Citrus Sinensis ID: 006225

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-----

MPIAMRRTRRGGGRPRNHLQNDEDLTVKPLNDAPPAAPPSQQKRHQQHSLDSPSTSDQPNNEPIPKYQGNLRWVSRRRRARVAKPKFVKKTESREEKLLNDEVGSLSIGEEVKEKQDEEEGLPSNSNVNDVESILRELSSSVEEPELEAEQLRINDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNSSTDLDARSESSDDFSYSFKVQYLPPIVLTCLLPKSYPSHLPPYFTISARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSLSYLGFNEEIVLGPYGVACIGDRRAISESVSPDVDIPSIRSYNHERCHENFLKSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKLLGDEEFERWESLMLQKTLESMSDVAYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRERRHVGVVCMTPEIKLRILQERQNSSQVKEGQKQREHEMINELLSVKEILRDAKQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKAIDGYDHFRTGTCELFPQEMIRDWEERLNARQVVAQIQADMFDEHGLSCPNCRQFNAKVGNNNHMFCWACQIHYCYLCKKIVRRSTQHYGPKGCKQHTVG

ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHcccccccccHHHHHccHHHHHHHHHHHHHHccccccccccccccccEEEEEEEcccccEEEEEEcccccccccccccccccccEEEEEEcccEEEEEEcccccccccccEEEEEcccccHHHHHHHHHHHHHHHHHccccEEEHHHHHHHHHccHHHccccccHHccccccccccccccccccccccccHHHHHHHcHHHHHHHHcccccccccccccccccccEEccccccccHHHHHHHHHHHHHccccEEEEcccccccccccHHHHHHcccHHHHHHHHHHHHHHHHHccccEEEccccccccEEcccccEEccccccccccccccccccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccEEEccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcHHHcccccccccccccEEEcccccEEcccccccccccccccccccccccccccccccccc

ccEEEEcccccccccHHHHHcccccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccccHHccccccccccccccccHHcccccccHHHHHHHHHHHHHccccccccHHHHHHcHHHHHHHHHHHHHHccccEEEEEccccccccEEEEEEEcccccEEEEEccccccccccccccccccEEEEEEEcccEEEEEEcccccccccccEEEEEEccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHccccccEEEcccccccccccHHHcccccHHHHHHHHHHccHHHHHHHHcccccccEEEEccccccccEEcccccHHHHHHHHHHHEEEEccccEEEEEcccccccccccHHHHHHHccHHHHHHHHHHHHHHHHHcccccEEcccccccEEEcccccccccccccEHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccEEEEccccccEEccccccEEEHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccEccccccEEEEHHHHHHHHHHHHHHEcccccccccccccccccc

mpiamrrtrrgggrprnhlqndedltvkplndappaappsqqkrhqqhsldspstsdqpnnepipkyqgnlrwVSRRRRarvakpkfvkkTESREEKLlndevgslsigeevkekqdeeeglpsnsnvnDVESILRELsssveepeleaEQLRINDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTaklnsstdldarsessddfsysfkvqylppivltcllpksypshlppyftISARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNsslsylgfneeivlgpygvacigdrraisesvspdvdipsirsynhercheNFLKSFHECRIcfsefagtdfvrlpchhffcwKCMKTYLDIhisegtvsklqcpdakcggmvppsllkkllgDEEFERWESLMLQKTLEsmsdvaycprcetpciedeeqhaqCSKCFYSFCTlcrerrhvgvvcmtPEIKLRILQERqnssqvkeGQKQREHEMINELLSVKEILRDakqcpsckmaisrtegcnkivcnncgqyfcyrcnkaidgydhfrtgtcelfpqEMIRDWEERLNARQVVAQIQADmfdehglscpncrqfnakvgnnnhmFCWACQIHYCYLCKKIVRrstqhygpkgckqhtvg

mpiamrrtrrgggrprnhlqndedltvkPLNDAPPAAPPSQQKRHQQHSldspstsdqpnnepipkyqgnlrwvsrrrrarvakpkfvkktesreekllndevgslsigeevkekqdeeeglpsnsnvndvESILRELSSSVEEPELEAEQLRINDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHvetldgltvtAKLNSSTDLDARSESSDDFSYSFKVQYLPPIVLTCLLPKSYPSHLPPYFTISARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSLSYLGFNEEIVLGPYGVACIGDRRAisesvspdvdipSIRSYNHERCHENFLKSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKLLGDEEFERWESLMLQKTLESMSDVAYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRERRHVGVVCMTPEIKLRilqerqnssqvkegqkqreHEMINELLSVKEILRDAKQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKAIDGYDHFRTGTCELFPQEMIRDWEERLNARQVVAQIQADMFDEHGLSCPNCRQFNAKVGNNNHMFCWACQIHYCYLCKKIVRRSTQhygpkgckqhtvg

MPIAMrrtrrgggrprNHLQNDEDLTVKPLNDAPPAAPPSQQKRHQQHSLDSPSTSDQPNNEPIPKYQGNLrwvsrrrrarvaKPKFVKKTESREEKLLNDEVGSLSIGeevkekqdeeeGLPSNSNVNDVESIlrelsssveepeleaeqlRINDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNSSTDLDARSESSDDFSYSFKVQYLPPIVLTCLLPKSYPSHLPPYFTISARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSLSYLGFNEEIVLGPYGVACIGDRRAISESVSPDVDIPSIRSYNHERCHENFLKSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKLLGDEEFERWESLMLQKTLESMSDVAYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRERRHVGVVCMTPEIKLRILQERQNSSQVKEGQKQREHEMINELLSVKEILRDAKQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKAIDGYDHFRTGTCELFPQEMIRDWEERLNARQVVAQIQADMFDEHGLSCPNCRQFNAKVGNNNHMFCWACQIHYCYLCKKIVRRSTQHYGPKGCKQHTVG

******************************************************************************************************************************************************************LLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKL***************FSYSFKVQYLPPIVLTCLLPKSYPSHLPPYFTISARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSLSYLGFNEEIVLGPYGVACIGDRRAISESVSPDVDIPSIRSYNHERCHENFLKSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKLLGDEEFERWESLMLQKTLESMSDVAYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRERRHVGVVCMTPEIKLRIL*********************NELLSVKEILRDAKQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKAIDGYDHFRTGTCELFPQEMIRDWEERLNARQVVAQIQADMFDEHGLSCPNCRQFNAKVGNNNHMFCWACQIHYCYLCKKIVRRST**************

********************NDEDLTVKP************************************************************************************************SNVNDVESI***********************SQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKL****************SYSFKVQYLPPIVLTCLLPKSYPSHLPPYFTISARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSLSYLGFNEEIVLGPYGVACIGDRRAISE****************************ECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKLLGDEEFERWESLMLQKTLESMSDVAYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRERRHVGVVCMTPEIKLR************************ELLSVKEILRDAKQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKAIDGYDHFRTGTCELFPQEM***************QIQADMFDEHGLSCPNCRQFNAKVGNNNHMFCWACQIHYCYLCKKIVRRSTQHYGPK*CKQ****

***************RNHLQNDEDLTVKPLNDAP**************************NEPIPKYQGNLRWVSRRRRARVAKPKFVKKTESREEKLLNDEVGSLSIGE***************SNVNDVESILRELSSSVEEPELEAEQLRINDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNSST***********FSYSFKVQYLPPIVLTCLLPKSYPSHLPPYFTISARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSLSYLGFNEEIVLGPYGVACIGDRRAISESVSPDVDIPSIRSYNHERCHENFLKSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKLLGDEEFERWESLMLQKTLESMSDVAYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRERRHVGVVCMTPEIKLRILQER**************HEMINELLSVKEILRDAKQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKAIDGYDHFRTGTCELFPQEMIRDWEERLNARQVVAQIQADMFDEHGLSCPNCRQFNAKVGNNNHMFCWACQIHYCYLCKKIVRRSTQ*************

*******TRRGGGRPRNHLQNDEDLTVKPLNDA****************************************************KF**K*E*********************************SNVNDVESILRELSSSVEEPELEAEQLRINDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNS**********SDDFSYSFKVQYLPPIVLTCLLPKSYPSHLPPYFTISARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSLSYLGFNEEIVLGPYGVACIGDRRAISESVSPDVDIPSIRSYNHERCHENFLKSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKLLGDEEFERWESLMLQKTLESMSDVAYCPRCETPCIEDEEQHAQCSKCFYSFCTLCRERRHVGVVCMTPEIKLRILQERQNSSQVKEGQKQREHEMINELLSVKEILRDAKQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKAIDGYDHFRTGTCELFPQEMIRDWEERLNARQVVAQIQADMFDEHGLSCPNCRQFNAKVGNNNHMFCWACQIHYCYLCKKIVRRS***************

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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		655	2.2.26 [Sep-21-2011]
Q9JI90		485	E3 ubiquitin-protein liga	yes	no	0.607	0.820	0.304	1e-50
Q9UBS8		474	E3 ubiquitin-protein liga	yes	no	0.604	0.835	0.299	4e-48
Q9US46		435	E3 ubiquitin-protein liga	yes	no	0.586	0.882	0.265	1e-30
Q04638		464	Translation termination i	yes	no	0.331	0.467	0.278	1e-19
Q54CX4		903	Uncharacterized protein D	no	no	0.293	0.212	0.306	3e-19
A4IIY1		292	Probable E3 ubiquitin-pro	no	no	0.314	0.705	0.265	3e-15
Q925F3		292	Probable E3 ubiquitin-pro	no	no	0.314	0.705	0.265	3e-15
Q6DH94		293	Probable E3 ubiquitin-pro	no	no	0.316	0.706	0.253	4e-15
P50876		292	Probable E3 ubiquitin-pro	no	no	0.314	0.705	0.261	3e-14
Q6T486		520	Probable E3 ubiquitin-pro	no	no	0.351	0.442	0.251	1e-13

>sp\|Q9JI90\|RNF14_MOUSE E3 ubiquitin-protein ligase RNF14 OS=Mus musculus GN=Rnf14 PE=2 SV=2	Back alignment and function desciption

 Score =  202 bits (513), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 137/450 (30%), Positives = 220/450 (48%), Gaps = 52/450 (11%)

Query: 157 QSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNSSTDLDARSES 216
           ++Q DELLAL SIY    F   +   ++  +  ++++      +    NS+       ES
Sbjct: 7   EAQEDELLALASIYDADEF--RKAESVQGGETRIYLDLPQNFKIFVSGNSN-------ES 57

Query: 217 SDDFSYSFKVQYLPPIVLTCLLPKSYPSHLPPYFTISARWLNSTKISNLCSMLESIWIDQ 276
             +  + + + +LPP+VL   LP  YPS  PP FT+S +WL+ T++S LC  L+++W + 
Sbjct: 58  LQNSGFEYTICFLPPLVLNFELPPDYPSSSPPSFTLSGKWLSPTQLSALCKHLDNLWEEH 117

Query: 277 PGQEILYQWIEWLQNSSLSYLGF------------------------NEEIVLGPYGVAC 312
            G+ +L+ W+++L+  +L+YL                          + E+ +G    A 
Sbjct: 118 RGRVVLFAWMQFLKEETLTYLNIVSPFELKMGSQKKVQRRATAQASSSTELGVGGAAAAD 177

Query: 313 IGDRRAISESVSPDVD-----IPSIRSYNHERCHENFLKSFHECRICFSEFAGTD-FVRL 366
           +     + E    DV+     I  I  +N  R  + F      C ICF E  G+D    L
Sbjct: 178 VDQEETVDERAVQDVESLSSLIQEILDFNQARQTKCFNSKLFLCSICFCEKLGSDCMYFL 237

Query: 367 PCHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCGGMVPPSLLKKLLGDEEFERWESLML 426
            C H +C  C+K Y +I I +G V  L CP+ +C  +  P  +K+L+  + F R++ L+L
Sbjct: 238 ECKHVYCKACLKDYFEIQIKDGQVKCLNCPEPQCPSVATPGQVKELVEADLFARYDRLLL 297

Query: 427 QKTLESMSDVAYCPR--CETPCIEDE-EQHAQCSKCFYSFCTLCRERRHVGVVCMTPEIK 483
           Q TL+ M+DV YCPR  C+ P +++     A CS C ++FCTLCR   H    C     K
Sbjct: 298 QSTLDLMADVVYCPRPCCQLPVMQEPGGTMAICSSCNFAFCTLCRLTYHGLSPCKVTAEK 357

Query: 484 LRILQER--QNSSQVKEGQKQRE-----HEMINELLSVKEILRDAKQCPSCKMAISRTEG 536
           L  L+    Q     K   +QR       + + E+ S   + +++K CP C   I + +G
Sbjct: 358 LIDLRNEYLQADEATKRFLEQRYGKRVIQKALEEMESKDWLEKNSKSCPCCGTPIQKLDG 417

Query: 537 CNKIVCNNCGQYFCYRCNKAI---DGYDHF 563
           CNK+ C  C QYFC+ C  ++   + Y HF
Sbjct: 418 CNKMTCTGCMQYFCWICMGSLSRANPYRHF 447

Might act as an E3 ubiquitin-protein ligase which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates, which could be nuclear proteins. Could play a role as a coactivator for androgen- and, to a lesser extent, progesterone-dependent transcription.
Mus musculus (taxid: 10090)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp\|Q9UBS8\|RNF14_HUMAN E3 ubiquitin-protein ligase RNF14 OS=Homo sapiens GN=RNF14 PE=1 SV=1	Back alignment and function description

>sp\|Q9US46\|ITT1_SCHPO E3 ubiquitin-protein ligase itt1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=itt1 PE=4 SV=1	Back alignment and function description

>sp\|Q04638\|ITT1_YEAST Translation termination inhibitor protein ITT1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ITT1 PE=1 SV=1	Back alignment and function description

>sp\|Q54CX4\|Y5521_DICDI Uncharacterized protein DDB_G0292642 OS=Dictyostelium discoideum GN=DDB_G0292642 PE=4 SV=2	Back alignment and function description

>sp\|A4IIY1\|R144A_XENTR Probable E3 ubiquitin-protein ligase RNF144A OS=Xenopus tropicalis GN=rnf144a PE=2 SV=1	Back alignment and function description

>sp\|Q925F3\|R144A_MOUSE Probable E3 ubiquitin-protein ligase RNF144A OS=Mus musculus GN=Rnf144a PE=1 SV=1	Back alignment and function description

>sp\|Q6DH94\|R1442_DANRE Probable E3 ubiquitin-protein ligase RNF144A-B OS=Danio rerio GN=rnf144ab PE=2 SV=1	Back alignment and function description

>sp\|P50876\|R144A_HUMAN Probable E3 ubiquitin-protein ligase RNF144A OS=Homo sapiens GN=RNF144A PE=1 SV=2	Back alignment and function description

>sp\|Q6T486\|RBRA_DICDI Probable E3 ubiquitin-protein ligase rbrA OS=Dictyostelium discoideum GN=rbrA 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		655
297742068		662	unnamed protein product [Vitis vinifera]	0.940	0.930	0.660	0.0
225427151		868	PREDICTED: uncharacterized protein LOC10	0.940	0.709	0.660	0.0
224138168		642	predicted protein [Populus trichocarpa]	0.839	0.856	0.701	0.0
297851676		682	predicted protein [Arabidopsis lyrata su	0.981	0.942	0.581	0.0
15223171		688	ubiquitin-protein ligase RNF14 [Arabidop	0.981	0.934	0.568	0.0
449436832		638	PREDICTED: E3 ubiquitin-protein ligase R	0.966	0.992	0.600	0.0
357485119		630	E3 ubiquitin-protein ligase RNF14 [Medic	0.829	0.861	0.628	0.0
255573469		578	ring finger protein, putative [Ricinus c	0.682	0.773	0.734	0.0
357168323		633	PREDICTED: E3 ubiquitin-protein ligase R	0.755	0.781	0.570	1e-175
414585671		645	TPA: hypothetical protein ZEAMMB73_09119	0.786	0.798	0.548	1e-172

>gi\|297742068\|emb\|CBI33855.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  866 bits (2238), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 418/633 (66%), Positives = 496/633 (78%), Gaps = 17/633 (2%)

Query: 40  SQQKRHQQHSLDSPSTSDQPNNEPIPKYQGNLRWVSRRRRARVAKPKFVKKTESREEKLL 99
           SQ       +L SP  +   +  P  + + N +WVSR +RA VAK  FVKK+E      +
Sbjct: 30  SQPDTTSHENLQSPQPTHDSDFHPKSQSRPNSKWVSRNQRAHVAKTTFVKKSEVGSGSEV 89

Query: 100 NDEVGSLSI-------------GEEVKEKQDEEEGLPSNSNVNDVESILRELSSSVEEPE 146
           N++                    E+    ++  E      +V+DV S L +L   VEEPE
Sbjct: 90  NEQKQEEDEQKQGEEEEGEGPRNEQTDLNEEVVEASDFTHDVDDVGSRLEKLVVGVEEPE 149

Query: 147 LEAEQLRINDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNS 206
           L  ++LRIN Q Q DELLA++SIYGD+VFILDRQ+ L+S QIHVH+E L  LTVTAKLNS
Sbjct: 150 LSEDRLRINAQLQEDELLAMQSIYGDNVFILDRQQGLQSFQIHVHIEALGELTVTAKLNS 209

Query: 207 STDLDARSESSDDFSYSFKVQYLPPIVLTCLLPKSYPSHLPPYFTISARWLNSTKISNLC 266
           S+     S+ SDDFSYSF VQYLPPIVLTCLLPK+YPSHLPPYFTIS +WL+S  IS LC
Sbjct: 210 SSGRTTESDGSDDFSYSFNVQYLPPIVLTCLLPKAYPSHLPPYFTISVQWLDSISISKLC 269

Query: 267 SMLESIWIDQPGQEILYQWIEWLQNSSLSYLGFNEEIVLGPYGVACIGDRRAISESVSPD 326
           SML+S+W +QPGQE+LYQW+EWL +S LSYLGF++EIVLGPY +    DRRAIS SVS D
Sbjct: 270 SMLDSLWKEQPGQEVLYQWVEWLHSSCLSYLGFDKEIVLGPYNMGNSEDRRAISGSVSLD 329

Query: 327 VDIPSIRSYNHERCHENFLKSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHIS 386
           VDIPS++SYN E+ HENF K+FHEC ICF+E+AGT+F++LPC HFFCWKCMKTY ++H+ 
Sbjct: 330 VDIPSMKSYNDEKRHENFSKNFHECCICFTEYAGTEFIKLPCQHFFCWKCMKTYSEMHVK 389

Query: 387 EGTVSKLQCPDAKCGGMVPPSLLKKLLGDEEFERWESLMLQKTLESMSDVAYCPRCETPC 446
           EGT S+L CP+ KC  MVPP LLK+LLGDEEFE WESLMLQKTLESMSD+ YCPRCET C
Sbjct: 390 EGTGSQLLCPETKCRAMVPPVLLKRLLGDEEFEHWESLMLQKTLESMSDMTYCPRCETIC 449

Query: 447 IEDEEQHAQCSKCFYSFCTLCRERRHVGVVCMTPEIKLRILQERQNSSQVKEGQKQREHE 506
           IEDE+QHAQCSKCF+SFCTLCR+RRHVG+ CMTPE+KL ILQ RQ+SSQ+K+ Q+++E E
Sbjct: 450 IEDEDQHAQCSKCFFSFCTLCRDRRHVGLECMTPEVKLHILQGRQHSSQLKDEQRKKERE 509

Query: 507 MINELLSVKEILRDAKQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKAIDGYDHFRTG 566
           MINELLSVKEILRDAKQCPSCKMAISRTEGCNK+VCNNCGQYFCYRCN+AIDGY+HFR  
Sbjct: 510 MINELLSVKEILRDAKQCPSCKMAISRTEGCNKMVCNNCGQYFCYRCNQAIDGYEHFRDS 569

Query: 567 TCELFPQEMIR----DWEERLNARQVVAQIQADMFDEHGLSCPNCRQFNAKVGNNNHMFC 622
            CELFPQEMI+    DWE RLN RQVV QIQA++F + G SCP CRQ N KVGNNNH+FC
Sbjct: 570 ACELFPQEMIQNWEWDWEARLNQRQVVGQIQAELFADRGHSCPICRQINVKVGNNNHIFC 629

Query: 623 WACQIHYCYLCKKIVRRSTQHYGPKGCKQHTVG 655
           W+CQ HYCYLCK+IVRRS+QH+GPKGCKQHTVG
Sbjct: 630 WSCQSHYCYLCKEIVRRSSQHFGPKGCKQHTVG 662

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|225427151\|ref\|XP_002277376.1\| PREDICTED: uncharacterized protein LOC100262589 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224138168\|ref\|XP_002326535.1\| predicted protein [Populus trichocarpa] gi\|222833857\|gb\|EEE72334.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|297851676\|ref\|XP_002893719.1\| predicted protein [Arabidopsis lyrata subsp. lyrata] gi\|297339561\|gb\|EFH69978.1\| predicted protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi|15223171|ref|NP_174512.1| ubiquitin-protein ligase RNF14 [Arabidopsis thaliana] gi|8920608|gb|AAF81330.1|AC007767_10 Contains similarity to ring finger protein 14 from Homo sapiens gb|NM_004290. It contains an IBR domain PF|01485 [Arabidopsis thaliana] gi|12597865|gb|AAG60174.1|AC084110_7 hypothetical protein [Arabidopsis thaliana] gi|20466165|gb|AAM20400.1| RING finger protein, putative [Arabidopsis thaliana] gi|25083846|gb|AAN72126.1| RING finger protein, putative [Arabidopsis thaliana] gi|332193345|gb|AEE31466.1| ubiquitin-protein ligase RNF14 [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|449436832\|ref\|XP_004136196.1\| PREDICTED: E3 ubiquitin-protein ligase RNF14-like [Cucumis sativus] gi\|449525814\|ref\|XP_004169911.1\| PREDICTED: E3 ubiquitin-protein ligase RNF14-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|357485119\|ref\|XP_003612847.1\| E3 ubiquitin-protein ligase RNF14 [Medicago truncatula] gi\|355514182\|gb\|AES95805.1\| E3 ubiquitin-protein ligase RNF14 [Medicago truncatula]	Back alignment and taxonomy information

>gi\|255573469\|ref\|XP_002527660.1\| ring finger protein, putative [Ricinus communis] gi\|223532965\|gb\|EEF34731.1\| ring finger protein, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|357168323\|ref\|XP_003581592.1\| PREDICTED: E3 ubiquitin-protein ligase RNF14-like [Brachypodium distachyon]	Back alignment and taxonomy information

>gi\|414585671\|tpg\|DAA36242.1\| TPA: hypothetical protein ZEAMMB73_091196 [Zea mays]	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		655
TAIR\|locus:2028316		688	NHL8 "NDR1/HIN1-like 8" [Arabi	0.763	0.726	0.675	3e-204
UNIPROTKB\|F1NEG7		470	LOC100859099 "Uncharacterized	0.392	0.546	0.328	1.4e-59
UNIPROTKB\|F1RM50		474	RNF14 "Uncharacterized protein	0.380	0.525	0.342	5.5e-59
MGI\|MGI:1929668		485	Rnf14 "ring finger protein 14"	0.380	0.513	0.349	1e-58
ZFIN\|ZDB-GENE-040625-65		459	rnf14 "ring finger protein 14"	0.377	0.538	0.347	2e-58
UNIPROTKB\|A2VDU5		474	RNF14 "Ring finger protein 14"	0.380	0.525	0.346	4.6e-58
UNIPROTKB\|E2QX80		474	RNF14 "Uncharacterized protein	0.380	0.525	0.346	1.4e-57
UNIPROTKB\|Q9UBS8		474	RNF14 "E3 ubiquitin-protein li	0.383	0.529	0.343	5.2e-57
DICTYBASE\|DDB_G0270130		588	DDB_G0270130 "E3 ubiquitin-pro	0.406	0.452	0.273	2.8e-44
WB\|WBGene00018966		437	F56D2.5 [Caenorhabditis elegan	0.593	0.890	0.272	2.8e-38

TAIR\|locus:2028316 NHL8 "NDR1/HIN1-like 8" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1976 (700.6 bits), Expect = 3.0e-204, P = 3.0e-204
 Identities = 344/509 (67%), Positives = 419/509 (82%)

Query:   153 RINDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNSSTDLDA 212
             ++NDQ Q DELLAL  IYG ++FI DR  D+R  Q+HV+VE     T++ KLN   D   
Sbjct:   183 KMNDQLQEDELLALGYIYGGNMFIFDRYNDMRYFQVHVNVEATSEYTISTKLNLQAD--- 239

Query:   213 RSESSDDFSYSFKVQYLPPIVLTCLLPKSYPSHLPPYFTISARWLNSTKISNLCSMLESI 272
              S+ S+DF YSFK Q+LPPIVL CLLPK+YPSHLPPYF IS +W+N  KIS+LCS L+S+
Sbjct:   240 SSKESEDFLYSFKAQHLPPIVLKCLLPKAYPSHLPPYFLISVQWMNPDKISSLCSKLDSL 299

Query:   273 WIDQPGQEILYQWIEWLQNSSLSYLGFNEEIVLGPYGVACIGDRRAISESVSPDVDIPSI 332
             W +QPGQE+LYQW +WLQNSS+S+LGF+ EIVLGPYGV C  D+RA+S S SPD DIP I
Sbjct:   300 WSEQPGQEVLYQWTDWLQNSSISHLGFDNEIVLGPYGVTCSRDKRAVSGSRSPDSDIPYI 359

Query:   333 RSYNHERCHENFLKSFHECRICFSEFAGTDFVRLPCHHFFCWKCMKTYLDIHISEGTVSK 392
             RSY+ E+ H++FL+S HEC ICFSE AG DFV+LPC HFFC KCMKTY DIH++EGTV+K
Sbjct:   360 RSYDDEKRHDSFLQSLHECCICFSESAGIDFVKLPCQHFFCLKCMKTYTDIHVTEGTVNK 419

Query:   393 LQCPDAKCGGMVPPSLLKKLLGDEEFERWESLMLQKTLESMSDVAYCPRCETPCIEDEEQ 452
             L+CPD+KCG  VPP +LK+LLGDE +ERWE+LMLQKTLESM+DVAYCPRCETPCIEDEEQ
Sbjct:   420 LKCPDSKCGETVPPGILKRLLGDEAYERWETLMLQKTLESMTDVAYCPRCETPCIEDEEQ 479

Query:   453 HAQCSKCFYSFCTLCRERRHVGVVCMTPEIKLRILQERQNSSQVKEGQKQREHEMINELL 512
              A C KC++SFCTLC+E+RHVGV CM+PE++L+ILQERQ+SS++ E Q+++E EMINE++
Sbjct:   480 LALCFKCYFSFCTLCKEKRHVGVACMSPELRLQILQERQDSSRLGEEQRRKEKEMINEIM 539

Query:   513 SVKEILRDAKQCPSCKMAISRTEGCNKIVCNNCGQYFCYRCNKAIDGYDHFRTGTCELFP 572
             SVK I++ AKQCPSCK+AISRT GCNK+VCNNCGQYFCYRCN+AI GY+HF  G CELFP
Sbjct:   540 SVKVIMKSAKQCPSCKIAISRTGGCNKMVCNNCGQYFCYRCNEAITGYEHFSEGKCELFP 599

Query:   573 QEMIRDWEERLNARQVVAQIQADMF------DEHGLSCPNCRQFNAKVGNNNHMFCWACQ 626
             QE I++W E +N RQV+ QIQA +F       + G  CPNCRQFN K GNNNH+FCWACQ
Sbjct:   600 QEAIQEWNEMMNERQVIGQIQAQLFAQGGQFPQRGQLCPNCRQFNGKAGNNNHLFCWACQ 659

Query:   627 IHYCYLCKKIVRRSTQHYGPKGCKQHTVG 655
              H+CYLCKK+V++S QHYGPKGCKQHT G
Sbjct:   660 AHFCYLCKKVVKKSAQHYGPKGCKQHTDG 688

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006487 "protein N-linked glycosylation" evidence=RCA

GO:0006499 "N-terminal protein myristoylation" evidence=RCA

GO:0009610 "response to symbiotic fungus" evidence=RCA

UNIPROTKB\|F1NEG7 LOC100859099 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|F1RM50 RNF14 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

MGI\|MGI:1929668 Rnf14 "ring finger protein 14" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-040625-65 rnf14 "ring finger protein 14" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|A2VDU5 RNF14 "Ring finger protein 14" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2QX80 RNF14 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9UBS8 RNF14 "E3 ubiquitin-protein ligase RNF14" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0270130 DDB_G0270130 "E3 ubiquitin-protein ligase RNF14" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

WB\|WBGene00018966 F56D2.5 [Caenorhabditis elegans (taxid:6239)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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		655
pfam05773		113	pfam05773, RWD, RWD domain	2e-18
smart00591		107	smart00591, RWD, domain in RING finger and WD repe	2e-17
smart00647		64	smart00647, IBR, In Between Ring fingers	8e-10
pfam01485		63	pfam01485, IBR, IBR domain	1e-08
pfam13639		46	pfam13639, zf-RING_2, Ring finger domain	1e-05
pfam01485		63	pfam01485, IBR, IBR domain	0.001
smart00184		40	smart00184, RING, Ring finger	0.001
cd00162		45	cd00162, RING, RING-finger (Really Interesting New	0.001
TIGR01240		305	TIGR01240, mevDPdecarb, diphosphomevalonate decarb	0.001
smart00647		64	smart00647, IBR, In Between Ring fingers	0.003

>gnl\|CDD\|218742 pfam05773, RWD, RWD domain	Back alignment and domain information

 Score = 81.2 bits (201), Expect = 2e-18
 Identities = 34/140 (24%), Positives = 58/140 (41%), Gaps = 29/140 (20%)

Query: 155 NDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNSSTDLDARS 214
           + + Q +EL ALESIY D      ++    +  I + + T +                  
Sbjct: 2   SKELQEEELEALESIYPDEFEDEVKESSPPTFTIKLKLLTSEA----------------- 44

Query: 215 ESSDDFSYSFKVQYLPPIVLTCLLPKSYPSHLPPYFTISARWLNSTK-ISNLCSMLESIW 273
                     +   L  +VLT  LP+ YP   PP  ++S+ WL   +    L   LE + 
Sbjct: 45  ----------ESSPLVSLVLTFTLPEDYP-DEPPKISLSSPWLLRDQDKLQLLKELEELA 93

Query: 274 IDQPGQEILYQWIEWLQNSS 293
            +  G+ ++++ IEWLQ + 
Sbjct: 94  EENLGEVMIFELIEWLQENL 113

This domain was identified in WD40 repeat proteins and Ring finger domain proteins. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices. Length = 113

>gnl\|CDD\|214735 smart00591, RWD, domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain	Back alignment and domain information

>gnl\|CDD\|214763 smart00647, IBR, In Between Ring fingers	Back alignment and domain information

>gnl\|CDD\|216524 pfam01485, IBR, IBR domain	Back alignment and domain information

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

>gnl\|CDD\|216524 pfam01485, IBR, IBR domain	Back alignment and domain information

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

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

Back alignment and domain information

>gnl\|CDD\|130307 TIGR01240, mevDPdecarb, diphosphomevalonate decarboxylase	Back alignment and domain information

>gnl\|CDD\|214763 smart00647, IBR, In Between Ring fingers	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		655
KOG1814		445	consensus Predicted E3 ubiquitin ligase [Posttrans	100.0
KOG1812		384	consensus Predicted E3 ubiquitin ligase [Posttrans	99.92
KOG1815		444	consensus Predicted E3 ubiquitin ligase [Posttrans	99.91
KOG1814		445	consensus Predicted E3 ubiquitin ligase [Posttrans	99.88
KOG0006		446	consensus E3 ubiquitin-protein ligase (Parkin prot	99.83
KOG1812		384	consensus Predicted E3 ubiquitin ligase [Posttrans	99.72
PF05773		113	RWD: RWD domain; InterPro: IPR006575 The RWD eukar	99.66
smart00591		107	RWD domain in RING finger and WD repeat containing	99.63
KOG4018		215	consensus Uncharacterized conserved protein, conta	99.51
KOG4445		368	consensus Uncharacterized conserved protein, conta	99.2
KOG1815		444	consensus Predicted E3 ubiquitin ligase [Posttrans	98.94
smart00647		64	IBR In Between Ring fingers. the domains occurs be	98.74
KOG0006		446	consensus E3 ubiquitin-protein ligase (Parkin prot	98.64
smart00647		64	IBR In Between Ring fingers. the domains occurs be	98.58
PF01485		64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	98.52
PF01485		64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	98.27
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.22
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	98.05
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	97.85
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	97.85
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	97.84
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	97.83
KOG1035		1351	consensus eIF-2alpha kinase GCN2 [Translation, rib	97.71
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	97.71
PF14634		44	zf-RING_5: zinc-RING finger domain	97.68
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	97.63
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	97.49
KOG0823		230	consensus Predicted E3 ubiquitin ligase [Posttrans	97.42
KOG2177		386	consensus Predicted E3 ubiquitin ligase [Posttrans	97.34
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	97.28
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	97.19
KOG2164		513	consensus Predicted E3 ubiquitin ligase [Posttrans	97.12
PHA02926		242	zinc finger-like protein; Provisional	97.06
PHA02929		238	N1R/p28-like protein; Provisional	97.02
TIGR00599		397	rad18 DNA repair protein rad18. This family is bas	96.97
KOG0317		293	consensus Predicted E3 ubiquitin ligase, integral	96.87
COG5540		374	RING-finger-containing ubiquitin ligase [Posttrans	96.69
KOG1002		791	consensus Nucleotide excision repair protein RAD16	96.53
KOG0978		698	consensus E3 ubiquitin ligase involved in syntaxin	96.19
KOG0287		442	consensus Postreplication repair protein RAD18 [Re	96.15
TIGR00570		309	cdk7 CDK-activating kinase assembly factor MAT1. A	96.14
KOG4628		348	consensus Predicted E3 ubiquitin ligase [Posttrans	96.14
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	95.4
PF11789		57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	95.36
PF14835		65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	95.1
COG5219		1525	Uncharacterized conserved protein, contains RING Z	94.99
PF04564		73	U-box: U-box domain; InterPro: IPR003613 Quality c	94.77
KOG0309		1081	consensus Conserved WD40 repeat-containing protein	94.73
PF11793		70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	94.57
COG5574		271	PEX10 RING-finger-containing E3 ubiquitin ligase [	94.28
COG5243		491	HRD1 HRD ubiquitin ligase complex, ER membrane com	93.33
COG5432		391	RAD18 RING-finger-containing E3 ubiquitin ligase [	92.7
PF10571		26	UPF0547: Uncharacterised protein family UPF0547; I	92.66
KOG1039		344	consensus Predicted E3 ubiquitin ligase [Posttrans	92.42
PF10571		26	UPF0547: Uncharacterised protein family UPF0547; I	91.9
KOG0824		324	consensus Predicted E3 ubiquitin ligase [Posttrans	91.85
KOG4367		699	consensus Predicted Zn-finger protein [Function un	91.55
KOG0828		636	consensus Predicted E3 ubiquitin ligase [Posttrans	91.01
KOG2660		331	consensus Locus-specific chromosome binding protei	90.45
PF09297		32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	89.73
KOG2879		298	consensus Predicted E3 ubiquitin ligase [Posttrans	89.68
PHA00626		59	hypothetical protein	89.32
KOG0825		1134	consensus PHD Zn-finger protein [General function	88.99
smart00744		49	RINGv The RING-variant domain is a C4HC3 zinc-fing	88.64
KOG4185		296	consensus Predicted E3 ubiquitin ligase [Posttrans	88.03
KOG1428		3738	consensus Inhibitor of type V adenylyl cyclases/Ne	87.66
PF13719		37	zinc_ribbon_5: zinc-ribbon domain	87.65
KOG4739		233	consensus Uncharacterized protein involved in syna	87.64
PF05883		134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	87.63
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	87.62
KOG1645		463	consensus RING-finger-containing E3 ubiquitin liga	87.52
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	87.26
smart00661		52	RPOL9 RNA polymerase subunit 9.	86.73
KOG4159		398	consensus Predicted E3 ubiquitin ligase [Posttrans	85.67
KOG0823		230	consensus Predicted E3 ubiquitin ligase [Posttrans	85.67
PF13717		36	zinc_ribbon_4: zinc-ribbon domain	85.62
PF13248		26	zf-ribbon_3: zinc-ribbon domain	85.49
KOG0311		381	consensus Predicted E3 ubiquitin ligase [Posttrans	85.4
PF12861		85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	85.35
COG5152		259	Uncharacterized conserved protein, contains RING a	85.28
smart00661		52	RPOL9 RNA polymerase subunit 9.	85.17
KOG0978		698	consensus E3 ubiquitin ligase involved in syntaxin	84.8
PF14570		48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	84.76
PLN00172		147	ubiquitin conjugating enzyme; Provisional	84.34
PF14803		34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	84.12
PF13719		37	zinc_ribbon_5: zinc-ribbon domain	82.97
PRK00398		46	rpoP DNA-directed RNA polymerase subunit P; Provis	82.94
PLN03086		567	PRLI-interacting factor K; Provisional	82.63
PHA00626		59	hypothetical protein	81.75
KOG3299		206	consensus Uncharacterized conserved protein [Funct	81.52
PF13240		23	zinc_ribbon_2: zinc-ribbon domain	81.13
PF12773		50	DZR: Double zinc ribbon	80.77
PRK04023		1121	DNA polymerase II large subunit; Validated	80.02

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

Probab=100.00  E-value=1.2e-64  Score=521.15  Aligned_cols=407  Identities=38%  Similarity=0.679  Sum_probs=342.9

Q ss_pred             hchHHHHHHHHHHHHHhcCCCeeeeccCCCCceEEEEEeeccCCCceEEeecCCCCccccCCCCCCCcccccccccCCcE
Q 006225          153 RINDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNSSTDLDARSESSDDFSYSFKVQYLPPI  232 (655)
Q Consensus       153 ~~n~e~Q~~EleaLeSIY~d~~~~~~~~~~~~~f~i~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~v~~LPpi  232 (655)
                      ++|.++|++||+||+|||+++.+........+.|+|++.+++.-++.+..+.+...+    ++.  ...+++++.+||||
T Consensus         3 ~dn~~~qedEL~AL~siy~e~~~~~~~~~~~~~~~ir~ni~v~f~~~~~~~vnie~~----s~~--~~~f~~~~~~lPpi   76 (445)
T KOG1814|consen    3 EDNRELQEDELEALESIYPENEFRKVSYWEDGEFEIRLNIEVNFEILYSPKVNIEGT----SDS--MDLFSLPLDHLPPI   76 (445)
T ss_pred             chHHHHHHHHHHHHHHhccccccccccccccccceeEeeeeccceeecccccccccc----ccc--ccccccccccCCCe
Confidence            468999999999999999988776554444467888887666555544444332221    111  12378999999999


Q ss_pred             EEEEEcCCCCCCCCCCeEEeecccCCHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHhhccccccccccceecCCCCccc
Q 006225          233 VLTCLLPKSYPSHLPPYFTISARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSLSYLGFNEEIVLGPYGVAC  312 (655)
Q Consensus       233 ~L~~~lP~~YPs~~pP~~~l~s~wL~~~~l~~L~~~L~~~~ee~~G~~~lf~~ie~lqe~~~~~l~~~~~~~l~~~~~~~  312 (655)
                      .|.|.||++||+.+||.|.|++.||+.++++.|++.      +.+|..++|+|.+||++...+++++...++|.++....
T Consensus        77 vlkf~LP~~YPs~spP~f~l~s~Wmn~~q~~~lc~~------el~~i~~~~q~m~~l~~~~~s~l~~i~~~~lki~~~~~  150 (445)
T KOG1814|consen   77 VLKFHLPNDYPSVSPPKFELKSYWMNPDQKSALCSK------ELRLIEELNQMMDFLKESTISILNLIAPFELKIISQKE  150 (445)
T ss_pred             eeeeecCCccccCCCCceeeehcccCHHHhhhccch------hhccceeHHHHHHHHHHHHHHHHHhcccceeccchhhh
Confidence            999999999999999999999999999999999887      67899999999999999999999999999998877665


Q ss_pred             cCCcccccccCCCCCCchhhhccchhhhhhhccccccccccccccccCCCeE-ecCCCCcccHhhHHHHHHHHhhcCCcc
Q 006225          313 IGDRRAISESVSPDVDIPSIRSYNHERCHENFLKSFHECRICFSEFAGTDFV-RLPCHHFFCWKCMKTYLDIHISEGTVS  391 (655)
Q Consensus       313 ~~d~~~~~~~~s~~~~~~~l~~~n~~~~~~~f~~~~~~C~IC~e~~~~~~~~-~l~C~H~fC~~Cl~~yi~~~i~~g~~~  391 (655)
                      ..+.++..  .+++.+++.+++|++++..+.|.++.+.|.|||++..|...+ .++|+|+||+.|++.|++..|++|.+.
T Consensus       151 ~~~~~~~~--~~~~sl~~~Il~~deea~~~~F~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~  228 (445)
T KOG1814|consen  151 FPALIRQG--ESIDSLKKEILQFDEEATLEKFVNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVS  228 (445)
T ss_pred             cccccccc--cChHHHHHHHHhhhHHHHHHHHHhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceee
Confidence            55554443  467778899999999999999999999999999999985544 469999999999999999999999999


Q ss_pred             eeccCCCCCCCCCCcccccccCChHHHHHHHHHHHHHHhhcCCCcccccC--CCCCcccc-cccccccccccceeecccc
Q 006225          392 KLQCPDAKCGGMVPPSLLKKLLGDEEFERWESLMLQKTLESMSDVAYCPR--CETPCIED-EEQHAQCSKCFYSFCTLCR  468 (655)
Q Consensus       392 ~i~CP~~~C~~~l~~~~i~~ll~~e~~ery~~~~~~~~l~~~~~~~~CP~--C~~~~~~~-~~~~~~C~~C~~~fC~~C~  468 (655)
                      .++||+++|+...++..++.+|+.++++||+.+++++.++.+.|.+|||+  |+.++..+ ....+.|.+|.++||+.|+
T Consensus       229 ~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l~lqk~l~~msdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk  308 (445)
T KOG1814|consen  229 CLKCPDPKCGSVAPPGQVKELVGDELFARYEKLMLQKTLELMSDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCK  308 (445)
T ss_pred             eecCCCCCCcccCCchHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCChhhccCccccCchhhhhhhccCccHHHHHHH
Confidence            99999999999999999999999999999999999999999999999998  99997544 4578999999999999999


Q ss_pred             ccccCCcCCCchHHH-HHHHHHhhc--chhhhhhhhHHH----HHHHHHHHhHHHHhcccccCccccceeEEecCcCcee
Q 006225          469 ERRHVGVVCMTPEIK-LRILQERQN--SSQVKEGQKQRE----HEMINELLSVKEILRDAKQCPSCKMAISRTEGCNKIV  541 (655)
Q Consensus       469 ~~~H~~~sC~~~~~~-~~~~~e~~~--~~~~~~~~~~~e----~e~~~e~l~~~~i~~~~k~CP~C~~~iek~~Gcn~m~  541 (655)
                      ..||+...|...+.+ ..+..++..  .+......+++.    .+++++.++++|+..|.++||.|+++|++++|||+|+
T Consensus       309 ~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~  388 (445)
T KOG1814|consen  309 LTWHGVSPCKVKAEKLIELYLEYLEADEARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMH  388 (445)
T ss_pred             HhhcCCCcccCchHHHHHHHHHHhhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCcccee
Confidence            999999999755333 222222222  222233334444    7788899999999999999999999999999999999


Q ss_pred             ccccCeeeeccccccc---cCCCCCCCCCCCCChh
Q 006225          542 CNNCGQYFCYRCNKAI---DGYDHFRTGTCELFPQ  573 (655)
Q Consensus       542 C~~C~~~FC~~C~~~~---~~~~H~~~~~C~~~~~  573 (655)
                      |..|++.|||.|....   +||.||+...+..|+.
T Consensus       389 C~~c~~~fc~~c~~~l~~~nPYkHF~e~~s~c~~~  423 (445)
T KOG1814|consen  389 CTKCGTYFCWICAELLYPENPYKHFSEPGSECYGQ  423 (445)
T ss_pred             eccccccceeehhhhcCCCChhhhhcCCcCccccc
Confidence            9999999999999887   5799999998877754

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

>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

>PF05773 RWD: RWD domain; InterPro: IPR006575 The RWD eukaryotic domain is found in RING finger (IPR001841 from INTERPRO) and WD repeat (IPR001680 from INTERPRO) containing proteins and DEXDc-like helicase (IPR001410 from INTERPRO) subfamily related to the ubiquitin-conjugating enzymes domain (IPR000608 from INTERPRO)	Back alignment and domain information

>smart00591 RWD domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain	Back alignment and domain information

>KOG4018 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]	Back alignment and domain information

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

>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>smart00647 IBR In Between Ring fingers	Back alignment and domain information

>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>smart00647 IBR In Between Ring fingers	Back alignment and domain information

>PF01485 IBR: IBR domain; InterPro: IPR002867 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

>PF01485 IBR: IBR domain; InterPro: IPR002867 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

>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

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

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

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

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

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

>KOG1035 consensus eIF-2alpha kinase GCN2 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

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

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

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

Back alignment and domain information

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

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

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

>smart00184 RING Ring finger	Back alignment and domain information

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

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

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

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

>TIGR00599 rad18 DNA repair protein rad18	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

>COG5540 RING-finger-containing 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

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

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

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

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

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

>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C	Back alignment and domain information

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

>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]	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

>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]	Back alignment and domain information

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

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

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

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

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines	Back alignment and domain information

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

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines	Back alignment and domain information

>KOG0824 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

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

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

>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains	Back alignment and domain information

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

>PHA00626 hypothetical protein	Back alignment and domain information

>KOG0825 consensus PHD Zn-finger protein [General function prediction only]	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

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

>PF13719 zinc_ribbon_5: zinc-ribbon domain	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

>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

>KOG0802 consensus 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

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

>smart00661 RPOL9 RNA polymerase subunit 9	Back alignment and domain information

>KOG4159 consensus Predicted E3 ubiquitin ligase [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

>PF13717 zinc_ribbon_4: zinc-ribbon domain	Back alignment and domain information

>PF13248 zf-ribbon_3: zinc-ribbon domain	Back alignment and domain information

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

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

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

>smart00661 RPOL9 RNA polymerase subunit 9	Back alignment and domain information

>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]	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

>PLN00172 ubiquitin conjugating enzyme; Provisional	Back alignment and domain information

>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C	Back alignment and domain information

>PF13719 zinc_ribbon_5: zinc-ribbon domain	Back alignment and domain information

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional	Back alignment and domain information

>PLN03086 PRLI-interacting factor K; Provisional	Back alignment and domain information

>PHA00626 hypothetical protein	Back alignment and domain information

>KOG3299 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>PF13240 zinc_ribbon_2: zinc-ribbon domain	Back alignment and domain information

>PF12773 DZR: Double zinc ribbon	Back alignment and domain information

>PRK04023 DNA polymerase II large subunit; Validated	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		655
1wim_A		94	Solution Structure Of The Ring Finger Domain Of The		2e-04

>pdb|1WIM|A Chain A, Solution Structure Of The Ring Finger Domain Of The Human Ubcm4-Interacting Protein 4 Length = 94

Back alignment and structure

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/82 (25%), Positives = 43/82 (52%), Gaps = 3/82 (3%)
Query: 351 CRICFSEFAGTDFVRLP-CHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKC--GGMVPPS 407
           C++C  E+       +  C   FC  C+K Y+++ I EG  + + CPDA C   G +  +
Sbjct: 8   CKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQEN 67
Query: 408 LLKKLLGDEEFERWESLMLQKT 429
            ++ ++  E  +R++ L  +++
Sbjct: 68  EIECMVAAEIMQRYKKLQFERS 89

PyMOL of 1wim

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		655
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	3e-23
2day_A		128	Ring finger protein 25; ligase, metal-binding, UB1	7e-17
2ebm_A		128	RWD domain-containing protein 1; alpha+beta sandwi	1e-14
1ukx_A		137	GCN2, GCN2 EIF2alpha kinase; UBC-like fold, triple	2e-14
2yz0_A		138	Serine/threonine-protein kinase GCN2; A-B-B-B-B-A-	3e-14
2dax_A		152	Protein C21ORF6; RWD domain, alpha+beta sandwich f	4e-14
2ebk_A		128	RWD domain-containing protein 3; alpha+beta sandwi	5e-14
2daw_A		154	RWD domain containing protein 2; alpha+beta sandwi	2e-12
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-12
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-11
1wd2_A		60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	1e-09
2ct7_A		86	Ring finger protein 31; IBR, structural genomics,	4e-07
2ct7_A		86	Ring finger protein 31; IBR, structural genomics,	5e-04
2ect_A		78	Ring finger protein 126; metal binding protein, st	1e-04
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	2e-04
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	2e-04
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	3e-04
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	3e-04
2jmo_A		80	Parkin; IBR, E3 ligase, zinc binding domain, RBR;	4e-04
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	5e-04
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	5e-04
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	7e-04

>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 Length = 94	Back alignment and structure

 Score = 93.4 bits (232), Expect = 3e-23
 Identities = 22/88 (25%), Positives = 44/88 (50%), Gaps = 3/88 (3%)

Query: 349 HECRICFSEFAGTDFVRLP-CHHFFCWKCMKTYLDIHISEGTVSKLQCPDAKCG--GMVP 405
             C++C  E+       +  C   FC  C+K Y+++ I EG  + + CPDA C   G + 
Sbjct: 6   SGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQ 65

Query: 406 PSLLKKLLGDEEFERWESLMLQKTLESM 433
            + ++ ++  E  +R++ L  +++  S 
Sbjct: 66  ENEIECMVAAEIMQRYKKLQFERSGPSS 93

PyMOL of 1wim

>2day_A Ring finger protein 25; ligase, metal-binding, UB1 conjugation, UB1 conjugation pathway, RWD domain, alpha+beta sandwich fold, structural genomics; NMR {Homo sapiens} SCOP: d.20.1.3 PDB: 2dmf_A Length = 128	Back alignment and structure

>2ebm_A RWD domain-containing protein 1; alpha+beta sandwich fold, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 128	Back alignment and structure

>1ukx_A GCN2, GCN2 EIF2alpha kinase; UBC-like fold, triple beta-turns, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.20.1.3 Length = 137	Back alignment and structure

>2yz0_A Serine/threonine-protein kinase GCN2; A-B-B-B-B-A-A, amino acid starvation signal response, EIF2alpha kinase, transferase; NMR {Saccharomyces cerevisiae} Length = 138	Back alignment and structure

>2dax_A Protein C21ORF6; RWD domain, alpha+beta sandwich fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.20.1.3 Length = 152	Back alignment and structure

>2ebk_A RWD domain-containing protein 3; alpha+beta sandwich fold, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 128	Back alignment and structure

>2daw_A RWD domain containing protein 2; alpha+beta sandwich fold, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.20.1.3 Length = 154	Back alignment and structure

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

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

>1wd2_A Ariadne-1 protein homolog; ring, IBR, triad, zinc finger, ligase; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 60	Back alignment and structure

>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4 Length = 86	Back alignment and structure

>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4 Length = 86	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

>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

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

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

>2jmo_A Parkin; IBR, E3 ligase, zinc binding domain, RBR; NMR {Homo sapiens} Length = 80	Back alignment and structure

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

>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

>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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		655
2yz0_A		138	Serine/threonine-protein kinase GCN2; A-B-B-B-B-A-	99.82
2ebm_A		128	RWD domain-containing protein 1; alpha+beta sandwi	99.81
1ukx_A		137	GCN2, GCN2 EIF2alpha kinase; UBC-like fold, triple	99.81
2ebk_A		128	RWD domain-containing protein 3; alpha+beta sandwi	99.8
2day_A		128	Ring finger protein 25; ligase, metal-binding, UB1	99.8
2dax_A		152	Protein C21ORF6; RWD domain, alpha+beta sandwich f	99.78
2daw_A		154	RWD domain containing protein 2; alpha+beta sandwi	99.75
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.53
1wd2_A		60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	99.52
1wd2_A		60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	99.22
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.92
2ct7_A		86	Ring finger protein 31; IBR, structural genomics,	98.81
2jmo_A		80	Parkin; IBR, E3 ligase, zinc binding domain, RBR;	98.6
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	98.35
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	98.26
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	98.24
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	98.22
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	98.2
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	98.18
1t1h_A		78	Gspef-atpub14, armadillo repeat containing protein	98.16
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	98.16
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	98.14
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	98.13
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	98.12
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	98.12
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	98.12
2ct7_A		86	Ring finger protein 31; IBR, structural genomics,	98.11
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	98.11
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	98.11
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	98.1
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	98.07
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	98.05
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	98.0
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	97.99
2yu4_A		94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	97.97
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	97.96
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	97.96
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	97.94
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	97.93
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	97.91
2ect_A		78	Ring finger protein 126; metal binding protein, st	97.86
1z6u_A		150	NP95-like ring finger protein isoform B; structura	97.82
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	97.82
4ayc_A		138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	97.8
2kr4_A		85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	97.79
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	97.78
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	97.78
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	97.77
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	97.76
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	97.76
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	97.75
2jmo_A		80	Parkin; IBR, E3 ligase, zinc binding domain, RBR;	97.75
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	97.71
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	97.7
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	97.69
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	97.67
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	97.67
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	97.63
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	97.59
1wgm_A		98	Ubiquitin conjugation factor E4A; ubiquitinating e	97.55
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	97.54
2kre_A		100	Ubiquitin conjugation factor E4 B; U-box domain, E	97.52
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	97.48
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	97.43
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	97.39
4ic3_A		74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	97.36
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	97.19
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	97.19
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	97.16
2f42_A		179	STIP1 homology and U-box containing protein 1; cha	97.08
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	97.05
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	96.98
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	96.92
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	96.88
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	96.85
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	96.85
2ea5_A		68	Cell growth regulator with ring finger domain prot	96.75
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	95.86
3t6p_A		345	Baculoviral IAP repeat-containing protein 2; ring,	95.83
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	95.71
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	95.26
2bay_A		61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	94.47
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	92.63
2jrp_A		81	Putative cytoplasmic protein; two-zinc binding pro	92.27
3vk6_A		101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	90.62
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	90.31
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	90.29
2cs3_A		93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	88.73
2jun_A		101	Midline-1; B-BOX, TRIM, ring finger, alternative s	88.06
3vk6_A		101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	87.76
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	87.26
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	86.13
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	86.03
3j20_Y		50	30S ribosomal protein S27AE; archaea, archaeal, KI	85.73
1vq8_Z		83	50S ribosomal protein L37AE; ribosome 50S, protein	85.39
2ect_A		78	Ring finger protein 126; metal binding protein, st	85.25
4ayc_A		138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	85.2
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	84.72
3nw0_A		238	Non-structural maintenance of chromosomes element	84.16
2a7l_A		136	Hypothetical ubiquitin-conjugating enzyme LOC55284	83.86
2jrp_A		81	Putative cytoplasmic protein; two-zinc binding pro	83.66
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	83.25
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	82.98
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	82.32
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	81.99
1t1h_A		78	Gspef-atpub14, armadillo repeat containing protein	81.0
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	80.98
3bzh_A		194	Ubiquitin-conjugating enzyme E2 E1; structural gen	80.78
2fo3_A		125	Ubiquitin-conjugating enzyme; SGC, UBC, structural	80.49
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	80.46

>2yz0_A Serine/threonine-protein kinase GCN2; A-B-B-B-B-A-A, amino acid starvation signal response, EIF2alpha kinase, transferase; NMR {Saccharomyces cerevisiae}	Back alignment and structure

Probab=99.82  E-value=6.1e-20  Score=170.45  Aligned_cols=114  Identities=21%  Similarity=0.258  Sum_probs=91.2

Q ss_pred             hhchHHHHHHHHHHHHHhcCCCeeeeccC------CCCceEEEEEeeccCCCceEEeecCCCCccccCCCCCCCcccccc
Q 006225          152 LRINDQSQGDELLALESIYGDSVFILDRQ------RDLRSCQIHVHVETLDGLTVTAKLNSSTDLDARSESSDDFSYSFK  225 (655)
Q Consensus       152 ~~~n~e~Q~~EleaLeSIY~d~~~~~~~~------~~~~~f~i~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  225 (655)
                      |.++.|+|++||+||+|||+|++..++..      +....|+|.|.....+                      +      
T Consensus         8 ~~~~~e~q~~EleaL~SIY~d~~~~~~~~~~~~~~~~~~~f~I~l~~~~~~----------------------~------   59 (138)
T 2yz0_A            8 LDQYYEIQCNELEAIRSIYMDDFTDLTKRKSSWDKQPQIIFEITLRSVDKE----------------------P------   59 (138)
T ss_dssp             HHHHHHHHHHHHHHHHTTSSSSEECCSTTSSSSCSSCCSCEEEEEECSSCS----------------------S------
T ss_pred             ccchHHHHHHHHHHHHHHChhhheecccccccccCCCCcEEEEEEecCCCC----------------------C------
Confidence            56788999999999999999998876542      1224566665421100                      0      


Q ss_pred             cccCCcEEEEEEcCCCCCCCCCCeEEee-cccCCHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHhhccccc
Q 006225          226 VQYLPPIVLTCLLPKSYPSHLPPYFTIS-ARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSSLSY  296 (655)
Q Consensus       226 v~~LPpi~L~~~lP~~YPs~~pP~~~l~-s~wL~~~~l~~L~~~L~~~~ee~~G~~~lf~~ie~lqe~~~~~  296 (655)
                        .-.+|.|.|.||++||++ ||.|.|. +.||++.+++.|.+.|.++|+++.|++|||+||+||||.+..+
T Consensus        60 --~~~~~~L~~~~p~~YP~~-~P~i~l~~~~~L~~~~~~~L~~~L~~~~~e~~G~~mif~lv~~lqe~l~~~  128 (138)
T 2yz0_A           60 --VESSITLHFAMTPMYPYT-APEIEFKNVQNVMDSQLQMLKSEFKKIHNTSRGQEIIFEITSFTQEKLDEF  128 (138)
T ss_dssp             --CCCEEEEEEECCSSTTSS-CCEEEEECCCSCCSHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHHH
T ss_pred             --CceEEEEEEECCCCCCCC-CCeEEEecCCCCCHHHHHHHHHHHHHHHHHhCCCEEHHHHHHHHHHHHHHH
Confidence              002489999999999976 9999995 5799999999999999999999999999999999999998765

PyMOL of 2yz0

>2ebm_A RWD domain-containing protein 1; alpha+beta sandwich fold, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1ukx_A GCN2, GCN2 EIF2alpha kinase; UBC-like fold, triple beta-turns, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.20.1.3	Back alignment and structure

>2ebk_A RWD domain-containing protein 3; alpha+beta sandwich fold, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2day_A Ring finger protein 25; ligase, metal-binding, UB1 conjugation, UB1 conjugation pathway, RWD domain, alpha+beta sandwich fold, structural genomics; NMR {Homo sapiens} SCOP: d.20.1.3 PDB: 2dmf_A	Back alignment and structure

>2dax_A Protein C21ORF6; RWD domain, alpha+beta sandwich fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.20.1.3	Back alignment and structure

>2daw_A RWD domain containing protein 2; alpha+beta sandwich fold, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.20.1.3	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

>1wd2_A Ariadne-1 protein homolog; ring, IBR, triad, zinc finger, ligase; NMR {Homo sapiens} SCOP: g.44.1.1	Back alignment and structure

>1wd2_A Ariadne-1 protein homolog; ring, IBR, triad, zinc finger, ligase; NMR {Homo sapiens} SCOP: g.44.1.1	Back alignment and structure

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

>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4	Back alignment and structure

>2jmo_A Parkin; IBR, E3 ligase, zinc binding domain, RBR; 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

>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

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

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

>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

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

>1jm7_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

>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

>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

>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

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

>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4	Back alignment and structure

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

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

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

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

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

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

>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

>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

>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

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

>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

>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

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

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

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

>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

>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

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

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

>2jmo_A Parkin; IBR, E3 ligase, zinc binding domain, RBR; 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

>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

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, 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

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

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

>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

>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

>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

>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

>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

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

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

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

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

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

>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

>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

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

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

>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

>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

>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

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

>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

>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

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}	Back alignment and structure

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

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

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

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

>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

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

>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

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

>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}	Back alignment and structure

>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...	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

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

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

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

>2a7l_A Hypothetical ubiquitin-conjugating enzyme LOC55284; structural genomics consortium, (SGC), ligase; 1.82A {Homo sapiens} SCOP: d.20.1.1	Back alignment and structure

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}	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

>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

>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

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

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

>3bzh_A Ubiquitin-conjugating enzyme E2 E1; structural genomics consortium, ubiquitin-conjuga enzyme, ligase, SGC, UBL conjugation pathway; 1.60A {Homo sapiens} PDB: 1y6l_A	Back alignment and structure

>2fo3_A Ubiquitin-conjugating enzyme; SGC, UBC, structural genomics, structural genomics consortium, unknown function; 1.86A {Plasmodium vivax} SCOP: d.20.1.1	Back alignment and structure

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

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		655
d2daya1		115	d.20.1.3 (A:8-122) E3 ubiquitin-protein ligase RNF	3e-20
d1wima_		94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	3e-18
d2daxa1		140	d.20.1.3 (A:8-147) Uncharacterized protein C21orf6	7e-18
d1ukxa_		137	d.20.1.3 (A:) EIF2-alpha kinase 4 (GCN2-like prote	2e-16
d2dawa1		141	d.20.1.3 (A:8-148) RWD domain-containing protein 2	2e-14
d2ct7a1		73	g.44.1.4 (A:8-80) Ring finger protein 31 {Human (H	5e-10
d2ct7a1		73	g.44.1.4 (A:8-80) Ring finger protein 31 {Human (H	1e-08
d2ct7a1		73	g.44.1.4 (A:8-80) Ring finger protein 31 {Human (H	5e-04
d1wd2a_		60	g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Ho	2e-09
d1wd2a_		60	g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Ho	5e-04
d1jm7a_		103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	0.001
d1fbva4		79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	0.001
d1bora_		56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	0.002
d1chca_		68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	0.002
d1rmda2		86	g.44.1.1 (A:1-86) V(D)J recombination activating p	0.002
d1iyma_		55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	0.002

>d2daya1 d.20.1.3 (A:8-122) E3 ubiquitin-protein ligase RNF25 {Human (Homo sapiens) [TaxId: 9606]} Length = 115	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: UBC-like
superfamily: UBC-like
family: RWD domain
domain: E3 ubiquitin-protein ligase RNF25
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 84.2 bits (208), Expect = 3e-20
 Identities = 24/136 (17%), Positives = 46/136 (33%), Gaps = 25/136 (18%)

Query: 155 NDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNSSTDLDARS 214
            D     E+  LESIY D + ++         +I++ +                      
Sbjct: 2   EDWVLPSEVEVLESIYLDELQVIKGNGRTSPWEIYITLH--------------------P 41

Query: 215 ESSDDFSYSFKVQYLPPIVLTCLLPKSYPSHLPPYFTISARWLNSTKISNLCSMLESIWI 274
            +++D              L   +P  YP  +P     + R L+  +I  +  +L  +  
Sbjct: 42  ATAEDQD-----SQYVCFTLVLQVPAEYPHEVPQISIRNPRGLSDEQIHTILQVLGHVAK 96

Query: 275 DQPGQEILYQWIEWLQ 290
              G  +LY+ IE  +
Sbjct: 97  AGLGTAMLYELIEKGK 112

PyMOL of d2daya1

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

>d2daxa1 d.20.1.3 (A:8-147) Uncharacterized protein C21orf6 {Human (Homo sapiens) [TaxId: 9606]} Length = 140	Back information, alignment and structure

>d1ukxa_ d.20.1.3 (A:) EIF2-alpha kinase 4 (GCN2-like protein) {Mouse (Mus musculus) [TaxId: 10090]} Length = 137	Back information, alignment and structure

>d2dawa1 d.20.1.3 (A:8-148) RWD domain-containing protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 141	Back information, alignment and structure

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]} Length = 73	Back information, alignment and structure

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]} Length = 73	Back information, alignment and structure

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]} Length = 73	Back information, alignment and structure

>d1wd2a_ g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Homo sapiens) [TaxId: 9606]} Length = 60	Back information, alignment and structure

>d1wd2a_ g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Homo sapiens) [TaxId: 9606]} Length = 60	Back information, alignment and structure

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

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

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

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

>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

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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		655
d2daya1		115	E3 ubiquitin-protein ligase RNF25 {Human (Homo sap	99.81
d1ukxa_		137	EIF2-alpha kinase 4 (GCN2-like protein) {Mouse (Mu	99.79
d2daxa1		140	Uncharacterized protein C21orf6 {Human (Homo sapie	99.75
d2dawa1		141	RWD domain-containing protein 2 {Human (Homo sapie	99.74
d1wd2a_		60	Ariadne-1 protein homolog {Human (Homo sapiens) [T	99.57
d1wima_		94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	99.49
d1wd2a_		60	Ariadne-1 protein homolog {Human (Homo sapiens) [T	99.22
d2ct7a1		73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	98.95
d2ct7a1		73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	98.72
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	98.29
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	98.19
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	98.16
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	98.06
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	98.01
d1t1ha_		78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	97.98
d1bora_		56	Acute promyelocytic leukaemia proto-oncoprotein PM	97.86
d2c2la2		80	STIP1 homology and U box-containing protein 1, STU	97.84
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	97.83
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	97.81
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	97.79
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	97.75
d2baya1		56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	97.71
d1vyxa_		60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	97.08
d3dplr1		88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	96.6
d1wgma_		98	Ubiquitin conjugation factor E4A {Human (Homo sapi	96.47
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	92.8
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	91.83
d2cs3a1		80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	91.78
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	89.58
d2akla2		38	Hypothetical protein PA0128, N-terminal domain {Ps	88.73
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	83.96
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	83.63
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	83.34
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	82.34

>d2daya1 d.20.1.3 (A:8-122) E3 ubiquitin-protein ligase RNF25 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: UBC-like
superfamily: UBC-like
family: RWD domain
domain: E3 ubiquitin-protein ligase RNF25
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=4.6e-20  Score=163.72  Aligned_cols=114  Identities=22%  Similarity=0.294  Sum_probs=87.0

Q ss_pred             hHHHHHHHHHHHHHhcCCCeeeeccCCCCceEEEEEeeccCCCceEEeecCCCCccccCCCCCCCcccccccccCCcEEE
Q 006225          155 NDQSQGDELLALESIYGDSVFILDRQRDLRSCQIHVHVETLDGLTVTAKLNSSTDLDARSESSDDFSYSFKVQYLPPIVL  234 (655)
Q Consensus       155 n~e~Q~~EleaLeSIY~d~~~~~~~~~~~~~f~i~i~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~v~~LPpi~L  234 (655)
                      +++.+++||+||+|||+|++..+...+....+++.|.+.          +....+       ..        +...++.|
T Consensus         2 ~~~~~~~EleaL~SIY~d~~~~~~~~~~~~~~~~~i~~~----------~~~~~~-------~~--------~~~~~v~L   56 (115)
T d2daya1           2 EDWVLPSEVEVLESIYLDELQVIKGNGRTSPWEIYITLH----------PATAED-------QD--------SQYVCFTL   56 (115)
T ss_dssp             CCCHHHHHHHHHHHHSTTTEEEECCTTSSCCEEEEEEEC----------CSCCSS-------SS--------CCCCEEEE
T ss_pred             cchhHHHHHHHHHhHCCCceEEeccCCCCCCeEEEEEEe----------cCCCCC-------Cc--------ccceEEEE
Confidence            456789999999999999998776543333333333221          111000       00        11234999


Q ss_pred             EEEcCCCCCCCCCCeEEeecccCCHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHhhcc
Q 006225          235 TCLLPKSYPSHLPPYFTISARWLNSTKISNLCSMLESIWIDQPGQEILYQWIEWLQNSS  293 (655)
Q Consensus       235 ~~~lP~~YPs~~pP~~~l~s~wL~~~~l~~L~~~L~~~~ee~~G~~~lf~~ie~lqe~~  293 (655)
                      .|.||++||++.||.+.+++.||+..++..|.+.|.++|+++.|++|||+||+|+||.+
T Consensus        57 ~~~~p~~YP~~~P~i~~~~~~~l~~~~~~~L~~~l~~~~~e~~G~~mif~lv~~~qE~L  115 (115)
T d2daya1          57 VLQVPAEYPHEVPQISIRNPRGLSDEQIHTILQVLGHVAKAGLGTAMLYELIEKGKEIL  115 (115)
T ss_dssp             EEEECSSTTSSCCEEEEEEEESSCHHHHHHHHHHHHHHHHHTTTSCCHHHHHHHHHHHH
T ss_pred             EEEcCCCCCCCCCcEEeeccCCCCHHHHHHHHHHHHHHHHHcCCCEEHHHHHHHHHhhC
Confidence            99999999999777777788999999999999999999999999999999999999864

PyMOL of d2daya1

>d1ukxa_ d.20.1.3 (A:) EIF2-alpha kinase 4 (GCN2-like protein) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2daxa1 d.20.1.3 (A:8-147) Uncharacterized protein C21orf6 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2dawa1 d.20.1.3 (A:8-148) RWD domain-containing protein 2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wd2a_ g.44.1.1 (A:) Ariadne-1 protein homolog {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

>d1wd2a_ g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {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

>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

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

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

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

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

>d1jm7b_ g.44.1.1 (B:) bard1 RING 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

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

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

>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

>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

>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

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

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

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

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

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

>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}	Back information, alignment and structure

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

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

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

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