Citrus Sinensis ID: 027504

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--

MASGFAESTSVPSQNPSCVGNSANDAGGFECNICFELAQDPIVTLCGHLFCWPCLYRWLHHHSHSQECPVCKAVVQEEKLVPLYGRGKTQTDPRSKSYPGIDIPSRPAGQRPETAPPPEASYFPNLGFGLMGGFMPMATARIGNFTMGFAGLFPSLFNIQFHGFPDATVYGTTSGFPNGFSAFHGGHVHGFPQPSRGQQADNVLKNLLLLIGLFVILALLFW

cccccccccccccccccccccccccccccccccccccccccEEccccccccHHHHHHHHcccccccccccccccccccccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHc

ccccccccccccccccccccccccccccEEEEEEHccccccEEEcccccccHHHHHHHHHccccccccccEEEEEccccEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccEccccccccccccccHcHEcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHc

masgfaestsvpsqnpscvgnsandaggfecnicfelaqdpivtlcghlfcwpclyrwlhhhshsqecpvckavvqeeklvplygrgktqtdprsksypgidipsrpagqrpetapppeasyfpnlgfglmggfmpmatarignftmgfaglfpslfniqfhgfpdatvygttsgfpngfsafhgghvhgfpqpsrgqqADNVLKNLLLLIGLFVILALLFW

masgfaestsvpsqnpsCVGNSANDAGGFECNICFELAQDPIVTLCGHLFCWPCLYRWLHHHSHSQECPVCKAVVQEEKLVplygrgktqtdprsksypgidipsrpagQRPETAPPPEASYFPNLGFGLMGGFMPMATARIGNFTMGFAGLFPSLFNIQFHGFPDATVYGTTSGFPNGFSAFHGGHVHGFPQPSRGQQADNVLKNLLLLIGLFVILALLFW

MASGFAESTSVPSQNPSCVGNSANDAGGFECNICFELAQDPIVTLCGHLFCWPCLYRWLHHHSHSQECPVCKAVVQEEKLVPLYGRGKTQTDPRSKSYPGIDIPSRPAGQRPETAPPPEASYFPNlgfglmggfmPMATARIGNFTMGFAGLFPSLFNIQFHGFPDATVYGTTSGFPNGFSAFHGGHVHGFPQPSRGQQADnvlknlllliglfvilallfW

*************************AGGFECNICFELAQDPIVTLCGHLFCWPCLYRWLHHHSHSQECPVCKAVVQEEKLVPLYG************************************YFPNLGFGLMGGFMPMATARIGNFTMGFAGLFPSLFNIQFHGFPDATVYGTTSGFPNGFSAFHGGHVHGFP*******ADNVLKNLLLLIGLFVILALLFW

******************************CNICFELAQDPIVTLCGHLFCWPCLYRWLHHHSHSQECPVCKAVVQEEKLVPLY****************************************NLGFGLMGGFMPMATARIGNFTMGFAGLFPSLFNIQFHGFPDATVYGTTSGFPNGF***********************LKNLLLLIGLFVILALLFW

*******************GNSANDAGGFECNICFELAQDPIVTLCGHLFCWPCLYRWLHHHSHSQECPVCKAVVQEEKLVPLYGRG*********SYPGIDIPSRP*********PPEASYFPNLGFGLMGGFMPMATARIGNFTMGFAGLFPSLFNIQFHGFPDATVYGTTSGFPNGFSAFHGGHVHGFPQPSRGQQADNVLKNLLLLIGLFVILALLFW

*************************AGGFECNICFELAQDPIVTLCGHLFCWPCLYRWLHHHSHSQECPVCKAVVQEEKLVPLYGRG********************************ASYFPNLGFGLMGGFMPMATARIGNFTMGFAGLFPSLFNIQFHGFPDATVYGTTSGFPNGFSAFHGGHVHGFPQPSRGQQADNVLKNLLLLIGLFVILALLFW

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHo

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooHHHHHHHHHHHHHHHHHHHi

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoo

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

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		222	2.2.26 [Sep-21-2011]
Q09463		235	RING finger protein 5 OS=	yes	no	0.905	0.855	0.342	4e-27
Q91YT2		192	E3 ubiquitin-protein liga	yes	no	0.477	0.552	0.486	8e-26
Q5ZIR9		194	E3 ubiquitin-protein liga	yes	no	0.400	0.458	0.531	1e-25
Q99942		180	E3 ubiquitin-protein liga	yes	no	0.513	0.633	0.480	2e-24
Q568Y3		192	E3 ubiquitin-protein liga	yes	no	0.391	0.453	0.531	2e-24
Q96GF1		192	E3 ubiquitin-protein liga	no	no	0.391	0.453	0.531	2e-24
Q5M807		180	E3 ubiquitin-protein liga	no	no	0.513	0.633	0.480	2e-24
O35445		180	E3 ubiquitin-protein liga	no	no	0.513	0.633	0.480	2e-24
Q5RFK9		192	E3 ubiquitin-protein liga	no	no	0.391	0.453	0.531	2e-24
Q6PC78		194	E3 ubiquitin-protein liga	no	no	0.355	0.407	0.558	9e-24

>sp\|Q09463\|RNF5_CAEEL RING finger protein 5 OS=Caenorhabditis elegans GN=rnf-5 PE=1 SV=1	Back alignment and function desciption

 Score =  121 bits (304), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 85/248 (34%), Positives = 115/248 (46%), Gaps = 47/248 (18%)

Query: 6   AESTSVPSQNPSCVGNSANDAGGFECNICFELAQDPIVTLCGHLFCWPCLYRWLHHHSHS 65
           A  T  PS+ P+   N  +++  FECNIC + A+D +V+LCGHLFCWPCL +WL    ++
Sbjct: 2   ASETKAPSEEPTSSSNK-DESARFECNICLDAAKDAVVSLCGHLFCWPCLSQWLDTRPNN 60

Query: 66  QECPVCKAVVQEEKLVPLYGRGKTQTDPRSKSYPGIDIPSRPAGQRPETAPPPEA----- 120
           Q CPVCK+ +   K+VP+YGRG   +DPR K      +P RP GQR E  PPP++     
Sbjct: 61  QVCPVCKSAIDGNKVVPIYGRGGDSSDPRKK------VPPRPKGQRSE--PPPQSFAGFN 112

Query: 121 ---------SYFPNL----GFGLMGGFMPMATARIGNFTMGF-AGLFPSLFNIQFHGFPD 166
                       PN+    G G + G  P+       F + F  G+FP  F   F G  +
Sbjct: 113 WGGDGGMMGGGGPNVHFSFGIGTVNGLFPLM------FMLPFIQGIFPLSFVASFFGNGN 166

Query: 167 ATVYGTTSGFPNGFSAFHG-------------GHVHGFPQPSRGQQADNVLKNLLLLIGL 213
                   G   G     G             GH       SR  Q +  L N+   IG 
Sbjct: 167 QGAAAAGGGNGGGNDGNDGTHAHTHGHTHGPRGHGESAAPGSRMAQEEEYLSNIFKYIGF 226

Query: 214 FVILALLF 221
           F++  LLF
Sbjct: 227 FMLFWLLF 234

Caenorhabditis elegans (taxid: 6239)

>sp\|Q91YT2\|RN185_MOUSE E3 ubiquitin-protein ligase RNF185 OS=Mus musculus GN=Rnf185 PE=2 SV=1	Back alignment and function description

>sp\|Q5ZIR9\|RN185_CHICK E3 ubiquitin-protein ligase RNF185 OS=Gallus gallus GN=RNF185 PE=2 SV=1	Back alignment and function description

>sp\|Q99942\|RNF5_HUMAN E3 ubiquitin-protein ligase RNF5 OS=Homo sapiens GN=RNF5 PE=1 SV=1	Back alignment and function description

>sp\|Q568Y3\|RN185_RAT E3 ubiquitin-protein ligase RNF185 OS=Rattus norvegicus GN=Rnf185 PE=2 SV=1	Back alignment and function description

>sp\|Q96GF1\|RN185_HUMAN E3 ubiquitin-protein ligase RNF185 OS=Homo sapiens GN=RNF185 PE=1 SV=1	Back alignment and function description

>sp\|Q5M807\|RNF5_RAT E3 ubiquitin-protein ligase RNF5 OS=Rattus norvegicus GN=Rnf5 PE=2 SV=1	Back alignment and function description

>sp\|O35445\|RNF5_MOUSE E3 ubiquitin-protein ligase RNF5 OS=Mus musculus GN=Rnf5 PE=1 SV=1	Back alignment and function description

>sp\|Q5RFK9\|RN185_PONAB E3 ubiquitin-protein ligase RNF185 OS=Pongo abelii GN=RNF185 PE=2 SV=1	Back alignment and function description

>sp\|Q6PC78\|RN185_DANRE E3 ubiquitin-protein ligase RNF185 OS=Danio rerio GN=rnf185 PE=2 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		222
118488873		227	unknown [Populus trichocarpa x Populus d	1.0	0.977	0.731	6e-92
224096906		230	predicted protein [Populus trichocarpa]	1.0	0.965	0.721	6e-86
449448400		229	PREDICTED: E3 ubiquitin-protein ligase R	1.0	0.969	0.764	7e-86
255585132		233	rnf5, putative [Ricinus communis] gi\|223	0.927	0.884	0.778	2e-81
147851991		232	hypothetical protein VITISV_043720 [Viti	0.995	0.952	0.709	2e-80
255644744		205	unknown [Glycine max]	0.869	0.941	0.747	2e-79
225430860		226	PREDICTED: uncharacterized protein LOC10	0.990	0.973	0.665	3e-76
297825287		226	zinc finger family protein [Arabidopsis	0.977	0.960	0.652	2e-75
224067343		227	predicted protein [Populus trichocarpa]	0.990	0.969	0.669	7e-75
225428562		229	PREDICTED: E3 ubiquitin-protein ligase R	0.995	0.965	0.653	8e-75

>gi\|118488873\|gb\|ABK96246.1\| unknown [Populus trichocarpa x Populus deltoides]	Back alignment and taxonomy information

 Score =  342 bits (878), Expect = 6e-92,   Method: Compositional matrix adjust.
 Identities = 166/227 (73%), Positives = 183/227 (80%), Gaps = 5/227 (2%)

Query: 1   MASGFAESTSVPSQNPSCVGNSANDAGGFECNICFELAQDPIVTLCGHLFCWPCLYRWLH 60
           M SG+ ESTSV  ++ S   N+  DAG FECNICFELAQDPIVTLCGHLFCWPCLYRWLH
Sbjct: 1   MESGYEESTSVRLESSSFSSNNGTDAGDFECNICFELAQDPIVTLCGHLFCWPCLYRWLH 60

Query: 61  HHSHSQECPVCKAVVQEEKLVPLYGRGKTQTDPRSKSYPGIDIPSRPAGQRPETAPPPEA 120
           HHSHS ECPVCKA++QEEKLVPLYGRGKTQ DPRSKSYPGIDIP+RP+GQRPETAPPP+A
Sbjct: 61  HHSHSHECPVCKAIIQEEKLVPLYGRGKTQADPRSKSYPGIDIPTRPSGQRPETAPPPDA 120

Query: 121 SYFPNLGFGLMGGFMPMATARIGNFTMGFA----GLFPSLFNIQFHGFPDATVYGTTSGF 176
           +  P+ GFG+ GGFMP A  RIG FT+  A     LFPSLFNIQF G+PDATVYGTTSGF
Sbjct: 121 NNLPHFGFGMPGGFMPAAPTRIGGFTISTAFGGLSLFPSLFNIQFQGYPDATVYGTTSGF 180

Query: 177 PNGFSAFHGGHVHGF-PQPSRGQQADNVLKNLLLLIGLFVILALLFW 222
           P GF  FHG   H F P  +RGQQADNVLKNL   IG  V+LALL+W
Sbjct: 181 PYGFHGFHGNRTHRFPPATTRGQQADNVLKNLFFFIGFLVVLALLWW 227

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224096906\|ref\|XP_002310781.1\| predicted protein [Populus trichocarpa] gi\|222853684\|gb\|EEE91231.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449448400\|ref\|XP_004141954.1\| PREDICTED: E3 ubiquitin-protein ligase RMA1H1-like [Cucumis sativus] gi\|449487905\|ref\|XP_004157859.1\| PREDICTED: E3 ubiquitin-protein ligase RMA1H1-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|255585132\|ref\|XP_002533271.1\| rnf5, putative [Ricinus communis] gi\|223526896\|gb\|EEF29103.1\| rnf5, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|147851991\|emb\|CAN79067.1\| hypothetical protein VITISV_043720 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255644744\|gb\|ACU22874.1\| unknown [Glycine max]	Back alignment and taxonomy information

>gi\|225430860\|ref\|XP_002269155.1\| PREDICTED: uncharacterized protein LOC100246078 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297825287\|ref\|XP_002880526.1\| zinc finger family protein [Arabidopsis lyrata subsp. lyrata] gi\|297326365\|gb\|EFH56785.1\| zinc finger family protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|224067343\|ref\|XP_002302470.1\| predicted protein [Populus trichocarpa] gi\|222844196\|gb\|EEE81743.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|225428562\|ref\|XP_002284651.1\| PREDICTED: E3 ubiquitin-protein ligase RNF5 [Vitis vinifera] gi\|147795942\|emb\|CAN60863.1\| hypothetical protein VITISV_016726 [Vitis vinifera]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		222
TAIR\|locus:2049023		227	AT2G23780 [Arabidopsis thalian	0.855	0.837	0.668	1.5e-67
TAIR\|locus:2016437		226	AT1G19310 [Arabidopsis thalian	0.797	0.783	0.608	3.4e-61
TAIR\|locus:2037294		137	AT1G74990 [Arabidopsis thalian	0.581	0.941	0.530	1.1e-34
DICTYBASE\|DDB_G0285333		281	DDB_G0285333 "RING finger prot	0.581	0.459	0.479	6.2e-30
WB\|WBGene00004381		235	rnf-5 [Caenorhabditis elegans	0.783	0.740	0.391	2.7e-29
UNIPROTKB\|Q09463		235	rnf-5 "RING finger protein 5"	0.783	0.740	0.391	2.7e-29
UNIPROTKB\|F1PCX5		192	RNF185 "Uncharacterized protei	0.689	0.796	0.420	3.1e-28
UNIPROTKB\|Q96GF1		192	RNF185 "E3 ubiquitin-protein l	0.689	0.796	0.420	3.1e-28
UNIPROTKB\|F2Z4Y3		192	RNF185 "Uncharacterized protei	0.689	0.796	0.420	3.1e-28
MGI\|MGI:1922078		192	Rnf185 "ring finger protein 18	0.702	0.812	0.419	3.9e-28

TAIR\|locus:2049023 AT2G23780 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 686 (246.5 bits), Expect = 1.5e-67, P = 1.5e-67
 Identities = 137/205 (66%), Positives = 152/205 (74%)

Query:     1 MASGFAESTSVPSQNPSCVGNSANDAGG-FECNICFELAQDPIVTLCGHLFCWPCLYRWL 59
             M +G  ES++  S + S   N  ND GG FECNICFELAQDPIVTLCGHLFCWPCLYRWL
Sbjct:     1 MVNG--ESSTSTSYSDS--NNDTNDQGGDFECNICFELAQDPIVTLCGHLFCWPCLYRWL 56

Query:    60 HHHSHSQECPVCKAVVQEEKLVPLYGRGKTQTDPRSKSYPGIDIPSRPAGQRPETA-PPP 118
             HHHSHSQECPVCKAVVQ++KLVPLYGRGK QTDPRSK YPG+ IP+RP GQRPETA PPP
Sbjct:    57 HHHSHSQECPVCKAVVQDDKLVPLYGRGKNQTDPRSKRYPGLRIPNRPTGQRPETAAPPP 116

Query:   119 E---ASYFPNXXXXXXXXXXPM-ATARIGNFTMGFAGLFPSLFNIQFHGFPDATVYGTTS 174
             +   AS F N          PM AT R GNF+MGF GL PSLFN QFHGF DAT+YG+T 
Sbjct:   117 QPEAASNFFNYGIGLMGGIMPMMATTRFGNFSMGFGGLLPSLFNFQFHGFHDATLYGSTP 176

Query:   175 GFPNGFSAFHGGHVHGFPQPSRGQQ 199
             G+P G   +H G   G P P RGQ+
Sbjct:   177 GYPYG--GYHNGF-RGVP-P-RGQE 196

GO:0005634 "nucleus" evidence=ISM

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

GO:0006661 "phosphatidylinositol biosynthetic process" evidence=RCA

TAIR\|locus:2016437 AT1G19310 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2037294 AT1G74990 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0285333 DDB_G0285333 "RING finger protein 185" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

WB\|WBGene00004381 rnf-5 [Caenorhabditis elegans (taxid:6239)]	Back alignment and assigned GO terms

UNIPROTKB\|Q09463 rnf-5 "RING finger protein 5" [Caenorhabditis elegans (taxid:6239)]	Back alignment and assigned GO terms

UNIPROTKB\|F1PCX5 RNF185 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|Q96GF1 RNF185 "E3 ubiquitin-protein ligase RNF185" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|F2Z4Y3 RNF185 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

MGI\|MGI:1922078 Rnf185 "ring finger protein 185" [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)
Q09463	RNF5_CAEEL	No assigned EC number	0.3427	0.9054	0.8553	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	LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_Genewise1_v1.C_LG_VII3310	hypothetical protein (230 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	fgenesh4_pm.C_scaffold_86000046	hypothetical protein (276 aa)	•	0.800
	estExt_fgenesh4_pg.C_LG_VI0994	hypothetical protein (249 aa)	•	0.800
	estExt_Genewise1_v1.C_LG_XI1160	hypothetical protein (243 aa)	•	0.800
	estExt_Genewise1_v1.C_LG_IV1734	hypothetical protein (245 aa)	•	0.800

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		222
PLN03208		193	PLN03208, PLN03208, E3 ubiquitin-protein ligase RM	1e-26
pfam13923		45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	3e-12
cd00162		45	cd00162, RING, RING-finger (Really Interesting New	5e-12
pfam13639		46	pfam13639, zf-RING_2, Ring finger domain	3e-10
COG5574		271	COG5574, PEX10, RING-finger-containing E3 ubiquiti	3e-10
smart00184		40	smart00184, RING, Ring finger	6e-10
TIGR00599		397	TIGR00599, rad18, DNA repair protein rad18	8e-08
pfam00097		40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	9e-07
COG5432		391	COG5432, RAD18, RING-finger-containing E3 ubiquiti	2e-06
pfam13920		49	pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RI	1e-05
COG5540		374	COG5540, COG5540, RING-finger-containing ubiquitin	2e-05
PHA02929		238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	9e-05
COG5152		259	COG5152, COG5152, Uncharacterized conserved protei	2e-04
pfam13445		55	pfam13445, zf-RING_LisH, RING-type zinc-finger, Li	6e-04
pfam12861		85	pfam12861, zf-Apc11, Anaphase-promoting complex su	0.002
PHA02926		242	PHA02926, PHA02926, zinc finger-like protein; Prov	0.004

>gnl\|CDD\|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2; Provisional	Back alignment and domain information

 Score =  100 bits (251), Expect = 1e-26
 Identities = 47/99 (47%), Positives = 66/99 (66%), Gaps = 20/99 (20%)

Query: 25  DAGG-FECNICFELAQDPIVTLCGHLFCWPCLYRWLHHHSHSQE-------------CPV 70
           D+GG F+CNIC +  +DP+VTLCGHLFCWPC+++W +  ++S++             CPV
Sbjct: 14  DSGGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPV 73

Query: 71  CKAVVQEEKLVPLYGRGKTQTDPRSKSYPGIDIPSRPAG 109
           CK+ V E  LVP+YGRG  Q  P+S    G ++PSRP+G
Sbjct: 74  CKSDVSEATLVPIYGRG--QKAPQS----GSNVPSRPSG 106

Length = 193

>gnl\|CDD\|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger)	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\|222279 pfam13639, zf-RING_2, Ring finger domain	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

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

>gnl\|CDD\|233043 TIGR00599, rad18, DNA repair protein rad18	Back alignment and domain information

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

>gnl\|CDD\|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]	Back alignment and domain information

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

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

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

>gnl\|CDD\|227481 COG5152, COG5152, Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|222135 pfam13445, zf-RING_LisH, RING-type zinc-finger, LisH dimerisation motif	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\|165237 PHA02926, PHA02926, zinc finger-like protein; Provisional	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		222
KOG0823		230	consensus Predicted E3 ubiquitin ligase [Posttrans	100.0
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	100.0
KOG0317		293	consensus Predicted E3 ubiquitin ligase, integral	99.38
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.33
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.27
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	99.24
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.15
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.1
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.09
PHA02929		238	N1R/p28-like protein; Provisional	99.03
KOG2164		513	consensus Predicted E3 ubiquitin ligase [Posttrans	99.02
TIGR00599		397	rad18 DNA repair protein rad18. This family is bas	99.01
PF04564		73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.98
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.96
COG5574		271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.93
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	98.9
COG5243		491	HRD1 HRD ubiquitin ligase complex, ER membrane com	98.9
PHA02926		242	zinc finger-like protein; Provisional	98.82
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.8
PF14634		44	zf-RING_5: zinc-RING finger domain	98.79
KOG0287		442	consensus Postreplication repair protein RAD18 [Re	98.78
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.77
KOG4628		348	consensus Predicted E3 ubiquitin ligase [Posttrans	98.7
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	98.68
COG5432		391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.59
KOG2177		386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.53
COG5540		374	RING-finger-containing ubiquitin ligase [Posttrans	98.51
KOG0978		698	consensus E3 ubiquitin ligase involved in syntaxin	98.47
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	98.46
PF12861		85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.39
PF14835		65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.35
TIGR00570		309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.27
KOG4159		398	consensus Predicted E3 ubiquitin ligase [Posttrans	98.1
KOG4172		62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.06
KOG4265		349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.04
KOG0311		381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.99
KOG0824		324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.92
KOG1785		563	consensus Tyrosine kinase negative regulator CBL [	97.9
PF11789		57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.84
KOG2660		331	consensus Locus-specific chromosome binding protei	97.83
KOG1734		328	consensus Predicted RING-containing E3 ubiquitin l	97.75
PF11793		70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.75
KOG1645		463	consensus RING-finger-containing E3 ubiquitin liga	97.74
KOG0297		391	consensus TNF receptor-associated factor [Signal t	97.72
KOG0828		636	consensus Predicted E3 ubiquitin ligase [Posttrans	97.7
COG5152		259	Uncharacterized conserved protein, contains RING a	97.69
KOG1002		791	consensus Nucleotide excision repair protein RAD16	97.63
KOG2879		298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.6
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.53
smart00744		49	RINGv The RING-variant domain is a C4HC3 zinc-fing	97.47
KOG1813		313	consensus Predicted E3 ubiquitin ligase [Posttrans	97.43
KOG0827		465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.42
KOG4692		489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.38
KOG3039		303	consensus Uncharacterized conserved protein [Funct	97.37
KOG1039		344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.33
COG5219		1525	Uncharacterized conserved protein, contains RING Z	97.23
KOG0826		357	consensus Predicted E3 ubiquitin ligase involved i	97.19
COG5222		427	Uncharacterized conserved protein, contains RING Z	97.15
KOG1493		84	consensus Anaphase-promoting complex (APC), subuni	97.09
KOG0825		1134	consensus PHD Zn-finger protein [General function	96.99
KOG1571		355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.93
KOG4275		350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.93
COG5194		88	APC11 Component of SCF ubiquitin ligase and anapha	96.88
PF05290		140	Baculo_IE-1: Baculovirus immediate-early protein (	96.84
PF04641		260	Rtf2: Rtf2 RING-finger	96.74
KOG1001		674	consensus Helicase-like transcription factor HLTF/	96.48
PF14447		55	Prok-RING_4: Prokaryotic RING finger family 4	96.15
KOG4739		233	consensus Uncharacterized protein involved in syna	96.01
KOG1814		445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.96
PF07800		162	DUF1644: Protein of unknown function (DUF1644); In	95.66
KOG1941		518	consensus Acetylcholine receptor-associated protei	95.64
KOG4185		296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.58
KOG2930		114	consensus SCF ubiquitin ligase, Rbx1 component [Po	95.51
KOG3002		299	consensus Zn finger protein [General function pred	95.43
KOG3970		299	consensus Predicted E3 ubiquitin ligase [Posttrans	95.36
PF14570		48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.33
PHA03096		284	p28-like protein; Provisional	95.09
KOG4367		699	consensus Predicted Zn-finger protein [Function un	95.01
COG5236		493	Uncharacterized conserved protein, contains RING Z	94.93
KOG2817		394	consensus Predicted E3 ubiquitin ligase [Posttrans	94.9
KOG4445		368	consensus Uncharacterized conserved protein, conta	94.54
KOG3800		300	consensus Predicted E3 ubiquitin ligase containing	94.39
PHA02825		162	LAP/PHD finger-like protein; Provisional	94.37
KOG4362		684	consensus Transcriptional regulator BRCA1 [Replica	94.31
KOG1428		3738	consensus Inhibitor of type V adenylyl cyclases/Ne	94.14
PF08746		43	zf-RING-like: RING-like domain; InterPro: IPR01485	94.11
COG5175		480	MOT2 Transcriptional repressor [Transcription]	93.79
KOG2114		933	consensus Vacuolar assembly/sorting protein PEP5/V	93.55
PHA02862		156	5L protein; Provisional	93.2
PF02891		50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	92.98
PF10272		358	Tmpp129: Putative transmembrane protein precursor;	92.84
PF12906		47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	92.81
KOG0298		1394	consensus DEAD box-containing helicase-like transc	92.48
KOG1952		950	consensus Transcription factor NF-X1, contains NFX	91.97
KOG1815		444	consensus Predicted E3 ubiquitin ligase [Posttrans	91.94
PF10367		109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	91.84
KOG3161		861	consensus Predicted E3 ubiquitin ligase [Posttrans	91.72
PF05883		134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	91.38
KOG1940		276	consensus Zn-finger protein [General function pred	91.03
KOG1812		384	consensus Predicted E3 ubiquitin ligase [Posttrans	90.8
COG5220		314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	90.75
KOG1100		207	consensus Predicted E3 ubiquitin ligase [Posttrans	90.37
PF03854		50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	90.15
COG5183		1175	SSM4 Protein involved in mRNA turnover and stabili	89.72
KOG3268		234	consensus Predicted E3 ubiquitin ligase [Posttrans	89.67
KOG0825		1134	consensus PHD Zn-finger protein [General function	89.54
KOG3579		352	consensus Predicted E3 ubiquitin ligase [Posttrans	89.09
COG5109		396	Uncharacterized conserved protein, contains RING Z	88.34
KOG3113		293	consensus Uncharacterized conserved protein [Funct	88.34
KOG3039		303	consensus Uncharacterized conserved protein [Funct	88.32
KOG2932		389	consensus E3 ubiquitin ligase involved in ubiquiti	87.74
KOG2034		911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	87.43
KOG3899		381	consensus Uncharacterized conserved protein [Funct	83.9
KOG3053		293	consensus Uncharacterized conserved protein [Funct	83.8

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

Probab=100.00  E-value=2.5e-35  Score=249.33  Aligned_cols=179  Identities=44%  Similarity=0.870  Sum_probs=122.2

Q ss_pred             CCCCCccccccccCCCCcEEcccCCccCHhHHHHHHHhcCCCCCCCcccccccccccccccCCCCC-CCCCCCCCCCCCC
Q 027504           24 NDAGGFECNICFELAQDPIVTLCGHLFCWPCLYRWLHHHSHSQECPVCKAVVQEEKLVPLYGRGKT-QTDPRSKSYPGID  102 (222)
Q Consensus        24 ~~~~~~~C~ICl~~~~~pv~l~CGH~FC~~Cl~~wl~~~~~~~~CPvCr~~v~~~~l~p~~~~~~~-~~d~~~k~~~~~~  102 (222)
                      .+...++|+||+|..+|||++.|||+|||+||++|++.+..++.|||||..|+.++|+|+|++|.. .++++++.     
T Consensus        43 ~~~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYGrG~~~~~~~~~~~-----  117 (230)
T KOG0823|consen   43 RDGGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYGRGSKKPSDPRKKD-----  117 (230)
T ss_pred             CCCCceeeeeeccccCCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEeeeccCCCCCCCccccc-----
Confidence            467889999999999999999999999999999999999889999999999999999999999984 66776654     


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCccccccc-------ccCccchhccccCCCCccccCCCCC
Q 027504          103 IPSRPAGQRPETAPPPEASYFPNLGFGLMGGFMPMATARIGNFTMGFA-------GLFPSLFNIQFHGFPDATVYGTTSG  175 (222)
Q Consensus       103 ip~Rp~~~r~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~g~~~~~~g-------~~~p~~f~~~~~~~~~~~~~~~~~~  175 (222)
                      +|+||+++|.+++.+...+ ...|++...|........+...+++++|       +++|.+|..        +.||....
T Consensus       118 vP~RP~~~R~e~~~p~~~~-~~~~g~r~~g~~~~~~~~~~f~~s~~i~~~~~~v~~~~p~~~~~--------~lf~~~~~  188 (230)
T KOG0823|consen  118 VPPRPAGQRYESKRPTPQN-RGNHGFRFFGFRLGEESSNRFMYSFGIGLFGDPVMGLFPFGLYT--------RLFGTDET  188 (230)
T ss_pred             CCCCCCCccccccCCCCcc-ccccccccccccccccCCcceeEEeecccCCCceeeecccccee--------eecCCCCC
Confidence            8999999998865442111 1112322121110000111112233322       244433333        33443333


Q ss_pred             CCCCCccCCCCCCCCCCCCC-chhhHHHHHHHHHHHHHHHHHHHHHhC
Q 027504          176 FPNGFSAFHGGHVHGFPQPS-RGQQADNVLKNLLLLIGLFVILALLFW  222 (222)
Q Consensus       176 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~~~l~~~  222 (222)
                      ++ . .+.   . ...+++. ++||++++|+++++|+++++++||+++
T Consensus       189 ~~-~-~~~---~-~~~~~~~~r~~q~e~~ls~~f~~~~~~~~~~l~~~  230 (230)
T KOG0823|consen  189 FP-A-DTP---R-PSPARPLGRQMQRENSLSRVFLFLACFFVSWLLVI  230 (230)
T ss_pred             cc-c-cCC---C-CCCCccccccchhhcccccchhhhhhhheeeeeeC
Confidence            33 1 111   0 1123334 889999999999999999999999874

>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

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

>smart00504 Ubox Modified RING finger domain	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

>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

>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

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

>TIGR00599 rad18 DNA repair protein rad18	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

>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

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

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

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

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

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

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

>smart00184 RING Ring finger	Back alignment and domain information

>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

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

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

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

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

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

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

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

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

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

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

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

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

>KOG0824 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

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

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

>KOG1734 consensus Predicted RING-containing 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

>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

>KOG0828 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

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

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

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

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

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

>KOG0827 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

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

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

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

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

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]	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

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

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

>KOG4275 consensus Predicted 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

>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

>PF04641 Rtf2: Rtf2 RING-finger	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

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4	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

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

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

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

>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

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

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

>KOG4367 consensus Predicted Zn-finger protein [Function unknown]	Back alignment and domain information

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

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

>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]	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

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

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

>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

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

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

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

>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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

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

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

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

>KOG1815 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

>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

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

>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

>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

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

>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]	Back alignment and domain information

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]	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

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

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		222
1jm7_A		112	Solution Structure Of The Brca1/bard1 Ring-domain H		3e-06
2ecj_A		58	Solution Structure Of The Ring Domain Of The Human		2e-05

>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain Heterodimer Length = 112

Back alignment and structure

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 18/44 (40%), Positives = 27/44 (61%)
Query: 29 FECNICFELAQDPIVTLCGHLFCWPCLYRWLHHHSHSQECPVCK 72
           EC IC EL ++P+ T C H+FC  C+ + L+      +CP+CK
Sbjct: 22 LECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCK 65

PyMOL of 1jm7

>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human Tripartite Motif-Containing Protein 39 Length = 58

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		222
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	1e-21
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	8e-20
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	1e-19
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	3e-19
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	1e-18
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	1e-18
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	2e-16
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	3e-16
4epo_C		149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	3e-16
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	3e-14
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	3e-14
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	1e-13
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	1e-13
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	2e-13
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	5e-13
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	6e-13
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	2e-12
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	2e-12
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	4e-12
1z6u_A		150	NP95-like ring finger protein isoform B; structura	5e-12
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	5e-12
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	6e-12
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	8e-12
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	2e-11
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	2e-11
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	2e-11
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	3e-11
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-10
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-09
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	5e-10
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	6e-10
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	7e-10
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	9e-10
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	1e-09
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	2e-09
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	6e-09
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	4e-08
2bay_A		61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	9e-08
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	1e-07
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	3e-07
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	5e-07
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	9e-07
2ect_A		78	Ring finger protein 126; metal binding protein, st	2e-06
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	2e-06
3nw0_A		238	Non-structural maintenance of chromosomes element	4e-06
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	5e-06
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	6e-06
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	9e-06
2kre_A		100	Ubiquitin conjugation factor E4 B; U-box domain, E	2e-05
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	2e-05
2kr4_A		85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	4e-05
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	4e-05
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	5e-05
2yu4_A		94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	5e-05
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	5e-05
3m62_A		968	Ubiquitin conjugation factor E4; armadillo-like re	7e-05
2cs3_A		93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	1e-04
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	2e-04
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	2e-04
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	2e-04
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	4e-04
2ko5_A		99	Ring finger protein Z; lassa fever virus-Z, negati	6e-04
2f42_A		179	STIP1 homology and U-box containing protein 1; cha	7e-04
1wd2_A		60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	9e-04

>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

 Score = 84.6 bits (209), Expect = 1e-21
 Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 3/57 (5%)

Query: 29 FECNICFELAQDP-IVTLCGHLFCWPCLYRWLHHHSHSQECPVCKAVVQEEKLVPLY 84
          F C IC E  +D  +   C  L C+ C+ RWL       +CP C+A +Q  +LV   
Sbjct: 23 FRCFICMEKLRDARLCPHCSKLCCFSCIRRWL--TEQRAQCPHCRAPLQLRELVNCR 77

PyMOL of 3lrq

>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

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

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

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

>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

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

>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

>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

>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

>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

>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

>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

>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

>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

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

>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

>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

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

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 58	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

>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

>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

>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

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

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

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

>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

>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

>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

>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

>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 Length = 61	Back alignment and structure

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

>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

>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

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

>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 Length = 281	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

>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

>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

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 74	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 Length = 100	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

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus} Length = 85	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

>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

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 94	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

>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 Length = 968	Back alignment and structure

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3 Length = 93	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 Length = 64	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* Length = 63	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

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

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C Length = 179	Back alignment and structure

>1wd2_A Ariadne-1 protein homolog; ring, IBR, triad, zinc finger, ligase; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 60	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		222
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	99.61
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	99.59
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	99.57
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	99.57
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	99.56
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	99.54
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	99.53
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	99.53
1t1h_A		78	Gspef-atpub14, armadillo repeat containing protein	99.52
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	99.52
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	99.52
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.52
2ect_A		78	Ring finger protein 126; metal binding protein, st	99.51
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.51
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	99.5
1wgm_A		98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.47
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.47
2kr4_A		85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.46
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	99.46
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	99.44
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	99.43
2kre_A		100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.43
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.41
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	99.4
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	99.4
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	99.39
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.38
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.36
2yu4_A		94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.36
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.35
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	99.35
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.34
4ayc_A		138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.33
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	99.33
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	99.32
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	99.32
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	99.31
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	99.31
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.3
1z6u_A		150	NP95-like ring finger protein isoform B; structura	99.29
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.29
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.29
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.25
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.25
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	99.25
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.24
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.23
2f42_A		179	STIP1 homology and U-box containing protein 1; cha	99.22
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	99.22
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	99.22
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	99.19
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.18
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	99.16
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.14
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.11
2ea5_A		68	Cell growth regulator with ring finger domain prot	99.1
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.09
2bay_A		61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	99.08
4ic3_A		74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.07
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	99.06
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	99.03
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.0
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	98.98
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	98.8
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.79
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.78
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	98.77
3t6p_A		345	Baculoviral IAP repeat-containing protein 2; ring,	98.66
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.39
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.31
3vk6_A		101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.73
3nw0_A		238	Non-structural maintenance of chromosomes element	97.03
2ko5_A		99	Ring finger protein Z; lassa fever virus-Z, negati	96.9
3m62_A		968	Ubiquitin conjugation factor E4; armadillo-like re	96.67
2jun_A		101	Midline-1; B-BOX, TRIM, ring finger, alternative s	96.27
2cs3_A		93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	96.09
3i2d_A		371	E3 SUMO-protein ligase SIZ1; signal transduction,	88.54
4fo9_A		360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	86.57
1x64_A		89	Alpha-actinin-2 associated LIM protein; LIM domain	86.47
2lv9_A		98	Histone-lysine N-methyltransferase MLL5; zinc fing	83.93
1weo_A		93	Cellulose synthase, catalytic subunit (IRX3); stru	83.33
2lri_C		66	Autoimmune regulator; Zn binding protein domain, a	83.06

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

Probab=99.61  E-value=8.5e-16  Score=107.78  Aligned_cols=64  Identities=28%  Similarity=0.512  Sum_probs=54.3

Q ss_pred             CCCCCCCCCCccccccccCCCCcEEc-ccCCccCHhHHHHHHHhcCCCCCCCcccccccccccccccC
Q 027504           19 VGNSANDAGGFECNICFELAQDPIVT-LCGHLFCWPCLYRWLHHHSHSQECPVCKAVVQEEKLVPLYG   85 (222)
Q Consensus        19 ~~~~~~~~~~~~C~ICl~~~~~pv~l-~CGH~FC~~Cl~~wl~~~~~~~~CPvCr~~v~~~~l~p~~~   85 (222)
                      +.+.+...+.++|+||++.+.+|+++ +|||.||..||.+|++.   ...||+||+.+..++++++..
T Consensus         6 ~~~~~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~---~~~CP~Cr~~~~~~~~~~~~~   70 (72)
T 2djb_A            6 SGNLSELTPYILCSICKGYLIDATTITECLHTFCKSCIVRHFYY---SNRCPKCNIVVHQTQPLSGPS   70 (72)
T ss_dssp             CCCCCCCCGGGSCTTTSSCCSSCEECSSSCCEECHHHHHHHHHH---CSSCTTTCCCCCSSCSCCCCS
T ss_pred             hhhHhhcCCCCCCCCCChHHHCcCEECCCCCHHHHHHHHHHHHc---CCcCCCcCcccCcccccccCC
Confidence            44556667889999999999999997 99999999999999984   568999999999877665543

PyMOL of 2djb

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

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

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

>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

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

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

>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

>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

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

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

>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

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; 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

>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

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

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

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

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

>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

>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

>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

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

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

>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

>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

>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

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

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

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

>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

>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

>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

>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

>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

>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

>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

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

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

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

>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

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

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

>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

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; 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

>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

>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

>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

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

>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

>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

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

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

>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

>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

>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

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

>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

>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

>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

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3	Back alignment and structure

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

>4fo9_A E3 SUMO-protein ligase PIAS2; E3 ligase, pinit domain, SP-ring domain, structural GE consortium, SGC; 2.39A {Homo sapiens} PDB: 2asq_B	Back alignment and structure

>1x64_A Alpha-actinin-2 associated LIM protein; LIM domain, PDZ and LIM domain 3, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3	Back alignment and structure

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}	Back alignment and structure

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1	Back alignment and structure

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

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		222
d1jm7a_		103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	3e-18
d1fbva4		79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	9e-15
d1rmda2		86	g.44.1.1 (A:1-86) V(D)J recombination activating p	2e-13
d1chca_		68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	3e-13
d1bora_		56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	9e-11
d1iyma_		55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	3e-10
d1t1ha_		78	g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cre	2e-09
d1jm7b_		97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	4e-09
d1vyxa_		60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	1e-08
d1g25a_		65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	5e-08
d2c2la2		80	g.44.1.2 (A:225-304) STIP1 homology and U box-cont	6e-08
d2baya1		56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	8e-08
d3dplr1		88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	9e-08
d1ur6b_		52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	2e-07
d1v87a_		114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	7e-06
d1wima_		94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	1e-05
d1wd2a_		60	g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Ho	0.001

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


class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.7 bits (183), Expect = 3e-18
 Identities = 19/54 (35%), Positives = 30/54 (55%)

Query: 29 FECNICFELAQDPIVTLCGHLFCWPCLYRWLHHHSHSQECPVCKAVVQEEKLVP 82
           EC IC EL ++P+ T C H+FC  C+ + L+      +CP+CK  + +  L  
Sbjct: 22 LECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQE 75

PyMOL of d1jm7a_

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

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

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

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

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 65	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]} Length = 80	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

>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

>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

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

>d1wd2a_ g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Homo sapiens) [TaxId: 9606]} Length = 60	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		222
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.51
d1t1ha_		78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.49
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	99.48
d2c2la2		80	STIP1 homology and U box-containing protein 1, STU	99.48
d2baya1		56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.47
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.46
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	99.37
d1wgma_		98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.37
d1bora_		56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.31
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.29
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	99.27
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.27
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.27
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.19
d3dplr1		88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.02
d1vyxa_		60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.93
d1wima_		94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.43
d2cs3a1		80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	94.46
d1weoa_		93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	89.82
d1weva_		88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	88.68
d1wewa_		78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	86.06
d1wema_		76	Death associated transcription factor 1, Datf1 (DI	86.04
d1wesa_		71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	83.29
d1wepa_		79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	80.5

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=3.8e-15  Score=110.20  Aligned_cols=61  Identities=31%  Similarity=0.746  Sum_probs=52.7

Q ss_pred             CCccccccccCCCCcEEcccCCccCHhHHHHHHHhcCCCCCCCcccccccccccccccCCC
Q 027504           27 GGFECNICFELAQDPIVTLCGHLFCWPCLYRWLHHHSHSQECPVCKAVVQEEKLVPLYGRG   87 (222)
Q Consensus        27 ~~~~C~ICl~~~~~pv~l~CGH~FC~~Cl~~wl~~~~~~~~CPvCr~~v~~~~l~p~~~~~   87 (222)
                      +.++|+||++.+.+|+.++|||+||..||.+|++.+.....||+||+.+..+++.+++...
T Consensus        20 ~~l~CpIC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l~~n~~l~   80 (103)
T d1jm7a_          20 KILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFS   80 (103)
T ss_dssp             HHTSCSSSCCCCSSCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCCCSSS
T ss_pred             cCcCCCccCchhCCeEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhCCcCHHHH
Confidence            4578999999999999999999999999999998655557899999999887777765543

PyMOL of d1jm7a_

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

>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

>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

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

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

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {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

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

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

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

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

>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

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}	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

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

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

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

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

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

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