Citrus Sinensis ID: 023614

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280
MSDVPPPQPPKPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLELLEC
ccccccccccccccEEEEcccccHHHHHHHHHHHHHccccEEEcccccccccccccccccccHHHHHHHHHHHcccccEEEEEEEEccccccccccccccccEEEEEcccccccccccccHHHHHHHHHccccHHHHHHccccHHHHHHHHHHcccccccccEEEEEEcccHHHHHHHHHHcccccccHHHHHHHHcHHccccEEEHHHHHHHHcccccHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHccccccccccccEEEccccccc
ccccccccccccccEHHHHHHHHHHHHHHHHHHHHHHccEEEEccccccEEEEEcccccccccHHHHHHHHHHHHHHHHHHHcEEEEccccccccccccccEEEEEEEccccccHHHcccHHHHHHHHHccccHHHHHHccccHHHHHHHHHHccEEEcccEEEEEEcccHHHHHHHHHHccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHccHHHHHHHHccccEEEcHccccccHHHHHHHHHHHHHHHHHcccccHHHcccEEEEcccccc
msdvpppqppkprilIREVFEFNLISEFERIRALIdrypiismdtefpgvvvrpdsnirhrdpaanynglkANVDLLNLIQIGltlsdeegnlpdlgsgstyyiwefnfkdfdiarHAHALDSVELLKRQgidfeknrefgiDSVRFAELLMSSglvlnkdvtwvTFHSAYDFGYLVKCltqrvlpekLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVervvgkshqagsdSLLTLHAFLKIkdkhfgneyELQKYANVLhglellec
msdvpppqppkpriliREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGkshqagsdslLTLHAFLKIKDKHFGNEYELQKYANVLHGLELLEC
MSDVpppqppkpRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLELLEC
*************ILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLEL***
**********KPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLELLEC
*********PKPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLELLEC
***********PRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLELLEC
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSDVPPPQPPKPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLELLEC
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query280 2.2.26 [Sep-21-2011]
Q9FMS6278 Probable CCR4-associated yes no 0.942 0.949 0.600 4e-86
Q9LXM2280 Probable CCR4-associated no no 0.982 0.982 0.586 8e-85
Q9LEU4277 Probable CCR4-associated no no 0.914 0.924 0.541 1e-74
Q9SKZ2275 Probable CCR4-associated no no 0.917 0.934 0.534 1e-73
Q9S9P2286 Probable CCR4-associated no no 0.967 0.947 0.508 3e-71
Q9SAI2274 Probable CCR4-associated no no 0.914 0.934 0.530 2e-69
Q9UFF9292 CCR4-NOT transcription co yes no 0.932 0.893 0.448 3e-56
Q9D8X5292 CCR4-NOT transcription co yes no 0.932 0.893 0.448 3e-56
O74856335 Poly(A) ribonuclease pop2 yes no 0.892 0.746 0.453 5e-56
Q60809285 CCR4-NOT transcription co no no 0.896 0.880 0.465 2e-55
>sp|Q9FMS6|CAF1K_ARATH Probable CCR4-associated factor 1 homolog 11 OS=Arabidopsis thaliana GN=CAF1-11 PE=2 SV=1 Back     alignment and function desciption
 Score =  318 bits (814), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 161/268 (60%), Positives = 207/268 (77%), Gaps = 4/268 (1%)

Query: 14  ILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNI-RHRDPAANYNGLKA 72
           I+IR+V+ +NL SEF+ IR +++ YP ISMDTEFPGV+ + D ++ R  +P   YN LK+
Sbjct: 12  IVIRDVWAYNLESEFDLIRGIVEDYPFISMDTEFPGVIYKADLDVLRRGNPNYLYNLLKS 71

Query: 73  NVDLLNLIQIGLTLSDEEGNLPDLG-SGSTYYIWEFNFKDFDIARHAHALDSVELLKRQG 131
           NVD L+LIQ+GLTLSD +GNLPDLG   +  YIWEFNF+DFD+ R  HA DS+ELL+R G
Sbjct: 72  NVDALSLIQVGLTLSDADGNLPDLGGQKNRRYIWEFNFRDFDVERDPHAPDSIELLRRHG 131

Query: 132 IDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSE 191
           IDFE+NR  G++S RFAEL+MSSGL+ N+ V+WVTFHSAYDFGYLVK LT+R LP  L E
Sbjct: 132 IDFERNRREGVESERFAELMMSSGLICNESVSWVTFHSAYDFGYLVKILTRRQLPVALRE 191

Query: 192 FVTRVGVFFGEKVYDVKHLIRFCTC-LYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHA 250
           F+  +  FFG++VYDVKH++RFC   LYGGLDRV ++L V R VGK HQAGSDSLLT  A
Sbjct: 192 FLGLLRAFFGDRVYDVKHIMRFCEQRLYGGLDRVARSLEVNRAVGKCHQAGSDSLLTWQA 251

Query: 251 FLKIKDKHFGNEYELQKYANVLHGLELL 278
           F +++D +F  E   +K+A VL+GLE+ 
Sbjct: 252 FQRMRDLYF-VEDGAEKHAGVLYGLEVF 278
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|Q9LXM2|CAF1I_ARATH Probable CCR4-associated factor 1 homolog 9 OS=Arabidopsis thaliana GN=CAF1-9 PE=2 SV=1 Back     alignment and function description
>sp|Q9LEU4|CAF1J_ARATH Probable CCR4-associated factor 1 homolog 10 OS=Arabidopsis thaliana GN=CAF1-10 PE=2 SV=1 Back     alignment and function description
>sp|Q9SKZ2|CAF1G_ARATH Probable CCR4-associated factor 1 homolog 7 OS=Arabidopsis thaliana GN=CAF1-7 PE=2 SV=2 Back     alignment and function description
>sp|Q9S9P2|CAF1B_ARATH Probable CCR4-associated factor 1 homolog 2 OS=Arabidopsis thaliana GN=CAF1-2 PE=2 SV=1 Back     alignment and function description
>sp|Q9SAI2|CAF1F_ARATH Probable CCR4-associated factor 1 homolog 6 OS=Arabidopsis thaliana GN=CAF1-6 PE=2 SV=1 Back     alignment and function description
>sp|Q9UFF9|CNOT8_HUMAN CCR4-NOT transcription complex subunit 8 OS=Homo sapiens GN=CNOT8 PE=1 SV=1 Back     alignment and function description
>sp|Q9D8X5|CNOT8_MOUSE CCR4-NOT transcription complex subunit 8 OS=Mus musculus GN=Cnot8 PE=2 SV=1 Back     alignment and function description
>sp|O74856|CAF1_SCHPO Poly(A) ribonuclease pop2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=caf1 PE=1 SV=2 Back     alignment and function description
>sp|Q60809|CNOT7_MOUSE CCR4-NOT transcription complex subunit 7 OS=Mus musculus GN=Cnot7 PE=1 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query280
224091915295 predicted protein [Populus trichocarpa] 0.95 0.901 0.725 1e-108
224140049296 predicted protein [Populus trichocarpa] 0.989 0.935 0.676 1e-107
356505410274 PREDICTED: probable CCR4-associated fact 0.942 0.963 0.686 1e-100
356572602274 PREDICTED: probable CCR4-associated fact 0.942 0.963 0.682 2e-99
358343557 445 CCR4-associated factor [Medicago truncat 0.964 0.606 0.672 2e-97
255578601292 ccr4-associated factor, putative [Ricinu 0.942 0.904 0.660 2e-97
359481632280 PREDICTED: probable CCR4-associated fact 0.957 0.957 0.640 3e-94
147792345278 hypothetical protein VITISV_021407 [Viti 0.953 0.960 0.638 5e-94
225440749278 PREDICTED: probable CCR4-associated fact 0.953 0.960 0.638 7e-94
225464848278 PREDICTED: probable CCR4-associated fact 0.946 0.953 0.656 8e-94
>gi|224091915|ref|XP_002309398.1| predicted protein [Populus trichocarpa] gi|222855374|gb|EEE92921.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  398 bits (1022), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 198/273 (72%), Positives = 229/273 (83%), Gaps = 7/273 (2%)

Query: 14  ILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRP---DSNIRHRDPAANYNGL 70
           +LIR V+  NL  EF+ IR+ IDRYP+ISMDTEFPG+VVRP   D   RHRDP A+Y  L
Sbjct: 23  VLIRSVWADNLEEEFKFIRSEIDRYPLISMDTEFPGIVVRPVAGDPYNRHRDPTAHYLSL 82

Query: 71  KANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQ 130
           KANVDLLNLIQIGLT++DE+GNLPDLG     +IWEFNF+DFD+A  AHA DSVELL+RQ
Sbjct: 83  KANVDLLNLIQIGLTIADEDGNLPDLGFKDLCFIWEFNFRDFDVAHDAHAHDSVELLRRQ 142

Query: 131 GIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLS 190
           GIDFEKNRE GIDSV+FAEL+MSSGLVLN+ V+WVTFH AYDFGYLVKCLT +VLPE L+
Sbjct: 143 GIDFEKNRELGIDSVKFAELMMSSGLVLNQSVSWVTFHCAYDFGYLVKCLTHKVLPEGLN 202

Query: 191 EFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHA 250
           EF+  V VFFG++VYD+KH+IRFC  LYGGLDRVCK LGV+RV+GKSHQAGSDSLLTLHA
Sbjct: 203 EFLGLVRVFFGDRVYDIKHIIRFCAGLYGGLDRVCKELGVDRVIGKSHQAGSDSLLTLHA 262

Query: 251 FLKIKDKHF----GNEYELQKYANVLHGLELLE 279
           +LKIKDK+F     N+  L KYANVLHGLEL +
Sbjct: 263 YLKIKDKYFFKDKDNDRGLDKYANVLHGLELFD 295

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224140049|ref|XP_002323399.1| predicted protein [Populus trichocarpa] gi|222868029|gb|EEF05160.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356505410|ref|XP_003521484.1| PREDICTED: probable CCR4-associated factor 1 homolog 11-like [Glycine max] Back     alignment and taxonomy information
>gi|356572602|ref|XP_003554457.1| PREDICTED: probable CCR4-associated factor 1 homolog 11-like [Glycine max] Back     alignment and taxonomy information
>gi|358343557|ref|XP_003635867.1| CCR4-associated factor [Medicago truncatula] gi|355501802|gb|AES83005.1| CCR4-associated factor [Medicago truncatula] Back     alignment and taxonomy information
>gi|255578601|ref|XP_002530162.1| ccr4-associated factor, putative [Ricinus communis] gi|223530323|gb|EEF32217.1| ccr4-associated factor, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|359481632|ref|XP_003632649.1| PREDICTED: probable CCR4-associated factor 1 homolog 9-like isoform 2 [Vitis vinifera] Back     alignment and taxonomy information
>gi|147792345|emb|CAN61475.1| hypothetical protein VITISV_021407 [Vitis vinifera] Back     alignment and taxonomy information
>gi|225440749|ref|XP_002281138.1| PREDICTED: probable CCR4-associated factor 1 homolog 9-like isoform 1 [Vitis vinifera] Back     alignment and taxonomy information
>gi|225464848|ref|XP_002271636.1| PREDICTED: probable CCR4-associated factor 1 homolog 9-like [Vitis vinifera] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query280
TAIR|locus:2176307278 CAF1b "CCR4- associated factor 0.939 0.946 0.599 1.2e-81
TAIR|locus:2095715280 CAF1a "CCR4- associated factor 0.932 0.932 0.609 7.6e-80
TAIR|locus:2183765277 AT5G10960 [Arabidopsis thalian 0.914 0.924 0.541 3.7e-71
TAIR|locus:2045512275 AT2G32070 [Arabidopsis thalian 0.917 0.934 0.538 5.5e-70
TAIR|locus:2200532286 AT1G15920 [Arabidopsis thalian 0.921 0.902 0.518 1.2e-65
DICTYBASE|DDB_G0284217 367 DDB_G0284217 "CAF1 family prot 0.896 0.683 0.461 1.6e-56
ZFIN|ZDB-GENE-040426-2845285 cnot8 "CCR4-NOT transcription 0.9 0.884 0.467 6.1e-55
UNIPROTKB|F1NYH4291 CNOT8 "Uncharacterized protein 0.9 0.865 0.463 5.5e-54
UNIPROTKB|E1BJH0292 CNOT8 "Uncharacterized protein 0.9 0.863 0.463 5.5e-54
UNIPROTKB|E2RID4292 CNOT8 "Uncharacterized protein 0.9 0.863 0.463 5.5e-54
TAIR|locus:2176307 CAF1b "CCR4- associated factor 1b" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 819 (293.4 bits), Expect = 1.2e-81, P = 1.2e-81
 Identities = 160/267 (59%), Positives = 206/267 (77%)

Query:    14 ILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHR-DPAANYNGLKA 72
             I+IR+V+ +NL SEF+ IR +++ YP ISMDTEFPGV+ + D ++  R +P   YN LK+
Sbjct:    12 IVIRDVWAYNLESEFDLIRGIVEDYPFISMDTEFPGVIYKADLDVLRRGNPNYLYNLLKS 71

Query:    73 NVDLLNLIQIGLTLSDEEGNLPDLGSGSTY-YIWEFNFKDFDIARHAHALDSVELLKRQG 131
             NVD L+LIQ+GLTLSD +GNLPDLG      YIWEFNF+DFD+ R  HA DS+ELL+R G
Sbjct:    72 NVDALSLIQVGLTLSDADGNLPDLGGQKNRRYIWEFNFRDFDVERDPHAPDSIELLRRHG 131

Query:   132 IDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSE 191
             IDFE+NR  G++S RFAEL+MSSGL+ N+ V+WVTFHSAYDFGYLVK LT+R LP  L E
Sbjct:   132 IDFERNRREGVESERFAELMMSSGLICNESVSWVTFHSAYDFGYLVKILTRRQLPVALRE 191

Query:   192 FVTRVGVFFGEKVYDVKHLIRFCTC-LYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHA 250
             F+  +  FFG++VYDVKH++RFC   LYGGLDRV ++L V R VGK HQAGSDSLLT  A
Sbjct:   192 FLGLLRAFFGDRVYDVKHIMRFCEQRLYGGLDRVARSLEVNRAVGKCHQAGSDSLLTWQA 251

Query:   251 FLKIKDKHFGNEYELQKYANVLHGLEL 277
             F +++D +F  +   +K+A VL+GLE+
Sbjct:   252 FQRMRDLYFVED-GAEKHAGVLYGLEV 277
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:2095715 CAF1a "CCR4- associated factor 1a" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2183765 AT5G10960 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2045512 AT2G32070 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2200532 AT1G15920 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0284217 DDB_G0284217 "CAF1 family protein" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-040426-2845 cnot8 "CCR4-NOT transcription complex, subunit 8" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|F1NYH4 CNOT8 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|E1BJH0 CNOT8 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2RID4 CNOT8 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q9FMS6CAF1K_ARATH3, ., 1, ., 1, 3, ., 40.60070.94280.9496yesno
Q9D8X5CNOT8_MOUSENo assigned EC number0.44810.93210.8938yesno
Q9UFF9CNOT8_HUMANNo assigned EC number0.44810.93210.8938yesno

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

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query280
pfam04857235 pfam04857, CAF1, CAF1 family ribonuclease 2e-92
COG5228299 COG5228, POP2, mRNA deadenylase subunit [RNA proce 1e-78
>gnl|CDD|147159 pfam04857, CAF1, CAF1 family ribonuclease Back     alignment and domain information 
 Score =  272 bits (698), Expect = 2e-92
 Identities = 123/242 (50%), Positives = 150/242 (61%), Gaps = 12/242 (4%)

Query: 17  REVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDL 76
           REV+  N   EF+ IR  ID Y  I++DTEFPGVV RP  +         Y  L+ NVD 
Sbjct: 1   REVWRSNFHEEFKEIRQAIDSYDFIAIDTEFPGVVARPIGS-FRSTSDYRYQALRKNVDR 59

Query: 77  LNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEK 136
           L +IQ+GLTL DE+GNLPD     +YY W+FNF  F++    +A  S+E L +QG DF K
Sbjct: 60  LKIIQLGLTLFDEKGNLPD-----SYYTWQFNFSLFNLEEDFYAPSSIEFLAKQGFDFNK 114

Query: 137 NREFGIDSVRFAELLMSSGLVLN-KDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTR 195
           +R  GI  +RFAELL SSGL LN   VTWVTFH  YDFGYL+K LT   LPE L +F+  
Sbjct: 115 HRREGIPYLRFAELLGSSGLFLNISSVTWVTFHGLYDFGYLLKLLTGGPLPETLDDFLEL 174

Query: 196 VGVFFGEKVYDVKHLIRFCTCLYG----GLDRVCKALGVERVVGKSHQAGSDSLLTLHAF 251
           +   F  +VYD K+L +FC  L G    GL  +   LGV R VG+ HQAGSDSLLT   F
Sbjct: 175 LRELFP-RVYDTKYLAKFCFELDGGSNGGLQELADLLGVNRRVGRLHQAGSDSLLTALVF 233

Query: 252 LK 253
            K
Sbjct: 234 FK 235

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] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 280
KOG0304239 consensus mRNA deadenylase subunit [RNA processing 100.0
COG5228299 POP2 mRNA deadenylase subunit [RNA processing and 100.0
PF04857262 CAF1: CAF1 family ribonuclease; InterPro: IPR00694 100.0
PRK07942232 DNA polymerase III subunit epsilon; Provisional 98.95
smart00479169 EXOIII exonuclease domain in DNA-polymerase alpha 98.93
KOG1990 564 consensus Poly(A)-specific exoribonuclease PARN [R 98.9
cd06133176 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o 98.7
PRK09145202 DNA polymerase III subunit epsilon; Validated 98.69
cd06131167 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl 98.67
cd06134189 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. 98.66
PRK05168211 ribonuclease T; Provisional 98.58
PRK07748207 sporulation inhibitor KapD; Provisional 98.56
cd06130156 DNA_pol_III_epsilon_like an uncharacterized bacter 98.5
PRK05711240 DNA polymerase III subunit epsilon; Provisional 98.5
TIGR00573217 dnaq exonuclease, DNA polymerase III, epsilon subu 98.37
PRK07740244 hypothetical protein; Provisional 98.36
PRK06310250 DNA polymerase III subunit epsilon; Validated 98.34
cd06127159 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh 98.33
PRK06063 313 DNA polymerase III subunit epsilon; Provisional 98.31
TIGR01406225 dnaQ_proteo DNA polymerase III, epsilon subunit, P 98.3
PRK09146239 DNA polymerase III subunit epsilon; Validated 98.24
PRK06807 313 DNA polymerase III subunit epsilon; Validated 98.2
TIGR01298200 RNaseT ribonuclease T. in gamma-subdivision Proteo 98.17
PRK07247195 DNA polymerase III subunit epsilon; Validated 98.16
cd06136177 TREX1_2 DEDDh 3'-5' exonuclease domain of three pr 98.14
PRK06195 309 DNA polymerase III subunit epsilon; Validated 98.13
PRK08517257 DNA polymerase III subunit epsilon; Provisional 98.05
PRK08074 928 bifunctional ATP-dependent DNA helicase/DNA polyme 98.05
PRK07246 820 bifunctional ATP-dependent DNA helicase/DNA polyme 98.01
PRK07883 557 hypothetical protein; Validated 97.99
TIGR01405 1213 polC_Gram_pos DNA polymerase III, alpha chain, Gra 97.98
PRK06722281 exonuclease; Provisional 97.93
TIGR01407 850 dinG_rel DnaQ family exonuclease/DinG family helic 97.91
PRK11779 476 sbcB exonuclease I; Provisional 97.8
cd06138183 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain o 97.79
PF00929164 RNase_T: Exonuclease; InterPro: IPR013520 This ent 97.77
PRK07983219 exodeoxyribonuclease X; Provisional 97.7
PRK05601 377 DNA polymerase III subunit epsilon; Validated 97.68
PRK06309232 DNA polymerase III subunit epsilon; Validated 97.66
PTZ00315 582 2'-phosphotransferase; Provisional 97.65
PRK09182294 DNA polymerase III subunit epsilon; Validated 97.64
cd06144152 REX4_like DEDDh 3'-5' exonuclease domain of RNA ex 97.55
PRK00448 1437 polC DNA polymerase III PolC; Validated 97.47
COG0847243 DnaQ DNA polymerase III, epsilon subunit and relat 97.32
cd06137161 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the 97.15
cd06145150 REX1_like DEDDh 3'-5' exonuclease domain of RNA ex 96.87
PRK05359181 oligoribonuclease; Provisional 96.7
cd06149157 ISG20 DEDDh 3'-5' exonuclease domain of Interferon 96.63
PF01612176 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR00 95.65
COG0349 361 Rnd Ribonuclease D [Translation, ribosomal structu 95.58
cd06135173 Orn DEDDh 3'-5' exonuclease domain of oligoribonuc 95.24
cd06146193 mut-7_like_exo DEDDy 3'-5' exonuclease domain of C 95.06
cd06141170 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and 94.52
PRK05755 880 DNA polymerase I; Provisional 94.51
PRK10829 373 ribonuclease D; Provisional 94.38
TIGR01388 367 rnd ribonuclease D. This model describes ribonucle 91.55
cd06129161 RNaseD_like DEDDy 3'-5' exonuclease domain of RNas 91.34
COG2176 1444 PolC DNA polymerase III, alpha subunit (gram-posit 84.04
PF13482164 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 83.33
PF10108209 DNA_pol_B_exo2: Predicted 3'-5' exonuclease relate 81.16
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification] Back     alignment and domain information 
Probab=100.00  E-value=6.9e-93  Score=620.73  Aligned_cols=237  Identities=58%  Similarity=0.937  Sum_probs=230.6

Q ss_pred             eEEecCccCHHHHHHHHHHHhhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeeeeeccCCCCCC
Q 023614           15 LIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLP   94 (280)
Q Consensus        15 ~i~eVw~~Nl~~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGlt~~~~~g~~p   94 (280)
                      .|||||++|+++||++||++|++||||||||||||++.+|.+.|+++. +++|+.||+|||.+++||+|||++|++|++|
T Consensus         1 ~ireVW~~Nl~~Em~~Ir~~v~~y~~IamDTEFPGvv~rp~~~f~s~~-d~~Y~~lk~NVd~lklIQlGlTlsd~~Gn~p   79 (239)
T KOG0304|consen    1 FIREVWRSNLEEEMALIRECVKDYPYIAMDTEFPGVVARPIGTFRSSD-DYHYQTLKCNVDNLKLIQLGLTLSDEKGNLP   79 (239)
T ss_pred             ChhHHHHHhHHHHHHHHHHHHHhCCeeEecCcCCceeeecCccccCCh-HHHHHHHHhchhhhhhhheeeeeeccCCCCC
Confidence            379999999999999999999999999999999999999999999887 9999999999999999999999999999999


Q ss_pred             CCCCCCCceEEEEeccccCcCcCCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceEEEeccchhHH
Q 023614           95 DLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFG  174 (280)
Q Consensus        95 ~~~~~~~~~~wqFNF~~F~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~Wvtfhg~yD~g  174 (280)
                      .+|    ..+|||||++|++.+|+++++||+||+++||||.|++++||+..+|+|+|++||++++++|+||||||+||||
T Consensus        80 ~~g----~~tWqfNF~dF~~~~D~~a~~SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YDfg  155 (239)
T KOG0304|consen   80 DCG----TDTWQFNFSDFNLEKDMYAQDSIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHSGYDFG  155 (239)
T ss_pred             CCC----CceeEEecccCCchhhccchhhHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeeccchHH
Confidence            764    5799999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhcc--ccchHHHHHHHcCCCccCCCccchhhhHHHHHHHHH
Q 023614          175 YLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTC--LYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFL  252 (280)
Q Consensus       175 yL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~--l~~~L~~la~~L~v~r~~g~~hqAGsDs~lT~~~F~  252 (280)
                      ||+|+||+++||++.++|.+.++++||. +||+|||++.|.+  +++||++||+.|+|+| +|++|||||||+||+.+|+
T Consensus       156 YLlK~Lt~~~LP~~~~eF~~~v~~~fp~-vYDiK~l~~~c~~~~l~~GL~~lA~~L~~~R-vG~~HqAGSDSlLT~~~F~  233 (239)
T KOG0304|consen  156 YLLKILTGKPLPETEEEFFEIVRQLFPF-VYDVKYLMKFCEGLSLKGGLQRLADLLGLKR-VGIAHQAGSDSLLTARVFF  233 (239)
T ss_pred             HHHHHHcCCCCcchHHHHHHHHHHHcch-hhhHHHHHHhhhhhhhhcCHHHHHHHhCCCe-eecccccCcHHHHHHHHHH
Confidence            9999999999999999999999999999 9999999999965  8999999999999999 9999999999999999999


Q ss_pred             HHHHhh
Q 023614          253 KIKDKH  258 (280)
Q Consensus       253 ~l~~~~  258 (280)
                      ||++.|
T Consensus       234 kl~~~f  239 (239)
T KOG0304|consen  234 KLKELF  239 (239)
T ss_pred             HHHhcC
Confidence            999864

>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification] Back     alignment and domain information
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation Back     alignment and domain information
>PRK07942 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases Back     alignment and domain information
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair] Back     alignment and domain information
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins Back     alignment and domain information
>PRK09145 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins Back     alignment and domain information
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T Back     alignment and domain information
>PRK05168 ribonuclease T; Provisional Back     alignment and domain information
>PRK07748 sporulation inhibitor KapD; Provisional Back     alignment and domain information
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III Back     alignment and domain information
>PRK05711 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family Back     alignment and domain information
>PRK07740 hypothetical protein; Provisional Back     alignment and domain information
>PRK06310 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family Back     alignment and domain information
>PRK06063 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial Back     alignment and domain information
>PRK09146 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06807 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>TIGR01298 RNaseT ribonuclease T Back     alignment and domain information
>PRK07247 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins Back     alignment and domain information
>PRK06195 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK08517 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07883 hypothetical protein; Validated Back     alignment and domain information
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type Back     alignment and domain information
>PRK06722 exonuclease; Provisional Back     alignment and domain information
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative Back     alignment and domain information
>PRK11779 sbcB exonuclease I; Provisional Back     alignment and domain information
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins Back     alignment and domain information
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III Back     alignment and domain information
>PRK07983 exodeoxyribonuclease X; Provisional Back     alignment and domain information
>PRK05601 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06309 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PTZ00315 2'-phosphotransferase; Provisional Back     alignment and domain information
>PRK09182 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins Back     alignment and domain information
>PRK00448 polC DNA polymerase III PolC; Validated Back     alignment and domain information
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair] Back     alignment and domain information
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins Back     alignment and domain information
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins Back     alignment and domain information
>PRK05359 oligoribonuclease; Provisional Back     alignment and domain information
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins Back     alignment and domain information
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides Back     alignment and domain information
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins Back     alignment and domain information
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins Back     alignment and domain information
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>PRK10829 ribonuclease D; Provisional Back     alignment and domain information
>TIGR01388 rnd ribonuclease D Back     alignment and domain information
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins Back     alignment and domain information
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair] Back     alignment and domain information
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A Back     alignment and domain information
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query280
2p51_A333 Crystal Structure Of The S. Pombe Pop2p Deadenylati 3e-57
4gmj_B285 Structure Of Human Not1 Mif4g Domain Co-Crystallize 1e-56
2d5r_A252 Crystal Structure Of A Tob-Hcaf1 Complex Length = 2 2e-56
4b8c_A288 Nuclease Module Of The Yeast Ccr4-Not Complex Lengt 4e-39
4b8a_B286 Structure Of Yeast Not1 Mif4g Domain Co-Crystallize 4e-39
1uoc_A289 X-Ray Structure Of The Rnase Domain Of The Yeast Po 4e-39
>pdb|2P51|A Chain A, Crystal Structure Of The S. Pombe Pop2p Deadenylation Subunit Length = 333 Back     alignment and structure 
Iteration: 1

 Score =  218 bits (555), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 118/260 (45%), Positives = 165/260 (63%), Gaps = 10/260 (3%)
Query: 16  IREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVD 75
           IR+V+  NL  E   I +LI+RYP++SMDTEFPGVV RP    +  D   +Y  L+ANVD
Sbjct: 23  IRDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVARPLGVFKSSD-DYHYQTLRANVD 81
Query: 76  LLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFE 135
            L +IQIGL LSDEEGN P          W+FNF  F++    +A +S+ELL + GIDF+
Sbjct: 82  SLKIIQIGLALSDEEGNAPVEAC-----TWQFNFT-FNLQDDMYAPESIELLTKSGIDFK 135
Query: 136 KNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTR 195
           K++E GI+   FAELL+ SGLVL ++VTW+TFHS YDF YL+K +TQ  LP +  EF   
Sbjct: 136 KHQEVGIEPADFAELLIGSGLVLQEEVTWITFHSGYDFAYLLKAMTQIPLPAEYEEFYKI 195
Query: 196 VGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIK 255
           + ++F  K YD+K++++       GL  +   L + R +G  HQAGSD+LLT   F +I+
Sbjct: 196 LCIYF-PKNYDIKYIMKSVLNNSKGLQDIADDLQIHR-IGPQHQAGSDALLTARIFFEIR 253
Query: 256 DKHFGNEYELQKYANVLHGL 275
            ++F    +  +  N L+GL
Sbjct: 254 SRYFDGSID-SRMLNQLYGL 272
>pdb|4GMJ|B Chain B, Structure Of Human Not1 Mif4g Domain Co-Crystallized With Caf1 Length = 285 Back     alignment and structure
>pdb|2D5R|A Chain A, Crystal Structure Of A Tob-Hcaf1 Complex Length = 252 Back     alignment and structure
>pdb|4B8C|A Chain A, Nuclease Module Of The Yeast Ccr4-Not Complex Length = 288 Back     alignment and structure
>pdb|4B8A|B Chain B, Structure Of Yeast Not1 Mif4g Domain Co-Crystallized With Caf1 Length = 286 Back     alignment and structure
>pdb|1UOC|A Chain A, X-Ray Structure Of The Rnase Domain Of The Yeast Pop2 Protein Length = 289 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query280
2p51_A333 SPCC18.06C protein; DEDD nuclease fold, hydrolase, 5e-98
1uoc_A289 POP2; hydrolase, DEDD nuclease, mRNA degradation, 4e-97
2d5r_A252 CCR4-NOT transcription complex subunit 7; poly(A) 1e-93
2a1r_A 430 Poly(A)-specific ribonuclease PARN; DEDD, nuclease 4e-24
2a1r_A430 Poly(A)-specific ribonuclease PARN; DEDD, nuclease 3e-09
3d45_A 507 Poly(A)-specific ribonuclease PARN; CAP analogue, 2e-22
>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A Length = 333 Back     alignment and structure
 Score =  290 bits (742), Expect = 5e-98
 Identities = 117/275 (42%), Positives = 164/275 (59%), Gaps = 10/275 (3%)

Query: 1   MSDVPPPQPPKPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRH 60
              +           IR+V+  NL  E   I +LI+RYP++SMDTEFPGVV RP    + 
Sbjct: 8   YPALGVDGISSQISPIRDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVARPLGVFKS 67

Query: 61  RDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHA 120
                +Y  L+ANVD L +IQIGL LSDEEGN P          W+FNF  F++    +A
Sbjct: 68  -SDDYHYQTLRANVDSLKIIQIGLALSDEEGNAPV-----EACTWQFNFT-FNLQDDMYA 120

Query: 121 LDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCL 180
            +S+ELL + GIDF+K++E GI+   FAELL+ SGLVL ++VTW+TFHS YDF YL+K +
Sbjct: 121 PESIELLTKSGIDFKKHQEVGIEPADFAELLIGSGLVLQEEVTWITFHSGYDFAYLLKAM 180

Query: 181 TQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQA 240
           TQ  LP +  EF   + ++F  K YD+K++++       GL  +   L + R +G  HQA
Sbjct: 181 TQIPLPAEYEEFYKILCIYFP-KNYDIKYIMKSVLNNSKGLQDIADDLQIHR-IGPQHQA 238

Query: 241 GSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGL 275
           GSD+LLT   F +I+ ++F       +  N L+GL
Sbjct: 239 GSDALLTARIFFEIRSRYFDGS-IDSRMLNQLYGL 272
>1uoc_A POP2; hydrolase, DEDD nuclease, mRNA degradation, poly(A) tail, transcription regulation, repressor, phosphorylation.; 2.3A {Saccharomyces cerevisiae} SCOP: c.55.3.9 Length = 289 Back     alignment and structure
>2d5r_A CCR4-NOT transcription complex subunit 7; poly(A) deadenylase, antiproliferative protein, transcription; 2.50A {Homo sapiens} SCOP: c.55.3.9 Length = 252 Back     alignment and structure
>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase-RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A Length = 430 Back     alignment and structure
>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase-RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A Length = 430 Back     alignment and structure
>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus} Length = 507 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query280
2p51_A333 SPCC18.06C protein; DEDD nuclease fold, hydrolase, 100.0
4gmj_B285 CCR4-NOT transcription complex subunit 7; mRNA dec 100.0
2d5r_A252 CCR4-NOT transcription complex subunit 7; poly(A) 100.0
1uoc_A289 POP2; hydrolase, DEDD nuclease, mRNA degradation, 100.0
3d45_A507 Poly(A)-specific ribonuclease PARN; CAP analogue, 100.0
2a1r_A430 Poly(A)-specific ribonuclease PARN; DEDD, nuclease 100.0
3v9w_A235 Ribonuclease T; DEDD nucleases family, EXO-nucleas 98.86
1w0h_A204 3'-5' exonuclease ERI1; nuclease domain, hydrolase 98.76
2f96_A224 Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas 98.72
2p1j_A186 POLIII, DNA polymerase III POLC-type; structural g 98.62
3cg7_A308 CRN-4, cell death-related nuclease 4; hydrolase, a 98.61
1zbh_A299 3'-5' exonuclease ERI1; histone mRNA 3'-END-specif 98.58
2gui_A194 DNA polymerase III epsilon subunit; DNA polymerase 98.55
2xri_A224 ERI1 exoribonuclease 3; hydrolase, metal binding; 98.53
3mxm_B242 Three prime repair exonuclease 1; RNAse H-like fol 98.49
1y97_A238 Three prime repair exonuclease 2; TREX2, hydrolase 98.38
1zbu_A349 ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; 98.38
2qxf_A 482 Exodeoxyribonuclease I; alpha-beta domain, DNAQ su 98.38
3u3y_B314 Three prime repair exonuclease 1; RNAse H fold, 3' 98.36
1wlj_A189 Interferon stimulated gene 20KDA; exoribonuclease, 98.01
2igi_A180 Oligoribonuclease; RNAse, exoribonuclease, exonucl 98.01
2gbz_A194 Oligoribonuclease; ORN, deddh, structural genomics 97.6
3tr8_A186 Oligoribonuclease; transcription, hydrolase; 2.50A 97.52
2kfn_A 605 Klenow fragment of DNA polymerase I; complex (poly 95.97
3saf_A 428 Exosome component 10; exoribonuclease, RNA exosome 91.76
>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A Back     alignment and structure
Probab=100.00  E-value=1.9e-93  Score=666.36  Aligned_cols=268  Identities=44%  Similarity=0.731  Sum_probs=248.6

Q ss_pred             CCCCCCCCCCCCCceEEecCccCHHHHHHHHHHHhhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccce
Q 023614            1 MSDVPPPQPPKPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLI   80 (280)
Q Consensus         1 ~~~~~~~~~~~~~~~i~eVw~~Nl~~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~ii   80 (280)
                      |++++.|+++++.+.|||||++||++||+.|+++|++|+||||||||||++++|.+.++++. ++||+++|+|||.++||
T Consensus         8 ~~~~~~~~~~~~~~~IreVw~~Nleee~~~Ir~~i~~~~fVAmDtEFpGvv~rp~g~f~~~~-e~~Yq~lR~NVd~l~iI   86 (333)
T 2p51_A            8 YPALGVDGISSQISPIRDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVARPLGVFKSSD-DYHYQTLRANVDSLKII   86 (333)
T ss_dssp             ----------CCSCSEEEECTTTHHHHHHHHHHHTTTSCEEEEEEECCCCCCCCCSCCSSSH-HHHHHHHHHHHHHSCCC
T ss_pred             CCccccCCCCCCCcEEEEehHhHHHHHHHHHHHHHhhCCEEEEeeeccccccccccccCCCH-HHHHHHHHHhhhhccce
Confidence            56677888889999999999999999999999999999999999999999999998898877 99999999999999999


Q ss_pred             eeeeeeccCCCCCCCCCCCCCceEEEEeccccCcCcCCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCC
Q 023614           81 QIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNK  160 (280)
Q Consensus        81 QlGlt~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~  160 (280)
                      |||||+++++|+.|.     .+++|||||+ |++.+|+|+++||+||+++||||+|++++||++.+|+|+|++||||+++
T Consensus        87 QlGLt~fd~~G~~p~-----~~~twqFNF~-F~~~~d~~~~~SI~fL~~~G~DF~k~~~~GI~~~~F~elL~~SGLvl~~  160 (333)
T 2p51_A           87 QIGLALSDEEGNAPV-----EACTWQFNFT-FNLQDDMYAPESIELLTKSGIDFKKHQEVGIEPADFAELLIGSGLVLQE  160 (333)
T ss_dssp             EEEEEEECTTSCCCT-----TCSEEEEEBC-CCTTTSCCCHHHHHHHHHTTCCHHHHHHHCBCHHHHHHHHHTTTSSSCT
T ss_pred             EEEEEEEccCCCCCC-----CceeEEEEEE-ECCcccccCHHHHHHHHHcCCChhHHHHcCCCHHHHHHHHHhcCcccCC
Confidence            999999999999985     3799999999 9999999999999999999999999999999999999999999999999


Q ss_pred             CceEEEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhccccchHHHHHHHcCCCccCCCccch
Q 023614          161 DVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQA  240 (280)
Q Consensus       161 ~v~Wvtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~l~~~L~~la~~L~v~r~~g~~hqA  240 (280)
                      +|+||+|||+||||||+|+|||++||+++++|+++|+.+||+ |||||||++.|.++++||++||+.|+|+| +|++|||
T Consensus       161 ~V~Witfhg~YDfgyLlK~Lt~~~LP~~~~eF~~~l~~~FP~-iYD~K~l~~~~~~l~ggL~~lA~~L~v~R-ig~~HqA  238 (333)
T 2p51_A          161 EVTWITFHSGYDFAYLLKAMTQIPLPAEYEEFYKILCIYFPK-NYDIKYIMKSVLNNSKGLQDIADDLQIHR-IGPQHQA  238 (333)
T ss_dssp             TCEEEESSCHHHHHHHHHHHHCSCCCSSHHHHHHHHHHHSSS-EEEHHHHHTTTTCCCCCHHHHHHHTTCCC-CSCTTSH
T ss_pred             CceEEEeccchhHHHHHHHhcCCCCCCCHHHHHHHHHHHCcc-hhhHHHHHHHhccccCCHHHHHHHcCCCc-cCcchhh
Confidence            999999999999999999999999999999999999999998 99999999999999999999999999999 9999999


Q ss_pred             hhhHHHHHHHHHHHHHhhCCCccccccccceEecCCCC
Q 023614          241 GSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLELL  278 (280)
Q Consensus       241 GsDs~lT~~~F~~l~~~~~~~~~~~~~~~g~i~Gl~~~  278 (280)
                      |||||||++||+||++.+|++. +.++++|+||||+..
T Consensus       239 GsDSlLT~~~F~kl~~~~f~~~-~~~~~~g~l~Gl~~~  275 (333)
T 2p51_A          239 GSDALLTARIFFEIRSRYFDGS-IDSRMLNQLYGLGST  275 (333)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTS-CCGGGTTCCTTC---
T ss_pred             hhHHHHHHHHHHHHHHHhcCCC-chhhhCCEEeccCcC
Confidence            9999999999999999999775 578999999999865
>4gmj_B CCR4-NOT transcription complex subunit 7; mRNA decay, deadenylase, RNA bindin; HET: GOL; 2.70A {Homo sapiens} Back     alignment and structure
>2d5r_A CCR4-NOT transcription complex subunit 7; poly(A) deadenylase, antiproliferative protein, transcription; 2.50A {Homo sapiens} SCOP: c.55.3.9 Back     alignment and structure
>1uoc_A POP2; hydrolase, DEDD nuclease, mRNA degradation, poly(A) tail, transcription regulation, repressor, phosphorylation.; 2.3A {Saccharomyces cerevisiae} SCOP: c.55.3.9 Back     alignment and structure
>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus} Back     alignment and structure
>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase-RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A Back     alignment and structure
>3v9w_A Ribonuclease T; DEDD nucleases family, EXO-nucleases, hydrolase-DNA complex; HET: DNA; 1.70A {Escherichia coli} PDB: 3ngy_A 3v9u_A* 3ngz_A* 3va3_A* 3v9z_A* 3nh0_A 3nh2_A 3nh1_A* 3v9s_A* 3v9x_A* 3va0_A* 2is3_A Back     alignment and structure
>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5 Back     alignment and structure
>2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PS protein structure initiative, midwest center for structural genomics; 2.09A {Pseudomonas aeruginosa} SCOP: c.55.3.5 Back     alignment and structure
>2p1j_A POLIII, DNA polymerase III POLC-type; structural genomics, exonuclease, PSI-2, protein structure initiative; HET: DNA; 2.50A {Thermotoga maritima MSB8} Back     alignment and structure
>3cg7_A CRN-4, cell death-related nuclease 4; hydrolase, apoptosis, 3'-5' exonuclease, deddh; 2.50A {Caenorhabditis elegans} PDB: 3cm5_A 3cm6_A Back     alignment and structure
>1zbh_A 3'-5' exonuclease ERI1; histone mRNA 3'-END-specific recognition, structures of 3'- exonuclease and ITS RNA complex, hydrolase/RNA complex; HET: AMP; 3.00A {Homo sapiens} Back     alignment and structure
>2gui_A DNA polymerase III epsilon subunit; DNA polymerase proofreading domain, transferase; HET: DNA U5P; 1.60A {Escherichia coli} SCOP: c.55.3.5 PDB: 1j54_A* 1j53_A* 2ido_A* 2xy8_A* Back     alignment and structure
>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens} Back     alignment and structure
>3mxm_B Three prime repair exonuclease 1; RNAse H-like fold, polyproline type II helix, hydrolase-DNA; HET: DNA; 1.75A {Mus musculus} SCOP: c.55.3.5 PDB: 3mxj_B 2ioc_B 3mxi_B* 3b6o_A* 2o4g_A* 3b6p_A* 2o4i_A 2oa8_A Back     alignment and structure
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5 Back     alignment and structure
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens} Back     alignment and structure
>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* Back     alignment and structure
>3u3y_B Three prime repair exonuclease 1; RNAse H fold, 3' exonuclease, homodimer, hydrolase-DNA compl; HET: BU1; 2.28A {Mus musculus} PDB: 3u6f_B* Back     alignment and structure
>1wlj_A Interferon stimulated gene 20KDA; exoribonuclease, hydrolase; HET: U5P; 1.90A {Homo sapiens} SCOP: c.55.3.5 Back     alignment and structure
>2igi_A Oligoribonuclease; RNAse, exoribonuclease, exonuclease, hydrolase, mRNA decay; 1.70A {Escherichia coli} SCOP: c.55.3.5 PDB: 1yta_A 1j9a_A Back     alignment and structure
>2gbz_A Oligoribonuclease; ORN, deddh, structural genomics, hydrolase; 2.30A {Xanthomonas campestris PV} Back     alignment and structure
>3tr8_A Oligoribonuclease; transcription, hydrolase; 2.50A {Coxiella burnetii} Back     alignment and structure
>2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA), exonuclease, transferase, transferase/DNA complex; HET: US1; 2.03A {Escherichia coli} SCOP: c.55.3.5 e.8.1.1 PDB: 1d9f_A* 1d9d_A* 1krp_A* 1ksp_A* 1qsl_A* 1kfs_A* 2kfz_A* 2kzm_A* 2kzz_A* 1dpi_A* 1kfd_A* 1kln_A* 1d8y_A* Back     alignment and structure
>3saf_A Exosome component 10; exoribonuclease, RNA exosome, hydrolase; 2.50A {Homo sapiens} PDB: 3sag_A 3sah_A 2cpr_A Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 280
d2d5ra1252 c.55.3.9 (A:11-262) CCR4-NOT transcription complex 2e-98
d1uoca_286 c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast ( 6e-98
>d2d5ra1 c.55.3.9 (A:11-262) CCR4-NOT transcription complex subunit 7, CAF1 {Human (Homo sapiens) [TaxId: 9606]} Length = 252 Back     information, alignment and structure

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

 Score =  287 bits (735), Expect = 2e-98
 Identities = 120/260 (46%), Positives = 165/260 (63%), Gaps = 9/260 (3%)

Query: 16  IREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVD 75
           I EV+  NL  E ++IR +I +Y  ++MDTEFPGVV RP    R  +    Y  L+ NVD
Sbjct: 2   ICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRS-NADYQYQLLRCNVD 60

Query: 76  LLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFE 135
           LL +IQ+GLT  +E+G  P          W+FNFK F++    +A DS+ELL   GI F+
Sbjct: 61  LLKIIQLGLTFMNEQGEYP-----PGTSTWQFNFK-FNLTEDMYAQDSIELLTTSGIQFK 114

Query: 136 KNREFGIDSVRFAELLMSSGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTR 195
           K+ E GI++  FAELLM+SG+VL + V W++FHS YDFGYL+K LT   LPE+  +F   
Sbjct: 115 KHEEEGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEI 174

Query: 196 VGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIK 255
           + +FF   +YDVK+L++ C  L GGL  V + L +ER +G  HQAGSDSLLT  AF K++
Sbjct: 175 LRLFFP-VIYDVKYLMKSCKNLKGGLQEVAEQLELER-IGPQHQAGSDSLLTGMAFFKMR 232

Query: 256 DKHFGNEYELQKYANVLHGL 275
           +  F +  +  KY   L+GL
Sbjct: 233 EMFFEDHIDDAKYCGHLYGL 252
>d1uoca_ c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 286 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query280
d1uoca_286 Pop2 RNase D domain {Baker's yeast (Saccharomyces 100.0
d2d5ra1252 CCR4-NOT transcription complex subunit 7, CAF1 {Hu 100.0
d2guia1174 N-terminal exonuclease domain of the epsilon subun 98.73
d1w0ha_200 Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960 98.6
d1y97a1228 Three prime repair exonuclease 2, TREX2 {Human (Ho 98.43
d2f96a1202 Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287 98.42
d2qxfa1 467 Exonuclease I {Escherichia coli K12 (Escherichia c 98.21
d3b6oa1226 Three prime repair exonuclease 1, TREX1 {Mouse (Mu 98.15
d1wlja_173 Interferon-stimulated gene 20 kDa protein, ISG20 { 97.93
d1yt3a3193 Ribonuclease D, catalytic domain {Escherichia coli 96.97
d2hbka2292 Exosome complex exonuclease RRP6 {Baker's yeast (S 96.74
d1kfsa1195 Exonuclease domain of prokaryotic DNA polymerase { 95.82
d2igia1180 Oligoribonuclease {Escherichia coli [TaxId: 562]} 93.58
>d1uoca_ c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: CAF1-like ribonuclease
domain: Pop2 RNase D domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.7e-87  Score=617.45  Aligned_cols=266  Identities=36%  Similarity=0.662  Sum_probs=240.0

Q ss_pred             CCCCCCCCCceEEecCccCHHHHHHHHHHHhhhCCeeEeeeccccccccCCCCCCCCChhhhHHHHHhccccccceeeee
Q 023614            5 PPPQPPKPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGL   84 (280)
Q Consensus         5 ~~~~~~~~~~~i~eVw~~Nl~~e~~~I~~~i~~~~fIAiDtEFpGv~~~~~~~~~~~~~e~rY~~lk~nVd~~~iiQlGl   84 (280)
                      |.-.|++..+.|||||++||++||+.|+++|++|+||||||||||++++|.+.+++++ ++||+++|+|||.+++||+||
T Consensus         2 ~~~~p~~~~~~i~dVw~~N~~~e~~~i~~~i~~~~fvaiD~EF~Gi~~~~~~~~~~t~-d~~Y~~lr~nvd~~~iiQlGl   80 (286)
T d1uoca_           2 PIFLPPPNYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSKV-DYHYQTMRANVDFLNPIQLGL   80 (286)
T ss_dssp             CCCCCCGGGGCCEEECTTTHHHHHHHHHHHTTTSCEEEEEEEEEC----------CHH-HHHHHHHHHHHTTCEEEEEEE
T ss_pred             CCcCCCCCeEEEEEchhhhHHHHHHHHHHHHhcCCEEEEeeeecCcccCCCCCCCCCH-HHHHHHHHHhHhhcceeEEee
Confidence            4344667779999999999999999999999999999999999999999988887776 999999999999999999999


Q ss_pred             eeccCCCCCCCCCCCCCceEEEEeccccCcCcCCCchhHHHHHHHcCCCchhhhhcCCChHHHHHHHHHcccccCCCceE
Q 023614           85 TLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGIDFEKNREFGIDSVRFAELLMSSGLVLNKDVTW  164 (280)
Q Consensus        85 t~~~~~g~~p~~~~~~~~~~wqFNF~~F~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~e~l~~Sglv~~~~v~W  164 (280)
                      |+|+++|+.|..    .+++|||||+ |+..+|+|+++||+||+++||||||++++|||+.+|+|+|.+||++++++++|
T Consensus        81 t~f~~~g~~~~~----~~~~w~FNF~-f~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~F~~ll~~s~l~~~~~~~w  155 (286)
T d1uoca_          81 SLSDANGNKPDN----GPSTWQFNFE-FDPKKEIMSTESLELLRKSGINFEKHENLGIDVFEFSQLLMDSGLMMDDSVTW  155 (286)
T ss_dssp             EEECTTCCCCSS----SCSEEEEEBC-CCTTCCCCCHHHHHHHHHTTCCHHHHHHHCBCHHHHHHHHHTSSCSSCTTSEE
T ss_pred             eeecccCCCCCC----CceEEEEEEE-ecCccccccHHHHHHHHHcCCChHHHHHcCCCHHHHHHHHHhccccccCCcce
Confidence            999999998853    4789999999 99999999999999999999999999999999999999999999999999999


Q ss_pred             EEeccchhHHHHHHHhhCCCCCCCHHHHHHHHhhhcCCCccchHHHHHhhcccc---------------chHHHHHHHcC
Q 023614          165 VTFHSAYDFGYLVKCLTQRVLPEKLSEFVTRVGVFFGEKVYDVKHLIRFCTCLY---------------GGLDRVCKALG  229 (280)
Q Consensus       165 vtfhg~yD~gyL~k~l~~~~LP~~~~~F~~~l~~~Fp~~iyD~K~la~~~~~l~---------------~~L~~la~~L~  229 (280)
                      |+|||+||||||+|+|+|+|||+++++|+++++.+||. +||||||++.+.+++               .||++||+.|+
T Consensus       156 i~fhg~yD~~yl~k~l~~~~LP~~~~eF~~~v~~~FP~-iyDtK~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~ia~~l~  234 (286)
T d1uoca_         156 ITYHAAYDLGFLINILMNDSMPNNKEDFEWWVHQYMPN-FYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELG  234 (286)
T ss_dssp             EESSTTHHHHHHHHHHTTSCCCSSHHHHHHHHHHHCSS-EEEHHHHHHHHTTTCC-------------CCSHHHHHHHTT
T ss_pred             EEecchHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCCc-ceeHHHHHHHhhccccccccchhhhhccccCCHHHHHHhcC
Confidence            99999999999999999999999999999999999998 999999999886543               48999999999


Q ss_pred             CCccCCCccchhhhHHHHHHHHHHHHHhhC---CCccccccccceEecCCCC
Q 023614          230 VERVVGKSHQAGSDSLLTLHAFLKIKDKHF---GNEYELQKYANVLHGLELL  278 (280)
Q Consensus       230 v~r~~g~~hqAGsDs~lT~~~F~~l~~~~~---~~~~~~~~~~g~i~Gl~~~  278 (280)
                      ++| +|++||||||||||++||++|++.+.   .+.++.++|.|+||||+.+
T Consensus       235 v~~-~g~~HeAG~DSllT~~~F~~l~~~~~~~f~~~~~~~~~~g~l~Gl~~~  285 (286)
T d1uoca_         235 LPR-FSIFTTTGGQSLLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGIDGD  285 (286)
T ss_dssp             CCC-CGGGGSHHHHHHHHHHHHHHHHHHTTTBCTTSCBGGGGTTCSSCCTTC
T ss_pred             CCc-cCCCcchHHHHHHHHHHHHHHHHHHHhhccCCccHHHhCCEEeCCCCC
Confidence            999 99999999999999999999998654   3456789999999999875
>d2d5ra1 c.55.3.9 (A:11-262) CCR4-NOT transcription complex subunit 7, CAF1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2guia1 c.55.3.5 (A:7-180) N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1w0ha_ c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1y97a1 c.55.3.5 (A:1-228) Three prime repair exonuclease 2, TREX2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2f96a1 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d2qxfa1 c.55.3.5 (A:8-474) Exonuclease I {Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333]} Back     information, alignment and structure
>d3b6oa1 c.55.3.5 (A:9-234) Three prime repair exonuclease 1, TREX1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1wlja_ c.55.3.5 (A:) Interferon-stimulated gene 20 kDa protein, ISG20 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1yt3a3 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2hbka2 c.55.3.5 (A:129-420) Exosome complex exonuclease RRP6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1kfsa1 c.55.3.5 (A:324-518) Exonuclease domain of prokaryotic DNA polymerase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2igia1 c.55.3.5 (A:1-180) Oligoribonuclease {Escherichia coli [TaxId: 562]} Back     information, alignment and structure