Citrus Sinensis ID: 027829

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-------22
MSDVPPPQPPKPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFGFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLELLEC
ccccccccccccccEEEEcccccHHHHHHHHHHHHHcccEEEEEccccccEEccccccccccccHHHHHHHHHcccccEEEEEEEEEcccccccccccccccEEEEEEcccccccccccHHHHHHHHHHccccccccEEEEEEEccccccHHHHHcccHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHccccccccccccEEEccccccc
ccccccccccccccEHHHHHHHHHHHHHHHHHHHHHcccEEEEccccccEEEEEccccccccHHHHHHHHHHHHHHHHHHHHcEEEEcccccccccccccccEEEEEEccccccHHccccHHHHHHHHHcccEEcccEEEEEEcccHHHHHHHHHHccHHHHHHHccccEEccHccccccHHHHHHHHHHHHHHHHHcccccHHHcccEEEEccEEcc
msdvpppqppkprilIREVFEFNLISEFERIRALIdrypiismdtefpgvvvrpdsnirhrdpaanynglkANVDLLNLIQIGltlsdeegnlpdlgsgstyyiwefnfkdfdiarHAHALDSVELLKRQGlvlnkdvtwvtfhsaydfgfctclyggldRVCKALGVervvgkshqagsdSLLTLHAFLKIkdkhfgneyELQKYANVLhglellec
msdvpppqppkpriliREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFGFCTCLYGGLDRVCKALGVERVVGkshqagsdslLTLHAFLKIKDKHFGNEYELQKYANVLHGLELLEC
MSDVpppqppkpRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFGFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLELLEC
*************ILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFGFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLEL***
**********KPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFGFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLELLEC
*********PKPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFGFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLELLEC
**********KPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFGFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLELLEC
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSDVPPPQPPKPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGLVLNKDVTWVTFHSAYDFGFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLELLEC
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 ?
Query218 2.2.26 [Sep-21-2011]
Q9LXM2280 Probable CCR4-associated yes no 0.977 0.760 0.455 2e-53
Q9FMS6278 Probable CCR4-associated no no 0.926 0.726 0.455 9e-53
Q9LEU4277 Probable CCR4-associated no no 0.894 0.703 0.406 7e-47
Q9S9P2286 Probable CCR4-associated no no 0.963 0.734 0.396 4e-44
Q9SKZ2275 Probable CCR4-associated no no 0.899 0.712 0.390 5e-43
Q9SAI2274 Probable CCR4-associated no no 0.894 0.711 0.402 9e-42
O74856335 Poly(A) ribonuclease pop2 yes no 0.866 0.564 0.355 3e-32
Q60809285 CCR4-NOT transcription co yes no 0.871 0.666 0.351 4e-31
Q3ZC01285 CCR4-NOT transcription co yes no 0.871 0.666 0.351 4e-31
Q3KQ85285 CCR4-NOT transcription co N/A no 0.871 0.666 0.351 5e-31
>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 desciption
 Score =  208 bits (529), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 129/283 (45%), Positives = 162/283 (57%), Gaps = 70/283 (24%)

Query: 1   MSDVPPPQPPKP---RILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSN 57
           M+ + P +  KP    ++ REV+  NL SEFE I  +ID YP ISMDTEFPGV+ +  S+
Sbjct: 1   MAIIKPNRDLKPDGVTVVTREVWAENLESEFELISEIIDDYPFISMDTEFPGVIFK--SD 58

Query: 58  IRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSG-STYYIWEFNFKDFDIAR 116
           +R  +P   Y  LKANVD L+LIQ+GLTLSD  GNLPDLG      +IWEFNF+DFD+AR
Sbjct: 59  LRFTNPDDLYTLLKANVDALSLIQVGLTLSDVNGNLPDLGDDLHRGFIWEFNFRDFDVAR 118

Query: 117 HAHALDSVELLKRQ------------------------GLVLNKDVTWVTFHSAYDFG-- 150
            AHA DS+ELL+RQ                        GLV N++V+WVTFHSAYDFG  
Sbjct: 119 DAHAPDSIELLRRQGIDFERNCRDGVESERFAELMMSSGLVCNEEVSWVTFHSAYDFGYL 178

Query: 151 ------------------------------------FCT-CLYGGLDRVCKALGVERVVG 173
                                               FC   L+GGLDRV + L V R VG
Sbjct: 179 MKILTRRELPGALGEFKRVMRVLFGERVYDVKHMMKFCERRLFGGLDRVARTLEVNRAVG 238

Query: 174 KSHQAGSDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGLELL 216
           K HQAGSDSLLT HAF +++D +F  +   +K+A VL+GLE+ 
Sbjct: 239 KCHQAGSDSLLTWHAFQRMRDLYFVQDGP-EKHAGVLYGLEVF 280
Ubiquitous transcription factor required for a diverse set of processes. It is a component of the CCR4 complex involved in the control of gene expression.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 1EC: .EC: 1EC: 3EC: .EC: 4
>sp|Q9FMS6|CAF1K_ARATH Probable CCR4-associated factor 1 homolog 11 OS=Arabidopsis thaliana GN=CAF1-11 PE=2 SV=1 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|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|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|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|O74856|CAF1_SCHPO Poly(A) ribonuclease pop2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=caf1 PE=1 SV=2 Back     alignment and function description
>sp|Q60809|CNOT7_MOUSE CCR4-NOT transcription complex subunit 7 OS=Mus musculus GN=Cnot7 PE=1 SV=1 Back     alignment and function description
>sp|Q3ZC01|CNOT7_BOVIN CCR4-NOT transcription complex subunit 7 OS=Bos taurus GN=CNOT7 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

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 ?
Query218
224091915295 predicted protein [Populus trichocarpa] 0.935 0.691 0.553 2e-69
224140049296 predicted protein [Populus trichocarpa] 0.986 0.726 0.517 2e-67
356505410274 PREDICTED: probable CCR4-associated fact 0.926 0.737 0.518 1e-62
356572602274 PREDICTED: probable CCR4-associated fact 0.926 0.737 0.511 9e-62
255578601292 ccr4-associated factor, putative [Ricinu 0.926 0.691 0.496 4e-60
358343557 445 CCR4-associated factor [Medicago truncat 0.954 0.467 0.501 2e-59
225464848278 PREDICTED: probable CCR4-associated fact 0.931 0.730 0.501 9e-59
147839203265 hypothetical protein VITISV_015622 [Viti 0.917 0.754 0.498 6e-58
449443480277 PREDICTED: probable CCR4-associated fact 0.922 0.725 0.483 2e-56
359481632280 PREDICTED: probable CCR4-associated fact 0.944 0.735 0.474 2e-56
>gi|224091915|ref|XP_002309398.1| predicted protein [Populus trichocarpa] gi|222855374|gb|EEE92921.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  267 bits (683), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 151/273 (55%), Positives = 173/273 (63%), Gaps = 69/273 (25%)

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

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

Query: 131 ------------------------GLVLNKDVTWVTFHSAYDFG---------------- 150
                                   GLVLN+ V+WVTFH AYDFG                
Sbjct: 143 GIDFEKNRELGIDSVKFAELMMSSGLVLNQSVSWVTFHCAYDFGYLVKCLTHKVLPEGLN 202

Query: 151 ----------------------FCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHA 188
                                 FC  LYGGLDRVCK LGV+RV+GKSHQAGSDSLLTLHA
Sbjct: 203 EFLGLVRVFFGDRVYDIKHIIRFCAGLYGGLDRVCKELGVDRVIGKSHQAGSDSLLTLHA 262

Query: 189 FLKIKDKHF----GNEYELQKYANVLHGLELLE 217
           +LKIKDK+F     N+  L KYANVLHGLEL +
Sbjct: 263 YLKIKDKYFFKDKDNDRGLDKYANVLHGLELFD 295

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224140049|ref|XP_002323399.1| predicted protein [Populus trichocarpa] gi|222868029|gb|EEF05160.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356505410|ref|XP_003521484.1| PREDICTED: probable CCR4-associated factor 1 homolog 11-like [Glycine max] Back     alignment and taxonomy information
>gi|356572602|ref|XP_003554457.1| PREDICTED: probable CCR4-associated factor 1 homolog 11-like [Glycine max] Back     alignment and taxonomy information
>gi|255578601|ref|XP_002530162.1| ccr4-associated factor, putative [Ricinus communis] gi|223530323|gb|EEF32217.1| ccr4-associated factor, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|358343557|ref|XP_003635867.1| CCR4-associated factor [Medicago truncatula] gi|355501802|gb|AES83005.1| CCR4-associated factor [Medicago truncatula] Back     alignment and taxonomy information
>gi|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|449443480|ref|XP_004139505.1| PREDICTED: probable CCR4-associated factor 1 homolog 11-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|359481632|ref|XP_003632649.1| PREDICTED: probable CCR4-associated factor 1 homolog 9-like isoform 2 [Vitis vinifera] Back     alignment and taxonomy information

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 ?
Query218
TAIR|locus:2176307278 CAF1b "CCR4- associated factor 0.545 0.428 0.578 4.1e-59
TAIR|locus:2095715280 CAF1a "CCR4- associated factor 0.536 0.417 0.608 6.6e-59
TAIR|locus:2183765277 AT5G10960 [Arabidopsis thalian 0.564 0.444 0.48 2.6e-45
TAIR|locus:2200532286 AT1G15920 [Arabidopsis thalian 0.564 0.430 0.465 2.5e-41
TAIR|locus:2045512275 AT2G32070 [Arabidopsis thalian 0.541 0.429 0.478 2.8e-40
ZFIN|ZDB-GENE-061013-29286 cnot7 "CCR4-NOT transcription 0.522 0.398 0.446 3e-38
WB|WBGene00000369310 ccf-1 [Caenorhabditis elegans 0.513 0.361 0.378 4e-35
DICTYBASE|DDB_G0284217 367 DDB_G0284217 "CAF1 family prot 0.527 0.313 0.450 1.3e-34
UNIPROTKB|Q5ZJV9285 CNOT7 "CCR4-NOT transcription 0.522 0.4 0.446 4.8e-31
UNIPROTKB|Q3ZC01285 CNOT7 "CCR4-NOT transcription 0.522 0.4 0.446 4.8e-31
TAIR|locus:2176307 CAF1b "CCR4- associated factor 1b" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 362 (132.5 bits), Expect = 4.1e-59, Sum P(3) = 4.1e-59
 Identities = 70/121 (57%), Positives = 92/121 (76%)

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

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

Query:   132 L 132
             +
Sbjct:   132 I 132
GO:0003676 "nucleic acid binding" evidence=IEA
GO:0004540 "ribonuclease activity" evidence=ISS
GO:0005634 "nucleus" evidence=ISM
GO:0009451 "RNA modification" evidence=ISS
GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=IMP
GO:0008408 "3'-5' exonuclease activity" evidence=IDA
GO:0042742 "defense response to bacterium" evidence=IEP
GO:0000165 "MAPK cascade" evidence=RCA
GO:0002679 "respiratory burst involved in defense response" evidence=RCA
GO:0009693 "ethylene biosynthetic process" evidence=RCA
GO:0009738 "abscisic acid mediated signaling pathway" evidence=RCA
GO:0009814 "defense response, incompatible interaction" evidence=RCA
GO:0009873 "ethylene mediated signaling pathway" evidence=RCA
GO:0010200 "response to chitin" evidence=RCA
GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA
GO:0035556 "intracellular signal transduction" evidence=RCA
TAIR|locus:2095715 CAF1a "CCR4- associated factor 1a" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2183765 AT5G10960 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2200532 AT1G15920 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2045512 AT2G32070 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-061013-29 cnot7 "CCR4-NOT transcription complex, subunit 7" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
WB|WBGene00000369 ccf-1 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0284217 DDB_G0284217 "CAF1 family protein" [Dictyostelium discoideum (taxid:44689)] 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

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

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 ?
Query218
pfam04857235 pfam04857, CAF1, CAF1 family ribonuclease 8e-56
COG5228299 COG5228, POP2, mRNA deadenylase subunit [RNA proce 1e-46
>gnl|CDD|147159 pfam04857, CAF1, CAF1 family ribonuclease Back     alignment and domain information 
 Score =  177 bits (450), Expect = 8e-56
 Identities = 88/241 (36%), Positives = 107/241 (44%), Gaps = 72/241 (29%)

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

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

Query: 137 -------------------------DVTWVTFHSAYDFGF-------------------C 152
                                     VTWVTFH  YDFG+                    
Sbjct: 115 HRREGIPYLRFAELLGSSGLFLNISSVTWVTFHGLYDFGYLLKLLTGGPLPETLDDFLEL 174

Query: 153 TCLY----------------------GGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFL 190
                                     GGL  +   LGV R VG+ HQAGSDSLLT   F 
Sbjct: 175 LRELFPRVYDTKYLAKFCFELDGGSNGGLQELADLLGVNRRVGRLHQAGSDSLLTALVFF 234

Query: 191 K 191
           K
Sbjct: 235 K 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 218
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
smart00479169 EXOIII exonuclease domain in DNA-polymerase alpha 98.08
PRK07942232 DNA polymerase III subunit epsilon; Provisional 98.0
cd06131167 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonucl 97.87
PRK09145202 DNA polymerase III subunit epsilon; Validated 97.7
PRK06063 313 DNA polymerase III subunit epsilon; Provisional 97.47
cd06133176 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain o 97.46
PRK07748207 sporulation inhibitor KapD; Provisional 97.39
TIGR00573217 dnaq exonuclease, DNA polymerase III, epsilon subu 97.24
PRK08074 928 bifunctional ATP-dependent DNA helicase/DNA polyme 97.15
PRK06310250 DNA polymerase III subunit epsilon; Validated 97.15
PRK07247195 DNA polymerase III subunit epsilon; Validated 97.1
cd06136177 TREX1_2 DEDDh 3'-5' exonuclease domain of three pr 97.09
cd06130156 DNA_pol_III_epsilon_like an uncharacterized bacter 97.08
PRK05168211 ribonuclease T; Provisional 97.08
PRK08517257 DNA polymerase III subunit epsilon; Provisional 97.06
PRK06807 313 DNA polymerase III subunit epsilon; Validated 97.03
KOG1990 564 consensus Poly(A)-specific exoribonuclease PARN [R 97.01
TIGR01406225 dnaQ_proteo DNA polymerase III, epsilon subunit, P 96.99
PRK05711240 DNA polymerase III subunit epsilon; Provisional 96.94
PRK07883 557 hypothetical protein; Validated 96.84
PRK07740244 hypothetical protein; Provisional 96.84
PRK09146239 DNA polymerase III subunit epsilon; Validated 96.8
PRK06195 309 DNA polymerase III subunit epsilon; Validated 96.68
TIGR01407 850 dinG_rel DnaQ family exonuclease/DinG family helic 96.55
PRK07246 820 bifunctional ATP-dependent DNA helicase/DNA polyme 96.42
cd06127159 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh 96.21
PRK07983219 exodeoxyribonuclease X; Provisional 96.11
PRK11779 476 sbcB exonuclease I; Provisional 95.85
TIGR01405 1213 polC_Gram_pos DNA polymerase III, alpha chain, Gra 95.47
PRK09182294 DNA polymerase III subunit epsilon; Validated 95.4
PRK00448 1437 polC DNA polymerase III PolC; Validated 95.15
PRK05601 377 DNA polymerase III subunit epsilon; Validated 93.01
COG0847243 DnaQ DNA polymerase III, epsilon subunit and relat 92.95
cd06134189 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. 92.6
PF00929164 RNase_T: Exonuclease; InterPro: IPR013520 This ent 92.35
PRK06722281 exonuclease; Provisional 89.81
TIGR01298200 RNaseT ribonuclease T. in gamma-subdivision Proteo 88.95
cd06144152 REX4_like DEDDh 3'-5' exonuclease domain of RNA ex 88.86
cd06149157 ISG20 DEDDh 3'-5' exonuclease domain of Interferon 86.42
PRK05755 880 DNA polymerase I; Provisional 84.51
PRK06309232 DNA polymerase III subunit epsilon; Validated 81.17
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification] Back     alignment and domain information 
Probab=100.00  E-value=6e-77  Score=508.86  Aligned_cols=176  Identities=58%  Similarity=0.977  Sum_probs=168.5

Q ss_pred             eEEEeccccHHHHHHHHHHhhhcCCeEEEeccccceeecCCCCCCCCCcccchHHHhhhcccccceeeeeeeecCCCCCC
Q 027829           15 LIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLSDEEGNLP   94 (218)
Q Consensus        15 ~I~eVwa~NleeE~~~I~~~i~~~~yIAmDtEFPGvv~~p~~~~~~~~~~~~Y~~lk~NVd~l~iIQlGit~~~~~G~~p   94 (218)
                      .||+||++|+++||++||++|++||||||||||||++++|.+.|+++. |++||+||+|||.+|+||+|||++|++|++|
T Consensus         1 ~ireVW~~Nl~~Em~~Ir~~v~~y~~IamDTEFPGvv~rp~~~f~s~~-d~~Y~~lk~NVd~lklIQlGlTlsd~~Gn~p   79 (239)
T KOG0304|consen    1 FIREVWRSNLEEEMALIRECVKDYPYIAMDTEFPGVVARPIGTFRSSD-DYHYQTLKCNVDNLKLIQLGLTLSDEKGNLP   79 (239)
T ss_pred             ChhHHHHHhHHHHHHHHHHHHHhCCeeEecCcCCceeeecCccccCCh-HHHHHHHHhchhhhhhhheeeeeeccCCCCC
Confidence            479999999999999999999999999999999999999999999888 9999999999999999999999999999999


Q ss_pred             CCCCCCCceeEEEeeeeeccccCCCchhHHHHHHhcC------------------------ccccCCeeEEeeccccccc
Q 027829           95 DLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQG------------------------LVLNKDVTWVTFHSAYDFG  150 (218)
Q Consensus        95 ~~~~~~~~~~wqFNF~~Fd~~~d~~~~~SI~lL~~~G------------------------lv~~~~v~WvtFhg~yDfg  150 (218)
                      .+|    .++|||||++||+.+|+++++||+||+++|                        ++++++|+|||||||||||
T Consensus        80 ~~g----~~tWqfNF~dF~~~~D~~a~~SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YDfg  155 (239)
T KOG0304|consen   80 DCG----TDTWQFNFSDFNLEKDMYAQDSIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHSGYDFG  155 (239)
T ss_pred             CCC----CceeEEecccCCchhhccchhhHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeeccchHH
Confidence            775    469999999999999999999999999999                        7889999999999999999


Q ss_pred             -------------------------------------ccc--cccCcHHHHHHHhCccccCCCCCCchhHHHHHHHHHHH
Q 027829          151 -------------------------------------FCT--CLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLK  191 (218)
Q Consensus       151 -------------------------------------~~~--~l~ggL~~vA~~L~v~r~~g~~hqAGsdsllT~~~F~k  191 (218)
                                                           +|.  +++|||++||+.|+|+| +|++||||||||||+++|+|
T Consensus       156 YLlK~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK~l~~~c~~~~l~~GL~~lA~~L~~~R-vG~~HqAGSDSlLT~~~F~k  234 (239)
T KOG0304|consen  156 YLLKILTGKPLPETEEEFFEIVRQLFPFVYDVKYLMKFCEGLSLKGGLQRLADLLGLKR-VGIAHQAGSDSLLTARVFFK  234 (239)
T ss_pred             HHHHHHcCCCCcchHHHHHHHHHHHcchhhhHHHHHHhhhhhhhhcCHHHHHHHhCCCe-eecccccCcHHHHHHHHHHH
Confidence                                                 574  48999999999999999 99999999999999999999


Q ss_pred             HHHhh
Q 027829          192 IKDKH  196 (218)
Q Consensus       192 l~~~~  196 (218)
                      ||+.|
T Consensus       235 l~~~f  239 (239)
T KOG0304|consen  235 LKELF  239 (239)
T ss_pred             HHhcC
Confidence            99864

>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
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases Back     alignment and domain information
>PRK07942 DNA polymerase III subunit epsilon; 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
>PRK09145 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06063 DNA polymerase III subunit epsilon; Provisional 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
>PRK07748 sporulation inhibitor KapD; Provisional Back     alignment and domain information
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family Back     alignment and domain information
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06310 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07247 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins Back     alignment and domain information
>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
>PRK05168 ribonuclease T; Provisional Back     alignment and domain information
>PRK08517 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK06807 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair] Back     alignment and domain information
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial Back     alignment and domain information
>PRK05711 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK07883 hypothetical protein; Validated Back     alignment and domain information
>PRK07740 hypothetical protein; Provisional 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
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative Back     alignment and domain information
>PRK07246 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
>PRK07983 exodeoxyribonuclease X; Provisional Back     alignment and domain information
>PRK11779 sbcB exonuclease I; Provisional Back     alignment and domain information
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type 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
>PRK05601 DNA polymerase III subunit epsilon; 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
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T 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
>PRK06722 exonuclease; Provisional Back     alignment and domain information
>TIGR01298 RNaseT ribonuclease T 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
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>PRK06309 DNA polymerase III subunit epsilon; Validated 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 ?
Query218
2p51_A333 Crystal Structure Of The S. Pombe Pop2p Deadenylati 3e-33
4gmj_B285 Structure Of Human Not1 Mif4g Domain Co-Crystallize 3e-32
2d5r_A252 Crystal Structure Of A Tob-Hcaf1 Complex Length = 2 4e-32
4b8a_B286 Structure Of Yeast Not1 Mif4g Domain Co-Crystallize 5e-24
4b8c_A288 Nuclease Module Of The Yeast Ccr4-Not Complex Lengt 6e-24
1uoc_A289 X-Ray Structure Of The Rnase Domain Of The Yeast Po 6e-24
>pdb|2P51|A Chain A, Crystal Structure Of The S. Pombe Pop2p Deadenylation Subunit Length = 333 Back     alignment and structure 
Iteration: 1

 Score =  138 bits (347), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 92/259 (35%), Positives = 125/259 (48%), Gaps = 70/259 (27%)
Query: 16  IREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVD 75
           IR+V+  NL  E   I +LI+RYP++SMDTEFPGVV RP    +  D   +Y  L+ANVD
Sbjct: 23  IRDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVARPLGVFKSSD-DYHYQTLRANVD 81
Query: 76  LLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKR------ 129
            L +IQIGL LSDEEGN P          W+FNF  F++    +A +S+ELL +      
Sbjct: 82  SLKIIQIGLALSDEEGNAPVEAC-----TWQFNFT-FNLQDDMYAPESIELLTKSGIDFK 135
Query: 130 ------------------QGLVLNKDVTWVTFHSAYDFGF-------------------C 152
                              GLVL ++VTW+TFHS YDF +                    
Sbjct: 136 KHQEVGIEPADFAELLIGSGLVLQEEVTWITFHSGYDFAYLLKAMTQIPLPAEYEEFYKI 195
Query: 153 TCLY------------------GGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIKD 194
            C+Y                   GL  +   L + R +G  HQAGSD+LLT   F +I+ 
Sbjct: 196 LCIYFPKNYDIKYIMKSVLNNSKGLQDIADDLQIHR-IGPQHQAGSDALLTARIFFEIRS 254
Query: 195 KHFGNEYELQKYANVLHGL 213
           ++F    +  +  N L+GL
Sbjct: 255 RYFDGSID-SRMLNQLYGL 272
>pdb|4GMJ|B Chain B, Structure Of Human Not1 Mif4g Domain Co-Crystallized With Caf1 Length = 285 Back     alignment and structure
>pdb|2D5R|A Chain A, Crystal Structure Of A Tob-Hcaf1 Complex Length = 252 Back     alignment and structure
>pdb|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 ?
Query218
2p51_A333 SPCC18.06C protein; DEDD nuclease fold, hydrolase, 3e-59
1uoc_A289 POP2; hydrolase, DEDD nuclease, mRNA degradation, 3e-59
2d5r_A252 CCR4-NOT transcription complex subunit 7; poly(A) 6e-57
2a1r_A 430 Poly(A)-specific ribonuclease PARN; DEDD, nuclease 2e-19
3d45_A 507 Poly(A)-specific ribonuclease PARN; CAP analogue, 3e-19
>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 =  188 bits (479), Expect = 3e-59
 Identities = 89/274 (32%), Positives = 121/274 (44%), Gaps = 70/274 (25%)

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

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

Query: 121 LDSVELLKRQG------------------------LVLNKDVTWVTFHSAYDFGF----- 151
            +S+ELL + G                        LVL ++VTW+TFHS YDF +     
Sbjct: 121 PESIELLTKSGIDFKKHQEVGIEPADFAELLIGSGLVLQEEVTWITFHSGYDFAYLLKAM 180

Query: 152 --------------------------------CTCLYGGLDRVCKALGVERVVGKSHQAG 179
                                                 GL  +   L + R +G  HQAG
Sbjct: 181 TQIPLPAEYEEFYKILCIYFPKNYDIKYIMKSVLNNSKGLQDIADDLQIHR-IGPQHQAG 239

Query: 180 SDSLLTLHAFLKIKDKHFGNEYELQKYANVLHGL 213
           SD+LLT   F +I+ ++F       +  N L+GL
Sbjct: 240 SDALLTARIFFEIRSRYFDGS-IDSRMLNQLYGL 272
>1uoc_A POP2; hydrolase, DEDD nuclease, mRNA degradation, poly(A) tail, transcription regulation, repressor, phosphorylation.; 2.3A {Saccharomyces cerevisiae} SCOP: c.55.3.9 Length = 289 Back     alignment and structure
>2d5r_A CCR4-NOT transcription complex subunit 7; poly(A) deadenylase, antiproliferative protein, transcription; 2.50A {Homo sapiens} SCOP: c.55.3.9 Length = 252 Back     alignment and structure
>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase-RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A Length = 430 Back     alignment and structure
>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus} Length = 507 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

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 218
d1uoca_286 c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast ( 2e-61
d2d5ra1252 c.55.3.9 (A:11-262) CCR4-NOT transcription complex 7e-61
>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 =  191 bits (486), Expect = 2e-61
 Identities = 78/290 (26%), Positives = 118/290 (40%), Gaps = 87/290 (30%)

Query: 5   PPPQ-PPKPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDP 63
           PP   PP   + +R+V++ NL SEF  IR L+ +Y  +S+ TEF G + RP         
Sbjct: 1   PPIFLPPPNYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGT-FRSKV 59

Query: 64  AANYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDS 123
             +Y  ++ANVD LN IQ+GL+LSD  GN PD    +    W+FNF+ FD  +   + +S
Sbjct: 60  DYHYQTMRANVDFLNPIQLGLSLSDANGNKPD----NGPSTWQFNFE-FDPKKEIMSTES 114

Query: 124 VELLKRQG------------------------LVLNKDVTWVTFHSAYDFGF-------- 151
           +ELL++ G                        L+++  VTW+T+H+AYD GF        
Sbjct: 115 LELLRKSGINFEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMND 174

Query: 152 --------------------------------------------CTCLYGGLDRVCKALG 167
                                                              L  +   LG
Sbjct: 175 SMPNNKEDFEWWVHQYMPNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELG 234

Query: 168 VERVVGKSHQAGSDSLLTLHAFLKIKDKH---FGNEYELQKYANVLHGLE 214
           + R        G  SLL L +F ++       F N  +  KY  V++G++
Sbjct: 235 LPRF-SIFTTTGGQSLLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGID 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 ?
Query218
d1uoca_286 Pop2 RNase D domain {Baker's yeast (Saccharomyces 100.0
d2d5ra1252 CCR4-NOT transcription complex subunit 7, CAF1 {Hu 100.0
d2guia1174 N-terminal exonuclease domain of the epsilon subun 98.13
d2qxfa1 467 Exonuclease I {Escherichia coli K12 (Escherichia c 98.06
d2f96a1202 Ribonuclease T {Pseudomonas aeruginosa [TaxId: 287 97.94
d1w0ha_200 Exonuclease ERI1 {Human (Homo sapiens) [TaxId: 960 97.92
d1y97a1228 Three prime repair exonuclease 2, TREX2 {Human (Ho 97.72
d3b6oa1226 Three prime repair exonuclease 1, TREX1 {Mouse (Mu 96.98
d1wlja_173 Interferon-stimulated gene 20 kDa protein, ISG20 { 96.78
d2hbka2292 Exosome complex exonuclease RRP6 {Baker's yeast (S 95.03
d1kfsa1195 Exonuclease domain of prokaryotic DNA polymerase { 91.78
d1yt3a3193 Ribonuclease D, catalytic domain {Escherichia coli 84.49
>d1uoca_ c.55.3.9 (A:) Pop2 RNase D domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: CAF1-like ribonuclease
domain: Pop2 RNase D domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=0  Score=439.71  Aligned_cols=202  Identities=37%  Similarity=0.665  Sum_probs=184.2

Q ss_pred             CCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCEEEEECCCCCEEECCCCCCCCCCCCCCHHHHHHHCCCCCCEEEEEEEE
Q ss_conf             99999851887164568999999998651299389941235201068999989994202387863001211023232341
Q 027829            8 QPPKPRILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVDLLNLIQIGLTLS   87 (218)
Q Consensus         8 ~~~~~~~~IreVwa~Nle~E~~~I~~li~~~~yIAiDtEFPGvv~~p~g~~~~~~~~~~Y~~lk~NVd~l~iIQlGitl~   87 (218)
                      .|++..+.|||||++||++||++|+++|++|+||||||||||++++|.+.+++++ |+||+++|+|||.+++||+|||++
T Consensus         5 ~p~~~~~~i~dVw~~N~~~e~~~i~~~i~~~~fvaiD~EF~Gi~~~~~~~~~~t~-d~~Y~~lr~nvd~~~iiQlGlt~f   83 (286)
T d1uoca_           5 LPPPNYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSKV-DYHYQTMRANVDFLNPIQLGLSLS   83 (286)
T ss_dssp             CCCGGGGCCEEECTTTHHHHHHHHHHHTTTSCEEEEEEEEEC----------CHH-HHHHHHHHHHHTTCEEEEEEEEEE
T ss_pred             CCCCCEEEEEECHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCCCCCCCCCH-HHHHHHHHHHHHHCCEEEEEEEEE
T ss_conf             8998847999820535999999999998429989994150684357887778998-999999998674455467766531


Q ss_pred             CCCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCHHHHHHHHHCC------------------------CCCCCCEEEEEE
Q ss_conf             68899889999997004898322224466777566899998629------------------------302587018950
Q 027829           88 DEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQG------------------------LVLNKDVTWVTF  143 (218)
Q Consensus        88 ~~~G~~p~~~~~~~~~~WqFNF~~Fd~~~d~~~~~Si~lL~~~G------------------------lv~~~~v~WvtF  143 (218)
                      +++|+.|..    .+++|||||+ |+..+|+|+++||+||+++|                        ++++++++||||
T Consensus        84 ~~~g~~~~~----~~~~w~FNF~-f~~~~d~~~~~Si~fL~~~G~DF~k~~~~GI~~~~F~~ll~~s~l~~~~~~~wi~f  158 (286)
T d1uoca_          84 DANGNKPDN----GPSTWQFNFE-FDPKKEIMSTESLELLRKSGINFEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITY  158 (286)
T ss_dssp             CTTCCCCSS----SCSEEEEEBC-CCTTCCCCCHHHHHHHHHTTCCHHHHHHHCBCHHHHHHHHHTSSCSSCTTSEEEES
T ss_pred             CCCCCCCCC----CCEEEEEEEE-ECCCCCCCCHHHHHHHHHCCCCHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCEEEE
T ss_conf             356877888----8438999778-65865554578999999859985899874997888999998655430688516882


Q ss_pred             CCCCCCC-------------------------------------CCC---------------CCCCCHHHHHHHHCCCCC
Q ss_conf             0443100-------------------------------------146---------------546768889978196223
Q 027829          144 HSAYDFG-------------------------------------FCT---------------CLYGGLDRVCKALGVERV  171 (218)
Q Consensus       144 hg~yDfg-------------------------------------~~~---------------~l~ggL~~vA~~L~v~r~  171 (218)
                      ||+||||                                     .|.               ..++||+++|+.|+|+| 
T Consensus       159 hg~yD~~yl~k~l~~~~LP~~~~eF~~~v~~~FP~iyDtK~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~ia~~l~v~~-  237 (286)
T d1uoca_         159 HAAYDLGFLINILMNDSMPNNKEDFEWWVHQYMPNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELGLPR-  237 (286)
T ss_dssp             STTHHHHHHHHHHTTSCCCSSHHHHHHHHHHHCSSEEEHHHHHHHHTTTCC-------------CCSHHHHHHHTTCCC-
T ss_pred             CCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCEEHHHHHHHHHCCCCCCCCCHHHHHCCCCCCHHHHHHHCCCCC-
T ss_conf             2457899999998488899789999999999877430599999975101464211001110002378788888549986-


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHC---CCCCCCCCCCCEEECCCCC
Q ss_conf             79999853579999999999997507---9920000003237426988
Q 027829          172 VGKSHQAGSDSLLTLHAFLKIKDKHF---GNEYELQKYANVLHGLELL  216 (218)
Q Consensus       172 ~g~~hqAGsdsllt~~~F~kl~~~~f---~~~~~~~~~~g~l~Gl~~~  216 (218)
                      +|.+|||||||+||++||++|++.++   .+.++..+|.|+||||+.+
T Consensus       238 ~g~~HeAG~DSllT~~~F~~l~~~~~~~f~~~~~~~~~~g~l~Gl~~~  285 (286)
T d1uoca_         238 FSIFTTTGGQSLLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGIDGD  285 (286)
T ss_dssp             CGGGGSHHHHHHHHHHHHHHHHHHTTTBCTTSCBGGGGTTCSSCCTTC
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCEEECCCCC
T ss_conf             577755387899999999999998876546996478849777177889
>d2d5ra1 c.55.3.9 (A:11-262) CCR4-NOT transcription complex subunit 7, CAF1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2guia1 c.55.3.5 (A:7-180) N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2qxfa1 c.55.3.5 (A:8-474) Exonuclease I {Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333]} 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
>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
>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
>d1yt3a3 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure