Citrus Sinensis ID: 013469

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--

MGASYLVISAASTILSFVGLQFWTEFSLDKLRTDGLVVENVIHLESANRVLELLLRSYATVALLANFVLNVFVLINLCLKTIFFGELYPAETRKFVERLINYVIYKGTFLPLVIPPTVFQAGLWSVWLTVLCSLKMFQALARDRLERLNASPSATPWTYFRVFSALLFVLAVDIFWIRMCLLLFKTLDSSMFLLLFFEPLSVAFETMQAILVHGFQLLDIWLHHSAGNSTNCARSKFFDTLAAGSLLEWKGILIRNFGFFLDMATLLMALGHYIHIWWLRGMAFHLVDAILFLNIRALLSAIIKRIKGFIKLRIALGHLHAALPDATSEELRAYDDECAICREPMAKAKKLLCNHLFHLACLRSWLDQGLNEMYSCPTCRKPLFVGRREIEANSRPGEVSSDEQLARQLSMGLDRQNNTGQTLPTGVFPNQTQPPVEGSPWS

cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHcccccEEEccccccccEEcccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccc

ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHcccHHHHHcccEEEHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHccccEEEEcHHcccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

MGASYLVISAASTILSFVGLQFWTEFSLDKLRTDGLVVENVIHLESANRVLELLLRSYATVALLANFVLNVFVLINLCLKtiffgelypaETRKFVERLINYVIYkgtflplvipptvfqaGLWSVWLTVLCSLKMFQALARDRLERlnaspsatpwTYFRVFSALLFVLAVDIFWIRMCLLLFKTLDSSMFLLLFFEPLSVAFETMQAILVHGFQLLDIWLhhsagnstncarsKFFDTLAAGSLLEWKGILIRNFGFFLDMATLLMALGHYIHIWWLRGMAFHLVDAILFLNIRALLSAIIKRIKGFIKLRIALGHlhaalpdatseELRAYDDECAICREPMAKAKKLLCNHLFHLACLRSWLDQGLnemyscptcrkplfvgrreieansrpgevssdEQLARQLSMgldrqnntgqtlptgvfpnqtqppvegspws

MGASYLVISAASTILSFVGLQFWTEFSLDKLRTDGLVVENVIHLESANRVLELLLRSYATVALLANFVLNVFVLINLCLKTIFFGELYPAETRKFVERLINYVIYKGTFLPLVIPPTVFQAGLWSVWLTVLCSLKMFQALARDRLERLNASPSATPWTYFRVFSALLFVLAVDIFWIRMCLLLFKTLDSSMFLLLFFEPLSVAFETMQAILVHGFQLLDIWLHHSAGNSTNCARSKFFDTLAAGSLLEWKGILIRNFGFFLDMATLLMALGHYIHIWWLRGMAFHLVDAILFLNIRALLSAIIKRIKGFIKLRIALGHLHAALPDATSEELRAYDDECAICREPMAKAKKLLCNHLFHLACLRSWLDQGLNEMYSCPTCRKPLFVGRREIEansrpgevssdeQLARQLSMGLDRQNNTGQtlptgvfpnqtqppvegspws

MGASYLVISAASTILSFVGLQFWTEFSLDKLRTDGLVVENVIHLESANRVLELLLRSYATvallanfvlnvfvlINLCLKTIFFGELYPAETRKFVERLINYVIYKGTFLPLVIPPTVFQAGLWSVWLTVLCSLKMFQALARDRLERLNASPSATPWTYFRVFSALLFVLAVDIFWIRMCLLLFKTLDSSMFLLLFFEPLSVAFETMQAILVHGFQLLDIWLHHSAGNSTNCARSKFFDTLAAGSLLEWKGILIRNFGFFLDMATLLMALGHYIHIWWLRGMAFHLVDAILFLNIRALLSAIIKRIKGFIKLRIALGHLHAALPDATSEELRAYDDECAICREPMAKAKKLLCNHLFHLACLRSWLDQGLNEMYSCPTCRKPLFVGRREIEANSRPGEVSSDEQLARQLSMGLDRQNNTGQTLPTGVFPNQTQPPVEGSPWS

****YLVISAASTILSFVGLQFWTEFSLDKLRTDGLVVENVIHLESANRVLELLLRSYATVALLANFVLNVFVLINLCLKTIFFGELYPAETRKFVERLINYVIYKGTFLPLVIPPTVFQAGLWSVWLTVLCSLKMFQALARDRLERLNASPSATPWTYFRVFSALLFVLAVDIFWIRMCLLLFKTLDSSMFLLLFFEPLSVAFETMQAILVHGFQLLDIWLHHSAGNSTNCARSKFFDTLAAGSLLEWKGILIRNFGFFLDMATLLMALGHYIHIWWLRGMAFHLVDAILFLNIRALLSAIIKRIKGFIKLRIALGHLHAALPDATSEELRAYDDECAICREPMAKAKKLLCNHLFHLACLRSWLDQGLNEMYSCPTCRKPLFVGR*******************************************************

**ASYLVISAASTILSFVGLQFWTEFSLDKLRTDGLVVENVIHLESANRVLELLLRSYATVALLANFVLNVFVLINLCLKTIFFGELYPAETRKFVERLINYVIYKGTFLPLVIPPTVFQAGLWSVWLTVLCSLKMFQALARDRLERLNASPSATPWTYFRVFSALLFVLAVDIFWIRMCLLLFKTLDSSMFLLLFFEPLSVAFETMQAILVHGFQLLDIWLHHSAGNSTNCARSKFFDTLAAGSLLEWKGILIRNFGFFLDMATLLMALGHYIHIWWLRGMAFHLVDAILFLNIRALLSAIIKRIKGFIKLRIALGHLHAALPDATSEELRAYDDECAICREPMAKAKKLLCNHLFHLACLRSWLDQGLNEMYSCPTCRK*************************************************************

MGASYLVISAASTILSFVGLQFWTEFSLDKLRTDGLVVENVIHLESANRVLELLLRSYATVALLANFVLNVFVLINLCLKTIFFGELYPAETRKFVERLINYVIYKGTFLPLVIPPTVFQAGLWSVWLTVLCSLKMFQALARDRLERLNASPSATPWTYFRVFSALLFVLAVDIFWIRMCLLLFKTLDSSMFLLLFFEPLSVAFETMQAILVHGFQLLDIWLHHSAGNSTNCARSKFFDTLAAGSLLEWKGILIRNFGFFLDMATLLMALGHYIHIWWLRGMAFHLVDAILFLNIRALLSAIIKRIKGFIKLRIALGHLHAALPDATSEELRAYDDECAICREPMAKAKKLLCNHLFHLACLRSWLDQGLNEMYSCPTCRKPLFVGRREIE**************ARQLSMGLDRQNNTGQTLPTGVFPNQT**********

*GASYLVISAASTILSFVGLQFWTEFSLDKLRTDGLVVENVIHLESANRVLELLLRSYATVALLANFVLNVFVLINLCLKTIFFGELYPAETRKFVERLINYVIYKGTFLPLVIPPTVFQAGLWSVWLTVLCSLKMFQALARDRLERLNASPSATPWTYFRVFSALLFVLAVDIFWIRMCLLLFKTLDSSMFLLLFFEPLSVAFETMQAILVHGFQLLDIWLHHSAGNSTNCARSKFFDTLAAGSLLEWKGILIRNFGFFLDMATLLMALGHYIHIWWLRGMAFHLVDAILFLNIRALLSAIIKRIKGFIKLRIALGHLHAALPDATSEELRAYDDECAICREPMAKAKKLLCNHLFHLACLRSWLDQGLNEMYSCPTCRKPLFV*********************************************************

iHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

oooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

SSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooHHHHHHHHHHHHHHHHHiiiHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHHiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

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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		442	2.2.26 [Sep-21-2011]
Q8VYC8		578	E3 ubiquitin protein liga	yes	no	0.981	0.750	0.722	0.0
Q8W4Q5		577	E3 ubiquitin protein liga	no	no	0.986	0.755	0.698	0.0
Q9R049		643	E3 ubiquitin-protein liga	yes	no	0.753	0.517	0.291	5e-27
Q9UKV5		643	E3 ubiquitin-protein liga	yes	no	0.753	0.517	0.288	7e-27
Q803I8		625	E3 ubiquitin-protein liga	no	no	0.642	0.454	0.275	7e-20
Q5XHH7		595	E3 ubiquitin-protein liga	N/A	no	0.640	0.475	0.265	6e-19
Q6NRL6		605	E3 ubiquitin-protein liga	N/A	no	0.640	0.467	0.265	2e-18
Q9DBY1		612	E3 ubiquitin-protein liga	no	no	0.685	0.495	0.267	6e-18
Q86TM6		617	E3 ubiquitin-protein liga	no	no	0.685	0.491	0.267	7e-18
Q20798		610	E3 ubiquitin-protein liga	yes	no	0.671	0.486	0.260	5e-15

>sp\|Q8VYC8\|RIN2_ARATH E3 ubiquitin protein ligase RIN2 OS=Arabidopsis thaliana GN=RIN2 PE=1 SV=1	Back alignment and function desciption

 Score =  665 bits (1715), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 317/439 (72%), Positives = 369/439 (84%), Gaps = 5/439 (1%)

Query: 1   MGASYLVISAASTILSFVGLQFWTEFSLDKLRTDGLVVENVIHLESANRVLELLLRSYAT 60
           MG  YL +S AST LSFVGLQ WTE SLD+LR DGL+ +N I L  +   LELLL SY T
Sbjct: 1   MGIKYLPVSVASTALSFVGLQVWTELSLDRLRADGLIAKN-ISLGDSEHALELLLGSYFT 59

Query: 61  VALLANFVLNVFVLINLCLKTIFFGELYPAETRKFVERLINYVIYKGTFLPLVIPPTVFQ 120
           +ALL NFVLNV++L+ L LKT+FFG+LY  ET+K VERL NY+IYKGTFLPLVIPPT+FQ
Sbjct: 60  IALLTNFVLNVYILLVLSLKTLFFGDLYDVETKKLVERLANYIIYKGTFLPLVIPPTIFQ 119

Query: 121 AGLWSVWLTVLCSLKMFQALARDRLERLNASPSATPWTYFRVFSALLFVLAVDIFWIRMC 180
             LW+VWLTVLC+LKMFQALARDRLERLNASPS+TPWTYFRV+S L  VL+VD+FWI++ 
Sbjct: 120 GVLWTVWLTVLCTLKMFQALARDRLERLNASPSSTPWTYFRVYSVLFLVLSVDMFWIKLS 179

Query: 181 LLLFKTLDSSMFLLLFFEPLSVAFETMQAILVHGFQLLDIWLHHSAGNSTNCARSKFFDT 240
           L+ + T+ S+++LLL FEP S+AFET+QA+L+HGFQLLD+W++H A  +++C RSKF D+
Sbjct: 180 LMTYNTIGSAVYLLLLFEPCSIAFETLQALLIHGFQLLDMWINHLAVKNSDCQRSKFIDS 239

Query: 241 LAAGSLLEWKGILIRNFGFFLDMATLLMALGHYIHIWWLRGMAFHLVDAILFLNIRALLS 300
           + AGSLLEWKG+L RN GFFLDMATL+MALGHY+HIWWL G+AFHLVDA+LFLNIRALLS
Sbjct: 240 MTAGSLLEWKGLLNRNLGFFLDMATLVMALGHYLHIWWLHGIAFHLVDAVLFLNIRALLS 299

Query: 301 AIIKRIKGFIKLRIALGHLHAALPDATSEELRAYDDECAICREPMAKAKKLLCNHLFHLA 360
           AI+KRIKG+IKLRIALG LHAALPDATSEELRAYDDECAICREPMAKAK+L CNHLFHL 
Sbjct: 300 AILKRIKGYIKLRIALGALHAALPDATSEELRAYDDECAICREPMAKAKRLHCNHLFHLG 359

Query: 361 CLRSWLDQGLNEMYSCPTCRKPLFVGRREIEANSRPGEVSSDEQLARQLSMGLDRQNNTG 420
           CLRSWLDQGLNE+YSCPTCRKPLFVGR E E N R  EVSSDEQLARQ    L+RQNN  
Sbjct: 360 CLRSWLDQGLNEVYSCPTCRKPLFVGRTENEVNPRTVEVSSDEQLARQ----LERQNNPV 415

Query: 421 QTLPTGVFPNQTQPPVEGS 439
             L TG+FP +    VE  
Sbjct: 416 HALATGLFPAEVPDSVEND 434

E3 ubiquitin protein ligase that acts as positive regulator of RPM1- and RPS2-dependent hypersensitive response (HR), in association with RIN3. Probably not required for RPM1 degradation during HR.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp\|Q8W4Q5\|RIN3_ARATH E3 ubiquitin protein ligase RIN3 OS=Arabidopsis thaliana GN=RIN3 PE=1 SV=2	Back alignment and function description

>sp\|Q9R049\|AMFR_MOUSE E3 ubiquitin-protein ligase AMFR OS=Mus musculus GN=Amfr PE=1 SV=2	Back alignment and function description

>sp\|Q9UKV5\|AMFR_HUMAN E3 ubiquitin-protein ligase AMFR OS=Homo sapiens GN=AMFR PE=1 SV=2	Back alignment and function description

>sp\|Q803I8\|SYVN1_DANRE E3 ubiquitin-protein ligase synoviolin OS=Danio rerio GN=syvn1 PE=2 SV=2	Back alignment and function description

>sp\|Q5XHH7\|SYVNB_XENLA E3 ubiquitin-protein ligase synoviolin B OS=Xenopus laevis GN=syvn1-b PE=2 SV=1	Back alignment and function description

>sp\|Q6NRL6\|SYVNA_XENLA E3 ubiquitin-protein ligase synoviolin A OS=Xenopus laevis GN=syvn1-a PE=2 SV=1	Back alignment and function description

>sp\|Q9DBY1\|SYVN1_MOUSE E3 ubiquitin-protein ligase synoviolin OS=Mus musculus GN=Syvn1 PE=1 SV=3	Back alignment and function description

>sp\|Q86TM6\|SYVN1_HUMAN E3 ubiquitin-protein ligase synoviolin OS=Homo sapiens GN=SYVN1 PE=1 SV=2	Back alignment and function description

>sp\|Q20798\|HRD1_CAEEL E3 ubiquitin-protein ligase hrd-1 OS=Caenorhabditis elegans GN=sel-11 PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		442
255539769		585	protein binding protein, putative [Ricin	0.993	0.750	0.784	0.0
224071523		581	predicted protein [Populus trichocarpa]	0.990	0.753	0.752	0.0
224125224		571	predicted protein [Populus trichocarpa]	0.961	0.744	0.750	0.0
225466103		587	PREDICTED: E3 ubiquitin protein ligase R	0.997	0.751	0.773	0.0
357455727		589	E3 ubiquitin-protein ligase synoviolin [	0.997	0.748	0.723	0.0
356508268		586	PREDICTED: E3 ubiquitin protein ligase R	0.997	0.752	0.725	0.0
297803598		578	hypothetical protein ARALYDRAFT_492309 [	0.981	0.750	0.724	0.0
297792453		577	predicted protein [Arabidopsis lyrata su	0.986	0.755	0.718	0.0
22328916		578	E3 ubiquitin protein ligase RIN2 [Arabid	0.981	0.750	0.722	0.0
356517740		586	PREDICTED: E3 ubiquitin protein ligase R	0.997	0.752	0.723	0.0

>gi\|255539769\|ref\|XP_002510949.1\| protein binding protein, putative [Ricinus communis] gi\|223550064\|gb\|EEF51551.1\| protein binding protein, putative [Ricinus communis]	Back alignment and taxonomy information

 Score =  726 bits (1874), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 346/441 (78%), Positives = 389/441 (88%), Gaps = 2/441 (0%)

Query: 1   MGASYLVISAASTILSFVGLQFWTEFSLDKLRTDGLVVENVIHLESANRVLELLLRSYAT 60
           MGA YL ISAA T LSFVGL+ WTE SL+KL+++GL+ EN I+ E+ANR LELLL SYAT
Sbjct: 1   MGAGYLAISAACTALSFVGLKCWTELSLEKLKSEGLISENFINPENANRALELLLGSYAT 60

Query: 61  VALLANFVLNVFVLINLCLKTIFFGELYPAETRKFVERLINYVIYKGTFLPLVIPPTVFQ 120
           +ALLA+FV N F+L+NL LKTIFF ELYP+ETRK +ERL+NYVIYKGTFLPLVIP T+FQ
Sbjct: 61  IALLASFVFNAFILLNLSLKTIFFAELYPSETRKLMERLVNYVIYKGTFLPLVIPATIFQ 120

Query: 121 AGLWSVWLTVLCSLKMFQALARDRLERLNASPSATPWTYFRVFSALLFVLAVDIFWIRMC 180
           AGLWS WLTVLCSLKMFQALARDRLERLNASPSA PWTYFRV+S LL VL+VD FWIR+C
Sbjct: 121 AGLWSSWLTVLCSLKMFQALARDRLERLNASPSAMPWTYFRVYSVLLLVLSVDFFWIRLC 180

Query: 181 LLLFKTLDSSMFLLLFFEPLSVAFETMQAILVHGFQLLDIWLHHSAGNSTNCARSKFFDT 240
            L+++TLD+SMF+LLF+EP S+AFETMQA+LVHGFQLLDIW HHSAGN  NC R KFFD 
Sbjct: 181 WLIYRTLDTSMFMLLFYEPFSIAFETMQAMLVHGFQLLDIWFHHSAGNDANCQRFKFFDP 240

Query: 241 LAAGSLLEWKGILIRNFGFFLDMATLLMALGHYIHIWWLRGMAFHLVDAILFLNIRALLS 300
           +AAGSL EWKGILIRN GF LDMATLLMALGHY+HIWWL G+AFHLVDA+LFLNIRALLS
Sbjct: 241 IAAGSLSEWKGILIRNLGFSLDMATLLMALGHYMHIWWLHGVAFHLVDAVLFLNIRALLS 300

Query: 301 AIIKRIKGFIKLRIALGHLHAALPDATSEELRAYDDECAICREPMAKAKKLLCNHLFHLA 360
           AIIKR++GF+KLRIALG LHAALPDATSEELRAYDDECAICREPMAKAKKL C+HLFHLA
Sbjct: 301 AIIKRVRGFVKLRIALGALHAALPDATSEELRAYDDECAICREPMAKAKKLHCSHLFHLA 360

Query: 361 CLRSWLDQGLNEMYSCPTCRKPLFVGRREIEANSRPGEVSSDEQLARQLSMGLDRQNNTG 420
           CLRSWLDQGLNEMYSCPTCRKPLFVGR + E +    +VS+DEQLARQ+S GLD+QN   
Sbjct: 361 CLRSWLDQGLNEMYSCPTCRKPLFVGRPDNEPSRHRRDVSADEQLARQISEGLDQQN--A 418

Query: 421 QTLPTGVFPNQTQPPVEGSPW 441
            TLP GVFPNQ +  +EGSPW
Sbjct: 419 PTLPAGVFPNQMRNSIEGSPW 439

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224071523\|ref\|XP_002303501.1\| predicted protein [Populus trichocarpa] gi\|222840933\|gb\|EEE78480.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|224125224\|ref\|XP_002329924.1\| predicted protein [Populus trichocarpa] gi\|222871161\|gb\|EEF08292.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|225466103\|ref\|XP_002266334.1\| PREDICTED: E3 ubiquitin protein ligase RIN2 [Vitis vinifera] gi\|296084203\|emb\|CBI24591.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|357455727\|ref\|XP_003598144.1\| E3 ubiquitin-protein ligase synoviolin [Medicago truncatula] gi\|355487192\|gb\|AES68395.1\| E3 ubiquitin-protein ligase synoviolin [Medicago truncatula]	Back alignment and taxonomy information

>gi\|356508268\|ref\|XP_003522880.1\| PREDICTED: E3 ubiquitin protein ligase RIN2-like [Glycine max]	Back alignment and taxonomy information

>gi\|297803598\|ref\|XP_002869683.1\| hypothetical protein ARALYDRAFT_492309 [Arabidopsis lyrata subsp. lyrata] gi\|297315519\|gb\|EFH45942.1\| hypothetical protein ARALYDRAFT_492309 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|297792453\|ref\|XP_002864111.1\| predicted protein [Arabidopsis lyrata subsp. lyrata] gi\|297309946\|gb\|EFH40370.1\| predicted protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi|22328916|ref|NP_194253.2| E3 ubiquitin protein ligase RIN2 [Arabidopsis thaliana] gi|30686808|ref|NP_849552.1| E3 ubiquitin protein ligase RIN2 [Arabidopsis thaliana] gi|75304438|sp|Q8VYC8.1|RIN2_ARATH RecName: Full=E3 ubiquitin protein ligase RIN2; AltName: Full=AMF receptor-like protein 1A; AltName: Full=RPM1-interacting protein 2 gi|18176187|gb|AAL60000.1| unknown protein [Arabidopsis thaliana] gi|332659628|gb|AEE85028.1| E3 ubiquitin protein ligase RIN2 [Arabidopsis thaliana] gi|332659629|gb|AEE85029.1| E3 ubiquitin protein ligase RIN2 [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|356517740\|ref\|XP_003527544.1\| PREDICTED: E3 ubiquitin protein ligase RIN2-like [Glycine max]	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		442
TAIR\|locus:2122674		578	RIN2 "RPM1 interacting protein	0.977	0.747	0.702	1.2e-166
TAIR\|locus:2093422		492	Hrd1A "homolog of yeast Hrd1"	0.352	0.317	0.341	1e-23
TAIR\|locus:2014993		460	Hrd1B "homolog of yeast Hrd1"	0.389	0.373	0.305	1.5e-22
UNIPROTKB\|Q5XHH7		595	syvn1-b "E3 ubiquitin-protein	0.298	0.221	0.363	1.4e-20
RGD\|1311551		643	Amfr "autocrine motility facto	0.334	0.230	0.325	1.6e-20
UNIPROTKB\|Q6NRL6		605	syvn1-a "E3 ubiquitin-protein	0.298	0.218	0.358	2.5e-18
UNIPROTKB\|F1MWZ9		646	AMFR "Uncharacterized protein"	0.346	0.236	0.348	2.5e-18
ZFIN\|ZDB-GENE-030131-7166		625	syvn1 "synovial apoptosis inhi	0.300	0.212	0.335	7.3e-18
MGI\|MGI:1921376		612	Syvn1 "synovial apoptosis inhi	0.626	0.452	0.272	2.7e-14
MGI\|MGI:1345634		643	Amfr "autocrine motility facto	0.346	0.237	0.348	9.3e-18

TAIR\|locus:2122674 RIN2 "RPM1 interacting protein 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1621 (575.7 bits), Expect = 1.2e-166, P = 1.2e-166
 Identities = 307/437 (70%), Positives = 356/437 (81%)

Query:     1 MGASYLVISAASTILSFVGLQFWTEFSLDKLRTDGLVVENVIHLESANRVLELLLRSYAT 60
             MG  YL +S AST LSFVGLQ WTE SLD+LR DGL+ +N I L  +   LELLL SY T
Sbjct:     1 MGIKYLPVSVASTALSFVGLQVWTELSLDRLRADGLIAKN-ISLGDSEHALELLLGSYFT 59

Query:    61 XXXXXXXXXXXXXXINLCLKTIFFGELYPAETRKFVERLINYVIYKGTFLPLVIPPTVFQ 120
                           + L LKT+FFG+LY  ET+K VERL NY+IYKGTFLPLVIPPT+FQ
Sbjct:    60 IALLTNFVLNVYILLVLSLKTLFFGDLYDVETKKLVERLANYIIYKGTFLPLVIPPTIFQ 119

Query:   121 AGLWSVWLTVLCSLKMFQALARDRLERLNASPSATPWTYFRVFSALLFVLAVDIFWIRMC 180
               LW+VWLTVLC+LKMFQALARDRLERLNASPS+TPWTYFRV+S L  VL+VD+FWI++ 
Sbjct:   120 GVLWTVWLTVLCTLKMFQALARDRLERLNASPSSTPWTYFRVYSVLFLVLSVDMFWIKLS 179

Query:   181 LLLFKTLDSSMFLLLFFEPLSVAFETMQAILVHGFQLLDIWLHHSAGNSTNCARSKFFDT 240
             L+ + T+ S+++LLL FEP S+AFET+QA+L+HGFQLLD+W++H A  +++C RSKF D+
Sbjct:   180 LMTYNTIGSAVYLLLLFEPCSIAFETLQALLIHGFQLLDMWINHLAVKNSDCQRSKFIDS 239

Query:   241 LAAGSLLEWKGILIRNFGFFLDMATLLMALGHYIHIWWLRGMAFHLVDAILFLNIRALLS 300
             + AGSLLEWKG+L RN GFFLDMATL+MALGHY+HIWWL G+AFHLVDA+LFLNIRALLS
Sbjct:   240 MTAGSLLEWKGLLNRNLGFFLDMATLVMALGHYLHIWWLHGIAFHLVDAVLFLNIRALLS 299

Query:   301 AIIKRIKGFIKLRIALGHLHAALPDATSEELRAYDDECAICREPMAKAKKLLCNHLFHLA 360
             AI+KRIKG+IKLRIALG LHAALPDATSEELRAYDDECAICREPMAKAK+L CNHLFHL 
Sbjct:   300 AILKRIKGYIKLRIALGALHAALPDATSEELRAYDDECAICREPMAKAKRLHCNHLFHLG 359

Query:   361 CLRSWLDQGLNEMYSCPTCRKPLFVGRREIEANSRPGEVSSDEQLARQLSMGLDRQNNTG 420
             CLRSWLDQGLNE+YSCPTCRKPLFVGR E E N R  EVSSDEQLARQL    +RQNN  
Sbjct:   360 CLRSWLDQGLNEVYSCPTCRKPLFVGRTENEVNPRTVEVSSDEQLARQL----ERQNNPV 415

Query:   421 QTLPTGVFPNQTQPPVE 437
               L TG+FP +    VE
Sbjct:   416 HALATGLFPAEVPDSVE 432

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

GO:0004842 "ubiquitin-protein ligase activity" evidence=ISS;IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005886 "plasma membrane" evidence=IDA

GO:0034052 "positive regulation of plant-type hypersensitive response" evidence=IGI

TAIR\|locus:2093422 Hrd1A "homolog of yeast Hrd1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2014993 Hrd1B "homolog of yeast Hrd1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5XHH7 syvn1-b "E3 ubiquitin-protein ligase synoviolin B" [Xenopus laevis (taxid:8355)]	Back alignment and assigned GO terms

RGD\|1311551 Amfr "autocrine motility factor receptor, E3 ubiquitin protein ligase" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q6NRL6 syvn1-a "E3 ubiquitin-protein ligase synoviolin A" [Xenopus laevis (taxid:8355)]	Back alignment and assigned GO terms

UNIPROTKB\|F1MWZ9 AMFR "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-030131-7166 syvn1 "synovial apoptosis inhibitor 1, synoviolin" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

MGI\|MGI:1921376 Syvn1 "synovial apoptosis inhibitor 1, synoviolin" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

MGI\|MGI:1345634 Amfr "autocrine motility factor receptor" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8VYC8	RIN2_ARATH	6, ., 3, ., 2, ., -	0.7220	0.9819	0.7508	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	6.3.2	0.691

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		442
COG5243		491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	1e-17
pfam13639		46	pfam13639, zf-RING_2, Ring finger domain	4e-12
cd00162		45	cd00162, RING, RING-finger (Really Interesting New	6e-12
pfam12678		73	pfam12678, zf-rbx1, RING-H2 zinc finger	8e-09
smart00184		40	smart00184, RING, Ring finger	9e-09
pfam00097		40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	1e-07
pfam13923		45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	1e-07
COG5540		374	COG5540, COG5540, RING-finger-containing ubiquitin	1e-06
COG5194		88	COG5194, APC11, Component of SCF ubiquitin ligase	2e-04
PHA02929		238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	2e-04
pfam12861		85	pfam12861, zf-Apc11, Anaphase-promoting complex su	4e-04
COG5574		271	COG5574, PEX10, RING-finger-containing E3 ubiquiti	0.003

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

 Score = 84.6 bits (209), Expect = 1e-17
 Identities = 88/410 (21%), Positives = 145/410 (35%), Gaps = 78/410 (19%)

Query: 57  SYATVALLANFVLNVFVLINLCLKTIFFGELYPAETRKFVERLINYVIYKGTFLPLVIPP 116
           S   + +  N +L +F LI   LKT+ FG L   E     E+L   +      L  +   
Sbjct: 39  SPVHITIGLNVILLLFFLIANALKTLLFGSLRTFELELLYEQLWITLT---EILLAI--- 92

Query: 117 TVFQAGL---WSVWLTVLCSLKMFQALARDRLERLNASPSATPWTYFRVFSALLFVLAV- 172
           +VF+  +   + + L+ L   K+F  +   R ERL    +   +  F  FS   F+L++ 
Sbjct: 93  SVFREAISFSFFMLLSTLLFAKVFHWILSFRTERLQIQSTDQRFHIFSRFSCAYFLLSIL 152

Query: 173 DIFWIRMCLLLFKTLDSSMFLLLFFEPLSVAFETMQAILVHGFQLLDIWLHHSAGNSTNC 232
           D   I +C+     +D S  L LF    SV    + +                   ST  
Sbjct: 153 DASLIYLCISSEHLIDKST-LFLFVCEFSVLLLNLTSEANKLCVYNYEARDDDDERST-- 209

Query: 233 ARSKFFDTLAAGSLLEWKGILIRNFGFFLDMATLLMALGHYIHIWWLRGMAFHLVDAI-- 290
                                   + F L++         Y  +  L      +      
Sbjct: 210 ------------------------YLFRLEVC--------YDGLTLLAYSLLFMYQFPYV 237

Query: 291 -----LFLNIRALLSAIIKRIKGFIKLRIALGHLHAALPDATSEELRAYDDECAICREPM 345
                L   +     A+ +RI+   + R A   L+A  P AT E+L   D  C IC + M
Sbjct: 238 RVPIYLIRQMYTCFYALFRRIREHARFRRATKDLNAMYPTATEEQLTNSDRTCTICMDEM 297

Query: 346 -------------AKAKKLLCNHLFHLACLRSWLDQGLNEMYSCPTCRKPLFVGRREIEA 392
                           K+L C H+ HL CL++WL++      +CP CR+P+   +    +
Sbjct: 298 FHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER----QQTCPICRRPVIFDQS---S 350

Query: 393 NSRPGEVSSDEQLARQLSMGLDRQNNTGQTLPTGVFPNQTQ--PPVEGSP 440
            +       + Q+A Q+       +NT  T       N +    P   + 
Sbjct: 351 PTPASPNVRNTQIATQVPN----PDNTPTTTAVPGITNSSNQGDPQASTF 396

Length = 491

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

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

>gnl\|CDD\|214546 smart00184, RING, 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\|206094 pfam13923, zf-C3HC4_2, 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\|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\|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional	Back alignment and domain information

>gnl\|CDD\|193335 pfam12861, zf-Apc11, Anaphase-promoting complex subunit 11 RING-H2 finger	Back alignment and domain information

>gnl\|CDD\|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		442
COG5243		491	HRD1 HRD ubiquitin ligase complex, ER membrane com	100.0
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	100.0
KOG4628		348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.47
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.31
PHA02929		238	N1R/p28-like protein; Provisional	99.15
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.15
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	99.12
KOG0317		293	consensus Predicted E3 ubiquitin ligase, integral	99.1
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.03
PF12861		85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.99
KOG0823		230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.96
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.95
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.85
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	98.84
COG5540		374	RING-finger-containing ubiquitin ligase [Posttrans	98.82
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	98.8
PHA02926		242	zinc finger-like protein; Provisional	98.72
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.71
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.68
KOG1734		328	consensus Predicted RING-containing E3 ubiquitin l	98.67
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.65
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.59
TIGR00599		397	rad18 DNA repair protein rad18. This family is bas	98.54
COG5574		271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.53
COG5194		88	APC11 Component of SCF ubiquitin ligase and anapha	98.53
KOG1493		84	consensus Anaphase-promoting complex (APC), subuni	98.53
KOG2164		513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.53
PF14634		44	zf-RING_5: zinc-RING finger domain	98.41
KOG0828		636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.35
PF04564		73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.31
KOG0287		442	consensus Postreplication repair protein RAD18 [Re	98.23
KOG2930		114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.18
COG5432		391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.13
KOG0824		324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.07
TIGR00570		309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.0
KOG2177		386	consensus Predicted E3 ubiquitin ligase [Posttrans	97.94
PF11793		70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.91
COG5219		1525	Uncharacterized conserved protein, contains RING Z	97.9
KOG4172		62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.85
smart00744		49	RINGv The RING-variant domain is a C4HC3 zinc-fing	97.84
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.81
KOG4265		349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.79
PF14835		65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.7
KOG0827		465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.7
KOG1785		563	consensus Tyrosine kinase negative regulator CBL [	97.68
KOG0978		698	consensus E3 ubiquitin ligase involved in syntaxin	97.65
KOG1039		344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.56
PF13705		508	TRC8_N: TRC8 N-terminal domain	97.53
KOG0311		381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.51
KOG4159		398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.33
KOG2114		933	consensus Vacuolar assembly/sorting protein PEP5/V	97.3
KOG1941		518	consensus Acetylcholine receptor-associated protei	97.3
KOG2879		298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.29
KOG1645		463	consensus RING-finger-containing E3 ubiquitin liga	97.28
KOG1002		791	consensus Nucleotide excision repair protein RAD16	97.13
KOG0825		1134	consensus PHD Zn-finger protein [General function	97.09
KOG0297		391	consensus TNF receptor-associated factor [Signal t	96.96
KOG1571		355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.88
KOG4692		489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.85
KOG3970		299	consensus Predicted E3 ubiquitin ligase [Posttrans	96.82
PF10367		109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.8
PF11789		57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	96.67
KOG4275		350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.6
COG5152		259	Uncharacterized conserved protein, contains RING a	96.56
PHA02825		162	LAP/PHD finger-like protein; Provisional	96.46
KOG1813		313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.39
KOG1428		3738	consensus Inhibitor of type V adenylyl cyclases/Ne	96.34
KOG4445		368	consensus Uncharacterized conserved protein, conta	96.12
COG5222		427	Uncharacterized conserved protein, contains RING Z	96.12
PHA02862		156	5L protein; Provisional	96.1
KOG1814		445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.07
KOG2660		331	consensus Locus-specific chromosome binding protei	96.04
PF14447		55	Prok-RING_4: Prokaryotic RING finger family 4	95.81
COG5236		493	Uncharacterized conserved protein, contains RING Z	95.59
PF12906		47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	95.54
KOG2034		911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	95.45
PF10272		358	Tmpp129: Putative transmembrane protein precursor;	95.25
PF14570		48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.22
KOG3039		303	consensus Uncharacterized conserved protein [Funct	95.05
KOG1952		950	consensus Transcription factor NF-X1, contains NFX	94.76
COG5175		480	MOT2 Transcriptional repressor [Transcription]	94.67
KOG4185		296	consensus Predicted E3 ubiquitin ligase [Posttrans	94.55
KOG0826		357	consensus Predicted E3 ubiquitin ligase involved i	94.48
PHA03096		284	p28-like protein; Provisional	94.17
PF05290		140	Baculo_IE-1: Baculovirus immediate-early protein (	94.11
PF07800		162	DUF1644: Protein of unknown function (DUF1644); In	93.6
KOG1001		674	consensus Helicase-like transcription factor HLTF/	93.43
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	92.99
PF05883		134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	92.75
KOG0827		465	consensus Predicted E3 ubiquitin ligase [Posttrans	92.52
PF04641		260	Rtf2: Rtf2 RING-finger	91.43
KOG4739		233	consensus Uncharacterized protein involved in syna	91.42
KOG1940		276	consensus Zn-finger protein [General function pred	90.77
COG5183		1175	SSM4 Protein involved in mRNA turnover and stabili	90.52
KOG3268		234	consensus Predicted E3 ubiquitin ligase [Posttrans	90.36
PF08746		43	zf-RING-like: RING-like domain; InterPro: IPR01485	90.13
KOG3800		300	consensus Predicted E3 ubiquitin ligase containing	88.68
KOG3053		293	consensus Uncharacterized conserved protein [Funct	88.12
KOG3161		861	consensus Predicted E3 ubiquitin ligase [Posttrans	87.91
KOG2932		389	consensus E3 ubiquitin ligase involved in ubiquiti	87.84
KOG1100		207	consensus Predicted E3 ubiquitin ligase [Posttrans	87.75
KOG4367		699	consensus Predicted Zn-finger protein [Function un	87.05
KOG0298		1394	consensus DEAD box-containing helicase-like transc	86.38
KOG2817		394	consensus Predicted E3 ubiquitin ligase [Posttrans	85.98
KOG0801		205	consensus Predicted E3 ubiquitin ligase [Posttrans	85.6
KOG3899		381	consensus Uncharacterized conserved protein [Funct	85.57
PF03854		50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	85.12
KOG4362		684	consensus Transcriptional regulator BRCA1 [Replica	84.71
COG5220		314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	84.68
KOG3002		299	consensus Zn finger protein [General function pred	82.4
KOG0309		1081	consensus Conserved WD40 repeat-containing protein	81.81
KOG1609		323	consensus Protein involved in mRNA turnover and st	80.88

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

Probab=100.00  E-value=5.6e-43  Score=337.04  Aligned_cols=324  Identities=24%  Similarity=0.374  Sum_probs=235.9

Q ss_pred             HHHHHHHhhHHHHhHhhhhhccccchhhcccCcchhHHHHHHHhh-chhHHHHHHHHHHHHHHHHHHHHHHHhcccCcHH
Q 013469           12 STILSFVGLQFWTEFSLDKLRTDGLVVENVIHLESANRVLELLLR-SYATVALLANFVLNVFVLINLCLKTIFFGELYPA   90 (442)
Q Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-s~~~~~vl~N~~~~~~~l~~~~lq~lfFG~LR~~   90 (442)
                      |...+++++.-+.+-++.             .....|++++.-+| |++.++++.|++++.+.++++++++++||+||..
T Consensus         6 y~l~~~Vl~~l~~~~~~~-------------~s~t~ys~l~~t~~ls~~hi~i~~~~ill~~~l~~~~l~~llFGsLr~~   72 (491)
T COG5243           6 YVLASLVLFGLSVLLSLY-------------SSATVYSALVMTSQLSPVHITIGLNVILLLFFLIANALKTLLFGSLRTF   72 (491)
T ss_pred             hhHHHHHHHHHHHHHHHh-------------ccceeeeeeeeeeccCcchhHHHHHHHHHHHHHHHHHHHHHhhhhhHHH
Confidence            455566666555554443             34567788888888 9999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhcccccCchhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCcch--HHHHHHHHHH
Q 013469           91 ETRKFVERLINYVIYKGTFLPLVIPPTVFQAGLWSVWLTVLCSLKMFQALARDRLERLNASPSATPWT--YFRVFSALLF  168 (442)
Q Consensus        91 E~e~l~er~~~~~~~k~~fl~~vi~~~~~~~~~w~~~F~~L~~lK~fh~l~~dRve~l~~sp~~~~~~--h~R~~~lL~~  168 (442)
                      |.|+++|++| |++. ++.++..++++.-.. .+...+..|+++|+||||+++|.|... -.++..+.  .-|..+.+.+
T Consensus        73 E~e~~~E~l~-~tlt-~~ll~iS~F~e~i~f-s~~~l~~~Ll~~kvfhwil~~R~er~~-~~st~~~~~ifSrfS~~~~l  148 (491)
T COG5243          73 ELELLYEQLW-ITLT-EILLAISVFREAISF-SFFMLLSTLLFAKVFHWILSFRTERLQ-IQSTDQRFHIFSRFSCAYFL  148 (491)
T ss_pred             HHHHHHHhhH-HHHH-HHHHHHHHHHhhHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
Confidence            9999999999 3333 455554455542211 345677888999999999999999763 22334444  4699999999


Q ss_pred             HHHHHHHHHHHHHHHhhhCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCcccccchhhhhhhccchhh
Q 013469          169 VLAVDIFWIRMCLLLFKTLDSSMFLLLFFEPLSVAFETMQAILVHGFQLLDIWLHHSAGNSTNCARSKFFDTLAAGSLLE  248 (442)
Q Consensus       169 ll~~d~~~i~~~~~~~~~~g~~~~ll~~fE~~~l~~~~l~~~l~~~~~l~d~~~~~~~~~~~~~~~~~~~~~~~~~~~we  248 (442)
                      +.++|...|..|+..-...+.++..++..|+..+. ..+++.                . +..+...  ++.+++   -+
T Consensus       149 L~ild~~li~~CiSs~~liD~~~lfL~~c~F~~~l-l~l~s~----------------~-n~~cV~n--~~~~dd---Dd  205 (491)
T COG5243         149 LSILDASLIYLCISSEHLIDKSTLFLFVCEFSVLL-LNLTSE----------------A-NKLCVYN--YEARDD---DD  205 (491)
T ss_pred             HHHHhHHHHHHHhhhHhhhhhhHHHHHHHHHHHHH-HHHHHh----------------h-cccceee--cccccc---cc
Confidence            99999999999997544444444333444432211 111111                0 1011000  000011   13


Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCh
Q 013469          249 WKGILIRNFGFFLDMATLLMALGHYIHIWWLRGMAFHLVDAILFLNIRALLSAIIKRIKGFIKLRIALGHLHAALPDATS  328 (442)
Q Consensus       249 ~kg~~i~~~ef~~dl~~~~~~l~~~~~~~~~~g~~~~i~~~v~~~~ir~~~~~l~~r~~~~~~~r~~~~~~~~~~~~~~~  328 (442)
                      .|..+.++.|+.-|=++++.+...+...+..+.+|+.+++.++ ..+    .++.+|++.+.+++++.+++++.+|.+++
T Consensus       206 ~rs~~~f~~~v~y~g~tllays~l~~~~~~~~r~Pi~l~r~~~-t~~----~AL~~~i~~~~~~~r~~kdl~~~~~t~t~  280 (491)
T COG5243         206 ERSTYLFRLEVCYDGLTLLAYSLLFMYQFPYVRVPIYLIRQMY-TCF----YALFRRIREHARFRRATKDLNAMYPTATE  280 (491)
T ss_pred             cceeeeeeeehHHHHHHHHHHHHHHHhhccchhchHHHHHHHH-HHH----HHHHHHHHHHHHHHHHhhHHHhhcchhhh
Confidence            4556667777888877777776666666777788988888753 333    46778899999999999999999999999


Q ss_pred             hhhccCCCCCccCcccc-c------------CCccccCcccchHHHHHHHHHhCCCCCCCccccccCCc
Q 013469          329 EELRAYDDECAICREPM-A------------KAKKLLCNHLFHLACLRSWLDQGLNEMYSCPTCRKPLF  384 (442)
Q Consensus       329 ~el~~~~~~C~IC~e~~-~------------~~~~LpCgH~FH~~Cl~~Wl~~~~~~~~~CP~CR~~l~  384 (442)
                      |++.+.|..|.||+|++ .            .||+|||||++|.+|++.|+++    +++||+||.++.
T Consensus       281 eql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ER----qQTCPICr~p~i  345 (491)
T COG5243         281 EQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER----QQTCPICRRPVI  345 (491)
T ss_pred             hhhcCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHh----ccCCCcccCccc
Confidence            99998999999999995 3            3599999999999999999999    699999999953

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

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

>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

>PHA02929 N1R/p28-like protein; Provisional	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

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional	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

>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

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

>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

>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

>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

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

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

>PHA02926 zinc finger-like protein; Provisional	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

>KOG0320 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

>smart00184 RING Ring finger	Back alignment and domain information

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

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

>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

>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

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

>KOG0828 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

>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]	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

>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1	Back alignment and domain information

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

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

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

>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

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

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

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

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

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

>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [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

>PF13705 TRC8_N: TRC8 N-terminal domain	Back alignment and domain information

>KOG0311 consensus Predicted E3 ubiquitin ligase [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

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

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

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

>KOG1645 consensus RING-finger-containing 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

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

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

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

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

>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

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

>KOG4275 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

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

>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

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

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

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

>KOG1814 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

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

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

>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A	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

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

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]	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

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

>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

>PHA03096 p28-like protein; Provisional	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

>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

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

>KOG0802 consensus 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

>KOG0827 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

>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]	Back alignment and domain information

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

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

>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

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

>KOG4367 consensus Predicted Zn-finger protein [Function unknown]	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

>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0801 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

>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

>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]	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

>KOG3002 consensus 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

>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]	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		442
2ect_A		78	Solution Structure Of The Zinc Finger, C3hc4 Type (		1e-06

>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

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 23/50 (46%), Positives = 30/50 (60%), Gaps = 7/50 (14%)
Query: 337 ECAICREPMA---KAKKLLCNHLFHLACLRSWLDQGLNEMYSCPTCRKPL 383
           EC +C+E  A     ++L CNHLFH +C+  WL+Q      SCP CRK L
Sbjct: 17  ECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQ----HDSCPVCRKSL 62

PyMOL of 2ect

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		442
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	3e-14
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	4e-14
2ect_A		78	Ring finger protein 126; metal binding protein, st	2e-13
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	3e-12
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	5e-12
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	7e-12
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	3e-11
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	3e-11
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	7e-11
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	1e-10
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	1e-10
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	5e-10
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	9e-10
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	1e-09
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	3e-09
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	3e-09
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	4e-09
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	6e-09
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	1e-08
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	1e-08
4epo_C		149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	2e-08
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	2e-08
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	3e-08
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	5e-08
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	5e-08
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	7e-08
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	1e-07
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	1e-07
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	3e-07
1z6u_A		150	NP95-like ring finger protein isoform B; structura	3e-07
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	5e-07
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	5e-07
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	8e-07
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	8e-07
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	9e-07
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	1e-06
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	1e-06
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	3e-06
1fp0_A		88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	6e-06
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	7e-06
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	7e-06
2yql_A		56	PHD finger protein 21A; PHD domain, structural gen	8e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-06
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	9e-06
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-05
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	1e-05
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	1e-05
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	1e-05
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	2e-05
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	3e-05
3nw0_A		238	Non-structural maintenance of chromosomes element	3e-05
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	5e-05
1xwh_A		66	Autoimmune regulator; PHD domain, Zn binding domai	1e-04
2l5u_A		61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	2e-04
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	2e-04
2puy_A		60	PHD finger protein 21A; PHD finger, histone CODE,	2e-04
1mm2_A		61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	3e-04
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	4e-04
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	5e-04
1wev_A		88	Riken cDNA 1110020M19; structural genomics, PHD do	5e-04
3v43_A		112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	6e-04
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	7e-04
3vk6_A		101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	8e-04
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	9e-04

>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

 Score = 67.9 bits (165), Expect = 3e-14
 Identities = 20/80 (25%), Positives = 30/80 (37%), Gaps = 19/80 (23%)

Query: 327 TSEELRAYDDECAICREPMAKA------------------KKLLCNHLFHLACLRSWLDQ 368
           T E   A +++C IC E +A A                  +   C+H FHL CL +    
Sbjct: 17  TEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCN 76

Query: 369 GLNEMY-SCPTCRKPLFVGR 387
           G  +    CP+C+       
Sbjct: 77  GNKDGSLQCPSCKTIYGEKT 96

PyMOL of 1v87

>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

>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

>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

>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

>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

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

>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

>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

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

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

>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

>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

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens} Length = 92	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

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens} Length = 74	Back alignment and structure

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, chromosomal protein, DNA repair, metal-binding; 2.12A {Homo sapiens} Length = 115	Back alignment and structure

>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

>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

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 72	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} Length = 124	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

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 66	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

>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

>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 Length = 118	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} Length = 150	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} Length = 170	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 Length = 116	Back alignment and structure

>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster} Length = 381	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} Length = 141	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

>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

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 73	Back alignment and structure

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus} Length = 85	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 Length = 88	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 Length = 117	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

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 56	Back alignment and structure

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

>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

>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

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 88	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} Length = 79	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 Length = 165	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 Length = 112	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

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 85	Back alignment and structure

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A Length = 66	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} Length = 61	Back alignment and structure

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 63	Back alignment and structure

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens} Length = 60	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 Length = 61	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

>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} Length = 267	Back alignment and structure

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2 Length = 88	Back alignment and structure

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A Length = 112	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

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus} Length = 101	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 Length = 65	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		442
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.36
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	99.34
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.34
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	99.34
2ect_A		78	Ring finger protein 126; metal binding protein, st	99.34
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	99.33
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	99.31
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.31
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.31
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	99.3
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.3
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	99.3
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	99.3
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.29
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	99.27
4ayc_A		138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.27
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	99.26
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.24
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	99.24
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	99.23
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	99.22
1t1h_A		78	Gspef-atpub14, armadillo repeat containing protein	99.21
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	99.2
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	99.19
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.16
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.14
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	99.14
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	99.14
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.13
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	99.13
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	99.13
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.13
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.1
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	99.09
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.09
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	99.09
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	99.04
2kr4_A		85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.02
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.02
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	99.02
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.02
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.01
1z6u_A		150	NP95-like ring finger protein isoform B; structura	99.01
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	99.0
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	98.99
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	98.98
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.97
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	98.97
2kre_A		100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.97
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	98.95
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.93
1wgm_A		98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.93
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.92
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.91
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	98.9
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	98.87
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	98.81
2f42_A		179	STIP1 homology and U-box containing protein 1; cha	98.79
4ic3_A		74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.73
2yu4_A		94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.72
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	98.71
2ea5_A		68	Cell growth regulator with ring finger domain prot	98.7
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.64
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.55
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.48
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.48
2bay_A		61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.44
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.4
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.3
3t6p_A		345	Baculoviral IAP repeat-containing protein 2; ring,	98.26
3vk6_A		101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.0
3nw0_A		238	Non-structural maintenance of chromosomes element	97.75
2jun_A		101	Midline-1; B-BOX, TRIM, ring finger, alternative s	93.92
2ko5_A		99	Ring finger protein Z; lassa fever virus-Z, negati	93.5
1wil_A		89	KIAA1045 protein; ring finger domain, structural g	93.28
2lri_C		66	Autoimmune regulator; Zn binding protein domain, a	92.6
3m62_A		968	Ubiquitin conjugation factor E4; armadillo-like re	92.05
1mm2_A		61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	88.29
2k16_A		75	Transcription initiation factor TFIID subunit 3; p	88.2
1f62_A		51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	86.42
2l5u_A		61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	85.44
3u5n_A		207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	84.79
3o36_A		184	Transcription intermediary factor 1-alpha; TRIM24,	84.68
2yql_A		56	PHD finger protein 21A; PHD domain, structural gen	81.24
1fp0_A		88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	80.75

>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

Probab=99.36  E-value=4.9e-13  Score=102.16  Aligned_cols=51  Identities=31%  Similarity=0.790  Sum_probs=43.3

Q ss_pred             cCCCCCccCcccccC---CccccCcccchHHHHHHHHHhCCCCCCCccccccCCcCCC
Q 013469          333 AYDDECAICREPMAK---AKKLLCNHLFHLACLRSWLDQGLNEMYSCPTCRKPLFVGR  387 (442)
Q Consensus       333 ~~~~~C~IC~e~~~~---~~~LpCgH~FH~~Cl~~Wl~~~~~~~~~CP~CR~~l~~~~  387 (442)
                      +.+..|+||++.+..   ++.+||||.||..|+.+|+.+    +.+||+||+++....
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~----~~~CP~Cr~~~~~~~   65 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLIT----NKKCPICRVDIEAQL   65 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHH----CSBCTTTCSBSCSCC
T ss_pred             CCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHc----CCCCcCcCccccCcC
Confidence            456789999999854   366899999999999999998    578999999987653

PyMOL of 2kiz

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; 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

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

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring 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

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

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

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

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

>2ecy_A TNF receptor-associated factor 3; metal binding protein, 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

>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

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, 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

>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

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

>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

>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

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

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

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

>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

>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

>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

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {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

>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

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

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

>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

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

>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

>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

>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

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

>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

>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

>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

>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

>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

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

>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

>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

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

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

>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

>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

>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

>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

>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

>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

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

>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

>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

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

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*	Back alignment and structure

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A	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

>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

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		442
d1fbva4		79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	2e-12
d1chca_		68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	3e-12
d1iyma_		55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	8e-12
d1bora_		56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	3e-11
d3dplr1		88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	2e-09
d1jm7a_		103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	3e-09
d1g25a_		65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	4e-09
d1v87a_		114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	4e-09
d1vyxa_		60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	1e-08
d1rmda2		86	g.44.1.1 (A:1-86) V(D)J recombination activating p	1e-08
d1ur6b_		52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	5e-08
d1mm2a_		61	g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens	5e-07
d1jm7b_		97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	7e-07
d1fp0a1		70	g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-	4e-06
d1we9a_		64	g.50.1.2 (A:) PHD finger protein At5g26210 {Thale	5e-06
d1f62a_		51	g.50.1.2 (A:) Williams-Beuren syndrome transcripti	2e-05
d1weva_		88	g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus mu	2e-05
d1weea_		72	g.50.1.2 (A:) PHD finger protein At1g33420 {Thale	3e-05
d1wima_		94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	4e-05
d1t1ha_		78	g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cre	2e-04
d2baya1		56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	6e-04
d1wema_		76	g.50.1.2 (A:) Death associated transcription facto	0.004

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


class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.0 bits (145), Expect = 2e-12
 Identities = 19/64 (29%), Positives = 23/64 (35%), Gaps = 9/64 (14%)

Query: 326 ATSEELRAY------DDECAICREPMAKAKKLLCNHLFHLACLRSWLDQGLNEMYSCPTC 379
            T E+   Y         C IC E     K   C HL   +CL SW +        CP C
Sbjct: 8   VTQEQYELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQ---GCPFC 64

Query: 380 RKPL 383
           R  +
Sbjct: 65  RCEI 68

PyMOL of d1fbva4

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

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

>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

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

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

>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

>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

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

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]} Length = 70	Back information, alignment and structure

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 64	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

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]} Length = 88	Back information, alignment and structure

>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 72	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

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 78	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

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 76	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		442
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	99.42
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.4
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.37
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.29
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	99.29
d3dplr1		88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.29
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	99.27
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.24
d2baya1		56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.22
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.18
d1bora_		56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.15
d2c2la2		80	STIP1 homology and U box-containing protein 1, STU	99.1
d1t1ha_		78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.08
d1vyxa_		60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.01
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.94
d1wgma_		98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.68
d1wima_		94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.12
d1f62a_		51	Williams-Beuren syndrome transcription factor, WST	92.43
d1wila_		89	Hypothetical protein KIAA1045 {Human (Homo sapiens	91.41
d1fp0a1		70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	88.19
d1mm2a_		61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	88.05
d1we9a_		64	PHD finger protein At5g26210 {Thale cress (Arabido	85.2
d1wesa_		71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	81.22
d2cs3a1		80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	81.08

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=99.42  E-value=4.5e-14  Score=106.25  Aligned_cols=48  Identities=31%  Similarity=0.776  Sum_probs=42.0

Q ss_pred             CCCCCccCcccccCCc-cccCcccchHHHHHHHHHhCCCCCCCccccccCCcC
Q 013469          334 YDDECAICREPMAKAK-KLLCNHLFHLACLRSWLDQGLNEMYSCPTCRKPLFV  385 (442)
Q Consensus       334 ~~~~C~IC~e~~~~~~-~LpCgH~FH~~Cl~~Wl~~~~~~~~~CP~CR~~l~~  385 (442)
                      ..+.|+||++.+.++. .+||||.||..|+.+|+++    +.+||+||+++..
T Consensus         4 ~~d~C~IC~~~~~~~~~~~~C~H~Fc~~Ci~~w~~~----~~~CP~CR~~i~~   52 (68)
T d1chca_           4 VAERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQ----NPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCSCEEETTTTEEESTTHHHHHHHH----SCSTTTTCCCCCC
T ss_pred             CCCCCccCCcCccCCcEEeCCCCcCcHHHHHHHHHh----CCcCCCCCcchHh
Confidence            4678999999998764 4799999999999999998    5899999998753

PyMOL of d1chca_

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

>d1fbva4 g.44.1.1 (A:356-434) CBL {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

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

>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

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

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}	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

>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

>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

>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

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

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

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

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

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure