Citrus Sinensis ID: 003865

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-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790

MAQVMNMAVDSLDRRRKDKSSAGDDNGNGNGNDNEDNIDNNNNNSAPQSSPPPPPPPARRRERDSRERRDDRDLDRPPPNRRGPDYYDRNRSPPPPMPRERDRDYKRRSTVSPPPPPLPYRDRRHSPPPRRSPPYKRSRRDDGGYEPRRGSPRGGFGPDRRFGYDYTGGYEREMGGRPGYGDERPHGRFAGRSSGGYQSGPSEWDSSRGGYGDASNTGSTQREGLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWYFSSFTLFLLCTLRCSYYMCFVCRLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSGTLDLGPSVNASSSNKLGQTSEPNSDDDVDNGGKRRRHGRGPAKETDLLSAAPKAHPISSEPRRIQVDIEQAQALVRKLDSEKGITENILCGSDNDKMNREKSHGSTGPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETSEAKGLRHVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQDPLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPDAPGGTPVMQQPMPKDRPLRRKLGPDNRLKDERGNRRDRDYRANGSDRYDRSDNAQASDFPSNDDVPEGANRDESMFDTFGGQGIRVAPPFPSDIPPPPVLMPVPGAGPLGPFVPAPPEVAMQMIRDQGGPPFEGGGRHGRPGPQISGPGPILLSPAFRQDPRRIRSYQDLDAPEDEVTVMDYRSL

cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHcccccHHHHHHHcccccHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

ccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHccccHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccEEEEEccccccccHHHHHHHHHHHHHHHHHccHcccccccccccccEEEccccccccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHccccHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccEEEcccccccccEEEEEcccc

MAQVMNMAVDSldrrrkdkssagddngngngndnednidnnnnnsapqssppppppparrrerdsrerrddrdldrpppnrrgpdyydrnrsppppmprerdrdykrrstvsppppplpyrdrrhsppprrsppykrsrrddggyeprrgsprggfgpdrrfgydytggyeremggrpgygderphgrfagrssggyqsgpsewdssrggygdasntgstqrEGLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFfdahkdeewyfSSFTLFLLCTLRCSYYMCfvcrlkdkyhptnLVAVIERRNDLARKVAKDFLLDLQsgtldlgpsvnasssnklgqtsepnsdddvdnggkrrrhgrgpaketdllsaapkahpisseprrIQVDIEQAQALVRKLdsekgitenilcgsdndkmnrekshgstgpviIIRGltsvkglegvELLDTLITYLWRIHgvdyygmvetseakglrhvraegkssditnngAEWEKKLDFRWQerlrsqdpleiMTAKDKIDAAAVDALDPFVRKirdekygwkygcgakgctklFHAAEFVHKHLKLKHPELVIELTSKVREELYFQnymndpdapggtpvmqqpmpkdrplrrklgpdnrlkdergnrrdrdyrangsdrydrsdnaqasdfpsnddvpeganrdesmfdtfggqgirvappfpsdippppvlmpvpgagplgpfvpappeVAMQMIRdqggppfegggrhgrpgpqisgpgpillspafrqdprrirsyqdldapedevtvMDYRSL

MAQVMNMAVdsldrrrkdkssagddngngngndNEDNIDNNNnnsapqssppppppparrrerdsrerrddrdldrpppnrrgpdyydrnrsppppmprerdrdykrrstvsppppplpyrdrrhsppprrsppykrsrrddggyeprrgsprggfgpdrrfGYDYTGGYEREMGGRPGYGDERPHGRFAGRSSGGYQSGPSEWDSSRGGYGDASNTGSTQREGLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWYFSSFTLFLLCTLRCSYYMCFVCRLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSGTLDLGPSVNAsssnklgqtsepnsdddvdnggkrrrhgrgpaketdllsaapkahpisseprriQVDIEQAQALVrkldsekgitenilcgsdndkmnrekshgstgpviiIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETSEAKGlrhvraegkssditnngaewekKLDFRWQERLRSQDPLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPDAPGGTPVMQQPMpkdrplrrklgpdnrlkdergnrrdrdyrangsdrydrsdnaqasdfpsnddvpegANRDESMFDTFGGQGIRVAPPFPSDIPPPPVLMPVPGAGPLGPFVPAPPEVAMQMIRDQGGPPFEGGGRHGRPGPQISGPGPILLSPAFRQDPRRIRsyqdldapedevtvmdyrsl

MAQVMNMAVDSLDRRRKDKSsagddngngngndnednidnnnnnsapqssppppppparrrerdsrerrddrdldrpppnrrgpdyydrnrsppppmprerdrdYKRRSTVSppppplpyrdrrhsppprrsppykrsrrddGGYEprrgsprggfgpdrrfgYDYTGGYEREMGGRPGYGDERPHGRFAGRSSGGYQSGPSEWDSSRGGYGDASNTGSTQREGLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWYfssftlfllctlrcsYYMCFVCRLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSGTLDLGPSVNASSSNKLGQTSEPNSDDDVDNGGKRRRHGRGPAKETDLLSAAPKAHPISSEPRRIQVDIEQAQALVRKLDSEKGITENILCGSDNDKMNREKSHGSTGPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETSEAKGLRHVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQDPLEIMTakdkidaaavdaldPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPDAPGGTPVMQQPMPKDRPLRRKLGPDNRLKDERGNRRDRDYRANGSDRYDRSDNAQASDFPSNDDVPEGANRDESMFDTFGGQGIRVAppfpsdippppvlmpvpgagplgpFVPAPPEVAMQMIRDQggppfegggrhgrpgpQISGPGPILLSPAFRQDPRRIRSYQDLDAPEDEVTVMDYRSL

***********************************************************************************************************************************************************************************************************************************YKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWYFSSFTLFLLCTLRCSYYMCFVCRLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSG***************************************************************************************IL*****************GPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETS**********************EWEKKLDFRWQERLR***PLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYM*********************************************************************************************************************************************************************************************

***********************************************************************************************************************************************************************************************************************************YKQFIQELE*************EYKSEYISTQKRVFFDAHKDEEWYFSSFTLFL***************LKDKYHPTNLV**********RKVAKDFLLDLQSGTLDLG**********************************************************IQVDIEQAQALVRKLDS**GI*************************************EGVELLDTLITYLWRIHGVDYYGMVETSEAK*******************EWEKKLDFRWQERLRSQDPLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDP**********************************************************************************************************************************************************************SYQDLDAPEDEVTVMDYRSL

*************************NGNGNGNDNEDNIDNNNN*******************************DRPPPNRRGPDYYDRNRSP*********************PPPLPYR******************************PRGGFGPDRRFGYDYTGGYEREMGGRPGYGDERPHGRFAG*****************************QREGLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWYFSSFTLFLLCTLRCSYYMCFVCRLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSGTLDLGPSVNA*********************************ETDLLSAAPKAHPISSEPRRIQVDIEQAQALVRKLDSEKGITENILCGSDNDKMNREKSHGSTGPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETSEAKGLRHVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQDPLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPDAPGGTPVMQQPMPKDRPLRRKLGPDNRLKDERGNRRDRDYRANGSDRYDRSDNAQASDFPSNDDVPEGANRDESMFDTFGGQGIRVAPPFPSDIPPPPVLMPVPGAGPLGPFVPAPPEVAMQMIRDQGGPPFEGGGRHGRPGPQISGPGPILLSPAFRQDPRRIRSYQDLDAPEDEVTVMDYRSL

**Q******************************************************************************************************************************************************GGFGPDRRFGYDYTGGYEREMGGRPGYGDERPHGRFAGRSSGGYQSGPSEWDSS**GY******G*TQREGLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWYFSSFTLFLLCTLRCSYYMCFVCRLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSGTLDL******************************************************SEPRRIQVDIEQAQALVRKLDSEKGITE*IL***************STGPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETSEAKGLRHVRAEGK****TNNGAEWEKKLDFRWQERLRSQDPLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPD*********************************************DRYDRSDNAQASDFPSNDDVPEGANRDESMFDTFGGQGIRVAPPFPSDIPPPPVLMPVPGAGPLGPFVPAPPEVAMQMIRDQGGPPFEG*GRHGRPGPQISGPGPILLSPAFRQDPRRIRSYQDLDAPEDEVTVMDYRSL

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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		790	2.2.26 [Sep-21-2011]
Q9ZVD0		720	Serrate RNA effector mole	yes	no	0.827	0.908	0.699	0.0
B4LIK8		963	Serrate RNA effector mole	N/A	no	0.221	0.181	0.263	2e-09
Q5TUF1		967	Serrate RNA effector mole	yes	no	0.274	0.224	0.272	2e-09
B3MJ69		948	Serrate RNA effector mole	N/A	no	0.187	0.156	0.308	3e-09
Q17FR9		937	Serrate RNA effector mole	N/A	no	0.191	0.161	0.311	5e-09
B4QCR6		947	Serrate RNA effector mole	N/A	no	0.187	0.156	0.301	7e-09
B4MR46		1000	Serrate RNA effector mole	N/A	no	0.208	0.165	0.291	8e-09
B4II37		947	Serrate RNA effector mole	N/A	no	0.187	0.156	0.301	9e-09
Q28WQ8		951	Serrate RNA effector mole	yes	no	0.181	0.150	0.310	1e-08
B4H732		951	Serrate RNA effector mole	N/A	no	0.181	0.150	0.310	1e-08

>sp\|Q9ZVD0\|SRRT_ARATH Serrate RNA effector molecule OS=Arabidopsis thaliana GN=SE PE=1 SV=2	Back alignment and function desciption

 Score =  904 bits (2336), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 504/721 (69%), Positives = 567/721 (78%), Gaps = 67/721 (9%)

Query: 74  LDRPPPNRRGPDYYDRNRSPPPPMPRERDRDYKRRSTVSPPPPPLPYRDRRHSPPPRRSP 133
           ++RPPPNRR     +R+RSP PP PR   RDYKRR ++SPP    PYRDRRHSPP RRSP
Sbjct: 63  IERPPPNRR-----ERDRSPLPP-PR---RDYKRRPSLSPP---PPYRDRRHSPPQRRSP 110

Query: 134 PYKRSRRDDGGYEPRRGSPRGGFGP-DRRFGYDYTGGYEREMGGRPGYGDERPHGRFAGR 192
           P KR RRDD GY+ RRGSPRGG+GP DRRFGYD+ GGY+REMGGRPGYGDERPHGRF GR
Sbjct: 111 PQKRYRRDDNGYDGRRGSPRGGYGPPDRRFGYDHGGGYDREMGGRPGYGDERPHGRFMGR 170

Query: 193 SSGGYQSGPSEWDSSRGGYGDASNTGSTQREGLMSYKQFIQELEDDILPAEAERRYQEYK 252
               YQ    +W+  RGGYGDASN+G+ QR+GLMSYKQFIQELEDDILP+EAERRYQEYK
Sbjct: 171 ----YQ----DWEGGRGGYGDASNSGNPQRDGLMSYKQFIQELEDDILPSEAERRYQEYK 222

Query: 253 SEYISTQKRVFFDAHKDEEWYFSSFTLFLLCTLRCSYYMCFVCRLKDKYHPTNLVAVIER 312
           SEYI+TQKR FF+ HK+E+W                        LK+KYHPTNL++VIER
Sbjct: 223 SEYITTQKRAFFNTHKEEDW------------------------LKNKYHPTNLLSVIER 258

Query: 313 RNDLARKVAKDFLLDLQSGTLDLGPSVNASSSNKLGQTSEPNSDDDVDNGGKRRRHGRGP 372
           RNDLA+KVAKDFLLDLQSGTLDLGP+V A   NK G+TSEPNS+D+    GKR+RHG G 
Sbjct: 259 RNDLAQKVAKDFLLDLQSGTLDLGPAVTAL--NKSGRTSEPNSEDEAAGVGKRKRHGMGG 316

Query: 373 AKETDLLSAAPKAHPISSEPRRIQVDIEQAQALVRKLDSEKGITENILCGSDNDKMNREK 432
           AKE +LLSAAPKA   +S+P+RI  D+EQ QALVRKLDSEK I EN+L GS+ +K  REK
Sbjct: 317 AKENELLSAAPKAPSFTSDPKRILTDVEQTQALVRKLDSEKKIEENVLQGSETEKSGREK 376

Query: 433 SH-GSTGPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETSEAKGLRHVRAE 491
            H GSTGPV+IIRGLTSVKGLEGVELLDTL+TYLWR+HG+DYYG VET+EAKGLRHVRAE
Sbjct: 377 LHSGSTGPVVIIRGLTSVKGLEGVELLDTLVTYLWRVHGLDYYGKVETNEAKGLRHVRAE 436

Query: 492 GKSSDITNNGAEWEKKLDFRWQERLRSQDPLEIMTAKDKIDAAAVDALDPFVRKIRDEKY 551
           GK SD    G E E K D  WQERL+ QDPLE+M AK+KIDAAA +ALDP VRKIRDEKY
Sbjct: 437 GKVSDA--KGDENESKFDSHWQERLKGQDPLEVMAAKEKIDAAATEALDPHVRKIRDEKY 494

Query: 552 GWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPDAPGGTP 611
           GWKYGCGAKGCTKLFHAAEFV+KHLKLKH ELV ELT+KVREELYFQNYMNDP+APGG P
Sbjct: 495 GWKYGCGAKGCTKLFHAAEFVYKHLKLKHTELVTELTTKVREELYFQNYMNDPNAPGGQP 554

Query: 612 VMQQPMPKDRPLRRKLGPDNRLKDERGNRRDRDYRANGSDRYDRSDNAQASDFPSNDDVP 671
             QQ  P+DRP+RRK   +NRL+D+RG RR+RD RANG+DR DRS++ Q  D   ND   
Sbjct: 555 ATQQSGPRDRPIRRKPSMENRLRDDRGGRRERDGRANGNDRNDRSEDQQRGD---ND--- 608

Query: 672 EGANRDESMFDTFGGQGIRVAPPFPSDIPPPPVLMPVPGAGPLGPFVPAPPEVAMQMIRD 731
            G N  E  +D FGGQG    PPF SDI PPP+LMPVPGAGPLGPFVPAPPEVAMQM RD
Sbjct: 609 -GGNPGEVGYDAFGGQGGVHVPPFLSDINPPPMLMPVPGAGPLGPFVPAPPEVAMQMFRD 667

Query: 732 QGG--PPFEGGGRHGRPGPQISGPGPILLSPAFRQDPRRIRSYQDLDAPEDEVTVMDYRS 789
             G  PPFEG GR         GP P LLSPAFRQDPRR+RSYQDLDAPE+EVTV+DYRS
Sbjct: 668 PSGPNPPFEGSGR--------GGPAPFLLSPAFRQDPRRLRSYQDLDAPEEEVTVIDYRS 719

Query: 790 L 790
           L
Sbjct: 720 L 720

Acts as a mediator between the cap-binding complex (CBC) and both the pre-mRNA splicing and primary microRNAs (miRNAs) processing machinery. Required for proper processing of primary miRNAs to miRNAs, thereby playing a role in RNA-mediated gene silencing (RNAi) by miRNAs. Does not participate in sense post-transcriptional gene silencing. Acts as a regulator of meristem activity and adaxial leaf fate via the miRNA gene-silencing pathway by regulating the expression of PHB and by limiting the competence of shoot tissue to respond to KNOX expression. Its function is however not limited to miRNA-mediated repression of leaf polarity genes, but rather acts as a general regulator of primary microRNAs processing. Also critical for the accumulation of the trans-acting small interfering RNA (ta-siRNA). Required for pre-mRNA splicing.
Arabidopsis thaliana (taxid: 3702)

>sp\|B4LIK8\|SRRT_DROVI Serrate RNA effector molecule homolog OS=Drosophila virilis GN=Ars2 PE=3 SV=1	Back alignment and function description

>sp\|Q5TUF1\|SRRT_ANOGA Serrate RNA effector molecule homolog OS=Anopheles gambiae GN=Ars2 PE=3 SV=3	Back alignment and function description

>sp\|B3MJ69\|SRRT_DROAN Serrate RNA effector molecule homolog OS=Drosophila ananassae GN=Ars2 PE=3 SV=1	Back alignment and function description

>sp\|Q17FR9\|SRRT_AEDAE Serrate RNA effector molecule homolog OS=Aedes aegypti GN=Ars2 PE=3 SV=1	Back alignment and function description

>sp\|B4QCR6\|SRRT_DROSI Serrate RNA effector molecule homolog OS=Drosophila simulans GN=Ars2 PE=3 SV=1	Back alignment and function description

>sp\|B4MR46\|SRRT_DROWI Serrate RNA effector molecule homolog OS=Drosophila willistoni GN=Ars2 PE=3 SV=1	Back alignment and function description

>sp\|B4II37\|SRRT_DROSE Serrate RNA effector molecule homolog OS=Drosophila sechellia GN=Ars2 PE=3 SV=2	Back alignment and function description

>sp\|Q28WQ8\|SRRT_DROPS Serrate RNA effector molecule homolog OS=Drosophila pseudoobscura pseudoobscura GN=Ars2 PE=3 SV=2	Back alignment and function description

>sp\|B4H732\|SRRT_DROPE Serrate RNA effector molecule homolog OS=Drosophila persimilis GN=Ars2 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
Query		790
255561268		823	arsenite-resistance protein, putative [R	0.936	0.899	0.749	0.0
296083972		735	unnamed protein product [Vitis vinifera]	0.921	0.990	0.740	0.0
449452660		755	PREDICTED: serrate RNA effector molecule	0.941	0.985	0.725	0.0
449452662		751	PREDICTED: serrate RNA effector molecule	0.936	0.985	0.722	0.0
225465363		748	PREDICTED: serrate RNA effector molecule	0.848	0.895	0.717	0.0
296085418		724	unnamed protein product [Vitis vinifera]	0.820	0.895	0.707	0.0
359479066		605	PREDICTED: serrate RNA effector molecule	0.758	0.990	0.787	0.0
297822357		718	hypothetical protein ARALYDRAFT_481593 [	0.827	0.910	0.698	0.0
18401322		720	serrate RNA effector molecule [Arabidops	0.827	0.908	0.699	0.0
147804970		1184	hypothetical protein VITISV_035521 [Viti	0.736	0.491	0.723	0.0

>gi\|255561268\|ref\|XP_002521645.1\| arsenite-resistance protein, putative [Ricinus communis] gi\|223539157\|gb\|EEF40752.1\| arsenite-resistance protein, putative [Ricinus communis]	Back alignment and taxonomy information

 Score = 1111 bits (2874), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 601/802 (74%), Positives = 665/802 (82%), Gaps = 62/802 (7%)

Query: 1   MAQVMNMAVDSLDRR-----RKDKSSAGDDNGNGNGNDNEDNIDNNNNNSAPQSSPPPPP 55
           MA+V+NM VDSLDRR     RK+KSSA  D+   +         NN+      S      
Sbjct: 72  MAEVINMPVDSLDRRGRERDRKEKSSA--DDPQSSSPPPPHPHQNNSRRRDRDSRDRDFD 129

Query: 56  PPARRRERDSRERRDDRDLDRPPPNRRGPDYYDRN----RSPPPPMPRERDRDYKRRSTV 111
            P    +                 NRR  D+Y+RN    RSPP P PRER+R+YKRR+++
Sbjct: 130 RPPPPPQ-----------------NRR--DFYERNHNHHRSPPLP-PREREREYKRRNSL 169

Query: 112 SPPPPPLPYRDRRHSPPPRRSPPYKRSRRDDGGYEPRRGSPRGGFGP-DRRFGYDYTGGY 170
           SPPP  +PYRDRRHSPP RRSPPYKRSRRDDGGY+ RRGSPRGGFGP DRRFGYDY GGY
Sbjct: 170 SPPP--IPYRDRRHSPPARRSPPYKRSRRDDGGYDGRRGSPRGGFGPGDRRFGYDYGGGY 227

Query: 171 EREMGGRPGYGDERPHGRFAGRSSGGYQSGPSEWDSSRGGYGDASNTGSTQREGLMSYKQ 230
           EREMGGRPGY D+RP GR+ GR+ GGYQSGPSEWDS RG Y DASNT STQREGLMSYKQ
Sbjct: 228 EREMGGRPGYPDDRPRGRYMGRA-GGYQSGPSEWDSGRGNYIDASNTMSTQREGLMSYKQ 286

Query: 231 FIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWYFSSFTLFLLCTLRCSYY 290
           FIQELEDD+LPAEAERRYQEYKSEYISTQKRVFF+AHKDEEW                  
Sbjct: 287 FIQELEDDVLPAEAERRYQEYKSEYISTQKRVFFEAHKDEEW------------------ 328

Query: 291 MCFVCRLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSGTLDLGPSVNASSSNKLGQT 350
                 LKDKYHPTNLVAVIERRN+LARK AKDFLLDLQSGTLDLGP +N  SSNK GQT
Sbjct: 329 ------LKDKYHPTNLVAVIERRNELARKAAKDFLLDLQSGTLDLGPGINVLSSNKSGQT 382

Query: 351 SEPNSDDDVDNGGKRRRHGRGPAKETDLLSAAPKAHPISSEPRRIQVDIEQAQALVRKLD 410
           S+PNSDD+VD  GKRRRHGR PAKE D+LSAAPKAHP+SSEPRRIQ+D+EQAQALVRKLD
Sbjct: 383 SDPNSDDEVDTSGKRRRHGRAPAKENDILSAAPKAHPVSSEPRRIQIDVEQAQALVRKLD 442

Query: 411 SEKGITENILCGSDNDKMNREKSHGST-GPVIIIRGLTSVKGLEGVELLDTLITYLWRIH 469
           SEKGI ENIL GSDN+KMNREK HGS+ GPVIIIRGLTSVKGLEG+ELLDTLITYLWR+H
Sbjct: 443 SEKGIEENILGGSDNEKMNREKPHGSSSGPVIIIRGLTSVKGLEGIELLDTLITYLWRVH 502

Query: 470 GVDYYGMVETSEAKGLRHVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQDPLEIMTAKD 529
           G+DYY MVET+EAKG+RHVRAEGKSSD+ N+G EWEKKLD RWQERLRSQDPLE+MTAK+
Sbjct: 503 GLDYYRMVETTEAKGVRHVRAEGKSSDVNNSGMEWEKKLDSRWQERLRSQDPLEVMTAKE 562

Query: 530 KIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTS 589
           KI+A AV++LDP+VRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELV+ELTS
Sbjct: 563 KIEATAVESLDPYVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVMELTS 622

Query: 590 KVREELYFQNYMNDPDAPGGTPVMQQPMPKDRPLRRKLGPDNRLKDERGNRRDRDYRANG 649
           K+RE+LYFQNYMNDPDAPGGTPVMQQP+PKD+P RRKLGP+NRLKDERGNRR+ D RANG
Sbjct: 623 KLREDLYFQNYMNDPDAPGGTPVMQQPLPKDKPQRRKLGPENRLKDERGNRREHDSRANG 682

Query: 650 SDRYDRSDNAQASDFPSNDDVPEGANRDESMFDTFGGQGIRVAPPFPSDIPPPPVLMPVP 709
           S+R+DRS+N Q  DF SN+D P+G N D+ M+D FGGQGI V P FPSDIPPPPVLMPVP
Sbjct: 683 SERFDRSENPQTGDFQSNNDGPDGGNHDDGMYDNFGGQGIHV-PSFPSDIPPPPVLMPVP 741

Query: 710 GAGPLGPFVPAPPEVAMQMIRDQGG-PPFEGGGRHGRPGPQISGPGPILLSPAFRQDPRR 768
           GAGPLGPFVPAPPEVAM+M R+QGG PPFE GGR+GRPGPQ+SGP PILLSPAFRQDPRR
Sbjct: 742 GAGPLGPFVPAPPEVAMRMFREQGGPPPFESGGRNGRPGPQLSGPAPILLSPAFRQDPRR 801

Query: 769 IRSYQDLDAPEDEVTVMDYRSL 790
           IRSYQDLDAP+DEVTV+DYRSL
Sbjct: 802 IRSYQDLDAPDDEVTVIDYRSL 823

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|296083972\|emb\|CBI24360.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449452660\|ref\|XP_004144077.1\| PREDICTED: serrate RNA effector molecule-like isoform 1 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449452662\|ref\|XP_004144078.1\| PREDICTED: serrate RNA effector molecule-like isoform 2 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|225465363\|ref\|XP_002273262.1\| PREDICTED: serrate RNA effector molecule-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|296085418\|emb\|CBI29150.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|359479066\|ref\|XP_002270387.2\| PREDICTED: serrate RNA effector molecule [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297822357\|ref\|XP_002879061.1\| hypothetical protein ARALYDRAFT_481593 [Arabidopsis lyrata subsp. lyrata] gi\|297324900\|gb\|EFH55320.1\| hypothetical protein ARALYDRAFT_481593 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi|18401322|ref|NP_565635.1| serrate RNA effector molecule [Arabidopsis thaliana] gi|75339076|sp|Q9ZVD0.2|SRRT_ARATH RecName: Full=Serrate RNA effector molecule gi|14486602|gb|AAK63206.1|AF311221_1 C2H2 zinc-finger protein SERRATE [Arabidopsis thaliana] gi|16226331|gb|AAL16137.1|AF428305_1 At2g27100/T20P8.15 [Arabidopsis thaliana] gi|14532582|gb|AAK64019.1| unknown protein [Arabidopsis thaliana] gi|20197420|gb|AAC77868.2| expressed protein [Arabidopsis thaliana] gi|23296648|gb|AAN13138.1| unknown protein [Arabidopsis thaliana] gi|23506033|gb|AAN28876.1| At2g27100/T20P8.15 [Arabidopsis thaliana] gi|330252842|gb|AEC07936.1| serrate RNA effector molecule [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|147804970\|emb\|CAN71440.1\| hypothetical protein VITISV_035521 [Vitis vinifera]	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		790
TAIR\|locus:2059294		720	SE "SERRATE" [Arabidopsis thal	0.603	0.662	0.646	1.1e-205
DICTYBASE\|DDB_G0277375		1068	DDB_G0277375 "RNA recognition	0.082	0.060	0.454	2.8e-24
UNIPROTKB\|B4QCR6		947	Ars2 "Serrate RNA effector mol	0.201	0.167	0.297	1.2e-17
UNIPROTKB\|Q6INH5		844	srrt-b "Serrate RNA effector m	0.278	0.260	0.264	2.2e-17
UNIPROTKB\|B3N3F7		947	Ars2 "Serrate RNA effector mol	0.268	0.223	0.265	3.1e-17
UNIPROTKB\|B4KLY7		980	Ars2 "Serrate RNA effector mol	0.187	0.151	0.295	3.3e-17
UNIPROTKB\|B3MJ69		948	Ars2 "Serrate RNA effector mol	0.2	0.166	0.290	1.2e-16
UNIPROTKB\|B4II37		947	Ars2 "Serrate RNA effector mol	0.294	0.246	0.264	2e-16
FB\|FBgn0033062		943	Ars2 [Drosophila melanogaster	0.201	0.168	0.297	2.3e-16
UNIPROTKB\|Q17FR9		937	Ars2 "Serrate RNA effector mol	0.122	0.103	0.33	3.3e-16

TAIR\|locus:2059294 SE "SERRATE" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1563 (555.3 bits), Expect = 1.1e-205, Sum P(2) = 1.1e-205
 Identities = 320/495 (64%), Positives = 360/495 (72%)

Query:   297 LKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSGTLDLGPSVNASSSNKLGQTSEPNSD 356
             LK+KYHPTNL++VIERRNDLA+KVAKDFLLDLQSGTLDLGP+V A   NK G+TSEPNS+
Sbjct:   243 LKNKYHPTNLLSVIERRNDLAQKVAKDFLLDLQSGTLDLGPAVTAL--NKSGRTSEPNSE 300

Query:   357 DDVDNGGKRRRHGRGPAKETDLLSAAPKAHPISSEPRRIQVDIEQAQALVRKLDSEKGIT 416
             D+    GKR+RHG G AKE +LLSAAPKA   +S+P+RI  D+EQ QALVRKLDSEK I 
Sbjct:   301 DEAAGVGKRKRHGMGGAKENELLSAAPKAPSFTSDPKRILTDVEQTQALVRKLDSEKKIE 360

Query:   417 ENILCGSDNDKMNREKSH-GSTGPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYG 475
             EN+L GS+ +K  REK H GSTGPV+IIRGLTSVKGLEGVELLDTL+TYLWR+HG+DYYG
Sbjct:   361 ENVLQGSETEKSGREKLHSGSTGPVVIIRGLTSVKGLEGVELLDTLVTYLWRVHGLDYYG 420

Query:   476 MVETSEAKGLRHVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQDPLEIMTXXXXXXXXX 535
              VET+EAKGLRHVRAEGK SD    G E E K D  WQERL+ QDPLE+M          
Sbjct:   421 KVETNEAKGLRHVRAEGKVSDA--KGDENESKFDSHWQERLKGQDPLEVMAAKEKIDAAA 478

Query:   536 XXXXXPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREEL 595
                  P VRKIRDEKYGWKYGCGAKGCTKLFHAAEFV+KHLKLKH ELV ELT+KVREEL
Sbjct:   479 TEALDPHVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVYKHLKLKHTELVTELTTKVREEL 538

Query:   596 YFQNYMNDPDAPGGTPVMQQPMPKDRPLRRKLGPDNRLKDERGNRRDRDYRANGSDRYDR 655
             YFQNYMNDP+APGG P  QQ  P+DRP+RRK   +NRL+D+RG RR+RD RANG+DR DR
Sbjct:   539 YFQNYMNDPNAPGGQPATQQSGPRDRPIRRKPSMENRLRDDRGGRRERDGRANGNDRNDR 598

Query:   656 SDNAQASDFPSNDDVPEGANRDESMFDTFGGQGIRVAXXXXXXXXXXXXXXXXXXXXXXX 715
             S++ Q  D   ND    G N  E  +D FGGQG                           
Sbjct:   599 SEDQQRGD---ND----GGNPGEVGYDAFGGQGGVHVPPFLSDINPPPMLMPVPGAGPLG 651

Query:   716 XFVPAPPEVAMQMIRDQXXXXXXXXXXXXXXXXQISGPGPILLSPAFRQDPRRIRSYQDL 775
              FVPAPPEVAMQM RD                    GP P LLSPAFRQDPRR+RSYQDL
Sbjct:   652 PFVPAPPEVAMQMFRDPSGPNPPFEGSGR------GGPAPFLLSPAFRQDPRRLRSYQDL 705

Query:   776 DAPEDEVTVMDYRSL 790
             DAPE+EVTV+DYRSL
Sbjct:   706 DAPEEEVTVIDYRSL 720

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;ISS;IDA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0048367 "shoot system development" evidence=IMP

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA;TAS

GO:0016568 "chromatin modification" evidence=TAS

GO:0009507 "chloroplast" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0048509 "regulation of meristem development" evidence=IMP

GO:2000011 "regulation of adaxial/abaxial pattern formation" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0010267 "production of ta-siRNAs involved in RNA interference" evidence=IMP

GO:0031053 "primary miRNA processing" evidence=IMP

GO:0010445 "nuclear dicing body" evidence=IDA

GO:0016607 "nuclear speck" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0008380 "RNA splicing" evidence=IMP

GO:0000398 "mRNA splicing, via spliceosome" evidence=RCA

GO:0007346 "regulation of mitotic cell cycle" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

DICTYBASE\|DDB_G0277375 DDB_G0277375 "RNA recognition motif-containing protein RRM" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

UNIPROTKB\|B4QCR6 Ars2 "Serrate RNA effector molecule homolog" [Drosophila simulans (taxid:7240)]	Back alignment and assigned GO terms

UNIPROTKB\|Q6INH5 srrt-b "Serrate RNA effector molecule homolog B" [Xenopus laevis (taxid:8355)]	Back alignment and assigned GO terms

UNIPROTKB\|B3N3F7 Ars2 "Serrate RNA effector molecule homolog" [Drosophila erecta (taxid:7220)]	Back alignment and assigned GO terms

UNIPROTKB\|B4KLY7 Ars2 "Serrate RNA effector molecule homolog" [Drosophila mojavensis (taxid:7230)]	Back alignment and assigned GO terms

UNIPROTKB\|B3MJ69 Ars2 "Serrate RNA effector molecule homolog" [Drosophila ananassae (taxid:7217)]	Back alignment and assigned GO terms

UNIPROTKB\|B4II37 Ars2 "Serrate RNA effector molecule homolog" [Drosophila sechellia (taxid:7238)]	Back alignment and assigned GO terms

FB\|FBgn0033062 Ars2 [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

UNIPROTKB\|Q17FR9 Ars2 "Serrate RNA effector molecule homolog" [Aedes aegypti (taxid:7159)]	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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9ZVD0	SRRT_ARATH	No assigned EC number	0.6990	0.8278	0.9083	yes	no

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		790
pfam12066		110	pfam12066, DUF3546, Domain of unknown function (DU	4e-27
PRK14086		617	PRK14086, dnaA, chromosomal replication initiation	6e-06
PHA03307		1352	PHA03307, PHA03307, transcriptional regulator ICP4	3e-04
PRK12678		672	PRK12678, PRK12678, transcription termination fact	4e-04
PHA03247		3151	PHA03247, PHA03247, large tegument protein UL36; P	4e-04
PHA03247		3151	PHA03247, PHA03247, large tegument protein UL36; P	6e-04
PHA03307		1352	PHA03307, PHA03307, transcriptional regulator ICP4	0.001
TIGR01642		509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.002
PHA03307		1352	PHA03307, PHA03307, transcriptional regulator ICP4	0.003
PHA03321		694	PHA03321, PHA03321, tegument protein VP11/12; Prov	0.003
pfam05750		300	pfam05750, Rubella_Capsid, Rubella capsid protein	0.004

>gnl\|CDD\|192930 pfam12066, DUF3546, Domain of unknown function (DUF3546)	Back alignment and domain information

 Score =  105 bits (265), Expect = 4e-27
 Identities = 43/108 (39%), Positives = 57/108 (52%), Gaps = 24/108 (22%)

Query: 227 SYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWYFSSFTLFLLCTLR 286
           ++KQF++  +DDI PAEAE+RYQEYK+E+   Q + FFD HKDEEW              
Sbjct: 1   TFKQFLESQDDDISPAEAEKRYQEYKTEFRRKQLQDFFDQHKDEEW-------------- 46

Query: 287 CSYYMCFVCRLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSGTLD 334
                      ++KYHP  L    E R +L +     FL  L+SGT D
Sbjct: 47  ----------FREKYHPEELAKRREERRELRKNRLNVFLELLESGTFD 84

This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 93 to 114 amino acids in length. This domain has two completely conserved Y residues that may be functionally important. Length = 110

>gnl\|CDD\|237605 PRK14086, dnaA, chromosomal replication initiation protein; Provisional	Back alignment and domain information

>gnl\|CDD\|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional	Back alignment and domain information

>gnl\|CDD\|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional	Back alignment and domain information

>gnl\|CDD\|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional	Back alignment and domain information

>gnl\|CDD\|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional	Back alignment and domain information

>gnl\|CDD\|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional	Back alignment and domain information

>gnl\|CDD\|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

>gnl\|CDD\|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional	Back alignment and domain information

>gnl\|CDD\|223041 PHA03321, PHA03321, tegument protein VP11/12; Provisional	Back alignment and domain information

>gnl\|CDD\|114474 pfam05750, Rubella_Capsid, Rubella capsid protein	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		790
KOG2295		648	consensus C2H2 Zn-finger protein [General function	100.0
PF04959		214	ARS2: Arsenite-resistance protein 2; InterPro: IPR	100.0
PF12066		110	DUF3546: Domain of unknown function (DUF3546); Int	99.9
KOG2295		648	consensus C2H2 Zn-finger protein [General function	98.85
PF13821		55	DUF4187: Domain of unknown function (DUF4187)	98.03
PF13894		24	zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP	89.29
PF00096		23	zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR0070	88.79
KOG3973		465	consensus Uncharacterized conserved glycine-rich p	83.98
KOG0921		1282	consensus Dosage compensation complex, subunit MLE	82.52
PF12756		100	zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB:	82.04
KOG1924		1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	81.53

>KOG2295 consensus C2H2 Zn-finger protein [General function prediction only]	Back alignment and domain information

Probab=100.00  E-value=2.9e-89  Score=745.95  Aligned_cols=595  Identities=28%  Similarity=0.324  Sum_probs=501.5

Q ss_pred             CCCCCCCCCCCC---CCcccccchhhhhhccCCCCCCCCCCCCCCCCcCCCCCCCCCCCccchhhhcccCCCCCCCCCCC
Q 003865           43 NNSAPQSSPPPP---PPPARRRERDSRERRDDRDLDRPPPNRRGPDYYDRNRSPPPPMPRERDRDYKRRSTVSPPPPPLP  119 (790)
Q Consensus        43 ~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  119 (790)
                      .-++|-|++|+-   .+++-++.+++|.+++++|+++++..++   |-|+..-|+      +.++++++.+.++++   +
T Consensus        27 ~r~~p~S~sp~geqs~~~p~r~t~kkr~~~~dddi~e~~p~kr---ynd~k~dp~------~qq~~~~f~a~k~ee---w   94 (648)
T KOG2295|consen   27 ERSQPRSQSPPGEQSAYHPERSTFKKRLNSYDDDIRESGPYKR---YNDYKIDPR------TQQNAVFFEAHKDEE---W   94 (648)
T ss_pred             CCCCccccCCCccccccCcccchHHHhhcccccccccCCCccc---ccccCCCCc------hhhhHHHHHhcCCcc---h
Confidence            334444444444   3355678899999999999999966654   777776665      337888888888877   9


Q ss_pred             CCCCCCCCC--CCCCCCccCccCCCCCCCCCCCCCCCCCCC-CCCccccCCCCcccccCCCCCCCCCCCCCCCCCCCCCC
Q 003865          120 YRDRRHSPP--PRRSPPYKRSRRDDGGYEPRRGSPRGGFGP-DRRFGYDYTGGYEREMGGRPGYGDERPHGRFAGRSSGG  196 (790)
Q Consensus       120 ~~~rr~Sp~--~~~sPp~kR~rrd~~g~d~~rg~p~~~~g~-dr~~G~d~~gg~~~~~gg~~~y~~~~~~G~~~~r~~~g  196 (790)
                      ||+++|+++  -++++++++.+++..+|+.+++.|.++++. |++|+|+|+++|.+++++..++.....++..+++-+  
T Consensus        95 yr~k~h~d~~~k~r~~~~g~yqn~~q~f~~r~e~~~~~~~~~D~~fada~~~~~d~~vv~~~g~te~~~r~~l~qk~e--  172 (648)
T KOG2295|consen   95 YRKKYHPDATEKLRNSLHGTYQNRLQVFYARTERGFFESHCLDAWFADAIWVMLDQGVVKEEGGTEKSLRRALYQKFE--  172 (648)
T ss_pred             hhhccCCChHHHHHHHHHHHHHHHHHHHHHhhcccccccCCcccchhhhHhhhhhhhhhcccCCCcccHHHHHHHHhh--
Confidence            999999999  888999999998888999999999999998 999999999999999999999999999998888876  


Q ss_pred             CCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccc
Q 003865          197 YQSGPSEWDSSRGGYGDASNTGSTQREGLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWYFSS  276 (790)
Q Consensus       197 ~~~~p~~~~~g~~g~~~~~~~~~~~~~~lmsFKQFl~~~~DdIspeEA~~rYqEYK~ef~~~Qi~~FFe~HKdEeW~~~~  276 (790)
                            + ..+.+||.++...+..+....|++|+     +|++++.++...|++| .+|. +|..+||+-||...|    
T Consensus       173 ------D-e~~~~gy~De~~~gt~e~e~kkssk~-----ddd~d~s~~ee~e~e~-se~~-tqksa~~n~hke~sl----  234 (648)
T KOG2295|consen  173 ------D-EGLDAGYKDEFQLGTAEDEIKKSSKP-----DDDTDDSILEENEPEL-SEWG-TQKSANDNTHKECSL----  234 (648)
T ss_pred             ------h-ccccccccccccCCCcchhhhcccCc-----ccccCcccccccchhh-hhhh-hhhhhhhhhhHHHHH----
Confidence                  4 56789999999989899999999999     9999999999999999 8888 999999999999999    


Q ss_pred             chhhhhhhhccccchhhhhhhhhhcCCchhHHHHH-------------HHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCc
Q 003865          277 FTLFLLCTLRCSYYMCFVCRLKDKYHPTNLVAVIE-------------RRNDLARKVAKDFLLDLQSGTLDLGPSVNASS  343 (790)
Q Consensus       277 ~~~~~~~~~~~~~~~~~~~~~~~KYhP~~~~~~~~-------------~r~~~~~~~ak~f~~~l~~G~ld~~p~v~a~~  343 (790)
                                          |+.+|+|.+++++|+             +++.+|.++++.|+..++++++++++.+.|. 
T Consensus       235 --------------------l~rni~Pnis~aeIe~~ck~i~~~lrfals~~~aek~~~r~lwv~fk~~~ni~~a~~aL-  293 (648)
T KOG2295|consen  235 --------------------LVRNILPNISVAEIENLCKGIPGFLRFALSTINAEKNFERRLWVTFKRGTNIKEACWAL-  293 (648)
T ss_pred             --------------------HHhccCCcccHHHHHHHhccCchheeeeccCchHHHHHHHHhhHhhccccchHHHHHHh-
Confidence                                999999999999975             6889999999999999999999999877776 


Q ss_pred             cCCCCCCCCCCCCccccCCCcccccCCCCCccccccc-cCCCCCCCCCchhHHHHHHHHHHHHHHHHhhhcCcccccccC
Q 003865          344 SNKLGQTSEPNSDDDVDNGGKRRRHGRGPAKETDLLS-AAPKAHPISSEPRRIQVDIEQAQALVRKLDSEKGITENILCG  422 (790)
Q Consensus       344 ~~k~g~~sD~nsed~~~~~~kr~r~G~~~~k~~d~l~-~aPka~Pi~S~peRI~kDLeQAr~LV~kLDaEkGIe~NpL~~  422 (790)
                       ++.+-++.++++++....+++.|++-+-.+...+++ +|+|++.+.+.+-||..+.+|+..|+.+|+.++-|..|++.-
T Consensus       294 -n~irl~s~~~se~en~~i~rrvr~~~Gia~~keiasn~a~k~~~lldk~irl~~~a~~t~al~tkl~s~n~i~kni~d~  372 (648)
T KOG2295|consen  294 -NGIRLRSNFLSESENPDITRRVRPINGIAKHKEIASNAAQKLKNLLDKLIRLIDRASQTQALVTKLSSPNPIAKNIEDR  372 (648)
T ss_pred             -hhccccccccccccccCccceeccCCchhhHHHHHHHHHHhhhHHHhhhHHHhhcccccccchhhccCCCHHHHHHHHH
Confidence             455667888999888888999999988777777666 799999999999999999999999999999999999997665


Q ss_pred             CCCccccccccC-CCCCCeeeeccccccCCccchhhHHHHHHHHHHHhhcccccccccc------cccccccccCCCCCC
Q 003865          423 SDNDKMNREKSH-GSTGPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETS------EAKGLRHVRAEGKSS  495 (790)
Q Consensus       423 ~d~~k~d~eks~-gs~gPi~i~egl~eV~dle~~k~LDllI~YLRrVHsvDYYc~~E~d------ercGi~HvR~~~~s~  495 (790)
                      ..+.++..|+.+ |+.+|.+++||+..+.++..+++||+||+|||+||++|||+.+||+      ++||++|||+++..+
T Consensus       373 l~te~S~eE~e~~gssg~e~p~eg~~~er~d~~lk~LDll~~YLr~VhslDfyn~~ey~~e~~mpnrcgl~hvR~~~~vs  452 (648)
T KOG2295|consen  373 LKTEASMEEDELLGSSGPEVPIEGLTSERDDIRLKLLDLLAEYLRIVHSLDFYNSKEYESEDAMPNRCGLIHVRGKGFVS  452 (648)
T ss_pred             hhhhcchhhhhhcCCCCCcCccccCccccchhHHHHHHHHHHHHHHHHhcccccccccchhhhcccccCceeecccCCCC
Confidence            555454445545 3888999999999999999999999999999999999999999986      389999999984432


Q ss_pred             CCCcchhhhHHhhHHHHHHHhhcCChhhHhhhhhhHHHHHHHhhhHHHHhhhhcccCcccccCCCCCcccccchhhHHHH
Q 003865          496 DITNNGAEWEKKLDFRWQERLRSQDPLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKH  575 (790)
Q Consensus       496 ~~ts~~~eWeKklD~~~q~rL~~~d~le~l~gkekID~al~e~ve~fVkk~~DEk~g~KwrC~l~gCtKLFKgpEFVrKH  575 (790)
                      .  ....+|++++++.|+.+|...++++.+-.++++++.++++|++||.+|++|+++|||+|+|++|+|||||+|||+||
T Consensus       453 ~--~ev~e~es~f~s~le~~l~~~~~lee~eakkkg~k~~e~eve~~v~s~t~e~~kdKy~C~lsgc~KlF~gpEFvrKH  530 (648)
T KOG2295|consen  453 S--KEVGEEESIFLSDLENNLACLLELEEEEAKKKGAKDVEDEVENFVDSNTMELDKDKYLCPLSGCAKLFKGPEFVRKH  530 (648)
T ss_pred             c--ccchhHHHHHHHHhhhcccccccchHHHHHHhcccCHHHHHHHHHHHHHHHhhcccccCCCcchHhhccCHHHHHHH
Confidence            2  24678999999999999988888887777888888899999999999999999999999999999999999999999


Q ss_pred             HhhhChhHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCCCCccccccCCCCCccccccCCccccccccCCCCCCCC
Q 003865          576 LKLKHPELVIELTSKVREELYFQNYMNDPDAPGGTPVMQQPMPKDRPLRRKLGPDNRLKDERGNRRDRDYRANGSDRYDR  655 (790)
Q Consensus       576 I~nKH~E~Veev~~Kv~E~~yFnNYl~DP~RP~~~pv~qq~~~~~~~~~~~~~~~~r~~~~r~~~~~~~~~~~g~~r~~~  655 (790)
                      |++||.|||+++++   |++||||||+||+||..+++ +|+.|.+.++.+        |+++|++|.-       .|+  
T Consensus       531 i~~KH~d~leeirk---ea~ffnnYl~Dp~rp~~pe~-~~q~prd~qIl~--------r~~~gG~r~~-------~r~--  589 (648)
T KOG2295|consen  531 INKKHKDKLEEIRK---EAIFFNNYLLDPCRPMDPEV-VSQSPRDLQILN--------RGPYGGFRNY-------NRN--  589 (648)
T ss_pred             HHHHHHHHHHHHHH---HHHHHHhhccCccccCCCcc-ccCCCCcccccc--------CCCCCCccCC-------CCC--
Confidence            99999999999984   89999999999999999999 777787777633        3445554430       011  


Q ss_pred             CCCCcCCCCCCCCCCCCCCCCCccccccCCCCCccCCCCCCCCCCCCCccccCCCCCCCCCCCCCChHHHHHHHHhcCCC
Q 003865          656 SDNAQASDFPSNDDVPEGANRDESMFDTFGGQGIRVAPPFPSDIPPPPVLMPVPGAGPLGPFVPAPPEVAMQMIRDQGGP  735 (790)
Q Consensus       656 ~~~~~~~~~~~~~~~~~~~~~~~~m~d~~g~~~~~~~~~f~~~~~~pp~lmpvpgagplGpfvpaPp~~~m~m~~~~g~~  735 (790)
                                    -..++++...-+|.|||+|                      |+|.|||-                 
T Consensus       590 --------------~~dg~~p~~~g~d~fgg~G----------------------a~~sg~~p-----------------  616 (648)
T KOG2295|consen  590 --------------YTDGTTPYGRGRDEFGGSG----------------------ASPSGPQP-----------------  616 (648)
T ss_pred             --------------CCCCCCCCCCCCCcccCCC----------------------CCCCCCCC-----------------
Confidence                          1334455555568888866                      33556553                 


Q ss_pred             CCCCCCCCCCCCCCCCCCCccccCCCCCCCCccCCccccCCCCCCCccc
Q 003865          736 PFEGGGRHGRPGPQISGPGPILLSPAFRQDPRRIRSYQDLDAPEDEVTV  784 (790)
Q Consensus       736 ~~~~~g~~~~~~p~~~gp~~~~~~p~~~~dpr~~r~Y~DLDaP~~~v~v  784 (790)
                      ||.++|..            +...|.|+     |+||||||||+++|+|
T Consensus       617 pf~gqg~~------------f~~~p~~R-----~vsYqDLDAPddev~~  648 (648)
T KOG2295|consen  617 PFSGQGGM------------FHRRPRYR-----LVSYQDLDAPDDEVPE  648 (648)
T ss_pred             CcccCCCC------------cCCCcccc-----cccccccCCccccCCC
Confidence            45544311            33455544     9999999999999986

>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []	Back alignment and domain information

>PF12066 DUF3546: Domain of unknown function (DUF3546); InterPro: IPR021933 This presumed domain is functionally uncharacterised	Back alignment and domain information

>KOG2295 consensus C2H2 Zn-finger protein [General function prediction only]	Back alignment and domain information

>PF13821 DUF4187: Domain of unknown function (DUF4187)	Back alignment and domain information

>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A	Back alignment and domain information

>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]	Back alignment and domain information

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]	Back alignment and domain information

>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A	Back alignment and domain information

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		790
3ax1_A		358	Molecular Insights Into Mirna Processing By Arabido		1e-149

>pdb|3AX1|A Chain A, Molecular Insights Into Mirna Processing By Arabidopsis Serrate Length = 358

Back alignment and structure

Iteration: 1

Score = 525 bits (1352), Expect = e-149, Method: Compositional matrix adjust. Identities = 264/379 (69%), Positives = 296/379 (78%), Gaps = 29/379 (7%) Query: 224 GLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWYXXXXXXXXXX 283 GLMSYKQFIQELEDDILP+EAERRYQEYKSEYI+TQKR FF+ HK+E+W Sbjct: 1 GLMSYKQFIQELEDDILPSEAERRYQEYKSEYITTQKRAFFNTHKEEDW----------- 49 Query: 284 XXXXXYYMCFVCRLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSGTLDLGPSVNASS 343 LK+KYHPTNL++VIERRNDLA+KVAKDFLLDLQSGTLDLGP+V A Sbjct: 50 -------------LKNKYHPTNLLSVIERRNDLAQKVAKDFLLDLQSGTLDLGPAVTAL- 95 Query: 344 SNKLGQTSEPNSDDDVDNGGKRRRHGRGPAKETDLLSAAPKAHPISSEPRRIQVDIEQAQ 403 NK G+TSEPNS+D+ GKR+RHG G AKE +LLSAAPKA +S+P+RI D+EQ Q Sbjct: 96 -NKSGRTSEPNSEDEAAGVGKRKRHGMGGAKENELLSAAPKAPSFTSDPKRILTDVEQTQ 154 Query: 404 ALVRKLDSEKGITENILCGSDNDKMNREKSH-GSTGPVIIIRGLTSVKGLEGVELLDTLI 462 ALVRKLDSEK I EN+L GS+ +K REK H GSTGPV+IIRGLTSVKGLEGVELLDTL+ Sbjct: 155 ALVRKLDSEKKIEENVLQGSETEKSGREKLHSGSTGPVVIIRGLTSVKGLEGVELLDTLV 214 Query: 463 TYLWRIHGVDYYGMVETSEAKGLRHVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQDPL 522 TYLWR+HG+DYYG VET+EAKGLRHVRAEGK SD G E E K D WQERL+ QDPL Sbjct: 215 TYLWRVHGLDYYGKVETNEAKGLRHVRAEGKVSDA--KGDENESKFDSHWQERLKGQDPL 272 Query: 523 EIMTXXXXXXXXXXXXXXPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPE 582 E+M P VRKIRDEKYGWKYGCGAKGCTKLFHAAEFV+KHLKLKH E Sbjct: 273 EVMAAKEKIDAAATEALDPHVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVYKHLKLKHTE 332 Query: 583 LVIELTSKVREELYFQNYM 601 LV ELT+KVREELYFQNY+ Sbjct: 333 LVTELTTKVREELYFQNYL 351

PyMOL of 3ax1

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		790
3ax1_A		358	Serrate RNA effector molecule; miRNA processing, p	1e-113
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05
3pgw_S		437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-04

>3ax1_A Serrate RNA effector molecule; miRNA processing, protein binding; 2.74A {Arabidopsis thaliana} Length = 358	Back alignment and structure

 Score =  347 bits (891), Expect = e-113
 Identities = 275/385 (71%), Positives = 309/385 (80%), Gaps = 29/385 (7%)

Query: 224 GLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWYFSSFTLFLLC 283
           GLMSYKQFIQELEDDILP+EAERRYQEYKSEYI+TQKR FF+ HK+E+W           
Sbjct: 1   GLMSYKQFIQELEDDILPSEAERRYQEYKSEYITTQKRAFFNTHKEEDW----------- 49

Query: 284 TLRCSYYMCFVCRLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSGTLDLGPSVNASS 343
                        LK+KYHPTNL++VIERRNDLA+KVAKDFLLDLQSGTLDLGP+V A  
Sbjct: 50  -------------LKNKYHPTNLLSVIERRNDLAQKVAKDFLLDLQSGTLDLGPAVTAL- 95

Query: 344 SNKLGQTSEPNSDDDVDNGGKRRRHGRGPAKETDLLSAAPKAHPISSEPRRIQVDIEQAQ 403
            NK G+TSEPNS+D+    GKR+RHG G AKE +LLSAAPKA   +S+P+RI  D+EQ Q
Sbjct: 96  -NKSGRTSEPNSEDEAAGVGKRKRHGMGGAKENELLSAAPKAPSFTSDPKRILTDVEQTQ 154

Query: 404 ALVRKLDSEKGITENILCGSDNDKMNREKSH-GSTGPVIIIRGLTSVKGLEGVELLDTLI 462
           ALVRKLDSEK I EN+L GS+ +K  REK H GSTGPV+IIRGLTSVKGLEGVELLDTL+
Sbjct: 155 ALVRKLDSEKKIEENVLQGSETEKSGREKLHSGSTGPVVIIRGLTSVKGLEGVELLDTLV 214

Query: 463 TYLWRIHGVDYYGMVETSEAKGLRHVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQDPL 522
           TYLWR+HG+DYYG VET+EAKGLRHVRAEGK SD    G E E K D  WQERL+ QDPL
Sbjct: 215 TYLWRVHGLDYYGKVETNEAKGLRHVRAEGKVSD--AKGDENESKFDSHWQERLKGQDPL 272

Query: 523 EIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPE 582
           E+M AK+KIDAAA +ALDP VRKIRDEKYGWKYGCGAKGCTKLFHAAEFV+KHLKLKH E
Sbjct: 273 EVMAAKEKIDAAATEALDPHVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVYKHLKLKHTE 332

Query: 583 LVIELTSKVREELYFQNYMNDPDAP 607
           LV ELT+KVREELYFQNY+      
Sbjct: 333 LVTELTTKVREELYFQNYLEHHHHH 357

PyMOL of 3ax1

>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

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		790
3ax1_A		358	Serrate RNA effector molecule; miRNA processing, p	100.0
2d9h_A		78	Zinc finger protein 692; ZF-C2H2 domain, structura	84.82
2adr_A		60	ADR1; transcription regulation, zinc finger,; NMR	84.5
1x5w_A		70	Zinc finger protein 64, isoforms 1; ZNF338, nuclea	82.11
1bbo_A		57	Human enhancer-binding protein MBP-1; DNA-binding	82.06
2yt9_A		95	Zinc finger-containing protein 1; C2H2, structural	81.31
2lv2_A		85	Insulinoma-associated protein 1; structural genomi	81.26
1klr_A		30	Zinc finger Y-chromosomal protein; transcription;	80.81

>3ax1_A Serrate RNA effector molecule; miRNA processing, protein binding; 2.74A {Arabidopsis thaliana}	Back alignment and structure

Probab=100.00  E-value=1e-99  Score=808.33  Aligned_cols=354  Identities=77%  Similarity=1.199  Sum_probs=286.8

Q ss_pred             CCCCHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhhhhhccccchhhhhhhhhhcCC
Q 003865          224 GLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWYFSSFTLFLLCTLRCSYYMCFVCRLKDKYHP  303 (790)
Q Consensus       224 ~lmsFKQFl~~~~DdIspeEA~~rYqEYK~ef~~~Qi~~FFe~HKdEeW~~~~~~~~~~~~~~~~~~~~~~~~~~~KYhP  303 (790)
                      +||||||||++|+|+|||+||+++|++||++|+++|++.||++||+++|                        |++||||
T Consensus         1 glmsFKqFl~~~~D~isp~eA~~~Y~eYk~e~~~~q~~~FF~~HK~e~W------------------------freKY~P   56 (358)
T 3ax1_A            1 GLMSYKQFIQELEDDILPSEAERRYQEYKSEYITTQKRAFFNTHKEEDW------------------------LKNKYHP   56 (358)
T ss_dssp             CCCCHHHHGGGTTTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSHH------------------------HHHHHCH
T ss_pred             CCcCHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHH------------------------HHHhcCc
Confidence            5899999999999999999999999999999999999999999999999                        9999999


Q ss_pred             chhHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCccCCCCCCCCCCCCccccCCCcccccCCCCCccccccccCC
Q 003865          304 TNLVAVIERRNDLARKVAKDFLLDLQSGTLDLGPSVNASSSNKLGQTSEPNSDDDVDNGGKRRRHGRGPAKETDLLSAAP  383 (790)
Q Consensus       304 ~~~~~~~~~r~~~~~~~ak~f~~~l~~G~ld~~p~v~a~~~~k~g~~sD~nsed~~~~~~kr~r~G~~~~k~~d~l~~aP  383 (790)
                      +++++++++|+++|++.|+.|+++|++|+||++|+++++  +++|.++|++++|+++.++|++++||++.+++|++++||
T Consensus        57 ~~l~~~~~~R~e~ak~~a~~F~~~L~~G~ld~~~~~~~~--~~~~~~~~~~~~d~~~~~~k~~~~g~~~~~~~d~~~~ap  134 (358)
T 3ax1_A           57 TNLLSVIERRNDLAQKVAKDFLLDLQSGTLDLGPAVTAL--NKSGRTSEPNSEDEAAGVGKRKRHGMGGAKENELLSAAP  134 (358)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCSBSSCC--C-----------------------------------CCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCccccc--cccCCCCCCChhhhhhccccccccCCCcccccchhhccc
Confidence            999999999999999999999999999999999888884  678888999999999988999999999999999999999


Q ss_pred             CCCCCCCchhHHHHHHHHHHHHHHHHhhhcCcccccccCCCCccccccccCC-CCCCeeeeccccccCCccchhhHHHHH
Q 003865          384 KAHPISSEPRRIQVDIEQAQALVRKLDSEKGITENILCGSDNDKMNREKSHG-STGPVIIIRGLTSVKGLEGVELLDTLI  462 (790)
Q Consensus       384 ka~Pi~S~peRI~kDLeQAr~LV~kLDaEkGIe~NpL~~~d~~k~d~eks~g-s~gPi~i~egl~eV~dle~~k~LDllI  462 (790)
                      ++||+||+|+||++||+||++||++||+|+||++|+|+..+++.++.++++. ++||++|++++.++++|+++++||++|
T Consensus       135 ~~~P~~S~p~RI~~Dle~a~~Lv~kLD~e~gie~n~l~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~l~~~~~LD~~i  214 (358)
T 3ax1_A          135 KAPSFTSDPKRILTDVEQTQALVRKLDSEKKIEENVLQGSETEKSGREKLHSGSTGPVVIIRGLTSVKGLEGVELLDTLV  214 (358)
T ss_dssp             BCCGGGSCHHHHHHHHHHHHHHHHHHHHHHTCCCCTTC---------------CCCCCEEECCSSCCEEECSHHHHHHHH
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHHHHHhhCCcccccccccccccccccccccCCCcchhhccccchhhhhhHHHHHHHH
Confidence            9999999999999999999999999999999999999998887777778775 899999999999999999999999999


Q ss_pred             HHHHHHhhcccccccccccccccccccCCCCCCCCCcchhhhHHhhHHHHHHHhhcCChhhHhhhhhhHHHHHHHhhhHH
Q 003865          463 TYLWRIHGVDYYGMVETSEAKGLRHVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQDPLEIMTAKDKIDAAAVDALDPF  542 (790)
Q Consensus       463 ~YLRrVHsvDYYc~~E~dercGi~HvR~~~~s~~~ts~~~eWeKklD~~~q~rL~~~d~le~l~gkekID~al~e~ve~f  542 (790)
                      +|||+||||||||++|++++||++|||++.++.+  .+..+|+++|+++|+.+|+.+++++.++|+++||++++++|++|
T Consensus       215 ~YLRrVH~~dYY~~~E~~~~~g~~HvR~~~~~~~--~~~~~we~~ld~~w~~~l~~~dp~~~~lg~k~ie~~~~e~l~~~  292 (358)
T 3ax1_A          215 TYLWRVHGLDYYGKVETNEAKGLRHVRAEGKVSD--AKGDENESKFDSHWQERLKGQDPLEVMAAKEKIDAAATEALDPH  292 (358)
T ss_dssp             HHHHHHHCEEGGGTEECTTCCSBCCBC------------CHHHHHHHHHHHHHHHSCCHHHHHHCHHHHHHHHHHHHGGG
T ss_pred             HHHHHHHcccccceEeecCccccCeecCCCCCCC--CchhhHHHHHHHHHHHHHcccChHHHHhcCccHHHHHHHHHHHH
Confidence            9999999999999999999999999999876543  25678999999999999999999998989999999999999999


Q ss_pred             HHhhhhcccCcccccCCCCCcccccchhhHHHHHhhhChhHHHHHHHHHHHHHHHhhhccCCC
Q 003865          543 VRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPD  605 (790)
Q Consensus       543 Vkk~~DEk~g~KwrC~l~gCtKLFKgpEFVrKHI~nKH~E~Veev~~Kv~E~~yFnNYl~DP~  605 (790)
                      |+|++||+|||||+|++++|+|||||+|||+|||+|||+|+|++++++|+|.+||+|||.--+
T Consensus       293 v~k~~dE~~gwK~~C~~~~C~KLFk~~eFV~KHi~~KH~e~v~~~~~~v~~~~~~~~~~~~~~  355 (358)
T 3ax1_A          293 VRKIRDEKYGWKYGCGAKGCTKLFHAAEFVYKHLKLKHTELVTELTTKVREELYFQNYLEHHH  355 (358)
T ss_dssp             EEEEECSSSSEEEEECSSSCCCEESSHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHhhcccccccCCCCCCcCcccCCHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            999999999999999999999999999999999999999999999999999999999996433

PyMOL of 3ax1

>2d9h_A Zinc finger protein 692; ZF-C2H2 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2adr_A ADR1; transcription regulation, zinc finger,; NMR {Saccharomyces cerevisiae} SCOP: g.37.1.1 g.37.1.1	Back alignment and structure

>1x5w_A Zinc finger protein 64, isoforms 1; ZNF338, nuclear protein, DNA binding, transcription, C2H2 type zinc finger, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1	Back alignment and structure

>1bbo_A Human enhancer-binding protein MBP-1; DNA-binding protein; HET: ABA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1 PDB: 3znf_A 4znf_A	Back alignment and structure

>2yt9_A Zinc finger-containing protein 1; C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1 g.37.1.1	Back alignment and structure

>2lv2_A Insulinoma-associated protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}	Back alignment and structure

>1klr_A Zinc finger Y-chromosomal protein; transcription; NMR {Synthetic} SCOP: g.37.1.1 PDB: 5znf_A 1kls_A 1xrz_A* 7znf_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		790
d2glia5		29	Five-finger GLI1 {Human (Homo sapiens) [TaxId: 960	94.74
d1ubdc1		28	Ying-yang 1 (yy1, zinc finger domain) {Human (Homo	89.44
d2glia3		30	Five-finger GLI1 {Human (Homo sapiens) [TaxId: 960	85.78
d2ct1a2		36	Transcriptional repressor CTCF {Human (Homo sapien	85.46
d1ubdc4		28	Ying-yang 1 (yy1, zinc finger domain) {Human (Homo	85.08
d1zfda_		32	SWI5 zinc-finger domains {Baker's yeast (Saccharom	84.15
d2dlka2		36	Zinc finger protein 692, ZNF692 {Human (Homo sapie	82.7
d2glia1		32	Five-finger GLI1 {Human (Homo sapiens) [TaxId: 960	82.03
d1sp2a_		31	Transcription factor sp1 {Human (Homo sapiens) [Ta	81.79
d1ubdc3		30	Ying-yang 1 (yy1, zinc finger domain) {Human (Homo	81.29
d1a1ia1		29	ZIF268 {Mouse (Mus musculus) [TaxId: 10090]}	80.7
d2dlka1		30	Zinc finger protein 692, ZNF692 {Human (Homo sapie	80.53

>d2glia5 g.37.1.1 (A:229-257) Five-finger GLI1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Five-finger GLI1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.74  E-value=0.0061  Score=42.60  Aligned_cols=27  Identities=37%  Similarity=0.678  Sum_probs=25.6

Q ss_pred             cccCCCCCcccccchhhHHHHHhhhCh
Q 003865          555 YGCGAKGCTKLFHAAEFVHKHLKLKHP  581 (790)
Q Consensus       555 wrC~l~gCtKLFKgpEFVrKHI~nKH~  581 (790)
                      |-|.+.+|+|-+-.|.=++|||++.|+
T Consensus         3 Y~Ck~~gC~K~YtdPSSLRKH~k~~HG   29 (29)
T d2glia5           3 YVCKLPGCTKRYTDPSSLRKHVKTVHG   29 (29)
T ss_dssp             EECCSTTTCCEESSHHHHHHHHHHSCC
T ss_pred             eecccCCCCcccCCHHHHHHHHHhhCC
Confidence            789999999999999999999999984

PyMOL of d2glia5

>d1ubdc1 g.37.1.1 (C:295-322) Ying-yang 1 (yy1, zinc finger domain) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2glia3 g.37.1.1 (A:168-197) Five-finger GLI1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ct1a2 g.37.1.1 (A:8-43) Transcriptional repressor CTCF {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ubdc4 g.37.1.1 (C:381-408) Ying-yang 1 (yy1, zinc finger domain) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1zfda_ g.37.1.1 (A:) SWI5 zinc-finger domains {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2dlka2 g.37.1.1 (A:38-73) Zinc finger protein 692, ZNF692 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2glia1 g.37.1.1 (A:103-134) Five-finger GLI1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1sp2a_ g.37.1.1 (A:) Transcription factor sp1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ubdc3 g.37.1.1 (C:351-380) Ying-yang 1 (yy1, zinc finger domain) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1a1ia1 g.37.1.1 (A:103-131) ZIF268 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2dlka1 g.37.1.1 (A:8-37) Zinc finger protein 692, ZNF692 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure