Citrus Sinensis ID: 039128

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----

MEDQTVLTVKSNAEPEKISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRRPYNHFPSICVMLHRLLLKMYPIAYKMREIEILEDERRYDFFSPQLDNHACGPLVDNECHHLNDSMQFSRIFCGSSSKTGSHENMEQLESVSVAMNNGTSEQSSIEGITVAGKKLPPNELNHNCKQISIVDVLCTACKQLLIHPVVLNCGHVYCETCIITPTVQQLKCEVCQCLNPNGFPKVCLELDQFLEEQFSKEYALRRDVILNHEFATMCSMGAGKSGFISSSGAKGEHSSWLADAHSKVHVGVGCDSCGTGQFCLALKLYLTITWMLLYAAYRLLDRDEDKICHPSFVDFSKRFEDDEGMAGKSSRFDSLIVETQAMHGGEHVSQRLFAVQELAR

cccccccccccccccccccccccccccHHcccccccccccHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHcHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHccccEEEccccHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHEEEccccccccHHHHHHHHHHHHHc

cccccEccccccccHHHcccHccccHHHHHHccccEcccccHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHccHHHHHHHccccEEcccccHHHHHHHHccccccccccccccccccccccEEHHHHHHHHHHcHHHHHHHHHHHHHcccccccccccccccccccccccccccEEcccccccEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccEccccccccccccccccccccEEEEEEHHccccHHHHHHHHHHHHHHc

medqtvltvksnaepekishsfrccicldllykpivlscghiscfwcvhrsmnglreshcpicrrpynhfpSICVMLHRLLLKMYPIAYKMREIEilederrydffspqldnhacgplvdnechhlndsmqfsrifcgsssktgshenmeQLESVSVAMnngtseqssiegitvagkklppnelnhnckqiSIVDVLCTACKqllihpvvlncghvycetciitptvqQLKCEvcqclnpngfpkVCLELDQFLEEQFSKEYALRRDVILNHEFatmcsmgagksgfisssgakgehsswladahskvhvgvgcdscgtgqFCLALKLYLTITWMLLYAAYRLLdrdedkichpsfvdfskrfeddegmagkssrfdSLIVETQamhggehvSQRLFAVQELAR

medqtvltvksnaepekishsFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRRPYNHFPSICVMLHRLLLKMYPIAYKMREIEILEDERRYDFFSPQLDNHACGPLVDNECHHLNDSMQFSRIFCGSSSKTGSHENMEQLESVSVAMNNGTSEQSSIEGITVAGKKLPPNELNHNCKQISIVDVLCTACKQLLIHPVVLNCGHVYCETCIITPTVQQLKCEVCQCLNPNGFPKVCLELDQFLEEQFSKEYALRRDVILNHEFATMCSMGAGKSGFISSSGAKGEHSSWLADAHSKVHVGVGCDSCGTGQFCLALKLYLTITWMLLYAAYRLLDRDEDKICHPSFVDFSKRFEDDEGMAGKSSRFDSLIVETQamhggehvsQRLFAVQELAR

*****************ISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRRPYNHFPSICVMLHRLLLKMYPIAYKMREIEILEDERRYDFFSPQLDNHACGPLVDNECHHLNDSMQFSRIFC*********************************************ELNHNCKQISIVDVLCTACKQLLIHPVVLNCGHVYCETCIITPTVQQLKCEVCQCLNPNGFPKVCLELDQFLEEQFSKEYALRRDVILNHEFATMCSMGAGKSGFI**********SWLADAHSKVHVGVGCDSCGTGQFCLALKLYLTITWMLLYAAYRLLDRDEDKICHPSFVDFSK*******************************************

*********************FRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRRPYNHFPSICVMLHRLLLKMYP********************SPQLDNHACGPLVDNECHHLNDSMQFSRIFCGSSSKTGSHENMEQLESVSVAMNNGTSE***********************KQISIVDVLCTACKQLLIHPVVLNCGHVYCETCIITPTVQQLK************PKVCLELDQFLEEQF*********************************************AHSKVHVGVGCDSCGTGQFCLALKLYLTITWMLLYAAYRLLDRDEDKICHPSFVDFSKRFE*********SRFDSLIVETQAMHGGEHVSQRLFAVQELA*

***********NAEPEKISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRRPYNHFPSICVMLHRLLLKMYPIAYKMREIEILEDERRYDFFSPQLDNHACGPLVDNECHHLNDSMQFSRIFCGSSSKTGSHENMEQLESVSVAMNNGTSEQSSIEGITVAGKKLPPNELNHNCKQISIVDVLCTACKQLLIHPVVLNCGHVYCETCIITPTVQQLKCEVCQCLNPNGFPKVCLELDQFLEEQFSKEYALRRDVILNHEFATMCSMGAGKSGF************WLADAHSKVHVGVGCDSCGTGQFCLALKLYLTITWMLLYAAYRLLDRDEDKICHPSFVDFSKRFEDDEGMAGKSSRFDSLIVETQAMHGGEHVSQRLFAVQELAR

*****VLT**SNAEPEKISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRRPYNHFPSICVMLHRLLLKMYPIAYKMREIEILEDERRYDFFSPQLDNHACGPLVDNECHHLN*SMQ**********************************************************QISIVDVLCTACKQLLIHPVVLNCGHVYCETCIITPTVQQLKCEVCQCLNPNGFPKVCLELDQFLEEQFSKEYALRRDVILNH*************************SSWLADAHSKVHVGVGCDSCGTGQFCLALKLYLTITWMLLYAAYRLLDRDEDKICHPSFVDFSKR********GKSSRFDSLIVETQAMHGGEHVSQRLFAVQELAR

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		404	2.2.26 [Sep-21-2011]
Q8LBL5		410	E3 ubiquitin-protein liga	yes	no	0.737	0.726	0.422	3e-63
Q5PQN2		450	Bifunctional apoptosis re	yes	no	0.195	0.175	0.317	3e-06
Q9NZS9		450	Bifunctional apoptosis re	yes	no	0.190	0.171	0.307	4e-06
Q8R079		450	Bifunctional apoptosis re	yes	no	0.195	0.175	0.305	7e-06
Q5D7I6		551	Tripartite motif-containi	N/A	no	0.160	0.117	0.356	7e-05
Q9P3U8		468	Uncharacterized RING fing	yes	no	0.155	0.134	0.328	0.0001
B8B5U8		321	Probable E3 ubiquitin-pro	N/A	no	0.121	0.152	0.396	0.0002
Q7XI73		321	Probable E3 ubiquitin-pro	no	no	0.121	0.152	0.396	0.0002
Q1L5Z9		754	LON peptidase N-terminal	no	no	0.202	0.108	0.270	0.0005
Q5BN31		494	Tripartite motif-containi	N/A	no	0.163	0.133	0.358	0.0006

>sp\|Q8LBL5\|PRT1_ARATH E3 ubiquitin-protein ligase PRT1 OS=Arabidopsis thaliana GN=PRT1 PE=2 SV=2	Back alignment and function desciption

 Score =  243 bits (619), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 137/324 (42%), Positives = 186/324 (57%), Gaps = 26/324 (8%)

Query: 7   LTVKSN-AEPEKISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRR 65
           +T+K++ ++ E+I   F CC+CL+LLYKPIVLSCGH+SCFWCVH+SMNG RESHCPICR 
Sbjct: 8   ITMKNDESQEEEIPDQFLCCVCLELLYKPIVLSCGHLSCFWCVHKSMNGFRESHCPICRD 67

Query: 66  PYNHFPSICVMLHRLLLKMYPIAYKMREIEILEDERRYDFFSPQLDNHACGPLVDNECHH 125
           PY HFPS+C  L+ LL KMYP+A+K RE ++L++E+  + FSPQ+D      LV +    
Sbjct: 68  PYVHFPSVCQKLYFLLKKMYPLAHKKREEQVLKEEQERECFSPQID------LVLDLSVC 121

Query: 126 LNDSMQFSRIFCGSSSKTGSHENMEQLESVSVAMNNGTSEQSSIEGITVAGKKLPPNELN 185
             DS+  S           ++          +       E +  + + V   +L  +  N
Sbjct: 122 SGDSLNVSDKQKVEECSNAANLLSSSSSRGDIPCIPKNQEPTDAKALNVHENELLKD--N 179

Query: 186 HNCKQISIVDVLCTACKQLLIHPVVLNCGHVYCETCII--TPTVQQLKCEVCQCLNPNGF 243
              KQIS  D+LC+ACK+LL+ PVVLNCGHVYCE C++      +++KC+ C   +P GF
Sbjct: 180 KVSKQISKDDLLCSACKELLVRPVVLNCGHVYCEGCVVDMAEESEKIKCQECNVCDPRGF 239

Query: 244 PKVCLELDQFLEEQFSKEYALRRDVILNHEFATMCSMGAGKSGFISS--------SGAKG 295
           PKVCL L+Q LEE F +EY  R   +         ++     G I S        S    
Sbjct: 240 PKVCLILEQLLEENFPEEYNSRSSKVQK-------TLAHNSKGNIQSYLKEGPSLSNDNN 292

Query: 296 EHSSWLADAHSKVHVGVGCDSCGT 319
               WLA+  S VH G GCDSCG 
Sbjct: 293 NDDPWLANPGSNVHFGAGCDSCGV 316

E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins. Functions in the N-end rule pathway of protein degradation, where it specifically recognizes and ubiquitinates proteins with a N-terminal bulky aromatic amino acid. Does not act on aliphatic hydrophobic and basic N-terminal residues containing proteins.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp\|Q5PQN2\|BFAR_RAT Bifunctional apoptosis regulator OS=Rattus norvegicus GN=Bfar PE=2 SV=1	Back alignment and function description

>sp\|Q9NZS9\|BFAR_HUMAN Bifunctional apoptosis regulator OS=Homo sapiens GN=BFAR PE=1 SV=1	Back alignment and function description

>sp\|Q8R079\|BFAR_MOUSE Bifunctional apoptosis regulator OS=Mus musculus GN=Bfar PE=1 SV=1	Back alignment and function description

>sp\|Q5D7I6\|TRIM5_ALOSA Tripartite motif-containing protein 5 OS=Alouatta sara GN=TRIM5 PE=3 SV=1	Back alignment and function description

>sp\|Q9P3U8\|YJ95_SCHPO Uncharacterized RING finger protein C548.05c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPCC548.05c PE=4 SV=1	Back alignment and function description

>sp\|B8B5U8\|BAHL2_ORYSI Probable E3 ubiquitin-protein ligase BAH1-like 1 OS=Oryza sativa subsp. indica GN=OsI_27296 PE=3 SV=1	Back alignment and function description

>sp\|Q7XI73\|BAHL2_ORYSJ Probable E3 ubiquitin-protein ligase BAH1-like 2 OS=Oryza sativa subsp. japonica GN=Os07g0673200 PE=2 SV=1	Back alignment and function description

>sp\|Q1L5Z9\|LONF2_HUMAN LON peptidase N-terminal domain and RING finger protein 2 OS=Homo sapiens GN=LONRF2 PE=2 SV=3	Back alignment and function description

>sp\|Q5BN31\|TRIM5_SAIBB Tripartite motif-containing protein 5 OS=Saimiri boliviensis boliviensis GN=TRIM5 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		404
118486134		469	unknown [Populus trichocarpa]	0.742	0.639	0.531	4e-83
224065338		382	predicted protein [Populus trichocarpa]	0.740	0.782	0.532	1e-81
225465447		470	PREDICTED: E3 ubiquitin-protein ligase P	0.777	0.668	0.494	4e-81
297744343		451	unnamed protein product [Vitis vinifera]	0.722	0.647	0.496	8e-75
356566399		421	PREDICTED: E3 ubiquitin-protein ligase P	0.740	0.710	0.479	1e-73
356524509		394	PREDICTED: E3 ubiquitin-protein ligase P	0.680	0.697	0.458	9e-72
449443740		359	PREDICTED: E3 ubiquitin-protein ligase P	0.690	0.777	0.474	4e-71
255560167		399	conserved hypothetical protein [Ricinus	0.665	0.674	0.477	5e-69
388515267		410	unknown [Medicago truncatula]	0.757	0.746	0.468	1e-68
357505275		452	E3 ubiquitin-protein ligase PRT1 [Medica	0.764	0.683	0.428	9e-67

>gi\|118486134\|gb\|ABK94910.1\| unknown [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  315 bits (806), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 169/318 (53%), Positives = 210/318 (66%), Gaps = 18/318 (5%)

Query: 16  EKISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRRPYNHFPSICV 75
           E+ S SFRC +CLDLLYKPIVLSCGHISCFWCVH+SM+GLRES+CPICR PYNHFP+IC 
Sbjct: 31  EEFSDSFRCSVCLDLLYKPIVLSCGHISCFWCVHKSMSGLRESNCPICRHPYNHFPTICQ 90

Query: 76  MLHRLLLKMYPIAYKMREIEILEDERRYDFFSPQLDNHACGPLVDNECHHLNDSMQ---- 131
           MLH LL K+YP+ Y  RE + LE+E    FFSPQ     C    D + HH  D       
Sbjct: 91  MLHFLLFKLYPMVYTRREEQTLEEEMEMGFFSPQFGYKECNS--DLKHHHPRDRKHALDS 148

Query: 132 -FSRI--FCGSSSKTGSHENMEQLESVSVAMNNGTSEQS--SIEGITVAGKKLPPNELNH 186
            F R   FCGS+ +  S +++  +++ ++++ N   +++   I+  +V    LP ++ N 
Sbjct: 149 CFFRNGEFCGSTQQIESVKSVSMIQAPTMSIPNKVCDENCCMIKPDSVEENNLPEDKSNR 208

Query: 187 NCKQISIVDVLCTACKQLLIHPVVLNCGHVYCETCIITPTVQQLKCEVCQCLNPNGFPKV 246
           NCKQ+SI DV C+ CKQLL HPVVLNCGHVYCETC I P  + L C+VCQ L+P GFPKV
Sbjct: 209 NCKQVSIADVQCSTCKQLLFHPVVLNCGHVYCETC-IGPVNEMLTCQVCQSLHPRGFPKV 267

Query: 247 CLELDQFLEEQFSKEYALR------RDVILNHEFATMCSMGAGKSGFISSSGAKGEHSSW 300
           CLE D FLEE F  EYA+R      + V +  +    CS  A +  F SSS    E+ SW
Sbjct: 268 CLEFDHFLEEYFPTEYAMRIEAVQAKQVPVKFQHPITCSTKASEKSFQSSSATTRENLSW 327

Query: 301 LADAHSKVHVGVGCDSCG 318
            AD HSKVHVGVGCDSCG
Sbjct: 328 RADPHSKVHVGVGCDSCG 345

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224065338\|ref\|XP_002301781.1\| predicted protein [Populus trichocarpa] gi\|222843507\|gb\|EEE81054.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|225465447\|ref\|XP_002266086.1\| PREDICTED: E3 ubiquitin-protein ligase PRT1-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297744343\|emb\|CBI37313.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356566399\|ref\|XP_003551419.1\| PREDICTED: E3 ubiquitin-protein ligase PRT1-like [Glycine max]	Back alignment and taxonomy information

>gi\|356524509\|ref\|XP_003530871.1\| PREDICTED: E3 ubiquitin-protein ligase PRT1-like [Glycine max]	Back alignment and taxonomy information

>gi\|449443740\|ref\|XP_004139635.1\| PREDICTED: E3 ubiquitin-protein ligase PRT1-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|255560167\|ref\|XP_002521101.1\| conserved hypothetical protein [Ricinus communis] gi\|223539670\|gb\|EEF41252.1\| conserved hypothetical protein [Ricinus communis]	Back alignment and taxonomy information

>gi\|388515267\|gb\|AFK45695.1\| unknown [Medicago truncatula]	Back alignment and taxonomy information

>gi\|357505275\|ref\|XP_003622926.1\| E3 ubiquitin-protein ligase PRT1 [Medicago truncatula] gi\|355497941\|gb\|AES79144.1\| E3 ubiquitin-protein ligase PRT1 [Medicago truncatula]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		404
TAIR\|locus:2087278		410	PRT1 "proteolysis 1" [Arabidop	0.747	0.736	0.433	7.4e-66
UNIPROTKB\|H3BRQ5		109	BFAR "Bifunctional apoptosis r	0.222	0.825	0.296	5.4e-09
UNIPROTKB\|G3MWZ9		844	TRIM34 "Uncharacterized protei	0.198	0.094	0.329	8.9e-08
UNIPROTKB\|F1NNQ7		632	Gga.54568 "Uncharacterized pro	0.153	0.098	0.338	2e-07
TAIR\|locus:2037294		137	AT1G74990 [Arabidopsis thalian	0.126	0.372	0.384	3.8e-07
RGD\|1304791		450	Bfar "bifunctional apoptosis r	0.222	0.2	0.318	6.4e-07
UNIPROTKB\|F1RLR6		319	BFAR "Uncharacterized protein"	0.220	0.278	0.292	6.8e-07
UNIPROTKB\|F6XV32		449	BFAR "Uncharacterized protein"	0.222	0.200	0.307	8.3e-07
UNIPROTKB\|E2QZD5		450	BFAR "Uncharacterized protein"	0.222	0.2	0.307	8.4e-07
UNIPROTKB\|H3BPQ8		89	BFAR "Bifunctional apoptosis r	0.150	0.685	0.370	1e-06

TAIR\|locus:2087278 PRT1 "proteolysis 1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 670 (240.9 bits), Expect = 7.4e-66, P = 7.4e-66
 Identities = 138/318 (43%), Positives = 191/318 (60%)

Query:     7 LTVKSN-AEPEKISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRR 65
             +T+K++ ++ E+I   F CC+CL+LLYKPIVLSCGH+SCFWCVH+SMNG RESHCPICR 
Sbjct:     8 ITMKNDESQEEEIPDQFLCCVCLELLYKPIVLSCGHLSCFWCVHKSMNGFRESHCPICRD 67

Query:    66 PYNHFPSICVMLHRLLLKMYPIAYKMREIEILEDERRYDFFSPQLDNHACGPLVDNECHH 125
             PY HFPS+C  L+ LL KMYP+A+K RE ++L++E+  + FSPQ+D      +   +  +
Sbjct:    68 PYVHFPSVCQKLYFLLKKMYPLAHKKREEQVLKEEQERECFSPQIDLVLDLSVCSGDSLN 127

Query:   126 LNDSMQFSRIFCGSSSKTGSHENMEQLESVSVAMNNGTSEQSSIEGITVAGKKLPPNELN 185
             ++D  +     C +++   S  +      +     N   E +  + + V   +L  +  N
Sbjct:   128 VSDKQKVEE--CSNAANLLSSSSSRG--DIPCIPKN--QEPTDAKALNVHENELLKD--N 179

Query:   186 HNCKQISIVDVLCTACKQLLIHPVVLNCGHVYCETCII--TPTVQQLKCEVCQCLNPNGF 243
                KQIS  D+LC+ACK+LL+ PVVLNCGHVYCE C++      +++KC+ C   +P GF
Sbjct:   180 KVSKQISKDDLLCSACKELLVRPVVLNCGHVYCEGCVVDMAEESEKIKCQECNVCDPRGF 239

Query:   244 PKVCLELDQFLEEQFSKEYALRRDVI---LNHEFATMCSMGAGKSGFISSSGAKGEHSSW 300
             PKVCL L+Q LEE F +EY  R   +   L H           K G  S S        W
Sbjct:   240 PKVCLILEQLLEENFPEEYNSRSSKVQKTLAHNSKGNIQSYL-KEG-PSLSNDNNNDDPW 297

Query:   301 LADAHSKVHVGVGCDSCG 318
             LA+  S VH G GCDSCG
Sbjct:   298 LANPGSNVHFGAGCDSCG 315

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000151 "ubiquitin ligase complex" evidence=TAS

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

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=TAS

UNIPROTKB\|H3BRQ5 BFAR "Bifunctional apoptosis regulator" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|G3MWZ9 TRIM34 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NNQ7 Gga.54568 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

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

RGD\|1304791 Bfar "bifunctional apoptosis regulator" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|F1RLR6 BFAR "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|F6XV32 BFAR "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|E2QZD5 BFAR "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|H3BPQ8 BFAR "Bifunctional apoptosis regulator" [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

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

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		404
TIGR00599		397	TIGR00599, rad18, DNA repair protein rad18	4e-06
cd00162		45	cd00162, RING, RING-finger (Really Interesting New	4e-06
pfam13923		45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	1e-05
pfam13639		46	pfam13639, zf-RING_2, Ring finger domain	7e-05
COG5574		271	COG5574, PEX10, RING-finger-containing E3 ubiquiti	1e-04
COG5152		259	COG5152, COG5152, Uncharacterized conserved protei	1e-04
COG5432		391	COG5432, RAD18, RING-finger-containing E3 ubiquiti	3e-04
smart00184		40	smart00184, RING, Ring finger	4e-04
PLN03208		193	PLN03208, PLN03208, E3 ubiquitin-protein ligase RM	8e-04
pfam13920		49	pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RI	0.001

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

 Score = 48.5 bits (115), Expect = 4e-06
 Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 2/46 (4%)

Query: 21 SFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRRP 66
          S RC IC D    P++ SC H  C  C+ R ++   +  CP+CR  
Sbjct: 26 SLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLS--NQPKCPLCRAE 69

All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 397

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

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

>gnl\|CDD\|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

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

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

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		404
KOG3039		303	consensus Uncharacterized conserved protein [Funct	99.35
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.28
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.18
TIGR00599		397	rad18 DNA repair protein rad18. This family is bas	99.16
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	99.08
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	99.02
TIGR00599		397	rad18 DNA repair protein rad18. This family is bas	98.94
PF14835		65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.94
COG5432		391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.94
KOG0287		442	consensus Postreplication repair protein RAD18 [Re	98.92
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	98.91
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.9
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	98.88
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.87
PF04564		73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.84
KOG0287		442	consensus Postreplication repair protein RAD18 [Re	98.82
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.81
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.78
KOG0823		230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.76
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.72
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	98.71
KOG0823		230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.71
PF04564		73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.71
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.69
KOG0317		293	consensus Predicted E3 ubiquitin ligase, integral	98.68
KOG0317		293	consensus Predicted E3 ubiquitin ligase, integral	98.68
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.65
PF14835		65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.63
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	98.63
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.59
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.59
PHA02929		238	N1R/p28-like protein; Provisional	98.58
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.56
COG5432		391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.56
PF14634		44	zf-RING_5: zinc-RING finger domain	98.53
KOG4159		398	consensus Predicted E3 ubiquitin ligase [Posttrans	98.51
PF14634		44	zf-RING_5: zinc-RING finger domain	98.5
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	98.49
PHA02929		238	N1R/p28-like protein; Provisional	98.49
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	98.43
KOG2177		386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.41
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.41
KOG0824		324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.4
KOG2177		386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.36
PHA02926		242	zinc finger-like protein; Provisional	98.36
KOG2660		331	consensus Locus-specific chromosome binding protei	98.35
KOG2164		513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.33
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.31
KOG2660		331	consensus Locus-specific chromosome binding protei	98.23
COG5574		271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.22
COG5574		271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.2
PHA02926		242	zinc finger-like protein; Provisional	98.16
KOG4367		699	consensus Predicted Zn-finger protein [Function un	98.15
KOG0311		381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.11
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	98.1
KOG0311		381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.07
KOG4159		398	consensus Predicted E3 ubiquitin ligase [Posttrans	98.03
COG5152		259	Uncharacterized conserved protein, contains RING a	97.98
TIGR00570		309	cdk7 CDK-activating kinase assembly factor MAT1. A	97.94
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	97.94
KOG2164		513	consensus Predicted E3 ubiquitin ligase [Posttrans	97.9
COG5152		259	Uncharacterized conserved protein, contains RING a	97.9
TIGR00570		309	cdk7 CDK-activating kinase assembly factor MAT1. A	97.8
KOG1813		313	consensus Predicted E3 ubiquitin ligase [Posttrans	97.73
PF11789		57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.67
KOG0978		698	consensus E3 ubiquitin ligase involved in syntaxin	97.64
KOG1813		313	consensus Predicted E3 ubiquitin ligase [Posttrans	97.64
PF12861		85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	97.6
KOG4628		348	consensus Predicted E3 ubiquitin ligase [Posttrans	97.58
KOG0824		324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.53
KOG0978		698	consensus E3 ubiquitin ligase involved in syntaxin	97.44
COG5243		491	HRD1 HRD ubiquitin ligase complex, ER membrane com	97.44
KOG4628		348	consensus Predicted E3 ubiquitin ligase [Posttrans	97.41
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	97.4
KOG4172		62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.35
COG5540		374	RING-finger-containing ubiquitin ligase [Posttrans	97.35
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	97.33
COG5243		491	HRD1 HRD ubiquitin ligase complex, ER membrane com	97.3
COG5222		427	Uncharacterized conserved protein, contains RING Z	97.28
KOG2879		298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.24
COG5540		374	RING-finger-containing ubiquitin ligase [Posttrans	97.21
KOG2879		298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.17
PF11789		57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.15
KOG4172		62	consensus Predicted E3 ubiquitin ligase [Posttrans	96.94
KOG0825		1134	consensus PHD Zn-finger protein [General function	96.93
KOG0297		391	consensus TNF receptor-associated factor [Signal t	96.93
COG5222		427	Uncharacterized conserved protein, contains RING Z	96.89
KOG4265		349	consensus Predicted E3 ubiquitin ligase [Posttrans	96.87
KOG0297		391	consensus TNF receptor-associated factor [Signal t	96.75
PF12861		85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	96.74
KOG4265		349	consensus Predicted E3 ubiquitin ligase [Posttrans	96.42
smart00744		49	RINGv The RING-variant domain is a C4HC3 zinc-fing	96.28
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	96.24
KOG1002		791	consensus Nucleotide excision repair protein RAD16	96.24
PF14447		55	Prok-RING_4: Prokaryotic RING finger family 4	96.21
KOG1039		344	consensus Predicted E3 ubiquitin ligase [Posttrans	96.18
KOG1645		463	consensus RING-finger-containing E3 ubiquitin liga	96.15
KOG1940		276	consensus Zn-finger protein [General function pred	96.09
KOG4367		699	consensus Predicted Zn-finger protein [Function un	95.88
KOG1002		791	consensus Nucleotide excision repair protein RAD16	95.82
KOG0825		1134	consensus PHD Zn-finger protein [General function	95.78
KOG1039		344	consensus Predicted E3 ubiquitin ligase [Posttrans	95.77
PF11793		70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	95.72
KOG1785		563	consensus Tyrosine kinase negative regulator CBL [	95.6
KOG1785		563	consensus Tyrosine kinase negative regulator CBL [	95.37
COG5219		1525	Uncharacterized conserved protein, contains RING Z	95.29
PF14447		55	Prok-RING_4: Prokaryotic RING finger family 4	95.25
KOG4692		489	consensus Predicted E3 ubiquitin ligase [Posttrans	95.23
KOG1734		328	consensus Predicted RING-containing E3 ubiquitin l	95.09
KOG1734		328	consensus Predicted RING-containing E3 ubiquitin l	94.98
KOG4739		233	consensus Uncharacterized protein involved in syna	94.87
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	94.86
KOG4692		489	consensus Predicted E3 ubiquitin ligase [Posttrans	94.84
KOG0828		636	consensus Predicted E3 ubiquitin ligase [Posttrans	94.69
COG5194		88	APC11 Component of SCF ubiquitin ligase and anapha	94.67
KOG1571		355	consensus Predicted E3 ubiquitin ligase [Posttrans	94.51
KOG0828		636	consensus Predicted E3 ubiquitin ligase [Posttrans	94.25
KOG1493		84	consensus Anaphase-promoting complex (APC), subuni	94.11
KOG4275		350	consensus Predicted E3 ubiquitin ligase [Posttrans	94.01
smart00744		49	RINGv The RING-variant domain is a C4HC3 zinc-fing	93.93
PF14570		48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	93.91
PF04641		260	Rtf2: Rtf2 RING-finger	93.83
KOG1814		445	consensus Predicted E3 ubiquitin ligase [Posttrans	93.63
KOG0827		465	consensus Predicted E3 ubiquitin ligase [Posttrans	93.52
KOG4185		296	consensus Predicted E3 ubiquitin ligase [Posttrans	93.46
KOG1812		384	consensus Predicted E3 ubiquitin ligase [Posttrans	93.42
KOG1001		674	consensus Helicase-like transcription factor HLTF/	93.33
PF14570		48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	93.23
KOG0826		357	consensus Predicted E3 ubiquitin ligase involved i	93.14
KOG3800		300	consensus Predicted E3 ubiquitin ligase containing	93.11
KOG1571		355	consensus Predicted E3 ubiquitin ligase [Posttrans	93.0
KOG3002		299	consensus Zn finger protein [General function pred	92.99
PF11793		70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	92.99
KOG4275		350	consensus Predicted E3 ubiquitin ligase [Posttrans	92.97
KOG2817		394	consensus Predicted E3 ubiquitin ligase [Posttrans	92.55
KOG3800		300	consensus Predicted E3 ubiquitin ligase containing	92.38
KOG3039		303	consensus Uncharacterized conserved protein [Funct	92.21
KOG1645		463	consensus RING-finger-containing E3 ubiquitin liga	92.09
KOG4739		233	consensus Uncharacterized protein involved in syna	91.87
COG5236		493	Uncharacterized conserved protein, contains RING Z	91.82
COG5236		493	Uncharacterized conserved protein, contains RING Z	91.81
KOG0826		357	consensus Predicted E3 ubiquitin ligase involved i	91.55
KOG1941		518	consensus Acetylcholine receptor-associated protei	91.51
cd02342		43	ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger pre	91.5
PF02891		50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	91.43
KOG0827		465	consensus Predicted E3 ubiquitin ligase [Posttrans	91.43
KOG1493		84	consensus Anaphase-promoting complex (APC), subuni	91.12
KOG3161		861	consensus Predicted E3 ubiquitin ligase [Posttrans	91.11
KOG3002		299	consensus Zn finger protein [General function pred	91.07
KOG1001		674	consensus Helicase-like transcription factor HLTF/	90.91
KOG4185		296	consensus Predicted E3 ubiquitin ligase [Posttrans	90.73
COG5194		88	APC11 Component of SCF ubiquitin ligase and anapha	90.32
KOG1814		445	consensus Predicted E3 ubiquitin ligase [Posttrans	90.03
KOG3970		299	consensus Predicted E3 ubiquitin ligase [Posttrans	89.86
PF07800		162	DUF1644: Protein of unknown function (DUF1644); In	89.81
KOG2930		114	consensus SCF ubiquitin ligase, Rbx1 component [Po	89.07
PF08746		43	zf-RING-like: RING-like domain; InterPro: IPR01485	88.67
COG5219		1525	Uncharacterized conserved protein, contains RING Z	88.66
KOG4362		684	consensus Transcriptional regulator BRCA1 [Replica	88.53
KOG2114		933	consensus Vacuolar assembly/sorting protein PEP5/V	88.37
PF04641		260	Rtf2: Rtf2 RING-finger	88.06
KOG1428		3738	consensus Inhibitor of type V adenylyl cyclases/Ne	87.87
COG5175		480	MOT2 Transcriptional repressor [Transcription]	87.8
PF10367		109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	87.39
KOG2114		933	consensus Vacuolar assembly/sorting protein PEP5/V	86.98
PF10367		109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	86.42
PF03854		50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	85.25
KOG4445		368	consensus Uncharacterized conserved protein, conta	84.73
KOG2817		394	consensus Predicted E3 ubiquitin ligase [Posttrans	84.67
KOG1940		276	consensus Zn-finger protein [General function pred	84.12
KOG2930		114	consensus SCF ubiquitin ligase, Rbx1 component [Po	84.08
COG5175		480	MOT2 Transcriptional repressor [Transcription]	83.92
KOG2113		394	consensus Predicted RNA binding protein, contains	83.84
KOG4362		684	consensus Transcriptional regulator BRCA1 [Replica	83.29
PF05290		140	Baculo_IE-1: Baculovirus immediate-early protein (	83.25
PHA02825		162	LAP/PHD finger-like protein; Provisional	82.83
KOG3161		861	consensus Predicted E3 ubiquitin ligase [Posttrans	81.89
PHA02862		156	5L protein; Provisional	81.35
cd02334		49	ZZ_dystrophin Zinc finger, ZZ type. Zinc finger pr	81.05
KOG2932		389	consensus E3 ubiquitin ligase involved in ubiquiti	81.05
PF05290		140	Baculo_IE-1: Baculovirus immediate-early protein (	80.92

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

Probab=99.35  E-value=2.7e-12  Score=117.30  Aligned_cols=201  Identities=14%  Similarity=0.121  Sum_probs=119.1

Q ss_pred             cccCCCcccccccccccCcEEccCCCcccHHHHHHhHcCCCCCCCCCCCcCCCCCCchhHHHHHHHHHHchHHHHHHHHH
Q 039128           16 EKISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRRPYNHFPSICVMLHRLLLKMYPIAYKMREIE   95 (404)
Q Consensus        16 ~~l~~~l~C~IC~~~l~~Pv~l~CGH~fC~~Ci~~~~~~~~~~~CP~CR~~~~~~~~~~~~l~~~l~~~~~~~~~~r~~~   95 (404)
                      ..+.+...|++|+..+++||.++=||+||++||.+++..+++                  .....|..+   +.+.|.++
T Consensus        38 DsiK~FdcCsLtLqPc~dPvit~~GylfdrEaILe~ilaqKk------------------e~arrlkay---ekqrr~ee   96 (303)
T KOG3039|consen   38 DSIKPFDCCSLTLQPCRDPVITPDGYLFDREAILEYILAQKK------------------EIARRLKAY---EKQRRAEE   96 (303)
T ss_pred             cccCCcceeeeecccccCCccCCCCeeeeHHHHHHHHHHHHH------------------HHHHHHHHH---HHHHHhhh
Confidence            455677899999999999999999999999999998763211                  111122211   22221111


Q ss_pred             HHHHHhhhc---CCCCCCCCC--------------------CCCCCccCCCcCC----CccccccccccCCCCCCCCcc-
Q 039128           96 ILEDERRYD---FFSPQLDNH--------------------ACGPLVDNECHHL----NDSMQFSRIFCGSSSKTGSHE-  147 (404)
Q Consensus        96 ~~e~~~~~~---~~~p~~~~~--------------------~~g~~~~~~~~~~----~~~~~~~~s~~~~ss~~~s~e-  147 (404)
                      ..+..+...   .+..+|...                    .++....+ ....    ......++++|.|+..|.... 
T Consensus        97 d~e~qra~~q~~~~~~eF~~~e~~~~s~al~r~~~~~~ae~~a~~~~~~-~~~~sn~~~d~~k~lpsFWlPs~tP~A~at  175 (303)
T KOG3039|consen   97 DKEEQRAMSQKARRLDEFDQQESTPESSALPRNPDTNSAEDAASFHGAN-SVSTSNMEEDKLKTLPSFWLPSLTPTAAAT  175 (303)
T ss_pred             hHHHHHHHhhhHHHHHHHHhhccccccccccCCCCcchhhhccCccccC-CccccCccccccccccceecCccCchhhhh
Confidence            111111110   011112110                    00000001 0000    011112788999888875543 


Q ss_pred             hhhhcccccccCCCCCCcccccccccccCCCCCCCccccccc--cccccceeeeecccCccCce----ecccCCcchHHh
Q 039128          148 NMEQLESVSVAMNNGTSEQSSIEGITVAGKKLPPNELNHNCK--QISIVDVLCTACKQLLIHPV----VLNCGHVYCETC  221 (404)
Q Consensus       148 ~~e~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~C~iC~~~~~~p~----~l~CgH~fC~~C  221 (404)
                      .++.+..+..+...    ..+++.++|..+.|+..+.+....  ......+.||||.+.|++.+    .-+|||+||..|
T Consensus       176 klekP~~~v~CP~s----~kplklkdL~~VkFT~l~s~~~et~l~a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ec  251 (303)
T KOG3039|consen  176 KLEKPSTTVVCPVS----GKPLKLKDLFAVKFTPLNSEETETKLIAASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKEC  251 (303)
T ss_pred             cccCCCceeeccCC----CCccchhhcceeeeeecCCchhhhhhhhhccceecccchhhhcCccceEEeccCCcEeeHHH
Confidence            34444444433322    346778889998887754433321  22336799999999999864    338999999999


Q ss_pred             hcccccccCCCccCCcccCCC
Q 039128          222 IITPTVQQLKCEVCQCLNPNG  242 (404)
Q Consensus       222 l~~~~~~~~~CP~Cr~~~~~~  242 (404)
                      ++.++.....||+|..++.+.
T Consensus       252 vEklir~D~v~pv~d~plkdr  272 (303)
T KOG3039|consen  252 VEKLIRKDMVDPVTDKPLKDR  272 (303)
T ss_pred             HHHhccccccccCCCCcCccc
Confidence            999999999999999987653

>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

>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

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

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

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

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

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

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

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

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

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

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional	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

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

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

>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

>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

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

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

>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

>KOG0823 consensus Predicted 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

>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A	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

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

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

>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B	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

>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

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

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

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

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

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

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

>PF14634 zf-RING_5: zinc-RING finger domain	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

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

Back alignment and domain information

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

>smart00184 RING Ring finger	Back alignment and domain information

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

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

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

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

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

>smart00184 RING Ring finger	Back alignment and domain information

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

>COG5574 PEX10 RING-finger-containing 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

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

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

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

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

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

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

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

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1	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

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

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

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

>KOG1813 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>KOG2879 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

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

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

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

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

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

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

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

>KOG4265 consensus Predicted 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>KOG4692 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

>KOG1734 consensus Predicted RING-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

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

>KOG4692 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

>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

>KOG1571 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

>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

>KOG4275 consensus Predicted 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

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

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

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

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

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

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

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

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

>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

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

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

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

>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

>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

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

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

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

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

>cd02342 ZZ_UBA_plant Zinc finger, ZZ type	Back alignment and domain information

>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

>KOG0827 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

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

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

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

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

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

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

>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

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

>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO)	Back alignment and domain information

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

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

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

>PF04641 Rtf2: Rtf2 RING-finger	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

>COG5175 MOT2 Transcriptional repressor [Transcription]	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

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

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

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

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

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

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

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

>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]	Back alignment and domain information

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

>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0	Back alignment and domain information

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

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

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

>cd02334 ZZ_dystrophin Zinc finger, ZZ type	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

>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		404
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	9e-12
4epo_C		149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	4e-11
4epo_C		149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	3e-06
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	5e-11
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	9e-07
1z6u_A		150	NP95-like ring finger protein isoform B; structura	9e-11
1z6u_A		150	NP95-like ring finger protein isoform B; structura	5e-04
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	7e-10
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	4e-06
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	3e-09
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	5e-09
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	5e-07
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	8e-09
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	1e-08
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	1e-08
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	2e-08
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	4e-04
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	4e-08
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	4e-04
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	4e-08
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	2e-04
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	5e-08
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	5e-08
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	8e-08
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	1e-07
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	8e-04
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	1e-07
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	2e-07
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	8e-04
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	3e-07
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	3e-07
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	3e-07
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	3e-07
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	5e-04
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	4e-07
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	8e-07
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	9e-07
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	1e-06
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	1e-06
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	6e-04
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	2e-06
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	3e-04
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-06
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	4e-04
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	2e-06
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	9e-06
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	2e-05
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	7e-05
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	1e-04
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	3e-04
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	3e-04
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	4e-04

>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

 Score = 61.1 bits (148), Expect = 9e-12
 Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 16  EKISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRRPYNHFPSICV 75
            K+  +F+C  C +L+++PI   C H  C  C+ RS    +   CP CR       ++ V
Sbjct: 47  SKVEETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRA-QVFSCPACRYDLGRSYAMQV 105

Query: 76  --MLHRLLLKMYPIAYKMR 92
              L  +L +++P     R
Sbjct: 106 NQPLQTVLNQLFPGYGNGR 124

PyMOL of 3fl2

>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

>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

>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

>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

>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

>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

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

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

>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

>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

>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc binuclear cluster, zinc finger, DNA-binding protein; 2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1 Length = 116	Back alignment and structure

>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

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

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens} Length = 141	Back alignment and structure

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens} Length = 141	Back alignment and structure

>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

>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

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

>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

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A Length = 118	Back alignment and structure

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A Length = 118	Back alignment and structure

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

>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

>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

>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

>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

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

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

>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

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

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

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 56	Back alignment and structure

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 56	Back alignment and structure

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

>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

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A Length = 108	Back alignment and structure

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

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

>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

>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

>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

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

>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase complex, ring zinc-finger, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 2yhn_A Length = 79	Back alignment and structure

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 74	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		404
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.77
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.45
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.43
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.43
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.4
1t1h_A		78	Gspef-atpub14, armadillo repeat containing protein	99.4
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	99.37
4ayc_A		138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.37
2kr4_A		85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.37
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.36
4ayc_A		138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.36
2kre_A		100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.36
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.36
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	99.36
1z6u_A		150	NP95-like ring finger protein isoform B; structura	99.34
2kr4_A		85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.34
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	99.34
2kre_A		100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.33
1t1h_A		78	Gspef-atpub14, armadillo repeat containing protein	99.33
1wgm_A		98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.32
1wgm_A		98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.32
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	99.31
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.3
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	99.29
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	99.27
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.27
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	99.26
1z6u_A		150	NP95-like ring finger protein isoform B; structura	99.26
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.25
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	99.24
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.23
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	99.23
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	99.23
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.23
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	99.2
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	99.2
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	99.19
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.18
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	99.18
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	99.18
2yu4_A		94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.17
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	99.17
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.17
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	99.16
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	99.16
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.15
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	99.15
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	99.15
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	99.14
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	99.13
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	99.13
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	99.13
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	99.12
2yu4_A		94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.12
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.11
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	99.1
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.08
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	99.08
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	99.07
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	99.06
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	99.06
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	99.05
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	99.05
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.04
2f42_A		179	STIP1 homology and U-box containing protein 1; cha	99.04
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.04
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	99.04
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	99.04
2ect_A		78	Ring finger protein 126; metal binding protein, st	99.03
2f42_A		179	STIP1 homology and U-box containing protein 1; cha	99.02
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	99.02
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	99.01
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	99.01
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.01
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	99.0
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	99.0
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	99.0
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	98.99
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	98.99
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	98.98
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	98.98
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.97
2ect_A		78	Ring finger protein 126; metal binding protein, st	98.96
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.96
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	98.95
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	98.95
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	98.94
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	98.94
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	98.92
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	98.92
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	98.92
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	98.91
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	98.91
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	98.91
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	98.91
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	98.9
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	98.89
4ic3_A		74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.89
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	98.89
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	98.88
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.87
4ic3_A		74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.83
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	98.83
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	98.82
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.8
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	98.79
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	98.74
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.73
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	98.7
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.65
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	98.64
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.64
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.62
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.6
2ea5_A		68	Cell growth regulator with ring finger domain prot	98.57
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.57
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	98.55
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.55
2ea5_A		68	Cell growth regulator with ring finger domain prot	98.55
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	98.54
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	98.46
2bay_A		61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.44
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	98.44
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.42
3t6p_A		345	Baculoviral IAP repeat-containing protein 2; ring,	98.38
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.37
3t6p_A		345	Baculoviral IAP repeat-containing protein 2; ring,	98.3
2bay_A		61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.3
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	98.24
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	98.18
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	98.12
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	97.95
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	97.94
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	97.55
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	97.49
3vk6_A		101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.12
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	96.91
3vk6_A		101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	96.88
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	96.88
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	96.04
3m62_A		968	Ubiquitin conjugation factor E4; armadillo-like re	95.78
2jun_A		101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.55
3nw0_A		238	Non-structural maintenance of chromosomes element	95.54
2jun_A		101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.46
3m62_A		968	Ubiquitin conjugation factor E4; armadillo-like re	94.83
2ffw_A		78	Midline-1; B-BOX, ring finger, zinc-finger, ligase	94.29
3nw0_A		238	Non-structural maintenance of chromosomes element	91.95
2ko5_A		99	Ring finger protein Z; lassa fever virus-Z, negati	89.93
2cs3_A		93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	86.65
3i2d_A		371	E3 SUMO-protein ligase SIZ1; signal transduction,	82.19

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

Probab=99.77  E-value=5.8e-20  Score=156.15  Aligned_cols=107  Identities=28%  Similarity=0.615  Sum_probs=87.3

Q ss_pred             CCCcccccccccccCc-------EEccCCCcccHHHHHHhHcCCCCCCCCCCCcCCCCCCchhHHHHHHHHHHchHHHHH
Q 039128           19 SHSFRCCICLDLLYKP-------IVLSCGHISCFWCVHRSMNGLRESHCPICRRPYNHFPSICVMLHRLLLKMYPIAYKM   91 (404)
Q Consensus        19 ~~~l~C~IC~~~l~~P-------v~l~CGH~fC~~Ci~~~~~~~~~~~CP~CR~~~~~~~~~~~~l~~~l~~~~~~~~~~   91 (404)
                      .+.+.|+||++.+.+|       +.++|||+||..||.+|+.  ....||+||+.+........                
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~--~~~~CP~Cr~~~~~~~l~~l----------------   66 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK--NANTCPTCRKKINHKRYHPI----------------   66 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHT--TCSBCTTTCCBCTTTCEEEC----------------
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHH--hCCCCCCCCCcCcccccccc----------------
Confidence            5679999999999998       9999999999999999998  45589999997653111000                


Q ss_pred             HHHHHHHHHhhhcCCCCCCCCCCCCCCccCCCcCCCccccccccccCCCCCCCCcchhhhcccccccCCCCCCccccccc
Q 039128           92 REIEILEDERRYDFFSPQLDNHACGPLVDNECHHLNDSMQFSRIFCGSSSKTGSHENMEQLESVSVAMNNGTSEQSSIEG  171 (404)
Q Consensus        92 r~~~~~e~~~~~~~~~p~~~~~~~g~~~~~~~~~~~~~~~~~~s~~~~ss~~~s~e~~e~~~~~s~~~~~~~~~~~~~~~  171 (404)
                                                                                                      
T Consensus        67 --------------------------------------------------------------------------------   66 (133)
T 4ap4_A           67 --------------------------------------------------------------------------------   66 (133)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             ccccCCCCCCCccccccccccccceeeeecccCccCc-------eecccCCcchHHhhcccccccCCCccCCcccCC
Q 039128          172 ITVAGKKLPPNELNHNCKQISIVDVLCTACKQLLIHP-------VVLNCGHVYCETCIITPTVQQLKCEVCQCLNPN  241 (404)
Q Consensus       172 ~~~~~~~~~~~~~~~~~~~~~~~~~~C~iC~~~~~~p-------~~l~CgH~fC~~Cl~~~~~~~~~CP~Cr~~~~~  241 (404)
                                        ....+...|+||++.+.+|       +.++|||+||..|+.+|+.....||+||..+..
T Consensus        67 ------------------~i~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~  125 (133)
T 4ap4_A           67 ------------------YIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH  125 (133)
T ss_dssp             ------------------BCSSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             ------------------ccCCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCCh
Confidence                              0002345799999999887       888999999999999998888999999998754

PyMOL of 4ap4

>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

>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

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

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

>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

>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

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

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

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

>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

>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

>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

>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

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

>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

>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

>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

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2	Back alignment and structure

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

>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

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

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

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

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

>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

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

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

>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

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

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

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

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

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

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

>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

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

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

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

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

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

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

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

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

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

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

>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

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

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens}	Back alignment and structure

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

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

>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

>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

>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

>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

>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

>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

>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

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

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

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

>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

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

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

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

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

>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

>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

>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

>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

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

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

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

>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

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

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

>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

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

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

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

>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

>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

>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

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

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

>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

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

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

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

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

>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

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

>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

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

>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

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

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

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

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

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

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

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

>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

>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

>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

>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

>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

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

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

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

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

>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

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

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

>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

>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

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

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

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

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

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

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

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

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

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A	Back alignment and structure

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

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

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

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A	Back alignment and structure

>2ffw_A Midline-1; B-BOX, ring finger, zinc-finger, ligase; NMR {Homo sapiens}	Back alignment and structure

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

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

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

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		404
d1rmda2		86	g.44.1.1 (A:1-86) V(D)J recombination activating p	6e-09
d1rmda2		86	g.44.1.1 (A:1-86) V(D)J recombination activating p	0.001
d1jm7a_		103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	6e-08
d1fbva4		79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	6e-08
d1fbva4		79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	0.002
d1bora_		56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	9e-08
d1bora_		56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	0.004
d1chca_		68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	3e-06
d1t1ha_		78	g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cre	4e-05
d1jm7b_		97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	6e-05
d2c2la2		80	g.44.1.2 (A:225-304) STIP1 homology and U box-cont	2e-04
d1ur6b_		52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	0.002
d1g25a_		65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	0.003
d1iyma_		55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	0.004

>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


class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.7 bits (121), Expect = 6e-09
 Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 15 PEKISHSFRCCICLDLLYKPIVLSCGHISCFWCVHRSMNGLRESHCPICRRPYN 68
          P     S  C IC  +L  P+  SC H+ C  C+ R +     S+CP CR P  
Sbjct: 17 PAHFVKSISCQICEHILADPVETSCKHLFCRICILRCLKV-MGSYCPSCRYPCF 69

PyMOL of d1rmda2

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

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

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

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

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

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

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

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80	Back information, alignment and structure

>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

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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		404
d2c2la2		80	STIP1 homology and U box-containing protein 1, STU	99.38
d2c2la2		80	STIP1 homology and U box-containing protein 1, STU	99.36
d1t1ha_		78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.35
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	99.34
d1t1ha_		78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.34
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.33
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.32
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.27
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	99.24
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.2
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.19
d1wgma_		98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.18
d1wgma_		98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.12
d2baya1		56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.11
d1bora_		56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.1
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.07
d1bora_		56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.07
d2baya1		56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.05
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	99.01
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	98.99
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	98.94
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	98.93
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	98.91
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	98.89
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	98.85
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	98.83
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	98.61
d3dplr1		88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	98.49
d1vyxa_		60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.47
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	98.43
d3dplr1		88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	98.39
d1vyxa_		60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.2
d1wima_		94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	97.76
d1wima_		94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	97.75
d2cs3a1		80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	83.84

>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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.38  E-value=4.8e-14  Score=107.80  Aligned_cols=66  Identities=11%  Similarity=-0.016  Sum_probs=57.7

Q ss_pred             ccceeeeecccCccCceecccCCcchHHhhccccc-ccCCCccCCcccCCCCCcchHHHHHHHHHHh
Q 039128          193 IVDVLCTACKQLLIHPVVLNCGHVYCETCIITPTV-QQLKCEVCQCLNPNGFPKVCLELDQFLEEQF  258 (404)
Q Consensus       193 ~~~~~C~iC~~~~~~p~~l~CgH~fC~~Cl~~~~~-~~~~CP~Cr~~~~~~~~~~~~~l~~~l~~~~  258 (404)
                      -+++.|+||+++|.+||+++|||+||+.||..++. ....||.|+..+....+.+|..|+++|+++.
T Consensus         5 P~~l~CpIc~~l~~dPv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~l~pN~~L~~~I~~~l   71 (80)
T d2c2la2           5 PDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAMKEVIDAFI   71 (80)
T ss_dssp             CSTTBCTTTCSBCSSEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEECHHHHHHHHHHH
T ss_pred             CccccCcCcCchhhhhcccCCcCeecHHHHHHHHhcCCccCCCccccccccccccHHHHHHHHHHHH
Confidence            36789999999999999999999999999999864 5567999999987666788999999997654

PyMOL of d2c2la2

>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

>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

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

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {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

>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

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

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

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

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

>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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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