Citrus Sinensis ID: 039490

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420---

MGNNVREEIMDLDLNLDPSDPSNGSVLGLGSLLNELETAHGRIEERIRQLEAVTSRARQRQRWRQGQSNTQMVNVSLEPTVSSVPSEVSLLSGECSINPQVRTIENVKTGKRGSSHLIAKALGIHTDTKRAGAGGGEFFDCNICLDMARDPVLTCCGHLFCWSCFYQLPYAYRNVKECPACNGEVTDASIIPIYGNGNSNDLQKLKSKESCLKVPPRPLARRIESVRQQLVNRRPVSTPIEVRIQQFNSIVDAARHQTGSLDLDAAVRSGELEVNDPLLHISRVLPASISSLSSALTSAMDSAERLVGDLEAYINSDNLRRNHQEFSHADTDSVSLISADVQAGSQSLDMATEIDSGVPRSASSVRTDVPTNIVRLQSEIRDTAMEVNLNAPHSSSSRRRSASLRASDVDSGICRELRRRRLR

cccccccccccccccccccccccccccccccccccHHHHccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccEEEccccccccHHHHHHccccccccccccccccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHccccccHHHHHccccccccHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHHcccc

cccccccccEEccccccccccccccccccccHHHHHHcHccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEHccccccEEEcccccccHHHHHHHHHccccccccccEEEEEccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHEcccccccccccccHHHHHHcHHHHHcccccccccccccccccccHHHHHHHHcccccccccHEEccccccccccccccccccEEEEEccccccccEEEEcccccccccccccccccccccccccccccHHHccc

MGNNVREEIMDldlnldpsdpsngsvlGLGSLLNELETAHGRIEERIRQLEAVTSRARQRQRwrqgqsntqMVNVsleptvssvpsevsllsgecsinpqvrtienvktgkrgsSHLIAKALGihtdtkragagggeffdcnicldmardpvltccghlfcwscfyqlpyayrnvkecpacngevtdasiipiygngnsndlqklkskesclkvpprplaRRIESVRQQLvnrrpvstpiEVRIQQFNSIVDAARhqtgsldldaavrsgelevndpllhiSRVLPASISSLSSALTSAMDSAERLVGDLEAyinsdnlrrnhqefshadtdsvSLISADVQAGSQSLDMAteidsgvprsassvrtdvptNIVRLQSEIRDTAMevnlnaphssssrrrsaslrasdvdsgICRELRRRRLR

MGNNVREEIMDLDLNLDPSDPSNGSVLGLGSLLNELETAHGRIEERIRQLEAVTSRArqrqrwrqgqsntqmvnvSLEPTVSSVPSEVSLlsgecsinpqvrtienvktgkrgssHLIAKALGIHTDTKRAGAGGGEFFDCNICLDMARDPVLTCCGHLFCWSCFYQLPYAYRNVKECPACNGEVTDASIIPIYGNGNSNDLQKLKSKESCLKVPPRPLARRIESvrqqlvnrrpvstpievRIQQFNSIVDAARHQTGSLDLDAAVRSGELEVNDPLLHISRVLPASISSLSSALTSAMDSAERLVGDLEAYINSDNLRRNHQEFSHADTDSVSLISADVQAGSQSLDMATEIDsgvprsassvrtdvptNIVRLQSEIRDTamevnlnaphssssrrrsaslrasdvdsgicrelrrrrlr

MGNNVREEIMdldlnldpsdpsngsvlglgsllneleTAHGRIEERIRQLEAVTSrarqrqrwrqgqSNTQMVNvsleptvssvpsevsllsGECSINPQVRTIENVKTGKRGSSHLIAKALGIHTDTKRAGAGGGEFFDCNICLDMARDPVLTCCGHLFCWSCFYQLPYAYRNVKECPACNGEVTDASIIPIYGNGNSNDLQKLKSKESCLKVPPRPLARRIESVRQQLVNRRPVSTPIEVRIQQFNSIVDAARHQTGSLDLDAAVRSGELEVNDPLLHIsrvlpasisslssaltsamdsaERLVGDLEAYINSDNLRRNHQEFSHADTDSVSLISADVQAGSQSLDMATEIDSGVPRSASSVRTDVPTNIVRLQSEIRDTAMEVNLNAPHssssrrrsaslrasDVDSGICrelrrrrlr

*******************************************************************************************************************HLIAKALGIHTDTKRAGAGGGEFFDCNICLDMARDPVLTCCGHLFCWSCFYQLPYAYRNVKECPACNGEVTDASIIPIYGNG**************************************VSTPIEVRIQQFNSIVDAARHQTGSLDLDAAVRSGELEVNDPLLHISRVLPA*******************VGDLEAYI*************************************************************************************************************

******E***DLDLN*****************LNELE*******************************************************************************************************CNICLDMARDPVLTCCGHLFCWSCFYQLPYAYRNVKECPACNGEVTDASIIPIYGNG*****************************************************************************************************************************************************************************************************************************R****

MGNNVREEIMDLDLNLDPSDPSNGSVLGLGSLLNELETAHGRIEERIRQLEA****************NTQMVNVSLEPTVSSVPSEVSLLSGECSINPQVRTIENVKTGKRGSSHLIAKALGIHTDTKRAGAGGGEFFDCNICLDMARDPVLTCCGHLFCWSCFYQLPYAYRNVKECPACNGEVTDASIIPIYGNGNSNDLQKLKSKESCLKVPPRPLARRIESVRQQLVNRRPVSTPIEVRIQQFNSIVDAARHQTGSLDLDAAVRSGELEVNDPLLHISRVLPASISSLSSALTSAMDSAERLVGDLEAYINSDNLRRNHQEFSHADTDSVSLISADVQAGSQSLDMATEIDSGVPRSASSVRTDVPTNIVRLQSEIRDTAMEVNL********************DSGICRELRRRRLR

********IMDLDL*LDP*********GLGSLLNELETAHGRIEERIRQLEAVTSRARQRQRWRQGQSNTQMVNVSLE*********************************************************GEFFDCNICLDMARDPVLTCCGHLFCWSCFYQLPYAYRNVKECPACNGEVTDASIIPIYGNG***************************************STPIEVRIQQFNSIVDAARHQTGSLDLDAAVRSGELEVNDPLLHISRVLPASISSLSSALTSAMDSAERLVGDLEAYINS********************************D***EI****************TNI******IRDTAMEVN***********************************

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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MGNNVREEIMDLDLNLDPSDPSNGSVLGLGSLxxxxxxxxxxxxxxxxxxxxxTSRARQRQRWRQGQSNTQMVNVSLEPTVSSVPSEVSLLSGECSINPQVRTIENVKTGKRGSSHLIAKALGIHTDTKRAGAGGGEFFDCNICLDMARDPVLTCCGHLFCWSCFYQLPYAYRNVKECPACNGEVTDASIIPIYGNGNSNDLQKLKSKESCLKVPPRPLARRIESVRQQLVNRRPVSTPIEVRIQQFNSIVDAARHQTGSLDLDAAVRSGELEVNDPLLHISRVLPASISSLSSALTSAMDSAERLVGDLEAYINSDNLRRNHQEFSHADTDSVSLISADVQAGSQSLDMATEIDSGVPRSASSVRTDVPTNIVRLQSEIRDTAMEVNLNAPHSSSSRRRSASLRASDVDSGICRELRRRRLR

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		423	2.2.26 [Sep-21-2011]
P93030		193	E3 ubiquitin-protein liga	no	no	0.196	0.430	0.419	3e-16
Q8GUK7		243	E3 ubiquitin-protein liga	no	no	0.302	0.526	0.326	1e-14
Q99942		180	E3 ubiquitin-protein liga	yes	no	0.198	0.466	0.388	1e-14
Q09463		235	RING finger protein 5 OS=	yes	no	0.198	0.357	0.430	2e-14
Q91YT2		192	E3 ubiquitin-protein liga	yes	no	0.236	0.520	0.370	2e-14
Q5M807		180	E3 ubiquitin-protein liga	yes	no	0.184	0.433	0.392	4e-14
O35445		180	E3 ubiquitin-protein liga	yes	no	0.184	0.433	0.392	4e-14
Q6R567		252	E3 ubiquitin-protein liga	N/A	no	0.196	0.329	0.393	5e-14
Q568Y3		192	E3 ubiquitin-protein liga	no	no	0.189	0.416	0.406	6e-14
Q96GF1		192	E3 ubiquitin-protein liga	no	no	0.189	0.416	0.406	7e-14

>sp\|P93030\|RMA2_ARATH E3 ubiquitin-protein ligase RMA2 OS=Arabidopsis thaliana GN=RMA2 PE=1 SV=1	Back alignment and function desciption

 Score = 87.0 bits (214), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 44/105 (41%), Positives = 58/105 (55%), Gaps = 22/105 (20%)

Query: 127 DTKRAGAGGGEFFDCNICLDMARDPVLTCCGHLFCWSCFYQLPYAYRNVKE--------- 177
           DT    +GG   FDCNICLD  RDPV+T CGHLFCW C ++  YA  N ++         
Sbjct: 9   DTTLVDSGGD--FDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKR 66

Query: 178 ----CPACNGEVTDASIIPIYGNGNSNDLQKLKSKESCLKVPPRP 218
               CP C  +V++A+++PIYG G        K+ +S   VP RP
Sbjct: 67  EPPKCPVCKSDVSEATLVPIYGRGQ-------KAPQSGSNVPSRP 104

E3 ubiquitin-protein ligase that promotes the ubiquitination and proteasomal degradation of the auxin-binding protein ERABP1.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp\|Q8GUK7\|RMA3_ARATH E3 ubiquitin-protein ligase RMA3 OS=Arabidopsis thaliana GN=RMA3 PE=1 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\|Q09463\|RNF5_CAEEL RING finger protein 5 OS=Caenorhabditis elegans GN=rnf-5 PE=1 SV=1	Back alignment and function description

>sp\|Q91YT2\|RN185_MOUSE E3 ubiquitin-protein ligase RNF185 OS=Mus musculus GN=Rnf185 PE=2 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\|Q6R567\|RMA1_CAPAN E3 ubiquitin-protein ligase RMA1H1 OS=Capsicum annuum GN=RMA1H1 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

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		423
224120906		466	predicted protein [Populus trichocarpa]	0.955	0.866	0.496	9e-93
224106616		465	predicted protein [Populus trichocarpa]	0.945	0.860	0.506	2e-91
449466743		451	PREDICTED: uncharacterized protein LOC10	0.969	0.909	0.480	5e-91
225450313		436	PREDICTED: uncharacterized protein LOC10	0.955	0.926	0.496	2e-84
147768913		427	hypothetical protein VITISV_024463 [Viti	0.933	0.925	0.492	2e-81
297741217		392	unnamed protein product [Vitis vinifera]	0.860	0.928	0.449	2e-69
357470139		506	RING finger protein [Medicago truncatula	0.803	0.671	0.442	1e-60
356544206		398	PREDICTED: uncharacterized protein LOC10	0.825	0.876	0.376	2e-59
255640203		398	unknown [Glycine max]	0.825	0.876	0.376	2e-59
262192727		376	hypothetical protein [Nicotiana tabacum]	0.860	0.968	0.398	2e-59

>gi\|224120906\|ref\|XP_002330855.1\| predicted protein [Populus trichocarpa] gi\|222872677\|gb\|EEF09808.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  347 bits (889), Expect = 9e-93,   Method: Compositional matrix adjust.
 Identities = 215/433 (49%), Positives = 273/433 (63%), Gaps = 29/433 (6%)

Query: 10  MDLDLNLDPSDPSNGSVLGLGSLLNELETAHGRIEERIRQLEAVTSRARQRQRWRQGQSN 69
           MDLDLN +P  PSN S+LGL S+ +ELE  HG IEER+RQLEAVT RARQRQRWRQ    
Sbjct: 1   MDLDLNQEPLYPSNDSLLGLASIRDELENTHGHIEERLRQLEAVTFRARQRQRWRQSHFT 60

Query: 70  TQMVNVSLEPTVSSVPSEVSLLSGECSINPQVRTIENVKTGKRGSSHLIAKALGIHTDTK 129
            Q VNVS+EP   +V S+  LL GE S+  + R  E  K GKR S++LIAKALG + + K
Sbjct: 61  PQTVNVSVEPATVNVRSDGGLLIGEASVATEERRDEMNKFGKRKSTYLIAKALGRNGNGK 120

Query: 130 RAGAGGGEFFDCNICLDMARDPVLTCCGHLFCWSCFYQLPYAYRNVKECPACNGEVTDAS 189
           +A       FDCNICLDMA+DP+LT CGHLFCW CFYQL Y Y NVKECP C  EVTD S
Sbjct: 121 KARTDRRSVFDCNICLDMAQDPILTSCGHLFCWPCFYQLSYVYSNVKECPVCVEEVTDTS 180

Query: 190 IIPIYGNGNSNDLQKLKSKESCLKVPPRPLARRIESVRQQLVNRRPVSTPIEVRIQQFNS 249
           IIPIYGNGNS D +KLK KES LKVPPRP A+R+ESVRQQL+N    S+ IE R++   +
Sbjct: 181 IIPIYGNGNSYDNKKLKLKESGLKVPPRPSAQRVESVRQQLINHGAFSSSIEERMRYIGN 240

Query: 250 IVDAA------------------------RHQTG----SLDLDAAVRSGELEVNDPLLHI 281
           ++ A                         R  T     S+  D++     ++V+  L   
Sbjct: 241 VLIAMGEIPPSEGLDGVPLESDRISFLANRTSTSQALPSIGADSSQHHRSVQVSRLLFQG 300

Query: 282 SRVLPASISSLSSALTSAMDSAERLVGDLEAYINSDNLRRNHQEFSH-ADTDSVSLISAD 340
           +  L +  S+++SA+ SAM+S ERL  DL A ++S   RRNHQ+ S  AD DS S I+A 
Sbjct: 301 AASLSSFSSAVNSAMESAMESTERLFEDLGAILHSHRGRRNHQQSSRPADRDSFSSIAAV 360

Query: 341 VQAGSQSLDMATEIDSGVPRSASSVRTDVPTNIVRLQSEIRDTAMEVNLNAPHSSSSRRR 400
           +Q  SQ+ D   + DS +P+SASS R D    + +L+S    TA+E N + P SSSSRRR
Sbjct: 361 IQPDSQNPDTVADADSTLPQSASSSRPDDVVTVSQLESHRTGTAIESNFSVPLSSSSRRR 420

Query: 401 SASLRASDVDSGI 413
           +   R S+VD+ +
Sbjct: 421 NLVFRLSEVDNSV 433

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224106616\|ref\|XP_002314225.1\| predicted protein [Populus trichocarpa] gi\|222850633\|gb\|EEE88180.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449466743\|ref\|XP_004151085.1\| PREDICTED: uncharacterized protein LOC101212429 [Cucumis sativus] gi\|449501587\|ref\|XP_004161409.1\| PREDICTED: uncharacterized protein LOC101226819 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|225450313\|ref\|XP_002272445.1\| PREDICTED: uncharacterized protein LOC100246046 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|147768913\|emb\|CAN75887.1\| hypothetical protein VITISV_024463 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297741217\|emb\|CBI32168.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|357470139\|ref\|XP_003605354.1\| RING finger protein [Medicago truncatula] gi\|355506409\|gb\|AES87551.1\| RING finger protein [Medicago truncatula]	Back alignment and taxonomy information

>gi\|356544206\|ref\|XP_003540545.1\| PREDICTED: uncharacterized protein LOC100793230 [Glycine max]	Back alignment and taxonomy information

>gi\|255640203\|gb\|ACU20392.1\| unknown [Glycine max]	Back alignment and taxonomy information

>gi\|262192727\|gb\|ACY30433.1\| hypothetical protein [Nicotiana tabacum]	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		423
TAIR\|locus:2050533		413	AT2G44410 [Arabidopsis thalian	0.380	0.389	0.476	4.6e-46
TAIR\|locus:2095833		436	AT3G58030 [Arabidopsis thalian	0.382	0.371	0.421	7.9e-30
TAIR\|locus:2064584		425	AT2G42030 [Arabidopsis thalian	0.349	0.348	0.419	1.4e-25
TAIR\|locus:2016437		226	AT1G19310 [Arabidopsis thalian	0.208	0.389	0.426	3.1e-19
TAIR\|locus:2049023		227	AT2G23780 [Arabidopsis thalian	0.210	0.392	0.406	6.5e-19
TAIR\|locus:2037294		137	AT1G74990 [Arabidopsis thalian	0.260	0.802	0.375	1.7e-18
TAIR\|locus:2123663		193	RMA2 "RING membrane-anchor 2"	0.196	0.430	0.419	3.3e-17
UNIPROTKB\|F1N0B8		180	RNF5 "Uncharacterized protein"	0.205	0.483	0.387	1e-16
UNIPROTKB\|A4IFC2		192	RNF185 "RNF185 protein" [Bos t	0.208	0.458	0.416	1.3e-16
UNIPROTKB\|E2QS10		180	RNF5 "Uncharacterized protein"	0.205	0.483	0.387	1.3e-16

TAIR\|locus:2050533 AT2G44410 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 411 (149.7 bits), Expect = 4.6e-46, Sum P(3) = 4.6e-46
 Identities = 81/170 (47%), Positives = 106/170 (62%)

Query:   102 RTIENVKTGKRGSSHLIAKALGIHTDTKRAGAGGGEFFDCNICLDMARDPVLTCCGHLFC 161
             R+ E +       ++LIAKAL +    K +   GG FFDCNICL+ A DP+LTCCGHLFC
Sbjct:    90 RSRERLVENGENKTYLIAKALNME---KTSSVPGG-FFDCNICLEKAEDPILTCCGHLFC 145

Query:   162 WSCFYQLPYAYRNVKECPACNGEVTDASIIPIYGNGNSNDLQKLKSKESCLKVPPRPLAR 221
             W CFYQLP  Y N+KECP C+GEVTDA +IPIYGNG+  D  K K ++  + +PPRP A+
Sbjct:   146 WGCFYQLPLIYLNIKECPVCDGEVTDAEVIPIYGNGDDCDGTKPKLEDCGISLPPRPNAK 205

Query:   222 RIESVRQQLVNRRPVSTPIEVRIQQFNSIVDAARHQTGSLDLDAAVRSGE 271
             R+ESVRQ+++NR     P        N  ++  R    S+ L A  +  E
Sbjct:   206 RVESVRQKIINRGNPFFP-----GHENEAIEHIRRTIDSIGLQALAQGDE 250

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

TAIR\|locus:2095833 AT3G58030 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2064584 AT2G42030 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

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

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

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

TAIR\|locus:2123663 RMA2 "RING membrane-anchor 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|F1N0B8 RNF5 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|A4IFC2 RNF185 "RNF185 protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2QS10 RNF5 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		423
PLN03208		193	PLN03208, PLN03208, E3 ubiquitin-protein ligase RM	7e-21
pfam13923		45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	2e-10
smart00184		40	smart00184, RING, Ring finger	3e-09
cd00162		45	cd00162, RING, RING-finger (Really Interesting New	4e-09
pfam13639		46	pfam13639, zf-RING_2, Ring finger domain	6e-07
COG5574		271	COG5574, PEX10, RING-finger-containing E3 ubiquiti	3e-06
pfam13920		49	pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RI	6e-06
pfam00097		40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	1e-05
pfam04641		254	pfam04641, Rtf2, Replication termination factor 2	7e-04
COG5152		259	COG5152, COG5152, Uncharacterized conserved protei	0.001
TIGR00599		397	TIGR00599, rad18, DNA repair protein rad18	0.004

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

 Score = 89.4 bits (221), Expect = 7e-21
 Identities = 44/105 (41%), Positives = 58/105 (55%), Gaps = 22/105 (20%)

Query: 127 DTKRAGAGGGEFFDCNICLDMARDPVLTCCGHLFCWSCFYQLPYAYRNVKE--------- 177
           DT    +GG   FDCNICLD  RDPV+T CGHLFCW C ++  YA  N ++         
Sbjct: 9   DTTLVDSGGD--FDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKR 66

Query: 178 ----CPACNGEVTDASIIPIYGNGNSNDLQKLKSKESCLKVPPRP 218
               CP C  +V++A+++PIYG G        K+ +S   VP RP
Sbjct: 67  EPPKCPVCKSDVSEATLVPIYGRGQ-------KAPQSGSNVPSRP 104

Length = 193

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

>gnl\|CDD\|214546 smart00184, RING, 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\|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger)	Back alignment and domain information

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

>gnl\|CDD\|218188 pfam04641, Rtf2, Replication termination factor 2	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\|233043 TIGR00599, rad18, DNA repair protein rad18	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		423
KOG1002		791	consensus Nucleotide excision repair protein RAD16	99.97
KOG1001		674	consensus Helicase-like transcription factor HLTF/	99.83
KOG0823		230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.73
KOG0298		1394	consensus DEAD box-containing helicase-like transc	99.54
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	99.5
KOG0389		941	consensus SNF2 family DNA-dependent ATPase [Chroma	99.45
KOG0385		971	consensus Chromatin remodeling complex WSTF-ISWI,	99.32
PLN03142		1033	Probable chromatin-remodeling complex ATPase chain	99.28
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.26
KOG0384		1373	consensus Chromodomain-helicase DNA-binding protei	99.24
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	99.22
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.2
KOG0317		293	consensus Predicted E3 ubiquitin ligase, integral	99.14
KOG4439		901	consensus RNA polymerase II transcription terminat	99.09
KOG0392		1549	consensus SNF2 family DNA-dependent ATPase domain-	99.05
TIGR00599		397	rad18 DNA repair protein rad18. This family is bas	99.03
PF04564		73	U-box: U-box domain; InterPro: IPR003613 Quality c	99.02
KOG2164		513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.98
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.95
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.95
PHA02929		238	N1R/p28-like protein; Provisional	98.93
COG0553		866	HepA Superfamily II DNA/RNA helicases, SNF2 family	98.92
KOG0287		442	consensus Postreplication repair protein RAD18 [Re	98.92
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.87
KOG0391		1958	consensus SNF2 family DNA-dependent ATPase [Genera	98.84
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	98.83
KOG0390		776	consensus DNA repair protein, SNF2 family [Replica	98.82
KOG0388		1185	consensus SNF2 family DNA-dependent ATPase [Replic	98.79
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.74
COG5432		391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.72
COG5574		271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.71
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	98.7
KOG0978		698	consensus E3 ubiquitin ligase involved in syntaxin	98.7
PHA02926		242	zinc finger-like protein; Provisional	98.68
PF14634		44	zf-RING_5: zinc-RING finger domain	98.64
KOG0387		923	consensus Transcription-coupled repair protein CSB	98.64
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.61
PF14835		65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.55
KOG2177		386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.49
KOG0386		1157	consensus Chromatin remodeling complex SWI/SNF, co	98.45
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	98.37
TIGR00570		309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.35
KOG4628		348	consensus Predicted E3 ubiquitin ligase [Posttrans	98.34
KOG1000		689	consensus Chromatin remodeling protein HARP/SMARCA	98.26
COG5540		374	RING-finger-containing ubiquitin ligase [Posttrans	98.23
COG5243		491	HRD1 HRD ubiquitin ligase complex, ER membrane com	98.16
PF12861		85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.15
KOG0311		381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.05
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	97.98
KOG0824		324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.97
PRK04914		956	ATP-dependent helicase HepA; Validated	97.93
COG5152		259	Uncharacterized conserved protein, contains RING a	97.93
PF11789		57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.92
KOG4159		398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.85
KOG4172		62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.85
KOG2879		298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.83
KOG1015		1567	consensus Transcription regulator XNP/ATRX, DEAD-b	97.72
KOG1813		313	consensus Predicted E3 ubiquitin ligase [Posttrans	97.69
KOG1785		563	consensus Tyrosine kinase negative regulator CBL [	97.64
KOG2660		331	consensus Locus-specific chromosome binding protei	97.6
COG5222		427	Uncharacterized conserved protein, contains RING Z	97.56
KOG1734		328	consensus Predicted RING-containing E3 ubiquitin l	97.51
KOG1645		463	consensus RING-finger-containing E3 ubiquitin liga	97.49
KOG0297		391	consensus TNF receptor-associated factor [Signal t	97.41
KOG4265		349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.4
KOG0825		1134	consensus PHD Zn-finger protein [General function	97.34
PF11793		70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.32
PF04641		260	Rtf2: Rtf2 RING-finger	97.31
KOG3039		303	consensus Uncharacterized conserved protein [Funct	97.28
KOG0828		636	consensus Predicted E3 ubiquitin ligase [Posttrans	97.28
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.25
KOG1039		344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.23
KOG4692		489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.16
COG5219		1525	Uncharacterized conserved protein, contains RING Z	97.03
KOG0827		465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.99
PF14447		55	Prok-RING_4: Prokaryotic RING finger family 4	96.95
smart00744		49	RINGv The RING-variant domain is a C4HC3 zinc-fing	96.89
KOG4275		350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.8
KOG1571		355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.67
KOG4739		233	consensus Uncharacterized protein involved in syna	96.62
KOG0826		357	consensus Predicted E3 ubiquitin ligase involved i	96.56
KOG1493		84	consensus Anaphase-promoting complex (APC), subuni	96.38
KOG0383		696	consensus Predicted helicase [General function pre	96.32
PF05290		140	Baculo_IE-1: Baculovirus immediate-early protein (	96.31
KOG1016		1387	consensus Predicted DNA helicase, DEAD-box superfa	96.25
KOG1814		445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.13
KOG4367		699	consensus Predicted Zn-finger protein [Function un	96.06
COG5236		493	Uncharacterized conserved protein, contains RING Z	95.75
COG5194		88	APC11 Component of SCF ubiquitin ligase and anapha	95.68
KOG3800		300	consensus Predicted E3 ubiquitin ligase containing	95.61
KOG1941		518	consensus Acetylcholine receptor-associated protei	95.51
KOG4185		296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.41
KOG2817		394	consensus Predicted E3 ubiquitin ligase [Posttrans	95.4
cd00079		131	HELICc Helicase superfamily c-terminal domain; ass	95.32
PF07800		162	DUF1644: Protein of unknown function (DUF1644); In	94.68
KOG3002		299	consensus Zn finger protein [General function pred	94.6
PF14570		48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	94.59
PHA03096		284	p28-like protein; Provisional	94.58
KOG2932		389	consensus E3 ubiquitin ligase involved in ubiquiti	94.47
KOG4362		684	consensus Transcriptional regulator BRCA1 [Replica	94.43
COG5175		480	MOT2 Transcriptional repressor [Transcription]	94.36
KOG1952		950	consensus Transcription factor NF-X1, contains NFX	94.25
KOG3161		861	consensus Predicted E3 ubiquitin ligase [Posttrans	94.24
KOG3970		299	consensus Predicted E3 ubiquitin ligase [Posttrans	94.04
PF10367		109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	93.88
KOG4445		368	consensus Uncharacterized conserved protein, conta	93.85
KOG2114		933	consensus Vacuolar assembly/sorting protein PEP5/V	93.56
KOG3039		303	consensus Uncharacterized conserved protein [Funct	93.12
COG5220		314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	92.55
KOG3113		293	consensus Uncharacterized conserved protein [Funct	92.41
KOG3268		234	consensus Predicted E3 ubiquitin ligase [Posttrans	92.15
PF02891		50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	92.11
KOG2034		911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	91.67
PRK13766		773	Hef nuclease; Provisional	90.9
PF05883		134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	90.7
KOG2930		114	consensus SCF ubiquitin ligase, Rbx1 component [Po	90.48
KOG1812		384	consensus Predicted E3 ubiquitin ligase [Posttrans	90.43
KOG1428		3738	consensus Inhibitor of type V adenylyl cyclases/Ne	90.31
TIGR00603		732	rad25 DNA repair helicase rad25. All proteins in t	90.17
KOG1100		207	consensus Predicted E3 ubiquitin ligase [Posttrans	89.84
PF10272		358	Tmpp129: Putative transmembrane protein precursor;	89.73
KOG3579		352	consensus Predicted E3 ubiquitin ligase [Posttrans	89.45
COG5109		396	Uncharacterized conserved protein, contains RING Z	89.37
PF08746		43	zf-RING-like: RING-like domain; InterPro: IPR01485	89.2
PF00271		78	Helicase_C: Helicase conserved C-terminal domain;	87.98
PF03854		50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	87.59
PHA02862		156	5L protein; Provisional	87.36
PHA02825		162	LAP/PHD finger-like protein; Provisional	86.27
KOG1940		276	consensus Zn-finger protein [General function pred	85.21
PF12906		47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	83.6
PF07191		70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	83.55
KOG0825		1134	consensus PHD Zn-finger protein [General function	81.49
KOG0331		519	consensus ATP-dependent RNA helicase [RNA processi	81.41
KOG1815		444	consensus Predicted E3 ubiquitin ligase [Posttrans	80.42

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

Probab=99.97  E-value=2.8e-33  Score=283.58  Aligned_cols=191  Identities=17%  Similarity=0.184  Sum_probs=149.6

Q ss_pred             CCccccccccccccCcEEccCCCccchhhHhhhhhh--cCCCCCCCCCCcccCCCCceecccCCCchhhhhhhhhcccCC
Q 039490          136 GEFFDCNICLDMARDPVLTCCGHLFCWSCFYQLPYA--YRNVKECPACNGEVTDASIIPIYGNGNSNDLQKLKSKESCLK  213 (423)
Q Consensus       136 ~e~~~C~ICle~~~~pv~~~CGH~FC~~Ci~~~~~~--~~~~~~CP~Cr~~i~~~~l~~~~~~~~~~~~~k~~~~~~~~~  213 (423)
                      ..+..|.+|.++.++++.+.|.|.||+.|+.+|...  .....+||+|...++.+.-.|....-.. ...+....-..++
T Consensus       534 k~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~alek~~l-~~Fk~sSIlnRin  612 (791)
T KOG1002|consen  534 KGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPALEKTDL-KGFKASSILNRIN  612 (791)
T ss_pred             cCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchhhhhcch-hhhhhHHHhhhcc
Confidence            456799999999999999999999999999998542  2345889999999887644443321111 1112122224567


Q ss_pred             CCCCCCchhhHHHHHHHHhc-CCCCCCceEEcccchhHHHHHHHhhhhCCCCcccc---------cchhcccCCCCCcce
Q 039490          214 VPPRPLARRIESVRQQLVNR-RPVSTPIEVRIQQFNSIVDAARHQTGSLDLDAAVR---------SGELEVNDPLLHISR  283 (423)
Q Consensus       214 ~~~~~~stKieaLr~~L~~~-~~~p~~K~iVFSQftsfLdlle~~L~~~gi~~~~~---------d~~l~~f~~~dp~~~  283 (423)
                      +..+.+++|||+|++.|... ..+-+.|+|||||||+|||+|++.|.+.|+.++..         |.+|+.| +.++.|+
T Consensus       613 m~~~qsSTKIEAL~EEl~~l~~rd~t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F-~nd~~c~  691 (791)
T KOG1002|consen  613 MDDWQSSTKIEALVEELYFLRERDRTAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYF-KNDIDCR  691 (791)
T ss_pred             hhhhcchhHHHHHHHHHHHHHHcccchhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHh-ccCCCeE
Confidence            77899999999999988866 67888999999999999999999999999997764         4566889 9999999


Q ss_pred             EEEecccccccccchhc-------hhhhhhhccccceeeccccCccccccCCCC
Q 039490          284 VLPASISSLSSALTSAM-------DSAERLVGDLEAYINSDNLRRNHQEFSHAD  330 (423)
Q Consensus       284 VLL~SLkaggvGLN~~l-------~~A~~~~~~~qa~~r~hriGq~~~~~~~~~  330 (423)
                      |||+|||||||+||++-       +|=|..+-+.||-+|+||||  |.+|+...
T Consensus       692 vfLvSLkAGGVALNLteASqVFmmDPWWNpaVe~Qa~DRiHRIG--Q~rPvkvv  743 (791)
T KOG1002|consen  692 VFLVSLKAGGVALNLTEASQVFMMDPWWNPAVEWQAQDRIHRIG--QYRPVKVV  743 (791)
T ss_pred             EEEEEeccCceEeeechhceeEeecccccHHHHhhhhhhHHhhc--CccceeEE
Confidence            99999999999999754       33333322379999999999  78888443

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

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

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

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]	Back alignment and domain information

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]	Back alignment and domain information

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional	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

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]	Back alignment and domain information

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

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

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

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]	Back alignment and domain information

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]	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

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

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

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

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

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

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

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]	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

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]	Back alignment and domain information

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]	Back alignment and domain information

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

>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]	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

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

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

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

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]	Back alignment and domain information

>smart00184 RING Ring finger	Back alignment and domain information

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

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

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]	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

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

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

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]	Back alignment and domain information

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

>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [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

>KOG0311 consensus Predicted E3 ubiquitin ligase [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

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

>PRK04914 ATP-dependent helicase HepA; Validated	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

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

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

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]	Back alignment and domain information

>KOG1813 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

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

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

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

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

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

>KOG4265 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

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

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

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

>KOG0828 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

>KOG1039 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

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

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

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4	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

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

>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]	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

>KOG0383 consensus Predicted helicase [General function prediction only]	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

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [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

>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

>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

>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

>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

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

>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

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

>KOG3002 consensus Zn finger protein [General function prediction only]	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

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

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

>COG5175 MOT2 Transcriptional repressor [Transcription]	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

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

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

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

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

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

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

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

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

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

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

>PRK13766 Hef nuclease; Provisional	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

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

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

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

>TIGR00603 rad25 DNA repair helicase rad25	Back alignment and domain information

>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

>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

>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

>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins	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

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

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

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

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

>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length	Back alignment and domain information

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

>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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		423
1jm7_A		112	Solution Structure Of The Brca1/bard1 Ring-domain H		7e-06
2ysl_A		73	Solution Structure Of The Ring Domain (1-66) From T		6e-04

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

Back alignment and structure

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 18/54 (33%), Positives = 31/54 (57%)
Query: 137 EFFDCNICLDMARDPVLTCCGHLFCWSCFYQLPYAYRNVKECPACNGEVTDASI 190
           +  +C ICL++ ++PV T C H+FC  C  +L    +   +CP C  ++T  S+
Sbjct: 20  KILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL 73

PyMOL of 1jm7

>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From Tripartite Motif-containing Protein 31 Length = 73

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		423
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	1e-16
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	6e-16
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	1e-15
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	1e-15
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	9e-15
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	2e-14
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	4e-14
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	2e-11
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	4e-11
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	7e-11
4epo_C		149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	2e-10
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	2e-10
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	2e-10
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	4e-10
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-07
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	7e-10
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	7e-10
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	8e-10
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	8e-10
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	3e-09
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	3e-09
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	3e-09
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	3e-09
1z6u_A		150	NP95-like ring finger protein isoform B; structura	3e-09
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	4e-09
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	1e-08
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	2e-08
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	3e-08
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	3e-08
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	3e-08
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	4e-08
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	5e-08
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	8e-08
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	2e-07
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	2e-07
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	4e-06
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	4e-06
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	5e-06
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	6e-06
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	2e-05
2ea5_A		68	Cell growth regulator with ring finger domain prot	3e-05
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	5e-05
3t6p_A		345	Baculoviral IAP repeat-containing protein 2; ring,	6e-05
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	7e-05
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	2e-04
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	2e-04

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

 Score = 72.9 bits (179), Expect = 1e-16
 Identities = 21/66 (31%), Positives = 27/66 (40%), Gaps = 10/66 (15%)

Query: 136 GEFFDCNICLDM-------ARDPVLTCCGHLFCWSCFYQLPYAYRNVKECPACNGEVTDA 188
           G    C IC+D         R  V T CGH+FC  C      + +N   CP C  ++   
Sbjct: 1   GAMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRD---SLKNANTCPTCRKKINHK 57

Query: 189 SIIPIY 194
              PIY
Sbjct: 58  RYHPIY 63

PyMOL of 2xeu

>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

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

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

>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

>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

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

>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

>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

>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

>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

>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

>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

>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

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

>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

>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

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

>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

>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

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

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

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

>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

>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

>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

>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

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

>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

>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 Length = 79	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

>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

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75	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} Length = 68	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

>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 Length = 345	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

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		423
1t1h_A		78	Gspef-atpub14, armadillo repeat containing protein	99.48
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.47
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.46
2kre_A		100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.45
2kr4_A		85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.45
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	99.45
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	99.43
1wgm_A		98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.42
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	99.4
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	99.4
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	99.38
2yu4_A		94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.37
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	99.36
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	99.36
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.36
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.34
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	99.34
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	99.33
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	99.32
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	99.32
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	99.32
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	99.31
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	99.31
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.3
1z6u_A		150	NP95-like ring finger protein isoform B; structura	99.29
4ayc_A		138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.28
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	99.26
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	99.26
2f42_A		179	STIP1 homology and U-box containing protein 1; cha	99.25
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	99.24
2ect_A		78	Ring finger protein 126; metal binding protein, st	99.24
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	99.23
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.23
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	99.2
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.19
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	99.18
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.18
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	99.16
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.15
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	99.14
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	99.14
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.13
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.13
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.12
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.11
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	99.1
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	99.09
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	99.08
1z5z_A		271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.07
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.05
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	99.05
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	99.04
3mwy_W		800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.03
4ic3_A		74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.98
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	98.98
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.97
1z3i_X		644	Similar to RAD54-like; recombination ATPase helica	98.92
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	98.92
2bay_A		61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.91
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	98.88
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.85
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.82
2ea5_A		68	Cell growth regulator with ring finger domain prot	98.78
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.76
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	98.76
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.75
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.62
3t6p_A		345	Baculoviral IAP repeat-containing protein 2; ring,	98.62
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	98.62
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	98.54
3hgt_A		328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	98.53
1z63_A		500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.46
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	98.26
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.0
3vk6_A		101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.92
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	97.91
1wp9_A		494	ATP-dependent RNA helicase, putative; ATPase, DNA	97.48
3dmq_A		968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	97.05
2jgn_A		185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	96.67
3nw0_A		238	Non-structural maintenance of chromosomes element	96.61
3m62_A		968	Ubiquitin conjugation factor E4; armadillo-like re	96.58
1t5i_A		172	C_terminal domain of A probable ATP-dependent RNA	96.51
2hjv_A		163	ATP-dependent RNA helicase DBPA; parallel alpha-be	96.25
2jun_A		101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.97
3tbk_A		555	RIG-I helicase domain; DECH helicase, ATP binding,	95.9
1fuk_A		165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	95.76
2p6n_A		191	ATP-dependent RNA helicase DDX41; DEAD, structural	95.73
2rb4_A		175	ATP-dependent RNA helicase DDX25; rossmann fold, s	95.58
2yjt_D		170	ATP-dependent RNA helicase SRMB, regulator of ribo	93.84
4a2p_A		556	RIG-I, retinoic acid inducible protein I; hydrolas	94.82
2fwr_A		472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	94.64
4a2w_A		936	RIG-I, retinoic acid inducible protein I; hydrolas	93.8
4a2q_A		797	RIG-I, retinoic acid inducible protein I; hydrolas	93.75
2ko5_A		99	Ring finger protein Z; lassa fever virus-Z, negati	93.11
3i2d_A		371	E3 SUMO-protein ligase SIZ1; signal transduction,	91.69
3eaq_A		212	Heat resistant RNA dependent ATPase; DEAD box RNA	91.59
4fo9_A		360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	91.46
2cs3_A		93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	91.11
1xti_A		391	Probable ATP-dependent RNA helicase P47; alpha-bet	91.06
1hv8_A		367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	88.74
1s2m_A		400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	87.6
2ykg_A		696	Probable ATP-dependent RNA helicase DDX58; hydrola	87.52
2oca_A		510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	85.33
2j0s_A		410	ATP-dependent RNA helicase DDX48; mRNA processing,	82.88
1wil_A		89	KIAA1045 protein; ring finger domain, structural g	82.53
3i32_A		300	Heat resistant RNA dependent ATPase; RNA helicase,	82.41
2lv9_A		98	Histone-lysine N-methyltransferase MLL5; zinc fing	81.72
3h1t_A		590	Type I site-specific restriction-modification syst	80.9

>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

Probab=99.48  E-value=1.6e-14  Score=113.69  Aligned_cols=67  Identities=25%  Similarity=0.423  Sum_probs=57.9

Q ss_pred             CCCccccccccccccCcEEccCCCccchhhHhhhhhhcCCCCCCCCCCcccCCCCceecccCCCchhhh
Q 039490          135 GGEFFDCNICLDMARDPVLTCCGHLFCWSCFYQLPYAYRNVKECPACNGEVTDASIIPIYGNGNSNDLQ  203 (423)
Q Consensus       135 ~~e~~~C~ICle~~~~pv~~~CGH~FC~~Ci~~~~~~~~~~~~CP~Cr~~i~~~~l~~~~~~~~~~~~~  203 (423)
                      ..+.+.|+||++.+.+|++++|||+||..||..|+.  .+...||+|+..+...++.+++.+.+.+..+
T Consensus         5 ~~~~~~C~IC~~~~~~Pv~~~CgH~fc~~Ci~~~~~--~~~~~CP~C~~~~~~~~l~~n~~l~~~i~~~   71 (78)
T 1t1h_A            5 FPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLD--AGHKTCPKSQETLLHAGLTPNYVLKSLIALW   71 (78)
T ss_dssp             CSSSSSCTTTSCCCSSEEEETTTEEEEHHHHHHHHT--TTCCBCTTTCCBCSSCCCEECTTTHHHHHHH
T ss_pred             CcccCCCCCccccccCCEEcCCCCeecHHHHHHHHH--HCcCCCCCCcCCCChhhCccCHHHHHHHHHH
Confidence            356789999999999999999999999999999965  3477899999999988899988876665544

PyMOL of 1t1h

>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

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

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

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

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, 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

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

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

>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

>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

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

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

>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

>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

>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

>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

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

>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

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

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

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

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

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

>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

>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

>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

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

>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

>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

>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

>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

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

>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

>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

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

>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

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

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

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19	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

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

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}	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

>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

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

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19	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

>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

>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

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {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

>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

>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

>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

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

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

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

>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

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A	Back alignment and structure

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A	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

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

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

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19	Back alignment and structure

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}	Back alignment and structure

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}	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

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19	Back alignment and structure

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}	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

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}	Back alignment and structure

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19	Back alignment and structure

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}	Back alignment and structure

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}	Back alignment and structure

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}	Back alignment and structure

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*	Back alignment and structure

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*	Back alignment and structure

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}	Back alignment and structure

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}	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

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A	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

>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

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A	Back alignment and structure

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19	Back alignment and structure

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A	Back alignment and structure

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*	Back alignment and structure

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}	Back alignment and structure

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A	Back alignment and structure

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

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}	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

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}	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		423
d1jm7a_		103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	4e-12
d1fbva4		79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	4e-12
d1bora_		56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	9e-11
d1rmda2		86	g.44.1.1 (A:1-86) V(D)J recombination activating p	3e-10
d1t1ha_		78	g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cre	4e-08
d1chca_		68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	6e-08
d2c2la2		80	g.44.1.2 (A:225-304) STIP1 homology and U box-cont	8e-08
d2baya1		56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	2e-07
d1iyma_		55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	6e-06
d1g25a_		65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	9e-05
d1wima_		94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	1e-04
d1vyxa_		60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	4e-04
d1ur6b_		52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	4e-04
d1jm7b_		97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	4e-04

>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 = 60.5 bits (146), Expect = 4e-12
 Identities = 18/56 (32%), Positives = 31/56 (55%)

Query: 137 EFFDCNICLDMARDPVLTCCGHLFCWSCFYQLPYAYRNVKECPACNGEVTDASIIP 192
           +  +C ICL++ ++PV T C H+FC  C  +L    +   +CP C  ++T  S+  
Sbjct: 20  KILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQE 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

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

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

>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

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

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

>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

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97	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		423
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.5
d1t1ha_		78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.48
d2c2la2		80	STIP1 homology and U box-containing protein 1, STU	99.44
d1z3ix1		346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.4
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	99.39
d2baya1		56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.36
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.33
d1wgma_		98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.33
d1bora_		56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.29
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.28
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.24
d1z5za1		244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.2
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	99.18
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.14
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	99.12
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	98.94
d3dplr1		88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	98.74
d1vyxa_		60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.72
d1wima_		94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.22
d2fwra1		200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	97.94
d1wp9a2		286	putative ATP-dependent RNA helicase PF2015 {Pyroco	97.08
d1t5ia_		168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	96.06
d1hv8a2		155	Putative DEAD box RNA helicase {Archaeon Methanoco	95.79
d1s2ma2		171	Putative ATP-dependent RNA helicase DHH1 {Baker's	95.1
d2rb4a1		168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	93.9
d1fuka_		162	Initiation factor 4a {Baker's yeast (Saccharomyces	92.64
d2cs3a1		80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	91.57
d1wesa_		71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	81.08
d1wila_		89	Hypothetical protein KIAA1045 {Human (Homo sapiens	80.71
d1t5la2		181	Nucleotide excision repair enzyme UvrB {Bacillus c	80.17

>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=99.50  E-value=3.4e-15  Score=122.68  Aligned_cols=65  Identities=28%  Similarity=0.703  Sum_probs=55.2

Q ss_pred             CccccccccccccCcEEccCCCccchhhHhhhhhhcCCCCCCCCCCcccCCCCceecccCCCchh
Q 039490          137 EFFDCNICLDMARDPVLTCCGHLFCWSCFYQLPYAYRNVKECPACNGEVTDASIIPIYGNGNSND  201 (423)
Q Consensus       137 e~~~C~ICle~~~~pv~~~CGH~FC~~Ci~~~~~~~~~~~~CP~Cr~~i~~~~l~~~~~~~~~~~  201 (423)
                      +.+.||||+++|.+|+.++|||+||..||..|+........||.||.++...++.+++.+.++++
T Consensus        20 ~~l~CpIC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l~~n~~l~~~ve   84 (103)
T d1jm7a_          20 KILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVE   84 (103)
T ss_dssp             HHTSCSSSCCCCSSCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCCCSSSHHHH
T ss_pred             cCcCCCccCchhCCeEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhCCcCHHHHHHHH
Confidence            45689999999999999999999999999999875555678999999998888877776655443

PyMOL of d1jm7a_

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

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}	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

>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

>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

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

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

>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}	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

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

>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

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	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

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

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

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}	Back information, alignment and structure