Citrus Sinensis ID: 018282

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-------36

MGGKENVPQTTNTGGEVCRVESAEDSRCSLDKEVGLPSCRVCQCAESDKRGDVALAYLGITLPVQKPEAEATPKSNGDTQQPDGEKNLVNNESGYVQFISPDGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAKNIRVSDFKKVLIALKDFEALRERTATGEPNPAHVHTSSGVDPDAVAAIRRQRLSEISLWFSPHSSNNNHTYSNSTAVSQVVSEQPLSTVTEDVVAAENPATKWAVEGTGILLATGLLTVTLAWLIAPRVGKKTAKSGLHILLGGICALTVVVFFRFFVLTRIKYGPARYWAILFVFWFLVFGIWASRTHGAHTT

ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHHHHHcccccccccccccccccEEcccccccccccccccccccccccEEEEEcHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcHHHHHEEEEEEEEEEEEEEccccHHHHHHHHHHHHHHHHHHccccccccc

ccccccccccccccccccccHHccccccccccHccccccEEEcccccHcccccHHEEEEccccccccccccccccccccccccccccccccccccEEccccccEEEEEEEccccccccccccccEEEEEcccHHHHHHHHHHHHHHHHHcccccEEEEcccEEEEcccccccHEEEEEHHHHHHHHccccccccccEccccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccHHHEHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHEEEEEEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHccccccccc

mggkenvpqttntggevcrvesaedsrcsldkevglpscrvcqcaesdkrGDVALAYLGItlpvqkpeaeatpksngdtqqpdgeknlvnnesgyvqfispdgevficntntdlemgpchnqdtlielgcscrgdlALVHYGCALKWFVnhgstaceicgngaknirvsDFKKVLIALKDFEALRErtatgepnpahvhtssgvdpdAVAAIRRQRLSEIslwfsphssnnnhtysnsTAVSQvvseqplstvTEDVVaaenpatkwavEGTGILLATGLLTVTLAWLiaprvgkktaKSGLHILLGGICALTVVVFFRFFVLTRIKYGPARYWAILFVFWFLVFGIwasrthgahtt

mggkenvpqttntggevcrvesaedsrcsldkevglpscRVCQCAESDKRGDVALAYLGITLpvqkpeaeatpksngdtqqpdgEKNLVNNESGYVQFISPDGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNgaknirvsDFKKVLIALKDFEALRERTAtgepnpahvhtssgvdpdAVAAIRRQRLSEISLWFSPHSSNNNHTYSNSTAVSQVVSEQPLSTVTEDVVAAENPATKWAVEGTGILLATGLLTVTLAWLIAPRVGKKTAKSGLHILLGGICALTVVVFFRFFVLTRIKYGPARYWAILFVFWFLVFGIWASRTHGAHTT

MGGKENVPQTTNTGGEVCRVESAEDSRCSLDKEVGLPSCRVCQCAESDKRGDVALAYLGITLPVQKPEAEATPKSNGDTQQPDGEKNLVNNESGYVQFISPDGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAKNIRVSDFKKVLIALKDFEALRERTATGEPNPAHVHTSSGVDPDAVAAIRRQRLSEISLWFSPhssnnnhtysnstAVSQVVSEQPLSTVTEDVVAAENPATKWAVEgtgillatglltvtlawlIAPRVGKKTAKSGLHILLGGICAltvvvffrffvltrIKYGPARYWAILFVFWFLVFGIWASRTHGAHTT

*******************************KEVGLPSCRVCQCAESDKRGDVALAYLGITLPV****************************SGYVQFISPDGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAKNIRVSDFKKVLIALKDFEAL***************************IR**RLSEISLWF****************************VTEDVVAAENPATKWAVEGTGILLATGLLTVTLAWLIAPRVGKKTAKSGLHILLGGICALTVVVFFRFFVLTRIKYGPARYWAILFVFWFLVFGIWAS********

********************************************************************************************************VFICNTNTD***********LIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAKNIRVSDFKKVLIAL*********************TSSGVDPDAVAAIRRQRLSEISLWFSPHSSNNNH**********************DVVAAENPATKWAVEGTGILLATGLLTVTLAWLIAPRVGKKTAKSGLHILLGGICALTVVVFFRFFVLTRIKYGPARYWAILFVFWFLVFGIWA**T******

************TGGEVC**********SLDKEVGLPSCRVCQCAESDKRGDVALAYLGITLPVQKP***************DGEKNLVNNESGYVQFISPDGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAKNIRVSDFKKVLIALKDFEALRERTATGEPNPAHVHTSSGVDPDAVAAIRRQRLSEISLWFSPHSSNNNHTYSNSTAVSQVVSEQPLSTVTEDVVAAENPATKWAVEGTGILLATGLLTVTLAWLIAPRVGKKTAKSGLHILLGGICALTVVVFFRFFVLTRIKYGPARYWAILFVFWFLVFGIWASRTHGAHTT

*********************************VGLPSCRVCQCAESDKRGDVALAYLGITLPVQK***************************GYVQFISPDGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAKNIRVSDFKKVLIALKDFEALRERTATGEPNPAHVHTSSGVDPDAVAAIRRQRLSEISLWFSPHSS*************************EDVVAAENPATKWAVEGTGILLATGLLTVTLAWLIAPRVGKKTAKSGLHILLGGICALTVVVFFRFFVLTRIKYGPARYWAILFVFWFLVFGIWAS********

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooHHHHHHHHHHHHHHHHHHiiiiiiii

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHooooooooHHHHHHHHHHHHHHHHHHiiiiiiii

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooHHHHHHHHHHHHHHHHHHHiiiiiii

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiii

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooHHHHHHHHHHHHHHHHHHiiiiiiii

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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

No hits with e-value below 0.001 by BLAST

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		358
224083528		368	predicted protein [Populus trichocarpa]	0.986	0.959	0.718	1e-146
224096125		367	predicted protein [Populus trichocarpa]	0.927	0.904	0.755	1e-143
225438355		365	PREDICTED: uncharacterized protein LOC10	0.958	0.939	0.702	1e-134
297806947		369	zinc finger family protein [Arabidopsis	0.944	0.915	0.662	1e-127
18415916		363	RING/FYVE/PHD zinc finger-containing pro	0.946	0.933	0.662	1e-125
16209722		363	AT5g63780/MBK5_26 [Arabidopsis thaliana]	0.946	0.933	0.662	1e-125
145334333		370	RING/FYVE/PHD zinc finger-containing pro	0.944	0.913	0.661	1e-125
449457315		367	PREDICTED: uncharacterized protein LOC10	0.969	0.945	0.650	1e-124
356526954		363	PREDICTED: uncharacterized protein LOC10	0.972	0.958	0.663	1e-123
357520123		358	Zinc finger protein [Medicago truncatula	0.972	0.972	0.647	1e-122

>gi\|224083528\|ref\|XP_002307061.1\| predicted protein [Populus trichocarpa] gi\|222856510\|gb\|EEE94057.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  522 bits (1345), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 268/373 (71%), Positives = 301/373 (80%), Gaps = 20/373 (5%)

Query: 1   MGGKENVPQTTNTG--GEVCRVESAED----SRCSLDKEVGLPSCRVCQCAESDKRGDVA 54
           M  KENV Q  ++G   +      +ED    SRCSLD   G+ +CRVCQCAESDKRGDVA
Sbjct: 1   MMSKENVSQPISSGVRNDGHSPSESEDLGTGSRCSLD--AGIATCRVCQCAESDKRGDVA 58

Query: 55  LAYLGITLPVQ---------KPEAEATPKSNGDTQQPDGEKNLVNNESGYVQFISPDGEV 105
           L +LGI  P+Q         KPE++  P  N +  +   +      ESG V+F SP+GEV
Sbjct: 59  LGFLGIVPPLQEARKSSGAVKPESKEVPL-NAEADRFHSKNT--GRESGLVEFFSPEGEV 115

Query: 106 FICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAKN 165
           FICNT+TDLE+G CH QD LIELGCSC+ DLALVHY CALKWFVNHGST CEICG+ A N
Sbjct: 116 FICNTDTDLELGSCHQQDLLIELGCSCKSDLALVHYACALKWFVNHGSTVCEICGHVAIN 175

Query: 166 IRVSDFKKVLIALKDFEALRERTATGEPNPAHVHTSSGVDPDAVAAIRRQRLSEISLWFS 225
           IR SDFKKV++ALKD+EALRERTATG+PNPA VH S+GVDPDAVAA+RRQRLSEISLWF 
Sbjct: 176 IRTSDFKKVMVALKDYEALRERTATGDPNPAQVHASAGVDPDAVAAVRRQRLSEISLWFC 235

Query: 226 PHSSNNNHTYSNSTAVSQVVSEQPLSTVTEDVVAAENPATKWAVEGTGILLATGLLTVTL 285
           PH++N N+  +NS AVSQVVSEQPL+TVTED+V A+N ATKWAVEGTGILLATGLLTVTL
Sbjct: 236 PHNNNTNNYNNNSAAVSQVVSEQPLNTVTEDIVPADNRATKWAVEGTGILLATGLLTVTL 295

Query: 286 AWLIAPRVGKKTAKSGLHILLGGICALTVVVFFRFFVLTRIKYGPARYWAILFVFWFLVF 345
           AWLIAPRVGKKTAKSGLHILLGGICALTVV+FFRF VLTRIKYGPARYWAILFVFWFLVF
Sbjct: 296 AWLIAPRVGKKTAKSGLHILLGGICALTVVIFFRFIVLTRIKYGPARYWAILFVFWFLVF 355

Query: 346 GIWASRTHGAHTT 358
           GIWASRTH AHTT
Sbjct: 356 GIWASRTHDAHTT 368

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224096125\|ref\|XP_002310542.1\| predicted protein [Populus trichocarpa] gi\|222853445\|gb\|EEE90992.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|225438355\|ref\|XP_002273487.1\| PREDICTED: uncharacterized protein LOC100243998 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297806947\|ref\|XP_002871357.1\| zinc finger family protein [Arabidopsis lyrata subsp. lyrata] gi\|297317194\|gb\|EFH47616.1\| zinc finger family protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi|18415916|ref|NP_568206.1| RING/FYVE/PHD zinc finger-containing protein [Arabidopsis thaliana] gi|145334331|ref|NP_001078547.1| RING/FYVE/PHD zinc finger-containing protein [Arabidopsis thaliana] gi|13548333|emb|CAC35880.1| putative protein [Arabidopsis thaliana] gi|26451043|dbj|BAC42627.1| unknown protein [Arabidopsis thaliana] gi|94442419|gb|ABF18997.1| At5g08750 [Arabidopsis thaliana] gi|332003961|gb|AED91344.1| RING/FYVE/PHD zinc finger-containing protein [Arabidopsis thaliana] gi|332003962|gb|AED91345.1| RING/FYVE/PHD zinc finger-containing protein [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|16209722\|gb\|AAL14416.1\| AT5g63780/MBK5_26 [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|145334333\|ref\|NP_001078548.1\| RING/FYVE/PHD zinc finger-containing protein [Arabidopsis thaliana] gi\|332003963\|gb\|AED91346.1\| RING/FYVE/PHD zinc finger-containing protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|449457315\|ref\|XP_004146394.1\| PREDICTED: uncharacterized protein LOC101218157 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356526954\|ref\|XP_003532080.1\| PREDICTED: uncharacterized protein LOC100805323 [Glycine max]	Back alignment and taxonomy information

>gi\|357520123\|ref\|XP_003630350.1\| Zinc finger protein [Medicago truncatula] gi\|355524372\|gb\|AET04826.1\| Zinc finger protein [Medicago truncatula]	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		358
TAIR\|locus:505006592		370	AT5G08750 [Arabidopsis thalian	0.972	0.940	0.553	3.8e-101
TAIR\|locus:2160619		367	SHA1 "shoot apical meristem ar	0.966	0.942	0.517	1.7e-89
TAIR\|locus:2040949		222	AT2G34200 [Arabidopsis thalian	0.122	0.198	0.522	2.2e-07
TAIR\|locus:2175158		494	AT5G60580 [Arabidopsis thalian	0.256	0.186	0.356	4.4e-07
TAIR\|locus:2065620		207	AT2G37950 [Arabidopsis thalian	0.251	0.434	0.37	4.6e-07
TAIR\|locus:2166399		204	AT5G05830 [Arabidopsis thalian	0.114	0.200	0.536	8e-07
TAIR\|locus:2043664		240	AT2G45530 [Arabidopsis thalian	0.284	0.425	0.3	1.1e-06
TAIR\|locus:2081076		426	AT3G06330 [Arabidopsis thalian	0.175	0.147	0.376	4.5e-06
TAIR\|locus:2150084		206	AT5G01070 [Arabidopsis thalian	0.220	0.383	0.361	4.9e-06
TAIR\|locus:2144890		411	AT5G18760 "AT5G18760" [Arabido	0.173	0.150	0.382	7.1e-06

TAIR\|locus:505006592 AT5G08750 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1003 (358.1 bits), Expect = 3.8e-101, P = 3.8e-101
 Identities = 203/367 (55%), Positives = 243/367 (66%)

Query:     4 KENVPQTTNTG-----GEVCRVESAEDSRCSLDKEVGLPSCRVCQCAESDKRGDVALAYL 58
             KEN  +TT+ G         + E  E  R S DK+ GLP+CRVCQCAESD+RGD AL +L
Sbjct:    10 KENQLETTDCGVSDHGSPPIKNEEHEAPRYSSDKDTGLPTCRVCQCAESDRRGDAALGFL 69

Query:    59 GITLPVQKPEAEATPKSNGDTQQPDGEKNLVNNESGYVQFISPDGEVFICNTNTDLEMGP 118
             GIT PV +P      +SN   +  D   ++V + SG+++ ISPDGEVF+C  N D+EMG 
Sbjct:    70 GITPPVSEPR-----RSNAGEETVDQRSSVVKS-SGFIELISPDGEVFVC-ANDDIEMGA 122

Query:   119 CHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAKNIRVSDFKKVLIAL 178
               ++D L+ELGCSC+ DLALVHY CALKWFVNHGST CEICG   +NIR  DF KV+IAL
Sbjct:   123 WQHRDKLLELGCSCKNDLALVHYACALKWFVNHGSTVCEICGKTTENIRTVDFNKVVIAL 182

Query:   179 KDFEALRERTATGEPNPAHVH---TSSGVDPDAVAAIRRQRLSEISLWFSPXXXX----X 231
             KD+ ALRERTA G+PNP  V+   +SSG+DPDAVAAIRRQRLSEISLWF P         
Sbjct:   183 KDYAALRERTADGDPNPVVVNNNTSSSGIDPDAVAAIRRQRLSEISLWFGPHCSTNNNNS 242

Query:   232 XXXXXXXXAVSQVVSEQPLSTVTEDVVAAENPATKWAVEXXXXXXXXXXXXXXXXXXIAP 291
                     A SQV SEQP+  V  D++  E+ ATKWAVE                  IAP
Sbjct:   243 SNSAAAGTASSQVTSEQPVGIVNFDILPMESRATKWAVEGTGILLATGLLTVTLAWLIAP 302

Query:   292 RVGKKTAKSGLHILLGGICAXXXXXXXXXXXXXXIKYGPARYWAILFVFWFLVFGIWASR 351
             RVGK+TAKSGLHILLGG+CA              I+YGPARYWAILFVFWFLVFGIWASR
Sbjct:   303 RVGKRTAKSGLHILLGGLCALTVVIFFRFVVLTRIRYGPARYWAILFVFWFLVFGIWASR 362

Query:   352 THGAHTT 358
             +H +H++
Sbjct:   363 SHASHSS 369

GO:0005634 "nucleus" evidence=ISM

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

TAIR\|locus:2160619 SHA1 "shoot apical meristem arrest 1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2040949 AT2G34200 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2175158 AT5G60580 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2065620 AT2G37950 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2166399 AT5G05830 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2043664 AT2G45530 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2081076 AT3G06330 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2150084 AT5G01070 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2144890 AT5G18760 "AT5G18760" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		358
pfam12906		47	pfam12906, RINGv, RING-variant domain	2e-09
smart00744		49	smart00744, RINGv, The RING-variant domain is a C4	8e-08

>gnl\|CDD\|221845 pfam12906, RINGv, RING-variant domain	Back alignment and domain information

 Score = 52.8 bits (127), Expect = 2e-09
 Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 3/44 (6%)

Query: 119 CHNQDT---LIELGCSCRGDLALVHYGCALKWFVNHGSTACEIC 159
           C   +     +   C CRG L  VH  C  +W    G+T CEIC
Sbjct: 4   CLEGEEEDEPLIRPCRCRGSLKYVHQSCLERWLKTSGNTTCEIC 47

Length = 47

>gnl\|CDD\|128983 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		358
smart00744		49	RINGv The RING-variant domain is a C4HC3 zinc-fing	99.56
KOG1609		323	consensus Protein involved in mRNA turnover and st	99.51
PHA02825		162	LAP/PHD finger-like protein; Provisional	99.49
PF12906		47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	99.49
PHA02862		156	5L protein; Provisional	99.42
COG5183		1175	SSM4 Protein involved in mRNA turnover and stabili	99.05
KOG3053		293	consensus Uncharacterized conserved protein [Funct	98.47
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	96.04
PHA02929		238	N1R/p28-like protein; Provisional	95.2
KOG4628		348	consensus Predicted E3 ubiquitin ligase [Posttrans	94.79
PF12861		85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	94.31
KOG1493		84	consensus Anaphase-promoting complex (APC), subuni	93.29
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	93.08
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	91.99
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	91.71
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	91.68
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	91.5
PHA02926		242	zinc finger-like protein; Provisional	91.5
PF11793		70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	91.37
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	89.94
PF08510		126	PIG-P: PIG-P; InterPro: IPR013717 PIG-P (phosphati	88.77
COG5243		491	HRD1 HRD ubiquitin ligase complex, ER membrane com	87.63
COG5219		1525	Uncharacterized conserved protein, contains RING Z	87.51
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	85.91
COG5540		374	RING-finger-containing ubiquitin ligase [Posttrans	82.23

>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

Probab=99.56  E-value=2.8e-15  Score=109.33  Aligned_cols=49  Identities=33%  Similarity=0.786  Sum_probs=42.9

Q ss_pred             ceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccc
Q 018282          104 EVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICG  160 (358)
Q Consensus       104 eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~  160 (358)
                      .||||+   +.+     +.++++++||.|+|+++++|++||++|+..+++++||||+
T Consensus         1 ~CrIC~---~~~-----~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICH---DEG-----DEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCC---CCC-----CCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            599998   211     2457789999999999999999999999999999999996

Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class

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

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

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

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

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

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]	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

>KOG4628 consensus Predicted 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

>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

>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

>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

>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

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

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

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

>smart00184 RING Ring finger	Back alignment and domain information

>PF08510 PIG-P: PIG-P; InterPro: IPR013717 PIG-P (phosphatidylinositol N-acetylglucosaminyltransferase subunit P) is an enzyme involved in GPI anchor biosynthesis []	Back alignment and domain information

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

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

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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		358
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	9e-09
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	1e-07

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

 Score = 50.5 bits (121), Expect = 9e-09
 Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 1/43 (2%)

Query: 119 CH-NQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICG 160
           C+          C C G+L  VH  C   W     +TAC+ICG
Sbjct: 12  CNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICG 54

PyMOL of 1vyx

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		358
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	99.6
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	99.4
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	96.99
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	96.72
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	96.52
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	96.49
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	96.33
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	96.21
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	96.21
2ect_A		78	Ring finger protein 126; metal binding protein, st	96.16
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	95.97
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	95.92
1t1h_A		78	Gspef-atpub14, armadillo repeat containing protein	95.81
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	95.58
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	95.41
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	95.4
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	95.18
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	95.04
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	94.97
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	94.97
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	94.82
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	94.72
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	94.72
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	94.63
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	94.51
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	94.4
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	94.4
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	94.34
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	94.16
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	94.16
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	94.14
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	94.05
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	93.88
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	93.56
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	93.45
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	92.66
1z6u_A		150	NP95-like ring finger protein isoform B; structura	92.45
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	92.35
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	92.25
4ayc_A		138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	91.34
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	91.31
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	90.34
1wgm_A		98	Ubiquitin conjugation factor E4A; ubiquitinating e	90.19
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	90.16
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	90.04
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	89.67
3nw0_A		238	Non-structural maintenance of chromosomes element	88.57
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	88.07
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	87.96
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	87.72
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	87.03
2kre_A		100	Ubiquitin conjugation factor E4 B; U-box domain, E	86.9
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	86.75
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	86.7
2f42_A		179	STIP1 homology and U-box containing protein 1; cha	85.84
2kr4_A		85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	84.04
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	84.03
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	83.76
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	82.47
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	81.66

>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

Probab=99.60  E-value=1.5e-16  Score=117.99  Aligned_cols=54  Identities=33%  Similarity=0.668  Sum_probs=46.3

Q ss_pred             CCCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccccccc
Q 018282          101 PDGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAK  164 (358)
Q Consensus       101 pE~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~  164 (358)
                      .+..||||+.    +.      ++.+++||.|+|+++++|+.||++|++.+++.+||+|++.|.
T Consensus         5 ~~~~CrIC~~----~~------~~~l~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            5 DVPVCWICNE----EL------GNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             SCCEETTTTE----EC------SCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCEeEEeec----CC------CCceecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            4667999982    11      123679999999999999999999999999999999999986

PyMOL of 1vyx

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring 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

>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

>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

>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

>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

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

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

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

>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

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding 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

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

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

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

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

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

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

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

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

>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

>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

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

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

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

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

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

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

>2ckl_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

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

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

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

>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

>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

>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

>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

>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

>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

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

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

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {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

>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

>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

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

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

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

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

>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

>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

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		358
d1vyxa_		60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.12
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	96.86
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	96.66
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	96.43
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	96.12
d3dplr1		88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	95.81
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	95.58
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	94.45
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	93.38
d1t1ha_		78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	92.32
d2baya1		56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	91.66
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	90.13
d1wima_		94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	88.54
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	86.85
d1wgma_		98	Ubiquitin conjugation factor E4A {Human (Homo sapi	85.21
d2c2la2		80	STIP1 homology and U box-containing protein 1, STU	83.51

>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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=99.12  E-value=7.5e-12  Score=89.61  Aligned_cols=53  Identities=34%  Similarity=0.686  Sum_probs=45.4

Q ss_pred             CCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccccccc
Q 018282          102 DGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAK  164 (358)
Q Consensus       102 E~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~  164 (358)
                      +..|+||++  +.        ++.+..||.|+|...++|+.||++|++.+++.+|++|++.|+
T Consensus         6 ~~~C~IC~~--~~--------~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           6 VPVCWICNE--EL--------GNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CCEETTTTE--EC--------SCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCccCCc--cC--------CCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            467999982  11        234678999999999999999999999999999999999986

PyMOL of d1vyxa_

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

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

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

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

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

>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

>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

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

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

>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

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

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