAGIPMRDLVAGCAVGKVDGVIVLDLNKEEDNYGEADMPVAIM 190

Query: 187 PTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLE 230
           P L ++TLLQ+D  L    F + ++LA +G K +    RE L  
Sbjct: 191 PRLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQLQREALKS 234

Length = 244

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

 Score =  258 bits (660), Expect = 2e-87
 Identities = 102/213 (47%), Positives = 145/213 (68%), Gaps = 1/213 (0%)

Query: 18  EMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANF 77
           E+R ++ E+G +  ADGSA  E GN K+IAAVYGPREV  +  Q+ D+A++R  Y+MA F
Sbjct: 1   ELRPIKIEVGVLKNADGSAYVEWGNNKIIAAVYGPREVHPRHLQLPDRAVIRVRYNMAPF 60

Query: 78  STGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINA 137
           S  +R R P  DRR  EIS VI++ +E  I+    PR+ ID+FV+VLQAD GTR A +NA
Sbjct: 61  SVDERKR-PGPDRREIEISKVIKEALEPAIILEEFPRTAIDVFVEVLQADAGTRVAGLNA 119

Query: 138 ATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQM 197
           A+LAL DAGIPMRD+V +C+AG ++   +LDLN  ED+ G  D+ + ++P L ++TLLQ+
Sbjct: 120 ASLALADAGIPMRDLVAACAAGKVDGKIVLDLNKEEDNYGEADMPIAMMPNLGEITLLQL 179

Query: 198 DAKLPTNTFEDVMQLAIEGCKAVANYIREVLLE 230
           D  L  + F+  ++LA +GCK +    +E L  
Sbjct: 180 DGDLTPDEFKQAIELAKKGCKRIYELQKEALKR 212

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

 Score =  249 bits (637), Expect = 8e-84
 Identities = 107/224 (47%), Positives = 146/224 (65%), Gaps = 1/224 (0%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           +G+RLDGR+P E+R ++ E G +  ADGSA  E G TK++AAVYGPRE   +  Q+ D+A
Sbjct: 6   DGVRLDGRKPDELRPIKIEAGVLKNADGSAYLEFGGTKILAAVYGPREAHPRHLQLPDRA 65

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
           ++R  Y MA FST +R R P   RR  EIS VIR+ +E  IL    PR+ ID+F++VLQA
Sbjct: 66  VLRVRYHMAPFSTDERKR-PGPSRREIEISKVIREALEPAILLEQFPRTVIDVFIEVLQA 124

Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGIL 186
           DGGTR A + AA+LAL DAGIPMRD+V   + G ++   +LDL+  ED  G  D+ V I+
Sbjct: 125 DGGTRCAGLTAASLALADAGIPMRDLVVGVAVGKVDGVVVLDLSEEEDMYGEADMPVAIM 184

Query: 187 PTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLE 230
           P   ++TLLQ+D  L  + F   + LA+EG K +    RE L +
Sbjct: 185 PKTGEITLLQLDGDLTPDEFRQALDLAVEGIKRIYEIQREALKK 228

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

 Score =  246 bits (631), Expect = 6e-83
 Identities = 90/228 (39%), Positives = 132/228 (57%), Gaps = 2/228 (0%)

Query: 4   VSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMS 63
            S +G+R DGR+P E+R ++   G +  A+GS++ E GNTKVI  V GPRE   +  + +
Sbjct: 3   ESEDGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGT 62

Query: 64  DQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQV 123
            +  +  EY M   ST +R ++     R+ EIS +I + + A I   L+P S IDI   V
Sbjct: 63  GKGWLTAEYGMLPRSTDERKKREADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDV 122

Query: 124 LQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTV 183
           LQADGGTR+A I  A+LAL DAGIP+RD+V + S G ++   +LDL+Y EDSA   D+ V
Sbjct: 123 LQADGGTRTASITGASLALADAGIPLRDLVAAISVGIVDGVIVLDLDYEEDSAAEADMNV 182

Query: 184 GILPT--LDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLL 229
            +     L ++  L  D     +   +++ LAI+GC  +    RE L 
Sbjct: 183 VMTGNGGLVEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQREALA 230

Length = 230

>gnl|CDD|206776 cd11371, RNase_PH_MTR3, MTR3 subunit of eukaryotic exosome

 Score =  201 bits (514), Expect = 2e-65
 Identities = 82/212 (38%), Positives = 124/212 (58%), Gaps = 2/212 (0%)

Query: 19  MRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFS 78
           +R +  + G V++A GSA  E+GNTKVI +VYGPR +     + SD+  + CE   A F+
Sbjct: 1   IRPIFLKTGVVSQAKGSAYVELGNTKVICSVYGPRPIP-GRTEFSDRGRLNCEVKFAPFA 59

Query: 79  TGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAA 138
           T  R R+   D    E+S ++ Q +E  +     P+SQID+FV VL++DG   +A I AA
Sbjct: 60  TPGR-RRHGQDSEERELSSLLHQALEPAVRLEKYPKSQIDVFVTVLESDGSVLAAAITAA 118

Query: 139 TLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMD 198
           +LAL DAGI M D+VT+CSA  +    LLD    E+ A    V +  +P+L++VT L   
Sbjct: 119 SLALADAGIEMYDLVTACSAALIGDELLLDPTREEEEASSGGVMLAYMPSLNQVTQLWQS 178

Query: 199 AKLPTNTFEDVMQLAIEGCKAVANYIREVLLE 230
            ++  +  E+ + L I+GC  +   +R+ LLE
Sbjct: 179 GEMDVDQLEEALDLCIDGCNRIHPVVRQALLE 210

The MTR3 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Length = 210

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

 Score =  154 bits (390), Expect = 1e-46
 Identities = 62/218 (28%), Positives = 102/218 (46%), Gaps = 22/218 (10%)

Query: 20  RQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFST 79
           R +  E G + +ADGSA+ ++GNTKVI AV GP        +  D+  +     ++  + 
Sbjct: 2   RPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVE-PDKLERPDKGTLYVNVEISPGAV 60

Query: 80  GDRMRKPKGDRRSTEISLVIRQTMEACILTHLM---PRSQIDIFVQVLQADGGTRSACIN 136
           G+R +         EIS ++ +T+EA ++       P   + + +QVL  DGG   AC N
Sbjct: 61  GERRQ-GPPGDEEMEISRLLERTIEASVILDKSTRKPSWVLYVDIQVLSRDGGLLDACWN 119

Query: 137 AATLALQDAGIP-------------MRDIVTSCSAGYL-NSTPLLDLNYVEDSAGGPDVT 182
           AA  AL+DAGIP             M+D++ + S G + +   LLD    E+      +T
Sbjct: 120 AAIAALKDAGIPRVFVDERSPPLLLMKDLIVAVSVGGISDGVLLLDPTGEEEELADSTLT 179

Query: 183 VGILPTLDKVTLLQMDAKLP--TNTFEDVMQLAIEGCK 218
           V +  +  K+ LL         T   ++ ++LA +   
Sbjct: 180 VAVDKS-GKLCLLSKVGGGSLDTEEIKECLELAKKRSL 216

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

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

 Score =  146 bits (370), Expect = 1e-44
 Identities = 52/131 (39%), Positives = 74/131 (56%), Gaps = 2/131 (1%)

Query: 18  EMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANF 77
           E+R +  E G +++ADGSA+ E+G+TKV+A V GP E   K +       +  EY  + F
Sbjct: 1   ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPPQKERD-FFPGELTVEYEESPF 59

Query: 78  STGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINA 137
           ++G+R    +   R  E+S +I + +   I     PR +I I V VL  DG    A INA
Sbjct: 60  ASGERPE-GRPSEREIELSRLIDRALRPSIPLEGYPRWEIRIDVTVLSDDGSLLDAAINA 118

Query: 138 ATLALQDAGIP 148
           A+LAL DAGIP
Sbjct: 119 ASLALADAGIP 129

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

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

 Score =  142 bits (360), Expect = 2e-42
 Identities = 60/215 (27%), Positives = 105/215 (48%), Gaps = 24/215 (11%)

Query: 19  MRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFS 78
           +R L  E+G +++ADGSA F  G+T V+AAVYGP EV+   +++ D+A +          
Sbjct: 1   LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKL-RKELPDRATLEVIV------ 53

Query: 79  TGDRMRKPK---GDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACI 135
                 +PK      +   + L++R T+E  IL HL PR+ I + +QVLQ DG   +  I
Sbjct: 54  ------RPKSGLPGVKEKLLELLLRSTLEPIILLHLHPRTLISVVLQVLQDDGSLLACAI 107

Query: 136 NAATLALQDAGIPMRDIVTSCSAGYLNSTPLL---DLNYVEDSAGGPDVTVGILPTLDKV 192
           NAA LAL DAG+PM+ +  + +        ++        +++      T     + ++ 
Sbjct: 108 NAACLALLDAGVPMKGLFAAVTCAITEDGEIILDPTAEEEKEAKAV--ATFAF-DSGEEK 164

Query: 193 TLLQMDAK--LPTNTFEDVMQLAIEGCKAVANYIR 225
            L+  +++           ++LA     A+ ++ R
Sbjct: 165 NLVLSESEGSFTEEELFACLELAQAASAAIFDFYR 199

The RRP46 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Length = 199

>gnl|CDD|206767 cd11362, RNase_PH_bact, Ribonuclease PH

 Score =  105 bits (265), Expect = 6e-28
 Identities = 61/184 (33%), Positives = 89/184 (48%), Gaps = 22/184 (11%)

Query: 18  EMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNK-SQQMSDQAL--VRCEYSM 74
           ++R +    G    A+GS + E G+TKV+        V+ K    +  +    V  EYSM
Sbjct: 1   QLRPISITRGFNKHAEGSVLIEFGDTKVLCTA----SVEEKVPPFLRGKGKGWVTAEYSM 56

Query: 75  ANFSTGDRMR----KPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGT 130
              ST +R +    K K   R+ EI  +I +++ A +    +    I I   VLQADGGT
Sbjct: 57  LPRSTHERTQREASKGKQSGRTQEIQRLIGRSLRAAVDLEALGERTITIDCDVLQADGGT 116

Query: 131 RSACINAATLALQDA-----------GIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGP 179
           R+A I  A +AL DA             P++  V + S G ++  PLLDL+Y EDSA   
Sbjct: 117 RTASITGAYVALADAVDKLVEKGVLEENPLKHFVAAVSVGIVDGEPLLDLDYEEDSAADV 176

Query: 180 DVTV 183
           D+ V
Sbjct: 177 DMNV 180

Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Structurally all members of this family form hexameric rings (trimers of dimers). Bacterial RNase PH forms a homohexameric ring, and removes nucleotide residues following the -CCA terminus of tRNA. Length = 227

>gnl|CDD|178914 PRK00173, rph, ribonuclease PH; Reviewed

 Score =  104 bits (262), Expect = 2e-27
 Identities = 67/196 (34%), Positives = 96/196 (48%), Gaps = 30/196 (15%)

Query: 10  RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVI--AAVYG--PREVQNKSQQMSDQ 65
           R DGR   ++R +         A+GS + E G+TKV+  A+V    PR ++ + Q     
Sbjct: 2   RPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQ----- 56

Query: 66  ALVRCEYSMANFSTGDRMR------KPKGDRRSTEISLVIRQTMEACI-LTHLMPRSQID 118
             V  EY M   +T  R        K  G  R+ EI  +I +++ A + L  L  R  I 
Sbjct: 57  GWVTAEYGMLPRATHTRNDREAAKGKQGG--RTQEIQRLIGRSLRAVVDLKALGER-TIT 113

Query: 119 IFVQVLQADGGTRSACINAATLALQDA-----------GIPMRDIVTSCSAGYLNSTPLL 167
           I   V+QADGGTR+A I  A +AL DA             P++D V + S G ++  P+L
Sbjct: 114 IDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLKDQVAAVSVGIVDGEPVL 173

Query: 168 DLNYVEDSAGGPDVTV 183
           DL+Y EDSA   D+ V
Sbjct: 174 DLDYEEDSAAETDMNV 189

Length = 238

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

 Score =  101 bits (253), Expect = 3e-26
 Identities = 67/190 (35%), Positives = 95/190 (50%), Gaps = 18/190 (9%)

Query: 10  RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVR 69
           R DGR+P ++R +      +  A+GS + E GNTKV+       +V     + S +  + 
Sbjct: 1   RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVP-PFLRGSGEGWIT 59

Query: 70  CEYSMANFSTGDRMR----KPKGDRRSTEISLVIRQTMEACI-LTHLMPRSQIDIFVQVL 124
            EY M   +T  R R    K K   R+ EI  +I + + A + L  L  R  I I   V+
Sbjct: 60  AEYGMLPRATQTRNRRESAKGKQSGRTQEIQRLIGRALRAVVDLEALGER-TIWIDCDVI 118

Query: 125 QADGGTRSACINAATLALQDA-----------GIPMRDIVTSCSAGYLNSTPLLDLNYVE 173
           QADGGTR+A I  A +AL DA             P+RD V + S G ++  P+LDL+Y E
Sbjct: 119 QADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAAVSVGIVDGEPVLDLDYEE 178

Query: 174 DSAGGPDVTV 183
           DSA   D+ V
Sbjct: 179 DSAADVDMNV 188

This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and modification of tRNA precursors. This model is restricted absolutely to bacteria. Related families outside the model include proteins described as probable exosome complex exonucleases (rRNA processing) and polyribonucleotide nucleotidyltransferases (mRNA degradation). The most divergent member within the family is RNase PH from Deinococcus radiodurans [Transcription, RNA processing]. Length = 236

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

 Score = 69.1 bits (169), Expect = 2e-13
 Identities = 70/260 (26%), Positives = 112/260 (43%), Gaps = 64/260 (24%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           EG+R+DGR  T++R L AE+  + +  GSA+FE G T+++        +    QQ+   +
Sbjct: 333 EGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVT--TLNMLKMEQQIDSLS 390

Query: 67  LVRCE-----YSMANFSTGD--RMRKPKGDRRS------TEISLV------------IRQ 101
               +     Y+   +STG+  R+  PK  RR        E +LV            IRQ
Sbjct: 391 PETSKRYMHHYNFPPYSTGETGRVGSPK--RREIGHGALAERALVPVLPSREEFPYAIRQ 448

Query: 102 TMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL 161
             EA                  L ++G T    + A+TL+L +AG+P++  V   + G +
Sbjct: 449 VSEA------------------LGSNGSTSMGSVCASTLSLLNAGVPLKAPVAGIAMGLI 490

Query: 162 NSTPLLDLNYV--------EDSAGGPDVTVGILPTLDKVTLLQMDAKL---PTNTFEDVM 210
           +     +  YV        ED+ G  D  V    T + VT LQ+D KL   P      V+
Sbjct: 491 SDEVDGETRYVALTDILGAEDAFGDMDFKVA--GTSEFVTALQLDTKLDGIPA----SVL 544

Query: 211 QLAIEGCKAVANYIREVLLE 230
             A++  +     I +V+ E
Sbjct: 545 ASALKQARDARLAILDVMAE 564

Sohlberg, et al present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase. Length = 719

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

 Score = 68.0 bits (167), Expect = 3e-13
 Identities = 70/243 (28%), Positives = 112/243 (46%), Gaps = 34/243 (13%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-YG-PREVQNKSQQMSD 64
             +R+DGR   E+R +  E+G + +  GSA+F  G T+ +  V  G PR+ Q       +
Sbjct: 310 GKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGE 369

Query: 65  QALVRCEYSMANF---STGD--RMRKPKGDRRSTEI---SLVIRQTMEACILTHLMPRSQ 116
               +      NF   S G+  RM  P   RR  EI   +L  R       L  ++P  +
Sbjct: 370 YK--KRFLLHYNFPPFSVGETGRMGSPG--RR--EIGHGALAERA------LAPVLPSEE 417

Query: 117 -----IDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL----NSTPLL 167
                I +  ++L+++G +  A +   +LAL DAG+P++  V   + G +        L 
Sbjct: 418 EFPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLS 477

Query: 168 DLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREV 227
           D+   ED  G  D+   +  T D +T LQMD K+   T E +M+ A+E  K    +I  V
Sbjct: 478 DILGDEDHLG--DMDFKVAGTDDGITALQMDIKIKGITKE-IMKKALEQAKGARLHILIV 534

Query: 228 LLE 230
           + E
Sbjct: 535 MNE 537

Length = 692

>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 63.3 bits (155), Expect = 1e-11
 Identities = 65/238 (27%), Positives = 105/238 (44%), Gaps = 53/238 (22%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVY--GPREVQNKSQQMSD 64
           EG R+DGR    +R +  E+G + +  GSA+F  G T+ +        R+ Q     + D
Sbjct: 308 EGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQI----IDD 363

Query: 65  QALVRCE-----YSMANFSTGD--RMRKPKGDRRSTEI---SLVIRQTMEACILTHLMPR 114
                 +     Y+   +S G+  R+  P   RR  EI   +L  R       L  ++P 
Sbjct: 364 LEGEYRKRFMLHYNFPPYSVGEVGRVGGPG--RR--EIGHGALAERA------LKAVLPS 413

Query: 115 SQ-----IDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLL-- 167
            +     I +  ++L+++G +  A +   +LAL DAG+P++  V   + G      L+  
Sbjct: 414 EEEFPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMG------LIKE 467

Query: 168 -DLNYV--------EDSAGGPDVTV-GILPTLDKVTLLQMDAKLPTNTFEDVMQLAIE 215
            D  +         ED  G  D  V G   T D +T LQMD K+   T E +M+ A+E
Sbjct: 468 GDERFAVLSDILGDEDHLGDMDFKVAG---TRDGITALQMDIKIDGITRE-IMEQALE 521

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family) [Transcription, Degradation of RNA]. Length = 684

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

 Score = 61.0 bits (149), Expect = 3e-11
 Identities = 66/232 (28%), Positives = 110/232 (47%), Gaps = 33/232 (14%)

Query: 18  EMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-YGPREVQNKSQQMSDQALVR--CEYSM 74
           E+R +  E+G + +  GSA+F  G T+V+  V  G  E   K   +  +   R    Y+ 
Sbjct: 1   EIRPISCEVGLLPRTHGSALFTRGETQVLCTVTLGTLEDAQKIDSLGGEKSKRFMLHYNF 60

Query: 75  ANFSTGD--RMRKPKGDRRSTEI---SLVIRQTMEACILTHLMPRSQ-----IDIFVQVL 124
             +S G+  R+  P   RR  EI   +L  R       L  ++P  +     I +  +VL
Sbjct: 61  PPYSVGETGRVGGPG--RR--EIGHGALAERA------LLPVLPSPEDFPYTIRVVSEVL 110

Query: 125 QADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTP-----LLDLNYVEDSAGGP 179
           +++G +  A +   +LAL DAG+P++  V   + G +         L D+  +ED  G  
Sbjct: 111 ESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLITEGIDDYRVLTDILGLEDHLGDM 170

Query: 180 DVTV-GILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLE 230
           D  V G   T D +T LQMD K+P  T E +M+ A++  K    +I +++ +
Sbjct: 171 DFKVAG---TRDGITALQMDIKIPGITLE-IMREALQQAKEGRLHILDIMEK 218

Polyribonucleotide nucleotidyltransferase (PNPase) is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally, all members of this family form hexameric rings. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction and in quality control of ribosomal RNA precursors, with the second repeat containing the active site. PNPase is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E. Length = 223

>gnl|CDD|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase; Provisional

 Score = 62.6 bits (152), Expect = 3e-11
 Identities = 57/222 (25%), Positives = 103/222 (46%), Gaps = 17/222 (7%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-YGPREVQNKSQQMSDQ 65
            G R DGR P E+R + +  G + +A GSA+F  G T+ +A V  G +++  +   + D 
Sbjct: 436 GGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDA 495

Query: 66  ALVR---CEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQ 122
             V+    +YS      G+  R     RR     ++  + +E  + +       I +   
Sbjct: 496 DEVKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFPYTIRVEST 555

Query: 123 VLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL--------NSTPLL--DLNYV 172
           + +++G +  A +    LALQDAG+P++  +   + G +        + +PL+  D+   
Sbjct: 556 ITESNGSSSMASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGGDGSPLILSDITGS 615

Query: 173 EDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAI 214
           ED++G  D  V      D +T  QMD K+   T   +M+ A+
Sbjct: 616 EDASGDMDFKVA--GNEDGITAFQMDIKVGGITLP-IMERAL 654

Length = 891

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

 Score = 57.2 bits (139), Expect = 8e-10
 Identities = 20/44 (45%), Positives = 30/44 (68%)

Query: 6  PEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV 49
           +G R+DGR   E R +  E G + KA+GSA+ ++GNT+V+A V
Sbjct: 13 EKGKRIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGV 56

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

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

 Score = 49.9 bits (120), Expect = 1e-08
 Identities = 17/68 (25%), Positives = 33/68 (48%), Gaps = 2/68 (2%)

Query: 151 DIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMD--AKLPTNTFED 208
             V + + G ++   +LD    E+S    D+T+ +  T + V L++    A+L      +
Sbjct: 1   GPVAAVTVGKIDGELVLDPTLEEESLADSDLTIVVAGTGEIVALMKEGGGAELTEEELLE 60

Query: 209 VMQLAIEG 216
            ++LA EG
Sbjct: 61  ALELAHEG 68

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

>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional

 Score = 53.5 bits (130), Expect = 3e-08
 Identities = 66/265 (24%), Positives = 105/265 (39%), Gaps = 78/265 (29%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVY--GPREVQNKSQQMSD 64
           EG+R+DGR+  E+R +  E+G + +  GSA+F  G T+ +        R+     Q +  
Sbjct: 312 EGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLRDE----QIIDG 367

Query: 65  QALVRCE-----YSMANFSTGD--RMRKPKGDRRSTEI--------SL------------ 97
                 +     Y+   +S G+  R+  P   RR  EI        +L            
Sbjct: 368 LEGEYKKRFMLHYNFPPYSVGETGRVGSPG--RR--EIGHGALAERALEPVLPSEEEFPY 423

Query: 98  VIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCS 157
            IR   E                  +L+++G +  A +  ++LAL DAG+P++  V   +
Sbjct: 424 TIRVVSE------------------ILESNGSSSMASVCGSSLALMDAGVPIKAPVAGIA 465

Query: 158 AGYLNSTPLL---DLNYV--------EDSAGGPDVTV-GILPTLDKVTLLQMDAKLPTNT 205
            G       L      Y         ED  G  D  V G   T D +T LQMD K+   T
Sbjct: 466 MG-------LIKEGDKYAVLTDILGDEDHLGDMDFKVAG---TRDGITALQMDIKIDGIT 515

Query: 206 FEDVMQLAIEGCKAVANYIREVLLE 230
            E +++ A+E  K    +I   + E
Sbjct: 516 RE-ILEEALEQAKEGRLHILGKMNE 539

Length = 693

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

 Score = 52.2 bits (126), Expect = 4e-08
 Identities = 20/43 (46%), Positives = 31/43 (72%)

Query: 7  EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV 49
          +G R+DGR+  E R +  E G + KA+GSA+ ++GNT+V+A V
Sbjct: 22 KGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGV 64

Length = 271

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

 Score = 50.1 bits (120), Expect = 2e-07
 Identities = 44/160 (27%), Positives = 69/160 (43%), Gaps = 31/160 (19%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-------YGPREVQNKS 59
           +G+R+DGR   E R L  E G + KA+GSA+ ++GNT+V+  V       +     +   
Sbjct: 21  KGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIGEPFPDTPNEGV- 79

Query: 60  QQMSDQALVRCEYS-MA--NFSTGDRMRKPKGDRRSTEISLVIRQTM---EACILTHLMP 113
                  +V  E S +A  +F  G        D  + E+S V+ + +   +A  L  L  
Sbjct: 80  ------LVVNVELSPLASPSFEPGPP------DELAIELSRVVDRGLRESKAIDLEKLCI 127

Query: 114 RSQ-----IDIFVQVLQADGGTRSACINAATLALQDAGIP 148
                   + + V VL  DG    A   AA  AL +  +P
Sbjct: 128 EEGKKVWVVFVDVHVLDYDGNLIDAASLAAVAALLNTRVP 167

Length = 272

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

 Score = 47.1 bits (113), Expect = 2e-06
 Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 3/43 (6%)

Query: 7  EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV 49
          EGLRLDGR   E R ++   G      G     +G T+V+A V
Sbjct: 15 EGLRLDGRGLDEFRPIKITFG---LEYGCVEVSLGKTRVLAQV 54

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

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

 Score = 46.0 bits (110), Expect = 5e-06
 Identities = 17/43 (39%), Positives = 27/43 (62%)

Query: 7  EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV 49
          E +R DGR   E R     +G+++ ADGSA+ ++GNT V+  +
Sbjct: 15 ENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGI 57

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

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

 Score = 40.3 bits (95), Expect = 4e-04
 Identities = 38/154 (24%), Positives = 68/154 (44%), Gaps = 19/154 (12%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           + +R DGR   + R +  E G ++  +GSA   +GNT V+  V    EV +   +  ++ 
Sbjct: 16  QNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKA--EVGSPDPETPNKG 73

Query: 67  L----VRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACI---LTHL--MPRSQ- 116
                V C  + +    G       G+  +TE+S  + + +++     L+ L  +P  Q 
Sbjct: 74  RLEFFVDCSPNASPEFEGRG-----GEELATELSSALERALKSGSAIDLSKLCIVPGKQC 128

Query: 117 --IDIFVQVLQADGGTRSACINAATLALQDAGIP 148
             + + V VL++ G    A   A   AL +  IP
Sbjct: 129 WVLYVDVLVLESGGNLLDAISIAVKAALFNTRIP 162

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	241
TIGR02065	230	ECX1 archaeal exosome-like complex exonuclease 1.	100.0
PRK03983	244	exosome complex exonuclease Rrp41; Provisional	100.0
KOG1068	245	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
PRK00173	238	rph ribonuclease PH; Reviewed	100.0
COG0689	230	Rph RNase PH [Translation, ribosomal structure and	100.0
TIGR01966	236	RNasePH ribonuclease PH. This bacterial enzyme, ri	100.0
PRK04282	271	exosome complex RNA-binding protein Rrp42; Provisi	100.0
COG2123	272	RNase PH-related exoribonuclease [Translation, rib	100.0
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	100.0
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	100.0
KOG1069	217	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	100.0
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	100.0
KOG1614	291	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	100.0
KOG1612	288	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
KOG1613	298	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	100.0
PF01138	132	RNase_PH: 3' exoribonuclease family, domain 1 This	99.97
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.96
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	99.93
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.91
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.83
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.75
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	99.66
PF03725	68	RNase_PH_C: 3' exoribonuclease family, domain 2 Th	99.33

>TIGR02065 ECX1 archaeal exosome-like complex exonuclease 1

Probab=100.00  E-value=5.8e-54  Score=359.43  Aligned_cols=228  Identities=46%  Similarity=0.770  Sum_probs=215.4

Q ss_pred             ccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCccccc
Q 026213            3 FVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDR   82 (241)
Q Consensus         3 ~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~   82 (241)
                      .|+++|+|+|||.++|+|++++++|+++++||||++++|+|+|+|+|+||++.+.+....++++.++|++++.||++..+
T Consensus         2 ~~~~~~~R~DGR~~~e~R~~~~~~g~~~~a~GSa~~~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~~~a~~~~   81 (230)
T TIGR02065         2 LILEDGVRLDGRKPDELRPIKIEAGVLKNADGSAYVEFGGTKIIAAVYGPREMHPRHLQLPDRAVLRVRYHMAPFSTDER   81 (230)
T ss_pred             cccCCCcCCCCCCcccccCeEEEECCCCCCCeEEEEEECCcEEEEEEeCCCccccccccCCCceEEEEEEEeCCcccCCc
Confidence            57899999999999999999999999999999999999999999999999988766666789999999999999998765


Q ss_pred             CCCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEEEeeeC
Q 026213           83 MRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLN  162 (241)
Q Consensus        83 ~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs~~~~~  162 (241)
                      +.. .+++++.+++++|++++++++.++.||++.|+|+++||++||++++|++||+++||.|+||||+++++++++++++
T Consensus        82 ~~~-~~~~~~~~~s~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~DG~~~~aai~aa~lAL~dagIp~~~~v~avtv~~~~  160 (230)
T TIGR02065        82 KRP-GPSRREIEISKVIREALEPAILLEQFPRTAIDVFIEVLQADAGTRCAGLTAASLALADAGIPMRDLVVGVAVGKVD  160 (230)
T ss_pred             cCC-CCCccHHHHHHHHHHHHHHHhChhhcCCeEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCCccccceeeEEEEEEC
Confidence            543 4677888999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          163 STPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLEN  231 (241)
Q Consensus       163 ~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~  231 (241)
                      +.+|+|||.+||..+.+.++|+++++.+++++++++|.++++++.++++.|.++|++++++|++.|+++
T Consensus       161 ~~~v~Dpt~~Ee~~~~~~l~va~~~~~~~i~~i~~~g~~~~e~~~~~l~~a~~~~~~l~~~~~~~l~~~  229 (230)
T TIGR02065       161 GVVVLDLNEEEDMYGEADMPVAMMPKLGEITLLQLDGDMTPDEFRQALDLAVKGIKIIYQIQREALKNK  229 (230)
T ss_pred             CeEEECCCHHHhhcCCCceEEEEeCCCCCEEEEEEecCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            999999999999999999999998888999999999999999999999999999999999999999876

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

>PRK03983 exosome complex exonuclease Rrp41; Provisional

Probab=100.00  E-value=1e-53  Score=360.93  Aligned_cols=234  Identities=47%  Similarity=0.789  Sum_probs=220.1

Q ss_pred             cccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccc
Q 026213            2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGD   81 (241)
Q Consensus         2 ~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~   81 (241)
                      +|++++|+|+|||.++|+|++++++|++++++|||++++|+|+|+|+|+||.+...+....++++.+.|++++.|+++..
T Consensus         7 ~~~~~~~~R~DGR~~~~~R~i~i~~G~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~p~~~~~   86 (244)
T PRK03983          7 KLILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSVDE   86 (244)
T ss_pred             hhhccCCCCCCCCCcCcccceEEEeCCCCCCCeEEEEEECCeEEEEEEecCCccccccccCCCcEEEEEEEEcCCCcccc
Confidence            58899999999999999999999999999999999999999999999999998877766778999999999999999876


Q ss_pred             cCCCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEEEeee
Q 026213           82 RMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL  161 (241)
Q Consensus        82 ~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs~~~~  161 (241)
                      +... .+++++.+++++|+++|++++.++.||++.|+|+++||++|||++++++||+++||.|+||||++++++++++++
T Consensus        87 ~~~~-~~~~~~~~~s~~l~~~l~~~i~~~~~p~~~I~I~i~VL~~DG~~~~aai~Aa~lAL~dagIp~~~~v~avtv~~~  165 (244)
T PRK03983         87 RKRP-GPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKV  165 (244)
T ss_pred             ccCC-CCChhHHHHHHHHHHHHHHhccHHhCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHhcCCccccceeEEEEEEE
Confidence            5433 467788899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          162 NSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLE  236 (241)
Q Consensus       162 ~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~~~~  236 (241)
                      ++.+++|||..||..+.+.++|+++++.++|++++++|.++++++.++++.|.+.+++++++|+++|+++..+..
T Consensus       166 ~~~~i~DPt~~Ee~~~~~~l~va~~~~~~~I~~l~~~G~~~~~~~~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~  240 (244)
T PRK03983        166 DGVIVLDLNKEEDNYGEADMPVAIMPRLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQLQREALKSKYGEIA  240 (244)
T ss_pred             CCEEEECCCHHHhccCCceEEEEEECCCCCEEEEEEecCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            999999999999999999999999878899999999999999999999999999999999999999999877543

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

Probab=100.00  E-value=2.3e-51  Score=334.86  Aligned_cols=240  Identities=54%  Similarity=0.854  Sum_probs=226.9

Q ss_pred             CcccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCccc
Q 026213            1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTG   80 (241)
Q Consensus         1 ~~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~   80 (241)
                      +++...+|.|.|||.++|+|++..+.|++++++||||+++|||||+|.|+||+|++......++++.++|.++.++|++.
T Consensus         5 ~~~~seeg~r~dgRr~~elR~i~~~~g~~~~a~GSay~E~GnTKVl~aV~GPre~~~~~~~~~~~a~lnc~~~~a~Fst~   84 (245)
T KOG1068|consen    5 YETLSEEGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCEVSSAQFSTG   84 (245)
T ss_pred             ccccCccccccCCCChhHhhhhhhhcCccccCCccchhhcCCeEEEEEEeCCcccccccccccccceEEEEEeeeccccc
Confidence            57888999999999999999999999999999999999999999999999999987655557899999999999999999


Q ss_pred             ccCCCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEEEee
Q 026213           81 DRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGY  160 (241)
Q Consensus        81 ~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs~~~  160 (241)
                      ++++..+.+.++++++.+|+++|+++|.++.||+++|+|+|+|++|||+.+++|+||+.+||.|+||||+|+++++|+++
T Consensus        85 ~r~~~~~~~rr~~e~s~~L~~afe~~I~~~lyPrsqIDI~v~VleddG~~laa~inaatlAL~daGI~m~D~i~~~t~~l  164 (245)
T KOG1068|consen   85 DRKKRPKGDRREKELSLMLQQAFEPVILLELYPRSQIDIYVQVLEDDGSNLAAAINAATLALADAGIPMYDLITACTAGL  164 (245)
T ss_pred             hhccCCCccHHHHHHHHHHHHHHHHHHHhhhCccccceEEEEEEECCCccHHHHHHHHHHHHHHcCCChhhhhhhceeee
Confidence            98765567889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhC
Q 026213          161 LNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRRG  240 (241)
Q Consensus       161 ~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~~~~~~~~  240 (241)
                      .++..++||+..||......+||++.+..++|..+|+++.++.+.|...++.+.+.|+++++.++..+.++.++..-..+
T Consensus       165 ~~~~~l~Dl~~~eesa~~~~ltVa~l~~~~~i~~l~~~~~~~~d~l~~vl~~a~~~c~~v~~~l~~~l~~~l~~~~~~~~  244 (245)
T KOG1068|consen  165 ADGTPLLDLTSLEESARAPGLTVAALPNREEIALLQLDERLHCDHLETVLELAIAGCKRVYERLRLVLREHLKNAESALS  244 (245)
T ss_pred             cCCccccccccchhhccCCceEEEEecCcceEEEEEecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcc
Confidence            99999999999999988889999998999999999999999999999999999999999999999999999998765543

>PRK00173 rph ribonuclease PH; Reviewed

Probab=100.00  E-value=6.1e-48  Score=324.39  Aligned_cols=219  Identities=31%  Similarity=0.430  Sum_probs=199.5

Q ss_pred             CCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCC----
Q 026213            9 LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR----   84 (241)
Q Consensus         9 ~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~----   84 (241)
                      +|+|||.++|+|++++++|++++++|||++++|+|+|+|+|+++.+.+ +....+++|.++|+|.++|+++.++..    
T Consensus         1 ~R~DGR~~~e~R~i~~~~g~~~~a~GSa~v~~G~T~Vla~V~~~~~~p-~~~~~~~~g~l~v~~~~~p~a~~~~~~~~~~   79 (238)
T PRK00173          1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVP-RFLKGQGQGWVTAEYGMLPRATHTRNDREAA   79 (238)
T ss_pred             CCCCCCCcccccCeEEEeCCCCCCCeeEEEEecCcEEEEEEEcCCCCC-CccCCCCcEEEEEEEecCCCCCccccccccc
Confidence            599999999999999999999999999999999999999999875433 122456889999999999999887632    


Q ss_pred             CCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhC-----------CCCCCCee
Q 026213           85 KPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDA-----------GIPMRDIV  153 (241)
Q Consensus        85 ~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~-----------gip~~~~~  153 (241)
                      .|+++.++.+++++|+++|+++++++.||++.++|+++||++|||+++|++||+++||+|+           ++||+++|
T Consensus        80 ~g~~~~~~~~~sr~i~r~lr~~i~l~~l~~~~i~v~v~VL~~DG~~~~aai~Aa~~AL~da~~~~~~~~~~~~ip~~~~~  159 (238)
T PRK00173         80 KGKQGGRTQEIQRLIGRSLRAVVDLKALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLKDQV  159 (238)
T ss_pred             CCCCCccHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhhhccCcccCCcccCce
Confidence            3466778899999999999999999999998899999999999999999999999999999           99999999


Q ss_pred             EEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee---cCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          154 TSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA---KLPTNTFEDVMQLAIEGCKAVANYIREVLL  229 (241)
Q Consensus       154 ~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g---~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~  229 (241)
                      +++|++++++.+|+|||.+||..+.+.++|++ ++.++|++++++|   .++++++.++++.|.+.++++++++++.|.
T Consensus       160 ~~vt~~~~~~~~lvDpt~~Ee~~~~~~l~v~~-~~~~~i~~v~~~g~g~~~~~e~l~~~i~~A~~~~~~l~~~~~~~l~  237 (238)
T PRK00173        160 AAVSVGIVDGEPVLDLDYEEDSAAETDMNVVM-TGSGGFVEVQGTAEGAPFSREELDALLDLAEKGIAELVALQKAALA  237 (238)
T ss_pred             eEEEEEEECCEEEECCCHHHHhcCCceEEEEE-CCCCCEEEEEccCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999999999987 5678999999843   699999999999999999999999999885

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

Probab=100.00  E-value=8.4e-48  Score=315.40  Aligned_cols=225  Identities=40%  Similarity=0.622  Sum_probs=210.6

Q ss_pred             cCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccC
Q 026213            4 VSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRM   83 (241)
Q Consensus         4 ~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~   83 (241)
                      ...++.|+|||.++|.|++.++.|++++++||+++++|+|+|+|+|+||.|.+.+....++.+++.++|.+.|+++.+|.
T Consensus         3 ~~~~~~R~dgR~~delR~i~~~~~~~~~a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~ey~m~p~sT~~R~   82 (230)
T COG0689           3 ESEDGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLPRSTDERK   82 (230)
T ss_pred             CcccCcCCCCCCcccccceEEEeccccCCCccEEEEeCCeEEEEEEecCCCCCChhhcCCCceEEEEEEecccccccccc
Confidence            45689999999999999999999999999999999999999999999999888777777889999999999999997765


Q ss_pred             CCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEEEeeeCC
Q 026213           84 RKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNS  163 (241)
Q Consensus        84 ~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs~~~~~~  163 (241)
                      .+.....++++++++|.++|+++++++.||+.+|+|++.|+++||+...|++||+++||+|+|+||.++++|+|+|+.++
T Consensus        83 ~~~~~~gR~~eisrli~~al~~~i~L~~~p~~~I~i~~dVlqaDggTrta~It~A~lAL~DAgipl~~~vaaiSvgi~~~  162 (230)
T COG0689          83 KREADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVGIVDG  162 (230)
T ss_pred             cccccccchhHHHHHHHHHHHHHhhhhhcCccEEEEEEEEEECCCCeeeehhhHHHHHHHHcCCchhhheeEeEEEEECC
Confidence            44322237889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEeCCccccccCCCcEEEEEcCCCC--cEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          164 TPLLDLNYVEDSAGGPDVTVGILPTLD--KVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVL  228 (241)
Q Consensus       164 ~~i~DPt~~Ee~~~~~~~~v~~~~~~~--~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~l  228 (241)
                      .+++||+..|++.+...+.|++.++.+  +|.+++.+|+|+.++|.+++++|.+.|+++++.++++|
T Consensus       163 ~~~lDl~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~~~~~~del~~lL~la~~g~~~~~~~~~~al  229 (230)
T COG0689         163 VIVLDLDYEEDSAAEADMNVVMTGNGGLVEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQREAL  229 (230)
T ss_pred             ceEecCcchhhcccccCceEEEEecCCeEEEEEEeccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999998887877  89999999999999999999999999999999999887

>TIGR01966 RNasePH ribonuclease PH

Probab=100.00  E-value=3.6e-47  Score=319.44  Aligned_cols=217  Identities=32%  Similarity=0.463  Sum_probs=195.9

Q ss_pred             CCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCC----C
Q 026213           10 RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR----K   85 (241)
Q Consensus        10 R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~----~   85 (241)
                      |+|||+++|+|++++++|++++++|||++++|+|+|+|+|+++.+.+. ....+++|.+.|++.+.|+++..+..    .
T Consensus         1 R~DGR~~~e~R~i~i~~G~~~~A~GSa~v~~G~T~Vla~V~~~~~~p~-~~~~~~~g~l~v~~~~~p~a~~~~~~r~~~~   79 (236)
T TIGR01966         1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPP-FLRGSGEGWITAEYGMLPRATQTRNRRESAK   79 (236)
T ss_pred             CCCCCCCCCccCeEEEeCCcCCCCceEEEEecCCEEEEEEEccCccCC-cccCCCcEEEEEEEecCCCCCCCCccccccC
Confidence            899999999999999999999999999999999999999997543221 12235789999999999999886521    2


Q ss_pred             CCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhC-----------CCCCCCeeE
Q 026213           86 PKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDA-----------GIPMRDIVT  154 (241)
Q Consensus        86 ~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~-----------gip~~~~~~  154 (241)
                      |+++.++.+++++|+++|+++++++.||++.|+|+++||++|||+++|++||+++||.|+           ++||+++|+
T Consensus        80 g~~~~~~~e~~~~i~r~lr~~i~l~~l~~~~i~I~v~VL~~DG~~~~aai~Aa~aAL~da~~~~~~~~~~~~ip~~~~~~  159 (236)
T TIGR01966        80 GKQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVA  159 (236)
T ss_pred             CCCCccHHHHHHHHHHHHHHhcCHhhcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHHHHhhhhcCcccCCCccCcee
Confidence            455567888999999999999999999999999999999999999999999999999999           999999999


Q ss_pred             EEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEee---ecCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          155 SCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMD---AKLPTNTFEDVMQLAIEGCKAVANYIREVL  228 (241)
Q Consensus       155 ~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~---g~~~~~~l~~~l~~a~~~~~~i~~~i~~~l  228 (241)
                      ++|++++++.+|+|||.+||..+.+.++++++ +.++|++++++   +.++++++.++++.|.++++++++.|+++|
T Consensus       160 ~vt~~~~~~~~v~Dpt~~Ee~~~~~~l~l~~~-~~~~i~~i~~~g~~~~~~~~~l~~~i~~a~~~~~~l~~~~~~~l  235 (236)
T TIGR01966       160 AVSVGIVDGEPVLDLDYEEDSAADVDMNVVMT-GSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQKQAL  235 (236)
T ss_pred             EEEEEEECCEEEECCChhHHhccCceEEEEEc-CCCCEEEEEecCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999874 57899999984   469999999999999999999999999986

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

>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional

Probab=100.00  E-value=1.1e-45  Score=316.65  Aligned_cols=222  Identities=22%  Similarity=0.313  Sum_probs=197.8

Q ss_pred             cCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccC
Q 026213            4 VSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRM   83 (241)
Q Consensus         4 ~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~   83 (241)
                      ++++|+|+|||.++|+|++.+++|++++++|||++++|+|+|+|+|+++  +..|....|++|.+.|++++.|+++... 
T Consensus        19 ~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~vl~~V~~~--~~~p~~~~~~~g~i~~~v~~~~~a~~~~-   95 (271)
T PRK04282         19 LLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLE--IGEPFPDTPNEGVLIVNAELLPLASPTF-   95 (271)
T ss_pred             HHhcCCCCCCCCCccccCeEEEeCCccCCCcEEEEEECCCEEEEEEEEE--EecCCCCCCCCCEEEEEEEECCCcCccc-
Confidence            3578999999999999999999999999999999999999999999963  3344445678999999999999987654 


Q ss_pred             CCCCCCchhHHHHHHHHHHHHHh--hccCCC---C---ccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCC-------
Q 026213           84 RKPKGDRRSTEISLVIRQTMEAC--ILTHLM---P---RSQIDIFVQVLQADGGTRSACINAATLALQDAGIP-------  148 (241)
Q Consensus        84 ~~~~~~~~~~~l~~~l~~~l~~~--i~l~~~---p---~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip-------  148 (241)
                      ..+.+++++.+++++|++++++.  ++++.+   |   .|.|+|+++||++|||++||+++|+++||.|+++|       
T Consensus        96 ~~~~~~~~~~~l~~~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG~~~daa~~Aa~aAL~~~~iP~~~~~~~  175 (271)
T PRK04282         96 EPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEGED  175 (271)
T ss_pred             cCCCCCHHHHHHHHHHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhCCCCcEEEcCC
Confidence            34567778889999999999886  444433   4   49999999999999999999999999999999995       


Q ss_pred             -------------CCCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEee--ecCCHHHHHHHHHHH
Q 026213          149 -------------MRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMD--AKLPTNTFEDVMQLA  213 (241)
Q Consensus       149 -------------~~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~--g~~~~~~l~~~l~~a  213 (241)
                                   |+++|+++|++++++.+|+|||.+||..+.+.++|+++ ..|+++++++.  |+++++++.++++.|
T Consensus       176 ~~~~~~~~~~~l~~~~~p~~vt~~~~~~~~v~Dpt~~Ee~~~~~~l~va~~-~~g~i~~l~~~g~~~~~~~~l~~~i~~A  254 (271)
T PRK04282        176 GVVDKLGEDFPLPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTD-EDGNIVAIQKSGIGSFTEEEVDKAIDIA  254 (271)
T ss_pred             ceeccCCCcccCCCCCeeEEEEEEEECCEEEECCCHHHHhhcCceEEEEEC-CCCcEEEEEcCCCCCCCHHHHHHHHHHH
Confidence                         99999999999999999999999999999999999985 56799999975  469999999999999


Q ss_pred             HHHHHHHHHHHHHHHH
Q 026213          214 IEGCKAVANYIREVLL  229 (241)
Q Consensus       214 ~~~~~~i~~~i~~~l~  229 (241)
                      .+.++++++.++++|+
T Consensus       255 ~~~~~~l~~~~~~~l~  270 (271)
T PRK04282        255 LEKAKELREKLKEALG  270 (271)
T ss_pred             HHHHHHHHHHHHHHhc
Confidence            9999999999999874

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

Probab=100.00  E-value=4.8e-43  Score=290.04  Aligned_cols=222  Identities=21%  Similarity=0.310  Sum_probs=201.5

Q ss_pred             cCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccC
Q 026213            4 VSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRM   83 (241)
Q Consensus         4 ~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~   83 (241)
                      +++.|+|+|||.++|+|++.+++|+++.++|||+|++|+|+|+|+|+.  ++.+|+++.|++|.+.+++...|++.... 
T Consensus        18 ll~~g~R~DGR~~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK~--eig~Pf~DtP~eG~~~~n~El~Plas~~f-   94 (272)
T COG2123          18 LLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKA--EIGEPFPDTPNEGVLVVNVELSPLASPSF-   94 (272)
T ss_pred             HhccCcccCCCCcccccceEEEeCceecCCCcEEEEecCeEEEEEEEc--ccCCCCCCCCCCceEEeeeeeeccccccc-
Confidence            356899999999999999999999999999999999999999999998  67889999999999999999888887654 


Q ss_pred             CCCCCCchhHHHHHHHHHHHHHh--hccCCC---C---ccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCC-------
Q 026213           84 RKPKGDRRSTEISLVIRQTMEAC--ILTHLM---P---RSQIDIFVQVLQADGGTRSACINAATLALQDAGIP-------  148 (241)
Q Consensus        84 ~~~~~~~~~~~l~~~l~~~l~~~--i~l~~~---p---~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip-------  148 (241)
                      ..|+++....++++.++|.++.+  ++++++   +   .|.+.+++++|++|||++||++.|+++||+++++|       
T Consensus        95 E~Gppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~Da~~lA~~aAL~~t~vP~~~~~~~  174 (272)
T COG2123          95 EPGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAAVAALLNTRVPKAVEVGD  174 (272)
T ss_pred             cCCCCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHhcCCCceeecCC
Confidence            34677888889999999999874  555554   2   49999999999999999999999999999999988       


Q ss_pred             ---------------CCCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEee--ecCCHHHHHHHHH
Q 026213          149 ---------------MRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMD--AKLPTNTFEDVMQ  211 (241)
Q Consensus       149 ---------------~~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~--g~~~~~~l~~~l~  211 (241)
                                     +.+.|+++|++++++.+++|||.+||..+++.++|.+ ++.++|+.+++.  |.++++.+.+|++
T Consensus       175 ~~~v~~~~~~~~pl~~~~~pi~vt~a~ig~~lvvDPsleEe~v~d~~ltit~-~~~~~Iv~iqK~g~~~~~~~~~~~~~~  253 (272)
T COG2123         175 GEIVIEVEEEPVPLPVSNPPISVTFAKIGNVLVVDPSLEEELVADGRLTITV-NEDGEIVAIQKVGGGSITESDLEKALK  253 (272)
T ss_pred             cceeecccCCCcccccCCCceEEEEEEECCEEEeCCCcchhhhcCceEEEEE-CCCCcEEEEEEcCCCcCCHHHHHHHHH
Confidence                           4788999999999999999999999999999999987 688999999985  4699999999999


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 026213          212 LAIEGCKAVANYIREVLL  229 (241)
Q Consensus       212 ~a~~~~~~i~~~i~~~l~  229 (241)
                      .|.+.+.++...+.+.|+
T Consensus       254 ~A~~~~~kl~~~~~~~L~  271 (272)
T COG2123         254 TALSKAEKLREALKEALK  271 (272)
T ss_pred             HHHHHHHHHHHHHHHhhc
Confidence            999999999999988875

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=100.00  E-value=8.7e-43  Score=329.61  Aligned_cols=230  Identities=25%  Similarity=0.391  Sum_probs=206.5

Q ss_pred             cccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEE-EcCcccccccc--CCCCceEEEEEEeecCCc
Q 026213            2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-YGPREVQNKSQ--QMSDQALVRCEYSMANFS   78 (241)
Q Consensus         2 ~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V-~~p~e~~~~~~--~~~~~~~i~v~~~~~~~~   78 (241)
                      +|++++|.|+|||.++|+|++++++|+++++||||+|+.|+|+|+|+| .||.+..++.+  ...+.+.+.++|+++||+
T Consensus       303 ~~il~~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSa~~~~G~Tqvl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs  382 (684)
T TIGR03591       303 ERILKEGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQIIDDLEGEYRKRFMLHYNFPPYS  382 (684)
T ss_pred             HHHhcCCCCCCCCCCCCcCceEEEeCCCCCCCceEEEEeCCeEEEEEEecCCcccccCCcccCCCccEEEEEEEEcCCCC
Confidence            588999999999999999999999999999999999999999999999 58865543322  124579999999999999


Q ss_pred             ccccCCCCCCCchhHHHHHHHHHHHHHhhcc-CCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEE
Q 026213           79 TGDRMRKPKGDRRSTEISLVIRQTMEACILT-HLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCS  157 (241)
Q Consensus        79 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l-~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs  157 (241)
                      ++++++.+.+++++.+++++++++|++++++ +.|| |+|+|+++||++|||.++|+++|+++||+|+||||++.+++++
T Consensus       383 ~~e~~~~g~~~rrei~~~~l~~ral~~~i~~~~~~p-~tI~v~~~VLesdGs~~~Aai~aaslAL~dAgvP~~~~Vagvs  461 (684)
T TIGR03591       383 VGEVGRVGGPGRREIGHGALAERALKAVLPSEEEFP-YTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIA  461 (684)
T ss_pred             CCCcCCCCCCChHHHHHHHHHHHHHHHhcCccccCC-eEEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCCcCCEEEEE
Confidence            9998777778899999999999999999986 7899 5799999999999999999999999999999999999999999


Q ss_pred             EeeeC-C----eeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeec---CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          158 AGYLN-S----TPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAK---LPTNTFEDVMQLAIEGCKAVANYIREVLL  229 (241)
Q Consensus       158 ~~~~~-~----~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~---~~~~~l~~~l~~a~~~~~~i~~~i~~~l~  229 (241)
                      +|+++ +    .+++||+..|+..++..++|+. +.. .|++++++++   ++.+.+.++++.|.+++.+|++.|++++.
T Consensus       462 ~gli~~~~~~~~il~D~~~~Ed~~~d~d~~va~-t~~-gI~~lq~d~k~~~i~~~~l~~al~~a~~~~~~I~~~m~~~l~  539 (684)
T TIGR03591       462 MGLIKEGDERFAVLSDILGDEDHLGDMDFKVAG-TRD-GITALQMDIKIDGITREIMEQALEQAKEGRLHILGEMNKVIS  539 (684)
T ss_pred             EEEEcCCCcceEEEeCCChHHHhcCCceEEEEE-cCC-ceEEEEEEcCcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99994 2    4899999999999999999975 344 4999999754   69999999999999999999999999999


Q ss_pred             HHHHH
Q 026213          230 ENTKQ  234 (241)
Q Consensus       230 ~~~~~  234 (241)
                      ++.++
T Consensus       540 ~~~~~  544 (684)
T TIGR03591       540 EPRAE  544 (684)
T ss_pred             hhhcc
Confidence            98653

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=100.00  E-value=3e-42  Score=326.67  Aligned_cols=230  Identities=25%  Similarity=0.411  Sum_probs=204.4

Q ss_pred             cccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEE-EcCcccccccc--CCCCceEEEEEEeecCCc
Q 026213            2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-YGPREVQNKSQ--QMSDQALVRCEYSMANFS   78 (241)
Q Consensus         2 ~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V-~~p~e~~~~~~--~~~~~~~i~v~~~~~~~~   78 (241)
                      +||+++|.|+|||.++|+|++++++|+++++||||+|+.|+|+|+|+| .||....++..  ...+.+.+.++|+++||+
T Consensus       307 ~~il~~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSal~~~G~T~Vl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~pfs  386 (693)
T PRK11824        307 RRILEEGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLRDEQIIDGLEGEYKKRFMLHYNFPPYS  386 (693)
T ss_pred             HHHhcCCCCCCCCCcCcccceEEEeCCCCCCCceEEEEECCeEEEEEEecCCCcccccccccCCCCcEEEEEEEEcCCCC
Confidence            589999999999999999999999999999999999999999999999 47743222211  123679999999999999


Q ss_pred             ccccCCCCCCCchhHHHHHHHHHHHHHhhcc-CCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEE
Q 026213           79 TGDRMRKPKGDRRSTEISLVIRQTMEACILT-HLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCS  157 (241)
Q Consensus        79 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l-~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs  157 (241)
                      ++++++.+.+++++.+++++++++|++++++ +.|| |+|+|+++||++|||.++|+++|+++||+|+||||++++++++
T Consensus       387 ~~e~~~~~~~~rre~~~~~li~ral~~vi~~~~~~p-~~I~v~~~VLe~dGs~~~Aai~aaslAL~dAgvP~~~~Va~vs  465 (693)
T PRK11824        387 VGETGRVGSPGRREIGHGALAERALEPVLPSEEEFP-YTIRVVSEILESNGSSSMASVCGSSLALMDAGVPIKAPVAGIA  465 (693)
T ss_pred             CCCcCCCCCCChhHHHHHHHHHHHHHHhcCcccCCC-EEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCccCceeEEE
Confidence            9988777778899999999999999999998 6888 5999999999999999999999999999999999999999999


Q ss_pred             EeeeC-C---eeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeec---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          158 AGYLN-S---TPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAK---LPTNTFEDVMQLAIEGCKAVANYIREVLLE  230 (241)
Q Consensus       158 ~~~~~-~---~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~---~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~  230 (241)
                      +|+++ +   .+++||+..|+..++..++|+. +..+ |++++++++   ++.+.+.++++.|.+++.+|++.|.+++.+
T Consensus       466 ~gli~~~~~~~il~D~~~~Ed~~~d~d~~va~-t~~g-i~~lq~d~k~~~i~~~~l~~al~~a~~g~~~I~~~M~~aI~~  543 (693)
T PRK11824        466 MGLIKEGDKYAVLTDILGDEDHLGDMDFKVAG-TRDG-ITALQMDIKIDGITREILEEALEQAKEGRLHILGKMNEAISE  543 (693)
T ss_pred             EEEEcCCCceEEEcCCChhhHhhCCceEEEEe-cCCc-eEEEEEecccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            99994 3   3889999999999999999975 3444 999998754   699999999999999999999999999976


Q ss_pred             HHHH
Q 026213          231 NTKQ  234 (241)
Q Consensus       231 ~~~~  234 (241)
                      ..+.
T Consensus       544 ~r~~  547 (693)
T PRK11824        544 PRAE  547 (693)
T ss_pred             Chhh
Confidence            6543

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

Probab=100.00  E-value=1.7e-41  Score=267.60  Aligned_cols=208  Identities=27%  Similarity=0.435  Sum_probs=187.4

Q ss_pred             CCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCCCCCCCchhHHHHH
Q 026213           18 EMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISL   97 (241)
Q Consensus        18 e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~~~l~~   97 (241)
                      ++|++.++.|+++++|||+.|++|+|+|+|+|+||.+++.+. +.+++..++|.++...         |.++..++.+++
T Consensus         4 ~lr~~~cei~iLsr~dGSs~fsqgdT~V~c~V~GP~dvk~r~-E~~~katleVi~rp~~---------G~~~~~eK~~e~   73 (217)
T KOG1069|consen    4 RLRGIACEISILSRPDGSSEFSQGDTKVICSVYGPIDVKARQ-EDPEKATLEVIWRPKS---------GVNGTVEKVLER   73 (217)
T ss_pred             hhhhhhhhhceecCCCCccceecCCcEEEEEeeCCcchhhcc-cCchhceEEEEEeccc---------CcchHHHHHHHH
Confidence            789999999999999999999999999999999999987654 5688899999997432         344567889999


Q ss_pred             HHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEEEeeeCC-eeEEeCCcccccc
Q 026213           98 VIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNS-TPLLDLNYVEDSA  176 (241)
Q Consensus        98 ~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs~~~~~~-~~i~DPt~~Ee~~  176 (241)
                      .|++++++.|.++.||+..|+|.+||+++||+.+++|+|||++||.|+||||+++++++++++.++ .+++|||..+++.
T Consensus        74 iI~~tl~~~I~l~l~Prt~iqVsiqvv~ddgs~LacaINaAclALvDaGIpl~~mfcai~~~~~~d~~lv~Dpt~~qek~  153 (217)
T KOG1069|consen   74 IIRKTLSKAIILELYPRTTIQVSIQVVEDDGSTLACAINAACLALVDAGIPLRSMFCAISCALHEDGVLVLDPTAKQEKI  153 (217)
T ss_pred             HHHHHHHHhheeeecCCceEEEEEEEEecCCcchHHHHHHHHHHHHhcCCchHHhhhhceEEEecCccEEECCcHHhhhh
Confidence            999999999999999999999999999999999999999999999999999999999999999854 8999999999997


Q ss_pred             CCCcEEEEEc---CCCCcEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          177 GGPDVTVGIL---PTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQL  235 (241)
Q Consensus       177 ~~~~~~v~~~---~~~~~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~~~  235 (241)
                      +.+..++++.   ....+++.++..|.++.+++..+++.|+..++++++++++.|++..++.
T Consensus       154 ~~~~~~lsf~~~~~~~~~vi~s~t~G~~~~d~lf~~le~a~~~~~~~f~f~r~~~q~~~s~~  215 (217)
T KOG1069|consen  154 STARATLSFEGGSLGEPKVIISETNGEKSEDQLFYVLELAQAAAQSLFPFYREVLQRKYSKS  215 (217)
T ss_pred             hhceEEEEEecCCCCCcceEEEeccCCCCHHHHHHHHHhhHHHHHHHHHHHHHHHHhhcCcc
Confidence            7777666652   2356888889999999999999999999999999999999999887654

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=100.00  E-value=1.2e-40  Score=310.47  Aligned_cols=228  Identities=26%  Similarity=0.398  Sum_probs=203.7

Q ss_pred             CcccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEc-Ccccccccc--CCCCceEEEEEEeecCC
Q 026213            1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYG-PREVQNKSQ--QMSDQALVRCEYSMANF   77 (241)
Q Consensus         1 ~~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~-p~e~~~~~~--~~~~~~~i~v~~~~~~~   77 (241)
                      +|+++++|.|+|||.++++|++++++|+++++||||+++.|+|+|+|.++. |.+..+..+  ..++.+.+.|+|+++||
T Consensus       327 r~~il~~g~R~DGR~~~eiR~i~~~~g~l~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~~~~~~~~YnfpPF  406 (719)
T TIGR02696       327 RERVLTEGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPPY  406 (719)
T ss_pred             HHHHhcCCCCCCCCCccccccceeecCCCCCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccccceEEEEEeCCCC
Confidence            378999999999999999999999999999999999999999999998863 332222111  12457888999999999


Q ss_pred             cccccCCCCCCCchhHHHHHHHHHHHHHhhc-cCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEE
Q 026213           78 STGDRMRKPKGDRRSTEISLVIRQTMEACIL-THLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSC  156 (241)
Q Consensus        78 ~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~-l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~v  156 (241)
                      +++++++.+.+++++.+++++++++|++++. ++.||++ |.+.++||++||+...|++||+++||+||||||+++++++
T Consensus       407 St~er~~~~~~~RReighg~La~rALe~vI~~~e~fP~T-IrvvseVLeSdGSss~AsIcaasLALmDAGVPmkd~VAgi  485 (719)
T TIGR02696       407 STGETGRVGSPKRREIGHGALAERALVPVLPSREEFPYA-IRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAGI  485 (719)
T ss_pred             cccCCCCCCCCCccHHHHHHHHHHHHHHhhCcHhhCCCE-EEEEEEeeccCCcHHHHHHHHHHHHHHHcCcchhheeeEE
Confidence            9999888777888999999999999999997 6999996 8899999999999999999999999999999999999999


Q ss_pred             EEeeeCC----e----eEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeecC---CHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          157 SAGYLNS----T----PLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKL---PTNTFEDVMQLAIEGCKAVANYIR  225 (241)
Q Consensus       157 s~~~~~~----~----~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~~---~~~~l~~~l~~a~~~~~~i~~~i~  225 (241)
                      ++|++++    .    +++||+..|+...+..+.++  ++.+.|++++++|++   +.+.+.+++++|.+++.+|++.|+
T Consensus       486 s~Gli~e~~~~~~~~~iL~Di~g~ED~~Gdmdfkva--gt~~gIt~lQmd~ki~gi~~e~l~~aL~~A~~g~~~Il~~m~  563 (719)
T TIGR02696       486 AMGLISDEVDGETRYVALTDILGAEDAFGDMDFKVA--GTSEFVTALQLDTKLDGIPASVLASALKQARDARLAILDVMA  563 (719)
T ss_pred             EEEEeccccCCCcceeEEeCCCchhhhcCCceEEEE--ecCCCEEEEEEEeeECCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999933    2    89999999999988888875  567899999999875   889999999999999999999999


Q ss_pred             HHHHHH
Q 026213          226 EVLLEN  231 (241)
Q Consensus       226 ~~l~~~  231 (241)
                      ++|...
T Consensus       564 ~al~~p  569 (719)
T TIGR02696       564 EAIDTP  569 (719)
T ss_pred             HHHhCc
Confidence            999877

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

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=100.00  E-value=2.7e-39  Score=307.05  Aligned_cols=230  Identities=25%  Similarity=0.396  Sum_probs=204.7

Q ss_pred             cccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEE-cCccccccccC---CCCceEEEEEEeecCC
Q 026213            2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVY-GPREVQNKSQQ---MSDQALVRCEYSMANF   77 (241)
Q Consensus         2 ~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~-~p~e~~~~~~~---~~~~~~i~v~~~~~~~   77 (241)
                      +||+.+|.|+|||.++|.|++.+++|.++++||||+|++|+|+|+|+|+ ||.+..++.+.   .+....+.++|+++|+
T Consensus       431 ~~i~~~g~R~DGR~~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVLatVtlGp~~~~q~~d~l~~~~~~~~f~~~y~fPPf  510 (891)
T PLN00207        431 RRIVEGGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEVKRFYLQYSFPPS  510 (891)
T ss_pred             HHHhcCCCCCCCCCcCccceEEEEeCCcCCCCceEEEEECCeEEEEEEEecCccccccccccccccceeeEEEEEEcCCC
Confidence            5789999999999999999999999999999999999999999999996 88765443222   1346788899999999


Q ss_pred             cccccCCCCCCCchhHHHHHHHHHHHHHhhccC-CCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEE
Q 026213           78 STGDRMRKPKGDRRSTEISLVIRQTMEACILTH-LMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSC  156 (241)
Q Consensus        78 ~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~-~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~v  156 (241)
                      +++++++.+.+++++.+++++++++|++++..+ .|| |+|+|+++||++||+..+|++||+++||+|+||||++.++++
T Consensus       511 s~ge~~r~g~psrREi~hg~L~eRALrpvip~~~~fP-~tIrV~~~VLesDGSssmAaV~aaSLALmDAGIPmk~~VAGv  589 (891)
T PLN00207        511 CVGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFP-YTIRVESTITESNGSSSMASVCGGCLALQDAGVPVKCPIAGI  589 (891)
T ss_pred             CCccccCCCCCCHHHHHHHHHHHHHHHHhCCcccCCC-EEEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCccCceeEE
Confidence            998877777788899999999999999999985 899 599999999999999999999999999999999999999999


Q ss_pred             EEeee-C-------Ce--eEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeec---CCHHHHHHHHHHHHHHHHHHHHH
Q 026213          157 SAGYL-N-------ST--PLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAK---LPTNTFEDVMQLAIEGCKAVANY  223 (241)
Q Consensus       157 s~~~~-~-------~~--~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~---~~~~~l~~~l~~a~~~~~~i~~~  223 (241)
                      ++|++ +       +.  +++||+..|+..++..|.|+  ++.+.|++++++++   ++.+.+.++++.|.+++.+|.+.
T Consensus       590 svGli~d~~~~~~~g~~~IL~Dp~g~Ed~~gdmDfkVA--gT~~gIt~iqmd~k~~gis~e~l~eAL~~A~~g~~~Il~~  667 (891)
T PLN00207        590 AMGMVLDTEEFGGDGSPLILSDITGSEDASGDMDFKVA--GNEDGITAFQMDIKVGGITLPIMERALLQAKDGRKHILAE  667 (891)
T ss_pred             EEEEEecccccCCCCcEEEEeCCCHHHHhcCCceEEEE--ecccceEEEEEecccCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            99998 3       23  55799999999999888887  46679999999764   58999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 026213          224 IREVLLENTKQ  234 (241)
Q Consensus       224 i~~~l~~~~~~  234 (241)
                      |++++.+...+
T Consensus       668 M~~~i~~pr~~  678 (891)
T PLN00207        668 MSKCSPPPSKR  678 (891)
T ss_pred             HHHHHhhhhhh
Confidence            99999877653

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

Probab=100.00  E-value=3.7e-39  Score=260.97  Aligned_cols=229  Identities=23%  Similarity=0.295  Sum_probs=202.1

Q ss_pred             cCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccC
Q 026213            4 VSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRM   83 (241)
Q Consensus         4 ~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~   83 (241)
                      .++.|.|.|||++.|+|.+.+++|   .-.||+.+++|+|+|+|.|+.  ++.+|+.+.|.+|.+++...+.|++...-.
T Consensus        17 alk~g~R~DgR~l~efR~lei~fG---ke~gs~~vt~G~Tkvm~~vt~--~ia~Py~dRP~eG~~~I~telsPmA~~sfE   91 (291)
T KOG1614|consen   17 ALKAGLRFDGRSLEEFRDLEIEFG---KEYGSVLVTMGNTKVMARVTA--QIAQPYIDRPHEGSFSIFTELSPMASPSFE   91 (291)
T ss_pred             HHHhcccccccchhhhhceEEEec---cccccEEEEecCeeEEEEeeh--hhcCcccCCCCCCeeeeeeccccccccccC
Confidence            467899999999999999999999   578999999999999999998  678899999999999998888888866432


Q ss_pred             CCCCCCchhHHHHHHHHHHHHH--hhccCCCC------ccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCC-------
Q 026213           84 RKPKGDRRSTEISLVIRQTMEA--CILTHLMP------RSQIDIFVQVLQADGGTRSACINAATLALQDAGIP-------  148 (241)
Q Consensus        84 ~~~~~~~~~~~l~~~l~~~l~~--~i~l~~~p------~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip-------  148 (241)
                       .|..+..+.++.++|+++++.  ++++|.+.      .|.|++++++|+.|||++||+..|+.+||++.+-|       
T Consensus        92 -~Gr~~~~~v~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlvDaA~iAviaaL~hFrrPdvTv~g~  170 (291)
T KOG1614|consen   92 -PGRKGESEVELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLVDAACIAVIAALMHFRRPDVTVGGE  170 (291)
T ss_pred             -CCCccchHHHHHHHHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCeehhHHHHHHHHHHhcCCCCcccccc
Confidence             345567788999999999987  45556442      49999999999999999999999999999999943       


Q ss_pred             ----------------CCCeeEEEEEeeeC--CeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeec--CCHHHHHH
Q 026213          149 ----------------MRDIVTSCSAGYLN--STPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAK--LPTNTFED  208 (241)
Q Consensus       149 ----------------~~~~~~~vs~~~~~--~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~--~~~~~l~~  208 (241)
                                      ++|+|+|+||++++  +..|+|||..||...++.++|++ ++++++|.+++.|.  ++..++..
T Consensus       171 ev~ihp~eEr~PvPL~I~HmPIC~tf~ffnkG~ivviDpt~~Ee~~~dGs~vVt~-Nk~rEVc~i~k~G~~~~~~~~i~~  249 (291)
T KOG1614|consen  171 EVIIHPVEEREPVPLSIHHMPICFTFGFFNKGEIVVIDPTEKEEAVMDGSMVVTM-NKNREVCAIQKSGGEILDESVIER  249 (291)
T ss_pred             eeEecChhccCCcceeeeeccceEEEEEecCceEEEeCCcHHHHhccCceEEEEE-cCCccEEEEecCCCccccHHHHHH
Confidence                            69999999999996  46789999999999999999975 68899999998653  68999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 026213          209 VMQLAIEGCKAVANYIREVLLENTKQLECRR  239 (241)
Q Consensus       209 ~l~~a~~~~~~i~~~i~~~l~~~~~~~~~~~  239 (241)
                      |...|...+.++...+.+.|+++..++-+++
T Consensus       250 C~k~A~~~a~~vt~ii~e~l~~d~~~r~~~~  280 (291)
T KOG1614|consen  250 CYKLAKDRAVEVTGIILEALEEDQRERSAQK  280 (291)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            9999999999999999999999988876654

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=100.00  E-value=1.6e-32  Score=259.90  Aligned_cols=204  Identities=24%  Similarity=0.371  Sum_probs=179.6

Q ss_pred             cceEEEeCCC-CCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccc-----cCCCCCCCchhH
Q 026213           20 RQLRAEIGNV-AKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGD-----RMRKPKGDRRST   93 (241)
Q Consensus        20 R~i~i~~~~l-~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~-----~~~~~~~~~~~~   93 (241)
                      |++.+++|.+ ++|+|||++++|+|+|+|+|++|.+.+    +..+...++|+|...+++.+.     .++.|+|++++.
T Consensus         5 R~i~ie~G~la~~AdGSa~v~~G~T~VlatV~~~~~~~----~~~df~pL~vey~e~~~A~gkipg~f~kReg~p~~~ei   80 (684)
T TIGR03591         5 RTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAK----EGQDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSEKET   80 (684)
T ss_pred             ccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCC----CCCceEeEEEEEEehhhhccCCCCCcccCCCCCCHHHH
Confidence            8999999999 579999999999999999999987542    224678999999977765542     233467889999


Q ss_pred             HHHHHHHHHHHHhhccCCCCc---cEEEEEEEEEeCCCchH-h-HHHHHHHHHHHhCCCCCCCeeEEEEEeeeCCeeEEe
Q 026213           94 EISLVIRQTMEACILTHLMPR---SQIDIFVQVLQADGGTR-S-ACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLD  168 (241)
Q Consensus        94 ~l~~~l~~~l~~~i~l~~~p~---~~i~i~v~il~~dG~~l-~-a~i~a~~~AL~~~gip~~~~~~~vs~~~~~~~~i~D  168 (241)
                      +++++|++.++++     ||+   |.|+|+++||++||+.. + +++||+++||.+++||++++++++++|+++|.+++|
T Consensus        81 l~srlIdR~lrpl-----fp~~~~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~idg~~ild  155 (684)
T TIGR03591        81 LTSRLIDRPIRPL-----FPKGFRNEVQVVATVLSYDPENDPDILAIIGASAALAISGIPFNGPIAAVRVGYIDGQYVLN  155 (684)
T ss_pred             HHHHHHhhHHHHh-----cCCCCCceEEEEEEEEecCcCCchHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCEEEEc
Confidence            9999999999886     565   89999999999999975 4 999999999999999999999999999999999999


Q ss_pred             CCccccccCCCcEEEEEcCCCCcEEEEEeeec-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          169 LNYVEDSAGGPDVTVGILPTLDKVTLLQMDAK-LPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ  234 (241)
Q Consensus       169 Pt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~-~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~~  234 (241)
                      ||.+|+..++..++|+  .+.+.+++++.++. ++.+++.++++.|.++++++.+++++.++++.+.
T Consensus       156 Pt~~E~~~s~~~l~va--~t~~~i~mie~~~~~i~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~~~  220 (684)
T TIGR03591       156 PTVDELEKSDLDLVVA--GTKDAVLMVESEAKELSEEVMLGAIEFGHEEIQPVIEAIEELAEEAGKE  220 (684)
T ss_pred             CCHHHHhhCCceEEEE--ccCCcEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence            9999999999888886  45578999998765 9999999999999999999999999999888754

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).

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

Probab=100.00  E-value=1.7e-31  Score=217.65  Aligned_cols=222  Identities=17%  Similarity=0.225  Sum_probs=181.7

Q ss_pred             CCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCC-eEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCC
Q 026213            6 PEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGN-TKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR   84 (241)
Q Consensus         6 ~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~-T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~   84 (241)
                      +..+|+|||.++|+|++.+++|+++++||||+|++|+ |.|+++|+.  |+..|+.+.|+++.+.+.+++.|-++++-. 
T Consensus        18 e~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVKa--Evg~~~~~~p~egk~~~~VD~S~sasp~f~-   94 (288)
T KOG1612|consen   18 EPDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKA--EVGSPDDETPVEGKYLFFVDCSPSASPQFQ-   94 (288)
T ss_pred             CcccccCCcCccccceEEEEeccccCCCCcEEEEecCCceEEEEEee--eccCccccCCCCCeEEEEEEecCCcCcccc-
Confidence            4679999999999999999999999999999999998 899999998  666677777888888777777776654322 


Q ss_pred             CCCC-CchhHHHHHHHHHHHHH---hhccCC---CC--ccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCC-------
Q 026213           85 KPKG-DRRSTEISLVIRQTMEA---CILTHL---MP--RSQIDIFVQVLQADGGTRSACINAATLALQDAGIP-------  148 (241)
Q Consensus        85 ~~~~-~~~~~~l~~~l~~~l~~---~i~l~~---~p--~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip-------  148 (241)
                       |+. +....++...++++|.+   .+++..   -|  +|.|+|++.+++.|||++||+..|+.+||-++.+|       
T Consensus        95 -gRggde~~~eltsaLq~~l~~~~sgv~ls~L~lt~~~~W~i~VDvlVi~s~gn~~dAiS~Ai~~AL~~T~lPkv~v~~d  173 (288)
T KOG1612|consen   95 -GRGGDELVEELTSALQRVLNSLGSGVDLSKLQLTPGYCWKIYVDVLVISSDGNLLDAISIAIYAALNNTRLPKVIVAFD  173 (288)
T ss_pred             -CCChhhHHHHHHHHHHHHHhCcCcccchhheeccCCeeEEEEEeEEEEecCCCHHHHHHHHHHHHHhcccCCccccccc
Confidence             222 23344677777777766   133332   23  59999999999999999999999999999999988       


Q ss_pred             --------------------CCCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEee--ecCCHHHH
Q 026213          149 --------------------MRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMD--AKLPTNTF  206 (241)
Q Consensus       149 --------------------~~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~--g~~~~~~l  206 (241)
                                          ...+|+-++++.++..+++|||.+||.++...+.|++ ...|-+..++.-  |.+.++-+
T Consensus       174 d~~~~~i~~s~~~Yd~~~~~~~~~P~ivtlskIG~~~lVD~T~eEe~~a~s~l~Isv-~a~givs~~r~VG~G~l~~s~i  252 (288)
T KOG1612|consen  174 DDGEVEILLSDEEYDLMVKLVENVPLIVTLSKIGTNMLVDPTAEEESVANSGLLISV-SAGGIVSCTRSVGLGDLDPSSI  252 (288)
T ss_pred             cCCceeeccCcccchhhhhhcccCCEEEEEEeecceEEccCCccHHHhhhcceEEEE-ecCcceEEEEEecCCCCChhhH
Confidence                                2456889999999999999999999999999999998 455655555553  45889999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          207 EDVMQLAIEGCKAVANYIREVLLENT  232 (241)
Q Consensus       207 ~~~l~~a~~~~~~i~~~i~~~l~~~~  232 (241)
                      .++++++.+-...++..+.+.|.+..
T Consensus       253 ~~mle~~~~~~e~l~~~l~k~L~~~e  278 (288)
T KOG1612|consen  253 PEMLEQGKAVVETLAPDLVKSLENEE  278 (288)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHhhhhh
Confidence            99999999999999988888887643

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

Probab=100.00  E-value=9.4e-33  Score=223.41  Aligned_cols=217  Identities=21%  Similarity=0.282  Sum_probs=179.2

Q ss_pred             cCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccC
Q 026213            4 VSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRM   83 (241)
Q Consensus         4 ~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~   83 (241)
                      .+.+++|+|||...|+|.+.++.|.++.+|||+.++.|+|.|+|++++  |+..|..+.|++|.+..+|.++|.++. +.
T Consensus        31 hLse~~RpdgR~lgefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~--ei~epstdapdeg~Iv~n~~lpplcs~-r~  107 (298)
T KOG1613|consen   31 HLSEGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKA--EIAEPSTDAPDEGDIVPNYALPPLCSS-RF  107 (298)
T ss_pred             HhhcccCcchhhhhHHhhhheecCceeccCcHHHHhcCCcEEEEEeee--eecccccCCCCCcceeecccCCccccc-CC
Confidence            467899999999999999999999999999999999999999999999  777888888999999999999898875 44


Q ss_pred             CCCCCCchhHHHHHHHHHHHHHhhc--cCC---C---CccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCC------
Q 026213           84 RKPKGDRRSTEISLVIRQTMEACIL--THL---M---PRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPM------  149 (241)
Q Consensus        84 ~~~~~~~~~~~l~~~l~~~l~~~i~--l~~---~---p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~------  149 (241)
                      ++|+|++.++-++..|..++.++-.  ++.   +   ..|.++.++.+|+.||+++|+|++|.++||.+..+|.      
T Consensus       108 RpG~p~dea~viSq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG~~fDa~w~al~aAlknvklP~a~ide~  187 (298)
T KOG1613|consen  108 RPGPPTDEAQVISQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDGPVFDACWNALMAALKNVKLPRAFIDER  187 (298)
T ss_pred             CCCCCchHHHHHHHHHHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCCcHHHHHHHHHHHHHhcCCCceeeeccc
Confidence            5678888888999999888876533  332   2   3499999999999999999999999999999999982      


Q ss_pred             -------------------------CCeeE-----EEEEe-eeCCee-EEeCCccccccCCCcEEEEEcCCCCcEEEEEe
Q 026213          150 -------------------------RDIVT-----SCSAG-YLNSTP-LLDLNYVEDSAGGPDVTVGILPTLDKVTLLQM  197 (241)
Q Consensus       150 -------------------------~~~~~-----~vs~~-~~~~~~-i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~  197 (241)
                                               ...++     ..|.. ++++.+ +.|||.+||....+.+||.. .+.|+++.+.+
T Consensus       188 ~~~~~~t~e~~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~vl~~~li~adpT~eEE~l~~~~lTIvl-dss~n~v~l~k  266 (298)
T KOG1613|consen  188 ASDLRMTIEEIICDQTLTVPLMLNAENRAFASQNSDFSEEEVLDDVLIAADPTEEEETLITSTLTIVL-DSSGNYVQLTK  266 (298)
T ss_pred             chhhhhhHHHHHHhhhhcchhhhccccccccccCCCccHHHhhcceeEecCCCchhhhhhhceEEEEE-cCCCCEEEEEe
Confidence                                     11111     11222 344444 59999999999999999966 46677777765


Q ss_pred             -ee--cCCHHHHHHHHHHHHHHHHHHHHHH
Q 026213          198 -DA--KLPTNTFEDVMQLAIEGCKAVANYI  224 (241)
Q Consensus       198 -~g--~~~~~~l~~~l~~a~~~~~~i~~~i  224 (241)
                       +|  ...++.++.|+++|+.+++++.+.+
T Consensus       267 ~GG~al~~~~~iK~c~elar~Rakelk~~~  296 (298)
T KOG1613|consen  267 VGGGALITPEMIKRCLELARVRAKELKTRF  296 (298)
T ss_pred             cCcccccCHHHHHHHHHHHHHHHHHHHHHh
Confidence             44  2567999999999999999988765

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=100.00  E-value=2.2e-31  Score=252.75  Aligned_cols=206  Identities=21%  Similarity=0.320  Sum_probs=179.1

Q ss_pred             CcceEEEeCCCC-CCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccc-----cCCCCCCCchh
Q 026213           19 MRQLRAEIGNVA-KADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGD-----RMRKPKGDRRS   92 (241)
Q Consensus        19 ~R~i~i~~~~l~-~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~-----~~~~~~~~~~~   92 (241)
                      -|++.+++|.+. +|+|||++++|+|+|+|+|++|.+.+    +..+...++|+|...+++.+.     .++.|+|++++
T Consensus        13 ~r~i~~e~G~ia~qAdGSa~v~~G~T~VlatV~~~~~~~----~~~df~pL~v~y~e~~~A~gkiP~~f~kreg~pse~e   88 (693)
T PRK11824         13 GRTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPK----EGQDFFPLTVDYEEKTYAAGKIPGGFFKREGRPSEKE   88 (693)
T ss_pred             CccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCC----CCCCeeeeEEEEEehhhhccCCCcccccCCCCCChHH
Confidence            379999999995 69999999999999999999987632    235678899999987776442     22346788899


Q ss_pred             HHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCch-Hh-HHHHHHHHHHHhCCCCCCCeeEEEEEeeeCCeeEEeCC
Q 026213           93 TEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGT-RS-ACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLN  170 (241)
Q Consensus        93 ~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~-l~-a~i~a~~~AL~~~gip~~~~~~~vs~~~~~~~~i~DPt  170 (241)
                      ..++++|++.++++..  ..++|.++|+++||++||+. .+ +++||+++||.+++||+++.++++++|+++|.+|+|||
T Consensus        89 il~srlIdR~lrplfp--~~~~~~i~I~~~VL~~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~i~g~~ivdPt  166 (693)
T PRK11824         89 TLTSRLIDRPIRPLFP--KGFRNEVQVVATVLSVDPENDPDILAMIGASAALSISGIPFNGPIAAVRVGYIDGEFVLNPT  166 (693)
T ss_pred             HHHHHHHhhhHHHhCC--CCCCeEEEEEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCEEEEcCC
Confidence            9999999999999642  23479999999999999976 45 89999999999999999999999999999999999999


Q ss_pred             ccccccCCCcEEEEEcCCCCcEEEEEeee-cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          171 YVEDSAGGPDVTVGILPTLDKVTLLQMDA-KLPTNTFEDVMQLAIEGCKAVANYIREVLLENT  232 (241)
Q Consensus       171 ~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g-~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~  232 (241)
                      .+|+..++..++|+.  +.+.+++++.+| .++.+++.++++.|.++++++.+.+++.++++.
T Consensus       167 ~~E~~~s~~~l~va~--t~~~i~mie~~~~~l~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~  227 (693)
T PRK11824        167 VEELEESDLDLVVAG--TKDAVLMVESEAKELSEEVMLEAIEFGHEAIQELIDAQEELAAEAG  227 (693)
T ss_pred             HHHHhhCcceEEEEE--ccCceEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            999999999998875  345899999876 499999999999999999999999999998776

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

Probab=99.97  E-value=5e-30  Score=196.99  Aligned_cols=130  Identities=39%  Similarity=0.542  Sum_probs=116.4

Q ss_pred             CCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCC-CceEEEEEEeecCCcccccCCCCCCCchhHHHH
Q 026213           18 EMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMS-DQALVRCEYSMANFSTGDRMRKPKGDRRSTEIS   96 (241)
Q Consensus        18 e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~-~~~~i~v~~~~~~~~~~~~~~~~~~~~~~~~l~   96 (241)
                      |+|++.+++|++++++|||+|++|+|+|+|+|++|.+.+ |....+ ..|.+.+++++.|++....+..+.++..+.+++
T Consensus         1 e~R~i~i~~~~~~~a~GSa~v~~G~T~V~~~V~~~~~~~-~~~~~~~~~g~~~v~v~~~~~~~~~~~~~~~~~~~~~~l~   79 (132)
T PF01138_consen    1 ELRPISIETGVLPRADGSARVSLGNTKVICSVKGPIEPP-PSNERDDAEGRLTVEVEFSPFASPSFRRGGRPDEEERELS   79 (132)
T ss_dssp             CBEEEEEEESSSSSSSEEEEEEETTEEEEEEEEEEEEGC-SCSTTSSSSEEEEEEEEECCCGSTSSSSSSSTHHHHHHHH
T ss_pred             CCccEEEEeCCCCCCCeEEEEEECCeEEEEEEEeccccc-chhcccCCCceEEEEEEeccccccccccccccchhHHHHH
Confidence            799999999999999999999999999999999987662 333322 358999999999998877655456778888999


Q ss_pred             HHHHHHHHHhhccCCCCccEEEEEEEEEeCCC-chHhHHHHHHHHHHHhCCCC
Q 026213           97 LVIRQTMEACILTHLMPRSQIDIFVQVLQADG-GTRSACINAATLALQDAGIP  148 (241)
Q Consensus        97 ~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG-~~l~a~i~a~~~AL~~~gip  148 (241)
                      ++|+++|++++.++.||+|+|+|+++|+++|| |++++++||+++||+|+|||
T Consensus        80 ~~l~~~l~~~~~~~~~~~~~i~v~v~vl~~dG~~~~~a~~~A~~~AL~~~~iP  132 (132)
T PF01138_consen   80 SLLERALRSSILLEGYPRWQIHVDVQVLSDDGGNLLDAAINAACLALLDAGIP  132 (132)
T ss_dssp             HHHHHHHHHTBSTTTTSSEEEEEEEEEEECSSSSHHHHHHHHHHHHHHHHTCS
T ss_pred             HHHhhhccccccccccCceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCC
Confidence            99999999999999999999999999999999 99999999999999999998

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

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.96  E-value=1.4e-27  Score=227.42  Aligned_cols=207  Identities=18%  Similarity=0.227  Sum_probs=180.8

Q ss_pred             cceEEEeCCC-CCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCccccc-----CCCCCCCchhH
Q 026213           20 RQLRAEIGNV-AKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDR-----MRKPKGDRRST   93 (241)
Q Consensus        20 R~i~i~~~~l-~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~-----~~~~~~~~~~~   93 (241)
                      |.+.+++|.+ .+|+||+.+++|+|.|+|+|....+.+    +..++..+.|+|.-..++.+..     ++-|+|++++.
T Consensus        89 ~~~~~etG~~a~qA~gav~v~~g~t~vl~t~~~~~~~~----~~~dF~PLtV~y~Ek~~AaGkipggf~kREgrp~d~ei  164 (891)
T PLN00207         89 RHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPS----EPSDFFPLSVHYQERFSAAGRTSGGFFKREGRTKDHEV  164 (891)
T ss_pred             EEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEeccCCC----CCCCccceeEeeeeehhhcCccCCceeccCCCCChHHH
Confidence            5799999988 489999999999999999998644322    2357889999998666665542     22367888999


Q ss_pred             HHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCc--hHhHHHHHHHHHHHhCCCCCCCeeEEEEEeeeCCeeEEeCCc
Q 026213           94 EISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGG--TRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNY  171 (241)
Q Consensus        94 ~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~--~l~a~i~a~~~AL~~~gip~~~~~~~vs~~~~~~~~i~DPt~  171 (241)
                      .++++|+|.+++++..+.||+++|.+  +||++||+  ...+++||+++||.++||||++.+.||++|+++|++|+|||.
T Consensus       165 L~sRlIdR~lRPlfp~~~~~etQI~i--~VLsaDg~~~pd~~AInAASaAL~~SgIP~~gpVaAVrVG~idg~~VlnPt~  242 (891)
T PLN00207        165 LICRLIDRPLRPTMPKGFYHETQILS--WVLSYDGLHSPDSLAVTAAGIAVALSEVPNLKAIAGVRVGLIGGKFIVNPTT  242 (891)
T ss_pred             HHHHHHCccchhhccccCCCCcEEEE--EEEeeCCCCChhhHHHHHHHHHHHhhCCCccCceEEEEEEEECCEEEECCCH
Confidence            99999999999999999999877765  89999998  679999999999999999999999999999999999999999


Q ss_pred             cccccCCCcEEEEEcCCCCcEEEEEeeec-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          172 VEDSAGGPDVTVGILPTLDKVTLLQMDAK-LPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ  234 (241)
Q Consensus       172 ~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~-~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~~  234 (241)
                      .|+..++..+.|+.  ..+.|++++.+++ ++.+++.++++.|.++++.+++++++.++++.+.
T Consensus       243 ~E~~~s~ldLvvag--t~~~IvMIE~~a~e~see~l~~Al~~a~~aik~i~~~~~el~~~~gk~  304 (891)
T PLN00207        243 KEMEESELDLIMAG--TDSAILMIEGYCNFLPEEKLLEAVEVGQDAVRAICKEIEVLVKKCGKP  304 (891)
T ss_pred             HHHhcCCeeEEEEE--cCCeEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence            99998888887764  4567999999886 5999999999999999999999999999888765

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

Probab=99.93  E-value=4.6e-25  Score=196.85  Aligned_cols=221  Identities=24%  Similarity=0.332  Sum_probs=190.6

Q ss_pred             ccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcC-cccccccc--CCCC-ceEEEEEEeecCCc
Q 026213            3 FVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGP-REVQNKSQ--QMSD-QALVRCEYSMANFS   78 (241)
Q Consensus         3 ~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p-~e~~~~~~--~~~~-~~~i~v~~~~~~~~   78 (241)
                      .|+..|.|.|||..++.|++.++.+.++..|||++|+.|.|+|+|+|+.. .+..++.+  ..++ ...+..+|.|+|++
T Consensus       352 ~i~~~gkR~DGR~ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~~~~~~FmLhY~FPPya  431 (760)
T KOG1067|consen  352 RILEEGKRCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNGINFMLHYEFPPYA  431 (760)
T ss_pred             HHHhcccccCCcchhhhcccceecCccccccchhhhhcCceeEEEEEEcCCHHHhhhhhhhccCccCceEEEEeccCCcc
Confidence            35678999999999999999999999999999999999999999999842 22222221  1233 34899999999999


Q ss_pred             ccccCCCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEEE
Q 026213           79 TGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSA  158 (241)
Q Consensus        79 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs~  158 (241)
                      +++-.+.+.+++++.....+-+++|.+++. +.||. +|+|.-.|++.+|+-..|.+++-++||+|+|+|++.-++++.+
T Consensus       432 t~Evgkig~~nRRE~GhgaLAEkaL~~vlP-~dfPf-tIRv~SeVleSnGSsSMASvCGGslALmDaGvPv~a~vAGvai  509 (760)
T KOG1067|consen  432 TNEVGKIGGLNRRELGHGALAEKALLPVLP-EDFPF-TIRVTSEVLESNGSSSMASVCGGSLALMDAGVPVSAHVAGVAI  509 (760)
T ss_pred             ccccccccCCcccccCchhHhhhhhhccCc-ccCce-EEEEeeeeeecCCcchHHhhhcchhhhhhcCCccccccceeEE
Confidence            999888888889988888899999999998 88998 8999999999999999999999999999999999999999999


Q ss_pred             eeeC-----------CeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          159 GYLN-----------STPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREV  227 (241)
Q Consensus       159 ~~~~-----------~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~  227 (241)
                      |++-           -.++.|....|+-..+..+.||  .+++-++.+    .++.+-+.++++.|..+-.+|.+.|.++
T Consensus       510 Glvt~td~e~g~i~dyriltDIlGiEd~~GDMDFKiA--Gt~dGvTA~----gi~l~Iv~eal~~a~~ar~~Il~~m~k~  583 (760)
T KOG1067|consen  510 GLVTKTDPEKGEIEDYRILTDILGIEDYNGDMDFKIA--GTNDGVTAL----GIPLKIVMEALQKAREARLQILDIMEKN  583 (760)
T ss_pred             EeEeccCcccCCcccceeehhhcchhhhcCCcceeec--cccCcceec----CCcHHHHHHHHHhhhHHHHHHHHHHHhh
Confidence            9862           1588999999999888899987  455667666    4788999999999999999999999887


Q ss_pred             HHHH
Q 026213          228 LLEN  231 (241)
Q Consensus       228 l~~~  231 (241)
                      +.+.
T Consensus       584 i~~P  587 (760)
T KOG1067|consen  584 INSP  587 (760)
T ss_pred             cCCc
Confidence            6543

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

Probab=99.91  E-value=5.8e-24  Score=195.09  Aligned_cols=229  Identities=24%  Similarity=0.356  Sum_probs=199.0

Q ss_pred             ccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEc-Ccccccccc--CCCCceEEEEEEeecCCcc
Q 026213            3 FVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYG-PREVQNKSQ--QMSDQALVRCEYSMANFST   79 (241)
Q Consensus         3 ~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~-p~e~~~~~~--~~~~~~~i~v~~~~~~~~~   79 (241)
                      +|+..++|+|||..++.|++.++.|+++++|||+.+..|.|+.++.++. +....+-.+  ..+....+..+|+|+||+.
T Consensus       306 ~Il~~~vR~DGR~~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TLG~~~d~Qvid~l~~e~~krfm~hYNFPp~Sv  385 (692)
T COG1185         306 LILEGKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLHYNFPPFSV  385 (692)
T ss_pred             HHhcCCcccCCCCcceeeeeeEEecCCCCccchhhhccCCCcceEEEEcCCcchhhhhhhccchhhhheeeeccCCCCCc
Confidence            5788999999999999999999999999999999999999998888863 221112111  2223567889999999999


Q ss_pred             cccCCCCCCCchhHHHHHHHHHHHHHhhc-cCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEEE
Q 026213           80 GDRMRKPKGDRRSTEISLVIRQTMEACIL-THLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSA  158 (241)
Q Consensus        80 ~~~~~~~~~~~~~~~l~~~l~~~l~~~i~-l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs~  158 (241)
                      ++.++.+.|++++....++-++++.+++. .+.||+ +|++.-.|++.+|+-..|.+++.++||+++|+|++..++++..
T Consensus       386 GE~g~~g~p~RREiGHG~LA~Ral~~vlp~~e~fpy-tiRvVsEi~eSNGSsSmaSVCg~sLaLmdAGVPIk~pVAGIAM  464 (692)
T COG1185         386 GETGRMGSPGRREIGHGALAERALAPVLPSEEEFPY-TIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAM  464 (692)
T ss_pred             cccCCCCCCCcccccCchhhHHHHhhhCCchhcCCc-eeeeeehhhcccCcccchhhhhhHHHHHhCCCcccccccchhc
Confidence            99988888999999999999999999998 578998 8999999999999999999999999999999999999999999


Q ss_pred             eeeC-C---eeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee---cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          159 GYLN-S---TPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA---KLPTNTFEDVMQLAIEGCKAVANYIREVLLEN  231 (241)
Q Consensus       159 ~~~~-~---~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g---~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~  231 (241)
                      |++. +   .++.|....|+...+..|-|+  .+.+-++.++++-   .++.+.+.+++..|+.+..++...|.+++.+.
T Consensus       465 GLI~eg~~~~vLsDI~G~EDhlGDMDFKVA--GT~~GiTAlQMDiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~p  542 (692)
T COG1185         465 GLIKEGDKYAVLSDILGDEDHLGDMDFKVA--GTDDGITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEP  542 (692)
T ss_pred             cceecCCceEeeccccccccccCCceeEEe--cCCCcceeeeeeeeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            9983 2   477899999988888889987  4667888998873   47899999999999999999999999999988


Q ss_pred             HHH
Q 026213          232 TKQ  234 (241)
Q Consensus       232 ~~~  234 (241)
                      .++
T Consensus       543 r~e  545 (692)
T COG1185         543 RKE  545 (692)
T ss_pred             hhh
Confidence            754

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.83  E-value=4.3e-19  Score=166.50  Aligned_cols=207  Identities=14%  Similarity=0.161  Sum_probs=170.4

Q ss_pred             cceEEEeCCC-CCCceeEEEEe-CCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCccccc-----CCCCCCCchh
Q 026213           20 RQLRAEIGNV-AKADGSAVFEM-GNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDR-----MRKPKGDRRS   92 (241)
Q Consensus        20 R~i~i~~~~l-~~a~GSa~v~~-G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~-----~~~~~~~~~~   92 (241)
                      |.+.+++|-+ .+||||+.+++ |+|.|+|+|....+.+    +..++.++.|+|.-..++.+..     ++-++|++++
T Consensus        17 ~~~~~etG~~A~qA~Gav~v~~~G~t~vl~t~~~~~~~~----~~~dF~PLtV~y~Ek~yA~GkiPggf~kREgrps~~e   92 (719)
T TIGR02696        17 RTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPK----DQFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDA   92 (719)
T ss_pred             EEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecCCCC----CCCCCcceeEeeeehhhhcCccCCceeccCCCCChhh
Confidence            4799999988 48999999999 9999999998643321    2357899999998766666543     2236788888


Q ss_pred             HHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCc--hHhHHHHHHHHHHHhCCCCCCCeeEEEEEeeeCCeeEEeCC
Q 026213           93 TEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGG--TRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLN  170 (241)
Q Consensus        93 ~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~--~l~a~i~a~~~AL~~~gip~~~~~~~vs~~~~~~~~i~DPt  170 (241)
                      ...+++|+|.++|+..- .|.+ -++|.+++|+.|+.  .--.++||+++||.-++||+.+.+.++.+|.++|++|++||
T Consensus        93 iL~sRliDR~iRPLFp~-~~~~-e~qi~~~vls~D~~~~pdvla~~~ASaAl~iSdiPf~gPv~~vrVg~i~g~~viNPt  170 (719)
T TIGR02696        93 ILTCRLIDRPLRPSFVK-GLRN-EVQVVVTVLSLNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIDGQWVAFPT  170 (719)
T ss_pred             hHHHHhhCCCCccCCCC-CCCc-ceEEEEEEEEcCCCCChHHHHHHHHHHHHHhcCCCCCCceEEEEEEEECCEEEECcC
Confidence            89999999999998763 3333 57778889998884  45689999999999999999999999999999999999999


Q ss_pred             ccccccCCCcEEEEEcC--C-CCcEEEEEe------------eec-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          171 YVEDSAGGPDVTVGILP--T-LDKVTLLQM------------DAK-LPTNTFEDVMQLAIEGCKAVANYIREVLLENT  232 (241)
Q Consensus       171 ~~Ee~~~~~~~~v~~~~--~-~~~i~~~~~------------~g~-~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~  232 (241)
                      ..|.+.++-.++|+...  + .+.+++++.            +++ ++.+.+.+++..|.+..+.+.+++++......
T Consensus       171 ~~~~~~s~ldLvvagt~~~~~~~~i~MiE~~a~~~~~~~~~~~a~e~~e~~~~~Ai~~a~~~i~~~~~~~~~l~~~~g  248 (719)
T TIGR02696       171 HEQLEGAVFDMVVAGRVLENGDVAIMMVEAEATEKTWDLVKGGAEAPTEEVVAEGLEAAKPFIKVLCRAQADLAEKAA  248 (719)
T ss_pred             HHHHhhCeeeEEEEeeecCCCCccEEEEecCCccccccccccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            99998888888887521  1 238999997            443 79999999999999999999999999665554

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=99.75  E-value=9.5e-17  Score=147.94  Aligned_cols=204  Identities=22%  Similarity=0.326  Sum_probs=172.7

Q ss_pred             cceEEEeCCC-CCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCccccc-----CCCCCCCchhH
Q 026213           20 RQLRAEIGNV-AKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDR-----MRKPKGDRRST   93 (241)
Q Consensus        20 R~i~i~~~~l-~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~-----~~~~~~~~~~~   93 (241)
                      |++.+++|.+ .+|+||+++++|+|.|+++|.+.. .    .+..|+.++.|+|.-..++.++.     ++-|+|++++.
T Consensus        14 ~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~-~----~~~~dF~PLtV~y~Ek~yaaGkiPGgf~kREGrpse~e~   88 (692)
T COG1185          14 RTLTLETGKIARQANGAVLVRYGDTVVLATVVASK-P----KEGQDFFPLTVNYEEKTYAAGKIPGGFFKREGRPSEKEI   88 (692)
T ss_pred             eeEEEEcchhhhhcCccEEEEECCeEEEEEEeecC-C----CCCCCccceeEeeeeehhccCcCCCcccccCCCCCccch
Confidence            8899999998 489999999999999999999854 2    13468899999998666666643     22367888898


Q ss_pred             HHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCc--hHhHHHHHHHHHHHhCCCCCCCeeEEEEEeeeCCeeEEeCCc
Q 026213           94 EISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGG--TRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNY  171 (241)
Q Consensus        94 ~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~--~l~a~i~a~~~AL~~~gip~~~~~~~vs~~~~~~~~i~DPt~  171 (241)
                      ..+++|+|-++++.... |- --++|.++|++.|+.  .--.+++++++||.-++||+...+.++.+|+++|.++++||.
T Consensus        89 L~sRLIDRpiRPlFp~g-~~-~evqIv~tvls~D~~~~pdi~a~~gaSaAl~is~iPf~gpi~~vrvg~idg~~vlNPt~  166 (692)
T COG1185          89 LTSRLIDRPIRPLFPKG-FR-NEVQIVNTVLSVDPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDGIFVLNPTL  166 (692)
T ss_pred             hhhhhcccccccccchh-hc-cceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCccCccceEEEEEECCEEEECCCh
Confidence            99999999998877532 22 257788889999885  446889999999999999999999999999999999999999


Q ss_pred             cccccCCCcEEEEEcCCCCcEEEEEeeec-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          172 VEDSAGGPDVTVGILPTLDKVTLLQMDAK-LPTNTFEDVMQLAIEGCKAVANYIREVLLENT  232 (241)
Q Consensus       172 ~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~-~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~  232 (241)
                      .|.+.+...++|+  .+...|.+++.+.. ++.+++.+++..+.+..+.+.+++++......
T Consensus       167 ~e~~~s~lDlvVA--GT~~aV~MVE~~a~~l~E~~ml~Av~fg~~~~~~~~~~qe~l~~~~g  226 (692)
T COG1185         167 EELEESKLDLVVA--GTKDAVNMVESEADELDEEVMLEAVEFGHEAIQSVINAQEELALEVG  226 (692)
T ss_pred             HHhhhcceeeEec--CChhhhheeecccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            9998888888876  56668999998864 78999999999999999999999999887766

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

Probab=99.66  E-value=7.3e-16  Score=138.41  Aligned_cols=209  Identities=19%  Similarity=0.244  Sum_probs=164.9

Q ss_pred             CCcceEEEeCCCC-CCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCccccc-----CCCCCCCch
Q 026213           18 EMRQLRAEIGNVA-KADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDR-----MRKPKGDRR   91 (241)
Q Consensus        18 e~R~i~i~~~~l~-~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~-----~~~~~~~~~   91 (241)
                      --|.+.+++|.+. .|+||+.++.|+|.|+++|..-.   +|+  .+++..+.|+|.....+.+..     ++-+.+.++
T Consensus        54 GnR~i~~etGklaRfAngsvvv~~GeT~Vm~Tv~~a~---~PS--p~qFlPL~VdYqeK~aAvGRip~~fmRREg~tkdk  128 (760)
T KOG1067|consen   54 GNREILFETGKLARFANGSVVVQMGETAVMTTVVLAD---KPS--PPQFLPLVVDYQEKFAAVGRIPGNFMRREGRTKDK  128 (760)
T ss_pred             CCeEEEEecchhhhhcCCcEEEccCCeEEEEEEEecC---CCC--ccccceEEEehhhhhhhhccCCCcccccccCCcch
Confidence            5699999999996 59999999999999999998632   333  245888999997543333321     122345556


Q ss_pred             hHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCc--hHhHHHHHHHHHHHhCCCCCCCeeEEEEEeeeCCeeEEeC
Q 026213           92 STEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGG--TRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDL  169 (241)
Q Consensus        92 ~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~--~l~a~i~a~~~AL~~~gip~~~~~~~vs~~~~~~~~i~DP  169 (241)
                      +....++|++.+++...-..|.  ..++-..+|..||-  .--.++|++++||..+.+|+...+.++.+|+++|++|++|
T Consensus       129 EiL~~rLidrsirplfp~g~~~--etqi~~n~Ls~dG~~~pdvlainaas~Al~lsdvpw~gpig~vRigLi~Ge~vVNP  206 (760)
T KOG1067|consen  129 EILTGRLIDRPIRPLFPKGFYH--ETQILCNVLSSDGVHDPDVLAINAASAALSLSDVPWNGPIGAVRIGLIDGEFVVNP  206 (760)
T ss_pred             hheeeeccccccccCCcccchh--HHHHHhhheecccccCchHHHHhHHHHHhhhccCCCCCceeeeEeeeecceEEeCc
Confidence            6666778888877766443333  33444567888883  3457899999999999999999999999999999999999


Q ss_pred             CccccccCCCcEEEEEcCCCCcEEEEEeeec-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          170 NYVEDSAGGPDVTVGILPTLDKVTLLQMDAK-LPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQL  235 (241)
Q Consensus       170 t~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~-~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~~~  235 (241)
                      |..|.+.+.-.+.++.  .+.++++++..+. +..+++.+++..+.+.++.+.+.|....+++.+++
T Consensus       207 T~kEmssS~Lnlvvag--t~~~~vmle~~s~~i~qqdl~~Aikvg~~~~q~~i~~i~~L~k~~Gk~K  271 (760)
T KOG1067|consen  207 TRKEMSSSQLNLVVAG--TKSQTVMLEGSSNNILQQDLLHAIKVGVKEAQQIIQGIERLAKKYGKQK  271 (760)
T ss_pred             chhhhhhccceeEEEe--ccceEEEEEcccccccHHHHHHHHHhccHHHHHHHHHHHHHHHHhCccc
Confidence            9999999998888875  4789999997764 78999999999999999999999999888877655

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

Probab=99.33  E-value=5e-12  Score=85.71  Aligned_cols=66  Identities=20%  Similarity=0.279  Sum_probs=56.2

Q ss_pred             CeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeec--CCHHHHHHHHHHHHHH
Q 026213          151 DIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAK--LPTNTFEDVMQLAIEG  216 (241)
Q Consensus       151 ~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~--~~~~~l~~~l~~a~~~  216 (241)
                      |+|+++|++++++.+++|||.+||..+.+.++++++++.+.+..++.+|.  ++++++.++++.|.++
T Consensus         1 ~~~~avt~~~i~~~~v~Dpt~~Ee~~~~~~l~~~~~~~~~~~~~~~~~g~~~~~~~~l~~~i~~A~~~   68 (68)
T PF03725_consen    1 DPPVAVTVGIIDGELVVDPTAEEESLSDSSLTLAVDGTGNICTLQKSGGGSELSEDQLEEAIELAKKA   68 (68)
T ss_dssp             SEEEEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSSEEEEEEEEESSEEEHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEECCEEEECCCHHHHhhcCCcEEEEEECCCCEEEEEEcCCCCCCCHHHHHHHHHHHhcC
Confidence            58999999999999999999999999999999999766555566677765  9999999999999874

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	241
2nn6_B	249	Structure Of The Human Rna Exosome Composed Of Rrp4		5e-70
2pnz_A	249	Crystal Structure Of The P. Abyssi Exosome Rnase Ph		7e-59
3l7z_B	245	Crystal Structure Of The S. Solfataricus Archaeal E		3e-55
2br2_B	248	Rnase Ph Core Of The Archaeal Exosome Length = 248		3e-55
2je6_B	250	Structure Of A 9-Subunit Archaeal Exosome Length =		3e-54
2wnr_B	240	The Structure Of Methanothermobacter Thermautotroph		3e-52
2ba0_F	258	Archaeal Exosome Core Length = 258		2e-48
3m7n_D	258	Archaeoglobus Fulgidus Exosome With Rna Bound To Th		3e-48
4ifd_B	248	Crystal Structure Of An 11-subunit Eukaryotic Exoso		4e-40
2wp8_B	246	Yeast Rrp44 Nuclease Length = 246		6e-40
1r6m_A	239	Crystal Structure Of The Trna Processing Enzyme Rna		2e-18
1r6l_A	239	Crystal Structure Of The Trna Processing Enzyme Rna		2e-17
2nn6_F	272	Structure Of The Human Rna Exosome Composed Of Rrp4		5e-17
1udn_A	255	Crystal Structure Of The Trna Processing Enzyme Rna		2e-15
2nn6_D	237	Structure Of The Human Rna Exosome Composed Of Rrp4		8e-15
1udq_A	255	Crystal Structure Of The Trna Processing Enzyme Rna		1e-14
1udo_A	255	Crystal Structure Of The Trna Processing Enzyme Rna		1e-14
1uds_A	255	Crystal Structure Of The Trna Processing Enzyme Rna		2e-14
3dd6_A	255	Crystal Structure Of Rph, An Exoribonuclease From B		2e-14
1oyp_A	245	Crystal Structure Of The Phosphorolytic Exoribonucl		1e-13
1oys_A	245	Crystal Structure Of The Phosphorolytic Exoribonucl		2e-13
3hkm_A	246	Crystal Structure Of Rice(Oryza Sativa) Rrp46 Lengt		1e-12
3b4t_A	262	Crystal Structure Of Mycobacterium Tuberculosis Rna		2e-12
3krn_A	222	Crystal Structure Of C. Elegans Cell-Death-Related		4e-11
1e3p_A	757	Tungstate Derivative Of Streptomyces Antibioticus P		2e-09
4ifd_D	245	Crystal Structure Of An 11-subunit Eukaryotic Exoso		3e-09
3gcm_A	549	Crystal Structure Of E. Coli Polynucleotide Phospho		3e-09
3h1c_A	549	Crystal Structure Of Polynucleotide Phosphorylase (		3e-09
3cdj_A	559	Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCA		3e-09
3cdi_A	723	Crystal Structure Of E. Coli Pnpase Length = 723		3e-09
4aim_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		8e-08
3u1k_A	630	Crystal Structure Of Human Pnpase Length = 630		9e-08
4aid_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		9e-08
4am3_A	717	Crystal Structure Of C. Crescentus Pnpase Bound To		9e-08
1e3h_A	757	Semet Derivative Of Streptomyces Antibioticus Pnpas		6e-07
3l7z_A	271	Crystal Structure Of The S. Solfataricus Archaeal E		6e-05
2nn6_C	278	Structure Of The Human Rna Exosome Composed Of Rrp4		9e-05
2je6_A	277	Structure Of A 9-Subunit Archaeal Exosome Length =		5e-04
2br2_A	275	Rnase Ph Core Of The Archaeal Exosome Length = 275		6e-04

>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 =  260 bits (664), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 120/235 (51%), Positives = 175/235 (74%), Gaps = 1/235 (0%)
Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQ-NKS 59
           +E +S +G R+DGRR  E+R+++A +G  A+ADGSA  E GNTK +A VYGP E++ +++
Sbjct: 8   LELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRA 67
Query: 60  QQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDI 119
           + + D+ALV C+YS A FSTG+R R+P GDR+S E+ L +RQT EA ILT L PRSQIDI
Sbjct: 68  RALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDI 127
Query: 120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGP 179
           +VQVLQADGGT +AC+NAATLA+ DAGIPMRD V +CSAG+++ T L DL++VE++AGGP
Sbjct: 128 YVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAGGP 187
Query: 180 DVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ 234
            + + +LP   ++ LL+MDA+L  +  E V++ A +  + V   +  V+ ++ ++
Sbjct: 188 QLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVRE 242

>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 =  223 bits (568), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 111/231 (48%), Positives = 154/231 (66%), Gaps = 1/231 (0%)
Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
           ++ +   G R+DGR+  E+R ++ E+G +  A+GSA  E G  K+IAAVYGPRE+  K  
Sbjct: 8   LKLIDENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHL 67
Query: 61  QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
           Q  D+A++R  Y+MA FS  +R +KP  DRRS EIS VI+  +E  ++  + PR+ ID+F
Sbjct: 68  QRPDRAILRVRYNMAPFSVEER-KKPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVF 126
Query: 121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180
           ++VLQAD GTR A I AA+LAL DAGIPMRD+V +C+AG +    +LDLN  ED+ G  D
Sbjct: 127 IEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKIEGEIVLDLNKEEDNYGEAD 186
Query: 181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLEN 231
           V V I+P  + +TLLQMD  L  + F + ++LAI+G KAV    RE L E 
Sbjct: 187 VPVAIMPLKNDITLLQMDGYLTKDEFIEAVKLAIKGAKAVYQKQREALKEK 237

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

Iteration: 1
 Score =  211 bits (537), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 99/232 (42%), Positives = 150/232 (64%), Gaps = 3/232 (1%)
Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           +G R DGR+P E+R ++ E+G +  ADGSA+FEMGNTK IAAVYGP+E+  +   + D+A
Sbjct: 13  DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRA 72
Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
           ++R  Y M  FST +R + P   RR  E+S VIR+ +E+ +L  L PR+ ID+F ++LQA
Sbjct: 73  VLRVRYHMTPFSTDER-KNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQA 131
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGIL 186
           D G+R   + AA+LAL DAGIPMRD++   + G  +   +LDLN  ED  G  D+ + ++
Sbjct: 132 DAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLNETEDMWGEADMPIAMM 191
Query: 187 PTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECR 238
           P+L++VTL Q++  +  + F     LA++G   + N  RE L   +K +E +
Sbjct: 192 PSLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREAL--KSKYVEFK 241

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

Iteration: 1
 Score =  211 bits (536), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 99/232 (42%), Positives = 150/232 (64%), Gaps = 3/232 (1%)
Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           +G R DGR+P E+R ++ E+G +  ADGSA+FEMGNTK IAAVYGP+E+  +   + D+A
Sbjct: 16  DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRA 75
Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
           ++R  Y M  FST +R + P   RR  E+S VIR+ +E+ +L  L PR+ ID+F ++LQA
Sbjct: 76  VLRVRYHMTPFSTDER-KNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQA 134
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGIL 186
           D G+R   + AA+LAL DAGIPMRD++   + G  +   +LDLN  ED  G  D+ + ++
Sbjct: 135 DAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLNETEDMWGEADMPIAMM 194
Query: 187 PTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECR 238
           P+L++VTL Q++  +  + F     LA++G   + N  RE L   +K +E +
Sbjct: 195 PSLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREAL--KSKYVEFK 244

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

Iteration: 1
 Score =  208 bits (529), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 98/232 (42%), Positives = 149/232 (64%), Gaps = 3/232 (1%)
Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           +G R DGR+P E+R ++ E+G +  ADGSA+FEMGNTK IAAVYGP+E+  +   + D+A
Sbjct: 18  DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRA 77
Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
           ++R  Y M  FST +R + P   RR  E+S VIR+ +E+ +L  L PR+ ID+F ++LQA
Sbjct: 78  VLRVRYHMTPFSTDER-KNPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQA 136
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGIL 186
           D G+R   + AA+LAL DAGIPMRD++   + G  +   +LDLN  E   G  D+ + ++
Sbjct: 137 DAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLNETEAMWGEADMPIAMM 196
Query: 187 PTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECR 238
           P+L++VTL Q++  +  + F     LA++G   + N  RE L   +K +E +
Sbjct: 197 PSLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREAL--KSKYVEFK 246

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

Iteration: 1
 Score =  201 bits (510), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 102/220 (46%), Positives = 140/220 (63%), Gaps = 1/220 (0%)
Query: 9   LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALV 68
           +R DGR   E+R L+ E G + +ADGS+  E G  K++ AVYGPRE Q +  Q  D+A++
Sbjct: 16  VREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVI 75
Query: 69  RCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADG 128
           RC Y+MA FS  +R R P  DRRS EIS +  + +   ++    PRS ID+F++VL+A+G
Sbjct: 76  RCRYNMAPFSVEERKR-PGPDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEG 134
Query: 129 GTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPT 188
           GTR A I AA++AL DAGIPMRD+V +C+AG +    +LDL+  ED  G  DV V ILP 
Sbjct: 135 GTRCAGITAASVALADAGIPMRDMVVACAAGKVGDQVVLDLSEEEDKEGQADVPVAILPR 194
Query: 189 LDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVL 228
             ++TLLQ D  L    FE  + LA+EGC  +    +E L
Sbjct: 195 TREITLLQSDGNLTPEEFERALDLAVEGCLRIHEVQKEAL 234

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

Iteration: 1
 Score =  189 bits (479), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 99/226 (43%), Positives = 143/226 (63%), Gaps = 4/226 (1%)
Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           +GLRLDGR+  E+R ++ E   + +ADGS   EMG  KVIAAV+GPREV  +  Q   +A
Sbjct: 14  DGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKA 73
Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
           ++R  Y+MA FS  +R R P  DRRS EIS V ++  EA I+  L PRS IDIFV+VLQA
Sbjct: 74  IIRYRYNMAPFSVEERKR-PGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQA 132
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGIL 186
           D G+R+AC+NAA++AL DAG+PM+ ++TS + G  +   +LD    ED+ G  D+    L
Sbjct: 133 DAGSRTACLNAASVALVDAGVPMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFL 192
Query: 187 ---PTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLL 229
                ++ + LLQMD ++  +  +  ++LA +G   +    RE +L
Sbjct: 193 IRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAIL 238

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

Iteration: 1
 Score =  188 bits (477), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 99/226 (43%), Positives = 143/226 (63%), Gaps = 4/226 (1%)
Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           +GLRLDGR+  E+R ++ E   + +ADGS   EMG  KVIAAV+GPREV  +  Q   +A
Sbjct: 14  DGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKA 73
Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
           ++R  Y+MA FS  +R R P  DRRS EIS V ++  EA I+  L PRS IDIFV+VLQA
Sbjct: 74  IIRYRYNMAPFSVEERKR-PGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQA 132
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGIL 186
           D G+R+AC+NAA++AL DAG+PM+ ++TS + G  +   +LD    ED+ G  D+    L
Sbjct: 133 DAGSRTACLNAASVALVDAGVPMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFL 192
Query: 187 ---PTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLL 229
                ++ + LLQMD ++  +  +  ++LA +G   +    RE +L
Sbjct: 193 IRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAIL 238

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

Iteration: 1
 Score =  161 bits (407), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 89/236 (37%), Positives = 142/236 (60%), Gaps = 3/236 (1%)
Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIG-NVAKADGSAVFEMGNTKVIAAVYGPREVQNKS 59
           +E  SPEGLRLDGRR  E+R+  + I  +   ADGS+  E GN K+I  V GP+E + KS
Sbjct: 6   LEIYSPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKS 65
Query: 60  QQMSDQALVRCEYSMANFSTGDRMRKP-KGDRRSTEISLVIRQTMEACILTHLMPRSQID 118
           Q  + +AL+    ++  FS  +R +   K +RR  EI   + +  E  ++ ++ PR+ ID
Sbjct: 66  QMDTSKALLNVSVNITKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVID 125
Query: 119 IFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGG 178
           I + VL+ DGG   + IN  TLAL DAGI M D ++  S G  ++TPLLD N +E++A  
Sbjct: 126 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEENAMS 185
Query: 179 PDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ 234
             VT+G++   +K++LL ++ K+P +  E+V+ + I G   V + + E L ++ ++
Sbjct: 186 T-VTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQK 240

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

Iteration: 1
 Score =  160 bits (405), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 89/236 (37%), Positives = 142/236 (60%), Gaps = 3/236 (1%)
Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIG-NVAKADGSAVFEMGNTKVIAAVYGPREVQNKS 59
           +E  SPEGLRLDGRR  E+R+  + I  +   ADGS+  E GN K+I  V GP+E + KS
Sbjct: 4   LEIYSPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKS 63
Query: 60  QQMSDQALVRCEYSMANFSTGDRMRKP-KGDRRSTEISLVIRQTMEACILTHLMPRSQID 118
           Q  + +AL+    ++  FS  +R +   K +RR  EI   + +  E  ++ ++ PR+ ID
Sbjct: 64  QMDTSKALLNVSVNINKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVID 123
Query: 119 IFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGG 178
           I + VL+ DGG   + IN  TLAL DAGI M D ++  S G  ++TPLLD N +E++A  
Sbjct: 124 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEENAMS 183
Query: 179 PDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ 234
             VT+G++   +K++LL ++ K+P +  E+V+ + I G   V + + E L ++ ++
Sbjct: 184 T-VTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQK 238

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

Iteration: 1
 Score = 89.4 bits (220), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 64/193 (33%), Positives = 97/193 (50%), Gaps = 24/193 (12%)
Query: 10  RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYG----PREVQNKSQQMSDQ 65
           R  GR   ++R +R        A+GS + E G+TKVI  V      PR ++ + Q     
Sbjct: 3   RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQ----- 57
Query: 66  ALVRCEYSMANFSTGDRMRKP----KGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFV 121
             +  EY M   STG+R ++     K   R+ EI  +I +++ A +    +  + + I  
Sbjct: 58  GWLTAEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDC 117
Query: 122 QVLQADGGTRSACINAATLALQDA-----------GIPMRDIVTSCSAGYLNSTPLLDLN 170
            V+QADGGTR+A I  AT+AL DA           G P++ +V + S G     P+LDL+
Sbjct: 118 DVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIYQGVPVLDLD 177
Query: 171 YVEDSAGGPDVTV 183
           Y+EDSA   D+ V
Sbjct: 178 YLEDSAAETDLNV 190

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

Iteration: 1
 Score = 85.9 bits (211), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 63/193 (32%), Positives = 95/193 (49%), Gaps = 24/193 (12%)
Query: 10  RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYG----PREVQNKSQQMSDQ 65
           R  GR   ++R +R        A+GS + E G+TKVI  V      PR ++ + Q     
Sbjct: 3   RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRFLKGQGQ----- 57
Query: 66  ALVRCEYSMANFSTGDRMRKP----KGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFV 121
             +  EY     STG+R ++     K   R+ EI  +I +++ A +    +  + + I  
Sbjct: 58  GWLTAEYGXLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDC 117
Query: 122 QVLQADGGTRSACINAATLALQDA-----------GIPMRDIVTSCSAGYLNSTPLLDLN 170
            V+QADGGTR+A I  AT+AL DA           G P++  V + S G     P+LDL+
Sbjct: 118 DVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQXVAAVSVGIYQGVPVLDLD 177
Query: 171 YVEDSAGGPDVTV 183
           Y+EDSA   D+ V
Sbjct: 178 YLEDSAAETDLNV 190

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

Iteration: 1
 Score = 84.3 bits (207), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 118/231 (51%), Gaps = 16/231 (6%)
Query: 14  RRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSD--------- 64
           R PT +R + A  G +++A GSA  E G TKV+ AV GPR+ +   +             
Sbjct: 31  RDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPA 90
Query: 65  --QALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQ 122
             +  + C++  A F+ G R R P G     E++L +++ +E  +     PR+Q+++   
Sbjct: 91  ALRGRLLCDFRRAPFA-GRRRRAPPGGCEERELALALQEALEPAVRLGRYPRAQLEVSAL 149
Query: 123 VLQADGGTRSACINAATLALQDAGIPMRDIVTSCS---AGYLNSTPLLDLNYVEDSAGGP 179
           +L+  G   +A + AA LAL DAG+ M D+V  C    A     T LLD   +E+     
Sbjct: 150 LLEDGGSALAAALTAAALALADAGVEMYDLVVGCGLSLAPGPAPTWLLDPTRLEEERAAA 209
Query: 180 DVTVGILPTLDKVT-LLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLL 229
            +TV ++P L++V  LL       T ++ + ++L +EGC+ +   +++ L+
Sbjct: 210 GLTVALMPVLNQVAGLLGSGEGGLTESWAEAVRLGLEGCQRLYPVLQQSLV 260

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

Iteration: 1
 Score = 79.0 bits (193), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 64/191 (33%), Positives = 95/191 (49%), Gaps = 18/191 (9%)
Query: 9   LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALV 68
           +R DGR+  ++R +  +   +   +GS +   G TKVI        V N  +    Q  +
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKG-QGWI 59
Query: 69  RCEYSMANFSTGDR-MRKPKGDR---RSTEISLVIRQTMEACI-LTHLMPRSQIDIFVQV 123
             EYSM   +T  R +R+    R   R+ EI  +I + M   + LT +  R+ I +   V
Sbjct: 60  TAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERT-IWVDCDV 118
Query: 124 LQADGGTRSACINAATLALQDAGI-----------PMRDIVTSCSAGYLNSTPLLDLNYV 172
           +QADGGTR+A I  A +A+ DA I           P++D V + S G +N   LLDLN+ 
Sbjct: 119 IQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNFE 178
Query: 173 EDSAGGPDVTV 183
           EDSA   D+ V
Sbjct: 179 EDSAAQVDMNV 189

>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 = 77.0 bits (188), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 47/138 (34%), Positives = 75/138 (54%), Gaps = 18/138 (13%)
Query: 19  MRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA----LVRCEYSM 74
           +R    E   +++ DGSA F  G+T V+A VYGP EV+  S+++ ++A    ++R +  +
Sbjct: 30  LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVK-VSKEIFNKATLEVILRPKIGL 88
Query: 75  ANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSAC 134
              +   R R             +IR T EA +L  L PR+ I + +QV+   G   + C
Sbjct: 89  PGVAEKSRER-------------LIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACC 135
Query: 135 INAATLALQDAGIPMRDI 152
           +NAA +AL DAG+PMR +
Sbjct: 136 LNAACMALVDAGVPMRAL 153

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

Iteration: 1
 Score = 76.6 bits (187), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 63/191 (32%), Positives = 94/191 (49%), Gaps = 18/191 (9%)
Query: 9   LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALV 68
           +R DGR+  ++R +  +   +   +GS +   G TKVI        V N  +    Q  +
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKG-QGWI 59
Query: 69  RCEYSMANFSTGDR-MRKPKGDR---RSTEISLVIRQTMEACI-LTHLMPRSQIDIFVQV 123
             EYSM   +T  R +R+    R   R+ EI  +I + M   + LT +  R+ I +   V
Sbjct: 60  TAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERT-IWVDCDV 118
Query: 124 LQADGGTRSACINAATLALQDAGI-----------PMRDIVTSCSAGYLNSTPLLDLNYV 172
           +QADGG R+A I  A +A+ DA I           P++D V + S G +N   LLDLN+ 
Sbjct: 119 IQADGGARTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNFE 178
Query: 173 EDSAGGPDVTV 183
           EDSA   D+ V
Sbjct: 179 EDSAAQVDMNV 189

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

Iteration: 1
 Score = 76.3 bits (186), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/191 (32%), Positives = 92/191 (48%), Gaps = 18/191 (9%)
Query: 9   LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALV 68
           +R DGR+  ++R +  +   +   +GS +   G TKVI        V N  +    Q  +
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKG-QGWI 59
Query: 69  RCEYSMANFSTGDRMRKPKGDRR----STEISLVIRQTMEACI-LTHLMPRSQIDIFVQV 123
             EYSM   +T  R  +     R    + EI  +I + M   + LT +  R+ I +   V
Sbjct: 60  TAEYSMLPRATQQRTIRESVQGRIGGATHEIQRMIGRAMRTAVELTKIGERT-IWVDCDV 118
Query: 124 LQADGGTRSACINAATLALQDAGI-----------PMRDIVTSCSAGYLNSTPLLDLNYV 172
           +QADGGTR+A I  A +A+ DA I           P++D V + S G +N   LLDLN+ 
Sbjct: 119 IQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNFE 178
Query: 173 EDSAGGPDVTV 183
           EDSA   D+ V
Sbjct: 179 EDSAAQVDMNV 189

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

Iteration: 1
 Score = 75.5 bits (184), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 63/191 (32%), Positives = 94/191 (49%), Gaps = 18/191 (9%)
Query: 9   LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALV 68
           +R DGR+  ++R +  +   +   +GS +   G TKVI        V N  +    Q  +
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKG-QGWI 59
Query: 69  RCEYSMANFSTGDR-MRKPKGDR---RSTEISLVIRQTMEACI-LTHLMPRSQIDIFVQV 123
             EYSM   +T  R +R+    R   R+ EI  +I + M   + LT +  R+ I +   V
Sbjct: 60  TAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERT-IWVDCDV 118
Query: 124 LQADGGTRSACINAATLALQDAGI-----------PMRDIVTSCSAGYLNSTPLLDLNYV 172
           +QADGGT +A I  A +A+ DA I           P++D V + S G +N   LLDLN+ 
Sbjct: 119 IQADGGTATAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNFE 178
Query: 173 EDSAGGPDVTV 183
           EDSA   D+ V
Sbjct: 179 EDSAAQVDMNV 189

>pdb|3DD6|A Chain A, Crystal Structure Of Rph, An Exoribonuclease From Bacillus Anthracis At 1.7 A Resolution Length = 255

Iteration: 1
 Score = 75.5 bits (184), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 57/191 (29%), Positives = 91/191 (47%), Gaps = 17/191 (8%)
Query: 9   LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALV 68
           +R+DGR  TE+R +      +   +GS + E+G+TKVI +      V     +   +  V
Sbjct: 11  MRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERV-PPFMRGEGKGWV 69
Query: 69  RCEYSMANFSTGDRM----RKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVL 124
             EY+M   +T  R      K K   R+ EI  +I + + A +    +    + I   V+
Sbjct: 70  TAEYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWIDCDVI 129
Query: 125 QADGGTRSACINAATLAL-----------QDAGIPMRDIVTSCSAGYLNSTP-LLDLNYV 172
           QADGGTR+A I  A +A+           + + IP++D + + S G +     +LDLNY 
Sbjct: 130 QADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEEQGVVLDLNYA 189
Query: 173 EDSAGGPDVTV 183
           EDS    D+ V
Sbjct: 190 EDSKADVDMNV 200

>pdb|1OYP|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease Rnase Ph From Bacillus Subtilis Length = 245

Iteration: 1
 Score = 73.6 bits (179), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 74/250 (29%), Positives = 118/250 (47%), Gaps = 27/250 (10%)
Query: 9   LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQM---SDQ 65
           +R DGR+  E+R +  ++  ++  +GS +   GNTKVI        V+++         +
Sbjct: 1   MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNA----SVEDRVPPFLRGGGK 56
Query: 66  ALVRCEYSMANFSTGDRM----RKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFV 121
             +  EYSM   +T  R      K K   R+ EI  +I + + A +    +    I I  
Sbjct: 57  GWITAEYSMLPRATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDC 116
Query: 122 QVLQADGGTRSACINAATLA-------LQDAGI----PMRDIVTSCSAGYLNSTP-LLDL 169
            V+QADGGTR+A I  A LA       L  AG     P+ D + + S G       LLDL
Sbjct: 117 DVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDL 176
Query: 170 NYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFED---VMQLAIEGCKAVANYIRE 226
           NY EDS+   D+ V I+    +   LQ   +  T + ED   ++ LA +G + + +  +E
Sbjct: 177 NYEEDSSAEVDMNV-IMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKE 235
Query: 227 VLLENTKQLE 236
           VL ++  +L+
Sbjct: 236 VLGDSLPELK 245

>pdb|1OYS|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease Rnase Ph From Bacillus Subtilis Length = 245

Iteration: 1
 Score = 72.8 bits (177), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 74/250 (29%), Positives = 117/250 (46%), Gaps = 27/250 (10%)
Query: 9   LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQM---SDQ 65
           +R DGR+  E+R +  ++  ++  +GS +   GNTKVI        V+++         +
Sbjct: 1   MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNA----SVEDRVPPFLRGGGK 56
Query: 66  ALVRCEYSM----ANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFV 121
             +  EYSM     N  T     K K   R+ EI  +I + + A +    +    I I  
Sbjct: 57  GWITAEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDC 116
Query: 122 QVLQADGGTRSACINAATLA-------LQDAGI----PMRDIVTSCSAGYLNSTP-LLDL 169
            V+QADGGTR+A I  A LA       L  AG     P+ D + + S G       LLDL
Sbjct: 117 DVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDL 176
Query: 170 NYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFED---VMQLAIEGCKAVANYIRE 226
           NY EDS+   D+ V I+    +   LQ   +  T + ED   ++ LA +G + + +  +E
Sbjct: 177 NYEEDSSAEVDMNV-IMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKE 235
Query: 227 VLLENTKQLE 236
           VL ++  +L+
Sbjct: 236 VLGDSLPELK 245

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 46/169 (27%), Positives = 80/169 (47%), Gaps = 11/169 (6%)
Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           E  R DGR P ++R        + +A GSA +  G+T V+AAVYGP+    K +   ++A
Sbjct: 2   EESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGEN-PEKA 60
Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
            +   +       G         ++  E  + +++T+++  L  + P +   + +QV+  
Sbjct: 61  SIEVVWKPMTGQIG---------KQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGN 111
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL-NSTPLLDLNYVED 174
           DG      INA   AL  AGIP++ +  +   G L +   +LD N  E+
Sbjct: 112 DGSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLEDGEVILDTNKAEE 160

>pdb|3B4T|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph, The Mycobacterium Tuberculosis Structural Genomics Consortium Target Rv1340 Length = 262

Iteration: 1
 Score = 69.3 bits (168), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 111/240 (46%), Gaps = 25/240 (10%)
Query: 10  RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVR 69
           R DGR   E+R +    G      GS + E G+TKV+        V  + ++ +    + 
Sbjct: 7   REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVP-RWRKATGLGWLT 65
Query: 70  CEYSM---ANFSTGDRMR-KPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQ 125
            EY+M   A  S  DR   + +   R+ EIS +I +++ ACI    +  + I I   VLQ
Sbjct: 66  AEYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQ 125
Query: 126 ADGGTRSACINAATLALQDAGI------------PMRDIVTSCSAGYLNSTPLLDLNYVE 173
           ADGGTR+A I  A +AL DA              P+   + + S G ++    +DL Y E
Sbjct: 126 ADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVVDGRIRVDLPYEE 185
Query: 174 DSAGGPDVTVGILPTLDKVTLLQMD-----AKLPTNTFEDVMQLAIEGCKAVANYIREVL 228
           DS    +V + ++ T D  TL+++      A    +T + ++ +A+  C  +    R+ L
Sbjct: 186 DSRA--EVDMNVVAT-DTGTLVEIQGTGEGATFARSTLDKLLDMALGACDTLFAAQRDAL 242

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

Iteration: 1
 Score = 64.7 bits (156), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 39/134 (29%), Positives = 63/134 (47%), Gaps = 12/134 (8%)
Query: 19  MRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFS 78
           +R++R E+  +  ADGSA F  G T + A+  GP +V   + + SD+A+          +
Sbjct: 5   LREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVH--ASKASDEAM----------T 52
Query: 79  TGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAA 138
                R   GD +   ++ +I  T+   I   L P + I + V  +Q DG   +  IN A
Sbjct: 53  LDISYRANCGDNKFNVLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAVAINGA 112
Query: 139 TLALQDAGIPMRDI 152
             AL D G+P   +
Sbjct: 113 CFALLDNGMPFETV 126

>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase Gpsi Enzyme Length = 757

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 109/242 (45%), Gaps = 18/242 (7%)
Query: 2   EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQ 61
           E V  E  R+DGR  T++R L AE+  + +  GSA+FE G T+++        +    QQ
Sbjct: 348 ERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTT--LNMLRMEQQ 405
Query: 62  MSDQALVRCEYSMAN-----FSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQ 116
           +   + V  +  M N     +S G+  R     RR      +  + +   + T       
Sbjct: 406 LDTLSPVTRKRYMHNYNFPPYSVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYA 465
Query: 117 IDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL--------NSTPLLD 168
           I    + L ++G T    + A+T++L +AG+P++  V   + G +        +   L D
Sbjct: 466 IRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIAMGLISQEINGETHYVALTD 525
Query: 169 LNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVL 228
           +   ED+ G  D+   +  T + VT LQ+D KL       V+  A++  +    +I +V+
Sbjct: 526 ILGAEDAFG--DMDFKVAGTKEFVTALQLDTKL-DGIPASVLAAALKQARDARLHILDVM 582
Query: 229 LE 230
           +E
Sbjct: 583 ME 584

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 60/242 (24%), Positives = 107/242 (44%), Gaps = 36/242 (14%)
Query: 10  RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ---QMSDQA 66
           RLD     +   ++AEIG +   DGS+ F   +TKVI +V GP E + + +   Q++ + 
Sbjct: 13  RLDSAEKKKKMSVQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEI 72
Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVL-- 124
           +VR    +A  +T +++ + K           +R  +   I  H  PR    I  Q+L  
Sbjct: 73  IVRPAKGVA--TTREKVLEDK-----------LRAVLTPLITRHCYPRQLCQITCQILES 119
Query: 125 ---QADGGTR--SACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGP 179
              +A+   R  S CINAA LAL DAGI +  +  S     +  T  +    V+ +A   
Sbjct: 120 GEDEAEFSLRELSCCINAAFLALVDAGIALNSMCASIPIAIIKDTSDI---IVDPTAEQL 176
Query: 180 DVTVGIL----------PTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLL 229
            +++ +             +  V LL  +     +    +++L  + C+ +   IR ++ 
Sbjct: 177 KISLSVHTLALEFVNGGKVVKNVLLLDSNGDFNEDQLFSLLELGEQKCQELVTNIRRIIQ 236
Query: 230 EN 231
           +N
Sbjct: 237 DN 238

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 104/226 (46%), Gaps = 10/226 (4%)
Query: 10  RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTK--VIAAVYGPREVQNKSQQMSDQA- 66
           R+DGR    +R L    G + +  GSA+F  G T+  V A +   R+ Q   + M ++  
Sbjct: 315 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTD 374
Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
                Y+   +S G+        RR      + ++ + A +         + +  ++ ++
Sbjct: 375 TFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVRVVSEITES 434
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL----NSTPLLDLNYVEDSAGGPDVT 182
           +G +  A +  A+LAL DAG+P++  V   + G +    N   L D+   ED  G  D+ 
Sbjct: 435 NGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDILGDEDHLG--DMD 492
Query: 183 VGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVL 228
             +  + D ++ LQMD K+   T +++MQ+A+   K    +I  V+
Sbjct: 493 FKVAGSRDGISALQMDIKIEGIT-KEIMQVALNQAKGARLHILGVM 537

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 104/226 (46%), Gaps = 10/226 (4%)
Query: 10  RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTK--VIAAVYGPREVQNKSQQMSDQA- 66
           R+DGR    +R L    G + +  GSA+F  G T+  V A +   R+ Q   + M ++  
Sbjct: 315 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTD 374
Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
                Y+   +S G+        RR      + ++ + A +         + +  ++ ++
Sbjct: 375 TFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVRVVSEITES 434
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL----NSTPLLDLNYVEDSAGGPDVT 182
           +G +  A +  A+LAL DAG+P++  V   + G +    N   L D+   ED  G  D+ 
Sbjct: 435 NGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDILGDEDHLG--DMD 492
Query: 183 VGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVL 228
             +  + D ++ LQMD K+   T +++MQ+A+   K    +I  V+
Sbjct: 493 FKVAGSRDGISALQMDIKIEGIT-KEIMQVALNQAKGARLHILGVM 537

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 103/226 (45%), Gaps = 10/226 (4%)
Query: 10  RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTK--VIAAVYGPREVQNKSQQMSDQA- 66
           R+DGR    +R L    G + +  GSA+F  G T+  V A +   R+ Q   + M ++  
Sbjct: 321 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTD 380
Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
                Y+   +S G+        RR      + ++ + A +         + +  ++ ++
Sbjct: 381 TFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVRVVSEITES 440
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL----NSTPLLDLNYVEDSAGGPDVT 182
           +G +  A +  A+LAL DAG+P++  V   + G +    N   L D+   ED  G  D+ 
Sbjct: 441 NGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDILGDEDHLG--DMD 498
Query: 183 VGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVL 228
             +  + D ++ LQMD K+   T E +MQ+A+   K    +I  V+
Sbjct: 499 FKVAGSRDGISALQMDIKIEGITKE-IMQVALNQAKGARLHILGVM 543

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 103/226 (45%), Gaps = 10/226 (4%)
Query: 10  RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTK--VIAAVYGPREVQNKSQQMSDQA- 66
           R+DGR    +R L    G + +  GSA+F  G T+  V A +   R+ Q   + M ++  
Sbjct: 321 RIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTD 380
Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
                Y+   +S G+        RR      + ++ + A +         + +  ++ ++
Sbjct: 381 TFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVRVVSEITES 440
Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL----NSTPLLDLNYVEDSAGGPDVT 182
           +G +  A +  A+LAL DAG+P++  V   + G +    N   L D+   ED  G  D+ 
Sbjct: 441 NGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDILGDEDHLG--DMD 498
Query: 183 VGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVL 228
             +  + D ++ LQMD K+   T E +MQ+A+   K    +I  V+
Sbjct: 499 FKVAGSRDGISALQMDIKIEGITKE-IMQVALNQAKGARLHILGVM 543

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 53/203 (26%), Positives = 91/203 (44%), Gaps = 13/203 (6%)
Query: 8   GLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV---YGPREVQNKSQQMSD 64
           GLR+DGR    +R +  E+G + +  GSA+F  G T+ I       G  E    + + + 
Sbjct: 329 GLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTY 388
Query: 65  QALVRCEYSMANFSTGD--RMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQ 122
           +      Y+   +S G+  RM  P G R      L  R            P + I +  +
Sbjct: 389 KESFLLHYNFPPYSVGETGRMGSP-GRREIGHGKLAWRALRPMLPTKEDFPYT-IRLVSE 446
Query: 123 VLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL----NSTPLLDLNYVEDSAGG 178
           + +++G +  A +  ++LA+ DAG+P+   V+  + G +        L D+   ED  G 
Sbjct: 447 ITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLG- 505
Query: 179 PDVTVGILPTLDKVTLLQMDAKL 201
            D+   +  T + +T LQMD K+
Sbjct: 506 -DMDFKVAGTSEGLTSLQMDIKI 527

>pdb|3U1K|A Chain A, Crystal Structure Of Human Pnpase Length = 630

Iteration: 1
 Score = 53.5 bits (127), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 58/224 (25%), Positives = 95/224 (42%), Gaps = 30/224 (13%)
Query: 10  RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-YGPREVQNKSQQ------- 61
           R DGR  T +R +  E+       GSA+F+ G T+V+  V +   E   KS Q       
Sbjct: 319 RCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITAING 378
Query: 62  MSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRS---QID 118
           + D+  +   Y    ++T +  +    +RR      +  + +   I     PR     I 
Sbjct: 379 IKDKNFM-LHYEFPPYATNEIGKVTGLNRRELGHGALAEKALYPVI-----PRDFPFTIR 432
Query: 119 IFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTP-----------LL 167
           +  +VL+++G +  A     +LAL D+G+P+   V   + G +  T            L 
Sbjct: 433 VTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEKGEIEDYRLLT 492
Query: 168 DLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQ 211
           D+  +ED  G  D+   I  T   +T LQ D KLP    + VM+
Sbjct: 493 DILGIEDYNG--DMDFKIAGTNKGITALQADIKLPGIPIKIVME 534

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 49/201 (24%), Positives = 90/201 (44%), Gaps = 9/201 (4%)
Query: 8   GLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV---YGPREVQNKSQQMSD 64
           GLR+DGR    +R +  E+G + +  GSA+F  G T+ I       G  E    + + + 
Sbjct: 329 GLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTY 388
Query: 65  QALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVL 124
           +      Y+   +S G+  R     RR      +  + +   + T       I +  ++ 
Sbjct: 389 KESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSEIT 448
Query: 125 QADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL----NSTPLLDLNYVEDSAGGPD 180
           +++G +  A +  ++LA+ DAG+P+   V+  + G +        L D+   ED  G  D
Sbjct: 449 ESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLG--D 506
Query: 181 VTVGILPTLDKVTLLQMDAKL 201
           +   +  T + +T LQMD K+
Sbjct: 507 MDFKVAGTSEGLTSLQMDIKI 527

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 53/203 (26%), Positives = 91/203 (44%), Gaps = 13/203 (6%)
Query: 8   GLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV---YGPREVQNKSQQMSD 64
           GLR+DGR    +R +  E+G + +  GSA+F  G T+ I       G  E    + + + 
Sbjct: 320 GLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTY 379
Query: 65  QALVRCEYSMANFSTGD--RMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQ 122
           +      Y+   +S G+  RM  P G R      L  R            P + I +  +
Sbjct: 380 KESFLLHYNFPPYSVGETGRMGSP-GRREIGHGKLAWRALRPMLPTKEDFPYT-IRLVSE 437
Query: 123 VLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL----NSTPLLDLNYVEDSAGG 178
           + +++G +  A +  ++LA+ DAG+P+   V+  + G +        L D+   ED  G 
Sbjct: 438 ITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLG- 496
Query: 179 PDVTVGILPTLDKVTLLQMDAKL 201
            D+   +  T + +T LQMD K+
Sbjct: 497 -DMDFKVAGTSEGLTSLQMDIKI 518

>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI Enzyme Length = 757

Iteration: 1
 Score = 51.2 bits (121), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 56/212 (26%), Positives = 95/212 (44%), Gaps = 15/212 (7%)
Query: 2   EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQ 61
           E V  E  R+DGR  T++R L AE+  + +  GSA+FE G T+++  V     ++ + Q 
Sbjct: 348 ERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQIL-GVTTLNXLRXEQQL 406
Query: 62  MSDQALVR----CEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQI 117
            +   + R      Y+   +S G+  R     RR      +  + +   + T       I
Sbjct: 407 DTLSPVTRKRYXHNYNFPPYSVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYAI 466
Query: 118 DIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL--------NSTPLLDL 169
               + L ++G T    + A+T +L +AG+P++  V   + G +        +   L D+
Sbjct: 467 RQVSEALGSNGSTSXGSVCASTXSLLNAGVPLKAPVAGIAXGLISQEINGETHYVALTDI 526
Query: 170 NYVEDSAGGPDVTVGILPTLDKVTLLQMDAKL 201
              ED+ G  D  V    T + VT LQ+D KL
Sbjct: 527 LGAEDAFGDXDFKVA--GTKEFVTALQLDTKL 556

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 57/224 (25%), Positives = 100/224 (44%), Gaps = 28/224 (12%)
Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAA----VYGPRE-VQNKSQQ 61
           +G+R DGR+ T+ R L   +    KADGSA+ ++G T V+A     +  P E   N+   
Sbjct: 25  KGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNL 84
Query: 62  MSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTM---EACILTHLMPRSQID 118
           + +  L+   Y+   F  G        D  + E++ V+ +++   +A  LT L+      
Sbjct: 85  IVNVELLPLAYT--TFEPG------PPDENAIELARVVDRSLRDSKALDLTKLVIEPGKS 136
Query: 119 IF-----VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNY-- 171
           ++     V VL   G    AC  A+  AL +  +   + ++      +   P   LNY  
Sbjct: 137 VWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQISVNKNEVVGKLP---LNYPV 193
Query: 172 VEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIE 215
           V  S    D  + + P LD+ ++  MDAK+  +   D+  + I+
Sbjct: 194 VTISVAKVDKYLVVDPDLDEESI--MDAKISFSYTPDLKIVGIQ 235

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 40/153 (26%), Positives = 58/153 (37%), Gaps = 17/153 (11%)
Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           E  R DGR   E R     IG+++ ADGSA+ ++GNT VI  V    E    S    D+ 
Sbjct: 22  ENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKA--EFAAPSTDAPDKG 79
Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLV--------IRQTMEACILTHLMPRSQID 118
            V     +    +      P G+        +        I Q  + CI     P   + 
Sbjct: 80  YVVPNVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCI----SPGKLVW 135
Query: 119 IF---VQVLQADGGTRSACINAATLALQDAGIP 148
           +    +  L  DG    AC  A   AL++  +P
Sbjct: 136 VLYCDLICLDYDGNILDACTFALLAALKNVQLP 168

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 58/225 (25%), Positives = 97/225 (43%), Gaps = 26/225 (11%)
Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAA----VYGPRE-VQNKSQQ 61
           +G+R DGR+ T+ R L   +    KADGSA+ ++G T V+A     +  P E   N+   
Sbjct: 27  KGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNL 86
Query: 62  MSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTM---EACILTHLMPRSQID 118
           + +  L+   Y    F  G        D  + E++ V+ +++   +A  LT L+      
Sbjct: 87  IVNVELLPLAYE--TFEPG------PPDENAIELARVVDRSLRDSKALDLTKLVIEPGKS 138
Query: 119 IF-----VQVLQADGGTRSACINAATLALQDAGI-PMRDIVTSCSAGYLNSTPLLDLNY- 171
           ++     V VL   G    AC  A+  AL +  +  +       S         L LNY 
Sbjct: 139 VWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYP 198
Query: 172 -VEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIE 215
            V  S    D  + + P LD+ ++  MDAK+  +   D+  + I+
Sbjct: 199 VVTISVAKVDKYLVVDPDLDEESI--MDAKISFSYTPDLKIVGIQ 241

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 58/225 (25%), Positives = 97/225 (43%), Gaps = 26/225 (11%)
Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAA----VYGPRE-VQNKSQQ 61
           +G+R DGR+ T+ R L   +    KADGSA+ ++G T V+A     +  P E   N+   
Sbjct: 25  KGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNL 84
Query: 62  MSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTM---EACILTHLMPRSQID 118
           + +  L+   Y    F  G        D  + E++ V+ +++   +A  LT L+      
Sbjct: 85  IVNVELLPLAYE--TFEPG------PPDENAIELARVVDRSLRDSKALDLTKLVIEPGKS 136
Query: 119 IF-----VQVLQADGGTRSACINAATLALQDAGI-PMRDIVTSCSAGYLNSTPLLDLNY- 171
           ++     V VL   G    AC  A+  AL +  +  +       S         L LNY 
Sbjct: 137 VWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYP 196
Query: 172 -VEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIE 215
            V  S    D  + + P LD+ ++  MDAK+  +   D+  + I+
Sbjct: 197 VVTISVAKVDKYLVVDPDLDEESI--MDAKISFSYTPDLKIVGIQ 239

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	241
2nn6_B	249	Exosome complex exonuclease RRP41; RNA, exosome, P	1e-112
2wp8_B	246	Exosome complex component SKI6; nucleus, hydrolase	1e-105
2po1_A	249	Probable exosome complex exonuclease 1; RNAse PH,	1e-104
2wnr_B	240	Probable exosome complex exonuclease 1; phosphate	1e-103
2je6_B	250	RRP41, exosome complex exonuclease 1; nuclease, hy	1e-95
3m7n_D	258	Probable exosome complex exonuclease 1; exosome, R	7e-93
2nn6_F	272	MTR3, exosome component 6; RNA, exosome, PM/SCL, p	5e-90
2nn6_D	237	Exosome complex exonuclease RRP46; RNA, exosome, P	2e-87
3krn_A	222	Protein C14A4.5, confirmed by transcript evidence;	4e-80
3hkm_A	246	OS03G0854200 protein; RNAse PH domain, phosphoryla	4e-78
3dd6_A	255	Ribonuclease PH; exoribonuclease, tRNA maturation,	4e-77
1udn_A	255	Ribonuclease PH, RNAse PH; transferase, riken stru	9e-75
1r6l_A	239	Ribonuclease PH; beta-alpha-beta-alpha fold, hexam	7e-72
3b4t_A	262	Ribonuclease PH; RNAse, tRNA nucleotidyltransferas	3e-69
1oys_A	245	Ribonuclease PH; transferase, tRNA processing; 2.4	5e-59
2po1_B	277	Probable exosome complex exonuclease 2; RNAse PH,	2e-47
2wnr_A	271	Probable exosome complex exonuclease 2; phosphate	1e-46
3m7n_G	259	Probable exosome complex exonuclease 2; exosome, R	1e-43
2je6_A	277	RRP42, exosome complex exonuclease 2; nuclease, hy	2e-42
2nn6_C	278	Exosome complex exonuclease RRP43; RNA, exosome, P	9e-37
2nn6_E	305	Exosome complex exonuclease RRP42; RNA, exosome, P	1e-32
2nn6_A	358	Polymyositis/scleroderma autoantigen 1; RNA, exoso	2e-29
2wp8_A	305	Exosome complex component RRP45; nucleus, hydrolas	4e-27
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	8e-13
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	1e-11
3gme_A	549	Polyribonucleotide nucleotidyltransferase; protein	2e-11
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	1e-09
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	4e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04

>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 =  322 bits (827), Expect = e-112
 Identities = 121/241 (50%), Positives = 175/241 (72%), Gaps = 1/241 (0%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQN-KS 59
           +E +S +G R+DGRR  E+R+++A +G  A+ADGSA  E GNTK +A VYGP E++  ++
Sbjct: 8   LELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRA 67

Query: 60  QQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDI 119
           + + D+ALV C+YS A FSTG+R R+P GDR+S E+ L +RQT EA ILT L PRSQIDI
Sbjct: 68  RALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDI 127

Query: 120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGP 179
           +VQVLQADGGT +AC+NAATLA+ DAGIPMRD V +CSAG+++ T L DL++VE++AGGP
Sbjct: 128 YVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAGGP 187

Query: 180 DVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRR 239
            + + +LP   ++ LL+MDA+L  +  E V++ A +  + V   +  V+ ++ ++     
Sbjct: 188 QLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVREASILL 247

Query: 240 G 240
           G
Sbjct: 248 G 248

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

 Score =  304 bits (781), Expect = e-105
 Identities = 89/237 (37%), Positives = 141/237 (59%), Gaps = 3/237 (1%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAK-ADGSAVFEMGNTKVIAAVYGPREVQNKS 59
           +E  SPEGLRLDGRR  E+R+  + I      ADGS+  E GN K+I  V GP+E + KS
Sbjct: 4   LEIYSPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKS 63

Query: 60  QQMSDQALVRCEYSMANFSTGDRMR-KPKGDRRSTEISLVIRQTMEACILTHLMPRSQID 118
           Q  + +AL+    ++  FS  +R +   K +RR  EI   + +  E  ++ ++ PR+ ID
Sbjct: 64  QMDTSKALLNVSVNINKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVID 123

Query: 119 IFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGG 178
           I + VL+ DGG   + IN  TLAL DAGI M D ++  S G  ++TPLLD N +E++A  
Sbjct: 124 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEENAMS 183

Query: 179 PDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQL 235
             VT+G++   +K++LL ++ K+P +  E+V+ + I G   V + + E L ++ ++ 
Sbjct: 184 -TVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQKR 239

>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 =  300 bits (770), Expect = e-104
 Identities = 110/235 (46%), Positives = 155/235 (65%), Gaps = 1/235 (0%)

Query: 1   MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ 60
           ++ +   G R+DGR+  E+R ++ E+G +  A+GSA  E G  K+IAAVYGPRE+  K  
Sbjct: 8   LKLIDENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHL 67

Query: 61  QMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIF 120
           Q  D+A++R  Y+MA FS  +R + P  DRRS EIS VI+  +E  ++  + PR+ ID+F
Sbjct: 68  QRPDRAILRVRYNMAPFSVEERKK-PGPDRRSIEISKVIKGALEPALILEMFPRTAIDVF 126

Query: 121 VQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPD 180
           ++VLQAD GTR A I AA+LAL DAGIPMRD+V +C+AG +    +LDLN  ED+ G  D
Sbjct: 127 IEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKIEGEIVLDLNKEEDNYGEAD 186

Query: 181 VTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQL 235
           V V I+P  + +TLLQMD  L  + F + ++LAI+G KAV    RE L E   ++
Sbjct: 187 VPVAIMPLKNDITLLQMDGYLTKDEFIEAVKLAIKGAKAVYQKQREALKEKYLKI 241

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

 Score =  298 bits (765), Expect = e-103
 Identities = 102/229 (44%), Positives = 143/229 (62%), Gaps = 1/229 (0%)

Query: 2   EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQ 61
           +  +   +R DGR   E+R L+ E G + +ADGS+  E G  K++ AVYGPRE Q +  Q
Sbjct: 9   QLKTSPSVREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQ 68

Query: 62  MSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFV 121
             D+A++RC Y+MA FS  +R R P  DRRS EIS +  + +   ++    PRS ID+F+
Sbjct: 69  RPDRAVIRCRYNMAPFSVEERKR-PGPDRRSVEISKITAEALRPALILEKFPRSVIDVFI 127

Query: 122 QVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDV 181
           +VL+A+GGTR A I AA++AL DAGIPMRD+V +C+AG +    +LDL+  ED  G  DV
Sbjct: 128 EVLEAEGGTRCAGITAASVALADAGIPMRDMVVACAAGKVGDQVVLDLSEEEDKEGQADV 187

Query: 182 TVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLE 230
            V ILP   ++TLLQ D  L    FE  + LA+EGC  +    +E L +
Sbjct: 188 PVAILPRTREITLLQSDGNLTPEEFERALDLAVEGCLRIHEVQKEALRK 236

>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 =  279 bits (715), Expect = 1e-95
 Identities = 96/234 (41%), Positives = 146/234 (62%), Gaps = 1/234 (0%)

Query: 2   EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQ 61
           + +  +G R DGR+P E+R ++ E+G +  ADGSA+FEMGNTK IAAVYGP+E+  +   
Sbjct: 13  KLILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLS 72

Query: 62  MSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFV 121
           + D+A++R  Y M  FST +R   P   RR  E+S VIR+ +E+ +L  L PR+ ID+F 
Sbjct: 73  LPDRAVLRVRYHMTPFSTDERKN-PAPSRREIELSKVIREALESAVLVELFPRTAIDVFT 131

Query: 122 QVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDV 181
           ++LQAD G+R   + AA+LAL DAGIPMRD++   + G  +   +LDLN  E   G  D+
Sbjct: 132 EILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLNETEAMWGEADM 191

Query: 182 TVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQL 235
            + ++P+L++VTL Q++  +  + F     LA++G   + N  RE L     + 
Sbjct: 192 PIAMMPSLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREALKSKYVEF 245

>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 =  272 bits (698), Expect = 7e-93
 Identities = 100/237 (42%), Positives = 147/237 (62%), Gaps = 4/237 (1%)

Query: 2   EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQ 61
           E +  +GLRLDGR+  E+R ++ E   + +ADGS   EMG  KVIAAV+GPREV  +  Q
Sbjct: 9   EKLIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQ 68

Query: 62  MSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFV 121
              +A++R  Y+MA FS  +R R P  DRRS EIS V ++  EA I+  L PRS IDIFV
Sbjct: 69  DPSKAIIRYRYNMAPFSVEERKR-PGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFV 127

Query: 122 QVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDV 181
           +VLQAD G+R+AC+NAA++AL DAG+PM+ ++TS + G  +   +LD    ED+ G  D+
Sbjct: 128 EVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKADGQLVLDPMKEEDNFGEADM 187

Query: 182 TVGILP---TLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQL 235
               L     ++ + LLQMD ++  +  +  ++LA +G   +    RE +L    ++
Sbjct: 188 PFAFLIRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAILRRYIEV 244

>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 =  265 bits (680), Expect = 5e-90
 Identities = 65/248 (26%), Positives = 120/248 (48%), Gaps = 16/248 (6%)

Query: 3   FVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNK---- 58
           + + E      R PT +R + A  G +++A GSA  E G TKV+ AV GPR+ +      
Sbjct: 20  YAADEEEAPGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGG 79

Query: 59  -------SQQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHL 111
                      + +  + C++  A F+   R R P G     E++L +++ +E  +    
Sbjct: 80  GPAGAGGEAPAALRGRLLCDFRRAPFAGRRR-RAPPGGCEERELALALQEALEPAVRLGR 138

Query: 112 MPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL---NSTPLLD 168
            PR+Q+++   +L+  G   +A + AA LAL DAG+ M D+V  C          T LLD
Sbjct: 139 YPRAQLEVSALLLEDGGSALAAALTAAALALADAGVEMYDLVVGCGLSLAPGPAPTWLLD 198

Query: 169 LNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTN-TFEDVMQLAIEGCKAVANYIREV 227
              +E+      +TV ++P L++V  L    +     ++ + ++L +EGC+ +   +++ 
Sbjct: 199 PTRLEEERAAAGLTVALMPVLNQVAGLLGSGEGGLTESWAEAVRLGLEGCQRLYPVLQQS 258

Query: 228 LLENTKQL 235
           L+   ++ 
Sbjct: 259 LVRAARRR 266

>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 =  258 bits (660), Expect = 2e-87
 Identities = 57/236 (24%), Positives = 95/236 (40%), Gaps = 12/236 (5%)

Query: 1   MEFVSPEGLRLDGRRP-TEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKS 59
            +  +  G     R P   +R    E   +++ DGSA F  G+T V+A VYGP EV+   
Sbjct: 11  AKIRAENGTGSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVS- 69

Query: 60  QQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDI 119
                    +  ++ A      R +             +IR T EA +L  L PR+ I +
Sbjct: 70  ---------KEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITV 120

Query: 120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNS-TPLLDLNYVEDSAGG 178
            +QV+   G   + C+NAA +AL DAG+PMR +    +    +  T +LD    ++    
Sbjct: 121 VLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEAR 180

Query: 179 PDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ 234
             +T  +     K+ +            +  +  A    + V  + RE L     +
Sbjct: 181 AVLTFALDSVERKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYRESLQRRYSK 236

>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 =  238 bits (610), Expect = 4e-80
 Identities = 48/218 (22%), Positives = 84/218 (38%), Gaps = 15/218 (6%)

Query: 16  PTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMA 75
              +R++R E+  +  ADGSA F  G T + A+  GP +V   S+   +   +   Y   
Sbjct: 2   AGRLREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVH-ASKASDEAMTLDISY--- 57

Query: 76  NFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACI 135
                   R   GD +   ++ +I  T+   I   L P + I + V  +Q DG   +  I
Sbjct: 58  --------RANCGDNKFNVLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAVAI 109

Query: 136 NAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLD---KV 192
           N A  AL D G+P   +        +    ++D    +++A    V   +    D   +V
Sbjct: 110 NGACFALLDNGMPFETVFCGVLIVRVKDELIIDPTAKQEAASTGRVLFSVCKGSDGHPEV 169

Query: 193 TLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLE 230
             +           E    LA     A+ ++ + V+  
Sbjct: 170 CAMDAIGHWDFIQLEAAWSLAQPSASAIFDFYKTVMKR 207

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

 Score =  234 bits (599), Expect = 4e-78
 Identities = 48/245 (19%), Positives = 98/245 (40%), Gaps = 27/245 (11%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           E  R DGR P ++R        + +A GSA +  G+T V+AAVYGP+    +  +  ++A
Sbjct: 2   EESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGT-RKGENPEKA 60

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
            +   +       G         ++  E  + +++T+++  L  + P +   + +QV+  
Sbjct: 61  SIEVVWKPMTGQIG---------KQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGN 111

Query: 127 DGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNS-TPLLDLNYVEDSAGGPDVTVGI 185
           DG      INA   AL  AGIP++ +  +   G L     +LD N  E+        +  
Sbjct: 112 DGSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLEDGEVILDTNKAEEQQLKSFAHLVF 171

Query: 186 LPTLDKVTLLQMDAK----------------LPTNTFEDVMQLAIEGCKAVANYIREVLL 229
             +    +  + + K                +    +   ++  +     +++++R  L 
Sbjct: 172 PNSRKSASSKEPNQKEEDSERGLITSITHGVMSEEDYFSCIERGLAASSRISDFMRTTLQ 231

Query: 230 ENTKQ 234
           +    
Sbjct: 232 KQAPG 236

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

 Score =  232 bits (594), Expect = 4e-77
 Identities = 64/254 (25%), Positives = 110/254 (43%), Gaps = 21/254 (8%)

Query: 2   EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQ 61
                  +R+DGR  TE+R +      +   +GS + E+G+TKVI +      V     +
Sbjct: 4   SHHHHHHMRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVP-PFMR 62

Query: 62  MSDQALVRCEYSMANFSTGDRMR----KPKGDRRSTEISLVIRQTMEACILTHLMPRSQI 117
              +  V  EY+M   +T  R      K K   R+ EI  +I + + A +    +    +
Sbjct: 63  GEGKGWVTAEYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGERTV 122

Query: 118 DIFVQVLQADGGTRSACINAATLALQD-----------AGIPMRDIVTSCSAGYLNSTP- 165
            I   V+QADGGTR+A I  A +A+             + IP++D + + S G +     
Sbjct: 123 WIDCDVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEEQGV 182

Query: 166 LLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAK---LPTNTFEDVMQLAIEGCKAVAN 222
           +LDLNY EDS    D+ V I+    +   +Q   +          +++  A +G   + +
Sbjct: 183 VLDLNYAEDSKADVDMNV-IMTGKGQFVEVQGTGEEATFSRAQLNELLDAAEQGIFQLID 241

Query: 223 YIREVLLENTKQLE 236
             +E L +    +E
Sbjct: 242 IQKEALGDIVSHIE 255

>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 =  226 bits (578), Expect = 9e-75
 Identities = 65/245 (26%), Positives = 109/245 (44%), Gaps = 18/245 (7%)

Query: 9   LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALV 68
           +R DGR+  ++R +  +   +   +GS +   G TKVI        V N  +    Q  +
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKG-KGQGWI 59

Query: 69  RCEYSMANFSTGDRMRKP----KGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVL 124
             EYSM   +T  R  +     +   R+ EI  +I + M   +    +    I +   V+
Sbjct: 60  TAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVI 119

Query: 125 QADGGTRSACINAATLALQDAGI-----------PMRDIVTSCSAGYLNSTPLLDLNYVE 173
           QADGGTR+A I  A +A+ DA I           P++D V + S G +N   LLDLN+ E
Sbjct: 120 QADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNFEE 179

Query: 174 DSAGGPDVTVGILPT--LDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLEN 231
           DSA   D+ V    +  L +V  +  +     +    ++ LA +G   +    +++ +  
Sbjct: 180 DSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTKDELIKMLDLAQKGINELIELQKKLYVIQ 239

Query: 232 TKQLE 236
             + E
Sbjct: 240 DGKWE 244

>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 =  218 bits (557), Expect = 7e-72
 Identities = 71/239 (29%), Positives = 112/239 (46%), Gaps = 20/239 (8%)

Query: 10  RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVR 69
           R  GR   ++R +R        A+GS + E G+TKVI  V     V  +  +   Q  + 
Sbjct: 3   RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVP-RFLKGQGQGWLT 61

Query: 70  CEYSMANFSTGDRMRKP----KGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQ 125
            EY M   STG+R ++     K   R+ EI  +I +++ A +    +  + + I   V+Q
Sbjct: 62  AEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQ 121

Query: 126 ADGGTRSACINAATLALQDA-----------GIPMRDIVTSCSAGYLNSTPLLDLNYVED 174
           ADGGTR+A I  AT+AL DA           G P++ +V + S G     P+LDL+Y+ED
Sbjct: 122 ADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIYQGVPVLDLDYLED 181

Query: 175 SAGGPDVTVGILPTLDKVTLLQMDAK---LPTNTFEDVMQLAIEGCKAVANYIREVLLE 230
           SA   D+ V +         +Q  A+           +++LA +G + +    R  L E
Sbjct: 182 SAAETDLNVVMTDA-GGFIEVQGTAEGAPFRPAELNAMLELAQQGMQELFELQRAALAE 239

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

 Score =  212 bits (542), Expect = 3e-69
 Identities = 63/238 (26%), Positives = 105/238 (44%), Gaps = 21/238 (8%)

Query: 10  RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVR 69
           R DGR   E+R +    G      GS + E G+TKV+        V  + ++ +    + 
Sbjct: 7   REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGV-PRWRKATGLGWLT 65

Query: 70  CEYSMANFSTGDRMR----KPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQ 125
            EY+M   +T  R      + +   R+ EIS +I +++ ACI    +  + I I   VLQ
Sbjct: 66  AEYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQ 125

Query: 126 ADGGTRSACINAATLALQDAGI------------PMRDIVTSCSAGYLNSTPLLDLNYVE 173
           ADGGTR+A I  A +AL DA              P+   + + S G ++    +DL Y E
Sbjct: 126 ADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVVDGRIRVDLPYEE 185

Query: 174 DSAGGPDVTVGILPTLDKVTLLQMDAK---LPTNTFEDVMQLAIEGCKAVANYIREVL 228
           DS    D+ V +      +  +Q   +      +T + ++ +A+  C  +    R+ L
Sbjct: 186 DSRAEVDMNV-VATDTGTLVEIQGTGEGATFARSTLDKLLDMALGACDTLFAAQRDAL 242

>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 =  185 bits (473), Expect = 5e-59
 Identities = 69/247 (27%), Positives = 112/247 (45%), Gaps = 21/247 (8%)

Query: 9   LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALV 68
           +R DGR+  E+R +  ++  ++  +GS +   GNTKVI        V     +   +  +
Sbjct: 1   MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVP-PFLRGGGKGWI 59

Query: 69  RCEYSMANFSTGDRMR----KPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVL 124
             EYSM   +T  +      K K   R+ EI  +I + + A +    +    I I   V+
Sbjct: 60  TAEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVI 119

Query: 125 QADGGTRSACINAATLALQDA-----------GIPMRDIVTSCSAGYLNSTP-LLDLNYV 172
           QADGGTR+A I  A LA+  A             P+ D + + S G       LLDLNY 
Sbjct: 120 QADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYE 179

Query: 173 EDSAGGPDVTVGILPTLDKVTLLQMDAKLPT---NTFEDVMQLAIEGCKAVANYIREVLL 229
           EDS+   D+ V I+    +   LQ   +  T        ++ LA +G + + +  +EVL 
Sbjct: 180 EDSSAEVDMNV-IMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLG 238

Query: 230 ENTKQLE 236
           ++  +L+
Sbjct: 239 DSLPELK 245

>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 =  157 bits (398), Expect = 2e-47
 Identities = 44/258 (17%), Positives = 95/258 (36%), Gaps = 35/258 (13%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           EG R+D R   + R +  E+G + KA+GSA+ ++G+T+V+  +     +        +  
Sbjct: 24  EGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKT--SLGEPFPDTPNMG 81

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQT--------MEACILTHLMPRSQID 118
           ++     +   ++         D R+ E++ VI +         +E  ++        + 
Sbjct: 82  VMTTNVELVPLASPTFEP-GPPDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVF 140

Query: 119 IFVQVLQADGGTRSACINAATLALQDAGIP---------------------MRDIVTSCS 157
           I V VL  DG    A   AA  AL +A +P                     +  I    +
Sbjct: 141 IDVHVLDHDGNLMDAIGIAAIAALLNARVPKVRYNEETGEVETLDETEPLPVEKIPVPVT 200

Query: 158 AGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMD--AKLPTNTFEDVMQLAIE 215
              + +  ++D +  E+      +T+    T   ++ +Q               ++ A +
Sbjct: 201 FAKIGNILVVDPSLDEELVMDGKITITTDET-GHISAVQKSEGGAFKLEEVMYAVETAFK 259

Query: 216 GCKAVANYIREVLLENTK 233
             + +   I E + +  +
Sbjct: 260 KAEEIRKLILEAVEKAKQ 277

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

 Score =  154 bits (392), Expect = 1e-46
 Identities = 44/253 (17%), Positives = 95/253 (37%), Gaps = 36/253 (14%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
              R+DGR   E R +  E G ++KA+GS+  ++GNT++I  V    ++        +  
Sbjct: 22  NKERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKP--QIGEPFPDTPEMG 79

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEA---------CILTHLMPRSQI 117
           ++     +   ++         D RS E+S V+ + +           CI+        +
Sbjct: 80  VILTNSELLPMASPTFEP-GPPDERSVELSRVVDRCIRESRMIDLEKLCIIEG-SKVWML 137

Query: 118 DIFVQVLQADGGTRSACINAATLALQDAGIP--------------------MRDIVTSCS 157
            + + ++  DG    A + A   AL D  IP                    +      C+
Sbjct: 138 FLDLHIIDYDGNLFDAAVLATVAALLDTRIPAAEVEDGEVVINREKMQPLPVNRKALMCT 197

Query: 158 AGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLP--TNTFEDVMQLAIE 215
              + +  +LD +  E+      +++G+      +  +Q   + P   +     + +A+E
Sbjct: 198 FAKIGNEIVLDPSLEEEDILTARISIGVTEE-GSICAMQKGGEGPLTRDDVLKAVSIAVE 256

Query: 216 GCKAVANYIREVL 228
               +  Y+ + +
Sbjct: 257 KVPQLIEYLDKSM 269

>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 =  146 bits (371), Expect = 1e-43
 Identities = 45/245 (18%), Positives = 95/245 (38%), Gaps = 29/245 (11%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           +  R+DGR   E R++      + KA+GSA+ ++G+T+V+  V    +         D+ 
Sbjct: 20  DNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGV--KMQPGEPYPDTPDRG 77

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEA---------CILTHLMPRSQI 117
           ++     +   ++         D  S E++ V+ + +            I         +
Sbjct: 78  VIIVNAELVPLASPTF-EPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEG-EKVWIV 135

Query: 118 DIFVQVLQADGGTRSACINAATLALQDAGIP-------------MRDIVTSCSAGYLNST 164
            + +  L  DG    A   AA  AL +  +P             +RD+  S ++  + + 
Sbjct: 136 FVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLPVRDLPVSVTSLIVGNK 195

Query: 165 PLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLP--TNTFEDVMQLAIEGCKAVAN 222
            L+D +  E S G   +T+      D V  +Q           F++++ ++I   + +  
Sbjct: 196 YLVDPSREEMSVGDTTLTITTDKD-DNVVAMQKSGGYLLDEKLFDELLDVSINCARKLRE 254

Query: 223 YIREV 227
             +E+
Sbjct: 255 KFKEI 259

>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 =  144 bits (365), Expect = 2e-42
 Identities = 44/253 (17%), Positives = 92/253 (36%), Gaps = 35/253 (13%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           +G+R DGR+ T+ R L   +    KADGSA+ ++G T V+A      E+    +   +Q 
Sbjct: 27  KGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGT--KLEIDKPYEDTPNQG 84

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTME--ACI----LTHLMPRSQIDIF 120
            +     +   +          D  + E++ V+ +++     +    L     +S   ++
Sbjct: 85  NLIVNVELLPLAYETFEP-GPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVW 143

Query: 121 V--QVLQADGGTRSACINAATLALQDAGIP---------------------MRDIVTSCS 157
           +   VL   G    AC  A+  AL +  +                      +   V + S
Sbjct: 144 LDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVVTIS 203

Query: 158 AGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTN--TFEDVMQLAIE 215
              ++   ++D +  E+S     ++    P   K+  +Q   K   +    +     A  
Sbjct: 204 VAKVDKYLVVDPDLDEESIMDAKISFSYTPD-LKIVGIQKSGKGSMSLQDIDQAENTARS 262

Query: 216 GCKAVANYIREVL 228
               +   +++ L
Sbjct: 263 TAVKLLEELKKHL 275

>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 =  129 bits (326), Expect = 9e-37
 Identities = 55/255 (21%), Positives = 87/255 (34%), Gaps = 37/255 (14%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           E  R DGR   E R     IG+++ ADGSA+ ++GNT VI  V    E    S    D+ 
Sbjct: 22  ENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKA--EFAAPSTDAPDKG 79

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHL--------MPRSQID 118
            V     +    +      P G+  +   S  I   +E   +                + 
Sbjct: 80  YVVPNVDLPPLCSSRFRSGPPGE-EAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLY 138

Query: 119 IFVQVLQADGGTRSACINAATLALQDAGIP----------------------MRDIVTSC 156
             +  L  DG    AC  A   AL++  +P                      +R    + 
Sbjct: 139 CDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETALAEVNLKKKSYLNIRTHPVAT 198

Query: 157 SAGYLNSTPLL-DLNYVEDSAGGPDVTVGILPTLDKVTLLQMD--AKLPTNTFEDVMQLA 213
           S    + T L+ D    E+      +T+ +     K+  L     + L     +D M  A
Sbjct: 199 SFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEE-GKLCCLHKPGGSGLTGAKLQDCMSRA 257

Query: 214 IEGCKAVANYIREVL 228
           +   K V   + EV+
Sbjct: 258 VTRHKEVKKLMDEVI 272

>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 =  119 bits (299), Expect = 1e-32
 Identities = 41/270 (15%), Positives = 94/270 (34%), Gaps = 41/270 (15%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           E LR+DGR   + R +  E   V+   GSA  ++G+T ++  V    E+     +  ++ 
Sbjct: 34  EDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKA--EMGTPKLEKPNEG 91

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQT--------MEACILTHLMPRSQID 118
            +      +  +T +   +  GD   TEI+  + +         ++   ++       + 
Sbjct: 92  YLEFFVDCSASATPEFEGRG-GDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLY 150

Query: 119 IFVQVLQADGGTRSACINAATLALQDAGIP---------------------------MRD 151
           + V +L+  G    A   A   AL +  IP                           + +
Sbjct: 151 VDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLEDEEGSKDIELSDDPYDCIRLSVEN 210

Query: 152 IVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQM--DAKLPTNTFEDV 209
           +    +   +    ++D    E++     + V +      VT ++      L   +  ++
Sbjct: 211 VPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSK-GVVTCMRKVGKGSLDPESIFEM 269

Query: 210 MQLAIEGCKAVANYIREVLLENTKQLECRR 239
           M+      K +   ++ V+ +       R+
Sbjct: 270 METGKRVGKVLHASLQSVVHKEESLGPKRQ 299

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

 Score =  112 bits (281), Expect = 2e-29
 Identities = 38/268 (14%), Positives = 85/268 (31%), Gaps = 42/268 (15%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           E  RLDGR+  + R +R   G      G  + E+G T+V+  V    E+ +     + + 
Sbjct: 37  EKKRLDGRQTYDYRNIRISFGT---DYGCCIVELGKTRVLGQVSC--ELVSPKLNRATEG 91

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHL--------MPRSQID 118
           ++     ++  +        +      +++ ++ + +                    QI 
Sbjct: 92  ILFFNLELSQMAAPAF-EPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIR 150

Query: 119 IFVQVLQADGGTRSACINAATLALQDAGIP-----------------------MRDIVTS 155
           + + +L  DG    A   AA +AL     P                       +  +   
Sbjct: 151 VDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDPVPLSIHHMPIC 210

Query: 156 CSAGYLN--STPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMD--AKLPTNTFEDVMQ 211
            S  +    +  L+D N  E+      + + +     ++  +Q      L  +      +
Sbjct: 211 VSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKH-REICTIQSSGGIMLLKDQVLRCSK 269

Query: 212 LAIEGCKAVANYIREVLLENTKQLECRR 239
           +A      +   I + L  + K  +   
Sbjct: 270 IAGVKVAEITELILKALENDQKVRKEGG 297

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

 Score =  104 bits (261), Expect = 4e-27
 Identities = 38/274 (13%), Positives = 77/274 (28%), Gaps = 51/274 (18%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           +  RLDGR   + R +    G      G    +MGNTKV   +    ++    +    + 
Sbjct: 21  QNYRLDGRSFDQFRDVEITFGK---EFGDVSVKMGNTKVHCRISC--QIAQPYEDRPFEG 75

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHL--------MPRSQID 118
           L      ++  +                 S +I +++       +             + 
Sbjct: 76  LFVISTEISPMAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVR 135

Query: 119 IFVQVLQADGGTRSACINAATLALQDAGIP-----------------------MRDIVTS 155
             V  L  DGG   A   A    L     P                       +  I   
Sbjct: 136 ADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQIIVHPVNEREPVPLGILHIPIC 195

Query: 156 CSAGYLNSTP--------------LLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMD-AK 200
            +  + N                 ++D    E+      +TV +    + V + +     
Sbjct: 196 VTFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLNKNREVVQVSKAGGLP 255

Query: 201 LPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ 234
           +   T       A    + + + I ++L E++++
Sbjct: 256 MDALTLMKCCHEAYSIIEKITDQILQLLKEDSEK 289

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

 Score = 66.4 bits (163), Expect = 8e-13
 Identities = 59/251 (23%), Positives = 103/251 (41%), Gaps = 41/251 (16%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-YGPREVQNKSQQMSDQ 65
           E  R DGR  T +R +  E+       GSA+F+ G T+V+  V +   E   KS Q+   
Sbjct: 316 EYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITA 375

Query: 66  ALVRCE------YSMANFSTGD--RMRKPKGDRRSTEI---SLVIRQTMEACILTHLMPR 114
                +      Y    ++T +  ++      RR  E+   +L  +       L  ++PR
Sbjct: 376 INGIKDKNFMLHYEFPPYATNEIGKVTGLN--RR--ELGHGALAEKA------LYPVIPR 425

Query: 115 S---QIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL---NSTPLLD 168
                I +  +VL+++G +  A     +LAL D+G+P+   V   + G +   +      
Sbjct: 426 DFPFTIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEKGEI 485

Query: 169 LNYV--------EDSAGGPDVTV-GILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKA 219
            +Y         ED  G  D  + G   T   +T LQ D KLP    + ++  AI+    
Sbjct: 486 EDYRLLTDILGIEDYNGDMDFKIAG---TNKGITALQADIKLPGIPIK-IVMEAIQQASV 541

Query: 220 VANYIREVLLE 230
               I +++ +
Sbjct: 542 AKKEILQIMNK 552

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A Length = 757

 Score = 62.6 bits (153), Expect = 1e-11
 Identities = 67/250 (26%), Positives = 116/250 (46%), Gaps = 44/250 (17%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVY--GPREVQNKSQQMSD 64
           E  R+DGR  T++R L AE+  + +  GSA+FE G T+++        R      QQ+  
Sbjct: 353 EKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRME----QQLDT 408

Query: 65  QALVRCE-----YSMANFSTGD--RMRKPKGDRRSTEI---SLVIRQTMEACILTHLMPR 114
            + V  +     Y+   +S G+  R+  PK  RR  EI   +L  R       +  ++P 
Sbjct: 409 LSPVTRKRYMHNYNFPPYSVGETGRVGSPK--RR--EIGHGALAERA------IVPVLPT 458

Query: 115 SQ-----IDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDL 169
            +     I    + L ++G T    + A+T++L +AG+P++  V   + G ++     + 
Sbjct: 459 REEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIAMGLISQEINGET 518

Query: 170 NYV--------EDSAGGPDVTV-GILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAV 220
           +YV        ED+ G  D  V G   T + VT LQ+D KL       V+  A++  +  
Sbjct: 519 HYVALTDILGAEDAFGDMDFKVAG---TKEFVTALQLDTKLDGIPAS-VLAAALKQARDA 574

Query: 221 ANYIREVLLE 230
             +I +V++E
Sbjct: 575 RLHILDVMME 584

>3gme_A Polyribonucleotide nucleotidyltransferase; protein-RNA complex, cytoplasm, nucleotidyltransferase, RNA- binding, transferase, hydrolase; 2.40A {Escherichia coli E24377A} PDB: 3gll_A 3gcm_A 3h1c_A 3cdj_A Length = 549

 Score = 62.1 bits (152), Expect = 2e-11
 Identities = 63/246 (25%), Positives = 106/246 (43%), Gaps = 40/246 (16%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVY--GPREVQNKSQQMSD 64
              R+DGR    +R L    G + +  GSA+F  G T+ +        R+      Q+ D
Sbjct: 312 GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDA-----QVLD 366

Query: 65  QALVRCE------YSMANFSTGD--RMRKPKGDRRSTEI---SLVIRQTMEACILTHLMP 113
           + +          Y+   +S G+   +  PK  RR  EI    L  R       +  +MP
Sbjct: 367 ELMGERTDTFLFHYNFPPYSVGETGMVGSPK--RR--EIGHGRLAKRG------VLAVMP 416

Query: 114 RSQ-----IDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL----NST 164
                   + +  ++ +++G +  A +  A+LAL DAG+P++  V   + G +    N  
Sbjct: 417 DMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYV 476

Query: 165 PLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYI 224
            L D+   ED  G  D  V    + D ++ LQMD K+   T E +MQ+A+   K    +I
Sbjct: 477 VLSDILGDEDHLGDMDFKVA--GSRDGISALQMDIKIEGITKE-IMQVALNQAKGARLHI 533

Query: 225 REVLLE 230
             V+ +
Sbjct: 534 LGVMEQ 539

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

 Score = 56.7 bits (138), Expect = 1e-09
 Identities = 65/247 (26%), Positives = 107/247 (43%), Gaps = 42/247 (17%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVY--GPREVQNKSQQMSD 64
              R+DGR    +R L    G + +  GSA+F  G T+ +        R+     Q + +
Sbjct: 318 GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDA----QVLDE 373

Query: 65  QALVRCE-----YSMANFSTGD--RMRKPKGDRRSTEI---SLVIRQTMEACILTHLMPR 114
               R +     Y+   +S G+   +  PK  RR  EI    L  R       +  +MP 
Sbjct: 374 LMGERTDTFLFHYNFPPYSVGETGMVGSPK--RR--EIGHGRLAKRG------VLAVMPD 423

Query: 115 SQ-----IDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL-----NST 164
                  + +  ++ +++G +  A +  A+LAL DAG+P++  V   + G L     N  
Sbjct: 424 MDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMG-LVKEGDNYV 482

Query: 165 PLLDLNYVEDSAGGPDVTV-GILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANY 223
            L D+   ED  G  D  V G   + D ++ LQMD K+   T E +MQ+A+   K    +
Sbjct: 483 VLSDILGDEDHLGDMDFKVAG---SRDGISALQMDIKIEGITKE-IMQVALNQAKGARLH 538

Query: 224 IREVLLE 230
           I  V+ +
Sbjct: 539 ILGVMEQ 545

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

 Score = 55.2 bits (134), Expect = 4e-09
 Identities = 63/247 (25%), Positives = 105/247 (42%), Gaps = 42/247 (17%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVY--GPREVQNKSQQMSD 64
            GLR+DGR    +R +  E+G + +  GSA+F  G T+ I         +      Q  D
Sbjct: 328 TGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDE-----QFID 382

Query: 65  QALVRCE------YSMANFSTGD--RMRKPKGDRRSTEI---SLVIRQTMEACILTHLMP 113
                 +      Y+   +S G+  RM  P   RR  EI    L  R       L  ++P
Sbjct: 383 ALEGTYKESFLLHYNFPPYSVGETGRMGSPG--RR--EIGHGKLAWRA------LRPMLP 432

Query: 114 RSQ-----IDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL----NST 164
             +     I +  ++ +++G +  A +  ++LA+ DAG+P+   V+  + G +       
Sbjct: 433 TKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFA 492

Query: 165 PLLDLNYVEDSAGGPDVTV-GILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANY 223
            L D+   ED  G  D  V G   T + +T LQMD K+   T   +M+ A+   K    +
Sbjct: 493 VLSDILGDEDHLGDMDFKVAG---TSEGLTSLQMDIKIAGITPA-IMEQALAQAKEGRAH 548

Query: 224 IREVLLE 230
           I   + +
Sbjct: 549 ILGEMNK 555

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

 Score = 45.2 bits (106), Expect = 1e-05
 Identities = 36/258 (13%), Positives = 75/258 (29%), Gaps = 50/258 (19%)

Query: 15  RPTEMRQLRAEIGNVAKADGSAVFEM---GNTKVIAAVYGPREVQNK----------SQQ 61
           R     +LR  +  +  A    +  +   G T V   V    +VQ K             
Sbjct: 133 RLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNC 192

Query: 62  MSDQALVR-----CEYSMANF-STGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRS 115
            S + ++            N+ S  D     K   R   I   +R+ ++    +      
Sbjct: 193 NSPETVLEMLQKLLYQIDPNWTSRSDHSSNIK--LRIHSIQAELRRLLK----SKPYENC 246

Query: 116 QI---DIF-VQVLQA-DGG------TRSACINAATLALQDAGIPMRDIVTSCSAGYLNST 164
            +   ++   +   A +        TR   +     A     I +     +     L   
Sbjct: 247 LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMT-----LTPD 301

Query: 165 PLLDL--NYVEDSAGG-PDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVA 221
            +  L   Y++      P   +   P    ++++    +    T+++   +    C  + 
Sbjct: 302 EVKSLLLKYLDCRPQDLPREVLTTNPRR--LSIIAESIRDGLATWDNWKHV---NCDKLT 356

Query: 222 NYIREVLLENTKQLECRR 239
             I E  L   +  E R+
Sbjct: 357 T-IIESSLNVLEPAEYRK 373

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

 Score = 40.6 bits (94), Expect = 3e-04
 Identities = 31/248 (12%), Positives = 78/248 (31%), Gaps = 44/248 (17%)

Query: 11  LDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYG-------PREVQNKSQQMS 63
           L+   P E R++   +         +VF   +  +   +           +V     ++ 
Sbjct: 363 LNVLEPAEYRKMFDRL---------SVFPP-SAHIPTILLSLIWFDVIKSDVMVVVNKLH 412

Query: 64  DQALVRCEYSMANFSTGD---RMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQID-- 118
             +LV  +   +  S       ++    +  +   S+V    +     +  +    +D  
Sbjct: 413 KYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQY 472

Query: 119 IFVQV----LQADGGTRSACINAATLALQ--DAGIPMRDIVTSCSAGYLNSTPLLDL--- 169
            +  +       +   R        L  +  +  I       + S   LN+  L  L   
Sbjct: 473 FYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNT--LQQLKFY 530

Query: 170 -NYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVL 228
             Y+ D+    +  V  +       L +++  L  + + D++++A+            + 
Sbjct: 531 KPYICDNDPKYERLVNAILDF----LPKIEENLICSKYTDLLRIALM------AEDEAIF 580

Query: 229 LENTKQLE 236
            E  KQ++
Sbjct: 581 EEAHKQVQ 588

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	241
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
2wp8_B	246	Exosome complex component SKI6; nucleus, hydrolase	100.0
2je6_B	250	RRP41, exosome complex exonuclease 1; nuclease, hy	100.0
3m7n_D	258	Probable exosome complex exonuclease 1; exosome, R	100.0
2nn6_F	272	MTR3, exosome component 6; RNA, exosome, PM/SCL, p	100.0
2nn6_D	237	Exosome complex exonuclease RRP46; RNA, exosome, P	100.0
3dd6_A	255	Ribonuclease PH; exoribonuclease, tRNA maturation,	100.0
3b4t_A	262	Ribonuclease PH; RNAse, tRNA nucleotidyltransferas	100.0
1oys_A	245	Ribonuclease PH; transferase, tRNA processing; 2.4	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
2po1_B	277	Probable exosome complex exonuclease 2; RNAse PH,	100.0
3hkm_A	246	OS03G0854200 protein; RNAse PH domain, phosphoryla	100.0
3m7n_G	259	Probable exosome complex exonuclease 2; exosome, R	100.0
2je6_A	277	RRP42, exosome complex exonuclease 2; nuclease, hy	100.0
2wnr_A	271	Probable exosome complex exonuclease 2; phosphate	100.0
2nn6_C	278	Exosome complex exonuclease RRP43; RNA, exosome, P	100.0
2nn6_E	305	Exosome complex exonuclease RRP42; RNA, exosome, P	100.0
2nn6_A	358	Polymyositis/scleroderma autoantigen 1; RNA, exoso	100.0
2wp8_A	305	Exosome complex component RRP45; nucleus, hydrolas	100.0
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
3krn_A	222	Protein C14A4.5, confirmed by transcript evidence;	100.0
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	100.0
3gme_A	549	Polyribonucleotide nucleotidyltransferase; protein	99.97
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	99.96
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.96
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.96

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

Probab=100.00  E-value=9.3e-57  Score=377.61  Aligned_cols=232  Identities=44%  Similarity=0.733  Sum_probs=212.8

Q ss_pred             CcccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCccc
Q 026213            1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTG   80 (241)
Q Consensus         1 ~~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~   80 (241)
                      ||+++++|+|+|||.++|+|++.+++|++++++|||+|++|+|+|+|+|++|.+...|....++++.+.++|+++|++++
T Consensus         8 ~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~g~l~~~~~~~p~a~~   87 (240)
T 2wnr_B            8 DQLKTSPSVREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIRCRYNMAPFSVE   87 (240)
T ss_dssp             -------CCCTTSCCTTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECCSSSSCCSSSCEEEEEEEECTTSSS
T ss_pred             eEeecccCccCCCCCcCCccCeEEEeCCCCCCCEEEEEEECCeEEEEEEEcCCCCCcccccCCCcEEEEEEEEeCCCCcC
Confidence            79999999999999999999999999999999999999999999999999998876666667899999999999999998


Q ss_pred             ccCCCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEEEee
Q 026213           81 DRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGY  160 (241)
Q Consensus        81 ~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs~~~  160 (241)
                      +++ .++++.++.+++++|+++|+++++++.||+|+|+|+++||++|||+++|+++|+++||+|+|+||+++|+++|+|+
T Consensus        88 ~~~-~~~~~~~~~~l~~ll~r~l~~~i~l~~~p~~~I~i~~~VL~~dG~~~~a~i~aa~~AL~da~iP~~~~v~avs~g~  166 (240)
T 2wnr_B           88 ERK-RPGPDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEGGTRCAGITAASVALADAGIPMRDMVVACAAGK  166 (240)
T ss_dssp             SCC-CSSCCHHHHHHHHHHHHHHGGGBCGGGSTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTTCCBSSCCEEEEEEE
T ss_pred             Ccc-CCCCChhHHHHHHHHHHHHHHhcCHHHCCCcEEEEEEEEEeCCCCHHHHHHHHHHHHHHHcCCccccceeeEEEEE
Confidence            876 5578899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          161 LNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTK  233 (241)
Q Consensus       161 ~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~  233 (241)
                      +++.+++||+..||..+++.++|+++++.++++.++++|.++++++.++++.|.++++++++.++++|.++.+
T Consensus       167 ~~~~~l~Dp~~~Ee~~~~~~~~v~~~~~~~~i~~lq~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~  239 (240)
T 2wnr_B          167 VGDQVVLDLSEEEDKEGQADVPVAILPRTREITLLQSDGNLTPEEFERALDLAVEGCLRIHEVQKEALRKRYG  239 (240)
T ss_dssp             SSSSEEESCCSHHHHSCSEEEEEEEETTTTEEEEEEEEECBCHHHHHHHHHHHHHHHHHHHHHHHHHHHC---
T ss_pred             ECCEEEeCCCHHHhccCCceEEEEEECCCCCEEEEEEEcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            9999999999999999999999998788899999999999999999999999999999999999999988754

>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=1e-56  Score=379.28  Aligned_cols=239  Identities=50%  Similarity=0.860  Sum_probs=221.2

Q ss_pred             CcccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCcccccc-ccCCCCceEEEEEEeecCCcc
Q 026213            1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNK-SQQMSDQALVRCEYSMANFST   79 (241)
Q Consensus         1 ~~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~-~~~~~~~~~i~v~~~~~~~~~   79 (241)
                      ||||+++|+|+|||.++|+|++.+++|++++++|||+|++|+|+|+|+|++|.+.+.+ ....++++.+.++|+++|+++
T Consensus         8 ~~~i~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~g~~~~~~~~~~~~~~~g~l~~~~~~~p~a~   87 (249)
T 2nn6_B            8 LELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATFST   87 (249)
T ss_dssp             ---CCBTTBCSSSSCTTSCCCEEEEESCSSSSSEEEEEEESSCEEEEEEEEEEECCSSSCCCCCSSCCEEEEEEECTTTS
T ss_pred             hhhcccCCcCCCCCCcCCcCCeEEEeCCCCCCCeEEEEEECCeEEEEEEEccCCccccccccCCCcEEEEEEEEcCCCcc
Confidence            7999999999999999999999999999999999999999999999999998765332 234688999999999999999


Q ss_pred             cccCCCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEEEe
Q 026213           80 GDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAG  159 (241)
Q Consensus        80 ~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs~~  159 (241)
                      +++.+.++++.++.+++++|+++|+++++++.||+|+|+|+++||++|||+++|++||+++||+|+||||+++|+++|+|
T Consensus        88 ~~~~~~~~~~~~~~~~~~ll~r~l~~~i~~~~~p~~~I~i~~~VL~~dG~~~~A~i~aa~~AL~da~iPl~~~v~avs~g  167 (249)
T 2nn6_B           88 GERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAG  167 (249)
T ss_dssp             SSCCCTTTSTHHHHHHHHHHHHHHHHTTCGGGCTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTCCCCSSCCEEEEEE
T ss_pred             cccccCCCCCHhHHHHHHHHHHHHHHhcCHHHCCCcEEEEEEEEEeCCCCHHHHHHHHHHHHHHhcCCcccCCeeeEEEE
Confidence            98876778899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 026213          160 YLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRR  239 (241)
Q Consensus       160 ~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~~~~~~~  239 (241)
                      ++++.+++||+..||..+.+.++|+++++.++++.++++|+++.+++.+++++|.++++++++.++++|.++.++.....
T Consensus       168 ~~~~~~l~Dp~~~Ee~~~~~~~~v~~~~~~~~i~~lq~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~~~~~~  247 (249)
T 2nn6_B          168 FVDGTALADLSHVEEAAGGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVREASILL  247 (249)
T ss_dssp             EETTEEEESCCHHHHTSSCCCEEEEEETTTTEEEEEEECSCCBTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC--
T ss_pred             EECCeEEECCChHHhccCCcEEEEEEECCCCCEEEEEEECCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence            99999999999999999999999998778899999999999999999999999999999999999999999988765443

>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=7.4e-56  Score=373.95  Aligned_cols=235  Identities=47%  Similarity=0.765  Sum_probs=222.1

Q ss_pred             CcccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCccc
Q 026213            1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTG   80 (241)
Q Consensus         1 ~~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~   80 (241)
                      ||+++++|+|+|||.++|+|++.+++|++++++|||+|++|+|+|+|+|+||.+...|....++++.+.++|+++|++++
T Consensus         8 ~~~~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~g~l~v~~~~~p~a~~   87 (249)
T 2po1_A            8 LKLIDENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILRVRYNMAPFSVE   87 (249)
T ss_dssp             -CCSBCSSCBTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEEECSSGGGCCSSSCEEEEEEEECGGGSS
T ss_pred             eEEecccCccCCCCCcccccCEEEEeCCcCCCCEEEEEEECCcEEEEEEEcCcccCcccccCCCceEEEEEEEeCCcccc
Confidence            68999999999999999999999999999999999999999999999999998876656677899999999999999998


Q ss_pred             ccCCCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEEEee
Q 026213           81 DRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGY  160 (241)
Q Consensus        81 ~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs~~~  160 (241)
                      +++ .+.++.++.+++++|+++|+++++++.||+|.|+|+++||++||++++|+++|+++||+|+||||+++|+++++|+
T Consensus        88 ~~~-~~~~~~~~~~~s~li~r~l~~~i~l~~~p~~~i~I~~~VL~~dG~~~~aai~aa~~AL~da~iP~~~~v~avs~g~  166 (249)
T 2po1_A           88 ERK-KPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGK  166 (249)
T ss_dssp             SCC-CSSCCHHHHHHHHHHHHHHGGGBCGGGSTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTTCCBSSCCEEEEEEE
T ss_pred             ccc-CCCCCHHHHHHHHHHHHHHHhhccHHHCCCCEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCccCceEEEEEEE
Confidence            765 3457889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          161 LNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLE  236 (241)
Q Consensus       161 ~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~~~~  236 (241)
                      +++.+++||+..||..+++.++|+++++.+++++++++|.++++++.++++.|.++++++++.+++++.++.+++.
T Consensus       167 ~~~~~l~Dp~~~Ee~~~~~~l~va~~~~~~~i~~~~~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~~~  242 (249)
T 2po1_A          167 IEGEIVLDLNKEEDNYGEADVPVAIMPLKNDITLLQMDGYLTKDEFIEAVKLAIKGAKAVYQKQREALKEKYLKIA  242 (249)
T ss_dssp             ETTEEEESCCHHHHHTCSEEEEEEEEGGGTEEEEECCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             ECCEEEecCcHHHhccCCceEEEEEECCCCCEEEEEEEcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            9999999999999999999999998778899999999999999999999999999999999999999999887654

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

Probab=100.00  E-value=1.2e-55  Score=372.15  Aligned_cols=236  Identities=37%  Similarity=0.600  Sum_probs=208.1

Q ss_pred             CcccCCCCCCCCCCCCCCCcceEEEeCCCCCC-ceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcc
Q 026213            1 MEFVSPEGLRLDGRRPTEMRQLRAEIGNVAKA-DGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFST   79 (241)
Q Consensus         1 ~~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a-~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~   79 (241)
                      ||||+++|+|+|||.++|+|++.+++|+++++ +|||+|++|+|+|+|+|++|.+...+....++++.+.|+|+++|+++
T Consensus         4 ~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~aa~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~~g~l~v~~~~~p~a~   83 (246)
T 2wp8_B            4 LEIYSPEGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNINKFSK   83 (246)
T ss_dssp             CCSSCTTSCCTTSCCTTCCCCEEEEECSCTTTCSEEEEEEETTEEEEEEEEEEEC------CCSSSEEEEEEEEEC----
T ss_pred             hhhhcccCccCCCCCcCCccCeEEEeCCCCCCCCceEEEEECCeEEEEEEEecCCcccccccCCCcEEEEEEEEeCCccc
Confidence            89999999999999999999999999999999 99999999999999999998875455556789999999999999999


Q ss_pred             cccCCC-CCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEEE
Q 026213           80 GDRMRK-PKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSA  158 (241)
Q Consensus        80 ~~~~~~-~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs~  158 (241)
                      +++.++ ++++.++.+++++|+++|+++++++.||+|.|+|+++||++||++++|++||+++||+++||||+++|+++++
T Consensus        84 ~~~~~r~g~~~~~~~~~s~li~r~l~~~i~~~~~p~~~I~i~~~VL~~dG~~~~aai~aa~~AL~~a~iP~~~~v~avs~  163 (246)
T 2wp8_B           84 FERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISV  163 (246)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHBCTTTSCSEEEEEEEEEEECCSCHHHHHHHHHHHHHHHHTCCBSSCEEEEEE
T ss_pred             ccccccCCCCChhHHHHHHHHHHHHHHhhhHHHCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHHcCCcccCceeEEEE
Confidence            987655 5677899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026213          159 GYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLEC  237 (241)
Q Consensus       159 ~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~~~~~  237 (241)
                      |++++.+++||+.+|| .+.+.++|+++++.+++++++++|+++.+++.++++.|.++++++++.+++++.++.++...
T Consensus       164 g~~~~~~l~Dp~~~Ee-~~~~~l~v~~~~~~~~i~~i~~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~~~~  241 (246)
T 2wp8_B          164 GLYDTTPLLDTNSLEE-NAMSTVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQKRVS  241 (246)
T ss_dssp             EEETTEEESSCCHHHH-HHSEEEEEEEETTSSCEEEEEECSCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--
T ss_pred             EEECCEEEECCCchhh-ccCceEEEEEeCCCCCEEEEEecCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            9999999999999999 99999999887788999999999999999999999999999999999999999999887554

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

Probab=100.00  E-value=6.5e-55  Score=368.45  Aligned_cols=233  Identities=41%  Similarity=0.747  Sum_probs=220.5

Q ss_pred             cccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccc
Q 026213            2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGD   81 (241)
Q Consensus         2 ~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~   81 (241)
                      |||+++|+|+|||.++|+|++.+++|++++++|||+|++|+|+|+|+|++|.+...|....++++.+.|+|+++|+++++
T Consensus        13 ~~~l~~~~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~g~~e~~~~~~~~~~~g~l~v~~~~~p~a~~~   92 (250)
T 2je6_B           13 KLILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDE   92 (250)
T ss_dssp             CSBCTTSCBTTSCCTTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECSSGGGSCSSSCEEEEEEEECTTSSSS
T ss_pred             ceecCCCccCCCCCccCcCCeEEEeCCCCCCCeEEEEEECCcEEEEEEEcccccccccccCCCcEEEEEEEEeCCCccCC
Confidence            78999999999999999999999999999999999999999999999999987765566678999999999999999988


Q ss_pred             cCCCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEEEeee
Q 026213           82 RMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL  161 (241)
Q Consensus        82 ~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs~~~~  161 (241)
                      ++ .++++.++.+++++|+++|+++++++.||+|.|+|+++||++||++++|+++|+++||+++|||++++|+++++|++
T Consensus        93 ~~-~g~~~~~e~~~s~li~r~l~~~i~~~~~p~~~i~I~~~VL~~DG~~~~aai~aa~~AL~~a~iP~~~~v~avsvg~~  171 (250)
T 2je6_B           93 RK-NPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKA  171 (250)
T ss_dssp             CC-CSSCCHHHHHHHHHHHHHHHTTBCGGGSTTEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCBSSCCEEEEEEEE
T ss_pred             cc-CCCCChhHHHHHHHHHHHHHhhcCHhhCCCcEEEEEEEEEeCCCCHHHHHHHHHHHHHHhcCCCccCceEEEEEEEE
Confidence            76 56788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          162 NSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQL  235 (241)
Q Consensus       162 ~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~~~  235 (241)
                      ++.+++|||.+||..+++.++|+++++.++|++++++|.++.+++.++++.|.++++++++++++++.++.+++
T Consensus       172 ~~~~l~Dpt~~Ee~~~~~~l~va~~~~~~~i~~v~~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~~  245 (250)
T 2je6_B          172 DGVIILDLNETEAMWGEADMPIAMMPSLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREALKSKYVEF  245 (250)
T ss_dssp             TTEEEESCCHHHHHHSSEEEEEEEEGGGTEEEEEEEEECBCHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGC--
T ss_pred             CCEEEeCCCHHHHhcCCceEEEEEECCCCCEEEEEEEcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            99999999999999999999999877789999999999999999999999999999999999999999887665

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

Probab=100.00  E-value=1.5e-54  Score=366.86  Aligned_cols=231  Identities=43%  Similarity=0.702  Sum_probs=217.2

Q ss_pred             cccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccc
Q 026213            2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGD   81 (241)
Q Consensus         2 ~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~   81 (241)
                      ++|. +|.|+|||.++|+|++++++|++++++|||+|++|+|+|+|+|+||.+...+....++++.+.++|+++|+++++
T Consensus        10 ~~i~-~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~g~l~~~~~~~P~s~~~   88 (258)
T 3m7n_D           10 KLIV-DGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKAIIRYRYNMAPFSVEE   88 (258)
T ss_dssp             CSEE-TTEETTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEEECSSSTTCCSSSCEEEEEEEECGGGSSS
T ss_pred             HHHh-cCCCCCCCCcCCccCeEEEECCCCCCCceEEEEECCeEEEEEEEcccCCCCccccCCCceEEEEEEEeCCccccc
Confidence            5666 899999999999999999999999999999999999999999999988765555678999999999999999987


Q ss_pred             cCCCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEEEeee
Q 026213           82 RMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL  161 (241)
Q Consensus        82 ~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs~~~~  161 (241)
                      +++ +.++.++.+++++|+++|+++++++.||+|.|+|+++||++||+.++|++||+++||+|+||||+++|+++++|++
T Consensus        89 r~~-~~~~~re~ei~~li~r~l~~~i~~~~~p~~~I~V~~~VL~~DG~~~~Aai~aa~lAL~dagiP~~~~v~avsvg~i  167 (258)
T 3m7n_D           89 RKR-PGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKA  167 (258)
T ss_dssp             CCC-SSCCHHHHHHHHHHHHHHHTTBCGGGSTTEEEEEEEEEEECCTTHHHHHHHHHHHHHHHTTCCBSSEEEEEEEEEE
T ss_pred             ccC-CCCCHHHHHHHHHHHHHHHhhcCHHhCCceEEEEEEEEEEcCCCHHHHHHHHHHHHHHhcCCCCCCceEEEEEEEE
Confidence            654 4688899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCeeEEeCCccccccCCCcEEEEEcCCC---CcEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          162 NSTPLLDLNYVEDSAGGPDVTVGILPTL---DKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ  234 (241)
Q Consensus       162 ~~~~i~DPt~~Ee~~~~~~~~v~~~~~~---~~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~~  234 (241)
                      ++.+++||+..|+..++..++|++++..   ++|+.++++|.++++++.+++++|.++++++++.++++|.++.++
T Consensus       168 ~~~~llDpt~~Ee~~~~~d~~va~~~~~~~~~~I~~lq~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~  243 (258)
T 3m7n_D          168 DGQLVLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAILRRYIE  243 (258)
T ss_dssp             TTEEEESCCHHHHHHSSEEEEEEEEEETTEEEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEECCCHHHHhccCceEEEEEEcCCCCCCCEEEEEecCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            9999999999999999999999885566   899999999999999999999999999999999999999998775

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

Probab=100.00  E-value=3.2e-52  Score=356.00  Aligned_cols=236  Identities=27%  Similarity=0.475  Sum_probs=208.5

Q ss_pred             cccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccC-----------CCCceEEEE
Q 026213            2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQ-----------MSDQALVRC   70 (241)
Q Consensus         2 ~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~-----------~~~~~~i~v   70 (241)
                      +|+.+++.|+|||.++|+|++++++|+++++||||+|++|+|+|+|+|++|.+.+...+.           .++++.+.|
T Consensus        19 ~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~g~l~v   98 (272)
T 2nn6_F           19 LYAADEEEAPGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAALRGRLLC   98 (272)
T ss_dssp             ----------CCCCSSCCCCCCCCCSCCSSSSEEECCCSSSCEEEEEEEEEECC-------------------CBCEEEE
T ss_pred             ccccccCccCCCCCccccCCeEEEeCCCCCCCeEEEEEeCCeEEEEEEECCCcccccccccccccccccccCCCceEEEE
Confidence            467789999999999999999999999999999999999999999999998866432211           567899999


Q ss_pred             EEeecCCcccccCCCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCC
Q 026213           71 EYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMR  150 (241)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~  150 (241)
                      +|.+.|+++++++. ++++.++.+++++|+++|+++++++.||+|.|+|+++||++||++++|++||+++||+++|||++
T Consensus        99 ~~~~~p~a~~~~~~-~~~~~~e~~~s~li~r~l~~~i~~~~~p~~~I~I~~~VL~~DG~~~~aai~aa~~AL~da~iP~~  177 (272)
T 2nn6_F           99 DFRRAPFAGRRRRA-PPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVEMY  177 (272)
T ss_dssp             EEEECTTSSSSCCC-SCCHHHHHHHHHHHHHHHTTTBCSTTSBTCEEEEEEEEEECCSSHHHHHHHHHHHHHHHHCCCBS
T ss_pred             EEEecCCCcCCccC-CCCCHHHHHHHHHHHHHHHHhccHHHCCceEEEEEEEEEeCCCCHHHHHHHHHHHHHHHcCCccc
Confidence            99999999987654 57888999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CeeEEEEEee---eCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeecCCH-HHHHHHHHHHHHHHHHHHHHHHH
Q 026213          151 DIVTSCSAGY---LNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPT-NTFEDVMQLAIEGCKAVANYIRE  226 (241)
Q Consensus       151 ~~~~~vs~~~---~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~~~~-~~l~~~l~~a~~~~~~i~~~i~~  226 (241)
                      ++++++++++   .++.+|+|||..||..+...++|+++++.++|++++++|.++. +++.++++.|.++++++++++++
T Consensus       178 ~~v~avsvg~~~~~~~~~llDpt~~Ee~~~~~~l~va~~~~~~~I~~i~~~g~~~~~~~l~~~l~~A~~~~~~i~~~~~~  257 (272)
T 2nn6_F          178 DLVVGCGLSLAPGPAPTWLLDPTRLEEERAAAGLTVALMPVLNQVAGLLGSGEGGLTESWAEAVRLGLEGCQRLYPVLQQ  257 (272)
T ss_dssp             SCCEEEECCCCSCSSCCCCSSCCTTTGGGCSSEEEEEEETTTTEEEEEEEECCSSCTTTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcEEEEEEEEeeccCCeEEeCCCHHHhccCCceEEEEEeCCCCCEEEEEEecCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999   8889999999999999999999998888899999999999999 99999999999999999999999


Q ss_pred             HHHHHHHHHHhh
Q 026213          227 VLLENTKQLECR  238 (241)
Q Consensus       227 ~l~~~~~~~~~~  238 (241)
                      ++.++.+++.+.
T Consensus       258 ~l~~~~~~~~~~  269 (272)
T 2nn6_F          258 SLVRAARRRGAA  269 (272)
T ss_dssp             HHHHHHHHHHTT
T ss_pred             HHHHHHHhhccc
Confidence            999999987764

>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=2.4e-50  Score=337.88  Aligned_cols=219  Identities=26%  Similarity=0.375  Sum_probs=187.4

Q ss_pred             CCCCCCCCCCCCC----CCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCccc
Q 026213            5 SPEGLRLDGRRPT----EMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTG   80 (241)
Q Consensus         5 ~~~~~R~DGR~~~----e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~   80 (241)
                      +.+|+|+|||.++    |+|++.+++|++++++|||+|++|+|+|+|+|++|.+.+ |..+.++++.++++|.  |+.  
T Consensus        12 ~~~~~R~DGR~~~~~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~g~~~~~-~~~~~~~~g~l~~~~~--p~~--   86 (237)
T 2nn6_D           12 KIRAENGTGSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVK-VSKEIFNKATLEVILR--PKI--   86 (237)
T ss_dssp             ---------------CCCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECC-------CCEEEEEEEE--CSS--
T ss_pred             CccCccCCCCCCCCccccccceEEEeCCCCCCCEEEEEEECCcEEEEEEeCCCccc-ccccCCCcEEEEEEec--CCC--
Confidence            3568999999999    999999999999999999999999999999999988653 3445678898888775  543  


Q ss_pred             ccCCCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEEEee
Q 026213           81 DRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGY  160 (241)
Q Consensus        81 ~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs~~~  160 (241)
                           |+++.++++++++|+++|+++++++.||+|+|+|+++||++|||+++|++||+++||+|+||||+++|+++++|+
T Consensus        87 -----g~~~~~e~~~~~li~r~l~~~i~~~~~p~~~I~I~~~VL~~dG~~~~aai~aa~~AL~da~iP~~~~v~avs~g~  161 (237)
T 2nn6_D           87 -----GLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACAL  161 (237)
T ss_dssp             -----SCCCHHHHHHHHHHHHHHHHHCGGGCSSSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCEEEEEEEE
T ss_pred             -----CCCCccHHHHHHHHHHHHHHHhchhcCCceEEEEEEEEEECCCcHHHHHHHHHHHHHHHcCCCcccCeeeEEEEE
Confidence                 356788999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             e-CCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          161 L-NSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTK  233 (241)
Q Consensus       161 ~-~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~  233 (241)
                      + ++.+++||+..||..+.+.++|+++++.++++.+++.|.++.+++.+++++|.++++++++.++++|+++.+
T Consensus       162 ~~~~~~llDp~~~Ee~~~~~~~~v~~~~~~~~i~~lq~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~  235 (237)
T 2nn6_D          162 DSDGTLVLDPTSKQEKEARAVLTFALDSVERKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYRESLQRRYS  235 (237)
T ss_dssp             CTTCCEEESCCHHHHHHCSEEEEEEEETTTCCCCEEEEEESCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             ecCCcEEeCCCHHHHhccCCceEEEEcCCCCCEEEEEEeCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            9 789999999999999999999998877779999999999999999999999999999999999999998754

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

Probab=100.00  E-value=4e-49  Score=333.27  Aligned_cols=226  Identities=28%  Similarity=0.392  Sum_probs=206.2

Q ss_pred             CCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCC--
Q 026213            7 EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR--   84 (241)
Q Consensus         7 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~--   84 (241)
                      ...|.|||.++|+|++++++|++++++|||++++|+|+|+|+|++|.+.+ +..+.+++|.+.++|+++|+++.++.+  
T Consensus         9 ~~~~~~~R~~~e~R~i~i~~g~~~~A~GSa~v~~G~T~Vl~~V~~~~~~p-~~~~~~~~g~l~v~~~~~P~a~~~~~~Re   87 (255)
T 3dd6_A            9 HHMRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVP-PFMRGEGKGWVTAEYAMIPRATEQRTIRE   87 (255)
T ss_dssp             --CCCCSCCTTCCCCEEEEESCSSSSSEEEEEEETTEEEEEEEEEESCCC-GGGTTSSCCEEEEEEEECTTSSSSCCCCC
T ss_pred             cccccCCCCcCCCCCEEEEECCCCCCCeEEEEEECCeEEEEEEEecCCCC-CCCCCCCceEEEEEEEECCCccccccccc
Confidence            45899999999999999999999999999999999999999999976432 345668899999999999999988643  


Q ss_pred             --CCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhC-----------CCCCCC
Q 026213           85 --KPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDA-----------GIPMRD  151 (241)
Q Consensus        85 --~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~-----------gip~~~  151 (241)
                        .|++++++.+++++|+++|+++++++.||+|+|+|+++||++||++++|++||+++||.++           +|||++
T Consensus        88 ~~~g~~~~~~~eisrli~r~lr~~i~~~~l~~~~I~V~~~VL~~DG~~~~aai~aa~~AL~~a~~p~~~~g~~~~iPl~~  167 (255)
T 3dd6_A           88 SSKGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWIDCDVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKD  167 (255)
T ss_dssp             CC-CCCCHHHHHHHHHHHHHHHHHBCHHHHCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTSSSSCCBSS
T ss_pred             ccCCCCCHHHHHHHHHHHHHHHHhcChhhcCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHHhhhhhhhcCcccCCCccC
Confidence              2678899999999999999999999999999999999999999999999999999999999           999999


Q ss_pred             eeEEEEEeeeCCeeE-EeCCccccccCCCcEEEEEcCCCCcEEEEEeee---cCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          152 IVTSCSAGYLNSTPL-LDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA---KLPTNTFEDVMQLAIEGCKAVANYIREV  227 (241)
Q Consensus       152 ~~~~vs~~~~~~~~i-~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g---~~~~~~l~~~l~~a~~~~~~i~~~i~~~  227 (241)
                      +|+++++|++++.++ +|||..||..++..++|++ +..++|++++++|   .++.+++.++++.|.+.+++++++++++
T Consensus       168 ~v~avsvg~i~g~~vllDpt~~Ee~~~~~~l~Va~-~~~g~i~~vq~~g~~~~~~~~~l~~~l~~A~~~~~~i~~~~~~~  246 (255)
T 3dd6_A          168 YLAATSVGIVEEQGVVLDLNYAEDSKADVDMNVIM-TGKGQFVEVQGTGEEATFSRAQLNELLDAAEQGIFQLIDIQKEA  246 (255)
T ss_dssp             CEEEEEEEEETTTEEEESCCHHHHHTEEEEEEEEE-ETTSCEEEEEEEESSSCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ceeEEEEEEECCEEEEeCCCHHHHhhcCceEEEEE-cCCCcEEEEEecCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999988 9999999999999999975 6788999999864   5999999999999999999999999999


Q ss_pred             HHHHHHH
Q 026213          228 LLENTKQ  234 (241)
Q Consensus       228 l~~~~~~  234 (241)
                      +++..++
T Consensus       247 l~~~~~~  253 (255)
T 3dd6_A          247 LGDIVSH  253 (255)
T ss_dssp             HGGGGGG
T ss_pred             HHHHHhh
Confidence            9876543

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

Probab=100.00  E-value=2e-49  Score=336.97  Aligned_cols=227  Identities=28%  Similarity=0.380  Sum_probs=205.4

Q ss_pred             CCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCCC
Q 026213            6 PEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMRK   85 (241)
Q Consensus         6 ~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~~   85 (241)
                      ..|+|+|||.++|+|++.+++|++++++|||+|++|+|+|+|+|++|.+.+. ....++++++.|+|+++|++++++.++
T Consensus         3 ~~g~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~~~~~~p~-~~~~~~~g~l~v~~~~~p~a~~~~~~R   81 (262)
T 3b4t_A            3 HVSKREDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPR-WRKATGLGWLTAEYAMLPSATHSRSDR   81 (262)
T ss_dssp             --CCSTTSCCTTCCCCEEEEETSSSSSSEEEEEEETTEEEEEEEEEEESCC-----CCSCCEEEEEEEECGGGSSSCCCC
T ss_pred             CCCcCCCCCCCcCcCCeEEEeCCcCCCCeEEEEEECCCEEEEEEEecCcCCC-ccCCCCceEEEEEEEeCCCcccccccc
Confidence            3589999999999999999999999999999999999999999999764321 223368899999999999998876432


Q ss_pred             ----CCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhC------------CCCC
Q 026213           86 ----PKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDA------------GIPM  149 (241)
Q Consensus        86 ----~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~------------gip~  149 (241)
                          |+++.++.+++++|+++|+++++++.||+|+|+|+++||++||++++|++||+++||+++            +|||
T Consensus        82 e~~~G~~~~~~~~isrli~r~lr~~i~~~~l~~~~I~i~~~VL~~DG~~~~aai~aa~~AL~~a~~~~~~~~~~~~~ip~  161 (262)
T 3b4t_A           82 ESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPL  161 (262)
T ss_dssp             HHHHTSCCHHHHHHHHHHHHHHHTTBCHHHHCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTCCSSSCCB
T ss_pred             ccCCCCCCHHHHHHHHHHHHHHHHhcCHhHCCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhhccCCccccCCcc
Confidence                578899999999999999999999999999999999999999999999999999999999            9999


Q ss_pred             CCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee---cCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          150 RDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA---KLPTNTFEDVMQLAIEGCKAVANYIRE  226 (241)
Q Consensus       150 ~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g---~~~~~~l~~~l~~a~~~~~~i~~~i~~  226 (241)
                      +++|++++++++++.+++|||.+||..+...++|++ +..++++++++.|   .++.+++.++++.|.++++++++.+++
T Consensus       162 ~~~v~avsvg~~~g~~l~Dpt~~Ee~~~~~~l~va~-~~~g~i~~i~~~g~~~~~~~~~l~~~l~~A~~~~~~i~~~~~~  240 (262)
T 3b4t_A          162 SCAIAAVSVGVVDGRIRVDLPYEEDSRAEVDMNVVA-TDTGTLVEIQGTGEGATFARSTLDKLLDMALGACDTLFAAQRD  240 (262)
T ss_dssp             CSCEEEEEEEEETTEEEESCCHHHHTTCSEEEEEEE-ETTSCEEEEEECSSCCCBCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCceeEEEEEEECCEEEECCCHHHHhccCceEEEEE-cCCCCEEEEEeeCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999987 5678999999975   699999999999999999999999999


Q ss_pred             HHHHHHHH
Q 026213          227 VLLENTKQ  234 (241)
Q Consensus       227 ~l~~~~~~  234 (241)
                      +++++.++
T Consensus       241 ~l~~~~~~  248 (262)
T 3b4t_A          241 ALALPYPG  248 (262)
T ss_dssp             HHTSCCSS
T ss_pred             HHhcchhc
Confidence            99876554

>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=1.5e-49  Score=334.79  Aligned_cols=224  Identities=29%  Similarity=0.381  Sum_probs=185.4

Q ss_pred             CCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCC----
Q 026213            9 LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR----   84 (241)
Q Consensus         9 ~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~----   84 (241)
                      +|+|||.++|+|++.+++|++++++|||+|++|+|+|+|+|++|.+.+ +....+++|.+.++|+++|++++++..    
T Consensus         1 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p-~~~~~~~~g~l~~~~~~~p~a~~~~~~Re~~   79 (245)
T 1oys_A            1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVP-PFLRGGGKGWITAEYSMLPQATNQQTIQESS   79 (245)
T ss_dssp             CCTTSCCTTCCCCEEEECC-----CCCEEEEETTEEEEEEEEEESCCC-GGGTTSCCCEEEEEEEC--------------
T ss_pred             CCCCCCCCCCcCCeEEEeCCCCCCCEEEEEEECCeEEEEEEEeccccC-CccCCCCceEEEEEEEeCCCcCccccccccc
Confidence            499999999999999999999999999999999999999999976432 123457899999999999999987632    


Q ss_pred             CCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCC-----------CCCCCee
Q 026213           85 KPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAG-----------IPMRDIV  153 (241)
Q Consensus        85 ~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~g-----------ip~~~~~  153 (241)
                      .|+++.++++++++|+++|+++++++.||+|.|+|+++||++|||+++|++||+++||+|+|           +||+++|
T Consensus        80 ~G~~~~~~~eis~li~r~l~~~i~~~~l~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~~~~~~~~~~~~ipl~~~v  159 (245)
T 1oys_A           80 KGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFL  159 (245)
T ss_dssp             -----CHHHHHHHHHHHHHHHTBCHHHHCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTSSSSCCBCSCE
T ss_pred             CCCCchHHHHHHHHHHHHHHHhcCHhHCCCEEEEEEEEEEeCCCCHHHHHHHHHHHHHHhccchhcccCcccccCCCCce
Confidence            35688899999999999999999999999999999999999999999999999999999999           9999999


Q ss_pred             EEEEEeeeCCeeE-EeCCccccccCCCcEEEEEcCCCCcEEEEEeee---cCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          154 TSCSAGYLNSTPL-LDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA---KLPTNTFEDVMQLAIEGCKAVANYIREVLL  229 (241)
Q Consensus       154 ~~vs~~~~~~~~i-~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g---~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~  229 (241)
                      +++|+|++++.++ +||+..||..+++.++|++ ++.|+++.+++.|   .++++++.+++++|.++++++++.++++|.
T Consensus       160 ~avs~g~~~g~~vl~Dp~~~Ee~~~~~~~~v~~-~~~g~i~~iq~~g~~~~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~  238 (245)
T 1oys_A          160 AAISVGIDKEQGILLDLNYEEDSSAEVDMNVIM-TGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLG  238 (245)
T ss_dssp             EEEEEEEETTTEEEESCCHHHHHHEEEEEEEEE-ETTSCEEEEEEEESSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             eEEEEEEECCEEEEecCCHHHHhcCCCcEEEEE-cCCCcEEEEEEeCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999998888 9999999999999999987 5778999999865   699999999999999999999999999998


Q ss_pred             HHHHH
Q 026213          230 ENTKQ  234 (241)
Q Consensus       230 ~~~~~  234 (241)
                      ++.++
T Consensus       239 ~~~~~  243 (245)
T 1oys_A          239 DSLPE  243 (245)
T ss_dssp             -----
T ss_pred             hhhhh
Confidence            87553

>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=2.1e-48  Score=329.42  Aligned_cols=220  Identities=27%  Similarity=0.383  Sum_probs=202.1

Q ss_pred             CCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCC----
Q 026213            9 LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR----   84 (241)
Q Consensus         9 ~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~----   84 (241)
                      +|+|||.++|+|++.+++|++++++|||+|++|+|+|+|+|++|.+.+ +....+++|.+.++|.++|+++.++..    
T Consensus         1 ~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~~~~~~p-~~~~~~~~g~l~~~~~~~P~a~~~r~~Re~~   79 (255)
T 1udn_A            1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVP-NWLKGKGQGWITAEYSMLPRATQQRTIRESV   79 (255)
T ss_dssp             -CTTSCCTTCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEESCCC-GGGTTSSCCEEEEEEEECSCCTTSCCCCSST
T ss_pred             CCCCCCCCCCccCeEEEECCCCCCCEEEEEEECCEEEEEEEEcCCcCC-CCCCCCCceEEEEEEEcCCCccccccccccC
Confidence            499999999999999999999999999999999999999999976442 233457899999999999999987632    


Q ss_pred             CCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCC-----------CCCCCee
Q 026213           85 KPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAG-----------IPMRDIV  153 (241)
Q Consensus        85 ~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~g-----------ip~~~~~  153 (241)
                      .|+++.++++++++|+++|+++++++.||+|+|+|+++||++||++++|++||+++||+|+|           +||+++|
T Consensus        80 ~G~~~~~~~eisrli~r~lr~~i~~~~l~~~~i~I~~~VL~~DG~~~~aai~aa~~AL~da~~~~~~~~~~~~ipl~~~v  159 (255)
T 1udn_A           80 QGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFV  159 (255)
T ss_dssp             TCSCCHHHHHHHHHHHHHHHHHBCGGGGCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTSSSSCCBCCCE
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHhhcchhcccCcccCCCccCce
Confidence            36788999999999999999999999999999999999999999999999999999999999           9999999


Q ss_pred             EEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee---cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          154 TSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA---KLPTNTFEDVMQLAIEGCKAVANYIREVLLE  230 (241)
Q Consensus       154 ~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g---~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~  230 (241)
                      ++++++++++.+++||+.+||..++..++|++ +..++++.+++.|   .++++++.++++.|.++++++++++++++.+
T Consensus       160 ~avsvg~~~g~~llDpt~~Ee~~~~~~l~va~-~~~g~i~~~q~~g~~~~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~  238 (255)
T 1udn_A          160 AAVSVGIVNDRILLDLNFEEDSAAQVDMNVVG-TGSGRLSEVHTMGEEYSFTKDELIKMLDLAQKGINELIELQKKLYVI  238 (255)
T ss_dssp             EEEEEEEETTEEEESCCHHHHHTCSEEEEEEE-ETTSCEEEEEEEESSCCCCHHHHHHHHHHHHHHHHHHHHHHHTTEEE
T ss_pred             eEEEEEEECCEEEECCCHHHHhhCCCCEEEEE-eCCCCEEEEEEeCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999987 5677999999864   6999999999999999999999999998765

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

Probab=100.00  E-value=2.4e-48  Score=326.32  Aligned_cols=218  Identities=32%  Similarity=0.455  Sum_probs=198.7

Q ss_pred             CCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCCC----
Q 026213           10 RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMRK----   85 (241)
Q Consensus        10 R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~~----   85 (241)
                      |+|||.++|+|++.+++|++++++|||++++|+|+|+|+|++|.+.+ +....+++|.+.++|.+.|+++.++..+    
T Consensus         3 R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~~~~~~p-~~~~~~~~g~l~v~~~~~p~~~~~r~~Re~~~   81 (239)
T 1r6l_A            3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVP-RFLKGQGQGWLTAEYGMLPRSTGERNQREASR   81 (239)
T ss_dssp             CTTCCCTTCCCCEEEESSCSSSSSEEEEEEETTEEEEEEEEEEESCS-SCCC---CCEEEEEEEECTTSSSSCCCCHHHH
T ss_pred             CCCCCCCCCcCCeEEEeCCcCCCCeEEEEEECCEEEEEEEEccCccC-CccCCCCcEEEEEEEEeCCCccccccccccCC
Confidence            99999999999999999999999999999999999999999976432 1223468899999999999999876332    


Q ss_pred             CCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCC-----------CCCCCeeE
Q 026213           86 PKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAG-----------IPMRDIVT  154 (241)
Q Consensus        86 ~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~g-----------ip~~~~~~  154 (241)
                      |+++.++++++++|+++|+++++++.||+|+|+|+++||++||++++|++||+++||+|++           +||+++|+
T Consensus        82 G~~~~~~~~isrli~r~l~~~i~~~~l~~~~i~I~~~VL~~DG~~~~aai~aa~~AL~da~~~~~~~~~~~~ip~~~~~~  161 (239)
T 1r6l_A           82 GKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVA  161 (239)
T ss_dssp             TSCCHHHHHHHHHHHHHHHHTBCGGGTCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCBCCCEE
T ss_pred             CCCcHHHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhcchhcccCcccccCccCcee
Confidence            6788999999999999999999999999999999999999999999999999999999999           99999999


Q ss_pred             EEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee---cCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          155 SCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA---KLPTNTFEDVMQLAIEGCKAVANYIREVLL  229 (241)
Q Consensus       155 ~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g---~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~  229 (241)
                      ++|+|++++.+++|||.+||..+...++|++ ++.++++.+++.|   .++++++.++++.|.+++++++++++++++
T Consensus       162 avs~g~~~~~~l~Dpt~~Ee~~~~~~l~va~-~~~g~i~~~~~~g~~~~~~~~~l~~~l~~a~~~~~~i~~~~~~~l~  238 (239)
T 1r6l_A          162 AVSVGIYQGVPVLDLDYLEDSAAETDLNVVM-TDAGGFIEVQGTAEGAPFRPAELNAMLELAQQGMQELFELQRAALA  238 (239)
T ss_dssp             EEEEEEETTEEEESCCHHHHHHCSEEEEEEE-ETTSCEEEEEEEESSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             EEEEEEECCEEEECCCHHHHhcCCceEEEEE-eCCCCEEEEEEeCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999987 5667999999864   699999999999999999999999999875

>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-48  Score=330.66  Aligned_cols=223  Identities=20%  Similarity=0.275  Sum_probs=203.3

Q ss_pred             CCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEE-cCccccccccCCCCceEEEEEEeecCCcccccC
Q 026213            5 SPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVY-GPREVQNKSQQMSDQALVRCEYSMANFSTGDRM   83 (241)
Q Consensus         5 ~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~-~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~   83 (241)
                      +++|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|+ +|.+   |..+.++++.+.++|+++|++++.+.
T Consensus        22 l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~---p~~~~~~~g~l~~~~~~~p~a~~~~~   98 (277)
T 2po1_B           22 LKEGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLGE---PFPDTPNMGVMTTNVELVPLASPTFE   98 (277)
T ss_dssp             HHTTCCTTSCCTTCCCCEEEEECCSTTSSEEEEEEETTEEEEEEEEEEEEC---CCTTCTTSCEEEEEEEECGGGCTTCC
T ss_pred             HhcCCCCCCCCCCCcCCeEEEeCCcCCCCeEEEEEECCeEEEEEEEecccC---CCCCCCCceEEEEEEEeCCCcccccc
Confidence            4689999999999999999999999999999999999999999999 5443   33456889999999999999987653


Q ss_pred             CCCCCCchhHHHHHHHHHHHHH--hhccCCC---C---ccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCC---------
Q 026213           84 RKPKGDRRSTEISLVIRQTMEA--CILTHLM---P---RSQIDIFVQVLQADGGTRSACINAATLALQDAG---------  146 (241)
Q Consensus        84 ~~~~~~~~~~~l~~~l~~~l~~--~i~l~~~---p---~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~g---------  146 (241)
                       .++++.++.+++++|+++|++  +++++.|   |   .|.|+|+++||++|||+++|+++|+++||+|+|         
T Consensus        99 -~g~~~~~~~~l~~li~r~l~~s~~idl~~L~i~pg~~~w~i~id~~VL~~dG~~~~a~i~aa~~AL~da~~p~~~~~~~  177 (277)
T 2po1_B           99 -PGPPDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVFIDVHVLDHDGNLMDAIGIAAIAALLNARVPKVRYNEE  177 (277)
T ss_dssp             -SSSCCHHHHHHHHHHHHHHHTTTSBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHHCEEEEEEECTT
T ss_pred             -CCCCChHHHHHHHHHHHHHhhcccccHHHccccCCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcCCCcEEEeCC
Confidence             457888999999999999998  5888866   5   389999999999999999999999999999999         


Q ss_pred             ------------CCCCCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEee--ecCCHHHHHHHHHH
Q 026213          147 ------------IPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMD--AKLPTNTFEDVMQL  212 (241)
Q Consensus       147 ------------ip~~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~--g~~~~~~l~~~l~~  212 (241)
                                  +||+++|+++|+|++++.+++||+..||..+.+.++|++ +..|+++.+++.  +.++.+++.++++.
T Consensus       178 ~~~~~~~~~~~~ipl~~~~~avs~g~~~~~~l~Dp~~~Ee~~~~~~~~v~~-~~~g~i~~lq~~g~~~~~~~~l~~~l~~  256 (277)
T 2po1_B          178 TGEVETLDETEPLPVEKIPVPVTFAKIGNILVVDPSLDEELVMDGKITITT-DETGHISAVQKSEGGAFKLEEVMYAVET  256 (277)
T ss_dssp             TCCEEEEEEEEECCBCCCCEEEEEEEETTEEEESCCHHHHHHCSEEEEEEE-CTTSCEEEEEEESSCCCCHHHHHHHHHH
T ss_pred             CceeecccccccccccCceEEEEEEEECCEEEeCCCHHHHhhCCCcEEEEE-cCCCCEEEEEccCCCCCCHHHHHHHHHH
Confidence                        899999999999999999999999999999999999987 566899999987  57999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 026213          213 AIEGCKAVANYIREVLLENT  232 (241)
Q Consensus       213 a~~~~~~i~~~i~~~l~~~~  232 (241)
                      |.++++++++.++++|++..
T Consensus       257 A~~~~~~l~~~~~~~l~~~~  276 (277)
T 2po1_B          257 AFKKAEEIRKLILEAVEKAK  276 (277)
T ss_dssp             HHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhhcc
Confidence            99999999999999998753

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

Probab=100.00  E-value=4.8e-48  Score=324.87  Aligned_cols=219  Identities=21%  Similarity=0.375  Sum_probs=183.2

Q ss_pred             CCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCCCC
Q 026213            7 EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMRKP   86 (241)
Q Consensus         7 ~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~~~   86 (241)
                      +|.|+|||.++|+|++++++|++++++|||+|++|+|+|+|+|++|.+.+ +..+.++++.+++++  +|.       .+
T Consensus         2 eg~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~g~~~~~-~~~~~~~~~~~~~~~--~P~-------~g   71 (246)
T 3hkm_A            2 EESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGT-RKGENPEKASIEVVW--KPM-------TG   71 (246)
T ss_dssp             ---CTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEECCCEECC-CTTSCSSSCEEEEEE--ECS-------SS
T ss_pred             CCcCCCCCCCCCcCCeEEEECCCCCCCeEEEEEECCeEEEEEEecCcCCC-cccCCCccEEEEEEe--CCC-------CC
Confidence            68999999999999999999999999999999999999999999987543 444567777776654  452       13


Q ss_pred             CCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEEEeee-CCee
Q 026213           87 KGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYL-NSTP  165 (241)
Q Consensus        87 ~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs~~~~-~~~~  165 (241)
                      +++.++++++++|+++|+++++++.||+|.|+|+++||++||++++|++||+++||+++||||+++|+++++|++ ++.+
T Consensus        72 ~~~~~~~e~~~li~r~l~~l~~~~~~~~~~I~v~~~VL~~dG~~~~aai~aa~~AL~dagiP~~~~v~avs~g~~~~g~~  151 (246)
T 3hkm_A           72 QIGKQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDGSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLEDGEV  151 (246)
T ss_dssp             CCCTTHHHHHHHHHHHHHHHBCTTSSCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCBSSCEEEEEEEECTTSCE
T ss_pred             CCChhHHHHHHHHHHHHHHhcCccCCCcEEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCCCCceEEEEEEEEECCEE
Confidence            466788999999999999999999999999999999999999999999999999999999999999999999998 8899


Q ss_pred             EEeCCccccccCCCcEEEEEcCCCCcEEEEE------------------eeecCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          166 LLDLNYVEDSAGGPDVTVGILPTLDKVTLLQ------------------MDAKLPTNTFEDVMQLAIEGCKAVANYIREV  227 (241)
Q Consensus       166 i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~------------------~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~  227 (241)
                      ++||+..||..++..++|+++.+  .++.++                  ..|.++++++.++++.|.++++++.++++++
T Consensus       152 llDpt~~Ee~~~~~~~~va~~~~--~i~~lq~~g~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~  229 (246)
T 3hkm_A          152 ILDTNKAEEQQLKSFAHLVFPNS--RKSASSKEPNQKEEDSERGLITSITHGVMSEEDYFSCIERGLAASSRISDFMRTT  229 (246)
T ss_dssp             EESCCHHHHTTCSEEEEEEEEC----------------------CCCEEEEECEEHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             EECCCHHHHhcCCeeEEEEEeCC--ceEEEeecccccccccccceeeeeccCCcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999987533  244444                  3578999999999999999999999999999


Q ss_pred             HHHHHHHHHh
Q 026213          228 LLENTKQLEC  237 (241)
Q Consensus       228 l~~~~~~~~~  237 (241)
                      |+++.++-..
T Consensus       230 l~~~~~~~~~  239 (246)
T 3hkm_A          230 LQKQAPGDVL  239 (246)
T ss_dssp             TC--------
T ss_pred             HHhhhhchhh
Confidence            9998877543

>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=1.8e-47  Score=324.44  Aligned_cols=218  Identities=21%  Similarity=0.286  Sum_probs=197.5

Q ss_pred             CCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCC
Q 026213            5 SPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR   84 (241)
Q Consensus         5 ~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~   84 (241)
                      +++|+|+|||.++|+|++.+++|++++++|||++++|+|+|+|+|+++.  ..|....++++.+.++|+++|+++++++ 
T Consensus        18 l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~--~~p~~~~~~~g~l~v~~~~~p~a~~~~~-   94 (259)
T 3m7n_G           18 LRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQP--GEPYPDTPDRGVIIVNAELVPLASPTFE-   94 (259)
T ss_dssp             HHTTCCTTCCCTTCCCCEEEEETSSTTSSEEEEEEETTEEEEEEEEEEE--ECCCSSCTTSCEEEEEEECCTTSCTTCC-
T ss_pred             HhcCCCCCCCCCccccCeEEEeCCcCCCCceEEEEECCcEEEEEEEecc--cCCCCCCCCceEEEEEEEeCCccccccc-
Confidence            3589999999999999999999999999999999999999999999742  2233456788999999999999998764 


Q ss_pred             CCCCCchhHHHHHHHHHHHHH--hhccCCC---Cc---cEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCC---------
Q 026213           85 KPKGDRRSTEISLVIRQTMEA--CILTHLM---PR---SQIDIFVQVLQADGGTRSACINAATLALQDAGI---------  147 (241)
Q Consensus        85 ~~~~~~~~~~l~~~l~~~l~~--~i~l~~~---p~---~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gi---------  147 (241)
                      .|++++++.+++++|+++|++  +++++.|   |+   |.|+|+++||++|||+++|+++|+++||.++++         
T Consensus        95 ~g~~~~~~~~~srli~r~lr~s~~i~l~~L~i~pg~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~iP~~~~~~~~  174 (259)
T 3m7n_G           95 PGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGE  174 (259)
T ss_dssp             SSSSCHHHHHHHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHTCEECTGGGTSSS
T ss_pred             CCCCChHHHHHHHHHHHHHhhcCCccHHHhcccCCcEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHhCCCCeEEecCCc
Confidence            467889999999999999999  7888876   73   999999999999999999999999999999999         


Q ss_pred             ----CCCCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEee--ecCCHHHHHHHHHHHHHHHHHHH
Q 026213          148 ----PMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMD--AKLPTNTFEDVMQLAIEGCKAVA  221 (241)
Q Consensus       148 ----p~~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~--g~~~~~~l~~~l~~a~~~~~~i~  221 (241)
                          ||+++|+++|+|++++.+++|||.+||..+++.++|+++ ..|+++.+++.  +.++++++.++++.|.++++++.
T Consensus       175 ~~~lp~~~~~~avtvg~~~~~~l~Dpt~~Ee~~~~~~l~va~~-~~g~i~~i~~~g~~~~~~~~l~~~l~~a~~~~~~l~  253 (259)
T 3m7n_G          175 DYLLPVRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITTD-KDDNVVAMQKSGGYLLDEKLFDELLDVSINCARKLR  253 (259)
T ss_dssp             CEECCBCCCCEEEEEEEETTEEEESCCTTGGGGCSCEEEEEEC-TTSCEEEEEEESSCCBCHHHHHHHHHHHHHHHHHHH
T ss_pred             eecccccCceeEEEEEEECCEEEECCCHHHHhhCCCcEEEEEe-CCCcEEEEECCCCCCcCHHHHHHHHHHHHHHHHHHH
Confidence                799999999999999999999999999999999999874 56899999986  47999999999999999999999


Q ss_pred             HHHHH
Q 026213          222 NYIRE  226 (241)
Q Consensus       222 ~~i~~  226 (241)
                      ++|++
T Consensus       254 ~~~~~  258 (259)
T 3m7n_G          254 EKFKE  258 (259)
T ss_dssp             HTTC-
T ss_pred             HHHhh
Confidence            98765

>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=1.7e-47  Score=327.63  Aligned_cols=222  Identities=18%  Similarity=0.234  Sum_probs=201.6

Q ss_pred             cCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccC
Q 026213            4 VSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRM   83 (241)
Q Consensus         4 ~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~   83 (241)
                      ++++|+|+|||.++|+|++.+++|++++++|||++++|+|+|+|+|+++  ...|....++++.+.++|+++|+++++++
T Consensus        24 ~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~--~~~p~~~~~~~g~l~v~~~~~p~a~~~~~  101 (277)
T 2je6_A           24 LFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLE--IDKPYEDTPNQGNLIVNVELLPLAYETFE  101 (277)
T ss_dssp             TGGGTBCTTSCBTTCCCCEEEEETCSTTSSEEEEEEETTEEEEEEEEEE--EECCCTTCTTCCEEEEEEEECTTSCTTCC
T ss_pred             HHhcCCCCCCCCcCcccCeEEEeCCcCCCCeEEEEEECCeEEEEEEEee--eeCCCCCCCCccEEEEEEEeCCccCcccc
Confidence            4568999999999999999999999999999999999999999999952  22333456889999999999999998754


Q ss_pred             CCCCCCchhHHHHHHHHHHHHH--hhccCCC------CccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCC---------
Q 026213           84 RKPKGDRRSTEISLVIRQTMEA--CILTHLM------PRSQIDIFVQVLQADGGTRSACINAATLALQDAG---------  146 (241)
Q Consensus        84 ~~~~~~~~~~~l~~~l~~~l~~--~i~l~~~------p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~g---------  146 (241)
                       .|++++++.+++++|+++|++  +++++.|      ++|.|+|+++||++|||+++|+++|+++||++++         
T Consensus       102 -~g~~~~~~~~is~li~r~lr~~~~i~~~~l~i~~g~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~~p~v~~~~~  180 (277)
T 2je6_A          102 -PGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSN  180 (277)
T ss_dssp             -CSSCCHHHHHHHHHHHHHHHHTTCSCGGGGEEETTTEEEEEEEEEEEEECCSCHHHHHHHHHHHHHHTCEEEEEECC--
T ss_pred             -cCCCChHHHHHHHHHHHHHhccCCcCHHHceeecCceEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcCCCeEEecCC
Confidence             467888999999999999999  4788887      3699999999999999999999999999999999         


Q ss_pred             ------------CCCCCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEee--ecCCHHHHHHHHHH
Q 026213          147 ------------IPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMD--AKLPTNTFEDVMQL  212 (241)
Q Consensus       147 ------------ip~~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~--g~~~~~~l~~~l~~  212 (241)
                                  +||+++|+++++|++++.+++|||.+||..+++.++|++ +..|+++++++.  +.++.+++.++++.
T Consensus       181 ~~~~~~~~~~~~ip~~~~~~avsvg~~~~~~l~Dpt~~Ee~~~~~~l~va~-~~~g~i~~v~~~g~~~~~~~~l~~~l~~  259 (277)
T 2je6_A          181 GISVNKNEVVGKLPLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSY-TPDLKIVGIQKSGKGSMSLQDIDQAENT  259 (277)
T ss_dssp             -CEEEEEEEEEECCCSCCCEEEEEEEETTEEEESCCHHHHHHCSEEEEEEE-CTTCCEEEEEEESSSCEEHHHHHHHHHH
T ss_pred             cceEeccCccccccccCCeEEEEEEEECCEEecCCCHHHHhcCCCcEEEEE-eCCCCEEEEECCCCCCCCHHHHHHHHHH
Confidence                        999999999999999999999999999999999999987 456899999987  46899999999999


Q ss_pred             HHHHHHHHHHHHHHHHH
Q 026213          213 AIEGCKAVANYIREVLL  229 (241)
Q Consensus       213 a~~~~~~i~~~i~~~l~  229 (241)
                      |.++++++++.++++++
T Consensus       260 A~~~~~~i~~~~~~~l~  276 (277)
T 2je6_A          260 ARSTAVKLLEELKKHLG  276 (277)
T ss_dssp             HHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHhc
Confidence            99999999999998873

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

Probab=100.00  E-value=3.6e-47  Score=324.72  Aligned_cols=221  Identities=19%  Similarity=0.299  Sum_probs=200.6

Q ss_pred             cCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEE-cCccccccccCCCCceEEEEEEeecCCccccc
Q 026213            4 VSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVY-GPREVQNKSQQMSDQALVRCEYSMANFSTGDR   82 (241)
Q Consensus         4 ~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~-~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~   82 (241)
                      ++++|+|+|||+++|+|++.+++|++++++|||++++|+|+|+|+|+ +|.   .|....++++.+.++|.++|++++++
T Consensus        19 ~l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~---~p~~~~~~~g~l~v~~~~~p~a~~~~   95 (271)
T 2wnr_A           19 LINNKERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKPQIG---EPFPDTPEMGVILTNSELLPMASPTF   95 (271)
T ss_dssp             HHHTTCCTTCCCTTCCCCEEEEESCSTTSSEEEEEEETTEEEEEEEEEEEE---CCCTTCTTCCEEEEEEEECGGGCTTC
T ss_pred             HHhcCCCCCCCCcccccCeEEEeCccCCCCeEEEEEECCeEEEEEEEeeee---cCCCCCCCceEEEEEEEeCCcccccc
Confidence            35689999999999999999999999999999999999999999999 443   23345688999999999999998875


Q ss_pred             CCCCCCCchhHHHHHHHHHHHHH--hhccCCC---C---ccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCC--------
Q 026213           83 MRKPKGDRRSTEISLVIRQTMEA--CILTHLM---P---RSQIDIFVQVLQADGGTRSACINAATLALQDAG--------  146 (241)
Q Consensus        83 ~~~~~~~~~~~~l~~~l~~~l~~--~i~l~~~---p---~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~g--------  146 (241)
                      + .|++++++.+++++|+++|++  +++++.|   |   .|.|+|+++||++|||+++|+++|+++||++++        
T Consensus        96 ~-~g~~~~~~~~~s~li~r~lr~s~~i~l~~l~i~pg~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~~p~~~~~~  174 (271)
T 2wnr_A           96 E-PGPPDERSVELSRVVDRCIRESRMIDLEKLCIIEGSKVWMLFLDLHIIDYDGNLFDAAVLATVAALLDTRIPAAEVED  174 (271)
T ss_dssp             C-CSSCCHHHHHHHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHHCEEEEEEEET
T ss_pred             c-CCCCchHHHHHHHHHHHHHhccCCccHHHccccCCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcCCCeEEecC
Confidence            3 467889999999999999999  5777876   4   499999999999999999999999999999999        


Q ss_pred             ------------CCCCCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEee--ecCCHHHHHHHHHH
Q 026213          147 ------------IPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMD--AKLPTNTFEDVMQL  212 (241)
Q Consensus       147 ------------ip~~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~--g~~~~~~l~~~l~~  212 (241)
                                  +||+++|+++|+|++++.+++|||.+||..+++.++|++ +..|+++++++.  +.++.+++.++++.
T Consensus       175 ~~~~~~~~~~~~ip~~~~~~avt~g~~~~~~l~Dpt~~Ee~~~~~~l~va~-~~~~~i~~i~~~g~~~~~~~~l~~~l~~  253 (271)
T 2wnr_A          175 GEVVINREKMQPLPVNRKALMCTFAKIGNEIVLDPSLEEEDILTARISIGV-TEEGSICAMQKGGEGPLTRDDVLKAVSI  253 (271)
T ss_dssp             TEEEEEEEEEEECCBCCCEEEEEEEEETTEEEESCCHHHHTTCSEEEEEEE-ETTSCEEEEEEESSSCBCHHHHHHHHHH
T ss_pred             CceeeccCcccccCccCCeEEEEEEEECCEEEeCCCHHHHhcCCCcEEEEE-eCCCCEEEEECCCCCCCCHHHHHHHHHH
Confidence                        999999999999999999999999999999999999987 456899999987  47999999999999


Q ss_pred             HHHHHHHHHHHHHHHHH
Q 026213          213 AIEGCKAVANYIREVLL  229 (241)
Q Consensus       213 a~~~~~~i~~~i~~~l~  229 (241)
                      |.++++++++.++++++
T Consensus       254 a~~~~~~i~~~~~~~l~  270 (271)
T 2wnr_A          254 AVEKVPQLIEYLDKSMT  270 (271)
T ss_dssp             HHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHhC
Confidence            99999999999998874

>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=9.8e-48  Score=329.35  Aligned_cols=223  Identities=22%  Similarity=0.249  Sum_probs=202.1

Q ss_pred             CCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCC
Q 026213            5 SPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR   84 (241)
Q Consensus         5 ~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~   84 (241)
                      +++|+|+|||+++|+|++.+++|++++++|||++++|+|+|+|+|+++..  .|....++++.+.++|+++|+++++++ 
T Consensus        20 l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~--~p~~~~~~~g~l~v~~~~~p~a~~~~~-   96 (278)
T 2nn6_C           20 LKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFA--APSTDAPDKGYVVPNVDLPPLCSSRFR-   96 (278)
T ss_dssp             HHTSCCTTSCCSCCCCSCCEEETCCSSSSEEEEEEETTEEEEEEEEEEEC--CCCSSSTTCCCCEEEEECCSSSCTTSC-
T ss_pred             HhcCCCCCCCCcccccCeEEEeCCccCCCceEEEEeCCeEEEEEEEEEee--cCCCCCCCccEEEEEEEeCCccCcccc-
Confidence            47899999999999999999999999999999999999999999999643  344445789999999999999998754 


Q ss_pred             CCCCCchhHHHHHHHHHHHHH--hhccCCC------CccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCC---------
Q 026213           85 KPKGDRRSTEISLVIRQTMEA--CILTHLM------PRSQIDIFVQVLQADGGTRSACINAATLALQDAGI---------  147 (241)
Q Consensus        85 ~~~~~~~~~~l~~~l~~~l~~--~i~l~~~------p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gi---------  147 (241)
                      .|+++.++.+++++|+++|++  +++++.|      +.|.|+|+++||++|||+++|+++|+++||+++||         
T Consensus        97 ~g~~~~~~~~~s~li~r~l~~s~~i~l~~L~i~pg~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~iP~v~~~~~~  176 (278)
T 2nn6_C           97 SGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEET  176 (278)
T ss_dssp             SSSCCHHHHHHHHHHHHHHHHHCCSCHHHHCSSBTTBCEEEEEEEEESSCCSCTTHHHHHHHHHHHHTCCCCCCCBCSSS
T ss_pred             CCCCcHHHHHHHHHHHHHHhccCCCCHHHCEEeCCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhCCCCeEEEeCCC
Confidence            467888999999999999996  6766654      46999999999999999999999999999999996         


Q ss_pred             -------------CCCCeeEEEEEeeeCC-eeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee--cCCHHHHHHHHH
Q 026213          148 -------------PMRDIVTSCSAGYLNS-TPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA--KLPTNTFEDVMQ  211 (241)
Q Consensus       148 -------------p~~~~~~~vs~~~~~~-~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g--~~~~~~l~~~l~  211 (241)
                                   ||+++|+++++|++++ .+++|||.+||..+.+.++|++ +..|+++++++.|  .++.+++.++++
T Consensus       177 ~~~~~~~~~~~~lp~~~~~~avs~g~~~~~~~l~Dpt~~Ee~~~~~~l~va~-~~~g~i~~v~~~g~~~~~~~~l~~~l~  255 (278)
T 2nn6_C          177 ALAEVNLKKKSYLNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVM-DEEGKLCCLHKPGGSGLTGAKLQDCMS  255 (278)
T ss_dssp             BCCCTTSCCCSCSCCSCCCEEEEEEECTTTCCEESCCTTTTTSCSEEEEEEE-CTTCCEEEEEESCCSCCCHHHHHHHHH
T ss_pred             cceecCcccccccccCCceEEEEEEEECCceEEECCCHHHHhhcCceEEEEE-cCCCcEEEEEccCCCCCCHHHHHHHHH
Confidence                         7999999999999998 9999999999999999999987 4667999999987  799999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 026213          212 LAIEGCKAVANYIREVLLEN  231 (241)
Q Consensus       212 ~a~~~~~~i~~~i~~~l~~~  231 (241)
                      .|.++++++++.+++++++.
T Consensus       256 ~a~~~~~~i~~~~~~~l~~~  275 (278)
T 2nn6_C          256 RAVTRHKEVKKLMDEVIKSM  275 (278)
T ss_dssp             HHHHHHHHHHHHHHTTTTTT
T ss_pred             HHHHHHHHHHHHHHHHHHhh
Confidence            99999999999999988764

>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=2.2e-46  Score=324.70  Aligned_cols=228  Identities=18%  Similarity=0.198  Sum_probs=201.7

Q ss_pred             CCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCC
Q 026213            5 SPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR   84 (241)
Q Consensus         5 ~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~   84 (241)
                      +++|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|+++.  ..|....++++.+.++|++.|++++.++ 
T Consensus        32 l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~e~--~~p~~~~~~~g~l~~~v~~~p~a~~~~~-  108 (305)
T 2nn6_E           32 VQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEM--GTPKLEKPNEGYLEFFVDCSASATPEFE-  108 (305)
T ss_dssp             HHTTCCSSSCCSSCCCCCEEEECCCTTSSSEEEEEETTEEEEEECCCCC--SCCCSSSCSSCCEEEECCCCTTTCSSCC-
T ss_pred             HhcCCCCCCCCCcCccCeEEEeCcccCCCcEEEEEECCeEEEEEEEEEe--eCCCcCCCCceEEEEEEEeCCCcCcccc-
Confidence            3679999999999999999999999999999999999999999999954  3344456888999999999999987653 


Q ss_pred             CCCCCchhHHHHHHHHHHHHH--hhccC---CCC---ccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCC-----
Q 026213           85 KPKGDRRSTEISLVIRQTMEA--CILTH---LMP---RSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRD-----  151 (241)
Q Consensus        85 ~~~~~~~~~~l~~~l~~~l~~--~i~l~---~~p---~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~-----  151 (241)
                      .+.++.++.+++++|+++|++  +++++   .+|   .|.|+|+++||++|||+++|+++|+++||.++++|+.+     
T Consensus       109 ~r~~~~~~~~isrli~r~lr~s~~idl~~L~i~p~~~~w~i~idv~VL~~DG~~~daai~aa~~AL~~a~iP~~~~~~~~  188 (305)
T 2nn6_E          109 GRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLEDE  188 (305)
T ss_dssp             TTSTHHHHHHHHHHHHHHHHHSCCSCSSSSCSSTTTCCCCEEEEEEECCCCSSHHHHHHHHHHHTTTTCCCCEEEEECC-
T ss_pred             CCCCchHHHHHHHHHHHHHhhcCcccHHHheeccCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcCCCeEEEecCC
Confidence            234557888999999999999  67777   567   38999999999999999999999999999999999643     


Q ss_pred             ----------------------eeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee--cCCHHHHH
Q 026213          152 ----------------------IVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA--KLPTNTFE  207 (241)
Q Consensus       152 ----------------------~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g--~~~~~~l~  207 (241)
                                            +|+++|+|++++.+|+|||.+||..+++.++|++ +..++|+++++.|  .++.+++.
T Consensus       189 ~~~~~i~~~~d~~~~~~l~l~~~p~avt~g~i~~~~l~Dpt~~Ee~~~~~~l~Va~-~~~g~i~~i~~~g~~~l~~~~l~  267 (305)
T 2nn6_E          189 EGSKDIELSDDPYDCIRLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSV-TSKGVVTCMRKVGKGSLDPESIF  267 (305)
T ss_dssp             -----EEEEESSCCCSCCCCTTCCCCEEEEESSSSEESSCCHHHHTSCSEEEEECC-CSSSCCCEEEEEESSCBCHHHHH
T ss_pred             CCceeeeccCcccccccccccCceEEEEEEEECCEEEECCCHHHHhhcCCcEEEEE-cCCCCEEEEEccCCCCCCHHHHH
Confidence                                  4789999999999999999999999999999986 4568899999876  79999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          208 DVMQLAIEGCKAVANYIREVLLENTKQLE  236 (241)
Q Consensus       208 ~~l~~a~~~~~~i~~~i~~~l~~~~~~~~  236 (241)
                      ++++.|.++++++.+.+++++.++.+.+.
T Consensus       268 ~~l~~A~~~~~~i~~~~~~~l~~~~~~~~  296 (305)
T 2nn6_E          268 EMMETGKRVGKVLHASLQSVVHKEESLGP  296 (305)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHC-CC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            99999999999999999999998776443

>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=3.9e-45  Score=321.76  Aligned_cols=226  Identities=16%  Similarity=0.205  Sum_probs=202.2

Q ss_pred             CCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCC
Q 026213            5 SPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR   84 (241)
Q Consensus         5 ~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~   84 (241)
                      +++|+|+|||.++|+|++.+++|   +++|||+|++|+|+|+|+|++|.+.  |....++++.+.++|+++|+++++++.
T Consensus        35 L~~g~R~DGR~~~e~R~i~ie~g---~A~GSa~v~~G~T~VL~tV~~e~~~--p~~~~~~~g~l~~~v~~~p~a~~~~~~  109 (358)
T 2nn6_A           35 IEEKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVS--PKLNRATEGILFFNLELSQMAAPAFEP  109 (358)
T ss_dssp             HHTTCCTTSCCTTCCCCCEEEEC---SSTTEEEEESSSCEEEEEECCEEEC--CCSTTTTSCCEEEEEEECTTTCSSCCS
T ss_pred             HhcCCCCCCCCccccCCeEEEEe---cCCcEEEEEECCcEEEEEEEecccC--CcccCCCCcEEEEEEEecCCccccccC
Confidence            46899999999999999999999   8999999999999999999997543  333457889999999999999887543


Q ss_pred             CCCCCchhHHHHHHHHHHHHHhhcc--CCC------CccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCC--------
Q 026213           85 KPKGDRRSTEISLVIRQTMEACILT--HLM------PRSQIDIFVQVLQADGGTRSACINAATLALQDAGIP--------  148 (241)
Q Consensus        85 ~~~~~~~~~~l~~~l~~~l~~~i~l--~~~------p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip--------  148 (241)
                       ++++.++.+++++|+++|+++..+  +.+      ++|.|+|+++||++|||+++|+++|+++||.++++|        
T Consensus       110 -g~~s~~e~eisrli~r~Lr~s~~idl~~LcI~pg~~~w~I~Vdv~VL~~DGn~~dAai~Aa~aAL~da~iP~v~~~~~~  188 (358)
T 2nn6_A          110 -GRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDE  188 (358)
T ss_dssp             -SSTHHHHTHHHHHHHHHHHHHTCBCSSSSCSBTTTBEEEEEEEEEECSCCSCCHHHHHHHHHHHHHHCCCCCCBCCTTC
T ss_pred             -CCCCHHHHHHHHHHHHHhhhccccchHhhcccCCCccEEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhCcCcEEeeCCe
Confidence             567888999999999999996544  322      679999999999999999999999999999999999        


Q ss_pred             ---------------CCCeeEEEEEeee--CCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee--cCCHHHHHHH
Q 026213          149 ---------------MRDIVTSCSAGYL--NSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA--KLPTNTFEDV  209 (241)
Q Consensus       149 ---------------~~~~~~~vs~~~~--~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g--~~~~~~l~~~  209 (241)
                                     ++++|+++|+|++  ++.+|+||+..||..+++.++|++ +..|+|+.+++.|  .++.+++.++
T Consensus       189 v~i~~~~~~~~~~l~i~~~p~avsvgl~~~~~~illDPt~~Ee~~~~~~l~Va~-t~~g~I~~lqk~G~~~ls~~~l~~~  267 (358)
T 2nn6_A          189 VTLYTPEERDPVPLSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAM-NKHREICTIQSSGGIMLLKDQVLRC  267 (358)
T ss_dssp             CBCCHHHHTSCCCCCBCCCEEEEEEEECTTTSSEEESCCHHHHHHCSCEEEEEE-ETTTEEEEEEEESCCCCCHHHHHHH
T ss_pred             eEecccccccccccCccCCEEEEEEEEEeeCCEEEECCCHHHHhhcCccEEEEE-cCCCeEEEEEeCCCCCCCHHHHHHH
Confidence                           8999999999987  789999999999999999999985 6778999999765  4899999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026213          210 MQLAIEGCKAVANYIREVLLENTKQLEC  237 (241)
Q Consensus       210 l~~a~~~~~~i~~~i~~~l~~~~~~~~~  237 (241)
                      ++.|.++++++.+.+++++.++.+++-+
T Consensus       268 l~~A~~~~~~i~~~~~~~l~~~~~~r~~  295 (358)
T 2nn6_A          268 SKIAGVKVAEITELILKALENDQKVRKE  295 (358)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHhhhh
Confidence            9999999999999999999998887644

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

Probab=100.00  E-value=5.7e-45  Score=315.92  Aligned_cols=226  Identities=17%  Similarity=0.188  Sum_probs=184.2

Q ss_pred             CCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCC
Q 026213            5 SPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR   84 (241)
Q Consensus         5 ~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~   84 (241)
                      +++|+|+|||.++|+|++.+++|   +++|||+|++|+|+|+|+|++|..  .|....++++.+.+++.+.|++....+ 
T Consensus        19 l~~~~R~DGR~~~e~R~i~i~~g---~a~GSa~v~~G~T~Vl~~V~~~~~--~p~~~~~~~g~~~~~ve~~~~~~~~~~-   92 (305)
T 2wp8_A           19 LRQNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGNTKVHCRISCQIA--QPYEDRPFEGLFVISTEISPMAGSQFE-   92 (305)
T ss_dssp             HTTTCCTTSCCTTCCCCEEEEEC---SSTTEEEEEETTEEEEEEEEEEEC---CCSSCTTCCEEEEEECCC---------
T ss_pred             HhhCCCCCCCCCcccCCeEEEEc---CCCcEEEEEECCeEEEEEEecccc--CCcccCCCCcEEEEEEEECCCCCcccc-
Confidence            46899999999999999999999   899999999999999999999643  333446788999999999998876542 


Q ss_pred             CCCCC-chhHHHHHHHHHHHH--HhhccCCC---Cc---cEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCC-------
Q 026213           85 KPKGD-RRSTEISLVIRQTME--ACILTHLM---PR---SQIDIFVQVLQADGGTRSACINAATLALQDAGIP-------  148 (241)
Q Consensus        85 ~~~~~-~~~~~l~~~l~~~l~--~~i~l~~~---p~---~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip-------  148 (241)
                      .|+++ .++.+++++|+++|+  .+++++.+   |+   |.|+|+++||++|||+++|+++|+++||+++|+|       
T Consensus        93 ~g~~~~~~~~~is~li~r~l~~s~~idl~~L~i~pg~~~w~I~id~~VL~~DG~~~dAai~aa~~AL~~a~iP~~~~~~~  172 (305)
T 2wp8_A           93 NGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGE  172 (305)
T ss_dssp             --------------CHHHHHHHTTSBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHHCEECCCBCTTS
T ss_pred             CCCCChhHHHHHHHHHHHHHhhccCcCHHHccccCCcEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHHhCCCeEEecCC
Confidence            35666 888999999999999  56777755   53   9999999999999999999999999999999999       


Q ss_pred             ----------------CCCeeEEEEEeeeC--------------CeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEee
Q 026213          149 ----------------MRDIVTSCSAGYLN--------------STPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMD  198 (241)
Q Consensus       149 ----------------~~~~~~~vs~~~~~--------------~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~  198 (241)
                                      |++.|+++|+|+++              +.+++||+.+||..+++.++|++ +..|+++.+++.
T Consensus       173 ~~~i~~~~~~~~~~l~~~~~pvavs~g~i~~~~~~~~~~~~~~~~~~l~Dpt~~Ee~~~~~~l~Va~-~~~g~i~~l~~~  251 (305)
T 2wp8_A          173 QIIVHPVNEREPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTL-NKNREVVQVSKA  251 (305)
T ss_dssp             SCCBCCSSSSCCEECCBSCCCEEEEEEECC---------------CEEESCCHHHHHHCSEEEEEEE-CTTSEEEEEEEE
T ss_pred             ceEecccccccccccccccCeEEEEEEEEccccccccccccccCCeEEeCCCHHHHhccCCcEEEEE-cCCCcEEEEEec
Confidence                            67899999999997              78999999999999999999987 567899999987


Q ss_pred             e--cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026213          199 A--KLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLEC  237 (241)
Q Consensus       199 g--~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~~~~~  237 (241)
                      |  .++.+++.+++++|.+++++|++.++++|.++.+++.+
T Consensus       252 g~~~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~r~~  292 (305)
T 2wp8_A          252 GGLPMDALTLMKCCHEAYSIIEKITDQILQLLKEDSEKRNK  292 (305)
T ss_dssp             EEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            5  69999999999999999999999999999999888744

>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=3e-45  Score=335.26  Aligned_cols=228  Identities=21%  Similarity=0.313  Sum_probs=198.8

Q ss_pred             cccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEE-EcCccccccc--cCCCCceEEEEEEeecCCc
Q 026213            2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-YGPREVQNKS--QQMSDQALVRCEYSMANFS   78 (241)
Q Consensus         2 ~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V-~~p~e~~~~~--~~~~~~~~i~v~~~~~~~~   78 (241)
                      ++|+++|.|+|||.++|+|++.+++|+++++||||+|++|+|+|+|+| +||.+..++.  ...++.+++.++|+++||+
T Consensus       307 ~~il~~g~R~DGR~~~elRpi~i~~g~l~~a~GSal~~~G~T~Vl~~Vt~gp~~~~~~~~~l~~~~~g~~~~~y~~~P~s  386 (549)
T 3gme_A          307 SRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTDTFLFHYNFPPYS  386 (549)
T ss_dssp             HHHHHTCCCTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEC---------------CCEEEEEECCGGG
T ss_pred             HHHhcCCCCCCCCCCCCccceEEEECCCCCCCceEEEEECCeEEEEEEEecCcccccCccccCCCCceEEEEEEEeCCCC
Confidence            467889999999999999999999999999999999999999999999 6987654322  2234789999999999999


Q ss_pred             ccccCCCCCCCchhHHHHHHHHHHHHHhhc-cCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEE
Q 026213           79 TGDRMRKPKGDRRSTEISLVIRQTMEACIL-THLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCS  157 (241)
Q Consensus        79 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~-l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs  157 (241)
                      ++++++.+.++.++.+++++++++|+++++ .+.||+ +|+|+++||++|||.++|++||+++||+|+||||++++++++
T Consensus       387 t~e~~~~g~~~~Reie~~~li~raL~~vI~~~~~~P~-tI~V~~~VLesDGs~~~AsI~aa~lAL~DAGvPm~~~Vaavs  465 (549)
T 3gme_A          387 VGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPY-TVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIA  465 (549)
T ss_dssp             TTCCCCSSCCCSSHHHHHHHHHHHHTTTCCCTTTCCC-EEEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCCSSCCEEEE
T ss_pred             cCCcccCCCCChhHHHHHHHHHHHHHHhcCccccCCe-EEEEEEEEEECCCCHHHHHHHHHHHHHHhCCCCcccceeEEE
Confidence            999877778899999999999999999999 578997 599999999999999999999999999999999999999999


Q ss_pred             EeeeCC----eeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeec---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          158 AGYLNS----TPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAK---LPTNTFEDVMQLAIEGCKAVANYIREVLLE  230 (241)
Q Consensus       158 ~~~~~~----~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~---~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~  230 (241)
                      +|++++    .+++||+..|+..++..+.|+.  +.+.++.++++++   |+.+++.+++++|.+++.+|++.++++|.+
T Consensus       466 ~Gli~~g~~~~iL~D~~~~Ed~~~d~d~~Va~--t~~gitalqmd~ki~G~s~~~l~~~L~~A~~g~~~I~~~m~~al~~  543 (549)
T 3gme_A          466 MGLVKEGDNYVVLSDILGDEDHLGDMDFKVAG--SRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQAINA  543 (549)
T ss_dssp             EEEEEETTEEEEEESCCHHHHHHSSEEEEEEE--CSSCEEEEEEEECCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCS
T ss_pred             EEEEcCCCceEEEecCChHHHccCCceEEEEe--cCCCeEEEEEccccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999965    6889999999999998999874  4455888888754   699999999999999999999999999876


Q ss_pred             HH
Q 026213          231 NT  232 (241)
Q Consensus       231 ~~  232 (241)
                      ..
T Consensus       544 pr  545 (549)
T 3gme_A          544 PR  545 (549)
T ss_dssp             CC
T ss_pred             hh
Confidence            54

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

Probab=100.00  E-value=1.2e-43  Score=333.57  Aligned_cols=227  Identities=23%  Similarity=0.348  Sum_probs=204.9

Q ss_pred             cccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEE-EcCcccccccc--CCCCceEEEEEEeecCCc
Q 026213            2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-YGPREVQNKSQ--QMSDQALVRCEYSMANFS   78 (241)
Q Consensus         2 ~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V-~~p~e~~~~~~--~~~~~~~i~v~~~~~~~~   78 (241)
                      ++|+++|.|+|||.++|+|++.+++|++++++|||+|++|+|+|+|+| +||.+..++.+  ..++.+.+.++|+++||+
T Consensus       323 ~~il~~g~R~DGR~~~elRpI~ie~gvl~~a~GSAl~~~G~TkVl~~Vt~Gp~~~~~~~d~l~~~~~g~~~~~y~~~P~s  402 (726)
T 4aid_A          323 RGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYKESFLLHYNFPPYS  402 (726)
T ss_dssp             HHHHSSSBCTTSCBTTCCCCEEEEECSSTTSSEEEEEEETTEEEEEEEEEECGGGSEEEEETTEEEEECEEEEEECCGGG
T ss_pred             HHHhcCCCCCCCCCCCCccceEEEECCCCCCCceEEEEeCCeEEEEEEEeCCCCcccccccccCCCceEEEEEEEeCCCc
Confidence            468889999999999999999999999999999999999999999999 79887654332  235789999999999999


Q ss_pred             ccccCCCCCCCchhHHHHHHHHHHHHHhhc-cCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEE
Q 026213           79 TGDRMRKPKGDRRSTEISLVIRQTMEACIL-THLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCS  157 (241)
Q Consensus        79 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~-l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs  157 (241)
                      ++++++.+++++++.+++++++++|+++++ .+.||+ +|+|+++||++|||.++|++||+++||+|+||||++++++++
T Consensus       403 t~er~~~g~~~~Reie~~~li~raL~~vI~~~~~~P~-tI~V~~~VLesDGs~~~AsI~aa~lAL~DAGIPm~~~Vaavs  481 (726)
T 4aid_A          403 VGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPY-TIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIA  481 (726)
T ss_dssp             GTCCCCCSSCCHHHHHHHHHHHHHHGGGSCCTTTCCC-EEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCCEEEE
T ss_pred             ccccccCCCcchhhHHHHHHHHHHHHHhcCccccCCe-EEEEEEEEEEcCCcHHHHHHHHHHHHHHhcCCccccCeeEEE
Confidence            999887788899999999999999999999 588998 599999999999999999999999999999999999999999


Q ss_pred             EeeeCC----eeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee---cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          158 AGYLNS----TPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA---KLPTNTFEDVMQLAIEGCKAVANYIREVLLE  230 (241)
Q Consensus       158 ~~~~~~----~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g---~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~  230 (241)
                      +|++++    .+++||+..|+..++..+.|+.  +.+.++.++++|   .|+.+++.+++++|.+++.+|++.|+++|.+
T Consensus       482 vGli~~g~~~~iLlD~~~~Ed~~gd~d~~Va~--t~~gIt~lQ~d~k~~~~s~e~l~~aL~~A~~g~~~I~~~m~~al~~  559 (726)
T 4aid_A          482 MGLILEQDGFAVLSDILGDEDHLGDMDFKVAG--TSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEMNKAMDA  559 (726)
T ss_dssp             EEEEECSSCEEEEESCCTTGGGGSSEEEEEEE--ETTEEEEEEEEECSSCCCHHHHHHHHHHHHHHHHHHHHHHHTTCSS
T ss_pred             EEEEcCCCceEEEecCChhHHhcCCceEEEEe--cCCceEEEEecCCcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999953    4778999999998888888863  455699999987   4699999999999999999999999998875


Q ss_pred             H
Q 026213          231 N  231 (241)
Q Consensus       231 ~  231 (241)
                      +
T Consensus       560 ~  560 (726)
T 4aid_A          560 P  560 (726)
T ss_dssp             C
T ss_pred             h
Confidence            4

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

Probab=100.00  E-value=3.3e-43  Score=327.62  Aligned_cols=226  Identities=23%  Similarity=0.308  Sum_probs=202.2

Q ss_pred             cccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCcc-cccccc------CCCCceEEEEEEee
Q 026213            2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPRE-VQNKSQ------QMSDQALVRCEYSM   74 (241)
Q Consensus         2 ~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e-~~~~~~------~~~~~~~i~v~~~~   74 (241)
                      ++|+++|.|+|||.++|+|++++++|+++++||||+|++|+|+|+|+|++|.. ..++.+      ..++.+.+.++|++
T Consensus       311 ~~il~~g~R~DGR~~~elRpi~i~~g~l~~a~GSal~~~G~T~Vl~~Vt~~~~~~~~~~d~~~~~l~~~~~g~~~~~y~~  390 (630)
T 3u1k_A          311 SIVLNEYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITAINGIKDKNFMLHYEF  390 (630)
T ss_dssp             HHHHHHSCCTTSCCTTCCCCEEEEECCSTTSSEEEEEEETTEEEEEEEEEECGGGGSCSSHHHHHHHCCCGGGEEEEEEC
T ss_pred             HHHhcCCCCCCCCCCccccceEEEECCCCCCCceEEEEECCeEEEEEEEcCCCCchhcccccccccCCCCceEEEEEEEe
Confidence            46788999999999999999999999999999999999999999999998432 221111      13678899999999


Q ss_pred             cCCcccccCCCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeE
Q 026213           75 ANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVT  154 (241)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~  154 (241)
                      +||+++++++.|.+++++.+++++++++|+++++ +.||+ +|+|+++||++|||.++|++||+++||+|+||||+++++
T Consensus       391 ~P~st~e~~~~g~~~rREi~~~~Li~raLr~vi~-~~~p~-tI~V~~~VLesDGs~~~AsI~aa~lAL~dAGIPl~~~Va  468 (630)
T 3u1k_A          391 PPYATNEIGKVTGLNRRELGHGALAEKALYPVIP-RDFPF-TIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVA  468 (630)
T ss_dssp             CGGGGTCCCCCSSCCHHHHHHHHHHHHHHGGGSC-TTCSS-EEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCCE
T ss_pred             cCCcccccccCCCCChHHHHHHHHHHHHHHhhCc-ccCCe-EEEEEEEEEEcCCCHHHHHHHHHHHHHHhCCCCcccceE
Confidence            9999999877788899999999999999999997 56886 699999999999999999999999999999999999999


Q ss_pred             EEEEeeeC------C-----eeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee---cCCHHHHHHHHHHHHHHHHHH
Q 026213          155 SCSAGYLN------S-----TPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA---KLPTNTFEDVMQLAIEGCKAV  220 (241)
Q Consensus       155 ~vs~~~~~------~-----~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g---~~~~~~l~~~l~~a~~~~~~i  220 (241)
                      ++++|+++      +     .+++||+..|+..++..+.|+. +..| ++.++++|   .|+.+++.+++++|.+++.+|
T Consensus       469 avs~gli~~~~~~~g~~~~~~iLlD~~~~Ed~~~d~d~~Va~-t~~g-It~lQ~~~k~~~~s~~~l~~aL~~A~~g~~~I  546 (630)
T 3u1k_A          469 GVAIGLVTKTDPEKGEIEDYRLLTDILGIEDYNGDMDFKIAG-TNKG-ITALQADIKLPGIPIKIVMEAIQQASVAKKEI  546 (630)
T ss_dssp             EEEEEEEEEECSSSSCEEEEEEEESCCHHHHHTSSEEEEEEE-CSSC-EEEEEEEECSSCBCHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEecCCCcccccccCceEEecCCHHHHhhCcceEEEEe-cCCc-eEEEEecCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            99999987      3     6999999999999888899874 4555 99999987   579999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 026213          221 ANYIREVLLEN  231 (241)
Q Consensus       221 ~~~i~~~l~~~  231 (241)
                      ++.+++++.+.
T Consensus       547 ~~~m~~al~~~  557 (630)
T 3u1k_A          547 LQIMNKTISKP  557 (630)
T ss_dssp             HHHHHHHCSSC
T ss_pred             HHHHHHHHHHH
Confidence            99999998765

>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=2.5e-43  Score=333.74  Aligned_cols=227  Identities=25%  Similarity=0.386  Sum_probs=206.9

Q ss_pred             cccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEE-EcCcccccccc--CCCCceEEEEEEeecCCc
Q 026213            2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-YGPREVQNKSQ--QMSDQALVRCEYSMANFS   78 (241)
Q Consensus         2 ~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V-~~p~e~~~~~~--~~~~~~~i~v~~~~~~~~   78 (241)
                      ++|+++|.|+|||.++|+|++.+++|+++++||||+|++|+|+|+|+| .||.+..++.+  ..++.+.+.++|+++|++
T Consensus       348 ~~i~~~g~R~DGR~~~elRpI~ie~gvl~~a~GSAl~~~G~TqVL~~Vt~Gp~~~~~~~d~l~~~~~g~~~~~y~f~P~s  427 (757)
T 1e3p_A          348 ERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPPYS  427 (757)
T ss_dssp             HHHHHTCBCTTSCBTTCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEEEGGGSEECCSSSSCCEESEEEEEECCGGG
T ss_pred             HHHhcCCCCCCCCCcccccceeEEeCCCCCCCEEEEEEECCcEEEEEEEecCCCccccccccCCCCceEEEEEEEeCCcc
Confidence            467789999999999999999999999999999999999999999999 58876655433  246789999999999999


Q ss_pred             ccccCCCCCCCchhHHHHHHHHHHHHHhhc-cCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEE
Q 026213           79 TGDRMRKPKGDRRSTEISLVIRQTMEACIL-THLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCS  157 (241)
Q Consensus        79 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~-l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs  157 (241)
                      ++++++.+.+++++.+++++++++|+++++ .+.||+ +|+|+++||++|||.++|+++|+++||+|+||||++++++++
T Consensus       428 t~e~~~~g~~~~reie~~~li~raL~~vI~~~~~~P~-tI~V~~~VLesDGs~~~Asi~aa~lAL~dAgIP~k~~Vaavs  506 (757)
T 1e3p_A          428 VGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPY-AIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIA  506 (757)
T ss_dssp             GTCCCCCSSCCHHHHHHHHHHHHHHGGGCCCTTTSCE-EEEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCCSSCCEEEE
T ss_pred             cccccCCCCCchhHHHHHHHHHHHHHHhccccccCCE-EEEEEEEEEECCCCHHHHHHHHHHHHHHHcCCCcccceEEEE
Confidence            998877778899999999999999999998 588996 599999999999999999999999999999999999999999


Q ss_pred             Eeee----CC----eeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeec---CCHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          158 AGYL----NS----TPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAK---LPTNTFEDVMQLAIEGCKAVANYIRE  226 (241)
Q Consensus       158 ~~~~----~~----~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~---~~~~~l~~~l~~a~~~~~~i~~~i~~  226 (241)
                      +|++    ++    .+++||+..|+..++..++|+  ++.+.|+.++++|+   ++.+++.++++.|.+++.+|++.|++
T Consensus       507 ~gli~eg~dg~~~~~iLlDp~~~Ed~~gd~d~~Va--~t~~~It~lQ~~gk~~gi~~e~l~~aL~~A~~~~~~I~~~m~~  584 (757)
T 1e3p_A          507 MGLISQEINGETHYVALTDILGAEDAFGDMDFKVA--GTKEFVTALQLDTKLDGIPASVLAAALKQARDARLHILDVMME  584 (757)
T ss_dssp             EEEEEEESSSCEEEEEEESCCHHHHHHCSEEEEEE--ECSSSEEEEEEEECSSCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEecCCCCccceeEEeCCCHHHHhccCceEEEE--ecCCeEEEEEEcCCccccCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999    43    789999999999999999997  35578999999875   59999999999999999999999999


Q ss_pred             HHHHH
Q 026213          227 VLLEN  231 (241)
Q Consensus       227 ~l~~~  231 (241)
                      +|.++
T Consensus       585 al~~~  589 (757)
T 1e3p_A          585 AIDTP  589 (757)
T ss_dssp             HCSSC
T ss_pred             Hhccc
Confidence            98765

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

Probab=100.00  E-value=7.4e-43  Score=329.51  Aligned_cols=229  Identities=20%  Similarity=0.299  Sum_probs=194.4

Q ss_pred             cccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEE-EcCcccccc-c-cCCCCceEEEEEEeecCCc
Q 026213            2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAV-YGPREVQNK-S-QQMSDQALVRCEYSMANFS   78 (241)
Q Consensus         2 ~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V-~~p~e~~~~-~-~~~~~~~~i~v~~~~~~~~   78 (241)
                      ++|++++.|+|||.++|+|++.+++|++++++|||+|++|+|+|+|+| .+|.+..+. + ...++.+.+.++|+++|++
T Consensus       313 ~~i~~~g~R~DGR~~~elRpI~ie~gvl~~a~GSAl~~~G~TqVL~~Vt~gp~e~~~~~d~l~~~~~g~~~~~y~~~P~s  392 (723)
T 3cdi_A          313 SRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTDTFLFHYNFPPYS  392 (723)
T ss_dssp             HHHHTTCCCTTSCCTTCCCCEEEEESCSTTSSEEEEEEETTEEEEEEEEECC-------------CTTSEEEEEECCGGG
T ss_pred             HHHhccCcCCCCCCccccccceEEeCCCCCCCeEEEEEECCcEEEEEEEecCcccccCCcccCCCCceEEEEEEecCCCC
Confidence            467889999999999999999999999999999999999999999999 688764321 1 1235778999999999999


Q ss_pred             ccccCCCCCCCchhHHHHHHHHHHHHHhhcc-CCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEE
Q 026213           79 TGDRMRKPKGDRRSTEISLVIRQTMEACILT-HLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCS  157 (241)
Q Consensus        79 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l-~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs  157 (241)
                      ++++++.+.+++++.+++++++++|++++++ +.||+ +|+|+++||++|||+++|+++|+++||+|+||||++++++++
T Consensus       393 t~e~~r~g~p~~REi~~~~li~raL~~vI~~~~~~p~-tI~Vd~~VLesdGs~~~Asi~aa~lAL~dAgVPl~~~vaavs  471 (723)
T 3cdi_A          393 VGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPY-TVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIA  471 (723)
T ss_dssp             GTCCCCC-----CTTHHHHHHHHHHHTTSCCSSSSCS-CEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCCEEEE
T ss_pred             ccccccCCCCCHHHHHHHHHHHHHHHHhcCcccCCCE-EEEEEEEEEeCCCCHHHHHHHHHHHHHhcCCCCcccceeeEE
Confidence            9988766777889999999999999999986 67885 699999999999999999999999999999999999999999


Q ss_pred             EeeeC-C---eeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee---cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          158 AGYLN-S---TPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA---KLPTNTFEDVMQLAIEGCKAVANYIREVLLE  230 (241)
Q Consensus       158 ~~~~~-~---~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g---~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~  230 (241)
                      +|+++ |   .+++||+..|+..++..++|+. +..| ++.++++|   .++.+++.++++.|.+++.+|++.|+++|.+
T Consensus       472 ~gli~~g~~~~iL~Dp~~~Ed~~~d~d~~Va~-t~~g-I~~lq~~gk~~~is~e~l~~~l~~A~~~~~~I~~~m~~al~~  549 (723)
T 3cdi_A          472 MGLVKEGDNYVVLSDILGDEDHLGDMDFKVAG-SRDG-ISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQAINA  549 (723)
T ss_dssp             EEEEEETTEEEEESSCCGGGGGGCSEEEEEEE-CSSC-EEEEEEEECSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC-
T ss_pred             EEEEcCCCceEEEECCChHHhhhccceeeecc-cCCc-eEEEEeCCccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            99995 4   4899999999999999999975 4555 99999974   5899999999999999999999999999987


Q ss_pred             HHH
Q 026213          231 NTK  233 (241)
Q Consensus       231 ~~~  233 (241)
                      +.+
T Consensus       550 ~~~  552 (723)
T 3cdi_A          550 PRG  552 (723)
T ss_dssp             ---
T ss_pred             cch
Confidence            754

>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=9.4e-46  Score=306.96  Aligned_cols=209  Identities=22%  Similarity=0.319  Sum_probs=167.9

Q ss_pred             CCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCCCCCCCchhHHH
Q 026213           16 PTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEI   95 (241)
Q Consensus        16 ~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~~~l   95 (241)
                      .+|+|++++++|++++++|||+|++|+|+|+|+|++|.+.+ +..+.++++.++++|.  |+++       +++++  ++
T Consensus         2 ~~e~R~i~ie~g~l~~A~GSa~v~~G~T~Vl~~V~~~~e~~-~~~~~~~~~~l~v~~~--p~~G-------~~~~~--e~   69 (222)
T 3krn_A            2 AGRLREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVH-ASKASDEAMTLDISYR--ANCG-------DNKFN--VL   69 (222)
T ss_dssp             -CCCCCBCCBSCCC----CCCBCCBTTCEEECCCCSSCC--------------CCCSS--CCCC---------CCS--SC
T ss_pred             CCcccceEEEECCCCCCCeEEEEEECCcEEEEEEECCCCCc-ccccCCceEEEEEEEc--CCCC-------CCCHH--HH
Confidence            57999999999999999999999999999999999998664 3345577888776654  5542       23333  78


Q ss_pred             HHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCeeEEEEEeeeCCeeEEeCCccccc
Q 026213           96 SLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDS  175 (241)
Q Consensus        96 ~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~~~~vs~~~~~~~~i~DPt~~Ee~  175 (241)
                      +++|++.|++++.++.||+|.|+|+++||++||++++|++||+++||.++||||+++++++++|+++|.+++|||..|+.
T Consensus        70 ~~li~r~l~~~i~~~~~p~~~I~I~~~VL~~DG~~~~aai~aa~~AL~dagiP~~~~v~avsvg~~~g~~llDpt~~Ee~  149 (222)
T 3krn_A           70 NNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAVAINGACFALLDNGMPFETVFCGVLIVRVKDELIIDPTAKQEA  149 (222)
T ss_dssp             TTHHHHC--CCSCC-----CCCCCCCEEEECCSCHHHHHHHGGGTTTTTTTCCTTSCCCCCCCEECSSSEESSCCTTTTT
T ss_pred             HHHHHHHHHHhccHHhCCCcEEEEEEEEEECCCChHHHHHHHHHHHHHHCCCCccCcEEEEEEEEECCEEEeCCCHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCcEEEEE---cCCCCcEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          176 AGGPDVTVGI---LPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQLE  236 (241)
Q Consensus       176 ~~~~~~~v~~---~~~~~~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~~~~  236 (241)
                      .++..++|++   +++.++|++++++|.++.+++.++++.|.++++++.++++++++++.++..
T Consensus       150 ~~~~~l~va~~~~~~~~~~i~~vq~~g~~~~~~l~~~l~~a~~~~~~i~~~~~~~l~~~~~~~~  213 (222)
T 3krn_A          150 ASTGRVLFSVCKGSDGHPEVCAMDAIGHWDFIQLEAAWSLAQPSASAIFDFYKTVMKRKLSVDE  213 (222)
T ss_dssp             SCC-CCCCEECCCSSSSCCEEEECCBSSCTTHHHHTHHHHTTHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             ccCccEEEEEEccCCCCCCEEEEEEeCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchh
Confidence            9999999998   766799999999999999999999999999999999999999999887754

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

Probab=100.00  E-value=1.2e-33  Score=263.43  Aligned_cols=209  Identities=18%  Similarity=0.268  Sum_probs=182.5

Q ss_pred             CCcceEEEeCCCCC-CceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCccccc-----CCCCCCCch
Q 026213           18 EMRQLRAEIGNVAK-ADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDR-----MRKPKGDRR   91 (241)
Q Consensus        18 e~R~i~i~~~~l~~-a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~-----~~~~~~~~~   91 (241)
                      .-|++++++|.+.+ |+|||++++|+|+|+|+|++|.+.+ +   . +++.+.|+|+..+++.+..     ++.++|+.+
T Consensus        13 ~~R~i~ietG~~a~qA~GSa~v~~G~T~VL~tv~~~~~~~-~---~-df~pL~v~y~~~~~a~g~iPg~f~kRegrps~~   87 (630)
T 3u1k_A           13 GNRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKPS-P---S-QFMPLVVDYRQKAAAAGRIPTNYLRREVGTSDK   87 (630)
T ss_dssp             SSSEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCC-S---S-SSCCEEEEEECSEETTTTEECTTC-----CCHH
T ss_pred             CCEEEEEEeCCccccCCeeEEEEECCeEEEEEEEecCCCC-C---C-CeeEEEEEEEecccccCCCCccccccCCCCCHH
Confidence            35899999999986 9999999999999999999987543 1   1 6777999999888886421     122468889


Q ss_pred             hHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCch--HhHHHHHHHHHHHhCCCCCCCeeEEEEEeeeCCeeEEeC
Q 026213           92 STEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGT--RSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDL  169 (241)
Q Consensus        92 ~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~--l~a~i~a~~~AL~~~gip~~~~~~~vs~~~~~~~~i~DP  169 (241)
                      +.+++++|++.|++++.+..||..  +|+++||+.||+.  ..+++||+++||.++||||++.++++++|+++|++|+||
T Consensus        88 e~lisRlIdR~lRp~~~~~~~~~~--qI~~~VLs~Dg~~~~~~aai~aAs~AL~~s~iP~~~~vaav~vg~i~g~~vldP  165 (630)
T 3u1k_A           88 EILTSRIIDRSIRPLFPAGYFYDT--QVLCNLLAVDGVNEPDVLAINGASVALSLSDIPWNGPVGAVRIGIIDGEYVVNP  165 (630)
T ss_dssp             HHHHHHHHHHHHGGGSCTTCCCCE--EEEEEEEECCSSSCHHHHHHHHHHHHHHHSSSCCCCCCEEEEEEEETTEEEESC
T ss_pred             HHHHHHHHhHHhhhcccccCCCce--EEEEEEEECCCCCCHHHHHHHHHHHHHhccCCCcCCCeEEEEEEEECCEEEECC
Confidence            999999999999999998877764  5788899999997  789999999999999999999999999999999999999


Q ss_pred             CccccccCCCcEEEEEcCCCCcEEEEEeeec-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          170 NYVEDSAGGPDVTVGILPTLDKVTLLQMDAK-LPTNTFEDVMQLAIEGCKAVANYIREVLLENTKQ  234 (241)
Q Consensus       170 t~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~-~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~~  234 (241)
                      |.+|++.+...++|+++ ..+++++++.+|. ++.+++.++++.|.+.++++++++++.+++..+.
T Consensus       166 t~~E~~~s~~dl~Va~t-~~~~i~mve~~~~~~se~~~~~al~~a~~~~~~l~~~~~~~~~~~~~~  230 (630)
T 3u1k_A          166 TRKEMSSSTLNLVVAGA-PKSQIVMLEASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVT  230 (630)
T ss_dssp             CHHHHHTEEEEEEEEEE-TTTEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CHHHHhhCCceEEEEEc-cCCcEEEEECCCccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence            99999999999999875 5678999999876 9999999999999999999999999999887643

>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=99.97  E-value=1.5e-28  Score=225.04  Aligned_cols=207  Identities=19%  Similarity=0.280  Sum_probs=173.1

Q ss_pred             CcceEEEeCCCC-CCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCccccc-----CCCCCCCchh
Q 026213           19 MRQLRAEIGNVA-KADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDR-----MRKPKGDRRS   92 (241)
Q Consensus        19 ~R~i~i~~~~l~-~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~-----~~~~~~~~~~   92 (241)
                      -|++++++|.+. +|+||+++++|+|+|+|+|+++.+.+    +..+...+.|+|....++.+..     ++-|+|+.++
T Consensus        13 ~R~i~ietg~~ak~A~GSvlv~~GdT~Vl~tv~~~~~~~----~g~df~Pltv~Y~e~~~a~G~iPg~~~~REGrps~~~   88 (549)
T 3gme_A           13 QHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAK----PGQDFFPLTVNYQERTYAAGRIPGSFFRREGRPSEGE   88 (549)
T ss_dssp             TEEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCC----TTCCSCCEEEEEEECGGGTTCCCSCC-----CCCHHH
T ss_pred             CEEEEEEECCccCCCCeEEEEEECCEEEEEEEEecCCCC----CCCCCccceeeeeeehhhcccCCCcCcCcCCCCChhh
Confidence            589999999886 59999999999999999999976432    2235566999997433332221     1127889999


Q ss_pred             HHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchH--hHHHHHHHHHHHhCCCCCCCeeEEEEEeeeCCeeEEeCC
Q 026213           93 TEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTR--SACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLN  170 (241)
Q Consensus        93 ~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l--~a~i~a~~~AL~~~gip~~~~~~~vs~~~~~~~~i~DPt  170 (241)
                      .+++++|+|.|+++++...+.  .++|+++||+.||+..  .+++||+++||..++||+++.+.++++|+++|++|+|||
T Consensus        89 ~l~~RlIdR~lRplfp~~~~~--evqI~~~Vls~D~~~~pd~~ai~gAs~AL~~s~iP~~gpvaaV~Vg~i~g~~vlnPt  166 (549)
T 3gme_A           89 TLIARLIDRPIRPLFPEGFVN--EVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPT  166 (549)
T ss_dssp             HHHHHHHHHHHGGGSCTTCCS--CEEEEEEEEECCSSSCHHHHHHHHHHHHHHHHCSCCCCCCEEEEEEEETTEEEESCC
T ss_pred             hHHHHHhCCccccccccCCcc--cEEEEEEEEecCCCCcHHHHHHHHHHHHHhccCCCcCCCeeEEEEEEECCEEEECCC
Confidence            999999999999998776544  5788899999998553  588999999999999999999999999999999999999


Q ss_pred             ccccccCCCcEEEEEcCCCCcEEEEEeee-cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          171 YVEDSAGGPDVTVGILPTLDKVTLLQMDA-KLPTNTFEDVMQLAIEGCKAVANYIREVLLENTK  233 (241)
Q Consensus       171 ~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g-~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~  233 (241)
                      .+|++.++..++|+.  +.+.+++++.+| .|+.+++.++++.|.+.++++++++++.+++..+
T Consensus       167 ~~e~~~s~~dl~va~--t~~~i~mve~e~~~~se~~~~~al~~a~~~i~~l~~~q~~~~~~~~~  228 (549)
T 3gme_A          167 QDELKESKLDLVVAG--TEAAVLMVESEAELLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGK  228 (549)
T ss_dssp             TTTTTTCSBCEEEEE--CSSCEEEEEEEEEEECHHHHHHHHHHHHHHTHHHHHHHHHHHHHHCC
T ss_pred             HHHHhhCceEEEEEe--cCCeEEEEEccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            999999999999975  334599999886 6999999999999999999999999999988654

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

Probab=99.96  E-value=2.4e-28  Score=229.89  Aligned_cols=206  Identities=20%  Similarity=0.230  Sum_probs=175.1

Q ss_pred             CCcceEEEeCCCC-CCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEee-------cCCcccccCCCCCCC
Q 026213           18 EMRQLRAEIGNVA-KADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSM-------ANFSTGDRMRKPKGD   89 (241)
Q Consensus        18 e~R~i~i~~~~l~-~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~-------~~~~~~~~~~~~~~~   89 (241)
                      .-|++++++|.+. +|+||+++++|+|+|+|+|+++.+.+    +..+..++.++|..       .|.....|  -|+|+
T Consensus        26 ~~R~i~ietg~~ak~A~GSvlv~~GdT~VL~tv~~~~~~~----~g~df~pltveY~ek~~a~G~iPg~~~~R--EGrps   99 (726)
T 4aid_A           26 GGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQK----PGQDFFPLTVNYQEKTFAAGKIPGGFFKR--EGRPS   99 (726)
T ss_dssp             TTEEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCC----TTCCSCCEEEEEEECGGGGTCCCCSTTCS--CCSCC
T ss_pred             CCeeEEEEECCccCCCCeeEEEEECCeEEEEEEEecCCCC----CCCCCcCceeeeeeehhhcccCCCcccCC--CCCCC
Confidence            3689999999876 59999999999999999999976432    22356679999973       34332222  27899


Q ss_pred             chhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCch--HhHHHHHHHHHHHhCCCCCCCeeEEEEEeeeCCeeEE
Q 026213           90 RRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGT--RSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLL  167 (241)
Q Consensus        90 ~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~--l~a~i~a~~~AL~~~gip~~~~~~~vs~~~~~~~~i~  167 (241)
                      .++.+++++|.|.|+++++...+  +.++|+++||+.||+.  -.+++||+++||.++++|+++.+.++++|+++|++|+
T Consensus       100 ~~~~li~RlIdR~lRplf~~~~~--~evqI~~~Vls~Dg~~~~d~~ai~gAs~AL~~s~iP~~~~vaaV~Vg~i~g~~vl  177 (726)
T 4aid_A          100 EKETLVSRLIDRPIRPLFVKGFK--NEVQVVVTVLQHDLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVL  177 (726)
T ss_dssp             HHHHHHHHHHHHHHGGGBCTTCC--SCEEEEEEEEECCSSSCHHHHHHHHHHHHHHHHTCSBCCCCEEEEEEEETTEEEE
T ss_pred             chhhhHHHHhCCccccccccCCc--cceEEEEEEEecCCCCChhHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCEEEE
Confidence            99999999999999999886654  4688889999999864  3679999999999999999999999999999999999


Q ss_pred             eCCccccccCCCcEEEEEcCCCCcEEEEEeee-cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          168 DLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA-KLPTNTFEDVMQLAIEGCKAVANYIREVLLENTK  233 (241)
Q Consensus       168 DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g-~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~  233 (241)
                      |||.+|++.++..++|+. +.. .+++++.++ .|+.+++.+++++|.+.++++++++++.+++..+
T Consensus       178 dPt~~E~~~s~~dl~va~-t~~-~i~mve~~~~~~se~~~~~al~~a~~~i~~l~~~q~~~~~~~g~  242 (726)
T 4aid_A          178 NPTLDEMKESKMDLVVAG-TAD-AVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAK  242 (726)
T ss_dssp             SCCHHHHHTCSEEEEEEE-CSS-CEEEEEEEESSBCHHHHHHHHHHHHHHTHHHHHHHHHHHHHHCC
T ss_pred             CCCHHHHhhCceeEEEEE-eCC-eEEEEEccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            999999999999999975 333 499999876 5999999999999999999999999999987654

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

Probab=99.96  E-value=4e-28  Score=229.22  Aligned_cols=206  Identities=19%  Similarity=0.279  Sum_probs=175.1

Q ss_pred             cceEEEeCCC-CCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCccccc-----CCCCCCCchhH
Q 026213           20 RQLRAEIGNV-AKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDR-----MRKPKGDRRST   93 (241)
Q Consensus        20 R~i~i~~~~l-~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~-----~~~~~~~~~~~   93 (241)
                      |++.+++|.+ .+|+||+++++|+|+|+|+|+++.+.+    +..+...+.|+|....++.+..     ++.|+|+.++.
T Consensus        20 r~i~ietg~ia~qA~GSv~v~~G~T~Vl~tv~~~~~~~----~~~~f~pltv~y~ek~~a~g~ipg~f~kReGrpse~e~   95 (723)
T 3cdi_A           20 HTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAK----PGQDFFPLTVNYQERTYAAGRIPGSFFRREGRPSEGET   95 (723)
T ss_dssp             EEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCC----SSCCSCCEEEEEEECGGGGTCCCC-------CCCHHHH
T ss_pred             EEEEEEeCccccCCCeeEEEEECCEEEEEEEEecCCCC----CCCCeeeEEEEEeEeccccccCCCccccCCCCCChHHh
Confidence            5999999988 589999999999999999999975332    1236677999998654444431     22378899999


Q ss_pred             HHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCch-H-hHHHHHHHHHHHhCCCCCCCeeEEEEEeeeCCeeEEeCCc
Q 026213           94 EISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGT-R-SACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNY  171 (241)
Q Consensus        94 ~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~-l-~a~i~a~~~AL~~~gip~~~~~~~vs~~~~~~~~i~DPt~  171 (241)
                      +++++|+|.|++++....  +|.++|+++||+.||+. . .+++||+++||..+++|+.+.+.++++|+++|.+|+|||.
T Consensus        96 l~sRlIdR~lRplfp~~~--~~~vqv~~~vls~Dg~~~~d~~ai~aAsaAL~~s~iP~~~pv~av~vg~i~g~~v~nPt~  173 (723)
T 3cdi_A           96 LIARLIDRPIRPLFPEGF--VNEVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQ  173 (723)
T ss_dssp             HHHHHHHHHHGGGSCTTC--CSCEEEEEEEEECCTTSCHHHHHHHHHHHHHHHHTSSCCCCCCCEEEEEETTEEEESCCT
T ss_pred             HHHHHhCccchhcccccC--cceEEEEEEEEEcCCCCCHHHHHHHHHHHHHHhcCCCCCCCeEEEEEEEECCEEEECcCH
Confidence            999999999999876543  57899999999999985 4 4999999999999999999999999999999999999999


Q ss_pred             cccccCCCcEEEEEcCCCCcEEEEEeeec-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          172 VEDSAGGPDVTVGILPTLDKVTLLQMDAK-LPTNTFEDVMQLAIEGCKAVANYIREVLLENTK  233 (241)
Q Consensus       172 ~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~-~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~  233 (241)
                      +|++.++..++|+.  +.+.+++++.++. ++.+++.++++.|.+.++++.+++++.+++..+
T Consensus       174 ~e~~~s~~~lvvag--t~~~i~mve~~~~~~se~~~~~al~~a~~~~~~l~~~~~~~~~~~~~  234 (723)
T 3cdi_A          174 DELKESKLDLVVAG--TEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGK  234 (723)
T ss_dssp             TGGGGCSEEEEEEE--CSSCEEEEEEEEEEECHHHHHHHHHHHHHHTHHHHHHHHHHHHHTCC
T ss_pred             HHHHhCCceEEEEc--cCCEEEEEeCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            99999999999874  4456999998765 999999999999999999999999999987654

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=99.96  E-value=1.6e-27  Score=225.97  Aligned_cols=209  Identities=15%  Similarity=0.158  Sum_probs=175.7

Q ss_pred             CcceEEEeCCC-CCCceeEEEEe-CCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccc-----cCCCCCCCch
Q 026213           19 MRQLRAEIGNV-AKADGSAVFEM-GNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGD-----RMRKPKGDRR   91 (241)
Q Consensus        19 ~R~i~i~~~~l-~~a~GSa~v~~-G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~-----~~~~~~~~~~   91 (241)
                      -|++++++|.+ .+|+||+++++ |+|+|+|+|++|.+.+    +..++..+.|+|+...++.+.     .++-|+|+.+
T Consensus        36 ~r~i~~etg~la~qA~GSv~v~~~G~T~Vl~tv~~~~~~~----~~~df~pLtv~y~ek~~a~g~iPg~f~~REGrps~~  111 (757)
T 1e3p_A           36 TRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPK----DQLDFFPLTVDVEERMYAAGKIPGSFFRREGRPSED  111 (757)
T ss_dssp             EEEEEEEESSSCTTSSEEEEEEETTTEEEEEEEEEEEEEC----TTCSSCCEEEEEEECGGGGTCCCCSTTSSCCSCCHH
T ss_pred             CEeEEEEECccccCCCeEEEEEECCCeEEEEEEEecCCCC----CCCCCccEEEEEEecccccccCCCcccccCcCCChH
Confidence            48999999987 58999999999 9999999999976543    123567799999744333322     1223788899


Q ss_pred             hHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCch--HhHHHHHHHHHHHhCCCCCCCeeEEEEEeeeCCeeEEeC
Q 026213           92 STEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGT--RSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDL  169 (241)
Q Consensus        92 ~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~--l~a~i~a~~~AL~~~gip~~~~~~~vs~~~~~~~~i~DP  169 (241)
                      +++++++|.|.|+++++...+  ..++|+++||+.||..  ..+++||+++||.+++||+++.+.|+++|+++|++|+||
T Consensus       112 e~l~~RlIdR~LRplfp~~~~--~evqv~~~Vls~D~~~~~~~~ai~gAs~AL~~s~iP~~~~vaav~vg~~~g~~vlnP  189 (757)
T 1e3p_A          112 AILTCRLIDRPLRPSFKKGLR--NEIQVVATIMALNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFP  189 (757)
T ss_dssp             HHHHHHHHHHHHGGGBCTTBC--EEEEEEEEEEECCTTSCCHHHHHHHHHHHHHHTTSSBCCCCEEEEEEEETTEEEESC
T ss_pred             HHHHHHHHCCcchhccccCCC--CceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCCCCceEEEEEEEECCEEEECC
Confidence            999999999999998765432  3699999999999864  899999999999999999999999999999999999999


Q ss_pred             CccccccCCCcEEEEEcC---CCCcEEEEEe------------e-ecCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          170 NYVEDSAGGPDVTVGILP---TLDKVTLLQM------------D-AKLPTNTFEDVMQLAIEGCKAVANYIREVLLENTK  233 (241)
Q Consensus       170 t~~Ee~~~~~~~~v~~~~---~~~~i~~~~~------------~-g~~~~~~l~~~l~~a~~~~~~i~~~i~~~l~~~~~  233 (241)
                      |.+|++.+...++|+...   +.+.+.+++.            + +.++.+++.++++.|.+.++++++++++.+++..+
T Consensus       190 t~~e~~~s~~dl~va~t~~~~~~~~i~mvE~q~t~~~~~~~~~~~~~~se~~l~~al~~a~~~i~~l~~~q~~~~~~~~~  269 (757)
T 1e3p_A          190 THTELEDAVFDMVVAGRVLEDGDVAIMMVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLAAKAAK  269 (757)
T ss_dssp             CHHHHTTEEEEEEEEEEECTTSCEEEEEEEEEECSSHHHHHHTTCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CHHHHhcCceeEEEEeccccCCCCcEEEEEEecccccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            999999988889987531   2677899988            2 46999999999999999999999999999886544

---

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	241
d2nn6b1	145	d.14.1.4 (B:6-150) Exosome complex exonuclease RRP	5e-36
d2je6b1	148	d.14.1.4 (B:8-155) Exosome complex exonuclease 1,	7e-36
d2ba0d1	144	d.14.1.4 (D:10-153) Exosome complex exonuclease 1,	3e-34
d2nn6e1	187	d.14.1.4 (E:5-191) Exosome complex exonuclease RRP	6e-32
d2nn6c1	181	d.14.1.4 (C:7-187) Exosome complex exonuclease RRP	8e-32
d2ba0g1	176	d.14.1.4 (G:3-178) Exosome complex exonuclease 2,E	8e-32
d1e3ha3	137	d.14.1.4 (A:346-482) Polynucleotide phosphorylase/	4e-31
d1r6la1	151	d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Pseu	2e-30
d2nn6d1	122	d.14.1.4 (D:25-146) Exosome complex exonuclease RR	1e-28
d2nn6a1	184	d.14.1.4 (A:1-184) Exosome complex exonuclease RRP	1e-28
d2nn6f1	147	d.14.1.4 (F:29-175) Exosome complex exonuclease MT	1e-28
d1udsa1	149	d.14.1.4 (A:2-150) Ribonuclease PH, domain 1 {Aqui	1e-27
d1oysa1	151	d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Baci	4e-27
d2je6a1	191	d.14.1.4 (A:1-191) Exosome complex exonuclease 2,E	3e-25
d1e3ha2	149	d.14.1.4 (A:3-151) Polynucleotide phosphorylase/gu	3e-20
d2nn6f2	95	d.101.1.1 (F:176-270) Exosome complex exonuclease	8e-18
d2nn6b2	90	d.101.1.1 (B:151-240) Exosome complex exonuclease	3e-16
d2je6b2	86	d.101.1.1 (B:156-241) Exosome complex exonuclease	6e-16
d2ba0g2	79	d.101.1.1 (G:179-257) Exosome complex exonuclease	5e-11
d2ba0d2	99	d.101.1.1 (D:154-252) Exosome complex exonuclease	8e-11
d2nn6d2	89	d.101.1.1 (D:147-235) Exosome complex exonuclease	1e-10
d1udsa2	105	d.101.1.1 (A:151-255) Ribonuclease PH, domain 2 {A	2e-09
d2je6a2	84	d.101.1.1 (A:192-275) Exosome complex exonuclease	8e-09
d1r6la2	88	d.101.1.1 (A:152-239) Ribonuclease PH, domain 2 {P	9e-09
d2nn6e2	94	d.101.1.1 (E:192-285) Exosome complex exonuclease	2e-08
d2nn6c2	89	d.101.1.1 (C:188-276) Exosome complex exonuclease	3e-08
d2nn6a2	118	d.101.1.1 (A:185-302) Exosome complex exonuclease	1e-07
d1oysa2	86	d.101.1.1 (A:152-237) Ribonuclease PH, domain 2 {B	2e-07
d1e3ha6	96	d.101.1.1 (A:483-578) Polynucleotide phosphorylase	5e-05

>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 =  122 bits (307), Expect = 5e-36
 Identities = 87/145 (60%), Positives = 115/145 (79%), Gaps = 1/145 (0%)

Query: 4   VSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQ-NKSQQM 62
           +S +G R+DGRR  E+R+++A +G  A+ADGSA  E GNTK +A VYGP E++ ++++ +
Sbjct: 1   LSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARAL 60

Query: 63  SDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQ 122
            D+ALV C+YS A FSTG+R R+P GDR+S E+ L +RQT EA ILT L PRSQIDI+VQ
Sbjct: 61  PDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQ 120

Query: 123 VLQADGGTRSACINAATLALQDAGI 147
           VLQADGGT +AC+NAATLA+ DAGI
Sbjct: 121 VLQADGGTYAACVNAATLAVLDAGI 145

>d2je6b1 d.14.1.4 (B:8-155) Exosome complex exonuclease 1, ECX1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 148

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 1, ECX1
species: Sulfolobus solfataricus [TaxId: 2287]

 Score =  122 bits (306), Expect = 7e-36
 Identities = 70/141 (49%), Positives = 98/141 (69%), Gaps = 1/141 (0%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           +G R DGR+P E+R ++ E+G +  ADGSA+FEMGNTK IAAVYGP+E+  +   + D+A
Sbjct: 9   DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRA 68

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
           ++R  Y M  FST +R   P   RR  E+S VIR+ +E+ +L  L PR+ ID+F ++LQA
Sbjct: 69  VLRVRYHMTPFSTDERKN-PAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQA 127

Query: 127 DGGTRSACINAATLALQDAGI 147
           D G+R   + AA+LAL DAGI
Sbjct: 128 DAGSRLVSLMAASLALADAGI 148

>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 =  118 bits (295), Expect = 3e-34
 Identities = 76/141 (53%), Positives = 100/141 (70%), Gaps = 1/141 (0%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           +GLRLDGR+  E+R ++ E   + +ADGS   EMG  KVIAAV+GPREV  +  Q   +A
Sbjct: 5   DGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKA 64

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
           ++R  Y+MA FS  +R R P  DRRS EIS V ++  EA I+  L PRS IDIFV+VLQA
Sbjct: 65  IIRYRYNMAPFSVEERKR-PGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQA 123

Query: 127 DGGTRSACINAATLALQDAGI 147
           D G+R+AC+NAA++AL DAG+
Sbjct: 124 DAGSRTACLNAASVALVDAGV 144

>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 =  113 bits (284), Expect = 6e-32
 Identities = 36/189 (19%), Positives = 62/189 (32%), Gaps = 30/189 (15%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           E LR+DGR   + R +  E   V+   GSA  ++G+T ++  V          +      
Sbjct: 16  EDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEG-- 73

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHL--------MPRSQID 118
            +      +  +T +      GD   TEI+  + +         L             + 
Sbjct: 74  YLEFFVDCSASATPEFEG-RGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLY 132

Query: 119 IFVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGG 178
           + V +L+  G    A   A   AL +  IP                    +  +ED  G 
Sbjct: 133 VDVLLLECGGNLFDAISIAVKAALFNTRIP-------------------RVRVLEDEEGS 173

Query: 179 PDVTVGILP 187
            D+ +   P
Sbjct: 174 KDIELSDDP 182

>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 =  112 bits (282), Expect = 8e-32
 Identities = 39/176 (22%), Positives = 61/176 (34%), Gaps = 17/176 (9%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           E  R DGR   E R     IG+++ ADGSA+ ++GNT VI  V       +      D+ 
Sbjct: 14  ENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPS--TDAPDKG 71

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIR-------QTMEACILTHLMPRSQIDI 119
            V     +    +      P G+        +            E   ++       +  
Sbjct: 72  YVVPNVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYC 131

Query: 120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIVTSCSAGYLNSTPLLDLNYVEDS 175
            +  L  DG    AC  A   AL++  +P   I           T L ++N  + S
Sbjct: 132 DLICLDYDGNILDACTFALLAALKNVQLPEVTIN--------EETALAEVNLKKKS 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 =  112 bits (282), Expect = 8e-32
 Identities = 32/154 (20%), Positives = 60/154 (38%), Gaps = 9/154 (5%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           +  R+DGR   E R++      + KA+GSA+ ++G+T+V+  V              D+ 
Sbjct: 18  DNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPY--PDTPDRG 75

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIR--QTMEACILTHLMPR-----SQIDI 119
           ++     +   ++      P  +       +V R  +  EA  L+ L+         + +
Sbjct: 76  VIIVNAELVPLASPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFV 135

Query: 120 FVQVLQADGGTRSACINAATLALQDAGIPMRDIV 153
            +  L  DG    A   AA  AL +  +P     
Sbjct: 136 DIHALDDDGNLLDASALAAIAALMNTKVPAERFD 169

>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 =  109 bits (274), Expect = 4e-31
 Identities = 30/137 (21%), Positives = 59/137 (43%), Gaps = 3/137 (2%)

Query: 17  TEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREV---QNKSQQMSDQALVRCEYS 73
           T++R L AE+  + +  GSA+FE G T+++            Q  +     +      Y+
Sbjct: 1   TDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYN 60

Query: 74  MANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSA 133
              +S G+  R     RR      +  + +   + T       I    + L ++G T   
Sbjct: 61  FPPYSVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMG 120

Query: 134 CINAATLALQDAGIPMR 150
            + A+T++L +AG+P++
Sbjct: 121 SVCASTMSLLNAGVPLK 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 =  108 bits (270), Expect = 2e-30
 Identities = 43/145 (29%), Positives = 70/145 (48%), Gaps = 5/145 (3%)

Query: 10  RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVR 69
           R  GR   ++R +R        A+GS + E G+TKVI  V        +  +   Q  + 
Sbjct: 3   RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESG-VPRFLKGQGQGWLT 61

Query: 70  CEYSMANFSTGDRMRKPKGDRRSTEISL----VIRQTMEACILTHLMPRSQIDIFVQVLQ 125
            EY M   STG+R ++     +    +L    +I +++ A +    +  + + I   V+Q
Sbjct: 62  AEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQ 121

Query: 126 ADGGTRSACINAATLALQDAGIPMR 150
           ADGGTR+A I  AT+AL DA   ++
Sbjct: 122 ADGGTRTASITGATVALIDALAVLK 146

>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 =  103 bits (257), Expect = 1e-28
 Identities = 41/130 (31%), Positives = 62/130 (47%), Gaps = 10/130 (7%)

Query: 18  EMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANF 77
            +R    E   +++ DGSA F  G+T V+A VYGP EV+   +           ++ A  
Sbjct: 3   SLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKE----------IFNKATL 52

Query: 78  STGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINA 137
               R +             +IR T EA +L  L PR+ I + +QV+   G   + C+NA
Sbjct: 53  EVILRPKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNA 112

Query: 138 ATLALQDAGI 147
           A +AL DAG+
Sbjct: 113 ACMALVDAGV 122

>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 =  104 bits (261), Expect = 1e-28
 Identities = 26/155 (16%), Positives = 53/155 (34%), Gaps = 14/155 (9%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           E  RLDGR+  + R +R   G      G  + E+G T+V+  V             + + 
Sbjct: 20  EKKRLDGRQTYDYRNIRISFGT---DYGCCIVELGKTRVLGQVSCELVSPK--LNRATEG 74

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMP--------RSQID 118
           ++     ++  +        +      +++ ++ + +                    QI 
Sbjct: 75  ILFFNLELSQMAAPAF-EPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIR 133

Query: 119 IFVQVLQADGGTRSACINAATLALQDAGIPMRDIV 153
           + + +L  DG    A   AA +AL     P   + 
Sbjct: 134 VDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQ 168

>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 =  103 bits (257), Expect = 1e-28
 Identities = 43/146 (29%), Positives = 73/146 (50%), Gaps = 12/146 (8%)

Query: 13  GRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNK-----------SQQ 61
            R PT +R + A  G +++A GSA  E G TKV+ AV GPR+ +                
Sbjct: 2   TRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAP 61

Query: 62  MSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFV 121
            + +  + C++  A F+   R   P G     E++L +++ +E  +     PR+Q+++  
Sbjct: 62  AALRGRLLCDFRRAPFAGRRRRA-PPGGCEERELALALQEALEPAVRLGRYPRAQLEVSA 120

Query: 122 QVLQADGGTRSACINAATLALQDAGI 147
            +L+  G   +A + AA LAL DAG+
Sbjct: 121 LLLEDGGSALAAALTAAALALADAGV 146

>d1udsa1 d.14.1.4 (A:2-150) Ribonuclease PH, domain 1 {Aquifex aeolicus [TaxId: 63363]} Length = 149

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Ribonuclease PH, domain 1
species: Aquifex aeolicus [TaxId: 63363]

 Score =  101 bits (251), Expect = 1e-27
 Identities = 34/145 (23%), Positives = 54/145 (37%), Gaps = 3/145 (2%)

Query: 10  RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQ-ALV 68
           R DGR+  ++R +  +   +   +GS +   G TKVI        V N  +         
Sbjct: 1   RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNWLKGKGQGWITA 60

Query: 69  RCEYSMANFSTGDRMRKPKGDRRST--EISLVIRQTMEACILTHLMPRSQIDIFVQVLQA 126
                             +G       EI  +I + M   +    +    I +   V+QA
Sbjct: 61  EYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQA 120

Query: 127 DGGTRSACINAATLALQDAGIPMRD 151
           DGGT +A I  A +A+ DA I +  
Sbjct: 121 DGGTATAAITGAFVAVADAIIKLHK 145

>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 =   99 bits (248), Expect = 4e-27
 Identities = 41/144 (28%), Positives = 63/144 (43%), Gaps = 3/144 (2%)

Query: 9   LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ---QMSDQ 65
           +R DGR+  E+R +  ++  ++  +GS +   GNTKVI        V    +   +    
Sbjct: 1   MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWIT 60

Query: 66  ALVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQ 125
           A         N  T     K K   R+ EI  +I + + A +    +    I I   V+Q
Sbjct: 61  AEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQ 120

Query: 126 ADGGTRSACINAATLALQDAGIPM 149
           ADGGTR+A I  A LA+  A   +
Sbjct: 121 ADGGTRTASITGAFLAMAIAIGKL 144

>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 = 96.4 bits (239), Expect = 3e-25
 Identities = 31/150 (20%), Positives = 56/150 (37%), Gaps = 9/150 (6%)

Query: 7   EGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQA 66
           +G+R DGR+ T+ R L   +    KADGSA+ ++G T V+A      +     +   +Q 
Sbjct: 25  KGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPY--EDTPNQG 82

Query: 67  LVRCEYSMANFSTGDRMRKPKGDRRSTEISLVIR-------QTMEACILTHLMPRSQIDI 119
            +     +   +       P  +       +V R         +   ++        + +
Sbjct: 83  NLIVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWL 142

Query: 120 FVQVLQADGGTRSACINAATLALQDAGIPM 149
            V VL   G    AC  A+  AL +  +  
Sbjct: 143 DVYVLDYGGNVLDACTLASVAALYNTKVYK 172

>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 = 81.7 bits (201), Expect = 3e-20
 Identities = 26/132 (19%), Positives = 47/132 (35%), Gaps = 3/132 (2%)

Query: 20  RQLRAEIGNVAK-ADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFS 78
           R +R E G +A+ A GSAV  + +  ++ +     +            +   E   A   
Sbjct: 18  RTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDVEERMYAAGK 77

Query: 79  T--GDRMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACIN 136
                  R+ +    +     +I + +       L    Q+   +  L  D       IN
Sbjct: 78  IPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVVAIN 137

Query: 137 AATLALQDAGIP 148
           AA+ + Q AG+P
Sbjct: 138 AASASTQLAGLP 149

>d2nn6f2 d.101.1.1 (F:176-270) Exosome complex exonuclease MTR3 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease MTR3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.9 bits (181), Expect = 8e-18
 Identities = 21/91 (23%), Positives = 44/91 (48%), Gaps = 4/91 (4%)

Query: 149 MRDIVTSCSAG---YLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKL-PTN 204
           M D+V  C          T LLD   +E+      +TV ++P L++V  L    +   T 
Sbjct: 1   MYDLVVGCGLSLAPGPAPTWLLDPTRLEEERAAAGLTVALMPVLNQVAGLLGSGEGGLTE 60

Query: 205 TFEDVMQLAIEGCKAVANYIREVLLENTKQL 235
           ++ + ++L +EGC+ +   +++ L+   ++ 
Sbjct: 61  SWAEAVRLGLEGCQRLYPVLQQSLVRAARRR 91

>d2nn6b2 d.101.1.1 (B:151-240) Exosome complex exonuclease RRP41 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.7 bits (170), Expect = 3e-16
 Identities = 32/88 (36%), Positives = 58/88 (65%)

Query: 148 PMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFE 207
           PMRD V +CSAG+++ T L DL++VE++AGGP + + +LP   ++ LL+MDA+L  +  E
Sbjct: 1   PMRDFVCACSAGFVDGTALADLSHVEEAAGGPQLALALLPASGQIALLEMDARLHEDHLE 60

Query: 208 DVMQLAIEGCKAVANYIREVLLENTKQL 235
            V++ A +  + V   +  V+ ++ ++ 
Sbjct: 61  RVLEAAAQAARDVHTLLDRVVRQHVREA 88

>d2je6b2 d.101.1.1 (B:156-241) Exosome complex exonuclease 1, ECX1 {Sulfolobus solfataricus [TaxId: 2287]} Length = 86

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]

 Score = 68.4 bits (167), Expect = 6e-16
 Identities = 26/83 (31%), Positives = 45/83 (54%)

Query: 148 PMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFE 207
           PMRD++   + G  +   +LDLN  E   G  D+ + ++P+L++VTL Q++  +  + F 
Sbjct: 1   PMRDLIAGVAVGKADGVIILDLNETEAMWGEADMPIAMMPSLNQVTLFQLNGSMTPDEFR 60

Query: 208 DVMQLAIEGCKAVANYIREVLLE 230
               LA++G   + N  RE L  
Sbjct: 61  QAFDLAVKGINIIYNLEREALKS 83

>d2ba0g2 d.101.1.1 (G:179-257) Exosome complex exonuclease 2, ECX2 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 79

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

 Score = 55.2 bits (133), Expect = 5e-11
 Identities = 15/80 (18%), Positives = 36/80 (45%), Gaps = 3/80 (3%)

Query: 148 PMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTN--T 205
           P+RD+  S ++  + +  L+D +  E S G   +T+      D V  +Q       +   
Sbjct: 1   PVRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITTDKD-DNVVAMQKSGGYLLDEKL 59

Query: 206 FEDVMQLAIEGCKAVANYIR 225
           F++++ ++I   + +    +
Sbjct: 60  FDELLDVSINCARKLREKFK 79

>d2ba0d2 d.101.1.1 (D:154-252) Exosome complex exonuclease 1, ECX1 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 1, ECX1
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 55.1 bits (132), Expect = 8e-11
 Identities = 23/86 (26%), Positives = 43/86 (50%), Gaps = 3/86 (3%)

Query: 148 PMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILP---TLDKVTLLQMDAKLPTN 204
           PM+ ++TS + G  +   +LD    ED+ G  D+    L     ++ + LLQMD ++  +
Sbjct: 1   PMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMDGRMTRD 60

Query: 205 TFEDVMQLAIEGCKAVANYIREVLLE 230
             +  ++LA +G   +    RE +L 
Sbjct: 61  EVKQAIELAKKGALQIYEMQREAILR 86

>d2nn6d2 d.101.1.1 (D:147-235) Exosome complex exonuclease RRP46 {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP46
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (131), Expect = 1e-10
 Identities = 13/82 (15%), Positives = 27/82 (32%), Gaps = 1/82 (1%)

Query: 148 PMRDIVTSCSAG-YLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTF 206
           PMR +    +     + T +LD    ++      +T  +     K+ +            
Sbjct: 1   PMRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFALDSVERKLLMSSTKGLYSDTEL 60

Query: 207 EDVMQLAIEGCKAVANYIREVL 228
           +  +  A    + V  + RE L
Sbjct: 61  QQCLAAAQAASQHVFRFYRESL 82

>d1udsa2 d.101.1.1 (A:151-255) Ribonuclease PH, domain 2 {Aquifex aeolicus [TaxId: 63363]} Length = 105

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Aquifex aeolicus [TaxId: 63363]

 Score = 51.9 bits (124), Expect = 2e-09
 Identities = 23/92 (25%), Positives = 42/92 (45%), Gaps = 2/92 (2%)

Query: 147 IPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILP--TLDKVTLLQMDAKLPTN 204
            P++D V + S G +N   LLDLN+ EDSA   D+ V       L +V  +  +     +
Sbjct: 3   TPIKDFVAAVSVGIVNDRILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYSFTKD 62

Query: 205 TFEDVMQLAIEGCKAVANYIREVLLENTKQLE 236
               ++ LA +G   +    +++ +    + E
Sbjct: 63  ELIKMLDLAQKGINELIELQKKLYVIQDGKWE 94

>d2je6a2 d.101.1.1 (A:192-275) Exosome complex exonuclease 2, ECX2 {Sulfolobus solfataricus [TaxId: 2287]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 2, ECX2
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 49.2 bits (117), Expect = 8e-09
 Identities = 11/82 (13%), Positives = 29/82 (35%), Gaps = 1/82 (1%)

Query: 148 PMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAK-LPTNTF 206
           P+   V + S   ++   ++D +  E+S     ++    P L  V + +     +     
Sbjct: 1   PLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSYTPDLKIVGIQKSGKGSMSLQDI 60

Query: 207 EDVMQLAIEGCKAVANYIREVL 228
           +     A      +   +++ L
Sbjct: 61  DQAENTARSTAVKLLEELKKHL 82

>d1r6la2 d.101.1.1 (A:152-239) Ribonuclease PH, domain 2 {Pseudomonas aeruginosa [TaxId: 287]} Length = 88

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]

 Score = 49.2 bits (117), Expect = 9e-09
 Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 4/88 (4%)

Query: 146 GIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAK---LP 202
           G P++ +V + S G     P+LDL+Y+EDSA   D+ V ++        +Q  A+     
Sbjct: 2   GNPLKQMVAAVSVGIYQGVPVLDLDYLEDSAAETDLNV-VMTDAGGFIEVQGTAEGAPFR 60

Query: 203 TNTFEDVMQLAIEGCKAVANYIREVLLE 230
                 +++LA +G + +    R  L E
Sbjct: 61  PAELNAMLELAQQGMQELFELQRAALAE 88

>d2nn6e2 d.101.1.1 (E:192-285) Exosome complex exonuclease RRP42 {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP42
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.4 bits (115), Expect = 2e-08
 Identities = 9/86 (10%), Positives = 32/86 (37%), Gaps = 3/86 (3%)

Query: 147 IPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPT--N 204
           + + ++    +   +    ++D    E++     + V +      VT ++   K      
Sbjct: 1   LSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSK-GVVTCMRKVGKGSLDPE 59

Query: 205 TFEDVMQLAIEGCKAVANYIREVLLE 230
           +  ++M+      K +   ++ V+ +
Sbjct: 60  SIFEMMETGKRVGKVLHASLQSVVHK 85

>d2nn6c2 d.101.1.1 (C:188-276) Exosome complex exonuclease RRP43 {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.9 bits (114), Expect = 3e-08
 Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 149 MRDIVTSCSAGYLNSTP-LLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA--KLPTNT 205
           +R    + S    + T  ++D    E+      +T+ +     K+  L       L    
Sbjct: 2   IRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEE-GKLCCLHKPGGSGLTGAK 60

Query: 206 FEDVMQLAIEGCKAVANYIREVL 228
            +D M  A+   K V   + EV+
Sbjct: 61  LQDCMSRAVTRHKEVKKLMDEVI 83

>d2nn6a2 d.101.1.1 (A:185-302) Exosome complex exonuclease RRP45 {Human (Homo sapiens) [TaxId: 9606]} Length = 118

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP45
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.8 bits (111), Expect = 1e-07
 Identities = 11/96 (11%), Positives = 29/96 (30%), Gaps = 5/96 (5%)

Query: 148 PMRDIVTSCSAGYLNS--TPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMD--AKLPT 203
            +  +    S  +       L+D N  E+      + + +     ++  +Q      L  
Sbjct: 2   SIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKH-REICTIQSSGGIMLLK 60

Query: 204 NTFEDVMQLAIEGCKAVANYIREVLLENTKQLECRR 239
           +      ++A      +   I + L  + K  +   
Sbjct: 61  DQVLRCSKIAGVKVAEITELILKALENDQKVRKEGG 96

>d1oysa2 d.101.1.1 (A:152-237) Ribonuclease PH, domain 2 {Bacillus subtilis [TaxId: 1423]} Length = 86

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]

 Score = 45.3 bits (107), Expect = 2e-07
 Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 5/86 (5%)

Query: 147 IPMRDIVTSCSAGYLN-STPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAK---LP 202
            P+ D + + S G       LLDLNY EDS+   D+ V +  +  +   LQ   +     
Sbjct: 2   NPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGS-GRFVELQGTGEEATFS 60

Query: 203 TNTFEDVMQLAIEGCKAVANYIREVL 228
                 ++ LA +G + + +  +EVL
Sbjct: 61  REDLNGLLGLAEKGIQELIDKQKEVL 86

>d1e3ha6 d.101.1.1 (A:483-578) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5 {Streptomyces antibioticus [TaxId: 1890]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
species: Streptomyces antibioticus [TaxId: 1890]

 Score = 39.0 bits (91), Expect = 5e-05
 Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 4/86 (4%)

Query: 145 AGIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTN 204
           AGI M  +++    G  +   L D+   ED+ G  D  V    T + VT LQ+D KL   
Sbjct: 4   AGIAM-GLISQEINGETHYVALTDILGAEDAFGDMDFKVA--GTKEFVTALQLDTKLDGI 60

Query: 205 TFEDVMQLAIEGCKAVANYIREVLLE 230
               V+  A++  +    +I +V++E
Sbjct: 61  PAS-VLAAALKQARDARLHILDVMME 85

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	241
d2ba0d1	144	Exosome complex exonuclease 1, ECX1 {Archaeoglobus	100.0
d2je6b1	148	Exosome complex exonuclease 1, ECX1 {Sulfolobus so	100.0
d2nn6b1	145	Exosome complex exonuclease RRP41 {Human (Homo sap	100.0
d1udsa1	149	Ribonuclease PH, domain 1 {Aquifex aeolicus [TaxId	100.0
d1r6la1	151	Ribonuclease PH, domain 1 {Pseudomonas aeruginosa	100.0
d1oysa1	151	Ribonuclease PH, domain 1 {Bacillus subtilis [TaxI	100.0
d2ba0g1	176	Exosome complex exonuclease 2,ECX2 {Archaeoglobus	99.98
d1e3ha3	137	Polynucleotide phosphorylase/guanosine pentaphosph	99.98
d2nn6c1	181	Exosome complex exonuclease RRP43 {Human (Homo sap	99.97
d2je6a1	191	Exosome complex exonuclease 2,ECX2 {Sulfolobus sol	99.97
d2nn6e1	187	Exosome complex exonuclease RRP42 {Human (Homo sap	99.97
d2nn6d1	122	Exosome complex exonuclease RRP46 {Human (Homo sap	99.97
d2nn6f1	147	Exosome complex exonuclease MTR3 {Human (Homo sapi	99.96
d2nn6a1	184	Exosome complex exonuclease RRP45 {Human (Homo sap	99.96
d1e3ha2	149	Polynucleotide phosphorylase/guanosine pentaphosph	99.89
d2nn6d2	89	Exosome complex exonuclease RRP46 {Human (Homo sap	99.74
d2nn6b2	90	Exosome complex exonuclease RRP41 {Human (Homo sap	99.73
d2je6b2	86	Exosome complex exonuclease 1, ECX1 {Sulfolobus so	99.69
d2nn6a2	118	Exosome complex exonuclease RRP45 {Human (Homo sap	99.67
d2nn6e2	94	Exosome complex exonuclease RRP42 {Human (Homo sap	99.66
d2je6a2	84	Exosome complex exonuclease 2, ECX2 {Sulfolobus so	99.65
d2ba0g2	79	Exosome complex exonuclease 2, ECX2 {Archaeoglobus	99.64
d2nn6c2	89	Exosome complex exonuclease RRP43 {Human (Homo sap	99.62
d2nn6f2	95	Exosome complex exonuclease MTR3 {Human (Homo sapi	99.58
d1r6la2	88	Ribonuclease PH, domain 2 {Pseudomonas aeruginosa	99.5
d2ba0d2	99	Exosome complex exonuclease 1, ECX1 {Archaeoglobus	99.49
d1oysa2	86	Ribonuclease PH, domain 2 {Bacillus subtilis [TaxI	99.26
d1udsa2	105	Ribonuclease PH, domain 2 {Aquifex aeolicus [TaxId	99.25
d1e3ha5	111	Polynucleotide phosphorylase/guanosine pentaphosph	97.9
d1e3ha6	96	Polynucleotide phosphorylase/guanosine pentaphosph	97.17

>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=9.4e-39  Score=246.28  Aligned_cols=143  Identities=53%  Similarity=0.851  Sum_probs=132.5

Q ss_pred             cCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccC
Q 026213            4 VSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRM   83 (241)
Q Consensus         4 ~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~   83 (241)
                      |+++|+|+|||.++|+|++++++|++++++|||+|++|+|+|+|+|++|.+.+.+..+.++++.+.+++++.|++++.+.
T Consensus         2 ~~~~g~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~   81 (144)
T d2ba0d1           2 LIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKAIIRYRYNMAPFSVEERK   81 (144)
T ss_dssp             CBCSSCBTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEEECCSGGGCCSSSCEEEEEEEECTTSSSSCC
T ss_pred             cccCCcCCCCCCCCCccCeEEEECCCCCCCceEEEEEcccceEEEEeccchhhhhhcccccceEEEEEEecCCccccccc
Confidence            56789999999999999999999999999999999999999999999999887666667889999999999999988765


Q ss_pred             CCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCC
Q 026213           84 RKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGI  147 (241)
Q Consensus        84 ~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gi  147 (241)
                      . +.++.++.+++++|+++++++++++.||+|.|+|+|+||++||++++||+||+++||+|+||
T Consensus        82 ~-~~~~~~~~~l~~~l~~~l~~~i~~~~~~~~~i~v~v~VL~~DG~~~~a~i~aa~lAL~daGI  144 (144)
T d2ba0d1          82 R-PGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACLNAASVALVDAGV  144 (144)
T ss_dssp             C-SSCCHHHHHHHHHHHHHHHTTBCGGGCTTEEEEEEEEEEECCTTHHHHHHHHHHHHHHHHTC
T ss_pred             c-cCCCchhhhhhhhhhhhhccccchhhcCCeEEEEEEEEEccCCCHHHHHHHHHHHHHHHcCC
Confidence            4 34667788999999999999999999999999999999999999999999999999999997

>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=1.7e-38  Score=245.99  Aligned_cols=145  Identities=48%  Similarity=0.850  Sum_probs=135.0

Q ss_pred             cccCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccc
Q 026213            2 EFVSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGD   81 (241)
Q Consensus         2 ~~~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~   81 (241)
                      .+|+++|+|+|||.++|+|++++++|+++++||||+|++|+|+|+|+|++|.|...+..+.++++.+.|+++++|+++..
T Consensus         4 ~~i~~~g~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~~~v~~~~~~~~~~~   83 (148)
T d2je6b1           4 KLILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTDE   83 (148)
T ss_dssp             CSBCTTSCBTTSCCTTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECSSGGGSCSSSCEEEEEEEECTTSSSS
T ss_pred             eEecCCCccCCCCCCCCccCeEEEECCCCCCCEEEEEEcCCccEEeecccCccccchhhcCCcceEEEEEEEeccccccc
Confidence            36899999999999999999999999999999999999999999999999998877777778999999999999999876


Q ss_pred             cCCCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCC
Q 026213           82 RMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGI  147 (241)
Q Consensus        82 ~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gi  147 (241)
                      +.. +.++.++.+++++|+++++++++++.||++.|+|+++||++||++++|++||+++||+|+||
T Consensus        84 ~~~-~~~~~~~~el~~~l~~~l~~~i~~~~~p~~~i~v~v~VL~~DG~~~~a~i~aa~~AL~daGI  148 (148)
T d2je6b1          84 RKN-PAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGI  148 (148)
T ss_dssp             CCC-SSCCHHHHHHHHHHHHHHHTTBCGGGSTTEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTC
T ss_pred             ccc-ccccchhHHHHHHHHHHhhccccHHHcCCEEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCC
Confidence            543 35677888999999999999999999999999999999999999999999999999999997

>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=2.8e-38  Score=243.87  Aligned_cols=144  Identities=60%  Similarity=0.977  Sum_probs=131.9

Q ss_pred             cCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCcccccc-ccCCCCceEEEEEEeecCCccccc
Q 026213            4 VSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNK-SQQMSDQALVRCEYSMANFSTGDR   82 (241)
Q Consensus         4 ~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~-~~~~~~~~~i~v~~~~~~~~~~~~   82 (241)
                      |+++|+|+|||.++|+|++++++|++++++|||+|++|+|+|+|+|++|.+.+.+ ....++++.++|+++++|+++..+
T Consensus         1 ~~e~g~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~~v~v~~~~~~~~~~~~   80 (145)
T d2nn6b1           1 LSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATFSTGER   80 (145)
T ss_dssp             CCBTTBCSSSSCTTSCCCEEEEESCSSSSSEEEEEEESSCEEEEEEEEEEECCSSSCCCCCSSCCEEEEEEECTTTSSSC
T ss_pred             CCCCCccCCCCCCCCccCeEEEECCCCCCCceEEEEeCCceEEEEEEeccccccchhhccccceeEEEEeeecCcccccc
Confidence            4679999999999999999999999999999999999999999999999866432 234578999999999999999877


Q ss_pred             CCCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCC
Q 026213           83 MRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGI  147 (241)
Q Consensus        83 ~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gi  147 (241)
                      ...+.++.++.+++++|+++|++++.++.||+|.|+|+++||++|||+++|++||+++||+|+||
T Consensus        81 ~~~~~~~~~~~~l~~~l~~~l~~~i~~~~~~~~~I~v~v~VL~~DG~l~~a~i~aa~lAL~daGI  145 (145)
T d2nn6b1          81 KRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGI  145 (145)
T ss_dssp             CCTTTSTHHHHHHHHHHHHHHHHTTCGGGCTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTCC
T ss_pred             cccCCCCchhhhHHHHHHHhhhcccchHhhCceeeEEEEEEEeCCCCHHHHHHHHHHHHHHHcCC
Confidence            66556677888999999999999999999999999999999999999999999999999999997

>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=3.6e-35  Score=227.32  Aligned_cols=140  Identities=29%  Similarity=0.372  Sum_probs=124.0

Q ss_pred             CCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCC----C
Q 026213           10 RLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR----K   85 (241)
Q Consensus        10 R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~----~   85 (241)
                      |+|||.++|+|++.+++|++++++|||+|++|+|+|+|+|++|.+.+. ....++++.+.+++.++|++......    .
T Consensus         1 R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~   79 (149)
T d1udsa1           1 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPN-WLKGKGQGWITAEYSMLPRATQQRTIRESVQ   79 (149)
T ss_dssp             CTTSCCTTCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEESCCCG-GGTTSSCCEEEEEEEECSEETTEECCCSSSS
T ss_pred             CCCCCCCCCccCeEEEeCCCCCCCEEEEEEECCCEEEEEEEeeccccc-cccCCCceeEEeeecchhhcccccccccccc
Confidence            899999999999999999999999999999999999999999865432 34567899999999999987654322    2


Q ss_pred             CCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCC
Q 026213           86 PKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMR  150 (241)
Q Consensus        86 ~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~  150 (241)
                      +.+......++.++++.+++++.++.||+|.|+|+|+||++|||+++|++||+++||+|+||||+
T Consensus        80 ~~~~~~~~~~~~~l~~~l~~~i~l~~~~~~~i~v~v~VL~~DG~l~da~~~A~~~AL~dagipm~  144 (149)
T d1udsa1          80 GRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQADGGTATAAITGAFVAVADAIIKLH  144 (149)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHBCGGGSCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccchhHHHHHHHhhhhheehhhhcCCceEEEEEEEEccCCCHHHHHHHHHHHHHHHhChHHH
Confidence            33455667889999999999999999999999999999999999999999999999999999986

>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=2.9e-34  Score=222.55  Aligned_cols=141  Identities=33%  Similarity=0.442  Sum_probs=121.0

Q ss_pred             CCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCCC---
Q 026213            9 LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMRK---   85 (241)
Q Consensus         9 ~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~~---   85 (241)
                      -|+|||+++|+|++++++|+++++||||+|++|+|+|+|+|++|.+.+ +..+.++++.+.+++.++|++.......   
T Consensus         2 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~   80 (151)
T d1r6la1           2 NRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVP-RFLKGQGQGWLTAEYGMLPRSTGERNQREAS   80 (151)
T ss_dssp             CCTTCCCTTCCCCEEEESSCSSSSSEEEEEEETTEEEEEEEEEEESCS-SCCC---CCEEEEEEEECTTSSSSCCCCHHH
T ss_pred             CCCCCCCCCCccCeEEEeCCCCCCCEEEEEEeCCCEEEEEEEeccccc-ccccCCCceeEEEEEEecCccccccccccCC
Confidence            499999999999999999999999999999999999999999986553 2345578999999999999887654322   


Q ss_pred             -CCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCC
Q 026213           86 -PKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMR  150 (241)
Q Consensus        86 -~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~  150 (241)
                       +.....+.++..++.+.+.+.+.++.||+|+|+|+++||++|||+++|+++|+++||+|+||||+
T Consensus        81 ~~~~~~~~~~~~~~l~~~~~~~~~l~~~~~~~i~v~v~VL~~DG~~~da~~~Aa~~AL~dagip~~  146 (151)
T d1r6la1          81 RGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADGGTRTASITGATVALIDALAVLK  146 (151)
T ss_dssp             HTSCCHHHHHHHHHHHHHHHHTBCGGGTCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CccccccchhHHHHHHhhhhhccchhhhCceEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhcHHHH
Confidence             12334556788899999999999999999999999999999999999999999999999999984

>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=100.00  E-value=4.8e-34  Score=221.37  Aligned_cols=139  Identities=31%  Similarity=0.370  Sum_probs=109.0

Q ss_pred             CCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCC----
Q 026213            9 LRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR----   84 (241)
Q Consensus         9 ~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~----   84 (241)
                      +|+|||.++|+|++++++|+++++||||+|++|+|+|+|+|++|.+. .+....++++.+.+++.+.|++...+..    
T Consensus         1 lR~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~   79 (151)
T d1oysa1           1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRV-PPFLRGGGKGWITAEYSMLPQATNQQTIQESS   79 (151)
T ss_dssp             CCTTSCCTTCCCCEEEECC-----CCCEEEEETTEEEEEEEEEESCC-CGGGTTSCCCEEEEEEEC--------------
T ss_pred             CCCCCCCCCCccCeEEEeCCCCCCCEEEEEEEcCCEEEEEEEecccc-cccccccccceeeeeeeecccccccccccccc
Confidence            69999999999999999999999999999999999999999976433 3455668899999999998888765422    


Q ss_pred             CCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCC
Q 026213           85 KPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIP  148 (241)
Q Consensus        85 ~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip  148 (241)
                      .+.+...+.+++.++++.+++++.++.||+|+|+|+++||++|||+++|++||+++||+|+.++
T Consensus        80 ~~~~~~~~~~~~~~l~~~l~~~i~l~~~~~~~i~v~v~VL~~DG~l~~a~i~Aa~~AL~dA~~~  143 (151)
T d1oysa1          80 KGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGK  143 (151)
T ss_dssp             -----CHHHHHHHHHHHHHHHTBCHHHHCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcccchhhHHhHHHHHHhhhhhhhhhhccceEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHH
Confidence            2334567778999999999999999999999999999999999999999999999999998654

>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=99.98  E-value=4.7e-32  Score=215.23  Aligned_cols=145  Identities=20%  Similarity=0.253  Sum_probs=123.8

Q ss_pred             CCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCC
Q 026213            5 SPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR   84 (241)
Q Consensus         5 ~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~   84 (241)
                      +++|+|+|||.++|+|++++++|++++++|||+|++|+|+|+|+|+++  ...|....+++|.+.+++.+.|++...+..
T Consensus        16 l~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~~--~~~p~~~~~~~g~~~~~v~~~~~~~~~~~~   93 (176)
T d2ba0g1          16 LRDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQ--PGEPYPDTPDRGVIIVNAELVPLASPTFEP   93 (176)
T ss_dssp             HTTTCCTTCCCTTCCCCEEEEECCCTTSSEEEEEEETTEEEEEEEEEE--EECCCTTCTTCCEEEEEEECCTTTCTTSCS
T ss_pred             HHhCCCCCCCCCCCccCeEEEeCccCCCCeEEEEEeCCcEEEEEEecc--ccccccccCCCceeeeeeEeccccCccccC
Confidence            468999999999999999999999999999999999999999999974  334455678899999999999988776543


Q ss_pred             CCCCCchhHHHHHHHHHHHHHh--hccCC------CCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCCe
Q 026213           85 KPKGDRRSTEISLVIRQTMEAC--ILTHL------MPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRDI  152 (241)
Q Consensus        85 ~~~~~~~~~~l~~~l~~~l~~~--i~l~~------~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~~  152 (241)
                       +.++.....+++++++++.+.  ++++.      ++.|.|+|+++||++|||+++|+++|+++||+|+|||+..+
T Consensus        94 -~~~~~~~~~~~~~l~~~~~~~~~i~~e~L~i~~~~~~~~i~i~v~VL~~DG~l~dA~~~A~~~AL~da~iP~~~~  168 (176)
T d2ba0g1          94 -GPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERF  168 (176)
T ss_dssp             -SSCCHHHHHHHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHTTCEECTGGG
T ss_pred             -CCCCchhHHHHHHHHHhhccccccchhhccCCCCCceEEEEEEEEEEeCCCCHHHHHHHHHHHHHHHcCCCcEEe
Confidence             356677788999999998764  33332      34599999999999999999999999999999999998654

>d1e3ha3 d.14.1.4 (A:346-482) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 {Streptomyces antibioticus [TaxId: 1890]}

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

Probab=99.98  E-value=7.9e-32  Score=205.51  Aligned_cols=134  Identities=22%  Similarity=0.332  Sum_probs=118.0

Q ss_pred             CCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccC---CCCceEEEEEEeecCCcccccCCCCCCCchhH
Q 026213           17 TEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQ---MSDQALVRCEYSMANFSTGDRMRKPKGDRRST   93 (241)
Q Consensus        17 ~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~---~~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~~   93 (241)
                      .|+|++++++|+++++||||+|++|+|+|+|+|++|.+.+.+..+   ......+.+++...|+.+..+++.+.++.++.
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            489999999999999999999999999999999998755432211   12345677888888988877766677888999


Q ss_pred             HHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCC
Q 026213           94 EISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMR  150 (241)
Q Consensus        94 ~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~  150 (241)
                      ++++.+.+++++++.++.||+|+|+|+++||++||++++|++||+++||+|+||||+
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            999999999999999999999999999999999999999999999999999999995

>d2nn6c1 d.14.1.4 (C:7-187) Exosome complex exonuclease RRP43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=5.5e-31  Score=209.49  Aligned_cols=143  Identities=24%  Similarity=0.280  Sum_probs=119.3

Q ss_pred             cCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccC
Q 026213            4 VSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRM   83 (241)
Q Consensus         4 ~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~   83 (241)
                      ++++|+|+|||.++|+|++++++|++++++|||++++|+|+|+|+|+++...  +....++++.+.+++...+++.....
T Consensus        11 ~l~~giR~DGR~~~e~R~~~i~~g~l~~a~GSa~v~~G~T~v~~~v~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (181)
T d2nn6c1          11 FLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAA--PSTDAPDKGYVVPNVDLPPLCSSRFR   88 (181)
T ss_dssp             HHHTSCCTTSCCSCCCCSCCEEETCCSSSSEEEEEEETTEEEEEEEEEEECC--CCSSSTTCCCCEEEEECCSSSCTTSC
T ss_pred             HHhcCCCCCCcCCCCccCeEEEeCCcCCCCeEEEEEeCCcEEEEEEeccccc--cccccCCCceeeeeeeeecccccccc
Confidence            3468999999999999999999999999999999999999999999996543  34455677888888887777665432


Q ss_pred             CCCCCCchhHHHHHHHHHHHHHh--------hccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCC
Q 026213           84 RKPKGDRRSTEISLVIRQTMEAC--------ILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPM  149 (241)
Q Consensus        84 ~~~~~~~~~~~l~~~l~~~l~~~--------i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~  149 (241)
                       .+.+......+.+++++.+.+.        +.++.+|.|.|+|+++||++|||++||+++|+++||+|++||+
T Consensus        89 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~~~~~~i~i~v~vl~~DG~l~da~~~A~~~AL~d~~iP~  161 (181)
T d2nn6c1          89 -SGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPE  161 (181)
T ss_dssp             -SSSCCHHHHHHHHHHHHHHHHHCCSCHHHHCSSBTTBCEEEEEEEEESSCCSCTTHHHHHHHHHHHHTCCCCC
T ss_pred             -ccCCCchhhhhHHHHHHHHHhhhhhhhhhccccCCcceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCCe
Confidence             2344556667888888887654        2345678899999999999999999999999999999999996

>d2je6a1 d.14.1.4 (A:1-191) Exosome complex exonuclease 2,ECX2 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease 2,ECX2
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.97  E-value=9.1e-31  Score=210.33  Aligned_cols=144  Identities=22%  Similarity=0.244  Sum_probs=121.5

Q ss_pred             cCCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccC
Q 026213            4 VSPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRM   83 (241)
Q Consensus         4 ~~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~   83 (241)
                      ++++|+|+|||.++|+|++++++|++++++|||+|++|+|+|+|+|++|...  |....++.+.+.+++...+++...+.
T Consensus        22 ~l~~giR~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~a~V~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (191)
T d2je6a1          22 LFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDK--PYEDTPNQGNLIVNVELLPLAYETFE   99 (191)
T ss_dssp             TGGGTBCTTSCBTTCCCCEEEEETCSTTSSEEEEEEETTEEEEEEEEEEEEC--CCTTCTTCCEEEEEEEECTTSCTTCC
T ss_pred             HHhcCCCCCCcCCCCccCeEEEECCccCcCceEEEEcCCceEEEEEEecccC--chhccCccCccccccccccccccccc
Confidence            5679999999999999999999999999999999999999999999997643  34456788999999988887765433


Q ss_pred             CCCCCCchhHHHHHHHHHHHHHhhcc--C------CCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCC
Q 026213           84 RKPKGDRRSTEISLVIRQTMEACILT--H------LMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMR  150 (241)
Q Consensus        84 ~~~~~~~~~~~l~~~l~~~l~~~i~l--~------~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~  150 (241)
                       .+.+......++++|++.+.+...+  +      .++.|.|+|+++||++|||++||+++|+++||+|+|||+.
T Consensus       100 -~~~~~~~~~~l~~~l~~~~~~~~~id~~~l~i~~~~~~w~I~v~v~VL~~DG~l~dA~~~A~~~AL~da~iP~v  173 (191)
T d2je6a1         100 -PGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKV  173 (191)
T ss_dssp             -CSSCCHHHHHHHHHHHHHHHHTTCSCGGGGEEETTTEEEEEEEEEEEEECCSCHHHHHHHHHHHHHHTCEEEEE
T ss_pred             -cccCCcchhHHHHHHHHhhcchhhcccccccccCccccEEEEEEEEEEcCCCCHHHHHHHHHHHHHHHcCCCeE
Confidence             2345566778899999998765332  2      2446999999999999999999999999999999999953

>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=99.97  E-value=2.8e-31  Score=212.68  Aligned_cols=142  Identities=21%  Similarity=0.214  Sum_probs=121.6

Q ss_pred             CCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCC
Q 026213            5 SPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR   84 (241)
Q Consensus         5 ~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~   84 (241)
                      +++|+|+|||.++|+|++.+++|++++++|||+|++|+|+|+|+|++|...  |....++++.+.+++++.|+++.....
T Consensus        14 l~~~iR~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~~~~~--~~~~~~~~g~~~~~v~~~~~~~~~~~~   91 (187)
T d2nn6e1          14 VQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGT--PKLEKPNEGYLEFFVDCSASATPEFEG   91 (187)
T ss_dssp             HHTTCCSSSCCSSCCCCCEEEECCCTTSSSEEEEEETTEEEEEECCCCCSC--CCSSSCSSCCEEEECCCCTTTCSSCCT
T ss_pred             HhhCCCCCCcCCCCccCeEEEeCccCCCCceEEEEeCCceEEEEEEecccc--ccccccccceeeeeeeeccccccCcCC
Confidence            358999999999999999999999999999999999999999999997543  445567889999999988888765432


Q ss_pred             CCCCCchhHHHHHHHHHHHHHhhcc--C------CCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCC
Q 026213           85 KPKGDRRSTEISLVIRQTMEACILT--H------LMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPM  149 (241)
Q Consensus        85 ~~~~~~~~~~l~~~l~~~l~~~i~l--~------~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~  149 (241)
                       +.++....++++++++.|++...+  +      .++.|.|+|+++||++||++++|+++|+++||.|+++|.
T Consensus        92 -~~~~~~~~~ls~~l~~~l~~~~~~d~~~L~i~~~~~~w~i~v~v~vL~~DG~~~da~~~A~~~AL~d~~iP~  163 (187)
T d2nn6e1          92 -RGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPR  163 (187)
T ss_dssp             -TSTHHHHHHHHHHHHHHHHHSCCSCSSSSCSSTTTCCCCEEEEEEECCCCSSHHHHHHHHHHHTTTTCCCCE
T ss_pred             -CCcchHHHHHHHHHHHHhccccccchhhheecCCCccEEEEEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCE
Confidence             345566778899999999875432  2      356799999999999999999999999999999999994

>d2nn6d1 d.14.1.4 (D:25-146) Exosome complex exonuclease RRP46 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP46
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=2.8e-30  Score=193.03  Aligned_cols=121  Identities=34%  Similarity=0.515  Sum_probs=105.1

Q ss_pred             CCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCCCCCCCchhHHHH
Q 026213           17 TEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMRKPKGDRRSTEIS   96 (241)
Q Consensus        17 ~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~~~l~   96 (241)
                      .|+|++.+++|+++++||||+|++|+|+|+|+|+||.+.+. ..+.++++.++|+++...         +.++.++++++
T Consensus         2 ~elR~i~~~~gvl~~adGSa~~~~G~T~Vi~~V~gP~e~~~-~~~~~~~~~~~v~~~~~~---------~~~~~~~~~~~   71 (122)
T d2nn6d1           2 CSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKV-SKEIFNKATLEVILRPKI---------GLPGVAEKSRE   71 (122)
T ss_dssp             CCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECC-------CCEEEEEEEECSS---------SCCCHHHHHHH
T ss_pred             CccceEEEEECCCCCCCeEEEEEECCcEEEEEEEecccccc-hhhCcCCCceEEEeeeec---------CCCCchhhHHH
Confidence            48999999999999999999999999999999999987654 345567888888886321         24556788999


Q ss_pred             HHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCC
Q 026213           97 LVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGI  147 (241)
Q Consensus        97 ~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gi  147 (241)
                      ++|+++|++++.++.||+|+|+|+++|+++||++++|++||+++||+|+||
T Consensus        72 ~~l~~~l~~~i~~~~~p~~~i~i~v~Vl~~DG~~~~a~ina~~lAL~dagI  122 (122)
T d2nn6d1          72 RLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGV  122 (122)
T ss_dssp             HHHHHHHHHHCGGGCSSSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHhhhhcccchhhcCCeEEEEEEEEEcCCCChhHHHHHHHHHHHHHcCC
Confidence            999999999999999999999999999999999999999999999999997

>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=99.96  E-value=4.2e-30  Score=197.78  Aligned_cols=135  Identities=32%  Similarity=0.553  Sum_probs=115.3

Q ss_pred             CCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCcccccccc-----------CCCCceEEEEEEeecCCcccc
Q 026213           13 GRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQ-----------QMSDQALVRCEYSMANFSTGD   81 (241)
Q Consensus        13 GR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~-----------~~~~~~~i~v~~~~~~~~~~~   81 (241)
                      .|+++|+|++++++|++++++|||+|++|+|+|+|+|++|.+.+.+..           ..+..+.+.+++.+.|+++..
T Consensus         2 ~R~~~e~R~i~i~~gvi~~a~GSa~v~~G~T~V~~~V~gp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (147)
T d2nn6f1           2 TRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAALRGRLLCDFRRAPFAGRR   81 (147)
T ss_dssp             CCCSSCCCCCCCCCSCCSSSSEEECCCSSSCEEEEEEEEEECC-------------------CBCEEEEEEEECTTSSSS
T ss_pred             CCCCCCccceEEEeCCCCCCCEEEEEEECCeEEEEEEeccccccccccCCccccccccccccccceeEEEEEecCCcccc
Confidence            599999999999999999999999999999999999999886543211           123457888999999998776


Q ss_pred             cCCCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCC
Q 026213           82 RMRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIP  148 (241)
Q Consensus        82 ~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip  148 (241)
                      +.. +.+..++.+++.++.+.+++++.++.||+|.|+|+++||++|||+++||+||+++||+|+||+
T Consensus        82 ~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~i~v~v~Vl~~DG~l~~a~i~A~~~AL~daGIe  147 (147)
T d2nn6f1          82 RRA-PPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVE  147 (147)
T ss_dssp             CCC-SCCHHHHHHHHHHHHHHHTTTBCSTTSBTCEEEEEEEEEECCSSHHHHHHHHHHHHHHHHCCC
T ss_pred             ccc-cCCccchhhhhhhhhhcccccccccccCCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHhCCC
Confidence            543 344566778999999999999999999999999999999999999999999999999999985

>d2nn6a1 d.14.1.4 (A:1-184) Exosome complex exonuclease RRP45 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP45
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=3.3e-29  Score=200.00  Aligned_cols=141  Identities=19%  Similarity=0.232  Sum_probs=117.6

Q ss_pred             CCCCCCCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEeecCCcccccCC
Q 026213            5 SPEGLRLDGRRPTEMRQLRAEIGNVAKADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYSMANFSTGDRMR   84 (241)
Q Consensus         5 ~~~~~R~DGR~~~e~R~i~i~~~~l~~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~   84 (241)
                      +++|+|+|||+++|+|++.+++|   .++|||+|++|+|+|+|+|+++...  |....++++.+.+++.+.++++.... 
T Consensus        18 l~~~~R~DGR~~~e~R~~~i~~g---~a~GSa~v~~G~T~V~~~V~~~~~~--p~~~~~~~g~~~~~v~~~~~~~~~~~-   91 (184)
T d2nn6a1          18 IEEKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVS--PKLNRATEGILFFNLELSQMAAPAFE-   91 (184)
T ss_dssp             HHTTCCTTSCCTTCCCCCEEEEC---SSTTEEEEESSSCEEEEEECCEEEC--CCSTTTTSCCEEEEEEECTTTCSSCC-
T ss_pred             HhhCcCCCCCCCCCcCCeEEEec---CCCCEEEEEeCCCEEEEEEEecccc--ccccCCCccceeEEEEeccccCcccc-
Confidence            35799999999999999999998   5899999999999999999996533  34456888999999998888765443 


Q ss_pred             CCCCCchhHHHHHHHHHHHHHhhc--cC------CCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCCCCC
Q 026213           85 KPKGDRRSTEISLVIRQTMEACIL--TH------LMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIPMRD  151 (241)
Q Consensus        85 ~~~~~~~~~~l~~~l~~~l~~~i~--l~------~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip~~~  151 (241)
                      .+.++.++..++++|++.+.....  ++      .++.|.|+|+++||++|||++||+++|+++||+|+++|...
T Consensus        92 ~~~~~~~~~~l~~~l~~~~~~~~~~d~~~L~i~~~~~~w~i~i~v~VL~~DG~~~da~~~a~~~AL~~~~iP~v~  166 (184)
T d2nn6a1          92 PGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVS  166 (184)
T ss_dssp             SSSTHHHHTHHHHHHHHHHHHHTCBCSSSSCSBTTTBEEEEEEEEEECSCCSCCHHHHHHHHHHHHHHCCCCCCB
T ss_pred             cCCCCchhHHHHHHHHhhhhhhhhhhhhhhccccccCcEEEEEEEEEECCCCCHHHHHHHHHHHHHHhhCCCeEE
Confidence            234556677889999999887533  33      23469999999999999999999999999999999999644

>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=99.89  E-value=6.6e-23  Score=157.44  Aligned_cols=136  Identities=20%  Similarity=0.191  Sum_probs=108.6

Q ss_pred             CCCCCCCCCCCcceEEEeCCCC-CCceeEEEEeCCeEEEEEEEcCccccccccCCCCceEEEEEEe--ecC---Cccccc
Q 026213            9 LRLDGRRPTEMRQLRAEIGNVA-KADGSAVFEMGNTKVIAAVYGPREVQNKSQQMSDQALVRCEYS--MAN---FSTGDR   82 (241)
Q Consensus         9 ~R~DGR~~~e~R~i~i~~~~l~-~a~GSa~v~~G~T~Vi~~V~~p~e~~~~~~~~~~~~~i~v~~~--~~~---~~~~~~   82 (241)
                      .+.|+|.+.+ |++++++|.+. +|||||++++|+|+|+|+++.+.+...   ...+...+.+.+.  +.+   +.++..
T Consensus         8 ~~~~~~~~~~-R~i~ie~G~lakqA~GSalv~~G~T~vl~ta~~~~~~~~---~~~~~~~~~v~~~~~~~~~~~~~~~~~   83 (149)
T d1e3ha2           8 AVIDNGAFGT-RTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPK---DQLDFFPLTVDVEERMYAAGKIPGSFF   83 (149)
T ss_dssp             EEEECGGGCE-EEEEEEESSSCTTSSEEEEEEETTTEEEEEEEEECSSCC---TTCSSCCEEEEEEECGGGGTCCCCSTT
T ss_pred             EEEeCCcCCC-cEEEEEeCcccccCCceEEEEECCcEEEEEeeecccccc---cccccCCceeEEEEecccccccccccc
Confidence            4678887777 99999999995 799999999999999999987543322   1223344444443  322   223334


Q ss_pred             CCCCCCCchhHHHHHHHHHHHHHhhccCCCCccEEEEEEEEEeCCCchHhHHHHHHHHHHHhCCCC
Q 026213           83 MRKPKGDRRSTEISLVIRQTMEACILTHLMPRSQIDIFVQVLQADGGTRSACINAATLALQDAGIP  148 (241)
Q Consensus        83 ~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~i~i~v~il~~dG~~l~a~i~a~~~AL~~~gip  148 (241)
                      ++.+++++++.+.+++|++.|++++..+.++..+|.++|.+++.||+...+++||+++||+++|||
T Consensus        84 rre~~~~~reil~~rlidR~Lrpl~p~~~~~~~qI~~~vl~~d~d~~~~~aai~aAs~AL~~agIP  149 (149)
T d1e3ha2          84 RREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLP  149 (149)
T ss_dssp             SSCCSCCHHHHHHHHHHHHHHHHHBCTTBCSCEEEEEEEEECCTTSCCHHHHHHHHHHHHHHTTCS
T ss_pred             ccccccchHHHHHHHHHHHHHHhhccccCCCceEEEEEEEEeCCCCChHHHHHHHHHHHHHhcCCC
Confidence            455678999999999999999999998888888999999999999999999999999999999998

>d2nn6d2 d.101.1.1 (D:147-235) Exosome complex exonuclease RRP46 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP46
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=4e-18  Score=119.32  Aligned_cols=87  Identities=15%  Similarity=0.212  Sum_probs=82.8

Q ss_pred             CCCCeeEEEEEeee-CCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          148 PMRDIVTSCSAGYL-NSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIRE  226 (241)
Q Consensus       148 p~~~~~~~vs~~~~-~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~  226 (241)
                      ||+++++|+++|+. +|.+++|||..||..+.+.++++++++.++++.++..|+++++++.++++.|.++|.+|++++++
T Consensus         1 Pm~~~v~av~~~~~~dg~~vlDpt~~Ee~~~~~~~~~a~~~~~~~i~~~~~~g~~s~~~~~~~l~~a~~~~~~I~~~~r~   80 (89)
T d2nn6d2           1 PMRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFALDSVERKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYRE   80 (89)
T ss_dssp             CCSSCEEEEEEEECTTCCEEESCCHHHHHHCSEEEEEEEETTTCCCCEEEEEESCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCEeEEEEEEEcCCceeeCCCHHHHhhcceEEEEEEEcCCCeEEEEeecCCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999988 67999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             HHHHHHHH
Q 026213          227 VLLENTKQ  234 (241)
Q Consensus       227 ~l~~~~~~  234 (241)
                      .|+++.+|
T Consensus        81 ~l~k~~~k   88 (89)
T d2nn6d2          81 SLQRRYSK   88 (89)
T ss_dssp             HHHHHTCC
T ss_pred             HHHHHhcC
Confidence            99988765

>d2nn6b2 d.101.1.1 (B:151-240) Exosome complex exonuclease RRP41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=9.1e-18  Score=117.71  Aligned_cols=87  Identities=37%  Similarity=0.739  Sum_probs=84.4

Q ss_pred             CCCCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          148 PMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREV  227 (241)
Q Consensus       148 p~~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~  227 (241)
                      ||+++++|+++|++++.+++|||..|+..+.+.++|+++++.++|++++.+|.++++++.++++.|.++|++++++++++
T Consensus         1 Pm~d~V~avs~g~~~~~~llDp~~~E~~~~~~~l~va~~~~~~~I~~~~~~g~~~~~~~~~~l~~a~~~~~~i~~~~~~~   80 (90)
T d2nn6b2           1 PMRDFVCACSAGFVDGTALADLSHVEEAAGGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRV   80 (90)
T ss_dssp             CCSSCCEEEEEEEETTEEEESCCHHHHTSSCCCEEEEEETTTTEEEEEEECSCCBTTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCeEEEEEEEECCEEeeCCccccccccccceEEEEEecCCCEEEEEEecccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHH
Q 026213          228 LLENTKQ  234 (241)
Q Consensus       228 l~~~~~~  234 (241)
                      ++++.++
T Consensus        81 l~~~~~e   87 (90)
T d2nn6b2          81 VRQHVRE   87 (90)
T ss_dssp             HHHHHHH
T ss_pred             HHhhhhh
Confidence            9998875

>d2je6b2 d.101.1.1 (B:156-241) Exosome complex exonuclease 1, ECX1 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 1, ECX1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.69  E-value=5.5e-17  Score=112.70  Aligned_cols=83  Identities=31%  Similarity=0.606  Sum_probs=80.2

Q ss_pred             CCCCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeecCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          148 PMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKLPTNTFEDVMQLAIEGCKAVANYIREV  227 (241)
Q Consensus       148 p~~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i~~~  227 (241)
                      ||+++++|+++|++++.+++|||..|++.+...++|+++++.++|+.++.+|.++++++.++++.|.++|.+|+++++++
T Consensus         1 Pm~d~V~avsvg~~d~~~llDp~~~E~~~~~~~l~va~~~~~~~i~~~~~~g~~~~~~~~~~l~~a~~~~~~I~~~~~e~   80 (86)
T d2je6b2           1 PMRDLIAGVAVGKADGVIILDLNETEAMWGEADMPIAMMPSLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREA   80 (86)
T ss_dssp             CBSSCCEEEEEEEETTEEEESCCHHHHHHSSEEEEEEEEGGGTEEEEEEEEECBCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCeEEEEEEEECCEEEEecchhhhhcCceeEEEEEeCCCCeEEEEeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999999999999999999999999888899999999999999999999999999999999999999


Q ss_pred             HHH
Q 026213          228 LLE  230 (241)
Q Consensus       228 l~~  230 (241)
                      |++
T Consensus        81 l~~   83 (86)
T d2je6b2          81 LKS   83 (86)
T ss_dssp             HHG
T ss_pred             HHh
Confidence            985

>d2nn6a2 d.101.1.1 (A:185-302) Exosome complex exonuclease RRP45 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP45
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=2.8e-16  Score=115.35  Aligned_cols=91  Identities=12%  Similarity=0.123  Sum_probs=82.6

Q ss_pred             CCCCCeeEEEEEeeeC--CeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee--cCCHHHHHHHHHHHHHHHHHHHH
Q 026213          147 IPMRDIVTSCSAGYLN--STPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA--KLPTNTFEDVMQLAIEGCKAVAN  222 (241)
Q Consensus       147 ip~~~~~~~vs~~~~~--~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g--~~~~~~l~~~l~~a~~~~~~i~~  222 (241)
                      ++++|+|+++||++++  +.+|+|||..||..+++.++|+++ ..++|+.+++.|  .++++++.+|++.|.++++++++
T Consensus         1 L~i~h~Pi~vT~~~~~~g~~~lvDPt~~EE~~~~~~ltv~~n-~~gei~~l~k~Gg~~l~~~~l~~~~~~A~~~~~el~~   79 (118)
T d2nn6a2           1 LSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMN-KHREICTIQSSGGIMLLKDQVLRCSKIAGVKVAEITE   79 (118)
T ss_dssp             CCBCCCEEEEEEEECTTTSSEEESCCHHHHHHCSCEEEEEEE-TTTEEEEEEEESCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcCceEEEEEEEEEecCCeEEECCCHHHHhCCCCcEEEEEe-CCCcEEEEEecCCcccCHHHHHHHHHHHHHHHHHHHH
Confidence            4789999999999985  578999999999999999999885 678999999864  69999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhh
Q 026213          223 YIREVLLENTKQLECR  238 (241)
Q Consensus       223 ~i~~~l~~~~~~~~~~  238 (241)
                      .++++|+++.+++-..
T Consensus        80 ~i~~aLk~~~~~R~~~   95 (118)
T d2nn6a2          80 LILKALENDQKVRKEG   95 (118)
T ss_dssp             HHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhhhhh
Confidence            9999999999888654

>d2nn6e2 d.101.1.1 (E:192-285) Exosome complex exonuclease RRP42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=4.5e-17  Score=114.96  Aligned_cols=89  Identities=10%  Similarity=0.132  Sum_probs=80.6

Q ss_pred             CCCCCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee--cCCHHHHHHHHHHHHHHHHHHHHHH
Q 026213          147 IPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA--KLPTNTFEDVMQLAIEGCKAVANYI  224 (241)
Q Consensus       147 ip~~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g--~~~~~~l~~~l~~a~~~~~~i~~~i  224 (241)
                      ++++++|+++|++++++.+|+|||.+||..+++.++|++ +..|+|+.+++.|  +++++++.+|++.|.+.++++++.+
T Consensus         1 L~i~~~Pv~vT~~~i~~~~lvDpt~~EE~~~~~~l~v~~-~~~g~i~~l~k~G~~~l~~~~i~~~i~~A~~~~~el~~~l   79 (94)
T d2nn6e2           1 LSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSV-TSKGVVTCMRKVGKGSLDPESIFEMMETGKRVGKVLHASL   79 (94)
T ss_dssp             CCCTTCCCCEEEEESSSSEESSCCHHHHTSCSEEEEECC-CSSSCCCEEEEEESSCBCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcCceEEEEEEEEECCEEEECCCHHHHhccCceEEEEE-cCCCcEEEEEecCCCccCHHHHHHHHHHHHHHHHHHHHHH
Confidence            478899999999999999999999999999999999986 5679999999865  5899999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 026213          225 REVLLENTKQLE  236 (241)
Q Consensus       225 ~~~l~~~~~~~~  236 (241)
                      +++|++..+.+-
T Consensus        80 ~~~L~~~e~~~~   91 (94)
T d2nn6e2          80 QSVVHKEESLGP   91 (94)
T ss_dssp             HHHHHHHHC-CC
T ss_pred             HHHHHHHhhccc
Confidence            999988776543

>d2je6a2 d.101.1.1 (A:192-275) Exosome complex exonuclease 2, ECX2 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 2, ECX2
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.65  E-value=3.6e-16  Score=108.00  Aligned_cols=80  Identities=13%  Similarity=0.136  Sum_probs=74.7

Q ss_pred             CCCCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee--cCCHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          148 PMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA--KLPTNTFEDVMQLAIEGCKAVANYIR  225 (241)
Q Consensus       148 p~~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g--~~~~~~l~~~l~~a~~~~~~i~~~i~  225 (241)
                      |+++.|+++|++++++.+|+|||.+||..+++.++|+++ .+++++.+++.|  .++++++.++++.|.+.++++++.++
T Consensus         1 P~~~~~~~vt~~~i~~~~lvDpt~~EE~~~~~~l~v~~~-~~g~i~~~~k~g~~~~~~~~i~~~i~~A~~~~~~l~~~l~   79 (84)
T d2je6a2           1 PLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSYT-PDLKIVGIQKSGKGSMSLQDIDQAENTARSTAVKLLEELK   79 (84)
T ss_dssp             CCSCCCEEEEEEEETTEEEESCCHHHHHHCSEEEEEEEC-TTCCEEEEEEESSSCEEHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCeEEEEEEEECCEEEecCCHHHHHhcCCceeeeec-CCCceeeEEeccCCcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            899999999999999999999999999999999999985 568999998754  58999999999999999999999999


Q ss_pred             HHH
Q 026213          226 EVL  228 (241)
Q Consensus       226 ~~l  228 (241)
                      ++|
T Consensus        80 ~~l   82 (84)
T d2je6a2          80 KHL   82 (84)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            987

>d2ba0g2 d.101.1.1 (G:179-257) Exosome complex exonuclease 2, ECX2 {Archaeoglobus fulgidus [TaxId: 2234]}

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

Probab=99.64  E-value=3.2e-16  Score=106.92  Aligned_cols=76  Identities=21%  Similarity=0.337  Sum_probs=70.0

Q ss_pred             CCCCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee--cCCHHHHHHHHHHHHHHHHHHHHHH
Q 026213          148 PMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA--KLPTNTFEDVMQLAIEGCKAVANYI  224 (241)
Q Consensus       148 p~~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g--~~~~~~l~~~l~~a~~~~~~i~~~i  224 (241)
                      |++++|+++|++++++.+|+|||.+||..+++.++|++ +.+|+++.+++.|  .++.+++.+|++.|.+.++++.+.+
T Consensus         1 Pv~~~Pv~vT~~~~~~~~lvDpt~eEE~~~~~~iti~~-~~~g~i~~~~k~G~~~~~~~~i~~~i~~A~~~~~~l~e~l   78 (79)
T d2ba0g2           1 PVRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITT-DKDDNVVAMQKSGGYLLDEKLFDELLDVSINCARKLREKF   78 (79)
T ss_dssp             CBCCCCEEEEEEEETTEEEESCCTTGGGGCSCEEEEEE-CTTSCEEEEEEESSCCBCHHHHHHHHHHHHHHHHHHTTTT
T ss_pred             CCCCceEEEEEEEECCEEEECCCHHHHhcCCceEEEEE-cCCCCEEEEEccCCCCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence            89999999999999999999999999999999999987 4668999999865  5899999999999999999987654

>d2nn6c2 d.101.1.1 (C:188-276) Exosome complex exonuclease RRP43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease RRP43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=4.5e-16  Score=108.65  Aligned_cols=82  Identities=20%  Similarity=0.215  Sum_probs=74.2

Q ss_pred             CCCeeEEEEEeeeCCe-eEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee--cCCHHHHHHHHHHHHHHHHHHHHHHH
Q 026213          149 MRDIVTSCSAGYLNST-PLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA--KLPTNTFEDVMQLAIEGCKAVANYIR  225 (241)
Q Consensus       149 ~~~~~~~vs~~~~~~~-~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g--~~~~~~l~~~l~~a~~~~~~i~~~i~  225 (241)
                      ++++|+++|++++++. +|+|||.+||..+++.++|++ +.+|+++.+++.|  +++++++.+|++.|.+++++++++++
T Consensus         2 i~~~Pi~vT~~~~~~~~~lvDpt~~EE~~~~~~lti~~-~~~g~i~~l~k~G~~~l~~~~l~~~~~~A~~~~~~l~~~l~   80 (89)
T d2nn6c2           2 IRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVM-DEEGKLCCLHKPGGSGLTGAKLQDCMSRAVTRHKEVKKLMD   80 (89)
T ss_dssp             CSCCCEEEEEEECTTTCCEESCCTTTTTSCSEEEEEEE-CTTCCEEEEEESCCSCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCEEEEEEEEECCEEEEEcCCHHHHhcCCceEEEEE-cCCCCEEEEEecCCcccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6799999999999764 788999999999999999987 4678999999865  68999999999999999999999999


Q ss_pred             HHHHHH
Q 026213          226 EVLLEN  231 (241)
Q Consensus       226 ~~l~~~  231 (241)
                      ++|++.
T Consensus        81 ~al~~~   86 (89)
T d2nn6c2          81 EVIKSM   86 (89)
T ss_dssp             TTTTTT
T ss_pred             HHHHhc
Confidence            988754

>d2nn6f2 d.101.1.1 (F:176-270) Exosome complex exonuclease MTR3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease MTR3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=3e-15  Score=105.61  Aligned_cols=89  Identities=24%  Similarity=0.440  Sum_probs=82.7

Q ss_pred             CCCeeEEEEEeeeC---CeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeeecC-CHHHHHHHHHHHHHHHHHHHHHH
Q 026213          149 MRDIVTSCSAGYLN---STPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDAKL-PTNTFEDVMQLAIEGCKAVANYI  224 (241)
Q Consensus       149 ~~~~~~~vs~~~~~---~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g~~-~~~~l~~~l~~a~~~~~~i~~~i  224 (241)
                      |+|+++++|+++.+   +.+++||+..||..+.+.++|+++++.++|+.++.+|.+ +.+.+.+++++|.++|.+|++.+
T Consensus         1 M~D~V~acs~~~~~~~~~~~llD~~~~Ee~~~~~~~~va~~p~~~~i~~~~~~G~~~~~d~l~~~lela~~g~~~I~~i~   80 (95)
T d2nn6f2           1 MYDLVVGCGLSLAPGPAPTWLLDPTRLEEERAAAGLTVALMPVLNQVAGLLGSGEGGLTESWAEAVRLGLEGCQRLYPVL   80 (95)
T ss_dssp             BSSCCEEEECCCCSCSSCCCCSSCCTTTGGGCSSEEEEEEETTTTEEEEEEEECCSSCTTTTHHHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEEEEeecCCCCcEEECCCHHHhcCCCCcEEEEEcCCCceeEEEEEecccchHHHHHHHHHHHHHHHHHHHHHH
Confidence            78999999999975   578999999999999999999999999999999999985 66899999999999999999999


Q ss_pred             HHHHHHHHHHHHh
Q 026213          225 REVLLENTKQLEC  237 (241)
Q Consensus       225 ~~~l~~~~~~~~~  237 (241)
                      +++|.++.+++-.
T Consensus        81 ~~aL~~~~~k~~~   93 (95)
T d2nn6f2          81 QQSLVRAARRRGA   93 (95)
T ss_dssp             HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhhc
Confidence            9999999998754

>d1r6la2 d.101.1.1 (A:152-239) Ribonuclease PH, domain 2 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.50  E-value=5.6e-14  Score=97.49  Aligned_cols=83  Identities=28%  Similarity=0.472  Sum_probs=76.7

Q ss_pred             CCCCCCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee---cCCHHHHHHHHHHHHHHHHHHHH
Q 026213          146 GIPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA---KLPTNTFEDVMQLAIEGCKAVAN  222 (241)
Q Consensus       146 gip~~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g---~~~~~~l~~~l~~a~~~~~~i~~  222 (241)
                      |+||++.++||++|+++|++++|||.+|+..++..+.|+. +..++++.++.+|   .|+.+++.++++.|.+.++++++
T Consensus         2 g~P~~~~VaavsvG~idg~~vld~~~~E~~~~~~Dl~va~-t~~g~i~~iq~~ge~~~~sed~~~~al~~A~~~i~~i~~   80 (88)
T d1r6la2           2 GNPLKQMVAAVSVGIYQGVPVLDLDYLEDSAAETDLNVVM-TDAGGFIEVQGTAEGAPFRPAELNAMLELAQQGMQELFE   80 (88)
T ss_dssp             SCCBCCCEEEEEEEEETTEEEESCCHHHHHHCSEEEEEEE-ETTSCEEEEEEEESSSCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcCCCccEEEEEEECCEEEecCcHHhhccCceeEEEEE-eCCCCEEeehhhcccCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999999999999999999999999975 6778888888765   58999999999999999999999


Q ss_pred             HHHHHHH
Q 026213          223 YIREVLL  229 (241)
Q Consensus       223 ~i~~~l~  229 (241)
                      .++++|.
T Consensus        81 ~Qkeal~   87 (88)
T d1r6la2          81 LQRAALA   87 (88)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHhc
Confidence            9999875

>d2ba0d2 d.101.1.1 (D:154-252) Exosome complex exonuclease 1, ECX1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 1, ECX1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.49  E-value=8.5e-14  Score=98.75  Aligned_cols=86  Identities=28%  Similarity=0.441  Sum_probs=77.7

Q ss_pred             CCCCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEE---EEEeeecCCHHHHHHHHHHHHHHHHHHHHHH
Q 026213          148 PMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVT---LLQMDAKLPTNTFEDVMQLAIEGCKAVANYI  224 (241)
Q Consensus       148 p~~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~---~~~~~g~~~~~~l~~~l~~a~~~~~~i~~~i  224 (241)
                      ||+++++|+++|++++.+++||+..|+..+...+++++.++.+.+.   +.+.+|.++++++.++++.|.++|++|++++
T Consensus         1 Pm~~~V~avsvG~~d~~~llDp~~~E~~~~~~~l~va~~~~~~~~~ei~~~~~~~~~~~~~~~~~l~~a~~~~~~I~~~~   80 (99)
T d2ba0d2           1 PMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQ   80 (99)
T ss_dssp             CBSSEEEEEEEEEETTEEEESCCHHHHHHSSEEEEEEEEEETTEEEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCcEEEEEEEEECCEEEEcCCcchhhcccCceEEEEecCcceEEEEEEEeccccchHHHHHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999999999999999999999998877766654   4455789999999999999999999999999


Q ss_pred             HHHHHHHHH
Q 026213          225 REVLLENTK  233 (241)
Q Consensus       225 ~~~l~~~~~  233 (241)
                      ++++++...
T Consensus        81 ~~alk~~~~   89 (99)
T d2ba0d2          81 REAILRRYI   89 (99)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHhhhhh
Confidence            999988654

>d1oysa2 d.101.1.1 (A:152-237) Ribonuclease PH, domain 2 {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Bacillus subtilis [TaxId: 1423]

Probab=99.26  E-value=1.1e-11  Score=85.32  Aligned_cols=81  Identities=28%  Similarity=0.401  Sum_probs=71.4

Q ss_pred             CCCCCeeEEEEEeeeCCe-eEEeCCccccccCCCcEEEEEcCCCCcEEEEEeee---cCCHHHHHHHHHHHHHHHHHHHH
Q 026213          147 IPMRDIVTSCSAGYLNST-PLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMDA---KLPTNTFEDVMQLAIEGCKAVAN  222 (241)
Q Consensus       147 ip~~~~~~~vs~~~~~~~-~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~g---~~~~~~l~~~l~~a~~~~~~i~~  222 (241)
                      .||++.++||++|+++|. +++||+.+|+..++..+.|+. +..|+++.++.+|   .++.+++.+++++|.+.+++|++
T Consensus         2 ~P~~~~VaavsvG~i~~~~vlldl~~~Ed~~~~~D~~va~-t~~g~i~~iq~~ge~~~~s~d~~~~al~lA~~gi~~I~~   80 (86)
T d1oysa2           2 NPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIM-TGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELID   80 (86)
T ss_dssp             CCBCSCEEEEEEEEETTTEEEESCCHHHHHHEEEEEEEEE-ETTSCEEEEEEEESSCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCccCcccEEEEEEEcCCcEECCCHHHHhcCCCcceEEEE-eCCCCEEEEEEeeccCcccHHHHHHHHHHHHHHHHHHHH
Confidence            599999999999999886 568999999999999999975 5678887777654   59999999999999999999999


Q ss_pred             HHHHHH
Q 026213          223 YIREVL  228 (241)
Q Consensus       223 ~i~~~l  228 (241)
                      ..+++|
T Consensus        81 ~Qkeal   86 (86)
T d1oysa2          81 KQKEVL   86 (86)
T ss_dssp             HHHHHC
T ss_pred             HHHHhC
Confidence            998875

>d1udsa2 d.101.1.1 (A:151-255) Ribonuclease PH, domain 2 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Ribonuclease PH, domain 2
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.25  E-value=1.1e-11  Score=88.30  Aligned_cols=82  Identities=24%  Similarity=0.415  Sum_probs=72.3

Q ss_pred             CCCCCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCCCCcEEEEEe---eecCCHHHHHHHHHHHHHHHHHHHHH
Q 026213          147 IPMRDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQM---DAKLPTNTFEDVMQLAIEGCKAVANY  223 (241)
Q Consensus       147 ip~~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~---~g~~~~~~l~~~l~~a~~~~~~i~~~  223 (241)
                      .||++.++||++|+++|.+|+||+..|+..++..+.|+.. ..+.+..++.   ++.++.+++.++++.|.+.+++|+++
T Consensus         3 ~P~~~~VaAVsvG~idg~~vldp~~~Ed~~~~~dl~va~t-~~g~~~ei~~~~e~~~~see~~~eal~~a~~~i~~i~~~   81 (105)
T d1udsa2           3 TPIKDFVAAVSVGIVNDRILLDLNFEEDSAAQVDMNVVGT-GSGRLSEVHTMGEEYSFTKDELIKMLDLAQKGINELIEL   81 (105)
T ss_dssp             CCBCCCEEEEEEEEETTEEEESCCHHHHHTCSEEEEEEEE-TTSCEEEEEEEESSCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCccCCceEEEEEEECCEEeecCCHHHHhcCccceeEEEe-cCCcchhhhhhhccccccHHHHHHHHHHHHHHHHHHHHH
Confidence            6999999999999999999999999999999999999874 4566655544   46799999999999999999999999


Q ss_pred             HHHHHH
Q 026213          224 IREVLL  229 (241)
Q Consensus       224 i~~~l~  229 (241)
                      .+++|.
T Consensus        82 Qke~l~   87 (105)
T d1udsa2          82 QKKLYV   87 (105)
T ss_dssp             HHTTEE
T ss_pred             HHHHHh
Confidence            988764

>d1e3ha5 d.101.1.1 (A:152-262) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
species: Streptomyces antibioticus [TaxId: 1890]

Probab=97.90  E-value=1.9e-05  Score=55.74  Aligned_cols=84  Identities=8%  Similarity=-0.039  Sum_probs=67.7

Q ss_pred             CCeeEEEEEeeeCCeeEEeCCccccccCCCcEEEEEcCC---CCcEEEEEeeec-------------CCHHHHHHHHHHH
Q 026213          150 RDIVTSCSAGYLNSTPLLDLNYVEDSAGGPDVTVGILPT---LDKVTLLQMDAK-------------LPTNTFEDVMQLA  213 (241)
Q Consensus       150 ~~~~~~vs~~~~~~~~i~DPt~~Ee~~~~~~~~v~~~~~---~~~i~~~~~~g~-------------~~~~~l~~~l~~a  213 (241)
                      ++.+.||.+|+++|.+|++||.+|...++..+.|+-...   ...+.+++..+.             ++.+.+.++++.|
T Consensus         2 ~GPvgaVRVg~idge~viNPt~~el~~S~ldLvVaGt~~~~~~~~v~mie~~~~e~~~~mie~~a~e~~E~~~~~ai~~a   81 (111)
T d1e3ha5           2 SGPIGGVRVALIRGQWVAFPTHTELEDAVFDMVVAGRVLEDGDVAIMMVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAA   81 (111)
T ss_dssp             CCCCEEEEEEEETTEEEESCCHHHHTTEEEEEEEEEEECTTSCEEEEEEEEEECTTHHHHHHTTCCCCCHHHHHHHHHHH
T ss_pred             CCCEEEEEEEEECCEEEECCCHHHHhcCceEEEEeecccccchHHHHHHHhcchhHHHHHHHhccccccHHHHHHHHHHH
Confidence            467789999999999999999999998888888875322   234666665542             5788999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 026213          214 IEGCKAVANYIREVLLENTK  233 (241)
Q Consensus       214 ~~~~~~i~~~i~~~l~~~~~  233 (241)
                      .+..+++.+.+++..++..+
T Consensus        82 ~~~i~~~i~~q~el~~~~gk  101 (111)
T d1e3ha5          82 KPFIKVLCKAQADLAAKAAK  101 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHHHHCC
Confidence            99999999999888877554

>d1e3ha6 d.101.1.1 (A:483-578) Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5 {Streptomyces antibioticus [TaxId: 1890]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
species: Streptomyces antibioticus [TaxId: 1890]

Probab=97.17  E-value=0.00091  Score=44.91  Aligned_cols=77  Identities=23%  Similarity=0.307  Sum_probs=64.9

Q ss_pred             eEEEEEeeeCC--------eeEEeCCccccccCCCcEEEEEcCCCCcEEEEEee---ecCCHHHHHHHHHHHHHHHHHHH
Q 026213          153 VTSCSAGYLNS--------TPLLDLNYVEDSAGGPDVTVGILPTLDKVTLLQMD---AKLPTNTFEDVMQLAIEGCKAVA  221 (241)
Q Consensus       153 ~~~vs~~~~~~--------~~i~DPt~~Ee~~~~~~~~v~~~~~~~~i~~~~~~---g~~~~~~l~~~l~~a~~~~~~i~  221 (241)
                      ++++++|++.+        .++.|....|+...+..|-||-  +.+-|+.+|++   ..++.+.+.++++.|+++..+|.
T Consensus         3 VAGIamGLi~~~~~~~~~~~iLtDI~G~ED~~GDMDFKVAG--T~~GITa~QmDiKi~Gi~~~il~~Al~qAk~gR~~IL   80 (96)
T d1e3ha6           3 VAGIAMGLISQEINGETHYVALTDILGAEDAFGDMDFKVAG--TKEFVTALQLDTKLDGIPASVLAAALKQARDARLHIL   80 (96)
T ss_dssp             CEEEEEEEEEEEETTEEEEEEESSCCSHHHHHCSEEEEEEE--CSSCEEEEEEEECCSCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             cceeeeeeeeccCCCCccEEEEeeccCchhhccCccccccc--CcccceeeeeeecccCCCHHHHHHHHHHHHHHHHHHH
Confidence            46788888721        4789999999999999999985  44459999997   45899999999999999999999


Q ss_pred             HHHHHHHHHH
Q 026213          222 NYIREVLLEN  231 (241)
Q Consensus       222 ~~i~~~l~~~  231 (241)
                      +.|.+++.+.
T Consensus        81 ~~M~~~i~~p   90 (96)
T d1e3ha6          81 DVMMEAIDTP   90 (96)
T ss_dssp             HHHHHHCSSC
T ss_pred             HHHHHHhccc
Confidence            9999987543