Citrus Sinensis ID: 026177

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--

MSFVFRGSRADLETGFPGFIPERRTVRIHAGRPVNSNSLAFLVTVLLLFMILNSHQMSSNFLLWIVLGIFLLATSLRMYATCQQLHAQAQAHAVASGLLGHTELRLQMPPAIAFASRGRLQGLRLQLALLDREFDELDYETLRALDADNVPTAASMSEEEINTLPVHKYKVSGSQSGASSMQLGSSSSPAEKKLETSISVGNLKTEDELTCTVCLEQVNVGEIVRSLPCLHQQNVWLLSVVT

ccEEEEcccccccccccccccccccEEccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHcccccHHHHHHHHHccccccHHcHHHHHHHccccccccccccHHHHHccccEEEEEccccccccccccccccccHHHHcccccccccccccccccccccccccccccEEEEcccccccccccccccc

ccEEEEcccccHccccccccccccEEEEEcccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEcccccHHHHcHHHHHHHHHHHHHHcHHHHHccHHHHHHHccccccccccccHHHHHcccEEEEEEccccccccccccccccccHHHcccccccccccccccccEEEEEccccccccHHEccccHHccEEEEEEEEc

msfvfrgsradletgfpgfiperrtvrihagrpvnsnSLAFLVTVLLLFMILNSHQMSSNFLLWIVLGIFLLATSLRMYATCQQLHAQAQAHAVASGLLGhtelrlqmppaiafASRGRLQGLRLQLALLDREFDELDYETLRaldadnvptaasmseeeintlpvhkykvsgsqsgassmqlgsssspaekKLETSIsvgnlktedeltCTVCleqvnvgeivrslpclhqqNVWLLSVVT

msfvfrgsradletgfpgfipeRRTVRihagrpvnsNSLAFLVTVLLLFMILNSHQMSSNFLLWIVLGIFLLATSLRMYATCQQLHAQAQAHAVASGLLGHTELRLQMPPAIAFASRGRLQGLRLQLALLDREFDELDYETLRALDADNVPTAASMSEEEINTLPVHKYKVSGSQSGASsmqlgsssspaeKKLETSISvgnlktedelTCTVCLEQVNVGEIvrslpclhqqnvwllsvvt

MSFVFRGSRADLETGFPGFIPERRTVRIHAGRPVNSNSLAFLVTVLLLFMILNSHQMSSNFLLWIVLGIFLLATSLRMYATCqqlhaqaqahaVASGLLGHTELRLQMPPAIAFASrgrlqglrlqlallDREFDELDYETLRALDADNVPTAASMSEEEINTLPVHKYKVsgsqsgassmqlgssssPAEKKLETSISVGNLKTEDELTCTVCLEQVNVGEIVRSLPCLHQQNVWLLSVVT

***********LETGFPGFIPERRTVRIHAGRPVNSNSLAFLVTVLLLFMILNSHQMSSNFLLWIVLGIFLLATSLRMYATCQQLHAQAQAHAVASGLLGHTELRLQMPPAIAFASRGRLQGLRLQLALLDREFDELDYETLRALD********************************************************LKTEDELTCTVCLEQVNVGEIVRSLPCLHQQNVWLLSV**

*SFVFR*SRADLETGFPGFIPERRTVRIHAGRPVNSNSLAFLVTVLLLFMILNSHQMSSNFLLWIVLGIFLLATSLRMYA*******************GHTELRLQMPPAIAFASRGRLQGLRLQLALLDREFDELDYETLR******************NTLPVH***************************************DELTCTVCLEQVNVGEIVRSLPCLHQQNVWLLSVVT

MSFVFRGSRADLETGFPGFIPERRTVRIHAGRPVNSNSLAFLVTVLLLFMILNSHQMSSNFLLWIVLGIFLLATSLRMYATCQQLHAQAQAHAVASGLLGHTELRLQMPPAIAFASRGRLQGLRLQLALLDREFDELDYETLRALDADNVPTAASMSEEEINTLPVHKYK************************ETSISVGNLKTEDELTCTVCLEQVNVGEIVRSLPCLHQQNVWLLSVVT

*SFVFRGSRADLETGFPGFIPERRTVRIHAGRPVNSNSLAFLVTVLLLFMILNSHQMSSNFLLWIVLGIFLLATSLRMYATCQQLHAQAQAHA***GLLGHTELRLQMPPAIAFASRGRLQGLRLQLALLDREFDELDYETLRALDADNVP*AASMSEEEINTLPVHKYKVSG*********************************DELTCTVCLEQVNVGEIVRSLPCLHQQNVWLLSVVT

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiHHHHHHHHHHHHHHHHooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHoooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		242	2.2.26 [Sep-21-2011]
Q9M2S6		273	E3 ubiquitin-protein liga	yes	no	0.950	0.842	0.717	8e-88

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

 Score =  323 bits (827), Expect = 8e-88,   Method: Compositional matrix adjust.
 Identities = 168/234 (71%), Positives = 189/234 (80%), Gaps = 4/234 (1%)

Query: 1   MSFVFRGSRADLETGFPG-FIPERRTVRIHAGRPVNSNSLAFLVTVLLLFMILNSHQMSS 59
           MSFVFRGSR DLE+GF G F+PERR +R+H  RPVNSNSLAFLVTVLLLFMILNSHQM  
Sbjct: 1   MSFVFRGSRGDLESGFSGGFLPERRAMRVHGARPVNSNSLAFLVTVLLLFMILNSHQMPP 60

Query: 60  NFLLWIVLGIFLLATSLRMYATC-QQLHAQAQAHAVASGLLGHTELRLQMPPAIAFASRG 118
           NFLLW+VLG+FL+AT+LRMYATC Q         A ASGL  HTELRL +PP+IA A+RG
Sbjct: 61  NFLLWLVLGVFLMATTLRMYATCQQLQAHAQAQAAAASGLFSHTELRLHVPPSIALATRG 120

Query: 119 RLQGLRLQLALLDREFDELDYETLRALDADNVPTAASMSEEEINTLPVHKYKVSGSQSGA 178
           RLQGLRLQLALLDREFD+LDYETLRALD+DNV T  SMSEEEIN LPVHKYKV   ++G 
Sbjct: 121 RLQGLRLQLALLDREFDDLDYETLRALDSDNVST-TSMSEEEINALPVHKYKVLDPENGC 179

Query: 179 SSMQLGSSSSPAEKKLETSISVGNLKTEDELTCTVCLEQVNVGEIVRSLPCLHQ 232
           S  +  S+SS AEK L+ S +     TEDELTC+VCLEQV VGEIVR+LPCLHQ
Sbjct: 180 SLAKQASTSSSAEKMLD-SANESKKGTEDELTCSVCLEQVTVGEIVRTLPCLHQ 232

E3 ubiquitin-protein ligase that acts as a positive regulator of abscisic acid-related stress signal transduction.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

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		242
359486786		275	PREDICTED: E3 ubiquitin-protein ligase S	0.958	0.843	0.769	3e-92
224104393		275	predicted protein [Populus trichocarpa]	0.954	0.84	0.740	1e-91
359807355		274	uncharacterized protein LOC100777936 [Gl	0.958	0.846	0.794	1e-91
363807434		274	uncharacterized protein LOC100816448 [Gl	0.958	0.846	0.786	9e-91
449441410		275	PREDICTED: E3 ubiquitin-protein ligase S	0.958	0.843	0.770	2e-90
307136233		275	protein binding protein [Cucumis melo su	0.958	0.843	0.770	3e-90
255581543		276	protein binding protein, putative [Ricin	0.958	0.840	0.753	6e-89
147779997		262	hypothetical protein VITISV_012400 [Viti	0.909	0.839	0.755	1e-88
297820308		272	zinc finger family protein [Arabidopsis	0.950	0.845	0.721	2e-88
224109496		276	predicted protein [Populus trichocarpa]	0.958	0.840	0.770	7e-87

>gi\|359486786\|ref\|XP_002283148.2\| PREDICTED: E3 ubiquitin-protein ligase SDIR1-like [Vitis vinifera] gi\|296086209\|emb\|CBI31650.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  343 bits (880), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 180/234 (76%), Positives = 204/234 (87%), Gaps = 2/234 (0%)

Query: 1   MSFVFRGSRADLETGFPGFIPERRTVRIHAGRPVNSNSLAFLVTVLLLFMILNSHQMSSN 60
           MSFVFRGSRAD+E+GFPGFIPERR VR+HA RPVN+NSLAFLVTVLLLFMILNSHQMS N
Sbjct: 1   MSFVFRGSRADIESGFPGFIPERRAVRVHAARPVNTNSLAFLVTVLLLFMILNSHQMSPN 60

Query: 61  FLLWIVLGIFLLATSLRMYATC-QQLHAQAQAHAVASGLLGHTELRLQMPPAIAFASRGR 119
           FL+W+VLGIFL+AT+LRMYATC Q         A ASGLLGHTELRL MPP+IA A+RGR
Sbjct: 61  FLIWLVLGIFLMATTLRMYATCQQLQAQAQAHAAAASGLLGHTELRLHMPPSIALATRGR 120

Query: 120 LQGLRLQLALLDREFDELDYETLRALDADNVPTAASMSEEEINTLPVHKYKVSGSQSGAS 179
           LQGLRLQLALLDREFD+LDYETLRALD++NVPT  SMSEEEIN LPVHKYKV+G+Q G S
Sbjct: 121 LQGLRLQLALLDREFDDLDYETLRALDSENVPTTPSMSEEEINALPVHKYKVAGTQGGGS 180

Query: 180 SMQLGSSSSPAEKKLETSISVGNLKT-EDELTCTVCLEQVNVGEIVRSLPCLHQ 232
           SMQ GSSS+ AEKK + + +V + K  +DELTC+VCLEQVNVGE++RSLPCLHQ
Sbjct: 181 SMQQGSSSASAEKKQDINNAVASTKAPDDELTCSVCLEQVNVGELIRSLPCLHQ 234

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224104393\|ref\|XP_002313422.1\| predicted protein [Populus trichocarpa] gi\|222849830\|gb\|EEE87377.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|359807355\|ref\|NP_001241380.1\| uncharacterized protein LOC100777936 [Glycine max] gi\|255645784\|gb\|ACU23384.1\| unknown [Glycine max]	Back alignment and taxonomy information

>gi\|363807434\|ref\|NP_001242131.1\| uncharacterized protein LOC100816448 [Glycine max] gi\|255641194\|gb\|ACU20874.1\| unknown [Glycine max]	Back alignment and taxonomy information

>gi\|449441410\|ref\|XP_004138475.1\| PREDICTED: E3 ubiquitin-protein ligase SDIR1-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|307136233\|gb\|ADN34069.1\| protein binding protein [Cucumis melo subsp. melo]	Back alignment and taxonomy information

>gi\|255581543\|ref\|XP_002531577.1\| protein binding protein, putative [Ricinus communis] gi\|223528807\|gb\|EEF30813.1\| protein binding protein, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|147779997\|emb\|CAN60068.1\| hypothetical protein VITISV_012400 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297820308\|ref\|XP_002878037.1\| zinc finger family protein [Arabidopsis lyrata subsp. lyrata] gi\|297323875\|gb\|EFH54296.1\| zinc finger family protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|224109496\|ref\|XP_002315216.1\| predicted protein [Populus trichocarpa] gi\|222864256\|gb\|EEF01387.1\| predicted protein [Populus trichocarpa]	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		242
TAIR\|locus:2100021		273	SDIR1 "SALT- AND DROUGHT-INDUC	0.950	0.842	0.628	8.9e-70
DICTYBASE\|DDB_G0282479		320	DDB_G0282479 "E3 ubiquitin-pro	0.119	0.090	0.413	1.6e-06
TAIR\|locus:2010582		634	AT1G04790 [Arabidopsis thalian	0.095	0.036	0.521	2.3e-05

TAIR\|locus:2100021 SDIR1 "SALT- AND DROUGHT-INDUCED RING FINGER1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 707 (253.9 bits), Expect = 8.9e-70, P = 8.9e-70
 Identities = 147/234 (62%), Positives = 164/234 (70%)

Query:     1 MSFVFRGSRADLETGFPG-FIPERRTVRIHAGRPVNSNSLAFLVTVLLLFMILNSHQMSS 59
             MSFVFRGSR DLE+GF G F+PERR +R+H  RPVNSNSLAFLVTVLLLFMILNSHQM  
Sbjct:     1 MSFVFRGSRGDLESGFSGGFLPERRAMRVHGARPVNSNSLAFLVTVLLLFMILNSHQMPP 60

Query:    60 NFLLWIVLGIFLLATSLRMYATCXXXXXXXXX-XXVASGLLGHTELRLQMPPAIAFASXX 118
             NFLLW+VLG+FL+AT+LRMYATC             ASGL  HTELRL +PP+IA A+  
Sbjct:    61 NFLLWLVLGVFLMATTLRMYATCQQLQAHAQAQAAAASGLFSHTELRLHVPPSIALATRG 120

Query:   119 XXXXXXXXXXXXDREFDELDYETLRALDADNVPTAASMSEEEINTLPVHKYKVXXXXXXX 178
                         DREFD+LDYETLRALD+DNV T  SMSEEEIN LPVHKYKV       
Sbjct:   121 RLQGLRLQLALLDREFDDLDYETLRALDSDNVSTT-SMSEEEINALPVHKYKVLDPENGC 179

Query:   179 XXXXXXXXXXPAEKKLETSISVGNLKTEDELTCTVCLEQVNVGEIVRSLPCLHQ 232
                        AEK L+ S +     TEDELTC+VCLEQV VGEIVR+LPCLHQ
Sbjct:   180 SLAKQASTSSSAEKMLD-SANESKKGTEDELTCSVCLEQVTVGEIVRTLPCLHQ 232

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009414 "response to water deprivation" evidence=IEP

GO:0009651 "response to salt stress" evidence=IEP

GO:0009737 "response to abscisic acid stimulus" evidence=IEP

GO:0009789 "positive regulation of abscisic acid mediated signaling pathway" evidence=IMP

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IDA

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0006301 "postreplication repair" evidence=RCA

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

GO:0009086 "methionine biosynthetic process" evidence=RCA

DICTYBASE\|DDB_G0282479 DDB_G0282479 "E3 ubiquitin-protein ligase DMA2" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

TAIR\|locus:2010582 AT1G04790 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9M2S6	SDIR1_ARATH	6, ., 3, ., 2, ., -	0.7179	0.9504	0.8424	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		242
pfam13639		46	pfam13639, zf-RING_2, Ring finger domain	0.003

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

 Score = 34.7 bits (80), Expect = 0.003
 Identities = 10/22 (45%), Positives = 13/22 (59%)

Query: 210 TCTVCLEQVNVGEIVRSLPCLH 231
            C +CL++   GE V  LPC H
Sbjct: 2   ECPICLDEFEPGEEVVVLPCGH 23

Length = 46

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		242
KOG4628		348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.22
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	98.42
COG5540		374	RING-finger-containing ubiquitin ligase [Posttrans	98.08
KOG0801		205	consensus Predicted E3 ubiquitin ligase [Posttrans	97.72
PHA02929		238	N1R/p28-like protein; Provisional	97.49
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	97.16
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	97.08
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	97.04
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	96.75
COG5243		491	HRD1 HRD ubiquitin ligase complex, ER membrane com	96.74
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	96.37
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	96.18
PF14634		44	zf-RING_5: zinc-RING finger domain	96.14
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	96.02
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	94.3
PHA02926		242	zinc finger-like protein; Provisional	93.71
KOG4445		368	consensus Uncharacterized conserved protein, conta	93.52
PF10367		109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	93.23
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	92.65
KOG1734		328	consensus Predicted RING-containing E3 ubiquitin l	92.23
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	90.25
smart00744		49	RINGv The RING-variant domain is a C4HC3 zinc-fing	89.94
PF12861		85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	86.46
PF11793		70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	86.21
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	85.24
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	84.31
PF14446		54	Prok-RING_1: Prokaryotic RING finger family 1	83.11

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

Probab=99.22  E-value=5e-12  Score=118.66  Aligned_cols=56  Identities=30%  Similarity=0.706  Sum_probs=47.4

Q ss_pred             CCCCHHHHhcCCeEEeeccCCCCCCCcccCCCCCCcccccccccccccccCCCCCcccccccccccCCceeEEcCCCCcc
Q 026177          154 ASMSEEEINTLPVHKYKVSGSQSGASSMQLGSSSSPAEKKLETSISVGNLKTEDELTCTVCLEQVNVGEIVRSLPCLHQQ  233 (242)
Q Consensus       154 ~G~See~I~aLPv~kyk~~~~~~gss~~~~~Ss~~~~e~~~ds~~~~g~~k~~~e~tCsICLEdF~~GE~VR~LPC~H~F  233 (242)
                      ..+.+..+.++|+++|+.....                              ....+|+||||+|++||+||.|||.|.|
T Consensus       205 ~r~~k~~l~~~p~~~f~~~~~~------------------------------~~~~~CaIClEdY~~GdklRiLPC~H~F  254 (348)
T KOG4628|consen  205 NRLIKRLLKKLPVRTFTKGDDE------------------------------DATDTCAICLEDYEKGDKLRILPCSHKF  254 (348)
T ss_pred             hhhHHHHHhhCCcEEecccccc------------------------------CCCceEEEeecccccCCeeeEecCCCch
Confidence            4789999999999999976421                              1226999999999999999999999999


Q ss_pred             cc-----hhhc
Q 026177          234 NV-----WLLS  239 (242)
Q Consensus       234 H~-----wLls  239 (242)
                      |.     ||..
T Consensus       255 H~~CIDpWL~~  265 (348)
T KOG4628|consen  255 HVNCIDPWLTQ  265 (348)
T ss_pred             hhccchhhHhh
Confidence            96     8865

>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

>COG5540 RING-finger-containing 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

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

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

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

Back alignment and domain information

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

>smart00184 RING Ring finger	Back alignment and domain information

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

>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

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

>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_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

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

>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]	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

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

>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [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

>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

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

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

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

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

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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		242
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	9e-08
2ect_A		78	Ring finger protein 126; metal binding protein, st	2e-07
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	2e-07
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	2e-07
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	4e-07
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	4e-06
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	3e-04

>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

 Score = 47.7 bits (114), Expect = 9e-08
 Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 5/48 (10%)

Query: 189 PAEK----KLET-SISVGNLKTEDELTCTVCLEQVNVGEIVRSLPCLH 231
           PA K     L    ++  +     E+ C +C  +   G++   LPC H
Sbjct: 16  PASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHH 63

PyMOL of 2l0b

>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

>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

>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

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

>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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		242
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.21
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	98.99
2ect_A		78	Ring finger protein 126; metal binding protein, st	98.55
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	98.48
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	98.46
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	98.46
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	98.33
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	98.19
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	98.08
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	98.01
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	97.99
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	97.96
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	97.93
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	97.84
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	97.83
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	97.82
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	97.78
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	97.73
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	97.71
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	97.64
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	97.59
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	97.53
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	97.48
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	97.43
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	97.43
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	97.4
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	97.39
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	97.38
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	97.31
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	97.29
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	97.25
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	97.25
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	97.19
4ayc_A		138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	97.17
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	97.06
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	97.03
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	96.98
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	96.98
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	96.97
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	96.86
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	96.77
1t1h_A		78	Gspef-atpub14, armadillo repeat containing protein	96.69
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	96.68
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	96.61
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	96.51
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	96.32
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	96.2
1z6u_A		150	NP95-like ring finger protein isoform B; structura	96.17
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	96.03
2ea5_A		68	Cell growth regulator with ring finger domain prot	95.96
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	95.95
4ic3_A		74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	95.88
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	95.86
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	95.74
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	95.67
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	95.22
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	95.15
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	93.37
3t6p_A		345	Baculoviral IAP repeat-containing protein 2; ring,	93.19
1wgm_A		98	Ubiquitin conjugation factor E4A; ubiquitinating e	92.68
2yu4_A		94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	90.44
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	90.05
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	88.4
2jun_A		101	Midline-1; B-BOX, TRIM, ring finger, alternative s	88.02
2kr4_A		85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	87.57
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	86.78
2kre_A		100	Ubiquitin conjugation factor E4 B; U-box domain, E	85.11
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	83.7
2f42_A		179	STIP1 homology and U-box containing protein 1; cha	80.62

>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

Probab=99.21  E-value=1.2e-11  Score=93.04  Aligned_cols=56  Identities=23%  Similarity=0.457  Sum_probs=47.2

Q ss_pred             CCCCCCCHHHHhcCCeEEeeccCCCCCCCcccCCCCCCcccccccccccccccCCCCCcccccccccccCCceeEEcCCC
Q 026177          151 PTAASMSEEEINTLPVHKYKVSGSQSGASSMQLGSSSSPAEKKLETSISVGNLKTEDELTCTVCLEQVNVGEIVRSLPCL  230 (242)
Q Consensus       151 ~~~~G~See~I~aLPv~kyk~~~~~~gss~~~~~Ss~~~~e~~~ds~~~~g~~k~~~e~tCsICLEdF~~GE~VR~LPC~  230 (242)
                      ....|+|++.|++||.++++....                             ...++.+|+||+++|..|+.++.|||+
T Consensus        12 ~~~~~~s~~~i~~lp~~~~~~~~~-----------------------------~~~~~~~C~IC~~~~~~~~~~~~l~C~   62 (91)
T 2l0b_A           12 VANPPASKESIDALPEILVTEDHG-----------------------------AVGQEMCCPICCSEYVKGDVATELPCH   62 (91)
T ss_dssp             SCCCCCCHHHHHTSCEEECCTTCS-----------------------------SSSSCSEETTTTEECCTTCEEEEETTT
T ss_pred             cCCCCCCHHHHHhCCCeeeccccc-----------------------------ccCCCCCCcccChhhcCCCcEEecCCC
Confidence            445689999999999998876431                             114668999999999999999999999


Q ss_pred             Ccccc
Q 026177          231 HQQNV  235 (242)
Q Consensus       231 H~FH~  235 (242)
                      |.||.
T Consensus        63 H~Fh~   67 (91)
T 2l0b_A           63 HYFHK   67 (91)
T ss_dssp             EEEEH
T ss_pred             ChHHH
Confidence            99996

PyMOL of 2l0b

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

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

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

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

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

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

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

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

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

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

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

>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

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

>2ecj_A Tripartite motif-containing protein 39; TRIM39, 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

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; 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

>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

>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

>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

>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

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

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

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

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

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

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

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

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

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

>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

>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

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

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

>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

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

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

>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

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

>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

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

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A*	Back alignment and structure

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

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

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

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B	Back alignment and structure

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

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C	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		242
d1iyma_		55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	1e-04

>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 = 36.8 bits (85), Expect = 1e-04
 Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 1/27 (3%)

Query: 206 EDELTCTVCLEQVNVGEIVRSLP-CLH 231
           +D + C VCL ++  GE  R LP C H
Sbjct: 3   DDGVECAVCLAELEDGEEARFLPRCGH 29

PyMOL of d1iyma_

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		242
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	98.79
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	98.12
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	97.99
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	97.83
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	97.71
d1bora_		56	Acute promyelocytic leukaemia proto-oncoprotein PM	97.63
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	97.42
d1wima_		94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	97.42
d3dplr1		88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	97.42
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	96.78
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	96.67
d1vyxa_		60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	96.6
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	95.76
d1t1ha_		78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	94.26
d2baya1		56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	93.58
d2c2la2		80	STIP1 homology and U box-containing protein 1, STU	93.55
d1wewa_		78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	80.18

>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=98.79  E-value=1.1e-09  Score=74.73  Aligned_cols=35  Identities=43%  Similarity=0.825  Sum_probs=30.4

Q ss_pred             CCCcccccccccccCCceeEEcC-CCCcccc-----hhhcC
Q 026177          206 EDELTCTVCLEQVNVGEIVRSLP-CLHQQNV-----WLLSV  240 (242)
Q Consensus       206 ~~e~tCsICLEdF~~GE~VR~LP-C~H~FH~-----wLls~  240 (242)
                      +++.+|+||+++|+.||.+++|| |+|.||.     |+.+.
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~   43 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSH   43 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTC
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhC
Confidence            35678999999999999999997 9999996     87654

PyMOL of d1iyma_

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

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

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

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

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

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

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

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

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

>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

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

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

>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

>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

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure