Citrus Sinensis ID: 023590

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
MKGDLQLEQFSERNPSDADPLLGSQEVSDAPVVSSPSSSSSSEIKDEDIENGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLRVELFEDNSWRKIKFRLFVARDVFFVFLAVQTIIAAMGGFAYLMDKDGAFRNSFSDGWDRILSKHPIPFYYCIELLLWVGSLGLFPCIYGSMLCPGYRFCCHFCHSWYSLWFPCCYHGYSKDLAETLPYSYQEGAHKGKIGFLLSSRNLCYAFYIDIGFVNLLALDL
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcccccccccccccccccccccHHHHHHHHHHHHHHHcccccccccccccccccccEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHccccHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHcccEEEccccccccccccccccccccccccccccccEEEcccccEEEEEEEEHHHHHHcccc
ccccEEccccccccccccccccccccccccccccccccccccccccHHccccccccEEEEEcccccccccccccccccccHHHHHHHHHHHHHHcccccccccccccccEEEEEEEcccccHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHcccHHHHHHHccccHHHHHEEEEEEHHHHcHHHHHHcccccHHHHHHHHHcccccEEEcccccccHHHHHHccccccccccccccEEEEEEcccccEEEEEEEHHHHHHHHccc
mkgdlqleqfsernpsdadpllgsqevsdapvvsspsssssseikdediengslpccriclendgepddelispcmckgtqqFVHRACLDHWrsvkegfafshcttckAQFHLRVELfednswrkIKFRLFVARDVFFVFLAVQTIIAAMGGFAylmdkdgafrnsfsdgwdrilskhpipfYYCIELLLWVGslglfpciygsmlcpgyrfcchfchswyslwfpccyhgyskdlaetlpysyqegahkgkIGFLLSSRNLCYAFYIDIGFVNLLALDL
MKGDLQLEQFSERNPSDADPLLGSqevsdapvvsspsssssseikdediengsLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLRVELFEDNSWRKIKFRLFVARDVFFVFLAVQTIIAAMGGFAYLMDKDGAFRNSFSDGWDRILSKHPIPFYYCIELLLWVGSLGLFPCIYGSMLCPGYRFCCHFCHSWYSLWFPCCYHGYSKDLAETLPYSYQEGAHKGKIGFLLSSRNLCYAFYIDIGFVNLLALDL
MKGDLQLEQFSERNPSDADPLLGSQEVSDApvvsspssssssEIKDEDIENGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLRVELFEDNSWRKIKFRLFVARDVFFVFLAVQTIIAAMGGFAYLMDKDGAFRNSFSDGWDRILSKHPIPFYYCIELLLWVGSLGLFPCIYGSMLCPGYRFCCHFCHSWYSLWFPCCYHGYSKDLAETLPYSYQEGAHKGKIGFLLSSRNLCYAFYIDIGFVNLLALDL
****************************************************SLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLRVELFEDNSWRKIKFRLFVARDVFFVFLAVQTIIAAMGGFAYLMDKDGAFRNSFSDGWDRILSKHPIPFYYCIELLLWVGSLGLFPCIYGSMLCPGYRFCCHFCHSWYSLWFPCCYHGYSKDLAETLPYSYQEGAHKGKIGFLLSSRNLCYAFYIDIGFVNLLAL**
********************************************************CRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLRVELFEDNSWRKIKFRLFVARDVFFVFLAVQTIIAAMGGFAYLMDKDGAFRNSFSDGWDRILSKHPIPFYYCIELLLWVGSLGLFPCIYGSMLCPGYRFCCHFCHSWYSLWFPCCYHGYSKD*****************IGFLLSSRNLCYAFYIDIGFVNLLALDL
******************DPLLGSQE**********************IENGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLRVELFEDNSWRKIKFRLFVARDVFFVFLAVQTIIAAMGGFAYLMDKDGAFRNSFSDGWDRILSKHPIPFYYCIELLLWVGSLGLFPCIYGSMLCPGYRFCCHFCHSWYSLWFPCCYHGYSKDLAETLPYSYQEGAHKGKIGFLLSSRNLCYAFYIDIGFVNLLALDL
****************************************************SLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLRVELFEDNSWRKIKFRLFVARDVFFVFLAVQTIIAAMGGFAYLMDKDGAFRNSFSDGWDRILSKHPIPFYYCIELLLWVGSLGLFPCIYGSMLCPGYRFCCHFCHSWYSLWFPCCYHGYSKDLAETLPYSYQEGAHKGKIGFLLSSRNLCYAFYIDIGFVNLLALDL
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiii
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MKGDLQLEQFSERNPSDADPLLGSQEVSDAPVVSSPSSSSSSEIKDEDIENGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLRVELFEDNSWRKIKFRLFVARDVFFVFLAVQTIIAAMGGFAYLMDKDGAFRNSFSDGWDRILSKHPIPFYYCIELLLWVGSLGLFPCIYGSMLCPGYRFCCHFCHSWYSLWFPCCYHGYSKDLAETLPYSYQEGAHKGKIGFLLSSRNLCYAFYIDIGFVNLLALDL
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 ?
Query280 2.2.26 [Sep-21-2011]
Q8TCQ1289 E3 ubiquitin-protein liga yes no 0.535 0.519 0.260 8e-07
Q9DBD2286 E3 ubiquitin-protein liga yes no 0.492 0.482 0.282 1e-06
Q5XH39264 E3 ubiquitin-protein liga N/A no 0.464 0.492 0.279 1e-06
Q28IK8264 E3 ubiquitin-protein liga yes no 0.464 0.492 0.279 1e-06
Q6NZQ8289 E3 ubiquitin-protein liga no no 0.517 0.501 0.25 3e-06
Q5T0T0291 E3 ubiquitin-protein liga no no 0.392 0.378 0.286 1e-05
O60103 1242 ERAD-associated E3 ubiqui yes no 0.267 0.060 0.325 1e-05
Q0IH10252 E3 ubiquitin-protein liga N/A no 0.185 0.206 0.421 2e-05
Q68FA7251 E3 ubiquitin-protein liga no no 0.185 0.207 0.421 2e-05
Q5XIE5253 E3 ubiquitin-protein liga no no 0.185 0.205 0.421 3e-05
>sp|Q8TCQ1|MARH1_HUMAN E3 ubiquitin-protein ligase MARCH1 OS=Homo sapiens GN=MARCH1 PE=1 SV=1 Back     alignment and function desciption
 Score = 54.3 bits (129), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 44/169 (26%), Positives = 72/169 (42%), Gaps = 19/169 (11%)

Query: 1   MKGDL----QLEQFSERNPSDADPLLGSQEVSDAPVV-SSPSSSSSSEI--KDEDIENGS 53
           + GDL    Q    +E++P  +     +   + +P   ++P S S   +    +DI    
Sbjct: 24  ISGDLADASQTSTLNEKSPGRSASRSSNISKASSPTTGTAPRSQSRLSVCPSTQDI---- 79

Query: 54  LPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHL 113
              CRIC   +G+ +  LI+PC C GT +FVH++CL  W    +      C  CK  F +
Sbjct: 80  ---CRIC-HCEGDEESPLITPCRCTGTLRFVHQSCLHQWIKSSDTRC---CELCKYDFIM 132

Query: 114 RVELFEDNSWRKIKFRLFVARDVF-FVFLAVQTIIAAMGGFAYLMDKDG 161
             +L     W K++      R +F  V   V  I   +     L+D+  
Sbjct: 133 ETKLKPLRKWEKLQMTTSERRKIFCSVTFHVIAITCVVWSLYVLIDRTA 181
E3 ubiquitin-protein ligase that mediates ubiquitination of TFRC, CD86, FAS and MHC class II proteins, such as HLA-DR alpha and beta, and promotes their subsequent endocytosis and sorting to lysosomes via multivesicular bodies. By constitutively ubiquitinating MHC class II proteins in immature dendritic cells, down-regulates their cell surface localization thus sequestering them in the intracellular endosomal system.
Homo sapiens (taxid: 9606)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -
>sp|Q9DBD2|MARH8_MOUSE E3 ubiquitin-protein ligase MARCH8 OS=Mus musculus GN=March8 PE=2 SV=1 Back     alignment and function description
>sp|Q5XH39|MARH8_XENLA E3 ubiquitin-protein ligase MARCH8 OS=Xenopus laevis GN=march8 PE=2 SV=2 Back     alignment and function description
>sp|Q28IK8|MARH8_XENTR E3 ubiquitin-protein ligase MARCH8 OS=Xenopus tropicalis GN=march8 PE=2 SV=1 Back     alignment and function description
>sp|Q6NZQ8|MARH1_MOUSE E3 ubiquitin-protein ligase MARCH1 OS=Mus musculus GN=March1 PE=1 SV=2 Back     alignment and function description
>sp|Q5T0T0|MARH8_HUMAN E3 ubiquitin-protein ligase MARCH8 OS=Homo sapiens GN=MARCH8 PE=1 SV=1 Back     alignment and function description
>sp|O60103|DOA10_SCHPO ERAD-associated E3 ubiquitin-protein ligase doa10 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=doa10 PE=1 SV=1 Back     alignment and function description
>sp|Q0IH10|MARH3_XENLA E3 ubiquitin-protein ligase MARCH3 OS=Xenopus laevis GN=march3 PE=2 SV=1 Back     alignment and function description
>sp|Q68FA7|MARH3_XENTR E3 ubiquitin-protein ligase MARCH3 OS=Xenopus tropicalis GN=march3 PE=2 SV=1 Back     alignment and function description
>sp|Q5XIE5|MARH3_RAT E3 ubiquitin-protein ligase MARCH3 OS=Rattus norvegicus GN=March3 PE=1 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query280
359484644304 PREDICTED: uncharacterized protein LOC10 0.689 0.634 0.771 6e-85
297738903 438 unnamed protein product [Vitis vinifera] 0.635 0.406 0.811 5e-83
449464344305 PREDICTED: uncharacterized protein LOC10 0.692 0.636 0.746 5e-83
363807700309 uncharacterized protein LOC100818950 [Gl 0.703 0.637 0.727 5e-80
357477907312 E3 ubiquitin-protein ligase MARCH3 [Medi 0.707 0.634 0.740 1e-79
388520119307 unknown [Lotus japonicus] 0.692 0.631 0.729 2e-79
363806756300 uncharacterized protein LOC100782178 [Gl 0.885 0.826 0.570 2e-79
224091379310 predicted protein [Populus trichocarpa] 0.660 0.596 0.755 6e-76
255576972318 protein binding protein, putative [Ricin 0.717 0.632 0.695 2e-74
224114355308 predicted protein [Populus trichocarpa] 0.685 0.623 0.684 1e-73
>gi|359484644|ref|XP_002281763.2| PREDICTED: uncharacterized protein LOC100254401 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  320 bits (819), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 155/201 (77%), Positives = 170/201 (84%), Gaps = 8/201 (3%)

Query: 1   MKGDLQLEQFSERNPSDADPLLGSQEVSDAPVVSSPSSSSSSEIKDEDIENGSLPCCRIC 60
           MKG++QLE   ERNP D+DPLL +Q        +  S+ SSSEI  EDIE GS+PCCRIC
Sbjct: 1   MKGEVQLEPSGERNPRDSDPLLENQ--------ADSSTGSSSEINSEDIEAGSVPCCRIC 52

Query: 61  LENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLRVELFED 120
           LE DGEPDDELISPCMCKGTQQFVHR+CLDHWRSVKEGFAFSHCTTCKAQ+HL+V LFED
Sbjct: 53  LECDGEPDDELISPCMCKGTQQFVHRSCLDHWRSVKEGFAFSHCTTCKAQYHLQVALFED 112

Query: 121 NSWRKIKFRLFVARDVFFVFLAVQTIIAAMGGFAYLMDKDGAFRNSFSDGWDRILSKHPI 180
           NSWRKIKFRLFVARDVF VFLAVQT+I AMGGFAY+MDKDGAFRNSFSDGWDRILS+HPI
Sbjct: 113 NSWRKIKFRLFVARDVFLVFLAVQTVIGAMGGFAYIMDKDGAFRNSFSDGWDRILSRHPI 172

Query: 181 PFYYCIELLLWVGSLGLFPCI 201
           PFYYCI +L +   LG F  I
Sbjct: 173 PFYYCIGVLAFFVLLGFFGLI 193

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|297738903|emb|CBI28148.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|449464344|ref|XP_004149889.1| PREDICTED: uncharacterized protein LOC101220313 [Cucumis sativus] gi|449533550|ref|XP_004173737.1| PREDICTED: uncharacterized LOC101220313 [Cucumis sativus] Back     alignment and taxonomy information
>gi|363807700|ref|NP_001241911.1| uncharacterized protein LOC100818950 [Glycine max] gi|255641889|gb|ACU21213.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|357477907|ref|XP_003609239.1| E3 ubiquitin-protein ligase MARCH3 [Medicago truncatula] gi|355510294|gb|AES91436.1| E3 ubiquitin-protein ligase MARCH3 [Medicago truncatula] Back     alignment and taxonomy information
>gi|388520119|gb|AFK48121.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|363806756|ref|NP_001242276.1| uncharacterized protein LOC100782178 [Glycine max] gi|255641332|gb|ACU20943.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|224091379|ref|XP_002309239.1| predicted protein [Populus trichocarpa] gi|222855215|gb|EEE92762.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|255576972|ref|XP_002529371.1| protein binding protein, putative [Ricinus communis] gi|223531191|gb|EEF33038.1| protein binding protein, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|224114355|ref|XP_002332377.1| predicted protein [Populus trichocarpa] gi|222832201|gb|EEE70678.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query280
TAIR|locus:2197434321 AT1G11020 [Arabidopsis thalian 0.807 0.704 0.610 6.3e-69
TAIR|locus:2008056250 AT1G50440 [Arabidopsis thalian 0.503 0.564 0.470 1.3e-29
UNIPROTKB|B9EJE7138 MARCH3 "Membrane-associated ri 0.228 0.463 0.375 1.2e-08
WB|WBGene00008433206 D2089.2 [Caenorhabditis elegan 0.228 0.310 0.4 1.3e-08
UNIPROTKB|D6RGC4545 MARCH1 "E3 ubiquitin-protein l 0.539 0.277 0.283 2.7e-08
UNIPROTKB|F1NAM1185 MARCH3 "Uncharacterized protei 0.185 0.281 0.421 6.2e-08
UNIPROTKB|F1MM17272 MARCH1 "Uncharacterized protei 0.353 0.363 0.326 1.2e-07
UNIPROTKB|Q8TCQ1289 MARCH1 "E3 ubiquitin-protein l 0.353 0.342 0.317 3.3e-07
UNIPROTKB|E1C485688 MARCH7 "Uncharacterized protei 0.264 0.107 0.358 3.3e-07
UNIPROTKB|F1NSN9235 MARCH1 "Uncharacterized protei 0.310 0.370 0.326 3.6e-07
TAIR|locus:2197434 AT1G11020 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 699 (251.1 bits), Expect = 6.3e-69, P = 6.3e-69
 Identities = 146/239 (61%), Positives = 167/239 (69%)

Query:     1 MKGDLQLEQFSERNPSDADPLLGSQEVSDAXXXXXXXXXX--XXEIK-DEDIEN--GSLP 55
             M+G++QL+    +  SD+ PLLG    S +              EIK +ED+EN   S P
Sbjct:     2 MQGEVQLQPPDSQKLSDSAPLLGDHTNSSSASPSAASVVAGNSDEIKAEEDLENDASSAP 61

Query:    56 CCRICLENDGEP-DDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLR 114
             CCRICLE+D E   DELISPCMCKGTQQFVHR+CLDHWRSVKEGFAFSHCTTCKAQFHLR
Sbjct:    62 CCRICLEDDSELLGDELISPCMCKGTQQFVHRSCLDHWRSVKEGFAFSHCTTCKAQFHLR 121

Query:   115 VELFEDN-SWR-KIKFRLFVARDVFFVFLAVQTIIAAMGGFAYLMDKDGAFRNSFSDGWD 172
             VE FEDN SWR K KFRLFVARDV  VFLAVQT+IA M GFAY+MDKDG FRNSF+D WD
Sbjct:   122 VEPFEDNNSWRRKAKFRLFVARDVLLVFLAVQTVIAVMAGFAYMMDKDGEFRNSFNDDWD 181

Query:   173 RILSKHPIPFYYCIELLLW---VGSLGLF-PCIYGSMLCPGYRFCCHFCHSWYSL-WFP 226
             RILSKHPIPFYYCI ++ +    G LG+   C   +   P    C + C+ W  L  FP
Sbjct:   182 RILSKHPIPFYYCIGVISFFVLTGFLGIILHCSALNGNDPRMAGCQNCCYGWGVLDCFP 240
GO:0008270 "zinc ion binding" evidence=IEA;ISS
TAIR|locus:2008056 AT1G50440 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|B9EJE7 MARCH3 "Membrane-associated ring finger (C3HC4) 3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
WB|WBGene00008433 D2089.2 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
UNIPROTKB|D6RGC4 MARCH1 "E3 ubiquitin-protein ligase MARCH1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1NAM1 MARCH3 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F1MM17 MARCH1 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|Q8TCQ1 MARCH1 "E3 ubiquitin-protein ligase MARCH1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E1C485 MARCH7 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F1NSN9 MARCH1 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer6.3.20.691

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query280
smart0074449 smart00744, RINGv, The RING-variant domain is a C4 3e-13
pfam1290647 pfam12906, RINGv, RING-variant domain 1e-09
COG5183 1175 COG5183, SSM4, Protein involved in mRNA turnover a 1e-08
>gnl|CDD|128983 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 
 Score = 62.3 bits (152), Expect = 3e-13
 Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 4/53 (7%)

Query: 56  CCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCK 108
            CRIC +   +  D L+SPC CKG+ ++VH+ CL+ W +         C  CK
Sbjct: 1   ICRICHDEG-DEGDPLVSPCRCKGSLKYVHQECLERWINESGN---KTCEICK 49

Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Classical RING domain: C-x (2) -C-x (9-39)-C-x(1-3)-H-x(2-3)-C-x(2)-C-x(4-48) -C-x(2)-C. Length = 49
>gnl|CDD|221845 pfam12906, RINGv, RING-variant domain Back     alignment and domain information
>gnl|CDD|227510 COG5183, SSM4, Protein involved in mRNA turnover and stability [RNA processing and modification] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 280
PHA02825162 LAP/PHD finger-like protein; Provisional 99.78
PHA02862156 5L protein; Provisional 99.78
COG5183 1175 SSM4 Protein involved in mRNA turnover and stabili 99.68
smart0074449 RINGv The RING-variant domain is a C4HC3 zinc-fing 99.66
PF1290647 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A. 99.62
KOG3053293 consensus Uncharacterized conserved protein [Funct 99.57
KOG1609323 consensus Protein involved in mRNA turnover and st 99.39
PF1363944 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 96.86
PF1179370 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A. 96.23
PHA02929238 N1R/p28-like protein; Provisional 95.89
PLN03208193 E3 ubiquitin-protein ligase RMA2; Provisional 95.7
KOG4628348 consensus Predicted E3 ubiquitin ligase [Posttrans 95.55
PF1286185 zf-Apc11: Anaphase-promoting complex subunit 11 RI 94.91
COG5243491 HRD1 HRD ubiquitin ligase complex, ER membrane com 94.82
cd0016245 RING RING-finger (Really Interesting New Gene) dom 93.64
PF1267873 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 93.33
COG5540374 RING-finger-containing ubiquitin ligase [Posttrans 93.15
PHA02926242 zinc finger-like protein; Provisional 93.15
KOG0802543 consensus E3 ubiquitin ligase [Posttranslational m 92.87
PF1392050 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); 92.82
smart0018439 RING Ring finger. E3 ubiquitin-protein ligase acti 91.99
KOG0823230 consensus Predicted E3 ubiquitin ligase [Posttrans 91.8
KOG0828636 consensus Predicted E3 ubiquitin ligase [Posttrans 90.3
PF0009741 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I 88.68
KOG149384 consensus Anaphase-promoting complex (APC), subuni 88.51
smart0050463 Ubox Modified RING finger domain. Modified RING fi 87.76
KOG0825 1134 consensus PHD Zn-finger protein [General function 87.27
PF1392339 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); 85.72
KOG0317293 consensus Predicted E3 ubiquitin ligase, integral 85.37
>PHA02825 LAP/PHD finger-like protein; Provisional Back     alignment and domain information 
Probab=99.78  E-value=2.6e-19  Score=154.89  Aligned_cols=74  Identities=23%  Similarity=0.580  Sum_probs=63.3

Q ss_pred             cCCCCCCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeeeeeeeccccccccce
Q 023590           49 IENGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLRVELFEDNSWRKIKF  128 (280)
Q Consensus        49 ~~~~~~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~~~~~~~~~W~~l~~  128 (280)
                      +++...+.||||++++    +++.+||+|+||++|||++||++|+..++   ...||+|+++|.++...+++++|.--+.
T Consensus         3 ~~s~~~~~CRIC~~~~----~~~~~PC~CkGs~k~VH~sCL~rWi~~s~---~~~CeiC~~~Y~i~~~~kpl~~W~~~~~   75 (162)
T PHA02825          3 DVSLMDKCCWICKDEY----DVVTNYCNCKNENKIVHKECLEEWINTSK---NKSCKICNGPYNIKKNYKKCTKWRCSFR   75 (162)
T ss_pred             CcCCCCCeeEecCCCC----CCccCCcccCCCchHHHHHHHHHHHhcCC---CCcccccCCeEEEEEecCCCccccccCc
Confidence            4567788999999753    24679999999999999999999999875   5799999999999988899999976554


Q ss_pred             e
Q 023590          129 R  129 (280)
Q Consensus       129 ~  129 (280)
                      .
T Consensus        76 d   76 (162)
T PHA02825         76 D   76 (162)
T ss_pred             c
Confidence            4

>PHA02862 5L protein; Provisional Back     alignment and domain information
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification] 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
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A Back     alignment and domain information
>KOG3053 consensus Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification] 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
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A Back     alignment and domain information
>PHA02929 N1R/p28-like protein; Provisional Back     alignment and domain information
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional Back     alignment and domain information
>KOG4628 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
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H) Back     alignment and domain information
>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
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>PHA02926 zinc finger-like protein; Provisional Back     alignment and domain information
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>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
>smart00184 RING Ring finger Back     alignment and domain information
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>smart00504 Ubox Modified RING finger domain Back     alignment and domain information
>KOG0825 consensus PHD Zn-finger protein [General function prediction only] 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
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query280
2d8s_A80 Solution Structure Of The Ring Domain Of The Human 2e-04
>pdb|2D8S|A Chain A, Solution Structure Of The Ring Domain Of The Human Cellular Modulator Of Immune Recognition Protein Length = 80 Back     alignment and structure 
Iteration: 1

 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 57  CRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLRVE 116
           CRIC   +G+ +  LI+PC C G+  FVH+ACL  W    +      C  CK +F +  +
Sbjct: 18  CRIC-HCEGDDESPLITPCHCTGSLHFVHQACLQQWIKSSDTRC---CELCKYEFIMETK 73
Query: 117 LFEDNS 122
           L   +S
Sbjct: 74  LSGPSS 79

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query280
2d8s_A80 Cellular modulator of immune recognition; C-MIR, m 1e-18
1vyx_A60 ORF K3, K3RING; zinc-binding protein, ring domain, 5e-16
>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80 Back     alignment and structure
 Score = 77.3 bits (190), Expect = 1e-18
 Identities = 31/89 (34%), Positives = 44/89 (49%), Gaps = 11/89 (12%)

Query: 34  SSPSSSSSSEIKDEDIENGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWR 93
           SS SS +S     +DI       CRIC   +G+ +  LI+PC C G+  FVH+ACL  W 
Sbjct: 2   SSGSSGTSITPSSQDI-------CRICHC-EGDDESPLITPCHCTGSLHFVHQACLQQWI 53

Query: 94  SVKEGFAFSHCTTCKAQFHLRVELFEDNS 122
              +      C  CK +F +  +L   +S
Sbjct: 54  KSSDT---RCCELCKYEFIMETKLSGPSS 79
>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3 Length = 60 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query280
1vyx_A60 ORF K3, K3RING; zinc-binding protein, ring domain, 99.72
2d8s_A80 Cellular modulator of immune recognition; C-MIR, m 99.64
2kiz_A69 E3 ubiquitin-protein ligase arkadia; ring-H2 finge 97.7
2l0b_A91 E3 ubiquitin-protein ligase praja-1; zinc finger, 97.55
1iym_A55 EL5; ring-H2 finger, ubiquitin ligase, DNA binding 97.53
2ect_A78 Ring finger protein 126; metal binding protein, st 97.51
1x4j_A75 Ring finger protein 38; structural genomics, NPPSF 97.49
2ep4_A74 Ring finger protein 24; zinc binding, ubiquitin, E 97.46
1v87_A114 Deltex protein 2; ring-H2 domain, zinc-binding dom 97.29
2ecm_A55 Ring finger and CHY zinc finger domain- containing 97.27
2ysl_A73 Tripartite motif-containing protein 31; ring-type 97.15
2ecl_A81 Ring-box protein 2; RNF7, ring domian, zinc-bindin 97.15
2ct2_A88 Tripartite motif protein 32; zinc-finger protein H 97.07
2ysj_A63 Tripartite motif-containing protein 31; ring-type 96.98
2ea6_A69 Ring finger protein 4; RNF4, RES4-26, ring domain, 96.94
2d8t_A71 Dactylidin, ring finger protein 146; RNF146, ring 96.9
2csy_A81 Zinc finger protein 183-like 1; ring finger protei 96.83
2ecw_A85 Tripartite motif-containing protein 30; metal bind 96.8
2yur_A74 Retinoblastoma-binding protein 6; P53-associated c 96.75
1chc_A68 Equine herpes virus-1 ring domain; viral protein; 96.59
2ecn_A70 Ring finger protein 141; RNF141, ring domain, zinc 96.49
2ecv_A85 Tripartite motif-containing protein 5; metal bindi 96.44
3ng2_A71 RNF4, snurf, ring finger protein 4; ring domain, E 96.38
2djb_A72 Polycomb group ring finger protein 6; PCGF6, ring 96.31
2ecy_A66 TNF receptor-associated factor 3; metal binding pr 96.31
2xeu_A64 Ring finger protein 4; transcription, zinc-finger, 96.29
3dpl_R106 Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST 96.21
2ecj_A58 Tripartite motif-containing protein 39; TRIM39, ri 95.99
1e4u_A78 Transcriptional repressor NOT4; gene regulation, t 95.73
4a0k_B117 E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi 95.68
3ztg_A92 E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR 95.62
2ct0_A74 Non-SMC element 1 homolog; ring domain, structural 95.47
2y1n_A389 E3 ubiquitin-protein ligase; ligase-transferase co 95.46
1t1h_A78 Gspef-atpub14, armadillo repeat containing protein 95.35
1jm7_A112 BRCA1, breast cancer type 1 susceptibility protein 95.3
3k1l_B381 Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A 95.09
3lrq_A100 E3 ubiquitin-protein ligase TRIM37; structural gen 95.06
4ayc_A138 E3 ubiquitin-protein ligase RNF8; DNA damage, K63 95.03
3fl2_A124 E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA 94.65
2y43_A99 E3 ubiquitin-protein ligase RAD18; DNA repair, met 94.6
2ckl_B165 Ubiquitin ligase protein RING2; BMI1, RING1B, poly 94.59
1g25_A65 CDK-activating kinase assembly factor MAT1; ring f 94.48
2egp_A79 Tripartite motif-containing protein 34; ZF-C3HC4 d 94.46
1z6u_A150 NP95-like ring finger protein isoform B; structura 93.93
3hct_A118 TNF receptor-associated factor 6; cross-brace, bet 93.8
4ap4_A133 E3 ubiquitin ligase RNF4; ligase-signalling protei 93.71
1rmd_A116 RAG1; V(D)J recombination, antibody, MAD, ring fin 93.56
2ckl_A108 Polycomb group ring finger protein 4; BMI1, RING1B 93.15
4ic3_A74 E3 ubiquitin-protein ligase XIAP; ring domain, zin 92.91
3knv_A141 TNF receptor-associated factor 2; cross-brace, alt 92.87
3l11_A115 E3 ubiquitin-protein ligase RNF168; E3 ligase, rin 91.9
2ea5_A68 Cell growth regulator with ring finger domain prot 91.47
1wgm_A98 Ubiquitin conjugation factor E4A; ubiquitinating e 91.22
2vje_A64 E3 ubiquitin-protein ligase MDM2; proto-oncogene, 91.2
2vje_B63 MDM4 protein; proto-oncogene, phosphorylation, alt 91.07
4ap4_A133 E3 ubiquitin ligase RNF4; ligase-signalling protei 90.34
2kr4_A85 Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri 88.8
1jm7_B117 BARD1, BRCA1-associated ring domain protein 1; rin 88.71
2ecg_A75 Baculoviral IAP repeat-containing protein 4; BIRC4 88.64
3nw0_A238 Non-structural maintenance of chromosomes element 87.95
2c2l_A281 CHIP, carboxy terminus of HSP70-interacting protei 87.74
2kre_A100 Ubiquitin conjugation factor E4 B; U-box domain, E 86.92
2yho_A79 E3 ubiquitin-protein ligase mylip; ligase, E2 liga 85.36
3hcs_A170 TNF receptor-associated factor 6; cross-brace, bet 83.77
1weu_A91 Inhibitor of growth family, member 4; structural g 81.38
3t6p_A345 Baculoviral IAP repeat-containing protein 2; ring, 80.95
1bor_A56 Transcription factor PML; proto-oncogene, nuclear 80.9
>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
Probab=99.72  E-value=1.4e-18  Score=126.73  Aligned_cols=57  Identities=32%  Similarity=0.790  Sum_probs=49.6

Q ss_pred             CCCCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeee
Q 023590           52 GSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLR  114 (280)
Q Consensus        52 ~~~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~  114 (280)
                      .+.+.||||+++.   ++++++||+|+||+++||+.||++|+..++   ...||+|+++|+++
T Consensus         4 ~~~~~CrIC~~~~---~~~l~~PC~C~gs~~~~H~~Cl~~W~~~~~---~~~C~~C~~~~~~r   60 (60)
T 1vyx_A            4 EDVPVCWICNEEL---GNERFRACGCTGELENVHRSCLSTWLTISR---NTACQICGVVYNTR   60 (60)
T ss_dssp             CSCCEETTTTEEC---SCCCCCSCCCSSGGGSCCHHHHHHHHHHHT---CSBCTTTCCBCCCC
T ss_pred             CCCCEeEEeecCC---CCceecCcCCCCchhhhHHHHHHHHHHhCC---CCccCCCCCeeecC
Confidence            4567999999753   457999999999999999999999999875   37999999999874
>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; 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
>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
>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1 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
>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1 Back     alignment and structure
>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A Back     alignment and structure
>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>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
>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus} Back     alignment and structure
>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens} Back     alignment and structure
>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} 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
>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus} Back     alignment and structure
>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens} Back     alignment and structure
>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 4f52_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A Back     alignment and structure
>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B Back     alignment and structure
>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
>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens} Back     alignment and structure
>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>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
>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
>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
>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster} 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
>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C 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
>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens} Back     alignment and structure
>2ckl_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
>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
>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
>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
>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus} 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
>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
>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A 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
>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
>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
>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
>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A Back     alignment and structure
>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B* Back     alignment and structure
>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus} 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
>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
>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, 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
>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
>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
>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
>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
>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2 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
>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

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 280
d1vyxa_60 g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do 1e-06
d1g25a_65 g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi 1e-04
>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60 Back     information, alignment and structure

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 42.9 bits (100), Expect = 1e-06
 Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 6/66 (9%)

Query: 49  IENGSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCK 108
           +E+  +P C IC E   E  +E    C C G  + VHR+CL  W ++      + C  C 
Sbjct: 1   MEDEDVPVCWICNE---ELGNERFRACGCTGELENVHRSCLSTWLTI---SRNTACQICG 54

Query: 109 AQFHLR 114
             ++ R
Sbjct: 55  VVYNTR 60
>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 65 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 ?
Query280
d1vyxa_60 IE1B protein (ORF K3), N-terminal domain {Kaposi's 99.43
d1iyma_55 EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45 97.44
d1ur6b_52 Not-4 N-terminal RING finger domain {Human (Homo s 97.35
d1v87a_114 Deltex protein 2 RING-H2 domain {Mouse (Mus muscul 97.25
d1chca_68 Immediate early protein, IEEHV {Equine herpesvirus 97.16
d3dplr188 RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase 97.1
d1fbva479 CBL {Human (Homo sapiens) [TaxId: 9606]} 97.08
d1g25a_65 TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9 96.56
d1jm7a_103 brca1 RING domain {Human (Homo sapiens) [TaxId: 96 96.04
d1rmda286 V(D)J recombination activating protein 1 (RAG1), d 95.35
d2baya156 Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac 94.92
d1bora_56 Acute promyelocytic leukaemia proto-oncoprotein PM 91.48
d1jm7b_97 bard1 RING domain {Human (Homo sapiens) [TaxId: 96 89.66
d1wima_94 UbcM4-interacting protein 4 (KIAA0161) {Human (Hom 88.97
d1t1ha_78 E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi 87.34
d1wgma_98 Ubiquitin conjugation factor E4A {Human (Homo sapi 85.79
d2c2la280 STIP1 homology and U box-containing protein 1, STU 85.69
>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
class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=99.43  E-value=1.7e-14  Score=102.26  Aligned_cols=57  Identities=32%  Similarity=0.790  Sum_probs=49.2

Q ss_pred             CCCCcceEeccCCCCCCCccccccccCCCCcccchhhHHHHHHhhcCccccccccccceeeee
Q 023590           52 GSLPCCRICLENDGEPDDELISPCMCKGTQQFVHRACLDHWRSVKEGFAFSHCTTCKAQFHLR  114 (280)
Q Consensus        52 ~~~~~CRIC~~~~~e~~~~LIsPC~CkGSlkyVH~~CL~~Wi~~s~~~~~~~CElCk~~y~~~  114 (280)
                      .+.++|+||+++.   +++++.||.|+|+.+++|+.||++|++.++   ..+|++|+++|+++
T Consensus         4 ed~~~C~IC~~~~---~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~---~~~CP~Cr~~~~~k   60 (60)
T d1vyxa_           4 EDVPVCWICNEEL---GNERFRACGCTGELENVHRSCLSTWLTISR---NTACQICGVVYNTR   60 (60)
T ss_dssp             CSCCEETTTTEEC---SCCCCCSCCCSSGGGSCCHHHHHHHHHHHT---CSBCTTTCCBCCCC
T ss_pred             CCCCCCccCCccC---CCceeEecccCCCCCEEcHHHHHHHHhhCC---CCCCcccCCeeecC
Confidence            4567899999753   467899999999999999999999998875   36899999999864
>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} 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
>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} 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
>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
>d1fbva4 g.44.1.1 (A:356-434) CBL {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
>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
>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {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
>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]} 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
>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