Citrus Sinensis ID: 023268

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----

MSAMLKEQLVKVFSLMKPGMLFQYEPELDAFLEFLIWRFSIWVDKPTPGNALMNLRYRDERAVETRAKVRTGLEGPGLTNAQKIWYCIATVGGQYLWARLQSFSAFRRWGDSEQRPLARRAWILIQRIEALYKAASFGNLLIFLYTGRYRNLIERALRARLVYGTPNMNRAVSFEYMNRQLVWNEFSEMLLLLLPLLNSSTVKGLFGPFSKDKSSSSEEDVTTCPICQASPTTPFLALPCQHRYCYYCLRTRCAASPSFRCSRCNEPVIAMQRHGVINPKISSQ

cHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHccccccccHHHHcccEEcccccHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHccEEEccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccc

cHHHHHHHHHHHHHHccccHHHHcHHHHHHHHHHHHHHHHEccccccHHHHHHccEEccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHccccccccccccccccccccccccccccccccEEEEHHHHHHHHcccccccccccccHHHHEEccccccccccc

MSAMLKEQLVKVFSLmkpgmlfqyePELDAFLEFLIWRFSIwvdkptpgnalmnlryrDERAVETRAKvrtglegpgltnaqKIWYCIATVGGQYLWARLQSFSAFrrwgdseqrpLARRAWILIQRIEALYKAASFGNLLIFLYTGRYRNLIERALRARLvygtpnmnravSFEYMNRQLVWNEFSEMLLLLLPllnsstvkglfgpfskdksssseedvttcpicqaspttpflalpcqhrycyyclrtrcaaspsfrcsrcnepviamqrhgvinpkissq

MSAMLKEQLVKVFSLMKPGMLFQYEPELDAFLEFLIWRFSIWvdkptpgnalmnlryrdERAVETRAkvrtglegpgltnaqKIWYCIATVGGQYLWARLQSFSAFRRWGDSEQRPLARRAWILIQRIEALYKAASFGNLLIFLYTGRYRNLIERALRARLVYGTPNMNRAVSFEYMNRQLVWNEFSEMLLLLLPLLNSSTVKGLFGPFSKDKSSSSEEDVTTCPIcqaspttpflalPCQHRYCYYCLRTRCAASPSFRCSRCNEPviamqrhgvinpkissq

MSAMLKEQLVKVFSLMKPGMLFQYEPELDAFLEFLIWRFSIWVDKPTPGNALMNLRYRDERAVETRAKVRTGLEGPGLTNAQKIWYCIATVGGQYLWARLQSFSAFRRWGDSEQRPLARRAWILIQRIEALYKAASFGNLLIFLYTGRYRNLIERALRARLVYGTPNMNRAVSFEYMNRQLVWNEFSEMlllllpllNSSTVKGLFGPFskdksssseedVTTCPICQASPTTPFLALPCQHRYCYYCLRTRCAASPSFRCSRCNEPVIAMQRHGVINPKISSQ

*******QLVKVFSLMKPGMLFQYEPELDAFLEFLIWRFSIWVDKPTPGNALMNLRYRDERAVETRAKVRTGLEGPGLTNAQKIWYCIATVGGQYLWARLQSFSAFRRWGDSEQRPLARRAWILIQRIEALYKAASFGNLLIFLYTGRYRNLIERALRARLVYGTPNMNRAVSFEYMNRQLVWNEFSEMLLLLLPLLNSSTVKGLFG**************TTCPICQASPTTPFLALPCQHRYCYYCLRTRCAASPSFRCSRCNEPVIAMQRHGV********

MSAMLKEQLVKVFSLMKPGMLFQYEPELDAFLEFLIWRFSIWVDKPTPGNALMNLRYRDERAVET*********GPGLTNAQKIWYCIATVGGQYLWARLQSFSAFRRWGDSEQRPLARRAWILIQRIEALYKAASFGNLLIFLYTGRYRNLIERALRARLVYGTP*******FEYMNRQLVWNEFSEMLLLLLPLLNSSTVKGLFGPFSK******EEDVTTCPICQASPTTPFLALPCQHRYCYYCLRTRCAASPSFRCSRCNEPVIAMQ************

MSAMLKEQLVKVFSLMKPGMLFQYEPELDAFLEFLIWRFSIWVDKPTPGNALMNLRYRDERAVETRAKVRTGLEGPGLTNAQKIWYCIATVGGQYLWARLQSFSAFRRWGDSEQRPLARRAWILIQRIEALYKAASFGNLLIFLYTGRYRNLIERALRARLVYGTPNMNRAVSFEYMNRQLVWNEFSEMLLLLLPLLNSSTVKGLFGPF*************TCPICQASPTTPFLALPCQHRYCYYCLRTRCAASPSFRCSRCNEPVIAMQRHGVINPKISSQ

MSAMLKEQLVKVFSLMKPGMLFQYEPELDAFLEFLIWRFSIWVDKPTPGNALMNLRYRDERA***R*KVRTGLEGPGLTNAQKIWYCIATVGGQYLWARLQSFSAFRRWGDSEQRPLARRAWILIQRIEALYKAASFGNLLIFLYTGRYRNLIERALRARLVYGTPNMNRAVSFEYMNRQLVWNEFSEMLLLLLPLLNSSTVKGLFGPFSKDKSS****DVTTCPICQASPTTPFLALPCQHRYCYYCLRTRCAASPSFRCSRCNEPVIAMQRHGVI*******

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		284	2.2.26 [Sep-21-2011]
Q9CA86		333	Peroxisome biogenesis pro	yes	no	0.985	0.840	0.812	1e-133
Q75JQ3		423	Peroxisome biogenesis fac	yes	no	0.950	0.638	0.311	1e-44
P24392		305	Peroxisome biogenesis fac	yes	no	0.873	0.813	0.322	3e-34
P55098		305	Peroxisome biogenesis fac	no	no	0.897	0.836	0.307	2e-33
P28328		305	Peroxisome biogenesis fac	yes	no	0.887	0.826	0.300	8e-33
Q06438		304	Peroxisome biogenesis fac	yes	no	0.897	0.838	0.303	3e-32
P51021		554	Peroxisomal biogenesis fa	yes	no	0.841	0.431	0.315	9e-31
Q99155		381	Peroxisomal biogenesis fa	yes	no	0.887	0.661	0.304	3e-29
Q01964		461	Peroxisomal biogenesis fa	yes	no	0.795	0.490	0.248	2e-08
P32800		271	Peroxisomal biogenesis fa	yes	no	0.253	0.265	0.358	0.0003

>sp\|Q9CA86\|PEX2_ARATH Peroxisome biogenesis protein 2 OS=Arabidopsis thaliana GN=PEX2 PE=1 SV=1	Back alignment and function desciption

 Score =  473 bits (1217), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 229/282 (81%), Positives = 254/282 (90%), Gaps = 2/282 (0%)

Query: 1   MSAMLKEQLVKVFSLMKPGMLFQYEPELDAFLEFLIWRFSIWVDKPTPGNALMNLRYRDE 60
           MSAMLKEQLVKVF+LMKPGMLFQYEPELDAFLEFLIWRFSIWVDKPTPGNALMNLRYRDE
Sbjct: 52  MSAMLKEQLVKVFTLMKPGMLFQYEPELDAFLEFLIWRFSIWVDKPTPGNALMNLRYRDE 111

Query: 61  RAVETR--AKVRTGLEGPGLTNAQKIWYCIATVGGQYLWARLQSFSAFRRWGDSEQRPLA 118
           R V  +   KVRTGLEGPGLT+ QKIWYC+A+VGGQYL++RLQSFSAFRRWGDSEQRPLA
Sbjct: 112 RGVVAQHLGKVRTGLEGPGLTSPQKIWYCVASVGGQYLFSRLQSFSAFRRWGDSEQRPLA 171

Query: 119 RRAWILIQRIEALYKAASFGNLLIFLYTGRYRNLIERALRARLVYGTPNMNRAVSFEYMN 178
           RR W L+QRIE +YKAASF NLL FLYTGRYRNLIE+AL+ARLVY +P+MNR+VSFEYMN
Sbjct: 172 RRLWTLVQRIEGIYKAASFLNLLSFLYTGRYRNLIEKALKARLVYRSPHMNRSVSFEYMN 231

Query: 179 RQLVWNEFSEMLLLLLPLLNSSTVKGLFGPFSKDKSSSSEEDVTTCPICQASPTTPFLAL 238
           RQLVWNEFSEMLLLLLPLLNSS VK +  PF+KDKSSS++ED  TCPICQ  P  PF+AL
Sbjct: 232 RQLVWNEFSEMLLLLLPLLNSSAVKNILSPFAKDKSSSTKEDTVTCPICQVDPAIPFIAL 291

Query: 239 PCQHRYCYYCLRTRCAASPSFRCSRCNEPVIAMQRHGVINPK 280
           PCQHRYCYYC+RTRCA++ SFRC RCNEPV+A+QR GV + K
Sbjct: 292 PCQHRYCYYCIRTRCASAASFRCLRCNEPVVAIQREGVSSGK 333

Might act directly in a photomorphogenetic pathway negatively regulated by DET1, which is involved in peroxisome assembly and matrix protein import. Could be part of a complex responsible for the monoubiquitination of PEX5.
Arabidopsis thaliana (taxid: 3702)

>sp\|Q75JQ3\|PEX2_DICDI Peroxisome biogenesis factor 2 OS=Dictyostelium discoideum GN=pex2 PE=3 SV=1	Back alignment and function description

>sp\|P24392\|PEX2_RAT Peroxisome biogenesis factor 2 OS=Rattus norvegicus GN=Pex2 PE=2 SV=1	Back alignment and function description

>sp\|P55098\|PEX2_MOUSE Peroxisome biogenesis factor 2 OS=Mus musculus GN=Pex2 PE=2 SV=1	Back alignment and function description

>sp\|P28328\|PEX2_HUMAN Peroxisome biogenesis factor 2 OS=Homo sapiens GN=PEX2 PE=1 SV=2	Back alignment and function description

>sp\|Q06438\|PEX2_CRIGR Peroxisome biogenesis factor 2 OS=Cricetulus griseus GN=PEX2 PE=1 SV=1	Back alignment and function description

>sp\|P51021\|PEX2_PODAS Peroxisomal biogenesis factor 2 OS=Podospora anserina GN=PEX2 PE=3 SV=1	Back alignment and function description

>sp\|Q99155\|PEX2_YARLI Peroxisomal biogenesis factor 2 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=PEX2 PE=3 SV=2	Back alignment and function description

>sp\|Q01964\|PEX2_PICPA Peroxisomal biogenesis factor 2 OS=Komagataella pastoris GN=PEX2 PE=3 SV=1	Back alignment and function description

>sp\|P32800\|PEX2_YEAST Peroxisomal biogenesis factor 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PEX2 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		284
357513377		438	Peroxisome assembly protein [Medicago tr	0.978	0.634	0.881	1e-139
356526111		330	PREDICTED: peroxisome biogenesis protein	0.975	0.839	0.884	1e-139
225442563		346	PREDICTED: peroxisome biogenesis protein	0.964	0.791	0.872	1e-137
356523018		331	PREDICTED: peroxisome biogenesis protein	0.975	0.836	0.877	1e-137
356523016		333	PREDICTED: peroxisome biogenesis protein	0.975	0.831	0.867	1e-136
224074005		340	predicted protein [Populus trichocarpa]	0.968	0.808	0.901	1e-135
449524581		360	PREDICTED: peroxisome biogenesis protein	0.964	0.761	0.843	1e-132
224059114		341	predicted protein [Populus trichocarpa]	0.975	0.812	0.877	1e-131
18412518		333	peroxin-2 [Arabidopsis thaliana] gi\|3409	0.985	0.840	0.812	1e-131
42572185		282	peroxin-2 [Arabidopsis thaliana] gi\|3321	0.985	0.992	0.812	1e-130

>gi\|357513377\|ref\|XP_003626977.1\| Peroxisome assembly protein [Medicago truncatula] gi\|355520999\|gb\|AET01453.1\| Peroxisome assembly protein [Medicago truncatula]	Back alignment and taxonomy information

 Score =  501 bits (1289), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 245/278 (88%), Positives = 260/278 (93%)

Query: 1   MSAMLKEQLVKVFSLMKPGMLFQYEPELDAFLEFLIWRFSIWVDKPTPGNALMNLRYRDE 60
           MSAMLKEQLVKVF+LMKPGMLFQYE ELDAFLEFLIWRFSIWVDKPTPG ALMNLRYRDE
Sbjct: 159 MSAMLKEQLVKVFTLMKPGMLFQYEAELDAFLEFLIWRFSIWVDKPTPGIALMNLRYRDE 218

Query: 61  RAVETRAKVRTGLEGPGLTNAQKIWYCIATVGGQYLWARLQSFSAFRRWGDSEQRPLARR 120
           RAVE+R KVRTGLEGPGLT AQK+WYCIATVGGQY+WARLQSFSAFRRWGD+EQRPLARR
Sbjct: 219 RAVESRDKVRTGLEGPGLTVAQKLWYCIATVGGQYIWARLQSFSAFRRWGDTEQRPLARR 278

Query: 121 AWILIQRIEALYKAASFGNLLIFLYTGRYRNLIERALRARLVYGTPNMNRAVSFEYMNRQ 180
            WILIQRIE +Y+AASFGNLLIFL TGRYRNLIER LRARLVYG+PNMNRAVSFEYMNRQ
Sbjct: 279 LWILIQRIEGIYRAASFGNLLIFLCTGRYRNLIERVLRARLVYGSPNMNRAVSFEYMNRQ 338

Query: 181 LVWNEFSEMLLLLLPLLNSSTVKGLFGPFSKDKSSSSEEDVTTCPICQASPTTPFLALPC 240
           LVWNEFSEMLLLLLPLLNSS+VK L  PFSKDKSSSS ED T CPICQA+P  PF+ALPC
Sbjct: 339 LVWNEFSEMLLLLLPLLNSSSVKNLLRPFSKDKSSSSGEDSTACPICQATPIIPFVALPC 398

Query: 241 QHRYCYYCLRTRCAASPSFRCSRCNEPVIAMQRHGVIN 278
           QHRYCYYCLRTRCAA+PSFRC RCNEPV+AMQRHG ++
Sbjct: 399 QHRYCYYCLRTRCAAAPSFRCLRCNEPVVAMQRHGGVS 436

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|356526111\|ref\|XP_003531663.1\| PREDICTED: peroxisome biogenesis protein 2-like [Glycine max]	Back alignment and taxonomy information

>gi\|225442563\|ref\|XP_002279072.1\| PREDICTED: peroxisome biogenesis protein 2 [Vitis vinifera] gi\|297743241\|emb\|CBI36108.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356523018\|ref\|XP_003530139.1\| PREDICTED: peroxisome biogenesis protein 2-like isoform 2 [Glycine max]	Back alignment and taxonomy information

>gi\|356523016\|ref\|XP_003530138.1\| PREDICTED: peroxisome biogenesis protein 2-like isoform 1 [Glycine max]	Back alignment and taxonomy information

>gi\|224074005\|ref\|XP_002304212.1\| predicted protein [Populus trichocarpa] gi\|222841644\|gb\|EEE79191.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449524581\|ref\|XP_004169300.1\| PREDICTED: peroxisome biogenesis protein 2-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|224059114\|ref\|XP_002299722.1\| predicted protein [Populus trichocarpa] gi\|222846980\|gb\|EEE84527.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi|18412518|ref|NP_565222.1| peroxin-2 [Arabidopsis thaliana] gi|34098692|sp|Q9CA86.1|PEX2_ARATH RecName: Full=Peroxisome biogenesis protein 2; AltName: Full=E3 ubiquitin-protein ligase PEX2; AltName: Full=Peroxin-2; Short=AtPEX2; Short=AthPEX2; AltName: Full=Pex2p gi|12324593|gb|AAG52254.1|AC011717_22 putative RING finger protein; 84236-82024 [Arabidopsis thaliana] gi|17381214|gb|AAL36419.1| unknown protein [Arabidopsis thaliana] gi|20465819|gb|AAM20014.1| unknown protein [Arabidopsis thaliana] gi|332198180|gb|AEE36301.1| peroxin-2 [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|42572185\|ref\|NP_974183.1\| peroxin-2 [Arabidopsis thaliana] gi\|332198181\|gb\|AEE36302.1\| peroxin-2 [Arabidopsis thaliana]	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		284
TAIR\|locus:2017804		333	TED3 "REVERSAL OF THE DET PHEN	0.985	0.840	0.755	1.3e-116
DICTYBASE\|DDB_G0272234		423	pex2 "peroxisomal biogenesis f	0.690	0.463	0.338	2.2e-42
ZFIN\|ZDB-GENE-070530-2		312	pex2 "peroxisomal biogenesis f	0.880	0.801	0.329	1.2e-33
UNIPROTKB\|F1RWL5		305	PEX2 "Uncharacterized protein"	0.904	0.842	0.298	7.7e-32
UNIPROTKB\|F6R7C3		305	PEX2 "Uncharacterized protein"	0.933	0.868	0.287	8.8e-31
UNIPROTKB\|E2R4P2		305	PEX2 "Uncharacterized protein"	0.873	0.813	0.300	1.3e-29
UNIPROTKB\|Q5ZM64		304	PEX2 "Uncharacterized protein"	0.904	0.845	0.305	9.1e-29
RGD\|61814		305	Pex2 "peroxisomal biogenesis f	0.897	0.836	0.285	2.4e-28
UNIPROTKB\|Q06438		304	PEX2 "Peroxisome biogenesis fa	0.897	0.838	0.282	3.9e-28
MGI\|MGI:107486		305	Pex2 "peroxisomal biogenesis f	0.897	0.836	0.282	1.7e-27

TAIR\|locus:2017804 TED3 "REVERSAL OF THE DET PHENOTYPE 3" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1149 (409.5 bits), Expect = 1.3e-116, P = 1.3e-116
 Identities = 213/282 (75%), Positives = 235/282 (83%)

Query:     1 MSAMLKEQLVKVFSLMKPGMLFQYEPELDAFLEFLIWRFSIWVDKPTPGNALMNLRYRDE 60
             MSAMLKEQLVKVF+LMKPGMLFQYEPELDAFLEFLIWRFSIWVDKPTPGNALMNLRYRDE
Sbjct:    52 MSAMLKEQLVKVFTLMKPGMLFQYEPELDAFLEFLIWRFSIWVDKPTPGNALMNLRYRDE 111

Query:    61 RAVETR--AKVRTGLEGPGLTNAQKIWYCIATVGGQYLWARLQSFSAFRRWGDSEQRPLA 118
             R V  +   KVRTGLEGPGLT+ QKIWYC+A+VGGQYL++RLQSFSAFRRWGDSEQRPLA
Sbjct:   112 RGVVAQHLGKVRTGLEGPGLTSPQKIWYCVASVGGQYLFSRLQSFSAFRRWGDSEQRPLA 171

Query:   119 RRAWILIQRIEALYKAASFGNLLIFLYTGRYRNLIERALRARLVYGTPNMNRAVSFEYMN 178
             RR W L+QRIE +YKAASF NLL FLYTGRYRNLIE+AL+ARLVY +P+MNR+VSFEYMN
Sbjct:   172 RRLWTLVQRIEGIYKAASFLNLLSFLYTGRYRNLIEKALKARLVYRSPHMNRSVSFEYMN 231

Query:   179 RQLVWNEFSEMXXXXXXXXNSSTVKGLFGPFXXXXXXXXXXXVTTCPICQASPTTPFLAL 238
             RQLVWNEFSEM        NSS VK +  PF             TCPICQ  P  PF+AL
Sbjct:   232 RQLVWNEFSEMLLLLLPLLNSSAVKNILSPFAKDKSSSTKEDTVTCPICQVDPAIPFIAL 291

Query:   239 PCQHRYCYYCLRTRCAASPSFRCSRCNEPVIAMQRHGVINPK 280
             PCQHRYCYYC+RTRCA++ SFRC RCNEPV+A+QR GV + K
Sbjct:   292 PCQHRYCYYCIRTRCASAASFRCLRCNEPVVAIQREGVSSGK 333

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

GO:0005777 "peroxisome" evidence=IDA

GO:0007031 "peroxisome organization" evidence=IMP

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0006635 "fatty acid beta-oxidation" evidence=RCA;IMP

GO:0016558 "protein import into peroxisome matrix" evidence=RCA;IMP

GO:0009506 "plasmodesma" evidence=IDA

GO:0006869 "lipid transport" evidence=RCA

GO:0006888 "ER to Golgi vesicle-mediated transport" evidence=RCA

GO:0006891 "intra-Golgi vesicle-mediated transport" evidence=RCA

GO:0010351 "lithium ion transport" evidence=RCA

GO:0044265 "cellular macromolecule catabolic process" evidence=RCA

GO:0009640 "photomorphogenesis" evidence=IMP

DICTYBASE\|DDB_G0272234 pex2 "peroxisomal biogenesis factor 2" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-070530-2 pex2 "peroxisomal biogenesis factor 2" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|F1RWL5 PEX2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|F6R7C3 PEX2 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2R4P2 PEX2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5ZM64 PEX2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

RGD\|61814 Pex2 "peroxisomal biogenesis factor 2" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q06438 PEX2 "Peroxisome biogenesis factor 2" [Cricetulus griseus (taxid:10029)]	Back alignment and assigned GO terms

MGI\|MGI:107486 Pex2 "peroxisomal biogenesis factor 2" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P28328	PEX2_HUMAN	No assigned EC number	0.3003	0.8873	0.8262	yes	no
Q06438	PEX2_CRIGR	No assigned EC number	0.3035	0.8978	0.8388	yes	no
P24392	PEX2_RAT	No assigned EC number	0.3223	0.8732	0.8131	yes	no
Q9CA86	PEX2_ARATH	No assigned EC number	0.8120	0.9859	0.8408	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00034358001	SubName- Full=Chromosome chr9 scaffold_7, whole genome shotgun sequence; (346 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00032261001	SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (400 aa)	•	•	0.463
	GSVIVG00032871001	SubName- Full=Chromosome undetermined scaffold_62, whole genome shotgun sequence; (393 aa)		•	0.455

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		284
pfam04757		215	pfam04757, Pex2_Pex12, Pex2 / Pex12 amino terminal	5e-40
cd00162		45	cd00162, RING, RING-finger (Really Interesting New	4e-08
pfam00097		40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	4e-07
pfam13923		45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	4e-06
smart00184		40	smart00184, RING, Ring finger	3e-05
pfam13639		46	pfam13639, zf-RING_2, Ring finger domain	0.004

>gnl\|CDD\|218247 pfam04757, Pex2_Pex12, Pex2 / Pex12 amino terminal region	Back alignment and domain information

 Score =  138 bits (349), Expect = 5e-40
 Identities = 59/215 (27%), Positives = 93/215 (43%), Gaps = 21/215 (9%)

Query: 1   MSAMLKEQLVKVFSLMK-PGMLFQYEPELDAFLEFLIWRFSIWVDKPTPGNALMNLRYRD 59
           + ++L+ QL  +   +     L  Y  EL   L+ L  R ++     T G     L+  +
Sbjct: 4   LESLLRPQLRYILRYLAGARFLLNYFDELKLLLKLLYERLTLLRGNATLGEEFYGLKRVN 63

Query: 60  ERAVETRAKVRTGLEGPGLTNAQKIWYCIATVGGQYLWARLQSFSAFRRWGDSEQRP--- 116
           E             EG  L+  Q++   +  V G YL  +L S        D E      
Sbjct: 64  EDD-----------EGRLLSRKQRLLSLLLLVLGPYLLRKLDSLLERLLEEDLENSLLRQ 112

Query: 117 -----LARRAWILIQRIEALYKAASFGNLLIFLYTGRYRNLIERALRARLVYGTPN-MNR 170
                L RR   L   + AL +  +  + L+FL+ G Y +L +R L  R V    + + R
Sbjct: 113 SRLSRLKRRLLKLYPALNALLELLNLLHFLLFLFGGTYYSLSKRLLGIRYVRLNQSDLER 172

Query: 171 AVSFEYMNRQLVWNEFSEMLLLLLPLLNSSTVKGL 205
            VS+E++ R L+W  F E+LL LLPLL  +++  L
Sbjct: 173 NVSYEFLGRLLLWQLFVELLLFLLPLLLPASLFFL 207

This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (pfam00097) domain. Length = 215

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

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

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

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		284
KOG2879		298	consensus Predicted E3 ubiquitin ligase [Posttrans	100.0
PF04757		229	Pex2_Pex12: Pex2 / Pex12 amino terminal region; In	100.0
KOG0317		293	consensus Predicted E3 ubiquitin ligase, integral	100.0
KOG0826		357	consensus Predicted E3 ubiquitin ligase involved i	99.97
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.17
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	99.1
KOG0823		230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.09
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.01
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.95
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.89
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	98.88
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.87
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	98.78
PHA02929		238	N1R/p28-like protein; Provisional	98.77
COG5574		271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.74
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	98.69
KOG2164		513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.68
PHA02926		242	zinc finger-like protein; Provisional	98.62
TIGR00599		397	rad18 DNA repair protein rad18. This family is bas	98.61
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.56
PF14835		65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.53
COG5432		391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.53
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.49
KOG0287		442	consensus Postreplication repair protein RAD18 [Re	98.47
KOG0978		698	consensus E3 ubiquitin ligase involved in syntaxin	98.45
PF14634		44	zf-RING_5: zinc-RING finger domain	98.45
PF04564		73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.43
KOG0311		381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.22
TIGR00570		309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.13
PF11789		57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	98.13
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	98.13
KOG0824		324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.11
KOG2177		386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.03
KOG4172		62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.92
COG5243		491	HRD1 HRD ubiquitin ligase complex, ER membrane com	97.87
COG5222		427	Uncharacterized conserved protein, contains RING Z	97.72
COG5152		259	Uncharacterized conserved protein, contains RING a	97.7
COG5540		374	RING-finger-containing ubiquitin ligase [Posttrans	97.65
KOG2660		331	consensus Locus-specific chromosome binding protei	97.65
KOG4628		348	consensus Predicted E3 ubiquitin ligase [Posttrans	97.61
KOG1785		563	consensus Tyrosine kinase negative regulator CBL [	97.58
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	97.52
KOG0297		391	consensus TNF receptor-associated factor [Signal t	97.5
KOG1813		313	consensus Predicted E3 ubiquitin ligase [Posttrans	97.49
KOG4159		398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.42
KOG1734		328	consensus Predicted RING-containing E3 ubiquitin l	97.4
PF12861		85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	97.37
KOG4692		489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.25
KOG1002		791	consensus Nucleotide excision repair protein RAD16	97.22
KOG4265		349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.18
KOG0828		636	consensus Predicted E3 ubiquitin ligase [Posttrans	96.84
PF14447		55	Prok-RING_4: Prokaryotic RING finger family 4	96.63
KOG1039		344	consensus Predicted E3 ubiquitin ligase [Posttrans	96.5
KOG2932		389	consensus E3 ubiquitin ligase involved in ubiquiti	96.5
KOG1571		355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.41
KOG3039		303	consensus Uncharacterized conserved protein [Funct	96.16
PF02891		50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	96.15
KOG1001		674	consensus Helicase-like transcription factor HLTF/	96.03
PF04641		260	Rtf2: Rtf2 RING-finger	96.02
KOG1645		463	consensus RING-finger-containing E3 ubiquitin liga	95.93
KOG1941		518	consensus Acetylcholine receptor-associated protei	95.89
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	95.72
KOG4739		233	consensus Uncharacterized protein involved in syna	95.71
KOG4367		699	consensus Predicted Zn-finger protein [Function un	95.48
COG5219		1525	Uncharacterized conserved protein, contains RING Z	95.22
smart00744		49	RINGv The RING-variant domain is a C4HC3 zinc-fing	95.2
KOG0825		1134	consensus PHD Zn-finger protein [General function	95.08
KOG4275		350	consensus Predicted E3 ubiquitin ligase [Posttrans	95.02
PF14570		48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	94.87
COG5175		480	MOT2 Transcriptional repressor [Transcription]	94.4
PF11793		70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	94.18
COG5236		493	Uncharacterized conserved protein, contains RING Z	94.18
KOG0827		465	consensus Predicted E3 ubiquitin ligase [Posttrans	93.86
PF05290		140	Baculo_IE-1: Baculovirus immediate-early protein (	93.03
KOG4185		296	consensus Predicted E3 ubiquitin ligase [Posttrans	92.38
KOG2114		933	consensus Vacuolar assembly/sorting protein PEP5/V	91.96
KOG1493		84	consensus Anaphase-promoting complex (APC), subuni	91.43
KOG3800		300	consensus Predicted E3 ubiquitin ligase containing	91.38
KOG3039		303	consensus Uncharacterized conserved protein [Funct	91.14
KOG3002		299	consensus Zn finger protein [General function pred	90.8
KOG1814		445	consensus Predicted E3 ubiquitin ligase [Posttrans	90.34
PF07800		162	DUF1644: Protein of unknown function (DUF1644); In	90.13
COG5194		88	APC11 Component of SCF ubiquitin ligase and anapha	89.42
KOG2817		394	consensus Predicted E3 ubiquitin ligase [Posttrans	88.87
KOG3970		299	consensus Predicted E3 ubiquitin ligase [Posttrans	88.59
PF10367		109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	88.39
PHA02825		162	LAP/PHD finger-like protein; Provisional	87.87
KOG2034		911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	85.77
KOG2930		114	consensus SCF ubiquitin ligase, Rbx1 component [Po	85.14
PHA03096		284	p28-like protein; Provisional	85.12
PF07191		70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	84.79
KOG3579		352	consensus Predicted E3 ubiquitin ligase [Posttrans	84.78
COG5220		314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	84.56
PF07975		51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	83.68
PF10497		105	zf-4CXXC_R1: Zinc-finger domain of monoamine-oxida	83.4
PF08746		43	zf-RING-like: RING-like domain; InterPro: IPR01485	83.13
PRK04023		1121	DNA polymerase II large subunit; Validated	83.09
KOG4362		684	consensus Transcriptional regulator BRCA1 [Replica	82.29
KOG3161		861	consensus Predicted E3 ubiquitin ligase [Posttrans	82.09
PHA02862		156	5L protein; Provisional	81.64
KOG2979		262	consensus Protein involved in DNA repair [General	81.53
PF03854		50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	81.25

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

Probab=100.00  E-value=2.3e-40  Score=282.66  Aligned_cols=263  Identities=39%  Similarity=0.671  Sum_probs=220.4

Q ss_pred             ChhHHHHHHHHHHHhcCCCccccChHHHHHHHHHHHHHHhhccCCCCcchhccCceeccchhhhhhhhhccCCCCCCCch
Q 023268            1 MSAMLKEQLVKVFSLMKPGMLFQYEPELDAFLEFLIWRFSIWVDKPTPGNALMNLRYRDERAVETRAKVRTGLEGPGLTN   80 (284)
Q Consensus         1 ~~~~l~~~l~~v~~~~~p~~~~~~~~El~lll~~l~~~~t~~~~~~T~Ge~~~~L~~~~~~~~~~~~~~~~~~~~~~ls~   80 (284)
                      ++.++.+|+.+++....|+...++++|.+++++.+++.++.+..+.|+|+...|++|.++.....+    ..     +  
T Consensus        29 ls~~l~~qf~~~F~~~~p~~~~r~epe~~~vl~~~iw~~si~~~~~T~Gqall~v~y~~ek~~~~r----~~-----l--   97 (298)
T KOG2879|consen   29 LSFLLWSQFVSIFLYYKPGLLLRVEPELDAVLDSAIWFFSIYSVDDTVGQALLNVAYIFEKLPVLR----VV-----L--   97 (298)
T ss_pred             HHHHHHHHHHHHHHhcCchhhhhhcHHHhHHHHHHHHheeccCCCCcccchhhhHHhhhccCceEE----Ee-----e--
Confidence            467899999999999999999999999999999999999999999999999999999987642111    00     1  


Q ss_pred             hHHHHHHHHHHhhhhHHHHHHhHHhhhhcCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHhce
Q 023268           81 AQKIWYCIATVGGQYLWARLQSFSAFRRWGDSEQRPLARRAWILIQRIEALYKAASFGNLLIFLYTGRYRNLIERALRAR  160 (284)
Q Consensus        81 ~~r~~~~l~~v~~pYl~~kl~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~l~~~~~Fl~~g~y~sl~~Rllglr  160 (284)
                      .-++++.+..+++.|+..|.+ ....+.+...    .-.+++..+.+++.++.++.+.|++.||..|+++++.++++|++
T Consensus        98 ~g~IW~~v~sig~~~~~~r~q-m~l~r~~~~~----~~~~~~~~v~~ve~i~~~~~~~n~l~fL~~gr~~tlie~il~~~  172 (298)
T KOG2879|consen   98 EGKIWTHVFSIGGSWLEERNQ-MDLFRAGWVN----LTPKLITSVFMVEGILKALGMLNLLSFLYRGRMYTLIEAILGLG  172 (298)
T ss_pred             cceEEEEeccccCCchhhhhH-HHHHHhhhhh----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHhccc
Confidence            114455567889999999976 2222222111    22356778888999999999999999999999999999999999


Q ss_pred             eecCCCCCcccchhhhhhhHHHHHHHHHHHHHHhhhccchhhhcccccCCCC----C--CCCCCCCcccccccCCCCCCC
Q 023268          161 LVYGTPNMNRAVSFEYMNRQLVWNEFSEMLLLLLPLLNSSTVKGLFGPFSKD----K--SSSSEEDVTTCPICQASPTTP  234 (284)
Q Consensus       161 ~~~~~~~~~~~~~~~~lnr~l~w~~~~e~l~~~l~~~~~~~~~~~l~~~~~~----~--~~~~~~~~~~C~iC~~~~~~p  234 (284)
                      +++..+...|.++||||||||+||+|.|++.+++|+++.+++++.++++..+    +  .++....+.+||+|.+.+++|
T Consensus       173 si~~~~~~~R~ig~eY~NReLlW~~F~e~ll~~lp~I~~~k~r~~l~sw~~~l~~ap~~sss~~t~~~~C~~Cg~~PtiP  252 (298)
T KOG2879|consen  173 SILHFPYFNRSIGYEYQNRELLWNAFREVLLLTLPFINFRKLRRVLKSWKLDLDRAPKFSSSTGTSDTECPVCGEPPTIP  252 (298)
T ss_pred             hhhhcccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCcccccccCCceeeccCCCCCCC
Confidence            9999999999999999999999999999999999999999988866655443    2  234557889999999999999


Q ss_pred             CeeccCcCcccHHHHHHHHhcCCCCccCCCCcCcccccccccCCC
Q 023268          235 FLALPCQHRYCYYCLRTRCAASPSFRCSRCNEPVIAMQRHGVINP  279 (284)
Q Consensus       235 ~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~C~~~~~~~~~~~~~~~  279 (284)
                      ++..+|||+|||+|+.+....+..+.||.|+.++..+++.++.+|
T Consensus       253 ~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~lq~sgv~~~  297 (298)
T KOG2879|consen  253 HVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEPLQASGVKSP  297 (298)
T ss_pred             eeeccccceeehhhhhhhhcchhhcccCccCCCCcchhhccCCCC
Confidence            988889999999999998876667999999999999998888654

>PF04757 Pex2_Pex12: Pex2 / Pex12 amino terminal region; InterPro: IPR006845 This region is the N-terminal part of a number of peroxisomal biogenesis proteins, including Pex2, Pex10 and Pex12, which contain two predicted transmembrane segments	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

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

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

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

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

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

>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

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

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

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

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

>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

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

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

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

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

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

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

>smart00184 RING Ring finger	Back alignment and domain information

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

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

>PF14634 zf-RING_5: zinc-RING finger domain	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

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

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

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

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

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

>KOG4172 consensus Predicted E3 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

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

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

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

>KOG4628 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

>KOG0802 consensus 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

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

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

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

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

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

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

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

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

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

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

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

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

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

>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

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

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

>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [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

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]	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

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

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

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

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

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

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

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

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

>COG5236 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

>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

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

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

>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

>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

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

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

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

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

>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

>KOG2817 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

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

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

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

>PHA03096 p28-like protein; Provisional	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

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

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

>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair	Back alignment and domain information

>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression	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

>PRK04023 DNA polymerase II large subunit; Validated	Back alignment and domain information

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

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

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

>KOG2979 consensus Protein involved in DNA repair [General function prediction only]	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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		284
1chc_A		68	Structure Of The C3hc4 Domain By 1h-Nuclear Magneti		2e-04

>pdb|1CHC|A Chain A, Structure Of The C3hc4 Domain By 1h-Nuclear Magnetic Resonance Spectroscopy; A New Structural Class Of Zinc- Finger Length = 68

Back alignment and structure

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 224 CPICQASPTTPFLALPCQHRYCYYCLRTRCAASPSFRCSRCNEPV 268
           CPIC   P+   +ALPC H +CY C+      +P+  C  C  PV
Sbjct: 8   CPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPT--CPLCKVPV 50

PyMOL of 1chc

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		284
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	1e-08
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	8e-08
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	8e-08
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	4e-07
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	7e-07
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	7e-07
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	1e-06
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	1e-06
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	2e-06
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	2e-06
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	2e-06
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	3e-06
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	4e-06
4epo_C		149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	5e-06
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	1e-05
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	1e-05
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	2e-05
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	2e-05
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	2e-05
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	2e-05
1z6u_A		150	NP95-like ring finger protein isoform B; structura	2e-05
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	2e-05
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	3e-05
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	5e-05
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	7e-05
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	7e-05
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	1e-04
3vk6_A		101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	1e-04
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	1e-04
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	3e-04
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	3e-04
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	3e-04
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	4e-04
3nw0_A		238	Non-structural maintenance of chromosomes element	5e-04
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	5e-04
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	6e-04
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	7e-04

>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

 Score = 50.6 bits (121), Expect = 1e-08
 Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 9/69 (13%)

Query: 212 DKSSSSEEDVT-TCPICQASPTTPFLALPCQHRYCYYCLRTRCAASPSFRCSRCNEPVIA 270
               S EE++   C IC+ +   P +   C+H +C  C      A+P  RC  C++P   
Sbjct: 5   SSGGSEEEEIPFRCFICRQAFQNPVV-TKCRHYFCESCALEHFRATP--RCYICDQPT-- 59

Query: 271 MQRHGVINP 279
               G+ NP
Sbjct: 60  ---GGIFNP 65

PyMOL of 2csy

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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 65	Back alignment and structure

>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

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens} Length = 170	Back alignment and structure

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens} Length = 150	Back alignment and structure

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

>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

>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

>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

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

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

>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

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

>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

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

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

>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

>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

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		284
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	99.3
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.26
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	99.25
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	99.21
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	99.19
1t1h_A		78	Gspef-atpub14, armadillo repeat containing protein	99.19
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	99.16
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	99.15
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	99.15
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	99.15
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.12
4ayc_A		138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.12
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.11
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	99.11
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.1
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	99.09
2kr4_A		85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.08
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	99.08
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	99.07
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	99.07
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	99.06
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.06
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	99.06
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.06
2kre_A		100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.04
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	99.03
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	99.03
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	99.02
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.02
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.0
1z6u_A		150	NP95-like ring finger protein isoform B; structura	99.0
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.0
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.0
2ect_A		78	Ring finger protein 126; metal binding protein, st	98.99
1wgm_A		98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.99
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	98.99
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	98.98
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	98.97
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	98.97
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	98.93
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	98.93
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	98.93
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	98.92
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.91
2yu4_A		94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.91
2f42_A		179	STIP1 homology and U-box containing protein 1; cha	98.9
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	98.89
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	98.88
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	98.86
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	98.86
4ic3_A		74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.84
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.83
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.82
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.8
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.77
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.74
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	98.73
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	98.71
2ea5_A		68	Cell growth regulator with ring finger domain prot	98.69
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	98.63
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.62
2bay_A		61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.57
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.52
3vk6_A		101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.47
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	98.41
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.41
3t6p_A		345	Baculoviral IAP repeat-containing protein 2; ring,	98.41
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	98.21
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	97.84
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	97.27
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	97.19
3nw0_A		238	Non-structural maintenance of chromosomes element	96.39
2jun_A		101	Midline-1; B-BOX, TRIM, ring finger, alternative s	94.92
3i2d_A		371	E3 SUMO-protein ligase SIZ1; signal transduction,	94.05
4fo9_A		360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	93.73
2ko5_A		99	Ring finger protein Z; lassa fever virus-Z, negati	92.36
2cs3_A		93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	91.58
3m62_A		968	Ubiquitin conjugation factor E4; armadillo-like re	88.23
1weo_A		93	Cellulose synthase, catalytic subunit (IRX3); stru	87.86
1wd2_A		60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	82.2
2lbm_A		142	Transcriptional regulator ATRX; metal binding prot	80.83

>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

Probab=99.30  E-value=3.4e-12  Score=90.49  Aligned_cols=55  Identities=27%  Similarity=0.631  Sum_probs=46.3

Q ss_pred             CCCCcccccccCCCCCCCCeecc-CcCcccHHHHHHHHhcCCCCccCCCCcCccccc
Q 023268          217 SEEDVTTCPICQASPTTPFLALP-CQHRYCYYCLRTRCAASPSFRCSRCNEPVIAMQ  272 (284)
Q Consensus       217 ~~~~~~~C~iC~~~~~~p~~~~~-CgH~fC~~Ci~~~~~~~~~~~CP~C~~~~~~~~  272 (284)
                      ...+...|+||.+.+.+| ++++ |||.||..||..|+.......||+||+++...+
T Consensus        11 ~~~~~~~C~IC~~~~~~p-~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           11 PIPDELLCLICKDIMTDA-VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             CSCGGGSCSSSCCCCTTC-EECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTT
T ss_pred             cCCCCCCCcCCChHHhCC-eEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCcc
Confidence            456789999999999999 5678 999999999999998644579999999766444

PyMOL of 2yur

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

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

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

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

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

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

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

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

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

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

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

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; 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

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

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

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

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

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

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

>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

>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

>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

>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

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

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

>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

>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

>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

>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

>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

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

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

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

>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

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

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

>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

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

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

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

>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

>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

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

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

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

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

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

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

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

>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

>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

>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

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

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

>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

>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

>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

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

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

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

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

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

>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

>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

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

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

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A	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		284
d1chca_		68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	2e-06
d1fbva4		79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-05
d1bora_		56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	2e-05
d1rmda2		86	g.44.1.1 (A:1-86) V(D)J recombination activating p	5e-05
d1jm7a_		103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	7e-05
d1jm7b_		97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	8e-05
d1vyxa_		60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	2e-04
d1g25a_		65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	3e-04
d2baya1		56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	0.002

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


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

 Score = 42.6 bits (100), Expect = 2e-06
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 6/55 (10%)

Query: 214 SSSSEEDVTTCPICQASPTTPFLALPCQHRYCYYCLRTRCAASPSFRCSRCNEPV 268
           ++ +E     CPIC   P+   +ALPC H +CY C+      +P+  C  C  PV
Sbjct: 2   ATVAER----CPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPT--CPLCKVPV 50

PyMOL of d1chca_

>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

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

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

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

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

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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		284
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	99.26
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.26
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	99.26
d2baya1		56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.22
d2c2la2		80	STIP1 homology and U box-containing protein 1, STU	99.14
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.13
d1t1ha_		78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.09
d1bora_		56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.04
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.02
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.01
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.99
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	98.9
d1wgma_		98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.78
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	98.67
d3dplr1		88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	98.61
d1vyxa_		60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.54
d1wima_		94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	97.96
d2cs3a1		80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	93.26
d1weoa_		93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	90.35
d1z60a1		59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	86.06

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

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

Probab=99.26  E-value=1.7e-12  Score=88.89  Aligned_cols=50  Identities=34%  Similarity=0.862  Sum_probs=43.2

Q ss_pred             cccccccCCCCCCCCeeccCcCcccHHHHHHHHhcCCCCccCCCCcCccccc
Q 023268          221 VTTCPICQASPTTPFLALPCQHRYCYYCLRTRCAASPSFRCSRCNEPVIAMQ  272 (284)
Q Consensus       221 ~~~C~iC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~C~~~~~~~~  272 (284)
                      ...|+||++.+.+|.+.++|||.||..|+..|+..  +..||+||.++....
T Consensus         5 ~d~C~IC~~~~~~~~~~~~C~H~Fc~~Ci~~w~~~--~~~CP~CR~~i~~~~   54 (68)
T d1chca_           5 AERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQ--NPTCPLCKVPVESVV   54 (68)
T ss_dssp             CCCCSSCCSCCCSCEEETTTTEEESTTHHHHHHHH--SCSTTTTCCCCCCEE
T ss_pred             CCCCccCCcCccCCcEEeCCCCcCcHHHHHHHHHh--CCcCCCCCcchHhhc
Confidence            45799999999888677899999999999999986  468999999987543

PyMOL of d1chca_

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

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

>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

>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

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

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

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

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

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {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

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

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

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

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

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

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

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

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

>d1z60a1 g.49.1.2 (A:328-386) TFIIH p44 subunit cysteine-rich domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure