Citrus Sinensis ID: 048735

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-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------58
RRDLGDHGDDLRWRFPPPENNSRHPVTTSQQSHVASQNLHLIPIYQKPNQQDYHVENPSLQNPTTQDQLSGHLHYSNYPYDKSLAMEPSTCRCRTPESGLSRPSQFAAPRPPLSQYLPYPIPLNQAQYSFINSLPTSFPLENHETIDLQSGFDLQSGFEGLNIDGLGLPRPNNLTVQRNLVAATNRYATTNNASPSYSNLSHGFLSDHHHLGSSTNASSRYNNFYARARHHHHRTSYSSIEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRHPEIVQLILDPYGNYVIQTAWDVSQGRRIRQTLYDLVVDNSPFLQSHMYGKNVLAKVRGNKNRFHNRVAMW
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHccccccHHHHHHHHccccHHHHHHHHHHHHHccccHHHHcccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHcccccccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHcccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHcccHHHHHHHHHHHHccHHHHHHHccccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHccccccccccccc
ccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccHHHHHHHccccccccccccccccEEcccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccHHHHHHccHHHHHHHcccHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHccccEHHHHccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHcEEEHcccccHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHccHHHHHHHHHHHcccHHHHHHHHcHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHccccccEEEc
rrdlgdhgddlrwrfpppennsrhpvttsqqshvasqnlhlipiyqkpnqqdyhvenpslqnpttqdqlsghlhysnypydkslamepstcrcrtpesglsrpsqfaaprpplsqylpypiplnqaqysfinslptsfplenhetidlqsgfdlqsgfeglnidglglprpnnltVQRNLVAATNryattnnaspsysnlshgflsdhhhlgsstnassRYNNFYARarhhhhrtsyssIEELRGRIILVAKDEQGCRFLQkkvdernpiDIEMILSEVIDDLHELMRHQSANHLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLdageyptrqqLTQEQQSLLVSALKNITVSlsksphgnhvikrclqkfppdyTKDLLEEIAENCLDLatdrsgccllqyCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRHPEIVQLIldpygnyviqtawdvsqgrriRQTLYDLvvdnspflqshmygkNVLAKVRGNKNRFHNRVAMW
rrdlgdhgddlrwrfpppennsrhpVTTSQQSHVASQNLHLIPIYQKPNQQDYHVENPSLQNPTTQDQLSGHLHYSNYPYDKSLAMEPSTCRCRTPESGLSRPSQFAAPRPPLSQYLPYPIPLNQAQYSFINSLPTSFPLENHETIDLQSGFDLQSGFEGLNIDGLGLPRPNNLTVQRNLVAATNRYATTNNASPSYSNLSHGFLSDHHHLGSSTNASSRYNNFYARARHHhhrtsyssieeLRGRIILVAKDEQGCRflqkkvdernpidIEMILSEVIDDLHELMRHQSANHLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLVSALKNITVSlsksphgnhvIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRHPEIVQLILDPYGNYVIQTAWDVSQGRRIRQTLYDLVVDNspflqshmygknvlakvrgnknrfhnrvamw
rrdlgdhgddlrwrFPPPENNSRHPVTTSQQSHVASQNLHLIPIYQKPNQQDYHVENPSLQNPTTQDQLSGHLHYSNYPYDKSLAMEPSTCRCRTPESGLSRPSQFAAPRPPLSQYLPYPIPLNQAQYSFINSLPTSFPLENHETIDLQSGFDLQSGFEGLNIDGLGLPRPNNLTVQRNLVaatnryattnnaSPSYSNLSHGFLSDHHHLGSSTNASSRYNNFYARARHHHHRTSYSSIEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRHPEIVQLILDPYGNYVIQTAWDVSQGRRIRQTLYDLVVDNSPFLQSHMYGKNVLAKVRGNKNRFHNRVAMW
***************************************HLIPIY*********************************************************************QYLPYPIPLNQAQYSFINSLPTSFPLENHETIDLQSGFDLQSGFEGLNIDGLGLPRPNNLTVQRNLVAATNRYA******************************************************LRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDA***************LLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRHPEIVQLILDPYGNYVIQTAWDVSQGRRIRQTLYDLVVDNSPFLQSHMYGKNVLAKVRG************
**********************************************************************************************************************************************************************************************************************************************SIEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRHPEIVQLILDPYGNYVIQTAWDVSQGRRIRQTLYDLVVDNSPFLQSHMYGKNVLAKVRGN******RVAMW
RRDLGDHGDDLRWRFPPPEN**************ASQNLHLIPIYQKPNQQDYHVENPSLQNPTTQDQLSGHLHYSNYPYDKSLAMEPS****************FAAPRPPLSQYLPYPIPLNQAQYSFINSLPTSFPLENHETIDLQSGFDLQSGFEGLNIDGLGLPRPNNLTVQRNLVAATNRYATTNNASPSYSNLSHGFLSDHHHLGSSTNASSRYNNFYARAR*********SIEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRHPEIVQLILDPYGNYVIQTAWDVSQGRRIRQTLYDLVVDNSPFLQSHMYGKNVLAKVRGNKNRFHNRVAMW
*****DHGDDLRWRFP***********************H*IPIYQKPNQQDYHVENPSLQNPTTQDQLSGHLHYSNYPYDKSLAMEPSTCRCRTPESGLSRPSQFAAPRPPLSQYLPYPIPLNQAQYSFINSLPTSFPLENHETIDLQSGFDLQSGFEGLNIDGLGLPRPNNLTVQRNLVAATNRYATTNNASPSYSNLSHGFLSDHHHLGSSTNASSRYNNFYARARHHHHRTSYSSIEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRHPEIVQLILDPYGNYVIQTAWDVSQGRRIRQTLYDLVVDNSPFLQSHMYGKNVLAKVRGNKNRFHNRVAMW
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RRDLGDHGDDLRWRFPPPENNSRHPVTTSQQSHVASQNLHLIPIYQKPNQQDYHVENPSLQNPTTQDQLSGHLHYSNYPYDKSLAMEPSTCRCRTPESGLSRPSQFAAPRPPLSQYLPYPIPLNQAQYSFINSLPTSFPLENHETIDLQSGFDLQSGFEGLNIDGLGLPRPNNLTVQRNLVAATNRYATTNNASPSYSNLSHGFLSDHHHLGSSTNASSRYNNFYARARHHHHRTSYSSIEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRHPEIVQLILDPYGNYVIQTAWDVSQGRRIRQTLYDLVVDNSPFLQSHMYGKNVLAKVRGNKNRFHNRVAMW
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 ?
Query579 2.2.26 [Sep-21-2011]
Q9LVC3596 Pumilio homolog 12 OS=Ara yes no 0.561 0.545 0.414 1e-70
Q9C9R6650 Putative pumilio homolog no no 0.621 0.553 0.334 1e-55
Q9LM20515 Putative pumilio homolog no no 0.550 0.619 0.373 2e-55
Q9LDW3556 Pumilio homolog 11 OS=Ara no no 0.544 0.566 0.379 9e-53
Q1PFN9564 Pumilio homolog 9 OS=Arab no no 0.540 0.554 0.373 4e-48
Q09829780 Pumilio domain-containing yes no 0.530 0.393 0.302 2e-43
Q9LP21528 Putative pumilio homolog no no 0.540 0.592 0.351 4e-42
Q92359681 Pumilio domain-containing no no 0.533 0.453 0.318 5e-42
P25339888 Pumilio homology domain f yes no 0.519 0.338 0.340 9e-40
Q4PSD1518 Pumilio homolog 14 OS=Ara no no 0.613 0.685 0.321 8e-38
>sp|Q9LVC3|PUM12_ARATH Pumilio homolog 12 OS=Arabidopsis thaliana GN=APUM12 PE=2 SV=2 Back     alignment and function desciption
 Score =  268 bits (684), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 138/333 (41%), Positives = 215/333 (64%), Gaps = 8/333 (2%)

Query: 237 YSSIEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLI 296
           Y+SI E RG+I  +AKD+ GCRFLQ+   E++  DIEMI +E+ID + ELM     N+L+
Sbjct: 272 YNSIAEARGKIYYLAKDQHGCRFLQRIFSEKDGNDIEMIFNEIIDYISELMMDPFGNYLV 331

Query: 297 QKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQS 356
           QKL+ V NE+Q  +++ S+      L++I  D+ G+R +QK+++  +        +E+ S
Sbjct: 332 QKLLEVCNEDQRMQIVHSITRKPGLLIKISCDMHGTRAVQKIVETAK-------REEEIS 384

Query: 357 LLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQ 416
           +++SALK+  V L K+ +GNHV++RCLQ   P   K L E    +C++LATDR GCC+LQ
Sbjct: 385 IIISALKHGIVHLIKNVNGNHVVQRCLQYLLPYCGKFLFEAAITHCVELATDRHGCCVLQ 444

Query: 417 YCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFA 476
            C+  ++ EQK  L++++ +NA +LS+  +GNYV+QY+  L++   T +++ QL G Y  
Sbjct: 445 KCLGYSEGEQKQHLVSEIASNALLLSQDPFGNYVLQYVFELQLQWATFEILEQLEGNYTE 504

Query: 477 LSLGKCSSNVVQKCLLESGEEQSTGIINEIIRHPEIVQLILDPYGNYVIQTAWDVSQGRR 536
           LS+ KCSSNVV+KCL  + ++    II E+I +  + Q++LDPYGNYVIQ A   S+G  
Sbjct: 505 LSMQKCSSNVVEKCLKLADDKHRARIIRELINYGRLDQVMLDPYGNYVIQAALKQSKG-N 563

Query: 537 IRQTLYDLVVDNSPFLQSHMYGKNVLAKVRGNK 569
           +   L D +  N   L+++ YGK VL+ +   K
Sbjct: 564 VHALLVDAIKLNISSLRTNPYGKKVLSALSSKK 596
Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.
Arabidopsis thaliana (taxid: 3702)
>sp|Q9C9R6|PUM7_ARATH Putative pumilio homolog 7, chloroplastic OS=Arabidopsis thaliana GN=APUM7 PE=3 SV=2 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|Q9LDW3|PUM11_ARATH Pumilio homolog 11 OS=Arabidopsis thaliana GN=APUM11 PE=3 SV=2 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|Q09829|YAD3_SCHPO Pumilio domain-containing protein C4G8.03c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC4G8.03c PE=4 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|Q92359|YDHE_SCHPO Pumilio domain-containing protein C6G9.14 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC6G9.14 PE=4 SV=1 Back     alignment and function description
>sp|P25339|PUF4_YEAST Pumilio homology domain family member 4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PUF4 PE=1 SV=2 Back     alignment and function description
>sp|Q4PSD1|PUM14_ARATH Pumilio homolog 14 OS=Arabidopsis thaliana GN=APUM14 PE=2 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query579
359492558574 PREDICTED: putative pumilio homolog 7, c 0.576 0.581 0.448 5e-78
255555215644 Pumilio domain-containing protein C6G9.1 0.571 0.513 0.447 1e-73
255538126542 RNA binding protein, putative [Ricinus c 0.557 0.595 0.433 2e-71
255564824 771 RNA binding protein, putative [Ricinus c 0.550 0.413 0.422 1e-70
224136880509 predicted protein [Populus trichocarpa] 0.559 0.636 0.418 5e-70
224052863620 predicted protein [Populus trichocarpa] 0.611 0.570 0.398 6e-70
22327888596 pumilio 12 [Arabidopsis thaliana] gi|313 0.561 0.545 0.414 9e-69
224067236486 predicted protein [Populus trichocarpa] 0.554 0.660 0.418 2e-68
297793151598 APUM12 [Arabidopsis lyrata subsp. lyrata 0.561 0.543 0.411 3e-68
224056214614 predicted protein [Populus trichocarpa] 0.569 0.537 0.428 4e-67
>gi|359492558|ref|XP_003634432.1| PREDICTED: putative pumilio homolog 7, chloroplastic-like [Vitis vinifera] Back     alignment and taxonomy information
 Score =  298 bits (763), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 154/343 (44%), Positives = 237/343 (69%), Gaps = 9/343 (2%)

Query: 222 NNFYARARHHHHRTSYSSIEELRGRIILVAKDEQGCRFLQKKVDERNPI-DIEMILSEVI 280
           NN +      +   +Y  +E+ RGR++ +A ++ GCRFLQ+K+     + +IEMI SEVI
Sbjct: 228 NNHFNHQLQQYLSLNYLCLEDFRGRVVPLAMNQHGCRFLQEKLQNNVTVKEIEMIFSEVI 287

Query: 281 DDLHELMRHQSANHLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLD 340
             + +LM  Q  N+++QKL+ + NEEQ T+++LS  ++Q +L+ IC ++ G+RVMQKLL 
Sbjct: 288 HHVAQLMLDQFGNYVVQKLVEICNEEQRTQILLSATTNQYQLIFICLNMHGTRVMQKLL- 346

Query: 341 AGEYPTRQQLTQEQQSLLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAE 400
             EY T    T EQ S+ +SAL  +TV+L+K   G+HVI+ CL+ F       L++E+AE
Sbjct: 347 --EYLT----TPEQISIAMSALWPVTVALTKDTSGHHVIQHCLKLFSCQDNMYLIKEVAE 400

Query: 401 NCLDLATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIP 460
           NC ++AT+RSGCC+LQ C+  +Q E + +L+A+++ANA  L+E  YGNYVVQ+++GLKIP
Sbjct: 401 NCFEIATNRSGCCVLQSCVENSQGELREQLMAEIIANALPLAEDRYGNYVVQHLMGLKIP 460

Query: 461 QVTADVVAQLAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRHPEIVQLILDPY 520
           +V  +++ Q  G + +LS  K  SNVV+K L+ES +EQS+ II E++R P +  L+LDP+
Sbjct: 461 EVITNLLKQFEGTFISLSCNKYGSNVVEKFLIESKDEQSSQIIIELLRSPNVSMLLLDPF 520

Query: 521 GNYVIQTAWDVSQGRRIRQTLYDLVVDNSPFLQSHMYGKNVLA 563
           GN+VIQ+A  VS+G  IR  L +LV  ++P ++S++YGK VL 
Sbjct: 521 GNFVIQSALSVSKG-HIRNALVNLVRLHAPSMRSNLYGKKVLT 562

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255555215|ref|XP_002518644.1| Pumilio domain-containing protein C6G9.14, putative [Ricinus communis] gi|223542025|gb|EEF43569.1| Pumilio domain-containing protein C6G9.14, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|255538126|ref|XP_002510128.1| RNA binding protein, putative [Ricinus communis] gi|223550829|gb|EEF52315.1| RNA binding protein, putative [Ricinus communis] 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|224136880|ref|XP_002326968.1| predicted protein [Populus trichocarpa] gi|222835283|gb|EEE73718.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224052863|ref|XP_002297618.1| predicted protein [Populus trichocarpa] gi|222844876|gb|EEE82423.1| predicted protein [Populus trichocarpa] 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|224067236|ref|XP_002302423.1| predicted protein [Populus trichocarpa] gi|222844149|gb|EEE81696.1| predicted protein [Populus trichocarpa] 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|224056214|ref|XP_002298759.1| predicted protein [Populus trichocarpa] gi|222846017|gb|EEE83564.1| predicted protein [Populus trichocarpa] 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 ?
Query579
TAIR|locus:2167111596 PUM12 "pumilio 12" [Arabidopsi 0.561 0.545 0.414 4e-67
TAIR|locus:2015036515 PUM8 "pumilio 8" [Arabidopsis 0.550 0.619 0.376 1.9e-53
TAIR|locus:2194699650 PUM7 "pumilio 7" [Arabidopsis 0.621 0.553 0.338 2.4e-53
DICTYBASE|DDB_G02899871036 DDB_G0289987 "Pumilio homology 0.550 0.307 0.367 6.6e-52
TAIR|locus:2138258556 PUM11 "pumilio 11" [Arabidopsi 0.544 0.566 0.382 1.1e-50
TAIR|locus:2011349564 PUM9 "pumilio 9" [Arabidopsis 0.540 0.554 0.376 1.1e-50
ASPGD|ASPL0000057098650 AN10071 [Emericella nidulans ( 0.542 0.483 0.354 2.3e-48
POMBASE|SPAC4G8.03c780 SPAC4G8.03c "RNA-binding prote 0.528 0.392 0.304 2.6e-44
TAIR|locus:2011360528 PUM10 "pumilio 10" [Arabidopsi 0.540 0.592 0.354 3.9e-44
POMBASE|SPAC6G9.14681 SPAC6G9.14 "RNA-binding protei 0.552 0.469 0.314 2.1e-43
TAIR|locus:2167111 PUM12 "pumilio 12" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 682 (245.1 bits), Expect = 4.0e-67, P = 4.0e-67
 Identities = 138/333 (41%), Positives = 215/333 (64%)

Query:   237 YSSIEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLI 296
             Y+SI E RG+I  +AKD+ GCRFLQ+   E++  DIEMI +E+ID + ELM     N+L+
Sbjct:   272 YNSIAEARGKIYYLAKDQHGCRFLQRIFSEKDGNDIEMIFNEIIDYISELMMDPFGNYLV 331

Query:   297 QKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQS 356
             QKL+ V NE+Q  +++ S+      L++I  D+ G+R +QK+++  +        +E+ S
Sbjct:   332 QKLLEVCNEDQRMQIVHSITRKPGLLIKISCDMHGTRAVQKIVETAK-------REEEIS 384

Query:   357 LLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQ 416
             +++SALK+  V L K+ +GNHV++RCLQ   P   K L E    +C++LATDR GCC+LQ
Sbjct:   385 IIISALKHGIVHLIKNVNGNHVVQRCLQYLLPYCGKFLFEAAITHCVELATDRHGCCVLQ 444

Query:   417 YCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFA 476
              C+  ++ EQK  L++++ +NA +LS+  +GNYV+QY+  L++   T +++ QL G Y  
Sbjct:   445 KCLGYSEGEQKQHLVSEIASNALLLSQDPFGNYVLQYVFELQLQWATFEILEQLEGNYTE 504

Query:   477 LSLGKCSSNVVQKCLLESGEEQSTGIINEIIRHPEIVQLILDPYGNYVIQTAWDVSQGRR 536
             LS+ KCSSNVV+KCL  + ++    II E+I +  + Q++LDPYGNYVIQ A   S+G  
Sbjct:   505 LSMQKCSSNVVEKCLKLADDKHRARIIRELINYGRLDQVMLDPYGNYVIQAALKQSKGN- 563

Query:   537 IRQTLYDLVVDNSPFLQSHMYGKNVLAKVRGNK 569
             +   L D +  N   L+++ YGK VL+ +   K
Sbjct:   564 VHALLVDAIKLNISSLRTNPYGKKVLSALSSKK 596
GO:0003723 "RNA binding" evidence=IEA;ISS
GO:0005737 "cytoplasm" evidence=ISM;IDA
GO:0005634 "nucleus" evidence=IDA
TAIR|locus:2015036 PUM8 "pumilio 8" [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
DICTYBASE|DDB_G0289987 DDB_G0289987 "Pumilio homology domain family member 4" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
TAIR|locus:2138258 PUM11 "pumilio 11" [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
ASPGD|ASPL0000057098 AN10071 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
POMBASE|SPAC4G8.03c SPAC4G8.03c "RNA-binding protein (predicted)" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
TAIR|locus:2011360 PUM10 "pumilio 10" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
POMBASE|SPAC6G9.14 SPAC6G9.14 "RNA-binding protein (predicted)" [Schizosaccharomyces pombe (taxid:4896)] 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 ?
Query579
cd07920322 cd07920, Pumilio, Pumilio-family RNA binding domai 3e-91
COG5099777 COG5099, COG5099, RNA-binding protein of the Puf f 2e-45
cd07920322 cd07920, Pumilio, Pumilio-family RNA binding domai 5e-21
cd07920322 cd07920, Pumilio, Pumilio-family RNA binding domai 2e-20
pfam0080634 pfam00806, PUF, Pumilio-family RNA binding repeat 0.002
smart0002536 smart00025, Pumilio, Pumilio-like repeats 0.004
>gnl|CDD|153420 cd07920, Pumilio, Pumilio-family RNA binding domain Back     alignment and domain information 
 Score =  283 bits (726), Expect = 3e-91
 Identities = 121/325 (37%), Positives = 196/325 (60%), Gaps = 16/325 (4%)

Query: 245 GRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKLIGVLN 304
           G I+  AKD+ G RFLQ+K++E  P + E+I  E++  + ELM     N++IQKL     
Sbjct: 10  GHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGT 69

Query: 305 EEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLVSALKN 364
           EEQ  +L+  ++     ++R+  D+ G RV+QKLL++        +++EQ SLLV  L+ 
Sbjct: 70  EEQRLQLLEKILGH---VVRLSLDMYGCRVIQKLLES--------ISEEQISLLVKELRG 118

Query: 365 ITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQYCIPLAQE 424
             V L K  +GNHVI++C++KFPP+  + +++    NC+ L+T   GC ++Q C+    E
Sbjct: 119 HVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALSTHPYGCRVIQRCLEHCSE 178

Query: 425 EQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFALSLGKCSS 484
           EQ+  L+ +++ +A  L +  +GNYVVQ++L L  P  T+ ++ +L G    LS  K +S
Sbjct: 179 EQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFAS 238

Query: 485 NVVQKCLLESGEEQSTGIINEII----RHPEIVQLILDPYGNYVIQTAWDVSQGRRIRQT 540
           NVV+KCL  + +E+   II+EI+        +  L+ D YGNYVIQTA DV++    R+ 
Sbjct: 239 NVVEKCLKHASKEERELIIDEILASGNETSALDTLMKDQYGNYVIQTALDVAKE-EQREL 297

Query: 541 LYDLVVDNSPFLQSHMYGKNVLAKV 565
           L + +  + P L+   YGK++LAK+
Sbjct: 298 LVEAIRPHLPSLRKSPYGKHILAKL 322

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
>gnl|CDD|201452 pfam00806, PUF, Pumilio-family RNA binding repeat Back     alignment and domain information
>gnl|CDD|214475 smart00025, Pumilio, Pumilio-like repeats Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 579
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 99.97
KOG2049536 consensus Translational repressor MPT5/PUF4 and re 99.96
KOG2188650 consensus Predicted RNA-binding protein, contains 99.96
KOG2050 652 consensus Puf family RNA-binding protein [Translat 99.96
KOG2188650 consensus Predicted RNA-binding protein, contains 99.83
KOG2050 652 consensus Puf family RNA-binding protein [Translat 99.81
KOG4574 1007 consensus RNA-binding protein (contains RRM and Pu 99.72
KOG45741007 consensus RNA-binding protein (contains RRM and Pu 99.22
PF07990385 NABP: Nucleic acid binding protein NABP; InterPro: 98.46
PF0080635 PUF: Pumilio-family RNA binding repeat; InterPro: 98.2
PF0080635 PUF: Pumilio-family RNA binding repeat; InterPro: 97.88
smart0002536 Pumilio Pumilio-like repeats. Pumilio-like repeats 97.79
smart0002536 Pumilio Pumilio-like repeats. Pumilio-like repeats 97.6
PRK05686339 fliG flagellar motor switch protein G; Validated 91.07
PRK05686339 fliG flagellar motor switch protein G; Validated 90.58
PF08144148 CPL: CPL (NUC119) domain; InterPro: IPR012959 This 89.43
PF08144148 CPL: CPL (NUC119) domain; InterPro: IPR012959 This 87.72
TIGR00207338 fliG flagellar motor switch protein FliG. The fliG 84.33
>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=4e-66  Score=552.46  Aligned_cols=322  Identities=28%  Similarity=0.458  Sum_probs=312.6

Q ss_pred             ccHHHHhhhHHHHhcCCCccHHHHhhhccCCH-HHHHHHHHHHHHHHHHHhcCcchhHHHHHHHhhccHHHHHHHHHHHH
Q 048735          238 SSIEELRGRIILVAKDEQGCRFLQKKVDERNP-IDIEMILSEVIDDLHELMRHQSANHLIQKLIGVLNEEQMTKLILSVV  316 (579)
Q Consensus       238 ~~L~ei~Gki~eLa~Dq~gSr~LQ~lLe~~~~-e~~~~I~~ei~~~~~~L~~D~~Gs~VIQkLle~~s~eq~~~I~~~l~  316 (579)
                      ..+.++.|+++++++||+||||||+.|+.+++ +++..||++|.+.+.+||+|.||||||||++|+++.+++..+...+.
T Consensus       172 l~~~~~~~~~v~f~~Dq~GsrfiQqkl~~~~~~~ek~~if~ei~~~~~~L~~dvFGNyvIQkffE~gt~~q~~~l~~~~~  251 (503)
T KOG1488|consen  172 LELVDIPGHLVEFAKDQHGSRFIQQKLETASDNEEKQAVFDEILPPALELMTDVFGNYVIQKFFEHGTEDQRNLLHSQIK  251 (503)
T ss_pred             ccccccCCCceeecCCcccchHHHHhccccccHHHHHHHHHHHHHHHHHHHHHHhcCchhhhhhccCCHHHHHHHHHHHH
Confidence            34788899999999999999999999999988 99999999999999999999999999999999999999999999999


Q ss_pred             hhchhhhhhhccccCCHHHHHHHHhcCCCCccCCCHHHHHHHHHHHHhhHhHhccCCCCchhhhhhccccCccchHHHHH
Q 048735          317 SSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLE  396 (579)
Q Consensus       317 ~~~g~~~~La~d~~GsrVLQklLe~~~~~~~~~~~~eq~~~l~~eL~~~i~~L~~D~~GnhVlQklLe~~~~~~~~~Ii~  396 (579)
                         +++..||.|+||||||||+|+.+        +.++...|++||.++++.+++|++||||||||+|+.+++.+++|++
T Consensus       252 ---g~v~~Lsld~ygCRVIQkale~i--------d~~~~~~Li~ELd~~vl~~v~DQngnHViQK~ie~~p~~~~~Fiv~  320 (503)
T KOG1488|consen  252 ---GHVLELSLDMYGCRVIQKALEKV--------DVSLQIQLIDELDGHLLKCVKDQNGNHVIQKCIETLPPDAWQFIVD  320 (503)
T ss_pred             ---hhhhhhhcccccchhHHHHHHhc--------CHHHHHHHHHHHHhhHHHHHhhcccceehhhhhhccChHHHHHHHH
Confidence               99999999999999999999999        7999999999999999999999999999999999999999999999


Q ss_pred             HHHH--hhHhhccCCCchhHHHHhhhhCCHHHHHHHHHHHHHHHHHHhhCcchhHHHHHHHhcCChhhHHHHHHHHHHhH
Q 048735          397 EIAE--NCLDLATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRY  474 (579)
Q Consensus       397 ~l~~--~l~~La~~k~Gs~VVQklLe~~~~~~~~~Lv~~L~~~l~~La~D~~GnyVIQ~iLe~~~~~~r~~Ii~~L~g~~  474 (579)
                      .+.+  ++..+++|+|||+|||++||+|+++++..|+++|..++..|+.|+|||||||++|+++.+..+..|+++|.+++
T Consensus       321 ~f~~~~~~~~ls~~~YGCRVIQr~lE~c~~~~~~~i~~ei~~~~~~L~~dQygNYVIQHVie~g~~~~~~~I~~~l~~~l  400 (503)
T KOG1488|consen  321 FFSGDDNLLELSTHKYGCRVIQRILEHCSEDQKQPLMEEIIRNCDQLAQDQYGNYVIQHVIEHGSPYRDTIIIKCLLGNL  400 (503)
T ss_pred             HhcCCCceeEeeccCcccHHHHHHhhcCChHhhhHHHHHHHHHHHHHHhhhhhhHHHHHHHhcCChhhhhhHHHHHHhhH
Confidence            9998  99999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhcCCcchHHHHHHHHhhcCHHHHHHHHHHHhCh-----hhHHHhhcCcChHHHHHHHHhcCCcHHHHHHHHHHHHhhH
Q 048735          475 FALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRH-----PEIVQLILDPYGNYVIQTAWDVSQGRRIRQTLYDLVVDNS  549 (579)
Q Consensus       475 ~~Ls~~k~GS~VVEk~L~~a~~~~r~~Ii~eL~~~-----~~l~~L~~d~~GnyVVQklL~~~~~~~~re~Ll~~L~~~l  549 (579)
                      ++||.|||+|+|||+|+.+++..+|..|++|+++.     +.|..|++|+|||||||++++.|.+ .+|++|..+|++|+
T Consensus       401 l~~Sq~KfASnVVEk~~~~a~~~~r~~i~~Ei~~~~~~~~~~L~~mmkdQYgNYVVQkmi~~~~~-~q~~~i~~rI~~h~  479 (503)
T KOG1488|consen  401 LSMSQHKFASNVVEKAFLFAPPLLRALIMNEIFPGYVEHPDALDIMMKDQYGNYVVQKMIDICGP-EQRELIKSRVKPHA  479 (503)
T ss_pred             HHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCccCCccHHHHHHHHhhhhhHHHHHHHhcCH-HHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999985     4799999999999999999999988 89999999999999


Q ss_pred             HHHhhCCchHHHHHHHHhcccc
Q 048735          550 PFLQSHMYGKNVLAKVRGNKNR  571 (579)
Q Consensus       550 ~~L~~~~~G~~Vv~kl~~~~~~  571 (579)
                      ..|++++||+||+++|++....
T Consensus       480 ~~Lrk~syGKhIia~lek~~~~  501 (503)
T KOG1488|consen  480 SRLRKFSYGKHIIAKLEKLRSK  501 (503)
T ss_pred             HHHccCccHHHHHHHHHHhccc
Confidence            9999999999999999987653

>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
>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
>KOG2050 consensus Puf family RNA-binding protein [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
>PF07990 NABP: Nucleic acid binding protein NABP; InterPro: IPR012940 This domain occurs in some putative nucleic acid binding proteins 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
>PRK05686 fliG flagellar motor switch protein G; Validated Back     alignment and domain information
>PRK05686 fliG flagellar motor switch protein G; Validated 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
>TIGR00207 fliG flagellar motor switch protein FliG 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 ?
Query579
4dzs_A357 Crystal Structure Of Yeast Puf4p Rna Binding Domain 5e-39
3bx2_A335 Puf4 Rna Binding Domain Bound To Ho Endonuclease Rn 2e-38
3bwt_A333 Crystal Structure Of The Rna Binding Domain Of Puf4 2e-38
3bx3_A335 Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR Re 1e-36
3gvo_A351 Structure And Rna Binding Of The Mouse Pumilio-2 Pu 1e-31
3q0q_A351 Crystal Structure Of The Pumilio-Homology Domain Fr 1e-30
3bsb_A343 Crystal Structure Of Human Pumilio1 In Complex With 6e-30
1ib2_A349 Crystal Structure Of A Pumilio-Homology Domain Leng 6e-30
2yjy_A350 A Specific And Modular Binding Code For Cytosine Re 8e-29
3h3d_X323 Drosophila Pumilio Rna Binding Domain (Puf Domain) 4e-27
3h3d_X323 Drosophila Pumilio Rna Binding Domain (Puf Domain) 1e-08
3k49_A369 Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr R 3e-20
3v71_A382 Crystal Structure Of Puf-6 In Complex With 5be13 Rn 8e-13
3qg9_A413 Crystal Structure Of Fbf-2GLD-1 Fbea A7u Mutant Com 7e-11
3k5q_A412 Crystal Structure Of Fbf-2FBE COMPLEX Length = 412 7e-11
3qgb_A413 Crystal Structure Of Fbf-2 R288y Mutant In Complex 5e-10
>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 
Iteration: 1

 Score =  159 bits (401), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 111/326 (34%), Positives = 178/326 (54%), Gaps = 19/326 (5%)
Query: 214 STNASSRYNNFYARARHHHHRTSYSSIEELRGRIILVAKDEQGCRFLQKKVDERNPIDIE 273
           ++NA++  +    R      R + + +++  G I  + KD+ GCRFLQK++D       +
Sbjct: 4   TSNATNSNSAEKQRKIEESSRFADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAAD 63
Query: 274 MILSEVIDDLHELMRHQSANHLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSR 333
            I  E  D   ELM     N+LIQKL+  +  EQ  +++L+ +SS    + I  +  G+R
Sbjct: 64  AIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQ--RIVLTKISSPH-FVEISLNPHGTR 120
Query: 334 VMQKLLDAGEYPTRQQLTQEQQSLLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKD 393
            +QKL++  +       T E+  ++V +L+  TV LSK  +GNHVI++CLQ+  P+  + 
Sbjct: 121 ALQKLIECIK-------TDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQF 173
Query: 394 LLEEIAENCLDLATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQY 453
           + + I+++C+D+AT R GCC+LQ C+     EQ   L   ++A    L+   +GNYVVQY
Sbjct: 174 IFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQY 233
Query: 454 ILGLKIPQ----VTADVVAQLAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRH 509
           I+  +  +     T  +V  L  R   LS+ K  SNV++K L       S  +I EI+ +
Sbjct: 234 IITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKIL--KTAIVSEPMILEILNN 291
Query: 510 ---PEIVQLILDPYGNYVIQTAWDVS 532
                I  L+ D YGNYV+QTA D+S
Sbjct: 292 GGETGIQSLLNDSYGNYVLQTALDIS 317
>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|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|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|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|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|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|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna Length = 382 Back     alignment and structure
>pdb|3QG9|A Chain A, Crystal Structure Of Fbf-2GLD-1 Fbea A7u Mutant Complex Length = 413 Back     alignment and structure
>pdb|3K5Q|A Chain A, Crystal Structure Of Fbf-2FBE COMPLEX Length = 412 Back     alignment and structure
>pdb|3QGB|A Chain A, Crystal Structure Of Fbf-2 R288y Mutant In Complex With Gld-1 Fbea Length = 413 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 ?
Query579
3gvo_A351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 4e-98
3gvo_A351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 4e-39
3gvo_A 351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 1e-23
3gvo_A351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 2e-23
3k49_A369 MRNA-binding protein PUF3; PUF3, pumilio, RNA bind 9e-91
3k49_A 369 MRNA-binding protein PUF3; PUF3, pumilio, RNA bind 2e-23
3k49_A369 MRNA-binding protein PUF3; PUF3, pumilio, RNA bind 2e-10
3bwt_A333 Protein PUF4; pumilio, RNA binding, HO endonucleas 2e-86
3bwt_A333 Protein PUF4; pumilio, RNA binding, HO endonucleas 1e-35
3bwt_A 333 Protein PUF4; pumilio, RNA binding, HO endonucleas 6e-23
3v71_A382 PUF (pumilio/FBF) domain-containing protein 7, CO 6e-72
3v71_A382 PUF (pumilio/FBF) domain-containing protein 7, CO 5e-28
3v71_A 382 PUF (pumilio/FBF) domain-containing protein 7, CO 2e-17
3v71_A382 PUF (pumilio/FBF) domain-containing protein 7, CO 1e-15
3v71_A382 PUF (pumilio/FBF) domain-containing protein 7, CO 6e-08
3v71_A382 PUF (pumilio/FBF) domain-containing protein 7, CO 5e-05
3k62_A412 FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa 9e-63
3k62_A412 FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa 2e-30
3k62_A 412 FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa 8e-27
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-07
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-07
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-06
>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 =  301 bits (773), Expect = 4e-98
 Identities = 83/331 (25%), Positives = 174/331 (52%), Gaps = 17/331 (5%)

Query: 240 IEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKL 299
           + +L G I+  ++D+ G RF+Q+K++   P + +++ +E++   ++LM     N++IQK 
Sbjct: 21  LRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKF 80

Query: 300 IGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLV 359
               + +Q   L   +   +  +L +   + G RV+QK L++        ++ +QQS +V
Sbjct: 81  FEFGSLDQKLALATRI---RGHVLPLALQMYGCRVIQKALES--------ISSDQQSEMV 129

Query: 360 SALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQYCI 419
             L    +   K  +GNHV+++C++   P   + +++        L+T   GC ++Q  +
Sbjct: 130 KELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRIL 189

Query: 420 PLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGRYFALSL 479
                EQ   ++ ++  +   L +  YGNYV+Q++L    P+  + +V+++ G+  ALS 
Sbjct: 190 EHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQ 249

Query: 480 GKCSSNVVQKCLLESGEEQSTGIINEIIRHPE-----IVQLILDPYGNYVIQTAWDVSQG 534
            K +SNVV+KC+  +   +   +I+E+    +     +  ++ D Y NYV+Q   D+++ 
Sbjct: 250 HKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEP 309

Query: 535 RRIRQTLYDLVVDNSPFLQSHMYGKNVLAKV 565
              R+ +   +  +   L+ + YGK++LAK+
Sbjct: 310 -AQRKIIMHKIRPHITTLRKYTYGKHILAKL 339
>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
>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
>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
>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
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query579
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
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
3bwt_A333 Protein PUF4; pumilio, RNA binding, HO endonucleas 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=1.7e-63  Score=526.04  Aligned_cols=339  Identities=26%  Similarity=0.449  Sum_probs=321.3

Q ss_pred             CCCCcccchhhhhhhccCCCCCcccHHHHhhhHHHHhcCCCccHHHHhhhccCCHHHHHHHHHHHHHHHHHHhcCcchhH
Q 048735          215 TNASSRYNNFYARARHHHHRTSYSSIEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANH  294 (579)
Q Consensus       215 ~~~~~~~~~~~~~~~~~~~~~~~~~L~ei~Gki~eLa~Dq~gSr~LQ~lLe~~~~e~~~~I~~ei~~~~~~L~~D~~Gs~  294 (579)
                      +.++..|++|++.      +..-..|+|++|+++++|+||+|||+||++|+.+++++++.||+++.+++.+||+|+||||
T Consensus         2 ~~~~~l~e~~r~~------~~~~~~l~~~~g~i~~la~dq~gsR~lQ~~l~~~~~~~~~~i~~ei~~~~~~L~~d~~gn~   75 (351)
T 3gvo_A            2 TGRSRLLEDFRNN------RFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNY   75 (351)
T ss_dssp             -CCCHHHHHHHTT------CCTTCCGGGGTTCHHHHHTSHHHHHHHHHHHHHCCHHHHHHHHHHHGGGHHHHHTSTTHHH
T ss_pred             CCccHHHHHHhCC------CCCCcCHHHHHhHHHHHhcCCcchHHHHHHHhhCCHHHHHHHHHHHHHhHHHHHhChhhhH
Confidence            4566777776543      2333579999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhccHHHHHHHHHHHHhhchhhhhhhccccCCHHHHHHHHhcCCCCccCCCHHHHHHHHHHHHhhHhHhccCCC
Q 048735          295 LIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLVSALKNITVSLSKSPH  374 (579)
Q Consensus       295 VIQkLle~~s~eq~~~I~~~l~~~~g~~~~La~d~~GsrVLQklLe~~~~~~~~~~~~eq~~~l~~eL~~~i~~L~~D~~  374 (579)
                      ||||++++++++++..|++.+.   |++.+|+.|+|||||||++++.+        ..+++..+++++.+++..|+.|++
T Consensus        76 vvQklle~~~~~~~~~i~~~i~---g~~~~l~~~~~G~rvvQk~le~~--------~~~~~~~i~~el~~~~~~L~~d~~  144 (351)
T 3gvo_A           76 VIQKFFEFGSLDQKLALATRIR---GHVLPLALQMYGCRVIQKALESI--------SSDQQSEMVKELDGHVLKCVKDQN  144 (351)
T ss_dssp             HHHHHHHHCCHHHHHHHHHHHT---TCHHHHHTSTTHHHHHHHHHHHS--------CHHHHHHHHGGGTTCHHHHHHSTT
T ss_pred             HHHHHHhhCCHHHHHHHHHHHH---hhHHHHhhCHHhHHHHHHHHHhC--------CHHHHHHHHHHhhhhHHHHHHhhh
Confidence            9999999999999999999999   99999999999999999999999        688889999999999999999999


Q ss_pred             CchhhhhhccccCccchHHHHHHHHHhhHhhccCCCchhHHHHhhhhCCHHHHHHHHHHHHHHHHHHhhCcchhHHHHHH
Q 048735          375 GNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYI  454 (579)
Q Consensus       375 GnhVlQklLe~~~~~~~~~Ii~~l~~~l~~La~~k~Gs~VVQklLe~~~~~~~~~Lv~~L~~~l~~La~D~~GnyVIQ~i  454 (579)
                      ||||+|+++++++++.+.+|++.+.+++..+++|+|||+|||++|+.++++++..|++++.+++..|++|+|||||||++
T Consensus       145 Gn~ViQk~l~~~~~~~~~~i~~~~~~~~~~ls~~~~G~~Vvq~~le~~~~~~~~~ii~~l~~~~~~L~~d~~Gn~ViQ~~  224 (351)
T 3gvo_A          145 GNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHV  224 (351)
T ss_dssp             HHHHHHHHHHHSCGGGTHHHHHHTTTTHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHHHHTTHHHHHTSTTHHHHHHHH
T ss_pred             hhHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhCcHhHHHHHHHHHHCCHHHHHHHHHHHhhhHHhcCCCchHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcCChhhHHHHHHHHHHhHHhhcCCcchHHHHHHHHhhcCHHHHHHHHHHHhCh-----hhHHHhhcCcChHHHHHHHH
Q 048735          455 LGLKIPQVTADVVAQLAGRYFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIRH-----PEIVQLILDPYGNYVIQTAW  529 (579)
Q Consensus       455 Le~~~~~~r~~Ii~~L~g~~~~Ls~~k~GS~VVEk~L~~a~~~~r~~Ii~eL~~~-----~~l~~L~~d~~GnyVVQklL  529 (579)
                      |+.++++.+..|++.+.+++..||+|||||+|||+||+++++++|+.|+++++..     +.+..|+.|+|||||||++|
T Consensus       225 l~~~~~~~~~~i~~~l~~~~~~Ls~~k~gs~Vvek~l~~~~~~~r~~ii~el~~~~~~~~~~l~~l~~d~ygnyViq~~L  304 (351)
T 3gvo_A          225 LEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMI  304 (351)
T ss_dssp             HHHSCHHHHHHHHHTTTTCHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHHHHSCEETTEEHHHHHHHSTTHHHHHHHHH
T ss_pred             HHhCchhhHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHhCCHHHHHHHHHHHhcccCCCChHHHHccCCcchHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999962     26999999999999999999


Q ss_pred             hcCCcHHHHHHHHHHHHhhHHHHhhCCchHHHHHHHHhcccc
Q 048735          530 DVSQGRRIRQTLYDLVVDNSPFLQSHMYGKNVLAKVRGNKNR  571 (579)
Q Consensus       530 ~~~~~~~~re~Ll~~L~~~l~~L~~~~~G~~Vv~kl~~~~~~  571 (579)
                      +.+++ ++|+.|+++|++++..|++++||++|++++++...+
T Consensus       305 ~~~~~-~~r~~i~~~i~~~~~~L~~~~~g~~i~~kl~~~~~~  345 (351)
T 3gvo_A          305 DMAEP-AQRKIIMHKIRPHITTLRKYTYGKHILAKLEKYYLK  345 (351)
T ss_dssp             HHCCH-HHHHHHHHHHGGGHHHHTTSTTTHHHHHHHHHHTC-
T ss_pred             HhCCH-HHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHhh
Confidence            99998 899999999999999999999999999999987653
>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
>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
>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 579
d1m8za_339 a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [Ta 8e-65
>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 =  213 bits (543), Expect = 8e-65
 Identities = 85/337 (25%), Positives = 170/337 (50%), Gaps = 17/337 (5%)

Query: 234 RTSYSSIEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSAN 293
           R     + E+ G I+  ++D+ G RF+Q K++   P + +++ +E++   ++LM     N
Sbjct: 13  RYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGN 72

Query: 294 HLIQKLIGVLNEEQMTKLILSVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQE 353
           ++IQK     + EQ   L   +   +  +L +   + G RV+QK L+         +  +
Sbjct: 73  YVIQKFFEFGSLEQKLALAERI---RGHVLSLALQMYGCRVIQKALE--------FIPSD 121

Query: 354 QQSLLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKDLLEEIAENCLDLATDRSGCC 413
           QQ+ +V  L    +   K  +GNHV+++C++   P   + +++        L+T   GC 
Sbjct: 122 QQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCR 181

Query: 414 LLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGR 473
           ++Q  +     +Q   ++ ++  +   L +  YGNYV+Q++L    P+  + +VA++ G 
Sbjct: 182 VIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGN 241

Query: 474 YFALSLGKCSSNVVQKCLLESGEEQSTGIINEII-----RHPEIVQLILDPYGNYVIQTA 528
              LS  K +SNVV+KC+  +   +   +I+E+       H  +  ++ D Y NYV+Q  
Sbjct: 242 VLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKM 301

Query: 529 WDVSQGRRIRQTLYDLVVDNSPFLQSHMYGKNVLAKV 565
            DV++    R+ +   +  +   L+ + YGK++LAK+
Sbjct: 302 IDVAEP-GQRKIVMHKIRPHIATLRKYTYGKHILAKL 337

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query579
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=2.5e-56  Score=464.99  Aligned_cols=322  Identities=26%  Similarity=0.460  Sum_probs=308.8

Q ss_pred             CCCcccHHHHhhhHHHHhcCCCccHHHHhhhccCCHHHHHHHHHHHHHHHHHHhcCcchhHHHHHHHhhccHHHHHHHHH
Q 048735          234 RTSYSSIEELRGRIILVAKDEQGCRFLQKKVDERNPIDIEMILSEVIDDLHELMRHQSANHLIQKLIGVLNEEQMTKLIL  313 (579)
Q Consensus       234 ~~~~~~L~ei~Gki~eLa~Dq~gSr~LQ~lLe~~~~e~~~~I~~ei~~~~~~L~~D~~Gs~VIQkLle~~s~eq~~~I~~  313 (579)
                      +.+-..|++++|+++++|+||+|||+||++|+.+++++++.||+++.+++.+||+|+|||||+|+|+++++++++..|++
T Consensus        13 ~~~~~~l~~~~g~~~~~~~~q~gSr~lQ~~l~~~~~~~~~~I~~~l~~~~~~L~~~~~gn~vvqkll~~~~~~~~~~i~~   92 (339)
T d1m8za_          13 RYPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAE   92 (339)
T ss_dssp             CCTTCCGGGGTTCHHHHHTSHHHHHHHHHHHHHCCHHHHHHHHHHHGGGHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHH
T ss_pred             CCCCCcHHHHHhHHHHHhcCchhhHHHHHHHhhCCHHHHHHHHHHHHHHHHHHhhCcccchhHHHHHhhCCHHHHHHHHH
Confidence            33444599999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhchhhhhhhccccCCHHHHHHHHhcCCCCccCCCHHHHHHHHHHHHhhHhHhccCCCCchhhhhhccccCccchHH
Q 048735          314 SVVSSQQRLLRICDDLSGSRVMQKLLDAGEYPTRQQLTQEQQSLLVSALKNITVSLSKSPHGNHVIKRCLQKFPPDYTKD  393 (579)
Q Consensus       314 ~l~~~~g~~~~La~d~~GsrVLQklLe~~~~~~~~~~~~eq~~~l~~eL~~~i~~L~~D~~GnhVlQklLe~~~~~~~~~  393 (579)
                      .+.   +++.+|+.|+||++|||++++.+        ..++...+++++.+++..++.|++|+||++++++.++++.+..
T Consensus        93 ~l~---~~~~~L~~~~~gs~Vvq~l~~~~--------~~~~~~~l~~el~~~~~~l~~d~~~~~v~~~~l~~~~~~~~~~  161 (339)
T d1m8za_          93 RIR---GHVLSLALQMYGCRVIQKALEFI--------PSDQQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQF  161 (339)
T ss_dssp             HHT---TCHHHHHTSTTHHHHHHHHHHHS--------CHHHHHHHHHTTTTCHHHHHHSTTHHHHHHHHHHHSCGGGGHH
T ss_pred             HHH---hhHHHHhcccccchHHHhhhccC--------CHHHHHHHHHHHhhhhHHHhcCCCcchHHHHHHHhcCHHHHHH
Confidence            999   99999999999999999999998        6788888999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhHhhccCCCchhHHHHhhhhCCHHHHHHHHHHHHHHHHHHhhCcchhHHHHHHHhcCChhhHHHHHHHHHHh
Q 048735          394 LLEEIAENCLDLATDRSGCCLLQYCIPLAQEEQKARLIADVVANAYVLSEHSYGNYVVQYILGLKIPQVTADVVAQLAGR  473 (579)
Q Consensus       394 Ii~~l~~~l~~La~~k~Gs~VVQklLe~~~~~~~~~Lv~~L~~~l~~La~D~~GnyVIQ~iLe~~~~~~r~~Ii~~L~g~  473 (579)
                      |++.+.+.+.++++|++||+++|++++.++++++..+++++.+++..|++|++||||+|++|+.++++.++.|++.|.++
T Consensus       162 i~~~~~~~~~~l~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~L~~~~~G~~vvq~~l~~~~~~~~~~i~~~l~~~  241 (339)
T d1m8za_         162 IIDAFKGQVFALSTHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGN  241 (339)
T ss_dssp             HHHHTTTTHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHHHHHTHHHHTTSTTHHHHHHHHHHHSCHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHhCcchhHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhcCCcchHHHHHHHHhhcCHHHHHHHHHHHhC-----hhhHHHhhcCcChHHHHHHHHhcCCcHHHHHHHHHHHHhh
Q 048735          474 YFALSLGKCSSNVVQKCLLESGEEQSTGIINEIIR-----HPEIVQLILDPYGNYVIQTAWDVSQGRRIRQTLYDLVVDN  548 (579)
Q Consensus       474 ~~~Ls~~k~GS~VVEk~L~~a~~~~r~~Ii~eL~~-----~~~l~~L~~d~~GnyVVQklL~~~~~~~~re~Ll~~L~~~  548 (579)
                      +.+|+.+++||+|||+|++.++++.+..++++++.     .+.+..|+.|+|||||||++|+.+++ ++++.|+++|+++
T Consensus       242 ~~~l~~~k~gS~vve~~l~~~~~~~~~~~~~~l~~~~~~~~~~l~~L~~d~~gn~Viq~~l~~~~~-~~~~~i~~~l~~~  320 (339)
T d1m8za_         242 VLVLSQHKFASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEP-GQRKIVMHKIRPH  320 (339)
T ss_dssp             HHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHHHHHCEETTEEHHHHHHTSTTHHHHHHHHHHHSCH-HHHHHHHHTTGGG
T ss_pred             HHHHHcchhHHHHHHHHHHhCCHHHHHHHHHHHHhcccCchHHHHHHHcCCcccHHHHHHHHhCCH-HHHHHHHHHHHHH
Confidence            99999999999999999999999999999998863     13699999999999999999999998 9999999999999


Q ss_pred             HHHHhhCCchHHHHHHHHh
Q 048735          549 SPFLQSHMYGKNVLAKVRG  567 (579)
Q Consensus       549 l~~L~~~~~G~~Vv~kl~~  567 (579)
                      +++|+.++||++|+++|.+
T Consensus       321 ~~~L~~~~~G~~v~~~l~~  339 (339)
T d1m8za_         321 IATLRKYTYGKHILAKLEK  339 (339)
T ss_dssp             HHHHTTSSTHHHHHHHHC-
T ss_pred             HHHHhcCCcHHHHHHHHhC
Confidence            9999999999999999863
>d1m8za_ a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure