Citrus Sinensis ID: 025541

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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-------220-------230-------240-------250-
Protein Sequence
MSYYTPSCCSSPPKSSSVSAELKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWSSLRMRTSLHTNNVDEISRAELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASSELSDIQQETIQESSVTENADGASDQQRSEAYEEPQAVEHSESRNEDGSTLQNGPKEQGRSSHSLDHEREVRDTTNETGEHEQSRRIPDLTLKSP
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHcccccHHHHHHcccEEEEccccccccccEEEccccccccEEEcccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHcccccccccccHHHHHHccEEEEEccccccccccEEEHcccccccEEEEcccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEcccccccccccccccccccEEEccccEEccc
Coil and Loop (DISEMBL)
msyytpsccssppksssvsAELKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWSSLRMRTSLHTNNVDEISRAELGLKKELREMLPIViykesfsirdtqcsVCLADYqaedklqqipacghafhMDCIDhwltthttcplcrlsllapakasselsDIQQETIqessvtenadgasdqqrseayeepqavehsesrnedgstlqngpkeqgrsshsldherevrdttnetgeheqsrripdltlksp
Flexible Loop (DISEMBL)
msyytpsccssppksSSVSAELKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWsslrmrtslhtnnvdeisraELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASSELSDIQQETiqessvtenadgASDQQRSEAYEEPqavehsesrnedgstlqngpkeqgrsshsldherevrdttnetgeheqsrripdltlksp
Low Complexity Region (SEG)
MSYYTpsccssppksssvsAELKVYQAFIFSVPifftfillllfylfylrrrrVDWSSLRMRTSLHTNNVDEISRAELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASSELSDIQQETIQESSVTENADGASDQQRSEAYEEPQAVEHSESRNEDGSTLQNGPKEQGRSSHSLDHEREVRDTTNETGEHEQSRRIPDLTLKSP
Disordered region (IsUnstruct)
********************ELKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWSSLRMRTSLHTNNVDEISRAELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA****************************************************************************************************
Disordered Region (DISOPRED)
************************YQAFIFSVPIFFTFILLLLFYLFYLRRRR******************************LREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLL**********************************************************************************************D******
Disordered Region (DISEMBL)
*******************AELKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWSSLRMRTSLHTNNVDEISRAELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPA**************************************************************************************************
Disordered Region (DISPRO)
*******************AELKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVD**********************LGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA**************************************************************************************EQSRRIPDLTLKS*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSYYTPSCCSSPPKSSSVSAELKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWSSLRMRTSLHTNNVDEISRAELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASSELSDIQQETIQESSVTENADGASDQQRSEAYEEPQAVEHSESRNEDGSTLQNGPKEQGRSSHSLDHEREVRDTTNETGEHEQSRRIPDLTLKSP
Positional Conservation
no confident homologs detected

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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	251	2.2.26 [Sep-21-2011]
Q9SN28	236	RING-H2 finger protein AT	yes	no	0.848	0.902	0.5	9e-56
Q570X5	261	RING-H2 finger protein AT	no	no	0.533	0.513	0.683	4e-47
Q9SN27	225	E3 ubiquitin-protein liga	no	no	0.808	0.902	0.459	4e-44
Q84TF5	174	RING-H2 zinc finger prote	no	no	0.521	0.752	0.451	6e-22
Q8GW38	369	RING-H2 finger protein AT	no	no	0.442	0.300	0.360	4e-17
Q9XF63	324	RING-H2 finger protein AT	no	no	0.517	0.401	0.308	2e-16
Q940Q4	472	RING-H2 finger protein AT	no	no	0.270	0.144	0.471	5e-16
Q9ZV53	423	Putative RING-H2 finger p	no	no	0.326	0.193	0.440	9e-16
O64763	378	E3 ubiquitin-protein liga	no	no	0.486	0.322	0.3	1e-15
Q9FL42	159	Putative RING-H2 finger p	no	no	0.597	0.943	0.310	4e-15

>sp|Q9SN28|ATL7_ARATH RING-H2 finger protein ATL7 OS=Arabidopsis thaliana GN=ATL7 PE=2 SV=1

 Score =  216 bits (551), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 114/228 (50%), Positives = 149/228 (65%), Gaps = 15/228 (6%)

Query: 1   MSYYTPSCCSSP----PKSSSVSAELKVYQAFIFSVPIFFTFILLLLFYLFYLRRR---R 53
           MSY  P+    P    P +S+ S +LK+YQAFIFSVPI FTFI+L + Y+ YLRR     
Sbjct: 1   MSYSDPNQNPIPETYAPSNSTESEKLKLYQAFIFSVPICFTFIVLFVLYVIYLRRNSTTN 60

Query: 54  VDWSSLRMRTSLHTNNVDEISRAELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQA 113
           VDWSSL MR        + +S AELGL K++REMLP+VIYKESF ++D+QCSVCL DYQA
Sbjct: 61  VDWSSLGMRGGTFVPTNNNLSTAELGLSKDIREMLPVVIYKESFIVKDSQCSVCLGDYQA 120

Query: 114 EDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASSELSDIQQETIQESSVT 173
           E+KLQQ+P+CGH FHM+CID WLT+HTTCPLCRLSL+   K S +LS    E +   S  
Sbjct: 121 EEKLQQMPSCGHTFHMECIDLWLTSHTTCPLCRLSLI--PKPSLDLSHQSTEIV---SSI 175

Query: 174 ENADGASDQQRSEAYEEPQAVEHS---ESRNEDGSTLQNGPKEQGRSS 218
           EN++G     + ++    +A+ H+   E  N D   +    +E  R+S
Sbjct: 176 ENSNGGEASTQPDSQSATEAISHTDDVEEGNRDSQEVSKETEENDRNS 223

Arabidopsis thaliana (taxid: 3702)

>sp|Q570X5|ATL58_ARATH RING-H2 finger protein ATL58 OS=Arabidopsis thaliana GN=ATL58 PE=2 SV=1

 Score =  188 bits (477), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 93/136 (68%), Positives = 108/136 (79%), Gaps = 2/136 (1%)

Query: 15  SSSVSAELKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWSSLRMRTSLHTNNVDEIS 74
           +++ S ELK+YQAFIFSVPI FTFI+L LFYL YLRR   D SSL MRT+    N   +S
Sbjct: 13  AATSSPELKLYQAFIFSVPICFTFIILFLFYLIYLRRSSSDLSSLGMRTTFIPGN--SLS 70

Query: 75  RAELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDH 134
             ELGL KELREMLPIV++KESF++ D+QCSVCL DYQ  DKLQQIP C H FHMDCID 
Sbjct: 71  TIELGLSKELREMLPIVVFKESFTVMDSQCSVCLGDYQPNDKLQQIPVCKHTFHMDCIDL 130

Query: 135 WLTTHTTCPLCRLSLL 150
           WLT+HTTCPLCRL+L+
Sbjct: 131 WLTSHTTCPLCRLALI 146

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SN27|ATL59_ARATH E3 ubiquitin-protein ligase ATL59 OS=Arabidopsis thaliana GN=ATL59 PE=1 SV=1

 Score =  178 bits (451), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 103/224 (45%), Positives = 136/224 (60%), Gaps = 21/224 (9%)

Query: 1   MSYYTPSCCSSPPKSSSVSAELKVYQAFIFSVPIFFTFILLLLFYLFYLRRR---RVDWS 57
           MS+  P   +  P +S+ S  LK    FI  VPI    I+LL+ Y+  +RR     VDWS
Sbjct: 1   MSFIDPR--TYIPSNSTESQILKF--TFIVCVPICVILIVLLVLYI--MRRNSNTNVDWS 54

Query: 58  SLRMRTSLHTNNVDEISRAELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKL 117
           SL     + TNN   +S AELGL K++REMLPIVIYKESF++ DTQCSVCL DYQAE+KL
Sbjct: 55  SLG--GFVPTNN--NLSTAELGLSKDIREMLPIVIYKESFTVNDTQCSVCLGDYQAEEKL 110

Query: 118 QQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASSELSDIQQETIQESSVTENAD 177
           QQ+P+CGH FHM+CID WLT+HTTCPLCRLSL+          D+  ++I+  S  EN +
Sbjct: 111 QQMPSCGHTFHMECIDLWLTSHTTCPLCRLSLIPKPSV-----DLSHQSIEIVSSIENTN 165

Query: 178 GASDQQRSEAYEEPQAVEH---SESRNEDGSTLQNGPKEQGRSS 218
           G     + ++    +A+ H    E  N D   +    +E  R+S
Sbjct: 166 GGEASTQPDSQSATEAIIHIDDVEEGNRDSIEVVKESEENDRNS 209

E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8, UBC10, UBC11, and UBC34 in vitro.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q84TF5|RHA4A_ARATH RING-H2 zinc finger protein RHA4a OS=Arabidopsis thaliana GN=RHA4A PE=2 SV=1

 Score =  104 bits (260), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 61/135 (45%), Positives = 88/135 (65%), Gaps = 4/135 (2%)

Query: 19  SAELKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWSS----LRMRTSLHTNNVDEIS 74
           + +LK+YQAFIFS+PI F+ IL LLFYLFYL+RR    SS    +   +S H  +    S
Sbjct: 16  AIQLKLYQAFIFSIPILFSIILFLLFYLFYLKRRASSLSSPSPMILPVSSSHQTSSHLPS 75

Query: 75  RAELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDH 134
              L +K EL++ L +V++ E    RD+ C VCL +++ +++L ++P C H FH+DCI  
Sbjct: 76  VCLLDVKVELKDKLHVVLFNEELGTRDSLCCVCLGEFELKEELVEMPLCKHIFHLDCIHL 135

Query: 135 WLTTHTTCPLCRLSL 149
           WL +H TCPLCR S+
Sbjct: 136 WLYSHNTCPLCRSSV 150

Arabidopsis thaliana (taxid: 3702)

>sp|Q8GW38|ATL47_ARATH RING-H2 finger protein ATL47 OS=Arabidopsis thaliana GN=ATL47 PE=2 SV=1

 Score = 88.6 bits (218), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 49/136 (36%), Positives = 77/136 (56%), Gaps = 25/136 (18%)

Query: 34  IFFTFILLLLFYLFYLRRRRVDWSSLRMRTSLHTNNVDEISRAEL--------------G 79
           IFF   +L L   +YL+++R + SS    +   +N   E S ++               G
Sbjct: 63  IFFICSILHLLVRYYLKKKRSNLSS----SPNESNQNPEFSDSDTYQRQLQQLFHLHDSG 118

Query: 80  LKKELREMLPIVIYKESFSIRDTQ----CSVCLADYQAEDKLQQIPACGHAFHMDCIDHW 135
           L + L + LP+ +YKE   I+ T+    C+VCL ++  +DKL+ +P C HAFH+DCID W
Sbjct: 119 LDQALIDALPVFLYKE---IKGTKEPFDCAVCLCEFSEDDKLRLLPNCSHAFHIDCIDTW 175

Query: 136 LTTHTTCPLCRLSLLA 151
           L +++TCPLCR +L +
Sbjct: 176 LLSNSTCPLCRGTLFS 191

Arabidopsis thaliana (taxid: 3702)

>sp|Q9XF63|ATL3_ARATH RING-H2 finger protein ATL3 OS=Arabidopsis thaliana GN=ATL3 PE=2 SV=1

 Score = 86.3 bits (212), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 42/136 (30%), Positives = 72/136 (52%), Gaps = 6/136 (4%)

Query: 88  LPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRL 147
           LPIV +++       +CS+CL++    DK + +P C H+FH++CID W  +H+TCP+CR 
Sbjct: 111 LPIVFFRQDSCKDGLECSICLSELVKGDKARLLPKCNHSFHVECIDMWFQSHSTCPICRN 170

Query: 148 SLLAPAKASSELSDIQQETIQESSVTENADGASDQQRSEAYEEPQAV------EHSESRN 201
           ++L P +ASS+  +   +  + +  T N   A  Q  + + E P  V      +   + N
Sbjct: 171 TVLGPEQASSKRVEQVPDNAENAGTTNNNHDALSQLSTSSPEFPTNVLVWGRQDQVSTGN 230

Query: 202 EDGSTLQNGPKEQGRS 217
            +  T ++G    G S
Sbjct: 231 TNVGTQEDGAAGNGAS 246

Arabidopsis thaliana (taxid: 3702)

>sp|Q940Q4|ATL13_ARATH RING-H2 finger protein ATL13 OS=Arabidopsis thaliana GN=ATL13 PE=2 SV=2

 Score = 84.7 bits (208), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 33/70 (47%), Positives = 48/70 (68%), Gaps = 2/70 (2%)

Query: 79  GLKKELREMLPIVIYKESFSIRDT--QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWL 136
           G+ +   + LP+  YK    +++    C+VCL +++ EDKL+ +P C HAFHMDCID WL
Sbjct: 107 GVDQSFIDTLPVFHYKSIIGLKNYPFDCAVCLCEFETEDKLRLLPKCSHAFHMDCIDTWL 166

Query: 137 TTHTTCPLCR 146
            +H+TCPLCR
Sbjct: 167 LSHSTCPLCR 176

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZV53|ATL49_ARATH Putative RING-H2 finger protein ATL49 OS=Arabidopsis thaliana GN=ATL49 PE=3 SV=1

 Score = 84.0 bits (206), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 37/84 (44%), Positives = 53/84 (63%), Gaps = 2/84 (2%)

Query: 79  GLKKELREMLPIVIYKE--SFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWL 136
           G+ + L + LP+  YK      I    C VCL +++ EDKL+ +P C HAFH++CID WL
Sbjct: 99  GVDQSLIDTLPVFHYKSIVGLKISPFDCPVCLCEFETEDKLRLLPKCSHAFHVECIDTWL 158

Query: 137 TTHTTCPLCRLSLLAPAKASSELS 160
            +H+TCPLCR +LL+   +   LS
Sbjct: 159 LSHSTCPLCRSNLLSGFSSHHNLS 182

May be involved in female gametophyte development.

Arabidopsis thaliana (taxid: 3702)

>sp|O64763|ATL9_ARATH E3 ubiquitin-protein ligase ATL9 OS=Arabidopsis thaliana GN=ATL9 PE=1 SV=1

 Score = 83.2 bits (204), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 39/130 (30%), Positives = 66/130 (50%), Gaps = 8/130 (6%)

Query: 29  IFSVPIFFTFILLLLFYLFYLRRRRVDWSSLRMRTSLHTNNVDEISR----AELGLKKEL 84
           +  + + F  I  ++F   + RR    +S   +  S   +   ++ R       GL  E 
Sbjct: 52  VVVITVLFLVIFFMVFGSIFCRRSNAQFSRSSIFRSTDADAESQVVRIRRLTARGLDAEA 111

Query: 85  REMLPIVIYKESFSIR----DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHT 140
            E  P  +Y E  ++R      +C+VCL +++ ++ L+ +P C H FH DC+D WL+ H+
Sbjct: 112 IETFPTFLYSEVKAVRIGKGGVECAVCLCEFEDDETLRLMPPCCHVFHADCVDVWLSEHS 171

Query: 141 TCPLCRLSLL 150
           TCPLCR  L+
Sbjct: 172 TCPLCRADLV 181

E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 in vitro. May be involved in the early steps of the plant defense signaling pathway.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9FL42|ATL69_ARATH Putative RING-H2 finger protein ATL69 OS=Arabidopsis thaliana GN=ATL69 PE=3 SV=1

 Score = 81.6 bits (200), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 50/161 (31%), Positives = 80/161 (49%), Gaps = 11/161 (6%)

Query: 11  SPPKSSSVSAELKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWSSLRMRTSLHTNNV 70
           SPP S      L    A   S+ +  +FI+L  +     +    D ++  +   L +   
Sbjct: 5   SPPASG---VGLGYGIAIAVSILVLISFIMLASYICIRSKSTGRDEATSDVVLDLPSPAA 61

Query: 71  DEISRAELGLKKELREMLPIVIYKESFSI---RDTQCSVCLADYQAEDKLQQIPACGHAF 127
           +     +LGL + + E  P ++  +S  +    +  CS+CL DY+A + ++ IP C H F
Sbjct: 62  E----VKLGLDRPVIESYPRIVLGDSRRLPRPNNGPCSICLCDYEAREPVRCIPECNHCF 117

Query: 128 HMDCIDHWLTTHTTCPLCRLSLLAPAKASSELSDIQQETIQ 168
           H DC+D WL T  TCPLCR S  AP++ ++ LSD+     Q
Sbjct: 118 HTDCVDEWLRTSATCPLCRNS-PAPSRLATPLSDLVPLAFQ 157

Arabidopsis thaliana (taxid: 3702)

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	251
255561478	337	protein with unknown function [Ricinus c	0.908	0.676	0.611	2e-58
297809223	237	zinc finger family protein [Arabidopsis	0.896	0.949	0.487	9e-56
15234955	236	RING-H2 finger protein ATL7 [Arabidopsis	0.848	0.902	0.5	5e-54
357470167	226	RING finger family protein [Medicago tru	0.768	0.853	0.559	1e-52
359493589	221	PREDICTED: RING-H2 finger protein ATL7-l	0.848	0.963	0.601	4e-52
224124408	171	predicted protein [Populus trichocarpa]	0.649	0.953	0.646	3e-51
145336373	261	RING-H2 finger protein ATL58 [Arabidopsi	0.533	0.513	0.683	2e-45
12322389	508	unknown protein; 73879-71181 [Arabidopsi	0.533	0.263	0.683	7e-45
356532271	219	PREDICTED: RING-H2 finger protein ATL7-l	0.725	0.831	0.552	3e-43
115446717	233	Os02g0557300 [Oryza sativa Japonica Grou	0.848	0.914	0.526	2e-42

>gi|255561478|ref|XP_002521749.1| protein with unknown function [Ricinus communis] gi|223538962|gb|EEF40559.1| protein with unknown function [Ricinus communis]

 Score =  231 bits (590), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 143/234 (61%), Positives = 166/234 (70%), Gaps = 6/234 (2%)

Query: 18  VSAELKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWSSLRMRTSLHTNNVDEISRAE 77
            S ELK+YQAFIFSVPIFFTF+LL LFYLFYLRRRRVDW+SLRMR +L  +  D I RAE
Sbjct: 22  ASTELKLYQAFIFSVPIFFTFVLLFLFYLFYLRRRRVDWASLRMRANLQGS--DNIFRAE 79

Query: 78  LGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT 137
           LGLKKE+REMLPI++YKESFS++DTQC VCL DYQAED+LQQIPACGH FHM CIDHWL 
Sbjct: 80  LGLKKEVREMLPIIVYKESFSVKDTQCPVCLGDYQAEDRLQQIPACGHTFHMVCIDHWLA 139

Query: 138 THTTCPLCRLSLLAPAKASSELSDIQQETIQESSVTENADGASDQQRS--EAYEEPQAVE 195
            HTTCPLCRLSL+APAK  +E  + Q E  QES V  +    S Q  S   +  E  +  
Sbjct: 140 NHTTCPLCRLSLVAPAKVPTESPNNQVEAGQESFVAVSGGETSAQSGSGPGSCGESNSRG 199

Query: 196 HSESRNEDGSTLQNGPKEQGRSSHSLDHEREVRDTTNETGEHEQSRRIPDLTLK 249
            SE RNED  T  +  +E+ R S S D  +EVRD   E+ E E  R   +L LK
Sbjct: 200 LSEPRNEDSGTAHSSAEEEERRSQSADQGKEVRDEKKESEERENIRE--ELKLK 251

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297809223|ref|XP_002872495.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata] gi|297318332|gb|EFH48754.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  222 bits (566), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 121/248 (48%), Positives = 157/248 (63%), Gaps = 23/248 (9%)

Query: 1   MSYYTPSCCSSP----PKSSSVSAELKVYQAFIFSVPIFFTFILLLLFYLFYLRRR---R 53
           MSY  P+    P    P +S+ S +LK+YQAFIFSVPI FTFI+L + Y+ YLRR     
Sbjct: 1   MSYSDPNQNPIPETYAPSNSTESEKLKLYQAFIFSVPICFTFIVLFVLYVIYLRRNSTTN 60

Query: 54  VDWSSLRMRTSLHTNNVDEISRAELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQA 113
           VDWSSL MR  +     + +S AELGL K++REMLPIVIYKESF+++D+QCSVCLADYQA
Sbjct: 61  VDWSSLGMRGGIFVPTNNNLSTAELGLSKDVREMLPIVIYKESFTVKDSQCSVCLADYQA 120

Query: 114 EDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASSELSDIQQETIQESSVT 173
           E+KLQQ+PACGH FHM+CID WLT+HTTCPLCRLSL+   K S +LS   Q+T +  S  
Sbjct: 121 EEKLQQMPACGHTFHMECIDRWLTSHTTCPLCRLSLI--PKPSLDLS---QQTPEIVSPI 175

Query: 174 ENADGASDQQRSEAYEEPQAVEHSESRNEDGSTLQNGPKEQGRSSHSLDHEREVRDTTNE 233
           EN +G     + ++    +A+ H     +DG       +E  R S  +  E    +  N 
Sbjct: 176 ENFNGGEASAQPDSQSTTEAISHI----DDG-------QEGNRDSQEVSKEPAEENDPNS 224

Query: 234 TGEHEQSR 241
            G  +  R
Sbjct: 225 VGTSDGCR 232

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15234955|ref|NP_192753.1| RING-H2 finger protein ATL7 [Arabidopsis thaliana] gi|68565338|sp|Q9SN28.1|ATL7_ARATH RecName: Full=RING-H2 finger protein ATL7 gi|4538979|emb|CAB39767.1| putative protein [Arabidopsis thaliana] gi|7267711|emb|CAB78138.1| putative protein [Arabidopsis thaliana] gi|21689651|gb|AAM67447.1| unknown protein [Arabidopsis thaliana] gi|332657448|gb|AEE82848.1| RING-H2 finger protein ATL7 [Arabidopsis thaliana]

 Score =  216 bits (551), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 114/228 (50%), Positives = 149/228 (65%), Gaps = 15/228 (6%)

Query: 1   MSYYTPSCCSSP----PKSSSVSAELKVYQAFIFSVPIFFTFILLLLFYLFYLRRR---R 53
           MSY  P+    P    P +S+ S +LK+YQAFIFSVPI FTFI+L + Y+ YLRR     
Sbjct: 1   MSYSDPNQNPIPETYAPSNSTESEKLKLYQAFIFSVPICFTFIVLFVLYVIYLRRNSTTN 60

Query: 54  VDWSSLRMRTSLHTNNVDEISRAELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQA 113
           VDWSSL MR        + +S AELGL K++REMLP+VIYKESF ++D+QCSVCL DYQA
Sbjct: 61  VDWSSLGMRGGTFVPTNNNLSTAELGLSKDIREMLPVVIYKESFIVKDSQCSVCLGDYQA 120

Query: 114 EDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASSELSDIQQETIQESSVT 173
           E+KLQQ+P+CGH FHM+CID WLT+HTTCPLCRLSL+   K S +LS    E +   S  
Sbjct: 121 EEKLQQMPSCGHTFHMECIDLWLTSHTTCPLCRLSLI--PKPSLDLSHQSTEIV---SSI 175

Query: 174 ENADGASDQQRSEAYEEPQAVEHS---ESRNEDGSTLQNGPKEQGRSS 218
           EN++G     + ++    +A+ H+   E  N D   +    +E  R+S
Sbjct: 176 ENSNGGEASTQPDSQSATEAISHTDDVEEGNRDSQEVSKETEENDRNS 223

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357470167|ref|XP_003605368.1| RING finger family protein [Medicago truncatula] gi|355506423|gb|AES87565.1| RING finger family protein [Medicago truncatula]

 Score =  212 bits (539), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 118/211 (55%), Positives = 151/211 (71%), Gaps = 18/211 (8%)

Query: 20  AELKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWSSLRMRTS---LHTNNVDEISRA 76
           AELK+Y+AFIFSVPIFFT ILL LFY+FYLR RRVDWSS+RMR+     H +N +  S +
Sbjct: 23  AELKLYRAFIFSVPIFFTLILLFLFYVFYLRPRRVDWSSIRMRSVSVLQHHHNNNATSTS 82

Query: 77  ELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWL 136
           +LGLKKELREMLPI++Y ESFS++DTQCSVCL DYQ ED+LQQIPACGH FHM CID WL
Sbjct: 83  DLGLKKELREMLPIIVYNESFSVKDTQCSVCLLDYQPEDRLQQIPACGHTFHMSCIDLWL 142

Query: 137 TTHTTCPLCRLSLLAPAKASSELSDIQQETIQESSVTENADGASDQQRSEAYEEPQAVEH 196
           ++H+TCPLCRLSLL  AK+S+E+S++Q            A    + +  ++ EE  A+E 
Sbjct: 143 SSHSTCPLCRLSLLPTAKSSTEISEMQ------------ATSNEEMEMQQSDEETLAMEF 190

Query: 197 SESRNE---DGSTLQNGPKEQGRSSHSLDHE 224
           S+SR+    + S +QN   E     H ++ E
Sbjct: 191 SDSRSTRHLETSVIQNVSGEAAIDDHRIEVE 221

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359493589|ref|XP_002266319.2| PREDICTED: RING-H2 finger protein ATL7-like [Vitis vinifera] gi|297734760|emb|CBI16994.3| unnamed protein product [Vitis vinifera]

 Score =  210 bits (535), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 139/231 (60%), Positives = 161/231 (69%), Gaps = 18/231 (7%)

Query: 10  SSPPKSSSVSAELKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWSSLRMRTSLHTNN 69
           S PP   S SAELK+YQAFIFSVPIFFTFILLLLFYLFYLRRRRVDW+SLRMR+S+  N+
Sbjct: 6   SDPPSCCSASAELKLYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWASLRMRSSMQ-ND 64

Query: 70  VDEISR-AELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFH 128
            D  S  +ELGLKKE+REMLPI+++KESFS+ DTQCSVCLADYQAED+LQQIPACGH FH
Sbjct: 65  ADHASGVSELGLKKEVREMLPIIVFKESFSVSDTQCSVCLADYQAEDRLQQIPACGHTFH 124

Query: 129 MDCIDHWLTTHTTCPLCRLSLLAPAKASSELSDIQQETIQESSVTENADGASDQQRSEAY 188
           MDCIDHWL THTTCPLCRLSL A A+  +E   I         + E   G S +Q     
Sbjct: 125 MDCIDHWLATHTTCPLCRLSLTAAARTPAEPLTI---------LVETPHGTSPEQT---- 171

Query: 189 EEPQAVEHSESRNEDGSTLQNGPKE-QGRSSHSLDHEREVRDTTNETGEHE 238
            +P   + S+ RNE+   +     E +G SS   D E   RD  NE   HE
Sbjct: 172 -QPD-TQVSQPRNENERAVHTTTMEAEGGSSECDDCETGTRDARNENERHE 220

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224124408|ref|XP_002319324.1| predicted protein [Populus trichocarpa] gi|222857700|gb|EEE95247.1| predicted protein [Populus trichocarpa]

 Score =  207 bits (527), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 106/164 (64%), Positives = 117/164 (71%), Gaps = 1/164 (0%)

Query: 78  LGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT 137
           +GLKKELREMLPI++YKESFS+RDTQC VCL DYQAEDKLQQIPACGH FHMDCIDHWL 
Sbjct: 1   MGLKKELREMLPIIVYKESFSVRDTQCPVCLGDYQAEDKLQQIPACGHTFHMDCIDHWLA 60

Query: 138 THTTCPLCRLSLLAPAKASSELSDIQQETIQESSVTENADGASDQQRSEAYEEPQAVEHS 197
            H TCPLCRLSLL   KA SE    Q ET+QESS  EN + AS Q R E+ EE QA   S
Sbjct: 61  NHITCPLCRLSLLPSVKAPSEPPRNQVETVQESSAAENGEEASVQPRPESCEESQATPLS 120

Query: 198 ESRNEDGSTLQNGPKEQGRSSHSLDHEREVRDTTNETGEHEQSR 241
           +S +E+  TLQN   E+ R S   D  RE R   NE  EHE SR
Sbjct: 121 QSMDEESGTLQNSAGEEQR-SECADQGREFRFARNEAEEHENSR 163

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145336373|ref|NP_174614.2| RING-H2 finger protein ATL58 [Arabidopsis thaliana] gi|68565103|sp|Q570X5.1|ATL58_ARATH RecName: Full=RING-H2 finger protein ATL58 gi|62318524|dbj|BAD94869.1| hypothetical protein [Arabidopsis thaliana] gi|332193478|gb|AEE31599.1| RING-H2 finger protein ATL58 [Arabidopsis thaliana]

 Score =  188 bits (477), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 93/136 (68%), Positives = 108/136 (79%), Gaps = 2/136 (1%)

Query: 15  SSSVSAELKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWSSLRMRTSLHTNNVDEIS 74
           +++ S ELK+YQAFIFSVPI FTFI+L LFYL YLRR   D SSL MRT+    N   +S
Sbjct: 13  AATSSPELKLYQAFIFSVPICFTFIILFLFYLIYLRRSSSDLSSLGMRTTFIPGN--SLS 70

Query: 75  RAELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDH 134
             ELGL KELREMLPIV++KESF++ D+QCSVCL DYQ  DKLQQIP C H FHMDCID 
Sbjct: 71  TIELGLSKELREMLPIVVFKESFTVMDSQCSVCLGDYQPNDKLQQIPVCKHTFHMDCIDL 130

Query: 135 WLTTHTTCPLCRLSLL 150
           WLT+HTTCPLCRL+L+
Sbjct: 131 WLTSHTTCPLCRLALI 146

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|12322389|gb|AAG51221.1|AC051630_18 unknown protein; 73879-71181 [Arabidopsis thaliana]

 Score =  186 bits (473), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 93/136 (68%), Positives = 108/136 (79%), Gaps = 2/136 (1%)

Query: 15  SSSVSAELKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWSSLRMRTSLHTNNVDEIS 74
           +++ S ELK+YQAFIFSVPI FTFI+L LFYL YLRR   D SSL MRT+    N   +S
Sbjct: 13  AATSSPELKLYQAFIFSVPICFTFIILFLFYLIYLRRSSSDLSSLGMRTTFIPGN--SLS 70

Query: 75  RAELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDH 134
             ELGL KELREMLPIV++KESF++ D+QCSVCL DYQ  DKLQQIP C H FHMDCID 
Sbjct: 71  TIELGLSKELREMLPIVVFKESFTVMDSQCSVCLGDYQPNDKLQQIPVCKHTFHMDCIDL 130

Query: 135 WLTTHTTCPLCRLSLL 150
           WLT+HTTCPLCRL+L+
Sbjct: 131 WLTSHTTCPLCRLALI 146

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356532271|ref|XP_003534697.1| PREDICTED: RING-H2 finger protein ATL7-like [Glycine max]

 Score =  181 bits (459), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 116/210 (55%), Positives = 137/210 (65%), Gaps = 28/210 (13%)

Query: 21  ELKVYQAFIFSVPIFFTFILLLLFYLFYLR-RRRVDWSSLRMRTSLHTNNVDEISRAELG 79
           ELK+Y+AFIF VPIFFT ILL LFYLFYLR R R+ W S   R   + N  + IS   LG
Sbjct: 28  ELKLYRAFIFCVPIFFTLILLFLFYLFYLRPRTRLHWIS-HFRLPSNNNRNNAISTLGLG 86

Query: 80  LKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH 139
           L KELREMLPI++YKESFS++DTQCSVCL DYQAED+LQQIPACGH FHM CID WL TH
Sbjct: 87  LNKELREMLPIIVYKESFSVKDTQCSVCLLDYQAEDRLQQIPACGHTFHMSCIDLWLATH 146

Query: 140 TTCPLCRLSLLAPAKASSELSDIQQETIQESSVTENADGASDQQRSEAYEEPQAVEHSES 199
           TTCPLCR SLL  AK+S++ SD+Q                         EE QA+E SES
Sbjct: 147 TTCPLCRFSLLTTAKSSTQASDMQNN-----------------------EETQAMEFSES 183

Query: 200 ---RNEDGSTLQNGPKEQGRSSHSLDHERE 226
              R+ + +  QN   E   S+H +D E +
Sbjct: 184 TSPRDLETNVFQNVSGEVAISTHCIDVEGQ 213

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115446717|ref|NP_001047138.1| Os02g0557300 [Oryza sativa Japonica Group] gi|113536669|dbj|BAF09052.1| Os02g0557300 [Oryza sativa Japonica Group] gi|215695052|dbj|BAG90243.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  178 bits (452), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 127/241 (52%), Positives = 163/241 (67%), Gaps = 28/241 (11%)

Query: 7   SCCSSPPKS--SSVSAELKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWSSLRMRTS 64
           SC S  P    S+ S ELK+YQAFIFSVP+FFTF+LLL FYLFYLRRRR +W SLRMRT 
Sbjct: 2   SCTSPDPPDYCSAASPELKLYQAFIFSVPVFFTFVLLLFFYLFYLRRRRANWQSLRMRT- 60

Query: 65  LHTNNV--DEISRAELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPA 122
              NN+   +  R E G+KKE+REMLP+V++KESF IR+TQCSVCLADYQ +++LQ+IP 
Sbjct: 61  ---NNLIRGDNPRLECGIKKEMREMLPVVVFKESFLIRETQCSVCLADYQPDERLQRIPP 117

Query: 123 CGHAFHMDCIDHWLTTHTTCPLCRLSLL-APAKASSELSDIQQETIQESSVTENADGASD 181
           CGH FH+DCIDHWL+T+TTCPLCR+SLL +P  AS +  D++ +T++E+S       + D
Sbjct: 118 CGHTFHIDCIDHWLSTNTTCPLCRVSLLPSPKTASIDPVDLEAQTVEENS-------SLD 170

Query: 182 QQRSEAYEEPQAVEHSESRNEDGSTLQN--GPKEQGRSSHSLDHEREVRDTTNETGEHEQ 239
            Q    Y+E +  E+  +R ED +  Q   GP  Q       + E  VR TT    E E 
Sbjct: 171 VQ----YQEGRIDEN--TRQEDQTLQQGSEGPTHQAEE----NEETSVRVTTEPQVEAEG 220

Query: 240 S 240
           S
Sbjct: 221 S 221

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

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	251
TAIR|locus:2124695	236	AT4G10150 [Arabidopsis thalian	0.760	0.809	0.490	6.4e-44
TAIR|locus:2007008	261	AT1G33480 [Arabidopsis thalian	0.836	0.804	0.436	4.8e-39
TAIR|locus:2124700	225	AT4G10160 [Arabidopsis thalian	0.621	0.693	0.523	2.1e-38
TAIR|locus:1006230395	174	AT4G24015 "AT4G24015" [Arabido	0.605	0.873	0.331	1.9e-19
UNIPROTKB|Q8H7N9	353	LOC_Os03g08920 "E3 ubiquitin-p	0.422	0.300	0.431	1.1e-18
TAIR|locus:2122363	345	AT4G09120 [Arabidopsis thalian	0.454	0.330	0.333	4.8e-18
TAIR|locus:2193992	324	ATL3 [Arabidopsis thaliana (ta	0.545	0.422	0.316	7.5e-18
TAIR|locus:2118666	472	AT4G30400 [Arabidopsis thalian	0.394	0.209	0.411	4e-17
TAIR|locus:2054049	423	MEE16 "maternal effect embryo	0.326	0.193	0.440	2.8e-16
TAIR|locus:505006547	367	AT4G33565 [Arabidopsis thalian	0.482	0.329	0.328	2.9e-16

TAIR|locus:2124695 AT4G10150 [Arabidopsis thaliana (taxid:3702)]

 Score = 463 (168.0 bits), Expect = 6.4e-44, P = 6.4e-44
 Identities = 101/206 (49%), Positives = 131/206 (63%)

Query:    21 ELKVYQAFIFSVP---XXXXXXXXXXXXXXXXXXXXVDWSSLRMR--TSLHTNNVDEISR 75
             +LK+YQAFIFSVP                       VDWSSL MR  T + TNN   +S 
Sbjct:    25 KLKLYQAFIFSVPICFTFIVLFVLYVIYLRRNSTTNVDWSSLGMRGGTFVPTNN--NLST 82

Query:    76 AELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHW 135
             AELGL K++REMLP+VIYKESF ++D+QCSVCL DYQAE+KLQQ+P+CGH FHM+CID W
Sbjct:    83 AELGLSKDIREMLPVVIYKESFIVKDSQCSVCLGDYQAEEKLQQMPSCGHTFHMECIDLW 142

Query:   136 LTTHTTCPLCRLSLLAPAKASSELSDIQQETIQESSVTENADGASDQQRSEAYEEPQAVE 195
             LT+HTTCPLCRLSL+ P K S +LS    E +  SS+ EN++G     + ++    +A+ 
Sbjct:   143 LTSHTTCPLCRLSLI-P-KPSLDLSHQSTEIV--SSI-ENSNGGEASTQPDSQSATEAIS 197

Query:   196 HS---ESRNEDGSTLQNGPKEQGRSS 218
             H+   E  N D   +    +E  R+S
Sbjct:   198 HTDDVEEGNRDSQEVSKETEENDRNS 223

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2007008 AT1G33480 [Arabidopsis thaliana (taxid:3702)]

 Score = 417 (151.9 bits), Expect = 4.8e-39, P = 4.8e-39
 Identities = 96/220 (43%), Positives = 124/220 (56%)

Query:    21 ELKVYQAFIFSVPXXXXXXXXXXXXXXXXXXXXVDWSSLRMRTSLHTNNVDEISRAELGL 80
             ELK+YQAFIFSVP                     D SSL MRT+    N   +S  ELGL
Sbjct:    19 ELKLYQAFIFSVPICFTFIILFLFYLIYLRRSSSDLSSLGMRTTFIPGN--SLSTIELGL 76

Query:    81 KKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHT 140
              KELREMLPIV++KESF++ D+QCSVCL DYQ  DKLQQIP C H FHMDCID WLT+HT
Sbjct:    77 SKELREMLPIVVFKESFTVMDSQCSVCLGDYQPNDKLQQIPVCKHTFHMDCIDLWLTSHT 136

Query:   141 TCPLCRLSLLAPAKASSELSDIQQETIQESSVTENADGASDQQRSEAYEEPQAVEHSESR 200
             TCPLCRL+L+ P+++       Q + +  S V+ + +  S Q  SE           ES 
Sbjct:   137 TCPLCRLALI-PSRSRQS----QDDPVP-SLVSPDEE-VSSQPESEPVNHRVVSTQPESE 189

Query:   201 NEDGSTLQNGPKEQGRSSH-SLDHEREVRDTTNETGEHEQ 239
               + S + + P+ Q   +H  +  + E +   +    HEQ
Sbjct:   190 PVNHSGVSSQPESQPVVNHRGVSSQPESQPVNHINDGHEQ 229

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2124700 AT4G10160 [Arabidopsis thaliana (taxid:3702)]

 Score = 411 (149.7 bits), Expect = 2.1e-38, P = 2.1e-38
 Identities = 88/168 (52%), Positives = 113/168 (67%)

Query:    54 VDWSSLRMRTSLHTNNVDEISRAELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQA 113
             VDWSSL     + TNN   +S AELGL K++REMLPIVIYKESF++ DTQCSVCL DYQA
Sbjct:    51 VDWSSLG--GFVPTNN--NLSTAELGLSKDIREMLPIVIYKESFTVNDTQCSVCLGDYQA 106

Query:   114 EDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASSELSDIQQETIQESSVT 173
             E+KLQQ+P+CGH FHM+CID WLT+HTTCPLCRLSL+ P K S +LS    ++I+  S  
Sbjct:   107 EEKLQQMPSCGHTFHMECIDLWLTSHTTCPLCRLSLI-P-KPSVDLS---HQSIEIVSSI 161

Query:   174 ENADGASDQQRSEAYEEPQAVEHS---ESRNEDGSTLQNGPKEQGRSS 218
             EN +G     + ++    +A+ H    E  N D   +    +E  R+S
Sbjct:   162 ENTNGGEASTQPDSQSATEAIIHIDDVEEGNRDSIEVVKESEENDRNS 209

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

TAIR|locus:1006230395 AT4G24015 "AT4G24015" [Arabidopsis thaliana (taxid:3702)]

 Score = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 52/157 (33%), Positives = 82/157 (52%)

Query:    21 ELKVYQAFIFSVPXXXXXXXXXXXXXXXXXXXXVDWSS----LRMRTSLHTNNVDEISRA 76
             +LK+YQAFIFS+P                       SS    +   +S H  +    S  
Sbjct:    18 QLKLYQAFIFSIPILFSIILFLLFYLFYLKRRASSLSSPSPMILPVSSSHQTSSHLPSVC 77

Query:    77 ELGLKKELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWL 136
              L +K EL++ L +V++ E    RD+ C VCL +++ +++L ++P C H FH+DCI  WL
Sbjct:    78 LLDVKVELKDKLHVVLFNEELGTRDSLCCVCLGEFELKEELVEMPLCKHIFHLDCIHLWL 137

Query:   137 TTHTTCPLCRLSL-LAPAKASSELSDIQQETIQESSV 172
              +H TCPLCR S+ ++  K S +  +   ++ Q S V
Sbjct:   138 YSHNTCPLCRSSVSISSTKTSVDDDNDHPDSPQTSPV 174

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q8H7N9 LOC_Os03g08920 "E3 ubiquitin-protein ligase Os03g0188200" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 226 (84.6 bits), Expect = 1.1e-18, P = 1.1e-18
 Identities = 50/116 (43%), Positives = 69/116 (59%)

Query:    74 SRAELGLKKELREMLPIVIY---KESFSIRD--TQCSVCLADYQAEDKLQQIPACGHAFH 128
             SRA  GL KE+ E  P  +Y   K   + +    +C+VCLA++   D+L+ +PAC H FH
Sbjct:    98 SRASRGLDKEVVEAFPTAVYGDVKARMAAKSGPLECAVCLAEFADSDELRVLPACCHVFH 157

Query:   129 MDCIDHWLTTHTTCPLCRLSLLAP--AKASSELSDIQ--QETIQESSVTENADGAS 180
              DCID WL    TCPLCR +L AP  + A++E SD+   +E +QE   +E  D AS
Sbjct:   158 PDCIDPWLAAAVTCPLCRANLTAPPVSLAAAESSDLTAPEEAVQEEE-SEELDEAS 212

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

GO:0016567 "protein ubiquitination" evidence=IDA

TAIR|locus:2122363 AT4G09120 [Arabidopsis thaliana (taxid:3702)]

 Score = 200 (75.5 bits), Expect = 4.8e-18, Sum P(2) = 4.8e-18
 Identities = 40/120 (33%), Positives = 71/120 (59%)

Query:    74 SRAELGLKKELREMLPIVIYKESFSIR----DTQCSVCLADYQAEDKLQQIPACGHAFHM 129
             SRA  GL+KE+ E  P  +Y E   ++      +C++CL++++ ++ L+ +P C H FH 
Sbjct:    89 SRARRGLEKEVIESFPTFLYSEVKGLKIGKGGVECAICLSEFEDQETLRWMPPCSHTFHA 148

Query:   130 DCIDHWLTTHTTCPLCRLSL-LAPAKASSELS-DIQQETIQESSVTENADGASDQQRSEA 187
             +CID WL++ +TCP+CR +L L P ++   L+ D++   +Q+     +  G S   RS +
Sbjct:   149 NCIDVWLSSWSTCPVCRANLSLKPGESYPYLNMDVETGGVQKLPNERSLTGNSVTTRSRS 208

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

TAIR|locus:2193992 ATL3 [Arabidopsis thaliana (taxid:3702)]

 Score = 217 (81.4 bits), Expect = 7.5e-18, P = 7.5e-18
 Identities = 45/142 (31%), Positives = 78/142 (54%)

Query:    88 LPIVIYKESFSIRD-TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCR 146
             LPIV +++  S +D  +CS+CL++    DK + +P C H+FH++CID W  +H+TCP+CR
Sbjct:   111 LPIVFFRQD-SCKDGLECSICLSELVKGDKARLLPKCNHSFHVECIDMWFQSHSTCPICR 169

Query:   147 LSLLAPAKASSELSDIQQETIQESSVTENADGASDQQRSEAYEEPQ--AVEHSESRNEDG 204
              ++L P +ASS+  +   +  + +  T N   A  Q  + + E P    V   + +   G
Sbjct:   170 NTVLGPEQASSKRVEQVPDNAENAGTTNNNHDALSQLSTSSPEFPTNVLVWGRQDQVSTG 229

Query:   205 STLQNGPKEQGRSSHSLDHERE 226
             +T   G +E G + +     +E
Sbjct:   230 NT-NVGTQEDGAAGNGASQSQE 250

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2118666 AT4G30400 [Arabidopsis thaliana (taxid:3702)]

 Score = 217 (81.4 bits), Expect = 4.0e-17, P = 4.0e-17
 Identities = 44/107 (41%), Positives = 63/107 (58%)

Query:    79 GLKKELREMLPIVIYKESFSIRDT--QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWL 136
             G+ +   + LP+  YK    +++    C+VCL +++ EDKL+ +P C HAFHMDCID WL
Sbjct:   107 GVDQSFIDTLPVFHYKSIIGLKNYPFDCAVCLCEFETEDKLRLLPKCSHAFHMDCIDTWL 166

Query:   137 TTHTTCPLCRLSLLAPAKASSELSDIQQETIQESSVTENADGASDQQ 183
              +H+TCPLCR SLL      S+LS  Q        V E+A   S ++
Sbjct:   167 LSHSTCPLCRSSLL------SDLSSHQDPRSSFLLVLESASDHSSRE 207

GO:0005634 "nucleus" evidence=ISM

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

GO:0080167 "response to karrikin" evidence=IEP

TAIR|locus:2054049 MEE16 "maternal effect embryo arrest 16" [Arabidopsis thaliana (taxid:3702)]

 Score = 208 (78.3 bits), Expect = 2.8e-16, P = 2.8e-16
 Identities = 37/84 (44%), Positives = 53/84 (63%)

Query:    79 GLKKELREMLPIVIYKE--SFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWL 136
             G+ + L + LP+  YK      I    C VCL +++ EDKL+ +P C HAFH++CID WL
Sbjct:    99 GVDQSLIDTLPVFHYKSIVGLKISPFDCPVCLCEFETEDKLRLLPKCSHAFHVECIDTWL 158

Query:   137 TTHTTCPLCRLSLLAPAKASSELS 160
              +H+TCPLCR +LL+   +   LS
Sbjct:   159 LSHSTCPLCRSNLLSGFSSHHNLS 182

GO:0005634 "nucleus" evidence=ISM

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

GO:0009793 "embryo development ending in seed dormancy" evidence=IMP

TAIR|locus:505006547 AT4G33565 [Arabidopsis thaliana (taxid:3702)]

 Score = 206 (77.6 bits), Expect = 2.9e-16, P = 2.9e-16
 Identities = 43/131 (32%), Positives = 72/131 (54%)

Query:    78 LGLKKELREMLPIVIY-KESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWL 136
             +GL   +   + +  Y K+   +  T CSVCL++++ E+ L+ +P C HAFH+ CID WL
Sbjct:   190 IGLNPTVISSIKVCQYSKKDGVVEGTDCSVCLSEFEEEETLRLLPKCKHAFHLYCIDTWL 249

Query:   137 TTHTTCPLCRLSLLAPAKASSELSDIQQETIQESSVT---ENADGASDQ--QRSEAYEEP 191
              +HT CPLCR    AP   ++ + D   E ++E SV    EN D   ++  +  + +   
Sbjct:   250 RSHTNCPLCR----APIVEANTMIDDHSEGLEEISVMIPEENGDDTDEEIEEERDGFVSN 305

Query:   192 QAVEHSESRNE 202
              + +H ES+ +
Sbjct:   306 ISRDHGESQQQ 316

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

GO:0005886 "plasma membrane" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9SN28	ATL7_ARATH	No assigned EC number	0.5	0.8486	0.9025	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh2_kg.6__2997__AT4G10150.1 annotation not avaliable (237 aa) (Arabidopsis lyrata)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	251
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	8e-15
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	3e-11
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	2e-10
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	6e-08
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	4e-07
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	8e-07
smart00184	40	smart00184, RING, Ring finger	1e-06
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	1e-06
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	7e-06
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	9e-06
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	5e-05

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

 Score = 66.3 bits (162), Expect = 8e-15
 Identities = 19/44 (43%), Positives = 31/44 (70%), Gaps = 1/44 (2%)

Query: 103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCR 146
           +C +CL +++  +++  +P CGH FH +C+D WL +  TCPLCR
Sbjct: 2   ECPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLCR 44

Length = 46

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

 Score = 57.4 bits (139), Expect = 3e-11
 Identities = 23/64 (35%), Positives = 29/64 (45%), Gaps = 9/64 (14%)

Query: 92  IYKESFSIRDTQCSVCL---------ADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTC 142
           +   S+ I D  C++C               +D       CGHAFH+ CI  WL T  TC
Sbjct: 10  VALWSWDIEDDVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTC 69

Query: 143 PLCR 146
           PLCR
Sbjct: 70  PLCR 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|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 = 54.8 bits (132), Expect = 2e-10
 Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 4/45 (8%)

Query: 103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWL-TTHTTCPLCR 146
           +C +CL ++    +   +  CGH F   CID WL +   TCPLCR
Sbjct: 1   ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCR 42

Length = 45

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

 Score = 52.7 bits (126), Expect = 6e-08
 Identities = 40/176 (22%), Positives = 63/176 (35%), Gaps = 38/176 (21%)

Query: 22  LKVYQAFIFSVPIFFTFILLLLFYLFYLRRRRVDWSSLRMRTSLHTNNVDEISRAELGLK 81
           L +YQ     VPI+    +   FY  + RR R      R                     
Sbjct: 229 LFMYQFPYVRVPIYLIRQMYTCFYALF-RRIREHARFRR-------------------AT 268

Query: 82  KELREMLPIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPA----------CGHAFHMDC 131
           K+L  M P    +E  +  D  C++C+ D       + +P           CGH  H+ C
Sbjct: 269 KDLNAMYPTAT-EEQLTNSDRTCTICM-DEMFHPDHEPLPRGLDMTPKRLPCGHILHLHC 326

Query: 132 IDHWLTTHTTCPLCRLSLL----APAKASSELSDIQQETIQESSVTENADGASDQQ 183
           + +WL    TCP+CR  ++    +P  AS  + + Q  T       +N    +   
Sbjct: 327 LKNWLERQQTCPICRRPVIFDQSSPTPASPNVRNTQIATQ--VPNPDNTPTTTAVP 380

Length = 491

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

 Score = 45.6 bits (108), Expect = 4e-07
 Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 3/46 (6%)

Query: 101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCR 146
           + +C +CL      D +   P CGH F  +CI  +L   + CP+CR
Sbjct: 2   ELECPICLDLL--RDPVVLTP-CGHVFCRECILRYLKKKSKCPICR 44

Length = 45

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

 Score = 48.2 bits (115), Expect = 8e-07
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 7/72 (9%)

Query: 82  KELREMLPIVI--YKESFSI-RDTQCSVCLAD-YQAEDK---LQQIPACGHAFHMDCIDH 134
           K+  + +P V+  Y++ ++  +D +C++C+   Y  E K      +  C H F ++CID 
Sbjct: 152 KKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDI 211

Query: 135 WLTTHTTCPLCR 146
           W     TCP+CR
Sbjct: 212 WKKEKNTCPVCR 223

Length = 238

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

 Score = 44.0 bits (104), Expect = 1e-06
 Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 4/43 (9%)

Query: 104 CSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHT-TCPLC 145
           C +CL +Y        +P CGH F   CI  WL +   TCP+C
Sbjct: 1   CPICLEEY--LKDPVILP-CGHTFCRSCIRKWLESGNNTCPIC 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|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

 Score = 48.5 bits (115), Expect = 1e-06
 Identities = 18/51 (35%), Positives = 35/51 (68%), Gaps = 2/51 (3%)

Query: 103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHT-TCPLCRLSLLAP 152
           +C++C++++   D+L+ +P C H FH+ C+D WL  ++  CP+CR ++  P
Sbjct: 325 ECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPPP 374

Length = 374

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

 Score = 41.7 bits (98), Expect = 7e-06
 Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 4/43 (9%)

Query: 104 CSVCLADYQAEDKLQQIPACGHAFHMDCIDHWL-TTHTTCPLC 145
           C +CL +   +D +  +P CGH F   CI  WL + + TCPLC
Sbjct: 1   CPICLEEP--KDPVTILP-CGHLFCSKCILSWLESGNVTCPLC 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

>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 = 42.5 bits (100), Expect = 9e-06
 Identities = 14/24 (58%), Positives = 14/24 (58%)

Query: 123 CGHAFHMDCIDHWLTTHTTCPLCR 146
           C HAFH  CI  WL T   CPL R
Sbjct: 54  CNHAFHDHCIYRWLDTKGVCPLDR 77

Length = 88

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

 Score = 40.5 bits (95), Expect = 5e-05
 Identities = 15/27 (55%), Positives = 17/27 (62%), Gaps = 3/27 (11%)

Query: 123 CGHAFHMDCIDHWLTTHTT---CPLCR 146
           C H FHM CI  WL T T+   CP+CR
Sbjct: 52  CKHNFHMHCILKWLATETSKGLCPMCR 78

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	251
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.78
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.62
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.57
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.38
PHA02929	238	N1R/p28-like protein; Provisional	99.37
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.3
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.09
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.08
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.08
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.05
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.04
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.04
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.01
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.98
PHA02926	242	zinc finger-like protein; Provisional	98.96
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.94
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.91
PF14634	44	zf-RING_5: zinc-RING finger domain	98.86
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.84
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.77
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.76
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.76
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.7
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.65
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.6
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.6
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.59
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.54
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.45
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.4
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.37
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.29
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.23
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.23
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.19
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.16
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.12
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.05
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.97
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.96
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.87
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.85
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.81
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.73
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.72
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.71
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.7
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.68
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.66
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.62
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.44
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.3
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.26
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.22
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.2
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.17
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.11
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.08
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	96.98
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	96.88
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	96.86
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	96.85
KOG2660	331	consensus Locus-specific chromosome binding protei	96.8
PHA02862	156	5L protein; Provisional	96.72
KOG3039	303	consensus Uncharacterized conserved protein [Funct	96.67
COG5222	427	Uncharacterized conserved protein, contains RING Z	96.66
PHA02825	162	LAP/PHD finger-like protein; Provisional	96.55
KOG1002	791	consensus Nucleotide excision repair protein RAD16	96.54
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.54
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.53
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.43
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.32
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	96.27
COG5152	259	Uncharacterized conserved protein, contains RING a	96.19
PHA03096	284	p28-like protein; Provisional	96.09
PF04641	260	Rtf2: Rtf2 RING-finger	96.05
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.88
COG5236	493	Uncharacterized conserved protein, contains RING Z	95.78
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	95.69
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	95.63
KOG4739	233	consensus Uncharacterized protein involved in syna	95.42
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	95.32
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	95.26
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	94.98
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	94.95
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	94.89
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	94.85
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	94.81
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	94.5
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	94.26
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	94.13
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	93.53
KOG1001	674	consensus Helicase-like transcription factor HLTF/	93.47
KOG1940	276	consensus Zn-finger protein [General function pred	93.41
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	93.23
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	93.21
KOG0298	1394	consensus DEAD box-containing helicase-like transc	92.88
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	92.58
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	92.27
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	91.83
KOG3899	381	consensus Uncharacterized conserved protein [Funct	90.99
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	90.63
KOG3002	299	consensus Zn finger protein [General function pred	90.12
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	89.55
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	89.28
PF01102	122	Glycophorin_A: Glycophorin A; InterPro: IPR001195	89.1
KOG3113	293	consensus Uncharacterized conserved protein [Funct	88.33
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	88.25
KOG1609	323	consensus Protein involved in mRNA turnover and st	88.13
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	87.79
KOG3053	293	consensus Uncharacterized conserved protein [Funct	86.37
KOG0269	839	consensus WD40 repeat-containing protein [Function	85.93
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	85.34
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	84.0
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	83.82
KOG0825	1134	consensus PHD Zn-finger protein [General function	82.58
KOG1829	580	consensus Uncharacterized conserved protein, conta	82.23
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	81.47

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

Probab=99.78  E-value=9.1e-19  Score=154.73  Aligned_cols=76  Identities=36%  Similarity=0.816  Sum_probs=65.3

Q ss_pred             cCCCHHHHhhCCceeeccCCCCCc-ccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCC-CCccccCcccCCCC
Q 025541           78 LGLKKELREMLPIVIYKESFSIRD-TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHT-TCPLCRLSLLAPAK  154 (251)
Q Consensus        78 ~~~~~~~~~~lp~~~~~~~~~~~~-~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~-~CP~Cr~~~~~~~~  154 (251)
                      .++.+++++++|...+........ +.|+||+|+|..++++++|| |+|.||..||++||.... .||+||+++.....
T Consensus       205 ~r~~k~~l~~~p~~~f~~~~~~~~~~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~~  282 (348)
T KOG4628|consen  205 NRLIKRLLKKLPVRTFTKGDDEDATDTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDSG  282 (348)
T ss_pred             hhhHHHHHhhCCcEEeccccccCCCceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCCCCCC
Confidence            357899999999999887655433 59999999999999999999 999999999999999875 49999998876544

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

Probab=99.62  E-value=1.7e-15  Score=132.90  Aligned_cols=72  Identities=28%  Similarity=0.833  Sum_probs=56.8

Q ss_pred             CCHHHHhhCCceeeccCCCCCccccccccccc-ccC---------CceeEcCCCCCcccHhhHHHHHhcCCCCccccCcc
Q 025541           80 LKKELREMLPIVIYKESFSIRDTQCSVCLADY-QAE---------DKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSL  149 (251)
Q Consensus        80 ~~~~~~~~lp~~~~~~~~~~~~~~C~IC~~~~-~~~---------~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~  149 (251)
                      ..|++.+.+|.+..++ ...+|..|.|||+++ ..+         .+.+.+| |||+||.+|++.|++++++||+||.++
T Consensus       267 ~~kdl~~~~~t~t~eq-l~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~  344 (491)
T COG5243         267 ATKDLNAMYPTATEEQ-LTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPV  344 (491)
T ss_pred             HhhHHHhhcchhhhhh-hcCCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCcc
Confidence            4567777777766444 466788999999995 333         2557888 999999999999999999999999996


Q ss_pred             cCCC
Q 025541          150 LAPA  153 (251)
Q Consensus       150 ~~~~  153 (251)
                      ....
T Consensus       345 ifd~  348 (491)
T COG5243         345 IFDQ  348 (491)
T ss_pred             cccc
Confidence            5443

>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=99.57  E-value=7.3e-16  Score=97.73  Aligned_cols=44  Identities=41%  Similarity=1.282  Sum_probs=40.2

Q ss_pred             ccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCcccc
Q 025541          102 TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCR  146 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr  146 (251)
                      ++|+||+++|..++.+..++ |||+||.+||..|+..+.+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHhCCcCCccC
Confidence            36999999999888999998 999999999999999999999997

...

>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=99.38  E-value=3.2e-13  Score=94.86  Aligned_cols=48  Identities=42%  Similarity=1.039  Sum_probs=36.9

Q ss_pred             CCCcccccccccccccC----------CceeEcCCCCCcccHhhHHHHHhcCCCCcccc
Q 025541           98 SIRDTQCSVCLADYQAE----------DKLQQIPACGHAFHMDCIDHWLTTHTTCPLCR  146 (251)
Q Consensus        98 ~~~~~~C~IC~~~~~~~----------~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr  146 (251)
                      +..++.|+||++.|...          -.+...+ |||.||..||.+||..+.+||+||
T Consensus        16 ~~~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   16 DIADDNCAICREPLEDPCPECQAPQDECPIVWGP-CGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             SSCCSBETTTTSBTTSTTCCHHHCTTTS-EEEET-TSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             cCcCCcccccChhhhChhhhhcCCccccceEecc-cCCCEEHHHHHHHHhcCCcCCCCC
Confidence            33456699999999332          2344444 999999999999999999999997

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 ....

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.37  E-value=4.1e-13  Score=114.13  Aligned_cols=76  Identities=24%  Similarity=0.643  Sum_probs=57.7

Q ss_pred             hhcCCCHHHHhhCCceeeccC---CCCCcccccccccccccCCc----eeEcCCCCCcccHhhHHHHHhcCCCCccccCc
Q 025541           76 AELGLKKELREMLPIVIYKES---FSIRDTQCSVCLADYQAEDK----LQQIPACGHAFHMDCIDHWLTTHTTCPLCRLS  148 (251)
Q Consensus        76 ~~~~~~~~~~~~lp~~~~~~~---~~~~~~~C~IC~~~~~~~~~----~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~  148 (251)
                      ...+..+..++.+|.+..+-.   ....+.+|+||++.+..+..    +.+++.|+|.||..||.+|+..+.+||+||..
T Consensus       146 ~k~~~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~  225 (238)
T PHA02929        146 KKGKNYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTP  225 (238)
T ss_pred             HhcchhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCE
Confidence            345568888999998764422   22346889999999865431    23444599999999999999999999999998


Q ss_pred             ccC
Q 025541          149 LLA  151 (251)
Q Consensus       149 ~~~  151 (251)
                      +..
T Consensus       226 ~~~  228 (238)
T PHA02929        226 FIS  228 (238)
T ss_pred             eeE
Confidence            753

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

Probab=99.30  E-value=1.3e-12  Score=112.22  Aligned_cols=52  Identities=35%  Similarity=1.124  Sum_probs=47.6

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHh-cCCCCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT-THTTCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~~  152 (251)
                      .+.+|+|||+.|..+++++++| |.|.||..|+.+|+. .+..||+||..++++
T Consensus       322 ~GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iPPp  374 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPPP  374 (374)
T ss_pred             CCceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCCCC
Confidence            4578999999999999999999 999999999999998 678899999998763

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

Probab=99.09  E-value=9.5e-11  Score=100.42  Aligned_cols=50  Identities=34%  Similarity=0.875  Sum_probs=42.8

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPA  153 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  153 (251)
                      ....|.|||+....+   ..+| |||+||..||..|+..+..||+||..+.+.+
T Consensus       238 a~~kC~LCLe~~~~p---SaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~psk  287 (293)
T KOG0317|consen  238 ATRKCSLCLENRSNP---SATP-CGHIFCWSCILEWCSEKAECPLCREKFQPSK  287 (293)
T ss_pred             CCCceEEEecCCCCC---CcCc-CcchHHHHHHHHHHccccCCCcccccCCCcc
Confidence            457899999998654   4566 9999999999999999999999999887643

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

Probab=99.08  E-value=6.2e-11  Score=84.30  Aligned_cols=51  Identities=35%  Similarity=0.805  Sum_probs=39.4

Q ss_pred             cccccccccccccC--------C-ceeEcCCCCCcccHhhHHHHHhc---CCCCccccCcccC
Q 025541          101 DTQCSVCLADYQAE--------D-KLQQIPACGHAFHMDCIDHWLTT---HTTCPLCRLSLLA  151 (251)
Q Consensus       101 ~~~C~IC~~~~~~~--------~-~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~~~~~  151 (251)
                      ++.|.||+..|...        + -..++..|+|.||..||.+||..   +..||+||+.+..
T Consensus        21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~   83 (85)
T PF12861_consen   21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF   83 (85)
T ss_pred             CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence            77899999998632        1 12234469999999999999985   4689999998743

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

Probab=99.08  E-value=6.2e-11  Score=113.10  Aligned_cols=53  Identities=34%  Similarity=0.968  Sum_probs=45.4

Q ss_pred             CCCcccccccccccccCCc--eeEcCCCCCcccHhhHHHHHhcCCCCccccCcccC
Q 025541           98 SIRDTQCSVCLADYQAEDK--LQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus        98 ~~~~~~C~IC~~~~~~~~~--~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      ...+..|+||++.+..+..  .++++ |+|+||..|++.|++++++||+||..+..
T Consensus       288 ~~~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~~~  342 (543)
T KOG0802|consen  288 ALSDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVLYD  342 (543)
T ss_pred             hhcCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhhhc
Confidence            3457889999999987644  67787 99999999999999999999999995543

>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=99.05  E-value=1.7e-10  Score=72.23  Aligned_cols=44  Identities=43%  Similarity=1.262  Sum_probs=36.4

Q ss_pred             cccccccccccCCceeEcCCCCCcccHhhHHHHHhc-CCCCccccCcc
Q 025541          103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSL  149 (251)
Q Consensus       103 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~  149 (251)
                      +|+||++.+.  ..+...+ |||.||..|+..|+.. ...||+||..+
T Consensus         1 ~C~iC~~~~~--~~~~~~~-C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFR--EPVVLLP-CGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhh--CceEecC-CCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            4999999983  3455555 9999999999999997 77899998764

>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=99.04  E-value=1.5e-10  Score=71.30  Aligned_cols=39  Identities=36%  Similarity=1.129  Sum_probs=32.7

Q ss_pred             ccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccc
Q 025541          104 CSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLC  145 (251)
Q Consensus       104 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~C  145 (251)
                      |+||++.+..  .+..++ |||.||..||.+|+..+..||+|
T Consensus         1 C~iC~~~~~~--~~~~~~-CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTP-CGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECT-TSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC--cCEECC-CCCchhHHHHHHHHHCcCCCcCC
Confidence            8999998876  445676 99999999999999998999998

>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=99.04  E-value=1.5e-10  Score=75.15  Aligned_cols=46  Identities=30%  Similarity=0.936  Sum_probs=38.6

Q ss_pred             cccccccccccccCCceeEcCCCCCc-ccHhhHHHHHhcCCCCccccCccc
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHA-FHMDCIDHWLTTHTTCPLCRLSLL  150 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~  150 (251)
                      +..|.||++...   .+..+| |||. ||..|+..|+.....||+||+++.
T Consensus         2 ~~~C~iC~~~~~---~~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPR---DVVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBS---SEEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCC---ceEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            467999999865   466777 9999 999999999999999999999874

...

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.01  E-value=2.5e-10  Score=93.47  Aligned_cols=49  Identities=29%  Similarity=0.784  Sum_probs=39.8

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc----------------CCCCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT----------------HTTCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----------------~~~CP~Cr~~~~~~  152 (251)
                      ++.+|+||++.+..+   .+++ |||.||+.||.+|+..                ...||+||..+...
T Consensus        17 ~~~~CpICld~~~dP---VvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~   81 (193)
T PLN03208         17 GDFDCNICLDQVRDP---VVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEA   81 (193)
T ss_pred             CccCCccCCCcCCCc---EEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChh
Confidence            467899999998654   4565 9999999999999852                34799999998653

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

Probab=98.98  E-value=2.5e-10  Score=91.42  Aligned_cols=51  Identities=27%  Similarity=0.651  Sum_probs=42.2

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccC
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      ..-+.|+|||+.+.....  +..+|||+||..||+..+.....||+|++.|..
T Consensus       129 ~~~~~CPiCl~~~sek~~--vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~  179 (187)
T KOG0320|consen  129 EGTYKCPICLDSVSEKVP--VSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH  179 (187)
T ss_pred             ccccCCCceecchhhccc--cccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence            345789999999987543  323699999999999999999999999987654

>PHA02926 zinc finger-like protein; Provisional

Probab=98.96  E-value=3.4e-10  Score=93.80  Aligned_cols=52  Identities=25%  Similarity=0.789  Sum_probs=39.6

Q ss_pred             CcccccccccccccC-----CceeEcCCCCCcccHhhHHHHHhcC------CCCccccCcccC
Q 025541          100 RDTQCSVCLADYQAE-----DKLQQIPACGHAFHMDCIDHWLTTH------TTCPLCRLSLLA  151 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~-----~~~~~~~~C~H~fh~~Ci~~wl~~~------~~CP~Cr~~~~~  151 (251)
                      .+.+|+|||+.+..+     ....+++.|+|.||..||+.|...+      .+||+||..+..
T Consensus       169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~  231 (242)
T PHA02926        169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN  231 (242)
T ss_pred             CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence            467899999986432     1234565799999999999999753      459999997653

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

Probab=98.94  E-value=4.9e-10  Score=93.46  Aligned_cols=52  Identities=27%  Similarity=0.651  Sum_probs=41.8

Q ss_pred             CCCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc---CCCCccccCcccCCC
Q 025541           98 SIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT---HTTCPLCRLSLLAPA  153 (251)
Q Consensus        98 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~~~~~~~  153 (251)
                      .....+|.|||+..+.+   +++. |||+||+.||.+||..   .+.||+||..+....
T Consensus        44 ~~~~FdCNICLd~akdP---VvTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~   98 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDP---VVTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT   98 (230)
T ss_pred             CCCceeeeeeccccCCC---EEee-cccceehHHHHHHHhhcCCCeeCCccccccccce
Confidence            45678999999987764   4444 9999999999999985   456999999886544

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

Probab=98.91  E-value=6.4e-10  Score=77.14  Aligned_cols=51  Identities=33%  Similarity=0.679  Sum_probs=38.8

Q ss_pred             cccccccccccc-----------CC-ceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCC
Q 025541          102 TQCSVCLADYQA-----------ED-KLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAP  152 (251)
Q Consensus       102 ~~C~IC~~~~~~-----------~~-~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  152 (251)
                      +.|+||+..|..           ++ -+.....|.|.||..||.+||..+..||++|+.+...
T Consensus        21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~   83 (88)
T COG5194          21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLA   83 (88)
T ss_pred             chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEe
Confidence            568888776632           22 2333445999999999999999999999999987653

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.86  E-value=1.9e-09  Score=68.12  Aligned_cols=44  Identities=30%  Similarity=0.887  Sum_probs=37.9

Q ss_pred             cccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccC
Q 025541          103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRL  147 (251)
Q Consensus       103 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~  147 (251)
                      .|+||++.|.......+++ |||+||..|+..+......||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~-CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTS-CGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcc-cCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            4999999996566777786 9999999999999866778999985

>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=98.84  E-value=1.7e-09  Score=67.16  Aligned_cols=39  Identities=41%  Similarity=1.193  Sum_probs=33.3

Q ss_pred             ccccccccccCCceeEcCCCCCcccHhhHHHHHh--cCCCCccc
Q 025541          104 CSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT--THTTCPLC  145 (251)
Q Consensus       104 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~--~~~~CP~C  145 (251)
                      |+||++.+..+.  ..++ |||.||..||.+|+.  ....||+|
T Consensus         1 C~iC~~~~~~~~--~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPV--ILLP-CGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEE--EETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCCC--EEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence            899999987643  5676 999999999999999  56679998

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 ....

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

Probab=98.77  E-value=4.5e-09  Score=65.63  Aligned_cols=38  Identities=32%  Similarity=0.990  Sum_probs=28.3

Q ss_pred             ccccccccccCCceeEcCCCCCcccHhhHHHHHhcC----CCCccc
Q 025541          104 CSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH----TTCPLC  145 (251)
Q Consensus       104 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP~C  145 (251)
                      |+||++-|..+   ..++ |||.|+..||..|+...    ..||.|
T Consensus         1 CpiC~~~~~~P---v~l~-CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDP---VSLP-CGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSE---EE-S-SSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCc---cccC-CcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999865   4555 99999999999999753    469987

>smart00184 RING Ring finger

Probab=98.76  E-value=6.2e-09  Score=62.81  Aligned_cols=38  Identities=42%  Similarity=1.219  Sum_probs=32.0

Q ss_pred             ccccccccccCCceeEcCCCCCcccHhhHHHHHh-cCCCCccc
Q 025541          104 CSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT-THTTCPLC  145 (251)
Q Consensus       104 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~C  145 (251)
                      |+||++..   .....++ |+|.||..|+..|+. .+..||+|
T Consensus         1 C~iC~~~~---~~~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEEL---KDPVVLP-CGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCC---CCcEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence            78999883   3556676 999999999999998 66779987

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)

>smart00504 Ubox Modified RING finger domain

Probab=98.76  E-value=1e-08  Score=69.52  Aligned_cols=46  Identities=24%  Similarity=0.515  Sum_probs=40.0

Q ss_pred             ccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccC
Q 025541          102 TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      ..|+||++.|..+   .+++ |||+|++.||.+|+..+.+||+|+..+..
T Consensus         2 ~~Cpi~~~~~~~P---v~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~~   47 (63)
T smart00504        2 FLCPISLEVMKDP---VILP-SGQTYERRAIEKWLLSHGTDPVTGQPLTH   47 (63)
T ss_pred             cCCcCCCCcCCCC---EECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence            4699999999875   4566 99999999999999988899999988744

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

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

Probab=98.70  E-value=3.3e-09  Score=73.04  Aligned_cols=51  Identities=33%  Similarity=0.722  Sum_probs=38.4

Q ss_pred             CcccccccccccccCC---------ceeEcCCCCCcccHhhHHHHHhc---CCCCccccCccc
Q 025541          100 RDTQCSVCLADYQAED---------KLQQIPACGHAFHMDCIDHWLTT---HTTCPLCRLSLL  150 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~---------~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~~~~  150 (251)
                      .+..|.||+.+|...-         -..++..|.|.||..||.+|+..   +..||+||+.+.
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            4558999999985321         22233359999999999999974   557999999764

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

Probab=98.65  E-value=1.1e-08  Score=74.52  Aligned_cols=53  Identities=32%  Similarity=0.707  Sum_probs=40.2

Q ss_pred             CCcccccccccccc-------------cCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccC
Q 025541           99 IRDTQCSVCLADYQ-------------AEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus        99 ~~~~~C~IC~~~~~-------------~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      ..-+.|+||+..+.             ..+-+.....|.|.||..||.+||+.++.||+|.++...
T Consensus        44 i~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~~  109 (114)
T KOG2930|consen   44 IVVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWVF  109 (114)
T ss_pred             eeechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcceeE
Confidence            34577999986652             122334444699999999999999999999999887643

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

Probab=98.60  E-value=1.9e-08  Score=85.40  Aligned_cols=51  Identities=31%  Similarity=0.844  Sum_probs=41.8

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHH-HHhcCCC-CccccCcccCCC
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDH-WLTTHTT-CPLCRLSLLAPA  153 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~-wl~~~~~-CP~Cr~~~~~~~  153 (251)
                      ..++.|+||++....+   ..++ |||+||..||.. |-..+.- ||+||+.+.+.+
T Consensus       213 ~~d~kC~lC~e~~~~p---s~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~  265 (271)
T COG5574         213 LADYKCFLCLEEPEVP---SCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK  265 (271)
T ss_pred             ccccceeeeecccCCc---cccc-ccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence            3578899999987654   5565 999999999999 8777665 999999887654

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.60  E-value=3.7e-08  Score=89.68  Aligned_cols=49  Identities=27%  Similarity=0.653  Sum_probs=41.8

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  152 (251)
                      ....|+||++.|..+   .+++ |||.||..||..|+.....||+||..+...
T Consensus        25 ~~l~C~IC~d~~~~P---vitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~   73 (397)
T TIGR00599        25 TSLRCHICKDFFDVP---VLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQES   73 (397)
T ss_pred             cccCCCcCchhhhCc---cCCC-CCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence            356899999998765   3566 999999999999999888999999988654

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

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

Probab=98.59  E-value=5.9e-08  Score=88.59  Aligned_cols=50  Identities=28%  Similarity=0.828  Sum_probs=39.0

Q ss_pred             cccccccccccccC--------------CceeEcCCCCCcccHhhHHHHHh-cCCCCccccCcccC
Q 025541          101 DTQCSVCLADYQAE--------------DKLQQIPACGHAFHMDCIDHWLT-THTTCPLCRLSLLA  151 (251)
Q Consensus       101 ~~~C~IC~~~~~~~--------------~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~  151 (251)
                      -.+|+|||.++.--              ....+.| |.|+||..|+.+|+. .+-.||.||.++++
T Consensus       571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tP-C~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTP-CHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             cccceEeccccceeeccCcchhhhhhhhccccccc-hHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            46799999886321              1133456 999999999999999 56689999999864

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

Probab=98.54  E-value=1.6e-08  Score=85.96  Aligned_cols=54  Identities=28%  Similarity=0.684  Sum_probs=44.2

Q ss_pred             CCcccccccccccccCC-------ceeEcCCCCCcccHhhHHHHHh--cCCCCccccCcccCCC
Q 025541           99 IRDTQCSVCLADYQAED-------KLQQIPACGHAFHMDCIDHWLT--THTTCPLCRLSLLAPA  153 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~-------~~~~~~~C~H~fh~~Ci~~wl~--~~~~CP~Cr~~~~~~~  153 (251)
                      .++..|+||-..+....       .+..+. |+|+||..||+.|..  .+++||.|+..+....
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVdl~r  284 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKR  284 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhhHhh
Confidence            45788999999887655       566776 999999999999965  5789999998776543

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

Probab=98.45  E-value=1.3e-07  Score=59.13  Aligned_cols=38  Identities=32%  Similarity=0.914  Sum_probs=22.5

Q ss_pred             cccccccccc-CCceeEcCCCCCcccHhhHHHHHhcC----CCCc
Q 025541          104 CSVCLADYQA-EDKLQQIPACGHAFHMDCIDHWLTTH----TTCP  143 (251)
Q Consensus       104 C~IC~~~~~~-~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP  143 (251)
                      |+||++ |.. .....+|+ |||+|+++||.+|+..+    ..||
T Consensus         1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 754 44567888 99999999999999843    3576

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

Probab=98.40  E-value=1.2e-07  Score=87.26  Aligned_cols=49  Identities=31%  Similarity=0.736  Sum_probs=39.1

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcC-----CCCccccCcccCCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH-----TTCPLCRLSLLAPA  153 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~-----~~CP~Cr~~~~~~~  153 (251)
                      +..||||++....+.   .+ .|||+||..||.+++...     ..||+||..+...+
T Consensus       186 ~~~CPICL~~~~~p~---~t-~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kd  239 (513)
T KOG2164|consen  186 DMQCPICLEPPSVPV---RT-NCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKD  239 (513)
T ss_pred             CCcCCcccCCCCccc---cc-ccCceeeHHHHHHHHhhhcccCCccCCchhhhccccc
Confidence            788999999876542   33 399999999999988643     46999999887744

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

Probab=98.37  E-value=3e-07  Score=59.33  Aligned_cols=42  Identities=26%  Similarity=0.883  Sum_probs=32.6

Q ss_pred             cccccccccccCCceeEcCCCC-----CcccHhhHHHHHhc--CCCCcccc
Q 025541          103 QCSVCLADYQAEDKLQQIPACG-----HAFHMDCIDHWLTT--HTTCPLCR  146 (251)
Q Consensus       103 ~C~IC~~~~~~~~~~~~~~~C~-----H~fh~~Ci~~wl~~--~~~CP~Cr  146 (251)
                      .|.||++. ..+....+.| |.     |.||..|+.+|+..  +.+||+|+
T Consensus         1 ~CrIC~~~-~~~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDE-GDEGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCC-CCCCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            38999983 3444555787 85     89999999999974  45899995

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

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.29  E-value=6.8e-07  Score=78.52  Aligned_cols=53  Identities=28%  Similarity=0.616  Sum_probs=39.0

Q ss_pred             cccccccccc-cccCC-ceeEcCCCCCcccHhhHHHHHh-cCCCCccccCcccCCCC
Q 025541          101 DTQCSVCLAD-YQAED-KLQQIPACGHAFHMDCIDHWLT-THTTCPLCRLSLLAPAK  154 (251)
Q Consensus       101 ~~~C~IC~~~-~~~~~-~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~~~~  154 (251)
                      +..||||... |..+. .+.+.+ |||.||..|+...+. ....||.|+..+.....
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~-CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~f   58 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGSGSCPECDTPLRKNNF   58 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCC-CCCcccHHHHHHHhcCCCCCCCCCCCccchhhc
Confidence            4679999986 33333 333444 999999999999664 45689999998876553

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).

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

Probab=98.23  E-value=4.5e-07  Score=79.52  Aligned_cols=52  Identities=23%  Similarity=0.687  Sum_probs=43.7

Q ss_pred             ccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCCCCCC
Q 025541          102 TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASS  157 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~~~  157 (251)
                      ..|.||.+-|..+   .++| |+|.||.-||+.+|..+..||.|+..+....-...
T Consensus        24 LRC~IC~eyf~ip---~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n   75 (442)
T KOG0287|consen   24 LRCGICFEYFNIP---MITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNN   75 (442)
T ss_pred             HHHhHHHHHhcCc---eecc-ccchHHHHHHHHHhccCCCCCceecccchhhhhhh
Confidence            4699999998754   5566 99999999999999999999999998876654433

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

Probab=98.23  E-value=2.5e-07  Score=64.32  Aligned_cols=50  Identities=24%  Similarity=0.767  Sum_probs=23.2

Q ss_pred             cccccccccccc-cCCc-eeEc--CCCCCcccHhhHHHHHhc----C-------CCCccccCccc
Q 025541          101 DTQCSVCLADYQ-AEDK-LQQI--PACGHAFHMDCIDHWLTT----H-------TTCPLCRLSLL  150 (251)
Q Consensus       101 ~~~C~IC~~~~~-~~~~-~~~~--~~C~H~fh~~Ci~~wl~~----~-------~~CP~Cr~~~~  150 (251)
                      +.+|.||+..+. .+.. ..+-  +.|++.||..||.+||..    +       ..||.|+.+|.
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~   66 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS   66 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence            357999999865 3222 2222  269999999999999973    1       14999998874

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

Probab=98.19  E-value=8.1e-07  Score=76.45  Aligned_cols=47  Identities=30%  Similarity=0.675  Sum_probs=39.8

Q ss_pred             ccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCC
Q 025541          102 TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAP  152 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  152 (251)
                      ..|-||-+-|..+   ..++ |||.||.-||+..|..+..||+||.+....
T Consensus        26 lrC~IC~~~i~ip---~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~~~es   72 (391)
T COG5432          26 LRCRICDCRISIP---CETT-CGHTFCSLCIRRHLGTQPFCPVCREDPCES   72 (391)
T ss_pred             HHhhhhhheeecc---eecc-cccchhHHHHHHHhcCCCCCccccccHHhh
Confidence            5699999988754   3344 999999999999999999999999977543

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

Probab=98.16  E-value=1.3e-06  Score=61.27  Aligned_cols=49  Identities=22%  Similarity=0.459  Sum_probs=37.2

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhc-CCCCccccCcccCCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSLLAPA  153 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~  153 (251)
                      ...|+|+.+-|..+   .++| |||.|.+.||..|+.. +.+||+|+.++....
T Consensus         4 ~f~CpIt~~lM~dP---Vi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~   53 (73)
T PF04564_consen    4 EFLCPITGELMRDP---VILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSESD   53 (73)
T ss_dssp             GGB-TTTSSB-SSE---EEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGG
T ss_pred             ccCCcCcCcHhhCc---eeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCccc
Confidence            46799999999865   4566 9999999999999998 889999998886543

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 ....

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

Probab=98.12  E-value=9.3e-07  Score=86.30  Aligned_cols=52  Identities=23%  Similarity=0.745  Sum_probs=38.6

Q ss_pred             CCccccccccccccc---CCceeEcCCCCCcccHhhHHHHHhc--CCCCccccCccc
Q 025541           99 IRDTQCSVCLADYQA---EDKLQQIPACGHAFHMDCIDHWLTT--HTTCPLCRLSLL  150 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~---~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~  150 (251)
                      .+-.+|+||+..+..   .-.-...+.|.|.||..|+.+|+..  +.+||+||..+.
T Consensus      1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            456789999977641   1122233359999999999999985  668999997764

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

Probab=98.05  E-value=1.7e-06  Score=75.24  Aligned_cols=44  Identities=30%  Similarity=0.863  Sum_probs=38.3

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRL  147 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~  147 (251)
                      +...|+||++.|..+   .+++ |+|.||..||..++.....||.||.
T Consensus        12 ~~~~C~iC~~~~~~p---~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   12 EELTCPICLEYFREP---VLLP-CGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             ccccChhhHHHhhcC---cccc-ccchHhHHHHHHhcCCCcCCcccCC
Confidence            456899999999987   6777 9999999999999885568999993

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

Probab=97.97  E-value=2.4e-06  Score=77.58  Aligned_cols=48  Identities=31%  Similarity=0.871  Sum_probs=38.3

Q ss_pred             CcccccccccccccCCc-eeEcCCCCCcccHhhHHHHHhcCCCCccccCccc
Q 025541          100 RDTQCSVCLADYQAEDK-LQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLL  150 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~-~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  150 (251)
                      +-.+|+|||+.|..... ++.+. |.|.||..|+..|..  .+||+||....
T Consensus       174 ELPTCpVCLERMD~s~~gi~t~~-c~Hsfh~~cl~~w~~--~scpvcR~~q~  222 (493)
T KOG0804|consen  174 ELPTCPVCLERMDSSTTGILTIL-CNHSFHCSCLMKWWD--SSCPVCRYCQS  222 (493)
T ss_pred             cCCCcchhHhhcCccccceeeee-cccccchHHHhhccc--CcChhhhhhcC
Confidence            45789999999976542 33344 999999999999965  48999998765

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

Probab=97.96  E-value=3.2e-06  Score=75.40  Aligned_cols=48  Identities=31%  Similarity=1.016  Sum_probs=34.0

Q ss_pred             ccccccccccccCCceeEcCCCCCcccHhhHHHHHhc---CCCCccccCcc
Q 025541          102 TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT---HTTCPLCRLSL  149 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~~~  149 (251)
                      ..|.||.+-+-....+.-+..|||+||..|+.+|+..   +..||.|+-.+
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~   55 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL   55 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence            4699994433333333333359999999999999985   35799998433

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

Probab=97.87  E-value=2.3e-06  Score=75.57  Aligned_cols=56  Identities=27%  Similarity=0.530  Sum_probs=44.2

Q ss_pred             CCCcccccccccccccCCceeEcCCCCCcccHhhHHHHHh-cCCCCccccCcccCCCCCC
Q 025541           98 SIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT-THTTCPLCRLSLLAPAKAS  156 (251)
Q Consensus        98 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~~~~~~  156 (251)
                      ...+..|+|||+-++..   +..+.|.|.||..||..-+. .++.||.||+.+.......
T Consensus        40 ~~~~v~c~icl~llk~t---mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr   96 (381)
T KOG0311|consen   40 FDIQVICPICLSLLKKT---MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLR   96 (381)
T ss_pred             hhhhhccHHHHHHHHhh---cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCC
Confidence            34567899999988754   33347999999999999887 4789999999987665443

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

Probab=97.85  E-value=7.8e-06  Score=73.28  Aligned_cols=54  Identities=24%  Similarity=0.831  Sum_probs=40.8

Q ss_pred             CCcccccccccccccCC----ceeEcCCCCCcccHhhHHHHHh--c-----CCCCccccCcccCC
Q 025541           99 IRDTQCSVCLADYQAED----KLQQIPACGHAFHMDCIDHWLT--T-----HTTCPLCRLSLLAP  152 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~----~~~~~~~C~H~fh~~Ci~~wl~--~-----~~~CP~Cr~~~~~~  152 (251)
                      ..+.+|.||++......    ...++|.|.|.||..||+.|-.  +     .+.||.||......
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v  223 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFV  223 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccc
Confidence            34778999999876543    1334567999999999999984  3     46799999866443

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

Probab=97.81  E-value=5.1e-06  Score=55.86  Aligned_cols=48  Identities=23%  Similarity=0.616  Sum_probs=23.9

Q ss_pred             ccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCCC
Q 025541          102 TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAK  154 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~  154 (251)
                      ..|++|.+-+..+..   +..|.|+||..||..-+..  .||+|+.+....+.
T Consensus         8 LrCs~C~~~l~~pv~---l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD~   55 (65)
T PF14835_consen    8 LRCSICFDILKEPVC---LGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQDI   55 (65)
T ss_dssp             TS-SSS-S--SS-B------SSS--B-TTTGGGGTTT--B-SSS--B-S-SS-
T ss_pred             cCCcHHHHHhcCCce---eccCccHHHHHHhHHhcCC--CCCCcCChHHHHHH
Confidence            369999999876532   2369999999999885553  49999988765443

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

Probab=97.73  E-value=9.6e-06  Score=78.20  Aligned_cols=48  Identities=29%  Similarity=0.737  Sum_probs=37.8

Q ss_pred             ccccccccccccCCceeEcCCCCCcccHhhHHHHHh-cCCCCccccCcccCCC
Q 025541          102 TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT-THTTCPLCRLSLLAPA  153 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~~~  153 (251)
                      ..|+.|-..+...    +++.|+|+||..|+..-+. ++..||.|...+.+.+
T Consensus       644 LkCs~Cn~R~Kd~----vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD  692 (698)
T KOG0978|consen  644 LKCSVCNTRWKDA----VITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND  692 (698)
T ss_pred             eeCCCccCchhhH----HHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence            4699999666542    3335999999999999887 6889999988876544

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

Probab=97.72  E-value=7e-06  Score=78.94  Aligned_cols=52  Identities=23%  Similarity=0.496  Sum_probs=41.6

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPA  153 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  153 (251)
                      ...|++|+..+.........+ |+|+||..||..|-..-++||+||..+....
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~  174 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGEFGEVK  174 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhhhheee
Confidence            345888887776655555555 9999999999999999999999999776443

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

Probab=97.71  E-value=0.00015  Score=60.59  Aligned_cols=76  Identities=20%  Similarity=0.540  Sum_probs=60.5

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhc--------CCCCccccCcccCCCCCCCcchhHHHhhhhcccc
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT--------HTTCPLCRLSLLAPAKASSELSDIQQETIQESSV  172 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--------~~~CP~Cr~~~~~~~~~~~~~~~~~~~~~~~~~~  172 (251)
                      +.-|..|--.+..++.++..  |-|+||.+|+..|-..        .-.||.|...++++.....+.-+...+...+...
T Consensus        50 ~pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva~aLre~L~qvNW  127 (299)
T KOG3970|consen   50 NPNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVSPVAEALREQLKQVNW  127 (299)
T ss_pred             CCCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccchhHHHHHHHHHhhhH
Confidence            45699999999999888765  9999999999999753        3369999999999988888777766666666655


Q ss_pred             ccCCCC
Q 025541          173 TENADG  178 (251)
Q Consensus       173 ~~~~~~  178 (251)
                      ...+-|
T Consensus       128 aRagLG  133 (299)
T KOG3970|consen  128 ARAGLG  133 (299)
T ss_pred             HhhccC
Confidence            554443

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

Probab=97.70  E-value=2.2e-05  Score=70.65  Aligned_cols=49  Identities=35%  Similarity=0.853  Sum_probs=38.0

Q ss_pred             cccccccccccccCC-ceeEcCCCCCcccHhhHHHHHhc--CCCCccccCcc
Q 025541          101 DTQCSVCLADYQAED-KLQQIPACGHAFHMDCIDHWLTT--HTTCPLCRLSL  149 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~-~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~  149 (251)
                      ..+|+||++++.... .-.+.+.|||.|...||++||.+  ...||.|....
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka   55 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA   55 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence            468999999987544 33444579999999999999963  34699997654

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

Probab=97.68  E-value=2.5e-05  Score=69.39  Aligned_cols=48  Identities=23%  Similarity=0.702  Sum_probs=40.2

Q ss_pred             CcccccccccccccCCceeEcCCCCC-cccHhhHHHHHhcCCCCccccCcccC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGH-AFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H-~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      ...+|.|||.+-.   .+.+|| |.| -.|..|-+....+++.||+||+++..
T Consensus       289 ~gkeCVIClse~r---dt~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~  337 (349)
T KOG4265|consen  289 SGKECVICLSESR---DTVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIEE  337 (349)
T ss_pred             CCCeeEEEecCCc---ceEEec-chhhehhHhHHHHHHHhhcCCCccccchHh
Confidence            3568999998754   567898 999 58999999887788899999998854

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

Probab=97.66  E-value=1.3e-05  Score=51.82  Aligned_cols=46  Identities=24%  Similarity=0.659  Sum_probs=33.5

Q ss_pred             cccccccccccccCCceeEcCCCCC-cccHhhHHHHHh-cCCCCccccCccc
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGH-AFHMDCIDHWLT-THTTCPLCRLSLL  150 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H-~fh~~Ci~~wl~-~~~~CP~Cr~~~~  150 (251)
                      +++|.||++.-..  .+..  .||| -.|..|-.+.++ .+..||+||+++.
T Consensus         7 ~dECTICye~pvd--sVlY--tCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    7 SDECTICYEHPVD--SVLY--TCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             ccceeeeccCcch--HHHH--HcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            4789999987543  2222  3999 478888655444 7889999999874

>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.62  E-value=2.6e-05  Score=67.67  Aligned_cols=48  Identities=23%  Similarity=0.573  Sum_probs=38.3

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhc-CCCCccccCcccCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSLLAP  152 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~  152 (251)
                      ..+|+||+.....+   ..++ |+|.||..||+.-... +.+|++||.++...
T Consensus         7 ~~eC~IC~nt~n~P---v~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    7 KKECLICYNTGNCP---VNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             CCcceeeeccCCcC---cccc-ccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            45799999887654   4455 9999999999987665 56799999998643

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

Probab=97.44  E-value=4.8e-05  Score=65.95  Aligned_cols=53  Identities=26%  Similarity=0.735  Sum_probs=42.9

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc-----------------------CCCCccccCcccCC
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-----------------------HTTCPLCRLSLLAP  152 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-----------------------~~~CP~Cr~~~~~~  152 (251)
                      .....|.|||.-|..+....+++ |-|.||..|+.++|.-                       +..||+||..+...
T Consensus       113 ~p~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e  188 (368)
T KOG4445|consen  113 HPNGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIE  188 (368)
T ss_pred             CCCCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccc
Confidence            34567999999999998788887 9999999999888731                       12599999987643

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

Probab=97.30  E-value=0.00043  Score=59.52  Aligned_cols=51  Identities=29%  Similarity=0.477  Sum_probs=38.2

Q ss_pred             CCCCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc--CCCCccccCccc
Q 025541           97 FSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT--HTTCPLCRLSLL  150 (251)
Q Consensus        97 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~  150 (251)
                      ....+.+|++|-+.-..+  .... +|+|+||+-||..-+..  ..+||.|-..+.
T Consensus       235 ~~t~~~~C~~Cg~~PtiP--~~~~-~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  235 TGTSDTECPVCGEPPTIP--HVIG-KCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cccCCceeeccCCCCCCC--eeec-cccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            344578899999876554  2233 49999999999987663  478999977665

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

Probab=97.26  E-value=9.7e-05  Score=49.11  Aligned_cols=42  Identities=21%  Similarity=0.677  Sum_probs=27.1

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc--CCCCcc
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT--HTTCPL  144 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~  144 (251)
                      -...|||.+..|..+  ++-. .|+|+|-+..|..||.+  ...||+
T Consensus        10 ~~~~CPiT~~~~~~P--V~s~-~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFEDP--VKSK-KCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SSE--EEES-SS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhhCC--cCcC-CCCCeecHHHHHHHHHhcCCCCCCC
Confidence            356799999999865  3333 49999999999999943  456998

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

Probab=97.22  E-value=0.0001  Score=66.14  Aligned_cols=46  Identities=33%  Similarity=0.893  Sum_probs=37.2

Q ss_pred             ccccccccccccc-CCceeEcCCCCCcccHhhHHHHHhc--CCCCccccC
Q 025541          101 DTQCSVCLADYQA-EDKLQQIPACGHAFHMDCIDHWLTT--HTTCPLCRL  147 (251)
Q Consensus       101 ~~~C~IC~~~~~~-~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~  147 (251)
                      +.-|..|-+.+.- +..+..+| |.|+||..|+...|..  ..+||.||+
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            3459999998854 34566787 9999999999999975  457999984

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

Probab=97.20  E-value=0.00013  Score=65.62  Aligned_cols=47  Identities=28%  Similarity=0.885  Sum_probs=37.6

Q ss_pred             cccccccccccCCceeEcCCCCCcccHhhHHHHHhc--CCCCccccCcccCCC
Q 025541          103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT--HTTCPLCRLSLLAPA  153 (251)
Q Consensus       103 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~~~~  153 (251)
                      -|-||-+.   ...+++-| |||..|..|+..|-..  .++||.||..+....
T Consensus       371 LCKICaen---dKdvkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte  419 (563)
T KOG1785|consen  371 LCKICAEN---DKDVKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTE  419 (563)
T ss_pred             HHHHhhcc---CCCccccc-ccchHHHHHHHhhcccCCCCCCCceeeEecccc
Confidence            49999865   33566777 9999999999999753  678999999886543

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

Probab=97.17  E-value=0.00021  Score=65.80  Aligned_cols=54  Identities=26%  Similarity=0.693  Sum_probs=45.1

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCCCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKAS  156 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~~  156 (251)
                      .+..|+||+..+..+...  . .|||.||..|+..|+..+..||.|+..+.......
T Consensus        20 ~~l~C~~C~~vl~~p~~~--~-~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~   73 (391)
T KOG0297|consen   20 ENLLCPICMSVLRDPVQT--T-TCGHRFCAGCLLESLSNHQKCPVCRQELTQAEELP   73 (391)
T ss_pred             ccccCccccccccCCCCC--C-CCCCcccccccchhhccCcCCcccccccchhhccC
Confidence            457899999999876543  3 49999999999999999999999998887665554

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

Probab=97.11  E-value=0.00025  Score=64.91  Aligned_cols=49  Identities=37%  Similarity=0.857  Sum_probs=41.8

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccC
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      ..+..|.||+..+..+   ..+| |||.||..||.+-+.....||.||..+..
T Consensus        82 ~sef~c~vc~~~l~~p---v~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   82 RSEFECCVCSRALYPP---VVTP-CGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cchhhhhhhHhhcCCC---cccc-ccccccHHHHHHHhccCCCCccccccccc
Confidence            3578999999888764   4556 99999999999988888889999999875

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

Probab=97.08  E-value=0.00033  Score=71.55  Aligned_cols=65  Identities=23%  Similarity=0.605  Sum_probs=46.7

Q ss_pred             HhhCCceeecc--CCCCCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcC----------CCCccccCccc
Q 025541           85 REMLPIVIYKE--SFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH----------TTCPLCRLSLL  150 (251)
Q Consensus        85 ~~~lp~~~~~~--~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----------~~CP~Cr~~~~  150 (251)
                      .+-||-+..+.  ..+..|+.|-||+-+--.....+.+. |+|+||..|.+.-|.+.          -.||+|+.++.
T Consensus      3468 E~CLPCl~Cdks~tkQD~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3468 EHCLPCLHCDKSATKQDADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             hhcccccccChhhhhcccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            33455443332  23456788999998876666777885 99999999998777643          25999998874

>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=96.98  E-value=0.00028  Score=54.64  Aligned_cols=36  Identities=22%  Similarity=0.641  Sum_probs=30.0

Q ss_pred             cccccccccccccCCceeEcCCCC------CcccHhhHHHHHh
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACG------HAFHMDCIDHWLT  137 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~------H~fh~~Ci~~wl~  137 (251)
                      ..+|.||++.+.....+..++ ||      |+||..|+.+|-.
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHHh
Confidence            468999999998855666776 76      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.

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

Probab=96.88  E-value=0.002  Score=56.74  Aligned_cols=48  Identities=25%  Similarity=0.500  Sum_probs=37.3

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcc
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSL  149 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~  149 (251)
                      .....|+||+.....+-.+.   .-|-+||+.||-.++..+..||+=..++
T Consensus       298 ~~~~~CpvClk~r~Nptvl~---vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~  345 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPTVLE---VSGYVFCYPCIFSYVVNYGHCPVTGYPA  345 (357)
T ss_pred             CccccChhHHhccCCCceEE---ecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence            34568999999877653332   2699999999999999999999864443

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

Probab=96.86  E-value=0.00082  Score=42.81  Aligned_cols=40  Identities=25%  Similarity=0.899  Sum_probs=27.3

Q ss_pred             ccccccccccCCceeEcCCCC-----CcccHhhHHHHHh--cCCCCccc
Q 025541          104 CSVCLADYQAEDKLQQIPACG-----HAFHMDCIDHWLT--THTTCPLC  145 (251)
Q Consensus       104 C~IC~~~~~~~~~~~~~~~C~-----H~fh~~Ci~~wl~--~~~~CP~C  145 (251)
                      |-||++.-.... ..+.| |+     -..|..|+.+|+.  .+..|++|
T Consensus         1 CrIC~~~~~~~~-~li~p-C~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISP-CRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-S-SS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecc-cccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            679999876655 44566 65     4789999999998  45679887

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

Probab=96.85  E-value=0.00035  Score=55.47  Aligned_cols=40  Identities=28%  Similarity=0.711  Sum_probs=31.6

Q ss_pred             CceeeccCC-CCCcccccccccccccCCceeEcCCCCCcccH
Q 025541           89 PIVIYKESF-SIRDTQCSVCLADYQAEDKLQQIPACGHAFHM  129 (251)
Q Consensus        89 p~~~~~~~~-~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~  129 (251)
                      |.+.|.++. .....+|.|||+++..++.+..|| |-.+||+
T Consensus       164 PrlsYNdDVL~ddkGECvICLEdL~~GdtIARLP-CLCIYHK  204 (205)
T KOG0801|consen  164 PRLSYNDDVLKDDKGECVICLEDLEAGDTIARLP-CLCIYHK  204 (205)
T ss_pred             cccccccchhcccCCcEEEEhhhccCCCceeccc-eEEEeec
Confidence            444454442 334578999999999999999999 9999996

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

Probab=96.80  E-value=0.00026  Score=62.37  Aligned_cols=50  Identities=22%  Similarity=0.574  Sum_probs=40.0

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPA  153 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  153 (251)
                      ..+|.+|-.-|.....+  . .|-|.||+.||...|.....||+|...+-...
T Consensus        15 ~itC~LC~GYliDATTI--~-eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t~   64 (331)
T KOG2660|consen   15 HITCRLCGGYLIDATTI--T-ECLHTFCKSCIVKYLEESKYCPTCDIVIHKTH   64 (331)
T ss_pred             ceehhhccceeecchhH--H-HHHHHHHHHHHHHHHHHhccCCccceeccCcc
Confidence            45799998877654332  2 59999999999999999999999988775543

>PHA02862 5L protein; Provisional

Probab=96.72  E-value=0.0012  Score=51.64  Aligned_cols=47  Identities=21%  Similarity=0.641  Sum_probs=35.6

Q ss_pred             cccccccccccccCCceeEcCCCC-----CcccHhhHHHHHhc--CCCCccccCcccCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACG-----HAFHMDCIDHWLTT--HTTCPLCRLSLLAP  152 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~-----H~fh~~Ci~~wl~~--~~~CP~Cr~~~~~~  152 (251)
                      ++.|-||+++-...    .-| |.     ...|..|+.+|+..  +..|++|+.+....
T Consensus         2 ~diCWIC~~~~~e~----~~P-C~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik   55 (156)
T PHA02862          2 SDICWICNDVCDER----NNF-CGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK   55 (156)
T ss_pred             CCEEEEecCcCCCC----ccc-ccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence            35799999985433    244 64     58999999999974  56799999987643

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.67  E-value=0.0016  Score=55.21  Aligned_cols=54  Identities=13%  Similarity=0.289  Sum_probs=47.2

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPA  153 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  153 (251)
                      .-+.|+||.+.+.......+|..|||+|+.+|..+.+.....||+|-.++...+
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrd  273 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRD  273 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccc
Confidence            346799999999998888888889999999999999999999999988876543

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

Probab=96.66  E-value=0.0043  Score=54.05  Aligned_cols=50  Identities=32%  Similarity=0.717  Sum_probs=37.7

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHh-cCCCCccc-cCcccCCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT-THTTCPLC-RLSLLAPA  153 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~C-r~~~~~~~  153 (251)
                      ...|+.|..-+..+.+.   +.|+|.||..||..-|. ..+.||.| |+++....
T Consensus       274 ~LkCplc~~Llrnp~kT---~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld~  325 (427)
T COG5222         274 SLKCPLCHCLLRNPMKT---PCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDG  325 (427)
T ss_pred             cccCcchhhhhhCcccC---ccccchHHHHHHhhhhhhccccCCCcccccchhhc
Confidence            36799998877665433   46999999999987765 67899999 55665543

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=96.55  E-value=0.0023  Score=50.90  Aligned_cols=50  Identities=24%  Similarity=0.697  Sum_probs=36.7

Q ss_pred             CCCcccccccccccccCCceeEcCCCCC-----cccHhhHHHHHhc--CCCCccccCcccCC
Q 025541           98 SIRDTQCSVCLADYQAEDKLQQIPACGH-----AFHMDCIDHWLTT--HTTCPLCRLSLLAP  152 (251)
Q Consensus        98 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H-----~fh~~Ci~~wl~~--~~~CP~Cr~~~~~~  152 (251)
                      ...+..|-||+++...  .  ..| |..     ..|..|+..|+..  ...|++|+......
T Consensus         5 s~~~~~CRIC~~~~~~--~--~~P-C~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          5 SLMDKCCWICKDEYDV--V--TNY-CNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCCCeeEecCCCCCC--c--cCC-cccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            4456789999988532  1  235 553     6799999999984  55799999877544

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

Probab=96.54  E-value=0.0011  Score=61.85  Aligned_cols=50  Identities=24%  Similarity=0.660  Sum_probs=38.6

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc-----CCCCccccCcccCC
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-----HTTCPLCRLSLLAP  152 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-----~~~CP~Cr~~~~~~  152 (251)
                      .+..+|.+|.++-+..   ... .|.|.||+.||..++..     +-+||.|...+.-.
T Consensus       534 k~~~~C~lc~d~aed~---i~s-~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD  588 (791)
T KOG1002|consen  534 KGEVECGLCHDPAEDY---IES-SCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             cCceeecccCChhhhh---Hhh-hhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            3567899999886643   334 39999999999999863     56899998877554

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

Probab=96.54  E-value=0.002  Score=41.03  Aligned_cols=45  Identities=29%  Similarity=0.656  Sum_probs=23.1

Q ss_pred             ccccccccccCCceeEcC-CCCCcccHhhHHHHHh-cCCCCccccCcc
Q 025541          104 CSVCLADYQAEDKLQQIP-ACGHAFHMDCIDHWLT-THTTCPLCRLSL  149 (251)
Q Consensus       104 C~IC~~~~~~~~~~~~~~-~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~  149 (251)
                      |++|.+++...+. ...| .|++.++..|...-+. ....||-||.+.
T Consensus         1 cp~C~e~~d~~d~-~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDK-DFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCT-T--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCC-ccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            7899999944432 2333 5899999999999886 478999999864

>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=96.53  E-value=0.00092  Score=49.79  Aligned_cols=32  Identities=38%  Similarity=0.827  Sum_probs=26.5

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHH
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCID  133 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~  133 (251)
                      .+..|++|...+..+ ...+.| |||+||..|+.
T Consensus        77 ~~~~C~vC~k~l~~~-~f~~~p-~~~v~H~~C~~  108 (109)
T PF10367_consen   77 ESTKCSVCGKPLGNS-VFVVFP-CGHVVHYSCIK  108 (109)
T ss_pred             CCCCccCcCCcCCCc-eEEEeC-CCeEEeccccc
Confidence            456799999999874 566777 99999999985

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 [].

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

Probab=96.43  E-value=0.0014  Score=59.39  Aligned_cols=37  Identities=22%  Similarity=0.724  Sum_probs=32.6

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHh
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT  137 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~  137 (251)
                      ....|.||+++.....-...+| |+|+||+.|+..++.
T Consensus       183 slf~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~  219 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFT  219 (445)
T ss_pred             hcccceeeehhhcCcceeeecc-cchHHHHHHHHHHHH
Confidence            4568999999987767888898 999999999999986

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

Probab=96.32  E-value=0.0027  Score=56.49  Aligned_cols=50  Identities=24%  Similarity=0.581  Sum_probs=41.2

Q ss_pred             CCCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccC
Q 025541           98 SIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus        98 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      ..++..|+||+..-   ......| |+|.=|+.||.+.|...+.|=.|+..+..
T Consensus       419 ~sEd~lCpICyA~p---i~Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  419 DSEDNLCPICYAGP---INAVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             CcccccCcceeccc---chhhccC-CCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            45788999998642   2345566 99999999999999999999999988764

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

Probab=96.27  E-value=0.0016  Score=63.85  Aligned_cols=50  Identities=28%  Similarity=0.744  Sum_probs=37.3

Q ss_pred             CCCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc-------CCCCccccC
Q 025541           98 SIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-------HTTCPLCRL  147 (251)
Q Consensus        98 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-------~~~CP~Cr~  147 (251)
                      ...-++|.||++.+.....+---..|-|+||..||..|-..       ...||.|+.
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            34568899999999876544322247799999999999763       235999973

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

Probab=96.19  E-value=0.0026  Score=52.22  Aligned_cols=47  Identities=23%  Similarity=0.552  Sum_probs=38.7

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      ...|.||.++|..+.   +. .|||.||..|...-++....|-+|.+....
T Consensus       196 PF~C~iCKkdy~spv---vt-~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G  242 (259)
T COG5152         196 PFLCGICKKDYESPV---VT-ECGHSFCSLCAIRKYQKGDECGVCGKATYG  242 (259)
T ss_pred             ceeehhchhhccchh---hh-hcchhHHHHHHHHHhccCCcceecchhhcc
Confidence            457999999998753   33 499999999999888888999999776543

>PHA03096 p28-like protein; Provisional

Probab=96.09  E-value=0.003  Score=55.56  Aligned_cols=48  Identities=23%  Similarity=0.519  Sum_probs=33.6

Q ss_pred             ccccccccccccC----CceeEcCCCCCcccHhhHHHHHhc---CCC---CccccCcc
Q 025541          102 TQCSVCLADYQAE----DKLQQIPACGHAFHMDCIDHWLTT---HTT---CPLCRLSL  149 (251)
Q Consensus       102 ~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~---~~~---CP~Cr~~~  149 (251)
                      -.|.||++.....    ..--.++.|.|.||..||+.|...   ..+   ||.|+..+
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~~~~~  236 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRLNTVI  236 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccchhhHH
Confidence            4699999987542    233356689999999999999863   234   55555444

>PF04641 Rtf2: Rtf2 RING-finger

Probab=96.05  E-value=0.0064  Score=52.95  Aligned_cols=56  Identities=18%  Similarity=0.418  Sum_probs=42.2

Q ss_pred             CCCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCCC
Q 025541           98 SIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAK  154 (251)
Q Consensus        98 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~  154 (251)
                      ....+.|||...+|........+-.|||+|...+|...- ....||+|-.++...+.
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~Di  165 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEEDI  165 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccCCE
Confidence            345688999999996544444443499999999999973 35679999988875543

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.88  E-value=0.0057  Score=54.22  Aligned_cols=57  Identities=19%  Similarity=0.377  Sum_probs=41.1

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHh-cCCCCccccCcccCCCCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT-THTTCPLCRLSLLAPAKAS  156 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~~~~~~  156 (251)
                      +++-|++|+++|...++-..--+||...|.-|....-+ .+..||-||.....+....
T Consensus        13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~   70 (480)
T COG5175          13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRY   70 (480)
T ss_pred             ccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeE
Confidence            34559999999987766544335998888888665433 3678999999887766543

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

Probab=95.78  E-value=0.0093  Score=53.05  Aligned_cols=53  Identities=25%  Similarity=0.597  Sum_probs=41.0

Q ss_pred             ccCCCCCcccccccccccccCCceeEcCCCCCcccHhhHHHH--HhcCCCCccccCccc
Q 025541           94 KESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHW--LTTHTTCPLCRLSLL  150 (251)
Q Consensus        94 ~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w--l~~~~~CP~Cr~~~~  150 (251)
                      .++.+.++..|.||-+.+.   ...++| |+|..|--|-.+.  |..++.||+||....
T Consensus        54 addtDEen~~C~ICA~~~T---Ys~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE~e  108 (493)
T COG5236          54 ADDTDEENMNCQICAGSTT---YSARYP-CGHQICHACAVRLRALYMQKGCPLCRTETE  108 (493)
T ss_pred             ccccccccceeEEecCCce---EEEecc-CCchHHHHHHHHHHHHHhccCCCccccccc
Confidence            3445566788999998875   567788 9999999997543  567889999998653

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

Probab=95.69  E-value=0.0042  Score=60.98  Aligned_cols=42  Identities=29%  Similarity=0.804  Sum_probs=32.3

Q ss_pred             ccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcc
Q 025541          102 TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSL  149 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~  149 (251)
                      ..|..|--.+..+. +-.  .|||.||.+|+.   .....||.|+..+
T Consensus       841 skCs~C~~~LdlP~-VhF--~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  841 SKCSACEGTLDLPF-VHF--LCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeecccCCccccce-eee--ecccHHHHHhhc---cCcccCCccchhh
Confidence            57999998887652 222  399999999999   4566899998733

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

Probab=95.63  E-value=0.0059  Score=53.17  Aligned_cols=47  Identities=19%  Similarity=0.386  Sum_probs=39.2

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      .+.|-||...|..+..   . .|+|.||..|-..-++....|++|.+.+..
T Consensus       241 Pf~c~icr~~f~~pVv---t-~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g  287 (313)
T KOG1813|consen  241 PFKCFICRKYFYRPVV---T-KCGHYFCEVCALKPYQKGEKCYVCSQQTHG  287 (313)
T ss_pred             Cccccccccccccchh---h-cCCceeehhhhccccccCCcceeccccccc
Confidence            4569999999987633   3 499999999999988888999999877654

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

Probab=95.42  E-value=0.0064  Score=51.60  Aligned_cols=44  Identities=27%  Similarity=0.677  Sum_probs=31.5

Q ss_pred             cccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCccc
Q 025541          103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLL  150 (251)
Q Consensus       103 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  150 (251)
                      .|--|..--. ++...++. |+|+||..|...-  ....||+|++.+-
T Consensus         5 hCn~C~~~~~-~~~f~LTa-C~HvfC~~C~k~~--~~~~C~lCkk~ir   48 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLTA-CRHVFCEPCLKAS--SPDVCPLCKKSIR   48 (233)
T ss_pred             EeccccccCC-CCceeeee-chhhhhhhhcccC--Cccccccccceee
Confidence            3666654433 55666665 9999999998763  2338999999864

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

Probab=95.32  E-value=0.0032  Score=54.71  Aligned_cols=43  Identities=23%  Similarity=0.695  Sum_probs=32.1

Q ss_pred             cccccccccccccCCceeEcCCCCC-cccHhhHHHHHhcCCCCccccCcccC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGH-AFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H-~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      +.-|.|||+...   ....|+ ||| +-|.+|-+..    +.||+||+.+..
T Consensus       300 ~~LC~ICmDaP~---DCvfLe-CGHmVtCt~CGkrm----~eCPICRqyi~r  343 (350)
T KOG4275|consen  300 RRLCAICMDAPR---DCVFLE-CGHMVTCTKCGKRM----NECPICRQYIVR  343 (350)
T ss_pred             HHHHHHHhcCCc---ceEEee-cCcEEeehhhcccc----ccCchHHHHHHH
Confidence            567999998754   456777 999 4577786553    379999987754

>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=95.26  E-value=0.01  Score=37.03  Aligned_cols=41  Identities=22%  Similarity=0.680  Sum_probs=22.7

Q ss_pred             ccccccccccCCceeEcCCCCCcccHhhHHHHHhcCC--CCccc
Q 025541          104 CSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHT--TCPLC  145 (251)
Q Consensus       104 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~--~CP~C  145 (251)
                      |.+|.+-+..++.-... .|+=.+|..|+..++....  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~-~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNR-DCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS---S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCC-ccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            66777776665333222 4888999999999998654  79988

; PDB: 3NW0_A 2CT0_A.

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

Probab=94.98  E-value=0.016  Score=46.92  Aligned_cols=30  Identities=33%  Similarity=0.946  Sum_probs=24.5

Q ss_pred             CCCCcccHhhHHHHHhc----C-------CCCccccCcccC
Q 025541          122 ACGHAFHMDCIDHWLTT----H-------TTCPLCRLSLLA  151 (251)
Q Consensus       122 ~C~H~fh~~Ci~~wl~~----~-------~~CP~Cr~~~~~  151 (251)
                      +||.-||.-|+..||+.    .       ..||.|-.++..
T Consensus       189 qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pial  229 (234)
T KOG3268|consen  189 QCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIAL  229 (234)
T ss_pred             ccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCccee
Confidence            59999999999999973    1       149999888754

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

Probab=94.95  E-value=0.016  Score=52.49  Aligned_cols=29  Identities=24%  Similarity=0.945  Sum_probs=22.7

Q ss_pred             CCCcccHhhHHHHHhcC-------------CCCccccCcccC
Q 025541          123 CGHAFHMDCIDHWLTTH-------------TTCPLCRLSLLA  151 (251)
Q Consensus       123 C~H~fh~~Ci~~wl~~~-------------~~CP~Cr~~~~~  151 (251)
                      |.-.+|.+|+-+|+..+             -.||+||+.+..
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi  352 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI  352 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence            56788999999998642             259999998653

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

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

Probab=94.89  E-value=0.014  Score=52.33  Aligned_cols=44  Identities=30%  Similarity=0.677  Sum_probs=31.2

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      ...|.||+++...   ...+| |||+-|  |..-... ...||+||..+..
T Consensus       305 p~lcVVcl~e~~~---~~fvp-cGh~cc--ct~cs~~-l~~CPvCR~rI~~  348 (355)
T KOG1571|consen  305 PDLCVVCLDEPKS---AVFVP-CGHVCC--CTLCSKH-LPQCPVCRQRIRL  348 (355)
T ss_pred             CCceEEecCCccc---eeeec-CCcEEE--chHHHhh-CCCCchhHHHHHH
Confidence            4569999998765   56677 999966  6554322 3349999987643

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

Probab=94.85  E-value=0.002  Score=58.00  Aligned_cols=51  Identities=31%  Similarity=0.679  Sum_probs=42.2

Q ss_pred             cccccccccccccC-CceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCC
Q 025541          101 DTQCSVCLADYQAE-DKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAP  152 (251)
Q Consensus       101 ~~~C~IC~~~~~~~-~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  152 (251)
                      ...|+||...+... +.+..+. |||.+|..||.+||.....||.|+..+...
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~-~g~~~~~~kL~k~L~~~~kl~~~~rel~~~  247 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIV-CGHIYHHGKLSKWLATKRKLPSCRRELPKN  247 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHh-hcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence            34699999998765 4555554 999999999999999988999999988643

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=94.81  E-value=0.019  Score=37.51  Aligned_cols=46  Identities=24%  Similarity=0.490  Sum_probs=32.2

Q ss_pred             ccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCC
Q 025541          102 TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPA  153 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  153 (251)
                      ..|-.|...-   .+-.++| |+|+.+..|..-+  +-+-||.|.+++...+
T Consensus         8 ~~~~~~~~~~---~~~~~~p-CgH~I~~~~f~~~--rYngCPfC~~~~~~~~   53 (55)
T PF14447_consen    8 QPCVFCGFVG---TKGTVLP-CGHLICDNCFPGE--RYNGCPFCGTPFEFDD   53 (55)
T ss_pred             eeEEEccccc---ccccccc-ccceeeccccChh--hccCCCCCCCcccCCC
Confidence            3466665442   2345677 9999999998764  4457999998886543

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

Probab=94.50  E-value=0.016  Score=50.86  Aligned_cols=43  Identities=28%  Similarity=0.662  Sum_probs=30.9

Q ss_pred             cccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCccc
Q 025541          103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLL  150 (251)
Q Consensus       103 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  150 (251)
                      .|--|-..+..  .-+++| |.|+||.+|-+.  ...+.||.|-..|.
T Consensus        92 fCd~Cd~PI~I--YGRmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~Vq  134 (389)
T KOG2932|consen   92 FCDRCDFPIAI--YGRMIP-CKHVFCLECARS--DSDKICPLCDDRVQ  134 (389)
T ss_pred             eecccCCccee--eecccc-cchhhhhhhhhc--CccccCcCcccHHH
Confidence            36667655443  567888 999999999865  34668999966553

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

Probab=94.26  E-value=0.029  Score=49.61  Aligned_cols=47  Identities=32%  Similarity=0.840  Sum_probs=38.3

Q ss_pred             ccccccccccccCC---ceeEcCCCCCcccHhhHHHHHhc-CCCCccccCcc
Q 025541          102 TQCSVCLADYQAED---KLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSL  149 (251)
Q Consensus       102 ~~C~IC~~~~~~~~---~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~  149 (251)
                      ..|-||-++|...+   ..+++. |||.|+..|+.+.+.. ...||.||...
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~-c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLK-CGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccc-cCceehHhHHHHHhcCceeeccCCCCcc
Confidence            46999999998763   455564 9999999999998875 45799999986

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=94.13  E-value=0.065  Score=34.96  Aligned_cols=35  Identities=29%  Similarity=0.816  Sum_probs=30.6

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHH
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDH  134 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~  134 (251)
                      ....|++|-+.|..++.+.+-|.||-.+|+.|-..
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            34679999999998888888999999999999765

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

Probab=93.53  E-value=0.033  Score=55.20  Aligned_cols=36  Identities=28%  Similarity=0.676  Sum_probs=28.5

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHh
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT  137 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~  137 (251)
                      .++.|.+|...+... .-.+.| |||.||++||.+-..
T Consensus       816 p~d~C~~C~~~ll~~-pF~vf~-CgH~FH~~Cl~~~v~  851 (911)
T KOG2034|consen  816 PQDSCDHCGRPLLIK-PFYVFP-CGHCFHRDCLIRHVL  851 (911)
T ss_pred             CccchHHhcchhhcC-cceeee-ccchHHHHHHHHHHH
Confidence            567899999888664 445566 999999999987653

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

Probab=93.47  E-value=0.029  Score=55.10  Aligned_cols=47  Identities=30%  Similarity=0.751  Sum_probs=36.4

Q ss_pred             ccccccccccccCCceeEcCCCCCcccHhhHHHHHhc--CCCCccccCcccCCC
Q 025541          102 TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT--HTTCPLCRLSLLAPA  153 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~~~~  153 (251)
                      ..|.||++    .+.....+ |+|.||..|+..-+..  ...||+||..+....
T Consensus       455 ~~c~ic~~----~~~~~it~-c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~  503 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITR-CGHDFCVECLKKSIQQSENAPCPLCRNVLKEKK  503 (674)
T ss_pred             cccccccc----cccceeec-ccchHHHHHHHhccccccCCCCcHHHHHHHHHH
Confidence            68999999    23445555 9999999999998874  336999998776544

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

Probab=93.41  E-value=0.046  Score=47.72  Aligned_cols=45  Identities=24%  Similarity=0.642  Sum_probs=36.4

Q ss_pred             ccccccccccccCCc-eeEcCCCCCcccHhhHHHHHhcCCCCccccC
Q 025541          102 TQCSVCLADYQAEDK-LQQIPACGHAFHMDCIDHWLTTHTTCPLCRL  147 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~-~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~  147 (251)
                      .-||||.+.+..... +..++ |||.-|..|+......+-+||+|.+
T Consensus       159 ~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  159 FNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             CCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc
Confidence            349999998765443 44555 9999999999999887799999987

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

Probab=93.23  E-value=0.049  Score=53.15  Aligned_cols=40  Identities=30%  Similarity=0.753  Sum_probs=28.5

Q ss_pred             cccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCcc
Q 025541          103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPL  144 (251)
Q Consensus       103 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~  144 (251)
                      .|.||.-.+..... ... .|+|+-|..|.+.|+.....||.
T Consensus      1030 ~C~~C~l~V~gss~-~Cg-~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1030 QCAICHLAVRGSSN-FCG-TCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeeEeeEeeccch-hhc-cccccccHHHHHHHHhcCCcCCC
Confidence            36666555433222 223 39999999999999999999984

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

Probab=93.21  E-value=0.028  Score=53.82  Aligned_cols=43  Identities=21%  Similarity=0.576  Sum_probs=31.4

Q ss_pred             ccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccC
Q 025541          102 TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRL  147 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~  147 (251)
                      ..|.||+..|....-..+.+.|||..|.+|+....  +.+|| |+.
T Consensus        12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly--n~scp-~~~   54 (861)
T KOG3161|consen   12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY--NASCP-TKR   54 (861)
T ss_pred             hhchHHHHHHHHHhcCcccccccchHHHHHHHhHh--hccCC-CCc
Confidence            35999998886554444444699999999998854  45788 543

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

Probab=92.88  E-value=0.034  Score=57.15  Aligned_cols=45  Identities=27%  Similarity=0.773  Sum_probs=37.1

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCc
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLS  148 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~  148 (251)
                      -..|.||++.+..-..+.   .|||.+|..|+..|+..+..||+|+..
T Consensus      1153 ~~~c~ic~dil~~~~~I~---~cgh~~c~~c~~~~l~~~s~~~~~ksi 1197 (1394)
T KOG0298|consen 1153 HFVCEICLDILRNQGGIA---GCGHEPCCRCDELWLYASSRCPICKSI 1197 (1394)
T ss_pred             ccchHHHHHHHHhcCCee---eechhHhhhHHHHHHHHhccCcchhhh
Confidence            347999999987433332   499999999999999999999999743

>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=92.58  E-value=0.06  Score=33.97  Aligned_cols=29  Identities=28%  Similarity=0.812  Sum_probs=21.9

Q ss_pred             CC-CcccHhhHHHHHhcCCCCccccCcccC
Q 025541          123 CG-HAFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus       123 C~-H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      |. |..|..|+...|.+...||+|..+++.
T Consensus        18 C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen   18 CSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             -SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             ecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            76 999999999999999999999988864

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.

>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=92.27  E-value=0.16  Score=40.52  Aligned_cols=37  Identities=22%  Similarity=0.549  Sum_probs=22.1

Q ss_pred             cccccccccccccCCceeEcC---C-----CC-CcccHhhHHHHHh
Q 025541          101 DTQCSVCLADYQAEDKLQQIP---A-----CG-HAFHMDCIDHWLT  137 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~---~-----C~-H~fh~~Ci~~wl~  137 (251)
                      +..|+|||+--....-+.-..   +     |+ -.-|..||+++-+
T Consensus         2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            568999998755432221111   1     44 2457889998864

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.

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

Probab=91.83  E-value=0.13  Score=46.85  Aligned_cols=45  Identities=22%  Similarity=0.473  Sum_probs=38.5

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcC---CCCccc
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH---TTCPLC  145 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~---~~CP~C  145 (251)
                      .-..|||=.+.-.....+..+. |||+..++-|.+..+..   ..||.|
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYC  380 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYC  380 (394)
T ss_pred             ceeecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCC
Confidence            4578999998888888888897 99999999999987643   579999

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=90.99  E-value=0.12  Score=45.20  Aligned_cols=29  Identities=21%  Similarity=0.643  Sum_probs=23.2

Q ss_pred             CCCcccHhhHHHHHhc-------------CCCCccccCcccC
Q 025541          123 CGHAFHMDCIDHWLTT-------------HTTCPLCRLSLLA  151 (251)
Q Consensus       123 C~H~fh~~Ci~~wl~~-------------~~~CP~Cr~~~~~  151 (251)
                      |...+|..|+-+|+..             +-+||+||+.+.-
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci  366 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCI  366 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEE
Confidence            6788999999999852             3469999997754

>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=90.63  E-value=0.08  Score=44.95  Aligned_cols=49  Identities=31%  Similarity=0.676  Sum_probs=36.2

Q ss_pred             Ccccccccccc-cccC-CceeEcCCCCCcccHhhHHHHHhcC-CCCc--cccCc
Q 025541          100 RDTQCSVCLAD-YQAE-DKLQQIPACGHAFHMDCIDHWLTTH-TTCP--LCRLS  148 (251)
Q Consensus       100 ~~~~C~IC~~~-~~~~-~~~~~~~~C~H~fh~~Ci~~wl~~~-~~CP--~Cr~~  148 (251)
                      .+..||||..+ |-.+ .++.+.|.|-|..|..|+++.+.+. ..||  -|.+-
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kI   62 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKI   62 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHH
Confidence            45679999875 3333 3455566799999999999999864 5798  77543

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

Probab=90.12  E-value=0.19  Score=44.60  Aligned_cols=43  Identities=28%  Similarity=0.629  Sum_probs=33.7

Q ss_pred             CcccccccccccccCCceeEcCCC--CCcccHhhHHHHHhcCCCCccccCccc
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPAC--GHAFHMDCIDHWLTTHTTCPLCRLSLL  150 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C--~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  150 (251)
                      .-.+||||.+.+..+..     +|  ||+.|..|-.+   ....||.||.++.
T Consensus        47 ~lleCPvC~~~l~~Pi~-----QC~nGHlaCssC~~~---~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   47 DLLDCPVCFNPLSPPIF-----QCDNGHLACSSCRTK---VSNKCPTCRLPIG   91 (299)
T ss_pred             hhccCchhhccCcccce-----ecCCCcEehhhhhhh---hcccCCccccccc
Confidence            34679999999987522     36  79999999874   4567999999886

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

Probab=89.55  E-value=0.24  Score=48.96  Aligned_cols=52  Identities=21%  Similarity=0.647  Sum_probs=38.9

Q ss_pred             CcccccccccccccCCceeEcCCCC-----CcccHhhHHHHHhc--CCCCccccCcccCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACG-----HAFHMDCIDHWLTT--HTTCPLCRLSLLAPA  153 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~-----H~fh~~Ci~~wl~~--~~~CP~Cr~~~~~~~  153 (251)
                      ++..|-||..+-..++.+. -| |.     ...|..|+.+|+.-  ...|-+|+.++.-.+
T Consensus        11 d~~~CRICr~e~~~d~pLf-hP-CKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~   69 (1175)
T COG5183          11 DKRSCRICRTEDIRDDPLF-HP-CKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKD   69 (1175)
T ss_pred             cchhceeecCCCCCCCcCc-cc-ccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeee
Confidence            4578999999877666554 34 54     46899999999984  557999998775443

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

Probab=89.28  E-value=0.41  Score=41.85  Aligned_cols=52  Identities=29%  Similarity=0.620  Sum_probs=36.8

Q ss_pred             cccccccc-cccCCceeEcCCCCCcccHhhHHHHHhc-CCCCccccCcccCCCC
Q 025541          103 QCSVCLAD-YQAEDKLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSLLAPAK  154 (251)
Q Consensus       103 ~C~IC~~~-~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~~  154 (251)
                      .|++|.-. |..++...+...|+|..|..|++..+.. ...||-|-..+-....
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nf   55 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNNF   55 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhccc
Confidence            49999864 4444433333359999999999998875 5579999776654443

>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane

Probab=89.10  E-value=0.67  Score=35.60  Aligned_cols=19  Identities=26%  Similarity=0.457  Sum_probs=8.7

Q ss_pred             HHHHHHHHHHHHHHHHhhc
Q 025541           35 FFTFILLLLFYLFYLRRRR   53 (251)
Q Consensus        35 ~~~~i~~~~~~~~~~~~~~   53 (251)
                      +++++.++++++|+++|++
T Consensus        74 ~aGvIg~Illi~y~irR~~   92 (122)
T PF01102_consen   74 MAGVIGIILLISYCIRRLR   92 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHHh
Confidence            3334444444455555444

Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.33  E-value=0.5  Score=40.57  Aligned_cols=58  Identities=12%  Similarity=0.268  Sum_probs=42.2

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCCCCCCcc
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASSEL  159 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~~~~~  159 (251)
                      ....|+|=--+|........+-.|||+|-..-+.+.  ...+|++|.+.+...+......
T Consensus       110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~dvIvlNg  167 (293)
T KOG3113|consen  110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDDVIVLNG  167 (293)
T ss_pred             ceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccCeEeeCC
Confidence            456799988888765544444459999999988874  4678999999887766544333

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

Probab=88.25  E-value=0.45  Score=36.88  Aligned_cols=54  Identities=20%  Similarity=0.516  Sum_probs=37.1

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHh---cCCCCccccCcccCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT---THTTCPLCRLSLLAPA  153 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~---~~~~CP~Cr~~~~~~~  153 (251)
                      .-.+|-||.+.-.+..-+.----||-..|..|-...++   .+..||.|+..+....
T Consensus        79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS  135 (140)
T ss_pred             CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence            34689999987654332221114999999998765544   4788999999886543

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

Probab=88.13  E-value=0.31  Score=43.15  Aligned_cols=52  Identities=21%  Similarity=0.698  Sum_probs=38.1

Q ss_pred             cccccccccccccCCc-eeEcCCCC-----CcccHhhHHHHHh--cCCCCccccCcccCCC
Q 025541          101 DTQCSVCLADYQAEDK-LQQIPACG-----HAFHMDCIDHWLT--THTTCPLCRLSLLAPA  153 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~-~~~~~~C~-----H~fh~~Ci~~wl~--~~~~CP~Cr~~~~~~~  153 (251)
                      +..|-||..+...... ....| |.     +..|+.|+..|+.  ....|..|........
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~p-C~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~~  137 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISP-CSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINVG  137 (323)
T ss_pred             CCcEEEEecccccccccccccC-ccccCcHHHHHHHHHHhhhccccCeeeecccccceecc
Confidence            4679999997654322 34455 64     6789999999998  5667999988666553

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

Probab=87.79  E-value=0.29  Score=47.17  Aligned_cols=49  Identities=24%  Similarity=0.711  Sum_probs=39.6

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCCCC
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKA  155 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~  155 (251)
                      .....|.||+.++    ..+..+ |.   |..|+..|+..+..||+|+..+......
T Consensus       477 ~~~~~~~~~~~~~----~~~~~~-~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~~  525 (543)
T KOG0802|consen  477 EPNDVCAICYQEM----SARITP-CS---HALCLRKWLYVQEVCPLCHTYMKEDDFL  525 (543)
T ss_pred             cccCcchHHHHHH----Hhcccc-cc---chhHHHhhhhhccccCCCchhhhccccc
Confidence            3467799999998    445555 88   9999999999999999999888765543

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.37  E-value=0.34  Score=41.66  Aligned_cols=52  Identities=21%  Similarity=0.638  Sum_probs=35.5

Q ss_pred             CCCcccccccccccccCCce-eEcCCCC-----CcccHhhHHHHHhcC--------CCCccccCccc
Q 025541           98 SIRDTQCSVCLADYQAEDKL-QQIPACG-----HAFHMDCIDHWLTTH--------TTCPLCRLSLL  150 (251)
Q Consensus        98 ~~~~~~C~IC~~~~~~~~~~-~~~~~C~-----H~fh~~Ci~~wl~~~--------~~CP~Cr~~~~  150 (251)
                      ...+..|=||+..=++.... -+-| |.     |-.|..|+..|+..+        .+||-|+....
T Consensus        17 ~e~eR~CWiCF~TdeDn~~a~WV~P-CrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi   82 (293)
T KOG3053|consen   17 QELERCCWICFATDEDNRLAAWVHP-CRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI   82 (293)
T ss_pred             cccceeEEEEeccCcccchhhhccc-ccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence            34567799999764443322 2334 53     889999999999632        25999988654

>KOG0269 consensus WD40 repeat-containing protein [Function unknown]

Probab=85.93  E-value=0.68  Score=45.53  Aligned_cols=41  Identities=22%  Similarity=0.500  Sum_probs=31.3

Q ss_pred             ccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCcc
Q 025541          102 TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPL  144 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~  144 (251)
                      ..|.+|-..+..  ....-+.|||.=|..|+++|+.....||.
T Consensus       780 ~~CtVC~~vi~G--~~~~c~~C~H~gH~sh~~sw~~~~s~ca~  820 (839)
T KOG0269|consen  780 AKCTVCDLVIRG--VDVWCQVCGHGGHDSHLKSWFFKASPCAK  820 (839)
T ss_pred             cCceeecceeee--eEeecccccccccHHHHHHHHhcCCCCcc
Confidence            358888766542  33344479999999999999998888876

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

Probab=85.34  E-value=0.29  Score=45.03  Aligned_cols=38  Identities=24%  Similarity=0.760  Sum_probs=27.6

Q ss_pred             CcccccccccccccC-CceeEcCCCCCcccHhhHHHHHhc
Q 025541          100 RDTQCSVCLADYQAE-DKLQQIPACGHAFHMDCIDHWLTT  138 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~-~~~~~~~~C~H~fh~~Ci~~wl~~  138 (251)
                      ...+|.||+.+.... ....+. .|+|.||..|+.+.+..
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~-~C~H~fC~~C~k~~iev  183 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVL-KCGHRFCKDCVKQHIEV  183 (384)
T ss_pred             ccccCccCccccccHhhhHHHh-cccchhhhHHhHHHhhh
Confidence            356799999444333 444434 59999999999999874

>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=84.00  E-value=0.96  Score=29.00  Aligned_cols=42  Identities=19%  Similarity=0.608  Sum_probs=20.3

Q ss_pred             cccccccccccCCceeEcCCCCCcccHhhHHHHHhc-----CCCCccccCc
Q 025541          103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-----HTTCPLCRLS  148 (251)
Q Consensus       103 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-----~~~CP~Cr~~  148 (251)
                      .|+|....+..  .++... |.|.-|.+ +..||..     .-.||+|.++
T Consensus         4 ~CPls~~~i~~--P~Rg~~-C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    4 RCPLSFQRIRI--PVRGKN-CKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             B-TTTSSB-SS--EEEETT---SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eCCCCCCEEEe--CccCCc-CcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            58998888766  455554 99986544 5566653     3469999763

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.

>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins

Probab=83.82  E-value=6.4  Score=29.65  Aligned_cols=22  Identities=18%  Similarity=0.303  Sum_probs=16.0

Q ss_pred             HHHhcCCCCccccCcccCCCCC
Q 025541          134 HWLTTHTTCPLCRLSLLAPAKA  155 (251)
Q Consensus       134 ~wl~~~~~CP~Cr~~~~~~~~~  155 (251)
                      +.|.+...|+.|++++..+...
T Consensus        80 KmLGr~D~CM~C~~pLTLd~~l  101 (114)
T PF11023_consen   80 KMLGRVDACMHCKEPLTLDPSL  101 (114)
T ss_pred             hhhchhhccCcCCCcCccCchh
Confidence            3455667899999999876544

; GO: 0005887 integral to plasma membrane

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

Probab=82.58  E-value=0.72  Score=45.59  Aligned_cols=52  Identities=12%  Similarity=0.223  Sum_probs=36.7

Q ss_pred             CcccccccccccccCCc---eeEcCCCCCcccHhhHHHHHhc------CCCCccccCcccC
Q 025541          100 RDTQCSVCLADYQAEDK---LQQIPACGHAFHMDCIDHWLTT------HTTCPLCRLSLLA  151 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~---~~~~~~C~H~fh~~Ci~~wl~~------~~~CP~Cr~~~~~  151 (251)
                      ..+.|.||..++..++.   .-.+..|+|.||..||..|+.+      +-.|++|..-|..
T Consensus        95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~s  155 (1134)
T KOG0825|consen   95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGS  155 (1134)
T ss_pred             cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhh
Confidence            45779999988877332   1122259999999999999863      3358888776643

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

Probab=82.23  E-value=0.46  Score=45.73  Aligned_cols=42  Identities=21%  Similarity=0.746  Sum_probs=26.2

Q ss_pred             Ccccccccccc-----cccCCceeEcCCCCCcccHhhHHHHHhcCCCCccc
Q 025541          100 RDTQCSVCLAD-----YQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLC  145 (251)
Q Consensus       100 ~~~~C~IC~~~-----~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~C  145 (251)
                      ....|.||...     |.. +.++.--.|+++||.+|+..   .+..||.|
T Consensus       510 ~gfiCe~Cq~~~iiyPF~~-~~~~rC~~C~avfH~~C~~r---~s~~CPrC  556 (580)
T KOG1829|consen  510 KGFICELCQHNDIIYPFET-RNTRRCSTCLAVFHKKCLRR---KSPCCPRC  556 (580)
T ss_pred             CeeeeeeccCCCccccccc-ccceeHHHHHHHHHHHHHhc---cCCCCCch
Confidence            35668888332     221 22232225999999999876   33449999

>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=81.47  E-value=1.8  Score=40.68  Aligned_cols=37  Identities=32%  Similarity=0.805  Sum_probs=29.9

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT  138 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~  138 (251)
                      .....|.||.+.+..  .+..+. |+|.|+..|...++..
T Consensus        68 ~~~~~c~ic~~~~~~--~~~~~~-c~H~~c~~cw~~yl~~  104 (444)
T KOG1815|consen   68 KGDVQCGICVESYDG--EIIGLG-CGHPFCPPCWTGYLGT  104 (444)
T ss_pred             CccccCCcccCCCcc--hhhhcC-CCcHHHHHHHHHHhhh
Confidence            456789999999865  444554 9999999999999874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	251
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		6e-12
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		9e-08
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		2e-07
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		1e-06
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		7e-06
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		2e-04

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 23/48 (47%), Positives = 38/48 (79%)
Query: 103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLL 150
           +C+VCLA+ +  ++ + +P CGH FH +C+D WL +H+TCPLCRL+++
Sbjct: 7   ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 24/57 (42%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 104 CSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASSELS 160
           C+VCL D++  D+L   P C HAFH  C+  WL     CPLC + +L  A+ S   S
Sbjct: 18  CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLSGPSS 73

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 20/45 (44%), Positives = 29/45 (64%), Gaps = 1/45 (2%)
Query: 102 TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCR 146
           T C VC+ D+++   L+ +P C H FH  C+D WL  + TCP+CR
Sbjct: 24  TLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICR 67

>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 = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA 151
           +C VC  DY   + ++Q+P C H FH  CI  WL  H +CP+CR SL  
Sbjct: 17  ECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTG 64

>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain Length = 69

Iteration: 1
 Score = 47.4 bits (111), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 17/47 (36%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSL 149
           +C++CL+  +  + ++++P C H FH  C+D WL T+  CP+CR+ +
Sbjct: 16  KCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDI 61

>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 = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 82  KELREMLPIVIYKESFSI--RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH 139
           KE  + LP ++  E      ++  C +C ++Y   D   ++P C H FH  C+  WL   
Sbjct: 19  KESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKS 77
Query: 140 TTCPLCRLSLLAP 152
            TCP+CR     P
Sbjct: 78  GTCPVCRCMFPPP 90

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	251
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	3e-26
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	5e-25
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	2e-24
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	7e-22
2ect_A	78	Ring finger protein 126; metal binding protein, st	2e-21
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	1e-20
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	6e-19
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	3e-18
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	5e-16
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	8e-14
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	2e-13
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	9e-13
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	3e-12
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	7e-12
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	9e-11
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	1e-08
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	2e-08
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	6e-08
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	8e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-07
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-05
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-07
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	3e-07
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	3e-07
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	1e-06
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	7e-06
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	1e-05
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	1e-05
3nw0_A	238	Non-structural maintenance of chromosomes element	2e-05
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	4e-05
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	1e-04
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	2e-04
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	2e-04
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	3e-04
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	3e-04
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	5e-04
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	8e-04

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

 Score = 96.1 bits (240), Expect = 3e-26
 Identities = 23/50 (46%), Positives = 38/50 (76%)

Query: 101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLL 150
             +C+VCLA+ +  ++ + +P CGH FH +C+D WL +H+TCPLCRL+++
Sbjct: 5   GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

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

 Score = 93.2 bits (232), Expect = 5e-25
 Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 2/69 (2%)

Query: 86  EMLPIVIYK-ESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPL 144
             LP   +   +     T C VC+ D+++   L+ +P C H FH  C+D WL  + TCP+
Sbjct: 7   GQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPI 65

Query: 145 CRLSLLAPA 153
           CR      +
Sbjct: 66  CRADSGPSS 74

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

 Score = 92.0 bits (229), Expect = 2e-24
 Identities = 23/76 (30%), Positives = 34/76 (44%), Gaps = 3/76 (3%)

Query: 79  GLKKELREMLPIVIYKESFSIR--DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWL 136
              KE  + LP ++  E       +  C +C ++Y   D   ++P C H FH  C+  WL
Sbjct: 16  PASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWL 74

Query: 137 TTHTTCPLCRLSLLAP 152
               TCP+CR     P
Sbjct: 75  QKSGTCPVCRCMFPPP 90

>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 = 85.1 bits (211), Expect = 7e-22
 Identities = 19/57 (33%), Positives = 36/57 (63%), Gaps = 1/57 (1%)

Query: 101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASS 157
           + +C++CL+  +  + ++++P C H FH  C+D WL T+  CP+CR+ + A   + S
Sbjct: 14  EEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQLPSES 69

>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 = 84.0 bits (208), Expect = 2e-21
 Identities = 23/58 (39%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASSE 158
             +C VC  DY   + ++Q+P C H FH  CI  WL  H +CP+CR SL     A++ 
Sbjct: 15  GLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATNP 71

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

 Score = 82.1 bits (203), Expect = 1e-20
 Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASS 157
              C+VCL D++  D+L   P C HAFH  C+  WL     CPLC + +L  A+ S 
Sbjct: 15  HELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLSG 70

>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 = 76.9 bits (190), Expect = 6e-19
 Identities = 14/51 (27%), Positives = 19/51 (37%)

Query: 101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA 151
            + C +CL D      +  +  CGH  H  C +  L     CPLC      
Sbjct: 5   SSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSSG 55

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

 Score = 75.7 bits (186), Expect = 3e-18
 Identities = 15/46 (32%), Positives = 23/46 (50%)

Query: 101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCR 146
              C  C A+ + ED +     C H+FH  C+  W+  +  CPLC+
Sbjct: 26  MDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71

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

 Score = 69.7 bits (171), Expect = 5e-16
 Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 5/58 (8%)

Query: 100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASS 157
            + +C +C+     + +   I  C H+F   CID W   H  CP+CRL +    ++S 
Sbjct: 14  DEEECCICM-----DGRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANESSG 66

>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 = 64.8 bits (157), Expect = 8e-14
 Identities = 17/55 (30%), Positives = 21/55 (38%)

Query: 92  IYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCR 146
           I +        +C    A   +E+       C HAFH  CI  WL T   CPL  
Sbjct: 42  ICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

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

 Score = 62.4 bits (152), Expect = 2e-13
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 3/67 (4%)

Query: 101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASSELS 160
             +C +CL D    +    +P C HAF   CI  W+  + TCPLC++ + +        S
Sbjct: 5   AERCPICLEDP--SNYSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVESVVHTIESDS 61

Query: 161 DIQQETI 167
           +   + I
Sbjct: 62  EFGDQLI 68

>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 = 62.2 bits (150), Expect = 9e-13
 Identities = 17/55 (30%), Positives = 21/55 (38%)

Query: 92  IYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCR 146
           I +        +C    A   +E+       C HAFH  CI  WL T   CPL  
Sbjct: 53  ICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

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

 Score = 59.5 bits (144), Expect = 3e-12
 Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 3/52 (5%)

Query: 101 DTQCSVCLADYQAEDKLQQIPA---CGHAFHMDCIDHWLTTHTTCPLCRLSL 149
              C +C+  Y    +  ++     CGH F   C+   L    TCP CR  +
Sbjct: 15  TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66

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

 Score = 58.2 bits (141), Expect = 7e-12
 Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 3/53 (5%)

Query: 100 RDTQCSVCLADYQAEDKLQQIPA---CGHAFHMDCIDHWLTTHTTCPLCRLSL 149
               C +C+  Y    +  ++     CGH F   C+   L    TCP CR  +
Sbjct: 2   AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54

>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 = 55.6 bits (134), Expect = 9e-11
 Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 3/52 (5%)

Query: 101 DTQCSVCLADYQAEDKLQQIPA---CGHAFHMDCIDHWLTTHTTCPLCRLSL 149
              C +C+  Y    +  ++     CGH F   C+   L    TCP CR  +
Sbjct: 10  TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61

>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 = 50.7 bits (121), Expect = 1e-08
 Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 15/83 (18%)

Query: 103 QCSVCLADYQAEDKLQ---QIPACGHAFHMDCIDHWLTT-HTTCPLCRLSL----LAPAK 154
           +C +C+      +KL+     P C       CI  WLT     CP CR  L    L   +
Sbjct: 24  RCFICM------EKLRDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVNCR 77

Query: 155 ASSELSDIQQETIQESSVTENAD 177
            + E++  Q +T+Q  S+T++ +
Sbjct: 78  WAEEVTQ-QLDTLQLCSLTKHEE 99

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

 Score = 49.4 bits (118), Expect = 2e-08
 Identities = 12/46 (26%), Positives = 16/46 (34%), Gaps = 4/46 (8%)

Query: 101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCR 146
             +C++CL        L     C H F   C+         C LCR
Sbjct: 15  VPECAICLQTCVHPVSL----PCKHVFCYLCVKGASWLGKRCALCR 56

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

 Score = 47.9 bits (114), Expect = 6e-08
 Identities = 13/68 (19%), Positives = 21/68 (30%), Gaps = 4/68 (5%)

Query: 103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASSELSDI 162
           +C +C   +Q     +    C H F   C          C +C          + EL   
Sbjct: 17  RCFICRQAFQNPVVTK----CRHYFCESCALEHFRATPRCYICDQPTGGIFNPAKELMAK 72

Query: 163 QQETIQES 170
            Q++   S
Sbjct: 73  LQKSGPSS 80

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

 Score = 47.4 bits (113), Expect = 8e-08
 Identities = 12/47 (25%), Positives = 15/47 (31%), Gaps = 3/47 (6%)

Query: 103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSL 149
            CS+C            I  C H F   CI         CP C + +
Sbjct: 17  LCSICKGYLIDA---TTITECLHTFCKSCIVRHFYYSNRCPKCNIVV 60

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

 Score = 47.9 bits (113), Expect = 2e-07
 Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 3/49 (6%)

Query: 101 DTQCSVCLADYQAEDKLQQIPA---CGHAFHMDCIDHWLTTHTTCPLCR 146
              C +C+  Y    +  ++     CGH F   C+   L    TCP CR
Sbjct: 7   TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 55

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

 Score = 42.8 bits (100), Expect = 1e-05
 Identities = 13/46 (28%), Positives = 18/46 (39%)

Query: 104 CSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSL 149
           C    ++     +L     CGH F   C+   L    TCP CR  +
Sbjct: 78  CMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 123

>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 = 47.1 bits (112), Expect = 2e-07
 Identities = 19/95 (20%), Positives = 34/95 (35%), Gaps = 4/95 (4%)

Query: 103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASSELSDI 162
            C +C   +        I  C H+F   CI  +L T   CP+C + +       +  SD 
Sbjct: 17  MCVLCGGYFIDA---TTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDK 73

Query: 163 QQETIQESSVTENADGASDQQRSEAYEEPQAVEHS 197
             + I    V         ++R + Y    + + +
Sbjct: 74  TLQDIVYKLV-PGLFKNEMKRRRDFYAAHPSADAA 107

>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 = 45.7 bits (108), Expect = 3e-07
 Identities = 11/55 (20%), Positives = 23/55 (41%), Gaps = 5/55 (9%)

Query: 94  KESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH--TTCPLCR 146
           +E++      C++C   +    + Q    CG   H+ C+  +  ++    CP C 
Sbjct: 8   RETYPDAVKICNIC---HSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCN 59

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

 Score = 46.3 bits (110), Expect = 3e-07
 Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 9/50 (18%)

Query: 103 QCSVCLADYQAEDKLQ---QIPACGHAFHMDCIDHWLTTHTTCPLCRLSL 149
           +C +C       +       IP C H +   CI  +L+  T CP C +++
Sbjct: 24  RCGICF------EYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTV 67

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

 Score = 47.5 bits (112), Expect = 1e-06
 Identities = 11/61 (18%), Positives = 19/61 (31%), Gaps = 15/61 (24%)

Query: 101 DTQCSVCLA----DYQAEDKLQQIPACGHAFHMDCIDHWLTT-----------HTTCPLC 145
           + +C++C A      +          C    H  C++ W  T              CP C
Sbjct: 308 ELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFC 367

Query: 146 R 146
           +
Sbjct: 368 K 368

>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 = 43.3 bits (101), Expect = 7e-06
 Identities = 11/65 (16%), Positives = 20/65 (30%), Gaps = 19/65 (29%)

Query: 101 DTQCSVCLADYQA--------------EDKLQQIPACGHAFHMDCIDHWL-----TTHTT 141
           +  C +C+                      + ++  C HAFH+ C+              
Sbjct: 25  EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQ 84

Query: 142 CPLCR 146
           CP C+
Sbjct: 85  CPSCK 89

>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 = 45.1 bits (106), Expect = 1e-05
 Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 5/50 (10%)

Query: 101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHT-TCPLCRLSL 149
              C +C  +    DK  +I  CGH     C+  W  +    CP CR  +
Sbjct: 332 FQLCKICAEN----DKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 377

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

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 4/50 (8%)

Query: 100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSL 149
            + QC +C   +           C H+F   CI+ W+     CP+CR  +
Sbjct: 63  NELQCIICSEYF----IEAVTLNCAHSFCSYCINEWMKRKIECPICRKDI 108

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens} Length = 238

 Score = 44.0 bits (103), Expect = 2e-05
 Identities = 11/57 (19%), Positives = 23/57 (40%), Gaps = 5/57 (8%)

Query: 92  IYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH--TTCPLCR 146
             +E++      C++C   +    + Q    CG   H+ C+  +  ++    CP C 
Sbjct: 171 YIRETYPDAVKICNIC---HSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCN 224

>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 = 39.7 bits (93), Expect = 4e-05
 Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 11/49 (22%)

Query: 103 QCSVCLADYQAEDKLQ---QIPACGHAFHMDCIDHWLTTHT--TCPLCR 146
            C +C       D +     IP CG+++  +CI   L      TCP C 
Sbjct: 17  LCLICK------DIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCH 59

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 65

 Score = 38.8 bits (90), Expect = 1e-04
 Identities = 13/51 (25%), Positives = 16/51 (31%), Gaps = 2/51 (3%)

Query: 101 DTQCSVCLAD-YQAEDKLQQIPACGHAFHMDCIDHWLTTHT-TCPLCRLSL 149
           D  C  C    Y+       +  CGH     C+D         CP C   L
Sbjct: 3   DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B Length = 78

 Score = 38.2 bits (88), Expect = 2e-04
 Identities = 11/47 (23%), Positives = 17/47 (36%), Gaps = 1/47 (2%)

Query: 101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTT-CPLCR 146
             +C +C+   + +D       CG+     C     T     CP CR
Sbjct: 11  PVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACR 57

>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 = 39.2 bits (91), Expect = 2e-04
 Identities = 12/47 (25%), Positives = 14/47 (29%), Gaps = 5/47 (10%)

Query: 101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHT-TCPLCR 146
             QC  C               C H    DC+D        +CP CR
Sbjct: 52  TFQCICCQELVFRPITT----VCQHNVCKDCLDRSFRAQVFSCPACR 94

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 88

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 3/47 (6%)

Query: 103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHT---TCPLCR 146
           +C +C+  +  E    ++  CGH     C++  L +      CP C 
Sbjct: 17  ECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCS 63

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

 Score = 38.4 bits (89), Expect = 3e-04
 Identities = 14/102 (13%), Positives = 34/102 (33%), Gaps = 7/102 (6%)

Query: 98  SIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHT-TCPLCRLSLLAPAKAS 156
           S+ + QC +C+        L     C H     C    +   +  CP CR  + +  +  
Sbjct: 12  SLSECQCGICMEILVEPVTLP----CNHTLCKPCFQSTVEKASLCCPFCRRRVSSWTRYH 67

Query: 157 SELSDIQQETIQESSVTENADGASDQQRSEAYEEPQAVEHSE 198
           +  + +    +    + +       + R+   E  +  +  +
Sbjct: 68  TRRNSLVNVELWT--IIQKHYPRECKLRASGQESEEVADDYQ 107

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

 Score = 37.1 bits (86), Expect = 5e-04
 Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 11/49 (22%)

Query: 103 QCSVCLADYQAEDKLQ---QIPACGHAFHMDCIDHWLTTHT--TCPLCR 146
            C +C       D +     IP CG+++  +CI   L      TCP C 
Sbjct: 15  LCLICK------DIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCH 57

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

 Score = 38.0 bits (88), Expect = 8e-04
 Identities = 16/53 (30%), Positives = 21/53 (39%), Gaps = 10/53 (18%)

Query: 101 DTQCSVCLADYQAEDKLQQ---IPACGHAFHMDCID-HWLTTHTTCPLCRLSL 149
           +  C +CL      D L+       C H F  DCI     + +  CP CR  L
Sbjct: 54  ELMCPICL------DMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKL 100

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	251
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.71
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.63
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.58
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.57
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.57
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.57
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.53
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.46
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.45
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.44
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.44
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.42
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.41
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.37
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.36
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.36
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.36
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.34
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.33
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.32
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.28
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.27
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.27
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.26
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.25
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.24
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.24
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.21
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.21
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.2
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.18
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.18
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.17
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.17
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.16
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.15
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.13
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.12
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.11
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.1
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.07
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.07
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.03
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.02
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.01
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.01
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.98
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.98
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.97
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.97
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.95
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.94
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.94
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.9
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.89
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.88
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.82
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.82
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.81
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.7
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.69
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.67
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.64
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.63
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.61
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.6
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.52
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.4
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.37
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.37
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.35
3nw0_A	238	Non-structural maintenance of chromosomes element	98.05
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	96.42
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.0
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	94.07
1we9_A	64	PHD finger family protein; structural genomics, PH	91.0
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	90.98
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	89.17
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	88.93
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	88.1
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	87.16
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	85.82
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	85.75
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	85.08
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	84.7
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	84.09
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	83.44
2jwa_A	44	Receptor tyrosine-protein kinase ERBB-2; transmemb	83.37
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	83.15
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	81.83
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	81.07

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

Probab=99.71  E-value=1.5e-17  Score=121.02  Aligned_cols=78  Identities=29%  Similarity=0.640  Sum_probs=67.5

Q ss_pred             hhhhhcCCCHHHHhhCCceeeccCC--CCCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCccc
Q 025541           73 ISRAELGLKKELREMLPIVIYKESF--SIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLL  150 (251)
Q Consensus        73 ~~~~~~~~~~~~~~~lp~~~~~~~~--~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  150 (251)
                      ......+++++.++.||.+.+....  ...+..|+||++.|..+..++.++ |||.||..||..|+..+.+||+||..+.
T Consensus        10 ~~~~~~~~s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   88 (91)
T 2l0b_A           10 HMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCMFP   88 (91)
T ss_dssp             CSSCCCCCCHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTTCCBSS
T ss_pred             CCcCCCCCCHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCcCccCC
Confidence            3345668999999999999887654  345678999999999988888998 9999999999999999999999999886


Q ss_pred             C
Q 025541          151 A  151 (251)
Q Consensus       151 ~  151 (251)
                      .
T Consensus        89 ~   89 (91)
T 2l0b_A           89 P   89 (91)
T ss_dssp             C
T ss_pred             C
Confidence            5

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

Probab=99.63  E-value=1.7e-16  Score=111.05  Aligned_cols=67  Identities=33%  Similarity=0.833  Sum_probs=56.4

Q ss_pred             HhhCCceeeccCC-CCCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCC
Q 025541           85 REMLPIVIYKESF-SIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAP  152 (251)
Q Consensus        85 ~~~lp~~~~~~~~-~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  152 (251)
                      ++.||...+.... ..++..|+||++.|..+..++.++ |+|.||..||.+|+..+.+||+||+.+.+.
T Consensus         6 i~~lp~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A            6 SGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             CSSCCCEEBCSSSCSSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             HhhCCcEEecCccccCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            3467777766543 346678999999999988889998 999999999999999999999999988653

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

Probab=99.58  E-value=1e-15  Score=100.42  Aligned_cols=51  Identities=45%  Similarity=1.206  Sum_probs=46.0

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCccc
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLL  150 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  150 (251)
                      ++..|+||++.|..++.+..++.|||.||..||.+|+..+.+||+||+.+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            456899999999988888888679999999999999999999999999874

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

Probab=99.57  E-value=2.3e-15  Score=104.85  Aligned_cols=55  Identities=40%  Similarity=0.957  Sum_probs=49.2

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKA  155 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~  155 (251)
                      .+..|+||++.|..+..+.+++ |+|.||..||.+|+..+.+||+||..+......
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   68 (74)
T 2ep4_A           14 LHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQL   68 (74)
T ss_dssp             CSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSSCCSC
T ss_pred             CCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCccccccccc
Confidence            4678999999999988888888 999999999999999999999999998765543

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

Probab=99.57  E-value=2.3e-15  Score=105.92  Aligned_cols=57  Identities=40%  Similarity=0.910  Sum_probs=50.2

Q ss_pred             CCCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCCCC
Q 025541           98 SIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKA  155 (251)
Q Consensus        98 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~  155 (251)
                      ...+..|+||++.|..+..++.++ |+|.||..||..|+..+.+||+||..+......
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   68 (78)
T 2ect_A           12 VGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTA   68 (78)
T ss_dssp             SSSSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSC
T ss_pred             CCCCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCccCCcccC
Confidence            345678999999999888888898 999999999999999999999999999775544

>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=99.57  E-value=3.2e-15  Score=102.65  Aligned_cols=54  Identities=33%  Similarity=0.947  Sum_probs=48.1

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCC
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPA  153 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  153 (251)
                      ..+..|+||++.|..+..++.++ |||.||..||..|+..+.+||+||..+....
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   65 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQL   65 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCSCC
T ss_pred             CCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccCcC
Confidence            35678999999998888888898 9999999999999999999999999987643

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

Probab=99.53  E-value=4.6e-15  Score=105.43  Aligned_cols=53  Identities=26%  Similarity=0.741  Sum_probs=43.3

Q ss_pred             CCccccccccccccc-----------CCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccC
Q 025541           99 IRDTQCSVCLADYQA-----------EDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~-----------~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      .++..|+||++.|..           ++.+++++.|+|.||..||.+||..+.+||+||+.+..
T Consensus        13 ~~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   76 (81)
T 2ecl_A           13 VECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVV   76 (81)
T ss_dssp             CCCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCE
T ss_pred             CCCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcch
Confidence            356779999888854           34455665699999999999999999999999998754

>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=99.46  E-value=3.7e-14  Score=92.79  Aligned_cols=50  Identities=30%  Similarity=0.731  Sum_probs=42.9

Q ss_pred             CcccccccccccccC-CceeEcCCCCCcccHhhHHHHHhcCCCCccccCccc
Q 025541          100 RDTQCSVCLADYQAE-DKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLL  150 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~-~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  150 (251)
                      .+..|+||++.|..+ ..+..++ |+|.||..||.+|+..+.+||+||..+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLP-CGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECT-TSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecC-CCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            457899999999654 3566776 9999999999999999999999998874

>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=99.45  E-value=8e-14  Score=105.05  Aligned_cols=52  Identities=21%  Similarity=0.541  Sum_probs=42.0

Q ss_pred             CcccccccccccccCC---------------ceeEcCCCCCcccHhhHHHHH-----hcCCCCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAED---------------KLQQIPACGHAFHMDCIDHWL-----TTHTTCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~---------------~~~~~~~C~H~fh~~Ci~~wl-----~~~~~CP~Cr~~~~~~  152 (251)
                      .+..|+||++.|..+.               .++.++ |+|+||..||..|+     ..+.+||+||..+...
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCC-CCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            4568999999996643               334676 99999999999999     4567999999988654

>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=99.44  E-value=5.7e-14  Score=104.70  Aligned_cols=52  Identities=31%  Similarity=0.629  Sum_probs=43.5

Q ss_pred             CCCcccccccccccccCC---------------ceeEcCCCCCcccHhhHHHHHhcCCCCccccCccc
Q 025541           98 SIRDTQCSVCLADYQAED---------------KLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLL  150 (251)
Q Consensus        98 ~~~~~~C~IC~~~~~~~~---------------~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  150 (251)
                      ...++.|+||++.|....               .++.++ |+|.||..||.+||..+.+||+||+.+.
T Consensus        34 d~~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           34 DIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             SSCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCCCCccCChhHhCcCchhhccccccCCccceEeecc-cCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            345788999999987541               255566 9999999999999999999999999864

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

Probab=99.44  E-value=6.9e-14  Score=96.31  Aligned_cols=54  Identities=26%  Similarity=0.660  Sum_probs=45.3

Q ss_pred             CCcccccccccccccC----CceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCC
Q 025541           99 IRDTQCSVCLADYQAE----DKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPA  153 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  153 (251)
                      .++..|+||++.+..+    ..+..++ |||.||..||.+|+..+.+||+||..+....
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   65 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKR   65 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCCCS
T ss_pred             CCCCCCcccChhhhccccccCCeEeCC-CCChHhHHHHHHHHHcCCCCCCCCCccChhh
Confidence            3467899999998763    4456776 9999999999999999999999999987543

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

Probab=99.42  E-value=9e-14  Score=95.05  Aligned_cols=51  Identities=27%  Similarity=0.712  Sum_probs=43.2

Q ss_pred             CCcccccccccccccC----CceeEcCCCCCcccHhhHHHHHhcCCCCccccCccc
Q 025541           99 IRDTQCSVCLADYQAE----DKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLL  150 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  150 (251)
                      ..+..|+||++.|..+    ..+..++ |||.||..||..|+..+..||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   67 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKIN   67 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECS-SSCEEEHHHHHHHHHHCSSCTTTCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCC-CCChhcHHHHHHHHHcCCCCCCCCCccC
Confidence            3567899999999764    3346676 9999999999999999999999999875

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

Probab=99.41  E-value=8.6e-14  Score=93.72  Aligned_cols=52  Identities=27%  Similarity=0.684  Sum_probs=43.7

Q ss_pred             CcccccccccccccC----CceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAE----DKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  152 (251)
                      ++..|+||++.+..+    ..+..++ |||.||..||.+|+..+.+||+||..+...
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   57 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   57 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEET-TSCEEEHHHHHHHHHHCSBCTTTCCBCTTT
T ss_pred             CCCCCCccChhhhCccccCCCEEeCC-CCCchhHHHHHHHHHcCCCCCCCCccCCcc
Confidence            356899999998753    3446676 999999999999999999999999988653

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

Probab=99.37  E-value=4.7e-13  Score=94.68  Aligned_cols=55  Identities=25%  Similarity=0.738  Sum_probs=45.4

Q ss_pred             CCcccccccccccccCCceeEcCCCC-----CcccHhhHHHHHhcC--CCCccccCcccCCCCC
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACG-----HAFHMDCIDHWLTTH--TTCPLCRLSLLAPAKA  155 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~-----H~fh~~Ci~~wl~~~--~~CP~Cr~~~~~~~~~  155 (251)
                      .++..|.||++++..+..+ ++| |+     |.||..||.+||..+  .+||+||..+......
T Consensus        13 ~~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~~~   74 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMETKL   74 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCCCS
T ss_pred             CCCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCccc
Confidence            3567899999999877665 687 96     999999999999865  5899999998765543

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

Probab=99.36  E-value=3.9e-13  Score=91.80  Aligned_cols=49  Identities=35%  Similarity=0.887  Sum_probs=42.3

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      .+..|+||++.+..  .+..++ |||.||..||..|+..+.+||+||..+..
T Consensus         4 ~~~~C~IC~~~~~~--~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCeeCCccccC--CcEecC-CCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            35689999999864  346777 99999999999999999999999998854

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

Probab=99.36  E-value=1.9e-13  Score=93.91  Aligned_cols=50  Identities=32%  Similarity=0.974  Sum_probs=43.4

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAK  154 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~  154 (251)
                      .+..|+||++.+..    ..++ |||.||..||..|+..+..||+||..+.....
T Consensus        14 ~~~~C~IC~~~~~~----~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   63 (70)
T 2ecn_A           14 DEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGANE   63 (70)
T ss_dssp             CCCCCSSSCCSCCS----EEET-TTEEECHHHHHHSSCCCSSCHHHHHCTTCCCC
T ss_pred             CCCCCeeCCcCccC----cccC-CCCcccHHHHHHHHHCcCcCCCcCCcccCCCc
Confidence            45789999999876    5676 99999999999999999999999999876543

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

Probab=99.36  E-value=7.8e-13  Score=91.50  Aligned_cols=53  Identities=21%  Similarity=0.436  Sum_probs=43.7

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKA  155 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~  155 (251)
                      .+..|+||++.+..+  +..++ |||.||..||..|+..+..||+||..+......
T Consensus        14 ~~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   66 (72)
T 2djb_A           14 PYILCSICKGYLIDA--TTITE-CLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPL   66 (72)
T ss_dssp             GGGSCTTTSSCCSSC--EECSS-SCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSC
T ss_pred             CCCCCCCCChHHHCc--CEECC-CCCHHHHHHHHHHHHcCCcCCCcCcccCccccc
Confidence            467899999998763  33346 999999999999999999999999998765443

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

Probab=99.34  E-value=3.3e-13  Score=93.12  Aligned_cols=50  Identities=26%  Similarity=0.609  Sum_probs=42.5

Q ss_pred             CCCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccC
Q 025541           98 SIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus        98 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      ...+..|+||++.+..+   ..++ |||.||..||..|+..+..||+||..+..
T Consensus        12 ~~~~~~C~IC~~~~~~~---~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (71)
T 2d8t_A           12 SLTVPECAICLQTCVHP---VSLP-CKHVFCYLCVKGASWLGKRCALCRQEIPE   61 (71)
T ss_dssp             SSSCCBCSSSSSBCSSE---EEET-TTEEEEHHHHHHCTTCSSBCSSSCCBCCH
T ss_pred             CCCCCCCccCCcccCCC---EEcc-CCCHHHHHHHHHHHHCCCcCcCcCchhCH
Confidence            34567899999998653   5566 99999999999999999999999998854

>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=99.33  E-value=1.3e-13  Score=104.31  Aligned_cols=53  Identities=30%  Similarity=0.603  Sum_probs=2.1

Q ss_pred             CCCcccccccccccccCC---------------ceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccC
Q 025541           98 SIRDTQCSVCLADYQAED---------------KLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus        98 ~~~~~~C~IC~~~~~~~~---------------~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      +..++.|+||++.|....               .+..++ |+|.||..||.+||..+.+||+||+++..
T Consensus        45 d~~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~-C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~  112 (117)
T 4a0k_B           45 DIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEF  112 (117)
T ss_dssp             CCCC-----------------------------------------------------------------
T ss_pred             cCCCCcCeECChhhcCcChhhhcccccccccccccccCC-cCceEcHHHHHHHHHcCCcCCCCCCeeee
Confidence            445788999999997532               222345 99999999999999999999999998643

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

Probab=99.32  E-value=1.5e-12  Score=93.30  Aligned_cols=53  Identities=21%  Similarity=0.646  Sum_probs=44.5

Q ss_pred             CCcccccccccccccCCc-eeEcCCCCCcccHhhHHHHHhcC---CCCccccCcccCC
Q 025541           99 IRDTQCSVCLADYQAEDK-LQQIPACGHAFHMDCIDHWLTTH---TTCPLCRLSLLAP  152 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~-~~~~~~C~H~fh~~Ci~~wl~~~---~~CP~Cr~~~~~~  152 (251)
                      .....|+||++.|..... .+.++ |||.||..||..|+..+   ..||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             cCCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            346789999999987554 66777 99999999999999875   7899999987654

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

Probab=99.28  E-value=2.8e-12  Score=90.70  Aligned_cols=48  Identities=19%  Similarity=0.412  Sum_probs=41.6

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCccc
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLL  150 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  150 (251)
                      .....|+||++.|..+   .+++ |||.||..||..|+.....||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQNP---VVTK-CRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCSE---EECT-TSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcCe---eEcc-CCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            3457899999999653   4576 9999999999999999999999999985

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

Probab=99.27  E-value=4.4e-12  Score=88.21  Aligned_cols=52  Identities=27%  Similarity=0.646  Sum_probs=41.9

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcC--CCCccccCcccCCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH--TTCPLCRLSLLAPAK  154 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~--~~CP~Cr~~~~~~~~  154 (251)
                      .+..|+||++.|..+   ..++.|||.||..||..|+..+  ..||+||..+...+.
T Consensus        14 ~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~~   67 (74)
T 2yur_A           14 DELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA   67 (74)
T ss_dssp             GGGSCSSSCCCCTTC---EECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTTT
T ss_pred             CCCCCcCCChHHhCC---eEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCccc
Confidence            467899999999764   3454599999999999999865  689999998665443

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

Probab=99.27  E-value=4.1e-12  Score=86.23  Aligned_cols=49  Identities=22%  Similarity=0.596  Sum_probs=40.8

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHh-cCCCCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT-THTTCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~~  152 (251)
                      .+..|+||++.+..+..   ++ |||.||..||..|+. .+..||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~p~~---~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           14 DKYKCEKCHLVLCSPKQ---TE-CGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCEECTTTCCEESSCCC---CS-SSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             cCCCCCCCChHhcCeeE---CC-CCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            45789999999976533   55 999999999999995 567899999998654

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

Probab=99.26  E-value=1.5e-12  Score=101.47  Aligned_cols=47  Identities=28%  Similarity=0.857  Sum_probs=41.0

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      +..|+||++.|..+   ..+| |||.||..||..|+..+.+||+||.++..
T Consensus        53 ~~~C~iC~~~~~~~---~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           53 ELQCIICSEYFIEA---VTLN-CAHSFCSYCINEWMKRKIECPICRKDIKS   99 (138)
T ss_dssp             HSBCTTTCSBCSSE---EEET-TSCEEEHHHHHHHTTTCSBCTTTCCBCCC
T ss_pred             cCCCcccCcccCCc---eECC-CCCCccHHHHHHHHHcCCcCCCCCCcCCC
Confidence            45799999999753   4566 99999999999999999999999998854

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

Probab=99.25  E-value=5.4e-12  Score=87.18  Aligned_cols=49  Identities=33%  Similarity=0.720  Sum_probs=40.8

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHh---cCCCCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT---THTTCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~---~~~~CP~Cr~~~~~~  152 (251)
                      .+..|+||++.+..   ...++ |||.||..||..|+.   .+..||+||..+...
T Consensus        19 ~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           19 EEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCBCTTTCSBCSS---EEECT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCC
T ss_pred             cCCEeccCCcccCC---eEEcC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcc
Confidence            46789999999874   34566 999999999999997   456899999988654

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

Probab=99.24  E-value=7e-12  Score=87.05  Aligned_cols=51  Identities=18%  Similarity=0.511  Sum_probs=42.0

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcC--CCCccccCcccCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH--TTCPLCRLSLLAPA  153 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~--~~CP~Cr~~~~~~~  153 (251)
                      ....|+||++.+..++..  . .|+|.||..||.+||+.+  .+||+||..+....
T Consensus        14 ~i~~C~IC~~~i~~g~~C--~-~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~   66 (74)
T 2ct0_A           14 AVKICNICHSLLIQGQSC--E-TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEI   66 (74)
T ss_dssp             SSCBCSSSCCBCSSSEEC--S-SSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCC
T ss_pred             CCCcCcchhhHcccCCcc--C-CCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCC
Confidence            446899999999865433  2 599999999999999977  89999999886543

>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=99.24  E-value=2.7e-12  Score=94.57  Aligned_cols=51  Identities=25%  Similarity=0.616  Sum_probs=41.7

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcC-CCCccccCcccCCCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH-TTCPLCRLSLLAPAK  154 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~-~~CP~Cr~~~~~~~~  154 (251)
                      +..|+||++.|..  .+..++ |||.||..||..|+..+ ..||+||..+.....
T Consensus        22 ~~~C~IC~~~~~~--p~~~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~l   73 (100)
T 3lrq_A           22 VFRCFICMEKLRD--ARLCPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPLQLREL   73 (100)
T ss_dssp             HTBCTTTCSBCSS--EEECTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGC
T ss_pred             CCCCccCCccccC--ccccCC-CCChhhHHHHHHHHHHCcCCCCCCCCcCCHHHh
Confidence            4679999999975  232266 99999999999999987 699999999865443

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

Probab=99.21  E-value=1.2e-11  Score=86.70  Aligned_cols=50  Identities=24%  Similarity=0.555  Sum_probs=42.3

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc-CCCCccccCcccCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSLLAPA  153 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~  153 (251)
                      .+..|+||++.|..+   ..++ |||.||..||..|+.. +.+||+||..+....
T Consensus         7 ~~~~C~IC~~~~~~P---v~~~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~   57 (78)
T 1t1h_A            7 EYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLHAG   57 (78)
T ss_dssp             SSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCC
T ss_pred             ccCCCCCccccccCC---EEcC-CCCeecHHHHHHHHHHCcCCCCCCcCCCChhh
Confidence            467899999999764   4456 9999999999999987 789999999987543

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

Probab=99.21  E-value=9.6e-12  Score=84.14  Aligned_cols=51  Identities=25%  Similarity=0.592  Sum_probs=40.8

Q ss_pred             ccccccccc-ccccCCce-eEcCCCCCcccHhhHHHHHhc-CCCCccccCcccCC
Q 025541          101 DTQCSVCLA-DYQAEDKL-QQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSLLAP  152 (251)
Q Consensus       101 ~~~C~IC~~-~~~~~~~~-~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~  152 (251)
                      +..|+||++ .+..+... ..++ |||.||..||..|+.. ...||+||..+...
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   56 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCcCCcCCCCccCCCccCeecCC-CCCHhHHHHHHHHHHcCCCcCCCCCCccccc
Confidence            567999999 77766543 3455 9999999999999764 56799999998654

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

Probab=99.20  E-value=7.5e-12  Score=96.06  Aligned_cols=53  Identities=26%  Similarity=0.684  Sum_probs=44.6

Q ss_pred             CcccccccccccccC----CceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCC
Q 025541          100 RDTQCSVCLADYQAE----DKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPA  153 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  153 (251)
                      ++..|+||++.|..+    ..+..++ |||.||..||.+|+..+.+||+||+.+....
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKR   62 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBCTTTC
T ss_pred             CCCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcCcccc
Confidence            457899999999764    3446676 9999999999999999999999999886543

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

Probab=99.18  E-value=1.5e-11  Score=87.08  Aligned_cols=49  Identities=24%  Similarity=0.647  Sum_probs=41.6

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc------CCCCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT------HTTCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~------~~~CP~Cr~~~~~~  152 (251)
                      .+..|+||++.+..+   ..++ |||.||..||..|+..      ...||+||..+...
T Consensus        18 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           18 EEVTCPICLELLKEP---VSAD-CNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             TTTSCTTTCSCCSSC---EECT-TSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTT
T ss_pred             cCCCCcCCChhhCcc---eeCC-CCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHH
Confidence            467899999998764   3576 9999999999999987      67899999988653

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

Probab=99.18  E-value=1.1e-11  Score=91.01  Aligned_cols=49  Identities=24%  Similarity=0.706  Sum_probs=41.1

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAP  152 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  152 (251)
                      +..|+||++.|..+  +..++ |||.||..||..|+..+..||+||..+...
T Consensus        22 ~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   70 (99)
T 2y43_A           22 LLRCGICFEYFNIA--MIIPQ-CSHNYCSLCIRKFLSYKTQCPTCCVTVTEP   70 (99)
T ss_dssp             HTBCTTTCSBCSSE--EECTT-TCCEEEHHHHHHHHTTCCBCTTTCCBCCGG
T ss_pred             CCCcccCChhhCCc--CEECC-CCCHhhHHHHHHHHHCCCCCCCCCCcCChh
Confidence            46799999999753  22235 999999999999999999999999988753

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

Probab=99.17  E-value=2.5e-11  Score=86.00  Aligned_cols=49  Identities=27%  Similarity=0.756  Sum_probs=41.6

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc------CCCCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT------HTTCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~------~~~CP~Cr~~~~~~  152 (251)
                      .+..|+||++.+..+   ..++ |||.||..||..|+..      ...||+||..+...
T Consensus        18 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecv_A           18 EEVTCPICLELLTQP---LSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPE   72 (85)
T ss_dssp             CCCCCTTTCSCCSSC---BCCS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSS
T ss_pred             CCCCCCCCCcccCCc---eeCC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHH
Confidence            457899999998764   3456 9999999999999987      78899999998754

>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=99.17  E-value=1.8e-11  Score=91.21  Aligned_cols=50  Identities=26%  Similarity=0.614  Sum_probs=42.1

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  152 (251)
                      .+..|+||++.|..  .+..++ |||.||..||..|+..+..||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           14 PHLMCVLCGGYFID--ATTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGTBCTTTSSBCSS--EEEETT-TCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             CcCCCccCChHHhC--cCEeCC-CCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            35689999999875  333346 999999999999999999999999998764

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

Probab=99.16  E-value=2.5e-11  Score=81.49  Aligned_cols=42  Identities=36%  Similarity=0.839  Sum_probs=35.6

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHh---cCCCCccc
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT---THTTCPLC  145 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~---~~~~CP~C  145 (251)
                      .+..|+||++.+..+   ..++ |||.||..||..|+.   .+..||+|
T Consensus        19 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           19 EEVICPICLDILQKP---VTID-CGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCBCTTTCSBCSSC---EECT-TSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             cCCCCCcCCchhCCe---EEeC-CCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            467899999998754   4566 999999999999998   45689998

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

Probab=99.15  E-value=7.3e-12  Score=87.82  Aligned_cols=49  Identities=24%  Similarity=0.653  Sum_probs=41.1

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc-------CCCCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-------HTTCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-------~~~CP~Cr~~~~~~  152 (251)
                      .+..|+||++.|..+   ..++ |||.||..||..|+..       ...||+||..+...
T Consensus        11 ~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~   66 (79)
T 2egp_A           11 EEVTCPICLELLTEP---LSLD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFE   66 (79)
T ss_dssp             CCCEETTTTEECSSC---CCCS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSS
T ss_pred             cCCCCcCCCcccCCe---eECC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHh
Confidence            467899999999764   3466 9999999999999986       56899999998653

>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=99.13  E-value=3.6e-11  Score=91.82  Aligned_cols=47  Identities=28%  Similarity=0.554  Sum_probs=40.0

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcC-CCCccccCcccC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH-TTCPLCRLSLLA  151 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~-~~CP~Cr~~~~~  151 (251)
                      +..|+||++.|..+   ..++ |||.||..||..|+..+ ..||+||..+..
T Consensus        52 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           52 TFQCICCQELVFRP---ITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HTBCTTTSSBCSSE---EECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             CCCCCcCChHHcCc---EEee-CCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            46799999999853   4566 99999999999999854 489999999976

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

Probab=99.12  E-value=3.3e-11  Score=79.30  Aligned_cols=42  Identities=38%  Similarity=0.953  Sum_probs=35.1

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHh---cCCCCccc
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT---THTTCPLC  145 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~---~~~~CP~C  145 (251)
                      .+..|+||++.+..+   ..++ |||.||..||..|+.   .+..||+|
T Consensus        14 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           14 VEASCSVCLEYLKEP---VIIE-CGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCBCSSSCCBCSSC---CCCS-SCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cCCCCccCCcccCcc---EeCC-CCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            457899999999865   3466 999999999999954   56789998

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

Probab=99.11  E-value=6.3e-11  Score=85.58  Aligned_cols=50  Identities=26%  Similarity=0.612  Sum_probs=40.4

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc--CCCCccccCcccC
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT--HTTCPLCRLSLLA  151 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~~  151 (251)
                      ..+..|+||++.|..+   ..++.|||.||..||..|+..  +..||+||..+..
T Consensus        11 ~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~   62 (92)
T 3ztg_A           11 PDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS   62 (92)
T ss_dssp             CTTTEETTTTEECSSC---EECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSCC
T ss_pred             CcCCCCCCCChhhcCc---eECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCCC
Confidence            3567899999999764   345449999999999999974  3689999999743

>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=99.10  E-value=3.8e-11  Score=96.17  Aligned_cols=49  Identities=31%  Similarity=0.710  Sum_probs=41.2

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc-CCCCccccCcccC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSLLA  151 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~  151 (251)
                      .+..|+||++.|..  .+..++ |||.||..||..|+.. +..||+||..+..
T Consensus        53 ~~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           53 SELMCPICLDMLKN--TMTTKE-CLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHBCTTTSSBCSS--EEEETT-TCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCcccChHhhC--cCEeCC-CCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            45689999999975  344446 9999999999999997 7889999999864

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

Probab=99.07  E-value=5.2e-11  Score=91.31  Aligned_cols=53  Identities=26%  Similarity=0.676  Sum_probs=43.7

Q ss_pred             CCcccccccccccccC----CceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCC
Q 025541           99 IRDTQCSVCLADYQAE----DKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAP  152 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  152 (251)
                      .....|+||++.|...    .....++ |||.||..||.+|+..+.+||+||..+...
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  126 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK  126 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEET-TSBEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCCccccccccCcceEeCC-CCChhhHHHHHHHHHcCCCCCCCCCcCChh
Confidence            3467899999998753    2335665 999999999999999999999999988653

>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=99.07  E-value=7.8e-11  Score=88.04  Aligned_cols=49  Identities=24%  Similarity=0.613  Sum_probs=40.5

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcC---CCCccccCcccCCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH---TTCPLCRLSLLAPA  153 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~---~~CP~Cr~~~~~~~  153 (251)
                      ...|+||++.+..+   ..++ |||.||..||..|+..+   ..||+||..+....
T Consensus        21 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   72 (112)
T 1jm7_A           21 ILECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS   72 (112)
T ss_dssp             HTSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTT
T ss_pred             CCCCcccChhhcCe---EECC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhh
Confidence            35799999998764   3356 99999999999999865   38999999887654

>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=99.03  E-value=1.1e-10  Score=92.18  Aligned_cols=48  Identities=23%  Similarity=0.492  Sum_probs=40.9

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCC-CCccccCcccCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHT-TCPLCRLSLLAP  152 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~-~CP~Cr~~~~~~  152 (251)
                      ...|+||++.|..+   ..++ |||.||..||..|+.... .||+||..+...
T Consensus        78 ~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           78 SFMCVCCQELVYQP---VTTE-CFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HTBCTTTSSBCSSE---EECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CCEeecCChhhcCC---EEcC-CCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            46799999998754   4466 999999999999998654 899999998765

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

Probab=99.02  E-value=2.1e-10  Score=80.56  Aligned_cols=55  Identities=20%  Similarity=0.432  Sum_probs=41.7

Q ss_pred             CCcccccccccccccCCcee-EcCCCCCcccHhhHHHHHh-cCCCCccccCcccCCCC
Q 025541           99 IRDTQCSVCLADYQAEDKLQ-QIPACGHAFHMDCIDHWLT-THTTCPLCRLSLLAPAK  154 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~-~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~~~~  154 (251)
                      .++..|+||++.+...+... -++ |||.||..|+..|+. ....||+||+.+.....
T Consensus         9 ~~~~~CpICle~~~~~d~~~~p~~-CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~   65 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPEDPA   65 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTTCCSST-TSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSS
T ss_pred             ccCCcCCccCccCccccccccccC-CCCCcCHHHHHHHHhcCCCCCCCCCCccCCCch
Confidence            35678999999986543322 234 999999999999875 46789999999876543

>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=99.01  E-value=4.5e-11  Score=90.03  Aligned_cols=48  Identities=23%  Similarity=0.690  Sum_probs=40.6

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc-CCCCccccCcccC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSLLA  151 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~  151 (251)
                      .+..|+||++.|..+   ..++ |||.||..||..|+.. +..||+||..+..
T Consensus        14 ~~~~C~iC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           14 SECQCGICMEILVEP---VTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHBCTTTCSBCSSC---EECT-TSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCccCCcccCce---eEcC-CCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            457899999998754   4566 9999999999999976 6789999999864

>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=99.01  E-value=1.4e-10  Score=87.89  Aligned_cols=49  Identities=31%  Similarity=0.661  Sum_probs=41.3

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCC-CCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHT-TCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~-~CP~Cr~~~~~~  152 (251)
                      .+..|+||++.+..+   ..++ |||.||..||..|+..+. .||+||..+...
T Consensus        17 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           17 SKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             GGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCcCChhhcCe---EECC-cCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            457899999998754   4566 999999999999998754 999999998653

>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=98.98  E-value=1.7e-10  Score=86.90  Aligned_cols=49  Identities=24%  Similarity=0.552  Sum_probs=41.3

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhc-CCCCccccCcccCCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSLLAPA  153 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~  153 (251)
                      +..|+||++.+..+   ..++ |||.||..||..|+.. +..||+||..+....
T Consensus        23 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (116)
T 1rmd_A           23 SISCQICEHILADP---VETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (116)
T ss_dssp             HTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCcHhcCc---EEcC-CCCcccHHHHHHHHhHCcCcCCCCCCCCCHhh
Confidence            45799999998753   4466 9999999999999986 779999999987644

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

Probab=98.98  E-value=2.6e-10  Score=81.39  Aligned_cols=49  Identities=16%  Similarity=0.157  Sum_probs=42.7

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  152 (251)
                      ....|+||++-|..+   .+++ |||.|++.||..|+..+.+||+||..+...
T Consensus        13 ~~~~CpI~~~~m~dP---V~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~   61 (85)
T 2kr4_A           13 DEFRDPLMDTLMTDP---VRLP-SGTVMDRSIILRHLLNSPTDPFNRQMLTES   61 (85)
T ss_dssp             TTTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             hheECcccCchhcCC---eECC-CCCEECHHHHHHHHhcCCCCCCCcCCCChH
Confidence            467899999999864   4566 999999999999999889999999988654

>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=98.97  E-value=2.1e-10  Score=77.23  Aligned_cols=50  Identities=18%  Similarity=0.425  Sum_probs=39.9

Q ss_pred             CCcccccccccccccCCceeEcCCCCCc-ccHhhHHHHHhcCCCCccccCccc
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHA-FHMDCIDHWLTTHTTCPLCRLSLL  150 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~  150 (251)
                      ..+..|.||++..... .+..+| |||. ||..|+..|...+..||+||+++.
T Consensus         5 ~~~~~C~IC~~~~~~~-~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            5 NLLKPCSLCEKRPRDG-NIIHGR-TGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GGGSBCTTTSSSBSCE-EEEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             CcCCCCcccCCcCCCe-EEEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            3456899999986542 122347 9998 999999999988889999999874

>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=98.97  E-value=2.5e-10  Score=77.10  Aligned_cols=48  Identities=19%  Similarity=0.454  Sum_probs=39.5

Q ss_pred             CcccccccccccccCCcee-EcCCCCCc-ccHhhHHHHHhcCCCCccccCccc
Q 025541          100 RDTQCSVCLADYQAEDKLQ-QIPACGHA-FHMDCIDHWLTTHTTCPLCRLSLL  150 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~-~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~  150 (251)
                      ++..|.||++.....  +. .+| |||. |+..|+..|+..+..||+||+++.
T Consensus         7 ~~~~C~IC~~~~~~~--~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            7 AIEPCVICQGRPKNG--CIVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             GGSCCTTTSSSCSCE--EEEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CcCCCCcCCCCCCCE--EEECCC-CCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            456899999987543  22 238 9999 899999999998899999999874

>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=98.95  E-value=3.4e-10  Score=83.32  Aligned_cols=50  Identities=16%  Similarity=0.163  Sum_probs=43.2

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPA  153 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  153 (251)
                      ....|+||++-|..+   .+++ |||.|++.||..|+..+.+||+||.++....
T Consensus        28 ~~~~CpI~~~~m~dP---V~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~   77 (100)
T 2kre_A           28 DEFRDPLMDTLMTDP---VRLP-SGTIMDRSIILRHLLNSPTDPFNRQTLTESM   77 (100)
T ss_dssp             TTTBCTTTCSBCSSE---EEET-TTEEEEHHHHHHHTTSCSBCSSSCCBCCTTS
T ss_pred             HhhCCcCccCcccCC---eECC-CCCEEchHHHHHHHHcCCCCCCCCCCCChhh
Confidence            467899999999865   4566 9999999999999998899999999987643

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

Probab=98.94  E-value=2.7e-10  Score=74.76  Aligned_cols=48  Identities=23%  Similarity=0.609  Sum_probs=39.1

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCC
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPA  153 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  153 (251)
                      .+...|+||++.|..+   +.++ |||.||..||..|   ...||+||+.+....
T Consensus         4 ~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCCSSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             ccCCCceEeCCccCCe---EEcC-CCCcccHHHHccC---CCCCCcCCcEeecCC
Confidence            3456799999999864   5576 9999999999884   568999999887544

>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=98.94  E-value=7.3e-10  Score=81.22  Aligned_cols=50  Identities=14%  Similarity=0.094  Sum_probs=43.1

Q ss_pred             CcccccccccccccCCceeEcCCCC-CcccHhhHHHHHhcCCCCccccCcccCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACG-HAFHMDCIDHWLTTHTTCPLCRLSLLAPA  153 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~-H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  153 (251)
                      .+..|+||++-|..+   .+++ || |.|++.||..|+..+.+||+||.++....
T Consensus        21 ~~~~CpI~~~~m~dP---V~~~-cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~   71 (98)
T 1wgm_A           21 DEFLDPIMSTLMCDP---VVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQ   71 (98)
T ss_dssp             TTTBCTTTCSBCSSE---EECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTT
T ss_pred             HhcCCcCccccccCC---eECC-CCCeEECHHHHHHHHHhCCCCCCCCCCCChhh
Confidence            467899999999865   4566 99 99999999999998899999999987643

>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=98.90  E-value=3.8e-10  Score=88.20  Aligned_cols=49  Identities=22%  Similarity=0.474  Sum_probs=40.7

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCC-CCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHT-TCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~-~CP~Cr~~~~~~  152 (251)
                      .+..|+||++.+..+   ..++ |||.||..||..|+.... .||+||.++...
T Consensus        30 ~~~~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   79 (141)
T 3knv_A           30 AKYLCSACRNVLRRP---FQAQ-CGHRYCSFCLASILSSGPQNCAACVHEGIYE   79 (141)
T ss_dssp             GGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHGGGSCEECHHHHHTTCCC
T ss_pred             cCcCCCCCChhhcCc---EECC-CCCccCHHHHHHHHhcCCCCCCCCCCccccc
Confidence            467899999999765   4466 999999999999998654 899999987543

>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=98.89  E-value=7.8e-10  Score=99.40  Aligned_cols=48  Identities=25%  Similarity=0.765  Sum_probs=41.0

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHh-cCCCCccccCcccCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT-THTTCPLCRLSLLAP  152 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~~  152 (251)
                      ...|+||++.+..   +..+| |||.||..|+..|+. .+..||+||..+...
T Consensus       332 ~~~C~ICle~~~~---pv~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          332 FQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SSBCTTTSSSBCC---EEEET-TCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCCccCcCCCC---eEEeC-CCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            3689999999854   45677 999999999999999 688999999988653

>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=98.88  E-value=5.2e-10  Score=84.51  Aligned_cols=47  Identities=23%  Similarity=0.559  Sum_probs=39.2

Q ss_pred             cccccccccccccCCceeEc-CCCCCcccHhhHHHHHhcCCCCccccCcccCCC
Q 025541          101 DTQCSVCLADYQAEDKLQQI-PACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPA  153 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~-~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  153 (251)
                      ...|+||++.|..+   ..+ + |||.||..||..|+.  ..||+||..+....
T Consensus        22 ~~~C~IC~~~~~~p---v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~   69 (117)
T 1jm7_B           22 LLRCSRCTNILREP---VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAWIQD   69 (117)
T ss_dssp             TTSCSSSCSCCSSC---BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCSCSS
T ss_pred             CCCCCCCChHhhCc---cEeCC-CCCHHHHHHHHHHhc--CCCcCCCCcCcccc
Confidence            46799999999764   344 5 999999999999998  78999999986543

>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=98.82  E-value=2.6e-09  Score=77.61  Aligned_cols=49  Identities=18%  Similarity=0.518  Sum_probs=38.8

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcC------CCCcc--ccCc-ccC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH------TTCPL--CRLS-LLA  151 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~------~~CP~--Cr~~-~~~  151 (251)
                      .+..|+||++.|..+   .+++.|||.|++.||..|+..+      .+||+  |+.. +..
T Consensus         6 ~~~~CPI~~~~~~dP---V~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~   63 (94)
T 2yu4_A            6 SGFTCPITKEEMKKP---VKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRK   63 (94)
T ss_dssp             SCCBCTTTCSBCSSE---EEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCG
T ss_pred             cEeECcCcCchhcCC---EEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCH
Confidence            467899999999864   3342499999999999999853      48999  9876 443

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

Probab=98.82  E-value=8.7e-10  Score=96.76  Aligned_cols=52  Identities=23%  Similarity=0.642  Sum_probs=39.6

Q ss_pred             CCcccccccccccccCCce----eEcCCCCCcccHhhHHHHHhcC-----------CCCccccCccc
Q 025541           99 IRDTQCSVCLADYQAEDKL----QQIPACGHAFHMDCIDHWLTTH-----------TTCPLCRLSLL  150 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~----~~~~~C~H~fh~~Ci~~wl~~~-----------~~CP~Cr~~~~  150 (251)
                      ....+|+||+..+..+..+    -..+.|+|.||..||.+||.+.           ..||+||+++.
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            3567899999998763222    2223599999999999999742           36999999875

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

Probab=98.81  E-value=8.9e-10  Score=76.46  Aligned_cols=43  Identities=26%  Similarity=0.741  Sum_probs=36.1

Q ss_pred             cccccccccccccCCceeEcCCCCCc-ccHhhHHHHHhcCCCCccccCcccC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHA-FHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      +..|+||++.+..   ...+| |||. ||..|+..|    ..||+||..+..
T Consensus        24 ~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           24 EKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HTBCTTTSSSBCC---EEEET-TCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             CCCCCCCCCCCCC---EEEcC-CCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            4579999998764   45667 9999 999999999    789999998753

>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=98.70  E-value=6.3e-09  Score=89.35  Aligned_cols=49  Identities=14%  Similarity=0.142  Sum_probs=41.3

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc-CCCCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~  152 (251)
                      ....|+||++.|..+   .+++ |||.||+.||..|+.. +.+||+||.++...
T Consensus       207 ~~~~c~i~~~~~~dP---v~~~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~  256 (281)
T 2c2l_A          207 DYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQE  256 (281)
T ss_dssp             STTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCGG
T ss_pred             cccCCcCcCCHhcCC---eECC-CCCEECHHHHHHHHHHCCCCCcCCCCCCchh
Confidence            578899999999865   4566 9999999999999986 44599999988644

>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=98.69  E-value=7.1e-09  Score=83.18  Aligned_cols=49  Identities=31%  Similarity=0.666  Sum_probs=41.1

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcC-CCCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH-TTCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~-~~CP~Cr~~~~~~  152 (251)
                      +...|+||++.|..+   ..++ |||.||..||..|+... ..||+||..+...
T Consensus        17 ~~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           17 SKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             GGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCChhhcCc---EECC-CCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            467899999999764   4466 99999999999999864 4999999988654

>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=98.67  E-value=9.9e-09  Score=74.35  Aligned_cols=48  Identities=23%  Similarity=0.643  Sum_probs=39.8

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc--------CCCCcc--ccCc
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT--------HTTCPL--CRLS  148 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--------~~~CP~--Cr~~  148 (251)
                      ...+|+||++.+..++.+...+ |||.||..|+..|+..        ...||.  |+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~-CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCC-CCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            3568999999998776666666 9999999999999863        236999  9987

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.64  E-value=2e-08  Score=68.42  Aligned_cols=48  Identities=23%  Similarity=0.602  Sum_probs=38.3

Q ss_pred             CCCcccccccccccccCCceeEcCCCCCc-ccHhhHHHHHhcCCCCccccCcccCCC
Q 025541           98 SIRDTQCSVCLADYQAEDKLQQIPACGHA-FHMDCIDHWLTTHTTCPLCRLSLLAPA  153 (251)
Q Consensus        98 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  153 (251)
                      ...+..|.||++...   .+..+| |||. ||..|+..    ...||+||..+...-
T Consensus        12 ~~~~~~C~IC~~~~~---~~v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i~~~~   60 (68)
T 2ea5_A           12 EENSKDCVVCQNGTV---NWVLLP-CRHTCLCDGCVKY----FQQCPMCRQFVQESF   60 (68)
T ss_dssp             CCCSSCCSSSSSSCC---CCEETT-TTBCCSCTTHHHH----CSSCTTTCCCCCCEE
T ss_pred             CCCCCCCCCcCcCCC---CEEEEC-CCChhhhHHHHhc----CCCCCCCCcchhceE
Confidence            345678999998765   456788 9999 99999984    468999999886543

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

Probab=98.63  E-value=1.8e-08  Score=66.99  Aligned_cols=47  Identities=26%  Similarity=0.681  Sum_probs=36.7

Q ss_pred             CcccccccccccccCCceeEcCCCC--C---cccHhhHHHHHhc--CCCCccccCccc
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACG--H---AFHMDCIDHWLTT--HTTCPLCRLSLL  150 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~--H---~fh~~Ci~~wl~~--~~~CP~Cr~~~~  150 (251)
                      +...|.||+++..  ..+ ++| |.  |   .||..||.+|+..  +.+||+|+..+.
T Consensus         5 ~~~~CrIC~~~~~--~~l-~~P-C~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            5 DVPVCWICNEELG--NER-FRA-CGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             SCCEETTTTEECS--CCC-CCS-CCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCEeEEeecCCC--Cce-ecC-cCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            4568999999843  233 577 65  4   9999999999974  678999998774

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

Probab=98.61  E-value=9.7e-09  Score=71.29  Aligned_cols=44  Identities=25%  Similarity=0.724  Sum_probs=35.2

Q ss_pred             cccccccccccccCCceeEcCCCCCc-ccHhhHHHHHhcCCCCccccCcccCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHA-FHMDCIDHWLTTHTTCPLCRLSLLAP  152 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~~  152 (251)
                      +..|+||++.+..   +..+| |||. ||..|+..    ...||+||..+...
T Consensus        25 ~~~C~IC~~~~~~---~~~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           25 EKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEA----VDKCPMCYTVITFK   69 (75)
T ss_dssp             HHSCSSSCSSCCC---BCCSS-SCCCCBCHHHHHH----CSBCTTTCCBCCCC
T ss_pred             CCCCCcCCCCCCC---EEEec-CCCHHHHHHHhhC----CCCCccCCceecCc
Confidence            4579999998765   34567 9999 99999965    36899999988653

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

Probab=98.60  E-value=1.9e-08  Score=81.40  Aligned_cols=50  Identities=14%  Similarity=0.111  Sum_probs=41.6

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc-CCCCccccCcccCC
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSLLAP  152 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~  152 (251)
                      .....|+||++-|..+   .+++ |||.|++.||..|+.. +.+||+|+.++...
T Consensus       104 p~~f~CPI~~elm~DP---V~~~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~  154 (179)
T 2f42_A          104 PDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFDPVTRSPLTQD  154 (179)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             cHhhcccCccccCCCC---eECC-CCCEECHHHHHHHHHhCCCCCCCCcCCCChh
Confidence            3578899999999864   4556 9999999999999986 35799999988654

>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=98.52  E-value=2e-08  Score=70.57  Aligned_cols=44  Identities=27%  Similarity=0.647  Sum_probs=35.9

Q ss_pred             cccccccccccccCCceeEcCCCCCc-ccHhhHHHHHhcCCCCccccCcccCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHA-FHMDCIDHWLTTHTTCPLCRLSLLAP  152 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~~  152 (251)
                      +..|+||++.+..   +..+| |||. ||..|+..|    ..||+||..+...
T Consensus        18 ~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~   62 (79)
T 2yho_A           18 AMLCMVCCEEEIN---STFCP-CGHTVCCESCAAQL----QSCPVCRSRVEHV   62 (79)
T ss_dssp             HTBCTTTSSSBCC---EEEET-TCBCCBCHHHHTTC----SBCTTTCCBCCEE
T ss_pred             CCEeEEeCcccCc---EEEEC-CCCHHHHHHHHHhc----CcCCCCCchhhCe
Confidence            3579999998753   56677 9999 999999987    3899999988653

>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=98.40  E-value=1.2e-07  Score=80.55  Aligned_cols=51  Identities=25%  Similarity=0.541  Sum_probs=40.7

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcC--CCCcc--ccCcccCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH--TTCPL--CRLSLLAPA  153 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~--~~CP~--Cr~~~~~~~  153 (251)
                      .+..||||++.|..+  ++.+. |||.|++.||..|+..+  ..||+  ||..+....
T Consensus       180 ~el~CPIcl~~f~DP--Vts~~-CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~d  234 (267)
T 3htk_C          180 IELTCPITCKPYEAP--LISRK-CNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRD  234 (267)
T ss_dssp             CCSBCTTTSSBCSSE--EEESS-SCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGG
T ss_pred             eeeECcCccCcccCC--eeeCC-CCCcccHHHHHHHHHhCCCCCCCcccccCcCchhh
Confidence            467799999999764  33344 99999999999999854  57999  999876543

>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=98.37  E-value=1e-07  Score=63.46  Aligned_cols=48  Identities=10%  Similarity=0.179  Sum_probs=40.1

Q ss_pred             ccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCC
Q 025541          102 TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAP  152 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  152 (251)
                      ..|+||++.|..+   .+++.|||+|.+.||.+||..+.+||+++.++...
T Consensus         4 ~~CpIs~~~m~dP---V~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~   51 (61)
T 2bay_A            4 MLCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   51 (61)
T ss_dssp             CCCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             EEecCCCCCCCCC---EEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChh
Confidence            5799999999864   34423999999999999999888899999988543

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

Probab=98.37  E-value=2.4e-07  Score=66.86  Aligned_cols=46  Identities=26%  Similarity=0.496  Sum_probs=38.9

Q ss_pred             cccccccccccCCceeEcCCCCCcccHhhHHHHHh-cCCCCccccCcccC
Q 025541          103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT-THTTCPLCRLSLLA  151 (251)
Q Consensus       103 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~  151 (251)
                      -|.+|--++..  ..+++| |+|+||.+|+..|.+ ..++||+|+.++..
T Consensus         3 fC~~C~~Pi~i--ygRmIP-CkHvFCydCa~~~~~~~~k~Cp~C~~~V~r   49 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMIP-CKHVFCYDCAILHEKKGDKMCPGCSDPVQR   49 (101)
T ss_dssp             BCTTTCSBCSE--EEEEET-TCCEEEHHHHHHHHHTTCCBCTTTCCBCSE
T ss_pred             ecCccCCCeEE--Eeeecc-ccccHHHHHHHHHHhccCCCCcCcCCeeee
Confidence            38888877755  778898 999999999999986 56899999998864

>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=98.35  E-value=9.3e-08  Score=85.11  Aligned_cols=44  Identities=30%  Similarity=0.788  Sum_probs=36.7

Q ss_pred             CcccccccccccccCCceeEcCCCCCc-ccHhhHHHHHhcCCCCccccCcccC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHA-FHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      ++..|+||++.+..   +..+| |||. ||..|+..|    ..||+||..+..
T Consensus       294 ~~~~C~IC~~~~~~---~v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          294 EERTCKVCMDKEVS---VVFIP-CGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             TTCBCTTTSSSBCC---EEEET-TCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             CCCCCCccCCcCCc---eEEcC-CCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            35689999999864   45667 9999 999999998    689999998753

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

Probab=98.05  E-value=4e-06  Score=70.81  Aligned_cols=50  Identities=18%  Similarity=0.543  Sum_probs=40.1

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcC--CCCccccCcccCCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH--TTCPLCRLSLLAPA  153 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~--~~CP~Cr~~~~~~~  153 (251)
                      -..|.||.+-+..+.   ..+.|+|.||..|+..|+..+  ..||.|+..+....
T Consensus       180 i~~C~iC~~iv~~g~---~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~  231 (238)
T 3nw0_A          180 VKICNICHSLLIQGQ---SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEI  231 (238)
T ss_dssp             CCBCTTTCSBCSSCE---ECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCC
T ss_pred             CCcCcchhhHHhCCc---ccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCC
Confidence            567999999988652   233499999999999999864  48999999876553

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=95.00  E-value=0.015  Score=41.74  Aligned_cols=34  Identities=15%  Similarity=0.417  Sum_probs=25.7

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHH
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHW  135 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w  135 (251)
                      +..|.||++.+..+....-+. |+|.||..|+..+
T Consensus         3 e~~C~~C~~~~~~~av~~C~~-C~~~~C~~Cl~~~   36 (101)
T 2jun_A            3 KVLCQFCDQDPAQDAVKTCVT-CEVSYCDECLKAT   36 (101)
T ss_dssp             CCBCTTCCSSSCCBCCEEETT-TTEEECHHHHHHH
T ss_pred             CCCCcCCCCCCCCCceEECCc-CChHHhHHHCHHH
Confidence            467999998754433444465 9999999999984

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

Probab=94.07  E-value=0.049  Score=36.24  Aligned_cols=46  Identities=24%  Similarity=0.462  Sum_probs=33.3

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc----CCCCccccCcc
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT----HTTCPLCRLSL  149 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~~  149 (251)
                      .+..|.||.+.   + .+..--.|...||..|+.+.|..    .-.||.|....
T Consensus        11 ~~~~C~vC~~~---~-~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           11 PGARCGVCGDG---T-DVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             TTCCCTTTSCC---T-TCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCcCCCCCC---C-eEEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            45679999753   3 33344459999999999988764    34799997654

>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=91.00  E-value=0.065  Score=35.16  Aligned_cols=50  Identities=24%  Similarity=0.464  Sum_probs=34.1

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHh-----cCCCCccccCc
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT-----THTTCPLCRLS  148 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-----~~~~CP~Cr~~  148 (251)
                      .++..|+||...+......+.--.|..-||..|+.--..     ....||.|+..
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            345679999988864444443335889999999864321     35679999653

>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=90.98  E-value=0.21  Score=34.58  Aligned_cols=34  Identities=29%  Similarity=0.642  Sum_probs=22.8

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHH
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHW  135 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w  135 (251)
                      .|..|.||- .+.......-- -|+-+||..|+++-
T Consensus        14 ~D~~C~VC~-~~t~~~l~pCR-vC~RvfH~~CL~r~   47 (89)
T 1wil_A           14 NDEMCDVCE-VWTAESLFPCR-VCTRVFHDGCLRRM   47 (89)
T ss_dssp             CSCCCTTTC-CCCSSCCSSCS-SSSSCCCHHHHHHH
T ss_pred             CCcccCccc-cccccceeccc-cccccccHhhcccc
Confidence            577899995 22222222222 38999999999996

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=89.17  E-value=0.17  Score=40.54  Aligned_cols=48  Identities=25%  Similarity=0.488  Sum_probs=34.1

Q ss_pred             ccccccccccccCCc---eeEcCCCCCcccHhhHHH------HHh-----cCCCCccccCcc
Q 025541          102 TQCSVCLADYQAEDK---LQQIPACGHAFHMDCIDH------WLT-----THTTCPLCRLSL  149 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~---~~~~~~C~H~fh~~Ci~~------wl~-----~~~~CP~Cr~~~  149 (251)
                      ..|+||...|..++.   .+.--.|..-||..|+.-      -+.     ..-.||.|+..-
T Consensus         3 ~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~   64 (183)
T 3lqh_A            3 NFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERH   64 (183)
T ss_dssp             CBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSS
T ss_pred             CcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCC
Confidence            469999999987752   444445899999999732      121     157899997754

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

Probab=88.93  E-value=0.26  Score=31.99  Aligned_cols=45  Identities=27%  Similarity=0.637  Sum_probs=31.7

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc----CCCCccccC
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT----HTTCPLCRL  147 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~  147 (251)
                      ..+..|.||...   + .+..--.|...||..|+..-+..    .-.||.|+.
T Consensus         9 ~~~~~C~vC~~~---g-~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A            9 DHQDYCEVCQQG---G-EIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CCCSSCTTTSCC---S-SEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCCccCCCC---C-cEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            346779999863   3 34444458899999999975542    346999965

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=88.10  E-value=0.19  Score=33.99  Aligned_cols=52  Identities=15%  Similarity=0.323  Sum_probs=34.9

Q ss_pred             CCCcccccccccccccCCceeEcCCCCCcccHhhHHHHHh----cCCCCccccCccc
Q 025541           98 SIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLT----THTTCPLCRLSLL  150 (251)
Q Consensus        98 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~----~~~~CP~Cr~~~~  150 (251)
                      ......|.||..... +..++.--.|.--||..|+..-+.    ....||.|+..+.
T Consensus        15 ~~~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~   70 (75)
T 2k16_A           15 GNQIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIK   70 (75)
T ss_dssp             SCEEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHC
T ss_pred             CCCCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchh
Confidence            334566999987753 333333335889999999976443    2456999976553

>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=87.16  E-value=0.2  Score=32.61  Aligned_cols=47  Identities=23%  Similarity=0.543  Sum_probs=31.8

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc----CCCCccccCcc
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT----HTTCPLCRLSL  149 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~~  149 (251)
                      ..+..|.||.+.   + .+..--.|...||..|+.+-|..    .-.||.|+...
T Consensus         7 ~~~~~C~vC~~~---g-~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            7 HHMEFCRVCKDG---G-ELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---S-SCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCCcCCCCCCC---C-CEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            456779999853   3 23333358899999999865543    34699997654

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=85.82  E-value=0.33  Score=30.06  Aligned_cols=44  Identities=27%  Similarity=0.658  Sum_probs=29.2

Q ss_pred             cccccccccccCCceeEcCCCCCcccHhhHHHHHhc----CCCCccccC
Q 025541          103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT----HTTCPLCRL  147 (251)
Q Consensus       103 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~  147 (251)
                      .|.||...-..+..+ .--.|...||..|+.+=|..    .-.||.|+.
T Consensus         2 ~C~vC~~~~~~~~ll-~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDDKLI-LCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCE-ECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCEE-ECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            488898654333333 33359999999999764442    346999964

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=85.75  E-value=0.22  Score=40.50  Aligned_cols=48  Identities=25%  Similarity=0.468  Sum_probs=33.9

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc----CCCCccccCccc
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT----HTTCPLCRLSLL  150 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~~~  150 (251)
                      ..+..|.+|...   + .+..-..|...||..|+.+-+..    ...||.|+..-.
T Consensus         5 ~~~~~C~~C~~~---g-~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~~   56 (207)
T 3u5n_A            5 PNEDWCAVCQNG---G-DLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGK   56 (207)
T ss_dssp             SSCSSBTTTCCC---E-EEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSSS
T ss_pred             CCCCCCCCCCCC---C-ceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCccc
Confidence            345679999854   2 34444468999999999876653    347999986543

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=85.08  E-value=0.25  Score=39.42  Aligned_cols=47  Identities=28%  Similarity=0.550  Sum_probs=33.1

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc----CCCCccccCccc
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT----HTTCPLCRLSLL  150 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~~~  150 (251)
                      .++.|.+|.+.   ++ +..-..|.-.||..|+.+-+..    .-.||.|+..-.
T Consensus         3 ~~~~C~~C~~~---g~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   53 (184)
T 3o36_A            3 NEDWCAVCQNG---GE-LLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSK   53 (184)
T ss_dssp             SCSSCTTTCCC---SS-CEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSSS
T ss_pred             CCCccccCCCC---Ce-eeecCCCCcccCccccCCCCCCCCCCCEECccccCccc
Confidence            35679999854   33 3444458999999999876653    346999986543

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=84.70  E-value=0.15  Score=32.48  Aligned_cols=46  Identities=35%  Similarity=0.703  Sum_probs=31.3

Q ss_pred             CCCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc----CCCCccccC
Q 025541           98 SIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT----HTTCPLCRL  147 (251)
Q Consensus        98 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~  147 (251)
                      ...+..|.||...   + .+..-..|...||..|+.+-|..    .-.||.|..
T Consensus         6 ~~~~~~C~vC~~~---g-~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            6 SGHEDFCSVCRKS---G-QLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             CSSCCSCSSSCCS---S-CCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCCccCCCC---C-eEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            3456779999874   3 33333359999999999865543    335888853

>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=84.09  E-value=0.34  Score=35.28  Aligned_cols=47  Identities=28%  Similarity=0.608  Sum_probs=30.9

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc----CCCCcccc
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT----HTTCPLCR  146 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr  146 (251)
                      ..++.|.||.+.-...+.+.-. .|+..||..|+...+..    ...||.|+
T Consensus         5 ~~~~~C~~C~~~g~~~~ll~C~-~C~~~~H~~Cl~~~~~~~~~~~W~C~~C~   55 (111)
T 2ysm_A            5 SSGANCAVCDSPGDLLDQFFCT-TCGQHYHGMCLDIAVTPLKRAGWQCPECK   55 (111)
T ss_dssp             CCCSCBTTTCCCCCTTTSEECS-SSCCEECTTTTTCCCCTTTSTTCCCTTTC
T ss_pred             CCCCCCcCCCCCCCCcCCeECC-CCCCCcChHHhCCccccccccCccCCcCC
Confidence            4567899998764322223333 59999999999876642    33566664

>2kgg_A Histone demethylase jarid1A; PHD finger, histone modification, leukemia, alternative splicing, chromatin regulator, developmental protein; NMR {Homo sapiens} PDB: 2kgi_A* 3gl6_A*

Probab=83.44  E-value=1.1  Score=27.82  Aligned_cols=44  Identities=18%  Similarity=0.341  Sum_probs=29.5

Q ss_pred             cccccccccccCCceeEcC-CCCCcccHhhHHHH----HhcCCCCcccc
Q 025541          103 QCSVCLADYQAEDKLQQIP-ACGHAFHMDCIDHW----LTTHTTCPLCR  146 (251)
Q Consensus       103 ~C~IC~~~~~~~~~~~~~~-~C~H~fh~~Ci~~w----l~~~~~CP~Cr  146 (251)
                      .|.||...+..+...+.-- .|..-||..|+.--    ...+..||.|+
T Consensus         4 ~cc~C~~p~~~~~~mI~Cd~~C~~WfH~~Cvgl~~~~~~~~~~~C~~C~   52 (52)
T 2kgg_A            4 AAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA   52 (52)
T ss_dssp             SCTTCCCCCCTTCCEEECTTTTCCEEETTTTTCCHHHHHHSCCCCSCC-
T ss_pred             cCCCCcCccCCCCcEEEeCCCCCccCcccccCCCccccCCCCEECCCCC
Confidence            4789998886555444443 48889999997421    13567899885

>2jwa_A Receptor tyrosine-protein kinase ERBB-2; transmembrane helix dimer, protein kinase receptor membrane domain, ATP-binding, glycoprotein; NMR {Homo sapiens} PDB: 2ks1_A

Probab=83.37  E-value=2.1  Score=25.83  Aligned_cols=29  Identities=17%  Similarity=0.304  Sum_probs=13.8

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 025541           24 VYQAFIFSVPIFFTFILLLLFYLFYLRRRR   53 (251)
Q Consensus        24 ~~~~~~~~v~i~~~~i~~~~~~~~~~~~~~   53 (251)
                      ...+...+++++ +++++.+.+++++++++
T Consensus        11 ~~~Ia~~vVGvl-l~vi~~l~~~~~~RRR~   39 (44)
T 2jwa_A           11 LTSIISAVVGIL-LVVVLGVVFGILIKRRQ   39 (44)
T ss_dssp             HHHHHHHHHHHH-HHHHHHHHHHHHHHHHC
T ss_pred             ccchHHHHHHHH-HHHHHHHHHHhheehhh
Confidence            334455555533 44444444444555444

>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=83.15  E-value=0.9  Score=29.86  Aligned_cols=47  Identities=21%  Similarity=0.433  Sum_probs=32.1

Q ss_pred             CcccccccccccccCCceeEcC-CCCCcccHhhHHHH------Hh----cCCCCcccc
Q 025541          100 RDTQCSVCLADYQAEDKLQQIP-ACGHAFHMDCIDHW------LT----THTTCPLCR  146 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~-~C~H~fh~~Ci~~w------l~----~~~~CP~Cr  146 (251)
                      ....|++|...+......+.-- .|.--||..|+.--      |.    ....||.|+
T Consensus         7 ~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvglt~~~~~~l~~e~~~~w~C~~C~   64 (65)
T 2vpb_A            7 PVYPCGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTCM   64 (65)
T ss_dssp             --CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHTCCHHHHHHHHHCTTEEECCHHHH
T ss_pred             CcCcCccCCCccCCCCCeEecccCccccCchhccCCCHHHHHHhhccCCCcEECcCcc
Confidence            3467999999987766665554 58999999997311      11    144688885

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=81.83  E-value=0.41  Score=31.54  Aligned_cols=46  Identities=26%  Similarity=0.594  Sum_probs=31.8

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc----CCCCccccCc
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT----HTTCPLCRLS  148 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~  148 (251)
                      ..+..|.||.+.   + .+..-..|...||..|+.+-|..    .-.||.|...
T Consensus         6 ~~~~~C~vC~~~---g-~ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~   55 (66)
T 1xwh_A            6 KNEDECAVCRDG---G-ELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQA   55 (66)
T ss_dssp             SCCCSBSSSSCC---S-SCEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHT
T ss_pred             CCCCCCccCCCC---C-CEEEcCCCChhhcccccCCCcCcCCCCCeECccccCc
Confidence            356789999864   3 33333358999999999865442    3469999653

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=81.07  E-value=0.17  Score=32.76  Aligned_cols=46  Identities=33%  Similarity=0.737  Sum_probs=31.7

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc----CCCCccccCcc
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT----HTTCPLCRLSL  149 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~~  149 (251)
                      .+..|.||...   +. +..-..|.-.||..|+.+-|..    .-.||.|....
T Consensus         4 ~~~~C~vC~~~---g~-ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   53 (60)
T 2puy_A            4 HEDFCSVCRKS---GQ-LLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQM   53 (60)
T ss_dssp             CCSSCTTTCCC---SS-CEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHH
T ss_pred             CCCCCcCCCCC---Cc-EEEcCCCCcCEECCcCCCCcCCCCCCceEChhccChh
Confidence            46779999864   33 3333359999999999865542    34699996543

---

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	251
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	8e-19
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	6e-12
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	3e-11
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	6e-10
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	4e-09
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-07
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	2e-07
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	3e-07
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	1e-06
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	2e-06
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	8e-05
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	1e-04
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	0.001
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	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 = 75.3 bits (185), Expect = 8e-19
 Identities = 23/50 (46%), Positives = 38/50 (76%)

Query: 101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLL 150
             +C+VCLA+ +  ++ + +P CGH FH +C+D WL +H+TCPLCRL+++
Sbjct: 5   GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 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 = 57.3 bits (138), Expect = 6e-12
 Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 3/65 (4%)

Query: 103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASSELSDI 162
           +C +CL D            C HAF   CI  W+  + TCPLC++ + +        S+ 
Sbjct: 7   RCPICLEDPSNYSM---ALPCLHAFCYVCITRWIRQNPTCPLCKVPVESVVHTIESDSEF 63

Query: 163 QQETI 167
             + I
Sbjct: 64  GDQLI 68

>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 = 55.9 bits (134), Expect = 3e-11
 Identities = 17/69 (24%), Positives = 22/69 (31%), Gaps = 14/69 (20%)

Query: 92  IYKESFSIRDTQCSVCLADYQAEDKLQQIPA--------------CGHAFHMDCIDHWLT 137
           +   ++ I    C++C           Q                 C HAFH  CI  WL 
Sbjct: 12  VALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLK 71

Query: 138 THTTCPLCR 146
           T   CPL  
Sbjct: 72  TRQVCPLDN 80

>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 = 51.3 bits (122), Expect = 6e-10
 Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 1/45 (2%)

Query: 103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTT-CPLCR 146
           +C +C+   + +D       CG+     C     T     CP CR
Sbjct: 2   ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACR 46

>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 = 49.8 bits (118), Expect = 4e-09
 Identities = 13/53 (24%), Positives = 17/53 (32%), Gaps = 2/53 (3%)

Query: 99  IRDTQCSVCLADYQAEDKLQQIPA-CGHAFHMDCIDHWLTT-HTTCPLCRLSL 149
           + D  C  C         L+ +   CGH     C+D         CP C   L
Sbjct: 1   MDDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

>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 = 46.1 bits (109), Expect = 1e-07
 Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 5/47 (10%)

Query: 104 CSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSL 149
           C +C  + +    ++  P CGH     C+  W  +    CP CR  +
Sbjct: 26  CKICAENDK---DVKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEI 68

>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 = 44.9 bits (105), Expect = 2e-07
 Identities = 11/46 (23%), Positives = 15/46 (32%), Gaps = 3/46 (6%)

Query: 104 CSVCLADYQAEDKLQQIP-ACGHAFHMDCIDHWLTTH--TTCPLCR 146
           C +C  +   E              H  C+  WLT    T C +C 
Sbjct: 9   CWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICG 54

>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 = 45.8 bits (107), Expect = 3e-07
 Identities = 11/64 (17%), Positives = 22/64 (34%), Gaps = 5/64 (7%)

Query: 89  PIVIYKESFSIRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-----HTTCP 143
             +I  E  ++      +  +       + ++  C HAFH+ C+              CP
Sbjct: 27  DCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCP 86

Query: 144 LCRL 147
            C+ 
Sbjct: 87  SCKT 90

>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 = 42.6 bits (100), Expect = 1e-06
 Identities = 11/54 (20%), Positives = 18/54 (33%), Gaps = 7/54 (12%)

Query: 104 CSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKASS 157
           C  C A+ +    L     C H     C++        CP+C+      A   +
Sbjct: 9   CQQCQAEAKCPKLL----PCLHTLCSGCLEAS---GMQCPICQAPWPLGADTPA 55

>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 = 42.6 bits (100), Expect = 2e-06
 Identities = 15/59 (25%), Positives = 20/59 (33%), Gaps = 10/59 (16%)

Query: 103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH-TTCPLCRL-----SLLAPAKA 155
            C +C              +C H F   CI   L    + CP CR       L +P K+
Sbjct: 25  SCQICEHIL----ADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLESPVKS 79

>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 = 38.5 bits (89), Expect = 8e-05
 Identities = 13/50 (26%), Positives = 19/50 (38%), Gaps = 7/50 (14%)

Query: 103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH---TTCPLCRLSL 149
           +C +CL       K      C H F   C+   L      + CPLC+  +
Sbjct: 23  ECPICLELI----KEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 68

>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 = 38.1 bits (88), Expect = 1e-04
 Identities = 11/54 (20%), Positives = 18/54 (33%), Gaps = 9/54 (16%)

Query: 101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHT--------TCPLCR 146
            + C +CL +Y  E     I  C   F   C+  ++            +CP   
Sbjct: 5   SSGCKLCLGEYPVEQMTT-IAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA 57

>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 = 34.3 bits (78), Expect = 0.001
 Identities = 5/46 (10%), Positives = 14/46 (30%), Gaps = 3/46 (6%)

Query: 104 CSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSL 149
           C++     +   +    P     F    ++ ++      P+    L
Sbjct: 3   CAISGKVPR---RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPL 45

>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 = 34.0 bits (77), Expect = 0.003
 Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 5/47 (10%)

Query: 103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSL 149
           +CS C    +    L     C H F  +C+   +   T CP+C    
Sbjct: 24  RCSRCTNILREPVCL---GGCEHIFCSNCVSDCI--GTGCPVCYTPA 65

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	251
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.71
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.51
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.49
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.48
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.44
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.42
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.4
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.3
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.23
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.21
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.16
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.12
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.0
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.96
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.96
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.86
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.59
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	93.34
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	92.88
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	90.79
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	87.59
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	86.51
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	85.07
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	84.06
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	83.6
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	82.69
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	81.77

>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=99.71  E-value=1.9e-18  Score=112.27  Aligned_cols=51  Identities=45%  Similarity=1.206  Sum_probs=46.4

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCccc
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLL  150 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  150 (251)
                      ++.+|+||+++|..++.+..++.|+|.||..||.+|+..+.+||+||+++.
T Consensus         4 d~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            346799999999999888888779999999999999999999999999874

>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=99.51  E-value=3.7e-15  Score=100.76  Aligned_cols=47  Identities=36%  Similarity=0.931  Sum_probs=41.3

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCccc
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLL  150 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  150 (251)
                      .+.|+||++.+..  .++.++ |||.||.+||.+|+..+.+||+||+++.
T Consensus         5 ~d~C~IC~~~~~~--~~~~~~-C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           5 AERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCccCCcCccC--CcEEeC-CCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            4679999999864  456677 9999999999999999999999999874

>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=99.49  E-value=3.8e-15  Score=95.27  Aligned_cols=48  Identities=23%  Similarity=0.526  Sum_probs=40.1

Q ss_pred             cccccccccccCCcee-EcCCCCCcccHhhHHHHHhc-CCCCccccCcccC
Q 025541          103 QCSVCLADYQAEDKLQ-QIPACGHAFHMDCIDHWLTT-HTTCPLCRLSLLA  151 (251)
Q Consensus       103 ~C~IC~~~~~~~~~~~-~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~  151 (251)
                      +|+||+++|..++... .++ |||.||..||.+|+.. +.+||+||+++..
T Consensus         2 eCpICl~~~~~~~~~~~~~~-CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSS-SSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecC-CCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            6999999998765544 445 9999999999999985 5579999998854

>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=99.48  E-value=1.1e-14  Score=103.27  Aligned_cols=52  Identities=31%  Similarity=0.611  Sum_probs=42.6

Q ss_pred             CCcccccccccccccCC---------------ceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccC
Q 025541           99 IRDTQCSVCLADYQAED---------------KLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLA  151 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~---------------~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  151 (251)
                      ..++.|+||++.+....               .+..++ |||+||..||.+||..+.+||+||+++..
T Consensus        19 ~~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   85 (88)
T d3dplr1          19 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEF   85 (88)
T ss_dssp             SCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCCE
T ss_pred             CCCCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCcccc
Confidence            34667999999886532               345666 99999999999999999999999998753

>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=99.44  E-value=3.9e-14  Score=105.19  Aligned_cols=53  Identities=21%  Similarity=0.504  Sum_probs=41.2

Q ss_pred             CCcccccccccccccC---------------CceeEcCCCCCcccHhhHHHHHhcC-----CCCccccCcccCC
Q 025541           99 IRDTQCSVCLADYQAE---------------DKLQQIPACGHAFHMDCIDHWLTTH-----TTCPLCRLSLLAP  152 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~---------------~~~~~~~~C~H~fh~~Ci~~wl~~~-----~~CP~Cr~~~~~~  152 (251)
                      ..+..|+||++.|...               ..+.+++ |+|+||..||..||..+     .+||+||..+...
T Consensus        23 ~~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          23 APEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             cccccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            3466899999998542               2355666 99999999999999743     4799999887554

>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=99.42  E-value=5.7e-14  Score=93.91  Aligned_cols=52  Identities=27%  Similarity=0.572  Sum_probs=40.6

Q ss_pred             CcccccccccccccC-C-ceeEcCCCCCcccHhhHHHHHhc-CCCCccccCcccCC
Q 025541          100 RDTQCSVCLADYQAE-D-KLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSLLAP  152 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~-~-~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~  152 (251)
                      ++..|+||++.+..+ . .+.+++ |||.||..||..|+.. +..||+||+.+...
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCCCCcCCceeecCCceEEEeCc-cChHhhHHHHHHHhCcCcCCCCCCCcCcccc
Confidence            457899999986433 2 344565 9999999999999965 56799999988543

>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=99.40  E-value=1.4e-13  Score=95.45  Aligned_cols=50  Identities=24%  Similarity=0.741  Sum_probs=41.5

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhc-CCCCccccCcccCCCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSLLAPAK  154 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~~  154 (251)
                      ...|+||++.+..   +++++ |||.||..||..||.. +++||+||..+.....
T Consensus        23 ~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~   73 (79)
T d1fbva4          23 FQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP   73 (79)
T ss_dssp             TTBCTTTSSSBCC---EECSS-SCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCC
T ss_pred             CCCCccCCCcCCC---eEEeC-CCCeeeHHHHHHHHHHCcCcCCCCCcCccCCce
Confidence            3569999998864   56777 9999999999999974 5789999999976443

>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=99.30  E-value=2.6e-13  Score=87.87  Aligned_cols=47  Identities=11%  Similarity=0.187  Sum_probs=40.0

Q ss_pred             cccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCC
Q 025541          103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAP  152 (251)
Q Consensus       103 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  152 (251)
                      .|+||++.|..+   .+++.|||+||+.||.+||..+.+||+||.++...
T Consensus         2 ~C~Ic~~~~~~P---v~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~   48 (56)
T d2baya1           2 LCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   48 (56)
T ss_dssp             CCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             CCccCCchHHhc---CccCCCCCcccHHHHHHHHhhccCCCccCCcCCHH
Confidence            599999999753   34445999999999999999999999999988653

>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=99.23  E-value=1.1e-12  Score=84.82  Aligned_cols=47  Identities=23%  Similarity=0.608  Sum_probs=38.7

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAK  154 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~  154 (251)
                      ...|+||++.|..+   +++| |||.||..||.+|   +.+||+||+++.....
T Consensus         6 ~l~C~IC~~~~~~p---~~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~~   52 (56)
T d1bora_           6 FLRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGAD   52 (56)
T ss_dssp             CSSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCSS
T ss_pred             CCCCcccCcccCCC---EEec-CCCHHhHHHHHcC---CCcCcCCCCcccCCCC
Confidence            35799999999764   5677 9999999999876   5689999999976554

>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=99.21  E-value=2.8e-12  Score=90.03  Aligned_cols=47  Identities=26%  Similarity=0.561  Sum_probs=39.5

Q ss_pred             ccccccccccccCCceeEcCCCCCcccHhhHHHHHhc-CCCCccccCcccCC
Q 025541          102 TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSLLAP  152 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~  152 (251)
                      ..|+||++.|..   ..+++ |||.||+.||.+|++. +..||+||.++...
T Consensus        24 l~C~IC~~~~~~---pv~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~   71 (86)
T d1rmda2          24 ISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (86)
T ss_dssp             TBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             cCCccCCcchhc---ceecC-CCChhhHHHHHHHHhhCCCcCcccCCCCChh
Confidence            479999999875   35676 9999999999999974 56899999988654

>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=99.16  E-value=1e-11  Score=90.24  Aligned_cols=48  Identities=25%  Similarity=0.652  Sum_probs=39.6

Q ss_pred             ccccccccccccCCceeEcCCCCCcccHhhHHHHHhcC---CCCccccCcccCCC
Q 025541          102 TQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH---TTCPLCRLSLLAPA  153 (251)
Q Consensus       102 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~---~~CP~Cr~~~~~~~  153 (251)
                      ..|+||++.|..+   ..++ |||.||..||..|+..+   ..||+||..+....
T Consensus        22 l~CpIC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   72 (103)
T d1jm7a_          22 LECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS   72 (103)
T ss_dssp             TSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTT
T ss_pred             cCCCccCchhCCe---EEcC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhh
Confidence            4699999999764   3466 99999999999999764   47999999886544

>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=99.12  E-value=1.4e-11  Score=80.70  Aligned_cols=52  Identities=21%  Similarity=0.445  Sum_probs=37.7

Q ss_pred             CCcccccccccccccCCcee-EcCCCCCcccHhhHHHHHh--cCCCCccccCccc
Q 025541           99 IRDTQCSVCLADYQAEDKLQ-QIPACGHAFHMDCIDHWLT--THTTCPLCRLSLL  150 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~-~~~~C~H~fh~~Ci~~wl~--~~~~CP~Cr~~~~  150 (251)
                      .+...|.||++.+....... ...+|+|.||..||.+|+.  .+.+||+||+.+.
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            34567999999886542221 1113569999999999996  4568999999864

>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=99.00  E-value=6.3e-11  Score=84.99  Aligned_cols=50  Identities=22%  Similarity=0.472  Sum_probs=39.2

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCCCC
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAKA  155 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~  155 (251)
                      ...|+||++.|..+  +...+ |||.||..||.+|+.  ..||.||..+......
T Consensus        22 ~l~C~IC~~~~~~p--v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~l~   71 (97)
T d1jm7b_          22 LLRCSRCTNILREP--VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLK   71 (97)
T ss_dssp             TTSCSSSCSCCSSC--BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCC
T ss_pred             cCCCccCCchhhcC--ceeCC-CCCchhHHHHHHHHh--ccccccCCcCchhhCc
Confidence            34799999999765  33344 999999999999985  4699999988665433

>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=98.96  E-value=2.3e-10  Score=78.59  Aligned_cols=50  Identities=24%  Similarity=0.555  Sum_probs=41.9

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc-CCCCccccCcccCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSLLAPA  153 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~  153 (251)
                      ++..|+||++-|..+   .+++ |||.||+.||..|+.. ...||.|+..+....
T Consensus         7 ~~l~CpIc~~~m~dP---V~~~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~   57 (78)
T d1t1ha_           7 EYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLHAG   57 (78)
T ss_dssp             SSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCC
T ss_pred             ccCCCcCcCchhhCc---eEcc-CCCcchHHHHHHHHHHCCCCCCcccccCCccc
Confidence            467899999999875   3566 9999999999999986 467999999887644

>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=98.96  E-value=1.7e-10  Score=79.66  Aligned_cols=50  Identities=14%  Similarity=0.137  Sum_probs=41.5

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc-CCCCccccCcccCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT-HTTCPLCRLSLLAPA  153 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~  153 (251)
                      ++..|+||++-|..+   ..++ |||.|++.||.+|+.. +.+||.||..+....
T Consensus         6 ~~l~CpIc~~l~~dP---v~~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~   56 (80)
T d2c2la2           6 DYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQ   56 (80)
T ss_dssp             STTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCGGG
T ss_pred             ccccCcCcCchhhhh---cccC-CcCeecHHHHHHHHhcCCccCCCccccccccc
Confidence            467899999999865   3566 9999999999999975 567999999876543

>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=98.86  E-value=1.1e-09  Score=78.56  Aligned_cols=52  Identities=13%  Similarity=0.075  Sum_probs=42.9

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCccccCcccCCCC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCRLSLLAPAK  154 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~  154 (251)
                      .+..|+||++-|..+   .+++.|||.|++.||..||..+..||+||.++....-
T Consensus        21 ~~f~CPI~~~lm~dP---V~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L   72 (98)
T d1wgma_          21 DEFLDPIMSTLMCDP---VVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQI   72 (98)
T ss_dssp             TTTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTS
T ss_pred             HHhCCcCchhHHHHH---HhcccccchhhHHHHHHHHHhcCCcccccccccchhh
Confidence            468899999999865   4566345689999999999999999999999876443

>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=98.59  E-value=1e-08  Score=72.52  Aligned_cols=47  Identities=21%  Similarity=0.576  Sum_probs=37.4

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhcC--------CCCccccC
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTH--------TTCPLCRL  147 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~--------~~CP~Cr~  147 (251)
                      ....|+||++++...+.+..++ |+|.||..|+..|+..+        -.||.|+-
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCcCccCCCcccCCceEEECC-CCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            4568999999998776677666 99999999999999631        25998643

>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=93.34  E-value=0.016  Score=34.85  Aligned_cols=44  Identities=32%  Similarity=0.689  Sum_probs=31.0

Q ss_pred             cccccccccccCCceeEcCCCCCcccHhhHHHHHhc----CCCCccccC
Q 025541          103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT----HTTCPLCRL  147 (251)
Q Consensus       103 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~  147 (251)
                      .|.||...-..+ .+..-..|...||..|+..-+..    .-.||.||.
T Consensus         2 ~C~vC~~~~~~~-~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCC-CEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            588997665444 33344469999999999886653    336999975

>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=92.88  E-value=0.016  Score=36.57  Aligned_cols=49  Identities=24%  Similarity=0.499  Sum_probs=35.1

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHH---h--cCCCCccccCc
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWL---T--THTTCPLCRLS  148 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl---~--~~~~CP~Cr~~  148 (251)
                      ....|.||...+..+..++.--.|+..||..|+..-.   .  .+..||.|+..
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            4567999998877665555444699999999995311   1  24679999754

>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=90.79  E-value=0.078  Score=34.88  Aligned_cols=35  Identities=29%  Similarity=0.680  Sum_probs=25.4

Q ss_pred             CCcccccccccccccCCceeEcCCCCCcccHhhHHHH
Q 025541           99 IRDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHW  135 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w  135 (251)
                      ..|..|.|| +.+.......-- -|+-+||..|+++-
T Consensus        13 ~~D~mC~vC-~v~t~~~l~pCR-vCtRv~H~~CL~r~   47 (89)
T d1wila_          13 VNDEMCDVC-EVWTAESLFPCR-VCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTT-CCCCSSCCSSCS-SSSSCCCHHHHHHH
T ss_pred             CcCcccccc-Ccccccceecce-eecchhhHHHHHHh
Confidence            457889999 666555443222 38899999999986

>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=87.59  E-value=0.15  Score=32.53  Aligned_cols=45  Identities=33%  Similarity=0.645  Sum_probs=30.1

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHHHHHhc----CCCCccccCcc
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT----HTTCPLCRLSL  149 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~~  149 (251)
                      ...|.||.+.   ++ +..--.|...||..|+.+.+..    .-.||.|+...
T Consensus         7 c~~C~~C~~~---~~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           7 ATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             SSCCSSSCSS---SC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCCCCc---CE-EEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            4457777543   33 3333359999999999987753    34699996543

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=86.51  E-value=0.68  Score=30.38  Aligned_cols=55  Identities=16%  Similarity=0.338  Sum_probs=37.6

Q ss_pred             CCcccccccccccccCC--ceeE-cCCCCCcccHhhHHHHHh-cCCCCccccCcccCCC
Q 025541           99 IRDTQCSVCLADYQAED--KLQQ-IPACGHAFHMDCIDHWLT-THTTCPLCRLSLLAPA  153 (251)
Q Consensus        99 ~~~~~C~IC~~~~~~~~--~~~~-~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~~~  153 (251)
                      .....|.||-+.+....  .+.+ .-.|+--.|+.|..-=.+ .++.||-|+..+....
T Consensus        14 ~~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Ykr~k   72 (93)
T d1weoa_          14 LDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKRLR   72 (93)
T ss_dssp             CSSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCCCT
T ss_pred             cccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhhhhc
Confidence            34568999999875332  1211 124778899999875443 6789999998886543

>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=85.07  E-value=0.13  Score=31.75  Aligned_cols=46  Identities=24%  Similarity=0.582  Sum_probs=30.9

Q ss_pred             CcccccccccccccCCceeEcCCCCCcccHhhHHHHHhc----CCCCccccCcc
Q 025541          100 RDTQCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTT----HTTCPLCRLSL  149 (251)
Q Consensus       100 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~~  149 (251)
                      .+..|.||.+.   +. +..--.|.-.||..|+...+..    ...||.|+...
T Consensus         8 ~~~~C~~C~~~---g~-lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           8 HMEFCRVCKDG---GE-LLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SCSSCTTTCCC---SS-CBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CcCCCcCCCCC---Ce-EEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            34569999753   32 3333358999999999765543    34699997654

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 8
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.06  E-value=0.61  Score=30.11  Aligned_cols=46  Identities=20%  Similarity=0.455  Sum_probs=30.9

Q ss_pred             ccccccccccCCceeEcCCCCCcccHhhHH--HHH-h--cCCCCccccCcc
Q 025541          104 CSVCLADYQAEDKLQQIPACGHAFHMDCID--HWL-T--THTTCPLCRLSL  149 (251)
Q Consensus       104 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~--~wl-~--~~~~CP~Cr~~~  149 (251)
                      |-||...+......+.--.|.--||..|+.  ... .  .+..||.|+...
T Consensus        14 ~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~   64 (79)
T d1wepa_          14 YCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             EeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCc
Confidence            449998776554444444689999999984  222 1  246899997644

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.60  E-value=0.14  Score=34.04  Aligned_cols=49  Identities=24%  Similarity=0.495  Sum_probs=31.9

Q ss_pred             cccccccccccccC-CceeEcCCCCCcccHhhHHHHHh--------cCCCCccccCcc
Q 025541          101 DTQCSVCLADYQAE-DKLQQIPACGHAFHMDCIDHWLT--------THTTCPLCRLSL  149 (251)
Q Consensus       101 ~~~C~IC~~~~~~~-~~~~~~~~C~H~fh~~Ci~~wl~--------~~~~CP~Cr~~~  149 (251)
                      ...|.||....... ..++.--.|...||..|+...+.        ....||.|....
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~   73 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQM   73 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHH
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchH
Confidence            35699998754332 23443446999999999874331        145799996543

>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=82.69  E-value=0.61  Score=29.67  Aligned_cols=46  Identities=22%  Similarity=0.494  Sum_probs=29.6

Q ss_pred             cccccccccccccCCceeEcCCCCCcccHhhHH----H--H---HhcCCCCccccCc
Q 025541          101 DTQCSVCLADYQAEDKLQQIPACGHAFHMDCID----H--W---LTTHTTCPLCRLS  148 (251)
Q Consensus       101 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~----~--w---l~~~~~CP~Cr~~  148 (251)
                      ...| ||......+. ++.--.|.--||..|+.    .  .   ......||.|+..
T Consensus        16 ~~~C-iC~~~~~~~~-mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~   70 (76)
T d1wema_          16 ALYC-ICRQPHNNRF-MICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             CCCS-TTCCCCCSSC-EEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             cCEE-ECCCccCCCe-EEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCc
Confidence            3457 8987765443 34444588999999982    1  1   1235789999643

>d1y02a2 g.50.1.1 (A:20-70) Rififylin (FYVE-RING finger protein Sakura) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Rififylin (FYVE-RING finger protein Sakura)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.77  E-value=0.089  Score=31.54  Aligned_cols=44  Identities=25%  Similarity=0.551  Sum_probs=28.5

Q ss_pred             cccccccccccCCceeEcCCCCCcccHhhHHHHHhcCCCCcccc
Q 025541          103 QCSVCLADYQAEDKLQQIPACGHAFHMDCIDHWLTTHTTCPLCR  146 (251)
Q Consensus       103 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr  146 (251)
                      .|.+|...|..-..-..-..||.+|+..|....-.....|..|.
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C~   45 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQ   45 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhHh
Confidence            48889888865443333336999999999766544556677774