Citrus Sinensis ID: 028200

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210--
Protein Sequence
MGGCCCCSSKGVERNSTPAYYYYPRASEERLPLSSHHGAGSALSRGLLVDTNLETSVPDAYRPPPAPTPFDANVRHPQTPPVVQEICSNKSDPSVQTTPVPVQDTLGGNSQETSSKCDDLKEPESKTVANVELESTKELEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPVDY
Secondary Structure (PSIPRED)
cccccccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccEEcccccccccccccccccccccEEEccccccccHHHHHHHHHcccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccEcccccccHcccccccccccccccccccHHHHccccHHHHccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEccccccccHcccccccccccEcccccccccccccHHccccccccEEccccccccHHHHHHHHHccccccccccEEEEcccccc
Coil and Loop (DISEMBL)
mggccccsskgvernstpayyyypraseerlplsshhgagsalsrgllvdtnletsvpdayrpppaptpfdanvrhpqtppvvqeicsnksdpsvqttpvpvqdtlggnsqetsskcddlkepesktvanveLESTKELEVELSKSVHHVVAVIEeedvcptcleeydaenpriiTKCEHHFHLACIFEwmersdtcpvcnqemifdlpvdy
Flexible Loop (DISEMBL)
mggccccsskgvernstpAYYYYPRASEERLPLSSHHGAGSALSRGLLVDTNLETSVPDAYRPPPAPTPFDANVRHPQTPPVVQEICSNKSDPSVQTtpvpvqdtlggnsqetsskcddlkepesktvanvelestkeLEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPVDY
Low Complexity Region (SEG)
MGGCCCCSSKGVERNSTPAYYYYPRASEERLPLSSHHGAGSALSRGLLVDTNLETSVpdayrpppaptpfdaNVRHPQTPPVVQEICSNKSDPSVQTTPVPVQDTLGGNSQETSSKCDDLKEPESKTVANVELESTKELEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPVDY
Disordered region (IsUnstruct)
***CCCCSSKGVERNSTPAYYYYP*********************************************************************************************************************ELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL****
Disordered Region (DISOPRED)
*GGC***SSKGV**NSTPAYYY***********************************************************************************************************************************IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD*****
Disordered Region (DISEMBL)
MGGCCCCSSKGVERNSTPAYYYYPRASEERLPLSSHHGAGSALSRGLLVDTNLETSVPDAYRPPPAPTPFDANVRHPQTPPVVQEICSNKSDPSVQTTPVPVQDTL********************TVANVELESTKELEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPVDY
Disordered Region (DISPRO)
*GGCCCCSSKGVERNSTPAYYYYPRASEERLPLSSHHGAGSALSRGLLVDTNLETSVPDAYRPPPAPTPFDANVRHPQ*********************************************************************HHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MGGCCCCSSKGVERNSTPAYYYYPRASEERLPLSSHHGAGSALSRGLLVDTNLETSVPDAYRPPPAPTPFDANVRHPQTPPVVQEICSNKSDPSVQTTPVPVQDTLGGNSQETSSKCDDLKEPESKTVANVELESTKELEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPVDY
Positional Conservation
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	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	212	2.2.26 [Sep-21-2011]
Q8LE94	231	E3 ubiquitin-protein liga	no	no	0.693	0.636	0.368	5e-22
Q4TU14	371	E3 ubiquitin-protein liga	no	no	0.254	0.145	0.407	6e-09
Q9ZT42	375	E3 ubiquitin-protein liga	no	no	0.334	0.189	0.356	4e-08
Q7TMV1	668	E3 ubiquitin-protein liga	yes	no	0.240	0.076	0.377	3e-06
Q5RBT7	664	E3 ubiquitin-protein liga	yes	no	0.240	0.076	0.377	5e-06
Q8WU17	664	E3 ubiquitin-protein liga	yes	no	0.240	0.076	0.377	5e-06
Q9SG96	181	RING-H2 finger protein AT	no	no	0.235	0.276	0.372	6e-06
Q7KRW1	809	Protein TRC8 homolog OS=D	yes	no	0.268	0.070	0.342	7e-06
Q9SL78	390	Putative RING-H2 finger p	no	no	0.212	0.115	0.413	8e-06
Q9CY62	165	E3 ubiquitin-protein liga	no	no	0.259	0.333	0.363	1e-05

>sp|Q8LE94|RING3_ARATH E3 ubiquitin-protein ligase At3g02290 OS=Arabidopsis thaliana GN=At3g02290 PE=2 SV=1

 Score =  104 bits (259), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 59/160 (36%), Positives = 91/160 (56%), Gaps = 13/160 (8%)

Query: 57  VPDAYRPPPAPTPFDANVRHPQTPPVVQEICSN---------KSDPSVQTTPVPVQDTLG 107
           + +A+R  P P P+DA+ R+ ++    +E  S+         +SD    +    V     
Sbjct: 73  LSEAFRSTPRPLPYDADPRYFRSLVSRREKGSSHSHEEVEPLRSDSDADSESFGVGGCKW 132

Query: 108 GNSQETSSKCDDLKEPESKTVANVELESTKELEVELSKSVHHVVAVIEEEDVCPTCLEEY 167
            N++ T S  D  +E  SK+   +    +K +  +      ++  + E+EDVCPTCLEEY
Sbjct: 133 ANNKSTLSDKDSKEEYSSKSSLRILRSRSKSIMAD----SENMYILSEDEDVCPTCLEEY 188

Query: 168 DAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD 207
            +ENP+I+TKC HHFHL+CI+EWMERS+ CPVC + M F+
Sbjct: 189 TSENPKIVTKCSHHFHLSCIYEWMERSENCPVCGKVMEFN 228

Mediates E2-dependent protein ubiquitination.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|Q4TU14|RHF1A_ARATH E3 ubiquitin-protein ligase RHF1A OS=Arabidopsis thaliana GN=RHF1A PE=1 SV=1

 Score = 60.8 bits (146), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 32/54 (59%)

Query: 157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPV 210
           +D C  CLE +  ++P  +T C+H +HL CI EW +RS  CP+C Q  +   P 
Sbjct: 43  DDACSICLEPFTLQDPSTVTSCKHEYHLQCIIEWSQRSKECPICWQLFVLRDPA 96

E3 ubiquitin-protein ligase involved in the positive regulation of the gametogenesis progression. Mediates the proteasomal degradation of KRP6, a cyclin-dependent kinase inhibitor which accumulates during meiosis and blocks the progression of subsequent mitoses during gametophyte development. Functions in association with RHF2A. Possesses E3 ubiquitin ligase activity in vitro.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9ZT42|RHF2A_ARATH E3 ubiquitin-protein ligase RHF2A OS=Arabidopsis thaliana GN=RHF2A PE=2 SV=1

 Score = 58.2 bits (139), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 140 EVELSKSVHHVVAVIEE--EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTC 197
           E  L+ +   V   I++  +D C  CLE +   +P  +T C+H +HL CI EW +RS  C
Sbjct: 11  EGHLTSAAAFVEGGIQDACDDACSICLESFCESDPSTLTSCKHEYHLQCILEWCQRSSQC 70

Query: 198 PVCNQEMIFDLPV 210
           P+C Q +    P 
Sbjct: 71  PMCWQSISLKDPT 83

Probable E3 ubiquitin-protein ligase involved in the positive regulation of the gametogenesis progression. Required for the degradation of KRP6, a cyclin-dependent kinase inhibitor which accumulates during meiosis and blocks the progression of subsequent mitoses during gametophytes development. Functions in association with RHF1A.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q7TMV1|RN139_MOUSE E3 ubiquitin-protein ligase RNF139 OS=Mus musculus GN=Rnf139 PE=1 SV=1

 Score = 52.0 bits (123), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 20/53 (37%), Positives = 31/53 (58%), Gaps = 2/53 (3%)

Query: 155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD 207
           E +DVC  C  E+       IT C H+FH  C+ +W+   DTCP+C+Q++  +
Sbjct: 542 EIDDVCAICYHEFTTSAR--ITPCNHYFHALCLRKWLYIQDTCPMCHQKVYIE 592

E3-ubiquitin ligase; acts as a negative regulator of the cell proliferation through mechanisms involving G2/M arrest and cell death. Required for MHC class I ubiquitination in cells expressing the cytomegalovirus protein US2 before dislocation from the endoplasmic reticulum (ER). Affects SREBP processing by hindering the SREBP/SCAP complex translocation from the ER to the Golgi, thereby reducing SREBF2 target gene expression. Required for INSIG1 ubiquitination. May be required for EIF3 complex ubiquitination. May function as a signaling receptor.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q5RBT7|RN139_PONAB E3 ubiquitin-protein ligase RNF139 OS=Pongo abelii GN=RNF139 PE=2 SV=1

 Score = 51.2 bits (121), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 2/53 (3%)

Query: 155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD 207
           E  DVC  C  E+       IT C H+FH  C+ +W+   DTCP+C+Q++  +
Sbjct: 542 EINDVCAICYHEFTTSAR--ITPCNHYFHALCLRKWLYIQDTCPMCHQKVYIE 592

E3-ubiquitin ligase; acts as a negative regulator of the cell proliferation through mechanisms involving G2/M arrest and cell death. Required for MHC class I ubiquitination in cells expressing the cytomegalovirus protein US2 before dislocation from the endoplasmic reticulum (ER). Affects SREBP processing by hindering the SREBP/SCAP complex translocation from the ER to the Golgi, thereby reducing SREBF2 target gene expression. Required for INSIG1 ubiquitination. May be required for EIF3 complex ubiquitination. May function as a signaling receptor.

Pongo abelii (taxid: 9601)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q8WU17|RN139_HUMAN E3 ubiquitin-protein ligase RNF139 OS=Homo sapiens GN=RNF139 PE=1 SV=1

 Score = 51.2 bits (121), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 2/53 (3%)

Query: 155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD 207
           E  DVC  C  E+       IT C H+FH  C+ +W+   DTCP+C+Q++  +
Sbjct: 542 EINDVCAICYHEFTTSAR--ITPCNHYFHALCLRKWLYIQDTCPMCHQKVYIE 592

E3-ubiquitin ligase; acts as a negative regulator of the cell proliferation through mechanisms involving G2/M arrest and cell death. Required for MHC class I ubiquitination in cells expressing the cytomegalovirus protein US2 before dislocation from the endoplasmic reticulum (ER). Affects SREBP processing by hindering the SREBP/SCAP complex translocation from the ER to the Golgi, thereby reducing SREBF2 target gene expression. Required for INSIG1 ubiquitination. May be required for EIF3 complex ubiquitination. May function as a signaling receptor.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9SG96|ATL72_ARATH RING-H2 finger protein ATL72 OS=Arabidopsis thaliana GN=ATL72 PE=2 SV=1

 Score = 50.8 bits (120), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 160 CPTCLEEY-DAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLP 209
           C  CL ++ D E  R++ KC H FH+ CI  W+    +CP C Q ++ + P
Sbjct: 114 CLICLGDFEDGEKVRVLPKCNHGFHVRCIDTWLLSRSSCPTCRQSLLLEQP 164

Arabidopsis thaliana (taxid: 3702)

>sp|Q7KRW1|TRC8_DROME Protein TRC8 homolog OS=Drosophila melanogaster GN=Trc8 PE=1 SV=1

 Score = 50.8 bits (120), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 13/70 (18%)

Query: 146 SVHHVVAVIEE--------EDVCPTCLEE-YDAENPRIITKCEHHFHLACIFEWMERSDT 196
           +VH + A+ E         +DVC  C +E Y A+    IT+C H FH  C+ +W+   D 
Sbjct: 599 AVHKISALPEATPAQLQAFDDVCAICYQEMYSAK----ITRCRHFFHGVCLRKWLYVQDR 654

Query: 197 CPVCNQEMIF 206
           CP+C++ M++
Sbjct: 655 CPLCHEIMMY 664

Plays a role in growth inhibition that is dependent upon COP9 signalosome subunits CSN5 and CSN6. May modulate signalosome levels or compartmentalization. Probably functions in the same or a related pathway to VHL during early midline development.

Drosophila melanogaster (taxid: 7227)

>sp|Q9SL78|ATL12_ARATH Putative RING-H2 finger protein ATL12 OS=Arabidopsis thaliana GN=ATL12 PE=3 SV=1

 Score = 50.4 bits (119), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 19/46 (41%), Positives = 29/46 (63%), Gaps = 1/46 (2%)

Query: 160 CPTCLEEY-DAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEM 204
           C  CL ++ D E  R++ KC H FH+ CI +W+E+  TCP+C   +
Sbjct: 124 CSVCLSKFEDVEILRLLPKCRHAFHIGCIDQWLEQHATCPLCRNRV 169

Arabidopsis thaliana (taxid: 3702)

>sp|Q9CY62|RN181_MOUSE E3 ubiquitin-protein ligase RNF181 OS=Mus musculus GN=Rnf181 PE=2 SV=1

 Score = 50.1 bits (118), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 33/55 (60%)

Query: 150 VVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEM 204
           V++  + +  CP CL E++AE   I   C H FH  CI  W+ ++++CP+C  E+
Sbjct: 78  VISSAKADLKCPVCLLEFEAEETVIEMPCHHLFHSNCILPWLSKTNSCPLCRHEL 132

E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	212
225426204	213	PREDICTED: E3 ubiquitin-protein ligase A	0.976	0.971	0.687	3e-77
255537531	212	protein binding protein, putative [Ricin	0.995	0.995	0.688	5e-75
224053875	212	predicted protein [Populus trichocarpa]	0.990	0.990	0.638	2e-65
449452294	211	PREDICTED: E3 ubiquitin-protein ligase A	0.990	0.995	0.594	7e-65
297742211	227	unnamed protein product [Vitis vinifera]	0.867	0.810	0.670	2e-64
359806791	213	uncharacterized protein LOC100816369 [Gl	0.990	0.985	0.574	1e-60
224074986	255	predicted protein [Populus trichocarpa]	0.995	0.827	0.562	7e-59
255648202	212	unknown [Glycine max]	0.910	0.910	0.569	1e-56
356513367	213	PREDICTED: uncharacterized protein LOC10	0.910	0.906	0.566	3e-55
297801436	212	zinc finger family protein [Arabidopsis	0.976	0.976	0.537	8e-54

>gi|225426204|ref|XP_002280000.1| PREDICTED: E3 ubiquitin-protein ligase At3g02290-like [Vitis vinifera]

 Score =  293 bits (750), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 143/208 (68%), Positives = 165/208 (79%), Gaps = 1/208 (0%)

Query: 1   MGGCCCCSSKGVERNSTPAYYYYPRASEERLPLSSHHGAGSALSRGLLVDTNLETSVPDA 60
           MGGCCCCSSKG E N TPAYYY PRASEE  PLSSHHGA S LS GLLVDTNL TS PD 
Sbjct: 1   MGGCCCCSSKGTELNGTPAYYYCPRASEEHEPLSSHHGAASTLSTGLLVDTNLGTSPPDT 60

Query: 61  YRPPPAPTPFDANVRHPQTPPVVQEICSNKSDPSVQTT-PVPVQDTLGGNSQETSSKCDD 119
           YRPPPAP P+D ++ HPQTPPV +E C NK+D  VQTT    + + + GN  ET +KC+D
Sbjct: 61  YRPPPAPIPYDVDLGHPQTPPVAEESCVNKNDTVVQTTNSGSLGEAVEGNMLETLAKCED 120

Query: 120 LKEPESKTVANVELESTKELEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCE 179
           LK+ + K +A  EL S+KE EVELSKS   +V+  +EEDVCPTCLEEYDAENP+I+TKCE
Sbjct: 121 LKQSDCKMLAQSELTSSKETEVELSKSGDPIVSSTDEEDVCPTCLEEYDAENPKIVTKCE 180

Query: 180 HHFHLACIFEWMERSDTCPVCNQEMIFD 207
           HHFHLACI EWMERSDTCPVC++EMIF+
Sbjct: 181 HHFHLACILEWMERSDTCPVCDKEMIFN 208

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255537531|ref|XP_002509832.1| protein binding protein, putative [Ricinus communis] gi|223549731|gb|EEF51219.1| protein binding protein, putative [Ricinus communis]

 Score =  286 bits (731), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 146/212 (68%), Positives = 169/212 (79%), Gaps = 1/212 (0%)

Query: 1   MGGCCCCSSKGVERNSTPAYYYYPRASEERLPLSSHHGAGSALSRGLLVDTNLETSVPDA 60
           MGGCCCCSSKG E NS PAYYYYPRASEE +PLSS HG+ + LS GLLVDTNL+TSVPDA
Sbjct: 1   MGGCCCCSSKGAEINSAPAYYYYPRASEEHVPLSSRHGSVATLSTGLLVDTNLDTSVPDA 60

Query: 61  YRPPPAPTPFDANVRHPQTPPVVQEICSNKSDPSVQTT-PVPVQDTLGGNSQETSSKCDD 119
           YRPPP P PF+  +  PQTP   QE  S+K D +VQTT    VQ+T   N++ETS KC+D
Sbjct: 61  YRPPPPPIPFEMAIGCPQTPQGAQETSSDKDDGTVQTTNSGSVQETTYTNTRETSIKCED 120

Query: 120 LKEPESKTVANVELESTKELEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCE 179
           +KEP+ K   N+EL+S KELEVE SKSV  +V+  EEEDVCPTCLEEYDAENP+I TKCE
Sbjct: 121 VKEPDCKAQTNLELDSAKELEVEFSKSVELLVSATEEEDVCPTCLEEYDAENPKITTKCE 180

Query: 180 HHFHLACIFEWMERSDTCPVCNQEMIFDLPVD 211
           HHFHL+CI EWMERSDTCPVC++EMI D P+D
Sbjct: 181 HHFHLSCILEWMERSDTCPVCDKEMIIDPPLD 212

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224053875|ref|XP_002298023.1| predicted protein [Populus trichocarpa] gi|222845281|gb|EEE82828.1| predicted protein [Populus trichocarpa]

 Score =  254 bits (649), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 136/213 (63%), Positives = 166/213 (77%), Gaps = 3/213 (1%)

Query: 1   MGGCCCCSSKGV-ERNSTPAYYYYPRASEERLPLSSHHGAGSALSRGLLVDTNLETSVPD 59
           MGGCCCCSSKG  + NS P YYYYPRA  E +PLSSHH AGSALS GLLVDTNL+TSVPD
Sbjct: 1   MGGCCCCSSKGAAQSNSAPPYYYYPRAPAEHVPLSSHHAAGSALSTGLLVDTNLDTSVPD 60

Query: 60  AYRPPPAPTPFDANVRHPQTPPVVQEICSNKSDPSVQTT-PVPVQDTLGGNSQETSSKCD 118
           AYRPPPAP PFD  V H QT    +E C +K+D ++QTT     Q+  G N++ETS++C+
Sbjct: 61  AYRPPPAPMPFDVAVGHLQTLHRSRETCGDKNDGALQTTNSASGQENTGLNTRETSAECE 120

Query: 119 DLKEPESKTVANVELESTKELEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKC 178
           D+KE + K   N EL++ KELE+ELSKSV  +V+  EEED CP CLEEYD ENP++ITKC
Sbjct: 121 DVKELDCKAQINSELDAAKELEIELSKSVEPLVSATEEED-CPICLEEYDLENPKLITKC 179

Query: 179 EHHFHLACIFEWMERSDTCPVCNQEMIFDLPVD 211
           EHHFHL+CI EWMERS++CPVC++E+I D P+D
Sbjct: 180 EHHFHLSCILEWMERSESCPVCDKEVIIDPPID 212

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452294|ref|XP_004143894.1| PREDICTED: E3 ubiquitin-protein ligase At3g02290-like [Cucumis sativus]

 Score =  252 bits (644), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 126/212 (59%), Positives = 151/212 (71%), Gaps = 2/212 (0%)

Query: 1   MGGCCCCSSKGVERNSTPAYYYYPRASEERLPLSSHHGAGSALSRGLLVDTNLETSVPDA 60
           MGGCCCCSSKG E N  P YYYYPRASEE +PLS         S GLLVDTNL+TS+PD 
Sbjct: 1   MGGCCCCSSKGTESNIAPGYYYYPRASEEHVPLSPLR-TPREFSTGLLVDTNLDTSIPDT 59

Query: 61  YRPPPAPTPFDANVRHPQTPPVVQEICSNKSDPSVQTTPV-PVQDTLGGNSQETSSKCDD 119
           YR PP P P+D  +  P TPPVVQEI   K++ + QTT    +Q+T   N++ETS+KC+ 
Sbjct: 60  YRSPPLPMPYDVVLTSPLTPPVVQEISCYKNEAAAQTTNSNTIQETACINTRETSAKCEG 119

Query: 120 LKEPESKTVANVELESTKELEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCE 179
           + E + K   + E+++ KE E ELSK V   V  IEEEDVCP CLEEYD ENP++ TKCE
Sbjct: 120 VDESDCKKHTDFEVDALKESENELSKGVESAVLPIEEEDVCPICLEEYDGENPKLTTKCE 179

Query: 180 HHFHLACIFEWMERSDTCPVCNQEMIFDLPVD 211
           HHFHLACI EWMERSD CPVC+QEM+F  P+D
Sbjct: 180 HHFHLACILEWMERSDICPVCDQEMVFSSPID 211

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297742211|emb|CBI34360.3| unnamed protein product [Vitis vinifera]

 Score =  250 bits (639), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 124/185 (67%), Positives = 146/185 (78%), Gaps = 1/185 (0%)

Query: 24  PRASEERLPLSSHHGAGSALSRGLLVDTNLETSVPDAYRPPPAPTPFDANVRHPQTPPVV 83
           PRASEE  PLSSHHGA S LS GLLVDTNL TS PD YRPPPAP P+D ++ HPQTPPV 
Sbjct: 38  PRASEEHEPLSSHHGAASTLSTGLLVDTNLGTSPPDTYRPPPAPIPYDVDLGHPQTPPVA 97

Query: 84  QEICSNKSDPSVQTT-PVPVQDTLGGNSQETSSKCDDLKEPESKTVANVELESTKELEVE 142
           +E C NK+D  VQTT    + + + GN  ET +KC+DLK+ + K +A  EL S+KE EVE
Sbjct: 98  EESCVNKNDTVVQTTNSGSLGEAVEGNMLETLAKCEDLKQSDCKMLAQSELTSSKETEVE 157

Query: 143 LSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQ 202
           LSKS   +V+  +EEDVCPTCLEEYDAENP+I+TKCEHHFHLACI EWMERSDTCPVC++
Sbjct: 158 LSKSGDPIVSSTDEEDVCPTCLEEYDAENPKIVTKCEHHFHLACILEWMERSDTCPVCDK 217

Query: 203 EMIFD 207
           EMIF+
Sbjct: 218 EMIFN 222

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359806791|ref|NP_001241561.1| uncharacterized protein LOC100816369 [Glycine max] gi|255641755|gb|ACU21148.1| unknown [Glycine max]

 Score =  238 bits (607), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 123/214 (57%), Positives = 161/214 (75%), Gaps = 4/214 (1%)

Query: 1   MGGCCCC--SSKGVERNSTPAYYYYPRASEERLPLSSHHGAGSALSRGLLVDTNLETSVP 58
           MGGCCCC  S+K    ++ PAYYYYPRASEE +PLSSH GA SA S  LLVDTNL+TS P
Sbjct: 1   MGGCCCCCCSAKETVLSAPPAYYYYPRASEEHVPLSSHQGAASAFSGRLLVDTNLDTSSP 60

Query: 59  DAYRPPPAPTPFDANVRHPQTPPVVQEICSNKSDPSVQTTPV-PVQDTLGGNSQETSSKC 117
           D YRPPPAP PF+  +   QTPP  QEI S+K++ S+ +T    +Q+ + G++  TS+K 
Sbjct: 61  DTYRPPPAPIPFNVTLGTTQTPPAAQEIRSDKNNTSLHSTNSNAIQEPVAGDNHGTSAKL 120

Query: 118 DDLKEPESKTVANVELESTKELEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITK 177
           ++LKE + K   ++EL+S K  E+EL+KS    + V+EEED CP CLEEYDAENP++ TK
Sbjct: 121 EELKESDCKVQTDLELDSAKGSEIELAKS-GKPIDVVEEEDTCPICLEEYDAENPKLATK 179

Query: 178 CEHHFHLACIFEWMERSDTCPVCNQEMIFDLPVD 211
           C+HHFHLACI EWMERS+TCPVC+Q+++FD P++
Sbjct: 180 CDHHFHLACILEWMERSETCPVCDQDLVFDPPIE 213

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224074986|ref|XP_002304508.1| predicted protein [Populus trichocarpa] gi|222841940|gb|EEE79487.1| predicted protein [Populus trichocarpa]

 Score =  232 bits (592), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 122/217 (56%), Positives = 156/217 (71%), Gaps = 6/217 (2%)

Query: 1   MGGCCCCSSKGV--ERNSTPAYYYYPRASEERLPLSSHHGAGSAL-SRGLLVDTNLETSV 57
           MGGCCC S+ G   + N+ P ++YYPR SEE + LSSH   GS L S GLLVDTNL+TSV
Sbjct: 39  MGGCCCGSANGAADQFNNAPPFFYYPRTSEEHVSLSSHQAPGSVLQSTGLLVDTNLDTSV 98

Query: 58  PDAYRPPPAPTPFDANVRHPQTPPVVQEICSNKSDPSVQTT-PVPVQDTLGGNSQETSSK 116
           PDAYRPPPAP PFDA V  PQTP  ++E+  +K+  ++QTT     Q+    N++E  +K
Sbjct: 99  PDAYRPPPAPIPFDAAVGRPQTPGRLREVRGDKNHGALQTTTSASGQENTALNTREPLAK 158

Query: 117 CDDLKEPESKTVANVELESTKELEVELSKSVHHVVAVIEEEDV--CPTCLEEYDAENPRI 174
           C+D K+ + K   N E  S KELE+ELSK V  +V+  EEE+   CP CLEEYD ENP++
Sbjct: 159 CEDAKDLDCKVQINSEPGSAKELEIELSKLVEPLVSATEEEEEEDCPICLEEYDLENPKL 218

Query: 175 ITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPVD 211
            TKCEHH+HL+CI EWMERS++CPVC++EMIFD P+D
Sbjct: 219 TTKCEHHYHLSCILEWMERSESCPVCDKEMIFDPPID 255

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255648202|gb|ACU24554.1| unknown [Glycine max]

 Score =  224 bits (572), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 111/195 (56%), Positives = 144/195 (73%), Gaps = 2/195 (1%)

Query: 18  PAYYYYPRASEERLPLSSHHGAGSALSRGLLVDTNLETSVPDAYRPPPAPTPFDANVRHP 77
           PAYYYYPRASEE +PLSSH GA SA S  LLVDTNL+TS PD YRPPPAP PF+  +   
Sbjct: 19  PAYYYYPRASEEHVPLSSHPGAASAFSGRLLVDTNLDTSSPDTYRPPPAPIPFNVTLGTT 78

Query: 78  QTPPVVQEICSNKSDPSV-QTTPVPVQDTLGGNSQETSSKCDDLKEPESKTVANVELEST 136
           QTPP  QEI S+K++ S+  T    +Q+ +  +   TS+K ++ KE E K   ++EL+S 
Sbjct: 79  QTPPAAQEIRSDKNNTSLPSTNSNAIQEPVARDIHGTSAKLEEPKESECKVQTDLELDSA 138

Query: 137 KELEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDT 196
           K  E+EL+KS    + ++EEED CP CLEEYDAENP++ T C+HHFHLACI EWMERS+T
Sbjct: 139 KGSEIELAKS-GKPIDLVEEEDACPICLEEYDAENPKLATNCDHHFHLACILEWMERSET 197

Query: 197 CPVCNQEMIFDLPVD 211
           CPVC+Q+++FD P++
Sbjct: 198 CPVCDQDLVFDPPIE 212

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356513367|ref|XP_003525385.1| PREDICTED: uncharacterized protein LOC100790079 [Glycine max]

 Score =  220 bits (561), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 111/196 (56%), Positives = 144/196 (73%), Gaps = 3/196 (1%)

Query: 18  PAYYY-YPRASEERLPLSSHHGAGSALSRGLLVDTNLETSVPDAYRPPPAPTPFDANVRH 76
           PAYYY YPRASEE +PLSSH GA SA S  LLVDTNL+TS PD YRPPPAP PF+  +  
Sbjct: 19  PAYYYQYPRASEEHVPLSSHPGAASAFSGRLLVDTNLDTSSPDTYRPPPAPIPFNVTLGT 78

Query: 77  PQTPPVVQEICSNKSDPSV-QTTPVPVQDTLGGNSQETSSKCDDLKEPESKTVANVELES 135
            QTPP  QEI S+K++ S+  T    +Q+ +  +   TS+K ++ KE E K   ++EL+S
Sbjct: 79  TQTPPAAQEIRSDKNNTSLPSTNSNAIQEPVARDIHGTSAKLEEPKESECKVQTDLELDS 138

Query: 136 TKELEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD 195
            K  E+EL+KS    + ++EEED CP CLEEYDAENP++ T C+HHFHLACI EWMERS+
Sbjct: 139 AKGSEIELAKS-GKPIDLVEEEDACPICLEEYDAENPKLATNCDHHFHLACILEWMERSE 197

Query: 196 TCPVCNQEMIFDLPVD 211
           TCPVC+Q+++FD P++
Sbjct: 198 TCPVCDQDLVFDPPIE 213

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297801436|ref|XP_002868602.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata] gi|297314438|gb|EFH44861.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  215 bits (548), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 116/216 (53%), Positives = 152/216 (70%), Gaps = 9/216 (4%)

Query: 1   MGGCCCCSS-KGVERNSTPAYYYYPRASEERLPLSS-HHGAGSALSRGLLV-DTNLETSV 57
           MGGCCCCSS +  + ++ PAYYYYPRA+EER+PLSS H+   SA+S G++V DTNLETS 
Sbjct: 1   MGGCCCCSSSRRADVDNGPAYYYYPRATEERVPLSSAHNRTSSAISTGVVVVDTNLETSS 60

Query: 58  PDAYRPPPAPTPFDANVRHPQTPPVVQE-ICSNKSDPSVQTTPV-PVQDTLGGNSQETSS 115
           PDAY PPP P PFD  +  PQTP   +E  C +  + SV +      Q+T+ G +    +
Sbjct: 61  PDAYIPPPLPIPFDVAIGVPQTPASAEEATCVDIREVSVDSANTESAQETVDGITIGVPT 120

Query: 116 KCDDLKEPESKTVANVELESTKELEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRII 175
            C   KE + K    ++LEST+E++ +LSK+V      IEEE+ CP CLEEYD ENP+++
Sbjct: 121 TCSH-KETDCKIQTEIDLESTEEIDPKLSKAVF---IPIEEEEDCPICLEEYDIENPKLV 176

Query: 176 TKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPVD 211
            KC+HHFHLACI EWMERS+TCPVCN+EM+FD P+D
Sbjct: 177 AKCDHHFHLACILEWMERSETCPVCNKEMVFDSPLD 212

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	212
TAIR|locus:2177881	212	AT5G41350 [Arabidopsis thalian	0.976	0.976	0.486	6.7e-49
TAIR|locus:505006415	190	RHB1A "RING-H2 finger B1A" [Ar	0.490	0.547	0.471	1.1e-38
TAIR|locus:2076542	231	AT3G02290 [Arabidopsis thalian	0.566	0.519	0.411	7.8e-23
TAIR|locus:2143251	232	AT5G15790 [Arabidopsis thalian	0.514	0.469	0.435	4.9e-21
UNIPROTKB|C9J1C6	139	RNF181 "E3 ubiquitin-protein l	0.273	0.417	0.362	8e-11
UNIPROTKB|Q9P0P0	153	RNF181 "E3 ubiquitin-protein l	0.273	0.379	0.362	8e-11
TAIR|locus:2129525	371	RHF1A "RING-H2 group F1A" [Ara	0.25	0.142	0.415	7.8e-10
TAIR|locus:2165735	163	AT5G42200 [Arabidopsis thalian	0.349	0.453	0.342	1.2e-08
MGI|MGI:1913760	165	Rnf181 "ring finger protein 18	0.273	0.351	0.362	1.6e-08
UNIPROTKB|F1SVB7	153	RNF181 "Uncharacterized protei	0.273	0.379	0.362	2e-08

TAIR|locus:2177881 AT5G41350 [Arabidopsis thaliana (taxid:3702)]

 Score = 510 (184.6 bits), Expect = 6.7e-49, P = 6.7e-49
 Identities = 105/216 (48%), Positives = 142/216 (65%)

Query:     1 MGGCCCCSS-KGVERNSTPAYYYYPRASEERLPLSS-HHGAGSALSRGLLV-DTNLETSV 57
             MGGCCCCSS +  + ++ PAYYYYPRA+EER+PLSS H+   SA+S G++V DTNLETS 
Sbjct:     1 MGGCCCCSSSRRADVDNGPAYYYYPRATEERVPLSSAHNRTSSAISTGVVVVDTNLETSS 60

Query:    58 XXXXXXXXXXXXXXXNVRHPQTPPVVQEI-CSNKSDPSVQTTPVP-VQDTLGGNSQETSS 115
                             +  PQTP   +E  C +  + SV +      Q+T+ G +    +
Sbjct:    61 PDAYIPPPLPTPFDVPIGIPQTPASGEEATCVDIREVSVDSANTESAQETVDGITLGVPT 120

Query:   116 KCDDLKEPESKTVANVELESTKELEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRII 175
              C   KE +SK    ++LEST+E++ +LSK+V   + + EEED CP CLEEYD ENP+++
Sbjct:   121 TCSH-KETDSKIQTEIDLESTEEIDPKLSKAVF--IPIEEEED-CPICLEEYDIENPKLV 176

Query:   176 TKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPVD 211
              KC+HHFHLACI EWMERS+TCPVCN+EM+FD  +D
Sbjct:   177 AKCDHHFHLACILEWMERSETCPVCNKEMVFDSTLD 212

GO:0005634 "nucleus" evidence=ISM

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

GO:0005739 "mitochondrion" evidence=IDA

GO:0006914 "autophagy" evidence=RCA

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=RCA

TAIR|locus:505006415 RHB1A "RING-H2 finger B1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 289 (106.8 bits), Expect = 1.1e-38, Sum P(2) = 1.1e-38
 Identities = 50/106 (47%), Positives = 74/106 (69%)

Query:   102 VQDTLGGNSQETSSKCDDLKEPESKTVANVELESTKELEVELSKSVHHVVAVIEEEDVCP 161
             ++  + G+S ET + C+DL E + KT+A+  + S ++ +   SK     + V EEED CP
Sbjct:    83 IKGRMSGSSFETLATCEDLGESDCKTLASSVILSPRKSD--FSKHQGLKILVDEEEDCCP 140

Query:   162 TCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD 207
              C E+YD ENPR+ TKCEH FHL+C+ EW+ERSD CP+C++E++FD
Sbjct:   141 ICFEDYDVENPRLTTKCEHEFHLSCLLEWIERSDRCPICDKEVVFD 186

GO:0005634 "nucleus" evidence=ISM

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

GO:0048573 "photoperiodism, flowering" evidence=RCA

TAIR|locus:2076542 AT3G02290 [Arabidopsis thaliana (taxid:3702)]

 Score = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 51/124 (41%), Positives = 77/124 (62%)

Query:    84 QEICSNKSDPSVQTTPVPVQDTLGGNSQETSSKCDDLKEPESKTVANVELESTKELEVEL 143
             +E+   +SD    +    V      N++ T S  D  +E  SK+   +    +K +  + 
Sbjct:   109 EEVEPLRSDSDADSESFGVGGCKWANNKSTLSDKDSKEEYSSKSSLRILRSRSKSIMAD- 167

Query:   144 SKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQE 203
             S++++    + E+EDVCPTCLEEY +ENP+I+TKC HHFHL+CI+EWMERS+ CPVC + 
Sbjct:   168 SENMY---ILSEDEDVCPTCLEEYTSENPKIVTKCSHHFHLSCIYEWMERSENCPVCGKV 224

Query:   204 MIFD 207
             M F+
Sbjct:   225 MEFN 228

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2143251 AT5G15790 [Arabidopsis thaliana (taxid:3702)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 51/117 (43%), Positives = 71/117 (60%)

Query:    90 KSDPSVQTTPVPVQDTLGGNSQETSSKCDDLKEPESKTVANVELESTKELEVELSKSVHH 149
             +SD  V +    V+ +   N    S   +D KE  S++   + L+S       +S S   
Sbjct:   120 RSDADVDSESFSVEGSKWANKLIISG--EDSKEEFSRSSRRI-LQSRT-----MSTSNEG 171

Query:   150 VVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIF 206
             +    ++EDVCPTCLEEY +ENP+I+TKC HHFHL+CI+EWMERS+ CPVC + M F
Sbjct:   172 LYITSDDEDVCPTCLEEYISENPKIVTKCSHHFHLSCIYEWMERSENCPVCGKVMEF 228

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

UNIPROTKB|C9J1C6 RNF181 "E3 ubiquitin-protein ligase RNF181" [Homo sapiens (taxid:9606)]

 Score = 128 (50.1 bits), Expect = 8.0e-11, Sum P(2) = 8.0e-11
 Identities = 21/58 (36%), Positives = 33/58 (56%)

Query:   150 VVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD 207
             V+   + E  CP CL E++ E   I   C H FH +CI  W+ ++++CP+C  E+  D
Sbjct:    66 VIRGSQAELKCPVCLLEFEEEETAIEMPCHHLFHSSCILPWLSKTNSCPLCRYELPTD 123

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q9P0P0 RNF181 "E3 ubiquitin-protein ligase RNF181" [Homo sapiens (taxid:9606)]

 Score = 128 (50.1 bits), Expect = 8.0e-11, Sum P(2) = 8.0e-11
 Identities = 21/58 (36%), Positives = 33/58 (56%)

Query:   150 VVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD 207
             V+   + E  CP CL E++ E   I   C H FH +CI  W+ ++++CP+C  E+  D
Sbjct:    66 VIRGSQAELKCPVCLLEFEEEETAIEMPCHHLFHSSCILPWLSKTNSCPLCRYELPTD 123

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=IEA

TAIR|locus:2129525 RHF1A "RING-H2 group F1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 148 (57.2 bits), Expect = 7.8e-10, P = 7.8e-10
 Identities = 22/53 (41%), Positives = 32/53 (60%)

Query:   157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLP 209
             +D C  CLE +  ++P  +T C+H +HL CI EW +RS  CP+C Q  +   P
Sbjct:    43 DDACSICLEPFTLQDPSTVTSCKHEYHLQCIIEWSQRSKECPICWQLFVLRDP 95

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0016020 "membrane" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0009561 "megagametogenesis" evidence=IGI

GO:0010498 "proteasomal protein catabolic process" evidence=IDA

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0051726 "regulation of cell cycle" evidence=IGI

GO:0055046 "microgametogenesis" evidence=IGI

GO:0000165 "MAPK cascade" evidence=RCA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009617 "response to bacterium" evidence=RCA

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=RCA

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

GO:0031348 "negative regulation of defense response" evidence=RCA

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

TAIR|locus:2165735 AT5G42200 [Arabidopsis thaliana (taxid:3702)]

 Score = 130 (50.8 bits), Expect = 1.2e-08, P = 1.2e-08
 Identities = 26/76 (34%), Positives = 39/76 (51%)

Query:   135 STKELEVELSKSVHHVVAVIEEEDVCPTCLEEYDA-ENPRIITKCEHHFHLACIFEWMER 193
             S  ELE ++ K     +AVI     C  CLE+ ++ ++ R++  C H FH  C   W+  
Sbjct:    80 SVLELE-KIPKLTGRELAVIARSTECAVCLEDIESGQSTRLVPGCNHGFHQLCADTWLSN 138

Query:   194 SDTCPVCNQEMIFDLP 209
                CPVC  E+  +LP
Sbjct:   139 HTVCPVCRAELAPNLP 154

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

MGI|MGI:1913760 Rnf181 "ring finger protein 181" [Mus musculus (taxid:10090)]

 Score = 129 (50.5 bits), Expect = 1.6e-08, P = 1.6e-08
 Identities = 21/58 (36%), Positives = 34/58 (58%)

Query:   150 VVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD 207
             V++  + +  CP CL E++AE   I   C H FH  CI  W+ ++++CP+C  E+  D
Sbjct:    78 VISSAKADLKCPVCLLEFEAEETVIEMPCHHLFHSNCILPWLSKTNSCPLCRHELPTD 135

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|F1SVB7 RNF181 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 128 (50.1 bits), Expect = 2.0e-08, P = 2.0e-08
 Identities = 21/58 (36%), Positives = 32/58 (55%)

Query:   150 VVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD 207
             V+   + E  CP CL E++ E   I   C H FH  CI  W+ ++++CP+C  E+  D
Sbjct:    66 VIRGSQAELKCPVCLLEFEEEETAIEMPCHHLFHSGCILPWLSKTNSCPLCRHELPTD 123

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	212
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	3e-10
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	5e-09
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	4e-08
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	5e-07
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	9e-07
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	1e-06
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	3e-06
smart00184	40	smart00184, RING, Ring finger	3e-05
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	5e-05
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	7e-05
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	2e-04
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	2e-04

>gnl|CDD|221705 pfam12678, zf-rbx1, RING-H2 zinc finger

 Score = 54.4 bits (131), Expect = 3e-10
 Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 10/56 (17%)

Query: 156 EEDVCPTCLEEYDA----------ENPRIITKCEHHFHLACIFEWMERSDTCPVCN 201
           E+DVC  C   +D           + P +  +C H FHL CI  W++  +TCP+C 
Sbjct: 18  EDDVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73

There are 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding. The protein, of which this domain is the conserved region, participates in diverse functions relevant to chromosome metabolism and cell cycle control. Length = 73

>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain

 Score = 50.1 bits (120), Expect = 5e-09
 Identities = 17/46 (36%), Positives = 27/46 (58%)

Query: 158 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQE 203
           D CP CL+E++     ++  C H FH  C+ +W+  S+TCP+C   
Sbjct: 1   DECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

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

 Score = 47.4 bits (113), Expect = 4e-08
 Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 3/45 (6%)

Query: 160 CPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD-TCPVCNQE 203
           CP CLEE+    P ++  C H F  +CI +W++    TCP+C   
Sbjct: 2   CPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44

Length = 45

>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

 Score = 49.2 bits (117), Expect = 5e-07
 Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 10/61 (16%)

Query: 157 EDVCPTCLEEY----DAENPRIITK------CEHHFHLACIFEWMERSDTCPVCNQEMIF 206
           +  C  C++E         PR +        C H  HL C+  W+ER  TCP+C + +IF
Sbjct: 287 DRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVIF 346

Query: 207 D 207
           D
Sbjct: 347 D 347

Length = 491

>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger)

 Score = 44.0 bits (104), Expect = 9e-07
 Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 2/47 (4%)

Query: 156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQ 202
           EE  CP CL+     +P ++T C H F   CI  ++++   CP+C  
Sbjct: 1   EELECPICLDLL--RDPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

>gnl|CDD|227521 COG5194, APC11, Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

 Score = 44.8 bits (106), Expect = 1e-06
 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 2/51 (3%)

Query: 158 DVCPTCLEEYDAEN--PRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIF 206
             CP C       +  P +   C H FH  CI+ W++    CP+  Q  + 
Sbjct: 32  GTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVL 82

Length = 88

>gnl|CDD|193335 pfam12861, zf-Apc11, Anaphase-promoting complex subunit 11 RING-H2 finger

 Score = 43.6 bits (103), Expect = 3e-06
 Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 13/66 (19%)

Query: 154 IEEEDVCPTCLEEYDA----------ENPRIITKCEHHFHLACIFEWMERSDT---CPVC 200
              +DVC  C   +D           + P +  KC+H+FH+ CI +W+    +   CP+C
Sbjct: 18  TPSDDVCGICRVSFDGTCPQCKFPGDDCPLVWGKCKHNFHMHCILKWLATETSKGLCPMC 77

Query: 201 NQEMIF 206
            Q  +F
Sbjct: 78  RQTFVF 83

Apc11 is one of the subunits of the anaphase-promoting complex or cyclosome. The APC subunits are cullin family proteins with ubiquitin ligase activity. Polyubiquitination marks proteins for degradation by the 26S proteasome and is carried out by a cascade of enzymes that includes ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and is responsible for recruiting E2s to the APC and for mediating the subsequent transfer of ubiquitin to APC substrates in vivo. In Saccharomyces cerevisiae this RING-H2 finger protein defines the minimal ubiquitin ligase activity of the APC, and the integrity of the RING-H2 finger is essential for budding yeast cell viability. Length = 85

>gnl|CDD|214546 smart00184, RING, Ring finger

 Score = 39.8 bits (93), Expect = 3e-05
 Identities = 20/42 (47%), Positives = 27/42 (64%), Gaps = 3/42 (7%)

Query: 160 CPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD-TCPVC 200
           CP CLEEY  ++P I   C H F  +CI +W+E  + TCP+C
Sbjct: 1   CPICLEEYL-KDPVI-LPCGHTFCRSCIRKWLESGNNTCPIC 40

E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s). Length = 40

>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

 Score = 43.5 bits (102), Expect = 5e-05
 Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 5/68 (7%)

Query: 143  LSKSVHHVVAVIEEEDVCPTCLEEYDAENP--RIITKCEHHFHLACIFEWMERS--DTCP 198
              K++    +  EE  +C + L+  D   P  R  T C++ FH  C+++W   S    CP
Sbjct: 1458 WKKNIDEKFSGHEECAICYSVLDMVDRSLPSKRCAT-CKNKFHTRCLYKWFASSARSNCP 1516

Query: 199  VCNQEMIF 206
            +C  E+ F
Sbjct: 1517 LCRSEITF 1524

Length = 1525

>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

 Score = 42.7 bits (100), Expect = 7e-05
 Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 1/46 (2%)

Query: 160 CPTCLEEYDAENPRIITKCEHHFHLACIFEWM-ERSDTCPVCNQEM 204
           C  C+  +   +   +  C+H FH+ C+ +W+   S+ CPVC   +
Sbjct: 326 CAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAI 371

Length = 374

>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional

 Score = 40.9 bits (96), Expect = 2e-04
 Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 7/58 (12%)

Query: 154 IEEEDVCPTCLEE-YDAENPR----IITKCEHHFHLACIFEWMERSDTCPVCNQEMIF 206
            ++E  C  C+E+ YD E       I++ C H F + CI  W +  +TCPVC    I 
Sbjct: 173 KDKE--CAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFIS 228

Length = 238

>gnl|CDD|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger)

 Score = 37.1 bits (86), Expect = 2e-04
 Identities = 19/42 (45%), Positives = 24/42 (57%), Gaps = 3/42 (7%)

Query: 160 CPTCLEEYDAENPRIITKCEHHFHLACIFEWME-RSDTCPVC 200
           CP CLEE   ++P  I  C H F   CI  W+E  + TCP+C
Sbjct: 1   CPICLEEP--KDPVTILPCGHLFCSKCILSWLESGNVTCPLC 40

The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway. Length = 40

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	212
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.69
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.53
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.51
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.38
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.36
PHA02929	238	N1R/p28-like protein; Provisional	99.35
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.27
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.27
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.26
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.24
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.23
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.22
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.15
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.14
PF14634	44	zf-RING_5: zinc-RING finger domain	99.14
PHA02926	242	zinc finger-like protein; Provisional	99.11
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	99.1
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.09
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.04
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.03
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.0
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.99
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.92
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.89
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.86
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.8
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.65
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.61
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.58
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.55
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.46
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.44
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.39
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.35
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.29
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.26
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.25
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.18
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.16
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.1
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.09
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.96
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.81
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.77
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.61
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.56
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.55
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	97.54
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.47
COG5152	259	Uncharacterized conserved protein, contains RING a	97.44
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	97.33
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.32
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.25
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.25
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.25
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	97.17
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	97.06
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.04
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	97.02
KOG2660	331	consensus Locus-specific chromosome binding protei	96.99
KOG3039	303	consensus Uncharacterized conserved protein [Funct	96.98
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.96
PHA02862	156	5L protein; Provisional	96.95
PHA02825	162	LAP/PHD finger-like protein; Provisional	96.71
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	96.56
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.45
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.31
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	96.31
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.27
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.25
PHA03096	284	p28-like protein; Provisional	96.14
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	96.14
KOG1002	791	consensus Nucleotide excision repair protein RAD16	96.13
PF04641	260	Rtf2: Rtf2 RING-finger	96.09
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	95.96
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	95.93
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	95.84
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.64
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.39
COG5236	493	Uncharacterized conserved protein, contains RING Z	95.36
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	95.05
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	95.01
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	94.91
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	94.88
KOG1940	276	consensus Zn-finger protein [General function pred	94.88
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	94.5
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	94.44
KOG1001	674	consensus Helicase-like transcription factor HLTF/	94.29
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	93.92
KOG3053	293	consensus Uncharacterized conserved protein [Funct	93.81
COG5222	427	Uncharacterized conserved protein, contains RING Z	93.73
KOG3002	299	consensus Zn finger protein [General function pred	93.73
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	92.31
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	92.11
KOG0298	1394	consensus DEAD box-containing helicase-like transc	92.09
KOG1609	323	consensus Protein involved in mRNA turnover and st	91.75
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	91.08
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	89.67
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	88.44
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	88.39
KOG1829	580	consensus Uncharacterized conserved protein, conta	87.82
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	87.52
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	87.05
COG5109	396	Uncharacterized conserved protein, contains RING Z	86.99
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	86.88
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	86.86
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	86.4
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	85.56
KOG0825	1134	consensus PHD Zn-finger protein [General function	85.08
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	83.94
KOG3899	381	consensus Uncharacterized conserved protein [Funct	83.87
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	83.66
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	83.07
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	80.97
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	80.46

>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

Probab=99.69  E-value=1.1e-17  Score=104.91  Aligned_cols=44  Identities=45%  Similarity=1.152  Sum_probs=40.2

Q ss_pred             CccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCccc
Q 028200          158 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCN  201 (212)
Q Consensus       158 ~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr  201 (212)
                      +.|+||++.|..++..+.++|||.||.+||.+|++++.+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence            46999999998888899999999999999999999999999997

...

>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.53  E-value=5.5e-15  Score=129.00  Aligned_cols=52  Identities=38%  Similarity=0.957  Sum_probs=46.9

Q ss_pred             CccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCC-CCcccccccCCCC
Q 028200          158 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDT-CPVCNQEMIFDLP  209 (212)
Q Consensus       158 ~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~t-CPvCr~~l~~~~~  209 (212)
                      +.|+||||+|..|+.+++|+|+|.||..||++||.+..+ ||+||+.+.....
T Consensus       230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~~  282 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDSG  282 (348)
T ss_pred             ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCCCC
Confidence            489999999999999999999999999999999988755 9999998865543

>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

Probab=99.51  E-value=1.4e-14  Score=100.50  Aligned_cols=46  Identities=37%  Similarity=1.006  Sum_probs=37.4

Q ss_pred             CCCccccccccccC----------CCCeEEcCCCCcccHHHHHHHHhcCCCCCccc
Q 028200          156 EEDVCPTCLEEYDA----------ENPRIITKCEHHFHLACIFEWMERSDTCPVCN  201 (212)
Q Consensus       156 e~~~C~ICle~~~~----------~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr  201 (212)
                      .++.|+||++.|..          +.++...+|||.||..||.+||+++.+||+||
T Consensus        18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            45569999999932          24556678999999999999999999999997

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....

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

Probab=99.38  E-value=3.3e-13  Score=95.11  Aligned_cols=53  Identities=36%  Similarity=0.967  Sum_probs=44.2

Q ss_pred             CCCccccccccccC----------CCCeEEcCCCCcccHHHHHHHHhc---CCCCCcccccccCCC
Q 028200          156 EEDVCPTCLEEYDA----------ENPRIITKCEHHFHLACIFEWMER---SDTCPVCNQEMIFDL  208 (212)
Q Consensus       156 e~~~C~ICle~~~~----------~~~~~~l~C~H~FH~~CI~~Wl~~---~~tCPvCr~~l~~~~  208 (212)
                      ++++|.||+..|+.          +.+++.-.|+|.||..||.+||+.   ++.||+||+++.+++
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k~   85 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFKE   85 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeeeCC
Confidence            47779999999974          235666789999999999999975   478999999998764

>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

Probab=99.36  E-value=3.8e-13  Score=116.96  Aligned_cols=54  Identities=33%  Similarity=0.955  Sum_probs=46.0

Q ss_pred             cCCCcccccccc-ccCCC---------CeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEE-YDAEN---------PRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~-~~~~~---------~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      .++..|.||+|+ |..++         .+..++|||+||..|++.||+|+++||+||.++.+|.
T Consensus       285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~ifd~  348 (491)
T COG5243         285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVIFDQ  348 (491)
T ss_pred             CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCcccccc
Confidence            456689999999 55542         3467999999999999999999999999999988775

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.35  E-value=4.5e-13  Score=112.21  Aligned_cols=50  Identities=32%  Similarity=0.853  Sum_probs=41.9

Q ss_pred             CCCccccccccccCCCC-----eEEcCCCCcccHHHHHHHHhcCCCCCccccccc
Q 028200          156 EEDVCPTCLEEYDAENP-----RIITKCEHHFHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~-----~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      .+..|+||++.+.....     .++++|+|.||..||.+|++++.+||+||+.+.
T Consensus       173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~  227 (238)
T PHA02929        173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI  227 (238)
T ss_pred             CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence            35679999999754331     356789999999999999999999999999875

>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

Probab=99.27  E-value=3.8e-12  Score=81.76  Aligned_cols=46  Identities=28%  Similarity=0.782  Sum_probs=39.5

Q ss_pred             CCccccccccccCCCCeEEcCCCCc-ccHHHHHHHHhcCCCCCccccccc
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHH-FHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~-FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      +..|.||++....   .+.++|||. |+..|+.+|+++..+||+||+.+.
T Consensus         2 ~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRD---VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSS---EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCc---eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            4569999998654   788999999 999999999999999999999874

...

>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

Probab=99.27  E-value=3.2e-12  Score=77.92  Aligned_cols=39  Identities=44%  Similarity=1.142  Sum_probs=33.9

Q ss_pred             cccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcc
Q 028200          160 CPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVC  200 (212)
Q Consensus       160 C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvC  200 (212)
                      |+||++.+..  +.+.++|||.||..||.+|++.+.+||+|
T Consensus         1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC--cCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence            8999998855  56789999999999999999999999998

>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.26  E-value=2.5e-12  Score=109.30  Aligned_cols=49  Identities=27%  Similarity=0.811  Sum_probs=45.0

Q ss_pred             CCccccccccccCCCCeEEcCCCCcccHHHHHHHHh-cCCCCCccccccc
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME-RSDTCPVCNQEMI  205 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~-~~~tCPvCr~~l~  205 (212)
                      .-.|+|||+.|..++...+|||.|.||..||.+||. -++.||+||.+++
T Consensus       323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP  372 (374)
T COG5540         323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP  372 (374)
T ss_pred             CceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence            456999999998888899999999999999999998 6789999999885

>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)

Probab=99.24  E-value=7.8e-12  Score=77.15  Aligned_cols=44  Identities=39%  Similarity=1.092  Sum_probs=37.8

Q ss_pred             ccccccccccCCCCeEEcCCCCcccHHHHHHHHhc-CCCCCcccccc
Q 028200          159 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-SDTCPVCNQEM  204 (212)
Q Consensus       159 ~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~-~~tCPvCr~~l  204 (212)
                      .|+||++.+  .+...+++|||.||..|+..|++. +..||+||+.+
T Consensus         1 ~C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEF--REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhh--hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            499999998  445667779999999999999998 77899999864

>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.23  E-value=1.8e-11  Score=96.91  Aligned_cols=54  Identities=28%  Similarity=0.664  Sum_probs=45.3

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLP  209 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~~  209 (212)
                      +.-..|||||+.|.... .+.++|||+||..||+..++...+||+|++.|..+..
T Consensus       129 ~~~~~CPiCl~~~sek~-~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~  182 (187)
T KOG0320|consen  129 EGTYKCPICLDSVSEKV-PVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQF  182 (187)
T ss_pred             ccccCCCceecchhhcc-ccccccchhHHHHHHHHHHHhCCCCCCcccccchhhh
Confidence            44568999999996533 3569999999999999999999999999998866543

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.22  E-value=8.7e-12  Score=100.77  Aligned_cols=51  Identities=27%  Similarity=0.696  Sum_probs=41.1

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc----------------CCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER----------------SDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~----------------~~tCPvCr~~l~~~~  208 (212)
                      .++..|+||++.+..   .++++|||.||..||.+|+..                ..+||+||..+....
T Consensus        16 ~~~~~CpICld~~~d---PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~   82 (193)
T PLN03208         16 GGDFDCNICLDQVRD---PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT   82 (193)
T ss_pred             CCccCCccCCCcCCC---cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence            345679999998754   567899999999999999853                247999999886544

>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.15  E-value=1.6e-11  Score=101.06  Aligned_cols=51  Identities=31%  Similarity=0.790  Sum_probs=41.6

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc---CCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER---SDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~---~~tCPvCr~~l~~~~  208 (212)
                      .....|.||||.-++   .+++.|||.||..||++||..   ++.|||||..|..+.
T Consensus        45 ~~~FdCNICLd~akd---PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~   98 (230)
T KOG0823|consen   45 GGFFDCNICLDLAKD---PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT   98 (230)
T ss_pred             CCceeeeeeccccCC---CEEeecccceehHHHHHHHhhcCCCeeCCccccccccce
Confidence            445679999996543   667889999999999999966   467999999887665

>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]

Probab=99.14  E-value=1.9e-11  Score=103.43  Aligned_cols=54  Identities=30%  Similarity=0.696  Sum_probs=45.5

Q ss_pred             ccCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCCCC
Q 028200          154 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPV  210 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~~~  210 (212)
                      .+....|.||||.-..   ...++|||+||..||.+|...+..||+||..+.-.+.|
T Consensus       236 ~~a~~kC~LCLe~~~~---pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskvi  289 (293)
T KOG0317|consen  236 PEATRKCSLCLENRSN---PSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKVI  289 (293)
T ss_pred             CCCCCceEEEecCCCC---CCcCcCcchHHHHHHHHHHccccCCCcccccCCCccee
Confidence            3556789999997543   66899999999999999999999999999988766543

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.14  E-value=3.7e-11  Score=75.14  Aligned_cols=44  Identities=32%  Similarity=0.785  Sum_probs=39.7

Q ss_pred             ccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccc
Q 028200          159 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQ  202 (212)
Q Consensus       159 ~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~  202 (212)
                      .|+||++.|..+....+|.|||+||..||..++.....||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            39999999976778899999999999999999967788999986

>PHA02926 zinc finger-like protein; Provisional

Probab=99.11  E-value=4.9e-11  Score=97.78  Aligned_cols=57  Identities=25%  Similarity=0.612  Sum_probs=42.8

Q ss_pred             CCCccccccccccCC------CCeEEcCCCCcccHHHHHHHHhcC------CCCCcccccccCCCCCCC
Q 028200          156 EEDVCPTCLEEYDAE------NPRIITKCEHHFHLACIFEWMERS------DTCPVCNQEMIFDLPVDY  212 (212)
Q Consensus       156 e~~~C~ICle~~~~~------~~~~~l~C~H~FH~~CI~~Wl~~~------~tCPvCr~~l~~~~~~~~  212 (212)
                      ++.+|+||||.....      ...++.+|+|.||..||.+|.+.+      .+||+||+.+.+=.|-.|
T Consensus       169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I~pSrf  237 (242)
T PHA02926        169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNITMSKF  237 (242)
T ss_pred             CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeeeccccc
Confidence            467799999986321      124567899999999999999753      469999998866555443

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

Probab=99.10  E-value=4.6e-11  Score=82.44  Aligned_cols=54  Identities=30%  Similarity=0.691  Sum_probs=43.7

Q ss_pred             CCccccccccccC-------------CCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCCCC
Q 028200          157 EDVCPTCLEEYDA-------------ENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPV  210 (212)
Q Consensus       157 ~~~C~ICle~~~~-------------~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~~~  210 (212)
                      -|+|+||..-|..             +-++..-.|.|.||..||.+||..++.||++|+.+.+.++.
T Consensus        20 id~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~~~~   86 (88)
T COG5194          20 IDVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLADGG   86 (88)
T ss_pred             cchhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEeccc
Confidence            4678888877633             22455567999999999999999999999999999877653

>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A

Probab=99.09  E-value=8.7e-11  Score=72.78  Aligned_cols=38  Identities=29%  Similarity=0.838  Sum_probs=30.0

Q ss_pred             cccccccccCCCCeEEcCCCCcccHHHHHHHHhcC----CCCCcc
Q 028200          160 CPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS----DTCPVC  200 (212)
Q Consensus       160 C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~----~tCPvC  200 (212)
                      |+||++.|..   .+.++|||.|+..||.+|.+..    ..||+|
T Consensus         1 CpiC~~~~~~---Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKD---PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SS---EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCC---ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            8999999976   7889999999999999999764    369988

>smart00504 Ubox Modified RING finger domain

Probab=99.04  E-value=2.4e-10  Score=76.36  Aligned_cols=48  Identities=23%  Similarity=0.402  Sum_probs=41.6

Q ss_pred             CccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          158 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       158 ~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      ..|+||++.+..   .++++|||.|+..||.+|++.+.+||+|++.+..++
T Consensus         2 ~~Cpi~~~~~~~---Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~   49 (63)
T smart00504        2 FLCPISLEVMKD---PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHED   49 (63)
T ss_pred             cCCcCCCCcCCC---CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhh
Confidence            469999998865   467899999999999999999999999999885544

Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.

>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

Probab=99.03  E-value=2.3e-10  Score=70.24  Aligned_cols=39  Identities=44%  Similarity=1.182  Sum_probs=33.8

Q ss_pred             cccccccccCCCCeEEcCCCCcccHHHHHHHHh--cCCCCCcc
Q 028200          160 CPTCLEEYDAENPRIITKCEHHFHLACIFEWME--RSDTCPVC  200 (212)
Q Consensus       160 C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~--~~~tCPvC  200 (212)
                      |+||++.+..  +.++++|||.||..||.+|++  ....||+|
T Consensus         1 C~iC~~~~~~--~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFED--PVILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSS--EEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccC--CCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            8999998865  345899999999999999998  45679998

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....

>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.00  E-value=1.3e-10  Score=108.59  Aligned_cols=49  Identities=35%  Similarity=0.867  Sum_probs=42.8

Q ss_pred             CCCccccccccccCCCC--eEEcCCCCcccHHHHHHHHhcCCCCCcccccc
Q 028200          156 EEDVCPTCLEEYDAENP--RIITKCEHHFHLACIFEWMERSDTCPVCNQEM  204 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~--~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l  204 (212)
                      ..+.|+||+|.+..+..  ...++|+|+||..|++.||+++++||+||..+
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~  340 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVL  340 (543)
T ss_pred             cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhh
Confidence            46789999999866543  66789999999999999999999999999944

>smart00184 RING Ring finger

Probab=98.99  E-value=4.1e-10  Score=66.96  Aligned_cols=38  Identities=42%  Similarity=1.189  Sum_probs=32.9

Q ss_pred             cccccccccCCCCeEEcCCCCcccHHHHHHHHh-cCCCCCcc
Q 028200          160 CPTCLEEYDAENPRIITKCEHHFHLACIFEWME-RSDTCPVC  200 (212)
Q Consensus       160 C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~-~~~tCPvC  200 (212)
                      |+||++..   ...+.++|||.||..||..|++ .+.+||+|
T Consensus         1 C~iC~~~~---~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEEL---KDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCC---CCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            78999973   3477889999999999999998 66789997

E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)

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

Probab=98.92  E-value=1.6e-10  Score=79.18  Aligned_cols=52  Identities=31%  Similarity=0.827  Sum_probs=41.5

Q ss_pred             CCccccccccccCC----------CCeEEcCCCCcccHHHHHHHHhc---CCCCCcccccccCCC
Q 028200          157 EDVCPTCLEEYDAE----------NPRIITKCEHHFHLACIFEWMER---SDTCPVCNQEMIFDL  208 (212)
Q Consensus       157 ~~~C~ICle~~~~~----------~~~~~l~C~H~FH~~CI~~Wl~~---~~tCPvCr~~l~~~~  208 (212)
                      .++|.||...|+.-          -|++.-.|.|.||..||.+|+..   +..||+||+++.+++
T Consensus        20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~~e   84 (84)
T KOG1493|consen   20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQFKE   84 (84)
T ss_pred             CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEecC
Confidence            44899999999652          34555569999999999999954   467999999987753

>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]

Probab=98.89  E-value=2e-10  Score=83.05  Aligned_cols=69  Identities=28%  Similarity=0.522  Sum_probs=51.0

Q ss_pred             HHHhhhcccccccc-ccCCCccccccccccC-------------CC-CeEEcCCCCcccHHHHHHHHhcCCCCCcccccc
Q 028200          140 EVELSKSVHHVVAV-IEEEDVCPTCLEEYDA-------------EN-PRIITKCEHHFHLACIFEWMERSDTCPVCNQEM  204 (212)
Q Consensus       140 ~~~~~~~~~~~~~~-~ee~~~C~ICle~~~~-------------~~-~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l  204 (212)
                      ..+++|+....... +..-|.|+||..-+..             ++ .+.--.|.|.||..||.+||+.++.||+|.++.
T Consensus        28 rF~lKKWnAvAlWaWDi~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW  107 (114)
T KOG2930|consen   28 RFELKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEW  107 (114)
T ss_pred             ceEEeeeeeeeeeeeeeeechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence            34567776554443 3567889999865411             12 234456999999999999999999999999998


Q ss_pred             cCCC
Q 028200          205 IFDL  208 (212)
Q Consensus       205 ~~~~  208 (212)
                      .++.
T Consensus       108 ~~qr  111 (114)
T KOG2930|consen  108 VFQR  111 (114)
T ss_pred             eEee
Confidence            8765

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.86  E-value=1.7e-09  Score=96.78  Aligned_cols=51  Identities=25%  Similarity=0.636  Sum_probs=43.4

Q ss_pred             ccCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCC
Q 028200          154 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD  207 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~  207 (212)
                      .+....|+||++.|..   .++++|||.||..||..|+.....||+|+..+...
T Consensus        23 Le~~l~C~IC~d~~~~---PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~   73 (397)
T TIGR00599        23 LDTSLRCHICKDFFDV---PVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES   73 (397)
T ss_pred             cccccCCCcCchhhhC---ccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence            3567789999999854   45789999999999999999988999999987543

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A

Probab=98.80  E-value=4e-09  Score=65.53  Aligned_cols=38  Identities=37%  Similarity=0.912  Sum_probs=24.5

Q ss_pred             cccccccc-cCCCCeEEcCCCCcccHHHHHHHHhcC----CCCC
Q 028200          160 CPTCLEEY-DAENPRIITKCEHHFHLACIFEWMERS----DTCP  198 (212)
Q Consensus       160 C~ICle~~-~~~~~~~~l~C~H~FH~~CI~~Wl~~~----~tCP  198 (212)
                      |+||+| | ..+++.++|+|||.|+.+||.+|++++    -+||
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 7 557788899999999999999999864    2576

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

Probab=98.65  E-value=2.3e-08  Score=63.89  Aligned_cols=42  Identities=29%  Similarity=0.890  Sum_probs=32.9

Q ss_pred             ccccccccccCCCCeEEcCCC-----CcccHHHHHHHHhcC--CCCCccc
Q 028200          159 VCPTCLEEYDAENPRIITKCE-----HHFHLACIFEWMERS--DTCPVCN  201 (212)
Q Consensus       159 ~C~ICle~~~~~~~~~~l~C~-----H~FH~~CI~~Wl~~~--~tCPvCr  201 (212)
                      .|.||++..+.++ ....||.     |.||..|+.+|+..+  .+||+|+
T Consensus         1 ~CrIC~~~~~~~~-~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEGDEGD-PLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCCCCCCC-eeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4999999444444 4567884     999999999999654  5899995

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 Class

>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.61  E-value=1.8e-08  Score=84.54  Aligned_cols=51  Identities=29%  Similarity=0.675  Sum_probs=42.1

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHH-HHhcCC-CCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFE-WMERSD-TCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~-Wl~~~~-tCPvCr~~l~~~~  208 (212)
                      +.+..|+||+|....   ...++|||+||..||.. |-.++- .||+||+....++
T Consensus       213 ~~d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~  265 (271)
T COG5574         213 LADYKCFLCLEEPEV---PSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK  265 (271)
T ss_pred             ccccceeeeecccCC---cccccccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence            456789999997544   77899999999999999 987764 5999999876554

>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A

Probab=98.58  E-value=8.5e-09  Score=70.85  Aligned_cols=51  Identities=27%  Similarity=0.690  Sum_probs=25.4

Q ss_pred             CCcccccccccc-CCC-C-eEE--cCCCCcccHHHHHHHHhc-----------CCCCCcccccccCC
Q 028200          157 EDVCPTCLEEYD-AEN-P-RII--TKCEHHFHLACIFEWMER-----------SDTCPVCNQEMIFD  207 (212)
Q Consensus       157 ~~~C~ICle~~~-~~~-~-~~~--l~C~H~FH~~CI~~Wl~~-----------~~tCPvCr~~l~~~  207 (212)
                      +..|+||+..+. .+. + ++.  ..|++.||..||.+||..           .++||.|+++|.++
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~   68 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS   68 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence            345999999875 322 2 222  369999999999999964           14699999988654

>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.55  E-value=3.7e-08  Score=89.36  Aligned_cols=49  Identities=31%  Similarity=0.737  Sum_probs=39.9

Q ss_pred             CCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC-----CCCCcccccccCCC
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS-----DTCPVCNQEMIFDL  208 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~-----~tCPvCr~~l~~~~  208 (212)
                      +..|||||+....   ..+|.|||+||..||...+...     ..||+||..|..++
T Consensus       186 ~~~CPICL~~~~~---p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kd  239 (513)
T KOG2164|consen  186 DMQCPICLEPPSV---PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKD  239 (513)
T ss_pred             CCcCCcccCCCCc---ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccc
Confidence            6679999997654   5567799999999999988654     68999999876544

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

Probab=98.46  E-value=1.1e-07  Score=65.84  Aligned_cols=50  Identities=24%  Similarity=0.382  Sum_probs=38.7

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc-CCCCCcccccccCCC
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-SDTCPVCNQEMIFDL  208 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~-~~tCPvCr~~l~~~~  208 (212)
                      ++..|+|+.+.+..   .+++++||.|...+|.+|+++ ..+||+|++.+..++
T Consensus         3 ~~f~CpIt~~lM~d---PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~   53 (73)
T PF04564_consen    3 DEFLCPITGELMRD---PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESD   53 (73)
T ss_dssp             GGGB-TTTSSB-SS---EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGG
T ss_pred             cccCCcCcCcHhhC---ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCccc
Confidence            35679999999876   678899999999999999998 889999999876544

Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....

>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.44  E-value=7.2e-08  Score=87.02  Aligned_cols=51  Identities=29%  Similarity=0.792  Sum_probs=39.8

Q ss_pred             cCCCccccccccccC---CCC-----------eEEcCCCCcccHHHHHHHHh-cCCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDA---ENP-----------RIITKCEHHFHLACIFEWME-RSDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~---~~~-----------~~~l~C~H~FH~~CI~~Wl~-~~~tCPvCr~~l~  205 (212)
                      +....|+||+..++.   +.+           -..+||.|+||..|+..||. .+-.||+||..+.
T Consensus       569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP  634 (636)
T KOG0828|consen  569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP  634 (636)
T ss_pred             hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence            344569999988733   211           34579999999999999999 5669999999875

>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.39  E-value=7.7e-08  Score=80.97  Aligned_cols=52  Identities=29%  Similarity=0.710  Sum_probs=41.7

Q ss_pred             cCCCccccccccccCCC-------CeEEcCCCCcccHHHHHHHH--hcCCCCCcccccccC
Q 028200          155 EEEDVCPTCLEEYDAEN-------PRIITKCEHHFHLACIFEWM--ERSDTCPVCNQEMIF  206 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~-------~~~~l~C~H~FH~~CI~~Wl--~~~~tCPvCr~~l~~  206 (212)
                      .++.+|+||-..++...       ..-.|.|+|.||..||+-|-  -++.+||.|++.+..
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl  282 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDL  282 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhH
Confidence            45668999998885533       45678999999999999998  457899999987643

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=98.35  E-value=1.6e-07  Score=83.88  Aligned_cols=49  Identities=35%  Similarity=0.906  Sum_probs=39.3

Q ss_pred             cCCCccccccccccCCCCe-EEcCCCCcccHHHHHHHHhcCCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPR-IITKCEHHFHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~-~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      -+-.+||||||.++..... +.+.|.|.||..|+.+|  ...+|||||....
T Consensus       173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w--~~~scpvcR~~q~  222 (493)
T KOG0804|consen  173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKW--WDSSCPVCRYCQS  222 (493)
T ss_pred             ccCCCcchhHhhcCccccceeeeecccccchHHHhhc--ccCcChhhhhhcC
Confidence            4566899999999776544 44669999999999999  4566999997544

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

Probab=98.29  E-value=2.4e-07  Score=80.31  Aligned_cols=48  Identities=27%  Similarity=0.695  Sum_probs=42.3

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      ++-..|.||.|.|..   ..+++|+|.||.-||...|..+..||.|+.++.
T Consensus        21 D~lLRC~IC~eyf~i---p~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~   68 (442)
T KOG0287|consen   21 DDLLRCGICFEYFNI---PMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVT   68 (442)
T ss_pred             HHHHHHhHHHHHhcC---ceeccccchHHHHHHHHHhccCCCCCceecccc
Confidence            345579999999977   668899999999999999999999999998764

>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.26  E-value=4.5e-07  Score=79.90  Aligned_cols=56  Identities=32%  Similarity=0.762  Sum_probs=42.5

Q ss_pred             CCCccccccccccCCC-----CeEEcCCCCcccHHHHHHHH--hc-----CCCCCcccccccCCCCCC
Q 028200          156 EEDVCPTCLEEYDAEN-----PRIITKCEHHFHLACIFEWM--ER-----SDTCPVCNQEMIFDLPVD  211 (212)
Q Consensus       156 e~~~C~ICle~~~~~~-----~~~~l~C~H~FH~~CI~~Wl--~~-----~~tCPvCr~~l~~~~~~~  211 (212)
                      .+.+|.||+|....-.     -.|+.+|.|.||..||.+|.  ++     .+.||.||....+--+.+
T Consensus       160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~  227 (344)
T KOG1039|consen  160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSS  227 (344)
T ss_pred             ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccc
Confidence            4667999999874422     23446799999999999998  44     578999999876555443

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

Probab=98.25  E-value=3.7e-07  Score=76.89  Aligned_cols=46  Identities=37%  Similarity=0.851  Sum_probs=40.0

Q ss_pred             ccCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccc
Q 028200          154 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQ  202 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~  202 (212)
                      .+++..|+||++.|...   .+++|+|.||..||..|+...-.||.||.
T Consensus        10 ~~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   10 LQEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             ccccccChhhHHHhhcC---ccccccchHhHHHHHHhcCCCcCCcccCC
Confidence            35677899999999764   78999999999999999986678999993

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

Probab=98.18  E-value=7e-07  Score=85.96  Aligned_cols=52  Identities=27%  Similarity=0.892  Sum_probs=40.2

Q ss_pred             cCCCccccccccccC-CC---CeEEcCCCCcccHHHHHHHHhcC--CCCCcccccccC
Q 028200          155 EEEDVCPTCLEEYDA-EN---PRIITKCEHHFHLACIFEWMERS--DTCPVCNQEMIF  206 (212)
Q Consensus       155 ee~~~C~ICle~~~~-~~---~~~~l~C~H~FH~~CI~~Wl~~~--~tCPvCr~~l~~  206 (212)
                      +....|+||+..... +.   ...+..|.|.||..|+++|++.+  ++||+||.++.+
T Consensus      1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseitf 1524 (1525)
T COG5219        1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEITF 1524 (1525)
T ss_pred             CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccccc
Confidence            455579999988752 11   23455699999999999999875  689999988865

>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

Probab=98.16  E-value=8.8e-07  Score=75.45  Aligned_cols=47  Identities=26%  Similarity=0.517  Sum_probs=41.4

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEM  204 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l  204 (212)
                      +.-+.|-||-+.|..   ...++|||.||.-||...|..+.-||+||.+.
T Consensus        23 Ds~lrC~IC~~~i~i---p~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~   69 (391)
T COG5432          23 DSMLRCRICDCRISI---PCETTCGHTFCSLCIRRHLGTQPFCPVCREDP   69 (391)
T ss_pred             hhHHHhhhhhheeec---ceecccccchhHHHHHHHhcCCCCCccccccH
Confidence            345579999998876   66889999999999999999999999999864

>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B

Probab=98.10  E-value=5.6e-07  Score=60.08  Aligned_cols=50  Identities=30%  Similarity=0.658  Sum_probs=25.8

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      ++-..|+||.+.+..  ++.+..|+|+||..||.+-+.  ..||+|+.+...++
T Consensus         5 e~lLrCs~C~~~l~~--pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD   54 (65)
T PF14835_consen    5 EELLRCSICFDILKE--PVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQD   54 (65)
T ss_dssp             HHTTS-SSS-S--SS---B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS
T ss_pred             HHhcCCcHHHHHhcC--CceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHH
Confidence            345679999998744  667789999999999988544  34999999876665

>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.09  E-value=4.2e-07  Score=79.23  Aligned_cols=53  Identities=23%  Similarity=0.709  Sum_probs=41.3

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc-CCCCCcccccccCCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-SDTCPVCNQEMIFDLP  209 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~-~~tCPvCr~~l~~~~~  209 (212)
                      ..+..|+|||+-+..  ......|.|.||.+||.+-|+. ++.||.||+.+.-+-.
T Consensus        41 ~~~v~c~icl~llk~--tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Skrs   94 (381)
T KOG0311|consen   41 DIQVICPICLSLLKK--TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRS   94 (381)
T ss_pred             hhhhccHHHHHHHHh--hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccccc
Confidence            346679999998854  2334569999999999999976 5789999998865443

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

Probab=97.96  E-value=1.3e-06  Score=82.65  Aligned_cols=54  Identities=26%  Similarity=0.487  Sum_probs=44.3

Q ss_pred             CCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCCCC
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPV  210 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~~~  210 (212)
                      ...|+|||-.|..+......+|+|.||..||..|-+.-++||+||.++.--..+
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~V~  176 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEVKVL  176 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhheeeee
Confidence            446999999997665555677999999999999999999999999987543333

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

Probab=97.81  E-value=5.7e-06  Score=78.47  Aligned_cols=49  Identities=31%  Similarity=0.614  Sum_probs=41.8

Q ss_pred             CCccccccccccCCCCeEEcCCCCcccHHHHHHHHh-cCCCCCcccccccCCC
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME-RSDTCPVCNQEMIFDL  208 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~-~~~tCPvCr~~l~~~~  208 (212)
                      -..|+.|-..|..   .++++|+|.||..||..-++ |..+||.|...+-.+|
T Consensus       643 ~LkCs~Cn~R~Kd---~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD  692 (698)
T KOG0978|consen  643 LLKCSVCNTRWKD---AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND  692 (698)
T ss_pred             ceeCCCccCchhh---HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence            4489999998876   77899999999999999995 4678999999886655

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

Probab=97.77  E-value=1.7e-05  Score=52.22  Aligned_cols=43  Identities=33%  Similarity=0.758  Sum_probs=29.8

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc--CCCCCc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER--SDTCPV  199 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~--~~tCPv  199 (212)
                      .-...|||.+..|.  +|++...|||.|-.+.|.+||++  ...||+
T Consensus         9 ~~~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen    9 TISLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             B--SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             EeccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            44668999999884  57888899999999999999944  457998

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

Probab=97.61  E-value=3.3e-05  Score=77.36  Aligned_cols=50  Identities=32%  Similarity=0.803  Sum_probs=43.7

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC----------CCCCcccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS----------DTCPVCNQEM  204 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~----------~tCPvCr~~l  204 (212)
                      +.+|+|.||+-+--..-|.+.|.|+|+||..|...-|++.          -+||+|+.+|
T Consensus      3484 D~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~I 3543 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKI 3543 (3738)
T ss_pred             ccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchh
Confidence            4678999999988778889999999999999999888764          3799999876

>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]

Probab=97.56  E-value=3.2e-05  Score=69.76  Aligned_cols=52  Identities=33%  Similarity=0.777  Sum_probs=42.9

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      ++...|+||...+..  +...+.|||.||..||.+|+..+..||+|++.+....
T Consensus        19 ~~~l~C~~C~~vl~~--p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~   70 (391)
T KOG0297|consen   19 DENLLCPICMSVLRD--PVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAE   70 (391)
T ss_pred             cccccCccccccccC--CCCCCCCCCcccccccchhhccCcCCcccccccchhh
Confidence            456779999998755  3434689999999999999999999999998876544

>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.55  E-value=5.7e-05  Score=66.25  Aligned_cols=48  Identities=25%  Similarity=0.632  Sum_probs=39.7

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCc-ccHHHHHHHHhcCCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHH-FHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~-FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      +....|.|||.+-..   ..+|||.|. .|.+|.+.-.-+.+.||+||+.+.
T Consensus       288 ~~gkeCVIClse~rd---t~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~  336 (349)
T KOG4265|consen  288 ESGKECVICLSESRD---TVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIE  336 (349)
T ss_pred             cCCCeeEEEecCCcc---eEEecchhhehhHhHHHHHHHhhcCCCccccchH
Confidence            346689999997654   778999996 799999997767889999999763

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

Probab=97.54  E-value=0.0003  Score=67.61  Aligned_cols=49  Identities=33%  Similarity=0.717  Sum_probs=38.2

Q ss_pred             ccCCCccccccccccCCCCeE-EcCCCCcccHHHHHHHHhcC-------CCCCcccc
Q 028200          154 IEEEDVCPTCLEEYDAENPRI-ITKCEHHFHLACIFEWMERS-------DTCPVCNQ  202 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~~~-~l~C~H~FH~~CI~~Wl~~~-------~tCPvCr~  202 (212)
                      ..+...|.||+|.+....++. ...|=|+||+.||.+|-+..       -.||.|..
T Consensus       188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs  244 (950)
T KOG1952|consen  188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS  244 (950)
T ss_pred             hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence            455668999999997655443 45689999999999999653       25999983

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

Probab=97.47  E-value=3.4e-05  Score=66.18  Aligned_cols=51  Identities=25%  Similarity=0.744  Sum_probs=42.5

Q ss_pred             CccccccccccCCCCeEEcCCCCcccHHHHHHHHhc-----------------------CCCCCcccccccCCC
Q 028200          158 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-----------------------SDTCPVCNQEMIFDL  208 (212)
Q Consensus       158 ~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~-----------------------~~tCPvCr~~l~~~~  208 (212)
                      ..|.|||--|......+.+.|-|.||..|+-+.|.-                       ...|||||..|..+.
T Consensus       116 gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~  189 (368)
T KOG4445|consen  116 GQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEE  189 (368)
T ss_pred             CceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccc
Confidence            359999999988888899999999999999887731                       236999999886553

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

Probab=97.44  E-value=4.4e-05  Score=61.91  Aligned_cols=45  Identities=27%  Similarity=0.761  Sum_probs=40.5

Q ss_pred             CCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccc
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEM  204 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l  204 (212)
                      ...|.||-++|..   ++++.|||.||..|...-++.-.+|-+|.+.+
T Consensus       196 PF~C~iCKkdy~s---pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t  240 (259)
T COG5152         196 PFLCGICKKDYES---PVVTECGHSFCSLCAIRKYQKGDECGVCGKAT  240 (259)
T ss_pred             ceeehhchhhccc---hhhhhcchhHHHHHHHHHhccCCcceecchhh
Confidence            4489999999977   67899999999999999999999999998865

>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A

Probab=97.33  E-value=0.00013  Score=46.04  Aligned_cols=40  Identities=28%  Similarity=0.904  Sum_probs=27.9

Q ss_pred             cccccccccCCCCeEEcCCC-----CcccHHHHHHHHhc--CCCCCcc
Q 028200          160 CPTCLEEYDAENPRIITKCE-----HHFHLACIFEWMER--SDTCPVC  200 (212)
Q Consensus       160 C~ICle~~~~~~~~~~l~C~-----H~FH~~CI~~Wl~~--~~tCPvC  200 (212)
                      |-||++.-..+. ..+.||.     -..|..|+.+|+..  +.+|++|
T Consensus         1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            789999876655 4567773     58899999999974  5679988

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

Probab=97.32  E-value=6.2e-05  Score=66.69  Aligned_cols=48  Identities=33%  Similarity=0.682  Sum_probs=39.8

Q ss_pred             cCCCccccccccccC-CCCeEEcCCCCcccHHHHHHHHhcC--CCCCcccc
Q 028200          155 EEEDVCPTCLEEYDA-ENPRIITKCEHHFHLACIFEWMERS--DTCPVCNQ  202 (212)
Q Consensus       155 ee~~~C~ICle~~~~-~~~~~~l~C~H~FH~~CI~~Wl~~~--~tCPvCr~  202 (212)
                      +-+..|..|-|.|.. .+.+..++|.|+||..|+.+.|+++  .+||-||+
T Consensus       363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            446689999999844 3456679999999999999999876  57999995

>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]

Probab=97.25  E-value=0.00012  Score=65.18  Aligned_cols=51  Identities=29%  Similarity=0.720  Sum_probs=41.4

Q ss_pred             CCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc--CCCCCcccccccCCCCC
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER--SDTCPVCNQEMIFDLPV  210 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~--~~tCPvCr~~l~~~~~~  210 (212)
                      ...|-||-|.   +..+.+-+|||..|..|+..|-..  .++||.||.+|+..+++
T Consensus       369 FeLCKICaen---dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~v  421 (563)
T KOG1785|consen  369 FELCKICAEN---DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPV  421 (563)
T ss_pred             HHHHHHhhcc---CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEeccccce
Confidence            3469999884   344778899999999999999844  47899999999876654

>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.25  E-value=0.00018  Score=64.74  Aligned_cols=48  Identities=27%  Similarity=0.722  Sum_probs=41.6

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      ..+..|.||+..+..   .+.++|||.||..||.+-|..+..||.||.++.
T Consensus        82 ~sef~c~vc~~~l~~---pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~  129 (398)
T KOG4159|consen   82 RSEFECCVCSRALYP---PVVTPCGHSFCLECLDRSLDQETECPLCRDELV  129 (398)
T ss_pred             cchhhhhhhHhhcCC---CccccccccccHHHHHHHhccCCCCcccccccc
Confidence            456679999887755   667899999999999999998999999999875

>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.25  E-value=6.4e-05  Score=48.50  Aligned_cols=45  Identities=24%  Similarity=0.625  Sum_probs=32.6

Q ss_pred             CccccccccccCCCCeEEcCCCCc-ccHHHHHHHHh-cCCCCCccccccc
Q 028200          158 DVCPTCLEEYDAENPRIITKCEHH-FHLACIFEWME-RSDTCPVCNQEMI  205 (212)
Q Consensus       158 ~~C~ICle~~~~~~~~~~l~C~H~-FH~~CI~~Wl~-~~~tCPvCr~~l~  205 (212)
                      +.|.||+|.-..   .++--|||. .|..|-.+-++ .+..||+||.++.
T Consensus         8 dECTICye~pvd---sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    8 DECTICYEHPVD---SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             cceeeeccCcch---HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            669999985422   234569996 67888665444 6889999999763

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=97.17  E-value=0.00023  Score=61.85  Aligned_cols=35  Identities=20%  Similarity=0.552  Sum_probs=27.4

Q ss_pred             EEcCCCCcccHHHHHHHH-hcCCCCCcccccccCCC
Q 028200          174 IITKCEHHFHLACIFEWM-ERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       174 ~~l~C~H~FH~~CI~~Wl-~~~~tCPvCr~~l~~~~  208 (212)
                      .+..|||.||..||...+ .....||+|++.+..+.
T Consensus        22 ~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~   57 (309)
T TIGR00570        22 MVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNN   57 (309)
T ss_pred             ccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence            344899999999999955 55678999998775443

All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.06  E-value=0.00018  Score=61.59  Aligned_cols=45  Identities=27%  Similarity=0.613  Sum_probs=40.4

Q ss_pred             CCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccc
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEM  204 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l  204 (212)
                      .+.|-||...|..   .+++.|+|.||..|-..-+++...|.+|.+.+
T Consensus       241 Pf~c~icr~~f~~---pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t  285 (313)
T KOG1813|consen  241 PFKCFICRKYFYR---PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQT  285 (313)
T ss_pred             Ccccccccccccc---chhhcCCceeehhhhccccccCCcceeccccc
Confidence            3469999999976   67899999999999999999999999998876

>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.04  E-value=0.00025  Score=62.82  Aligned_cols=27  Identities=41%  Similarity=1.178  Sum_probs=23.6

Q ss_pred             EcCCCCcccHHHHHHHHhcC---CCCCccc
Q 028200          175 ITKCEHHFHLACIFEWMERS---DTCPVCN  201 (212)
Q Consensus       175 ~l~C~H~FH~~CI~~Wl~~~---~tCPvCr  201 (212)
                      +-.|||+||..|+.+|++.-   ..||+|+
T Consensus        23 i~~cGhifh~~cl~qwfe~~Ps~R~cpic~   52 (465)
T KOG0827|consen   23 IGTCGHIFHTTCLTQWFEGDPSNRGCPICQ   52 (465)
T ss_pred             ccchhhHHHHHHHHHHHccCCccCCCCcee
Confidence            44599999999999999873   5799998

>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length

Probab=97.02  E-value=0.00027  Score=54.15  Aligned_cols=36  Identities=17%  Similarity=0.421  Sum_probs=29.7

Q ss_pred             CCccccccccccCCCCeEEcCCC------CcccHHHHHHHHh
Q 028200          157 EDVCPTCLEEYDAENPRIITKCE------HHFHLACIFEWME  192 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~------H~FH~~CI~~Wl~  192 (212)
                      ...|.||++.+.....++.+.||      |.||..|+.+|-+
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence            45699999999775567777785      9999999999943

The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.

>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]

Probab=96.99  E-value=0.0002  Score=62.20  Aligned_cols=51  Identities=27%  Similarity=0.565  Sum_probs=41.2

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD  207 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~  207 (212)
                      ....+|.+|--.|...  ..++.|-|.||.+||.+.|+.++.||.|+..+-..
T Consensus        13 n~~itC~LC~GYliDA--TTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   13 NPHITCRLCGGYLIDA--TTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             ccceehhhccceeecc--hhHHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            3456799998887553  34567999999999999999999999998766433

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.98  E-value=0.00062  Score=57.06  Aligned_cols=55  Identities=13%  Similarity=0.274  Sum_probs=47.9

Q ss_pred             CCCccccccccccCCCCeEEc-CCCCcccHHHHHHHHhcCCCCCcccccccCCCCC
Q 028200          156 EEDVCPTCLEEYDAENPRIIT-KCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPV  210 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l-~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~~~  210 (212)
                      ...+||||.+.+....+...| +|||+|+.+|+.+.++.-..||||.+.+..++.|
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI  275 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDII  275 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceE
Confidence            456899999999877776665 5999999999999999999999999999887755

>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.96  E-value=0.00086  Score=57.02  Aligned_cols=49  Identities=33%  Similarity=0.676  Sum_probs=39.8

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc--CCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER--SDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~--~~tCPvCr~~l~  205 (212)
                      ....+|++|-+.  +..|-+..+|+|+||.-||..-+.-  +-+||.|.....
T Consensus       237 t~~~~C~~Cg~~--PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  237 TSDTECPVCGEP--PTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cCCceeeccCCC--CCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            456689999885  4567788899999999999987653  468999988764

>PHA02862 5L protein; Provisional

Probab=96.95  E-value=0.00051  Score=53.12  Aligned_cols=47  Identities=21%  Similarity=0.620  Sum_probs=35.4

Q ss_pred             CCccccccccccCCCCeEEcCC-----CCcccHHHHHHHHhc--CCCCCcccccccCC
Q 028200          157 EDVCPTCLEEYDAENPRIITKC-----EHHFHLACIFEWMER--SDTCPVCNQEMIFD  207 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C-----~H~FH~~CI~~Wl~~--~~tCPvCr~~l~~~  207 (212)
                      .+.|-||+++-+.+    .-||     ....|..|+.+|++.  +..|++|+.+..++
T Consensus         2 ~diCWIC~~~~~e~----~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik   55 (156)
T PHA02862          2 SDICWICNDVCDER----NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK   55 (156)
T ss_pred             CCEEEEecCcCCCC----cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence            35799999986432    2455     478999999999965  46799999987543

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=96.71  E-value=0.0014  Score=51.57  Aligned_cols=49  Identities=29%  Similarity=0.706  Sum_probs=36.1

Q ss_pred             ccCCCccccccccccCCCCeEEcCC--CC---cccHHHHHHHHhcC--CCCCcccccccC
Q 028200          154 IEEEDVCPTCLEEYDAENPRIITKC--EH---HFHLACIFEWMERS--DTCPVCNQEMIF  206 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~~~~l~C--~H---~FH~~CI~~Wl~~~--~tCPvCr~~l~~  206 (212)
                      ...+..|-||.++....    .-||  ..   ..|.+|+.+|+..+  .+|++|+++..+
T Consensus         5 s~~~~~CRIC~~~~~~~----~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i   60 (162)
T PHA02825          5 SLMDKCCWICKDEYDVV----TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNI   60 (162)
T ss_pred             CCCCCeeEecCCCCCCc----cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEE
Confidence            45677899999885432    2355  33   67999999999664  579999987644

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=96.56  E-value=0.0012  Score=42.73  Aligned_cols=47  Identities=26%  Similarity=0.491  Sum_probs=36.4

Q ss_pred             CccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCCC
Q 028200          158 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLP  209 (212)
Q Consensus       158 ~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~~  209 (212)
                      ..|-.|...   +....+++|||..+..|..-|  +.+-||+|.+.+..+++
T Consensus         8 ~~~~~~~~~---~~~~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~~~~~   54 (55)
T PF14447_consen    8 QPCVFCGFV---GTKGTVLPCGHLICDNCFPGE--RYNGCPFCGTPFEFDDP   54 (55)
T ss_pred             eeEEEcccc---ccccccccccceeeccccChh--hccCCCCCCCcccCCCC
Confidence            345555543   444678999999999998865  88899999999987775

>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

Probab=96.45  E-value=0.0022  Score=46.79  Aligned_cols=33  Identities=24%  Similarity=0.555  Sum_probs=27.0

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHH
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIF  188 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~  188 (212)
                      .++..|+||-..+.. ....+.||||.||..|+.
T Consensus        76 ~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence            345669999999865 556778999999999975

Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].

>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.31  E-value=0.0024  Score=56.24  Aligned_cols=48  Identities=23%  Similarity=0.660  Sum_probs=40.7

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      .|++.|+||.-.   ....+..||+|.-|.+||.+-|-+++.|=.|+..+.
T Consensus       420 sEd~lCpICyA~---pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~  467 (489)
T KOG4692|consen  420 SEDNLCPICYAG---PINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVI  467 (489)
T ss_pred             cccccCcceecc---cchhhccCCCCchHHHHHHHHHhcCCeeeEecceee
Confidence            567789999763   334667899999999999999999999999998764

>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.31  E-value=0.0025  Score=57.01  Aligned_cols=37  Identities=24%  Similarity=0.723  Sum_probs=29.3

Q ss_pred             cCCCCeEEcCCCCcccHHHHHHHHhc--CCCCCcccccc
Q 028200          168 DAENPRIITKCEHHFHLACIFEWMER--SDTCPVCNQEM  204 (212)
Q Consensus       168 ~~~~~~~~l~C~H~FH~~CI~~Wl~~--~~tCPvCr~~l  204 (212)
                      ..++....+.|||.|...||.+||-+  ...||.|..+-
T Consensus        17 ~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka   55 (463)
T KOG1645|consen   17 AGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA   55 (463)
T ss_pred             cCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence            34555677899999999999999953  35799997654

>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.27  E-value=0.0024  Score=57.18  Aligned_cols=46  Identities=22%  Similarity=0.383  Sum_probs=38.3

Q ss_pred             CCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc--------CCCCCcccc
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER--------SDTCPVCNQ  202 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~--------~~tCPvCr~  202 (212)
                      -..|.||+++....+..+.++|+|+||..|+...+..        .-+||-++-
T Consensus       184 lf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  184 LFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             cccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            3469999999988788999999999999999999854        246887653

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

Probab=96.25  E-value=0.0043  Score=39.26  Aligned_cols=45  Identities=27%  Similarity=0.646  Sum_probs=22.8

Q ss_pred             cccccccccCCCC-eEEcCCCCcccHHHHHHHHh-cCCCCCcccccc
Q 028200          160 CPTCLEEYDAENP-RIITKCEHHFHLACIFEWME-RSDTCPVCNQEM  204 (212)
Q Consensus       160 C~ICle~~~~~~~-~~~l~C~H~FH~~CI~~Wl~-~~~tCPvCr~~l  204 (212)
                      ||+|.++++.... ..--+||+.++..|...-++ ..+.||-||+..
T Consensus         1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            7999999944332 22235799999999999886 478999999864

>PHA03096 p28-like protein; Provisional

Probab=96.14  E-value=0.003  Score=54.66  Aligned_cols=45  Identities=33%  Similarity=0.696  Sum_probs=31.3

Q ss_pred             CccccccccccCC-----CCeEEcCCCCcccHHHHHHHHhcC---CCCCcccc
Q 028200          158 DVCPTCLEEYDAE-----NPRIITKCEHHFHLACIFEWMERS---DTCPVCNQ  202 (212)
Q Consensus       158 ~~C~ICle~~~~~-----~~~~~l~C~H~FH~~CI~~Wl~~~---~tCPvCr~  202 (212)
                      ..|.||+|.....     --.++..|.|.||..||..|...+   .+||.||.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            5699999986432     113345699999999999999543   34554443

>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

Probab=96.14  E-value=0.0024  Score=40.04  Aligned_cols=43  Identities=30%  Similarity=0.798  Sum_probs=26.6

Q ss_pred             cccccccccCCCCeEEcCC-CCcccHHHHHHHHhcCCCCCcccccccCC
Q 028200          160 CPTCLEEYDAENPRIITKC-EHHFHLACIFEWMERSDTCPVCNQEMIFD  207 (212)
Q Consensus       160 C~ICle~~~~~~~~~~l~C-~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~  207 (212)
                      |--|+-....     +..| .|..|..|+...|.+++.||+|.++++.+
T Consensus         5 CKsCWf~~k~-----Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen    5 CKSCWFANKG-----LIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             --SS-S--SS-----EEE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             ChhhhhcCCC-----eeeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            6667654433     5568 69999999999999999999999988754

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.

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

Probab=96.13  E-value=0.0023  Score=59.05  Aligned_cols=52  Identities=35%  Similarity=0.689  Sum_probs=41.1

Q ss_pred             ccCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc-----CCCCCcccccccCCC
Q 028200          154 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-----SDTCPVCNQEMIFDL  208 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~-----~~tCPvCr~~l~~~~  208 (212)
                      ..++..|.+|-+.-+.   .+.+.|.|.||.-||.+++..     +-+||+|-..+..|.
T Consensus       533 nk~~~~C~lc~d~aed---~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDl  589 (791)
T KOG1002|consen  533 NKGEVECGLCHDPAED---YIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDL  589 (791)
T ss_pred             ccCceeecccCChhhh---hHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccc
Confidence            3556689999986443   678899999999999988853     468999988876653

>PF04641 Rtf2: Rtf2 RING-finger

Probab=96.09  E-value=0.0057  Score=52.26  Aligned_cols=53  Identities=23%  Similarity=0.508  Sum_probs=41.7

Q ss_pred             cCCCccccccccccCCCCeEE-cCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRII-TKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~-l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      .....|||...+|......+. -+|||+|-..+|.+- .....||+|.+.+...+
T Consensus       111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~f~~~D  164 (260)
T PF04641_consen  111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKPFTEED  164 (260)
T ss_pred             CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCccccCC
Confidence            556789999999965544444 479999999999996 34668999999886544

>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.96  E-value=0.0015  Score=56.12  Aligned_cols=42  Identities=21%  Similarity=0.676  Sum_probs=31.4

Q ss_pred             CCccccccccccCCCCeEEcCCCCcc-cHHHHHHHHhcCCCCCccccccc
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHHF-HLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~F-H~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      ...|.||++.-..   .+.|.|||.. |.+|=..    =+.|||||+.|+
T Consensus       300 ~~LC~ICmDaP~D---CvfLeCGHmVtCt~CGkr----m~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPRD---CVFLECGHMVTCTKCGKR----MNECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCcc---eEEeecCcEEeehhhccc----cccCchHHHHHH
Confidence            5679999996544   7789999964 6666443    348999999763

>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.93  E-value=0.0057  Score=50.80  Aligned_cols=50  Identities=26%  Similarity=0.544  Sum_probs=40.0

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc--------CCCCCcccccccC
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER--------SDTCPVCNQEMIF  206 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~--------~~tCPvCr~~l~~  206 (212)
                      -...|..|-..+..++. +.|-|-|.||.+|+.+|--.        .-.||.|.++|.-
T Consensus        49 Y~pNC~LC~t~La~gdt-~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP  106 (299)
T KOG3970|consen   49 YNPNCRLCNTPLASGDT-TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP  106 (299)
T ss_pred             CCCCCceeCCccccCcc-eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence            34469999888877774 46779999999999999854        2479999998863

>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.84  E-value=0.0063  Score=48.79  Aligned_cols=53  Identities=23%  Similarity=0.610  Sum_probs=36.7

Q ss_pred             cCCCccccccccccCCC----CeEEcCCCCcccHHHHHHHHhc------C-----CCCCcccccccCC
Q 028200          155 EEEDVCPTCLEEYDAEN----PRIITKCEHHFHLACIFEWMER------S-----DTCPVCNQEMIFD  207 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~----~~~~l~C~H~FH~~CI~~Wl~~------~-----~tCPvCr~~l~~~  207 (212)
                      ++...|.||+-.--.|.    ..--..||.-||.-|+..||+.      +     +.||+|-+++..+
T Consensus       163 d~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK  230 (234)
T KOG3268|consen  163 DELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK  230 (234)
T ss_pred             hhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence            34446999976432222    1223569999999999999964      1     5799999887554

>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.64  E-value=0.0078  Score=53.08  Aligned_cols=44  Identities=30%  Similarity=0.708  Sum_probs=32.9

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCccccccc
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      ..+.|.||+++...   .+.++|||.-+  |+.--.. ..+||+||+.+.
T Consensus       304 ~p~lcVVcl~e~~~---~~fvpcGh~cc--ct~cs~~-l~~CPvCR~rI~  347 (355)
T KOG1571|consen  304 QPDLCVVCLDEPKS---AVFVPCGHVCC--CTLCSKH-LPQCPVCRQRIR  347 (355)
T ss_pred             CCCceEEecCCccc---eeeecCCcEEE--chHHHhh-CCCCchhHHHHH
Confidence            45579999998755   67899999966  7666432 334999998763

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.39  E-value=0.01  Score=52.08  Aligned_cols=53  Identities=25%  Similarity=0.579  Sum_probs=37.1

Q ss_pred             ccccCCCccccccccccCCCCeE-EcCCCCcccHHHHHHHHh-cCCCCCcccccc
Q 028200          152 AVIEEEDVCPTCLEEYDAENPRI-ITKCEHHFHLACIFEWME-RSDTCPVCNQEM  204 (212)
Q Consensus       152 ~~~ee~~~C~ICle~~~~~~~~~-~l~C~H~FH~~CI~~Wl~-~~~tCPvCr~~l  204 (212)
                      .+++++|.||.|+|+++..+.-. --+||-..|.-|...--+ -++.||.||...
T Consensus         9 ~sedeed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y   63 (480)
T COG5175           9 NSEDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKY   63 (480)
T ss_pred             ccccccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhc
Confidence            45567778999999997655333 356898877777554322 257899999854

>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=95.36  E-value=0.016  Score=51.07  Aligned_cols=50  Identities=24%  Similarity=0.478  Sum_probs=39.5

Q ss_pred             ccccCCCccccccccccCCCCeEEcCCCCcccHHHHHHH--HhcCCCCCcccccc
Q 028200          152 AVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEW--MERSDTCPVCNQEM  204 (212)
Q Consensus       152 ~~~ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~W--l~~~~tCPvCr~~l  204 (212)
                      ..+|++..|-||-+.+..   ..++||+|..|.-|-.+-  |=..+.||+||.++
T Consensus        56 dtDEen~~C~ICA~~~TY---s~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          56 DTDEENMNCQICAGSTTY---SARYPCGHQICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             ccccccceeEEecCCceE---EEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence            345777789999987765   668999999999998653  33467899999864

>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)

Probab=95.05  E-value=0.0097  Score=36.76  Aligned_cols=41  Identities=22%  Similarity=0.600  Sum_probs=22.1

Q ss_pred             cccccccccCCCCeEEcCCCCcccHHHHHHHHhcCC--CCCcc
Q 028200          160 CPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD--TCPVC  200 (212)
Q Consensus       160 C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~--tCPvC  200 (212)
                      |.+|-+....|..-....|+=.+|..|+..+++...  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            567777665543222225888999999999997765  79988

; PDB: 3NW0_A 2CT0_A.

>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.01  E-value=0.02  Score=51.18  Aligned_cols=47  Identities=26%  Similarity=0.513  Sum_probs=40.3

Q ss_pred             CccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC---CCCCcccccc
Q 028200          158 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS---DTCPVCNQEM  204 (212)
Q Consensus       158 ~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~---~tCPvCr~~l  204 (212)
                      .+|||=.++-..+||+..|.|||+...+=|.+-.+..   -+||+|-.+.
T Consensus       335 F~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~  384 (394)
T KOG2817|consen  335 FICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ  384 (394)
T ss_pred             eecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence            3899999999999999999999999999999966543   4799996543

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

Probab=94.91  E-value=0.012  Score=51.44  Aligned_cols=51  Identities=29%  Similarity=0.705  Sum_probs=40.9

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      +...||||+-.-  .|+.++.-=|-+||..||...+...+.|||=..++.+++
T Consensus       299 ~~~~CpvClk~r--~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~v~~  349 (357)
T KOG0826|consen  299 DREVCPVCLKKR--QNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPASVDH  349 (357)
T ss_pred             ccccChhHHhcc--CCCceEEecceEEeHHHHHHHHHhcCCCCccCCcchHHH
Confidence            445799999865  445555556999999999999999999999877766554

>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=94.88  E-value=0.0015  Score=58.09  Aligned_cols=48  Identities=19%  Similarity=0.475  Sum_probs=40.2

Q ss_pred             ccccccccccCC-CCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccC
Q 028200          159 VCPTCLEEYDAE-NPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIF  206 (212)
Q Consensus       159 ~C~ICle~~~~~-~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~  206 (212)
                      .|+||.+.|... +....+.|||.+|.+||.+||.....||-|+.++..
T Consensus       198 sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~  246 (465)
T KOG0827|consen  198 SLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPK  246 (465)
T ss_pred             hhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhh
Confidence            599999988554 334457799999999999999999999999998753

>KOG1940 consensus Zn-finger protein [General function prediction only]

Probab=94.88  E-value=0.014  Score=50.12  Aligned_cols=45  Identities=31%  Similarity=0.605  Sum_probs=37.2

Q ss_pred             Ccccccccccc-CCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccc
Q 028200          158 DVCPTCLEEYD-AENPRIITKCEHHFHLACIFEWMERSDTCPVCNQ  202 (212)
Q Consensus       158 ~~C~ICle~~~-~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~  202 (212)
                      ..||||.|.+. ....+..++|||.-|..|..+-....=+||+|.+
T Consensus       159 ~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  159 FNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             CCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence            34999999863 3455667999999999999988877789999987

>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

Probab=94.50  E-value=0.042  Score=43.28  Aligned_cols=33  Identities=21%  Similarity=0.609  Sum_probs=22.5

Q ss_pred             CCccccccccccCCCCeEEcCCC-------------CcccHHHHHHHHh
Q 028200          157 EDVCPTCLEEYDAENPRIITKCE-------------HHFHLACIFEWME  192 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~-------------H~FH~~CI~~Wl~  192 (212)
                      +.+||||||--   +..++|.|.             -.-|..|+++.-+
T Consensus         2 d~~CpICme~P---HNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    2 DVTCPICMEHP---HNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CccCceeccCC---CceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            55799999953   335666663             3457889998753

The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.

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

Probab=94.44  E-value=0.02  Score=55.62  Aligned_cols=42  Identities=29%  Similarity=0.777  Sum_probs=34.5

Q ss_pred             CccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccc
Q 028200          158 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEM  204 (212)
Q Consensus       158 ~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l  204 (212)
                      .+|.+|--..  +-|.+...|||.||..|+.   +....||-|+.++
T Consensus       841 skCs~C~~~L--dlP~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  841 SKCSACEGTL--DLPFVHFLCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeecccCCcc--ccceeeeecccHHHHHhhc---cCcccCCccchhh
Confidence            4799997766  4478889999999999998   5667899998743

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

Probab=94.29  E-value=0.011  Score=56.90  Aligned_cols=47  Identities=26%  Similarity=0.674  Sum_probs=38.2

Q ss_pred             CccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC--CCCCcccccccCCC
Q 028200          158 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS--DTCPVCNQEMIFDL  208 (212)
Q Consensus       158 ~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~--~tCPvCr~~l~~~~  208 (212)
                      ..|.||++    .+..+.+.|+|.||..|+.+-++..  ..||+||..+..+.
T Consensus       455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~  503 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKK  503 (674)
T ss_pred             cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHH
Confidence            57999999    4457789999999999999988664  36999998765443

>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=93.92  E-value=0.021  Score=45.15  Aligned_cols=29  Identities=24%  Similarity=0.533  Sum_probs=26.0

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccH
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHL  184 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~  184 (212)
                      +.-+|.||||++..++.+..|+|--+||+
T Consensus       176 dkGECvICLEdL~~GdtIARLPCLCIYHK  204 (205)
T KOG0801|consen  176 DKGECVICLEDLEAGDTIARLPCLCIYHK  204 (205)
T ss_pred             cCCcEEEEhhhccCCCceeccceEEEeec
Confidence            44469999999999999999999999996

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.81  E-value=0.027  Score=47.61  Aligned_cols=50  Identities=26%  Similarity=0.704  Sum_probs=35.6

Q ss_pred             ccCCCccccccccccCCCCe--EEcCC-----CCcccHHHHHHHHhcC--------CCCCcccccc
Q 028200          154 IEEEDVCPTCLEEYDAENPR--IITKC-----EHHFHLACIFEWMERS--------DTCPVCNQEM  204 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~~--~~l~C-----~H~FH~~CI~~Wl~~~--------~tCPvCr~~l  204 (212)
                      .+.+..|=||+..=+ ++..  -+-||     .|..|..|+..|+..+        -+||.|+.+.
T Consensus        17 ~e~eR~CWiCF~Tde-Dn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY   81 (293)
T KOG3053|consen   17 QELERCCWICFATDE-DNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY   81 (293)
T ss_pred             cccceeEEEEeccCc-ccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence            355678999998532 3322  23456     5999999999999553        2699999875

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

Probab=93.73  E-value=0.04  Score=47.68  Aligned_cols=49  Identities=29%  Similarity=0.550  Sum_probs=35.7

Q ss_pred             CccccccccccCCCCeEEcCCCCcccHHHHHHHHhc-CCCCCcc-cccccCCC
Q 028200          158 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-SDTCPVC-NQEMIFDL  208 (212)
Q Consensus       158 ~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~-~~tCPvC-r~~l~~~~  208 (212)
                      ..|+.|---.  .++....-|+|.||.+||...|-- -..||.| |+.++.+.
T Consensus       275 LkCplc~~Ll--rnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld~  325 (427)
T COG5222         275 LKCPLCHCLL--RNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDG  325 (427)
T ss_pred             ccCcchhhhh--hCcccCccccchHHHHHHhhhhhhccccCCCcccccchhhc
Confidence            5799987754  344444458999999999988855 4689999 55555443

>KOG3002 consensus Zn finger protein [General function prediction only]

Probab=93.73  E-value=0.036  Score=48.35  Aligned_cols=43  Identities=26%  Similarity=0.583  Sum_probs=34.0

Q ss_pred             CCCccccccccccCCCCeEEcCC--CCcccHHHHHHHHhcCCCCCccccccc
Q 028200          156 EEDVCPTCLEEYDAENPRIITKC--EHHFHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C--~H~FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      +-..||||.+.+..    -+.+|  ||.-|..|-.   +.++.||.||.+|.
T Consensus        47 ~lleCPvC~~~l~~----Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   47 DLLDCPVCFNPLSP----PIFQCDNGHLACSSCRT---KVSNKCPTCRLPIG   91 (299)
T ss_pred             hhccCchhhccCcc----cceecCCCcEehhhhhh---hhcccCCccccccc
Confidence            34469999998865    24678  8999999976   46889999999875

>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]

Probab=92.31  E-value=0.076  Score=51.19  Aligned_cols=30  Identities=30%  Similarity=0.815  Sum_probs=25.8

Q ss_pred             CCCeEEcCCCCcccHHHHHHHHhcCCCCCc
Q 028200          170 ENPRIITKCEHHFHLACIFEWMERSDTCPV  199 (212)
Q Consensus       170 ~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPv  199 (212)
                      +...++..|+|+.|.+|..+|++....||-
T Consensus      1040 gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1040 GSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             ccchhhccccccccHHHHHHHHhcCCcCCC
Confidence            344566789999999999999999999984

>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]

Probab=92.11  E-value=0.095  Score=50.90  Aligned_cols=54  Identities=33%  Similarity=0.743  Sum_probs=41.6

Q ss_pred             cCCCccccccccccCCCCeEE-cCCC---CcccHHHHHHHHhcC--CCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRII-TKCE---HHFHLACIFEWMERS--DTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~-l~C~---H~FH~~CI~~Wl~~~--~tCPvCr~~l~~~~  208 (212)
                      ++...|.||.-+-..++++.. -+|.   -..|.+|+.+||.-+  .+|-+|..++.+++
T Consensus        10 ~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~   69 (1175)
T COG5183          10 EDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKD   69 (1175)
T ss_pred             ccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeee
Confidence            445679999998877776643 2342   568999999999765  57999999988775

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

Probab=92.09  E-value=0.038  Score=55.93  Aligned_cols=44  Identities=30%  Similarity=0.638  Sum_probs=36.9

Q ss_pred             CCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccc
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQ  202 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~  202 (212)
                      ...|.||++....  -..+..|||.|+..|+..|+..+..||+|+.
T Consensus      1153 ~~~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1153 HFVCEICLDILRN--QGGIAGCGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred             ccchHHHHHHHHh--cCCeeeechhHhhhHHHHHHHHhccCcchhh
Confidence            3489999998752  2346679999999999999999999999974

>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]

Probab=91.75  E-value=0.1  Score=45.06  Aligned_cols=48  Identities=27%  Similarity=0.697  Sum_probs=36.3

Q ss_pred             CCccccccccccCCCC-eEEcCCC-----CcccHHHHHHHHh--cCCCCCcccccc
Q 028200          157 EDVCPTCLEEYDAENP-RIITKCE-----HHFHLACIFEWME--RSDTCPVCNQEM  204 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~-~~~l~C~-----H~FH~~CI~~Wl~--~~~tCPvCr~~l  204 (212)
                      +..|-||.++....+. ....+|.     +..|..|+..|+.  .+..|.+|....
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~  133 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFF  133 (323)
T ss_pred             CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccc
Confidence            4679999997754332 4456773     7789999999997  567899998754

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

Probab=91.08  E-value=0.11  Score=50.91  Aligned_cols=39  Identities=28%  Similarity=0.614  Sum_probs=31.4

Q ss_pred             cccCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHh
Q 028200          153 VIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME  192 (212)
Q Consensus       153 ~~ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~  192 (212)
                      ..+-.+.|.||.-.+.. .+-.+.+|||.||.+||.+-+.
T Consensus       813 v~ep~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v~  851 (911)
T KOG2034|consen  813 VLEPQDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHVL  851 (911)
T ss_pred             EecCccchHHhcchhhc-CcceeeeccchHHHHHHHHHHH
Confidence            34667789999887744 3677889999999999998773

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=89.67  E-value=0.47  Score=30.71  Aligned_cols=46  Identities=17%  Similarity=0.556  Sum_probs=33.5

Q ss_pred             CCccccccccccC-CCCeEEcCCCCcccHHHHHHHHhcCCCCCc--ccccccC
Q 028200          157 EDVCPTCLEEYDA-ENPRIITKCEHHFHLACIFEWMERSDTCPV--CNQEMIF  206 (212)
Q Consensus       157 ~~~C~ICle~~~~-~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPv--Cr~~l~~  206 (212)
                      ...|++|-+.|.. ++.++...||=-+|..|..+    ...|-+  |...+.+
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~~~c~~~~~~   53 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCINYSCGTGFEW   53 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEeccCCCCccc
Confidence            4569999999974 45566677999999999654    566665  6655443

>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=88.44  E-value=0.23  Score=46.86  Aligned_cols=49  Identities=35%  Similarity=0.775  Sum_probs=40.9

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPV  210 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~~~  210 (212)
                      +..+.|.||+++.    ....++|.   |.-|+.+|+..+..||+|++.+..++..
T Consensus       477 ~~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~~  525 (543)
T KOG0802|consen  477 EPNDVCAICYQEM----SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDDFL  525 (543)
T ss_pred             cccCcchHHHHHH----Hhcccccc---chhHHHhhhhhccccCCCchhhhccccc
Confidence            4567799999988    24456777   9999999999999999999998887754

>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

Probab=88.39  E-value=0.62  Score=29.57  Aligned_cols=43  Identities=23%  Similarity=0.550  Sum_probs=21.0

Q ss_pred             CccccccccccCCCCeEEcCCCCcccHHHHHHHHhc---C--CCCCccccc
Q 028200          158 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER---S--DTCPVCNQE  203 (212)
Q Consensus       158 ~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~---~--~tCPvCr~~  203 (212)
                      ..|||....+  ..|++...|.|.-+.+ +..||+.   .  -.||+|++.
T Consensus         3 L~CPls~~~i--~~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRI--RIPVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB---SSEEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEE--EeCccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            3588888876  4477778899985432 3445533   2  259999863

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.

>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]

Probab=87.82  E-value=0.2  Score=47.40  Aligned_cols=44  Identities=27%  Similarity=0.725  Sum_probs=31.1

Q ss_pred             cCCCcccccccc-----ccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCccc
Q 028200          155 EEEDVCPTCLEE-----YDAENPRIITKCEHHFHLACIFEWMERSDTCPVCN  201 (212)
Q Consensus       155 ee~~~C~ICle~-----~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr  201 (212)
                      .....|.||...     |..++......|+++||.+|+..   .+.-||.|-
T Consensus       509 ~~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r---~s~~CPrC~  557 (580)
T KOG1829|consen  509 GKGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRR---KSPCCPRCE  557 (580)
T ss_pred             cCeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhc---cCCCCCchH
Confidence            456678888433     34455666788999999999554   445599994

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

Probab=87.52  E-value=0.23  Score=43.28  Aligned_cols=29  Identities=28%  Similarity=0.843  Sum_probs=22.2

Q ss_pred             EEcCCCCcccHHHHHHHHhcCCCCCcccccc
Q 028200          174 IITKCEHHFHLACIFEWMERSDTCPVCNQEM  204 (212)
Q Consensus       174 ~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l  204 (212)
                      ++.+|.|+||++|...  ..-+.||.|...+
T Consensus       105 RmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen  105 RMIPCKHVFCLECARS--DSDKICPLCDDRV  133 (389)
T ss_pred             cccccchhhhhhhhhc--CccccCcCcccHH
Confidence            4689999999999654  3346799996543

>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=87.05  E-value=0.23  Score=47.24  Aligned_cols=43  Identities=19%  Similarity=0.482  Sum_probs=31.8

Q ss_pred             CCccccccccccCC-CCeEEcCCCCcccHHHHHHHHhcCCCCCcccc
Q 028200          157 EDVCPTCLEEYDAE-NPRIITKCEHHFHLACIFEWMERSDTCPVCNQ  202 (212)
Q Consensus       157 ~~~C~ICle~~~~~-~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~  202 (212)
                      -..|+||+..|-.+ -..+.+.|||..|..|+..-..  .+|| |+.
T Consensus        11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn--~scp-~~~   54 (861)
T KOG3161|consen   11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN--ASCP-TKR   54 (861)
T ss_pred             HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh--ccCC-CCc
Confidence            44699999888443 3456788999999999998644  4588 543

>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=86.99  E-value=0.45  Score=41.64  Aligned_cols=46  Identities=26%  Similarity=0.520  Sum_probs=37.7

Q ss_pred             CccccccccccCCCCeEEcCCCCcccHHHHHHHHhc---CCCCCccccc
Q 028200          158 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER---SDTCPVCNQE  203 (212)
Q Consensus       158 ~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~---~~tCPvCr~~  203 (212)
                      ..||+=-|.-..+|++.++.|||+.-.+=++..-++   .-+||+|-..
T Consensus       337 FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~~  385 (396)
T COG5109         337 FICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPEM  385 (396)
T ss_pred             eeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCcc
Confidence            389999999899999999999999998888774433   2479999654

>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=86.88  E-value=0.22  Score=44.95  Aligned_cols=38  Identities=29%  Similarity=0.645  Sum_probs=28.5

Q ss_pred             CCcccccc-ccccCCCCeEEcCCCCcccHHHHHHHHhcC
Q 028200          157 EDVCPTCL-EEYDAENPRIITKCEHHFHLACIFEWMERS  194 (212)
Q Consensus       157 ~~~C~ICl-e~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~  194 (212)
                      ..+|.||+ +....+.-..+..|+|.||..|+.+-++.+
T Consensus       146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~  184 (384)
T KOG1812|consen  146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK  184 (384)
T ss_pred             cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh
Confidence            55799999 444443434468899999999999988754

>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]

Probab=86.86  E-value=0.16  Score=48.77  Aligned_cols=45  Identities=29%  Similarity=0.727  Sum_probs=36.4

Q ss_pred             CCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC---CCCCcccccc
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS---DTCPVCNQEM  204 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~---~tCPvCr~~l  204 (212)
                      ...|+||++.|..   .+.++|.|.|+..|+..-|+..   ..||+|+..+
T Consensus        21 ~lEc~ic~~~~~~---p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~   68 (684)
T KOG4362|consen   21 ILECPICLEHVKE---PSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDI   68 (684)
T ss_pred             hccCCceeEEeec---cchhhhhHHHHhhhhhceeeccCccccchhhhhhh
Confidence            4569999999866   3788999999999998877554   5799998654

>smart00249 PHD PHD zinc finger

Probab=86.40  E-value=0.43  Score=28.56  Aligned_cols=31  Identities=19%  Similarity=0.487  Sum_probs=23.2

Q ss_pred             ccccccccccCCCCeEEcCCCCcccHHHHHH
Q 028200          159 VCPTCLEEYDAENPRIITKCEHHFHLACIFE  189 (212)
Q Consensus       159 ~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~  189 (212)
                      .|.+|......+..+..-.|...||..|+..
T Consensus         1 ~C~~C~~~~~~~~~i~C~~C~~~~H~~C~~~   31 (47)
T smart00249        1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGP   31 (47)
T ss_pred             CcccCCCcCCCCCEEECCCCCchhhhhhCCC
Confidence            4788888765555455567999999999854

The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=85.56  E-value=0.61  Score=38.33  Aligned_cols=43  Identities=23%  Similarity=0.719  Sum_probs=32.3

Q ss_pred             cCCCcccccccc-----ccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccc
Q 028200          155 EEEDVCPTCLEE-----YDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQ  202 (212)
Q Consensus       155 ee~~~C~ICle~-----~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~  202 (212)
                      ..+..|-||-..     |+.++......|+-+||..|..     +..||-|..
T Consensus       150 ~kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~-----~~~CpkC~R  197 (202)
T PF13901_consen  150 QKGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR-----KKSCPKCAR  197 (202)
T ss_pred             hCCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC-----CCCCCCcHh
Confidence            346678888753     4555667778899999999976     267999943

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

Probab=85.08  E-value=0.5  Score=46.03  Aligned_cols=49  Identities=16%  Similarity=0.266  Sum_probs=34.8

Q ss_pred             CCCccccccccccC-C---CCeEEcCCCCcccHHHHHHHHhc------CCCCCcccccc
Q 028200          156 EEDVCPTCLEEYDA-E---NPRIITKCEHHFHLACIFEWMER------SDTCPVCNQEM  204 (212)
Q Consensus       156 e~~~C~ICle~~~~-~---~~~~~l~C~H~FH~~CI~~Wl~~------~~tCPvCr~~l  204 (212)
                      +.+.|.||+.++.. .   ....+-.|+|.||..||..|+.+      .-.|+.|..-|
T Consensus        95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci  153 (1134)
T KOG0825|consen   95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV  153 (1134)
T ss_pred             cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence            45678888888855 1   12223449999999999999965      34588887644

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

Probab=83.94  E-value=0.86  Score=39.29  Aligned_cols=36  Identities=22%  Similarity=0.533  Sum_probs=28.9

Q ss_pred             CCCCeEEcCCCCcccHHHHHHHHhcC-CCCCcccccc
Q 028200          169 AENPRIITKCEHHFHLACIFEWMERS-DTCPVCNQEM  204 (212)
Q Consensus       169 ~~~~~~~l~C~H~FH~~CI~~Wl~~~-~tCPvCr~~l  204 (212)
                      ....+..|+|||.|+..|+.+-+... ..||.||...
T Consensus        18 ~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen   18 GDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             cccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            34446678899999999999987665 5699999974

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=83.87  E-value=0.54  Score=40.75  Aligned_cols=31  Identities=19%  Similarity=0.563  Sum_probs=23.5

Q ss_pred             CCCcccHHHHHHHHh-------------cCCCCCcccccccCCC
Q 028200          178 CEHHFHLACIFEWME-------------RSDTCPVCNQEMIFDL  208 (212)
Q Consensus       178 C~H~FH~~CI~~Wl~-------------~~~tCPvCr~~l~~~~  208 (212)
                      |.-..|.+|+-+|+.             .+-+||.||+.+...+
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~d  368 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRD  368 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEee
Confidence            456778899998883             3568999999875543

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

Probab=83.66  E-value=0.68  Score=41.43  Aligned_cols=51  Identities=22%  Similarity=0.694  Sum_probs=33.6

Q ss_pred             cCCCccccccccccCCCCeEEcCC---------------------CCcccHHHHHHHHhc-------------CCCCCcc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKC---------------------EHHFHLACIFEWMER-------------SDTCPVC  200 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C---------------------~H~FH~~CI~~Wl~~-------------~~tCPvC  200 (212)
                      ++.+.|--|+..-  .+.++.-.|                     .=..|.+|+-+|+-.             +-.||.|
T Consensus       269 ~e~e~CigC~~~~--~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtC  346 (358)
T PF10272_consen  269 QELEPCIGCMQAQ--PNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTC  346 (358)
T ss_pred             cccCCccccccCC--CCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCC
Confidence            6777899998752  222222222                     345689999999932             3479999


Q ss_pred             cccccCC
Q 028200          201 NQEMIFD  207 (212)
Q Consensus       201 r~~l~~~  207 (212)
                      |+.+..-
T Consensus       347 Ra~FCil  353 (358)
T PF10272_consen  347 RAKFCIL  353 (358)
T ss_pred             cccceee
Confidence            9987543

They are purported to be transmembrane protein-precursors but their function is unknown.

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=83.07  E-value=0.65  Score=45.18  Aligned_cols=45  Identities=22%  Similarity=0.588  Sum_probs=34.2

Q ss_pred             CCccccccccccC-C---CCeEEcCCCCcccHHHHHHHHhcCCCCCcccc
Q 028200          157 EDVCPTCLEEYDA-E---NPRIITKCEHHFHLACIFEWMERSDTCPVCNQ  202 (212)
Q Consensus       157 ~~~C~ICle~~~~-~---~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~  202 (212)
                      +..|.-|++.... +   +..+++.|||.||..|+.--+.+++ |-.|..
T Consensus       784 e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~-~~~~~~  832 (846)
T KOG2066|consen  784 EERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA-CNIESG  832 (846)
T ss_pred             hhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc-cChhhc
Confidence            3369999988742 2   4677899999999999988877665 666643

>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=80.97  E-value=0.64  Score=29.04  Aligned_cols=44  Identities=23%  Similarity=0.519  Sum_probs=30.1

Q ss_pred             ccccccccccCCCCeEEcCCCCcccHHHHHHHHhc------CCCCCcccc
Q 028200          159 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER------SDTCPVCNQ  202 (212)
Q Consensus       159 ~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~------~~tCPvCr~  202 (212)
                      .|.||......+.-+..-.|+..||..|+..=.+.      .-.||.|+.
T Consensus         1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~   50 (51)
T PF00628_consen    1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP   50 (51)
T ss_dssp             EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred             eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence            48899985554555555679999999998765431      235777753

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....

>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]

Probab=80.46  E-value=0.68  Score=39.09  Aligned_cols=48  Identities=27%  Similarity=0.720  Sum_probs=34.6

Q ss_pred             CCcccccccc-ccCCCCeE-EcC-CCCcccHHHHHHHHhcC-CCCC--cccccc
Q 028200          157 EDVCPTCLEE-YDAENPRI-ITK-CEHHFHLACIFEWMERS-DTCP--VCNQEM  204 (212)
Q Consensus       157 ~~~C~ICle~-~~~~~~~~-~l~-C~H~FH~~CI~~Wl~~~-~tCP--vCr~~l  204 (212)
                      +..||||..+ |-..+-++ +-| |=|..|.+|+++-+.+. ..||  -|.+-+
T Consensus        10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL   63 (314)
T COG5220          10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL   63 (314)
T ss_pred             cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence            4479999976 33333333 334 99999999999999764 6799  787643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	212
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		9e-06
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		2e-05
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		5e-05
4epo_C	149	Crystal Structure Of Rnf8 Bound To The Ubc13MMS2 HE		2e-04
4ayc_A	138	Rnf8 Ring Domain Structure Length = 138		2e-04
4ayc_B	138	Rnf8 Ring Domain Structure Length = 138		2e-04
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		4e-04
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		5e-04

>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger Protein 24 Length = 74

Iteration: 1
 Score = 46.6 bits (109), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 16/48 (33%), Positives = 28/48 (58%)
Query: 158 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI 205
           ++C  CLE++   +   I  C+H FH  C+ +W+E    CP+CN  ++
Sbjct: 16  ELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVL 63

>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring Finger) Domain Of Ring Finger Protein 126 Length = 78

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 4/61 (6%)
Query: 144 SKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQE 203
           S +  HV + +E    CP C E+Y          C H FH +CI  W+E+ D+CPVC + 
Sbjct: 6   SGTEEHVGSGLE----CPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKS 61
Query: 204 M 204
           +
Sbjct: 62  L 62

>pdb|2L0B|A Chain A, Solution Nmr Structure Of Zinc Finger Domain Of E3 Ubiquitin-Protein Ligase Praja-1 From Homo Sapiens, Northeast Structural Genomics Consortium (Nesg) Target Hr4710b Length = 91

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 18/50 (36%), Positives = 26/50 (52%)
Query: 152 AVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCN 201
             + +E  CP C  EY   +      C H+FH  C+  W+++S TCPVC 
Sbjct: 35  GAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCR 84

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 130 NVELESTKE----LEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLA 185
           N ELE TKE    ++ +  + + H+  V+E E  C  C  EY  E   +   C H F   
Sbjct: 33  NKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIIC-SEYFIEA--VTLNCAHSFCSY 89
Query: 186 CIFEWMERSDTCPVCNQEM 204
           CI EWM+R   CP+C +++
Sbjct: 90  CINEWMKRKIECPICRKDI 108

>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure Length = 138

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 130 NVELESTKE----LEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLA 185
           N ELE TKE    ++ +  + + H+  V+E E  C  C  EY  E   +   C H F   
Sbjct: 22  NKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIIC-SEYFIEA--VTLNCAHSFCSY 78
Query: 186 CIFEWMERSDTCPVCNQEM 204
           CI EWM+R   CP+C +++
Sbjct: 79  CINEWMKRKIECPICRKDI 97

>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure Length = 138

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 130 NVELESTKE----LEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLA 185
           N ELE TKE    ++ +  + + H+  V+E E  C  C  EY  E   +   C H F   
Sbjct: 22  NKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIIC-SEYFIEA--VTLNCAHSFCSY 78
Query: 186 CIFEWMERSDTCPVCNQEM 204
           CI EWM+R   CP+C +++
Sbjct: 79  CINEWMKRKIECPICRKDI 97

>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein 38 Length = 75

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 13/48 (27%), Positives = 28/48 (58%)
Query: 156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQE 203
           E+ +C  C+ ++++     +  C H FH  C+ +W++ + TCP+C  +
Sbjct: 22  EQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRAD 69

>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5 Length = 55

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 160 CPTCLEEY-DAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI 205
           C  CL E  D E  R + +C H FH  C+  W+    TCP+C   ++
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	212
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	6e-14
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	2e-12
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	6e-11
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	8e-11
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	8e-11
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	1e-10
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	2e-10
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	4e-10
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	4e-10
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	5e-10
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	5e-10
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	1e-09
2ect_A	78	Ring finger protein 126; metal binding protein, st	1e-09
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	3e-09
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	5e-09
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	7e-09
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	8e-09
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	2e-08
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	2e-08
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	7e-08
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	1e-07
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	3e-07
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	7e-07
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	5e-06
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	7e-06
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	1e-05
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	3e-05
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	4e-05
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	6e-05
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	8e-05
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	9e-05
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	2e-04
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	3e-04
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	4e-04
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	9e-04

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

 Score = 63.8 bits (155), Expect = 6e-14
 Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 155 EEEDVCPTCLEEYDAEN-PRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIF 206
           +  D C  C  E   E+   +  +C H FH  C+  W+++++ CP+C Q+ + 
Sbjct: 24  QVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVV 76

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1 Length = 68

 Score = 59.3 bits (144), Expect = 2e-12
 Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 2/49 (4%)

Query: 155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQE 203
              + CP CLE+    N  +   C H F   CI  W+ ++ TCP+C   
Sbjct: 3   TVAERCPICLEDP--SNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVP 49

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A Length = 55

 Score = 55.0 bits (133), Expect = 6e-11
 Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 1/46 (2%)

Query: 157 EDVCPTCLEEY-DAENPRIITKCEHHFHLACIFEWMERSDTCPVCN 201
              CP CLE+   +     +  C H  H  C  E ++    CP+C+
Sbjct: 5   SSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCS 50

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

 Score = 55.2 bits (133), Expect = 8e-11
 Identities = 16/51 (31%), Positives = 28/51 (54%)

Query: 155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI 205
              ++C  CLE++   +   I  C+H FH  C+ +W+E    CP+CN  ++
Sbjct: 13  NLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVL 63

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

 Score = 55.1 bits (133), Expect = 8e-11
 Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 4/57 (7%)

Query: 144 SKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVC 200
           S      V  + +E+ C  C++        +I  C H F   CI +W +R   CP+C
Sbjct: 2   SSGSSGRVKQLTDEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRNCPIC 54

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

 Score = 55.0 bits (133), Expect = 1e-10
 Identities = 18/53 (33%), Positives = 26/53 (49%)

Query: 152 AVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEM 204
             + +E  CP C  EY   +      C H+FH  C+  W+++S TCPVC    
Sbjct: 35  GAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMF 87

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1 Length = 55

 Score = 53.7 bits (130), Expect = 2e-10
 Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 154 IEEEDVCPTCLEEY-DAENPRIITKCEHHFHLACIFEWMERSDTCPVC 200
           +++   C  CL E  D E  R + +C H FH  C+  W+    TCP+C
Sbjct: 2   MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLC 49

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

 Score = 53.2 bits (128), Expect = 4e-10
 Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 4/48 (8%)

Query: 160 CPTCLEEY----DAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQE 203
           CP C++ Y          + T+C H F   C+ + ++ ++TCP C ++
Sbjct: 6   CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKK 53

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

 Score = 53.0 bits (127), Expect = 4e-10
 Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 4/48 (8%)

Query: 160 CPTCLEEYD----AENPRIITKCEHHFHLACIFEWMERSDTCPVCNQE 203
           CP C++ Y          + T+C H F   C+ + ++ ++TCP C ++
Sbjct: 18  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKK 65

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens} Length = 69

 Score = 52.8 bits (127), Expect = 5e-10
 Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 2/58 (3%)

Query: 155 EEEDVCPTCLEEY-DAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPVD 211
           + E+ C  CL    + E+ R +  C H FH  C+ +W+  +  CP+C  ++   LP +
Sbjct: 12  DTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQLPSE 68

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

 Score = 52.8 bits (127), Expect = 5e-10
 Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 2/53 (3%)

Query: 151 VAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQE 203
           ++ +    +C  C       +   IT+C H F  +CI      S+ CP CN  
Sbjct: 9   LSELTPYILCSICKGYLI--DATTITECLHTFCKSCIVRHFYYSNRCPKCNIV 59

>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

 Score = 52.1 bits (125), Expect = 1e-09
 Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 4/48 (8%)

Query: 160 CPTCLEEYD----AENPRIITKCEHHFHLACIFEWMERSDTCPVCNQE 203
           CP C++ Y          + T+C H F   C+ + ++ ++TCP C ++
Sbjct: 13  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKK 60

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 78

 Score = 52.0 bits (125), Expect = 1e-09
 Identities = 18/51 (35%), Positives = 26/51 (50%)

Query: 154 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEM 204
           +     CP C E+Y          C H FH +CI  W+E+ D+CPVC + +
Sbjct: 12  VGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSL 62

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 75

 Score = 50.8 bits (122), Expect = 3e-09
 Identities = 14/47 (29%), Positives = 28/47 (59%), Gaps = 2/47 (4%)

Query: 155 EEEDVCPTCLEEY-DAENPRIITKCEHHFHLACIFEWMERSDTCPVC 200
            E+ +C  C+ ++   +  R++  C H FH  C+ +W++ + TCP+C
Sbjct: 21  SEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPIC 66

>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

 Score = 51.0 bits (122), Expect = 5e-09
 Identities = 15/62 (24%), Positives = 22/62 (35%), Gaps = 3/62 (4%)

Query: 144 SKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD-TCPVCNQ 202
           S      V  I E   C  C+E+    + R+   C      +CI  W+      CP C  
Sbjct: 9   SHMDEQSVESIAEVFRCFICMEK--LRDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRA 66

Query: 203 EM 204
            +
Sbjct: 67  PL 68

>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

 Score = 51.0 bits (122), Expect = 7e-09
 Identities = 14/68 (20%), Positives = 30/68 (44%), Gaps = 2/68 (2%)

Query: 143 LSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQ 202
           + ++    +  +    +C  C   +   +   I +C H F   CI  ++E S  CP+C+ 
Sbjct: 1   MHRTTRIKITELNPHLMCVLCGGYF--IDATTIIECLHSFCKTCIVRYLETSKYCPICDV 58

Query: 203 EMIFDLPV 210
           ++    P+
Sbjct: 59  QVHKTRPL 66

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus} Length = 117

 Score = 51.0 bits (121), Expect = 8e-09
 Identities = 13/47 (27%), Positives = 17/47 (36%)

Query: 160 CPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIF 206
                     E       C H FH  CI  W++    CP+ N+E  F
Sbjct: 66  QANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEF 112

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81

 Score = 49.1 bits (117), Expect = 2e-08
 Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 6/52 (11%)

Query: 155 EEEDV---CPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQE 203
           EEE++   C  C + +  +NP ++TKC H+F  +C  E    +  C +C+Q 
Sbjct: 10  EEEEIPFRCFICRQAF--QNP-VVTKCRHYFCESCALEHFRATPRCYICDQP 58

>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 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A Length = 106

 Score = 49.4 bits (117), Expect = 2e-08
 Identities = 13/47 (27%), Positives = 17/47 (36%)

Query: 160 CPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIF 206
                     E       C H FH  CI  W++    CP+ N+E  F
Sbjct: 55  QANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEF 101

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

 Score = 49.3 bits (117), Expect = 7e-08
 Identities = 30/105 (28%), Positives = 48/105 (45%), Gaps = 12/105 (11%)

Query: 109 NSQETSSKCDDLKEPESKTVA-----NVELESTKE----LEVELSKSVHHVVAVIEEEDV 159
             QE  +  ++L   +    A     N ELE TKE    ++ +  + + H+  V+E E  
Sbjct: 7   GFQEHWALMEELNRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQ 66

Query: 160 CPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEM 204
           C  C E +      +   C H F   CI EWM+R   CP+C +++
Sbjct: 67  CIICSEYF--IEA-VTLNCAHSFCSYCINEWMKRKIECPICRKDI 108

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

 Score = 47.1 bits (112), Expect = 1e-07
 Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 2/53 (3%)

Query: 151 VAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQE 203
           +  I++   C  C E +      II +C H++   CI +++     CP C   
Sbjct: 16  MKTIDDLLRCGICFEYF--NIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVT 66

>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

 Score = 49.0 bits (116), Expect = 3e-07
 Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 4/51 (7%)

Query: 155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME-RSDTCPVCNQEM 204
               +C  C E  + ++ +I   C H    +C+  W E     CP C  E+
Sbjct: 330 STFQLCKICAE--NDKDVKI-EPCGHLMCTSCLTSWQESEGQGCPFCRCEI 377

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

 Score = 44.4 bits (105), Expect = 7e-07
 Identities = 13/54 (24%), Positives = 20/54 (37%), Gaps = 3/54 (5%)

Query: 155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL 208
                C  CL+     +P +   C+H F   C+         C +C QE+  D 
Sbjct: 13  LTVPECAICLQTC--VHP-VSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDF 63

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

 Score = 43.6 bits (102), Expect = 5e-06
 Identities = 14/55 (25%), Positives = 26/55 (47%), Gaps = 4/55 (7%)

Query: 152 AVIEEEDVCPTCLEEY----DAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQ 202
           A+      CP C++ Y          + T+C H F   C+ + ++ ++TCP C +
Sbjct: 2   AMGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 56

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 74

 Score = 41.8 bits (98), Expect = 7e-06
 Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 4/57 (7%)

Query: 155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD--TCPVCNQEMIFDLP 209
           +   +C  C         +    C    HL C+ ++ + +    CP CN     ++P
Sbjct: 13  DAVKICNICHSL--LIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIP 67

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1 Length = 114

 Score = 42.5 bits (99), Expect = 1e-05
 Identities = 19/86 (22%), Positives = 28/86 (32%), Gaps = 22/86 (25%)

Query: 135 STKELEVELSKSVHHVVAVIEEEDVCPTCLEEYDA---------------ENPRIITKCE 179
           S+ E E  + K    +      E+ C  C+E+                       +TKC 
Sbjct: 5   SSGEPEQVIRKYTEELKV--APEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCS 62

Query: 180 HHFHLACIFEWMERSD-----TCPVC 200
           H FHL C+       +      CP C
Sbjct: 63  HAFHLLCLLAMYCNGNKDGSLQCPSC 88

>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster} Length = 381

 Score = 42.9 bits (100), Expect = 3e-05
 Identities = 22/150 (14%), Positives = 37/150 (24%), Gaps = 33/150 (22%)

Query: 74  VRHPQTPPVVQEICSNKSDPSVQTTPVPVQDTLGGNSQETSSKCDDLKEPESKTVANVEL 133
           +  P        +        V      ++  L        S+ +  K           L
Sbjct: 236 IADPFACIASMSLKIIGPTEEVA----RLRHVLSDGLSNWDSEMNIHKN----------L 281

Query: 134 ESTKELEVELSKSVHHVVAVIEEEDV---CPTCLEEY--DAENPRII---TKCEHHFHLA 185
               +L             + EE++    C  C        E P +     KC    H  
Sbjct: 282 LRMFDLCYFPMPDWSDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAV 341

Query: 186 CIFEWMERSD-----------TCPVCNQEM 204
           C+ EW +               CP C  ++
Sbjct: 342 CLEEWFKTLMDGKTFLEVSFGQCPFCKAKL 371

>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

 Score = 40.7 bits (95), Expect = 4e-05
 Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 4/53 (7%)

Query: 151 VAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQE 203
           +  +E+   C  C        P  +  CEH F   C+ + +     CPVC   
Sbjct: 16  LDRLEKLLRCSRCTNILR--EPVCLGGCEHIFCSNCVSDCIGTG--CPVCYTP 64

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 39.1 bits (91), Expect = 6e-05
 Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 8/63 (12%)

Query: 155 EEEDVCPTCLEEYDAENPRIITKCE-----HHFHLACIFEWMERSDT--CPVCNQEMIFD 207
             +D+C  C  E D E+P +IT C      H  H AC+ +W++ SDT  C +C  E I +
Sbjct: 13  SSQDICRICHCEGDDESP-LITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIME 71

Query: 208 LPV 210
             +
Sbjct: 72  TKL 74

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

 Score = 39.0 bits (91), Expect = 8e-05
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 4/52 (7%)

Query: 154 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD--TCPVCNQE 203
           I +E +C  C +     +  +I  C + +   CI   +  SD  TCP C+Q 
Sbjct: 12  IPDELLCLICKDIMT--DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQN 61

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

 Score = 38.2 bits (89), Expect = 9e-05
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 4/54 (7%)

Query: 151 VAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS-DTCPVCNQE 203
           V  +E++  C  C       +P   T+C H F  +C+   +  S   C  C + 
Sbjct: 9   VKTVEDKYKCEKCHLVL--CSP-KQTECGHRFCESCMAALLSSSSPKCTACQES 59

>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

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 4/86 (4%)

Query: 120 LKEPESKTVANVELESTKELEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCE 179
           ++E +S      E+ ++ +            ++ +EE   C  C E      P I T C+
Sbjct: 15  IREDKSNAKLWNEVLASLKDRPASGSPFQLFLSKVEETFQCICCQELV--FRP-ITTVCQ 71

Query: 180 HHFHLACIFEWME-RSDTCPVCNQEM 204
           H+    C+      +  +CP C  ++
Sbjct: 72  HNVCKDCLDRSFRAQVFSCPACRYDL 97

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

 Score = 37.8 bits (88), Expect = 3e-04
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 4/52 (7%)

Query: 154 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD--TCPVCNQE 203
           I +E +C  C +     +  +I  C + +   CI   +  SD  TCP C+Q 
Sbjct: 10  IPDELLCLICKDIMT--DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQN 59

>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

 Score = 37.8 bits (88), Expect = 4e-04
 Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 6/57 (10%)

Query: 150 VVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD---TCPVCNQE 203
           V+  +++   CP CLE      P + TKC+H F   C+ + + +      CP+C  +
Sbjct: 14  VINAMQKILECPICLELIK--EP-VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKND 67

>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} Length = 267

 Score = 38.4 bits (88), Expect = 9e-04
 Identities = 19/67 (28%), Positives = 27/67 (40%), Gaps = 7/67 (10%)

Query: 150 VVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDT--CPV--CNQEMI 205
            +   + E  CP   + Y  E P I  KC H F    I  +++   T  CP   C+Q + 
Sbjct: 174 QIEGGKIELTCPITCKPY--EAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVS 231

Query: 206 F-DLPVD 211
             D   D
Sbjct: 232 MRDFVRD 238

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	212
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.68
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.67
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.65
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.64
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.64
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.62
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.62
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.6
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.58
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.57
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.57
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.57
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.55
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.53
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.53
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.51
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.51
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.5
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.5
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.49
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.48
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.47
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.47
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.46
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.45
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.41
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.41
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.4
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.4
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.39
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.37
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.37
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.37
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.37
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.37
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.36
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.36
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.34
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.33
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.3
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.28
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.27
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.27
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.25
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.24
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.23
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.23
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.22
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.21
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.2
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.18
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.18
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.18
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.12
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.11
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.09
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.08
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.04
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.03
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.98
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.95
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.93
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.91
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.85
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.84
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.8
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.8
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.78
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.76
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.6
3nw0_A	238	Non-structural maintenance of chromosomes element	98.24
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.16
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	97.19
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	96.39
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	93.82
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	93.08
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	91.99
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	91.69
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	91.57
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	90.04
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	89.49
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	89.38
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	88.25
1we9_A	64	PHD finger family protein; structural genomics, PH	88.15
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	87.37
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	87.04
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	87.04
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	87.01
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	86.25
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	85.97
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	85.95
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	84.71
2yt5_A	66	Metal-response element-binding transcription facto	84.04
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	81.98
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	81.54
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	81.4
4fo9_A	360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	81.36
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	80.08
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	80.01

>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}

Probab=99.68  E-value=5e-17  Score=109.93  Aligned_cols=56  Identities=27%  Similarity=0.722  Sum_probs=49.8

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPV  210 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~~~  210 (212)
                      ++...|+||++.|..+...+.++|||.||..||.+|++++.+||+||+.+...-+.
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   67 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLPS   67 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCSCCCC
T ss_pred             CCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccCcCCC
Confidence            45667999999998878888999999999999999999999999999998766553

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

Probab=99.67  E-value=2.9e-17  Score=106.18  Aligned_cols=52  Identities=27%  Similarity=0.760  Sum_probs=46.1

Q ss_pred             cCCCccccccccccCCCCeEEcC-CCCcccHHHHHHHHhcCCCCCcccccccC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITK-CEHHFHLACIFEWMERSDTCPVCNQEMIF  206 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~-C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~  206 (212)
                      +++..|+||++.|..++....++ |||.||..||.+|++++.+||+||+.+.+
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~v   55 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV   55 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSCC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeEC
Confidence            45667999999998877777776 99999999999999999999999998753

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

Probab=99.65  E-value=1.3e-16  Score=109.24  Aligned_cols=54  Identities=30%  Similarity=0.838  Sum_probs=48.1

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      +++..|+||++.|........++|+|.||..||.+|++.+.+||+||+.+..-.
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA   66 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCSSCC
T ss_pred             CCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCccccccc
Confidence            456679999999988888888899999999999999999999999999886544

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

Probab=99.64  E-value=5.9e-17  Score=111.48  Aligned_cols=53  Identities=25%  Similarity=0.785  Sum_probs=47.7

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD  207 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~  207 (212)
                      ++...|+||++.|..++.++.++|+|.||..||.+|++.+.+||+||+.+...
T Consensus        21 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A           21 SEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             SSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             CCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            45678999999998888788899999999999999999999999999988643

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

Probab=99.64  E-value=1.4e-16  Score=110.18  Aligned_cols=55  Identities=33%  Similarity=0.769  Sum_probs=49.0

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLP  209 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~~  209 (212)
                      ++...|+||++.|......+.++|+|.||..||.+|++++.+||+||+.+...+.
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   67 (78)
T 2ect_A           13 GSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNT   67 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCSCS
T ss_pred             CCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCccc
Confidence            4566899999999888888889999999999999999999999999999876553

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

Probab=99.62  E-value=1.8e-16  Score=113.27  Aligned_cols=51  Identities=35%  Similarity=0.805  Sum_probs=46.8

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      +++..|+|||+.|..++..+.++|||.||..||.+|++.+.+||+||+.+.
T Consensus        38 ~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   88 (91)
T 2l0b_A           38 GQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFP   88 (91)
T ss_dssp             SSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCBCTTTCCBSS
T ss_pred             CCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCcCcCcCccCC
Confidence            456789999999988888888999999999999999999999999999875

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

Probab=99.62  E-value=1.9e-16  Score=110.85  Aligned_cols=53  Identities=28%  Similarity=0.772  Sum_probs=42.6

Q ss_pred             cCCCccccccccccC-----------CC-CeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCC
Q 028200          155 EEEDVCPTCLEEYDA-----------EN-PRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD  207 (212)
Q Consensus       155 ee~~~C~ICle~~~~-----------~~-~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~  207 (212)
                      .+++.|+||++.|..           ++ ...+++|+|.||..||.+||+++.+||+||+.+.+.
T Consensus        13 ~~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   77 (81)
T 2ecl_A           13 VECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQ   77 (81)
T ss_dssp             CCCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEE
T ss_pred             CCCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchh
Confidence            356668888888843           33 344556999999999999999999999999988654

>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

Probab=99.60  E-value=5.3e-16  Score=100.07  Aligned_cols=51  Identities=25%  Similarity=0.610  Sum_probs=44.1

Q ss_pred             cCCCccccccccccC-CCCeEEcCCCCcccHHHHHHHHhcCCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDA-ENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~-~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      .++..|+||++.|.. ++..+.++|+|.||..||.+|++.+.+||+||+.+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            3 SGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             SCCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            345679999999944 456788999999999999999999999999999764

>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

Probab=99.58  E-value=1.1e-15  Score=112.33  Aligned_cols=53  Identities=28%  Similarity=0.606  Sum_probs=45.3

Q ss_pred             cCCCccccccccccCC---------------CCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCC
Q 028200          155 EEEDVCPTCLEEYDAE---------------NPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD  207 (212)
Q Consensus       155 ee~~~C~ICle~~~~~---------------~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~  207 (212)
                      .+++.|+||++.|...               ..++.++|+|.||..||.+||+++.+||+||+.+.++
T Consensus        35 ~~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~~~  102 (106)
T 3dpl_R           35 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQ  102 (106)
T ss_dssp             SCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCCEE
T ss_pred             CCCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCCcCcCCCCcceee
Confidence            4577899999999753               2467789999999999999999999999999987653

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

Probab=99.57  E-value=1.1e-15  Score=103.56  Aligned_cols=55  Identities=24%  Similarity=0.638  Sum_probs=47.4

Q ss_pred             cCCCccccccccccC----CCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCCC
Q 028200          155 EEEDVCPTCLEEYDA----ENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLP  209 (212)
Q Consensus       155 ee~~~C~ICle~~~~----~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~~  209 (212)
                      +++..|+||++.|..    +...+.++|||.||..||.+|++++.+||+||+.+..++.
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   66 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   66 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSC
T ss_pred             CCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChhhe
Confidence            456779999999854    3556889999999999999999999999999999876654

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

Probab=99.57  E-value=2.9e-15  Score=102.21  Aligned_cols=55  Identities=27%  Similarity=0.514  Sum_probs=47.3

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCCCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPVD  211 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~~~~  211 (212)
                      ++...|+||++.|..  ++.+++|||.||..||.+|++.+.+||+||+.+..++++.
T Consensus        13 ~~~~~C~IC~~~~~~--p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   67 (72)
T 2djb_A           13 TPYILCSICKGYLID--ATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLS   67 (72)
T ss_dssp             CGGGSCTTTSSCCSS--CEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSCC
T ss_pred             CCCCCCCCCChHHHC--cCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCcccccc
Confidence            456679999999865  4555699999999999999999999999999998887764

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

Probab=99.57  E-value=1.7e-15  Score=101.82  Aligned_cols=51  Identities=25%  Similarity=0.720  Sum_probs=44.2

Q ss_pred             cCCCccccccccccC----CCCeEEcCCCCcccHHHHHHHHhcCCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDA----ENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~----~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      .+...|+||++.|..    +...+.++|||.||..||.+|++.+.+||+||+.+.
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   67 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN   67 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccC
Confidence            556779999999854    344578999999999999999999999999999875

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

Probab=99.55  E-value=3.3e-15  Score=104.48  Aligned_cols=54  Identities=39%  Similarity=0.873  Sum_probs=46.1

Q ss_pred             ccCCCccccccccccCCCCeEEcCCC-----CcccHHHHHHHHhcCC--CCCcccccccCCC
Q 028200          154 IEEEDVCPTCLEEYDAENPRIITKCE-----HHFHLACIFEWMERSD--TCPVCNQEMIFDL  208 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~~~~l~C~-----H~FH~~CI~~Wl~~~~--tCPvCr~~l~~~~  208 (212)
                      ..+++.|.|||++|..++.+ +++|.     |.||..||.+||+.++  +||+||+.+.++.
T Consensus        12 ~~~~~~C~IC~~~~~~~~~l-~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~   72 (80)
T 2d8s_A           12 PSSQDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMET   72 (80)
T ss_dssp             CTTSCCCSSSCCCCCSSSCE-ECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCC
T ss_pred             CCCCCCCeEcCccccCCCee-EeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCc
Confidence            35567899999999887776 58996     9999999999998764  8999999997765

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

Probab=99.53  E-value=2.8e-15  Score=99.33  Aligned_cols=53  Identities=25%  Similarity=0.674  Sum_probs=45.4

Q ss_pred             CCCccccccccccC----CCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          156 EEDVCPTCLEEYDA----ENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       156 e~~~C~ICle~~~~----~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      ++..|+||++.|..    +...+.++|||.||..||.+|++++.+||+||+.+..++
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   58 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR   58 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTTC
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCccc
Confidence            35679999999854    345678999999999999999999999999999987654

>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

Probab=99.53  E-value=7.6e-15  Score=108.55  Aligned_cols=52  Identities=31%  Similarity=0.652  Sum_probs=41.8

Q ss_pred             CCCccccccccccCCC---------------CeEEcCCCCcccHHHHHHHH-----hcCCCCCcccccccCC
Q 028200          156 EEDVCPTCLEEYDAEN---------------PRIITKCEHHFHLACIFEWM-----ERSDTCPVCNQEMIFD  207 (212)
Q Consensus       156 e~~~C~ICle~~~~~~---------------~~~~l~C~H~FH~~CI~~Wl-----~~~~tCPvCr~~l~~~  207 (212)
                      .++.|+|||+.|....               ...+++|+|.||..||.+||     +.+.+||+||+.+...
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            3457999999995532               34478999999999999999     4567999999987543

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

Probab=99.51  E-value=4.3e-15  Score=100.57  Aligned_cols=50  Identities=30%  Similarity=0.775  Sum_probs=44.1

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      .+...|+||++.+..    +.++|||.||..||.+|++++.+||+||+.+...+
T Consensus        13 ~~~~~C~IC~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGAN   62 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCCC
T ss_pred             CCCCCCeeCCcCccC----cccCCCCcccHHHHHHHHHCcCcCCCcCCcccCCC
Confidence            456679999999865    67899999999999999999999999999887554

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

Probab=99.51  E-value=7.2e-15  Score=99.95  Aligned_cols=49  Identities=22%  Similarity=0.435  Sum_probs=43.0

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIF  206 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~  206 (212)
                      .+...|+||++.|..   .+.++|||.||..||.+|++.+.+||+||+.+..
T Consensus        13 ~~~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (71)
T 2d8t_A           13 LTVPECAICLQTCVH---PVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPE   61 (71)
T ss_dssp             SSCCBCSSSSSBCSS---EEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCCH
T ss_pred             CCCCCCccCCcccCC---CEEccCCCHHHHHHHHHHHHCCCcCcCcCchhCH
Confidence            456679999999855   5678999999999999999999999999998753

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

Probab=99.50  E-value=9.7e-15  Score=98.19  Aligned_cols=49  Identities=33%  Similarity=0.826  Sum_probs=42.8

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      +++..|+||++.+.  ++.+.++|||.||..||.+|++++.+||+||+.+.
T Consensus         3 ~~~~~C~IC~~~~~--~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~   51 (68)
T 1chc_A            3 TVAERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCCCSSCCSCCC--SCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCCCeeCCcccc--CCcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhH
Confidence            34667999999985  35678999999999999999999999999999874

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

Probab=99.50  E-value=2.8e-14  Score=100.42  Aligned_cols=54  Identities=24%  Similarity=0.566  Sum_probs=45.9

Q ss_pred             cCCCccccccccccCCCC-eEEcCCCCcccHHHHHHHHhcC---CCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENP-RIITKCEHHFHLACIFEWMERS---DTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~-~~~l~C~H~FH~~CI~~Wl~~~---~tCPvCr~~l~~~~  208 (212)
                      ++...|+||++.|...+. .+.++|||.||..||.+|++.+   .+||+||+.+..++
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   70 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITS   70 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCSS
T ss_pred             cCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccchh
Confidence            556789999999976553 6788999999999999999886   78999999886653

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus}

Probab=99.49  E-value=2.3e-15  Score=112.49  Aligned_cols=53  Identities=28%  Similarity=0.606  Sum_probs=1.6

Q ss_pred             cCCCccccccccccCC---------------CCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCC
Q 028200          155 EEEDVCPTCLEEYDAE---------------NPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD  207 (212)
Q Consensus       155 ee~~~C~ICle~~~~~---------------~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~  207 (212)
                      .+++.|+||++.|...               ..+..++|+|.||..||.+||+++.+||+||+++.++
T Consensus        46 ~~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~~  113 (117)
T 4a0k_B           46 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQ  113 (117)
T ss_dssp             CCC-----------------------------------------------------------------
T ss_pred             CCCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeeeee
Confidence            4567899999999642               1334468999999999999999999999999987654

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens}

Probab=99.48  E-value=3.1e-14  Score=97.63  Aligned_cols=51  Identities=24%  Similarity=0.518  Sum_probs=42.4

Q ss_pred             cCCCccccccccccCCCCeEEcC-CCCcccHHHHHHHHhcC--CCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITK-CEHHFHLACIFEWMERS--DTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~-C~H~FH~~CI~~Wl~~~--~tCPvCr~~l~~~~  208 (212)
                      +++..|+||++.|..   .+.++ |||.||..||.+|++.+  .+||+||+.+...+
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           13 PDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             CGGGSCSSSCCCCTT---CEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTT
T ss_pred             CCCCCCcCCChHHhC---CeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCcc
Confidence            456689999999864   45688 99999999999999876  68999999865444

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

Probab=99.47  E-value=4.2e-14  Score=96.25  Aligned_cols=51  Identities=31%  Similarity=0.704  Sum_probs=43.1

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHh---cCCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME---RSDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~---~~~tCPvCr~~l~~~~  208 (212)
                      ++...|+||++.|..   .+.++|||.||..||.+|++   ...+||+||+.+..++
T Consensus        18 ~~~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           18 QEEVICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCCBCTTTCSBCSS---EEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             ccCCEeccCCcccCC---eEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            456789999999874   56779999999999999997   4568999999987654

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

Probab=99.47  E-value=3.4e-14  Score=95.14  Aligned_cols=51  Identities=24%  Similarity=0.544  Sum_probs=42.7

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHh-cCCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME-RSDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~-~~~tCPvCr~~l~~~~  208 (212)
                      ++...|+||++.+..   .+.++|||.||..||.+|++ .+.+||+||+.+..++
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   64 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCS---PKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDK   64 (66)
T ss_dssp             CCCEECTTTCCEESS---CCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTT
T ss_pred             CcCCCCCCCChHhcC---eeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhh
Confidence            456789999999864   34589999999999999994 5678999999987664

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

Probab=99.46  E-value=5.3e-14  Score=97.96  Aligned_cols=48  Identities=27%  Similarity=0.613  Sum_probs=42.4

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      ++...|+||++.|..   .++++|||.||..||.+|++...+||+||+.+.
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQN---PVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCS---EEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcC---eeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            446689999999855   567999999999999999999999999999875

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

Probab=99.45  E-value=2.5e-14  Score=109.56  Aligned_cols=49  Identities=35%  Similarity=0.782  Sum_probs=43.1

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIF  206 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~  206 (212)
                      +++..|+||++.|..   .++++|||.||..||.+|++++.+||+||+.+..
T Consensus        51 ~~~~~C~iC~~~~~~---~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           51 ENELQCIICSEYFIE---AVTLNCAHSFCSYCINEWMKRKIECPICRKDIKS   99 (138)
T ss_dssp             HHHSBCTTTCSBCSS---EEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCC
T ss_pred             cccCCCcccCcccCC---ceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCC
Confidence            455679999999865   5678999999999999999999999999998753

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

Probab=99.41  E-value=1.4e-13  Score=94.99  Aligned_cols=51  Identities=22%  Similarity=0.477  Sum_probs=43.8

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc-CCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-SDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~-~~tCPvCr~~l~~~~  208 (212)
                      .++..|+||++.|..   .++++|||.||..||.+|++. +.+||+||+.+..++
T Consensus         6 ~~~~~C~IC~~~~~~---Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~   57 (78)
T 1t1h_A            6 PEYFRCPISLELMKD---PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAG   57 (78)
T ss_dssp             SSSSSCTTTSCCCSS---EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCC
T ss_pred             cccCCCCCccccccC---CEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChhh
Confidence            456789999999865   567899999999999999987 789999999886554

>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}

Probab=99.41  E-value=5.7e-14  Score=101.90  Aligned_cols=52  Identities=23%  Similarity=0.625  Sum_probs=43.4

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC-CCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS-DTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~-~tCPvCr~~l~~~~  208 (212)
                      +++..|+||++.|..  ++.+++|||.||..||.+|++.+ .+||+||+.+..++
T Consensus        20 ~~~~~C~IC~~~~~~--p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (100)
T 3lrq_A           20 AEVFRCFICMEKLRD--ARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRE   72 (100)
T ss_dssp             HHHTBCTTTCSBCSS--EEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCCCCCccCCccccC--ccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHHH
Confidence            456679999999964  44349999999999999999988 69999999886544

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

Probab=99.40  E-value=1.3e-13  Score=94.75  Aligned_cols=53  Identities=21%  Similarity=0.610  Sum_probs=44.8

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC--CCCCcccccccCCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS--DTCPVCNQEMIFDLP  209 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~--~tCPvCr~~l~~~~~  209 (212)
                      +..+.|+||++.|..+  .....|+|.||..||.+||+.+  .+||+||+.+.++.+
T Consensus        13 ~~i~~C~IC~~~i~~g--~~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~~   67 (74)
T 2ct0_A           13 DAVKICNICHSLLIQG--QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIP   67 (74)
T ss_dssp             SSSCBCSSSCCBCSSS--EECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCCC
T ss_pred             CCCCcCcchhhHcccC--CccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCCC
Confidence            4566799999999764  3455899999999999999887  899999999987654

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

Probab=99.40  E-value=3.2e-13  Score=94.02  Aligned_cols=51  Identities=37%  Similarity=0.724  Sum_probs=43.3

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc------CCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER------SDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~------~~tCPvCr~~l~~~~  208 (212)
                      ++...|+||++.|..   .+.++|||.||..||.+|++.      ...||+||+.+..++
T Consensus        17 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~   73 (85)
T 2ecw_A           17 KEEVTCPICLELLKE---PVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGN   73 (85)
T ss_dssp             CTTTSCTTTCSCCSS---CEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTC
T ss_pred             ccCCCCcCCChhhCc---ceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHh
Confidence            456679999999865   457899999999999999988      678999999886553

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

Probab=99.39  E-value=3.1e-13  Score=89.49  Aligned_cols=43  Identities=37%  Similarity=0.851  Sum_probs=36.9

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHh---cCCCCCcc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME---RSDTCPVC  200 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~---~~~tCPvC  200 (212)
                      +++..|+||++.|..   .+.++|||.||..||.+|++   ...+||+|
T Consensus        18 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           18 QEEVICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCBCTTTCSBCSS---CEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             ccCCCCCcCCchhCC---eEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            556789999999864   45679999999999999998   45689998

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

Probab=99.37  E-value=1.9e-13  Score=102.80  Aligned_cols=54  Identities=24%  Similarity=0.669  Sum_probs=45.9

Q ss_pred             cCCCccccccccccC----CCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDA----ENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~----~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      .++..|+||++.|..    +...+.++|||.||..||.+|++.+.+||+||+.+..+.
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR   62 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTC
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCcccc
Confidence            356679999999854    355588999999999999999999999999999886544

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

Probab=99.37  E-value=4.5e-13  Score=89.31  Aligned_cols=53  Identities=21%  Similarity=0.585  Sum_probs=41.7

Q ss_pred             CCCccccccc-cccCCC-CeEEcCCCCcccHHHHHHHHhc-CCCCCcccccccCCC
Q 028200          156 EEDVCPTCLE-EYDAEN-PRIITKCEHHFHLACIFEWMER-SDTCPVCNQEMIFDL  208 (212)
Q Consensus       156 e~~~C~ICle-~~~~~~-~~~~l~C~H~FH~~CI~~Wl~~-~~tCPvCr~~l~~~~  208 (212)
                      ++..|+||++ .|.... ..+.++|||.||..||.+|+.+ +.+||+||+.+..++
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   57 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSN   57 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCC
T ss_pred             CCCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCcccccc
Confidence            3567999999 675432 3356899999999999999765 468999999886554

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

Probab=99.37  E-value=8.6e-14  Score=96.04  Aligned_cols=50  Identities=34%  Similarity=0.717  Sum_probs=42.6

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc-------CCCCCcccccccCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-------SDTCPVCNQEMIFD  207 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~-------~~tCPvCr~~l~~~  207 (212)
                      +++..|+||++.|..   .+.++|||.||..||.+|++.       ..+||+||+.+..+
T Consensus        10 ~~~~~C~IC~~~~~~---p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~   66 (79)
T 2egp_A           10 QEEVTCPICLELLTE---PLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFE   66 (79)
T ss_dssp             CCCCEETTTTEECSS---CCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSS
T ss_pred             ccCCCCcCCCcccCC---eeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHh
Confidence            567789999999865   446899999999999999987       67899999988654

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

Probab=99.37  E-value=3.9e-13  Score=93.57  Aligned_cols=51  Identities=31%  Similarity=0.668  Sum_probs=43.2

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc------CCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER------SDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~------~~tCPvCr~~l~~~~  208 (212)
                      ++...|+||++.|..   .+.++|||.||..||.+|++.      ...||+||+.+..++
T Consensus        17 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~   73 (85)
T 2ecv_A           17 KEEVTCPICLELLTQ---PLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPEN   73 (85)
T ss_dssp             CCCCCCTTTCSCCSS---CBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSS
T ss_pred             cCCCCCCCCCcccCC---ceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHh
Confidence            456779999999865   456799999999999999987      789999999887544

>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

Probab=99.37  E-value=3.3e-13  Score=98.94  Aligned_cols=52  Identities=25%  Similarity=0.586  Sum_probs=44.1

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      +++..|+||++.|..  ++.+++|||.||..||.+|++.+.+||+||+.+....
T Consensus        13 ~~~~~C~IC~~~~~~--p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   64 (108)
T 2ckl_A           13 NPHLMCVLCGGYFID--ATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTR   64 (108)
T ss_dssp             GGGTBCTTTSSBCSS--EEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSSC
T ss_pred             CCcCCCccCChHHhC--cCEeCCCCChhhHHHHHHHHHhCCcCcCCCccccccC
Confidence            456779999999864  4444599999999999999999999999999887653

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

Probab=99.36  E-value=5.9e-13  Score=94.64  Aligned_cols=48  Identities=25%  Similarity=0.602  Sum_probs=40.9

Q ss_pred             cCCCccccccccccCCCCeEEcC-CCCcccHHHHHHHHhcC--CCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITK-CEHHFHLACIFEWMERS--DTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~-C~H~FH~~CI~~Wl~~~--~tCPvCr~~l~  205 (212)
                      +++..|+||++.|..   .+.++ |||.||..||.+|+..+  .+||+||+.+.
T Consensus        11 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           11 PDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CTTTEETTTTEECSS---CEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CcCCCCCCCChhhcC---ceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            567789999999864   45778 99999999999999765  58999999874

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

Probab=99.36  E-value=3e-13  Score=97.56  Aligned_cols=50  Identities=24%  Similarity=0.648  Sum_probs=42.2

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIF  206 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~  206 (212)
                      ++...|+||++.|..  ++.+++|||.||..||.+|++.+.+||+||+.+..
T Consensus        20 ~~~~~C~IC~~~~~~--p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           20 DDLLRCGICFEYFNI--AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HHHTBCTTTCSBCSS--EEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCCCcccCChhhCC--cCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            345679999999865  44445999999999999999999999999998764

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

Probab=99.34  E-value=5.7e-13  Score=86.46  Aligned_cols=43  Identities=44%  Similarity=0.983  Sum_probs=36.2

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHH---hcCCCCCcc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWM---ERSDTCPVC  200 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl---~~~~tCPvC  200 (212)
                      ++...|+||++.|..   .+.++|||.||..||.+|+   +++.+||+|
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKE---PVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSS---CCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccCCCCccCCcccCc---cEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            456789999999965   3568999999999999995   456789998

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

Probab=99.33  E-value=6.6e-13  Score=99.66  Aligned_cols=49  Identities=27%  Similarity=0.465  Sum_probs=42.2

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCC-CCCcccccccC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD-TCPVCNQEMIF  206 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~-tCPvCr~~l~~  206 (212)
                      ++...|+||++.|..   .+.++|||.||..||..|++... +||+||+.+..
T Consensus        50 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           50 EETFQCICCQELVFR---PITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHHTBCTTTSSBCSS---EEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             ccCCCCCcCChHHcC---cEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            456689999999975   56789999999999999998654 99999998865

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

Probab=99.30  E-value=7.9e-13  Score=99.34  Aligned_cols=55  Identities=24%  Similarity=0.630  Sum_probs=46.8

Q ss_pred             ccCCCccccccccccC----CCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          154 IEEEDVCPTCLEEYDA----ENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~----~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      .++...|+||++.|..    +...+.++|||.||..||.+|++.+.+||+||+.+..++
T Consensus        69 ~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~  127 (133)
T 4ap4_A           69 GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR  127 (133)
T ss_dssp             SSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChhc
Confidence            3566779999999854    345578999999999999999999999999999987654

>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

Probab=99.28  E-value=1.1e-12  Score=96.35  Aligned_cols=50  Identities=28%  Similarity=0.718  Sum_probs=41.6

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCC---CCCcccccccCCC
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD---TCPVCNQEMIFDL  208 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~---tCPvCr~~l~~~~  208 (212)
                      +...|+||++.|..   .+.++|||.||..||.+|++.+.   +||+||+.+..++
T Consensus        20 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   72 (112)
T 1jm7_A           20 KILECPICLELIKE---PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS   72 (112)
T ss_dssp             HHTSCSSSCCCCSS---CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTT
T ss_pred             CCCCCcccChhhcC---eEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhh
Confidence            45579999999854   34589999999999999998764   8999999886554

>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

Probab=99.27  E-value=1.8e-12  Score=96.55  Aligned_cols=50  Identities=32%  Similarity=0.681  Sum_probs=43.0

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCC-CCCcccccccCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD-TCPVCNQEMIFD  207 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~-tCPvCr~~l~~~  207 (212)
                      ++...|+||++.|..   .+.++|||.||..||.+|++.+. +||+||+.+..+
T Consensus        16 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           16 ESKYECPICLMALRE---AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             CGGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCcCChhhcC---eEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            556789999999865   46789999999999999998875 999999988654

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

Probab=99.27  E-value=2.5e-12  Score=99.96  Aligned_cols=50  Identities=22%  Similarity=0.517  Sum_probs=43.0

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCC-CCCcccccccCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD-TCPVCNQEMIFD  207 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~-tCPvCr~~l~~~  207 (212)
                      ++...|+||++.|..   .+.++|||.||..||.+|++... +||+||+.+..+
T Consensus        76 ~~~~~C~IC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           76 EQSFMCVCCQELVYQ---PVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHHTBCTTTSSBCSS---EEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             ccCCEeecCChhhcC---CEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            356689999999865   56689999999999999998765 899999998765

>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

Probab=99.25  E-value=2.3e-12  Score=95.56  Aligned_cols=50  Identities=22%  Similarity=0.485  Sum_probs=42.6

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc-CCCCCcccccccCCC
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-SDTCPVCNQEMIFDL  208 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~-~~tCPvCr~~l~~~~  208 (212)
                      ++..|+||++.|..   .+.++|||.||..||.+|++. ..+||+||+.+...+
T Consensus        22 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (116)
T 1rmd_A           22 KSISCQICEHILAD---PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (116)
T ss_dssp             HHTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCcHhcC---cEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhh
Confidence            45679999999865   566899999999999999987 679999999886543

>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}

Probab=99.24  E-value=9e-13  Score=97.57  Aligned_cols=48  Identities=25%  Similarity=0.553  Sum_probs=41.1

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc-CCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-SDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~-~~tCPvCr~~l~  205 (212)
                      +++..|+||++.|..   .+.++|||.||..||.+|++. ..+||+||+.+.
T Consensus        13 ~~~~~C~iC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   61 (115)
T 3l11_A           13 LSECQCGICMEILVE---PVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVS   61 (115)
T ss_dssp             HHHHBCTTTCSBCSS---CEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCH
T ss_pred             CCCCCCccCCcccCc---eeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccC
Confidence            456679999999864   567799999999999999976 678999999875

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

Probab=99.23  E-value=6e-12  Score=88.64  Aligned_cols=51  Identities=14%  Similarity=0.029  Sum_probs=44.8

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      .++..|+||++.|..   .++++|||.|+..||.+|+..+.+||+||+.+..++
T Consensus        12 p~~~~CpI~~~~m~d---PV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~   62 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTD---PVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTESM   62 (85)
T ss_dssp             CTTTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             chheECcccCchhcC---CeECCCCCEECHHHHHHHHhcCCCCCCCcCCCChHh
Confidence            457789999999976   677889999999999999999999999999886543

>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

Probab=99.23  E-value=3.7e-12  Score=100.08  Aligned_cols=49  Identities=27%  Similarity=0.735  Sum_probs=41.4

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc-CCCCCcccccccC
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-SDTCPVCNQEMIF  206 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~-~~tCPvCr~~l~~  206 (212)
                      +...|+||++.|..  ++.+++|||.||..||.+|++. +.+||+||+.+..
T Consensus        53 ~~~~C~IC~~~~~~--p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           53 SELMCPICLDMLKN--TMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHBCTTTSSBCSS--EEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCcccChHhhC--cCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            45579999999864  4555699999999999999987 7889999998853

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

Probab=99.22  E-value=4.5e-12  Score=97.57  Aligned_cols=51  Identities=20%  Similarity=0.560  Sum_probs=43.2

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCC-CCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD-TCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~-tCPvCr~~l~~~~  208 (212)
                      ++...|+||++.|..   .+.++|||.||..||.+|++... +||+||+++.+++
T Consensus        29 ~~~~~C~IC~~~~~~---pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   80 (141)
T 3knv_A           29 EAKYLCSACRNVLRR---PFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYEE   80 (141)
T ss_dssp             CGGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHGGGSCEECHHHHHTTCCCT
T ss_pred             CcCcCCCCCChhhcC---cEECCCCCccCHHHHHHHHhcCCCCCCCCCCcccccc
Confidence            566789999999865   46789999999999999998765 8999999875543

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

Probab=99.21  E-value=1.2e-11  Score=85.88  Aligned_cols=55  Identities=20%  Similarity=0.477  Sum_probs=41.8

Q ss_pred             ccCCCccccccccccCCCCeEE-cCCCCcccHHHHHHHHhc-CCCCCcccccccCCC
Q 028200          154 IEEEDVCPTCLEEYDAENPRII-TKCEHHFHLACIFEWMER-SDTCPVCNQEMIFDL  208 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~~~~-l~C~H~FH~~CI~~Wl~~-~~tCPvCr~~l~~~~  208 (212)
                      .+++..|+||++.+...+..+. ++|||.||..||.+|++. ...||+||+.+....
T Consensus         8 ~~~~~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~   64 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDP   64 (78)
T ss_dssp             CCCCCBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCS
T ss_pred             cccCCcCCccCccCccccccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCc
Confidence            3567789999998865443322 359999999999999853 578999999875443

>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

Probab=99.20  E-value=1.5e-11  Score=89.02  Aligned_cols=51  Identities=12%  Similarity=0.066  Sum_probs=45.2

Q ss_pred             cCCCccccccccccCCCCeEEcCCC-CcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCE-HHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~-H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      .++..||||++.|..   .++++|| |.|+..||.+|+..+.+||+||+.+..++
T Consensus        20 p~~~~CpI~~~~m~d---PV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~   71 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQ   71 (98)
T ss_dssp             CTTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTT
T ss_pred             cHhcCCcCccccccC---CeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChhh
Confidence            457789999999976   6788999 99999999999999999999999987654

>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

Probab=99.18  E-value=1.5e-11  Score=89.20  Aligned_cols=51  Identities=14%  Similarity=0.040  Sum_probs=44.9

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      .++..||||++.|..   +++++|||.|+..||.+|+..+.+||+||+.+..++
T Consensus        27 p~~~~CpI~~~~m~d---PV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~   77 (100)
T 2kre_A           27 PDEFRDPLMDTLMTD---PVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESM   77 (100)
T ss_dssp             STTTBCTTTCSBCSS---EEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCTTS
T ss_pred             cHhhCCcCccCcccC---CeECCCCCEEchHHHHHHHHcCCCCCCCCCCCChhh
Confidence            457789999999976   667889999999999999998899999999987654

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

Probab=99.18  E-value=2.5e-12  Score=83.52  Aligned_cols=48  Identities=19%  Similarity=0.407  Sum_probs=40.2

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      ++...|+||++.|..   .+.++|||.||..||..|   ..+||+||+.+..+.
T Consensus         4 ~~~~~C~IC~~~~~~---p~~l~CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T 1bor_A            4 FQFLRCQQCQAEAKC---PKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCCSSCSSSCSSCBC---CSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             ccCCCceEeCCccCC---eEEcCCCCcccHHHHccC---CCCCCcCCcEeecCC
Confidence            456789999999975   457899999999999885   678999999986654

>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

Probab=99.18  E-value=1.2e-11  Score=82.48  Aligned_cols=48  Identities=25%  Similarity=0.506  Sum_probs=40.1

Q ss_pred             cCCCccccccccccCCCCeEEc--CCCCc-ccHHHHHHHHhcCCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIIT--KCEHH-FHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l--~C~H~-FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      +++..|+||++.+..   .+.+  +|||. |+..|+..|++.+..||+||+.+.
T Consensus         6 ~~~~~C~IC~~~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            6 NAIEPCVICQGRPKN---GCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             GGGSCCTTTSSSCSC---EEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CCcCCCCcCCCCCCC---EEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            345679999998654   3444  99999 899999999999999999999874

>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*

Probab=99.12  E-value=3.4e-11  Score=80.02  Aligned_cols=48  Identities=19%  Similarity=0.433  Sum_probs=39.7

Q ss_pred             cCCCccccccccccCCCCeEEc--CCCCc-ccHHHHHHHHhcCCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIIT--KCEHH-FHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l--~C~H~-FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      +....|+||++....   ..++  +|||. |+..|+.+|.+++.+||+||+.+.
T Consensus         5 ~~~~~C~IC~~~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            5 NLLKPCSLCEKRPRD---GNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GGGSBCTTTSSSBSC---EEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             CcCCCCcccCCcCCC---eEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            345679999997643   3344  99998 999999999999899999999874

>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

Probab=99.11  E-value=1e-11  Score=92.32  Aligned_cols=50  Identities=26%  Similarity=0.565  Sum_probs=40.6

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      ++...|+||++.|..  ++.+++|||.||..||..|+.  ..||+||+.+...+
T Consensus        20 ~~~~~C~IC~~~~~~--pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~   69 (117)
T 1jm7_B           20 EKLLRCSRCTNILRE--PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQD   69 (117)
T ss_dssp             HHTTSCSSSCSCCSS--CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSS
T ss_pred             hhCCCCCCCChHhhC--ccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCcccc
Confidence            456779999999854  443339999999999999998  78999999885543

>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*

Probab=99.09  E-value=4.6e-11  Score=105.58  Aligned_cols=49  Identities=27%  Similarity=0.611  Sum_probs=42.3

Q ss_pred             CCccccccccccCCCCeEEcCCCCcccHHHHHHHHh-cCCCCCcccccccCCC
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME-RSDTCPVCNQEMIFDL  208 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~-~~~tCPvCr~~l~~~~  208 (212)
                      ...|+||++.+..   .+.++|||.||..||..|++ .+.+||+||+.+....
T Consensus       332 ~~~C~ICle~~~~---pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~  381 (389)
T 2y1n_A          332 FQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE  381 (389)
T ss_dssp             SSBCTTTSSSBCC---EEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEEE
T ss_pred             CCCCCccCcCCCC---eEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCce
Confidence            4579999998854   67899999999999999998 7889999999876543

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

Probab=99.08  E-value=2.1e-11  Score=83.48  Aligned_cols=43  Identities=28%  Similarity=0.654  Sum_probs=37.5

Q ss_pred             CCCccccccccccCCCCeEEcCCCCc-ccHHHHHHHHhcCCCCCccccccc
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHH-FHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~-FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      ++..|+||++.+..   .+.++|||. ||..||..|    .+||+||+.+.
T Consensus        23 ~~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~   66 (74)
T 4ic3_A           23 EEKLCKICMDRNIA---IVFVPCGHLVTCKQCAEAV----DKCPMCYTVIT   66 (74)
T ss_dssp             HHTBCTTTSSSBCC---EEEETTCCBCCCHHHHTTC----SBCTTTCCBCS
T ss_pred             cCCCCCCCCCCCCC---EEEcCCCChhHHHHhhhcC----ccCCCcCcCcc
Confidence            45679999998755   678899999 999999999    88999999874

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.04  E-value=6.7e-11  Score=84.72  Aligned_cols=48  Identities=23%  Similarity=0.518  Sum_probs=39.5

Q ss_pred             cCCCccccccccccCCCCeEEc-CCCCcccHHHHHHHHhcC------CCCCc--cccc-cc
Q 028200          155 EEEDVCPTCLEEYDAENPRIIT-KCEHHFHLACIFEWMERS------DTCPV--CNQE-MI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l-~C~H~FH~~CI~~Wl~~~------~tCPv--Cr~~-l~  205 (212)
                      .++..||||++.|..   .+++ .|||.|+..||.+|+..+      .+||+  |++. +.
T Consensus         5 ~~~~~CPI~~~~~~d---PV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~   62 (94)
T 2yu4_A            5 SSGFTCPITKEEMKK---PVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIR   62 (94)
T ss_dssp             SSCCBCTTTCSBCSS---EEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBC
T ss_pred             CcEeECcCcCchhcC---CEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccC
Confidence            567789999999865   5566 599999999999999764      48999  9866 43

>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}

Probab=99.03  E-value=8.8e-11  Score=92.53  Aligned_cols=50  Identities=32%  Similarity=0.681  Sum_probs=42.5

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCC-CCCcccccccCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD-TCPVCNQEMIFD  207 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~-tCPvCr~~l~~~  207 (212)
                      ++...|+||++.|..   .+.++|||.||..||.+|++.+. +||+||+.+..+
T Consensus        16 ~~~~~C~IC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           16 ESKYECPICLMALRE---AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             CGGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCChhhcC---cEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            566789999999865   46689999999999999998754 999999988654

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

Probab=98.98  E-value=3.9e-10  Score=74.25  Aligned_cols=49  Identities=29%  Similarity=0.659  Sum_probs=39.0

Q ss_pred             cCCCccccccccccCCCCeEEcCCC--C---cccHHHHHHHHhc--CCCCCcccccccC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCE--H---HFHLACIFEWMER--SDTCPVCNQEMIF  206 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~--H---~FH~~CI~~Wl~~--~~tCPvCr~~l~~  206 (212)
                      +++..|.||+++.  ++++ ++||.  |   .||..||.+|+..  +.+||+|+..+.+
T Consensus         4 ~~~~~CrIC~~~~--~~~l-~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            4 EDVPVCWICNEEL--GNER-FRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEEC--SCCC-CCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCEeEEeecCC--CCce-ecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            5677899999974  3344 57864  4   9999999999965  5789999998765

>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

Probab=98.95  E-value=2.9e-10  Score=95.31  Aligned_cols=51  Identities=16%  Similarity=0.090  Sum_probs=42.8

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCC-CCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD-TCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~-tCPvCr~~l~~~~  208 (212)
                      .+...|+||++.|..   +++++|||.||..||.+|+..+. +||+||+.+...+
T Consensus       206 ~~~~~c~i~~~~~~d---Pv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~  257 (281)
T 2c2l_A          206 PDYLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQ  257 (281)
T ss_dssp             CSTTBCTTTCSBCSS---EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGG
T ss_pred             CcccCCcCcCCHhcC---CeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCchhc
Confidence            356689999999976   67889999999999999998754 5999999886443

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

Probab=98.93  E-value=1.7e-10  Score=99.82  Aligned_cols=51  Identities=25%  Similarity=0.608  Sum_probs=39.4

Q ss_pred             cCCCccccccccccC-CCCe-E---EcCCCCcccHHHHHHHHhcC-----------CCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDA-ENPR-I---ITKCEHHFHLACIFEWMERS-----------DTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~-~~~~-~---~l~C~H~FH~~CI~~Wl~~~-----------~tCPvCr~~l~  205 (212)
                      ++...|+||++.+.. +... .   .++|+|.||..||++||+..           ++||+||+.|.
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs  372 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLS  372 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEE
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCC
Confidence            345579999999865 3211 1   25799999999999999763           57999999874

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

Probab=98.91  E-value=3.1e-10  Score=77.73  Aligned_cols=45  Identities=29%  Similarity=0.692  Sum_probs=36.5

Q ss_pred             CCCccccccccccCCCCeEEcCCCCc-ccHHHHHHHHhcCCCCCcccccccCC
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHH-FHLACIFEWMERSDTCPVCNQEMIFD  207 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~-FH~~CI~~Wl~~~~tCPvCr~~l~~~  207 (212)
                      +...|+||++.+..   .+.++|||. ||..|+..    ...||+||+.+...
T Consensus        24 ~~~~C~IC~~~~~~---~~~~pCgH~~~C~~C~~~----~~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           24 EEKLCKICMDRNIA---IVFVPCGHLVTCKQCAEA----VDKCPMCYTVITFK   69 (75)
T ss_dssp             HHHSCSSSCSSCCC---BCCSSSCCCCBCHHHHHH----CSBCTTTCCBCCCC
T ss_pred             CCCCCCcCCCCCCC---EEEecCCCHHHHHHHhhC----CCCCccCCceecCc
Confidence            34569999998754   567899999 99999964    47899999988543

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

Probab=98.85  E-value=1.3e-09  Score=86.84  Aligned_cols=51  Identities=18%  Similarity=0.096  Sum_probs=43.3

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC-CCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS-DTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~-~tCPvCr~~l~~~~  208 (212)
                      .+...||||++.|..   +++++|||.|+..||.+|+..+ .+||+|++.+...+
T Consensus       104 p~~f~CPI~~elm~D---PV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~  155 (179)
T 2f42_A          104 PDYLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQ  155 (179)
T ss_dssp             CGGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             cHhhcccCccccCCC---CeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChhh
Confidence            467789999999976   6778999999999999999875 46999999886543

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.84  E-value=2.1e-09  Score=72.38  Aligned_cols=45  Identities=22%  Similarity=0.504  Sum_probs=37.4

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCc-ccHHHHHHHHhcCCCCCcccccccC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHH-FHLACIFEWMERSDTCPVCNQEMIF  206 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~-FH~~CI~~Wl~~~~tCPvCr~~l~~  206 (212)
                      ++...|.||++....   .+.++|||. ||..|+..    ...||+||+.+..
T Consensus        13 ~~~~~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~~   58 (68)
T 2ea5_A           13 ENSKDCVVCQNGTVN---WVLLPCRHTCLCDGCVKY----FQQCPMCRQFVQE   58 (68)
T ss_dssp             CCSSCCSSSSSSCCC---CEETTTTBCCSCTTHHHH----CSSCTTTCCCCCC
T ss_pred             CCCCCCCCcCcCCCC---EEEECCCChhhhHHHHhc----CCCCCCCCcchhc
Confidence            456679999997654   778999999 99999984    5789999998753

>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

Probab=98.80  E-value=9.1e-10  Score=76.35  Aligned_cols=43  Identities=28%  Similarity=0.614  Sum_probs=36.4

Q ss_pred             CCCccccccccccCCCCeEEcCCCCc-ccHHHHHHHHhcCCCCCccccccc
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHH-FHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~-FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      ++..|+||++.+..   .+.++|||. ||..|+..|    ..||+||+.+.
T Consensus        17 ~~~~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~   60 (79)
T 2yho_A           17 EAMLCMVCCEEEIN---STFCPCGHTVCCESCAAQL----QSCPVCRSRVE   60 (79)
T ss_dssp             HHTBCTTTSSSBCC---EEEETTCBCCBCHHHHTTC----SBCTTTCCBCC
T ss_pred             CCCEeEEeCcccCc---EEEECCCCHHHHHHHHHhc----CcCCCCCchhh
Confidence            34569999998754   778999999 999999988    38999999764

>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

Probab=98.80  E-value=1.8e-09  Score=71.25  Aligned_cols=50  Identities=12%  Similarity=0.231  Sum_probs=42.5

Q ss_pred             CccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCCC
Q 028200          158 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLP  209 (212)
Q Consensus       158 ~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~~  209 (212)
                      ..|+|+++.+..  +++..++||.|...||.+||+++++||+.++.+..++.
T Consensus         4 ~~CpIs~~~m~d--PV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~L   53 (61)
T 2bay_A            4 MLCAISGKVPRR--PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEI   53 (61)
T ss_dssp             CCCTTTCSCCSS--EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGC
T ss_pred             EEecCCCCCCCC--CEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhhc
Confidence            569999999864  44433899999999999999999999999999877664

>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

Probab=98.78  E-value=2.4e-09  Score=76.34  Aligned_cols=48  Identities=29%  Similarity=0.675  Sum_probs=38.8

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC--------CCCCc--cccc
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS--------DTCPV--CNQE  203 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~--------~tCPv--Cr~~  203 (212)
                      +...|+||++.+.......+++|||.||..||..|++.+        -+||.  |+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            456799999999765545556899999999999999642        37999  9987

>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}

Probab=98.76  E-value=2.8e-09  Score=89.33  Aligned_cols=51  Identities=31%  Similarity=0.639  Sum_probs=41.9

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC--CCCCc--ccccccCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS--DTCPV--CNQEMIFD  207 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~--~tCPv--Cr~~l~~~  207 (212)
                      ..+..||||++.|..  |++.+.|||.|+..||.+|++.+  .+||+  |++.+...
T Consensus       179 ~~el~CPIcl~~f~D--PVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~  233 (267)
T 3htk_C          179 KIELTCPITCKPYEA--PLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMR  233 (267)
T ss_dssp             BCCSBCTTTSSBCSS--EEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGG
T ss_pred             ceeeECcCccCcccC--CeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchh
Confidence            456689999999954  56667999999999999999865  47999  99977543

>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

Probab=98.60  E-value=8e-09  Score=90.28  Aligned_cols=44  Identities=23%  Similarity=0.629  Sum_probs=38.1

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCc-ccHHHHHHHHhcCCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHH-FHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~-FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      +++..|+||++.+..   .+.++|||. ||..||..|    ..||+||+.+.
T Consensus       293 ~~~~~C~IC~~~~~~---~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~  337 (345)
T 3t6p_A          293 QEERTCKVCMDKEVS---VVFIPCGHLVVCQECAPSL----RKCPICRGIIK  337 (345)
T ss_dssp             HTTCBCTTTSSSBCC---EEEETTCCEEECTTTGGGC----SBCTTTCCBCC
T ss_pred             cCCCCCCccCCcCCc---eEEcCCCChhHhHHHHhcC----CcCCCCCCCcc
Confidence            356689999998865   677899999 999999998    78999999874

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

Probab=98.24  E-value=8.7e-07  Score=73.55  Aligned_cols=52  Identities=21%  Similarity=0.607  Sum_probs=42.8

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCC--CCCcccccccCCCC
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD--TCPVCNQEMIFDLP  209 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~--tCPvCr~~l~~~~~  209 (212)
                      .-..|.||.+....+  ..+..|+|.||..|+.+|++.+.  +||.|+..+..+.|
T Consensus       179 ~i~~C~iC~~iv~~g--~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~~  232 (238)
T 3nw0_A          179 AVKICNICHSLLIQG--QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIP  232 (238)
T ss_dssp             TCCBCTTTCSBCSSC--EECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCCC
T ss_pred             CCCcCcchhhHHhCC--cccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCC
Confidence            356799999998764  44556999999999999998754  89999999877654

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

Probab=98.16  E-value=1.2e-06  Score=62.62  Aligned_cols=45  Identities=20%  Similarity=0.521  Sum_probs=35.9

Q ss_pred             ccccccccccCCCCeEEcCCCCcccHHHHHHHHhc-CCCCCccccccc
Q 028200          159 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-SDTCPVCNQEMI  205 (212)
Q Consensus       159 ~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~-~~tCPvCr~~l~  205 (212)
                      .|++|--.+..  -.++.+|.|+||.+|+..|.++ .++||.|+..+.
T Consensus         3 fC~~C~~Pi~i--ygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~   48 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQ   48 (101)
T ss_dssp             BCTTTCSBCSE--EEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCS
T ss_pred             ecCccCCCeEE--EeeeccccccHHHHHHHHHHhccCCCCcCcCCeee
Confidence            37788766533  3567899999999999999865 589999998763

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=96.39  E-value=0.0018  Score=45.87  Aligned_cols=36  Identities=17%  Similarity=0.402  Sum_probs=27.5

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHHH-HH
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFE-WM  191 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~-Wl  191 (212)
                      ++..|+||++.|...-....+.|+|.||..|+.. |.
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~~h~   38 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKATHP   38 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETTTTEEECHHHHHHHSC
T ss_pred             CCCCCcCCCCCCCCCceEECCcCChHHhHHHCHHHhc
Confidence            3567999998754333344599999999999998 54

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

Probab=93.82  E-value=0.042  Score=36.12  Aligned_cols=46  Identities=22%  Similarity=0.473  Sum_probs=35.1

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC----CCCCcccccc
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS----DTCPVCNQEM  204 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~----~tCPvCr~~l  204 (212)
                      ....|.||.+   .++.+..-.|...||..|+...|...    =.||.|....
T Consensus        11 ~~~~C~vC~~---~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           11 PGARCGVCGD---GTDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             TTCCCTTTSC---CTTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCcCCCCC---CCeEEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            3456999986   35556666799999999999888653    3699997654

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=93.08  E-value=0.026  Score=40.71  Aligned_cols=39  Identities=21%  Similarity=0.330  Sum_probs=30.1

Q ss_pred             ccCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHh
Q 028200          154 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME  192 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~  192 (212)
                      ..+++.|.||.+.-+.++-+....|+..||..||..++.
T Consensus         4 ~~~~~~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~~~   42 (111)
T 2ysm_A            4 GSSGANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVT   42 (111)
T ss_dssp             CCCCSCBTTTCCCCCTTTSEECSSSCCEECTTTTTCCCC
T ss_pred             CCCCCCCcCCCCCCCCcCCeECCCCCCCcChHHhCCccc
Confidence            356788999998654444466678999999999988764

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=91.99  E-value=0.032  Score=37.38  Aligned_cols=51  Identities=20%  Similarity=0.453  Sum_probs=35.1

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc----CCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER----SDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~----~~tCPvCr~~l~  205 (212)
                      ++...|.||......+.-+..-.|.-.||..|+..-+..    .-.||.|+..+.
T Consensus        16 ~~~~~C~~C~~~~~~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~   70 (75)
T 2k16_A           16 NQIWICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIK   70 (75)
T ss_dssp             CEEECBTTTTBCCSSCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHC
T ss_pred             CCCcCCCCCCCCCCCCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchh
Confidence            345579999887653333444568999999999765432    235999987653

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=91.69  E-value=0.089  Score=32.36  Aligned_cols=44  Identities=23%  Similarity=0.607  Sum_probs=31.5

Q ss_pred             ccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC----CCCCcccc
Q 028200          159 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS----DTCPVCNQ  202 (212)
Q Consensus       159 ~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~----~tCPvCr~  202 (212)
                      .|.||...-..++-+..-.|...||..|+..=|...    =.||.|+.
T Consensus         2 ~C~vC~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            488998765555556666799999999997544332    24999965

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

Probab=91.57  E-value=0.08  Score=34.08  Aligned_cols=46  Identities=26%  Similarity=0.707  Sum_probs=33.4

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc----CCCCCccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER----SDTCPVCNQE  203 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~----~~tCPvCr~~  203 (212)
                      ..++.|.||...   ++.+..-.|...||..|+..-|..    .=.||.|++.
T Consensus         9 ~~~~~C~vC~~~---g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            9 DHQDYCEVCQQG---GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             CCCSSCTTTSCC---SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCCccCCCC---CcEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            456679999873   444555668999999999986543    2369999764

>1wil_A KIAA1045 protein; ring finger domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: g.50.1.3

Probab=90.04  E-value=0.18  Score=34.69  Aligned_cols=34  Identities=26%  Similarity=0.606  Sum_probs=23.7

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHHHH
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEW  190 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~W  190 (212)
                      .++.|.|| +.|..+...-.=-|+-+||..|+.+-
T Consensus        14 ~D~~C~VC-~~~t~~~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           14 NDEMCDVC-EVWTAESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CSCCCTTT-CCCCSSCCSSCSSSSSCCCHHHHHHH
T ss_pred             CCcccCcc-ccccccceeccccccccccHhhcccc
Confidence            56679998 45555442222237999999999995

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=89.49  E-value=0.038  Score=34.92  Aligned_cols=46  Identities=24%  Similarity=0.591  Sum_probs=33.1

Q ss_pred             ccCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC----CCCCcccc
Q 028200          154 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS----DTCPVCNQ  202 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~----~tCPvCr~  202 (212)
                      ...++.|.||...   ++.+..-.|...||..|+.+-|...    =.||.|..
T Consensus         6 ~~~~~~C~vC~~~---g~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            6 SGHEDFCSVCRKS---GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             CSSCCSCSSSCCS---SCCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCCccCCCC---CeEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            3557789999874   4556666799999999998655432    24888854

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A

Probab=89.38  E-value=0.063  Score=34.59  Aligned_cols=48  Identities=17%  Similarity=0.444  Sum_probs=33.8

Q ss_pred             ccCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC----CCCCcccccc
Q 028200          154 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS----DTCPVCNQEM  204 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~----~tCPvCr~~l  204 (212)
                      +..++.|.||.+   .++.+..-.|...||..|+..-|...    =.||.|+...
T Consensus         6 d~~~~~C~vC~~---~g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            6 DHHMEFCRVCKD---GGELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             CSSCSSCTTTCC---CSSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             cCCCCcCCCCCC---CCCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            345667999986   34445556689999999998655432    2599997654

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=88.25  E-value=0.046  Score=35.04  Aligned_cols=48  Identities=25%  Similarity=0.627  Sum_probs=34.6

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC----CCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS----DTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~----~tCPvCr~~l~  205 (212)
                      ..++.|.||...   ++.+..-.|...||..|+.+-|...    =.||.|...+.
T Consensus         3 ~~~~~C~vC~~~---g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~   54 (60)
T 2puy_A            3 IHEDFCSVCRKS---GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQML   54 (60)
T ss_dssp             CCCSSCTTTCCC---SSCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHH
T ss_pred             CCCCCCcCCCCC---CcEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccChhh
Confidence            346679999873   4556666799999999998655432    25999976554

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=88.15  E-value=0.26  Score=31.65  Aligned_cols=50  Identities=26%  Similarity=0.521  Sum_probs=34.4

Q ss_pred             ccCCCccccccccccCCCCe-EEcCCCCcccHHHHHHHHh-----cCCCCCccccc
Q 028200          154 IEEEDVCPTCLEEYDAENPR-IITKCEHHFHLACIFEWME-----RSDTCPVCNQE  203 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~~-~~l~C~H~FH~~CI~~Wl~-----~~~tCPvCr~~  203 (212)
                      .++...|+||...+..+... ..-.|...||..|+.--..     ..-.||.|+..
T Consensus         3 ~~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            3 SGSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             CSSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            35667799999988544333 3356899999999865332     23469999653

>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

Probab=87.37  E-value=0.41  Score=46.66  Aligned_cols=50  Identities=12%  Similarity=0.094  Sum_probs=42.4

Q ss_pred             CCCccccccccccCCCCeEEcCCC-CcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCE-HHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~-H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      ++..|||=++.+..   +++++-| +.|-...|.+||.+..+||+=|+.+...+
T Consensus       890 ~~F~cPIs~~lM~D---PVilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~  940 (968)
T 3m62_A          890 DEFLDPLMYTIMKD---PVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLED  940 (968)
T ss_dssp             GGGBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGG
T ss_pred             HHhCCcchhhHHhC---CeEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCCccc
Confidence            45679999998866   6778887 68999999999999999999999886543

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=87.04  E-value=0.12  Score=33.65  Aligned_cols=47  Identities=28%  Similarity=0.552  Sum_probs=34.0

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC----CCCCcccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS----DTCPVCNQEM  204 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~----~tCPvCr~~l  204 (212)
                      ..++.|.||...   ++.+..-.|...||..|+.+-|...    =.||.|...-
T Consensus         6 ~~~~~C~vC~~~---g~ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~~   56 (66)
T 1xwh_A            6 KNEDECAVCRDG---GELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQAT   56 (66)
T ss_dssp             SCCCSBSSSSCC---SSCEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHTC
T ss_pred             CCCCCCccCCCC---CCEEEcCCCChhhcccccCCCcCcCCCCCeECccccCcc
Confidence            456789999873   4556666799999999998655432    2599996643

>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=87.04  E-value=0.046  Score=38.28  Aligned_cols=49  Identities=16%  Similarity=0.521  Sum_probs=34.7

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc----CCCCCccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER----SDTCPVCNQE  203 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~----~~tCPvCr~~  203 (212)
                      .+...|.||...-..+..+..-.|...||..|+.+=|..    .=.||.|...
T Consensus        14 ~~~~~C~vC~~~~~~~~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~   66 (92)
T 2e6r_A           14 IDSYICQVCSRGDEDDKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILA   66 (92)
T ss_dssp             CCCCCCSSSCCSGGGGGCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHH
T ss_pred             cCCCCCccCCCcCCCCCEEEcCCCCchhccccCCCCcccCCCCCcCCccCcCc
Confidence            456679999987554445556679999999999754432    1249999764

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=87.01  E-value=0.31  Score=33.85  Aligned_cols=51  Identities=20%  Similarity=0.520  Sum_probs=36.6

Q ss_pred             ccCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC----CCCCcccccccCC
Q 028200          154 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS----DTCPVCNQEMIFD  207 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~----~tCPvCr~~l~~~  207 (212)
                      .+.++.|.||...   ++.+..-.|.-.||..|+.+=|...    =.||.|+..-..+
T Consensus        22 d~n~~~C~vC~~~---g~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~~~k   76 (88)
T 1fp0_A           22 DDSATICRVCQKP---GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLK   76 (88)
T ss_dssp             SSSSSCCSSSCSS---SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCSSC
T ss_pred             CCCCCcCcCcCCC---CCEEECCCCCCceecccCCCCCCCCcCCCcCCccccCCCccc
Confidence            3556789999974   4556666789999999998766442    2599998654443

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*

Probab=86.25  E-value=0.61  Score=30.31  Aligned_cols=34  Identities=24%  Similarity=0.570  Sum_probs=24.6

Q ss_pred             cCCCccccccccccCCCCeEE-c-CCCCcccHHHHH
Q 028200          155 EEEDVCPTCLEEYDAENPRII-T-KCEHHFHLACIF  188 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~-l-~C~H~FH~~CI~  188 (212)
                      +....|++|...|..+...+. - .|.-.||..|+-
T Consensus         6 ~~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvg   41 (65)
T 2vpb_A            6 DPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTG   41 (65)
T ss_dssp             ---CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHT
T ss_pred             CCcCcCccCCCccCCCCCeEecccCccccCchhccC
Confidence            455679999999876655544 4 699999999974

>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

Probab=85.97  E-value=1.3  Score=30.13  Aligned_cols=39  Identities=18%  Similarity=0.309  Sum_probs=29.4

Q ss_pred             cCCCccccccccccCCCCeEEcC-CCCcccHHHHHHHHhc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITK-CEHHFHLACIFEWMER  193 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~-C~H~FH~~CI~~Wl~~  193 (212)
                      .....|.+|.|.++..+-+.... =.|.||..|-...+++
T Consensus        13 ~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~   52 (93)
T 2cs3_A           13 SGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   52 (93)
T ss_dssp             CCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHh
Confidence            34567999999998766443211 1799999999999976

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=85.95  E-value=1.1  Score=32.15  Aligned_cols=32  Identities=22%  Similarity=0.449  Sum_probs=24.1

Q ss_pred             CCccccccccc------cCCCCeEEcCCCCcccHHHHH
Q 028200          157 EDVCPTCLEEY------DAENPRIITKCEHHFHLACIF  188 (212)
Q Consensus       157 ~~~C~ICle~~------~~~~~~~~l~C~H~FH~~CI~  188 (212)
                      ...|.||+..-      ..++.+....|+..||..||.
T Consensus         5 ~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~   42 (112)
T 3v43_A            5 IPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLK   42 (112)
T ss_dssp             CSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHT
T ss_pred             CccccccCCchhhCcCCCchhceEhhhcCCCCCCchhc
Confidence            45699999752      334556667899999999995

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

Probab=84.71  E-value=0.97  Score=34.09  Aligned_cols=46  Identities=24%  Similarity=0.473  Sum_probs=33.9

Q ss_pred             ccCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc-----------CCCCCcccc
Q 028200          154 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-----------SDTCPVCNQ  202 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~-----------~~tCPvCr~  202 (212)
                      +..++.|.||-+   .++.+..-.|...||..||.+=|.+           .=.||+|+.
T Consensus        60 Dg~~d~C~vC~~---GG~LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~  116 (142)
T 2lbm_A           60 DGMDEQCRWCAE---GGNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHP  116 (142)
T ss_dssp             TSCBCSCSSSCC---CSSEEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCC
T ss_pred             CCCCCeecccCC---CCcEEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccC
Confidence            455778999997   3554555679999999999976531           235999975

>2yt5_A Metal-response element-binding transcription factor 2; zinc-regulated factor 1, ZIRF1, metal-response element DNA-binding protein M96; NMR {Mus musculus}

Probab=84.04  E-value=0.33  Score=31.31  Aligned_cols=51  Identities=25%  Similarity=0.533  Sum_probs=34.6

Q ss_pred             cCCCccccccccccC--CCCeEEcCCCCcccHHHHHHHHh-------cCCCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDA--ENPRIITKCEHHFHLACIFEWME-------RSDTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~--~~~~~~l~C~H~FH~~CI~~Wl~-------~~~tCPvCr~~l~  205 (212)
                      .++..|.||......  +..+..-.|.-.||..|+..-|.       ..=.|+.|.....
T Consensus         4 ~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~~   63 (66)
T 2yt5_A            4 GSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFATT   63 (66)
T ss_dssp             CCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTTS
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCccc
Confidence            456789999986532  34444466999999999886442       1235998876543

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

Probab=81.98  E-value=1.1  Score=39.02  Aligned_cols=48  Identities=21%  Similarity=0.495  Sum_probs=34.6

Q ss_pred             ccccccccccCCCCeEEcCCCCc--ccHHHHHHHHhcC--CCCCcccccccCCC
Q 028200          159 VCPTCLEEYDAENPRIITKCEHH--FHLACIFEWMERS--DTCPVCNQEMIFDL  208 (212)
Q Consensus       159 ~C~ICle~~~~~~~~~~l~C~H~--FH~~CI~~Wl~~~--~tCPvCr~~l~~~~  208 (212)
                      .|||=+..+  ..|.....|.|.  |-+.=+....++.  -.||+|.+.+.+.+
T Consensus       251 ~CPlS~~ri--~~PvRg~~C~HlQCFDl~sfL~~~~~~~~W~CPIC~k~~~~~d  302 (371)
T 3i2d_A          251 QCPISYTRM--KYPSKSINCKHLQCFDALWFLHSQLQIPTWQCPVCQIDIALEN  302 (371)
T ss_dssp             BCTTTSSBC--SSEEEETTCCSSCCEEHHHHHHHHHHSCCCBCTTTCCBCCGGG
T ss_pred             cCCCccccc--cccCcCCcCCCcceECHHHHHHHhhcCCceeCCCCCcccCHHH
Confidence            799877766  457888899998  6665555554443  46999999876544

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=81.54  E-value=0.19  Score=33.94  Aligned_cols=44  Identities=18%  Similarity=0.559  Sum_probs=30.4

Q ss_pred             ccccccccccCCCCeEEcCCCCcccHHHHHHHHhc-----CCCCCcccc
Q 028200          159 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-----SDTCPVCNQ  202 (212)
Q Consensus       159 ~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~-----~~tCPvCr~  202 (212)
                      .|.||...-..+..+..-.|...||..|+.+=|..     .=.||.|..
T Consensus        28 ~C~vC~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   76 (77)
T 2e6s_A           28 SCRVCGGKHEPNMQLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKT   76 (77)
T ss_dssp             SCSSSCCCCCSTTEEECSSSCCEEETTSSSSCCSSCCCSSCCCCTTTCC
T ss_pred             CCcCcCCcCCCCCEEEcCCCCccccccccCCCccCCCCCCCcCCcCccC
Confidence            68999865444554555679999999999854432     125888864

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=81.40  E-value=1.2  Score=29.35  Aligned_cols=49  Identities=22%  Similarity=0.404  Sum_probs=32.1

Q ss_pred             ccCCCccccccccc--cCCCCeEEcCCCCcccHHHHHHHHhc--CCCCCcccc
Q 028200          154 IEEEDVCPTCLEEY--DAENPRIITKCEHHFHLACIFEWMER--SDTCPVCNQ  202 (212)
Q Consensus       154 ~ee~~~C~ICle~~--~~~~~~~~l~C~H~FH~~CI~~Wl~~--~~tCPvCr~  202 (212)
                      ..+.+.|.||...-  ..+..+..-.|.-.||..|+..-+.-  .=.||.|+.
T Consensus        13 ~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~   65 (71)
T 2ku3_A           13 IDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQ   65 (71)
T ss_dssp             CCSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcC
Confidence            45677899998764  23333444568999999999753211  224888854

>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

Probab=81.36  E-value=1.2  Score=38.66  Aligned_cols=49  Identities=24%  Similarity=0.512  Sum_probs=35.9

Q ss_pred             CccccccccccCCCCeEEcCCCCc--ccHHHHHHHHhcC--CCCCcccccccCCC
Q 028200          158 DVCPTCLEEYDAENPRIITKCEHH--FHLACIFEWMERS--DTCPVCNQEMIFDL  208 (212)
Q Consensus       158 ~~C~ICle~~~~~~~~~~l~C~H~--FH~~CI~~Wl~~~--~tCPvCr~~l~~~~  208 (212)
                      ..|||=+..+  ..|.....|.|.  |-+.=+....++.  -.||+|.+.+.+++
T Consensus       216 L~CPlS~~ri--~~P~Rg~~C~HlqCFDl~sfL~~~~~~~~W~CPiC~k~~~~~d  268 (360)
T 4fo9_A          216 LMCPLGKMRL--TIPCRAVTCTHLQCFDAALYLQMNEKKPTWICPVCDKKAAYES  268 (360)
T ss_dssp             SBCTTTCSBC--SSEEEETTCCCCCCEEHHHHHHHHHHSCCCBCTTTCSBCCGGG
T ss_pred             eeCCCcccee--ccCCcCCCCCCCccCCHHHHHHHHhhCCCeECCCCCcccCHHH
Confidence            3699887776  447788899999  7766666655544  46999999886654

>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2

Probab=80.08  E-value=0.95  Score=30.34  Aligned_cols=48  Identities=23%  Similarity=0.406  Sum_probs=31.2

Q ss_pred             cCCCccccccccccCCCC-eEEcCCCCcccHHHHHHHHh-----cCCCCCccccc
Q 028200          155 EEEDVCPTCLEEYDAENP-RIITKCEHHFHLACIFEWME-----RSDTCPVCNQE  203 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~-~~~l~C~H~FH~~CI~~Wl~-----~~~tCPvCr~~  203 (212)
                      .+...| ||...++.+.. +..-.|...||..|+.--..     ..-.||.|+..
T Consensus        10 ~~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~   63 (79)
T 1wep_A           10 LVPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAV   63 (79)
T ss_dssp             CCCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTT
T ss_pred             CCccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCcccc
Confidence            344456 99988753333 33456899999999853221     23469999864

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=80.01  E-value=0.46  Score=33.44  Aligned_cols=45  Identities=20%  Similarity=0.305  Sum_probs=31.2

Q ss_pred             CCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc---CCCCCcccc
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER---SDTCPVCNQ  202 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~---~~tCPvCr~  202 (212)
                      ...| ||-.....+.-+..-.|.-.||..|+..=+..   .-.||.|+.
T Consensus        28 ~vrC-iC~~~~~~~~mi~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~   75 (98)
T 2lv9_A           28 VTRC-ICGFTHDDGYMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQP   75 (98)
T ss_dssp             BCCC-TTSCCSCSSCEEEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSS
T ss_pred             CEEe-ECCCccCCCcEEEcCCCCCcCcCcCCCCCccCCCCCEECCCCcC
Confidence            3457 89877665554555678999999998653322   236999974

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	212
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	3e-13
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-10
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	2e-10
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	6e-07
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	8e-07
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	9e-07
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	4e-06
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	2e-05
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	1e-04
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	2e-04
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	2e-04
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	3e-04
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	4e-04
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	0.003

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 59.9 bits (145), Expect = 3e-13
 Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 154 IEEEDVCPTCLEEY-DAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI 205
           +++   C  CL E  D E  R + +C H FH  C+  W+    TCP+C   ++
Sbjct: 2   MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 53.0 bits (127), Expect = 1e-10
 Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 158 DVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEM 204
           + CP CLE+    N  +   C H F   CI  W+ ++ TCP+C   +
Sbjct: 6   ERCPICLEDP--SNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPV 50

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 2e-10
 Identities = 16/66 (24%), Positives = 20/66 (30%), Gaps = 15/66 (22%)

Query: 156 EEDVCPTCLEEYDA---------------ENPRIITKCEHHFHLACIFEWMERSDTCPVC 200
             D C  C                     E       C H FH  CI  W++    CP+ 
Sbjct: 20  VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLD 79

Query: 201 NQEMIF 206
           N+E  F
Sbjct: 80  NREWEF 85

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

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

 Score = 43.8 bits (103), Expect = 6e-07
 Identities = 13/51 (25%), Positives = 20/51 (39%), Gaps = 4/51 (7%)

Query: 155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME-RSDTCPVCNQEM 204
               +C  C E    ++ +I   C H    +C+  W E     CP C  E+
Sbjct: 21  STFQLCKICAEND--KDVKI-EPCGHLMCTSCLTSWQESEGQGCPFCRCEI 68

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 8e-07
 Identities = 9/51 (17%), Positives = 17/51 (33%), Gaps = 3/51 (5%)

Query: 156 EEDVCPTCLEEY--DAENPRIITKCEHHFHLACIFEWME-RSDTCPVCNQE 203
           ++  CP C      +     ++  C H    +C+       +  CP C   
Sbjct: 2   DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTP 52

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

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 = 42.5 bits (99), Expect = 9e-07
 Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 4/53 (7%)

Query: 155 EEEDVCPTCLEEYDA--ENPRIITKCEHHFHLACIFEWMERSD--TCPVCNQE 203
           E+  VC  C EE           T    + H +C+  W+  S    C +C   
Sbjct: 4   EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVV 56

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

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 = 42.0 bits (98), Expect = 4e-06
 Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 6/60 (10%)

Query: 147 VHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD---TCPVCNQE 203
           V +V+  +++   CP CLE    + P + TKC+H F   C+ + + +      CP+C  +
Sbjct: 11  VQNVINAMQKILECPICLELI--KEP-VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKND 67

>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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.5 bits (92), Expect = 2e-05
 Identities = 16/69 (23%), Positives = 22/69 (31%), Gaps = 11/69 (15%)

Query: 135 STKELEVELSKSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME-R 193
           STK L V+             +   C  C          + T C+H F   CI   ++  
Sbjct: 8   STKLLAVDFPAHF-------VKSISCQICEHIL---ADPVETSCKHLFCRICILRCLKVM 57

Query: 194 SDTCPVCNQ 202
              CP C  
Sbjct: 58  GSYCPSCRY 66

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 1e-04
 Identities = 9/47 (19%), Positives = 16/47 (34%), Gaps = 2/47 (4%)

Query: 160 CPTCLEEYDAENPRI-ITKCEHHFHLACIFEWMERSDT-CPVCNQEM 204
           CP C+E  + ++       C +     C        +  CP C +  
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPY 49

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 2e-04
 Identities = 14/65 (21%), Positives = 23/65 (35%), Gaps = 8/65 (12%)

Query: 155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME--------RSDTCPVCNQEMIF 206
                C  CL EY  E    I +C+  F   C+ +++E         + +CP        
Sbjct: 3   SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQG 62

Query: 207 DLPVD 211
            L  +
Sbjct: 63  HLQEN 67

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (85), Expect = 2e-04
 Identities = 13/59 (22%), Positives = 20/59 (33%), Gaps = 4/59 (6%)

Query: 145 KSVHHVVAVIEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQE 203
                 +  +E+   C  C        P  +  CEH F   C+ + +     CPVC   
Sbjct: 10  AHSRAALDRLEKLLRCSRCTNIL--REPVCLGGCEHIFCSNCVSDCI--GTGCPVCYTP 64

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.2 bits (81), Expect = 3e-04
 Identities = 10/49 (20%), Positives = 16/49 (32%), Gaps = 6/49 (12%)

Query: 155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQE 203
            +   C  C  E   + P++   C H     C+         CP+C   
Sbjct: 4   FQFLRCQQCQAEA--KCPKL-LPCLHTLCSGCLEAS---GMQCPICQAP 46

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.5 bits (83), Expect = 4e-04
 Identities = 20/86 (23%), Positives = 28/86 (32%), Gaps = 22/86 (25%)

Query: 135 STKELEVELSKSVHHVVAVIEEEDVCPTCLE---------------EYDAENPRIITKCE 179
           S+ E E  + K    +    EE+  C  C+E                        +TKC 
Sbjct: 5   SSGEPEQVIRKYTEELKVAPEED--CIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCS 62

Query: 180 HHFHLACIFEWMERSD-----TCPVC 200
           H FHL C+       +      CP C
Sbjct: 63  HAFHLLCLLAMYCNGNKDGSLQCPSC 88

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 32.8 bits (74), Expect = 0.003
 Identities = 6/46 (13%), Positives = 19/46 (41%), Gaps = 2/46 (4%)

Query: 159 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEM 204
           +C    +      P +  K    F  + + ++++ +   P+ N+ +
Sbjct: 2   LCAISGKVP--RRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPL 45

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	212
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.76
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.62
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.6
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.58
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.57
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.54
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.52
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.5
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.41
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.39
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.36
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.34
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.23
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.21
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.2
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.01
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.76
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	95.48
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	92.85
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	92.71
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	92.71
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	88.77
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	87.67
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	86.89
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	86.0
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	84.73

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=99.76  E-value=1.2e-19  Score=116.82  Aligned_cols=52  Identities=27%  Similarity=0.781  Sum_probs=45.4

Q ss_pred             cCCCccccccccccCCCCeEEc-CCCCcccHHHHHHHHhcCCCCCcccccccC
Q 028200          155 EEEDVCPTCLEEYDAENPRIIT-KCEHHFHLACIFEWMERSDTCPVCNQEMIF  206 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l-~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~  206 (212)
                      +++..|+|||++|..++.++.+ .|+|.||..||.+||+++++||+||+.|++
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~v   55 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV   55 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSCC
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeEC
Confidence            4566799999999887766655 699999999999999999999999998863

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=99.62  E-value=7.9e-17  Score=107.68  Aligned_cols=47  Identities=34%  Similarity=0.875  Sum_probs=41.7

Q ss_pred             CCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCccccccc
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMI  205 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~  205 (212)
                      .+.|+||++.|.  ++.+.++|||.||..||.+||+++.+||+||+++.
T Consensus         5 ~d~C~IC~~~~~--~~~~~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           5 AERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCCC--SCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCccCCcCcc--CCcEEeCCCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            456999999985  35678999999999999999999999999999873

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=2.5e-16  Score=110.43  Aligned_cols=52  Identities=29%  Similarity=0.635  Sum_probs=44.2

Q ss_pred             CCCccccccccccCCC---------------CeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCC
Q 028200          156 EEDVCPTCLEEYDAEN---------------PRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFD  207 (212)
Q Consensus       156 e~~~C~ICle~~~~~~---------------~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~  207 (212)
                      .++.|+||++.+....               .+..++|||.||..||.+||+.+++||+||+++.++
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   86 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQ   86 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCCEE
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCCcCCCCCCccccc
Confidence            4556999999885422               467789999999999999999999999999998765

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=6e-16  Score=102.42  Aligned_cols=53  Identities=19%  Similarity=0.483  Sum_probs=42.0

Q ss_pred             CCCcccccccccc--CCCCeEEcCCCCcccHHHHHHHHhc-CCCCCcccccccCCC
Q 028200          156 EEDVCPTCLEEYD--AENPRIITKCEHHFHLACIFEWMER-SDTCPVCNQEMIFDL  208 (212)
Q Consensus       156 e~~~C~ICle~~~--~~~~~~~l~C~H~FH~~CI~~Wl~~-~~tCPvCr~~l~~~~  208 (212)
                      ++.+|+||++.+.  ......+++|||.||..||.+|+++ +.+||+||+.+..++
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~   57 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSN   57 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCccccc
Confidence            4567999999863  2344567899999999999999965 568999999885543

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

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

Probab=99.57  E-value=1.1e-15  Score=104.88  Aligned_cols=51  Identities=27%  Similarity=0.656  Sum_probs=43.3

Q ss_pred             CCccccccccccCCCCeEEcCCCCcccHHHHHHHHh-cCCCCCcccccccCCCCC
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWME-RSDTCPVCNQEMIFDLPV  210 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~-~~~tCPvCr~~l~~~~~~  210 (212)
                      ...|+||++.+..   .++++|||.||..||.+||+ ++++||+||+.|.....+
T Consensus        23 ~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~i   74 (79)
T d1fbva4          23 FQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPI   74 (79)
T ss_dssp             TTBCTTTSSSBCC---EECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCCS
T ss_pred             CCCCccCCCcCCC---eEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCcee
Confidence            4569999998864   67899999999999999997 457899999999765544

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=7.4e-16  Score=97.55  Aligned_cols=48  Identities=19%  Similarity=0.470  Sum_probs=39.9

Q ss_pred             ccccccccccCCCC-eEEcCCCCcccHHHHHHHHhcC-CCCCcccccccC
Q 028200          159 VCPTCLEEYDAENP-RIITKCEHHFHLACIFEWMERS-DTCPVCNQEMIF  206 (212)
Q Consensus       159 ~C~ICle~~~~~~~-~~~l~C~H~FH~~CI~~Wl~~~-~tCPvCr~~l~~  206 (212)
                      .|+|||++|..++. ...++|||.||..||.+|++.. .+||+||+.+..
T Consensus         2 eCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            49999999976544 4456899999999999999864 579999998753

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=3.4e-15  Score=109.06  Aligned_cols=51  Identities=29%  Similarity=0.594  Sum_probs=40.7

Q ss_pred             CCccccccccccC---------------CCCeEEcCCCCcccHHHHHHHHhcC-----CCCCcccccccCC
Q 028200          157 EDVCPTCLEEYDA---------------ENPRIITKCEHHFHLACIFEWMERS-----DTCPVCNQEMIFD  207 (212)
Q Consensus       157 ~~~C~ICle~~~~---------------~~~~~~l~C~H~FH~~CI~~Wl~~~-----~tCPvCr~~l~~~  207 (212)
                      ++.|+||++.+..               ...+.+++|+|.||..||.+||+++     .+||+||+.+-.+
T Consensus        25 ~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             cccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            4469999998743               2346678999999999999999864     4899999877544

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.50  E-value=2.5e-15  Score=96.46  Aligned_cols=50  Identities=14%  Similarity=0.280  Sum_probs=43.6

Q ss_pred             ccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCCCC
Q 028200          159 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLPV  210 (212)
Q Consensus       159 ~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~~~  210 (212)
                      .|+||++.+.  ++++...|||.||..||.+||+++++||+||+.+..++.+
T Consensus         2 ~C~Ic~~~~~--~Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dLi   51 (56)
T d2baya1           2 LCAISGKVPR--RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIV   51 (56)
T ss_dssp             CCTTTCSCCS--SEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCE
T ss_pred             CCccCCchHH--hcCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhce
Confidence            6999999885  4566667999999999999999999999999999877654

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

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=99.41  E-value=5.4e-14  Score=91.27  Aligned_cols=53  Identities=25%  Similarity=0.406  Sum_probs=40.0

Q ss_pred             ccCCCccccccccccCCCC--eEEcCCCCcccHHHHHHHHhc--CCCCCcccccccC
Q 028200          154 IEEEDVCPTCLEEYDAENP--RIITKCEHHFHLACIFEWMER--SDTCPVCNQEMIF  206 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~--~~~l~C~H~FH~~CI~~Wl~~--~~tCPvCr~~l~~  206 (212)
                      +++..+|+||++++.....  .....|+|.||..||.+|++.  +.+||+||+++.+
T Consensus         3 ded~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           3 DEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             TCSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            4667789999998864321  122335699999999999954  5689999998765

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.39  E-value=6.5e-14  Score=97.38  Aligned_cols=49  Identities=22%  Similarity=0.510  Sum_probs=41.0

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC-CCCCcccccccCC
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS-DTCPVCNQEMIFD  207 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~-~tCPvCr~~l~~~  207 (212)
                      ++..|+||++.|..   .++++|||.||..||.+|++.. .+||+||..+...
T Consensus        22 ~~l~C~IC~~~~~~---pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~   71 (86)
T d1rmda2          22 KSISCQICEHILAD---PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (86)
T ss_dssp             HHTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             cCcCCccCCcchhc---ceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChh
Confidence            34579999999865   6788999999999999999754 5899999987543

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

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]

Probab=99.36  E-value=8.1e-14  Score=99.96  Aligned_cols=51  Identities=27%  Similarity=0.715  Sum_probs=41.3

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCC---CCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSD---TCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~---tCPvCr~~l~~~~  208 (212)
                      ++...|+||++.|..   .+.++|||.||..||.+|+++.+   +||+||+.+...+
T Consensus        19 ~~~l~CpIC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   72 (103)
T d1jm7a_          19 QKILECPICLELIKE---PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS   72 (103)
T ss_dssp             HHHTSCSSSCCCCSS---CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTT
T ss_pred             ccCcCCCccCchhCC---eEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhh
Confidence            345569999999864   45689999999999999997753   7999999885443

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=7.1e-14  Score=89.53  Aligned_cols=48  Identities=19%  Similarity=0.429  Sum_probs=40.0

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCCC
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDLP  209 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~~  209 (212)
                      +...|+||++.|..   .++++|||.||..||.+|   +.+||+||+.+.....
T Consensus         5 ~~l~C~IC~~~~~~---p~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~~   52 (56)
T d1bora_           5 QFLRCQQCQAEAKC---PKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGAD   52 (56)
T ss_dssp             CCSSCSSSCSSCBC---CSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCCSS
T ss_pred             CCCCCcccCcccCC---CEEecCCCHHhHHHHHcC---CCcCcCCCCcccCCCC
Confidence            34589999999865   457899999999999877   6789999999976654

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.23  E-value=6.2e-13  Score=94.23  Aligned_cols=50  Identities=26%  Similarity=0.565  Sum_probs=40.3

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~  208 (212)
                      ++...|+||++.|..  ++.+++|||.||..||.+|+.  .+||+||+.+...+
T Consensus        20 ~~~l~C~IC~~~~~~--pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~   69 (97)
T d1jm7b_          20 EKLLRCSRCTNILRE--PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQD   69 (97)
T ss_dssp             HHTTSCSSSCSCCSS--CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSS
T ss_pred             hhcCCCccCCchhhc--CceeCCCCCchhHHHHHHHHh--ccccccCCcCchhh
Confidence            345679999999954  555678999999999999985  45999999876544

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

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=99.21  E-value=5.1e-12  Score=85.86  Aligned_cols=51  Identities=22%  Similarity=0.481  Sum_probs=43.1

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC-CCCCcccccccCCC
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS-DTCPVCNQEMIFDL  208 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~-~tCPvCr~~l~~~~  208 (212)
                      .++..|+||++.|..   .++++|||.|+..||.+|++.+ .+||+|+..+..++
T Consensus         6 P~~l~CpIc~~~m~d---PV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~   57 (78)
T d1t1ha_           6 PEYFRCPISLELMKD---PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAG   57 (78)
T ss_dssp             SSSSSCTTTSCCCSS---EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCC
T ss_pred             CccCCCcCcCchhhC---ceEccCCCcchHHHHHHHHHHCCCCCCcccccCCccc
Confidence            357789999999965   5678999999999999999875 57999999886554

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.20  E-value=3.7e-12  Score=87.04  Aligned_cols=50  Identities=16%  Similarity=0.107  Sum_probs=42.5

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhc-CCCCCcccccccCCC
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMER-SDTCPVCNQEMIFDL  208 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~-~~tCPvCr~~l~~~~  208 (212)
                      ++..|+||++.|..   .++++|||.|+..||.+|+.+ +.+||+||+.+..++
T Consensus         6 ~~l~CpIc~~l~~d---Pv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~   56 (80)
T d2c2la2           6 DYLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQ   56 (80)
T ss_dssp             STTBCTTTCSBCSS---EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGG
T ss_pred             ccccCcCcCchhhh---hcccCCcCeecHHHHHHHHhcCCccCCCccccccccc
Confidence            56789999999966   568999999999999999975 457999999876543

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Ubiquitin conjugation factor E4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.01  E-value=1e-10  Score=82.77  Aligned_cols=51  Identities=12%  Similarity=0.068  Sum_probs=43.2

Q ss_pred             CCCccccccccccCCCCeEEcCCC-CcccHHHHHHHHhcCCCCCcccccccCCCC
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCE-HHFHLACIFEWMERSDTCPVCNQEMIFDLP  209 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~-H~FH~~CI~~Wl~~~~tCPvCr~~l~~~~~  209 (212)
                      ++..||||++.|..   .++++|+ |.|+..||.+||+++.+||+||+.+..++.
T Consensus        21 ~~f~CPI~~~lm~d---PV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L   72 (98)
T d1wgma_          21 DEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQI   72 (98)
T ss_dssp             TTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTS
T ss_pred             HHhCCcCchhHHHH---HHhcccccchhhHHHHHHHHHhcCCcccccccccchhh
Confidence            46789999999976   6677765 579999999999999999999999876553

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.76  E-value=1.2e-09  Score=76.22  Aligned_cols=45  Identities=29%  Similarity=0.626  Sum_probs=37.2

Q ss_pred             CCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC--------CCCCccc
Q 028200          157 EDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS--------DTCPVCN  201 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~--------~tCPvCr  201 (212)
                      ...|+||++++..++...+++|+|.||..||..|++.+        -+||.|+
T Consensus         5 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           5 SSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            45699999999777767778999999999999999642        2699854

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

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.48  E-value=0.0031  Score=37.72  Aligned_cols=44  Identities=23%  Similarity=0.607  Sum_probs=32.8

Q ss_pred             ccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC----CCCCcccc
Q 028200          159 VCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS----DTCPVCNQ  202 (212)
Q Consensus       159 ~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~----~tCPvCr~  202 (212)
                      .|.||...-..++-+..-.|...||..|+..-+...    =.||.|+.
T Consensus         2 ~C~vC~~~~~~~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            488998765555555556799999999999877543    25999975

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.85  E-value=0.0082  Score=37.21  Aligned_cols=48  Identities=17%  Similarity=0.444  Sum_probs=34.4

Q ss_pred             ccCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC----CCCCcccccc
Q 028200          154 IEEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS----DTCPVCNQEM  204 (212)
Q Consensus       154 ~ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~----~tCPvCr~~l  204 (212)
                      ++.++.|.||.+   .++-+..-.|.-.||..||...+...    =.||.|+...
T Consensus         6 d~~~~~C~~C~~---~g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           6 DHHMEFCRVCKD---GGELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             CSSCSSCTTTCC---CSSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             cCCcCCCcCCCC---CCeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            345667999986   34545556789999999998766442    3699997644

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.71  E-value=0.032  Score=36.55  Aligned_cols=35  Identities=26%  Similarity=0.571  Sum_probs=25.4

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHH
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEW  190 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~W  190 (212)
                      ..+..|.|| +.|..+...-.=-|+.+||..|+.+-
T Consensus        13 ~~D~mC~vC-~v~t~~~l~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          13 VNDEMCDVC-EVWTAESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTT-CCCCSSCCSSCSSSSSCCCHHHHHHH
T ss_pred             CcCcccccc-CcccccceecceeecchhhHHHHHHh
Confidence            346679999 88876543222237999999999985

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.71  E-value=0.021  Score=36.23  Aligned_cols=48  Identities=21%  Similarity=0.567  Sum_probs=34.3

Q ss_pred             cCCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcC----CCCCccccccc
Q 028200          155 EEEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERS----DTCPVCNQEMI  205 (212)
Q Consensus       155 ee~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~----~tCPvCr~~l~  205 (212)
                      +...+|.||..   .++.+..-.|...||..|+...+...    =.||.|+....
T Consensus         5 d~c~~C~~C~~---~~~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   56 (70)
T d1fp0a1           5 DSATICRVCQK---PGDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   56 (70)
T ss_dssp             SSSSCCSSSCS---SSCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             CCCCCCCCCCC---cCEEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCc
Confidence            34456777765   45556666799999999999887553    25999976543

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=88.77  E-value=0.091  Score=32.35  Aligned_cols=48  Identities=31%  Similarity=0.621  Sum_probs=33.5

Q ss_pred             CCCccccccccccCCCCeE-EcCCCCcccHHHHHHHH---h--cCCCCCccccc
Q 028200          156 EEDVCPTCLEEYDAENPRI-ITKCEHHFHLACIFEWM---E--RSDTCPVCNQE  203 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~-~l~C~H~FH~~CI~~Wl---~--~~~tCPvCr~~  203 (212)
                      ....|.||...+..++..+ .-.|+..||..|+..=.   .  ..-.||.|+..
T Consensus         5 ~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            3456999999886665544 56799999999986321   1  12369999753

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.67  E-value=0.46  Score=29.91  Aligned_cols=37  Identities=19%  Similarity=0.331  Sum_probs=28.2

Q ss_pred             CCccccccccccCCCCeEEcC-CCCcccHHHHHHHHhc
Q 028200          157 EDVCPTCLEEYDAENPRIITK-CEHHFHLACIFEWMER  193 (212)
Q Consensus       157 ~~~C~ICle~~~~~~~~~~l~-C~H~FH~~CI~~Wl~~  193 (212)
                      ...|.+|.|.+++.+-+.... =+|.||..|-+..+++
T Consensus         8 ~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~   45 (80)
T d2cs3a1           8 PLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   45 (80)
T ss_dssp             SCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             ceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHh
Confidence            467999999998766443211 1799999999999976

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Death associated transcription factor 1, Datf1 (DIO-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.89  E-value=0.26  Score=31.02  Aligned_cols=46  Identities=22%  Similarity=0.497  Sum_probs=30.2

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHH------HHH---hcCCCCCcccc
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIF------EWM---ERSDTCPVCNQ  202 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~------~Wl---~~~~tCPvCr~  202 (212)
                      +...| ||...+..+.-+..-.|.-.||..|+.      ..+   ...-.||.|+.
T Consensus        15 ~~~~C-iC~~~~~~~~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~   69 (76)
T d1wema_          15 NALYC-ICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTI   69 (76)
T ss_dssp             TCCCS-TTCCCCCSSCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHH
T ss_pred             CcCEE-ECCCccCCCeEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcC
Confidence            34458 898776554444456789999999982      111   22357999964

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

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: TFIIH p44 subunit cysteine-rich domain
domain: TFIIH p44 subunit cysteine-rich domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.00  E-value=0.086  Score=32.23  Aligned_cols=45  Identities=22%  Similarity=0.535  Sum_probs=31.5

Q ss_pred             CCCccccccccccCCCCeEEcCCCCcccHHHHHHHHhcCCCCCcc
Q 028200          156 EEDVCPTCLEEYDAENPRIITKCEHHFHLACIFEWMERSDTCPVC  200 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l~C~H~FH~~CI~~Wl~~~~tCPvC  200 (212)
                      ....|--|+..+.....-...+|+++|+.+|=.--=+.-..||-|
T Consensus        14 ~~~~C~gC~~~l~~~~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKDQHVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTTSEEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCCCceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            345699999888654334467899999999944322444679987

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

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=84.73  E-value=0.29  Score=31.21  Aligned_cols=47  Identities=19%  Similarity=0.463  Sum_probs=30.2

Q ss_pred             CCCccccccccccCCCCeEEc---CCCCcccHHHHHH----H--Hh---cCCCCCcccccc
Q 028200          156 EEDVCPTCLEEYDAENPRIIT---KCEHHFHLACIFE----W--ME---RSDTCPVCNQEM  204 (212)
Q Consensus       156 e~~~C~ICle~~~~~~~~~~l---~C~H~FH~~CI~~----W--l~---~~~tCPvCr~~l  204 (212)
                      +...| ||......+ ..+..   .|...||..|+--    +  ..   ..-.||.|+...
T Consensus        15 ~~~~C-~C~~~~~~~-~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T d1wewa_          15 IKVRC-VCGNSLETD-SMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCCCC-SSCCCCCCS-CEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             CccEe-ECCCccCCC-cEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcC
Confidence            34457 999877544 34555   4999999999831    1  11   124699997643