Citrus Sinensis ID: 038950

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-------
MAVVSKILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMKNRYELEESAFDGFLYGMDSRIERKPAEIMMLQYMQPLMIPQPLLVPTQFHHPLALSYYVPA
cccccEEEEEcHHHHHHHHHHHHHHHHHcccEEEccEEcccccccccccccHHHHHHHHcccccccEEEEEEEEEccccccEEEEEEEccccccccccccHHHHHHHHHccccHHHHHHccccccccHHHHHHHHHHccccccEEEEccccHHHHHHHHHHcccccccHHHHHHHHHHHcccEEHHHHHHHHHccccccccHHHHHHHHcccEEccccccccHHHHHHHHHHHHHHHHccccccccccEEEEcccccccccHHHHHccccccccccccccccccccccccccccccc
ccHHHHHHHHHHHHHHHHHHHHHHHHHHccEEEEccccccEEEEccccccccHHHEEEEHcHHHHHHHHHcEEEEccccccccEEEEEccccccHHHcccHHHHHHHHHccccHHHHHHccccHHHHHHHHHHccEEEcccEEEEEEcccHHHHHHHHHHccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHcccccHHHHHHHHccccEcccccccccHHHHHHHHHHHHHHHHccccccccEEEEEccccccccccccccccccccccccccccccccccccccccccccc
MAVVSKILNVWCENFEIVMRFLDKLLNCFnvlsidtefpgflrntprnapavesyndlkfnvdCTHLIQLGitlsdkegkisytfefnfsdfdlkkdlhagdsIQLLkdsgldfdkirkdgiprcvfAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIftndalpptaeaFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARILNvkrhggahhagsdSLLTAAVFAEMKNRYELEESAFdgflygmdsrierkPAEIMMLQYmqplmipqpllvptqfhhplalsyyvpa
MAVVSKILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRHggahhagsdsLLTAAVFAEMKNRYELEESAFDGFLYGMDSRIERKPAEIMMLQYMQPLMIPQPLLVPTQFHHPLALSYYVPA
MAVVSKILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCqglqglklglsklARILNVKRHGGAHHAGSDSLLTAAVFAEMKNRYELEESAFDGFLYGMDSRIERKPAEIMMLQYMQPLMIPQPLLVPTQFHHPLALSYYVPA
**VVSKILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMKNRYELEESAFDGFLYGMDSRIERKPAEIMMLQYMQPLMIPQPLLVPTQFHHPLALSYYV**
***VSKI*NVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMKNRYELEESAFDGFLYGMDSR*****************************************
MAVVSKILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMKNRYELEESAFDGFLYGMDSRIERKPAEIMMLQYMQPLMIPQPLLVPTQFHHPLALSYYVPA
*AVVSKILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMKNRYELEESAFDGFLYGMDSRIERKPAEIMMLQYMQPLMIPQPLLVPTQFHHPLALSYYVP*
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MAVVSKILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMKNRYELEESAFDGFLYGMDSRIERKPAEIMMLQYMQPLMIPQPLLVPTQFHHPLALSYYVPA
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 ?
Query297 2.2.26 [Sep-21-2011]
Q9LXM4239 Putative CCR4-associated yes no 0.723 0.899 0.474 2e-48
O64773278 Probable CCR4-associated no no 0.750 0.802 0.458 9e-47
Q9SFX6310 Putative CCR4-associated no no 0.754 0.722 0.460 2e-44
Q9SHJ0360 Probable CCR4-associated no no 0.956 0.788 0.375 2e-42
Q9C6M9302 Putative CCR4-associated no no 0.754 0.741 0.460 7e-42
Q9FMS6278 Probable CCR4-associated no no 0.828 0.884 0.392 2e-41
Q9SKZ2275 Probable CCR4-associated no no 0.824 0.890 0.378 4e-40
Q9LXM2280 Probable CCR4-associated no no 0.841 0.892 0.373 1e-38
Q3KQ85285 CCR4-NOT transcription co N/A no 0.831 0.866 0.355 1e-38
A4II96285 CCR4-NOT transcription co yes no 0.831 0.866 0.359 2e-38
>sp|Q9LXM4|CAF1H_ARATH Putative CCR4-associated factor 1 homolog 8 OS=Arabidopsis thaliana GN=CAF1-8 PE=3 SV=1 Back     alignment and function desciption
 Score =  192 bits (488), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 103/217 (47%), Positives = 137/217 (63%), Gaps = 2/217 (0%)

Query: 19  MRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLIQLGITLSDKE 78
           M  ++  L  +  ++IDTEFP  LR T ++A   E Y D+ F+VD   LIQLG+TL D  
Sbjct: 1   MSLIEDCLRSYRFIAIDTEFPSTLRETTQHATDEERYMDMSFSVDRAKLIQLGLTLFDIN 60

Query: 79  GKISYTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVFAPRFLEVLSKH 138
           G+I  T+E NFSDF +  D     SI+ L+ +GLD  KIR++GI    F      +L K 
Sbjct: 61  GRIGGTWEINFSDFGVD-DARNEKSIEFLRRNGLDLRKIREEGIRIEGFFSEMFWMLKKT 119

Query: 139 RENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQG 198
           R N+ WVTFHG YD+AYL+K FT +ALP T+E FS   A    SV+D+KV+AG C+GL  
Sbjct: 120 RRNITWVTFHGSYDIAYLLKGFTGEALPVTSERFSKAVARVLGSVYDLKVMAGRCEGLSS 179

Query: 199 LKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEM 235
            +LGL  LA    + R G AHHAGS++ LTA VFA++
Sbjct: 180 -RLGLETLAHEFGLNRVGTAHHAGSNNELTAMVFAKV 215
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|O64773|CAF1E_ARATH Probable CCR4-associated factor 1 homolog 5 OS=Arabidopsis thaliana GN=CAF1-5 PE=2 SV=1 Back     alignment and function description
>sp|Q9SFX6|CAF1C_ARATH Putative CCR4-associated factor 1 homolog 3 OS=Arabidopsis thaliana GN=CAF1-3 PE=1 SV=1 Back     alignment and function description
>sp|Q9SHJ0|CAF1A_ARATH Probable CCR4-associated factor 1 homolog 1 OS=Arabidopsis thaliana GN=CAF1-1 PE=2 SV=1 Back     alignment and function description
>sp|Q9C6M9|CAF1D_ARATH Putative CCR4-associated factor 1 homolog 4 OS=Arabidopsis thaliana GN=CAF1-4 PE=1 SV=1 Back     alignment and function description
>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 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|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|Q3KQ85|CNOT7_XENLA CCR4-NOT transcription complex subunit 7 OS=Xenopus laevis GN=cnot7 PE=2 SV=1 Back     alignment and function description
>sp|A4II96|CNOT7_XENTR CCR4-NOT transcription complex subunit 7 OS=Xenopus tropicalis 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 ?
Query297
224143029305 predicted protein [Populus trichocarpa] 0.841 0.819 0.507 9e-62
224141777224 predicted protein [Populus trichocarpa] 0.754 1.0 0.535 7e-59
449458674300 PREDICTED: probable CCR4-associated fact 0.845 0.836 0.452 8e-53
297815542266 predicted protein [Arabidopsis lyrata su 0.720 0.804 0.502 3e-48
449467363262 PREDICTED: probable CCR4-associated fact 0.835 0.946 0.426 7e-47
15229910239 putative CCR4-associated factor 1-8 [Ara 0.723 0.899 0.474 1e-46
449443480277 PREDICTED: probable CCR4-associated fact 0.824 0.884 0.417 7e-46
15219931278 putative CCR4-associated factor 1-5 [Ara 0.750 0.802 0.458 5e-45
15217727310 putative CCR4-associated factor 1-3 [Ara 0.754 0.722 0.460 2e-42
255565745281 ccr4-associated factor, putative [Ricinu 0.821 0.868 0.398 3e-42
>gi|224143029|ref|XP_002324825.1| predicted protein [Populus trichocarpa] gi|222866259|gb|EEF03390.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  243 bits (619), Expect = 9e-62,   Method: Compositional matrix adjust.
 Identities = 128/252 (50%), Positives = 171/252 (67%), Gaps = 2/252 (0%)

Query: 6   KILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCT 65
           KI  VW +NF+  +  LD  L  F V+S DTEFPGF RNTP +A  +  Y DLK NVD  
Sbjct: 10  KITAVWRQNFKREIFRLDAALFRFPVVSFDTEFPGFFRNTPIDATDLTRYEDLKHNVDPL 69

Query: 66  HLIQLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRC 125
            LIQ GIT++D  GKI  T+EFN   FDL KDL    SIQ L+D+G+DFDK+R+DGI   
Sbjct: 70  RLIQFGITVADASGKIGGTWEFNLR-FDLSKDLFVSQSIQFLQDNGIDFDKLRRDGIDFD 128

Query: 126 VFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFFQSVFD 185
           +FA     V++KHR NL WVTFHGLYD+++ ++  TN  LP +   F+ +  + F  V D
Sbjct: 129 MFAQLLSRVVAKHR-NLCWVTFHGLYDLSHTLRTVTNRPLPHSLAGFTSLLGIVFGDVVD 187

Query: 186 IKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMKNRYELEESA 245
           IK +A +CQGL+G +LGL+ +A+IL V+R GGAH AGSDSLLTA V+ +M+  Y+++ + 
Sbjct: 188 IKYMARFCQGLRGGELGLAAIAKILKVERVGGAHQAGSDSLLTARVYTKMRMVYKIDGTL 247

Query: 246 FDGFLYGMDSRI 257
             G LYG+ +RI
Sbjct: 248 CVGCLYGVSARI 259

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224141777|ref|XP_002324241.1| predicted protein [Populus trichocarpa] gi|222865675|gb|EEF02806.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449458674|ref|XP_004147072.1| PREDICTED: probable CCR4-associated factor 1 homolog 1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|297815542|ref|XP_002875654.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297321492|gb|EFH51913.1| predicted protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|449467363|ref|XP_004151393.1| PREDICTED: probable CCR4-associated factor 1 homolog 9-like [Cucumis sativus] gi|449484866|ref|XP_004157002.1| PREDICTED: probable CCR4-associated factor 1 homolog 9-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|15229910|ref|NP_190010.1| putative CCR4-associated factor 1-8 [Arabidopsis thaliana] gi|75335619|sp|Q9LXM4.1|CAF1H_ARATH RecName: Full=Putative CCR4-associated factor 1 homolog 8 gi|7649375|emb|CAB88992.1| CCR4-associated factor 1-like protein [Arabidopsis thaliana] gi|332644359|gb|AEE77880.1| putative CCR4-associated factor 1-8 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|449443480|ref|XP_004139505.1| PREDICTED: probable CCR4-associated factor 1 homolog 11-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|15219931|ref|NP_176342.1| putative CCR4-associated factor 1-5 [Arabidopsis thaliana] gi|75318497|sp|O64773.1|CAF1E_ARATH RecName: Full=Probable CCR4-associated factor 1 homolog 5 gi|3056583|gb|AAC13894.1|AAC13894 T1F9.4 [Arabidopsis thaliana] gi|332195720|gb|AEE33841.1| putative CCR4-associated factor 1-5 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|15217727|ref|NP_174103.1| putative CCR4-associated factor 1-3 [Arabidopsis thaliana] gi|75337186|sp|Q9SFX6.1|CAF1C_ARATH RecName: Full=Putative CCR4-associated factor 1 homolog 3 gi|6693029|gb|AAF24955.1|AC012375_18 T22C5.28 [Arabidopsis thaliana] gi|12320883|gb|AAG50574.1|AC079280_5 hypothetical protein [Arabidopsis thaliana] gi|332192759|gb|AEE30880.1| putative CCR4-associated factor 1-3 [Arabidopsis thaliana] 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

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 ?
Query297
TAIR|locus:2197669278 AT1G61470 [Arabidopsis thalian 0.892 0.953 0.402 1.7e-41
TAIR|locus:2095705239 AT3G44240 [Arabidopsis thalian 0.744 0.924 0.439 1.7e-41
TAIR|locus:2010414302 AT1G27890 [Arabidopsis thalian 0.925 0.910 0.402 3.6e-41
TAIR|locus:2029826310 AT1G27820 [Arabidopsis thalian 0.919 0.880 0.402 1.6e-40
TAIR|locus:2009220360 AT1G06450 [Arabidopsis thalian 0.952 0.786 0.350 5.5e-38
TAIR|locus:2176307278 CAF1b "CCR4- associated factor 0.828 0.884 0.377 2.4e-37
TAIR|locus:2095715280 CAF1a "CCR4- associated factor 0.841 0.892 0.361 3.5e-36
DICTYBASE|DDB_G0284217367 DDB_G0284217 "CAF1 family prot 0.828 0.670 0.352 7.2e-36
TAIR|locus:2045512275 AT2G32070 [Arabidopsis thalian 0.824 0.890 0.359 9.2e-36
ZFIN|ZDB-GENE-040426-2845285 cnot8 "CCR4-NOT transcription 0.845 0.880 0.352 1.9e-35
TAIR|locus:2197669 AT1G61470 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 440 (159.9 bits), Expect = 1.7e-41, P = 1.7e-41
 Identities = 112/278 (40%), Positives = 158/278 (56%)

Query:    10 VWCENFEIVMRFL-DKLLNCFNVLSIDTEFPGFLRNTPRNAPAVESYNDLKFNVDCTHLI 68
             VW  N +  M  + D L +C N ++IDTEFPG L+ TP +A     Y D+KFNVD THLI
Sbjct:     5 VWRWNKQAEMNSIRDCLKHC-NSIAIDTEFPGCLKETPMDASDEIRYRDMKFNVDNTHLI 63

Query:    69 QLGITLSDKEGKISYTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVFA 128
             QLG+TL  K G I+ T+E N SDF+  K L    SI  LK++GLD DKIR++GI    F 
Sbjct:    64 QLGLTLFGK-G-ITKTWEINLSDFNESKSLKNDKSIAFLKNNGLDLDKIREEGIGIEEFF 121

Query:   129 PRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSG-VAALFFQSVFDIK 187
               F ++L++    ++WVTF G YD AYL+K  T   LP T++ F   V  L  + V+D+K
Sbjct:   122 MEFSQILNEKHGKMRWVTFQGSYDKAYLLKGLTRKPLPETSKEFDETVQQLLGRFVYDVK 181

Query:   188 VVAGYCXXXXXXXXXXXXXARILNVKRHGGAHHAGSDSLLTAAVFAEMKNRYELEESAFD 247
              +AG C             A +L ++R G AHHAGSDS LTA VF ++   ++L  S  +
Sbjct:   182 KMAGLCSGLSSRFGLQRI-ADVLQMRRVGKAHHAGSDSELTARVFTKLI--FDLVNSRKE 238

Query:   248 GFLYGMDSRIERKPAEIMMLQYMQPLMIPQPLL-VPTQ 284
                     R + +  ++   Q+ Q LM+ +  + +P Q
Sbjct:   239 S----TGRRADDQQYQLEQQQHQQQLMMTRCYIPIPVQ 272
GO:0003676 "nucleic acid binding" evidence=IEA
GO:0004540 "ribonuclease activity" evidence=ISS
GO:0005634 "nucleus" evidence=IEA
GO:0009451 "RNA modification" evidence=ISS
TAIR|locus:2095705 AT3G44240 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2010414 AT1G27890 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2029826 AT1G27820 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2009220 AT1G06450 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2176307 CAF1b "CCR4- associated factor 1b" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2095715 CAF1a "CCR4- associated factor 1a" [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
TAIR|locus:2045512 AT2G32070 [Arabidopsis thaliana (taxid:3702)] 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

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) ?
Q9D8X5CNOT8_MOUSENo assigned EC number0.35090.85180.8664yesno
Q9UFF9CNOT8_HUMANNo assigned EC number0.35090.85180.8664yesno
A4II96CNOT7_XENTRNo assigned EC number0.35900.83160.8666yesno

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 ?
Query297
pfam04857235 pfam04857, CAF1, CAF1 family ribonuclease 2e-67
COG5228299 COG5228, POP2, mRNA deadenylase subunit [RNA proce 2e-45
>gnl|CDD|147159 pfam04857, CAF1, CAF1 family ribonuclease Back     alignment and domain information 
 Score =  209 bits (535), Expect = 2e-67
 Identities = 95/239 (39%), Positives = 134/239 (56%), Gaps = 18/239 (7%)

Query: 9   NVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAP--AVESYNDLKFNVDCTH 66
            VW  NF    + + + ++ ++ ++IDTEFPG +     +    +   Y  L+ NVD   
Sbjct: 2   EVWRSNFHEEFKEIRQAIDSYDFIAIDTEFPGVVARPIGSFRSTSDYRYQALRKNVDRLK 61

Query: 67  LIQLGITLSDKEGKIS---YTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIP 123
           +IQLG+TL D++G +    YT++FNFS F+L++D +A  SI+ L   G DF+K R++GIP
Sbjct: 62  IIQLGLTLFDEKGNLPDSYYTWQFNFSLFNLEEDFYAPSSIEFLAKQGFDFNKHRREGIP 121

Query: 124 RCVFAPR------FLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAA 177
              FA        FL + S       WVTFHGLYD  YL+K+ T   LP T + F  +  
Sbjct: 122 YLRFAELLGSSGLFLNISSVT-----WVTFHGLYDFGYLLKLLTGGPLPETLDDFLELLR 176

Query: 178 LFFQSVFDIKVVAGYCQGLQG-LKLGLSKLARILNVKRH-GGAHHAGSDSLLTAAVFAE 234
             F  V+D K +A +C  L G    GL +LA +L V R  G  H AGSDSLLTA VF +
Sbjct: 177 ELFPRVYDTKYLAKFCFELDGGSNGGLQELADLLGVNRRVGRLHQAGSDSLLTALVFFK 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 297
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 99.16
PRK07942232 DNA polymerase III subunit epsilon; Provisional 98.8
smart00479169 EXOIII exonuclease domain in DNA-polymerase alpha 98.8
cd06133176 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o 98.6
PRK09145202 DNA polymerase III subunit epsilon; Validated 98.55
cd06134189 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. 98.47
PRK07748207 sporulation inhibitor KapD; Provisional 98.46
PRK05168211 ribonuclease T; Provisional 98.38
cd06131167 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl 98.37
cd06130156 DNA_pol_III_epsilon_like an uncharacterized bacter 98.3
PRK07740244 hypothetical protein; Provisional 98.28
TIGR00573217 dnaq exonuclease, DNA polymerase III, epsilon subu 98.27
PRK05711240 DNA polymerase III subunit epsilon; Provisional 98.24
PRK06807313 DNA polymerase III subunit epsilon; Validated 98.15
PRK06063313 DNA polymerase III subunit epsilon; Provisional 98.1
cd06127159 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh 98.05
PRK07247195 DNA polymerase III subunit epsilon; Validated 98.03
PRK09146239 DNA polymerase III subunit epsilon; Validated 98.03
PRK06195309 DNA polymerase III subunit epsilon; Validated 97.95
TIGR01406225 dnaQ_proteo DNA polymerase III, epsilon subunit, P 97.94
TIGR01298200 RNaseT ribonuclease T. in gamma-subdivision Proteo 97.91
PRK06310250 DNA polymerase III subunit epsilon; Validated 97.91
PRK06722281 exonuclease; Provisional 97.82
PRK08517257 DNA polymerase III subunit epsilon; Provisional 97.74
PRK07883 557 hypothetical protein; Validated 97.73
TIGR01407 850 dinG_rel DnaQ family exonuclease/DinG family helic 97.72
PRK08074 928 bifunctional ATP-dependent DNA helicase/DNA polyme 97.68
TIGR01405 1213 polC_Gram_pos DNA polymerase III, alpha chain, Gra 97.66
PRK05601377 DNA polymerase III subunit epsilon; Validated 97.64
PRK07246 820 bifunctional ATP-dependent DNA helicase/DNA polyme 97.62
cd06138183 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain o 97.6
PTZ00315 582 2'-phosphotransferase; Provisional 97.5
PF00929164 RNase_T: Exonuclease; InterPro: IPR013520 This ent 97.5
PRK11779 476 sbcB exonuclease I; Provisional 97.4
cd06144152 REX4_like DEDDh 3'-5' exonuclease domain of RNA ex 97.32
cd06136177 TREX1_2 DEDDh 3'-5' exonuclease domain of three pr 97.31
PRK09182294 DNA polymerase III subunit epsilon; Validated 96.99
cd06149157 ISG20 DEDDh 3'-5' exonuclease domain of Interferon 96.92
COG0847243 DnaQ DNA polymerase III, epsilon subunit and relat 96.88
PRK00448 1437 polC DNA polymerase III PolC; Validated 96.84
cd06145150 REX1_like DEDDh 3'-5' exonuclease domain of RNA ex 96.83
PRK06309232 DNA polymerase III subunit epsilon; Validated 96.79
PRK07983219 exodeoxyribonuclease X; Provisional 96.6
COG0349 361 Rnd Ribonuclease D [Translation, ribosomal structu 95.59
PRK05359181 oligoribonuclease; Provisional 95.45
cd06141170 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and 94.02
PRK10829 373 ribonuclease D; Provisional 93.9
PRK05755 880 DNA polymerase I; Provisional 93.62
cd06135173 Orn DEDDh 3'-5' exonuclease domain of oligoribonuc 92.91
cd06146193 mut-7_like_exo DEDDy 3'-5' exonuclease domain of C 92.61
cd06137161 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the 91.67
TIGR01388 367 rnd ribonuclease D. This model describes ribonucle 91.61
PF01612176 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR00 90.77
cd06129161 RNaseD_like DEDDy 3'-5' exonuclease domain of RNas 89.56
PF13482164 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 81.59
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification] Back     alignment and domain information 
Probab=100.00  E-value=2.7e-86  Score=589.60  Aligned_cols=228  Identities=45%  Similarity=0.732  Sum_probs=221.8

Q ss_pred             eeeeeccccHHHHHHHHHHHhhcCCeeEEeccccCcccCCC--CCCChhHHHHHHhhccccccceEEEeEEeccCCCcce
Q 038950            6 KILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTP--RNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKISY   83 (297)
Q Consensus         6 ~i~eVw~~N~~~el~~I~~~i~~~~fIAiDtEFpGv~~~p~--~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p~   83 (297)
                      .|||||++|+++||+.||++|++|+||||||||||++.+|.  |+++.+++|+.||+|||.+++||+|||++|++|+.|+
T Consensus         1 ~ireVW~~Nl~~Em~~Ir~~v~~y~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlGlTlsd~~Gn~p~   80 (239)
T KOG0304|consen    1 FIREVWRSNLEEEMALIRECVKDYPYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLGLTLSDEKGNLPD   80 (239)
T ss_pred             ChhHHHHHhHHHHHHHHHHHHHhCCeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhheeeeeeccCCCCCC
Confidence            47999999999999999999999999999999999999998  7799999999999999999999999999999999994


Q ss_pred             ----eEEEeeecCCCCCCCCchhhHHHHHhcCCChhhhhhCCCCCcch--hhhhccccccCCCCceeEEeecchhHHHHH
Q 038950           84 ----TFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVF--APRFLEVLSKHRENLKWVTFHGLYDVAYLV  157 (297)
Q Consensus        84 ----~wqFNF~~Fd~~~d~~~~~SI~fL~~~GfDFnk~~~~GI~~~~F--ll~~SGLv~~~~~~~~Witfh~~yD~~yL~  157 (297)
                          +|||||++|++.+|+++++||+||+++|+||.|+++.||+..+|  ++++||++++  ++++|||||||||||||+
T Consensus        81 ~g~~tWqfNF~dF~~~~D~~a~~SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~--~~V~WvTFhs~YDfgYLl  158 (239)
T KOG0304|consen   81 CGTDTWQFNFSDFNLEKDMYAQDSIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLD--ENVTWVTFHSGYDFGYLL  158 (239)
T ss_pred             CCCceeEEecccCCchhhccchhhHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhcc--CceEEEEeeccchHHHHH
Confidence                99999999999999999999999999999999999999999999  9999999999  999999999999999999


Q ss_pred             HHhcCCCCCCChHHHHHHHHhccCcccchhHHHHhccc--cCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHH
Q 038950          158 KIFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQG--LQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEM  235 (297)
Q Consensus       158 k~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~~--l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl  235 (297)
                      |+||+++||++.++|.+.++.+||.+||+|||++.|.+  +++   ||++||+.|++.|+|.+|||||||+||+++|+||
T Consensus       159 K~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK~l~~~c~~~~l~~---GL~~lA~~L~~~RvG~~HqAGSDSlLT~~~F~kl  235 (239)
T KOG0304|consen  159 KILTGKPLPETEEEFFEIVRQLFPFVYDVKYLMKFCEGLSLKG---GLQRLADLLGLKRVGIAHQAGSDSLLTARVFFKL  235 (239)
T ss_pred             HHHcCCCCcchHHHHHHHHHHHcchhhhHHHHHHhhhhhhhhc---CHHHHHHHhCCCeeecccccCcHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999965  777   9999999999999999999999999999999999


Q ss_pred             HHh
Q 038950          236 KNR  238 (297)
Q Consensus       236 ~~~  238 (297)
                      ++.
T Consensus       236 ~~~  238 (239)
T KOG0304|consen  236 KEL  238 (239)
T ss_pred             Hhc
Confidence            853

>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
>PRK09145 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T Back     alignment and domain information
>PRK07748 sporulation inhibitor KapD; Provisional 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
>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
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family Back     alignment and domain information
>PRK05711 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK06807 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06063 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family Back     alignment and domain information
>PRK07247 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK09146 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06195 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial Back     alignment and domain information
>TIGR01298 RNaseT ribonuclease T Back     alignment and domain information
>PRK06310 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06722 exonuclease; Provisional Back     alignment and domain information
>PRK08517 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK07883 hypothetical protein; Validated Back     alignment and domain information
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative Back     alignment and domain information
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type Back     alignment and domain information
>PRK05601 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
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins Back     alignment and domain information
>PTZ00315 2'-phosphotransferase; Provisional 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
>PRK11779 sbcB exonuclease I; 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
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins Back     alignment and domain information
>PRK09182 DNA polymerase III subunit epsilon; Validated 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
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK00448 polC DNA polymerase III PolC; Validated Back     alignment and domain information
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins Back     alignment and domain information
>PRK06309 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07983 exodeoxyribonuclease X; Provisional Back     alignment and domain information
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK05359 oligoribonuclease; Provisional Back     alignment and domain information
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins Back     alignment and domain information
>PRK10829 ribonuclease D; Provisional Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional 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
>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
>TIGR01388 rnd ribonuclease D 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
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins 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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query297
2p51_A333 Crystal Structure Of The S. Pombe Pop2p Deadenylati 6e-35
4gmj_B285 Structure Of Human Not1 Mif4g Domain Co-Crystallize 2e-34
2d5r_A252 Crystal Structure Of A Tob-Hcaf1 Complex Length = 2 5e-34
1uoc_A289 X-Ray Structure Of The Rnase Domain Of The Yeast Po 1e-19
4b8a_B286 Structure Of Yeast Not1 Mif4g Domain Co-Crystallize 1e-19
4b8c_A288 Nuclease Module Of The Yeast Ccr4-Not Complex Lengt 1e-19
>pdb|2P51|A Chain A, Crystal Structure Of The S. Pombe Pop2p Deadenylation Subunit Length = 333 Back     alignment and structure 
Iteration: 1

 Score =  144 bits (363), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 94/262 (35%), Positives = 140/262 (53%), Gaps = 24/262 (9%)
Query: 4   VSKILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVES-----YNDL 58
           +S I +VW  N +  M  +  L+  + V+S+DTEFPG +    R     +S     Y  L
Sbjct: 20  ISPIRDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVA---RPLGVFKSSDDYHYQTL 76
Query: 59  KFNVDCTHLIQLGITLSDKEGKI---SYTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFD 115
           + NVD   +IQ+G+ LSD+EG     + T++FNF+ F+L+ D++A +SI+LL  SG+DF 
Sbjct: 77  RANVDSLKIIQIGLALSDEEGNAPVEACTWQFNFT-FNLQDDMYAPESIELLTKSGIDFK 135
Query: 116 KIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGV 175
           K ++ GI    FA   +      +E + W+TFH  YD AYL+K  T   LP   E F  +
Sbjct: 136 KHQEVGIEPADFAELLIGSGLVLQEEVTWITFHSGYDFAYLLKAMTQIPLPAEYEEFYKI 195
Query: 176 AALFFQSVFDIKVVAGYCXXXXXXXXXXXXXARILNVKRHGGAHHAGSDSLLTAAVFAEM 235
             ++F   +DIK +                 A  L + R G  H AGSD+LLTA +F E+
Sbjct: 196 LCIYFPKNYDIKYI---MKSVLNNSKGLQDIADDLQIHRIGPQHQAGSDALLTARIFFEI 252
Query: 236 KNRYELEESAFDGFLYGMDSRI 257
           ++RY      FDG    +DSR+
Sbjct: 253 RSRY------FDG---SIDSRM 265
>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|1UOC|A Chain A, X-Ray Structure Of The Rnase Domain Of The Yeast Pop2 Protein Length = 289 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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query297
1uoc_A289 POP2; hydrolase, DEDD nuclease, mRNA degradation, 3e-73
2p51_A333 SPCC18.06C protein; DEDD nuclease fold, hydrolase, 9e-73
2d5r_A252 CCR4-NOT transcription complex subunit 7; poly(A) 3e-70
3d45_A 507 Poly(A)-specific ribonuclease PARN; CAP analogue, 1e-15
3d45_A507 Poly(A)-specific ribonuclease PARN; CAP analogue, 4e-07
2a1r_A 430 Poly(A)-specific ribonuclease PARN; DEDD, nuclease 6e-15
2a1r_A430 Poly(A)-specific ribonuclease PARN; DEDD, nuclease 8e-12
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-07
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-06
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 8e-04
1zbu_A349 ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; 8e-06
1w0h_A204 3'-5' exonuclease ERI1; nuclease domain, hydrolase 2e-05
1zbh_A299 3'-5' exonuclease ERI1; histone mRNA 3'-END-specif 3e-05
>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
 Score =  226 bits (576), Expect = 3e-73
 Identities = 71/274 (25%), Positives = 127/274 (46%), Gaps = 25/274 (9%)

Query: 6   KILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTPRN--APAVESYNDLKFNVD 63
            + +VW  N       + +L++ +N +SI TEF G L        +     Y  ++ NVD
Sbjct: 15  FVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSKVDYHYQTMRANVD 74

Query: 64  CTHLIQLGITLSDKEGKI----SYTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRK 119
             + IQLG++LSD  G        T++FNF +FD KK++ + +S++LL+ SG++F+K   
Sbjct: 75  FLNPIQLGLSLSDANGNKPDNGPSTWQFNF-EFDPKKEIMSTESLELLRKSGINFEKHEN 133

Query: 120 DGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALF 179
            GI    F+   ++      +++ W+T+H  YD+ +L+ I  ND++P   E F      +
Sbjct: 134 LGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNNKEDFEWWVHQY 193

Query: 180 FQSVFDIKVVAGYCQGLQG------------LKLGLSKLARILNVKRHGGAHHAGSDSLL 227
             + +D+ +V    Q  +              +  L+ LA  L + R       G  SLL
Sbjct: 194 MPNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELGLPRFSIFTTTGGQSLL 253

Query: 228 TAAVFAEMKNRY------ELEESAFDGFLYGMDS 255
               F ++            + + + G +YG+D 
Sbjct: 254 MLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGIDG 287
>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
>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
>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
>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
>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
>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
>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
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens} Length = 349 Back     alignment and structure
>1w0h_A 3'-5' exonuclease ERI1; nuclease domain, hydrolase; HET: AMP; 1.59A {Homo sapiens} SCOP: c.55.3.5 Length = 204 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} Length = 299 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query297
2d5r_A252 CCR4-NOT transcription complex subunit 7; poly(A) 100.0
4gmj_B285 CCR4-NOT transcription complex subunit 7; mRNA dec 100.0
2p51_A333 SPCC18.06C protein; DEDD nuclease fold, hydrolase, 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
1w0h_A204 3'-5' exonuclease ERI1; nuclease domain, hydrolase 98.64
3v9w_A235 Ribonuclease T; DEDD nucleases family, EXO-nucleas 98.57
2f96_A224 Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolas 98.45
2gui_A194 DNA polymerase III epsilon subunit; DNA polymerase 98.39
1zbh_A299 3'-5' exonuclease ERI1; histone mRNA 3'-END-specif 98.37
3cg7_A308 CRN-4, cell death-related nuclease 4; hydrolase, a 98.35
2p1j_A186 POLIII, DNA polymerase III POLC-type; structural g 98.32
2xri_A224 ERI1 exoribonuclease 3; hydrolase, metal binding; 98.29
3mxm_B242 Three prime repair exonuclease 1; RNAse H-like fol 98.19
1zbu_A349 ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; 98.15
1y97_A238 Three prime repair exonuclease 2; TREX2, hydrolase 98.04
2qxf_A 482 Exodeoxyribonuclease I; alpha-beta domain, DNAQ su 98.01
3u3y_B314 Three prime repair exonuclease 1; RNAse H fold, 3' 97.88
1wlj_A189 Interferon stimulated gene 20KDA; exoribonuclease, 97.73
2igi_A180 Oligoribonuclease; RNAse, exoribonuclease, exonucl 97.31
2gbz_A194 Oligoribonuclease; ORN, deddh, structural genomics 96.84
3tr8_A186 Oligoribonuclease; transcription, hydrolase; 2.50A 96.24
2kfn_A 605 Klenow fragment of DNA polymerase I; complex (poly 95.6
3saf_A428 Exosome component 10; exoribonuclease, RNA exosome 85.4
>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
Probab=100.00  E-value=7.6e-87  Score=613.25  Aligned_cols=242  Identities=38%  Similarity=0.673  Sum_probs=234.1

Q ss_pred             eeeeeccccHHHHHHHHHHHhhcCCeeEEeccccCcccCCC--CCCChhHHHHHHhhccccccceEEEeEEeccCCCcc-
Q 038950            6 KILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTP--RNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKIS-   82 (297)
Q Consensus         6 ~i~eVw~~N~~~el~~I~~~i~~~~fIAiDtEFpGv~~~p~--~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p-   82 (297)
                      .|||||++||++||+.|+++|++|+||||||||||++++|.  +++++++||+++|+|||.++|||+|||+++++|+.| 
T Consensus         1 ~i~eVw~~Nl~~e~~~I~~~i~~~~fvAmDtEFpGvv~rp~g~f~~~~~~~Y~~lr~nVd~l~iIQlGlt~~~~~g~~p~   80 (252)
T 2d5r_A            1 RICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVDLLKIIQLGLTFMNEQGEYPP   80 (252)
T ss_dssp             CEEEECGGGHHHHHHHHHHHHHHCCEEEEEEECCCCCCCCCSCCSSHHHHHHHHHHHHHTTCCCCEEEEEEECTTSCCCS
T ss_pred             CeEEehhhhHHHHHHHHHHHHhhCCEEEEEeeecceecccCCCCCCCHHHHHHHHHHhhhhcceeEEEEEEEccCCCCCC
Confidence            48999999999999999999999999999999999999986  778899999999999999999999999999999987 


Q ss_pred             --eeEEEeeecCCCCCCCCchhhHHHHHhcCCChhhhhhCCCCCcch--hhhhccccccCCCCceeEEeecchhHHHHHH
Q 038950           83 --YTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVF--APRFLEVLSKHRENLKWVTFHGLYDVAYLVK  158 (297)
Q Consensus        83 --~~wqFNF~~Fd~~~d~~~~~SI~fL~~~GfDFnk~~~~GI~~~~F--ll~~SGLv~~~~~~~~Witfh~~yD~~yL~k  158 (297)
                        .+|||||+ |++++|+|+++||+||+++||||+|++++|||+..|  +++.||||++  ++++||+|||+||||||+|
T Consensus        81 ~~~~wqFNF~-F~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~F~ell~~sglvl~--~~v~Witfhg~yDf~yL~k  157 (252)
T 2d5r_A           81 GTSTWQFNFK-FNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELLMTSGVVLC--EGVKWLSFHSGYDFGYLIK  157 (252)
T ss_dssp             SCCEEEEEBC-CCTTTSCCCHHHHHHHHHHTCCHHHHHHHCBCHHHHHHHHHTTTSSSS--SSCEEEESSCHHHHHHHHH
T ss_pred             CceeEEEEEE-ECCcccccCHHHHHHHHHcCCChhHHHhcCCCHHHHHHHHHhcCcccC--CCceEEEecCcchHHHHHH
Confidence              39999999 999999999999999999999999999999999999  8999999999  8999999999999999999


Q ss_pred             HhcCCCCCCChHHHHHHHHhccCcccchhHHHHhccccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH-H
Q 038950          159 IFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK-N  237 (297)
Q Consensus       159 ~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~-~  237 (297)
                      +|||++||+++++|.++++.+||+|||||||++.|.++++   ||++||+.||++|+|++|||||||+||++||+||+ .
T Consensus       158 ~L~~~~LP~~~~~F~~~l~~~FP~iyD~K~l~~~~~~l~~---gL~~la~~L~v~r~g~~HqAGsDsllT~~~F~km~~~  234 (252)
T 2d5r_A          158 ILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKG---GLQEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREM  234 (252)
T ss_dssp             HHHTSCCCSSHHHHHHHHHHHCSCEEEHHHHGGGCTTCCS---SHHHHHHHHTCCCCSSTTSHHHHHHHHHHHHHHHHHH
T ss_pred             HhcCCCCCCCHHHHHHHHHHHCcchhhHHHHHHHhcccCC---CHHHHHHHcCCCccCcccchhhhHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999998888   99999999999999999999999999999999999 7


Q ss_pred             hcCCc--ccccCceeecC
Q 038950          238 RYELE--ESAFDGFLYGM  253 (297)
Q Consensus       238 ~f~~~--~~~~~g~l~Gl  253 (297)
                      +|++.  .++++|+||||
T Consensus       235 ~f~~~~~~~~~~g~l~gl  252 (252)
T 2d5r_A          235 FFEDHIDDAKYCGHLYGL  252 (252)
T ss_dssp             TSCSSCCHHHHTTBCTTC
T ss_pred             hcCCCCCHHHcCCEecCC
Confidence            88765  56999999997
>4gmj_B CCR4-NOT transcription complex subunit 7; mRNA decay, deadenylase, RNA bindin; HET: GOL; 2.70A {Homo sapiens} Back     alignment and structure
>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation; 1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>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
>1zbu_A ERI-1 homolog, 3'-5' exonuclease ERI1; hydrolase; HET: AMP; 3.00A {Homo sapiens} Back     alignment and structure
>1y97_A Three prime repair exonuclease 2; TREX2, hydrolase; 2.50A {Homo sapiens} SCOP: c.55.3.5 Back     alignment and structure
>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 297
d2d5ra1252 c.55.3.9 (A:11-262) CCR4-NOT transcription complex 4e-69
d1uoca_286 c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast ( 5e-68
d2f96a1202 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas ae 0.001
d1w0ha_200 c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapien 0.002
>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 =  213 bits (543), Expect = 4e-69
 Identities = 89/255 (34%), Positives = 143/255 (56%), Gaps = 12/255 (4%)

Query: 6   KILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAV--ESYNDLKFNVD 63
           +I  VW  N +  M+ + +++  +N +++DTEFPG +        +     Y  L+ NVD
Sbjct: 1   RICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVD 60

Query: 64  CTHLIQLGITLSDKEGKISY---TFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKD 120
              +IQLG+T  +++G+      T++FNF  F+L +D++A DSI+LL  SG+ F K  ++
Sbjct: 61  LLKIIQLGLTFMNEQGEYPPGTSTWQFNFK-FNLTEDMYAQDSIELLTTSGIQFKKHEEE 119

Query: 121 GIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFF 180
           GI    FA   +       E +KW++FH  YD  YL+KI TN  LP     F  +  LFF
Sbjct: 120 GIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFF 179

Query: 181 QSVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMKNRY- 239
             ++D+K +   C+ L+G   GL ++A  L ++R G  H AGSDSLLT   F +M+  + 
Sbjct: 180 PVIYDVKYLMKSCKNLKG---GLQEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFF 236

Query: 240 --ELEESAFDGFLYG 252
              ++++ + G LYG
Sbjct: 237 EDHIDDAKYCGHLYG 251
>d1uoca_ c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 286 Back     information, alignment and structure
>d2f96a1 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287]} Length = 202 Back     information, alignment and structure
>d1w0ha_ c.55.3.5 (A:) Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 9606]} Length = 200 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 ?
Query297
d2d5ra1252 CCR4-NOT transcription complex subunit 7, CAF1 {Hu 100.0
d1uoca_286 Pop2 RNase D domain {Baker's yeast (Saccharomyces 100.0
d1w0ha_200 Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960 98.62
d2guia1174 N-terminal exonuclease domain of the epsilon subun 98.56
d2f96a1202 Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287 98.44
d1y97a1228 Three prime repair exonuclease 2, TREX2 {Human (Ho 98.28
d2qxfa1 467 Exonuclease I {Escherichia coli K12 (Escherichia c 97.95
d3b6oa1226 Three prime repair exonuclease 1, TREX1 {Mouse (Mu 97.82
d1wlja_173 Interferon-stimulated gene 20 kDa protein, ISG20 { 97.62
d1yt3a3193 Ribonuclease D, catalytic domain {Escherichia coli 97.01
d2hbka2292 Exosome complex exonuclease RRP6 {Baker's yeast (S 95.64
d1kfsa1195 Exonuclease domain of prokaryotic DNA polymerase { 95.34
d2igia1180 Oligoribonuclease {Escherichia coli [TaxId: 562]} 85.15
>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=6.5e-83  Score=585.44  Aligned_cols=242  Identities=38%  Similarity=0.673  Sum_probs=232.6

Q ss_pred             eeeeeccccHHHHHHHHHHHhhcCCeeEEeccccCcccCCC--CCCChhHHHHHHhhccccccceEEEeEEeccCCCcc-
Q 038950            6 KILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTP--RNAPAVESYNDLKFNVDCTHLIQLGITLSDKEGKIS-   82 (297)
Q Consensus         6 ~i~eVw~~N~~~el~~I~~~i~~~~fIAiDtEFpGv~~~p~--~~~t~eerY~~lk~nVd~~~iiQlGLt~~~~~g~~p-   82 (297)
                      +|||||++||++||+.|+++|++|+||||||||||++++|.  +++++|+||+++|+||+.+++||+|||+++++|+.| 
T Consensus         1 ~i~eV~~~Nf~e~~~~i~~~i~~~~fVAiD~EF~G~~~~~~~~~~~t~~~~Y~~lr~nv~~~~iiQ~Glt~~~~~g~~~~   80 (252)
T d2d5ra1           1 RICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVDLLKIIQLGLTFMNEQGEYPP   80 (252)
T ss_dssp             CEEEECGGGHHHHHHHHHHHHHHCCEEEEEEECCCCCCCCCSCCSSHHHHHHHHHHHHHTTCCCCEEEEEEECTTSCCCS
T ss_pred             CeEEehhhhHHHHHHHHHHHHhcCCEEEEeeeccCcccCCCCccCCCHHHHHHHHHHHHhhcceeEEEEEeecccCCCCC
Confidence            58999999999999999999999999999999999999886  777899999999999999999999999999999887 


Q ss_pred             --eeEEEeeecCCCCCCCCchhhHHHHHhcCCChhhhhhCCCCCcch--hhhhccccccCCCCceeEEeecchhHHHHHH
Q 038950           83 --YTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKDGIPRCVF--APRFLEVLSKHRENLKWVTFHGLYDVAYLVK  158 (297)
Q Consensus        83 --~~wqFNF~~Fd~~~d~~~~~SI~fL~~~GfDFnk~~~~GI~~~~F--ll~~SGLv~~~~~~~~Witfh~~yD~~yL~k  158 (297)
                        .+|||||+ |+.++|+|+++||+||+++||||||++++|||+..|  +++.||++++  ++++||+|||+|||+||+|
T Consensus        81 ~~~~w~FNf~-~~~~~~~~~~~Si~fL~~~G~DF~k~~~~GI~~~~f~~~l~~s~~~~~--~~~~wv~f~g~yD~~yl~k  157 (252)
T d2d5ra1          81 GTSTWQFNFK-FNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELLMTSGVVLC--EGVKWLSFHSGYDFGYLIK  157 (252)
T ss_dssp             SCCEEEEEBC-CCTTTSCCCHHHHHHHHHHTCCHHHHHHHCBCHHHHHHHHHTTTSSSS--SSCEEEESSCHHHHHHHHH
T ss_pred             CceeEEEEEE-eCCcccccCHHHHHHHHHcCCChHHHHHcCCCHHHHHHHHHhhhhhhc--CCCcEEEecchhHHHHHHH
Confidence              49999999 999999999999999999999999999999999999  8899999999  8999999999999999999


Q ss_pred             HhcCCCCCCChHHHHHHHHhccCcccchhHHHHhccccCCCcchHHHHHHHcCCcccCCCcccchHHHHHHHHHHHHH-H
Q 038950          159 IFTNDALPPTAEAFSGVAALFFQSVFDIKVVAGYCQGLQGLKLGLSKLARILNVKRHGGAHHAGSDSLLTAAVFAEMK-N  237 (297)
Q Consensus       159 ~l~g~~LP~t~~eF~~~l~~~FP~vyDtK~~a~~~~~l~~~~~~L~~la~~L~v~r~g~~HqAGsDSllT~~vF~kl~-~  237 (297)
                      +|+|++||+++++|++.++.+||++||||||++.|.++++   ||++||+.||++|+|++||||||||||++||++|+ .
T Consensus       158 ~l~~~~LP~~~~eF~~~v~~~FP~vyDtK~l~~~~~~~~~---~L~~la~~L~v~~~g~~H~AG~DsllT~~~F~~l~~~  234 (252)
T d2d5ra1         158 ILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKG---GLQEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREM  234 (252)
T ss_dssp             HHHTSCCCSSHHHHHHHHHHHCSCEEEHHHHGGGCTTCCS---SHHHHHHHHTCCCCSSTTSHHHHHHHHHHHHHHHHHH
T ss_pred             HHcCCCCCCCHHHHHHHHHHHCchHhhHHHHHhhccCCCc---hHHHHHHHcCCCCCCCCcchhHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999998888   99999999999999999999999999999999999 7


Q ss_pred             hcCCc--ccccCceeecC
Q 038950          238 RYELE--ESAFDGFLYGM  253 (297)
Q Consensus       238 ~f~~~--~~~~~g~l~Gl  253 (297)
                      ++++.  ..+++|+||||
T Consensus       235 ~~~~~~~~~~~~g~i~Gl  252 (252)
T d2d5ra1         235 FFEDHIDDAKYCGHLYGL  252 (252)
T ss_dssp             TSCSSCCHHHHTTBCTTC
T ss_pred             HhcCCCcHHHhCCcccCC
Confidence            77654  57899999997
>d1uoca_ c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1w0ha_ c.55.3.5 (A:) Exonuclease ERI1 {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
>d2f96a1 c.55.3.5 (A:19-220) Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287]} 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