Citrus Sinensis ID: 041693

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------

VALHINLGETNVSSSTAEAISSEGYRLTFNDDKVSLSCQLFDSIRLDIELTCPVCLETVFDPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLCRKAGVYQGAIHLTELGILLSRSCREYWEKRLQIERVERVKQAKEYWENQCRAFMGI

cEEEEEccccccccccccccccccccccccccccHHccccHHHccccccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc

cEEEEEccccccccccccccccccccccccccccEEEEEccccccEcccccccHHHHHcccccEcccccHHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc

valhinlgetnvsssTAEAissegyrltfnddkvsLSCQLFDSIRLdieltcpvcletvfdpvsltcGHILckmcacsaasvsivdglkladptekcplcrkagvyqGAIHLTELGILLSRSCREYWEKRLQIERVERVKQAKEYWENQCRAFMGI

valhinlgetnvssstaEAISSEGYRLTFNDDKVSLSCQLFDSIRLDIELTCPVCLETVFDPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLCRKAGVYQGAIHLTELGILLSRSCREYWEKRLQIERVERVKQAKeywenqcrafmgi

VALHINLGETNVSSSTAEAISSEGYRLTFNDDKVSLSCQLFDSIRLDIELTCPVCLETVFDPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLCRKAGVYQGAIHLTELGILLSRSCREYWEKRLQIERVERVKQAKEYWENQCRAFMGI

***********************GYRLTFNDDKVSLSCQLFDSIRLDIELTCPVCLETVFDPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLCRKAGVYQGAIHLTELGILLSRSCREYWEKRLQIERVERVKQAKEYWENQCRAF***

VALHI*****************EGYRLTFNDDKVSLSCQLFDSIRLDIELTCPVCLETVFDPVSLTCGHILCKMCACSAASVSIV********TEKCPLCRKAGVYQGAIHLTELGILLS**************************ENQCRAFMGI

VALHINLGETN*********SSEGYRLTFNDDKVSLSCQLFDSIRLDIELTCPVCLETVFDPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLCRKAGVYQGAIHLTELGILLSRSCREYWEKRLQIERVERVKQAKEYWENQCRAFMGI

VALHINLGE*********AISSEGYRLTFNDDKVSLSCQLFDSIRLDIELTCPVCLETVFDPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLCRKAGVYQGAIHLTELGILLSRSCREYWEKRLQIERVERVKQAKEYWENQCRAFMGI

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

SSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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VALHINLGETNVSSSTAEAISSEGYRLTFNDDKVSLSCQLFDSIRLDIELTCPVCLETVFDPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLCRKAGVYQGAIHLTELGILLSRSCREYWEKRLQIERVERVKQAKEYWENQCRAFMGI

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		156	2.2.26 [Sep-21-2011]
Q9SRX9		335	E3 ubiquitin-protein liga	yes	no	1.0	0.465	0.607	2e-53
B8B5U8		321	Probable E3 ubiquitin-pro	N/A	no	0.987	0.479	0.589	2e-51
Q7XI73		321	Probable E3 ubiquitin-pro	yes	no	0.987	0.479	0.589	2e-51
Q8GW10		335	Probable E3 ubiquitin-pro	no	no	0.961	0.447	0.448	2e-33
Q7XZZ3		339	Probable E3 ubiquitin-pro	no	no	0.993	0.457	0.388	9e-33
A2XK56		339	Probable E3 ubiquitin-pro	N/A	no	0.993	0.457	0.388	9e-33
Q495X7		471	Tripartite motif-containi	yes	no	0.551	0.182	0.35	2e-06
Q3ZEE5		493	Tripartite motif-containi	N/A	no	0.301	0.095	0.415	4e-06
Q8IYM9		498	E3 ubiquitin-protein liga	no	no	0.352	0.110	0.360	1e-05
Q5D7I2		494	Tripartite motif-containi	N/A	no	0.307	0.097	0.415	2e-05

>sp\|Q9SRX9\|BAH1_ARATH E3 ubiquitin-protein ligase BAH1 OS=Arabidopsis thaliana GN=BAH1 PE=1 SV=1	Back alignment and function desciption

 Score =  207 bits (528), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 99/163 (60%), Positives = 126/163 (77%), Gaps = 7/163 (4%)

Query: 1   VALHINLGETNVSS-----STAEAISS--EGYRLTFNDDKVSLSCQLFDSIRLDIELTCP 53
           +A HINL E+   S     S    + +  +G  LTF+D K  LSC+L DS+++DI+LTC 
Sbjct: 173 MAFHINLKESKKESGATITSPPPPVHALFDGCALTFDDGKPLLSCELSDSVKVDIDLTCS 232

Query: 54  VCLETVFDPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLCRKAGVYQGAIHLT 113
           +CL+TVFDP+SLTCGHI C MCACSAASV++VDGLK A+ TEKCPLCR+ GVY+GA+HL 
Sbjct: 233 ICLDTVFDPISLTCGHIYCYMCACSAASVNVVDGLKTAEATEKCPLCREDGVYKGAVHLD 292

Query: 114 ELGILLSRSCREYWEKRLQIERVERVKQAKEYWENQCRAFMGI 156
           EL ILL RSCR+YWE+R + ER ER++QAKEYW+ QCR+F GI
Sbjct: 293 ELNILLKRSCRDYWEERRKTERAERLQQAKEYWDYQCRSFTGI 335

Mediates E2-dependent protein ubiquitination. Plays a role in salicylic acid-mediated negative feedback regulation of salicylic acid (SA) accumulation. May be involved in the overall regulation of SA, benzoic acid and phenylpropanoid biosynthesis. Controls the adaptability to nitrogen limitation by channeling the phenylpropanoid metabolic flux to the induced anthocyanin synthesis.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp\|B8B5U8\|BAHL2_ORYSI Probable E3 ubiquitin-protein ligase BAH1-like 1 OS=Oryza sativa subsp. indica GN=OsI_27296 PE=3 SV=1	Back alignment and function description

>sp\|Q7XI73\|BAHL2_ORYSJ Probable E3 ubiquitin-protein ligase BAH1-like 2 OS=Oryza sativa subsp. japonica GN=Os07g0673200 PE=2 SV=1	Back alignment and function description

>sp\|Q8GW10\|BAH1L_ARATH Probable E3 ubiquitin-protein ligase BAH1-like OS=Arabidopsis thaliana GN=RF178 PE=2 SV=1	Back alignment and function description

>sp\|Q7XZZ3\|BAHL1_ORYSJ Probable E3 ubiquitin-protein ligase BAH1-like 1 OS=Oryza sativa subsp. japonica GN=Os03g0650900 PE=2 SV=1	Back alignment and function description

>sp\|A2XK56\|BAHL1_ORYSI Probable E3 ubiquitin-protein ligase BAH1-like 1 OS=Oryza sativa subsp. indica GN=OsI_12825 PE=3 SV=1	Back alignment and function description

>sp\|Q495X7\|TRI60_HUMAN Tripartite motif-containing protein 60 OS=Homo sapiens GN=TRIM60 PE=2 SV=2	Back alignment and function description

>sp\|Q3ZEE5\|TRIM5_HYLLA Tripartite motif-containing protein 5 OS=Hylobates lar GN=TRIM5 PE=3 SV=1	Back alignment and function description

>sp\|Q8IYM9\|TRI22_HUMAN E3 ubiquitin-protein ligase TRIM22 OS=Homo sapiens GN=TRIM22 PE=1 SV=1	Back alignment and function description

>sp\|Q5D7I2\|TRIM5_PITPI Tripartite motif-containing protein 5 OS=Pithecia pithecia GN=TRIM5 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		156
225437340		324	PREDICTED: E3 ubiquitin-protein ligase B	0.993	0.478	0.711	1e-61
224128498		320	predicted protein [Populus trichocarpa]	0.993	0.484	0.711	6e-61
224068330		320	predicted protein [Populus trichocarpa]	0.993	0.484	0.673	3e-59
255564140		330	ubiquitin-protein ligase, putative [Rici	1.0	0.472	0.700	3e-59
255564136		226	ubiquitin-protein ligase, putative [Rici	1.0	0.690	0.694	6e-59
37725955		227	heavy metal-induced putative protein 1,	0.993	0.682	0.698	7e-58
356505572		324	PREDICTED: E3 ubiquitin-protein ligase B	0.993	0.478	0.679	1e-57
357442533		316	E3 ubiquitin-protein ligase BAH1 [Medica	0.993	0.490	0.692	3e-57
356572738		324	PREDICTED: E3 ubiquitin-protein ligase B	0.993	0.478	0.685	3e-57
388496098		169	unknown [Lotus japonicus]	0.993	0.917	0.685	4e-57

>gi\|225437340\|ref\|XP_002265436.1\| PREDICTED: E3 ubiquitin-protein ligase BAH1 [Vitis vinifera] gi\|297743873\|emb\|CBI36843.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  240 bits (613), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 111/156 (71%), Positives = 133/156 (85%), Gaps = 1/156 (0%)

Query: 1   VALHINLGETNVSSSTAEAISSEGYRLTFNDDKVSLSCQLFDSIRLDIELTCPVCLETVF 60
           +A HINL E+   S  A A+  +G  LTFND K SLSC+LFDS++LDI+LTC +CL+TVF
Sbjct: 170 MAFHINLRESKAKSRKAPALF-DGCSLTFNDGKPSLSCELFDSVKLDIDLTCSICLDTVF 228

Query: 61  DPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLCRKAGVYQGAIHLTELGILLS 120
           DPVSLTCGHI C MCACSAASV+IVDGLK+A+P EKCPLCR+AGVY+GA+HL EL ILLS
Sbjct: 229 DPVSLTCGHIFCYMCACSAASVTIVDGLKIAEPKEKCPLCREAGVYEGAVHLEELNILLS 288

Query: 121 RSCREYWEKRLQIERVERVKQAKEYWENQCRAFMGI 156
           RSC EYWE+RLQ ER ER++QAKE+WE+QCRAFMG+
Sbjct: 289 RSCHEYWEQRLQTERTERIRQAKEHWESQCRAFMGV 324

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224128498\|ref\|XP_002320347.1\| predicted protein [Populus trichocarpa] gi\|222861120\|gb\|EEE98662.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|224068330\|ref\|XP_002302708.1\| predicted protein [Populus trichocarpa] gi\|222844434\|gb\|EEE81981.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|255564140\|ref\|XP_002523067.1\| ubiquitin-protein ligase, putative [Ricinus communis] gi\|223537629\|gb\|EEF39252.1\| ubiquitin-protein ligase, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|255564136\|ref\|XP_002523065.1\| ubiquitin-protein ligase, putative [Ricinus communis] gi\|223537627\|gb\|EEF39250.1\| ubiquitin-protein ligase, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|37725955\|gb\|AAO27261.1\| heavy metal-induced putative protein 1, partial [Pisum sativum]	Back alignment and taxonomy information

>gi\|356505572\|ref\|XP_003521564.1\| PREDICTED: E3 ubiquitin-protein ligase BAH1-like isoform 1 [Glycine max]	Back alignment and taxonomy information

>gi\|357442533\|ref\|XP_003591544.1\| E3 ubiquitin-protein ligase BAH1 [Medicago truncatula] gi\|355480592\|gb\|AES61795.1\| E3 ubiquitin-protein ligase BAH1 [Medicago truncatula]	Back alignment and taxonomy information

>gi\|356572738\|ref\|XP_003554523.1\| PREDICTED: E3 ubiquitin-protein ligase BAH1-like [Glycine max]	Back alignment and taxonomy information

>gi\|388496098\|gb\|AFK36115.1\| unknown [Lotus japonicus]	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		156
TAIR\|locus:2024675		335	NLA "nitrogen limitation adapt	1.0	0.465	0.607	2.4e-51
TAIR\|locus:2064935		335	AT2G38920 [Arabidopsis thalian	0.961	0.447	0.448	6.7e-33
UNIPROTKB\|C9J060		203	TRIM22 "E3 ubiquitin-protein l	0.352	0.270	0.360	8e-11
UNIPROTKB\|C9JIU5		227	TRIM22 "E3 ubiquitin-protein l	0.352	0.242	0.360	2.2e-10
UNIPROTKB\|E1BM69		497	LOC516599 "Uncharacterized pro	0.435	0.136	0.373	1.2e-09
UNIPROTKB\|Q8IYM9		498	TRIM22 "E3 ubiquitin-protein l	0.352	0.110	0.360	6.8e-09
UNIPROTKB\|E1BSU9		274	LOC416147 "Uncharacterized pro	0.346	0.197	0.406	1.2e-08
UNIPROTKB\|Q5C8U4		515	TRIM5 "Tripartite motif-contai	0.314	0.095	0.415	2e-08
RGD\|1310896		488	Trim6 "tripartite motif contai	0.378	0.120	0.358	2.7e-08
UNIPROTKB\|D6RAS2		90	TRIM60 "Tripartite motif-conta	0.519	0.9	0.368	5.3e-08

TAIR\|locus:2024675 NLA "nitrogen limitation adaptation" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 533 (192.7 bits), Expect = 2.4e-51, P = 2.4e-51
 Identities = 99/163 (60%), Positives = 126/163 (77%)

Query:     1 VALHINLGETNVSS-----STAEAISS--EGYRLTFNDDKVSLSCQLFDSIRLDIELTCP 53
             +A HINL E+   S     S    + +  +G  LTF+D K  LSC+L DS+++DI+LTC 
Sbjct:   173 MAFHINLKESKKESGATITSPPPPVHALFDGCALTFDDGKPLLSCELSDSVKVDIDLTCS 232

Query:    54 VCLETVFDPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLCRKAGVYQGAIHLT 113
             +CL+TVFDP+SLTCGHI C MCACSAASV++VDGLK A+ TEKCPLCR+ GVY+GA+HL 
Sbjct:   233 ICLDTVFDPISLTCGHIYCYMCACSAASVNVVDGLKTAEATEKCPLCREDGVYKGAVHLD 292

Query:   114 ELGILLSRSCREYWEKRLQIERVERVKQAKEYWENQCRAFMGI 156
             EL ILL RSCR+YWE+R + ER ER++QAKEYW+ QCR+F GI
Sbjct:   293 ELNILLKRSCRDYWEERRKTERAERLQQAKEYWDYQCRSFTGI 335

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0010167 "response to nitrate" evidence=IMP

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

GO:0009626 "plant-type hypersensitive response" evidence=IMP

GO:0009627 "systemic acquired resistance" evidence=IMP

GO:0009697 "salicylic acid biosynthetic process" evidence=IMP

GO:0009751 "response to salicylic acid stimulus" evidence=IEP

GO:0010337 "regulation of salicylic acid metabolic process" evidence=IMP

GO:0042742 "defense response to bacterium" evidence=IMP

GO:0080021 "response to benzoic acid stimulus" evidence=IEP;IMP

GO:0006817 "phosphate ion transport" evidence=RCA

GO:0016036 "cellular response to phosphate starvation" evidence=RCA

TAIR\|locus:2064935 AT2G38920 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|C9J060 TRIM22 "E3 ubiquitin-protein ligase TRIM22" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|C9JIU5 TRIM22 "E3 ubiquitin-protein ligase TRIM22" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BM69 LOC516599 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|Q8IYM9 TRIM22 "E3 ubiquitin-protein ligase TRIM22" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BSU9 LOC416147 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5C8U4 TRIM5 "Tripartite motif-containing protein 5" [Chlorocebus pygerythrus (taxid:60710)]	Back alignment and assigned GO terms

RGD\|1310896 Trim6 "tripartite motif containing 6" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|D6RAS2 TRIM60 "Tripartite motif-containing protein 60" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	6.3.2	LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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		156
COG5574		271	COG5574, PEX10, RING-finger-containing E3 ubiquiti	1e-04
cd00162		45	cd00162, RING, RING-finger (Really Interesting New	2e-04
pfam13923		45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	3e-04
PLN03208		193	PLN03208, PLN03208, E3 ubiquitin-protein ligase RM	6e-04
pfam13445		55	pfam13445, zf-RING_LisH, RING-type zinc-finger, Li	0.001
pfam13639		46	pfam13639, zf-RING_2, Ring finger domain	0.004

>gnl\|CDD\|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 16/50 (32%), Positives = 20/50 (40%), Gaps = 9/50 (18%)

Query: 52  CPVCLETVFDPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLCR 101
           C +CLE    P    CGH+ C  C   + +             E CPLCR
Sbjct: 218 CFLCLEEPEVPSCTPCGHLFCLSCLLISWT---------KKKYEFCPLCR 258

Length = 271

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

Back alignment and domain information

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

>gnl\|CDD\|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2; Provisional	Back alignment and domain information

>gnl\|CDD\|222135 pfam13445, zf-RING_LisH, RING-type zinc-finger, LisH dimerisation motif	Back alignment and domain information

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		156
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.61
TIGR00599		397	rad18 DNA repair protein rad18. This family is bas	99.52
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	99.49
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	99.45
KOG0287		442	consensus Postreplication repair protein RAD18 [Re	99.45
PF04564		73	U-box: U-box domain; InterPro: IPR003613 Quality c	99.44
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.34
PF14835		65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	99.34
KOG0823		230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.32
COG5432		391	RAD18 RING-finger-containing E3 ubiquitin ligase [	99.3
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.3
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.25
KOG0317		293	consensus Predicted E3 ubiquitin ligase, integral	99.22
PHA02929		238	N1R/p28-like protein; Provisional	99.21
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.18
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	99.18
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.15
PHA02926		242	zinc finger-like protein; Provisional	99.07
PF14634		44	zf-RING_5: zinc-RING finger domain	99.07
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	99.04
KOG2660		331	consensus Locus-specific chromosome binding protei	99.03
KOG2177		386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.99
KOG2164		513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.98
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.93
COG5574		271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.81
KOG0311		381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.73
KOG4159		398	consensus Predicted E3 ubiquitin ligase [Posttrans	98.7
TIGR00570		309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.69
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	98.67
KOG0978		698	consensus E3 ubiquitin ligase involved in syntaxin	98.57
COG5222		427	Uncharacterized conserved protein, contains RING Z	98.45
PF12861		85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.42
PF11789		57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	98.38
COG5152		259	Uncharacterized conserved protein, contains RING a	98.36
KOG0824		324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.33
COG5243		491	HRD1 HRD ubiquitin ligase complex, ER membrane com	98.3
KOG0802		543	consensus E3 ubiquitin ligase [Posttranslational m	98.27
KOG1813		313	consensus Predicted E3 ubiquitin ligase [Posttrans	98.25
KOG2879		298	consensus Predicted E3 ubiquitin ligase [Posttrans	98.16
KOG0297		391	consensus TNF receptor-associated factor [Signal t	98.12
KOG4628		348	consensus Predicted E3 ubiquitin ligase [Posttrans	98.09
COG5540		374	RING-finger-containing ubiquitin ligase [Posttrans	98.05
KOG1002		791	consensus Nucleotide excision repair protein RAD16	97.83
PF11793		70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.8
KOG1645		463	consensus RING-finger-containing E3 ubiquitin liga	97.78
KOG1039		344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.74
PF04641		260	Rtf2: Rtf2 RING-finger	97.72
KOG4367		699	consensus Predicted Zn-finger protein [Function un	97.68
KOG4172		62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.63
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.54
KOG4692		489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.47
KOG4265		349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.45
KOG3039		303	consensus Uncharacterized conserved protein [Funct	97.38
KOG1785		563	consensus Tyrosine kinase negative regulator CBL [	97.31
KOG4185		296	consensus Predicted E3 ubiquitin ligase [Posttrans	97.29
KOG0828		636	consensus Predicted E3 ubiquitin ligase [Posttrans	97.15
KOG0825		1134	consensus PHD Zn-finger protein [General function	97.11
KOG1814		445	consensus Predicted E3 ubiquitin ligase [Posttrans	97.07
KOG1493		84	consensus Anaphase-promoting complex (APC), subuni	97.0
KOG1734		328	consensus Predicted RING-containing E3 ubiquitin l	96.97
PF14447		55	Prok-RING_4: Prokaryotic RING finger family 4	96.91
KOG4275		350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.88
smart00744		49	RINGv The RING-variant domain is a C4HC3 zinc-fing	96.83
PF14570		48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.81
COG5194		88	APC11 Component of SCF ubiquitin ligase and anapha	96.77
COG5219		1525	Uncharacterized conserved protein, contains RING Z	96.75
KOG1571		355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.73
KOG0827		465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.61
KOG3800		300	consensus Predicted E3 ubiquitin ligase containing	96.59
PF07800		162	DUF1644: Protein of unknown function (DUF1644); In	96.55
PF02891		50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	96.54
KOG3161		861	consensus Predicted E3 ubiquitin ligase [Posttrans	96.39
KOG4739		233	consensus Uncharacterized protein involved in syna	96.35
KOG1001		674	consensus Helicase-like transcription factor HLTF/	96.35
KOG0826		357	consensus Predicted E3 ubiquitin ligase involved i	96.3
KOG3002		299	consensus Zn finger protein [General function pred	96.3
KOG2817		394	consensus Predicted E3 ubiquitin ligase [Posttrans	96.23
KOG1812		384	consensus Predicted E3 ubiquitin ligase [Posttrans	96.22
KOG1941		518	consensus Acetylcholine receptor-associated protei	95.9
KOG4362		684	consensus Transcriptional regulator BRCA1 [Replica	95.89
KOG3039		303	consensus Uncharacterized conserved protein [Funct	95.88
PF05290		140	Baculo_IE-1: Baculovirus immediate-early protein (	95.62
KOG3970		299	consensus Predicted E3 ubiquitin ligase [Posttrans	95.52
COG5175		480	MOT2 Transcriptional repressor [Transcription]	95.31
PF10367		109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	95.14
COG5236		493	Uncharacterized conserved protein, contains RING Z	94.79
KOG2930		114	consensus SCF ubiquitin ligase, Rbx1 component [Po	94.71
PF03854		50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	94.36
PHA03096		284	p28-like protein; Provisional	94.29
KOG3113		293	consensus Uncharacterized conserved protein [Funct	93.87
KOG1815		444	consensus Predicted E3 ubiquitin ligase [Posttrans	93.76
COG5109		396	Uncharacterized conserved protein, contains RING Z	93.56
KOG1952		950	consensus Transcription factor NF-X1, contains NFX	93.45
KOG2114		933	consensus Vacuolar assembly/sorting protein PEP5/V	93.34
KOG1428		3738	consensus Inhibitor of type V adenylyl cyclases/Ne	93.16
KOG0298		1394	consensus DEAD box-containing helicase-like transc	93.05
KOG2932		389	consensus E3 ubiquitin ligase involved in ubiquiti	92.7
PF08746		43	zf-RING-like: RING-like domain; InterPro: IPR01485	92.17
KOG1940		276	consensus Zn-finger protein [General function pred	92.08
KOG3579		352	consensus Predicted E3 ubiquitin ligase [Posttrans	91.92
PF07191		70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	91.62
COG5220		314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	91.6
PF10497		105	zf-4CXXC_R1: Zinc-finger domain of monoamine-oxida	91.05
KOG1100		207	consensus Predicted E3 ubiquitin ligase [Posttrans	90.69
KOG3268		234	consensus Predicted E3 ubiquitin ligase [Posttrans	90.57
PF10571		26	UPF0547: Uncharacterised protein family UPF0547; I	88.75
COG3813		84	Uncharacterized protein conserved in bacteria [Fun	88.72
PHA02825		162	LAP/PHD finger-like protein; Provisional	88.53
PF10235		90	Cript: Microtubule-associated protein CRIPT; Inter	87.94
PF05883		134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	87.57
PF06906		57	DUF1272: Protein of unknown function (DUF1272); In	87.21
PF10272		358	Tmpp129: Putative transmembrane protein precursor;	85.86
KOG0825		1134	consensus PHD Zn-finger protein [General function	85.42
KOG2169		636	consensus Zn-finger transcription factor [Transcri	83.78
KOG3899		381	consensus Uncharacterized conserved protein [Funct	82.67
KOG4445		368	consensus Uncharacterized conserved protein, conta	82.6
KOG2979		262	consensus Protein involved in DNA repair [General	81.94
KOG4718		235	consensus Non-SMC (structural maintenance of chrom	80.2
PHA02862		156	5L protein; Provisional	80.05

>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

Probab=99.61  E-value=4.7e-16  Score=87.25  Aligned_cols=42  Identities=40%  Similarity=0.942  Sum_probs=30.8

Q ss_pred             CccccccCCCCeeccCCCcccHhhHHHHHhhhhhccccCCCCCCCCCCC
Q 041693           52 CPVCLETVFDPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLC  100 (156)
Q Consensus        52 C~IC~~~~~~Pv~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~~~~~CP~C  100 (156)
                      ||||+++|.+|++++|||+||..||.+++.     .  .......||.|
T Consensus         1 CpiC~~~~~~Pv~l~CGH~FC~~Cl~~~~~-----~--~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDPVSLPCGHSFCRSCLERLWK-----E--PSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSEEE-SSSSEEEHHHHHHHHC-----C--SSSST---SSS
T ss_pred             CCccchhhCCccccCCcCHHHHHHHHHHHH-----c--cCCcCCCCcCC
Confidence            899999999999999999999999999982     1  11233789987

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

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

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

>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]	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

>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

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

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

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

>KOG0320 consensus Predicted 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

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

>PHA02929 N1R/p28-like protein; Provisional	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

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

>PHA02926 zinc finger-like protein; Provisional	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

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

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

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

>smart00184 RING Ring finger	Back alignment and domain information

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

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

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

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1	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

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

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

>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger	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

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

>KOG0824 consensus Predicted 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

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

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

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

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

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

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

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

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

>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

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

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

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

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

>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

>KOG4185 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

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

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

>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

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

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

>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function	Back alignment and domain information

>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]	Back alignment and domain information

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

>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG3002 consensus Zn finger protein [General function prediction only]	Back alignment and domain information

>KOG2817 consensus Predicted E3 ubiquitin ligase [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

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

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

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

>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0	Back alignment and domain information

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

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

>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1	Back alignment and domain information

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

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

>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

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

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

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

>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]	Back alignment and domain information

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

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

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

>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO)	Back alignment and domain information

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

>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length	Back alignment and domain information

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

>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression	Back alignment and domain information

>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG3268 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

>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]	Back alignment and domain information

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

>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production	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

>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length	Back alignment and domain information

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

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

>KOG2169 consensus Zn-finger transcription factor [Transcription]	Back alignment and domain information

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

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

>KOG2979 consensus Protein involved in DNA repair [General function prediction only]	Back alignment and domain information

>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]	Back alignment and domain information

>PHA02862 5L protein; Provisional	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		156
2egp_A		79	Solution Structure Of The Ring-Finger Domain From H		3e-05
2ecv_A		85	Solution Structure Of The Zinc Finger, C3hc4 Type (		4e-05
1jm7_A		112	Solution Structure Of The Brca1/bard1 Ring-domain H		1e-04

>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human Tripartite Motif Protein 34 Length = 79

Back alignment and structure

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 31/52 (59%), Gaps = 4/52 (7%)
Query: 49  ELTCPVCLETVFDPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLC 100
           E+TCP+CLE + +P+SL CGH LC+ C     +VS  + +        CP+C
Sbjct: 12  EVTCPICLELLTEPLSLDCGHSLCRAC----ITVSNKEAVTSMGGKSSCPVC 59

PyMOL of 2egp

>pdb|2ECV|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring Finger) Domain Of Tripartite Motif-Containing Protein 5 Length = 85

Back alignment and structure

>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain Heterodimer Length = 112

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		156
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	1e-10
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	2e-10
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	5e-10
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	7e-10
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	4e-09
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	4e-09
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	4e-09
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	9e-09
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	2e-08
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	2e-08
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	3e-08
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	3e-08
1z6u_A		150	NP95-like ring finger protein isoform B; structura	4e-08
4epo_C		149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	7e-08
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	8e-08
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	8e-08
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	9e-08
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	2e-07
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	5e-07
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	5e-07
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	7e-07
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	1e-06
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	1e-06
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	2e-06
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-06
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	3e-06
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	4e-06
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	6e-06
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	6e-06
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	1e-05
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	2e-05
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	5e-05
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	8e-04

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, chromosomal protein, DNA repair, metal-binding; 2.12A {Homo sapiens} Length = 115	Back alignment and structure

 Score = 54.9 bits (132), Expect = 1e-10
 Identities = 24/110 (21%), Positives = 39/110 (35%), Gaps = 17/110 (15%)

Query: 49  ELTCPVCLETVFDPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLCRKAGVYQG 108
           E  C +C+E + +PV+L C H LCK C  S           +   +  CP CR+      
Sbjct: 15  ECQCGICMEILVEPVTLPCNHTLCKPCFQST----------VEKASLCCPFCRRRVSSWT 64

Query: 109 AIHL-------TELGILLSRSCREYWEKRLQIERVERVKQAKEYWENQCR 151
             H         EL  ++ +      + R   +  E V    +      +
Sbjct: 65  RYHTRRNSLVNVELWTIIQKHYPRECKLRASGQESEEVADDYQPVRLLSK 114

PyMOL of 3l11

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 112	Back alignment and structure

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

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus} Length = 85	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

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens} Length = 79	Back alignment and structure

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 85	Back alignment and structure

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

>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

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 63	Back alignment and structure

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A* Length = 389	Back alignment and structure

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens} Length = 124	Back alignment and structure

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens} Length = 150	Back alignment and structure

>4epo_C E3 ubiquitin-protein ligase RNF8; coiled-coil, E3 ubiquitin ligase, protein binding complex; 4.80A {Homo sapiens} Length = 149	Back alignment and structure

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 58	Back alignment and structure

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 117	Back alignment and structure

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 56	Back alignment and structure

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A Length = 118	Back alignment and structure

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B Length = 165	Back alignment and structure

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens} Length = 99	Back alignment and structure

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens} Length = 74	Back alignment and structure

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

>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc binuclear cluster, zinc finger, DNA-binding protein; 2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1 Length = 116	Back alignment and structure

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens} Length = 141	Back alignment and structure

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A Length = 108	Back alignment and structure

>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

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

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 69	Back alignment and structure

>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

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus} Length = 71	Back alignment and structure

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

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens} Length = 170	Back alignment and structure

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		156
1t1h_A		78	Gspef-atpub14, armadillo repeat containing protein	99.73
2kr4_A		85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.72
3ztg_A		92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.72
2kre_A		100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.7
1wgm_A		98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.69
2y43_A		99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.67
2ckl_A		108	Polycomb group ring finger protein 4; BMI1, RING1B	99.67
4ayc_A		138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.66
1jm7_B		117	BARD1, BRCA1-associated ring domain protein 1; rin	99.65
3fl2_A		124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.65
3l11_A		115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.64
3lrq_A		100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.62
2yu4_A		94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.62
2ysl_A		73	Tripartite motif-containing protein 31; ring-type	99.61
2djb_A		72	Polycomb group ring finger protein 6; PCGF6, ring	99.6
2ecy_A		66	TNF receptor-associated factor 3; metal binding pr	99.6
1z6u_A		150	NP95-like ring finger protein isoform B; structura	99.59
2yur_A		74	Retinoblastoma-binding protein 6; P53-associated c	99.59
1jm7_A		112	BRCA1, breast cancer type 1 susceptibility protein	99.59
2csy_A		81	Zinc finger protein 183-like 1; ring finger protei	99.56
2c2l_A		281	CHIP, carboxy terminus of HSP70-interacting protei	99.56
2f42_A		179	STIP1 homology and U-box containing protein 1; cha	99.56
2egp_A		79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.56
2ecw_A		85	Tripartite motif-containing protein 30; metal bind	99.56
2ysj_A		63	Tripartite motif-containing protein 31; ring-type	99.55
2ckl_B		165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.54
2d8t_A		71	Dactylidin, ring finger protein 146; RNF146, ring	99.54
2ecv_A		85	Tripartite motif-containing protein 5; metal bindi	99.52
3knv_A		141	TNF receptor-associated factor 2; cross-brace, alt	99.52
2ct2_A		88	Tripartite motif protein 32; zinc-finger protein H	99.51
3ng2_A		71	RNF4, snurf, ring finger protein 4; ring domain, E	99.51
3hct_A		118	TNF receptor-associated factor 6; cross-brace, bet	99.5
1g25_A		65	CDK-activating kinase assembly factor MAT1; ring f	99.49
2ecj_A		58	Tripartite motif-containing protein 39; TRIM39, ri	99.49
2ea6_A		69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.47
1rmd_A		116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.47
1bor_A		56	Transcription factor PML; proto-oncogene, nuclear	99.46
3htk_C		267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	99.46
2xeu_A		64	Ring finger protein 4; transcription, zinc-finger,	99.45
2ect_A		78	Ring finger protein 126; metal binding protein, st	99.44
1iym_A		55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.44
1e4u_A		78	Transcriptional repressor NOT4; gene regulation, t	99.43
2ecn_A		70	Ring finger protein 141; RNF141, ring domain, zinc	99.41
3hcs_A		170	TNF receptor-associated factor 6; cross-brace, bet	99.41
2l0b_A		91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.4
2kiz_A		69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.4
1chc_A		68	Equine herpes virus-1 ring domain; viral protein;	99.39
2ecm_A		55	Ring finger and CHY zinc finger domain- containing	99.39
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.36
1x4j_A		75	Ring finger protein 38; structural genomics, NPPSF	99.35
2ep4_A		74	Ring finger protein 24; zinc binding, ubiquitin, E	99.34
1v87_A		114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.27
4ic3_A		74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.25
2ecg_A		75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.24
1wim_A		94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.21
2vje_A		64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.2
2ecl_A		81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.19
2y1n_A		389	E3 ubiquitin-protein ligase; ligase-transferase co	99.16
4ap4_A		133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.14
2bay_A		61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	99.1
2vje_B		63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.1
3dpl_R		106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.07
2yho_A		79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	99.06
2ea5_A		68	Cell growth regulator with ring finger domain prot	99.04
3t6p_A		345	Baculoviral IAP repeat-containing protein 2; ring,	98.89
4a0k_B		117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	98.8
2d8s_A		80	Cellular modulator of immune recognition; C-MIR, m	98.67
2ct0_A		74	Non-SMC element 1 homolog; ring domain, structural	98.32
3vk6_A		101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.21
3k1l_B		381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	97.95
3m62_A		968	Ubiquitin conjugation factor E4; armadillo-like re	97.88
1vyx_A		60	ORF K3, K3RING; zinc-binding protein, ring domain,	97.87
2jun_A		101	Midline-1; B-BOX, TRIM, ring finger, alternative s	97.49
3nw0_A		238	Non-structural maintenance of chromosomes element	96.48
2cs3_A		93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	95.41
2ko5_A		99	Ring finger protein Z; lassa fever virus-Z, negati	94.89
3i2d_A		371	E3 SUMO-protein ligase SIZ1; signal transduction,	94.34
4fo9_A		360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	93.6
2lbm_A		142	Transcriptional regulator ATRX; metal binding prot	87.58
1weo_A		93	Cellulose synthase, catalytic subunit (IRX3); stru	84.82
2lri_C		66	Autoimmune regulator; Zn binding protein domain, a	83.97
3mjh_B		34	Early endosome antigen 1; protein-zinc finger comp	83.77
1vfy_A		73	Phosphatidylinositol-3-phosphate binding FYVE doma	83.56
1m3v_A		122	FLIN4, fusion of the LIM interacting domain of LDB	83.51
1joc_A		125	EEA1, early endosomal autoantigen 1; FYVE domain,	81.61
3ql9_A		129	Transcriptional regulator ATRX; zinc finger, trans	80.48
1z2q_A		84	LM5-1; membrane protein, FYVE domain, zinc-finger;	80.41
2yw8_A		82	RUN and FYVE domain-containing protein 1; structur	80.34
2l5u_A		61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	80.32
2xqn_T		126	Testin, TESS; metal-binding protein, cytoskeleton,	80.06

>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

Probab=99.73  E-value=1.9e-18  Score=108.77  Aligned_cols=70  Identities=19%  Similarity=0.299  Sum_probs=58.2

Q ss_pred             CCCCcccCccccccCCCCeeccCCCcccHhhHHHHHhhhhhccccCCCCCCCCCCCCcCcccCCccchhhHHHHHHHHHH
Q 041693           45 RLDIELTCPVCLETVFDPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLCRKAGVYQGAIHLTELGILLSRSCR  124 (156)
Q Consensus        45 ~~~~~l~C~IC~~~~~~Pv~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~~~~~n~~l~~l~~  124 (156)
                      .+.+++.||||+++|.+|++++|||+||+.||.+|+.          .+...||.||..+......    .|..+.++++
T Consensus         4 ~~~~~~~C~IC~~~~~~Pv~~~CgH~fc~~Ci~~~~~----------~~~~~CP~C~~~~~~~~l~----~n~~l~~~i~   69 (78)
T 1t1h_A            4 EFPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLD----------AGHKTCPKSQETLLHAGLT----PNYVLKSLIA   69 (78)
T ss_dssp             CCSSSSSCTTTSCCCSSEEEETTTEEEEHHHHHHHHT----------TTCCBCTTTCCBCSSCCCE----ECTTTHHHHH
T ss_pred             CCcccCCCCCccccccCCEEcCCCCeecHHHHHHHHH----------HCcCCCCCCcCCCChhhCc----cCHHHHHHHH
Confidence            4578899999999999999999999999999999981          3367899999998765543    5667777777


Q ss_pred             HHHH
Q 041693          125 EYWE  128 (156)
Q Consensus       125 ~~~~  128 (156)
                      .|..
T Consensus        70 ~~~~   73 (78)
T 1t1h_A           70 LWCE   73 (78)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7754

PyMOL of 1t1h

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

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

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

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

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

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

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens}	Back alignment and structure

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, CHR protein, DNA repair, metal-binding, nucleus; 2.12A {Homo sapiens}	Back alignment and structure

>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

>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

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

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

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

>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

>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

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

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

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens}	Back alignment and structure

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

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

>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

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

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

>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

>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

>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

>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

>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

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding 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

>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

>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

>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

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

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

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

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

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

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} 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

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

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

>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

>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

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; 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

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

>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

>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

>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

>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

>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

>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

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

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

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

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

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A	Back alignment and structure

>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

>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

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

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

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

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

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

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

>3mjh_B Early endosome antigen 1; protein-zinc finger complex, beta BETA alpha fold, beta HAIR RAB5A GTPase, EEA1, protein transport; HET: GTP; 2.03A {Homo sapiens}	Back alignment and structure

>1vfy_A Phosphatidylinositol-3-phosphate binding FYVE domain of protein VPS27; endosome maturation, intracellular trafficking; 1.15A {Saccharomyces cerevisiae} SCOP: g.50.1.1	Back alignment and structure

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3	Back alignment and structure

>1joc_A EEA1, early endosomal autoantigen 1; FYVE domain, inositol 3-phosphate binding, membrane protein; HET: ITP; 2.20A {Homo sapiens} SCOP: g.50.1.1 h.1.21.1 PDB: 1hyi_A* 1hyj_A	Back alignment and structure

>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A	Back alignment and structure

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}	Back alignment and structure

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A	Back alignment and structure

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

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens}	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		156
d1jm7a_		103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	7e-08
d1bora_		56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	5e-07
d1rmda2		86	g.44.1.1 (A:1-86) V(D)J recombination activating p	2e-06
d1fbva4		79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-05
d1t1ha_		78	g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cre	7e-05
d1wima_		94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	2e-04
d1chca_		68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	5e-04

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


class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 7e-08
 Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 8/58 (13%)

Query: 45  RLDIELTCPVCLETVFDPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLCRK 102
            +   L CP+CLE + +PVS  C HI CK C        ++  L       +CPLC+ 
Sbjct: 17  AMQKILECPICLELIKEPVSTKCDHIFCKFC--------MLKLLNQKKGPSQCPLCKN 66

PyMOL of d1jm7a_

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

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

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

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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		156
d1t1ha_		78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.75
d2c2la2		80	STIP1 homology and U box-containing protein 1, STU	99.75
d1jm7a_		103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.71
d1jm7b_		97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.67
d1rmda2		86	V(D)J recombination activating protein 1 (RAG1), d	99.65
d1wgma_		98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.63
d2baya1		56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.57
d1fbva4		79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.55
d1bora_		56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.51
d1g25a_		65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.44
d1chca_		68	Immediate early protein, IEEHV {Equine herpesvirus	99.43
d1iyma_		55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.41
d1ur6b_		52	Not-4 N-terminal RING finger domain {Human (Homo s	99.34
d1v87a_		114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.15
d3dplr1		88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.01
d1vyxa_		60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.87
d1wima_		94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.68
d2cs3a1		80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	96.01
d1wila_		89	Hypothetical protein KIAA1045 {Human (Homo sapiens	91.68
d2jnea1		71	Hypothetical protein YfgJ {Escherichia coli [TaxId	88.03
d1f62a_		51	Williams-Beuren syndrome transcription factor, WST	86.6
d1vfya_		67	vps27p protein {Baker's yeast (Saccharomyces cerev	84.14
d1weoa_		93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	83.84
d1dvpa2		72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	83.67
d1z60a1		59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	82.3

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.75  E-value=3.6e-19  Score=110.87  Aligned_cols=71  Identities=18%  Similarity=0.291  Sum_probs=59.5

Q ss_pred             CCCCcccCccccccCCCCeeccCCCcccHhhHHHHHhhhhhccccCCCCCCCCCCCCcCcccCCccchhhHHHHHHHHHH
Q 041693           45 RLDIELTCPVCLETVFDPVSLTCGHILCKMCACSAASVSIVDGLKLADPTEKCPLCRKAGVYQGAIHLTELGILLSRSCR  124 (156)
Q Consensus        45 ~~~~~l~C~IC~~~~~~Pv~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~~~~~n~~l~~l~~  124 (156)
                      .+.++|.||||+++|.+||+++|||+||+.||.+|+          ......||.|+.++...+..    .|..|+++++
T Consensus         4 eiP~~l~CpIc~~~m~dPV~~~cgh~fc~~ci~~~~----------~~~~~~cP~~~~~l~~~~l~----pN~~L~~~I~   69 (78)
T d1t1ha_           4 EFPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWL----------DAGHKTCPKSQETLLHAGLT----PNYVLKSLIA   69 (78)
T ss_dssp             CCSSSSSCTTTSCCCSSEEEETTTEEEEHHHHHHHH----------TTTCCBCTTTCCBCSSCCCE----ECTTTHHHHH
T ss_pred             CCCccCCCcCcCchhhCceEccCCCcchHHHHHHHH----------HHCCCCCCcccccCCccccc----chHHHHHHHH
Confidence            456889999999999999999999999999999998          13456799999998766553    5778888888


Q ss_pred             HHHHH
Q 041693          125 EYWEK  129 (156)
Q Consensus       125 ~~~~~  129 (156)
                      .|..+
T Consensus        70 ~~~~~   74 (78)
T d1t1ha_          70 LWCES   74 (78)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87653

PyMOL of d1t1ha_

>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

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

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

>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

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

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

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

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

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {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

>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

>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

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

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

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

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

>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

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

>d1vfya_ g.50.1.1 (A:) vps27p protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

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

>d1dvpa2 g.50.1.1 (A:149-220) Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

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