Citrus Sinensis ID: 006991

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620--

MVPKFKPSPLRIRSFCTKTVQQNPHHWPIKQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISYLSEAQESTVKVRMGNPMAVDHATKSSSSPALSVADTVFIERVRSRVKHWKNACTDSDIKTEAALVTSLRKIVLGGEQFGSRPSMTIDVCSERQVQLVLKMLEDFSDVLVPLIIPAKGGGTQAVRAVLTSSDEDKDLLKRELQTFEFEQNKRVRGFREVIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILKITPDAIESSDDFLASAINRYANIFYSLPGSSQEPTNEEIRGWTNDKRKVSCEDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFKNVMNSKAVSGPLREMVSDGLKAAGYETYQRVCSSGLWESALADALDKTLASHNCLSEAAYETKQSEIYLSNELINLAEL

ccccccccHHHHccccccccccccccccEEEEccccHHHHHHHHHHHcccccEEEEEcccccccccccccccccccHHHHHHHHHHHcccccEEEEEEEcEEEcccccccccEEEEccccHHHcccccccEEEEccHHHHHHHHccccccHHHHcccccccHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHcccccEEEEEEcccccccEEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHccccEEEccHHHHHHHHHHHccccccccHHHHHHHHHHHcccEEEHHHHHHHHccccccccHHHHHHHHHcccccccEEccccccccccccccHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHHcccccccEEEEEEcccEEEEEEcccccHHHHHHHHHHcccccHHHHHHHccccccccHHHHHHHHccccccHHHHHHHHHHHccccccccHHccccccHHccccccccccc

ccccccccHHHHHHHHccccccccccccHHHHcHHHHHHHHHHHHHHHHcccEEEEEEEEccccccccccccccccHHHHHHHHHHHHHHcEEEEEEEEEEEEccccEEEEEEEEEEcccccccccccccEEEEEHHHHHHHHHccccHHHHHHcccccccHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccccEEEEEEcccccEEEEEEEccHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEccHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccEEcHHHHHHHcccccccccHHHHHHHHcccccccccccccccccccHHHHccHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHcccccccccccccccccccccccEEccccEEEEEcccccccHHHHHHHHHHHcccccEEEEEEEEcccEEEEEEccccHHHHHHHHcccccccccHHHHHHccccccccHHHHHHHcccccHHHHHHHHHHHHcccccccccccccccccEEcccccEccccc

mvpkfkpsplrirSFCTKTvqqnphhwpikqitkTNFNESLSEIKNHISSSDFIAVSLqntgsfsspwhrvstfdtpetAYLKAKFAAERFQILQFAICpfklqaskviaypynfhlfprdelkmgmpsysftcQTSYLTAMAKegfdfntciyDGISYLSEAQESTVKvrmgnpmavdhatksssspalsvadTVFIERVRSRVKHWknactdsdiKTEAALVTSLRKIVlggeqfgsrpsmtidvCSERQVQLVLKMLEDFSDVLvpliipakgggtQAVRAVLTSSDEDKDLLKRELQTFEFEQNKRVRGFREVIDLISAsqkplvahnslndftfihskflaplppnmNEFICSLRLAFPQVIDVnyllkdigpvkkmtNISATIAYLKNrffapiemeipnqanenegkihgHNVVKICQLFGKLCSilkitpdaiesSDDFLASAINRYANIfyslpgssqeptneeirgwtndkrkvscEDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIvvfgkpglsntfknvmnskavsgplrEMVSDGLKAAGYETYQRVCSSGLWESALADALDKTLAshnclseaayETKQSEIYLSNELINLAEL

mvpkfkpsplrirSFCTKtvqqnphhwpikqiTKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISYLSEAQESTVKVRMGNPMAVDhatksssspalsvADTVFIERVRSRVkhwknactdsdikteAALVTSLRKIVLGgeqfgsrpsmtidVCSERQVQLVLKMLEDFSDVLVPLIipakgggtqAVRAVLtssdedkdLLKRELqtfefeqnkrvrgFREVIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLkdigpvkkMTNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILKITPDAIESSDDFLASAINRYANIFYslpgssqeptneeirgwtndkrkvsCEDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFgkpglsntfkNVMNSKAVSGPLREMVSDGLKAAGYETYQRVCSSGLWESALADALDKTLASHNCLSEaayetkqseiylsnelinlael

***********IRSFCTKTVQQNPHHWPIKQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISYLSE****************************SVADTVFIERVRSRVKHWKNACTDSDIKTEAALVTSLRKIVLGGEQFGSRPSMTIDVCSERQVQLVLKMLEDFSDVLVPLIIPAKGGGTQAVRAVLT********LKRELQTFEFEQNKRVRGFREVIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILKITPDAIESSDDFLASAINRYANIFYSL***********IRGWTNDKRKVSCEDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFKNVMNSKAVSGPLREMVSDGLKAAGYETYQRVCSSGLWESALADALDKTLASHNCLSEAAYETKQSEIYLSNELI*****

****************************IKQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRV*TFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISYLSEAQEST************************VADTVFIERVRSRVKHWKNACTDS***TEAALVTSLRK*************MTIDVCSERQVQLVLKMLEDFSDVLVPLIIPAKGGGTQAVRAVLT***********************VRGFREVIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIG***********IAYLKNRFFAPI***********EGKIHGHNVVKICQLFGKLCSILK*****************NRYANIFYSL**********************SCEDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFKNVMN*********EMVSDGLKAAGYETYQRVCSSGLWESALAD*************************LSNELINLAEL

********PLRIRSFCTKTVQQNPHHWPIKQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISYLSEAQESTVKVRMGNPMAV************SVADTVFIERVRSRVKHWKNACTDSDIKTEAALVTSLRKIVLGGEQFGSRPSMTIDVCSERQVQLVLKMLEDFSDVLVPLIIPAKGGGTQAVRAVLTSSDEDKDLLKRELQTFEFEQNKRVRGFREVIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILKITPDAIESSDDFLASAINRYANIFYSLPG*********IRGWTNDKRKVSCEDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFKNVMNSKAVSGPLREMVSDGLKAAGYETYQRVCSSGLWESALADALDKTLASHNCLSEAAYETKQSEIYLSNELINLAEL

****FKPSPLRIRSFCTKTVQQNPHHWPIKQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISYLSEAQESTVKVRMGNPM*************LSVADTVFIERVRSRVKHWKNACTDS*****AALVTSLRKIVLGGEQFGSRPSMTIDVCSERQVQLVLKMLEDFSDVLVPLIIPAKGGGTQAVRAVLTSSDEDKDLLKRELQTFEFEQNKRVRGFREVIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKICQLFGKLCSILKITPDAIESSDDFLASAINRYANIFYSLPGSS***TNEEIRGWTNDKRKVSCEDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFKNVMNSKAVSGPLREMVSDGLKAAGYETYQRVCSSGLWESALADALDKTLAS************QSEIYLSNELINL**L

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		622	2.2.26 [Sep-21-2011]
Q8W4C3		618	Poly(A)-specific ribonucl	yes	no	0.958	0.964	0.557	0.0
Q9LG26		689	Poly(A)-specific ribonucl	no	no	0.929	0.838	0.264	1e-59
Q90ZA1		631	Poly(A)-specific ribonucl	N/A	no	0.530	0.522	0.263	2e-26
P69341		638	Poly(A)-specific ribonucl	yes	no	0.546	0.532	0.256	4e-24
O95453		639	Poly(A)-specific ribonucl	yes	no	0.561	0.546	0.255	3e-23
Q5RC51		639	Poly(A)-specific ribonucl	yes	no	0.561	0.546	0.255	4e-23
Q8VDG3		624	Poly(A)-specific ribonucl	no	no	0.546	0.544	0.256	2e-21
Q8NA58		520	Poly(A)-specific ribonucl	no	no	0.432	0.517	0.271	8e-19
Q5R6R6		520	Poly(A)-specific ribonucl	no	no	0.435	0.521	0.264	1e-18
Q7ZU92		660	Poly(A)-specific ribonucl	yes	no	0.221	0.209	0.328	1e-15

>sp\|Q8W4C3\|PARNL_ARATH Poly(A)-specific ribonuclease PARN-like OS=Arabidopsis thaliana GN=At3g25430 PE=2 SV=1	Back alignment and function desciption

 Score =  680 bits (1755), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 342/613 (55%), Positives = 452/613 (73%), Gaps = 17/613 (2%)

Query: 17  TKTVQQNPHHWPIKQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDT 76
           TKT+ Q    W +KQ+ K+NF+ +L EI+  I SSDFIA+SLQNTGS+++ WHRVS  DT
Sbjct: 16  TKTLNQG--RWSVKQVKKSNFHVTLDEIRTSIDSSDFIALSLQNTGSYAAAWHRVSAIDT 73

Query: 77  PETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRDELKMGMPSYSFTCQT 136
           P+T+YLKAK+AAER+QILQFA+CPF LQ SK+  +PYNFHLFPRDELK GMPSYSF+CQ 
Sbjct: 74  PQTSYLKAKYAAERYQILQFALCPFSLQGSKLTVHPYNFHLFPRDELKCGMPSYSFSCQA 133

Query: 137 SYLTAMAKEGFDFNTCIYDGISYLSEAQESTVKVRMGNPMAVDHATKSSSSPALSVADTV 196
           S LTAMA+EGFDFN CIY+GISYLS AQES  K    NP+  D  T  SSSPA +VADTV
Sbjct: 134 SRLTAMAREGFDFNICIYEGISYLSRAQESASKFLSENPILADSVT-VSSSPA-TVADTV 191

Query: 197 FIERVRSRVKHWKNACTDSDIKT-EAALVTSLRKIVLGGEQFGSRPSMTIDVCSERQVQL 255
           F+ R+RSRVK+W+ +C DS  KT +  LV+SLR++VLG EQ+GSR  +TIDVCSERQVQL
Sbjct: 192 FVGRIRSRVKNWRQSCIDSGSKTGDDDLVSSLRRLVLGSEQYGSRLCLTIDVCSERQVQL 251

Query: 256 VLKMLEDFSDVLVPLIIPAKGGGTQAVRAVLTSSDEDKDLLKRELQTFEFEQNKRVRGFR 315
           +L+ML +FSD +VPL++ +K  GTQAVR V  SS EDKDL KREL+  E E+N+RVRGFR
Sbjct: 252 ILEMLTEFSDDVVPLLVASKSRGTQAVRTVFMSSKEDKDLFKRELKDLEKEENRRVRGFR 311

Query: 316 EVIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKD 375
           EV+D IS+SQKP+V+ N L+DFT IH+KFL PLP N+++F  SL  AFP V+D++  +K+
Sbjct: 312 EVVDFISSSQKPVVSQNYLSDFTSIHAKFLGPLPSNVDDFSSSLSSAFPNVVDLSQFMKE 371

Query: 376 IGPVKKMTNISATIAYLKNRFFAPIEMEIPNQA---NENEG-KIHGHNVVKICQLFGKLC 431
           I P+  ++N+ A ++ L NRFFAP+++E+ NQ      +EG + HG N V I QLF KLC
Sbjct: 372 ISPLSNISNLPAAMSSL-NRFFAPVDVEVANQGCPVKLDEGHQSHGQNAVMISQLFAKLC 430

Query: 432 SILKITPDAIESSDDFLASAINRYANIFYSLPGSSQEPTNEEIRGWTNDKRKVSCEDVVF 491
           +I K     I+S++DF A A + +AN   S+   S+   +E ++ W+ + R+VS E++VF
Sbjct: 431 TIQKSDLSTIQSNEDFQALASDEHAN---SVTSCSKNAGDENVKVWSKNSRRVSSENLVF 487

Query: 492 LWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTF-KNVMNSKA 550
           +WG  ++++A  LKN+LQ SH VFA  F+V+ +DRS AI+VF + G S TF   V N + 
Sbjct: 488 IWGLGKKMTAAKLKNVLQKSHPVFAREFDVKYIDRSSAILVFWESGPSETFLSAVNNEEQ 547

Query: 551 VSGPLREMVSDGLKAAGYETYQRVCSSGLWESALADALDKTLASHNCLSEAAYETKQSEI 610
           + G LREMV++GL+ AGYETY+R C  G WE+ LA++LDK L S +  ++   +TK SEI
Sbjct: 548 LDGSLREMVAEGLRGAGYETYKRACRLGFWEADLAESLDKALESSD--TDPDSDTKPSEI 605

Query: 611 YLSNEL-INLAEL 622
             SNEL IN  EL
Sbjct: 606 DWSNELAINFDEL 618

3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 1EC: .EC: 1EC: 3EC: .EC: 4

>sp\|Q9LG26\|PARN_ARATH Poly(A)-specific ribonuclease PARN OS=Arabidopsis thaliana GN=PARN PE=1 SV=2	Back alignment and function description

>sp\|Q90ZA1\|PARN_XENLA Poly(A)-specific ribonuclease PARN OS=Xenopus laevis GN=parn PE=1 SV=1	Back alignment and function description

>sp\|P69341\|PARN_BOVIN Poly(A)-specific ribonuclease PARN OS=Bos taurus GN=PARN PE=1 SV=2	Back alignment and function description

>sp\|O95453\|PARN_HUMAN Poly(A)-specific ribonuclease PARN OS=Homo sapiens GN=PARN PE=1 SV=1	Back alignment and function description

>sp\|Q5RC51\|PARN_PONAB Poly(A)-specific ribonuclease PARN OS=Pongo abelii GN=PARN PE=2 SV=1	Back alignment and function description

>sp\|Q8VDG3\|PARN_MOUSE Poly(A)-specific ribonuclease PARN OS=Mus musculus GN=Parn PE=1 SV=1	Back alignment and function description

>sp\|Q8NA58\|PNDC1_HUMAN Poly(A)-specific ribonuclease PARN-like domain-containing protein 1 OS=Homo sapiens GN=PNLDC1 PE=2 SV=2	Back alignment and function description

>sp\|Q5R6R6\|PNDC1_PONAB Poly(A)-specific ribonuclease PARN-like domain-containing protein 1 OS=Pongo abelii GN=PNLDC1 PE=2 SV=1	Back alignment and function description

>sp\|Q7ZU92\|PARN_DANRE Poly(A)-specific ribonuclease PARN OS=Danio rerio GN=parn PE=1 SV=2	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		622
255572662		624	ribonuclease, putative [Ricinus communis	0.982	0.979	0.642	0.0
224136934		626	predicted protein [Populus trichocarpa]	0.982	0.976	0.623	0.0
224132034		628	predicted protein [Populus trichocarpa]	0.982	0.972	0.592	0.0
15230837		618	Poly(A)-specific ribonuclease PARN-like	0.958	0.964	0.557	0.0
356527283		619	PREDICTED: poly(A)-specific ribonuclease	0.954	0.959	0.548	0.0
9279724		1115	unnamed protein product [Arabidopsis tha	0.938	0.523	0.556	0.0
449502106		610	PREDICTED: LOW QUALITY PROTEIN: poly(A)-	0.966	0.985	0.537	0.0
449462471		610	PREDICTED: poly(A)-specific ribonuclease	0.966	0.985	0.535	0.0
297831446		1055	predicted protein [Arabidopsis lyrata su	0.922	0.544	0.555	0.0
224129918		544	predicted protein [Populus trichocarpa]	0.842	0.963	0.548	0.0

>gi\|255572662\|ref\|XP_002527264.1\| ribonuclease, putative [Ricinus communis] gi\|223533357\|gb\|EEF35108.1\| ribonuclease, putative [Ricinus communis]	Back alignment and taxonomy information

 Score =  822 bits (2122), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 399/621 (64%), Positives = 487/621 (78%), Gaps = 10/621 (1%)

Query: 9   PLRI--RSFCTKTVQQNPH---HWPIKQITKTNFNESLSEIKNHISSSDFIAVSLQNTGS 63
           PLR+  R FCTK      H    W +KQITK+NF +SL EI +HI  SDFI++SL+ TGS
Sbjct: 7   PLRLQRRLFCTKIHHHRAHTHNQWNVKQITKSNFADSLPEINSHIMCSDFISISLKTTGS 66

Query: 64  FSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRDEL 123
           FSSPWHRVS FDTP+ AYLK+K AAE+FQILQ A+CPF + ASKV AYPYNFHLFPRDEL
Sbjct: 67  FSSPWHRVSPFDTPDVAYLKSKHAAEKFQILQLAVCPFTVSASKVTAYPYNFHLFPRDEL 126

Query: 124 KMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISYLSEAQESTVKVRMGNPMAVDHATK 183
             GMPSYSF+C TSYLT M +EGFDFN C+ DGISYLS AQES  +VRM NP       +
Sbjct: 127 NSGMPSYSFSCHTSYLTKMVQEGFDFNACVNDGISYLSRAQESAARVRMKNPFLAKDIVE 186

Query: 184 SSSSPALSVADTVFIERVRSRVKHWKNACTDSDIKTEAALVTSLRKIVLGGEQFGSRPSM 243
           S+S+P   VAD+VF++R RSRVK+WKNACTD+   T+ ALV SLRK+VLG E++ SRP +
Sbjct: 187 STSTPG--VADSVFVQRTRSRVKNWKNACTDTS-STDEALVKSLRKLVLGLEEYNSRPCI 243

Query: 244 TIDVCSERQVQLVLKMLEDFSDVLVPLIIPAKGGGTQAVRAVLTSSDEDKDLLKRELQTF 303
            IDVCSERQV LV++ML++F+D LVPLI+PAKGGGTQAVR VLTSS ED+DLL+ ELQ  
Sbjct: 244 NIDVCSERQVHLVIEMLQEFADDLVPLIVPAKGGGTQAVRVVLTSSKEDRDLLQMELQNL 303

Query: 304 EFEQNKRVRGFREVIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAF 363
           E EQNK++RGFREVIDLIS S+KP+V+HNSLND  FIHSKFLAPLPP+M EF CSLRL F
Sbjct: 304 EDEQNKKIRGFREVIDLISGSEKPVVSHNSLNDLAFIHSKFLAPLPPSMEEFTCSLRLVF 363

Query: 364 PQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKI 423
           PQVIDVN+L+K+I P+KK+TNI    +YLKN FFAP++MEIP  A  NEGKIHGHNV++I
Sbjct: 364 PQVIDVNHLMKEISPLKKVTNIPMATSYLKNWFFAPVDMEIPFPAMVNEGKIHGHNVMRI 423

Query: 424 CQLFGKLCSILKITPDAIESSDDFLASAINRYANIFYSLPGSSQEPTNEEIRGWTNDKRK 483
           CQLF KLC ILK+ P++I+S++  LASAI  Y NIF       QEPT+E++R WTN+ RK
Sbjct: 424 CQLFAKLCYILKLAPNSIQSNEKNLASAIEAYVNIFSPYFPGPQEPTDEDVRIWTNNTRK 483

Query: 484 VSCEDVVFLWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFK 543
           VSC+D+VFLWGFR R+SAG+LK++LQ SH+VF+E F+VR VD+SCAIVVF +PGLSNT  
Sbjct: 484 VSCQDLVFLWGFRYRMSAGMLKSLLQQSHKVFSEEFDVRFVDKSCAIVVFWEPGLSNTLL 543

Query: 544 NVM-NSKAVSGPLREMVSDGLKAAGYETYQRVCSSGLWESALADALDKTLASHNCLSEAA 602
           +V+  S  + GPLREMVS+G++AA Y+TY RVC  GLW   LAD+LDK LA  +  S++ 
Sbjct: 544 DVLKGSSEIVGPLREMVSEGVRAASYDTYNRVCRLGLWHENLADSLDKALADTDHPSDSD 603

Query: 603 YETKQSEIYLSNE-LINLAEL 622
             T  S  Y  +E +INL EL
Sbjct: 604 SVTSSSNTYWCHEWMINLDEL 624

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224136934\|ref\|XP_002326981.1\| predicted protein [Populus trichocarpa] gi\|222835296\|gb\|EEE73731.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|224132034\|ref\|XP_002321239.1\| predicted protein [Populus trichocarpa] gi\|222862012\|gb\|EEE99554.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi|15230837|ref|NP_189170.1| Poly(A)-specific ribonuclease PARN-like protein [Arabidopsis thaliana] gi|75162449|sp|Q8W4C3.1|PARNL_ARATH RecName: Full=Poly(A)-specific ribonuclease PARN-like; AltName: Full=Polyadenylate-specific ribonuclease-like protein gi|17065176|gb|AAL32742.1| Unknown protein [Arabidopsis thaliana] gi|30725444|gb|AAP37744.1| At3g25430 [Arabidopsis thaliana] gi|332643489|gb|AEE77010.1| Poly(A)-specific ribonuclease PARN-like protein [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|356527283\|ref\|XP_003532241.1\| PREDICTED: poly(A)-specific ribonuclease PARN-like [Glycine max]	Back alignment and taxonomy information

>gi\|9279724\|dbj\|BAB01314.1\| unnamed protein product [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|449502106\|ref\|XP_004161545.1\| PREDICTED: LOW QUALITY PROTEIN: poly(A)-specific ribonuclease PARN-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449462471\|ref\|XP_004148964.1\| PREDICTED: poly(A)-specific ribonuclease PARN-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|297831446\|ref\|XP_002883605.1\| predicted protein [Arabidopsis lyrata subsp. lyrata] gi\|297329445\|gb\|EFH59864.1\| predicted protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|224129918\|ref\|XP_002320703.1\| predicted protein [Populus trichocarpa] gi\|222861476\|gb\|EEE99018.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		622
TAIR\|locus:2094533		618	AT3G25430 [Arabidopsis thalian	0.958	0.964	0.556	4.1e-175
TAIR\|locus:2012100		689	AHG2 "ABA-HYPERSENSITIVE GERMI	0.596	0.538	0.297	3.7e-62
UNIPROTKB\|F1NEI8		631	F1NEI8 "Uncharacterized protei	0.221	0.218	0.328	1.1e-22
UNIPROTKB\|F6XU41		638	PARN "Uncharacterized protein"	0.221	0.216	0.335	1.3e-22
ZFIN\|ZDB-GENE-040426-880		660	parn "poly(A)-specific ribonuc	0.221	0.209	0.328	1.4e-22
UNIPROTKB\|P69341		638	PARN "Poly(A)-specific ribonuc	0.221	0.216	0.335	3.2e-22
UNIPROTKB\|E2QZA0		496	PARN "Uncharacterized protein"	0.221	0.278	0.331	3.7e-22
RGD\|1565449		624	Parn "poly(A)-specific ribonuc	0.281	0.280	0.291	6.7e-22
UNIPROTKB\|O95453		639	PARN "Poly(A)-specific ribonuc	0.221	0.215	0.335	1.1e-21
MGI\|MGI:1921358		624	Parn "poly(A)-specific ribonuc	0.281	0.280	0.291	1.1e-21

TAIR\|locus:2094533 AT3G25430 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1701 (603.8 bits), Expect = 4.1e-175, P = 4.1e-175
 Identities = 341/613 (55%), Positives = 454/613 (74%)

Query:    17 TKTVQQNPHHWPIKQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDT 76
             TKT+ Q    W +KQ+ K+NF+ +L EI+  I SSDFIA+SLQNTGS+++ WHRVS  DT
Sbjct:    16 TKTLNQG--RWSVKQVKKSNFHVTLDEIRTSIDSSDFIALSLQNTGSYAAAWHRVSAIDT 73

Query:    77 PETAYLKAKFAAERFQILQFAICPFKLQASKVIAYPYNFHLFPRDELKMGMPSYSFTCQT 136
             P+T+YLKAK+AAER+QILQFA+CPF LQ SK+  +PYNFHLFPRDELK GMPSYSF+CQ 
Sbjct:    74 PQTSYLKAKYAAERYQILQFALCPFSLQGSKLTVHPYNFHLFPRDELKCGMPSYSFSCQA 133

Query:   137 SYLTAMAKEGFDFNTCIYDGISYLSEAQESTVKVRMGNPMAVDHATKSSSSPALSVADTV 196
             S LTAMA+EGFDFN CIY+GISYLS AQES  K    NP+  D  T SSS PA +VADTV
Sbjct:   134 SRLTAMAREGFDFNICIYEGISYLSRAQESASKFLSENPILADSVTVSSS-PA-TVADTV 191

Query:   197 FIERVRSRVKHWKNACTDSDIKT-EAALVTSLRKIVLGGEQFGSRPSMTIDVCSERQVQL 255
             F+ R+RSRVK+W+ +C DS  KT +  LV+SLR++VLG EQ+GSR  +TIDVCSERQVQL
Sbjct:   192 FVGRIRSRVKNWRQSCIDSGSKTGDDDLVSSLRRLVLGSEQYGSRLCLTIDVCSERQVQL 251

Query:   256 VLKMLEDFSDVLVPLIIPAKGGGTQAVRAVLTSSDEDKDLLKRELQTFEFEQNKRVRGFR 315
             +L+ML +FSD +VPL++ +K  GTQAVR V  SS EDKDL KREL+  E E+N+RVRGFR
Sbjct:   252 ILEMLTEFSDDVVPLLVASKSRGTQAVRTVFMSSKEDKDLFKRELKDLEKEENRRVRGFR 311

Query:   316 EVIDLISASQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKD 375
             EV+D IS+SQKP+V+ N L+DFT IH+KFL PLP N+++F  SL  AFP V+D++  +K+
Sbjct:   312 EVVDFISSSQKPVVSQNYLSDFTSIHAKFLGPLPSNVDDFSSSLSSAFPNVVDLSQFMKE 371

Query:   376 IGPVKKMTNISATIAYLKNRFFAPIEMEIPNQA---NENEG-KIHGHNVVKICQLFGKLC 431
             I P+  ++N+ A ++ L NRFFAP+++E+ NQ      +EG + HG N V I QLF KLC
Sbjct:   372 ISPLSNISNLPAAMSSL-NRFFAPVDVEVANQGCPVKLDEGHQSHGQNAVMISQLFAKLC 430

Query:   432 SILKITPDAIESSDDFLASAINRYANIFYSLPGSSQEPTNEEIRGWTNDKRKVSCEDVVF 491
             +I K     I+S++DF A A + +AN   S+   S+   +E ++ W+ + R+VS E++VF
Sbjct:   431 TIQKSDLSTIQSNEDFQALASDEHAN---SVTSCSKNAGDENVKVWSKNSRRVSSENLVF 487

Query:   492 LWGFRERISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFKNVMNSKA- 550
             +WG  ++++A  LKN+LQ SH VFA  F+V+ +DRS AI+VF + G S TF + +N++  
Sbjct:   488 IWGLGKKMTAAKLKNVLQKSHPVFAREFDVKYIDRSSAILVFWESGPSETFLSAVNNEEQ 547

Query:   551 VSGPLREMVSDGLKAAGYETYQRVCSSGLWESALADALDKTLASHNCLSEAAYETKQSEI 610
             + G LREMV++GL+ AGYETY+R C  G WE+ LA++LDK L S +  ++   +TK SEI
Sbjct:   548 LDGSLREMVAEGLRGAGYETYKRACRLGFWEADLAESLDKALESSD--TDPDSDTKPSEI 605

Query:   611 YLSNEL-INLAEL 622
               SNEL IN  EL
Sbjct:   606 DWSNELAINFDEL 618

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004540 "ribonuclease activity" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0009451 "RNA modification" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM

TAIR\|locus:2012100 AHG2 "ABA-HYPERSENSITIVE GERMINATION 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NEI8 F1NEI8 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|F6XU41 PARN "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-040426-880 parn "poly(A)-specific ribonuclease (deadenylation nuclease)" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|P69341 PARN "Poly(A)-specific ribonuclease PARN" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2QZA0 PARN "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

RGD\|1565449 Parn "poly(A)-specific ribonuclease" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|O95453 PARN "Poly(A)-specific ribonuclease PARN" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

MGI\|MGI:1921358 Parn "poly(A)-specific ribonuclease (deadenylation nuclease)" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

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)
Q8W4C3	PARNL_ARATH	3, ., 1, ., 1, 3, ., 4	0.5579	0.9581	0.9644	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.13.4	0.946
3rd Layer	3.1.13	0.963

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		622
pfam04857		235	pfam04857, CAF1, CAF1 family ribonuclease	3e-26
pfam04857		235	pfam04857, CAF1, CAF1 family ribonuclease	5e-12

>gnl\|CDD\|147159 pfam04857, CAF1, CAF1 family ribonuclease	Back alignment and domain information

 Score =  107 bits (269), Expect = 3e-26
 Identities = 38/138 (27%), Positives = 62/138 (44%), Gaps = 14/138 (10%)

Query: 30  KQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAE 89
           +++ ++NF+E   EI+  I S DFIA+  +  G  + P    S   T +  Y   +   +
Sbjct: 1   REVWRSNFHEEFKEIRQAIDSYDFIAIDTEFPGVVARPIG--SFRSTSDYRYQALRKNVD 58

Query: 90  RFQILQFAICPFKL---QASKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEG 146
           R +I+Q  +  F            + +NF LF  +E              S +  +AK+G
Sbjct: 59  RLKIIQLGLTLFDEKGNLPDSYYTWQFNFSLFNLEE---------DFYAPSSIEFLAKQG 109

Query: 147 FDFNTCIYDGISYLSEAQ 164
           FDFN    +GI YL  A+
Sbjct: 110 FDFNKHRREGIPYLRFAE 127

The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom#resolution. Length = 235

>gnl\|CDD\|147159 pfam04857, CAF1, CAF1 family ribonuclease	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		622
PF04857		262	CAF1: CAF1 family ribonuclease; InterPro: IPR00694	100.0
KOG0304		239	consensus mRNA deadenylase subunit [RNA processing	99.97
KOG1990		564	consensus Poly(A)-specific exoribonuclease PARN [R	99.96
COG5228		299	POP2 mRNA deadenylase subunit [RNA processing and	99.87
PF08675		87	RNA_bind: RNA binding domain; InterPro: IPR014789	99.57
PRK07740		244	hypothetical protein; Provisional	97.19
cd06131		167	DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl	97.06
PRK06195		309	DNA polymerase III subunit epsilon; Validated	96.98
TIGR01406		225	dnaQ_proteo DNA polymerase III, epsilon subunit, P	96.97
cd02637		65	R3H_PARN R3H domain of Poly(A)-specific ribonuclea	96.9
PRK05711		240	DNA polymerase III subunit epsilon; Provisional	96.86
cd06134		189	RNaseT DEDDh 3'-5' exonuclease domain of RNase T.	96.86
PF10309		62	DUF2414: Protein of unknown function (DUF2414); In	96.84
PRK07942		232	DNA polymerase III subunit epsilon; Provisional	96.83
TIGR00573		217	dnaq exonuclease, DNA polymerase III, epsilon subu	96.79
PRK06063		313	DNA polymerase III subunit epsilon; Provisional	96.74
cd06130		156	DNA_pol_III_epsilon_like an uncharacterized bacter	96.66
PRK06807		313	DNA polymerase III subunit epsilon; Validated	96.59
PRK09145		202	DNA polymerase III subunit epsilon; Validated	96.59
PRK05168		211	ribonuclease T; Provisional	96.53
TIGR01298		200	RNaseT ribonuclease T. in gamma-subdivision Proteo	96.49
PRK09146		239	DNA polymerase III subunit epsilon; Validated	96.48
cd06145		150	REX1_like DEDDh 3'-5' exonuclease domain of RNA ex	96.37
cd06137		161	DEDDh_RNase DEDDh 3'-5' exonuclease domain of the	96.27
PRK07983		219	exodeoxyribonuclease X; Provisional	96.24
cd06127		159	DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh	95.98
PRK06309		232	DNA polymerase III subunit epsilon; Validated	95.72
smart00479		169	EXOIII exonuclease domain in DNA-polymerase alpha	95.71
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	95.65
PRK07883		557	hypothetical protein; Validated	95.61
cd06144		152	REX4_like DEDDh 3'-5' exonuclease domain of RNA ex	95.36
TIGR01405		1213	polC_Gram_pos DNA polymerase III, alpha chain, Gra	95.36
PRK06722		281	exonuclease; Provisional	95.29
PRK07247		195	DNA polymerase III subunit epsilon; Validated	95.19
PRK06310		250	DNA polymerase III subunit epsilon; Validated	95.09
PRK05601		377	DNA polymerase III subunit epsilon; Validated	94.96
KOG4483		528	consensus Uncharacterized conserved protein [Funct	94.92
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	94.9
cd06149		157	ISG20 DEDDh 3'-5' exonuclease domain of Interferon	94.9
PRK07748		207	sporulation inhibitor KapD; Provisional	94.84
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	94.6
PRK08517		257	DNA polymerase III subunit epsilon; Provisional	94.4
PRK00448		1437	polC DNA polymerase III PolC; Validated	93.9
PF00929		164	RNase_T: Exonuclease; InterPro: IPR013520 This ent	91.87
cd06133		176	ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o	91.01
cd06133		176	ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o	90.53
cd06136		177	TREX1_2 DEDDh 3'-5' exonuclease domain of three pr	90.36
cd06138		183	ExoI_N N-terminal DEDDh 3'-5' exonuclease domain o	89.65
COG0847		243	DnaQ DNA polymerase III, epsilon subunit and relat	88.65
PRK05168		211	ribonuclease T; Provisional	87.41
PRK09182		294	DNA polymerase III subunit epsilon; Validated	86.96
PRK09145		202	DNA polymerase III subunit epsilon; Validated	86.29
PF01612		176	DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR00	86.25
PF00076		70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	85.94
PTZ00315		582	2'-phosphotransferase; Provisional	85.41
smart00479		169	EXOIII exonuclease domain in DNA-polymerase alpha	84.26
PF11608		90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	82.56
PF08777		105	RRM_3: RNA binding motif; InterPro: IPR014886 This	81.99
PRK11779		476	sbcB exonuclease I; Provisional	81.96

>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation	Back alignment and domain information

Probab=100.00  E-value=1.7e-63  Score=512.64  Aligned_cols=246  Identities=38%  Similarity=0.600  Sum_probs=197.4

Q ss_pred             EEcCcccHHHHHHHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeee-ecCC---
Q 006991           30 KQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPF-KLQA---  105 (622)
Q Consensus        30 ~dVt~~NF~~~l~~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f-~~~~---  105 (622)
                      ||||++||+++||.|+++|++|+|||||+||||+...+.+.  ..+|+++||+++|.+|++|+|+|+|||+| +.++   
T Consensus         1 m~Vt~~Nf~~~l~~i~~~i~~~~fvaiD~EftGl~~~~~~~--~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~   78 (262)
T PF04857_consen    1 MEVTRSNFEEELPEILQAISKADFVAIDTEFTGLVSKPPRS--RFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIP   78 (262)
T ss_dssp             EEE-CCCHHHHHHHHHHHHHHSSEEEEEEEES-S-SSS-SH--CSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEE
T ss_pred             CcccHHHHHHHHHHHHHHHhhCCEEEEEeeccccccCCCcc--ccccHHHHHHHHHHhhcccccceeeEEEeecccccCC
Confidence            89999999999999999999999999999999997654322  89999999999999999999999999999 4444   


Q ss_pred             CceeeEeeEEeecCccccccCCCCCceeechhHHHHHHHcCCCcchhhhcccccCCHHHHHHHHHHhCCCccccccccCC
Q 006991          106 SKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISYLSEAQESTVKVRMGNPMAVDHATKSS  185 (622)
Q Consensus       106 ~~y~~~~fNF~lfp~~~~~~~~~d~~f~~q~sSl~FL~~~gFDFnk~~~~GI~YLs~~eE~~~r~~~~~~~~~~~~~~~~  185 (622)
                      .+|.+|+|||++||..        +.|+ |++||+||++||||||+|+++||||+++.||+.++                
T Consensus        79 ~~~~~~~~nf~~f~~~--------~~~~-~~~sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~----------------  133 (262)
T PF04857_consen   79 SSYNVWPFNFYLFPLD--------RDFS-QASSLQFLRKNGFDFNKWFRDGIPYLSFAEEEKAR----------------  133 (262)
T ss_dssp             CCEEEEEEEBSTTSTT--------TCEE-EHHHHHHHHHTT--HHHHHHH-B-HHHHHHHHHHH----------------
T ss_pred             ceeEEEEeeeeccccc--------ccee-cchhHHHHHHcccCHHHHHHhCCCcccccccchhh----------------
Confidence            5789999999999974        4677 99999999999999999999999999988775421                


Q ss_pred             CCCCCCcccHHHHHHHHHHHHHHHhhccCCCchhhHHHHHHHHHHHhcCcccCCCCCccccccchHHHHHHHHHHHhccC
Q 006991          186 SSPALSVADTVFIERVRSRVKHWKNACTDSDIKTEAALVTSLRKIVLGGEQFGSRPSMTIDVCSERQVQLVLKMLEDFSD  265 (622)
Q Consensus       186 ~~~~~~~~d~~fi~~v~~~I~eWl~~~~~~~~~~~~~l~~~l~~~~~~~e~~~~~p~l~l~~~~~~q~~Lv~q~l~~~~~  265 (622)
                                                                                                      
T Consensus       134 --------------------------------------------------------------------------------  133 (262)
T PF04857_consen  134 --------------------------------------------------------------------------------  133 (262)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CcceeeeccCCCCceEEEEEEccChHHHHHHHHHhhHHHHhhhhccccHHHHHHHHHhCCCCEEechhHHHHHHHHHhcc
Q 006991          266 VLVPLIIPAKGGGTQAVRAVLTSSDEDKDLLKRELQTFEFEQNKRVRGFREVIDLISASQKPLVAHNSLNDFTFIHSKFL  345 (622)
Q Consensus       266 ~l~~~~v~~k~g~~~~vrvi~~~~~eek~~l~~e~~~~e~e~~~~~~GFr~Vi~~L~~skKpIVGHN~llDL~~iy~~F~  345 (622)
                                                                  +.+|||.|++++.+++||||||||++||+|||++|+
T Consensus       134 --------------------------------------------~~~g~~~v~~~~~~~~~p~Vghn~~~Dl~~l~~~f~  169 (262)
T PF04857_consen  134 --------------------------------------------ELLGFSGVIDALKSSKKPIVGHNGLYDLMYLYKKFI  169 (262)
T ss_dssp             --------------------------------------------HHHHTCCCSSHCHCC-SEEEESSTHHHHHHHHHHHT
T ss_pred             --------------------------------------------hhHHHHHHHHHhhccCCcEEEeChHhHHHHHHHHhc
Confidence                                                        123788889999999999999999999999999999


Q ss_pred             CCCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCceeecCCC----C-------CCCC-c
Q 006991          346 APLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEMEIPNQ----A-------NENE-G  413 (622)
Q Consensus       346 gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~p~ve~~~~----~-------~~~~-~  413 (622)
                      ||||++++||++.++++||.|||||||++...  ...++|+.+.+.+.... .++.+..+..    .       ..+. .
T Consensus       170 ~~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~--~~~~~L~~l~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~  246 (262)
T PF04857_consen  170 GPLPETLEEFKELLRELFPRIYDTKYLAEECP--GKSTSLQELAEELGIRR-NPSSISSPEGFPSYDEEKNNFPMFGEKA  246 (262)
T ss_dssp             TS--SSHHHHHHHHHHHSSSEEEHHHHHTSTT--TS-SSHHHHHHHTTSTT-----EEE-TTS-------------SS-T
T ss_pred             CCCCCCHHHHHHHHHHHCcccccHHHHHHhcc--ccccCHHHHHHHhCCCc-cccccccccccccccccccccccCCCCC
Confidence            99999999999999999999999999998765  24567888888775433 2222222210    1       1234 7


Q ss_pred             ccchhhHHHHHHHHHH
Q 006991          414 KIHGHNVVKICQLFGK  429 (622)
Q Consensus       414 h~AGyDA~mTg~vF~~  429 (622)
                      |+|||||||||+||++
T Consensus       247 HeAGyDA~mTg~~F~~  262 (262)
T PF04857_consen  247 HEAGYDAYMTGCVFIK  262 (262)
T ss_dssp             TSHHHHHHHHHHHHHH
T ss_pred             CCcchHHHHHHHHHcC
Confidence            9999999999999986

The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.

>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]	Back alignment and domain information

>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]	Back alignment and domain information

>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]	Back alignment and domain information

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)	Back alignment and domain information

>PRK07740 hypothetical protein; Provisional	Back alignment and domain information

>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins	Back alignment and domain information

>PRK06195 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial	Back alignment and domain information

>cd02637 R3H_PARN R3H domain of Poly(A)-specific ribonuclease (PARN)	Back alignment and domain information

>PRK05711 DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T	Back alignment and domain information

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function	Back alignment and domain information

>PRK07942 DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family	Back alignment and domain information

>PRK06063 DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III	Back alignment and domain information

>PRK06807 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK09145 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK05168 ribonuclease T; Provisional	Back alignment and domain information

>TIGR01298 RNaseT ribonuclease T	Back alignment and domain information

>PRK09146 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins	Back alignment and domain information

>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins	Back alignment and domain information

>PRK07983 exodeoxyribonuclease X; Provisional	Back alignment and domain information

>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family	Back alignment and domain information

>PRK06309 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases	Back alignment and domain information

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK07883 hypothetical protein; Validated	Back alignment and domain information

>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins	Back alignment and domain information

>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type	Back alignment and domain information

>PRK06722 exonuclease; Provisional	Back alignment and domain information

>PRK07247 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK06310 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK05601 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative	Back alignment and domain information

>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins	Back alignment and domain information

>PRK07748 sporulation inhibitor KapD; Provisional	Back alignment and domain information

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK08517 DNA polymerase III subunit epsilon; Provisional	Back alignment and domain information

>PRK00448 polC DNA polymerase III PolC; Validated	Back alignment and domain information

>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III	Back alignment and domain information

>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins	Back alignment and domain information

>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins	Back alignment and domain information

>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins	Back alignment and domain information

>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins	Back alignment and domain information

>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK05168 ribonuclease T; Provisional	Back alignment and domain information

>PRK09182 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PRK09145 DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides	Back alignment and domain information

>PF00076 RRM_1: RNA recognition motif	Back alignment and domain information

>PTZ00315 2'-phosphotransferase; Provisional	Back alignment and domain information

>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases	Back alignment and domain information

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes	Back alignment and domain information

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation	Back alignment and domain information

>PRK11779 sbcB exonuclease I; Provisional	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		622
2a1r_A		430	Crystal Structure Of Parn Nuclease Domain Length =		3e-24
3d45_A		507	Crystal Structure Of Mouse Parn In Complex With M7g		3e-22

>pdb|2A1R|A Chain A, Crystal Structure Of Parn Nuclease Domain Length = 430

Back alignment and structure

Iteration: 1

Score = 110 bits (274), Expect = 3e-24, Method: Compositional matrix adjust. Identities = 98/384 (25%), Positives = 176/384 (45%), Gaps = 35/384 (9%) Query: 31 QITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVST--FDTPETAYLKAKFAA 88 +I ++NF +L ++ I +DF A+ + +G P T FDTPE Y K K + Sbjct: 2 EIIRSNFKSNLHKVYQAIEEADFFAIDGEFSGISDGPSVSALTNGFDTPEERYQKLKKHS 61 Query: 89 ERFQILQFAICPFKLQA--SKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEG 146 F + QF +C FK SK I +NF++FP+ P F CQ+S + +A +G Sbjct: 62 MDFLLFQFGLCTFKYDYTDSKYITKSFNFYVFPK-PFNRSSPDVKFVCQSSSIDFLASQG 120 Query: 147 FDFNTCIYDGISYLSEAQESTVKVRMGNPMAVDHATKSSSSPALSVADTVFIERVRSRVK 206 FDFN +GI YL++ +E ++ + + ++++ + ALS V Sbjct: 121 FDFNKVFRNGIPYLNQEEERQLREQYD-----EKRSQANGAGALSY------------VS 163 Query: 207 HWKNACTDSDIKTEAALVTSLRKIVLGGEQFGSRPSMTIDVCSERQVQLVLKMLEDFSDV 266 + C + + + + + + + Q ++ ++ C+ Q +L+ + L Sbjct: 164 PNTSKCPVTIPEDQKKFIDQVVEKIEDLLQSEENKNLDLEPCTGFQRKLIYQTL----SW 219 Query: 267 LVPLIIPAKGGGTQAV-RAVLTSSDEDKDLLKRELQTFEFEQNK--RVRGFREVIDLISA 323 P I + T+ R ++ S ++++ +RE Q EQ + GF VI I+ Sbjct: 220 KYPKGIHVETLETEKKERYIVISKVDEEERKRREQQKHAKEQEELNDAVGFSRVIHAIAN 279 Query: 324 SQKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMT 383 S K ++ HN L D +F PLP +++EF FP+++D L+ P K + Sbjct: 280 SGKLVIGHNMLLDVMHTVHQFYCPLPADLSEFKEMTTCVFPRLLDTK-LMASTQPFKDII 338 Query: 384 NISATIAYLKNRF----FAPIEME 403 N + ++A L+ R F P ++E Sbjct: 339 N-NTSLAELEKRLKETPFNPPKVE 361

PyMOL of 2a1r

>pdb|3D45|A Chain A, Crystal Structure Of Mouse Parn In Complex With M7gpppg Length = 507

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		622
3d45_A		507	Poly(A)-specific ribonuclease PARN; CAP analogue,	3e-77
2a1r_A		430	Poly(A)-specific ribonuclease PARN; DEDD, nuclease	2e-73
1uoc_A		289	POP2; hydrolase, DEDD nuclease, mRNA degradation,	1e-14
2d5r_A		252	CCR4-NOT transcription complex subunit 7; poly(A)	6e-14
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-13
2p51_A		333	SPCC18.06C protein; DEDD nuclease fold, hydrolase,	5e-12
2p51_A		333	SPCC18.06C protein; DEDD nuclease fold, hydrolase,	5e-04

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus} Length = 507	Back alignment and structure

 Score =  253 bits (647), Expect = 3e-77
 Identities = 106/554 (19%), Positives = 200/554 (36%), Gaps = 63/554 (11%)

Query: 31  QITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSP--WHRVSTFDTPETAYLKAKFAA 88
           +I ++NF  +L ++   I  +DF A+  + +G    P      S FDTPE  Y K K  +
Sbjct: 4   EIIRSNFKINLHKVYQAIEEADFFAIDGEFSGISDGPSVTALTSGFDTPEERYQKLKKHS 63

Query: 89  ERFQILQFAICPFKLQ--ASKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEG 146
             F + QF +C FK     SK +   +NF++FP+       P   F CQ+S +  +A +G
Sbjct: 64  MDFLLFQFGLCAFKYDHTDSKHVTKSFNFYVFPK-PFSRSSPDVKFVCQSSSIDFLASQG 122

Query: 147 FDFNTCIYDGISYLSEAQESTVKVRMGNPMAVDHATKSSSSPALSVA--DTVFIERVRSR 204
           FDFN     GI YL++ +E  ++ +     +  +   + +   +++      FI++V  +
Sbjct: 123 FDFNKVFCSGIPYLNQEEERQLREQFDEKRSQANGAGALAKCPVTIPEDQKKFIDQVIEK 182

Query: 205 VKHWKNACTDSDIKTEAALVTSLRKIVLGGEQFGSRPSMTIDVCSERQVQLVLKMLEDFS 264
           ++ +  +                            + S+ +D C+  Q +L+ + L    
Sbjct: 183 IEDFLQS--------------------------EEKRSLELDPCTGFQRKLIYQTLSWKY 216

Query: 265 DVLVPLIIPAKGGGTQAVRAVLTSSDEDKDLLKRELQTFEFEQNKRVRGFREVIDLISAS 324
              + +         + +       +E++   ++E  T E E+     GF  VI  I+ S
Sbjct: 217 PKGIHVETLETDKKERHIVIS-KVDEEERKRREQEKYTKEQEELNDAVGFSRVIHAIANS 275

Query: 325 QKPLVAHNSLNDFTFIHSKFLAPLPPNMNEFICSLRLAFPQVIDVNYLLK--DIGPVKKM 382
            K +V HN L D      +F  PLP ++NEF       FP+++D   +        +   
Sbjct: 276 GKLVVGHNMLLDVMHTIHQFYCPLPADLNEFKEMAICVFPRLLDTKLMASTQPFKDIINN 335

Query: 383 TNISATIAYLKNRFFAPIEMEIPNQ-----ANENEGKIHGHNVVKICQLFGKLCSILKIT 437
           T+++     LK   F P ++E             +    G++       F  + + L   
Sbjct: 336 TSLAELEKRLKETPFDPPKVESAEGFPSYDTASEQLHEAGYDAYITGLCFISMANYLGSL 395

Query: 438 PDAIESSDDFLASAINRYANIFYSLPGSSQEPTNEEIRGWTNDKRKVSCEDVVFLWGFRE 497
               +      +  I  + N  + +        N                D V    F +
Sbjct: 396 LSPPKMCVSARSKLIEPFFNKLFLMRVMDIPYLN------LEGPDLQPKRDHVLHVTFPK 449

Query: 498 RISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFKNVMNSKAVSGPLRE 557
                 L  +      +      +  +D + A V   +P       N             
Sbjct: 450 EWKTSDLYQLFSAFGNI-----QISWIDDTSAFVSLSQPEQVQIAVNTSKY--------- 495

Query: 558 MVSDGLKAAGYETY 571
             ++  +   Y  Y
Sbjct: 496 --AESYRIQTYAEY 507

PyMOL of 3d45

>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase-RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A Length = 430	Back alignment and structure

>1uoc_A POP2; hydrolase, DEDD nuclease, mRNA degradation, poly(A) tail, transcription regulation, repressor, phosphorylation.; 2.3A {Saccharomyces cerevisiae} SCOP: c.55.3.9 Length = 289	Back alignment and structure

>2d5r_A CCR4-NOT transcription complex subunit 7; poly(A) deadenylase, antiproliferative protein, transcription; 2.50A {Homo sapiens} SCOP: c.55.3.9 Length = 252	Back alignment and structure

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

>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A Length = 333	Back alignment and structure

>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A Length = 333	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		622
3d45_A		507	Poly(A)-specific ribonuclease PARN; CAP analogue,	100.0
2a1r_A		430	Poly(A)-specific ribonuclease PARN; DEDD, nuclease	100.0
4gmj_B		285	CCR4-NOT transcription complex subunit 7; mRNA dec	100.0
2p51_A		333	SPCC18.06C protein; DEDD nuclease fold, hydrolase,	100.0
2d5r_A		252	CCR4-NOT transcription complex subunit 7; poly(A)	100.0
1uoc_A		289	POP2; hydrolase, DEDD nuclease, mRNA degradation,	100.0
1whv_A		100	Poly(A)-specific ribonuclease; RNA recognition mot	99.46
3ctr_A		101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	99.23
1ug8_A		87	Poly(A)-specific ribonuclease; R3H domain, poly(A)	98.68
2gui_A		194	DNA polymerase III epsilon subunit; DNA polymerase	96.58
1wlj_A		189	Interferon stimulated gene 20KDA; exoribonuclease,	96.5
2p1j_A		186	POLIII, DNA polymerase III POLC-type; structural g	96.21
1w0h_A		204	3'-5' exonuclease ERI1; nuclease domain, hydrolase	95.95
1zbh_A		299	3'-5' exonuclease ERI1; histone mRNA 3'-END-specif	95.76
3mxm_B		242	Three prime repair exonuclease 1; RNAse H-like fol	95.56
3v9w_A		235	Ribonuclease T; DEDD nucleases family, EXO-nucleas	95.3
2f96_A		224	Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas	95.07
3u3y_B		314	Three prime repair exonuclease 1; RNAse H fold, 3'	94.59
1zbu_A		349	ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase;	94.32
2xri_A		224	ERI1 exoribonuclease 3; hydrolase, metal binding;	94.19
1y97_A		238	Three prime repair exonuclease 2; TREX2, hydrolase	93.86
3cg7_A		308	CRN-4, cell death-related nuclease 4; hydrolase, a	92.76
2igi_A		180	Oligoribonuclease; RNAse, exoribonuclease, exonucl	92.15
2diu_A		96	KIAA0430 protein; structural genomics, RRM domain,	91.62
2gbz_A		194	Oligoribonuclease; ORN, deddh, structural genomics	90.32
2dnp_A		90	RNA-binding protein 14; RRM domain, RBD, structura	89.28
1x4c_A		108	Splicing factor, arginine/serine-rich 1; structura	89.21
2f96_A		224	Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas	89.05
3v9w_A		235	Ribonuclease T; DEDD nucleases family, EXO-nucleas	88.11
1x5s_A		102	Cold-inducible RNA-binding protein; structure geno	86.79
1nu4_A		97	U1A RNA binding domain; RNA recognition motif, U1	86.2
2fc8_A		102	NCL protein; structure genomics, RRM_1 domain, str	86.13
2dgx_A		96	KIAA0430 protein; RRM domain, structural genomics,	85.59
2fc9_A		101	NCL protein; structure genomics, RRM_1 domain, str	84.81
2cq0_A		103	Eukaryotic translation initiation factor 3 subunit	84.46
2cpi_A		111	CCR4-NOT transcription complex subunit 4; RNA reco	84.28
2cqc_A		95	Arginine/serine-rich splicing factor 10; RNA recog	84.07
2dgt_A		92	RNA-binding protein 30; RRM domain, structural gen	84.02
2dgo_A		115	Cytotoxic granule-associated RNA binding protein 1	83.9
2dnm_A		103	SRP46 splicing factor; RRM domain, RBD, structural	83.86
2cq3_A		103	RNA-binding protein 9; RRM domain, structural geno	83.84
1x5u_A		105	Splicing factor 3B subunit 4 (spliceosome associat	83.66
2a3j_A		127	U1 small nuclear ribonucleoprotein A; computationa	83.49
3beg_B		115	Splicing factor, arginine/serine-rich 1; kinase, S	82.63
2p1j_A		186	POLIII, DNA polymerase III POLC-type; structural g	81.84
2dgp_A		106	Bruno-like 4, RNA binding protein; RRM domain, str	81.83
2ytc_A		85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	81.25
1wex_A		104	Hypothetical protein (riken cDNA 2810036L13); stru	81.2
2dnz_A		95	Probable RNA-binding protein 23; RNA recognition m	81.03
2igi_A		180	Oligoribonuclease; RNAse, exoribonuclease, exonucl	80.99
2e5h_A		94	Zinc finger CCHC-type and RNA-binding motif- conta	80.92
2dhg_A		104	TRNA selenocysteine associated protein (SECP43); R	80.91
2dgu_A		103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	80.82
3bs9_A		87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	80.61
2dnh_A		105	Bruno-like 5, RNA binding protein; RRM domain, RBD	80.59

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}	Back alignment and structure

Probab=100.00  E-value=5.2e-103  Score=870.78  Aligned_cols=480  Identities=22%  Similarity=0.330  Sum_probs=332.7

Q ss_pred             eEEcCcccHHHHHHHHHHhhcCCCeEEEecCCCCccCCCCCC--CCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCC-
Q 006991           29 IKQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHR--VSTFDTPETAYLKAKFAAERFQILQFAICPFKLQA-  105 (622)
Q Consensus        29 i~dVt~~NF~~~l~~i~~~I~~a~FVAiD~EftGi~~~~~~~--~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~-  105 (622)
                      |||||++||+++|+.|+++|++|+|||||+|||||...+...  .+.++|+++||+++|.+|+.|+|||+|||+|++++ 
T Consensus         2 ~m~V~~~Nf~~~l~~i~~~i~~~~fvaiD~Ef~Gi~~~~~~~~~~~~~~t~~~~Y~~~r~~v~~~~iiQlGlt~f~~~~~   81 (507)
T 3d45_A            2 PMEIIRSNFKINLHKVYQAIEEADFFAIDGEFSGISDGPSVTALTSGFDTPEERYQKLKKHSMDFLLFQFGLCAFKYDHT   81 (507)
T ss_dssp             CEEECHHHHHHHHHHHHHHHHHCSEEEEEEEESCSCC--------CBSCCHHHHHHHHHHHHTTBCEEEEEEEEEEECSS
T ss_pred             CeEEeHHhHHHHHHHHHHHHhcCCEEEEeeeccCcCCCCCccccccccCCHHHHHHHHHHHHHhcccceEEEEEEecCCC
Confidence            699999999999999999999999999999999997543211  24589999999999999999999999999999987 


Q ss_pred             -CceeeEeeEEeecCccccccCCCCCceeechhHHHHHHHcCCCcchhhhcccccCCHHHHHHHHHHhCCCccccccc--
Q 006991          106 -SKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISYLSEAQESTVKVRMGNPMAVDHAT--  182 (622)
Q Consensus       106 -~~y~~~~fNF~lfp~~~~~~~~~d~~f~~q~sSl~FL~~~gFDFnk~~~~GI~YLs~~eE~~~r~~~~~~~~~~~~~--  182 (622)
                       .+|.+||||||+||+.. +.+.+|++|+||++||+||++||||||+|+++|||||+++||+.+++++.+++...+..  
T Consensus        82 ~~~~~~~~fNf~~fp~~~-~~~~~d~~~~~~~~Si~fL~~~GfDFnk~~~~GI~yl~~~ee~~~~~~~~~~~~~~~~~~~  160 (507)
T 3d45_A           82 DSKHVTKSFNFYVFPKPF-SRSSPDVKFVCQSSSIDFLASQGFDFNKVFCSGIPYLNQEEERQLREQFDEKRSQANGAGA  160 (507)
T ss_dssp             SSCEEEEEEEEEBCCCCC-SSSSCCCEEEEEHHHHHHHHTTTCCHHHHHTTCBCBCCHHHHHHHHHHSCC----------
T ss_pred             CCceeEEeEEEEecCccc-cccCcccceeecHHHHHHHHHcCCChhhHHhcCCCCCChHHHHHHHHHHHhhhhhhhcccc
Confidence             68999999999999852 23467899999999999999999999999999999999999999999998765543210  


Q ss_pred             cCCCCCCCCcccHHHHHHHHHHHHHHHhhccCCCchhhHHHHHHHHHHHhcCcccCCCCCccccccchHHHHHHHHHHHh
Q 006991          183 KSSSSPALSVADTVFIERVRSRVKHWKNACTDSDIKTEAALVTSLRKIVLGGEQFGSRPSMTIDVCSERQVQLVLKMLED  262 (622)
Q Consensus       183 ~~~~~~~~~~~d~~fi~~v~~~I~eWl~~~~~~~~~~~~~l~~~l~~~~~~~e~~~~~p~l~l~~~~~~q~~Lv~q~l~~  262 (622)
                      ....+..++.++++|+++++++|++|+++..+                          +.+++++||++||+||||+|++
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~I~~wl~~~~~--------------------------~~l~i~~~n~~~r~Lv~q~l~~  214 (507)
T 3d45_A          161 LAKCPVTIPEDQKKFIDQVIEKIEDFLQSEEK--------------------------RSLELDPCTGFQRKLIYQTLSW  214 (507)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccCCcccCCHHHHHHHHHHHHHHHHHHhcCCC--------------------------CccccCCCcHHHHHHHHHHHHH
Confidence            01111125678899999999999999976321                          1367889999999999999999


Q ss_pred             ccCCcceeeeccCCCCceEEEEEEccChHHHHHHHHHhhHHHHhhhhccccHHHHHHHHHhCCCCEEechhHHHHHHHHH
Q 006991          263 FSDVLVPLIIPAKGGGTQAVRAVLTSSDEDKDLLKRELQTFEFEQNKRVRGFREVIDLISASQKPLVAHNSLNDFTFIHS  342 (622)
Q Consensus       263 ~~~~l~~~~v~~k~g~~~~vrvi~~~~~eek~~l~~e~~~~e~e~~~~~~GFr~Vi~~L~~skKpIVGHN~llDL~~iy~  342 (622)
                      +||+++.+......+....+.| .+.+++++..++++.+..+++.+.+++|||+||++|++++|||||||||+||||||+
T Consensus       215 ~fp~~v~~~~~~~~~~~~~i~v-~~~~~e~~~~~~~~~~~~~~~~~~~~~Gfr~v~~~L~~~~kpiVgHN~l~Dl~~l~~  293 (507)
T 3d45_A          215 KYPKGIHVETLETDKKERHIVI-SKVDEEERKRREQEKYTKEQEELNDAVGFSRVIHAIANSGKLVVGHNMLLDVMHTIH  293 (507)
T ss_dssp             --------------------------------------CCSTHHHHHHHSBTHHHHHHHHHHCCEEEESSCHHHHHHHHH
T ss_pred             hCCCceEeeeccCCCcceeEEE-EeCCHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhCCCeEEEechHHHHHHHHH
Confidence            9999875432111222233433 344455555566666666678899999999999999999999999999999999999


Q ss_pred             hccCCCCCCHHHHHHHHHccCCCccchhhHHhhhC--cccccCchHHHHHHHHhcCCCCceeecCCCC-C----CCCccc
Q 006991          343 KFLAPLPPNMNEFICSLRLAFPQVIDVNYLLKDIG--PVKKMTNISATIAYLKNRFFAPIEMEIPNQA-N----ENEGKI  415 (622)
Q Consensus       343 ~F~gpLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~--~~~~~~~L~~~~~~l~~~~~~~p~ve~~~~~-~----~~~~h~  415 (622)
                      +|+||||++++|||+.+|++||.|||||||++..+  .+...++|+++++.|.+.++.+|+|+++... +    .+..|+
T Consensus       294 ~F~~pLP~~~~eFk~~i~~lFP~i~DTK~la~~~~~~~~~~~~~L~~l~~~l~~~~~~~p~i~~~~~~~~y~~~~~~~He  373 (507)
T 3d45_A          294 QFYCPLPADLNEFKEMAICVFPRLLDTKLMASTQPFKDIINNTSLAELEKRLKETPFDPPKVESAEGFPSYDTASEQLHE  373 (507)
T ss_dssp             HHTCSCCSSHHHHHHHHHHHCSCEEEHHHHTTSTTHHHHCCCCCHHHHHHHTTSTTCCCCCEEECTTSCCCC----CCCC
T ss_pred             HhcCCCCCCHHHHHHHHHHhCCceeEhHhhhhcCccccccCCCCHHHHHHHHhccCCCCCeEEecccccccccCCCCccc
Confidence            99999999999999999999999999999997632  2224789999999999888889999887542 2    356799


Q ss_pred             chhhHHHHHHHHHHHHHHhcc---CCCCCCCCcHHHHhhhhhhhccccCCCCCCCCCCCccccCCCCCCCCCCcCCEEEE
Q 006991          416 HGHNVVKICQLFGKLCSILKI---TPDAIESSDDFLASAINRYANIFYSLPGSSQEPTNEEIRGWTNDKRKVSCEDVVFL  492 (622)
Q Consensus       416 AGyDA~mTg~vF~~l~~~l~~---~~~~~~s~~~~~~~~l~~~~N~l~~~~~~~~~~~d~~~~~l~g~~~~~~~~~vv~i  492 (622)
                      |||||||||+||++||++||.   ..+...   ...+.+|++|+|+|++  ++   +.|++|+||+|+|+.++|++|++ 
T Consensus       374 AGyDA~mTg~~F~kl~~~l~~~~~~~~~~~---~~~~~~l~~~~N~l~l--~~---~~d~~~i~l~g~d~~~~R~~vl~-  444 (507)
T 3d45_A          374 AGYDAYITGLCFISMANYLGSLLSPPKMCV---SARSKLIEPFFNKLFL--MR---VMDIPYLNLEGPDLQPKRDHVLH-  444 (507)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCC------------CCSCSSSGGGTTEECC--CS---BSSCCSEESSSCCCCCCGGGEEE-
T ss_pred             HHHHHHHHHHHHHHHHHHHhhccCCccccc---ccchhHHHhhheeeee--ec---cCCCceeeCCCCCCCCCcCcEEE-
Confidence            999999999999999999985   111100   1235689999999999  55   57899999999999999999666 


Q ss_pred             eccccccchhHHHHhhhhhhhccccceEEEEecCceEEEEecCCCchhHHHHHhhhcc
Q 006991          493 WGFRERISAGILKNMLQGSHEVFAEAFNVRMVDRSCAIVVFGKPGLSNTFKNVMNSKA  550 (622)
Q Consensus       493 ~~f~~~~~~~~i~~~l~~~~~~F~~~~~V~~id~t~a~V~~~~~~~~~~~l~~~~~~~  550 (622)
                      |+||++|+..+|.++++    .|| .++|+|||+|||||+|+++++|+++|++++++.
T Consensus       445 v~f~~~~~~~~i~~~fs----~fg-~v~V~widdt~a~V~~~~~~~a~~~l~~~~~~~  497 (507)
T 3d45_A          445 VTFPKEWKTSDLYQLFS----AFG-NIQISWIDDTSAFVSLSQPEQVQIAVNTSKYAE  497 (507)
T ss_dssp             EECCTTCCHHHHHHHGG----GGC-CCEEEECSSSEEEEECSCHHHHHHHHHHHTTCS
T ss_pred             EeCCCCCCHHHHHHHHH----hcC-CEEEEEEcCCeEEEEECCHHHHHHHHHHHHhCC
Confidence            89999999999888775    566 389999999999999999999999999998764

PyMOL of 3d45

>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase-RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A	Back alignment and structure

>4gmj_B CCR4-NOT transcription complex subunit 7; mRNA decay, deadenylase, RNA bindin; HET: GOL; 2.70A {Homo sapiens}	Back alignment and structure

>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A	Back alignment and structure

>2d5r_A CCR4-NOT transcription complex subunit 7; poly(A) deadenylase, antiproliferative protein, transcription; 2.50A {Homo sapiens} SCOP: c.55.3.9	Back alignment and structure

>1uoc_A POP2; hydrolase, DEDD nuclease, mRNA degradation, poly(A) tail, transcription regulation, repressor, phosphorylation.; 2.3A {Saccharomyces cerevisiae} SCOP: c.55.3.9	Back alignment and structure

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*	Back alignment and structure

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}	Back alignment and structure

>1ug8_A Poly(A)-specific ribonuclease; R3H domain, poly(A)-specific 3'-exoribonuclease, PARN, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.68.7.1	Back alignment and structure

>2gui_A DNA polymerase III epsilon subunit; DNA polymerase proofreading domain, transferase; HET: DNA U5P; 1.60A {Escherichia coli} SCOP: c.55.3.5 PDB: 1j54_A* 1j53_A* 2ido_A* 2xy8_A*	Back alignment and structure

>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5	Back alignment and structure

>2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics, exonuclease, PSI-2, protein structure initiative; HET: DNA; 2.50A {Thermotoga maritima MSB8}	Back alignment and structure

>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5	Back alignment and structure

>1zbh_A 3'-5' exonuclease ERI1; histone mRNA 3'-END-specific recognition, structures of 3'- exonuclease and ITS RNA complex, hydrolase/RNA complex; HET: AMP; 3.00A {Homo sapiens}	Back alignment and structure

>3mxm_B Three prime repair exonuclease 1; RNAse H-like fold, polyproline type II helix, hydrolase-DNA; HET: DNA; 1.75A {Mus musculus} SCOP: c.55.3.5 PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A* 3b6p_A* 2o4i_A 2oa8_A	Back alignment and structure

>3v9w_A Ribonuclease T; DEDD nucleases family, EXO-nucleases, hydrolase-DNA complex; HET: DNA; 1.70A {Escherichia coli} PDB: 3ngy_A 3v9u_A* 3ngz_A* 3va3_A* 3v9z_A* 3nh0_A 3nh2_A 3nh1_A* 3v9s_A* 3v9x_A* 3va0_A* 2is3_A	Back alignment and structure

>2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PS protein structure initiative, midwest center for structural genomics; 2.09A {Pseudomonas aeruginosa} SCOP: c.55.3.5	Back alignment and structure

>3u3y_B Three prime repair exonuclease 1; RNAse H fold, 3' exonuclease, homodimer, hydrolase-DNA compl; HET: BU1; 2.28A {Mus musculus} PDB: 3u6f_B*	Back alignment and structure

>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens}	Back alignment and structure

>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens}	Back alignment and structure

>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5	Back alignment and structure

>3cg7_A CRN-4, cell death-related nuclease 4; hydrolase, apoptosis, 3'-5' exonuclease, deddh; 2.50A {Caenorhabditis elegans} PDB: 3cm5_A 3cm6_A	Back alignment and structure

>2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase, mRNA decay; 1.70A {Escherichia coli} SCOP: c.55.3.5 PDB: 1yta_A 1j9a_A	Back alignment and structure

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, hydrolase; 2.30A {Xanthomonas campestris PV}	Back alignment and structure

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PS protein structure initiative, midwest center for structural genomics; 2.09A {Pseudomonas aeruginosa} SCOP: c.55.3.5	Back alignment and structure

>3v9w_A Ribonuclease T; DEDD nucleases family, EXO-nucleases, hydrolase-DNA complex; HET: DNA; 1.70A {Escherichia coli} PDB: 3ngy_A 3v9u_A* 3ngz_A* 3va3_A* 3v9z_A* 3nh0_A 3nh2_A 3nh1_A* 3v9s_A* 3v9x_A* 3va0_A* 2is3_A	Back alignment and structure

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...	Back alignment and structure

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A	Back alignment and structure

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}	Back alignment and structure

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A	Back alignment and structure

>2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics, exonuclease, PSI-2, protein structure initiative; HET: DNA; 2.50A {Thermotoga maritima MSB8}	Back alignment and structure

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A	Back alignment and structure

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase, mRNA decay; 1.70A {Escherichia coli} SCOP: c.55.3.5 PDB: 1yta_A 1j9a_A	Back alignment and structure

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A	Back alignment and structure

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}	Back alignment and structure

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		622
d2d5ra1		252	c.55.3.9 (A:11-262) CCR4-NOT transcription complex	4e-21
d2d5ra1		252	c.55.3.9 (A:11-262) CCR4-NOT transcription complex	1e-04
d1uoca_		286	c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (	2e-18
d1uoca_		286	c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (	6e-05

>d2d5ra1 c.55.3.9 (A:11-262) CCR4-NOT transcription complex subunit 7, CAF1 {Human (Homo sapiens) [TaxId: 9606]} Length = 252	Back information, alignment and structure


class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: CAF1-like ribonuclease
domain: CCR4-NOT transcription complex subunit 7, CAF1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 91.1 bits (226), Expect = 4e-21
 Identities = 19/150 (12%), Positives = 45/150 (30%), Gaps = 15/150 (10%)

Query: 29  IKQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAA 88
           I ++   N +E + +I+  I   +++A+  +  G  + P          +  Y   +   
Sbjct: 2   ICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIG--EFRSNADYQYQLLRCNV 59

Query: 89  ERFQILQFAICPFKLQ---ASKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKE 145
           +  +I+Q  +     Q         + +NF     +                 +  +   
Sbjct: 60  DLLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTE----------DMYAQDSIELLTTS 109

Query: 146 GFDFNTCIYDGISYLSEAQESTVKVRMGNP 175
           G  F     +GI     A+       +   
Sbjct: 110 GIQFKKHEEEGIETQYFAELLMTSGVVLCE 139

PyMOL of d2d5ra1

>d2d5ra1 c.55.3.9 (A:11-262) CCR4-NOT transcription complex subunit 7, CAF1 {Human (Homo sapiens) [TaxId: 9606]} Length = 252	Back information, alignment and structure

>d1uoca_ c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 286	Back information, alignment and structure

>d1uoca_ c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 286	Back information, alignment and structure

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		622
d2d5ra1		252	CCR4-NOT transcription complex subunit 7, CAF1 {Hu	100.0
d1uoca_		286	Pop2 RNase D domain {Baker's yeast (Saccharomyces	100.0
d1whva_		100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	99.48
d1ug8a_		87	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	98.58
d1wlja_		173	Interferon-stimulated gene 20 kDa protein, ISG20 {	96.74
d2guia1		174	N-terminal exonuclease domain of the epsilon subun	95.9
d1y97a1		228	Three prime repair exonuclease 2, TREX2 {Human (Ho	94.65
d3b6oa1		226	Three prime repair exonuclease 1, TREX1 {Mouse (Mu	94.01
d1x5ua1		93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	89.61
d2cqca1		83	Arginine/serine-rich splicing factor 10 {Human (Ho	89.6
d1wg4a_		98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	89.32
d3begb1		87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	89.23
d1x4da1		89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	88.8
d2b0ga1		83	Splicesomal U1A protein {Drosophila melanogaster [	88.75
d2cqpa1		86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	87.85
d1wexa_		104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	87.7
d2f96a1		202	Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287	86.61
d2cq3a1		93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	86.6
d1yt3a3		193	Ribonuclease D, catalytic domain {Escherichia coli	86.2
d1nu4a_		91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	85.01
d2f96a1		202	Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287	84.95
d1x4ga1		96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	84.38
d2cpja1		86	Non-POU domain-containing octamer-binding protein,	84.27
d2cq0a1		90	Eukaryotic translation initiation factor 3 subunit	84.0
d2guia1		174	N-terminal exonuclease domain of the epsilon subun	83.97
d2cqia1		90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	83.56
d1x4fa1		99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	82.99
d2cpza1		102	CUG triplet repeat RNA-binding protein 1 {Human (H	82.63
d2cq1a1		88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	82.48
d1w0ha_		200	Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960	81.82
d1fxla2		85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	80.61
d2f9da1		114	Pre-mRNA branch site protein p14 {Human (Homo sapi	80.39

>d2d5ra1 c.55.3.9 (A:11-262) CCR4-NOT transcription complex subunit 7, CAF1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: CAF1-like ribonuclease
domain: CCR4-NOT transcription complex subunit 7, CAF1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.9e-53  Score=429.22  Aligned_cols=232  Identities=18%  Similarity=0.262  Sum_probs=195.2

Q ss_pred             ceEEcCcccHHHHHHHHHHhhcCCCeEEEecCCCCccCCCCCCCCCCCCHHHHHHHHHhhhhcccceeEEeeeeecCC--
Q 006991           28 PIKQITKTNFNESLSEIKNHISSSDFIAVSLQNTGSFSSPWHRVSTFDTPETAYLKAKFAAERFQILQFAICPFKLQA--  105 (622)
Q Consensus        28 ~i~dVt~~NF~~~l~~i~~~I~~a~FVAiD~EftGi~~~~~~~~~~~dt~eerY~~~k~~a~~f~iiQ~Gl~~f~~~~--  105 (622)
                      .|+|||++||+++++.|+++|++|+|||||+||||+..++  .....+|+++||+++|.||+.|.+||+|||+|++++  
T Consensus         1 ~i~eV~~~Nf~e~~~~i~~~i~~~~fVAiD~EF~G~~~~~--~~~~~~t~~~~Y~~lr~nv~~~~iiQ~Glt~~~~~g~~   78 (252)
T d2d5ra1           1 RICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARP--IGEFRSNADYQYQLLRCNVDLLKIIQLGLTFMNEQGEY   78 (252)
T ss_dssp             CEEEECGGGHHHHHHHHHHHHHHCCEEEEEEECCCCCCCC--CSCCSSHHHHHHHHHHHHHTTCCCCEEEEEEECTTSCC
T ss_pred             CeEEehhhhHHHHHHHHHHHHhcCCEEEEeeeccCcccCC--CCccCCCHHHHHHHHHHHHhhcceeEEEEEeecccCCC
Confidence            4899999999999999999999999999999999996543  356778999999999999999999999999999987  


Q ss_pred             -CceeeEeeEEeecCccccccCCCCCceeechhHHHHHHHcCCCcchhhhcccccCCHHHHHHHHHHhCCCccccccccC
Q 006991          106 -SKVIAYPYNFHLFPRDELKMGMPSYSFTCQTSYLTAMAKEGFDFNTCIYDGISYLSEAQESTVKVRMGNPMAVDHATKS  184 (622)
Q Consensus       106 -~~y~~~~fNF~lfp~~~~~~~~~d~~f~~q~sSl~FL~~~gFDFnk~~~~GI~YLs~~eE~~~r~~~~~~~~~~~~~~~  184 (622)
                       ..+.+|+|||+++|+          .++|+++||+||++|||||||++++||||....|.-                  
T Consensus        79 ~~~~~~w~FNf~~~~~----------~~~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~~~l------------------  130 (252)
T d2d5ra1          79 PPGTSTWQFNFKFNLT----------EDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELL------------------  130 (252)
T ss_dssp             CSSCCEEEEEBCCCTT----------TSCCCHHHHHHHHHHTCCHHHHHHHCBCHHHHHHHH------------------
T ss_pred             CCCceeEEEEEEeCCc----------ccccCHHHHHHHHHcCCChHHHHHcCCCHHHHHHHH------------------
Confidence             468999999997774          468999999999999999999999999994321110                  


Q ss_pred             CCCCCCCcccHHHHHHHHHHHHHHHhhccCCCchhhHHHHHHHHHHHhcCcccCCCCCccccccchHHHHHHHHHHHhcc
Q 006991          185 SSSPALSVADTVFIERVRSRVKHWKNACTDSDIKTEAALVTSLRKIVLGGEQFGSRPSMTIDVCSERQVQLVLKMLEDFS  264 (622)
Q Consensus       185 ~~~~~~~~~d~~fi~~v~~~I~eWl~~~~~~~~~~~~~l~~~l~~~~~~~e~~~~~p~l~l~~~~~~q~~Lv~q~l~~~~  264 (622)
                                               .                                                      
T Consensus       131 -------------------------~------------------------------------------------------  131 (252)
T d2d5ra1         131 -------------------------M------------------------------------------------------  131 (252)
T ss_dssp             -------------------------H------------------------------------------------------
T ss_pred             -------------------------H------------------------------------------------------
Confidence                                     0                                                      


Q ss_pred             CCcceeeeccCCCCceEEEEEEccChHHHHHHHHHhhHHHHhhhhccccHHHHHHHHHhCCCCEEechhHHHHHHHHHhc
Q 006991          265 DVLVPLIIPAKGGGTQAVRAVLTSSDEDKDLLKRELQTFEFEQNKRVRGFREVIDLISASQKPLVAHNSLNDFTFIHSKF  344 (622)
Q Consensus       265 ~~l~~~~v~~k~g~~~~vrvi~~~~~eek~~l~~e~~~~e~e~~~~~~GFr~Vi~~L~~skKpIVGHN~llDL~~iy~~F  344 (622)
                                ..|                                          .+...++++||||+++|++|++++|
T Consensus       132 ----------~s~------------------------------------------~~~~~~~~wv~f~g~yD~~yl~k~l  159 (252)
T d2d5ra1         132 ----------TSG------------------------------------------VVLCEGVKWLSFHSGYDFGYLIKIL  159 (252)
T ss_dssp             ----------TTT------------------------------------------SSSSSSCEEEESSCHHHHHHHHHHH
T ss_pred             ----------hhh------------------------------------------hhhcCCCcEEEecchhHHHHHHHHH
Confidence                      000                                          0011246799999999999999999


Q ss_pred             cC-CCCCCHHHHHHHHHccCCCccchhhHHhhhCcccccCchHHHHHHHHhcCCCCceeecCCCCCCCCcccchhhHHHH
Q 006991          345 LA-PLPPNMNEFICSLRLAFPQVIDVNYLLKDIGPVKKMTNISATIAYLKNRFFAPIEMEIPNQANENEGKIHGHNVVKI  423 (622)
Q Consensus       345 ~g-pLP~t~~EFk~~i~~lFP~I~DTKyLa~~~~~~~~~~~L~~~~~~l~~~~~~~p~ve~~~~~~~~~~h~AGyDA~mT  423 (622)
                      +| |||++++||++.+|.+||.|||||||++...+++  .+|.++.+.|.-    +         ..+..|+||||||||
T Consensus       160 ~~~~LP~~~~eF~~~v~~~FP~vyDtK~l~~~~~~~~--~~L~~la~~L~v----~---------~~g~~H~AG~DsllT  224 (252)
T d2d5ra1         160 TNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLK--GGLQEVAEQLEL----E---------RIGPQHQAGSDSLLT  224 (252)
T ss_dssp             HTSCCCSSHHHHHHHHHHHCSCEEEHHHHGGGCTTCC--SSHHHHHHHHTC----C---------CCSSTTSHHHHHHHH
T ss_pred             cCCCCCCCHHHHHHHHHHHCchHhhHHHHHhhccCCC--chHHHHHHHcCC----C---------CCCCCcchhHHHHHH
Confidence            96 9999999999999999999999999999876654  357776666621    1         135689999999999


Q ss_pred             HHHHHHHHHHhc
Q 006991          424 CQLFGKLCSILK  435 (622)
Q Consensus       424 g~vF~~l~~~l~  435 (622)
                      |.||++|++.+.
T Consensus       225 ~~~F~~l~~~~~  236 (252)
T d2d5ra1         225 GMAFFKMREMFF  236 (252)
T ss_dssp             HHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHh
Confidence            999999999883

PyMOL of d2d5ra1

>d1uoca_ c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1ug8a_ d.68.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1wlja_ c.55.3.5 (A:) Interferon-stimulated gene 20 kDa protein, ISG20 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2guia1 c.55.3.5 (A:7-180) N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1y97a1 c.55.3.5 (A:1-228) Three prime repair exonuclease 2, TREX2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d3b6oa1 c.55.3.5 (A:9-234) Three prime repair exonuclease 1, TREX1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2f96a1 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287]}	Back information, alignment and structure

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1yt3a3 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2f96a1 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287]}	Back information, alignment and structure

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2guia1 c.55.3.5 (A:7-180) N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1w0ha_ c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure