Citrus Sinensis ID: 047627

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-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420--
METSRTHPVSETQLNNLSLSFENLQVNDPSYSSFNEIHPSPPVPLYPQSTWAVPSLSGRSTVPNLSGTSNPQYETITSSNFQTPLGFQANPFQHCANSGILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNCLKYRITVNYIVEEFLLNSDQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLVTKLQQNLDSLRFGYGKHVYNFIKDCDLQN
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccHHcccccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHcccHHHHHHHHHHHHHcHHHHHHHHHcccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHcccccHHHHHHHHHcccHHHHHHHHcccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHcc
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccEEEEcHccccHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHccccHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHcccEEEEEEcccccHHHHHHHHcccccHHHHHHHHHHHcccEEEEccccccHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
metsrthpvsetqlnnLSLSFEnlqvndpsyssfneihpsppvplypqstwavpslsgrstvpnlsgtsnpqyetitssnfqtplgfqanpfqhcanSGILLLAQDEQGSQYLQEkltsgdsrfLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNfidemkgprrKQILYLISVNAASlsrnfsgnyVVQHVLELEDPYLIETICFSLRghyidlsltkcgsfvVQNCLKYRITVNYIVEEFLLNSDQIFRVACDKYGNYVIQTALIEtmrpnslhLHQRLVTKLQQNLDSLRFGYGKHVYNFIKDCDLQN
metsrthpvsetqlnnLSLSFENLQVNDPSYSSFNEIHPSPPVPLYPQSTWAVPSLSGRSTVPNLSGTSNPQYETITSSNFQTPLGFQANPFQHCANSGILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKavanrppllDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNCLKYRITVNYIVEEFLLNSDQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLVTKLQQNLDSLRFGYGKHVYNFIKDCDLQN
METSRTHPVSETQLNNLSLSFENLQVNDPSYSSFNEIHPSPPVPLYPQSTWAVPSLSGRSTVPNLSGTSNPQYETITSSNFQTPLGFQANPFQHCANSGILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNCLKYRITVNYIVEEFLLNSDQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLVTKLQQNLDSLRFGYGKHVYNFIKDCDLQN
********************************************************************************FQTPLGFQANPFQHCANSGILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNCLKYRITVNYIVEEFLLNSDQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLVTKLQQNLDSLRFGYGKHVYNFIKDCD***
******************************************************************************************PFQHCANSGILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNCLKYRITVNYIVEEFLLNSDQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLVTKLQQNLDSLRFGYGKHVYNFIKDCDL**
***********TQLNNLSLSFENLQVNDPSYSSFNEIHPSPPVPLYPQSTWAVPSLSGRSTVPNLSGTSNPQYETITSSNFQTPLGFQANPFQHCANSGILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNCLKYRITVNYIVEEFLLNSDQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLVTKLQQNLDSLRFGYGKHVYNFIKDCDLQN
****************LSLSFENLQVNDPSYSSFNEIHPSPPVPLYPQSTWAVPSLSGRSTV**************************ANPFQHCANSGILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNCLKYRITVNYIVEEFLLNSDQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLVTKLQQNLDSLRFGYGKHVYNFIKDCDL**
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
METSRTHPVSETQLNNLSLSFENLQVNDPSYSSFNEIHPSPPVPLYPQSTWAVPSLSGRSTVPNLSGTSNPQYETITSSNFQTPLGFQANPFQHCANSGILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQILYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNCLKYRITVNYIVEEFLLNSDQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLVTKLQQNLDSLRFGYGKHVYNFIKDCDLQN
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 ?
Query422 2.2.26 [Sep-21-2011]
Q9LVC3596 Pumilio homolog 12 OS=Ara yes no 0.729 0.516 0.316 5e-39
Q9LXC5517 Putative pumilio homolog no no 0.744 0.607 0.290 2e-32
Q9LM20515 Putative pumilio homolog no no 0.672 0.551 0.275 2e-30
Q9C9R6650 Putative pumilio homolog no no 0.680 0.441 0.282 3e-29
Q9LDW3556 Pumilio homolog 11 OS=Ara no no 0.646 0.491 0.306 5e-28
Q9LVG3327 Pumilio homolog 18 OS=Ara no no 0.618 0.798 0.312 6e-23
Q1PFN9564 Pumilio homolog 9 OS=Arab no no 0.670 0.501 0.275 1e-22
Q9LSS8327 Putative pumilio homolog no no 0.618 0.798 0.312 2e-22
O81465477 Pumilio homolog 15 OS=Ara no no 0.739 0.654 0.271 1e-21
Q9LP21528 Putative pumilio homolog no no 0.680 0.543 0.285 1e-20
>sp|Q9LVC3|PUM12_ARATH Pumilio homolog 12 OS=Arabidopsis thaliana GN=APUM12 PE=2 SV=2 Back     alignment and function desciption
 Score =  162 bits (409), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 101/319 (31%), Positives = 179/319 (56%), Gaps = 11/319 (3%)

Query: 96  ANSGILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIET 155
           A   I  LA+D+ G ++LQ   +  D   ++ +FN + ++  +++ + +  ++  K +E 
Sbjct: 278 ARGKIYYLAKDQHGCRFLQRIFSEKDGNDIEMIFNEIIDYISELMMDPFGNYLVQKLLEV 337

Query: 156 CNEDQLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRL 215
           CNEDQ ++I   IT +  L ++ S D  G+ +++K+++  A R   + +++ ALK     
Sbjct: 338 CNEDQRMQIVHSITRKPGLLIKISCDMHGTRAVQKIVE-TAKREEEISIIISALKHGIVH 396

Query: 216 LMMTKPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPR 275
           L+    G+ VV +CL+ +  +  K  F+++AA+ HC+ LA    GC  +   +   +G +
Sbjct: 397 LIKNVNGNHVVQRCLQYLLPYCGK--FLFEAAITHCVELATDRHGCCVLQKCLGYSEGEQ 454

Query: 276 RKQILYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFV 335
           ++ ++  I+ NA  LS++  GNYV+Q+V EL+  +    I   L G+Y +LS+ KC S V
Sbjct: 455 KQHLVSEIASNALLLSQDPFGNYVLQYVFELQLQWATFEILEQLEGNYTELSMQKCSSNV 514

Query: 336 VQNCLKYRITVN--YIVEEFLLNSDQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLV 393
           V+ CLK     +   I+ E L+N  ++ +V  D YGNYVIQ AL    + +  ++H  LV
Sbjct: 515 VEKCLKLADDKHRARIIRE-LINYGRLDQVMLDPYGNYVIQAAL----KQSKGNVHALLV 569

Query: 394 TKLQQNLDSLRFG-YGKHV 411
             ++ N+ SLR   YGK V
Sbjct: 570 DAIKLNISSLRTNPYGKKV 588
Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.
Arabidopsis thaliana (taxid: 3702)
>sp|Q9LXC5|PUM21_ARATH Putative pumilio homolog 21 OS=Arabidopsis thaliana GN=APUM21 PE=3 SV=1 Back     alignment and function description
>sp|Q9LM20|PUM8_ARATH Putative pumilio homolog 8, chloroplastic OS=Arabidopsis thaliana GN=APUM8 PE=3 SV=2 Back     alignment and function description
>sp|Q9C9R6|PUM7_ARATH Putative pumilio homolog 7, chloroplastic OS=Arabidopsis thaliana GN=APUM7 PE=3 SV=2 Back     alignment and function description
>sp|Q9LDW3|PUM11_ARATH Pumilio homolog 11 OS=Arabidopsis thaliana GN=APUM11 PE=3 SV=2 Back     alignment and function description
>sp|Q9LVG3|PUM18_ARATH Pumilio homolog 18 OS=Arabidopsis thaliana GN=APUM18 PE=2 SV=1 Back     alignment and function description
>sp|Q1PFN9|PUM9_ARATH Pumilio homolog 9 OS=Arabidopsis thaliana GN=APUM9 PE=2 SV=1 Back     alignment and function description
>sp|Q9LSS8|PUM19_ARATH Putative pumilio homolog 19 OS=Arabidopsis thaliana GN=APUM19 PE=3 SV=2 Back     alignment and function description
>sp|O81465|PUM15_ARATH Pumilio homolog 15 OS=Arabidopsis thaliana GN=APUM15 PE=3 SV=1 Back     alignment and function description
>sp|Q9LP21|PUM10_ARATH Putative pumilio homolog 10 OS=Arabidopsis thaliana GN=APUM10 PE=3 SV=2 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 ?
Query422
255544718483 conserved hypothetical protein [Ricinus 0.959 0.838 0.346 2e-53
255553119471 RNA binding protein, putative [Ricinus c 0.966 0.866 0.344 3e-52
224117628502 predicted protein [Populus trichocarpa] 0.874 0.735 0.318 1e-46
224056741497 predicted protein [Populus trichocarpa] 0.921 0.782 0.313 5e-42
147798084507 hypothetical protein VITISV_039435 [Viti 0.703 0.585 0.346 6e-38
22327888 596 pumilio 12 [Arabidopsis thaliana] gi|313 0.729 0.516 0.316 4e-37
297793151 598 APUM12 [Arabidopsis lyrata subsp. lyrata 0.729 0.515 0.316 7e-37
255564824 771 RNA binding protein, putative [Ricinus c 0.727 0.398 0.314 7e-36
255545698 1204 conserved hypothetical protein [Ricinus 0.663 0.232 0.319 2e-35
8809626 604 unnamed protein product [Arabidopsis tha 0.729 0.509 0.308 3e-35
>gi|255544718|ref|XP_002513420.1| conserved hypothetical protein [Ricinus communis] gi|223547328|gb|EEF48823.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
 Score =  216 bits (550), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 163/471 (34%), Positives = 244/471 (51%), Gaps = 66/471 (14%)

Query: 2   ETSRTHPVSETQLNNLSLSFENLQ-VNDPSYSS--------FN----------------- 35
           ET +++   ++ +++LS S ENL  +N   YSS        FN                 
Sbjct: 13  ETPKSNLFVDSAIDSLSFSVENLSLINGDGYSSIGSNNSLAFNGEFSASRTQETTPDIQE 72

Query: 36  ---EIHPSPPV-PLYPQSTWAVPSLSGRSTVPNLSGTSNPQYETITSSNFQT-------P 84
              E+  +P + PLYP   WAV      STV   +G     +      NFQ+       P
Sbjct: 73  TGLEMSRTPVLTPLYPDGIWAV----NYSTVN--AGIHLSSFHGYHDMNFQSNNYDGASP 126

Query: 85  LGFQANPFQHCANS-----------GILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVS 133
              Q +    C  S             ++ A  +QGS++LQ+ L   +S F  K+   V+
Sbjct: 127 SAIQESNENSCMVSQDFIPSMQNQESFIMFASTQQGSKHLQDLLAYSNSDFASKLLETVT 186

Query: 134 EFTFQI------ICNQYARFVFGKFIETCNEDQLLRITLQITSQDQLFVQASVDKFGSSS 187
               +I      + +QY   V  K I++CN+ QL  I  +IT  D+ FVQ   +  GS  
Sbjct: 187 ASVVEIPVINYLMVDQYGCHVCSKLIDSCNDKQLALILERITRNDEQFVQICCNINGSKM 246

Query: 188 IRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKNDFIYQAA 247
           I+KL+K V  R  L+  +  +L + F  L + + GS VV+ C++ +     ++  +Y+AA
Sbjct: 247 IKKLIKKV-KRSCLICYMTVSLYKGFCQLAINQIGSYVVVFCMDCL--DVKQSALLYEAA 303

Query: 248 LEHCLYLACHEQGCINMNNFIDEMKGPRRKQILYLISVNAASLSRNFSGNYVVQHVLELE 307
           + HCL LA    GC+++NNFID ++G  R+ +L LIS NA  LS++ SGN+VVQ VLELE
Sbjct: 304 ISHCLILATDATGCVSINNFIDRIQGSHRQTLLELISDNAVFLSQDPSGNHVVQKVLELE 363

Query: 308 DPYLIETICFSLRGHYIDLSLTKCGSFVVQNCLKYRITVNYIVEEFLL-NSDQIFRVACD 366
           +P +   I   L+GHY  LS  K GS VV+ CL  +  V Y+V++ L   S Q+ ++A D
Sbjct: 364 NPIINAKIGAQLKGHYARLSFQKWGSHVVEKCLVSQPIV-YVVQDLLTCGSSQLSQIARD 422

Query: 367 KYGNYVIQTALIETMRPNSLHLHQRLVTKLQQNLDSLRFGYGKHVYNFIKD 417
           ++GNYVIQ AL  T + N + LH  L+  L+ NL++L+ GYGK VY  I D
Sbjct: 423 QFGNYVIQKALKVTKKKN-ITLHLILLNSLKPNLNALQNGYGKKVYRLIMD 472

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255553119|ref|XP_002517602.1| RNA binding protein, putative [Ricinus communis] gi|223543234|gb|EEF44766.1| RNA binding protein, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|224117628|ref|XP_002317626.1| predicted protein [Populus trichocarpa] gi|222860691|gb|EEE98238.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224056741|ref|XP_002299000.1| predicted protein [Populus trichocarpa] gi|222846258|gb|EEE83805.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|147798084|emb|CAN67257.1| hypothetical protein VITISV_039435 [Vitis vinifera] Back     alignment and taxonomy information
>gi|22327888|ref|NP_200462.2| pumilio 12 [Arabidopsis thaliana] gi|313471423|sp|Q9LVC3.2|PUM12_ARATH RecName: Full=Pumilio homolog 12; Short=APUM-12; Short=AtPUM12 gi|332009392|gb|AED96775.1| pumilio 12 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297793151|ref|XP_002864460.1| APUM12 [Arabidopsis lyrata subsp. lyrata] gi|297310295|gb|EFH40719.1| APUM12 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|255564824|ref|XP_002523406.1| RNA binding protein, putative [Ricinus communis] gi|223537356|gb|EEF38985.1| RNA binding protein, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|255545698|ref|XP_002513909.1| conserved hypothetical protein [Ricinus communis] gi|223546995|gb|EEF48492.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
>gi|8809626|dbj|BAA97177.1| unnamed protein product [Arabidopsis thaliana] 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 ?
Query422
TAIR|locus:2167111596 PUM12 "pumilio 12" [Arabidopsi 0.729 0.516 0.319 1.2e-43
DICTYBASE|DDB_G02899871036 DDB_G0289987 "Pumilio homology 0.834 0.339 0.276 4.3e-34
TAIR|locus:2144711517 PUM21 "pumilio 21" [Arabidopsi 0.917 0.748 0.278 4.6e-34
TAIR|locus:2015036515 PUM8 "pumilio 8" [Arabidopsis 0.668 0.547 0.294 3.1e-32
TAIR|locus:2138258556 PUM11 "pumilio 11" [Arabidopsi 0.642 0.487 0.311 1.5e-31
TAIR|locus:2194699650 PUM7 "pumilio 7" [Arabidopsis 0.862 0.56 0.277 4.1e-31
ASPGD|ASPL0000057098650 AN10071 [Emericella nidulans ( 0.850 0.552 0.265 2.2e-28
TAIR|locus:2164165327 PUM18 "pumilio 18" [Arabidopsi 0.616 0.795 0.318 3.9e-28
TAIR|locus:2144010327 PUM19 "pumilio 19" [Arabidopsi 0.616 0.795 0.318 1.3e-27
TAIR|locus:2011349564 PUM9 "pumilio 9" [Arabidopsis 0.670 0.501 0.275 5.7e-25
TAIR|locus:2167111 PUM12 "pumilio 12" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 433 (157.5 bits), Expect = 1.2e-43, Sum P(2) = 1.2e-43
 Identities = 102/319 (31%), Positives = 180/319 (56%)

Query:    96 ANSGILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIET 155
             A   I  LA+D+ G ++LQ   +  D   ++ +FN + ++  +++ + +  ++  K +E 
Sbjct:   278 ARGKIYYLAKDQHGCRFLQRIFSEKDGNDIEMIFNEIIDYISELMMDPFGNYLVQKLLEV 337

Query:   156 CNEDQLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRL 215
             CNEDQ ++I   IT +  L ++ S D  G+ +++K+++  A R   + +++ ALK     
Sbjct:   338 CNEDQRMQIVHSITRKPGLLIKISCDMHGTRAVQKIVET-AKREEEISIIISALKHGIVH 396

Query:   216 LMMTKPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPR 275
             L+    G+ VV +CL+ +  +  K  F+++AA+ HC+ LA    GC  +   +   +G +
Sbjct:   397 LIKNVNGNHVVQRCLQYLLPYCGK--FLFEAAITHCVELATDRHGCCVLQKCLGYSEGEQ 454

Query:   276 RKQILYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFV 335
             ++ ++  I+ NA  LS++  GNYV+Q+V EL+  +    I   L G+Y +LS+ KC S V
Sbjct:   455 KQHLVSEIASNALLLSQDPFGNYVLQYVFELQLQWATFEILEQLEGNYTELSMQKCSSNV 514

Query:   336 VQNCLKYRITVNY--IVEEFLLNSDQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLV 393
             V+ CLK     +   I+ E L+N  ++ +V  D YGNYVIQ AL ++ + N   +H  LV
Sbjct:   515 VEKCLKLADDKHRARIIRE-LINYGRLDQVMLDPYGNYVIQAALKQS-KGN---VHALLV 569

Query:   394 TKLQQNLDSLRFG-YGKHV 411
               ++ N+ SLR   YGK V
Sbjct:   570 DAIKLNISSLRTNPYGKKV 588
GO:0003723 "RNA binding" evidence=IEA;ISS
GO:0005737 "cytoplasm" evidence=ISM;IDA
GO:0005634 "nucleus" evidence=IDA
DICTYBASE|DDB_G0289987 DDB_G0289987 "Pumilio homology domain family member 4" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
TAIR|locus:2144711 PUM21 "pumilio 21" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2015036 PUM8 "pumilio 8" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2138258 PUM11 "pumilio 11" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2194699 PUM7 "pumilio 7" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
ASPGD|ASPL0000057098 AN10071 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
TAIR|locus:2164165 PUM18 "pumilio 18" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2144010 PUM19 "pumilio 19" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2011349 PUM9 "pumilio 9" [Arabidopsis thaliana (taxid:3702)] 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 ?
Query422
cd07920322 cd07920, Pumilio, Pumilio-family RNA binding domai 2e-58
COG5099777 COG5099, COG5099, RNA-binding protein of the Puf f 2e-24
cd07920 322 cd07920, Pumilio, Pumilio-family RNA binding domai 5e-05
cd07920322 cd07920, Pumilio, Pumilio-family RNA binding domai 0.001
>gnl|CDD|153420 cd07920, Pumilio, Pumilio-family RNA binding domain Back     alignment and domain information 
 Score =  193 bits (493), Expect = 2e-58
 Identities = 94/318 (29%), Positives = 160/318 (50%), Gaps = 17/318 (5%)

Query: 100 ILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNED 159
           I+  A+D+ GS++LQ+KL        + +F+ +     +++ + +  +V  K  E   E+
Sbjct: 12  IVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEE 71

Query: 160 QLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMT 219
           Q L++  +I       V+ S+D +G   I+KL++++      + L++K L+     L+  
Sbjct: 72  QRLQLLEKILGH---VVRLSLDMYGCRVIQKLLESI--SEEQISLLVKELRGHVVELVKD 126

Query: 220 KPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQI 279
           + G+ V+ +C+E+         FI  A   +C+ L+ H  GC  +   ++     +R+ +
Sbjct: 127 QNGNHVIQKCIEKFPPE--DLQFIIDAFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPL 184

Query: 280 LYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNC 339
           L  I  +A  L ++  GNYVVQHVLEL DP     I   L G+ + LS  K  S VV+ C
Sbjct: 185 LEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNVVEKC 244

Query: 340 LKYRITV--NYIVEEFL---LNSDQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLVT 394
           LK+        I++E L     +  +  +  D+YGNYVIQTAL            + LV 
Sbjct: 245 LKHASKEERELIIDEILASGNETSALDTLMKDQYGNYVIQTALDVA----KEEQRELLVE 300

Query: 395 KLQQNLDSLR-FGYGKHV 411
            ++ +L SLR   YGKH+
Sbjct: 301 AIRPHLPSLRKSPYGKHI 318

Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats. Length = 322
>gnl|CDD|227430 COG5099, COG5099, RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|153420 cd07920, Pumilio, Pumilio-family RNA binding domain Back     alignment and domain information
>gnl|CDD|153420 cd07920, Pumilio, Pumilio-family RNA binding domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 422
KOG1488503 consensus Translational repressor Pumilio/PUF3 and 100.0
cd07920322 Pumilio Pumilio-family RNA binding domain. Puf rep 100.0
KOG2049536 consensus Translational repressor MPT5/PUF4 and re 100.0
COG5099777 RNA-binding protein of the Puf family, translation 100.0
cd07920322 Pumilio Pumilio-family RNA binding domain. Puf rep 100.0
KOG1488503 consensus Translational repressor Pumilio/PUF3 and 100.0
KOG2050 652 consensus Puf family RNA-binding protein [Translat 99.97
KOG2049536 consensus Translational repressor MPT5/PUF4 and re 99.97
COG5099777 RNA-binding protein of the Puf family, translation 99.96
KOG2188650 consensus Predicted RNA-binding protein, contains 99.95
KOG2050 652 consensus Puf family RNA-binding protein [Translat 99.94
KOG2188650 consensus Predicted RNA-binding protein, contains 99.89
KOG4574 1007 consensus RNA-binding protein (contains RRM and Pu 99.72
KOG4574 1007 consensus RNA-binding protein (contains RRM and Pu 99.38
PF0080635 PUF: Pumilio-family RNA binding repeat; InterPro: 98.49
PF0080635 PUF: Pumilio-family RNA binding repeat; InterPro: 98.16
smart0002536 Pumilio Pumilio-like repeats. Pumilio-like repeats 98.13
smart0002536 Pumilio Pumilio-like repeats. Pumilio-like repeats 97.61
PF08144148 CPL: CPL (NUC119) domain; InterPro: IPR012959 This 92.94
PF08144148 CPL: CPL (NUC119) domain; InterPro: IPR012959 This 92.34
PF04286367 DUF445: Protein of unknown function (DUF445); Inte 83.17
PRK05686339 fliG flagellar motor switch protein G; Validated 82.38
KOG19241102 consensus RhoA GTPase effector DIA/Diaphanous [Sig 80.09
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information 
Probab=100.00  E-value=3.6e-67  Score=519.82  Aligned_cols=314  Identities=24%  Similarity=0.395  Sum_probs=299.9

Q ss_pred             chhHhhhcccCcccHHHHHhhcCCCH-HHHHHHHHHHHHHHHHhhccccchHHHHHHHhhCCHHHHHHHHHHHhhcCchH
Q 047627           97 NSGILLLAQDEQGSQYLQEKLTSGDS-RFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLLRITLQITSQDQLF  175 (422)
Q Consensus        97 ~~~v~~l~~d~~gsrvlQ~~L~~~~~-e~~~~I~~ei~~~~~~L~~d~~gn~vvQkLi~~~~~~q~~~i~~~l~~~~~~i  175 (422)
                      .|.++++++||+|||+||..|+.+.+ +++..||++|.+.+.+||+|.||||||||++|+++.+|+..+...+.   +++
T Consensus       178 ~~~~v~f~~Dq~GsrfiQqkl~~~~~~~ek~~if~ei~~~~~~L~~dvFGNyvIQkffE~gt~~q~~~l~~~~~---g~v  254 (503)
T KOG1488|consen  178 PGHLVEFAKDQHGSRFIQQKLETASDNEEKQAVFDEILPPALELMTDVFGNYVIQKFFEHGTEDQRNLLHSQIK---GHV  254 (503)
T ss_pred             CCCceeecCCcccchHHHHhccccccHHHHHHHHHHHHHHHHHHHHHHhcCchhhhhhccCCHHHHHHHHHHHH---hhh
Confidence            46899999999999999999999988 99999999999999999999999999999999999999999999999   999


Q ss_pred             HHhhhcccchHHHHHHHHhhcCChhHHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHhccCcchhhHHHHHHhh--hHHH
Q 047627          176 VQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKNDFIYQAALE--HCLY  253 (422)
Q Consensus       176 ~~La~~~~Gs~VvQkll~~~~~~~~~~~~i~~~l~~~~~~L~~d~~gshViQ~~l~~~~~~~~~~~~i~~~l~~--~~~~  253 (422)
                      ..||.|+|||||+||+|+... ...+.+++.+ |.+++..+++|+||+||||||+++.+.  +...+|++.+.+  ++..
T Consensus       255 ~~Lsld~ygCRVIQkale~id-~~~~~~Li~E-Ld~~vl~~v~DQngnHViQK~ie~~p~--~~~~Fiv~~f~~~~~~~~  330 (503)
T KOG1488|consen  255 LELSLDMYGCRVIQKALEKVD-VSLQIQLIDE-LDGHLLKCVKDQNGNHVIQKCIETLPP--DAWQFIVDFFSGDDNLLE  330 (503)
T ss_pred             hhhhcccccchhHHHHHHhcC-HHHHHHHHHH-HHhhHHHHHhhcccceehhhhhhccCh--HHHHHHHHHhcCCCceeE
Confidence            999999999999999999998 5555555555 799999999999999999999999999  999999999998  9999


Q ss_pred             HhcCcCCcHHHHHHHhccChhhHHHHHHHHHHhHHhhhhcCChhHHHHHhhccCChhhHHHHHHHHHHHHHHhhcCcchH
Q 047627          254 LACHEQGCINMNNFIDEMKGPRRKQILYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGS  333 (422)
Q Consensus       254 la~~~~Gs~vlq~ll~~~~~~~~~~L~~~l~~~~~~L~~d~~Gn~VvQ~lL~~~~~~~~~~ii~~l~~~~~~Ls~~k~GS  333 (422)
                      +|+|+|||+|||++||+|..+++..++++|..++..|+.|+|||||||++|++++++.+..|+++|.+++..|+.|||+|
T Consensus       331 ls~~~YGCRVIQr~lE~c~~~~~~~i~~ei~~~~~~L~~dQygNYVIQHVie~g~~~~~~~I~~~l~~~ll~~Sq~KfAS  410 (503)
T KOG1488|consen  331 LSTHKYGCRVIQRILEHCSEDQKQPLMEEIIRNCDQLAQDQYGNYVIQHVIEHGSPYRDTIIIKCLLGNLLSMSQHKFAS  410 (503)
T ss_pred             eeccCcccHHHHHHhhcCChHhhhHHHHHHHHHHHHHHhhhhhhHHHHHHHhcCChhhhhhHHHHHHhhHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999888999999999999999999999


Q ss_pred             HHHHHHhcc--hhhHHHHHHHHhc----CChhHHHhhcChhhhHHHHHHHhhcCCCCcHHHHHHHHHHHHHhHHHHhc-h
Q 047627          334 FVVQNCLKY--RITVNYIVEEFLL----NSDQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLVTKLQQNLDSLRF-G  406 (422)
Q Consensus       334 ~Vvek~l~~--~~~r~~Ii~el~~----~~~~l~~L~~d~~GnyVvq~~L~~~~~~~~~~~~~~l~~~l~~~~~~L~~-~  406 (422)
                      ||||+||.+  ...|..|++|++.    ..+.+..|+.|+|||||||++++.+.+    ++++.|..+|++|+..|+. +
T Consensus       411 nVVEk~~~~a~~~~r~~i~~Ei~~~~~~~~~~L~~mmkdQYgNYVVQkmi~~~~~----~q~~~i~~rI~~h~~~Lrk~s  486 (503)
T KOG1488|consen  411 NVVEKAFLFAPPLLRALIMNEIFPGYVEHPDALDIMMKDQYGNYVVQKMIDICGP----EQRELIKSRVKPHASRLRKFS  486 (503)
T ss_pred             HHHHHHHhhCCHHHHHHHHHHhcCCccCCccHHHHHHHHhhhhhHHHHHHHhcCH----HHHHHHHHHHHHHHHHHccCc
Confidence            999999999  6789999999998    237999999999999999999999988    8999999999999999999 9


Q ss_pred             hhhHHHHHHHhhhcc
Q 047627          407 YGKHVYNFIKDCDLQ  421 (422)
Q Consensus       407 ~G~~V~~~l~~~~~~  421 (422)
                      |||||+++++++.-+
T Consensus       487 yGKhIia~lek~~~~  501 (503)
T KOG1488|consen  487 YGKHIIAKLEKLRSK  501 (503)
T ss_pred             cHHHHHHHHHHhccc
Confidence            999999999998754

>cd07920 Pumilio Pumilio-family RNA binding domain Back     alignment and domain information
>KOG2049 consensus Translational repressor MPT5/PUF4 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd07920 Pumilio Pumilio-family RNA binding domain Back     alignment and domain information
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG2050 consensus Puf family RNA-binding protein [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG2049 consensus Translational repressor MPT5/PUF4 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG2188 consensus Predicted RNA-binding protein, contains Pumilio domains [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG2050 consensus Puf family RNA-binding protein [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG2188 consensus Predicted RNA-binding protein, contains Pumilio domains [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only] Back     alignment and domain information
>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only] Back     alignment and domain information
>PF00806 PUF: Pumilio-family RNA binding repeat; InterPro: IPR001313 The drosophila pumilio gene codes for an unusual protein that binds through the Puf domain that usually occurs as a tandem repeat of eight domains Back     alignment and domain information
>PF00806 PUF: Pumilio-family RNA binding repeat; InterPro: IPR001313 The drosophila pumilio gene codes for an unusual protein that binds through the Puf domain that usually occurs as a tandem repeat of eight domains Back     alignment and domain information
>smart00025 Pumilio Pumilio-like repeats Back     alignment and domain information
>smart00025 Pumilio Pumilio-like repeats Back     alignment and domain information
>PF08144 CPL: CPL (NUC119) domain; InterPro: IPR012959 This C-terminal domain is found in Penguin-like proteins (CPL) and is associated with Pumilio like repeats [] Back     alignment and domain information
>PF08144 CPL: CPL (NUC119) domain; InterPro: IPR012959 This C-terminal domain is found in Penguin-like proteins (CPL) and is associated with Pumilio like repeats [] Back     alignment and domain information
>PF04286 DUF445: Protein of unknown function (DUF445); InterPro: IPR007383 This entry contains proteins of unknown function Back     alignment and domain information
>PRK05686 fliG flagellar motor switch protein G; Validated Back     alignment and domain information
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton] 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 ?
Query422
3q0q_A351 Crystal Structure Of The Pumilio-Homology Domain Fr 8e-21
4dzs_A357 Crystal Structure Of Yeast Puf4p Rna Binding Domain 4e-20
4dzs_A357 Crystal Structure Of Yeast Puf4p Rna Binding Domain 3e-04
3bx2_A335 Puf4 Rna Binding Domain Bound To Ho Endonuclease Rn 5e-20
3bx2_A335 Puf4 Rna Binding Domain Bound To Ho Endonuclease Rn 4e-04
3bwt_A333 Crystal Structure Of The Rna Binding Domain Of Puf4 5e-20
3bwt_A333 Crystal Structure Of The Rna Binding Domain Of Puf4 4e-04
3bx3_A335 Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR Re 1e-19
3bx3_A335 Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR Re 3e-05
3gvo_A351 Structure And Rna Binding Of The Mouse Pumilio-2 Pu 7e-19
1ib2_A349 Crystal Structure Of A Pumilio-Homology Domain Leng 4e-16
3bsb_A343 Crystal Structure Of Human Pumilio1 In Complex With 5e-16
3h3d_X323 Drosophila Pumilio Rna Binding Domain (Puf Domain) 8e-16
2yjy_A350 A Specific And Modular Binding Code For Cytosine Re 5e-15
3k49_A 369 Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr R 1e-05
>pdb|3Q0Q|A Chain A, Crystal Structure Of The Pumilio-Homology Domain From Human Pumilio2 In Complex With P38alpha Nrea Length = 351 Back     alignment and structure 
Iteration: 1

 Score = 98.2 bits (243), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 80/330 (24%), Positives = 158/330 (47%), Gaps = 16/330 (4%)
Query: 100 ILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNED 159
           I+  +QD+ GS+++Q+KL          VFN + +  +Q++ + +  +V  KF E  + D
Sbjct: 26  IVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLD 85
Query: 160 QLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMT 219
           Q L +  +I       +  ++  +G   I+K ++++++   ++  ++K L       +  
Sbjct: 86  QKLALATRIRGH---VLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKCVKD 142
Query: 220 KPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQI 279
           + G+ VV +C+E +        FI  A       L+ H  GC  +   ++     +   I
Sbjct: 143 QNGNHVVQKCIECV--QPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPI 200
Query: 280 LYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNC 339
           L  +  +   L ++  GNYV+QHVLE   P     I   +RG  + LS  K  S VV+ C
Sbjct: 201 LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKC 260
Query: 340 LKY--RITVNYIVEEFLLNSD----QIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLV 393
           + +  R     +++E    +D     ++ +  D+Y NYV+Q  +I+   P    +   ++
Sbjct: 261 VTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQK-MIDMAEPAQRKI---IM 316
Query: 394 TKLQQNLDSLR-FGYGKHVYNFIKDCDLQN 422
            K++ ++ +LR + YGKH+   ++   L+N
Sbjct: 317 HKIRPHITTLRKYTYGKHILAKLEKYYLKN 346
>pdb|4DZS|A Chain A, Crystal Structure Of Yeast Puf4p Rna Binding Domain In Complex With Ho-4be Mutant Rna Length = 357 Back     alignment and structure
>pdb|4DZS|A Chain A, Crystal Structure Of Yeast Puf4p Rna Binding Domain In Complex With Ho-4be Mutant Rna Length = 357 Back     alignment and structure
>pdb|3BX2|A Chain A, Puf4 Rna Binding Domain Bound To Ho Endonuclease Rna 3' Utr Recognition Sequence Length = 335 Back     alignment and structure
>pdb|3BX2|A Chain A, Puf4 Rna Binding Domain Bound To Ho Endonuclease Rna 3' Utr Recognition Sequence Length = 335 Back     alignment and structure
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From Saccharomyces Cerevisiae Length = 333 Back     alignment and structure
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From Saccharomyces Cerevisiae Length = 333 Back     alignment and structure
>pdb|3BX3|A Chain A, Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR Recognition Sequence Length = 335 Back     alignment and structure
>pdb|3BX3|A Chain A, Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR Recognition Sequence Length = 335 Back     alignment and structure
>pdb|3GVO|A Chain A, Structure And Rna Binding Of The Mouse Pumilio-2 Puf Domain Length = 351 Back     alignment and structure
>pdb|1IB2|A Chain A, Crystal Structure Of A Pumilio-Homology Domain Length = 349 Back     alignment and structure
>pdb|3BSB|A Chain A, Crystal Structure Of Human Pumilio1 In Complex With Cyclinb Reverse Rna Length = 343 Back     alignment and structure
>pdb|3H3D|X Chain X, Drosophila Pumilio Rna Binding Domain (Puf Domain) Length = 323 Back     alignment and structure
>pdb|2YJY|A Chain A, A Specific And Modular Binding Code For Cytosine Recognition In Puf Domains Length = 350 Back     alignment and structure
>pdb|3K49|A Chain A, Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr Recognition Sequence Site B Length = 369 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 ?
Query422
3bwt_A333 Protein PUF4; pumilio, RNA binding, HO endonucleas 9e-62
3bwt_A 333 Protein PUF4; pumilio, RNA binding, HO endonucleas 4e-17
3bwt_A333 Protein PUF4; pumilio, RNA binding, HO endonucleas 1e-07
3bwt_A 333 Protein PUF4; pumilio, RNA binding, HO endonucleas 3e-04
3gvo_A351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 2e-58
3gvo_A 351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 3e-15
3gvo_A351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 3e-14
3k49_A369 MRNA-binding protein PUF3; PUF3, pumilio, RNA bind 1e-54
3k49_A 369 MRNA-binding protein PUF3; PUF3, pumilio, RNA bind 4e-14
3k49_A369 MRNA-binding protein PUF3; PUF3, pumilio, RNA bind 7e-07
3v71_A382 PUF (pumilio/FBF) domain-containing protein 7, CO 3e-45
3v71_A 382 PUF (pumilio/FBF) domain-containing protein 7, CO 1e-10
3v71_A382 PUF (pumilio/FBF) domain-containing protein 7, CO 2e-08
3k62_A412 FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa 1e-34
3k62_A412 FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa 4e-07
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-06
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 5e-06
>3bwt_A Protein PUF4; pumilio, RNA binding, HO endonuclease, transcription, RNA binding protein; 2.69A {Saccharomyces cerevisiae} PDB: 4dzs_A 3bx2_A 3bx3_A Length = 333 Back     alignment and structure
 Score =  201 bits (514), Expect = 9e-62
 Identities = 77/325 (23%), Positives = 149/325 (45%), Gaps = 15/325 (4%)

Query: 100 ILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNED 159
           I  L +D+ G ++LQ++L    S+  D +F    ++T +++ + +  ++  K +E    +
Sbjct: 15  IHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTE 74

Query: 160 QLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMT 219
           Q + +T   +     FV+ S++  G+ +++KL++ +        +V+ +L+     L   
Sbjct: 75  QRIVLTKISSPH---FVEISLNPHGTRALQKLIECIKT-DEEAQIVVDSLRPYTVQLSKD 130

Query: 220 KPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQI 279
             G+ V+ +CL+          FI+ A  + C+ +A H  GC  +   +D     +   +
Sbjct: 131 LNGNHVIQKCLQ--RLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNL 188

Query: 280 LYLISVNAASLSRNFSGNYVVQHVLELEDP----YLIETICFSLRGHYIDLSLTKCGSFV 335
              +      L+ +  GNYVVQ+++  E           I   L+   I+LS+ K GS V
Sbjct: 189 CDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNV 248

Query: 336 VQNCLKYRITVNYIVEEFLLNS--DQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLV 393
           ++  LK  I    ++ E L N     I  +  D YGNYV+QTAL +     + +L++RL 
Sbjct: 249 IEKILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTAL-DISHKQNDYLYKRLS 307

Query: 394 TKLQQNLDSL--RFGYGKHVYNFIK 416
             +   L        +GK +   + 
Sbjct: 308 EIVAPLLVGPIRNTPHGKRIIGMLH 332
>3bwt_A Protein PUF4; pumilio, RNA binding, HO endonuclease, transcription, RNA binding protein; 2.69A {Saccharomyces cerevisiae} PDB: 4dzs_A 3bx2_A 3bx3_A Length = 333 Back     alignment and structure
>3bwt_A Protein PUF4; pumilio, RNA binding, HO endonuclease, transcription, RNA binding protein; 2.69A {Saccharomyces cerevisiae} PDB: 4dzs_A 3bx2_A 3bx3_A Length = 333 Back     alignment and structure
>3bwt_A Protein PUF4; pumilio, RNA binding, HO endonuclease, transcription, RNA binding protein; 2.69A {Saccharomyces cerevisiae} PDB: 4dzs_A 3bx2_A 3bx3_A Length = 333 Back     alignment and structure
>3gvo_A Pumilio 2, pumilio homolog 2; RNA-binding, PUF domain, RNA binding protein; HET: DTD; 1.60A {Mus musculus} PDB: 3gvt_A 3q0q_A 3q0r_A 3q0s_A 1ib2_A 1m8w_A 1m8x_A 1m8y_A 1m8z_A 3q0l_A 3q0m_A 3q0n_A 3q0o_A 3q0p_A 2yjy_A 3bsx_A 3bsb_A 3h3d_X Length = 351 Back     alignment and structure
>3gvo_A Pumilio 2, pumilio homolog 2; RNA-binding, PUF domain, RNA binding protein; HET: DTD; 1.60A {Mus musculus} PDB: 3gvt_A 3q0q_A 3q0r_A 3q0s_A 1ib2_A 1m8w_A 1m8x_A 1m8y_A 1m8z_A 3q0l_A 3q0m_A 3q0n_A 3q0o_A 3q0p_A 2yjy_A 3bsx_A 3bsb_A 3h3d_X Length = 351 Back     alignment and structure
>3gvo_A Pumilio 2, pumilio homolog 2; RNA-binding, PUF domain, RNA binding protein; HET: DTD; 1.60A {Mus musculus} PDB: 3gvt_A 3q0q_A 3q0r_A 3q0s_A 1ib2_A 1m8w_A 1m8x_A 1m8y_A 1m8z_A 3q0l_A 3q0m_A 3q0n_A 3q0o_A 3q0p_A 2yjy_A 3bsx_A 3bsb_A 3h3d_X Length = 351 Back     alignment and structure
>3k49_A MRNA-binding protein PUF3; PUF3, pumilio, RNA binding, mitochondrial mRNA,, membrane, mitochondrion; HET: CIT; 2.50A {Saccharomyces cerevisiae} PDB: 3k4e_A Length = 369 Back     alignment and structure
>3k49_A MRNA-binding protein PUF3; PUF3, pumilio, RNA binding, mitochondrial mRNA,, membrane, mitochondrion; HET: CIT; 2.50A {Saccharomyces cerevisiae} PDB: 3k4e_A Length = 369 Back     alignment and structure
>3k49_A MRNA-binding protein PUF3; PUF3, pumilio, RNA binding, mitochondrial mRNA,, membrane, mitochondrion; HET: CIT; 2.50A {Saccharomyces cerevisiae} PDB: 3k4e_A Length = 369 Back     alignment and structure
>3v71_A PUF (pumilio/FBF) domain-containing protein 7, CO transcript evidence; PUF repeats, RNA binding protein-RNA complex; HET: EPE; 2.90A {Caenorhabditis elegans} Length = 382 Back     alignment and structure
>3v71_A PUF (pumilio/FBF) domain-containing protein 7, CO transcript evidence; PUF repeats, RNA binding protein-RNA complex; HET: EPE; 2.90A {Caenorhabditis elegans} Length = 382 Back     alignment and structure
>3v71_A PUF (pumilio/FBF) domain-containing protein 7, CO transcript evidence; PUF repeats, RNA binding protein-RNA complex; HET: EPE; 2.90A {Caenorhabditis elegans} Length = 382 Back     alignment and structure
>3k62_A FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding factor, PUF, RNA-binding specificity, base flipping, base stacking; 1.90A {Caenorhabditis elegans} PDB: 3k5y_A 3k5z_A 3k61_A 3k5q_A 3k64_A 3qg9_A 3v6y_A 3v74_A 3qgc_A 3qgb_A Length = 412 Back     alignment and structure
>3k62_A FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding factor, PUF, RNA-binding specificity, base flipping, base stacking; 1.90A {Caenorhabditis elegans} PDB: 3k5y_A 3k5z_A 3k61_A 3k5q_A 3k64_A 3qg9_A 3v6y_A 3v74_A 3qgc_A 3qgb_A Length = 412 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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query422
3gvo_A351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 100.0
3k62_A412 FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa 100.0
3bwt_A333 Protein PUF4; pumilio, RNA binding, HO endonucleas 100.0
3k49_A369 MRNA-binding protein PUF3; PUF3, pumilio, RNA bind 100.0
3v71_A382 PUF (pumilio/FBF) domain-containing protein 7, CO 100.0
3gvo_A351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 100.0
3k49_A369 MRNA-binding protein PUF3; PUF3, pumilio, RNA bind 100.0
3bwt_A333 Protein PUF4; pumilio, RNA binding, HO endonucleas 100.0
3v71_A382 PUF (pumilio/FBF) domain-containing protein 7, CO 100.0
3k62_A412 FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa 100.0
>3gvo_A Pumilio 2, pumilio homolog 2; RNA-binding, PUF domain, RNA binding protein; HET: DTD; 1.60A {Mus musculus} SCOP: a.118.1.8 PDB: 3gvt_A 3q0q_A 3q0r_A 3q0s_A 1ib2_A 1m8w_A 1m8x_A 1m8y_A 1m8z_A 3q0l_A 3q0m_A 3q0n_A 3q0o_A 3q0p_A 2yjy_A 3bsx_A 3bsb_A 3h3d_X Back     alignment and structure
Probab=100.00  E-value=9.1e-65  Score=501.25  Aligned_cols=319  Identities=24%  Similarity=0.410  Sum_probs=302.8

Q ss_pred             hhhhcchhHhhhcccCcccHHHHHhhcCCCHHHHHHHHHHHHHHHHHhhccccchHHHHHHHhhCCHHHHHHHHHHHhhc
Q 047627           92 FQHCANSGILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLLRITLQITSQ  171 (422)
Q Consensus        92 f~~l~~~~v~~l~~d~~gsrvlQ~~L~~~~~e~~~~I~~ei~~~~~~L~~d~~gn~vvQkLi~~~~~~q~~~i~~~l~~~  171 (422)
                      +.++. |+++++|+||+|||+||++|+.+++++++.||+++.+++.+||+|+||||||||++++|+++++..|++.+.  
T Consensus        21 l~~~~-g~i~~la~dq~gsR~lQ~~l~~~~~~~~~~i~~ei~~~~~~L~~d~~gn~vvQklle~~~~~~~~~i~~~i~--   97 (351)
T 3gvo_A           21 LRDLI-GHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLDQKLALATRIR--   97 (351)
T ss_dssp             GGGGT-TCHHHHHTSHHHHHHHHHHHHHCCHHHHHHHHHHHGGGHHHHHTSTTHHHHHHHHHHHCCHHHHHHHHHHHT--
T ss_pred             HHHHH-hHHHHHhcCCcchHHHHHHHhhCCHHHHHHHHHHHHHhHHHHHhChhhhHHHHHHHhhCCHHHHHHHHHHHH--
Confidence            56775 799999999999999999999999999999999999999999999999999999999999999999999999  


Q ss_pred             CchHHHhhhcccchHHHHHHHHhhcCChhHHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHhccCcchhhHHHHHHhhhH
Q 047627          172 DQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKNDFIYQAALEHC  251 (422)
Q Consensus       172 ~~~i~~La~~~~Gs~VvQkll~~~~~~~~~~~~i~~~l~~~~~~L~~d~~gshViQ~~l~~~~~~~~~~~~i~~~l~~~~  251 (422)
                       |++++|+.|+|||+|+|++++.+.  .++...+.+++.+++..|++|++||||+|++++..++  +.+..|++.+.+++
T Consensus        98 -g~~~~l~~~~~G~rvvQk~le~~~--~~~~~~i~~el~~~~~~L~~d~~Gn~ViQk~l~~~~~--~~~~~i~~~~~~~~  172 (351)
T 3gvo_A           98 -GHVLPLALQMYGCRVIQKALESIS--SDQQSEMVKELDGHVLKCVKDQNGNHVVQKCIECVQP--QSLQFIIDAFKGQV  172 (351)
T ss_dssp             -TCHHHHHTSTTHHHHHHHHHHHSC--HHHHHHHHGGGTTCHHHHHHSTTHHHHHHHHHHHSCG--GGTHHHHHHTTTTH
T ss_pred             -hhHHHHhhCHHhHHHHHHHHHhCC--HHHHHHHHHHhhhhHHHHHHhhhhhHHHHHHHHhCCH--HHHHHHHHHHHHHH
Confidence             999999999999999999999998  4555667777999999999999999999999999988  89999999999999


Q ss_pred             HHHhcCcCCcHHHHHHHhccChhhHHHHHHHHHHhHHhhhhcCChhHHHHHhhccCChhhHHHHHHHHHHHHHHhhcCcc
Q 047627          252 LYLACHEQGCINMNNFIDEMKGPRRKQILYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKC  331 (422)
Q Consensus       252 ~~la~~~~Gs~vlq~ll~~~~~~~~~~L~~~l~~~~~~L~~d~~Gn~VvQ~lL~~~~~~~~~~ii~~l~~~~~~Ls~~k~  331 (422)
                      ..+++|+|||+|+|++|++++++++..+++++.+++..|++|+|||||||++|+.++++.++.|++.+.+++..||++||
T Consensus       173 ~~ls~~~~G~~Vvq~~le~~~~~~~~~ii~~l~~~~~~L~~d~~Gn~ViQ~~l~~~~~~~~~~i~~~l~~~~~~Ls~~k~  252 (351)
T 3gvo_A          173 FVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKF  252 (351)
T ss_dssp             HHHHTSTTHHHHHHHHHHHSCHHHHHHHHHHHHTTHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHTTTTCHHHHHTSTT
T ss_pred             HHHHhCcHhHHHHHHHHHHCCHHHHHHHHHHHhhhHHhcCCCchHHHHHHHHHHhCchhhHHHHHHHHHHHHHHHhcCcH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHhcc--hhhHHHHHHHHhcC----ChhHHHhhcChhhhHHHHHHHhhcCCCCcHHHHHHHHHHHHHhHHHHhc
Q 047627          332 GSFVVQNCLKY--RITVNYIVEEFLLN----SDQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLVTKLQQNLDSLRF  405 (422)
Q Consensus       332 GS~Vvek~l~~--~~~r~~Ii~el~~~----~~~l~~L~~d~~GnyVvq~~L~~~~~~~~~~~~~~l~~~l~~~~~~L~~  405 (422)
                      ||+|||+||+.  +..|..|+++++..    .+.+..|+.|+|||||||++|+.+++    .+++.|++.|+|+++.|+.
T Consensus       253 gs~Vvek~l~~~~~~~r~~ii~el~~~~~~~~~~l~~l~~d~ygnyViq~~L~~~~~----~~r~~i~~~i~~~~~~L~~  328 (351)
T 3gvo_A          253 ASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEP----AQRKIIMHKIRPHITTLRK  328 (351)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHSCEETTEEHHHHHHHSTTHHHHHHHHHHHCCH----HHHHHHHHHHGGGHHHHTT
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHhcccCCCChHHHHccCCcchHHHHHHHHHhCCH----HHHHHHHHHHHHHHHHHhc
Confidence            99999999999  67899999999961    13799999999999999999999988    8999999999999999999


Q ss_pred             -hhhhHHHHHHHhhhccC
Q 047627          406 -GYGKHVYNFIKDCDLQN  422 (422)
Q Consensus       406 -~~G~~V~~~l~~~~~~~  422 (422)
                       +||++|+++++++--++
T Consensus       329 ~~~g~~i~~kl~~~~~~~  346 (351)
T 3gvo_A          329 YTYGKHILAKLEKYYLKN  346 (351)
T ss_dssp             STTTHHHHHHHHHHTC--
T ss_pred             CCchHHHHHHHHHHHhhc
Confidence             99999999999986553
>3k62_A FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding factor, PUF, RNA-binding specificity, base flipping, base stacking; 1.90A {Caenorhabditis elegans} PDB: 3k5y_A 3k5z_A 3k61_A 3k5q_A 3k64_A 3qg9_A 3v6y_A 3v74_A 3qgc_A 3qgb_A Back     alignment and structure
>3bwt_A Protein PUF4; pumilio, RNA binding, HO endonuclease, transcription, RNA binding protein; 2.69A {Saccharomyces cerevisiae} PDB: 4dzs_A 3bx2_A 3bx3_A Back     alignment and structure
>3k49_A MRNA-binding protein PUF3; PUF3, pumilio, RNA binding, mitochondrial mRNA,, membrane, mitochondrion; HET: CIT; 2.50A {Saccharomyces cerevisiae} SCOP: a.118.1.0 PDB: 3k4e_A Back     alignment and structure
>3v71_A PUF (pumilio/FBF) domain-containing protein 7, CO transcript evidence; PUF repeats, RNA binding protein-RNA complex; HET: EPE; 2.90A {Caenorhabditis elegans} Back     alignment and structure
>3gvo_A Pumilio 2, pumilio homolog 2; RNA-binding, PUF domain, RNA binding protein; HET: DTD; 1.60A {Mus musculus} SCOP: a.118.1.8 PDB: 3gvt_A 3q0q_A 3q0r_A 3q0s_A 1ib2_A 1m8w_A 1m8x_A 1m8y_A 1m8z_A 3q0l_A 3q0m_A 3q0n_A 3q0o_A 3q0p_A 2yjy_A 3bsx_A 3bsb_A 3h3d_X Back     alignment and structure
>3k49_A MRNA-binding protein PUF3; PUF3, pumilio, RNA binding, mitochondrial mRNA,, membrane, mitochondrion; HET: CIT; 2.50A {Saccharomyces cerevisiae} SCOP: a.118.1.0 PDB: 3k4e_A Back     alignment and structure
>3bwt_A Protein PUF4; pumilio, RNA binding, HO endonuclease, transcription, RNA binding protein; 2.69A {Saccharomyces cerevisiae} PDB: 4dzs_A 3bx2_A 3bx3_A Back     alignment and structure
>3v71_A PUF (pumilio/FBF) domain-containing protein 7, CO transcript evidence; PUF repeats, RNA binding protein-RNA complex; HET: EPE; 2.90A {Caenorhabditis elegans} Back     alignment and structure
>3k62_A FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding factor, PUF, RNA-binding specificity, base flipping, base stacking; 1.90A {Caenorhabditis elegans} PDB: 3k5y_A 3k5z_A 3k61_A 3k5q_A 3k64_A 3qg9_A 3v6y_A 3v74_A 3qgc_A 3qgb_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 422
d1m8za_339 a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [Ta 1e-44
d1m8za_339 a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [Ta 8e-11
d1m8za_ 339 a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [Ta 4e-09
>d1m8za_ a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 339 Back     information, alignment and structure

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Pumilio repeat
domain: Pumilio 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  156 bits (394), Expect = 1e-44
 Identities = 72/323 (22%), Positives = 144/323 (44%), Gaps = 18/323 (5%)

Query: 100 ILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNED 159
           I+  +QD+ GS+++Q KL          VFN + +  +Q++ + +  +V  KF E  + +
Sbjct: 26  IMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLE 85

Query: 160 QLLRITLQITSQDQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMT 219
           Q L +  +I       +  ++  +G   I+K +          + +++ L       +  
Sbjct: 86  QKLALAERIRGH---VLSLALQMYGCRVIQKAL--EFIPSDQQNEMVRELDGHVLKCVKD 140

Query: 220 KPGSSVVLQCLEQIYHHNNKNDFIYQAALEHCLYLACHEQGCINMNNFIDEMKGPRRKQI 279
           + G+ VV +C+E +        FI  A       L+ H  GC  +   ++     +   I
Sbjct: 141 QNGNHVVQKCIECV--QPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPI 198

Query: 280 LYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKCGSFVVQNC 339
           L  +  +   L ++  GNYV+QHVLE   P     I   +RG+ + LS  K  S VV+ C
Sbjct: 199 LEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKC 258

Query: 340 LKY------RITVNYIVEEFLLNSDQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLV 393
           + +       + ++ +          ++ +  D+Y NYV+Q  + +   P      + ++
Sbjct: 259 VTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMI-DVAEP---GQRKIVM 314

Query: 394 TKLQQNLDSLR-FGYGKHVYNFI 415
            K++ ++ +LR + YGKH+   +
Sbjct: 315 HKIRPHIATLRKYTYGKHILAKL 337
>d1m8za_ a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 339 Back     information, alignment and structure
>d1m8za_ a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 339 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 ?
Query422
d1m8za_339 Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]} 100.0
d1m8za_339 Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]} 100.0
>d1m8za_ a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Pumilio repeat
domain: Pumilio 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.6e-58  Score=452.25  Aligned_cols=314  Identities=24%  Similarity=0.392  Sum_probs=297.6

Q ss_pred             hhhhcchhHhhhcccCcccHHHHHhhcCCCHHHHHHHHHHHHHHHHHhhccccchHHHHHHHhhCCHHHHHHHHHHHhhc
Q 047627           92 FQHCANSGILLLAQDEQGSQYLQEKLTSGDSRFLDKVFNVVSEFTFQIICNQYARFVFGKFIETCNEDQLLRITLQITSQ  171 (422)
Q Consensus        92 f~~l~~~~v~~l~~d~~gsrvlQ~~L~~~~~e~~~~I~~ei~~~~~~L~~d~~gn~vvQkLi~~~~~~q~~~i~~~l~~~  171 (422)
                      ++++. |+++++|+||+|||+||++|+.+++++++.||+++.+++.+||+|+|||||+|+|+++|+++++..|++.+.  
T Consensus        19 l~~~~-g~~~~~~~~q~gSr~lQ~~l~~~~~~~~~~I~~~l~~~~~~L~~~~~gn~vvqkll~~~~~~~~~~i~~~l~--   95 (339)
T d1m8za_          19 LREIA-GHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERIR--   95 (339)
T ss_dssp             GGGGT-TCHHHHHTSHHHHHHHHHHHHHCCHHHHHHHHHHHGGGHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHHHT--
T ss_pred             HHHHH-hHHHHHhcCchhhHHHHHHHhhCCHHHHHHHHHHHHHHHHHHhhCcccchhHHHHHhhCCHHHHHHHHHHHH--
Confidence            56775 799999999999999999999999999999999999999999999999999999999999999999999999  


Q ss_pred             CchHHHhhhcccchHHHHHHHHhhcCChhHHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHhccCcchhhHHHHHHhhhH
Q 047627          172 DQLFVQASVDKFGSSSIRKLMKAVANRPPLLDLVMKALKRLFRLLMMTKPGSSVVLQCLEQIYHHNNKNDFIYQAALEHC  251 (422)
Q Consensus       172 ~~~i~~La~~~~Gs~VvQkll~~~~~~~~~~~~i~~~l~~~~~~L~~d~~gshViQ~~l~~~~~~~~~~~~i~~~l~~~~  251 (422)
                       +++..|+.|+||++|+|++++.+. + .+...+.+++.+++..++.|.+|+||+|++++.+++  +..+.+++.+.+++
T Consensus        96 -~~~~~L~~~~~gs~Vvq~l~~~~~-~-~~~~~l~~el~~~~~~l~~d~~~~~v~~~~l~~~~~--~~~~~i~~~~~~~~  170 (339)
T d1m8za_          96 -GHVLSLALQMYGCRVIQKALEFIP-S-DQQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQP--QSLQFIIDAFKGQV  170 (339)
T ss_dssp             -TCHHHHHTSTTHHHHHHHHHHHSC-H-HHHHHHHHTTTTCHHHHHHSTTHHHHHHHHHHHSCG--GGGHHHHHHTTTTH
T ss_pred             -hhHHHHhcccccchHHHhhhccCC-H-HHHHHHHHHHhhhhHHHhcCCCcchHHHHHHHhcCH--HHHHHHHHHHHHHH
Confidence             999999999999999999999987 4 455556667999999999999999999999999988  89999999999999


Q ss_pred             HHHhcCcCCcHHHHHHHhccChhhHHHHHHHHHHhHHhhhhcCChhHHHHHhhccCChhhHHHHHHHHHHHHHHhhcCcc
Q 047627          252 LYLACHEQGCINMNNFIDEMKGPRRKQILYLISVNAASLSRNFSGNYVVQHVLELEDPYLIETICFSLRGHYIDLSLTKC  331 (422)
Q Consensus       252 ~~la~~~~Gs~vlq~ll~~~~~~~~~~L~~~l~~~~~~L~~d~~Gn~VvQ~lL~~~~~~~~~~ii~~l~~~~~~Ls~~k~  331 (422)
                      .++++|++||+++|++++.++++++..+++++.+++..|+.|+|||||+|++|++++++.++.|++.|++++.+|+++||
T Consensus       171 ~~l~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~L~~~~~G~~vvq~~l~~~~~~~~~~i~~~l~~~~~~l~~~k~  250 (339)
T d1m8za_         171 FALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKF  250 (339)
T ss_dssp             HHHHTSTTHHHHHHHHHHHSCHHHHHHHHHHHHHTHHHHTTSTTHHHHHHHHHHHSCHHHHHHHHHHHTTCHHHHHTSTT
T ss_pred             HHHHhCcchhHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHcCCHHHHHHHHHHHHhhHHHHHcchh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHhcc--hhhHHHHHHHHhc----CChhHHHhhcChhhhHHHHHHHhhcCCCCcHHHHHHHHHHHHHhHHHHhc
Q 047627          332 GSFVVQNCLKY--RITVNYIVEEFLL----NSDQIFRVACDKYGNYVIQTALIETMRPNSLHLHQRLVTKLQQNLDSLRF  405 (422)
Q Consensus       332 GS~Vvek~l~~--~~~r~~Ii~el~~----~~~~l~~L~~d~~GnyVvq~~L~~~~~~~~~~~~~~l~~~l~~~~~~L~~  405 (422)
                      ||+|+|+|++.  +..+..++.+++.    ..+.+..|+.|+|||||||++|+.+++    .+++.|+++|.+++++|+.
T Consensus       251 gS~vve~~l~~~~~~~~~~~~~~l~~~~~~~~~~l~~L~~d~~gn~Viq~~l~~~~~----~~~~~i~~~l~~~~~~L~~  326 (339)
T d1m8za_         251 ASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEP----GQRKIVMHKIRPHIATLRK  326 (339)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHCEETTEEHHHHHHTSTTHHHHHHHHHHHSCH----HHHHHHHHTTGGGHHHHTT
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHhcccCchHHHHHHHcCCcccHHHHHHHHhCCH----HHHHHHHHHHHHHHHHHhc
Confidence            99999999998  6678888988875    345799999999999999999999998    8999999999999999999


Q ss_pred             -hhhhHHHHHHHh
Q 047627          406 -GYGKHVYNFIKD  417 (422)
Q Consensus       406 -~~G~~V~~~l~~  417 (422)
                       +||++|++++++
T Consensus       327 ~~~G~~v~~~l~~  339 (339)
T d1m8za_         327 YTYGKHILAKLEK  339 (339)
T ss_dssp             SSTHHHHHHHHC-
T ss_pred             CCcHHHHHHHHhC
Confidence             999999999875
>d1m8za_ a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure