Citrus Sinensis ID: 015426

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

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

MTYADFCQFCASFIQHILEMRIVRTDGMDDQYSVLIRFDSQDSADKFYQHFNGRQFNSLEEEVCHVLFTVDVQFTGYTGSLEHVQPAPASSTEQPSCPVCLERLDQDTSGILTTICNHSFHCSCISKWTDSSCPVCRYCQQQPEKSICFVCQTSENLWMCVICGFVGCGRYKGGHAIIHWKETEHCYSLELETQRVWDYAGDNYVHRLIQSKTDGKLVELNSHCLHGKDNCGSCDCVDSGTSDALLSSKVEAIVNEYNELLAAQLENQKIYYETLLQEAKEETEKIISEAVKKAIAQKLQKMQAKLDRCVREKKFLDDLNENLLKNQEMWKAKISEIEEREKMALRAKDDKIQDSEAQLRDLMAYLEAEKTLQQLSISNEIKDGTVLPMSVESSTSTGTKGKGKKIQ

ccHHHHHHHHHHHHccccEEEEEEccccccEEEEEEEEccHHHHHHHHHHHccccccccccccEEEEEEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccEEEEEEcccccccccccHHHHHHHcccccEEEEEccEEEEEcccccEEEcccccccccccHHccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccEEEEccccccccccccccccccc

ccHHHHHHHHHHHHHHHcEEEEEEcccccccEEEEEEEccHHHHHHHHHHHccccccccccccEEEEEEEEEEEEccccccccccccccccccccccccEEEcccccccEEEEEEccccccHHHHHHcccccccEEEEEcccccccccccccccccEEEEEEEcccccccccccHHHHHHHHcccEEEEEcccccEEEccccccEEEEEEEccccEEEEEccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHcccEEEEccccccccccccccccccc

MTYADFCQFCASFIQHILEMRIVrtdgmddqysVLIRFDSQDSADKFYQhfngrqfnsleEEVCHVLFTVDVQftgytgslehvqpapassteqpscpvclerldqdtSGILTTICnhsfhcsciskwtdsscpvcrycqqqpeksicfvcqtsenlwmCVICGfvgcgrykgghaiIHWKETEHCYSLELETQRvwdyagdnyvHRLIQSKTDGKLVELNshclhgkdncgscdcvdsgtsdaLLSSKVEAIVNEYNELLAAQLENQKIYYETLLQEAKEETEKIISEAVKKAIAQKLQKMQAKLDRCVREKKFLDDLNENLLKNQEMWKAKISEIEEREKMALRAKDDKIQDSEAQLRDLMAYLEAEKTLQQLSIsneikdgtvlpmsvesststgtkgkgkkiq

MTYADFCQFCASFIQHILEMRIVRTDGMDDQYSVLIRFDSQDSADKFYQHFNGRQFNSLEEEVCHVLFTVDVQFTGYTGSLEHVQPAPASSTEQPSCPVCLERLDQDTSGILTTICNHSFHCSCISKWTDSSCPVCRYCQQQPEKSICFVCQTSENLWMCVICGFVGCGRYKGGHAIIHWKETEHCYSLELETQRVWDYAGDNYVHRLIQSKTDGKLVELNSHCLHGKDNCGSCDCVDSGTSDALLSSKVEAIVNEYNELLAAQLENQKIYYETLLQEAKEETEKIISEAVKKAIAQKLQKMQAKLDRCVREKKFLDDLNENLLKNQEMWKAKISEIEEREKMAlrakddkiqdSEAQLRDLMAYLEAEKTLQQLSIsneikdgtvlpmsvesststgtkgkgkkiq

**YADFCQFCASFIQHILEMRIVRTDGMDDQYSVLIRFDSQDSADKFYQHFNGRQFNSLEEEVCHVLFTVDVQFTGYTGSLE**************CPVCLERLDQDTSGILTTICNHSFHCSCISKWTDSSCPVCRYCQQQPEKSICFVCQTSENLWMCVICGFVGCGRYKGGHAIIHWKETEHCYSLELETQRVWDYAGDNYVHRLIQSKTDGKLVELNSHCLHGKDNCGSCDCVDSGTSDALLSSKVEAIVNEYNELLAAQLENQKIYYETLLQEAKEETEKIISEAVKKAIAQKLQKMQAKLDRCVREKKFLDDLNENLLKNQEMWK********************************AYL*****************************************

MTYADFCQFCASFIQHILEMRIVRTDGMDDQYSVLIRFDSQDSADKFYQHFNGRQFNSLEEEVCHVLFTVDVQFT****************TEQPSCPVCLERLDQDTSGILTTICNHSFHCSCISKWTDSSCPVCR*******************LWMCVICGFVGCGRYKGGHAIIHWKETEHCYSLELETQRVWDYAGDNYVHRLIQSKTDG*****************************************YNELLAAQLENQKIYY*************************************************************************************QLRDLMAY******************************************

MTYADFCQFCASFIQHILEMRIVRTDGMDDQYSVLIRFDSQDSADKFYQHFNGRQFNSLEEEVCHVLFTVDVQFTGYTGSLEH*************CPVCLERLDQDTSGILTTICNHSFHCSCISKWTDSSCPVCRYCQQQPEKSICFVCQTSENLWMCVICGFVGCGRYKGGHAIIHWKETEHCYSLELETQRVWDYAGDNYVHRLIQSKTDGKLVELNSHCLHGKDNCGSCDCVDSGTSDALLSSKVEAIVNEYNELLAAQLENQKIYYETLLQEAKEETEKIISEAVKKAIAQKLQKMQAKLDRCVREKKFLDDLNENLLKNQEMWKAKISEIEEREKMALRAKDDKIQDSEAQLRDLMAYLEAEKTLQQLSISNEIKDGTVLPM******************

MTYADFCQFCASFIQHILEMRIVRTDGMDDQYSVLIRFDSQDSADKFYQHFNGRQFNSLEEEVCHVLFTVDVQFTGYTG***HVQPAPASSTEQPSCPVCLERLDQDTSGILTTICNHSFHCSCISKWTDSSCPVCRYCQQQPEKSICFVCQTSENLWMCVICGFVGCGRYKGGHAIIHWKETEHCYSLELETQRVWDYAGDNYVHRLIQSKTDGKLVELNSH********************ALLSSKVEAIVNEYNELLAAQLENQKIYYETLLQEAKEETEKIISEAVKKAIAQKLQKMQAKLDRCVREKKFLDDLNENLLKNQEMWKAKISEIEEREKMALRAKDDKIQDSEAQLRDLMAYLEAEKTLQQLSISNEIKDGTVLPMS*****************

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MTYADFCQFCASFIQHILEMRIVRTDGMDDQYSVLIRFDSQDSADKFYQHFNGRQFNSLEEEVCHVLFTVDVQFTGYTGSLEHVQPAPASSTEQPSCPVCLERLDQDTSGILTTICNHSFHCSCISKWTDSSCPVCRYCQQQPEKSICFVCQTSENLWMCVICGFVGCGRYKGGHAIIHWKETEHCYSLELETQRVWDYAGDNYVHRLIQSKTDGKLVELNSHCLHGKDNCGSCDCVDSGTSDALLSSKVEAIVNEYNELLxxxxxxxxxxxxxxxxxxxxxTEKIISEAVxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxEKMALRAKDDKIQDSEAQLRDLMAYLEAEKTLQQLSISNEIKDGTVLPMSVESSTSTGTKGKGKKIQ

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		407	2.2.26 [Sep-21-2011]
Q7Z569		592	BRCA1-associated protein	yes	no	0.894	0.614	0.389	2e-75
Q99MP8		591	BRCA1-associated protein	yes	no	0.943	0.649	0.380	8e-75
O13747		547	RING finger protein ETP1	yes	no	0.882	0.656	0.381	6e-66
P38748		585	RING finger protein ETP1	yes	no	0.901	0.627	0.347	1e-61
Q95QN6		590	Uncharacterized RING fing	yes	no	0.823	0.567	0.354	4e-61
Q7ZUM8		695	Ubiquitin carboxyl-termin	no	no	0.346	0.202	0.295	4e-08
Q9H0E7		712	Ubiquitin carboxyl-termin	no	no	0.176	0.101	0.386	5e-08
D2HBJ8		711	Ubiquitin carboxyl-termin	no	no	0.154	0.088	0.412	6e-08
Q0V9G5		652	Ubiquitin carboxyl-termin	no	no	0.189	0.118	0.375	7e-08
Q5XGZ2		690	Ubiquitin carboxyl-termin	N/A	no	0.189	0.111	0.375	8e-08

>sp\|Q7Z569\|BRAP_HUMAN BRCA1-associated protein OS=Homo sapiens GN=BRAP PE=1 SV=2	Back alignment and function desciption

 Score =  283 bits (723), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 161/413 (38%), Positives = 240/413 (58%), Gaps = 49/413 (11%)

Query: 1   MTYADFCQFCASFIQHILEMRIVRTDGMDDQYSVLIRFDSQDSADKFYQHFNGRQFNSLE 60
           MT  D  +F A F + I +M+I+R D   +QY VLI+F +Q  AD FY   NGRQFNS+E
Sbjct: 172 MTSHDLMKFVAPFNEVIEQMKIIR-DSTPNQYMVLIKFRAQADADSFYMTCNGRQFNSIE 230

Query: 61  EEVCHVLFTVDVQFTGYTGSLEHVQPAPASSTEQPSCPVCLERLDQDTSGILTTICNHSF 120
           ++VC +++   V+      S +         TE P C VCLER+D+  +GILTT+CNHSF
Sbjct: 231 DDVCQLVY---VERAEVLKSEDGASLPVMDLTELPKCTVCLERMDESVNGILTTLCNHSF 287

Query: 121 HCSCISKWTDSSCPVCRYCQ-QQP-EKSICFVCQTSENLWMCVICGFVGCGRYKGGHAII 178
           H  C+ +W D++CPVCRYCQ  +P E++ CF C   ENLW+C+ICG +GCGRY   HA  
Sbjct: 288 HSQCLQRWDDTTCPVCRYCQTPEPVEENKCFECGVQENLWICLICGHIGCGRYVSRHAYK 347

Query: 179 HWKETEHCYSLELETQRVWDYAGDNYVHRLIQSKTDGKLVELNSHCLHGKDNCGSCDCVD 238
           H++ET+H Y+++L   RVWDYAGDNYVHRL+ SKTDGK+V+              C+   
Sbjct: 348 HFEETQHTYAMQLTNHRVWDYAGDNYVHRLVASKTDGKIVQY------------ECE--- 392

Query: 239 SGTSDALLSSKVEAIVNEYNELLAAQLENQKIYYET-LLQEAKEETEKIISEAVK-KAIA 296
               D     K++A+  EY+ LL +QLE+Q+IY+E  +++  K+  E+I +   K K   
Sbjct: 393 ---GDTCQEEKIDALQLEYSYLLTSQLESQRIYWENKIVRIEKDTAEEINNMKTKFKETI 449

Query: 297 QKLQKMQAKLDRCVREKKFLD---------------------DLNENLLKNQEMWKAKIS 335
           +K   ++ KL+  ++EK+ ++                     ++N+ L  NQ + + K+ 
Sbjct: 450 EKCDNLEHKLNDLLKEKQSVERKCTQLNTKVAKLTNELKEEQEMNKCLRANQVLLQNKLK 509

Query: 336 EIEEREKMALRAKDDKIQDSEAQLRDLMAYLEAEKTLQQLS--ISNEIKDGTV 386
           E E   K     KD +I + + QLRD+M YLE ++ +  L      EI++G +
Sbjct: 510 EEERVLKETCDQKDLQITEIQEQLRDVMFYLETQQKINHLPAETRQEIQEGQI 562

Negatively regulates MAP kinase activation by limiting the formation of Raf/MEK complexes probably by inactivation of the KSR1 scaffold protein. Also acts as a Ras responsive E3 ubiquitin ligase that, on activation of Ras, is modified by auto-polyubiquitination resulting in the release of inhibition of Raf/MEK complex formation. May also act as a cytoplasmic retention protein with a role in regulating nuclear transport.
Homo sapiens (taxid: 9606)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp\|Q99MP8\|BRAP_MOUSE BRCA1-associated protein OS=Mus musculus GN=Brap PE=1 SV=1	Back alignment and function description

>sp\|O13747\|EPT1_SCHPO RING finger protein ETP1 homolog OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC16E8.13 PE=3 SV=1	Back alignment and function description

>sp\|P38748\|ETP1_YEAST RING finger protein ETP1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ETP1 PE=1 SV=1	Back alignment and function description

>sp\|Q95QN6\|YQOE_CAEEL Uncharacterized RING finger protein EEED8.16 OS=Caenorhabditis elegans GN=EEED8.16 PE=4 SV=1	Back alignment and function description

>sp\|Q7ZUM8\|UBP44_DANRE Ubiquitin carboxyl-terminal hydrolase 44 OS=Danio rerio GN=usp44 PE=2 SV=1	Back alignment and function description

>sp\|Q9H0E7\|UBP44_HUMAN Ubiquitin carboxyl-terminal hydrolase 44 OS=Homo sapiens GN=USP44 PE=1 SV=2	Back alignment and function description

>sp\|D2HBJ8\|UBP44_AILME Ubiquitin carboxyl-terminal hydrolase 44 OS=Ailuropoda melanoleuca GN=USP44 PE=3 SV=1	Back alignment and function description

>sp\|Q0V9G5\|UBP44_XENTR Ubiquitin carboxyl-terminal hydrolase 44 OS=Xenopus tropicalis GN=usp44 PE=2 SV=1	Back alignment and function description

>sp\|Q5XGZ2\|UP44B_XENLA Ubiquitin carboxyl-terminal hydrolase 44-B OS=Xenopus laevis GN=usp44-b PE=2 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		407
255579210		500	brca1-associated protein, putative [Rici	0.990	0.806	0.799	0.0
224094254		411	predicted protein [Populus trichocarpa]	0.992	0.982	0.812	0.0
356558602		477	PREDICTED: BRCA1-associated protein-like	0.985	0.840	0.722	1e-179
449491057		507	PREDICTED: BRCA1-associated protein-like	0.955	0.767	0.742	1e-179
302143251		464	unnamed protein product [Vitis vinifera]	0.904	0.793	0.771	1e-174
225465123		439	PREDICTED: BRCA1-associated protein-like	0.904	0.838	0.771	1e-173
297822067		466	hypothetical protein ARALYDRAFT_901299 [	0.948	0.828	0.714	1e-169
79323080		479	BRCA1-associated protein [Arabidopsis th	0.936	0.795	0.708	1e-167
357455393		525	Ubiquitin carboxyl-terminal hydrolase [M	0.926	0.718	0.727	1e-166
449436170		520	PREDICTED: LOW QUALITY PROTEIN: BRCA1-as	0.955	0.748	0.681	1e-162

>gi\|255579210\|ref\|XP_002530451.1\| brca1-associated protein, putative [Ricinus communis] gi\|223529996\|gb\|EEF31921.1\| brca1-associated protein, putative [Ricinus communis]	Back alignment and taxonomy information

 Score =  693 bits (1789), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 323/404 (79%), Positives = 365/404 (90%), Gaps = 1/404 (0%)

Query: 1   MTYADFCQFCASFIQHILEMRIVRTDGMDDQYSVLIRFDSQDSADKFYQHFNGRQFNSLE 60
           MTYADFCQFCASFI HI EMRIVR DGM+D+YS+LIRFDSQ+S DKFYQHFNGRQFNSLE
Sbjct: 89  MTYADFCQFCASFIPHISEMRIVRNDGMEDRYSILIRFDSQESTDKFYQHFNGRQFNSLE 148

Query: 61  EEVCHVLFTVDVQFTGYTGSLEHVQPAPASSTEQPSCPVCLERLDQDTSGILTTICNHSF 120
           E+VC VLFTVDVQFTGY+GSL+  QP+PAS+TEQPSCPVCLERLDQD  GILTTICNHSF
Sbjct: 149 EDVCRVLFTVDVQFTGYSGSLD-TQPSPASTTEQPSCPVCLERLDQDMGGILTTICNHSF 207

Query: 121 HCSCISKWTDSSCPVCRYCQQQPEKSICFVCQTSENLWMCVICGFVGCGRYKGGHAIIHW 180
           HCSCISKWTDSSCPVCRYCQQQPEKS CFVCQTSENLW+CVICGFVGCGRYK  HAI HW
Sbjct: 208 HCSCISKWTDSSCPVCRYCQQQPEKSTCFVCQTSENLWLCVICGFVGCGRYKEEHAIRHW 267

Query: 181 KETEHCYSLELETQRVWDYAGDNYVHRLIQSKTDGKLVELNSHCLHGKDNCGSCDCVDSG 240
           KET+HCYSLELETQRVW+Y  DNYVHRLI SKTDGKLVELNSHC+H  D CGSC+CV++G
Sbjct: 268 KETQHCYSLELETQRVWNYISDNYVHRLILSKTDGKLVELNSHCVHANDGCGSCECVNTG 327

Query: 241 TSDALLSSKVEAIVNEYNELLAAQLENQKIYYETLLQEAKEETEKIISEAVKKAIAQKLQ 300
            S+ALL+SKVEAIVNEYNELLA QLE QK+Y+ETLLQE KEETE+ ISEAVKKA+AQ+LQ
Sbjct: 328 ISEALLNSKVEAIVNEYNELLATQLETQKLYFETLLQEVKEETEREISEAVKKAVAQRLQ 387

Query: 301 KMQAKLDRCVREKKFLDDLNENLLKNQEMWKAKISEIEEREKMALRAKDDKIQDSEAQLR 360
           K+Q+KLDRC++EKKFLD+L+ENL+KNQE+WKAK+ EIEEREK AL+ KDDKIQD E QL+
Sbjct: 388 KLQSKLDRCLKEKKFLDELDENLVKNQEIWKAKVLEIEEREKTALKMKDDKIQDLEEQLK 447

Query: 361 DLMAYLEAEKTLQQLSISNEIKDGTVLPMSVESSTSTGTKGKGK 404
           DLM YLEA K ++Q+S+S+EIKDGTVLP+ VESS+ T +    K
Sbjct: 448 DLMVYLEAGKPMEQVSVSDEIKDGTVLPLLVESSSRTNSPRSKK 491

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224094254\|ref\|XP_002310111.1\| predicted protein [Populus trichocarpa] gi\|222853014\|gb\|EEE90561.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356558602\|ref\|XP_003547593.1\| PREDICTED: BRCA1-associated protein-like [Glycine max]	Back alignment and taxonomy information

>gi\|449491057\|ref\|XP_004158786.1\| PREDICTED: BRCA1-associated protein-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|302143251\|emb\|CBI20546.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|225465123\|ref\|XP_002273039.1\| PREDICTED: BRCA1-associated protein-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297822067\|ref\|XP_002878916.1\| hypothetical protein ARALYDRAFT_901299 [Arabidopsis lyrata subsp. lyrata] gi\|297324755\|gb\|EFH55175.1\| hypothetical protein ARALYDRAFT_901299 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi|79323080|ref|NP_001031419.1| BRCA1-associated protein [Arabidopsis thaliana] gi|3413712|gb|AAC31235.1| hypothetical protein [Arabidopsis thaliana] gi|50253504|gb|AAT71954.1| At2g26000 [Arabidopsis thaliana] gi|53850529|gb|AAU95441.1| At2g26000 [Arabidopsis thaliana] gi|312274870|gb|ADQ57815.1| BRIZ2 [Arabidopsis thaliana] gi|330252688|gb|AEC07782.1| BRCA1-associated protein [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|357455393\|ref\|XP_003597977.1\| Ubiquitin carboxyl-terminal hydrolase [Medicago truncatula] gi\|355487025\|gb\|AES68228.1\| Ubiquitin carboxyl-terminal hydrolase [Medicago truncatula]	Back alignment and taxonomy information

>gi\|449436170\|ref\|XP_004135867.1\| PREDICTED: LOW QUALITY PROTEIN: BRCA1-associated protein-like [Cucumis sativus]	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		407
TAIR\|locus:2057469		479	BRIZ2 "AT2G26000" [Arabidopsis	0.941	0.799	0.709	5.5e-157
TAIR\|locus:2060045		488	BRIZ1 "AT2G42160" [Arabidopsis	0.943	0.786	0.503	1.8e-112
DICTYBASE\|DDB_G0270200		687	DDB_G0270200 "BRCA1-associated	0.663	0.393	0.462	7.5e-78
UNIPROTKB\|F1NJH4		556	BRAP "Uncharacterized protein"	0.921	0.674	0.398	1.7e-73
UNIPROTKB\|F1NR06		585	BRAP "Uncharacterized protein"	0.921	0.641	0.398	1.7e-73
UNIPROTKB\|F1PGI5		592	BRAP "Uncharacterized protein"	0.923	0.635	0.389	5.3e-72
ZFIN\|ZDB-GENE-040718-168		578	brap "BRCA1 associated protein	0.923	0.650	0.386	5.3e-72
UNIPROTKB\|A6H716		592	BRAP "BRAP protein" [Bos tauru	0.923	0.635	0.389	6.7e-72
UNIPROTKB\|J3KNN7		562	BRAP "BRCA1-associated protein	0.923	0.669	0.386	1.4e-71
UNIPROTKB\|Q7Z569		592	BRAP "BRCA1-associated protein	0.923	0.635	0.386	1.4e-71

TAIR\|locus:2057469 BRIZ2 "AT2G26000" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1530 (543.6 bits), Expect = 5.5e-157, P = 5.5e-157
 Identities = 274/386 (70%), Positives = 328/386 (84%)

Query:     1 MTYADFCQFCASFIQHILEMRIVRTDGMDDQYSVLIRFDSQDSADKFYQHFNGRQFNSLE 60
             MTYADFCQFC SFIQHIL+MR VR D ++++YS+LIRFDSQ+S D F+QHF G+QFNSL+
Sbjct:    71 MTYADFCQFCGSFIQHILDMRTVRNDDIENRYSILIRFDSQESTDTFFQHFRGKQFNSLD 130

Query:    61 EEVCHVLFTVDVQFTGYTGSLEHVQPAPASSTEQPSCPVCLERLDQDTSGILTTICNHSF 120
             E+VC +LF +DVQFTGY+GS++H QP+ A   EQP+CPVCLERLDQDT GILTT+CNHSF
Sbjct:   131 EDVCRLLFALDVQFTGYSGSIDHTQPSAAGPIEQPTCPVCLERLDQDTGGILTTMCNHSF 190

Query:   121 HCSCISKWTDSSCPVCRYCQQQPEKSICFVCQTSENLWMCVICGFVGCGRYKGGHAIIHW 180
             HCSCIS W DSSCPVCRYCQQQPE S+C VCQT+ENLWMCVICG VGCGRYK GHA  HW
Sbjct:   191 HCSCISNWPDSSCPVCRYCQQQPENSVCCVCQTTENLWMCVICGVVGCGRYKEGHARRHW 250

Query:   181 KETEHCYSLELETQRVWDYAGDNYVHRLIQSKTDGKLVELNSHCLHGKDNCGSCDCVDSG 240
             +ETEHCYSLELETQRVWDYAGDNYVHRLIQSKTDGKLVELNSH    KD CGSC+  DSG
Sbjct:   251 EETEHCYSLELETQRVWDYAGDNYVHRLIQSKTDGKLVELNSHGSLSKDGCGSCEYSDSG 310

Query:   241 TSDALLSSKVEAIVNEYNELLAAQLENQKIYYETLLQEAKEETEKIISEAVKKAIAQKLQ 300
              +DALL+SKV+ I++EYNELL AQLENQK Y+E LLQ  KEETE+ ISEA  KAI+Q+LQ
Sbjct:   311 MTDALLNSKVDMIISEYNELLQAQLENQKQYFEKLLQNVKEETEQKISEAASKAISQRLQ 370

Query:   301 KMQAKLDRCVREKKFLDDLNENLLKNQEMWKAKISEIEEREKMALRAKDDKIQDSEAQLR 360
             K+Q + DRCV+EK+FL+DLNENL+KN+++W  KI+E++EREK A+RAKD+KIQ  E QL 
Sbjct:   371 KLQTRFDRCVKEKQFLEDLNENLVKNKDVWSTKITEMKEREKKAVRAKDEKIQGLEEQLG 430

Query:   361 DLMAYLEAEKTLQQLSISNEIKDGTV 386
             +LMA ++ E    ++S + E++D TV
Sbjct:   431 NLMAQMDGES---EVSETKEVQDATV 453

GO:0003824 "catalytic activity" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000151 "ubiquitin ligase complex" evidence=IC

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

GO:0010029 "regulation of seed germination" evidence=IMP

GO:0043130 "ubiquitin binding" evidence=IDA

GO:0046982 "protein heterodimerization activity" evidence=IDA

GO:0009688 "abscisic acid biosynthetic process" evidence=RCA

TAIR\|locus:2060045 BRIZ1 "AT2G42160" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0270200 DDB_G0270200 "BRCA1-associated protein" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NJH4 BRAP "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NR06 BRAP "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|F1PGI5 BRAP "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-040718-168 brap "BRCA1 associated protein" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|A6H716 BRAP "BRAP protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|J3KNN7 BRAP "BRCA1-associated protein" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|Q7Z569 BRAP "BRCA1-associated protein" [Homo sapiens (taxid:9606)]	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

Your Input:
	estExt_Genewise1_v1.C_LG_VII2767	hypothetical protein (412 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

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		407
cd12437		82	cd12437, RRM_BRAP2_like, RNA recognition motif in	5e-36
pfam07576		110	pfam07576, BRAP2, BRCA1-associated protein 2	9e-30
pfam02148		63	pfam02148, zf-UBP, Zn-finger in ubiquitin-hydrolas	2e-22
cd12718		84	cd12718, RRM_BRAP2, RNA recognition motif in BRCA1	8e-22
smart00290		50	smart00290, ZnF_UBP, Ubiquitin Carboxyl-terminal H	4e-19
cd12717		82	cd12717, RRM_ETP1, RNA recognition motif in yeast	2e-13
pfam13639		46	pfam13639, zf-RING_2, Ring finger domain	3e-08
cd00162		45	cd00162, RING, RING-finger (Really Interesting New	3e-08
COG5207		749	COG5207, UBP14, Isopeptidase T [Posttranslational	2e-06
smart00184		40	smart00184, RING, Ring finger	6e-06
pfam12678		73	pfam12678, zf-rbx1, RING-H2 zinc finger	9e-06
pfam13923		45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	6e-05
pfam12072		201	pfam12072, DUF3552, Domain of unknown function (DU	6e-05
TIGR03319		514	TIGR03319, RNase_Y, ribonuclease Y	1e-04
PRK12704		520	PRK12704, PRK12704, phosphodiesterase; Provisional	2e-04
pfam00097		40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	2e-04
TIGR02169		1164	TIGR02169, SMC_prok_A, chromosome segregation prot	3e-04
COG5540		374	COG5540, COG5540, RING-finger-containing ubiquitin	3e-04
TIGR02168		1179	TIGR02168, SMC_prok_B, chromosome segregation prot	4e-04
PRK12704		520	PRK12704, PRK12704, phosphodiesterase; Provisional	7e-04
PRK00409		782	PRK00409, PRK00409, recombination and DNA strand e	0.001
COG0419		908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
COG5219		1525	COG5219, COG5219, Uncharacterized conserved protei	0.003
cd00590		72	cd00590, RRM_SF, RNA recognition motif (RRM) super	0.003
pfam06991		277	pfam06991, Prp19_bind, Splicing factor, Prp19-bind	0.004
pfam12861		85	pfam12861, zf-Apc11, Anaphase-promoting complex su	0.004
COG5194		88	COG5194, APC11, Component of SCF ubiquitin ligase	0.004

>gnl\|CDD\|240883 cd12437, RRM_BRAP2_like, RNA recognition motif in BRCA1-associated protein (BRAP2) and similar proteins	Back alignment and domain information

 Score =  126 bits (319), Expect = 5e-36
 Identities = 42/73 (57%), Positives = 53/73 (72%)

Query: 1  MTYADFCQFCASFIQHILEMRIVRTDGMDDQYSVLIRFDSQDSADKFYQHFNGRQFNSLE 60
          MT AD C FC SFIQ I +MRI+R +G  ++Y VLI+F SQ+ AD FY  FNG+ FNSLE
Sbjct: 10 MTSADLCTFCGSFIQQISDMRILRNEGRGNRYMVLIKFRSQEDADSFYNDFNGKPFNSLE 69

Query: 61 EEVCHVLFTVDVQ 73
           EVCH++F   V+
Sbjct: 70 PEVCHLVFVKSVE 82

This subfamily corresponds to the RRM domain of BRAP2, also termed impedes mitogenic signal propagation (IMP), or ring finger protein 52, or renal carcinoma antigen NY-REN-63, a novel cytoplasmic protein interacting with the two functional nuclear localisation signal (NLS) motifs of BRCA1, a nuclear protein linked to breast cancer. It also binds to the SV40 large T antigen NLS motif and the bipartite NLS motif found in mitosin. BRAP2 may serve as a cytoplasmic retention protein and play a role in the regulation of nuclear protein transport. The family also includes RING finger protein ETP1 and its homologs found in fungi. ETP1, also termed BRAP2 homolog, or ethanol tolerance protein 1, is the yeast homolog of BRCA1-associated protein (BRAP2) found in vertebrates. It may be involved in ethanol and salt-induced transcriptional activation of the NHA1 promoter and heat shock protein genes (HSP12 and HSP26), and participate in ethanol-induced turnover of the low-affinity hexose transporter Hxt3p. Members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C3HC4-type ring finger domain and a UBP-type zinc finger. . Length = 82

>gnl\|CDD\|191791 pfam07576, BRAP2, BRCA1-associated protein 2	Back alignment and domain information

>gnl\|CDD\|216903 pfam02148, zf-UBP, Zn-finger in ubiquitin-hydrolases and other protein	Back alignment and domain information

>gnl\|CDD\|241162 cd12718, RRM_BRAP2, RNA recognition motif in BRCA1-associated protein (BRAP2)	Back alignment and domain information

>gnl\|CDD\|197632 smart00290, ZnF_UBP, Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger	Back alignment and domain information

>gnl\|CDD\|241161 cd12717, RRM_ETP1, RNA recognition motif in yeast RING finger protein ETP1 and similar proteins	Back alignment and domain information

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

>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)

Back alignment and domain information

>gnl\|CDD\|227532 COG5207, UBP14, Isopeptidase T [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

>gnl\|CDD\|221705 pfam12678, zf-rbx1, RING-H2 zinc 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\|221408 pfam12072, DUF3552, Domain of unknown function (DUF3552)	Back alignment and domain information

>gnl\|CDD\|188306 TIGR03319, RNase_Y, ribonuclease Y	Back alignment and domain information

>gnl\|CDD\|237177 PRK12704, PRK12704, phosphodiesterase; Provisional	Back alignment and domain information

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

>gnl\|CDD\|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type	Back alignment and domain information

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

>gnl\|CDD\|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type	Back alignment and domain information

>gnl\|CDD\|237177 PRK12704, PRK12704, phosphodiesterase; Provisional	Back alignment and domain information

>gnl\|CDD\|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed	Back alignment and domain information

>gnl\|CDD\|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily	Back alignment and domain information

>gnl\|CDD\|219256 pfam06991, Prp19_bind, Splicing factor, Prp19-binding domain	Back alignment and domain information

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

>gnl\|CDD\|227521 COG5194, APC11, Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		407
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	100.0
PF07576		110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	99.9
PF02148		63	zf-UBP: Zn-finger in ubiquitin-hydrolases and othe	99.5
KOG0944		763	consensus Ubiquitin-specific protease UBP14 [Postt	99.13
COG5207		749	UBP14 Isopeptidase T [Posttranslational modificati	99.03
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	98.9
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.85
smart00290		50	ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like	98.75
KOG4628		348	consensus Predicted E3 ubiquitin ligase [Posttrans	98.72
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.7
cd02669		440	Peptidase_C19M A subfamily of Peptidase C19. Pepti	98.61
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	98.55
PHA02929		238	N1R/p28-like protein; Provisional	98.55
COG5540		374	RING-finger-containing ubiquitin ligase [Posttrans	98.51
KOG1873		877	consensus Ubiquitin-specific protease [Posttransla	98.43
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	98.43
PHA02926		242	zinc finger-like protein; Provisional	98.41
KOG0317		293	consensus Predicted E3 ubiquitin ligase, integral	98.4
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.39
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.39
TIGR00599		397	rad18 DNA repair protein rad18. This family is bas	98.39
PF14634		44	zf-RING_5: zinc-RING finger domain	98.36
KOG0823		230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.32
TIGR00570		309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.23
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.22
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.21
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.17
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	98.16
KOG2177		386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.16
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	98.06
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.01
PF14835		65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.97
KOG0287		442	consensus Postreplication repair protein RAD18 [Re	97.95
COG5432		391	RAD18 RING-finger-containing E3 ubiquitin ligase [	97.94
COG5243		491	HRD1 HRD ubiquitin ligase complex, ER membrane com	97.91
PF12861		85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	97.88
KOG4367		699	consensus Predicted Zn-finger protein [Function un	97.81
KOG0825		1134	consensus PHD Zn-finger protein [General function	97.68
KOG2164		513	consensus Predicted E3 ubiquitin ligase [Posttrans	97.65
COG5574		271	PEX10 RING-finger-containing E3 ubiquitin ligase [	97.49
PF04564		73	U-box: U-box domain; InterPro: IPR003613 Quality c	97.46
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	97.38
COG5194		88	APC11 Component of SCF ubiquitin ligase and anapha	97.28
KOG0978		698	consensus E3 ubiquitin ligase involved in syntaxin	97.25
KOG0824		324	consensus Predicted E3 ubiquitin ligase [Posttrans	96.99
KOG1734		328	consensus Predicted RING-containing E3 ubiquitin l	96.96
smart00744		49	RINGv The RING-variant domain is a C4HC3 zinc-fing	96.92
KOG0827		465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.87
KOG0828		636	consensus Predicted E3 ubiquitin ligase [Posttrans	96.68
PF11793		70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	96.54
KOG0311		381	consensus Predicted E3 ubiquitin ligase [Posttrans	96.42
KOG1493		84	consensus Anaphase-promoting complex (APC), subuni	96.4
PF00038		312	Filament: Intermediate filament protein; InterPro:	96.38
KOG1039		344	consensus Predicted E3 ubiquitin ligase [Posttrans	96.07
KOG1645		463	consensus RING-finger-containing E3 ubiquitin liga	95.89
KOG4739		233	consensus Uncharacterized protein involved in syna	95.8
KOG4159		398	consensus Predicted E3 ubiquitin ligase [Posttrans	95.79
PF00038		312	Filament: Intermediate filament protein; InterPro:	95.45
KOG0297		391	consensus TNF receptor-associated factor [Signal t	95.04
PF14570		48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.01
KOG4265		349	consensus Predicted E3 ubiquitin ligase [Posttrans	94.96
COG5219		1525	Uncharacterized conserved protein, contains RING Z	94.86
KOG2879		298	consensus Predicted E3 ubiquitin ligase [Posttrans	94.76
KOG2930		114	consensus SCF ubiquitin ligase, Rbx1 component [Po	94.68
KOG4185		296	consensus Predicted E3 ubiquitin ligase [Posttrans	94.64
PF11789		57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	94.56
COG1579		239	Zn-ribbon protein, possibly nucleic acid-binding [	94.5
KOG1785		563	consensus Tyrosine kinase negative regulator CBL [	94.24
KOG1941		518	consensus Acetylcholine receptor-associated protei	94.12
COG5152		259	Uncharacterized conserved protein, contains RING a	94.04
PF06785		401	UPF0242: Uncharacterised protein family (UPF0242);	93.9
PF10212		518	TTKRSYEDQ: Predicted coiled-coil domain-containing	93.88
PF10168		717	Nup88: Nuclear pore component; InterPro: IPR019321	93.86
KOG1940		276	consensus Zn-finger protein [General function pred	93.71
KOG2660		331	consensus Locus-specific chromosome binding protei	93.61
KOG4445		368	consensus Uncharacterized conserved protein, conta	93.37
PF05883		134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	93.2
PF04641		260	Rtf2: Rtf2 RING-finger	93.06
COG5175		480	MOT2 Transcriptional repressor [Transcription]	92.9
PF07227		446	DUF1423: Protein of unknown function (DUF1423); In	92.88
PF12325		120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	92.84
PF14259		70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	92.82
KOG4172		62	consensus Predicted E3 ubiquitin ligase [Posttrans	92.77
KOG0977		546	consensus Nuclear envelope protein lamin, intermed	92.76
KOG3970		299	consensus Predicted E3 ubiquitin ligase [Posttrans	92.65
KOG1571		355	consensus Predicted E3 ubiquitin ligase [Posttrans	92.65
KOG0161		1930	consensus Myosin class II heavy chain [Cytoskeleto	92.61
PF10367		109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	92.38
KOG1813		313	consensus Predicted E3 ubiquitin ligase [Posttrans	92.25
PF06005		72	DUF904: Protein of unknown function (DUF904); Inte	92.06
PRK09039		343	hypothetical protein; Validated	91.67
KOG0971		1243	consensus Microtubule-associated protein dynactin	91.47
COG5185		622	HEC1 Protein involved in chromosome segregation, i	91.12
KOG0250		1074	consensus DNA repair protein RAD18 (SMC family pro	90.71
KOG1002		791	consensus Nucleotide excision repair protein RAD16	90.69
PF09731		582	Mitofilin: Mitochondrial inner membrane protein; I	90.55
PF14447		55	Prok-RING_4: Prokaryotic RING finger family 4	90.44
PF07926		132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	90.42
KOG2932		389	consensus E3 ubiquitin ligase involved in ubiquiti	90.33
KOG4275		350	consensus Predicted E3 ubiquitin ligase [Posttrans	90.02
PF00076		70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	89.85
cd00590		74	RRM RRM (RNA recognition motif), also known as RBD	89.72
KOG0982		502	consensus Centrosomal protein Nuf [Cell cycle cont	89.44
KOG0971		1243	consensus Microtubule-associated protein dynactin	89.38
KOG3161		861	consensus Predicted E3 ubiquitin ligase [Posttrans	89.35
PF07800		162	DUF1644: Protein of unknown function (DUF1644); In	89.06
PRK09039		343	hypothetical protein; Validated	88.9
PRK12704		520	phosphodiesterase; Provisional	88.71
PF09304		107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	88.39
KOG0995		581	consensus Centromere-associated protein HEC1 [Cell	88.39
KOG4460		741	consensus Nuclear pore complex, Nup88/rNup84 compo	88.23
PF07888		546	CALCOCO1: Calcium binding and coiled-coil domain (	88.08
COG5222		427	Uncharacterized conserved protein, contains RING Z	88.07
KOG1814		445	consensus Predicted E3 ubiquitin ligase [Posttrans	88.05
KOG1029		1118	consensus Endocytic adaptor protein intersectin [S	87.98
KOG1001		674	consensus Helicase-like transcription factor HLTF/	87.66
PF12718		143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	87.65
PRK10361		475	DNA recombination protein RmuC; Provisional	87.38
PF09726		697	Macoilin: Transmembrane protein; InterPro: IPR0191	87.28
KOG3039		303	consensus Uncharacterized conserved protein [Funct	87.14
KOG3759		621	consensus Uncharacterized RUN domain protein [Sign	87.0
KOG1952		950	consensus Transcription factor NF-X1, contains NFX	86.93
KOG0161		1930	consensus Myosin class II heavy chain [Cytoskeleto	86.86
PF15397		258	DUF4618: Domain of unknown function (DUF4618)	86.69
PRK00409		782	recombination and DNA strand exchange inhibitor pr	86.52
KOG3268		234	consensus Predicted E3 ubiquitin ligase [Posttrans	86.44
TIGR03319		514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	86.4
PRK10884		206	SH3 domain-containing protein; Provisional	86.23
PF10211		189	Ax_dynein_light: Axonemal dynein light chain; Inte	86.19
KOG2114		933	consensus Vacuolar assembly/sorting protein PEP5/V	86.03
PF12906		47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	85.61
COG2433		652	Uncharacterized conserved protein [Function unknow	85.49
smart00360		71	RRM RNA recognition motif.	85.44
PF15070		617	GOLGA2L5: Putative golgin subfamily A member 2-lik	85.19
PF11932		251	DUF3450: Protein of unknown function (DUF3450); In	85.11
PF10168		717	Nup88: Nuclear pore component; InterPro: IPR019321	85.0
KOG3002		299	consensus Zn finger protein [General function pred	84.88
PHA02562		562	46 endonuclease subunit; Provisional	84.59
PF09726		697	Macoilin: Transmembrane protein; InterPro: IPR0191	84.26
KOG4005		292	consensus Transcription factor XBP-1 [Transcriptio	84.02
KOG0996		1293	consensus Structural maintenance of chromosome pro	83.96
KOG0298		1394	consensus DEAD box-containing helicase-like transc	83.78
PHA02825		162	LAP/PHD finger-like protein; Provisional	83.73
COG1579		239	Zn-ribbon protein, possibly nucleic acid-binding [	83.72
PF07798		177	DUF1640: Protein of unknown function (DUF1640); In	83.45
KOG0996		1293	consensus Structural maintenance of chromosome pro	83.34
PF09731		582	Mitofilin: Mitochondrial inner membrane protein; I	83.26
smart00362		72	RRM_2 RNA recognition motif.	83.24
PF14662		193	CCDC155: Coiled-coil region of CCDC155	83.07
PF04912		388	Dynamitin: Dynamitin ; InterPro: IPR006996 Dynamit	83.0
COG2433		652	Uncharacterized conserved protein [Function unknow	82.32
PHA03096		284	p28-like protein; Provisional	81.78
PF12128		1201	DUF3584: Protein of unknown function (DUF3584); In	81.68
smart00787		312	Spc7 Spc7 kinetochore protein. This domain is foun	81.68
PF08317		325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	81.56
PF04111		314	APG6: Autophagy protein Apg6; InterPro: IPR007243	81.53
PF04111		314	APG6: Autophagy protein Apg6; InterPro: IPR007243	81.16
PRK00106		535	hypothetical protein; Provisional	81.08
COG1196		1163	Smc Chromosome segregation ATPases [Cell division	80.63
COG3883		265	Uncharacterized protein conserved in bacteria [Fun	80.53
KOG1428		3738	consensus Inhibitor of type V adenylyl cyclases/Ne	80.26
KOG1853		333	consensus LIS1-interacting protein NUDE [Cytoskele	80.04

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

Probab=100.00  E-value=3.4e-99  Score=735.60  Aligned_cols=391  Identities=54%  Similarity=0.936  Sum_probs=340.8

Q ss_pred             CChhHHhHhhHHHHHhhheeEEEeeCCCCCeeEEEEeccChhhHhhHhhhcCCcccccCCCceeEEEEEeeEEEeccCCC
Q 015426            1 MTYADFCQFCASFIQHILEMRIVRTDGMDDQYSVLIRFDSQDSADKFYQHFNGRQFNSLEEEVCHVLFTVDVQFTGYTGS   80 (407)
Q Consensus         1 ~~~~d~~~f~~~~~~~i~~~r~ir~~~~~~~y~vll~f~~~~~a~~f~~~~~g~~f~~l~~~~c~~v~v~~v~~~~~~~~   80 (407)
                      ||++|||+|+++|..+|.+||||| |++||+|||||+|++|++|+.||.+|||++||++++++||++||.+|+++.+.. 
T Consensus        86 mt~~Dll~F~~~~~~~I~~irivR-d~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~le~e~Chll~V~~ve~~~s~d-  163 (493)
T KOG0804|consen   86 MTSHDLLRFCASFIKQISDIRIVR-DGMPNRYMVLIKFRDQADADTFYEEFNGKQFNSLEPEVCHLLYVDRVEVTESED-  163 (493)
T ss_pred             ccHHHHHHHHHHHhhhhheeEEee-cCCCceEEEEEEeccchhHHHHHHHcCCCcCCCCCccceeEEEEEEEEEEeccc-
Confidence            899999999999999999999999 999999999999999999999999999999999999999999999999995433 


Q ss_pred             CCcCCCCCCCCCCCCcccccccccccCCCceeeecCCCccchhccccccCCCCCCcccccCCC--CccceeecccCCCcc
Q 015426           81 LEHVQPAPASSTEQPSCPVCLERLDQDTSGILTTICNHSFHCSCISKWTDSSCPVCRYCQQQP--EKSICFVCQTSENLW  158 (407)
Q Consensus        81 ~~~~~~~~~~~~e~~~C~iCle~~~~~~~~~~~~~C~H~F~~~Cl~~w~~~~CP~Cr~~~~~~--~~~~C~~C~~~~~l~  158 (407)
                        .+.+++++++|+||||||||+||++++|++++.|+|+||..|+..|++.+||+||+...|.  +...|..|+..++||
T Consensus       164 --~as~~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~~scpvcR~~q~p~~ve~~~c~~c~~~~~Lw  241 (493)
T KOG0804|consen  164 --GASEPPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWDSSCPVCRYCQSPSVVESSLCLACGCTEDLW  241 (493)
T ss_pred             --CCCCCCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhcccCcChhhhhhcCcchhhhhhhhhhcccccEE
Confidence              3444566789999999999999999999999999999999999999999999999987621  578999999999999


Q ss_pred             cccccCccccccCCccccccccccCCceeEeecCceeEEeccCCcchhhhhhhcccCceeeecccCCCC-CCCCCCCCCC
Q 015426          159 MCVICGFVGCGRYKGGHAIIHWKETEHCYSLELETQRVWDYAGDNYVHRLIQSKTDGKLVELNSHCLHG-KDNCGSCDCV  237 (407)
Q Consensus       159 ~Cl~Cg~~~Cgr~~~~Ha~~H~~~t~H~~~~~l~~~~v~cy~cd~~vhrl~~~~~dgkl~e~~~~~~~~-~~~~~~~~~~  237 (407)
                      +|++||++|||||..+||++||++|+|+|+|+++|+|||||++|+|||||+++++|||+|+....+..+ .+.++.+...
T Consensus       242 icliCg~vgcgrY~eghA~rHweet~H~yalel~tqrVWDYAGDnYVhRl~~~~~dGklve~~~~~~~~~~~~~~~~~~~  321 (493)
T KOG0804|consen  242 ICLICGNVGCGRYKEGHARRHWEETGHCYALELETQRVWDYAGDNYVHRLPQSKTDGKLVESSTEGDDSRKDDCDSLELE  321 (493)
T ss_pred             EEEEccceecccccchhHHHHHHhhcceEEEeecceeeeecccchhhhhccccCCCCceEEeccccccccccCcceEEee
Confidence            999999999999999999999999999999999999999999999999999999999999999888663 2333333333


Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 015426          238 DSGTSDALLSSKVEAIVNEYNELLAAQLENQKIYYETLLQEAKE-ETEKIISEAVKKAIAQKLQKMQAKLDRCVREKKFL  316 (407)
Q Consensus       238 ~~~~~~~~~~~k~~~~~~ey~~lL~~qle~qr~~~E~~l~~l~~-~~~~~l~~~~~~~~~~~l~~l~~~l~~~~~e~~~l  316 (407)
                      .+.+.....+....-....+..+.++||+.||+||+.++.++.. +.+....++..+.++.++++++.+++++.+|++++
T Consensus       322 ~s~ll~sqleSqr~y~e~~~~e~~qsqlen~k~~~e~~~~e~~~l~~~~~~~e~~kk~~e~k~~q~q~k~~k~~kel~~~  401 (493)
T KOG0804|consen  322 YSPLLTSQLESQRKYYEQIMSEYEQSQLENQKQYYELLITEADSLKQESSDLEAEKKIVERKLQQLQTKLKKCQKELKEE  401 (493)
T ss_pred             cchhhhhhhhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333344445557888888888888777766 55556667788889999999999999999999999


Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhHhHHHHhhhccccCCCCcEEeecCCCCCCC
Q 015426          317 DDLNENLLKNQEMWKAKISEIEEREKMALRAKDDKIQDSEAQLRDLMAYLEAEKTLQQLSISNEIKDGTVLPMSVESSTS  396 (407)
Q Consensus       317 ~eln~~l~~~~~~l~~kl~~~~~~~~~~~~~~~~~i~~Leeq~~dLm~~l~~~~~~~~~~~~~ei~~G~v~~~~~~~~~~  396 (407)
                      +|+|+.|.+|+..|+.++++++++.+.++..++++|+||+||+|||||||++|+||+  ++.++|++|||++.+.+++++
T Consensus       402 ~E~n~~l~knq~vw~~kl~~~~e~~~~~~~s~d~~I~dLqEQlrDlmf~le~qqklk--~dt~eIqegtI~~~~~s~~~~  479 (493)
T KOG0804|consen  402 REENKKLIKNQDVWRGKLKELEEREKEALGSKDEKITDLQEQLRDLMFFLEAQQKLK--SDTDEIQEGTILITQISPSSS  479 (493)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHheehhhhhhhh--cchhhhcCceeeccCCCCCcc
Confidence            999999999999999999999999999999999999999999999999999999998  445599999998775554443


Q ss_pred             C
Q 015426          397 T  397 (407)
Q Consensus       397 ~  397 (407)
                      +
T Consensus       480 ~  480 (493)
T KOG0804|consen  480 S  480 (493)
T ss_pred             c
Confidence            3

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []	Back alignment and domain information

>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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

>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

>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

>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger	Back alignment and domain information

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

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

>cd02669 Peptidase_C19M A subfamily of Peptidase C19	Back alignment and domain information

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

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

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

>KOG1873 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

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

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

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

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

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

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

>KOG0823 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

>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

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

>KOG0320 consensus Predicted 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

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

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

>smart00184 RING Ring finger	Back alignment and domain information

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

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

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

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

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

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

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

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

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

>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis	Back alignment and domain information

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

>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]	Back alignment and domain information

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

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

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

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

>KOG0827 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

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

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

>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope	Back alignment and domain information

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

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

>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

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

>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope	Back alignment and domain information

>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]	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

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

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

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

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

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

>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]	Back alignment and domain information

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

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]	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

>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function	Back alignment and domain information

>PF10212 TTKRSYEDQ: Predicted coiled-coil domain-containing protein; InterPro: IPR019348 This entry represents a C-terminal 500 residue region, which contains a conserved TTKRSYEDQ motif	Back alignment and domain information

>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs	Back alignment and domain information

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

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

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

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

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

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

>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []	Back alignment and domain information

>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []	Back alignment and domain information

>PF14259 RRM_6: RNA recognition motif (a	Back alignment and domain information

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

>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]	Back alignment and domain information

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

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

>KOG0161 consensus Myosin class II heavy chain [Cytoskeleton]	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

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

>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation	Back alignment and domain information

>PRK09039 hypothetical protein; Validated	Back alignment and domain information

>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]	Back alignment and domain information

>COG5185 HEC1 Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]	Back alignment and domain information

>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]	Back alignment and domain information

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

>PF09731 Mitofilin: Mitochondrial inner membrane protein; InterPro: IPR019133 Mitofilin controls mitochondrial cristae morphology	Back alignment and domain information

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

>PF07926 TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro: IPR012929 This domain is found in a number of proteins, including TPR protein (P12270 from SWISSPROT) and yeast myosin-like proteins 1 (MLP1, Q02455 from SWISSPROT) and 2 (MLP2, P40457 from SWISSPROT)	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

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

>PF00076 RRM_1: RNA recognition motif	Back alignment and domain information

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability	Back alignment and domain information

>KOG0982 consensus Centrosomal protein Nuf [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]	Back alignment and domain information

>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]	Back alignment and domain information

>KOG3161 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

>PRK09039 hypothetical protein; Validated	Back alignment and domain information

>PRK12704 phosphodiesterase; Provisional	Back alignment and domain information

>PF09304 Cortex-I_coil: Cortexillin I, coiled coil; InterPro: IPR015383 This domain is predominantly found in the actin-bundling protein cortexillin I from Dictyostelium discoideum (Slime mold)	Back alignment and domain information

>KOG0995 consensus Centromere-associated protein HEC1 [Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>PF07888 CALCOCO1: Calcium binding and coiled-coil domain (CALCOCO1) like; InterPro: IPR012852 Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein expressed by Mus musculus (CoCoA, Q8CGU1 from SWISSPROT)	Back alignment and domain information

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [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

>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]	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

>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells	Back alignment and domain information

>PRK10361 DNA recombination protein RmuC; Provisional	Back alignment and domain information

>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes	Back alignment and domain information

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

>KOG3759 consensus Uncharacterized RUN domain protein [Signal transduction mechanisms]	Back alignment and domain information

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

>KOG0161 consensus Myosin class II heavy chain [Cytoskeleton]	Back alignment and domain information

>PF15397 DUF4618: Domain of unknown function (DUF4618)	Back alignment and domain information

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed	Back alignment and domain information

>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF	Back alignment and domain information

>PRK10884 SH3 domain-containing protein; Provisional	Back alignment and domain information

>PF10211 Ax_dynein_light: Axonemal dynein light chain; InterPro: IPR019347 Axonemal dynein light chain proteins play a dynamic role in flagellar and cilial motility	Back alignment and domain information

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

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

>COG2433 Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>smart00360 RRM RNA recognition motif	Back alignment and domain information

>PF15070 GOLGA2L5: Putative golgin subfamily A member 2-like protein 5	Back alignment and domain information

>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function	Back alignment and domain information

>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs	Back alignment and domain information

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

>PHA02562 46 endonuclease subunit; Provisional	Back alignment and domain information

>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes	Back alignment and domain information

>KOG4005 consensus Transcription factor XBP-1 [Transcription]	Back alignment and domain information

>KOG0996 consensus Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]	Back alignment and domain information

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

>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]	Back alignment and domain information

>PF07798 DUF1640: Protein of unknown function (DUF1640); InterPro: IPR024461 This family consists of uncharacterised proteins	Back alignment and domain information

>KOG0996 consensus Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

>PF09731 Mitofilin: Mitochondrial inner membrane protein; InterPro: IPR019133 Mitofilin controls mitochondrial cristae morphology	Back alignment and domain information

>smart00362 RRM_2 RNA recognition motif	Back alignment and domain information

>PF14662 CCDC155: Coiled-coil region of CCDC155	Back alignment and domain information

>PF04912 Dynamitin: Dynamitin ; InterPro: IPR006996 Dynamitin is a subunit of the microtubule-dependent motor complex, it is also implicated in cell adhesion by binding to macrophage-enriched myristoylated alanine-rice C kinase substrate (MacMARCKS) []	Back alignment and domain information

>COG2433 Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

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

>PF12128 DUF3584: Protein of unknown function (DUF3584); InterPro: IPR021979 This family consist of uncharacterised bacterial proteins	Back alignment and domain information

>smart00787 Spc7 Spc7 kinetochore protein	Back alignment and domain information

>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association []	Back alignment and domain information

>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells	Back alignment and domain information

>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells	Back alignment and domain information

>PRK00106 hypothetical protein; Provisional	Back alignment and domain information

>COG1196 Smc Chromosome segregation ATPases [Cell division and chromosome partitioning]	Back alignment and domain information

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]	Back alignment and domain information

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

>KOG1853 consensus LIS1-interacting protein NUDE [Cytoskeleton]	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		407
2uzg_A		97	Zf-Ubp Domain Of Vdu1 Length = 97		3e-05
2ect_A		78	Solution Structure Of The Zinc Finger, C3hc4 Type (		5e-04

>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring Finger) Domain Of Ring Finger Protein 126 Length = 78

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		407
2i50_A		126	Ubiquitin carboxyl-terminal hydrolase 16; alpha/be	2e-31
3c5k_A		109	HD6, histone deacetylase 6; HDAC6, zinc finger, ac	8e-28
2uzg_A		97	Ubiquitin carboxyl-terminal hydrolase 33; UBL conj	3e-25
2g45_A		129	Ubiquitin carboxyl-terminal hydrolase 5; zinc fing	4e-23
2ida_A		102	Hypothetical protein; zinc binding protein, struct	7e-21
3ihp_A		854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	2e-09
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-09
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	2e-09
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	3e-09
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	3e-09
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	4e-09
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	6e-09
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	8e-09
2ect_A		78	Ring finger protein 126; metal binding protein, st	8e-09
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	9e-09
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	1e-08
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	1e-08
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	2e-08
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	2e-08
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	3e-08
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	5e-08
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	7e-08
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-07
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	5e-07
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	7e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	3e-06
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	4e-06
1z6u_A		150	NP95-like ring finger protein isoform B; structura	5e-06
3mhs_A		476	Ubiquitin carboxyl-terminal hydrolase 8; multi-pro	6e-06
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	8e-06
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	1e-05
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-05
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	3e-05
2dfs_A		1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-05
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	3e-05
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	4e-05
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	6e-05
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	6e-05
1i84_S		1184	Smooth muscle myosin heavy chain; muscle protein,	9e-05
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	1e-04
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	1e-04
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	1e-04
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	2e-04
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	2e-04
4epo_C		149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	2e-04
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	2e-04
3lvg_D		190	LCB, clathrin light chain B; SELF assembly, coated	3e-04
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	3e-04
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	3e-04
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	4e-04
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	4e-04
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	6e-04
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	7e-04

>2i50_A Ubiquitin carboxyl-terminal hydrolase 16; alpha/beta zinc-finger, ring-finger, ZNF-UBP, metalloprotein, ubiquitin-binding protein, USP; NMR {Homo sapiens} Length = 126	Back alignment and structure

 Score =  115 bits (289), Expect = 2e-31
 Identities = 28/121 (23%), Positives = 49/121 (40%), Gaps = 11/121 (9%)

Query: 110 GILTTICNHSFHCSCISKW----TDSSCPVCRYCQQQ--PEKSICFVCQTSENLWMCVIC 163
           G    +C H               +    +C+ C+     +       +   ++W+C+ C
Sbjct: 1   GSHMPVCRHIRKGLEQGNLKKALVNVEWNICQDCKTDNKVKDKAEEETEEKPSVWLCLKC 60

Query: 164 GFVGCGRY-KGGHAIIHW---KETEHCYSLELETQRVWDYAGDNYVHRLIQSKTDGKLVE 219
           G  GCGR  +  HA+ H+   +   HC  L L+   VW Y  DN V     ++  G++V+
Sbjct: 61  GHQGCGRNSQEQHALKHYLTPRSEPHCLVLSLDNWSVWCYVCDNEVQYCSSNQ-LGQVVD 119

Query: 220 L 220
            
Sbjct: 120 Y 120

PyMOL of 2i50

>3c5k_A HD6, histone deacetylase 6; HDAC6, zinc finger, actin-binding, chromatin regulator, cytoplasm, hydrolase, metal-binding, nucleus, phosphoprotein; 1.55A {Homo sapiens} PDB: 3gv4_A 3phd_A Length = 109	Back alignment and structure

>2g45_A Ubiquitin carboxyl-terminal hydrolase 5; zinc finger, hydrolase; 1.99A {Homo sapiens} SCOP: g.44.1.5 PDB: 2g43_A 2l80_A Length = 129	Back alignment and structure

>2ida_A Hypothetical protein; zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Rhodopseudomonas palustris} SCOP: g.44.1.5 Length = 102	Back alignment and structure

>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {Homo sapiens} Length = 854	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

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

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

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens} Length = 91	Back alignment and structure

>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

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1 Length = 55	Back alignment and structure

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

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 78	Back alignment and structure

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1 Length = 68	Back alignment and structure

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

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

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 75	Back alignment and structure

>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

>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

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens} Length = 69	Back alignment and structure

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

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus} Length = 133	Back alignment and structure

>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

>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

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

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

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens} Length = 124	Back alignment and structure

>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

>3mhs_A Ubiquitin carboxyl-terminal hydrolase 8; multi-protein complex, hydrolase-transcription regulator-Pro binding complex, acetylation, cytoplasm; 1.89A {Saccharomyces cerevisiae} PDB: 3mhh_A 3m99_A Length = 476	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

>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

>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

>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

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080	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

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

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus} Length = 117	Back alignment and structure

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A Length = 106	Back alignment and structure

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184	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

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1 Length = 114	Back alignment and structure

>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

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

>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

>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

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190	Back alignment and structure

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

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

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 112	Back alignment and structure

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

>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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		407
2g45_A		129	Ubiquitin carboxyl-terminal hydrolase 5; zinc fing	99.73
2i50_A		126	Ubiquitin carboxyl-terminal hydrolase 16; alpha/be	99.7
3c5k_A		109	HD6, histone deacetylase 6; HDAC6, zinc finger, ac	99.65
2uzg_A		97	Ubiquitin carboxyl-terminal hydrolase 33; UBL conj	99.58
2ida_A		102	Hypothetical protein; zinc binding protein, struct	99.56
3ihp_A		854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	99.52
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	98.99
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.98
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	98.98
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	98.97
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	98.95
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	98.94
4ayc_A		138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	98.94
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	98.91
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	98.91
2ect_A		78	Ring finger protein 126; metal binding protein, st	98.91
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	98.91
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	98.91
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	98.91
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	98.9
3mhs_A		476	Ubiquitin carboxyl-terminal hydrolase 8; multi-pro	98.89
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	98.89
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	98.89
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	98.89
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	98.88
1t1h_A		78	Gspef-atpub14, armadillo repeat containing protein	98.88
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	98.88
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	98.87
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	98.87
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	98.86
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	98.85
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	98.84
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	98.83
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	98.83
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	98.82
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	98.82
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	98.81
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.81
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	98.8
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	98.79
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	98.78
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	98.77
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	98.77
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	98.73
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	98.73
1wgm_A		98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.73
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	98.72
2kr4_A		85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.69
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	98.68
2kre_A		100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.67
4ic3_A		74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.67
1z6u_A		150	NP95-like ring finger protein isoform B; structura	98.66
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	98.65
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	98.64
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	98.61
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.57
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.55
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	98.51
2yu4_A		94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.49
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	98.48
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	98.46
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.39
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.37
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.34
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	98.34
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	98.32
2f42_A		179	STIP1 homology and U-box containing protein 1; cha	98.32
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.28
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.23
3t6p_A		345	Baculoviral IAP repeat-containing protein 2; ring,	98.23
2ea5_A		68	Cell growth regulator with ring finger domain prot	98.17
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.17
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	97.96
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	97.88
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	97.73
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	97.58
2bay_A		61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	97.47
3vk6_A		101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.3
2jun_A		101	Midline-1; B-BOX, TRIM, ring finger, alternative s	96.53
2dfs_A		1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	94.6
3nw0_A		238	Non-structural maintenance of chromosomes element	94.58
3ghg_A		562	Fibrinogen alpha chain; triple-stranded coiled coi	93.36
3hnw_A		138	Uncharacterized protein; coiled-coil, structural g	92.99
3tnu_B		129	Keratin, type II cytoskeletal 5; coiled-coil, stru	91.94
3ol1_A		119	Vimentin; structural genomics, PSI-2, protein stru	91.75
3tnu_A		131	Keratin, type I cytoskeletal 14; coiled-coil, stru	91.39
2v71_A		189	Nuclear distribution protein NUDE-like 1; developm	91.13
2dfs_A		1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	89.99
3mq9_A		471	Bone marrow stromal antigen 2 fused to maltose-BI	89.85
2dgw_A		91	Probable RNA-binding protein 19; RRM domain, struc	89.2
3na7_A		256	HP0958; flagellar biogenesis, flagellum export, C4	88.71
3ghg_A		562	Fibrinogen alpha chain; triple-stranded coiled coi	88.33
3na7_A		256	HP0958; flagellar biogenesis, flagellum export, C4	88.11
1gs9_A		165	Apolipoprotein E, APOE4; lipid transport, heparin-	87.33
3oja_B		597	Anopheles plasmodium-responsive leucine-rich REPE	87.23
3mq9_A		471	Bone marrow stromal antigen 2 fused to maltose-BI	86.24
3r2p_A		185	Apolipoprotein A-I; amphipathic alpha-helix, major	85.9
1nfn_A		191	Apolipoprotein E3; lipid transport, heparin-bindin	85.84
1deq_A		390	Fibrinogen (alpha chain); coiled-coil, blood clott	85.75
3oja_B		597	Anopheles plasmodium-responsive leucine-rich REPE	85.36
3s4r_A		93	Vimentin; alpha-helix, cytoskeleton, intermediate	84.99
3vkg_A		3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	83.98
2lri_C		66	Autoimmune regulator; Zn binding protein domain, a	83.3
2fy1_A		116	RNA-binding motif protein, Y chromosome, family 1	83.22
2ko5_A		99	Ring finger protein Z; lassa fever virus-Z, negati	83.09
2lem_A		216	Apolipoprotein A-I; lipid transport; NMR {Mus musc	83.04
2ysm_A		111	Myeloid/lymphoid or mixed-lineage leukemia protein	83.03
2a01_A		243	Apolipoprotein A-I; four-helix bundle, lipid trans	83.0
2dgv_A		92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	82.75
2dhg_A		104	TRNA selenocysteine associated protein (SECP43); R	82.57
3bs9_A		87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	82.32
2dng_A		103	Eukaryotic translation initiation factor 4H; RRM d	81.83
3bas_A		89	Myosin heavy chain, striated muscle/general contro	81.79
2d9p_A		103	Polyadenylate-binding protein 3; RRM domain, struc	81.51
2do4_A		100	Squamous cell carcinoma antigen recognized by T- c	81.31
2dnh_A		105	Bruno-like 5, RNA binding protein; RRM domain, RBD	80.94
2v66_B		111	Nuclear distribution protein NUDE-like 1; structur	80.87
2cq3_A		103	RNA-binding protein 9; RRM domain, structural geno	80.86
2ywk_A		95	Putative RNA-binding protein 11; RRM-domain, struc	80.8
1m1j_A		491	Fibrinogen alpha subunit; coiled coils, disulfide	80.51
2cqi_A		103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	80.3

>2g45_A Ubiquitin carboxyl-terminal hydrolase 5; zinc finger, hydrolase; 1.99A {Homo sapiens} SCOP: g.44.1.5 PDB: 2g43_A 2l80_A	Back alignment and structure

Probab=99.73  E-value=4.1e-19  Score=150.70  Aligned_cols=84  Identities=29%  Similarity=0.518  Sum_probs=67.9

Q ss_pred             hccccccCCCCCCcccccC----------CCCccceeecccCCCcccccccCccccccCC------ccccccccccCCce
Q 015426          123 SCISKWTDSSCPVCRYCQQ----------QPEKSICFVCQTSENLWMCVICGFVGCGRYK------GGHAIIHWKETEHC  186 (407)
Q Consensus       123 ~Cl~~w~~~~CP~Cr~~~~----------~~~~~~C~~C~~~~~l~~Cl~Cg~~~Cgr~~------~~Ha~~H~~~t~H~  186 (407)
                      .|+..|.+..||+|++...          ++....|..|+...++|+||+||++||||+.      ++||..||.+++|+
T Consensus         2 ~~~~~W~~e~~~~C~h~~~l~q~~~~~~~~~~~~~C~~C~~~~~LwlCL~CG~vgCgr~~~~g~g~~~HA~~H~~~t~H~   81 (129)
T 2g45_A            2 QEVQAWDGEVRQVSKHAFSLKQLDNPARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYP   81 (129)
T ss_dssp             ---------CCEECTTTTTCCCCSSCCCCCCCBCCCSSSSCCSSEEEETTTCCEEECCBCTTSCBCCSHHHHHHHHHCCC
T ss_pred             hHHHhhcCCCCCCCCCcCcccccccccccCCCCCcCccccCcCceEEeccCCccccCccccCCCCcCcHHHHHhhhcCCC
Confidence            6889999888999988742          2345689999999999999999999999997      89999999999999


Q ss_pred             eEeecCc-----eeEEeccCCcchh
Q 015426          187 YSLELET-----QRVWDYAGDNYVH  206 (407)
Q Consensus       187 ~~~~l~~-----~~v~cy~cd~~vh  206 (407)
                      +++.+.+     ++||||.||+||+
T Consensus        82 l~v~l~t~~~~~~~vwcY~cd~~V~  106 (129)
T 2g45_A           82 LAVKLGTITPDGADVYSYDEDDMVL  106 (129)
T ss_dssp             EEEETTCCBTTBCCEEETTTTEEEE
T ss_pred             EEEECCCCCCCCCeEEECCCCCEeE
Confidence            9999998     6999999999995

PyMOL of 2g45

>2i50_A Ubiquitin carboxyl-terminal hydrolase 16; alpha/beta zinc-finger, ring-finger, ZNF-UBP, metalloprotein, ubiquitin-binding protein, USP; NMR {Homo sapiens}	Back alignment and structure

>3c5k_A HD6, histone deacetylase 6; HDAC6, zinc finger, actin-binding, chromatin regulator, cytoplasm, hydrolase, metal-binding, nucleus, phosphoprotein; 1.55A {Homo sapiens} PDB: 3gv4_A 3phd_A	Back alignment and structure

>2ida_A Hypothetical protein; zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Rhodopseudomonas palustris} SCOP: g.44.1.5	Back alignment and structure

>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {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

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

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

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

>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

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

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; 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

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

>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

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

>3mhs_A Ubiquitin carboxyl-terminal hydrolase 8; multi-protein complex, hydrolase-transcription regulator-Pro binding complex, acetylation, cytoplasm; 1.89A {Saccharomyces cerevisiae} PDB: 3mhh_A 4fjc_A 4fk5_A 4fip_A 3m99_A	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

>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

>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

>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

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

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

>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

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

>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

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

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

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens}	Back alignment and structure

>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

>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

>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

>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

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

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

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

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

>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

>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

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

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

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A	Back alignment and structure

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B	Back alignment and structure

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

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

>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

>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

>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

>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

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

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus}	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

>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G*	Back alignment and structure

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}	Back alignment and structure

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}	Back alignment and structure

>3tnu_A Keratin, type I cytoskeletal 14; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}	Back alignment and structure

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus}	Back alignment and structure

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus}	Back alignment and structure

>3mq9_A Bone marrow stromal antigen 2 fused to maltose-BI periplasmic protein; HIV, antiviral protein; 2.80A {Escherichia coli}	Back alignment and structure

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}	Back alignment and structure

>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G*	Back alignment and structure

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}	Back alignment and structure

>1gs9_A Apolipoprotein E, APOE4; lipid transport, heparin-binding, plasma, lipid binding protein; 1.7A {Homo sapiens} SCOP: a.24.1.1 PDB: 1or3_A 1or2_A 1le4_A 1bz4_A 1lpe_A 1le2_A	Back alignment and structure

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}	Back alignment and structure

>3mq9_A Bone marrow stromal antigen 2 fused to maltose-BI periplasmic protein; HIV, antiviral protein; 2.80A {Escherichia coli}	Back alignment and structure

>3r2p_A Apolipoprotein A-I; amphipathic alpha-helix, major protein of high density lipop (HDL), lipid binding, plasma, lipid transport; 2.20A {Homo sapiens} PDB: 1gw3_A 1gw4_A	Back alignment and structure

>1nfn_A Apolipoprotein E3; lipid transport, heparin-binding, plasma protein, HDL, VLDL; 1.80A {Homo sapiens} SCOP: a.24.1.1 PDB: 1h7i_A 1ea8_A 1b68_A 1nfo_A 2kc3_A 1ya9_A	Back alignment and structure

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}	Back alignment and structure

>3s4r_A Vimentin; alpha-helix, cytoskeleton, intermediate filament, structural; 2.45A {Homo sapiens} PDB: 3ssu_A	Back alignment and structure

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*	Back alignment and structure

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

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}	Back alignment and structure

>2lem_A Apolipoprotein A-I; lipid transport; NMR {Mus musculus}	Back alignment and structure

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}	Back alignment and structure

>2a01_A Apolipoprotein A-I; four-helix bundle, lipid transport; HET: AC9; 2.40A {Homo sapiens} PDB: 3k2s_A* 1av1_A 3j00_0*	Back alignment and structure

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A	Back alignment and structure

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}	Back alignment and structure

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}	Back alignment and structure

>3bas_A Myosin heavy chain, striated muscle/general control protein GCN4 chimera; alpha-helical coiled coil, disorder, salt links; 2.30A {Argopecten irradians} SCOP: h.1.26.1 PDB: 1nkn_A 3bat_A	Back alignment and structure

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A	Back alignment and structure

>2v66_B Nuclear distribution protein NUDE-like 1; structural protein, developmental protein, structural protei phosphorylation, transport, microtubule; 2.10A {Homo sapiens}	Back alignment and structure

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}	Back alignment and structure

>1m1j_A Fibrinogen alpha subunit; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: h.1.8.1 PDB: 1ei3_A	Back alignment and structure

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	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		407
d2uzga1		95	g.44.1.5 (A:36-130) Ubiquitin carboxyl-terminal hy	2e-20
d2g45a1		113	g.44.1.5 (A:173-285) Ubiquitin carboxyl-terminal h	4e-18
d2idaa1		102	g.44.1.5 (A:1-102) Hypothetical protein RPA1320 {R	8e-18
d1iyma_		55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	1e-09
d1chca_		68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-07
d1ur6b_		52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	5e-07
d1bora_		56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	5e-07
d1rmda2		86	g.44.1.1 (A:1-86) V(D)J recombination activating p	9e-07
d1fbva4		79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-06
d1g25a_		65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	1e-05
d1jm7b_		97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	2e-05
d3dplr1		88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	2e-05
d1jm7a_		103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	5e-05
d1vyxa_		60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	2e-04

>d2uzga1 g.44.1.5 (A:36-130) Ubiquitin carboxyl-terminal hydrolase 33, UBP33 {Human (Homo sapiens) [TaxId: 9606]} Length = 95	Back information, alignment and structure


class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Zf-UBP
domain: Ubiquitin carboxyl-terminal hydrolase 33, UBP33
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 83.5 bits (206), Expect = 2e-20
 Identities = 28/81 (34%), Positives = 39/81 (48%), Gaps = 3/81 (3%)

Query: 129 TDSSCPVCRYCQQQPEKSICFVCQ-TSENLWMCV--ICGFVGCGRYKGGHAIIHWKETEH 185
            DS   + +    Q     C  C+    NLW C+   C +VGCG  +  H+ IH +ET+H
Sbjct: 7   LDSVGEITKEDLIQKSLGTCQDCKVQGPNLWACLENRCSYVGCGESQVDHSTIHSQETKH 66

Query: 186 CYSLELETQRVWDYAGDNYVH 206
             ++ L T RVW YA    V 
Sbjct: 67  YLTVNLTTLRVWCYACSKEVF 87

PyMOL of d2uzga1

>d2g45a1 g.44.1.5 (A:173-285) Ubiquitin carboxyl-terminal hydrolase 5, UBP5 {Human (Homo sapiens) [TaxId: 9606]} Length = 113	Back information, alignment and structure

>d2idaa1 g.44.1.5 (A:1-102) Hypothetical protein RPA1320 {Rhodopseudomonas palustris [TaxId: 1076]} Length = 102	Back information, alignment and structure

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

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

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52	Back information, alignment and structure

>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

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

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

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88	Back information, alignment and structure

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

>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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		407
d2g45a1		113	Ubiquitin carboxyl-terminal hydrolase 5, UBP5 {Hum	99.57
d2uzga1		95	Ubiquitin carboxyl-terminal hydrolase 33, UBP33 {H	99.56
d2idaa1		102	Hypothetical protein RPA1320 {Rhodopseudomonas pal	99.44
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.15
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	99.06
d1bora_		56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.03
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	98.92
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.92
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	98.87
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	98.87
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	98.86
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	98.86
d2c2la2		80	STIP1 homology and U box-containing protein 1, STU	98.73
d1t1ha_		78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.7
d2baya1		56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	98.67
d3dplr1		88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	98.66
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	98.57
d1vyxa_		60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.44
d1wgma_		98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.35
d1wima_		94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	97.63
d1gs9a_		144	Apolipoprotein E {Human (Homo sapiens), E4 [TaxId:	88.23
d1cvja1		80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	86.72
d1p1ta_		104	Cleavage stimulation factor, 64 kda subunit {Human	84.75
d1fxla1		82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	84.58
d1fxla2		85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	82.82
d1no8a_		78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	82.64
d1we9a_		64	PHD finger protein At5g26210 {Thale cress (Arabido	82.36
d2cqca1		83	Arginine/serine-rich splicing factor 10 {Human (Ho	82.27
d2cqia1		90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	81.87
d2cqpa1		86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	81.85
d2ghpa2		75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	81.07
d2adca1		109	Polypyrimidine tract-binding protein {Human (Homo	80.1
d1b7fa2		85	Sex-lethal protein {Drosophila melanogaster [TaxId	80.05

>d2g45a1 g.44.1.5 (A:173-285) Ubiquitin carboxyl-terminal hydrolase 5, UBP5 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Zf-UBP
domain: Ubiquitin carboxyl-terminal hydrolase 5, UBP5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=2.1e-16  Score=128.72  Aligned_cols=65  Identities=34%  Similarity=0.601  Sum_probs=59.5

Q ss_pred             CCCccceeecccCCCcccccccCccccccCC------ccccccccccCCceeEeecCc-----eeEEeccCCcchh
Q 015426          142 QPEKSICFVCQTSENLWMCVICGFVGCGRYK------GGHAIIHWKETEHCYSLELET-----QRVWDYAGDNYVH  206 (407)
Q Consensus       142 ~~~~~~C~~C~~~~~l~~Cl~Cg~~~Cgr~~------~~Ha~~H~~~t~H~~~~~l~~-----~~v~cy~cd~~vh  206 (407)
                      ++....|..|+...++|+||+||++||||+.      ++||..||.+++|++++.+.+     .++|||.||+||.
T Consensus        21 ~p~~~~C~~C~~~~~lWlCL~CG~vgCgR~~~~~~~~~~HA~~H~~~t~H~l~v~l~t~~~~~~~vwCY~cd~~V~   96 (113)
T d2g45a1          21 PPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLGTITPDGADVYSYDEDDMVL   96 (113)
T ss_dssp             CCCBCCCSSSSCCSSEEEETTTCCEEECCBCTTSCBCCSHHHHHHHHHCCCEEEETTCCBTTBCCEEETTTTEEEE
T ss_pred             CCCCCcccCCCCcCCEEEEecCCCCccCcccccCCCCChHHHHHHHhcCCCEEEEecCCCCCCceEEEecCCCEEE
Confidence            4667889999999999999999999999985      889999999999999999865     5799999999985

PyMOL of d2g45a1

>d2uzga1 g.44.1.5 (A:36-130) Ubiquitin carboxyl-terminal hydrolase 33, UBP33 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2idaa1 g.44.1.5 (A:1-102) Hypothetical protein RPA1320 {Rhodopseudomonas palustris [TaxId: 1076]}	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

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

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {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

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

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

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

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

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

>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

>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

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

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

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

>d1gs9a_ a.24.1.1 (A:) Apolipoprotein E {Human (Homo sapiens), E4 [TaxId: 9606]}	Back information, alignment and structure

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

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

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure