Citrus Sinensis ID: 004566

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-----

MMFHAQSSSRNHCSLLAVLSRKFVDDKQKQAATDDKPKYPFPEIASSGRLEVHLLSSPSTDEFRRLLESSEPNIVYLQGEKINDSEEIGSLVWGDVDLSTPEALCGLFGSTLPTTVYLEIPNGENFAEALHSRGVPYVIYWKHSFSCYAACHFLQALLSVVQSSCSHTWDAFQLAHASFRLYCVRNNIVMASNSQKGSSKLGPHLLGDPPKIDIALSEMDVQGEENSPENLPAIKIYDDDVTMRFLVCGVPCTLDTSLLGPLEDGLNALLNIEIRGSKLHNRTSAPPPPLQAGAFSRGVVTMRCDLSTCSSAHISLLVSGSAQTCFNDQLLENHIKNELIENSQLVHALPNSGDNRLPPSEPRKSASIACGASVFEVSMKVSTWASQVLRQLAPDVSYRSLVMLGIASIQGLSVASFEKDDAERLLFFCTRQGKADHTENSVLTRPPSWLTSPAPSRKRSEPCRESKGVESENVCNVRPKLNSAAMRPIPHTRHYKMLPFSGFSEIERYDGDQVKANLPVAPLKHSSAGPTPVTHRKSLSSSYQAQQIISLNPLPLKKHGCGRAPIQVCSEEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEYELAHDDVDGECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVTNFKKKSQKTSNGY

ccccccccccccEEEEEEEccccccccccccccccccccccccccccccEEEEEcccccHHHHHHHHHHccccEEEEcccccccccccccccccccccccHHHHHHHHccccccEEEEEccccHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHcEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccEEEEEEcccccccccccccHHHHHHHHHHHHHccccccccccccccccccccccccEEEEEEccccccccEEEEEEEccccccccHHHHHHHHHHHHHHcccEEEEcccccccccccccccccccccccccEEEEEEEEHHHHHHHHHHHccccccHHHHHHHHccccccccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccccccccccccHHHHHcccccHHHHHHHHHHHcccEEcccccccccHHHcccccccccccccccHHHHHHHHHHHHHHHHHcccccccccEEccccccccccEEcccccccccccccccccccccccccccccEEEEcccccccccccccccccccc

ccccccccccccEEEEEEEcccccccccccccccccccccccHHcccccEEEEEEccccHHHHHHHHHHHcccEEEEEccccccccccccEEEcccccccHHHHHHHcccccccEEEEEcccHHHHHHHHHHccccEEEEEcccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHEEEEEEccccccccccccccccccccHcccccccccccccccHHHccccccccccEEEEccccEEEEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHccccEEEEEEEEccccccEEEEEEEccHHHHccHHHHHHHHHHHHHHHcccEEEccccccccccccccccccEEcccccEEEEEEEcHHHHHHHHHHHcccccHHHHHHHEEEEEcccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccEEcccccccccccccccccccccHHHHHHHHHHHHHHcccccccccccHHHccHHHHccHHHcHHHHHHHHHHccccEccccccccccHcHHccccccccccccccHHHHHHHHHHHHHHHHHcccccccEEEEEEccccccEEEcccccccHccccccccccccHHHcccccccEEEcccccccccccccccccccc

mmfhaqsssrnhCSLLAVLSRKfvddkqkqaatddkpkypfpeiassgrlevhllsspstDEFRRLLEssepnivylqgekindseeigslvwgdvdlstpealcglfgstlpttvyleipngenFAEALHSRGVPYVIYWKHSFSCYAACHFLQALLSVVQSSCSHTWDAFQLAHASFRLYCVRNNivmasnsqkgssklgphllgdppkidialsemdvqgeenspenlpaikiydddvtMRFLVCGvpctldtsllgpleDGLNALLNIEIRgsklhnrtsapppplqagafsrgVVTMrcdlstcssAHISLLVSgsaqtcfnDQLLENHIKneliensqlvhalpnsgdnrlppseprksasiacGASVFEVSMKVSTWASQVLRQLAPDVSYRSLVMLGIASIQglsvasfeKDDAERLLFFCTrqgkadhtensvltrppswltspapsrkrsepcreskgvesenvcnvrpklnsaamrpiphtrhykmlpfsgfseierydgdqvkanlpvaplkhssagptpvthrkslsssyqaqqiislnplplkkhgcgrapiqvcseEEFLRDVMQFLILRghtrlvpqgglaefpDAILNAKRLDLFNLYREVVsrggfhvgnginwKGQVFSKMrnhtltnrmtgvgnTLKRHYETYLLEYELahddvdgeccllchssaagdwvncgicgewahfgcdrrqglgafkdyaktdgleyvcpqcsvtnfkkksqktsngy

mmfhaqsssrnhcSLLAVLSRKFVDDKQKqaatddkpkypfpeiassgrlevhlLSSPSTDEFRRLLESSEPNIVYLQGEKINDSEEIGSLVWGDVDLSTPEALCGLFGSTLPTTVYLEIPNGENFAEALHSRGVPYVIYWKHSFSCYAACHFLQALLSVVQSSCSHTWDAFQLAHASFRLYCVRNNIVMASNSQKGSSKLGPHLLGDPPKIDIALSEMDVQGEENSPENLPAIKIYDDDVTMRFLVCGVPCTLDTSLLGPLEDGLNALLNIEIRGSKLHNRTSAPPPPLQAGAFSRGVVTMRCDLSTCSSAHISLLVSGSAQTCFNDQLLENHIKNELIENSQLVHALPNSGDNRLPPSEPRKSASIACGASVFEVSMKVSTWASQVLRQLAPDVSYRSLVMLGIASIQGLSVASFEKDDAERLLFFCTrqgkadhtensvltrppswltspapsrkrsepcreskgvesenvcnvrpklnsaamrpiphtrhYKMLPFSGFSEIERYDGDQVKANLPVAPLKHSSAGPTPVTHRKSLSSSYQAQQIISLNPLPLKKHGCGRAPIQVCSEEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRggfhvgnginwKGQVFSKMRNhtltnrmtgvgntLKRHYETYLLEYELAHDDVDGECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLeyvcpqcsvtnfkkksqktsngy

MMFHAQSSSRNHCSLLAVLSRKFVddkqkqaatddkpkYPFPEIASSGRLEVHLLSSPSTDEFRRLLESSEPNIVYLQGEKINDSEEIGSLVWGDVDLSTPEALCGLFGSTLPTTVYLEIPNGENFAEALHSRGVPYVIYWKHSFSCYAACHFLQALLSVVQSSCSHTWDAFQLAHASFRLYCVRNNIVMASNSQKGSSKLGPHLLGDPPKIDIALSEMDVQGEENSPENLPAIKIYDDDVTMRFLVCGVPCTLDTSLLGPLEDGLNALLNIEIRGSKLHNRTSAPPPPLQAGAFSRGVVTMRCDLSTCSSAHISLLVSGSAQTCFNDQLLENHIKNELIENSQLVHALPNSGDNRLPPSEPRKSASIACGASVFEVSMKVSTWASQVLRQLAPDVSYRSLVMLGIASIQGLSVASFEKDDAERLLFFCTRQGKADHTENSVLTRPPSWLTSPAPSRKRSEPCRESKGVESENVCNVRPKLNSAAMRPIPHTRHYKMLPFSGFSEIERYDGDQVKANLPVAPLKHSSAGPTPVTHRKSLSSSYQAQQIISLNPLPLKKHGCGRAPIQVCSEEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEYELAHDDVDGECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVTNFKKKSQKTSNGY

**************LLAVLS****************************************************NIVYLQGEKINDSEEIGSLVWGDVDLSTPEALCGLFGSTLPTTVYLEIPNGENFAEALHSRGVPYVIYWKHSFSCYAACHFLQALLSVVQSSCSHTWDAFQLAHASFRLYCVRNNIVM*****************************************PAIKIYDDDVTMRFLVCGVPCTLDTSLLGPLEDGLNALLNIEIRG****************GAFSRGVVTMRCDLSTCSSAHISLLVSGSAQTCFNDQLLENHIKNELIENSQLV*********************IACGASVFEVSMKVSTWASQVLRQLAPDVSYRSLVMLGIASIQGLSVASFEKDDAERLLFFCTRQ***********************************************************TRHYKMLPFSGFSEIERY*************************************QIISLNPLPLKKHGCGRAPIQVCSEEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEYELAHDDVDGECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVTN************

************CSLLAVLS**********************EIASSGRLEVHLLSSPSTDEFRRLLESSEPNIVYLQGE*******I**LVWGDVDLSTPEALCGLFGSTLPTTVYLEIPNGENFAEALHSRGVPYVIYWKHSFSCYAACHFLQALLSVVQSSCSHTWDAFQLAHASFRLYCVRNNIV*********SKLGPHLLGDPPKI********************AIKIYDDDVTMRFLVCGVPCTLDTSLLGPLEDGLNALLNIEIRGSKLHNRTSA*PPPLQAGAFSRGVVTMRCDLSTCSSAHISLLVSGSAQTCFNDQLLENHIKNELIENSQ***********************IACGASVFEVSMKVSTWASQVLRQLAPDVSYRSLVMLGIASIQGLSVASFEKDDAERLLFFCTRQGKADH**********************************************************************************************************************************VCSEEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEYELAHDDVDGECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCS***************

**********NHCSLLAVLSRKFV***********KPKYPFPEIASSGRLEVHLLSSPSTDEFRRLLESSEPNIVYLQGEKINDSEEIGSLVWGDVDLSTPEALCGLFGSTLPTTVYLEIPNGENFAEALHSRGVPYVIYWKHSFSCYAACHFLQALLSVVQSSCSHTWDAFQLAHASFRLYCVRNNIVMASNSQKGSSKLGPHLLGDPPKIDIALSEMDVQGEENSPENLPAIKIYDDDVTMRFLVCGVPCTLDTSLLGPLEDGLNALLNIEIRGSKLHNRTSAPPPPLQAGAFSRGVVTMRCDLSTCSSAHISLLVSGSAQTCFNDQLLENHIKNELIENSQLVHALPNS***************IACGASVFEVSMKVSTWASQVLRQLAPDVSYRSLVMLGIASIQGLSVASFEKDDAERLLFFCTRQGKADHTENSVLTRPPS*************************VCNVRPKLNSAAMRPIPHTRHYKMLPFSGFSEIERYDGDQVKANLPVAPLKH*******************AQQIISLNPLPLKKHGCGRAPIQVCSEEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEYELAHDDVDGECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVTNF***********

**********NHCSLLAVLSRKF*************PKYPFPEIASSGRLEVHLLSSPSTDEFRRLLESSEPNIVYLQGEKINDSEEIGSLVWGDVDLSTPEALCGLFGSTLPTTVYLEIPNGENFAEALHSRGVPYVIYWKHSFSCYAACHFLQALLSVVQSSCSHTWDAFQLAHASFRLYCVRNNIVMAS*****SSKLGPHLLGDPPKIDIALSEMD******SPENLPAIKIYDDDVTMRFLVCGVPCTLDTSLLGPLEDGLNALLNIEIRGSKLHNRTSAPPPPLQAGAFSRGVVTMRCDLSTCSSAHISLLVSGSAQTCFNDQLLENHIKNELIENSQLVHALPN*********EPRKSASIACGASVFEVSMKVSTWASQVLRQLAPDVSYRSLVMLGIASIQGLSVASFEKDDAERLLFFCTRQGKADHTENSVLTRPPSWLT*********************************************MLP*S********************************************QQIISLNPLPLKKHGCGRAPIQVCSEEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEYELAHDDVDGECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKTDGLEYVCPQCSVTNF***********

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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		745	2.2.26 [Sep-21-2011]
Q6NQ79		747	AT-rich interactive domai	yes	no	0.993	0.990	0.714	0.0

>sp\|Q6NQ79\|ARID4_ARATH AT-rich interactive domain-containing protein 4 OS=Arabidopsis thaliana GN=ARID4 PE=2 SV=1	Back alignment and function desciption

 Score = 1090 bits (2819), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 532/745 (71%), Positives = 622/745 (83%), Gaps = 5/745 (0%)

Query: 2   MFHAQSSSRNHCSLLAVLS-RKFVDDKQKQAATDDKPKYPFPEIASSGRLEVHLLSSPST 60
           MFH Q  SRN C+++AV+S  +  D   +   T  +PKYPFP+++SSGRL+  +L++P+ 
Sbjct: 1   MFHGQGFSRNRCNVVAVVSGAELCDTNNQIDGTSHQPKYPFPDLSSSGRLKFQVLNNPTP 60

Query: 61  DEFRRLLESSEPNIVYLQGEKINDSEEIGSLVWGDVDLSTPEALCGLFGSTLPTTVYLEI 120
           +EF+  + SS  + VYLQGE   DS+E+G LV G  D STP+AL  LFGSTLPTTVYLE+
Sbjct: 61  EEFQVAVNSSATDFVYLQGEHSGDSDEVGPLVLGYTDFSTPDALVTLFGSTLPTTVYLEL 120

Query: 121 PNGENFAEALHSRGVPYVIYWKHSFSCYAACHFLQALLSVVQSSCSHTWDAFQLAHASFR 180
           PNGE  A+AL+S+GV YVIYWK+ FS YAACHF  +L SV+QSSCS TWD F +A ASFR
Sbjct: 121 PNGEELAQALYSKGVQYVIYWKNVFSKYAACHFRHSLFSVIQSSCSDTWDVFHVAEASFR 180

Query: 181 LYCVRNNIVMASNS-QKGSSKLGPHLLGDPPKIDIALSEMDVQGEENSPENLPAIKIYDD 239
           LYC  +N V+ SNS +K + ++GP LLG+PPKID+   E D   EENS E+LP+IKIYD+
Sbjct: 181 LYCTSDNAVLPSNSNRKMNYEMGPCLLGEPPKIDVVSPEADELEEENSLESLPSIKIYDE 240

Query: 240 DVTMRFLVCGVPCTLDTSLLGPLEDGLNALLNIEIRGSKLHNRTSAPPPPLQAGAFSRGV 299
           DVT+RFL+CG PCT+DT LLG L DGLNALL IE+RGSKLHNR+SAP PPLQAG F+RGV
Sbjct: 241 DVTVRFLLCGPPCTVDTFLLGSLMDGLNALLRIEMRGSKLHNRSSAPAPPLQAGTFTRGV 300

Query: 300 VTMRCDLSTCSSAHISLLVSGSAQTCFNDQLLENHIKNELIENSQLVHALPNSGDNRLPP 359
           VTMRCD+STCSSAHIS+LVSG+AQTCF+DQLLENHIK+E++E  QLVH++ NS + +   
Sbjct: 301 VTMRCDVSTCSSAHISMLVSGNAQTCFSDQLLENHIKHEVVEKIQLVHSVVNSEETKRGF 360

Query: 360 SEPRKSASIACGASVFEVSMKVSTWASQVLRQLAPDVSYRSLVMLGIASIQGLSVASFEK 419
           SEPR+SASIACGASV EVSM+V TWA QVLRQLAPDVSYRSLV+LG+ASIQGLSVASFEK
Sbjct: 361 SEPRRSASIACGASVCEVSMQVPTWALQVLRQLAPDVSYRSLVVLGVASIQGLSVASFEK 420

Query: 420 DDAERLLFFCTRQGKADHTENSVLTRPPSWLTSPAPSRKRSEPCRESKGVESENVCNVRP 479
           DDAERLLFFC +Q       +++L++ P+WLT P P+RKRSEPCRESK  E EN      
Sbjct: 421 DDAERLLFFCGQQINDTSNHDALLSKIPNWLTPPLPTRKRSEPCRESK--EIENGGPTSR 478

Query: 480 KLNSAAMRPIPHTRHYKMLPFSGFSEIERYDGDQVKANLPVAPLKHSSAGPTPVTHRKSL 539
           K+N AA+RPIPHTR +KM+PFSG+SEI R+DGD  K +LP+ P KH ++G TPVTHRK+ 
Sbjct: 479 KINVAALRPIPHTRRHKMIPFSGYSEIGRFDGDHTKGSLPMPP-KHGASGGTPVTHRKAF 537

Query: 540 SSSYQAQQIISLNPLPLKKHGCGRAPIQVCSEEEFLRDVMQFLILRGHTRLVPQGGLAEF 599
           S SYQ +QIISLNPLPLKKH CGRA IQVCSEEEFLRDVMQFL++RGHTRLVP GGLAEF
Sbjct: 538 SGSYQRKQIISLNPLPLKKHDCGRAHIQVCSEEEFLRDVMQFLLIRGHTRLVPPGGLAEF 597

Query: 600 PDAILNAKRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRH 659
           PDA+LN+KRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRH
Sbjct: 598 PDAVLNSKRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRH 657

Query: 660 YETYLLEYELAHDDVDGECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKT 719
           YETYLLEYE AHDDVDGECCL+C SS AGDWVNCG CGEWAHFGCDRR GLGAFKDYAKT
Sbjct: 658 YETYLLEYEYAHDDVDGECCLICRSSTAGDWVNCGSCGEWAHFGCDRRPGLGAFKDYAKT 717

Query: 720 DGLEYVCPQCSVTNFKKKSQKTSNG 744
           DGLEYVCP CSV+N++KKSQKTSNG
Sbjct: 718 DGLEYVCPNCSVSNYRKKSQKTSNG 742

Arabidopsis thaliana (taxid: 3702)

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		745
224141545		745	predicted protein [Populus trichocarpa]	0.994	0.994	0.812	0.0
255550299		749	DNA binding protein, putative [Ricinus c	0.936	0.931	0.846	0.0
225444591		739	PREDICTED: AT-rich interactive domain-co	0.981	0.989	0.777	0.0
297742936		746	unnamed protein product [Vitis vinifera]	0.997	0.995	0.753	0.0
356556430		750	PREDICTED: uncharacterized protein LOC10	0.995	0.989	0.726	0.0
356530473		752	PREDICTED: uncharacterized protein LOC10	0.997	0.988	0.729	0.0
42565391		747	ARID/BRIGHT DNA-binding domain-containin	0.993	0.990	0.714	0.0
297818776		748	ARID/BRIGHT DNA-binding domain-containin	0.994	0.990	0.714	0.0
7649364		717	putative protein [Arabidopsis thaliana]	0.953	0.990	0.681	0.0
357514291		769	Fiber protein Fb21 [Medicago truncatula]	0.987	0.957	0.651	0.0

>gi\|224141545\|ref\|XP_002324130.1\| predicted protein [Populus trichocarpa] gi\|222865564\|gb\|EEF02695.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score = 1231 bits (3185), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 608/748 (81%), Positives = 649/748 (86%), Gaps = 7/748 (0%)

Query: 2   MFHAQSSSRNHCSLLAVLSRKFVDDKQKQAATDDKPKYPFPEIASSGRLEVHLLSSPSTD 61
           MFHAQ   RNHC+LLAVL  K    +QK   +DDKP+YP PE+ S+GRLEV +L++PSTD
Sbjct: 1   MFHAQGPLRNHCTLLAVLCGK--SGEQKLPLSDDKPRYPLPELESTGRLEVQVLNNPSTD 58

Query: 62  EFRRLLESSEPNIVYLQGEKINDSEEIGSLVWGDVDLSTPEALCGLFGSTLPTTVYLEIP 121
           EFR++L+S EP+IVY QGE++ D EEIGSL W DV LSTPE+LCGLFGSTLP TVYLE+P
Sbjct: 59  EFRQVLQSLEPSIVYFQGEQVEDREEIGSLRWADVGLSTPESLCGLFGSTLPPTVYLEMP 118

Query: 122 NGENFAEALHSRGVPYVIYWKHSFSCYAACHFLQALLSVVQSSCSHTWDAFQLAHASFRL 181
           NGE  AEALHS+GVPYVIYWK +FSCYAA HF QALLSVVQSSCSHT DAFQLAHASFRL
Sbjct: 119 NGEKLAEALHSKGVPYVIYWKSAFSCYAASHFRQALLSVVQSSCSHTCDAFQLAHASFRL 178

Query: 182 YCVRNNIVMASNSQKGSSKLGPHLLGDPPKIDIALSEMDVQGEENSPENLPAIKIYDDDV 241
           YCV+NN   ASNSQK   K GP LLGDPPK DI+L E D QGEE S   LPAIKIYDDDV
Sbjct: 179 YCVQNNNTPASNSQKVGGKPGPRLLGDPPKFDISLPEADDQGEEGSSGALPAIKIYDDDV 238

Query: 242 TMRFLVCGVPCTLDTSLLGPLEDGLNALLNIEIRGSKLHNRTSAPPPPLQAGAFSRGVVT 301
           TMRFLVCG+  TLD   LG LEDGLNALLNIEIRGSKLHNRTSAPPPPLQAG FSRGVVT
Sbjct: 239 TMRFLVCGLTGTLDACALGSLEDGLNALLNIEIRGSKLHNRTSAPPPPLQAGTFSRGVVT 298

Query: 302 MRCDLSTCSSAHISLLVSGSAQTCFNDQLLENHIKNELIENSQLVHALPNSGDNRLPPSE 361
           MRCDLSTCSSAHISLLVSGSAQ CFNDQLLENHIK+ELIENSQLVHA  +S +++ P SE
Sbjct: 299 MRCDLSTCSSAHISLLVSGSAQNCFNDQLLENHIKSELIENSQLVHASTSSDESKSPSSE 358

Query: 362 PRKSASIACGASVFEVSMKVSTWASQVLRQLAPDVSYRSLVMLGIASIQGLSVASFEKDD 421
           PRKSASIACGASVFEVSMKV TWASQVLRQLAPDV+YRSLVMLGIASIQGLSVASFEKDD
Sbjct: 359 PRKSASIACGASVFEVSMKVPTWASQVLRQLAPDVTYRSLVMLGIASIQGLSVASFEKDD 418

Query: 422 AERLLFFCTRQGKADHTENSVLTRPPSWLTSPAPSRKRSEPCRESK----GVESENVCNV 477
           A+RLLFFCT+Q K  H  N VLTR PSWL  PAP RKR EP RE+K    G   EN  N 
Sbjct: 419 ADRLLFFCTKQSKDPHPRNPVLTRHPSWLIPPAPCRKRYEPSRETKPLTFGCGGENGGNF 478

Query: 478 RPKLNSAAMRPIPHTRHYKMLPFSGFSEIERYDGDQVKANLPVAPLKHSSAGPTPVTHRK 537
           + KL  AAMRPIPHTR +KMLPFSGF E ERYDG+Q K +LP  P KHS  GP PVTHRK
Sbjct: 479 KQKLYVAAMRPIPHTRRHKMLPFSGFLEAERYDGEQTKPSLPPPP-KHSVVGPAPVTHRK 537

Query: 538 SLSSSYQAQQIISLNPLPLKKHGCGRAPIQVCSEEEFLRDVMQFLILRGHTRLVPQGGLA 597
           SLS+SYQAQQIISLNPLPLKKHGCGR+PIQ CSEEEFLRDVMQFLILRGH+RLVPQGGLA
Sbjct: 538 SLSNSYQAQQIISLNPLPLKKHGCGRSPIQACSEEEFLRDVMQFLILRGHSRLVPQGGLA 597

Query: 598 EFPDAILNAKRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLK 657
           EFPDAILNAKRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLK
Sbjct: 598 EFPDAILNAKRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLK 657

Query: 658 RHYETYLLEYELAHDDVDGECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYA 717
           RHYETYLLEYELAHDDVDGECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYA
Sbjct: 658 RHYETYLLEYELAHDDVDGECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYA 717

Query: 718 KTDGLEYVCPQCSVTNFKKKSQKTSNGY 745
           KTDGLEY+CP CS+ NFKKKSQK +NGY
Sbjct: 718 KTDGLEYICPHCSIANFKKKSQKNANGY 745

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255550299\|ref\|XP_002516200.1\| DNA binding protein, putative [Ricinus communis] gi\|223544686\|gb\|EEF46202.1\| DNA binding protein, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|225444591\|ref\|XP_002277324.1\| PREDICTED: AT-rich interactive domain-containing protein 4 [Vitis vinifera] gi\|297738501\|emb\|CBI27746.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297742936\|emb\|CBI35803.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356556430\|ref\|XP_003546529.1\| PREDICTED: uncharacterized protein LOC100775894 [Glycine max]	Back alignment and taxonomy information

>gi\|356530473\|ref\|XP_003533805.1\| PREDICTED: uncharacterized protein LOC100808357 [Glycine max]	Back alignment and taxonomy information

>gi|42565391|ref|NP_189910.2| ARID/BRIGHT DNA-binding domain-containing protein [Arabidopsis thaliana] gi|75223288|sp|Q6NQ79.1|ARID4_ARATH RecName: Full=AT-rich interactive domain-containing protein 4; Short=ARID domain-containing protein 4 gi|34849889|gb|AAQ82841.1| At3g43240 [Arabidopsis thaliana] gi|332644257|gb|AEE77778.1| ARID/BRIGHT DNA-binding domain-containing protein [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|297818776\|ref\|XP_002877271.1\| ARID/BRIGHT DNA-binding domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi\|297323109\|gb\|EFH53530.1\| ARID/BRIGHT DNA-binding domain-containing protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|7649364\|emb\|CAB89045.1\| putative protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|357514291\|ref\|XP_003627434.1\| Fiber protein Fb21 [Medicago truncatula] gi\|355521456\|gb\|AET01910.1\| Fiber protein Fb21 [Medicago truncatula]	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		745
TAIR\|locus:2084731		747	AT3G43240 [Arabidopsis thalian	0.993	0.990	0.708	7.9e-291

TAIR\|locus:2084731 AT3G43240 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 2793 (988.2 bits), Expect = 7.9e-291, P = 7.9e-291
 Identities = 528/745 (70%), Positives = 616/745 (82%)

Query:     2 MFHAQSSSRNHCSLLAVLS-RKFVXXXXXXXXXXXXXXYPFPEIASSGRLEVHLLSSPST 60
             MFH Q  SRN C+++AV+S  +                YPFP+++SSGRL+  +L++P+ 
Sbjct:     1 MFHGQGFSRNRCNVVAVVSGAELCDTNNQIDGTSHQPKYPFPDLSSSGRLKFQVLNNPTP 60

Query:    61 DEFRRLLESSEPNIVYLQGEKINDSEEIGSLVWGDVDLSTPEALCGLFGSTLPTTVYLEI 120
             +EF+  + SS  + VYLQGE   DS+E+G LV G  D STP+AL  LFGSTLPTTVYLE+
Sbjct:    61 EEFQVAVNSSATDFVYLQGEHSGDSDEVGPLVLGYTDFSTPDALVTLFGSTLPTTVYLEL 120

Query:   121 PNGENFAEALHSRGVPYVIYWKHSFSCYAACHFLQALLSVVQSSCSHTWDAFQLAHASFR 180
             PNGE  A+AL+S+GV YVIYWK+ FS YAACHF  +L SV+QSSCS TWD F +A ASFR
Sbjct:   121 PNGEELAQALYSKGVQYVIYWKNVFSKYAACHFRHSLFSVIQSSCSDTWDVFHVAEASFR 180

Query:   181 LYCVRNNIVMASNS-QKGSSKLGPHLLGDPPKIDIALSEMDVQGEENSPENLPAIKIYDD 239
             LYC  +N V+ SNS +K + ++GP LLG+PPKID+   E D   EENS E+LP+IKIYD+
Sbjct:   181 LYCTSDNAVLPSNSNRKMNYEMGPCLLGEPPKIDVVSPEADELEEENSLESLPSIKIYDE 240

Query:   240 DVTMRFLVCGVPCTLDTSLLGPLEDGLNALLNIEIRGSKLHNRTSAPPPPLQAGAFSRGV 299
             DVT+RFL+CG PCT+DT LLG L DGLNALL IE+RGSKLHNR+SAP PPLQAG F+RGV
Sbjct:   241 DVTVRFLLCGPPCTVDTFLLGSLMDGLNALLRIEMRGSKLHNRSSAPAPPLQAGTFTRGV 300

Query:   300 VTMRCDLSTCSSAHISLLVSGSAQTCFNDQLLENHIKNELIENSQLVHALPNSGDNRLPP 359
             VTMRCD+STCSSAHIS+LVSG+AQTCF+DQLLENHIK+E++E  QLVH++ NS + +   
Sbjct:   301 VTMRCDVSTCSSAHISMLVSGNAQTCFSDQLLENHIKHEVVEKIQLVHSVVNSEETKRGF 360

Query:   360 SEPRKSASIACGASVFEVSMKVSTWASQVLRQLAPDVSYRSLVMLGIASIQGLSVASFEK 419
             SEPR+SASIACGASV EVSM+V TWA QVLRQLAPDVSYRSLV+LG+ASIQGLSVASFEK
Sbjct:   361 SEPRRSASIACGASVCEVSMQVPTWALQVLRQLAPDVSYRSLVVLGVASIQGLSVASFEK 420

Query:   420 DDAERLLFFCTRQGKADHTENSVLTRPPSWLTSPAPSRKRSEPCRESKGVESENVCNVRP 479
             DDAERLLFFC +Q       +++L++ P+WLT P P+RKRSEPCRESK  E EN      
Sbjct:   421 DDAERLLFFCGQQINDTSNHDALLSKIPNWLTPPLPTRKRSEPCRESK--EIENGGPTSR 478

Query:   480 KLNSAAMRPIPHTRHYKMLPFSGFSEIERYDGDQVKANLPVAPLKHSSAGPTPVTHRKSL 539
             K+N AA+RPIPHTR +KM+PFSG+SEI R+DGD  K +LP+ P KH ++G TPVTHRK+ 
Sbjct:   479 KINVAALRPIPHTRRHKMIPFSGYSEIGRFDGDHTKGSLPMPP-KHGASGGTPVTHRKAF 537

Query:   540 SSSYQAQQIISLNPLPLKKHGCGRAPIQVCSEEEFLRDVMQFLILRGHTRLVPQGGLAEF 599
             S SYQ +QIISLNPLPLKKH CGRA IQVCSEEEFLRDVMQFL++RGHTRLVP GGLAEF
Sbjct:   538 SGSYQRKQIISLNPLPLKKHDCGRAHIQVCSEEEFLRDVMQFLLIRGHTRLVPPGGLAEF 597

Query:   600 PDAILNAKRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRH 659
             PDA+LN+KRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRH
Sbjct:   598 PDAVLNSKRLDLFNLYREVVSRGGFHVGNGINWKGQVFSKMRNHTLTNRMTGVGNTLKRH 657

Query:   660 YETYLLEYELAHDDVDGECCLLCHSSAAGDWVNCGICGEWAHFGCDRRQGLGAFKDYAKT 719
             YETYLLEYE AHDDVDGECCL+C SS AGDWVNCG CGEWAHFGCDRR GLGAFKDYAKT
Sbjct:   658 YETYLLEYEYAHDDVDGECCLICRSSTAGDWVNCGSCGEWAHFGCDRRPGLGAFKDYAKT 717

Query:   720 DGLEYVCPQCSVTNFKKKSQKTSNG 744
             DGLEYVCP CSV+N++KKSQKTSNG
Sbjct:   718 DGLEYVCPNCSVSNYRKKSQKTSNG 742


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.134   0.409    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      745       731   0.00087  121 3  11 22  0.40    34
                                                     37  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  628 (67 KB)
  Total size of DFA:  404 KB (2195 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  66.54u 0.09s 66.63t   Elapsed:  00:00:03
  Total cpu time:  66.54u 0.09s 66.63t   Elapsed:  00:00:03
  Start:  Mon May 20 22:23:00 2013   End:  Mon May 20 22:23:03 2013

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA;ISS

GO:0008270 "zinc ion binding" evidence=IEA

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)
Q6NQ79	ARID4_ARATH	No assigned EC number	0.7140	0.9932	0.9906	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		745
smart01014		88	smart01014, ARID, ARID/BRIGHT DNA binding domain	3e-17
pfam01388		90	pfam01388, ARID, ARID/BRIGHT DNA binding domain	2e-10
smart00501		93	smart00501, BRIGHT, BRIGHT, ARID (A/T-rich interac	2e-05

>gnl\|CDD\|198082 smart01014, ARID, ARID/BRIGHT DNA binding domain	Back alignment and domain information

 Score = 76.9 bits (190), Expect = 3e-17
 Identities = 34/99 (34%), Positives = 46/99 (46%), Gaps = 14/99 (14%)

Query: 571 EEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGFH-VGNG 629
            E FL  + +F+  RG                ++  K LDL+ LYR V  RGGF  V   
Sbjct: 3   RELFLDRLRKFMEKRGTPLDKIP---------VIGGKPLDLYRLYRAVQKRGGFDKVTKK 53

Query: 630 INWKGQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEYE 668
             WK QV  ++    +    T  G +L++HYE YLL YE
Sbjct: 54  KKWK-QVARELG---IPPSATSAGTSLRKHYEKYLLPYE 88

Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. Length = 88

>gnl\|CDD\|216473 pfam01388, ARID, ARID/BRIGHT DNA binding domain	Back alignment and domain information

>gnl\|CDD\|128777 smart00501, BRIGHT, BRIGHT, ARID (A/T-rich interaction domain) domain	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		745
smart00501		93	BRIGHT BRIGHT, ARID (A/T-rich interaction domain)	99.85
PF01388		92	ARID: ARID/BRIGHT DNA binding domain; InterPro: IP	99.81
KOG2744		512	consensus DNA-binding proteins Bright/BRCAA1/RBP1	99.66
KOG2510		532	consensus SWI-SNF chromatin-remodeling complex pro	98.83
PF00628		51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	98.32
smart00249		47	PHD PHD zinc finger. The plant homeodomain (PHD) f	98.22
KOG1973		274	consensus Chromatin remodeling protein, contains P	97.9
KOG0825		1134	consensus PHD Zn-finger protein [General function	97.44
PF12770		287	CHAT: CHAT domain	97.35
KOG1632		345	consensus Uncharacterized PHD Zn-finger protein [G	96.84
KOG1244		336	consensus Predicted transcription factor Requiem/N	96.83
KOG4299		613	consensus PHD Zn-finger protein [General function	96.44
KOG1512		381	consensus PHD Zn-finger protein [General function	96.33
KOG4443		694	consensus Putative transcription factor HALR/MLL3,	95.51
KOG0957		707	consensus PHD finger protein [General function pre	95.49
KOG1245		1404	consensus Chromatin remodeling complex WSTF-ISWI,	95.28
PF07227		446	DUF1423: Protein of unknown function (DUF1423); In	95.24
KOG0383		696	consensus Predicted helicase [General function pre	94.63
COG5034		271	TNG2 Chromatin remodeling protein, contains PhD zi	92.81
KOG0955		1051	consensus PHD finger protein BR140/LIN-49 [General	92.35
KOG1246		904	consensus DNA-binding protein jumonji/RBP2/SMCY, c	92.28
KOG4323		464	consensus Polycomb-like PHD Zn-finger protein [Gen	91.24
COG5141		669	PHD zinc finger-containing protein [General functi	88.32
KOG1844		508	consensus PHD Zn-finger proteins [General function	83.68
KOG1632		345	consensus Uncharacterized PHD Zn-finger protein [G	81.96

>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain	Back alignment and domain information

Probab=99.85  E-value=1.7e-21  Score=170.14  Aligned_cols=89  Identities=30%  Similarity=0.568  Sum_probs=81.0

Q ss_pred             CHHHHHHHHHHHHHHhCCccccCCCCCCCCCCcccCCeechhhHHHHHHHhcCceeeccC-CCChHHHHhhccCCCCCCc
Q 004566          570 SEEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGFHVGNG-INWKGQVFSKMRNHTLTNR  648 (745)
Q Consensus       570 ~~EeFL~dL~qFhesRGtp~eiP~G~ls~fP~PvVgGK~LDLykLYreV~sRGGF~kVnk-kkWk~EV~~~Mgn~~~p~t  648 (745)
                      +.++|+++|++||+.+|+++..         .|+|+|++||||+||++|+++|||++|+. ++|. +|+++|+   ++.+
T Consensus         2 ~~~~F~~~L~~F~~~~g~~~~~---------~P~i~g~~vdL~~Ly~~V~~~GG~~~v~~~~~W~-~Va~~lg---~~~~   68 (93)
T smart00501        2 ERVLFLDRLYKFMEERGSPLKK---------IPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWK-EIARELG---IPDT   68 (93)
T ss_pred             cHHHHHHHHHHHHHHcCCcCCc---------CCeECCEeCcHHHHHHHHHHccCHHHHcCCCCHH-HHHHHhC---CCcc
Confidence            5789999999999999998753         57999999999999999999999999965 5799 9999999   5566


Q ss_pred             cccHHHHHHHHHHHhhhhhhhcc
Q 004566          649 MTGVGNTLKRHYETYLLEYELAH  671 (745)
Q Consensus       649 ~TSag~~LK~hYERyLleYE~aH  671 (745)
                      ++++++.||++|+|||++||..+
T Consensus        69 ~~~~~~~lk~~Y~k~L~~yE~~~   91 (93)
T smart00501       69 STSAASSLRKHYERYLLPFERFL   91 (93)
T ss_pred             cchHHHHHHHHHHHHhHHHHHHh
Confidence            89999999999999999999865

DNA-binding domain containing a helix-turn-helix structure

>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans	Back alignment and domain information

>KOG2744 consensus DNA-binding proteins Bright/BRCAA1/RBP1 and related proteins containing BRIGHT domain [Transcription]	Back alignment and domain information

>KOG2510 consensus SWI-SNF chromatin-remodeling complex protein [Chromatin structure and dynamics]	Back alignment and domain information

>PF00628 PHD: PHD-finger; InterPro: IPR019787 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

>smart00249 PHD PHD zinc finger	Back alignment and domain information

>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]	Back alignment and domain information

>KOG0825 consensus PHD Zn-finger protein [General function prediction only]	Back alignment and domain information

>PF12770 CHAT: CHAT domain	Back alignment and domain information

>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]	Back alignment and domain information

>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]	Back alignment and domain information

>KOG4299 consensus PHD Zn-finger protein [General function prediction only]	Back alignment and domain information

>KOG1512 consensus PHD Zn-finger protein [General function prediction only]	Back alignment and domain information

>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]	Back alignment and domain information

>KOG0957 consensus PHD finger protein [General function prediction only]	Back alignment and domain information

>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]	Back alignment and domain information

>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []	Back alignment and domain information

>KOG0383 consensus Predicted helicase [General function prediction only]	Back alignment and domain information

>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]	Back alignment and domain information

>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]	Back alignment and domain information

>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]	Back alignment and domain information

>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]	Back alignment and domain information

>COG5141 PHD zinc finger-containing protein [General function prediction only]	Back alignment and domain information

>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]	Back alignment and domain information

>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		745
2jxj_A		96	Histone demethylase jarid1A; ARID domain, chromati	1e-17
2rq5_A		121	Protein jumonji; developmental protein, nucleus, r	1e-16
1ig6_A		107	MRF-2, modulator recognition factor 2; DNA binding	5e-16
2jrz_A		117	Histone demethylase jarid1C; bright/ARID domain, h	1e-15
2eqy_A		122	RBP2 like, jumonji, at rich interactive domain 1B;	2e-15
2lm1_A		107	Lysine-specific demethylase LID; structural genomi	5e-15
2cxy_A		125	BAF250B subunit, HBAF250B; DNA-binding domain, str	2e-14
1c20_A		128	DEAD ringer protein; DNA-binding domain, ARID, AT-	7e-13
1kkx_A		123	Transcription regulatory protein ADR6; ARID, DNA-b	9e-13
2kk0_A		145	AT-rich interactive domain-containing protein 3A;	4e-12
2li6_A		116	SWI/SNF chromatin-remodeling complex subunit SWI1;	1e-11
2k16_A		75	Transcription initiation factor TFIID subunit 3; p	6e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-05
3kqi_A		75	GRC5, PHD finger protein 2; metal-binding, zinc-fi	2e-04
1wep_A		79	PHF8; structural genomics, PHD domain, riken struc	4e-04
3lqh_A		183	Histone-lysine N-methyltransferase MLL; PHD finger	6e-04
1wem_A		76	Death associated transcription factor 1; structura	8e-04

>2jxj_A Histone demethylase jarid1A; ARID domain, chromatin regulator, developmental protein, dioxygenase, iron, metal-binding, nucleus, oxidoreductase; NMR {Homo sapiens} Length = 96	Back alignment and structure

 Score = 77.6 bits (191), Expect = 1e-17
 Identities = 32/107 (29%), Positives = 47/107 (43%), Gaps = 16/107 (14%)

Query: 564 APIQVCSEEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGG 623
            P+      +FL  + +F  L+G T  +P           +  K LDL+ L + V S+GG
Sbjct: 1   GPLGSRVRLDFLDQLAKFWELQGSTLKIPV----------VERKILDLYALSKIVASKGG 50

Query: 624 FHVGNGIN-WKGQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEYEL 669
           F +      W  +V S++          G G+ LK HYE  L  YEL
Sbjct: 51  FEMVTKEKKWS-KVGSRLG----YLPGKGTGSLLKSHYERILYPYEL 92

PyMOL of 2jxj

>2rq5_A Protein jumonji; developmental protein, nucleus, repressor, transcription, transcription regulation; NMR {Mus musculus} Length = 121	Back alignment and structure

>1ig6_A MRF-2, modulator recognition factor 2; DNA binding protein, DNA-binding motif, protein-DNA interaction; NMR {Homo sapiens} SCOP: a.4.3.1 PDB: 2oeh_A Length = 107	Back alignment and structure

>2jrz_A Histone demethylase jarid1C; bright/ARID domain, helical, structural genomics, structural genomics consortium, SGC, oxidoreductase; NMR {Homo sapiens} PDB: 2yqe_A Length = 117	Back alignment and structure

>2eqy_A RBP2 like, jumonji, at rich interactive domain 1B; ARID domain, structural genomics, NPPSFA; NMR {Mus musculus} Length = 122	Back alignment and structure

>2lm1_A Lysine-specific demethylase LID; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Drosophila melanogaster} Length = 107	Back alignment and structure

>2cxy_A BAF250B subunit, HBAF250B; DNA-binding domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.60A {Homo sapiens} PDB: 2eh9_A 1ryu_A Length = 125	Back alignment and structure

>1c20_A DEAD ringer protein; DNA-binding domain, ARID, AT-rich interaction domain, DNA- binding protein; NMR {Drosophila melanogaster} SCOP: a.4.3.1 PDB: 1kqq_A Length = 128	Back alignment and structure

>1kkx_A Transcription regulatory protein ADR6; ARID, DNA-binding domain, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.4.3.1 PDB: 1kn5_A Length = 123	Back alignment and structure

>2kk0_A AT-rich interactive domain-containing protein 3A; DEAD ringer, AT-rich interaction domain, NESG, ARID, cytopla binding, nucleus, phosphoprotein; NMR {Homo sapiens} Length = 145	Back alignment and structure

>2li6_A SWI/SNF chromatin-remodeling complex subunit SWI1; ligand binding, DNA binding protein; NMR {Saccharomyces cerevisiae} Length = 116	Back alignment and structure

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A* Length = 75	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

>3kqi_A GRC5, PHD finger protein 2; metal-binding, zinc-finger, histone-binding, NUC protein; HET: M3L; 1.78A {Homo sapiens} Length = 75	Back alignment and structure

>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2 Length = 79	Back alignment and structure

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A Length = 183	Back alignment and structure

>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2 Length = 76	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		745
d1ryua_		120	a.4.3.1 (A:) SWI-SNF complex protein p270, SMARCF1	4e-16
d1ig6a_		107	a.4.3.1 (A:) MRF-2 DNA-binding domain {Human (Homo	1e-15
d1kkxa_		102	a.4.3.1 (A:) Transcription regulator Adr6 (Swi1) {	2e-15
d1c20a_		128	a.4.3.1 (A:) DNA-binding domain from the dead ring	2e-14
d1wewa_		78	g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale c	0.002
d1wepa_		79	g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus mus	0.004

>d1ryua_ a.4.3.1 (A:) SWI-SNF complex protein p270, SMARCF1 {Human (Homo sapiens) [TaxId: 9606]} Length = 120	Back information, alignment and structure


class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: ARID-like
family: ARID domain
domain: SWI-SNF complex protein p270, SMARCF1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 72.6 bits (178), Expect = 4e-16
 Identities = 18/103 (17%), Positives = 37/103 (35%), Gaps = 15/103 (14%)

Query: 571 EEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGF-HVGNG 629
            + ++   + F   +                  +  K LDL+ LY  V   GG   V   
Sbjct: 21  RKMWVDRYLAFTEEKAMGMTNLP---------AVGRKPLDLYRLYVSVKEIGGLTQVNKN 71

Query: 630 INWKGQVFSKMRNHTLTNRMTGVGNTLKRHYETYLLEYELAHD 672
             W+ ++ + +   T ++      ++LK+ Y   L  +E   +
Sbjct: 72  KKWR-ELATNLNVGTSSS----AASSLKKQYIQCLYAFECKIE 109

PyMOL of d1ryua_

>d1ig6a_ a.4.3.1 (A:) MRF-2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 107	Back information, alignment and structure

>d1kkxa_ a.4.3.1 (A:) Transcription regulator Adr6 (Swi1) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 102	Back information, alignment and structure

>d1c20a_ a.4.3.1 (A:) DNA-binding domain from the dead ringer protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 128	Back information, alignment and structure

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 78	Back information, alignment and structure

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]} Length = 79	Back information, alignment and structure

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		745
d1ig6a_		107	MRF-2 DNA-binding domain {Human (Homo sapiens) [Ta	99.83
d1ryua_		120	SWI-SNF complex protein p270, SMARCF1 {Human (Homo	99.83
d1c20a_		128	DNA-binding domain from the dead ringer protein {F	99.82
d1kkxa_		102	Transcription regulator Adr6 (Swi1) {Baker's yeast	99.76
d1mm2a_		61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	98.47
d1wepa_		79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	98.32
d1fp0a1		70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	98.24
d1f62a_		51	Williams-Beuren syndrome transcription factor, WST	98.23
d1weva_		88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	98.23
d1we9a_		64	PHD finger protein At5g26210 {Thale cress (Arabido	98.18
d1wesa_		71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	98.05
d1wewa_		78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	97.88
d1weea_		72	PHD finger protein At1g33420 {Thale cress (Arabido	97.83
d1wema_		76	Death associated transcription factor 1, Datf1 (DI	97.62
d2pnxa1		51	Inhibitor of growth protein 4, Ing4 {Homo sapiens	97.58
d1wila_		89	Hypothetical protein KIAA1045 {Human (Homo sapiens	83.17

>d1ig6a_ a.4.3.1 (A:) MRF-2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: ARID-like
family: ARID domain
domain: MRF-2 DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=5.4e-22  Score=160.03  Aligned_cols=91  Identities=21%  Similarity=0.418  Sum_probs=82.8

Q ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEECHHHHHHHHHHHCCCEEECCCC-CCHHHHHHHCCCCCCCC
Q ss_conf             99888999999999981982324899988777730178102166789998723942202577-87688986413877898
Q 004566          569 CSEEEFLRDVMQFLILRGHTRLVPQGGLAEFPDAILNAKRLDLFNLYREVVSRGGFHVGNGI-NWKGQVFSKMRNHTLTN  647 (745)
Q Consensus       569 ~~eEeFL~dL~kFhesRGtp~eiP~G~ls~lP~PvVgGK~LDLykLYkeV~sRGGF~kVnkk-kWk~EV~s~Lgn~~~p~  647 (745)
                      ++++.|+++|++||++||+++..         .|+++||+||||+||.+|+++|||++|+.. .|. +|+.+|+   .+.
T Consensus         2 ~e~~~Fl~~L~~F~~~rg~~~~~---------~P~i~gk~vDL~~Ly~~V~~~GG~~~V~~~~~W~-~ia~~lg---~~~   68 (107)
T d1ig6a_           2 ADEQAFLVALYKYMKERKTPIER---------IPYLGFKQINLWTMFQAAQKLGGYETITARRQWK-HIYDELG---GNP   68 (107)
T ss_dssp             HHHHHHHHHHHHHHHTTTCCGGG---------CCCSSSSSCCHHHHHHHHHHTTHHHHHHHHTTHH-HHHHHHT---CCT
T ss_pred             CCHHHHHHHHHHHHHHCCCCCCC---------CCEECCCCCCHHHHHHHHHHHCCHHHCCCCCCHH-HHHHHHC---CCC
T ss_conf             54999999999999985998875---------8828982541999999999967705336506199-9999868---898


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             5346789999999995553320167
Q 004566          648 RMTGVGNTLKRHYETYLLEYELAHD  672 (745)
Q Consensus       648 t~Tsag~~LK~hYERyLleYE~aHD  672 (745)
                      .+|++++.||++|++||++||..+.
T Consensus        69 ~~~~~~~~Lk~~Y~~~L~~yE~~~~   93 (107)
T d1ig6a_          69 GSTSAATCTRRHYERLILPYERFIK   93 (107)
T ss_dssp             TCTTTTTTHHHHHHHHTTTTHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7787999999999999999998870

PyMOL of d1ig6a_

>d1ryua_ a.4.3.1 (A:) SWI-SNF complex protein p270, SMARCF1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1c20a_ a.4.3.1 (A:) DNA-binding domain from the dead ringer protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1kkxa_ a.4.3.1 (A:) Transcription regulator Adr6 (Swi1) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1wesa_ g.50.1.2 (A:) PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2pnxa1 g.50.1.2 (A:195-245) Inhibitor of growth protein 4, Ing4 {Homo sapiens [TaxId: 9606]}	Back information, alignment and structure

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure