Citrus Sinensis ID: 025079

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-------26

MKRVRDMEVMYYQLAKSSYQDSLKVLEADIQHANALAAAIPRAKGGARLQMKLVYDHWAPLFWFLLQWVNSSCMCVLPRYLNFFHILVYKVSADDRPSLTSPGRKATIREFYGVILPSLQRLHSNLRELDDAKIENLEIGSFDRMRGDSQVGSADLEREDECGICLEPCTKMVLPNCCHAMCIKCYRNWNTKSESCPFCRGSMKRVNSEDLWVLTCTDDVIDPETVSKEDLLRFYLYINSLPKDYPDALFVVYYEYLI

cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEEEEEccccccHHHHHHHHHHHcccccccccccccEEEEEEEEEcccccccccccccccHHHHHHHHcHHHHHHccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccEEEcccccccccccccHHHHHHHHHcccccccccccccHHHHHHccc

cccHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHccccccccEEEEEEEcccHHHHHHHHHHHHcccccHHHHHHHccEEEEEEEEEcccccccccHcHHcHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHccccccccccccccccHHHccEEccccccEEccccccHHHHHHHHHHHHccccccccHHHccEcccccEEEEEcccccccHHHHHHHHHHHHHHHHHHcccccccHHEHHHHHHcc

MKRVRDMEVMYYQLAKSSYQDSLKVLEADIQHANALAAAIPRAKGGARLQMKLVYDHWAPLFWFLLQWVNsscmcvlprylNFFHILVYKvsaddrpsltspgrkaTIREFYGVILPSLQRLHSNLRelddakienleigsfdrmrgdsqvgsadleredecgiclepctkmvlpncchamcikcyrnwntksescpfcrgsmkrvnsedlwvltctddvidpetvskeDLLRFYLYINslpkdypdaLFVVYYEYLI

MKRVRDMEVMYYQLAKSSYQDSLKVLEADIQHANALAAAIPRAKGGARLQMKLVYDHWAPLFWFLLQWVNSSCMCVLPRYLNFFHILVYKVsaddrpsltspgrkatiREFYGVILPSLQRLHSNLRELDDAKIEnleigsfdrmrgDSQVGSADLEREDECGICLEPCTKMVLPNCCHAMCIKCYRNWNTKSESCPFCRGSMKRVNSEDLWVLTCTDDVIDPETVSKEDLLRFYLYInslpkdypdaLFVVYYEYLI

********VMYYQLAKSSYQDSLKVLEADIQHANALAAAIPRAKGGARLQMKLVYDHWAPLFWFLLQWVNSSCMCVLPRYLNFFHILVYKVSA***********KATIREFYGVILPSLQRLHSNLRELDDAKIENLEI********************DECGICLEPCTKMVLPNCCHAMCIKCYRNWNTKSESCPFCRGSMKRVNSEDLWVLTCTDDVIDPETVSKEDLLRFYLYINSLPKDYPDALFVVYYEYL*

*****D****YY**********LKVLEADIQHANALAAAIPRAKGGARLQMKLVYDHWAPLFWFLLQWVNSSCMCVLPRYLNFFHILVYKVSADDRPSLTSPGRKATIREFYGVILPSLQ****************************************ECGICLEPCTKMVLPNCCHAMCIKCYRNWNTKSESCPFCRGSMKRVNSEDLWVLTCTDDVIDPETVSKEDLLRFYLYINSLPKDYPDALFVVYYEYLI

********VMYYQLAKSSYQDSLKVLEADIQHANALAAAIPRAKGGARLQMKLVYDHWAPLFWFLLQWVNSSCMCVLPRYLNFFHILVYKVSADDRPSLTSPGRKATIREFYGVILPSLQRLHSNLRELDDAKIENLEIGSFDRMRG************DECGICLEPCTKMVLPNCCHAMCIKCYRNWNTKSESCPFCRGSMKRVNSEDLWVLTCTDDVIDPETVSKEDLLRFYLYINSLPKDYPDALFVVYYEYLI

**RVRDMEVMYYQLAKSSYQDSLKVLEADIQHANALAAAIPRAKGGARLQMKLVYDHWAPLFWFLLQWVNSSCMCVLPRYLNFFHILVYKVSADDRPSLTSPGRKATIREFYGVILPSLQRLHSNLRELDDAKIENLEIGSFDRM*GDSQVGSADLEREDECGICLEPCTKMVLPNCCHAMCIKCYRNWNTKSESCPFCRGSMKRVNSEDLWVLTCTDDVIDPETVSKEDLLRFYLYINSLPKDYPDALFVVYYEYLI

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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		258	2.2.26 [Sep-21-2011]
Q5ZM74		230	RING finger protein 141 O	yes	no	0.209	0.234	0.385	2e-05
Q6IV56		222	RING finger protein 141 O	yes	no	0.220	0.256	0.366	3e-05
Q32L15		230	RING finger protein 141 O	yes	no	0.220	0.247	0.366	5e-05
Q2XNS1		231	RING finger protein 141 O	yes	no	0.220	0.246	0.366	5e-05
Q6IV57		230	RING finger protein 141 O	yes	no	0.220	0.247	0.366	5e-05
Q5R7K8		230	RING finger protein 141 O	yes	no	0.220	0.247	0.366	5e-05
Q8WVD5		230	RING finger protein 141 O	yes	no	0.220	0.247	0.366	5e-05
Q99MB7		230	RING finger protein 141 O	yes	no	0.220	0.247	0.366	5e-05
Q7ZX20		540	E3 ubiquitin-protein liga	N/A	no	0.255	0.122	0.328	0.0002
Q9SL78		390	Putative RING-H2 finger p	no	no	0.383	0.253	0.324	0.0002

>sp\|Q5ZM74\|RN141_CHICK RING finger protein 141 OS=Gallus gallus GN=RNF141 PE=2 SV=1	Back alignment and function desciption

 Score = 49.7 bits (117), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 3/57 (5%)

Query: 159 EDECGICLEPCTKMVLPNCCHAMCIKCYRNWNTKSESCPFCRGSMKRVNSEDLWVLT 215
           EDEC IC++    ++LP C H+ C KC   W+ +  SCP CR  +    + D WV++
Sbjct: 152 EDECCICMDGRVDLILP-CAHSFCQKCIDKWSDRHRSCPVCRRQV--TGAGDSWVVS 205

Gallus gallus (taxid: 9031)

>sp\|Q6IV56\|RN141_DANRE RING finger protein 141 OS=Danio rerio GN=rnf141 PE=2 SV=2	Back alignment and function description

>sp\|Q32L15\|RN141_BOVIN RING finger protein 141 OS=Bos taurus GN=RNF141 PE=2 SV=1	Back alignment and function description

>sp\|Q2XNS1\|RN141_CANFA RING finger protein 141 OS=Canis familiaris GN=RNF141 PE=2 SV=1	Back alignment and function description

>sp\|Q6IV57\|RN141_RAT RING finger protein 141 OS=Rattus norvegicus GN=Rnf141 PE=2 SV=1	Back alignment and function description

>sp\|Q5R7K8\|RN141_PONAB RING finger protein 141 OS=Pongo abelii GN=RNF141 PE=2 SV=1	Back alignment and function description

>sp\|Q8WVD5\|RN141_HUMAN RING finger protein 141 OS=Homo sapiens GN=RNF141 PE=1 SV=1	Back alignment and function description

>sp\|Q99MB7\|RN141_MOUSE RING finger protein 141 OS=Mus musculus GN=Rnf141 PE=2 SV=2	Back alignment and function description

>sp\|Q7ZX20\|RNF8A_XENLA E3 ubiquitin-protein ligase RNF8-A OS=Xenopus laevis GN=rnf8-a PE=2 SV=1	Back alignment and function description

>sp\|Q9SL78\|ATL12_ARATH Putative RING-H2 finger protein ATL12 OS=Arabidopsis thaliana GN=ATL12 PE=3 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		258
224100091		254	predicted protein [Populus trichocarpa]	0.976	0.992	0.755	1e-112
255547928		254	ubiquitin-protein ligase, putative [Rici	0.976	0.992	0.755	1e-112
224107701		254	predicted protein [Populus trichocarpa]	0.976	0.992	0.755	1e-111
225425930		254	PREDICTED: uncharacterized protein LOC10	0.976	0.992	0.712	1e-105
449435023		253	PREDICTED: uncharacterized protein LOC10	0.965	0.984	0.703	1e-102
449450409		251	PREDICTED: uncharacterized protein LOC10	0.965	0.992	0.689	1e-100
169219251		251	putative protein-binding/zinc ion-bindin	0.965	0.992	0.685	1e-100
297851138		251	protein binding protein [Arabidopsis lyr	0.953	0.980	0.708	8e-99
18395478		251	RING/U-box domain-containing protein [Ar	0.953	0.980	0.708	1e-98
356512343		256	PREDICTED: uncharacterized protein LOC10	0.976	0.984	0.710	2e-98

>gi\|224100091\|ref\|XP_002311740.1\| predicted protein [Populus trichocarpa] gi\|222851560\|gb\|EEE89107.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  411 bits (1056), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 192/254 (75%), Positives = 225/254 (88%), Gaps = 2/254 (0%)

Query: 7   MEVMYYQLAKSSYQDSLKVLEADIQHANALAAAIPRAKGGARLQMKLVYDHWAPLFWFLL 66
           ME+M+YQL+ SSYQDSLKVLEADIQHANALAAAIPR K GARLQMKLVY+ WAPL +FLL
Sbjct: 1   MEMMHYQLSNSSYQDSLKVLEADIQHANALAAAIPRGKDGARLQMKLVYNRWAPLLFFLL 60

Query: 67  QWVNSSCMCVLPRYLNFFHILVYKVSADDRPSLTSPGRKATIREFYGVILPSLQRLHSNL 126
           Q ++ SC+C+LPRYLNFFH+L+YKV +D RPSL+  GRKATIREFYGVI PSLQRLHSNL
Sbjct: 61  QRIDCSCICLLPRYLNFFHVLLYKVYSDGRPSLSKHGRKATIREFYGVISPSLQRLHSNL 120

Query: 127 RELDDAKIENLEIGSF--DRMRGDSQVGSADLEREDECGICLEPCTKMVLPNCCHAMCIK 184
            EL+D K +N  + S   +++ GD+++ + DLEREDECGICLEPCTKMVLPNCCHAMCIK
Sbjct: 121 EELEDVKGDNSGMESLCKNKVEGDNKLANIDLEREDECGICLEPCTKMVLPNCCHAMCIK 180

Query: 185 CYRNWNTKSESCPFCRGSMKRVNSEDLWVLTCTDDVIDPETVSKEDLLRFYLYINSLPKD 244
           CYRNWNT+SESCPFCRGS+KRVNSEDLWVLTC ++V+D + VSKEDL RFYLY+NSLPKD
Sbjct: 181 CYRNWNTRSESCPFCRGSLKRVNSEDLWVLTCNNEVVDTKAVSKEDLSRFYLYVNSLPKD 240

Query: 245 YPDALFVVYYEYLI 258
           Y D+LF++YYEYLI
Sbjct: 241 YHDSLFLMYYEYLI 254

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255547928\|ref\|XP_002515021.1\| ubiquitin-protein ligase, putative [Ricinus communis] gi\|223546072\|gb\|EEF47575.1\| ubiquitin-protein ligase, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|224107701\|ref\|XP_002314569.1\| predicted protein [Populus trichocarpa] gi\|222863609\|gb\|EEF00740.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|225425930\|ref\|XP_002272699.1\| PREDICTED: uncharacterized protein LOC100240870 [Vitis vinifera] gi\|297738321\|emb\|CBI27522.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449435023\|ref\|XP_004135295.1\| PREDICTED: uncharacterized protein LOC101206911 [Cucumis sativus] gi\|449512970\|ref\|XP_004164192.1\| PREDICTED: uncharacterized protein LOC101223721 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449450409\|ref\|XP_004142955.1\| PREDICTED: uncharacterized protein LOC101204614 [Cucumis sativus] gi\|449494510\|ref\|XP_004159565.1\| PREDICTED: uncharacterized protein LOC101226593 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|169219251\|gb\|ACA50446.1\| putative protein-binding/zinc ion-binding protein [Cucumis sativus]	Back alignment and taxonomy information

>gi\|297851138\|ref\|XP_002893450.1\| protein binding protein [Arabidopsis lyrata subsp. lyrata] gi\|297339292\|gb\|EFH69709.1\| protein binding protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|18395478\|ref\|NP_564218.1\| RING/U-box domain-containing protein [Arabidopsis thaliana] gi\|9743332\|gb\|AAF97956.1\|AC000103_6 F21J9.10 [Arabidopsis thaliana] gi\|21553664\|gb\|AAM62757.1\| unknown [Arabidopsis thaliana] gi\|24030317\|gb\|AAN41327.1\| unknown protein [Arabidopsis thaliana] gi\|332192409\|gb\|AEE30530.1\| RING/U-box domain-containing protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|356512343\|ref\|XP_003524879.1\| PREDICTED: uncharacterized protein LOC100790422 [Glycine max]	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		258
TAIR\|locus:2024026		251	AT1G24440 [Arabidopsis thalian	0.953	0.980	0.708	1.6e-95
TAIR\|locus:505006120		260	AT1G13195 [Arabidopsis thalian	0.957	0.95	0.667	2.5e-88
TAIR\|locus:505006703		242	AT5G58787 "AT5G58787" [Arabido	0.899	0.958	0.451	4.8e-55
TAIR\|locus:2149750		242	AIRP2 "ABA Insensitive RING Pr	0.906	0.966	0.454	2.1e-52
UNIPROTKB\|E1BTQ2		136	RNF8 "Uncharacterized protein"	0.255	0.485	0.328	1.1e-06
UNIPROTKB\|I3LUY7		135	I3LUY7 "Uncharacterized protei	0.255	0.488	0.328	2.4e-06
UNIPROTKB\|Q5ZM74		230	RNF141 "RING finger protein 14	0.209	0.234	0.385	2.8e-06
ZFIN\|ZDB-GENE-040625-71		222	rnf141 "ring finger protein 14	0.290	0.337	0.329	4.4e-06
UNIPROTKB\|Q32L15		230	RNF141 "RING finger protein 14	0.220	0.247	0.366	6.6e-06
UNIPROTKB\|F1Q4F0		230	RNF141 "RING finger protein 14	0.220	0.247	0.366	6.6e-06

TAIR\|locus:2024026 AT1G24440 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 950 (339.5 bits), Expect = 1.6e-95, P = 1.6e-95
 Identities = 180/254 (70%), Positives = 206/254 (81%)

Query:    10 MYYQLAKSSYQDSLKVLEADIQHANALAAAIPRAKGGARLQMKLVYDHWAPLFWFLLQWV 69
             MYYQL KSSY+DSLK+LEADI+HAN LAA IP  K G RLQMKLV  + AP F FLLQW+
Sbjct:     1 MYYQLTKSSYRDSLKILEADIEHANGLAAEIPMGKSGVRLQMKLVCSNLAPFFIFLLQWM 60

Query:    70 NSSCMCVLPRYLNFFHILVYKVSADDRPSLTSPGRKATIREFYGVILPSLQRLHSNLREL 129
             + SC+  LPRY +FFHIL+YKV AD R + +  GRKATIREFYGVILPSL+RLH N  +L
Sbjct:    61 DFSCL--LPRYFDFFHILIYKVRADGRWNRSRYGRKATIREFYGVILPSLERLHINFADL 118

Query:   130 DDAKI-----ENLEIGSFDRMRGDSQVGSADLEREDECGICLEPCTKMVLPNCCHAMCIK 184
              D  +     + +    +D + G   + S DLEREDECGICLEPCTKMVLPNCCHAMCIK
Sbjct:   119 PDESLWYPNPKAITKKQYD-IEGSRYMNSIDLEREDECGICLEPCTKMVLPNCCHAMCIK 177

Query:   185 CYRNWNTKSESCPFCRGSMKRVNSEDLWVLTCTDDVIDPETVSKEDLLRFYLYINSLPKD 244
             CYRNWNTKSESCPFCRGS+KRVNSEDLWVLTC +DV+DPETV+KEDLLRFYL+INSLPKD
Sbjct:   178 CYRNWNTKSESCPFCRGSIKRVNSEDLWVLTCDEDVVDPETVTKEDLLRFYLHINSLPKD 237

Query:   245 YPDALFVVYYEYLI 258
             YP+A F+VY EYLI
Sbjct:   238 YPEAAFLVYNEYLI 251

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

TAIR\|locus:505006120 AT1G13195 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:505006703 AT5G58787 "AT5G58787" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2149750 AIRP2 "ABA Insensitive RING Protein 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BTQ2 RNF8 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|I3LUY7 I3LUY7 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5ZM74 RNF141 "RING finger protein 141" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-040625-71 rnf141 "ring finger protein 141" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|Q32L15 RNF141 "RING finger protein 141" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|F1Q4F0 RNF141 "RING finger protein 141" [Canis lupus familiaris (taxid:9615)]	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	LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_fgenesh4_pm.C_LG_VIII0763	hypothetical protein (254 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		258
pfam13639		46	pfam13639, zf-RING_2, Ring finger domain	2e-07
cd00162		45	cd00162, RING, RING-finger (Really Interesting New	2e-07
PHA02929		238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	7e-07
pfam13923		45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	8e-07
smart00184		40	smart00184, RING, Ring finger	3e-06
pfam13920		49	pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RI	2e-05
pfam00097		40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	5e-05
PHA02926		242	PHA02926, PHA02926, zinc finger-like protein; Prov	0.002

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

 Score = 46.6 bits (111), Expect = 2e-07
 Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 3/46 (6%)

Query: 160 DECGICLEPCT---KMVLPNCCHAMCIKCYRNWNTKSESCPFCRGS 202
           DEC ICL+      ++V+  C H    +C   W   S +CP CR  
Sbjct: 1   DECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

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

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

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

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

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

>gnl\|CDD\|165237 PHA02926, PHA02926, zinc finger-like protein; Provisional	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		258
KOG1039		344	consensus Predicted E3 ubiquitin ligase [Posttrans	99.71
PHA02929		238	N1R/p28-like protein; Provisional	99.25
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	99.18
PHA02926		242	zinc finger-like protein; Provisional	99.16
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.16
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.15
KOG0317		293	consensus Predicted E3 ubiquitin ligase, integral	99.14
KOG0823		230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.04
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.01
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.99
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	98.97
COG5243		491	HRD1 HRD ubiquitin ligase complex, ER membrane com	98.88
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	98.85
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.84
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	98.83
TIGR00599		397	rad18 DNA repair protein rad18. This family is bas	98.79
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.79
KOG4628		348	consensus Predicted E3 ubiquitin ligase [Posttrans	98.74
PF14634		44	zf-RING_5: zinc-RING finger domain	98.71
KOG0287		442	consensus Postreplication repair protein RAD18 [Re	98.71
PF12861		85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.71
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.65
KOG2164		513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.62
COG5540		374	RING-finger-containing ubiquitin ligase [Posttrans	98.62
COG5432		391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.58
COG5574		271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.56
KOG4172		62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.48
PF04564		73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.39
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	98.36
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.34
TIGR00570		309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.32
KOG2177		386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.26
KOG4265		349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.08
PF14835		65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.05
KOG4159		398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.96
COG5194		88	APC11 Component of SCF ubiquitin ligase and anapha	97.96
KOG1785		563	consensus Tyrosine kinase negative regulator CBL [	97.95
KOG0978		698	consensus E3 ubiquitin ligase involved in syntaxin	97.86
KOG0828		636	consensus Predicted E3 ubiquitin ligase [Posttrans	97.83
KOG1734		328	consensus Predicted RING-containing E3 ubiquitin l	97.79
KOG1493		84	consensus Anaphase-promoting complex (APC), subuni	97.76
COG5219		1525	Uncharacterized conserved protein, contains RING Z	97.72
PF11793		70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.64
KOG0824		324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.61
KOG0311		381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.58
KOG1002		791	consensus Nucleotide excision repair protein RAD16	97.54
COG5152		259	Uncharacterized conserved protein, contains RING a	97.52
KOG2879		298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.42
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.35
KOG0297		391	consensus TNF receptor-associated factor [Signal t	97.35
KOG4692		489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.31
smart00744		49	RINGv The RING-variant domain is a C4HC3 zinc-fing	97.3
PHA03096		284	p28-like protein; Provisional	97.28
KOG1813		313	consensus Predicted E3 ubiquitin ligase [Posttrans	97.24
KOG0827		465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.12
KOG2930		114	consensus SCF ubiquitin ligase, Rbx1 component [Po	97.07
PF11789		57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	96.9
KOG2660		331	consensus Locus-specific chromosome binding protei	96.78
KOG0825		1134	consensus PHD Zn-finger protein [General function	96.76
COG5236		493	Uncharacterized conserved protein, contains RING Z	96.65
KOG4275		350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.64
KOG1645		463	consensus RING-finger-containing E3 ubiquitin liga	96.56
KOG1571		355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.34
KOG4739		233	consensus Uncharacterized protein involved in syna	96.17
KOG4185		296	consensus Predicted E3 ubiquitin ligase [Posttrans	96.12
KOG3002		299	consensus Zn finger protein [General function pred	95.97
PF10367		109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	95.89
PF14570		48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.67
KOG1941		518	consensus Acetylcholine receptor-associated protei	95.35
KOG1001		674	consensus Helicase-like transcription factor HLTF/	95.26
PF07800		162	DUF1644: Protein of unknown function (DUF1644); In	95.09
KOG1428		3738	consensus Inhibitor of type V adenylyl cyclases/Ne	95.07
PHA02862		156	5L protein; Provisional	95.0
PF14447		55	Prok-RING_4: Prokaryotic RING finger family 4	94.89
PHA02825		162	LAP/PHD finger-like protein; Provisional	94.84
PF04641		260	Rtf2: Rtf2 RING-finger	94.62
KOG2114		933	consensus Vacuolar assembly/sorting protein PEP5/V	94.2
KOG3039		303	consensus Uncharacterized conserved protein [Funct	94.17
COG5222		427	Uncharacterized conserved protein, contains RING Z	94.15
PF10272		358	Tmpp129: Putative transmembrane protein precursor;	93.93
KOG4445		368	consensus Uncharacterized conserved protein, conta	93.81
KOG3268		234	consensus Predicted E3 ubiquitin ligase [Posttrans	93.3
COG5220		314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	93.22
KOG1814		445	consensus Predicted E3 ubiquitin ligase [Posttrans	92.97
KOG4367		699	consensus Predicted Zn-finger protein [Function un	92.52
KOG1100		207	consensus Predicted E3 ubiquitin ligase [Posttrans	92.42
COG5175		480	MOT2 Transcriptional repressor [Transcription]	92.38
KOG2932		389	consensus E3 ubiquitin ligase involved in ubiquiti	92.3
KOG3800		300	consensus Predicted E3 ubiquitin ligase containing	92.08
PF03854		50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	92.04
KOG1952		950	consensus Transcription factor NF-X1, contains NFX	92.0
PF05290		140	Baculo_IE-1: Baculovirus immediate-early protein (	91.63
KOG0826		357	consensus Predicted E3 ubiquitin ligase involved i	91.35
KOG0298		1394	consensus DEAD box-containing helicase-like transc	90.59
KOG3970		299	consensus Predicted E3 ubiquitin ligase [Posttrans	90.49
PF05883		134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	89.95
KOG2034		911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	89.44
PF12906		47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	89.31
PF08746		43	zf-RING-like: RING-like domain; InterPro: IPR01485	87.95
KOG4362		684	consensus Transcriptional regulator BRCA1 [Replica	87.74
PLN02638		1079	cellulose synthase A (UDP-forming), catalytic subu	87.59
PF14569		80	zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.	87.52
KOG1940		276	consensus Zn-finger protein [General function pred	86.41
KOG3799		169	consensus Rab3 effector RIM1 and related proteins,	85.67
KOG3899		381	consensus Uncharacterized conserved protein [Funct	82.86
PLN02189		1040	cellulose synthase	82.59
KOG2817		394	consensus Predicted E3 ubiquitin ligase [Posttrans	82.02
PLN02436		1094	cellulose synthase A	82.01
KOG1812		384	consensus Predicted E3 ubiquitin ligase [Posttrans	80.68

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

Probab=99.71  E-value=1.3e-18  Score=161.41  Aligned_cols=217  Identities=22%  Similarity=0.340  Sum_probs=160.8

Q ss_pred             HHhHHHHHHHHHhCCCcCCCceEEEEEeecCc-chHHHHHHHHhhcccccccccccceeEEEEEEee-cCCCCCcCcccc
Q 025079           27 EADIQHANALAAAIPRAKGGARLQMKLVYDHW-APLFWFLLQWVNSSCMCVLPRYLNFFHILVYKVS-ADDRPSLTSPGR  104 (258)
Q Consensus        27 ~~di~~an~la~~~p~~~~g~~~qm~l~y~~~-a~~~lfl~qw~d~~~~~~l~~~lgl~~iliy~vy-~dg~~~~s~~~r  104 (258)
                      +.+++++ |.+..+|+++.+..-+||++++.. .++..++++|+++.    .++ .|+..++++..+ .++..+++...|
T Consensus         2 d~~~~~~-tic~~~~~g~c~~g~~cr~~h~~~~~~~~~~~~~~~s~~----~~~-~~~~~~~~~~~~~~~~s~~~s~~~~   75 (344)
T KOG1039|consen    2 DLSLSQE-TICKYYQKGNCKFGDLCRLSHSLPDEEFATLLTPTTSSA----AAS-TGLSQSLIWANAVADASATMSVSSR   75 (344)
T ss_pred             ccccccc-hhhhhcccccccccceeeeeccCchhhcccccccccccc----ccc-cccchhhcccchhhccccccchhcc
Confidence            4578888 999999999999999999999777 78788899999776    343 678888899988 888888888777


Q ss_pred             --cccHHHHHHhhchhH---------HHHHhhhhhhh------------------HHhhhh-hhccc-ccccccCCCCCC
Q 025079          105 --KATIREFYGVILPSL---------QRLHSNLRELD------------------DAKIEN-LEIGS-FDRMRGDSQVGS  153 (258)
Q Consensus       105 --~asi~efy~~I~psl---------~qL~~~i~~~e------------------~~q~~~-~~~~~-~~~~~~~~~~~~  153 (258)
                        ..+++.++++.+++-         .+...+...+.                  ..++.. .+... .....+.++...
T Consensus        76 ~~~~~~~~s~~~~~~s~~~~~~~~~~~~~~~g~~~~~~~~~~~~~c~l~~~~pi~~~~~~~~~~~~~~~~~~~~~e~~~a  155 (344)
T KOG1039|consen   76 PVLTAIRASSSISEPSSTQENPYSNHGQCRFGNGDVTLNGNNPESCGLGTQHPICKRQYKNSMKRGSSCALSSAMERSFA  155 (344)
T ss_pred             cchhhhhhhhccccccccccCccccccccccCCcccccccccccccccccccchhHHHHhhhhcccccccchHhhhhccC
Confidence              788999999888872         11111111111                  111111 11110 111112222222


Q ss_pred             CCCCCcCccccccCCCCcc--------eecCCCCcccHhhHHHHh--cC-----CCCccccccccccccCCCceeecCCC
Q 025079          154 ADLEREDECGICLEPCTKM--------VLPNCCHAMCIKCYRNWN--TK-----SESCPFCRGSMKRVNSEDLWVLTCTD  218 (258)
Q Consensus       154 ~~~~~~~~C~ICle~~~~~--------vl~~C~H~FC~~Ci~~w~--~~-----~~~CP~CR~~l~~~~~~~~~~~~~~~  218 (258)
                      .....+.+|+||||.....        ++++|.|.||.+||+.|.  .+     +++||+||.+...++++..|+.+...
T Consensus       156 ~~~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~~Wv~t~~~  235 (344)
T KOG1039|consen  156 LQKSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSFWVETKEE  235 (344)
T ss_pred             cCccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccceeeeeccc
Confidence            2335578999999977653        458999999999999997  44     57999999999999999999999998


Q ss_pred             CccCCcccchHHHHHHHHHhhcCCCCCcchh
Q 025079          219 DVIDPETVSKEDLLRFYLYINSLPKDYPDAL  249 (258)
Q Consensus       219 d~vd~~~i~~E~l~Rl~~~i~~lP~~~p~~~  249 (258)
                      +..+.++..++...+...|+.+.+..-|..=
T Consensus       236 k~~li~e~~~~~s~~~c~yf~~~~g~cPf~s  266 (344)
T KOG1039|consen  236 KQKLIEEYEAEMSAKDCKYFSQGLGSCPFGS  266 (344)
T ss_pred             ccccHHHHHHHhhccchhhhcCCCCCCCCCC
Confidence            8888888888889999999998887777643

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

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

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

>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

>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

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

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

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

>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

>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

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

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

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

Back alignment and domain information

>TIGR00599 rad18 DNA repair protein rad18	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

>KOG4628 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

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

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

>smart00184 RING Ring finger	Back alignment and domain information

>KOG2164 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

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

>COG5574 PEX10 RING-finger-containing 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

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

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

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

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

>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

>KOG4159 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

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

>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [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

>KOG1734 consensus Predicted RING-containing 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

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

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

>KOG0824 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

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]	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

>KOG2879 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

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

>KOG4692 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

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

>KOG1813 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

>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [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

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

>KOG0825 consensus PHD Zn-finger protein [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

>KOG4275 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

>KOG1571 consensus Predicted 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

>KOG4185 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

>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

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

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

>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

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

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

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

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

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

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

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

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

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

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

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

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

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

>KOG1100 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

>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [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

>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

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

>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]	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

>KOG3970 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

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

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

>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

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

>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit	Back alignment and domain information

>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A	Back alignment and domain information

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

>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

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

>PLN02189 cellulose synthase	Back alignment and domain information

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

>PLN02436 cellulose synthase A	Back alignment and domain information

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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		258
2ecn_A		70	Solution Structure Of The Ring Domain Of The Human		4e-06
4epo_C		149	Crystal Structure Of Rnf8 Bound To The Ubc13MMS2 HE		4e-04

>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring Finger Protein 141 Length = 70

Back alignment and structure

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 156 LEREDECGICLEPCTKMVLPNCCHAMCIKCYRNWNTKSESCPFCRGSMKRVN 207
           L  E+EC IC++    ++LP C H+ C KC   W+ +  +CP CR  M   N
Sbjct: 12  LTDEEECCICMDGRADLILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGAN 62

PyMOL of 2ecn

>pdb|4EPO|C Chain C, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2 HETERODIMER Length = 149

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		258
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	4e-19
4epo_C		149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	4e-19
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	6e-12
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	2e-08
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	4e-08
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	5e-08
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	8e-08
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	9e-08
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-07
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	4e-07
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	9e-07
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	2e-06
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	2e-06
1z6u_A		150	NP95-like ring finger protein isoform B; structura	2e-06
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	4e-06
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	7e-06
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	8e-06
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	1e-05
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	2e-05
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	2e-05
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	2e-05
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	2e-05
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	3e-05
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	6e-05
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	6e-05
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	7e-05
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	7e-05
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	1e-04
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	1e-04
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	1e-04
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	2e-04
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	2e-04
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	2e-04
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	2e-04
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	2e-04
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	5e-04
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	6e-04
2ect_A		78	Ring finger protein 126; metal binding protein, st	6e-04
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	6e-04
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	7e-04
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	7e-04
2ea5_A		68	Cell growth regulator with ring finger domain prot	8e-04

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

 Score = 77.8 bits (192), Expect = 4e-19
 Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 155 DLEREDECGICLEPCTKMVLPNCCHAMCIKCYRNWNTKSESCPFCRGSMKRVNSE 209
            L  E+EC IC++    ++LP C H+ C KC   W+ +  +CP CR  M   N  
Sbjct: 11  QLTDEEECCICMDGRADLILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGANES 64

PyMOL of 2ecn

>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

>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

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

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens} Length = 100	Back alignment and structure

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

>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

>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

>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

>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

>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 Length = 64	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

>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

>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

>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* Length = 63	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

>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

>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

>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

>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

>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

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

>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

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

>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

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

>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

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

>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

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

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

>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

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

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 68	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		258
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.35
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	99.35
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	99.34
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	99.34
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.33
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	99.33
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.32
4ayc_A		138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.31
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	99.31
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	99.31
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	99.3
1t1h_A		78	Gspef-atpub14, armadillo repeat containing protein	99.3
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	99.29
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	99.29
2ect_A		78	Ring finger protein 126; metal binding protein, st	99.28
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.28
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	99.28
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	99.27
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	99.27
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	99.27
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	99.27
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.26
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	99.26
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	99.25
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.25
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.23
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.22
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.22
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	99.21
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	99.2
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	99.19
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.18
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.17
2kr4_A		85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.17
2kre_A		100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.14
1wgm_A		98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.14
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	99.14
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.13
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.12
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	99.11
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	99.11
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.11
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	99.1
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	99.1
1z6u_A		150	NP95-like ring finger protein isoform B; structura	99.09
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.06
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.04
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.04
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	99.03
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	99.03
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.03
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	98.99
4ic3_A		74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.97
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.97
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	98.95
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	98.95
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	98.88
2yu4_A		94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.84
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	98.83
2ea5_A		68	Cell growth regulator with ring finger domain prot	98.83
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.82
2f42_A		179	STIP1 homology and U-box containing protein 1; cha	98.81
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.73
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	98.7
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.57
3t6p_A		345	Baculoviral IAP repeat-containing protein 2; ring,	98.56
2bay_A		61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.46
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.4
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.39
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.28
3vk6_A		101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.04
3nw0_A		238	Non-structural maintenance of chromosomes element	97.19
2jun_A		101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.49
2ko5_A		99	Ring finger protein Z; lassa fever virus-Z, negati	93.49
2lri_C		66	Autoimmune regulator; Zn binding protein domain, a	90.99
1weo_A		93	Cellulose synthase, catalytic subunit (IRX3); stru	89.94
3u5n_A		207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	88.86
3m62_A		968	Ubiquitin conjugation factor E4; armadillo-like re	88.57
2l5u_A		61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	88.27
3o36_A		184	Transcription intermediary factor 1-alpha; TRIM24,	84.59
1mm2_A		61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	84.55
2yql_A		56	PHD finger protein 21A; PHD domain, structural gen	82.37

>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

Probab=99.35  E-value=6.9e-13  Score=94.16  Aligned_cols=52  Identities=25%  Similarity=0.650  Sum_probs=43.5

Q ss_pred             CCCCcCccccccCCCC---cceecCCCCcccHhhHHHHhcCCCCccccccccccc
Q 025079          155 DLEREDECGICLEPCT---KMVLPNCCHAMCIKCYRNWNTKSESCPFCRGSMKRV  206 (258)
Q Consensus       155 ~~~~~~~C~ICle~~~---~~vl~~C~H~FC~~Ci~~w~~~~~~CP~CR~~l~~~  206 (258)
                      +.+.+.+|+||++.+.   .++.++|||.||..|+.+|+..+.+||+||..+...
T Consensus        10 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           10 EEDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             STTCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             cCCCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            3355678999998774   456678999999999999998889999999998743

PyMOL of 2kiz

>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

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring 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

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} 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

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding 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

>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

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

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

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

>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

>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

>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

>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

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

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

>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

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

>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

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

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

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

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

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

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

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

>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

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

>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

>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

>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

>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

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

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

>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

>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

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

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

>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

>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

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

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

>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

>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

>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

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

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, 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

>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

>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

>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

>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

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

>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

>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

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_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

>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

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A	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

>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

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		258
d1iyma_		55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	6e-09
d1chca_		68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-08
d1fbva4		79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-08
d1rmda2		86	g.44.1.1 (A:1-86) V(D)J recombination activating p	3e-08
d1bora_		56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	1e-06
d1jm7a_		103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	3e-06
d3dplr1		88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	2e-05
d1g25a_		65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	2e-05
d1jm7b_		97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	7e-05
d1t1ha_		78	g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cre	2e-04
d2baya1		56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	6e-04
d1wgma_		98	g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Hu	9e-04
d1ur6b_		52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	0.002

>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 = 48.7 bits (116), Expect = 6e-09
 Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 4/49 (8%)

Query: 156 LEREDECGICLEP----CTKMVLPNCCHAMCIKCYRNWNTKSESCPFCR 200
           ++   EC +CL           LP C H    +C   W     +CP CR
Sbjct: 2   MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50

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

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

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

>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

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

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

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

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

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]} Length = 98	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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		258
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.45
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	99.39
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.37
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	99.28
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.25
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	99.25
d1bora_		56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.24
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.22
d2baya1		56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.22
d3dplr1		88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.18
d2c2la2		80	STIP1 homology and U box-containing protein 1, STU	99.16
d1t1ha_		78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.12
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.1
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.03
d1wgma_		98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.92
d1vyxa_		60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.92
d1wima_		94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.18
d1weoa_		93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	92.79
d1mm2a_		61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	87.39
d1fp0a1		70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	85.77
d1wila_		89	Hypothetical protein KIAA1045 {Human (Homo sapiens	84.35

>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=99.45  E-value=2e-14  Score=97.47  Aligned_cols=47  Identities=30%  Similarity=0.808  Sum_probs=40.3

Q ss_pred             CCcCccccccCCCCc----ceecCCCCcccHhhHHHHhcCCCCcccccccc
Q 025079          157 EREDECGICLEPCTK----MVLPNCCHAMCIKCYRNWNTKSESCPFCRGSM  203 (258)
Q Consensus       157 ~~~~~C~ICle~~~~----~vl~~C~H~FC~~Ci~~w~~~~~~CP~CR~~l  203 (258)
                      +++.+|+||++.+..    ..+++|+|.||..|+.+|+..+.+||+||.++
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i   53 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV   53 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCS
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEe
Confidence            445689999998864    34567999999999999999999999999876

PyMOL of d1iyma_

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

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

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

>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

>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

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

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

>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

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 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

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {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

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

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {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