Citrus Sinensis ID: 048245

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-------31
EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVHYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNKEIQKKK
cccHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHccHHHHHHHHHHHcccHHHHHHHHccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHccccHHHHHHHHHcccHHHHHHHHcccHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHccccccccHHHHccc
cccHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHccccHHHHHHHHHHHHcccccHHHHHHHcccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHccHHHHcccccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHccEHEEccccccHHHHHHHHHccccHHHHHHHHHcccHHHHHHHcccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEcc
EEGSQYLQEKlssgdsrildKLFWVVSGFTFElmsgqygrfVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMmtkpgssvilkclepsynhkndfIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAaslsrhrsgnyvvqhvlnledpfLIDAICFALRGhyvdlsltkcgSFVVQKFLKYQNAVHYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKygsnkeiqkkk
EEGSQYLQEklssgdsrilDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVvaqsppllYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVHYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALrvmkygsnkeiqkkk
EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVHYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNKEIQKKK
****************RILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVHYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKY**********
EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVHYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNKEIQKK*
***********SSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVHYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGS********
EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVHYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNKEIQKK*
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVHYIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNKEIQKKK
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 ?
Query309 2.2.26 [Sep-21-2011]
Q9LVC3596 Pumilio homolog 12 OS=Ara yes no 0.954 0.494 0.321 1e-36
Q9LM20515 Putative pumilio homolog no no 0.948 0.568 0.313 5e-29
Q9C9R6650 Putative pumilio homolog no no 0.948 0.450 0.3 3e-26
Q9LDW3556 Pumilio homolog 11 OS=Ara no no 0.860 0.478 0.325 6e-26
Q9LXC5517 Putative pumilio homolog no no 0.789 0.471 0.302 1e-25
Q1PFN9564 Pumilio homolog 9 OS=Arab no no 0.893 0.489 0.298 3e-23
Q9LVG3327 Pumilio homolog 18 OS=Ara no no 0.864 0.816 0.323 1e-22
Q9LP21528 Putative pumilio homolog no no 0.896 0.524 0.298 8e-22
Q9LSS8327 Putative pumilio homolog no no 0.864 0.816 0.32 9e-22
Q9FIE9332 Putative pumilio homolog no no 0.637 0.593 0.313 2e-18
>sp|Q9LVC3|PUM12_ARATH Pumilio homolog 12 OS=Arabidopsis thaliana GN=APUM12 PE=2 SV=2 Back     alignment and function desciption
 Score =  154 bits (388), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 97/302 (32%), Positives = 164/302 (54%), Gaps = 7/302 (2%)

Query: 1   EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIIL 60
           + G ++LQ   S  D   ++ +F  +  +  ELM   +G ++  K +E CNE Q   I+ 
Sbjct: 289 QHGCRFLQRIFSEKDGNDIEMIFNEIIDYISELMMDPFGNYLVQKLLEVCNEDQRMQIVH 348

Query: 61  KITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVI 120
            IT +  L +  S D  G+ +V+K+++   +   +   ++SALK     L+    G+ V+
Sbjct: 349 SITRKPGLLIKISCDMHGTRAVQKIVETAKREEEISI-IISALKHGIVHLIKNVNGNHVV 407

Query: 121 LKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAA 180
            +CL+    +   F+++AA+ HC+ LA    GC  L   +   +G +++ ++  I+ NA 
Sbjct: 408 QRCLQYLLPYCGKFLFEAAITHCVELATDRHGCCVLQKCLGYSEGEQKQHLVSEIASNAL 467

Query: 181 SLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVH- 239
            LS+   GNYV+Q+V  L+  +    I   L G+Y +LS+ KC S VV+K LK  +  H 
Sbjct: 468 LLSQDPFGNYVLQYVFELQLQWATFEILEQLEGNYTELSMQKCSSNVVEKCLKLADDKHR 527

Query: 240 -YIVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMK 298
             I+ EL+N  ++ QV  D YGNYVIQ AL    +Q + +VH  LV  ++ ++++LR   
Sbjct: 528 ARIIRELINYGRLDQVMLDPYGNYVIQAAL----KQSKGNVHALLVDAIKLNISSLRTNP 583

Query: 299 YG 300
           YG
Sbjct: 584 YG 585
Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.
Arabidopsis thaliana (taxid: 3702)
>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|Q9LXC5|PUM21_ARATH Putative pumilio homolog 21 OS=Arabidopsis thaliana GN=APUM21 PE=3 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|Q9LVG3|PUM18_ARATH Pumilio homolog 18 OS=Arabidopsis thaliana GN=APUM18 PE=2 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
>sp|Q9LSS8|PUM19_ARATH Putative pumilio homolog 19 OS=Arabidopsis thaliana GN=APUM19 PE=3 SV=2 Back     alignment and function description
>sp|Q9FIE9|PUM16_ARATH Putative pumilio homolog 16 OS=Arabidopsis thaliana GN=APUM16 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 ?
Query309
255553119 471 RNA binding protein, putative [Ricinus c 0.944 0.619 0.424 4e-49
255544718 483 conserved hypothetical protein [Ricinus 0.944 0.604 0.412 1e-47
147798084 507 hypothetical protein VITISV_039435 [Viti 0.844 0.514 0.386 3e-41
224117628 502 predicted protein [Populus trichocarpa] 0.870 0.535 0.375 3e-39
255564824 771 RNA binding protein, putative [Ricinus c 0.954 0.382 0.334 8e-38
297793151 598 APUM12 [Arabidopsis lyrata subsp. lyrata 0.954 0.493 0.327 3e-36
224056741 497 predicted protein [Populus trichocarpa] 0.867 0.539 0.366 7e-36
302775508321 hypothetical protein SELMODRAFT_94948 [S 0.941 0.906 0.323 1e-35
302756987322 hypothetical protein SELMODRAFT_75995 [S 0.941 0.903 0.323 1e-35
168015525347 predicted protein [Physcomitrella patens 0.951 0.847 0.317 2e-35
>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
 Score =  201 bits (511), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 129/304 (42%), Positives = 189/304 (62%), Gaps = 12/304 (3%)

Query: 1   EEGSQYLQEKLSSGDS-----RILDKLFWVVSGFTF--ELMSGQYGRFVFGKFIESCNES 53
           ++GS+YLQ+ L++ DS     +ILDK+   V G      LM  Q+G  V  K I+SCN+ 
Sbjct: 151 QQGSEYLQDLLATSDSYLTTSKILDKVTASVVGIPVINYLMVDQHGYHVCSKLIDSCNDI 210

Query: 54  QLALIILKITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMT 113
           QL LI+ +IT   + F+       GS  +KKLIK V +S  + Y  +S  K  ++ L + 
Sbjct: 211 QLTLILERITKNTEQFVRICCAINGSKMIKKLIKKVKRSCLISYLTVSLYKGFYQ-LAIN 269

Query: 114 KPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILH 173
           + GS V++ C++     +N  +Y+AA+ HCL LA    GC++ N FID ++GSRR+ +L 
Sbjct: 270 QIGSYVVVFCMDCLDIQQNALLYEAAISHCLILATDAIGCVSANKFIDRIQGSRRQTLLE 329

Query: 174 LISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLK 233
           LIS NA  LS+  SGN+VVQ VL LE+P +   I   L+GHYV LS  K GS VV+K L 
Sbjct: 330 LISDNAVFLSQDPSGNHVVQKVLGLENPIINAKIGAQLKGHYVRLSFQKWGSHVVEKCLV 389

Query: 234 YQNAVHYIVEELLN--SDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHL 291
            Q A+ Y V++LL   S Q+LQ+A D++GNYVIQ AL  T +++ +++H+ L+  L+ +L
Sbjct: 390 SQ-AMVYAVQDLLTCGSSQLLQIARDQFGNYVIQKALKVTKKKN-IALHRILLNSLEPNL 447

Query: 292 AALR 295
            ALR
Sbjct: 448 NALR 451

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>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
>gi|147798084|emb|CAN67257.1| hypothetical protein VITISV_039435 [Vitis vinifera] 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|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|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|224056741|ref|XP_002299000.1| predicted protein [Populus trichocarpa] gi|222846258|gb|EEE83805.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|302775508|ref|XP_002971171.1| hypothetical protein SELMODRAFT_94948 [Selaginella moellendorffii] gi|300161153|gb|EFJ27769.1| hypothetical protein SELMODRAFT_94948 [Selaginella moellendorffii] Back     alignment and taxonomy information
>gi|302756987|ref|XP_002961917.1| hypothetical protein SELMODRAFT_75995 [Selaginella moellendorffii] gi|300170576|gb|EFJ37177.1| hypothetical protein SELMODRAFT_75995 [Selaginella moellendorffii] Back     alignment and taxonomy information
>gi|168015525|ref|XP_001760301.1| predicted protein [Physcomitrella patens subsp. patens] gi|162688681|gb|EDQ75057.1| predicted protein [Physcomitrella patens subsp. patens] 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 ?
Query309
TAIR|locus:2167111596 PUM12 "pumilio 12" [Arabidopsi 0.954 0.494 0.321 1.4e-38
DICTYBASE|DDB_G02899871036 DDB_G0289987 "Pumilio homology 0.964 0.287 0.314 9.4e-33
TAIR|locus:2015036515 PUM8 "pumilio 8" [Arabidopsis 0.941 0.565 0.321 1.7e-31
TAIR|locus:2164165327 PUM18 "pumilio 18" [Arabidopsi 0.864 0.816 0.323 1.3e-29
TAIR|locus:2138258556 PUM11 "pumilio 11" [Arabidopsi 0.974 0.541 0.306 7.2e-29
TAIR|locus:2144010327 PUM19 "pumilio 19" [Arabidopsi 0.864 0.816 0.32 1.2e-28
ASPGD|ASPL0000057098650 AN10071 [Emericella nidulans ( 0.944 0.449 0.288 1.3e-28
TAIR|locus:2194699650 PUM7 "pumilio 7" [Arabidopsis 0.948 0.450 0.3 1.7e-28
TAIR|locus:2011349564 PUM9 "pumilio 9" [Arabidopsis 0.909 0.498 0.297 1.6e-26
TAIR|locus:2144711517 PUM21 "pumilio 21" [Arabidopsi 0.799 0.477 0.305 3.9e-26
TAIR|locus:2167111 PUM12 "pumilio 12" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 413 (150.4 bits), Expect = 1.4e-38, P = 1.4e-38
 Identities = 97/302 (32%), Positives = 164/302 (54%)

Query:     1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIIL 60
             + G ++LQ   S  D   ++ +F  +  +  ELM   +G ++  K +E CNE Q   I+ 
Sbjct:   289 QHGCRFLQRIFSEKDGNDIEMIFNEIIDYISELMMDPFGNYLVQKLLEVCNEDQRMQIVH 348

Query:    61 KITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVI 120
              IT +  L +  S D  G+ +V+K+++   +   +   ++SALK     L+    G+ V+
Sbjct:   349 SITRKPGLLIKISCDMHGTRAVQKIVETAKREEEISI-IISALKHGIVHLIKNVNGNHVV 407

Query:   121 LKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAA 180
              +CL+    +   F+++AA+ HC+ LA    GC  L   +   +G +++ ++  I+ NA 
Sbjct:   408 QRCLQYLLPYCGKFLFEAAITHCVELATDRHGCCVLQKCLGYSEGEQKQHLVSEIASNAL 467

Query:   181 SLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVHY 240
              LS+   GNYV+Q+V  L+  +    I   L G+Y +LS+ KC S VV+K LK  +  H 
Sbjct:   468 LLSQDPFGNYVLQYVFELQLQWATFEILEQLEGNYTELSMQKCSSNVVEKCLKLADDKHR 527

Query:   241 --IVEELLNSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMK 298
               I+ EL+N  ++ QV  D YGNYVIQ AL    +Q + +VH  LV  ++ ++++LR   
Sbjct:   528 ARIIRELINYGRLDQVMLDPYGNYVIQAAL----KQSKGNVHALLVDAIKLNISSLRTNP 583

Query:   299 YG 300
             YG
Sbjct:   584 YG 585
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:2015036 PUM8 "pumilio 8" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2164165 PUM18 "pumilio 18" [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:2144010 PUM19 "pumilio 19" [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:2194699 PUM7 "pumilio 7" [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
TAIR|locus:2144711 PUM21 "pumilio 21" [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 ?
Query309
cd07920322 cd07920, Pumilio, Pumilio-family RNA binding domai 2e-56
COG5099777 COG5099, COG5099, RNA-binding protein of the Puf f 2e-26
cd07920 322 cd07920, Pumilio, Pumilio-family RNA binding domai 6e-05
>gnl|CDD|153420 cd07920, Pumilio, Pumilio-family RNA binding domain Back     alignment and domain information 
 Score =  184 bits (470), Expect = 2e-56
 Identities = 94/308 (30%), Positives = 150/308 (48%), Gaps = 15/308 (4%)

Query: 1   EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIIL 60
           + GS++LQ+KL        + +F  +     ELM   +G +V  K  E   E Q   ++ 
Sbjct: 19  QHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLE 78

Query: 61  KITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVI 120
           KI     +  L S+D +G   ++KL++ +  S   +  ++  L+     L+  + G+ VI
Sbjct: 79  KIL--GHVVRL-SLDMYGCRVIQKLLESI--SEEQISLLVKELRGHVVELVKDQNGNHVI 133

Query: 121 LKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAA 180
            KC+E        FI  A   +C+ L+ H  GC  +   +++    +R+ +L  I  +A 
Sbjct: 134 QKCIEKFPPEDLQFIIDAFKGNCVALSTHPYGCRVIQRCLEHCSEEQREPLLEEILEHAL 193

Query: 181 SLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVH- 239
            L + + GNYVVQHVL L DP     I   L G+ V LS  K  S VV+K LK+ +    
Sbjct: 194 ELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNVVEKCLKHASKEER 253

Query: 240 -YIVEELLNS----DQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAAL 294
             I++E+L S      +  +  D+YGNYVIQTAL       +    + LV  ++ HL +L
Sbjct: 254 ELIIDEILASGNETSALDTLMKDQYGNYVIQTALDVA----KEEQRELLVEAIRPHLPSL 309

Query: 295 RVMKYGSN 302
           R   YG +
Sbjct: 310 RKSPYGKH 317

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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 309
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
COG5099777 RNA-binding protein of the Puf family, translation 100.0
KOG2049536 consensus Translational repressor MPT5/PUF4 and re 99.98
KOG2050 652 consensus Puf family RNA-binding protein [Translat 99.97
KOG2050 652 consensus Puf family RNA-binding protein [Translat 99.96
KOG2188650 consensus Predicted RNA-binding protein, contains 99.96
KOG2188650 consensus Predicted RNA-binding protein, contains 99.92
KOG4574 1007 consensus RNA-binding protein (contains RRM and Pu 99.74
KOG4574 1007 consensus RNA-binding protein (contains RRM and Pu 99.29
PF0080635 PUF: Pumilio-family RNA binding repeat; InterPro: 98.58
PF0080635 PUF: Pumilio-family RNA binding repeat; InterPro: 98.5
smart0002536 Pumilio Pumilio-like repeats. Pumilio-like repeats 98.16
smart0002536 Pumilio Pumilio-like repeats. Pumilio-like repeats 98.07
PF08144148 CPL: CPL (NUC119) domain; InterPro: IPR012959 This 94.67
PF08144148 CPL: CPL (NUC119) domain; InterPro: IPR012959 This 87.5
PRK05686339 fliG flagellar motor switch protein G; Validated 86.4
PF11510263 FA_FANCE: Fanconi Anaemia group E protein FANCE; I 80.35
>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=6e-64  Score=446.62  Aligned_cols=300  Identities=25%  Similarity=0.395  Sum_probs=287.8

Q ss_pred             CchhHHHHHHhccCCH-HHHHHHHHHHHhhHHHhccCcchhHHHHHHHhhcCHHHHHHHHHHHhcccchHHHhhccccCC
Q 048245            1 EEGSQYLQEKLSSGDS-RILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGS   79 (309)
Q Consensus         1 ~~gsr~lq~~l~~~~~-e~~~~i~~el~~~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~gs   79 (309)
                      |+|||++|..++..+. +++..+|+++.+.+.+||.|.+||||||+++++++++++..+...+.   +++..||.|+|||
T Consensus       188 q~GsrfiQqkl~~~~~~~ek~~if~ei~~~~~~L~~dvFGNyvIQkffE~gt~~q~~~l~~~~~---g~v~~Lsld~ygC  264 (503)
T KOG1488|consen  188 QHGSRFIQQKLETASDNEEKQAVFDEILPPALELMTDVFGNYVIQKFFEHGTEDQRNLLHSQIK---GHVLELSLDMYGC  264 (503)
T ss_pred             cccchHHHHhccccccHHHHHHHHHHHHHHHHHHHHHHhcCchhhhhhccCCHHHHHHHHHHHH---hhhhhhhcccccc
Confidence            7999999999999988 99999999999999999999999999999999999999999999999   9999999999999


Q ss_pred             HHHHHHHhhhcCChhHHHHHHHHHHHHHhHhhcCCCchHHHHHHhccCCCcchHHHHHHHHH--hHHHHhcCccccHHHH
Q 048245           80 SSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALE--HCLYLACHEQGCINLN  157 (309)
Q Consensus        80 ~vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~--~~~~l~~~~~gs~vvq  157 (309)
                      ||+|+.|+.. ......+++.+ +.+++..+++|++||||||++++..+++.+.++++.+.+  ++..+|+|+|||+|||
T Consensus       265 RVIQkale~i-d~~~~~~Li~E-Ld~~vl~~v~DQngnHViQK~ie~~p~~~~~Fiv~~f~~~~~~~~ls~~~YGCRVIQ  342 (503)
T KOG1488|consen  265 RVIQKALEKV-DVSLQIQLIDE-LDGHLLKCVKDQNGNHVIQKCIETLPPDAWQFIVDFFSGDDNLLELSTHKYGCRVIQ  342 (503)
T ss_pred             hhHHHHHHhc-CHHHHHHHHHH-HHhhHHHHHhhcccceehhhhhhccChHHHHHHHHHhcCCCceeEeeccCcccHHHH
Confidence            9999999999 66666666666 799999999999999999999999999999999999999  9999999999999999


Q ss_pred             HHHhccChHHHHHHHHHHHHhHHhhccCCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCc
Q 048245          158 NFIDNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNA  237 (309)
Q Consensus       158 ~~l~~~~~~~~~~l~~~l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~  237 (309)
                      ++++++++++...++++|..++..|+.|+|||||||++|+++++..+..|++++.+++++++.|||+|+|||+||..++.
T Consensus       343 r~lE~c~~~~~~~i~~ei~~~~~~L~~dQygNYVIQHVie~g~~~~~~~I~~~l~~~ll~~Sq~KfASnVVEk~~~~a~~  422 (503)
T KOG1488|consen  343 RILEHCSEDQKQPLMEEIIRNCDQLAQDQYGNYVIQHVIEHGSPYRDTIIIKCLLGNLLSMSQHKFASNVVEKAFLFAPP  422 (503)
T ss_pred             HHhhcCChHhhhHHHHHHHHHHHHHHhhhhhhHHHHHHHhcCChhhhhhHHHHHHhhHHHHHHHHHHHHHHHHHHhhCCH
Confidence            99999999999999999999999999999999999999999999888899999999999999999999999999999998


Q ss_pred             H--HHHHHHHhC-----chHHHHhhcCcChhHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHhhhcCCCccchhhhccC
Q 048245          238 V--HYIVEELLN-----SDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNKEIQKKK  309 (309)
Q Consensus       238 ~--~~i~~~l~~-----~~~l~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~g~~v~~k~~~  309 (309)
                      .  ..|++|++.     ++.|..|+.|+|||||||++++.+++    .+++.|+..+++|..+|+..+||++|+++|-|
T Consensus       423 ~~r~~i~~Ei~~~~~~~~~~L~~mmkdQYgNYVVQkmi~~~~~----~q~~~i~~rI~~h~~~Lrk~syGKhIia~lek  497 (503)
T KOG1488|consen  423 LLRALIMNEIFPGYVEHPDALDIMMKDQYGNYVVQKMIDICGP----EQRELIKSRVKPHASRLRKFSYGKHIIAKLEK  497 (503)
T ss_pred             HHHHHHHHHhcCCccCCccHHHHHHHHhhhhhHHHHHHHhcCH----HHHHHHHHHHHHHHHHHccCccHHHHHHHHHH
Confidence            8  889999998     26899999999999999999999988    99999999999999999999999999999854

>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
>COG5099 RNA-binding protein of the Puf family, translational repressor [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
>KOG2050 consensus Puf family RNA-binding protein [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
>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
>PRK05686 fliG flagellar motor switch protein G; Validated Back     alignment and domain information
>PF11510 FA_FANCE: Fanconi Anaemia group E protein FANCE; InterPro: IPR021025 Fanconi Anaemia (FA) is a cancer predisposition disorder characterised by chromosome fragility and hypersensitivity to genotoxic agents that suggest defects in the molecular mechanisms of DNA damage signalling and repair 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 ?
Query309
3bwt_A333 Crystal Structure Of The Rna Binding Domain Of Puf4 9e-20
3bwt_A333 Crystal Structure Of The Rna Binding Domain Of Puf4 3e-06
3bx2_A335 Puf4 Rna Binding Domain Bound To Ho Endonuclease Rn 1e-19
3bx2_A335 Puf4 Rna Binding Domain Bound To Ho Endonuclease Rn 4e-06
4dzs_A357 Crystal Structure Of Yeast Puf4p Rna Binding Domain 1e-19
4dzs_A357 Crystal Structure Of Yeast Puf4p Rna Binding Domain 3e-06
3bx3_A335 Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR Re 4e-19
3bx3_A335 Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR Re 3e-07
3q0q_A351 Crystal Structure Of The Pumilio-Homology Domain Fr 5e-14
3gvo_A351 Structure And Rna Binding Of The Mouse Pumilio-2 Pu 9e-13
3h3d_X323 Drosophila Pumilio Rna Binding Domain (Puf Domain) 3e-12
3h3d_X323 Drosophila Pumilio Rna Binding Domain (Puf Domain) 6e-10
3bsb_A343 Crystal Structure Of Human Pumilio1 In Complex With 7e-12
1ib2_A349 Crystal Structure Of A Pumilio-Homology Domain Leng 8e-12
2yjy_A350 A Specific And Modular Binding Code For Cytosine Re 1e-10
3k49_A369 Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr R 3e-07
3k49_A369 Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr R 6e-07
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From Saccharomyces Cerevisiae Length = 333 Back     alignment and structure 
Iteration: 1

 Score = 94.0 bits (232), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 76/282 (26%), Positives = 136/282 (48%), Gaps = 11/282 (3%)
Query: 1   EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIIL 60
           + G ++LQ++L    S+  D +F     +T ELM+  +G ++  K +E     Q  +++ 
Sbjct: 22  QHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQ-RIVLT 80
Query: 61  KITFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVI 120
           KI+     F+  S++  G+ +++KLI+ +         V+ +L+     L     G+ VI
Sbjct: 81  KISSPH--FVEISLNPHGTRALQKLIECIKTDEEAQI-VVDSLRPYTVQLSKDLNGNHVI 137
Query: 121 LKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAA 180
            KCL+        FI+ A  + C+ +A H  GC  L   +D+    +   +   +     
Sbjct: 138 QKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVD 197
Query: 181 SLSRHRSGNYVVQHVLNLEDP----FLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQN 236
            L+    GNYVVQ+++  E           I   L+   ++LS+ K GS V++K LK   
Sbjct: 198 KLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAI 257
Query: 237 AVHYIVEELLNS---DQILQVASDKYGNYVIQTALVETMRQD 275
               ++ E+LN+     I  + +D YGNYV+QTAL  + +Q+
Sbjct: 258 VSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQN 299
>pdb|3BWT|A Chain A, Crystal Structure Of The Rna Binding Domain Of Puf4 From Saccharomyces Cerevisiae Length = 333 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|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|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|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
>pdb|3GVO|A Chain A, Structure And Rna Binding Of The Mouse Pumilio-2 Puf Domain Length = 351 Back     alignment and structure
>pdb|3H3D|X Chain X, Drosophila Pumilio Rna Binding Domain (Puf Domain) Length = 323 Back     alignment and structure
>pdb|3H3D|X Chain X, Drosophila Pumilio Rna Binding Domain (Puf Domain) Length = 323 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|1IB2|A Chain A, Crystal Structure Of A Pumilio-Homology Domain Length = 349 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
>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 ?
Query309
3gvo_A351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 2e-59
3gvo_A 351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 7e-17
3gvo_A351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 9e-17
3bwt_A333 Protein PUF4; pumilio, RNA binding, HO endonucleas 2e-58
3bwt_A 333 Protein PUF4; pumilio, RNA binding, HO endonucleas 8e-19
3bwt_A 333 Protein PUF4; pumilio, RNA binding, HO endonucleas 2e-16
3bwt_A 333 Protein PUF4; pumilio, RNA binding, HO endonucleas 8e-08
3k49_A369 MRNA-binding protein PUF3; PUF3, pumilio, RNA bind 2e-55
3k49_A 369 MRNA-binding protein PUF3; PUF3, pumilio, RNA bind 2e-17
3v71_A382 PUF (pumilio/FBF) domain-containing protein 7, CO 9e-41
3v71_A382 PUF (pumilio/FBF) domain-containing protein 7, CO 1e-07
3v71_A 382 PUF (pumilio/FBF) domain-containing protein 7, CO 8e-05
3k62_A412 FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa 4e-32
3k62_A412 FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa 5e-15
3k62_A412 FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa 2e-10
3k62_A 412 FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa 3e-06
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-05
>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
 Score =  192 bits (491), Expect = 2e-59
 Identities = 68/307 (22%), Positives = 131/307 (42%), Gaps = 16/307 (5%)

Query: 3   GSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKI 62
           GS+++Q+KL          +F  +    ++LM+  +G +V  KF E  +  Q   +  +I
Sbjct: 37  GSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLDQKLALATRI 96

Query: 63  TFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILK 122
                +  L ++  +G   ++K ++ +  S      ++  L       +  + G+ V+ K
Sbjct: 97  R--GHVLPL-ALQMYGCRVIQKALESI--SSDQQSEMVKELDGHVLKCVKDQNGNHVVQK 151

Query: 123 CLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASL 182
           C+E        FI  A       L+ H  GC  +   +++    +   IL  +  +   L
Sbjct: 152 CIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQL 211

Query: 183 SRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKY--QNAVHY 240
            + + GNYV+QHVL    P     I   +RG  + LS  K  S VV+K + +  +     
Sbjct: 212 VQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERAL 271

Query: 241 IVEELL-----NSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALR 295
           +++E+          +  +  D+Y NYV+Q  +       R    + ++ K++ H+  LR
Sbjct: 272 LIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQR----KIIMHKIRPHITTLR 327

Query: 296 VMKYGSN 302
              YG +
Sbjct: 328 KYTYGKH 334
>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
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query309
3gvo_A351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 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
3k62_A412 FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa 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
2ilr_A264 Protein FACE, fanconi anemia group E protein; anti 85.11
>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=4.1e-65  Score=454.60  Aligned_cols=300  Identities=23%  Similarity=0.373  Sum_probs=286.8

Q ss_pred             CchhHHHHHHhccCCHHHHHHHHHHHHhhHHHhccCcchhHHHHHHHhhcCHHHHHHHHHHHhcccchHHHhhccccCCH
Q 048245            1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSS   80 (309)
Q Consensus         1 ~~gsr~lq~~l~~~~~e~~~~i~~el~~~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~gs~   80 (309)
                      |+|||++|++++.+++++++.+|+++.|++.+||.|+|||||+|+++++++++++..+++.+.   +++..++.|++|||
T Consensus        35 q~gsR~lQ~~l~~~~~~~~~~i~~ei~~~~~~L~~d~~gn~vvQklle~~~~~~~~~i~~~i~---g~~~~l~~~~~G~r  111 (351)
T 3gvo_A           35 QHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLDQKLALATRIR---GHVLPLALQMYGCR  111 (351)
T ss_dssp             HHHHHHHHHHHHHCCHHHHHHHHHHHGGGHHHHHTSTTHHHHHHHHHHHCCHHHHHHHHHHHT---TCHHHHHTSTTHHH
T ss_pred             CcchHHHHHHHhhCCHHHHHHHHHHHHHhHHHHHhChhhhHHHHHHHhhCCHHHHHHHHHHHH---hhHHHHhhCHHhHH
Confidence            689999999999999999999999999999999999999999999999999999999999999   99999999999999


Q ss_pred             HHHHHHhhhcCChhHHHHHHHHHHHHHhHhhcCCCchHHHHHHhccCCCcchHHHHHHHHHhHHHHhcCccccHHHHHHH
Q 048245           81 SVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFI  160 (309)
Q Consensus        81 vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~~~~gs~vvq~~l  160 (309)
                      |+|++++.+ ++ ++...+.+++.+++..|++|++||||+|++++.++++.+..+++.+.+++..+++|+|||+|+|+++
T Consensus       112 vvQk~le~~-~~-~~~~~i~~el~~~~~~L~~d~~Gn~ViQk~l~~~~~~~~~~i~~~~~~~~~~ls~~~~G~~Vvq~~l  189 (351)
T 3gvo_A          112 VIQKALESI-SS-DQQSEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRIL  189 (351)
T ss_dssp             HHHHHHHHS-CH-HHHHHHHGGGTTCHHHHHHSTTHHHHHHHHHHHSCGGGTHHHHHHTTTTHHHHHTSTTHHHHHHHHH
T ss_pred             HHHHHHHhC-CH-HHHHHHHHHhhhhHHHHHHhhhhhHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhCcHhHHHHHHHH
Confidence            999999999 54 4556666779999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccChHHHHHHHHHHHHhHHhhccCCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH--
Q 048245          161 DNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAV--  238 (309)
Q Consensus       161 ~~~~~~~~~~l~~~l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~~--  238 (309)
                      +.++++++..+++++.+++..|++|+|||||+|++|+.++|+.+..|++.+.+++.+||+|+|||+|+|+|++.+++.  
T Consensus       190 e~~~~~~~~~ii~~l~~~~~~L~~d~~Gn~ViQ~~l~~~~~~~~~~i~~~l~~~~~~Ls~~k~gs~Vvek~l~~~~~~~r  269 (351)
T 3gvo_A          190 EHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAER  269 (351)
T ss_dssp             HHSCHHHHHHHHHHHHTTHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHTTTTCHHHHHTSTTHHHHHHHHHHHSCHHHH
T ss_pred             HHCCHHHHHHHHHHHhhhHHhcCCCchHHHHHHHHHHhCchhhHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHhCCHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999988  


Q ss_pred             HHHHHHHhCc-----hHHHHhhcCcChhHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHhhhcCCCccchhhhccC
Q 048245          239 HYIVEELLNS-----DQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNKEIQKKK  309 (309)
Q Consensus       239 ~~i~~~l~~~-----~~l~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~g~~v~~k~~~  309 (309)
                      +.|+++++..     +.+..|++|+|||||||++|+.+++    ..|+.+++.|.|+++.|++++||++|+.|+.|
T Consensus       270 ~~ii~el~~~~~~~~~~l~~l~~d~ygnyViq~~L~~~~~----~~r~~i~~~i~~~~~~L~~~~~g~~i~~kl~~  341 (351)
T 3gvo_A          270 ALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEP----AQRKIIMHKIRPHITTLRKYTYGKHILAKLEK  341 (351)
T ss_dssp             HHHHHHHHSCEETTEEHHHHHHHSTTHHHHHHHHHHHCCH----HHHHHHHHHHGGGHHHHTTSTTTHHHHHHHHH
T ss_pred             HHHHHHHhcccCCCChHHHHccCCcchHHHHHHHHHhCCH----HHHHHHHHHHHHHHHHHhcCCchHHHHHHHHH
Confidence            7899999862     2699999999999999999999988    88999999999999999999999999998753
>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
>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
>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
>2ilr_A Protein FACE, fanconi anemia group E protein; antiparallel helical hairpin, helical repeat, FANC repeat, oncoprotein; 2.00A {Homo sapiens} 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 309
d1m8za_339 a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [Ta 1e-38
d1m8za_339 a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [Ta 1e-12
d1m8za_ 339 a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [Ta 7e-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 =  137 bits (345), Expect = 1e-38
 Identities = 71/313 (22%), Positives = 131/313 (41%), Gaps = 18/313 (5%)

Query: 3   GSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKI 62
           GS+++Q KL          +F  +    ++LM   +G +V  KF E  +  Q   +  +I
Sbjct: 35  GSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERI 94

Query: 63  TFQDQLFLLASVDKFGSSSVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILK 122
                  L  ++  +G   ++K ++ +         ++  L       +  + G+ V+ K
Sbjct: 95  RGH---VLSLALQMYGCRVIQKALEFI--PSDQQNEMVRELDGHVLKCVKDQNGNHVVQK 149

Query: 123 CLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFIDNMKGSRRKQILHLISVNAASL 182
           C+E        FI  A       L+ H  GC  +   +++    +   IL  +  +   L
Sbjct: 150 CIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQL 209

Query: 183 SRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAVHY-- 240
            + + GNYV+QHVL    P     I   +RG+ + LS  K  S VV+K + + +      
Sbjct: 210 VQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTERAV 269

Query: 241 IVEELL-----NSDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALR 295
           +++E+          +  +  D+Y NYV+Q  +       R    + ++ K++ H+A LR
Sbjct: 270 LIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQR----KIVMHKIRPHIATLR 325

Query: 296 VMKYGSNKEIQKK 308
              YG  K I  K
Sbjct: 326 KYTYG--KHILAK 336
>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
>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 ?
Query309
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=1.4e-58  Score=409.62  Aligned_cols=300  Identities=23%  Similarity=0.354  Sum_probs=283.6

Q ss_pred             CchhHHHHHHhccCCHHHHHHHHHHHHhhHHHhccCcchhHHHHHHHhhcCHHHHHHHHHHHhcccchHHHhhccccCCH
Q 048245            1 EEGSQYLQEKLSSGDSRILDKLFWVVSGFTFELMSGQYGRFVFGKFIESCNESQLALIILKITFQDQLFLLASVDKFGSS   80 (309)
Q Consensus         1 ~~gsr~lq~~l~~~~~e~~~~i~~el~~~~~~L~~~~~g~~vlq~li~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~gs~   80 (309)
                      |+|||+||++++++++++++.||+++.|++.+||.|+|||||+|+++++++++++..++..+.   +++..++.|++|++
T Consensus        33 q~gSr~lQ~~l~~~~~~~~~~I~~~l~~~~~~L~~~~~gn~vvqkll~~~~~~~~~~i~~~l~---~~~~~L~~~~~gs~  109 (339)
T d1m8za_          33 QHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERIR---GHVLSLALQMYGCR  109 (339)
T ss_dssp             HHHHHHHHHHHHHCCHHHHHHHHHHHGGGHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHHHT---TCHHHHHTSTTHHH
T ss_pred             chhhHHHHHHHhhCCHHHHHHHHHHHHHHHHHHhhCcccchhHHHHHhhCCHHHHHHHHHHHH---hhHHHHhcccccch
Confidence            579999999999999999999999999999999999999999999999999999999999999   99999999999999


Q ss_pred             HHHHHHhhhcCChhHHHHHHHHHHHHHhHhhcCCCchHHHHHHhccCCCcchHHHHHHHHHhHHHHhcCccccHHHHHHH
Q 048245           81 SVKKLIKVVAQSPPLLYHVMSALKRLFKFLMMTKPGSSVILKCLEPSYNHKNDFIYQAALEHCLYLACHEQGCINLNNFI  160 (309)
Q Consensus        81 vlq~ll~~~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vvq~~l~~~~~~~~~~l~~~l~~~~~~l~~~~~gs~vvq~~l  160 (309)
                      |+|++++.+ ++..... +..++.+++..++.|++|+||++++++.++++.+..+++.+.+++..+++|++||+++|+++
T Consensus       110 Vvq~l~~~~-~~~~~~~-l~~el~~~~~~l~~d~~~~~v~~~~l~~~~~~~~~~i~~~~~~~~~~l~~~~~g~~vlq~~l  187 (339)
T d1m8za_         110 VIQKALEFI-PSDQQNE-MVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRIL  187 (339)
T ss_dssp             HHHHHHHHS-CHHHHHH-HHHTTTTCHHHHHHSTTHHHHHHHHHHHSCGGGGHHHHHHTTTTHHHHHTSTTHHHHHHHHH
T ss_pred             HHHhhhccC-CHHHHHH-HHHHHhhhhHHHhcCCCcchHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhCcchhHHHHHHH
Confidence            999999998 5554444 45569999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccChHHHHHHHHHHHHhHHhhccCCChhHHHHHHhhcCChhhHHHHHHHHHHhHHHhccCcchhHHHHHHHhcCCcH--
Q 048245          161 DNMKGSRRKQILHLISVNAASLSRHRSGNYVVQHVLNLEDPFLIDAICFALRGHYVDLSLTKCGSFVVQKFLKYQNAV--  238 (309)
Q Consensus       161 ~~~~~~~~~~l~~~l~~~~~~l~~d~~g~~viq~ll~~~~~~~~~~i~~~l~~~~~~l~~~~~gs~vve~~l~~~~~~--  238 (309)
                      +.++++++..+++.+.+++..|+.|+|||||+|++|+.++++.++.|++.+.+++.++++|++||+|+|+|+..+++.  
T Consensus       188 ~~~~~~~~~~l~~~l~~~~~~L~~~~~G~~vvq~~l~~~~~~~~~~i~~~l~~~~~~l~~~k~gS~vve~~l~~~~~~~~  267 (339)
T d1m8za_         188 EHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASNVVEKCVTHASRTER  267 (339)
T ss_dssp             HHSCHHHHHHHHHHHHHTHHHHTTSTTHHHHHHHHHHHSCHHHHHHHHHHHTTCHHHHHTSTTHHHHHHHHHHHSCHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHcCCHHHHHHHHHHHHhhHHHHHcchhHHHHHHHHHHhCCHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999988  


Q ss_pred             HHHHHHHhC-----chHHHHhhcCcChhHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHhhhcCCCccchhhhccC
Q 048245          239 HYIVEELLN-----SDQILQVASDKYGNYVIQTALVETMRQDRLSVHQRLVTKLQQHLAALRVMKYGSNKEIQKKK  309 (309)
Q Consensus       239 ~~i~~~l~~-----~~~l~~L~~d~~g~~Viq~~l~~~~~~~~~~~~~~l~~~l~~~~~~L~~~~~g~~v~~k~~~  309 (309)
                      ..++.++..     .+.+..|+.|+|||||||++++.+++    .+++.+++.|.|+++.|+.++||++|+.||.|
T Consensus       268 ~~~~~~l~~~~~~~~~~l~~L~~d~~gn~Viq~~l~~~~~----~~~~~i~~~l~~~~~~L~~~~~G~~v~~~l~~  339 (339)
T d1m8za_         268 AVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEP----GQRKIVMHKIRPHIATLRKYTYGKHILAKLEK  339 (339)
T ss_dssp             HHHHHHHHHCEETTEEHHHHHHTSTTHHHHHHHHHHHSCH----HHHHHHHHTTGGGHHHHTTSSTHHHHHHHHC-
T ss_pred             HHHHHHHHhcccCchHHHHHHHcCCcccHHHHHHHHhCCH----HHHHHHHHHHHHHHHHHhcCCcHHHHHHHHhC
Confidence            666777653     34699999999999999999999998    89999999999999999999999999999976
>d1m8za_ a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure