Citrus Sinensis ID: 022773

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290--
MGVEDFSTDLDSNSNSSSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDIATDAHAPDSIELLRLQGIDFERNRKEGVDSVRFAELMMSSGLVCNESVSWVTFHSAYDFGYLVKILTRRSLPSGLDEFLTVLRVFFGNNIYDVKHIMRFCQSLYGGLDRVARTLDVSRAVGKCHQAGSDSLLTWHAFQKIRDVYFVHDGPEKHAGVLYGLEVY
ccccccccccccccccccccccEEEEcccccHHHHHHHHHHHHHcccEEEEEcEEccccccccccccccccccccccHHHHHHHHHccccccEEEEEEEEEccccccccccccccccEEEEEcccccccccccccHHHHHHHHHccccHHHHHHccccHHHHHHHHHHHcccccccccEEEEccccHHHHHHHHHHcccccccHHHHHHHHHHHccccEEHHHHHHHHHHcccccHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHcccccccccccEEEccccc
cccEEcccccccccccccccccEHHHHHHHHHHHHHHHHHHHHHHccEEEEccccccEEEEEccccccccccccccccHHHHHHHHHHHHHHHHHHcEEEEccccccccccccccccEEEEEEccccccHHHcccHHHHHHHHHccccHHHHHHccccHHHHHHHHHHccEEEcccEEEEEEcccHHHHHHHHHHccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHcHHHHHHHHccccEEEcHccccccHHHHHHHHHHHHHHHHHccccHHHHccEEEEcccc
mgvedfstdldsnsnssssnsIIIREVWASNLESEFELISQVidrypfismdtefpglvyrpdvdpstrpyfrqrkpsdhykvlKSNVDALNLIQVGLtlsdssgnlpdlgsggnnkfiwefnfrdfdiatdahapdSIELLRLQgidfernrkegvdSVRFAELMMSsglvcnesvswvtfhsaYDFGYLVKILtrrslpsgldEFLTVLRVFFGNNIYDVKHIMRFCQSLYGGLDRVARTLDVSRAvgkchqagsdslLTWHAFQKIRdvyfvhdgpekhagvlyglevy
mgvedfstdldsnsnssssnsiIIREVWASNLESEFELISQVIDRYPFISMDtefpglvyrpdvdpstrpyfrqrkpsdhykVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDIATDAHAPDSIELLrlqgidfernrKEGVDSVRFAELMMSSGLVCNESVSWVTFHSAYDFGYLVKILTRRSLPSGLDEFLTVLRVFFGNNIYDVKHIMRFCQSLYGGLDRVARTLDVSRAVGKCHQAGSDSLLTWHAFQKIRDVYFVHDGPEKhagvlyglevy
MGVEDFSTDLDsnsnssssnsiiiREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDIATDAHAPDSIELLRLQGIDFERNRKEGVDSVRFAELMMSSGLVCNESVSWVTFHSAYDFGYLVKILTRRSLPSGLDEFLTVLRVFFGNNIYDVKHIMRFCQSLYGGLDRVARTLDVSRAVGKCHQAGSDSLLTWHAFQKIRDVYFVHDGPEKHAGVLYGLEVY
*********************IIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDV***************HYKVLKSNVDALNLIQVGLTLSD******DLGSGGNNKFIWEFNFRDFDIATDAHAPDSIELLRLQGIDFERNRKEGVDSVRFAELMMSSGLVCNESVSWVTFHSAYDFGYLVKILTRRSLPSGLDEFLTVLRVFFGNNIYDVKHIMRFCQSLYGGLDRVARTLDVSRAVGKCHQAGSDSLLTWHAFQKIRDVYFVHDGPEKHAGVLYGL***
************************REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDIATDAHAPDSIELLRLQGIDFERNRKEGVDSVRFAELMMSSGLVCNESVSWVTFHSAYDFGYLVKILTRRSLPSGLDEFLTVLRVFFGNNIYDVKHIMRFCQSLYGGLDRVARTLDVSRAVGKCHQAGSDSLLTWHAFQKIRDVYFVHDGPEKHAGVLYGLEVY
*******************NSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDIATDAHAPDSIELLRLQGIDFERNRKEGVDSVRFAELMMSSGLVCNESVSWVTFHSAYDFGYLVKILTRRSLPSGLDEFLTVLRVFFGNNIYDVKHIMRFCQSLYGGLDRVARTLDVSRAVGKCHQAGSDSLLTWHAFQKIRDVYFVHDGPEKHAGVLYGLEVY
*******************NSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDIATDAHAPDSIELLRLQGIDFERNRKEGVDSVRFAELMMSSGLVCNESVSWVTFHSAYDFGYLVKILTRRSLPSGLDEFLTVLRVFFGNNIYDVKHIMRFCQSLYGGLDRVARTLDVSRAVGKCHQAGSDSLLTWHAFQKIRDVYFVHDGPEKHAGVLYGLEVY
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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MGVEDFSTDLDSNSNSSSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDIATDAHAPDSIELLRLQGIDFERNRKEGVDSVRFAELMMSSGLVCNESVSWVTFHSAYDFGYLVKILTRRSLPSGLDEFLTVLRVFFGNNIYDVKHIMRFCQSLYGGLDRVARTLDVSRAVGKCHQAGSDSLLTWHAFQKIRDVYFVHDGPEKHAGVLYGLEVY
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 ?
Query292 2.2.26 [Sep-21-2011]
Q9FMS6278 Probable CCR4-associated yes no 0.941 0.989 0.722 1e-118
Q9LXM2280 Probable CCR4-associated no no 0.904 0.942 0.732 1e-116
Q9SKZ2275 Probable CCR4-associated no no 0.890 0.945 0.549 4e-79
Q9LEU4277 Probable CCR4-associated no no 0.907 0.956 0.526 8e-77
Q9SAI2274 Probable CCR4-associated no no 0.883 0.941 0.525 4e-75
Q9S9P2286 Probable CCR4-associated no no 0.890 0.909 0.492 2e-69
Q9UIV1285 CCR4-NOT transcription co yes no 0.852 0.873 0.470 2e-60
Q5ZJV9285 CCR4-NOT transcription co no no 0.852 0.873 0.470 2e-60
Q60809285 CCR4-NOT transcription co yes no 0.852 0.873 0.470 2e-60
Q3ZC01285 CCR4-NOT transcription co yes no 0.852 0.873 0.470 2e-60
>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 =  423 bits (1088), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 203/281 (72%), Positives = 236/281 (83%), Gaps = 6/281 (2%)

Query: 13  NSNSSSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYF 72
            S +  S+ I+IR+VWA NLESEF+LI  +++ YPFISMDTEFPG++Y+ D+D       
Sbjct: 3   KSEADLSDVIVIRDVWAYNLESEFDLIRGIVEDYPFISMDTEFPGVIYKADLD-----VL 57

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

Query: 133 AHAPDSIELLRLQGIDFERNRKEGVDSVRFAELMMSSGLVCNESVSWVTFHSAYDFGYLV 192
            HAPDSIELLR  GIDFERNR+EGV+S RFAELMMSSGL+CNESVSWVTFHSAYDFGYLV
Sbjct: 118 PHAPDSIELLRRHGIDFERNRREGVESERFAELMMSSGLICNESVSWVTFHSAYDFGYLV 177

Query: 193 KILTRRSLPSGLDEFLTVLRVFFGNNIYDVKHIMRFC-QSLYGGLDRVARTLDVSRAVGK 251
           KILTRR LP  L EFL +LR FFG+ +YDVKHIMRFC Q LYGGLDRVAR+L+V+RAVGK
Sbjct: 178 KILTRRQLPVALREFLGLLRAFFGDRVYDVKHIMRFCEQRLYGGLDRVARSLEVNRAVGK 237

Query: 252 CHQAGSDSLLTWHAFQKIRDVYFVHDGPEKHAGVLYGLEVY 292
           CHQAGSDSLLTW AFQ++RD+YFV DG EKHAGVLYGLEV+
Sbjct: 238 CHQAGSDSLLTWQAFQRMRDLYFVEDGAEKHAGVLYGLEVF 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|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|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|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|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|Q9UIV1|CNOT7_HUMAN CCR4-NOT transcription complex subunit 7 OS=Homo sapiens GN=CNOT7 PE=1 SV=3 Back     alignment and function description
>sp|Q5ZJV9|CNOT7_CHICK CCR4-NOT transcription complex subunit 7 OS=Gallus gallus GN=CNOT7 PE=2 SV=1 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
>sp|Q3ZC01|CNOT7_BOVIN CCR4-NOT transcription complex subunit 7 OS=Bos taurus GN=CNOT7 PE=2 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 ?
Query292
224131812277 predicted protein [Populus trichocarpa] 0.931 0.981 0.829 1e-132
225464848278 PREDICTED: probable CCR4-associated fact 0.948 0.996 0.787 1e-128
147839203265 hypothetical protein VITISV_015622 [Viti 0.907 1.0 0.811 1e-126
356543624309 PREDICTED: probable CCR4-associated fact 0.931 0.880 0.768 1e-123
255638796309 unknown [Glycine max] 0.931 0.880 0.761 1e-122
356542778278 PREDICTED: probable CCR4-associated fact 0.952 1.0 0.733 1e-120
255565745281 ccr4-associated factor, putative [Ricinu 0.928 0.964 0.742 1e-118
356539219284 PREDICTED: probable CCR4-associated fact 0.941 0.968 0.720 1e-116
15242180278 putative CCR4-associated factor 1-11 [Ar 0.941 0.989 0.722 1e-116
297818892280 hypothetical protein ARALYDRAFT_484842 [ 0.900 0.939 0.743 1e-116
>gi|224131812|ref|XP_002328114.1| predicted protein [Populus trichocarpa] gi|222837629|gb|EEE75994.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  478 bits (1230), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 228/275 (82%), Positives = 252/275 (91%), Gaps = 3/275 (1%)

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

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

Query: 138 SIELLRLQGIDFERNRKEGVDSVRFAELMMSSGLVCNESVSWVTFHSAYDFGYLVKILTR 197
           SIELLR QGIDFERNR+EGVDS RFAELMMSSGLVCNESVSWVTFHSAYDFGYLVKILTR
Sbjct: 122 SIELLRRQGIDFERNREEGVDSARFAELMMSSGLVCNESVSWVTFHSAYDFGYLVKILTR 181

Query: 198 RSLPSGLDEFLTVLRVFFGNNIYDVKHIMRFCQSLYGGLDRVARTLDVSRAVGKCHQAGS 257
           R LPSGL  FL++LRVFFGNNIYDVKH+MRFC+SLYGGLDRVARTL+V+R VGKCHQAGS
Sbjct: 182 RELPSGLVGFLSLLRVFFGNNIYDVKHMMRFCKSLYGGLDRVARTLEVNREVGKCHQAGS 241

Query: 258 DSLLTWHAFQKIRDVYFVHDGPEKHAGVLYGLEVY 292
           DSLLTWHAFQK+RDV+FV DGPE+HAGVLYGLEV+
Sbjct: 242 DSLLTWHAFQKMRDVFFVKDGPEQHAGVLYGLEVF 276

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225464848|ref|XP_002271636.1| PREDICTED: probable CCR4-associated factor 1 homolog 9-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|147839203|emb|CAN76920.1| hypothetical protein VITISV_015622 [Vitis vinifera] Back     alignment and taxonomy information
>gi|356543624|ref|XP_003540260.1| PREDICTED: probable CCR4-associated factor 1 homolog 11-like [Glycine max] Back     alignment and taxonomy information
>gi|255638796|gb|ACU19702.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|356542778|ref|XP_003539842.1| PREDICTED: probable CCR4-associated factor 1 homolog 9-like [Glycine max] Back     alignment and taxonomy information
>gi|255565745|ref|XP_002523862.1| ccr4-associated factor, putative [Ricinus communis] gi|223536950|gb|EEF38588.1| ccr4-associated factor, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|356539219|ref|XP_003538097.1| PREDICTED: probable CCR4-associated factor 1 homolog 11 [Glycine max] Back     alignment and taxonomy information
>gi|15242180|ref|NP_197617.1| putative CCR4-associated factor 1-11 [Arabidopsis thaliana] gi|75334084|sp|Q9FMS6.1|CAF1K_ARATH RecName: Full=Probable CCR4-associated factor 1 homolog 11 gi|9757805|dbj|BAB08323.1| CCR4-associated factor-like protein [Arabidopsis thaliana] gi|17381058|gb|AAL36341.1| putative CCR4-associated factor [Arabidopsis thaliana] gi|25054979|gb|AAN71961.1| putative CCR4-associated factor [Arabidopsis thaliana] gi|332005618|gb|AED93001.1| putative CCR4-associated factor 1-11 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297818892|ref|XP_002877329.1| hypothetical protein ARALYDRAFT_484842 [Arabidopsis lyrata subsp. lyrata] gi|297323167|gb|EFH53588.1| hypothetical protein ARALYDRAFT_484842 [Arabidopsis lyrata subsp. lyrata] 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 ?
Query292
TAIR|locus:2095715280 CAF1a "CCR4- associated factor 0.890 0.928 0.743 1.5e-106
TAIR|locus:2176307278 CAF1b "CCR4- associated factor 0.900 0.946 0.739 1.5e-106
TAIR|locus:2045512275 AT2G32070 [Arabidopsis thalian 0.873 0.927 0.548 2.2e-73
TAIR|locus:2183765277 AT5G10960 [Arabidopsis thalian 0.869 0.916 0.537 5.5e-70
TAIR|locus:2200532286 AT1G15920 [Arabidopsis thalian 0.886 0.905 0.494 8.5e-65
UNIPROTKB|Q5ZJV9285 CNOT7 "CCR4-NOT transcription 0.845 0.866 0.473 1.2e-56
UNIPROTKB|Q3ZC01285 CNOT7 "CCR4-NOT transcription 0.845 0.866 0.473 1.2e-56
UNIPROTKB|E2RMU2285 CNOT7 "Uncharacterized protein 0.845 0.866 0.473 1.2e-56
UNIPROTKB|Q9UIV1285 CNOT7 "CCR4-NOT transcription 0.845 0.866 0.473 1.2e-56
MGI|MGI:1298230285 Cnot7 "CCR4-NOT transcription 0.845 0.866 0.473 1.2e-56
TAIR|locus:2095715 CAF1a "CCR4- associated factor 1a" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1054 (376.1 bits), Expect = 1.5e-106, P = 1.5e-106
 Identities = 200/269 (74%), Positives = 229/269 (85%)

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

Query:    85 KSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDIATDAHAPDSIELLRL 144
             K+NVDAL+LIQVGLTLSD +GNLPDLG   +  FIWEFNFRDFD+A DAHAPDSIELLR 
Sbjct:    72 KANVDALSLIQVGLTLSDVNGNLPDLGDDLHRGFIWEFNFRDFDVARDAHAPDSIELLRR 131

Query:   145 QGIDFERNRKEGVDSVRFAELMMSSGLVCNESVSWVTFHSAYDFGYLVKILTRRSLPSGL 204
             QGIDFERN ++GV+S RFAELMMSSGLVCNE VSWVTFHSAYDFGYL+KILTRR LP  L
Sbjct:   132 QGIDFERNCRDGVESERFAELMMSSGLVCNEEVSWVTFHSAYDFGYLMKILTRRELPGAL 191

Query:   205 DEFLTVLRVFFGNNIYDVKHIMRFCQS-LYGGLDRVARTLDVSRAVGKCHQAGSDSLLTW 263
              EF  V+RV FG  +YDVKH+M+FC+  L+GGLDRVARTL+V+RAVGKCHQAGSDSLLTW
Sbjct:   192 GEFKRVMRVLFGERVYDVKHMMKFCERRLFGGLDRVARTLEVNRAVGKCHQAGSDSLLTW 251

Query:   264 HAFQKIRDVYFVHDGPEKHAGVLYGLEVY 292
             HAFQ++RD+YFV DGPEKHAGVLYGLEV+
Sbjct:   252 HAFQRMRDLYFVQDGPEKHAGVLYGLEVF 280
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)] Back     alignment and assigned GO terms
TAIR|locus:2045512 AT2G32070 [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:2200532 AT1G15920 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q5ZJV9 CNOT7 "CCR4-NOT transcription complex subunit 7" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|Q3ZC01 CNOT7 "CCR4-NOT transcription complex subunit 7" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2RMU2 CNOT7 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|Q9UIV1 CNOT7 "CCR4-NOT transcription complex subunit 7" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
MGI|MGI:1298230 Cnot7 "CCR4-NOT transcription complex, subunit 7" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q60809CNOT7_MOUSENo assigned EC number0.47010.85270.8736yesno
Q9LXM2CAF1I_ARATH3, ., 1, ., 1, 3, ., 40.73260.90410.9428nono
Q9FMS6CAF1K_ARATH3, ., 1, ., 1, 3, ., 40.72240.94170.9892yesno
Q3ZC01CNOT7_BOVINNo assigned EC number0.47010.85270.8736yesno
A4II96CNOT7_XENTRNo assigned EC number0.46640.85270.8736yesno
Q9UIV1CNOT7_HUMANNo assigned EC number0.47010.85270.8736yesno

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 ?Alignment Graph ?Length ? Definition ? E-value ?
Query292
pfam04857235 pfam04857, CAF1, CAF1 family ribonuclease 1e-101
COG5228299 COG5228, POP2, mRNA deadenylase subunit [RNA proce 7e-80
>gnl|CDD|147159 pfam04857, CAF1, CAF1 family ribonuclease Back     alignment and domain information 
 Score =  295 bits (757), Expect = e-101
 Identities = 123/249 (49%), Positives = 156/249 (62%), Gaps = 19/249 (7%)

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

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

Query: 145 QGIDFERNRKEGVDSVRFAELMMSSGLVCNE-SVSWVTFHSAYDFGYLVKILTRRSLPSG 203
           QG DF ++R+EG+  +RFAEL+ SSGL  N  SV+WVTFH  YDFGYL+K+LT   LP  
Sbjct: 108 QGFDFNKHRREGIPYLRFAELLGSSGLFLNISSVTWVTFHGLYDFGYLLKLLTGGPLPET 167

Query: 204 LDEFLTVLRVFFGNNIYDVKHIMRFCQSLYG----GLDRVARTLDVSRAVGKCHQAGSDS 259
           LD+FL +LR  F   +YD K++ +FC  L G    GL  +A  L V+R VG+ HQAGSDS
Sbjct: 168 LDDFLELLRELFP-RVYDTKYLAKFCFELDGGSNGGLQELADLLGVNRRVGRLHQAGSDS 226

Query: 260 LLTWHAFQK 268
           LLT   F K
Sbjct: 227 LLTALVFFK 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 292
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
KOG1990 564 consensus Poly(A)-specific exoribonuclease PARN [R 99.31
PRK07942232 DNA polymerase III subunit epsilon; Provisional 98.86
smart00479169 EXOIII exonuclease domain in DNA-polymerase alpha 98.82
cd06133176 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o 98.64
cd06134189 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. 98.61
PRK09145202 DNA polymerase III subunit epsilon; Validated 98.59
PRK05168211 ribonuclease T; Provisional 98.59
cd06131167 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl 98.49
PRK07748207 sporulation inhibitor KapD; Provisional 98.46
PRK06310250 DNA polymerase III subunit epsilon; Validated 98.34
PRK05711240 DNA polymerase III subunit epsilon; Provisional 98.33
cd06130156 DNA_pol_III_epsilon_like an uncharacterized bacter 98.28
PRK07740244 hypothetical protein; Provisional 98.27
PRK06063 313 DNA polymerase III subunit epsilon; Provisional 98.27
TIGR00573217 dnaq exonuclease, DNA polymerase III, epsilon subu 98.26
TIGR01298200 RNaseT ribonuclease T. in gamma-subdivision Proteo 98.22
PRK09146239 DNA polymerase III subunit epsilon; Validated 98.21
PRK06807 313 DNA polymerase III subunit epsilon; Validated 98.19
TIGR01406225 dnaQ_proteo DNA polymerase III, epsilon subunit, P 98.09
PRK07247195 DNA polymerase III subunit epsilon; Validated 98.09
PRK08074 928 bifunctional ATP-dependent DNA helicase/DNA polyme 98.02
cd06127159 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh 97.99
PRK08517257 DNA polymerase III subunit epsilon; Provisional 97.98
PRK06195 309 DNA polymerase III subunit epsilon; Validated 97.95
cd06136177 TREX1_2 DEDDh 3'-5' exonuclease domain of three pr 97.91
PRK07883 557 hypothetical protein; Validated 97.9
PRK06722281 exonuclease; Provisional 97.84
TIGR01405 1213 polC_Gram_pos DNA polymerase III, alpha chain, Gra 97.83
PF00929164 RNase_T: Exonuclease; InterPro: IPR013520 This ent 97.82
PRK07246 820 bifunctional ATP-dependent DNA helicase/DNA polyme 97.8
TIGR01407 850 dinG_rel DnaQ family exonuclease/DinG family helic 97.73
PRK07983219 exodeoxyribonuclease X; Provisional 97.67
cd06138183 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain o 97.67
PRK05601 377 DNA polymerase III subunit epsilon; Validated 97.6
PRK11779 476 sbcB exonuclease I; Provisional 97.58
PTZ00315 582 2'-phosphotransferase; Provisional 97.57
PRK06309232 DNA polymerase III subunit epsilon; Validated 97.54
PRK09182294 DNA polymerase III subunit epsilon; Validated 97.38
PRK00448 1437 polC DNA polymerase III PolC; Validated 97.24
COG0847243 DnaQ DNA polymerase III, epsilon subunit and relat 97.19
PRK05359181 oligoribonuclease; Provisional 97.15
cd06144152 REX4_like DEDDh 3'-5' exonuclease domain of RNA ex 97.1
cd06137161 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the 97.03
cd06145150 REX1_like DEDDh 3'-5' exonuclease domain of RNA ex 96.43
cd06135173 Orn DEDDh 3'-5' exonuclease domain of oligoribonuc 95.63
COG0349 361 Rnd Ribonuclease D [Translation, ribosomal structu 94.44
PRK10829 373 ribonuclease D; Provisional 93.42
cd06146193 mut-7_like_exo DEDDy 3'-5' exonuclease domain of C 93.06
cd06141170 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and 92.6
PRK05755 880 DNA polymerase I; Provisional 91.04
TIGR01388 367 rnd ribonuclease D. This model describes ribonucle 90.21
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification] Back     alignment and domain information 
Probab=100.00  E-value=3.4e-86  Score=582.27  Aligned_cols=237  Identities=57%  Similarity=0.975  Sum_probs=230.0

Q ss_pred             EEEEeCccCHHHHHHHHHHHhhcCCceeccccccccccCCCCCCCCCCCCCCCCchHHHHHHHhhhccccceeeeeeeec
Q 022773           23 IIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSD  102 (292)
Q Consensus        23 ~v~eV~~~Nf~eel~~I~~~i~~~~fIAiDtEF~G~~~~~~~~~~~~~~~~~~t~e~rY~~lk~nvd~~~iiQlGLt~~~  102 (292)
                      .|||||+.|+++||++||++|++||||||||||||++.+|.+.+       +++.+++|+.||+|||.+++||+|||+++
T Consensus         1 ~ireVW~~Nl~~Em~~Ir~~v~~y~~IamDTEFPGvv~rp~~~f-------~s~~d~~Y~~lk~NVd~lklIQlGlTlsd   73 (239)
T KOG0304|consen    1 FIREVWRSNLEEEMALIRECVKDYPYIAMDTEFPGVVARPIGTF-------RSSDDYHYQTLKCNVDNLKLIQLGLTLSD   73 (239)
T ss_pred             ChhHHHHHhHHHHHHHHHHHHHhCCeeEecCcCCceeeecCccc-------cCChHHHHHHHHhchhhhhhhheeeeeec
Confidence            37999999999999999999999999999999999999999988       68999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCCCeeEEEEeecccCCCCCCCChhHHHHHHHcCCChhhhhhcCCChHHHHHHHHHcCccccCCcceEEe
Q 022773          103 SSGNLPDLGSGGNNKFIWEFNFRDFDIATDAHAPDSIELLRLQGIDFERNRKEGVDSVRFAELMMSSGLVCNESVSWVTF  182 (292)
Q Consensus       103 ~~g~~p~~g~~~~~~~~w~FNF~~F~~~~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wv~f  182 (292)
                      ++||.|..|+     .+|||||.+|++.+|+++++||+||+++|+||.|+.+.||+...|+|+|++||++++++++||||
T Consensus        74 ~~Gn~p~~g~-----~tWqfNF~dF~~~~D~~a~~SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTF  148 (239)
T KOG0304|consen   74 EKGNLPDCGT-----DTWQFNFSDFNLEKDMYAQDSIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTF  148 (239)
T ss_pred             cCCCCCCCCC-----ceeEEecccCCchhhccchhhHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEe
Confidence            9999997654     59999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eCchhHHHHHHHhCCCCCCCCHHHHHHHHHhhcCCcccchHHHHHhhhh--ccchHHHHHHHcCCCCCCCCCccchhhHH
Q 022773          183 HSAYDFGYLVKILTRRSLPSGLDEFLTVLRVFFGNNIYDVKHIMRFCQS--LYGGLDRVARTLDVSRAVGKCHQAGSDSL  260 (292)
Q Consensus       183 hg~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~F~P~iyDtK~la~~~~~--l~~~L~~la~~L~v~r~~g~~HqAGsDS~  260 (292)
                      |||||||||+|+||+++||++.++|.+.++.+| |.+||+|||++.|.+  +++||++||+.|+++| +|++|||||||+
T Consensus       149 hs~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~f-p~vYDiK~l~~~c~~~~l~~GL~~lA~~L~~~R-vG~~HqAGSDSl  226 (239)
T KOG0304|consen  149 HSGYDFGYLLKILTGKPLPETEEEFFEIVRQLF-PFVYDVKYLMKFCEGLSLKGGLQRLADLLGLKR-VGIAHQAGSDSL  226 (239)
T ss_pred             eccchHHHHHHHHcCCCCcchHHHHHHHHHHHc-chhhhHHHHHHhhhhhhhhcCHHHHHHHhCCCe-eecccccCcHHH
Confidence            999999999999999999999999999999999 999999999999965  8999999999999999 999999999999


Q ss_pred             HHHHHHHHHHHHh
Q 022773          261 LTWHAFQKIRDVY  273 (292)
Q Consensus       261 lT~~~F~~l~~~~  273 (292)
                      ||+++|+||++.|
T Consensus       227 LT~~~F~kl~~~f  239 (239)
T KOG0304|consen  227 LTARVFFKLKELF  239 (239)
T ss_pred             HHHHHHHHHHhcC
Confidence            9999999999864

>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
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair] 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
>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
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T Back     alignment and domain information
>PRK09145 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK05168 ribonuclease T; Provisional Back     alignment and domain information
>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
>PRK07748 sporulation inhibitor KapD; Provisional Back     alignment and domain information
>PRK06310 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK05711 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III Back     alignment and domain information
>PRK07740 hypothetical protein; Provisional Back     alignment and domain information
>PRK06063 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
>TIGR01298 RNaseT ribonuclease T 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
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial Back     alignment and domain information
>PRK07247 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family Back     alignment and domain information
>PRK08517 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK06195 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
>PRK07883 hypothetical protein; Validated Back     alignment and domain information
>PRK06722 exonuclease; Provisional Back     alignment and domain information
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type 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
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative Back     alignment and domain information
>PRK07983 exodeoxyribonuclease X; 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
>PRK05601 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK11779 sbcB exonuclease I; Provisional Back     alignment and domain information
>PTZ00315 2'-phosphotransferase; Provisional Back     alignment and domain information
>PRK06309 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK09182 DNA polymerase III subunit epsilon; Validated 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
>PRK05359 oligoribonuclease; Provisional 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
>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
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins Back     alignment and domain information
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK10829 ribonuclease D; Provisional 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
>TIGR01388 rnd ribonuclease D 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 ?
Query292
4gmj_B285 Structure Of Human Not1 Mif4g Domain Co-Crystallize 7e-61
2d5r_A252 Crystal Structure Of A Tob-Hcaf1 Complex Length = 2 1e-60
2p51_A333 Crystal Structure Of The S. Pombe Pop2p Deadenylati 8e-58
4b8a_B286 Structure Of Yeast Not1 Mif4g Domain Co-Crystallize 8e-39
4b8c_A288 Nuclease Module Of The Yeast Ccr4-Not Complex Lengt 9e-39
1uoc_A289 X-Ray Structure Of The Rnase Domain Of The Yeast Po 1e-38
>pdb|4GMJ|B Chain B, Structure Of Human Not1 Mif4g Domain Co-Crystallized With Caf1 Length = 285 Back     alignment and structure 
Iteration: 1

 Score =  230 bits (587), Expect = 7e-61,   Method: Compositional matrix adjust.
 Identities = 125/266 (46%), Positives = 175/266 (65%), Gaps = 19/266 (7%)
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  KSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDIATDAHAPDSIELLRL 144
           + NVD L +IQ+GLT  +  G  P   S       W+FNF+ F++  D +A DSIELL  
Sbjct: 66  RCNVDLLKIIQLGLTFMNEQGEYPPGTS------TWQFNFK-FNLTEDMYAQDSIELLTT 118
Query: 145 QGIDFERNRKEGVDSVRFAELMMSSGLVCNESVSWVTFHSAYDFGYLVKILTRRSLPSGL 204
            GI F+++ +EG+++  FAEL+M+SG+V  E V W++FHS YDFGYL+KILT  +LP   
Sbjct: 119 SGIQFKKHEEEGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEE 178
Query: 205 DEFLTVLRVFFGNNIYDVKHIMRFCQSLYGGLDRVARTLDVSRAVGKCHQAGSDSLLTWH 264
            +F  +LR+FF   IYDVK++M+ C++L GGL  VA  L++ R +G  HQAGSDSLLT  
Sbjct: 179 LDFFEILRLFF-PVIYDVKYLMKSCKNLKGGLQEVAEQLELER-IGPQHQAGSDSLLTGM 236
Query: 265 AFQKIRDVYFV-HDGPEKHAGVLYGL 289
           AF K+R+++F  H    K+ G LYGL
Sbjct: 237 AFFKMREMFFEDHIDDAKYCGHLYGL 262
>pdb|2D5R|A Chain A, Crystal Structure Of A Tob-Hcaf1 Complex Length = 252 Back     alignment and structure
>pdb|2P51|A Chain A, Crystal Structure Of The S. Pombe Pop2p Deadenylation Subunit Length = 333 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|4B8C|A Chain A, Nuclease Module Of The Yeast Ccr4-Not Complex Length = 288 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 ?
Query292
2p51_A333 SPCC18.06C protein; DEDD nuclease fold, hydrolase, 1e-106
1uoc_A289 POP2; hydrolase, DEDD nuclease, mRNA degradation, 1e-103
2d5r_A252 CCR4-NOT transcription complex subunit 7; poly(A) 1e-100
2a1r_A 430 Poly(A)-specific ribonuclease PARN; DEDD, nuclease 2e-31
2a1r_A430 Poly(A)-specific ribonuclease PARN; DEDD, nuclease 2e-08
3d45_A 507 Poly(A)-specific ribonuclease PARN; CAP analogue, 2e-28
3d45_A507 Poly(A)-specific ribonuclease PARN; CAP analogue, 1e-05
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-07
>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 =  311 bits (798), Expect = e-106
 Identities = 118/276 (42%), Positives = 168/276 (60%), Gaps = 16/276 (5%)

Query: 14  SNSSSSNSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFR 73
            +  SS    IR+VW++NL+ E  LI  +I+RYP +SMDTEFPG+V RP           
Sbjct: 13  VDGISSQISPIRDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVARPLGV-------F 65

Query: 74  QRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFDIATDA 133
           +     HY+ L++NVD+L +IQ+GL LSD  GN P           W+FNF  F++  D 
Sbjct: 66  KSSDDYHYQTLRANVDSLKIIQIGLALSDEEGNAPV------EACTWQFNFT-FNLQDDM 118

Query: 134 HAPDSIELLRLQGIDFERNRKEGVDSVRFAELMMSSGLVCNESVSWVTFHSAYDFGYLVK 193
           +AP+SIELL   GIDF+++++ G++   FAEL++ SGLV  E V+W+TFHS YDF YL+K
Sbjct: 119 YAPESIELLTKSGIDFKKHQEVGIEPADFAELLIGSGLVLQEEVTWITFHSGYDFAYLLK 178

Query: 194 ILTRRSLPSGLDEFLTVLRVFFGNNIYDVKHIMRFCQSLYGGLDRVARTLDVSRAVGKCH 253
            +T+  LP+  +EF  +L ++F    YD+K+IM+   +   GL  +A  L + R +G  H
Sbjct: 179 AMTQIPLPAEYEEFYKILCIYFP-KNYDIKYIMKSVLNNSKGLQDIADDLQIHR-IGPQH 236

Query: 254 QAGSDSLLTWHAFQKIRDVYFVHDGPEKHAGVLYGL 289
           QAGSD+LLT   F +IR  YF      +    LYGL
Sbjct: 237 QAGSDALLTARIFFEIRSRYFDGSIDSRMLNQLYGL 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
>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
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query292
4gmj_B285 CCR4-NOT transcription complex subunit 7; mRNA dec 100.0
1uoc_A289 POP2; hydrolase, DEDD nuclease, mRNA degradation, 100.0
2d5r_A252 CCR4-NOT transcription complex subunit 7; poly(A) 100.0
2p51_A333 SPCC18.06C protein; DEDD nuclease fold, hydrolase, 100.0
3d45_A507 Poly(A)-specific ribonuclease PARN; CAP analogue, 100.0
2a1r_A430 Poly(A)-specific ribonuclease PARN; DEDD, nuclease 100.0
1w0h_A204 3'-5' exonuclease ERI1; nuclease domain, hydrolase 98.78
3v9w_A235 Ribonuclease T; DEDD nucleases family, EXO-nucleas 98.71
1zbh_A299 3'-5' exonuclease ERI1; histone mRNA 3'-END-specif 98.58
2f96_A224 Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas 98.56
2xri_A224 ERI1 exoribonuclease 3; hydrolase, metal binding; 98.47
1zbu_A349 ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; 98.42
2gui_A194 DNA polymerase III epsilon subunit; DNA polymerase 98.4
2p1j_A186 POLIII, DNA polymerase III POLC-type; structural g 98.36
3mxm_B242 Three prime repair exonuclease 1; RNAse H-like fol 98.33
3cg7_A308 CRN-4, cell death-related nuclease 4; hydrolase, a 98.3
1y97_A238 Three prime repair exonuclease 2; TREX2, hydrolase 98.22
2qxf_A 482 Exodeoxyribonuclease I; alpha-beta domain, DNAQ su 98.16
1wlj_A189 Interferon stimulated gene 20KDA; exoribonuclease, 97.98
2igi_A180 Oligoribonuclease; RNAse, exoribonuclease, exonucl 97.97
3u3y_B314 Three prime repair exonuclease 1; RNAse H fold, 3' 97.93
2gbz_A194 Oligoribonuclease; ORN, deddh, structural genomics 97.62
3tr8_A186 Oligoribonuclease; transcription, hydrolase; 2.50A 97.51
2kfn_A 605 Klenow fragment of DNA polymerase I; complex (poly 95.16
>4gmj_B CCR4-NOT transcription complex subunit 7; mRNA decay, deadenylase, RNA bindin; HET: GOL; 2.70A {Homo sapiens} Back     alignment and structure
Probab=100.00  E-value=1e-88  Score=631.27  Aligned_cols=256  Identities=48%  Similarity=0.846  Sum_probs=246.2

Q ss_pred             CCcEEEEeCccCHHHHHHHHHHHhhcCCceeccccccccccCCCCCCCCCCCCCCCCchHHHHHHHhhhccccceeeeee
Q 022773           20 NSIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLT   99 (292)
Q Consensus        20 ~~~~v~eV~~~Nf~eel~~I~~~i~~~~fIAiDtEF~G~~~~~~~~~~~~~~~~~~t~e~rY~~lk~nvd~~~iiQlGLt   99 (292)
                      .+.+|||||++||++||+.|+++|++|+||||||||||++++|.+.+       .+++|+||+++|+|||.+++||+|||
T Consensus         8 ~~~~IreVw~~Nl~ee~~~I~~~i~~~~fVAiDtEFpGvv~rp~~~~-------~~t~d~~Y~~lr~nvd~l~iIQlGLt   80 (285)
T 4gmj_B            8 HSQRICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEF-------RSNADYQYQLLRCNVDLLKIIQLGLT   80 (285)
T ss_dssp             --CCEEEECHHHHHHHHHHHHHHHHHCCEEEEEEECCCCCCCCTTCC-------TTSTTHHHHHHHHHHTTSCCCEEEEE
T ss_pred             CCCeEEEechhHHHHHHHHHHHHHhcCCEEEEEEEecCccCCCCCcc-------CCCHHHHHHHHHHHHHhhcceeEEEE
Confidence            45679999999999999999999999999999999999999998887       88999999999999999999999999


Q ss_pred             eecCCCCCCCCCCCCCCeeEEEEeecccCCCCCCCChhHHHHHHHcCCChhhhhhcCCChHHHHHHHHHcCccccCCcce
Q 022773          100 LSDSSGNLPDLGSGGNNKFIWEFNFRDFDIATDAHAPDSIELLRLQGIDFERNRKEGVDSVRFAELMMSSGLVCNESVSW  179 (292)
Q Consensus       100 ~~~~~g~~p~~g~~~~~~~~w~FNF~~F~~~~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~w  179 (292)
                      +|+++|+.|.      .+++|||||+ |++.+|+|+++||+||++|||||||+.++|||+..|+|++++||++++++++|
T Consensus        81 ~f~~~g~~p~------~~~~wqFNF~-f~~~~d~~~~~SI~fL~~~G~DF~k~~~~GI~~~~f~ell~~sglvl~~~v~W  153 (285)
T 4gmj_B           81 FMNEQGEYPP------GTSTWQFNFK-FNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELLMTSGVVLCEGVKW  153 (285)
T ss_dssp             EECTTSCCCS------SCCEEEEEBC-CCTTTSCCCHHHHHHHHHHTCCHHHHHHHCBCHHHHHHHHHTSSSSSCTTCEE
T ss_pred             eeccCCCcCC------CeeEEEEEEE-eccccccccHHHHHHHHHcCCCHHHHHHcCCCHHHHHHHHHHhHHHhcCCCce
Confidence            9999999884      5789999999 99999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeCchhHHHHHHHhCCCCCCCCHHHHHHHHHhhcCCcccchHHHHHhhhhccchHHHHHHHcCCCCCCCCCccchhhH
Q 022773          180 VTFHSAYDFGYLVKILTRRSLPSGLDEFLTVLRVFFGNNIYDVKHIMRFCQSLYGGLDRVARTLDVSRAVGKCHQAGSDS  259 (292)
Q Consensus       180 v~fhg~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~F~P~iyDtK~la~~~~~l~~~L~~la~~L~v~r~~g~~HqAGsDS  259 (292)
                      |+|||+|||+||+|+|+|++||+++.+|+++++.+| |.|||||||++.|.++++||++||+.|+|+| +|++|||||||
T Consensus       154 vtfH~~yDf~yL~k~lt~~~LP~~~~eF~~~l~~~F-P~vYD~K~l~~~~~~l~ggL~~lA~~L~v~r-~g~~HqAGsDS  231 (285)
T 4gmj_B          154 LSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFF-PVIYDVKYLMKSCKNLKGGLQEVAEQLELER-IGPQHQAGSDS  231 (285)
T ss_dssp             EESSCHHHHHHHHHHHHTSCCCSSHHHHHHHHHHHC-SCEEEHHHHGGGSTTCCSCHHHHHHHTTCCC-CSCTTSHHHHH
T ss_pred             EEecchhhHHHHHHHHhCCCCCCCHHHHHHHHHHHC-chhhhHHHHHHhccccCChHHHHHHhCCCCC-CCCCCcchhHH
Confidence            999999999999999999999999999999999999 9999999999999999999999999999999 99999999999


Q ss_pred             HHHHHHHHHHHHHhcCCCC-CccccceEeccCC
Q 022773          260 LLTWHAFQKIRDVYFVHDG-PEKHAGVLYGLEV  291 (292)
Q Consensus       260 ~lT~~~F~~l~~~~~~~~~-~~~~~g~i~Gl~~  291 (292)
                      |||++||++|+++||++.+ .++|+|+|||||+
T Consensus       232 llT~~~F~kl~~~~f~~~~~~~~~~g~l~Glg~  264 (285)
T 4gmj_B          232 LLTGMAFFKMREMFFEDHIDDAKYCGHLYGLGS  264 (285)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCHHHHTTCCTTSST
T ss_pred             HHHHHHHHHHHHHHhcCCcchHHhCCEEeccCC
Confidence            9999999999999998654 5689999999985
>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
>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
>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A 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
>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5 Back     alignment and structure
>3v9w_A Ribonuclease T; DEDD nucleases family, EXO-nucleases, hydrolase-DNA complex; HET: DNA; 1.70A {Escherichia coli} PDB: 3ngy_A 3v9u_A* 3ngz_A* 3va3_A* 3v9z_A* 3nh0_A 3nh2_A 3nh1_A* 3v9s_A* 3v9x_A* 3va0_A* 2is3_A Back     alignment and structure
>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
>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
>2xri_A ERI1 exoribonuclease 3; hydrolase, metal binding; 2.15A {Homo sapiens} Back     alignment and structure
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; 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
>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
>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
>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
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5 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
>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
>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
>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

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 292
d1uoca_286 c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast ( 1e-103
d2d5ra1252 c.55.3.9 (A:11-262) CCR4-NOT transcription complex 1e-103
>d1uoca_ c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 286 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]

 Score =  301 bits (773), Expect = e-103
 Identities = 96/291 (32%), Positives = 156/291 (53%), Gaps = 34/291 (11%)

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

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

Query: 139 IELLRLQGIDFERNRKEGVDSVRFAELMMSSGLVCNESVSWVTFHSAYDFGYLVKILTRR 198
           +ELLR  GI+FE++   G+D   F++L+M SGL+ ++SV+W+T+H+AYD G+L+ IL   
Sbjct: 115 LELLRKSGINFEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMND 174

Query: 199 SLPSGLDEFLTVLRVFFGNNIYDVKHIMRFCQSLYG---------------GLDRVARTL 243
           S+P+  ++F   +  +   N YD+  + +  Q                    L  +A  L
Sbjct: 175 SMPNNKEDFEWWVHQYMP-NFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADEL 233

Query: 244 DVSRAVGKCHQAGSDSLLTWHAFQKIRDVYFVH----DGPEKHAGVLYGLE 290
            + R        G  SLL   +F ++  +            K+ GV+YG++
Sbjct: 234 GLPR-FSIFTTTGGQSLLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGID 283
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query292
d2d5ra1252 CCR4-NOT transcription complex subunit 7, CAF1 {Hu 100.0
d1uoca_286 Pop2 RNase D domain {Baker's yeast (Saccharomyces 100.0
d2guia1174 N-terminal exonuclease domain of the epsilon subun 98.63
d2f96a1202 Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287 98.53
d1w0ha_200 Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960 98.52
d1y97a1228 Three prime repair exonuclease 2, TREX2 {Human (Ho 98.29
d2qxfa1 467 Exonuclease I {Escherichia coli K12 (Escherichia c 98.13
d3b6oa1226 Three prime repair exonuclease 1, TREX1 {Mouse (Mu 98.11
d1wlja_173 Interferon-stimulated gene 20 kDa protein, ISG20 { 97.67
d1yt3a3193 Ribonuclease D, catalytic domain {Escherichia coli 97.07
d2hbka2292 Exosome complex exonuclease RRP6 {Baker's yeast (S 95.7
d1kfsa1195 Exonuclease domain of prokaryotic DNA polymerase { 94.38
d2igia1180 Oligoribonuclease {Escherichia coli [TaxId: 562]} 93.51
>d2d5ra1 c.55.3.9 (A:11-262) CCR4-NOT transcription complex subunit 7, CAF1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: CAF1-like ribonuclease
domain: CCR4-NOT transcription complex subunit 7, CAF1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=4.5e-85  Score=595.89  Aligned_cols=251  Identities=49%  Similarity=0.864  Sum_probs=242.5

Q ss_pred             EEEEeCccCHHHHHHHHHHHhhcCCceeccccccccccCCCCCCCCCCCCCCCCchHHHHHHHhhhccccceeeeeeeec
Q 022773           23 IIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSD  102 (292)
Q Consensus        23 ~v~eV~~~Nf~eel~~I~~~i~~~~fIAiDtEF~G~~~~~~~~~~~~~~~~~~t~e~rY~~lk~nvd~~~iiQlGLt~~~  102 (292)
                      +|+|||++||+|||+.|+++|++|+||||||||||++.+|.+.+       .+++|+||+++|+||+.+++||+|||+++
T Consensus         1 ~i~eV~~~Nf~e~~~~i~~~i~~~~fVAiD~EF~G~~~~~~~~~-------~~t~~~~Y~~lr~nv~~~~iiQ~Glt~~~   73 (252)
T d2d5ra1           1 RICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEF-------RSNADYQYQLLRCNVDLLKIIQLGLTFMN   73 (252)
T ss_dssp             CEEEECGGGHHHHHHHHHHHHHHCCEEEEEEECCCCCCCCCSCC-------SSHHHHHHHHHHHHHTTCCCCEEEEEEEC
T ss_pred             CeEEehhhhHHHHHHHHHHHHhcCCEEEEeeeccCcccCCCCcc-------CCCHHHHHHHHHHHHhhcceeEEEEEeec
Confidence            48999999999999999999999999999999999999988776       78999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCCCeeEEEEeecccCCCCCCCChhHHHHHHHcCCChhhhhhcCCChHHHHHHHHHcCccccCCcceEEe
Q 022773          103 SSGNLPDLGSGGNNKFIWEFNFRDFDIATDAHAPDSIELLRLQGIDFERNRKEGVDSVRFAELMMSSGLVCNESVSWVTF  182 (292)
Q Consensus       103 ~~g~~p~~g~~~~~~~~w~FNF~~F~~~~d~~~~~Si~fL~~~GfDFnk~~~~GI~~~~f~e~l~~Sglv~~~~~~wv~f  182 (292)
                      ++|+.|.      .+++|||||+ |+..+++|+++||+||++|||||||++++||||..|++++++||++++++++||+|
T Consensus        74 ~~g~~~~------~~~~w~FNf~-~~~~~~~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~~~l~~s~~~~~~~~~wv~f  146 (252)
T d2d5ra1          74 EQGEYPP------GTSTWQFNFK-FNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELLMTSGVVLCEGVKWLSF  146 (252)
T ss_dssp             TTSCCCS------SCCEEEEEBC-CCTTTSCCCHHHHHHHHHHTCCHHHHHHHCBCHHHHHHHHHTTTSSSSSSCEEEES
T ss_pred             ccCCCCC------CceeEEEEEE-eCCcccccCHHHHHHHHHcCCChHHHHHcCCCHHHHHHHHHhhhhhhcCCCcEEEe
Confidence            9999885      4789999999 99999999999999999999999999999999999999999999999999999999


Q ss_pred             eCchhHHHHHHHhCCCCCCCCHHHHHHHHHhhcCCcccchHHHHHhhhhccchHHHHHHHcCCCCCCCCCccchhhHHHH
Q 022773          183 HSAYDFGYLVKILTRRSLPSGLDEFLTVLRVFFGNNIYDVKHIMRFCQSLYGGLDRVARTLDVSRAVGKCHQAGSDSLLT  262 (292)
Q Consensus       183 hg~yD~~yL~k~l~~~~LP~~~~~F~~~l~~~F~P~iyDtK~la~~~~~l~~~L~~la~~L~v~r~~g~~HqAGsDS~lT  262 (292)
                      ||+|||+||+|+|+|+|||+++++|+++++.+| |.+||||||++.|.++++||++||+.||++| +|++||||||||||
T Consensus       147 ~g~yD~~yl~k~l~~~~LP~~~~eF~~~v~~~F-P~vyDtK~l~~~~~~~~~~L~~la~~L~v~~-~g~~H~AG~DsllT  224 (252)
T d2d5ra1         147 HSGYDFGYLIKILTNSNLPEEELDFFEILRLFF-PVIYDVKYLMKSCKNLKGGLQEVAEQLELER-IGPQHQAGSDSLLT  224 (252)
T ss_dssp             SCHHHHHHHHHHHHTSCCCSSHHHHHHHHHHHC-SCEEEHHHHGGGCTTCCSSHHHHHHHHTCCC-CSSTTSHHHHHHHH
T ss_pred             cchhHHHHHHHHHcCCCCCCCHHHHHHHHHHHC-chHhhHHHHHhhccCCCchHHHHHHHcCCCC-CCCCcchhHHHHHH
Confidence            999999999999999999999999999999999 9999999999999999999999999999999 99999999999999


Q ss_pred             HHHHHHHHHHhcCCCC-CccccceEecc
Q 022773          263 WHAFQKIRDVYFVHDG-PEKHAGVLYGL  289 (292)
Q Consensus       263 ~~~F~~l~~~~~~~~~-~~~~~g~i~Gl  289 (292)
                      ++||++|++++++++. .++++|+||||
T Consensus       225 ~~~F~~l~~~~~~~~~~~~~~~g~i~Gl  252 (252)
T d2d5ra1         225 GMAFFKMREMFFEDHIDDAKYCGHLYGL  252 (252)
T ss_dssp             HHHHHHHHHHTSCSSCCHHHHTTBCTTC
T ss_pred             HHHHHHHHHHHhcCCCcHHHhCCcccCC
Confidence            9999999999998654 57899999997
>d1uoca_ c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d2f96a1 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287]} 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
>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