Citrus Sinensis ID: 006926

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-------580-------590-------600-------610-------620-----

MASRTSPDTTMAAGDPPFPTKVSSISTTNENKGVSITRSHEVHGKSSTDGTSSAAGKSGSLSLDALAKAKKALQMQKELSEKLKKIATLSKGSSSDGSGKVQGPAATASDAAAAAAAASVQPPTSSVPAFPGLANITNIEAVKRAQELAAKMGFRQDPEFAPIINCFPGQPPVDAAVPQKPTKAPVLRVDALGREIDEHGNVVNRTKPSNLSTLKVNINKQKKDAFQILKPELEVDPNVNPHFDPRMGINKSKLLRPKRMTFQFVEEGKWSKEAEILRVKSQFGEAGAKERQAKQAQLAKAKGGTDINPNLIEVAERVITKEKPKDPIPEIEWWDAPLLLTGSYADISDDVTIEDKLKREKITIYVEHPRPIEPPAEPAPPPPQPLKLTKKEQKKLRTQRRLAREKDRQEMIRQGLIEPPKPKVKMSNLMKVLGSEATQDPTRLEKEIRSAAAEREQAHIDRNIARKLTPAERREKKERKLFDDPSSVETIVSVYKINDLSHPKTRFKVDVNAHENRLTGCAVICEGINVVVVEGGSKSIKRYGKLMLRRIDWAKAVKEEDEDEDETTDKPVNKCVLVWQGNVARPSFNRFFVHECMTEAAAKKVFADAGVAHYWDLAVNFNDEI

ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHccccccEEEccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHcccccccccccEEEEEEEcccccccccccccccccccccEEEEEEEcccEEEEEEccHHHHHHHHHHHHHHccccccccccccccccccccccccEEEEEEEEccccccccEEEEEcccHHHHHHHHHHccccHHHHHHHcccccc

cccccccccccccccccccEEEEEEcccccccccEEEEccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccHHHccccccccccccccccccccccccHcccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccHHccHHccccccccccccccccccccccEEEcccccEEcccccEEEcccccccccccccHcHHHHHHHHHcccccccccccccccccccccccccccccccccEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccHcccccccccEEEccHHHcccccccccccccHccccccccccEEEEEcccccccccccccccccccEccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEHHHHHHHHcHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccEEEEEEEEccccccccEEEEEEcHHHccccEEEEEcccccEEEEEccHHHHHHHHHHHHHHccccccccccccccccccccccccEEEEEEEccccccccccEEEEcccHHHHHHHHHHcccHHHHHHHHcccccc

masrtspdttmaagdppfptkvssisttnenkgvsitrshevhgksstdgtssaagksgsLSLDALAKAKKALQMQKELSEKLKKIATlskgsssdgsgkvqgpaatASDAAAAAAAasvqpptssvpafpglanitnIEAVKRAQELAAKmgfrqdpefapiincfpgqppvdaavpqkptkapvlRVDALGReidehgnvvnrtkpsnlstLKVNINKQKKDAFQilkpelevdpnvnphfdprmginkskllrpkrmtfqfveegkwsKEAEILRVKSQFGEAGAKERQAKQAQLAKakggtdinpnLIEVAERVItkekpkdpipeiewwdapllltgsyadisddvtiedKLKREKITiyvehprpieppaepappppqplkltKKEQKKLRTQRRLAREKDRQEMIRqglieppkpkvkmSNLMKVLgseatqdptRLEKEIRSAAAEREQAHIDRNIARKLTPAERREKKerklfddpssveTIVSVYKindlshpktrfkvdvnahenrltgCAVICEGINVVVVEGGSKSIKRYGKLMLRRIDWAKavkeedededettdkpvnkCVLVWqgnvarpsfnrfFVHECMTEAAAKKVFADAGVAHYWDLAVNFNDEI

masrtspdttmaagdppfptkvssisttNENKGvsitrshevhgksstdgtssaagksgSLSLDALAKAKKALQMQKELSEKLKKIatlskgsssdgsgkVQGPAATASDAAAAAAAASVQPPTSSVPAFPGLANITNIEAVKRAQELAAKMGFRQDPEFAPIINCFPGQPPVDAAVPQKPTKAPVLRVDALGreidehgnvvnrtkpsnlstlkvNINKQKKDAFQILKPELEVDPNVNPHFDPrmginkskllrpkRMTFQFveegkwskeaEILRVKSQFGEAGAKERQAKQAQLakakggtdinpnLIEVAERVitkekpkdpipeiewWDAPLLLTGSYADISDDVTIEDKLKREKITIYvehprpieppaepappppqplkltkkeqkklrtqrrlarekdrqemirqglieppkpkvkMSNLMKVLgseatqdptrLEKEIRSAAAereqahidrniarkltpaerrekkerklfddpssvetIVSVykindlshpktrFKVDVNAHENRLTGCAVICEGINVVvveggsksikrygKLMLRRIDWakavkeedededettdkpvnkcVLVWQGNVARPSFNRFFVHECMTEAAAKKVFADAGVAHYWDLAVNFNDEI

MASRTSPDTTMAAGDPPFPTKVSSISTTNENKGVSITRSHEVHgksstdgtssaagksgslsldalakakkalQMQKELSEKLKKIATLskgsssdgsgkVQGpaatasdaaaaaaaasvqpptssvpaFPGLANITNIEAVKRAQELAAKMGFRQDPEFAPIINCFPGQPPVDAAVPQKPTKAPVLRVDALGREIDEHGNVVNRTKPSNLSTLKVNINKQKKDAFQILKPELEVDPNVNPHFDPRMGINKSKLLRPKRMTFQFVEEGKWSKEAEILRVKSQFGEAGakerqakqaqlakakGGTDINPNLIEVAERVITKEKPKDPIPEIEWWDAPLLLTGSYADISDDVTIEDKLKREKITIYVEHprpieppaepappppqplkltkkeqkklrtqrRLAREKDRQEMIRQGLIEPPKPKVKMSNLMKVLGSEATQDPTRLEKEIRSAAAEREQAHIDRNIARKLTPAERREKKERKLFDDPSSVETIVSVYKINDLSHPKTRFKVDVNAHENRLTGCAVICEGINVVVVEGGSKSIKRYGKLMLRRIDWAKAVKeedededettdKPVNKCVLVWQGNVARPSFNRFFVHECMTEAAAKKVFADAGVAHYWDLAVNFNDEI

**********************************************************************************************************************************PGLANITNIEAVKRAQELAAKMGFRQDPEFAPIINCFPG*****************LRVDAL*********************************FQIL*****************************RMTFQFVEEGKWS***EIL********************************NLIEVAERVITK****DPIPEIEWWDAPLLLTGSYADISDDVTIEDKLKREKITIYV*************************************************************************************************************************VETIVSVYKINDLSHPKTRFKVDVNAHENRLTGCAVICEGINVVVVEGGSKSIKRYGKLMLRRIDWAKAV**************VNKCVLVWQGNVARPSFNRFFVHECMTEAAAKKVFADAGVAHYWDLAVNF****

************************************************************************************************************************************************************************************************************************************************************************VEEGKWSKEA*************************************IEVAERVITKEKPKDPIPEIEWWDAPLLLTGSYADISDDVTIEDKLKREKITIYVEHPRPI****************************************************KMSNLMKVLGSEATQDPTRLEKEIRSAA***********************************VETIVSVYKINDLSHPKTRFKVDVNAHENRLTGCAVICEGINVVVVEGGSKSIKRYGKLMLRRIDW*******************NKCVLVWQGNVARPSFNRFFVHECMTEAAAKKVFADAGVAHYWDLAVNFN***

************AGDPPFPTKVSSISTTNENKGVSI**********************GSLSLDALAKAKKALQMQKELSEKLKKIAT*************************************SVPAFPGLANITNIEAVKRAQELAAKMGFRQDPEFAPIINCFPGQPPVDAAVPQKPTKAPVLRVDALGREIDEHGNVVNRTKPSNLSTLKVNINKQKKDAFQILKPELEVDPNVNPHFDPRMGINKSKLLRPKRMTFQFVEEGKWSKEAEILRVKSQF******************KGGTDINPNLIEVAERVITKEKPKDPIPEIEWWDAPLLLTGSYADISDDVTIEDKLKREKITIYVEHPRPIEPPAEPAPPPPQPLKLT*******************QEMIRQGLIEPPKPKVKMSNLMKVLGSEATQDPTRLEKEIRSAAAEREQAHIDRNIARKLTPAERREKKERKLFDDPSSVETIVSVYKINDLSHPKTRFKVDVNAHENRLTGCAVICEGINVVVVEGGSKSIKRYGKLMLRRIDWAKAV************KPVNKCVLVWQGNVARPSFNRFFVHECMTEAAAKKVFADAGVAHYWDLAVNFNDEI

***************PPFPTKVSSIST*********************************LSLDALAKAKKALQMQKELSEKLKKIATLS******************************************LANITNIEAVKRAQELAAKMGFRQDPEFAPIINCFPGQPPVDAAVPQKPTKAPVLRVDALGREIDEHGNVVNRTKPSNLSTLKVNINKQKKDAFQILK**L******N***DPRMGINKSKLLRPKRMTFQFVEEGKWSKEAEILRVKSQFGEAGAKERQAKQAQLAKAKG***INPNLIEVAERVITKEKPKDPIPEIEWWDAPLLLTGSYADISDDVTIEDKLKREKITIYVEHPRPIEPPAEPAPPPPQPLKLTKKEQKKLRTQRRLAREKDRQEMIRQGLIEPPKPKVKMSNLMKVLGSEATQDPTRLEKEIRSAAAEREQAHIDRNIARKLTPAERREKKERKLFDDPSSVETIVSVYKINDLSHPKTRFKVDVNAHENRLTGCAVICEGINVVVVEGGSKSIKRYGKLMLRRIDWAKAVK********TTDKPVNKCVLVWQGNVARPSFNRFFVHECMTEAAAKKVFADAGVAHYWDLAVNFN***

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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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MASRTSPDTTMAAGDPPFPTKVSSISTTNENKGVSITRSHEVHGKSSTDGTSSAAGKSGSLSLDAxxxxxxxxxxxxxxxxxxxxxATLSKGSSSDGSGKVQGPAATASDAAAAAAAASVQPPTSSVPAFPGLANITNIEAVKRAQELAAKMGFRQDPEFAPIINCFPGQPPVDAAVPQKPTKAPVLRVDALGREIDEHGNVVNRTKPSNLSTLKVNINKQKKDAFQILKPELEVDPNVNPHFDPRMGINKSKLLRPKRMTFQFVEEGKWSKEAEILRVKSQFGEAGAKERQAKQAQLAKAKGGTDINPNLIEVAERVITKEKPKDPIPEIEWWDAPLLLTGSYADISDDVTIEDKLKREKITIYVEHPRPIEPPAEPAPPPPQPxxxxxxxxxxxxxxxxxxxxxxxQEMIRQGLIEPPKPKVKMSNLMKVLGSEATQDPTRLEKEIRSAAAEREQAHIDRNIARKLTPAERREKKERKLFDDPSSVETIVSVYKINDLSHPKTRFKVDVNAHENRLTGCAVICEGINVVVVEGGSKSIKRYGKLMLRRIDWAKAVKEEDEDEDETTDKPVNKCVLVWQGNVARPSFNRFFVHECMTEAAAKKVFADAGVAHYWDLAVNFNDEI

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
Query		625	2.2.26 [Sep-21-2011]
Q2KIA6		683	U4/U6 small nuclear ribon	yes	no	0.728	0.666	0.380	8e-72
Q5R5F1		683	U4/U6 small nuclear ribon	yes	no	0.656	0.600	0.403	1e-71
O43395		683	U4/U6 small nuclear ribon	yes	no	0.656	0.600	0.403	2e-71
Q922U1		683	U4/U6 small nuclear ribon	yes	no	0.656	0.600	0.405	2e-71
Q5ZJ85		684	U4/U6 small nuclear ribon	yes	no	0.675	0.616	0.393	1e-69
Q09856		542	Uncharacterized protein C	yes	no	0.633	0.730	0.337	7e-48
Q03338		469	U4/U6 small nuclear ribon	yes	no	0.592	0.788	0.267	4e-17

>sp\|Q2KIA6\|PRPF3_BOVIN U4/U6 small nuclear ribonucleoprotein Prp3 OS=Bos taurus GN=PRPF3 PE=2 SV=1	Back alignment and function desciption

 Score =  271 bits (694), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 199/523 (38%), Positives = 283/523 (54%), Gaps = 68/523 (13%)

Query: 113 AAAAAASVQPPTSSVPAFPGLANITNIEAVKRAQELAAKMGFRQDPEFAPIINCFPGQPP 172
           AA   AS+Q   +  P   G AN+  +  +         MG       AP        P 
Sbjct: 206 AAELQASIQAQLALKPGLIGNANMVGLANLH-------AMGI------AP--------PK 244

Query: 173 VDAAVPQKPTKAPVLRVDALGREIDEHGNVVNRTKPSNLSTLKVNINKQKKDAF-QILKP 231
           V+     KPT  P++ +D  GR +D  G  +  T    + TLK NI   K++ F Q LK 
Sbjct: 245 VELKDQTKPT--PLI-LDEQGRTVDATGKEIELT--HRMPTLKANIRAVKREQFKQQLKE 299

Query: 232 ELEVDPNVNPHFDPRMGINKSKLLRPKRMTFQFVEEGKWSKEAEILRVKSQFGEAGAKER 291
           +   D   N  FDPR+ I  S+    +R TF+F ++GK+ K A+ LR K+Q      ++ 
Sbjct: 300 KPSEDMESNTFFDPRVSIAPSQR---QRRTFKFHDKGKFEKIAQRLRTKAQL-----EKL 351

Query: 292 QAKQAQLAKAKGGTDINPNLIEVAERVITKEKPKDPIPEIEWWDAPLLLTGSYADISDDV 351
           QA+ +Q A+ K G   +  L  +A +   KE  +  IPEIEWWD+ ++  G       D+
Sbjct: 352 QAEISQAAR-KTGIHTSTRLALIAPK---KELKEGDIPEIEWWDSYIIPNGF------DL 401

Query: 352 TIEDKLKREK---ITIYVEHPRPIEPPAEPAPPPPQPLKLTKKEQKKLRTQRRLAREKDR 408
           T E+  KRE    IT  VEHP  + PP +   P    + LTKKEQKKLR Q R   +K+ 
Sbjct: 402 T-EENPKREDYFGITNLVEHPAQLNPPVDNDTPVTLGVYLTKKEQKKLRRQTRREAQKEL 460

Query: 409 QEMIRQGLIEPPKPKVKMSNLMKVLGSEATQDPTRLEKEIRSAAAEREQAHIDRNIARKL 468
           QE +R GL+ PP+PKV++SNLM+VLG+EA QDPT++E  +R+  A+R++AH + N ARKL
Sbjct: 461 QEKVRLGLMPPPEPKVRISNLMRVLGTEAVQDPTKVEAHVRAQMAKRQKAHEEANAARKL 520

Query: 469 TPAERREKKERKLFDDPSSVETIVSVYKINDLSHPKTRFKVDVNAHENRLTGCAVICEGI 528
           T AE+R+ K+ K   +  S    +SVY++ +LS+P  +FK++ NA +  LTG  V+ + +
Sbjct: 521 T-AEQRKVKKIKKLKEDISQGVHISVYRVRNLSNPAKKFKIEANAGQLYLTGVVVLHKDV 579

Query: 529 NVVVVEGGSKSIKRYGKLMLRRIDWAKAVKEEDEDEDETTD-----------KPVNKCVL 577
           NVVVVEGG K+ K++ +LML RI W       DE    T             K  NKCVL
Sbjct: 580 NVVVVEGGPKAQKKFKRLMLHRIKW-------DEQTSNTKGDDDEESDEEAVKKTNKCVL 632

Query: 578 VWQGNVARPSFNRFFVHECMTEAAAKKVFADAGVAHYWDLAVN 620
           VW+G     SF      +C TE  A++ F   G  HYWDLA++
Sbjct: 633 VWEGTAKDRSFGEMKFKQCPTENMAREHFKKHGAEHYWDLALS 675

Participates in pre-mRNA splicing. May play a role in the assembly of the U4/U5/U6 tri-snRNP complex.
Bos taurus (taxid: 9913)

>sp\|Q5R5F1\|PRPF3_PONAB U4/U6 small nuclear ribonucleoprotein Prp3 OS=Pongo abelii GN=PRPF3 PE=2 SV=1	Back alignment and function description

>sp\|O43395\|PRPF3_HUMAN U4/U6 small nuclear ribonucleoprotein Prp3 OS=Homo sapiens GN=PRPF3 PE=1 SV=2	Back alignment and function description

>sp\|Q922U1\|PRPF3_MOUSE U4/U6 small nuclear ribonucleoprotein Prp3 OS=Mus musculus GN=Prpf3 PE=1 SV=1	Back alignment and function description

>sp\|Q5ZJ85\|PRPF3_CHICK U4/U6 small nuclear ribonucleoprotein Prp3 OS=Gallus gallus GN=PRPF3 PE=2 SV=1	Back alignment and function description

>sp\|Q09856\|YAF2_SCHPO Uncharacterized protein C29E6.02 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC29E6.02 PE=4 SV=1	Back alignment and function description

>sp\|Q03338\|PRP3_YEAST U4/U6 small nuclear ribonucleoprotein PRP3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PRP3 PE=1 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
Query		625
297736440		882	unnamed protein product [Vitis vinifera]	0.995	0.705	0.756	0.0
449507556		923	PREDICTED: LOW QUALITY PROTEIN: U4/U6 sm	0.963	0.652	0.759	0.0
449451683		923	PREDICTED: U4/U6 small nuclear ribonucle	0.963	0.652	0.762	0.0
356495750		832	PREDICTED: U4/U6 small nuclear ribonucle	0.992	0.745	0.712	0.0
356540367		851	PREDICTED: U4/U6 small nuclear ribonucle	0.996	0.732	0.706	0.0
357444987		794	U4/U6 small nuclear ribonucleoprotein Pr	0.948	0.746	0.703	0.0
359486305		581	PREDICTED: U4/U6 small nuclear ribonucle	0.878	0.944	0.747	0.0
356574993		801	PREDICTED: U4/U6 small nuclear ribonucle	0.942	0.735	0.670	0.0
15217815		786	Pre-mRNA-splicing factor 3 [Arabidopsis	0.977	0.777	0.667	0.0
25090452		786	At1g28060/F13K9_16 [Arabidopsis thaliana	0.977	0.777	0.666	0.0

>gi\|297736440\|emb\|CBI25311.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  936 bits (2419), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 497/657 (75%), Positives = 557/657 (84%), Gaps = 35/657 (5%)

Query: 1   MASRTSPDTTMAAGDPPFPTKVSSISTTNENKGVSITRSHEVHGKSSTDGTSSAAGKSGS 60
           MA R  P+T++A   PP PTKVSSISTTNENKGVSITRSHEV GKSSTDGT+SAAGKSG+
Sbjct: 229 MAPRLVPETSLAPSLPP-PTKVSSISTTNENKGVSITRSHEVPGKSSTDGTTSAAGKSGN 287

Query: 61  LSLDALAKAKKALQMQKELSEKLKKIATLSKGS--SSDGS----------------GKVQ 102
           LSLDALAKAKKALQMQKELSEKLKKI  L+KG+  SSDGS                GK+ 
Sbjct: 288 LSLDALAKAKKALQMQKELSEKLKKIPLLNKGASPSSDGSPQLKPKEEVTLPSSTTGKLL 347

Query: 103 G--PAATASDAAA-----------AAAAASVQPPTSSVPAFPGLANITNIEAVKRAQELA 149
           G  P  TA++A +           AAAAASV P  S V A  GL ++ N EAVKRAQELA
Sbjct: 348 GSVPLTTATEAVSLVAMPSTSTLPAAAAASVMPSASGVGALAGLTSMPNFEAVKRAQELA 407

Query: 150 AKMGFRQDPEFAPIINCFPGQPPVDAAVPQKPTKAPVLRVDALGREIDEHGNVVNRTKPS 209
           AKMGFRQDPEFAP+IN FPGQ P D AV QKP KAPVLR+DALGREIDEHGNVVN  K +
Sbjct: 408 AKMGFRQDPEFAPLINMFPGQMPTDVAVQQKPAKAPVLRLDALGREIDEHGNVVNMPKLN 467

Query: 210 NLSTLKVNINKQKKDAFQILKPELEVDPNVNPHFDPRMGINKSKLLRPKRMTFQFVEEGK 269
           NLSTLKVNINKQKKDAFQILKPEL+VDP  NPHFD RMGI+K+KLLRPKRM FQFVEEGK
Sbjct: 468 NLSTLKVNINKQKKDAFQILKPELDVDPESNPHFDSRMGIDKNKLLRPKRMNFQFVEEGK 527

Query: 270 WSKEAEILRVKSQFGEAGAKERQAKQAQLAKAKGGTDINPNLIEVAERVITKEKPKDPIP 329
           WS++AEI+++KSQFGEA AKE +AKQAQLA+AK   DINPNLIEV+ERVI KEKPKD IP
Sbjct: 528 WSRDAEIIKLKSQFGEAQAKELKAKQAQLARAKAEPDINPNLIEVSERVIIKEKPKDQIP 587

Query: 330 EIEWWDAPLLLTGSYADISDDVTIEDKLKREKITIYVEHPRPIEPPAEPAPPPPQPLKLT 389
           E+EWWD P L +G+Y D    +T EDKLK +KITIY+EHPRPIEPPAEPAPPPPQPLKLT
Sbjct: 588 EVEWWDVPFLHSGTYGDTDGGIT-EDKLKMDKITIYLEHPRPIEPPAEPAPPPPQPLKLT 646

Query: 390 KKEQKKLRTQRRLAREKDRQEMIRQGLIEPPKPKVKMSNLMKVLGSEATQDPTRLEKEIR 449
           K+EQKKLRTQRRLAREKDRQEMIRQGLIEPPKPKVKMSNLMKVLGSEATQDPTRLE EIR
Sbjct: 647 KREQKKLRTQRRLAREKDRQEMIRQGLIEPPKPKVKMSNLMKVLGSEATQDPTRLEMEIR 706

Query: 450 SAAAEREQAHIDRNIARKLTPAERREKKERKLFDDPSSVETIVSVYKINDLSHPKTRFKV 509
           SAAAEREQAH+DRNIARKLTPAERREKKERKLFDDP+++ETIVSVYKINDLSHP+TRFKV
Sbjct: 707 SAAAEREQAHVDRNIARKLTPAERREKKERKLFDDPNTLETIVSVYKINDLSHPQTRFKV 766

Query: 510 DVNAHENRLTGCAVICEGINVVVVEGGSKSIKRYGKLMLRRIDWAKAVKEEDEDEDETTD 569
           D+NA ENRLTGCAVI +GI+VVVVEGGSK IKRYGKLML+RI+WA AV+ E +D+++  +
Sbjct: 767 DINAQENRLTGCAVISDGISVVVVEGGSKPIKRYGKLMLKRINWAAAVENE-DDDEDENE 825

Query: 570 KPVNKCVLVWQGNVARPSFNRFFVHECMTEAAAKKVFADAGVAHYWDLAVNFN-DEI 625
           KP+N CVLVWQG+VA+PSFN+F  H+C TEAAA+K+F+DAGV HYWDLAVNF+ D+I
Sbjct: 826 KPLNSCVLVWQGSVAKPSFNKFNFHQCRTEAAARKIFSDAGVGHYWDLAVNFSGDQI 882

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|449507556\|ref\|XP_004163065.1\| PREDICTED: LOW QUALITY PROTEIN: U4/U6 small nuclear ribonucleoprotein Prp3-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449451683\|ref\|XP_004143591.1\| PREDICTED: U4/U6 small nuclear ribonucleoprotein Prp3-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356495750\|ref\|XP_003516736.1\| PREDICTED: U4/U6 small nuclear ribonucleoprotein Prp3-like [Glycine max]	Back alignment and taxonomy information

>gi\|356540367\|ref\|XP_003538661.1\| PREDICTED: U4/U6 small nuclear ribonucleoprotein Prp3-like [Glycine max]	Back alignment and taxonomy information

>gi\|357444987\|ref\|XP_003592771.1\| U4/U6 small nuclear ribonucleoprotein Prp3 [Medicago truncatula] gi\|355481819\|gb\|AES63022.1\| U4/U6 small nuclear ribonucleoprotein Prp3 [Medicago truncatula]	Back alignment and taxonomy information

>gi\|359486305\|ref\|XP_002275798.2\| PREDICTED: U4/U6 small nuclear ribonucleoprotein Prp3-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356574993\|ref\|XP_003555627.1\| PREDICTED: U4/U6 small nuclear ribonucleoprotein Prp3-like [Glycine max]	Back alignment and taxonomy information

>gi\|15217815\|ref\|NP_174127.1\| Pre-mRNA-splicing factor 3 [Arabidopsis thaliana] gi\|12323002\|gb\|AAG51492.1\|AC069471_23 hypothetical protein [Arabidopsis thaliana] gi\|22022524\|gb\|AAM83220.1\| At1g28060/F13K9_16 [Arabidopsis thaliana] gi\|332192786\|gb\|AEE30907.1\| Pre-mRNA-splicing factor 3 [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|25090452\|gb\|AAN72305.1\| At1g28060/F13K9_16 [Arabidopsis thaliana]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		625
TAIR\|locus:2010519		786	AT1G28060 "AT1G28060" [Arabido	0.358	0.284	0.723	9.6e-174
TAIR\|locus:2082003		437	AT3G55930 "AT3G55930" [Arabido	0.456	0.652	0.531	3.5e-86
UNIPROTKB\|H9L3J2		684	RPRD2 "Uncharacterized protein	0.673	0.615	0.353	5.5e-61
UNIPROTKB\|F2Z4C4		683	PRPF3 "U4/U6 small nuclear rib	0.648	0.592	0.365	3.9e-60
UNIPROTKB\|Q2KIA6		683	PRPF3 "U4/U6 small nuclear rib	0.648	0.592	0.365	3.9e-60
UNIPROTKB\|E2R4I0		683	PRPF3 "Uncharacterized protein	0.648	0.592	0.365	3.9e-60
UNIPROTKB\|E7EVD1		634	PRPF3 "U4/U6 small nuclear rib	0.648	0.638	0.365	3.9e-60
UNIPROTKB\|O43395		683	PRPF3 "U4/U6 small nuclear rib	0.648	0.592	0.365	3.9e-60
UNIPROTKB\|I3LJQ7		683	PRPF3 "Uncharacterized protein	0.648	0.592	0.365	3.9e-60
RGD\|1310555		683	Prpf3 "PRP3 pre-mRNA processin	0.648	0.592	0.365	5e-60

TAIR\|locus:2010519 AT1G28060 "AT1G28060" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 859 (307.4 bits), Expect = 9.6e-174, Sum P(2) = 9.6e-174
 Identities = 162/224 (72%), Positives = 193/224 (86%)

Query:   401 RLAREKDRQEMIRQGLIEPPKPKVKMSNLMKVLGSEATQDPTRLEKEIRSAAAEREQAHI 460
             RLA+EK++QEMIRQGL+EPPK KVKMSNLMKVLGSEATQDPT+LEKEIR+AAAEREQAH 
Sbjct:   563 RLAKEKEKQEMIRQGLLEPPKAKVKMSNLMKVLGSEATQDPTKLEKEIRTAAAEREQAHT 622

Query:   461 DRNIARKLTPAERREKKERKLFDDPSSVETIVSVYKINDLSHPKTRFKVDVNAHENRLTG 520
             DRN ARKLTPAE+REKKERKLFDDP++VETIVSVYKI  LSHPKTRFKV++NA ENRLTG
Sbjct:   623 DRNAARKLTPAEKREKKERKLFDDPTTVETIVSVYKIKKLSHPKTRFKVEMNARENRLTG 682

Query:   521 CAVICEGINVVVVEGGSKSIKRYGKLMLRRIDWAKAVKXXXXXXXXXXXKPVNKCVLVWQ 580
             C+V+ + ++VVVVEG SK+IKRYGKLM++RI+W +A +              NKC LVWQ
Sbjct:   683 CSVMTDEMSVVVVEGKSKAIKRYGKLMMKRINWEEAERKEGNEDEEEEVNGGNKCWLVWQ 742

Query:   581 GNVARPSFNRFFVHECMTEAAAKKVFADAGVAHYWDLAVNFNDE 624
             G++ +PSF+RF VHEC+TE+ AKKVF DAGV HYWDLAVN++D+
Sbjct:   743 GSIGKPSFHRFHVHECVTESTAKKVFMDAGVVHYWDLAVNYSDD 786

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR\|locus:2082003 AT3G55930 "AT3G55930" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|H9L3J2 RPRD2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|F2Z4C4 PRPF3 "U4/U6 small nuclear ribonucleoprotein Prp3" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|Q2KIA6 PRPF3 "U4/U6 small nuclear ribonucleoprotein Prp3" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2R4I0 PRPF3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|E7EVD1 PRPF3 "U4/U6 small nuclear ribonucleoprotein Prp3" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|O43395 PRPF3 "U4/U6 small nuclear ribonucleoprotein Prp3" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|I3LJQ7 PRPF3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

RGD\|1310555 Prpf3 "PRP3 pre-mRNA processing factor 3 homolog (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]	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
Query		625
pfam08572		222	pfam08572, PRP3, pre-mRNA processing factor 3 (PRP	4e-83
pfam06544		127	pfam06544, DUF1115, Protein of unknown function (D	9e-46

>gnl\|CDD\|219911 pfam08572, PRP3, pre-mRNA processing factor 3 (PRP3)	Back alignment and domain information

 Score =  259 bits (665), Expect = 4e-83
 Identities = 115/234 (49%), Positives = 148/234 (63%), Gaps = 16/234 (6%)

Query: 240 NPHFDPRMGINKSKLLRPKRMTFQFVEEGKWSKEAEILRVKSQFGEAGAKERQ-AKQAQL 298
           NP+ DPRM   K K  + +R   QF+E+GK+S++AE LR +++  E  A+  + A+ A L
Sbjct: 2   NPYLDPRMAEAKRK--KRRRRGLQFIEKGKFSQQAEELRREAKLEEEEARISEEAQNAGL 59

Query: 299 AKAKGGTDINPNLIEVAERVITKEKPKDPIPEIEWWDAPLLLTGSYADISDDVTIEDKLK 358
             A            +AE++  KE P D +P+IEWWD P+L    Y D+ D+   +   +
Sbjct: 60  KSATD----------LAEKIPKKELPDD-VPDIEWWDMPILDDPDYNDLEDESDEDIDEE 108

Query: 359 REKITIYVEHPRPIEPPAEPAPPPP--QPLKLTKKEQKKLRTQRRLAREKDRQEMIRQGL 416
              IT Y+EHP PIEPP E   PPP   PL LTKKEQKKLR QRR  + K++QE IR GL
Sbjct: 109 MSSITNYIEHPVPIEPPWEAHYPPPIRPPLYLTKKEQKKLRRQRRKEKRKEKQERIRLGL 168

Query: 417 IEPPKPKVKMSNLMKVLGSEATQDPTRLEKEIRSAAAEREQAHIDRNIARKLTP 470
             PP PKVK+SNLM+VLGSEA QDPT++E E+R   AER QAH DRN  RKLT 
Sbjct: 169 EPPPPPKVKLSNLMRVLGSEAVQDPTKVEAEVRRQVAERRQAHEDRNEERKLTA 222

Pre-mRNA processing factor 3 (PRP3) is a U4/U6-associated splicing factor. The human PRP3 has been implicated in autosomal retinitis pigmentosa. Length = 222

>gnl\|CDD\|219080 pfam06544, DUF1115, Protein of unknown function (DUF1115)	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		625
KOG2769		522	consensus Putative u4/u6 small nuclear ribonucleop	100.0
PF08572		223	PRP3: pre-mRNA processing factor 3 (PRP3); InterPr	100.0
PF06544		128	DUF1115: Protein of unknown function (DUF1115); In	100.0
PF04940		93	BLUF: Sensors of blue-light using FAD; InterPro: I	95.57

>KOG2769 consensus Putative u4/u6 small nuclear ribonucleoprotein [RNA processing and modification]	Back alignment and domain information

Probab=100.00  E-value=2.2e-128  Score=1025.59  Aligned_cols=425  Identities=50%  Similarity=0.749  Sum_probs=374.7

Q ss_pred             ccccHHHHHHHHHHHHHhcCCCCCCCccccccCCCCCCCCCCC--CCCCCCCCceEecCCC--CeeccCCCeeeccCCCc
Q 006926          135 NITNIEAVKRAQELAAKMGFRQDPEFAPIINCFPGQPPVDAAV--PQKPTKAPVLRVDALG--REIDEHGNVVNRTKPSN  210 (625)
Q Consensus       135 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~--~~~~~kp~~L~lD~~G--R~ID~~G~vI~~~kp~~  210 (625)
                      +...+++++|++.|+..              ++++..+.+..+  +..|+++..|+.|+.|  |.||+.|++|. ++|..
T Consensus        94 s~~~~~~~~r~~~L~~~--------------~~~~~~t~~~~~~~a~~~tkg~~l~~~~le~~r~i~e~~~~i~-t~~~~  158 (522)
T KOG2769|consen   94 SKQILEAVKRPQELAQN--------------IQNSIRTPDMPISKAIKQTKGAVLRQDALEKKRKIDELGNVID-TKPSN  158 (522)
T ss_pred             hHHHHHHHhhhhhhccc--------------cccccCCcccchhhhhcccccceeehhhhhhhhhHhhhcchhh-ccccc
Confidence            34556899999998665              223333444445  6789999999999999  99999999999 78888


Q ss_pred             ccchhhhhhhhhhhHHHhcCCCcCCCCCCCCCCCCCCCCCcccccCCCccceeeccCchhHHHHHHHHHHhhhchHHHHH
Q 006926          211 LSTLKVNINKQKKDAFQILKPELEVDPNVNPHFDPRMGINKSKLLRPKRMTFQFVEEGKWSKEAEILRVKSQFGEAGAKE  290 (625)
Q Consensus       211 ~sTLKaNir~~k~e~f~~~k~~~~~~~~~npyfD~r~~~~~~k~~R~kR~~f~F~ekGKy~kqAe~lR~k~qlee~q~ee  290 (625)
                      .++|..|++                         ++ ...  ...| +|++|+||++|+|++.|++.|.++++     ++
T Consensus       159 ~~~li~n~d-------------------------~~-~~~--~~~r-~rr~f~f~e~gkf~~~an~~r~~a~l-----e~  204 (522)
T KOG2769|consen  159 LSGLIPNLD-------------------------PR-TKK--PRKR-GRRTFLFHESGKFIKLANRHRYKAQL-----ER  204 (522)
T ss_pred             ccccccccC-------------------------hh-hcc--chhc-cccceeecccchHHHHHHHHHHHHHH-----HH
Confidence            888877754                         33 111  2234 45699999999999999999988776     68


Q ss_pred             HHHHHHHHHHhcCCCCCCcchHHHHhhhhccCCCCCCCCccccccccccCCCCCCCCCcchhhhhhhccccccceeeCCC
Q 006926          291 RQAKQAQLAKAKGGTDINPNLIEVAERVITKEKPKDPIPEIEWWDAPLLLTGSYADISDDVTIEDKLKREKITIYVEHPR  370 (625)
Q Consensus       291 lk~~~a~~ak~k~~~~i~~~l~ei~e~~~~k~~~~~~iP~VEWWD~~iL~~~~y~~i~~~~~~~~~l~~~~It~yVEHPv  370 (625)
                      |+.++++++++.   ||++ ++.++...+     .++||+|||||..||+.+.|.+.+     ...+....||+|||||+
T Consensus       205 Lq~eis~~a~k~---gI~~-~~~la~~~p-----~~~iP~iEwwD~~il~~~d~~dEn-----~~~i~~~~it~~IeHP~  270 (522)
T KOG2769|consen  205 LQNEISQAARKT---GIST-ATKLALIAP-----KDDIPAIEWWDSNILTNDDTIDEN-----HLKIDQSIITNLIEHPI  270 (522)
T ss_pred             HHHHHHHHHHhc---CCch-hhhhhhccC-----CCCCchhhhhcccccccCCccccc-----chhhhHHHHHHHhcCCc
Confidence            999999999853   4766 667777654     389999999999999887433221     22333578999999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCccchhhhhhhhhccccCCCChHHHHHHHH
Q 006926          371 PIEPPAEPAPPPPQPLKLTKKEQKKLRTQRRLAREKDRQEMIRQGLIEPPKPKVKMSNLMKVLGSEATQDPTRLEKEIRS  450 (625)
Q Consensus       371 pi~pp~e~~~p~~~plyLTKKEqKKLRRqrR~e~~KEkQdKIRLGL~PPPpPKVKLSNLMrVLg~eAV~DPTkvEa~VR~  450 (625)
                      ||.||.++..|+++|||||||||||||||||+|++||+|+||||||+|||+|||||||||+|||+|||||||+||++||.
T Consensus       271 ~~~PP~e~~~p~~l~vyLTKKErKKLRRQ~R~ea~KEkqekIrLGL~~ppePKVKiSNLMrVLgsEAiqDPTK~E~~VR~  350 (522)
T KOG2769|consen  271 PMLPPAENLTPVSLPVYLTKKERKKLRRQRRKEARKEKQEKIRLGLEPPPEPKVKLSNLMRVLGSEAIQDPTKLEAEVRD  350 (522)
T ss_pred             ccCCCcccCCCCccceeecHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCcchHHHHHHHhhhccccCcHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhccCCHHHHHHHHHhhhcCCCCCCceEEEEEEEccCCCCccccccccccccccceeEEEEcCCceE
Q 006926          451 AAAEREQAHIDRNIARKLTPAERREKKERKLFDDPSSVETIVSVYKINDLSHPKTRFKVDVNAHENRLTGCAVICEGINV  530 (625)
Q Consensus       451 QmeeR~~~He~~NeeRKLT~EqRreKk~~K~~eD~~s~~v~vaVyrI~~LsnP~hrFKVd~NAqQl~LTG~~li~~~~nl  530 (625)
                      ||++|+++||++|++||||++||++|+.+|+.+|+ +.||||+||+|++|+||++||||++||+||+||||||++.+||+
T Consensus       351 Q~aeR~kaHe~~N~aRKLT~~qkreKk~rKl~ED~-st~v~~~V~r~K~l~~p~~rFKve~NAkql~ltG~~vl~~d~~v  429 (522)
T KOG2769|consen  351 QMAERQKAHEDENAARKLTPEQKREKKERKLFEDP-STGVHCSVYRIKNLQNPKKRFKVEMNAKQLQLTGVCVLHRDMNV  429 (522)
T ss_pred             HHHHHHHHhhhhhhhhcCCHHHHHHHHHhhhccCC-CceEEEEEEEEecccCCccceeeeechhhhceeeeEEEecCCcE
Confidence            99999999999999999999999999999999998 57999999999999999999999999999999999999999999


Q ss_pred             EEEecchhHHHHHhhhhhhccCccccccccCcCccccCCCCCCeeEEEEeeecCCCCCCCeeEEecCCHHHHHHHHHhcC
Q 006926          531 VVVEGGSKSIKRYGKLMLRRIDWAKAVKEEDEDEDETTDKPVNKCVLVWQGNVARPSFNRFFVHECMTEAAAKKVFADAG  610 (625)
Q Consensus       531 VVVEGG~KsiKkYkkLMl~RIkW~e~~~~~d~~~~e~~d~~~N~C~LVWEG~vk~r~F~~w~~k~c~te~~Are~L~k~~  610 (625)
                      ||||||+||||||++|||+||||+|++... .++|++.+..+|+|+|||||++.+|+|++|+|+.|+||.+||+||++||
T Consensus       430 vVvEGg~Ka~KkykrLMl~RIkW~e~~~~k-~d~~~e~~~~~N~C~lvWEG~~~rr~F~~~~~k~c~~e~~Ar~~f~k~g  508 (522)
T KOG2769|consen  430 VVVEGGPKAQKKYKRLMLKRIKWEEDFELK-KDEDEEAVNGGNKCVLVWEGTVQRRSFREFKFKECPTEKMAREFFEKHG  508 (522)
T ss_pred             EEEecCHHHHHHHHHHHHhhcCchhhhhhc-ccchhhccCCCceEEEEeeccccCCcccceeEEecCcHHHHHHHHHHcc
Confidence            999999999999999999999999996322 2556677889999999999999999999999999999999999999999


Q ss_pred             chhHHHHHhcccCC
Q 006926          611 VAHYWDLAVNFNDE  624 (625)
Q Consensus       611 ~ehYWdlA~~~~~~  624 (625)
                      |+||||||++|+..
T Consensus       509 veHyWdLa~s~s~~  522 (522)
T KOG2769|consen  509 VEHYWDLAYSYSVL  522 (522)
T ss_pred             hHHHHHHHhhccCC
Confidence            99999999999863

>PF08572 PRP3: pre-mRNA processing factor 3 (PRP3); InterPro: IPR013881 Pre-mRNA processing factor 3 (PRP3) is a U4/U6-associated splicing factor	Back alignment and domain information

>PF06544 DUF1115: Protein of unknown function (DUF1115); InterPro: IPR010541 This entry represents the C terminus of several eukaryotic RWD domain-containing proteins of unknown function	Back alignment and domain information

>PF04940 BLUF: Sensors of blue-light using FAD; InterPro: IPR007024 An FAD-binding domain, BLUF, exemplified by the N terminus of the AppA protein, (Q53119 from SWISSPROT), from Rhodobacter sphaeroides, is present in various proteins, primarily from Bacteria	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		625
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-13

>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

 Score = 71.8 bits (175), Expect = 4e-13
 Identities = 66/484 (13%), Positives = 129/484 (26%), Gaps = 151/484 (31%)

Query: 179 QKPTKAPVLRVDALGREIDEHGNVVNRTKPSNLSTLKVNINKQKKDAFQILKPELEVDPN 238
           +   + P +       + D   N        N+S L+    K ++ A   L+P      N
Sbjct: 99  KTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQ-PYLKLRQ-ALLELRPA----KN 152

Query: 239 VNPHFDPRM-GINKSKL----LRPKRMTFQFVEEGKWSKEAEILRVKSQFGEAGAKERQA 293
           V       + G  K+ +        ++  +   +  W                 + E   
Sbjct: 153 VLID---GVLGSGKTWVALDVCLSYKVQCKMDFKIFWLN----------LKNCNSPETVL 199

Query: 294 KQAQ-LAKAKGGTDINPNLIEVAERVITKEKPKDPIPEIEWWDAPLLLTGSYAD---ISD 349
           +  Q L        I+PN    ++        K  I  I+     LL +  Y +   +  
Sbjct: 200 EMLQKLL-----YQIDPNWTSRSDH---SSNIKLRIHSIQAELRRLLKSKPYENCLLVLL 251

Query: 350 DVTIEDKLK------------REK-ITIYVEHPRPIEPPAEPAPPPPQPLKLTKKEQKKL 396
           +V                   R K +T ++          +          LT  E K L
Sbjct: 252 NVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMT-----LTPDEVKSL 306

Query: 397 RTQRRLAREKDRQEMIRQGLIEPPKPKVKMSNL-MKVLGSEATQDPTRLEKEIRSAAAER 455
                L +  D      Q L   P+  +  +   + ++           +   +    ++
Sbjct: 307 -----LLKYLD---CRPQDL---PREVLTTNPRRLSIIAESIRDGLATWD-NWKHVNCDK 354

Query: 456 EQAHIDRNIARKLTPAERREKKERKLFDDPSSVETIVSVYKINDLSHPKTRFKVDVNAHE 515
               I+ ++   L PAE      RK+FD        +SV            F    +   
Sbjct: 355 LTTIIESSLN-VLEPAE-----YRKMFDR-------LSV------------FPPSAH--- 386

Query: 516 NRLTGCAVICEGINVVVVEGGSKSIKRYGKLMLRRIDWAKAVKEEDEDEDETTDKPVNKC 575
                       I  +++             ++    W   +K +        +K     
Sbjct: 387 ------------IPTILLS------------LI----WFDVIKSDVMVV---VNKLHKYS 415

Query: 576 VLVWQGNVARPSFNRFFVH--------ECMTEAAAKKVFADAGVAHY--------WDLAV 619
           ++       +P  +   +         +   E A  +      V HY         DL  
Sbjct: 416 LV-----EKQPKESTISIPSIYLELKVKLENEYALHRSI----VDHYNIPKTFDSDDLIP 466

Query: 620 NFND 623
            + D
Sbjct: 467 PYLD 470

PyMOL of 1vt4

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		625
1yrx_A		121	Hypothetical protein RSPH03001874; ferredoxin-like	96.64
2iyg_A		124	APPA, antirepressor of PPSR, sensor of blue light;	95.65
2hfn_A		153	Synechocystis photoreceptor (SLR1694); beta sheet	95.16
1x0p_A		143	Hypothetical protein TLL0078; BLUF, FAD, structura	95.11
2byc_A		137	Blue-light receptor of the BLUF-family; signaling	94.09
3gfz_A		413	Klebsiella pneumoniae BLRP1; TIM-barrel, EAL domai	90.83

>1yrx_A Hypothetical protein RSPH03001874; ferredoxin-like fold, flavin binding, photoreceptor, transcr; HET: FMN D9G; 2.30A {Rhodobacter sphaeroides 2} SCOP: d.58.10.2 PDB: 2bun_A*	Back alignment and structure

Probab=96.64  E-value=0.0038  Score=56.83  Aligned_cols=85  Identities=16%  Similarity=0.307  Sum_probs=67.9

Q ss_pred             ccccccccceeEEEEcCCceEEEEecchhHHHHHhhhhhhccCccccccccCcCccccCCCCCCeeEEEEeeecCCCCCC
Q 006926          510 DVNAHENRLTGCAVICEGINVVVVEGGSKSIKRYGKLMLRRIDWAKAVKEEDEDEDETTDKPVNKCVLVWQGNVARPSFN  589 (625)
Q Consensus       510 d~NAqQl~LTG~~li~~~~nlVVVEGG~KsiKkYkkLMl~RIkW~e~~~~~d~~~~e~~d~~~N~C~LVWEG~vk~r~F~  589 (625)
                      ..|-.+.++||+-+++.+.=+=|.||.+.++..    +..||.=               |..-..|..+-.|.+.+|.|.
T Consensus        30 r~~N~~~gITG~Ll~~~g~F~Q~LEG~~~~V~~----Ly~rI~~---------------D~RH~~v~~l~~~~i~~R~F~   90 (121)
T 1yrx_A           30 QAHNARAQLTGALFYSQGVFFQWLEGRPAAVAE----VMTHIQR---------------DRRHSNVEILAEEPIAKRRFA   90 (121)
T ss_dssp             HHHHHHHTCEEEEEEETTEEEEEEEECHHHHHH----HHHHHHT---------------CTTEEEEEEEEEEEESSCSCS
T ss_pred             HHhhhhcCCEEEEEEeCCEEEEEecCCHHHHHH----HHHHHhc---------------CCCcCCeEEEEeeeccccccC
Confidence            456678999999999999889999999999986    4467762               233456889999999999999


Q ss_pred             CeeEEecCCHHHHHHHHHhcCchhHHHHHhcccCCC
Q 006926          590 RFFVHECMTEAAAKKVFADAGVAHYWDLAVNFNDEI  625 (625)
Q Consensus       590 ~w~~k~c~te~~Are~L~k~~~ehYWdlA~~~~~~~  625 (625)
                      +|.|..+..+.            ..|.++..++.+|
T Consensus        91 ~WsM~~~~~~~------------~~~~l~~~~~~~~  114 (121)
T 1yrx_A           91 GWHMQLSCSEA------------DMRSLGLAESRQI  114 (121)
T ss_dssp             SEEEEECCCHH------------HHHHTTCCCCCCC
T ss_pred             CCcccccchHH------------HHHhhcccchhhh
Confidence            99999998774            5566666666655

PyMOL of 1yrx

>2iyg_A APPA, antirepressor of PPSR, sensor of blue light; signal transduction; HET: FMN; 2.3A {Rhodobacter sphaeroides} PDB: 2iyi_A*	Back alignment and structure

>2hfn_A Synechocystis photoreceptor (SLR1694); beta sheet ferredoxin-like fold, flavin binding protein, electron transport; HET: FMN; 1.80A {Synechocystis SP} PDB: 2hfo_A* 3mzi_A*	Back alignment and structure

>1x0p_A Hypothetical protein TLL0078; BLUF, FAD, structural genomics, electron transport; HET: FAD; 2.00A {Thermosynechococcus elongatus} SCOP: d.58.10.2	Back alignment and structure

>2byc_A Blue-light receptor of the BLUF-family; signaling protein, photoreceptor, flavin; HET: FMN; 1.9A {Rhodobacter sphaeroides} SCOP: d.58.10.2	Back alignment and structure

>3gfz_A Klebsiella pneumoniae BLRP1; TIM-barrel, EAL domain, BLUF domain, hydrolase, signaling PR; HET: C2E FMN; 2.05A {Klebsiella pneumoniae subsp} PDB: 3gfy_A* 3gfx_A* 3gg0_A* 3gg1_A* 2kb2_A*	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		625
d1yrxa1		114	Sensor of blue light AppA {Rhodobacter sphaeroides	95.73
d1x0pa1		142	Hypothetical protein Tll0078 {Thermosynechococcus	94.39
d2byca1		136	Blue light receptor BlrB {Rhodobacter sphaeroides	94.34
d1apsa_		98	Acylphosphatase {Horse (Equus caballus) [TaxId: 97	87.57
d2acya_		98	Acylphosphatase {Cow (Bos taurus) [TaxId: 9913]}	86.96

>d1yrxa1 d.58.10.2 (A:17-130) Sensor of blue light AppA {Rhodobacter sphaeroides [TaxId: 1063]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Acylphosphatase/BLUF domain-like
family: BLUF domain
domain: Sensor of blue light AppA
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=95.73  E-value=0.0078  Score=52.14  Aligned_cols=78  Identities=15%  Similarity=0.296  Sum_probs=64.2

Q ss_pred             ccccccccceeEEEEcCCceEEEEecchhHHHHHhhhhhhccCccccccccCcCccccCCCCCCeeEEEEeeecCCCCCC
Q 006926          510 DVNAHENRLTGCAVICEGINVVVVEGGSKSIKRYGKLMLRRIDWAKAVKEEDEDEDETTDKPVNKCVLVWQGNVARPSFN  589 (625)
Q Consensus       510 d~NAqQl~LTG~~li~~~~nlVVVEGG~KsiKkYkkLMl~RIkW~e~~~~~d~~~~e~~d~~~N~C~LVWEG~vk~r~F~  589 (625)
                      ..|-..+++||+-+++.+.=+=+.||.+-++..    ++.||.=               |..-..|.++-++.+..|.|.
T Consensus        26 ~~~N~~~gITG~Ll~~~~~F~Q~LEG~~~~V~~----l~~rI~~---------------D~RH~~v~~l~~~~i~~R~F~   86 (114)
T d1yrxa1          26 QAHNARAQLTGALFYSQGVFFQWLEGRPAAVAE----VMTHIQR---------------DRRHSNVEILAEEPIAKRRFA   86 (114)
T ss_dssp             HHHHHHHTCEEEEEEETTEEEEEEEECHHHHHH----HHHHHHT---------------CTTEEEEEEEEEEEESSCSCS
T ss_pred             HHhccccCCEEEEEEeCCEEEEEeeCCHHHHHH----HHHhccC---------------CCCcCceEEEeecccCccccC
Confidence            346677899999999998889999999999998    6778762               223346999999999999999


Q ss_pred             CeeEEecCCHHHHHHHH
Q 006926          590 RFFVHECMTEAAAKKVF  606 (625)
Q Consensus       590 ~w~~k~c~te~~Are~L  606 (625)
                      +|.|.....+.+.+...
T Consensus        87 ~W~M~~~~~~~d~~~l~  103 (114)
T d1yrxa1          87 GWHMQLSCSEADMRSLG  103 (114)
T ss_dssp             SEEEEECCCHHHHHHTT
T ss_pred             CCcCcCcccchHHHHhh
Confidence            99999988877776654

PyMOL of d1yrxa1

>d1x0pa1 d.58.10.2 (A:102-243) Hypothetical protein Tll0078 {Thermosynechococcus elongatus [TaxId: 146786]}	Back information, alignment and structure

>d2byca1 d.58.10.2 (A:1-136) Blue light receptor BlrB {Rhodobacter sphaeroides [TaxId: 1063]}	Back information, alignment and structure

>d1apsa_ d.58.10.1 (A:) Acylphosphatase {Horse (Equus caballus) [TaxId: 9796]}	Back information, alignment and structure

>d2acya_ d.58.10.1 (A:) Acylphosphatase {Cow (Bos taurus) [TaxId: 9913]}	Back information, alignment and structure