Psyllid ID: psy18119

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260---
Protein Sequence
MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGARGLGRKFQLGQLTGKKKEEESKS
Secondary Structure (PSIPRED)
cccccccccccccccccccccccEEEEEcccccccccEEEEEccEEEEEEEEccccccccccccccEEEEEEEEEEccccccccccccccccHHHHHHHHHHHHHHHHHccccccccEEEEEEEEEEccccHHHHHHHHHHHHHHHcccccccEEEEEEEEEEccEEEEccccccccccccccEEEEcccccEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHccc
Secondary Structure Prediction (SSPRO)
cccEEEcccccccccccccEEEEEEEEEcEccccccEEEEEcccEEEEEEEEccccccccccccccccEEEEEEcccccccccccccccccHHHHHHHHHHHcccccccccccccccEEEEEEEEEcccccccHHHHHHHHHHHHHccccccccEEEEEEEEEccEEEEcccccHHccccccEEEEEcccccEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHcHHccccHHHHHHHHcccHHHHHHcc
Coil and Loop (DISEMBL)
mdllteyggglrndgrrgheLRKIRCRlgvfsqsdgsayieqGNTKVLAAvygprpvrnksiKVHGSVLINFQYSMavfstgerktrprgdrktsEISLQLRQAVSAAImsevhprsqIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSAslagdtplvdishleetlggpnltvaalplSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGarglgrkfqlgqltgkkkeeesks
Flexible Loop (DISEMBL)
mdllteyggglrndgrrgheLRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAvfstgerktrprgdrktseisLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVagarglgrkfqlgqltgkkkeeesks
Low Complexity Region (SEG)
MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGARGLGRKFQLGQLTGKKKEEESKS
Disordered region (IsUnstruct)
*******************ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFS************************VSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGARGLGRKFQL**************
Disordered Region (DISOPRED)
*******GGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYG***************LINFQYSM***********************QLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQH******************************
Disordered Region (DISEMBL)
MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFST***************ISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGARGLGRKFQLGQ************
Disordered Region (DISPRO)
*DLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGARGLGRKFQLGQLTGK********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGARGLGRKFQLGQLTGKKKEEESKS
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	263	2.2.26 [Sep-21-2011]
Q9NPD3	245	Exosome complex component	yes	N/A	0.882	0.946	0.574	2e-76
Q7YRA3	245	Exosome complex component	yes	N/A	0.882	0.946	0.570	4e-76
Q921I9	245	Exosome complex component	yes	N/A	0.882	0.946	0.570	2e-75
A8WQQ5	240	Putative exosome complex	N/A	N/A	0.878	0.962	0.461	2e-52
Q17533	240	Putative exosome complex	yes	N/A	0.878	0.962	0.452	3e-51
B6YSI2	249	Probable exosome complex	yes	N/A	0.889	0.939	0.4	1e-44
C5A2B9	249	Probable exosome complex	yes	N/A	0.866	0.915	0.397	2e-44
O26779	240	Probable exosome complex	yes	N/A	0.844	0.925	0.408	5e-44
Q8U0L9	250	Probable exosome complex	yes	N/A	0.866	0.912	0.388	2e-43
Q5JIR6	249	Probable exosome complex	yes	N/A	0.866	0.915	0.388	3e-43

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

 Score =  285 bits (729), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 135/235 (57%), Positives = 178/235 (75%), Gaps = 3/235 (1%)

Query: 1   MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVR-N 59
           ++LL++ G   R DGRR  ELRKI+ R+GVF+Q+DGSAYIEQGNTK LA VYGP  +R +
Sbjct: 4   LELLSDQG--YRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGS 61

Query: 60  KSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQI 119
           ++  +    L+N QYS A FSTGERK RP GDRK+ E+ LQLRQ   AAI++++HPRSQI
Sbjct: 62  RARALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQI 121

Query: 120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLG 179
           DI+V+VLQADGG + ACVNAATLA++DAGIPMR++V ACSA     T L D+SH+EE  G
Sbjct: 122 DIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAG 181

Query: 180 GPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
           GP L +A LP SG++A++E+  +LH DHL RVL+ A +   D+H +LD  ++QH+
Sbjct: 182 GPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHV 236

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 =  284 bits (727), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 134/235 (57%), Positives = 178/235 (75%), Gaps = 3/235 (1%)

Query: 1   MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVR-N 59
           ++LL++ G   R DGRR  ELRKI+ R+GVF+Q+DGSAYIEQGNTK LA VYGP  +R +
Sbjct: 4   LELLSDQG--YRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGS 61

Query: 60  KSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQI 119
           ++  +    L+N QYS A FSTGERK RP GDRK+ E+ LQLRQ   AAI++++HPRSQI
Sbjct: 62  RARALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQI 121

Query: 120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLG 179
           DI+V+VLQADGG + ACVNAATLA++DAGIPMR++V ACSA     T L D+SH+EE  G
Sbjct: 122 DIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAG 181

Query: 180 GPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
           GP L +A LP SG++A++E+  +LH DHL +VL+ A +   D+H +LD  ++QH+
Sbjct: 182 GPQLALALLPASGQIALLEMDARLHEDHLEQVLEAAARASRDVHTVLDRVVRQHV 236

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

 Score =  281 bits (720), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 134/235 (57%), Positives = 177/235 (75%), Gaps = 3/235 (1%)

Query: 1   MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVR-N 59
           ++LL++ G   R DGRR  ELRKI+ R+GVF+Q+DGSAYIEQGNTK LA VYGP  +R +
Sbjct: 4   LELLSDQG--YRIDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGS 61

Query: 60  KSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQI 119
           +S  +    L+N QYS A FSTGERK RP GDRK+ E+ LQLRQ   AAI++++HPRSQI
Sbjct: 62  RSRALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQI 121

Query: 120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLG 179
           DI+V+VLQADGG + ACVNAATLA++DAGIPMR++V ACSA     T L D+SH+EE  G
Sbjct: 122 DIYVQVLQADGGTYAACVNAATLAVMDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAG 181

Query: 180 GPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
           GP L +A LP SG++A++E+  +LH DHL +VL+ A +    +H +LD  ++QH+
Sbjct: 182 GPQLALALLPASGQIALLEMDSRLHEDHLEQVLEAAAQAARGVHTLLDLVVRQHV 236

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|A8WQQ5|EXOS4_CAEBR Putative exosome complex component RRP41 OS=Caenorhabditis briggsae GN=exos-4.1 PE=3 SV=1

 Score =  205 bits (522), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 108/234 (46%), Positives = 147/234 (62%), Gaps = 3/234 (1%)

Query: 1   MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNK 60
           M +++E+G   R DGRR  ++R I  RLG+   ++GS Y+E GNTKVL AVYGP   +  
Sbjct: 1   MSIISEHG--FRMDGRRPAQIRNINTRLGLNRNAEGSCYLEHGNTKVLCAVYGPYESK-A 57

Query: 61  SIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQID 120
           S ++     I  QYS   FS  ERK RPRGDRK++EIS  L +A  + I++E  PRSQID
Sbjct: 58  SKRLEDRCAIVCQYSTTTFSGLERKNRPRGDRKSTEISRLLEKAFESVILTESFPRSQID 117

Query: 121 IFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGG 180
           IF EV+Q DG N  ACVNA +LAL DAGIPM+    A +  +    P+VD++  EET   
Sbjct: 118 IFCEVIQGDGSNLAACVNATSLALADAGIPMKGIASAATCGIVETKPIVDLTSREETDLL 177

Query: 181 PNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
           P +T+A +    +V ++EL  +LH+DHL  V+D A   CAD++  L    +QHL
Sbjct: 178 PRVTLATICGRDEVILVELQNRLHIDHLSVVMDAAKATCADVYECLAVVAQQHL 231

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.

Caenorhabditis briggsae (taxid: 6238)

>sp|Q17533|EXOS4_CAEEL Putative exosome complex component RRP41 OS=Caenorhabditis elegans GN=exos-4.1 PE=2 SV=2

 Score =  201 bits (512), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 106/234 (45%), Positives = 148/234 (63%), Gaps = 3/234 (1%)

Query: 1   MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNK 60
           M++++E+G   R DGRR  ++R I  RLG+   ++GS Y+E GNTKVL AVYGP   ++ 
Sbjct: 1   MNIISEHG--FRIDGRRPAQIRNINTRLGLNRNAEGSCYLEHGNTKVLCAVYGPYEGKS- 57

Query: 61  SIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQID 120
           S ++     I  QYS   FS  ERK R RGDRK++EIS  L +A  + I++E  PRSQ+D
Sbjct: 58  SKRIEDKCAIVCQYSATKFSGLERKNRTRGDRKSTEISRLLEKAFESVILTEAFPRSQLD 117

Query: 121 IFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGG 180
           IF EV+Q DG N  ACVNA +LAL DAGIPM+    A +  +    P+VD++  EET   
Sbjct: 118 IFCEVIQGDGSNLAACVNATSLALADAGIPMKGIASAATCGVVDGKPIVDLTSREETDLL 177

Query: 181 PNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
           P +T+A +    +V ++EL  +LH+DHL  V+D A   CAD++  L    +QHL
Sbjct: 178 PRVTLATICGRDEVILVELQNRLHIDHLSTVMDAAKATCADVYECLAVVAQQHL 231

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.

Caenorhabditis elegans (taxid: 6239)

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

 Score =  180 bits (456), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 94/235 (40%), Positives = 143/235 (60%), Gaps = 1/235 (0%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           G R DGR+ +ELR I+  +GV   +DGSAY+E G  K+LAAVYGPR +  K ++     +
Sbjct: 15  GRRIDGRKKYELRPIKMEVGVLKNADGSAYVEWGKNKILAAVYGPREIHPKHLQRPDRAI 74

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           +  +Y+MA FS  ERK +P  DR++ EIS  +R A+  A++ E+ PR+ IDIF+EVLQAD
Sbjct: 75  LRVRYNMAPFSVEERK-KPGPDRRSVEISKVIRGALEPALILEMFPRTAIDIFIEVLQAD 133

Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
            G   A + AA+LAL DAGIPMR+ V AC+A       ++D++  E+  G  ++ VA +P
Sbjct: 134 AGTRVAGITAASLALADAGIPMRDLVAACAAGKIEGEIVLDLNKEEDNYGEADVPVAIMP 193

Query: 190 LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGARGLG 244
           L   + ++++   L  D     +  A+KG   ++     A+K+  +K+A   G G
Sbjct: 194 LKNDITLLQMDGYLTRDEFIEAVRLAIKGAKAVYQKQREALKEKYLKIAEEVGGG 248

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 =  179 bits (453), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 91/229 (39%), Positives = 142/229 (62%), Gaps = 1/229 (0%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           G R DGRR +ELRKI   +GV   +DGSAYIE G  K+LAAVYGPR +  K ++   + +
Sbjct: 15  GRRIDGRRKYELRKIHMEVGVLKNADGSAYIEWGKNKILAAVYGPREIHPKHLQRPDTAV 74

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           +  +Y+MA FS  ERK +P  DR++ EIS  +R A+  A++ E+ PR+ +D+F+EVLQAD
Sbjct: 75  LRVRYNMAPFSVEERK-KPGPDRRSVEISKVIRGALEPALILEMFPRTVVDVFIEVLQAD 133

Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
            G   A + AA+LAL DAG+PMR+ V AC+A       ++D++  E+  G  ++ VA +P
Sbjct: 134 AGTRVAGITAASLALADAGVPMRDLVAACAAGKIDGEIVLDLNKDEDNYGEADVPVAIMP 193

Query: 190 LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVA 238
           L   + ++++   L  +     +  A+KG   ++     A+K+  +K+A
Sbjct: 194 LKNDITLLQMDGYLTKEEFIEAVKLAIKGAKAVYQKQREALKEKYLKIA 242

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|O26779|ECX1_METTH Probable exosome complex exonuclease 1 OS=Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) GN=MTH_683 PE=1 SV=1

 Score =  177 bits (450), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 91/223 (40%), Positives = 141/223 (63%), Gaps = 1/223 (0%)

Query: 11  LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLI 70
           +R DGR   ELR ++   G+  ++DGS+Y+E G  K+L AVYGPR  + + ++     +I
Sbjct: 16  VREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVI 75

Query: 71  NFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADG 130
             +Y+MA FS  ERK RP  DR++ EIS    +A+  A++ E  PRS ID+F+EVL+A+G
Sbjct: 76  RCRYNMAPFSVEERK-RPGPDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEG 134

Query: 131 GNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPL 190
           G  CA + AA++AL DAGIPMR+ VVAC+A   GD  ++D+S  E+  G  ++ VA LP 
Sbjct: 135 GTRCAGITAASVALADAGIPMRDMVVACAAGKVGDQVVLDLSEEEDKEGQADVPVAILPR 194

Query: 191 SGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQH 233
           + ++ +++    L  +   R LD A++GC  IH +   A+++ 
Sbjct: 195 TREITLLQSDGNLTPEEFERALDLAVEGCLRIHEVQKEALRKR 237

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

Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (taxid: 187420)

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 =  176 bits (446), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 89/229 (38%), Positives = 142/229 (62%), Gaps = 1/229 (0%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           G R DGR+ +ELR I+ ++GV   ++GSAYIE G  K++AAVYGPR +  K ++     +
Sbjct: 15  GRRLDGRKKYELRPIKMKVGVLKNANGSAYIEWGKNKIIAAVYGPREIHPKHLQRPDRAI 74

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           +  +Y+MA FS  ERK +P  DR++ EIS  +R A+  A++ E+ PR+ ID+F+EVLQAD
Sbjct: 75  LRVRYNMAPFSVEERK-KPGPDRRSIEISKVIRGALEPALILEMFPRTAIDVFIEVLQAD 133

Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
            G   A + AA+LAL DAGIPMR+ V ACSA       ++D++  E+  G  ++ VA +P
Sbjct: 134 AGTRVAGITAASLALADAGIPMRDLVAACSAGKIEGEIVLDLNKEEDNYGEADVPVAIMP 193

Query: 190 LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVA 238
           +   + ++++   L  +     +  A+KG   ++     A+K+  +K+A
Sbjct: 194 IKNDITLLQMDGYLTKEEFIEAVKLAIKGAKAVYQKQREALKEKYLKIA 242

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|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 =  175 bits (444), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 89/229 (38%), Positives = 140/229 (61%), Gaps = 1/229 (0%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           G R DGR+ +ELR I+  +GV   +DGSAY+E G  KVLAAVYGPR +  K ++     +
Sbjct: 15  GKRIDGRKKYELRPIKMEVGVLKNADGSAYVEWGKNKVLAAVYGPREIHPKHLQRPDRAI 74

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           +  +Y+MA FS  ERK +P  DR++ EIS  +R A+  A++  + PR+ ID+F+E+LQAD
Sbjct: 75  LRVRYNMAPFSVEERK-KPGPDRRSVEISKVIRGALEPALLLHMFPRTAIDVFIEILQAD 133

Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
            G   A + AA+LAL DAGIPM++ V AC+A       ++D++  E+  G  ++ VA +P
Sbjct: 134 AGTRVAGITAASLALADAGIPMKDLVAACAAGKIDGEIVLDLNKEEDNYGEADVPVAIMP 193

Query: 190 LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVA 238
           L   + ++++   L  D     +  A+KG   ++     A+K+  +K+A
Sbjct: 194 LKNDITLLQMDGYLTKDEFLEAVRLAIKGAKAVYQKQREALKEKYLKIA 242

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: -

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	263
312375907	246	hypothetical protein AND_13423 [Anophele	0.916	0.979	0.632	2e-87
157133589	245	exosome complex exonuclease RRP41, putat	0.908	0.975	0.626	2e-86
270010551	251	hypothetical protein TcasGA2_TC009968 [T	0.893	0.936	0.649	6e-86
189239465	249	PREDICTED: similar to exosome complex ex	0.889	0.939	0.644	2e-84
170070082	245	exosome complex exonuclease RRP41 [Culex	0.916	0.983	0.614	3e-84
405971078	245	Exosome complex exonuclease RRP41 [Crass	0.904	0.971	0.597	4e-83
291233253	246	PREDICTED: exosome component 4-like [Sac	0.874	0.934	0.606	6e-83
242005051	253	Exosome complex exonuclease RRP41, putat	0.863	0.897	0.627	4e-81
328712784	249	PREDICTED: exosome complex exonuclease R	0.916	0.967	0.593	2e-79
321465387	246	hypothetical protein DAPPUDRAFT_213979 [	0.866	0.926	0.606	3e-79

>gi|312375907|gb|EFR23155.1| hypothetical protein AND_13423 [Anopheles darlingi]

 Score =  327 bits (839), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 155/245 (63%), Positives = 199/245 (81%), Gaps = 4/245 (1%)

Query: 1   MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNK 60
           M+LL++ G  LR DGRR +ELR I+C+LGVFSQ DGSAY+EQGNTKVLAAVYGP    +K
Sbjct: 1   MELLSDQG--LRLDGRRANELRHIQCKLGVFSQPDGSAYVEQGNTKVLAAVYGPHQASSK 58

Query: 61  SIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQID 120
               H   ++N QYSMA FSTGERK RPRGDRK+ E+++ L+QA+SAAI  E++PRSQID
Sbjct: 59  KSN-HEEAIVNCQYSMATFSTGERKKRPRGDRKSQEMTIHLKQALSAAIKMELYPRSQID 117

Query: 121 IFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA-GDTPLVDISHLEETLG 179
           +++EVLQADGGN+CA VNAATLALIDAGI ++EYV AC+ASLA G+ PL+D+SHLEE  G
Sbjct: 118 VYIEVLQADGGNYCASVNAATLALIDAGICLKEYVCACTASLANGNVPLMDVSHLEENSG 177

Query: 180 GPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAG 239
           GP LTVA+LP SGK+A ME+SQ+ HLDHLP+VL+ ALKGC ++  ++D A+++H+ ++  
Sbjct: 178 GPTLTVASLPSSGKIAFMEMSQRFHLDHLPKVLETALKGCREVQNVIDRAVREHVTQLGQ 237

Query: 240 ARGLG 244
           A G G
Sbjct: 238 AGGWG 242

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157133589|ref|XP_001656263.1| exosome complex exonuclease RRP41, putative [Aedes aegypti] gi|157134369|ref|XP_001663263.1| exosome complex exonuclease RRP41, putative [Aedes aegypti] gi|108870517|gb|EAT34742.1| AAEL013045-PA [Aedes aegypti] gi|108870766|gb|EAT34991.1| AAEL012812-PA [Aedes aegypti]

 Score =  324 bits (831), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 154/246 (62%), Positives = 200/246 (81%), Gaps = 7/246 (2%)

Query: 1   MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPR--PVR 58
           M+LL++ G  LR DGRR +ELR+I+C+LGVFSQ DGSAYIEQGNTKVLAAVYGP   P +
Sbjct: 1   MELLSDEG--LRLDGRRANELRRIQCKLGVFSQPDGSAYIEQGNTKVLAAVYGPHQAPAK 58

Query: 59  NKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQ 118
             S   H  V++N QYSMA FSTGERK RPRGDRK+ E+++ L+QA+SAAI +E++P+SQ
Sbjct: 59  KSS---HEEVIVNCQYSMATFSTGERKRRPRGDRKSQEMTIHLQQALSAAIKTELYPKSQ 115

Query: 119 IDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETL 178
           ID+++EVL ADGGN+CA VNAATLALIDAGI ++EYV AC+ASLAG  PL+D+S+LEE  
Sbjct: 116 IDVYIEVLMADGGNYCASVNAATLALIDAGICLKEYVCACTASLAGKIPLMDVSNLEEMS 175

Query: 179 GGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVA 238
           GGP LTVA+LP SGK+A ME+SQ+ HLDHLP+VL+ AL+GC ++  I+D A+++H+ ++ 
Sbjct: 176 GGPTLTVASLPSSGKIAFMEMSQRFHLDHLPKVLETALQGCREVQKIIDQAVREHVTQLG 235

Query: 239 GARGLG 244
            A   G
Sbjct: 236 QAGDWG 241

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270010551|gb|EFA06999.1| hypothetical protein TcasGA2_TC009968 [Tribolium castaneum]

 Score =  323 bits (827), Expect = 6e-86,   Method: Compositional matrix adjust.
 Identities = 154/237 (64%), Positives = 193/237 (81%), Gaps = 2/237 (0%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVR-NKSIKVHGSV 68
           GLR DGRR  ELR+IRC+LGVF++ DGSAY+EQG TKVLAAVYGP  VR ++S   H S 
Sbjct: 12  GLRQDGRRADELRRIRCKLGVFTEPDGSAYLEQGLTKVLAAVYGPHQVRGSRSKAQHDSA 71

Query: 69  LINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQA 128
           ++N Q+SMAVFSTGERK RPRGDRK++EIS+ LRQA++AAI  E++P +QID++VEVL A
Sbjct: 72  VVNCQFSMAVFSTGERKKRPRGDRKSTEISIHLRQALTAAIKVELYPWTQIDVYVEVLHA 131

Query: 129 DGGNFCACVNAATLALIDAGIPMREYVVACSASLA-GDTPLVDISHLEETLGGPNLTVAA 187
           DGG + ACVNAATLALIDAGIP++EYV AC+ASLA  D PL+D+SH EE +GGP LTVAA
Sbjct: 132 DGGIYPACVNAATLALIDAGIPLKEYVCACTASLANNDVPLLDVSHQEEIIGGPTLTVAA 191

Query: 188 LPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGARGLG 244
           LP+SGK+ +ME+SQ+ H+DHL +VLD AL+GC DI +ILD A+K H+  V  + G  
Sbjct: 192 LPMSGKIVLMEMSQRFHVDHLQKVLDKALQGCKDIKSILDEAVKSHIQDVGSSTGWA 248

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189239465|ref|XP_975230.2| PREDICTED: similar to exosome complex exonuclease RRP41, putative [Tribolium castaneum]

 Score =  318 bits (814), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 152/236 (64%), Positives = 190/236 (80%), Gaps = 2/236 (0%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           GLR DGRR  ELR+IRC+LGVF++ DGSAY+EQG TKVLAAVYGP  V     + H S +
Sbjct: 12  GLRQDGRRADELRRIRCKLGVFTEPDGSAYLEQGLTKVLAAVYGPHQVGFAKAQ-HDSAV 70

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           +N Q+SMAVFSTGERK RPRGDRK++EIS+ LRQA++AAI  E++P +QID++VEVL AD
Sbjct: 71  VNCQFSMAVFSTGERKKRPRGDRKSTEISIHLRQALTAAIKVELYPWTQIDVYVEVLHAD 130

Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLA-GDTPLVDISHLEETLGGPNLTVAAL 188
           GG + ACVNAATLALIDAGIP++EYV AC+ASLA  D PL+D+SH EE +GGP LTVAAL
Sbjct: 131 GGIYPACVNAATLALIDAGIPLKEYVCACTASLANNDVPLLDVSHQEEIIGGPTLTVAAL 190

Query: 189 PLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGARGLG 244
           P+SGK+ +ME+SQ+ H+DHL +VLD AL+GC DI +ILD A+K H+  V  + G  
Sbjct: 191 PMSGKIVLMEMSQRFHVDHLQKVLDKALQGCKDIKSILDEAVKSHIQDVGSSTGWA 246

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170070082|ref|XP_001869459.1| exosome complex exonuclease RRP41 [Culex quinquefasciatus] gi|167866003|gb|EDS29386.1| exosome complex exonuclease RRP41 [Culex quinquefasciatus]

 Score =  317 bits (813), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 150/244 (61%), Positives = 195/244 (79%), Gaps = 3/244 (1%)

Query: 1   MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNK 60
           M+LL++ G  LR DGRR +ELR+I+C+LGVFSQ DGSAY+EQGNTKVLAAVYGP     K
Sbjct: 1   MELLSDEG--LRLDGRRSNELRRIQCKLGVFSQPDGSAYVEQGNTKVLAAVYGPHQAPAK 58

Query: 61  SIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQID 120
               H   ++N QYSMA FSTGERK RPRGDRK+ E+++ L+QA+SAAI ++++P+SQID
Sbjct: 59  KSN-HEECVVNCQYSMATFSTGERKKRPRGDRKSQEMTIHLQQALSAAIKTDLYPKSQID 117

Query: 121 IFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGG 180
           +++EVL ADGGN+CA VNAATLALIDAGI ++EYV AC+ASLAG  PL+D+S+LEE  GG
Sbjct: 118 VYIEVLMADGGNYCASVNAATLALIDAGICLKEYVCACTASLAGKVPLMDVSNLEEMSGG 177

Query: 181 PNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGA 240
           P LTVA+LP SGK+A ME+SQ+ HLDHLP VL+ AL+GC ++  I+D A++ H+ ++  A
Sbjct: 178 PTLTVASLPNSGKIAFMEMSQRFHLDHLPNVLETALQGCREVQKIIDQAVRDHVTQLGQA 237

Query: 241 RGLG 244
              G
Sbjct: 238 GDWG 241

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|405971078|gb|EKC35934.1| Exosome complex exonuclease RRP41 [Crassostrea gigas]

 Score =  313 bits (803), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 144/241 (59%), Positives = 195/241 (80%), Gaps = 3/241 (1%)

Query: 1   MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVR-N 59
           +DLL++ G   R DGRR HELRKI+C+LGVFSQ+DGSAY+EQGNTKVLAAVYGP  +R +
Sbjct: 4   LDLLSDQG--FRIDGRRSHELRKIQCKLGVFSQADGSAYVEQGNTKVLAAVYGPHEIRGS 61

Query: 60  KSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQI 119
           +S  +   VL+N QYSMA FST ERK RPRGDRK+ E+++ L+Q  +AAI++ +HPRSQI
Sbjct: 62  RSKLLQDKVLVNCQYSMATFSTSERKRRPRGDRKSQEMTMHLQQTFNAAILTSLHPRSQI 121

Query: 120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLG 179
           DIFVEVLQ+DGGN+CA VNAATLA+IDAGIPM++YV ACSAS  GD+P+VDI++LEE+ G
Sbjct: 122 DIFVEVLQSDGGNYCASVNAATLAVIDAGIPMKDYVCACSASYLGDSPIVDINYLEESSG 181

Query: 180 GPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAG 239
            P +TVA LP S ++  +E++ +LH D+L +V+D A+KGC D++ +LD  +++H+ +V  
Sbjct: 182 SPEITVAVLPKSEQIVFLEMNGRLHEDNLSKVVDMAVKGCKDVYGVLDRTVREHVSQVGS 241

Query: 240 A 240
           +
Sbjct: 242 S 242

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|291233253|ref|XP_002736568.1| PREDICTED: exosome component 4-like [Saccoglossus kowalevskii]

 Score =  313 bits (801), Expect = 6e-83,   Method: Compositional matrix adjust.
 Identities = 140/231 (60%), Positives = 188/231 (81%), Gaps = 1/231 (0%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRN-KSIKVHGSV 68
           G R DGRR HELRKIRCR+GVF Q+DGSAYIEQGNTKVLA VYGP  +   +S  +H  V
Sbjct: 11  GFRADGRRPHELRKIRCRMGVFRQADGSAYIEQGNTKVLATVYGPHEITGGRSKALHDKV 70

Query: 69  LINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQA 128
           L+N QYSMA FSTGERKTRP+GDR++ E+S+ LR+   AAI++ ++PRSQIDI+V+VLQ+
Sbjct: 71  LLNCQYSMATFSTGERKTRPKGDRRSQEMSMNLRRTFQAAILTHLYPRSQIDIYVQVLQS 130

Query: 129 DGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAAL 188
           DGGN+CACVNAATLA+IDAGIPMR+YV AC++SL  DTP+VDIS+LEE++G P + VA L
Sbjct: 131 DGGNYCACVNAATLAVIDAGIPMRDYVCACTSSLLEDTPVVDISYLEESVGSPEMVVALL 190

Query: 189 PLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAG 239
           P S ++ + + + +LH+D+L +VLD  +KGC D++ ILD ++++H+ +V+ 
Sbjct: 191 PKSEQIVLFQQNSRLHVDNLEKVLDMGIKGCTDVYGILDQSVREHVTEVSN 241

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|242005051|ref|XP_002423388.1| Exosome complex exonuclease RRP41, putative [Pediculus humanus corporis] gi|212506432|gb|EEB10650.1| Exosome complex exonuclease RRP41, putative [Pediculus humanus corporis]

 Score =  307 bits (786), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 143/228 (62%), Positives = 187/228 (82%), Gaps = 1/228 (0%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
            LR DGRR  ELR+IRC+LGVFSQ DGSAYIE GNTKVLAAVYGP  VR ++  +  + +
Sbjct: 9   NLRLDGRRASELRQIRCKLGVFSQPDGSAYIEMGNTKVLAAVYGPHQVRGRTKPLLDAAV 68

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           IN QYS AVFST ERK RPRGD+K+ E S+ L QA+SAAI +E++P+SQIDIFVEVLQ+D
Sbjct: 69  INCQYSSAVFSTEERKKRPRGDKKSQEKSMHLCQALSAAIKTELYPKSQIDIFVEVLQSD 128

Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDT-PLVDISHLEETLGGPNLTVAAL 188
           GG+F A VN +TLALIDAGIP++EYV +C+ASLA +  PLVD+++LEE+ GGP LT+A L
Sbjct: 129 GGSFSAAVNVSTLALIDAGIPLKEYVTSCTASLANENIPLVDVTYLEESCGGPTLTIATL 188

Query: 189 PLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIK 236
           PL+ K+A+ME+SQ+ HLDHL +VL+ A++GC +I  IL+ A+K+H+++
Sbjct: 189 PLAKKIALMEMSQRFHLDHLEKVLNTAMEGCKNIQVILNEAVKRHILQ 236

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328712784|ref|XP_001945013.2| PREDICTED: exosome complex exonuclease RRP41-like [Acyrthosiphon pisum]

 Score =  301 bits (772), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 146/246 (59%), Positives = 197/246 (80%), Gaps = 5/246 (2%)

Query: 1   MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVR-N 59
           MDLL+  G  LR DGRR  ELR+IRC++GVF+Q DGSAY+EQGNTKV+AA+YGP  +R N
Sbjct: 1   MDLLSRQG--LRTDGRRSGELRRIRCKMGVFNQPDGSAYLEQGNTKVVAAIYGPHEIRTN 58

Query: 60  KSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQI 119
           ++   + S +IN QYSMA FS  ERK RPR D K++E++L L+QA++ AI ++++P+SQI
Sbjct: 59  RAKAPNDSAVINCQYSMATFSRSERKRRPR-DNKSAELTLHLKQAMATAIKTDLYPKSQI 117

Query: 120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA-GDTPLVDISHLEETL 178
           DIFV+VLQ+DGGN+  CVNAATLALIDAGI M E+V++C++SLA G+TPLVDISHLEET+
Sbjct: 118 DIFVQVLQSDGGNYSVCVNAATLALIDAGIAMEEFVISCTSSLANGETPLVDISHLEETM 177

Query: 179 GGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVA 238
           GGP+LTVA LP+SGK+A++E SQ++H++HL  VL  A++GC  I+  L+  IK+H  ++ 
Sbjct: 178 GGPSLTVAILPISGKIAMLETSQRIHINHLEPVLTEAVRGCRYIYENLNKIIKKHYEEIG 237

Query: 239 GARGLG 244
           GA   G
Sbjct: 238 GALNWG 243

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321465387|gb|EFX76389.1| hypothetical protein DAPPUDRAFT_213979 [Daphnia pulex]

 Score =  300 bits (769), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 139/229 (60%), Positives = 181/229 (79%), Gaps = 1/229 (0%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVR-NKSIKVHGSV 68
           GLR DGR+ +ELR+IRC LG+FSQ+DGSAY+EQGNTKVLAAVYGP  +R +KS  +H   
Sbjct: 11  GLRIDGRKPNELRRIRCSLGIFSQADGSAYLEQGNTKVLAAVYGPHEIRGSKSKALHDKA 70

Query: 69  LINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQA 128
            +N QYS A FS GERK RPRGDRK++E+S  L +  +AAI +E++PRSQIDIFVEVLQA
Sbjct: 71  FVNCQYSTATFSMGERKRRPRGDRKSTEMSTHLEETFAAAIRTELYPRSQIDIFVEVLQA 130

Query: 129 DGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAAL 188
           DGGN+ ACVNAA +AL+DAG+P+++ VV+C+ASL  D PLVD++H+E + G P L V+ L
Sbjct: 131 DGGNYTACVNAAMMALVDAGVPLKDTVVSCTASLVKDVPLVDVNHVERSGGSPELVVSIL 190

Query: 189 PLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKV 237
           P SG++  M L+Q+ H+DHL +VLD A+KGC DI AIL+  +K HL K+
Sbjct: 191 PHSGEIVYMSLTQRFHIDHLSKVLDTAIKGCKDIGAILNEIMKGHLTKL 239

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	263
UNIPROTKB|Q9NPD3	245	EXOSC4 "Exosome complex compon	0.882	0.946	0.574	1.3e-70
UNIPROTKB|F1RSL0	245	EXOSC4 "Uncharacterized protei	0.882	0.946	0.574	1.6e-70
RGD|1310986	245	Exosc4 "exosome component 4" [	0.882	0.946	0.574	1.6e-70
FB|FBgn0032487	246	Ski6 "Ski6" [Drosophila melano	0.885	0.947	0.6	2.6e-70
UNIPROTKB|Q7YRA3	245	EXOSC4 "Exosome complex compon	0.882	0.946	0.570	2.6e-70
UNIPROTKB|E2RIM3	245	EXOSC4 "Uncharacterized protei	0.882	0.946	0.565	4.3e-70
MGI|MGI:1923576	245	Exosc4 "exosome component 4" [	0.912	0.979	0.555	7e-70
ZFIN|ZDB-GENE-040426-1702	245	exosc4 "exosome component 4" [	0.897	0.963	0.548	1.1e-69
TAIR|locus:2076710	241	RRP41 "AT3G61620" [Arabidopsis	0.806	0.879	0.504	7.2e-52
WB|WBGene00007201	240	exos-4.1 [Caenorhabditis elega	0.878	0.962	0.452	6e-48

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

 Score = 715 (256.8 bits), Expect = 1.3e-70, P = 1.3e-70
 Identities = 135/235 (57%), Positives = 176/235 (74%)

Query:     1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNK 60
             ++LL++ G   R DGRR  ELRKI+ R+GVF+Q+DGSAYIEQGNTK LA VYGP  +R  
Sbjct:     4 LELLSDQG--YRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGS 61

Query:    61 SIK-VHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQI 119
               + +    L+N QYS A FSTGERK RP GDRK+ E+ LQLRQ   AAI++++HPRSQI
Sbjct:    62 RARALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQI 121

Query:   120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLG 179
             DI+V+VLQADGG + ACVNAATLA++DAGIPMR++V ACSA     T L D+SH+EE  G
Sbjct:   122 DIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAG 181

Query:   180 GPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
             GP L +A LP SG++A++E+  +LH DHL RVL+ A +   D+H +LD  ++QH+
Sbjct:   182 GPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHV 236

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

 Score = 714 (256.4 bits), Expect = 1.6e-70, P = 1.6e-70
 Identities = 135/235 (57%), Positives = 178/235 (75%)

Query:     1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVR-N 59
             ++LL++ G   R DGRR  ELRKI+ R+GVF+Q+DGSAYIEQGNTK LA VYGP  +R +
Sbjct:     4 LELLSDQG--YRVDGRRARELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGS 61

Query:    60 KSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQI 119
             +S  +    L+N QYS A FSTGERK RP GDRK+ E+ LQLRQA  AAI++++HPRSQI
Sbjct:    62 RSRALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQAFEAAILTQLHPRSQI 121

Query:   120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLG 179
             DI+V+VLQADGG + ACVN ATLA++DAGIPMR++V ACSA     T L D+SH+EE  G
Sbjct:   122 DIYVQVLQADGGIYAACVNVATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAG 181

Query:   180 GPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
             GP L +A LP SG++A++E+  +LH DHL +VL+ A +   D+H +LD  ++QH+
Sbjct:   182 GPQLALALLPASGQIALLEMDARLHEDHLEQVLEAAAQAARDVHTVLDRVVRQHV 236

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

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

 Score = 714 (256.4 bits), Expect = 1.6e-70, P = 1.6e-70
 Identities = 135/235 (57%), Positives = 178/235 (75%)

Query:     1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVR-N 59
             ++LL++ G   R DGRR  ELRKI+ R+GVF+Q+DGSAYIEQGNTK LA VYGP  +R +
Sbjct:     4 LELLSDQG--YRIDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGS 61

Query:    60 KSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQI 119
             +S  +    L+N QYS A FSTGERK RP GDRK+ E+ LQLRQ   AAI++++HPRSQI
Sbjct:    62 RSRALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQI 121

Query:   120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLG 179
             DI+V+VLQADGG + ACVNAATLA++DAGIPMR++V ACSA     T L D+SH+EE  G
Sbjct:   122 DIYVQVLQADGGTYAACVNAATLAVMDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAG 181

Query:   180 GPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
             GP L +A LP SG++A++E+  +LH DHL +VL+ A +   D+H +LD  ++QH+
Sbjct:   182 GPQLALALLPASGQIALLEMDSRLHEDHLEQVLEAAAQAARDVHTLLDRVVRQHV 236

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

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

 Score = 712 (255.7 bits), Expect = 2.6e-70, P = 2.6e-70
 Identities = 144/240 (60%), Positives = 181/240 (75%)

Query:     2 DLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKS 61
             DLL+E G  LR DGRR HELR+I+C+LGVF Q DGSAY+EQGNTKVLAAVYGP   +   
Sbjct:     6 DLLSEQG--LRLDGRRPHELRRIKCKLGVFEQPDGSAYMEQGNTKVLAAVYGPHQAKGNQ 63

Query:    62 IKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDI 121
              +   SV IN QYS A FST ERK RPRGDRK+ E  L L+QA+SAAI SE++PRSQIDI
Sbjct:    64 TE---SV-INCQYSQATFSTAERKNRPRGDRKSLEFKLYLQQALSAAIKSELYPRSQIDI 119

Query:   122 FVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA-GDTPLVDISHLEETLGG 180
             +VEVLQ DG N+   +NAATLALIDAGI + E++VAC+ASL+  + PL DIS  EE  GG
Sbjct:   120 YVEVLQDDGANYAVALNAATLALIDAGICLNEFIVACTASLSKSNIPLTDISQFEEVSGG 179

Query:   181 PNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGA 240
             P LTVAALP + K+A +E+S++ H+DHL  V++ A+ GC +I  IL+ A+K+HL+ +  A
Sbjct:   180 PKLTVAALPTAEKIAFLEMSERFHIDHLGTVIETAMAGCREIRDILEAAVKEHLLHMGSA 239

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

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

 Score = 712 (255.7 bits), Expect = 2.6e-70, P = 2.6e-70
 Identities = 134/235 (57%), Positives = 176/235 (74%)

Query:     1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNK 60
             ++LL++ G   R DGRR  ELRKI+ R+GVF+Q+DGSAYIEQGNTK LA VYGP  +R  
Sbjct:     4 LELLSDQG--YRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGS 61

Query:    61 SIK-VHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQI 119
               + +    L+N QYS A FSTGERK RP GDRK+ E+ LQLRQ   AAI++++HPRSQI
Sbjct:    62 RARALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQI 121

Query:   120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLG 179
             DI+V+VLQADGG + ACVNAATLA++DAGIPMR++V ACSA     T L D+SH+EE  G
Sbjct:   122 DIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAG 181

Query:   180 GPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
             GP L +A LP SG++A++E+  +LH DHL +VL+ A +   D+H +LD  ++QH+
Sbjct:   182 GPQLALALLPASGQIALLEMDARLHEDHLEQVLEAAARASRDVHTVLDRVVRQHV 236

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

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

 Score = 710 (255.0 bits), Expect = 4.3e-70, P = 4.3e-70
 Identities = 133/235 (56%), Positives = 176/235 (74%)

Query:     1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNK 60
             ++LL++ G   R DGRR  ELRKI+ R+GVF+Q+DGSAYIEQGNTK LA VYGP  +R  
Sbjct:     4 LELLSDQG--YRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGS 61

Query:    61 SIK-VHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQI 119
               + +    L+N QYS A FSTGERK RP GDRK+ E+ L LRQ   AAI++++HPRSQI
Sbjct:    62 RARALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLHLRQTFEAAILTQLHPRSQI 121

Query:   120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLG 179
             DI+V+VLQADGG + ACVNAATLA++DAGIPMR++V ACSA    +T L D+SH+EE  G
Sbjct:   122 DIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDNTALADLSHVEEAAG 181

Query:   180 GPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
             GP L +A LP SG++A++E+  +LH DHL +VL+ A +   D+H +LD  ++QH+
Sbjct:   182 GPQLALALLPASGQIALLEMDARLHEDHLEQVLEAAARAARDVHTVLDRVVRQHV 236

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

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

 Score = 708 (254.3 bits), Expect = 7.0e-70, P = 7.0e-70
 Identities = 135/243 (55%), Positives = 181/243 (74%)

Query:     1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVR-N 59
             ++LL++ G   R DGRR  ELRKI+ R+GVF+Q+DGSAYIEQGNTK LA VYGP  +R +
Sbjct:     4 LELLSDQG--YRIDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGS 61

Query:    60 KSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQI 119
             +S  +    L+N QYS A FSTGERK RP GDRK+ E+ LQLRQ   AAI++++HPRSQI
Sbjct:    62 RSRALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQI 121

Query:   120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLG 179
             DI+V+VLQADGG + ACVNAATLA++DAGIPMR++V ACSA     T L D+SH+EE  G
Sbjct:   122 DIYVQVLQADGGTYAACVNAATLAVMDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAG 181

Query:   180 GPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAG 239
             GP L +A LP SG++A++E+  +LH DHL +VL+ A +    +H +LD  ++QH+ + + 
Sbjct:   182 GPQLALALLPASGQIALLEMDSRLHEDHLEQVLEAAAQAARGVHTLLDLVVRQHVQEASV 241

Query:   240 ARG 242
             + G
Sbjct:   242 SLG 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

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

 Score = 706 (253.6 bits), Expect = 1.1e-69, P = 1.1e-69
 Identities = 131/239 (54%), Positives = 181/239 (75%)

Query:     1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVR-N 59
             ++LL++ G   R DGR+  ELRK++ R+ VF+Q+DGSAY+EQGNTK LA VYGP  +R +
Sbjct:     4 LELLSDQG--YRLDGRKATELRKVQARMSVFAQADGSAYLEQGNTKALAVVYGPHEIRGS 61

Query:    60 KSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQI 119
             +S  +H   +IN QYSMA FST ERK RP GDRK+SE+SL L+Q   AA+++E++PRSQI
Sbjct:    62 RSKSLHDRAIINCQYSMATFSTAERKRRPHGDRKSSEMSLHLKQTFEAAVLTELYPRSQI 121

Query:   120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLG 179
             DI+V++LQADGGN+ ACVNAATLAL+DAGIPMR+YV ACSA    DTPL D+ H EE+ G
Sbjct:   122 DIYVKILQADGGNYSACVNAATLALVDAGIPMRDYVCACSAGFVEDTPLADLCHAEESGG 181

Query:   180 GPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVA 238
             G  L +A LP SG +A++++  +LH DHL  +++ A+  C +   +LD+ ++QHL +V+
Sbjct:   182 GTALALALLPRSGNIALLQMDARLHQDHLDTLMEAAMTACKEFSKVLDSVVRQHLEEVS 240

GO:0004527 "exonuclease activity" evidence=IEA

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

 Score = 538 (194.4 bits), Expect = 7.2e-52, P = 7.2e-52
 Identities = 108/214 (50%), Positives = 155/214 (72%)

Query:    10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSI-KVHGSV 68
             GLR DGRR +E+R+I   +GV S++DGSA  E GNTKV+AAVYGPR ++NKS  K +   
Sbjct:     8 GLRLDGRRFNEMRQIVAEVGVVSKADGSAVFEMGNTKVIAAVYGPREIQNKSQQKKNDHA 67

Query:    69 LINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQA 128
             ++  +YSMA FSTG+R+ R + DR+++E+SL +RQ + A I++E+ P SQIDIF++VLQA
Sbjct:    68 VVLCEYSMAQFSTGDRR-RQKFDRRSTELSLVIRQTMEACILTELMPHSQIDIFLQVLQA 126

Query:   129 DGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAAL 188
             DGG   AC+NAATLAL DAGIPMR+  V+CSA     TPL+D++++E++ GG ++TV  L
Sbjct:   127 DGGTRSACINAATLALADAGIPMRDLAVSCSAGYLNSTPLLDLNYVEDSAGGADVTVGIL 186

Query:   189 PLSGKVAVMELSQKLHLDHLPRVLDCALKGCADI 222
             P   KV+++++  KL ++    V   A +GC  I
Sbjct:   187 PKLDKVSLLQMDAKLPMETFETVFALASEGCKAI 220

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

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

 Score = 501 (181.4 bits), Expect = 6.0e-48, P = 6.0e-48
 Identities = 106/234 (45%), Positives = 148/234 (63%)

Query:     1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNK 60
             M++++E+G   R DGRR  ++R I  RLG+   ++GS Y+E GNTKVL AVYGP   ++ 
Sbjct:     1 MNIISEHG--FRIDGRRPAQIRNINTRLGLNRNAEGSCYLEHGNTKVLCAVYGPYEGKS- 57

Query:    61 SIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQID 120
             S ++     I  QYS   FS  ERK R RGDRK++EIS  L +A  + I++E  PRSQ+D
Sbjct:    58 SKRIEDKCAIVCQYSATKFSGLERKNRTRGDRKSTEISRLLEKAFESVILTEAFPRSQLD 117

Query:   121 IFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGG 180
             IF EV+Q DG N  ACVNA +LAL DAGIPM+    A +  +    P+VD++  EET   
Sbjct:   118 IFCEVIQGDGSNLAACVNATSLALADAGIPMKGIASAATCGVVDGKPIVDLTSREETDLL 177

Query:   181 PNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
             P +T+A +    +V ++EL  +LH+DHL  V+D A   CAD++  L    +QHL
Sbjct:   178 PRVTLATICGRDEVILVELQNRLHIDHLSTVMDAAKATCADVYECLAVVAQQHL 231

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, ., -	0.4080	0.8441	0.925	yes	N/A
Q5JIR6	ECX1_PYRKO	3, ., 1, ., 1, 3, ., -	0.3886	0.8669	0.9156	yes	N/A
Q8TYC1	ECX1_METKA	3, ., 1, ., 1, 3, ., -	0.3946	0.8441	0.9288	yes	N/A
B6YSI2	ECX1_THEON	3, ., 1, ., 1, 3, ., -	0.4	0.8897	0.9397	yes	N/A
Q9UXC2	ECX1_SULSO	3, ., 1, ., 1, 3, ., -	0.3612	0.8593	0.9112	yes	N/A
A0RXU1	ECX1_CENSY	3, ., 1, ., 1, 3, ., -	0.3716	0.8555	0.9259	yes	N/A
B1Y978	ECX1_PYRNV	3, ., 1, ., 1, 3, ., -	0.3695	0.8745	0.9349	yes	N/A
P46948	RRP41_YEAST	No assigned EC number	0.3539	0.8479	0.9065	yes	N/A
O29757	ECX1_ARCFU	3, ., 1, ., 1, 3, ., -	0.3982	0.8631	0.8798	yes	N/A
O42872	RRP41_SCHPO	No assigned EC number	0.4080	0.8441	0.9173	yes	N/A
Q97BZ5	ECX1_THEVO	3, ., 1, ., 1, 3, ., -	0.3793	0.8745	0.9274	yes	N/A
Q9YC03	ECX1_AERPE	3, ., 1, ., 1, 3, ., -	0.3826	0.8707	0.9308	yes	N/A
Q9HIP2	ECX1_THEAC	3, ., 1, ., 1, 3, ., -	0.4	0.8136	0.8629	yes	N/A
A6VEE1	RNPH_PSEA7	2, ., 7, ., 7, ., 5, 6	0.2773	0.8365	0.9205	yes	N/A
A1RST0	ECX1_PYRIL	3, ., 1, ., 1, 3, ., -	0.3405	0.8821	0.9430	yes	N/A
A3MUP1	ECX1_PYRCJ	3, ., 1, ., 1, 3, ., -	0.3580	0.8707	0.9308	yes	N/A
A2BKC0	ECX1_HYPBU	3, ., 1, ., 1, 3, ., -	0.3819	0.8821	0.9098	yes	N/A
Q975G8	ECX1_SULTO	3, ., 1, ., 1, 3, ., -	0.3766	0.8441	0.9135	yes	N/A
Q4JB27	ECX1_SULAC	3, ., 1, ., 1, 3, ., -	0.3815	0.8631	0.9341	yes	N/A
A9A5C9	ECX1_NITMS	3, ., 1, ., 1, 3, ., -	0.3665	0.8365	0.9016	yes	N/A
Q3K4M0	RNPH_PSEPF	2, ., 7, ., 7, ., 5, 6	0.2677	0.8212	0.9	yes	N/A
A4WM67	ECX1_PYRAR	3, ., 1, ., 1, 3, ., -	0.3521	0.8745	0.9349	yes	N/A
O59223	ECX1_PYRHO	3, ., 1, ., 1, 3, ., -	0.3826	0.8707	0.9196	yes	N/A
C3K479	RNPH_PSEFS	2, ., 7, ., 7, ., 5, 6	0.2677	0.8212	0.9	yes	N/A
P50597	RNPH_PSEAE	2, ., 7, ., 7, ., 5, 6	0.2773	0.8365	0.9205	yes	N/A
Q8ZVM9	ECX1_PYRAE	3, ., 1, ., 1, 3, ., -	0.3668	0.8707	0.9308	yes	N/A
Q9NPD3	EXOS4_HUMAN	No assigned EC number	0.5744	0.8821	0.9469	yes	N/A
B7V5M5	RNPH_PSEA8	2, ., 7, ., 7, ., 5, 6	0.2773	0.8365	0.9205	yes	N/A
Q9V119	ECX1_PYRAB	3, ., 1, ., 1, 3, ., -	0.3886	0.8669	0.9156	yes	N/A
Q7YRA3	EXOS4_BOVIN	No assigned EC number	0.5702	0.8821	0.9469	yes	N/A
Q8U0L9	ECX1_PYRFU	3, ., 1, ., 1, 3, ., -	0.3886	0.8669	0.912	yes	N/A
Q921I9	EXOS4_MOUSE	No assigned EC number	0.5702	0.8821	0.9469	yes	N/A
C5A2B9	ECX1_THEGJ	3, ., 1, ., 1, 3, ., -	0.3973	0.8669	0.9156	yes	N/A
A4Y0L7	RNPH_PSEMY	2, ., 7, ., 7, ., 5, 6	0.2669	0.8288	0.9121	yes	N/A
Q02E28	RNPH_PSEAB	2, ., 7, ., 7, ., 5, 6	0.2773	0.8365	0.9205	yes	N/A
Q17533	EXOS4_CAEEL	No assigned EC number	0.4529	0.8783	0.9625	yes	N/A

EC Number Prediction by EFICAz Software

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	263
cd11370	226	cd11370, RNase_PH_RRP41, RRP41 subunit of eukaryot	1e-126
PRK03983	244	PRK03983, PRK03983, exosome complex exonuclease Rr	1e-71
TIGR02065	230	TIGR02065, ECX1, archaeal exosome-like complex exo	1e-66
cd11366	214	cd11366, RNase_PH_archRRP41, RRP41 subunit of arch	3e-66
COG0689	230	COG0689, Rph, RNase PH [Translation, ribosomal str	3e-65
cd11371	210	cd11371, RNase_PH_MTR3, MTR3 subunit of eukaryotic	1e-58
cd11358	218	cd11358, RNase_PH, RNase PH-like 3'-5' exoribonucl	2e-43
pfam01138	129	pfam01138, RNase_PH, 3' exoribonuclease family, do	1e-42
cd11372	199	cd11372, RNase_PH_RRP46, RRP46 subunit of eukaryot	3e-35
cd11362	227	cd11362, RNase_PH_bact, Ribonuclease PH	2e-16
TIGR01966	236	TIGR01966, RNasePH, ribonuclease PH	3e-14
PRK00173	238	PRK00173, rph, ribonuclease PH; Reviewed	7e-12
cd11364	223	cd11364, RNase_PH_PNPase_2, Polyribonucleotide nuc	2e-09
cd11365	256	cd11365, RNase_PH_archRRP42, RRP42 subunit of arch	3e-09
cd11368	259	cd11368, RNase_PH_RRP45, RRP45 subunit of eukaryot	3e-09
pfam03725	68	pfam03725, RNase_PH_C, 3' exoribonuclease family,	7e-09
COG2123	272	COG2123, COG2123, RNase PH-related exoribonuclease	3e-08
COG1185	692	COG1185, Pnp, Polyribonucleotide nucleotidyltransf	4e-08
TIGR02696	719	TIGR02696, pppGpp_PNP, guanosine pentaphosphate sy	1e-07
cd11369	261	cd11369, RNase_PH_RRP43, RRP43 subunit of eukaryot	2e-07
TIGR03591	684	TIGR03591, polynuc_phos, polyribonucleotide nucleo	9e-07
cd11367	272	cd11367, RNase_PH_RRP42, RRP42 subunit of eukaryot	1e-06
PLN00207	891	PLN00207, PLN00207, polyribonucleotide nucleotidyl	5e-06
PRK04282	271	PRK04282, PRK04282, exosome complex RNA-binding pr	1e-05

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

 Score =  356 bits (917), Expect = e-126
 Identities = 132/225 (58%), Positives = 176/225 (78%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           GLR DGRR +ELR+IRCR+GVFS +DGSAY+EQGNTKVLAAVYGP   RN+S  +H   +
Sbjct: 1   GLRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNRSQALHDRAV 60

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           +N +YSMA FSTGERK R +GDR+++E+SL +RQ   A I++ ++PRSQIDI+V+VLQAD
Sbjct: 61  VNCEYSMATFSTGERKRRGKGDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQAD 120

Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
           GG   AC+NAATLALIDAGIPM++YV ACSA     TPL+D+++LEE+   P+LTVA LP
Sbjct: 121 GGLLAACINAATLALIDAGIPMKDYVCACSAGYLDSTPLLDLNYLEESGDLPDLTVAVLP 180

Query: 190 LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
            S KV ++++  +LHLD L +VL+ A++GC  I  I+D  +++H 
Sbjct: 181 KSDKVVLLQMESRLHLDRLEKVLELAIEGCKVIREIMDEVVREHT 225

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 =  219 bits (559), Expect = 1e-71
 Identities = 93/230 (40%), Positives = 142/230 (61%), Gaps = 1/230 (0%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           GLR DGR+  ELR I+  +GV   +DGSAY+E GN K++AAVYGPR +  + +++    +
Sbjct: 13  GLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAV 72

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           +  +Y+MA FS  ERK RP  DR++ EIS  +R+A+  AIM E+ PR+ ID+F+EVLQAD
Sbjct: 73  LRVRYNMAPFSVDERK-RPGPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQAD 131

Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
            G   A + AA+LAL DAGIPMR+ V  C+        ++D++  E+  G  ++ VA +P
Sbjct: 132 AGTRVAGITAASLALADAGIPMRDLVAGCAVGKVDGVIVLDLNKEEDNYGEADMPVAIMP 191

Query: 190 LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAG 239
             G++ +++L   L  +     L+ A KG   I+ +   A+K    ++A 
Sbjct: 192 RLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQLQREALKSKYGEIAE 241

Length = 244

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

 Score =  206 bits (526), Expect = 1e-66
 Identities = 96/223 (43%), Positives = 140/223 (62%), Gaps = 1/223 (0%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           G+R DGR+  ELR I+   GV   +DGSAY+E G TK+LAAVYGPR    + +++    +
Sbjct: 7   GVRLDGRKPDELRPIKIEAGVLKNADGSAYLEFGGTKILAAVYGPREAHPRHLQLPDRAV 66

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           +  +Y MA FST ERK RP   R+  EIS  +R+A+  AI+ E  PR+ ID+F+EVLQAD
Sbjct: 67  LRVRYHMAPFSTDERK-RPGPSRREIEISKVIREALEPAILLEQFPRTVIDVFIEVLQAD 125

Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
           GG  CA + AA+LAL DAGIPMR+ VV  +        ++D+S  E+  G  ++ VA +P
Sbjct: 126 GGTRCAGLTAASLALADAGIPMRDLVVGVAVGKVDGVVVLDLSEEEDMYGEADMPVAIMP 185

Query: 190 LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQ 232
            +G++ +++L   L  D   + LD A++G   I+ I   A+K+
Sbjct: 186 KTGEITLLQLDGDLTPDEFRQALDLAVEGIKRIYEIQREALKK 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|206771 cd11366, RNase_PH_archRRP41, RRP41 subunit of archaeal exosome

 Score =  204 bits (521), Expect = 3e-66
 Identities = 90/212 (42%), Positives = 135/212 (63%), Gaps = 1/212 (0%)

Query: 20  ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVF 79
           ELR I+  +GV   +DGSAY+E GN K++AAVYGPR V  + +++    +I  +Y+MA F
Sbjct: 1   ELRPIKIEVGVLKNADGSAYVEWGNNKIIAAVYGPREVHPRHLQLPDRAVIRVRYNMAPF 60

Query: 80  STGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNA 139
           S  ERK RP  DR+  EIS  +++A+  AI+ E  PR+ ID+FVEVLQAD G   A +NA
Sbjct: 61  SVDERK-RPGPDRREIEISKVIKEALEPAIILEEFPRTAIDVFVEVLQADAGTRVAGLNA 119

Query: 140 ATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMEL 199
           A+LAL DAGIPMR+ V AC+A       ++D++  E+  G  ++ +A +P  G++ +++L
Sbjct: 120 ASLALADAGIPMRDLVAACAAGKVDGKIVLDLNKEEDNYGEADMPIAMMPNLGEITLLQL 179

Query: 200 SQKLHLDHLPRVLDCALKGCADIHAILDTAIK 231
              L  D   + ++ A KGC  I+ +   A+K
Sbjct: 180 DGDLTPDEFKQAIELAKKGCKRIYELQKEALK 211

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

 Score =  202 bits (517), Expect = 3e-65
 Identities = 81/224 (36%), Positives = 120/224 (53%), Gaps = 2/224 (0%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           G+R DGR+  ELR I+   GV   ++GS+ IE GNTKV+  V GPR    + ++  G   
Sbjct: 7   GMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGW 66

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           +  +Y M   ST ERK R     +T EIS  + +A+ A I  E+ P S IDI  +VLQAD
Sbjct: 67  LTAEYGMLPRSTDERKKREADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQAD 126

Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
           GG   A +  A+LAL DAGIP+R+ V A S  +     ++D+ + E++    ++ V    
Sbjct: 127 GGTRTASITGASLALADAGIPLRDLVAAISVGIVDGVIVLDLDYEEDSAAEADMNVVMTG 186

Query: 190 LSGKVAV--MELSQKLHLDHLPRVLDCALKGCADIHAILDTAIK 231
             G V +  +        D L  +LD A+KGC ++  +   A+ 
Sbjct: 187 NGGLVEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQREALA 230

Length = 230

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

 Score =  185 bits (471), Expect = 1e-58
 Identities = 82/213 (38%), Positives = 125/213 (58%), Gaps = 4/213 (1%)

Query: 21  LRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKV-HGSVLINFQYSMAVF 79
           +R I  + GV SQ+ GSAY+E GNTKV+ +VYGPRP+  ++     G +    ++  A F
Sbjct: 1   IRPIFLKTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFSDRGRLNCEVKF--APF 58

Query: 80  STGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNA 139
           +T  R+   + D +  E+S  L QA+  A+  E +P+SQID+FV VL++DG    A + A
Sbjct: 59  ATPGRRRHGQ-DSEERELSSLLHQALEPAVRLEKYPKSQIDVFVTVLESDGSVLAAAITA 117

Query: 140 ATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMEL 199
           A+LAL DAGI M + V ACSA+L GD  L+D +  EE      + +A +P   +V  +  
Sbjct: 118 ASLALADAGIEMYDLVTACSAALIGDELLLDPTREEEEASSGGVMLAYMPSLNQVTQLWQ 177

Query: 200 SQKLHLDHLPRVLDCALKGCADIHAILDTAIKQ 232
           S ++ +D L   LD  + GC  IH ++  A+ +
Sbjct: 178 SGEMDVDQLEEALDLCIDGCNRIHPVVRQALLE 210

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

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

 Score =  146 bits (370), Expect = 2e-43
 Identities = 67/221 (30%), Positives = 102/221 (46%), Gaps = 22/221 (9%)

Query: 21  LRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFS 80
            R +    GV +Q+DGSA ++ GNTKV+ AV GP    +K  +      +     ++  +
Sbjct: 1   FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLERPD-KGTLYVNVEISPGA 59

Query: 81  TGERKTRPRGDRKTSEISLQLRQAVSAAIM---SEVHPRSQIDIFVEVLQADGGNFCACV 137
            GER+ +     +  EIS  L + + A+++   S   P   + + ++VL  DGG   AC 
Sbjct: 60  VGERR-QGPPGDEEMEISRLLERTIEASVILDKSTRKPSWVLYVDIQVLSRDGGLLDACW 118

Query: 138 NAATLALIDAGIP-------------MREYVVACSASLAGD-TPLVDISHLEETLGGPNL 183
           NAA  AL DAGIP             M++ +VA S     D   L+D +  EE L    L
Sbjct: 119 NAAIAALKDAGIPRVFVDERSPPLLLMKDLIVAVSVGGISDGVLLLDPTGEEEELADSTL 178

Query: 184 TVAALPLSGKVAVMELSQKLHLD--HLPRVLDCALKGCADI 222
           TVA    SGK+ ++       LD   +   L+ A K    +
Sbjct: 179 TVAVDK-SGKLCLLSKVGGGSLDTEEIKECLELAKKRSLHL 218

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

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

 Score =  141 bits (357), Expect = 1e-42
 Identities = 56/131 (42%), Positives = 73/131 (55%), Gaps = 2/131 (1%)

Query: 20  ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVF 79
           ELR I    GV SQ+DGSA +E G+TKVLA V GP     K        L   +Y  + F
Sbjct: 1   ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPPQKERDFFPGEL-TVEYEESPF 59

Query: 80  STGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNA 139
           ++GER    R   +  E+S  + +A+  +I  E +PR +I I V VL  DG    A +NA
Sbjct: 60  ASGERP-EGRPSEREIELSRLIDRALRPSIPLEGYPRWEIRIDVTVLSDDGSLLDAAINA 118

Query: 140 ATLALIDAGIP 150
           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 =  124 bits (314), Expect = 3e-35
 Identities = 53/158 (33%), Positives = 83/158 (52%), Gaps = 13/158 (8%)

Query: 21  LRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL-INFQYSMAVF 79
           LR + C LG+ S++DGSA   QG+T VLAAVYGP  V+ +      + L +  +    + 
Sbjct: 1   LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLP 60

Query: 80  STGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNA 139
              E+            + L LR  +   I+  +HPR+ I + ++VLQ DG      +NA
Sbjct: 61  GVKEK-----------LLELLLRSTLEPIILLHLHPRTLISVVLQVLQDDGSLLACAINA 109

Query: 140 ATLALIDAGIPMREYVVACSASLAGDTPLV-DISHLEE 176
           A LAL+DAG+PM+    A + ++  D  ++ D +  EE
Sbjct: 110 ACLALLDAGVPMKGLFAAVTCAITEDGEIILDPTAEEE 147

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 = 75.7 bits (187), Expect = 2e-16
 Identities = 55/176 (31%), Positives = 79/176 (44%), Gaps = 26/176 (14%)

Query: 20  ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVY----GPRPVRNKSIKVHGSVLINFQYS 75
           +LR I    G    ++GS  IE G+TKVL         P  +R K     G   +  +YS
Sbjct: 1   QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASVEEKVPPFLRGK-----GKGWVTAEYS 55

Query: 76  MAVFSTGERKTRPRGDRK----TSEISLQLRQAVSAAI-MSEVHPRSQIDIFVEVLQADG 130
           M   ST ER  R     K    T EI   + +++ AA+ +  +  R  I I  +VLQADG
Sbjct: 56  MLPRSTHERTQREASKGKQSGRTQEIQRLIGRSLRAAVDLEALGER-TITIDCDVLQADG 114

Query: 131 GNFCACVNAATLALIDA-----------GIPMREYVVACSASLAGDTPLVDISHLE 175
           G   A +  A +AL DA             P++ +V A S  +    PL+D+ + E
Sbjct: 115 GTRTASITGAYVALADAVDKLVEKGVLEENPLKHFVAAVSVGIVDGEPLLDLDYEE 170

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|131021 TIGR01966, RNasePH, ribonuclease PH

 Score = 69.7 bits (171), Expect = 3e-14
 Identities = 66/232 (28%), Positives = 104/232 (44%), Gaps = 26/232 (11%)

Query: 12  RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVL--AAVYG--PRPVRNKSIKVHGS 67
           R DGR+  +LR +         ++GS  IE GNTKVL  A+V    P  +R       G 
Sbjct: 1   RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGS-----GE 55

Query: 68  VLINFQYSMAVFSTGERKTRP----RGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFV 123
             I  +Y M   +T  R  R     +   +T EI   + +A+ A +  E      I I  
Sbjct: 56  GWITAEYGMLPRATQTRNRRESAKGKQSGRTQEIQRLIGRALRAVVDLEALGERTIWIDC 115

Query: 124 EVLQADGGNFCACVNAATLALIDA-----------GIPMREYVVACSASLAGDTPLVDIS 172
           +V+QADGG   A +  A +AL DA             P+R++V A S  +    P++D+ 
Sbjct: 116 DVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAAVSVGIVDGEPVLDLD 175

Query: 173 HLEETLGGPNLTVAALPLSGKVAVMELSQK--LHLDHLPRVLDCALKGCADI 222
           + E++    ++ V      G V V   +++     D L ++LD A KG  ++
Sbjct: 176 YEEDSAADVDMNVVMTGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIREL 227

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|178914 PRK00173, rph, ribonuclease PH; Reviewed

 Score = 63.2 bits (155), Expect = 7e-12
 Identities = 54/187 (28%), Positives = 82/187 (43%), Gaps = 32/187 (17%)

Query: 12  RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVL--AAVYG--PRPVRNKSIKVHGS 67
           R DGR   +LR +         ++GS  +E G+TKVL  A+V    PR ++ +     G 
Sbjct: 2   RPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQ-----GQ 56

Query: 68  VLINFQYSMAVFSTGERKTRP--RG--DRKTSEIS-L---QLRQAVSAAIMSEVHPRSQI 119
             +  +Y M   +T  R  R   +G    +T EI  L    LR  V    + E      I
Sbjct: 57  GWVTAEYGMLPRATHTRNDREAAKGKQGGRTQEIQRLIGRSLRAVVDLKALGE----RTI 112

Query: 120 DIFVEVLQADGGNFCACVNAATLALIDA-----------GIPMREYVVACSASLAGDTPL 168
            I  +V+QADGG   A +  A +AL DA             P+++ V A S  +    P+
Sbjct: 113 TIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKNPLKDQVAAVSVGIVDGEPV 172

Query: 169 VDISHLE 175
           +D+ + E
Sbjct: 173 LDLDYEE 179

Length = 238

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

 Score = 56.0 bits (136), Expect = 2e-09
 Identities = 54/177 (30%), Positives = 84/177 (47%), Gaps = 12/177 (6%)

Query: 20  ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKSIKVHGSVLINF--QYSM 76
           E+R I C +G+  ++ GSA   +G T+VL  V  G      K   + G     F   Y+ 
Sbjct: 1   EIRPISCEVGLLPRTHGSALFTRGETQVLCTVTLGTLEDAQKIDSLGGEKSKRFMLHYNF 60

Query: 77  AVFSTGE-RKTRPRGDRKTSEISLQLRQAVSAAIMS-EVHPRSQIDIFVEVLQADGGNFC 134
             +S GE  +    G R+    +L  R A+   + S E  P + I +  EVL+++G +  
Sbjct: 61  PPYSVGETGRVGGPGRREIGHGALAER-ALLPVLPSPEDFPYT-IRVVSEVLESNGSSSM 118

Query: 135 ACVNAATLALIDAGIPMREYVVACSASLAGDTP-----LVDISHLEETLGGPNLTVA 186
           A V   +LAL+DAG+P++  V   +  L  +       L DI  LE+ LG  +  VA
Sbjct: 119 ASVCGGSLALMDAGVPIKAPVAGIAMGLITEGIDDYRVLTDILGLEDHLGDMDFKVA 175

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|206770 cd11365, RNase_PH_archRRP42, RRP42 subunit of archaeal exosome

 Score = 56.1 bits (136), Expect = 3e-09
 Identities = 60/260 (23%), Positives = 97/260 (37%), Gaps = 66/260 (25%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-------YGPRPVRNKSI 62
           G R DGR   E R I    GV  +++GSA ++ GNT+VLA V       +   P  N+  
Sbjct: 15  GKRIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGVKLEVGEPFPDTP--NE-- 70

Query: 63  KVHGSVLINFQYS-MA--VFSTGERKTRP--------RGDRKTSEI---SLQLRQAVSAA 108
              G +++N +   +A   F  G              RG R++  I    L +       
Sbjct: 71  ---GVLIVNAELLPLASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVW 127

Query: 109 IMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP------------------ 150
           ++        IDI+  VL  DG  F A   AA  AL++  +P                  
Sbjct: 128 VVF-------IDIY--VLDYDGNLFDASALAAVAALLNTKVPEYEVDENEVIEVLGEELP 178

Query: 151 --MREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHL 208
             +    V+ + +  G   +VD +  EE +    +T+      G +  +   QK      
Sbjct: 179 LPVNTLPVSVTVAKIGGYIVVDPTLEEELVMDARITITIDE-DGNIVAL---QKGGGGSF 234

Query: 209 PR-----VLDCALKGCADIH 223
                   +D AL+  A++ 
Sbjct: 235 TEDEIDKAIDIALEKAAELR 254

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|206773 cd11368, RNase_PH_RRP45, RRP45 subunit of eukaryotic exosome

 Score = 56.0 bits (136), Expect = 3e-09
 Identities = 47/150 (31%), Positives = 62/150 (41%), Gaps = 28/150 (18%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYG----PRPVRNKSIKVH 65
           GLR DGR   E R I+     F    G   +  G T+VLA V      P+P R       
Sbjct: 16  GLRLDGRGLDEFRPIKIT---FGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPN----E 68

Query: 66  GSVLINFQYS-MAVFSTGERKTRPRGDRKTSEISLQLRQAV--SAAIMSE---VHPRS-- 117
           G + IN + S MA  S      RP  +    E+S  L +A+  S A+ +E   +      
Sbjct: 69  GILFINVELSPMA--SPAFEPGRPSEEEV--ELSRLLERALRDSRAVDTESLCIIAGEKV 124

Query: 118 -QIDIFVEVLQADGGNF--CACVNAATLAL 144
             I + V VL    GN    A + AA  AL
Sbjct: 125 WSIRVDVHVL-NHDGNLIDAASL-AAIAAL 152

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|217696 pfam03725, RNase_PH_C, 3' exoribonuclease family, domain 2

 Score = 50.6 bits (122), Expect = 7e-09
 Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 154 YVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMEL--SQKLHLDHLPRV 211
            V A +        ++D +  EE+L   +LT+        VA+M+     +L  + L   
Sbjct: 2   PVAAVTVGKIDGELVLDPTLEEESLADSDLTIVVAGTGEIVALMKEGGGAELTEEELLEA 61

Query: 212 LDCALKG 218
           L+ A +G
Sbjct: 62  LELAHEG 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|225034 COG2123, COG2123, RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]

 Score = 53.1 bits (128), Expect = 3e-08
 Identities = 56/271 (20%), Positives = 96/271 (35%), Gaps = 56/271 (20%)

Query: 3   LLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-------YGPR 55
           +L     G+R DGR   E R +    GV  +++GSA ++ GNT+V+  V       +   
Sbjct: 15  ILNLLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIGEPFPDT 74

Query: 56  PVRNKSIKVHGSVLINFQYSMAVFSTGERKTRP--------RGDRKTSEI---SLQLRQA 104
           P     + V    L         F  G              RG R++  I    L + + 
Sbjct: 75  PNEG--VLVVNVELSPLASP--SFEPGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEG 130

Query: 105 VSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP-------------- 150
               +   V     +D+   VL  DG    A   AA  AL++  +P              
Sbjct: 131 KKVWV---VF----VDVH--VLDYDGNLIDAASLAAVAALLNTRVPKAVEVGDGEIVIEV 181

Query: 151 --------MREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK 202
                   +    ++ + +  G+  +VD S  EE +    LT+  +   G++  ++    
Sbjct: 182 EEEPVPLPVSNPPISVTFAKIGNVLVVDPSLEEELVADGRLTI-TVNEDGEIVAIQKVGG 240

Query: 203 LHLDH--LPRVLDCALKGCADIHAILDTAIK 231
             +    L + L  AL     +   L  A+K
Sbjct: 241 GSITESDLEKALKTALSKAEKLREALKEALK 271

Length = 272

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

 Score = 53.3 bits (129), Expect = 4e-08
 Identities = 61/188 (32%), Positives = 88/188 (46%), Gaps = 23/188 (12%)

Query: 7   YGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKSIK-V 64
             G +R DGR G E+R I   +GV  ++ GSA   +G T+ L  V  G  P   + I  +
Sbjct: 308 LEGKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGT-PRDAQVIDIL 366

Query: 65  HGSVLINF--QYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMSEVHPRSQI 119
            G     F   Y+   FS GE  T   G     EI   +L  R A++  + SE      I
Sbjct: 367 EGEYKKRFLLHYNFPPFSVGE--TGRMGSPGRREIGHGALAER-ALAPVLPSEEEFPYTI 423

Query: 120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA------GDTPLV--DI 171
            +  E+L+++G +  A V   +LAL+DAG+P++  V    A +A      GD   V  DI
Sbjct: 424 RVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPV----AGIAMGLIKEGDKYAVLSDI 479

Query: 172 SHLEETLG 179
              E+ LG
Sbjct: 480 LGDEDHLG 487

Length = 692

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

 Score = 52.1 bits (125), Expect = 1e-07
 Identities = 71/244 (29%), Positives = 101/244 (41%), Gaps = 39/244 (15%)

Query: 9   GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAA-----------VYGPRPV 57
            G+R DGR   ++R +   + V  +  GSA  E+G T++L             +    P 
Sbjct: 333 EGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPE 392

Query: 58  RNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMSEVH 114
            +K    H        Y+   +STGE  T   G  K  EI   +L  R  V      E  
Sbjct: 393 TSKRYMHH--------YNFPPYSTGE--TGRVGSPKRREIGHGALAERALVPVLPSREEF 442

Query: 115 PRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDT-------- 166
           P + I    E L ++G      V A+TL+L++AG+P++  V   +  L  D         
Sbjct: 443 PYA-IRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAGIAMGLISDEVDGETRYV 501

Query: 167 PLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLP-RVLDCALKGCADIH-A 224
            L DI   E+  G  +  VA    S  V  ++L  K  LD +P  VL  ALK   D   A
Sbjct: 502 ALTDILGAEDAFGDMDFKVAG--TSEFVTALQLDTK--LDGIPASVLASALKQARDARLA 557

Query: 225 ILDT 228
           ILD 
Sbjct: 558 ILDV 561

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|206774 cd11369, RNase_PH_RRP43, RRP43 subunit of eukaryotic exosome

 Score = 50.2 bits (121), Expect = 2e-07
 Identities = 52/233 (22%), Positives = 77/233 (33%), Gaps = 60/233 (25%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYG----PRPVRNKSIKVH 65
            +R DGR   E R     +G  S +DGSA ++ GNT VL  +      P           
Sbjct: 16  NVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPD----E 71

Query: 66  GSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAI-MSEVHPRSQIDIF-- 122
           G ++ N      + S+  R   P      SE +  L   ++  +  S V    Q+ I   
Sbjct: 72  GYLVPNVDLP-PLCSSKFRPGPP------SEEAQVLSSFLADILLNSNVLDLEQLCIVPG 124

Query: 123 ---------VEVLQADGGNFCACVNAATLALIDAGIP-------MREYVV---------- 156
                    V  L  DG    A + A   AL +  +P           VV          
Sbjct: 125 KLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRLPAVTIDEETELVVVNPEERRPLNL 184

Query: 157 ---ACSASLA---GDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKL 203
                S + A       L D +  EE L    +TV          V++ + +L
Sbjct: 185 KNLPVSTTFAVFDDKHLLADPTAEEELLASGLVTV----------VVDENGEL 227

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|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase

 Score = 49.4 bits (119), Expect = 9e-07
 Identities = 48/156 (30%), Positives = 74/156 (47%), Gaps = 15/156 (9%)

Query: 9   GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKSI--KVH 65
            G R DGR    +R I   +GV  ++ GSA   +G T+ L     G    R++ I   + 
Sbjct: 308 EGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTE--RDEQIIDDLE 365

Query: 66  GSVLINF--QYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMS-EVHPRSQI 119
           G     F   Y+   +S GE      G     EI   +L  R A+ A + S E  P + I
Sbjct: 366 GEYRKRFMLHYNFPPYSVGE--VGRVGGPGRREIGHGALAER-ALKAVLPSEEEFPYT-I 421

Query: 120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYV 155
            +  E+L+++G +  A V   +LAL+DAG+P++  V
Sbjct: 422 RVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPV 457

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|206772 cd11367, RNase_PH_RRP42, RRP42 subunit of eukaryotic exosome

 Score = 48.0 bits (115), Expect = 1e-06
 Identities = 42/153 (27%), Positives = 66/153 (43%), Gaps = 19/153 (12%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYG----PRPVRNKSIKVH 65
            +RNDGR   + R I    GV S ++GSA +  GNT VL  V      P P         
Sbjct: 17  NIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPET------P 70

Query: 66  GSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSE-----VHPRSQI- 119
               + F    +  ++ E + R  G+   +E+S  L +A+ +    +     + P  Q  
Sbjct: 71  NKGRLEFFVDCSPNASPEFEGR-GGEELATELSSALERALKSGSAIDLSKLCIVPGKQCW 129

Query: 120 DIFVEVL-QADGGNFCACVNAAT-LALIDAGIP 150
            ++V+VL    GGN    ++ A   AL +  IP
Sbjct: 130 VLYVDVLVLESGGNLLDAISIAVKAALFNTRIP 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

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

 Score = 47.2 bits (112), Expect = 5e-06
 Identities = 49/192 (25%), Positives = 81/192 (42%), Gaps = 14/192 (7%)

Query: 9   GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKS---IKV 64
           GG R+DGR   E+R I    G+  ++ GSA   +G T+ LA V  G + +  +    +  
Sbjct: 436 GGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDA 495

Query: 65  HGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVE 124
                   QYS      GE        R+     +   +A+   + SE      I +   
Sbjct: 496 DEVKRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFPYTIRVEST 555

Query: 125 VLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDT--------PLV--DISHL 174
           + +++G +  A V    LAL DAG+P++  +   +  +  DT        PL+  DI+  
Sbjct: 556 ITESNGSSSMASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGGDGSPLILSDITGS 615

Query: 175 EETLGGPNLTVA 186
           E+  G  +  VA
Sbjct: 616 EDASGDMDFKVA 627

Length = 891

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

 Score = 45.3 bits (108), Expect = 1e-05
 Identities = 20/42 (47%), Positives = 27/42 (64%)

Query: 10 GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV 51
          G R DGR+  E R I    GV  +++GSA ++ GNT+VLA V
Sbjct: 23 GKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGV 64

Length = 271

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	263
TIGR02065	230	ECX1 archaeal exosome-like complex exonuclease 1.	100.0
PRK03983	244	exosome complex exonuclease Rrp41; Provisional	100.0
KOG1068|consensus	245		100.0
PRK00173	238	rph ribonuclease PH; Reviewed	100.0
TIGR01966	236	RNasePH ribonuclease PH. This bacterial enzyme, ri	100.0
COG0689	230	Rph RNase PH [Translation, ribosomal structure and	100.0
PRK04282	271	exosome complex RNA-binding protein Rrp42; Provisi	100.0
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	100.0
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	100.0
COG2123	272	RNase PH-related exoribonuclease [Translation, rib	100.0
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	100.0
KOG1069|consensus	217		100.0
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	100.0
KOG1614|consensus	291		100.0
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	100.0
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	100.0
KOG1612|consensus	288		99.98
KOG1613|consensus	298		99.97
PF01138	132	RNase_PH: 3' exoribonuclease family, domain 1 This	99.97
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	99.96
KOG1067|consensus	760		99.93
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.92
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	99.87
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	99.8
KOG1067|consensus	760		99.69
PF03725	68	RNase_PH_C: 3' exoribonuclease family, domain 2 Th	99.27

>TIGR02065 ECX1 archaeal exosome-like complex exonuclease 1

Probab=100.00  E-value=1.1e-52  Score=362.89  Aligned_cols=228  Identities=41%  Similarity=0.686  Sum_probs=212.9

Q ss_pred             cccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCc
Q psy18119          3 LLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTG   82 (263)
Q Consensus         3 ~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~   82 (263)
                      +|++  +|+|+|||.++|+|++++++|++++++|||++++|+|+|+|+|+||.+.+......++++.|+|+|+++||++.
T Consensus         2 ~~~~--~~~R~DGR~~~e~R~~~~~~g~~~~a~GSa~~~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~~~a~~   79 (230)
T TIGR02065         2 LILE--DGVRLDGRKPDELRPIKIEAGVLKNADGSAYVEFGGTKIIAAVYGPREMHPRHLQLPDRAVLRVRYHMAPFSTD   79 (230)
T ss_pred             cccC--CCcCCCCCCcccccCeEEEECCCCCCCeEEEEEECCcEEEEEEeCCCccccccccCCCceEEEEEEEeCCcccC
Confidence            4566  99999999999999999999999999999999999999999999998865543456889999999999999886


Q ss_pred             cccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEEe
Q psy18119         83 ERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASL  162 (263)
Q Consensus        83 ~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~~  162 (263)
                      ++++ +.+++++.+++++|+++|+++++++.||++.|+|+|+||++||++++|++||+++||+|+||||+++++++|+++
T Consensus        80 ~~~~-~~~~~~~~~~s~~l~~~l~~~i~~~~~p~~~i~i~v~vl~~DG~~~~aai~aa~lAL~dagIp~~~~v~avtv~~  158 (230)
T TIGR02065        80 ERKR-PGPSRREIEISKVIREALEPAILLEQFPRTAIDVFIEVLQADAGTRCAGLTAASLALADAGIPMRDLVVGVAVGK  158 (230)
T ss_pred             CccC-CCCCccHHHHHHHHHHHHHHHhChhhcCCeEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCCccccceeeEEEEE
Confidence            5543 346788899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        163 AGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQH  233 (263)
Q Consensus       163 ~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~  233 (263)
                      +++.+++|||..||..+.+.++|++++..++|+++++.|.++++++.++++.|.++|+.++++++++|+++
T Consensus       159 ~~~~~v~Dpt~~Ee~~~~~~l~va~~~~~~~i~~i~~~g~~~~e~~~~~l~~a~~~~~~l~~~~~~~l~~~  229 (230)
T TIGR02065       159 VDGVVVLDLNEEEDMYGEADMPVAMMPKLGEITLLQLDGDMTPDEFRQALDLAVKGIKIIYQIQREALKNK  229 (230)
T ss_pred             ECCeEEECCCHHHhhcCCCceEEEEeCCCCCEEEEEEecCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            99999999999999999999999998778999999999999999999999999999999999999999876

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=2.2e-52  Score=363.97  Aligned_cols=234  Identities=41%  Similarity=0.687  Sum_probs=217.0

Q ss_pred             ccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCC
Q psy18119          2 DLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFST   81 (263)
Q Consensus         2 e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~   81 (263)
                      +++++  +|+|+|||.++|+|++++++|++++++|||++++|+|+|+|+|+||.+........++++.++|+++++||++
T Consensus         7 ~~~~~--~~~R~DGR~~~~~R~i~i~~G~l~~a~GSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~l~v~~~~~p~~~   84 (244)
T PRK03983          7 KLILE--DGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSV   84 (244)
T ss_pred             hhhcc--CCCCCCCCCcCcccceEEEeCCCCCCCeEEEEEECCeEEEEEEecCCccccccccCCCcEEEEEEEEcCCCcc
Confidence            45676  9999999999999999999999999999999999999999999999887654345688999999999999998


Q ss_pred             ccccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEE
Q psy18119         82 GERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSAS  161 (263)
Q Consensus        82 ~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~  161 (263)
                      .++. +..+++++.+++++|+++|+++++++.||++.|+|+++||++|||+++|++||+++||+|+||||+++++++|++
T Consensus        85 ~~~~-~~~~~~~~~~~s~~l~~~l~~~i~~~~~p~~~I~I~i~VL~~DG~~~~aai~Aa~lAL~dagIp~~~~v~avtv~  163 (244)
T PRK03983         85 DERK-RPGPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVG  163 (244)
T ss_pred             cccc-CCCCChhHHHHHHHHHHHHHHhccHHhCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHhcCCccccceeEEEEE
Confidence            6554 334677889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy18119        162 LAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVA  238 (263)
Q Consensus       162 ~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~  238 (263)
                      ++++.+++|||..||+.+++.++|+++++.++|+++++.|.++.+++.++++.|.++|++++++|+++|+++..+..
T Consensus       164 ~~~~~~i~DPt~~Ee~~~~~~l~va~~~~~~~I~~l~~~G~~~~~~~~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~  240 (244)
T PRK03983        164 KVDGVIVLDLNKEEDNYGEADMPVAIMPRLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQLQREALKSKYGEIA  240 (244)
T ss_pred             EECCEEEECCCHHHhccCCceEEEEEECCCCCEEEEEEecCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            99999999999999999999999999777899999999999999999999999999999999999999998877543

>KOG1068|consensus

Probab=100.00  E-value=3.7e-51  Score=345.03  Aligned_cols=239  Identities=52%  Similarity=0.841  Sum_probs=228.1

Q ss_pred             CccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCC
Q psy18119          1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFS   80 (263)
Q Consensus         1 ~e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~   80 (263)
                      |+++++  +|+|.|||.++|.|+|..++|++.+++|||++++|||||+|.|+||++++..+...++++.++|.|..+.|+
T Consensus         5 ~~~~se--eg~r~dgRr~~elR~i~~~~g~~~~a~GSay~E~GnTKVl~aV~GPre~~~~~~~~~~~a~lnc~~~~a~Fs   82 (245)
T KOG1068|consen    5 YETLSE--EGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCEVSSAQFS   82 (245)
T ss_pred             ccccCc--cccccCCCChhHhhhhhhhcCccccCCccchhhcCCeEEEEEEeCCcccccccccccccceEEEEEeeeccc
Confidence            578999  999999999999999999999999999999999999999999999999887655578899999999999999


Q ss_pred             CccccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEE
Q psy18119         81 TGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSA  160 (263)
Q Consensus        81 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~  160 (263)
                      +..+++++..+.++++++.+|+++|+++|.++.||+++|+|+|+||++||+.+++|+||+.+||.|+||||+|+++++|+
T Consensus        83 t~~r~~~~~~~rr~~e~s~~L~~afe~~I~~~lyPrsqIDI~v~VleddG~~laa~inaatlAL~daGI~m~D~i~~~t~  162 (245)
T KOG1068|consen   83 TGDRKKRPKGDRREKELSLMLQQAFEPVILLELYPRSQIDIYVQVLEDDGSNLAAAINAATLALADAGIPMYDLITACTA  162 (245)
T ss_pred             cchhccCCCccHHHHHHHHHHHHHHHHHHHhhhCccccceEEEEEEECCCccHHHHHHHHHHHHHHcCCChhhhhhhcee
Confidence            99988878889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy18119        161 SLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGA  240 (263)
Q Consensus       161 ~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~~~  240 (263)
                      ++.++.+++||+..||......+||++.+..++|..+++.+.++.+.|...++.|..+|+++.+.++.++.+++.++...
T Consensus       163 ~l~~~~~l~Dl~~~eesa~~~~ltVa~l~~~~~i~~l~~~~~~~~d~l~~vl~~a~~~c~~v~~~l~~~l~~~l~~~~~~  242 (245)
T KOG1068|consen  163 GLADGTPLLDLTSLEESARAPGLTVAALPNREEIALLQLDERLHCDHLETVLELAIAGCKRVYERLRLVLREHLKNAESA  242 (245)
T ss_pred             eecCCccccccccchhhccCCceEEEEecCcceEEEEEecCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            99999999999999999999899999998889999999999999999999999999999999999999999998876654


Q ss_pred             C
Q psy18119        241 R  241 (263)
Q Consensus       241 ~  241 (263)
                      +
T Consensus       243 ~  243 (245)
T KOG1068|consen  243 L  243 (245)
T ss_pred             c
Confidence            3

>PRK00173 rph ribonuclease PH; Reviewed

Probab=100.00  E-value=2.1e-48  Score=337.63  Aligned_cols=219  Identities=27%  Similarity=0.381  Sum_probs=200.0

Q ss_pred             ccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCC---
Q psy18119         11 LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTR---   87 (263)
Q Consensus        11 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~---   87 (263)
                      +|+|||+++|+|++++++|++++++|||++++|+|+|+|+|++|...+.. ...++++.|+|+|.++||++.++.++   
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 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPRF-LKGQGQGWVTAEYGMLPRATHTRNDREAA   79 (238)
T ss_pred             CCCCCCCcccccCeEEEeCCCCCCCeeEEEEecCcEEEEEEEcCCCCCCc-cCCCCcEEEEEEEecCCCCCccccccccc
Confidence            59999999999999999999999999999999999999999987653321 23467899999999999998876433   


Q ss_pred             -CCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHc-----------CCCccCce
Q psy18119         88 -PRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDA-----------GIPMREYV  155 (263)
Q Consensus        88 -~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~da-----------gIp~~~~~  155 (263)
                       +++++++.+++++|+++|+++++++.||++.|+|+++||++|||+++|++||+++||+|+           ++||+++|
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             246677899999999999999999999998999999999999999999999999999999           99999999


Q ss_pred             eEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc---cCChhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        156 VACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ---KLHLDHLPRVLDCALKGCADIHAILDTAIK  231 (263)
Q Consensus       156 ~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G---~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~  231 (263)
                      +++|++++++.+|+|||..||..+++.++|++ +..++||++++.|   +++.+++.+|++.|.+++++++++++++|+
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            99999999999999999999999999999998 6788999999953   699999999999999999999999999885

>TIGR01966 RNasePH ribonuclease PH

Probab=100.00  E-value=2.9e-47  Score=330.12  Aligned_cols=217  Identities=29%  Similarity=0.400  Sum_probs=196.3

Q ss_pred             cCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCC----
Q psy18119         12 RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTR----   87 (263)
Q Consensus        12 R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~----   87 (263)
                      |+|||+++|+|++++++|++++|+|||++++|+|+|+|+|+++.+.+.. ...++++.++|++.++|+++..+.++    
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 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASVEEKVPPF-LRGSGEGWITAEYGMLPRATQTRNRRESAK   79 (236)
T ss_pred             CCCCCCCCCccCeEEEeCCcCCCCceEEEEecCCEEEEEEEccCccCCc-ccCCCcEEEEEEEecCCCCCCCCccccccC
Confidence            8999999999999999999999999999999999999999976543321 12357899999999999998765222    


Q ss_pred             CCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHc-----------CCCccCcee
Q psy18119         88 PRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDA-----------GIPMREYVV  156 (263)
Q Consensus        88 ~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~da-----------gIp~~~~~~  156 (263)
                      ++++.++.+++++|+++|+++++++.||++.|+|+|+||++|||+++||+||+++||+|+           +|||+++|+
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            234556889999999999999999999998999999999999999999999999999999           999999999


Q ss_pred             EEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEec---ccCChhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        157 ACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELS---QKLHLDHLPRVLDCALKGCADIHAILDTAI  230 (263)
Q Consensus       157 avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~---G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l  230 (263)
                      ++|++++++.+|+|||..||..+++.+++++ +..++||++++.   ++++++++.++++.|.+++++++++++++|
T Consensus       160 ~vt~~~~~~~~v~Dpt~~Ee~~~~~~l~l~~-~~~~~i~~i~~~g~~~~~~~~~l~~~i~~a~~~~~~l~~~~~~~l  235 (236)
T TIGR01966       160 AVSVGIVDGEPVLDLDYEEDSAADVDMNVVM-TGSGGFVEVQGTAEEGPFSRDELNKLLDLAKKGIRELIELQKQAL  235 (236)
T ss_pred             EEEEEEECCEEEECCChhHHhccCceEEEEE-cCCCCEEEEEecCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999 568999999995   369999999999999999999999999886

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

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

Probab=100.00  E-value=1.8e-47  Score=324.00  Aligned_cols=224  Identities=37%  Similarity=0.557  Sum_probs=209.9

Q ss_pred             ccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCcc
Q psy18119          4 LTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGE   83 (263)
Q Consensus         4 ~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~   83 (263)
                      ..+  ++.|+|||.++|.|+|+++.|++++++||+++++|+|+|+|+|+||.++.+.+...++++.++++|.+.|+++.+
T Consensus         3 ~~~--~~~R~dgR~~delR~i~~~~~~~~~a~GS~~~~~G~tkVic~vsGp~e~~p~~l~~~~~g~~t~ey~m~p~sT~~   80 (230)
T COG0689           3 ESE--DGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLPRSTDE   80 (230)
T ss_pred             Ccc--cCcCCCCCCcccccceEEEeccccCCCccEEEEeCCeEEEEEEecCCCCCChhhcCCCceEEEEEEecccccccc
Confidence            456  899999999999999999999999999999999999999999999998887666678999999999999999976


Q ss_pred             ccCCCCCCc-chHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEEe
Q psy18119         84 RKTRPRGDR-KTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASL  162 (263)
Q Consensus        84 ~~~~~~~~~-~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~~  162 (263)
                      +..+. .++ ++++++++|.++|+++++++.||++.|+|+|.|+++||+.+.|++||+++||+|+|+||+++++|+|+|+
T Consensus        81 R~~~~-~~~gR~~eisrli~~al~~~i~L~~~p~~~I~i~~dVlqaDggTrta~It~A~lAL~DAgipl~~~vaaiSvgi  159 (230)
T COG0689          81 RKKRE-ADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVGI  159 (230)
T ss_pred             ccccc-ccccchhHHHHHHHHHHHHHhhhhhcCccEEEEEEEEEECCCCeeeehhhHHHHHHHHcCCchhhheeEeEEEE
Confidence            65443 333 7899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCeeEecCCchhhhcCCCeEEEEEeCCCC--cEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        163 AGDTPLVDISHLEETLGGPNLTVAALPLSG--KVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAI  230 (263)
Q Consensus       163 ~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~--~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l  230 (263)
                      +++.+++||+..|++.+...++|++..+.+  +|..++..|+|++++|.+++++|.++|+++++.++++|
T Consensus       160 ~~~~~~lDl~~~Eds~~~~d~~v~~~~~~~~~ei~~~~~~~~~~~del~~lL~la~~g~~~~~~~~~~al  229 (230)
T COG0689         160 VDGVIVLDLDYEEDSAAEADMNVVMTGNGGLVEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQREAL  229 (230)
T ss_pred             ECCceEecCcchhhcccccCceEEEEecCCeEEEEEEeccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999987777  79999999999999999999999999999999999987

>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional

Probab=100.00  E-value=2.7e-44  Score=317.61  Aligned_cols=219  Identities=23%  Similarity=0.294  Sum_probs=194.2

Q ss_pred             CCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCC-CCCCCCcCCCCeEEEEEEEeeCCCCCccccC
Q psy18119          8 GGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPR-PVRNKSIKVHGSVLINFQYSMAVFSTGERKT   86 (263)
Q Consensus         8 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~-~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~   86 (263)
                      ++|+|+|||+++|+|++++++|++++++|||++++|+|+|+|+|+++. ++..   ..|++|.++|++.++|++...+. 
T Consensus        21 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~vl~~V~~~~~~p~~---~~~~~g~i~~~v~~~~~a~~~~~-   96 (271)
T PRK04282         21 KKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFP---DTPNEGVLIVNAELLPLASPTFE-   96 (271)
T ss_pred             hcCCCCCCCCCccccCeEEEeCCccCCCcEEEEEECCCEEEEEEEEEEecCCC---CCCCCCEEEEEEEECCCcCcccc-
Confidence            389999999999999999999999999999999999999999999632 3332   24678999999999999876542 


Q ss_pred             CCCCCcchHHHHHHHHHHHHhh--hccCCC---C---ceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCC--------
Q psy18119         87 RPRGDRKTSEISLQLRQAVSAA--IMSEVH---P---RSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP--------  150 (263)
Q Consensus        87 ~~~~~~~~~~l~~~l~~~l~~~--i~l~~~---p---~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp--------  150 (263)
                      .+++++++.+++++|+++|++.  ++++.|   |   .|.|+|+|+||++|||++||+++|+++||+|+++|        
T Consensus        97 ~~~~~~~~~~l~~~l~r~l~~~~~~dl~~L~I~~g~~~w~i~Vdv~VL~~dG~~~daa~~Aa~aAL~~~~iP~~~~~~~~  176 (271)
T PRK04282         97 PGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEGEDG  176 (271)
T ss_pred             CCCCCHHHHHHHHHHHHHHhccCCccHHHcEEecCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhCCCCcEEEcCCc
Confidence            3356778899999999999886  444444   3   47999999999999999999999999999999995        


Q ss_pred             ------------ccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHHHHHHHHHH
Q psy18119        151 ------------MREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRVLDCAL  216 (263)
Q Consensus       151 ------------~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l~~~i~~A~  216 (263)
                                  |+++|+++|++++++.+|+|||..||+.+++.++|++ +..|+|+++++.|  +++.+++.++++.|.
T Consensus       177 ~~~~~~~~~~l~~~~~p~~vt~~~~~~~~v~Dpt~~Ee~~~~~~l~va~-~~~g~i~~l~~~g~~~~~~~~l~~~i~~A~  255 (271)
T PRK04282        177 VVDKLGEDFPLPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITT-DEDGNIVAIQKSGIGSFTEEEVDKAIDIAL  255 (271)
T ss_pred             eeccCCCcccCCCCCeeEEEEEEEECCEEEECCCHHHHhhcCceEEEEE-CCCCcEEEEEcCCCCCCCHHHHHHHHHHHH
Confidence                        9999999999999999999999999999999999999 5678999999874  699999999999999


Q ss_pred             HHHHHHHHHHHHHHH
Q psy18119        217 KGCADIHAILDTAIK  231 (263)
Q Consensus       217 ~~~~~i~~~i~~~l~  231 (263)
                      +++++++++++++|+
T Consensus       256 ~~~~~l~~~~~~~l~  270 (271)
T PRK04282        256 EKAKELREKLKEALG  270 (271)
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999874

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=100.00  E-value=1.4e-43  Score=345.94  Aligned_cols=252  Identities=23%  Similarity=0.332  Sum_probs=223.7

Q ss_pred             ccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEE-cCCCCCCCC--cCCCCeEEEEEEEeeCC
Q psy18119          2 DLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVY-GPRPVRNKS--IKVHGSVLINFQYSMAV   78 (263)
Q Consensus         2 e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-gp~~~~~~~--~~~~~~~~l~v~~~~~~   78 (263)
                      +++.+  +|+|+|||.++|+||+++++|+++++||||+|++|+|+|+|+|+ ||.+..+..  .....++.+.++|+++|
T Consensus       303 ~~il~--~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSa~~~~G~Tqvl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~p  380 (684)
T TIGR03591       303 ERILK--EGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERDEQIIDDLEGEYRKRFMLHYNFPP  380 (684)
T ss_pred             HHHhc--CCCCCCCCCCCCcCceEEEeCCCCCCCceEEEEeCCeEEEEEEecCCcccccCCcccCCCccEEEEEEEEcCC
Confidence            45677  99999999999999999999999999999999999999999995 876543211  11245789999999999


Q ss_pred             CCCccccCCCCCCcchHHHHHHHHHHHHhhhcc-CCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeE
Q psy18119         79 FSTGERKTRPRGDRKTSEISLQLRQAVSAAIMS-EVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVA  157 (263)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l-~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~a  157 (263)
                      |+++++++.+++++++.+++++++++|++++++ +.||+ .|+|+++||++|||..+|+++|+++||+|+||||++.+++
T Consensus       381 fs~~e~~~~g~~~rrei~~~~l~~ral~~~i~~~~~~p~-tI~v~~~VLesdGs~~~Aai~aaslAL~dAgvP~~~~Vag  459 (684)
T TIGR03591       381 YSVGEVGRVGGPGRREIGHGALAERALKAVLPSEEEFPY-TIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAG  459 (684)
T ss_pred             CCCCCcCCCCCCChHHHHHHHHHHHHHHHhcCccccCCe-EEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCCcCCEEE
Confidence            999987765567889999999999999999986 78996 6999999999999999999999999999999999999999


Q ss_pred             EEEEecCC-----eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEeccc---CChhHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        158 CSASLAGD-----TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK---LHLDHLPRVLDCALKGCADIHAILDTA  229 (263)
Q Consensus       158 vt~~~~~~-----~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~---i~~~~l~~~i~~A~~~~~~i~~~i~~~  229 (263)
                      +|+|++++     .+++||+..|+..++..++|+. +..+ |+++++++.   ++.+.|.++++.|.+++.+++++|+++
T Consensus       460 vs~gli~~~~~~~~il~D~~~~Ed~~~d~d~~va~-t~~g-I~~lq~d~k~~~i~~~~l~~al~~a~~~~~~I~~~m~~~  537 (684)
T TIGR03591       460 IAMGLIKEGDERFAVLSDILGDEDHLGDMDFKVAG-TRDG-ITALQMDIKIDGITREIMEQALEQAKEGRLHILGEMNKV  537 (684)
T ss_pred             EEEEEEcCCCcceEEEeCCChHHHhcCCceEEEEE-cCCc-eEEEEEEcCcCCcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999952     5999999999999999999988 3444 999999754   699999999999999999999999999


Q ss_pred             HHHHHHHhhccCC-----CCccccccceecCCcc
Q psy18119        230 IKQHLIKVAGARG-----LGRKFQLGQLTGKKKE  258 (263)
Q Consensus       230 l~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~  258 (263)
                      +.++..+...+.+     .++....|.++|++|.
T Consensus       538 l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk  571 (684)
T TIGR03591       538 ISEPRAELSPYAPRIETIKINPDKIRDVIGPGGK  571 (684)
T ss_pred             HhhhhccccccCCeEEEEecCHHHHHhhcCCCcH
Confidence            9999988888877     3477778999999885

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=1.7e-42  Score=339.02  Aligned_cols=252  Identities=24%  Similarity=0.351  Sum_probs=219.2

Q ss_pred             ccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEE-cCCCCCCC--CcCCCCeEEEEEEEeeCC
Q psy18119          2 DLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVY-GPRPVRNK--SIKVHGSVLINFQYSMAV   78 (263)
Q Consensus         2 e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-gp~~~~~~--~~~~~~~~~l~v~~~~~~   78 (263)
                      ++|.+  +|+|+|||.++|+|++++++|+++++||||+|++|+|+|+|+|+ ||..+.+.  .....+++.+.++|+++|
T Consensus       307 ~~il~--~g~R~DGR~~~e~Rpi~~~~g~l~~a~GSal~~~G~T~Vl~~vt~g~~~~~~~~~~~~~~~~~~~~~~y~~~p  384 (693)
T PRK11824        307 RRILE--EGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLRDEQIIDGLEGEYKKRFMLHYNFPP  384 (693)
T ss_pred             HHHhc--CCCCCCCCCcCcccceEEEeCCCCCCCceEEEEECCeEEEEEEecCCCcccccccccCCCCcEEEEEEEEcCC
Confidence            46777  99999999999999999999999999999999999999999995 76432211  011236799999999999


Q ss_pred             CCCccccCCCCCCcchHHHHHHHHHHHHhhhcc-CCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeE
Q psy18119         79 FSTGERKTRPRGDRKTSEISLQLRQAVSAAIMS-EVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVA  157 (263)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l-~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~a  157 (263)
                      |+++++++.+++++++.+++++++++|++++++ +.||+ .|+|+++||++|||.++|+++|+++||+|+||||++++++
T Consensus       385 fs~~e~~~~~~~~rre~~~~~li~ral~~vi~~~~~~p~-~I~v~~~VLe~dGs~~~Aai~aaslAL~dAgvP~~~~Va~  463 (693)
T PRK11824        385 YSVGETGRVGSPGRREIGHGALAERALEPVLPSEEEFPY-TIRVVSEILESNGSSSMASVCGSSLALMDAGVPIKAPVAG  463 (693)
T ss_pred             CCCCCcCCCCCCChhHHHHHHHHHHHHHHhcCcccCCCE-EEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCccCceeE
Confidence            999887665567889999999999999999998 68995 8999999999999999999999999999999999999999


Q ss_pred             EEEEecCC----eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEeccc---CChhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        158 CSASLAGD----TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK---LHLDHLPRVLDCALKGCADIHAILDTAI  230 (263)
Q Consensus       158 vt~~~~~~----~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~---i~~~~l~~~i~~A~~~~~~i~~~i~~~l  230 (263)
                      +++|++++    .+++||+..|+..++..++|+. +..+ |++++++++   ++.+.+.++++.|.+++.+|++.|++++
T Consensus       464 vs~gli~~~~~~~il~D~~~~Ed~~~d~d~~va~-t~~g-i~~lq~d~k~~~i~~~~l~~al~~a~~g~~~I~~~M~~aI  541 (693)
T PRK11824        464 IAMGLIKEGDKYAVLTDILGDEDHLGDMDFKVAG-TRDG-ITALQMDIKIDGITREILEEALEQAKEGRLHILGKMNEAI  541 (693)
T ss_pred             EEEEEEcCCCceEEEcCCChhhHhhCCceEEEEe-cCCc-eEEEEEecccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999953    4889999999999999999998 3444 999998754   6999999999999999999999999999


Q ss_pred             HHHHHHhhccCCC-----CccccccceecCCcc
Q psy18119        231 KQHLIKVAGARGL-----GRKFQLGQLTGKKKE  258 (263)
Q Consensus       231 ~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~  258 (263)
                      .+.........+.     .+....|.++|.+|.
T Consensus       542 ~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~  574 (693)
T PRK11824        542 SEPRAELSPYAPRIETIKIPPDKIRDVIGPGGK  574 (693)
T ss_pred             cCChhhhcccCchheeecCCHHHHHHHhcCCch
Confidence            9888777766552     245557888888764

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

Probab=100.00  E-value=2.3e-41  Score=289.54  Aligned_cols=222  Identities=23%  Similarity=0.272  Sum_probs=189.9

Q ss_pred             cCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCC-CCCCCCcCCCCeEEEEEEEeeCCCCCcc
Q psy18119          5 TEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPR-PVRNKSIKVHGSVLINFQYSMAVFSTGE   83 (263)
Q Consensus         5 ~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~-~~~~~~~~~~~~~~l~v~~~~~~~~~~~   83 (263)
                      +.+++|+|+|||.++|+|++.|++|+++.++|||+|++|+|+|+|+|+... +|-+.   .|++|.+.+++...|.++..
T Consensus        17 ~ll~~g~R~DGR~~~efR~ieI~~~vi~ka~GSa~VklG~Tqvv~gvK~eig~Pf~D---tP~eG~~~~n~El~Plas~~   93 (272)
T COG2123          17 NLLKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIGEPFPD---TPNEGVLVVNVELSPLASPS   93 (272)
T ss_pred             HHhccCcccCCCCcccccceEEEeCceecCCCcEEEEecCeEEEEEEEcccCCCCCC---CCCCceEEeeeeeecccccc
Confidence            335699999999999999999999999999999999999999999999732 22221   34566555565555655544


Q ss_pred             ccCCCCCCcchHHHHHHHHHHHHh--hhccCCCC------ceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCC-----
Q psy18119         84 RKTRPRGDRKTSEISLQLRQAVSA--AIMSEVHP------RSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP-----  150 (263)
Q Consensus        84 ~~~~~~~~~~~~~l~~~l~~~l~~--~i~l~~~p------~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp-----  150 (263)
                      +... .+++.+.+++++++|.++.  +++++.+.      .|.+.++++||++|||++||++.|+++||+++++|     
T Consensus        94 fE~G-ppde~aielsrvvdr~lr~s~aiDlekL~I~~g~kvwvv~vDv~vld~DGnl~Da~~lA~~aAL~~t~vP~~~~~  172 (272)
T COG2123          94 FEPG-PPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVVFVDVHVLDYDGNLIDAASLAAVAALLNTRVPKAVEV  172 (272)
T ss_pred             ccCC-CCchhHHHHHHHHHHHHHhccCcchhheeEecCCEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHhcCCCceeec
Confidence            3322 3667889999999999998  46666542      38999999999999999999999999999999987     


Q ss_pred             -----------------ccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHHHHH
Q psy18119        151 -----------------MREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRV  211 (263)
Q Consensus       151 -----------------~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l~~~  211 (263)
                                       +.++|+++|++++++.+++|||.+||..+++.+||.+ ++.++|+.+++.|  .+++..+.+|
T Consensus       173 ~~~~~v~~~~~~~~pl~~~~~pi~vt~a~ig~~lvvDPsleEe~v~d~~ltit~-~~~~~Iv~iqK~g~~~~~~~~~~~~  251 (272)
T COG2123         173 GDGEIVIEVEEEPVPLPVSNPPISVTFAKIGNVLVVDPSLEEELVADGRLTITV-NEDGEIVAIQKVGGGSITESDLEKA  251 (272)
T ss_pred             CCcceeecccCCCcccccCCCceEEEEEEECCEEEeCCCcchhhhcCceEEEEE-CCCCcEEEEEEcCCCcCCHHHHHHH
Confidence                             5789999999999999999999999999999999999 6889999999985  6899999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q psy18119        212 LDCALKGCADIHAILDTAIK  231 (263)
Q Consensus       212 i~~A~~~~~~i~~~i~~~l~  231 (263)
                      ++.|.+.+.++.+.+.++|+
T Consensus       252 ~~~A~~~~~kl~~~~~~~L~  271 (272)
T COG2123         252 LKTALSKAEKLREALKEALK  271 (272)
T ss_pred             HHHHHHHHHHHHHHHHHhhc
Confidence            99999999999999988875

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=100.00  E-value=9.5e-42  Score=328.36  Aligned_cols=251  Identities=24%  Similarity=0.323  Sum_probs=220.4

Q ss_pred             ccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEc-CCCCCCC--CcCCCCeEEEEEEEeeCC
Q psy18119          2 DLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYG-PRPVRNK--SIKVHGSVLINFQYSMAV   78 (263)
Q Consensus         2 e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~g-p~~~~~~--~~~~~~~~~l~v~~~~~~   78 (263)
                      +++.+  ++.|+|||.++++|++++++|++++++|||+++.|+|+|+|.+.. |.+..+.  ....++...+.|+|+++|
T Consensus       328 ~~il~--~g~R~DGR~~~eiR~i~~~~g~l~~a~GSa~~~~G~Tqvl~~~tlG~~~~~q~~~~l~~~~~~~~~~~YnfpP  405 (719)
T TIGR02696       328 ERVLT--EGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILGVTTLNMLKMEQQIDSLSPETSKRYMHHYNFPP  405 (719)
T ss_pred             HHHhc--CCCCCCCCCccccccceeecCCCCCCCceEEEEecCcEEEEEEeCCCchhhhhcccccccccceEEEEEeCCC
Confidence            56777  999999999999999999999999999999999999999999874 4332221  111245677789999999


Q ss_pred             CCCccccCCCCCCcchHHHHHHHHHHHHhhhc-cCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeE
Q psy18119         79 FSTGERKTRPRGDRKTSEISLQLRQAVSAAIM-SEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVA  157 (263)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~-l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~a  157 (263)
                      |+++++++...+++++.+++++++++|+++++ ++.||++ |.+.++||++||+...|++||+++||+||||||++++++
T Consensus       406 FSt~er~~~~~~~RReighg~La~rALe~vI~~~e~fP~T-IrvvseVLeSdGSss~AsIcaasLALmDAGVPmkd~VAg  484 (719)
T TIGR02696       406 YSTGETGRVGSPKRREIGHGALAERALVPVLPSREEFPYA-IRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAG  484 (719)
T ss_pred             CcccCCCCCCCCCccHHHHHHHHHHHHHHhhCcHhhCCCE-EEEEEEeeccCCcHHHHHHHHHHHHHHHcCcchhheeeE
Confidence            99998887767788999999999999999997 6999996 889999999999999999999999999999999999999


Q ss_pred             EEEEecCC--------eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccC---ChhHHHHHHHHHHHHHHHHHHHH
Q psy18119        158 CSASLAGD--------TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKL---HLDHLPRVLDCALKGCADIHAIL  226 (263)
Q Consensus       158 vt~~~~~~--------~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i---~~~~l~~~i~~A~~~~~~i~~~i  226 (263)
                      +++|++++        .+++||+..|+...+..+.++.  ..+.|++++++|++   +.+.+.+++++|.++|.+++++|
T Consensus       485 is~Gli~e~~~~~~~~~iL~Di~g~ED~~Gdmdfkvag--t~~gIt~lQmd~ki~gi~~e~l~~aL~~A~~g~~~Il~~m  562 (719)
T TIGR02696       485 IAMGLISDEVDGETRYVALTDILGAEDAFGDMDFKVAG--TSEFVTALQLDTKLDGIPASVLASALKQARDARLAILDVM  562 (719)
T ss_pred             EEEEEeccccCCCcceeEEeCCCchhhhcCCceEEEEe--cCCCEEEEEEEeeECCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999943        2899999999999998888875  57999999999875   88999999999999999999999


Q ss_pred             HHHHHHHHHHhhccCCCC-----ccccccceecCCcc
Q psy18119        227 DTAIKQHLIKVAGARGLG-----RKFQLGQLTGKKKE  258 (263)
Q Consensus       227 ~~~l~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~  258 (263)
                      +++|... .+...+.+..     +....|.++|.+|.
T Consensus       563 ~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk  598 (719)
T TIGR02696       563 AEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGK  598 (719)
T ss_pred             HHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcH
Confidence            9999999 6677766633     66778999998874

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.

>KOG1069|consensus

Probab=100.00  E-value=1.2e-40  Score=271.94  Aligned_cols=207  Identities=28%  Similarity=0.423  Sum_probs=189.3

Q ss_pred             CCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCCCCCcchHHHHH
Q psy18119         20 ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISL   99 (263)
Q Consensus        20 e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~~~~~~~~~l~~   99 (263)
                      ..|++.++.|+++++|||+.|++|+|+|+|+|+||.+++.+ ++.+++..++|.+++...-         ++..++.+++
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 RLRGIACEISILSRPDGSSEFSQGDTKVICSVYGPIDVKAR-QEDPEKATLEVIWRPKSGV---------NGTVEKVLER   73 (217)
T ss_pred             hhhhhhhhhceecCCCCccceecCCcEEEEEeeCCcchhhc-ccCchhceEEEEEecccCc---------chHHHHHHHH
Confidence            68999999999999999999999999999999999998887 5789999999999865432         3456789999


Q ss_pred             HHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEEecCC-eeEecCCchhhhc
Q psy18119        100 QLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGD-TPLVDISHLEETL  178 (263)
Q Consensus       100 ~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~-~~lvDPt~~Ee~~  178 (263)
                      +|+++|+++|.++.||++.|+|.+||+++||+.+++|+|||++||.|+||||+++++++.+++.++ .+++|||..+|+.
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            999999999999999999999999999999999999999999999999999999999999999977 8999999999998


Q ss_pred             CCCeEEEEEeC---CCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        179 GGPNLTVAALP---LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIK  236 (263)
Q Consensus       179 ~~~~l~v~~~~---~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~  236 (263)
                      +.+..++++..   ...+++.++..|.++.+++..+++.|..++.+++.++++.+++..++
T Consensus       154 ~~~~~~lsf~~~~~~~~~vi~s~t~G~~~~d~lf~~le~a~~~~~~~f~f~r~~~q~~~s~  214 (217)
T KOG1069|consen  154 STARATLSFEGGSLGEPKVIISETNGEKSEDQLFYVLELAQAAAQSLFPFYREVLQRKYSK  214 (217)
T ss_pred             hhceEEEEEecCCCCCcceEEEeccCCCCHHHHHHHHHhhHHHHHHHHHHHHHHHHhhcCc
Confidence            87777777632   24689999999999999999999999999999999999999887654

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=100.00  E-value=9.4e-40  Score=320.35  Aligned_cols=252  Identities=23%  Similarity=0.319  Sum_probs=220.9

Q ss_pred             ccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEE-cCCCCCCCCcC---CCCeEEEEEEEeeC
Q psy18119          2 DLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVY-GPRPVRNKSIK---VHGSVLINFQYSMA   77 (263)
Q Consensus         2 e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-gp~~~~~~~~~---~~~~~~l~v~~~~~   77 (263)
                      ++|++  +|.|+|||.++|.|+|.+++|.+++++|||+|++|+|+|+|+|+ ||.+..+..+.   .+....+.++|+++
T Consensus       431 ~~i~~--~g~R~DGR~~~eiRpI~~e~G~Lp~A~GSAlf~~G~TqVLatVtlGp~~~~q~~d~l~~~~~~~~f~~~y~fP  508 (891)
T PLN00207        431 RRIVE--GGKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEVKRFYLQYSFP  508 (891)
T ss_pred             HHHhc--CCCCCCCCCcCccceEEEEeCCcCCCCceEEEEECCeEEEEEEEecCccccccccccccccceeeEEEEEEcC
Confidence            45677  99999999999999999999999999999999999999999997 78754432111   13456677999999


Q ss_pred             CCCCccccCCCCCCcchHHHHHHHHHHHHhhhccC-CCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCcee
Q psy18119         78 VFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSE-VHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVV  156 (263)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~-~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~  156 (263)
                      ||+.+++++.+++++++.+++++++++|+++++.+ .||+ .|+|+++||++||+..+|++||+++||+|+||||+++++
T Consensus       509 Pfs~ge~~r~g~psrREi~hg~L~eRALrpvip~~~~fP~-tIrV~~~VLesDGSssmAaV~aaSLALmDAGIPmk~~VA  587 (891)
T PLN00207        509 PSCVGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFPY-TIRVESTITESNGSSSMASVCGGCLALQDAGVPVKCPIA  587 (891)
T ss_pred             CCCCccccCCCCCCHHHHHHHHHHHHHHHHhCCcccCCCE-EEEEEEEEEeCCCChHHHHHHHHHHHHHhcCCCccCcee
Confidence            99988877666678899999999999999999885 7995 899999999999999999999999999999999999999


Q ss_pred             EEEEEec-C-------Ce--eEecCCchhhhcCCCeEEEEEeCCCCcEEEEEeccc---CChhHHHHHHHHHHHHHHHHH
Q psy18119        157 ACSASLA-G-------DT--PLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK---LHLDHLPRVLDCALKGCADIH  223 (263)
Q Consensus       157 avt~~~~-~-------~~--~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~---i~~~~l~~~i~~A~~~~~~i~  223 (263)
                      ++++|++ +       +.  +++||+..|+..++..|.|+.  ..+.|++++++++   ++.+.|.++++.|.+++.+++
T Consensus       588 GvsvGli~d~~~~~~~g~~~IL~Dp~g~Ed~~gdmDfkVAg--T~~gIt~iqmd~k~~gis~e~l~eAL~~A~~g~~~Il  665 (891)
T PLN00207        588 GIAMGMVLDTEEFGGDGSPLILSDITGSEDASGDMDFKVAG--NEDGITAFQMDIKVGGITLPIMERALLQAKDGRKHIL  665 (891)
T ss_pred             EEEEEEEecccccCCCCcEEEEeCCCHHHHhcCCceEEEEe--cccceEEEEEecccCCCCHHHHHHHHHHHHHHHHHHH
Confidence            9999999 2       23  567999999999999999997  4689999999864   589999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhccCCCC-----ccccccceecCCcc
Q psy18119        224 AILDTAIKQHLIKVAGARGLG-----RKFQLGQLTGKKKE  258 (263)
Q Consensus       224 ~~i~~~l~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~  258 (263)
                      +.|++++.....+...+.+..     +....|.++|.+|.
T Consensus       666 ~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGk  705 (891)
T PLN00207        666 AEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGK  705 (891)
T ss_pred             HHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCch
Confidence            999999999988888887743     77778889988774

>KOG1614|consensus

Probab=100.00  E-value=1.7e-38  Score=265.94  Aligned_cols=226  Identities=20%  Similarity=0.227  Sum_probs=190.8

Q ss_pred             CCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCC-CCCCCcCCCCeEEEEEEEeeCCCCCcccc
Q psy18119          7 YGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRP-VRNKSIKVHGSVLINFQYSMAVFSTGERK   85 (263)
Q Consensus         7 ~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~-~~~~~~~~~~~~~l~v~~~~~~~~~~~~~   85 (263)
                      .|.|.|.|||++.|+|.+++++|   .-.||+.+++|+|+|+|.|+.... |..   ..|.+|.+++...++|.+.+...
T Consensus        18 lk~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   18 LKAGLRFDGRSLEEFRDLEIEFG---KEYGSVLVTMGNTKVMARVTAQIAQPYI---DRPHEGSFSIFTELSPMASPSFE   91 (291)
T ss_pred             HHhcccccccchhhhhceEEEec---cccccEEEEecCeeEEEEeehhhcCccc---CCCCCCeeeeeeccccccccccC
Confidence            35899999999999999999999   478999999999999999997432 121   13455555555555555543322


Q ss_pred             CCCCCCcchHHHHHHHHHHHHh--hhccCCCC------ceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCC-------
Q psy18119         86 TRPRGDRKTSEISLQLRQAVSA--AIMSEVHP------RSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP-------  150 (263)
Q Consensus        86 ~~~~~~~~~~~l~~~l~~~l~~--~i~l~~~p------~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp-------  150 (263)
                      . ++.++.+.+++++|+++++.  +||+|.++      .|.|++++++|+.|||++|||+.|+.+||++++-|       
T Consensus        92 ~-Gr~~~~~v~l~Rliek~~R~S~aiD~EsLCI~aG~kvW~IRiDlhiLd~DGnlvDaA~iAviaaL~hFrrPdvTv~g~  170 (291)
T KOG1614|consen   92 P-GRKGESEVELSRLIEKALRRSKAIDTESLCIRAGEKVWLIRIDLHILDHDGNLVDAACIAVIAALMHFRRPDVTVGGE  170 (291)
T ss_pred             C-CCccchHHHHHHHHHHHHHhccccchHHHHhhhCCeEEEEEEEEEEEcCCCCeehhHHHHHHHHHHhcCCCCcccccc
Confidence            1 13457788999999999987  56666553      48999999999999999999999999999999933       


Q ss_pred             ----------------ccCceeEEEEEecC--CeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEeccc--CChhHHHH
Q psy18119        151 ----------------MREYVVACSASLAG--DTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK--LHLDHLPR  210 (263)
Q Consensus       151 ----------------~~~~~~avt~~~~~--~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~--i~~~~l~~  210 (263)
                                      |+|+|+|+||++++  +.+++|||..||...+|.++|++ |+.++||.+++.|.  ++..++..
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                            89999999999997  48899999999999999999999 78999999999985  58899999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy18119        211 VLDCALKGCADIHAILDTAIKQHLIKVAGA  240 (263)
Q Consensus       211 ~i~~A~~~~~~i~~~i~~~l~~~~~~~~~~  240 (263)
                      |.+.|...+.++...+.++|+++..++..+
T Consensus       250 C~k~A~~~a~~vt~ii~e~l~~d~~~r~~~  279 (291)
T KOG1614|consen  250 CYKLAKDRAVEVTGIILEALEEDQRERSAQ  279 (291)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            999999999999999999999998887766

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=100.00  E-value=1.7e-32  Score=268.25  Aligned_cols=207  Identities=17%  Similarity=0.231  Sum_probs=181.6

Q ss_pred             cceEEEeCCC-CCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCcc-----ccCCCCCCcchH
Q psy18119         22 RKIRCRLGVF-SQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGE-----RKTRPRGDRKTS   95 (263)
Q Consensus        22 R~i~i~~g~l-~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~-----~~~~~~~~~~~~   95 (263)
                      |++.+++|.+ ++|+|||++++|+|+|+|+|++|.++++.    .+++.|+|+|...+++.+.     .++.+++++++.
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 RTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKEG----QDFFPLTVNYQEKFYAAGKIPGGFFKREGRPSEKET   80 (684)
T ss_pred             ccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCCC----CceEeEEEEEEehhhhccCCCCCcccCCCCCCHHHH
Confidence            8999999999 57999999999999999999999886653    5789999999987765542     233446888999


Q ss_pred             HHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChh-H-HHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecCCc
Q psy18119         96 EISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNF-C-ACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISH  173 (263)
Q Consensus        96 ~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~-~-a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDPt~  173 (263)
                      +++++|+|.|+++++.. | .|.|+|+++||++||+.. + ||+||+++||++++|||++++++++++++++.+++|||.
T Consensus        81 l~srlIdR~lrplfp~~-~-~~~i~V~~~VLs~Dg~~~~d~aai~aAsaAL~~s~IP~~~~v~av~vg~idg~~ildPt~  158 (684)
T TIGR03591        81 LTSRLIDRPIRPLFPKG-F-RNEVQVVATVLSYDPENDPDILAIIGASAALAISGIPFNGPIAAVRVGYIDGQYVLNPTV  158 (684)
T ss_pred             HHHHHHhhHHHHhcCCC-C-CceEEEEEEEEecCcCCchHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCEEEEcCCH
Confidence            99999999999875422 2 268999999999999975 5 999999999999999999999999999999999999999


Q ss_pred             hhhhcCCCeEEEEEeCCCCcEEEEEeccc-CChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        174 LEETLGGPNLTVAALPLSGKVAVMELSQK-LHLDHLPRVLDCALKGCADIHAILDTAIKQHLIK  236 (263)
Q Consensus       174 ~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~-i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~  236 (263)
                      .|++.++..++|+.  ..+.+++++..+. ++.+++.++++.|.++++++.++++++++++...
T Consensus       159 ~E~~~s~~~l~va~--t~~~i~mie~~~~~i~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~~~  220 (684)
T TIGR03591       159 DELEKSDLDLVVAG--TKDAVLMVESEAKELSEEVMLGAIEFGHEEIQPVIEAIEELAEEAGKE  220 (684)
T ss_pred             HHHhhCCceEEEEc--cCCcEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence            99999999999986  4568899998764 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).

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=100.00  E-value=5.7e-32  Score=265.04  Aligned_cols=206  Identities=17%  Similarity=0.211  Sum_probs=181.3

Q ss_pred             CcceEEEeCCCC-CCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCcc-----ccCCCCCCcch
Q psy18119         21 LRKIRCRLGVFS-QSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGE-----RKTRPRGDRKT   94 (263)
Q Consensus        21 ~R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~-----~~~~~~~~~~~   94 (263)
                      -|++.+++|.++ +|+|||++++|+|+|+|+|++|.++++    ..+++.++|+|...+|+++.     .++.+++++++
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 GRTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPKE----GQDFFPLTVDYEEKTYAAGKIPGGFFKREGRPSEKE   88 (693)
T ss_pred             CccEEEEECCcCCCCCeEEEEEECCeEEEEEEEcCCCCCC----CCCeeeeEEEEEehhhhccCCCcccccCCCCCChHH
Confidence            378999999995 699999999999999999999988654    35789999999987776542     22334678899


Q ss_pred             HHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCCh-hH-HHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecCC
Q psy18119         95 SEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGN-FC-ACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDIS  172 (263)
Q Consensus        95 ~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~-~~-a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDPt  172 (263)
                      .+++++|+|.|+++++.  .++|.|+|+++||++||+. .+ +|+||+++||++++|||++.+++|+++++++.+++|||
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 TLTSRLIDRPIRPLFPK--GFRNEVQVVATVLSVDPENDPDILAMIGASAALSISGIPFNGPIAAVRVGYIDGEFVLNPT  166 (693)
T ss_pred             HHHHHHHhhhHHHhCCC--CCCeEEEEEEEEEeCCCCCcHHHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCEEEEcCC
Confidence            99999999999997642  2467999999999999976 55 89999999999999999999999999999999999999


Q ss_pred             chhhhcCCCeEEEEEeCCCCcEEEEEecc-cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        173 HLEETLGGPNLTVAALPLSGKVAVMELSQ-KLHLDHLPRVLDCALKGCADIHAILDTAIKQHL  234 (263)
Q Consensus       173 ~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G-~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~  234 (263)
                      ..|++.++..++|+..  .+.+++++..| .++.+++.++++.|.++++++.+++++++++..
T Consensus       167 ~~E~~~s~~~l~va~t--~~~i~mie~~~~~l~e~~l~~al~~a~~~~~~i~~~~~~~~~~~~  227 (693)
T PRK11824        167 VEELEESDLDLVVAGT--KDAVLMVESEAKELSEEVMLEAIEFGHEAIQELIDAQEELAAEAG  227 (693)
T ss_pred             HHHHhhCcceEEEEEc--cCceEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            9999999999999983  45899999876 599999999999999999999999999888766

>KOG1612|consensus

Probab=99.98  E-value=4.8e-30  Score=216.34  Aligned_cols=225  Identities=20%  Similarity=0.251  Sum_probs=182.8

Q ss_pred             CCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCC-eEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCcccc
Q psy18119          7 YGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGN-TKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERK   85 (263)
Q Consensus         7 ~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~-T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~   85 (263)
                      +.+.+|+|||.++++|||.++++++++++|||+|++|. |.|+++|+.....+..  +.|.++.+.+.+.+.|.+++++.
T Consensus        17 ~e~~iR~DGR~~~~~Rpi~vetdVlp~tNGSaRVk~g~~tdiivgVKaEvg~~~~--~~p~egk~~~~VD~S~sasp~f~   94 (288)
T KOG1612|consen   17 SEPDIRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKAEVGSPDD--ETPVEGKYLFFVDCSPSASPQFQ   94 (288)
T ss_pred             cCcccccCCcCccccceEEEEeccccCCCCcEEEEecCCceEEEEEeeeccCccc--cCCCCCeEEEEEEecCCcCcccc
Confidence            34889999999999999999999999999999999999 9999999985442221  23445556666666666665554


Q ss_pred             CCCCCCcchHHHHHHHHHHHHh--h-hccCCC---C--ceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCC-------
Q psy18119         86 TRPRGDRKTSEISLQLRQAVSA--A-IMSEVH---P--RSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP-------  150 (263)
Q Consensus        86 ~~~~~~~~~~~l~~~l~~~l~~--~-i~l~~~---p--~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp-------  150 (263)
                      +|+ .++...+|+..|+++|.+  + +++..+   |  .|.|.|++.|++.|||++||...|+++||.++.+|       
T Consensus        95 gRg-gde~~~eltsaLq~~l~~~~sgv~ls~L~lt~~~~W~i~VDvlVi~s~gn~~dAiS~Ai~~AL~~T~lPkv~v~~d  173 (288)
T KOG1612|consen   95 GRG-GDELVEELTSALQRVLNSLGSGVDLSKLQLTPGYCWKIYVDVLVISSDGNLLDAISIAIYAALNNTRLPKVIVAFD  173 (288)
T ss_pred             CCC-hhhHHHHHHHHHHHHHhCcCcccchhheeccCCeeEEEEEeEEEEecCCCHHHHHHHHHHHHHhcccCCccccccc
Confidence            432 456667899999999987  1 333221   2  47999999999999999999999999999999987       


Q ss_pred             --------------------ccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHH
Q psy18119        151 --------------------MREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHL  208 (263)
Q Consensus       151 --------------------~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l  208 (263)
                                          ...+|+-+|++.++..+++|||.+||.++...+.|.+ ++.+-+.++..-|  .+.++.+
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                                2347888999999999999999999999999999999 5667666666654  5889999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        209 PRVLDCALKGCADIHAILDTAIKQHLI  235 (263)
Q Consensus       209 ~~~i~~A~~~~~~i~~~i~~~l~~~~~  235 (263)
                      .+|++.+++-.+.++..+.+.|++.-.
T Consensus       253 ~~mle~~~~~~e~l~~~l~k~L~~~e~  279 (288)
T KOG1612|consen  253 PEMLEQGKAVVETLAPDLVKSLENEED  279 (288)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHhhhhhh
Confidence            999999999999999988888876543

>KOG1613|consensus

Probab=99.97  E-value=2.1e-30  Score=216.95  Aligned_cols=215  Identities=21%  Similarity=0.256  Sum_probs=175.0

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCC
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRP   88 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~   88 (263)
                      +++|+|||+..|+|.+.++.|.++.+|||+.++.|+|.|+|+|++..-.+.  +..|++|.+..+|.++|.++...+. +
T Consensus        34 e~~RpdgR~lgefRdt~in~g~IsTangSal~K~G~ttvi~~Ik~ei~eps--tdapdeg~Iv~n~~lpplcs~r~Rp-G  110 (298)
T KOG1613|consen   34 EGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKAEIAEPS--TDAPDEGDIVPNYALPPLCSSRFRP-G  110 (298)
T ss_pred             cccCcchhhhhHHhhhheecCceeccCcHHHHhcCCcEEEEEeeeeecccc--cCCCCCcceeecccCCcccccCCCC-C
Confidence            899999999999999999999999999999999999999999999543222  2467899999999999998765433 3


Q ss_pred             CCCcchHHHHHHHHHHHHhh--hccCCC------CceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCc---------
Q psy18119         89 RGDRKTSEISLQLRQAVSAA--IMSEVH------PRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPM---------  151 (263)
Q Consensus        89 ~~~~~~~~l~~~l~~~l~~~--i~l~~~------p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~---------  151 (263)
                      ++.+.++.+++.|...+.++  |+++.+      +-|.++.++.+|++||+++|+|++|.++||.+-.+|.         
T Consensus       111 ~p~dea~viSq~LhdtIl~S~ii~~k~Lci~~gKaawvlYadIicLd~dG~~fDa~w~al~aAlknvklP~a~ide~~~~  190 (298)
T KOG1613|consen  111 PPTDEAQVISQKLHDTILHSRIIPKKALCIKAGKAAWVLYADIICLDYDGPVFDACWNALMAALKNVKLPRAFIDERASD  190 (298)
T ss_pred             CCchHHHHHHHHHHHHHHhcCCcchhhheeeccceeeEEEEEEEEEcCCCcHHHHHHHHHHHHHhcCCCceeeecccchh
Confidence            57788888999998887764  444332      3478888999999999999999999999999999882         


Q ss_pred             ----------------------cCcee-----EEEEE-ecCCe-eEecCCchhhhcCCCeEEEEEeCCCCcEEEEEeccc
Q psy18119        152 ----------------------REYVV-----ACSAS-LAGDT-PLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK  202 (263)
Q Consensus       152 ----------------------~~~~~-----avt~~-~~~~~-~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~  202 (263)
                                            ...++     ..|.. ++++. ++.|||.+||..+++.+||+. ++.|+++.+.+.|.
T Consensus       191 ~~~t~e~~ic~~tlt~p~~ln~e~r~~~~~n~~fS~~~vl~~~li~adpT~eEE~l~~~~lTIvl-dss~n~v~l~k~GG  269 (298)
T KOG1613|consen  191 LRMTIEEIICDQTLTVPLMLNAENRAFASQNSDFSEEEVLDDVLIAADPTEEEETLITSTLTIVL-DSSGNYVQLTKVGG  269 (298)
T ss_pred             hhhhHHHHHHhhhhcchhhhccccccccccCCCccHHHhhcceeEecCCCchhhhhhhceEEEEE-cCCCCEEEEEecCc
Confidence                                  01111     12222 44554 459999999999999999999 57899998888763


Q ss_pred             ---CChhHHHHHHHHHHHHHHHHHHHHH
Q psy18119        203 ---LHLDHLPRVLDCALKGCADIHAILD  227 (263)
Q Consensus       203 ---i~~~~l~~~i~~A~~~~~~i~~~i~  227 (263)
                         .+++.+++|+++|..+++++.+.+.
T Consensus       270 ~al~~~~~iK~c~elar~Rakelk~~~~  297 (298)
T KOG1613|consen  270 GALITPEMIKRCLELARVRAKELKTRFN  297 (298)
T ss_pred             ccccCHHHHHHHHHHHHHHHHHHHHHhc
Confidence               5779999999999999999987664

>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=3e-29  Score=198.47  Aligned_cols=131  Identities=37%  Similarity=0.502  Sum_probs=116.0

Q ss_pred             CCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCCCCCcchHHHHH
Q psy18119         20 ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISL   99 (263)
Q Consensus        20 e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~~~~~~~~~l~~   99 (263)
                      |+|++.+++|++++++|||+|++|+|+|+|+|++|.+.++.....+..+.++|+++++|++....++.+.++..+.++++
T Consensus         1 e~R~i~i~~~~~~~a~GSa~v~~G~T~V~~~V~~~~~~~~~~~~~~~~g~~~v~v~~~~~~~~~~~~~~~~~~~~~~l~~   80 (132)
T PF01138_consen    1 ELRPISIETGVLPRADGSARVSLGNTKVICSVKGPIEPPPSNERDDAEGRLTVEVEFSPFASPSFRRGGRPDEEERELSS   80 (132)
T ss_dssp             CBEEEEEEESSSSSSSEEEEEEETTEEEEEEEEEEEEGCSCSTTSSSSEEEEEEEEECCCGSTSSSSSSSTHHHHHHHHH
T ss_pred             CCccEEEEeCCCCCCCeEEEEEECCeEEEEEEEecccccchhcccCCCceEEEEEEeccccccccccccccchhHHHHHH
Confidence            78999999999999999999999999999999999877543221223478899999889887766544457788899999


Q ss_pred             HHHHHHHhhhccCCCCceEEEEEEEEEeCCC-ChhHHHHHHHHHHHHHcCCC
Q psy18119        100 QLRQAVSAAIMSEVHPRSQIDIFVEVLQADG-GNFCACVNAATLALIDAGIP  150 (263)
Q Consensus       100 ~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG-~~~~a~i~Aa~~AL~dagIp  150 (263)
                      +|+++|++++.++.||+|.|+|+|+||++|| |++|+++||+++||+|+|||
T Consensus        81 ~l~~~l~~~~~~~~~~~~~i~v~v~vl~~dG~~~~~a~~~A~~~AL~~~~iP  132 (132)
T PF01138_consen   81 LLERALRSSILLEGYPRWQIHVDVQVLSDDGGNLLDAAINAACLALLDAGIP  132 (132)
T ss_dssp             HHHHHHHHTBSTTTTSSEEEEEEEEEEECSSSSHHHHHHHHHHHHHHHHTCS
T ss_pred             HHhhhccccccccccCceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCC
Confidence            9999999999999999999999999999999 99999999999999999998

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

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=99.96  E-value=9.4e-28  Score=236.08  Aligned_cols=207  Identities=18%  Similarity=0.183  Sum_probs=181.4

Q ss_pred             cceEEEeCCCC-CCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccc-----cCCCCCCcchH
Q psy18119         22 RKIRCRLGVFS-QSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGER-----KTRPRGDRKTS   95 (263)
Q Consensus        22 R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~-----~~~~~~~~~~~   95 (263)
                      |.+.+++|.+. +|+||+.++.|+|.|+|+|....+++.    ..+++.|.|+|....++.+..     ++.+++++++.
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 RHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPSE----PSDFFPLSVHYQERFSAAGRTSGGFFKREGRTKDHEV  164 (891)
T ss_pred             EEEEEEhhHHHHhCCCcEEEEECCeEEEEEEEeccCCCC----CCCccceeEeeeeehhhcCccCCceeccCCCCChHHH
Confidence            47999999885 699999999999999999997555443    357899999998766665432     44557888999


Q ss_pred             HHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCC--hhHHHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecCCc
Q psy18119         96 EISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGG--NFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISH  173 (263)
Q Consensus        96 ~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~--~~~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDPt~  173 (263)
                      .++++|+|.|+++++.+.||+++|  .++||++||+  ...+|+|||++||+++||||++.++||++|++++.+|+|||.
T Consensus       165 L~sRlIdR~lRPlfp~~~~~etQI--~i~VLsaDg~~~pd~~AInAASaAL~~SgIP~~gpVaAVrVG~idg~~VlnPt~  242 (891)
T PLN00207        165 LICRLIDRPLRPTMPKGFYHETQI--LSWVLSYDGLHSPDSLAVTAAGIAVALSEVPNLKAIAGVRVGLIGGKFIVNPTT  242 (891)
T ss_pred             HHHHHHCccchhhccccCCCCcEE--EEEEEeeCCCCChhhHHHHHHHHHHHhhCCCccCceEEEEEEEECCEEEECCCH
Confidence            999999999999999999998665  4589999998  568999999999999999999999999999999999999999


Q ss_pred             hhhhcCCCeEEEEEeCCCCcEEEEEeccc-CChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        174 LEETLGGPNLTVAALPLSGKVAVMELSQK-LHLDHLPRVLDCALKGCADIHAILDTAIKQHLIK  236 (263)
Q Consensus       174 ~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~-i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~  236 (263)
                      .|++.++..++|+.  ..+.|++++..+. ++++++.++++.|.++++.+.++++++++++...
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            99999999998887  3567999999886 5999999999999999999999999998887654

>KOG1067|consensus

Probab=99.93  E-value=1.1e-25  Score=207.33  Aligned_cols=241  Identities=24%  Similarity=0.289  Sum_probs=199.7

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCC-CCCC--CCcCCCCeE-EEEEEEeeCCCCCccc
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPR-PVRN--KSIKVHGSV-LINFQYSMAVFSTGER   84 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~-~~~~--~~~~~~~~~-~l~v~~~~~~~~~~~~   84 (263)
                      +|.|.|||..++.|+|.|+.+.++..+||++|+.|.|+|+|+|+.-. +...  ++-..++.+ .+-.+|.++|+++++.
T Consensus       356 ~gkR~DGR~ldelR~I~ce~~m~~~lHGSaLFqRGqTQvlctVtl~s~e~a~klD~l~~~~~~~~FmLhY~FPPyat~Ev  435 (760)
T KOG1067|consen  356 EGKRCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNGINFMLHYEFPPYATNEV  435 (760)
T ss_pred             cccccCCcchhhhcccceecCccccccchhhhhcCceeEEEEEEcCCHHHhhhhhhhccCccCceEEEEeccCCcccccc
Confidence            89999999999999999999999999999999999999999999622 2111  111122222 5667999999999998


Q ss_pred             cCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEEecC
Q psy18119         85 KTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAG  164 (263)
Q Consensus        85 ~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~  164 (263)
                      ++.+..++++.-...+-+++|.++++ +.||. .|+|.-.||++||+.-.|++.+-++||+|+|+|++.-+++|.+|++-
T Consensus       436 gkig~~nRRE~GhgaLAEkaL~~vlP-~dfPf-tIRv~SeVleSnGSsSMASvCGGslALmDaGvPv~a~vAGvaiGlvt  513 (760)
T KOG1067|consen  436 GKIGGLNRRELGHGALAEKALLPVLP-EDFPF-TIRVTSEVLESNGSSSMASVCGGSLALMDAGVPVSAHVAGVAIGLVT  513 (760)
T ss_pred             ccccCCcccccCchhHhhhhhhccCc-ccCce-EEEEeeeeeecCCcchHHhhhcchhhhhhcCCccccccceeEEEeEe
Confidence            88877888888778899999999998 78997 89999999999999999999999999999999999999999999873


Q ss_pred             C-----------eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        165 D-----------TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQH  233 (263)
Q Consensus       165 ~-----------~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~  233 (263)
                      +           .++.|....|+...+..+.|+.  +++.|+++    .++.+-+.+.+..|..+-.+|.+.|.+.+...
T Consensus       514 ~td~e~g~i~dyriltDIlGiEd~~GDMDFKiAG--t~dGvTA~----gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~P  587 (760)
T KOG1067|consen  514 KTDPEKGEIEDYRILTDILGIEDYNGDMDFKIAG--TNDGVTAL----GIPLKIVMEALQKAREARLQILDIMEKNINSP  587 (760)
T ss_pred             ccCcccCCcccceeehhhcchhhhcCCcceeecc--ccCcceec----CCcHHHHHHHHHhhhHHHHHHHHHHHhhcCCc
Confidence            2           6889999999999999999998  35667777    78889999999999999999999999888776


Q ss_pred             HHHhhccCCC-----CccccccceecCCc
Q psy18119        234 LIKVAGARGL-----GRKFQLGQLTGKKK  257 (263)
Q Consensus       234 ~~~~~~~~~~-----~~~~~~~~~~~~~~  257 (263)
                      .....++.+.     ....++-+|+|-+|
T Consensus       588 r~~~~~y~P~~~tlkv~~sk~~~lIGp~G  616 (760)
T KOG1067|consen  588 RGSDKEYSPVLETLKVSPSKRATLIGPGG  616 (760)
T ss_pred             ccCccccCceeeEEeecchhhheeecCcc
Confidence            6554444431     24444555665544

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

Probab=99.92  E-value=8e-25  Score=207.38  Aligned_cols=247  Identities=23%  Similarity=0.314  Sum_probs=212.6

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEc-CCCCCCCCc--CCCCeEEEEEEEeeCCCCCcccc
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYG-PRPVRNKSI--KVHGSVLINFQYSMAVFSTGERK   85 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~g-p~~~~~~~~--~~~~~~~l~v~~~~~~~~~~~~~   85 (263)
                      .++|+|||..++.||+.++.|++++.|||+++..|.|+.++.++. +....+-.+  ..+..-.+-.+|+++||+.++.+
T Consensus       310 ~~vR~DGR~~~~VRpi~~ev~~lpr~HGS~LFtRGeTQal~v~TLG~~~d~Qvid~l~~e~~krfm~hYNFPp~SvGE~g  389 (692)
T COG1185         310 GKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPRDAQVIDILEGEYKKRFLLHYNFPPFSVGETG  389 (692)
T ss_pred             CCcccCCCCcceeeeeeEEecCCCCccchhhhccCCCcceEEEEcCCcchhhhhhhccchhhhheeeeccCCCCCccccC
Confidence            899999999999999999999999999999999999999988884 322111111  11123334468999999999988


Q ss_pred             CCCCCCcchHHHHHHHHHHHHhhhc-cCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEEecC
Q psy18119         86 TRPRGDRKTSEISLQLRQAVSAAIM-SEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAG  164 (263)
Q Consensus        86 ~~~~~~~~~~~l~~~l~~~l~~~i~-l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~  164 (263)
                      +.+.+.+++.-..++-++++.++++ .+.||+ .|++.-.|++++|+-..|++++.++||+|+|+|++..++++..|++.
T Consensus       390 ~~g~p~RREiGHG~LA~Ral~~vlp~~e~fpy-tiRvVsEi~eSNGSsSmaSVCg~sLaLmdAGVPIk~pVAGIAMGLI~  468 (692)
T COG1185         390 RMGSPGRREIGHGALAERALAPVLPSEEEFPY-TIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIK  468 (692)
T ss_pred             CCCCCCcccccCchhhHHHHhhhCCchhcCCc-eeeeeehhhcccCcccchhhhhhHHHHHhCCCcccccccchhcccee
Confidence            8878888888888999999999998 578998 89999999999999999999999999999999999999999999985


Q ss_pred             C----eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc---cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy18119        165 D----TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ---KLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKV  237 (263)
Q Consensus       165 ~----~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G---~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~  237 (263)
                      +    .++-|....|+...+..+-|+.  ...-|++++++-   .++.+.+.+++..|+.+..++...|.+++.+...+.
T Consensus       469 eg~~~~vLsDI~G~EDhlGDMDFKVAG--T~~GiTAlQMDiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~el  546 (692)
T COG1185         469 EGDKYAVLSDILGDEDHLGDMDFKVAG--TDDGITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKEL  546 (692)
T ss_pred             cCCceEeeccccccccccCCceeEEec--CCCcceeeeeeeeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Confidence            4    6889999999999999999997  467899999884   579999999999999999999999999999999888


Q ss_pred             hccCCCC-----ccccccceecCCcc
Q psy18119        238 AGARGLG-----RKFQLGQLTGKKKE  258 (263)
Q Consensus       238 ~~~~~~~-----~~~~~~~~~~~~~~  258 (263)
                      ....++.     +.-..++++|.+|.
T Consensus       547 s~~aPri~t~~i~~dKI~dvIG~gGk  572 (692)
T COG1185         547 SPYAPRIETIKIDPDKIRDVIGPGGK  572 (692)
T ss_pred             hccCCceEEEccCHHHHhhccCCccc
Confidence            8888754     55567888888775

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=99.87  E-value=1.4e-20  Score=182.25  Aligned_cols=207  Identities=14%  Similarity=0.143  Sum_probs=173.7

Q ss_pred             cceEEEeCCCC-CCceeEEEEe-CCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccc-----cCCCCCCcch
Q psy18119         22 RKIRCRLGVFS-QSDGSAYIEQ-GNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGER-----KTRPRGDRKT   94 (263)
Q Consensus        22 R~i~i~~g~l~-~a~GSa~v~~-G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~-----~~~~~~~~~~   94 (263)
                      |++.+++|.+. +|+||+.+++ |+|.|+|+|....+++.    ..++++|.|+|....++.+..     +|.++|++++
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 RTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPKD----QFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDA   92 (719)
T ss_pred             EEEEEEcchhHhhCCceEEEEecCCeEEEEEEEecCCCCC----CCCCcceeEeeeehhhhcCccCCceeccCCCCChhh
Confidence            47999999885 6999999999 99999999997555443    357899999998766665433     4455788889


Q ss_pred             HHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChh--HHHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecCC
Q psy18119         95 SEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNF--CACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDIS  172 (263)
Q Consensus        95 ~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~--~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDPt  172 (263)
                      ...+|+|+|.++|+++- .|.+ .++|.++||+.|+..-  -.++|||++||.-++||+...+.+|.+|.+++++|++||
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            99999999999999863 3333 6888999999998653  468999999999999999999999999999999999999


Q ss_pred             chhhhcCCCeEEEEEeCC---CCcEEEEEe------------cc-cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        173 HLEETLGGPNLTVAALPL---SGKVAVMEL------------SQ-KLHLDHLPRVLDCALKGCADIHAILDTAIKQHL  234 (263)
Q Consensus       173 ~~Ee~~~~~~l~v~~~~~---~~~i~~i~~------------~G-~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~  234 (263)
                      ..|.+.++-.++|+....   .+.|++++.            .+ .++++.+.+++..|.+..+.+.+++++..+...
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            999999999999998321   348999997            33 489999999999999999999999988655444

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=99.80  E-value=2.3e-18  Score=163.76  Aligned_cols=211  Identities=17%  Similarity=0.183  Sum_probs=179.6

Q ss_pred             cceEEEeCCCC-CCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccc-----cCCCCCCcchH
Q psy18119         22 RKIRCRLGVFS-QSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGER-----KTRPRGDRKTS   95 (263)
Q Consensus        22 R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~-----~~~~~~~~~~~   95 (263)
                      |++.+++|.+. +|+|++++++|+|.|++++.+.. ++.    ..++++|.|+|....++.+..     ++.++|++++.
T Consensus        14 ~~l~~etg~~A~qa~gav~~~~gdt~vl~t~~~~~-~~~----~~dF~PLtV~y~Ek~yaaGkiPGgf~kREGrpse~e~   88 (692)
T COG1185          14 RTLTLETGKIARQANGAVLVRYGDTVVLATVVASK-PKE----GQDFFPLTVNYEEKTYAAGKIPGGFFKREGRPSEKEI   88 (692)
T ss_pred             eeEEEEcchhhhhcCccEEEEECCeEEEEEEeecC-CCC----CCCccceeEeeeeehhccCcCCCcccccCCCCCccch
Confidence            88999999885 69999999999999999999966 332    358999999998777666543     44557889999


Q ss_pred             HHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChh--HHHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecCCc
Q psy18119         96 EISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNF--CACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISH  173 (263)
Q Consensus        96 ~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~--~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDPt~  173 (263)
                      ..+|+|+|-+++.++.. |- ..++|.++|++.|+...  -.+++++++||.-++||+...+.++++|++++.+++.||.
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            99999999999887532 32 26889999999999764  4789999999999999999999999999999999999999


Q ss_pred             hhhhcCCCeEEEEEeCCCCcEEEEEecc-cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy18119        174 LEETLGGPNLTVAALPLSGKVAVMELSQ-KLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGAR  241 (263)
Q Consensus       174 ~Ee~~~~~~l~v~~~~~~~~i~~i~~~G-~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~~~~  241 (263)
                      .|-+.+.-.++|+.  +...|.+++... .++++++.+++..+.+..+.+.+++++.......+.+.+.
T Consensus       167 ~e~~~s~lDlvVAG--T~~aV~MVE~~a~~l~E~~ml~Av~fg~~~~~~~~~~qe~l~~~~g~~~~~~~  233 (692)
T COG1185         167 EELEESKLDLVVAG--TKDAVNMVESEADELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELE  233 (692)
T ss_pred             HHhhhcceeeEecC--ChhhhheeecccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccccc
Confidence            99999999999987  355899999876 5789999999999999999999999998877765555554

>KOG1067|consensus

Probab=99.69  E-value=2.1e-16  Score=146.55  Aligned_cols=207  Identities=18%  Similarity=0.196  Sum_probs=168.2

Q ss_pred             CCcceEEEeCCCCC-CceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCcc-----ccCCCCCCcc
Q psy18119         20 ELRKIRCRLGVFSQ-SDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGE-----RKTRPRGDRK   93 (263)
Q Consensus        20 e~R~i~i~~g~l~~-a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~-----~~~~~~~~~~   93 (263)
                      --|.+.+++|.+.+ |+||+.+..|+|.|+++|..-..|.+     +.+..+.|+|.....+.+.     .++..++.++
T Consensus        54 GnR~i~~etGklaRfAngsvvv~~GeT~Vm~Tv~~a~~PSp-----~qFlPL~VdYqeK~aAvGRip~~fmRREg~tkdk  128 (760)
T KOG1067|consen   54 GNREILFETGKLARFANGSVVVQMGETAVMTTVVLADKPSP-----PQFLPLVVDYQEKFAAVGRIPGNFMRREGRTKDK  128 (760)
T ss_pred             CCeEEEEecchhhhhcCCcEEEccCCeEEEEEEEecCCCCc-----cccceEEEehhhhhhhhccCCCcccccccCCcch
Confidence            56999999999975 99999999999999999998555554     2478999999754433322     1233345566


Q ss_pred             hHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChh--HHHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecC
Q psy18119         94 TSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNF--CACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDI  171 (263)
Q Consensus        94 ~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~--~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDP  171 (263)
                      +....++|++.+++......|.  ..++-+.+|..||-.-  --++|++++||.-+.||+...+.++.+|+++++++++|
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            6666788888888776544343  3556677899999654  35899999999999999999999999999999999999


Q ss_pred             CchhhhcCCCeEEEEEeCCCCcEEEEEecc-cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        172 SHLEETLGGPNLTVAALPLSGKVAVMELSQ-KLHLDHLPRVLDCALKGCADIHAILDTAIKQHLI  235 (263)
Q Consensus       172 t~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G-~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~  235 (263)
                      |..|.+.+.-.+.++.  ...++++++-.+ .+..+++.++++++.+.+.++...+....+++..
T Consensus       207 T~kEmssS~Lnlvvag--t~~~~vmle~~s~~i~qqdl~~Aikvg~~~~q~~i~~i~~L~k~~Gk  269 (760)
T KOG1067|consen  207 TRKEMSSSQLNLVVAG--TKSQTVMLEGSSNNILQQDLLHAIKVGVKEAQQIIQGIERLAKKYGK  269 (760)
T ss_pred             chhhhhhccceeEEEe--ccceEEEEEcccccccHHHHHHHHHhccHHHHHHHHHHHHHHHHhCc
Confidence            9999999999999998  388999999887 4789999999999999999999988887777644

>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=99.27  E-value=2.2e-11  Score=85.22  Aligned_cols=65  Identities=25%  Similarity=0.294  Sum_probs=54.3

Q ss_pred             CceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEE-EEEeccc--CChhHHHHHHHHHHHH
Q psy18119        153 EYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVA-VMELSQK--LHLDHLPRVLDCALKG  218 (263)
Q Consensus       153 ~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~-~i~~~G~--i~~~~l~~~i~~A~~~  218 (263)
                      |+|+++|++++++.+++|||..||..+++.+++++. .+++++ .++..|.  ++++++.++++.|.++
T Consensus         1 ~~~~avt~~~i~~~~v~Dpt~~Ee~~~~~~l~~~~~-~~~~~~~~~~~~g~~~~~~~~l~~~i~~A~~~   68 (68)
T PF03725_consen    1 DPPVAVTVGIIDGELVVDPTAEEESLSDSSLTLAVD-GTGNICTLQKSGGGSELSEDQLEEAIELAKKA   68 (68)
T ss_dssp             SEEEEEEEEEETTEEEES--HHHHHHSSEEEEEEEE-TTSSEEEEEEEEESSEEEHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEEEECCEEEECCCHHHHhhcCCcEEEEEE-CCCCEEEEEEcCCCCCCCHHHHHHHHHHHhcC
Confidence            689999999999999999999999999999999996 456665 4445554  9999999999999875

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	263
2nn6_B	249	Structure Of The Human Rna Exosome Composed Of Rrp4		2e-77
2wnr_B	240	The Structure Of Methanothermobacter Thermautotroph		4e-45
2pnz_A	249	Crystal Structure Of The P. Abyssi Exosome Rnase Ph		3e-44
2ba0_F	258	Archaeal Exosome Core Length = 258		4e-43
3m7n_D	258	Archaeoglobus Fulgidus Exosome With Rna Bound To Th		6e-43
2br2_B	248	Rnase Ph Core Of The Archaeal Exosome Length = 248		8e-41
3l7z_B	245	Crystal Structure Of The S. Solfataricus Archaeal E		1e-40
2je6_B	250	Structure Of A 9-Subunit Archaeal Exosome Length =		2e-40
4ifd_B	248	Crystal Structure Of An 11-subunit Eukaryotic Exoso		4e-34
2wp8_B	246	Yeast Rrp44 Nuclease Length = 246		5e-34
2nn6_F	272	Structure Of The Human Rna Exosome Composed Of Rrp4		4e-17
2nn6_D	237	Structure Of The Human Rna Exosome Composed Of Rrp4		1e-16
1r6m_A	239	Crystal Structure Of The Trna Processing Enzyme Rna		9e-15
1r6l_A	239	Crystal Structure Of The Trna Processing Enzyme Rna		7e-14
3hkm_A	246	Crystal Structure Of Rice(Oryza Sativa) Rrp46 Lengt		5e-13
1uds_A	255	Crystal Structure Of The Trna Processing Enzyme Rna		8e-13
1udn_A	255	Crystal Structure Of The Trna Processing Enzyme Rna		1e-12
1udq_A	255	Crystal Structure Of The Trna Processing Enzyme Rna		2e-12
1udo_A	255	Crystal Structure Of The Trna Processing Enzyme Rna		2e-12
1oyp_A	245	Crystal Structure Of The Phosphorolytic Exoribonucl		1e-09
3dd6_A	255	Crystal Structure Of Rph, An Exoribonuclease From B		5e-09
3b4t_A	262	Crystal Structure Of Mycobacterium Tuberculosis Rna		6e-09
3krn_A	222	Crystal Structure Of C. Elegans Cell-Death-Related		9e-09
1oys_A	245	Crystal Structure Of The Phosphorolytic Exoribonucl		1e-08
4ifd_D	245	Crystal Structure Of An 11-subunit Eukaryotic Exoso		2e-06
3cdi_A	723	Crystal Structure Of E. Coli Pnpase Length = 723		3e-06
3cdj_A	559	Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCA		3e-06
4aid_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		3e-06
4aim_A	726	Crystal Structure Of C. Crescentus Pnpase Bound To		3e-06
4am3_A	717	Crystal Structure Of C. Crescentus Pnpase Bound To		3e-06
3gcm_A	549	Crystal Structure Of E. Coli Polynucleotide Phospho		3e-06
3h1c_A	549	Crystal Structure Of Polynucleotide Phosphorylase (		3e-06
1e3p_A	757	Tungstate Derivative Of Streptomyces Antibioticus P		1e-04
3u1k_A	630	Crystal Structure Of Human Pnpase Length = 630		2e-04
4ifd_F	250	Crystal Structure Of An 11-subunit Eukaryotic Exoso		3e-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 =  285 bits (729), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 135/235 (57%), Positives = 178/235 (75%), Gaps = 3/235 (1%)
Query: 1   MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVR-N 59
           ++LL++ G   R DGRR  ELRKI+ R+GVF+Q+DGSAYIEQGNTK LA VYGP  +R +
Sbjct: 8   LELLSDQG--YRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGS 65
Query: 60  KSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQI 119
           ++  +    L+N QYS A FSTGERK RP GDRK+ E+ LQLRQ   AAI++++HPRSQI
Sbjct: 66  RARALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQI 125
Query: 120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLG 179
           DI+V+VLQADGG + ACVNAATLA++DAGIPMR++V ACSA     T L D+SH+EE  G
Sbjct: 126 DIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAG 185
Query: 180 GPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
           GP L +A LP SG++A++E+  +LH DHL RVL+ A +   D+H +LD  ++QH+
Sbjct: 186 GPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHV 240

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

Iteration: 1
 Score =  177 bits (450), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 91/223 (40%), Positives = 141/223 (63%), Gaps = 1/223 (0%)
Query: 11  LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLI 70
           +R DGR   ELR ++   G+  ++DGS+Y+E G  K+L AVYGPR  + + ++     +I
Sbjct: 16  VREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVI 75
Query: 71  NFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADG 130
             +Y+MA FS  ERK RP  DR++ EIS    +A+  A++ E  PRS ID+F+EVL+A+G
Sbjct: 76  RCRYNMAPFSVEERK-RPGPDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEG 134
Query: 131 GNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPL 190
           G  CA + AA++AL DAGIPMR+ VVAC+A   GD  ++D+S  E+  G  ++ VA LP 
Sbjct: 135 GTRCAGITAASVALADAGIPMRDMVVACAAGKVGDQVVLDLSEEEDKEGQADVPVAILPR 194
Query: 191 SGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQH 233
           + ++ +++    L  +   R LD A++GC  IH +   A+++ 
Sbjct: 195 TREITLLQSDGNLTPEEFERALDLAVEGCLRIHEVQKEALRKR 237

>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 =  174 bits (442), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 89/229 (38%), Positives = 141/229 (61%), Gaps = 1/229 (0%)
Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           G R DGR+ +ELR I+  +GV   ++GSAYIE G  K++AAVYGPR +  K ++     +
Sbjct: 15  GRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAI 74
Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           +  +Y+MA FS  ERK +P  DR++ EIS  ++ A+  A++ E+ PR+ ID+F+EVLQAD
Sbjct: 75  LRVRYNMAPFSVEERK-KPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQAD 133
Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
            G   A + AA+LAL DAGIPMR+ V AC+A       ++D++  E+  G  ++ VA +P
Sbjct: 134 AGTRVAGITAASLALADAGIPMRDLVAACAAGKIEGEIVLDLNKEEDNYGEADVPVAIMP 193
Query: 190 LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVA 238
           L   + ++++   L  D     +  A+KG   ++     A+K+  +K+A
Sbjct: 194 LKNDITLLQMDGYLTKDEFIEAVKLAIKGAKAVYQKQREALKEKYLKIA 242

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

Iteration: 1
 Score =  171 bits (432), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 92/231 (39%), Positives = 142/231 (61%), Gaps = 4/231 (1%)
Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           GLR DGR+  ELR I+    V  ++DGS Y+E G  KV+AAV+GPR V  + ++     +
Sbjct: 15  GLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKAI 74
Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           I ++Y+MA FS  ERK RP  DR++ EIS   ++A  A IM E+ PRS IDIFVEVLQAD
Sbjct: 75  IRYRYNMAPFSVEERK-RPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQAD 133
Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
            G+  AC+NAA++AL+DAG+PM+  + + +   A    ++D    E+  G  ++  A L 
Sbjct: 134 AGSRTACLNAASVALVDAGVPMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFLI 193
Query: 190 LSGK---VAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKV 237
            +GK   +A++++  ++  D + + ++ A KG   I+ +   AI +  I+V
Sbjct: 194 RNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAILRRYIEV 244

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

Iteration: 1
 Score =  170 bits (431), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 92/231 (39%), Positives = 142/231 (61%), Gaps = 4/231 (1%)
Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           GLR DGR+  ELR I+    V  ++DGS Y+E G  KV+AAV+GPR V  + ++     +
Sbjct: 15  GLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKAI 74
Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           I ++Y+MA FS  ERK RP  DR++ EIS   ++A  A IM E+ PRS IDIFVEVLQAD
Sbjct: 75  IRYRYNMAPFSVEERK-RPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQAD 133
Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
            G+  AC+NAA++AL+DAG+PM+  + + +   A    ++D    E+  G  ++  A L 
Sbjct: 134 AGSRTACLNAASVALVDAGVPMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFLI 193
Query: 190 LSGK---VAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKV 237
            +GK   +A++++  ++  D + + ++ A KG   I+ +   AI +  I+V
Sbjct: 194 RNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAILRRYIEV 244

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

Iteration: 1
 Score =  163 bits (413), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 82/227 (36%), Positives = 133/227 (58%), Gaps = 1/227 (0%)
Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           G R DGR+  ELR I+  LGV   +DGSA  E GNTK +AAVYGP+ +  + + +    +
Sbjct: 17  GKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAV 76
Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           +  +Y M  FST ERK  P   R+  E+S  +R+A+ +A++ E+ PR+ ID+F E+LQAD
Sbjct: 77  LRVRYHMTPFSTDERKN-PAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQAD 135
Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
            G+    + AA+LAL DAGIPMR+ +   +   A    ++D++  E+  G  ++ +A +P
Sbjct: 136 AGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLNETEDMWGEADMPIAMMP 195
Query: 190 LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIK 236
              +V + +L+  +  D   +  D A+KG   I+ +   A+K   ++
Sbjct: 196 SLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREALKSKYVE 242

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

Iteration: 1
 Score =  163 bits (412), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 82/227 (36%), Positives = 133/227 (58%), Gaps = 1/227 (0%)
Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           G R DGR+  ELR I+  LGV   +DGSA  E GNTK +AAVYGP+ +  + + +    +
Sbjct: 14  GKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAV 73
Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           +  +Y M  FST ERK  P   R+  E+S  +R+A+ +A++ E+ PR+ ID+F E+LQAD
Sbjct: 74  LRVRYHMTPFSTDERKN-PAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQAD 132
Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
            G+    + AA+LAL DAGIPMR+ +   +   A    ++D++  E+  G  ++ +A +P
Sbjct: 133 AGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLNETEDMWGEADMPIAMMP 192
Query: 190 LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIK 236
              +V + +L+  +  D   +  D A+KG   I+ +   A+K   ++
Sbjct: 193 SLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREALKSKYVE 239

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

Iteration: 1
 Score =  162 bits (409), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 82/227 (36%), Positives = 132/227 (58%), Gaps = 1/227 (0%)
Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           G R DGR+  ELR I+  LGV   +DGSA  E GNTK +AAVYGP+ +  + + +    +
Sbjct: 19  GKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAV 78
Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           +  +Y M  FST ERK  P   R+  E+S  +R+A+ +A++ E+ PR+ ID+F E+LQAD
Sbjct: 79  LRVRYHMTPFSTDERKN-PAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQAD 137
Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
            G+    + AA+LAL DAGIPMR+ +   +   A    ++D++  E   G  ++ +A +P
Sbjct: 138 AGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLNETEAMWGEADMPIAMMP 197
Query: 190 LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIK 236
              +V + +L+  +  D   +  D A+KG   I+ +   A+K   ++
Sbjct: 198 SLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREALKSKYVE 244

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

Iteration: 1
 Score =  141 bits (355), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 80/226 (35%), Positives = 125/226 (55%), Gaps = 3/226 (1%)
Query: 10  GLRNDGRRGHELRKIRCRLGVFSQS-DGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSV 68
           GLR DGRR +ELR+    +     + DGS+Y+EQGN K++  V GP+  R KS       
Sbjct: 13  GLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKA 72
Query: 69  LINFQYSMAVFSTGER-KTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQ 127
           L+N   ++  FS  ER K+  + +R+  EI   L +     +M  ++PR+ IDI + VL+
Sbjct: 73  LLNVSVNITKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLE 132
Query: 128 ADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAA 187
            DGG   + +N  TLALIDAGI M +Y+   S  L   TPL+D + LEE      +T+  
Sbjct: 133 QDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEEN-AMSTVTLGV 191
Query: 188 LPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQH 233
           +  S K++++ +  K+ LD L  VL   + G   +  ++D  +++H
Sbjct: 192 VGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKH 237

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

Iteration: 1
 Score =  140 bits (354), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 80/226 (35%), Positives = 125/226 (55%), Gaps = 3/226 (1%)
Query: 10  GLRNDGRRGHELRKIRCRLGVFSQS-DGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSV 68
           GLR DGRR +ELR+    +     + DGS+Y+EQGN K++  V GP+  R KS       
Sbjct: 11  GLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKA 70
Query: 69  LINFQYSMAVFSTGER-KTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQ 127
           L+N   ++  FS  ER K+  + +R+  EI   L +     +M  ++PR+ IDI + VL+
Sbjct: 71  LLNVSVNINKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLE 130
Query: 128 ADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAA 187
            DGG   + +N  TLALIDAGI M +Y+   S  L   TPL+D + LEE      +T+  
Sbjct: 131 QDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEEN-AMSTVTLGV 189
Query: 188 LPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQH 233
           +  S K++++ +  K+ LD L  VL   + G   +  ++D  +++H
Sbjct: 190 VGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKH 235

>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 = 85.1 bits (209), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 80/242 (33%), Positives = 123/242 (50%), Gaps = 24/242 (9%)
Query: 6   EYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPR---------- 55
           E   G R+  R    LR +  R G+ SQ+ GSAY+E G TKVL AV GPR          
Sbjct: 25  EEAPGTRDPTR----LRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGG 80
Query: 56  ---PVRNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSE 112
                      + G +L +F+   A F+ G R+  P G  +  E++L L++A+  A+   
Sbjct: 81  PAGAGGEAPAALRGRLLCDFR--RAPFA-GRRRRAPPGGCEERELALALQEALEPAVRLG 137
Query: 113 VHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA-GDTP--LV 169
            +PR+Q+++   +L+  G    A + AA LAL DAG+ M + VV C  SLA G  P  L+
Sbjct: 138 RYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVEMYDLVVGCGLSLAPGPAPTWLL 197
Query: 170 DISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHL-DHLPRVLDCALKGCADIHAILDT 228
           D + LEE      LTVA +P+  +VA +  S +  L +     +   L+GC  ++ +L  
Sbjct: 198 DPTRLEEERAAAGLTVALMPVLNQVAGLLGSGEGGLTESWAEAVRLGLEGCQRLYPVLQQ 257
Query: 229 AI 230
           ++
Sbjct: 258 SL 259

>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 = 83.2 bits (204), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 52/153 (33%), Positives = 78/153 (50%), Gaps = 12/153 (7%)
Query: 18  GHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVR-NKSIKVHGSVLINFQYSM 76
           G  LR   C   + S+ DGSA   QG+T VLA VYGP  V+ +K I    ++ +  +  +
Sbjct: 27  GCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKI 86
Query: 77  AVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCAC 136
            +    E K+R R  R T E          A ++  +HPR+ I + ++V+   G     C
Sbjct: 87  GLPGVAE-KSRERLIRNTCE----------AVVLGTLHPRTSITVVLQVVSDAGSLLACC 135
Query: 137 VNAATLALIDAGIPMREYVVACSASLAGDTPLV 169
           +NAA +AL+DAG+PMR      + +L  D  LV
Sbjct: 136 LNAACMALVDAGVPMRALFCGVACALDSDGTLV 168

>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 = 77.0 bits (188), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 111/238 (46%), Gaps = 18/238 (7%)
Query: 12  RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLIN 71
           R  GR   +LR IR        ++GS  +E G+TKV+  V     V  + +K  G   + 
Sbjct: 3   RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGV-PRFLKGQGQGWLT 61
Query: 72  FQYSMAVFSTGERKTR--PRGDR--KTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQ 127
            +Y M   STGER  R   RG +  +T EI   + +++ AA+       + + I  +V+Q
Sbjct: 62  AEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQ 121
Query: 128 ADGGNFCACVNAATLALIDA-----------GIPMREYVVACSASLAGDTPLVDISHLEE 176
           ADGG   A +  AT+ALIDA           G P+++ V A S  +    P++D+ +LE+
Sbjct: 122 ADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIYQGVPVLDLDYLED 181
Query: 177 TLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRVLDCALKGCADIHAILDTAIKQ 232
           +    +L V      G + V   ++        L  +L+ A +G  ++  +   A+ +
Sbjct: 182 SAAETDLNVVMTDAGGFIEVQGTAEGAPFRPAELNAMLELAQQGMQELFELQRAALAE 239

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

Iteration: 1
 Score = 74.3 bits (181), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 60/200 (30%), Positives = 95/200 (47%), Gaps = 16/200 (8%)
Query: 12  RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLIN 71
           R  GR   +LR IR        ++GS  +E G+TKV+  V     V  + +K  G   + 
Sbjct: 3   RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGV-PRFLKGQGQGWLT 61
Query: 72  FQYSMAVFSTGERKTR--PRGDR--KTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQ 127
            +Y     STGER  R   RG +  +T EI   + +++ AA+       + + I  +V+Q
Sbjct: 62  AEYGXLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQ 121
Query: 128 ADGGNFCACVNAATLALIDA-----------GIPMREYVVACSASLAGDTPLVDISHLEE 176
           ADGG   A +  AT+ALIDA           G P+++ V A S  +    P++D+ +LE+
Sbjct: 122 ADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQXVAAVSVGIYQGVPVLDLDYLED 181
Query: 177 TLGGPNLTVAALPLSGKVAV 196
           +    +L V      G + V
Sbjct: 182 SAAETDLNVVXTDAGGFIEV 201

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

Iteration: 1
 Score = 71.2 bits (173), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 47/167 (28%), Positives = 77/167 (46%), Gaps = 13/167 (7%)
Query: 12  RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRP-VRNKSIKVHGSVLI 70
           R DGR  ++LR   C      ++ GSA   QG+T VLAAVYGP+P  R        S+ +
Sbjct: 5   RADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRKGENPEKASIEV 64
Query: 71  NFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADG 130
            ++         E+           E  + L++ + +  +  VHP +   + ++V+  DG
Sbjct: 65  VWKPMTGQIGKQEK-----------EYEMTLKRTLQSICLLTVHPNTTTSVILQVVGNDG 113
Query: 131 GNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLV-DISHLEE 176
                 +NA   AL+ AGIP++   VA    +  D  ++ D +  EE
Sbjct: 114 SLLPCAINACCAALVFAGIPLKHLAVAIGCGVLEDGEVILDTNKAEE 160

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 117/245 (47%), Gaps = 25/245 (10%)
Query: 11  LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLI 70
           +R+DGR+  +LR +  +       +GS  I  G TKV+        V N  +K  G   I
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPN-WLKGKGQGWI 59
Query: 71  NFQYSMAVFSTGERKTRP----RGDRKTSEISLQLRQAVSAAI-MSEVHPRSQIDIFVEV 125
             +YSM   +T +R  R     R   +T EI   + +A+  A+ ++++  R+ I +  +V
Sbjct: 60  TAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERT-IWVDCDV 118
Query: 126 LQADGGNFCACVNAATLALIDAGI-----------PMREYVVACSASLAGDTPLVDISHL 174
           +QADGG   A +  A +A+ DA I           P++++V A S  +  D  L+D++  
Sbjct: 119 IQADGGTATAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNFE 178
Query: 175 EETLGGPNLTVAALPLSGK---VAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIK 231
           E++    ++ V     SG+   V  M        D L ++LD A KG   I+ +++   K
Sbjct: 179 EDSAAQVDMNVVGTG-SGRLSEVHTMGEEYSFTKDELIKMLDLAQKG---INELIELQKK 234
Query: 232 QHLIK 236
            ++I+
Sbjct: 235 LYVIQ 239

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 117/245 (47%), Gaps = 25/245 (10%)
Query: 11  LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLI 70
           +R+DGR+  +LR +  +       +GS  I  G TKV+        V N  +K  G   I
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPN-WLKGKGQGWI 59
Query: 71  NFQYSMAVFSTGERKTRP----RGDRKTSEISLQLRQAVSAAI-MSEVHPRSQIDIFVEV 125
             +YSM   +T +R  R     R   +T EI   + +A+  A+ ++++  R+ I +  +V
Sbjct: 60  TAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERT-IWVDCDV 118
Query: 126 LQADGGNFCACVNAATLALIDAGI-----------PMREYVVACSASLAGDTPLVDISHL 174
           +QADGG   A +  A +A+ DA I           P++++V A S  +  D  L+D++  
Sbjct: 119 IQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNFE 178
Query: 175 EETLGGPNLTVAALPLSGK---VAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIK 231
           E++    ++ V     SG+   V  M        D L ++LD A KG   I+ +++   K
Sbjct: 179 EDSAAQVDMNVVGTG-SGRLSEVHTMGEEYSFTKDELIKMLDLAQKG---INELIELQKK 234
Query: 232 QHLIK 236
            ++I+
Sbjct: 235 LYVIQ 239

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

Iteration: 1
 Score = 69.3 bits (168), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 117/245 (47%), Gaps = 25/245 (10%)
Query: 11  LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLI 70
           +R+DGR+  +LR +  +       +GS  I  G TKV+        V N  +K  G   I
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPN-WLKGKGQGWI 59
Query: 71  NFQYSMAVFSTGERKTRP----RGDRKTSEISLQLRQAVSAAI-MSEVHPRSQIDIFVEV 125
             +YSM   +T +R  R     R   +T EI   + +A+  A+ ++++  R+ I +  +V
Sbjct: 60  TAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERT-IWVDCDV 118
Query: 126 LQADGGNFCACVNAATLALIDAGI-----------PMREYVVACSASLAGDTPLVDISHL 174
           +QADGG   A +  A +A+ DA I           P++++V A S  +  D  L+D++  
Sbjct: 119 IQADGGARTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNFE 178
Query: 175 EETLGGPNLTVAALPLSGK---VAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIK 231
           E++    ++ V     SG+   V  M        D L ++LD A KG   I+ +++   K
Sbjct: 179 EDSAAQVDMNVVGTG-SGRLSEVHTMGEEYSFTKDELIKMLDLAQKG---INELIELQKK 234
Query: 232 QHLIK 236
            ++I+
Sbjct: 235 LYVIQ 239

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

Iteration: 1
 Score = 69.3 bits (168), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 116/245 (47%), Gaps = 25/245 (10%)
Query: 11  LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLI 70
           +R+DGR+  +LR +  +       +GS  I  G TKV+        V N  +K  G   I
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPN-WLKGKGQGWI 59
Query: 71  NFQYSMAVFSTGERKTRP----RGDRKTSEISLQLRQAVSAAI-MSEVHPRSQIDIFVEV 125
             +YSM   +T +R  R     R    T EI   + +A+  A+ ++++  R+ I +  +V
Sbjct: 60  TAEYSMLPRATQQRTIRESVQGRIGGATHEIQRMIGRAMRTAVELTKIGERT-IWVDCDV 118
Query: 126 LQADGGNFCACVNAATLALIDAGI-----------PMREYVVACSASLAGDTPLVDISHL 174
           +QADGG   A +  A +A+ DA I           P++++V A S  +  D  L+D++  
Sbjct: 119 IQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNFE 178
Query: 175 EETLGGPNLTVAALPLSGK---VAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIK 231
           E++    ++ V     SG+   V  M        D L ++LD A KG   I+ +++   K
Sbjct: 179 EDSAAQVDMNVVGTG-SGRLSEVHTMGEEYSFTKDELIKMLDLAQKG---INELIELQKK 234
Query: 232 QHLIK 236
            ++I+
Sbjct: 235 LYVIQ 239

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

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 58/185 (31%), Positives = 88/185 (47%), Gaps = 21/185 (11%)
Query: 11  LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVL--AAVYGPRPVRNKSIKVHGSV 68
           +R+DGR+  ELR I   L   S  +GS  I  GNTKV+  A+V    P     ++  G  
Sbjct: 1   MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVP---PFLRGGGKG 57
Query: 69  LINFQYSMAVFSTGERKTRPRGDRK----TSEISLQLRQAVSAAIMSEVHPRSQIDIFVE 124
            I  +YSM   +T +R  R     K    T EI   + +A+ A +  E      I I  +
Sbjct: 58  WITAEYSMLPRATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCD 117
Query: 125 VLQADGGNFCACVNAATLA-------LIDAGI----PMREYVVACSASLAGDTP-LVDIS 172
           V+QADGG   A +  A LA       LI AG     P+ +++ A S  +  +   L+D++
Sbjct: 118 VIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLN 177
Query: 173 HLEET 177
           + E++
Sbjct: 178 YEEDS 182

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 101/229 (44%), Gaps = 25/229 (10%)
Query: 11  LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLI 70
           +R DGR   ELR I          +GS  IE G+TKV+ +      V    ++  G   +
Sbjct: 11  MRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERV-PPFMRGEGKGWV 69
Query: 71  NFQYSMAVFSTGERKTRPRGDRK----TSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVL 126
             +Y+M   +T +R  R     K    T EI   + +A+ A +  E      + I  +V+
Sbjct: 70  TAEYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGERTVWIDCDVI 129
Query: 127 QADGGNFCACVNAATLALIDA-----------GIPMREYVVACSASLAGDTPLV-DISHL 174
           QADGG   A +  A +A++ A            IP+++Y+ A S  +  +  +V D+++ 
Sbjct: 130 QADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEEQGVVLDLNYA 189
Query: 175 EETLGGPNLTVAALPLSGKVAVMEL-----SQKLHLDHLPRVLDCALKG 218
           E++    ++ V    ++GK   +E+             L  +LD A +G
Sbjct: 190 EDSKADVDMNVI---MTGKGQFVEVQGTGEEATFSRAQLNELLDAAEQG 235

>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 = 57.8 bits (138), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 100/233 (42%), Gaps = 23/233 (9%)
Query: 12  RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVL--AAVYGPRPVRNKSIKVHGSVL 69
           R DGR  HELR +    G      GS  IE G+TKVL  A+V    P   +  K  G   
Sbjct: 7   REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVP---RWRKATGLGW 63
Query: 70  INFQYSM---AVFSTGERKT-RPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEV 125
           +  +Y+M   A  S  +R++ R R   +T EIS  + +++ A I       + I I  +V
Sbjct: 64  LTAEYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDV 123
Query: 126 LQADGGNFCACVNAATLALIDAGI------------PMREYVVACSASLAGDTPLVDISH 173
           LQADGG   A +  A +AL DA              P+   + A S  +      VD+ +
Sbjct: 124 LQADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVVDGRIRVDLPY 183
Query: 174 LEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRVLDCALKGCADIHA 224
            E++    ++ V A      V +    +        L ++LD AL  C  + A
Sbjct: 184 EEDSRAEVDMNVVATDTGTLVEIQGTGEGATFARSTLDKLLDMALGACDTLFA 236

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 38/132 (28%), Positives = 60/132 (45%), Gaps = 12/132 (9%)
Query: 21  LRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFS 80
           LR++RC L     +DGSA   QG T + A+  GP  V + S     ++ ++  Y      
Sbjct: 5   LREMRCELSFLKNADGSACFSQGATCIWASCSGPGDV-HASKASDEAMTLDISYRANC-- 61
Query: 81  TGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAA 140
                    GD K + ++  +   +S AI  E+ P + I + V  +Q DG      +N A
Sbjct: 62  ---------GDNKFNVLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAVAINGA 112
Query: 141 TLALIDAGIPMR 152
             AL+D G+P  
Sbjct: 113 CFALLDNGMPFE 124

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/185 (30%), Positives = 88/185 (47%), Gaps = 21/185 (11%)
Query: 11  LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVL--AAVYGPRPVRNKSIKVHGSV 68
           +R+DGR+  ELR I   L   S  +GS  I  GNTKV+  A+V    P     ++  G  
Sbjct: 1   MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVP---PFLRGGGKG 57
Query: 69  LINFQYSMAVFSTGERKTRPRGDRK----TSEISLQLRQAVSAAIMSEVHPRSQIDIFVE 124
            I  +YSM   +T ++  +     K    T EI   + +A+ A +  E      I I  +
Sbjct: 58  WITAEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCD 117
Query: 125 VLQADGGNFCACVNAATLA-------LIDAGI----PMREYVVACSASLAGDTP-LVDIS 172
           V+QADGG   A +  A LA       LI AG     P+ +++ A S  +  +   L+D++
Sbjct: 118 VIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLN 177
Query: 173 HLEET 177
           + E++
Sbjct: 178 YEEDS 182

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 39/163 (23%), Positives = 70/163 (42%), Gaps = 19/163 (11%)
Query: 12  RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGP-RPVRNKSIKVHGSVLI 70
           R D     +   ++  +G+    DGS+     +TKV+ +V GP  P   + +    ++ I
Sbjct: 13  RLDSAEKKKKMSVQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEI 72
Query: 71  NFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQA-- 128
             + +  V +T E+    +           LR  ++  I    +PR    I  ++L++  
Sbjct: 73  IVRPAKGVATTREKVLEDK-----------LRAVLTPLITRHCYPRQLCQITCQILESGE 121
Query: 129 DGGNFC-----ACVNAATLALIDAGIPMREYVVACSASLAGDT 166
           D   F       C+NAA LAL+DAGI +     +   ++  DT
Sbjct: 122 DEAEFSLRELSCCINAAFLALVDAGIALNSMCASIPIAIIKDT 164

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 57/190 (30%), Positives = 92/190 (48%), Gaps = 17/190 (8%)
Query: 9   GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVL-AAVYGPRPVRNKSI--KVH 65
           G  R DGR    +R +  R GV  ++ GSA   +G T+ L  A  G    R+  +  ++ 
Sbjct: 318 GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGT--ARDAQVLDELM 375
Query: 66  G--SVLINFQYSMAVFSTGERKTRPRGDRKTSEISL-QLRQAVSAAIMSEV--HPRSQID 120
           G  +    F Y+   +S GE  T   G  K  EI   +L +    A+M ++   P + + 
Sbjct: 376 GERTDTFLFHYNFPPYSVGE--TGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYT-VR 432
Query: 121 IFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA--GDTPLV--DISHLEE 176
           +  E+ +++G +  A V  A+LAL+DAG+P++  V   +  L   GD  +V  DI   E+
Sbjct: 433 VVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDILGDED 492
Query: 177 TLGGPNLTVA 186
            LG  +  VA
Sbjct: 493 HLGDMDFKVA 502

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 57/190 (30%), Positives = 92/190 (48%), Gaps = 17/190 (8%)
Query: 9   GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVL-AAVYGPRPVRNKSI--KVH 65
           G  R DGR    +R +  R GV  ++ GSA   +G T+ L  A  G    R+  +  ++ 
Sbjct: 318 GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGT--ARDAQVLDELM 375
Query: 66  G--SVLINFQYSMAVFSTGERKTRPRGDRKTSEISL-QLRQAVSAAIMSEV--HPRSQID 120
           G  +    F Y+   +S GE  T   G  K  EI   +L +    A+M ++   P + + 
Sbjct: 376 GERTDTFLFHYNFPPYSVGE--TGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYT-VR 432
Query: 121 IFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA--GDTPLV--DISHLEE 176
           +  E+ +++G +  A V  A+LAL+DAG+P++  V   +  L   GD  +V  DI   E+
Sbjct: 433 VVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDILGDED 492
Query: 177 TLGGPNLTVA 186
            LG  +  VA
Sbjct: 493 HLGDMDFKVA 502

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 52/186 (27%), Positives = 83/186 (44%), Gaps = 11/186 (5%)
Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTK-VLAAVYGPRPVRNKSIKVHGSV 68
           GLR DGR    +R I   +G+  ++ GSA   +G T+ ++ A  G          + G+ 
Sbjct: 329 GLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTY 388
Query: 69  LINF--QYSMAVFSTGE--RKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVE 124
             +F   Y+   +S GE  R   P G R+     L  R         E  P + I +  E
Sbjct: 389 KESFLLHYNFPPYSVGETGRMGSP-GRREIGHGKLAWRALRPMLPTKEDFPYT-IRLVSE 446
Query: 125 VLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA----GDTPLVDISHLEETLGG 180
           + +++G +  A V  ++LA++DAG+P+   V   +  L     G   L DI   E+ LG 
Sbjct: 447 ITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGD 506
Query: 181 PNLTVA 186
            +  VA
Sbjct: 507 MDFKVA 512

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 52/186 (27%), Positives = 83/186 (44%), Gaps = 11/186 (5%)
Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTK-VLAAVYGPRPVRNKSIKVHGSV 68
           GLR DGR    +R I   +G+  ++ GSA   +G T+ ++ A  G          + G+ 
Sbjct: 329 GLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTY 388
Query: 69  LINF--QYSMAVFSTGE--RKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVE 124
             +F   Y+   +S GE  R   P G R+     L  R         E  P + I +  E
Sbjct: 389 KESFLLHYNFPPYSVGETGRMGSP-GRREIGHGKLAWRALRPMLPTKEDFPYT-IRLVSE 446
Query: 125 VLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA----GDTPLVDISHLEETLGG 180
           + +++G +  A V  ++LA++DAG+P+   V   +  L     G   L DI   E+ LG 
Sbjct: 447 ITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGD 506
Query: 181 PNLTVA 186
            +  VA
Sbjct: 507 MDFKVA 512

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 52/186 (27%), Positives = 83/186 (44%), Gaps = 11/186 (5%)
Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTK-VLAAVYGPRPVRNKSIKVHGSV 68
           GLR DGR    +R I   +G+  ++ GSA   +G T+ ++ A  G          + G+ 
Sbjct: 320 GLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTY 379
Query: 69  LINF--QYSMAVFSTGE--RKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVE 124
             +F   Y+   +S GE  R   P G R+     L  R         E  P + I +  E
Sbjct: 380 KESFLLHYNFPPYSVGETGRMGSP-GRREIGHGKLAWRALRPMLPTKEDFPYT-IRLVSE 437
Query: 125 VLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA----GDTPLVDISHLEETLGG 180
           + +++G +  A V  ++LA++DAG+P+   V   +  L     G   L DI   E+ LG 
Sbjct: 438 ITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFAVLSDILGDEDHLGD 497
Query: 181 PNLTVA 186
            +  VA
Sbjct: 498 MDFKVA 503

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 57/190 (30%), Positives = 92/190 (48%), Gaps = 17/190 (8%)
Query: 9   GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVL-AAVYGPRPVRNKSI--KVH 65
           G  R DGR    +R +  R GV  ++ GSA   +G T+ L  A  G    R+  +  ++ 
Sbjct: 312 GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGT--ARDAQVLDELM 369
Query: 66  G--SVLINFQYSMAVFSTGERKTRPRGDRKTSEISL-QLRQAVSAAIMSEV--HPRSQID 120
           G  +    F Y+   +S GE  T   G  K  EI   +L +    A+M ++   P + + 
Sbjct: 370 GERTDTFLFHYNFPPYSVGE--TGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYT-VR 426
Query: 121 IFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA--GDTPLV--DISHLEE 176
           +  E+ +++G +  A V  A+LAL+DAG+P++  V   +  L   GD  +V  DI   E+
Sbjct: 427 VVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDILGDED 486
Query: 177 TLGGPNLTVA 186
            LG  +  VA
Sbjct: 487 HLGDMDFKVA 496

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 57/190 (30%), Positives = 92/190 (48%), Gaps = 17/190 (8%)
Query: 9   GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVL-AAVYGPRPVRNKSI--KVH 65
           G  R DGR    +R +  R GV  ++ GSA   +G T+ L  A  G    R+  +  ++ 
Sbjct: 312 GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGT--ARDAQVLDELM 369
Query: 66  G--SVLINFQYSMAVFSTGERKTRPRGDRKTSEISL-QLRQAVSAAIMSEV--HPRSQID 120
           G  +    F Y+   +S GE  T   G  K  EI   +L +    A+M ++   P + + 
Sbjct: 370 GERTDTFLFHYNFPPYSVGE--TGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYT-VR 426
Query: 121 IFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA--GDTPLV--DISHLEE 176
           +  E+ +++G +  A V  A+LAL+DAG+P++  V   +  L   GD  +V  DI   E+
Sbjct: 427 VVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDILGDED 486
Query: 177 TLGGPNLTVA 186
            LG  +  VA
Sbjct: 487 HLGDMDFKVA 496

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 65/237 (27%), Positives = 97/237 (40%), Gaps = 25/237 (10%)
Query: 12  RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL-- 69
           R DGR   ++R +   +    +  GSA  E+G T++L           + +     V   
Sbjct: 356 RIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRK 415
Query: 70  -INFQYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMSEVHPRSQIDIFVEV 125
                Y+   +S GE  T   G  K  EI   +L  R  V      E  P + I    E 
Sbjct: 416 RYMHNYNFPPYSVGE--TGRVGSPKRREIGHGALAERAIVPVLPTREEFPYA-IRQVSEA 472
Query: 126 LQADGGNFCACVNAATLALIDAGIPMREYVVA-----CSASLAGDT---PLVDISHLEET 177
           L ++G      V A+T++L++AG+P++  V        S  + G+T    L DI   E+ 
Sbjct: 473 LGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIAMGLISQEINGETHYVALTDILGAEDA 532
Query: 178 LGGPNLTVAALPLSGKVAVMELSQKLHLDHLP-RVLDCALKGCAD--IHAILDTAIK 231
            G  +  VA      K  V  L     LD +P  VL  ALK   D  +H ILD  ++
Sbjct: 533 FGDMDFKVAGT----KEFVTALQLDTKLDGIPASVLAAALKQARDARLH-ILDVMME 584

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 49/174 (28%), Positives = 78/174 (44%), Gaps = 18/174 (10%)
Query: 3   LLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKS 61
           +L EY    R DGR    LR + C + +F    GSA  ++G T+VL  V +       KS
Sbjct: 313 VLNEYK---RCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKS 369
Query: 62  IKV----HGSVLINF--QYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHP 115
            +V    +G    NF   Y    ++T E       +R+  E+      A++   +  V P
Sbjct: 370 DQVITAINGIKDKNFMLHYEFPPYATNEIGKVTGLNRR--ELG---HGALAEKALYPVIP 424
Query: 116 RS---QIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDT 166
           R     I +  EVL+++G +  A     +LAL+D+G+P+   V   +  L   T
Sbjct: 425 RDFPFTIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKT 478

>pdb|4IFD|F Chain F, Crystal Structure Of An 11-subunit Eukaryotic Exosome Complex Bound To Rna Length = 250

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 81/189 (42%), Gaps = 40/189 (21%)
Query: 17  RGHEL-RKIRCRLGVFSQSDGSAYIEQGN----TKVLAAVYGPRPVRNKSIKVHGSVLIN 71
           +G+E  +++    G     +GSA +E  +    T +++AVYGPR +R  S    G++ I 
Sbjct: 38  KGNESEQELSLHTGFIENCNGSALVEARSLGHQTSLISAVYGPRSIRG-SFTSQGTISIQ 96
Query: 72  FQYS-MAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVL---- 126
            +   +  ++T E K          E+S  L    ++ +    +P+S IDIFV +     
Sbjct: 97  LKNGLLEKYNTNELK----------EVSSFLMGIFNSVVNLSRYPKSGIDIFVYLTYDKD 146
Query: 127 -----QADGGN-----------FCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVD 170
                Q D                 C+ + TLAL DAGI   E V    A  A  T +  
Sbjct: 147 LTNNPQDDDSQSKMTSSQISSLIPHCITSITLALADAGI---ELVDMAGAGEANGTVVSF 203
Query: 171 ISHLEETLG 179
           I + EE +G
Sbjct: 204 IKNGEEIVG 212

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	263
2nn6_B	249	Exosome complex exonuclease RRP41; RNA, exosome, P	1e-104
2po1_A	249	Probable exosome complex exonuclease 1; RNAse PH,	3e-94
2wnr_B	240	Probable exosome complex exonuclease 1; phosphate	4e-92
2wp8_B	246	Exosome complex component SKI6; nucleus, hydrolase	8e-91
2je6_B	250	RRP41, exosome complex exonuclease 1; nuclease, hy	3e-89
3m7n_D	258	Probable exosome complex exonuclease 1; exosome, R	3e-88
2nn6_F	272	MTR3, exosome component 6; RNA, exosome, PM/SCL, p	6e-82
2nn6_D	237	Exosome complex exonuclease RRP46; RNA, exosome, P	4e-80
3dd6_A	255	Ribonuclease PH; exoribonuclease, tRNA maturation,	5e-70
3krn_A	222	Protein C14A4.5, confirmed by transcript evidence;	9e-70
1r6l_A	239	Ribonuclease PH; beta-alpha-beta-alpha fold, hexam	3e-68
3hkm_A	246	OS03G0854200 protein; RNAse PH domain, phosphoryla	2e-67
1udn_A	255	Ribonuclease PH, RNAse PH; transferase, riken stru	3e-67
3b4t_A	262	Ribonuclease PH; RNAse, tRNA nucleotidyltransferas	6e-63
1oys_A	245	Ribonuclease PH; transferase, tRNA processing; 2.4	4e-42
2po1_B	277	Probable exosome complex exonuclease 2; RNAse PH,	3e-39
2wnr_A	271	Probable exosome complex exonuclease 2; phosphate	2e-37
3m7n_G	259	Probable exosome complex exonuclease 2; exosome, R	5e-34
2nn6_C	278	Exosome complex exonuclease RRP43; RNA, exosome, P	5e-33
2je6_A	277	RRP42, exosome complex exonuclease 2; nuclease, hy	4e-32
2nn6_E	305	Exosome complex exonuclease RRP42; RNA, exosome, P	3e-30
2nn6_A	358	Polymyositis/scleroderma autoantigen 1; RNA, exoso	7e-25
2wp8_A	305	Exosome complex component RRP45; nucleus, hydrolas	1e-22
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	1e-05
3gme_A	549	Polyribonucleotide nucleotidyltransferase; protein	2e-04
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	4e-04
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	6e-04
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	9e-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 =  301 bits (772), Expect = e-104
 Identities = 136/243 (55%), Positives = 180/243 (74%), Gaps = 3/243 (1%)

Query: 1   MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRN- 59
           ++LL++   G R DGRR  ELRKI+ R+GVF+Q+DGSAYIEQGNTK LA VYGP  +R  
Sbjct: 8   LELLSD--QGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGS 65

Query: 60  KSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQI 119
           ++  +    L+N QYS A FSTGERK RP GDRK+ E+ LQLRQ   AAI++++HPRSQI
Sbjct: 66  RARALPDRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQI 125

Query: 120 DIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLG 179
           DI+V+VLQADGG + ACVNAATLA++DAGIPMR++V ACSA     T L D+SH+EE  G
Sbjct: 126 DIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAAG 185

Query: 180 GPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAG 239
           GP L +A LP SG++A++E+  +LH DHL RVL+ A +   D+H +LD  ++QH+ + + 
Sbjct: 186 GPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVREASI 245

Query: 240 ARG 242
             G
Sbjct: 246 LLG 248

>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 =  276 bits (708), Expect = 3e-94
 Identities = 89/230 (38%), Positives = 141/230 (61%), Gaps = 1/230 (0%)

Query: 9   GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSV 68
            G R DGR+ +ELR I+  +GV   ++GSAYIE G  K++AAVYGPR +  K ++     
Sbjct: 14  NGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRA 73

Query: 69  LINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQA 128
           ++  +Y+MA FS  ERK +P  DR++ EIS  ++ A+  A++ E+ PR+ ID+F+EVLQA
Sbjct: 74  ILRVRYNMAPFSVEERK-KPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQA 132

Query: 129 DGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAAL 188
           D G   A + AA+LAL DAGIPMR+ V AC+A       ++D++  E+  G  ++ VA +
Sbjct: 133 DAGTRVAGITAASLALADAGIPMRDLVAACAAGKIEGEIVLDLNKEEDNYGEADVPVAIM 192

Query: 189 PLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVA 238
           PL   + ++++   L  D     +  A+KG   ++     A+K+  +K+A
Sbjct: 193 PLKNDITLLQMDGYLTKDEFIEAVKLAIKGAKAVYQKQREALKEKYLKIA 242

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

 Score =  270 bits (693), Expect = 4e-92
 Identities = 91/225 (40%), Positives = 141/225 (62%), Gaps = 1/225 (0%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
            +R DGR   ELR ++   G+  ++DGS+Y+E G  K+L AVYGPR  + + ++     +
Sbjct: 15  SVREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAV 74

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           I  +Y+MA FS  ERK RP  DR++ EIS    +A+  A++ E  PRS ID+F+EVL+A+
Sbjct: 75  IRCRYNMAPFSVEERK-RPGPDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAE 133

Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP 189
           GG  CA + AA++AL DAGIPMR+ VVAC+A   GD  ++D+S  E+  G  ++ VA LP
Sbjct: 134 GGTRCAGITAASVALADAGIPMRDMVVACAAGKVGDQVVLDLSEEEDKEGQADVPVAILP 193

Query: 190 LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
            + ++ +++    L  +   R LD A++GC  IH +   A+++  
Sbjct: 194 RTREITLLQSDGNLTPEEFERALDLAVEGCLRIHEVQKEALRKRY 238

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

 Score =  267 bits (685), Expect = 8e-91
 Identities = 80/239 (33%), Positives = 129/239 (53%), Gaps = 5/239 (2%)

Query: 1   MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQS-DGSAYIEQGNTKVLAAVYGPRPVRN 59
           +++ +    GLR DGRR +ELR+    +     + DGS+Y+EQGN K++  V GP+  R 
Sbjct: 4   LEIYSP--EGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRL 61

Query: 60  KSIKVHGSVLINFQYSMAVFSTGERK-TRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQ 118
           KS       L+N   ++  FS  ER  +  + +R+  EI   L +     +M  ++PR+ 
Sbjct: 62  KSQMDTSKALLNVSVNINKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTV 121

Query: 119 IDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETL 178
           IDI + VL+ DGG   + +N  TLALIDAGI M +Y+   S  L   TPL+D + LEE  
Sbjct: 122 IDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEEN- 180

Query: 179 GGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKV 237
               +T+  +  S K++++ +  K+ LD L  VL   + G   +  ++D  +++H  K 
Sbjct: 181 AMSTVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQKR 239

>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 =  264 bits (676), Expect = 3e-89
 Identities = 82/230 (35%), Positives = 132/230 (57%), Gaps = 1/230 (0%)

Query: 9   GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSV 68
            G R DGR+  ELR I+  LGV   +DGSA  E GNTK +AAVYGP+ +  + + +    
Sbjct: 18  DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRA 77

Query: 69  LINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQA 128
           ++  +Y M  FST ERK  P   R+  E+S  +R+A+ +A++ E+ PR+ ID+F E+LQA
Sbjct: 78  VLRVRYHMTPFSTDERK-NPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQA 136

Query: 129 DGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAAL 188
           D G+    + AA+LAL DAGIPMR+ +   +   A    ++D++  E   G  ++ +A +
Sbjct: 137 DAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGVIILDLNETEAMWGEADMPIAMM 196

Query: 189 PLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVA 238
           P   +V + +L+  +  D   +  D A+KG   I+ +   A+K   ++  
Sbjct: 197 PSLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREALKSKYVEFK 246

>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 =  261 bits (670), Expect = 3e-88
 Identities = 90/228 (39%), Positives = 139/228 (60%), Gaps = 4/228 (1%)

Query: 9   GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSV 68
            GLR DGR+  ELR I+    V  ++DGS Y+E G  KV+AAV+GPR V  + ++     
Sbjct: 14  DGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKA 73

Query: 69  LINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQA 128
           +I ++Y+MA FS  ERK RP  DR++ EIS   ++A  A IM E+ PRS IDIFVEVLQA
Sbjct: 74  IIRYRYNMAPFSVEERK-RPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQA 132

Query: 129 DGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAAL 188
           D G+  AC+NAA++AL+DAG+PM+  + + +   A    ++D    E+  G  ++  A L
Sbjct: 133 DAGSRTACLNAASVALVDAGVPMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFL 192

Query: 189 PLSGK---VAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQH 233
             +GK   +A++++  ++  D + + ++ A KG   I+ +   AI + 
Sbjct: 193 IRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAILRR 240

>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 =  246 bits (629), Expect = 6e-82
 Identities = 72/247 (29%), Positives = 114/247 (46%), Gaps = 16/247 (6%)

Query: 9   GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNK-------- 60
                  R    LR +  R G+ SQ+ GSAY+E G TKVL AV GPR             
Sbjct: 24  EEEAPGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAG 83

Query: 61  ---SIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRS 117
                       +   +  A F+   R+  P G  +  E++L L++A+  A+    +PR+
Sbjct: 84  AGGEAPAALRGRLLCDFRRAPFAGRRRR-APPGGCEERELALALQEALEPAVRLGRYPRA 142

Query: 118 QIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA---GDTPLVDISHL 174
           Q+++   +L+  G    A + AA LAL DAG+ M + VV C  SLA     T L+D + L
Sbjct: 143 QLEVSALLLEDGGSALAAALTAAALALADAGVEMYDLVVGCGLSLAPGPAPTWLLDPTRL 202

Query: 175 EETLGGPNLTVAALPLSGKVAVMELSQKL-HLDHLPRVLDCALKGCADIHAILDTAIKQH 233
           EE      LTVA +P+  +VA +  S +    +     +   L+GC  ++ +L  ++ + 
Sbjct: 203 EEERAAAGLTVALMPVLNQVAGLLGSGEGGLTESWAEAVRLGLEGCQRLYPVLQQSLVRA 262

Query: 234 LIKVAGA 240
             +   A
Sbjct: 263 ARRRGAA 269

>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 =  240 bits (614), Expect = 4e-80
 Identities = 57/230 (24%), Positives = 92/230 (40%), Gaps = 12/230 (5%)

Query: 9   GGLRNDGR-RGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGS 67
            G  +  R  G  LR   C   + S+ DGSA   QG+T VLA VYGP  V+         
Sbjct: 17  NGTGSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVS------- 69

Query: 68  VLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQ 127
                 ++ A      R                +R    A ++  +HPR+ I + ++V+ 
Sbjct: 70  ---KEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVS 126

Query: 128 ADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGD-TPLVDISHLEETLGGPNLTVA 186
             G     C+NAA +AL+DAG+PMR      + +L  D T ++D +  +E      LT A
Sbjct: 127 DAGSLLACCLNAACMALVDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFA 186

Query: 187 ALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIK 236
              +  K+ +           L + L  A      +      ++++   K
Sbjct: 187 LDSVERKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYRESLQRRYSK 236

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

 Score =  215 bits (549), Expect = 5e-70
 Identities = 57/256 (22%), Positives = 109/256 (42%), Gaps = 21/256 (8%)

Query: 1   MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNK 60
           M     +   +R DGR   ELR I          +GS  IE G+TKV+ +      V   
Sbjct: 1   MGSSHHHHHHMRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVP-P 59

Query: 61  SIKVHGSVLINFQYSMAVFSTGERKTRPRG----DRKTSEISLQLRQAVSAAIMSEVHPR 116
            ++  G   +  +Y+M   +T +R  R         +T EI   + +A+ A +  E    
Sbjct: 60  FMRGEGKGWVTAEYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGE 119

Query: 117 SQIDIFVEVLQADGGNFCACVNAATLALID-----------AGIPMREYVVACSASLAGD 165
             + I  +V+QADGG   A +  A +A++            + IP+++Y+ A S  +  +
Sbjct: 120 RTVWIDCDVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEE 179

Query: 166 TPLV-DISHLEETLGGPNLTVAALPLSGKVAVMELSQK---LHLDHLPRVLDCALKGCAD 221
             +V D+++ E++    ++ V  +   G+   ++ + +        L  +LD A +G   
Sbjct: 180 QGVVLDLNYAEDSKADVDMNV-IMTGKGQFVEVQGTGEEATFSRAQLNELLDAAEQGIFQ 238

Query: 222 IHAILDTAIKQHLIKV 237
           +  I   A+   +  +
Sbjct: 239 LIDIQKEALGDIVSHI 254

>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 =  213 bits (544), Expect = 9e-70
 Identities = 49/218 (22%), Positives = 81/218 (37%), Gaps = 15/218 (6%)

Query: 20  ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVF 79
            LR++RC L     +DGSA   QG T + A+  GP  V         ++ ++  Y     
Sbjct: 4   RLREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASK-ASDEAMTLDISYRAN-- 60

Query: 80  STGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNA 139
                     GD K + ++  +   +S AI  E+ P + I + V  +Q DG      +N 
Sbjct: 61  ---------CGDNKFNVLNNIIHSTLSNAINLELFPHTTISVTVHGIQDDGSMGAVAING 111

Query: 140 ATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSG---KVAV 196
           A  AL+D G+P              D  ++D +  +E      +  +    S    +V  
Sbjct: 112 ACFALLDNGMPFETVFCGVLIVRVKDELIIDPTAKQEAASTGRVLFSVCKGSDGHPEVCA 171

Query: 197 MELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL 234
           M+         L      A    + I     T +K+ L
Sbjct: 172 MDAIGHWDFIQLEAAWSLAQPSASAIFDFYKTVMKRKL 209

>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 =  209 bits (535), Expect = 3e-68
 Identities = 65/238 (27%), Positives = 106/238 (44%), Gaps = 18/238 (7%)

Query: 12  RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLIN 71
           R  GR   +LR IR        ++GS  +E G+TKV+  V     V  + +K  G   + 
Sbjct: 3   RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVP-RFLKGQGQGWLT 61

Query: 72  FQYSMAVFSTGERKTRPRGDRK----TSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQ 127
            +Y M   STGER  R     K    T EI   + +++ AA+       + + I  +V+Q
Sbjct: 62  AEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQ 121

Query: 128 ADGGNFCACVNAATLALIDA-----------GIPMREYVVACSASLAGDTPLVDISHLEE 176
           ADGG   A +  AT+ALIDA           G P+++ V A S  +    P++D+ +LE+
Sbjct: 122 ADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIYQGVPVLDLDYLED 181

Query: 177 TLGGPNLTVAALPLSGKVAV--MELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQ 232
           +    +L V      G + V             L  +L+ A +G  ++  +   A+ +
Sbjct: 182 SAAETDLNVVMTDAGGFIEVQGTAEGAPFRPAELNAMLELAQQGMQELFELQRAALAE 239

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

 Score =  208 bits (531), Expect = 2e-67
 Identities = 49/244 (20%), Positives = 91/244 (37%), Gaps = 27/244 (11%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
             R DGR  ++LR   C      ++ GSA   QG+T VLAAVYGP+P   +  +      
Sbjct: 3   ESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGT-RKGENPEKAS 61

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           I   +       G+++          E  + L++ + +  +  VHP +   + ++V+  D
Sbjct: 62  IEVVWKPMTGQIGKQEK---------EYEMTLKRTLQSICLLTVHPNTTTSVILQVVGND 112

Query: 130 GGNFCACVNAATLALIDAGIPMREYVVACSASLAGD-TPLVDISHLEETLGGPNLTVAAL 188
           G      +NA   AL+ AGIP++   VA    +  D   ++D +  EE        +   
Sbjct: 113 GSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLEDGEVILDTNKAEEQQLKSFAHLVFP 172

Query: 189 P----------------LSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQ 232
                                +        +  +     ++  L   + I   + T +++
Sbjct: 173 NSRKSASSKEPNQKEEDSERGLITSITHGVMSEEDYFSCIERGLAASSRISDFMRTTLQK 232

Query: 233 HLIK 236
               
Sbjct: 233 QAPG 236

>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 =  208 bits (530), Expect = 3e-67
 Identities = 60/239 (25%), Positives = 105/239 (43%), Gaps = 20/239 (8%)

Query: 11  LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLI 70
           +R+DGR+  +LR +  +       +GS  I  G TKV+        V    +K  G   I
Sbjct: 1   MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVP-NWLKGKGQGWI 59

Query: 71  NFQYSMAVFSTGERKTRP----RGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVL 126
             +YSM   +T +R  R     R   +T EI   + +A+  A+         I +  +V+
Sbjct: 60  TAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVI 119

Query: 127 QADGGNFCACVNAATLALIDAGI-----------PMREYVVACSASLAGDTPLVDISHLE 175
           QADGG   A +  A +A+ DA I           P++++V A S  +  D  L+D++  E
Sbjct: 120 QADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDRILLDLNFEE 179

Query: 176 ETLGGPNLTVAALPLSGKVAVMELSQK---LHLDHLPRVLDCALKGCADIHAILDTAIK 231
           ++    ++ V     SG+++ +    +      D L ++LD A KG  ++  +      
Sbjct: 180 DSAAQVDMNVVGTG-SGRLSEVHTMGEEYSFTKDELIKMLDLAQKGINELIELQKKLYV 237

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

 Score =  197 bits (502), Expect = 6e-63
 Identities = 64/240 (26%), Positives = 98/240 (40%), Gaps = 21/240 (8%)

Query: 12  RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLIN 71
           R DGR  HELR +    G      GS  IE G+TKVL        V  +  K  G   + 
Sbjct: 7   REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVP-RWRKATGLGWLT 65

Query: 72  FQYSMAVFSTGERKTR----PRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQ 127
            +Y+M   +T  R  R     R   +T EIS  + +++ A I       + I I  +VLQ
Sbjct: 66  AEYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQ 125

Query: 128 ADGGNFCACVNAATLALIDAGI------------PMREYVVACSASLAGDTPLVDISHLE 175
           ADGG   A +  A +AL DA              P+   + A S  +      VD+ + E
Sbjct: 126 ADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVVDGRIRVDLPYEE 185

Query: 176 ETLGGPNLTVAALPLSGKVAVMELS---QKLHLDHLPRVLDCALKGCADIHAILDTAIKQ 232
           ++    ++ V     +G +  ++ +          L ++LD AL  C  + A    A+  
Sbjct: 186 DSRAEVDMNV-VATDTGTLVEIQGTGEGATFARSTLDKLLDMALGACDTLFAAQRDALAL 244

>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 =  143 bits (362), Expect = 4e-42
 Identities = 60/251 (23%), Positives = 103/251 (41%), Gaps = 31/251 (12%)

Query: 11  LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLI 70
           +R+DGR+  ELR I   L   S  +GS  I  GNTKV+        V    ++  G   I
Sbjct: 1   MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVP-PFLRGGGKGWI 59

Query: 71  NFQYSMAVFSTGERKTRPRG----DRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVL 126
             +YSM   +T ++  +         +T EI   + +A+ A +  E      I I  +V+
Sbjct: 60  TAEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVI 119

Query: 127 QADGGNFCACVNAATLALIDA-----------GIPMREYVVACSASLAGDTP-LVDISHL 174
           QADGG   A +  A LA+  A             P+ +++ A S  +  +   L+D+++ 
Sbjct: 120 QADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYE 179

Query: 175 EETLGGPNLTVA--------ALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAIL 226
           E++    ++ V          L  +G+ A            L  +L  A KG  ++    
Sbjct: 180 EDSSAEVDMNVIMTGSGRFVELQGTGEEATFSRED------LNGLLGLAEKGIQELIDKQ 233

Query: 227 DTAIKQHLIKV 237
              +   L ++
Sbjct: 234 KEVLGDSLPEL 244

>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 =  136 bits (345), Expect = 3e-39
 Identities = 51/258 (19%), Positives = 101/258 (39%), Gaps = 41/258 (15%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           G R D R   + R I   +GV  +++GSA ++ G+T+VL  +              G + 
Sbjct: 25  GKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLGEPFPDTPNMGVMT 84

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAV--SAAI------MSEVHPRSQIDI 121
            N    +   ++   +  P  +R   E++  + + +  S A+      +        + I
Sbjct: 85  TN--VELVPLASPTFEPGPPDER-AIELARVIDRGIRESKALNLEKMVIVPGKIVRVVFI 141

Query: 122 FVEVLQADGGNFCACVNAATLALIDAGIP---------------------MREYVVACSA 160
            V VL  DG    A   AA  AL++A +P                     + +  V  + 
Sbjct: 142 DVHVLDHDGNLMDAIGIAAIAALLNARVPKVRYNEETGEVETLDETEPLPVEKIPVPVTF 201

Query: 161 SLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK-----LHLDHLPRVLDCA 215
           +  G+  +VD S  EE +    +T+     +G ++ +   QK       L+ +   ++ A
Sbjct: 202 AKIGNILVVDPSLDEELVMDGKITITTDE-TGHISAV---QKSEGGAFKLEEVMYAVETA 257

Query: 216 LKGCADIHAILDTAIKQH 233
            K   +I  ++  A+++ 
Sbjct: 258 FKKAEEIRKLILEAVEKA 275

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

 Score =  132 bits (333), Expect = 2e-37
 Identities = 52/260 (20%), Positives = 99/260 (38%), Gaps = 50/260 (19%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYG----PRPVR-NKSIKV 64
             R DGR  HE R I    GV S+++GS+ ++ GNT+++  V      P P      +  
Sbjct: 23  KERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKPQIGEPFPDTPEMGV-- 80

Query: 65  HGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIM--------SEVHPR 116
                I     +   ++   +  P  +R + E+S  + + +  + M         E    
Sbjct: 81  -----ILTNSELLPMASPTFEPGPPDER-SVELSRVVDRCIRESRMIDLEKLCIIEGSKV 134

Query: 117 SQIDIFVEVLQADGGNFCACVNAATLALIDAGIP--------------------MREYVV 156
             + + + ++  DG  F A V A   AL+D  IP                    +    +
Sbjct: 135 WMLFLDLHIIDYDGNLFDAAVLATVAALLDTRIPAAEVEDGEVVINREKMQPLPVNRKAL 194

Query: 157 ACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK-----LHLDHLPRV 211
            C+ +  G+  ++D S  EE +    +++      G +  M   QK     L  D + + 
Sbjct: 195 MCTFAKIGNEIVLDPSLEEEDILTARISIGVTE-EGSICAM---QKGGEGPLTRDDVLKA 250

Query: 212 LDCALKGCADIHAILDTAIK 231
           +  A++    +   LD ++ 
Sbjct: 251 VSIAVEKVPQLIEYLDKSMT 270

>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 =  122 bits (309), Expect = 5e-34
 Identities = 49/249 (19%), Positives = 93/249 (37%), Gaps = 43/249 (17%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV----YGPRPVR-NKSIKV 64
             R DGR   E RK+     V  +++GSA ++ G+T+V+  V      P P   ++ +  
Sbjct: 21  NERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYPDTPDRGV-- 78

Query: 65  HGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAV--SAAIMSEV------HPR 116
                I     +   ++   +  P  +  + E++  + + +  S A+             
Sbjct: 79  -----IIVNAELVPLASPTFEPGPPDEN-SIELARVVDRGIRESEAVDLSKLVIEEGEKV 132

Query: 117 SQIDIFVEVLQADGGNFCACVNAATLALIDAGIP-------------MREYVVACSASLA 163
             + + +  L  DG    A   AA  AL++  +P             +R+  V+ ++ + 
Sbjct: 133 WIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGEDYLLPVRDLPVSVTSLIV 192

Query: 164 GDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK-----LHLDHLPRVLDCALKG 218
           G+  LVD S  E ++G   LT+        V  M   QK     L       +LD ++  
Sbjct: 193 GNKYLVDPSREEMSVGDTTLTITTDK-DDNVVAM---QKSGGYLLDEKLFDELLDVSINC 248

Query: 219 CADIHAILD 227
              +     
Sbjct: 249 ARKLREKFK 257

>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 =  120 bits (302), Expect = 5e-33
 Identities = 53/260 (20%), Positives = 88/260 (33%), Gaps = 37/260 (14%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
             R DGR   E R     +G  S +DGSA ++ GNT V+  V       +      G   
Sbjct: 23  NCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKG--Y 80

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIM--------SEVHPRSQIDI 121
           +     +    +   ++ P G+      S  +   +  + +        S       +  
Sbjct: 81  VVPNVDLPPLCSSRFRSGPPGEE-AQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYC 139

Query: 122 FVEVLQADGGNFCACVNAATLALIDAGIP----------------------MREYVVACS 159
            +  L  DG    AC  A   AL +  +P                      +R + VA S
Sbjct: 140 DLICLDYDGNILDACTFALLAALKNVQLPEVTINEETALAEVNLKKKSYLNIRTHPVATS 199

Query: 160 ASLAGDTP-LVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK--LHLDHLPRVLDCAL 216
            ++  DT  +VD +  EE L    LT+      GK+  +       L    L   +  A+
Sbjct: 200 FAVFDDTLLIVDPTGEEEHLATGTLTIVMDE-EGKLCCLHKPGGSGLTGAKLQDCMSRAV 258

Query: 217 KGCADIHAILDTAIKQHLIK 236
               ++  ++D  IK    K
Sbjct: 259 TRHKEVKKLMDEVIKSMKPK 278

>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 =  118 bits (297), Expect = 4e-32
 Identities = 45/258 (17%), Positives = 94/258 (36%), Gaps = 47/258 (18%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV---YGPRPVRNKSIKVHG 66
           G+R DGR+  + R +   L    ++DGSA ++ G T VLA              +    G
Sbjct: 28  GIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPN---QG 84

Query: 67  SVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAV--SAAI----MSEVHPRSQID 120
           ++++N    +   +    +  P  +    E++  + +++  S A+    +     +S   
Sbjct: 85  NLIVN--VELLPLAYETFEPGPPDEN-AIELARVVDRSLRDSKALDLTKLVIEPGKSVWT 141

Query: 121 IFVE--VLQADGGNFCACVNAATLALIDAGIP---------------------MREYVVA 157
           ++++  VL   G    AC  A+  AL +  +                      +   VV 
Sbjct: 142 VWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISVNKNEVVGKLPLNYPVVT 201

Query: 158 CSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK-----LHLDHLPRVL 212
            S +      +VD    EE++    ++ +  P   K+  +   QK     + L  + +  
Sbjct: 202 ISVAKVDKYLVVDPDLDEESIMDAKISFSYTP-DLKIVGI---QKSGKGSMSLQDIDQAE 257

Query: 213 DCALKGCADIHAILDTAI 230
           + A      +   L   +
Sbjct: 258 NTARSTAVKLLEELKKHL 275

>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 =  113 bits (284), Expect = 3e-30
 Identities = 48/261 (18%), Positives = 83/261 (31%), Gaps = 41/261 (15%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
            LR DGR   + R +     V S + GSA ++ G+T +L  V              G + 
Sbjct: 35  DLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLE 94

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIM--------SEVHPRSQIDI 121
                S +     E +    GD   +EI+  L +  +            S       + +
Sbjct: 95  FFVDCSASATPEFEGR---GGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYV 151

Query: 122 FVEVLQADGGNFCACVNAATLALIDAGIP---------------------------MREY 154
            V +L+  G  F A   A   AL +  IP                           +   
Sbjct: 152 DVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLEDEEGSKDIELSDDPYDCIRLSVENV 211

Query: 155 VVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELS--QKLHLDHLPRVL 212
               +    G   +VD +  EE     +L V+     G V  M       L  + +  ++
Sbjct: 212 PCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTS-KGVVTCMRKVGKGSLDPESIFEMM 270

Query: 213 DCALKGCADIHAILDTAIKQH 233
           +   +    +HA L + + + 
Sbjct: 271 ETGKRVGKVLHASLQSVVHKE 291

>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 =  100 bits (250), Expect = 7e-25
 Identities = 59/292 (20%), Positives = 97/292 (33%), Gaps = 52/292 (17%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYG----PRPVRNKSIKVH 65
             R DGR+ ++ R IR   G      G   +E G T+VL  V      P+  R       
Sbjct: 38  KKRLDGRQTYDYRNIRISFGT---DYGCCIVELGKTRVLGQVSCELVSPKLNRAT----E 90

Query: 66  GSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAV--SAAIMSEV------HPRS 117
           G +  N + S       E     R      +++  + + +  S  I +E           
Sbjct: 91  GILFFNLELSQMAAPAFEPG---RQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVW 147

Query: 118 QIDIFVEVLQADGGNFCACVNAATLALIDAGIP-----------------------MREY 154
           QI + + +L  DG    A   AA +AL     P                       +   
Sbjct: 148 QIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDPVPLSIHHM 207

Query: 155 VVACSASL--AGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELS--QKLHLDHLPR 210
            +  S +    G   LVD +  EE +    L +A      ++  ++ S    L  D + R
Sbjct: 208 PICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNK-HREICTIQSSGGIMLLKDQVLR 266

Query: 211 VLDCALKGCADIHAILDTAIKQHLI--KVAGARGLGRKFQLGQLTGKKKEEE 260
               A    A+I  ++  A++      K  G  G        ++T  K E+ 
Sbjct: 267 CSKIAGVKVAEITELILKALENDQKVRKEGGKFGFAESIANQRITAFKMEKA 318

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

 Score = 93.6 bits (232), Expect = 1e-22
 Identities = 40/274 (14%), Positives = 76/274 (27%), Gaps = 53/274 (19%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
             R DGR   + R +      F +  G   ++ GNTKV   +        +     G  +
Sbjct: 22  NYRLDGRSFDQFRDVEI---TFGKEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFV 78

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRS--------QIDI 121
           I+ + S    +  + +            S  + ++V  +   +V             +  
Sbjct: 79  ISTEISP--MAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRA 136

Query: 122 FVEVLQADGGNFCACVNAATLALIDAGIP-----------------------MREYVVAC 158
            V  L  DGG   A   A    L+    P                       +    +  
Sbjct: 137 DVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQIIVHPVNEREPVPLGILHIPICV 196

Query: 159 S--------------ASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK-- 202
           +                   +  ++D +  EE L    LTV     + +V  +  +    
Sbjct: 197 TFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTLNK-NREVVQVSKAGGLP 255

Query: 203 LHLDHLPRVLDCALKGCADIHAILDTAIKQHLIK 236
           +    L +    A      I   +   +K+   K
Sbjct: 256 MDALTLMKCCHEAYSIIEKITDQILQLLKEDSEK 289

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

 Score = 44.8 bits (107), Expect = 1e-05
 Identities = 44/162 (27%), Positives = 72/162 (44%), Gaps = 17/162 (10%)

Query: 9   GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKSIK---- 63
              R DGR    LR + C + +F    GSA  ++G T+VL  V +       KS +    
Sbjct: 316 EYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITA 375

Query: 64  VHGSVLINF--QYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMSEVHPRSQ 118
           ++G    NF   Y    ++T E            E+   +L  + A+   I  +  P + 
Sbjct: 376 INGIKDKNFMLHYEFPPYATNE--IGKVTGLNRRELGHGALAEK-ALYPVIPRDF-PFT- 430

Query: 119 IDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYV--VAC 158
           I +  EVL+++G +  A     +LAL+D+G+P+   V  VA 
Sbjct: 431 IRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAI 472

>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 = 41.3 bits (98), Expect = 2e-04
 Identities = 58/195 (29%), Positives = 82/195 (42%), Gaps = 27/195 (13%)

Query: 9   GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKSIKVHGS 67
           G  R DGR    +R +  R GV  ++ GSA   +G T+ L     G         ++ G 
Sbjct: 312 GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGE 371

Query: 68  VLINF--QYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMSEVHPRSQIDIF 122
               F   Y+   +S GE  T   G  K  EI    L  R  V A +          D F
Sbjct: 372 RTDTFLFHYNFPPYSVGE--TGMVGSPKRREIGHGRLAKR-GVLAVMPDM-------DKF 421

Query: 123 ------V-EVLQADGGNFCACVNAATLALIDAGIPMREYV--VACSASLAGD--TPLVDI 171
                 V E+ +++G +  A V  A+LAL+DAG+P++  V  +A      GD    L DI
Sbjct: 422 PYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSDI 481

Query: 172 SHLEETLGGPNLTVA 186
              E+ LG  +  VA
Sbjct: 482 LGDEDHLGDMDFKVA 496

>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 = 40.3 bits (95), Expect = 4e-04
 Identities = 46/200 (23%), Positives = 74/200 (37%), Gaps = 47/200 (23%)

Query: 9   GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPR----------PV 57
              R DGR   ++R +   +    +  GSA  E+G T++L                  PV
Sbjct: 353 EKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPV 412

Query: 58  RNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMSEVH 114
             K    +        Y+   +S GE  T   G  K  EI   +L  R A+   + +   
Sbjct: 413 TRKRYMHN--------YNFPPYSVGE--TGRVGSPKRREIGHGALAER-AIVPVLPTR-- 459

Query: 115 PRSQIDIF------V-EVLQADGGNFCACVNAATLALIDAGIPMREYV--VAC----SAS 161
                + F      V E L ++G      V A+T++L++AG+P++  V  +A        
Sbjct: 460 -----EEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIAMGLISQEI 514

Query: 162 LAGD--TPLVDISHLEETLG 179
                   L DI   E+  G
Sbjct: 515 NGETHYVALTDILGAEDAFG 534

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

 Score = 39.8 bits (94), Expect = 6e-04
 Identities = 55/196 (28%), Positives = 77/196 (39%), Gaps = 43/196 (21%)

Query: 9   GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVY-----------GPRPV 57
           G  R DGR    +R +  R GV  ++ GSA   +G T+ L                    
Sbjct: 318 GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGE 377

Query: 58  RNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMSEVH 114
           R  +   H        Y+   +S GE  T   G  K  EI    L  R  V A +     
Sbjct: 378 RTDTFLFH--------YNFPPYSVGE--TGMVGSPKRREIGHGRLAKR-GVLAVMPDM-- 424

Query: 115 PRSQIDIF------V-EVLQADGGNFCACVNAATLALIDAGIPMREYV--VACSASLAGD 165
                D F      V E+ +++G +  A V  A+LAL+DAG+P++  V  +A      GD
Sbjct: 425 -----DKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGD 479

Query: 166 --TPLVDISHLEETLG 179
               L DI   E+ LG
Sbjct: 480 NYVVLSDILGDEDHLG 495

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

 Score = 39.4 bits (93), Expect = 9e-04
 Identities = 41/160 (25%), Positives = 70/160 (43%), Gaps = 23/160 (14%)

Query: 9   GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKSIKVHGS 67
            GLR DGR    +R I   +G+  ++ GSA   +G T+ +     G          + G+
Sbjct: 328 TGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGT 387

Query: 68  VLINF--QYSMAVFSTGERKTRPRGDRKTSEI---SLQLRQAVSAAIMSEVHPRSQIDIF 122
              +F   Y+   +S GE  T   G     EI    L  R A+   + ++       + F
Sbjct: 388 YKESFLLHYNFPPYSVGE--TGRMGSPGRREIGHGKLAWR-ALRPMLPTK-------EDF 437

Query: 123 ------V-EVLQADGGNFCACVNAATLALIDAGIPMREYV 155
                 V E+ +++G +  A V  ++LA++DAG+P+   V
Sbjct: 438 PYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPV 477

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	263
2nn6_B	249	Exosome complex exonuclease RRP41; RNA, exosome, P	100.0
2wnr_B	240	Probable exosome complex exonuclease 1; phosphate	100.0
2po1_A	249	Probable exosome complex exonuclease 1; RNAse PH,	100.0
2wp8_B	246	Exosome complex component SKI6; nucleus, hydrolase	100.0
3m7n_D	258	Probable exosome complex exonuclease 1; exosome, R	100.0
2je6_B	250	RRP41, exosome complex exonuclease 1; nuclease, hy	100.0
2nn6_F	272	MTR3, exosome component 6; RNA, exosome, PM/SCL, p	100.0
3b4t_A	262	Ribonuclease PH; RNAse, tRNA nucleotidyltransferas	100.0
2nn6_D	237	Exosome complex exonuclease RRP46; RNA, exosome, P	100.0
1oys_A	245	Ribonuclease PH; transferase, tRNA processing; 2.4	100.0
3dd6_A	255	Ribonuclease PH; exoribonuclease, tRNA maturation,	100.0
1r6l_A	239	Ribonuclease PH; beta-alpha-beta-alpha fold, hexam	100.0
1udn_A	255	Ribonuclease PH, RNAse PH; transferase, riken stru	100.0
3hkm_A	246	OS03G0854200 protein; RNAse PH domain, phosphoryla	100.0
2po1_B	277	Probable exosome complex exonuclease 2; RNAse PH,	100.0
2je6_A	277	RRP42, exosome complex exonuclease 2; nuclease, hy	100.0
2wnr_A	271	Probable exosome complex exonuclease 2; phosphate	100.0
3m7n_G	259	Probable exosome complex exonuclease 2; exosome, R	100.0
2nn6_C	278	Exosome complex exonuclease RRP43; RNA, exosome, P	100.0
2nn6_A	358	Polymyositis/scleroderma autoantigen 1; RNA, exoso	100.0
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	100.0
3u1k_A	630	Polyribonucleotide nucleotidyltransferase 1, MITO;	100.0
2wp8_A	305	Exosome complex component RRP45; nucleus, hydrolas	100.0
2nn6_E	305	Exosome complex exonuclease RRP42; RNA, exosome, P	100.0
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	100.0
3gme_A	549	Polyribonucleotide nucleotidyltransferase; protein	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	99.97
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	99.97
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	99.96

>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=6.1e-55  Score=379.91  Aligned_cols=238  Identities=57%  Similarity=0.952  Sum_probs=220.5

Q ss_pred             CccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCC-CcCCCCeEEEEEEEeeCCC
Q psy18119          1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNK-SIKVHGSVLINFQYSMAVF   79 (263)
Q Consensus         1 ~e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~-~~~~~~~~~l~v~~~~~~~   79 (263)
                      ||++.+  +|+|+|||+++|+|++++++|++++++|||+|++|+|+|+|+|+||.+++.. ....++++.|.++|+++||
T Consensus         8 ~~~i~~--~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~g~~~~~~~~~~~~~~~g~l~~~~~~~p~   85 (249)
T 2nn6_B            8 LELLSD--QGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATF   85 (249)
T ss_dssp             ---CCB--TTBCSSSSCTTSCCCEEEEESCSSSSSEEEEEEESSCEEEEEEEEEEECCSSSCCCCCSSCCEEEEEEECTT
T ss_pred             hhhccc--CCcCCCCCCcCCcCCeEEEeCCCCCCCeEEEEEECCeEEEEEEEccCCccccccccCCCcEEEEEEEEcCCC
Confidence            688888  9999999999999999999999999999999999999999999998776432 2246889999999999999


Q ss_pred             CCccccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEE
Q psy18119         80 STGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACS  159 (263)
Q Consensus        80 ~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt  159 (263)
                      ++++++++++++.++.+++++|+++|+++++++.||+|.|+|+++||++|||+++|+++|+++||+|+||||+++|+++|
T Consensus        86 a~~~~~~~~~~~~~~~~~~~ll~r~l~~~i~~~~~p~~~I~i~~~VL~~dG~~~~A~i~aa~~AL~da~iPl~~~v~avs  165 (249)
T 2nn6_B           86 STGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACS  165 (249)
T ss_dssp             TSSSCCCTTTSTHHHHHHHHHHHHHHHHTTCGGGCTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTCCCCSSCCEEEE
T ss_pred             cccccccCCCCCHhHHHHHHHHHHHHHHhcCHHHCCCcEEEEEEEEEeCCCCHHHHHHHHHHHHHHhcCCcccCCeeeEE
Confidence            99887766678999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy18119        160 ASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAG  239 (263)
Q Consensus       160 ~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~~  239 (263)
                      ++++++.+++||+..||..+++.++|++++..++|+.+++.|+++.+++.++++.|.+++++++++++++|+++..++..
T Consensus       166 ~g~~~~~~l~Dp~~~Ee~~~~~~~~v~~~~~~~~i~~lq~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~~~~  245 (249)
T 2nn6_B          166 AGFVDGTALADLSHVEEAAGGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVREASI  245 (249)
T ss_dssp             EEEETTEEEESCCHHHHTSSCCCEEEEEETTTTEEEEEEECSCCBTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             EEEECCeEEECCChHHhccCCcEEEEEEECCCCCEEEEEEECCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            99999999999999999999999999997678999999999999999999999999999999999999999999887664


Q ss_pred             c
Q psy18119        240 A  240 (263)
Q Consensus       240 ~  240 (263)
                      .
T Consensus       246 ~  246 (249)
T 2nn6_B          246 L  246 (249)
T ss_dssp             -
T ss_pred             h
Confidence            4

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

Probab=100.00  E-value=1e-54  Score=376.58  Aligned_cols=232  Identities=40%  Similarity=0.683  Sum_probs=210.9

Q ss_pred             CccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCC
Q psy18119          1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFS   80 (263)
Q Consensus         1 ~e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~   80 (263)
                      ||++.+  +|+|+|||+++|+|++++++|++++++|||+|++|+|+|+|+|+||.+..+.....++++.|.++|+++|++
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   85 (240)
T 2wnr_B            8 DQLKTS--PSVREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKILVAVYGPREAQIRKLQRPDRAVIRCRYNMAPFS   85 (240)
T ss_dssp             ---------CCCTTSCCTTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECCSSSSCCSSSCEEEEEEEECTTS
T ss_pred             eEeecc--cCccCCCCCcCCccCeEEEeCCCCCCCEEEEEEECCeEEEEEEEcCCCCCcccccCCCcEEEEEEEEeCCCC
Confidence            688888  999999999999999999999999999999999999999999999877555333568899999999999999


Q ss_pred             CccccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEE
Q psy18119         81 TGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSA  160 (263)
Q Consensus        81 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~  160 (263)
                      +++++ ++.++.++++++++|+++|+++++++.||+|.|+|+++||++|||+++|+++|+++||+|+||||+++|+++|+
T Consensus        86 ~~~~~-~~~~~~~~~~l~~ll~r~l~~~i~l~~~p~~~I~i~~~VL~~dG~~~~a~i~aa~~AL~da~iP~~~~v~avs~  164 (240)
T 2wnr_B           86 VEERK-RPGPDRRSVEISKITAEALRPALILEKFPRSVIDVFIEVLEAEGGTRCAGITAASVALADAGIPMRDMVVACAA  164 (240)
T ss_dssp             SSSCC-CSSCCHHHHHHHHHHHHHHGGGBCGGGSTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTTCCBSSCCEEEEE
T ss_pred             cCCcc-CCCCChhHHHHHHHHHHHHHHhcCHHHCCCcEEEEEEEEEeCCCCHHHHHHHHHHHHHHHcCCccccceeeEEE
Confidence            98776 44688999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        161 SLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLI  235 (263)
Q Consensus       161 ~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~  235 (263)
                      +++++.+++||+..||..+++.++|++++..++|+.+++.|.++.+++.++++.|.++|+++++.++++|+++..
T Consensus       165 g~~~~~~l~Dp~~~Ee~~~~~~~~v~~~~~~~~i~~lq~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~  239 (240)
T 2wnr_B          165 GKVGDQVVLDLSEEEDKEGQADVPVAILPRTREITLLQSDGNLTPEEFERALDLAVEGCLRIHEVQKEALRKRYG  239 (240)
T ss_dssp             EESSSSEEESCCSHHHHSCSEEEEEEEETTTTEEEEEEEEECBCHHHHHHHHHHHHHHHHHHHHHHHHHHHC---
T ss_pred             EEECCEEEeCCCHHHhccCCceEEEEEECCCCCEEEEEEEcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999999999999778899999999999999999999999999999999999999988754

>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=8.2e-54  Score=372.82  Aligned_cols=236  Identities=39%  Similarity=0.659  Sum_probs=219.8

Q ss_pred             CccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCC
Q psy18119          1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFS   80 (263)
Q Consensus         1 ~e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~   80 (263)
                      ||++.+  +|+|+|||.++|+|++.+++|++++++|||+|++|+|+|+|+|+||.+..+.....++++.|.|+|+++||+
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   85 (249)
T 2po1_A            8 LKLIDE--NGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILRVRYNMAPFS   85 (249)
T ss_dssp             -CCSBC--SSCBTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEEECSSGGGCCSSSCEEEEEEEECGGG
T ss_pred             eEEecc--cCccCCCCCcccccCEEEEeCCcCCCCEEEEEEECCcEEEEEEEcCcccCcccccCCCceEEEEEEEeCCcc
Confidence            678887  999999999999999999999999999999999999999999999877655324568899999999999999


Q ss_pred             CccccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEE
Q psy18119         81 TGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSA  160 (263)
Q Consensus        81 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~  160 (263)
                      +++++. +.++.++.+++++|+++|+++++++.||+|.|+|+++||++|||+++|+++|+++||+|+||||+++|+++|+
T Consensus        86 ~~~~~~-~~~~~~~~~~s~li~r~l~~~i~l~~~p~~~i~I~~~VL~~dG~~~~aai~aa~~AL~da~iP~~~~v~avs~  164 (249)
T 2po1_A           86 VEERKK-PGPDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAA  164 (249)
T ss_dssp             SSSCCC-SSCCHHHHHHHHHHHHHHGGGBCGGGSTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTTCCBSSCCEEEEE
T ss_pred             cccccC-CCCCHHHHHHHHHHHHHHHhhccHHHCCCCEEEEEEEEEecCCCHHHHHHHHHHHHHHhcCCCccCceEEEEE
Confidence            987653 3478899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy18119        161 SLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAG  239 (263)
Q Consensus       161 ~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~~  239 (263)
                      +++++.+++||+..||..+++.++|++++..++|+++++.|.++.+++.++++.|.+++++++++++++++++..++..
T Consensus       165 g~~~~~~l~Dp~~~Ee~~~~~~l~va~~~~~~~i~~~~~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~~~~  243 (249)
T 2po1_A          165 GKIEGEIVLDLNKEEDNYGEADVPVAIMPLKNDITLLQMDGYLTKDEFIEAVKLAIKGAKAVYQKQREALKEKYLKIAQ  243 (249)
T ss_dssp             EEETTEEEESCCHHHHHTCSEEEEEEEEGGGTEEEEECCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             EEECCEEEecCcHHHhccCCceEEEEEECCCCCEEEEEEEcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            9999999999999999999999999997778999999999999999999999999999999999999999998876553

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

Probab=100.00  E-value=1e-53  Score=371.64  Aligned_cols=235  Identities=34%  Similarity=0.549  Sum_probs=207.0

Q ss_pred             CccccCCCCCccCCCCCCCCCcceEEEeCCCCCC-ceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCC
Q psy18119          1 MDLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQS-DGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVF   79 (263)
Q Consensus         1 ~e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a-~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~   79 (263)
                      ||++++  +|+|+|||.++|+|++.+++|+++++ +|||+|++|+|+|+|+|++|.++.+.....++++.|.|+|+++||
T Consensus         4 ~~~~~~--~~~R~DGR~~~e~R~i~i~~g~l~~aa~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~~g~l~v~~~~~p~   81 (246)
T 2wp8_B            4 LEIYSP--EGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNINKF   81 (246)
T ss_dssp             CCSSCT--TSCCTTSCCTTCCCCEEEEECSCTTTCSEEEEEEETTEEEEEEEEEEEC------CCSSSEEEEEEEEEC--
T ss_pred             hhhhcc--cCccCCCCCcCCccCeEEEeCCCCCCCCceEEEEECCeEEEEEEEecCCcccccccCCCcEEEEEEEEeCCc
Confidence            789998  99999999999999999999999999 999999999999999999988754422346899999999999999


Q ss_pred             CCccccCC-CCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEE
Q psy18119         80 STGERKTR-PRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVAC  158 (263)
Q Consensus        80 ~~~~~~~~-~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~av  158 (263)
                      +++++.++ +++++++.+++++|+++|+++++++.||+|.|+|+++||++|||+++|++||+++||+|+||||+++|+++
T Consensus        82 a~~~~~~r~g~~~~~~~~~s~li~r~l~~~i~~~~~p~~~I~i~~~VL~~dG~~~~aai~aa~~AL~~a~iP~~~~v~av  161 (246)
T 2wp8_B           82 SKFERSKSSHKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGI  161 (246)
T ss_dssp             ------------CHHHHHHHHHHHHHHHHHBCTTTSCSEEEEEEEEEEECCSCHHHHHHHHHHHHHHHHTCCBSSCEEEE
T ss_pred             ccccccccCCCCChhHHHHHHHHHHHHHHhhhHHHCCCeEEEEEEEEEECCCCHHHHHHHHHHHHHHHcCCcccCceeEE
Confidence            99887655 45678999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy18119        159 SASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVA  238 (263)
Q Consensus       159 t~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~  238 (263)
                      |+|++++.+++|||..|| .+++.++|++.+..++|+++++.|+++.+++.++++.|.+++++++++++++++++..+..
T Consensus       162 s~g~~~~~~l~Dp~~~Ee-~~~~~l~v~~~~~~~~i~~i~~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~~~  240 (246)
T 2wp8_B          162 SVGLYDTTPLLDTNSLEE-NAMSTVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQKRV  240 (246)
T ss_dssp             EEEEETTEEESSCCHHHH-HHSEEEEEEEETTSSCEEEEEECSCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-
T ss_pred             EEEEECCEEEECCCchhh-ccCceEEEEEeCCCCCEEEEEecCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            999999999999999999 9999999999777899999999999999999999999999999999999999999876543

>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=4e-53  Score=369.61  Aligned_cols=233  Identities=39%  Similarity=0.635  Sum_probs=216.2

Q ss_pred             ccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCC
Q psy18119          2 DLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFST   81 (263)
Q Consensus         2 e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~   81 (263)
                      ++|.   +|+|+|||.++|+|+|++++|++++++|||+|++|+|+|+|+|+||.++.+.....++++.|+++|+++||++
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~   86 (258)
T 3m7n_D           10 KLIV---DGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPEHLQDPSKAIIRYRYNMAPFSV   86 (258)
T ss_dssp             CSEE---TTEETTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEEECSSSTTCCSSSCEEEEEEEECGGGS
T ss_pred             HHHh---cCCCCCCCCcCCccCeEEEECCCCCCCceEEEEECCeEEEEEEEcccCCCCccccCCCceEEEEEEEeCCccc
Confidence            4455   7999999999999999999999999999999999999999999998876654345789999999999999998


Q ss_pred             ccccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEE
Q psy18119         82 GERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSAS  161 (263)
Q Consensus        82 ~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~  161 (263)
                      .++++ +++++++.+++++|+++|+++++++.||+|.|+|+++||++|||+++|+++|+++||+|+||||+++|+++|++
T Consensus        87 ~~r~~-~~~~~re~ei~~li~r~l~~~i~~~~~p~~~I~V~~~VL~~DG~~~~Aai~aa~lAL~dagiP~~~~v~avsvg  165 (258)
T 3m7n_D           87 EERKR-PGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVG  165 (258)
T ss_dssp             SSCCC-SSCCHHHHHHHHHHHHHHHTTBCGGGSTTEEEEEEEEEEECCTTHHHHHHHHHHHHHHHTTCCBSSEEEEEEEE
T ss_pred             ccccC-CCCCHHHHHHHHHHHHHHHhhcCHHhCCceEEEEEEEEEEcCCCHHHHHHHHHHHHHHhcCCCCCCceEEEEEE
Confidence            87654 35789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCeeEecCCchhhhcCCCeEEEEEeCCC---CcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy18119        162 LAGDTPLVDISHLEETLGGPNLTVAALPLS---GKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVA  238 (263)
Q Consensus       162 ~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~---~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~  238 (263)
                      ++++.+|+||+..||..+++.++|++++..   ++|+++++.|+++.+++.+++++|.++|++++++++++++++..+..
T Consensus       166 ~i~~~~llDpt~~Ee~~~~~d~~va~~~~~~~~~~I~~lq~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~~~  245 (258)
T 3m7n_D          166 KADGQLVLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMDGRMTRDEVKQAIELAKKGALQIYEMQREAILRRYIEVG  245 (258)
T ss_dssp             EETTEEEESCCHHHHHHSSEEEEEEEEEETTEEEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EECCEEEECCCHHHHhccCceEEEEEEcCCCCCCCEEEEEecCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            999999999999999999999999996567   89999999999999999999999999999999999999998776433

>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=5e-53  Score=368.10  Aligned_cols=232  Identities=36%  Similarity=0.625  Sum_probs=217.0

Q ss_pred             ccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCC
Q psy18119          2 DLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFST   81 (263)
Q Consensus         2 e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~   81 (263)
                      |++.+  +++|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|+||.++.+.....++++.|.|+|+++|+++
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~   90 (250)
T 2je6_B           13 KLILD--DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFST   90 (250)
T ss_dssp             CSBCT--TSCBTTSCCTTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECSSGGGSCSSSCEEEEEEEECTTSS
T ss_pred             ceecC--CCccCCCCCccCcCCeEEEeCCCCCCCeEEEEEECCcEEEEEEEcccccccccccCCCcEEEEEEEEeCCCcc
Confidence            67777  9999999999999999999999999999999999999999999998776543234688999999999999999


Q ss_pred             ccccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEE
Q psy18119         82 GERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSAS  161 (263)
Q Consensus        82 ~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~  161 (263)
                      ++++ ++++++++.+++++|+++|+++++++.||+|.|+|+++||++|||+++|+++|+++||+|+||||+++|+++|++
T Consensus        91 ~~~~-~g~~~~~e~~~s~li~r~l~~~i~~~~~p~~~i~I~~~VL~~DG~~~~aai~aa~~AL~~a~iP~~~~v~avsvg  169 (250)
T 2je6_B           91 DERK-NPAPSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVG  169 (250)
T ss_dssp             SSCC-CSSCCHHHHHHHHHHHHHHHTTBCGGGSTTEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCBSSCCEEEEEE
T ss_pred             CCcc-CCCCChhHHHHHHHHHHHHHhhcCHhhCCCcEEEEEEEEEeCCCCHHHHHHHHHHHHHHhcCCCccCceEEEEEE
Confidence            8775 556889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        162 LAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIK  236 (263)
Q Consensus       162 ~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~  236 (263)
                      ++++.+|+|||..||..+++.++|+++++.++|+++++.|.++.+++.++++.|.+++++++++++++++++..+
T Consensus       170 ~~~~~~l~Dpt~~Ee~~~~~~l~va~~~~~~~i~~v~~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~  244 (250)
T 2je6_B          170 KADGVIILDLNETEAMWGEADMPIAMMPSLNQVTLFQLNGSMTPDEFRQAFDLAVKGINIIYNLEREALKSKYVE  244 (250)
T ss_dssp             EETTEEEESCCHHHHHHSSEEEEEEEEGGGTEEEEEEEEECBCHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGC-
T ss_pred             EECCEEEeCCCHHHHhcCCceEEEEEECCCCCEEEEEEEcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            999999999999999999999999997678999999999999999999999999999999999999999887644

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

Probab=100.00  E-value=1e-50  Score=357.59  Aligned_cols=236  Identities=31%  Similarity=0.437  Sum_probs=207.2

Q ss_pred             ccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcC-----------CCCeEEE
Q psy18119          2 DLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIK-----------VHGSVLI   70 (263)
Q Consensus         2 e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~-----------~~~~~~l   70 (263)
                      +|+.+  +++|+|||.++|+|++.+++|++++++|||+|++|+|+|+|+|++|.++++..+.           .++++.+
T Consensus        19 ~~~~~--~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~g~l   96 (272)
T 2nn6_F           19 LYAAD--EEEAPGTRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAPAALRGRL   96 (272)
T ss_dssp             ------------CCCCSSCCCCCCCCCSCCSSSSEEECCCSSSCEEEEEEEEEECC-------------------CBCEE
T ss_pred             ccccc--cCccCCCCCccccCCeEEEeCCCCCCCeEEEEEeCCeEEEEEEECCCcccccccccccccccccccCCCceEE
Confidence            34555  8999999999999999999999999999999999999999999999876653110           4578999


Q ss_pred             EEEEeeCCCCCccccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCC
Q psy18119         71 NFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP  150 (263)
Q Consensus        71 ~v~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp  150 (263)
                      .|+|.+.|+++++++. +++++++++++++|+++|+++++++.||+|.|+|+++||++|||+++|+++|+++||+|+|||
T Consensus        97 ~v~~~~~p~a~~~~~~-~~~~~~e~~~s~li~r~l~~~i~~~~~p~~~I~I~~~VL~~DG~~~~aai~aa~~AL~da~iP  175 (272)
T 2nn6_F           97 LCDFRRAPFAGRRRRA-PPGGCEERELALALQEALEPAVRLGRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVE  175 (272)
T ss_dssp             EEEEEECTTSSSSCCC-SCCHHHHHHHHHHHHHHHTTTBCSTTSBTCEEEEEEEEEECCSSHHHHHHHHHHHHHHHHCCC
T ss_pred             EEEEEecCCCcCCccC-CCCCHHHHHHHHHHHHHHHHhccHHHCCceEEEEEEEEEeCCCCHHHHHHHHHHHHHHHcCCc
Confidence            9999999999987653 457889999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCceeEEEEEe---cCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCCh-hHHHHHHHHHHHHHHHHHHHH
Q psy18119        151 MREYVVACSASL---AGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHL-DHLPRVLDCALKGCADIHAIL  226 (263)
Q Consensus       151 ~~~~~~avt~~~---~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~-~~l~~~i~~A~~~~~~i~~~i  226 (263)
                      |+++++++++++   .++.+|+|||..||..+++.++|++++..++|+++++.|.++. ++|.++++.|.++++++++++
T Consensus       176 ~~~~v~avsvg~~~~~~~~~llDpt~~Ee~~~~~~l~va~~~~~~~I~~i~~~g~~~~~~~l~~~l~~A~~~~~~i~~~~  255 (272)
T 2nn6_F          176 MYDLVVGCGLSLAPGPAPTWLLDPTRLEEERAAAGLTVALMPVLNQVAGLLGSGEGGLTESWAEAVRLGLEGCQRLYPVL  255 (272)
T ss_dssp             BSSCCEEEECCCCSCSSCCCCSSCCTTTGGGCSSEEEEEEETTTTEEEEEEEECCSSCTTTTHHHHHHHHHHHHHHHHHH
T ss_pred             ccCcEEEEEEEEeeccCCeEEeCCCHHHhccCCceEEEEEeCCCCCEEEEEEecCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999   7789999999999999999999998778899999999999999 999999999999999999999


Q ss_pred             HHHHHHHHHHhhcc
Q psy18119        227 DTAIKQHLIKVAGA  240 (263)
Q Consensus       227 ~~~l~~~~~~~~~~  240 (263)
                      ++++++...++.+.
T Consensus       256 ~~~l~~~~~~~~~~  269 (272)
T 2nn6_F          256 QQSLVRAARRRGAA  269 (272)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhhccc
Confidence            99999998876654

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

Probab=100.00  E-value=6e-50  Score=350.88  Aligned_cols=239  Identities=28%  Similarity=0.309  Sum_probs=209.5

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCC-
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTR-   87 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~-   87 (263)
                      .|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|++|...+.. ...+++++|+|+|.++|++++++.+| 
T Consensus         4 ~g~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~-~~~~~~g~l~v~~~~~p~a~~~~~~Re   82 (262)
T 3b4t_A            4 VSKREDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVPRW-RKATGLGWLTAEYAMLPSATHSRSDRE   82 (262)
T ss_dssp             -CCSTTSCCTTCCCCEEEEETSSSSSSEEEEEEETTEEEEEEEEEEESCC-----CCSCCEEEEEEEECGGGSSSCCCCH
T ss_pred             CCcCCCCCCCcCcCCeEEEeCCcCCCCeEEEEEECCCEEEEEEEecCcCCCc-cCCCCceEEEEEEEeCCCccccccccc
Confidence            6899999999999999999999999999999999999999999997763321 12367888999999999999877554 


Q ss_pred             ---CCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHc------------CCCcc
Q psy18119         88 ---PRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDA------------GIPMR  152 (263)
Q Consensus        88 ---~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~da------------gIp~~  152 (263)
                         ++++.++++++++|+++|+++++++.||+|.|+|+++||++|||+++|+++|+++||+|+            +|||+
T Consensus        83 ~~~G~~~~~~~~isrli~r~lr~~i~~~~l~~~~I~i~~~VL~~DG~~~~aai~aa~~AL~~a~~~~~~~~~~~~~ip~~  162 (262)
T 3b4t_A           83 SVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAIDCDVLQADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLS  162 (262)
T ss_dssp             HHHTSCCHHHHHHHHHHHHHHHTTBCHHHHCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTCCSSSCCBC
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhcCHhHCCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhhhhhccCCccccCCccc
Confidence               357899999999999999999999999999999999999999999999999999999999            99999


Q ss_pred             CceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc---cCChhHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        153 EYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ---KLHLDHLPRVLDCALKGCADIHAILDTA  229 (263)
Q Consensus       153 ~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G---~i~~~~l~~~i~~A~~~~~~i~~~i~~~  229 (263)
                      ++|+++|++++++.+|+|||..||..+++.++|++ +..++|+++++.|   .++.++|.++++.|.+++++++++++++
T Consensus       163 ~~v~avsvg~~~g~~l~Dpt~~Ee~~~~~~l~va~-~~~g~i~~i~~~g~~~~~~~~~l~~~l~~A~~~~~~i~~~~~~~  241 (262)
T 3b4t_A          163 CAIAAVSVGVVDGRIRVDLPYEEDSRAEVDMNVVA-TDTGTLVEIQGTGEGATFARSTLDKLLDMALGACDTLFAAQRDA  241 (262)
T ss_dssp             SCEEEEEEEEETTEEEESCCHHHHTTCSEEEEEEE-ETTSCEEEEEECSSCCCBCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CceeEEEEEEECCEEEECCCHHHHhccCceEEEEE-cCCCCEEEEEeeCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999 5678999999986   6999999999999999999999999999


Q ss_pred             HHHHHHHhhccCCCCcccccc
Q psy18119        230 IKQHLIKVAGARGLGRKFQLG  250 (263)
Q Consensus       230 l~~~~~~~~~~~~~~~~~~~~  250 (263)
                      ++++..+...+.++. -++||
T Consensus       242 l~~~~~~~~~~~~~~-~~~~~  261 (262)
T 3b4t_A          242 LALPYPGVLPQGPPP-PKAFG  261 (262)
T ss_dssp             HTSCCSSCCC-----------
T ss_pred             HhcchhccCccCCCC-ccccC
Confidence            998877666655443 33444

>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=4.6e-49  Score=340.53  Aligned_cols=216  Identities=24%  Similarity=0.376  Sum_probs=186.5

Q ss_pred             CCccCCCCCCC----CCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccc
Q psy18119          9 GGLRNDGRRGH----ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGER   84 (263)
Q Consensus         9 ~~~R~DGR~~~----e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~   84 (263)
                      +++|+|||.++    |+|++++++|++++++|||+|++|+|+|+|+|+||.++++. ...++++.|+++|.  |++    
T Consensus        14 ~~~R~DGR~~~~~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~g~~~~~~~-~~~~~~g~l~~~~~--p~~----   86 (237)
T 2nn6_D           14 RAENGTGSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVS-KEIFNKATLEVILR--PKI----   86 (237)
T ss_dssp             -------------CCCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECC-------CCEEEEEEEE--CSS----
T ss_pred             cCccCCCCCCCCccccccceEEEeCCCCCCCEEEEEEECCcEEEEEEeCCCccccc-ccCCCcEEEEEEec--CCC----
Confidence            78999999999    99999999999999999999999999999999999876553 34678899988886  443    


Q ss_pred             cCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEEec-
Q psy18119         85 KTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA-  163 (263)
Q Consensus        85 ~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~~~-  163 (263)
                         ++++.++++++++|+++|+++++++.||+|.|+|+++||++|||+++|+++|+++||+|+||||+++|+++|++++ 
T Consensus        87 ---g~~~~~e~~~~~li~r~l~~~i~~~~~p~~~I~I~~~VL~~dG~~~~aai~aa~~AL~da~iP~~~~v~avs~g~~~  163 (237)
T 2nn6_D           87 ---GLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACALDS  163 (237)
T ss_dssp             ---SCCCHHHHHHHHHHHHHHHHHCGGGCSSSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCEEEEEEEECT
T ss_pred             ---CCCCccHHHHHHHHHHHHHHHhchhcCCceEEEEEEEEEECCCcHHHHHHHHHHHHHHHcCCCcccCeeeEEEEEec
Confidence               1357889999999999999999999999999999999999999999999999999999999999999999999999 


Q ss_pred             CCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        164 GDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHL  234 (263)
Q Consensus       164 ~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~  234 (263)
                      ++.+|+||+..||..+.+.++|++.+..++|+.+++.|+++.+++.++++.|.+++++++++++++++++.
T Consensus       164 ~~~~llDp~~~Ee~~~~~~~~v~~~~~~~~i~~lq~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~  234 (237)
T 2nn6_D          164 DGTLVLDPTSKQEKEARAVLTFALDSVERKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYRESLQRRY  234 (237)
T ss_dssp             TCCEEESCCHHHHHHCSEEEEEEEETTTCCCCEEEEEESCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCcEEeCCCHHHHhccCCceEEEEcCCCCCEEEEEEeCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            67999999999999999999999976556899999999999999999999999999999999999998874

>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=1.6e-49  Score=345.01  Aligned_cols=224  Identities=26%  Similarity=0.328  Sum_probs=186.2

Q ss_pred             ccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCC---
Q psy18119         11 LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTR---   87 (263)
Q Consensus        11 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~---   87 (263)
                      +|+|||.++|+|++.+++|++++++|||+|++|+|+|+|+|++|...+.. ...++++.|.++|.++|++++++.+|   
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 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPF-LRGGGKGWITAEYSMLPQATNQQTIQESS   79 (245)
T ss_dssp             CCTTSCCTTCCCCEEEECC-----CCCEEEEETTEEEEEEEEEESCCCGG-GTTSCCCEEEEEEEC--------------
T ss_pred             CCCCCCCCCCcCCeEEEeCCCCCCCEEEEEEECCeEEEEEEEeccccCCc-cCCCCceEEEEEEEeCCCcCccccccccc
Confidence            49999999999999999999999999999999999999999998764421 23578899999999999999877544   


Q ss_pred             -CCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcC-----------CCccCce
Q psy18119         88 -PRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAG-----------IPMREYV  155 (263)
Q Consensus        88 -~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dag-----------Ip~~~~~  155 (263)
                       ++++.++++++++|+++|+++++++.||++.|+|+|+||++|||+++|+++|+++||+|+|           +||+++|
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             2478899999999999999999999999999999999999999999999999999999999           9999999


Q ss_pred             eEEEEEecCCeeE-ecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc---cCChhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        156 VACSASLAGDTPL-VDISHLEETLGGPNLTVAALPLSGKVAVMELSQ---KLHLDHLPRVLDCALKGCADIHAILDTAIK  231 (263)
Q Consensus       156 ~avt~~~~~~~~l-vDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G---~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~  231 (263)
                      +++|++++++.++ +|||..||..+++.++|++ +..++|+.+++.|   +++.+++.+++++|.+++++++++++++++
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            9999999998777 9999999999999999999 6789999999985   699999999999999999999999999998


Q ss_pred             HHHHH
Q psy18119        232 QHLIK  236 (263)
Q Consensus       232 ~~~~~  236 (263)
                      ++..+
T Consensus       239 ~~~~~  243 (245)
T 1oys_A          239 DSLPE  243 (245)
T ss_dssp             -----
T ss_pred             hhhhh
Confidence            87654

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

Probab=100.00  E-value=1.1e-48  Score=341.05  Aligned_cols=224  Identities=25%  Similarity=0.352  Sum_probs=205.3

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCC-
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTR-   87 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~-   87 (263)
                      ...|.|||+++|+|++++++|++++++|||+|++|+|+|+|+|++|.+.++. .+.++++.|.|+|.++|+++.++.+| 
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 HHMRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATIEERVPPF-MRGEGKGWVTAEYAMIPRATEQRTIRE   87 (255)
T ss_dssp             --CCCCSCCTTCCCCEEEEESCSSSSSEEEEEEETTEEEEEEEEEESCCCGG-GTTSSCCEEEEEEEECTTSSSSCCCCC
T ss_pred             cccccCCCCcCCCCCEEEEECCCCCCCeEEEEEECCeEEEEEEEecCCCCCC-CCCCCceEEEEEEEECCCccccccccc
Confidence            5689999999999999999999999999999999999999999998653222 34678999999999999999887544 


Q ss_pred             ---CCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHc-----------CCCccC
Q psy18119         88 ---PRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDA-----------GIPMRE  153 (263)
Q Consensus        88 ---~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~da-----------gIp~~~  153 (263)
                         +++++++.+++++|+++|+++++++.||+|.|+|+++||++|||+++|+++|+++||+|+           +|||++
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               457899999999999999999999999999999999999999999999999999999999           999999


Q ss_pred             ceeEEEEEecCCeeE-ecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc---cCChhHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        154 YVVACSASLAGDTPL-VDISHLEETLGGPNLTVAALPLSGKVAVMELSQ---KLHLDHLPRVLDCALKGCADIHAILDTA  229 (263)
Q Consensus       154 ~~~avt~~~~~~~~l-vDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G---~i~~~~l~~~i~~A~~~~~~i~~~i~~~  229 (263)
                      +|+++|++++++.++ +|||..||..++..++|++ +..++|+++++.|   +++.+++.++++.|.+++++++++++++
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            999999999999888 9999999999999999998 6789999999975   6999999999999999999999999999


Q ss_pred             HHHHH
Q psy18119        230 IKQHL  234 (263)
Q Consensus       230 l~~~~  234 (263)
                      +++..
T Consensus       247 l~~~~  251 (255)
T 3dd6_A          247 LGDIV  251 (255)
T ss_dssp             HGGGG
T ss_pred             HHHHH
Confidence            87654

>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=2.8e-48  Score=336.05  Aligned_cols=219  Identities=28%  Similarity=0.389  Sum_probs=200.3

Q ss_pred             ccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCC---
Q psy18119         11 LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTR---   87 (263)
Q Consensus        11 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~---   87 (263)
                      .|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|++|...+.. ...++++.|.|+|.+.|+++.++.+|   
T Consensus         2 ~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~-~~~~~~g~l~v~~~~~p~~~~~r~~Re~~   80 (239)
T 1r6l_A            2 NRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRF-LKGQGQGWLTAEYGMLPRSTGERNQREAS   80 (239)
T ss_dssp             CCTTCCCTTCCCCEEEESSCSSSSSEEEEEEETTEEEEEEEEEEESCSSC-CC---CCEEEEEEEECTTSSSSCCCCHHH
T ss_pred             cCCCCCCCCCcCCeEEEeCCcCCCCeEEEEEECCEEEEEEEEccCccCCc-cCCCCcEEEEEEEEeCCCccccccccccC
Confidence            39999999999999999999999999999999999999999997654321 23468899999999999998876544   


Q ss_pred             -CCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcC-----------CCccCce
Q psy18119         88 -PRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAG-----------IPMREYV  155 (263)
Q Consensus        88 -~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dag-----------Ip~~~~~  155 (263)
                       ++++.++++++++|+++|+++++++.||+|.|+|+++||++|||+++|++||+++||+|+|           |||+++|
T Consensus        81 ~G~~~~~~~~isrli~r~l~~~i~~~~l~~~~i~I~~~VL~~DG~~~~aai~aa~~AL~da~~~~~~~~~~~~ip~~~~~  160 (239)
T 1r6l_A           81 RGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMV  160 (239)
T ss_dssp             HTSCCHHHHHHHHHHHHHHHHTBCGGGTCSEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCBCCCE
T ss_pred             CCCCcHHHHHHHHHHHHHHHHhcCHHHcCCeEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhcchhcccCcccccCccCce
Confidence             3578899999999999999999999999999999999999999999999999999999999           9999999


Q ss_pred             eEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc---cCChhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        156 VACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ---KLHLDHLPRVLDCALKGCADIHAILDTAIK  231 (263)
Q Consensus       156 ~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G---~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~  231 (263)
                      +++|++++++.+++|||..||..+++.++|++ +..++++.+++.|   +++.+++.++++.|.+++++++++++++++
T Consensus       161 ~avs~g~~~~~~l~Dpt~~Ee~~~~~~l~va~-~~~g~i~~~~~~g~~~~~~~~~l~~~l~~a~~~~~~i~~~~~~~l~  238 (239)
T 1r6l_A          161 AAVSVGIYQGVPVLDLDYLEDSAAETDLNVVM-TDAGGFIEVQGTAEGAPFRPAELNAMLELAQQGMQELFELQRAALA  238 (239)
T ss_dssp             EEEEEEEETTEEEESCCHHHHHHCSEEEEEEE-ETTSCEEEEEEEESSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             eEEEEEEECCEEEECCCHHHHhcCCceEEEEE-eCCCCEEEEEEeCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999 5778999999875   699999999999999999999999999875

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

Probab=100.00  E-value=1.4e-48  Score=340.88  Aligned_cols=220  Identities=27%  Similarity=0.369  Sum_probs=203.3

Q ss_pred             ccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCC---
Q psy18119         11 LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTR---   87 (263)
Q Consensus        11 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~---   87 (263)
                      +|+|||.++|+|++.+++|++++++|||+|++|+|+|+|+|++|...+.. ...++++.|.|+|.+.|+++.++.+|   
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 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNW-LKGKGQGWITAEYSMLPRATQQRTIRESV   79 (255)
T ss_dssp             -CTTSCCTTCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEESCCCGG-GTTSSCCEEEEEEEECSCCTTSCCCCSST
T ss_pred             CCCCCCCCCCccCeEEEECCCCCCCEEEEEEECCEEEEEEEEcCCcCCCC-CCCCCceEEEEEEEcCCCccccccccccC
Confidence            59999999999999999999999999999999999999999997764321 23578899999999999998877544   


Q ss_pred             -CCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcC-----------CCccCce
Q psy18119         88 -PRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAG-----------IPMREYV  155 (263)
Q Consensus        88 -~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dag-----------Ip~~~~~  155 (263)
                       ++++.++++++++|+++|+++++++.||+|.|+|+++||++|||+++|+++|+++||+|+|           |||+++|
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             3578899999999999999999999999999999999999999999999999999999999           9999999


Q ss_pred             eEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc---cCChhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        156 VACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ---KLHLDHLPRVLDCALKGCADIHAILDTAIKQ  232 (263)
Q Consensus       156 ~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G---~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~  232 (263)
                      +++|++++++.+|+|||..||..+++.++|++ +..++++.+++.|   +++.++|.++++.|.++++++++++++++++
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            99999999999999999999999999999999 5778999999874   6999999999999999999999999999876

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

Probab=100.00  E-value=7.1e-48  Score=334.24  Aligned_cols=216  Identities=23%  Similarity=0.348  Sum_probs=182.7

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCC
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRP   88 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~   88 (263)
                      +|+|+|||+++|+|++++++|++++++|||+|++|+|+|+|+|+||.+.++. ...++++.++++|.  |+.       +
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 EESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRK-GENPEKASIEVVWK--PMT-------G   71 (246)
T ss_dssp             ---CTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEECCCEECCCT-TSCSSSCEEEEEEE--CSS-------S
T ss_pred             CCcCCCCCCCCCcCCeEEEECCCCCCCeEEEEEECCeEEEEEEecCcCCCcc-cCCCccEEEEEEeC--CCC-------C
Confidence            6899999999999999999999999999999999999999999998765443 24577888877664  421       1


Q ss_pred             CCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEEec-CCee
Q psy18119         89 RGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLA-GDTP  167 (263)
Q Consensus        89 ~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~~~-~~~~  167 (263)
                      ++++++++++++|+++|+++++++.||+|.|+|+++||++|||+++|+++|+++||+|+||||+++|++++++++ ++.+
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            356778999999999999999999999999999999999999999999999999999999999999999999998 7799


Q ss_pred             EecCCchhhhcCCCeEEEEEeCCCCcEEEEEe------------------cccCChhHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        168 LVDISHLEETLGGPNLTVAALPLSGKVAVMEL------------------SQKLHLDHLPRVLDCALKGCADIHAILDTA  229 (263)
Q Consensus       168 lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~------------------~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~  229 (263)
                      |+|||..||..+++.++|++. .. .+|.+++                  .|.++++++.++++.|.+++++++++++++
T Consensus       152 llDpt~~Ee~~~~~~~~va~~-~~-~i~~lq~~g~~~~~~~~~~~i~~~~~g~~~~~~l~~~l~~A~~~~~~i~~~~~~~  229 (246)
T 3hkm_A          152 ILDTNKAEEQQLKSFAHLVFP-NS-RKSASSKEPNQKEEDSERGLITSITHGVMSEEDYFSCIERGLAASSRISDFMRTT  229 (246)
T ss_dssp             EESCCHHHHTTCSEEEEEEEE-C---------------------CCCEEEEECEEHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             EECCCHHHHhcCCeeEEEEEe-CC-ceEEEeecccccccccccceeeeeccCCcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999994 33 4666665                  567999999999999999999999999999


Q ss_pred             HHHHHHH
Q psy18119        230 IKQHLIK  236 (263)
Q Consensus       230 l~~~~~~  236 (263)
                      |+++..+
T Consensus       230 l~~~~~~  236 (246)
T 3hkm_A          230 LQKQAPG  236 (246)
T ss_dssp             TC-----
T ss_pred             HHhhhhc
Confidence            9877653

>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=1.9e-47  Score=337.59  Aligned_cols=220  Identities=22%  Similarity=0.288  Sum_probs=202.3

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEE-cCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCC
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVY-GPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTR   87 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~   87 (263)
                      +|+|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|+ +|.++..   ..++++.|.++|.++|++++.+. .
T Consensus        24 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~---~~~~~g~l~~~~~~~p~a~~~~~-~   99 (277)
T 2po1_B           24 EGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLGEPFP---DTPNMGVMTTNVELVPLASPTFE-P   99 (277)
T ss_dssp             TTCCTTSCCTTCCCCEEEEECCSTTSSEEEEEEETTEEEEEEEEEEEECCCT---TCTTSCEEEEEEEECGGGCTTCC-S
T ss_pred             cCCCCCCCCCCCcCCeEEEeCCcCCCCeEEEEEECCeEEEEEEEecccCCCC---CCCCceEEEEEEEeCCCcccccc-C
Confidence            79999999999999999999999999999999999999999999 6666543   35788999999999999987643 2


Q ss_pred             CCCCcchHHHHHHHHHHHHh--hhccCCC---C---ceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcC-----------
Q psy18119         88 PRGDRKTSEISLQLRQAVSA--AIMSEVH---P---RSQIDIFVEVLQADGGNFCACVNAATLALIDAG-----------  148 (263)
Q Consensus        88 ~~~~~~~~~l~~~l~~~l~~--~i~l~~~---p---~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dag-----------  148 (263)
                      ++++.++.+++++|+++|++  +++++.|   |   .|.|+|+++||++|||+++|+++|+++||+|+|           
T Consensus       100 g~~~~~~~~l~~li~r~l~~s~~idl~~L~i~pg~~~w~i~id~~VL~~dG~~~~a~i~aa~~AL~da~~p~~~~~~~~~  179 (277)
T 2po1_B          100 GPPDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVFIDVHVLDHDGNLMDAIGIAAIAALLNARVPKVRYNEETG  179 (277)
T ss_dssp             SSCCHHHHHHHHHHHHHHHTTTSBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHHCEEEEEEECTTTC
T ss_pred             CCCChHHHHHHHHHHHHHhhcccccHHHccccCCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcCCCcEEEeCCCc
Confidence            35788999999999999998  6888876   4   379999999999999999999999999999999           


Q ss_pred             ----------CCccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEec--ccCChhHHHHHHHHHH
Q psy18119        149 ----------IPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELS--QKLHLDHLPRVLDCAL  216 (263)
Q Consensus       149 ----------Ip~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~--G~i~~~~l~~~i~~A~  216 (263)
                                +||+++|+++|++++++.+++||+..||..+++.++|++ +..|+|+.+++.  |+++.+++.+++++|.
T Consensus       180 ~~~~~~~~~~ipl~~~~~avs~g~~~~~~l~Dp~~~Ee~~~~~~~~v~~-~~~g~i~~lq~~g~~~~~~~~l~~~l~~A~  258 (277)
T 2po1_B          180 EVETLDETEPLPVEKIPVPVTFAKIGNILVVDPSLDEELVMDGKITITT-DETGHISAVQKSEGGAFKLEEVMYAVETAF  258 (277)
T ss_dssp             CEEEEEEEEECCBCCCCEEEEEEEETTEEEESCCHHHHHHCSEEEEEEE-CTTSCEEEEEEESSCCCCHHHHHHHHHHHH
T ss_pred             eeecccccccccccCceEEEEEEEECCEEEeCCCHHHHhhCCCcEEEEE-cCCCCEEEEEccCCCCCCHHHHHHHHHHHH
Confidence                      899999999999999999999999999999999999999 567999999998  5799999999999999


Q ss_pred             HHHHHHHHHHHHHHHHH
Q psy18119        217 KGCADIHAILDTAIKQH  233 (263)
Q Consensus       217 ~~~~~i~~~i~~~l~~~  233 (263)
                      +++++++++++++|++.
T Consensus       259 ~~~~~l~~~~~~~l~~~  275 (277)
T 2po1_B          259 KKAEEIRKLILEAVEKA  275 (277)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhc
Confidence            99999999999999875

>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=1.1e-46  Score=332.74  Aligned_cols=218  Identities=19%  Similarity=0.197  Sum_probs=199.9

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEE-cCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCC
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVY-GPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTR   87 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~   87 (263)
                      +|+|+|||+++|+|++.+++|++++++|||++++|+|+|+|+|+ +|.++..   ..++++.|.|+|.++|+++++++ .
T Consensus        27 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~---~~~~~g~l~v~~~~~p~a~~~~~-~  102 (277)
T 2je6_A           27 KGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYE---DTPNQGNLIVNVELLPLAYETFE-P  102 (277)
T ss_dssp             GTBCTTSCBTTCCCCEEEEETCSTTSSEEEEEEETTEEEEEEEEEEEECCCT---TCTTCCEEEEEEEECTTSCTTCC-C
T ss_pred             cCCCCCCCCcCcccCeEEEeCCcCCCCeEEEEEECCeEEEEEEEeeeeCCCC---CCCCccEEEEEEEeCCccCcccc-c
Confidence            79999999999999999999999999999999999999999999 4555543   35788999999999999987653 3


Q ss_pred             CCCCcchHHHHHHHHHHHHh--hhccCCC------CceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcC-----------
Q psy18119         88 PRGDRKTSEISLQLRQAVSA--AIMSEVH------PRSQIDIFVEVLQADGGNFCACVNAATLALIDAG-----------  148 (263)
Q Consensus        88 ~~~~~~~~~l~~~l~~~l~~--~i~l~~~------p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dag-----------  148 (263)
                      +++++++.+++++|+++|++  +++++.|      +.|.|+|+++||++|||+++|+++|+++||++++           
T Consensus       103 g~~~~~~~~is~li~r~lr~~~~i~~~~l~i~~g~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~~p~v~~~~~~~  182 (277)
T 2je6_A          103 GPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGI  182 (277)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHTTCSCGGGGEEETTTEEEEEEEEEEEEECCSCHHHHHHHHHHHHHHTCEEEEEECC---C
T ss_pred             CCCChHHHHHHHHHHHHHhccCCcCHHHceeecCceEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcCCCeEEecCCcc
Confidence            45788999999999999999  4888887      3689999999999999999999999999999999           


Q ss_pred             ----------CCccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHHHHHHHHHH
Q psy18119        149 ----------IPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRVLDCAL  216 (263)
Q Consensus       149 ----------Ip~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l~~~i~~A~  216 (263)
                                +||+++|+++|++++++.+++|||..||..+++.++|++ +..++|+++++.|  +++.+++.++++.|.
T Consensus       183 ~~~~~~~~~~ip~~~~~~avsvg~~~~~~l~Dpt~~Ee~~~~~~l~va~-~~~g~i~~v~~~g~~~~~~~~l~~~l~~A~  261 (277)
T 2je6_A          183 SVNKNEVVGKLPLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSY-TPDLKIVGIQKSGKGSMSLQDIDQAENTAR  261 (277)
T ss_dssp             EEEEEEEEEECCCSCCCEEEEEEEETTEEEESCCHHHHHHCSEEEEEEE-CTTCCEEEEEEESSSCEEHHHHHHHHHHHH
T ss_pred             eEeccCccccccccCCeEEEEEEEECCEEecCCCHHHHhcCCCcEEEEE-eCCCCEEEEECCCCCCCCHHHHHHHHHHHH
Confidence                      999999999999999999999999999999999999999 5678999999984  799999999999999


Q ss_pred             HHHHHHHHHHHHHHH
Q psy18119        217 KGCADIHAILDTAIK  231 (263)
Q Consensus       217 ~~~~~i~~~i~~~l~  231 (263)
                      +++++++++++++++
T Consensus       262 ~~~~~i~~~~~~~l~  276 (277)
T 2je6_A          262 STAVKLLEELKKHLG  276 (277)
T ss_dssp             HHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999998874

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

Probab=100.00  E-value=1.3e-46  Score=331.31  Aligned_cols=218  Identities=21%  Similarity=0.284  Sum_probs=199.7

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEE-cCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCC
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVY-GPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTR   87 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~   87 (263)
                      +|+|+|||+++|+|++.+++|++++++|||++++|+|+|+|+|+ +|.+++.   ..++++.|.|+|.++|+++++++ .
T Consensus        22 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~---~~~~~g~l~v~~~~~p~a~~~~~-~   97 (271)
T 2wnr_A           22 NKERIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKPQIGEPFP---DTPEMGVILTNSELLPMASPTFE-P   97 (271)
T ss_dssp             TTCCTTCCCTTCCCCEEEEESCSTTSSEEEEEEETTEEEEEEEEEEEECCCT---TCTTCCEEEEEEEECGGGCTTCC-C
T ss_pred             cCCCCCCCCcccccCeEEEeCccCCCCeEEEEEECCeEEEEEEEeeeecCCC---CCCCceEEEEEEEeCCccccccc-C
Confidence            79999999999999999999999999999999999999999999 5666543   35789999999999999987643 3


Q ss_pred             CCCCcchHHHHHHHHHHHHh--hhccCCC---C---ceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcC-----------
Q psy18119         88 PRGDRKTSEISLQLRQAVSA--AIMSEVH---P---RSQIDIFVEVLQADGGNFCACVNAATLALIDAG-----------  148 (263)
Q Consensus        88 ~~~~~~~~~l~~~l~~~l~~--~i~l~~~---p---~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dag-----------  148 (263)
                      +++++++.+++++|+++|++  +++++.|   |   .|.|+|+++||++|||+++|+++|+++||+|++           
T Consensus        98 g~~~~~~~~~s~li~r~lr~s~~i~l~~l~i~pg~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~~p~~~~~~~~~  177 (271)
T 2wnr_A           98 GPPDERSVELSRVVDRCIRESRMIDLEKLCIIEGSKVWMLFLDLHIIDYDGNLFDAAVLATVAALLDTRIPAAEVEDGEV  177 (271)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHHCEEEEEEEETTEE
T ss_pred             CCCchHHHHHHHHHHHHHhccCCccHHHccccCCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcCCCeEEecCCce
Confidence            45788999999999999999  6887877   4   489999999999999999999999999999999           


Q ss_pred             ---------CCccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHHHHHHHHHHH
Q psy18119        149 ---------IPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRVLDCALK  217 (263)
Q Consensus       149 ---------Ip~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l~~~i~~A~~  217 (263)
                               +||+++|+++|++++++.+++|||..||..+++.++|++ +..++|+++++.|  +++.+++.++++.|.+
T Consensus       178 ~~~~~~~~~ip~~~~~~avt~g~~~~~~l~Dpt~~Ee~~~~~~l~va~-~~~~~i~~i~~~g~~~~~~~~l~~~l~~a~~  256 (271)
T 2wnr_A          178 VINREKMQPLPVNRKALMCTFAKIGNEIVLDPSLEEEDILTARISIGV-TEEGSICAMQKGGEGPLTRDDVLKAVSIAVE  256 (271)
T ss_dssp             EEEEEEEEECCBCCCEEEEEEEEETTEEEESCCHHHHTTCSEEEEEEE-ETTSCEEEEEEESSSCBCHHHHHHHHHHHHH
T ss_pred             eeccCcccccCccCCeEEEEEEEECCEEEeCCCHHHHhcCCCcEEEEE-eCCCCEEEEECCCCCCCCHHHHHHHHHHHHH
Confidence                     999999999999999999999999999999999999999 4678999999984  7999999999999999


Q ss_pred             HHHHHHHHHHHHHH
Q psy18119        218 GCADIHAILDTAIK  231 (263)
Q Consensus       218 ~~~~i~~~i~~~l~  231 (263)
                      ++++++++++++++
T Consensus       257 ~~~~i~~~~~~~l~  270 (271)
T 2wnr_A          257 KVPQLIEYLDKSMT  270 (271)
T ss_dssp             HHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHhC
Confidence            99999999998864

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

Probab=100.00  E-value=3.3e-46  Score=326.58  Aligned_cols=215  Identities=21%  Similarity=0.269  Sum_probs=195.6

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcC-CCCCCCCcCCCCeEEEEEEEeeCCCCCccccCC
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGP-RPVRNKSIKVHGSVLINFQYSMAVFSTGERKTR   87 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp-~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~   87 (263)
                      +|+|+|||+++|+|++.+++|++++++|||++++|+|+|+|+|+++ .++..   ..++++++.|+|.++|+++++++ +
T Consensus        20 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~~---~~~~~g~l~v~~~~~p~a~~~~~-~   95 (259)
T 3m7n_G           20 DNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYP---DTPDRGVIIVNAELVPLASPTFE-P   95 (259)
T ss_dssp             TTCCTTCCCTTCCCCEEEEETSSTTSSEEEEEEETTEEEEEEEEEEEECCCS---SCTTSCEEEEEEECCTTSCTTCC-S
T ss_pred             cCCCCCCCCCccccCeEEEeCCcCCCCceEEEEECCcEEEEEEEecccCCCC---CCCCceEEEEEEEeCCccccccc-C
Confidence            7999999999999999999999999999999999999999999964 33432   24678899999999999988764 3


Q ss_pred             CCCCcchHHHHHHHHHHHHh--hhccCCC---C-c--eEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCC----------
Q psy18119         88 PRGDRKTSEISLQLRQAVSA--AIMSEVH---P-R--SQIDIFVEVLQADGGNFCACVNAATLALIDAGI----------  149 (263)
Q Consensus        88 ~~~~~~~~~l~~~l~~~l~~--~i~l~~~---p-~--~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagI----------  149 (263)
                      +++++++.+++++|+++|++  +++++.|   | +  |.|+|+++||++|||+++|+++|+++||++++|          
T Consensus        96 g~~~~~~~~~srli~r~lr~s~~i~l~~L~i~pg~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~iP~~~~~~~~~  175 (259)
T 3m7n_G           96 GPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFDLGED  175 (259)
T ss_dssp             SSSCHHHHHHHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHTCEECTGGGTSSSC
T ss_pred             CCCChHHHHHHHHHHHHHhhcCCccHHHhcccCCcEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHhCCCCeEEecCCce
Confidence            46888999999999999999  7888876   6 3  899999999999999999999999999999999          


Q ss_pred             ---CccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHHHHHHHHHHHHHHHHHH
Q psy18119        150 ---PMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRVLDCALKGCADIHA  224 (263)
Q Consensus       150 ---p~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l~~~i~~A~~~~~~i~~  224 (263)
                         ||+++|+++|++++++.+++|||..||..+++.++|++ +..|+++++++.|  .++.+++.++++.|.++++++++
T Consensus       176 ~~lp~~~~~~avtvg~~~~~~l~Dpt~~Ee~~~~~~l~va~-~~~g~i~~i~~~g~~~~~~~~l~~~l~~a~~~~~~l~~  254 (259)
T 3m7n_G          176 YLLPVRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITT-DKDDNVVAMQKSGGYLLDEKLFDELLDVSINCARKLRE  254 (259)
T ss_dssp             EECCBCCCCEEEEEEEETTEEEESCCTTGGGGCSCEEEEEE-CTTSCEEEEEEESSCCBCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ecccccCceeEEEEEEECCEEEECCCHHHHhhCCCcEEEEE-eCCCcEEEEECCCCCCcCHHHHHHHHHHHHHHHHHHHH
Confidence               79999999999999999999999999999999999999 5678999999984  79999999999999999999998


Q ss_pred             HHHH
Q psy18119        225 ILDT  228 (263)
Q Consensus       225 ~i~~  228 (263)
                      ++++
T Consensus       255 ~~~~  258 (259)
T 3m7n_G          255 KFKE  258 (259)
T ss_dssp             TTC-
T ss_pred             HHhh
Confidence            8764

>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=2.1e-46  Score=330.99  Aligned_cols=220  Identities=22%  Similarity=0.236  Sum_probs=199.9

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCC
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRP   88 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~   88 (263)
                      +|+|+|||+++|+|++.+++|++++++|||++++|+|+|+|+|+++...+.  ...++++.|.|+|.++|+++++++ .+
T Consensus        22 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~p~--~~~~~~g~l~v~~~~~p~a~~~~~-~g   98 (278)
T 2nn6_C           22 ENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPS--TDAPDKGYVVPNVDLPPLCSSRFR-SG   98 (278)
T ss_dssp             TSCCTTSCCSCCCCSCCEEETCCSSSSEEEEEEETTEEEEEEEEEEECCCC--SSSTTCCCCEEEEECCSSSCTTSC-SS
T ss_pred             cCCCCCCCCcccccCeEEEeCCccCCCceEEEEeCCeEEEEEEEEEeecCC--CCCCCccEEEEEEEeCCccCcccc-CC
Confidence            799999999999999999999999999999999999999999999765322  124688999999999999988753 34


Q ss_pred             CCCcchHHHHHHHHHHHHh--hhccCCC------CceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCC-----------
Q psy18119         89 RGDRKTSEISLQLRQAVSA--AIMSEVH------PRSQIDIFVEVLQADGGNFCACVNAATLALIDAGI-----------  149 (263)
Q Consensus        89 ~~~~~~~~l~~~l~~~l~~--~i~l~~~------p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagI-----------  149 (263)
                      ++++++++++++|+++|++  +++++.|      +.|.|+|+++||++|||+++|+++|+++||+++||           
T Consensus        99 ~~~~~~~~~s~li~r~l~~s~~i~l~~L~i~pg~~~~~i~i~~~VL~~DG~~~~aai~aa~~AL~~a~iP~v~~~~~~~~  178 (278)
T 2nn6_C           99 PPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETAL  178 (278)
T ss_dssp             SCCHHHHHHHHHHHHHHHHHCCSCHHHHCSSBTTBCEEEEEEEEESSCCSCTTHHHHHHHHHHHHTCCCCCCCBCSSSBC
T ss_pred             CCcHHHHHHHHHHHHHHhccCCCCHHHCEEeCCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhCCCCeEEEeCCCcc
Confidence            5788999999999999995  6776654      46899999999999999999999999999999996           


Q ss_pred             -----------CccCceeEEEEEecCC-eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHHHHHHHHH
Q psy18119        150 -----------PMREYVVACSASLAGD-TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRVLDCA  215 (263)
Q Consensus       150 -----------p~~~~~~avt~~~~~~-~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l~~~i~~A  215 (263)
                                 ||+++|+++|++++++ .+++|||..||..+++.++|++ +..|+|+++++.|  +++.+++.++++.|
T Consensus       179 ~~~~~~~~~~lp~~~~~~avs~g~~~~~~~l~Dpt~~Ee~~~~~~l~va~-~~~g~i~~v~~~g~~~~~~~~l~~~l~~a  257 (278)
T 2nn6_C          179 AEVNLKKKSYLNIRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVM-DEEGKLCCLHKPGGSGLTGAKLQDCMSRA  257 (278)
T ss_dssp             CCTTSCCCSCSCCSCCCEEEEEEECTTTCCEESCCTTTTTSCSEEEEEEE-CTTCCEEEEEESCCSCCCHHHHHHHHHHH
T ss_pred             eecCcccccccccCCceEEEEEEEECCceEEECCCHHHHhhcCceEEEEE-cCCCcEEEEEccCCCCCCHHHHHHHHHHH
Confidence                       7999999999999999 9999999999999999999999 5678999999998  79999999999999


Q ss_pred             HHHHHHHHHHHHHHHHH
Q psy18119        216 LKGCADIHAILDTAIKQ  232 (263)
Q Consensus       216 ~~~~~~i~~~i~~~l~~  232 (263)
                      .++++++++++++++++
T Consensus       258 ~~~~~~i~~~~~~~l~~  274 (278)
T 2nn6_C          258 VTRHKEVKKLMDEVIKS  274 (278)
T ss_dssp             HHHHHHHHHHHHTTTTT
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            99999999999998865

>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=7.5e-45  Score=330.33  Aligned_cols=244  Identities=20%  Similarity=0.206  Sum_probs=208.7

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCC
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRP   88 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~   88 (263)
                      +++|+|||+++|+|++.+++|   +++|||+|++|+|+|+|+|++|...+..  ..+++++|.++|.++|+++.+++. +
T Consensus        37 ~g~R~DGR~~~e~R~i~ie~g---~A~GSa~v~~G~T~VL~tV~~e~~~p~~--~~~~~g~l~~~v~~~p~a~~~~~~-g  110 (358)
T 2nn6_A           37 EKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSPKL--NRATEGILFFNLELSQMAAPAFEP-G  110 (358)
T ss_dssp             TTCCTTSCCTTCCCCCEEEEC---SSTTEEEEESSSCEEEEEECCEEECCCS--TTTTSCCEEEEEEECTTTCSSCCS-S
T ss_pred             cCCCCCCCCccccCCeEEEEe---cCCcEEEEEECCcEEEEEEEecccCCcc--cCCCCcEEEEEEEecCCccccccC-C
Confidence            799999999999999999999   8999999999999999999997643321  247788899999999999877543 3


Q ss_pred             CCCcchHHHHHHHHHHHHhhh--ccCCC------CceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCC----------
Q psy18119         89 RGDRKTSEISLQLRQAVSAAI--MSEVH------PRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP----------  150 (263)
Q Consensus        89 ~~~~~~~~l~~~l~~~l~~~i--~l~~~------p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp----------  150 (263)
                      ++++++.+++++|+++|+++.  +++.+      |.|.|+|+++||++|||+++||++|+++||+++++|          
T Consensus       111 ~~s~~e~eisrli~r~Lr~s~~idl~~LcI~pg~~~w~I~Vdv~VL~~DGn~~dAai~Aa~aAL~da~iP~v~~~~~~v~  190 (358)
T 2nn6_A          111 RQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVT  190 (358)
T ss_dssp             STHHHHTHHHHHHHHHHHHHTCBCSSSSCSBTTTBEEEEEEEEEECSCCSCCHHHHHHHHHHHHHHCCCCCCBCCTTCCB
T ss_pred             CCCHHHHHHHHHHHHHhhhccccchHhhcccCCCccEEEEEEEEEEeCCCCHHHHHHHHHHHHHHHhCcCcEEeeCCeeE
Confidence            577888999999999999954  44433      679999999999999999999999999999999999          


Q ss_pred             -------------ccCceeEEEEEec--CCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHHHHHHH
Q psy18119        151 -------------MREYVVACSASLA--GDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRVLD  213 (263)
Q Consensus       151 -------------~~~~~~avt~~~~--~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l~~~i~  213 (263)
                                   |+++|+++|+|++  ++.+|+|||..||..+++.++|++ +..|+|+++++.|  +++.+++.+|++
T Consensus       191 i~~~~~~~~~~l~i~~~p~avsvgl~~~~~~illDPt~~Ee~~~~~~l~Va~-t~~g~I~~lqk~G~~~ls~~~l~~~l~  269 (358)
T 2nn6_A          191 LYTPEERDPVPLSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAM-NKHREICTIQSSGGIMLLKDQVLRCSK  269 (358)
T ss_dssp             CCHHHHTSCCCCCBCCCEEEEEEEECTTTSSEEESCCHHHHHHCSCEEEEEE-ETTTEEEEEEEESCCCCCHHHHHHHHH
T ss_pred             ecccccccccccCccCCEEEEEEEEEeeCCEEEECCCHHHHhhcCccEEEEE-cCCCeEEEEEeCCCCCCCHHHHHHHHH
Confidence                         8999999999987  679999999999999999999998 6788999999887  479999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhcc--CCCCccccccceecCCccc
Q psy18119        214 CALKGCADIHAILDTAIKQHLIKVAGA--RGLGRKFQLGQLTGKKKEE  259 (263)
Q Consensus       214 ~A~~~~~~i~~~i~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~  259 (263)
                      .|.++++++.++++++++++...+.+.  .|+..-....+++--+.|+
T Consensus       270 ~A~~~~~~i~~~~~~~l~~~~~~r~~~~~~gf~~~~~~~~~~~~~~~~  317 (358)
T 2nn6_A          270 IAGVKVAEITELILKALENDQKVRKEGGKFGFAESIANQRITAFKMEK  317 (358)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCCCSSCSHHHHSSSSEEEECC
T ss_pred             HHHHHHHHHHHHHHHHHHhHHHhhhhcccCCchhhccccceehhcccc
Confidence            999999999999999999987766543  2444444444444433333

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

Probab=100.00  E-value=3.1e-45  Score=355.58  Aligned_cols=251  Identities=21%  Similarity=0.276  Sum_probs=210.6

Q ss_pred             cccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEE-EcCCCCCCCCc--CCCCeEEEEEEEeeCCC
Q psy18119          3 LLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKSI--KVHGSVLINFQYSMAVF   79 (263)
Q Consensus         3 ~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V-~gp~~~~~~~~--~~~~~~~l~v~~~~~~~   79 (263)
                      .|.+  +|.|+|||.++|+|+|.+++|++++++|||+|++|+|+|+|+| .||.++.+..+  ..++++.+.++|+++||
T Consensus       324 ~il~--~g~R~DGR~~~elRpI~ie~gvl~~a~GSAl~~~G~TkVl~~Vt~Gp~~~~~~~d~l~~~~~g~~~~~y~~~P~  401 (726)
T 4aid_A          324 GILD--TGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYKESFLLHYNFPPY  401 (726)
T ss_dssp             HHHS--SSBCTTSCBTTCCCCEEEEECSSTTSSEEEEEEETTEEEEEEEEEECGGGSEEEEETTEEEEECEEEEEECCGG
T ss_pred             HHhc--CCCCCCCCCCCCccceEEEECCCCCCCceEEEEeCCeEEEEEEEeCCCCcccccccccCCCceEEEEEEEeCCC
Confidence            4555  8999999999999999999999999999999999999999999 68887654311  23578999999999999


Q ss_pred             CCccccCCCCCCcchHHHHHHHHHHHHhhhc-cCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEE
Q psy18119         80 STGERKTRPRGDRKTSEISLQLRQAVSAAIM-SEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVAC  158 (263)
Q Consensus        80 ~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~-l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~av  158 (263)
                      +++++++++.+++++.+++++++++|+++++ .+.||++ |+|+++||++|||+++|++||+++||+||||||+++++++
T Consensus       402 st~er~~~g~~~~Reie~~~li~raL~~vI~~~~~~P~t-I~V~~~VLesDGs~~~AsI~aa~lAL~DAGIPm~~~Vaav  480 (726)
T 4aid_A          402 SVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYT-IRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGI  480 (726)
T ss_dssp             GGTCCCCCSSCCHHHHHHHHHHHHHHGGGSCCTTTCCCE-EEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCCEEE
T ss_pred             cccccccCCCcchhhHHHHHHHHHHHHHhcCccccCCeE-EEEEEEEEEcCCcHHHHHHHHHHHHHHhcCCccccCeeEE
Confidence            9998877777899999999999999999998 5889985 9999999999999999999999999999999999999999


Q ss_pred             EEEecCC----eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc---cCChhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        159 SASLAGD----TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ---KLHLDHLPRVLDCALKGCADIHAILDTAIK  231 (263)
Q Consensus       159 t~~~~~~----~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G---~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~  231 (263)
                      ++|++++    .+++||+..|+..++..+.|+.  +.+.|+.+++.|   +|+.+.+.+++++|.++|.+|++.++++|.
T Consensus       481 svGli~~g~~~~iLlD~~~~Ed~~gd~d~~Va~--t~~gIt~lQ~d~k~~~~s~e~l~~aL~~A~~g~~~I~~~m~~al~  558 (726)
T 4aid_A          481 AMGLILEQDGFAVLSDILGDEDHLGDMDFKVAG--TSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEMNKAMD  558 (726)
T ss_dssp             EEEEEECSSCEEEEESCCTTGGGGSSEEEEEEE--ETTEEEEEEEEECSSCCCHHHHHHHHHHHHHHHHHHHHHHHTTCS
T ss_pred             EEEEEcCCCceEEEecCChhHHhcCCceEEEEe--cCCceEEEEecCCcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999964    5788999999999999999986  356699999987   469999999999999999999999999998


Q ss_pred             HHHHHhhccCCCC-----ccccccceecCCcc
Q psy18119        232 QHLIKVAGARGLG-----RKFQLGQLTGKKKE  258 (263)
Q Consensus       232 ~~~~~~~~~~~~~-----~~~~~~~~~~~~~~  258 (263)
                      ++..+.....+..     +....|.++|.+|.
T Consensus       559 ~~r~~~~~~ap~~~~~~i~~~ki~~vig~gg~  590 (726)
T 4aid_A          559 APRADVGDFAPKIETINIPTDKIREVIGSGGK  590 (726)
T ss_dssp             SCCSSCCSSCCC--------------------
T ss_pred             hhhhhhcccCCeEEEEeCCHHHHHhhcCCCch
Confidence            8765555555432     56667889998874

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

Probab=100.00  E-value=2.4e-45  Score=353.11  Aligned_cols=250  Identities=20%  Similarity=0.254  Sum_probs=219.6

Q ss_pred             cccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcC-CCCCCCCcC------CCCeEEEEEEEe
Q psy18119          3 LLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGP-RPVRNKSIK------VHGSVLINFQYS   75 (263)
Q Consensus         3 ~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp-~~~~~~~~~------~~~~~~l~v~~~   75 (263)
                      +|.+  +|+|+|||.++|+|+|++++|++++++|||+|++|+|+|+|+|++| ..+....+.      .++.+.+.++|.
T Consensus       312 ~il~--~g~R~DGR~~~elRpi~i~~g~l~~a~GSal~~~G~T~Vl~~Vt~~~~~~~~~~d~~~~~l~~~~~g~~~~~y~  389 (630)
T 3u1k_A          312 IVLN--EYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSDQVITAINGIKDKNFMLHYE  389 (630)
T ss_dssp             HHHH--HSCCTTSCCTTCCCCEEEEECCSTTSSEEEEEEETTEEEEEEEEEECGGGGSCSSHHHHHHHCCCGGGEEEEEE
T ss_pred             HHhc--CCCCCCCCCCccccceEEEECCCCCCCceEEEEECCeEEEEEEEcCCCCchhcccccccccCCCCceEEEEEEE
Confidence            4555  8999999999999999999999999999999999999999999984 333322111      256788999999


Q ss_pred             eCCCCCccccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCce
Q psy18119         76 MAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYV  155 (263)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~  155 (263)
                      ++||+++++++++.+++++.+++++++++|+++++ +.||+ .|+|+++||++|||.++|+++|+++||+|+||||++++
T Consensus       390 ~~P~st~e~~~~g~~~rREi~~~~Li~raLr~vi~-~~~p~-tI~V~~~VLesDGs~~~AsI~aa~lAL~dAGIPl~~~V  467 (630)
T 3u1k_A          390 FPPYATNEIGKVTGLNRRELGHGALAEKALYPVIP-RDFPF-TIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAV  467 (630)
T ss_dssp             CCGGGGTCCCCCSSCCHHHHHHHHHHHHHHGGGSC-TTCSS-EEEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCC
T ss_pred             ecCCcccccccCCCCChHHHHHHHHHHHHHHhhCc-ccCCe-EEEEEEEEEEcCCCHHHHHHHHHHHHHHhCCCCcccce
Confidence            99999998876667889999999999999999998 56997 59999999999999999999999999999999999999


Q ss_pred             eEEEEEecC------C-----eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc---cCChhHHHHHHHHHHHHHHH
Q psy18119        156 VACSASLAG------D-----TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ---KLHLDHLPRVLDCALKGCAD  221 (263)
Q Consensus       156 ~avt~~~~~------~-----~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G---~i~~~~l~~~i~~A~~~~~~  221 (263)
                      +++++|+++      +     .+++||+..|+..++..+.|+. +..+ |+.+++.|   +|+.+.|.+++++|.+++.+
T Consensus       468 aavs~gli~~~~~~~g~~~~~~iLlD~~~~Ed~~~d~d~~Va~-t~~g-It~lQ~~~k~~~~s~~~l~~aL~~A~~g~~~  545 (630)
T 3u1k_A          468 AGVAIGLVTKTDPEKGEIEDYRLLTDILGIEDYNGDMDFKIAG-TNKG-ITALQADIKLPGIPIKIVMEAIQQASVAKKE  545 (630)
T ss_dssp             EEEEEEEEEEECSSSSCEEEEEEEESCCHHHHHTSSEEEEEEE-CSSC-EEEEEEEECSSCBCHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEecCCCcccccccCceEEecCCHHHHhhCcceEEEEe-cCCc-eEEEEecCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            999999997      3     6999999999999999999998 4555 99999997   57999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhccCC-----CCccccccceecCCcc
Q psy18119        222 IHAILDTAIKQHLIKVAGARG-----LGRKFQLGQLTGKKKE  258 (263)
Q Consensus       222 i~~~i~~~l~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~  258 (263)
                      |++++++++++...+.....+     .++....|.++|++|.
T Consensus       546 I~~~m~~al~~~~~~~~~~ap~~~~~~I~~~kI~~vIG~gG~  587 (630)
T 3u1k_A          546 ILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGY  587 (630)
T ss_dssp             HHHHHHHHCSSCCSSCCTTCCEEEEEECCHHHHHHHHCGGGH
T ss_pred             HHHHHHHHHHHHHhhhcccCCeEEEEEeChhHhheeECCCCh
Confidence            999999999987665555555     3366777999999985

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

Probab=100.00  E-value=1.9e-44  Score=322.42  Aligned_cols=224  Identities=18%  Similarity=0.138  Sum_probs=181.8

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCC
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRP   88 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~   88 (263)
                      +|+|+|||+++|+|++.+++|   +++|||+|++|+|+|+|+|++|...+..  ..++++.+.+++.++|++....+ .+
T Consensus        21 ~~~R~DGR~~~e~R~i~i~~g---~a~GSa~v~~G~T~Vl~~V~~~~~~p~~--~~~~~g~~~~~ve~~~~~~~~~~-~g   94 (305)
T 2wp8_A           21 QNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGNTKVHCRISCQIAQPYE--DRPFEGLFVISTEISPMAGSQFE-NG   94 (305)
T ss_dssp             TTCCTTSCCTTCCCCEEEEEC---SSTTEEEEEETTEEEEEEEEEEEC-CCS--SCTTCCEEEEEECCC-----------
T ss_pred             hCCCCCCCCCcccCCeEEEEc---CCCcEEEEEECCeEEEEEEeccccCCcc--cCCCCcEEEEEEEECCCCCcccc-CC
Confidence            899999999999999999999   8999999999999999999997543221  24567777788887888766542 23


Q ss_pred             CCC-cchHHHHHHHHHHHH--hhhccCCC---Cc---eEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCC---------
Q psy18119         89 RGD-RKTSEISLQLRQAVS--AAIMSEVH---PR---SQIDIFVEVLQADGGNFCACVNAATLALIDAGIP---------  150 (263)
Q Consensus        89 ~~~-~~~~~l~~~l~~~l~--~~i~l~~~---p~---~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp---------  150 (263)
                      +++ .++.+++++|+++|+  .+|+++.|   |.   |.|+|+++||++|||+++|+++|+++||+|+|+|         
T Consensus        95 ~~~~~~~~~is~li~r~l~~s~~idl~~L~i~pg~~~w~I~id~~VL~~DG~~~dAai~aa~~AL~~a~iP~~~~~~~~~  174 (305)
T 2wp8_A           95 NITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQI  174 (305)
T ss_dssp             ------------CHHHHHHHTTSBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHHHCEECCCBCTTSSC
T ss_pred             CCChhHHHHHHHHHHHHHhhccCcCHHHccccCCcEEEEEEEEEEEEcCCCCHHHHHHHHHHHHHHHhCCCeEEecCCce
Confidence            456 888999999999999  57888765   42   7899999999999999999999999999999999         


Q ss_pred             --------------ccCceeEEEEEecC--------------CeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc-
Q psy18119        151 --------------MREYVVACSASLAG--------------DTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ-  201 (263)
Q Consensus       151 --------------~~~~~~avt~~~~~--------------~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G-  201 (263)
                                    |+++|+++|+|+++              +.+|+|||..||..+++.++|++ +..|+|+.+++.| 
T Consensus       175 ~i~~~~~~~~~~l~~~~~pvavs~g~i~~~~~~~~~~~~~~~~~~l~Dpt~~Ee~~~~~~l~Va~-~~~g~i~~l~~~g~  253 (305)
T 2wp8_A          175 IVHPVNEREPVPLGILHIPICVTFSFFNPQDTEENIKGETNSEISIIDATLKEELLRDGVLTVTL-NKNREVVQVSKAGG  253 (305)
T ss_dssp             CBCCSSSSCCEECCBSCCCEEEEEEECC---------------CEEESCCHHHHHHCSEEEEEEE-CTTSEEEEEEEEEE
T ss_pred             EecccccccccccccccCeEEEEEEEEccccccccccccccCCeEEeCCCHHHHhccCCcEEEEE-cCCCcEEEEEecCC
Confidence                          77899999999997              78999999999999999999999 5688999999997 


Q ss_pred             -cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy18119        202 -KLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAG  239 (263)
Q Consensus       202 -~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~~  239 (263)
                       +++.+++.+++++|.+++++|+++++++++++..++.+
T Consensus       254 ~~~~~~~l~~~l~~A~~~~~~i~~~~~~~l~~~~~~r~~  292 (305)
T 2wp8_A          254 LPMDALTLMKCCHEAYSIIEKITDQILQLLKEDSEKRNK  292 (305)
T ss_dssp             EEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence             69999999999999999999999999999998887654

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

Probab=100.00  E-value=3.5e-45  Score=327.10  Aligned_cols=223  Identities=22%  Similarity=0.254  Sum_probs=198.5

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCC
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRP   88 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~   88 (263)
                      +++|+|||+++|+|++.+++|++++++|||+|++|+|+|+|+|+++...+.  ...++++++.++|.++|++++.+.++ 
T Consensus        34 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~e~~~p~--~~~~~~g~l~~~v~~~p~a~~~~~~r-  110 (305)
T 2nn6_E           34 EDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPK--LEKPNEGYLEFFVDCSASATPEFEGR-  110 (305)
T ss_dssp             TTCCSSSCCSSCCCCCEEEECCCTTSSSEEEEEETTEEEEEECCCCCSCCC--SSSCSSCCEEEECCCCTTTCSSCCTT-
T ss_pred             cCCCCCCCCCcCccCeEEEeCcccCCCcEEEEEECCeEEEEEEEEEeeCCC--cCCCCceEEEEEEEeCCCcCccccCC-
Confidence            799999999999999999999999999999999999999999999754222  23567888999999999988765433 


Q ss_pred             CCCcchHHHHHHHHHHHHh--hhccC---CCC---ceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccC-------
Q psy18119         89 RGDRKTSEISLQLRQAVSA--AIMSE---VHP---RSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMRE-------  153 (263)
Q Consensus        89 ~~~~~~~~l~~~l~~~l~~--~i~l~---~~p---~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~-------  153 (263)
                      .+++++.+++++|+++|++  +|+++   .+|   .|.|+|+++||++|||+++|+++|+++||++++||+.+       
T Consensus       111 ~~~~~~~~isrli~r~lr~s~~idl~~L~i~p~~~~w~i~idv~VL~~DG~~~daai~aa~~AL~~a~iP~~~~~~~~~~  190 (305)
T 2nn6_E          111 GGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLEDEEG  190 (305)
T ss_dssp             STHHHHHHHHHHHHHHHHHSCCSCSSSSCSSTTTCCCCEEEEEEECCCCSSHHHHHHHHHHHTTTTCCCCEEEEECC---
T ss_pred             CCchHHHHHHHHHHHHHhhcCcccHHHheeccCcEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHhcCCCeEEEecCCCC
Confidence            2457889999999999999  67777   456   36799999999999999999999999999999999653       


Q ss_pred             --------------------ceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHHHHH
Q psy18119        154 --------------------YVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRV  211 (263)
Q Consensus       154 --------------------~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l~~~  211 (263)
                                          +|+++|++++++.+|+|||..||..+++.++|++ +..++|+++++.|  .++.+++.++
T Consensus       191 ~~~i~~~~d~~~~~~l~l~~~p~avt~g~i~~~~l~Dpt~~Ee~~~~~~l~Va~-~~~g~i~~i~~~g~~~l~~~~l~~~  269 (305)
T 2nn6_E          191 SKDIELSDDPYDCIRLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSV-TSKGVVTCMRKVGKGSLDPESIFEM  269 (305)
T ss_dssp             ---EEEEESSCCCSCCCCTTCCCCEEEEESSSSEESSCCHHHHTSCSEEEEECC-CSSSCCCEEEEEESSCBCHHHHHHH
T ss_pred             ceeeeccCcccccccccccCceEEEEEEEECCEEEECCCHHHHhhcCCcEEEEE-cCCCCEEEEEccCCCCCCHHHHHHH
Confidence                                4789999999999999999999999999999999 4578899999987  7999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        212 LDCALKGCADIHAILDTAIKQHLI  235 (263)
Q Consensus       212 i~~A~~~~~~i~~~i~~~l~~~~~  235 (263)
                      ++.|.++++++.+++++++++...
T Consensus       270 l~~A~~~~~~i~~~~~~~l~~~~~  293 (305)
T 2nn6_E          270 METGKRVGKVLHASLQSVVHKEES  293 (305)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999987665

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

Probab=100.00  E-value=1.2e-44  Score=354.13  Aligned_cols=251  Identities=21%  Similarity=0.281  Sum_probs=211.6

Q ss_pred             ccccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEE-cCCCCCCCCc--CCCCeEEEEEEEeeCC
Q psy18119          2 DLLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVY-GPRPVRNKSI--KVHGSVLINFQYSMAV   78 (263)
Q Consensus         2 e~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~-gp~~~~~~~~--~~~~~~~l~v~~~~~~   78 (263)
                      ++|.+  +++|+|||.++|+|+|.+++|++++++|||+|++|+|+|+|+|+ ||.++.++.+  ..++.+.+.++|+++|
T Consensus       348 ~~i~~--~g~R~DGR~~~elRpI~ie~gvl~~a~GSAl~~~G~TqVL~~Vt~Gp~~~~~~~d~l~~~~~g~~~~~y~f~P  425 (757)
T 1e3p_A          348 ERVIA--EKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPP  425 (757)
T ss_dssp             HHHHH--TCBCTTSCBTTCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEEEGGGSEECCSSSSCCEESEEEEEECCG
T ss_pred             HHHhc--CCCCCCCCCcccccceeEEeCCCCCCCEEEEEEECCcEEEEEEEecCCCccccccccCCCCceEEEEEEEeCC
Confidence            34556  89999999999999999999999999999999999999999995 8877654311  2567899999999999


Q ss_pred             CCCccccCCCCCCcchHHHHHHHHHHHHhhhc-cCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeE
Q psy18119         79 FSTGERKTRPRGDRKTSEISLQLRQAVSAAIM-SEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVA  157 (263)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~-l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~a  157 (263)
                      |+++++++++.+++++.+++++++++|+++++ .+.|||+ |+|+++||++|||+++|+++|+++||+|+||||++++++
T Consensus       426 ~st~e~~~~g~~~~reie~~~li~raL~~vI~~~~~~P~t-I~V~~~VLesDGs~~~Asi~aa~lAL~dAgIP~k~~Vaa  504 (757)
T 1e3p_A          426 YSVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYA-IRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAG  504 (757)
T ss_dssp             GGGTCCCCCSSCCHHHHHHHHHHHHHHGGGCCCTTTSCEE-EEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCCSSCCEE
T ss_pred             cccccccCCCCCchhHHHHHHHHHHHHHHhccccccCCEE-EEEEEEEEECCCCHHHHHHHHHHHHHHHcCCCcccceEE
Confidence            99998876667899999999999999999998 6889985 999999999999999999999999999999999999999


Q ss_pred             EEEEec----CC----eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEeccc---CChhHHHHHHHHHHHHHHHHHHHH
Q psy18119        158 CSASLA----GD----TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK---LHLDHLPRVLDCALKGCADIHAIL  226 (263)
Q Consensus       158 vt~~~~----~~----~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~---i~~~~l~~~i~~A~~~~~~i~~~i  226 (263)
                      +|++++    ++    .+++||+..|+..++..++|+.  +.++|+.+++.|.   ++.+.+.+|++.|.+++.+|++.|
T Consensus       505 vs~gli~eg~dg~~~~~iLlDp~~~Ed~~gd~d~~Va~--t~~~It~lQ~~gk~~gi~~e~l~~aL~~A~~~~~~I~~~m  582 (757)
T 1e3p_A          505 IAMGLISQEINGETHYVALTDILGAEDAFGDMDFKVAG--TKEFVTALQLDTKLDGIPASVLAAALKQARDARLHILDVM  582 (757)
T ss_dssp             EEEEEEEEESSSCEEEEEEESCCHHHHHHCSEEEEEEE--CSSSEEEEEEEECSSCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEecCCCCccceeEEeCCCHHHHhccCceEEEEe--cCCeEEEEEEcCCccccCHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999    43    7899999999999999999985  4688999999875   599999999999999999999999


Q ss_pred             HHHHHHHHHHhhccCCCC-----ccccccceecCCcc
Q psy18119        227 DTAIKQHLIKVAGARGLG-----RKFQLGQLTGKKKE  258 (263)
Q Consensus       227 ~~~l~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~  258 (263)
                      +++|.++ .+...+.+..     +.-..|+++|++|.
T Consensus       583 ~~al~~~-~~~~~~ap~~~~~~I~~~ki~~vIG~gGk  618 (757)
T 1e3p_A          583 MEAIDTP-DEMSPNAPRIITVKIPVDKIGEVIGPKRQ  618 (757)
T ss_dssp             HHHCSSC-CCCCTTSCBCCCC----------------
T ss_pred             HHHhccc-ccccccCceeEEEEEChHHeehcccccce
Confidence            9999887 5555554432     55677889988753

>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=1.3e-44  Score=341.87  Aligned_cols=227  Identities=23%  Similarity=0.354  Sum_probs=197.7

Q ss_pred             cccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEE-EcCCCCCCCC--cCCCCeEEEEEEEeeCCC
Q psy18119          3 LLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKS--IKVHGSVLINFQYSMAVF   79 (263)
Q Consensus         3 ~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V-~gp~~~~~~~--~~~~~~~~l~v~~~~~~~   79 (263)
                      .|.+  +|+|+|||.++|+|+|.+++|+++++||||+|++|+|+|+|+| .||.++.+..  ...++++.+.++|+++||
T Consensus       308 ~il~--~g~R~DGR~~~elRpi~i~~g~l~~a~GSal~~~G~T~Vl~~Vt~gp~~~~~~~~~l~~~~~g~~~~~y~~~P~  385 (549)
T 3gme_A          308 RVLA--GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTDTFLFHYNFPPY  385 (549)
T ss_dssp             HHHH--TCCCTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEC---------------CCEEEEEECCGG
T ss_pred             HHhc--CCCCCCCCCCCCccceEEEECCCCCCCceEEEEECCeEEEEEEEecCcccccCccccCCCCceEEEEEEEeCCC
Confidence            4555  8999999999999999999999999999999999999999999 5886654321  123578899999999999


Q ss_pred             CCccccCCCCCCcchHHHHHHHHHHHHhhhc-cCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEE
Q psy18119         80 STGERKTRPRGDRKTSEISLQLRQAVSAAIM-SEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVAC  158 (263)
Q Consensus        80 ~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~-l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~av  158 (263)
                      +++++++++.+++++.+++++++++|+++|+ .++||++ |+|+++||++|||.++|++||+++||+|+||||+++++++
T Consensus       386 st~e~~~~g~~~~Reie~~~li~raL~~vI~~~~~~P~t-I~V~~~VLesDGs~~~AsI~aa~lAL~DAGvPm~~~Vaav  464 (549)
T 3gme_A          386 SVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYT-VRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGI  464 (549)
T ss_dssp             GTTCCCCSSCCCSSHHHHHHHHHHHHTTTCCCTTTCCCE-EEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCCSSCCEEE
T ss_pred             CcCCcccCCCCChhHHHHHHHHHHHHHHhcCccccCCeE-EEEEEEEEECCCCHHHHHHHHHHHHHHhCCCCcccceeEE
Confidence            9998776667889999999999999999999 5789985 9999999999999999999999999999999999999999


Q ss_pred             EEEecCC----eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEeccc---CChhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        159 SASLAGD----TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK---LHLDHLPRVLDCALKGCADIHAILDTAIK  231 (263)
Q Consensus       159 t~~~~~~----~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~---i~~~~l~~~i~~A~~~~~~i~~~i~~~l~  231 (263)
                      ++|++++    .+++||+..|+..++..+.|+.  +.+.++.+++++.   |+.+++.+++++|.+++.+|++.+++++.
T Consensus       465 s~Gli~~g~~~~iL~D~~~~Ed~~~d~d~~Va~--t~~gitalqmd~ki~G~s~~~l~~~L~~A~~g~~~I~~~m~~al~  542 (549)
T 3gme_A          465 AMGLVKEGDNYVVLSDILGDEDHLGDMDFKVAG--SRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQAIN  542 (549)
T ss_dssp             EEEEEEETTEEEEEESCCHHHHHHSSEEEEEEE--CSSCEEEEEEEECCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             EEEEEcCCCceEEEecCChHHHccCCceEEEEe--cCCCeEEEEEccccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999976    7899999999999999999997  3456889988754   79999999999999999999999999987


Q ss_pred             HHH
Q psy18119        232 QHL  234 (263)
Q Consensus       232 ~~~  234 (263)
                      +..
T Consensus       543 ~pr  545 (549)
T 3gme_A          543 APR  545 (549)
T ss_dssp             SCC
T ss_pred             hhh
Confidence            643

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

Probab=100.00  E-value=6.1e-44  Score=347.91  Aligned_cols=251  Identities=22%  Similarity=0.320  Sum_probs=192.9

Q ss_pred             cccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEE-EcCCCCCCCC--cCCCCeEEEEEEEeeCCC
Q psy18119          3 LLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAV-YGPRPVRNKS--IKVHGSVLINFQYSMAVF   79 (263)
Q Consensus         3 ~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V-~gp~~~~~~~--~~~~~~~~l~v~~~~~~~   79 (263)
                      ++.+  +++|+|||.++|+|+|.+++|++++++|||+|++|+|+|+|+| .||.++++..  ...++.+.+.++|.++||
T Consensus       314 ~i~~--~g~R~DGR~~~elRpI~ie~gvl~~a~GSAl~~~G~TqVL~~Vt~gp~e~~~~~d~l~~~~~g~~~~~y~~~P~  391 (723)
T 3cdi_A          314 RVLA--GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGERTDTFLFHYNFPPY  391 (723)
T ss_dssp             HHHT--TCCCTTSCCTTCCCCEEEEESCSTTSSEEEEEEETTEEEEEEEEECC-------------CTTSEEEEEECCGG
T ss_pred             HHhc--cCcCCCCCCccccccceEEeCCCCCCCeEEEEEECCcEEEEEEEecCcccccCCcccCCCCceEEEEEEecCCC
Confidence            4566  8999999999999999999999999999999999999999999 5887643320  113566788899999999


Q ss_pred             CCccccCCCCCCcchHHHHHHHHHHHHhhhcc-CCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEE
Q psy18119         80 STGERKTRPRGDRKTSEISLQLRQAVSAAIMS-EVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVAC  158 (263)
Q Consensus        80 ~~~~~~~~~~~~~~~~~l~~~l~~~l~~~i~l-~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~av  158 (263)
                      +++++++.+.+++++.+++++++++|++++++ +.|||+ |+|+++||++|||+++|+++|+++||+|+||||+++++++
T Consensus       392 st~e~~r~g~p~~REi~~~~li~raL~~vI~~~~~~p~t-I~Vd~~VLesdGs~~~Asi~aa~lAL~dAgVPl~~~vaav  470 (723)
T 3cdi_A          392 SVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYT-VRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGI  470 (723)
T ss_dssp             GGTCCCCC-----CTTHHHHHHHHHHHTTSCCSSSSCSC-EEEEEEEEECSSCHHHHHHHHHHHHHHHTTCCCSSCCEEE
T ss_pred             CccccccCCCCCHHHHHHHHHHHHHHHHhcCcccCCCEE-EEEEEEEEeCCCCHHHHHHHHHHHHHhcCCCCcccceeeE
Confidence            99887655557788889999999999999996 779974 9999999999999999999999999999999999999999


Q ss_pred             EEEecC-C---eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc---cCChhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        159 SASLAG-D---TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ---KLHLDHLPRVLDCALKGCADIHAILDTAIK  231 (263)
Q Consensus       159 t~~~~~-~---~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G---~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~  231 (263)
                      |+++++ +   .+|+||+..||..+++.++|+. +..| |+.+++.|   +|+.++|.+++++|.+++.+|++.|+++|.
T Consensus       471 s~gli~~g~~~~iL~Dp~~~Ed~~~d~d~~Va~-t~~g-I~~lq~~gk~~~is~e~l~~~l~~A~~~~~~I~~~m~~al~  548 (723)
T 3cdi_A          471 AMGLVKEGDNYVVLSDILGDEDHLGDMDFKVAG-SRDG-ISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQAIN  548 (723)
T ss_dssp             EEEEEEETTEEEEESSCCGGGGGGCSEEEEEEE-CSSC-EEEEEEEECSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             EEEEEcCCCceEEEECCChHHhhhccceeeecc-cCCc-eEEEEeCCccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            999996 3   4999999999999999999997 4455 99999984   589999999999999999999999999999


Q ss_pred             HHHHHhhccCCCC-----ccccccceecCCcc
Q psy18119        232 QHLIKVAGARGLG-----RKFQLGQLTGKKKE  258 (263)
Q Consensus       232 ~~~~~~~~~~~~~-----~~~~~~~~~~~~~~  258 (263)
                      ++..+...+.+..     +....|.++|++|.
T Consensus       549 ~~~~~~~~~ap~~~~~~i~~~ki~~~ig~gGk  580 (723)
T 3cdi_A          549 APRGDISEFAPRIHTIKINPDKIKDVIGKGGS  580 (723)
T ss_dssp             --------------------------------
T ss_pred             hcchhccccCceEEEEEECHHHhcccccccce
Confidence            9887777666533     55666788888774

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

Probab=100.00  E-value=3.1e-45  Score=313.48  Aligned_cols=208  Identities=22%  Similarity=0.307  Sum_probs=167.6

Q ss_pred             CCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCCCCCcchHHH
Q psy18119         18 GHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEI   97 (263)
Q Consensus        18 ~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~~~~~~~~~l   97 (263)
                      ++|+|++++++|++++++|||+|++|+|+|+|+|+||.++++. ...+++++|+++|.  |++.       +++++  ++
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 AGRLREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHAS-KASDEAMTLDISYR--ANCG-------DNKFN--VL   69 (222)
T ss_dssp             -CCCCCBCCBSCCC----CCCBCCBTTCEEECCCCSSCC--------------CCCSS--CCCC---------CCS--SC
T ss_pred             CCcccceEEEECCCCCCCeEEEEEECCcEEEEEEECCCCCccc-ccCCceEEEEEEEc--CCCC-------CCCHH--HH
Confidence            5799999999999999999999999999999999999876654 34678888877765  4431       12222  78


Q ss_pred             HHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecCCchhhh
Q psy18119         98 SLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEET  177 (263)
Q Consensus        98 ~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDPt~~Ee~  177 (263)
                      +++|++.|+++++++.||+|.|+|+++||++||++++|++||+++||+|+||||++++++++++++++.+++|||..|+.
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             cCCCeEEEEE---eCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy18119        178 LGGPNLTVAA---LPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKV  237 (263)
Q Consensus       178 ~~~~~l~v~~---~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~  237 (263)
                      .+++.++|++   +++.++|+++++.|.++.+++.++++.|.++++++.++++++++++..+-
T Consensus       150 ~~~~~l~va~~~~~~~~~~i~~vq~~g~~~~~~l~~~l~~a~~~~~~i~~~~~~~l~~~~~~~  212 (222)
T 3krn_A          150 ASTGRVLFSVCKGSDGHPEVCAMDAIGHWDFIQLEAAWSLAQPSASAIFDFYKTVMKRKLSVD  212 (222)
T ss_dssp             SCC-CCCCEECCCSSSSCCEEEECCBSSCTTHHHHTHHHHTTHHHHHHHHHHHHHHHHHHHHC
T ss_pred             ccCccEEEEEEccCCCCCCEEEEEEeCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcch
Confidence            9999999999   66679999999999999999999999999999999999999999887643

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

Probab=100.00  E-value=8.2e-35  Score=280.04  Aligned_cols=213  Identities=17%  Similarity=0.205  Sum_probs=187.9

Q ss_pred             CCcceEEEeCCCCC-CceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCcc-----ccCCCCCCcc
Q psy18119         20 ELRKIRCRLGVFSQ-SDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGE-----RKTRPRGDRK   93 (263)
Q Consensus        20 e~R~i~i~~g~l~~-a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~-----~~~~~~~~~~   93 (263)
                      .-|++.+++|.+++ |+|||++++|+|+|+|+|++|.++++.     +++.|.|+|+..+++.+.     .++.++++++
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 GNRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKPSPS-----QFMPLVVDYRQKAAAAGRIPTNYLRREVGTSDK   87 (630)
T ss_dssp             SSSEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCCSS-----SSCCEEEEEECSEETTTTEECTTC-----CCHH
T ss_pred             CCEEEEEEeCCccccCCeeEEEEECCeEEEEEEEecCCCCCC-----CeeEEEEEEEecccccCCCCccccccCCCCCHH
Confidence            35899999999986 999999999999999999999886642     677899999988887642     2233468889


Q ss_pred             hHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCCh--hHHHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecC
Q psy18119         94 TSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGN--FCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDI  171 (263)
Q Consensus        94 ~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~--~~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDP  171 (263)
                      +.+++++|+|.|+++++++.||.  ++|+|+||++||+.  ..+|+||+++||++++|||++.+++|+++++++.+|+||
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 EILTSRIIDRSIRPLFPAGYFYD--TQVLCNLLAVDGVNEPDVLAINGASVALSLSDIPWNGPVGAVRIGIIDGEYVVNP  165 (630)
T ss_dssp             HHHHHHHHHHHHGGGSCTTCCCC--EEEEEEEEECCSSSCHHHHHHHHHHHHHHHSSSCCCCCCEEEEEEEETTEEEESC
T ss_pred             HHHHHHHHhHHhhhcccccCCCc--eEEEEEEEECCCCCCHHHHHHHHHHHHHhccCCCcCCCeEEEEEEEECCEEEECC
Confidence            99999999999999999888887  55789999999998  779999999999999999999999999999999999999


Q ss_pred             CchhhhcCCCeEEEEEeCCCCcEEEEEeccc-CChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy18119        172 SHLEETLGGPNLTVAALPLSGKVAVMELSQK-LHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGA  240 (263)
Q Consensus       172 t~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~-i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~~~  240 (263)
                      |..|++.++..++|+++ ..++|++++..|. ++++++.++++.|.++++.+++++++++++.....+.+
T Consensus       166 t~~E~~~s~~dl~Va~t-~~~~i~mve~~~~~~se~~~~~al~~a~~~~~~l~~~~~~~~~~~~~~~~~~  234 (630)
T 3u1k_A          166 TRKEMSSSTLNLVVAGA-PKSQIVMLEASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTP  234 (630)
T ss_dssp             CHHHHHTEEEEEEEEEE-TTTEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCCC
T ss_pred             CHHHHhhCCceEEEEEc-cCCcEEEEECCCccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCccC
Confidence            99999999999999995 5688999999886 99999999999999999999999999988877554444

>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=7.9e-30  Score=241.11  Aligned_cols=213  Identities=13%  Similarity=0.159  Sum_probs=180.6

Q ss_pred             CcceEEEeCCCC-CCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccc-----cCCCCCCcch
Q psy18119         21 LRKIRCRLGVFS-QSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGER-----KTRPRGDRKT   94 (263)
Q Consensus        21 ~R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~-----~~~~~~~~~~   94 (263)
                      -|++.+++|.+. +|+||+++++|+|+|+|+|+++.+++..    .+.+.|.|+|....++.+..     ++.++++.++
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 QHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPG----QDFFPLTVNYQERTYAAGRIPGSFFRREGRPSEGE   88 (549)
T ss_dssp             TEEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCCTT----CCSCCEEEEEEECGGGTTCCCSCC-----CCCHHH
T ss_pred             CEEEEEEECCccCCCCeEEEEEECCEEEEEEEEecCCCCCC----CCCccceeeeeeehhhcccCCCcCcCcCCCCChhh
Confidence            589999999886 5999999999999999999998765542    35677999997544443322     2335688999


Q ss_pred             HHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChh--HHHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecCC
Q psy18119         95 SEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNF--CACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDIS  172 (263)
Q Consensus        95 ~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~--~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDPt  172 (263)
                      .+++++|.|.|+++++...++.  ++|+++||+.||+..  .+++||+++||+.++||+++.+.+|++|++++.+++|||
T Consensus        89 ~l~~RlIdR~lRplfp~~~~~e--vqI~~~Vls~D~~~~pd~~ai~gAs~AL~~s~iP~~gpvaaV~Vg~i~g~~vlnPt  166 (549)
T 3gme_A           89 TLIARLIDRPIRPLFPEGFVNE--VQVIATVVSVNPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPT  166 (549)
T ss_dssp             HHHHHHHHHHHGGGSCTTCCSC--EEEEEEEEECCSSSCHHHHHHHHHHHHHHHHCSCCCCCCEEEEEEEETTEEEESCC
T ss_pred             hHHHHHhCCccccccccCCccc--EEEEEEEEecCCCCcHHHHHHHHHHHHHhccCCCcCCCeeEEEEEEECCEEEECCC
Confidence            9999999999999998776554  888999999998663  578999999999999999999999999999999999999


Q ss_pred             chhhhcCCCeEEEEEeCCCCcEEEEEecc-cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy18119        173 HLEETLGGPNLTVAALPLSGKVAVMELSQ-KLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGAR  241 (263)
Q Consensus       173 ~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G-~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~~~~  241 (263)
                      ..|++.++..++|+..  .+.|++++..| .++.+++.++++.|.++++.+.+++++++++.....+.+.
T Consensus       167 ~~e~~~s~~dl~va~t--~~~i~mve~e~~~~se~~~~~al~~a~~~i~~l~~~q~~~~~~~~~~~~~~~  234 (549)
T 3gme_A          167 QDELKESKLDLVVAGT--EAAVLMVESEAELLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQ  234 (549)
T ss_dssp             TTTTTTCSBCEEEEEC--SSCEEEEEEEEEEECHHHHHHHHHHHHHHTHHHHHHHHHHHHHHCCCCCCCC
T ss_pred             HHHHhhCceEEEEEec--CCeEEEEEccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCC
Confidence            9999999999999983  34599999886 6999999999999999999999999999988765544443

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

Probab=99.97  E-value=2.7e-29  Score=244.06  Aligned_cols=212  Identities=17%  Similarity=0.167  Sum_probs=180.3

Q ss_pred             CCcceEEEeCCCC-CCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCcc-----ccCCCCCCcc
Q psy18119         20 ELRKIRCRLGVFS-QSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGE-----RKTRPRGDRK   93 (263)
Q Consensus        20 e~R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~-----~~~~~~~~~~   93 (263)
                      .-|++.+++|.+. +|+||+++++|+|+|+|+|+++.++++.    .++++|.++|....++.+.     .++.++++.+
T Consensus        26 ~~R~i~ietg~~ak~A~GSvlv~~GdT~VL~tv~~~~~~~~g----~df~pltveY~ek~~a~G~iPg~~~~REGrps~~  101 (726)
T 4aid_A           26 GGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPG----QDFFPLTVNYQEKTFAAGKIPGGFFKREGRPSEK  101 (726)
T ss_dssp             TTEEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCCTT----CCSCCEEEEEEECGGGGTCCCCSTTCSCCSCCHH
T ss_pred             CCeeEEEEECCccCCCCeeEEEEECCeEEEEEEEecCCCCCC----CCCcCceeeeeeehhhcccCCCcccCCCCCCCch
Confidence            3689999999886 5999999999999999999998766542    3667799999754333321     1233568899


Q ss_pred             hHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChh--HHHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecC
Q psy18119         94 TSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNF--CACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDI  171 (263)
Q Consensus        94 ~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~--~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDP  171 (263)
                      +.+++++|.|.|+++++...++  .++|+|+||+.||+..  .+|+||+++||++++||+++.+.+|++|++++.+++||
T Consensus       102 ~~li~RlIdR~lRplf~~~~~~--evqI~~~Vls~Dg~~~~d~~ai~gAs~AL~~s~iP~~~~vaaV~Vg~i~g~~vldP  179 (726)
T 4aid_A          102 ETLVSRLIDRPIRPLFVKGFKN--EVQVVVTVLQHDLENDPDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNP  179 (726)
T ss_dssp             HHHHHHHHHHHHGGGBCTTCCS--CEEEEEEEEECCSSSCHHHHHHHHHHHHHHHHTCSBCCCCEEEEEEEETTEEEESC
T ss_pred             hhhHHHHhCCccccccccCCcc--ceEEEEEEEecCCCCChhHHHHHHHHHHHHhcCCCcCCCeEEEEEEEECCEEEECC
Confidence            9999999999999999877655  4888999999999753  57999999999999999999999999999999999999


Q ss_pred             CchhhhcCCCeEEEEEeCCCCcEEEEEecc-cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy18119        172 SHLEETLGGPNLTVAALPLSGKVAVMELSQ-KLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAG  239 (263)
Q Consensus       172 t~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G-~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~~  239 (263)
                      |..|++.++..++|+.. .. .|++++..+ .|+.+++.++++.|.++++.+.+++++++++.....+.
T Consensus       180 t~~E~~~s~~dl~va~t-~~-~i~mve~~~~~~se~~~~~al~~a~~~i~~l~~~q~~~~~~~g~~k~~  246 (726)
T 4aid_A          180 TLDEMKESKMDLVVAGT-AD-AVMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFA  246 (726)
T ss_dssp             CHHHHHTCSEEEEEEEC-SS-CEEEEEEEESSBCHHHHHHHHHHHHHHTHHHHHHHHHHHHHHCCCCCC
T ss_pred             CHHHHhhCceeEEEEEe-CC-eEEEEEccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccc
Confidence            99999999999999983 33 499999886 69999999999999999999999999998876544333

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

Probab=99.97  E-value=4.3e-29  Score=243.56  Aligned_cols=211  Identities=13%  Similarity=0.156  Sum_probs=180.1

Q ss_pred             cceEEEeCCC-CCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccc-----cCCCCCCcchH
Q psy18119         22 RKIRCRLGVF-SQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGER-----KTRPRGDRKTS   95 (263)
Q Consensus        22 R~i~i~~g~l-~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~-----~~~~~~~~~~~   95 (263)
                      |++.+++|.+ .+|+||+++++|+|+|+|+|+++.++++.    .+++.++|+|....++.+..     ++.+++++++.
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 HTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPG----QDFFPLTVNYQERTYAAGRIPGSFFRREGRPSEGET   95 (723)
T ss_dssp             EEEEEEESSSCTTSSEEEEEEETTEEEEEEEEECSSCCSS----CCSCCEEEEEEECGGGGTCCCC-------CCCHHHH
T ss_pred             EEEEEEeCccccCCCeeEEEEECCEEEEEEEEecCCCCCC----CCeeeEEEEEeEeccccccCCCccccCCCCCChHHh
Confidence            4899999988 47999999999999999999998766542    36778999999765554432     23446899999


Q ss_pred             HHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCCh-hH-HHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecCCc
Q psy18119         96 EISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGN-FC-ACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISH  173 (263)
Q Consensus        96 ~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~-~~-a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDPt~  173 (263)
                      +++++|+|.|+++++.+.++  .++|+++||++||+. .+ +|+|||++||+.++||+.+.+++|++|++++.+|+|||.
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 LIARLIDRPIRPLFPEGFVN--EVQVIATVVSVNPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQ  173 (723)
T ss_dssp             HHHHHHHHHHGGGSCTTCCS--CEEEEEEEEECCTTSCHHHHHHHHHHHHHHHHTSSCCCCCCCEEEEEETTEEEESCCT
T ss_pred             HHHHHhCccchhcccccCcc--eEEEEEEEEEcCCCCCHHHHHHHHHHHHHHhcCCCCCCCeEEEEEEEECCEEEECcCH
Confidence            99999999999998866544  599999999999996 44 999999999999999999999999999999999999999


Q ss_pred             hhhhcCCCeEEEEEeCCCCcEEEEEecc-cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy18119        174 LEETLGGPNLTVAALPLSGKVAVMELSQ-KLHLDHLPRVLDCALKGCADIHAILDTAIKQHLIKVAGA  240 (263)
Q Consensus       174 ~Ee~~~~~~l~v~~~~~~~~i~~i~~~G-~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~~~~~~  240 (263)
                      .|++.++..++|+.  +...+++++..+ .++++++.++++.|.+.++.+.+++++++++.....+.+
T Consensus       174 ~e~~~s~~~lvvag--t~~~i~mve~~~~~~se~~~~~al~~a~~~~~~l~~~~~~~~~~~~~~~~~~  239 (723)
T 3cdi_A          174 DELKESKLDLVVAG--TEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDW  239 (723)
T ss_dssp             TGGGGCSEEEEEEE--CSSCEEEEEEEEEEECHHHHHHHHHHHHHHTHHHHHHHHHHHHHTCCCCCCC
T ss_pred             HHHHhCCceEEEEc--cCCEEEEEeCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccC
Confidence            99999999999997  345599999776 499999999999999999999999999988765544444

>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-28  Score=240.27  Aligned_cols=209  Identities=15%  Similarity=0.137  Sum_probs=179.4

Q ss_pred             CcceEEEeCCC-CCCceeEEEEe-CCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCcc-----ccCCCCCCcc
Q psy18119         21 LRKIRCRLGVF-SQSDGSAYIEQ-GNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGE-----RKTRPRGDRK   93 (263)
Q Consensus        21 ~R~i~i~~g~l-~~a~GSa~v~~-G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~-----~~~~~~~~~~   93 (263)
                      -|++.+++|.+ .+|+||+++++ |+|+|+|+|++|.++++.    .+++.|+|+|....++.+.     .+|.++++.+
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 TRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQ----LDFFPLTVDVEERMYAAGKIPGSFFRREGRPSED  111 (757)
T ss_dssp             EEEEEEEESSSCTTSSEEEEEEETTTEEEEEEEEEEEEECTT----CSSCCEEEEEEECGGGGTCCCCSTTSSCCSCCHH
T ss_pred             CEeEEEEECccccCCCeEEEEEECCCeEEEEEEEecCCCCCC----CCCccEEEEEEecccccccCCCcccccCcCCChH
Confidence            48999999997 57999999999 999999999998776542    3567799999755444321     2334568899


Q ss_pred             hHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCCh--hHHHHHHHHHHHHHcCCCccCceeEEEEEecCCeeEecC
Q psy18119         94 TSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGN--FCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDI  171 (263)
Q Consensus        94 ~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~--~~a~i~Aa~~AL~dagIp~~~~~~avt~~~~~~~~lvDP  171 (263)
                      +++++++|.|.|+++++...  +..|+|+|+||+.||+.  ..+|+|||++||++++|||++.+.||++|++++.+++||
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 AILTCRLIDRPLRPSFKKGL--RNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFP  189 (757)
T ss_dssp             HHHHHHHHHHHHGGGBCTTB--CEEEEEEEEEEECCTTSCCHHHHHHHHHHHHHHTTSSBCCCCEEEEEEEETTEEEESC
T ss_pred             HHHHHHHHCCcchhccccCC--CCceEEEEEEEEECCCCCHHHHHHHHHHHHHhccCCCCCCceEEEEEEEECCEEEECC
Confidence            99999999999999987653  23699999999999976  889999999999999999999999999999999999999


Q ss_pred             CchhhhcCCCeEEEEEeC---CCCcEEEEEe-------------cccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        172 SHLEETLGGPNLTVAALP---LSGKVAVMEL-------------SQKLHLDHLPRVLDCALKGCADIHAILDTAIKQHLI  235 (263)
Q Consensus       172 t~~Ee~~~~~~l~v~~~~---~~~~i~~i~~-------------~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~l~~~~~  235 (263)
                      |..|++.++..++|+...   ..+.|.+++.             .+.++.+++.++++.|.++++.+.+++++++++...
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            999999999999999842   1667899998             347999999999999999999999999998876544

---

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	263
d2je6b1	148	d.14.1.4 (B:8-155) Exosome complex exonuclease 1,	3e-34
d2nn6b1	145	d.14.1.4 (B:6-150) Exosome complex exonuclease RRP	1e-33
d2ba0d1	144	d.14.1.4 (D:10-153) Exosome complex exonuclease 1,	2e-32
d1r6la1	151	d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Pseu	2e-30
d2ba0g1	176	d.14.1.4 (G:3-178) Exosome complex exonuclease 2,E	5e-30
d1e3ha3	137	d.14.1.4 (A:346-482) Polynucleotide phosphorylase/	5e-30
d2nn6e1	187	d.14.1.4 (E:5-191) Exosome complex exonuclease RRP	6e-30
d2nn6d1	122	d.14.1.4 (D:25-146) Exosome complex exonuclease RR	8e-30
d2nn6c1	181	d.14.1.4 (C:7-187) Exosome complex exonuclease RRP	7e-29
d2nn6f1	147	d.14.1.4 (F:29-175) Exosome complex exonuclease MT	2e-27
d1udsa1	149	d.14.1.4 (A:2-150) Ribonuclease PH, domain 1 {Aqui	1e-26
d1oysa1	151	d.14.1.4 (A:1-151) Ribonuclease PH, domain 1 {Baci	7e-26
d2nn6a1	184	d.14.1.4 (A:1-184) Exosome complex exonuclease RRP	7e-26
d2je6a1	191	d.14.1.4 (A:1-191) Exosome complex exonuclease 2,E	1e-23
d1e3ha2	149	d.14.1.4 (A:3-151) Polynucleotide phosphorylase/gu	1e-16
d2nn6b2	90	d.101.1.1 (B:151-240) Exosome complex exonuclease	5e-15
d2nn6f2	95	d.101.1.1 (F:176-270) Exosome complex exonuclease	2e-14
d2je6b2	86	d.101.1.1 (B:156-241) Exosome complex exonuclease	2e-12
d2nn6d2	89	d.101.1.1 (D:147-235) Exosome complex exonuclease	4e-12
d2ba0d2	99	d.101.1.1 (D:154-252) Exosome complex exonuclease	7e-09
d2ba0g2	79	d.101.1.1 (G:179-257) Exosome complex exonuclease	4e-08
d1r6la2	88	d.101.1.1 (A:152-239) Ribonuclease PH, domain 2 {P	8e-08
d2nn6c2	89	d.101.1.1 (C:188-276) Exosome complex exonuclease	2e-07
d1udsa2	105	d.101.1.1 (A:151-255) Ribonuclease PH, domain 2 {A	6e-07
d2nn6a2	118	d.101.1.1 (A:185-302) Exosome complex exonuclease	1e-06
d1oysa2	86	d.101.1.1 (A:152-237) Ribonuclease PH, domain 2 {B	2e-05
d2je6a2	84	d.101.1.1 (A:192-275) Exosome complex exonuclease	4e-05
d2nn6e2	94	d.101.1.1 (E:192-285) Exosome complex exonuclease	2e-04

>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 =  118 bits (297), Expect = 3e-34
 Identities = 62/140 (44%), Positives = 89/140 (63%), Gaps = 1/140 (0%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           G R DGR+  ELR I+  LGV   +DGSA  E GNTK +AAVYGP+ +  + + +    +
Sbjct: 10  GKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAV 69

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           +  +Y M  FST ERK      R+  E+S  +R+A+ +A++ E+ PR+ ID+F E+LQAD
Sbjct: 70  LRVRYHMTPFSTDERKNPAP-SRREIELSKVIREALESAVLVELFPRTAIDVFTEILQAD 128

Query: 130 GGNFCACVNAATLALIDAGI 149
            G+    + AA+LAL DAGI
Sbjct: 129 AGSRLVSLMAASLALADAGI 148

>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 =  117 bits (293), Expect = 1e-33
 Identities = 92/141 (65%), Positives = 113/141 (80%), Gaps = 1/141 (0%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVR-NKSIKVHGSV 68
           G R DGRR  ELRKI+ R+GVF+Q+DGSAYIEQGNTK LA VYGP  +R +++  +    
Sbjct: 5   GYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRA 64

Query: 69  LINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQA 128
           L+N QYS A FSTGERK RP GDRK+ E+ LQLRQ   AAI++++HPRSQIDI+V+VLQA
Sbjct: 65  LVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQA 124

Query: 129 DGGNFCACVNAATLALIDAGI 149
           DGG + ACVNAATLA++DAGI
Sbjct: 125 DGGTYAACVNAATLAVLDAGI 145

>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 =  114 bits (285), Expect = 2e-32
 Identities = 72/140 (51%), Positives = 97/140 (69%), Gaps = 1/140 (0%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
           GLR DGR+  ELR I+    V  ++DGS Y+E G  KV+AAV+GPR V  + ++     +
Sbjct: 6   GLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKAI 65

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQAD 129
           I ++Y+MA FS  ERK RP  DR++ EIS   ++A  A IM E+ PRS IDIFVEVLQAD
Sbjct: 66  IRYRYNMAPFSVEERK-RPGPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQAD 124

Query: 130 GGNFCACVNAATLALIDAGI 149
            G+  AC+NAA++AL+DAG+
Sbjct: 125 AGSRTACLNAASVALVDAGV 144

>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 =  109 bits (272), Expect = 2e-30
 Identities = 44/146 (30%), Positives = 70/146 (47%), Gaps = 5/146 (3%)

Query: 12  RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLIN 71
           R  GR   +LR IR        ++GS  +E G+TKV+  V        + +K  G   + 
Sbjct: 3   RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESG-VPRFLKGQGQGWLT 61

Query: 72  FQYSMAVFSTGERKTRPRGDRKTSEISLQ----LRQAVSAAIMSEVHPRSQIDIFVEVLQ 127
            +Y M   STGER  R     K    +L+    + +++ AA+       + + I  +V+Q
Sbjct: 62  AEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCDVIQ 121

Query: 128 ADGGNFCACVNAATLALIDAGIPMRE 153
           ADGG   A +  AT+ALIDA   +++
Sbjct: 122 ADGGTRTASITGATVALIDALAVLKK 147

>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 =  108 bits (271), Expect = 5e-30
 Identities = 30/152 (19%), Positives = 59/152 (38%), Gaps = 5/152 (3%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
             R DGR   E RK+     V  +++GSA ++ G+T+V+  V              G ++
Sbjct: 19  NERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYPDTPDRGVII 78

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPR-----SQIDIFVE 124
           +N +       T E         + + +  +  +   A  +S++          + + + 
Sbjct: 79  VNAELVPLASPTFEPGPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIH 138

Query: 125 VLQADGGNFCACVNAATLALIDAGIPMREYVV 156
            L  DG    A   AA  AL++  +P   + +
Sbjct: 139 ALDDDGNLLDASALAAIAALMNTKVPAERFDL 170

>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 =  107 bits (268), Expect = 5e-30
 Identities = 26/136 (19%), Positives = 51/136 (37%), Gaps = 3/136 (2%)

Query: 20  ELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVF 79
           ++R +   +    +  GSA  E+G T++L           + +     V          F
Sbjct: 2   DIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNF 61

Query: 80  ---STGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCAC 136
              S GE        R+         +A+   + +       I    E L ++G      
Sbjct: 62  PPYSVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGS 121

Query: 137 VNAATLALIDAGIPMR 152
           V A+T++L++AG+P++
Sbjct: 122 VCASTMSLLNAGVPLK 137

>d2nn6e1 d.14.1.4 (E:5-191) Exosome complex exonuclease RRP42 {Human (Homo sapiens) [TaxId: 9606]} Length = 187

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP42
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  109 bits (272), Expect = 6e-30
 Identities = 34/149 (22%), Positives = 56/149 (37%), Gaps = 11/149 (7%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
            LR DGR   + R +     V S + GSA ++ G+T +L  V              G   
Sbjct: 17  DLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEG--Y 74

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEV--------HPRSQIDI 121
           + F    +  +T E + R   D   +EI+  L +  +     ++             + +
Sbjct: 75  LEFFVDCSASATPEFEGRGGDDL-GTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYV 133

Query: 122 FVEVLQADGGNFCACVNAATLALIDAGIP 150
            V +L+  G  F A   A   AL +  IP
Sbjct: 134 DVLLLECGGNLFDAISIAVKAALFNTRIP 162

>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 =  106 bits (266), Expect = 8e-30
 Identities = 39/132 (29%), Positives = 58/132 (43%), Gaps = 10/132 (7%)

Query: 18  GHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMA 77
           G  LR   C   + S+ DGSA   QG+T VLA VYGP  V+               ++ A
Sbjct: 1   GCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKV----------SKEIFNKA 50

Query: 78  VFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACV 137
                 R                +R    A ++  +HPR+ I + ++V+   G     C+
Sbjct: 51  TLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCL 110

Query: 138 NAATLALIDAGI 149
           NAA +AL+DAG+
Sbjct: 111 NAACMALVDAGV 122

>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 =  106 bits (264), Expect = 7e-29
 Identities = 32/174 (18%), Positives = 57/174 (32%), Gaps = 17/174 (9%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
             R DGR   E R     +G  S +DGSA ++ GNT V+  V       +      G   
Sbjct: 15  NCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKG--Y 72

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLR-------QAVSAAIMSEVHPRSQIDIF 122
           +     +    +   ++ P G+                         +S       +   
Sbjct: 73  VVPNVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCD 132

Query: 123 VEVLQADGGNFCACVNAATLALIDAGIPMREYVVACSASLAGDTPLVDISHLEE 176
           +  L  DG    AC  A   AL +  +P          ++  +T L +++  ++
Sbjct: 133 LICLDYDGNILDACTFALLAALKNVQLPE--------VTINEETALAEVNLKKK 178

>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 =  101 bits (251), Expect = 2e-27
 Identities = 46/146 (31%), Positives = 70/146 (47%), Gaps = 12/146 (8%)

Query: 15  GRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNK-----------SIK 63
            R    LR +  R G+ SQ+ GSAY+E G TKVL AV GPR                   
Sbjct: 2   TRDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGPRQAEGGERGGGPAGAGGEAP 61

Query: 64  VHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFV 123
                 +   +  A F+   R+  P G  +  E++L L++A+  A+    +PR+Q+++  
Sbjct: 62  AALRGRLLCDFRRAPFAGRRRR-APPGGCEERELALALQEALEPAVRLGRYPRAQLEVSA 120

Query: 124 EVLQADGGNFCACVNAATLALIDAGI 149
            +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 = 98.8 bits (245), Expect = 1e-26
 Identities = 39/146 (26%), Positives = 67/146 (45%), Gaps = 5/146 (3%)

Query: 12  RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLIN 71
           R+DGR+  +LR +  +       +GS  I  G TKV+        V N  +K  G   I 
Sbjct: 1   RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNW-LKGKGQGWIT 59

Query: 72  FQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVH----PRSQIDIFVEVLQ 127
            +YSM   +T +R  R     +    + ++++ +  A+ + V         I +  +V+Q
Sbjct: 60  AEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIGRAMRTAVELTKIGERTIWVDCDVIQ 119

Query: 128 ADGGNFCACVNAATLALIDAGIPMRE 153
           ADGG   A +  A +A+ DA I + +
Sbjct: 120 ADGGTATAAITGAFVAVADAIIKLHK 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 = 97.3 bits (241), Expect = 7e-26
 Identities = 40/146 (27%), Positives = 62/146 (42%), Gaps = 3/146 (2%)

Query: 11  LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSI---KVHGS 67
           +R+DGR+  ELR I   L   S  +GS  I  GNTKV+        V        K   +
Sbjct: 1   MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWIT 60

Query: 68  VLINFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQ 127
              +         T +  ++ +   +T EI   + +A+ A +  E      I I  +V+Q
Sbjct: 61  AEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQ 120

Query: 128 ADGGNFCACVNAATLALIDAGIPMRE 153
           ADGG   A +  A LA+  A   + +
Sbjct: 121 ADGGTRTASITGAFLAMAIAIGKLIK 146

>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 = 98.3 bits (244), Expect = 7e-26
 Identities = 28/150 (18%), Positives = 51/150 (34%), Gaps = 14/150 (9%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVL 69
             R DGR+ ++ R IR   G      G   +E G T+VL  V         +       +
Sbjct: 21  KKRLDGRQTYDYRNIRISFGT---DYGCCIVELGKTRVLGQVSCELVSPKLNRA--TEGI 75

Query: 70  INFQYSMAVFSTGERKTRPRGDRKTSEISLQLRQA--------VSAAIMSEVHPRSQIDI 121
           + F   ++  +    +   R      +++  + +           +  +       QI +
Sbjct: 76  LFFNLELSQMAAPAFE-PGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRV 134

Query: 122 FVEVLQADGGNFCACVNAATLALIDAGIPM 151
            + +L  DG    A   AA +AL     P 
Sbjct: 135 DLHLLNHDGNIIDAASIAAIVALCHFRRPD 164

>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 = 92.2 bits (228), Expect = 1e-23
 Identities = 28/153 (18%), Positives = 51/153 (33%), Gaps = 5/153 (3%)

Query: 10  GLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHG-SV 68
           G+R DGR+  + R +   L    ++DGSA ++ G T VLA          +     G  +
Sbjct: 26  GIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYEDTPNQGNLI 85

Query: 69  LINFQYSMAVFSTGERKTRPRGDRKTSEIS----LQLRQAVSAAIMSEVHPRSQIDIFVE 124
           +      +A  +                +           ++  ++        + + V 
Sbjct: 86  VNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVY 145

Query: 125 VLQADGGNFCACVNAATLALIDAGIPMREYVVA 157
           VL   G    AC  A+  AL +  +   E    
Sbjct: 146 VLDYGGNVLDACTLASVAALYNTKVYKVEQHSN 178

>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 = 72.9 bits (178), Expect = 1e-16
 Identities = 20/132 (15%), Positives = 40/132 (30%), Gaps = 3/132 (2%)

Query: 22  RKIRCRLGVFS-QSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFS 80
           R IR   G  + Q+ GSA     +  ++ +           +      +   +   A   
Sbjct: 18  RTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDVEERMYAAGK 77

Query: 81  TGERKTRPRG--DRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVN 138
                 R  G            + + +  +    +    Q+   +  L  D       +N
Sbjct: 78  IPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVVAIN 137

Query: 139 AATLALIDAGIP 150
           AA+ +   AG+P
Sbjct: 138 AASASTQLAGLP 149

>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 = 66.6 bits (162), Expect = 5e-15
 Identities = 41/89 (46%), Positives = 61/89 (68%)

Query: 150 PMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLP 209
           PMR++V ACSA     T L D+SH+EE  GGP L +A LP SG++A++E+  +LH DHL 
Sbjct: 1   PMRDFVCACSAGFVDGTALADLSHVEEAAGGPQLALALLPASGQIALLEMDARLHEDHLE 60

Query: 210 RVLDCALKGCADIHAILDTAIKQHLIKVA 238
           RVL+ A +   D+H +LD  ++QH+ + +
Sbjct: 61  RVLEAAAQAARDVHTLLDRVVRQHVREAS 89

>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 = 65.0 bits (158), Expect = 2e-14
 Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 4/94 (4%)

Query: 151 MREYVVACSASLA---GDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHL-D 206
           M + VV C  SLA     T L+D + LEE      LTVA +P+  +VA +  S +  L +
Sbjct: 1   MYDLVVGCGLSLAPGPAPTWLLDPTRLEEERAAAGLTVALMPVLNQVAGLLGSGEGGLTE 60

Query: 207 HLPRVLDCALKGCADIHAILDTAIKQHLIKVAGA 240
                +   L+GC  ++ +L  ++ +   +   A
Sbjct: 61  SWAEAVRLGLEGCQRLYPVLQQSLVRAARRRGAA 94

>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 = 59.5 bits (144), Expect = 2e-12
 Identities = 19/82 (23%), Positives = 40/82 (48%)

Query: 150 PMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLP 209
           PMR+ +   +   A    ++D++  E   G  ++ +A +P   +V + +L+  +  D   
Sbjct: 1   PMRDLIAGVAVGKADGVIILDLNETEAMWGEADMPIAMMPSLNQVTLFQLNGSMTPDEFR 60

Query: 210 RVLDCALKGCADIHAILDTAIK 231
           +  D A+KG   I+ +   A+K
Sbjct: 61  QAFDLAVKGINIIYNLEREALK 82

>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 = 58.8 bits (142), Expect = 4e-12
 Identities = 15/88 (17%), Positives = 30/88 (34%), Gaps = 1/88 (1%)

Query: 150 PMREYVVACSASLAGDTP-LVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHL 208
           PMR      + +L  D   ++D +  +E      LT A   +  K+ +           L
Sbjct: 1   PMRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFALDSVERKLLMSSTKGLYSDTEL 60

Query: 209 PRVLDCALKGCADIHAILDTAIKQHLIK 236
            + L  A      +      ++++   K
Sbjct: 61  QQCLAAAQAASQHVFRFYRESLQRRYSK 88

>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 = 50.1 bits (119), Expect = 7e-09
 Identities = 18/92 (19%), Positives = 42/92 (45%), Gaps = 3/92 (3%)

Query: 150 PMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALP---LSGKVAVMELSQKLHLD 206
           PM+  + + +   A    ++D    E+  G  ++  A L        +A++++  ++  D
Sbjct: 1   PMKGMITSVAVGKADGQLVLDPMKEEDNFGEADMPFAFLIRNGKIESIALLQMDGRMTRD 60

Query: 207 HLPRVLDCALKGCADIHAILDTAIKQHLIKVA 238
            + + ++ A KG   I+ +   AI +  I+V 
Sbjct: 61  EVKQAIELAKKGALQIYEMQREAILRRYIEVG 92

>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 = 47.1 bits (112), Expect = 4e-08
 Identities = 18/79 (22%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 150 PMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK--LHLDH 207
           P+R+  V+ ++ + G+  LVD S  E ++G   LT+        V  M+ S    L    
Sbjct: 1   PVRDLPVSVTSLIVGNKYLVDPSREEMSVGDTTLTITTDK-DDNVVAMQKSGGYLLDEKL 59

Query: 208 LPRVLDCALKGCADIHAIL 226
              +LD ++     +    
Sbjct: 60  FDELLDVSINCARKLREKF 78

>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 = 46.9 bits (111), Expect = 8e-08
 Identities = 17/88 (19%), Positives = 42/88 (47%), Gaps = 4/88 (4%)

Query: 148 GIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK---LH 204
           G P+++ V A S  +    P++D+ +LE++    +L V  +  +G    ++ + +     
Sbjct: 2   GNPLKQMVAAVSVGIYQGVPVLDLDYLEDSAAETDLNV-VMTDAGGFIEVQGTAEGAPFR 60

Query: 205 LDHLPRVLDCALKGCADIHAILDTAIKQ 232
              L  +L+ A +G  ++  +   A+ +
Sbjct: 61  PAELNAMLELAQQGMQELFELQRAALAE 88

>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 = 45.6 bits (108), Expect = 2e-07
 Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 2/83 (2%)

Query: 151 MREYVVACSASLAGDTP-LVDISHLEETLGGPNLTVAALPLSGKVAV-MELSQKLHLDHL 208
           +R + VA S ++  DT  +VD +  EE L    LT+          +       L    L
Sbjct: 2   IRTHPVATSFAVFDDTLLIVDPTGEEEHLATGTLTIVMDEEGKLCCLHKPGGSGLTGAKL 61

Query: 209 PRVLDCALKGCADIHAILDTAIK 231
              +  A+    ++  ++D  IK
Sbjct: 62  QDCMSRAVTRHKEVKKLMDEVIK 84

>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 = 45.0 bits (106), Expect = 6e-07
 Identities = 18/80 (22%), Positives = 40/80 (50%), Gaps = 4/80 (5%)

Query: 149 IPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK---LHL 205
            P++++V A S  +  D  L+D++  E++    ++ V     SG+++ +    +      
Sbjct: 3   TPIKDFVAAVSVGIVNDRILLDLNFEEDSAAQVDMNVVGTG-SGRLSEVHTMGEEYSFTK 61

Query: 206 DHLPRVLDCALKGCADIHAI 225
           D L ++LD A KG  ++  +
Sbjct: 62  DELIKMLDLAQKGINELIEL 81

>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 = 44.5 bits (105), Expect = 1e-06
 Identities = 16/90 (17%), Positives = 29/90 (32%), Gaps = 3/90 (3%)

Query: 150 PMREYVVACSASL--AGDTPLVDISHLEETLGGPNLTVAALPLSGKVAV-MELSQKLHLD 206
            +    +  S +    G   LVD +  EE +    L +A         +       L  D
Sbjct: 2   SIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGIMLLKD 61

Query: 207 HLPRVLDCALKGCADIHAILDTAIKQHLIK 236
            + R    A    A+I  ++  A++     
Sbjct: 62  QVLRCSKIAGVKVAEITELILKALENDQKV 91

>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 = 39.6 bits (92), Expect = 2e-05
 Identities = 14/86 (16%), Positives = 37/86 (43%), Gaps = 5/86 (5%)

Query: 149 IPMREYVVACSASL-AGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK---LH 204
            P+ +++ A S  +      L+D+++ E++    ++ V     SG+   ++ + +     
Sbjct: 2   NPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTG-SGRFVELQGTGEEATFS 60

Query: 205 LDHLPRVLDCALKGCADIHAILDTAI 230
            + L  +L  A KG  ++       +
Sbjct: 61  REDLNGLLGLAEKGIQELIDKQKEVL 86

>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 = 38.8 bits (90), Expect = 4e-05
 Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 3/83 (3%)

Query: 150 PMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQK--LHLDH 207
           P+   VV  S +      +VD    EE++    ++ +  P   K+  ++ S K  + L  
Sbjct: 1   PLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSYTP-DLKIVGIQKSGKGSMSLQD 59

Query: 208 LPRVLDCALKGCADIHAILDTAI 230
           + +  + A      +   L   +
Sbjct: 60  IDQAENTARSTAVKLLEELKKHL 82

>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 = 37.2 bits (86), Expect = 2e-04
 Identities = 14/87 (16%), Positives = 31/87 (35%), Gaps = 3/87 (3%)

Query: 149 IPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELS--QKLHLD 206
           + +       +    G   +VD +  EE     +L V+     G V  M       L  +
Sbjct: 1   LSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTS-KGVVTCMRKVGKGSLDPE 59

Query: 207 HLPRVLDCALKGCADIHAILDTAIKQH 233
            +  +++   +    +HA L + + + 
Sbjct: 60  SIFEMMETGKRVGKVLHASLQSVVHKE 86

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	263
d2nn6b1	145	Exosome complex exonuclease RRP41 {Human (Homo sap	100.0
d2ba0d1	144	Exosome complex exonuclease 1, ECX1 {Archaeoglobus	100.0
d2je6b1	148	Exosome complex exonuclease 1, ECX1 {Sulfolobus so	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
d1e3ha3	137	Polynucleotide phosphorylase/guanosine pentaphosph	99.97
d2ba0g1	176	Exosome complex exonuclease 2,ECX2 {Archaeoglobus	99.97
d2nn6d1	122	Exosome complex exonuclease RRP46 {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	99.96
d2nn6c1	181	Exosome complex exonuclease RRP43 {Human (Homo sap	99.96
d2nn6f1	147	Exosome complex exonuclease MTR3 {Human (Homo sapi	99.96
d2nn6a1	184	Exosome complex exonuclease RRP45 {Human (Homo sap	99.95
d1e3ha2	149	Polynucleotide phosphorylase/guanosine pentaphosph	99.9
d2nn6b2	90	Exosome complex exonuclease RRP41 {Human (Homo sap	99.74
d2nn6d2	89	Exosome complex exonuclease RRP46 {Human (Homo sap	99.72
d2nn6a2	118	Exosome complex exonuclease RRP45 {Human (Homo sap	99.72
d2nn6e2	94	Exosome complex exonuclease RRP42 {Human (Homo sap	99.69
d2je6b2	86	Exosome complex exonuclease 1, ECX1 {Sulfolobus so	99.69
d2je6a2	84	Exosome complex exonuclease 2, ECX2 {Sulfolobus so	99.68
d2ba0g2	79	Exosome complex exonuclease 2, ECX2 {Archaeoglobus	99.67
d2nn6c2	89	Exosome complex exonuclease RRP43 {Human (Homo sap	99.66
d2nn6f2	95	Exosome complex exonuclease MTR3 {Human (Homo sapi	99.57
d1r6la2	88	Ribonuclease PH, domain 2 {Pseudomonas aeruginosa	99.54
d2ba0d2	99	Exosome complex exonuclease 1, ECX1 {Archaeoglobus	99.51
d1oysa2	86	Ribonuclease PH, domain 2 {Bacillus subtilis [TaxI	99.29
d1udsa2	105	Ribonuclease PH, domain 2 {Aquifex aeolicus [TaxId	99.25
d1e3ha5	111	Polynucleotide phosphorylase/guanosine pentaphosph	97.95
d1e3ha6	96	Polynucleotide phosphorylase/guanosine pentaphosph	97.22

>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=5.8e-38  Score=249.59  Aligned_cols=144  Identities=65%  Similarity=1.030  Sum_probs=131.7

Q ss_pred             ccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCC-CcCCCCeEEEEEEEeeCCCCCc
Q psy18119          4 LTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNK-SIKVHGSVLINFQYSMAVFSTG   82 (263)
Q Consensus         4 ~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~-~~~~~~~~~l~v~~~~~~~~~~   82 (263)
                      |++  +|+|+|||.++|+|++++++|++++++|||+|++|+|+|+|+|+||.+.+.. ..+.++++.++|+++++++++.
T Consensus         1 ~~e--~g~R~DGR~~~e~R~i~i~~g~~~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~~v~v~~~~~~~~~~   78 (145)
T d2nn6b1           1 LSD--QGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATFSTG   78 (145)
T ss_dssp             CCB--TTBCSSSSCTTSCCCEEEEESCSSSSSEEEEEEESSCEEEEEEEEEEECCSSSCCCCCSSCCEEEEEEECTTTSS
T ss_pred             CCC--CCccCCCCCCCCccCeEEEECCCCCCCceEEEEeCCceEEEEEEeccccccchhhccccceeEEEEeeecCcccc
Confidence            466  9999999999999999999999999999999999999999999998765432 2346889999999999999988


Q ss_pred             cccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCC
Q psy18119         83 ERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGI  149 (263)
Q Consensus        83 ~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagI  149 (263)
                      ++.+++.++.++.+++++|+++|+++++++.||++.|+|+|+||++|||+++||+||+++||+|+||
T Consensus        79 ~~~~~~~~~~~~~~l~~~l~~~l~~~i~~~~~~~~~I~v~v~VL~~DG~l~~a~i~aa~lAL~daGI  145 (145)
T d2nn6b1          79 ERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGI  145 (145)
T ss_dssp             SCCCTTTSTHHHHHHHHHHHHHHHHTTCGGGCTTEEEEEEEEEEECCSCHHHHHHHHHHHHHHHTCC
T ss_pred             cccccCCCCchhhhHHHHHHHhhhcccchHhhCceeeEEEEEEEeCCCCHHHHHHHHHHHHHHHcCC
Confidence            7766666778889999999999999999999999999999999999999999999999999999997

>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=3e-37  Score=245.06  Aligned_cols=140  Identities=51%  Similarity=0.813  Sum_probs=128.8

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCC
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRP   88 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~   88 (263)
                      +|+|+|||.++|+|++++++|++++++|||+|++|+|+|+|+|+||.+........++++.+.++++++|++...+.+ .
T Consensus         5 ~g~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~gp~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~-~   83 (144)
T d2ba0d1           5 DGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVFGPREVHPRHLQDPSKAIIRYRYNMAPFSVEERKR-P   83 (144)
T ss_dssp             SSCBTTSCCTTCCCCEEEEECCCSSSSEEEEEEETTEEEEEEEEEEEECCSGGGCCSSSCEEEEEEEECTTSSSSCCC-S
T ss_pred             CCcCCCCCCCCCccCeEEEECCCCCCCceEEEEEcccceEEEEeccchhhhhhcccccceEEEEEEecCCcccccccc-c
Confidence            899999999999999999999999999999999999999999999987665434568899999999999999876543 3


Q ss_pred             CCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCC
Q psy18119         89 RGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGI  149 (263)
Q Consensus        89 ~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagI  149 (263)
                      .++.++.+++++|+++|+++++++.||+|.|+|+|+||++|||+++||+||+++||+|+||
T Consensus        84 ~~~~~~~~l~~~l~~~l~~~i~~~~~~~~~i~v~v~VL~~DG~~~~a~i~aa~lAL~daGI  144 (144)
T d2ba0d1          84 GPDRRSIEISKVSKEAFEAVIMKELFPRSAIDIFVEVLQADAGSRTACLNAASVALVDAGV  144 (144)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTBCGGGCTTEEEEEEEEEEECCTTHHHHHHHHHHHHHHHHTC
T ss_pred             CCCchhhhhhhhhhhhhccccchhhcCCeEEEEEEEEEccCCCHHHHHHHHHHHHHHHcCC
Confidence            4677888999999999999999999999999999999999999999999999999999997

>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=4.4e-37  Score=245.33  Aligned_cols=144  Identities=44%  Similarity=0.730  Sum_probs=130.8

Q ss_pred             cccCCCCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCc
Q psy18119          3 LLTEYGGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTG   82 (263)
Q Consensus         3 ~~~~~~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~   82 (263)
                      +|.+  +|+|+|||.++|+|++++++|+++++||||+|++|+|+|+|+|+||.+........++++.++|++.++||++.
T Consensus         5 ~i~~--~g~R~DGR~~~e~R~i~i~~g~l~~adGSa~v~~G~T~Vl~~V~gp~e~~~~~~~~~~~~~~~v~~~~~~~~~~   82 (148)
T d2je6b1           5 LILD--DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVYGPKEMHPRHLSLPDRAVLRVRYHMTPFSTD   82 (148)
T ss_dssp             SBCT--TSCBTTSCCTTCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECSSGGGSCSSSCEEEEEEEECTTSSS
T ss_pred             EecC--CCccCCCCCCCCccCeEEEECCCCCCCEEEEEEcCCccEEeecccCccccchhhcCCcceEEEEEEEecccccc
Confidence            4555  99999999999999999999999999999999999999999999998766544456899999999999999987


Q ss_pred             cccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCC
Q psy18119         83 ERKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGI  149 (263)
Q Consensus        83 ~~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagI  149 (263)
                      .+..+ .+..++.+++++|+++|+++++++.||++.|+|+|+||++|||+++||+||+++||+|+||
T Consensus        83 ~~~~~-~~~~~~~el~~~l~~~l~~~i~~~~~p~~~i~v~v~VL~~DG~~~~a~i~aa~~AL~daGI  148 (148)
T d2je6b1          83 ERKNP-APSRREIELSKVIREALESAVLVELFPRTAIDVFTEILQADAGSRLVSLMAASLALADAGI  148 (148)
T ss_dssp             SCCCS-SCCHHHHHHHHHHHHHHHTTBCGGGSTTEEEEEEEEEEECSSCHHHHHHHHHHHHHHHTTC
T ss_pred             ccccc-cccchhHHHHHHHHHHhhccccHHHcCCEEEEEEEEEEEcCCCHHHHHHHHHHHHHHHcCC
Confidence            65433 3567788999999999999999999999999999999999999999999999999999997

>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=7.7e-35  Score=232.32  Aligned_cols=140  Identities=30%  Similarity=0.364  Sum_probs=123.4

Q ss_pred             cCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccC----C
Q psy18119         12 RNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKT----R   87 (263)
Q Consensus        12 R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~----~   87 (263)
                      |+|||+++|+|++++++|++++++|||+|++|+|+|+|+|++|.+.+.. ...++++.+++++.++|++......    .
T Consensus         1 R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~   79 (149)
T d1udsa1           1 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVPNW-LKGKGQGWITAEYSMLPRATQQRTIRESVQ   79 (149)
T ss_dssp             CTTSCCTTCCCCEEEEECCSSSSSEEEEEEETTEEEEEEEEEESCCCGG-GTTSSCCEEEEEEEECSEETTEECCCSSSS
T ss_pred             CCCCCCCCCccCeEEEeCCCCCCCEEEEEEECCCEEEEEEEeecccccc-ccCCCceeEEeeecchhhcccccccccccc
Confidence            8999999999999999999999999999999999999999998765432 3467889999999998887543221    1


Q ss_pred             CCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCcc
Q psy18119         88 PRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMR  152 (263)
Q Consensus        88 ~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~  152 (263)
                      ........++++++++.+++++.++.||+|.|+|+|+||++|||++||++||+++||+|+||||+
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            23456677899999999999999999999999999999999999999999999999999999997

>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=8.2e-34  Score=226.75  Aligned_cols=141  Identities=33%  Similarity=0.410  Sum_probs=120.8

Q ss_pred             ccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCC--
Q psy18119         11 LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRP--   88 (263)
Q Consensus        11 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~--   88 (263)
                      -|+|||+++|+|++++++|+++++||||+|++|+|+|+|+|++|.+.+.. ...++++.+.+++.+++++......+.  
T Consensus         2 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~~~~~~~   80 (151)
T d1r6la1           2 NRPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVSAESGVPRF-LKGQGQGWLTAEYGMLPRSTGERNQREAS   80 (151)
T ss_dssp             CCTTCCCTTCCCCEEEESSCSSSSSEEEEEEETTEEEEEEEEEEESCSSC-CC---CCEEEEEEEECTTSSSSCCCCHHH
T ss_pred             CCCCCCCCCCccCeEEEeCCCCCCCEEEEEEeCCCEEEEEEEeccccccc-ccCCCceeEEEEEEecCccccccccccCC
Confidence            49999999999999999999999999999999999999999998765433 245788999999999888765442211  


Q ss_pred             --CCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCcc
Q psy18119         89 --RGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMR  152 (263)
Q Consensus        89 --~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~  152 (263)
                        .......++++++.+.+.+.++++.||++.|+|+|+||++|||++||+++|+++||+|+||||+
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              2345566788999999999999999999999999999999999999999999999999999985

>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=1.1e-33  Score=225.90  Aligned_cols=140  Identities=31%  Similarity=0.353  Sum_probs=108.9

Q ss_pred             ccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccC----
Q psy18119         11 LRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKT----   86 (263)
Q Consensus        11 ~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~----   86 (263)
                      +|+|||+++|+|++++++|++++++|||+|++|+|+|+|+|++|.+.++. ...++++.++++|.+.|++...+..    
T Consensus         1 lR~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vl~~V~~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~~~~~~~   79 (151)
T d1oysa1           1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPF-LRGGGKGWITAEYSMLPQATNQQTIQESS   79 (151)
T ss_dssp             CCTTSCCTTCCCCEEEECC-----CCCEEEEETTEEEEEEEEEESCCCGG-GTTSCCCEEEEEEEC--------------
T ss_pred             CCCCCCCCCCccCeEEEeCCCCCCCEEEEEEEcCCEEEEEEEeccccccc-ccccccceeeeeeeecccccccccccccc
Confidence            69999999999999999999999999999999999999999986554443 3457889999999988887654322    


Q ss_pred             CCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCc
Q psy18119         87 RPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPM  151 (263)
Q Consensus        87 ~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~  151 (263)
                      ++..+..+.++++++++.|+++++++.||+|.|+|+|+||++|||+++|++||+++||+||.+++
T Consensus        80 ~~~~~~~~~~~~~~l~~~l~~~i~l~~~~~~~i~v~v~VL~~DG~l~~a~i~Aa~~AL~dA~~~~  144 (151)
T d1oysa1          80 KGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKL  144 (151)
T ss_dssp             -----CHHHHHHHHHHHHHHHTBCHHHHCSCEEEEEEEEEECSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcccchhhHHhHHHHHHhhhhhhhhhhccceEEEEEEEEcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            22345677889999999999999999999999999999999999999999999999999995543

>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=99.97  E-value=3.9e-31  Score=207.91  Aligned_cols=134  Identities=19%  Similarity=0.282  Sum_probs=117.3

Q ss_pred             CCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCC---cCCCCeEEEEEEEeeCCCCCccccCCCCCCcchH
Q psy18119         19 HELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKS---IKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTS   95 (263)
Q Consensus        19 ~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~---~~~~~~~~l~v~~~~~~~~~~~~~~~~~~~~~~~   95 (263)
                      +|+|++++++|+++++||||+|++|+|+|+|+|++|.+.+...   ........+.+++...||++..+++...++.++.
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            5899999999999999999999999999999999976433210   1223456677888888888777666667788999


Q ss_pred             HHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCcc
Q psy18119         96 EISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMR  152 (263)
Q Consensus        96 ~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~  152 (263)
                      ++++++++.|++++.++.||+|.|+|+++||++|||+++|++||+++||+|+||||+
T Consensus        81 ~~~~~i~~~l~~~i~~~~~~~~~I~v~v~vl~~DG~~~~aainAa~lAL~dAGIpmk  137 (137)
T d1e3ha3          81 GHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLK  137 (137)
T ss_dssp             HHHHHHHHHHGGGCCCTTTSCEEEEEEEEEEECSSCHHHHHHHHHHHHHHHHTCCCS
T ss_pred             ccchHHHHHHHhccchhhcCcEEEEEEEEEecCCCCHHHHHHHHHHHHHHHcCCccC
Confidence            999999999999999999999999999999999999999999999999999999996

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

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

Probab=99.97  E-value=1.2e-30  Score=213.44  Aligned_cols=144  Identities=19%  Similarity=0.220  Sum_probs=121.0

Q ss_pred             CCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCC-CCCCCcCCCCeEEEEEEEeeCCCCCccccC
Q psy18119          8 GGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRP-VRNKSIKVHGSVLINFQYSMAVFSTGERKT   86 (263)
Q Consensus         8 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~-~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~   86 (263)
                      ++|+|+|||.++|+|++++++|++++++|||++++|+|+|+|+|+++.. +.+   ..++++.+.+++.+++++...+.+
T Consensus        17 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~~~~~p~~---~~~~~g~~~~~v~~~~~~~~~~~~   93 (176)
T d2ba0g1          17 RDNERIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPYP---DTPDRGVIIVNAELVPLASPTFEP   93 (176)
T ss_dssp             TTTCCTTCCCTTCCCCEEEEECCCTTSSEEEEEEETTEEEEEEEEEEEECCCT---TCTTCCEEEEEEECCTTTCTTSCS
T ss_pred             HhCCCCCCCCCCCccCeEEEeCccCCCCeEEEEEeCCcEEEEEEecccccccc---ccCCCceeeeeeEeccccCccccC
Confidence            3899999999999999999999999999999999999999999997433 333   246778888999888888765543


Q ss_pred             CCCCCcchHHHHHHHHHHHHhh--hccCC------CCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCce
Q psy18119         87 RPRGDRKTSEISLQLRQAVSAA--IMSEV------HPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREYV  155 (263)
Q Consensus        87 ~~~~~~~~~~l~~~l~~~l~~~--i~l~~------~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~~  155 (263)
                       +.++.....+++++++++.+.  ++++.      .+.|.|+|+|+||++|||++||+++|+++||+|+|||+..+.
T Consensus        94 -~~~~~~~~~~~~~l~~~~~~~~~i~~e~L~i~~~~~~~~i~i~v~VL~~DG~l~dA~~~A~~~AL~da~iP~~~~~  169 (176)
T d2ba0g1          94 -GPPDENSIELARVVDRGIRESEAVDLSKLVIEEGEKVWIVFVDIHALDDDGNLLDASALAAIAALMNTKVPAERFD  169 (176)
T ss_dssp             -SSCCHHHHHHHHHHHHHHHHTTCBCGGGGEEETTTEEEEEEEEEEEEECSSCHHHHHHHHHHHHHTTCEECTGGGT
T ss_pred             -CCCCchhHHHHHHHHHhhccccccchhhccCCCCCceEEEEEEEEEEeCCCCHHHHHHHHHHHHHHHcCCCcEEec
Confidence             346677889999999998764  44433      335899999999999999999999999999999999998763

>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=4.7e-30  Score=197.84  Aligned_cols=121  Identities=30%  Similarity=0.527  Sum_probs=105.7

Q ss_pred             CCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCCCCCcchHHHH
Q psy18119         19 HELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRPRGDRKTSEIS   98 (263)
Q Consensus        19 ~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~~~~~~~~~l~   98 (263)
                      .|+|++.+++|+++++||||+|++|+|+|+|+|+||.+++++ .+.++++.++|++++...         .++.++++++
T Consensus         2 ~elR~i~~~~gvl~~adGSa~~~~G~T~Vi~~V~gP~e~~~~-~~~~~~~~~~v~~~~~~~---------~~~~~~~~~~   71 (122)
T d2nn6d1           2 CSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVS-KEIFNKATLEVILRPKIG---------LPGVAEKSRE   71 (122)
T ss_dssp             CCCCCEEEEESCCSSSSEEEEEEETTEEEEEEEEEEEECC-------CCEEEEEEEECSSS---------CCCHHHHHHH
T ss_pred             CccceEEEEECCCCCCCeEEEEEECCcEEEEEEEecccccch-hhCcCCCceEEEeeeecC---------CCCchhhHHH
Confidence            489999999999999999999999999999999999887665 356788999998874321         2456788999


Q ss_pred             HHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCC
Q psy18119         99 LQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGI  149 (263)
Q Consensus        99 ~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagI  149 (263)
                      ++|+++|+++++++.||+|.|+|+++||++|||+++|++||+++||+|+||
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

>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=4.6e-30  Score=212.50  Aligned_cols=144  Identities=19%  Similarity=0.180  Sum_probs=119.2

Q ss_pred             CCCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCC
Q psy18119          8 GGGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTR   87 (263)
Q Consensus         8 ~~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~   87 (263)
                      ++|+|+|||.++|+|++++++|++++++|||+|++|+|+|+|+|++|...+..  ..++.+.+.+++...+++...+. .
T Consensus        24 ~~giR~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~a~V~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~-~  100 (191)
T d2je6a1          24 EKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLAGTKLEIDKPYE--DTPNQGNLIVNVELLPLAYETFE-P  100 (191)
T ss_dssp             GGTBCTTSCBTTCCCCEEEEETCSTTSSEEEEEEETTEEEEEEEEEEEECCCT--TCTTCCEEEEEEEECTTSCTTCC-C
T ss_pred             hcCCCCCCcCCCCccCeEEEECCccCcCceEEEEcCCceEEEEEEecccCchh--ccCccCccccccccccccccccc-c
Confidence            38999999999999999999999999999999999999999999998765443  34677888888888777654432 2


Q ss_pred             CCCCcchHHHHHHHHHHHHhhh--ccCC------CCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCc
Q psy18119         88 PRGDRKTSEISLQLRQAVSAAI--MSEV------HPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREY  154 (263)
Q Consensus        88 ~~~~~~~~~l~~~l~~~l~~~i--~l~~------~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~  154 (263)
                      .........++++|++.+....  +++.      .+.|.|+|+|+||++|||++||+++|+++||+|+|||+..+
T Consensus       101 ~~~~~~~~~l~~~l~~~~~~~~~id~~~l~i~~~~~~w~I~v~v~VL~~DG~l~dA~~~A~~~AL~da~iP~v~~  175 (191)
T d2je6a1         101 GPPDENAIELARVVDRSLRDSKALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQ  175 (191)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHTTCSCGGGGEEETTTEEEEEEEEEEEEECCSCHHHHHHHHHHHHHHTCEEEEEEC
T ss_pred             ccCCcchhHHHHHHHHhhcchhhcccccccccCccccEEEEEEEEEEcCCCCHHHHHHHHHHHHHHHcCCCeEEe
Confidence            2355677889999999987643  3322      34689999999999999999999999999999999996443

>d2nn6e1 d.14.1.4 (E:5-191) Exosome complex exonuclease RRP42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Ribonuclease PH domain 1-like
domain: Exosome complex exonuclease RRP42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=3e-30  Score=212.95  Aligned_cols=140  Identities=24%  Similarity=0.254  Sum_probs=118.9

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCC
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRP   88 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~   88 (263)
                      +|+|+|||+++|+|++++++|++++++|||+|++|+|+|+|+|++|...+..  ..++++.+.+++.+++++.....++ 
T Consensus        16 ~~iR~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~V~~~V~~~~~~~~~--~~~~~g~~~~~v~~~~~~~~~~~~~-   92 (187)
T d2nn6e1          16 EDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKL--EKPNEGYLEFFVDCSASATPEFEGR-   92 (187)
T ss_dssp             TTCCSSSCCSSCCCCCEEEECCCTTSSSEEEEEETTEEEEEECCCCCSCCCS--SSCSSCCEEEECCCCTTTCSSCCTT-
T ss_pred             hCCCCCCcCCCCccCeEEEeCccCCCCceEEEEeCCceEEEEEEeccccccc--cccccceeeeeeeeccccccCcCCC-
Confidence            8999999999999999999999999999999999999999999997654442  3466778888888888876654332 


Q ss_pred             CCCcchHHHHHHHHHHHHhhh--ccCC------CCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCc
Q psy18119         89 RGDRKTSEISLQLRQAVSAAI--MSEV------HPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPM  151 (263)
Q Consensus        89 ~~~~~~~~l~~~l~~~l~~~i--~l~~------~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~  151 (263)
                      .++....+++++|++.|++..  +++.      ++.|.|+|+|+||++|||+++|+++|+++||+|++||.
T Consensus        93 ~~~~~~~~ls~~l~~~l~~~~~~d~~~L~i~~~~~~w~i~v~v~vL~~DG~~~da~~~A~~~AL~d~~iP~  163 (187)
T d2nn6e1          93 GGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPR  163 (187)
T ss_dssp             STHHHHHHHHHHHHHHHHHSCCSCSSSSCSSTTTCCCCEEEEEEECCCCSSHHHHHHHHHHHTTTTCCCCE
T ss_pred             CcchHHHHHHHHHHHHhccccccchhhheecCCCccEEEEEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCE
Confidence            345667789999999998854  3332      45789999999999999999999999999999999995

>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=99.96  E-value=2.1e-29  Score=206.20  Aligned_cols=141  Identities=20%  Similarity=0.214  Sum_probs=116.5

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCC
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRP   88 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~   88 (263)
                      +|+|+|||+++|+|++++++|++++++|||++++|+|+|+|+|++|..++..  ..++.+.+.+++...+++...... .
T Consensus        14 ~giR~DGR~~~e~R~~~i~~g~l~~a~GSa~v~~G~T~v~~~v~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~-~   90 (181)
T d2nn6c1          14 ENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPST--DAPDKGYVVPNVDLPPLCSSRFRS-G   90 (181)
T ss_dssp             TSCCTTSCCSCCCCSCCEEETCCSSSSEEEEEEETTEEEEEEEEEEECCCCS--SSTTCCCCEEEEECCSSSCTTSCS-S
T ss_pred             cCCCCCCcCCCCccCeEEEeCCcCCCCeEEEEEeCCcEEEEEEecccccccc--ccCCCceeeeeeeeeccccccccc-c
Confidence            7999999999999999999999999999999999999999999997654442  345567777788777766543322 2


Q ss_pred             CCCcchHHHHHHHHHHHHhhh--------ccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCcc
Q psy18119         89 RGDRKTSEISLQLRQAVSAAI--------MSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMR  152 (263)
Q Consensus        89 ~~~~~~~~l~~~l~~~l~~~i--------~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~  152 (263)
                      .+......+++.+++.+.+..        .++.+|.|.|+|+++||++|||++||+++|+++||+|++||+.
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~~~~~~~i~i~v~vl~~DG~l~da~~~A~~~AL~d~~iP~v  162 (181)
T d2nn6c1          91 PPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEV  162 (181)
T ss_dssp             SCCHHHHHHHHHHHHHHHHHCCSCHHHHCSSBTTBCEEEEEEEEESSCCSCTTHHHHHHHHHHHHTCCCCCC
T ss_pred             CCCchhhhhHHHHHHHHHhhhhhhhhhccccCCcceEEEEEEEEEecCCCCHHHHHHHHHHHHHHhcCCCeE
Confidence            345667788888888877542        2355778999999999999999999999999999999999973

>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=1.4e-29  Score=200.60  Aligned_cols=135  Identities=34%  Similarity=0.517  Sum_probs=114.8

Q ss_pred             CCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCc-----------CCCCeEEEEEEEeeCCCCCcc
Q psy18119         15 GRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSI-----------KVHGSVLINFQYSMAVFSTGE   83 (263)
Q Consensus        15 GR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~-----------~~~~~~~l~v~~~~~~~~~~~   83 (263)
                      .|.++|+|++++++|++++++|||+|++|+|+|+|+|++|.+++....           ..+..+.+.+++.+.++++..
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            599999999999999999999999999999999999999877554311           124457788899998988765


Q ss_pred             ccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCC
Q psy18119         84 RKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP  150 (263)
Q Consensus        84 ~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp  150 (263)
                      +.. .....++.+++.++.+.+.++++++.||+|.|+|+++||++|||+++||+||+++||+|+||.
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            432 235567789999999999999999999999999999999999999999999999999999984

>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=99.95  E-value=5.9e-28  Score=198.60  Aligned_cols=140  Identities=21%  Similarity=0.232  Sum_probs=114.2

Q ss_pred             CCccCCCCCCCCCcceEEEeCCCCCCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEeeCCCCCccccCCC
Q psy18119          9 GGLRNDGRRGHELRKIRCRLGVFSQSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYSMAVFSTGERKTRP   88 (263)
Q Consensus         9 ~~~R~DGR~~~e~R~i~i~~g~l~~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~~~~~~~~~~~~~~   88 (263)
                      +|+|+|||+++|+|++.+++|   .++|||+|++|+|+|+|+|++|...+..  ..++.+.+.+++.+.+++...... +
T Consensus        20 ~~~R~DGR~~~e~R~~~i~~g---~a~GSa~v~~G~T~V~~~V~~~~~~p~~--~~~~~g~~~~~v~~~~~~~~~~~~-~   93 (184)
T d2nn6a1          20 EKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSPKL--NRATEGILFFNLELSQMAAPAFEP-G   93 (184)
T ss_dssp             TTCCTTSCCTTCCCCCEEEEC---SSTTEEEEESSSCEEEEEECCEEECCCS--TTTTSCCEEEEEEECTTTCSSCCS-S
T ss_pred             hCcCCCCCCCCCcCCeEEEec---CCCCEEEEEeCCCEEEEEEEeccccccc--cCCCccceeEEEEeccccCccccc-C
Confidence            799999999999999999998   4899999999999999999997543332  246677788888877877654332 2


Q ss_pred             CCCcchHHHHHHHHHHHHhh--hccCC------CCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCCccCc
Q psy18119         89 RGDRKTSEISLQLRQAVSAA--IMSEV------HPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIPMREY  154 (263)
Q Consensus        89 ~~~~~~~~l~~~l~~~l~~~--i~l~~------~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp~~~~  154 (263)
                      .++.++.+++++|++.+...  ++++.      ++.|.|+|+|+||++|||++||+++|+++||+|++||...+
T Consensus        94 ~~~~~~~~l~~~l~~~~~~~~~~d~~~L~i~~~~~~w~i~i~v~VL~~DG~~~da~~~a~~~AL~~~~iP~v~v  167 (184)
T d2nn6a1          94 RQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSV  167 (184)
T ss_dssp             STHHHHTHHHHHHHHHHHHHTCBCSSSSCSBTTTBEEEEEEEEEECSCCSCCHHHHHHHHHHHHHHCCCCCCBC
T ss_pred             CCCchhHHHHHHHHhhhhhhhhhhhhhhccccccCcEEEEEEEEEECCCCCHHHHHHHHHHHHHHhhCCCeEEE
Confidence            34566778899999998875  33333      34689999999999999999999999999999999997553

>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=99.90  E-value=3e-23  Score=164.54  Aligned_cols=137  Identities=15%  Similarity=0.095  Sum_probs=109.2

Q ss_pred             CccCCCCCCCCCcceEEEeCCCC-CCceeEEEEeCCeEEEEEEEcCCCCCCCCcCCCCeEEEEEEEe--eCC---CCCcc
Q psy18119         10 GLRNDGRRGHELRKIRCRLGVFS-QSDGSAYIEQGNTKVLAAVYGPRPVRNKSIKVHGSVLINFQYS--MAV---FSTGE   83 (263)
Q Consensus        10 ~~R~DGR~~~e~R~i~i~~g~l~-~a~GSa~v~~G~T~Vi~~V~gp~~~~~~~~~~~~~~~l~v~~~--~~~---~~~~~   83 (263)
                      ..+.|+|.+.+ |+|++++|+++ +|||||++++|+|+|+|+++++......   ..+...+.+.+.  +.+   +....
T Consensus         7 ~~~~~~~~~~~-R~i~ie~G~lakqA~GSalv~~G~T~vl~ta~~~~~~~~~---~~~~~~~~v~~~~~~~~~~~~~~~~   82 (149)
T d1e3ha2           7 EAVIDNGAFGT-RTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKD---QLDFFPLTVDVEERMYAAGKIPGSF   82 (149)
T ss_dssp             EEEEECGGGCE-EEEEEEESSSCTTSSEEEEEEETTTEEEEEEEEECSSCCT---TCSSCCEEEEEEECGGGGTCCCCST
T ss_pred             EEEEeCCcCCC-cEEEEEeCcccccCCceEEEEECCcEEEEEeeeccccccc---ccccCCceeEEEEeccccccccccc
Confidence            35788888777 99999999996 6999999999999999999975443321   123344444443  222   22334


Q ss_pred             ccCCCCCCcchHHHHHHHHHHHHhhhccCCCCceEEEEEEEEEeCCCChhHHHHHHHHHHHHHcCCC
Q psy18119         84 RKTRPRGDRKTSEISLQLRQAVSAAIMSEVHPRSQIDIFVEVLQADGGNFCACVNAATLALIDAGIP  150 (263)
Q Consensus        84 ~~~~~~~~~~~~~l~~~l~~~l~~~i~l~~~p~~~I~v~v~VL~~dG~~~~a~i~Aa~~AL~dagIp  150 (263)
                      .++.+++++++.+++++|++.|+++++.+.++..+|.++|.+++.||+...|++||+++||+++|||
T Consensus        83 ~rre~~~~~reil~~rlidR~Lrpl~p~~~~~~~qI~~~vl~~d~d~~~~~aai~aAs~AL~~agIP  149 (149)
T d1e3ha2          83 FRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLP  149 (149)
T ss_dssp             TSSCCSCCHHHHHHHHHHHHHHHHHBCTTBCSCEEEEEEEEECCTTSCCHHHHHHHHHHHHHHTTCS
T ss_pred             cccccccchHHHHHHHHHHHHHHhhccccCCCceEEEEEEEEeCCCCChHHHHHHHHHHHHHhcCCC
Confidence            4555678999999999999999999998888888888888889999999999999999999999998

>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=99.74  E-value=1.3e-17  Score=120.57  Aligned_cols=88  Identities=47%  Similarity=0.871  Sum_probs=85.2

Q ss_pred             CccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        150 PMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTA  229 (263)
Q Consensus       150 p~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~  229 (263)
                      ||+++++|+|+|++++.+++|||..|++.+++.++|+++++.++|++++..|.++++++.++++.|.++|++++++++++
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            89999999999999999999999999999999999999899999999999999999999999999999999999999999


Q ss_pred             HHHHHHHh
Q psy18119        230 IKQHLIKV  237 (263)
Q Consensus       230 l~~~~~~~  237 (263)
                      ++++..+.
T Consensus        81 l~~~~~e~   88 (90)
T d2nn6b2          81 VRQHVREA   88 (90)
T ss_dssp             HHHHHHHH
T ss_pred             HHhhhhhc
Confidence            99998764

>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=99.72  E-value=1.1e-17  Score=120.61  Aligned_cols=86  Identities=16%  Similarity=0.195  Sum_probs=81.7

Q ss_pred             CccCceeEEEEEec-CCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        150 PMREYVVACSASLA-GDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDT  228 (263)
Q Consensus       150 p~~~~~~avt~~~~-~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~  228 (263)
                      ||+++++||++|++ ++.+++|||..||..+.+.++++++++.++|+.++..|+++++++.++++.|.++|++|++++++
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            89999999999998 55899999999999999999999988899999999999999999999999999999999999999


Q ss_pred             HHHHHHH
Q psy18119        229 AIKQHLI  235 (263)
Q Consensus       229 ~l~~~~~  235 (263)
                      +|+++..
T Consensus        81 ~l~k~~~   87 (89)
T d2nn6d2          81 SLQRRYS   87 (89)
T ss_dssp             HHHHHTC
T ss_pred             HHHHHhc
Confidence            9998754

>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=99.72  E-value=5e-17  Score=123.30  Aligned_cols=92  Identities=17%  Similarity=0.133  Sum_probs=84.8

Q ss_pred             CCccCceeEEEEEecC--CeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHHHHHHHHHHHHHHHHHH
Q psy18119        149 IPMREYVVACSASLAG--DTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRVLDCALKGCADIHA  224 (263)
Q Consensus       149 Ip~~~~~~avt~~~~~--~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l~~~i~~A~~~~~~i~~  224 (263)
                      ++++|+|+++||++++  +.+|+|||..||.++++.++|++ +..++||.+++.|  +++.+++.+|++.|.++++++++
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 LSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAM-NKHREICTIQSSGGIMLLKDQVLRCSKIAGVKVAEITE   79 (118)
T ss_dssp             CCBCCCEEEEEEEECTTTSSEEESCCHHHHHHCSCEEEEEE-ETTTEEEEEEEESCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcCceEEEEEEEEEecCCeEEECCCHHHHhCCCCcEEEEE-eCCCcEEEEEecCCcccCHHHHHHHHHHHHHHHHHHHH
Confidence            4789999999999986  47999999999999999999999 5789999999987  69999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhccC
Q psy18119        225 ILDTAIKQHLIKVAGAR  241 (263)
Q Consensus       225 ~i~~~l~~~~~~~~~~~  241 (263)
                      +++++|+++...+....
T Consensus        80 ~i~~aLk~~~~~R~~~~   96 (118)
T d2nn6a2          80 LILKALENDQKVRKEGG   96 (118)
T ss_dssp             HHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhhhhhh
Confidence            99999999998876654

>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=99.69  E-value=2.1e-17  Score=120.49  Aligned_cols=87  Identities=16%  Similarity=0.178  Sum_probs=80.9

Q ss_pred             CCccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHHHHHHHHHHHHHHHHHHHH
Q psy18119        149 IPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRVLDCALKGCADIHAIL  226 (263)
Q Consensus       149 Ip~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l~~~i~~A~~~~~~i~~~i  226 (263)
                      ++++++|+++||+++++.+|+|||..||.++++.++|++ +..|+||.+++.|  +++++++.+|+++|.++++++++.+
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            478999999999999999999999999999999999999 6789999999987  5899999999999999999999999


Q ss_pred             HHHHHHHHHH
Q psy18119        227 DTAIKQHLIK  236 (263)
Q Consensus       227 ~~~l~~~~~~  236 (263)
                      +++|++..+.
T Consensus        80 ~~~L~~~e~~   89 (94)
T d2nn6e2          80 QSVVHKEESL   89 (94)
T ss_dssp             HHHHHHHHC-
T ss_pred             HHHHHHHhhc
Confidence            9999887653

>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=9.5e-17  Score=115.03  Aligned_cols=84  Identities=23%  Similarity=0.423  Sum_probs=81.0

Q ss_pred             CccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccCChhHHHHHHHHHHHHHHHHHHHHHHH
Q psy18119        150 PMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKLHLDHLPRVLDCALKGCADIHAILDTA  229 (263)
Q Consensus       150 p~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i~~~  229 (263)
                      ||+++++|||+|++++.+++|||..|++.+++.++|+++++.++|++++..|.++++++.++++.|.++|++|+++++++
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             HHHH
Q psy18119        230 IKQH  233 (263)
Q Consensus       230 l~~~  233 (263)
                      |++.
T Consensus        81 l~~r   84 (86)
T d2je6b2          81 LKSK   84 (86)
T ss_dssp             HHGG
T ss_pred             HHhh
Confidence            9863

>d2je6a2 d.101.1.1 (A:192-275) Exosome complex exonuclease 2, ECX2 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a+b)
fold: Ribonuclease PH domain 2-like
superfamily: Ribonuclease PH domain 2-like
family: Ribonuclease PH domain 2-like
domain: Exosome complex exonuclease 2, ECX2
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.68  E-value=1.2e-16  Score=113.92  Aligned_cols=80  Identities=16%  Similarity=0.166  Sum_probs=76.0

Q ss_pred             CccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHHHHHHHHHHHHHHHHHHHHH
Q psy18119        150 PMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRVLDCALKGCADIHAILD  227 (263)
Q Consensus       150 p~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l~~~i~~A~~~~~~i~~~i~  227 (263)
                      |+++.|+++|++++++.+|+|||..||.++++.++|++ +.++++|.+++.|  +++++++.+|++.|.++++++++.++
T Consensus         1 P~~~~~~~vt~~~i~~~~lvDpt~~EE~~~~~~l~v~~-~~~g~i~~~~k~g~~~~~~~~i~~~i~~A~~~~~~l~~~l~   79 (84)
T d2je6a2           1 PLNYPVVTISVAKVDKYLVVDPDLDEESIMDAKISFSY-TPDLKIVGIQKSGKGSMSLQDIDQAENTARSTAVKLLEELK   79 (84)
T ss_dssp             CCSCCCEEEEEEEETTEEEESCCHHHHHHCSEEEEEEE-CTTCCEEEEEEESSSCEEHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCeEEEEEEEECCEEEecCCHHHHHhcCCceeeee-cCCCceeeEEeccCCcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999999999999999999999999 5689999999976  58999999999999999999999999


Q ss_pred             HHH
Q psy18119        228 TAI  230 (263)
Q Consensus       228 ~~l  230 (263)
                      ++|
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=99.67  E-value=9.4e-17  Score=113.21  Aligned_cols=76  Identities=24%  Similarity=0.374  Sum_probs=71.2

Q ss_pred             CccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHHHHHHHHHHHHHHHHHHHH
Q psy18119        150 PMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRVLDCALKGCADIHAIL  226 (263)
Q Consensus       150 p~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l~~~i~~A~~~~~~i~~~i  226 (263)
                      ||+++|+++|++++++.+|+|||..||..+++.++|++ +..|+||.+++.|  +++.+++.+|++.|.++++++.+.+
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            89999999999999999999999999999999999999 6789999999987  5899999999999999999987644

>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=99.66  E-value=1.5e-16  Score=114.73  Aligned_cols=82  Identities=24%  Similarity=0.287  Sum_probs=75.9

Q ss_pred             ccCceeEEEEEecCC-eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc--cCChhHHHHHHHHHHHHHHHHHHHHH
Q psy18119        151 MREYVVACSASLAGD-TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ--KLHLDHLPRVLDCALKGCADIHAILD  227 (263)
Q Consensus       151 ~~~~~~avt~~~~~~-~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G--~i~~~~l~~~i~~A~~~~~~i~~~i~  227 (263)
                      |+++|+++|++++++ .+|+|||..||..+++.++|++ +..|+||.+++.|  +++++++.+|++.|.+++++|+++++
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            689999999999977 5788999999999999999999 6789999999987  68999999999999999999999999


Q ss_pred             HHHHHH
Q psy18119        228 TAIKQH  233 (263)
Q Consensus       228 ~~l~~~  233 (263)
                      ++|++.
T Consensus        81 ~al~~~   86 (89)
T d2nn6c2          81 EVIKSM   86 (89)
T ss_dssp             TTTTTT
T ss_pred             HHHHhc
Confidence            998753

>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=99.57  E-value=7e-15  Score=107.05  Aligned_cols=89  Identities=28%  Similarity=0.374  Sum_probs=82.5

Q ss_pred             ccCceeEEEEEecC---CeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecccC-ChhHHHHHHHHHHHHHHHHHHHH
Q psy18119        151 MREYVVACSASLAG---DTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQKL-HLDHLPRVLDCALKGCADIHAIL  226 (263)
Q Consensus       151 ~~~~~~avt~~~~~---~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G~i-~~~~l~~~i~~A~~~~~~i~~~i  226 (263)
                      |+|++++||+++.+   +++|+||+..||..+.+.++|+++|+.++|+.++..|.+ +.+.+.+++++|.++|++|+.++
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   479999999999999999999999999999999999975 67899999999999999999999


Q ss_pred             HHHHHHHHHHhhc
Q psy18119        227 DTAIKQHLIKVAG  239 (263)
Q Consensus       227 ~~~l~~~~~~~~~  239 (263)
                      +++|.++..++..
T Consensus        81 ~~aL~~~~~k~~~   93 (95)
T d2nn6f2          81 QQSLVRAARRRGA   93 (95)
T ss_dssp             HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhhc
Confidence            9999999887654

>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=99.54  E-value=2.9e-14  Score=102.25  Aligned_cols=83  Identities=20%  Similarity=0.373  Sum_probs=77.8

Q ss_pred             CCCccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc---cCChhHHHHHHHHHHHHHHHHHH
Q psy18119        148 GIPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ---KLHLDHLPRVLDCALKGCADIHA  224 (263)
Q Consensus       148 gIp~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G---~i~~~~l~~~i~~A~~~~~~i~~  224 (263)
                      |+||++.++||++|++++++++|||..|+..++..+++++ +.+++++.++..|   .|+.+++.++++.|.++++++++
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            8999999999999999999999999999999999999998 5788988888775   59999999999999999999999


Q ss_pred             HHHHHHH
Q psy18119        225 ILDTAIK  231 (263)
Q Consensus       225 ~i~~~l~  231 (263)
                      +++++|.
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=99.51  E-value=6.3e-14  Score=102.61  Aligned_cols=88  Identities=23%  Similarity=0.404  Sum_probs=79.3

Q ss_pred             CccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcE---EEEEecccCChhHHHHHHHHHHHHHHHHHHHH
Q psy18119        150 PMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKV---AVMELSQKLHLDHLPRVLDCALKGCADIHAIL  226 (263)
Q Consensus       150 p~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i---~~i~~~G~i~~~~l~~~i~~A~~~~~~i~~~i  226 (263)
                      ||+++++||++|++++.+++||+..|+..++..+++++.+..+.+   .+.+..|.++.+.+.++++.|.++|++|++++
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            899999999999999999999999999999999999987766664   45566689999999999999999999999999


Q ss_pred             HHHHHHHHHHh
Q psy18119        227 DTAIKQHLIKV  237 (263)
Q Consensus       227 ~~~l~~~~~~~  237 (263)
                      ++++++.....
T Consensus        81 ~~alk~~~~~~   91 (99)
T d2ba0d2          81 REAILRRYIEV   91 (99)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHhhhhhhc
Confidence            99999876543

>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=99.29  E-value=7e-12  Score=89.11  Aligned_cols=81  Identities=17%  Similarity=0.284  Sum_probs=72.7

Q ss_pred             CCccCceeEEEEEecCCe-eEecCCchhhhcCCCeEEEEEeCCCCcEEEEEecc---cCChhHHHHHHHHHHHHHHHHHH
Q psy18119        149 IPMREYVVACSASLAGDT-PLVDISHLEETLGGPNLTVAALPLSGKVAVMELSQ---KLHLDHLPRVLDCALKGCADIHA  224 (263)
Q Consensus       149 Ip~~~~~~avt~~~~~~~-~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~G---~i~~~~l~~~i~~A~~~~~~i~~  224 (263)
                      .||++.++||++|++++. +++||+..|+..++..+.|++ +..|++..++..|   +++.+++.+++++|.++++++++
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 578999999999999999998 4678887777765   59999999999999999999999


Q ss_pred             HHHHHH
Q psy18119        225 ILDTAI  230 (263)
Q Consensus       225 ~i~~~l  230 (263)
                      +++++|
T Consensus        81 ~Qkeal   86 (86)
T d1oysa2          81 KQKEVL   86 (86)
T ss_dssp             HHHHHC
T ss_pred             HHHHhC
Confidence            999875

>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=1.4e-11  Score=90.64  Aligned_cols=81  Identities=22%  Similarity=0.386  Sum_probs=72.1

Q ss_pred             CCccCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEec---ccCChhHHHHHHHHHHHHHHHHHHH
Q psy18119        149 IPMREYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLSGKVAVMELS---QKLHLDHLPRVLDCALKGCADIHAI  225 (263)
Q Consensus       149 Ip~~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~---G~i~~~~l~~~i~~A~~~~~~i~~~  225 (263)
                      .||++.++||++|++++.+++||+..|+..++..++|++. ..+.+..++..   +.++.+++.++++.|.++|++|+++
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            6999999999999999999999999999999999999995 46766555544   6799999999999999999999998


Q ss_pred             HHHHH
Q psy18119        226 LDTAI  230 (263)
Q Consensus       226 i~~~l  230 (263)
                      ++++|
T Consensus        82 Qke~l   86 (105)
T d1udsa2          82 QKKLY   86 (105)
T ss_dssp             HHTTE
T ss_pred             HHHHH
Confidence            87764

>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=97.95  E-value=3.7e-05  Score=55.97  Aligned_cols=83  Identities=12%  Similarity=-0.038  Sum_probs=67.7

Q ss_pred             cCceeEEEEEecCCeeEecCCchhhhcCCCeEEEEEeCCC---CcEEEEEeccc-------------CChhHHHHHHHHH
Q psy18119        152 REYVVACSASLAGDTPLVDISHLEETLGGPNLTVAALPLS---GKVAVMELSQK-------------LHLDHLPRVLDCA  215 (263)
Q Consensus       152 ~~~~~avt~~~~~~~~lvDPt~~Ee~~~~~~l~v~~~~~~---~~i~~i~~~G~-------------i~~~~l~~~i~~A  215 (263)
                      ++.+.||.+|++++.+++.||..|-+.++-.+.|+.....   ..+.+++..+.             ++.+.+.++++.|
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            4567899999999999999999999999999999984322   34677776542             5788999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q psy18119        216 LKGCADIHAILDTAIKQHL  234 (263)
Q Consensus       216 ~~~~~~i~~~i~~~l~~~~  234 (263)
                      .+..+.+.+.+++..+...
T Consensus        82 ~~~i~~~i~~q~el~~~~g  100 (111)
T d1e3ha5          82 KPFIKVLCKAQADLAAKAA  100 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHC
Confidence            9999999988887766543

>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=97.22  E-value=0.0011  Score=45.94  Aligned_cols=77  Identities=22%  Similarity=0.267  Sum_probs=66.3

Q ss_pred             eeEEEEEecCC--------eeEecCCchhhhcCCCeEEEEEeCCCCcEEEEEec---ccCChhHHHHHHHHHHHHHHHHH
Q psy18119        155 VVACSASLAGD--------TPLVDISHLEETLGGPNLTVAALPLSGKVAVMELS---QKLHLDHLPRVLDCALKGCADIH  223 (263)
Q Consensus       155 ~~avt~~~~~~--------~~lvDPt~~Ee~~~~~~l~v~~~~~~~~i~~i~~~---G~i~~~~l~~~i~~A~~~~~~i~  223 (263)
                      ++++++|++.+        .++.|....|....+..|-|+.  ...-|+++|++   ..++.+.+.++++.|.++..+|.
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            46788888732        5789999999999999999998  35559999998   56899999999999999999999


Q ss_pred             HHHHHHHHHH
Q psy18119        224 AILDTAIKQH  233 (263)
Q Consensus       224 ~~i~~~l~~~  233 (263)
                      +.|.+++...
T Consensus        81 ~~M~~~i~~p   90 (96)
T d1e3ha6          81 DVMMEAIDTP   90 (96)
T ss_dssp             HHHHHHCSSC
T ss_pred             HHHHHHhccc
Confidence            9999887544