Citrus Sinensis ID: 004239

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------

MAQVMNMAVDSLDRRRKDKSSAGDDNGNGNGNDNEDNIDNNNNNSAPQSSPPPPPPPARRRERDSRERRDDRDLDRPPPNRRGPDYYDRNRSPPPPMPRERDRDYKRRSTVSPPPPPLPYRDRRHSPPPRRSPPYKRSRRDDGGYEPRRGSPRGGFGPDRRFGYDYTGGYEREMGGRPGYGDERPHGRFAGRSSGGYQSGPSEWDSSRGGYGDASNTGSTQREGLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSGTLDLGPSVNASSSNKLGQTSEPNSDDDVDNGGKRRRHGRGPAKETDLLSAAPKAHPISSEPRRIQVDIEQAQALVRKLDSEKGITENILCGSDNDKMNREKSHGSTGPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETSEAKGLRHVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQDPLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPDAPGGTPVMQQPMPKDRPLRRKLGPDNRLKDERGNRRDRDYRANGSDRYDRSDNAQASDFPSNDDVPEGANRDESMFDTFGGQGIRVAPPFPSDIPPPPVLMPVPGAGPLGPFVPAPPEVAMQMIRDQGGPPFEGGGRHGRPGPQISGPGPILLSPAFRQDPRRIRSYQDLDAPEDEVTVMDYRSL

cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccEEEccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

ccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccccccEccccccccccccccccccccEEEEEccccccccHHHHHHHHHHHHHHHHHccccccccccccccccEEEccccccccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHccccHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEcccccccccccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccEccccccccccEEEEEcccc

MAQVMNMAVDSldrrrkdkssagddngngngndnednidnnnnnsapqssppppppparrrerdsrerrddrdldrpppnrrgpdyydrnrsppppmprerdrdykrrstvsppppplpyrdrrhsppprrsppykrsrrddggyeprrgsprggfgpdrrfgydytggyeremggrpgygderphgrfagrssggyqsgpsewdssrggygdasntgstqrEGLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFfdahkdeewlkdkyhptnLVAVIERRNDLARKVAKDFLLDLQsgtldlgpsvnasssnklgqtsepnsdddvdnggkrrrhgrgpaketdllsaapkahpisseprrIQVDIEQAQALVRKLdsekgitenilcgsdndkmnrekshgstgpviIIRGltsvkglegvELLDTLITYLWRIHgvdyygmvetseakglrhvraegkssditnngAEWEKKLDFRWQerlrsqdpleiMTAKDKIDAAAVDALDPFVRKirdekygwkygcgakgctklFHAAEFVHKHLKLKHPELVIELTSKVREELYFQnymndpdapggtpvmqqpmpkdrplrrklgpdnrlkdergnrrdrdyrangsdrydrsdnaqasdfpsnddvpeganrdesmfdtfggqgirvappfpsdippppvlmpvpgagplgpfvpappeVAMQMIRdqggppfegggrhgrpgpqisgpgpillspafrqdprrirsyqdldapedevtvMDYRSL

MAQVMNMAVdsldrrrkdkssagddngngngndNEDNIDNNNnnsapqssppppppparrrerdsrerrddrdldrpppnrrgpdyydrnrsppppmprerdrdykrrstvsppppplpyrdrrhsppprrsppykrsrrddggyeprrgsprggfgpdrrfGYDYTGGYEREMGGRPGYGDERPHGRFAGRSSGGYQSGPSEWDSSRGGYGDASNTGSTQREGLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDeewlkdkyhptnLVAVIERRNDLARKVAKDFLLDLQSGTLDLGPSVNAsssnklgqtsepnsdddvdnggkrrrhgrgpaketdllsaapkahpisseprriQVDIEQAQALVrkldsekgitenilcgsdndkmnrekshgstgpviiIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETSEAKGlrhvraegkssditnngaewekKLDFRWQERLRSQDPLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPDAPGGTPVMQQPMpkdrplrrklgpdnrlkdergnrrdrdyrangsdrydrsdnaqasdfpsnddvpegANRDESMFDTFGGQGIRVAPPFPSDIPPPPVLMPVPGAGPLGPFVPAPPEVAMQMIRDQGGPPFEGGGRHGRPGPQISGPGPILLSPAFRQDPRRIRsyqdldapedevtvmdyrsl

MAQVMNMAVDSLDRRRKDKSsagddngngngndnednidnnnnnsapqssppppppparrrerdsrerrddrdldrpppnrrgpdyydrnrsppppmprerdrdYKRRSTVSppppplpyrdrrhsppprrsppykrsrrddGGYEprrgsprggfgpdrrfgYDYTGGYEREMGGRPGYGDERPHGRFAGRSSGGYQSGPSEWDSSRGGYGDASNTGSTQREGLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSGTLDLGPSVNASSSNKLGQTSEPNSDDDVDNGGKRRRHGRGPAKETDLLSAAPKAHPISSEPRRIQVDIEQAQALVRKLDSEKGITENILCGSDNDKMNREKSHGSTGPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETSEAKGLRHVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQDPLEIMTakdkidaaavdaldPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPDAPGGTPVMQQPMPKDRPLRRKLGPDNRLKDERGNRRDRDYRANGSDRYDRSDNAQASDFPSNDDVPEGANRDESMFDTFGGQGIRVAppfpsdippppvlmpvpgagplgpFVPAPPEVAMQMIRDQggppfegggrhgrpgpQISGPGPILLSPAFRQDPRRIRSYQDLDAPEDEVTVMDYRSL

***********************************************************************************************************************************************************************************************************************************YKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSG***************************************************************************************IL*****************GPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETS**********************EWEKKLDFRWQERLR***PLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYM*********************************************************************************************************************************************************************************************

******************************************************************************************************************************************************************************************************************************************************RYQEYKSEYISTQKRVFFDAHKDEEWLKDKYHPTNL***************KDFLLDLQSG********************************************TDLLSAAPKAHPISSEPRRIQVDIEQAQALVRKLDSEKGITENILC*******************************EGVELLDTLITYLWRIHGVDYYGMVETSEAKG*******************WEKKLDFRWQERLRSQDPLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMND******************************************************************************************************MPVPGAGPLGPFV*****************************************************YQDLDAPEDEVTVMDYRSL

*************************NGNGNGNDNEDNIDNNNN*******************************DRPPPNRRGPDYYDRNRSP*********************PPPLPYR******************************PRGGFGPDRRFGYDYTGGYEREMGGRPGYGDERPHGRFAG*****************************QREGLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSGTLDLGPSVNA*********************************ETDLLSAAPKAHPISSEPRRIQVDIEQAQALVRKLDSEKGITENILCGSDNDKMNREKSHGSTGPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETSEAKGLRHVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQDPLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPDAPGGTPVMQQPMPKDRPLRRKLGPDNRLKDERGNRRDRDYRANGSDRYDRSDNAQASDFPSNDDVPEGANRDESMFDTFGGQGIRVAPPFPSDIPPPPVLMPVPGAGPLGPFVPAPPEVAMQMIRDQGGPPFEGGGRHGRPGPQISGPGPILLSPAFRQDPRRIRSYQDLDAPEDEVTVMDYRSL

**Q**************************************************************************************************************************************************GSPRGGFGPDRRFGYDYTGGYEREMGGRPGYGDERPHGRFAGRSSGGYQS***********************EGLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSGTLDLG*****************************************************SEPRRIQVDIEQAQALVRKLDSEKGITENILCG*************STGPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETSEAKGLRHVRAEGK****TNNGAEWEKKLDFRWQERLRSQDPLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPD**********************************************RYDRSDNAQASDFPSNDDVPEGANRDESMFDTFGGQGIRVAPPFPSDIPPPPVLMPVPGAGPLGPFVPAPPEVAMQMIRDQGGPPFEG***HGRPGPQISGPGPILLSPAFRQDPRRIRSYQDLDAPEDEVTVMDYRSL

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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		766	2.2.26 [Sep-21-2011]
Q9ZVD0		720	Serrate RNA effector mole	yes	no	0.853	0.908	0.723	0.0
B4LIK8		963	Serrate RNA effector mole	N/A	no	0.228	0.181	0.295	3e-13
B3MJ69		948	Serrate RNA effector mole	N/A	no	0.171	0.138	0.309	1e-12
Q17FR9		937	Serrate RNA effector mole	N/A	no	0.261	0.213	0.301	1e-12
B3N3F7		947	Serrate RNA effector mole	N/A	no	0.198	0.160	0.296	2e-12
Q28WQ8		951	Serrate RNA effector mole	yes	no	0.229	0.185	0.308	2e-12
Q5TUF1		967	Serrate RNA effector mole	yes	no	0.261	0.206	0.316	2e-12
B4H732		951	Serrate RNA effector mole	N/A	no	0.229	0.185	0.308	2e-12
B4QCR6		947	Serrate RNA effector mole	N/A	no	0.218	0.176	0.276	3e-12
B4KLY7		980	Serrate RNA effector mole	N/A	no	0.232	0.181	0.315	3e-12

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

 Score =  917 bits (2371), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 504/697 (72%), Positives = 567/697 (81%), Gaps = 43/697 (6%)

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 SEYISTQKRVFFDAHKDEEWLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQSGTLDLG 312
           SEYI+TQKR FF+ HK+E+WLK+KYHPTNL++VIERRNDLA+KVAKDFLLDLQSGTLDLG
Sbjct: 223 SEYITTQKRAFFNTHKEEDWLKNKYHPTNLLSVIERRNDLAQKVAKDFLLDLQSGTLDLG 282

Query: 313 PSVNASSSNKLGQTSEPNSDDDVDNGGKRRRHGRGPAKETDLLSAAPKAHPISSEPRRIQ 372
           P+V A   NK G+TSEPNS+D+    GKR+RHG G AKE +LLSAAPKA   +S+P+RI 
Sbjct: 283 PAVTAL--NKSGRTSEPNSEDEAAGVGKRKRHGMGGAKENELLSAAPKAPSFTSDPKRIL 340

Query: 373 VDIEQAQALVRKLDSEKGITENILCGSDNDKMNREKSH-GSTGPVIIIRGLTSVKGLEGV 431
            D+EQ QALVRKLDSEK I EN+L GS+ +K  REK H GSTGPV+IIRGLTSVKGLEGV
Sbjct: 341 TDVEQTQALVRKLDSEKKIEENVLQGSETEKSGREKLHSGSTGPVVIIRGLTSVKGLEGV 400

Query: 432 ELLDTLITYLWRIHGVDYYGMVETSEAKGLRHVRAEGKSSDITNNGAEWEKKLDFRWQER 491
           ELLDTL+TYLWR+HG+DYYG VET+EAKGLRHVRAEGK SD    G E E K D  WQER
Sbjct: 401 ELLDTLVTYLWRVHGLDYYGKVETNEAKGLRHVRAEGKVSDA--KGDENESKFDSHWQER 458

Query: 492 LRSQDPLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKH 551
           L+ QDPLE+M AK+KIDAAA +ALDP VRKIRDEKYGWKYGCGAKGCTKLFHAAEFV+KH
Sbjct: 459 LKGQDPLEVMAAKEKIDAAATEALDPHVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVYKH 518

Query: 552 LKLKHPELVIELTSKVREELYFQNYMNDPDAPGGTPVMQQPMPKDRPLRRKLGPDNRLKD 611
           LKLKH ELV ELT+KVREELYFQNYMNDP+APGG P  QQ  P+DRP+RRK   +NRL+D
Sbjct: 519 LKLKHTELVTELTTKVREELYFQNYMNDPNAPGGQPATQQSGPRDRPIRRKPSMENRLRD 578

Query: 612 ERGNRRDRDYRANGSDRYDRSDNAQASDFPSNDDVPEGANRDESMFDTFGGQGIRVAPPF 671
           +RG RR+RD RANG+DR DRS++ Q  D   ND    G N  E  +D FGGQG    PPF
Sbjct: 579 DRGGRRERDGRANGNDRNDRSEDQQRGD---ND----GGNPGEVGYDAFGGQGGVHVPPF 631

Query: 672 PSDIPPPPVLMPVPGAGPLGPFVPAPPEVAMQMIRDQGG--PPFEGGGRHGRPGPQISGP 729
            SDI PPP+LMPVPGAGPLGPFVPAPPEVAMQM RD  G  PPFEG GR         GP
Sbjct: 632 LSDINPPPMLMPVPGAGPLGPFVPAPPEVAMQMFRDPSGPNPPFEGSGR--------GGP 683

Query: 730 GPILLSPAFRQDPRRIRSYQDLDAPEDEVTVMDYRSL 766
            P LLSPAFRQDPRR+RSYQDLDAPE+EVTV+DYRSL
Sbjct: 684 APFLLSPAFRQDPRRLRSYQDLDAPEEEVTVIDYRSL 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\|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\|B3N3F7\|SRRT_DROER Serrate RNA effector molecule homolog OS=Drosophila erecta GN=Ars2 PE=3 SV=1	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\|Q5TUF1\|SRRT_ANOGA Serrate RNA effector molecule homolog OS=Anopheles gambiae GN=Ars2 PE=3 SV=3	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

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

>sp\|B4KLY7\|SRRT_DROMO Serrate RNA effector molecule homolog OS=Drosophila mojavensis 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		766
255561268		823	arsenite-resistance protein, putative [R	0.966	0.899	0.772	0.0
296083972		735	unnamed protein product [Vitis vinifera]	0.950	0.990	0.763	0.0
449452660		755	PREDICTED: serrate RNA effector molecule	0.971	0.985	0.747	0.0
449452662		751	PREDICTED: serrate RNA effector molecule	0.966	0.985	0.745	0.0
225465363		748	PREDICTED: serrate RNA effector molecule	0.874	0.895	0.742	0.0
296085418		724	unnamed protein product [Vitis vinifera]	0.845	0.895	0.731	0.0
359479066		605	PREDICTED: serrate RNA effector molecule	0.781	0.990	0.818	0.0
297822357		718	hypothetical protein ARALYDRAFT_481593 [	0.853	0.910	0.722	0.0
18401322		720	serrate RNA effector molecule [Arabidops	0.853	0.908	0.723	0.0
147804970		1184	hypothetical protein VITISV_035521 [Viti	0.759	0.491	0.752	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 = 1124 bits (2907), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 601/778 (77%), Positives = 665/778 (85%), Gaps = 38/778 (4%)

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 FIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLKDKYHPTNLVAVIERRN 290
           FIQELEDD+LPAEAERRYQEYKSEYISTQKRVFF+AHKDEEWLKDKYHPTNLVAVIERRN
Sbjct: 287 FIQELEDDVLPAEAERRYQEYKSEYISTQKRVFFEAHKDEEWLKDKYHPTNLVAVIERRN 346

Query: 291 DLARKVAKDFLLDLQSGTLDLGPSVNASSSNKLGQTSEPNSDDDVDNGGKRRRHGRGPAK 350
           +LARK AKDFLLDLQSGTLDLGP +N  SSNK GQTS+PNSDD+VD  GKRRRHGR PAK
Sbjct: 347 ELARKAAKDFLLDLQSGTLDLGPGINVLSSNKSGQTSDPNSDDEVDTSGKRRRHGRAPAK 406

Query: 351 ETDLLSAAPKAHPISSEPRRIQVDIEQAQALVRKLDSEKGITENILCGSDNDKMNREKSH 410
           E D+LSAAPKAHP+SSEPRRIQ+D+EQAQALVRKLDSEKGI ENIL GSDN+KMNREK H
Sbjct: 407 ENDILSAAPKAHPVSSEPRRIQIDVEQAQALVRKLDSEKGIEENILGGSDNEKMNREKPH 466

Query: 411 GST-GPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETSEAKGLRHVRAEGK 469
           GS+ GPVIIIRGLTSVKGLEG+ELLDTLITYLWR+HG+DYY MVET+EAKG+RHVRAEGK
Sbjct: 467 GSSSGPVIIIRGLTSVKGLEGIELLDTLITYLWRVHGLDYYRMVETTEAKGVRHVRAEGK 526

Query: 470 SSDITNNGAEWEKKLDFRWQERLRSQDPLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGW 529
           SSD+ N+G EWEKKLD RWQERLRSQDPLE+MTAK+KI+A AV++LDP+VRKIRDEKYGW
Sbjct: 527 SSDVNNSGMEWEKKLDSRWQERLRSQDPLEVMTAKEKIEATAVESLDPYVRKIRDEKYGW 586

Query: 530 KYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPDAPGGTPVM 589
           KYGCGAKGCTKLFHAAEFVHKHLKLKHPELV+ELTSK+RE+LYFQNYMNDPDAPGGTPVM
Sbjct: 587 KYGCGAKGCTKLFHAAEFVHKHLKLKHPELVMELTSKLREDLYFQNYMNDPDAPGGTPVM 646

Query: 590 QQPMPKDRPLRRKLGPDNRLKDERGNRRDRDYRANGSDRYDRSDNAQASDFPSNDDVPEG 649
           QQP+PKD+P RRKLGP+NRLKDERGNRR+ D RANGS+R+DRS+N Q  DF SN+D P+G
Sbjct: 647 QQPLPKDKPQRRKLGPENRLKDERGNRREHDSRANGSERFDRSENPQTGDFQSNNDGPDG 706

Query: 650 ANRDESMFDTFGGQGIRVAPPFPSDIPPPPVLMPVPGAGPLGPFVPAPPEVAMQMIRDQG 709
            N D+ M+D FGGQGI V P FPSDIPPPPVLMPVPGAGPLGPFVPAPPEVAM+M R+QG
Sbjct: 707 GNHDDGMYDNFGGQGIHV-PSFPSDIPPPPVLMPVPGAGPLGPFVPAPPEVAMRMFREQG 765

Query: 710 G-PPFEGGGRHGRPGPQISGPGPILLSPAFRQDPRRIRSYQDLDAPEDEVTVMDYRSL 766
           G PPFE GGR+GRPGPQ+SGP PILLSPAFRQDPRRIRSYQDLDAP+DEVTV+DYRSL
Sbjct: 766 GPPPFESGGRNGRPGPQLSGPAPILLSPAFRQDPRRIRSYQDLDAPDDEVTVIDYRSL 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		766
TAIR\|locus:2059294		720	SE "SERRATE" [Arabidopsis thal	0.754	0.802	0.665	1.3e-211
DICTYBASE\|DDB_G0277375		1068	DDB_G0277375 "RNA recognition	0.150	0.107	0.355	6.4e-28
UNIPROTKB\|B4KLY7		980	Ars2 "Serrate RNA effector mol	0.159	0.124	0.346	4.9e-22
UNIPROTKB\|B4QCR6		947	Ars2 "Serrate RNA effector mol	0.187	0.152	0.319	1.6e-21
UNIPROTKB\|B3N3F7		947	Ars2 "Serrate RNA effector mol	0.259	0.210	0.292	3.9e-21
UNIPROTKB\|B3MJ69		948	Ars2 "Serrate RNA effector mol	0.271	0.219	0.276	1.2e-20
UNIPROTKB\|B4II37		947	Ars2 "Serrate RNA effector mol	0.190	0.154	0.298	1.7e-20
FB\|FBgn0033062		943	Ars2 [Drosophila melanogaster	0.160	0.130	0.343	3e-20
UNIPROTKB\|Q6INH5		844	srrt-b "Serrate RNA effector m	0.142	0.129	0.336	4.6e-20
UNIPROTKB\|B4LIK8		963	Ars2 "Serrate RNA effector mol	0.244	0.194	0.282	6.2e-20

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

 Score = 2012 (713.3 bits), Expect = 1.3e-211, Sum P(2) = 1.3e-211
 Identities = 402/604 (66%), Positives = 454/604 (75%)

Query:   164 YDYTGGYEREMGGRPGYGDERPHGRFAGRSSGGYQSGPSEWDSSRGGYGDASNTGSTQRE 223
             YD+ GGY+REMGGRPGYGDERPHGRF GR    YQ    +W+  RGGYGDASN+G+ QR+
Sbjct:   142 YDHGGGYDREMGGRPGYGDERPHGRFMGR----YQ----DWEGGRGGYGDASNSGNPQRD 193

Query:   224 GLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLKDKYHPTNLV 283
             GLMSYKQFIQELEDDILP+EAERRYQEYKSEYI+TQKR FF+ HK+E+WLK+KYHPTNL+
Sbjct:   194 GLMSYKQFIQELEDDILPSEAERRYQEYKSEYITTQKRAFFNTHKEEDWLKNKYHPTNLL 253

Query:   284 AVIERRNDLARKVAKDFLLDLQSGTLDLGPSVNASSSNKLGQTSEPNSDDDVDNGGKRRR 343
             +VIERRNDLA+KVAKDFLLDLQSGTLDLGP+V A   NK G+TSEPNS+D+    GKR+R
Sbjct:   254 SVIERRNDLAQKVAKDFLLDLQSGTLDLGPAVTAL--NKSGRTSEPNSEDEAAGVGKRKR 311

Query:   344 HGRGPAKETDLLSAAPKAHPISSEPRRIQVDIEQAQALVRKLDSEKGITENILCGSDNDK 403
             HG G AKE +LLSAAPKA   +S+P+RI  D+EQ QALVRKLDSEK I EN+L GS+ +K
Sbjct:   312 HGMGGAKENELLSAAPKAPSFTSDPKRILTDVEQTQALVRKLDSEKKIEENVLQGSETEK 371

Query:   404 MNREKSH-GSTGPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETSEAKGLR 462
               REK H GSTGPV+IIRGLTSVKGLEGVELLDTL+TYLWR+HG+DYYG VET+EAKGLR
Sbjct:   372 SGREKLHSGSTGPVVIIRGLTSVKGLEGVELLDTLVTYLWRVHGLDYYGKVETNEAKGLR 431

Query:   463 HVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQDPLEIMTXXXXXXXXXXXXXXPFVRKI 522
             HVRAEGK SD    G E E K D  WQERL+ QDPLE+M               P VRKI
Sbjct:   432 HVRAEGKVSDA--KGDENESKFDSHWQERLKGQDPLEVMAAKEKIDAAATEALDPHVRKI 489

Query:   523 RDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPDA 582
             RDEKYGWKYGCGAKGCTKLFHAAEFV+KHLKLKH ELV ELT+KVREELYFQNYMNDP+A
Sbjct:   490 RDEKYGWKYGCGAKGCTKLFHAAEFVYKHLKLKHTELVTELTTKVREELYFQNYMNDPNA 549

Query:   583 PGGTPVMQQPMPKDRPLRRKLGPDNRLKDERGNRRDRDYRANGSDRYDRSDNAQASDFPS 642
             PGG P  QQ  P+DRP+RRK   +NRL+D+RG RR+RD RANG+DR DRS++ Q  D   
Sbjct:   550 PGGQPATQQSGPRDRPIRRKPSMENRLRDDRGGRRERDGRANGNDRNDRSEDQQRGD--- 606

Query:   643 NDDVPEGANRDESMFDTFGGQGIRVAXXXXXXXXXXXXXXXXXXXXXXXXFVPAPPEVAM 702
             ND    G N  E  +D FGGQG                            FVPAPPEVAM
Sbjct:   607 ND----GGNPGEVGYDAFGGQGGVHVPPFLSDINPPPMLMPVPGAGPLGPFVPAPPEVAM 662

Query:   703 QMIRDQXXXXXXXXXXXXXXXXQISGPGPILLSPAFRQDPRRIRSYQDLDAPEDEVTVMD 762
             QM RD                    GP P LLSPAFRQDPRR+RSYQDLDAPE+EVTV+D
Sbjct:   663 QMFRDPSGPNPPFEGSGR------GGPAPFLLSPAFRQDPRRLRSYQDLDAPEEEVTVID 716

Query:   763 YRSL 766
             YRSL
Sbjct:   717 YRSL 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\|B4KLY7 Ars2 "Serrate RNA effector molecule homolog" [Drosophila mojavensis (taxid:7230)]	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\|B3N3F7 Ars2 "Serrate RNA effector molecule homolog" [Drosophila erecta (taxid:7220)]	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\|Q6INH5 srrt-b "Serrate RNA effector molecule homolog B" [Xenopus laevis (taxid:8355)]	Back alignment and assigned GO terms

UNIPROTKB\|B4LIK8 Ars2 "Serrate RNA effector molecule homolog" [Drosophila virilis (taxid:7244)]	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	0.7230	0.8537	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

Your Input:
	fgenesh2_kg.4__653__AT2G27100.1	annotation not avaliable (718 aa)
		(Arabidopsis lyrata)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

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		766
pfam12066		110	pfam12066, DUF3546, Domain of unknown function (DU	9e-32
PRK14086		617	PRK14086, dnaA, chromosomal replication initiation	1e-05
PHA03307		1352	PHA03307, PHA03307, transcriptional regulator ICP4	5e-04
PRK12678		672	PRK12678, PRK12678, transcription termination fact	6e-04
PHA03247		3151	PHA03247, PHA03247, large tegument protein UL36; P	7e-04
PHA03247		3151	PHA03247, PHA03247, large tegument protein UL36; P	8e-04
PHA03307		1352	PHA03307, PHA03307, transcriptional regulator ICP4	0.002
TIGR01642		509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.002

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

 Score =  119 bits (299), Expect = 9e-32
 Identities = 43/84 (51%), Positives = 57/84 (67%)

Query: 227 SYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLKDKYHPTNLVAVI 286
           ++KQF++  +DDI PAEAE+RYQEYK+E+   Q + FFD HKDEEW ++KYHP  L    
Sbjct: 1   TFKQFLESQDDDISPAEAEKRYQEYKTEFRRKQLQDFFDQHKDEEWFREKYHPEELAKRR 60

Query: 287 ERRNDLARKVAKDFLLDLQSGTLD 310
           E R +L +     FL  L+SGT D
Sbjct: 61  EERRELRKNRLNVFLELLESGTFD 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		766
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	99.92
KOG2295		648	consensus C2H2 Zn-finger protein [General function	98.99
PF13821		55	DUF4187: Domain of unknown function (DUF4187)	98.05
PF13894		24	zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP	88.94
PF00096		23	zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR0070	88.37
KOG1994		268	consensus Predicted RNA binding protein, contains	81.04
PF12756		100	zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB:	80.78

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

Probab=100.00  E-value=5.7e-86  Score=719.83  Aligned_cols=522  Identities=27%  Similarity=0.273  Sum_probs=446.8

Q ss_pred             CCCCCCCCCCCC---CCcccccchhhhhhccCCCCCCCCCCCCCCCCcCCCCCCCCCCCccchhhhhccCCCCCCCCCCC
Q 004239           43 NNSAPQSSPPPP---PPPARRRERDSRERRDDRDLDRPPPNRRGPDYYDRNRSPPPPMPRERDRDYKRRSTVSPPPPPLP  119 (766)
Q Consensus        43 ~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  119 (766)
                      .-++|-|++|+-   -+++-++.+++|.+++++|+++++..++   |-|+..-|+      +.+.+++..+.++++   +
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   777777666      237888888877776   9


Q ss_pred             CCCCCCCCC--CCCCCCccCccCCCCCCCCCCCCCCCCCCC-CCCCcccCCCCccccCCCCCCCCCCCCCCCCCCCCCCC
Q 004239          120 YRDRRHSPP--PRRSPPYKRSRRDDGGYEPRRGSPRGGFGP-DRRFGYDYTGGYEREMGGRPGYGDERPHGRFAGRSSGG  196 (766)
Q Consensus       120 ~~~rr~SP~--~~~spp~kr~rr~~~g~d~~~g~p~~~~g~-d~~~g~~~~~g~~~~~gg~~~~~~~~~~g~~~~~~~~g  196 (766)
                      ||+++|+++  -++++++++.+++..+|+++.+.+.++++. |.+|+|++..++.++|++..+++....++.++++..  
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  778999999998888999999999999998 999999999999999999999999999998888776  


Q ss_pred             CCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHhhc
Q 004239          197 YQSGPSEWDSSRGGYGDASNTGSTQREGLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLKDK  276 (766)
Q Consensus       197 ~~~~p~~~~~~~~g~~~~~~~~~~~~~~lmsFKqFl~~~eD~IspeEA~~rY~eYK~ef~~kq~r~FF~~HK~EeWFrEK  276 (766)
                            | ..+.+||.++..++..+....|++|+     +|++++..+...|++| .+|. .|..+||+.||...||..+
T Consensus       173 ------D-e~~~~gy~De~~~gt~e~e~kkssk~-----ddd~d~s~~ee~e~e~-se~~-tqksa~~n~hke~sll~rn  238 (648)
T KOG2295|consen  173 ------D-EGLDAGYKDEFQLGTAEDEIKKSSKP-----DDDTDDSILEENEPEL-SEWG-TQKSANDNTHKECSLLVRN  238 (648)
T ss_pred             ------h-ccccccccccccCCCcchhhhcccCc-----ccccCcccccccchhh-hhhh-hhhhhhhhhhHHHHHHHhc
Confidence                  3 45678999999889999999999998     9999999999999999 7887 8999999999999999999


Q ss_pred             cCCcchHHHHHHH-------------HHHHHHHHHHHHHHhhcCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCcccc
Q 004239          277 YHPTNLVAVIERR-------------NDLARKVAKDFLLDLQSGTLDLGPSVNASSSNKLGQTSEPNSDDDVDNGGKRRR  343 (766)
Q Consensus       277 Y~P~~l~~~~erR-------------~E~~~~aak~F~~dLesG~fD~~pgv~~~~sdksG~~sdpnse~e~~~~~Kr~R  343 (766)
                      |+|.++.+.++..             +.++...+..|+-.+.++++++++.+.+.  ++.+-++.++++.+...+.+|.|
T Consensus       239 i~Pnis~aeIe~~ck~i~~~lrfals~~~aek~~~r~lwv~fk~~~ni~~a~~aL--n~irl~s~~~se~en~~i~rrvr  316 (648)
T KOG2295|consen  239 ILPNISVAEIENLCKGIPGFLRFALSTINAEKNFERRLWVTFKRGTNIKEACWAL--NGIRLRSNFLSESENPDITRRVR  316 (648)
T ss_pred             cCCcccHHHHHHHhccCchheeeeccCchHHHHHHHHhhHhhccccchHHHHHHh--hhccccccccccccccCccceec
Confidence            9999988777643             33667778888888999999998766655  34444577888888777888888


Q ss_pred             cCCCCCCcccccc-cCCCCCCCCCChhHHHHHHHHHHHHHHHHhhhccccccccCCCCcccccccccC-CCCCCceeecc
Q 004239          344 HGRGPAKETDLLS-AAPKAHPISSEPRRIQVDIEQAQALVRKLDSEKGITENILCGSDNDKMNREKSH-GSTGPVIIIRG  421 (766)
Q Consensus       344 ~Gwv~~kesD~~s-~aPkahPi~S~p~RI~~DLeqAr~LV~kLDaEkGIe~n~L~~~d~~~~d~dks~-~s~gP~~i~rg  421 (766)
                      ++-+-.+...+++ +|+|.+.+.+.+-||..+.+|+..|+.+|++++-|..||+.......+..++.+ ++.+|++++++
T Consensus       317 ~~~Gia~~keiasn~a~k~~~lldk~irl~~~a~~t~al~tkl~s~n~i~kni~d~l~te~S~eE~e~~gssg~e~p~eg  396 (648)
T KOG2295|consen  317 PINGIAKHKEIASNAAQKLKNLLDKLIRLIDRASQTQALVTKLSSPNPIAKNIEDRLKTEASMEEDELLGSSGPEVPIEG  396 (648)
T ss_pred             cCCchhhHHHHHHHHHHhhhHHHhhhHHHhhcccccccchhhccCCCHHHHHHHHHhhhhcchhhhhhcCCCCCcCcccc
Confidence            8877666666555 799999999999999999999999999999999998888665443333334444 47889999999


Q ss_pred             cccccCcchhhHHHHHHHHHHHHhhcccccccccc------cccccccccCCCCCCCcCCchhhHHHhhHHHHHHHhhcC
Q 004239          422 LTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETS------EAKGLRHVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQ  495 (766)
Q Consensus       422 ~~~v~~le~ik~LDllI~YLRrVHsvDYY~~~E~d------ercgl~HvR~~~k~~~~~s~~~eW~KklD~~~q~rL~~~  495 (766)
                      ++.++++..+++||+||+|||+||++|||+.+||+      ++||++|||+++..+.  .+..+|+++|++.|+.+|...
T Consensus       397 ~~~er~d~~lk~LDll~~YLr~VhslDfyn~~ey~~e~~mpnrcgl~hvR~~~~vs~--~ev~e~es~f~s~le~~l~~~  474 (648)
T KOG2295|consen  397 LTSERDDIRLKLLDLLAEYLRIVHSLDFYNSKEYESEDAMPNRCGLIHVRGKGFVSS--KEVGEEESIFLSDLENNLACL  474 (648)
T ss_pred             CccccchhHHHHHHHHHHHHHHHHhcccccccccchhhhcccccCceeecccCCCCc--ccchhHHHHHHHHhhhccccc
Confidence            99999999999999999999999999999999987      4899999999854432  247789999999999999988


Q ss_pred             ChhhHhhhhhhHHHHHHHhhhhHHHhhhhcccCcccccCCCCCcccccchhHHHHHHhhhChHHHHHHHhhHHHHHHHhh
Q 004239          496 DPLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQN  575 (766)
Q Consensus       496 dple~l~~kekid~el~e~ve~fVkk~~dEk~g~K~rC~l~gCtKLFKgpEFVrKHI~nKH~E~Veev~~kv~E~~yFNN  575 (766)
                      ++++.+-++.++++..+++|++||.+|++|+++|||+|+|++|+|||||||||+|||++||.|||+++++   |++||||
T Consensus       475 ~~lee~eakkkg~k~~e~eve~~v~s~t~e~~kdKy~C~lsgc~KlF~gpEFvrKHi~~KH~d~leeirk---ea~ffnn  551 (648)
T KOG2295|consen  475 LELEEEEAKKKGAKDVEDEVENFVDSNTMELDKDKYLCPLSGCAKLFKGPEFVRKHINKKHKDKLEEIRK---EAIFFNN  551 (648)
T ss_pred             ccchHHHHHHhcccCHHHHHHHHHHHHHHHhhcccccCCCcchHhhccCHHHHHHHHHHHHHHHHHHHHH---HHHHHHh
Confidence            8888888888888889999999999999999999999999999999999999999999999999999997   8999999


Q ss_pred             hccCCCCCCCCCCCCCCCCCCcccc
Q 004239          576 YMNDPDAPGGTPVMQQPMPKDRPLR  600 (766)
Q Consensus       576 Yl~DP~RP~~~p~~~q~~~~~~~~~  600 (766)
                      ||+|||||..+++ +++.+.+..+.
T Consensus       552 Yl~Dp~rp~~pe~-~~q~prd~qIl  575 (648)
T KOG2295|consen  552 YLLDPCRPMDPEV-VSQSPRDLQIL  575 (648)
T ss_pred             hccCccccCCCcc-ccCCCCccccc
Confidence            9999999999988 66666666553

>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

>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]	Back alignment and domain information

>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A	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		766
3ax1_A		358	Molecular Insights Into Mirna Processing By Arabido		1e-153

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

Back alignment and structure

Iteration: 1

Score = 539 bits (1389), Expect = e-153, Method: Compositional matrix adjust. Identities = 264/355 (74%), Positives = 296/355 (83%), Gaps = 5/355 (1%) Query: 224 GLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLKDKYHPTNLV 283 GLMSYKQFIQELEDDILP+EAERRYQEYKSEYI+TQKR FF+ HK+E+WLK+KYHPTNL+ Sbjct: 1 GLMSYKQFIQELEDDILPSEAERRYQEYKSEYITTQKRAFFNTHKEEDWLKNKYHPTNLL 60 Query: 284 AVIERRNDLARKVAKDFLLDLQSGTLDLGPSVNASSSNKLGQTSEPNSDDDVDNGGKRRR 343 +VIERRNDLA+KVAKDFLLDLQSGTLDLGP+V A NK G+TSEPNS+D+ GKR+R Sbjct: 61 SVIERRNDLAQKVAKDFLLDLQSGTLDLGPAVTA--LNKSGRTSEPNSEDEAAGVGKRKR 118 Query: 344 HGRGPAKETDLLSAAPKAHPISSEPRRIQVDIEQAQALVRKLDSEKGITENILCGSDNDK 403 HG G AKE +LLSAAPKA +S+P+RI D+EQ QALVRKLDSEK I EN+L GS+ +K Sbjct: 119 HGMGGAKENELLSAAPKAPSFTSDPKRILTDVEQTQALVRKLDSEKKIEENVLQGSETEK 178 Query: 404 MNREKSH-GSTGPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETSEAKGLR 462 REK H GSTGPV+IIRGLTSVKGLEGVELLDTL+TYLWR+HG+DYYG VET+EAKGLR Sbjct: 179 SGREKLHSGSTGPVVIIRGLTSVKGLEGVELLDTLVTYLWRVHGLDYYGKVETNEAKGLR 238 Query: 463 HVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQDPLEIMTXXXXXXXXXXXXXXPFVRKI 522 HVRAEGK SD G E E K D WQERL+ QDPLE+M P VRKI Sbjct: 239 HVRAEGKVSDA--KGDENESKFDSHWQERLKGQDPLEVMAAKEKIDAAATEALDPHVRKI 296 Query: 523 RDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYM 577 RDEKYGWKYGCGAKGCTKLFHAAEFV+KHLKLKH ELV ELT+KVREELYFQNY+ Sbjct: 297 RDEKYGWKYGCGAKGCTKLFHAAEFVYKHLKLKHTELVTELTTKVREELYFQNYL 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		766
3ax1_A		358	Serrate RNA effector molecule; miRNA processing, p	1e-117
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04

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

 Score =  357 bits (915), Expect = e-117
 Identities = 275/361 (76%), Positives = 309/361 (85%), Gaps = 5/361 (1%)

Query: 224 GLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLKDKYHPTNLV 283
           GLMSYKQFIQELEDDILP+EAERRYQEYKSEYI+TQKR FF+ HK+E+WLK+KYHPTNL+
Sbjct: 1   GLMSYKQFIQELEDDILPSEAERRYQEYKSEYITTQKRAFFNTHKEEDWLKNKYHPTNLL 60

Query: 284 AVIERRNDLARKVAKDFLLDLQSGTLDLGPSVNASSSNKLGQTSEPNSDDDVDNGGKRRR 343
           +VIERRNDLA+KVAKDFLLDLQSGTLDLGP+V A   NK G+TSEPNS+D+    GKR+R
Sbjct: 61  SVIERRNDLAQKVAKDFLLDLQSGTLDLGPAVTAL--NKSGRTSEPNSEDEAAGVGKRKR 118

Query: 344 HGRGPAKETDLLSAAPKAHPISSEPRRIQVDIEQAQALVRKLDSEKGITENILCGSDNDK 403
           HG G AKE +LLSAAPKA   +S+P+RI  D+EQ QALVRKLDSEK I EN+L GS+ +K
Sbjct: 119 HGMGGAKENELLSAAPKAPSFTSDPKRILTDVEQTQALVRKLDSEKKIEENVLQGSETEK 178

Query: 404 MNREKSH-GSTGPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETSEAKGLR 462
             REK H GSTGPV+IIRGLTSVKGLEGVELLDTL+TYLWR+HG+DYYG VET+EAKGLR
Sbjct: 179 SGREKLHSGSTGPVVIIRGLTSVKGLEGVELLDTLVTYLWRVHGLDYYGKVETNEAKGLR 238

Query: 463 HVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQDPLEIMTAKDKIDAAAVDALDPFVRKI 522
           HVRAEGK SD    G E E K D  WQERL+ QDPLE+M AK+KIDAAA +ALDP VRKI
Sbjct: 239 HVRAEGKVSD--AKGDENESKFDSHWQERLKGQDPLEVMAAKEKIDAAATEALDPHVRKI 296

Query: 523 RDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPDA 582
           RDEKYGWKYGCGAKGCTKLFHAAEFV+KHLKLKH ELV ELT+KVREELYFQNY+     
Sbjct: 297 RDEKYGWKYGCGAKGCTKLFHAAEFVYKHLKLKHTELVTELTTKVREELYFQNYLEHHHH 356

Query: 583 P 583
            
Sbjct: 357 H 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

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		766
3ax1_A		358	Serrate RNA effector molecule; miRNA processing, p	100.0
2adr_A		60	ADR1; transcription regulation, zinc finger,; NMR	85.08
2lv2_A		85	Insulinoma-associated protein 1; structural genomi	84.01
1x5w_A		70	Zinc finger protein 64, isoforms 1; ZNF338, nuclea	83.36
1bbo_A		57	Human enhancer-binding protein MBP-1; DNA-binding	82.94
2d9h_A		78	Zinc finger protein 692; ZF-C2H2 domain, structura	82.9
2gqj_A		98	Zinc finger protein KIAA1196; ZF-C2H2 like domain,	80.67

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

Probab=100.00  E-value=3.2e-97  Score=790.19  Aligned_cols=353  Identities=78%  Similarity=1.202  Sum_probs=285.7

Q ss_pred             CCCCHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHhhccCCcchHHHHHHHHHHHHHHHHHHHHH
Q 004239          224 GLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLKDKYHPTNLVAVIERRNDLARKVAKDFLLD  303 (766)
Q Consensus       224 ~lmsFKqFl~~~eD~IspeEA~~rY~eYK~ef~~kq~r~FF~~HK~EeWFrEKY~P~~l~~~~erR~E~~~~aak~F~~d  303 (766)
                      +||||||||++|+|+|||+||+++|++||.+|.++|++.||++||+|+||+|||||+++++++++|++++++.++.|+++
T Consensus         1 glmsFKqFl~~~~D~isp~eA~~~Y~eYk~e~~~~q~~~FF~~HK~e~WfreKY~P~~l~~~~~~R~e~ak~~a~~F~~~   80 (358)
T 3ax1_A            1 GLMSYKQFIQELEDDILPSEAERRYQEYKSEYITTQKRAFFNTHKEEDWLKNKYHPTNLLSVIERRNDLAQKVAKDFLLD   80 (358)
T ss_dssp             CCCCHHHHGGGTTTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcCHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHhcCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCcccccCCCCCCcccccccCCCCCCCCCChhHHHHHHHHHHHHHH
Q 004239          304 LQSGTLDLGPSVNASSSNKLGQTSEPNSDDDVDNGGKRRRHGRGPAKETDLLSAAPKAHPISSEPRRIQVDIEQAQALVR  383 (766)
Q Consensus       304 LesG~fD~~pgv~~~~sdksG~~sdpnse~e~~~~~Kr~R~Gwv~~kesD~~s~aPkahPi~S~p~RI~~DLeqAr~LV~  383 (766)
                      |++|+||+++++++.  +++|.++++++++.++.++|++|+||++.+++|++++||++||+||+|+||++||+||++||+
T Consensus        81 L~~G~ld~~~~~~~~--~~~~~~~~~~~~d~~~~~~k~~~~g~~~~~~~d~~~~ap~~~P~~S~p~RI~~Dle~a~~Lv~  158 (358)
T 3ax1_A           81 LQSGTLDLGPAVTAL--NKSGRTSEPNSEDEAAGVGKRKRHGMGGAKENELLSAAPKAPSFTSDPKRILTDVEQTQALVR  158 (358)
T ss_dssp             HHTTCCCCCSBSSCC--C-----------------------------------CCCBCCGGGSCHHHHHHHHHHHHHHHH
T ss_pred             HHcCCCCCCCccccc--cccCCCCCCChhhhhhccccccccCCCcccccchhhcccCCCCCCCcHHHHHHHHHHHHHHHH
Confidence            999999998877774  677878899999888888899999999999999999999999999999999999999999999


Q ss_pred             HHhhhccccccccCCCCcccccccccCC-CCCCceeecccccccCcchhhHHHHHHHHHHHHhhcccccccccccccccc
Q 004239          384 KLDSEKGITENILCGSDNDKMNREKSHG-STGPVIIIRGLTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETSEAKGLR  462 (766)
Q Consensus       384 kLDaEkGIe~n~L~~~d~~~~d~dks~~-s~gP~~i~rg~~~v~~le~ik~LDllI~YLRrVHsvDYY~~~E~dercgl~  462 (766)
                      +||+|+||++|+|..+++...+.++++. ++||++|++++.++++++.+++||++|+|||+||||||||++||+++||++
T Consensus       159 kLD~e~gie~n~l~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~l~~~~~LD~~i~YLRrVH~~dYY~~~E~~~~~g~~  238 (358)
T 3ax1_A          159 KLDSEKKIEENVLQGSETEKSGREKLHSGSTGPVVIIRGLTSVKGLEGVELLDTLVTYLWRVHGLDYYGKVETNEAKGLR  238 (358)
T ss_dssp             HHHHHHTCCCCTTC---------------CCCCCEEECCSSCCEEECSHHHHHHHHHHHHHHHCEEGGGTEECTTCCSBC
T ss_pred             HHHHhhCCcccccccccccccccccccccCCCcchhhccccchhhhhhHHHHHHHHHHHHHHHcccccceEeecCccccC
Confidence            9999999999999998776677777775 789999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCCCcCCchhhHHHhhHHHHHHHhhcCChhhHhhhhhhHHHHHHHhhhhHHHhhhhcccCcccccCCCCCcccc
Q 004239          463 HVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQDPLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLF  542 (766)
Q Consensus       463 HvR~~~k~~~~~s~~~eW~KklD~~~q~rL~~~dple~l~~kekid~el~e~ve~fVkk~~dEk~g~K~rC~l~gCtKLF  542 (766)
                      |||++.++.+  .+..+|+++|+++|+.+|+..+|+++++++++|+++++++|++||++++||+|||||+|.+++|+|||
T Consensus       239 HvR~~~~~~~--~~~~~we~~ld~~w~~~l~~~dp~~~~lg~k~ie~~~~e~l~~~v~k~~dE~~gwK~~C~~~~C~KLF  316 (358)
T 3ax1_A          239 HVRAEGKVSD--AKGDENESKFDSHWQERLKGQDPLEVMAAKEKIDAAATEALDPHVRKIRDEKYGWKYGCGAKGCTKLF  316 (358)
T ss_dssp             CBC------------CHHHHHHHHHHHHHHHSCCHHHHHHCHHHHHHHHHHHHGGGEEEEECSSSSEEEEECSSSCCCEE
T ss_pred             eecCCCCCCC--CchhhHHHHHHHHHHHHHcccChHHHHhcCccHHHHHHHHHHHHHHHHhhcccccccCCCCCCcCccc
Confidence            9999877543  36678999999999999999999998889999999999999999999999999999999999999999


Q ss_pred             cchhHHHHHHhhhChHHHHHHHhhHHHHHHHhhhccCC
Q 004239          543 HAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDP  580 (766)
Q Consensus       543 KgpEFVrKHI~nKH~E~Veev~~kv~E~~yFNNYl~DP  580 (766)
                      ||+|||+|||+|||+|+|++++++|+|.+||+|||.--
T Consensus       317 k~~eFV~KHi~~KH~e~v~~~~~~v~~~~~~~~~~~~~  354 (358)
T 3ax1_A          317 HAAEFVYKHLKLKHTELVTELTTKVREELYFQNYLEHH  354 (358)
T ss_dssp             SSHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            99999999999999999999999999999999999643

PyMOL of 3ax1

>2adr_A ADR1; transcription regulation, zinc finger,; NMR {Saccharomyces cerevisiae} SCOP: 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

>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

>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

>2gqj_A Zinc finger protein KIAA1196; ZF-C2H2 like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

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		766
d2glia5		29	Five-finger GLI1 {Human (Homo sapiens) [TaxId: 960	95.14
d1ubdc1		28	Ying-yang 1 (yy1, zinc finger domain) {Human (Homo	90.67
d2glia3		30	Five-finger GLI1 {Human (Homo sapiens) [TaxId: 960	86.22
d2ct1a2		36	Transcriptional repressor CTCF {Human (Homo sapien	85.09
d1ubdc4		28	Ying-yang 1 (yy1, zinc finger domain) {Human (Homo	84.91
d1zfda_		32	SWI5 zinc-finger domains {Baker's yeast (Saccharom	84.62
d2glia1		32	Five-finger GLI1 {Human (Homo sapiens) [TaxId: 960	84.49
d2dlka2		36	Zinc finger protein 692, ZNF692 {Human (Homo sapie	83.54
d2dlka1		30	Zinc finger protein 692, ZNF692 {Human (Homo sapie	82.63
d1sp2a_		31	Transcription factor sp1 {Human (Homo sapiens) [Ta	82.36
d1ubdc3		30	Ying-yang 1 (yy1, zinc finger domain) {Human (Homo	82.06
d1ncsa_		47	SWI5 zinc-finger domains {Baker's yeast (Saccharom	81.91
d1a1ia1		29	ZIF268 {Mouse (Mus musculus) [TaxId: 10090]}	81.2

>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=95.14  E-value=0.0043  Score=43.01  Aligned_cols=27  Identities=37%  Similarity=0.678  Sum_probs=25.6

Q ss_pred             cccCCCCCcccccchhHHHHHHhhhCh
Q 004239          531 YGCGAKGCTKLFHAAEFVHKHLKLKHP  557 (766)
Q Consensus       531 ~rC~l~gCtKLFKgpEFVrKHI~nKH~  557 (766)
                      |-|.+.+|+|-+-.|.=++|||++.|+
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

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

>d2dlka1 g.37.1.1 (A:8-37) Zinc finger protein 692, ZNF692 {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

>d1ncsa_ g.37.1.1 (A:) SWI5 zinc-finger domains {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

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