Citrus Sinensis ID: 009499

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---

MGQRNMPCTSQMIDLEMDQQNRGYLLPEPCVVLGGVTSFPQPMQTIVRASGNTSSLDAHQHYDSAMFYGMPQYHGVHHHHAASVDLGASTASNLYVPYMPTLSSGMPVNHGSTDQLPSSRNFGVIGASAEEYGRNSHFMDNVRGSYKRKNTEGFPGSFQNLNAPASSSSSVAPLHPRHPDGVTPMDAACFSLPQYRGNGTPSIREVESQRSVRNRLVATGGMDPVLAHSHNHFIQGNFIGQPFQPAGWLEQPSDGGGSSWTQAPAIPYMHGSNVSGAPMDSGNMVVQRYPETAGNRNSSTFLQPPVNIQHLSFPHPPPPFQGIRNHNTNVHPQVAAASFRVPSSYRTMNISQDGSEMVPRHMGPVPPTGFRIYRSPREGPVPEALRQRSLPHLRVLPSDGVALLEIPDFYEVGNFIDRHRDMRLDIEDMSYEELLALGERIGNVNTGLSEEIVARQLKTRVYLSATNYINLEEPASKDQEPGSCIICQEDYRDNEKIGTLDCDHEYHAECLKKWLFIKNVCPICKSEALATKS

cccccccccccccccHHHcccccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccccccccHHHHHHHcccEEEEccccccccccccccccccccccccccccccccEEEEcccccccHHHHHHHHHHccccccccccccccccc

ccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccccHHHHEEEcHHHHHccccccccccccccccccccHHHHHHHHHHcccccccccHHHHHHHccccEEcccccccccccccccccccccEEEEEHHcccccccEEEcccccHHHHHHHHHHHHHcccccEEcccccccc

mgqrnmpctsqMIDLEMdqqnrgyllpepcvvlggvtsfpqpmqTIVRasgntssldahqhydsamfygmpqyhgvhhhhaasvdlgastasnlyvpymptlssgmpvnhgstdqlpssrnfgvigasaeeygrnshfmdnvrgsykrkntegfpgsfqnlnapasssssvaplhprhpdgvtpmdaacfslpqyrgngtpsirevESQRSVRNRLVatggmdpvlahshnhfiqgnfigqpfqpagwleqpsdgggsswtqapaipymhgsnvsgapmdsgnmvvqrypetagnrnsstflqppvniqhlsfphppppfqgirnhntnvhpqvaaasfrvpssyrtmnisqdgsemvprhmgpvpptgfriyrspregpvpealrqrslphlrvlpsdgvalleipdfyevgnfidrhrdmrldiEDMSYEELLALGERIGNVNTGLSEEIVARQLKTRVYLSATnyinleepaskdqepgsciicqedyrdnekigtldcdHEYHAECLKKWLFIKnvcpicksealatks

mgqrnmpcTSQMIDLEMDQQNRGYLLPEPCVVLGGVTSFPQPMQTIVRASGNTSSLDAHQHYDSAMFYGMPQYHGVHHHHAASVDLGASTASNLYVPYMPTLSSGMPVNHGSTDQLPSSRNFGVIGASaeeygrnshfmDNVRGSYKRKNTEGFPGSFQNLNAPASSSSSVAPLHPRHPDGVTPMDAACFSLPQYRGNgtpsirevesqrSVRNRLVATGGMDPVLAHSHNHFIQGNFIGQPFQPAGWLEQPSDGGGSSWTQAPAIPYMHGSNVSGAPMDSGNMVVQRYPETAGNRNSSTFLQPPVNIQHLSFPHPPPPFQGIRNHNTNVHPQVAAASFRVPSSYRTMNisqdgsemvprhMGPVPPTGFRIYRSPREGPVPEALRQRSLPHLRVLPSDGVALLEIPDFYEVGNFIDRHRDMRLDIEDMSYEELLALGERIGNVNTGLSEEIVARQLKTRVYLSATNYInleepaskdqepgsCIICQEDYRDNEKIGTLDCDHEYHAECLKKWLFIKNVCPICKSEALATKS

MGQRNMPCTSQMIDLEMDQQNRGYLLPEPCVVLGGVTSFPQPMQTIVRASGNTSSLDAHQHYDSAMFYGMPQYHGVHHHHAASVDLGASTASNLYVPYMPTLSSGMPVNHGSTDQLPSSRNFGVIGASAEEYGRNSHFMDNVRGSYKRKNTEGFPGSFQNLNAPAsssssVAPLHPRHPDGVTPMDAACFSLPQYRGNGTPSIREVESQRSVRNRLVATGGMDPVLAHSHNHFIQGNFIGQPFQPAGWLEQPSDGGGSSWTQAPAIPYMHGSNVSGAPMDSGNMVVQRYPETAGNRNSSTFLQPPVNIQHLSFPHPPPPFQGIRNHNTNVHPQVAAASFRVPSSYRTMNISQDGSEMVPRHMGPVPPTGFRIYRSPREGPVPEALRQRSLPHLRVLPSDGVALLEIPDFYEVGNFIDRHRDMRLDIEDMSYEELLALGERIGNVNTGLSEEIVARQLKTRVYLSATNYINLEEPASKDQEPGSCIICQEDYRDNEKIGTLDCDHEYHAECLKKWLFIKNVCPICKSEALATKS

*********************RGYLLPEPCVVLGGVTSFPQPMQTIV******************MFY**************************YV***********************************************************************************************************************LVATGGMDPVLAHSHNHFIQGNFIGQPFQPAGWL**********************************************************************************************************************************************HLRVLPSDGVALLEIPDFYEVGNFIDRHRDMRLDIEDMSYEELLALGERIGNVNTGLSEEIVARQLKTRVYLSATNYINL***********SCIICQEDYRDNEKIGTLDCDHEYHAECLKKWLFIKNVCPICKS*******

*********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************RVLPSDGVALLEIPDFYEVGNFIDRHRDMRLDIEDMSYEELLALGERIGNVNTGLSEEIVARQLKTRVY******************PGSCIICQEDYRDNEKIGTLDCDHEYHAECLKKWLFIKNVCPICKSEALA***

********TSQMIDLEMDQQNRGYLLPEPCVVLGGVTSFPQPMQTIVRASGNTSSLDAHQHYDSAMFYGMPQYHGVHHHHAASVDLGASTASNLYVPYMPTLSSGMPVNHGSTDQLPSSRNFGVIGASAEEYGRNSHFMDNVRGSYKRKNTEGFPGSFQNLNA************PRHPDGVTPMDAACFSLPQYRGNGTPSIREVESQRSVRNRLVATGGMDPVLAHSHNHFIQGNFIGQPFQPAGWLE********SWTQAPAIPYMHGSNVSGAPMDSGNMVVQRYPETAGNRNSSTFLQPPVNIQHLSFPHPPPPFQGIRNHNTNVHPQVAAASFRVPSSYRTMNISQDGSEMVPRHMGPVPPTGFRIYRSPREGPVPEALRQRSLPHLRVLPSDGVALLEIPDFYEVGNFIDRHRDMRLDIEDMSYEELLALGERIGNVNTGLSEEIVARQLKTRVYLSATNYINLEEPASKDQEPGSCIICQEDYRDNEKIGTLDCDHEYHAECLKKWLFIKNVCPICKSEALATKS

**********************GYLLPEPCVVLGGVTSFPQPMQTIVRASGNTSSLDAHQHYDSAMFYGMPQYHGVHHHHAASVDLGASTASNLYVPYMPTLSSGMPVNHGSTDQLPSSRNF*************SHF**NVRGSYKRKNTEGFPGSFQNL**********************PM*AACFS************************************************************************P***********************************TFLQPP***************************************************MVPRHMGPVPPTGFRIYRSPREGPVPEALRQRSLPHLRVLPSDGVALLEIPDFYEVGNFIDRHRDMRLDIEDMSYEELLALGERIGNVNTGLSEEIVARQLKTRVYLS****************PGSCIICQEDYRDNEKIGTLDCDHEYHAECLKKWLFIKNVCPICKSE******

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		533	2.2.26 [Sep-21-2011]
Q9LT17		340	E3 ubiquitin ligase BIG B	no	no	0.189	0.297	0.387	4e-16
Q8L649		248	E3 ubiquitin ligase BIG B	no	no	0.191	0.411	0.381	3e-15
Q3UHJ8		407	RING finger protein 44 OS	no	no	0.196	0.257	0.322	1e-11
Q08CG8		448	RING finger protein 44 OS	no	no	0.174	0.207	0.333	2e-11
Q4V7B8		350	RING finger protein 44 OS	yes	no	0.180	0.274	0.315	2e-11
Q8BI21		518	RING finger protein 38 OS	no	no	0.180	0.185	0.315	2e-11
Q9H0F5		515	RING finger protein 38 OS	yes	no	0.180	0.186	0.315	3e-11
Q7L0R7		432	RING finger protein 44 OS	no	no	0.174	0.215	0.314	3e-11
E9QAU8		347	RING finger protein 165 O	no	no	0.178	0.273	0.320	2e-09
Q6ZSG1		346	RING finger protein 165 O	no	no	0.178	0.274	0.320	3e-09

>sp\|Q9LT17\|BBR_ARATH E3 ubiquitin ligase BIG BROTHER-related OS=Arabidopsis thaliana GN=BBR PE=2 SV=1	Back alignment and function desciption

 Score = 86.7 bits (213), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 43/111 (38%), Positives = 63/111 (56%), Gaps = 10/111 (9%)

Query: 423 RLDIEDMSYEELLALGERIGNVNTGLSEEIVARQLKTRVYLSATNYINLEEPASKDQEPG 482
            +D +++SYEELLALG+ +G  + GLS + +A  L ++ Y    N     E         
Sbjct: 237 EMDPDELSYEELLALGDIVGTESRGLSADTIA-SLPSKRYKEGDNQNGTNE--------- 286

Query: 483 SCIICQEDYRDNEKIGTLDCDHEYHAECLKKWLFIKNVCPICKSEALATKS 533
           SC+IC+ DY D+E +  L C H YH+EC+  WL I  VCP+C +E   + S
Sbjct: 287 SCVICRLDYEDDEDLILLPCKHSYHSECINNWLKINKVCPVCSAEVSTSTS 337

E3 ubiquitin-ligase probably involved in organ size regulation.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp\|Q8L649\|BB_ARATH E3 ubiquitin ligase BIG BROTHER OS=Arabidopsis thaliana GN=BB PE=1 SV=1	Back alignment and function description

>sp\|Q3UHJ8\|RNF44_MOUSE RING finger protein 44 OS=Mus musculus GN=Rnf44 PE=2 SV=1	Back alignment and function description

>sp\|Q08CG8\|RNF44_DANRE RING finger protein 44 OS=Danio rerio GN=rnf44 PE=2 SV=1	Back alignment and function description

>sp\|Q4V7B8\|RNF44_RAT RING finger protein 44 OS=Rattus norvegicus GN=Rnf44 PE=2 SV=1	Back alignment and function description

>sp\|Q8BI21\|RNF38_MOUSE RING finger protein 38 OS=Mus musculus GN=Rnf38 PE=2 SV=1	Back alignment and function description

>sp\|Q9H0F5\|RNF38_HUMAN RING finger protein 38 OS=Homo sapiens GN=RNF38 PE=1 SV=4	Back alignment and function description

>sp\|Q7L0R7\|RNF44_HUMAN RING finger protein 44 OS=Homo sapiens GN=RNF44 PE=2 SV=1	Back alignment and function description

>sp\|E9QAU8\|RN165_MOUSE RING finger protein 165 OS=Mus musculus GN=Rnf165 PE=2 SV=1	Back alignment and function description

>sp\|Q6ZSG1\|RN165_HUMAN RING finger protein 165 OS=Homo sapiens GN=RNF165 PE=1 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		533
255554674		549	ring finger protein, putative [Ricinus c	0.984	0.956	0.652	0.0
224056535		535	predicted protein [Populus trichocarpa]	0.962	0.958	0.625	1e-178
224116702		517	predicted protein [Populus trichocarpa]	0.928	0.957	0.619	1e-175
225461582		543	PREDICTED: uncharacterized protein LOC10	0.966	0.948	0.569	1e-161
147855103		656	hypothetical protein VITISV_007038 [Viti	0.889	0.722	0.554	1e-139
302142938		489	unnamed protein product [Vitis vinifera]	0.842	0.918	0.489	1e-132
449438873		545	PREDICTED: uncharacterized protein LOC10	0.964	0.943	0.495	1e-126
356546838		528	PREDICTED: uncharacterized protein LOC10	0.934	0.943	0.450	1e-110
225429109		461	PREDICTED: uncharacterized protein LOC10	0.816	0.943	0.470	3e-94
225429088		460	PREDICTED: uncharacterized protein LOC10	0.816	0.945	0.459	3e-93

>gi\|255554674\|ref\|XP_002518375.1\| ring finger protein, putative [Ricinus communis] gi\|223542470\|gb\|EEF44011.1\| ring finger protein, putative [Ricinus communis]	Back alignment and taxonomy information

 Score =  685 bits (1767), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 356/546 (65%), Positives = 429/546 (78%), Gaps = 21/546 (3%)

Query: 1   MGQRNMPCTSQMIDLEMDQQNRGYLLPEPCVVLGGVTSFPQP-MQTIVRASGNTSSLDAH 59
           MGQRNM CTSQMIDLE+D+Q +GYL PEPC++LGGV++FPQ  +QT+V ASG+T+++DAH
Sbjct: 1   MGQRNMLCTSQMIDLEVDRQGQGYLHPEPCILLGGVSNFPQSDIQTMVTASGSTTNIDAH 60

Query: 60  ---QHYDSAMFYGMPQYHGVHHH---HAASVDLGASTASNLYVPYMPTLSSGMPVNHGST 113
              +HYDSA+FYGMPQYHGV HH   HA ++DLG +TASN YVPYM T SSG+P++HGS 
Sbjct: 61  RLPEHYDSAIFYGMPQYHGVQHHPQHHAPNLDLGVATASNFYVPYM-TPSSGIPLSHGSC 119

Query: 114 DQLPSSRNFGVIGASAEEYGRNSHFMDNVRGSYKRKNTEGFPGSFQNLNAPASSSSSVAP 173
           D LPSS ++GVIG S +EYG N+HFMDN RGSYKRKN EG PG+FQ +NA A SSSSV  
Sbjct: 120 DHLPSSTSYGVIGVSGDEYGMNNHFMDNARGSYKRKNAEGNPGNFQYVNASAGSSSSVLS 179

Query: 174 LHPRHPDGVTPMDAACFSLPQYRGNGTPSIREVESQRSVRNRLVATGGMDPVLAHSHNHF 233
              RHPDG++ MDA+ F+ PQYRGNG  SIREV S RSVRNR  ATG ++ VLAHS NHF
Sbjct: 180 T--RHPDGISLMDASSFASPQYRGNGILSIREVGSHRSVRNRSGATG-LESVLAHSQNHF 236

Query: 234 IQGNFIGQPFQPAG--WLEQ---PSDGGGSSWTQAPAIPYMHGSNVSGAPMDSGNMVVQR 288
           IQGN+IGQPFQPAG  W +Q    SD G  +W Q PAI YMHG+NV+G  +++G++V QR
Sbjct: 237 IQGNYIGQPFQPAGSLWADQHSSSSDAGTLAWNQNPAINYMHGNNVNGGSVETGSIVPQR 296

Query: 289 YPETAGNRNSSTFLQP-PVNIQHLSFPHPPPPFQGIRNHNTNVHPQVAAASFRVPSSYRT 347
           Y E + NR+++TFL P P NI+H +F HP PP QG+R HN NV PQV+AASFR  +SY +
Sbjct: 297 YHELSSNRSNTTFLHPSPPNIRHHNFHHPLPPIQGMRGHNLNVPPQVSAASFRGLTSYAS 356

Query: 348 ---MNISQDGSEMVPRHMGPVPPTGFRIYRSPREGPVPEA-LRQRSLPHLRVLPSDGVAL 403
              +N SQDG ++  RH G V PTG RIYR  R+G +PE  LR R+LPHLRVLP+D +A+
Sbjct: 357 QSNVNPSQDGLDIGVRHPGSVQPTGLRIYRPHRDGVIPETTLRHRNLPHLRVLPTDRIAV 416

Query: 404 LEIPDFYEVGNFIDRHRDMRLDIEDMSYEELLALGERIGNVNTGLSEEIVARQLKTRVYL 463
           LE PD+YEV N++D H DMRLDIEDMSYEELLALGERIG+VNTGLSEE +  QLKTR YL
Sbjct: 417 LEFPDYYEVENYVDHHSDMRLDIEDMSYEELLALGERIGSVNTGLSEETIRSQLKTRKYL 476

Query: 464 SATNYINLEEPASKDQEPGSCIICQEDYRDNEKIGTLDCDHEYHAECLKKWLFIKNVCPI 523
           S+   INLEE    DQE GSCIICQ++Y+  EKIGTLDC HEYHA+CLKKWL +KNVCPI
Sbjct: 477 SSPMSINLEEITCMDQELGSCIICQDEYKSKEKIGTLDCGHEYHADCLKKWLRVKNVCPI 536

Query: 524 CKSEAL 529
           CKSEAL
Sbjct: 537 CKSEAL 542

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224056535\|ref\|XP_002298898.1\| predicted protein [Populus trichocarpa] gi\|222846156\|gb\|EEE83703.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|224116702\|ref\|XP_002317370.1\| predicted protein [Populus trichocarpa] gi\|222860435\|gb\|EEE97982.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|225461582\|ref\|XP_002282878.1\| PREDICTED: uncharacterized protein LOC100264059 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|147855103\|emb\|CAN79595.1\| hypothetical protein VITISV_007038 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|302142938\|emb\|CBI20233.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449438873\|ref\|XP_004137212.1\| PREDICTED: uncharacterized protein LOC101205883 [Cucumis sativus] gi\|449526842\|ref\|XP_004170422.1\| PREDICTED: uncharacterized protein LOC101226032 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356546838\|ref\|XP_003541829.1\| PREDICTED: uncharacterized protein LOC100800642 [Glycine max]	Back alignment and taxonomy information

>gi\|225429109\|ref\|XP_002269505.1\| PREDICTED: uncharacterized protein LOC100251458 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|225429088\|ref\|XP_002269031.1\| PREDICTED: uncharacterized protein LOC100258411 [Vitis vinifera] gi\|147805611\|emb\|CAN62955.1\| hypothetical protein VITISV_018197 [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		533
TAIR\|locus:2009660		494	AT1G53190 [Arabidopsis thalian	0.560	0.605	0.507	1.4e-97
TAIR\|locus:2086305		486	AT3G15070 [Arabidopsis thalian	0.382	0.419	0.534	7.7e-70
TAIR\|locus:2124271		666	MBR2 "MED25 BINDING RING-H2 PR	0.219	0.175	0.5	8.7e-30
TAIR\|locus:2125284		497	AT4G31450 [Arabidopsis thalian	0.215	0.231	0.5	5.1e-27
TAIR\|locus:2160031		691	AT5G42940 [Arabidopsis thalian	0.232	0.179	0.488	6.7e-27
TAIR\|locus:2159634		525	AT5G10650 [Arabidopsis thalian	0.377	0.382	0.372	2e-26
TAIR\|locus:2028225		645	AT1G45180 [Arabidopsis thalian	0.249	0.206	0.448	4.1e-26
TAIR\|locus:2149378		520	AT5G24870 [Arabidopsis thalian	0.243	0.25	0.470	2e-25
TAIR\|locus:2027804		367	AT1G73760 [Arabidopsis thalian	0.234	0.340	0.384	7.2e-21
TAIR\|locus:2030933		368	AT1G17970 [Arabidopsis thalian	0.255	0.369	0.364	3.9e-19

TAIR\|locus:2009660 AT1G53190 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 710 (255.0 bits), Expect = 1.4e-97, Sum P(2) = 1.4e-97
 Identities = 173/341 (50%), Positives = 207/341 (60%)

Query:   213 RNRLVATGGMDPVL-AHSHNHFIQGNFIGQ-PFQPAG--WLEQP---SDGGGSSWTQAPA 265
             RNR  A   ++ VL +H+ N+FIQGN+ G  PF P G  W +Q    SDG  S W   P 
Sbjct:   165 RNRPGAVT-VNTVLPSHAPNNFIQGNYAGHHPFPPPGSMWYDQHHGRSDGSPSFW---PT 220

Query:   266 IPYMHGSNVSGAPMDSGNMVVQRYPETAGNRNSSTFLQP----PVNIQHLSFPHP-PPPF 320
              PYMHGSN+    ++S +            RN ++F+ P    P +  +    HP PPP 
Sbjct:   221 -PYMHGSNIFAGSIESSS------------RNPTSFMYPSQLNPRDHYYSHHHHPAPPPV 267

Query:   321 QGIRNHNTNVHPQVAA-ASFRVP-SSY---RTMNISQDGSEMVPRHMGPVPPTGFRIYRS 375
             QG+R  N  ++P  A+ AS+RVP  S+    TMN    GSEM   HMGPV PTGFRIY+ 
Sbjct:   268 QGMRGQNATLYPHTASSASYRVPPGSFTPQNTMNSGPLGSEMGSSHMGPVQPTGFRIYQH 327

Query:   376 -PREGPVPEA-LRQR--SLPHLRVLPSDGVALLEIPDFY--EVGNFIDRHRDMRLDIEDM 429
               R+  VP A LRQ    +P LRV+P D VALLE  DF      N ID HRDMRLDIE+M
Sbjct:   328 HQRDDSVPVATLRQHRGGVPRLRVMPDDEVALLEFGDFLGGSGNNHIDHHRDMRLDIEEM 387

Query:   430 SYEELLALGERIGNVNTGLSEEIVARQLKTRVYLSATNYIN-LEEPASKDQEPGSCIICQ 488
             SYEELLAL ERIG VNTGL EE V   LKTR   S  N+      P +KD E   C ICQ
Sbjct:   388 SYEELLALSERIGTVNTGLPEEDVKNHLKTRT-CSGINFEKESSSPRTKDLETEPCTICQ 446

Query:   489 EDYRDNEKIGTLDCDHEYHAECLKKWLFIKNVCPICKSEAL 529
             E +++ EKI TLDC HEYHAECL+KWL +KNVCPICKSEAL
Sbjct:   447 ESFKNEEKIATLDCGHEYHAECLEKWLIVKNVCPICKSEAL 487

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA;ISS

TAIR\|locus:2086305 AT3G15070 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2124271 MBR2 "MED25 BINDING RING-H2 PROTEIN 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2125284 AT4G31450 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2160031 AT5G42940 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2159634 AT5G10650 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2028225 AT1G45180 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2149378 AT5G24870 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2027804 AT1G73760 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2030933 AT1G17970 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		533
pfam13639		46	pfam13639, zf-RING_2, Ring finger domain	4e-14
cd00162		45	cd00162, RING, RING-finger (Really Interesting New	1e-10
pfam13923		45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	2e-08
pfam00097		40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	1e-07
COG5540		374	COG5540, COG5540, RING-finger-containing ubiquitin	1e-07
smart00184		40	smart00184, RING, Ring finger	3e-07
pfam12678		73	pfam12678, zf-rbx1, RING-H2 zinc finger	8e-07
COG5194		88	COG5194, APC11, Component of SCF ubiquitin ligase	6e-06
COG5243		491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	8e-05
PHA02929		238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	6e-04
pfam13920		49	pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RI	0.001
PHA02825		162	PHA02825, PHA02825, LAP/PHD finger-like protein; P	0.002
smart00249		47	smart00249, PHD, PHD zinc finger	0.003

>gnl\|CDD\|222279 pfam13639, zf-RING_2, Ring finger domain	Back alignment and domain information

 Score = 66.3 bits (162), Expect = 4e-14
 Identities = 18/46 (39%), Positives = 27/46 (58%)

Query: 482 GSCIICQEDYRDNEKIGTLDCDHEYHAECLKKWLFIKNVCPICKSE 527
             C IC +++   E++  L C H +H ECL KWL   N CP+C++ 
Sbjct: 1   DECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)

Back alignment and domain information

>gnl\|CDD\|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger)	Back alignment and domain information

>gnl\|CDD\|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger)	Back alignment and domain information

>gnl\|CDD\|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>gnl\|CDD\|214546 smart00184, RING, Ring finger	Back alignment and domain information

>gnl\|CDD\|221705 pfam12678, zf-rbx1, RING-H2 zinc finger	Back alignment and domain information

>gnl\|CDD\|227521 COG5194, APC11, Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]	Back alignment and domain information

>gnl\|CDD\|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>gnl\|CDD\|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional	Back alignment and domain information

>gnl\|CDD\|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger)	Back alignment and domain information

>gnl\|CDD\|177491 PHA02825, PHA02825, LAP/PHD finger-like protein; Provisional	Back alignment and domain information

>gnl\|CDD\|214584 smart00249, PHD, PHD zinc finger	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		533
KOG4628		348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.52
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.47
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.22
COG5540		374	RING-finger-containing ubiquitin ligase [Posttrans	99.18
PHA02929		238	N1R/p28-like protein; Provisional	99.13
COG5243		491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.13
KOG0317		293	consensus Predicted E3 ubiquitin ligase, integral	99.1
KOG0823		230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.02
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	99.0
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	98.9
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.87
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.87
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.86
PF12861		85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.86
PHA02926		242	zinc finger-like protein; Provisional	98.81
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	98.77
PF14634		44	zf-RING_5: zinc-RING finger domain	98.71
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	98.68
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.64
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.61
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.6
TIGR00599		397	rad18 DNA repair protein rad18. This family is bas	98.55
COG5194		88	APC11 Component of SCF ubiquitin ligase and anapha	98.48
COG5574		271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.45
KOG0828		636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.35
KOG1734		328	consensus Predicted RING-containing E3 ubiquitin l	98.28
COG5219		1525	Uncharacterized conserved protein, contains RING Z	98.23
smart00744		49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.23
KOG1493		84	consensus Anaphase-promoting complex (APC), subuni	98.23
KOG2164		513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.18
KOG2177		386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.12
PF04564		73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.11
PF11793		70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.04
KOG0287		442	consensus Postreplication repair protein RAD18 [Re	98.03
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.01
KOG2930		114	consensus SCF ubiquitin ligase, Rbx1 component [Po	97.97
COG5432		391	RAD18 RING-finger-containing E3 ubiquitin ligase [	97.92
KOG4265		349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.81
KOG0311		381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.76
KOG1039		344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.75
KOG0825		1134	consensus PHD Zn-finger protein [General function	97.7
KOG4445		368	consensus Uncharacterized conserved protein, conta	97.61
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.45
PF14835		65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.41
KOG1428		3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.22
KOG4172		62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.15
COG5152		259	Uncharacterized conserved protein, contains RING a	97.0
KOG0978		698	consensus E3 ubiquitin ligase involved in syntaxin	96.95
KOG4159		398	consensus Predicted E3 ubiquitin ligase [Posttrans	96.88
PF11789		57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	96.86
KOG0297		391	consensus TNF receptor-associated factor [Signal t	96.85
KOG1941		518	consensus Acetylcholine receptor-associated protei	96.8
KOG1785		563	consensus Tyrosine kinase negative regulator CBL [	96.76
KOG4275		350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.58
KOG2879		298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.52
PF05883		134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	96.37
KOG3970		299	consensus Predicted E3 ubiquitin ligase [Posttrans	96.27
KOG1002		791	consensus Nucleotide excision repair protein RAD16	96.26
KOG3039		303	consensus Uncharacterized conserved protein [Funct	96.24
PF12906		47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	96.11
PHA03096		284	p28-like protein; Provisional	96.01
PHA02825		162	LAP/PHD finger-like protein; Provisional	96.0
KOG4692		489	consensus Predicted E3 ubiquitin ligase [Posttrans	95.96
KOG1813		313	consensus Predicted E3 ubiquitin ligase [Posttrans	95.87
KOG2660		331	consensus Locus-specific chromosome binding protei	95.87
KOG0801		205	consensus Predicted E3 ubiquitin ligase [Posttrans	95.75
PHA02862		156	5L protein; Provisional	95.75
KOG0827		465	consensus Predicted E3 ubiquitin ligase [Posttrans	95.71
COG5236		493	Uncharacterized conserved protein, contains RING Z	95.61
KOG1952		950	consensus Transcription factor NF-X1, contains NFX	95.61
KOG1814		445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.34
PF04641		260	Rtf2: Rtf2 RING-finger	95.16
PF14570		48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.1
PF10367		109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	95.06
KOG1571		355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.01
COG5175		480	MOT2 Transcriptional repressor [Transcription]	94.69
COG5222		427	Uncharacterized conserved protein, contains RING Z	94.57
KOG2114		933	consensus Vacuolar assembly/sorting protein PEP5/V	94.4
KOG3268		234	consensus Predicted E3 ubiquitin ligase [Posttrans	93.85
KOG1001		674	consensus Helicase-like transcription factor HLTF/	93.5
KOG3053		293	consensus Uncharacterized conserved protein [Funct	93.31
KOG2034		911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	93.26
PF10272		358	Tmpp129: Putative transmembrane protein precursor;	93.11
PF14447		55	Prok-RING_4: Prokaryotic RING finger family 4	92.99
KOG0298		1394	consensus DEAD box-containing helicase-like transc	92.5
KOG1609		323	consensus Protein involved in mRNA turnover and st	92.37
KOG1940		276	consensus Zn-finger protein [General function pred	92.23
PF08746		43	zf-RING-like: RING-like domain; InterPro: IPR01485	92.11
COG5183		1175	SSM4 Protein involved in mRNA turnover and stabili	92.1
KOG0826		357	consensus Predicted E3 ubiquitin ligase involved i	91.68
PF03854		50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	90.8
KOG2932		389	consensus E3 ubiquitin ligase involved in ubiquiti	90.54
PF07800		162	DUF1644: Protein of unknown function (DUF1644); In	89.62
PF14446		54	Prok-RING_1: Prokaryotic RING finger family 1	89.43
KOG3002		299	consensus Zn finger protein [General function pred	89.39
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	87.17
KOG1812		384	consensus Predicted E3 ubiquitin ligase [Posttrans	86.72
KOG0825		1134	consensus PHD Zn-finger protein [General function	86.68
KOG0309		1081	consensus Conserved WD40 repeat-containing protein	86.36
COG5220		314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	86.02
PF05290		140	Baculo_IE-1: Baculovirus immediate-early protein (	84.74
KOG4362		684	consensus Transcriptional regulator BRCA1 [Replica	84.33
KOG1100		207	consensus Predicted E3 ubiquitin ligase [Posttrans	82.88
KOG3899		381	consensus Uncharacterized conserved protein [Funct	81.17

>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

Probab=99.52  E-value=9.2e-15  Score=151.84  Aligned_cols=74  Identities=28%  Similarity=0.807  Sum_probs=56.7

Q ss_pred             CCCHHHHHHhhcceeeecccccccccCCcCCCCCCCcccccccccCCCCceEEeCCCChhhHHHHHHHHhcC-CCCcccc
Q 009499          447 GLSEEIVARQLKTRVYLSATNYINLEEPASKDQEPGSCIICQEDYRDNEKIGTLDCDHEYHAECLKKWLFIK-NVCPICK  525 (533)
Q Consensus       447 glSee~I~~~L~~~~~~ss~~~~~~ee~~~~~eee~~C~ICLEey~~~e~v~~LpCgH~FH~~CI~qWL~~k-~sCPvCR  525 (533)
                      .+.+..+ +.++..+|+..         .+ ....+.|+||||+|+++|++++|||+|.||..||+.||... ..||+||
T Consensus       206 r~~k~~l-~~~p~~~f~~~---------~~-~~~~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK  274 (348)
T KOG4628|consen  206 RLIKRLL-KKLPVRTFTKG---------DD-EDATDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCK  274 (348)
T ss_pred             hhHHHHH-hhCCcEEeccc---------cc-cCCCceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCC
Confidence            3444444 44666666543         11 12226999999999999999999999999999999999986 5599999


Q ss_pred             cCcCCC
Q 009499          526 SEALAT  531 (533)
Q Consensus       526 ~~l~~~  531 (533)
                      +.+..+
T Consensus       275 ~di~~~  280 (348)
T KOG4628|consen  275 RDIRTD  280 (348)
T ss_pred             CcCCCC
Confidence            987653

>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A	Back alignment and domain information

>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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

>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PHA02929 N1R/p28-like protein; Provisional	Back alignment and domain information

>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional	Back alignment and domain information

>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)

Back alignment and domain information

>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A	Back alignment and domain information

>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A	Back alignment and domain information

>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger	Back alignment and domain information

>PHA02926 zinc finger-like protein; Provisional	Back alignment and domain information

>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF14634 zf-RING_5: zinc-RING finger domain	Back alignment and domain information

>smart00504 Ubox Modified RING finger domain	Back alignment and domain information

>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A	Back alignment and domain information

>smart00184 RING Ring finger	Back alignment and domain information

>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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

>TIGR00599 rad18 DNA repair protein rad18	Back alignment and domain information

>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]	Back alignment and domain information

>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]	Back alignment and domain information

>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins	Back alignment and domain information

>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis	Back alignment and domain information

>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A	Back alignment and domain information

>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]	Back alignment and domain information

>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A	Back alignment and domain information

>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]	Back alignment and domain information

>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]	Back alignment and domain information

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]	Back alignment and domain information

>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B	Back alignment and domain information

>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]	Back alignment and domain information

>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]	Back alignment and domain information

>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C	Back alignment and domain information

>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]	Back alignment and domain information

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]	Back alignment and domain information

>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]	Back alignment and domain information

>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length	Back alignment and domain information

>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]	Back alignment and domain information

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A	Back alignment and domain information

>PHA03096 p28-like protein; Provisional	Back alignment and domain information

>PHA02825 LAP/PHD finger-like protein; Provisional	Back alignment and domain information

>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]	Back alignment and domain information

>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PHA02862 5L protein; Provisional	Back alignment and domain information

>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]	Back alignment and domain information

>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]	Back alignment and domain information

>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF04641 Rtf2: Rtf2 RING-finger	Back alignment and domain information

>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B	Back alignment and domain information

>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1	Back alignment and domain information

>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>COG5175 MOT2 Transcriptional repressor [Transcription]	Back alignment and domain information

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]	Back alignment and domain information

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]	Back alignment and domain information

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans	Back alignment and domain information

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4	Back alignment and domain information

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]	Back alignment and domain information

>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]	Back alignment and domain information

>KOG1940 consensus Zn-finger protein [General function prediction only]	Back alignment and domain information

>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO)	Back alignment and domain information

>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]	Back alignment and domain information

>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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

>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function	Back alignment and domain information

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1	Back alignment and domain information

>KOG3002 consensus Zn finger protein [General function prediction only]	Back alignment and domain information

>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]	Back alignment and domain information

>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0	Back alignment and domain information

>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]	Back alignment and domain information

>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]	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		533
2ep4_A		74	Solution Structure Of Ring Finger From Human Ring F		2e-07
1x4j_A		75	Solution Structure Of Ring Finger In Ring Finger Pr		3e-07
2ect_A		78	Solution Structure Of The Zinc Finger, C3hc4 Type (		2e-04
2kiz_A		69	Solution Structure Of Arkadia Ring-H2 Finger Domain		7e-04

>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger Protein 24 Length = 74

Back alignment and structure

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 18/46 (39%), Positives = 29/46 (63%)
Query: 484 CIICQEDYRDNEKIGTLDCDHEYHAECLKKWLFIKNVCPICKSEAL 529
           C +C ED++  +++G   C H +H +CL KWL ++ VCP+C    L
Sbjct: 18  CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVL 63

PyMOL of 2ep4

>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein 38 Length = 75

Back alignment and structure

>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring Finger) Domain Of Ring Finger Protein 126 Length = 78

Back alignment and structure

>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain Length = 69

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		533
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	4e-18
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	3e-15
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	8e-15
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	1e-13
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	2e-13
2ect_A		78	Ring finger protein 126; metal binding protein, st	5e-13
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	9e-12
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	9e-12
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	2e-11
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	3e-11
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	5e-11
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	1e-10
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	2e-10
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-08
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	8e-04
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	3e-08
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	2e-07
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	3e-07
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	6e-07
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	9e-07
4epo_C		149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	1e-06
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	2e-06
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	2e-06
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	4e-06
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	4e-06
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	1e-05
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	1e-05
3nw0_A		238	Non-structural maintenance of chromosomes element	3e-05
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	3e-05
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	5e-05
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	5e-05
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	9e-05
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	2e-04
2ysm_A		111	Myeloid/lymphoid or mixed-lineage leukemia protein	3e-04
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	6e-04

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 74	Back alignment and structure

 Score = 77.9 bits (192), Expect = 4e-18
 Identities = 18/59 (30%), Positives = 30/59 (50%)

Query: 475 ASKDQEPGSCIICQEDYRDNEKIGTLDCDHEYHAECLKKWLFIKNVCPICKSEALATKS 533
             +      C +C ED++  +++G   C H +H +CL KWL ++ VCP+C    L    
Sbjct: 9   VKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQ 67

PyMOL of 2ep4

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 75	Back alignment and structure

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens} Length = 69	Back alignment and structure

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens} Length = 91	Back alignment and structure

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1 Length = 68	Back alignment and structure

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 78	Back alignment and structure

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 69	Back alignment and structure

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81	Back alignment and structure

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A Length = 55	Back alignment and structure

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70	Back alignment and structure

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus} Length = 71	Back alignment and structure

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens} Length = 64	Back alignment and structure

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1 Length = 55	Back alignment and structure

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus} Length = 133	Back alignment and structure

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus} Length = 133	Back alignment and structure

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81	Back alignment and structure

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 74	Back alignment and structure

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 72	Back alignment and structure

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A Length = 108	Back alignment and structure

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens} Length = 100	Back alignment and structure

>4epo_C E3 ubiquitin-protein ligase RNF8; coiled-coil, E3 ubiquitin ligase, protein binding complex; 4.80A {Homo sapiens} Length = 149	Back alignment and structure

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 71	Back alignment and structure

>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster} Length = 381	Back alignment and structure

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus} Length = 117	Back alignment and structure

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A Length = 106	Back alignment and structure

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3 Length = 60	Back alignment and structure

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B Length = 78	Back alignment and structure

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens} Length = 238	Back alignment and structure

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A* Length = 389	Back alignment and structure

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens} Length = 99	Back alignment and structure

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1 Length = 114	Back alignment and structure

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80	Back alignment and structure

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 94	Back alignment and structure

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens} Length = 111	Back alignment and structure

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 56	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		533
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.59
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	99.51
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	99.49
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.49
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.48
2ect_A		78	Ring finger protein 126; metal binding protein, st	99.46
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.39
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.39
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	99.38
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	99.36
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.35
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.32
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	99.31
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	99.3
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	99.29
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	99.29
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	99.27
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	99.26
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	99.26
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	99.25
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	99.23
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.23
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	99.22
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	99.21
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	99.16
4ayc_A		138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.16
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	99.15
1t1h_A		78	Gspef-atpub14, armadillo repeat containing protein	99.15
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	99.13
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.12
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.12
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.1
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.1
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	99.08
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.06
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	99.05
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	99.04
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	99.02
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.02
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.99
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	98.97
2kr4_A		85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.96
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.95
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.95
1z6u_A		150	NP95-like ring finger protein isoform B; structura	98.94
1wgm_A		98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.94
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	98.93
2kre_A		100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.92
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	98.88
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.87
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	98.87
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.82
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	98.81
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	98.8
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	98.74
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.73
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	98.71
4ic3_A		74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.69
2yu4_A		94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.67
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.64
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	98.61
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.61
2ea5_A		68	Cell growth regulator with ring finger domain prot	98.51
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.48
2f42_A		179	STIP1 homology and U-box containing protein 1; cha	98.47
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.46
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.35
2bay_A		61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.35
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.34
3t6p_A		345	Baculoviral IAP repeat-containing protein 2; ring,	98.22
3vk6_A		101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.7
3nw0_A		238	Non-structural maintenance of chromosomes element	97.49
2ko5_A		99	Ring finger protein Z; lassa fever virus-Z, negati	95.06
2jun_A		101	Midline-1; B-BOX, TRIM, ring finger, alternative s	94.59
2lri_C		66	Autoimmune regulator; Zn binding protein domain, a	93.85
1we9_A		64	PHD finger family protein; structural genomics, PH	90.39
1wil_A		89	KIAA1045 protein; ring finger domain, structural g	89.87
2k16_A		75	Transcription initiation factor TFIID subunit 3; p	89.32
2l5u_A		61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	87.12
1mm2_A		61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	86.88
3m62_A		968	Ubiquitin conjugation factor E4; armadillo-like re	85.82
1wem_A		76	Death associated transcription factor 1; structura	85.45
1fp0_A		88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	83.21
1wep_A		79	PHF8; structural genomics, PHD domain, riken struc	82.05
1f62_A		51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	82.04
2yql_A		56	PHD finger protein 21A; PHD domain, structural gen	81.8
2ysm_A		111	Myeloid/lymphoid or mixed-lineage leukemia protein	81.72
1weu_A		91	Inhibitor of growth family, member 4; structural g	80.89
2puy_A		60	PHD finger protein 21A; PHD finger, histone CODE,	80.82
2l43_A		88	N-teminal domain from histone H3.3, linker, PHD1 f	80.76
1wen_A		71	Inhibitor of growth family, member 4; ING1-like pr	80.74
3i2d_A		371	E3 SUMO-protein ligase SIZ1; signal transduction,	80.19
1wew_A		78	DNA-binding family protein; structural genomics, P	80.17

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens}	Back alignment and structure

Probab=99.59  E-value=1.4e-15  Score=128.49  Aligned_cols=78  Identities=23%  Similarity=0.492  Sum_probs=63.6

Q ss_pred             CCCCCCCHHHHHHhhcceeeecccccccccCCcCCCCCCCcccccccccCCCCceEEeCCCChhhHHHHHHHHhcCCCCc
Q 009499          443 NVNTGLSEEIVARQLKTRVYLSATNYINLEEPASKDQEPGSCIICQEDYRDNEKIGTLDCDHEYHAECLKKWLFIKNVCP  522 (533)
Q Consensus       443 ~v~~glSee~I~~~L~~~~~~ss~~~~~~ee~~~~~eee~~C~ICLEey~~~e~v~~LpCgH~FH~~CI~qWL~~k~sCP  522 (533)
                      ....+++++.| +.|+..++...         ....+++..|+||+++|..++.+..|+|+|.||..||++||+.+.+||
T Consensus        12 ~~~~~~s~~~i-~~lp~~~~~~~---------~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~CP   81 (91)
T 2l0b_A           12 VANPPASKESI-DALPEILVTED---------HGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCP   81 (91)
T ss_dssp             SCCCCCCHHHH-HTSCEEECCTT---------CSSSSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCBCT
T ss_pred             cCCCCCCHHHH-HhCCCeeeccc---------ccccCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCcCc
Confidence            45578899988 55666654422         122456788999999999999899999999999999999999999999


Q ss_pred             ccccCcCC
Q 009499          523 ICKSEALA  530 (533)
Q Consensus       523 vCR~~l~~  530 (533)
                      +||+++.+
T Consensus        82 ~Cr~~~~~   89 (91)
T 2l0b_A           82 VCRCMFPP   89 (91)
T ss_dssp             TTCCBSSC
T ss_pred             CcCccCCC
Confidence            99998865

PyMOL of 2l0b

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens}	Back alignment and structure

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1	Back alignment and structure

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}	Back alignment and structure

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1	Back alignment and structure

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A	Back alignment and structure

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus}	Back alignment and structure

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 4f52_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A	Back alignment and structure

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens}	Back alignment and structure

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1	Back alignment and structure

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus}	Back alignment and structure

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens}	Back alignment and structure

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus}	Back alignment and structure

>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C	Back alignment and structure

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2	Back alignment and structure

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens}	Back alignment and structure

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}	Back alignment and structure

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens}	Back alignment and structure

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens}	Back alignment and structure

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens}	Back alignment and structure

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A	Back alignment and structure

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1	Back alignment and structure

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens}	Back alignment and structure

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}	Back alignment and structure

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1	Back alignment and structure

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus}	Back alignment and structure

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, CHR protein, DNA repair, metal-binding, nucleus; 2.12A {Homo sapiens}	Back alignment and structure

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B	Back alignment and structure

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens}	Back alignment and structure

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2	Back alignment and structure

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A	Back alignment and structure

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B	Back alignment and structure

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1	Back alignment and structure

>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc binuclear cluster, zinc finger, DNA-binding protein; 2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1	Back alignment and structure

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens}	Back alignment and structure

>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A	Back alignment and structure

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B	Back alignment and structure

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A*	Back alignment and structure

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1	Back alignment and structure

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B*	Back alignment and structure

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2	Back alignment and structure

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A	Back alignment and structure

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3	Back alignment and structure

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens}	Back alignment and structure

>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster}	Back alignment and structure

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1	Back alignment and structure

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C	Back alignment and structure

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase complex, ring zinc-finger, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 2yhn_A	Back alignment and structure

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A	Back alignment and structure

>3htk_C E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}	Back alignment and structure

>3t6p_A Baculoviral IAP repeat-containing protein 2; ring, BIR, CARD, UBA, apoptosis, ubiquitin ligase, SMAC/ ubiquitin, caspase, IAP family, SMAC mimetic; 1.90A {Homo sapiens} PDB: 1qbh_A 2l9m_A 3eb5_A 3eb6_A 4auq_B	Back alignment and structure

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}	Back alignment and structure

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}	Back alignment and structure

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}	Back alignment and structure

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}	Back alignment and structure

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2	Back alignment and structure

>1wil_A KIAA1045 protein; ring finger domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: g.50.1.3	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*	Back alignment and structure

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}	Back alignment and structure

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A	Back alignment and structure

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A	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	Back alignment and structure

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2	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	Back alignment and structure

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2	Back alignment and structure

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}	Back alignment and structure

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2	Back alignment and structure

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}	Back alignment and structure

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}	Back alignment and structure

>1wen_A Inhibitor of growth family, member 4; ING1-like protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.50.1.2 PDB: 1wes_A	Back alignment and structure

>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus; 2.60A {Saccharomyces cerevisiae}	Back alignment and structure

>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		533
d1iyma_		55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	9e-15
d1chca_		68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	5e-12
d3dplr1		88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	7e-12
d1vyxa_		60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	1e-09
d1fbva4		79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	6e-09
d1g25a_		65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	3e-08
d1ur6b_		52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	3e-08
d1bora_		56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	5e-08
d1jm7a_		103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	2e-06
d1rmda2		86	g.44.1.1 (A:1-86) V(D)J recombination activating p	2e-05
d1wima_		94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	3e-05
d1v87a_		114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	3e-05
d1jm7b_		97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	9e-05
d1mm2a_		61	g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens	2e-04
d1f62a_		51	g.50.1.2 (A:) Williams-Beuren syndrome transcripti	0.001
d2baya1		56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	0.002

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55	Back information, alignment and structure


class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 66.4 bits (162), Expect = 9e-15
 Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 484 CIICQEDYRDNEKIGTL-DCDHEYHAECLKKWLFIKNVCPICKSEAL 529
           C +C  +  D E+   L  C H +HAEC+  WL   + CP+C+   +
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

PyMOL of d1iyma_

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68	Back information, alignment and structure

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88	Back information, alignment and structure

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60	Back information, alignment and structure

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79	Back information, alignment and structure

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 65	Back information, alignment and structure

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52	Back information, alignment and structure

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]} Length = 56	Back information, alignment and structure

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103	Back information, alignment and structure

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86	Back information, alignment and structure

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]} Length = 94	Back information, alignment and structure

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114	Back information, alignment and structure

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97	Back information, alignment and structure

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]} Length = 61	Back information, alignment and structure

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]} Length = 51	Back information, alignment and structure

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56	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		533
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.59
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	99.41
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.4
d3dplr1		88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.36
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	99.31
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.29
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.28
d2baya1		56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.1
d1bora_		56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.09
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.05
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	99.05
d1vyxa_		60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.01
d2c2la2		80	STIP1 homology and U box-containing protein 1, STU	98.89
d1t1ha_		78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.89
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.87
d1wgma_		98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.74
d1wima_		94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.43
d1f62a_		51	Williams-Beuren syndrome transcription factor, WST	91.82
d1mm2a_		61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	89.67
d1wewa_		78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	89.56
d1we9a_		64	PHD finger protein At5g26210 {Thale cress (Arabido	89.55
d1wila_		89	Hypothetical protein KIAA1045 {Human (Homo sapiens	87.66
d1wema_		76	Death associated transcription factor 1, Datf1 (DI	87.13
d1fp0a1		70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	86.26
d1wepa_		79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	84.5
d1wesa_		71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	80.19

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}	Back information, alignment and structure

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=99.59  E-value=1.9e-16  Score=121.09  Aligned_cols=51  Identities=31%  Similarity=0.850  Sum_probs=46.4

Q ss_pred             CCCCcccccccccCCCCceEEe-CCCChhhHHHHHHHHhcCCCCcccccCcC
Q 009499          479 QEPGSCIICQEDYRDNEKIGTL-DCDHEYHAECLKKWLFIKNVCPICKSEAL  529 (533)
Q Consensus       479 eee~~C~ICLEey~~~e~v~~L-pCgH~FH~~CI~qWL~~k~sCPvCR~~l~  529 (533)
                      +++.+|+||+++|..++.+..+ .|+|.||.+||++||+++++||+||++++
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            4556799999999999988887 59999999999999999999999999875

PyMOL of d1iyma_

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}	Back information, alignment and structure

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}	Back information, alignment and structure

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {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

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}	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

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

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}	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

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {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

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