Citrus Sinensis ID: 040167

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-------

MGSVCCCFHVEDFEDYMNPNSSVYRNCMCLSCFIQHVLNVYTSLFRRGDVHSVPSSIQGAASMTSTASLDNSLSDMYRSPPRPLPYDADPRYFRLQHEGLVSRREKGSSQFHEESEPLRSDNDVESESFSAGDKWNDSSCEDGSKEQRSKSSVTLSSAKSTAGFAYIYSPSEDEDVCPTCLEEYTPENPKIVTKCSHHFHLGCIYEWMERSENCPVCGKVMVFDETT

cccEEccccccccccccccccccccccccHHHHHHcccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccEEEccccccccHHHHHHHHHHccccccccccccccccc

cccEEEEcccccHHHccccccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccccccHccccccEEcccccccccccccHHccccccccEEEcccccccHHHHHHHHHHcccccccccEEEEcccc

mgsvcccfhvedfedymnpnssvyrncmCLSCFIQHVLNVYTSLfrrgdvhsvpssiqgAASMTstasldnslsdmyrspprplpydadpryfrLQHEglvsrrekgssqfheeseplrsdndvesesfsagdkwndsscedgskeqrskssvtlssakstagfayiyspsededvcptcleeytpenpkivtkcshhfHLGCIYEWmersencpvcgkvmvfdett

MGSVCCCFHVEDFEDYMNPNSSVYRNCMCLSCFIQHVLNVYTSLFRRGDVHSVPSSIQGAASMTSTASLDNSLSDMYRSPPRPLPYDADPRYFRLQHEGLVsrrekgssqfheeseplrsdndvesesfsagdkwndsscedgskeqrskssvtlssakstaGFAYIYSPSEDEDVCPTCLEEYTPENPKIVTKCSHHFHLGCIYEWMERSENCPVCGKVMVFDETT

MGSVCCCFHVEDFEDYMNPNSSVYRNCMCLSCFIQHVLNVYTSLFRRGDVHSVPSSIQGAASMTSTASLDNSLSDMYRSPPRPLPYDADPRYFRLQHEGLVSRREKGSSQFHEESEPLRSDNDVESESFSAGDKWNDSSCEDGSKEQRskssvtlssakstaGFAYIYSPSEDEDVCPTCLEEYTPENPKIVTKCSHHFHLGCIYEWMERSENCPVCGKVMVFDETT

***VCCCFHVEDFEDYMNPNSSVYRNCMCLSCFIQHVLNVYTSLFRRGDV****************************************************************************************************************GFAYIYSPSEDEDVCPTCLEEYTPENPKIVTKCSHHFHLGCIYEWMERSENCPVCGKVMVF****

MGSVCC*FHV************VYRNCMCLSCFIQHVLNV**************************************SPPRPLPYDADP*********************************************************************************EDEDVCPTCLEEYTPENPKIVTKCSHHFHLGCIYEWMERSENCPVCGKVMVF****

MGSVCCCFHVEDFEDYMNPNSSVYRNCMCLSCFIQHVLNVYTSLFRRGDVHSVPSSIQGAASMTSTASLDNSLSDMYRSPPRPLPYDADPRYFRLQHEGL*********************************************************AKSTAGFAYIYSPSEDEDVCPTCLEEYTPENPKIVTKCSHHFHLGCIYEWMERSENCPVCGKVMVFDETT

*GSVCCCFHVEDFEDYMNPNSSVYRNCMCLSCFIQHVLNVYTSLFRRGDV**V**********TSTASLDNSLSDMYRSPPRPLPYDADPRYFR*********************************************************************FAYIYSPSEDEDVCPTCLEEYTPENPKIVTKCSHHFHLGCIYEWMERSENCPVCGKVMVFD***

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		227	2.2.26 [Sep-21-2011]
Q8LE94		231	E3 ubiquitin-protein liga	no	no	0.977	0.961	0.628	2e-71
Q4TU14		371	E3 ubiquitin-protein liga	no	no	0.220	0.134	0.46	9e-10
Q9ZT42		375	E3 ubiquitin-protein liga	no	no	0.330	0.2	0.337	3e-08
Q0IJ20		695	RING finger protein 145 O	no	no	0.189	0.061	0.391	1e-05
Q5BIY5		695	RING finger protein 145 O	N/A	no	0.189	0.061	0.391	1e-05
Q9LF64		362	RING-H2 finger protein AT	no	no	0.317	0.198	0.370	1e-05
Q9D0C1		305	E3 ubiquitin-protein liga	yes	no	0.224	0.167	0.411	4e-05
Q9FHG8		210	Putative RING-H2 finger p	no	no	0.400	0.433	0.285	4e-05
Q9M2S6		273	E3 ubiquitin-protein liga	no	no	0.207	0.172	0.425	4e-05
Q08109		551	ERAD-associated E3 ubiqui	yes	no	0.308	0.127	0.308	4e-05

>sp\|Q8LE94\|RING3_ARATH E3 ubiquitin-protein ligase At3g02290 OS=Arabidopsis thaliana GN=At3g02290 PE=2 SV=1	Back alignment and function desciption

 Score =  268 bits (686), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 147/234 (62%), Positives = 170/234 (72%), Gaps = 12/234 (5%)

Query: 1   MGSVCCCFHVEDFEDYMNPNSSVYRNCMCLSCFIQHVLNVYTSLFRRGDVHSVPSSIQGA 60
           MG V  CF VED ++YMNPNSSVYRNC C+ C   + LN+Y S+FRRG+  S+PSS+Q  
Sbjct: 1   MGCVSSCFRVEDIDEYMNPNSSVYRNCPCIRCLAHNFLNLYISVFRRGETRSLPSSVQAT 60

Query: 61  ASMTSTASLDNSLSDMYRSPPRPLPYDADPRYFRLQHEGLVSRREKGSSQFHEESEPLRS 120
           AS+TS++S DN LS+ +RS PRPLPYDADPRYFR     LVSRREKGSS  HEE EPLRS
Sbjct: 61  ASITSSSSHDNFLSEAFRSTPRPLPYDADPRYFR----SLVSRREKGSSHSHEEVEPLRS 116

Query: 121 DNDVESESFSAGD-KW--NDSSCEDGSKEQRSKSSVTLSSAKS-----TAGFAYIYSPSE 172
           D+D +SESF  G  KW  N S+  D   ++   S  +L   +S      A    +Y  SE
Sbjct: 117 DSDADSESFGVGGCKWANNKSTLSDKDSKEEYSSKSSLRILRSRSKSIMADSENMYILSE 176

Query: 173 DEDVCPTCLEEYTPENPKIVTKCSHHFHLGCIYEWMERSENCPVCGKVMVFDET 226
           DEDVCPTCLEEYT ENPKIVTKCSHHFHL CIYEWMERSENCPVCGKVM F+ET
Sbjct: 177 DEDVCPTCLEEYTSENPKIVTKCSHHFHLSCIYEWMERSENCPVCGKVMEFNET 230

Mediates E2-dependent protein ubiquitination.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp\|Q4TU14\|RHF1A_ARATH E3 ubiquitin-protein ligase RHF1A OS=Arabidopsis thaliana GN=RHF1A PE=1 SV=1	Back alignment and function description

>sp\|Q9ZT42\|RHF2A_ARATH E3 ubiquitin-protein ligase RHF2A OS=Arabidopsis thaliana GN=RHF2A PE=2 SV=1	Back alignment and function description

>sp\|Q0IJ20\|RN145_XENTR RING finger protein 145 OS=Xenopus tropicalis GN=rnf145 PE=2 SV=1	Back alignment and function description

>sp\|Q5BIY5\|RN145_XENLA RING finger protein 145 OS=Xenopus laevis GN=rnf145 PE=2 SV=1	Back alignment and function description

>sp\|Q9LF64\|ATL52_ARATH RING-H2 finger protein ATL52 OS=Arabidopsis thaliana GN=ATL52 PE=2 SV=1	Back alignment and function description

>sp\|Q9D0C1\|RN115_MOUSE E3 ubiquitin-protein ligase RNF115 OS=Mus musculus GN=Rnf115 PE=1 SV=1	Back alignment and function description

>sp\|Q9FHG8\|ATL50_ARATH Putative RING-H2 finger protein ATL50 OS=Arabidopsis thaliana GN=ATL50 PE=3 SV=1	Back alignment and function description

>sp\|Q9M2S6\|SDIR1_ARATH E3 ubiquitin-protein ligase SDIR1 OS=Arabidopsis thaliana GN=SDIR1 PE=1 SV=1	Back alignment and function description

>sp\|Q08109\|HRD1_YEAST ERAD-associated E3 ubiquitin-protein ligase HRD1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=HRD1 PE=1 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		227
356526552		227	PREDICTED: E3 ubiquitin-protein ligase A	0.995	0.995	0.819	1e-106
255569920		570	60S ribosomal protein L7a, putative [Ric	0.964	0.384	0.812	1e-106
225451825		225	PREDICTED: E3 ubiquitin-protein ligase A	0.991	1.0	0.797	1e-103
224120794		225	predicted protein [Populus trichocarpa]	0.991	1.0	0.792	1e-103
358248876		229	uncharacterized protein LOC100777068 [Gl	1.0	0.991	0.762	1e-101
358248273		229	uncharacterized protein LOC100790104 [Gl	1.0	0.991	0.762	1e-101
363807934		226	uncharacterized protein LOC100790543 [Gl	0.991	0.995	0.779	1e-100
388511135		229	unknown [Lotus japonicus]	1.0	0.991	0.762	1e-100
449447440		227	PREDICTED: E3 ubiquitin-protein ligase A	1.0	1.0	0.757	8e-99
449481398		227	PREDICTED: E3 ubiquitin-protein ligase A	1.0	1.0	0.757	1e-98

>gi\|356526552\|ref\|XP_003531881.1\| PREDICTED: E3 ubiquitin-protein ligase At3g02290-like [Glycine max]	Back alignment and taxonomy information

 Score =  390 bits (1002), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 186/227 (81%), Positives = 205/227 (90%), Gaps = 1/227 (0%)

Query: 1   MGSVCCCFHVEDFEDYMNPNSSVYRNCMCLSCFIQHVLNVYTSLFRRGDVHSVPSSIQGA 60
           MG+VCCCF+V+DFEDYMNPNSSVYRNCMCLSCF+Q+ L VY S+FRRG+VH++PSSIQGA
Sbjct: 1   MGAVCCCFNVDDFEDYMNPNSSVYRNCMCLSCFVQNFLTVYESIFRRGEVHAIPSSIQGA 60

Query: 61  ASMTSTASLDNSLSDMYRSPPRPLPYDADPRYFRLQHEGLVSRREKGSSQFHEESEPLRS 120
           ASMTSTASLDNSLSDMYRSPPRPLPYDADPR+FR Q EGLVSRREKGSS  +EESEPLR 
Sbjct: 61  ASMTSTASLDNSLSDMYRSPPRPLPYDADPRFFRSQREGLVSRREKGSSHLNEESEPLRG 120

Query: 121 DNDVESESFSAGDKWNDSSCEDGSKEQRSKSSVTLSSAKSTAGFAYIYSPSEDEDVCPTC 180
           D D +SES ++G KWND+S EDGSKE RSKSSV LSSAK T G   +YS SE+EDVCPTC
Sbjct: 121 DVDADSESLNSGGKWNDTS-EDGSKEYRSKSSVRLSSAKLTTGAGVVYSSSEEEDVCPTC 179

Query: 181 LEEYTPENPKIVTKCSHHFHLGCIYEWMERSENCPVCGKVMVFDETT 227
           LEEYT ENPKIVTKCSHHFHLGCIYEWMERS++CPVCGKVMVFDETT
Sbjct: 180 LEEYTEENPKIVTKCSHHFHLGCIYEWMERSDSCPVCGKVMVFDETT 226

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255569920\|ref\|XP_002525923.1\| 60S ribosomal protein L7a, putative [Ricinus communis] gi\|223534752\|gb\|EEF36443.1\| 60S ribosomal protein L7a, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|225451825\|ref\|XP_002281596.1\| PREDICTED: E3 ubiquitin-protein ligase At3g02290 [Vitis vinifera] gi\|298204451\|emb\|CBI16931.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224120794\|ref\|XP_002330953.1\| predicted protein [Populus trichocarpa] gi\|222873147\|gb\|EEF10278.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|358248876\|ref\|NP_001240211.1\| uncharacterized protein LOC100777068 [Glycine max] gi\|255647555\|gb\|ACU24241.1\| unknown [Glycine max]	Back alignment and taxonomy information

>gi\|358248273\|ref\|NP_001240108.1\| uncharacterized protein LOC100790104 [Glycine max] gi\|255637513\|gb\|ACU19083.1\| unknown [Glycine max]	Back alignment and taxonomy information

>gi\|363807934\|ref\|NP_001241941.1\| uncharacterized protein LOC100790543 [Glycine max] gi\|255641258\|gb\|ACU20906.1\| unknown [Glycine max]	Back alignment and taxonomy information

>gi\|388511135\|gb\|AFK43629.1\| unknown [Lotus japonicus]	Back alignment and taxonomy information

>gi\|449447440\|ref\|XP_004141476.1\| PREDICTED: E3 ubiquitin-protein ligase At3g02290-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449481398\|ref\|XP_004156171.1\| PREDICTED: E3 ubiquitin-protein ligase At3g02290-like [Cucumis sativus]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		227
TAIR\|locus:2076542		231	AT3G02290 [Arabidopsis thalian	0.977	0.961	0.623	1.1e-73
TAIR\|locus:2143251		232	AT5G15790 [Arabidopsis thalian	0.995	0.974	0.593	9.9e-71
TAIR\|locus:2177881		212	AT5G41350 [Arabidopsis thalian	0.753	0.806	0.365	2.7e-25
TAIR\|locus:505006415		190	RHB1A "RING-H2 finger B1A" [Ar	0.237	0.284	0.574	1.1e-20
TAIR\|locus:2129525		371	RHF1A "RING-H2 group F1A" [Ara	0.215	0.132	0.469	1e-10
UNIPROTKB\|F1SVB7		153	RNF181 "Uncharacterized protei	0.251	0.372	0.385	2.4e-08
TAIR\|locus:2153654		151	AT5G05910 [Arabidopsis thalian	0.180	0.271	0.404	9.4e-08
UNIPROTKB\|Q3T0W3		153	RNF181 "E3 ubiquitin-protein l	0.251	0.372	0.368	1.2e-07
UNIPROTKB\|C9J1C6		139	RNF181 "E3 ubiquitin-protein l	0.251	0.410	0.368	1.6e-07
UNIPROTKB\|Q9P0P0		153	RNF181 "E3 ubiquitin-protein l	0.251	0.372	0.368	1.6e-07

TAIR\|locus:2076542 AT3G02290 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 744 (267.0 bits), Expect = 1.1e-73, P = 1.1e-73
 Identities = 146/234 (62%), Positives = 166/234 (70%)

Query:     1 MGSVCCCFHVEDFEDYMNPNSSVYRNCMCLSCFIQHVLNVYTSLFRRGDVHSVPSSIQGA 60
             MG V  CF VED ++YMNPNSSVYRNC C+ C   + LN+Y S+FRRG+  S+PSS+Q  
Sbjct:     1 MGCVSSCFRVEDIDEYMNPNSSVYRNCPCIRCLAHNFLNLYISVFRRGETRSLPSSVQAT 60

Query:    61 ASMTSTASLDNSLSDMYRSPPRPLPYDADPRYFRLQHEGLVSRREKGSSQFHEESEPLRS 120
             AS+TS++S DN LS+ +RS PRPLPYDADPRYFR     LVSRREKGSS  HEE EPLRS
Sbjct:    61 ASITSSSSHDNFLSEAFRSTPRPLPYDADPRYFR----SLVSRREKGSSHSHEEVEPLRS 116

Query:   121 DNDVESESFSAGD-KW--NDSSCED-GSKEQRXXXXXXXXXXXXXXGFAY----IYSPSE 172
             D+D +SESF  G  KW  N S+  D  SKE+                       +Y  SE
Sbjct:   117 DSDADSESFGVGGCKWANNKSTLSDKDSKEEYSSKSSLRILRSRSKSIMADSENMYILSE 176

Query:   173 DEDVCPTCLEEYTPENPKIVTKCSHHFHLGCIYEWMERSENCPVCGKVMVFDET 226
             DEDVCPTCLEEYT ENPKIVTKCSHHFHL CIYEWMERSENCPVCGKVM F+ET
Sbjct:   177 DEDVCPTCLEEYTSENPKIVTKCSHHFHLSCIYEWMERSENCPVCGKVMEFNET 230

GO:0005634 "nucleus" evidence=ISM

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

TAIR\|locus:2143251 AT5G15790 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2177881 AT5G41350 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:505006415 RHB1A "RING-H2 finger B1A" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2129525 RHF1A "RING-H2 group F1A" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|F1SVB7 RNF181 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

TAIR\|locus:2153654 AT5G05910 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|Q3T0W3 RNF181 "E3 ubiquitin-protein ligase RNF181" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|C9J1C6 RNF181 "E3 ubiquitin-protein ligase RNF181" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9P0P0 RNF181 "E3 ubiquitin-protein ligase RNF181" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	eugene3.01550025	hypothetical protein (226 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		227
pfam12678		73	pfam12678, zf-rbx1, RING-H2 zinc finger	2e-09
pfam13639		46	pfam13639, zf-RING_2, Ring finger domain	4e-09
COG5243		491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	9e-08
cd00162		45	cd00162, RING, RING-finger (Really Interesting New	3e-07
pfam13923		45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	5e-07
COG5194		88	COG5194, APC11, Component of SCF ubiquitin ligase	2e-05
COG5540		374	COG5540, COG5540, RING-finger-containing ubiquitin	3e-05
pfam12861		85	pfam12861, zf-Apc11, Anaphase-promoting complex su	3e-05
smart00184		40	smart00184, RING, Ring finger	4e-05
PHA02929		238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	5e-04
pfam00097		40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	0.001

>gnl\|CDD\|221705 pfam12678, zf-rbx1, RING-H2 zinc finger	Back alignment and domain information

 Score = 52.0 bits (125), Expect = 2e-09
 Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 10/62 (16%)

Query: 166 YIYSPSEDEDVCPTCLEEY----------TPENPKIVTKCSHHFHLGCIYEWMERSENCP 215
            ++S   ++DVC  C   +            + P +  +C H FHL CI  W++    CP
Sbjct: 11  ALWSWDIEDDVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCP 70

Query: 216 VC 217
           +C
Sbjct: 71  LC 72

There are 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding. The protein, of which this domain is the conserved region, participates in diverse functions relevant to chromosome metabolism and cell cycle control. Length = 73

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

>gnl\|CDD\|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

Back alignment and domain information

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

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

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

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

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

>gnl\|CDD\|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional	Back alignment and domain information

>gnl\|CDD\|215715 pfam00097, zf-C3HC4, 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		227
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.65
KOG4628		348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.54
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.47
COG5243		491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.42
PF12861		85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.39
PHA02929		238	N1R/p28-like protein; Provisional	99.34
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.29
COG5540		374	RING-finger-containing ubiquitin ligase [Posttrans	99.29
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.23
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	99.22
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.19
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	99.19
COG5194		88	APC11 Component of SCF ubiquitin ligase and anapha	99.12
KOG0823		230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.1
PF14634		44	zf-RING_5: zinc-RING finger domain	99.08
KOG0317		293	consensus Predicted E3 ubiquitin ligase, integral	99.08
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.07
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	99.01
PHA02926		242	zinc finger-like protein; Provisional	99.01
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	98.99
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.98
KOG1493		84	consensus Anaphase-promoting complex (APC), subuni	98.97
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.94
TIGR00599		397	rad18 DNA repair protein rad18. This family is bas	98.8
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.69
COG5574		271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.61
smart00744		49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.54
KOG2930		114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.5
KOG2164		513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.5
PF04564		73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.47
KOG0828		636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.46
PF11793		70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.44
KOG1734		328	consensus Predicted RING-containing E3 ubiquitin l	98.29
COG5219		1525	Uncharacterized conserved protein, contains RING Z	98.23
KOG2177		386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.22
KOG0287		442	consensus Postreplication repair protein RAD18 [Re	98.15
COG5432		391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.11
KOG1039		344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.1
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.04
KOG4265		349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.97
PF14835		65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.89
KOG0825		1134	consensus PHD Zn-finger protein [General function	97.76
KOG4445		368	consensus Uncharacterized conserved protein, conta	97.65
KOG4172		62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.62
KOG0311		381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.59
PF11789		57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.57
KOG0978		698	consensus E3 ubiquitin ligase involved in syntaxin	97.5
KOG1952		950	consensus Transcription factor NF-X1, contains NFX	97.5
KOG1428		3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.34
KOG0297		391	consensus TNF receptor-associated factor [Signal t	97.33
COG5152		259	Uncharacterized conserved protein, contains RING a	97.28
KOG1941		518	consensus Acetylcholine receptor-associated protei	97.26
PF12906		47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	97.19
KOG4159		398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.16
KOG1785		563	consensus Tyrosine kinase negative regulator CBL [	97.15
KOG2879		298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.96
KOG2660		331	consensus Locus-specific chromosome binding protei	96.84
KOG1813		313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.83
PF05883		134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	96.74
KOG1002		791	consensus Nucleotide excision repair protein RAD16	96.72
PHA02862		156	5L protein; Provisional	96.72
PHA02825		162	LAP/PHD finger-like protein; Provisional	96.68
KOG4692		489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.64
PF14447		55	Prok-RING_4: Prokaryotic RING finger family 4	96.48
PF14570		48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.44
PF10367		109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.15
KOG3268		234	consensus Predicted E3 ubiquitin ligase [Posttrans	96.05
KOG0801		205	consensus Predicted E3 ubiquitin ligase [Posttrans	95.88
PF03854		50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	95.85
PHA03096		284	p28-like protein; Provisional	95.79
KOG1814		445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.78
PF04641		260	Rtf2: Rtf2 RING-finger	95.72
COG5236		493	Uncharacterized conserved protein, contains RING Z	95.69
KOG3039		303	consensus Uncharacterized conserved protein [Funct	95.55
KOG4275		350	consensus Predicted E3 ubiquitin ligase [Posttrans	95.53
PF08746		43	zf-RING-like: RING-like domain; InterPro: IPR01485	95.19
KOG1571		355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.15
KOG1940		276	consensus Zn-finger protein [General function pred	95.13
KOG3970		299	consensus Predicted E3 ubiquitin ligase [Posttrans	94.62
COG5175		480	MOT2 Transcriptional repressor [Transcription]	94.58
COG5222		427	Uncharacterized conserved protein, contains RING Z	94.39
COG5183		1175	SSM4 Protein involved in mRNA turnover and stabili	93.39
KOG2114		933	consensus Vacuolar assembly/sorting protein PEP5/V	93.24
KOG3002		299	consensus Zn finger protein [General function pred	93.19
KOG2932		389	consensus E3 ubiquitin ligase involved in ubiquiti	92.94
KOG2817		394	consensus Predicted E3 ubiquitin ligase [Posttrans	92.74
KOG0827		465	consensus Predicted E3 ubiquitin ligase [Posttrans	92.74
KOG1001		674	consensus Helicase-like transcription factor HLTF/	92.41
KOG3053		293	consensus Uncharacterized conserved protein [Funct	92.13
KOG0309		1081	consensus Conserved WD40 repeat-containing protein	92.09
KOG0826		357	consensus Predicted E3 ubiquitin ligase involved i	92.02
KOG2034		911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	91.22
KOG0298		1394	consensus DEAD box-containing helicase-like transc	91.14
KOG1609		323	consensus Protein involved in mRNA turnover and st	90.66
KOG1812		384	consensus Predicted E3 ubiquitin ligase [Posttrans	90.4
PF07800		162	DUF1644: Protein of unknown function (DUF1644); In	90.08
PF10272		358	Tmpp129: Putative transmembrane protein precursor;	89.65
PF02891		50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	87.95
KOG4362		684	consensus Transcriptional regulator BRCA1 [Replica	86.59
PF14446		54	Prok-RING_1: Prokaryotic RING finger family 1	86.21
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	86.13
KOG1829		580	consensus Uncharacterized conserved protein, conta	85.75
PF05290		140	Baculo_IE-1: Baculovirus immediate-early protein (	83.52
KOG3899		381	consensus Uncharacterized conserved protein [Funct	81.0

>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

Probab=99.65  E-value=3.5e-17  Score=103.45  Aligned_cols=44  Identities=45%  Similarity=1.122  Sum_probs=40.3

Q ss_pred             cccccccccccCCCCceecCCCCccCHHHHHHHHhcCCCCCccC
Q 040167          175 DVCPTCLEEYTPENPKIVTKCSHHFHLGCIYEWMERSENCPVCG  218 (227)
Q Consensus       175 ~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr  218 (227)
                      ++|+||+++|..++.++.++|+|.||.+||.+|++++.+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence            47999999999888899999999999999999999999999997

...

>KOG4628 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

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

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

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

>KOG0320 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

>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

>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

>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

>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

>KOG0823 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

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

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

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

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

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

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

>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

>smart00184 RING Ring finger	Back alignment and domain information

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

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

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

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

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

>KOG2164 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

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

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

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

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

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

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

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

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

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

>KOG4265 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

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

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

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

>KOG0311 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

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

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

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

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

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

>KOG4275 consensus Predicted E3 ubiquitin ligase [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

>KOG1571 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

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

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

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

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

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

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

>KOG2817 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

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

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]	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

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

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

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

>KOG1812 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

>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans	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

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

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1	Back alignment and domain information

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

>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]	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

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		227
2ep4_A		74	Solution Structure Of Ring Finger From Human Ring F		5e-05
2ect_A		78	Solution Structure Of The Zinc Finger, C3hc4 Type (		2e-04
2l0b_A		91	Solution Nmr Structure Of Zinc Finger Domain Of E3		7e-04

>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger Protein 24 Length = 74

Back alignment and structure

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 15/43 (34%), Positives = 26/43 (60%)
Query: 175 DVCPTCLEEYTPENPKIVTKCSHHFHLGCIYEWMERSENCPVC 217
           ++C  CLE++ P +   +  C H FH  C+ +W+E  + CP+C
Sbjct: 16  ELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLC 58

PyMOL of 2ep4

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

Back alignment and structure

>pdb|2L0B|A Chain A, Solution Nmr Structure Of Zinc Finger Domain Of E3 Ubiquitin-Protein Ligase Praja-1 From Homo Sapiens, Northeast Structural Genomics Consortium (Nesg) Target Hr4710b Length = 91

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		227
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	2e-11
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	3e-11
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	3e-11
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	3e-10
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	4e-10
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	1e-09
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	1e-09
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	2e-09
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	2e-09
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	3e-09
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	4e-09
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	4e-09
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	5e-09
2ect_A		78	Ring finger protein 126; metal binding protein, st	7e-09
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	7e-09
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	3e-08
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	3e-08
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	1e-07
4epo_C		149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	1e-07
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	5e-07
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	1e-06
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	2e-06
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-06
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	2e-06
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	7e-06
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	1e-05
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	2e-05
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	7e-05
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	2e-04
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	3e-04
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	3e-04
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	4e-04
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	4e-04
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	6e-04
3nw0_A		238	Non-structural maintenance of chromosomes element	6e-04
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	7e-04

>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

 Score = 57.0 bits (138), Expect = 2e-11
 Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 2/47 (4%)

Query: 171 SEDEDVCPTCLEEYTPENPKIVTKCSHHFHLGCIYEWMERSENCPVC 217
           +   + CP CLE+    N  +   C H F   CI  W+ ++  CP+C
Sbjct: 2   ATVAERCPICLEDP--SNYSMALPCLHAFCYVCITRWIRQNPTCPLC 46

PyMOL of 1chc

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

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

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

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

>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

>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

>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

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

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

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

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

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

>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

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

>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

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

>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

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

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

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

>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

>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

>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

>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

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

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

>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

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

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		227
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.66
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	99.66
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.65
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.63
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	99.61
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.61
2ect_A		78	Ring finger protein 126; metal binding protein, st	99.6
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	99.58
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.55
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.54
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	99.54
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.51
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	99.51
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	99.51
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	99.5
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	99.49
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	99.48
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.47
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	99.47
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	99.47
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	99.47
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	99.46
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	99.46
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	99.43
4ayc_A		138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.4
1t1h_A		78	Gspef-atpub14, armadillo repeat containing protein	99.4
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.4
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	99.4
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	99.38
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.38
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	99.38
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	99.36
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	99.34
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.34
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	99.33
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.33
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.33
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	99.3
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.27
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.27
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	99.26
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	99.25
2kr4_A		85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.24
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.21
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.21
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.2
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	99.2
1z6u_A		150	NP95-like ring finger protein isoform B; structura	99.2
1wgm_A		98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.2
2kre_A		100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.19
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	99.19
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	99.17
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.16
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	99.09
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.07
2yu4_A		94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.06
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	99.05
4ic3_A		74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.04
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	99.01
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.97
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	98.94
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.91
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.86
2ea5_A		68	Cell growth regulator with ring finger domain prot	98.85
2f42_A		179	STIP1 homology and U-box containing protein 1; cha	98.85
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.76
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.76
2bay_A		61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.76
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.69
3t6p_A		345	Baculoviral IAP repeat-containing protein 2; ring,	98.54
3vk6_A		101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.16
3nw0_A		238	Non-structural maintenance of chromosomes element	98.01
2ko5_A		99	Ring finger protein Z; lassa fever virus-Z, negati	97.0
2jun_A		101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.95
2lri_C		66	Autoimmune regulator; Zn binding protein domain, a	95.02
1wil_A		89	KIAA1045 protein; ring finger domain, structural g	93.64
2ysm_A		111	Myeloid/lymphoid or mixed-lineage leukemia protein	91.23
1f62_A		51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	90.26
2l5u_A		61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	89.96
1mm2_A		61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	89.38
3m62_A		968	Ubiquitin conjugation factor E4; armadillo-like re	89.34
1fp0_A		88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	88.84
2puy_A		60	PHD finger protein 21A; PHD finger, histone CODE,	88.06
2k16_A		75	Transcription initiation factor TFIID subunit 3; p	87.95
2yql_A		56	PHD finger protein 21A; PHD domain, structural gen	87.74
1we9_A		64	PHD finger family protein; structural genomics, PH	86.75
2cs3_A		93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	86.65
1weo_A		93	Cellulose synthase, catalytic subunit (IRX3); stru	85.38
3i2d_A		371	E3 SUMO-protein ligase SIZ1; signal transduction,	84.22
4fo9_A		360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	83.78
3v43_A		112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	83.58
1xwh_A		66	Autoimmune regulator; PHD domain, Zn binding domai	83.36
2l43_A		88	N-teminal domain from histone H3.3, linker, PHD1 f	82.35
2e6s_A		77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	82.27
2lbm_A		142	Transcriptional regulator ATRX; metal binding prot	81.9
2vpb_A		65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	81.31

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

Probab=99.66  E-value=6.6e-17  Score=105.44  Aligned_cols=51  Identities=29%  Similarity=0.752  Sum_probs=46.1

Q ss_pred             CCCcccccccccccCCCCceecC-CCCccCHHHHHHHHhcCCCCCccCCCCc
Q 040167          172 EDEDVCPTCLEEYTPENPKIVTK-CSHHFHLGCIYEWMERSENCPVCGKVMV  222 (227)
Q Consensus       172 ~~~~~C~ICle~~~~~~~~~~l~-C~H~FH~~CI~~Wl~~~~tCPvCr~~v~  222 (227)
                      +++..|+||++.|..++..+.++ |+|.||..||.+|++.+.+||+||+.+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            45679999999999877777776 9999999999999999999999999875

PyMOL of 1iym

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; 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

>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

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, 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

>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

>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

>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

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

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

>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

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

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

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

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

>2ecy_A TNF receptor-associated factor 3; metal binding protein, 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

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

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

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger 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

>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

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; 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

>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

>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

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

>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

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

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

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

>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

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

>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

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

>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

>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

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

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

>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

>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

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

>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

>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

>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

>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

>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

>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

>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

>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

>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

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

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

>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

>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

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

>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

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

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

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

>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

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

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

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

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

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

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

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2	Back alignment and structure

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}	Back alignment and structure

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A	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

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2	Back alignment and structure

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}	Back alignment and structure

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*	Back alignment and structure

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2	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

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

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

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

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A	Back alignment and structure

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A	Back alignment and structure

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}	Back alignment and structure

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A	Back alignment and structure

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		227
d1iyma_		55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	2e-11
d1chca_		68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-09
d3dplr1		88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	9e-08
d1fbva4		79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-06
d1vyxa_		60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	8e-06
d1g25a_		65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	9e-06
d1jm7a_		103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	5e-05
d1wima_		94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	2e-04
d1bora_		56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	4e-04
d1ur6b_		52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	4e-04
d1rmda2		86	g.44.1.1 (A:1-86) V(D)J recombination activating p	4e-04
d1v87a_		114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	5e-04
d1jm7b_		97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	0.003

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


class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 55.6 bits (134), Expect = 2e-11
 Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 1/47 (2%)

Query: 172 EDEDVCPTCLEEYT-PENPKIVTKCSHHFHLGCIYEWMERSENCPVC 217
           +D   C  CL E    E  + + +C H FH  C+  W+     CP+C
Sbjct: 3   DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLC 49

PyMOL of d1iyma_

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

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

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

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

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

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

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

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

>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

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114	Back information, alignment and structure

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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		227
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.75
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	99.59
d3dplr1		88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.58
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.55
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	99.55
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.54
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.5
d2baya1		56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.43
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	99.37
d1vyxa_		60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.36
d1bora_		56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.35
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.35
d2c2la2		80	STIP1 homology and U box-containing protein 1, STU	99.21
d1t1ha_		78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.19
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.18
d1wgma_		98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.02
d1wima_		94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.72
d1f62a_		51	Williams-Beuren syndrome transcription factor, WST	94.95
d1fp0a1		70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	92.87
d1wila_		89	Hypothetical protein KIAA1045 {Human (Homo sapiens	92.86
d1mm2a_		61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	92.33
d2cs3a1		80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	88.13
d1weoa_		93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	86.38
d1z60a1		59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	84.37
d1we9a_		64	PHD finger protein At5g26210 {Thale cress (Arabido	84.02
d1wema_		76	Death associated transcription factor 1, Datf1 (DI	82.07

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=99.75  E-value=3.2e-19  Score=115.63  Aligned_cols=51  Identities=29%  Similarity=0.773  Sum_probs=45.2

Q ss_pred             CCCcccccccccccCCCCceec-CCCCccCHHHHHHHHhcCCCCCccCCCCc
Q 040167          172 EDEDVCPTCLEEYTPENPKIVT-KCSHHFHLGCIYEWMERSENCPVCGKVMV  222 (227)
Q Consensus       172 ~~~~~C~ICle~~~~~~~~~~l-~C~H~FH~~CI~~Wl~~~~tCPvCr~~v~  222 (227)
                      +++.+|+|||++|..++.++.+ .|+|.||..||.+||+++.+||+||++|.
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            4667899999999987766655 69999999999999999999999999875

PyMOL of d1iyma_

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

>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

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

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

>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

>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

>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

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

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

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

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

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

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

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

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

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

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

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

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

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

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

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure