Citrus Sinensis ID: 037508

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-------45
MLNSPGNRHLRDETTRFGSPSRGLPAAHFRRPRQESPRLPNTSLNEKSYFDETDLSAYFSHLNVNDRIFDNPVHHFPLVENGFFSHPCQEAEPINQDSSILNLLHNHNFDGLRSNGNELSSVPRNQWMSSLSLKRNQWLQDSFDCSSLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQRERLVAEIIANALLLAEDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSNVVERCLLESGEEQSTRIIIELLRSPNVSMLLMHPFGNYVIQSALLVSKVRLFSSPPISVCKPG
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccHHHHHHHHHHHHccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHccccHHHHHHHHHHHcccccHHHHHcccccHHHHHHHHHHccccHHHHHHHHHHHcccccHHHccccccHHHHHHHHHcccccHHHHHHHHHHcHHHHccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHcccHHHHHHHHHHHHccccHHHHHcccccHHHHHHHHHcccccccccccccccccc
cccccccccccccccEEcccccccccccccccccccccccccccccccccccccccHHHHHcccccHHcccccccccccccccccccccccccccccccccccHHHHHHHHccHHHHHHcccccccccccHcccHcccccccccccHHHHHcccHHHHHccHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHccHHHHHHHHHHHHHcccHHHHHHHcccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHccHHHHHHHHHHHcccHHHHHccccHHHHHHHHHHHccHHHHHHHHHHHcccHHHHHHcccHHHHHHHHHHHccHHHHHHHHHHccccHHHHHccccHHHHHHHHHHHccHHHHHHHHHHHHcccHHHHHHHcHHHHHHHHHHHHHccHHHHHHHHHHHcccc
mlnspgnrhlrdettrfgspsrglpaahfrrprqesprlpntslneksyfdetdlSAYFShlnvndrifdnpvhhfplvengffshpcqeaepinqdsSILNLLhnhnfdglrsngnelssvprnqwmsslSLKRNQwlqdsfdcsslrDLRGNIVALAKdqygcrhlqrtmsslpkEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALrpgavtltkdtnghYVIQYCVKHFSHEDTKYLLNEVADncygiatdksgccvlqhcveyskgaQRERLVAEIIANALLLAEDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSNVVERCLLESGEEQSTRIIIELLRspnvsmllmhpfgnYVIQSALLVSKVrlfssppisvckpg
mlnspgnrhlrdettrfgspsrglpaahfrrprqesprlpntslneKSYFDETDLSAYFSHLNVNDRIFDNPVHHFPLVENGFFSHPCQEAEPINQDSSILNLLHNHNFDGLRSNGNELSSVPRNQWMSSLSLKRNQWLQDSFDCSSLRDLRGNIVAlakdqygcrhlqrtmsslpkeEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQRERLVAEIIANALLLAEDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSNVVERCLLESGEEQSTRIIIELLRSPNVSMLLMHPFGNYVIQSALLVSKVRLfssppisvckpg
MLNSPGNRHLRDETTRFGSPSRGLPAAHFRRPRQESPRLPNTSLNEKSYFDETDLSAYFSHLNVNDRIFDNPVHHFPLVENGFFSHPCQEAEPINQDSSILNLLHNHNFDGLRSNGNELSSVPRNQWMSSLSLKRNQWLQDSFDCSSLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQRERlvaeiianalllaeDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSNVVERCLLESGEEQSTRIIIELLRSPNVSMLLMHPFGNYVIQSALLVSKVRLFSSPPISVCKPG
************************************************YFDETDLSAYFSHLNVNDRIFDNPVHHFPLVENGFFSHPCQEAEPINQDSSILNLLHNHNFDG******************SLSLKRNQWLQDSFDCSSLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQRERLVAEIIANALLLAEDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSNVVERCLLESGEEQSTRIIIELLRSPNVSMLLMHPFGNYVIQSALLVSKVRLFS**********
**************************************************************************************************************************************************SLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQRERLVAEIIANALLLAEDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSNVVERCLLESGEEQSTRIIIELLRSPNVSMLLMHPFGNYVIQSALLVSKVRLFSSPPISVCKP*
**********************GLPAAHFRRPRQESPRLPNTSLNEKSYFDETDLSAYFSHLNVNDRIFDNPVHHFPLVENGFFSHPCQEAEPINQDSSILNLLHNHNFDGLRSNGNELSSVPRNQWMSSLSLKRNQWLQDSFDCSSLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQRERLVAEIIANALLLAEDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSNVVERCLLESGEEQSTRIIIELLRSPNVSMLLMHPFGNYVIQSALLVSKVRLFSSP********
**************T**G***R************ESPRLPNTSLNEKSYFDETDLSAYFSHLNVNDRIFDNPVHHFPLVENGFFSHPCQEAEPINQDSSILNLLHNHNFDGLRSNGNELSSVPRNQWMSSLSLKRNQWLQDSFDCSSLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQRERLVAEIIANALLLAEDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSNVVERCLLESGEEQSTRIIIELLRSPNVSMLLMHPFGNYVIQSALLVSKVRLFSSPPISVCK**
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MLNSPGNRHLRDETTRFGSPSRGLPAAHFRRPRQESPRLPNTSLNEKSYFDETDLSAYFSHLNVNDRIFDNPVHHFPLVENGFFSHPCQEAEPINQDSSILNLLHNHNFDGLRSNGNELSSVPRNQWMSSLSLKRNQWLQDSFDCSSLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQRERLVAEIIANALLLAEDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSNVVERCLLESGEEQSTRIIIELLRSPNVSMLLMHPFGNYVIQSALLVSKVRLFSSPPISVCKPG
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 ?
Query449 2.2.26 [Sep-21-2011]
Q9C9R6650 Putative pumilio homolog yes no 0.645 0.446 0.481 3e-75
Q9LM20515 Putative pumilio homolog no no 0.665 0.580 0.461 3e-73
Q9LVC3596 Pumilio homolog 12 OS=Ara no no 0.599 0.451 0.434 3e-71
Q9LDW3556 Pumilio homolog 11 OS=Ara no no 0.679 0.548 0.451 5e-69
Q1PFN9564 Pumilio homolog 9 OS=Arab no no 0.734 0.585 0.415 2e-66
Q9LP21528 Putative pumilio homolog no no 0.643 0.547 0.407 2e-58
O81465477 Pumilio homolog 15 OS=Ara no no 0.630 0.593 0.415 2e-57
Q92359681 Pumilio domain-containing yes no 0.623 0.411 0.381 6e-56
Q09829780 Pumilio domain-containing no no 0.619 0.356 0.377 1e-52
Q9FMH4527 Putative pumilio homolog no no 0.674 0.574 0.384 3e-50
>sp|Q9C9R6|PUM7_ARATH Putative pumilio homolog 7, chloroplastic OS=Arabidopsis thaliana GN=APUM7 PE=3 SV=2 Back     alignment and function desciption
 Score =  282 bits (722), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 140/291 (48%), Positives = 199/291 (68%), Gaps = 1/291 (0%)

Query: 150 DLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVE 209
           D++G +  +AKDQ+GCR LQR        +  +IF EVI  V ELM+DPFGNY++QKL++
Sbjct: 333 DIQGYVYLMAKDQHGCRFLQRIFDEGTSVDAMIIFNEVIAHVVELMMDPFGNYLMQKLLD 392

Query: 210 LCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVT 269
           +C+EEQRT+I+L+ T +  QL+RI LN +G R V +L+E + + +QISLV  ALRPG + 
Sbjct: 393 VCTEEQRTQIVLVATEEPGQLIRISLNAYGTRVVQRLVETIRSGKQISLVKLALRPGFLD 452

Query: 270 LTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQRE 329
           L KD NG++VIQ C++  S ED K++ +     C  IAT + GCCVLQ C+ YS   QRE
Sbjct: 453 LIKDLNGNHVIQRCLQCLSTEDNKFIFDAATKFCTEIATHRHGCCVLQKCIAYSMRQQRE 512

Query: 330 RLVAEIIANALLLAEDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSNVVE 389
           +L+AEI  N+LLLA+D +GNY VQ ++ LR+P   A +L QL+GHYV  S  K+ S++VE
Sbjct: 513 KLIAEISRNSLLLAQDPFGNYAVQFVIELRIPSAVAMMLAQLKGHYVQLSMQKFSSHMVE 572

Query: 390 RCLLESGEEQSTRIIIELLRSPNVSMLLMHPFGNYVIQSALLVSKVRLFSS 440
           RCL+   E +  +I+ EL+  P+   LL  P+ N+VIQ+AL  +K  L +S
Sbjct: 573 RCLMHCPESRP-QIVRELVSVPHFDQLLQDPYANFVIQAALAATKGPLHAS 622
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|Q9LVC3|PUM12_ARATH Pumilio homolog 12 OS=Arabidopsis thaliana GN=APUM12 PE=2 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|Q9LP21|PUM10_ARATH Putative pumilio homolog 10 OS=Arabidopsis thaliana GN=APUM10 PE=3 SV=2 Back     alignment and function description
>sp|O81465|PUM15_ARATH Pumilio homolog 15 OS=Arabidopsis thaliana GN=APUM15 PE=3 SV=1 Back     alignment and function description
>sp|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|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|Q9FMH4|PUM13_ARATH Putative pumilio homolog 13 OS=Arabidopsis thaliana GN=APUM13 PE=3 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 ?
Query449
224067236486 predicted protein [Populus trichocarpa] 0.665 0.615 0.655 1e-110
224136880509 predicted protein [Populus trichocarpa] 0.636 0.561 0.659 1e-108
359492558 574 PREDICTED: putative pumilio homolog 7, c 0.659 0.515 0.625 1e-102
255538126542 RNA binding protein, putative [Ricinus c 0.639 0.529 0.616 4e-98
356518120508 PREDICTED: putative pumilio homolog 7, c 0.636 0.562 0.580 3e-92
356528751 763 PREDICTED: uncharacterized protein LOC10 0.634 0.373 0.529 5e-80
356557551 770 PREDICTED: pumilio homolog 2-like [Glyci 0.634 0.370 0.522 7e-80
358345510 679 Pumilio domain-containing protein [Medic 0.625 0.413 0.498 2e-79
225448285 810 PREDICTED: uncharacterized protein LOC10 0.639 0.354 0.508 1e-78
356512063451 PREDICTED: putative pumilio homolog 7, c 0.634 0.631 0.515 6e-78
>gi|224067236|ref|XP_002302423.1| predicted protein [Populus trichocarpa] gi|222844149|gb|EEE81696.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  406 bits (1043), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 198/302 (65%), Positives = 242/302 (80%), Gaps = 3/302 (0%)

Query: 134 KRNQWLQDSFDCSSLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCE 193
           +R  WLQD     S  DL G IVALAKDQ+GC+ LQR + S  +E+I+M+F EVID V  
Sbjct: 171 RRPPWLQDYV---SWEDLSGKIVALAKDQHGCKFLQRLIESATREQIDMLFYEVIDYVGG 227

Query: 194 LMIDPFGNYVVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNP 253
           L+ DPFGNYVVQKL+E+ SEEQRTR+L MLT  DFQLVRICL+ HG RAV KLL  +TNP
Sbjct: 228 LIADPFGNYVVQKLIEVISEEQRTRVLRMLTRTDFQLVRICLDVHGTRAVQKLLNCITNP 287

Query: 254 QQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGC 313
            Q+SLV++AL  GAV L KD+NGH+VIQ+ +KHFS +D KY+L +VA+ C+ IAT+KSGC
Sbjct: 288 LQVSLVVSALNQGAVALIKDSNGHHVIQHSMKHFSPQDNKYILKQVAEKCFEIATNKSGC 347

Query: 314 CVLQHCVEYSKGAQRERLVAEIIANALLLAEDCYGNYVVQHLLALRVPQITASLLRQLEG 373
           CVLQ CVEYS+G  R+RLVAEIIANALLLAED YGNYVVQH+L L++PQIT +LL Q EG
Sbjct: 348 CVLQRCVEYSEGEHRDRLVAEIIANALLLAEDHYGNYVVQHILDLKMPQITENLLTQFEG 407

Query: 374 HYVSFSCNKYGSNVVERCLLESGEEQSTRIIIELLRSPNVSMLLMHPFGNYVIQSALLVS 433
            Y++ SCNKYGSNVVE+CLL + E+QST+II+ELL +P  SMLL+ PFGN+VIQ AL VS
Sbjct: 408 SYMALSCNKYGSNVVEKCLLTTSEDQSTQIILELLSNPGASMLLVDPFGNFVIQKALSVS 467

Query: 434 KV 435
           + 
Sbjct: 468 QT 469

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>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|359492558|ref|XP_003634432.1| PREDICTED: putative pumilio homolog 7, chloroplastic-like [Vitis vinifera] 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|356518120|ref|XP_003527730.1| PREDICTED: putative pumilio homolog 7, chloroplastic-like [Glycine max] Back     alignment and taxonomy information
>gi|356528751|ref|XP_003532961.1| PREDICTED: uncharacterized protein LOC100780898 [Glycine max] Back     alignment and taxonomy information
>gi|356557551|ref|XP_003547079.1| PREDICTED: pumilio homolog 2-like [Glycine max] Back     alignment and taxonomy information
>gi|358345510|ref|XP_003636820.1| Pumilio domain-containing protein [Medicago truncatula] gi|358348879|ref|XP_003638469.1| Pumilio domain-containing protein [Medicago truncatula] gi|355502755|gb|AES83958.1| Pumilio domain-containing protein [Medicago truncatula] gi|355504404|gb|AES85607.1| Pumilio domain-containing protein [Medicago truncatula] Back     alignment and taxonomy information
>gi|225448285|ref|XP_002271130.1| PREDICTED: uncharacterized protein LOC100266352 [Vitis vinifera] Back     alignment and taxonomy information
>gi|356512063|ref|XP_003524740.1| PREDICTED: putative pumilio homolog 7, chloroplastic-like [Glycine max] 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 ?
Query449
TAIR|locus:2194699650 PUM7 "pumilio 7" [Arabidopsis 0.661 0.456 0.444 1.2e-67
TAIR|locus:2015036515 PUM8 "pumilio 8" [Arabidopsis 0.661 0.576 0.438 6e-64
TAIR|locus:2167111596 PUM12 "pumilio 12" [Arabidopsi 0.692 0.521 0.405 3e-62
TAIR|locus:2138258556 PUM11 "pumilio 11" [Arabidopsi 0.650 0.525 0.437 1.5e-60
TAIR|locus:2011349564 PUM9 "pumilio 9" [Arabidopsis 0.734 0.585 0.392 1.9e-58
TAIR|locus:2011360528 PUM10 "pumilio 10" [Arabidopsi 0.641 0.545 0.384 1.7e-52
DICTYBASE|DDB_G02899871036 DDB_G0289987 "Pumilio homology 0.636 0.276 0.374 1.9e-52
TAIR|locus:2133534477 PUM15 "pumilio 15" [Arabidopsi 0.630 0.593 0.395 5.6e-52
ASPGD|ASPL0000057098 650 AN10071 [Emericella nidulans ( 0.614 0.424 0.379 7.2e-52
POMBASE|SPAC6G9.14681 SPAC6G9.14 "RNA-binding protei 0.636 0.419 0.359 1.4e-48
TAIR|locus:2194699 PUM7 "pumilio 7" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 662 (238.1 bits), Expect = 1.2e-67, Sum P(2) = 1.2e-67
 Identities = 133/299 (44%), Positives = 191/299 (63%)

Query:   150 DLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVE 209
             D++G +  +AKDQ+GCR LQR        +  +IF EVI  V ELM+DPFGNY++QKL++
Sbjct:   333 DIQGYVYLMAKDQHGCRFLQRIFDEGTSVDAMIIFNEVIAHVVELMMDPFGNYLMQKLLD 392

Query:   210 LCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVT 269
             +C+EEQRT+I+L+ T +  QL+RI LN +G R V +L+E + + +QISLV  ALRPG + 
Sbjct:   393 VCTEEQRTQIVLVATEEPGQLIRISLNAYGTRVVQRLVETIRSGKQISLVKLALRPGFLD 452

Query:   270 LTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQRE 329
             L KD NG++VIQ C++  S ED K++ +     C  IAT + GCCVLQ C+ YS   QRE
Sbjct:   453 LIKDLNGNHVIQRCLQCLSTEDNKFIFDAATKFCTEIATHRHGCCVLQKCIAYSMRQQRE 512

Query:   330 RXXXXXXXXXXXXXXDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSNVVE 389
             +              D +GNY VQ ++ LR+P   A +L QL+GHYV  S  K+ S++VE
Sbjct:   513 KLIAEISRNSLLLAQDPFGNYAVQFVIELRIPSAVAMMLAQLKGHYVQLSMQKFSSHMVE 572

Query:   390 RCLLESGEEQSTRIIIELLRSPNVSMLLMHPFGNYVIQSALLVSKVRLFSSPPISVCKP 448
             RCL+   E +  +I+ EL+  P+   LL  P+ N+VIQ+AL  +K  L +S  + V +P
Sbjct:   573 RCLMHCPESRP-QIVRELVSVPHFDQLLQDPYANFVIQAALAATKGPLHASL-VEVIRP 629
GO:0003723 "RNA binding" evidence=IEA;ISS
GO:0009507 "chloroplast" evidence=ISM
GO:0003729 "mRNA binding" evidence=IPI
GO:0005737 "cytoplasm" evidence=IDA
TAIR|locus:2015036 PUM8 "pumilio 8" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2167111 PUM12 "pumilio 12" [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:2011349 PUM9 "pumilio 9" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2011360 PUM10 "pumilio 10" [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:2133534 PUM15 "pumilio 15" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
ASPGD|ASPL0000057098 AN10071 [Emericella nidulans (taxid:162425)] 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 ?
Query449
cd07920322 cd07920, Pumilio, Pumilio-family RNA binding domai 1e-110
COG5099777 COG5099, COG5099, RNA-binding protein of the Puf f 2e-61
cd07920322 cd07920, Pumilio, Pumilio-family RNA binding domai 2e-49
smart0002536 smart00025, Pumilio, Pumilio-like repeats 1e-07
pfam0080634 pfam00806, PUF, Pumilio-family RNA binding repeat 5e-07
pfam0080634 pfam00806, PUF, Pumilio-family RNA binding repeat 1e-04
smart0002536 smart00025, Pumilio, Pumilio-like repeats 0.003
>gnl|CDD|153420 cd07920, Pumilio, Pumilio-family RNA binding domain Back     alignment and domain information 
 Score =  326 bits (839), Expect = e-110
 Identities = 128/294 (43%), Positives = 193/294 (65%), Gaps = 9/294 (3%)

Query: 146 SSLRDLR-GNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVV 204
            +L+D++ G+IV  AKDQ+G R LQ+ +     EE E+IF E++  V ELM+DPFGNYV+
Sbjct: 2   LTLQDIKAGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVI 61

Query: 205 QKLVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALR 264
           QKL E  +EEQR ++L  +      +VR+ L+ +G R + KLLE++ + +QISL++  LR
Sbjct: 62  QKLFEHGTEEQRLQLLEKIL---GHVVRLSLDMYGCRVIQKLLESI-SEEQISLLVKELR 117

Query: 265 PGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSK 324
              V L KD NG++VIQ C++ F  ED +++++    NC  ++T   GC V+Q C+E+  
Sbjct: 118 GHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALSTHPYGCRVIQRCLEHCS 177

Query: 325 GAQRERLVAEIIANALLLAEDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYG 384
             QRE L+ EI+ +AL L +D +GNYVVQH+L L  P  T+ ++ +L G+ V  SC+K+ 
Sbjct: 178 EEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFA 237

Query: 385 SNVVERCLLESGEEQSTRIIIELLRSPN----VSMLLMHPFGNYVIQSALLVSK 434
           SNVVE+CL  + +E+   II E+L S N    +  L+   +GNYVIQ+AL V+K
Sbjct: 238 SNVVEKCLKHASKEERELIIDEILASGNETSALDTLMKDQYGNYVIQTALDVAK 291

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|214475 smart00025, Pumilio, Pumilio-like repeats Back     alignment and domain information
>gnl|CDD|201452 pfam00806, PUF, Pumilio-family RNA binding repeat 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 449
KOG1488503 consensus Translational repressor Pumilio/PUF3 and 100.0
cd07920322 Pumilio Pumilio-family RNA binding domain. Puf rep 100.0
KOG1488503 consensus Translational repressor Pumilio/PUF3 and 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
KOG2049536 consensus Translational repressor MPT5/PUF4 and re 100.0
COG5099777 RNA-binding protein of the Puf family, translation 100.0
KOG2050 652 consensus Puf family RNA-binding protein [Translat 99.97
KOG2188650 consensus Predicted RNA-binding protein, contains 99.96
KOG2050 652 consensus Puf family RNA-binding protein [Translat 99.89
KOG2188650 consensus Predicted RNA-binding protein, contains 99.75
KOG4574 1007 consensus RNA-binding protein (contains RRM and Pu 99.74
KOG45741007 consensus RNA-binding protein (contains RRM and Pu 99.53
PF0080635 PUF: Pumilio-family RNA binding repeat; InterPro: 98.41
smart0002536 Pumilio Pumilio-like repeats. Pumilio-like repeats 98.01
PF0080635 PUF: Pumilio-family RNA binding repeat; InterPro: 97.96
smart0002536 Pumilio Pumilio-like repeats. Pumilio-like repeats 97.8
PF08144148 CPL: CPL (NUC119) domain; InterPro: IPR012959 This 90.57
PF08144148 CPL: CPL (NUC119) domain; InterPro: IPR012959 This 90.33
PRK05686339 fliG flagellar motor switch protein G; Validated 89.22
>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=5.8e-58  Score=463.98  Aligned_cols=286  Identities=32%  Similarity=0.525  Sum_probs=271.8

Q ss_pred             HHHHHHHHHHHhcCccccHHHHHhhccCCH-HHHHHHHHHHHHHHHHhhcCCCccHHHHHHHhcCCHHHHHHHHHHhhCC
Q 037508          148 LRDLRGNIVALAKDQYGCRHLQRTMSSLPK-EEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTND  226 (449)
Q Consensus       148 l~~i~g~i~~La~d~~gsrvlQ~lLe~~~~-e~~~~i~~ei~~~~~~L~~d~~Gn~VvQklle~~~~~~~~~i~~~l~~~  226 (449)
                      +..+.|++++++.||+|||++|..++.++. +++..||+++.+.+.+||+|.||||||||++|+++++++..+...+.+ 
T Consensus       174 ~~~~~~~~v~f~~Dq~GsrfiQqkl~~~~~~~ek~~if~ei~~~~~~L~~dvFGNyvIQkffE~gt~~q~~~l~~~~~g-  252 (503)
T KOG1488|consen  174 LVDIPGHLVEFAKDQHGSRFIQQKLETASDNEEKQAVFDEILPPALELMTDVFGNYVIQKFFEHGTEDQRNLLHSQIKG-  252 (503)
T ss_pred             ccccCCCceeecCCcccchHHHHhccccccHHHHHHHHHHHHHHHHHHHHHHhcCchhhhhhccCCHHHHHHHHHHHHh-
Confidence            456789999999999999999999999987 999999999999999999999999999999999999999999999998 


Q ss_pred             chhhHHHhcCCchhHHHHHHHHhcCchHHHHHHHHHHhhchhchhcCcCccHHHHHHHhcCChhhHHHHHHHHHH--hHH
Q 037508          227 DFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVAD--NCY  304 (449)
Q Consensus       227 ~~~l~~L~~~~~G~~VvQklle~~~~~~~~~~I~~el~~~~~~L~~d~~Gn~ViQ~~L~~~~~~~~~~i~~~l~~--~~~  304 (449)
                        ++..||.++|||||||++|+.+....+.++| +||..++..++.|++||||||+|+++.+++.+++|++.+.+  ++.
T Consensus       253 --~v~~Lsld~ygCRVIQkale~id~~~~~~Li-~ELd~~vl~~v~DQngnHViQK~ie~~p~~~~~Fiv~~f~~~~~~~  329 (503)
T KOG1488|consen  253 --HVLELSLDMYGCRVIQKALEKVDVSLQIQLI-DELDGHLLKCVKDQNGNHVIQKCIETLPPDAWQFIVDFFSGDDNLL  329 (503)
T ss_pred             --hhhhhhcccccchhHHHHHHhcCHHHHHHHH-HHHHhhHHHHHhhcccceehhhhhhccChHHHHHHHHHhcCCCcee
Confidence              6999999999999999999999776666655 78899999999999999999999999999999999999999  999


Q ss_pred             hhhcCCchhHHHHHHHhhccHHHHHHHHHHHHHhHHHHhcCCChhHHHHHHhccCchhHHHHHHHHHHhhhhhhcCCcch
Q 037508          305 GIATDKSGCCVLQHCVEYSKGAQRERLVAEIIANALLLAEDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYG  384 (449)
Q Consensus       305 ~ls~~k~GS~Vvq~~L~~~~~~~~~~il~~l~~~l~~L~~d~~Gn~VIQ~lL~~~~~~~r~~li~~L~~~~~~Ls~~k~G  384 (449)
                      .+|+|+|||+|||++||+|.++++..++++|..++..|++|+|||||||++|+++++..+..|++.|.+++..||.+||+
T Consensus       330 ~ls~~~YGCRVIQr~lE~c~~~~~~~i~~ei~~~~~~L~~dQygNYVIQHVie~g~~~~~~~I~~~l~~~ll~~Sq~KfA  409 (503)
T KOG1488|consen  330 ELSTHKYGCRVIQRILEHCSEDQKQPLMEEIIRNCDQLAQDQYGNYVIQHVIEHGSPYRDTIIIKCLLGNLLSMSQHKFA  409 (503)
T ss_pred             EeeccCcccHHHHHHhhcCChHhhhHHHHHHHHHHHHHHhhhhhhHHHHHHHhcCChhhhhhHHHHHHhhHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999988889999999999999999999


Q ss_pred             hHHHHHHHhhcCHHHHHHHHHHHhcC-----CChhhhccCcChhHHHHHHhhhccccc
Q 037508          385 SNVVERCLLESGEEQSTRIIIELLRS-----PNVSMLLMHPFGNYVIQSALLVSKVRL  437 (449)
Q Consensus       385 S~Vvek~l~~~~~~~r~~ii~ell~~-----~~l~~L~~d~yGnyVvq~lL~~~~~~~  437 (449)
                      |+|||+|+.+++...|..|++|++..     +.|..|+.|+|||||||+||++|+.+.
T Consensus       410 SnVVEk~~~~a~~~~r~~i~~Ei~~~~~~~~~~L~~mmkdQYgNYVVQkmi~~~~~~q  467 (503)
T KOG1488|consen  410 SNVVEKAFLFAPPLLRALIMNEIFPGYVEHPDALDIMMKDQYGNYVVQKMIDICGPEQ  467 (503)
T ss_pred             HHHHHHHHhhCCHHHHHHHHHHhcCCccCCccHHHHHHHHhhhhhHHHHHHHhcCHHH
Confidence            99999999999999999999999973     467889999999999999999996643

>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
>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
>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
>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
>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
>smart00025 Pumilio Pumilio-like repeats 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
>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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query449
4dzs_A357 Crystal Structure Of Yeast Puf4p Rna Binding Domain 4e-45
3bx2_A335 Puf4 Rna Binding Domain Bound To Ho Endonuclease Rn 9e-45
3bwt_A333 Crystal Structure Of The Rna Binding Domain Of Puf4 9e-45
3bx3_A335 Puf4 T650cC724R MUTANT BOUND TO COX17 RNA 3' UTR Re 3e-43
3q0q_A351 Crystal Structure Of The Pumilio-Homology Domain Fr 1e-33
3k49_A369 Puf3 Rna Binding Domain Bound To Cox17 Rna 3' Utr R 2e-33
3h3d_X323 Drosophila Pumilio Rna Binding Domain (Puf Domain) 3e-33
3gvo_A351 Structure And Rna Binding Of The Mouse Pumilio-2 Pu 1e-32
3bsb_A343 Crystal Structure Of Human Pumilio1 In Complex With 3e-30
3bsb_A 343 Crystal Structure Of Human Pumilio1 In Complex With 1e-08
1ib2_A349 Crystal Structure Of A Pumilio-Homology Domain Leng 3e-30
1ib2_A 349 Crystal Structure Of A Pumilio-Homology Domain Leng 9e-09
2yjy_A350 A Specific And Modular Binding Code For Cytosine Re 4e-29
2yjy_A 350 A Specific And Modular Binding Code For Cytosine Re 9e-09
3qg9_A413 Crystal Structure Of Fbf-2GLD-1 Fbea A7u Mutant Com 2e-15
3k5q_A412 Crystal Structure Of Fbf-2FBE COMPLEX Length = 412 3e-15
3qgb_A413 Crystal Structure Of Fbf-2 R288y Mutant In Complex 2e-14
3v71_A382 Crystal Structure Of Puf-6 In Complex With 5be13 Rn 7e-08
>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 =  178 bits (452), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 103/288 (35%), Positives = 167/288 (57%), Gaps = 12/288 (4%)
Query: 153 GNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCS 212
           G+I +L KDQ+GCR LQ+ +  L  +  + IF E  D   ELM D FGNY++QKL+E  +
Sbjct: 35  GSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVT 94
Query: 213 EEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVTLTK 272
            EQR  +L  +++  F  V I LN HG RA+ KL+E +   ++  +V+ +LRP  V L+K
Sbjct: 95  TEQRI-VLTKISSPHF--VEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSK 151
Query: 273 DTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQRERXX 332
           D NG++VIQ C++    E+ +++ + ++D+C  IAT + GCCVLQ C+++    Q +   
Sbjct: 152 DLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLC 211
Query: 333 XXXXXXXXXXXXDCYGNYVVQHLLALRVPQ----ITASLLRQLEGHYVSFSCNKYGSNVV 388
                       D +GNYVVQ+++     +     T  ++  L+   +  S +K+GSNV+
Sbjct: 212 DKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVI 271
Query: 389 ERCLLESGEEQSTRIIIELLRS---PNVSMLLMHPFGNYVIQSALLVS 433
           E+ L  +    S  +I+E+L +     +  LL   +GNYV+Q+AL +S
Sbjct: 272 EKILKTAI--VSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDIS 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|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|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|3H3D|X Chain X, Drosophila Pumilio Rna Binding Domain (Puf Domain) Length = 323 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|3BSB|A Chain A, Crystal Structure Of Human Pumilio1 In Complex With Cyclinb Reverse Rna Length = 343 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|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|2YJY|A Chain A, A Specific And Modular Binding Code For Cytosine Recognition In Puf Domains Length = 350 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
>pdb|3V71|A Chain A, Crystal Structure Of Puf-6 In Complex With 5be13 Rna Length = 382 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 ?
Query449
3gvo_A351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 1e-107
3gvo_A351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 4e-53
3gvo_A 351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 4e-38
3gvo_A351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 1e-31
3gvo_A 351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 3e-26
3gvo_A351 Pumilio 2, pumilio homolog 2; RNA-binding, PUF dom 1e-06
3k49_A369 MRNA-binding protein PUF3; PUF3, pumilio, RNA bind 1e-103
3k49_A369 MRNA-binding protein PUF3; PUF3, pumilio, RNA bind 2e-44
3k49_A369 MRNA-binding protein PUF3; PUF3, pumilio, RNA bind 2e-21
3k49_A369 MRNA-binding protein PUF3; PUF3, pumilio, RNA bind 7e-10
3bwt_A333 Protein PUF4; pumilio, RNA binding, HO endonucleas 2e-99
3bwt_A 333 Protein PUF4; pumilio, RNA binding, HO endonucleas 9e-37
3bwt_A333 Protein PUF4; pumilio, RNA binding, HO endonucleas 7e-24
3bwt_A333 Protein PUF4; pumilio, RNA binding, HO endonucleas 1e-09
3bwt_A333 Protein PUF4; pumilio, RNA binding, HO endonucleas 1e-07
3v71_A382 PUF (pumilio/FBF) domain-containing protein 7, CO 4e-85
3v71_A382 PUF (pumilio/FBF) domain-containing protein 7, CO 3e-40
3v71_A382 PUF (pumilio/FBF) domain-containing protein 7, CO 6e-29
3v71_A382 PUF (pumilio/FBF) domain-containing protein 7, CO 3e-20
3v71_A382 PUF (pumilio/FBF) domain-containing protein 7, CO 4e-10
3k62_A412 FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa 7e-74
3k62_A412 FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa 3e-36
3k62_A 412 FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding fa 4e-21
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 4e-08
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 6e-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 =  321 bits (824), Expect = e-107
 Identities = 79/292 (27%), Positives = 157/292 (53%), Gaps = 9/292 (3%)

Query: 148 LRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKL 207
           LRDL G+IV  ++DQ+G R +Q+ +      E +++F E++    +LM D FGNYV+QK 
Sbjct: 21  LRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKF 80

Query: 208 VELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGA 267
            E  S +Q+  +   +      ++ + L  +G R + K LE++++ QQ  +V   L    
Sbjct: 81  FEFGSLDQKLALATRIRG---HVLPLALQMYGCRVIQKALESISSDQQSEMV-KELDGHV 136

Query: 268 VTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEYSKGAQ 327
           +   KD NG++V+Q C++    +  +++++      + ++T   GC V+Q  +E+    Q
Sbjct: 137 LKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQ 196

Query: 328 RERLVAEIIANALLLAEDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSNV 387
              ++ E+  +   L +D YGNYV+QH+L    P+  + ++ ++ G  ++ S +K+ SNV
Sbjct: 197 TLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNV 256

Query: 388 VERCLLESGEEQSTRIIIELLRSPNVS-----MLLMHPFGNYVIQSALLVSK 434
           VE+C+  +   +   +I E+    +        ++   + NYV+Q  + +++
Sbjct: 257 VEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAE 308
>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
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query449
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
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
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
3k49_A369 MRNA-binding protein PUF3; PUF3, pumilio, RNA bind 100.0
3bwt_A333 Protein PUF4; pumilio, RNA binding, HO endonucleas 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=3.9e-58  Score=462.24  Aligned_cols=287  Identities=27%  Similarity=0.503  Sum_probs=275.3

Q ss_pred             cHHHHHHHHHHHhcCccccHHHHHhhccCCHHHHHHHHHHHHHHHHHhhcCCCccHHHHHHHhcCCHHHHHHHHHHhhCC
Q 037508          147 SLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTND  226 (449)
Q Consensus       147 ~l~~i~g~i~~La~d~~gsrvlQ~lLe~~~~e~~~~i~~ei~~~~~~L~~d~~Gn~VvQklle~~~~~~~~~i~~~l~~~  226 (449)
                      .++++.|+++++|+||+|||+||++|+.+++++++.|++++.+++.+||+|+||||||||++++++++++..|++.+.+ 
T Consensus        20 ~l~~~~g~i~~la~dq~gsR~lQ~~l~~~~~~~~~~i~~ei~~~~~~L~~d~~gn~vvQklle~~~~~~~~~i~~~i~g-   98 (351)
T 3gvo_A           20 QLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRG-   98 (351)
T ss_dssp             CGGGGTTCHHHHHTSHHHHHHHHHHHHHCCHHHHHHHHHHHGGGHHHHHTSTTHHHHHHHHHHHCCHHHHHHHHHHHTT-
T ss_pred             CHHHHHhHHHHHhcCCcchHHHHHHHhhCCHHHHHHHHHHHHHhHHHHHhChhhhHHHHHHHhhCCHHHHHHHHHHHHh-
Confidence            5778999999999999999999999999999999999999999999999999999999999999999999999999998 


Q ss_pred             chhhHHHhcCCchhHHHHHHHHhcCchHHHHHHHHHHhhchhchhcCcCccHHHHHHHhcCChhhHHHHHHHHHHhHHhh
Q 037508          227 DFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGI  306 (449)
Q Consensus       227 ~~~l~~L~~~~~G~~VvQklle~~~~~~~~~~I~~el~~~~~~L~~d~~Gn~ViQ~~L~~~~~~~~~~i~~~l~~~~~~l  306 (449)
                        ++.+|+.|++||||||++++.++.+ +...+++++.+++..|++|++||||+|+++++.+++.+..|++.+.+++.++
T Consensus        99 --~~~~l~~~~~G~rvvQk~le~~~~~-~~~~i~~el~~~~~~L~~d~~Gn~ViQk~l~~~~~~~~~~i~~~~~~~~~~l  175 (351)
T 3gvo_A           99 --HVLPLALQMYGCRVIQKALESISSD-QQSEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVL  175 (351)
T ss_dssp             --CHHHHHTSTTHHHHHHHHHHHSCHH-HHHHHHGGGTTCHHHHHHSTTHHHHHHHHHHHSCGGGTHHHHHHTTTTHHHH
T ss_pred             --hHHHHhhCHHhHHHHHHHHHhCCHH-HHHHHHHHhhhhHHHHHHhhhhhHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence              6999999999999999999998765 4577889999999999999999999999999999999999999999999999


Q ss_pred             hcCCchhHHHHHHHhhccHHHHHHHHHHHHHhHHHHhcCCChhHHHHHHhccCchhHHHHHHHHHHhhhhhhcCCcchhH
Q 037508          307 ATDKSGCCVLQHCVEYSKGAQRERLVAEIIANALLLAEDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSN  386 (449)
Q Consensus       307 s~~k~GS~Vvq~~L~~~~~~~~~~il~~l~~~l~~L~~d~~Gn~VIQ~lL~~~~~~~r~~li~~L~~~~~~Ls~~k~GS~  386 (449)
                      ++|+|||+|+|+++++++++++..|++++.+++..|++|+|||||||++|+.++++.++.|++.+.+++..||.+||||+
T Consensus       176 s~~~~G~~Vvq~~le~~~~~~~~~ii~~l~~~~~~L~~d~~Gn~ViQ~~l~~~~~~~~~~i~~~l~~~~~~Ls~~k~gs~  255 (351)
T 3gvo_A          176 STHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASN  255 (351)
T ss_dssp             HTSTTHHHHHHHHHHHSCHHHHHHHHHHHHTTHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHTTTTCHHHHHTSTTHHH
T ss_pred             HhCcHhHHHHHHHHHHCCHHHHHHHHHHHhhhHHhcCCCchHHHHHHHHHHhCchhhHHHHHHHHHHHHHHHhcCcHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcCHHHHHHHHHHHhcC-----CChhhhccCcChhHHHHHHhhhccccc
Q 037508          387 VVERCLLESGEEQSTRIIIELLRS-----PNVSMLLMHPFGNYVIQSALLVSKVRL  437 (449)
Q Consensus       387 Vvek~l~~~~~~~r~~ii~ell~~-----~~l~~L~~d~yGnyVvq~lL~~~~~~~  437 (449)
                      |||+|++++++++|..|++|++..     +.+..|++|+|||||||++|+.++++.
T Consensus       256 Vvek~l~~~~~~~r~~ii~el~~~~~~~~~~l~~l~~d~ygnyViq~~L~~~~~~~  311 (351)
T 3gvo_A          256 VVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQ  311 (351)
T ss_dssp             HHHHHHHHSCHHHHHHHHHHHHSCEETTEEHHHHHHHSTTHHHHHHHHHHHCCHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHhcccCCCChHHHHccCCcchHHHHHHHHHhCCHHH
Confidence            999999999999999999999963     257899999999999999999988764
>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
>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
>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
>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

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 449
d1m8za_339 a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [Ta 2e-68
d1m8za_339 a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [Ta 7e-31
d1m8za_ 339 a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [Ta 1e-19
d1m8za_339 a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [Ta 2e-09
d1m8za_339 a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [Ta 0.002
>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 =  219 bits (559), Expect = 2e-68
 Identities = 78/297 (26%), Positives = 156/297 (52%), Gaps = 9/297 (3%)

Query: 143 FDCSSLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNY 202
           +    LR++ G+I+  ++DQ+G R +Q  +      E +++F E++    +LM+D FGNY
Sbjct: 14  YPNLQLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNY 73

Query: 203 VVQKLVELCSEEQRTRILLMLTNDDFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAA 262
           V+QK  E  S EQ+  +   +      ++ + L  +G R + K LE + + QQ  +V   
Sbjct: 74  VIQKFFEFGSLEQKLALAERIRG---HVLSLALQMYGCRVIQKALEFIPSDQQNEMV-RE 129

Query: 263 LRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGIATDKSGCCVLQHCVEY 322
           L    +   KD NG++V+Q C++    +  +++++      + ++T   GC V+Q  +E+
Sbjct: 130 LDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFALSTHPYGCRVIQRILEH 189

Query: 323 SKGAQRERLVAEIIANALLLAEDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNK 382
               Q   ++ E+  +   L +D YGNYV+QH+L    P+  + ++ ++ G+ +  S +K
Sbjct: 190 CLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHK 249

Query: 383 YGSNVVERCLLESGEEQSTRIIIELL-----RSPNVSMLLMHPFGNYVIQSALLVSK 434
           + SNVVE+C+  +   +   +I E+          +  ++   + NYV+Q  + V++
Sbjct: 250 FASNVVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAE 306
>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
>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 ?
Query449
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=4.8e-51  Score=405.95  Aligned_cols=287  Identities=26%  Similarity=0.491  Sum_probs=272.3

Q ss_pred             cHHHHHHHHHHHhcCccccHHHHHhhccCCHHHHHHHHHHHHHHHHHhhcCCCccHHHHHHHhcCCHHHHHHHHHHhhCC
Q 037508          147 SLRDLRGNIVALAKDQYGCRHLQRTMSSLPKEEIEMIFVEVIDRVCELMIDPFGNYVVQKLVELCSEEQRTRILLMLTND  226 (449)
Q Consensus       147 ~l~~i~g~i~~La~d~~gsrvlQ~lLe~~~~e~~~~i~~ei~~~~~~L~~d~~Gn~VvQklle~~~~~~~~~i~~~l~~~  226 (449)
                      .+++++|+++++|.||+|||+||++|+++++++++.|++++.+++.+||.|+|||||+|+++++++++++..|++.+.+ 
T Consensus        18 ~l~~~~g~~~~~~~~q~gSr~lQ~~l~~~~~~~~~~I~~~l~~~~~~L~~~~~gn~vvqkll~~~~~~~~~~i~~~l~~-   96 (339)
T d1m8za_          18 QLREIAGHIMEFSQDQHGSRFIQLKLERATPAERQLVFNEILQAAYQLMVDVFGNYVIQKFFEFGSLEQKLALAERIRG-   96 (339)
T ss_dssp             CGGGGTTCHHHHHTSHHHHHHHHHHHHHCCHHHHHHHHHHHGGGHHHHHTSTTHHHHHHHHHHHSCHHHHHHHHHHHTT-
T ss_pred             cHHHHHhHHHHHhcCchhhHHHHHHHhhCCHHHHHHHHHHHHHHHHHHhhCcccchhHHHHHhhCCHHHHHHHHHHHHh-
Confidence            4667899999999999999999999999999999999999999999999999999999999999999999999999998 


Q ss_pred             chhhHHHhcCCchhHHHHHHHHhcCchHHHHHHHHHHhhchhchhcCcCccHHHHHHHhcCChhhHHHHHHHHHHhHHhh
Q 037508          227 DFQLVRICLNTHGIRAVLKLLENLTNPQQISLVLAALRPGAVTLTKDTNGHYVIQYCVKHFSHEDTKYLLNEVADNCYGI  306 (449)
Q Consensus       227 ~~~l~~L~~~~~G~~VvQklle~~~~~~~~~~I~~el~~~~~~L~~d~~Gn~ViQ~~L~~~~~~~~~~i~~~l~~~~~~l  306 (449)
                        ++..|+.|++||+|||++++.+++. +...+++++.+++..++.|++|+||+|++++..+++.++.+++.+.+.+.++
T Consensus        97 --~~~~L~~~~~gs~Vvq~l~~~~~~~-~~~~l~~el~~~~~~l~~d~~~~~v~~~~l~~~~~~~~~~i~~~~~~~~~~l  173 (339)
T d1m8za_          97 --HVLSLALQMYGCRVIQKALEFIPSD-QQNEMVRELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFAL  173 (339)
T ss_dssp             --CHHHHHTSTTHHHHHHHHHHHSCHH-HHHHHHHTTTTCHHHHHHSTTHHHHHHHHHHHSCGGGGHHHHHHTTTTHHHH
T ss_pred             --hHHHHhcccccchHHHhhhccCCHH-HHHHHHHHHhhhhHHHhcCCCcchHHHHHHHhcCHHHHHHHHHHHHHHHHHH
Confidence              5999999999999999999998765 4556679999999999999999999999999999999999999999999999


Q ss_pred             hcCCchhHHHHHHHhhccHHHHHHHHHHHHHhHHHHhcCCChhHHHHHHhccCchhHHHHHHHHHHhhhhhhcCCcchhH
Q 037508          307 ATDKSGCCVLQHCVEYSKGAQRERLVAEIIANALLLAEDCYGNYVVQHLLALRVPQITASLLRQLEGHYVSFSCNKYGSN  386 (449)
Q Consensus       307 s~~k~GS~Vvq~~L~~~~~~~~~~il~~l~~~l~~L~~d~~Gn~VIQ~lL~~~~~~~r~~li~~L~~~~~~Ls~~k~GS~  386 (449)
                      ++|++||+++|++++.++++++..+++++.+++..|++|+|||||+|++|+.++++.++.|++.|++++.+|+.+++|||
T Consensus       174 ~~~~~g~~vlq~~l~~~~~~~~~~l~~~l~~~~~~L~~~~~G~~vvq~~l~~~~~~~~~~i~~~l~~~~~~l~~~k~gS~  253 (339)
T d1m8za_         174 STHPYGCRVIQRILEHCLPDQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVAEIRGNVLVLSQHKFASN  253 (339)
T ss_dssp             HTSTTHHHHHHHHHHHSCHHHHHHHHHHHHHTHHHHTTSTTHHHHHHHHHHHSCHHHHHHHHHHHTTCHHHHHTSTTHHH
T ss_pred             HhCcchhHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHcCCHHHHHHHHHHHHhhHHHHHcchhHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcCHHHHHHHHHHHhcC-----CChhhhccCcChhHHHHHHhhhccccc
Q 037508          387 VVERCLLESGEEQSTRIIIELLRS-----PNVSMLLMHPFGNYVIQSALLVSKVRL  437 (449)
Q Consensus       387 Vvek~l~~~~~~~r~~ii~ell~~-----~~l~~L~~d~yGnyVvq~lL~~~~~~~  437 (449)
                      |+|+|+..++++.+..++.+++..     +.+..|+.|+|||||||++|+.++++.
T Consensus       254 vve~~l~~~~~~~~~~~~~~l~~~~~~~~~~l~~L~~d~~gn~Viq~~l~~~~~~~  309 (339)
T d1m8za_         254 VVEKCVTHASRTERAVLIDEVCTMNDGPHSALYTMMKDQYANYVVQKMIDVAEPGQ  309 (339)
T ss_dssp             HHHHHHHHSCHHHHHHHHHHHHHCEETTEEHHHHHHTSTTHHHHHHHHHHHSCHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHhcccCchHHHHHHHcCCcccHHHHHHHHhCCHHH
Confidence            999999999999999999998742     347789999999999999999988754
>d1m8za_ a.118.1.8 (A:) Pumilio 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure