Citrus Sinensis ID: 024603

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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-------260-----
Protein Sequence
MSKGLVSEVIKMSLTCKETVSLWLFATMCAFGTGVLIRAMKRVLYAALTCIFALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQLLESAADGESLSKAALLSSLVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIKSSHGMLNLNRRFFFLFQVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDTDTW
Secondary Structure (PSIPRED)
ccccccEEEEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHccccccEEccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHcccccHHHHHcccccccccccccccHHHHHHcccEEEEcccccccccccccHHcccccccccccccccccccccccccHHHHHcccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHEHHEEEEEEEHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHccccHHHHHHHHHHHccccccccccHHHHHHccEEEEEcccccccccccccEEEHHHccccccEEEcccccccccHHHHHHHHHHcccccccHHHcccccccc
Coil and Loop (DISEMBL)
MSKGLVSEVIKMSLTCKETVSLWLFATMCAFGTGVLIRAMKRVLYAALTCIFALGGAIVGTIFgamkgqttetgflhgaGIGAVAGAITALQLLESAADGESLSKAALLSSLVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIKSSHGMLNLNRRFFFLFQVSTLETAYREvsdvydvtgvkglsEDMIQKLPECALHSEELIQLDNEIGCSIClekfeegdsarklpscghcfhsecvdkwltrngscpvcrecvckdtdtw
Flexible Loop (DISEMBL)
MSKGLVSEVIKMSLTCKETVSLWLFATMCAFGTGVLIRAMKRVLYAALTCIFALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQLLESAADGESLSKAALLSSLVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIKSSHGMLNLNRRFFFLFQVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLtrngscpvcrecvckdtdtw
Low Complexity Region (SEG)
MSKGLVSEVIKMSLTCKETVSLWLFATMCAFGTGVLIRAMKRVLYAALTCIFALGGAIVGTIFGAMKGQTTETGFLHgagigavagaiTALQLLESAADGEslskaallsslVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIKSSHGMlnlnrrffflfQVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDTDTW
Disordered region (IsUnstruct)
*****VSEVIKMSLTCKETVSLWLFATMCAFGTGVLIRAMKRVLYAALTCIFALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQLLESAADGESLSKAALLSSLVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIKSSHGMLNLNRRFFFLFQVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK*****
Disordered Region (DISOPRED)
******S*VIKMSLTCKETVSLWLFATMCAFGTGVLIRAMKRVLYAALTCIFALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQLLESAADGESLSKAALLSSLVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIKSSHGMLNLNRRFFFLFQVSTLE********************DMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR**********
Disordered Region (DISEMBL)
MSKGLVSEVIKMSLTCKETVSLWLFATMCAFGTGVLIRAMKRVLYAALTCIFALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQLLESAADGESLSKAALLSSLVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIKSSHGMLNLNRRFFFLFQVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDTDTW
Disordered Region (DISPRO)
*SKGLVSEVIKMSLTCKETVSLWLFATMCAFGTGVLIRAMKRVLYAALTCIFALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQLLESAADGESLSKAALLSSLVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIKSSHGMLNLNRRFFFLFQVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHHHooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSKGLVSEVIKMSLTCKETVSLWLFATMCAFGTGVLIRAMKRVLYAALTCIFALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQLLESAADGESLSKAALLSSLVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIKSSHGMLNLNRRFFFLFQVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDTDTW
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	265	2.2.26 [Sep-21-2011]
Q8GT75	236	NEP1-interacting protein	no	no	0.694	0.779	0.325	7e-32
Q8GT74	241	NEP1-interacting protein	no	no	0.694	0.763	0.325	1e-31
Q9FKX5	221	NEP1-interacting protein-	no	no	0.694	0.832	0.314	5e-29
Q8LBA0	223	NEP1-interacting protein-	no	no	0.709	0.843	0.341	9e-24
Q8L9W3	163	E3 ubiquitin-protein liga	no	no	0.422	0.687	0.367	1e-11
Q9FL42	159	Putative RING-H2 finger p	no	no	0.271	0.452	0.388	1e-11
P0CH01	372	Putative RING-H2 finger p	no	no	0.294	0.209	0.405	1e-11
Q7X843	349	RING-H2 finger protein AT	no	no	0.275	0.209	0.391	2e-11
Q8L9T5	304	RING-H2 finger protein AT	no	no	0.286	0.25	0.367	2e-11
Q9SG96	181	RING-H2 finger protein AT	no	no	0.381	0.558	0.349	3e-11

>sp|Q8GT75|NIP1_ARATH NEP1-interacting protein 1 OS=Arabidopsis thaliana GN=NIP1 PE=1 SV=2

 Score =  137 bits (345), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 73/224 (32%), Positives = 122/224 (54%), Gaps = 40/224 (17%)

Query: 43  VLYAALTCIFALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQLLESA----A 98
           +L A LT  FAL G ++G + GA+ GQ TE+GF+ GA +GA++GA+ ++++ ES+     
Sbjct: 41  ILSAVLTFFFALVGTLLGALTGALIGQETESGFIRGAAVGAISGAVFSIEVFESSLVLWK 100

Query: 99  DGES-----LSKAALLSSLVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIKSSHGMLN 153
             ES     L    ++ SL++G++  E + PA+L A Q Q+                   
Sbjct: 101 SNESRFGCLLYLIDVIVSLISGRLVRERIGPAMLSAVQSQMG------------------ 142

Query: 154 LNRRFFFLFQVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECALHSEELIQLD-NEIG 212
                        +++ + E+S ++D  G KGL+ D++ K+P+  +  +  +    N+  
Sbjct: 143 ------------AVDSTFEELSSIFDTGGSKGLTGDLVDKIPKIKITGKNNLDASGNKDS 190

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRE 256
           CS+CL+ F+ G++ R LP C H FH  C+D WL R+GSCP+CR 
Sbjct: 191 CSVCLQDFQLGETVRSLPHCHHMFHLPCIDNWLFRHGSCPMCRR 234

Intrinsic thylakoid membrane protein that fixes RPOT2 on the stromal side of the thylakoid membrane.
Arabidopsis thaliana (taxid: 3702)

>sp|Q8GT74|NIP2_ARATH NEP1-interacting protein 2 OS=Arabidopsis thaliana GN=NIP2 PE=1 SV=1

 Score =  137 bits (344), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 73/224 (32%), Positives = 121/224 (54%), Gaps = 40/224 (17%)

Query: 43  VLYAALTCIFALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQLLESAAD--- 99
           ++ A LT  FAL G ++G + GA+ GQ TE+GF+ GA IGA++GA+ ++++ ES+ D   
Sbjct: 46  IISAILTFFFALVGTLLGALTGALIGQETESGFIRGAAIGAISGAVFSIEVFESSLDLWK 105

Query: 100 ------GESLSKAALLSSLVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIKSSHGMLN 153
                 G  L    ++ SL++G++  E + PA+L A Q Q+                   
Sbjct: 106 SDESGFGCFLYLIDVIVSLLSGRLVRERIGPAMLSAVQSQMG------------------ 147

Query: 154 LNRRFFFLFQVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECALHSEELIQL-DNEIG 212
                        ++TA+ + + ++D  G KGL+ D+++K+P+  +         +N   
Sbjct: 148 ------------AVDTAFDDHTSLFDTGGSKGLTGDLVEKIPKMTITGNNNTDASENTDS 195

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRE 256
           CS+CL+ F+ G++ R LP C H FH  C+D WL R+GSCP+CR 
Sbjct: 196 CSVCLQDFQLGETVRSLPHCHHMFHLPCIDNWLLRHGSCPMCRR 239

Intrinsic thylakoid membrane protein that fixes RPOT2 on the stromal side of the thylakoid membrane.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FKX5|NIPL1_ARATH NEP1-interacting protein-like 1 OS=Arabidopsis thaliana GN=ATL27 PE=2 SV=1

 Score =  128 bits (321), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 73/232 (31%), Positives = 126/232 (54%), Gaps = 48/232 (20%)

Query: 37  IRAMKRVLYAAL-TCIFALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQLLE 95
           + A+   L++AL T  FAL G ++G + GA+ GQ TE+GF+ GA +GA++GA+ ++++ E
Sbjct: 24  VSALLANLFSALFTFFFALVGTLLGALTGALIGQETESGFIRGAAVGAISGAVFSIEVFE 83

Query: 96  SA----ADGES-----LSKAALLSSLVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIK 146
           S+       ES     L    +++SL++G++  E + PA+L A Q               
Sbjct: 84  SSLLLWQSDESGIGCLLYLIDVIASLLSGRLVRERIGPAMLSAVQS-------------- 129

Query: 147 SSHGMLNLNRRFFFLFQVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECAL--HSEEL 204
                           Q+  +E+ +++ +D++D    KGL+ D + ++P+  +   S E+
Sbjct: 130 ----------------QMGAVESQFQDHTDIFDTAISKGLTGDSLNRIPKVRITDTSPEI 173

Query: 205 IQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRE 256
           +       CS+CL+ F+ G++ R LP C H FH  C+DKWL R+ SCP+CR 
Sbjct: 174 VS------CSVCLQDFQVGETVRSLPHCHHMFHLPCIDKWLRRHASCPLCRR 219

May be involved in the early steps of the plant defense signaling pathway.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8LBA0|NIPL2_ARATH NEP1-interacting protein-like 2 OS=Arabidopsis thaliana GN=ATL24 PE=1 SV=2

 Score =  110 bits (276), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 79/231 (34%), Positives = 117/231 (50%), Gaps = 43/231 (18%)

Query: 38  RAMKRVLYAALTCIFALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQLLE-- 95
           R +  V   ALT IFA+ GA  G + GA+ G+  + G L GA +GAVAGAI ++++LE  
Sbjct: 24  RLIAGVFSGALTGIFAMAGAFTGAVTGAVAGRAAQYGVLRGAALGAVAGAILSVEVLEAS 83

Query: 96  --------SAADGESLSKAALLSSLVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIKS 147
                   S + G S S A  +  L  G++  E +   ++ ++ WQ              
Sbjct: 84  RAYWYLELSGSRGPS-SMADFVEQLFRGRLVDEQLMSTMINSHHWQ-------------- 128

Query: 148 SHGMLNLNRRFFFLFQVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECALHSEELIQL 207
                          ++S  + +Y E  DVY     +GLS D ++KLP C + S E+++ 
Sbjct: 129 --------------LRIS--DVSYEEREDVYGELEARGLSGDSLRKLP-CYIMSSEMVR- 170

Query: 208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECV 258
                C+ICL+  + G+  R LP C H FH  CVDKWL R+GSCP+CR+ V
Sbjct: 171 RQVTHCTICLQDIKTGEITRSLPKCDHTFHLVCVDKWLIRHGSCPICRQAV 221

May be involved in the early steps of the plant defense signaling pathway. Does not display E3 catalytic activity.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8L9W3|ATL23_ARATH E3 ubiquitin-protein ligase ATL23 OS=Arabidopsis thaliana GN=ATL23 PE=1 SV=2

 Score = 70.9 bits (172), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 43/117 (36%), Positives = 57/117 (48%), Gaps = 5/117 (4%)

Query: 141 FLEFIKSSHGMLNLNRRFFFLFQVSTLET--AYREVSDVYDVTGVKGLSEDMIQKLPECA 198
           F+  +    GM  +   + FL   ST       R    V  VTG KGLS   ++K+P+  
Sbjct: 33  FMALLLPCVGMCIVFLIYLFLLWCSTRRRIERLRFAEPVKPVTG-KGLSVLELEKIPK-- 89

Query: 199 LHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
           L   EL  +     C++CLE  E G S R +P C H FH  C D WL+ +  CPVCR
Sbjct: 90  LTGRELAVIARSTECAVCLEDIESGQSTRLVPGCNHGFHQLCADTWLSNHTVCPVCR 146

E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8, UBC10, UBC11, UBC28 and UBC29 in vitro.

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 = 70.1 bits (170), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 40/72 (55%)

Query: 185 GLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKW 244
           GL   +I+  P   L     +   N   CSICL  +E  +  R +P C HCFH++CVD+W
Sbjct: 66  GLDRPVIESYPRIVLGDSRRLPRPNNGPCSICLCDYEAREPVRCIPECNHCFHTDCVDEW 125

Query: 245 LTRNGSCPVCRE 256
           L  + +CP+CR 
Sbjct: 126 LRTSATCPLCRN 137

Arabidopsis thaliana (taxid: 3702)

>sp|P0CH01|AT21A_ARATH Putative RING-H2 finger protein ATL21A OS=Arabidopsis thaliana GN=ATL21A PE=3 SV=1

 Score = 70.1 bits (170), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 32/79 (40%), Positives = 47/79 (59%), Gaps = 1/79 (1%)

Query: 179 DVTGVKGLSEDMIQKLPECAL-HSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFH 237
           +V    GL E +I+   +  L  S  L   +++I C ICL ++   ++ R +P C HCFH
Sbjct: 285 EVIVTTGLDESIIESYKKTELGESRRLPGNNDDIVCPICLSEYASKETVRCIPECDHCFH 344

Query: 238 SECVDKWLTRNGSCPVCRE 256
           SEC+D WL  +GSCP+CR 
Sbjct: 345 SECIDVWLKIHGSCPLCRN 363

Arabidopsis thaliana (taxid: 3702)

>sp|Q7X843|ATL48_ARATH RING-H2 finger protein ATL48 OS=Arabidopsis thaliana GN=ATL48 PE=2 SV=2

 Score = 69.7 bits (169), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 185 GLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKW 244
           GL +  I  LP   L+    I L+    C++CL +F + D  R LP C H FH  C+D W
Sbjct: 180 GLDQTAIDALP-VFLYGNVTISLEQPFDCAVCLNEFSDTDKLRLLPVCSHAFHLHCIDTW 238

Query: 245 LTRNGSCPVCRECV 258
           L  N +CP+CR  +
Sbjct: 239 LLSNSTCPLCRRSL 252

Arabidopsis thaliana (taxid: 3702)

>sp|Q8L9T5|ATL2_ARATH RING-H2 finger protein ATL2 OS=Arabidopsis thaliana GN=ATL2 PE=2 SV=2

 Score = 69.3 bits (168), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 45/79 (56%), Gaps = 3/79 (3%)

Query: 180 VTGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSE 239
           V   +GL  ++I+ LP      E      + I C++CL +FEE ++ R LP+C H FH +
Sbjct: 89  VVASRGLDPNVIKSLPVFTFSDE---THKDPIECAVCLSEFEESETGRVLPNCQHTFHVD 145

Query: 240 CVDKWLTRNGSCPVCRECV 258
           C+D W   + +CP+CR  V
Sbjct: 146 CIDMWFHSHSTCPLCRSLV 164

May be involved in the early steps of the plant defense signaling pathway.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 69.3 bits (168), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 37/106 (34%), Positives = 54/106 (50%), Gaps = 5/106 (4%)

Query: 151 MLNLNRRFFFLFQVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECALHSEELIQLDNE 210
           +L + RRF    QVS    A   +  +   TG+K   +  ++++P   L+   +I +   
Sbjct: 57  VLRITRRFTSDDQVSNASNANANLGRLAAATGLK---KQALKQIP-VGLYGSGIIDM-KA 111

Query: 211 IGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRE 256
             C ICL  FE+G+  R LP C H FH  C+D WL    SCP CR+
Sbjct: 112 TECLICLGDFEDGEKVRVLPKCNHGFHVRCIDTWLLSRSSCPTCRQ 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	265
297737435	264	unnamed protein product [Vitis vinifera]	0.833	0.837	0.559	1e-70
224061431	245	predicted protein [Populus trichocarpa]	0.856	0.926	0.550	1e-69
359494038	180	PREDICTED: NEP1-interacting protein 2-li	0.675	0.994	0.535	3e-55
255583605	223	RING-H2 finger protein ATL2B, putative [	0.713	0.847	0.513	4e-53
351727337	236	uncharacterized protein LOC100305612 [Gl	0.743	0.834	0.48	1e-52
357494513	236	RING finger family protein [Medicago tru	0.728	0.817	0.495	9e-47
357494507	245	RING finger family protein [Medicago tru	0.815	0.881	0.450	5e-43
356524261	224	PREDICTED: NEP1-interacting protein 2-li	0.803	0.950	0.421	7e-42
356569798	210	PREDICTED: NEP1-interacting protein 2-li	0.716	0.904	0.395	2e-37
116830763	224	unknown [Arabidopsis thaliana]	0.822	0.973	0.363	2e-36

>gi|297737435|emb|CBI26636.3| unnamed protein product [Vitis vinifera]

 Score =  272 bits (695), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 142/254 (55%), Positives = 169/254 (66%), Gaps = 33/254 (12%)

Query: 10  IKMSLTCKETVSLWLFATMCAFGTGVLIRAMKRVLYAALTCIFALGGAIVGTIFGAMKGQ 69
           IK    C+E VS  +F+     G G++ R MK  + AA TCIFALGGA+VGTI GA+KGQ
Sbjct: 43  IKSHTMCREAVSFRVFSQTRDSGNGLVFRVMKSAVLAAFTCIFALGGAVVGTITGAIKGQ 102

Query: 70  TTETGFLHGAGIGAVAGAITALQLLESAADGESLSKAALLSSLVNGKVFMEWVSPAVLKA 129
           TTETGF  G+GIGAV GAITALQLLES A GESLSKAALL SLVNGKVFMEWVSPAVLKA
Sbjct: 103 TTETGFFRGSGIGAVTGAITALQLLESVAAGESLSKAALLCSLVNGKVFMEWVSPAVLKA 162

Query: 130 YQWQVSNHKMKFLEFIKSSHGMLNLNRRFFFLFQVSTLETAYREVSDVYDVTGVKGLSED 189
           YQWQ+S                              TLET Y E  D Y+++G KGL  +
Sbjct: 163 YQWQIS------------------------------TLETNYGETEDFYNISGAKGLPHN 192

Query: 190 MIQKLPECAL-HSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN 248
            I+KLP+    HS    ++ NEI C+ICL+ F++G+  R LPSC H FH ECVD+WLT +
Sbjct: 193 FIEKLPKSNFCHSNA--EMYNEISCTICLQDFKDGEMTRGLPSCRHYFHMECVDQWLTLH 250

Query: 249 GSCPVCRECVCKDT 262
           GSCP+CR+ VC DT
Sbjct: 251 GSCPMCRKDVCMDT 264

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224061431|ref|XP_002300476.1| predicted protein [Populus trichocarpa] gi|222847734|gb|EEE85281.1| predicted protein [Populus trichocarpa]

 Score =  268 bits (686), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 148/269 (55%), Positives = 172/269 (63%), Gaps = 42/269 (15%)

Query: 7   SEVIKMSLTCKETVSLWLFAT-MCAFGTGVLIRA-MKRVLYAALTCIFALGGAIVGTIFG 64
           S V K S  CKE VS W+FA  +  FGTG+ IR+ +K  + AA TCIFALGGA+VG+I G
Sbjct: 6   SGVTKASFRCKEAVSSWVFAAKLEGFGTGLFIRSVLKNSVLAASTCIFALGGALVGSIIG 65

Query: 65  AMKGQTTETGFLHGAGIGAVAGAITALQLLESAADGESLSKAALLSSLVNGKVFMEWVSP 124
           AMKGQTTETGFL G+G+GAVAGAITA+QLLES  +GE LSK ALL SL+NGKVFMEWV P
Sbjct: 66  AMKGQTTETGFLRGSGVGAVAGAITAVQLLESITNGEPLSKVALLHSLLNGKVFMEWVGP 125

Query: 125 AVLKAYQWQVSNHKMKFLEFIKSSHGMLNLNRRFFFLFQVSTLETAYREVSDVYDVTGVK 184
           AVLKAYQWQV+                               LET YRE+SD+YD + V+
Sbjct: 126 AVLKAYQWQVN------------------------------ALETTYREISDIYDTSEVR 155

Query: 185 GLSEDMIQKLPECALHSEELI------QLDNEIGCSICLEKF----EEGDSARKLPSCGH 234
           GLSED I+KLPEC   S+  I       L     C    +KF    ++GDS RKLP CGH
Sbjct: 156 GLSEDCIKKLPECIFKSDSNIVEQCCPALVVLFACRFLTKKFCQDFKDGDSMRKLPRCGH 215

Query: 235 CFHSECVDKWLTRNGSCPVCRECVCKDTD 263
            FH  C+DKWL  NGSCP CR  VC D D
Sbjct: 216 YFHLSCLDKWLATNGSCPNCRNSVCDDND 244

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359494038|ref|XP_002278195.2| PREDICTED: NEP1-interacting protein 2-like [Vitis vinifera]

 Score =  221 bits (562), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 120/224 (53%), Positives = 142/224 (63%), Gaps = 45/224 (20%)

Query: 40  MKRVLYAALTCIFALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQLLESAAD 99
           MK  + AA TCIFALGGA+VGTI GA+KGQTTETGF  G+GIGAV GAITALQLLES A 
Sbjct: 1   MKSAVLAAFTCIFALGGAVVGTITGAIKGQTTETGFFRGSGIGAVTGAITALQLLESVAA 60

Query: 100 GESLSKAALLSSLVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIKSSHGMLNLNRRFF 159
           GESLSKAALL SLVNGKVFMEW                                      
Sbjct: 61  GESLSKAALLCSLVNGKVFMEW-------------------------------------- 82

Query: 160 FLFQVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECAL-HSEELIQLDNEIGCSICLE 218
               +STLET Y E  D Y+++G KGL  + I+KLP+    HS    ++ NEI C+ICL+
Sbjct: 83  ----ISTLETNYGETEDFYNISGAKGLPHNFIEKLPKSNFCHSNA--EMYNEISCTICLQ 136

Query: 219 KFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDT 262
            F++G+  R LPSC H FH ECVD+WLT +GSCP+CR+ VC DT
Sbjct: 137 DFKDGEMTRGLPSCRHYFHMECVDQWLTLHGSCPMCRKDVCMDT 180

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255583605|ref|XP_002532558.1| RING-H2 finger protein ATL2B, putative [Ricinus communis] gi|223527713|gb|EEF29819.1| RING-H2 finger protein ATL2B, putative [Ricinus communis]

 Score =  214 bits (544), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 114/222 (51%), Positives = 143/222 (64%), Gaps = 33/222 (14%)

Query: 1   MSKGLVSEVIKMSLTCKETVSLWLFATMCAFGTGV-LIRAMKRVLYAALTCIFALGGAIV 59
           M+K L S +IK+ L C+E VS+ +   M  FGTG  +IR +K+ ++AA TCI ALGGA+V
Sbjct: 1   MTKWLFSGIIKVFLRCQEAVSMLVLGAMEGFGTGFFIIRMIKKAVFAAFTCILALGGAMV 60

Query: 60  GTIFGAMKGQTTETGFLHGAGIGAVAGAITALQLLESAADGESLSKAALLSSLVNGKVFM 119
           GT+ GAMKGQTTETGF+ G+GIGAVAGA+TA+QLLES ADGE  SK AL  SL+NGKVFM
Sbjct: 61  GTVIGAMKGQTTETGFIRGSGIGAVAGAVTAVQLLESVADGEPFSKVALFYSLMNGKVFM 120

Query: 120 EWVSPAVLKAYQWQVSNHKMKFLEFIKSSHGMLNLNRRFFFLFQVSTLETAYREVSDVYD 179
           EWVSPAVLKAYQW                              Q+S LET YRE+SD+ D
Sbjct: 121 EWVSPAVLKAYQW------------------------------QMSALETTYREISDILD 150

Query: 180 VTGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFE 221
            +G +GLSE++IQ LP+    S       N   CS+ +  F+
Sbjct: 151 TSGNRGLSENLIQNLPDFTFQSSNTYVNGNT--CSLAMSGFQ 190

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351727337|ref|NP_001237925.1| uncharacterized protein LOC100305612 [Glycine max] gi|255626083|gb|ACU13386.1| unknown [Glycine max]

 Score =  212 bits (540), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 108/225 (48%), Positives = 141/225 (62%), Gaps = 28/225 (12%)

Query: 34  GVLIRAMKRVLYAALTCIFALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQL 93
           G+  + +K+VL+A  TCI ALGG IVGTI G +KGQTTE GFL GAG GA+ GAI AL+L
Sbjct: 37  GLFTKIIKKVLFALFTCILALGGPIVGTIAGGIKGQTTEAGFLDGAGKGAITGAIAALEL 96

Query: 94  LESAADGESLSKAALLSSLVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIKSSHGMLN 153
           +   A  E +SK ALLSSL+NGK+FMEW+ PAV K YQ  V+                  
Sbjct: 97  INFDAFDEPISKVALLSSLLNGKIFMEWICPAVAKLYQLHVT------------------ 138

Query: 154 LNRRFFFLFQVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECALHSEELIQLDNEIGC 213
                     V+TLET  +EVSD+YD+ GV+G+  ++I KLP    +S ++++  N   C
Sbjct: 139 ----------VNTLETICQEVSDIYDIRGVRGIPHNVILKLPFQPFNSRKMLKSYNMSCC 188

Query: 214 SICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECV 258
           SIC + FE+G+  R LP C H FH EC+DKWL + GSCP+ R  V
Sbjct: 189 SICFQDFEDGELVRILPKCDHLFHLECIDKWLVQQGSCPMYRTYV 233

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357494513|ref|XP_003617545.1| RING finger family protein [Medicago truncatula] gi|355518880|gb|AET00504.1| RING finger family protein [Medicago truncatula]

 Score =  192 bits (489), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 111/224 (49%), Positives = 142/224 (63%), Gaps = 31/224 (13%)

Query: 36  LIRAMKRVLYAALTCIFALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQLLE 95
            ++AM+R L+AA TCI ALGG+I+GTI GA+KGQTTETGFL GAG GA+AGAI A++L+ 
Sbjct: 37  FMKAMERFLFAAFTCILALGGSIIGTIAGAIKGQTTETGFLDGAGKGAIAGAIAAIELMS 96

Query: 96  SAADGESLSKAALLSSLVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIKSSHGMLNLN 155
            A+  E  SK ALL SL+NGKVFMEW+ P V +AY                         
Sbjct: 97  FASVAEPFSKVALLRSLLNGKVFMEWICPTVAQAY------------------------- 131

Query: 156 RRFFFLFQVSTLETAYREV-SDVYDVTGVKGLSEDMIQKLPECALHSEELIQLDNEIGCS 214
                LF +++LETAY  V SD+YD  GVKG+ +  I KLP     S ++++L NE  CS
Sbjct: 132 -----LFYINSLETAYGAVLSDIYDDLGVKGMQQSCIMKLPCQQFSSNKMMKLYNESCCS 186

Query: 215 ICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECV 258
           IC++ FE  +  R LP C H FH EC+DKWL + GSCP+CR  V
Sbjct: 187 ICIQDFENEELVRLLPKCSHIFHLECIDKWLVQQGSCPICRTYV 230

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357494507|ref|XP_003617542.1| RING finger family protein [Medicago truncatula] gi|355518877|gb|AET00501.1| RING finger family protein [Medicago truncatula]

 Score =  180 bits (457), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 115/255 (45%), Positives = 148/255 (58%), Gaps = 39/255 (15%)

Query: 16  CKETVSLWLFATMCAFGTGVL---IRAMKRVLYAALTCIFALGGAIVGTIFGAMKGQTTE 72
           CKE +SL     + A G  V    +  +++VL+A  TCI ALGG+I+GTI GA+KGQTTE
Sbjct: 24  CKEVLSL---KALNAIGCSVFEQFMNVLEKVLFATFTCILALGGSIIGTITGAIKGQTTE 80

Query: 73  TGFLHGAGIGAVAGAITALQLLESA--ADGESLSKAALLSSLVNGKVFMEWVSPAVLKAY 130
            GFL GAG GA+AGAI A++ +  A  A GE  SK ALL SL+NGKVF EW+ P V +AY
Sbjct: 81  VGFLDGAGKGAIAGAIAAIEFMSFAYVAVGEPFSKVALLRSLLNGKVFTEWICPTVAEAY 140

Query: 131 QWQVSNHKMKFLEFIKSSHGMLNLNRRFFFLFQVSTLETAYREV-SDVYDVTGVKGLSED 189
                                         LF +++LET Y  V SD+YD  GVKG+   
Sbjct: 141 ------------------------------LFYINSLETGYEGVLSDMYDNMGVKGMPHS 170

Query: 190 MIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG 249
            I KLP     S ++++L NE  CSICL+ FE  +  R LP C H FH EC+DKWL + G
Sbjct: 171 CIMKLPFQQFCSNKMMKLYNESCCSICLQDFENEELVRILPKCSHIFHLECIDKWLIQQG 230

Query: 250 SCPVCRECVCKDTDT 264
           SCP+CR  V    ++
Sbjct: 231 SCPICRTYVVDHINS 245

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356524261|ref|XP_003530748.1| PREDICTED: NEP1-interacting protein 2-like [Glycine max]

 Score =  176 bits (447), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 105/249 (42%), Positives = 138/249 (55%), Gaps = 36/249 (14%)

Query: 7   SEVIKMSLTCKETVSLWLFATMCAFGTGVLIRAMKRVLYAALTCIFALGGAIVGTIFGAM 66
           S ++  +  CKE  SL + A    +   + I+    V+ A  TCI ALGG+I+G I GA+
Sbjct: 6   SGIMGATTWCKEVFSLRVLAGSVGYAVDLFIK----VVIAEFTCILALGGSIMGIIAGAI 61

Query: 67  KGQTTETGFLHGAGIGAVAGAITALQLLESAADGESLSKAALLSSLVNGKVFMEWVSPAV 126
           KG T   GFL GA  GAV GAI AL+L   AA  E LSK ALL SL+NGK+F+EW+ PAV
Sbjct: 62  KGHTRGAGFLDGACKGAVTGAIAALELPNIAACDEPLSKVALLRSLLNGKIFVEWICPAV 121

Query: 127 LKAYQWQVSNHKMKFLEFIKSSHGMLNLNRRFFFLFQVSTLETAYREVSDVYDVTGVKGL 186
            +AYQ  V          IKS                       Y +  D+     VKG+
Sbjct: 122 AQAYQCHVR---------IKSD---------------------IYND--DIVRGITVKGM 149

Query: 187 SEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT 246
           + ++IQKLP    +S ++ +L N+  CSIC + FE  +  R LP CGH FHS C+DKWL 
Sbjct: 150 AWNIIQKLPVQQFNSSKMFKLYNDSCCSICFQDFEYEEFVRTLPKCGHFFHSVCIDKWLV 209

Query: 247 RNGSCPVCR 255
           + GSCP+CR
Sbjct: 210 QQGSCPMCR 218

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356569798|ref|XP_003553083.1| PREDICTED: NEP1-interacting protein 2-like [Glycine max]

 Score =  162 bits (409), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 125/240 (52%), Gaps = 50/240 (20%)

Query: 16  CKETVSLWLFATMCAFGTGVLIRAMKRVLYAALTCIFALGGAIVGTIFGAMKGQTTETGF 75
           CKE  S+ + A    +   + I+    V+ A  TCI ALGG+IVG I GA+KG T   GF
Sbjct: 15  CKEVFSMRVLAGSGGYAVDLFIK----VVIAEFTCILALGGSIVGIIAGAIKGHTRGAGF 70

Query: 76  LHGAGIGAVAGAITALQLLESAADGESLSKAALLSSLVNGKVFMEWVSPAVLKAYQWQVS 135
           L GA  GAV GAI AL+LL  AA  E LSK ALL SL+NGK+FMEW+ PAV +AY   V 
Sbjct: 71  LDGACKGAVTGAIAALELLNIAAYDEPLSKVALLRSLLNGKLFMEWICPAVAQAYHCHVR 130

Query: 136 NHKMKFLEFIKSSHGMLNLNRRFFFLFQVSTLETAYREVSDVYDVTGVKGLSEDMIQKLP 195
                                                          ++G++ ++IQK P
Sbjct: 131 I----------------------------------------------IEGVAWNIIQKPP 144

Query: 196 ECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
               +S ++ +L N+  CSIC + FE+ +  R LP CGH FH  C+DKWL +  SCP+CR
Sbjct: 145 VQQFNSSKMFKLYNDSCCSICFQDFEDEEFVRTLPKCGHFFHLVCIDKWLVQRRSCPMCR 204

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116830763|gb|ABK28339.1| unknown [Arabidopsis thaliana]

 Score =  158 bits (399), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 95/261 (36%), Positives = 131/261 (50%), Gaps = 43/261 (16%)

Query: 6   VSEVIKMSLTCKETVSLWLFATMCAFGTGVLIRAMKRVLYAALTCIFALGGAIVGTIFGA 65
           +S++I +  T    VS W+   +         R +KR L  +   I A    +V  I GA
Sbjct: 3   ISKMILLKFT--YVVSFWITCVIFKMS-----RTIKRALLGSFIFILASASVVVAAIVGA 55

Query: 66  MKGQTTETGFLHGAGIGAVAGAITALQLLESAADG-ESLSKAALLSSLVNGKVFMEWVSP 124
           ++G TT+ GFL G+ +G VAG ITA+QL        + LSK ALL  +VNGK  M  V P
Sbjct: 56  IEGHTTDIGFLQGSVLGVVAGVITAVQLFGPVLHSDQPLSKVALLRRVVNGKAIMGLVRP 115

Query: 125 AVLKAYQWQVSNHKMKFLEFIKSSHGMLNLNRRFFFLFQVSTLETAYREVSDVYDVTG-V 183
            VLKAYQWQ+                                L+T+Y E S++YD     
Sbjct: 116 FVLKAYQWQII------------------------------ALDTSYMESSNLYDFNHEK 145

Query: 184 KGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDK 243
           KGLS+  IQ +P     SE       +  CSICL+ +EEG+  RKL  CGH FH  C+D+
Sbjct: 146 KGLSKSSIQNIPMFYNRSEH----QTKSSCSICLQDWEEGEVGRKLARCGHTFHMNCIDE 201

Query: 244 WLTRNGSCPVCRECVCKDTDT 264
           WL R  +CP+CR+ +  +T +
Sbjct: 202 WLLRQETCPICRDHLSHNTTS 222

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	265
TAIR|locus:4010713762	223	AT3G20395 [Arabidopsis thalian	0.362	0.430	0.425	4.9e-33
TAIR|locus:2125364	236	AT4G35840 [Arabidopsis thalian	0.350	0.394	0.382	2e-28
TAIR|locus:2019110	223	AT1G74410 [Arabidopsis thalian	0.362	0.430	0.444	2.5e-26
TAIR|locus:2156867	245	AT5G66070 [Arabidopsis thalian	0.788	0.853	0.296	4.6e-25
TAIR|locus:2011686	185	ATL8 [Arabidopsis thaliana (ta	0.271	0.389	0.410	8.4e-16
UNIPROTKB|Q9LRB7	325	EL5.1 "E3 ubiquitin-protein li	0.275	0.224	0.397	2.1e-14
TAIR|locus:2074678	158	AT3G11110 [Arabidopsis thalian	0.298	0.5	0.425	4.9e-14
TAIR|locus:2124695	236	AT4G10150 [Arabidopsis thalian	0.271	0.305	0.413	7.9e-14
TAIR|locus:2825708	197	AT1G20823 [Arabidopsis thalian	0.271	0.365	0.438	1.6e-13
TAIR|locus:2165735	163	AT5G42200 [Arabidopsis thalian	0.305	0.496	0.428	2.7e-13

TAIR|locus:4010713762 AT3G20395 [Arabidopsis thaliana (taxid:3702)]

 Score = 222 (83.2 bits), Expect = 4.9e-33, Sum P(2) = 4.9e-33
 Identities = 43/101 (42%), Positives = 61/101 (60%)

Query:   163 QVSTLETAYREVSDVYDVTGVK-GLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFE 221
             Q+  L+T+Y E S++YD    K GLS+  IQ +P     SE       +  CSICL+ +E
Sbjct:   124 QIIALDTSYMESSNLYDFNHEKKGLSKSSIQNIPMFYNRSEH----QTKSSCSICLQDWE 179

Query:   222 EGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDT 262
             EG+  RKL  CGH FH  C+D+WL R  +CP+CR+ +  +T
Sbjct:   180 EGEVGRKLARCGHTFHMNCIDEWLLRQETCPICRDHLSHNT 220

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2125364 AT4G35840 [Arabidopsis thaliana (taxid:3702)]

 Score = 231 (86.4 bits), Expect = 2.0e-28, Sum P(2) = 2.0e-28
 Identities = 36/94 (38%), Positives = 61/94 (64%)

Query:   163 QVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECALHSEELIQLD-NEIGCSICLEKFE 221
             Q+  +++ + E+S ++D  G KGL+ D++ K+P+  +  +  +    N+  CS+CL+ F+
Sbjct:   140 QMGAVDSTFEELSSIFDTGGSKGLTGDLVDKIPKIKITGKNNLDASGNKDSCSVCLQDFQ 199

Query:   222 EGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
              G++ R LP C H FH  C+D WL R+GSCP+CR
Sbjct:   200 LGETVRSLPHCHHMFHLPCIDNWLFRHGSCPMCR 233

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2019110 AT1G74410 [Arabidopsis thaliana (taxid:3702)]

 Score = 230 (86.0 bits), Expect = 2.5e-26, Sum P(2) = 2.5e-26
 Identities = 44/99 (44%), Positives = 61/99 (61%)

Query:   163 QVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEE 222
             Q+   + +Y E  DVY     +GLS D ++KLP C + S E+++      C+ICL+  + 
Sbjct:   128 QLRISDVSYEEREDVYGELEARGLSGDSLRKLP-CYIMSSEMVRRQ-VTHCTICLQDIKT 185

Query:   223 GDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD 261
             G+  R LP C H FH  CVDKWL R+GSCP+CR+ V KD
Sbjct:   186 GEITRSLPKCDHTFHLVCVDKWLIRHGSCPICRQAV-KD 223

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

GO:0010200 "response to chitin" evidence=IEP

TAIR|locus:2156867 AT5G66070 [Arabidopsis thaliana (taxid:3702)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 68/229 (29%), Positives = 120/229 (52%)

Query:    37 IRAMKRVLYAAL-TCIFALGGAIVGTIFGAMKGQTTETGFLHXXXXXXXXXXXTALQLLE 95
             + A+   L++AL T  FAL G ++G + GA+ GQ TE+GF+             ++++ E
Sbjct:    24 VSALLANLFSALFTFFFALVGTLLGALTGALIGQETESGFIRGAAVGAISGAVFSIEVFE 83

Query:    96 SA-----AD----GEXXXXXXXXXXXVNGKVFMEWVSPAVLKAYQWQVSNHKMKFLEFIK 146
             S+     +D    G            ++G++  E + PA+L A Q QV   ++ FL F  
Sbjct:    84 SSLLLWQSDESGIGCLLYLIDVIASLLSGRLVRERIGPAMLSAVQSQV---QLPFLFFDA 140

Query:   147 SSHGMXXXXXXXXXXXQVSTLETAYREVSDVYDVTGVKGLSEDMIQKLPECALHSEELIQ 206
             S               Q+  +E+ +++ +D++D    KGL+ D + ++P+  + ++   +
Sbjct:   141 S---FIILLNFCINNKQMGAVESQFQDHTDIFDTAISKGLTGDSLNRIPKVRI-TDTSPE 196

Query:   207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
             +   + CS+CL+ F+ G++ R LP C H FH  C+DKWL R+ SCP+CR
Sbjct:   197 I---VSCSVCLQDFQVGETVRSLPHCHHMFHLPCIDKWLRRHASCPLCR 242

GO:0005739 "mitochondrion" evidence=ISM

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

GO:0010200 "response to chitin" evidence=IEP;RCA

GO:0002679 "respiratory burst involved in defense response" evidence=RCA

GO:0035556 "intracellular signal transduction" evidence=RCA

TAIR|locus:2011686 ATL8 [Arabidopsis thaliana (taxid:3702)]

 Score = 173 (66.0 bits), Expect = 8.4e-16, Sum P(2) = 8.4e-16
 Identities = 30/73 (41%), Positives = 44/73 (60%)

Query:   184 KGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDK 243
             KGL + +++ LP+   +S +    +  + C+ICL +F  GD  R LP CGH FH  C+D 
Sbjct:    76 KGLKKKVLRSLPKLT-YSPDSPPAEKLVECAICLTEFAAGDELRVLPQCGHGFHVSCIDT 134

Query:   244 WLTRNGSCPVCRE 256
             WL  + SCP CR+
Sbjct:   135 WLGSHSSCPSCRQ 147

GO:0005634 "nucleus" evidence=ISM

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

GO:0009744 "response to sucrose stimulus" evidence=RCA

GO:0009750 "response to fructose stimulus" evidence=RCA

GO:0009855 "determination of bilateral symmetry" evidence=RCA

GO:0009944 "polarity specification of adaxial/abaxial axis" evidence=RCA

GO:0010014 "meristem initiation" evidence=RCA

GO:0010075 "regulation of meristem growth" evidence=RCA

UNIPROTKB|Q9LRB7 EL5.1 "E3 ubiquitin-protein ligase EL5" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 170 (64.9 bits), Expect = 2.1e-14, Sum P(2) = 2.1e-14
 Identities = 29/73 (39%), Positives = 45/73 (61%)

Query:   183 VKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVD 242
             ++ L   +  +    A   EE  + D+ + C++CL + E+G+ AR LP CGH FH+ECVD
Sbjct:   104 LRSLPVTVYSRSTAAAAAKEEEEEDDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVD 163

Query:   243 KWLTRNGSCPVCR 255
              WL  + +CP+CR
Sbjct:   164 MWLGSHSTCPLCR 176

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

GO:0005886 "plasma membrane" evidence=IDA

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0048364 "root development" evidence=IMP

GO:0051301 "cell division" evidence=IMP

TAIR|locus:2074678 AT3G11110 [Arabidopsis thaliana (taxid:3702)]

 Score = 181 (68.8 bits), Expect = 4.9e-14, P = 4.9e-14
 Identities = 34/80 (42%), Positives = 45/80 (56%)

Query:   185 GLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKW 244
             GL    I+ LP   L   E  + + E  C ICL  FEEG+  + LP C HC+H ECVD+W
Sbjct:    80 GLDPAEIRSLP-VVLCRRERAEEEEEKECCICLGGFEEGEKMKVLPPCSHCYHCECVDRW 138

Query:   245 LTRNGSCPVCRECVCKDTDT 264
             L    SCP+CR  +  D+ +
Sbjct:   139 LKTESSCPLCRVSIRVDSSS 158

GO:0005634 "nucleus" evidence=ISM

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

GO:0009741 "response to brassinosteroid stimulus" evidence=RCA

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

 Score = 179 (68.1 bits), Expect = 7.9e-14, P = 7.9e-14
 Identities = 31/75 (41%), Positives = 49/75 (65%)

Query:   181 TGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSEC 240
             T   GLS+D+ + LP   ++ E  I  D++  CS+CL  ++  +  +++PSCGH FH EC
Sbjct:    82 TAELGLSKDIREMLP-VVIYKESFIVKDSQ--CSVCLGDYQAEEKLQQMPSCGHTFHMEC 138

Query:   241 VDKWLTRNGSCPVCR 255
             +D WLT + +CP+CR
Sbjct:   139 IDLWLTSHTTCPLCR 153

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2825708 AT1G20823 [Arabidopsis thaliana (taxid:3702)]

 Score = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 32/73 (43%), Positives = 43/73 (58%)

Query:   184 KGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDK 243
             KGL + ++Q LP+    S E  + +    C+ICL +F  GD  R LP CGH FH  C+D 
Sbjct:    83 KGLKKKVLQSLPKLTF-SPESPESEKFAECAICLAEFSAGDELRVLPQCGHGFHVACIDT 141

Query:   244 WLTRNGSCPVCRE 256
             WL  + SCP CR+
Sbjct:   142 WLGSHSSCPSCRQ 154

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

GO:0009507 "chloroplast" evidence=ISM

GO:0010200 "response to chitin" evidence=IEP

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

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 36/84 (42%), Positives = 46/84 (54%)

Query:   172 REVSDVYDVTGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPS 231
             R    V  VTG KGLS   ++K+P+  L   EL  +     C++CLE  E G S R +P 
Sbjct:    66 RFAEPVKPVTG-KGLSVLELEKIPK--LTGRELAVIARSTECAVCLEDIESGQSTRLVPG 122

Query:   232 CGHCFHSECVDKWLTRNGSCPVCR 255
             C H FH  C D WL+ +  CPVCR
Sbjct:   123 CNHGFHQLCADTWLSNHTVCPVCR 146

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

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

GO:0016567 "protein ubiquitination" 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

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00027325001 SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (220 aa) (Vitis vinifera)

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	265
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	3e-16
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	5e-12
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	4e-09
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	1e-08
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	1e-08
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	1e-07
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	3e-07
smart00184	40	smart00184, RING, Ring finger	4e-07
COG5432	391	COG5432, RAD18, RING-finger-containing E3 ubiquiti	6e-06
TIGR00599	397	TIGR00599, rad18, DNA repair protein rad18	7e-05
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	1e-04
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	2e-04
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	3e-04
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	0.001

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

 Score = 70.1 bits (172), Expect = 3e-16
 Identities = 24/43 (55%), Positives = 31/43 (72%), Gaps = 1/43 (2%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
           C ICL++FE G+    LP CGH FH EC+DKWL  + +CP+CR
Sbjct: 3   CPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLCR 44

Length = 46

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

 Score = 59.0 bits (143), Expect = 5e-12
 Identities = 21/47 (44%), Positives = 27/47 (57%), Gaps = 4/47 (8%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWL-TRNGSCPVCRECV 258
           C ICLE+F E      L  CGH F   C+DKWL +   +CP+CR  +
Sbjct: 2   CPICLEEFRE---PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 56.2 bits (135), Expect = 4e-09
 Identities = 26/63 (41%), Positives = 31/63 (49%), Gaps = 10/63 (15%)

Query: 202 EELIQLDNE--------IGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR-NGSCP 252
             L  L  E        + C+IC+  F + D  R LP C H FH  CVDKWL   +  CP
Sbjct: 307 GSLKPLSIERAVEADKGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCP 365

Query: 253 VCR 255
           VCR
Sbjct: 366 VCR 368

Length = 374

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

 Score = 50.5 bits (121), Expect = 1e-08
 Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 9/52 (17%)

Query: 213 CSICLEKFEEGDSARKLPS---------CGHCFHSECVDKWLTRNGSCPVCR 255
           C+IC   F+      K P          CGH FH  C+ +WL    +CP+CR
Sbjct: 22  CAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 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|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger)

 Score = 49.8 bits (119), Expect = 1e-08
 Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 3/44 (6%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRE 256
           C ICL+   +      L  CGH F  EC+ ++L +   CP+CR 
Sbjct: 5   CPICLDLLRD---PVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 51.5 bits (123), Expect = 1e-07
 Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 12/67 (17%)

Query: 206 QLDNEIG-CSICLEKFEEGD----------SARKLPSCGHCFHSECVDKWLTRNGSCPVC 254
           QL N    C+IC+++    D          + ++LP CGH  H  C+  WL R  +CP+C
Sbjct: 282 QLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPIC 340

Query: 255 RECVCKD 261
           R  V  D
Sbjct: 341 RRPVIFD 347

Length = 491

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

 Score = 49.8 bits (119), Expect = 3e-07
 Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 4/58 (6%)

Query: 202 EELIQLDNEIGCSICLEKFEEGDSARK----LPSCGHCFHSECVDKWLTRNGSCPVCR 255
           E+L     +  C+IC+EK  + +        L +C H F  EC+D W     +CPVCR
Sbjct: 166 EKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCR 223

Length = 238

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

 Score = 45.2 bits (107), Expect = 4e-07
 Identities = 19/43 (44%), Positives = 26/43 (60%), Gaps = 4/43 (9%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWL-TRNGSCPVC 254
           C ICLE++ +      LP CGH F   C+ KWL + N +CP+C
Sbjct: 1   CPICLEEYLK--DPVILP-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|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

 Score = 46.6 bits (110), Expect = 6e-06
 Identities = 21/56 (37%), Positives = 27/56 (48%), Gaps = 4/56 (7%)

Query: 204 LIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVC 259
           L  LD+ + C IC  +     S     +CGH F S C+ + L     CPVCRE  C
Sbjct: 19  LKGLDSMLRCRICDCRI----SIPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPC 70

Length = 391

>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18

 Score = 43.1 bits (101), Expect = 7e-05
 Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 4/52 (7%)

Query: 204 LIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
           L  LD  + C IC + F+       L SC H F S C+ + L+    CP+CR
Sbjct: 20  LYPLDTSLRCHICKDFFD----VPVLTSCSHTFCSLCIRRCLSNQPKCPLCR 67

All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 397

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

 Score = 39.4 bits (92), Expect = 1e-04
 Identities = 19/47 (40%), Positives = 22/47 (46%), Gaps = 5/47 (10%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWL---TRNGSCPVCRE 256
           C  C  KF   D       C H FH  C+ KWL   T  G CP+CR+
Sbjct: 35  CPQC--KFPGDDCPLVWGKCKHNFHMHCILKWLATETSKGLCPMCRQ 79

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

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

 Score = 37.8 bits (88), Expect = 2e-04
 Identities = 19/43 (44%), Positives = 28/43 (65%), Gaps = 4/43 (9%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWL-TRNGSCPVC 254
           C ICLE+ ++  +   LP CGH F S+C+  WL + N +CP+C
Sbjct: 1   CPICLEEPKDPVTI--LP-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|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

 Score = 41.6 bits (97), Expect = 3e-04
 Identities = 19/50 (38%), Positives = 25/50 (50%), Gaps = 9/50 (18%)

Query: 213  CSICLEKFEEGDSARKLPS--CGHC---FHSECVDKWLTRNGS--CPVCR 255
            C+IC    +  D  R LPS  C  C   FH+ C+ KW   +    CP+CR
Sbjct: 1472 CAICYSVLDMVD--RSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCR 1519

Length = 1525

>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 = 37.1 bits (86), Expect = 0.001
 Identities = 11/25 (44%), Positives = 15/25 (60%)

Query: 232 CGHCFHSECVDKWLTRNGSCPVCRE 256
           C H FH  C+ +WL   G CP+ R+
Sbjct: 54  CNHAFHDHCIYRWLDTKGVCPLDRQ 78

Length = 88

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	265
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.73
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.52
PHA02929	238	N1R/p28-like protein; Provisional	99.42
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.25
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.24
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.23
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.1
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.05
PHA02926	242	zinc finger-like protein; Provisional	99.0
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.99
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	98.99
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.97
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.94
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.9
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.89
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.85
PF14634	44	zf-RING_5: zinc-RING finger domain	98.85
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.8
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.8
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.77
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.67
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.58
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.46
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.43
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.39
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.39
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.29
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.28
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.28
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.27
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.25
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.23
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.23
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.19
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.17
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.14
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.1
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.09
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.08
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.05
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.99
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.95
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.89
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	97.88
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.64
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.51
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.48
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.22
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.22
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.06
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.99
KOG1002	791	consensus Nucleotide excision repair protein RAD16	96.99
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.84
KOG2660	331	consensus Locus-specific chromosome binding protei	96.76
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.73
COG5152	259	Uncharacterized conserved protein, contains RING a	96.72
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.72
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.7
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	96.69
PF13441	45	Gly-zipper_YMGG: YMGG-like Gly-zipper	96.68
PF13436	118	Gly-zipper_OmpA: Glycine-zipper containing OmpA-li	96.64
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	96.54
PF13488	46	Gly-zipper_Omp: Glycine zipper	96.45
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.33
PHA02862	156	5L protein; Provisional	96.27
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	96.25
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	96.16
KOG3039	303	consensus Uncharacterized conserved protein [Funct	96.16
PF13441	45	Gly-zipper_YMGG: YMGG-like Gly-zipper	96.15
PF05433	42	Rick_17kDa_Anti: Glycine zipper 2TM domain; InterP	96.07
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.04
PHA03096	284	p28-like protein; Provisional	96.02
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.96
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	95.9
PHA02825	162	LAP/PHD finger-like protein; Provisional	95.67
PRK10510	219	putative outer membrane lipoprotein; Provisional	95.65
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	95.63
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	95.36
PF13488	46	Gly-zipper_Omp: Glycine zipper	95.33
PF13436	118	Gly-zipper_OmpA: Glycine-zipper containing OmpA-li	95.29
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	95.21
COG5236	493	Uncharacterized conserved protein, contains RING Z	95.18
KOG1940	276	consensus Zn-finger protein [General function pred	95.18
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	95.18
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	95.14
COG5175	480	MOT2 Transcriptional repressor [Transcription]	94.83
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	94.83
KOG3002	299	consensus Zn finger protein [General function pred	94.63
COG5222	427	Uncharacterized conserved protein, contains RING Z	94.61
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	94.31
PF04641	260	Rtf2: Rtf2 RING-finger	94.29
PRK10540	72	lipoprotein; Provisional	93.65
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	93.15
PRK11280	170	hypothetical protein; Provisional	93.0
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	92.96
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	92.72
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	92.6
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	92.29
KOG0298	1394	consensus DEAD box-containing helicase-like transc	92.27
KOG1001	674	consensus Helicase-like transcription factor HLTF/	92.2
PRK10540	72	lipoprotein; Provisional	92.08
TIGR03789	239	pdsO proteobacterial sortase system OmpA family pr	91.52
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	91.51
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	91.48
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	91.25
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	91.08
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	90.81
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	90.51
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	90.29
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	89.99
COG4803	170	Predicted membrane protein [Function unknown]	88.55
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	87.98
PF06897	102	DUF1269: Protein of unknown function (DUF1269); In	87.93
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	87.73
KOG3053	293	consensus Uncharacterized conserved protein [Funct	87.68
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	87.42
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	87.38
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	86.45
KOG1609	323	consensus Protein involved in mRNA turnover and st	86.02
KOG3579	352	consensus Predicted E3 ubiquitin ligase [Posttrans	85.65
PF05433	42	Rick_17kDa_Anti: Glycine zipper 2TM domain; InterP	85.28
PF06897	102	DUF1269: Protein of unknown function (DUF1269); In	84.95
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	84.82
KOG0269	839	consensus WD40 repeat-containing protein [Function	84.15
TIGR02865	764	spore_II_E stage II sporulation protein E. Stage I	83.36
TIGR00622	112	ssl1 transcription factor ssl1. This family is bas	83.13
KOG3113	293	consensus Uncharacterized conserved protein [Funct	83.07
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	82.23
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	82.09
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	81.72
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	81.49
KOG3899	381	consensus Uncharacterized conserved protein [Funct	81.22
PF05818	215	TraT: Enterobacterial TraT complement resistance p	80.98
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	80.82
PRK10510	219	putative outer membrane lipoprotein; Provisional	80.72
KOG2068	327	consensus MOT2 transcription factor [Transcription	80.54

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

Probab=99.73  E-value=6e-19  Score=163.44  Aligned_cols=80  Identities=36%  Similarity=0.796  Sum_probs=68.1

Q ss_pred             cCCCCCCHHHHhcCCcccccchhhhhcccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCC-ccccccccc
Q 024603          181 TGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGS-CPVCRECVC  259 (265)
Q Consensus       181 ~~~~gls~~~i~~lp~~~~~~~~~~~~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~s-CPvCR~~v~  259 (265)
                      .+.+.+.++.++++|..+++.....+  ....|+||+|+|+.++++|.|| |+|.||..||++||.++++ ||+||+++.
T Consensus       202 ~~~~r~~k~~l~~~p~~~f~~~~~~~--~~~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~  278 (348)
T KOG4628|consen  202 LRRNRLIKRLLKKLPVRTFTKGDDED--ATDTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIR  278 (348)
T ss_pred             hhhhhhHHHHHhhCCcEEeccccccC--CCceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCC
Confidence            35678899999999999988763322  1269999999999999999999 9999999999999998865 999999987


Q ss_pred             cCCC
Q 024603          260 KDTD  263 (265)
Q Consensus       260 ~~~~  263 (265)
                      +..+
T Consensus       279 ~~~~  282 (348)
T KOG4628|consen  279 TDSG  282 (348)
T ss_pred             CCCC
Confidence            6543

>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=99.52  E-value=3.5e-15  Score=99.26  Aligned_cols=44  Identities=61%  Similarity=1.427  Sum_probs=40.5

Q ss_pred             cccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccc
Q 024603          211 IGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR  255 (265)
Q Consensus       211 ~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR  255 (265)
                      ++|+||++++..++.+..+| |+|.||.+|+.+|++++.+||+||
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            37999999999999999998 999999999999999999999998

...

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.42  E-value=1.1e-13  Score=123.26  Aligned_cols=77  Identities=27%  Similarity=0.624  Sum_probs=61.4

Q ss_pred             CCCCHHHHhcCCcccccchhhhhcccCcccccccccccCCCe----eeecCCCCcccchhhHHHhhcCCCCccccccccc
Q 024603          184 KGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDS----ARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVC  259 (265)
Q Consensus       184 ~gls~~~i~~lp~~~~~~~~~~~~~~~~~C~ICle~~~~~~~----~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~  259 (265)
                      ++.+.+.++++|......+...+...+.+|+||++.+.+++.    ...++.|+|.||.+||.+|++.+.+||+||.++.
T Consensus       148 ~~~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~  227 (238)
T PHA02929        148 GKNYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI  227 (238)
T ss_pred             cchhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence            556889999999886555444345567899999999876542    2355569999999999999999999999999875


Q ss_pred             c
Q 024603          260 K  260 (265)
Q Consensus       260 ~  260 (265)
                      .
T Consensus       228 ~  228 (238)
T PHA02929        228 S  228 (238)
T ss_pred             E
Confidence            3

>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=99.25  E-value=4.9e-12  Score=93.28  Aligned_cols=45  Identities=40%  Similarity=0.996  Sum_probs=35.6

Q ss_pred             CcccccccccccCC----------CeeeecCCCCcccchhhHHHhhcCCCCccccc
Q 024603          210 EIGCSICLEKFEEG----------DSARKLPSCGHCFHSECVDKWLTRNGSCPVCR  255 (265)
Q Consensus       210 ~~~C~ICle~~~~~----------~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR  255 (265)
                      ++.|+||++.+.++          ..+... .|+|.||..||.+|++.+.+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~-~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWG-PCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEE-TTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEec-ccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            45699999999443          233334 4999999999999999999999998

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 ....

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

Probab=99.24  E-value=4.2e-12  Score=114.90  Aligned_cols=53  Identities=45%  Similarity=1.042  Sum_probs=47.9

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhc-CCCCcccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-RNGSCPVCRECVCK  260 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~-~~~sCPvCR~~v~~  260 (265)
                      .....+|+|||++|..+++++.+| |.|.||..|+++|+. .+..||+||.++++
T Consensus       320 a~~GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         320 ADKGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             cCCCceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            344589999999999999999999 999999999999998 56789999999875

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

Probab=99.23  E-value=2.3e-12  Score=119.32  Aligned_cols=70  Identities=29%  Similarity=0.797  Sum_probs=51.8

Q ss_pred             CCCCHHHHhcCCcccccchhhhhcccCccccccccccc-CC---------CeeeecCCCCcccchhhHHHhhcCCCCccc
Q 024603          184 KGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFE-EG---------DSARKLPSCGHCFHSECVDKWLTRNGSCPV  253 (265)
Q Consensus       184 ~gls~~~i~~lp~~~~~~~~~~~~~~~~~C~ICle~~~-~~---------~~~r~LP~CgH~FH~~CI~~WL~~~~sCPv  253 (265)
                      ....++.-+.+|..+...    -..++..|.||++++. .+         .+..+|| |||++|.+|++.|++++++||+
T Consensus       265 ~r~~kdl~~~~~t~t~eq----l~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPI  339 (491)
T COG5243         265 RRATKDLNAMYPTATEEQ----LTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPI  339 (491)
T ss_pred             HHHhhHHHhhcchhhhhh----hcCCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCc
Confidence            344555555555443221    1456789999999954 33         2446788 9999999999999999999999


Q ss_pred             ccccc
Q 024603          254 CRECV  258 (265)
Q Consensus       254 CR~~v  258 (265)
                      ||.++
T Consensus       340 Cr~p~  344 (491)
T COG5243         340 CRRPV  344 (491)
T ss_pred             ccCcc
Confidence            99995

>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=99.10  E-value=4.8e-11  Score=81.38  Aligned_cols=47  Identities=38%  Similarity=0.950  Sum_probs=39.4

Q ss_pred             CcccccccccccCCCeeeecCCCCcc-cchhhHHHhhcCCCCcccccccccc
Q 024603          210 EIGCSICLEKFEEGDSARKLPSCGHC-FHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r~LP~CgH~-FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      +..|.||++...+   ...+| |||. ||..|+.+|++.+..||+||+++.+
T Consensus         2 ~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~   49 (50)
T PF13920_consen    2 DEECPICFENPRD---VVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIES   49 (50)
T ss_dssp             HSB-TTTSSSBSS---EEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred             cCCCccCCccCCc---eEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence            5689999998665   56677 9999 9999999999999999999999864

...

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.05  E-value=9e-11  Score=101.06  Aligned_cols=52  Identities=31%  Similarity=0.784  Sum_probs=41.7

Q ss_pred             hcccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC----------------CCCccccccccccC
Q 024603          206 QLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR----------------NGSCPVCRECVCKD  261 (265)
Q Consensus       206 ~~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~----------------~~sCPvCR~~v~~~  261 (265)
                      +..++.+|+||++.+.++..   + .|||.||..||.+|+..                +..||+||.++...
T Consensus        14 ~~~~~~~CpICld~~~dPVv---T-~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~   81 (193)
T PLN03208         14 DSGGDFDCNICLDQVRDPVV---T-LCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEA   81 (193)
T ss_pred             cCCCccCCccCCCcCCCcEE---c-CCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChh
Confidence            34567899999999988644   4 49999999999999852                34799999998643

>PHA02926 zinc finger-like protein; Provisional

Probab=99.00  E-value=1.6e-10  Score=100.99  Aligned_cols=56  Identities=29%  Similarity=0.670  Sum_probs=43.1

Q ss_pred             hhhcccCcccccccccccCC-----CeeeecCCCCcccchhhHHHhhcCC------CCccccccccc
Q 024603          204 LIQLDNEIGCSICLEKFEEG-----DSARKLPSCGHCFHSECVDKWLTRN------GSCPVCRECVC  259 (265)
Q Consensus       204 ~~~~~~~~~C~ICle~~~~~-----~~~r~LP~CgH~FH~~CI~~WL~~~------~sCPvCR~~v~  259 (265)
                      ......+.+|+||+|...++     .....|+.|+|.||..||.+|.+.+      .+||+||....
T Consensus       164 ~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        164 VYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             HHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            33456689999999987442     2334677899999999999998743      45999999765

>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=98.99  E-value=3.1e-10  Score=73.46  Aligned_cols=39  Identities=46%  Similarity=1.217  Sum_probs=32.1

Q ss_pred             cccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccc
Q 024603          213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVC  254 (265)
Q Consensus       213 C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvC  254 (265)
                      |+||++.+.++  +..++ |||.||.+|+.+|++.+.+||+|
T Consensus         1 C~iC~~~~~~~--~~~~~-CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRDP--VVVTP-CGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SSE--EEECT-TSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccCc--CEECC-CCCchhHHHHHHHHHCcCCCcCC
Confidence            89999998883  23455 99999999999999999999998

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

Probab=98.99  E-value=2.3e-10  Score=103.14  Aligned_cols=51  Identities=31%  Similarity=0.805  Sum_probs=45.1

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccCC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDT  262 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~~  262 (265)
                      +.+..|.+||+..+++..+    .|||+||..||..|...+..||+||.+.++.+
T Consensus       237 ~a~~kC~LCLe~~~~pSaT----pCGHiFCWsCI~~w~~ek~eCPlCR~~~~psk  287 (293)
T KOG0317|consen  237 EATRKCSLCLENRSNPSAT----PCGHIFCWSCILEWCSEKAECPLCREKFQPSK  287 (293)
T ss_pred             CCCCceEEEecCCCCCCcC----cCcchHHHHHHHHHHccccCCCcccccCCCcc
Confidence            4568999999998887666    49999999999999999999999999987664

>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=98.97  E-value=3.6e-10  Score=73.46  Aligned_cols=44  Identities=48%  Similarity=1.190  Sum_probs=35.8

Q ss_pred             ccccccccccCCCeeeecCCCCcccchhhHHHhhcC-CCCcccccccc
Q 024603          212 GCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR-NGSCPVCRECV  258 (265)
Q Consensus       212 ~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~-~~sCPvCR~~v  258 (265)
                      +|+||++.+..  ..... .|+|.||..|+++|+.. +..||+||.++
T Consensus         1 ~C~iC~~~~~~--~~~~~-~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFRE--PVVLL-PCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhC--ceEec-CCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            59999999833  33334 49999999999999987 77899999864

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

Probab=98.94  E-value=5.2e-10  Score=84.28  Aligned_cols=52  Identities=35%  Similarity=0.745  Sum_probs=38.9

Q ss_pred             cCcccccccccccCCC--------e-eeecCCCCcccchhhHHHhhcC---CCCcccccccccc
Q 024603          209 NEIGCSICLEKFEEGD--------S-ARKLPSCGHCFHSECVDKWLTR---NGSCPVCRECVCK  260 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~--------~-~r~LP~CgH~FH~~CI~~WL~~---~~sCPvCR~~v~~  260 (265)
                      +++.|.||...|...-        . ...+-.|+|.||..||.+|+..   +..||+||++..-
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~   83 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF   83 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence            4778999988887321        1 1123369999999999999985   4679999998653

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

Probab=98.90  E-value=5.8e-10  Score=97.88  Aligned_cols=52  Identities=35%  Similarity=0.750  Sum_probs=43.5

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC---CCccccccccccCC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN---GSCPVCRECVCKDT  262 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~---~sCPvCR~~v~~~~  262 (265)
                      .....+|.|||+.-+++...    .|||.||+.||.+||..+   +.||+||..|..++
T Consensus        44 ~~~~FdCNICLd~akdPVvT----lCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~   98 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDPVVT----LCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT   98 (230)
T ss_pred             CCCceeeeeeccccCCCEEe----ecccceehHHHHHHHhhcCCCeeCCccccccccce
Confidence            34568999999999997766    599999999999999854   45999999886553

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

Probab=98.89  E-value=6.7e-10  Score=93.90  Aligned_cols=53  Identities=30%  Similarity=0.757  Sum_probs=43.7

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      .+....|+|||+.+.....+  -.+|||+||..||..-++....||+||+.|...
T Consensus       128 ~~~~~~CPiCl~~~sek~~v--sTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k  180 (187)
T KOG0320|consen  128 KEGTYKCPICLDSVSEKVPV--STKCGHVFCSQCIKDALKNTNKCPTCRKKITHK  180 (187)
T ss_pred             cccccCCCceecchhhcccc--ccccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence            34457899999999875532  127999999999999999999999999987644

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

Probab=98.85  E-value=1.3e-09  Score=71.96  Aligned_cols=38  Identities=39%  Similarity=0.984  Sum_probs=29.9

Q ss_pred             cccccccccCCCeeeecCCCCcccchhhHHHhhcCC----CCcccc
Q 024603          213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN----GSCPVC  254 (265)
Q Consensus       213 C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~----~sCPvC  254 (265)
                      |+||++.|.+|..+    .|||.||..||.+|.+..    ..||.|
T Consensus         1 CpiC~~~~~~Pv~l----~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDPVSL----PCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSEEE-----SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCcccc----CCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999997777    699999999999998754    359988

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.85  E-value=2.1e-09  Score=71.48  Aligned_cols=44  Identities=39%  Similarity=0.970  Sum_probs=37.7

Q ss_pred             ccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccc
Q 024603          212 GCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRE  256 (265)
Q Consensus       212 ~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~  256 (265)
                      .|+||++.+.+....+.++ |||+||..|+.++......||+||+
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            5999999996556677776 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=98.80  E-value=2.6e-09  Score=69.47  Aligned_cols=39  Identities=51%  Similarity=1.247  Sum_probs=33.5

Q ss_pred             cccccccccCCCeeeecCCCCcccchhhHHHhhc--CCCCcccc
Q 024603          213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT--RNGSCPVC  254 (265)
Q Consensus       213 C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~--~~~sCPvC  254 (265)
                      |+||++.+.++.  +.+| |+|.||..|+.+|++  ....||+|
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            899999988866  3465 999999999999998  55679998

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

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

Probab=98.80  E-value=1.6e-09  Score=107.45  Aligned_cols=51  Identities=39%  Similarity=1.057  Sum_probs=44.9

Q ss_pred             cccCcccccccccccCCCe--eeecCCCCcccchhhHHHhhcCCCCcccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDS--ARKLPSCGHCFHSECVDKWLTRNGSCPVCRECV  258 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~--~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v  258 (265)
                      ...+..|+||+|++..+..  ..++| |+|+||..|+.+|++++.+||+||..+
T Consensus       288 ~~~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~  340 (543)
T KOG0802|consen  288 ALSDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVL  340 (543)
T ss_pred             hhcCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhh
Confidence            3457899999999998754  66787 999999999999999999999999944

>smart00504 Ubox Modified RING finger domain

Probab=98.77  E-value=4.4e-09  Score=74.34  Aligned_cols=46  Identities=28%  Similarity=0.614  Sum_probs=40.4

Q ss_pred             cccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccccccc
Q 024603          211 IGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       211 ~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      ..|+||.+.+.++..   +| |||+|+..||.+|++.+.+||+|++++..
T Consensus         2 ~~Cpi~~~~~~~Pv~---~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~~   47 (63)
T smart00504        2 FLCPISLEVMKDPVI---LP-SGQTYERRAIEKWLLSHGTDPVTGQPLTH   47 (63)
T ss_pred             cCCcCCCCcCCCCEE---CC-CCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence            579999999999743   45 99999999999999998999999998843

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

>smart00184 RING Ring finger

Probab=98.67  E-value=1.4e-08  Score=63.60  Aligned_cols=38  Identities=50%  Similarity=1.328  Sum_probs=31.5

Q ss_pred             cccccccccCCCeeeecCCCCcccchhhHHHhhc-CCCCcccc
Q 024603          213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-RNGSCPVC  254 (265)
Q Consensus       213 C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~-~~~sCPvC  254 (265)
                      |+||++...   ....+| |+|.||..|+++|+. .+..||+|
T Consensus         1 C~iC~~~~~---~~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELK---DPVVLP-CGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCC---CcEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence            789998843   355566 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)

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.58  E-value=2.6e-08  Score=94.83  Aligned_cols=51  Identities=31%  Similarity=0.712  Sum_probs=43.9

Q ss_pred             hcccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccccccc
Q 024603          206 QLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       206 ~~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      ..+....|+||++.+..+..   +| |+|.||..|+..|+..+..||+||..+..
T Consensus        22 ~Le~~l~C~IC~d~~~~Pvi---tp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~   72 (397)
T TIGR00599        22 PLDTSLRCHICKDFFDVPVL---TS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQE   72 (397)
T ss_pred             ccccccCCCcCchhhhCccC---CC-CCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence            35567899999999988753   45 99999999999999988899999998764

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

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

Probab=98.46  E-value=7.7e-08  Score=71.22  Aligned_cols=29  Identities=38%  Similarity=1.047  Sum_probs=27.1

Q ss_pred             CCCcccchhhHHHhhcCCCCccccccccc
Q 024603          231 SCGHCFHSECVDKWLTRNGSCPVCRECVC  259 (265)
Q Consensus       231 ~CgH~FH~~CI~~WL~~~~sCPvCR~~v~  259 (265)
                      .|.|.||..||.+||..+..||++|++..
T Consensus        53 ~CnHaFH~HCI~rWL~Tk~~CPld~q~w~   81 (88)
T COG5194          53 VCNHAFHDHCIYRWLDTKGVCPLDRQTWV   81 (88)
T ss_pred             ecchHHHHHHHHHHHhhCCCCCCCCceeE
Confidence            59999999999999999999999999754

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

Probab=98.43  E-value=6.4e-08  Score=71.04  Aligned_cols=51  Identities=33%  Similarity=0.767  Sum_probs=36.8

Q ss_pred             cCcccccccccccCCCeee---------ecCCCCcccchhhHHHhhcC---CCCccccccccc
Q 024603          209 NEIGCSICLEKFEEGDSAR---------KLPSCGHCFHSECVDKWLTR---NGSCPVCRECVC  259 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r---------~LP~CgH~FH~~CI~~WL~~---~~sCPvCR~~v~  259 (265)
                      .++.|-||...|..--.--         .+-.|.|.||..||.+|+..   +..||+||+...
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            3458888888886422111         22259999999999999974   456999999754

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

Probab=98.39  E-value=1.2e-07  Score=84.75  Aligned_cols=51  Identities=31%  Similarity=0.718  Sum_probs=41.6

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHH-hhcCCCC-ccccccccccCC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDK-WLTRNGS-CPVCRECVCKDT  262 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~-WL~~~~s-CPvCR~~v~~~~  262 (265)
                      ..+..|+||++....+...    .|||+||..||.. |-+++.. ||+||+.+..+.
T Consensus       213 ~~d~kC~lC~e~~~~ps~t----~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~  265 (271)
T COG5574         213 LADYKCFLCLEEPEVPSCT----PCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK  265 (271)
T ss_pred             ccccceeeeecccCCcccc----cccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence            3477899999988775555    4999999999999 9777665 999999886543

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

Probab=98.39  E-value=1.5e-07  Score=90.92  Aligned_cols=47  Identities=32%  Similarity=0.790  Sum_probs=39.5

Q ss_pred             CcccccccccccCCCeeeecCCCCcccchhhHHHhhc-----CCCCcccccccccc
Q 024603          210 EIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-----RNGSCPVCRECVCK  260 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~-----~~~sCPvCR~~v~~  260 (265)
                      +..||||++....+...    .|||+||..||.+++.     ....||+||..|..
T Consensus       186 ~~~CPICL~~~~~p~~t----~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~  237 (513)
T KOG2164|consen  186 DMQCPICLEPPSVPVRT----NCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL  237 (513)
T ss_pred             CCcCCcccCCCCccccc----ccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence            78999999998776666    6999999999998875     34679999998764

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

Probab=98.29  E-value=1.6e-07  Score=68.61  Aligned_cols=51  Identities=33%  Similarity=0.827  Sum_probs=24.5

Q ss_pred             Cccccccccccc-CCCe-eeec--CCCCcccchhhHHHhhcC----C-------CCcccccccccc
Q 024603          210 EIGCSICLEKFE-EGDS-ARKL--PSCGHCFHSECVDKWLTR----N-------GSCPVCRECVCK  260 (265)
Q Consensus       210 ~~~C~ICle~~~-~~~~-~r~L--P~CgH~FH~~CI~~WL~~----~-------~sCPvCR~~v~~  260 (265)
                      +.+|.||++... +++. ....  ++|++.||..|+.+|+..    +       +.||.|+.+|.-
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence            468999999876 3222 2233  379999999999999862    1       249999998863

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

Probab=98.28  E-value=5e-07  Score=59.88  Aligned_cols=38  Identities=39%  Similarity=0.975  Sum_probs=22.3

Q ss_pred             cccccccccCC-CeeeecCCCCcccchhhHHHhhcCC----CCcc
Q 024603          213 CSICLEKFEEG-DSARKLPSCGHCFHSECVDKWLTRN----GSCP  252 (265)
Q Consensus       213 C~ICle~~~~~-~~~r~LP~CgH~FH~~CI~~WL~~~----~sCP  252 (265)
                      |+||.+ +.++ .....|| |||+||.+|+++++++.    .+||
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 7553 4457788 99999999999999843    3577

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

Probab=98.28  E-value=2.8e-07  Score=88.58  Aligned_cols=52  Identities=29%  Similarity=0.694  Sum_probs=40.1

Q ss_pred             ccCcccccccccccCCCe--------------eeecCCCCcccchhhHHHhhc-CCCCcccccccccc
Q 024603          208 DNEIGCSICLEKFEEGDS--------------ARKLPSCGHCFHSECVDKWLT-RNGSCPVCRECVCK  260 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~--------------~r~LP~CgH~FH~~CI~~WL~-~~~sCPvCR~~v~~  260 (265)
                      +....|+||+.++.-...              -...| |.|+||..|+.+|+. .+-.||+||.++++
T Consensus       569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tP-C~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTP-CHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             hccccceEeccccceeeccCcchhhhhhhhccccccc-hHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            445789999998863211              12346 999999999999999 45589999999864

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

Probab=98.27  E-value=3.5e-07  Score=80.72  Aligned_cols=47  Identities=47%  Similarity=0.944  Sum_probs=40.5

Q ss_pred             hcccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccc
Q 024603          206 QLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRE  256 (265)
Q Consensus       206 ~~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~  256 (265)
                      ...+...|+||++.|..+   ..+| |+|.||..|+..++.....||.||.
T Consensus         9 ~~~~~~~C~iC~~~~~~p---~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen    9 VLQEELTCPICLEYFREP---VLLP-CGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             hccccccChhhHHHhhcC---cccc-ccchHhHHHHHHhcCCCcCCcccCC
Confidence            345789999999999998   5566 9999999999999885567999993

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

Probab=98.25  E-value=5.5e-07  Score=66.19  Aligned_cols=49  Identities=22%  Similarity=0.533  Sum_probs=38.6

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC-CCCccccccccccC
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR-NGSCPVCRECVCKD  261 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~-~~sCPvCR~~v~~~  261 (265)
                      +...|+|+.+-+.+|..+    .+||+|...||.+|+.. +.+||+||+++...
T Consensus         3 ~~f~CpIt~~lM~dPVi~----~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~   52 (73)
T PF04564_consen    3 DEFLCPITGELMRDPVIL----PSGHTYERSAIERWLEQNGGTDPFTRQPLSES   52 (73)
T ss_dssp             GGGB-TTTSSB-SSEEEE----TTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred             cccCCcCcCcHhhCceeC----CcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence            467899999999997766    49999999999999998 78999999988653

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 ....

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

Probab=98.23  E-value=3e-07  Score=82.49  Aligned_cols=51  Identities=29%  Similarity=0.763  Sum_probs=42.4

Q ss_pred             ccCcccccccccccCCC-------eeeecCCCCcccchhhHHHhhc--CCCCccccccccc
Q 024603          208 DNEIGCSICLEKFEEGD-------SARKLPSCGHCFHSECVDKWLT--RNGSCPVCRECVC  259 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~-------~~r~LP~CgH~FH~~CI~~WL~--~~~sCPvCR~~v~  259 (265)
                      .++.-|+||-+.+...+       .+.+|. |+|.||..||+-|-.  ++++||.|++.+.
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVd  281 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVD  281 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhh
Confidence            35678999998887765       677786 999999999999954  6789999998774

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

Probab=98.23  E-value=7.6e-07  Score=60.63  Aligned_cols=42  Identities=26%  Similarity=0.869  Sum_probs=32.3

Q ss_pred             ccccccccccCCCeeeecCCCC-----cccchhhHHHhhcCC--CCccccc
Q 024603          212 GCSICLEKFEEGDSARKLPSCG-----HCFHSECVDKWLTRN--GSCPVCR  255 (265)
Q Consensus       212 ~C~ICle~~~~~~~~r~LP~Cg-----H~FH~~CI~~WL~~~--~sCPvCR  255 (265)
                      .|.||++ ..+++.....| |.     |.+|..|+.+|+..+  .+||+|+
T Consensus         1 ~CrIC~~-~~~~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGDEGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCCCCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4899998 33444445678 75     999999999999644  4899995

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

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

Probab=98.19  E-value=3.8e-07  Score=84.19  Aligned_cols=51  Identities=37%  Similarity=0.817  Sum_probs=44.2

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      .+.-+.|-||.+.|..+...   | |+|.||.-||.+.|..+..||.|+.++.+.
T Consensus        20 lD~lLRC~IC~eyf~ip~it---p-CsHtfCSlCIR~~L~~~p~CP~C~~~~~Es   70 (442)
T KOG0287|consen   20 LDDLLRCGICFEYFNIPMIT---P-CSHTFCSLCIRKFLSYKPQCPTCCVTVTES   70 (442)
T ss_pred             hHHHHHHhHHHHHhcCceec---c-ccchHHHHHHHHHhccCCCCCceecccchh
Confidence            44568999999999986555   5 999999999999999999999999887643

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

Probab=98.17  E-value=2e-07  Score=64.20  Aligned_cols=52  Identities=29%  Similarity=0.664  Sum_probs=40.2

Q ss_pred             CcccccccccccCCCeeeecCCCCc-ccchhhHHHhhc-CCCCccccccccccCCCCC
Q 024603          210 EIGCSICLEKFEEGDSARKLPSCGH-CFHSECVDKWLT-RNGSCPVCRECVCKDTDTW  265 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r~LP~CgH-~FH~~CI~~WL~-~~~sCPvCR~~v~~~~~~~  265 (265)
                      +.+|.||+|.-.+...-    .||| ..|.+|-.+.++ .+..||+||.++.+.-++|
T Consensus         7 ~dECTICye~pvdsVlY----tCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIkTY   60 (62)
T KOG4172|consen    7 SDECTICYEHPVDSVLY----TCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIKTY   60 (62)
T ss_pred             ccceeeeccCcchHHHH----HcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHHhh
Confidence            47999999886664444    5999 689999766555 7889999999997654443

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

Probab=98.14  E-value=8.7e-07  Score=80.38  Aligned_cols=49  Identities=39%  Similarity=0.820  Sum_probs=42.6

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVC  259 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~  259 (265)
                      .+..+.|-||-+.+..+...    .|||.||.-||...|..+..||+||.+-.
T Consensus        22 LDs~lrC~IC~~~i~ip~~T----tCgHtFCslCIR~hL~~qp~CP~Cr~~~~   70 (391)
T COG5432          22 LDSMLRCRICDCRISIPCET----TCGHTFCSLCIRRHLGTQPFCPVCREDPC   70 (391)
T ss_pred             chhHHHhhhhhheeecceec----ccccchhHHHHHHHhcCCCCCccccccHH
Confidence            34567899999998886666    69999999999999999999999998754

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

Probab=98.10  E-value=1.3e-06  Score=81.21  Aligned_cols=49  Identities=31%  Similarity=0.811  Sum_probs=42.3

Q ss_pred             ccCcccccccccccCCCeeeecCCCCc-ccchhhHHHhhcCCCCcccccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGH-CFHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH-~FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      +...+|.||+.+-.+   +..|| |.| ..|..|.+...-+++.||+||+++..
T Consensus       288 ~~gkeCVIClse~rd---t~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~  337 (349)
T KOG4265|consen  288 ESGKECVICLSESRD---TVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIEE  337 (349)
T ss_pred             cCCCeeEEEecCCcc---eEEec-chhhehhHhHHHHHHHhhcCCCccccchHh
Confidence            446899999998777   67788 999 79999999887788999999999864

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

Probab=98.09  E-value=1.2e-06  Score=83.42  Aligned_cols=49  Identities=37%  Similarity=0.986  Sum_probs=39.6

Q ss_pred             ccCcccccccccccCCCee-eecCCCCcccchhhHHHhhcCCCCccccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSA-RKLPSCGHCFHSECVDKWLTRNGSCPVCRECVC  259 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~-r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~  259 (265)
                      .+-.+|||||+.+.+.... +.. .|.|.||..|+.+|  ...+||+||--..
T Consensus       173 tELPTCpVCLERMD~s~~gi~t~-~c~Hsfh~~cl~~w--~~~scpvcR~~q~  222 (493)
T KOG0804|consen  173 TELPTCPVCLERMDSSTTGILTI-LCNHSFHCSCLMKW--WDSSCPVCRYCQS  222 (493)
T ss_pred             ccCCCcchhHhhcCccccceeee-ecccccchHHHhhc--ccCcChhhhhhcC
Confidence            3457999999999886633 334 49999999999999  6789999997554

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

Probab=98.08  E-value=1.1e-06  Score=89.81  Aligned_cols=54  Identities=26%  Similarity=0.816  Sum_probs=41.2

Q ss_pred             hcccCcccccccccccCCC---eeeecCCCCcccchhhHHHhhcCC--CCccccccccc
Q 024603          206 QLDNEIGCSICLEKFEEGD---SARKLPSCGHCFHSECVDKWLTRN--GSCPVCRECVC  259 (265)
Q Consensus       206 ~~~~~~~C~ICle~~~~~~---~~r~LP~CgH~FH~~CI~~WL~~~--~sCPvCR~~v~  259 (265)
                      +.+.-++|+||+..+..-+   .-.++|.|.|.||..|+.+|++..  .+||+||..++
T Consensus      1465 ~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1465 KFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             hcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            4466789999998776211   123466899999999999999854  57999997764

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

Probab=98.05  E-value=1.6e-06  Score=61.90  Aligned_cols=48  Identities=31%  Similarity=0.759  Sum_probs=26.5

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVC  259 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~  259 (265)
                      .+.-..|++|.+.+..|..+.   .|.|+||..||.+-+.  ..||+|+.+.-
T Consensus         4 le~lLrCs~C~~~l~~pv~l~---~CeH~fCs~Ci~~~~~--~~CPvC~~Paw   51 (65)
T PF14835_consen    4 LEELLRCSICFDILKEPVCLG---GCEHIFCSSCIRDCIG--SECPVCHTPAW   51 (65)
T ss_dssp             HHHTTS-SSS-S--SS-B------SSS--B-TTTGGGGTT--TB-SSS--B-S
T ss_pred             HHHhcCCcHHHHHhcCCceec---cCccHHHHHHhHHhcC--CCCCCcCChHH
Confidence            455689999999999976542   7999999999988654  34999998764

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

Probab=97.99  E-value=4.8e-06  Score=78.11  Aligned_cols=52  Identities=38%  Similarity=0.862  Sum_probs=41.7

Q ss_pred             ccCcccccccccccCCC----eeeecCCCCcccchhhHHHhh--cC-----CCCccccccccc
Q 024603          208 DNEIGCSICLEKFEEGD----SARKLPSCGHCFHSECVDKWL--TR-----NGSCPVCRECVC  259 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~----~~r~LP~CgH~FH~~CI~~WL--~~-----~~sCPvCR~~v~  259 (265)
                      ..+.+|.||++...+..    ....+|+|.|.||..||++|-  .+     .+.||.||....
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS  221 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence            45789999999987644    234568899999999999997  44     467999998764

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

Probab=97.95  E-value=1.4e-06  Score=80.85  Aligned_cols=51  Identities=31%  Similarity=0.678  Sum_probs=42.5

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhc-CCCCcccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-RNGSCPVCRECVCK  260 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~-~~~sCPvCR~~v~~  260 (265)
                      ...+..|+|||+-++.   .+..+.|.|.||.+||.+-++ ..+.||.||+.+..
T Consensus        40 ~~~~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S   91 (381)
T KOG0311|consen   40 FDIQVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS   91 (381)
T ss_pred             hhhhhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence            4567899999999887   455568999999999999887 45789999998753

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

Probab=97.89  E-value=2.3e-06  Score=77.97  Aligned_cols=55  Identities=31%  Similarity=0.689  Sum_probs=44.8

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhc-----------------------CCCCccccccccccCCC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-----------------------RNGSCPVCRECVCKDTD  263 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~-----------------------~~~sCPvCR~~v~~~~~  263 (265)
                      .....|.|||-.|.+++...+++ |.|+||..|+.++|.                       .+..||+||..+..+.+
T Consensus       113 ~p~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~~  190 (368)
T KOG4445|consen  113 HPNGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEEN  190 (368)
T ss_pred             CCCCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccccc
Confidence            45678999999999999888888 999999999976653                       11249999999876654

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

Probab=97.88  E-value=5.4e-06  Score=64.37  Aligned_cols=49  Identities=24%  Similarity=0.673  Sum_probs=35.9

Q ss_pred             CcccccccccccC-------------CCeeeecCCCCcccchhhHHHhhcCCCCcccccccc
Q 024603          210 EIGCSICLEKFEE-------------GDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECV  258 (265)
Q Consensus       210 ~~~C~ICle~~~~-------------~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v  258 (265)
                      -+.|+||...+-+             .+-...--.|.|.||..||.+||+.+..||+|.++-
T Consensus        46 vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW  107 (114)
T KOG2930|consen   46 VDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEW  107 (114)
T ss_pred             echhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence            4678888755422             111222225999999999999999999999998763

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

Probab=97.64  E-value=1.4e-05  Score=80.52  Aligned_cols=53  Identities=26%  Similarity=0.728  Sum_probs=42.6

Q ss_pred             hcccCcccccccccccCCCeeeecCCCCcccchhhHHHhhc-CCCCccccccccccCC
Q 024603          206 QLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-RNGSCPVCRECVCKDT  262 (265)
Q Consensus       206 ~~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~-~~~sCPvCR~~v~~~~  262 (265)
                      ....-..||.|-..+.+-...    +|+|.||..|+.+-+. ++..||.|...+..++
T Consensus       639 ~yK~~LkCs~Cn~R~Kd~vI~----kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD  692 (698)
T KOG0978|consen  639 EYKELLKCSVCNTRWKDAVIT----KCGHVFCEECVQTRYETRQRKCPKCNAAFGAND  692 (698)
T ss_pred             HHHhceeCCCccCchhhHHHH----hcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence            445678999999777773333    8999999999999886 6678999999886554

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

Probab=97.51  E-value=1.9e-05  Score=79.65  Aligned_cols=50  Identities=28%  Similarity=0.518  Sum_probs=42.4

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccc
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVC  259 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~  259 (265)
                      ....|++|+..+.+.......+ |+|+||..|++.|-+...+||+||..+.
T Consensus       122 ~~~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~EF~  171 (1134)
T KOG0825|consen  122 VENQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGEFG  171 (1134)
T ss_pred             hhhhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhhhh
Confidence            3467999999888876665565 9999999999999999999999998654

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

Probab=97.48  E-value=5e-05  Score=72.77  Aligned_cols=52  Identities=31%  Similarity=0.771  Sum_probs=45.0

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      .+++..|++|...+.++...  . .|||.||..|+.+|+..+..||.||..+...
T Consensus        18 ~~~~l~C~~C~~vl~~p~~~--~-~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~   69 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDPVQT--T-TCGHRFCAGCLLESLSNHQKCPVCRQELTQA   69 (391)
T ss_pred             CcccccCccccccccCCCCC--C-CCCCcccccccchhhccCcCCcccccccchh
Confidence            45678999999999998773  2 5999999999999999999999999877544

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

Probab=97.22  E-value=0.00013  Score=68.91  Aligned_cols=48  Identities=29%  Similarity=0.746  Sum_probs=38.3

Q ss_pred             cccccccccccCCCeeeecCCCCcccchhhHHHhhcC--CCCccccccccccCC
Q 024603          211 IGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR--NGSCPVCRECVCKDT  262 (265)
Q Consensus       211 ~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~--~~sCPvCR~~v~~~~  262 (265)
                      .-|-||-+.=++   ++.-| |||..|..|+..|-..  ..+||.||..+...+
T Consensus       370 eLCKICaendKd---vkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte  419 (563)
T KOG1785|consen  370 ELCKICAENDKD---VKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTE  419 (563)
T ss_pred             HHHHHhhccCCC---ccccc-ccchHHHHHHHhhcccCCCCCCCceeeEecccc
Confidence            569999776444   66777 9999999999999754  467999999886544

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

Probab=97.22  E-value=0.00014  Score=51.08  Aligned_cols=43  Identities=33%  Similarity=0.790  Sum_probs=29.0

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC--CCCccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR--NGSCPV  253 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~--~~sCPv  253 (265)
                      ..+..|||.+..+++|..-+   .|+|+|-.+.|.+|+.+  ...||+
T Consensus         9 ~~~~~CPiT~~~~~~PV~s~---~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen    9 TISLKCPITLQPFEDPVKSK---KCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             B--SB-TTTSSB-SSEEEES---SS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             EeccCCCCcCChhhCCcCcC---CCCCeecHHHHHHHHHhcCCCCCCC
Confidence            34689999999999876543   69999999999999944  346998

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

Probab=97.06  E-value=0.00029  Score=67.53  Aligned_cols=49  Identities=33%  Similarity=0.844  Sum_probs=42.8

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      ..+.+|.||+..+..+...   | |||.||..|+++-+.+...||.||..+.+
T Consensus        82 ~sef~c~vc~~~l~~pv~t---p-cghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   82 RSEFECCVCSRALYPPVVT---P-CGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cchhhhhhhHhhcCCCccc---c-ccccccHHHHHHHhccCCCCccccccccc
Confidence            4578999999999887666   5 99999999999988888899999988764

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

Probab=96.99  E-value=0.0002  Score=67.55  Aligned_cols=49  Identities=37%  Similarity=0.861  Sum_probs=40.3

Q ss_pred             ccCcccccccccccC-CCeeeecCCCCcccchhhHHHhhcCC--CCccccccc
Q 024603          208 DNEIGCSICLEKFEE-GDSARKLPSCGHCFHSECVDKWLTRN--GSCPVCREC  257 (265)
Q Consensus       208 ~~~~~C~ICle~~~~-~~~~r~LP~CgH~FH~~CI~~WL~~~--~sCPvCR~~  257 (265)
                      +.+..|-.|=+.+-. ++.+.-|| |.|+||..|+...|.++  .+||.||+-
T Consensus       363 e~~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Crkl  414 (518)
T KOG1941|consen  363 ETELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCRKL  414 (518)
T ss_pred             HHhhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHHHH
Confidence            446789999888854 56777898 99999999999999765  579999943

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

Probab=96.99  E-value=0.00031  Score=68.56  Aligned_cols=49  Identities=29%  Similarity=0.695  Sum_probs=40.0

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhc-----CCCCccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-----RNGSCPVCRECVC  259 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~-----~~~sCPvCR~~v~  259 (265)
                      ...+.+|-+|-+.-++....    .|.|.||..|+.++..     .+-+||+|...+.
T Consensus       533 nk~~~~C~lc~d~aed~i~s----~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls  586 (791)
T KOG1002|consen  533 NKGEVECGLCHDPAEDYIES----SCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS  586 (791)
T ss_pred             ccCceeecccCChhhhhHhh----hhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence            34568999999998886666    7999999999988875     3357999988764

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

Probab=96.84  E-value=0.00041  Score=63.33  Aligned_cols=46  Identities=28%  Similarity=0.556  Sum_probs=41.5

Q ss_pred             cccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccccccc
Q 024603          211 IGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       211 ~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      ..|-||.++|..|...    +|+|+||..|..+-+.....|++|.+....
T Consensus       242 f~c~icr~~f~~pVvt----~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g  287 (313)
T KOG1813|consen  242 FKCFICRKYFYRPVVT----KCGHYFCEVCALKPYQKGEKCYVCSQQTHG  287 (313)
T ss_pred             ccccccccccccchhh----cCCceeehhhhccccccCCcceeccccccc
Confidence            5699999999998888    899999999999988888999999987654

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

Probab=96.76  E-value=0.00035  Score=64.66  Aligned_cols=52  Identities=27%  Similarity=0.659  Sum_probs=44.5

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      ...-.+|.+|-..+.+...+   +.|-|.||..||.+.+.....||.|...+...
T Consensus        12 ~n~~itC~LC~GYliDATTI---~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   12 LNPHITCRLCGGYLIDATTI---TECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             cccceehhhccceeecchhH---HHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            34568999999999886655   36999999999999999999999999888654

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

Probab=96.73  E-value=0.00093  Score=62.49  Aligned_cols=49  Identities=24%  Similarity=0.455  Sum_probs=41.0

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVC  259 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~  259 (265)
                      ..++..|+||+..   +......| |+|.-|+.||.+.+.+.+.|=.|+..+.
T Consensus       419 ~sEd~lCpICyA~---pi~Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~  467 (489)
T KOG4692|consen  419 DSEDNLCPICYAG---PINAVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVI  467 (489)
T ss_pred             CcccccCcceecc---cchhhccC-CCCchHHHHHHHHHhcCCeeeEecceee
Confidence            3567899999765   34455566 9999999999999999999999998876

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

Probab=96.72  E-value=0.00058  Score=59.23  Aligned_cols=44  Identities=30%  Similarity=0.705  Sum_probs=39.5

Q ss_pred             cccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccccc
Q 024603          211 IGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECV  258 (265)
Q Consensus       211 ~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v  258 (265)
                      ..|.||-.+|..|...    .|||.||..|..+-++....|-+|-+..
T Consensus       197 F~C~iCKkdy~spvvt----~CGH~FC~~Cai~~y~kg~~C~~Cgk~t  240 (259)
T COG5152         197 FLCGICKKDYESPVVT----ECGHSFCSLCAIRKYQKGDECGVCGKAT  240 (259)
T ss_pred             eeehhchhhccchhhh----hcchhHHHHHHHHHhccCCcceecchhh
Confidence            5799999999998888    7999999999998888889999997653

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

Probab=96.72  E-value=0.0013  Score=44.56  Aligned_cols=45  Identities=31%  Similarity=0.685  Sum_probs=23.1

Q ss_pred             cccccccccCC-CeeeecCCCCcccchhhHHHhhc-CCCCcccccccc
Q 024603          213 CSICLEKFEEG-DSARKLPSCGHCFHSECVDKWLT-RNGSCPVCRECV  258 (265)
Q Consensus       213 C~ICle~~~~~-~~~r~LP~CgH~FH~~CI~~WL~-~~~sCPvCR~~v  258 (265)
                      |++|.+++... ....-. .|++..|..|..+-++ ....||-||++.
T Consensus         1 cp~C~e~~d~~d~~~~PC-~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPC-ECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SS-TTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccC-cCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            78999999432 233334 4899999999999886 578999999874

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

Probab=96.70  E-value=0.001  Score=60.20  Aligned_cols=51  Identities=24%  Similarity=0.450  Sum_probs=40.0

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC--CCcccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN--GSCPVCRECVCK  260 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~--~sCPvCR~~v~~  260 (265)
                      ...+.+|++|-++-..|...  . +|+|+||+.|+..-....  .+||.|-.++.+
T Consensus       236 ~t~~~~C~~Cg~~PtiP~~~--~-~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~  288 (298)
T KOG2879|consen  236 GTSDTECPVCGEPPTIPHVI--G-KCGHIYCYYCIATSRLWDASFTCPLCGENVEP  288 (298)
T ss_pred             ccCCceeeccCCCCCCCeee--c-cccceeehhhhhhhhcchhhcccCccCCCCcc
Confidence            34678999998887766555  2 499999999998866544  689999988763

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

Probab=96.69  E-value=0.0013  Score=58.05  Aligned_cols=55  Identities=25%  Similarity=0.629  Sum_probs=44.7

Q ss_pred             hcccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC--------CCCccccccccccCC
Q 024603          206 QLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR--------NGSCPVCRECVCKDT  262 (265)
Q Consensus       206 ~~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~--------~~sCPvCR~~v~~~~  262 (265)
                      +.+.+..|..|-..+..++.+|.  .|-|.||.+|+++|-..        ...||-|.++|.+..
T Consensus        46 DsDY~pNC~LC~t~La~gdt~RL--vCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~  108 (299)
T KOG3970|consen   46 DSDYNPNCRLCNTPLASGDTTRL--VCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPI  108 (299)
T ss_pred             hcCCCCCCceeCCccccCcceee--hhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCc
Confidence            45567889999999999988864  39999999999999652        236999999987654

>PF13441 Gly-zipper_YMGG: YMGG-like Gly-zipper

Probab=96.68  E-value=0.0016  Score=43.52  Aligned_cols=37  Identities=41%  Similarity=0.507  Sum_probs=22.4

Q ss_pred             HHhhhHHHHHHHhhhcccccccccccccccccchhhHH
Q 024603           52 FALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAIT   89 (265)
Q Consensus        52 ~~~~g~~~ga~~g~~~g~~~~~g~~~ga~~Ga~~gav~   89 (265)
                      .|+.|+..|+++|++.| ....|-+-||++|+++|+++
T Consensus         6 GA~iGA~~GA~iG~~~g-~~~~GA~iGA~~Ga~~G~~~   42 (45)
T PF13441_consen    6 GAAIGAAAGAVIGAIIG-NGGKGAAIGAAAGALAGAAI   42 (45)
T ss_pred             HHHHHHHHHHHHHHhhC-CCcccchhhhhhhhhhhhhh
Confidence            46677777777777777 33444555555555555443

>PF13436 Gly-zipper_OmpA: Glycine-zipper containing OmpA-like membrane domain

Probab=96.64  E-value=0.0012  Score=52.95  Aligned_cols=41  Identities=34%  Similarity=0.358  Sum_probs=31.1

Q ss_pred             HHHhhhHHHHHHHhhhcccccccccccccccccchhhHHHHH
Q 024603           51 IFALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQ   92 (265)
Q Consensus        51 ~~~~~g~~~ga~~g~~~g~~~~~g~~~ga~~Ga~~gav~s~e   92 (265)
                      .-+++|+++||++|++.|- ...|.+.||++||+.|++....
T Consensus        54 ~ga~~GA~~GA~~Ga~~G~-~~~ga~~GAa~Ga~~G~~~g~~   94 (118)
T PF13436_consen   54 GGAAIGAAAGAAIGAIIGG-NGRGAAIGAAAGAAVGAAAGAA   94 (118)
T ss_pred             HHHHHHHHHHHHHHhhcCC-CccchHHHHHHHHHHHHHhhhh
Confidence            3455777777777777776 6678888888888888887766

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

Probab=96.54  E-value=0.0019  Score=69.37  Aligned_cols=66  Identities=27%  Similarity=0.551  Sum_probs=47.4

Q ss_pred             hcCCcccccchhhhhcccCcccccccccccCCCeeeecCCCCcccchhhHHHhhc-----CC-----CCccccccccc
Q 024603          192 QKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-----RN-----GSCPVCRECVC  259 (265)
Q Consensus       192 ~~lp~~~~~~~~~~~~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~-----~~-----~sCPvCR~~v~  259 (265)
                      +-+|....+.+.. +.+.+..|-||+.+--......+|. |+|+||..|.+.-|+     ..     -+||+|+.++.
T Consensus      3469 ~CLPCl~Cdks~t-kQD~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3469 HCLPCLHCDKSAT-KQDADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             hcccccccChhhh-hcccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            3455555443323 5567889999998877767777886 999999999875544     22     25999998874

>PF13488 Gly-zipper_Omp: Glycine zipper

Probab=96.45  E-value=0.0019  Score=43.35  Aligned_cols=38  Identities=34%  Similarity=0.434  Sum_probs=23.0

Q ss_pred             hhhHHHHHHHhhhcccccccccccccccccchhhHHHHH
Q 024603           54 LGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQ   92 (265)
Q Consensus        54 ~~g~~~ga~~g~~~g~~~~~g~~~ga~~Ga~~gav~s~e   92 (265)
                      +.|+++|+++|+..+ .+..|.+-|+++|++.|+.+...
T Consensus         4 ~iGA~~Ga~iG~~~g-~~~~ga~iGa~vGa~~G~~ig~~   41 (46)
T PF13488_consen    4 AIGAAAGAAIGAATG-GPGKGAAIGAAVGAAVGAAIGNY   41 (46)
T ss_pred             HHHHHHHHHHHHHhC-CchhhHHHHHHHHHHHHHHHHHH
Confidence            445555555555444 23467777777777777776654

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

Probab=96.33  E-value=0.0034  Score=59.77  Aligned_cols=47  Identities=28%  Similarity=0.617  Sum_probs=38.4

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC--------CCCcccccc
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR--------NGSCPVCRE  256 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~--------~~sCPvCR~  256 (265)
                      ....|.||++.....+-...+| |+|+||..|+..++..        .-.||-+.-
T Consensus       183 slf~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             hcccceeeehhhcCcceeeecc-cchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            4578999999988878888999 9999999999998762        235876653

>PHA02862 5L protein; Provisional

Probab=96.27  E-value=0.0031  Score=52.14  Aligned_cols=46  Identities=22%  Similarity=0.532  Sum_probs=33.6

Q ss_pred             CcccccccccccCCCeeeecC-CC---CcccchhhHHHhhcC--CCCccccccccc
Q 024603          210 EIGCSICLEKFEEGDSARKLP-SC---GHCFHSECVDKWLTR--NGSCPVCRECVC  259 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r~LP-~C---gH~FH~~CI~~WL~~--~~sCPvCR~~v~  259 (265)
                      +..|-||.++-.+.  .  -| .|   -..-|.+|+.+|+..  +..||+||.+..
T Consensus         2 ~diCWIC~~~~~e~--~--~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~   53 (156)
T PHA02862          2 SDICWICNDVCDER--N--NFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN   53 (156)
T ss_pred             CCEEEEecCcCCCC--c--ccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence            45799999985443  2  34 23   357999999999974  456999998763

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

Probab=96.25  E-value=0.0025  Score=59.10  Aligned_cols=49  Identities=22%  Similarity=0.463  Sum_probs=39.9

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECV  258 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v  258 (265)
                      ..+...||+|+....++..+.   .-|-+||..|+.+.++.++.||+=-.+.
T Consensus       297 ~~~~~~CpvClk~r~Nptvl~---vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~  345 (357)
T KOG0826|consen  297 PPDREVCPVCLKKRQNPTVLE---VSGYVFCYPCIFSYVVNYGHCPVTGYPA  345 (357)
T ss_pred             CCccccChhHHhccCCCceEE---ecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence            345689999999988876653   3699999999999999999999855443

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

Probab=96.16  E-value=0.0026  Score=65.28  Aligned_cols=52  Identities=29%  Similarity=0.735  Sum_probs=41.8

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC-------CCccccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN-------GSCPVCRECVC  259 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~-------~sCPvCR~~v~  259 (265)
                      ....+|.||.+.+.....+-....|-|+||..||.+|-+..       =.||.|+....
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~  247 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK  247 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence            34579999999999887777777799999999999997632       14999985444

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.16  E-value=0.0042  Score=55.58  Aligned_cols=54  Identities=19%  Similarity=0.362  Sum_probs=47.8

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccCC
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDT  262 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~~  262 (265)
                      ....||+|.+.+.+......|.+|||+|+.+|..+.+.....||+|-+++.+.+
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            457899999999998888778789999999999999999999999998886543

>PF13441 Gly-zipper_YMGG: YMGG-like Gly-zipper

Probab=96.15  E-value=0.0032  Score=42.00  Aligned_cols=38  Identities=37%  Similarity=0.501  Sum_probs=34.1

Q ss_pred             hhhHHHHHHHhhhcccccccccccccccccchhhHHHHH
Q 024603           54 LGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQ   92 (265)
Q Consensus        54 ~~g~~~ga~~g~~~g~~~~~g~~~ga~~Ga~~gav~s~e   92 (265)
                      .-|+.+||.+||+.|.... .--+||.+||.+|++...-
T Consensus         4 ~~GA~iGA~~GA~iG~~~g-~~~~GA~iGA~~Ga~~G~~   41 (45)
T PF13441_consen    4 VRGAAIGAAAGAVIGAIIG-NGGKGAAIGAAAGALAGAA   41 (45)
T ss_pred             hhHHHHHHHHHHHHHHhhC-CCcccchhhhhhhhhhhhh
Confidence            5699999999999999998 7789999999999998754

>PF05433 Rick_17kDa_Anti: Glycine zipper 2TM domain; InterPro: IPR008816 This domain includes a putative two transmembrane alpha-helical region that contains glycine zipper motifs []

Probab=96.07  E-value=0.0021  Score=42.33  Aligned_cols=37  Identities=43%  Similarity=0.616  Sum_probs=26.2

Q ss_pred             hHHHHHHHhhhcccc--cccccccccccccchhhHHHHH
Q 024603           56 GAIVGTIFGAMKGQT--TETGFLHGAGIGAVAGAITALQ   92 (265)
Q Consensus        56 g~~~ga~~g~~~g~~--~~~g~~~ga~~Ga~~gav~s~e   92 (265)
                      |+++|+++|++.|..  .+++-..|+.+||+.||++..+
T Consensus         2 G~~~Ga~~Ga~~G~~ig~~~g~~~g~~~Ga~~Ga~~G~~   40 (42)
T PF05433_consen    2 GALIGAAVGAVAGSQIGGGNGRTLGAVAGAVAGALIGNQ   40 (42)
T ss_pred             chHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHhh
Confidence            455555555555554  3678888999999999998765

The domain is found in several Rickettsia genus specific 17 kDa surface antigen proteins [].; GO: 0019867 outer membrane

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

Probab=96.04  E-value=0.001  Score=60.76  Aligned_cols=43  Identities=28%  Similarity=0.810  Sum_probs=33.1

Q ss_pred             CcccccccccccCCCeeeecCCCCc-ccchhhHHHhhcCCCCcccccccccc
Q 024603          210 EIGCSICLEKFEEGDSARKLPSCGH-CFHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r~LP~CgH-~FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      +.-|.||++...+   ...|+ ||| .-|..|-...    ..||+||+.+..
T Consensus       300 ~~LC~ICmDaP~D---CvfLe-CGHmVtCt~CGkrm----~eCPICRqyi~r  343 (350)
T KOG4275|consen  300 RRLCAICMDAPRD---CVFLE-CGHMVTCTKCGKRM----NECPICRQYIVR  343 (350)
T ss_pred             HHHHHHHhcCCcc---eEEee-cCcEEeehhhcccc----ccCchHHHHHHH
Confidence            5679999887555   66776 999 6788886543    489999998764

>PHA03096 p28-like protein; Provisional

Probab=96.02  E-value=0.0029  Score=58.21  Aligned_cols=36  Identities=31%  Similarity=0.563  Sum_probs=29.6

Q ss_pred             cccccccccccCCC----eeeecCCCCcccchhhHHHhhc
Q 024603          211 IGCSICLEKFEEGD----SARKLPSCGHCFHSECVDKWLT  246 (265)
Q Consensus       211 ~~C~ICle~~~~~~----~~r~LP~CgH~FH~~CI~~WL~  246 (265)
                      -.|.||++......    .-..||.|.|.||..|+..|..
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~  218 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMT  218 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHH
Confidence            68999999887532    3345889999999999999976

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

Probab=95.96  E-value=0.0028  Score=59.47  Aligned_cols=47  Identities=32%  Similarity=0.632  Sum_probs=33.5

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      ......|.||++...+   ...+| |||.-|  |..-- +...+||+||+.+..
T Consensus       302 ~~~p~lcVVcl~e~~~---~~fvp-cGh~cc--ct~cs-~~l~~CPvCR~rI~~  348 (355)
T KOG1571|consen  302 LPQPDLCVVCLDEPKS---AVFVP-CGHVCC--CTLCS-KHLPQCPVCRQRIRL  348 (355)
T ss_pred             cCCCCceEEecCCccc---eeeec-CCcEEE--chHHH-hhCCCCchhHHHHHH
Confidence            3456789999998777   55566 999866  54432 234559999998754

>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=95.90  E-value=0.0036  Score=48.26  Aligned_cols=34  Identities=26%  Similarity=0.740  Sum_probs=27.8

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHH
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVD  242 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~  242 (265)
                      ..++..|++|-..+.. ......| |||.||..|++
T Consensus        75 i~~~~~C~vC~k~l~~-~~f~~~p-~~~v~H~~C~~  108 (109)
T PF10367_consen   75 ITESTKCSVCGKPLGN-SVFVVFP-CGHVVHYSCIK  108 (109)
T ss_pred             ECCCCCccCcCCcCCC-ceEEEeC-CCeEEeccccc
Confidence            3556789999999988 4555678 99999999975

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 [].

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=95.67  E-value=0.0082  Score=50.43  Aligned_cols=49  Identities=22%  Similarity=0.626  Sum_probs=35.3

Q ss_pred             cccCcccccccccccCCCeeeecC-CCCc---ccchhhHHHhhcCC--CCccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLP-SCGH---CFHSECVDKWLTRN--GSCPVCRECVC  259 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP-~CgH---~FH~~CI~~WL~~~--~sCPvCR~~v~  259 (265)
                      ...+..|-||.++-.+  ..  -| .|..   .-|.+|+.+|+..+  .+||+|+.+..
T Consensus         5 s~~~~~CRIC~~~~~~--~~--~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~   59 (162)
T PHA02825          5 SLMDKCCWICKDEYDV--VT--NYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN   59 (162)
T ss_pred             CCCCCeeEecCCCCCC--cc--CCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence            3456799999988542  22  24 3555   56999999999854  56999998763

>PRK10510 putative outer membrane lipoprotein; Provisional

Probab=95.65  E-value=0.01  Score=52.62  Aligned_cols=42  Identities=31%  Similarity=0.355  Sum_probs=29.0

Q ss_pred             HHhhhHHHHHHHhhhcccc--cccccccccccccchhhHHHHHH
Q 024603           52 FALGGAIVGTIFGAMKGQT--TETGFLHGAGIGAVAGAITALQL   93 (265)
Q Consensus        52 ~~~~g~~~ga~~g~~~g~~--~~~g~~~ga~~Ga~~gav~s~e~   93 (265)
                      -|++|+++||++|++.|=.  ...|-+-||++|+.+||.+.+..
T Consensus        38 ga~~Ga~~Ga~~G~~~g~~~~~~~~a~~ga~~G~~~G~~~g~~~   81 (219)
T PRK10510         38 GAGIGSLVGAGIGALSSSKKDRGKGALIGAAAGAALGGGVGYYM   81 (219)
T ss_pred             hhHHHHHHHHHHHhhhcCCCcccchhhhHhHHHhhhhhhhhhhh
Confidence            4556777777777776621  23477888888888888887664

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

Probab=95.63  E-value=0.0088  Score=40.20  Aligned_cols=41  Identities=37%  Similarity=0.977  Sum_probs=26.9

Q ss_pred             cccccccccCCCeeeecC-CCC---cccchhhHHHhhc--CCCCcccc
Q 024603          213 CSICLEKFEEGDSARKLP-SCG---HCFHSECVDKWLT--RNGSCPVC  254 (265)
Q Consensus       213 C~ICle~~~~~~~~r~LP-~Cg---H~FH~~CI~~WL~--~~~sCPvC  254 (265)
                      |-||+++-.+.. ....| .|.   ...|..|+.+|+.  .+.+|++|
T Consensus         1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            679999887766 23355 243   3789999999998  45679988

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

Probab=95.36  E-value=0.0064  Score=51.25  Aligned_cols=41  Identities=34%  Similarity=0.776  Sum_probs=32.2

Q ss_pred             CcccccchhhhhcccCcccccccccccCCCeeeecCCCCcccch
Q 024603          195 PECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHS  238 (265)
Q Consensus       195 p~~~~~~~~~~~~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~  238 (265)
                      |...++++  .-.++.-+|.|||||+..++.+.+|| |--+||+
T Consensus       164 PrlsYNdD--VL~ddkGECvICLEdL~~GdtIARLP-CLCIYHK  204 (205)
T KOG0801|consen  164 PRLSYNDD--VLKDDKGECVICLEDLEAGDTIARLP-CLCIYHK  204 (205)
T ss_pred             cccccccc--hhcccCCcEEEEhhhccCCCceeccc-eEEEeec
Confidence            55555443  23455689999999999999999999 9999985

>PF13488 Gly-zipper_Omp: Glycine zipper

Probab=95.33  E-value=0.0086  Score=40.19  Aligned_cols=38  Identities=39%  Similarity=0.506  Sum_probs=32.4

Q ss_pred             hhHHHHHHHhhhcccccccccccccccccchhhHHHHHH
Q 024603           55 GGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQL   93 (265)
Q Consensus        55 ~g~~~ga~~g~~~g~~~~~g~~~ga~~Ga~~gav~s~e~   93 (265)
                      .|+.+||++|+++|..+. +=..|+.+||..|+++..-+
T Consensus         1 ~Ga~iGA~~Ga~iG~~~g-~~~~ga~iGa~vGa~~G~~i   38 (46)
T PF13488_consen    1 IGAAIGAAAGAAIGAATG-GPGKGAAIGAAVGAAVGAAI   38 (46)
T ss_pred             CcHHHHHHHHHHHHHHhC-CchhhHHHHHHHHHHHHHHH
Confidence            489999999999999986 56889999999999887663

>PF13436 Gly-zipper_OmpA: Glycine-zipper containing OmpA-like membrane domain

Probab=95.29  E-value=0.0097  Score=47.78  Aligned_cols=41  Identities=37%  Similarity=0.412  Sum_probs=31.8

Q ss_pred             HHHhhhHHHHHHHhhhcccccccccccccccccchhhHHHHH
Q 024603           51 IFALGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQ   92 (265)
Q Consensus        51 ~~~~~g~~~ga~~g~~~g~~~~~g~~~ga~~Ga~~gav~s~e   92 (265)
                      -=+..|+++||++||+.|...+. --+|+++||.+||++...
T Consensus        50 ~~~~~ga~~GA~~GA~~Ga~~G~-~~~ga~~GAa~Ga~~G~~   90 (118)
T PF13436_consen   50 ENTAGGAAIGAAAGAAIGAIIGG-NGRGAAIGAAAGAAVGAA   90 (118)
T ss_pred             hhHHHHHHHHHHHHHHHHhhcCC-CccchHHHHHHHHHHHHH
Confidence            34677888888888888887766 677888888888888665

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

Probab=95.21  E-value=0.0083  Score=61.70  Aligned_cols=43  Identities=26%  Similarity=0.703  Sum_probs=34.0

Q ss_pred             CcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccccc
Q 024603          210 EIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECV  258 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v  258 (265)
                      ...|..|--+++-|..-  . .|||.||.+|+.   .....||-|+...
T Consensus       840 ~skCs~C~~~LdlP~Vh--F-~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTLDLPFVH--F-LCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCccccceee--e-ecccHHHHHhhc---cCcccCCccchhh
Confidence            36899998888876433  2 499999999998   4667899999744

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

Probab=95.18  E-value=0.013  Score=54.96  Aligned_cols=48  Identities=27%  Similarity=0.700  Sum_probs=37.6

Q ss_pred             hcccCcccccccccccCCCeeeecCCCCcccchhhHHHh--hcCCCCccccccc
Q 024603          206 QLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKW--LTRNGSCPVCREC  257 (265)
Q Consensus       206 ~~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~W--L~~~~sCPvCR~~  257 (265)
                      ..+++..|-||-+.+.-   ...+| |+|..|.-|..+.  |-.++.||+||..
T Consensus        57 tDEen~~C~ICA~~~TY---s~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE  106 (493)
T COG5236          57 TDEENMNCQICAGSTTY---SARYP-CGHQICHACAVRLRALYMQKGCPLCRTE  106 (493)
T ss_pred             cccccceeEEecCCceE---EEecc-CCchHHHHHHHHHHHHHhccCCCccccc
Confidence            45567889999887665   45677 9999999998654  4577899999974

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

Probab=95.18  E-value=0.0052  Score=56.16  Aligned_cols=51  Identities=31%  Similarity=0.687  Sum_probs=40.7

Q ss_pred             CcccccccccccCCCe-eeecCCCCcccchhhHHHhhcCCCCccccccccccCC
Q 024603          210 EIGCSICLEKFEEGDS-ARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDT  262 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~-~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~~  262 (265)
                      ...||||.+.+..... +..+| |||..|..|.......+-+||+|.+ +.+..
T Consensus       158 ~~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~-~~d~~  209 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK-PGDMS  209 (276)
T ss_pred             cCCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc-hHHHH
Confidence            4559999999887654 44565 9999999999999888899999998 54443

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=95.18  E-value=0.011  Score=41.10  Aligned_cols=47  Identities=32%  Similarity=0.627  Sum_probs=32.5

Q ss_pred             CcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccCC
Q 024603          210 EIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDT  262 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~~  262 (265)
                      ...|-.|...   +.+-..+| |+|..|..|.+-+  +-+.||+|-+++...+
T Consensus         7 ~~~~~~~~~~---~~~~~~~p-CgH~I~~~~f~~~--rYngCPfC~~~~~~~~   53 (55)
T PF14447_consen    7 EQPCVFCGFV---GTKGTVLP-CGHLICDNCFPGE--RYNGCPFCGTPFEFDD   53 (55)
T ss_pred             ceeEEEcccc---cccccccc-ccceeeccccChh--hccCCCCCCCcccCCC
Confidence            3445555333   23344566 9999999997664  6788999999987554

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

Probab=95.14  E-value=0.01  Score=50.86  Aligned_cols=50  Identities=30%  Similarity=0.751  Sum_probs=33.3

Q ss_pred             CcccccccccccCCCeee---ecCCCCcccchhhHHHhhcC-----C------CCccccccccc
Q 024603          210 EIGCSICLEKFEEGDSAR---KLPSCGHCFHSECVDKWLTR-----N------GSCPVCRECVC  259 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r---~LP~CgH~FH~~CI~~WL~~-----~------~sCPvCR~~v~  259 (265)
                      ...|.||+..--++...-   ---+||.-||.-|+..||+.     +      ..||.|..++.
T Consensus       165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia  228 (234)
T KOG3268|consen  165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA  228 (234)
T ss_pred             hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence            345777765544432211   11169999999999999972     1      24999999875

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=94.83  E-value=0.016  Score=54.13  Aligned_cols=56  Identities=27%  Similarity=0.574  Sum_probs=39.9

Q ss_pred             cCcccccccccccCCCeee-ecCCCCcccchhhHHHhhc-CCCCccccccccccCCCCC
Q 024603          209 NEIGCSICLEKFEEGDSAR-KLPSCGHCFHSECVDKWLT-RNGSCPVCRECVCKDTDTW  265 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r-~LP~CgH~FH~~CI~~WL~-~~~sCPvCR~~v~~~~~~~  265 (265)
                      ++..||.|++++...++-- -+| ||...|.-|...--. -+..||-||+...+++-.|
T Consensus        13 eed~cplcie~mditdknf~pc~-cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~   70 (480)
T COG5175          13 EEDYCPLCIEPMDITDKNFFPCP-CGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRY   70 (480)
T ss_pred             ccccCcccccccccccCCcccCC-cccHHHHHHHHHHHhhccCCChHhhhhccccceeE
Confidence            4456999999998765432 354 999888888655322 3578999999887665544

>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=94.83  E-value=0.015  Score=47.66  Aligned_cols=38  Identities=21%  Similarity=0.717  Sum_probs=29.7

Q ss_pred             CcccccccccccCCCeeeecCCCC------cccchhhHHHhhcCC
Q 024603          210 EIGCSICLEKFEEGDSARKLPSCG------HCFHSECVDKWLTRN  248 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r~LP~Cg------H~FH~~CI~~WL~~~  248 (265)
                      ..+|.||++.+.+..-+..++ |+      |.||.+|+.+|-+.+
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~~~~   69 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWRRER   69 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHHhhc
Confidence            679999999999855555555 65      899999999994433

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.

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

Probab=94.63  E-value=0.02  Score=53.14  Aligned_cols=47  Identities=23%  Similarity=0.504  Sum_probs=36.9

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      .+-.+||||.+.+..|..-  . .=||.-|..|-.+   ....||.||.++.+
T Consensus        46 ~~lleCPvC~~~l~~Pi~Q--C-~nGHlaCssC~~~---~~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   46 LDLLDCPVCFNPLSPPIFQ--C-DNGHLACSSCRTK---VSNKCPTCRLPIGN   92 (299)
T ss_pred             hhhccCchhhccCccccee--c-CCCcEehhhhhhh---hcccCCcccccccc
Confidence            4568999999999987655  1 1379999999753   57789999998863

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

Probab=94.61  E-value=0.019  Score=52.91  Aligned_cols=43  Identities=30%  Similarity=0.781  Sum_probs=35.6

Q ss_pred             cccccccccccCCCeeeecCCCCcccchhhHHHhhc-CCCCcccccc
Q 024603          211 IGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-RNGSCPVCRE  256 (265)
Q Consensus       211 ~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~-~~~sCPvCR~  256 (265)
                      +.|+.|-.-+.++.+.   |.|+|.||.+||..-|. ....||.|.+
T Consensus       275 LkCplc~~Llrnp~kT---~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRNPMKT---PCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhCcccC---ccccchHHHHHHhhhhhhccccCCCccc
Confidence            7899998888876554   68999999999987655 5678999976

>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=94.31  E-value=0.03  Score=36.91  Aligned_cols=41  Identities=27%  Similarity=0.814  Sum_probs=24.0

Q ss_pred             cccccccccCCCeeeecCCCCcccchhhHHHhhcCCC--Ccccc
Q 024603          213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG--SCPVC  254 (265)
Q Consensus       213 C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~--sCPvC  254 (265)
                      |.+|.+....+..-... .|+=.+|..|+.+++....  .||.|
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            66787777776655322 4999999999999998765  79987

; PDB: 3NW0_A 2CT0_A.

>PF04641 Rtf2: Rtf2 RING-finger

Probab=94.29  E-value=0.041  Score=49.86  Aligned_cols=54  Identities=19%  Similarity=0.492  Sum_probs=41.5

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      ......|||...++........+-.|||+|...++.+- .....||+|-.++...
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~f~~~  163 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKPFTEE  163 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCccccC
Confidence            34568999999999665555555459999999999987 2356799999887643

>PRK10540 lipoprotein; Provisional

Probab=93.65  E-value=0.091  Score=38.62  Aligned_cols=36  Identities=31%  Similarity=0.305  Sum_probs=23.3

Q ss_pred             hhhHHHHHHHhhhcccccccccccccccccchhhHHHHHH
Q 024603           54 LGGAIVGTIFGAMKGQTTETGFLHGAGIGAVAGAITALQL   93 (265)
Q Consensus        54 ~~g~~~ga~~g~~~g~~~~~g~~~ga~~Ga~~gav~s~e~   93 (265)
                      ..|+..|+++|++.|.    |-..|+.+||+.|+++..++
T Consensus        35 ~~Ga~~Ga~~Ga~~g~----g~~~g~~~Ga~~G~~~G~~v   70 (72)
T PRK10540         35 AIGAGAGALGGAVLTD----GSTLGTLGGAAVGGVIGHQV   70 (72)
T ss_pred             HHHHHHHHHHHHHhcC----CcHHHHHHHHHHHHHHhHhh
Confidence            3466666666666653    33367777888888777653

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

Probab=93.15  E-value=0.006  Score=57.77  Aligned_cols=51  Identities=31%  Similarity=0.677  Sum_probs=42.5

Q ss_pred             CcccccccccccCC-CeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          210 EIGCSICLEKFEEG-DSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       210 ~~~C~ICle~~~~~-~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      ...|+||.+.+... +.+..+ .|||.+|..|+.+||.....||.||+.+...
T Consensus       196 v~sl~I~~~slK~~y~k~~~~-~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~  247 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAI-VCGHIYHHGKLSKWLATKRKLPSCRRELPKN  247 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHH-hhcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence            46899999999876 444444 4999999999999999999999999988643

>PRK11280 hypothetical protein; Provisional

Probab=93.00  E-value=0.054  Score=46.18  Aligned_cols=41  Identities=22%  Similarity=0.371  Sum_probs=28.1

Q ss_pred             hhHHHHHHHhhhcccccc--cccccccccccchhhHHHHHHHh
Q 024603           55 GGAIVGTIFGAMKGQTTE--TGFLHGAGIGAVAGAITALQLLE   95 (265)
Q Consensus        55 ~g~~~ga~~g~~~g~~~~--~g~~~ga~~Ga~~gav~s~e~~~   95 (265)
                      .|+++||++|++.|..-+  +|=.-++++||++||++..++=+
T Consensus        66 ~Gtv~Gav~Gg~~G~~iGgG~Gr~~at~~Ga~~G~~~G~~i~~  108 (170)
T PRK11280         66 AGSVLGAVAGGVLGHQFGGGRGKDVATVAGALGGGYAGNQIQG  108 (170)
T ss_pred             hhHHHHHHHHHHhhhhccCCCccHHHHHHHHHHHHHHHHHHHH
Confidence            577777777777776543  34344677888888888877433

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

Probab=92.96  E-value=0.039  Score=51.03  Aligned_cols=45  Identities=31%  Similarity=0.722  Sum_probs=31.4

Q ss_pred             cccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccccccc
Q 024603          211 IGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       211 ~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      -.|--|  ++....--|..| |.|.||.+|...  ...+.||.|-..|..
T Consensus        91 HfCd~C--d~PI~IYGRmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~Vqr  135 (389)
T KOG2932|consen   91 HFCDRC--DFPIAIYGRMIP-CKHVFCLECARS--DSDKICPLCDDRVQR  135 (389)
T ss_pred             Eeeccc--CCcceeeecccc-cchhhhhhhhhc--CccccCcCcccHHHH
Confidence            345555  333334457788 999999999864  345689999887754

>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=92.72  E-value=0.07  Score=46.95  Aligned_cols=41  Identities=32%  Similarity=0.783  Sum_probs=30.8

Q ss_pred             cccccccccCCCeeeecCCCCc-ccchhhHHHhhcCCCCccccccccccC
Q 024603          213 CSICLEKFEEGDSARKLPSCGH-CFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       213 C~ICle~~~~~~~~r~LP~CgH-~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      |-.|-+.   +..+..+| |.| .+|..|-..    -..||+|+.+....
T Consensus       161 Cr~C~~~---~~~VlllP-CrHl~lC~~C~~~----~~~CPiC~~~~~s~  202 (207)
T KOG1100|consen  161 CRKCGER---EATVLLLP-CRHLCLCGICDES----LRICPICRSPKTSS  202 (207)
T ss_pred             ceecCcC---CceEEeec-ccceEeccccccc----CccCCCCcChhhce
Confidence            8788554   55588898 988 899999654    45699999876544

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

Probab=92.60  E-value=0.081  Score=43.25  Aligned_cols=54  Identities=22%  Similarity=0.473  Sum_probs=40.8

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhc---CCCCccccccccccCC
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT---RNGSCPVCRECVCKDT  262 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~---~~~sCPvCR~~v~~~~  262 (265)
                      .-.+|-||.|.-.+...+.--.-||-..|..|....++   .++.||+|+.+..+..
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            45789999988777555533335999999999876655   5678999999887654

>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=92.29  E-value=0.07  Score=35.98  Aligned_cols=31  Identities=26%  Similarity=0.731  Sum_probs=22.5

Q ss_pred             CC-CcccchhhHHHhhcCCCCccccccccccC
Q 024603          231 SC-GHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       231 ~C-gH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      .| .|+.|..|+...+.....||+|..+++..
T Consensus        17 ~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen   17 KCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             E-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             eecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            46 59999999999999999999999998754

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.

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

Probab=92.27  E-value=0.052  Score=58.27  Aligned_cols=48  Identities=33%  Similarity=0.870  Sum_probs=39.9

Q ss_pred             hcccCccccccccccc-CCCeeeecCCCCcccchhhHHHhhcCCCCccccccc
Q 024603          206 QLDNEIGCSICLEKFE-EGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCREC  257 (265)
Q Consensus       206 ~~~~~~~C~ICle~~~-~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~  257 (265)
                      +......|.||++.+. .+-..    .|||.+|..|...|+..+..||.|+..
T Consensus      1149 ~~~~~~~c~ic~dil~~~~~I~----~cgh~~c~~c~~~~l~~~s~~~~~ksi 1197 (1394)
T KOG0298|consen 1149 NLSGHFVCEICLDILRNQGGIA----GCGHEPCCRCDELWLYASSRCPICKSI 1197 (1394)
T ss_pred             HhhcccchHHHHHHHHhcCCee----eechhHhhhHHHHHHHHhccCcchhhh
Confidence            3445568999999998 44444    699999999999999999999999843

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

Probab=92.20  E-value=0.063  Score=54.99  Aligned_cols=44  Identities=32%  Similarity=0.785  Sum_probs=33.7

Q ss_pred             cccccccccccCCCeeeecCCCCcccchhhHHHhhcCC--CCccccccccc
Q 024603          211 IGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN--GSCPVCRECVC  259 (265)
Q Consensus       211 ~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~--~sCPvCR~~v~  259 (265)
                      ..|.||++ ...   .... .|+|.||.+|+.+-+...  ..||+||..+.
T Consensus       455 ~~c~ic~~-~~~---~~it-~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~  500 (674)
T KOG1001|consen  455 HWCHICCD-LDS---FFIT-RCGHDFCVECLKKSIQQSENAPCPLCRNVLK  500 (674)
T ss_pred             cccccccc-ccc---ceee-cccchHHHHHHHhccccccCCCCcHHHHHHH
Confidence            89999999 333   3334 499999999999887643  35999998764

>PRK10540 lipoprotein; Provisional

Probab=92.08  E-value=0.17  Score=37.16  Aligned_cols=13  Identities=31%  Similarity=0.677  Sum_probs=5.1

Q ss_pred             hHHHHHHHhhhcc
Q 024603           56 GAIVGTIFGAMKG   68 (265)
Q Consensus        56 g~~~ga~~g~~~g   68 (265)
                      |+++||++|++.|
T Consensus        55 g~~~Ga~~G~~~G   67 (72)
T PRK10540         55 GTLGGAAVGGVIG   67 (72)
T ss_pred             HHHHHHHHHHHHh
Confidence            3333444443333

>TIGR03789 pdsO proteobacterial sortase system OmpA family protein

Probab=91.52  E-value=0.079  Score=47.66  Aligned_cols=16  Identities=31%  Similarity=0.528  Sum_probs=10.0

Q ss_pred             cccccccchhhHHHHH
Q 024603           77 HGAGIGAVAGAITALQ   92 (265)
Q Consensus        77 ~ga~~Ga~~gav~s~e   92 (265)
                      -|+.+|++.|++++.+
T Consensus        61 ~G~~~G~~~G~~~g~~   76 (239)
T TIGR03789        61 VGAIIGGITGGLIGQA   76 (239)
T ss_pred             HHHHHHHHHHHHhhhh
Confidence            3666666666666655

A newly defined histidine kinase (TIGR03785) and response regulator (TIGR03787) gene pair occurs exclusively in Proteobacteria, mostly of marine origin, nearly all of which contain a subfamily 6 sortase (TIGR03784) and its single dedicated target protein (TIGR03788) adjacent to to the sortase. This protein family shows up in only in those species with the histidine kinase/response regulator gene pair, and often adjacent to that pair. It belongs to the OmpA protein family (pfam00691). Its function is unknown. We assign the gene symbol pdsO, for Proteobacterial Dedicated Sortase system OmpA family protein.

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

Probab=91.51  E-value=0.057  Score=54.30  Aligned_cols=45  Identities=31%  Similarity=0.589  Sum_probs=33.4

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccc
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRE  256 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~  256 (265)
                      +-..|+||+..|......-+-+.|||+.|..|+...  .+.+|| |+.
T Consensus        10 ~~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~   54 (861)
T KOG3161|consen   10 LLLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKR   54 (861)
T ss_pred             HHhhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCc
Confidence            346899998888765544444479999999999886  466788 554

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

Probab=91.48  E-value=0.06  Score=54.72  Aligned_cols=50  Identities=28%  Similarity=0.683  Sum_probs=40.3

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC---CCccccccccccC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN---GSCPVCRECVCKD  261 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~---~sCPvCR~~v~~~  261 (265)
                      ....+|+||.+.+.++..+    +|.|.||..|+..-+...   ..||+|+..+.+.
T Consensus        19 ~k~lEc~ic~~~~~~p~~~----kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~   71 (684)
T KOG4362|consen   19 QKILECPICLEHVKEPSLL----KCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKR   71 (684)
T ss_pred             hhhccCCceeEEeeccchh----hhhHHHHhhhhhceeeccCccccchhhhhhhhhh
Confidence            3468999999999998555    799999999998766644   4699999777543

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

Probab=91.25  E-value=0.13  Score=49.29  Aligned_cols=30  Identities=40%  Similarity=1.048  Sum_probs=23.8

Q ss_pred             cCCCCcccchhhHHHhhcCC--CCcccccccc
Q 024603          229 LPSCGHCFHSECVDKWLTRN--GSCPVCRECV  258 (265)
Q Consensus       229 LP~CgH~FH~~CI~~WL~~~--~sCPvCR~~v  258 (265)
                      -|.|||.|-.+||++||.+.  ..||.|....
T Consensus        24 sl~cghlFgs~cie~wl~k~~~~~cp~c~~ka   55 (463)
T KOG1645|consen   24 SLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA   55 (463)
T ss_pred             eecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence            34699999999999999522  3599998654

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

Probab=91.08  E-value=0.28  Score=46.65  Aligned_cols=29  Identities=34%  Similarity=0.984  Sum_probs=20.4

Q ss_pred             CCcccchhhHHHhhc-------------CCCCcccccccccc
Q 024603          232 CGHCFHSECVDKWLT-------------RNGSCPVCRECVCK  260 (265)
Q Consensus       232 CgH~FH~~CI~~WL~-------------~~~sCPvCR~~v~~  260 (265)
                      |...-|.+|+.+|+.             ++-.||+||+...-
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi  352 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI  352 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence            344557889988875             33459999998653

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

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=90.81  E-value=0.26  Score=34.18  Aligned_cols=41  Identities=34%  Similarity=0.852  Sum_probs=33.9

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccc
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPV  253 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPv  253 (265)
                      ....|++|-+.|.+++.+.+.|.|+--+|.+|.++    ...|-.
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~   44 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCIN   44 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEe
Confidence            45689999999998888889999999999999754    455544

>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=90.51  E-value=0.086  Score=47.24  Aligned_cols=50  Identities=24%  Similarity=0.565  Sum_probs=37.3

Q ss_pred             cCccccccccccc-CC-CeeeecCCCCcccchhhHHHhhcCC-CCcc--cccccc
Q 024603          209 NEIGCSICLEKFE-EG-DSARKLPSCGHCFHSECVDKWLTRN-GSCP--VCRECV  258 (265)
Q Consensus       209 ~~~~C~ICle~~~-~~-~~~r~LP~CgH~FH~~CI~~WL~~~-~sCP--vCR~~v  258 (265)
                      .+..||||..|.- .| ..+..-|.|-|..|.+|+++-+... ..||  -|-+-+
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL   63 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL   63 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence            3568999987753 33 3455567799999999999998754 5799  776544

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

Probab=90.29  E-value=0.13  Score=53.59  Aligned_cols=37  Identities=30%  Similarity=0.763  Sum_probs=28.7

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhh
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWL  245 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL  245 (265)
                      .+.+++|.+|...+... .-...| |||.||.+|+.+-.
T Consensus       814 ~ep~d~C~~C~~~ll~~-pF~vf~-CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  814 LEPQDSCDHCGRPLLIK-PFYVFP-CGHCFHRDCLIRHV  850 (911)
T ss_pred             ecCccchHHhcchhhcC-cceeee-ccchHHHHHHHHHH
Confidence            45678999999888764 344566 99999999997543

>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=89.99  E-value=0.34  Score=40.79  Aligned_cols=38  Identities=24%  Similarity=0.556  Sum_probs=23.3

Q ss_pred             cCcccccccccccCCCeeeecC---C-----CCc-ccchhhHHHhhc
Q 024603          209 NEIGCSICLEKFEEGDSARKLP---S-----CGH-CFHSECVDKWLT  246 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP---~-----CgH-~FH~~CI~~WL~  246 (265)
                      ++..||||||.-.+...+.--.   +     |+- .-|..|+++.-+
T Consensus         1 ed~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    1 EDVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CCccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            3568999999877654442100   1     443 346789987643

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.

>COG4803 Predicted membrane protein [Function unknown]

Probab=88.55  E-value=0.058  Score=45.01  Aligned_cols=19  Identities=37%  Similarity=0.669  Sum_probs=9.4

Q ss_pred             ccccccccccchhhHHHHH
Q 024603           74 GFLHGAGIGAVAGAITALQ   92 (265)
Q Consensus        74 g~~~ga~~Ga~~gav~s~e   92 (265)
                      |+.-||+.||++|++.-+.
T Consensus        82 G~avGAa~GAl~g~l~DvG  100 (170)
T COG4803          82 GMAVGAASGALSGSLTDVG  100 (170)
T ss_pred             HHHHHHhhhhhccceeecC
Confidence            4444455555555554443

>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair

Probab=87.98  E-value=0.53  Score=32.27  Aligned_cols=43  Identities=28%  Similarity=0.614  Sum_probs=22.5

Q ss_pred             cccccccccCC------CeeeecCCCCcccchhhHHHhhcCCCCccccc
Q 024603          213 CSICLEKFEEG------DSARKLPSCGHCFHSECVDKWLTRNGSCPVCR  255 (265)
Q Consensus       213 C~ICle~~~~~------~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR  255 (265)
                      |--|+..+..+      ......|+|++.||.+|=.---+.=..||-|-
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~   50 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE   50 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence            45566666664      34667889999999999433222335799884

It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.

>PF06897 DUF1269: Protein of unknown function (DUF1269); InterPro: IPR009200 There are currently no experimental data for members of this group or their homologues

Probab=87.93  E-value=0.15  Score=39.91  Aligned_cols=13  Identities=54%  Similarity=0.782  Sum_probs=5.8

Q ss_pred             ccccccccchhhH
Q 024603           76 LHGAGIGAVAGAI   88 (265)
Q Consensus        76 ~~ga~~Ga~~gav   88 (265)
                      +=||+.||++|++
T Consensus        23 ~~GA~~Gal~G~l   35 (102)
T PF06897_consen   23 AVGAAAGALAGAL   35 (102)
T ss_pred             HHHHHHHHHHhHH
Confidence            4444444444443

However, these proteins are predicted to contain two or more transmembrane segments.

>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=87.73  E-value=0.24  Score=33.63  Aligned_cols=43  Identities=19%  Similarity=0.552  Sum_probs=20.7

Q ss_pred             cccccccccccCCCeeeecCCCCcccchhhHHHhhcCC-----CCccccccc
Q 024603          211 IGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN-----GSCPVCREC  257 (265)
Q Consensus       211 ~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~-----~sCPvCR~~  257 (265)
                      +.|+|....+..|.+.  . .|.|.-|.+ ++.|+...     -.||+|.++
T Consensus         3 L~CPls~~~i~~P~Rg--~-~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRIPVRG--K-NCKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SSEEEE--T-T--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEeCccC--C-cCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            5788888888775544  3 599976544 34555422     359999874

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.

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.68  E-value=0.21  Score=45.21  Aligned_cols=52  Identities=29%  Similarity=0.661  Sum_probs=36.7

Q ss_pred             cccCcccccccccccCCCee-eecCCC-----CcccchhhHHHhhcCC--------CCccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSA-RKLPSC-----GHCFHSECVDKWLTRN--------GSCPVCRECVC  259 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~-r~LP~C-----gH~FH~~CI~~WL~~~--------~sCPvCR~~v~  259 (265)
                      .+.+..|-||+..=++.... -+-| |     .|..|..|+..|+..+        -+||.|+....
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            34567899999876665433 2234 5     4899999999998633        24999998653

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

Probab=87.42  E-value=0.24  Score=47.50  Aligned_cols=37  Identities=30%  Similarity=0.669  Sum_probs=27.8

Q ss_pred             cCcccccccccccCC-CeeeecCCCCcccchhhHHHhhc
Q 024603          209 NEIGCSICLEKFEEG-DSARKLPSCGHCFHSECVDKWLT  246 (265)
Q Consensus       209 ~~~~C~ICle~~~~~-~~~r~LP~CgH~FH~~CI~~WL~  246 (265)
                      ...+|.||..+...+ .... ...|+|.||.+|..+.+.
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~-~~~C~H~fC~~C~k~~ie  182 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFS-VLKCGHRFCKDCVKQHIE  182 (384)
T ss_pred             ccccCccCccccccHhhhHH-HhcccchhhhHHhHHHhh
Confidence            467999999555444 4444 446999999999998876

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

Probab=87.38  E-value=0.4  Score=45.81  Aligned_cols=48  Identities=19%  Similarity=0.450  Sum_probs=39.5

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC---CCccccccc
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN---GSCPVCREC  257 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~---~sCPvCR~~  257 (265)
                      ....|||=.+.-.+.....+|+ |||+.+.+-+++.-+..   ..||.|=..
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~e  383 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYCPVE  383 (394)
T ss_pred             ceeecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence            4478999988888888888887 99999999999987654   369999543

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

Probab=86.45  E-value=0.4  Score=43.86  Aligned_cols=32  Identities=41%  Similarity=0.858  Sum_probs=25.2

Q ss_pred             eeecCCCCcccchhhHHHhhcCC-CCcccccccc
Q 024603          226 ARKLPSCGHCFHSECVDKWLTRN-GSCPVCRECV  258 (265)
Q Consensus       226 ~r~LP~CgH~FH~~CI~~WL~~~-~sCPvCR~~v  258 (265)
                      .|.| +|||.+|..|+.+.+... ..||.||.+.
T Consensus        22 p~~l-~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen   22 PRVL-KCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             Cccc-ccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            3444 599999999998887654 4699999984

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

Probab=86.02  E-value=0.44  Score=43.43  Aligned_cols=49  Identities=31%  Similarity=0.732  Sum_probs=35.3

Q ss_pred             CcccccccccccCCCe-eeecCCCC-----cccchhhHHHhhc--CCCCccccccccc
Q 024603          210 EIGCSICLEKFEEGDS-ARKLPSCG-----HCFHSECVDKWLT--RNGSCPVCRECVC  259 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~-~r~LP~Cg-----H~FH~~CI~~WL~--~~~sCPvCR~~v~  259 (265)
                      +..|-||.++...... ....| |.     +..|..|+.+|+.  ....|.+|.....
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~p-C~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~  134 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISP-CSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI  134 (323)
T ss_pred             CCcEEEEecccccccccccccC-ccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence            4789999997765431 23344 53     6789999999998  4567999987553

>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=85.65  E-value=0.34  Score=44.48  Aligned_cols=36  Identities=22%  Similarity=0.625  Sum_probs=30.9

Q ss_pred             cCcccccccccccCCCeeeecCCC----CcccchhhHHHhhcCC
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSC----GHCFHSECVDKWLTRN  248 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~C----gH~FH~~CI~~WL~~~  248 (265)
                      ..+.|.+|.|.+++...+    +|    .|.||..|-++-++.+
T Consensus       267 apLcCTLC~ERLEDTHFV----QCPSVp~HKFCFPCSResIK~Q  306 (352)
T KOG3579|consen  267 APLCCTLCHERLEDTHFV----QCPSVPSHKFCFPCSRESIKQQ  306 (352)
T ss_pred             CceeehhhhhhhccCcee----ecCCCcccceecccCHHHHHhh
Confidence            348999999999998777    56    6999999999988855

>PF05433 Rick_17kDa_Anti: Glycine zipper 2TM domain; InterPro: IPR008816 This domain includes a putative two transmembrane alpha-helical region that contains glycine zipper motifs []

Probab=85.28  E-value=0.34  Score=31.86  Aligned_cols=33  Identities=39%  Similarity=0.557  Sum_probs=17.2

Q ss_pred             hhhHHHHHHHhhhc--ccccccccccccccccchh
Q 024603           54 LGGAIVGTIFGAMK--GQTTETGFLHGAGIGAVAG   86 (265)
Q Consensus        54 ~~g~~~ga~~g~~~--g~~~~~g~~~ga~~Ga~~g   86 (265)
                      ++|+++|+++|...  +--.-.|.+=|+.+|++.|
T Consensus         4 ~~Ga~~Ga~~G~~ig~~~g~~~g~~~Ga~~Ga~~G   38 (42)
T PF05433_consen    4 LIGAAVGAVAGSQIGGGNGRTLGAVAGAVAGALIG   38 (42)
T ss_pred             HHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHH
Confidence            34555555555444  4445555555555555554

The domain is found in several Rickettsia genus specific 17 kDa surface antigen proteins [].; GO: 0019867 outer membrane

>PF06897 DUF1269: Protein of unknown function (DUF1269); InterPro: IPR009200 There are currently no experimental data for members of this group or their homologues

Probab=84.95  E-value=0.88  Score=35.61  Aligned_cols=23  Identities=35%  Similarity=0.495  Sum_probs=15.8

Q ss_pred             hhHHHHHHHhhhccccccccccc
Q 024603           55 GGAIVGTIFGAMKGQTTETGFLH   77 (265)
Q Consensus        55 ~g~~~ga~~g~~~g~~~~~g~~~   77 (265)
                      +|+++||.+||+.|-.++.|+=+
T Consensus        20 ~G~~~GA~~Gal~G~l~d~gI~d   42 (102)
T PF06897_consen   20 LGAAVGAAAGALAGALSDYGIDD   42 (102)
T ss_pred             HHHHHHHHHHHHHhHHhhCCCCH
Confidence            67777777777777766666544

However, these proteins are predicted to contain two or more transmembrane segments.

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

Probab=84.82  E-value=0.46  Score=27.98  Aligned_cols=23  Identities=35%  Similarity=0.700  Sum_probs=15.3

Q ss_pred             ccccccccccCCCeeeecCCCCccc
Q 024603          212 GCSICLEKFEEGDSARKLPSCGHCF  236 (265)
Q Consensus       212 ~C~ICle~~~~~~~~r~LP~CgH~F  236 (265)
                      .||-|...+.  ...+..|.|||.|
T Consensus         2 ~CP~C~~~V~--~~~~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCPECGAEVP--ESAKFCPHCGYDF   24 (26)
T ss_pred             cCCCCcCCch--hhcCcCCCCCCCC
Confidence            4777776653  3455577888877

Several members are annotated as putative helicases.

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

Probab=84.15  E-value=0.78  Score=47.18  Aligned_cols=41  Identities=20%  Similarity=0.491  Sum_probs=31.2

Q ss_pred             cccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccc
Q 024603          211 IGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPV  253 (265)
Q Consensus       211 ~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPv  253 (265)
                      -.|.+|-..+..  .....+.|+|.-|.+|+.+|+..+..||.
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            468888555433  23346689999999999999998888876

>TIGR02865 spore_II_E stage II sporulation protein E

Probab=83.36  E-value=4.7  Score=42.18  Aligned_cols=55  Identities=18%  Similarity=0.414  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHh-----hhHHHHHHHhhhcccccc---------------ccccccccc-ccchhhHHHHHHH
Q 024603           40 MKRVLYAALTCIFAL-----GGAIVGTIFGAMKGQTTE---------------TGFLHGAGI-GAVAGAITALQLL   94 (265)
Q Consensus        40 ~~~~~~~~~~~~~~~-----~g~~~ga~~g~~~g~~~~---------------~g~~~ga~~-Ga~~gav~s~e~~   94 (265)
                      ++++++..+..+||.     +||.+|+++|.+.|.++.               .|++|..+. |...|=+++.-++
T Consensus       177 l~~il~~~~vl~~a~~gG~~~Gaa~Gv~~Gli~~l~~~~~~~~~~~~af~GLlaG~fk~~gK~g~~~g~~l~~~il  252 (764)
T TIGR02865       177 LENIIARLAVLLISYIGGSGAGAAGGVVIGVILGLANNANLYQIGVFGFAGLLGGIFKELGKIGTGIGYLVGFLIL  252 (764)
T ss_pred             HHHHHHHHHHHHHHHhcCchHhHHHHHHHHHHHHhcCccHHHHHHHHHHHHHHHHhhccCCcceeeHHHHHHHHHH
Confidence            455666666666663     367777777777777643               344454454 5555555555333

Stage II sporulation protein E (SpoIIE) is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation. By means of it protein phosphatase activity, located in the C-terminal region, it activates sigma-F. All proteins that score above the trusted cutoff to this model are found in endospore-forming Gram-positive bacteria. Surprisingly, a sequence from the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis is homologous, and scores between the trusted and noise cutoffs.

>TIGR00622 ssl1 transcription factor ssl1

Probab=83.13  E-value=1.3  Score=35.23  Aligned_cols=46  Identities=20%  Similarity=0.310  Sum_probs=35.0

Q ss_pred             CcccccccccccCC----------CeeeecCCCCcccchhhHHHhhcCCCCccccc
Q 024603          210 EIGCSICLEKFEEG----------DSARKLPSCGHCFHSECVDKWLTRNGSCPVCR  255 (265)
Q Consensus       210 ~~~C~ICle~~~~~----------~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR  255 (265)
                      ...|--|+..|.++          ......|+|++.||.+|-.-+-+.=..||-|.
T Consensus        55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~  110 (112)
T TIGR00622        55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI  110 (112)
T ss_pred             CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence            35699999988653          12345778999999999777766667899996

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

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=83.07  E-value=2.8  Score=37.97  Aligned_cols=52  Identities=17%  Similarity=0.363  Sum_probs=38.5

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccCC
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDT  262 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~~  262 (265)
                      ....|||=--++........+-.|||+|-..-+.+-  ....|++|...+..++
T Consensus       110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~d  161 (293)
T KOG3113|consen  110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDD  161 (293)
T ss_pred             ceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccC
Confidence            346799887777766555445569999998877664  4678999999876543

>smart00249 PHD PHD zinc finger

Probab=82.23  E-value=0.99  Score=28.60  Aligned_cols=31  Identities=23%  Similarity=0.614  Sum_probs=22.4

Q ss_pred             ccccccccccCCCeeeecCCCCcccchhhHHH
Q 024603          212 GCSICLEKFEEGDSARKLPSCGHCFHSECVDK  243 (265)
Q Consensus       212 ~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~  243 (265)
                      .|.+|.... ++..+.....|.+.||..|+..
T Consensus         1 ~C~~C~~~~-~~~~~i~C~~C~~~~H~~C~~~   31 (47)
T smart00249        1 YCSVCGKPD-DGGELLQCDGCDRWYHQTCLGP   31 (47)
T ss_pred             CcccCCCcC-CCCCEEECCCCCchhhhhhCCC
Confidence            377887766 4444555557999999999854

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

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

Probab=82.09  E-value=0.77  Score=47.32  Aligned_cols=23  Identities=35%  Similarity=1.054  Sum_probs=21.4

Q ss_pred             CCCcccchhhHHHhhcCCCCccc
Q 024603          231 SCGHCFHSECVDKWLTRNGSCPV  253 (265)
Q Consensus       231 ~CgH~FH~~CI~~WL~~~~sCPv  253 (265)
                      .|+|..|.+|...|++....||-
T Consensus      1047 ~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1047 TCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             cccccccHHHHHHHHhcCCcCCC
Confidence            59999999999999999999984

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

Probab=81.72  E-value=0.95  Score=47.01  Aligned_cols=51  Identities=24%  Similarity=0.618  Sum_probs=36.3

Q ss_pred             ccCcccccccccccCCCeeeecC-CCC---cccchhhHHHhhcCC--CCccccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLP-SCG---HCFHSECVDKWLTRN--GSCPVCRECVC  259 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP-~Cg---H~FH~~CI~~WL~~~--~sCPvCR~~v~  259 (265)
                      +++..|-||..+=..++.+- -| +|.   ...|.+|+-+|+...  ..|-+|+.+++
T Consensus        10 ~d~~~CRICr~e~~~d~pLf-hPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~   66 (1175)
T COG5183          10 EDKRSCRICRTEDIRDDPLF-HPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK   66 (1175)
T ss_pred             ccchhceeecCCCCCCCcCc-ccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence            44589999987655544442 23 343   468999999999854  46999998764

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

Probab=81.49  E-value=0.6  Score=31.07  Aligned_cols=44  Identities=27%  Similarity=0.647  Sum_probs=29.9

Q ss_pred             ccccccccccCCCeeeecCCCCcccchhhHHHhhc------CCCCcccccc
Q 024603          212 GCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT------RNGSCPVCRE  256 (265)
Q Consensus       212 ~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~------~~~sCPvCR~  256 (265)
                      .|.||.+. .+...+.....|+..||..|+..=..      ..-.||.|+.
T Consensus         1 ~C~vC~~~-~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~   50 (51)
T PF00628_consen    1 YCPVCGQS-DDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP   50 (51)
T ss_dssp             EBTTTTSS-CTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred             eCcCCCCc-CCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence            38899883 33444555667999999999864332      2346998874

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

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=81.22  E-value=0.66  Score=42.81  Aligned_cols=28  Identities=25%  Similarity=0.847  Sum_probs=21.7

Q ss_pred             CCcccchhhHHHhhc-------------CCCCccccccccc
Q 024603          232 CGHCFHSECVDKWLT-------------RNGSCPVCRECVC  259 (265)
Q Consensus       232 CgH~FH~~CI~~WL~-------------~~~sCPvCR~~v~  259 (265)
                      |...-|.+|+.+|+.             ++-+||+||++..
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fc  365 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFC  365 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceE
Confidence            566778899988764             4557999999765

>PF05818 TraT: Enterobacterial TraT complement resistance protein; InterPro: IPR008874 The traT gene is one of the F factor transfer genes and encodes an outer membrane protein which is involved in interactions between Escherichia coli and its surroundings []

Probab=80.98  E-value=1  Score=39.93  Aligned_cols=36  Identities=39%  Similarity=0.589  Sum_probs=19.1

Q ss_pred             hhHHHHHHHhhhcccccccccccccccc-cchhhHHHHH
Q 024603           55 GGAIVGTIFGAMKGQTTETGFLHGAGIG-AVAGAITALQ   92 (265)
Q Consensus        55 ~g~~~ga~~g~~~g~~~~~g~~~ga~~G-a~~gav~s~e   92 (265)
                      +|++.||.+|+..|-.+  +=-+|+++| .++||+++.-
T Consensus        88 gga~~Ga~~G~~~g~~~--~~~~g~~~G~GlaGalig~~  124 (215)
T PF05818_consen   88 GGALAGAATGAAIGAYN--SGSAGAAIGAGLAGALIGMI  124 (215)
T ss_pred             hhHHHHhHHhhhhcccc--CCccchhhhhhHHHhHHHHH
Confidence            45555555665555232  223455555 5666665554

The protein plays a role in preventing unproductive conjugation between bacteria carrying like plasmids.; GO: 0046999 regulation of conjugation, 0019867 outer membrane

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

Probab=80.82  E-value=0.74  Score=46.05  Aligned_cols=47  Identities=36%  Similarity=0.882  Sum_probs=38.1

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccCC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDT  262 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~~  262 (265)
                      +....|.+|+++.    ..+..| |.   |..|+.+|+..+..||+|+..+..++
T Consensus       477 ~~~~~~~~~~~~~----~~~~~~-~~---~~~~l~~~~~~~~~~pl~~~~~~~~~  523 (543)
T KOG0802|consen  477 EPNDVCAICYQEM----SARITP-CS---HALCLRKWLYVQEVCPLCHTYMKEDD  523 (543)
T ss_pred             cccCcchHHHHHH----Hhcccc-cc---chhHHHhhhhhccccCCCchhhhccc
Confidence            3457899999998    455555 88   89999999999999999998876443

>PRK10510 putative outer membrane lipoprotein; Provisional

Probab=80.72  E-value=0.81  Score=40.52  Aligned_cols=40  Identities=35%  Similarity=0.311  Sum_probs=30.9

Q ss_pred             hhHHHHHHHhhhcccccccc--cccccccccchhhHHHHHHH
Q 024603           55 GGAIVGTIFGAMKGQTTETG--FLHGAGIGAVAGAITALQLL   94 (265)
Q Consensus        55 ~g~~~ga~~g~~~g~~~~~g--~~~ga~~Ga~~gav~s~e~~   94 (265)
                      .|+.+||++||++|..++..  --.||++||..||.+.--+=
T Consensus        37 ~ga~~Ga~~Ga~~G~~~g~~~~~~~~a~~ga~~G~~~G~~~g   78 (219)
T PRK10510         37 IGAGIGSLVGAGIGALSSSKKDRGKGALIGAAAGAALGGGVG   78 (219)
T ss_pred             hhhHHHHHHHHHHHhhhcCCCcccchhhhHhHHHhhhhhhhh
Confidence            48999999999999887642  34678888888887776543

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=80.54  E-value=1.3  Score=41.40  Aligned_cols=51  Identities=31%  Similarity=0.654  Sum_probs=38.8

Q ss_pred             CcccccccccccCCCeeeecC-CCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          210 EIGCSICLEKFEEGDSARKLP-SCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r~LP-~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      ...|+||.++....+.. .+| .|+|..|..|...-...+.+||.||++....
T Consensus       249 ~~s~p~~~~~~~~~d~~-~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~~~  300 (327)
T KOG2068|consen  249 PPSCPICYEDLDLTDSN-FLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYERN  300 (327)
T ss_pred             CCCCCCCCCcccccccc-cccccccccchhhhhhcccccCCCCCccCCccccC
Confidence            37899999987433222 233 4899999999999888999999999876543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	265
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		3e-11
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		9e-09
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		1e-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 (		8e-07
4ayc_B	138	Rnf8 Ring Domain Structure Length = 138		3e-05
4ayc_A	138	Rnf8 Ring Domain Structure Length = 138		3e-05
4epo_C	149	Crystal Structure Of Rnf8 Bound To The Ubc13MMS2 HE		4e-05
2ecn_A	70	Solution Structure Of The Ring Domain Of The Human		3e-04

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 25/49 (51%), Positives = 37/49 (75%)
Query: 207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
           +D+ + C++CL + E+G+ AR LP CGH FH+ECVD WL  + +CP+CR
Sbjct: 2   MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 24/43 (55%), Positives = 29/43 (67%), Gaps = 1/43 (2%)
Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
           C+ICL   EEG+  R+LP C H FH  CVD+WL  N  CP+CR
Sbjct: 17  CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICR 58

>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 = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/69 (43%), Positives = 43/69 (62%), Gaps = 2/69 (2%)
Query: 187 SEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT 246
           S++ I  LPE  L +E+   +  E+ C IC  ++ +GD A +LP C H FH  CV  WL 
Sbjct: 18  SKESIDALPE-ILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQ 75
Query: 247 RNGSCPVCR 255
           ++G+CPVCR
Sbjct: 76  KSGTCPVCR 84

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 22/43 (51%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
           C +C+  FE     R LP C H FH++CVDKWL  N +CP+CR
Sbjct: 26  CVVCMCDFESRQLLRVLP-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 = 50.8 bits (120), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 29/44 (65%), Gaps = 1/44 (2%)
Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRE 256
           C +C E +  G+S R+LP C H FH  C+  WL ++ SCPVCR+
Sbjct: 18  CPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRK 60

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 4/49 (8%)
Query: 207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
           L+NE+ C IC E F E  +     +C H F S C+++W+ R   CP+CR
Sbjct: 50  LENELQCIICSEYFIEAVTL----NCAHSFCSYCINEWMKRKIECPICR 94

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 4/49 (8%)
Query: 207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
           L+NE+ C IC E F E  +     +C H F S C+++W+ R   CP+CR
Sbjct: 50  LENELQCIICSEYFIEAVTL----NCAHSFCSYCINEWMKRKIECPICR 94

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 4/49 (8%)
Query: 207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
           L+NE+ C IC E F E  +     +C H F S C+++W+ R   CP+CR
Sbjct: 61  LENELQCIICSEYFIEAVTL----NCAHSFCSYCINEWMKRKIECPICR 105

>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring Finger Protein 141 Length = 70

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 21/50 (42%), Positives = 30/50 (60%), Gaps = 5/50 (10%)
Query: 206 QLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
           QL +E  C IC++    G +   LP C H F  +C+DKW  R+ +CP+CR
Sbjct: 11  QLTDEEECCICMD----GRADLILP-CAHSFCQKCIDKWSDRHRNCPICR 55

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	265
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	1e-27
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	1e-23
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	6e-23
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	1e-22
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	1e-22
2ect_A	78	Ring finger protein 126; metal binding protein, st	4e-22
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	1e-18
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	5e-18
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	4e-15
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	5e-15
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	3e-14
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	9e-14
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	1e-13
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	7e-13
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	9e-13
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	1e-12
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	7e-12
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-07
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	1e-11
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	6e-11
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	8e-11
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	5e-10
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	5e-10
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	5e-10
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	5e-10
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	5e-10
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	6e-10
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	9e-10
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	2e-09
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	2e-09
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	2e-09
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	2e-09
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	6e-09
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	2e-08
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	4e-08
1z6u_A	150	NP95-like ring finger protein isoform B; structura	6e-07
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	7e-07
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	9e-07
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	3e-06
3nw0_A	238	Non-structural maintenance of chromosomes element	3e-06
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	6e-06
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	6e-06
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	8e-06
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	8e-06
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	1e-05
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	2e-05
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	3e-05
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	3e-05
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	7e-05
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	1e-04
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	1e-04
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	3e-04
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	6e-04
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	6e-04
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	8e-04

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

 Score =  101 bits (253), Expect = 1e-27
 Identities = 29/80 (36%), Positives = 44/80 (55%), Gaps = 2/80 (2%)

Query: 179 DVTGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHS 238
            +      S++ I  LPE  + +E+   +  E+ C IC  ++ +GD A +LP C H FH 
Sbjct: 10  HMVANPPASKESIDALPEILV-TEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHK 67

Query: 239 ECVDKWLTRNGSCPVCRECV 258
            CV  WL ++G+CPVCR   
Sbjct: 68  PCVSIWLQKSGTCPVCRCMF 87

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

 Score = 90.1 bits (224), Expect = 1e-23
 Identities = 25/76 (32%), Positives = 34/76 (44%), Gaps = 3/76 (3%)

Query: 187 SEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT 246
           S     +LP    +            C +C+  FE     R LP C H FH++CVDKWL 
Sbjct: 2   SSGSSGQLPSYRFNPNNHQSEQTL--CVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLK 58

Query: 247 RNGSCPVCRECVCKDT 262
            N +CP+CR      +
Sbjct: 59  ANRTCPICRADSGPSS 74

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

 Score = 87.6 bits (218), Expect = 6e-23
 Identities = 26/52 (50%), Positives = 38/52 (73%)

Query: 207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECV 258
           +D+ + C++CL + E+G+ AR LP CGH FH+ECVD WL  + +CP+CR  V
Sbjct: 2   MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

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

 Score = 87.5 bits (217), Expect = 1e-22
 Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 1/64 (1%)

Query: 201 SEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK 260
           S ++ +L+    C++CLE F+  D     P C H FH +C+ KWL     CP+C   V +
Sbjct: 6   SGKVKELNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQ 64

Query: 261 DTDT 264
               
Sbjct: 65  LAQL 68

>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 = 87.0 bits (216), Expect = 1e-22
 Identities = 28/54 (51%), Positives = 34/54 (62%), Gaps = 1/54 (1%)

Query: 202 EELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
           EE  + D E  C+ICL   EEG+  R+LP C H FH  CVD+WL  N  CP+CR
Sbjct: 6   EEGTEEDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICR 58

>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 = 86.3 bits (214), Expect = 4e-22
 Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 1/56 (1%)

Query: 206 QLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD 261
            + + + C +C E +  G+S R+LP C H FH  C+  WL ++ SCPVCR+ +   
Sbjct: 11  HVGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQ 65

>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 = 76.2 bits (188), Expect = 1e-18
 Identities = 15/48 (31%), Positives = 19/48 (39%)

Query: 208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
               GC ICLE          +  CGH  H  C ++ L     CP+C 
Sbjct: 3   SGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCS 50

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

 Score = 75.1 bits (185), Expect = 5e-18
 Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 5/64 (7%)

Query: 201 SEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK 260
           S  + QL +E  C IC++   +      LP C H F  +C+DKW  R+ +CP+CR  +  
Sbjct: 6   SGRVKQLTDEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTG 60

Query: 261 DTDT 264
             ++
Sbjct: 61  ANES 64

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

 Score = 67.4 bits (165), Expect = 4e-15
 Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 3/43 (6%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
           C ICLE     + +  LP C H F   C+ +W+ +N +CP+C+
Sbjct: 8   CPICLEDPS--NYSMALP-CLHAFCYVCITRWIRQNPTCPLCK 47

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

 Score = 67.6 bits (165), Expect = 5e-15
 Identities = 13/43 (30%), Positives = 22/43 (51%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
           C  C  + ++ D       C H FH+ C+  W+ +N  CP+C+
Sbjct: 29  CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71

>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 = 66.1 bits (161), Expect = 3e-14
 Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 4/65 (6%)

Query: 198 ALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR-NGSCPVCRE 256
            +  + +  +     C IC+EK  +   AR  P C       C+ +WLT     CP CR 
Sbjct: 10  HMDEQSVESIAEVFRCFICMEKLRD---ARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRA 66

Query: 257 CVCKD 261
            +   
Sbjct: 67  PLQLR 71

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

 Score = 63.8 bits (155), Expect = 9e-14
 Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 3/59 (5%)

Query: 201 SEELIQLDNEIGCSICLEKFEEGDSARKLPS---CGHCFHSECVDKWLTRNGSCPVCRE 256
           S   ++    + C IC++ + E     +L     CGH F S+C+   L    +CP CR+
Sbjct: 6   SGTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 64

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

 Score = 64.4 bits (157), Expect = 1e-13
 Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 3/54 (5%)

Query: 203 ELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRE 256
            +  +D+ + C IC E F     A  +P C H + S C+ K+L+    CP C  
Sbjct: 15  VMKTIDDLLRCGICFEYFNI---AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCV 65

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

 Score = 61.3 bits (149), Expect = 7e-13
 Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 3/50 (6%)

Query: 210 EIGCSICLEKFEEGDSARKLPS---CGHCFHSECVDKWLTRNGSCPVCRE 256
            + C IC++ + E     +L     CGH F S+C+   L    +CP CR+
Sbjct: 3   MVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 52

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

 Score = 61.3 bits (149), Expect = 9e-13
 Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 3/61 (4%)

Query: 201 SEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK 260
           S  L +L   I CSIC     +   A  +  C H F   C+ +    +  CP C   V +
Sbjct: 6   SGNLSELTPYILCSICKGYLID---ATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQ 62

Query: 261 D 261
            
Sbjct: 63  T 63

>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 = 61.0 bits (148), Expect = 1e-12
 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 3/52 (5%)

Query: 208 DNEIGCSICLEKFEEGDSARKLPS---CGHCFHSECVDKWLTRNGSCPVCRE 256
              + C IC++ + E     +L     CGH F S+C+   L    +CP CR+
Sbjct: 8   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 59

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

 Score = 60.6 bits (146), Expect = 7e-12
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 3/61 (4%)

Query: 208 DNEIGCSICLEKFEEGDSARKLP---SCGHCFHSECVDKWLTRNGSCPVCRECVCKDTDT 264
              + C IC++ + E     +L     CGH F S+C+   L    +CP CR+ +      
Sbjct: 5   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYH 64

Query: 265 W 265
            
Sbjct: 65  P 65

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

 Score = 48.6 bits (115), Expect = 1e-07
 Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 3/74 (4%)

Query: 191 IQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPS---CGHCFHSECVDKWLTR 247
             +          +      + C IC++ + E     +L     CGH F S+C+   L  
Sbjct: 53  TCRKKINHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN 112

Query: 248 NGSCPVCRECVCKD 261
             +CP CR+ +   
Sbjct: 113 ANTCPTCRKKINHK 126

>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 = 59.4 bits (144), Expect = 1e-11
 Identities = 14/55 (25%), Positives = 26/55 (47%), Gaps = 3/55 (5%)

Query: 204 LIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECV 258
           + +L+  + C +C   F +   A  +  C H F   C+ ++L  +  CP+C   V
Sbjct: 9   ITELNPHLMCVLCGGYFID---ATTIIECLHSFCKTCIVRYLETSKYCPICDVQV 60

>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 = 57.5 bits (138), Expect = 6e-11
 Identities = 21/99 (21%), Positives = 31/99 (31%), Gaps = 26/99 (26%)

Query: 181 TGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEG--------------DSA 226
           +G  G  E +I+K  E    + E         C IC+EK                     
Sbjct: 3   SGSSGEPEQVIRKYTEELKVAPEED-------CIICMEKLAVASGYSDMTDSKALGPMVV 55

Query: 227 RKLPSCGHCFHSECVDKWLTR-----NGSCPVCRECVCK 260
            +L  C H FH  C+           +  CP C+    +
Sbjct: 56  GRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGE 94

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

 Score = 58.1 bits (140), Expect = 8e-11
 Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 4/53 (7%)

Query: 206 QLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECV 258
            L+NE+ C IC E F E        +C H F S C+++W+ R   CP+CR+ +
Sbjct: 60  VLENELQCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDI 108

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

 Score = 58.3 bits (140), Expect = 5e-10
 Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 15/78 (19%)

Query: 194 LPECALHSEELIQLDNEIGCSICLEKFEEGDSARKL----PSCGHCFHSECVDKWL---- 245
           +P+ +   +   + + E+ C+IC     +G     +      C    H+ C+++W     
Sbjct: 292 MPDWSDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLM 351

Query: 246 -------TRNGSCPVCRE 256
                     G CP C+ 
Sbjct: 352 DGKTFLEVSFGQCPFCKA 369

>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 = 54.8 bits (131), Expect = 5e-10
 Identities = 10/43 (23%), Positives = 14/43 (32%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
           C          +       C H FH  C+ +WL     CP+  
Sbjct: 54  CQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

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

 Score = 53.7 bits (129), Expect = 5e-10
 Identities = 16/61 (26%), Positives = 22/61 (36%), Gaps = 4/61 (6%)

Query: 201 SEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK 260
           S           C+ICL+          LP C H F   CV         C +CR+ + +
Sbjct: 6   SGNTAPSLTVPECAICLQTCVH---PVSLP-CKHVFCYLCVKGASWLGKRCALCRQEIPE 61

Query: 261 D 261
           D
Sbjct: 62  D 62

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

 Score = 54.4 bits (131), Expect = 5e-10
 Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 5/58 (8%)

Query: 201 SEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG--SCPVCRE 256
             E   + +E+ C IC +   +   A  +P CG+ +  EC+   L  +   +CP C +
Sbjct: 4   GSEDDPIPDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQ 58

>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 = 54.9 bits (131), Expect = 5e-10
 Identities = 10/43 (23%), Positives = 14/43 (32%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
           C          +       C H FH  C+ +WL     CP+  
Sbjct: 65  CQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

>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 = 53.6 bits (129), Expect = 6e-10
 Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 5/58 (8%)

Query: 201 SEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG--SCPVCRE 256
           S E   + +E+ C IC +   +   A  +P CG+ +  EC+   L  +   +CP C +
Sbjct: 6   SGEDDPIPDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQ 60

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

 Score = 53.3 bits (128), Expect = 9e-10
 Identities = 10/44 (22%), Positives = 16/44 (36%), Gaps = 4/44 (9%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRE 256
           C IC + F+     +    C H F   C  +       C +C +
Sbjct: 18  CFICRQAFQNPVVTK----CRHYFCESCALEHFRATPRCYICDQ 57

>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 = 52.2 bits (125), Expect = 2e-09
 Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 5/46 (10%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGS--CPVCRE 256
           C+IC     +G   +   +CG   H  CV K+   N    CP C +
Sbjct: 18  CNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHCND 60

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

 Score = 52.8 bits (127), Expect = 2e-09
 Identities = 20/62 (32%), Positives = 27/62 (43%), Gaps = 3/62 (4%)

Query: 200 HSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG---SCPVCRE 256
            S  L  L   + C IC+E F E     KL  CGH    +C++K L  +     CP C +
Sbjct: 5   SSGNLDALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSK 64

Query: 257 CV 258
             
Sbjct: 65  IT 66

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

 Score = 56.7 bits (136), Expect = 2e-09
 Identities = 14/65 (21%), Positives = 22/65 (33%), Gaps = 5/65 (7%)

Query: 200 HSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWL-TRNGSCPVCRECV 258
           +            C IC E  ++    +  P CGH   + C+  W  +    CP CR  +
Sbjct: 322 YELYCEMGSTFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEI 377

Query: 259 CKDTD 263
                
Sbjct: 378 KGTEP 382

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

 Score = 53.4 bits (128), Expect = 2e-09
 Identities = 17/55 (30%), Positives = 21/55 (38%), Gaps = 5/55 (9%)

Query: 204 LIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECV 258
           L +L+  + CS C     E      L  C H F S CV   +     CPVC    
Sbjct: 16  LDRLEKLLRCSRCTNILRE---PVCLGGCEHIFCSNCVSDCI--GTGCPVCYTPA 65

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

 Score = 50.9 bits (121), Expect = 6e-09
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-RNGSCPVCRECVCKDTDTW 265
           ++ + C +C+E  E  D      +CG+     C  +  T  NG CP CR+   +D   +
Sbjct: 9   EDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAVY 67

>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 = 51.5 bits (123), Expect = 2e-08
 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 4/55 (7%)

Query: 207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWL-TRNGSCPVCRECVCK 260
           L +E+ C ICL+  +          C H F ++C+   L + N  CP CR+ +  
Sbjct: 51  LHSELMCPICLDMLKN---TMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS 102

>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 = 49.9 bits (119), Expect = 4e-08
 Identities = 17/59 (28%), Positives = 23/59 (38%), Gaps = 5/59 (8%)

Query: 201 SEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG-SCPVCRECV 258
            ++ I   +E  C IC+E   E      LP C H     C    + +    CP CR  V
Sbjct: 6   PKDAIPSLSECQCGICMEILVE---PVTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRV 60

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

 Score = 46.9 bits (111), Expect = 6e-07
 Identities = 14/57 (24%), Positives = 20/57 (35%), Gaps = 11/57 (19%)

Query: 204 LIQLDNEIGCSICLEKFEEGDSARKLP---SCGHCFHSECVDKWLTRNG-SCPVCRE 256
           L +L+    C  C E   +       P    C H    +C+ +       SCP CR 
Sbjct: 72  LKKLEQSFMCVCCQELVYQ-------PVTTECFHNVCKDCLQRSFKAQVFSCPACRH 121

>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 = 46.1 bits (109), Expect = 7e-07
 Identities = 13/70 (18%), Positives = 22/70 (31%), Gaps = 5/70 (7%)

Query: 188 EDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR 247
             +  +    +     L +++    C  C E             C H    +C+D+    
Sbjct: 30  ASLKDRPASGSPFQLFLSKVEETFQCICCQELVFR---PITTV-CQHNVCKDCLDRSFRA 85

Query: 248 NG-SCPVCRE 256
              SCP CR 
Sbjct: 86  QVFSCPACRY 95

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

 Score = 44.4 bits (105), Expect = 9e-07
 Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 11/60 (18%)

Query: 206 QLDNEIGCSICLEKFEEGDSARKLP---SCGHCFHSECVDKWLTRNG-SCPVCRECVCKD 261
            ++++  C  C             P    CGH F   C+   L+ +   C  C+E + KD
Sbjct: 11  TVEDKYKCEKCHLVLCS-------PKQTECGHRFCESCMAALLSSSSPKCTACQESIVKD 63

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

 Score = 44.1 bits (104), Expect = 3e-06
 Identities = 18/63 (28%), Positives = 23/63 (36%), Gaps = 12/63 (19%)

Query: 199 LHSEELIQ-LDNEIGCSICLEKFEEGDSARKLP---SCGHCFHSECVDKWLTRNGS-CPV 253
           L + +        I C IC     +       P   SC H F   C+ + L   GS CP 
Sbjct: 11  LLAVDFPAHFVKSISCQICEHILAD-------PVETSCKHLFCRICILRCLKVMGSYCPS 63

Query: 254 CRE 256
           CR 
Sbjct: 64  CRY 66

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

 Score = 45.9 bits (108), Expect = 3e-06
 Identities = 15/51 (29%), Positives = 20/51 (39%), Gaps = 5/51 (9%)

Query: 208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGS--CPVCRE 256
           D    C+IC     +G       +CG   H  CV K+   N    CP C +
Sbjct: 178 DAVKICNICHSLLIQGQ---SCETCGIRMHLPCVAKYFQSNAEPRCPHCND 225

>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 Length = 61

 Score = 42.0 bits (99), Expect = 6e-06
 Identities = 7/44 (15%), Positives = 16/44 (36%), Gaps = 3/44 (6%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRE 256
           C+I  +           P     F    +++++   G+ P+  E
Sbjct: 6   CAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNE 46

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

 Score = 44.3 bits (104), Expect = 6e-06
 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 5/57 (8%)

Query: 206 QLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGS-CPVCRECVCKD 261
            L+++  C ICL    E         CGH F   C+ K +   G  CPV  E + ++
Sbjct: 14  PLESKYECPICLMALREA----VQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN 66

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

 Score = 42.0 bits (99), Expect = 8e-06
 Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 13/64 (20%)

Query: 201 SEELIQLDNEIGCSICLEKFEEGDSARKLP---SCGHCFHSECVDKWLTRNG---SCPVC 254
            + + +L  E+ C ICL+  ++       P    CGH F  +C+ +    +     CP+C
Sbjct: 11  GQFVNKLQEEVICPICLDILQK-------PVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63

Query: 255 RECV 258
           +  V
Sbjct: 64  KTSV 67

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

 Score = 43.3 bits (102), Expect = 8e-06
 Identities = 17/55 (30%), Positives = 22/55 (40%), Gaps = 11/55 (20%)

Query: 206 QLDNEIGCSICLEKFEEGDSARKLP---SCGHCFHSECVDKWLTRNGS-CPVCRE 256
            L+++  C ICL    E            CGH F   C+ K +   G  CPV  E
Sbjct: 14  PLESKYECPICLMALRE-------AVQTPCGHRFCKACIIKSIRDAGHKCPVDNE 61

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

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 13/64 (20%)

Query: 201 SEELIQLDNEIGCSICLEKFEEGDSARKLP---SCGHCFHSECVDKWLTRNG---SCPVC 254
              +  +   + C ICLE  +E       P    C H F   C+ K L +      CP+C
Sbjct: 12  QNVINAMQKILECPICLELIKE-------PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLC 64

Query: 255 RECV 258
           +  +
Sbjct: 65  KNDI 68

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

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 12/59 (20%), Positives = 20/59 (33%), Gaps = 5/59 (8%)

Query: 206 QLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGS-CPVCRECVCKDTD 263
           +L+ +  CS C           +   CGH + S C+   L+     C  C      +  
Sbjct: 27  KLEAKYLCSACRNVLRR---PFQAQ-CGHRYCSFCLASILSSGPQNCAACVHEGIYEEG 81

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

 Score = 40.0 bits (94), Expect = 3e-05
 Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 7/46 (15%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECV 258
           C  C  + +     + LP C H   S C++        CP+C+   
Sbjct: 9   CQQCQAEAKC---PKLLP-CLHTLCSGCLEA---SGMQCPICQAPW 47

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

 Score = 40.4 bits (95), Expect = 3e-05
 Identities = 20/65 (30%), Positives = 25/65 (38%), Gaps = 16/65 (24%)

Query: 201 SEELIQLDNEIGCSICLEKFEEGDSARKLP---SCGHCFHSECVDKWLTRNG------SC 251
           S  L  +  E+ C ICLE  +E       P    C H F   C+      N       +C
Sbjct: 10  SSVLEMIKEEVTCPICLELLKE-------PVSADCNHSFCRACITLNYESNRNTDGKGNC 62

Query: 252 PVCRE 256
           PVCR 
Sbjct: 63  PVCRV 67

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

 Score = 39.6 bits (93), Expect = 7e-05
 Identities = 18/68 (26%), Positives = 21/68 (30%), Gaps = 17/68 (25%)

Query: 201 SEELIQLDNEIGCSICLEKFEEGDSARKLP---SCGHCFHSECVDKWLTRNG-------S 250
           S     +  E+ C ICLE   E       P    CGH     C+               S
Sbjct: 3   SGSSGNVQEEVTCPICLELLTE-------PLSLDCGHSLCRACITVSNKEAVTSMGGKSS 55

Query: 251 CPVCRECV 258
           CPVC    
Sbjct: 56  CPVCGISY 63

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

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 20/67 (29%), Positives = 27/67 (40%), Gaps = 16/67 (23%)

Query: 201 SEELIQLDNEIGCSICLEKFEEGDSARKLP---SCGHCFHSECVDKWLTRNG------SC 251
           S  L+ +  E+ C ICLE   +       P    CGH F   C+     ++       SC
Sbjct: 10  SGILVNVKEEVTCPICLELLTQ-------PLSLDCGHSFCQACLTANHKKSMLDKGESSC 62

Query: 252 PVCRECV 258
           PVCR   
Sbjct: 63  PVCRISY 69

>3htk_C E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae} Length = 267

 Score = 41.5 bits (96), Expect = 1e-04
 Identities = 11/53 (20%), Positives = 18/53 (33%), Gaps = 7/53 (13%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGS--CPV--CRECVCKD 261
           C I  + +E          C H F  + +  +L    +  CP   C + V   
Sbjct: 184 CPITCKPYEA---PLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMR 233

>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* Length = 63

 Score = 37.5 bits (87), Expect = 3e-04
 Identities = 11/44 (25%), Positives = 16/44 (36%), Gaps = 3/44 (6%)

Query: 213 CSICLEKFEEGDSARKLPSCGH-CFHSECVDKWLTRNGSCPVCR 255
           CS+C +     D        GH      C  +      SCP+C+
Sbjct: 10  CSLCEK--RPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICK 51

>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 Length = 64

 Score = 36.3 bits (84), Expect = 6e-04
 Identities = 14/44 (31%), Positives = 15/44 (34%), Gaps = 3/44 (6%)

Query: 213 CSICLEKFEEGDSARKLPSCGH-CFHSECVDKWLTRNGSCPVCR 255
           C IC       +        GH      C  K   RN  CPVCR
Sbjct: 11  CVICQG--RPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCR 52

>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 = 36.5 bits (84), Expect = 6e-04
 Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 2/54 (3%)

Query: 209 NEIGCSICLEKFEEGDSARKLPS-CGHCFHSECVDKWLTRN-GSCPVCRECVCK 260
           ++ GC  C        S + + + CGH     CVD    R  G+CP C   + K
Sbjct: 2   DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRK 55

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

 Score = 35.8 bits (83), Expect = 8e-04
 Identities = 23/60 (38%), Positives = 28/60 (46%), Gaps = 13/60 (21%)

Query: 201 SEELIQLDNEIGCSICLEKFEEGDSARKLP---SCGHCFHSECVDKW---LTRNGSCPVC 254
           S  L  L  E  CS+CLE  +E       P    CGH F   C+ +W   L R+  CPVC
Sbjct: 6   SGALENLQVEASCSVCLEYLKE-------PVIIECGHNFCKACITRWWEDLERDFPCPVC 58

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	265
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.7
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.64
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.57
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.54
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.54
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.53
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.46
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.45
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.44
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.43
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.42
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.41
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.41
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.36
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.35
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.34
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.33
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.32
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.3
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.29
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.28
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.27
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.26
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.26
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.24
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.24
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.24
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.24
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.23
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.23
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.22
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.2
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.19
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.19
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.16
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.16
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.15
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.14
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.13
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.13
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.12
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.11
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.1
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.09
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.07
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.05
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.05
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.03
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.03
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.0
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.99
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.99
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.99
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.96
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.95
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.93
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.85
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.85
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.77
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.77
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.77
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.76
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.75
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.73
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.71
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.59
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.56
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.46
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.45
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.39
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.16
3nw0_A	238	Non-structural maintenance of chromosomes element	97.94
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.32
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	95.21
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	94.54
1we9_A	64	PHD finger family protein; structural genomics, PH	94.25
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	92.4
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	92.14
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	91.68
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	91.15
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	90.3
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	90.28
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	90.07
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	89.13
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	88.64
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	87.11
1wee_A	72	PHD finger family protein; structural genomics, PH	87.06
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	86.88
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	86.84
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	86.43
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	86.28
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	86.19
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	86.07
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	85.97
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	85.52
1wem_A	76	Death associated transcription factor 1; structura	84.19
2yt5_A	66	Metal-response element-binding transcription facto	84.06
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	83.81
1z60_A	59	TFIIH basal transcription factor complex P44 subun	83.75
1weu_A	91	Inhibitor of growth family, member 4; structural g	83.73
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	83.3
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	83.24
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	81.33
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	81.06
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	80.68
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	80.45
1wew_A	78	DNA-binding family protein; structural genomics, P	80.02

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

Probab=99.70  E-value=1.4e-17  Score=126.21  Aligned_cols=80  Identities=35%  Similarity=0.773  Sum_probs=69.3

Q ss_pred             cccCCCCCCHHHHhcCCcccccchhhhhcccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccccc
Q 024603          179 DVTGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECV  258 (265)
Q Consensus       179 ~~~~~~gls~~~i~~lp~~~~~~~~~~~~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v  258 (265)
                      .....++++++.++.+|...+..... ...++..|+||++++..++.++.+| |+|.||..||.+|+..+.+||+||+++
T Consensus        10 ~~~~~~~~s~~~i~~lp~~~~~~~~~-~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~   87 (91)
T 2l0b_A           10 HMVANPPASKESIDALPEILVTEDHG-AVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCMF   87 (91)
T ss_dssp             CSSCCCCCCHHHHHTSCEEECCTTCS-SSSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTTCCBS
T ss_pred             CCcCCCCCCHHHHHhCCCeeeccccc-ccCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCcCccC
Confidence            44567899999999999988765432 3456789999999999999999998 999999999999999999999999988


Q ss_pred             cc
Q 024603          259 CK  260 (265)
Q Consensus       259 ~~  260 (265)
                      ..
T Consensus        88 ~~   89 (91)
T 2l0b_A           88 PP   89 (91)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

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

Probab=99.64  E-value=3.1e-17  Score=119.47  Aligned_cols=71  Identities=34%  Similarity=0.785  Sum_probs=59.3

Q ss_pred             HHHhcCCcccccchhhhhcccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccCC
Q 024603          189 DMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDT  262 (265)
Q Consensus       189 ~~i~~lp~~~~~~~~~~~~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~~  262 (265)
                      +.++.+|...++..+  ...++..|+||++++..++.++.+| |+|.||..|+.+|++.+.+||+||+++...+
T Consensus         4 ~~i~~lp~~~~~~~~--~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~   74 (75)
T 1x4j_A            4 GSSGQLPSYRFNPNN--HQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPSS   74 (75)
T ss_dssp             CCCSSCCCEEBCSSS--CSSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCCCC
T ss_pred             hhHhhCCcEEecCcc--ccCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCCCC
Confidence            445677777665432  2456789999999999999999998 9999999999999999999999999987654

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

Probab=99.57  E-value=1.1e-15  Score=104.36  Aligned_cols=52  Identities=50%  Similarity=1.210  Sum_probs=47.5

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVC  259 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~  259 (265)
                      +++.+|+||++++.+++....+|.|+|.||..|+.+|++.+.+||+||+++.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            4567999999999998888888889999999999999999999999999864

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

Probab=99.54  E-value=2.3e-15  Score=108.93  Aligned_cols=55  Identities=36%  Similarity=0.792  Sum_probs=49.6

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccCC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDT  262 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~~  262 (265)
                      ...+..|+||++++..++.++.+| |+|.||..|+.+|++.+.+||+||+++.+..
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2ep4_A           12 LNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA   66 (74)
T ss_dssp             CCCSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSSCC
T ss_pred             CCCCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCccccccc
Confidence            455789999999999999998998 9999999999999999999999999987543

>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=99.54  E-value=4e-15  Score=106.23  Aligned_cols=55  Identities=47%  Similarity=1.021  Sum_probs=49.2

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccCC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDT  262 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~~  262 (265)
                      ...+..|+||++.+..++.++.+| |+|.||..|+.+|+..+.+||+||+++....
T Consensus        11 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   65 (69)
T 2kiz_A           11 EDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQL   65 (69)
T ss_dssp             TTCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCSCC
T ss_pred             CCCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccCcC
Confidence            455689999999999888888898 9999999999999999999999999987543

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

Probab=99.53  E-value=4.3e-15  Score=108.59  Aligned_cols=54  Identities=39%  Similarity=1.046  Sum_probs=49.1

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      ...+..|+||++.+..++.++.+| |+|.||..||.+|++.+.+||+||+.+...
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (78)
T 2ect_A           12 VGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQ   65 (78)
T ss_dssp             SSSSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCCCCS
T ss_pred             CCCCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCccCCc
Confidence            456789999999999998888898 999999999999999999999999998654

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

Probab=99.46  E-value=1.7e-14  Score=106.88  Aligned_cols=51  Identities=27%  Similarity=0.692  Sum_probs=41.2

Q ss_pred             Cccccccccccc-----------CCCeeeecCCCCcccchhhHHHhhcCCCCcccccccccc
Q 024603          210 EIGCSICLEKFE-----------EGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       210 ~~~C~ICle~~~-----------~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      +..|+||++++.           .++.++.+|.|+|.||.+||++|++.+.+||+||+++..
T Consensus        15 ~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   76 (81)
T 2ecl_A           15 CDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVV   76 (81)
T ss_dssp             CSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCE
T ss_pred             CCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcch
Confidence            455666666664           455566777799999999999999999999999998754

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

Probab=99.45  E-value=2.6e-14  Score=102.29  Aligned_cols=54  Identities=35%  Similarity=0.891  Sum_probs=47.2

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccCCCCC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDTDTW  265 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~~~~~  265 (265)
                      ..++..|+||++.+.+    ..+| |+|.||..|+.+|+..+.+||+||+++...+..|
T Consensus        12 ~~~~~~C~IC~~~~~~----~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   65 (70)
T 2ecn_A           12 LTDEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGANESS   65 (70)
T ss_dssp             CCCCCCCSSSCCSCCS----EEET-TTEEECHHHHHHSSCCCSSCHHHHHCTTCCCCCC
T ss_pred             CCCCCCCeeCCcCccC----cccC-CCCcccHHHHHHHHHCcCcCCCcCCcccCCCccc
Confidence            3457899999999887    4566 9999999999999999999999999998877665

>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=2.4e-14  Score=102.40  Aligned_cols=54  Identities=28%  Similarity=0.724  Sum_probs=46.1

Q ss_pred             cccCcccccccccccCC----CeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEG----DSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~----~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      .+++..|+||++.+.++    .....+| |||.||..|+.+|++.+.+||+||+++...
T Consensus         7 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (71)
T 3ng2_A            7 PSGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   64 (71)
T ss_dssp             CTTCCBCTTTCCBHHHHHTTTCCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCCC
T ss_pred             CCCCCCCcccChhhhccccccCCeEeCC-CCChHhHHHHHHHHHcCCCCCCCCCccChh
Confidence            34678999999999875    4445666 999999999999999999999999998754

>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=99.43  E-value=7.7e-14  Score=109.01  Aligned_cols=52  Identities=29%  Similarity=0.616  Sum_probs=42.4

Q ss_pred             cCcccccccccccCCC---------------eeeecCCCCcccchhhHHHhh-----cCCCCccccccccccC
Q 024603          209 NEIGCSICLEKFEEGD---------------SARKLPSCGHCFHSECVDKWL-----TRNGSCPVCRECVCKD  261 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~---------------~~r~LP~CgH~FH~~CI~~WL-----~~~~sCPvCR~~v~~~  261 (265)
                      .+..|+||+++|..+.               .++.+| |+|.||..||.+|+     ..+.+||+||..+...
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            4568999999997654               333566 99999999999999     5677999999988644

>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=99.42  E-value=6e-14  Score=95.48  Aligned_cols=50  Identities=36%  Similarity=0.822  Sum_probs=43.3

Q ss_pred             cCcccccccccccCC-CeeeecCCCCcccchhhHHHhhcCCCCccccccccc
Q 024603          209 NEIGCSICLEKFEEG-DSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVC  259 (265)
Q Consensus       209 ~~~~C~ICle~~~~~-~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~  259 (265)
                      ++..|+||++++.++ +....+| |+|.||..|+.+|+..+.+||+||+++.
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            567899999999764 3456676 9999999999999999999999999875

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

Probab=99.41  E-value=5.8e-14  Score=99.59  Aligned_cols=53  Identities=28%  Similarity=0.735  Sum_probs=44.9

Q ss_pred             cccCcccccccccccCC----CeeeecCCCCcccchhhHHHhhcCCCCcccccccccc
Q 024603          207 LDNEIGCSICLEKFEEG----DSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~----~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      ..++..|+||++.+.++    ..+..+| |+|.||..|+.+|+..+.+||+||+++..
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           12 PSGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             TTCCCCCTTTCCCHHHHTTTTCCEEECS-SSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCCcccCccccccccccCCeEeCC-CCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            34678999999999875    3345666 99999999999999999999999998864

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

Probab=99.41  E-value=6.1e-14  Score=98.03  Aligned_cols=52  Identities=29%  Similarity=0.747  Sum_probs=44.5

Q ss_pred             cCcccccccccccCC----CeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          209 NEIGCSICLEKFEEG----DSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       209 ~~~~C~ICle~~~~~----~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      ++.+|+||++.+.++    .....+| |||.||..|+.+|++.+.+||+||+++...
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            467899999999875    3445666 999999999999999999999999998754

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

Probab=99.36  E-value=2.1e-13  Score=98.32  Aligned_cols=53  Identities=26%  Similarity=0.550  Sum_probs=44.5

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccCC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDT  262 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~~  262 (265)
                      .+++..|+||++.+.++..+  +| |+|.||..||.+|+..+.+||+||+++...+
T Consensus        12 ~~~~~~C~IC~~~~~~p~~~--~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   64 (72)
T 2djb_A           12 LTPYILCSICKGYLIDATTI--TE-CLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQ   64 (72)
T ss_dssp             CCGGGSCTTTSSCCSSCEEC--SS-SCCEECHHHHHHHHHHCSSCTTTCCCCCSSC
T ss_pred             cCCCCCCCCCChHHHCcCEE--CC-CCCHHHHHHHHHHHHcCCcCCCcCcccCccc
Confidence            45678999999999884332  35 9999999999999999999999999987654

>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=99.35  E-value=4.2e-13  Score=104.69  Aligned_cols=50  Identities=24%  Similarity=0.523  Sum_probs=42.4

Q ss_pred             cCcccccccccccCCC---------------eeeecCCCCcccchhhHHHhhcCCCCccccccccc
Q 024603          209 NEIGCSICLEKFEEGD---------------SARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVC  259 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~---------------~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~  259 (265)
                      ++..|+||++.|.++.               .++.+| |+|.||..||++||..+.+||+||++..
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecc-cCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            4678999999998651               245566 9999999999999999999999999853

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

Probab=99.34  E-value=3e-13  Score=96.04  Aligned_cols=49  Identities=35%  Similarity=0.804  Sum_probs=42.4

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccccccc
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      .+..|+||++.+.++.  ..+| |||.||..|+.+|+..+.+||+||+++..
T Consensus         4 ~~~~C~IC~~~~~~~~--~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSNYS--MALP-CLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCSCE--EETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCeeCCccccCCc--EecC-CCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            4678999999987643  4576 99999999999999999999999998753

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

Probab=99.33  E-value=5.4e-13  Score=99.03  Aligned_cols=54  Identities=31%  Similarity=0.755  Sum_probs=45.5

Q ss_pred             cccCcccccccccccCCCe-eeecCCCCcccchhhHHHhhcCC---CCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDS-ARKLPSCGHCFHSECVDKWLTRN---GSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~-~r~LP~CgH~FH~~CI~~WL~~~---~sCPvCR~~v~~~  261 (265)
                      ..+..+|+||++.+.+.+. ...+| |||.||..|+.+|+..+   .+||+||+++...
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           12 LREVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CCSCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             ccCCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            4567899999999998654 56676 99999999999999875   7899999987543

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

Probab=99.32  E-value=3.8e-13  Score=96.68  Aligned_cols=50  Identities=28%  Similarity=0.520  Sum_probs=43.0

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      ..++..|+||++.+.++   ..+| |+|.||..|+.+|+..+.+||+||+.+..
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            34568999999999875   3456 99999999999999999999999998863

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

Probab=99.30  E-value=1e-12  Score=92.96  Aligned_cols=51  Identities=25%  Similarity=0.673  Sum_probs=43.4

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhc-CCCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-RNGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~-~~~sCPvCR~~v~~~  261 (265)
                      ..++..|+||++.+.++..+   | |||.||..|+.+|+. .+..||+||+++..+
T Consensus        12 ~~~~~~C~IC~~~~~~p~~~---~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           12 VEDKYKCEKCHLVLCSPKQT---E-CGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCCCEECTTTCCEESSCCCC---S-SSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             CCcCCCCCCCChHhcCeeEC---C-CCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            34578999999999987664   4 999999999999994 567899999998765

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

Probab=99.29  E-value=9.2e-13  Score=95.57  Aligned_cols=53  Identities=25%  Similarity=0.697  Sum_probs=43.6

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC--CCccccccccccCC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN--GSCPVCRECVCKDT  262 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~--~sCPvCR~~v~~~~  262 (265)
                      ..++..|+||++.+.++..   +|.|||.||..||.+|+..+  .+||+||+++...+
T Consensus        12 ~~~~~~C~IC~~~~~~p~~---~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           12 IPDELLCLICKDIMTDAVV---IPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             SCGGGSCSSSCCCCTTCEE---CSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTT
T ss_pred             CCCCCCCcCCChHHhCCeE---cCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCcc
Confidence            4567899999999998655   44599999999999999865  68999999865443

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

Probab=99.28  E-value=1.4e-12  Score=93.60  Aligned_cols=52  Identities=31%  Similarity=0.731  Sum_probs=43.1

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhc---CCCCccccccccccCC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT---RNGSCPVCRECVCKDT  262 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~---~~~sCPvCR~~v~~~~  262 (265)
                      ..++..|+||++.+.++..   +| |||.||..|+.+|++   .+..||+||+++..++
T Consensus        17 ~~~~~~C~IC~~~~~~~~~---~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           17 LQEEVICPICLDILQKPVT---ID-CGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCCCBCTTTCSBCSSEEE---CT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             CccCCEeccCCcccCCeEE---cC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            4567899999999987443   45 999999999999997   4568999999987653

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

Probab=99.27  E-value=9.9e-13  Score=106.56  Aligned_cols=50  Identities=40%  Similarity=0.947  Sum_probs=43.2

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      +++..|+||++.+.++.   .+| |||.||..||.+|+..+.+||+||+++...
T Consensus        51 ~~~~~C~iC~~~~~~~~---~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           51 ENELQCIICSEYFIEAV---TLN-CAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             HHHSBCTTTCSBCSSEE---EET-TSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             cccCCCcccCcccCCce---ECC-CCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            44678999999998854   456 999999999999999999999999998643

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

Probab=99.26  E-value=1.8e-12  Score=96.10  Aligned_cols=54  Identities=22%  Similarity=0.600  Sum_probs=44.6

Q ss_pred             cccCcccccccccccCCCeeeecCCCC-----cccchhhHHHhhcCC--CCccccccccccCC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCG-----HCFHSECVDKWLTRN--GSCPVCRECVCKDT  262 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~Cg-----H~FH~~CI~~WL~~~--~sCPvCR~~v~~~~  262 (265)
                      ..++..|.||++++.+++.+ .+| |+     |.||..||++|+..+  .+||+||..+....
T Consensus        12 ~~~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~   72 (80)
T 2d8s_A           12 PSSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMET   72 (80)
T ss_dssp             CTTSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCC
T ss_pred             CCCCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCc
Confidence            34567899999999877766 588 86     999999999999865  48999999886443

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

Probab=99.26  E-value=1.4e-12  Score=95.98  Aligned_cols=49  Identities=20%  Similarity=0.482  Sum_probs=42.7

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVC  259 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~  259 (265)
                      .+....|+||++.+.++.   .+| |||.||..|+.+|+....+||+||+++.
T Consensus        12 ~~~~~~C~IC~~~~~~p~---~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           12 EEIPFRCFICRQAFQNPV---VTK-CRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCCSBCSSSCSBCCSEE---ECT-TSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCCcCCCchhcCee---Ecc-CCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            345689999999998854   456 9999999999999999999999999975

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

Probab=99.24  E-value=3.2e-12  Score=93.12  Aligned_cols=51  Identities=22%  Similarity=0.538  Sum_probs=43.7

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC-CCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR-NGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~-~~sCPvCR~~v~~~  261 (265)
                      ..++..|+||++.+.++..+   | |||.||..||.+|+.. +.+||+||+++...
T Consensus         5 ~~~~~~C~IC~~~~~~Pv~~---~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~   56 (78)
T 1t1h_A            5 FPEYFRCPISLELMKDPVIV---S-TGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             CSSSSSCTTTSCCCSSEEEE---T-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             CcccCCCCCccccccCCEEc---C-CCCeecHHHHHHHHHHCcCCCCCCcCCCChh
Confidence            35678999999999986554   5 9999999999999987 78899999988643

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

Probab=99.24  E-value=3.9e-12  Score=89.71  Aligned_cols=52  Identities=31%  Similarity=0.698  Sum_probs=41.9

Q ss_pred             cCcccccccc-cccCCCeee-ecCCCCcccchhhHHHhhcC-CCCccccccccccC
Q 024603          209 NEIGCSICLE-KFEEGDSAR-KLPSCGHCFHSECVDKWLTR-NGSCPVCRECVCKD  261 (265)
Q Consensus       209 ~~~~C~ICle-~~~~~~~~r-~LP~CgH~FH~~CI~~WL~~-~~sCPvCR~~v~~~  261 (265)
                      ++..|+||++ .+.++.... .+| |||.||..|+.+|+.+ +.+||+||+++...
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   56 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCcCCcCCCCccCCCccCeecCC-CCCHhHHHHHHHHHHcCCCcCCCCCCccccc
Confidence            3578999999 788876543 355 9999999999999764 46799999998654

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

Probab=99.24  E-value=2.5e-12  Score=101.87  Aligned_cols=53  Identities=28%  Similarity=0.752  Sum_probs=45.3

Q ss_pred             ccCcccccccccccCC----CeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          208 DNEIGCSICLEKFEEG----DSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~----~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      .++.+|+||++.+.++    .....+| |||.||..||.+|++.+.+||+||+.+...
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   61 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   61 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBCTTT
T ss_pred             CCCCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcCccc
Confidence            4578999999999875    3445666 999999999999999999999999988644

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

Probab=99.24  E-value=2.4e-12  Score=98.22  Aligned_cols=51  Identities=31%  Similarity=0.727  Sum_probs=43.1

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      ..++..|+||++.+.++..+  +| |||.||..|+.+|+..+.+||+||.++..
T Consensus        19 ~~~~~~C~IC~~~~~~p~~~--~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           19 IDDLLRCGICFEYFNIAMII--PQ-CSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HHHHTBCTTTCSBCSSEEEC--TT-TCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCCCCcccCChhhCCcCEE--CC-CCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            44568999999999884332  35 99999999999999999999999998864

>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=99.23  E-value=1.3e-12  Score=100.37  Aligned_cols=53  Identities=26%  Similarity=0.664  Sum_probs=43.8

Q ss_pred             hcccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC-CCccccccccccC
Q 024603          206 QLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN-GSCPVCRECVCKD  261 (265)
Q Consensus       206 ~~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~-~sCPvCR~~v~~~  261 (265)
                      ...++..|+||++.+.++..  .+| |||.||..||.+|+..+ ..||+||.++...
T Consensus        18 ~l~~~~~C~IC~~~~~~p~~--~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (100)
T 3lrq_A           18 SIAEVFRCFICMEKLRDARL--CPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPLQLR   71 (100)
T ss_dssp             HHHHHTBCTTTCSBCSSEEE--CTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             cCCCCCCCccCCccccCccc--cCC-CCChhhHHHHHHHHHHCcCCCCCCCCcCCHH
Confidence            45567899999999987443  155 99999999999999987 6999999998643

>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=99.23  E-value=9.7e-13  Score=104.39  Aligned_cols=51  Identities=24%  Similarity=0.524  Sum_probs=1.1

Q ss_pred             cCcccccccccccCCCe--------------eeecCCCCcccchhhHHHhhcCCCCccccccccc
Q 024603          209 NEIGCSICLEKFEEGDS--------------ARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVC  259 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~--------------~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~  259 (265)
                      +++.|+||+++|.++..              ...++.|+|.||..||++||+.+.+||+||++..
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~  111 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  111 (117)
T ss_dssp             CC---------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeee
Confidence            45799999999976321              2222349999999999999999999999999853

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

Probab=99.22  E-value=2.3e-12  Score=93.87  Aligned_cols=50  Identities=36%  Similarity=0.725  Sum_probs=42.8

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC-------CCCcccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR-------NGSCPVCRECVCK  260 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~-------~~sCPvCR~~v~~  260 (265)
                      ..++..|+||++.+.++..   +| |||.||..|+.+|+..       ...||+||+++..
T Consensus         9 ~~~~~~C~IC~~~~~~p~~---l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A            9 VQEEVTCPICLELLTEPLS---LD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             CCCCCEETTTTEECSSCCC---CS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCS
T ss_pred             cccCCCCcCCCcccCCeeE---CC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCH
Confidence            4567899999999988655   45 9999999999999986       5689999998864

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

Probab=99.20  E-value=5.9e-12  Score=92.39  Aligned_cols=51  Identities=33%  Similarity=0.718  Sum_probs=43.2

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC------CCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR------NGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~------~~sCPvCR~~v~~~  261 (265)
                      ..++..|+||++.+.++.   .+| |+|.||..|+.+|+..      ...||+||+++..+
T Consensus        16 ~~~~~~C~IC~~~~~~p~---~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           16 IKEEVTCPICLELLKEPV---SAD-CNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             CCTTTSCTTTCSCCSSCE---ECT-TSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTT
T ss_pred             CccCCCCcCCChhhCcce---eCC-CCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHH
Confidence            445789999999998865   456 9999999999999987      67899999988643

>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=99.19  E-value=7.4e-12  Score=97.01  Aligned_cols=53  Identities=26%  Similarity=0.672  Sum_probs=44.6

Q ss_pred             hcccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          206 QLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       206 ~~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      ...++..|+||++.+.++..  .+| |||.||..|+.+|+..+.+||+||..+...
T Consensus        11 ~~~~~~~C~IC~~~~~~p~~--~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           11 ELNPHLMCVLCGGYFIDATT--IIE-CLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             HHGGGTBCTTTSSBCSSEEE--ETT-TCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             ccCCcCCCccCChHHhCcCE--eCC-CCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            34567899999999987432  236 999999999999999999999999998754

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

Probab=99.19  E-value=7.5e-12  Score=91.84  Aligned_cols=51  Identities=37%  Similarity=0.808  Sum_probs=43.3

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC------CCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR------NGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~------~~sCPvCR~~v~~~  261 (265)
                      ..++..|+||++.+.++..   +| |||.||..|+.+|+..      ...||+||+.+...
T Consensus        16 ~~~~~~C~IC~~~~~~p~~---~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecv_A           16 VKEEVTCPICLELLTQPLS---LD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPE   72 (85)
T ss_dssp             CCCCCCCTTTCSCCSSCBC---CS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSS
T ss_pred             ccCCCCCCCCCcccCCcee---CC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHH
Confidence            4567899999999988654   45 9999999999999987      77899999988743

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

Probab=99.16  E-value=9.4e-12  Score=93.44  Aligned_cols=50  Identities=26%  Similarity=0.719  Sum_probs=41.8

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC--CCccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN--GSCPVCRECVC  259 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~--~sCPvCR~~v~  259 (265)
                      ..++..|+||++.+.++..+   |.|||.||..||.+|+..+  ..||+||+++.
T Consensus        10 ~~~~~~C~IC~~~~~~p~~~---~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           10 IPDELLCLICKDIMTDAVVI---PCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CCTTTEETTTTEECSSCEEC---TTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CCcCCCCCCCChhhcCceEC---CCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            45678999999999986544   4499999999999999743  58999999873

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

Probab=99.16  E-value=2e-11  Score=89.98  Aligned_cols=58  Identities=28%  Similarity=0.604  Sum_probs=43.7

Q ss_pred             cccCcccccccccccCCC-eeeecCCCCcccchhhHHHhhc-CCCCccccccccccCCCCC
Q 024603          207 LDNEIGCSICLEKFEEGD-SARKLPSCGHCFHSECVDKWLT-RNGSCPVCRECVCKDTDTW  265 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~-~~r~LP~CgH~FH~~CI~~WL~-~~~sCPvCR~~v~~~~~~~  265 (265)
                      .+++.+|+||++.+...+ ....+| |||.||..|+.+++. ....||+||+++...+..|
T Consensus         8 ~~~~~~CpICle~~~~~d~~~~p~~-CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~~~   67 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPEDPAVY   67 (78)
T ss_dssp             CCCCCBCTTTCCBCCTTTTTCCSST-TSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSSCC
T ss_pred             cccCCcCCccCccCccccccccccC-CCCCcCHHHHHHHHhcCCCCCCCCCCccCCCchhh
Confidence            456789999999886432 222244 999999999999875 4568999999997665443

>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=99.15  E-value=1e-11  Score=98.56  Aligned_cols=50  Identities=24%  Similarity=0.543  Sum_probs=42.4

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC-Ccccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG-SCPVCRECVCK  260 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~-sCPvCR~~v~~  260 (265)
                      ..++..|+||++.+.++..   +| |||.||..|+.+|+..+. .||+||+++..
T Consensus        49 ~~~~~~C~IC~~~~~~p~~---~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           49 VEETFQCICCQELVFRPIT---TV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHHHTBCTTTSSBCSSEEE---CT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             CccCCCCCcCChHHcCcEE---ee-CCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            3456899999999998644   45 999999999999998554 89999999865

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

Probab=99.14  E-value=1.7e-11  Score=85.69  Aligned_cols=44  Identities=32%  Similarity=0.788  Sum_probs=37.5

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhc---CCCCcccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT---RNGSCPVC  254 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~---~~~sCPvC  254 (265)
                      .+++..|+||++.+.++..   +| |||.||..||.+|++   .+.+||+|
T Consensus        17 ~~~~~~C~IC~~~~~~p~~---~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           17 LQEEVICPICLDILQKPVT---ID-CGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCBCTTTCSBCSSCEE---CT-TSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             CccCCCCCcCCchhCCeEE---eC-CCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            4567899999999998544   45 999999999999998   45689998

>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=99.13  E-value=1.9e-11  Score=101.64  Aligned_cols=50  Identities=30%  Similarity=0.705  Sum_probs=41.5

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC-CCCcccccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR-NGSCPVCRECVCK  260 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~-~~sCPvCR~~v~~  260 (265)
                      .++..|+||++.+.++..  .+| |||.||..|+.+|+.. +..||+||.++..
T Consensus        52 ~~~~~C~IC~~~~~~p~~--~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           52 HSELMCPICLDMLKNTMT--TKE-CLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHHBCTTTSSBCSSEEE--ETT-TCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCCcccChHhhCcCE--eCC-CCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            346799999999987432  245 9999999999999997 7789999998853

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

Probab=99.13  E-value=3.7e-11  Score=87.78  Aligned_cols=51  Identities=29%  Similarity=0.654  Sum_probs=42.9

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC--CCccccccccccCC
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN--GSCPVCRECVCKDT  262 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~--~sCPvCR~~v~~~~  262 (265)
                      ...+|+||++.+..++..   +.|+|.||..||.+||+.+  .+||+||++.....
T Consensus        14 ~i~~C~IC~~~i~~g~~C---~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~   66 (74)
T 2ct0_A           14 AVKICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEI   66 (74)
T ss_dssp             SSCBCSSSCCBCSSSEEC---SSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCC
T ss_pred             CCCcCcchhhHcccCCcc---CCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCC
Confidence            458999999999875543   3699999999999999987  78999999876443

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

Probab=99.12  E-value=2.7e-11  Score=82.95  Aligned_cols=44  Identities=43%  Similarity=1.040  Sum_probs=36.9

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhh---cCCCCcccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWL---TRNGSCPVC  254 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL---~~~~sCPvC  254 (265)
                      ..++..|+||++.+.++..   +| |+|.||..|+.+|+   ..+.+||+|
T Consensus        12 ~~~~~~C~IC~~~~~~p~~---~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           12 LQVEASCSVCLEYLKEPVI---IE-CGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             SCCCCBCSSSCCBCSSCCC---CS-SCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cccCCCCccCCcccCccEe---CC-CCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            4567899999999998754   45 99999999999995   456789998

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

Probab=99.11  E-value=1.5e-11  Score=97.44  Aligned_cols=53  Identities=28%  Similarity=0.752  Sum_probs=44.8

Q ss_pred             ccCcccccccccccCC----CeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          208 DNEIGCSICLEKFEEG----DSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~----~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      ++...|+||++.+.++    .....++ |||.||..|+++|++.+.+||+||.++.++
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            4578899999999864    2334555 999999999999999999999999998765

>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=99.10  E-value=2.4e-11  Score=94.09  Aligned_cols=50  Identities=34%  Similarity=0.731  Sum_probs=42.1

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC---CccccccccccC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG---SCPVCRECVCKD  261 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~---sCPvCR~~v~~~  261 (265)
                      .+...|+||++.+.++..   +| |||.||..|+.+|+..+.   +||+||.++...
T Consensus        19 ~~~~~C~IC~~~~~~p~~---~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (112)
T 1jm7_A           19 QKILECPICLELIKEPVS---TK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (112)
T ss_dssp             HHHTSCSSSCCCCSSCCB---CT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             cCCCCCcccChhhcCeEE---CC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHh
Confidence            456799999999988655   45 999999999999998654   899999988653

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

Probab=99.09  E-value=1.8e-11  Score=95.88  Aligned_cols=51  Identities=25%  Similarity=0.555  Sum_probs=43.1

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC-CCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR-NGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~-~~sCPvCR~~v~~~  261 (265)
                      ..++..|+||++.+.++..   +| |||.||..|+.+|+.. +.+||+||.++...
T Consensus        20 ~~~~~~C~IC~~~~~~p~~---~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (116)
T 1rmd_A           20 FVKSISCQICEHILADPVE---TS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (116)
T ss_dssp             HHHHTBCTTTCSBCSSEEE---CT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             ccCCCCCCCCCcHhcCcEE---cC-CCCcccHHHHHHHHhHCcCcCCCCCCCCCHh
Confidence            4456899999999988654   45 9999999999999986 67899999998653

>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=99.07  E-value=2.2e-11  Score=100.26  Aligned_cols=51  Identities=24%  Similarity=0.544  Sum_probs=43.4

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC-CccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG-SCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~-sCPvCR~~v~~~  261 (265)
                      ..++..|+||++.+.++..   +| |||.||..||.+|+.... .||+||.++...
T Consensus        75 l~~~~~C~IC~~~~~~pv~---~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           75 LEQSFMCVCCQELVYQPVT---TE-CFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHHHTBCTTTSSBCSSEEE---CT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CccCCEeecCChhhcCCEE---cC-CCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            4456899999999988655   55 999999999999998765 899999998765

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

Probab=99.05  E-value=2.8e-11  Score=85.64  Aligned_cols=52  Identities=29%  Similarity=0.469  Sum_probs=42.1

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcc-cchhhHHHhhcCCCCccccccccccC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHC-FHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~-FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      +++.+|+||++...+.. +..+| |||. ||.+|+.+|.+.+..||+||+++...
T Consensus         6 ~~~~~C~IC~~~~~~~~-~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~~   58 (64)
T 2vje_A            6 NAIEPCVICQGRPKNGC-IVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQMI   58 (64)
T ss_dssp             GGGSCCTTTSSSCSCEE-EEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCCEE
T ss_pred             CCcCCCCcCCCCCCCEE-EECCC-CCChhhHHHHHHHHHHcCCcCCCcCcchhce
Confidence            35678999999876632 21348 9999 89999999999889999999998653

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

Probab=99.05  E-value=7e-11  Score=91.01  Aligned_cols=51  Identities=10%  Similarity=0.120  Sum_probs=45.1

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      ..++..||||++.+.+|..+    .|||+||..||.+|+..+.+||+||.++...
T Consensus        26 ~p~~~~CpI~~~~m~dPV~~----~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~   76 (100)
T 2kre_A           26 APDEFRDPLMDTLMTDPVRL----PSGTIMDRSIILRHLLNSPTDPFNRQTLTES   76 (100)
T ss_dssp             CSTTTBCTTTCSBCSSEEEE----TTTEEEEHHHHHHHTTSCSBCSSSCCBCCTT
T ss_pred             CcHhhCCcCccCcccCCeEC----CCCCEEchHHHHHHHHcCCCCCCCCCCCChh
Confidence            35678999999999997776    4999999999999999899999999988653

>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=99.03  E-value=2.6e-11  Score=94.84  Aligned_cols=48  Identities=31%  Similarity=0.709  Sum_probs=41.1

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC-CCCccccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR-NGSCPVCRECVC  259 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~-~~sCPvCR~~v~  259 (265)
                      .++..|+||++.+.++..+   | |||.||..|+.+|+.. +..||+||+.+.
T Consensus        13 ~~~~~C~iC~~~~~~p~~~---~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   61 (115)
T 3l11_A           13 LSECQCGICMEILVEPVTL---P-CNHTLCKPCFQSTVEKASLCCPFCRRRVS   61 (115)
T ss_dssp             HHHHBCTTTCSBCSSCEEC---T-TSCEECHHHHCCCCCTTTSBCTTTCCBCH
T ss_pred             CCCCCCccCCcccCceeEc---C-CCCHHhHHHHHHHHhHCcCCCCCCCcccC
Confidence            3468999999999886544   5 9999999999999976 668999999875

>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=99.03  E-value=4.4e-11  Score=94.20  Aligned_cols=51  Identities=35%  Similarity=0.788  Sum_probs=43.1

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC-CccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG-SCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~-sCPvCR~~v~~~  261 (265)
                      .+++..|+||++.+.++.   .+| |||.||..|+.+|+..+. +||+||.++...
T Consensus        15 ~~~~~~C~IC~~~~~~p~---~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           15 LESKYECPICLMALREAV---QTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             CCGGGBCTTTCSBCSSEE---ECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCcCChhhcCeE---ECC-cCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            456789999999998863   355 999999999999998765 999999988653

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

Probab=99.00  E-value=1e-10  Score=87.33  Aligned_cols=51  Identities=12%  Similarity=0.172  Sum_probs=44.6

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      ..++..|+||++.+.+|..+   | |||+||..||.+|+..+.+||+||+++...
T Consensus        11 ~p~~~~CpI~~~~m~dPV~~---~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~   61 (85)
T 2kr4_A           11 APDEFRDPLMDTLMTDPVRL---P-SGTVMDRSIILRHLLNSPTDPFNRQMLTES   61 (85)
T ss_dssp             CCTTTBCTTTCSBCSSEEEC---T-TSCEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CchheECcccCchhcCCeEC---C-CCCEECHHHHHHHHhcCCCCCCCcCCCChH
Confidence            44678999999999997665   4 999999999999999889999999988643

>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=98.99  E-value=1.9e-10  Score=88.29  Aligned_cols=51  Identities=12%  Similarity=0.042  Sum_probs=44.8

Q ss_pred             cccCcccccccccccCCCeeeecCCCC-cccchhhHHHhhcCCCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCG-HCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~Cg-H~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      ..++..|+||++.+.+|..+    .|| |+||..||.+|+..+.+||+||+++...
T Consensus        19 ~p~~~~CpI~~~~m~dPV~~----~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~   70 (98)
T 1wgm_A           19 ACDEFLDPIMSTLMCDPVVL----PSSRVTVDRSTIARHLLSDQTDPFNRSPLTMD   70 (98)
T ss_dssp             CCTTTBCTTTCSBCSSEEEC----TTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTT
T ss_pred             CcHhcCCcCccccccCCeEC----CCCCeEECHHHHHHHHHhCCCCCCCCCCCChh
Confidence            34678999999999997765    499 9999999999999989999999988643

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

Probab=98.99  E-value=1.1e-10  Score=80.22  Aligned_cols=48  Identities=23%  Similarity=0.476  Sum_probs=39.8

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccCC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDT  262 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~~  262 (265)
                      .++..|+||++.+.++.   .+| |||.||..|+.+|   ...||+||+.+....
T Consensus         4 ~~~~~C~IC~~~~~~p~---~l~-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCPK---LLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCCSSCSSSCSSCBCCS---CST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             ccCCCceEeCCccCCeE---EcC-CCCcccHHHHccC---CCCCCcCCcEeecCC
Confidence            45788999999999864   455 9999999999884   678999999986543

>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=98.99  E-value=7.8e-11  Score=83.08  Aligned_cols=52  Identities=21%  Similarity=0.455  Sum_probs=41.9

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcc-cchhhHHHhhcCCCCccccccccccC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHC-FHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~-FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      +.+..|+||++...+.. +..+| |||. ||..|+.+|.+.+..||+||+++...
T Consensus         5 ~~~~~C~IC~~~~~~~~-~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~~   57 (63)
T 2vje_B            5 NLLKPCSLCEKRPRDGN-IIHGR-TGHLVTCFHCARRLKKAGASCPICKKEIQLV   57 (63)
T ss_dssp             GGGSBCTTTSSSBSCEE-EEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCCEE
T ss_pred             CcCCCCcccCCcCCCeE-EEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhhce
Confidence            34678999999876632 22347 9998 99999999998889999999998653

>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=98.96  E-value=1.7e-10  Score=90.66  Aligned_cols=50  Identities=30%  Similarity=0.594  Sum_probs=41.5

Q ss_pred             hcccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccccccc
Q 024603          206 QLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       206 ~~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      ...++..|+||++.+.++..+  .| |||.||..||.+|+.  ..||+||.++..
T Consensus        18 ~l~~~~~C~IC~~~~~~pv~~--~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~   67 (117)
T 1jm7_B           18 RLEKLLRCSRCTNILREPVCL--GG-CEHIFCSNCVSDCIG--TGCPVCYTPAWI   67 (117)
T ss_dssp             HHHHTTSCSSSCSCCSSCBCC--CS-SSCCBCTTTGGGGTT--TBCSSSCCBCSC
T ss_pred             hchhCCCCCCCChHhhCccEe--CC-CCCHHHHHHHHHHhc--CCCcCCCCcCcc
Confidence            345678999999999885433  25 999999999999987  889999999853

>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=98.95  E-value=1.8e-10  Score=93.90  Aligned_cols=50  Identities=24%  Similarity=0.505  Sum_probs=42.1

Q ss_pred             hcccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC-Cccccccccc
Q 024603          206 QLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG-SCPVCRECVC  259 (265)
Q Consensus       206 ~~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~-sCPvCR~~v~  259 (265)
                      ..+++..|+||++.+.++..   ++ |||.||..||.+|+.... +||+||.++.
T Consensus        27 ~l~~~~~C~IC~~~~~~pv~---~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~   77 (141)
T 3knv_A           27 KLEAKYLCSACRNVLRRPFQ---AQ-CGHRYCSFCLASILSSGPQNCAACVHEGI   77 (141)
T ss_dssp             GCCGGGBCTTTCSBCSSEEE---CT-TSCEEEHHHHHHHGGGSCEECHHHHHTTC
T ss_pred             cCCcCcCCCCCChhhcCcEE---CC-CCCccCHHHHHHHHhcCCCCCCCCCCccc
Confidence            34567899999999998744   45 999999999999998665 8999999763

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

Probab=98.93  E-value=1.1e-10  Score=84.78  Aligned_cols=50  Identities=26%  Similarity=0.644  Sum_probs=40.8

Q ss_pred             hcccCcccccccccccCCCeeeecCCCCcc-cchhhHHHhhcCCCCccccccccccCCC
Q 024603          206 QLDNEIGCSICLEKFEEGDSARKLPSCGHC-FHSECVDKWLTRNGSCPVCRECVCKDTD  263 (265)
Q Consensus       206 ~~~~~~~C~ICle~~~~~~~~r~LP~CgH~-FH~~CI~~WL~~~~sCPvCR~~v~~~~~  263 (265)
                      ..+++..|+||++.+.++   ..+| |||. ||..|+.+|    ..||+||+++.....
T Consensus        20 ~~~~~~~C~iC~~~~~~~---~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~~~   70 (74)
T 4ic3_A           20 RLQEEKLCKICMDRNIAI---VFVP-CGHLVTCKQCAEAV----DKCPMCYTVITFKQK   70 (74)
T ss_dssp             HHHHHTBCTTTSSSBCCE---EEET-TCCBCCCHHHHTTC----SBCTTTCCBCSEEEE
T ss_pred             cCccCCCCCCCCCCCCCE---EEcC-CCChhHHHHhhhcC----ccCCCcCcCccCcEE
Confidence            345567999999998774   4456 9999 999999998    889999999876543

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.85  E-value=7.4e-10  Score=80.39  Aligned_cols=51  Identities=25%  Similarity=0.638  Sum_probs=40.6

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcc-cchhhHHHhhcCCCCccccccccccCCCCC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHC-FHSECVDKWLTRNGSCPVCRECVCKDTDTW  265 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~-FH~~CI~~WL~~~~sCPvCR~~v~~~~~~~  265 (265)
                      .+++..|+||++.+.++.   .+| |||. ||..|+.+    ...||+||+++......|
T Consensus        22 ~~~~~~C~IC~~~~~~~~---~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i~~~~~i~   73 (75)
T 2ecg_A           22 LQEEKLCKICMDRNIAIV---FVP-CGHLVTCKQCAEA----VDKCPMCYTVITFKQKIF   73 (75)
T ss_dssp             HHHHHSCSSSCSSCCCBC---CSS-SCCCCBCHHHHHH----CSBCTTTCCBCCCCCBCC
T ss_pred             CCCCCCCCcCCCCCCCEE---Eec-CCCHHHHHHHhhC----CCCCccCCceecCcEEEe
Confidence            345678999999987744   456 9999 99999965    378999999998765544

>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=98.85  E-value=9.4e-10  Score=103.28  Aligned_cols=49  Identities=29%  Similarity=0.690  Sum_probs=41.7

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhc-CCCCccccccccccC
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-RNGSCPVCRECVCKD  261 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~-~~~sCPvCR~~v~~~  261 (265)
                      ....|+||++.+.++   ..+| |||.||..|+.+|+. .+.+||+||+++...
T Consensus       331 ~~~~C~ICle~~~~p---v~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          331 TFQLCKICAENDKDV---KIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SSSBCTTTSSSBCCE---EEET-TCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCCCccCcCCCCe---EEeC-CCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            347999999998774   4456 999999999999998 788999999988653

>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=98.77  E-value=1.3e-09  Score=90.75  Aligned_cols=51  Identities=33%  Similarity=0.727  Sum_probs=42.9

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC-CCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN-GSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~-~sCPvCR~~v~~~  261 (265)
                      .+++..|+||++.+.++..   +| |||.||..|+.+|+... .+||+||.++...
T Consensus        15 ~~~~~~C~IC~~~~~~pv~---~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           15 LESKYECPICLMALREAVQ---TP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             CCGGGBCTTTCSBCSSEEE---CT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCChhhcCcEE---CC-CCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            4567899999999998643   55 99999999999999865 4999999988653

>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=98.77  E-value=9.7e-10  Score=80.92  Aligned_cols=47  Identities=34%  Similarity=0.706  Sum_probs=38.2

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcc-cchhhHHHhhcCCCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHC-FHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~-FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      ..++..|+||++.+.+   ...+| |||. ||..|+.+|    ..||+||+++...
T Consensus        15 l~~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~   62 (79)
T 2yho_A           15 LKEAMLCMVCCEEEIN---STFCP-CGHTVCCESCAAQL----QSCPVCRSRVEHV   62 (79)
T ss_dssp             HHHHTBCTTTSSSBCC---EEEET-TCBCCBCHHHHTTC----SBCTTTCCBCCEE
T ss_pred             CCCCCEeEEeCcccCc---EEEEC-CCCHHHHHHHHHhc----CcCCCCCchhhCe
Confidence            3456789999998776   45567 9999 999999887    4999999988643

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

Probab=98.77  E-value=2.6e-09  Score=98.40  Aligned_cols=55  Identities=24%  Similarity=0.665  Sum_probs=42.2

Q ss_pred             cccCcccccccccccCCC----eeeecCCCCcccchhhHHHhhcCC-----------CCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGD----SARKLPSCGHCFHSECVDKWLTRN-----------GSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~----~~r~LP~CgH~FH~~CI~~WL~~~-----------~sCPvCR~~v~~~  261 (265)
                      .+...+|+||++.+.+..    ..-..++|+|.||..|+.+|++..           ++||+||+++...
T Consensus       305 ee~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~s  374 (381)
T 3k1l_B          305 DNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTS  374 (381)
T ss_dssp             CCSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGG
T ss_pred             ccCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCcc
Confidence            345689999999998722    222234799999999999999742           4699999998654

>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=98.76  E-value=1.8e-09  Score=95.44  Aligned_cols=49  Identities=20%  Similarity=0.285  Sum_probs=42.0

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC-CCcccccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN-GSCPVCRECVCK  260 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~-~sCPvCR~~v~~  260 (265)
                      .+...|+||++.+.+|..+   | |||+||..||.+|+..+ .+||+||.++..
T Consensus       206 ~~~~~c~i~~~~~~dPv~~---~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          206 PDYLCGKISFELMREPCIT---P-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             CSTTBCTTTCSBCSSEEEC---S-SCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CcccCCcCcCCHhcCCeEC---C-CCCEECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            4578999999999997665   4 99999999999999864 459999998864

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.75  E-value=2.8e-09  Score=76.24  Aligned_cols=48  Identities=29%  Similarity=0.643  Sum_probs=38.8

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcc-cchhhHHHhhcCCCCccccccccccCCC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHC-FHSECVDKWLTRNGSCPVCRECVCKDTD  263 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~-FH~~CI~~WL~~~~sCPvCR~~v~~~~~  263 (265)
                      .++..|.||++...+   +..+| |+|. ||..|+..    ...||+||+++....+
T Consensus        13 ~~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i~~~~~   61 (68)
T 2ea5_A           13 ENSKDCVVCQNGTVN---WVLLP-CRHTCLCDGCVKY----FQQCPMCRQFVQESFA   61 (68)
T ss_dssp             CCSSCCSSSSSSCCC---CEETT-TTBCCSCTTHHHH----CSSCTTTCCCCCCEEC
T ss_pred             CCCCCCCCcCcCCCC---EEEEC-CCChhhhHHHHhc----CCCCCCCCcchhceEE
Confidence            456789999998665   55677 9999 99999984    4789999999876443

>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=98.73  E-value=2.2e-09  Score=81.38  Aligned_cols=47  Identities=19%  Similarity=0.574  Sum_probs=39.6

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC------CCccc--cccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN------GSCPV--CREC  257 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~------~sCPv--CR~~  257 (265)
                      ..+..||||++.|.+|..+   |.|||+||..||.+|+..+      .+||+  |+..
T Consensus         5 ~~~~~CPI~~~~~~dPV~~---~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            5 SSGFTCPITKEEMKKPVKN---KVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             SSCCBCTTTCSBCSSEEEE---SSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             CcEeECcCcCchhcCCEEc---CCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            4578999999999997665   3499999999999999854      48999  9865

>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=98.71  E-value=4.8e-09  Score=79.18  Aligned_cols=48  Identities=23%  Similarity=0.614  Sum_probs=40.6

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC--------CCCccc--cccc
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR--------NGSCPV--CREC  257 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~--------~~sCPv--CR~~  257 (265)
                      +..+|+||++++..++.+...| |+|.||.+|+.+++..        ..+||.  ||..
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            4678999999999887776666 9999999999999863        236999  9988

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

Probab=98.59  E-value=1.3e-08  Score=86.24  Aligned_cols=50  Identities=20%  Similarity=0.288  Sum_probs=42.6

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC-CCcccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN-GSCPVCRECVCK  260 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~-~sCPvCR~~v~~  260 (265)
                      ..+...||||++.+.+|..+   | |||+||..||.+|+..+ .+||+||.++..
T Consensus       103 ip~~f~CPI~~elm~DPV~~---~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~  153 (179)
T 2f42_A          103 IPDYLCGKISFELMREPCIT---P-SGITYDRKDIEEHLQRVGHFDPVTRSPLTQ  153 (179)
T ss_dssp             CCGGGBCTTTCSBCSSEEEC---T-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CcHhhcccCccccCCCCeEC---C-CCCEECHHHHHHHHHhCCCCCCCCcCCCCh
Confidence            34578999999999997666   4 99999999999999864 469999998864

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

Probab=98.56  E-value=2.5e-08  Score=69.70  Aligned_cols=50  Identities=26%  Similarity=0.567  Sum_probs=37.7

Q ss_pred             cccCcccccccccccCCCeeeecC-CCCc---ccchhhHHHhhcC--CCCccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLP-SCGH---CFHSECVDKWLTR--NGSCPVCRECVC  259 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP-~CgH---~FH~~CI~~WL~~--~~sCPvCR~~v~  259 (265)
                      .++...|.||+++..+  .+ .+| .|.|   .||..|+.+|+..  +.+||+||.++.
T Consensus         3 ~~~~~~CrIC~~~~~~--~l-~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            3 DEDVPVCWICNEELGN--ER-FRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             TCSCCEETTTTEECSC--CC-CCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCEeEEeecCCCC--ce-ecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            3456789999998433  23 477 3445   9999999999974  578999998764

>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=98.46  E-value=2.8e-08  Score=92.16  Aligned_cols=50  Identities=30%  Similarity=0.723  Sum_probs=41.1

Q ss_pred             hcccCcccccccccccCCCeeeecCCCCcc-cchhhHHHhhcCCCCccccccccccCCC
Q 024603          206 QLDNEIGCSICLEKFEEGDSARKLPSCGHC-FHSECVDKWLTRNGSCPVCRECVCKDTD  263 (265)
Q Consensus       206 ~~~~~~~C~ICle~~~~~~~~r~LP~CgH~-FH~~CI~~WL~~~~sCPvCR~~v~~~~~  263 (265)
                      ..+++..|+||++.+.++   ..+| |||. ||..|+.+|    ..||+||.++...-.
T Consensus       291 ~l~~~~~C~IC~~~~~~~---v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i~~~~~  341 (345)
T 3t6p_A          291 RLQEERTCKVCMDKEVSV---VFIP-CGHLVVCQECAPSL----RKCPICRGIIKGTVR  341 (345)
T ss_dssp             HHHTTCBCTTTSSSBCCE---EEET-TCCEEECTTTGGGC----SBCTTTCCBCCEEEE
T ss_pred             hCcCCCCCCccCCcCCce---EEcC-CCChhHhHHHHhcC----CcCCCCCCCccCeEE
Confidence            345678999999998874   4456 9999 999999998    789999999875433

>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=98.45  E-value=4.5e-08  Score=87.28  Aligned_cols=50  Identities=24%  Similarity=0.576  Sum_probs=41.6

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC--CCccc--ccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN--GSCPV--CRECVCK  260 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~--~sCPv--CR~~v~~  260 (265)
                      ..+..||||++.|.+|...  . .|||.||..||.+|+..+  .+||+  ||+.+..
T Consensus       179 ~~el~CPIcl~~f~DPVts--~-~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~  232 (267)
T 3htk_C          179 KIELTCPITCKPYEAPLIS--R-KCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSM  232 (267)
T ss_dssp             BCCSBCTTTSSBCSSEEEE--S-SSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECG
T ss_pred             ceeeECcCccCcccCCeee--C-CCCCcccHHHHHHHHHhCCCCCCCcccccCcCch
Confidence            4567999999999997753  3 599999999999999864  46999  9997753

>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=98.39  E-value=9.5e-08  Score=66.89  Aligned_cols=49  Identities=14%  Similarity=0.275  Sum_probs=41.2

Q ss_pred             CcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          210 EIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      ...|+||++.+.++.   .+|.|||+|...||.+|++.+.+||++++++...
T Consensus         3 ~~~CpIs~~~m~dPV---~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~   51 (61)
T 2bay_A            3 HMLCAISGKVPRRPV---LSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   51 (61)
T ss_dssp             -CCCTTTCSCCSSEE---EETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             eEEecCCCCCCCCCE---EeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChh
Confidence            367999999999863   3434999999999999999888999999988644

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

Probab=98.16  E-value=1.1e-06  Score=67.21  Aligned_cols=46  Identities=26%  Similarity=0.538  Sum_probs=36.8

Q ss_pred             ccccccccccCCCeeeecCCCCcccchhhHHHhhc-CCCCcccccccccc
Q 024603          212 GCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-RNGSCPVCRECVCK  260 (265)
Q Consensus       212 ~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~-~~~sCPvCR~~v~~  260 (265)
                      .|++|--.+.  ...|..| |+|.||.+|+..|.+ +.++||.||.++..
T Consensus         3 fC~~C~~Pi~--iygRmIP-CkHvFCydCa~~~~~~~~k~Cp~C~~~V~r   49 (101)
T 3vk6_A            3 FCDKCGLPIK--VYGRMIP-CKHVFCYDCAILHEKKGDKMCPGCSDPVQR   49 (101)
T ss_dssp             BCTTTCSBCS--EEEEEET-TCCEEEHHHHHHHHHTTCCBCTTTCCBCSE
T ss_pred             ecCccCCCeE--EEeeecc-ccccHHHHHHHHHHhccCCCCcCcCCeeee
Confidence            4777754443  4677888 999999999999985 56889999998864

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

Probab=97.94  E-value=7.6e-06  Score=72.07  Aligned_cols=50  Identities=28%  Similarity=0.662  Sum_probs=41.4

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC--CccccccccccC
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG--SCPVCRECVCKD  261 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~--sCPvCR~~v~~~  261 (265)
                      ....|.||.+....+   ..+|.|+|.||..|+.+|++.+.  .||.|+.+.+..
T Consensus       179 ~i~~C~iC~~iv~~g---~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          179 AVKICNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             TCCBCTTTCSBCSSC---EECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSC
T ss_pred             CCCcCcchhhHHhCC---cccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCC
Confidence            357899999998875   44567999999999999998654  899999987644

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=95.32  E-value=0.0095  Score=44.55  Aligned_cols=36  Identities=14%  Similarity=0.421  Sum_probs=27.1

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHH-hh
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDK-WL  245 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~-WL  245 (265)
                      ++..|+||.+++..+....-++ |+|.||..|+.. |.
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~-C~~~~C~~Cl~~~h~   38 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVT-CEVSYCDECLKATHP   38 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETT-TTEEECHHHHHHHSC
T ss_pred             CCCCCcCCCCCCCCCceEECCc-CChHHhHHHCHHHhc
Confidence            4578999998765444443465 999999999998 53

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

Probab=94.54  E-value=0.03  Score=39.30  Aligned_cols=48  Identities=21%  Similarity=0.405  Sum_probs=35.5

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC----Cccccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG----SCPVCRECVC  259 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~----sCPvCR~~v~  259 (265)
                      .....|.||.+.    ..+.....|...||..|++..+....    .||.|+....
T Consensus        10 ~~~~~C~vC~~~----~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~   61 (66)
T 2lri_C           10 APGARCGVCGDG----TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDVT   61 (66)
T ss_dssp             CTTCCCTTTSCC----TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCCC
T ss_pred             CCCCCcCCCCCC----CeEEECCCCCCceecccCCCccCcCCCCCEECccccCCCc
Confidence            345679999753    33555667999999999988876543    5999987543

>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=94.25  E-value=0.022  Score=39.31  Aligned_cols=51  Identities=22%  Similarity=0.437  Sum_probs=37.4

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhc-----CCCCcccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-----RNGSCPVCRECV  258 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~-----~~~sCPvCR~~v  258 (265)
                      ++...|++|...+.+.........|...||..|+.--..     ..-.||.|+..-
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k~   59 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKS   59 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTT
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCcC
Confidence            456789999998876565666667999999999853221     345699998653

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

Probab=92.40  E-value=0.091  Score=36.06  Aligned_cols=47  Identities=23%  Similarity=0.565  Sum_probs=33.6

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC----CCccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN----GSCPVCREC  257 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~----~sCPvCR~~  257 (265)
                      ...+..|.+|.+.    ..+.....|...||..|+..-+...    =.||.|+..
T Consensus         8 ~~~~~~C~vC~~~----g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            8 TDHQDYCEVCQQG----GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             SCCCSSCTTTSCC----SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCCCccCCCC----CcEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            3456789999863    3455566799999999998755432    259999763

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

Probab=92.14  E-value=0.11  Score=37.98  Aligned_cols=40  Identities=20%  Similarity=0.402  Sum_probs=30.7

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR  247 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~  247 (265)
                      ...+.|.+|.+.+++...+.--..=+|.||..|-+..+++
T Consensus        13 ~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~   52 (93)
T 2cs3_A           13 SGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   52 (93)
T ss_dssp             CCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHh
Confidence            4568999999999998877211122799999999988874

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=91.68  E-value=0.074  Score=37.77  Aligned_cols=53  Identities=23%  Similarity=0.425  Sum_probs=37.5

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC----CCCccccccccccC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR----NGSCPVCRECVCKD  261 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~----~~sCPvCR~~v~~~  261 (265)
                      .+...|.||..... ++.......|...||..|+..-...    .-.||.|+..+.+.
T Consensus        16 ~~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~k~   72 (75)
T 2k16_A           16 NQIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKKD   72 (75)
T ss_dssp             CEEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHCSC
T ss_pred             CCCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchhhc
Confidence            34567999987753 4555566679999999999754432    33599999877543

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=91.15  E-value=0.053  Score=37.01  Aligned_cols=51  Identities=27%  Similarity=0.625  Sum_probs=36.2

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC----CccccccccccCCC
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG----SCPVCRECVCKDTD  263 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~----sCPvCR~~v~~~~~  263 (265)
                      .+..|.+|.+.   + .+.....|...||..|+..=+...+    .||.|+....+.++
T Consensus         4 ~~~~C~vC~~~---g-~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~~~~~   58 (60)
T 2puy_A            4 HEDFCSVCRKS---G-QLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQMLKKEE   58 (60)
T ss_dssp             CCSSCTTTCCC---S-SCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHHHTTT
T ss_pred             CCCCCcCCCCC---C-cEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccChhhchhc
Confidence            46789999864   3 3445667999999999986544322    49999887665543

>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=90.30  E-value=0.18  Score=37.05  Aligned_cols=35  Identities=20%  Similarity=0.500  Sum_probs=24.1

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHh
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKW  244 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~W  244 (265)
                      ..+..|.||- .+...+... ...|+..||..|+.+-
T Consensus        13 ~~D~~C~VC~-~~t~~~l~p-CRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           13 VNDEMCDVCE-VWTAESLFP-CRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTTC-CCCSSCCSS-CSSSSSCCCHHHHHHH
T ss_pred             CCCcccCccc-cccccceec-cccccccccHhhcccc
Confidence            4678999994 344433331 2248999999999985

>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=90.28  E-value=0.085  Score=36.20  Aligned_cols=49  Identities=20%  Similarity=0.418  Sum_probs=33.6

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC----Cccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG----SCPVCRECVC  259 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~----sCPvCR~~v~  259 (265)
                      ...+..|.+|.+.   + .+.....|...||..|+..-+....    .||.|+....
T Consensus         6 d~~~~~C~vC~~~---g-~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~   58 (61)
T 1mm2_A            6 DHHMEFCRVCKDG---G-ELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPAL   58 (61)
T ss_dssp             CSSCSSCTTTCCC---S-SCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTCC
T ss_pred             cCCCCcCCCCCCC---C-CEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCchh
Confidence            3456789999752   3 3444556889999999986544322    4999987543

>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens}

Probab=90.07  E-value=0.079  Score=40.45  Aligned_cols=49  Identities=24%  Similarity=0.510  Sum_probs=34.8

Q ss_pred             CcccccccccccCCCeeeecC-CCCcccchhhHHHh------h----cCCCCcccccccc
Q 024603          210 EIGCSICLEKFEEGDSARKLP-SCGHCFHSECVDKW------L----TRNGSCPVCRECV  258 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r~LP-~CgH~FH~~CI~~W------L----~~~~sCPvCR~~v  258 (265)
                      ...|+||...+.+........ .|...||..|+.-=      +    ..+-.||.|+..-
T Consensus         3 ~~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~   62 (105)
T 2xb1_A            3 VYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTK   62 (105)
T ss_dssp             CCBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTT
T ss_pred             cCCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcC
Confidence            457999999987665555664 79999999997311      1    0234699998754

>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=89.13  E-value=0.33  Score=32.00  Aligned_cols=45  Identities=18%  Similarity=0.335  Sum_probs=32.4

Q ss_pred             cccccccccccCCCeeeecC-CCCcccchhhHHHh----hcCCCCccccc
Q 024603          211 IGCSICLEKFEEGDSARKLP-SCGHCFHSECVDKW----LTRNGSCPVCR  255 (265)
Q Consensus       211 ~~C~ICle~~~~~~~~r~LP-~CgH~FH~~CI~~W----L~~~~sCPvCR  255 (265)
                      -.|.+|...+.++....... .|...||..|+.--    ...+-.||.|+
T Consensus         3 c~cc~C~~p~~~~~~mI~Cd~~C~~WfH~~Cvgl~~~~~~~~~~~C~~C~   52 (52)
T 2kgg_A            3 CAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA   52 (52)
T ss_dssp             CSCTTCCCCCCTTCCEEECTTTTCCEEETTTTTCCHHHHHHSCCCCSCC-
T ss_pred             ccCCCCcCccCCCCcEEEeCCCCCccCcccccCCCccccCCCCEECCCCC
Confidence            35789999887666666666 69999999997421    12556799986

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=88.64  E-value=0.098  Score=35.15  Aligned_cols=46  Identities=28%  Similarity=0.650  Sum_probs=32.5

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC----Ccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG----SCPVCRE  256 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~----sCPvCR~  256 (265)
                      ...+..|.+|.+.   + .+.....|...||..|+..=+....    .||.|+.
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            3456789999874   3 3445567999999999986554332    4999864

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=87.11  E-value=0.35  Score=35.84  Aligned_cols=47  Identities=28%  Similarity=0.590  Sum_probs=34.1

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC----Cccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG----SCPVCREC  257 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~----sCPvCR~~  257 (265)
                      ...+..|.+|.+.   + .+.....|.-.||..|++.=+...+    .||.|+..
T Consensus        22 d~n~~~C~vC~~~---g-~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~   72 (88)
T 1fp0_A           22 DDSATICRVCQKP---G-DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   72 (88)
T ss_dssp             SSSSSCCSSSCSS---S-CCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCC
T ss_pred             CCCCCcCcCcCCC---C-CEEECCCCCCceecccCCCCCCCCcCCCcCCccccCC
Confidence            4456789999864   3 3555667899999999977655432    49999864

>1wee_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=87.06  E-value=0.16  Score=35.92  Aligned_cols=51  Identities=24%  Similarity=0.445  Sum_probs=35.9

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHh----hcCCCCcccccccccc
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKW----LTRNGSCPVCRECVCK  260 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~W----L~~~~sCPvCR~~v~~  260 (265)
                      ....| ||.....+++.......|...||..|+.--    ...+-.||.|+..-.+
T Consensus        15 ~~~~C-~C~~~~~~g~~mI~Cd~C~~W~H~~Cvg~~~~~~~~~~~~C~~C~~~~~p   69 (72)
T 1wee_A           15 WKVDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELSGP   69 (72)
T ss_dssp             SEECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHHCSS
T ss_pred             cceEe-eCCCccCCCCcEEECCCCCCccCCeeeccCccccCCCcEECCCccCCCCC
Confidence            34678 798877666656666679999999998532    1234569999875443

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=86.88  E-value=0.27  Score=34.87  Aligned_cols=51  Identities=22%  Similarity=0.447  Sum_probs=35.9

Q ss_pred             cccCcccccccccc-cCCCeeeecCCCCcccchhhHHHhhcCC--CCccccccc
Q 024603          207 LDNEIGCSICLEKF-EEGDSARKLPSCGHCFHSECVDKWLTRN--GSCPVCREC  257 (265)
Q Consensus       207 ~~~~~~C~ICle~~-~~~~~~r~LP~CgH~FH~~CI~~WL~~~--~sCPvCR~~  257 (265)
                      ..++..|.||.+.- .+++.+.....|.-.||..|+..-....  =.||.|+..
T Consensus        13 ~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~~   66 (71)
T 2ku3_A           13 IDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQS   66 (71)
T ss_dssp             CCSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcCc
Confidence            44678899998763 3455666777899999999997432222  249999764

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=86.84  E-value=0.26  Score=36.37  Aligned_cols=53  Identities=21%  Similarity=0.421  Sum_probs=36.9

Q ss_pred             cccCcccccccccc-cCCCeeeecCCCCcccchhhHHHhhcCC--CCccccccccc
Q 024603          207 LDNEIGCSICLEKF-EEGDSARKLPSCGHCFHSECVDKWLTRN--GSCPVCRECVC  259 (265)
Q Consensus       207 ~~~~~~C~ICle~~-~~~~~~r~LP~CgH~FH~~CI~~WL~~~--~sCPvCR~~v~  259 (265)
                      .+++..|.||.+.- .+++.+.....|.-.||..|+..-+...  =.||.|+....
T Consensus        22 ~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~~   77 (88)
T 2l43_A           22 IDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRA   77 (88)
T ss_dssp             CCCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHTT
T ss_pred             CCCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCccc
Confidence            34568899998753 3445666777899999999997533222  24999987543

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*

Probab=86.43  E-value=0.48  Score=32.91  Aligned_cols=35  Identities=29%  Similarity=0.579  Sum_probs=27.4

Q ss_pred             cccCcccccccccccCCCeeeecC-CCCcccchhhH
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLP-SCGHCFHSECV  241 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP-~CgH~FH~~CI  241 (265)
                      .+....|++|...+.+.+..+... .|.-.||..|+
T Consensus         5 ~~~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cv   40 (65)
T 2vpb_A            5 SDPVYPCGICTNEVNDDQDAILCEASCQKWFHRICT   40 (65)
T ss_dssp             ----CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHH
T ss_pred             CCCcCcCccCCCccCCCCCeEecccCccccCchhcc
Confidence            345678999999998877777777 79999999997

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=86.28  E-value=0.44  Score=31.05  Aligned_cols=44  Identities=30%  Similarity=0.644  Sum_probs=30.3

Q ss_pred             ccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC----Ccccccc
Q 024603          212 GCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG----SCPVCRE  256 (265)
Q Consensus       212 ~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~----sCPvCR~  256 (265)
                      .|.||.+.-.. ..+.....|...||..|++.=+....    .||.|+.
T Consensus         2 ~C~vC~~~~~~-~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGED-DKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCC-SCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCC-CCEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            48888765433 34555667999999999975444322    4999975

>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2

Probab=86.19  E-value=0.48  Score=33.92  Aligned_cols=49  Identities=20%  Similarity=0.459  Sum_probs=33.9

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHh---h--cCCCCcccccccc
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKW---L--TRNGSCPVCRECV  258 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~W---L--~~~~sCPvCR~~v  258 (265)
                      ....| ||...+.+.........|...||..|+.--   .  ...-.||.|+..-
T Consensus        11 ~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A           11 VPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             CccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            34566 998887655555566679999999998421   1  1345699999754

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=86.07  E-value=0.25  Score=34.25  Aligned_cols=47  Identities=26%  Similarity=0.572  Sum_probs=33.3

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC----Ccccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG----SCPVCRECV  258 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~----sCPvCR~~v  258 (265)
                      ..+..|.||.+.   + .+.....|...||..|+..=+....    .||.|+..-
T Consensus         6 ~~~~~C~vC~~~---g-~ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~~   56 (66)
T 1xwh_A            6 KNEDECAVCRDG---G-ELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQAT   56 (66)
T ss_dssp             SCCCSBSSSSCC---S-SCEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHTC
T ss_pred             CCCCCCccCCCC---C-CEEEcCCCChhhcccccCCCcCcCCCCCeECccccCcc
Confidence            457789999863   3 3555667999999999986544322    499998643

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=85.97  E-value=0.33  Score=37.20  Aligned_cols=45  Identities=38%  Similarity=0.688  Sum_probs=32.2

Q ss_pred             ccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC----Ccccccc
Q 024603          212 GCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG----SCPVCRE  256 (265)
Q Consensus       212 ~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~----sCPvCR~  256 (265)
                      .|.||.+.-.++..+.....|...||..|++.-|....    .||.||.
T Consensus        63 ~C~vC~~~~~~~~~ll~Cd~C~~~yH~~Cl~p~l~~~P~~~W~C~~C~~  111 (112)
T 3v43_A           63 TCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRP  111 (112)
T ss_dssp             CBTTTCCCCCTTCCCEECTTTCCEECGGGCSSCCSSCCSSCCCCTTTSC
T ss_pred             ccccccCcCCCccceEEcCCCCCeeecccCCCCCCCCCCCCeECCCCCC
Confidence            68888765444445656667999999999976555332    5999985

>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A*

Probab=85.52  E-value=0.45  Score=38.86  Aligned_cols=49  Identities=24%  Similarity=0.547  Sum_probs=34.8

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhh-----cCCCCccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWL-----TRNGSCPVCREC  257 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL-----~~~~sCPvCR~~  257 (265)
                      ++...| +|.....+.........|...||..|+.--.     ...-.||.|+..
T Consensus         6 ~~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~   59 (174)
T 2ri7_A            6 DTKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST   59 (174)
T ss_dssp             -CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHH
T ss_pred             CCCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcch
Confidence            456778 9998876555566677899999999984211     234569999864

>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2

Probab=84.19  E-value=0.41  Score=33.96  Aligned_cols=49  Identities=22%  Similarity=0.431  Sum_probs=33.3

Q ss_pred             CcccccccccccCCCeeeecCCCCcccchhhHHHh---------hcCCCCcccccccccc
Q 024603          210 EIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKW---------LTRNGSCPVCRECVCK  260 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~W---------L~~~~sCPvCR~~v~~  260 (265)
                      ...| ||....... .......|...||..|+.--         ...+-.||.|+..-.+
T Consensus        16 ~~~C-~C~~~~~~~-~MI~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~~~p   73 (76)
T 1wem_A           16 ALYC-ICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILSGP   73 (76)
T ss_dssp             CCCS-TTCCCCCSS-CEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHSCS
T ss_pred             CCEE-ECCCccCCC-CEEEeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCccCc
Confidence            4567 898877643 44455579999999998421         1245679999876543

>2yt5_A Metal-response element-binding transcription factor 2; zinc-regulated factor 1, ZIRF1, metal-response element DNA-binding protein M96; NMR {Mus musculus}

Probab=84.06  E-value=0.35  Score=33.23  Aligned_cols=51  Identities=20%  Similarity=0.467  Sum_probs=36.2

Q ss_pred             ccCccccccccccc-CCCeeeecCCCCcccchhhHHHhhc-------CCCCcccccccc
Q 024603          208 DNEIGCSICLEKFE-EGDSARKLPSCGHCFHSECVDKWLT-------RNGSCPVCRECV  258 (265)
Q Consensus       208 ~~~~~C~ICle~~~-~~~~~r~LP~CgH~FH~~CI~~WL~-------~~~sCPvCR~~v  258 (265)
                      .++..|.||..... ++..+.....|...||..|+..=+.       ..=.||.|+...
T Consensus         4 ~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~   62 (66)
T 2yt5_A            4 GSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFAT   62 (66)
T ss_dssp             CCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTT
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCcc
Confidence            45688999987643 3455666778999999999875432       223599997654

>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC, structural genom type zinc finger, protein binding, zinc ION binding; 1.85A {Homo sapiens}

Probab=83.81  E-value=0.39  Score=33.67  Aligned_cols=47  Identities=21%  Similarity=0.556  Sum_probs=32.3

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhh---cCCCCcccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWL---TRNGSCPVCRE  256 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL---~~~~sCPvCR~  256 (265)
                      .+...| ||..... ++.......|...||..|+.---   ...-.||.|+.
T Consensus        17 ~~~~~C-iC~~~~~-~~~MIqCd~C~~WfH~~Cvgi~~~~~~~~~~C~~C~~   66 (68)
T 3o70_A           17 QGLVTC-FCMKPFA-GRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRD   66 (68)
T ss_dssp             TTCCCS-TTCCCCT-TCCEEECTTTCCEEETTTTTCCTTSCCSSCCCHHHHT
T ss_pred             CCceEe-ECCCcCC-CCCEEECCCCCccccccccCcCcccCCCcEECCCCCC
Confidence            445678 9987765 44455566799999999985322   23346999975

>1z60_A TFIIH basal transcription factor complex P44 subunit; basic transcription factor, zinc binding protein, ring finger; NMR {Homo sapiens} SCOP: g.49.1.2

Probab=83.75  E-value=0.9  Score=31.06  Aligned_cols=44  Identities=23%  Similarity=0.403  Sum_probs=31.6

Q ss_pred             CcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccc
Q 024603          210 EIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVC  254 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvC  254 (265)
                      ...|--|...+.+.. ....|+|++.||.+|=.---+.=..||-|
T Consensus        15 ~~~C~~C~~~~~~~~-~y~C~~C~~~FC~dCD~fiHe~Lh~CPgC   58 (59)
T 1z60_A           15 ERFCYGCQGELKDQH-VYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             CCEETTTTEECTTSE-EECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCcccccCcccCCCc-cEECCccCcCcccchhHHHHhhccCCcCC
Confidence            356999999886432 35688999999999943332333579988

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2

Probab=83.73  E-value=0.64  Score=34.56  Aligned_cols=48  Identities=27%  Similarity=0.560  Sum_probs=30.3

Q ss_pred             ccCcccccccccccCCCeeeecCC--CC-cccchhhHHHhhcC----CCCcccccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPS--CG-HCFHSECVDKWLTR----NGSCPVCRECVCK  260 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~--Cg-H~FH~~CI~~WL~~----~~sCPvCR~~v~~  260 (265)
                      .+...| ||.+... ++ ......  |. ..||..|+.  |..    +-.||.|+..-.+
T Consensus        34 ~e~~yC-iC~~~~~-g~-MI~CD~~dC~~~WfH~~CVg--l~~~p~g~W~Cp~C~~~~~k   88 (91)
T 1weu_A           34 NEPTYC-LCHQVSY-GE-MIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESGP   88 (91)
T ss_dssp             CCCBCS-TTCCBCC-SC-CCCCSCSSCSCCCCCSTTTT--CSSCCCSSCCCTTTCCCCSS
T ss_pred             CCCcEE-ECCCCCC-CC-EeEecCCCCCCCCEecccCC--cCcCCCCCEECcCccCcCCc
Confidence            345667 9988653 33 333444  55 689999996  332    2359999876543

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

Probab=83.30  E-value=0.57  Score=48.44  Aligned_cols=50  Identities=10%  Similarity=0.094  Sum_probs=42.6

Q ss_pred             ccCcccccccccccCCCeeeecCCCC-cccchhhHHHhhcCCCCccccccccccC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCG-HCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~Cg-H~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      .++..|||-++-+.+|..+   | -| |+|-..+|.+|+..+.+||+=|+++...
T Consensus       889 P~~F~cPIs~~lM~DPVil---p-sG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~  939 (968)
T 3m62_A          889 PDEFLDPLMYTIMKDPVIL---P-ASKMNIDRSTIKAHLLSDSTDPFNRMPLKLE  939 (968)
T ss_dssp             CGGGBCTTTCSBCSSEEEC---T-TTCCEEEHHHHHHHHTTCCBCTTTCCBCCGG
T ss_pred             cHHhCCcchhhHHhCCeEc---C-CCCEEECHHHHHHHHhcCCCCCCCCCCCCcc
Confidence            4467899999999997666   4 76 6999999999999999999999988643

>1wen_A Inhibitor of growth family, member 4; ING1-like protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.50.1.2 PDB: 1wes_A

Probab=83.24  E-value=0.76  Score=32.43  Aligned_cols=47  Identities=28%  Similarity=0.576  Sum_probs=30.1

Q ss_pred             ccCcccccccccccCCCeeeecCC--CC-cccchhhHHHhhcCC----CCccccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPS--CG-HCFHSECVDKWLTRN----GSCPVCRECVC  259 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~--Cg-H~FH~~CI~~WL~~~----~sCPvCR~~v~  259 (265)
                      .+...| ||.+... +. ......  |. ..||..|+.  |...    -.||.|+..-.
T Consensus        14 ~~~~~C-~C~~~~~-g~-MI~CD~~~C~~~wfH~~Cvg--l~~~p~g~w~Cp~C~~~~~   67 (71)
T 1wen_A           14 NEPTYC-LCHQVSY-GE-MIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESG   67 (71)
T ss_dssp             TSCCCS-TTCCCSC-SS-EECCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSCSS
T ss_pred             CCCCEE-ECCCCCC-CC-EeEeeCCCCCCccEecccCC--cCcCCCCCEECCCCCcccc
Confidence            345677 8987543 44 334445  65 699999997  3332    35999987543

>3c6w_A P28ING5, inhibitor of growth protein 5; chromatin, PHD, ING, epigenetics, alternative splicing, metal-binding, phosphoprotein, zinc; HET: M3L; 1.75A {Homo sapiens} PDB: 2pnx_A*

Probab=81.33  E-value=0.69  Score=31.40  Aligned_cols=43  Identities=33%  Similarity=0.665  Sum_probs=28.3

Q ss_pred             cCcccccccccccCCCeeeecCC--CC-cccchhhHHHhhcCC----CCcccccc
Q 024603          209 NEIGCSICLEKFEEGDSARKLPS--CG-HCFHSECVDKWLTRN----GSCPVCRE  256 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~--Cg-H~FH~~CI~~WL~~~----~sCPvCR~  256 (265)
                      +...| ||.+.. .++ ......  |. ..||..|+.  +...    -.||.|++
T Consensus         8 e~~yC-~C~~~~-~g~-mi~CD~~~C~~~wfH~~Cvg--l~~~p~~~w~Cp~C~~   57 (59)
T 3c6w_A            8 EPTYC-LCHQVS-YGE-MIGCDNPDCPIEWFHFACVD--LTTKPKGKWFCPRCVQ   57 (59)
T ss_dssp             CCEET-TTTEEC-CSE-EEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CCcEE-ECCCCC-CCC-eeEeeCCCCCCCCEecccCC--cccCCCCCEECcCccC
Confidence            45567 998764 343 444555  66 699999997  3322    35999975

>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=81.06  E-value=0.3  Score=36.23  Aligned_cols=49  Identities=22%  Similarity=0.381  Sum_probs=34.4

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC----Cccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG----SCPVCREC  257 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~----sCPvCR~~  257 (265)
                      .++..|.||.+.-. +..+.....|...||..|+..=+...+    .||.|+..
T Consensus        14 ~~~~~C~vC~~~~~-~~~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~   66 (92)
T 2e6r_A           14 IDSYICQVCSRGDE-DDKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILA   66 (92)
T ss_dssp             CCCCCCSSSCCSGG-GGGCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHH
T ss_pred             cCCCCCccCCCcCC-CCCEEEcCCCCchhccccCCCCcccCCCCCcCCccCcCc
Confidence            45568999987643 344556667999999999975443322    49999864

>2vnf_A ING 4, P29ING4, inhibitor of growth protein 4; acetylation, alternative splicing, anti-oncogene, cell cycle, coiled C nucleus, zinc, zinc-finger, ING4; HET: M3L; 1.76A {Homo sapiens} SCOP: g.50.1.2 PDB: 2k1j_A 2jmq_A 2qic_A*

Probab=80.68  E-value=0.72  Score=31.37  Aligned_cols=43  Identities=30%  Similarity=0.658  Sum_probs=27.7

Q ss_pred             cCcccccccccccCCCeeeecCC--CC-cccchhhHHHhhcCC----CCcccccc
Q 024603          209 NEIGCSICLEKFEEGDSARKLPS--CG-HCFHSECVDKWLTRN----GSCPVCRE  256 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~--Cg-H~FH~~CI~~WL~~~----~sCPvCR~  256 (265)
                      +...| ||.+... +. .....+  |. ..||..|+.  |...    -.||.|++
T Consensus         9 e~~~C-~C~~~~~-g~-mi~CD~cdC~~~wfH~~Cvg--l~~~p~g~w~C~~C~~   58 (60)
T 2vnf_A            9 EPTYC-LCHQVSY-GE-MIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQ   58 (60)
T ss_dssp             CCEET-TTTEECC-SE-EEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CCCEE-ECCCcCC-CC-EEEeCCCCCCCceEehhcCC--CCcCCCCCEECcCccC
Confidence            44566 8987643 33 444445  55 689999997  4332    35999975

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2

Probab=80.45  E-value=0.36  Score=35.50  Aligned_cols=53  Identities=17%  Similarity=0.458  Sum_probs=37.4

Q ss_pred             ccCcccccccccccC-CCeeeecCCCCcccchhhHHHhhc--------CCCCcccccccccc
Q 024603          208 DNEIGCSICLEKFEE-GDSARKLPSCGHCFHSECVDKWLT--------RNGSCPVCRECVCK  260 (265)
Q Consensus       208 ~~~~~C~ICle~~~~-~~~~r~LP~CgH~FH~~CI~~WL~--------~~~sCPvCR~~v~~  260 (265)
                      +.+..|.+|...-.. ...+.....|...||..|+..=+.        ..=.||.|+.....
T Consensus        14 e~~~~C~vC~~~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~~~~~~   75 (88)
T 1wev_A           14 EMGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKR   75 (88)
T ss_dssp             HHCCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHCC
T ss_pred             CCCCcCCCCCCCCCCCCCceEECCCCCCeEcCccCCCcccccccCCCCCCeeCccccchhhh
Confidence            356789999876432 345666778999999999976543        12259999876543

>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=80.02  E-value=0.8  Score=32.73  Aligned_cols=52  Identities=21%  Similarity=0.365  Sum_probs=34.1

Q ss_pred             ccCcccccccccccCCCeeeecC--CCCcccchhhHHHhh---------cCCCCccccccccccC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLP--SCGHCFHSECVDKWL---------TRNGSCPVCRECVCKD  261 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP--~CgH~FH~~CI~~WL---------~~~~sCPvCR~~v~~~  261 (265)
                      .....| ||-.....+ ..+...  .|...||..|+.---         ..+-.||.|+..-.+.
T Consensus        14 ~~~~~C-iC~~~~~~g-~MI~CD~~~C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~~~~~   76 (78)
T 1wew_A           14 EIKVRC-VCGNSLETD-SMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSGPS   76 (78)
T ss_dssp             CCCCCC-SSCCCCCCS-CEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCCSCC
T ss_pred             CCCEEe-ECCCcCCCC-CEEEECCccCCccccCEEEccccccccccccCCCCEECCCCCcccCCC
Confidence            345678 898875444 344444  699999999985211         1345699998765443

---

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	265
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	3e-20
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	2e-13
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	2e-12
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	6e-12
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	1e-10
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	4e-10
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	6e-10
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	1e-09
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	6e-09
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	1e-08
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	2e-08
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	4e-07
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	1e-05
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	1e-05
d1t1ha_	78	g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cre	2e-04

>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 = 79.5 bits (196), Expect = 3e-20
 Identities = 26/52 (50%), Positives = 38/52 (73%)

Query: 207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECV 258
           +D+ + C++CL + E+G+ AR LP CGH FH+ECVD WL  + +CP+CR  V
Sbjct: 2   MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>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 = 61.9 bits (150), Expect = 2e-13
 Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 3/46 (6%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECV 258
           C ICLE             C H F   C+ +W+ +N +CP+C+  V
Sbjct: 8   CPICLEDPSNYS---MALPCLHAFCYVCITRWIRQNPTCPLCKVPV 50

>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 = 59.2 bits (143), Expect = 2e-12
 Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 10/64 (15%)

Query: 201 SEELIQLDNEIG-----CSICLEKFEEGDSARKLPSCGHCFHSECVDKWL-TRNGSCPVC 254
           ++E  +L  E+G     C IC E  ++    +  P CGH   + C+  W  +    CP C
Sbjct: 9   TQEQYELYCEMGSTFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFC 64

Query: 255 RECV 258
           R  +
Sbjct: 65  RCEI 68

>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 = 57.0 bits (137), Expect = 6e-12
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-RNGSCPVCRECVCKD 261
           C +C+E  E  D      +CG+     C  +  T  NG CP CR+   +D
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED 52

>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 = 54.8 bits (131), Expect = 1e-10
 Identities = 14/60 (23%), Positives = 21/60 (35%), Gaps = 2/60 (3%)

Query: 196 ECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCR 255
            CA+    ++  D  I C          +       C H FH  C+ +WL     CP+  
Sbjct: 23  NCAICRNHIM--DLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 80

>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 = 52.9 bits (126), Expect = 4e-10
 Identities = 14/50 (28%), Positives = 18/50 (36%), Gaps = 2/50 (4%)

Query: 213 CSICLEKFEEGDSARKLP-SCGHCFHSECVDKWLT-RNGSCPVCRECVCK 260
           C  C        S + +   CGH     CVD       G+CP C   + K
Sbjct: 6   CPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRK 55

>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 = 53.5 bits (127), Expect = 6e-10
 Identities = 23/103 (22%), Positives = 35/103 (33%), Gaps = 26/103 (25%)

Query: 181 TGVKGLSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEE--------------GDSA 226
           +G  G  E +I+K  E        +++  E  C IC+EK                     
Sbjct: 3   SGSSGEPEQVIRKYTEE-------LKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVV 55

Query: 227 RKLPSCGHCFHSECVDKWLTR-----NGSCPVCRECVCKDTDT 264
            +L  C H FH  C+           +  CP C+    + T T
Sbjct: 56  GRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGT 98

>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 = 50.6 bits (121), Expect = 1e-09
 Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 7/52 (13%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDTDT 264
           C  C  + +     + LP C H   S C++        CP+C+       DT
Sbjct: 9   CQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGADT 53

>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 = 50.5 bits (120), Expect = 6e-09
 Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 13/79 (16%)

Query: 186 LSEDMIQKLPECALHSEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWL 245
           LS   ++++         +  +   + C ICLE  +E         C H F   C+ K L
Sbjct: 3   LSALRVEEV------QNVINAMQKILECPICLELIKE---PVSTK-CDHIFCKFCMLKLL 52

Query: 246 TRNG---SCPVCRECVCKD 261
            +      CP+C+  + K 
Sbjct: 53  NQKKGPSQCPLCKNDITKR 71

>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 = 49.4 bits (117), Expect = 1e-08
 Identities = 17/61 (27%), Positives = 21/61 (34%), Gaps = 5/61 (8%)

Query: 201 SEELIQLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK 260
              L +L+  + CS C     E      L  C H F S CV   +     CPVC      
Sbjct: 13  RAALDRLEKLLRCSRCTNILREP---VCLGGCEHIFCSNCVSDCI--GTGCPVCYTPAWI 67

Query: 261 D 261
            
Sbjct: 68  Q 68

>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 = 48.4 bits (115), Expect = 2e-08
 Identities = 16/55 (29%), Positives = 19/55 (34%), Gaps = 5/55 (9%)

Query: 207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGS-CPVCRECVCK 260
               I C IC     +        SC H F   C+ + L   GS CP CR     
Sbjct: 20  FVKSISCQICEHILAD----PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFP 70

>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 = 44.1 bits (103), Expect = 4e-07
 Identities = 11/48 (22%), Positives = 17/48 (35%), Gaps = 3/48 (6%)

Query: 213 CSICLEKFEEGDSARKLPS-CGHCFHSECVDKWLTRNG--SCPVCREC 257
           C IC E+           +      H  C+  WLT +   +C +C   
Sbjct: 9   CWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVV 56

>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 = 40.1 bits (93), Expect = 1e-05
 Identities = 7/49 (14%), Positives = 19/49 (38%), Gaps = 3/49 (6%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD 261
           C+I  +       + K       F    +++++   G+ P+  E +  +
Sbjct: 3   CAISGKVPRRPVLSPK---SRTIFEKSLLEQYVKDTGNDPITNEPLSIE 48

>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 = 40.8 bits (95), Expect = 1e-05
 Identities = 9/53 (16%), Positives = 18/53 (33%), Gaps = 9/53 (16%)

Query: 213 CSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT--------RNGSCPVCREC 257
           C +CL ++        +  C   F + C+ +++            SCP     
Sbjct: 8   CKLCLGEYPVEQMTT-IAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACP 59

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

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]

 Score = 37.4 bits (86), Expect = 2e-04
 Identities = 8/58 (13%), Positives = 14/58 (24%), Gaps = 4/58 (6%)

Query: 206 QLDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDTD 263
           +      C I LE  ++          G  +    + KWL          +       
Sbjct: 4   EFPEYFRCPISLELMKDPVIVS----TGQTYERSSIQKWLDAGHKTCPKSQETLLHAG 57

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	265
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.7
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.47
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.46
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.4
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.38
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.37
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.37
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.29
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.23
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.22
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.21
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.12
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.05
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.99
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.99
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.87
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.54
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	95.05
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	93.23
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	92.55
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	92.11
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	91.59
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	91.05
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	90.39
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	90.25
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	89.09
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	88.99
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	87.94
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	86.09
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	86.09

>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=99.70  E-value=3.1e-18  Score=116.97  Aligned_cols=52  Identities=50%  Similarity=1.210  Sum_probs=47.8

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVC  259 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~  259 (265)
                      +++.+|+||+++|.+++.++++|.|+|.||..|+.+|++.+.+||+||+++.
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            4567899999999999999988889999999999999999999999999873

>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=99.47  E-value=6.7e-15  Score=98.91  Aligned_cols=51  Identities=29%  Similarity=0.585  Sum_probs=41.2

Q ss_pred             cccccccccccCCCeeeecCCCCcccchhhHHHhhcCC-CCccccccccccC
Q 024603          211 IGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN-GSCPVCRECVCKD  261 (265)
Q Consensus       211 ~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~-~sCPvCR~~v~~~  261 (265)
                      .+|+||+++|..++....+..|||.||.+|+++|++.+ .+||+||+++.++
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~d   52 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED   52 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSCC
T ss_pred             CCCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCCC
Confidence            47999999998765543332499999999999999864 5799999998653

>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=99.46  E-value=8.1e-15  Score=103.69  Aligned_cols=48  Identities=35%  Similarity=0.825  Sum_probs=41.6

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccc
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVC  259 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~  259 (265)
                      ..++|+||++.+.++  .+.+| |+|.||..|+.+|++.+.+||+||+++.
T Consensus         4 ~~d~C~IC~~~~~~~--~~~~~-C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           4 VAERCPICLEDPSNY--SMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCCSSCCSCCCSC--EEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCCccCCcCccCC--cEEeC-CCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            356799999999764  34576 9999999999999999999999999885

>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=99.40  E-value=6.3e-14  Score=98.21  Aligned_cols=53  Identities=28%  Similarity=0.618  Sum_probs=41.4

Q ss_pred             cCcccccccccccCC-C-eeeecCCCCcccchhhHHHhhcC-CCCccccccccccCC
Q 024603          209 NEIGCSICLEKFEEG-D-SARKLPSCGHCFHSECVDKWLTR-NGSCPVCRECVCKDT  262 (265)
Q Consensus       209 ~~~~C~ICle~~~~~-~-~~r~LP~CgH~FH~~CI~~WL~~-~~sCPvCR~~v~~~~  262 (265)
                      ++..|+||++++..+ + ....+| |||.||..||.+|+.. +.+||+||+++...+
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~   57 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKSN   57 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCC
T ss_pred             CCCCCCcCCceeecCCceEEEeCc-cChHhhHHHHHHHhCcCcCCCCCCCcCccccc
Confidence            467999999987543 2 334455 9999999999999964 567999999986543

>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=99.38  E-value=9.9e-14  Score=102.79  Aligned_cols=50  Identities=24%  Similarity=0.523  Sum_probs=41.2

Q ss_pred             cCcccccccccccCCC---------------eeeecCCCCcccchhhHHHhhcCCCCccccccccc
Q 024603          209 NEIGCSICLEKFEEGD---------------SARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVC  259 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~---------------~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~  259 (265)
                      .++.|+||++.+.++.               .+..+| |+|.||..||.+||+.+.+||+||++..
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~   84 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWE   84 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCccc
Confidence            4567999998886533               245566 9999999999999999999999999864

>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=99.37  E-value=1.5e-13  Score=99.97  Aligned_cols=50  Identities=28%  Similarity=0.690  Sum_probs=41.8

Q ss_pred             CcccccccccccCCCeeeecCCCCcccchhhHHHhhc-CCCCccccccccccCCC
Q 024603          210 EIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-RNGSCPVCRECVCKDTD  263 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~-~~~sCPvCR~~v~~~~~  263 (265)
                      ...|+||++.+.+   .+.+| |||.||..||.+|+. ++.+||+||+++...+.
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            3569999998876   45677 999999999999997 45789999999976553

>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=99.37  E-value=1.1e-13  Score=106.84  Aligned_cols=52  Identities=29%  Similarity=0.599  Sum_probs=40.7

Q ss_pred             cCcccccccccccCC---------------CeeeecCCCCcccchhhHHHhhcC-----CCCccccccccccC
Q 024603          209 NEIGCSICLEKFEEG---------------DSARKLPSCGHCFHSECVDKWLTR-----NGSCPVCRECVCKD  261 (265)
Q Consensus       209 ~~~~C~ICle~~~~~---------------~~~r~LP~CgH~FH~~CI~~WL~~-----~~sCPvCR~~v~~~  261 (265)
                      .+..|+||++++..+               ..+..+| |+|.||..||.+|++.     +.+||+||..+...
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             ccccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            466899999998642               2345565 9999999999999974     34799999987544

>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=99.29  E-value=2.9e-13  Score=92.06  Aligned_cols=48  Identities=15%  Similarity=0.300  Sum_probs=41.8

Q ss_pred             cccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          211 IGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       211 ~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      ..|+||++.+.++...   |.|||.||.+||.+|++++++||+||+++..+
T Consensus         1 l~C~Ic~~~~~~Pv~~---~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~   48 (56)
T d2baya1           1 MLCAISGKVPRRPVLS---PKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   48 (56)
T ss_dssp             CCCTTTCSCCSSEEEE---TTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             CCCccCCchHHhcCcc---CCCCCcccHHHHHHHHhhccCCCccCCcCCHH
Confidence            3699999999885543   46999999999999999999999999998654

>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=99.23  E-value=1e-12  Score=97.08  Aligned_cols=50  Identities=26%  Similarity=0.561  Sum_probs=41.4

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhc-CCCCccccccccccC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLT-RNGSCPVCRECVCKD  261 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~-~~~sCPvCR~~v~~~  261 (265)
                      .+...|+||++.+.++.   .+| |||.||..||.+|++ ++.+||+||.++...
T Consensus        21 ~~~l~C~IC~~~~~~pv---~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~   71 (86)
T d1rmda2          21 VKSISCQICEHILADPV---ETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (86)
T ss_dssp             HHHTBCTTTCSBCSSEE---ECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             ccCcCCccCCcchhcce---ecC-CCChhhHHHHHHHHhhCCCcCcccCCCCChh
Confidence            35578999999998854   455 999999999999997 456899999988644

>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=99.22  E-value=1.1e-12  Score=89.18  Aligned_cols=48  Identities=25%  Similarity=0.539  Sum_probs=39.8

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccCCC
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKDTD  263 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~~~  263 (265)
                      +..+|+||++.+.++.   .+| |||.||..|+++|   +.+||+||+++....+
T Consensus         5 ~~l~C~IC~~~~~~p~---~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~~   52 (56)
T d1bora_           5 QFLRCQQCQAEAKCPK---LLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGAD   52 (56)
T ss_dssp             CCSSCSSSCSSCBCCS---CST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCSS
T ss_pred             CCCCCcccCcccCCCE---Eec-CCCHHhHHHHHcC---CCcCcCCCCcccCCCC
Confidence            4579999999998864   456 9999999999876   6689999999975543

>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=99.21  E-value=1.6e-12  Score=98.64  Aligned_cols=51  Identities=33%  Similarity=0.745  Sum_probs=42.0

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC---CCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN---GSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~---~sCPvCR~~v~~~  261 (265)
                      .++...|+||++.+.+|..   +| |||.||..||.+|+..+   ..||+||.++...
T Consensus        18 l~~~l~CpIC~~~~~~pv~---~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (103)
T d1jm7a_          18 MQKILECPICLELIKEPVS---TK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (103)
T ss_dssp             HHHHTSCSSSCCCCSSCCB---CT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             cccCcCCCccCchhCCeEE---cC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcCChh
Confidence            3456789999999988754   45 99999999999999765   3799999988643

>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=99.12  E-value=7.2e-12  Score=93.92  Aligned_cols=49  Identities=31%  Similarity=0.609  Sum_probs=40.3

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCK  260 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~  260 (265)
                      ..+..+|+||++.|.++..+  . .|||.||..||.+|+.  .+||.||.++..
T Consensus        19 l~~~l~C~IC~~~~~~pv~~--~-~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~   67 (97)
T d1jm7b_          19 LEKLLRCSRCTNILREPVCL--G-GCEHIFCSNCVSDCIG--TGCPVCYTPAWI   67 (97)
T ss_dssp             HHHTTSCSSSCSCCSSCBCC--C-SSSCCBCTTTGGGGTT--TBCSSSCCBCSC
T ss_pred             hhhcCCCccCCchhhcCcee--C-CCCCchhHHHHHHHHh--ccccccCCcCch
Confidence            45678999999999987543  3 4999999999999984  469999998754

>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=99.05  E-value=4.1e-11  Score=82.07  Aligned_cols=53  Identities=25%  Similarity=0.466  Sum_probs=40.0

Q ss_pred             cccCcccccccccccCCCeee-ecCCCCcccchhhHHHhhc--CCCCccccccccc
Q 024603          207 LDNEIGCSICLEKFEEGDSAR-KLPSCGHCFHSECVDKWLT--RNGSCPVCRECVC  259 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r-~LP~CgH~FH~~CI~~WL~--~~~sCPvCR~~v~  259 (265)
                      .++...|+||++++.++.... ...+|+|.||..|+.+|+.  ++.+||+||+++.
T Consensus         3 ded~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           3 DEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             TCSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            456788999999987654331 1223569999999999995  4568999999864

>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=98.99  E-value=9.8e-11  Score=84.13  Aligned_cols=51  Identities=22%  Similarity=0.533  Sum_probs=43.2

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC-CCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN-GSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~-~sCPvCR~~v~~~  261 (265)
                      ..++..|+||++.+.++..+   | |||.||..||.+|+..+ ..||.||.++...
T Consensus         5 iP~~l~CpIc~~~m~dPV~~---~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~   56 (78)
T d1t1ha_           5 FPEYFRCPISLELMKDPVIV---S-TGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             CSSSSSCTTTSCCCSSEEEE---T-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             CCccCCCcCcCchhhCceEc---c-CCCcchHHHHHHHHHHCCCCCCcccccCCcc
Confidence            34678999999999997654   5 99999999999999865 5799999988654

>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=98.99  E-value=6.1e-11  Score=85.71  Aligned_cols=50  Identities=20%  Similarity=0.302  Sum_probs=42.3

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC-CCCccccccccccC
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR-NGSCPVCRECVCKD  261 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~-~~sCPvCR~~v~~~  261 (265)
                      .++..|+||++.+.+|..   +| |||+||..||.+|+.. +.+||+||.++...
T Consensus         5 P~~l~CpIc~~l~~dPv~---~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~   55 (80)
T d2c2la2           5 PDYLCGKISFELMREPCI---TP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQE   55 (80)
T ss_dssp             CSTTBCTTTCSBCSSEEE---CS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCGG
T ss_pred             CccccCcCcCchhhhhcc---cC-CcCeecHHHHHHHHhcCCccCCCcccccccc
Confidence            467899999999999754   45 9999999999999975 55799999988643

>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=98.87  E-value=6e-10  Score=83.63  Aligned_cols=52  Identities=15%  Similarity=0.092  Sum_probs=43.8

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCccccccccccC
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRECVCKD  261 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~~v~~~  261 (265)
                      ..+++.||||.+.+.+|..+   |.|+|.|+..||.+|+..+..||+||+++...
T Consensus        19 ~P~~f~CPI~~~lm~dPV~~---~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~   70 (98)
T d1wgma_          19 ACDEFLDPIMSTLMCDPVVL---PSSRVTVDRSTIARHLLSDQTDPFNRSPLTMD   70 (98)
T ss_dssp             CCTTTBCTTTCSBCSSEEEC---TTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTT
T ss_pred             CcHHhCCcCchhHHHHHHhc---ccccchhhHHHHHHHHHhcCCcccccccccch
Confidence            34579999999999996655   54556999999999999999999999998653

>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=98.54  E-value=1.5e-08  Score=74.71  Aligned_cols=46  Identities=22%  Similarity=0.553  Sum_probs=37.1

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC--------CCccccc
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN--------GSCPVCR  255 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~--------~sCPvCR  255 (265)
                      ...+|+||++++...+..+.++ |+|.||.+|+.+|++.+        -+||.|+
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCCcCccCCCcccCCceEEECC-CCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            4678999999998777766665 99999999999998621        2599864

>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=95.05  E-value=0.0051  Score=40.98  Aligned_cols=52  Identities=21%  Similarity=0.414  Sum_probs=38.7

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHh---hc--CCCCcccccccccc
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKW---LT--RNGSCPVCRECVCK  260 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~W---L~--~~~sCPvCR~~v~~  260 (265)
                      .+..|.+|.+...+++.......|+..||..|+..=   ..  .+-.||.|+..-.+
T Consensus         5 ~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~~~p   61 (64)
T d1we9a_           5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKSGP   61 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTTCS
T ss_pred             CCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCcCCC
Confidence            467899999988777766677789999999998531   11  23469999875443

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.23  E-value=0.03  Score=38.17  Aligned_cols=39  Identities=21%  Similarity=0.408  Sum_probs=29.9

Q ss_pred             cCcccccccccccCCCeeeecCCCCcccchhhHHHhhcC
Q 024603          209 NEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTR  247 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~  247 (265)
                      ....|.+|.+.+++...+.--..=+|.||..|-+..+++
T Consensus         7 ~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~   45 (80)
T d2cs3a1           7 GPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   45 (80)
T ss_dssp             CSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHh
Confidence            458999999999998877211112799999999988873

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

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: TFIIH p44 subunit cysteine-rich domain
domain: TFIIH p44 subunit cysteine-rich domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.55  E-value=0.053  Score=35.55  Aligned_cols=46  Identities=22%  Similarity=0.413  Sum_probs=33.8

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVC  254 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvC  254 (265)
                      .....|--|...+.+ ......|+|++.||.+|=.---+.-..||-|
T Consensus        13 ~~~~~C~gC~~~l~~-~~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          13 NGERFCYGCQGELKD-QHVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             CSCCEETTTTEECTT-SEEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCCCccCCCCcCCC-CceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            456789999988865 4556788999999999954332344579988

>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=92.11  E-value=0.04  Score=34.62  Aligned_cols=44  Identities=30%  Similarity=0.644  Sum_probs=31.9

Q ss_pred             ccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC----Ccccccc
Q 024603          212 GCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG----SCPVCRE  256 (265)
Q Consensus       212 ~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~----sCPvCR~  256 (265)
                      .|.||...-.. ..+.....|...||..|++.-+...+    .||.||.
T Consensus         2 ~C~vC~~~~~~-~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGED-DKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCC-SCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCC-CCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            58888765433 44556678999999999988765433    4999985

>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=91.59  E-value=0.028  Score=36.93  Aligned_cols=47  Identities=19%  Similarity=0.412  Sum_probs=32.8

Q ss_pred             ccCcccccccccccCCCeeeecCCCCcccchhhHHHhhcCC----CCcccccccc
Q 024603          208 DNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRN----GSCPVCRECV  258 (265)
Q Consensus       208 ~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~----~sCPvCR~~v  258 (265)
                      ..+..|.+|.+.    ..+.....|.-.||..|+...+...    -.||.|+...
T Consensus         7 ~~~~~C~~C~~~----g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           7 HHMEFCRVCKDG----GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC----SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCcCCCcCCCCC----CeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            345679999752    3355556789999999997665532    2599998654

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=91.05  E-value=0.035  Score=38.24  Aligned_cols=50  Identities=22%  Similarity=0.434  Sum_probs=32.6

Q ss_pred             cCcccccccccccCCCeeeec--CCCCcccchhhHHH----hh--c---CCCCcccccccccc
Q 024603          209 NEIGCSICLEKFEEGDSARKL--PSCGHCFHSECVDK----WL--T---RNGSCPVCRECVCK  260 (265)
Q Consensus       209 ~~~~C~ICle~~~~~~~~r~L--P~CgH~FH~~CI~~----WL--~---~~~sCPvCR~~v~~  260 (265)
                      +...| ||.+....+..+ .+  ..|...||..|+.-    .-  .   .+-.||.|+..-.+
T Consensus        15 ~~~~C-~C~~~~~~~~~i-~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~~p   75 (78)
T d1wewa_          15 IKVRC-VCGNSLETDSMI-QCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSGP   75 (78)
T ss_dssp             CCCCC-SSCCCCCCSCEE-ECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCCSC
T ss_pred             CccEe-ECCCccCCCcEE-EEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcCCC
Confidence            34667 999877665544 34  25999999999831    10  1   13469999876543

>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=90.39  E-value=0.083  Score=35.48  Aligned_cols=45  Identities=24%  Similarity=0.543  Sum_probs=31.7

Q ss_pred             CcccccccccccCCCeeeecCCCCcccchhhHHHhhcCCC----Ccccccccc
Q 024603          210 EIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNG----SCPVCRECV  258 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~----sCPvCR~~v  258 (265)
                      ...|.+|.+.    ..+.....|...||..|+...+...+    .||.|+..-
T Consensus         7 c~~C~~C~~~----~~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           7 ATICRVCQKP----GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             SSCCSSSCSS----SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCCCCc----CEEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            4567777532    33556668999999999998765443    499997644

>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=90.25  E-value=0.04  Score=38.59  Aligned_cols=52  Identities=17%  Similarity=0.462  Sum_probs=35.4

Q ss_pred             ccCcccccccccccC-CCeeeecCCCCcccchhhHHHhhc-----C---CCCccccccccc
Q 024603          208 DNEIGCSICLEKFEE-GDSARKLPSCGHCFHSECVDKWLT-----R---NGSCPVCRECVC  259 (265)
Q Consensus       208 ~~~~~C~ICle~~~~-~~~~r~LP~CgH~FH~~CI~~WL~-----~---~~sCPvCR~~v~  259 (265)
                      +....|.||...... ...+.....|...||..|+...+.     .   .-.||.|+....
T Consensus        14 ~~~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~~   74 (88)
T d1weva_          14 EMGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMK   74 (88)
T ss_dssp             HHCCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHC
T ss_pred             cCcCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchHh
Confidence            345789999875443 345666778999999999864322     1   235999986543

>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=89.09  E-value=0.031  Score=35.65  Aligned_cols=45  Identities=18%  Similarity=0.452  Sum_probs=32.4

Q ss_pred             ccccccccccCCCeeeecCCCCcccchhhHHHhhcCCCCcccccc
Q 024603          212 GCSICLEKFEEGDSARKLPSCGHCFHSECVDKWLTRNGSCPVCRE  256 (265)
Q Consensus       212 ~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~WL~~~~sCPvCR~  256 (265)
                      .|.+|...|..-..-.....||++||..|..+.-.....|..|.+
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C~~   46 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQR   46 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhHhh
Confidence            588898888766555556689999999998766555667888864

>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=88.99  E-value=0.18  Score=34.55  Aligned_cols=48  Identities=21%  Similarity=0.500  Sum_probs=33.6

Q ss_pred             cccccccccccCCCeeeecCCCCcccchhhHH--Hh-hc--CCCCccccccccc
Q 024603          211 IGCSICLEKFEEGDSARKLPSCGHCFHSECVD--KW-LT--RNGSCPVCRECVC  259 (265)
Q Consensus       211 ~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~--~W-L~--~~~sCPvCR~~v~  259 (265)
                      ..| ||.+.+...........|.-.||..|+.  .. ..  .+-.||.|+....
T Consensus        13 v~C-iC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~g   65 (79)
T d1wepa_          13 VYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             eEe-ECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcC
Confidence            345 9998776665566677899999999984  11 11  2356999987543

>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {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 At1g33420
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=87.94  E-value=0.063  Score=36.15  Aligned_cols=49  Identities=24%  Similarity=0.479  Sum_probs=34.9

Q ss_pred             cccccccccccCCCeeeecCCCCcccchhhHHHh----hcCCCCcccccccccc
Q 024603          211 IGCSICLEKFEEGDSARKLPSCGHCFHSECVDKW----LTRNGSCPVCRECVCK  260 (265)
Q Consensus       211 ~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~W----L~~~~sCPvCR~~v~~  260 (265)
                      ..| ||.....+++.......|...||..|+..-    ....-.||.|+..-.+
T Consensus        17 ~~C-~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~~~~~~~~C~~C~~~~~p   69 (72)
T d1weea_          17 VDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELSGP   69 (72)
T ss_dssp             ECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHHCSS
T ss_pred             EEe-eCCCCcCCCCeEEEeCCCCCcCchhhcCCccccCCCCcEECcCCcCcCCc
Confidence            457 788777777666777789999999997532    1234469999876433

>d1wesa_ g.50.1.2 (A:) PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD Inhibitor of growth protein 2, Ing2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.09  E-value=0.21  Score=33.63  Aligned_cols=46  Identities=30%  Similarity=0.533  Sum_probs=26.9

Q ss_pred             CcccccccccccCCCeeee-cCCCC-cccchhhHHHhhcCC----CCccccccccc
Q 024603          210 EIGCSICLEKFEEGDSARK-LPSCG-HCFHSECVDKWLTRN----GSCPVCRECVC  259 (265)
Q Consensus       210 ~~~C~ICle~~~~~~~~r~-LP~Cg-H~FH~~CI~~WL~~~----~sCPvCR~~v~  259 (265)
                      ...| ||.+.. +++.+.. ...|. ..||..|+.  |...    -.||.||..-.
T Consensus        16 ~~~C-iC~~~~-~~~~i~c~~~~C~~~wfH~~Cvg--l~~~p~~~w~C~~C~~~~g   67 (71)
T d1wesa_          16 PTYC-LCNQVS-YGEMIGCDNEQCPIEWFHFSCVS--LTYKPKGKWYCPKCRGDSG   67 (71)
T ss_dssp             CCCS-TTCCCC-CSSEECCSCTTCSCCCEETTTTT--CSSCCSSCCCCTTTSSCCS
T ss_pred             CCEE-EeCCCC-CCCEEEEECCCCCCcCccCccCC--CCcCCCCcEECcCCccccC
Confidence            3455 998754 3333322 22354 479999984  3322    24999986543

>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=86.09  E-value=0.2  Score=34.90  Aligned_cols=36  Identities=22%  Similarity=0.564  Sum_probs=26.2

Q ss_pred             cccCcccccccccccCCCeeeecCCCCcccchhhHHHh
Q 024603          207 LDNEIGCSICLEKFEEGDSARKLPSCGHCFHSECVDKW  244 (265)
Q Consensus       207 ~~~~~~C~ICle~~~~~~~~r~LP~CgH~FH~~CI~~W  244 (265)
                      ...+..|.|| +.+...+.. -..-|+..||..|+.+-
T Consensus        12 v~~D~mC~vC-~v~t~~~l~-pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          12 VVNDEMCDVC-EVWTAESLF-PCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCSCCCTTT-CCCCSSCCS-SCSSSSSCCCHHHHHHH
T ss_pred             CCcCcccccc-Cccccccee-cceeecchhhHHHHHHh
Confidence            4567899999 666654443 22248899999999986