Citrus Sinensis ID: 048636

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150
Protein Sequence
MGAGDFSTDLDSSSNSSSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE
Secondary Structure (PSIPRED)
ccccccccccccccccccccccEEEEccHHcHHHHHHHHHHHHHcccEEEcccEEccccccccccccccccccccccHHHHHHHHHHHcccccEEEEEEEEccccccccccccccccEEEEEcccccccccccccHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccEHHHHHHHcHHHHHHHHHHHHHcccEEEEccccccEEEEEccccccccccccccccHHHHHHHHHHHHHHHHHHcEEEEccccccccccccccccEEEEEEcccccccHccccHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
mgagdfstdldsssnssssnsiIIREVWASNLESEFELISQVidrypfismdtefpglvyrpdvdpstrpyfrqrkpsdhykvlKSNVDALNLIQVGLtlsdssgnlpdlgsggnnkfiwefnfrdfdvatdahapdsIELLRLQGIDFE
Flexible Loop (DISEMBL)
mgagdfstdldsssnssssnsiIIREVWASNLESEFELISQVIDRYPFISMDtefpglvyrpdvdpstrpyfrqrkpsdhykVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIellrlqgidfe
Low Complexity Region (SEG)
MGAGDFSTDLDsssnssssnsiiiREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE
Disordered region (IsUnstruct)
*********************IIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDV***************HYKVLKSNVDALNLIQVGLTLSD******DLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRL******
Disordered Region (DISOPRED)
************************REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE
Disordered Region (DISEMBL)
********************SIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE
Disordered Region (DISPRO)
*******************NSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGAGDFSTDLDSSSNSSSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE
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	150	2.2.26 [Sep-21-2011]
Q9LXM2	280	Probable CCR4-associated	yes	no	0.813	0.435	0.684	2e-45
Q9FMS6	278	Probable CCR4-associated	no	no	0.886	0.478	0.630	1e-44
Q9SKZ2	275	Probable CCR4-associated	no	no	0.806	0.44	0.541	5e-33
Q9LEU4	277	Probable CCR4-associated	no	no	0.846	0.458	0.492	1e-30
Q9S9P2	286	Probable CCR4-associated	no	no	0.82	0.430	0.514	3e-30
Q9SAI2	274	Probable CCR4-associated	no	no	0.8	0.437	0.488	5e-28
O74856	335	Poly(A) ribonuclease pop2	yes	no	0.746	0.334	0.476	8e-25
P39008	433	Poly(A) ribonuclease POP2	yes	no	0.786	0.272	0.435	7e-21
Q9UIV1	285	CCR4-NOT transcription co	yes	no	0.746	0.392	0.429	1e-20
Q5ZJV9	285	CCR4-NOT transcription co	yes	no	0.746	0.392	0.429	1e-20

>sp|Q9LXM2|CAF1I_ARATH Probable CCR4-associated factor 1 homolog 9 OS=Arabidopsis thaliana GN=CAF1-9 PE=2 SV=1

 Score =  181 bits (458), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 89/130 (68%), Positives = 104/130 (80%), Gaps = 8/130 (6%)

Query: 21  SIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDH 80
           +++ REVWA NLESEFELIS++ID YPFISMDTEFPG++++ D+        R   P D 
Sbjct: 16  TVVTREVWAENLESEFELISEIIDDYPFISMDTEFPGVIFKSDL--------RFTNPDDL 67

Query: 81  YKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIE 140
           Y +LK+NVDAL+LIQVGLTLSD +GNLPDLG   +  FIWEFNFRDFDVA DAHAPDSIE
Sbjct: 68  YTLLKANVDALSLIQVGLTLSDVNGNLPDLGDDLHRGFIWEFNFRDFDVARDAHAPDSIE 127

Query: 141 LLRLQGIDFE 150
           LLR QGIDFE
Sbjct: 128 LLRRQGIDFE 137

Ubiquitous transcription factor required for a diverse set of processes. It is a component of the CCR4 complex involved in the control of gene expression.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 1EC: .EC: 1EC: 3EC: .EC: 4

>sp|Q9FMS6|CAF1K_ARATH Probable CCR4-associated factor 1 homolog 11 OS=Arabidopsis thaliana GN=CAF1-11 PE=2 SV=1

 Score =  178 bits (451), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 87/138 (63%), Positives = 106/138 (76%), Gaps = 5/138 (3%)

Query: 13  SSNSSSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYF 72
            S +  S+ I+IR+VWA NLESEF+LI  +++ YPFISMDTEFPG++Y+ D+D       
Sbjct: 3   KSEADLSDVIVIRDVWAYNLESEFDLIRGIVEDYPFISMDTEFPGVIYKADLDV-----L 57

Query: 73  RQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATD 132
           R+  P+  Y +LKSNVDAL+LIQVGLTLSD+ GNLPDLG   N ++IWEFNFRDFDV  D
Sbjct: 58  RRGNPNYLYNLLKSNVDALSLIQVGLTLSDADGNLPDLGGQKNRRYIWEFNFRDFDVERD 117

Query: 133 AHAPDSIELLRLQGIDFE 150
            HAPDSIELLR  GIDFE
Sbjct: 118 PHAPDSIELLRRHGIDFE 135

Ubiquitous transcription factor required for a diverse set of processes. It is a component of the CCR4 complex involved in the control of gene expression.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 4

>sp|Q9SKZ2|CAF1G_ARATH Probable CCR4-associated factor 1 homolog 7 OS=Arabidopsis thaliana GN=CAF1-7 PE=2 SV=2

 Score =  139 bits (351), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 71/131 (54%), Positives = 92/131 (70%), Gaps = 10/131 (7%)

Query: 20  NSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSD 79
           +SI IREVW  NLESE  LI +V+D +PF++MDTEFPG+V RP     T   +       
Sbjct: 8   DSIQIREVWNDNLESEMALIREVVDDFPFVAMDTEFPGIVCRPVGTFKTNTEY------- 60

Query: 80  HYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKF-IWEFNFRDFDVATDAHAPDS 138
           HY+ LK+NV+ L +IQ+GLT SD  GNLP  G+  +NK+ IW+FNFR+FD+ +D +A DS
Sbjct: 61  HYETLKTNVNILKMIQLGLTFSDEKGNLPTCGT--DNKYCIWQFNFREFDLESDIYATDS 118

Query: 139 IELLRLQGIDF 149
           IELLR  GIDF
Sbjct: 119 IELLRQSGIDF 129

Ubiquitous transcription factor required for a diverse set of processes. It is a component of the CCR4 complex involved in the control of gene expression.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 4

>sp|Q9LEU4|CAF1J_ARATH Probable CCR4-associated factor 1 homolog 10 OS=Arabidopsis thaliana GN=CAF1-10 PE=2 SV=1

 Score =  131 bits (329), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 68/138 (49%), Positives = 94/138 (68%), Gaps = 11/138 (7%)

Query: 14  SNSSSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFR 73
           + +   +SI+IREVW  NL  EF LI +++D++ +I+MDTEFPG+V +P    +T  Y  
Sbjct: 2   AETLKEDSIMIREVWDYNLVEEFALIREIVDKFSYIAMDTEFPGVVLKP---VATFKY-- 56

Query: 74  QRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKF-IWEFNFRDFDVATD 132
                 +Y+ LK NVD L LIQVGLT SD +GNLP  G+   +KF IW+FNFR+F++  D
Sbjct: 57  --NNDLNYRTLKENVDLLKLIQVGLTFSDENGNLPTCGT---DKFCIWQFNFREFNIGED 111

Query: 133 AHAPDSIELLRLQGIDFE 150
            +A +SIELLR  GIDF+
Sbjct: 112 IYASESIELLRQCGIDFK 129

Ubiquitous transcription factor required for a diverse set of processes. It is a component of the CCR4 complex involved in the control of gene expression.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 4

>sp|Q9S9P2|CAF1B_ARATH Probable CCR4-associated factor 1 homolog 2 OS=Arabidopsis thaliana GN=CAF1-2 PE=2 SV=1

 Score =  130 bits (327), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 70/136 (51%), Positives = 90/136 (66%), Gaps = 13/136 (9%)

Query: 20  NSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRP-DVDPSTRPYFRQRKPS 78
           ++I IREVW  NLE E  LI Q ID +P+++MDTEFPG+V +    +P+  PY      S
Sbjct: 12  DTIEIREVWNHNLEQEMALIEQSIDDFPYVAMDTEFPGIVCKTVTANPNPNPY------S 65

Query: 79  DHYK----VLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAH 134
            HY+     LK+NV+ L LIQ+GLTLSD  GNLP  G+  N + IW+FNFR+F+V +D  
Sbjct: 66  IHYEYNYDTLKANVNMLKLIQLGLTLSDEKGNLPTCGT--NKQCIWQFNFREFNVISDMF 123

Query: 135 APDSIELLRLQGIDFE 150
           A DSIELLR   ID E
Sbjct: 124 ALDSIELLRKSAIDLE 139

Ubiquitous transcription factor required for a diverse set of processes. It is a component of the CCR4 complex involved in the control of gene expression.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 4

>sp|Q9SAI2|CAF1F_ARATH Probable CCR4-associated factor 1 homolog 6 OS=Arabidopsis thaliana GN=CAF1-6 PE=2 SV=1

 Score =  123 bits (308), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 64/131 (48%), Positives = 86/131 (65%), Gaps = 11/131 (8%)

Query: 20  NSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRP-DVDPSTRPYFRQRKPS 78
           +SI IREVW  NL+ E +LI  V+D +P+++MDTEFPG+V RP     S   Y       
Sbjct: 8   DSIQIREVWNDNLQEEMDLIRDVVDDFPYVAMDTEFPGIVVRPVGTFKSNADY------- 60

Query: 79  DHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDS 138
            HY+ LK+NV+ L +IQ+GLT S+  GNLP  G+  +   IW+FNFR+FD+ +D  A DS
Sbjct: 61  -HYETLKTNVNILKMIQLGLTFSNEQGNLPTCGT--DKYCIWQFNFREFDLDSDIFALDS 117

Query: 139 IELLRLQGIDF 149
           IELL+  GID 
Sbjct: 118 IELLKQSGIDL 128

Ubiquitous transcription factor required for a diverse set of processes. It is a component of the CCR4 complex involved in the control of gene expression.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 4

>sp|O74856|CAF1_SCHPO Poly(A) ribonuclease pop2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=caf1 PE=1 SV=2

 Score =  112 bits (280), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 61/128 (47%), Positives = 82/128 (64%), Gaps = 16/128 (12%)

Query: 24  IREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRP-DVDPSTRPYFRQRKPSDHYK 82
           IR+VW++NL+ E  LI  +I+RYP +SMDTEFPG+V RP  V  S+  Y        HY+
Sbjct: 25  IRDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVARPLGVFKSSDDY--------HYQ 76

Query: 83  VLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELL 142
            L++NVD+L +IQ+GL LSD  GN P           W+FNF  F++  D +AP+SIELL
Sbjct: 77  TLRANVDSLKIIQIGLALSDEEGNAP------VEACTWQFNFT-FNLQDDMYAPESIELL 129

Query: 143 RLQGIDFE 150
              GIDF+
Sbjct: 130 TKSGIDFK 137

Acts as the catalytic component of the CCR4-NOT core complex, which in the nucleus seems to be a general transcription factor, and in the cytoplasm the major mRNA deadenylase involved in mRNA turnover. In vivo and in vitro, caf1 has 3'-exoribonuclease activity with a preference for poly(A) RNAs.

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

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 4

>sp|P39008|POP2_YEAST Poly(A) ribonuclease POP2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=POP2 PE=1 SV=2

 Score = 99.4 bits (246), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 57/131 (43%), Positives = 82/131 (62%), Gaps = 13/131 (9%)

Query: 20  NSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSD 79
           N + +R+VW SNL SEF +I Q++ +Y  +S+ TEF G + RP         FR  K   
Sbjct: 156 NYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGT------FR-SKVDY 208

Query: 80  HYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSI 139
           HY+ +++NVD LN IQ+GL+LSD++GN PD G        W+FNF +FD   +  + +S+
Sbjct: 209 HYQTMRANVDFLNPIQLGLSLSDANGNKPDNGPS-----TWQFNF-EFDPKKEIMSTESL 262

Query: 140 ELLRLQGIDFE 150
           ELLR  GI+FE
Sbjct: 263 ELLRKSGINFE 273

Acts as probably catalytic component of the CCR4-NOT core complex, which in the nucleus seems to be a general transcription factor, and in the cytoplasm the major mRNA deadenylase involved in mRNA turnover. In vitro, POP2 has 3'-exoribonuclease activity with a preference for poly(A) RNAs, but also degrades poly(U) and poly(C) RNAs. Is part of a glucose-sensing system involved in growth control in response to glucose availability.

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

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 4

>sp|Q9UIV1|CNOT7_HUMAN CCR4-NOT transcription complex subunit 7 OS=Homo sapiens GN=CNOT7 PE=1 SV=3

 Score = 98.6 bits (244), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 55/128 (42%), Positives = 76/128 (59%), Gaps = 16/128 (12%)

Query: 24  IREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDH-YK 82
           I EVWA NL+ E + I QVI +Y +++MDTEFPG+V         RP    R  +D+ Y+
Sbjct: 12  ICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVV--------ARPIGEFRSNADYQYQ 63

Query: 83  VLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELL 142
           +L+ NVD L +IQ+GLT  +  G  P   S       W+FNF+ F++  D +A DSIELL
Sbjct: 64  LLRCNVDLLKIIQLGLTFMNEQGEYPPGTS------TWQFNFK-FNLTEDMYAQDSIELL 116

Query: 143 RLQGIDFE 150
              GI F+
Sbjct: 117 TTSGIQFK 124

Ubiquitous transcription factor required for a diverse set of processes. It is a component of the CCR4 complex involved in the control of gene expression.

Homo sapiens (taxid: 9606)

>sp|Q5ZJV9|CNOT7_CHICK CCR4-NOT transcription complex subunit 7 OS=Gallus gallus GN=CNOT7 PE=2 SV=1

 Score = 98.6 bits (244), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 55/128 (42%), Positives = 76/128 (59%), Gaps = 16/128 (12%)

Query: 24  IREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDH-YK 82
           I EVWA NL+ E + I QVI +Y +++MDTEFPG+V         RP    R  +D+ Y+
Sbjct: 12  ICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVV--------ARPIGEFRSNADYQYQ 63

Query: 83  VLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELL 142
           +L+ NVD L +IQ+GLT  +  G  P   S       W+FNF+ F++  D +A DSIELL
Sbjct: 64  LLRCNVDLLKIIQLGLTFMNEQGEYPPGTS------TWQFNFK-FNLTEDMYAQDSIELL 116

Query: 143 RLQGIDFE 150
              GI F+
Sbjct: 117 TTSGIQFK 124

Ubiquitous transcription factor required for a diverse set of processes. It is a component of the CCR4 complex involved in the control of gene expression.

Gallus gallus (taxid: 9031)

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	150
224131812	277	predicted protein [Populus trichocarpa]	0.866	0.469	0.781	5e-54
229560489	199	CCR4-NOT [Dimocarpus longan]	0.846	0.638	0.753	1e-50
356542778	278	PREDICTED: probable CCR4-associated fact	0.84	0.453	0.746	3e-50
225464848	278	PREDICTED: probable CCR4-associated fact	0.893	0.482	0.712	1e-49
356543624	309	PREDICTED: probable CCR4-associated fact	0.873	0.423	0.720	9e-49
255638796	309	unknown [Glycine max]	0.873	0.423	0.713	4e-48
147839203	265	hypothetical protein VITISV_015622 [Viti	0.82	0.464	0.75	4e-48
356572602	274	PREDICTED: probable CCR4-associated fact	0.866	0.474	0.666	8e-45
356505410	274	PREDICTED: probable CCR4-associated fact	0.86	0.470	0.676	2e-44
356539219	284	PREDICTED: probable CCR4-associated fact	0.88	0.464	0.657	2e-44

>gi|224131812|ref|XP_002328114.1| predicted protein [Populus trichocarpa] gi|222837629|gb|EEE75994.1| predicted protein [Populus trichocarpa]

 Score =  215 bits (547), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 104/133 (78%), Positives = 116/133 (87%), Gaps = 3/133 (2%)

Query: 19  SNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPST-RPYFRQRKP 77
           S  I+IREVW+ NLESEFELI  +ID +PFISMDTEFPG+V+RP VDP+  R YFRQ KP
Sbjct: 4   SKEIVIREVWSCNLESEFELIRDLIDEFPFISMDTEFPGVVFRPPVDPTNNRNYFRQLKP 63

Query: 78  SDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPD 137
           SDHYK+LKSNVDALNLIQVGLTLSD+ GNLPDLG+G  N+FIWEFNFRDFDV  D+HAPD
Sbjct: 64  SDHYKILKSNVDALNLIQVGLTLSDAEGNLPDLGTG--NRFIWEFNFRDFDVERDSHAPD 121

Query: 138 SIELLRLQGIDFE 150
           SIELLR QGIDFE
Sbjct: 122 SIELLRRQGIDFE 134

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|229560489|gb|ACQ77596.1| CCR4-NOT [Dimocarpus longan]

 Score =  204 bits (518), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 101/134 (75%), Positives = 118/134 (88%), Gaps = 7/134 (5%)

Query: 17  SSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRK 76
           S+ ++I IREVW  NLESEFELI QVID YP+ISMDTEFPG++YR     S++PY  QR+
Sbjct: 6   SNPDTIKIREVWDFNLESEFELIRQVIDHYPYISMDTEFPGIIYR-----SSKPYHSQRQ 60

Query: 77  PSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAP 136
           PSDHY++LKSNVDALNLIQVGLTLSDSSGNLPDLG+  +N+FIW+FNFRDFDVA+DAHAP
Sbjct: 61  PSDHYELLKSNVDALNLIQVGLTLSDSSGNLPDLGT--DNQFIWQFNFRDFDVASDAHAP 118

Query: 137 DSIELLRLQGIDFE 150
           DSI+LLR QGIDFE
Sbjct: 119 DSIDLLRRQGIDFE 132

Source: Dimocarpus longan

Species: Dimocarpus longan

Genus: Dimocarpus

Family: Sapindaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356542778|ref|XP_003539842.1| PREDICTED: probable CCR4-associated factor 1 homolog 9-like [Glycine max]

 Score =  202 bits (515), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 97/130 (74%), Positives = 115/130 (88%), Gaps = 4/130 (3%)

Query: 20  NSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSD 79
           N I+IREVWASNLESEFELI ++IDRYPFISMDTEFPG+++RP VDP T+P+  + +PSD
Sbjct: 13  NPIVIREVWASNLESEFELIRELIDRYPFISMDTEFPGVIFRPHVDP-TKPFNHRNRPSD 71

Query: 80  HYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSI 139
           HY++LKSNVDALNLIQVGLTL+D++GNLPDL     N+ IWEFNFRDFDVA DA+APDSI
Sbjct: 72  HYRLLKSNVDALNLIQVGLTLTDAAGNLPDLAG---NRSIWEFNFRDFDVARDAYAPDSI 128

Query: 140 ELLRLQGIDF 149
           +LLR QGIDF
Sbjct: 129 DLLRRQGIDF 138

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225464848|ref|XP_002271636.1| PREDICTED: probable CCR4-associated factor 1 homolog 9-like [Vitis vinifera]

 Score =  200 bits (509), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 99/139 (71%), Positives = 114/139 (82%), Gaps = 5/139 (3%)

Query: 12  SSSNSSSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPY 71
           S  +  +S  ++IREVWA NLESEFELIS +ID+YPFISMDTEFPG+V+RP         
Sbjct: 3   SEDSDCNSKPVMIREVWAENLESEFELISDLIDQYPFISMDTEFPGVVFRP---SGGEQQ 59

Query: 72  FRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVAT 131
           FR R+PSDHY+ LKSNVDAL LIQVGLTLSD++GNLPDLG+G  N+FIWEFNFRDFDVA 
Sbjct: 60  FRLRRPSDHYRFLKSNVDALCLIQVGLTLSDANGNLPDLGTG--NRFIWEFNFRDFDVAR 117

Query: 132 DAHAPDSIELLRLQGIDFE 150
           DAHAPDSIELL  QGIDF+
Sbjct: 118 DAHAPDSIELLSRQGIDFD 136

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356543624|ref|XP_003540260.1| PREDICTED: probable CCR4-associated factor 1 homolog 11-like [Glycine max]

 Score =  197 bits (502), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 98/136 (72%), Positives = 111/136 (81%), Gaps = 5/136 (3%)

Query: 15  NSSSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQ 74
           N + S +I+IREVWASNLESEF+LI QVID YPFISMDTEFPG+V+RP     T+PY   
Sbjct: 33  NPNHSKTILIREVWASNLESEFQLIRQVIDDYPFISMDTEFPGVVFRPHTVDPTKPYL-- 90

Query: 75  RKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAH 134
             PS HY+ LKSNVDALNLIQ+GLTLSDS+GNLP LG+   N+FIWEFNFRDFDV  DAH
Sbjct: 91  -PPSVHYRFLKSNVDALNLIQIGLTLSDSNGNLPHLGTA--NRFIWEFNFRDFDVERDAH 147

Query: 135 APDSIELLRLQGIDFE 150
           APDSI+LLR QGIDF 
Sbjct: 148 APDSIDLLRRQGIDFR 163

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255638796|gb|ACU19702.1| unknown [Glycine max]

 Score =  196 bits (497), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 97/136 (71%), Positives = 110/136 (80%), Gaps = 5/136 (3%)

Query: 15  NSSSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQ 74
           N + S +I+IREVWASNLESEF+LI QVID YP ISMDTEFPG+V+RP     T+PY   
Sbjct: 33  NPNHSKTILIREVWASNLESEFQLIRQVIDDYPLISMDTEFPGVVFRPHTVDPTKPYL-- 90

Query: 75  RKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAH 134
             PS HY+ LKSNVDALNLIQ+GLTLSDS+GNLP LG+   N+FIWEFNFRDFDV  DAH
Sbjct: 91  -PPSVHYRFLKSNVDALNLIQIGLTLSDSNGNLPHLGTA--NRFIWEFNFRDFDVERDAH 147

Query: 135 APDSIELLRLQGIDFE 150
           APDSI+LLR QGIDF 
Sbjct: 148 APDSIDLLRRQGIDFR 163

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147839203|emb|CAN76920.1| hypothetical protein VITISV_015622 [Vitis vinifera]

 Score =  196 bits (497), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 96/128 (75%), Positives = 109/128 (85%), Gaps = 5/128 (3%)

Query: 23  IIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYK 82
           +IREVWA NLESEFELIS +ID+YPFISMDTEFPG+V+RP         FR R+PSDHY+
Sbjct: 1   MIREVWAENLESEFELISDLIDQYPFISMDTEFPGVVFRP---SGGEQQFRLRRPSDHYR 57

Query: 83  VLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELL 142
            LKSNVDAL LIQVGLTLSD++GNLPDLG+G  N+FIWEFNFRDFDVA DAH+PDSIELL
Sbjct: 58  FLKSNVDALCLIQVGLTLSDANGNLPDLGTG--NRFIWEFNFRDFDVARDAHSPDSIELL 115

Query: 143 RLQGIDFE 150
             QGIDF+
Sbjct: 116 SRQGIDFD 123

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356572602|ref|XP_003554457.1| PREDICTED: probable CCR4-associated factor 1 homolog 11-like [Glycine max]

 Score =  184 bits (468), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 90/135 (66%), Positives = 107/135 (79%), Gaps = 5/135 (3%)

Query: 16  SSSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQR 75
           + S  SI+ R VW+SNLESEF+LI  VID +P ISMDTEFPG+V RPD   +  P FR R
Sbjct: 2   AQSHGSILTRSVWSSNLESEFDLIRSVIDSFPLISMDTEFPGVVVRPD---ACDPSFRHR 58

Query: 76  KPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHA 135
           +P+ HY VLK+NVD L+LIQ+GLTLSD++GNLP LG+  +N FIWEFNFRDFDV  DAHA
Sbjct: 59  QPAAHYAVLKANVDRLHLIQIGLTLSDNAGNLPTLGT--SNAFIWEFNFRDFDVVRDAHA 116

Query: 136 PDSIELLRLQGIDFE 150
            DS+ELLR QGIDFE
Sbjct: 117 HDSVELLRRQGIDFE 131

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356505410|ref|XP_003521484.1| PREDICTED: probable CCR4-associated factor 1 homolog 11-like [Glycine max]

 Score =  183 bits (465), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 92/136 (67%), Positives = 108/136 (79%), Gaps = 7/136 (5%)

Query: 16  SSSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDV-DPSTRPYFRQ 74
           + S  SI+ R VW+SNLESEF+LI  VID +P ISMDTEFPG+V RPD  DPS    FR 
Sbjct: 2   AQSHGSILTRSVWSSNLESEFDLIRSVIDSFPLISMDTEFPGVVVRPDAGDPS----FRH 57

Query: 75  RKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAH 134
           R+P  HY VLK+NVD L+LIQ+GLTLSD++GNLP LG+  +N FIWEFNF+DFDVA DAH
Sbjct: 58  RQPVAHYAVLKANVDRLHLIQIGLTLSDNAGNLPTLGT--SNAFIWEFNFKDFDVARDAH 115

Query: 135 APDSIELLRLQGIDFE 150
           A DS+ELLR QGIDFE
Sbjct: 116 AHDSVELLRRQGIDFE 131

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356539219|ref|XP_003538097.1| PREDICTED: probable CCR4-associated factor 1 homolog 11 [Glycine max]

 Score =  183 bits (464), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 92/140 (65%), Positives = 115/140 (82%), Gaps = 8/140 (5%)

Query: 14  SNSSSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPY-- 71
           S + + + ++IR+VWASNLESEF+LI ++ID YPFISMDTEFPG+V+RP +DP T+PY  
Sbjct: 5   SENPNPDPVVIRQVWASNLESEFQLIRELIDHYPFISMDTEFPGVVFRPHLDP-TKPYNH 63

Query: 72  --FRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDV 129
               + + SDHY++LKSNVDALNLIQVGLTL+D++GNLPDL     N+ IWEFNFRDFDV
Sbjct: 64  RNNNRNRHSDHYRLLKSNVDALNLIQVGLTLTDAAGNLPDLAG---NRSIWEFNFRDFDV 120

Query: 130 ATDAHAPDSIELLRLQGIDF 149
           A DA+A DSI+LLR QGIDF
Sbjct: 121 ARDAYALDSIDLLRRQGIDF 140

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	150
TAIR|locus:2095715	280	CAF1a "CCR4- associated factor	0.786	0.421	0.706	5.2e-42
TAIR|locus:2176307	278	CAF1b "CCR4- associated factor	0.806	0.435	0.658	1.6e-40
TAIR|locus:2045512	275	AT2G32070 [Arabidopsis thalian	0.773	0.421	0.539	4.9e-30
TAIR|locus:2200532	286	AT1G15920 [Arabidopsis thalian	0.813	0.426	0.519	5e-28
TAIR|locus:2183765	277	AT5G10960 [Arabidopsis thalian	0.773	0.418	0.511	3.5e-27
POMBASE|SPCC18.06c	335	caf1 "CCR4-Not complex CAF1 fa	0.74	0.331	0.472	8.7e-24
DICTYBASE|DDB_G0285269	309	DDB_G0285269 "CAF1 family prot	0.746	0.362	0.460	9e-22
DICTYBASE|DDB_G0284217	367	DDB_G0284217 "CAF1 family prot	0.74	0.302	0.448	1.9e-21
FB|FBgn0036239	357	Pop2 "Pop2" [Drosophila melano	0.74	0.310	0.433	8e-21
SGD|S000005335	433	POP2 "RNase of the DEDD superf	0.753	0.260	0.452	2.4e-20

TAIR|locus:2095715 CAF1a "CCR4- associated factor 1a" [Arabidopsis thaliana (taxid:3702)]

 Score = 445 (161.7 bits), Expect = 5.2e-42, P = 5.2e-42
 Identities = 89/126 (70%), Positives = 101/126 (80%)

Query:    25 REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVL 84
             REVWA NLESEFELIS++ID YPFISMDTEFPG++++ D+        R   P D Y +L
Sbjct:    20 REVWAENLESEFELISEIIDDYPFISMDTEFPGVIFKSDL--------RFTNPDDLYTLL 71

Query:    85 KSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRL 144
             K+NVDAL+LIQVGLTLSD +GNLPDLG   +  FIWEFNFRDFDVA DAHAPDSIELLR 
Sbjct:    72 KANVDALSLIQVGLTLSDVNGNLPDLGDDLHRGFIWEFNFRDFDVARDAHAPDSIELLRR 131

Query:   145 QGIDFE 150
             QGIDFE
Sbjct:   132 QGIDFE 137

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004540 "ribonuclease activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0009451 "RNA modification" evidence=ISS

GO:0002213 "defense response to insect" evidence=IEP

GO:0009611 "response to wounding" evidence=IEP;RCA

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=IMP

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

GO:0042742 "defense response to bacterium" evidence=IEP

GO:0009612 "response to mechanical stimulus" evidence=RCA

GO:0009693 "ethylene biosynthetic process" evidence=RCA

GO:0009873 "ethylene mediated signaling pathway" evidence=RCA

GO:0010200 "response to chitin" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

TAIR|locus:2176307 CAF1b "CCR4- associated factor 1b" [Arabidopsis thaliana (taxid:3702)]

 Score = 431 (156.8 bits), Expect = 1.6e-40, P = 1.6e-40
 Identities = 83/126 (65%), Positives = 99/126 (78%)

Query:    25 REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVL 84
             R+VWA NLESEF+LI  +++ YPFISMDTEFPG++Y+ D+D       R+  P+  Y +L
Sbjct:    15 RDVWAYNLESEFDLIRGIVEDYPFISMDTEFPGVIYKADLD-----VLRRGNPNYLYNLL 69

Query:    85 KSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRL 144
             KSNVDAL+LIQVGLTLSD+ GNLPDLG   N ++IWEFNFRDFDV  D HAPDSIELLR 
Sbjct:    70 KSNVDALSLIQVGLTLSDADGNLPDLGGQKNRRYIWEFNFRDFDVERDPHAPDSIELLRR 129

Query:   145 QGIDFE 150
              GIDFE
Sbjct:   130 HGIDFE 135

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004540 "ribonuclease activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0009451 "RNA modification" evidence=ISS

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=IMP

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

GO:0042742 "defense response to bacterium" evidence=IEP

GO:0000165 "MAPK cascade" evidence=RCA

GO:0002679 "respiratory burst involved in defense response" evidence=RCA

GO:0009693 "ethylene biosynthetic process" evidence=RCA

GO:0009738 "abscisic acid mediated signaling pathway" evidence=RCA

GO:0009814 "defense response, incompatible interaction" evidence=RCA

GO:0009873 "ethylene mediated signaling pathway" evidence=RCA

GO:0010200 "response to chitin" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0035556 "intracellular signal transduction" evidence=RCA

TAIR|locus:2045512 AT2G32070 [Arabidopsis thaliana (taxid:3702)]

 Score = 332 (121.9 bits), Expect = 4.9e-30, P = 4.9e-30
 Identities = 68/126 (53%), Positives = 88/126 (69%)

Query:    25 REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVL 84
             REVW  NLESE  LI +V+D +PF++MDTEFPG+V RP     T   +       HY+ L
Sbjct:    13 REVWNDNLESEMALIREVVDDFPFVAMDTEFPGIVCRPVGTFKTNTEY-------HYETL 65

Query:    85 KSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKF-IWEFNFRDFDVATDAHAPDSIELLR 143
             K+NV+ L +IQ+GLT SD  GNLP  G+  +NK+ IW+FNFR+FD+ +D +A DSIELLR
Sbjct:    66 KTNVNILKMIQLGLTFSDEKGNLPTCGT--DNKYCIWQFNFREFDLESDIYATDSIELLR 123

Query:   144 LQGIDF 149
               GIDF
Sbjct:   124 QSGIDF 129

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:0006499 "N-terminal protein myristoylation" evidence=RCA

TAIR|locus:2200532 AT1G15920 [Arabidopsis thaliana (taxid:3702)]

 Score = 313 (115.2 bits), Expect = 5.0e-28, P = 5.0e-28
 Identities = 66/127 (51%), Positives = 85/127 (66%)

Query:    25 REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRP-DVDPSTRPYFRQRKPSDHYKV 83
             REVW  NLE E  LI Q ID +P+++MDTEFPG+V +    +P+  PY    + +  Y  
Sbjct:    17 REVWNHNLEQEMALIEQSIDDFPYVAMDTEFPGIVCKTVTANPNPNPYSIHYEYN--YDT 74

Query:    84 LKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLR 143
             LK+NV+ L LIQ+GLTLSD  GNLP  G+  N + IW+FNFR+F+V +D  A DSIELLR
Sbjct:    75 LKANVNMLKLIQLGLTLSDEKGNLPTCGT--NKQCIWQFNFREFNVISDMFALDSIELLR 132

Query:   144 LQGIDFE 150
                ID E
Sbjct:   133 KSAIDLE 139

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004540 "ribonuclease activity" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

GO:0009451 "RNA modification" evidence=ISS

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

TAIR|locus:2183765 AT5G10960 [Arabidopsis thaliana (taxid:3702)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 65/127 (51%), Positives = 87/127 (68%)

Query:    25 REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVL 84
             REVW  NL  EF LI +++D++ +I+MDTEFPG+V +P    +T  Y        +Y+ L
Sbjct:    13 REVWDYNLVEEFALIREIVDKFSYIAMDTEFPGVVLKP---VATFKYNNDL----NYRTL 65

Query:    85 KSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKF-IWEFNFRDFDVATDAHAPDSIELLR 143
             K NVD L LIQVGLT SD +GNLP  G+   +KF IW+FNFR+F++  D +A +SIELLR
Sbjct:    66 KENVDLLKLIQVGLTFSDENGNLPTCGT---DKFCIWQFNFREFNIGEDIYASESIELLR 122

Query:   144 LQGIDFE 150
               GIDF+
Sbjct:   123 QCGIDFK 129

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004540 "ribonuclease activity" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0009451 "RNA modification" evidence=ISS

GO:0000902 "cell morphogenesis" evidence=RCA

GO:0007030 "Golgi organization" evidence=RCA

GO:0007033 "vacuole organization" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0016049 "cell growth" evidence=RCA

GO:0048193 "Golgi vesicle transport" evidence=RCA

POMBASE|SPCC18.06c caf1 "CCR4-Not complex CAF1 family ribonuclease subunit Caf1" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 273 (101.2 bits), Expect = 8.7e-24, P = 8.7e-24
 Identities = 60/127 (47%), Positives = 81/127 (63%)

Query:    25 REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRP-DVDPSTRPYFRQRKPSDHYKV 83
             R+VW++NL+ E  LI  +I+RYP +SMDTEFPG+V RP  V  S+  Y        HY+ 
Sbjct:    26 RDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVARPLGVFKSSDDY--------HYQT 77

Query:    84 LKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLR 143
             L++NVD+L +IQ+GL LSD  GN P           W+FNF  F++  D +AP+SIELL 
Sbjct:    78 LRANVDSLKIIQIGLALSDEEGNAPV------EACTWQFNFT-FNLQDDMYAPESIELLT 130

Query:   144 LQGIDFE 150
               GIDF+
Sbjct:   131 KSGIDFK 137

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=IDA

GO:0003729 "mRNA binding" evidence=ISS

GO:0004535 "poly(A)-specific ribonuclease activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=ISO

GO:0005829 "cytosol" evidence=IDA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=ISO

GO:0030015 "CCR4-NOT core complex" evidence=ISO

GO:0046872 "metal ion binding" evidence=IDA

GO:0071276 "cellular response to cadmium ion" evidence=IMP

GO:0071585 "detoxification of cadmium ion" evidence=IMP

DICTYBASE|DDB_G0285269 DDB_G0285269 "CAF1 family protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 254 (94.5 bits), Expect = 9.0e-22, P = 9.0e-22
 Identities = 58/126 (46%), Positives = 81/126 (64%)

Query:    25 REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVL 84
             REVWA NLE E  LI +++D YP +++DTEFPG V +P ++ S R Y     P  +Y+ L
Sbjct:    48 REVWAHNLEYEMSLIRELVDIYPCVAIDTEFPGFVNKP-IE-SMRMY-----PDYNYQTL 100

Query:    85 KSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRL 144
             +SNVD L +IQ G+T SDS+G LP           W+FNF+ F +  D ++P +IELL+ 
Sbjct:   101 RSNVDLLKIIQFGITFSDSTGCLPV------PTCTWQFNFK-FSLKDDMYSPYAIELLKS 153

Query:   145 QGIDFE 150
              GIDF+
Sbjct:   154 CGIDFQ 159

GO:0005634 "nucleus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

DICTYBASE|DDB_G0284217 DDB_G0284217 "CAF1 family protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 251 (93.4 bits), Expect = 1.9e-21, P = 1.9e-21
 Identities = 57/127 (44%), Positives = 77/127 (60%)

Query:    25 REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSD-HYKV 83
             ++VW  NL+ E E I  ++D Y +I+MDTEFPG+V        TRP    R  SD HY+ 
Sbjct:    10 KDVWGYNLDEEMEKIRNLVDDYNYIAMDTEFPGIV--------TRPVGNFRSTSDYHYQT 61

Query:    84 LKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLR 143
             L+ NVD L +IQ+GLT SDS GNL            W+FNF+ F ++ D +A DSI+LL 
Sbjct:    62 LRLNVDQLKIIQLGLTFSDSEGNL------AKPTCTWQFNFK-FSLSEDMYAQDSIDLLS 114

Query:   144 LQGIDFE 150
               GI+F+
Sbjct:   115 RSGIEFK 121

GO:0005634 "nucleus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

FB|FBgn0036239 Pop2 "Pop2" [Drosophila melanogaster (taxid:7227)]

 Score = 245 (91.3 bits), Expect = 8.0e-21, P = 8.0e-21
 Identities = 55/127 (43%), Positives = 79/127 (62%)

Query:    25 REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVD-PSTRPYFRQRKPSDHYKV 83
             R+VW  NLE EF  I +V+ +Y +++MDTEFPG+V RP  +  ST  Y        HY++
Sbjct:    22 RDVWKQNLEEEFRTIRKVVQKYHYVAMDTEFPGVVARPVGEFRSTADY--------HYQL 73

Query:    84 LKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLR 143
             L+ NVD L +IQ+GLT  D  G  P    G +    W+FNF+ F+++ D +A DSI+LL+
Sbjct:    74 LRCNVDLLRIIQLGLTFMDDDGKTPP---GYST---WQFNFK-FNLSEDMYAQDSIDLLQ 126

Query:   144 LQGIDFE 150
               GI F+
Sbjct:   127 NSGIQFK 133

GO:0005634 "nucleus" evidence=ISS

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0007517 "muscle organ development" evidence=IMP

GO:0048666 "neuron development" evidence=IMP

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=IMP

GO:0030014 "CCR4-NOT complex" evidence=IDA

GO:0004535 "poly(A)-specific ribonuclease activity" evidence=IMP

GO:0007095 "mitotic G2 DNA damage checkpoint" evidence=IGI

GO:0022008 "neurogenesis" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

SGD|S000005335 POP2 "RNase of the DEDD superfamily" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 245 (91.3 bits), Expect = 2.4e-20, P = 2.4e-20
 Identities = 57/126 (45%), Positives = 80/126 (63%)

Query:    25 REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVL 84
             R+VW SNL SEF +I Q++ +Y  +S+ TEF G + RP     T   FR  K   HY+ +
Sbjct:   161 RDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPI---GT---FRS-KVDYHYQTM 213

Query:    85 KSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRL 144
             ++NVD LN IQ+GL+LSD++GN PD     N    W+FNF +FD   +  + +S+ELLR 
Sbjct:   214 RANVDFLNPIQLGLSLSDANGNKPD-----NGPSTWQFNF-EFDPKKEIMSTESLELLRK 267

Query:   145 QGIDFE 150
              GI+FE
Sbjct:   268 SGINFE 273

GO:0043332 "mating projection tip" evidence=IDA

GO:0004535 "poly(A)-specific ribonuclease activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA;IDA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0090305 "nucleic acid phosphodiester bond hydrolysis" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0004527 "exonuclease activity" evidence=IEA

GO:0032968 "positive regulation of transcription elongation from RNA polymerase II promoter" evidence=IDA;IPI

GO:0000932 "cytoplasmic mRNA processing body" evidence=IDA

GO:0000175 "3'-5'-exoribonuclease activity" evidence=IGI;IDA;IMP

GO:0030015 "CCR4-NOT core complex" evidence=IPI

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IPI

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=IMP;IDA

GO:0006368 "transcription elongation from RNA polymerase II promoter" 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: grail3.0066011001 hypothetical protein (277 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	150
pfam04857	235	pfam04857, CAF1, CAF1 family ribonuclease	2e-43
COG5228	299	COG5228, POP2, mRNA deadenylase subunit [RNA proce	7e-35

>gnl|CDD|147159 pfam04857, CAF1, CAF1 family ribonuclease

 Score =  142 bits (361), Expect = 2e-43
 Identities = 58/126 (46%), Positives = 73/126 (57%), Gaps = 13/126 (10%)

Query: 25  REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVL 84
           REVW SN   EF+ I Q ID Y FI++DTEFPG+V RP           +      Y+ L
Sbjct: 1   REVWRSNFHEEFKEIRQAIDSYDFIAIDTEFPGVVARPIG-------SFRSTSDYRYQAL 53

Query: 85  KSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRL 144
           + NVD L +IQ+GLTL D  GNLPD      + + W+FNF  F++  D +AP SIE L  
Sbjct: 54  RKNVDRLKIIQLGLTLFDEKGNLPD------SYYTWQFNFSLFNLEEDFYAPSSIEFLAK 107

Query: 145 QGIDFE 150
           QG DF 
Sbjct: 108 QGFDFN 113

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|227553 COG5228, POP2, mRNA deadenylase subunit [RNA processing and modification]

 Score =  122 bits (307), Expect = 7e-35
 Identities = 63/131 (48%), Positives = 83/131 (63%), Gaps = 14/131 (10%)

Query: 20  NSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSD 79
           N + IR+VW SNL SE  +I Q+I RY  +SMDTEFPG+V RP         F+      
Sbjct: 16  NYLFIRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARP------IGTFKS-SVDY 68

Query: 80  HYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSI 139
           HY+ L++NVD L +IQ+GL+LSD +GN P      N    W+FNF +FD+  D +A +SI
Sbjct: 69  HYQTLRANVDFLKIIQLGLSLSDENGNKP------NGPSTWQFNF-EFDLKKDMYATESI 121

Query: 140 ELLRLQGIDFE 150
           ELLR  GIDF+
Sbjct: 122 ELLRKSGIDFK 132

Length = 299

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	150
KOG0304	239	consensus mRNA deadenylase subunit [RNA processing	100.0
PF04857	262	CAF1: CAF1 family ribonuclease; InterPro: IPR00694	100.0
COG5228	299	POP2 mRNA deadenylase subunit [RNA processing and	100.0
KOG1990	564	consensus Poly(A)-specific exoribonuclease PARN [R	98.61
cd06133	176	ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o	93.64
PRK05168	211	ribonuclease T; Provisional	85.59
PRK09145	202	DNA polymerase III subunit epsilon; Validated	82.68
PF00929	164	RNase_T: Exonuclease; InterPro: IPR013520 This ent	82.12
cd06134	189	RNaseT DEDDh 3'-5' exonuclease domain of RNase T.	81.07
COG0349	361	Rnd Ribonuclease D [Translation, ribosomal structu	80.68

>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]

Probab=100.00  E-value=1.9e-40  Score=265.36  Aligned_cols=116  Identities=59%  Similarity=0.977  Sum_probs=109.1

Q ss_pred             eEEEecccCHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeec
Q 048636           23 IIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSD  102 (150)
Q Consensus        23 ~v~dV~~~Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~  102 (150)
                      .|||||+.|+++||..|+++|++|+||||||||||++.+|.     +.|.+  +.+++|+.||+|||.+++||+|||+++
T Consensus         1 ~ireVW~~Nl~~Em~~Ir~~v~~y~~IamDTEFPGvv~rp~-----~~f~s--~~d~~Y~~lk~NVd~lklIQlGlTlsd   73 (239)
T KOG0304|consen    1 FIREVWRSNLEEEMALIRECVKDYPYIAMDTEFPGVVARPI-----GTFRS--SDDYHYQTLKCNVDNLKLIQLGLTLSD   73 (239)
T ss_pred             ChhHHHHHhHHHHHHHHHHHHHhCCeeEecCcCCceeeecC-----ccccC--ChHHHHHHHHhchhhhhhhheeeeeec
Confidence            47999999999999999999999999999999999999998     67766  569999999999999999999999999


Q ss_pred             CCCCCCCCCCCCCCeeEEEEeccccCCCCCCcchhHHHHHHHcCCCCC
Q 048636          103 SSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE  150 (150)
Q Consensus       103 ~~g~~p~~g~~~~~~~~~~FNF~~F~~~~d~~~~sSi~FL~~~GfDFn  150 (150)
                      .+|++|..|     ..+|||||..|+..+|+++++||+||+++|+||.
T Consensus        74 ~~Gn~p~~g-----~~tWqfNF~dF~~~~D~~a~~SIElLr~~Gidf~  116 (239)
T KOG0304|consen   74 EKGNLPDCG-----TDTWQFNFSDFNLEKDMYAQDSIELLRRSGIDFE  116 (239)
T ss_pred             cCCCCCCCC-----CceeEEecccCCchhhccchhhHHHHHHcCcCHH
Confidence            999999664     4699999999999999999999999999999984

>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

Probab=100.00  E-value=6.5e-35  Score=239.15  Aligned_cols=113  Identities=40%  Similarity=0.697  Sum_probs=97.5

Q ss_pred             EEecccCHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeee-cC
Q 048636           25 REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLS-DS  103 (150)
Q Consensus        25 ~dV~~~Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f-~~  103 (150)
                      +|||++||+++|+.|+++|++|+|||||+||||+..++..    ..++   ++++||+++|+||+.+.|||+|||+| +.
T Consensus         1 m~Vt~~Nf~~~l~~i~~~i~~~~fvaiD~EftGl~~~~~~----~~~~---t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~   73 (262)
T PF04857_consen    1 MEVTRSNFEEELPEILQAISKADFVAIDTEFTGLVSKPPR----SRFD---TPEERYEKLRANVETFQIIQFGLTLFHDE   73 (262)
T ss_dssp             EEE-CCCHHHHHHHHHHHHHHSSEEEEEEEES-S-SSS-S----HCSS---HHHHHHHHHHHHHTTBEEEEEEEEEETTT
T ss_pred             CcccHHHHHHHHHHHHHHHhhCCEEEEEeeccccccCCCc----cccc---cHHHHHHHHHHhhcccccceeeEEEeecc
Confidence            6999999999999999999999999999999999988872    2333   78999999999999999999999999 66


Q ss_pred             CCCCCCCCCCCCCeeEEEEeccccCCCCCCcchhHHHHHHHcCCCCC
Q 048636          104 SGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE  150 (150)
Q Consensus       104 ~g~~p~~g~~~~~~~~~~FNF~~F~~~~d~~~~sSi~FL~~~GfDFn  150 (150)
                      +++.|.      .|.+|+|||++||..++.++++||+||++||||||
T Consensus        74 ~~~~~~------~~~~~~~nf~~f~~~~~~~~~~sl~FL~~~gfDFn  114 (262)
T PF04857_consen   74 DGNIPS------SYNVWPFNFYLFPLDRDFSQASSLQFLRKNGFDFN  114 (262)
T ss_dssp             TSEEEC------CEEEEEEEBSTTSTTTCEEEHHHHHHHHHTT--HH
T ss_pred             cccCCc------eeEEEEeeeeccccccceecchhHHHHHHcccCHH
Confidence            777653      58999999999999999889999999999999996

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.

>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]

Probab=100.00  E-value=2.4e-35  Score=237.49  Aligned_cols=116  Identities=52%  Similarity=0.882  Sum_probs=110.1

Q ss_pred             CceEEEecccCHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeee
Q 048636           21 SIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTL  100 (150)
Q Consensus        21 ~~~v~dV~~~Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~  100 (150)
                      -.+|||||+.|+..||..|+++|.+|++|+|||||||++++|.     |.|+++  .+.+||.||+|||-++|||+||++
T Consensus        17 ~~~irdVWk~NL~~Em~~I~qLi~rYn~vSmdTEFpGvvArPi-----G~FkSs--~dyhYQtlraNVD~LkiIQlGlsL   89 (299)
T COG5228          17 YLFIRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPI-----GTFKSS--VDYHYQTLRANVDFLKIIQLGLSL   89 (299)
T ss_pred             hHHHHHHHHhhHHHHHHHHHHHHHhCCceeeccccCceeeccc-----cccccc--chHHHHHHhcccchhhhhheeeee
Confidence            3579999999999999999999999999999999999999998     899984  599999999999999999999999


Q ss_pred             ecCCCCCCCCCCCCCCeeEEEEeccccCCCCCCcchhHHHHHHHcCCCCC
Q 048636          101 SDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE  150 (150)
Q Consensus       101 f~~~g~~p~~g~~~~~~~~~~FNF~~F~~~~d~~~~sSi~FL~~~GfDFn  150 (150)
                      .+++|+.|.      ..++|||||- |+..+|++.++||++|+++|+||.
T Consensus        90 SDe~GN~P~------~~sTWQFNF~-F~l~~dmya~ESieLL~ksgIdFk  132 (299)
T COG5228          90 SDENGNKPN------GPSTWQFNFE-FDLKKDMYATESIELLRKSGIDFK  132 (299)
T ss_pred             ccccCCCCC------CCceeEEEEE-ecchhhhcchHHHHHHHHcCCChh
Confidence            999999984      3799999999 999999999999999999999994

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

Probab=98.61  E-value=8e-09  Score=93.52  Aligned_cols=104  Identities=17%  Similarity=0.126  Sum_probs=83.3

Q ss_pred             ccCHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCCCCCC
Q 048636           29 ASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLP  108 (150)
Q Consensus        29 ~~Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~g~~p  108 (150)
                      +.||+. +..++..|+.+.|+|+|.|++|+...+..+  ...++   +++.+|+++|.++..+.++|+|+|+|.+++...
T Consensus         1 ~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~--~~~~~---~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~   74 (564)
T KOG1990|consen    1 RSNFES-LSLAELTVDEADLRRLRLVATGMTSAPWKA--GSTFD---TVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEA   74 (564)
T ss_pred             CCcccc-hhHHHhhcCHHHHHHHhhhhccceeccccc--ccchh---hhHHHHHHHHhhhhhheeeccccchhHHHhhhH
Confidence            468889 999999999999999999999998887521  12244   899999999999999999999999999987643


Q ss_pred             CCCCCCCCeeEEEEeccccCCC------CCCcchhHHHHHHHc
Q 048636          109 DLGSGGNNKFIWEFNFRDFDVA------TDAHAPDSIELLRLQ  145 (150)
Q Consensus       109 ~~g~~~~~~~~~~FNF~~F~~~------~d~~~~sSi~FL~~~  145 (150)
                             .+..-.+||++|+..      +.+|+.+++.|+.++
T Consensus        75 -------~~~~~~~n~~~~~~g~~~s~~~~~~~~~~~~~~~~~  110 (564)
T KOG1990|consen   75 -------LEMSTGGNFVVWSRGDSISSPEFLCQRSPVDFVARQ  110 (564)
T ss_pred             -------hhccCCCceeeeecCccccCCccceeecchhhhhhh
Confidence                   233345666666642      337899999998876

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

Probab=93.64  E-value=0.2  Score=37.44  Aligned_cols=59  Identities=15%  Similarity=0.069  Sum_probs=36.6

Q ss_pred             ceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCCCCCCCCCCCCCCeeEEEEecccc
Q 048636           48 FISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDF  127 (150)
Q Consensus        48 fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~g~~p~~g~~~~~~~~~~FNF~~F  127 (150)
                      ||.+|+|++|+......    ...                   -.|||+|....+.++.          ...-.|+.++-
T Consensus         1 ~vv~D~Ettg~~~~~~~----~~~-------------------~~IieIgav~v~~~~~----------~~~~~f~~~i~   47 (176)
T cd06133           1 YLVIDFEATCWEGNSKP----DYP-------------------NEIIEIGAVLVDVKTK----------EIIDTFSSYVK   47 (176)
T ss_pred             CEEEEeeccccCCCCCC----CCC-------------------cceEEEEEEEEEcCCC----------eEEeeeeeeEC
Confidence            79999999998643210    000                   1499999999887653          24556777766


Q ss_pred             CCCCCCcchhHH
Q 048636          128 DVATDAHAPDSI  139 (150)
Q Consensus       128 ~~~~d~~~~sSi  139 (150)
                      |......++.+.
T Consensus        48 P~~~~~i~~~~~   59 (176)
T cd06133          48 PVINPKLSDFCT   59 (176)
T ss_pred             CCcCCchhHHHH
Confidence            654233344333

This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho

>PRK05168 ribonuclease T; Provisional

Probab=85.59  E-value=2.1  Score=33.96  Aligned_cols=24  Identities=13%  Similarity=0.259  Sum_probs=20.4

Q ss_pred             HHHHHHHhhhCCceeccccccccc
Q 048636           36 FELISQVIDRYPFISMDTEFPGLV   59 (150)
Q Consensus        36 l~~I~~~i~~~~fIAiDtEF~Gl~   59 (150)
                      +.-|..-++...||++|+|-||+.
T Consensus         7 ~~~~~~~~~~~~~vv~D~ETTGl~   30 (211)
T PRK05168          7 LNPLKDRFRGFLPVVIDVETAGFN   30 (211)
T ss_pred             cchHHHHhcCCceEEEEeeCCCCC
Confidence            455777788999999999999985

>PRK09145 DNA polymerase III subunit epsilon; Validated

Probab=82.68  E-value=1.7  Score=33.96  Aligned_cols=22  Identities=18%  Similarity=0.280  Sum_probs=16.3

Q ss_pred             HHHHHhhhCCceeccccccccc
Q 048636           38 LISQVIDRYPFISMDTEFPGLV   59 (150)
Q Consensus        38 ~I~~~i~~~~fIAiDtEF~Gl~   59 (150)
                      .+.+.....+||+||+|.||+.
T Consensus        21 ~~~~~~~~~~~vviD~ETTGl~   42 (202)
T PRK09145         21 FLFEPPPPDEWVALDCETTGLD   42 (202)
T ss_pred             HHhcCCCCCCEEEEEeECCCCC
Confidence            3444445569999999999974

>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

Probab=82.12  E-value=3.3  Score=29.43  Aligned_cols=44  Identities=27%  Similarity=0.256  Sum_probs=29.8

Q ss_pred             eecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCCCCCCCCCCCCCCeeEEEEeccccC
Q 048636           49 ISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFD  128 (150)
Q Consensus        49 IAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~g~~p~~g~~~~~~~~~~FNF~~F~  128 (150)
                      |.+|+|++|+..+.                            -.|||+|.-..+.+..          ...-.|+.++.|
T Consensus         1 v~~D~Ettg~~~~~----------------------------~~iieig~v~~~~~~~----------~~~~~~~~~i~p   42 (164)
T PF00929_consen    1 VVFDTETTGLDPRQ----------------------------DEIIEIGAVKVDDDEN----------EEVESFNSLIRP   42 (164)
T ss_dssp             EEEEEEESSSTTTT----------------------------CTEEEEEEEEEETTTT----------EEEEEEEEEBEH
T ss_pred             cEEEeEcCCCCCCC----------------------------CeEEEEEEEEeeCCcc----------ccceeeeecccc
Confidence            67999999985321                            1389999988777542          244567777555


Q ss_pred             CC
Q 048636          129 VA  130 (150)
Q Consensus       129 ~~  130 (150)
                      ..
T Consensus        43 ~~   44 (164)
T PF00929_consen   43 EE   44 (164)
T ss_dssp             SS
T ss_pred             cc
Confidence            43

Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....

>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T

Probab=81.07  E-value=4.1  Score=31.68  Aligned_cols=33  Identities=15%  Similarity=0.249  Sum_probs=24.5

Q ss_pred             hhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCC
Q 048636           44 DRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSS  104 (150)
Q Consensus        44 ~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~  104 (150)
                      +.+.+|++|+|-||+.....                            .|||+|...+..+
T Consensus         3 ~~~~~vv~D~ETTGl~~~~d----------------------------~Iieigav~v~~~   35 (189)
T cd06134           3 RGFLPVVVDVETGGFNPQTD----------------------------ALLEIAAVTLEMD   35 (189)
T ss_pred             ccceeEEEEecCCCCCCCCC----------------------------eEEEEEEEEEEEC
Confidence            34678999999999853211                            2899999988753

RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.

>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]

Probab=80.68  E-value=1.2  Score=38.95  Aligned_cols=26  Identities=23%  Similarity=0.259  Sum_probs=21.3

Q ss_pred             HHHHHHHHHhhhCCceeccccccccc
Q 048636           34 SEFELISQVIDRYPFISMDTEFPGLV   59 (150)
Q Consensus        34 ~el~~I~~~i~~~~fIAiDtEF~Gl~   59 (150)
                      +++..+...+..+++|||||||-|+.
T Consensus         5 ~~l~~~~~~~~~~~~iAiDTEf~r~~   30 (361)
T COG0349           5 DLLAAACALLRGSKAIAIDTEFMRLR   30 (361)
T ss_pred             hHHHHHHHHhcCCCceEEeccccccc
Confidence            45666777788899999999999974

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	150
2p51_A	333	Crystal Structure Of The S. Pombe Pop2p Deadenylati		4e-25
4gmj_B	285	Structure Of Human Not1 Mif4g Domain Co-Crystallize		4e-21
2d5r_A	252	Crystal Structure Of A Tob-Hcaf1 Complex Length = 2		6e-21
4b8a_B	286	Structure Of Yeast Not1 Mif4g Domain Co-Crystallize		1e-20
1uoc_A	289	X-Ray Structure Of The Rnase Domain Of The Yeast Po		1e-20
4b8c_A	288	Nuclease Module Of The Yeast Ccr4-Not Complex Lengt		1e-20

>pdb|2P51|A Chain A, Crystal Structure Of The S. Pombe Pop2p Deadenylation Subunit Length = 333

Iteration: 1
 Score =  110 bits (274), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 60/127 (47%), Positives = 81/127 (63%), Gaps = 16/127 (12%)
Query: 25  REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRP-DVDPSTRPYFRQRKPSDHYKV 83
           R+VW++NL+ E  LI  +I+RYP +SMDTEFPG+V RP  V  S+  Y        HY+ 
Sbjct: 24  RDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVARPLGVFKSSDDY--------HYQT 75
Query: 84  LKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLR 143
           L++NVD+L +IQ+GL LSD  GN P           W+FNF  F++  D +AP+SIELL 
Sbjct: 76  LRANVDSLKIIQIGLALSDEEGNAPV------EACTWQFNFT-FNLQDDMYAPESIELLT 128
Query: 144 LQGIDFE 150
             GIDF+
Sbjct: 129 KSGIDFK 135

>pdb|4GMJ|B Chain B, Structure Of Human Not1 Mif4g Domain Co-Crystallized With Caf1 Length = 285

Iteration: 1
 Score = 96.7 bits (239), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 54/126 (42%), Positives = 75/126 (59%), Gaps = 16/126 (12%)
Query: 26  EVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDH-YKVL 84
           EVWA NL+ E + I QVI +Y +++MDTEFPG+V         RP    R  +D+ Y++L
Sbjct: 14  EVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVV--------ARPIGEFRSNADYQYQLL 65
Query: 85  KSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRL 144
           + NVD L +IQ+GLT  +  G  P   S       W+FNF+ F++  D +A DSIELL  
Sbjct: 66  RCNVDLLKIIQLGLTFMNEQGEYPPGTS------TWQFNFK-FNLTEDMYAQDSIELLTT 118
Query: 145 QGIDFE 150
            GI F+
Sbjct: 119 SGIQFK 124

>pdb|2D5R|A Chain A, Crystal Structure Of A Tob-Hcaf1 Complex Length = 252

Iteration: 1
 Score = 96.3 bits (238), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 54/126 (42%), Positives = 75/126 (59%), Gaps = 16/126 (12%)
Query: 26  EVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDH-YKVL 84
           EVWA NL+ E + I QVI +Y +++MDTEFPG+V         RP    R  +D+ Y++L
Sbjct: 4   EVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVV--------ARPIGEFRSNADYQYQLL 55
Query: 85  KSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRL 144
           + NVD L +IQ+GLT  +  G  P   S       W+FNF+ F++  D +A DSIELL  
Sbjct: 56  RCNVDLLKIIQLGLTFMNEQGEYPPGTS------TWQFNFK-FNLTEDMYAQDSIELLTT 108
Query: 145 QGIDFE 150
            GI F+
Sbjct: 109 SGIQFK 114

>pdb|4B8A|B Chain B, Structure Of Yeast Not1 Mif4g Domain Co-Crystallized With Caf1 Length = 286

Iteration: 1
 Score = 95.5 bits (236), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 56/126 (44%), Positives = 79/126 (62%), Gaps = 13/126 (10%)
Query: 25  REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVL 84
           R+VW SNL SEF +I Q++ +Y  +S+ TEF G + RP         FR  K   HY+ +
Sbjct: 14  RDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGT------FRS-KVDYHYQTM 66
Query: 85  KSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRL 144
           ++NVD LN IQ+GL+LSD++GN PD G        W+FNF +FD   +  + +S+ELLR 
Sbjct: 67  RANVDFLNPIQLGLSLSDANGNKPDNGPS-----TWQFNF-EFDPKKEIMSTESLELLRK 120
Query: 145 QGIDFE 150
            GI+FE
Sbjct: 121 SGINFE 126

>pdb|1UOC|A Chain A, X-Ray Structure Of The Rnase Domain Of The Yeast Pop2 Protein Length = 289

Iteration: 1
 Score = 95.5 bits (236), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 56/126 (44%), Positives = 79/126 (62%), Gaps = 13/126 (10%)
Query: 25  REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVL 84
           R+VW SNL SEF +I Q++ +Y  +S+ TEF G + RP         FR  K   HY+ +
Sbjct: 17  RDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGT------FRS-KVDYHYQTM 69
Query: 85  KSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRL 144
           ++NVD LN IQ+GL+LSD++GN PD G        W+FNF +FD   +  + +S+ELLR 
Sbjct: 70  RANVDFLNPIQLGLSLSDANGNKPDNGPS-----TWQFNF-EFDPKKEIMSTESLELLRK 123
Query: 145 QGIDFE 150
            GI+FE
Sbjct: 124 SGINFE 129

>pdb|4B8C|A Chain A, Nuclease Module Of The Yeast Ccr4-Not Complex Length = 288

Iteration: 1
 Score = 95.5 bits (236), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 56/126 (44%), Positives = 79/126 (62%), Gaps = 13/126 (10%)
Query: 25  REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVL 84
           R+VW SNL SEF +I Q++ +Y  +S+ TEF G + RP         FR  K   HY+ +
Sbjct: 16  RDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGT------FRS-KVDYHYQTM 68
Query: 85  KSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRL 144
           ++NVD LN IQ+GL+LSD++GN PD G        W+FNF +FD   +  + +S+ELLR 
Sbjct: 69  RANVDFLNPIQLGLSLSDANGNKPDNGPS-----TWQFNF-EFDPKKEIMSTESLELLRK 122
Query: 145 QGIDFE 150
            GI+FE
Sbjct: 123 SGINFE 128

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	150
1uoc_A	289	POP2; hydrolase, DEDD nuclease, mRNA degradation,	3e-42
2p51_A	333	SPCC18.06C protein; DEDD nuclease fold, hydrolase,	4e-40
2d5r_A	252	CCR4-NOT transcription complex subunit 7; poly(A)	2e-39
2a1r_A	430	Poly(A)-specific ribonuclease PARN; DEDD, nuclease	1e-27
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	2e-26

>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

 Score =  140 bits (355), Expect = 3e-42
 Identities = 55/134 (41%), Positives = 80/134 (59%), Gaps = 13/134 (9%)

Query: 17  SSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRK 76
              N + +R+VW SNL SEF +I Q++ +Y  +S+ TEF G + RP           + K
Sbjct: 9   PPPNYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGT-------FRSK 61

Query: 77  PSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAP 136
              HY+ +++NVD LN IQ+GL+LSD++GN PD     N    W+FNF  FD   +  + 
Sbjct: 62  VDYHYQTMRANVDFLNPIQLGLSLSDANGNKPD-----NGPSTWQFNFE-FDPKKEIMST 115

Query: 137 DSIELLRLQGIDFE 150
           +S+ELLR  GI+FE
Sbjct: 116 ESLELLRKSGINFE 129

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

 Score =  136 bits (343), Expect = 4e-40
 Identities = 60/138 (43%), Positives = 82/138 (59%), Gaps = 14/138 (10%)

Query: 13  SSNSSSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYF 72
             +  SS    IR+VW++NL+ E  LI  +I+RYP +SMDTEFPG+V RP          
Sbjct: 12  GVDGISSQISPIRDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVARPLGV------- 64

Query: 73  RQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATD 132
            +     HY+ L++NVD+L +IQ+GL LSD  GN P           W+FNF  F++  D
Sbjct: 65  FKSSDDYHYQTLRANVDSLKIIQIGLALSDEEGNAPV------EACTWQFNFT-FNLQDD 117

Query: 133 AHAPDSIELLRLQGIDFE 150
            +AP+SIELL   GIDF+
Sbjct: 118 MYAPESIELLTKSGIDFK 135

>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

 Score =  132 bits (334), Expect = 2e-39
 Identities = 53/127 (41%), Positives = 74/127 (58%), Gaps = 14/127 (11%)

Query: 24  IREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKV 83
           I EVWA NL+ E + I QVI +Y +++MDTEFPG+V RP  +        +      Y++
Sbjct: 2   ICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGE-------FRSNADYQYQL 54

Query: 84  LKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLR 143
           L+ NVD L +IQ+GLT  +  G  P   S       W+FNF+ F++  D +A DSIELL 
Sbjct: 55  LRCNVDLLKIIQLGLTFMNEQGEYPPGTS------TWQFNFK-FNLTEDMYAQDSIELLT 107

Query: 144 LQGIDFE 150
             GI F+
Sbjct: 108 TSGIQFK 114

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

 Score =  105 bits (261), Expect = 1e-27
 Identities = 31/126 (24%), Positives = 47/126 (37%), Gaps = 4/126 (3%)

Query: 26  EVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLK 85
           E+  SN +S    + Q I+   F ++D EF G+   P V   T  +     P + Y+ LK
Sbjct: 2   EIIRSNFKSNLHKVYQAIEEADFFAIDGEFSGISDGPSVSALTNGF---DTPEERYQKLK 58

Query: 86  SNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHA-PDSIELLRL 144
            +     L Q GL             +   N +++   F              SI+ L  
Sbjct: 59  KHSMDFLLFQFGLCTFKYDYTDSKYITKSFNFYVFPKPFNRSSPDVKFVCQSSSIDFLAS 118

Query: 145 QGIDFE 150
           QG DF 
Sbjct: 119 QGFDFN 124

>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

 Score =  102 bits (254), Expect = 2e-26
 Identities = 33/127 (25%), Positives = 48/127 (37%), Gaps = 6/127 (4%)

Query: 26  EVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLK 85
           E+  SN +     + Q I+   F ++D EF G+   P V   T  +     P + Y+ LK
Sbjct: 4   EIIRSNFKINLHKVYQAIEEADFFAIDGEFSGISDGPSVTALTSGF---DTPEERYQKLK 60

Query: 86  SNVDALNLIQVGLTLSD--SSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLR 143
            +     L Q GL       + +     S     F   F+    DV        SI+ L 
Sbjct: 61  KHSMDFLLFQFGLCAFKYDHTDSKHVTKSFNFYVFPKPFSRSSPDV-KFVCQSSSIDFLA 119

Query: 144 LQGIDFE 150
            QG DF 
Sbjct: 120 SQGFDFN 126

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	150
1uoc_A	289	POP2; hydrolase, DEDD nuclease, mRNA degradation,	100.0
2d5r_A	252	CCR4-NOT transcription complex subunit 7; poly(A)	100.0
2p51_A	333	SPCC18.06C protein; DEDD nuclease fold, hydrolase,	100.0
4gmj_B	285	CCR4-NOT transcription complex subunit 7; mRNA dec	100.0
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	100.0
2a1r_A	430	Poly(A)-specific ribonuclease PARN; DEDD, nuclease	100.0
2f96_A	224	Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas	93.67
3v9w_A	235	Ribonuclease T; DEDD nucleases family, EXO-nucleas	92.61
2igi_A	180	Oligoribonuclease; RNAse, exoribonuclease, exonucl	89.69
1w0h_A	204	3'-5' exonuclease ERI1; nuclease domain, hydrolase	87.79
2p1j_A	186	POLIII, DNA polymerase III POLC-type; structural g	87.28
2qxf_A	482	Exodeoxyribonuclease I; alpha-beta domain, DNAQ su	86.19
1zbh_A	299	3'-5' exonuclease ERI1; histone mRNA 3'-END-specif	83.29
2xri_A	224	ERI1 exoribonuclease 3; hydrolase, metal binding;	82.95

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

Probab=100.00  E-value=8.9e-43  Score=289.40  Aligned_cols=119  Identities=45%  Similarity=0.796  Sum_probs=103.0

Q ss_pred             CCCceEEEecccCHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeee
Q 048636           19 SNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGL   98 (150)
Q Consensus        19 ~~~~~v~dV~~~Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGl   98 (150)
                      ++.++|||||++||++||+.|+++|++|+||||||||||++.+|.     +.+++  ++++||+++|+||+.++|||+||
T Consensus        11 ~~~~~i~eVw~~Nl~~e~~~I~~~i~~~~fVAmDtEFpGvv~rp~-----g~f~~--~~d~~Yq~lr~nVd~l~iIQlGL   83 (289)
T 1uoc_A           11 PNYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPI-----GTFRS--KVDYHYQTMRANVDFLNPIQLGL   83 (289)
T ss_dssp             GGGGCCEEECTTTHHHHHHHHHHHTTTSCEEEEEEEEEC---------------C--HHHHHHHHHHHHHTTCEEEEEEE
T ss_pred             CCCcEEEEehhhhHHHHHHHHHHHHhhCCEEEEEeeecceeccCC-----cccCC--CHHHHHHHHHHhhhhccceEEEE
Confidence            446999999999999999999999999999999999999999987     66765  57999999999999999999999


Q ss_pred             eeecCCCCCCCCCCCCCCeeEEEEeccccCCCCCCcchhHHHHHHHcCCCCC
Q 048636           99 TLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE  150 (150)
Q Consensus        99 t~f~~~g~~p~~g~~~~~~~~~~FNF~~F~~~~d~~~~sSi~FL~~~GfDFn  150 (150)
                      |+|+++|+.|..     ++++|||||+ |+..+|+|+++||+||++||||||
T Consensus        84 t~~~~~g~~p~~-----~~~~wqFNF~-F~~~~d~~~~~SI~fL~~~G~DF~  129 (289)
T 1uoc_A           84 SLSDANGNKPDN-----GPSTWQFNFE-FDPKKEIMSTESLELLRKSGINFE  129 (289)
T ss_dssp             EEECTTCCCCSS-----SCSEEEEEBC-CCTTCCCCCHHHHHHHHHTTCCHH
T ss_pred             EEEccCCCcCCC-----CcceEEEEEE-ECCccccccHHHHHHHHHcCCChh
Confidence            999999998743     5899999999 999999999999999999999996

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

Probab=100.00  E-value=2.9e-42  Score=281.65  Aligned_cols=114  Identities=46%  Similarity=0.830  Sum_probs=107.6

Q ss_pred             eEEEecccCHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeec
Q 048636           23 IIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSD  102 (150)
Q Consensus        23 ~v~dV~~~Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~  102 (150)
                      .|||||++||++||+.|+++|++|+||||||||||++.+|.     +.+++  ++++||+++|+||+.++|||+|||+|+
T Consensus         1 ~i~eVw~~Nl~~e~~~I~~~i~~~~fvAmDtEFpGvv~rp~-----g~f~~--~~~~~Y~~lr~nVd~l~iIQlGlt~~~   73 (252)
T 2d5r_A            1 RICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPI-----GEFRS--NADYQYQLLRCNVDLLKIIQLGLTFMN   73 (252)
T ss_dssp             CEEEECGGGHHHHHHHHHHHHHHCCEEEEEEECCCCCCCCC-----SCCSS--HHHHHHHHHHHHHTTCCCCEEEEEEEC
T ss_pred             CeEEehhhhHHHHHHHHHHHHhhCCEEEEEeeecceecccC-----CCCCC--CHHHHHHHHHHhhhhcceeEEEEEEEc
Confidence            48999999999999999999999999999999999999886     67775  689999999999999999999999999


Q ss_pred             CCCCCCCCCCCCCCeeEEEEeccccCCCCCCcchhHHHHHHHcCCCCC
Q 048636          103 SSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE  150 (150)
Q Consensus       103 ~~g~~p~~g~~~~~~~~~~FNF~~F~~~~d~~~~sSi~FL~~~GfDFn  150 (150)
                      ++|+.|.      .+++|||||+ |+..+|+|+++||+||++||||||
T Consensus        74 ~~g~~p~------~~~~wqFNF~-F~~~~d~~~~~Si~fL~~~G~DF~  114 (252)
T 2d5r_A           74 EQGEYPP------GTSTWQFNFK-FNLTEDMYAQDSIELLTTSGIQFK  114 (252)
T ss_dssp             TTSCCCS------SCCEEEEEBC-CCTTTSCCCHHHHHHHHHHTCCHH
T ss_pred             cCCCCCC------CceeEEEEEE-ECCcccccCHHHHHHHHHcCCChh
Confidence            9999873      4899999999 999999999999999999999996

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

Probab=100.00  E-value=5e-42  Score=289.06  Aligned_cols=120  Identities=50%  Similarity=0.877  Sum_probs=111.3

Q ss_pred             CCCCCceEEEecccCHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeee
Q 048636           17 SSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQV   96 (150)
Q Consensus        17 ~~~~~~~v~dV~~~Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQl   96 (150)
                      .+.+.+.|||||++||++||+.|+++|++|+||||||||||++.+|.     +.+++  ++++||+++|+||+.++||||
T Consensus        16 ~~~~~~~IreVw~~Nleee~~~Ir~~i~~~~fVAmDtEFpGvv~rp~-----g~f~~--~~e~~Yq~lR~NVd~l~iIQl   88 (333)
T 2p51_A           16 ISSQISPIRDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVARPL-----GVFKS--SDDYHYQTLRANVDSLKIIQI   88 (333)
T ss_dssp             --CCSCSEEEECTTTHHHHHHHHHHHTTTSCEEEEEEECCCCCCCCC-----SCCSS--SHHHHHHHHHHHHHHSCCCEE
T ss_pred             CCCCCcEEEEehHhHHHHHHHHHHHHHhhCCEEEEeeeccccccccc-----cccCC--CHHHHHHHHHHhhhhccceEE
Confidence            45567899999999999999999999999999999999999999987     67876  579999999999999999999


Q ss_pred             eeeeecCCCCCCCCCCCCCCeeEEEEeccccCCCCCCcchhHHHHHHHcCCCCC
Q 048636           97 GLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE  150 (150)
Q Consensus        97 Glt~f~~~g~~p~~g~~~~~~~~~~FNF~~F~~~~d~~~~sSi~FL~~~GfDFn  150 (150)
                      |||+|+++|+.|.      .+++|||||+ |+..+|+|+++||+||++||||||
T Consensus        89 GLt~fd~~G~~p~------~~~twqFNF~-F~~~~d~~~~~SI~fL~~~G~DF~  135 (333)
T 2p51_A           89 GLALSDEEGNAPV------EACTWQFNFT-FNLQDDMYAPESIELLTKSGIDFK  135 (333)
T ss_dssp             EEEEECTTSCCCT------TCSEEEEEBC-CCTTTSCCCHHHHHHHHHTTCCHH
T ss_pred             EEEEEccCCCCCC------CceeEEEEEE-ECCcccccCHHHHHHHHHcCCChh
Confidence            9999999999873      4899999999 999999999999999999999996

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

Probab=100.00  E-value=7.1e-42  Score=283.59  Aligned_cols=117  Identities=45%  Similarity=0.813  Sum_probs=108.3

Q ss_pred             CCceEEEecccCHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeee
Q 048636           20 NSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLT   99 (150)
Q Consensus        20 ~~~~v~dV~~~Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt   99 (150)
                      ....|||||++||++||+.|+++|++|+||||||||||++.+|.     +.+.+  ++++||+++|.||+.++|||+|||
T Consensus         8 ~~~~IreVw~~Nl~ee~~~I~~~i~~~~fVAiDtEFpGvv~rp~-----~~~~~--t~d~~Y~~lr~nvd~l~iIQlGLt   80 (285)
T 4gmj_B            8 HSQRICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPI-----GEFRS--NADYQYQLLRCNVDLLKIIQLGLT   80 (285)
T ss_dssp             --CCEEEECHHHHHHHHHHHHHHHHHCCEEEEEEECCCCCCCCT-----TCCTT--STTHHHHHHHHHHTTSCCCEEEEE
T ss_pred             CCCeEEEechhHHHHHHHHHHHHHhcCCEEEEEEEecCccCCCC-----CccCC--CHHHHHHHHHHHHHhhcceeEEEE
Confidence            35689999999999999999999999999999999999999987     56655  689999999999999999999999


Q ss_pred             eecCCCCCCCCCCCCCCeeEEEEeccccCCCCCCcchhHHHHHHHcCCCCC
Q 048636          100 LSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE  150 (150)
Q Consensus       100 ~f~~~g~~p~~g~~~~~~~~~~FNF~~F~~~~d~~~~sSi~FL~~~GfDFn  150 (150)
                      +|+++|+.|.      .+++|||||+ |+..+|+|+++||+||++||||||
T Consensus        81 ~f~~~g~~p~------~~~~wqFNF~-f~~~~d~~~~~SI~fL~~~G~DF~  124 (285)
T 4gmj_B           81 FMNEQGEYPP------GTSTWQFNFK-FNLTEDMYAQDSIELLTTSGIQFK  124 (285)
T ss_dssp             EECTTSCCCS------SCCEEEEEBC-CCTTTSCCCHHHHHHHHHHTCCHH
T ss_pred             eeccCCCcCC------CeeEEEEEEE-eccccccccHHHHHHHHHcCCCHH
Confidence            9999999873      4899999999 999999999999999999999996

>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}

Probab=100.00  E-value=9.8e-37  Score=268.84  Aligned_cols=117  Identities=28%  Similarity=0.414  Sum_probs=100.8

Q ss_pred             EEEecccCHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecC
Q 048636           24 IREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDS  103 (150)
Q Consensus        24 v~dV~~~Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~  103 (150)
                      |+|||++||+++|+.|+++|++|+||||||||||+..++........++   ++++||+++|.||+.++|||+|||+|++
T Consensus         2 ~m~V~~~Nf~~~l~~i~~~i~~~~fvaiD~Ef~Gi~~~~~~~~~~~~~~---t~~~~Y~~~r~~v~~~~iiQlGlt~f~~   78 (507)
T 3d45_A            2 PMEIIRSNFKINLHKVYQAIEEADFFAIDGEFSGISDGPSVTALTSGFD---TPEERYQKLKKHSMDFLLFQFGLCAFKY   78 (507)
T ss_dssp             CEEECHHHHHHHHHHHHHHHHHCSEEEEEEEESCSCC--------CBSC---CHHHHHHHHHHHHTTBCEEEEEEEEEEE
T ss_pred             CeEEeHHhHHHHHHHHHHHHhcCCEEEEeeeccCcCCCCCccccccccC---CHHHHHHHHHHHHHhcccceEEEEEEec
Confidence            6899999999999999999999999999999999988775200001144   6899999999999999999999999999


Q ss_pred             CCCCCCCCCCCCCeeEEEEeccccCC-----CCC---CcchhHHHHHHHcCCCCC
Q 048636          104 SGNLPDLGSGGNNKFIWEFNFRDFDV-----ATD---AHAPDSIELLRLQGIDFE  150 (150)
Q Consensus       104 ~g~~p~~g~~~~~~~~~~FNF~~F~~-----~~d---~~~~sSi~FL~~~GfDFn  150 (150)
                      +|+.+       +|++|||||++||.     ..|   +|+++||+||++||||||
T Consensus        79 ~~~~~-------~~~~~~fNf~~fp~~~~~~~~d~~~~~~~~Si~fL~~~GfDFn  126 (507)
T 3d45_A           79 DHTDS-------KHVTKSFNFYVFPKPFSRSSPDVKFVCQSSSIDFLASQGFDFN  126 (507)
T ss_dssp             CSSSS-------CEEEEEEEEEBCCCCCSSSSCCCEEEEEHHHHHHHHTTTCCHH
T ss_pred             CCCCC-------ceeEEeEEEEecCccccccCcccceeecHHHHHHHHHcCCChh
Confidence            99865       69999999999997     445   999999999999999996

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

Probab=100.00  E-value=1.1e-34  Score=251.40  Aligned_cols=116  Identities=28%  Similarity=0.398  Sum_probs=101.1

Q ss_pred             EEecccCHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCC
Q 048636           25 REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSS  104 (150)
Q Consensus        25 ~dV~~~Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~  104 (150)
                      .|||++||++.|+.|+++|++|+||||||||||+..+|......+.++   ++++||+++|.||+.++|||+|||+|+++
T Consensus         1 M~V~r~nf~~~l~~i~~~i~~~~fVAiD~Ef~Gi~~~~~~~~~~~~~~---s~e~~Y~~lr~nv~~~~iiQlGlt~f~~~   77 (430)
T 2a1r_A            1 MEIIRSNFKSNLHKVYQAIEEADFFAIDGEFSGISDGPSVSALTNGFD---TPEERYQKLKKHSMDFLLFQFGLCTFKYD   77 (430)
T ss_dssp             CEECHHHHHHHHHHHHHHHHHCSEEEEEEEESCSCSSSCC-----CCC---CHHHHHHHHHHHTTTBCEEEEEEEEEEEE
T ss_pred             CceeHHHHHHHHHHHHHHHhcCCEEEEeeeeccccCCCccccccccCC---CHHHHHHHHHHHHhhcceeeEEEEEEeec
Confidence            389999999999999999999999999999999998875211113455   68999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCeeEEEEeccccCCC--------CCCcchhHHHHHHHcCCCCC
Q 048636          105 GNLPDLGSGGNNKFIWEFNFRDFDVA--------TDAHAPDSIELLRLQGIDFE  150 (150)
Q Consensus       105 g~~p~~g~~~~~~~~~~FNF~~F~~~--------~d~~~~sSi~FL~~~GfDFn  150 (150)
                      |+.+       +|++|||||++||..        .++|+++||+||++||||||
T Consensus        78 ~~~~-------~~~~~~fNF~~FP~~~~~~~~~~~~~~~~~Si~fL~~~GfDFn  124 (430)
T 2a1r_A           78 YTDS-------KYITKSFNFYVFPKPFNRSSPDVKFVCQSSSIDFLASQGFDFN  124 (430)
T ss_dssp             TTTT-------EEEEEEEEEEBCCCCSSSSSCCCEEEEEHHHHHHHHHTTCCHH
T ss_pred             CCCC-------ceeEEEEEEEeccccccccccchhhhccHHHHHHHHHcCCChh
Confidence            9865       699999999999642        35899999999999999996

>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

Probab=93.67  E-value=0.1  Score=40.05  Aligned_cols=53  Identities=19%  Similarity=0.155  Sum_probs=37.0

Q ss_pred             HHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecC--CCCCCCCCCCCCC
Q 048636           39 ISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDS--SGNLPDLGSGGNN  116 (150)
Q Consensus        39 I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~--~g~~p~~g~~~~~  116 (150)
                      +.+-+++..||+||+|.+|+....                            -.|||+|+..++.  +|+.         
T Consensus        22 ~~~~~~~~~~vviD~ETTGl~~~~----------------------------~~IieIg~v~~~~~~~g~i---------   64 (224)
T 2f96_A           22 MARRFRGYLPVVVDVETGGFNSAT----------------------------DALLEIAATTVGMDEKGFL---------   64 (224)
T ss_dssp             HHHHTTTEEEEEEEEEESSSCTTT----------------------------BCEEEEEEEEEEECTTSCE---------
T ss_pred             hhccccCCcEEEEEeeCCCCCCCC----------------------------CeeEEEEEEEEEEcCCCcc---------
Confidence            355678889999999999974110                            1399999999874  4541         


Q ss_pred             eeEEEEeccccC
Q 048636          117 KFIWEFNFRDFD  128 (150)
Q Consensus       117 ~~~~~FNF~~F~  128 (150)
                      .....|+.++-|
T Consensus        65 ~~~~~f~~lV~P   76 (224)
T 2f96_A           65 FPEHTYFFRIEP   76 (224)
T ss_dssp             EEEEEEEEEBCC
T ss_pred             cccceEEEEECC
Confidence            245667777555

>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

Probab=92.61  E-value=0.19  Score=38.80  Aligned_cols=57  Identities=12%  Similarity=0.099  Sum_probs=37.7

Q ss_pred             HHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecC--CCCCCCCCC
Q 048636           35 EFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDS--SGNLPDLGS  112 (150)
Q Consensus        35 el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~--~g~~p~~g~  112 (150)
                      ++..+...++...||++|+|.+|+....                            -.|||+|+..++.  +|+.     
T Consensus        26 ~~~~l~~~l~~~~~vviD~ETTGl~~~~----------------------------~~IieIgav~~~~~~~g~i-----   72 (235)
T 3v9w_A           26 QLTGLCDRFRGFYPVVIDVETAGFNAKT----------------------------DALLEIAAITLKMDEQGWL-----   72 (235)
T ss_dssp             ---CHHHHTTTEEEEEEEEEESSSCTTT----------------------------BCEEEEEEEEEEECTTSCE-----
T ss_pred             cccCchhcccCCcEEEEEEeCCCCCCCC----------------------------CeEEEEEEEEEEEcCCCcc-----
Confidence            4444666788899999999999984211                            1389999998763  4442     


Q ss_pred             CCCCeeEEEEeccccC
Q 048636          113 GGNNKFIWEFNFRDFD  128 (150)
Q Consensus       113 ~~~~~~~~~FNF~~F~  128 (150)
                          .....|+.++-|
T Consensus        73 ----~~~~~f~~~v~P   84 (235)
T 3v9w_A           73 ----MPDTTLHFHVEP   84 (235)
T ss_dssp             ----EEEEEEEEEBCC
T ss_pred             ----cccceEEEEECC
Confidence                245667776444

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

Probab=89.69  E-value=0.53  Score=34.53  Aligned_cols=46  Identities=17%  Similarity=0.149  Sum_probs=30.5

Q ss_pred             hCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCCCCCCCCCCCCCCeeEEEEec
Q 048636           45 RYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNF  124 (150)
Q Consensus        45 ~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~g~~p~~g~~~~~~~~~~FNF  124 (150)
                      ..+||++|+|.+|+....                            -.|||+|...++.+++          .....|+.
T Consensus         4 ~~~~v~iD~ETTGl~~~~----------------------------~~IieIg~v~~~~~~~----------~~~~~~~~   45 (180)
T 2igi_A            4 ENNLIWIDLEMTGLDPER----------------------------DRIIEIATLVTDANLN----------ILAEGPTI   45 (180)
T ss_dssp             GGCEEEEEEEESSSCTTT----------------------------CCEEEEEEEEECTTCC----------EEEEEEEE
T ss_pred             CCcEEEEEeeCCCCCCCC----------------------------CceEEEEEEEEcCCCc----------EecCCcce
Confidence            347999999999974110                            1399999997765543          23334777


Q ss_pred             cccC
Q 048636          125 RDFD  128 (150)
Q Consensus       125 ~~F~  128 (150)
                      ++-|
T Consensus        46 lv~P   49 (180)
T 2igi_A           46 AVHQ   49 (180)
T ss_dssp             ECCC
T ss_pred             EECC
Confidence            7444

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

Probab=87.79  E-value=1.8  Score=32.11  Aligned_cols=48  Identities=13%  Similarity=-0.053  Sum_probs=31.6

Q ss_pred             CceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecC-CCCCCCCCCCCCCeeEEEEecc
Q 048636           47 PFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDS-SGNLPDLGSGGNNKFIWEFNFR  125 (150)
Q Consensus        47 ~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~-~g~~p~~g~~~~~~~~~~FNF~  125 (150)
                      .||+||+|.+|+.....      .                  ..-.|||+|...++. +|+           ....|+.+
T Consensus        11 ~~vviD~ETTGl~~~~~------~------------------~~~~Iieigav~~~~~~g~-----------i~~~f~~l   55 (204)
T 1w0h_A           11 YICIIDFEATCEEGNPP------E------------------FVHEIIEFPVVLLNTHTLE-----------IEDTFQQY   55 (204)
T ss_dssp             EEEECCCEECCCTTCCT------T------------------SCCCEEEEEEEEEETTTCS-----------EEEEEEEE
T ss_pred             EEEEEEEecCCcCCCCC------C------------------CCCcEEEEEEEEEECCCCE-----------EeeeeeeE
Confidence            58999999999753211      0                  012499999999885 554           23457777


Q ss_pred             ccCC
Q 048636          126 DFDV  129 (150)
Q Consensus       126 ~F~~  129 (150)
                      +-|.
T Consensus        56 v~P~   59 (204)
T 1w0h_A           56 VRPE   59 (204)
T ss_dssp             BCCS
T ss_pred             ECCC
Confidence            5443

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

Probab=87.28  E-value=0.63  Score=34.56  Aligned_cols=17  Identities=29%  Similarity=0.438  Sum_probs=11.9

Q ss_pred             hhhCCceeccccccccc
Q 048636           43 IDRYPFISMDTEFPGLV   59 (150)
Q Consensus        43 i~~~~fIAiDtEF~Gl~   59 (150)
                      +...+||++|+|.+|+.
T Consensus         9 l~~~~~v~iD~ETTGl~   25 (186)
T 2p1j_A            9 FGDATFVVLDFETTGLD   25 (186)
T ss_dssp             ----CEEEEEEEESCSC
T ss_pred             CcCCCEEEEEEECCCCC
Confidence            46679999999999973

>2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily, SH3-like domain, produc structure, DNA damage, DNA repair, exonuclease; HET: TMP; 1.50A {Escherichia coli} SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A 3hl8_A* 3hp9_A*

Probab=86.19  E-value=0.69  Score=40.25  Aligned_cols=36  Identities=22%  Similarity=0.017  Sum_probs=27.0

Q ss_pred             hhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCCCC
Q 048636           43 IDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGN  106 (150)
Q Consensus        43 i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~g~  106 (150)
                      +....||++|+|.||+....                            -.|||+|...++.+|+
T Consensus         6 ~~~~~~vv~DlETTGl~p~~----------------------------d~IIEIgaV~vd~~g~   41 (482)
T 2qxf_A            6 KQQSTFLFHDYETFGTHPAL----------------------------DRPAQFAAIRTDSEFN   41 (482)
T ss_dssp             -CCCEEEEEEEEESSSCTTT----------------------------SCEEEEEEEEECTTSC
T ss_pred             CCCCCEEEEEEECCCCCCCC----------------------------CeEEEEEEEEEECCCe
Confidence            45678999999999984110                            1399999998887765

>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}

Probab=83.29  E-value=3.4  Score=33.09  Aligned_cols=49  Identities=12%  Similarity=-0.006  Sum_probs=32.0

Q ss_pred             CCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecC-CCCCCCCCCCCCCeeEEEEec
Q 048636           46 YPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDS-SGNLPDLGSGGNNKFIWEFNF  124 (150)
Q Consensus        46 ~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~-~g~~p~~g~~~~~~~~~~FNF  124 (150)
                      -.||+||+|.||+...+.      ..                  .-.|||+|+..++. +|+           ....|+.
T Consensus        78 ~~~vviD~ETTGl~~~~~------~~------------------~~~IIeIgaV~v~~~~g~-----------i~~~f~~  122 (299)
T 1zbh_A           78 DYICIIDFEATCEEGNPP------EF------------------VHEIIEFPVVLLNTHTLE-----------IEDTFQQ  122 (299)
T ss_dssp             SEEEEECCEECCCTTCCT------TC------------------CCCEEEEEEEEEETTTCC-----------EEEEEEE
T ss_pred             ceEEEEEeecccCCCCCC------CC------------------CCceEEEEEEEEECCCCe-----------Eeeeeee
Confidence            368999999999853211      00                  12499999999876 343           3456777


Q ss_pred             cccCC
Q 048636          125 RDFDV  129 (150)
Q Consensus       125 ~~F~~  129 (150)
                      ++-|.
T Consensus       123 lV~P~  127 (299)
T 1zbh_A          123 YVRPE  127 (299)
T ss_dssp             EBCCS
T ss_pred             eecCC
Confidence            75554

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

Probab=82.95  E-value=3  Score=31.81  Aligned_cols=46  Identities=13%  Similarity=0.033  Sum_probs=30.5

Q ss_pred             CceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCC-CCCCCCCCCCCCeeEEEEecc
Q 048636           47 PFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSS-GNLPDLGSGGNNKFIWEFNFR  125 (150)
Q Consensus        47 ~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~-g~~p~~g~~~~~~~~~~FNF~  125 (150)
                      .||+||+|.+|+....         +                 .-.|||+|...++.. ++           ....|+.+
T Consensus        32 ~~vviD~ETTGl~~~~---------d-----------------~~~IieIgav~v~~~~~~-----------i~~~f~~l   74 (224)
T 2xri_A           32 YFLVLDFEATCDKPQI---------H-----------------PQEIIEFPILKLNGRTME-----------IESTFHMY   74 (224)
T ss_dssp             EEEEECCEECCCC-CC---------S-----------------SCCEEEEEEEEEETTTCC-----------EEEEEEEE
T ss_pred             eEEEEEEEcCCCCCCC---------C-----------------CcceEEEEEEEEecCCcE-----------EeeeeeeE
Confidence            6899999999974211         0                 124999999988754 22           34567777


Q ss_pred             ccCC
Q 048636          126 DFDV  129 (150)
Q Consensus       126 ~F~~  129 (150)
                      +-|.
T Consensus        75 V~P~   78 (224)
T 2xri_A           75 VQPV   78 (224)
T ss_dssp             CCCS
T ss_pred             ECCC
Confidence            5543

---

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	150
d1uoca_	286	c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (	2e-43
d2d5ra1	252	c.55.3.9 (A:11-262) CCR4-NOT transcription complex	4e-41

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

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: CAF1-like ribonuclease
domain: Pop2 RNase D domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  142 bits (359), Expect = 2e-43
 Identities = 55/132 (41%), Positives = 81/132 (61%), Gaps = 13/132 (9%)

Query: 19  SNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPS 78
            N + +R+VW SNL SEF +I Q++ +Y  +S+ TEF G + RP           + K  
Sbjct: 8   PNYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARP-------IGTFRSKVD 60

Query: 79  DHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDS 138
            HY+ +++NVD LN IQ+GL+LSD++GN PD G        W+FNF +FD   +  + +S
Sbjct: 61  YHYQTMRANVDFLNPIQLGLSLSDANGNKPDNGPS-----TWQFNF-EFDPKKEIMSTES 114

Query: 139 IELLRLQGIDFE 150
           +ELLR  GI+FE
Sbjct: 115 LELLRKSGINFE 126

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

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 =  135 bits (342), Expect = 4e-41
 Identities = 52/127 (40%), Positives = 73/127 (57%), Gaps = 14/127 (11%)

Query: 24  IREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKV 83
           I EVWA NL+ E + I QVI +Y +++MDTEFPG+V RP  +        +      Y++
Sbjct: 2   ICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGE-------FRSNADYQYQL 54

Query: 84  LKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLR 143
           L+ NVD L +IQ+GLT  +  G  P           W+FNF+ F++  D +A DSIELL 
Sbjct: 55  LRCNVDLLKIIQLGLTFMNEQGEYPP------GTSTWQFNFK-FNLTEDMYAQDSIELLT 107

Query: 144 LQGIDFE 150
             GI F+
Sbjct: 108 TSGIQFK 114

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	150
d1uoca_	286	Pop2 RNase D domain {Baker's yeast (Saccharomyces	100.0
d2d5ra1	252	CCR4-NOT transcription complex subunit 7, CAF1 {Hu	100.0
d1w0ha_	200	Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960	93.36
d2f96a1	202	Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287	91.52
d1yt3a3	193	Ribonuclease D, catalytic domain {Escherichia coli	88.83
d1kfsa1	195	Exonuclease domain of prokaryotic DNA polymerase {	88.56
d2guia1	174	N-terminal exonuclease domain of the epsilon subun	83.76

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

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: CAF1-like ribonuclease
domain: Pop2 RNase D domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=4.2e-42  Score=283.04  Aligned_cols=120  Identities=45%  Similarity=0.791  Sum_probs=103.7

Q ss_pred             CCCCceEEEecccCHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeee
Q 048636           18 SSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVG   97 (150)
Q Consensus        18 ~~~~~~v~dV~~~Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlG   97 (150)
                      .++.+.|||||++||+++|+.|+++|++|+||||||||||++.++.     +.+.+  ++++||+++|+||+.+++||+|
T Consensus         7 ~~~~~~i~dVw~~N~~~e~~~i~~~i~~~~fvaiD~EF~Gi~~~~~-----~~~~~--t~d~~Y~~lr~nvd~~~iiQlG   79 (286)
T d1uoca_           7 PPNYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPI-----GTFRS--KVDYHYQTMRANVDFLNPIQLG   79 (286)
T ss_dssp             CGGGGCCEEECTTTHHHHHHHHHHHTTTSCEEEEEEEEEC---------------C--HHHHHHHHHHHHHTTCEEEEEE
T ss_pred             CCCeEEEEEchhhhHHHHHHHHHHHHhcCCEEEEeeeecCcccCCC-----CCCCC--CHHHHHHHHHHhHhhcceeEEe
Confidence            4457899999999999999999999999999999999999998876     45544  7899999999999999999999


Q ss_pred             eeeecCCCCCCCCCCCCCCeeEEEEeccccCCCCCCcchhHHHHHHHcCCCCC
Q 048636           98 LTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE  150 (150)
Q Consensus        98 lt~f~~~g~~p~~g~~~~~~~~~~FNF~~F~~~~d~~~~sSi~FL~~~GfDFn  150 (150)
                      ||+|+++|+.|..     .+++|||||+ |+..+|+|+++||+||++||||||
T Consensus        80 lt~f~~~g~~~~~-----~~~~w~FNF~-f~~~~d~~~~~Si~fL~~~G~DF~  126 (286)
T d1uoca_          80 LSLSDANGNKPDN-----GPSTWQFNFE-FDPKKEIMSTESLELLRKSGINFE  126 (286)
T ss_dssp             EEEECTTCCCCSS-----SCSEEEEEBC-CCTTCCCCCHHHHHHHHHTTCCHH
T ss_pred             eeeecccCCCCCC-----CceEEEEEEE-ecCccccccHHHHHHHHHcCCChH
Confidence            9999999998754     5899999999 999999999999999999999996

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

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=4.7e-41  Score=272.44  Aligned_cols=114  Identities=46%  Similarity=0.830  Sum_probs=106.1

Q ss_pred             eEEEecccCHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeec
Q 048636           23 IIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSD  102 (150)
Q Consensus        23 ~v~dV~~~Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~  102 (150)
                      .|||||++||+++|+.|+++|++|+||||||||||++.+|.     +.+.+  ++++||+++|.||+.+++||+|||+|+
T Consensus         1 ~i~eV~~~Nf~e~~~~i~~~i~~~~fVAiD~EF~G~~~~~~-----~~~~~--t~~~~Y~~lr~nv~~~~iiQ~Glt~~~   73 (252)
T d2d5ra1           1 RICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPI-----GEFRS--NADYQYQLLRCNVDLLKIIQLGLTFMN   73 (252)
T ss_dssp             CEEEECGGGHHHHHHHHHHHHHHCCEEEEEEECCCCCCCCC-----SCCSS--HHHHHHHHHHHHHTTCCCCEEEEEEEC
T ss_pred             CeEEehhhhHHHHHHHHHHHHhcCCEEEEeeeccCcccCCC-----CccCC--CHHHHHHHHHHHHhhcceeEEEEEeec
Confidence            48999999999999999999999999999999999998876     44544  689999999999999999999999999


Q ss_pred             CCCCCCCCCCCCCCeeEEEEeccccCCCCCCcchhHHHHHHHcCCCCC
Q 048636          103 SSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE  150 (150)
Q Consensus       103 ~~g~~p~~g~~~~~~~~~~FNF~~F~~~~d~~~~sSi~FL~~~GfDFn  150 (150)
                      ++|+.|.      .+.+|||||+ |+..+|+|+++||+||++||||||
T Consensus        74 ~~g~~~~------~~~~w~FNf~-~~~~~~~~~~~Si~fL~~~G~DF~  114 (252)
T d2d5ra1          74 EQGEYPP------GTSTWQFNFK-FNLTEDMYAQDSIELLTTSGIQFK  114 (252)
T ss_dssp             TTSCCCS------SCCEEEEEBC-CCTTTSCCCHHHHHHHHHHTCCHH
T ss_pred             ccCCCCC------CceeEEEEEE-eCCcccccCHHHHHHHHHcCCChH
Confidence            9998774      4899999999 888999999999999999999996

>d1w0ha_ c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Exonuclease ERI1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.36  E-value=0.12  Score=36.30  Aligned_cols=48  Identities=13%  Similarity=0.027  Sum_probs=32.1

Q ss_pred             ceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCCCCCCCCCCCCCCeeEEEEecccc
Q 048636           48 FISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDF  127 (150)
Q Consensus        48 fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~g~~p~~g~~~~~~~~~~FNF~~F  127 (150)
                      ||.+|+|.||......      ...                  -.|||+|.+.++..+.          ....+||.++-
T Consensus         8 ~iv~D~EtT~~~~~~~------~~~------------------~~Iieigav~~d~~~~----------~~~~~f~~~v~   53 (200)
T d1w0ha_           8 ICIIDFEATCEEGNPP------EFV------------------HEIIEFPVVLLNTHTL----------EIEDTFQQYVR   53 (200)
T ss_dssp             EEECCCEECCCTTCCT------TSC------------------CCEEEEEEEEEETTTC----------SEEEEEEEEBC
T ss_pred             EEEEEEecCCCCCCCC------CCC------------------CcEEEEEEEEEECCCC----------eEEEEEEEEEe
Confidence            8999999997643322      011                  1499999999886543          24567888765


Q ss_pred             CC
Q 048636          128 DV  129 (150)
Q Consensus       128 ~~  129 (150)
                      |.
T Consensus        54 P~   55 (200)
T d1w0ha_          54 PE   55 (200)
T ss_dssp             CS
T ss_pred             cC
Confidence            54

>d2f96a1 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Ribonuclease T
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=91.52  E-value=0.19  Score=34.57  Aligned_cols=31  Identities=16%  Similarity=0.205  Sum_probs=22.8

Q ss_pred             ceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCCCC
Q 048636           48 FISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGN  106 (150)
Q Consensus        48 fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~g~  106 (150)
                      +|.+|+|.||+....               +             .|||+|....+.+.+
T Consensus        13 ~Vv~D~ETTGl~~~~---------------~-------------~IIeigav~i~~~~~   43 (202)
T d2f96a1          13 PVVVDVETGGFNSAT---------------D-------------ALLEIAATTVGMDEK   43 (202)
T ss_dssp             EEEEEEEESSSCTTT---------------B-------------CEEEEEEEEEEECTT
T ss_pred             cEEEEEeCCCCCCCC---------------C-------------ceEEEEEEEEEeccc
Confidence            489999999983211               1             399999998876543

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

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Ribonuclease D, catalytic domain
species: Escherichia coli [TaxId: 562]

Probab=88.83  E-value=0.1  Score=37.78  Aligned_cols=27  Identities=22%  Similarity=0.495  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHhhhCCceeccccccccc
Q 048636           33 ESEFELISQVIDRYPFISMDTEFPGLV   59 (150)
Q Consensus        33 ~~el~~I~~~i~~~~fIAiDtEF~Gl~   59 (150)
                      +++|..+.+.+.+++.||+||||.|+.
T Consensus         9 ~~~l~~~~~~l~~~~~i~~DtE~~~~~   35 (193)
T d1yt3a3           9 DDALASLCEAVRAFPAIALDTEFVRTR   35 (193)
T ss_dssp             HHHHHHHHHHHTTSSEEEEEEEEECCS
T ss_pred             HHHHHHHHHHHhcCCeEEEECcccCCC
Confidence            356778888889999999999998864

>d1kfsa1 c.55.3.5 (A:324-518) Exonuclease domain of prokaryotic DNA polymerase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: Exonuclease domain of prokaryotic DNA polymerase
species: Escherichia coli [TaxId: 562]

Probab=88.56  E-value=0.12  Score=35.99  Aligned_cols=27  Identities=22%  Similarity=0.335  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHhhhCCceeccccccccc
Q 048636           33 ESEFELISQVIDRYPFISMDTEFPGLV   59 (150)
Q Consensus        33 ~~el~~I~~~i~~~~fIAiDtEF~Gl~   59 (150)
                      ++++..+.+.+.+++.||+|||.+|+.
T Consensus        13 ~~~l~~~l~~l~~~~~~a~DtEt~~l~   39 (195)
T d1kfsa1          13 EETLKAWIAKLEKAPVFAFDTETDSLD   39 (195)
T ss_dssp             HHHHHHHHHHHHHSSSEEEEEEESCSC
T ss_pred             HHHHHHHHHHHhcCCeEEEEeeeCCCC
Confidence            467777778889999999999999973

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

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: DnaQ-like 3'-5' exonuclease
domain: N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III
species: Escherichia coli [TaxId: 562]

Probab=83.76  E-value=0.47  Score=31.88  Aligned_cols=13  Identities=38%  Similarity=0.447  Sum_probs=11.2

Q ss_pred             ceecccccccccc
Q 048636           48 FISMDTEFPGLVY   60 (150)
Q Consensus        48 fIAiDtEF~Gl~~   60 (150)
                      +|.+|+|-||+..
T Consensus         2 ~vv~D~ETTGl~~   14 (174)
T d2guia1           2 QIVLDTETTGMNQ   14 (174)
T ss_dssp             EEEEEEEESCCCS
T ss_pred             EEEEEeeCCCCCc
Confidence            7899999999853