Citrus Sinensis ID: 040080

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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--
Protein Sequence
MVMAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVERSSIGSTSMSRDDVEKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRFGEESSRFSDIDVELREGVPTEGIELSDIRIELSDHVSFESSRPNQTDSNPSLLQDSSLETVL
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHcccccEEEEccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHccHHHHHHHccccccccHHHHHHccEEEEEccccccccccEEEEEccccccccEEEcccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHccc
Coil and Loop (DISEMBL)
MVMAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVerssigstsmsrddveklpCYEYlakskgsspieCAVCLdkfnkgdkcrllpicnhsfHAQCVDAwlltnpncpicrstansrrfgeessrfsdidvelregvptegielsDIRIELSdhvsfessrpnqtdsnpsllqdssletvl
Flexible Loop (DISEMBL)
MVMAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVErssigstsmsrddvEKLPCYEYLAkskgsspiECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRStansrrfgeessrfsdidvelregvptegielsdIRIELSDHVSFessrpnqtdsnpsllqdssletvl
Low Complexity Region (SEG)
MVMAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVERSSIGSTSMSRDDVEKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANsrrfgeessrfsDIDVELREGVPTEGIELSDIRIELSDHVSFESSRPNQTDSNPSLLQDSSLETVL
Disordered region (IsUnstruct)
**MAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMV****************KLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRS*********************************************************************
Disordered Region (DISOPRED)
MVMAIIISVIFLFLGIGALIFIHVCIVARTF****************************VEKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRST********************************************************************
Disordered Region (DISEMBL)
MVMAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVERSSIGSTSMSRDDVEKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRFGEESSRFSDIDVELREGVPTEGIELSDIRIELSDHV**************************
Disordered Region (DISPRO)
MVMAIIISVIFLFLGIGALIFIHVCIVAR***********************TSMSRDDVEKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTAN******************************************************************
Transmembrane Helix (TMHMM)
ooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVMAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVERSSIGSTSMSRDDVEKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRFGEESSRFSDIDVELREGVPTEGIELSDIRIELSDHVSFESSRPNQTDSNPSLLQDSSLETVL
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	192	2.2.26 [Sep-21-2011]
Q9FL07	376	RING-H2 finger protein AT	yes	no	0.442	0.226	0.444	5e-15
Q8W571	323	RING-H2 finger protein AT	no	no	0.656	0.390	0.335	6e-15
Q7X843	349	RING-H2 finger protein AT	no	no	0.640	0.352	0.335	2e-14
Q8GW38	369	RING-H2 finger protein AT	no	no	0.338	0.176	0.476	5e-14
Q8LGA5	368	E3 ubiquitin-protein liga	no	no	0.770	0.402	0.277	6e-14
Q8RXX9	398	E3 ubiquitin-protein liga	no	no	0.604	0.291	0.335	1e-13
Q9LY41	334	E3 ubiquitin-protein liga	no	no	0.364	0.209	0.426	2e-13
Q9LZV8	159	RING-H2 finger protein AT	no	no	0.447	0.540	0.351	2e-13
Q9XF63	324	RING-H2 finger protein AT	no	no	0.401	0.237	0.384	3e-13
Q9M0R6	302	Putative RING-H2 finger p	no	no	0.578	0.367	0.322	8e-13

>sp|Q9FL07|ATL46_ARATH RING-H2 finger protein ATL46 OS=Arabidopsis thaliana GN=ATL46 PE=2 SV=1

 Score = 80.9 bits (198), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 40/90 (44%), Positives = 56/90 (62%), Gaps = 5/90 (5%)

Query: 77  PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRFGEESSR 136
           P +CAVCL +F++ DK RLLP+C+H+FH  C+D WL +N  CP+CR T  S  F  E+  
Sbjct: 140 PFDCAVCLCEFSEKDKLRLLPMCSHAFHLNCIDTWLQSNSTCPLCRGTLFSPGFSMENPM 199

Query: 137 FSDIDV-ELREGVPTEG----IELSDIRIE 161
           F   D+ E  EGV   G    +E+ +I +E
Sbjct: 200 FDFDDIREDEEGVTENGSQKTMEIQEIVVE 229

Arabidopsis thaliana (taxid: 3702)

>sp|Q8W571|ATL32_ARATH RING-H2 finger protein ATL32 OS=Arabidopsis thaliana GN=ATL32 PE=2 SV=3

 Score = 80.5 bits (197), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 46/137 (33%), Positives = 70/137 (51%), Gaps = 11/137 (8%)

Query: 2   VMAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVERSSIGSTSMSRDDVE 61
           V A+++++ FL  G+ ++   H             RN        R  + +       VE
Sbjct: 49  VFAVLVTLFFL-TGLLSVYIRHCARSNPDSSTRYFRNRANDGSSRRGGLDNAV-----VE 102

Query: 62  KLPCYEY--LAKSK-GSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNC 118
             P + Y  + +SK GS  +ECA+CL++    +  RLLPICNH FH  C+D WL ++  C
Sbjct: 103 SFPVFAYSSVKESKIGSKDLECAICLNELEDHETVRLLPICNHLFHIDCIDTWLYSHATC 162

Query: 119 PICRS--TANSRRFGEE 133
           P+CRS  TA S + G+E
Sbjct: 163 PVCRSNLTAKSNKPGDE 179

Arabidopsis thaliana (taxid: 3702)

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

 Score = 79.0 bits (193), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 47/140 (33%), Positives = 76/140 (54%), Gaps = 17/140 (12%)

Query: 2   VMAIIIS---VIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVERSS--------I 50
           V+ ++IS   +I +FLG+  LIF  +   +  F   +   N    +   SS        +
Sbjct: 119 VLCLVISGLALIIVFLGVLYLIFKFLRKSSTLF--PIPHFNYNPDLFSFSSPQLQHLFFL 176

Query: 51  GSTSMSRDDVEKLPCYEYLAKSKG-SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVD 109
             + + +  ++ LP + Y   +     P +CAVCL++F+  DK RLLP+C+H+FH  C+D
Sbjct: 177 HDSGLDQTAIDALPVFLYGNVTISLEQPFDCAVCLNEFSDTDKLRLLPVCSHAFHLHCID 236

Query: 110 AWLLTNPNCPICR---STAN 126
            WLL+N  CP+CR   ST+N
Sbjct: 237 TWLLSNSTCPLCRRSLSTSN 256

Arabidopsis thaliana (taxid: 3702)

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

 Score = 77.4 bits (189), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 43/65 (66%)

Query: 60  VEKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCP 119
           ++ LP + Y        P +CAVCL +F++ DK RLLP C+H+FH  C+D WLL+N  CP
Sbjct: 124 IDALPVFLYKEIKGTKEPFDCAVCLCEFSEDDKLRLLPNCSHAFHIDCIDTWLLSNSTCP 183

Query: 120 ICRST 124
           +CR T
Sbjct: 184 LCRGT 188

Arabidopsis thaliana (taxid: 3702)

>sp|Q8LGA5|ATL31_ARATH E3 ubiquitin-protein ligase ATL31 OS=Arabidopsis thaliana GN=ATL31 PE=1 SV=2

 Score = 77.4 bits (189), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 43/155 (27%), Positives = 74/155 (47%), Gaps = 7/155 (4%)

Query: 16  IGALIFIHVCIVARTFRAGLIRNNVGGAMVERSSIGSTSMSR----DDVEKLPCYEY--- 68
           I AL F+    V      G +  +V  A   R  + + +++R    + +E  P + Y   
Sbjct: 53  IAALFFMGFFTVYIRHCTGAVDGSVTPAGGARRRVTNATVARGLDAETIETFPTFVYSEV 112

Query: 69  LAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSR 128
             +  G   +ECA+CL++F   +  RLLP C+H FH  C+ AWL  +  CP+CR+    +
Sbjct: 113 KTQKIGKGALECAICLNEFEDDETLRLLPKCDHVFHPHCIGAWLQGHVTCPVCRTNLAEQ 172

Query: 129 RFGEESSRFSDIDVELREGVPTEGIELSDIRIELS 163
               E    +D++ + +  VP   +EL  ++   S
Sbjct: 173 TPEPEVVVETDLEAQQQSAVPVPVVELPRVKFPRS 207

E3 ubiquitin-protein ligase that is required for the plant C/N response during seedling growth transition. May be involved in the early steps of the plant defense signaling pathway.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q8RXX9|ATL6_ARATH E3 ubiquitin-protein ligase ATL6 OS=Arabidopsis thaliana GN=ATL6 PE=1 SV=2

 Score = 76.3 bits (186), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 43/128 (33%), Positives = 71/128 (55%), Gaps = 12/128 (9%)

Query: 1   MVMAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVERSSIGSTSMSRDD- 59
           +++ I+I+ +F F+G  ++ F H   V     AG+  +  GGA   R+++ + +   D  
Sbjct: 51  VIVVILIAALF-FMGFFSIYFRHCSGVPD---AGV--SPAGGAR-SRATVNAAARGLDVS 103

Query: 60  -VEKLPCYEY---LAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN 115
            VE  P + Y     +  G   +ECA+CL++F   +  RLLP C+H FH  C+DAWL  +
Sbjct: 104 VVETFPTFLYSDVKTQKLGKGELECAICLNEFEDDETLRLLPKCDHVFHPHCIDAWLEAH 163

Query: 116 PNCPICRS 123
             CP+CR+
Sbjct: 164 VTCPVCRA 171

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

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9LY41|ATL4_ARATH E3 ubiquitin-protein ligase ATL4 OS=Arabidopsis thaliana GN=ATL4 PE=1 SV=1

 Score = 75.9 bits (185), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/82 (42%), Positives = 53/82 (64%), Gaps = 12/82 (14%)

Query: 45  VERSSIGSTSMSRDDVEKLPCYEYLAKSKGSSPI---ECAVCLDKFNKGDKCRLLPICNH 101
            ERSS+         ++ LP +++ + ++ SS +   +CAVCL KF   D+ RLLP+C H
Sbjct: 88  TERSSV---------LDSLPIFKFSSVTRRSSSMNSGDCAVCLSKFEPEDQLRLLPLCCH 138

Query: 102 SFHAQCVDAWLLTNPNCPICRS 123
           +FHA C+D WL++N  CP+CRS
Sbjct: 139 AFHADCIDIWLVSNQTCPLCRS 160

E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 in vitro.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9LZV8|ATL74_ARATH RING-H2 finger protein ATL74 OS=Arabidopsis thaliana GN=ATL74 PE=2 SV=1

 Score = 75.5 bits (184), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 54/91 (59%), Gaps = 5/91 (5%)

Query: 34  GLIRNNVGGAMVERSSIGSTSMSRDDVEKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKC 93
           GL  +   G + +R+ +      + +++K P  EY +     +  ECA+CL +F  G++ 
Sbjct: 64  GLSSSAAAGTVADRAGL-----KKRELKKFPVAEYGSGEVKIAATECAICLGEFADGERV 118

Query: 94  RLLPICNHSFHAQCVDAWLLTNPNCPICRST 124
           R+LP CNHSFH  C+D WL+++ +CP CR +
Sbjct: 119 RVLPPCNHSFHMSCIDTWLVSHSSCPNCRHS 149

Arabidopsis thaliana (taxid: 3702)

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

 Score = 74.7 bits (182), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 49/78 (62%), Gaps = 1/78 (1%)

Query: 47  RSSIGSTSMSRDDVEKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQ 106
           + ++ +T ++  ++  LP   +  +      +EC++CL +  KGDK RLLP CNHSFH +
Sbjct: 95  QDALSNTGLTSFELSSLPIV-FFRQDSCKDGLECSICLSELVKGDKARLLPKCNHSFHVE 153

Query: 107 CVDAWLLTNPNCPICRST 124
           C+D W  ++  CPICR+T
Sbjct: 154 CIDMWFQSHSTCPICRNT 171

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M0R6|ATL35_ARATH Putative RING-H2 finger protein ATL35 OS=Arabidopsis thaliana GN=ATL35 PE=3 SV=1

 Score = 73.6 bits (179), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 63/127 (49%), Gaps = 16/127 (12%)

Query: 2   VMAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVERSSIGSTSMSRDDVE 61
           V+AII+  IF+ L + A      C + +TF    +          R+  G   + ++ VE
Sbjct: 51  VIAIIVLAIFISLSMVA------CFLHKTFYRAEVEAASQEVFHSRARRG---LEKELVE 101

Query: 62  KLPCYEY-----LAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNP 116
             P + Y     L   KG   +ECA+CL +F   +  R +P C+H+FHA C+D WL +  
Sbjct: 102 SFPIFLYSEVKGLKIGKGG--VECAICLSEFVDKETLRWMPPCSHTFHANCIDVWLSSQS 159

Query: 117 NCPICRS 123
            CP CR+
Sbjct: 160 TCPACRA 166

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	192
359488847	188	PREDICTED: E3 ubiquitin-protein ligase A	0.911	0.930	0.561	2e-48
255552618	200	zinc finger protein, putative [Ricinus c	0.765	0.735	0.568	2e-44
359491594	146	PREDICTED: RING-H2 finger protein ATL48-	0.718	0.945	0.503	5e-36
388501546	188	unknown [Lotus japonicus]	0.901	0.920	0.415	7e-34
255540713	189	conserved hypothetical protein [Ricinus	0.755	0.767	0.463	5e-32
326516304	148	predicted protein [Hordeum vulgare subsp	0.645	0.837	0.380	2e-20
413944251	172	putative RING zinc finger domain superfa	0.645	0.720	0.372	6e-19
242066104	157	hypothetical protein SORBIDRAFT_04g02906	0.635	0.777	0.362	6e-19
242095466	168	hypothetical protein SORBIDRAFT_10g00986	0.645	0.738	0.351	7e-18
383172430	137	Pinus taeda anonymous locus 0_5128_01 ge	0.520	0.729	0.394	4e-17

>gi|359488847|ref|XP_003633831.1| PREDICTED: E3 ubiquitin-protein ligase ATL42-like [Vitis vinifera]

 Score =  197 bits (501), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 105/187 (56%), Positives = 127/187 (67%), Gaps = 12/187 (6%)

Query: 3   MAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVERSSIGSTSMSRDDVEK 62
           MAI+IS+I LFLGIG L+ IHVCIV R FR G       G MVER +  STSMS DD++K
Sbjct: 1   MAIVISLILLFLGIGVLVIIHVCIVGRAFRGGFGN----GRMVERGNPRSTSMSLDDLDK 56

Query: 63  LPCYEYLAKSKGSS-PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPIC 121
           LPC+ + AK KGSS P++CAVCLD F  GDKCRLLP+CNHSFHAQCVD+WLL  P CPIC
Sbjct: 57  LPCFHFQAKEKGSSSPVDCAVCLDNFKMGDKCRLLPLCNHSFHAQCVDSWLLKTPICPIC 116

Query: 122 RSTANSRRF----GEESSRFSDIDVELREGVPTEGIELSDIRIELSDH---VSFESSRPN 174
           R++A+ R+     GEESS FSD   ELRE   TE   + D  I+  D+   VS      N
Sbjct: 117 RTSADFRKGSLVSGEESSHFSDTGNELRESQTTERGHMGDAGIDSRDNPGAVSGIHLSSN 176

Query: 175 QTDSNPS 181
            + +NP+
Sbjct: 177 HSPNNPA 183

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255552618|ref|XP_002517352.1| zinc finger protein, putative [Ricinus communis] gi|223543363|gb|EEF44894.1| zinc finger protein, putative [Ricinus communis]

 Score =  184 bits (466), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 87/153 (56%), Positives = 111/153 (72%), Gaps = 6/153 (3%)

Query: 3   MAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVERSSIGSTSMSRDDVEK 62
           MAI++SVI LF+GIG L+FIH CI+ R+FR     N+  G+    S   +TS+S DD+EK
Sbjct: 1   MAIVVSVILLFVGIGLLVFIHACIIGRSFRNNDPANDPTGST--DSPGRTTSISADDLEK 58

Query: 63  LPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICR 122
           LP ++++AK KGSSP++CAVCLD F  GDKCRLLPIC HSFHAQCVD WLL  P CPICR
Sbjct: 59  LPSFDFIAKGKGSSPVDCAVCLDNFRAGDKCRLLPICKHSFHAQCVDEWLLKTPICPICR 118

Query: 123 STANSRR----FGEESSRFSDIDVELREGVPTE 151
           ++A SRR     GEESS  SD  +++R  + T+
Sbjct: 119 ASAGSRRGSVAIGEESSHLSDTSIDMRGNLTTD 151

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359491594|ref|XP_003634293.1| PREDICTED: RING-H2 finger protein ATL48-like [Vitis vinifera]

 Score =  155 bits (393), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 75/149 (50%), Positives = 100/149 (67%), Gaps = 11/149 (7%)

Query: 3   MAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVERSSIGSTSMSRDDVEK 62
           M I++S++ LF+GI  LI IHVCIV R FR    R    GAMV+R   G   MS+D+++K
Sbjct: 1   MEIVVSLVLLFVGIAVLIVIHVCIVGRAFR----RAYGNGAMVQRGGSGGLGMSQDELKK 56

Query: 63  LPCYEYLA---KSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCP 119
           LPC+EY A   +   +SP++CAVCL+ F KGDKCRLLP C H FH+QC+D+WLL  P CP
Sbjct: 57  LPCFEYKAVALEKASNSPVDCAVCLENFRKGDKCRLLPNCKHFFHSQCIDSWLLKTPICP 116

Query: 120 ICRSTANSRRF----GEESSRFSDIDVEL 144
           ICR+ A++ +     G+ES    D+  EL
Sbjct: 117 ICRTCASTPKISTFSGQESGISRDVGAEL 145

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388501546|gb|AFK38839.1| unknown [Lotus japonicus]

 Score =  149 bits (375), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 79/190 (41%), Positives = 112/190 (58%), Gaps = 17/190 (8%)

Query: 1   MVMAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVERSSIGSTSMSRDDV 60
           + MA+IIS++ +F+G+  L+ IHVC+     R G        +M ER + G  SMS+ D+
Sbjct: 13  LTMAVIISLVLIFVGLVFLVLIHVCLSEWFSRTGGGSGG---SMTERGANGGRSMSKKDL 69

Query: 61  EKLPCYEYLAKSKGS-SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCP 119
           EKLPCY+Y+AK   + SP++CAVCL+    GDKCRLLP+C HSFHAQCVD WLL  P CP
Sbjct: 70  EKLPCYDYVAKDNSTCSPVDCAVCLENLTTGDKCRLLPVCKHSFHAQCVDTWLLKTPICP 129

Query: 120 ICRSTANSRRFGEESSRFSDIDVELREGVPTEGIELSDIRIELSDHVSFESSRPNQTDSN 179
           ICRS+A S   G +        V++ E   +      ++ IE+ D+  F + R  Q +  
Sbjct: 130 ICRSSAGSSHSGNQ--------VQVVESGSSR-----NVAIEMMDNPIFGTPRSGQGEVE 176

Query: 180 PSLLQDSSLE 189
             + Q  + E
Sbjct: 177 SRVHQTGTAE 186

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255540713|ref|XP_002511421.1| conserved hypothetical protein [Ricinus communis] gi|223550536|gb|EEF52023.1| conserved hypothetical protein [Ricinus communis]

 Score =  142 bits (359), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 70/151 (46%), Positives = 95/151 (62%), Gaps = 6/151 (3%)

Query: 1   MVMAIIISVIFLFLGIGALIFIHVCIVARTFRAGL-IRNNVGGAMVERSSIGSTSMSRDD 59
           M M II+SV+ LF+GI  L+ IHVCIV R FR G      +G      S  G   +S ++
Sbjct: 1   MAMEIIVSVVLLFVGIAVLVAIHVCIVGRAFRRGYETGQEIGPGSFSSSRYGIKKISNEE 60

Query: 60  VEKLPCYEYLAKSK-GSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNC 118
           ++ LPC++Y A  K GSS  +C VCL+ FN GDKC+LLP C HSFH+QC+D+WL+  P C
Sbjct: 61  LKNLPCFDYKAAEKEGSSSSDCVVCLENFNVGDKCKLLPNCKHSFHSQCIDSWLVKTPIC 120

Query: 119 PICRSTANSRRFG----EESSRFSDIDVELR 145
           PICR+  N+ + G    +ESS    + VE+ 
Sbjct: 121 PICRTIVNTPKVGLVLRQESSISIAVGVEIH 151

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326516304|dbj|BAJ92307.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 48/126 (38%), Positives = 76/126 (60%), Gaps = 2/126 (1%)

Query: 5   IIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAM-VERSSIGSTSMSRDDVEKL 63
           + +SV+FL  G+  ++ +HV ++    R G +    G A   +R    +T ++ D++ +L
Sbjct: 4   MAVSVLFLIAGVVLMLALHVLVIVWAVRRGAVLRLRGAARERDREQGEATGLTADELGEL 63

Query: 64  PCYEYLAKSK-GSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICR 122
           PC ++ A +  G+   ECAVCL+ F  GD+CR+LP C+H FH QCVDAWL  +  CP+CR
Sbjct: 64  PCQDFKAAAVVGTGAGECAVCLEAFQGGDRCRVLPGCHHGFHTQCVDAWLRQSRRCPVCR 123

Query: 123 STANSR 128
           +    R
Sbjct: 124 AEVACR 129

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413944251|gb|AFW76900.1| putative RING zinc finger domain superfamily protein [Zea mays]

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 48/129 (37%), Positives = 70/129 (54%), Gaps = 5/129 (3%)

Query: 6   IISVIFLFLGIGALIFIHVCIVARTFRAGL-IRNNVGGAMVERSSI----GSTSMSRDDV 60
           I+SV+ L  G+  ++  H+ +V      GL  R +   A  +   +    G   +S  ++
Sbjct: 9   ILSVVLLIAGVAVMLVAHILVVFWALLRGLGSRGSSQHAANQEERVEDGRGRRGLSSGEL 68

Query: 61  EKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPI 120
             LPC+EY   +      +CAVCL+ F  GD+CR LP C HSFHA+CVD+WL  +  CP+
Sbjct: 69  ATLPCHEYFKAAADGETGDCAVCLEAFEAGDRCRQLPRCEHSFHAECVDSWLRKSSACPV 128

Query: 121 CRSTANSRR 129
           CR  A  RR
Sbjct: 129 CRVDAVDRR 137

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242066104|ref|XP_002454341.1| hypothetical protein SORBIDRAFT_04g029060 [Sorghum bicolor] gi|241934172|gb|EES07317.1| hypothetical protein SORBIDRAFT_04g029060 [Sorghum bicolor]

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 45/124 (36%), Positives = 71/124 (57%), Gaps = 2/124 (1%)

Query: 2   VMAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVERSSIGSTSMSRDDVE 61
           ++ + +SV+ L  G+ A++ +HV IV    R G++         +        +S +D+ 
Sbjct: 1   MVELTVSVLLLVAGVVAMLVLHVLIVVWALRRGVVLRAAASRRQDEERAAGQGLSPEDLN 60

Query: 62  KLPCYEYLAKSKGSSPI--ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCP 119
           +LPC+++     G+     ECAVCL+ F  GD+CR+LP C H FHAQCVD WL  +  CP
Sbjct: 61  ELPCHDHECSKAGAGAAGAECAVCLEAFQAGDRCRVLPRCEHGFHAQCVDQWLRKSRLCP 120

Query: 120 ICRS 123
           +CR+
Sbjct: 121 VCRA 124

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242095466|ref|XP_002438223.1| hypothetical protein SORBIDRAFT_10g009860 [Sorghum bicolor] gi|241916446|gb|EER89590.1| hypothetical protein SORBIDRAFT_10g009860 [Sorghum bicolor]

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 46/131 (35%), Positives = 72/131 (54%), Gaps = 7/131 (5%)

Query: 4   AIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVERS------SIGSTSMSR 57
           A I+SV  L +G+  ++ +H+ +V    R GL   + G     +         G   +S 
Sbjct: 5   AAILSVALLIVGVSLMLAVHILVVFWALRRGLGSRDTGQHANHQDQERVEDGHGRRGLSP 64

Query: 58  DDVEKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPN 117
            ++  LPC+++ A + G +  +CAVCL+ F  GD+CR LP C H FHA+CVD+WL  +  
Sbjct: 65  GELVTLPCHDFKA-ADGEAAGDCAVCLEAFQAGDRCRQLPRCEHCFHAECVDSWLRKSSK 123

Query: 118 CPICRSTANSR 128
           CP+CR+    R
Sbjct: 124 CPVCRADVVDR 134

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|383172430|gb|AFG69582.1| Pinus taeda anonymous locus 0_5128_01 genomic sequence gi|383172432|gb|AFG69583.1| Pinus taeda anonymous locus 0_5128_01 genomic sequence

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 47/119 (39%), Positives = 67/119 (56%), Gaps = 19/119 (15%)

Query: 17  GALIFIHVCIVA----RTFRAGLIRNNVGGAMVERSSIGSTSMSRDDVEKLPCYEYLAKS 72
           G L+ +H+ I      R  R  L +   G             +S+ +++KLPC+E+    
Sbjct: 1   GFLLLLHLWIAGSAHRRRLRPWLAQQGRG-------------LSQAELQKLPCFEFEVGG 47

Query: 73  KGSSPIECAVCLDKFNK--GDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR 129
              +   CAVCL++F K  G+KC+ LP CNH+FHA+C+DAWL   P CPICR+TA  RR
Sbjct: 48  SSCTDSSCAVCLEEFEKSGGEKCKTLPACNHTFHAKCLDAWLSRTPICPICRTTAGDRR 106

Source: Pinus taeda

Species: Pinus taeda

Genus: Pinus

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

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	192
TAIR|locus:2085914	411	AT3G18930 [Arabidopsis thalian	0.286	0.133	0.472	4.1e-17
TAIR|locus:2193992	324	ATL3 [Arabidopsis thaliana (ta	0.401	0.237	0.384	1.1e-16
TAIR|locus:2062008	227	AT2G47560 [Arabidopsis thalian	0.911	0.770	0.297	4.7e-16
TAIR|locus:2054049	423	MEE16 "maternal effect embryo	0.640	0.290	0.317	6.1e-16
TAIR|locus:2181032	159	DAFL2 "DAF-Like gene 2" [Arabi	0.583	0.704	0.311	9.8e-16
TAIR|locus:2090980	204	AT3G14320 [Arabidopsis thalian	0.604	0.568	0.325	1.7e-15
TAIR|locus:2146330	368	CNI1 "carbon/nitrogen insensit	0.838	0.437	0.284	1.8e-15
TAIR|locus:2197026	310	AT1G53820 [Arabidopsis thalian	0.244	0.151	0.531	3.3e-15
TAIR|locus:2199902	369	AT1G23980 [Arabidopsis thalian	0.333	0.173	0.5	3.9e-15
TAIR|locus:2118666	472	AT4G30400 [Arabidopsis thalian	0.645	0.262	0.314	4.7e-15

TAIR|locus:2085914 AT3G18930 [Arabidopsis thaliana (taxid:3702)]

 Score = 173 (66.0 bits), Expect = 4.1e-17, Sum P(3) = 4.1e-17
 Identities = 26/55 (47%), Positives = 41/55 (74%)

Query:    69 LAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRS 123
             + K+  ++  +CAVCL +F +GD  R LP+C H+FH +C+D WL ++PNCP+CR+
Sbjct:   145 VGKTSAANCRDCAVCLLEFEEGDYVRTLPLCFHAFHLECIDEWLRSHPNCPLCRT 199

GO:0005634 "nucleus" evidence=ISM

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

GO:0009693 "ethylene biosynthetic process" evidence=RCA

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

 Score = 190 (71.9 bits), Expect = 1.1e-16, Sum P(2) = 1.1e-16
 Identities = 30/78 (38%), Positives = 49/78 (62%)

Query:    47 RSSIGSTSMSRDDVEKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQ 106
             + ++ +T ++  ++  LP   +  +      +EC++CL +  KGDK RLLP CNHSFH +
Sbjct:    95 QDALSNTGLTSFELSSLPIV-FFRQDSCKDGLECSICLSELVKGDKARLLPKCNHSFHVE 153

Query:   107 CVDAWLLTNPNCPICRST 124
             C+D W  ++  CPICR+T
Sbjct:   154 CIDMWFQSHSTCPICRNT 171

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2062008 AT2G47560 [Arabidopsis thaliana (taxid:3702)]

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 55/185 (29%), Positives = 85/185 (45%)

Query:     5 IIISVIFLFLGIGALIFIHVCIVAR-TFRAG--LIRNNVGGAMVERS-SIGSTSMSRDDV 60
             ++ SVI LF+ +  ++  H    AR  FR     IR  +   +   S S    ++ +  +
Sbjct:    29 MLSSVIVLFVAVIMILCFHS--YARWLFRRHNRRIRRRIRSHLRTLSASPRDQALDQAVL 86

Query:    61 EKLPCYEYLAKSKG--SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNC 118
             +K+P + Y +K+        EC+VCL +F + D+ RLLP C HSFH  C+D W  +   C
Sbjct:    87 DKIPIFVYSSKNPPPPEEKEECSVCLSEFEEEDEGRLLPKCGHSFHVDCIDTWFRSRSTC 146

Query:   119 PICRSTANXXXXXXXXXXXXDIDVEL--REGVPTEGIELSDIRIELSDHVSFESSRPNQT 176
             P+CR+                        EG   E I+L+ I +++S  V FE S P   
Sbjct:   147 PLCRAPVQPPFQVIETGSSSSSSPLTFPTEGCEREPIDLAGIIVDISREVEFEGSNPGLP 206

Query:   177 DSNPS 181
               N S
Sbjct:   207 IENGS 211

GO:0005634 "nucleus" evidence=ISM

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

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

 Score = 205 (77.2 bits), Expect = 6.1e-16, P = 6.1e-16
 Identities = 40/126 (31%), Positives = 70/126 (55%)

Query:     1 MVMAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVG--GAMVERSSIGSTSMSRD 58
             +++ II+S+IF   G+  ++   +   +R  R     N     G + +  ++  + + + 
Sbjct:    44 LLIIIILSIIFFISGLLHILVKFLLTPSRESREDYFDNVTALQGQLQQLFNLHDSGVDQS 103

Query:    59 DVEKLPCYEYLA-KSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPN 117
              ++ LP + Y +      SP +C VCL +F   DK RLLP C+H+FH +C+D WLL++  
Sbjct:   104 LIDTLPVFHYKSIVGLKISPFDCPVCLCEFETEDKLRLLPKCSHAFHVECIDTWLLSHST 163

Query:   118 CPICRS 123
             CP+CRS
Sbjct:   164 CPLCRS 169

GO:0005634 "nucleus" evidence=ISM

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

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

TAIR|locus:2181032 DAFL2 "DAF-Like gene 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 197 (74.4 bits), Expect = 9.8e-16, P = 9.8e-16
 Identities = 38/122 (31%), Positives = 70/122 (57%)

Query:     1 MVMAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVGGAMVERSSIGSTSMSRDDV 60
             +++A ++  + L LG+ +++    C +   F  GL  +   G + +R+ +      + ++
Sbjct:    36 IILAALLCALILALGLNSILR---CAMRCGF--GLSSSAAAGTVADRAGL-----KKREL 85

Query:    61 EKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPI 120
             +K P  EY +     +  ECA+CL +F  G++ R+LP CNHSFH  C+D WL+++ +CP 
Sbjct:    86 KKFPVAEYGSGEVKIAATECAICLGEFADGERVRVLPPCNHSFHMSCIDTWLVSHSSCPN 145

Query:   121 CR 122
             CR
Sbjct:   146 CR 147

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

TAIR|locus:2090980 AT3G14320 [Arabidopsis thaliana (taxid:3702)]

 Score = 170 (64.9 bits), Expect = 1.7e-15, Sum P(2) = 1.7e-15
 Identities = 40/123 (32%), Positives = 58/123 (47%)

Query:     3 MAIIISVIFLFLGIGALIF--IHVCIVARTFRAGLIRNNVGGAMVE-RSSIGSTSMSRDD 59
             + I I   F F GI A++   I  C            NN G   +  +  +G        
Sbjct:    12 LGINIVFAFFFFGISAVVVSCIIKCYNTHDDDHDHDNNNDGHVSITIKERVGIKPYV--- 68

Query:    60 VEKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCP 119
             +  +P  ++  K      +EC VCL +   GDK R+LP C+H FH +C+D+WL +N  CP
Sbjct:    69 LRSIPIVDFNTKDF-KYVLECVVCLSELADGDKARVLPSCDHWFHVECIDSWLQSNSTCP 127

Query:   120 ICR 122
             ICR
Sbjct:   128 ICR 130

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

TAIR|locus:2146330 CNI1 "carbon/nitrogen insensitive 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 199 (75.1 bits), Expect = 1.8e-15, P = 1.8e-15
 Identities = 50/176 (28%), Positives = 83/176 (47%)

Query:     1 MVMAIIISVIFLFLGIGALIFIHVCIVA---RTFRAGLIRNNVGGAMVERSSIGSTSMSR 57
             +V+ ++I+ +F F+G    ++I  C  A       AG  R  V  A V R       +  
Sbjct:    47 VVVVVVIAALF-FMGFFT-VYIRHCTGAVDGSVTPAGGARRRVTNATVARG------LDA 98

Query:    58 DDVEKLPCYEYL-AKSK--GSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT 114
             + +E  P + Y   K++  G   +ECA+CL++F   +  RLLP C+H FH  C+ AWL  
Sbjct:    99 ETIETFPTFVYSEVKTQKIGKGALECAICLNEFEDDETLRLLPKCDHVFHPHCIGAWLQG 158

Query:   115 NPNCPICRSTANXXXXXXXXXXXXDIDVELREGVPTEGIELSDIRIELSDHVSFES 170
             +  CP+CR+               D++ + +  VP   +EL  ++   S H +  S
Sbjct:   159 HVTCPVCRTNLAEQTPEPEVVVETDLEAQQQSAVPVPVVELPRVKFPRS-HTTGHS 213

GO:0005576 "extracellular region" evidence=ISM

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

GO:0009737 "response to abscisic acid stimulus" evidence=IEP;RCA

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

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

GO:0016020 "membrane" evidence=IDA

GO:0043562 "cellular response to nitrogen levels" evidence=IMP

GO:0009814 "defense response, incompatible interaction" evidence=IEP

GO:0009816 "defense response to bacterium, incompatible interaction" evidence=IMP

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

GO:0007165 "signal transduction" evidence=RCA

GO:0009414 "response to water deprivation" evidence=RCA

GO:0009611 "response to wounding" evidence=RCA

GO:0009693 "ethylene biosynthetic process" evidence=RCA

GO:0009723 "response to ethylene stimulus" evidence=RCA

GO:0009733 "response to auxin stimulus" evidence=RCA

GO:0009738 "abscisic acid mediated signaling pathway" evidence=RCA

GO:0009753 "response to jasmonic acid stimulus" evidence=RCA

GO:0030968 "endoplasmic reticulum unfolded protein response" evidence=RCA

GO:0035556 "intracellular signal transduction" evidence=RCA

GO:0042538 "hyperosmotic salinity response" evidence=RCA

TAIR|locus:2197026 AT1G53820 [Arabidopsis thaliana (taxid:3702)]

 Score = 165 (63.1 bits), Expect = 3.3e-15, Sum P(2) = 3.3e-15
 Identities = 25/47 (53%), Positives = 32/47 (68%)

Query:    78 IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRST 124
             +ECAVCL     GDK R+LP CNH FH  C+D W  ++  CP+CR+T
Sbjct:   118 LECAVCLSDLVDGDKARVLPRCNHGFHVDCIDMWFQSHSTCPLCRNT 164

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2199902 AT1G23980 [Arabidopsis thaliana (taxid:3702)]

 Score = 196 (74.1 bits), Expect = 3.9e-15, P = 3.9e-15
 Identities = 33/66 (50%), Positives = 47/66 (71%)

Query:    60 VEKLPCYEYLAKSKGSS-PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNC 118
             ++ LP + Y  + KG+  P +CAVCL +F++ DK RLLP C+H+FH  C+D WLL+N  C
Sbjct:   124 IDALPVFLY-KEIKGTKEPFDCAVCLCEFSEDDKLRLLPNCSHAFHIDCIDTWLLSNSTC 182

Query:   119 PICRST 124
             P+CR T
Sbjct:   183 PLCRGT 188

GO:0005634 "nucleus" evidence=ISM

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

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

 Score = 198 (74.8 bits), Expect = 4.7e-15, P = 4.7e-15
 Identities = 40/127 (31%), Positives = 69/127 (54%)

Query:     1 MVMAIIISVIFLFLGIGALIFIHVCIVARTFRAGLIRNNVG--GAMVERSSIGSTSMSRD 58
             +++ II+S+IF   G+  L+   +   +   R     N     G + +   +  + + + 
Sbjct:    52 LLIIIILSIIFFISGLLHLLVRFLLTPSSRDREDYFDNVTALQGQLQQLFHLHDSGVDQS 111

Query:    59 DVEKLPCYEYLAK-SKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPN 117
              ++ LP + Y +     + P +CAVCL +F   DK RLLP C+H+FH  C+D WLL++  
Sbjct:   112 FIDTLPVFHYKSIIGLKNYPFDCAVCLCEFETEDKLRLLPKCSHAFHMDCIDTWLLSHST 171

Query:   118 CPICRST 124
             CP+CRS+
Sbjct:   172 CPLCRSS 178

GO:0005634 "nucleus" evidence=ISM

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

GO:0080167 "response to karrikin" evidence=IEP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	192
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	8e-15
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	3e-11
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	2e-10
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	8e-09
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	2e-07
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	3e-07
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	7e-07
smart00184	40	smart00184, RING, Ring finger	2e-06
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	5e-05
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	7e-05
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	3e-04
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	4e-04
TIGR00599	397	TIGR00599, rad18, DNA repair protein rad18	4e-04
COG5432	391	COG5432, RAD18, RING-finger-containing E3 ubiquiti	0.002

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

 Score = 65.1 bits (159), Expect = 8e-15
 Identities = 21/45 (46%), Positives = 32/45 (71%), Gaps = 1/45 (2%)

Query: 79  ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRS 123
           EC +CLD+F  G++  +LP C H FH +C+D WL ++  CP+CR+
Sbjct: 2   ECPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLCRA 45

Length = 46

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

 Score = 60.8 bits (147), Expect = 3e-11
 Identities = 25/47 (53%), Positives = 33/47 (70%), Gaps = 2/47 (4%)

Query: 78  IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPN-CPICRS 123
           +ECA+C+  F K D+ R+LP C+H FH  CVD WLL   N CP+CR+
Sbjct: 324 VECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRT 369

Length = 374

>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 = 53.6 bits (129), Expect = 2e-10
 Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 4/47 (8%)

Query: 79  ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRST 124
           EC +CL++F    +  +L  C H F   C+D WL +    CP+CR+ 
Sbjct: 1   ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44

Length = 45

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

 Score = 50.1 bits (120), Expect = 8e-09
 Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 9/52 (17%)

Query: 80  CAVCLDKF--------NKGDKCRL-LPICNHSFHAQCVDAWLLTNPNCPICR 122
           CA+C + F        + GD C +    C H+FH  C+  WL T   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|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional

 Score = 49.4 bits (118), Expect = 2e-07
 Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 4/63 (6%)

Query: 66  YEYLAKSKGSSPIECAVCLDK-FNKGDKCR---LLPICNHSFHAQCVDAWLLTNPNCPIC 121
            EY      S   ECA+C++K ++K  K     +L  CNH F  +C+D W      CP+C
Sbjct: 163 SEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVC 222

Query: 122 RST 124
           R+ 
Sbjct: 223 RTP 225

Length = 238

>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 = 46.4 bits (110), Expect = 3e-07
 Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 80  CAVCLDKFNKGDKCRLL-PICNHSFHAQCVDAWLLTNPNCPICRSTANSRRFGEE 133
           C  C      GD+C ++  +CNH+FH  C+  WL T   CP+ R T      G  
Sbjct: 34  CPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLADGGAI 88

Length = 88

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

 Score = 44.0 bits (104), Expect = 7e-07
 Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 3/48 (6%)

Query: 76  SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRS 123
             +EC +CLD         +L  C H F  +C+  +L     CPICR+
Sbjct: 1   EELECPICLDLL---RDPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 42.9 bits (101), Expect = 2e-06
 Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 4/43 (9%)

Query: 80  CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPN-CPIC 121
           C +CL+++       +LP C H+F   C+  WL +  N CPIC
Sbjct: 1   CPICLEEY--LKDPVILP-CGHTFCRSCIRKWLESGNNTCPIC 40

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

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

 Score = 40.2 bits (94), Expect = 5e-05
 Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 12/57 (21%)

Query: 80  CAVCLDKFN--------KGDKCRL-LPICNHSFHAQCVDAWLLTNPN---CPICRST 124
           C +C   F+         GD C L    C H+FH  C+  WL T  +   CP+CR T
Sbjct: 24  CGICRVSFDGTCPQCKFPGDDCPLVWGKCKHNFHMHCILKWLATETSKGLCPMCRQT 80

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

 Score = 42.3 bits (99), Expect = 7e-05
 Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 5/55 (9%)

Query: 79   ECAVC---LDKFNKGDKCRLLPICNHSFHAQCVDAWLLT--NPNCPICRSTANSR 128
            ECA+C   LD  ++    +    C + FH +C+  W  +    NCP+CRS     
Sbjct: 1471 ECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEITFV 1525

Length = 1525

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

 Score = 36.7 bits (85), Expect = 3e-04
 Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 4/43 (9%)

Query: 80  CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLL-TNPNCPIC 121
           C +CL++    D   +LP C H F ++C+ +WL   N  CP+C
Sbjct: 1   CPICLEEPK--DPVTILP-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|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

 Score = 40.0 bits (93), Expect = 4e-04
 Identities = 16/54 (29%), Positives = 21/54 (38%), Gaps = 11/54 (20%)

Query: 80  CAVCLDKF----------NKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRS 123
           C +C+D+                 + LP C H  H  C+  WL     CPICR 
Sbjct: 290 CTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRR 342

Length = 491

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

 Score = 40.0 bits (93), Expect = 4e-04
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 4/49 (8%)

Query: 76  SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRST 124
           + + C +C D F       +L  C+H+F + C+   L   P CP+CR+ 
Sbjct: 25  TSLRCHICKDFF----DVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAE 69

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|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

 Score = 37.8 bits (87), Expect = 0.002
 Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 4/43 (9%)

Query: 80  CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICR 122
           C +C  +            C H+F + C+   L T P CP+CR
Sbjct: 28  CRICDCRI----SIPCETTCGHTFCSLCIRRHLGTQPFCPVCR 66

Length = 391

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	192
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.8
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.62
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.5
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.43
PHA02929	238	N1R/p28-like protein; Provisional	99.42
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.37
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.35
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.27
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.21
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.19
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.16
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.13
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.11
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.09
PHA02926	242	zinc finger-like protein; Provisional	99.05
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.01
PF14634	44	zf-RING_5: zinc-RING finger domain	98.96
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.92
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.9
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.9
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.9
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.89
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.83
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.78
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.74
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.69
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.6
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.57
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.57
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.52
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.51
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.45
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.43
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.42
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.41
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.4
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.36
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.23
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.22
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.22
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.2
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.18
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.13
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.11
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.97
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.96
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.92
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.91
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.87
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.83
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.52
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.52
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.46
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	97.45
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.43
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.35
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.27
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	97.26
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	97.25
COG5152	259	Uncharacterized conserved protein, contains RING a	97.23
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.21
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.15
KOG3039	303	consensus Uncharacterized conserved protein [Funct	97.02
KOG2660	331	consensus Locus-specific chromosome binding protei	97.0
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.82
KOG1002	791	consensus Nucleotide excision repair protein RAD16	96.79
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.79
PHA02825	162	LAP/PHD finger-like protein; Provisional	96.76
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.75
PHA02862	156	5L protein; Provisional	96.73
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.7
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.57
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.57
COG5236	493	Uncharacterized conserved protein, contains RING Z	96.53
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.47
KOG4739	233	consensus Uncharacterized protein involved in syna	96.46
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	96.39
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	96.38
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	96.24
PF04641	260	Rtf2: Rtf2 RING-finger	96.22
PHA03096	284	p28-like protein; Provisional	96.21
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.87
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	95.86
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	95.46
PF02439	38	Adeno_E3_CR2: Adenovirus E3 region protein CR2; In	95.44
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	95.28
COG5222	427	Uncharacterized conserved protein, contains RING Z	95.03
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	95.0
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	94.69
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	94.61
KOG1001	674	consensus Helicase-like transcription factor HLTF/	94.37
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	94.33
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	94.23
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	94.2
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	94.14
KOG1940	276	consensus Zn-finger protein [General function pred	94.0
KOG3002	299	consensus Zn finger protein [General function pred	93.83
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	93.82
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	93.75
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	93.7
PF12273	130	RCR: Chitin synthesis regulation, resistance to Co	93.41
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	93.08
KOG0298	1394	consensus DEAD box-containing helicase-like transc	93.05
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	93.04
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	92.95
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	92.49
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	92.44
PF15050	133	SCIMP: SCIMP protein	91.84
KOG3053	293	consensus Uncharacterized conserved protein [Funct	91.63
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	91.38
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	90.59
KOG3113	293	consensus Uncharacterized conserved protein [Funct	89.41
PF01102	122	Glycophorin_A: Glycophorin A; InterPro: IPR001195	89.24
KOG3899	381	consensus Uncharacterized conserved protein [Funct	89.04
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	88.4
KOG0269	839	consensus WD40 repeat-containing protein [Function	88.29
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	87.52
PF01102	122	Glycophorin_A: Glycophorin A; InterPro: IPR001195	87.29
KOG0825	1134	consensus PHD Zn-finger protein [General function	85.53
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	84.59
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	83.99
KOG3842	429	consensus Adaptor protein Pellino [Signal transduc	83.93
KOG1609	323	consensus Protein involved in mRNA turnover and st	83.91
KOG1829	580	consensus Uncharacterized conserved protein, conta	83.69
KOG4367	699	consensus Predicted Zn-finger protein [Function un	83.59
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	82.06
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	81.97
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	81.54
PF12273	130	RCR: Chitin synthesis regulation, resistance to Co	81.1
TIGR00622	112	ssl1 transcription factor ssl1. This family is bas	80.13

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

Probab=99.80  E-value=2.1e-19  Score=148.88  Aligned_cols=77  Identities=32%  Similarity=0.858  Sum_probs=68.0

Q ss_pred             CCCCCHHHHhcCCceEeeccCCCCCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCC-CcccccccccCC
Q 040080           52 STSMSRDDVEKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPN-CPICRSTANSRR  129 (192)
Q Consensus        52 ~~~~~~~~i~~l~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~-CP~Cr~~~~~~~  129 (192)
                      ...+.++.++++|...|...+.......|+||+|+|..++.++.+| |+|.||..||++||..+.+ ||+||+++....
T Consensus       204 ~~r~~k~~l~~~p~~~f~~~~~~~~~~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~  281 (348)
T KOG4628|consen  204 RNRLIKRLLKKLPVRTFTKGDDEDATDTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDS  281 (348)
T ss_pred             hhhhHHHHHhhCCcEEeccccccCCCceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCCCCC
Confidence            4468889999999999998877655579999999999999999999 9999999999999988755 999999876543

>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=99.62  E-value=1.1e-16  Score=95.50  Aligned_cols=44  Identities=48%  Similarity=1.250  Sum_probs=40.1

Q ss_pred             CcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccc
Q 040080           78 IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICR  122 (192)
Q Consensus        78 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr  122 (192)
                      ++|+||++.|..++.+..++ |||.||.+||..|++++.+||+||
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            36999999999888999999 999999999999999999999997

...

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

Probab=99.50  E-value=1.8e-13  Score=113.08  Aligned_cols=53  Identities=34%  Similarity=0.873  Sum_probs=44.0

Q ss_pred             CCCCCcccccCcc-ccCCC---------ceEEcCCCCCcccHHhHHHHHcCCCCCccccccccc
Q 040080           74 GSSPIECAVCLDK-FNKGD---------KCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        74 ~~~~~~C~IC~~~-~~~~~---------~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      ..++..|.|||++ |..+.         ....+| |||+||..|++.|++++++||+||.++..
T Consensus       284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~if  346 (491)
T COG5243         284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPVIF  346 (491)
T ss_pred             cCCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCcccc
Confidence            4667889999999 55442         335688 99999999999999999999999999543

>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=99.43  E-value=1e-13  Score=91.46  Aligned_cols=45  Identities=36%  Similarity=0.908  Sum_probs=35.4

Q ss_pred             CCcccccCccccCC----------CceEEcCCCCCcccHHhHHHHHcCCCCCcccc
Q 040080           77 PIECAVCLDKFNKG----------DKCRLLPICNHSFHAQCVDAWLLTNPNCPICR  122 (192)
Q Consensus        77 ~~~C~IC~~~~~~~----------~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr  122 (192)
                      ++.|+||++.+...          -.+...+ |||.||..||.+|+..+.+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGP-CGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEET-TSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecc-cCCCEEHHHHHHHHhcCCcCCCCC
Confidence            44599999999422          2344445 999999999999999999999998

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

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.42  E-value=1.2e-13  Score=109.99  Aligned_cols=76  Identities=26%  Similarity=0.579  Sum_probs=56.7

Q ss_pred             CCCCCHHHHhcCCceEeeccC--CCCCCCcccccCccccCCC----ceEEcCCCCCcccHHhHHHHHcCCCCCccccccc
Q 040080           52 STSMSRDDVEKLPCYEYLAKS--KGSSPIECAVCLDKFNKGD----KCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTA  125 (192)
Q Consensus        52 ~~~~~~~~i~~l~~~~~~~~~--~~~~~~~C~IC~~~~~~~~----~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~  125 (192)
                      .....+..+..+|.+....+.  ....+.+|+||++.+..+.    .+..++.|+|.||..||..|+..+.+||+||.++
T Consensus       147 k~~~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~  226 (238)
T PHA02929        147 KGKNYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPF  226 (238)
T ss_pred             hcchhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEe
Confidence            344577888889987544332  2245678999999876543    1234445999999999999999999999999987


Q ss_pred             cc
Q 040080          126 NS  127 (192)
Q Consensus       126 ~~  127 (192)
                      ..
T Consensus       227 ~~  228 (238)
T PHA02929        227 IS  228 (238)
T ss_pred             eE
Confidence            53

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

Probab=99.37  E-value=5e-13  Score=107.33  Aligned_cols=51  Identities=25%  Similarity=0.762  Sum_probs=44.0

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      .....|.+||+....+   ..+| |||+||+.||..|...+..||+||..+.+.+
T Consensus       237 ~a~~kC~LCLe~~~~p---SaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~psk  287 (293)
T KOG0317|consen  237 EATRKCSLCLENRSNP---SATP-CGHIFCWSCILEWCSEKAECPLCREKFQPSK  287 (293)
T ss_pred             CCCCceEEEecCCCCC---CcCc-CcchHHHHHHHHHHccccCCCcccccCCCcc
Confidence            4457899999997655   4577 9999999999999999999999999987765

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

Probab=99.35  E-value=4.4e-13  Score=108.14  Aligned_cols=52  Identities=46%  Similarity=1.160  Sum_probs=46.8

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHc-CCCCCccccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLL-TNPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~  127 (192)
                      ..+.+|+|||+.|...+.++.+| |.|.||..|+++|+. .+..||+||.++++
T Consensus       321 ~~GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         321 DKGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCCceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            34578999999999999999999 999999999999998 47789999998865

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

Probab=99.27  E-value=2.5e-12  Score=100.49  Aligned_cols=58  Identities=24%  Similarity=0.594  Sum_probs=45.1

Q ss_pred             CCCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC---CCCCcccccccccCCCCCCCC
Q 040080           74 GSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT---NPNCPICRSTANSRRFGEESS  135 (192)
Q Consensus        74 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~~~~~~~~~~~~~  135 (192)
                      ....++|.|||+.-+.+   +++. |||+||+.||.+|+..   .+.||+||..+..++..+..+
T Consensus        44 ~~~~FdCNICLd~akdP---VvTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYG  104 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDP---VVTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYG  104 (230)
T ss_pred             CCCceeeeeeccccCCC---EEee-cccceehHHHHHHHhhcCCCeeCCccccccccceEEeeec
Confidence            35678999999986444   4455 9999999999999976   344999999998877544433

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

Probab=99.21  E-value=1.1e-11  Score=82.96  Aligned_cols=52  Identities=33%  Similarity=0.789  Sum_probs=39.4

Q ss_pred             CCcccccCccccC--------CCc-eEEcCCCCCcccHHhHHHHHcC---CCCCcccccccccC
Q 040080           77 PIECAVCLDKFNK--------GDK-CRLLPICNHSFHAQCVDAWLLT---NPNCPICRSTANSR  128 (192)
Q Consensus        77 ~~~C~IC~~~~~~--------~~~-~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~~~~~~  128 (192)
                      ++.|.||...|..        ++. ......|+|.||..||.+|+.+   +..||+||+++..+
T Consensus        21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k   84 (85)
T PF12861_consen   21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFK   84 (85)
T ss_pred             CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeeeC
Confidence            6679999988862        222 2233459999999999999986   46799999988654

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.19  E-value=1.9e-11  Score=93.89  Aligned_cols=55  Identities=25%  Similarity=0.746  Sum_probs=43.0

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC----------------CCCCcccccccccCCCCCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT----------------NPNCPICRSTANSRRFGEE  133 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----------------~~~CP~Cr~~~~~~~~~~~  133 (192)
                      .+..+|+||++.+..+   ..++ |||.||..||..|+..                ...||+||.++........
T Consensus        16 ~~~~~CpICld~~~dP---VvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPi   86 (193)
T PLN03208         16 GGDFDCNICLDQVRDP---VVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPI   86 (193)
T ss_pred             CCccCCccCCCcCCCc---EEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEe
Confidence            4567899999998654   4566 9999999999999852                2469999999977654433

>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=99.16  E-value=2.1e-11  Score=74.53  Aligned_cols=46  Identities=35%  Similarity=0.878  Sum_probs=38.5

Q ss_pred             CCcccccCccccCCCceEEcCCCCCc-ccHHhHHHHHcCCCCCcccccccc
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHS-FHAQCVDAWLLTNPNCPICRSTAN  126 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~  126 (192)
                      +..|.||++...   .+..+| |||. ||..|+..|+.....||+||+++.
T Consensus         2 ~~~C~iC~~~~~---~~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPR---DVVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBS---SEEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCC---ceEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            457999999853   457778 9999 999999999999999999999875

...

>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A

Probab=99.13  E-value=4.2e-11  Score=69.38  Aligned_cols=39  Identities=41%  Similarity=1.194  Sum_probs=32.5

Q ss_pred             ccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccc
Q 040080           80 CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPIC  121 (192)
Q Consensus        80 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~C  121 (192)
                      |+||++.+.+  .+..++ |||.||..|+..|++.+..||+|
T Consensus         1 C~iC~~~~~~--~~~~~~-CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTP-CGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECT-TSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC--cCEECC-CCCchhHHHHHHHHHCcCCCcCC
Confidence            8999999855  456677 99999999999999998889998

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

Probab=99.11  E-value=5.9e-11  Score=70.01  Aligned_cols=44  Identities=43%  Similarity=1.192  Sum_probs=36.5

Q ss_pred             cccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCccccccc
Q 040080           79 ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTA  125 (192)
Q Consensus        79 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~  125 (192)
                      +|+||++.+  .......+ |||.||..|+..|+.. +..||+||..+
T Consensus         1 ~C~iC~~~~--~~~~~~~~-C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEF--REPVVLLP-CGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhh--hCceEecC-CCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            499999998  33455556 9999999999999987 67799999764

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

Probab=99.09  E-value=4.9e-11  Score=89.66  Aligned_cols=54  Identities=28%  Similarity=0.727  Sum_probs=44.0

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRF  130 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~  130 (192)
                      .+-..|+|||+.+.....  ....|||+||..||..-++....||+||+.+..+.+
T Consensus       129 ~~~~~CPiCl~~~sek~~--vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~  182 (187)
T KOG0320|consen  129 EGTYKCPICLDSVSEKVP--VSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQF  182 (187)
T ss_pred             ccccCCCceecchhhccc--cccccchhHHHHHHHHHHHhCCCCCCcccccchhhh
Confidence            445679999999865433  333499999999999999999999999998877654

>PHA02926 zinc finger-like protein; Provisional

Probab=99.05  E-value=6.2e-11  Score=92.27  Aligned_cols=53  Identities=36%  Similarity=0.791  Sum_probs=40.0

Q ss_pred             CCCCcccccCccccCC-----CceEEcCCCCCcccHHhHHHHHcCC------CCCccccccccc
Q 040080           75 SSPIECAVCLDKFNKG-----DKCRLLPICNHSFHAQCVDAWLLTN------PNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~-----~~~~~~~~C~H~fh~~Ci~~wl~~~------~~CP~Cr~~~~~  127 (192)
                      +.+.+|+|||+..-..     ..-..++.|+|.||..||..|...+      .+||+||..+..
T Consensus       168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~  231 (242)
T PHA02926        168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN  231 (242)
T ss_pred             cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence            5578899999986322     1233565699999999999999753      359999998753

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

Probab=99.01  E-value=1.5e-10  Score=103.23  Aligned_cols=53  Identities=32%  Similarity=0.860  Sum_probs=44.9

Q ss_pred             CCCCcccccCccccCCCc--eEEcCCCCCcccHHhHHHHHcCCCCCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDK--CRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~--~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  128 (192)
                      .....|+||++.+..+..  ...++ |+|+||..|+..|++++++||+||..+...
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~~~~  343 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVLYDY  343 (543)
T ss_pred             hcCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhhhcc
Confidence            456789999999977543  56788 999999999999999999999999955443

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.96  E-value=6e-10  Score=66.22  Aligned_cols=44  Identities=32%  Similarity=0.882  Sum_probs=36.9

Q ss_pred             cccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccc
Q 040080           79 ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRS  123 (192)
Q Consensus        79 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~  123 (192)
                      .|+||++.|.......+++ |||+||..|+..+......||+||+
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            4999999995555666777 9999999999998855677999985

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

Probab=98.92  E-value=9e-10  Score=64.75  Aligned_cols=38  Identities=39%  Similarity=0.951  Sum_probs=28.9

Q ss_pred             ccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC----CCCccc
Q 040080           80 CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN----PNCPIC  121 (192)
Q Consensus        80 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP~C  121 (192)
                      |+||++.|..+   ..++ |||.|+..||..|.+..    ..||.|
T Consensus         1 CpiC~~~~~~P---v~l~-CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDP---VSLP-CGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSE---EE-S-SSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCc---cccC-CcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999766   5677 99999999999999763    259987

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

Probab=98.90  E-value=1.1e-09  Score=71.48  Aligned_cols=33  Identities=39%  Similarity=0.808  Sum_probs=29.5

Q ss_pred             CCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           97 PICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        97 ~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      ..|+|.||..||..||.++..||++|+++...+
T Consensus        52 G~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~~   84 (88)
T COG5194          52 GVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLAD   84 (88)
T ss_pred             EecchHHHHHHHHHHHhhCCCCCCCCceeEEec
Confidence            349999999999999999999999999986644

>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=98.90  E-value=1.4e-09  Score=63.53  Aligned_cols=39  Identities=44%  Similarity=1.185  Sum_probs=32.6

Q ss_pred             ccccCccccCCCceEEcCCCCCcccHHhHHHHHc--CCCCCccc
Q 040080           80 CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLL--TNPNCPIC  121 (192)
Q Consensus        80 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~--~~~~CP~C  121 (192)
                      |+||++.+..+  ...++ |||.||..|+..|+.  ....||+|
T Consensus         1 C~iC~~~~~~~--~~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDP--VILLP-CGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSE--EEETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCC--CEEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence            89999998554  34677 999999999999998  35569998

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 ....

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

Probab=98.90  E-value=1.8e-09  Score=92.41  Aligned_cols=52  Identities=31%  Similarity=0.812  Sum_probs=39.8

Q ss_pred             CCCCcccccCccccCC---C-----------ceEEcCCCCCcccHHhHHHHHcC-CCCCccccccccc
Q 040080           75 SSPIECAVCLDKFNKG---D-----------KCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~---~-----------~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~  127 (192)
                      ....+|+|||.++.--   .           ....+| |.|+||..|+..|+.. +-.||+||.++.+
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            3456799999987521   1           133457 9999999999999985 5589999998864

>smart00504 Ubox Modified RING finger domain

Probab=98.89  E-value=1.8e-09  Score=68.80  Aligned_cols=48  Identities=17%  Similarity=0.533  Sum_probs=41.0

Q ss_pred             CcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           78 IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        78 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      ..|+||++.+..+   ..++ |||+|+..||..|+..+.+||+|+.++....
T Consensus         2 ~~Cpi~~~~~~~P---v~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~   49 (63)
T smart00504        2 FLCPISLEVMKDP---VILP-SGQTYERRAIEKWLLSHGTDPVTGQPLTHED   49 (63)
T ss_pred             cCCcCCCCcCCCC---EECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCChhh
Confidence            4699999999775   4567 9999999999999998889999999885433

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

>smart00184 RING Ring finger

Probab=98.83  E-value=3e-09  Score=60.44  Aligned_cols=38  Identities=42%  Similarity=1.202  Sum_probs=31.7

Q ss_pred             ccccCccccCCCceEEcCCCCCcccHHhHHHHHc-CCCCCccc
Q 040080           80 CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLL-TNPNCPIC  121 (192)
Q Consensus        80 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~C  121 (192)
                      |+||++..   .....++ |||.||..|+..|+. .+..||+|
T Consensus         1 C~iC~~~~---~~~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEEL---KDPVVLP-CGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCC---CCcEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence            78999883   3456677 999999999999998 56679987

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

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

Probab=98.78  E-value=1.1e-09  Score=71.04  Aligned_cols=51  Identities=39%  Similarity=0.923  Sum_probs=37.6

Q ss_pred             CCcccccCccccC--------CCceE-EcCCCCCcccHHhHHHHHcC---CCCCccccccccc
Q 040080           77 PIECAVCLDKFNK--------GDKCR-LLPICNHSFHAQCVDAWLLT---NPNCPICRSTANS  127 (192)
Q Consensus        77 ~~~C~IC~~~~~~--------~~~~~-~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~~~~~  127 (192)
                      ++.|.||.-.|..        ++.+. ++..|.|.||..||.+|+..   +..||+||+.+..
T Consensus        20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~   82 (84)
T KOG1493|consen   20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQF   82 (84)
T ss_pred             CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence            3478888888852        23222 23459999999999999976   3459999998754

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.74  E-value=6.9e-09  Score=88.47  Aligned_cols=50  Identities=30%  Similarity=0.840  Sum_probs=42.4

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  128 (192)
                      .....|+||++.|..+   ..++ |||.||..||..|+.....||+||..+...
T Consensus        24 e~~l~C~IC~d~~~~P---vitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~   73 (397)
T TIGR00599        24 DTSLRCHICKDFFDVP---VLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQES   73 (397)
T ss_pred             ccccCCCcCchhhhCc---cCCC-CCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence            4467899999998665   3567 999999999999998888899999988654

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

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

Probab=98.69  E-value=7.9e-09  Score=82.40  Aligned_cols=51  Identities=25%  Similarity=0.718  Sum_probs=41.8

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHH-HHcCCCC-CcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDA-WLLTNPN-CPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~-wl~~~~~-CP~Cr~~~~~~~  129 (192)
                      ..+..|+||++....+   ..++ |||+||..||.. |-.++.. ||+||+...++.
T Consensus       213 ~~d~kC~lC~e~~~~p---s~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~  265 (271)
T COG5574         213 LADYKCFLCLEEPEVP---SCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK  265 (271)
T ss_pred             ccccceeeeecccCCc---cccc-ccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence            3477899999996554   5567 999999999999 8776665 999999887654

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

Probab=98.60  E-value=1.2e-08  Score=81.59  Aligned_cols=54  Identities=31%  Similarity=0.771  Sum_probs=43.6

Q ss_pred             CCCCcccccCccccCCC-------ceEEcCCCCCcccHHhHHHHHc--CCCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGD-------KCRLLPICNHSFHAQCVDAWLL--TNPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~-------~~~~~~~C~H~fh~~Ci~~wl~--~~~~CP~Cr~~~~~~~  129 (192)
                      .++..|+||-..+....       ..-.+. |+|+||..||+-|..  ++++||.|+..+..++
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVdl~r  284 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKR  284 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhhHhh
Confidence            56778999998886543       455677 999999999999984  4778999999887654

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

Probab=98.57  E-value=3.6e-08  Score=67.66  Aligned_cols=56  Identities=29%  Similarity=0.663  Sum_probs=41.8

Q ss_pred             CCCcccccCcccc-------------CCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCCCC
Q 040080           76 SPIECAVCLDKFN-------------KGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRFG  131 (192)
Q Consensus        76 ~~~~C~IC~~~~~-------------~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~  131 (192)
                      ..+.|+||...+-             .++....-..|+|.||..||..|+++++.||+|.+++...+++
T Consensus        45 ~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~~qr~g  113 (114)
T KOG2930|consen   45 VVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWVFQRYG  113 (114)
T ss_pred             eechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcceeEeecC
Confidence            3466999876541             1223333345999999999999999999999999988765543

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

Probab=98.57  E-value=3.6e-08  Score=85.09  Aligned_cols=52  Identities=27%  Similarity=0.604  Sum_probs=40.6

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC-----CCCcccccccccCCCCC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN-----PNCPICRSTANSRRFGE  132 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~-----~~CP~Cr~~~~~~~~~~  132 (192)
                      +..||||++....+   ..+. |||+||..||-.++...     ..||+||..+..++...
T Consensus       186 ~~~CPICL~~~~~p---~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~p  242 (513)
T KOG2164|consen  186 DMQCPICLEPPSVP---VRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLP  242 (513)
T ss_pred             CCcCCcccCCCCcc---cccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccccceee
Confidence            66799999985443   3344 99999999999988653     45999999998866443

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

Probab=98.52  E-value=3.3e-08  Score=81.33  Aligned_cols=49  Identities=31%  Similarity=0.856  Sum_probs=43.1

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      -..|.||.+.|..+   .++| |+|.||.-||+.+|..+..||.|+.++.+..
T Consensus        23 lLRC~IC~eyf~ip---~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~   71 (442)
T KOG0287|consen   23 LLRCGICFEYFNIP---MITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTESD   71 (442)
T ss_pred             HHHHhHHHHHhcCc---eecc-ccchHHHHHHHHHhccCCCCCceecccchhh
Confidence            45699999999776   5667 9999999999999999999999999887654

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

Probab=98.51  E-value=1.6e-08  Score=92.45  Aligned_cols=54  Identities=31%  Similarity=0.789  Sum_probs=40.1

Q ss_pred             CCCCCCcccccCcccc-CCC--ceEEcCCCCCcccHHhHHHHHcC--CCCCcccccccc
Q 040080           73 KGSSPIECAVCLDKFN-KGD--KCRLLPICNHSFHAQCVDAWLLT--NPNCPICRSTAN  126 (192)
Q Consensus        73 ~~~~~~~C~IC~~~~~-~~~--~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~  126 (192)
                      ...+..+|+||+..+. ...  +-...+.|.|.||..|+.+|+++  +++||+||..++
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            3367889999998765 111  11223349999999999999987  567999998765

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

Probab=98.45  E-value=1.5e-07  Score=57.04  Aligned_cols=42  Identities=26%  Similarity=0.804  Sum_probs=31.9

Q ss_pred             cccccCccccCCCceEEcCCCC-----CcccHHhHHHHHcCC--CCCcccc
Q 040080           79 ECAVCLDKFNKGDKCRLLPICN-----HSFHAQCVDAWLLTN--PNCPICR  122 (192)
Q Consensus        79 ~C~IC~~~~~~~~~~~~~~~C~-----H~fh~~Ci~~wl~~~--~~CP~Cr  122 (192)
                      .|.||++.. .++.....| |.     |.+|..|+..|+..+  .+||+|+
T Consensus         1 ~CrIC~~~~-~~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEG-DEGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCCC-CCCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            489999833 334445677 86     889999999999654  4799995

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

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

Probab=98.43  E-value=4.7e-08  Score=63.86  Aligned_cols=51  Identities=27%  Similarity=0.764  Sum_probs=24.4

Q ss_pred             CCcccccCccccCCCce--EEc--CCCCCcccHHhHHHHHcC---C--------CCCccccccccc
Q 040080           77 PIECAVCLDKFNKGDKC--RLL--PICNHSFHAQCVDAWLLT---N--------PNCPICRSTANS  127 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~--~~~--~~C~H~fh~~Ci~~wl~~---~--------~~CP~Cr~~~~~  127 (192)
                      +.+|.||+..+.....+  ..-  +.|++.||..||.+||..   .        .+||.|+.++.-
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            35799999987622221  221  359999999999999963   1        249999998864

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.42  E-value=2.4e-07  Score=76.30  Aligned_cols=54  Identities=22%  Similarity=0.586  Sum_probs=39.2

Q ss_pred             CCcccccCcc-ccCCC-ceEEcCCCCCcccHHhHHHHHcC-CCCCcccccccccCCCC
Q 040080           77 PIECAVCLDK-FNKGD-KCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRRFG  131 (192)
Q Consensus        77 ~~~C~IC~~~-~~~~~-~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~~~  131 (192)
                      +..||+|+.. |.+++ ...+.+ |||.||..|++..+.. ...||.|+.++....+.
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~-CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr   59 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFR   59 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCC-CCCcccHHHHHHHhcCCCCCCCCCCCccchhhcc
Confidence            3579999995 33333 223335 9999999999996644 55799999998776643

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

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

Probab=98.41  E-value=1.8e-07  Score=55.09  Aligned_cols=34  Identities=26%  Similarity=0.759  Sum_probs=21.0

Q ss_pred             ccccCccccCC-CceEEcCCCCCcccHHhHHHHHcCC
Q 040080           80 CAVCLDKFNKG-DKCRLLPICNHSFHAQCVDAWLLTN  115 (192)
Q Consensus        80 C~IC~~~~~~~-~~~~~~~~C~H~fh~~Ci~~wl~~~  115 (192)
                      |+||++ |... .....++ |||.|+.+|+..++.++
T Consensus         1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~   35 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKS   35 (43)
T ss_dssp             -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-
T ss_pred             CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcC
Confidence            899999 7553 3456688 99999999999999753

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

Probab=98.40  E-value=2.1e-07  Score=61.28  Aligned_cols=50  Identities=16%  Similarity=0.433  Sum_probs=38.2

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCcccccccccCC
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRR  129 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~  129 (192)
                      +.+.|+|+.+.|.++   .+++ +||.|...||..|+.. +.+||+|+.++....
T Consensus         3 ~~f~CpIt~~lM~dP---Vi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~   53 (73)
T PF04564_consen    3 DEFLCPITGELMRDP---VILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSESD   53 (73)
T ss_dssp             GGGB-TTTSSB-SSE---EEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGG
T ss_pred             cccCCcCcCcHhhCc---eeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCccc
Confidence            356799999999665   5567 9999999999999998 888999999887654

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 ....

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

Probab=98.36  E-value=1.8e-07  Score=75.65  Aligned_cols=49  Identities=29%  Similarity=0.683  Sum_probs=41.6

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      ...|-||-+.|..+   ..++ |||.||.-||...|..+..||+||.+..+..
T Consensus        25 ~lrC~IC~~~i~ip---~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~~~esr   73 (391)
T COG5432          25 MLRCRICDCRISIP---CETT-CGHTFCSLCIRRHLGTQPFCPVCREDPCESR   73 (391)
T ss_pred             HHHhhhhhheeecc---eecc-cccchhHHHHHHHhcCCCCCccccccHHhhh
Confidence            45699999998665   3455 9999999999999999999999999876644

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

Probab=98.23  E-value=5e-07  Score=75.67  Aligned_cols=54  Identities=30%  Similarity=0.784  Sum_probs=39.1

Q ss_pred             CcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC---CCCCcccccccccCCCC
Q 040080           78 IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT---NPNCPICRSTANSRRFG  131 (192)
Q Consensus        78 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~~~~~~~~~  131 (192)
                      ..|.||-+-+.....+.-+..|||+||..|+..|+..   +..||.|+-.+..+.+.
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~~~   61 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERHVA   61 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccceeee
Confidence            4699995544444444444459999999999999987   34699999666555444

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

Probab=98.22  E-value=4.5e-07  Score=77.21  Aligned_cols=49  Identities=33%  Similarity=0.883  Sum_probs=38.7

Q ss_pred             CCCCcccccCccccCCC-ceEEcCCCCCcccHHhHHHHHcCCCCCcccccccc
Q 040080           75 SSPIECAVCLDKFNKGD-KCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTAN  126 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~-~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  126 (192)
                      .+...|||||+.+.... .+.... |.|.||..|+..|  ...+||+||.-..
T Consensus       173 tELPTCpVCLERMD~s~~gi~t~~-c~Hsfh~~cl~~w--~~~scpvcR~~q~  222 (493)
T KOG0804|consen  173 TELPTCPVCLERMDSSTTGILTIL-CNHSFHCSCLMKW--WDSSCPVCRYCQS  222 (493)
T ss_pred             ccCCCcchhHhhcCccccceeeee-cccccchHHHhhc--ccCcChhhhhhcC
Confidence            34567999999997654 334445 9999999999999  4578999998655

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

Probab=98.22  E-value=3.4e-07  Score=55.63  Aligned_cols=46  Identities=26%  Similarity=0.561  Sum_probs=34.6

Q ss_pred             CCcccccCccccCCCceEEcCCCCCc-ccHHhHHHHHc-CCCCCcccccccc
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHS-FHAQCVDAWLL-TNPNCPICRSTAN  126 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~-~~~~CP~Cr~~~~  126 (192)
                      ..+|.||++.-.+.   .+-. |||. .|..|-.+-++ .+..||+||+++.
T Consensus         7 ~dECTICye~pvds---VlYt-CGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    7 SDECTICYEHPVDS---VLYT-CGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             ccceeeeccCcchH---HHHH-cchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            37899999974332   2233 9998 89999765444 6889999999884

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

Probab=98.20  E-value=2.1e-07  Score=77.12  Aligned_cols=56  Identities=29%  Similarity=0.523  Sum_probs=43.8

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCcccccccccCCCCCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRRFGEE  133 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~~~~~  133 (192)
                      ..+..|+||++-++..   +..+.|.|.||.+||..-++. ++.||.||+.+..+.....
T Consensus        41 ~~~v~c~icl~llk~t---mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr~   97 (381)
T KOG0311|consen   41 DIQVICPICLSLLKKT---MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLRI   97 (381)
T ss_pred             hhhhccHHHHHHHHhh---cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCCC
Confidence            4467799999988654   344559999999999988866 7789999999877654333

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

Probab=98.18  E-value=9.9e-07  Score=73.35  Aligned_cols=49  Identities=33%  Similarity=0.766  Sum_probs=41.4

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCc-ccHHhHHHHHcCCCCCccccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHS-FHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      ....+|.|||.+-   ....++| |.|. .|..|-+...-.++.||+||+++..
T Consensus       288 ~~gkeCVIClse~---rdt~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~  337 (349)
T KOG4265|consen  288 ESGKECVICLSES---RDTVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIEE  337 (349)
T ss_pred             cCCCeeEEEecCC---cceEEec-chhhehhHhHHHHHHHhhcCCCccccchHh
Confidence            3467899999984   4558899 9999 9999999977778889999998854

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

Probab=98.13  E-value=5.8e-07  Score=56.84  Aligned_cols=47  Identities=26%  Similarity=0.725  Sum_probs=23.3

Q ss_pred             CcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           78 IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        78 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      ..|++|.+-+..+   ..+..|.|+||..||..-+.  ..||+|+.+.-.++
T Consensus         8 LrCs~C~~~l~~p---v~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD   54 (65)
T PF14835_consen    8 LRCSICFDILKEP---VCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQD   54 (65)
T ss_dssp             TS-SSS-S--SS----B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS
T ss_pred             cCCcHHHHHhcCC---ceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHH
Confidence            4599999998654   33444999999999988544  35999999876544

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

Probab=98.11  E-value=1.1e-06  Score=71.53  Aligned_cols=45  Identities=33%  Similarity=0.882  Sum_probs=38.4

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRS  123 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~  123 (192)
                      .+...|+||++.|..+   ..++ |+|.||..|+..++.....||.||.
T Consensus        11 ~~~~~C~iC~~~~~~p---~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   11 QEELTCPICLEYFREP---VLLP-CGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             cccccChhhHHHhhcC---cccc-ccchHhHHHHHHhcCCCcCCcccCC
Confidence            4567899999999877   6778 9999999999999874456999994

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

Probab=97.97  E-value=4.3e-06  Score=70.60  Aligned_cols=54  Identities=31%  Similarity=0.845  Sum_probs=41.6

Q ss_pred             CCCcccccCccccC-CCceEEcCCCCCcccHHhHHHHHcC--CCCCcccccccccCC
Q 040080           76 SPIECAVCLDKFNK-GDKCRLLPICNHSFHAQCVDAWLLT--NPNCPICRSTANSRR  129 (192)
Q Consensus        76 ~~~~C~IC~~~~~~-~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~~~~  129 (192)
                      ....|+||++.+.- ++.....+.|||.|-.+||+.|+.+  ...||.|..+...+.
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~   59 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQ   59 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHHH
Confidence            35679999999864 4555555669999999999999964  345999988766554

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

Probab=97.96  E-value=3e-06  Score=71.43  Aligned_cols=46  Identities=26%  Similarity=0.827  Sum_probs=38.6

Q ss_pred             CcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC--CCCCccccccccc
Q 040080           78 IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT--NPNCPICRSTANS  127 (192)
Q Consensus        78 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~~  127 (192)
                      ..|-||-+.   ...+.+.| |||..|..|+..|-..  .++||.||..+.-
T Consensus       370 eLCKICaen---dKdvkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG  417 (563)
T KOG1785|consen  370 ELCKICAEN---DKDVKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG  417 (563)
T ss_pred             HHHHHhhcc---CCCccccc-ccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence            459999886   56778888 9999999999999855  5789999998754

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

Probab=97.92  E-value=5.6e-06  Score=67.41  Aligned_cols=51  Identities=25%  Similarity=0.428  Sum_probs=39.6

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCcccccccccCCCC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRRFG  131 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~~~  131 (192)
                      ..+|+||+....-+   ..++ |+|.||.-||+--..+ ..+|++||.++.+.-..
T Consensus         7 ~~eC~IC~nt~n~P---v~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids~i~~   58 (324)
T KOG0824|consen    7 KKECLICYNTGNCP---VNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDSTIDF   58 (324)
T ss_pred             CCcceeeeccCCcC---cccc-ccchhhhhhhcchhhcCCCCCceecCCCCcchhc
Confidence            45799999986444   5566 9999999999865544 56699999999775443

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

Probab=97.91  E-value=1.9e-06  Score=77.75  Aligned_cols=51  Identities=24%  Similarity=0.466  Sum_probs=40.8

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSR  128 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  128 (192)
                      ...|++|+..+..+......+ |+|.||..||..|.+.-.+||+||..+...
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v  173 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGEFGEV  173 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhhhhee
Confidence            345777777776554444566 999999999999999999999999987553

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

Probab=97.87  E-value=6.6e-06  Score=69.14  Aligned_cols=53  Identities=36%  Similarity=0.902  Sum_probs=39.3

Q ss_pred             CCCCcccccCccccCCC----ceEEcCCCCCcccHHhHHHHHc--C-----CCCCccccccccc
Q 040080           75 SSPIECAVCLDKFNKGD----KCRLLPICNHSFHAQCVDAWLL--T-----NPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~----~~~~~~~C~H~fh~~Ci~~wl~--~-----~~~CP~Cr~~~~~  127 (192)
                      ..+.+|.||++......    .-.++|+|.|.||..||+.|-.  +     .+.||.||.....
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~  222 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSF  222 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcccc
Confidence            34678999999874432    1234577999999999999983  3     3569999997643

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

Probab=97.83  E-value=4.5e-06  Score=75.40  Aligned_cols=50  Identities=24%  Similarity=0.683  Sum_probs=39.3

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCcccccccccCCC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRRF  130 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~~  130 (192)
                      -..|+.|-..+++.   .+.. |||+||..|+..-+.. +..||.|.+.|...++
T Consensus       643 ~LkCs~Cn~R~Kd~---vI~k-C~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv  693 (698)
T KOG0978|consen  643 LLKCSVCNTRWKDA---VITK-CGHVFCEECVQTRYETRQRKCPKCNAAFGANDV  693 (698)
T ss_pred             ceeCCCccCchhhH---HHHh-cchHHHHHHHHHHHHHhcCCCCCCCCCCCcccc
Confidence            35699999776443   3444 9999999999998866 6779999999876554

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

Probab=97.52  E-value=2.8e-05  Score=74.45  Aligned_cols=82  Identities=22%  Similarity=0.462  Sum_probs=56.8

Q ss_pred             hcCCceEeeccCC-CCCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC----------CCCcccccccccCC
Q 040080           61 EKLPCYEYLAKSK-GSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN----------PNCPICRSTANSRR  129 (192)
Q Consensus        61 ~~l~~~~~~~~~~-~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----------~~CP~Cr~~~~~~~  129 (192)
                      .-||......... ...++.|.||+.+-.....++.+. |+|+||..|.+.-|++.          -+||+|+.++....
T Consensus      3469 ~CLPCl~Cdks~tkQD~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH~~ 3547 (3738)
T KOG1428|consen 3469 HCLPCLHCDKSATKQDADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINHIV 3547 (3738)
T ss_pred             hcccccccChhhhhcccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhhHH
Confidence            3466665444332 356778999999877777888898 99999999998766542          24999999998766


Q ss_pred             CCCCCCcccchhhh
Q 040080          130 FGEESSRFSDIDVE  143 (192)
Q Consensus       130 ~~~~~~~~~~~~~~  143 (192)
                      ..+.-.+.....++
T Consensus      3548 LkDLldPiKel~ed 3561 (3738)
T KOG1428|consen 3548 LKDLLDPIKELYED 3561 (3738)
T ss_pred             HHHHHHHHHHHHHH
Confidence            54444433333333

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

Probab=97.52  E-value=4.2e-05  Score=62.40  Aligned_cols=53  Identities=25%  Similarity=0.670  Sum_probs=42.9

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHc------------------C-----CCCCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLL------------------T-----NPNCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~------------------~-----~~~CP~Cr~~~~~~  128 (192)
                      .....|.|||.-|..+.....++ |-|.||..|+..+|.                  .     ...||+||..+...
T Consensus       113 ~p~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e  188 (368)
T KOG4445|consen  113 HPNGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIE  188 (368)
T ss_pred             CCCCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccc
Confidence            44567999999999988888888 999999999977663                  1     23499999988654

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

Probab=97.46  E-value=0.00013  Score=45.54  Aligned_cols=42  Identities=19%  Similarity=0.654  Sum_probs=27.2

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC--CCCCcc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT--NPNCPI  120 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~  120 (192)
                      -...|||.+..|++  .+.... |||.|-...|.+|+.+  ...||+
T Consensus        10 ~~~~CPiT~~~~~~--PV~s~~-C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFED--PVKSKK-CGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SS--EEEESS-S--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhhC--CcCcCC-CCCeecHHHHHHHHHhcCCCCCCC
Confidence            35679999999865  455555 9999999999999944  344998

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

Probab=97.45  E-value=0.0003  Score=58.11  Aligned_cols=48  Identities=21%  Similarity=0.427  Sum_probs=37.5

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTA  125 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~  125 (192)
                      .+...|++|+....++..+.  . -|-+||..|+.+++.+++.||+=..+.
T Consensus       298 ~~~~~CpvClk~r~Nptvl~--v-SGyVfCY~Ci~~Yv~~~~~CPVT~~p~  345 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPTVLE--V-SGYVFCYPCIFSYVVNYGHCPVTGYPA  345 (357)
T ss_pred             CccccChhHHhccCCCceEE--e-cceEEeHHHHHHHHHhcCCCCccCCcc
Confidence            44567999999987763322  2 689999999999999999999854443

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

Probab=97.43  E-value=7.5e-05  Score=64.08  Aligned_cols=49  Identities=35%  Similarity=0.764  Sum_probs=41.7

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      ..+++|.||+..+..+   ..+| |||.||..||..-+.....||.||..+..
T Consensus        82 ~sef~c~vc~~~l~~p---v~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   82 RSEFECCVCSRALYPP---VVTP-CGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cchhhhhhhHhhcCCC---cccc-ccccccHHHHHHHhccCCCCccccccccc
Confidence            5678999999988665   4567 99999999999977777779999998875

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

Probab=97.35  E-value=0.0001  Score=63.53  Aligned_cols=52  Identities=23%  Similarity=0.633  Sum_probs=42.5

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      ..+..|++|...+..+...  .. |||.||..|+..|+..+..||.|+..+....
T Consensus        19 ~~~l~C~~C~~vl~~p~~~--~~-cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~   70 (391)
T KOG0297|consen   19 DENLLCPICMSVLRDPVQT--TT-CGHRFCAGCLLESLSNHQKCPVCRQELTQAE   70 (391)
T ss_pred             cccccCccccccccCCCCC--CC-CCCcccccccchhhccCcCCcccccccchhh
Confidence            4567899999998776221  34 9999999999999999999999998876544

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

Probab=97.27  E-value=0.00022  Score=56.00  Aligned_cols=50  Identities=28%  Similarity=0.674  Sum_probs=41.6

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC--------CCCCcccccccccC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT--------NPNCPICRSTANSR  128 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--------~~~CP~Cr~~~~~~  128 (192)
                      ...|..|-..+..++.++..  |-|+||++|++.|-..        ...||.|-.++.+.
T Consensus        50 ~pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp  107 (299)
T KOG3970|consen   50 NPNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP  107 (299)
T ss_pred             CCCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence            44599999999889887765  9999999999999854        23599999988764

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

Probab=97.26  E-value=8.3e-05  Score=55.50  Aligned_cols=41  Identities=29%  Similarity=0.626  Sum_probs=35.1

Q ss_pred             CceEeeccCCCCCCCcccccCccccCCCceEEcCCCCCcccH
Q 040080           64 PCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHA  105 (192)
Q Consensus        64 ~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~  105 (192)
                      |.+.|+......+..+|.|||+++..++.+..+| |-.+||.
T Consensus       164 PrlsYNdDVL~ddkGECvICLEdL~~GdtIARLP-CLCIYHK  204 (205)
T KOG0801|consen  164 PRLSYNDDVLKDDKGECVICLEDLEAGDTIARLP-CLCIYHK  204 (205)
T ss_pred             cccccccchhcccCCcEEEEhhhccCCCceeccc-eEEEeec
Confidence            4556666666677789999999999999999999 9999996

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

Probab=97.25  E-value=0.00011  Score=53.49  Aligned_cols=38  Identities=24%  Similarity=0.649  Sum_probs=31.3

Q ss_pred             CCcccccCccccCCCceEEcCCCC------CcccHHhHHHHHcCC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICN------HSFHAQCVDAWLLTN  115 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~------H~fh~~Ci~~wl~~~  115 (192)
                      ..+|+||++.+.....++.++ ||      |+||.+|+..|-+.+
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            568999999998866777777 77      899999999994333

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.

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

Probab=97.23  E-value=0.00012  Score=56.40  Aligned_cols=46  Identities=22%  Similarity=0.616  Sum_probs=38.7

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTA  125 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~  125 (192)
                      -++.|.||..+|..+   +... |||.||..|...-++....|-+|-+..
T Consensus       195 IPF~C~iCKkdy~sp---vvt~-CGH~FC~~Cai~~y~kg~~C~~Cgk~t  240 (259)
T COG5152         195 IPFLCGICKKDYESP---VVTE-CGHSFCSLCAIRKYQKGDECGVCGKAT  240 (259)
T ss_pred             Cceeehhchhhccch---hhhh-cchhHHHHHHHHHhccCCcceecchhh
Confidence            357899999999776   3444 999999999999888888999998754

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

Probab=97.21  E-value=0.00011  Score=61.97  Aligned_cols=46  Identities=33%  Similarity=0.863  Sum_probs=37.1

Q ss_pred             CCcccccCccccC-CCceEEcCCCCCcccHHhHHHHHcCC--CCCccccc
Q 040080           77 PIECAVCLDKFNK-GDKCRLLPICNHSFHAQCVDAWLLTN--PNCPICRS  123 (192)
Q Consensus        77 ~~~C~IC~~~~~~-~~~~~~~~~C~H~fh~~Ci~~wl~~~--~~CP~Cr~  123 (192)
                      +..|..|-+.+.. ++...-+| |.|+||..|+...+.++  .+||.||.
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            4569999998753 34556688 99999999999999775  45999994

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

Probab=97.15  E-value=0.00035  Score=58.32  Aligned_cols=49  Identities=22%  Similarity=0.530  Sum_probs=42.0

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      .++..|+||+..   +......| |+|.=|..||.+.+.+.+.|=.|++.+..
T Consensus       420 sEd~lCpICyA~---pi~Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  420 SEDNLCPICYAG---PINAVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             cccccCcceecc---cchhhccC-CCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            567789999987   44446778 99999999999999999999999998754

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.02  E-value=0.001  Score=53.08  Aligned_cols=57  Identities=18%  Similarity=0.314  Sum_probs=50.1

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCCCCCC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRFGEE  133 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~~~  133 (192)
                      -..|++|.+.+.+...+..+..|||+|+.+|+...+.....||+|-.++..++....
T Consensus       221 ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~L  277 (303)
T KOG3039|consen  221 RYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGL  277 (303)
T ss_pred             ceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEee
Confidence            457999999999988888886799999999999999889999999999988775544

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

Probab=97.00  E-value=0.00014  Score=60.12  Aligned_cols=50  Identities=22%  Similarity=0.585  Sum_probs=41.3

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      .....|.+|-..|.+...   .+.|-|-||.+||..++.....||.|...+-.
T Consensus        13 n~~itC~LC~GYliDATT---I~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~   62 (331)
T KOG2660|consen   13 NPHITCRLCGGYLIDATT---ITECLHTFCKSCIVKYLEESKYCPTCDIVIHK   62 (331)
T ss_pred             ccceehhhccceeecchh---HHHHHHHHHHHHHHHHHHHhccCCccceeccC
Confidence            456789999999876633   33499999999999999999999999987744

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

Probab=96.82  E-value=0.0012  Score=39.53  Aligned_cols=45  Identities=22%  Similarity=0.552  Sum_probs=22.3

Q ss_pred             ccccCccccCCC-ceEEcCCCCCcccHHhHHHHHcC-CCCCccccccc
Q 040080           80 CAVCLDKFNKGD-KCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTA  125 (192)
Q Consensus        80 C~IC~~~~~~~~-~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~  125 (192)
                      |++|.+++...+ ...--+ ||+.++..|...-+.. +..||-||.+.
T Consensus         1 cp~C~e~~d~~d~~~~PC~-Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCE-CGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SST-TS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccCc-CCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            789999984332 323334 8999999999887764 77899999864

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

Probab=96.79  E-value=0.00044  Score=60.58  Aligned_cols=50  Identities=24%  Similarity=0.663  Sum_probs=38.4

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-----CCCCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-----NPNCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-----~~~CP~Cr~~~~~~  128 (192)
                      .+..+|.+|-+.-+.   .+... |.|.||..|+..++..     +-+||+|...+...
T Consensus       534 k~~~~C~lc~d~aed---~i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD  588 (791)
T KOG1002|consen  534 KGEVECGLCHDPAED---YIESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             cCceeecccCChhhh---hHhhh-hhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            556789999998433   34455 9999999999888754     45699998877553

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

Probab=96.79  E-value=0.00027  Score=57.52  Aligned_cols=43  Identities=33%  Similarity=0.773  Sum_probs=34.3

Q ss_pred             CCcccccCccccCCCceEEcCCCCCc-ccHHhHHHHHcCCCCCccccccccc
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHS-FHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      ...|+|||+.   +..+..++ |||. -|.+|-...    +.||+||+.+..
T Consensus       300 ~~LC~ICmDa---P~DCvfLe-CGHmVtCt~CGkrm----~eCPICRqyi~r  343 (350)
T KOG4275|consen  300 RRLCAICMDA---PRDCVFLE-CGHMVTCTKCGKRM----NECPICRQYIVR  343 (350)
T ss_pred             HHHHHHHhcC---CcceEEee-cCcEEeehhhcccc----ccCchHHHHHHH
Confidence            4569999998   67788899 9998 788886552    379999997743

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=96.76  E-value=0.0019  Score=48.29  Aligned_cols=49  Identities=27%  Similarity=0.657  Sum_probs=36.2

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCC-----cccHHhHHHHHcCC--CCCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNH-----SFHAQCVDAWLLTN--PNCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H-----~fh~~Ci~~wl~~~--~~CP~Cr~~~~~~  128 (192)
                      ..+..|-||.+....  .  ..| |..     ..|.+|+..|+..+  ..|++|+++....
T Consensus         6 ~~~~~CRIC~~~~~~--~--~~P-C~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          6 LMDKCCWICKDEYDV--V--TNY-CNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCCeeEecCCCCCC--c--cCC-cccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            456789999988532  1  245 665     46999999999764  4599999988654

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

Probab=96.75  E-value=0.00027  Score=59.15  Aligned_cols=46  Identities=33%  Similarity=0.731  Sum_probs=33.4

Q ss_pred             CCCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccc
Q 040080           74 GSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTAN  126 (192)
Q Consensus        74 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  126 (192)
                      ...+..|.||+++..+   ...+| |||+-|  |..-- +...+||+||..+.
T Consensus       302 ~~~p~lcVVcl~e~~~---~~fvp-cGh~cc--ct~cs-~~l~~CPvCR~rI~  347 (355)
T KOG1571|consen  302 LPQPDLCVVCLDEPKS---AVFVP-CGHVCC--CTLCS-KHLPQCPVCRQRIR  347 (355)
T ss_pred             cCCCCceEEecCCccc---eeeec-CCcEEE--chHHH-hhCCCCchhHHHHH
Confidence            3556779999998644   57788 999965  65542 33455999999774

>PHA02862 5L protein; Provisional

Probab=96.73  E-value=0.0013  Score=48.37  Aligned_cols=46  Identities=22%  Similarity=0.608  Sum_probs=34.5

Q ss_pred             CcccccCccccCCCceEEcCCCC-----CcccHHhHHHHHcC--CCCCcccccccccC
Q 040080           78 IECAVCLDKFNKGDKCRLLPICN-----HSFHAQCVDAWLLT--NPNCPICRSTANSR  128 (192)
Q Consensus        78 ~~C~IC~~~~~~~~~~~~~~~C~-----H~fh~~Ci~~wl~~--~~~CP~Cr~~~~~~  128 (192)
                      ..|=||++.-...    ..| |.     ..-|.+|+..|+..  +..|++|+.+...+
T Consensus         3 diCWIC~~~~~e~----~~P-C~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik   55 (156)
T PHA02862          3 DICWICNDVCDER----NNF-CGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK   55 (156)
T ss_pred             CEEEEecCcCCCC----ccc-ccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence            5699999985332    345 65     46899999999976  34599999987554

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

Probab=96.70  E-value=0.00077  Score=57.35  Aligned_cols=48  Identities=23%  Similarity=0.663  Sum_probs=38.5

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC--------CCCCccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT--------NPNCPICRS  123 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--------~~~CP~Cr~  123 (192)
                      .....|.||++..........+| |+|+||..|+..++..        .-.||-+..
T Consensus       182 ~slf~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  182 NSLFDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             hhcccceeeehhhcCcceeeecc-cchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            44577999999987778888899 9999999999999853        123887655

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

Probab=96.57  E-value=0.00085  Score=54.78  Aligned_cols=48  Identities=21%  Similarity=0.533  Sum_probs=39.9

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTAN  126 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  126 (192)
                      .-++.|-||...|..+   ++.. |+|.||..|-..-++....|++|-++..
T Consensus       239 ~~Pf~c~icr~~f~~p---Vvt~-c~h~fc~~ca~~~~qk~~~c~vC~~~t~  286 (313)
T KOG1813|consen  239 LLPFKCFICRKYFYRP---VVTK-CGHYFCEVCALKPYQKGEKCYVCSQQTH  286 (313)
T ss_pred             cCCccccccccccccc---hhhc-CCceeehhhhccccccCCcceecccccc
Confidence            3456799999999776   4455 9999999999988888889999988664

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

Probab=96.57  E-value=0.0024  Score=51.69  Aligned_cols=51  Identities=25%  Similarity=0.540  Sum_probs=38.3

Q ss_pred             CCCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC--CCCCccccccccc
Q 040080           74 GSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT--NPNCPICRSTANS  127 (192)
Q Consensus        74 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~~  127 (192)
                      +....+|++|-+.-..+  ....+ |+|+||..||..-+..  .-+||.|-.+..+
T Consensus       236 ~t~~~~C~~Cg~~PtiP--~~~~~-C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~  288 (298)
T KOG2879|consen  236 GTSDTECPVCGEPPTIP--HVIGK-CGHIYCYYCIATSRLWDASFTCPLCGENVEP  288 (298)
T ss_pred             ccCCceeeccCCCCCCC--eeecc-ccceeehhhhhhhhcchhhcccCccCCCCcc
Confidence            36678999999985443  33445 9999999999986654  3579999877653

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

Probab=96.53  E-value=0.0031  Score=52.69  Aligned_cols=55  Identities=22%  Similarity=0.607  Sum_probs=40.0

Q ss_pred             eccCCCCCCCcccccCccccCCCceEEcCCCCCcccHHhHHHH--HcCCCCCccccccccc
Q 040080           69 LAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAW--LLTNPNCPICRSTANS  127 (192)
Q Consensus        69 ~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w--l~~~~~CP~Cr~~~~~  127 (192)
                      ++++...+...|.||-+.+   .....+| |+|..|--|--.-  |...+.||+||..+..
T Consensus        53 SaddtDEen~~C~ICA~~~---TYs~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE~e~  109 (493)
T COG5236          53 SADDTDEENMNCQICAGST---TYSARYP-CGHQICHACAVRLRALYMQKGCPLCRTETEA  109 (493)
T ss_pred             cccccccccceeEEecCCc---eEEEecc-CCchHHHHHHHHHHHHHhccCCCccccccce
Confidence            3334446667899999875   3446788 9999999997543  3457789999997754

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

Probab=96.47  E-value=0.0014  Score=45.69  Aligned_cols=33  Identities=24%  Similarity=0.731  Sum_probs=26.8

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHH
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVD  109 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~  109 (192)
                      .+...|++|-..+.. ......| |||+||..|+.
T Consensus        76 ~~~~~C~vC~k~l~~-~~f~~~p-~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGN-SVFVVFP-CGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCC-ceEEEeC-CCeEEeccccc
Confidence            345679999999976 4666678 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 [].

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

Probab=96.46  E-value=0.0015  Score=52.01  Aligned_cols=46  Identities=26%  Similarity=0.623  Sum_probs=32.9

Q ss_pred             ccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           80 CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        80 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      |.-|...-. ++...++. |+|+||..|...-  ....||+||.++....
T Consensus         6 Cn~C~~~~~-~~~f~LTa-C~HvfC~~C~k~~--~~~~C~lCkk~ir~i~   51 (233)
T KOG4739|consen    6 CNKCFRFPS-QDPFFLTA-CRHVFCEPCLKAS--SPDVCPLCKKSIRIIQ   51 (233)
T ss_pred             eccccccCC-CCceeeee-chhhhhhhhcccC--Cccccccccceeeeee
Confidence            666665544 55666666 9999999997762  2238999999876544

>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=96.39  E-value=0.0017  Score=38.10  Aligned_cols=41  Identities=27%  Similarity=0.858  Sum_probs=23.0

Q ss_pred             ccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCC--CCccc
Q 040080           80 CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNP--NCPIC  121 (192)
Q Consensus        80 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~--~CP~C  121 (192)
                      |.+|.+-...+....... |+-.+|..|+..++....  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~~-C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRD-CNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS---S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCCc-cCchHHHHHHHHHHhcCCCCCCcCC
Confidence            667777766653333223 888999999999998755  69987

; PDB: 3NW0_A 2CT0_A.

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

Probab=96.38  E-value=0.0016  Score=59.90  Aligned_cols=50  Identities=26%  Similarity=0.741  Sum_probs=38.8

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-------CCCCcccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-------NPNCPICRST  124 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-------~~~CP~Cr~~  124 (192)
                      ....+|.||++.+.....+-.-..|-|+||..||..|-.+       .-.||.|...
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv  245 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSV  245 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccch
Confidence            4457899999999876665554459999999999999865       1249999843

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

Probab=96.24  E-value=0.0041  Score=37.17  Aligned_cols=40  Identities=30%  Similarity=0.934  Sum_probs=25.6

Q ss_pred             ccccCccccCCCceEEcCCCCC-----cccHHhHHHHHcC--CCCCccc
Q 040080           80 CAVCLDKFNKGDKCRLLPICNH-----SFHAQCVDAWLLT--NPNCPIC  121 (192)
Q Consensus        80 C~IC~~~~~~~~~~~~~~~C~H-----~fh~~Ci~~wl~~--~~~CP~C  121 (192)
                      |-||++.-..... .+.| |+-     ..|..|+..|+..  +.+|++|
T Consensus         1 CrIC~~~~~~~~~-li~p-C~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDEP-LISP-CRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-S-SS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCCc-eecc-cccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            6789988655542 3345 653     6799999999974  5569887

>PF04641 Rtf2: Rtf2 RING-finger

Probab=96.22  E-value=0.0056  Score=49.96  Aligned_cols=57  Identities=19%  Similarity=0.395  Sum_probs=44.2

Q ss_pred             CCCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCCCC
Q 040080           74 GSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRFG  131 (192)
Q Consensus        74 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~  131 (192)
                      ......|||....|........+-.|||+|...++..- .....||+|-.++...+..
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~f~~~DiI  166 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKPFTEEDII  166 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCccccCCEE
Confidence            35667899999999666555555449999999999995 3356799999998866543

>PHA03096 p28-like protein; Provisional

Probab=96.21  E-value=0.0023  Score=52.76  Aligned_cols=46  Identities=22%  Similarity=0.559  Sum_probs=32.7

Q ss_pred             CcccccCccccCC----CceEEcCCCCCcccHHhHHHHHcC---CCCCccccc
Q 040080           78 IECAVCLDKFNKG----DKCRLLPICNHSFHAQCVDAWLLT---NPNCPICRS  123 (192)
Q Consensus        78 ~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~  123 (192)
                      ..|.||++.....    ..-..++.|.|.||..|+..|...   ..+||.||.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            6799999976532    122346779999999999999854   234555544

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.87  E-value=0.0044  Score=51.67  Aligned_cols=53  Identities=21%  Similarity=0.458  Sum_probs=37.7

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCcccccccccCC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRR  129 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~  129 (192)
                      ++-|+.|++.+...+.-..--+||-..|.-|...--.. +..||-||+......
T Consensus        14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~den   67 (480)
T COG5175          14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDEN   67 (480)
T ss_pred             cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccc
Confidence            44499999998766543333239988888887664333 678999999776554

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

Probab=95.86  E-value=0.0061  Score=46.38  Aligned_cols=32  Identities=28%  Similarity=0.807  Sum_probs=25.8

Q ss_pred             CCCCcccHHhHHHHHcC----C-------CCCcccccccccCC
Q 040080           98 ICNHSFHAQCVDAWLLT----N-------PNCPICRSTANSRR  129 (192)
Q Consensus        98 ~C~H~fh~~Ci~~wl~~----~-------~~CP~Cr~~~~~~~  129 (192)
                      +||.-||.-|+..||+.    .       ..||.|-.++..+.
T Consensus       189 qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKm  231 (234)
T KOG3268|consen  189 QCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKM  231 (234)
T ss_pred             ccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeec
Confidence            39999999999999964    1       24999998886553

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

Probab=95.46  E-value=0.00075  Score=57.02  Aligned_cols=52  Identities=23%  Similarity=0.553  Sum_probs=43.1

Q ss_pred             CCcccccCccccCC-CceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           77 PIECAVCLDKFNKG-DKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        77 ~~~C~IC~~~~~~~-~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      ...|+||...++.. +.+..+. |||.+|..|+.+|+.+...||.|+..+....
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~-~g~~~~~~kL~k~L~~~~kl~~~~rel~~~~  248 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIV-CGHIYHHGKLSKWLATKRKLPSCRRELPKNG  248 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHh-hcccchhhHHHHHHHHHHHhHHHHhhhhhhh
Confidence            45699999988654 4555566 9999999999999999888999999886544

>PF02439 Adeno_E3_CR2: Adenovirus E3 region protein CR2; InterPro: IPR003470 Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host []

Probab=95.44  E-value=0.037  Score=31.25  Aligned_cols=29  Identities=24%  Similarity=0.314  Sum_probs=20.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 040080            3 MAIIISVIFLFLGIGALIFIHVCIVARTF   31 (192)
Q Consensus         3 ~~iil~~~~~~~~i~~l~~~~~~~~~~~~   31 (192)
                      ++||.++++.++.+++.++.+.|.+++.+
T Consensus         6 IaIIv~V~vg~~iiii~~~~YaCcykk~~   34 (38)
T PF02439_consen    6 IAIIVAVVVGMAIIIICMFYYACCYKKHR   34 (38)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHcccc
Confidence            57778887777777777777766665443

This region called CR1 (conserved region 1) [] is found three times in Human adenovirus 19 (a subgroup D adenovirus) 49 kDa protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain.

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

Probab=95.28  E-value=0.009  Score=55.20  Aligned_cols=43  Identities=23%  Similarity=0.662  Sum_probs=32.7

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccccc
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTA  125 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~  125 (192)
                      ...|..|-..++.+  ..... |||.||..|+.   .+...||-|+...
T Consensus       840 ~skCs~C~~~LdlP--~VhF~-CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTLDLP--FVHFL-CGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCccccc--eeeee-cccHHHHHhhc---cCcccCCccchhh
Confidence            35799999988655  23334 99999999998   3556799998833

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

Probab=95.03  E-value=0.021  Score=46.99  Aligned_cols=43  Identities=28%  Similarity=0.768  Sum_probs=33.8

Q ss_pred             CcccccCccccCCCceEEcCCCCCcccHHhHHHHHc-CCCCCccccc
Q 040080           78 IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLL-TNPNCPICRS  123 (192)
Q Consensus        78 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~  123 (192)
                      ..|+.|..-+.++   ..++.|+|.||..||..-|. ....||.|..
T Consensus       275 LkCplc~~Llrnp---~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRNP---MKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhCc---ccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            6799998877554   34567999999999987664 4677999976

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=95.00  E-value=0.011  Score=36.29  Aligned_cols=44  Identities=27%  Similarity=0.619  Sum_probs=31.0

Q ss_pred             cccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccC
Q 040080           79 ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSR  128 (192)
Q Consensus        79 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  128 (192)
                      .|-.|...   +..-..+| |||+.+..|..-+  +-+-||.|-+++...
T Consensus         9 ~~~~~~~~---~~~~~~~p-CgH~I~~~~f~~~--rYngCPfC~~~~~~~   52 (55)
T PF14447_consen    9 PCVFCGFV---GTKGTVLP-CGHLICDNCFPGE--RYNGCPFCGTPFEFD   52 (55)
T ss_pred             eEEEcccc---cccccccc-ccceeeccccChh--hccCCCCCCCcccCC
Confidence            35555544   23335678 9999999998764  445699999988654

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

Probab=94.69  E-value=0.022  Score=47.08  Aligned_cols=48  Identities=27%  Similarity=0.672  Sum_probs=36.9

Q ss_pred             CcccccCccccCCC--ceEEcCCCCCcccHHhHHHHHcCC-CCCccccccc
Q 040080           78 IECAVCLDKFNKGD--KCRLLPICNHSFHAQCVDAWLLTN-PNCPICRSTA  125 (192)
Q Consensus        78 ~~C~IC~~~~~~~~--~~~~~~~C~H~fh~~Ci~~wl~~~-~~CP~Cr~~~  125 (192)
                      ..|-||-++|...+  .+.....|||.|+..|+..-+... ..||.||.+.
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            46999999998663  333333399999999999877663 4599999985

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

Probab=94.61  E-value=0.033  Score=41.70  Aligned_cols=34  Identities=24%  Similarity=0.716  Sum_probs=22.0

Q ss_pred             CCcccccCccccCCCceEEcC-----------CCCC-cccHHhHHHHHc
Q 040080           77 PIECAVCLDKFNKGDKCRLLP-----------ICNH-SFHAQCVDAWLL  113 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~-----------~C~H-~fh~~Ci~~wl~  113 (192)
                      +..|+|||+.-.+.   .+|-           .|+- .-|..|++++-+
T Consensus         2 d~~CpICme~PHNA---VLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    2 DVTCPICMEHPHNA---VLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CccCceeccCCCce---EEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            45799999985443   3322           1443 368899998753

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.

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

Probab=94.37  E-value=0.015  Score=53.53  Aligned_cols=48  Identities=27%  Similarity=0.733  Sum_probs=37.6

Q ss_pred             CcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC--CCCCcccccccccCCC
Q 040080           78 IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT--NPNCPICRSTANSRRF  130 (192)
Q Consensus        78 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~~~~~  130 (192)
                      ..|.||++    .+.+...+ |+|.||..|+..-+..  ...||.||..+..+..
T Consensus       455 ~~c~ic~~----~~~~~it~-c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l  504 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITR-CGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKL  504 (674)
T ss_pred             cccccccc----cccceeec-ccchHHHHHHHhccccccCCCCcHHHHHHHHHHH
Confidence            77999999    34455666 9999999999987755  2359999998876553

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

Probab=94.33  E-value=0.03  Score=47.60  Aligned_cols=30  Identities=23%  Similarity=0.728  Sum_probs=22.8

Q ss_pred             CCCcccHHhHHHHHcCC-------------CCCcccccccccC
Q 040080           99 CNHSFHAQCVDAWLLTN-------------PNCPICRSTANSR  128 (192)
Q Consensus        99 C~H~fh~~Ci~~wl~~~-------------~~CP~Cr~~~~~~  128 (192)
                      |.-++|.+|+-+|+.++             ..||+||+.+...
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCil  353 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCIL  353 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceee
Confidence            44567899999998542             3599999998654

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

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

Probab=94.23  E-value=0.041  Score=45.03  Aligned_cols=53  Identities=23%  Similarity=0.540  Sum_probs=38.2

Q ss_pred             cccccCcc-ccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCcccccccccCCCC
Q 040080           79 ECAVCLDK-FNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRRFG  131 (192)
Q Consensus        79 ~C~IC~~~-~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~~~  131 (192)
                      .|++|... |-+++.......|+|..|.+|++.-+.. ...||.|-..+....+.
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nfr   56 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNNFR   56 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhcccc
Confidence            49999875 4445443333349999999999998866 45699998877655543

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=94.20  E-value=0.082  Score=32.43  Aligned_cols=45  Identities=29%  Similarity=0.715  Sum_probs=35.2

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcc--cccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPI--CRST  124 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~--Cr~~  124 (192)
                      ....|++|-+.|.+++.+.+-|.||-.+|+.|.+.    ...|-.  |..+
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~~~c~~~   50 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCINYSCGTG   50 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEeccCCCC
Confidence            34569999999998888888888999999999654    455654  5443

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

Probab=94.14  E-value=0.037  Score=40.19  Aligned_cols=54  Identities=20%  Similarity=0.458  Sum_probs=37.1

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC---CCCCcccccccccCC
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT---NPNCPICRSTANSRR  129 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~~~~~~~  129 (192)
                      .-.+|.||.+.-.+..=+.--..||-..|..|....++.   +..||+|++++....
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            356799999975433211111239999999998765543   677999999987643

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

Probab=94.00  E-value=0.032  Score=45.70  Aligned_cols=46  Identities=24%  Similarity=0.704  Sum_probs=37.2

Q ss_pred             CCcccccCccccCCC-ceEEcCCCCCcccHHhHHHHHcCCCCCccccc
Q 040080           77 PIECAVCLDKFNKGD-KCRLLPICNHSFHAQCVDAWLLTNPNCPICRS  123 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~-~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~  123 (192)
                      ...||||.+.+.... .+..++ |||..|..|+......+-+||+|.+
T Consensus       158 ~~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             cCCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc
Confidence            445999999765543 444567 9999999999998877888999988

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

Probab=93.83  E-value=0.043  Score=45.63  Aligned_cols=47  Identities=19%  Similarity=0.482  Sum_probs=34.9

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      .+-.+||||.+.+..+  +..-. =||+.|..|=.+   ..+.||.||.++..
T Consensus        46 ~~lleCPvC~~~l~~P--i~QC~-nGHlaCssC~~~---~~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   46 LDLLDCPVCFNPLSPP--IFQCD-NGHLACSSCRTK---VSNKCPTCRLPIGN   92 (299)
T ss_pred             hhhccCchhhccCccc--ceecC-CCcEehhhhhhh---hcccCCcccccccc
Confidence            4566899999999776  22222 479999998653   56779999999874

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

Probab=93.82  E-value=0.033  Score=51.10  Aligned_cols=39  Identities=28%  Similarity=0.609  Sum_probs=27.7

Q ss_pred             ccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcc
Q 040080           80 CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPI  120 (192)
Q Consensus        80 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~  120 (192)
                      |+||--.+.. ....... |+|+.|.+|...|+.....||.
T Consensus      1031 C~~C~l~V~g-ss~~Cg~-C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1031 CAICHLAVRG-SSNFCGT-CGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeEeeEeec-cchhhcc-ccccccHHHHHHHHhcCCcCCC
Confidence            5555444322 2223344 9999999999999999999996

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

Probab=93.75  E-value=0.032  Score=51.97  Aligned_cols=36  Identities=22%  Similarity=0.532  Sum_probs=28.2

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHH
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWL  112 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl  112 (192)
                      ..+..|.+|...+... .-.+.| |||.||++|+..-.
T Consensus       815 ep~d~C~~C~~~ll~~-pF~vf~-CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  815 EPQDSCDHCGRPLLIK-PFYVFP-CGHCFHRDCLIRHV  850 (911)
T ss_pred             cCccchHHhcchhhcC-cceeee-ccchHHHHHHHHHH
Confidence            4467899999988665 445567 99999999997654

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

Probab=93.70  E-value=0.051  Score=46.35  Aligned_cols=48  Identities=19%  Similarity=0.425  Sum_probs=39.4

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCC---CCccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNP---NCPICRS  123 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~---~CP~Cr~  123 (192)
                      ...+.|||-.+.-...++...+. |||+...+-+..-.++..   .||.|=.
T Consensus       332 HSvF~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~  382 (394)
T KOG2817|consen  332 HSVFICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYCPV  382 (394)
T ss_pred             cceeecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence            45678999998887777878888 999999999999776644   4999933

>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls

Probab=93.41  E-value=0.08  Score=38.52  Aligned_cols=13  Identities=31%  Similarity=0.526  Sum_probs=5.6

Q ss_pred             HHHHHHHHHhhcc
Q 040080           21 FIHVCIVARTFRA   33 (192)
Q Consensus        21 ~~~~~~~~~~~r~   33 (192)
                      +++++..+|++|+
T Consensus        17 ~~~~~~~rRR~r~   29 (130)
T PF12273_consen   17 FLFYCHNRRRRRR   29 (130)
T ss_pred             HHHHHHHHHHhhc
Confidence            3333444444444

Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].

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

Probab=93.08  E-value=0.043  Score=43.27  Aligned_cols=40  Identities=38%  Similarity=0.822  Sum_probs=31.1

Q ss_pred             ccccCccccCCCceEEcCCCCCc-ccHHhHHHHHcCCCCCccccccccc
Q 040080           80 CAVCLDKFNKGDKCRLLPICNHS-FHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        80 C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      |-.|.+.   +..+..+| |.|. +|..|-..    -..||+|+.....
T Consensus       161 Cr~C~~~---~~~VlllP-CrHl~lC~~C~~~----~~~CPiC~~~~~s  201 (207)
T KOG1100|consen  161 CRKCGER---EATVLLLP-CRHLCLCGICDES----LRICPICRSPKTS  201 (207)
T ss_pred             ceecCcC---CceEEeec-ccceEeccccccc----CccCCCCcChhhc
Confidence            8888776   66788899 9998 99999654    3459999986643

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

Probab=93.05  E-value=0.031  Score=53.98  Aligned_cols=46  Identities=33%  Similarity=0.837  Sum_probs=37.9

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRS  123 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~  123 (192)
                      .....|.||++.+.+...+  .. |||.+|..|+..|+..+..||.|+.
T Consensus      1151 ~~~~~c~ic~dil~~~~~I--~~-cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRNQGGI--AG-CGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred             hcccchHHHHHHHHhcCCe--ee-echhHhhhHHHHHHHHhccCcchhh
Confidence            4456899999998754332  23 9999999999999999999999984

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

Probab=93.04  E-value=0.025  Score=50.92  Aligned_cols=44  Identities=25%  Similarity=0.590  Sum_probs=33.3

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccc
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRS  123 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~  123 (192)
                      -..|.||+..|....-..+..+|||..|..|+..-  .+.+|| |+.
T Consensus        11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~   54 (861)
T KOG3161|consen   11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKR   54 (861)
T ss_pred             HhhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCc
Confidence            34699999888766555555569999999999885  357898 544

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

Probab=92.95  E-value=0.043  Score=45.37  Aligned_cols=43  Identities=26%  Similarity=0.658  Sum_probs=29.1

Q ss_pred             cccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccc
Q 040080           79 ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTAN  126 (192)
Q Consensus        79 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  126 (192)
                      .|--|--.+.  ..-+.+| |.|+||.+|-..  ...+.||.|--.+.
T Consensus        92 fCd~Cd~PI~--IYGRmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~Vq  134 (389)
T KOG2932|consen   92 FCDRCDFPIA--IYGRMIP-CKHVFCLECARS--DSDKICPLCDDRVQ  134 (389)
T ss_pred             eecccCCcce--eeecccc-cchhhhhhhhhc--CccccCcCcccHHH
Confidence            4666654432  2335678 999999999765  33567999976553

>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=92.49  E-value=0.053  Score=43.31  Aligned_cols=55  Identities=27%  Similarity=0.603  Sum_probs=38.9

Q ss_pred             CCCcccccCcc-ccCCC-ceEEcCCCCCcccHHhHHHHHcCC-CCCc--ccccccccCCC
Q 040080           76 SPIECAVCLDK-FNKGD-KCRLLPICNHSFHAQCVDAWLLTN-PNCP--ICRSTANSRRF  130 (192)
Q Consensus        76 ~~~~C~IC~~~-~~~~~-~~~~~~~C~H~fh~~Ci~~wl~~~-~~CP--~Cr~~~~~~~~  130 (192)
                      .+..||||..+ |.+++ .+.+-|.|-|..|.+|++.-+... ..||  -|-.-+....+
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK~kf   68 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRKIKF   68 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHHhcc
Confidence            34579999986 33443 333446699999999999998775 4599  68775544443

>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=92.44  E-value=0.058  Score=32.03  Aligned_cols=44  Identities=25%  Similarity=0.649  Sum_probs=24.8

Q ss_pred             cccccCccccCCCceEEcCCCC-CcccHHhHHHHHcCCCCCcccccccccC
Q 040080           79 ECAVCLDKFNKGDKCRLLPICN-HSFHAQCVDAWLLTNPNCPICRSTANSR  128 (192)
Q Consensus        79 ~C~IC~~~~~~~~~~~~~~~C~-H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  128 (192)
                      .|--|+-...   .  ... |. |..|..|+...+.....||+|..+++.+
T Consensus         4 nCKsCWf~~k---~--Li~-C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen    4 NCKSCWFANK---G--LIK-CSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             ---SS-S--S---S--EEE--SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             cChhhhhcCC---C--eee-ecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            4666775532   2  223 65 9999999999999899999999988653

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.

>PF15050 SCIMP: SCIMP protein

Probab=91.84  E-value=0.37  Score=34.36  Aligned_cols=33  Identities=18%  Similarity=0.373  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCcc
Q 040080            3 MAIIISVIFLFLGIGALIFIHVCIVARTFRAGLI   36 (192)
Q Consensus         3 ~~iil~~~~~~~~i~~l~~~~~~~~~~~~r~~~~   36 (192)
                      |=||+++.++++++++-++ .+|.++|.+|++..
T Consensus         8 FWiiLAVaII~vS~~lglI-lyCvcR~~lRqGkk   40 (133)
T PF15050_consen    8 FWIILAVAIILVSVVLGLI-LYCVCRWQLRQGKK   40 (133)
T ss_pred             hHHHHHHHHHHHHHHHHHH-HHHHHHHHHHcccc
Confidence            3467777766665555444 45777787776644

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.63  E-value=0.085  Score=42.54  Aligned_cols=51  Identities=20%  Similarity=0.572  Sum_probs=34.7

Q ss_pred             CCCCCcccccCccccCCCce-EEcCCCC-----CcccHHhHHHHHcCC--------CCCccccccc
Q 040080           74 GSSPIECAVCLDKFNKGDKC-RLLPICN-----HSFHAQCVDAWLLTN--------PNCPICRSTA  125 (192)
Q Consensus        74 ~~~~~~C~IC~~~~~~~~~~-~~~~~C~-----H~fh~~Ci~~wl~~~--------~~CP~Cr~~~  125 (192)
                      ...+..|=||+..=++.... -+.| |.     |..|..|+..|+..+        -+||-|++..
T Consensus        17 ~e~eR~CWiCF~TdeDn~~a~WV~P-CrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY   81 (293)
T KOG3053|consen   17 QELERCCWICFATDEDNRLAAWVHP-CRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY   81 (293)
T ss_pred             cccceeEEEEeccCcccchhhhccc-ccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence            35567799999874433211 2234 53     789999999999542        1399999864

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

Probab=91.38  E-value=0.19  Score=46.66  Aligned_cols=53  Identities=21%  Similarity=0.550  Sum_probs=39.6

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCC-----cccHHhHHHHHcCCC--CCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNH-----SFHAQCVDAWLLTNP--NCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H-----~fh~~Ci~~wl~~~~--~CP~Cr~~~~~~~  129 (192)
                      .+...|-||..+-..+++.. .| |..     ..|.+|+.+|+.-+.  .|-+|+.++..++
T Consensus        10 ~d~~~CRICr~e~~~d~pLf-hP-CKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~   69 (1175)
T COG5183          10 EDKRSCRICRTEDIRDDPLF-HP-CKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKD   69 (1175)
T ss_pred             ccchhceeecCCCCCCCcCc-cc-ccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeee
Confidence            45578999998865555433 45 653     489999999998644  4999999987665

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

Probab=90.59  E-value=0.092  Score=48.00  Aligned_cols=61  Identities=31%  Similarity=0.768  Sum_probs=42.9

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC---CCCcccccccccCCCCCCCCcccchhh
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN---PNCPICRSTANSRRFGEESSRFSDIDV  142 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~---~~CP~Cr~~~~~~~~~~~~~~~~~~~~  142 (192)
                      ..+|+||+..+..+   ..+. |.|.|+..|+..-+...   ..||+|+..+..+.... ..+.++...
T Consensus        21 ~lEc~ic~~~~~~p---~~~k-c~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~s~~E-s~r~sq~vq   84 (684)
T KOG4362|consen   21 ILECPICLEHVKEP---SLLK-CDHIFLKFCLNKLFESKKGPKQCALCKSDIEKRSLRE-SPRFSQLSK   84 (684)
T ss_pred             hccCCceeEEeecc---chhh-hhHHHHhhhhhceeeccCccccchhhhhhhhhhhccc-cchHHHHHH
Confidence            45799999998776   3455 99999999998766543   45999998776655433 434444433

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.41  E-value=0.31  Score=39.34  Aligned_cols=55  Identities=15%  Similarity=0.262  Sum_probs=40.3

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCCCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRFG  131 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~  131 (192)
                      ...+.|+|---+|........+-.|||+|-..-+.+-  ...+|++|.+.+...+..
T Consensus       109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~dvI  163 (293)
T KOG3113|consen  109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDDVI  163 (293)
T ss_pred             cceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccCeE
Confidence            3456799988887655444445459999999888873  467899999988766533

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

Probab=89.24  E-value=0.66  Score=33.45  Aligned_cols=15  Identities=33%  Similarity=0.459  Sum_probs=7.7

Q ss_pred             HHHHHHHHHHHHHHH
Q 040080            3 MAIIISVIFLFLGIG   17 (192)
Q Consensus         3 ~~iil~~~~~~~~i~   17 (192)
                      .+||+++++.+++++
T Consensus        67 ~~Ii~gv~aGvIg~I   81 (122)
T PF01102_consen   67 IGIIFGVMAGVIGII   81 (122)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             eehhHHHHHHHHHHH
Confidence            455555555554433

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

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.04  E-value=0.21  Score=41.09  Aligned_cols=31  Identities=23%  Similarity=0.655  Sum_probs=24.5

Q ss_pred             CCCcccHHhHHHHHcC-------------CCCCcccccccccCC
Q 040080           99 CNHSFHAQCVDAWLLT-------------NPNCPICRSTANSRR  129 (192)
Q Consensus        99 C~H~fh~~Ci~~wl~~-------------~~~CP~Cr~~~~~~~  129 (192)
                      |...+|.+|+.+|+..             +.+||+||+.+...+
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~d  368 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRD  368 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEee
Confidence            6677899999988742             356999999987754

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

Probab=88.40  E-value=0.61  Score=28.08  Aligned_cols=43  Identities=21%  Similarity=0.566  Sum_probs=19.4

Q ss_pred             CcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-----CCCCcccccc
Q 040080           78 IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-----NPNCPICRST  124 (192)
Q Consensus        78 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-----~~~CP~Cr~~  124 (192)
                      ..|+|....+..  .++... |.|.-+.+ +..|+..     .-.||+|.++
T Consensus         3 L~CPls~~~i~~--P~Rg~~-C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRI--PVRGKN-CKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SS--EEEETT---SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEe--CccCCc-CcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            358888888744  556666 99984422 3445533     2249999864

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.

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

Probab=88.29  E-value=0.41  Score=44.17  Aligned_cols=40  Identities=20%  Similarity=0.507  Sum_probs=29.4

Q ss_pred             cccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcc
Q 040080           79 ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPI  120 (192)
Q Consensus        79 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~  120 (192)
                      .|.+|-..+..  ....-+.|||.-|.+|+.+|+..+..||.
T Consensus       781 ~CtVC~~vi~G--~~~~c~~C~H~gH~sh~~sw~~~~s~ca~  820 (839)
T KOG0269|consen  781 KCTVCDLVIRG--VDVWCQVCGHGGHDSHLKSWFFKASPCAK  820 (839)
T ss_pred             Cceeecceeee--eEeecccccccccHHHHHHHHhcCCCCcc
Confidence            57777765422  11223459999999999999999888876

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

Probab=87.52  E-value=0.35  Score=43.63  Aligned_cols=50  Identities=30%  Similarity=0.831  Sum_probs=39.6

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCCCCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRFGE  132 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~~  132 (192)
                      .....|.||+..+    ..+..+ |.   |..|+..|+..+..||+|+..+.......
T Consensus       477 ~~~~~~~~~~~~~----~~~~~~-~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~~~  526 (543)
T KOG0802|consen  477 EPNDVCAICYQEM----SARITP-CS---HALCLRKWLYVQEVCPLCHTYMKEDDFLS  526 (543)
T ss_pred             cccCcchHHHHHH----Hhcccc-cc---chhHHHhhhhhccccCCCchhhhcccccC
Confidence            4567899999997    334555 77   99999999999999999999887654333

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

Probab=87.29  E-value=1.1  Score=32.38  Aligned_cols=29  Identities=21%  Similarity=0.267  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 040080            4 AIIISVIFLFLGIGALIFIHVCIVARTFR   32 (192)
Q Consensus         4 ~iil~~~~~~~~i~~l~~~~~~~~~~~~r   32 (192)
                      +|++.++.+++|+++++++++|+.+|+++
T Consensus        65 ~i~~Ii~gv~aGvIg~Illi~y~irR~~K   93 (122)
T PF01102_consen   65 AIIGIIFGVMAGVIGIILLISYCIRRLRK   93 (122)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHS-
T ss_pred             ceeehhHHHHHHHHHHHHHHHHHHHHHhc
Confidence            45666666777777777666555544433

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

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

Probab=85.53  E-value=0.53  Score=43.77  Aligned_cols=52  Identities=8%  Similarity=0.133  Sum_probs=35.9

Q ss_pred             CCCCcccccCccccCC---CceEEcCCCCCcccHHhHHHHHcC------CCCCcccccccc
Q 040080           75 SSPIECAVCLDKFNKG---DKCRLLPICNHSFHAQCVDAWLLT------NPNCPICRSTAN  126 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~---~~~~~~~~C~H~fh~~Ci~~wl~~------~~~CP~Cr~~~~  126 (192)
                      .....|.+|+-++..+   ..+-.+.+|+|.||..||..|...      +-.|++|..-|.
T Consensus        94 a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~  154 (1134)
T KOG0825|consen   94 AESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVG  154 (1134)
T ss_pred             ccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhh
Confidence            3445688888887762   222223349999999999999854      334888887653

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

Probab=84.59  E-value=0.38  Score=41.55  Aligned_cols=39  Identities=26%  Similarity=0.578  Sum_probs=27.4

Q ss_pred             CCCCcccccCccccCC-CceEEcCCCCCcccHHhHHHHHcC
Q 040080           75 SSPIECAVCLDKFNKG-DKCRLLPICNHSFHAQCVDAWLLT  114 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~-~~~~~~~~C~H~fh~~Ci~~wl~~  114 (192)
                      ....+|.||+...... ....... |+|.||..|..+.+..
T Consensus       144 ~~~~~C~iC~~e~~~~~~~f~~~~-C~H~fC~~C~k~~iev  183 (384)
T KOG1812|consen  144 LPKEECGICFVEDPEAEDMFSVLK-CGHRFCKDCVKQHIEV  183 (384)
T ss_pred             cccccCccCccccccHhhhHHHhc-ccchhhhHHhHHHhhh
Confidence            3466899999444333 3333344 9999999999998864

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

Probab=83.99  E-value=3.5  Score=29.16  Aligned_cols=18  Identities=17%  Similarity=0.253  Sum_probs=13.4

Q ss_pred             HcCCCCCcccccccccCC
Q 040080          112 LLTNPNCPICRSTANSRR  129 (192)
Q Consensus       112 l~~~~~CP~Cr~~~~~~~  129 (192)
                      +.+...|+.|++++.-++
T Consensus        82 LGr~D~CM~C~~pLTLd~   99 (114)
T PF11023_consen   82 LGRVDACMHCKEPLTLDP   99 (114)
T ss_pred             hchhhccCcCCCcCccCc
Confidence            444557999999997654

; GO: 0005887 integral to plasma membrane

>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]

Probab=83.93  E-value=1.4  Score=36.82  Aligned_cols=52  Identities=23%  Similarity=0.540  Sum_probs=35.1

Q ss_pred             CCCCcccccCcccc---------------CC-CceEEcCCCCCcccHHhHHHHHcC---------CCCCccccccccc
Q 040080           75 SSPIECAVCLDKFN---------------KG-DKCRLLPICNHSFHAQCVDAWLLT---------NPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~---------------~~-~~~~~~~~C~H~fh~~Ci~~wl~~---------~~~CP~Cr~~~~~  127 (192)
                      ....+|++|+..-.               .+ -.-...| |||+--.+-..-|...         +..||.|-+.+..
T Consensus       339 ~~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~P-CGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~g  415 (429)
T KOG3842|consen  339 QRERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNP-CGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAG  415 (429)
T ss_pred             cccCcCCeeeeecceeeeeccccceeEecCCCcccccCC-cccccchhhhhHhhcCcCCCccccccccCcchhhhhcc
Confidence            45678999997521               00 0112356 9999888888888754         3459999887754

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

Probab=83.91  E-value=0.56  Score=38.79  Aligned_cols=51  Identities=24%  Similarity=0.611  Sum_probs=35.6

Q ss_pred             CCcccccCccccCCCc-eEEcCCCC-----CcccHHhHHHHHcC--CCCCcccccccccC
Q 040080           77 PIECAVCLDKFNKGDK-CRLLPICN-----HSFHAQCVDAWLLT--NPNCPICRSTANSR  128 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~-~~~~~~C~-----H~fh~~Ci~~wl~~--~~~CP~Cr~~~~~~  128 (192)
                      +..|-||..+...... ....| |.     +..|..|+..|+..  +..|..|.......
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~p-C~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~  136 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISP-CSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV  136 (323)
T ss_pred             CCcEEEEecccccccccccccC-ccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence            4679999997654321 23344 65     45799999999984  45699998866443

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

Probab=83.69  E-value=0.39  Score=43.38  Aligned_cols=45  Identities=27%  Similarity=0.728  Sum_probs=27.5

Q ss_pred             CCCCcccccCcc-----ccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccc
Q 040080           75 SSPIECAVCLDK-----FNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRS  123 (192)
Q Consensus        75 ~~~~~C~IC~~~-----~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~  123 (192)
                      ...+.|.+|...     |......+... |+++||..|+..   .+.-||-|-+
T Consensus       509 ~~gfiCe~Cq~~~iiyPF~~~~~~rC~~-C~avfH~~C~~r---~s~~CPrC~R  558 (580)
T KOG1829|consen  509 GKGFICELCQHNDIIYPFETRNTRRCST-CLAVFHKKCLRR---KSPCCPRCER  558 (580)
T ss_pred             cCeeeeeeccCCCcccccccccceeHHH-HHHHHHHHHHhc---cCCCCCchHH
Confidence            345678888331     11111222334 999999999665   3444999955

>KOG4367 consensus Predicted Zn-finger protein [Function unknown]

Probab=83.59  E-value=0.58  Score=40.70  Aligned_cols=36  Identities=25%  Similarity=0.695  Sum_probs=28.5

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT  114 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~  114 (192)
                      +++..|+||-.-|..+   +++| |+|.+|..|-..-+.+
T Consensus         2 eeelkc~vc~~f~~ep---iil~-c~h~lc~~ca~~~~~~   37 (699)
T KOG4367|consen    2 EEELKCPVCGSFYREP---IILP-CSHNLCQACARNILVQ   37 (699)
T ss_pred             cccccCceehhhccCc---eEee-cccHHHHHHHHhhccc
Confidence            3466799999988665   6788 9999999998865543

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=82.06  E-value=1.1  Score=35.21  Aligned_cols=42  Identities=29%  Similarity=0.741  Sum_probs=28.8

Q ss_pred             CCCcccccCcc-----ccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccc
Q 040080           76 SPIECAVCLDK-----FNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRS  123 (192)
Q Consensus        76 ~~~~C~IC~~~-----~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~  123 (192)
                      .++.|-+|-..     |+. +.+..-+.|+-+||..|...     ..||-|.+
T Consensus       151 kGfiCe~C~~~~~IfPF~~-~~~~~C~~C~~v~H~~C~~~-----~~CpkC~R  197 (202)
T PF13901_consen  151 KGFICEICNSDDIIFPFQI-DTTVRCPKCKSVFHKSCFRK-----KSCPKCAR  197 (202)
T ss_pred             CCCCCccCCCCCCCCCCCC-CCeeeCCcCccccchhhcCC-----CCCCCcHh
Confidence            35778888753     222 23444556999999999662     66999954

>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=81.97  E-value=0.8  Score=23.69  Aligned_cols=23  Identities=22%  Similarity=0.647  Sum_probs=12.4

Q ss_pred             cccccCccccCCCceEEcCCCCCcc
Q 040080           79 ECAVCLDKFNKGDKCRLLPICNHSF  103 (192)
Q Consensus        79 ~C~IC~~~~~~~~~~~~~~~C~H~f  103 (192)
                      .||-|...+..  ....-|.|||.|
T Consensus         2 ~CP~C~~~V~~--~~~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCPECGAEVPE--SAKFCPHCGYDF   24 (26)
T ss_pred             cCCCCcCCchh--hcCcCCCCCCCC
Confidence            36666666522  233344577766

Several members are annotated as putative helicases.

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

Probab=81.54  E-value=0.82  Score=35.96  Aligned_cols=48  Identities=23%  Similarity=0.529  Sum_probs=35.8

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTAN  126 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  126 (192)
                      .-..|.+|..-.-.+   +....||-.+|..|+..++.+...||.|.--++
T Consensus       180 nlk~Cn~Ch~LvIqg---~rCg~c~i~~h~~c~qty~q~~~~cphc~d~w~  227 (235)
T KOG4718|consen  180 NLKNCNLCHCLVIQG---IRCGSCNIQYHRGCIQTYLQRRDICPHCGDLWT  227 (235)
T ss_pred             HHHHHhHhHHHhhee---eccCcccchhhhHHHHHHhcccCcCCchhcccC
Confidence            345799999875443   222338888999999999999888999955443

>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls

Probab=81.10  E-value=1  Score=32.61  Aligned_cols=8  Identities=0%  Similarity=-0.052  Sum_probs=2.9

Q ss_pred             HHHHHHHH
Q 040080           22 IHVCIVAR   29 (192)
Q Consensus        22 ~~~~~~~~   29 (192)
                      +++.+..+
T Consensus        15 ~~~~~~~~   22 (130)
T PF12273_consen   15 FLFLFYCH   22 (130)
T ss_pred             HHHHHHHH
Confidence            33333333

Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].

>TIGR00622 ssl1 transcription factor ssl1

Probab=80.13  E-value=2.4  Score=30.03  Aligned_cols=46  Identities=22%  Similarity=0.382  Sum_probs=33.1

Q ss_pred             CCcccccCccccCC----------CceEEcCCCCCcccHHhHHHHHcCCCCCcccc
Q 040080           77 PIECAVCLDKFNKG----------DKCRLLPICNHSFHAQCVDAWLLTNPNCPICR  122 (192)
Q Consensus        77 ~~~C~IC~~~~~~~----------~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr  122 (192)
                      ...|--|+..|...          .....-+.|++.|+.+|-.-+-+.=..||-|-
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            34599999988542          11122455999999999888777666799995

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	192
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		4e-11
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		3e-09
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		1e-07
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		2e-06
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		4e-05
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		3e-04

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 25/47 (53%), Positives = 33/47 (70%)
Query: 78  IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRST 124
           +ECAVCL +   G++ R LP C H FHA+CVD WL ++  CP+CR T
Sbjct: 6   VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLT 52

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 28/62 (45%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 62  KLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPIC 121
           +LP Y +   +  S    C VC+  F      R+LP CNH FHA+CVD WL  N  CPIC
Sbjct: 8   QLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPIC 66
Query: 122 RS 123
           R+
Sbjct: 67  RA 68

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 23/44 (52%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 79  ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICR 122
           +C +CL    +G+  R LP C H FH  CVD WL+TN  CPICR
Sbjct: 16  KCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICR 58

>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 = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 75  SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRST 124
            S +EC VC + +  G+  R LP CNH FH  C+  WL  + +CP+CR +
Sbjct: 13  GSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKS 61

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 19/43 (44%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 80  CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICR 122
           C +C  ++ KGD    LP C+H FH  CV  WL  +  CP+CR
Sbjct: 43  CPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCR 84

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 80  CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPIC 121
           CAVCL+ F   D+  + P C H+FH +C+  WL     CP+C
Sbjct: 18  CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLC 58

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	192
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	3e-26
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	3e-23
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	2e-21
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	2e-20
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	3e-19
2ect_A	78	Ring finger protein 126; metal binding protein, st	1e-18
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	5e-16
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	2e-15
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	5e-14
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	1e-13
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	3e-12
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	4e-11
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	7e-11
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	5e-10
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	8e-10
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	8e-10
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	3e-09
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	2e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	5e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	4e-05
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	5e-08
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	1e-07
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-07
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	4e-07
3nw0_A	238	Non-structural maintenance of chromosomes element	7e-07
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	1e-06
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	1e-06
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	1e-06
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	2e-06
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	1e-05
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	3e-05
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	3e-05
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	3e-05
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	4e-05
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	3e-04
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	5e-04

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

 Score = 94.7 bits (236), Expect = 3e-26
 Identities = 29/68 (42%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 56  SRDDVEKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN 115
           S     +LP Y +   +  S    C VC+  F      R+LP CNH FHA+CVD WL  N
Sbjct: 2   SSGSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKAN 60

Query: 116 PNCPICRS 123
             CPICR+
Sbjct: 61  RTCPICRA 68

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

 Score = 86.5 bits (215), Expect = 3e-23
 Identities = 24/47 (51%), Positives = 32/47 (68%)

Query: 77  PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRS 123
            +ECAVCL +   G++ R LP C H FHA+CVD WL ++  CP+CR 
Sbjct: 5   GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRL 51

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

 Score = 82.8 bits (205), Expect = 2e-21
 Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 48  SSIGSTSMSRDDVEKLPCYEYLAKSKGS-SPIECAVCLDKFNKGDKCRLLPICNHSFHAQ 106
             + +   S++ ++ LP              + C +C  ++ KGD    LP C+H FH  
Sbjct: 10  HMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKP 68

Query: 107 CVDAWLLTNPNCPICR 122
           CV  WL  +  CP+CR
Sbjct: 69  CVSIWLQKSGTCPVCR 84

>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 = 79.7 bits (197), Expect = 2e-20
 Identities = 23/51 (45%), Positives = 31/51 (60%), Gaps = 1/51 (1%)

Query: 72  SKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICR 122
           ++  +  +C +CL    +G+  R LP C H FH  CVD WL+TN  CPICR
Sbjct: 9   TEEDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICR 58

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

 Score = 76.7 bits (189), Expect = 3e-19
 Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 71  KSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICR 122
             + +    CAVCL+ F   D+  + P C H+FH +C+  WL     CP+C 
Sbjct: 9   VKELNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCN 59

>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 = 75.5 bits (186), Expect = 1e-18
 Identities = 20/44 (45%), Positives = 27/44 (61%), Gaps = 1/44 (2%)

Query: 79  ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICR 122
           EC VC + +  G+  R LP CNH FH  C+  WL  + +CP+CR
Sbjct: 17  ECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCR 59

>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 = 68.1 bits (167), Expect = 5e-16
 Identities = 12/49 (24%), Positives = 18/49 (36%)

Query: 74  GSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICR 122
            S    C +CL+  +       +  C H  H  C +  L     CP+C 
Sbjct: 2   SSGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCS 50

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

 Score = 67.2 bits (164), Expect = 2e-15
 Identities = 15/43 (34%), Positives = 22/43 (51%)

Query: 80  CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICR 122
           C  C  +  + D   +   CNHSFH  C+  W+  N  CP+C+
Sbjct: 29  CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71

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

 Score = 63.2 bits (154), Expect = 5e-14
 Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 5/44 (11%)

Query: 79  ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICR 122
           EC +C+D         +LP C HSF  +C+D W   + NCPICR
Sbjct: 17  ECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICR 55

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

 Score = 62.0 bits (151), Expect = 1e-13
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 3/49 (6%)

Query: 79  ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANS 127
            C +CL+  +  +    LP C H+F   C+  W+  NP CP+C+    S
Sbjct: 7   RCPICLEDPS--NYSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVES 52

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

 Score = 58.4 bits (141), Expect = 3e-12
 Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 3/57 (5%)

Query: 75  SSPIECAVCLDKFNKGDKCRLLPI---CNHSFHAQCVDAWLLTNPNCPICRSTANSR 128
           S  + C +C+D +++  +   L +   C H F +QC+   L     CP CR   N +
Sbjct: 13  SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 69

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

 Score = 55.6 bits (134), Expect = 4e-11
 Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 3/59 (5%)

Query: 75  SSPIECAVCLDKFNKGDKCRLLPI---CNHSFHAQCVDAWLLTNPNCPICRSTANSRRF 130
           S  + C +C+D +++  +   L +   C H F +QC+   L     CP CR   N +R+
Sbjct: 8   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY 66

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

 Score = 54.8 bits (132), Expect = 7e-11
 Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 3/56 (5%)

Query: 78  IECAVCLDKFNKGDKCRLLPI---CNHSFHAQCVDAWLLTNPNCPICRSTANSRRF 130
           + C +C+D +++  +   L +   C H F +QC+   L     CP CR   N +R+
Sbjct: 4   VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY 59

>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 = 53.7 bits (128), Expect = 5e-10
 Identities = 12/43 (27%), Positives = 17/43 (39%)

Query: 80  CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICR 122
           C          +      +CNH+FH  C+  WL T   CP+  
Sbjct: 54  CQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

>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 = 8e-10
 Identities = 12/47 (25%), Positives = 16/47 (34%), Gaps = 5/47 (10%)

Query: 79  ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT--NPNCPICRS 123
            C +C     +G  C     C    H  CV  +  +   P CP C  
Sbjct: 17  ICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCND 60

>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 = 53.3 bits (127), Expect = 8e-10
 Identities = 12/43 (27%), Positives = 17/43 (39%)

Query: 80  CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICR 122
           C          +      +CNH+FH  C+  WL T   CP+  
Sbjct: 65  CQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens} Length = 100

 Score = 51.4 bits (123), Expect = 3e-09
 Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 4/54 (7%)

Query: 78  IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRRF 130
             C +C++K       RL P C+      C+  WL      CP CR+    R  
Sbjct: 23  FRCFICMEKLRD---ARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLREL 73

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

 Score = 48.2 bits (115), Expect = 2e-08
 Identities = 10/52 (19%), Positives = 18/52 (34%), Gaps = 3/52 (5%)

Query: 78  IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR 129
           I C++C            +  C H+F   C+      +  CP C    +  +
Sbjct: 16  ILCSICKGYLID---ATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQ 64

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

 Score = 49.0 bits (116), Expect = 5e-08
 Identities = 19/86 (22%), Positives = 37/86 (43%), Gaps = 3/86 (3%)

Query: 72  SKGSSPIECAVCLDKFNKGDKCRLLPI---CNHSFHAQCVDAWLLTNPNCPICRSTANSR 128
           + GS  + C +C+D +++  +   L +   C H F +QC+   L     CP CR   N +
Sbjct: 2   AMGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 61

Query: 129 RFGEESSRFSDIDVELREGVPTEGIE 154
           R+         +   +     +E ++
Sbjct: 62  RYHPIYIGSGTVSCPICMDGYSEIVQ 87

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

 Score = 40.5 bits (94), Expect = 4e-05
 Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 3/57 (5%)

Query: 77  PIECAVCLDKFN---KGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRF 130
            + C +C+D ++   +  +  +   C H F +QC+   L     CP CR   N +R+
Sbjct: 72  TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY 128

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

 Score = 47.5 bits (113), Expect = 5e-08
 Identities = 12/52 (23%), Positives = 14/52 (26%), Gaps = 4/52 (7%)

Query: 75  SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTAN 126
             P  C +C   F      +    C H F   C        P C IC     
Sbjct: 13  EIPFRCFICRQAFQNPVVTK----CRHYFCESCALEHFRATPRCYICDQPTG 60

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

 Score = 47.1 bits (112), Expect = 1e-07
 Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 3/51 (5%)

Query: 80  CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRF 130
           C +C + FN      ++P C+H++ + C+  +L     CP C  T      
Sbjct: 25  CGICFEYFNI---AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDL 72

>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 = 46.4 bits (110), Expect = 2e-07
 Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 3/52 (5%)

Query: 78  IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR 129
           + C +C   F        +  C HSF   C+  +L T+  CPIC    +  R
Sbjct: 16  LMCVLCGGYFID---ATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTR 64

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

 Score = 44.8 bits (106), Expect = 4e-07
 Identities = 15/44 (34%), Positives = 17/44 (38%), Gaps = 4/44 (9%)

Query: 79  ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICR 122
           ECA+CL           LP C H F   CV         C +CR
Sbjct: 17  ECAICLQTCVH---PVSLP-CKHVFCYLCVKGASWLGKRCALCR 56

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

 Score = 47.0 bits (111), Expect = 7e-07
 Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 5/59 (8%)

Query: 67  EYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT--NPNCPICRS 123
           +Y+ ++   +   C +C     +G  C     C    H  CV  +  +   P CP C  
Sbjct: 170 QYIRETYPDAVKICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCND 225

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

 Score = 45.4 bits (107), Expect = 1e-06
 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 4/52 (7%)

Query: 79  ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRF 130
           +C +C + F +      L  C HSF + C++ W+     CPICR    S+ +
Sbjct: 66  QCIICSEYFIE---AVTLN-CAHSFCSYCINEWMKRKIECPICRKDIKSKTY 113

>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 = 44.8 bits (105), Expect = 1e-06
 Identities = 15/76 (19%), Positives = 27/76 (35%), Gaps = 19/76 (25%)

Query: 68  YLAKSKGSSPIECAVCLDKFN--------------KGDKCRLLPICNHSFHAQCVDAWL- 112
           Y  + K +   +C +C++K                       L  C+H+FH  C+ A   
Sbjct: 16  YTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYC 75

Query: 113 ----LTNPNCPICRST 124
                 +  CP C++ 
Sbjct: 76  NGNKDGSLQCPSCKTI 91

>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 = 46.3 bits (109), Expect = 1e-06
 Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 5/56 (8%)

Query: 69  LAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPN-CPICRS 123
           L    GS+   C +C +        ++ P C H     C+ +W  +    CP CR 
Sbjct: 324 LYCEMGSTFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRC 375

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

 Score = 46.4 bits (109), Expect = 2e-06
 Identities = 13/60 (21%), Positives = 20/60 (33%), Gaps = 15/60 (25%)

Query: 79  ECAVCLDKFNKGDKCRLL----PICNHSFHAQCVDAWLLTNP-----------NCPICRS 123
            C +C      G +  L+      C    HA C++ W  T              CP C++
Sbjct: 310 RCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKA 369

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

 Score = 40.8 bits (96), Expect = 1e-05
 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 5/52 (9%)

Query: 75  SSPIECAVCLDKFNKGDKC-RLLPICNHSFHAQCVDAWLLTNPN---CPICR 122
              +EC +C++ F +     +LL  C H+   QC++  L ++ N   CP C 
Sbjct: 13  REVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCS 63

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

 Score = 40.5 bits (95), Expect = 3e-05
 Identities = 16/64 (25%), Positives = 24/64 (37%), Gaps = 7/64 (10%)

Query: 69  LAKSKGSSPIE--CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPN--CPICRST 124
           L       P E  C +C D         ++P C +S+  +C+   LL +    CP C   
Sbjct: 3   LGSEDDPIPDELLCLICKDIM---TDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQN 59

Query: 125 ANSR 128
             S 
Sbjct: 60  DVSP 63

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

 Score = 39.7 bits (93), Expect = 3e-05
 Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 5/52 (9%)

Query: 80  CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPN--CPICRSTANSRR 129
           C +C D         ++P C +S+  +C+   LL +    CP C     S  
Sbjct: 18  CLICKDIM---TDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD 66

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

 Score = 40.7 bits (95), Expect = 3e-05
 Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 5/51 (9%)

Query: 80  CAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRF 130
           C+ C +      +   L  C H F + CV   +     CP+C + A  +  
Sbjct: 25  CSRCTNIL---REPVCLGGCEHIFCSNCVSDCI--GTGCPVCYTPAWIQDL 70

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

 Score = 39.7 bits (92), Expect = 4e-05
 Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 6/69 (8%)

Query: 76  SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRRFGEES 134
            P+EC +C++     D       C +     C        N  CP CR     + + E+ 
Sbjct: 10  DPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACR-----KPYPEDP 64

Query: 135 SRFSDIDVE 143
           + +  +  E
Sbjct: 65  AVYKPLSQE 73

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

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 17/53 (32%), Positives = 21/53 (39%), Gaps = 4/53 (7%)

Query: 78  IECAVCLDKFNKGDKCRLLPICNHSFHAQC-VDAWLLTNPNCPICRSTANSRR 129
           + C +CLD             C H F A C + A    N  CP CR    S+R
Sbjct: 55  LMCPICLDMLKN---TMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKR 104

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

 Score = 35.8 bits (83), Expect = 5e-04
 Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 7/45 (15%)

Query: 79  ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRS 123
            C  C  +       +LLP C H+  + C++A  +    CPIC++
Sbjct: 8   RCQQCQAEAKCP---KLLP-CLHTLCSGCLEASGMQ---CPICQA 45

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	192
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.77
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.74
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.62
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.62
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.61
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.6
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.59
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.55
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.53
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.52
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.51
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.5
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.48
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.45
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.44
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.44
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.43
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.43
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.41
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.4
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.39
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.37
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.37
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.36
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.34
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.34
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.32
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.31
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.3
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.3
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.29
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.28
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.28
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.27
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.27
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.26
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.24
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.22
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.22
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.22
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.2
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.19
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.19
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.15
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.12
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.11
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.11
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.09
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.09
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.07
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.06
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.05
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.04
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.03
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.03
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.0
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.98
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.92
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.92
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.85
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.83
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.79
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.76
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.75
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.74
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.73
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.64
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.58
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.56
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.49
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.29
3nw0_A	238	Non-structural maintenance of chromosomes element	98.28
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	96.35
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	95.88
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.11
1we9_A	64	PHD finger family protein; structural genomics, PH	93.99
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	93.35
2l2t_A	44	Receptor tyrosine-protein kinase ERBB-4; transmemb	93.16
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	91.81
2ks1_B	44	Epidermal growth factor receptor; ERBB1, ERBB2, tr	91.51
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	91.5
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	90.93
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	90.7
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	90.46
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	90.33
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	90.02
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	89.82
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	89.81
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	89.78
2jwa_A	44	Receptor tyrosine-protein kinase ERBB-2; transmemb	89.38
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	88.62
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	88.21
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	88.12
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	87.94
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	87.64
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	87.48
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	87.43
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	87.0
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	86.57
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	86.17
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	86.01
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	85.48
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	85.23
1wem_A	76	Death associated transcription factor 1; structura	85.23
2yt5_A	66	Metal-response element-binding transcription facto	84.3
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	82.93
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	82.9
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	82.42
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	82.05
1weu_A	91	Inhibitor of growth family, member 4; structural g	81.9
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	81.83
1iij_A	35	ERBB-2 receptor protein-tyrosine kinase; alpha-hel	81.65
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	81.54
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	81.29
1wew_A	78	DNA-binding family protein; structural genomics, P	81.16
1wee_A	72	PHD finger family protein; structural genomics, PH	81.04
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	80.46

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

Probab=99.77  E-value=1e-18  Score=119.39  Aligned_cols=80  Identities=28%  Similarity=0.671  Sum_probs=69.2

Q ss_pred             ccCCCCCCCCHHHHhcCCceEeeccCC-CCCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccccc
Q 040080           47 RSSIGSTSMSRDDVEKLPCYEYLAKSK-GSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTA  125 (192)
Q Consensus        47 ~~~~~~~~~~~~~i~~l~~~~~~~~~~-~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~  125 (192)
                      .......+++++.++.||.+.+..... ......|+||++.|..++.+..++ |||.||..||..|+..+.+||+||+++
T Consensus         9 ~~~~~~~~~s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~   87 (91)
T 2l0b_A            9 SHMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCMF   87 (91)
T ss_dssp             CCSSCCCCCCHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTTCCBS
T ss_pred             CCCcCCCCCCHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCcCccC
Confidence            445567889999999999998876543 355678999999999888888899 999999999999999999999999988


Q ss_pred             cc
Q 040080          126 NS  127 (192)
Q Consensus       126 ~~  127 (192)
                      ..
T Consensus        88 ~~   89 (91)
T 2l0b_A           88 PP   89 (91)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

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

Probab=99.74  E-value=5.2e-19  Score=116.49  Aligned_cols=69  Identities=41%  Similarity=0.924  Sum_probs=61.5

Q ss_pred             HHhcCCceEeeccCCCCCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccC
Q 040080           59 DVEKLPCYEYLAKSKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSR  128 (192)
Q Consensus        59 ~i~~l~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  128 (192)
                      .++.||.+++.......+...|+||++.|..++.+..++ |+|.||..||..|+..+.+||+||+++.+.
T Consensus         5 ~i~~lp~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A            5 SSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             CCSSCCCEEBCSSSCSSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             hHhhCCcEEecCccccCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            467889998887776677889999999999988888899 999999999999999999999999988653

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

Probab=99.62  E-value=4.2e-16  Score=103.11  Aligned_cols=56  Identities=38%  Similarity=0.968  Sum_probs=49.5

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCCCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRFG  131 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~  131 (192)
                      .....|+||++.|..+..+..++ |+|.||..||..|+..+.+||+||+.+......
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   68 (78)
T 2ect_A           13 GSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTA   68 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSC
T ss_pred             CCCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCccCCcccC
Confidence            45678999999999888888888 999999999999999999999999999776543

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

Probab=99.62  E-value=1.9e-16  Score=97.82  Aligned_cols=52  Identities=48%  Similarity=1.141  Sum_probs=46.0

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTAN  126 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  126 (192)
                      .+..+|+||++.+..++.+..++.|||.||..||.+|+..+.+||+||+++.
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            3456899999999888777778679999999999999999999999999874

>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=99.61  E-value=6.6e-16  Score=99.77  Aligned_cols=53  Identities=43%  Similarity=1.065  Sum_probs=47.5

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  128 (192)
                      .....|+||++.|..+..+..++ |||.||..||..|+..+.+||+||+.+...
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             CCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            45678999999998888888899 999999999999999999999999998654

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

Probab=99.60  E-value=1.1e-15  Score=100.07  Aligned_cols=53  Identities=34%  Similarity=0.814  Sum_probs=47.5

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  128 (192)
                      .....|+||++.|..+..+..++ |+|.||..||..|+..+.+||+||+++...
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQL   65 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSSC
T ss_pred             CCCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCcccccc
Confidence            44678999999999888888888 999999999999999989999999998653

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

Probab=99.59  E-value=4.2e-16  Score=104.12  Aligned_cols=54  Identities=31%  Similarity=0.680  Sum_probs=43.1

Q ss_pred             CCCcccccCccccC-----------CCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           76 SPIECAVCLDKFNK-----------GDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        76 ~~~~C~IC~~~~~~-----------~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      ++..|+||++.|..           ++.+..++.|+|.||..||.+|+..+.+||+||+++....
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~   78 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQR   78 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchhh
Confidence            35568888888854           3445555559999999999999999999999999987654

>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=99.55  E-value=5.7e-15  Score=104.54  Aligned_cols=53  Identities=26%  Similarity=0.666  Sum_probs=42.5

Q ss_pred             CCCcccccCccccCCC---------------ceEEcCCCCCcccHHhHHHHH-----cCCCCCcccccccccCC
Q 040080           76 SPIECAVCLDKFNKGD---------------KCRLLPICNHSFHAQCVDAWL-----LTNPNCPICRSTANSRR  129 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~---------------~~~~~~~C~H~fh~~Ci~~wl-----~~~~~CP~Cr~~~~~~~  129 (192)
                      .+..|+||++.|..+.               .+..++ |+|.||..||..|+     ..+.+||+||+.+..+.
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~~   96 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKT   96 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCS
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCC-CCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCCC
Confidence            4568999999996543               333667 99999999999999     45678999999887653

>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=99.53  E-value=5.2e-15  Score=103.63  Aligned_cols=53  Identities=26%  Similarity=0.569  Sum_probs=44.0

Q ss_pred             CCCcccccCccccCCC---------------ceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           76 SPIECAVCLDKFNKGD---------------KCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~---------------~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      ++..|+||++.|...-               .+..++ |+|.||..||..||..+.+||+||+++....
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~~~~  103 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEFQK  103 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCCEEE
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecc-cCcEECHHHHHHHHHcCCcCcCCCCcceeec
Confidence            4677999999987541               245567 9999999999999999999999999976543

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

Probab=99.52  E-value=4.3e-15  Score=96.24  Aligned_cols=55  Identities=29%  Similarity=0.726  Sum_probs=46.0

Q ss_pred             CCCCcccccCccccCC----CceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCCC
Q 040080           75 SSPIECAVCLDKFNKG----DKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRF  130 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~  130 (192)
                      .+...|+||++.+..+    .....++ |||.||..||..|+..+.+||+||+++.....
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   66 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   66 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSC
T ss_pred             CCCCCCcccChhhhccccccCCeEeCC-CCChHhHHHHHHHHHcCCCCCCCCCccChhhe
Confidence            4567899999998653    4456677 99999999999999999999999999976543

>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=99.51  E-value=7.6e-15  Score=90.43  Aligned_cols=50  Identities=26%  Similarity=0.765  Sum_probs=42.5

Q ss_pred             CCCcccccCccccCC-CceEEcCCCCCcccHHhHHHHHcCCCCCcccccccc
Q 040080           76 SPIECAVCLDKFNKG-DKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTAN  126 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~-~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  126 (192)
                      +...|+||++.+..+ ..+..++ |||.||..||..|+..+.+||+||+++.
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            456799999998654 3466677 9999999999999998899999999764

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

Probab=99.50  E-value=7.2e-15  Score=94.55  Aligned_cols=52  Identities=29%  Similarity=0.688  Sum_probs=43.8

Q ss_pred             CCCCcccccCccccCC----CceEEcCCCCCcccHHhHHHHHcCCCCCccccccccc
Q 040080           75 SSPIECAVCLDKFNKG----DKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      .+...|+||++.+..+    ..+..++ |||.||..||..|+..+.+||+||.++..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECS-SSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCC-CCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            4567899999998653    3446677 99999999999999999999999998864

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

Probab=99.48  E-value=9.2e-15  Score=92.66  Aligned_cols=53  Identities=28%  Similarity=0.696  Sum_probs=44.3

Q ss_pred             CCCcccccCccccCC----CceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           76 SPIECAVCLDKFNKG----DKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      +...|+||++.+..+    ..+..++ |||.||..|+..|+..+.+||+||+++....
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   58 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKR   58 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEET-TSCEEEHHHHHHHHHHCSBCTTTCCBCTTTC
T ss_pred             CCCCCCccChhhhCccccCCCEEeCC-CCCchhHHHHHHHHHcCCCCCCCCccCCccc
Confidence            356799999998653    3446677 9999999999999999999999999987643

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

Probab=99.45  E-value=2.4e-14  Score=92.99  Aligned_cols=51  Identities=29%  Similarity=0.582  Sum_probs=43.4

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      .+...|+||++.+...   ..++ |||.||..||..|+..+.+||+||..+....
T Consensus        13 ~~~~~C~IC~~~~~~~---~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   63 (71)
T 2d8t_A           13 LTVPECAICLQTCVHP---VSLP-CKHVFCYLCVKGASWLGKRCALCRQEIPEDF   63 (71)
T ss_dssp             SSCCBCSSSSSBCSSE---EEET-TTEEEEHHHHHHCTTCSSBCSSSCCBCCHHH
T ss_pred             CCCCCCccCCcccCCC---EEcc-CCCHHHHHHHHHHHHCCCcCcCcCchhCHhh
Confidence            4567899999998554   5567 9999999999999999999999999987543

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

Probab=99.44  E-value=1.4e-13  Score=89.59  Aligned_cols=53  Identities=19%  Similarity=0.515  Sum_probs=43.6

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRF  130 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~  130 (192)
                      .+...|+||++.+..+  +..++ |||.||..||..|+..+.+||+||+++.....
T Consensus        13 ~~~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~   65 (72)
T 2djb_A           13 TPYILCSICKGYLIDA--TTITE-CLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQP   65 (72)
T ss_dssp             CGGGSCTTTSSCCSSC--EECSS-SCCEECHHHHHHHHHHCSSCTTTCCCCCSSCS
T ss_pred             CCCCCCCCCChHHHCc--CEECC-CCCHHHHHHHHHHHHcCCcCCCcCcccCcccc
Confidence            4567899999998653  33346 99999999999999888999999999876543

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

Probab=99.44  E-value=3.5e-14  Score=91.81  Aligned_cols=50  Identities=38%  Similarity=0.926  Sum_probs=43.2

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      .+...|+||++.+..    ..++ |||.||..|+..|+..+.+||+||+++....
T Consensus        13 ~~~~~C~IC~~~~~~----~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGAN   62 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEET-TTEEECHHHHHHSSCCCSSCHHHHHCTTCCC
T ss_pred             CCCCCCeeCCcCccC----cccC-CCCcccHHHHHHHHHCcCcCCCcCCcccCCC
Confidence            456789999999865    5677 9999999999999998999999999987543

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

Probab=99.43  E-value=7.1e-14  Score=89.77  Aligned_cols=49  Identities=33%  Similarity=0.897  Sum_probs=42.2

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      ....|+||++.+..  ....++ |||.||..|+..|+..+.+||+||+++..
T Consensus         4 ~~~~C~IC~~~~~~--~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCeeCCccccC--CcEecC-CCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            45679999999854  346778 99999999999999989999999998864

>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=99.43  E-value=1.1e-14  Score=103.49  Aligned_cols=54  Identities=26%  Similarity=0.626  Sum_probs=1.0

Q ss_pred             CCCcccccCccccCC-------------C--ceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCCC
Q 040080           76 SPIECAVCLDKFNKG-------------D--KCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRF  130 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~-------------~--~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~  130 (192)
                      .+..|+||++.|...             +  .+..++ |+|.||..||.+|+..+.+||+||+++...++
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~-C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~~k~  115 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEFQKY  115 (117)
T ss_dssp             CC--------------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCC-cCceEcHHHHHHHHHcCCcCCCCCCeeeeecc
Confidence            456899999999652             1  122245 99999999999999999999999999865543

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

Probab=99.41  E-value=2.1e-13  Score=90.64  Aligned_cols=53  Identities=23%  Similarity=0.588  Sum_probs=44.0

Q ss_pred             CCCCcccccCccccCCCceEEcCCCC-----CcccHHhHHHHHcCC--CCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICN-----HSFHAQCVDAWLLTN--PNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~-----H~fh~~Ci~~wl~~~--~~CP~Cr~~~~~~~  129 (192)
                      .+...|.||++++..++.+ ++| |+     |.||..||++|+..+  .+||+||+.+....
T Consensus        13 ~~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~   72 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMET   72 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCC
T ss_pred             CCCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCc
Confidence            4567899999999877665 578 96     999999999999875  48999999986543

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

Probab=99.40  E-value=3e-13  Score=91.03  Aligned_cols=54  Identities=26%  Similarity=0.736  Sum_probs=44.7

Q ss_pred             CCCCcccccCccccCCCc-eEEcCCCCCcccHHhHHHHHcCC---CCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDK-CRLLPICNHSFHAQCVDAWLLTN---PNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~-~~~~~~C~H~fh~~Ci~~wl~~~---~~CP~Cr~~~~~~~  129 (192)
                      .+...|+||++.|...+. ...++ |||.||..|+..|+..+   .+||+||..+....
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   70 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRITS   70 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCSS
T ss_pred             cCCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcccchh
Confidence            456789999999977553 56677 99999999999999875   67999999886543

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

Probab=99.39  E-value=3.6e-13  Score=89.53  Aligned_cols=48  Identities=25%  Similarity=0.671  Sum_probs=41.6

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTAN  126 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  126 (192)
                      .....|+||++.+..+   ..++ |||.||..||..|+....+||+||.++.
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQNP---VVTK-CRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCSE---EECT-TSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcCe---eEcc-CCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            4567899999998553   4577 9999999999999998889999999985

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

Probab=99.37  E-value=3.6e-13  Score=86.04  Aligned_cols=50  Identities=22%  Similarity=0.570  Sum_probs=41.3

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHc-CCCCCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLL-TNPNCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~~  128 (192)
                      .+...|+||++.+..+   ..++ |||.||..||..|+. .+.+||+||+++..+
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCSP---KQTE-CGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCCEECTTTCCEESSC---CCCS-SSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             CcCCCCCCCChHhcCe---eECC-CCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            4467899999999765   2356 999999999999995 467899999998754

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

Probab=99.37  E-value=5.1e-13  Score=86.88  Aligned_cols=51  Identities=24%  Similarity=0.645  Sum_probs=41.5

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHc---CCCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLL---TNPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~---~~~~CP~Cr~~~~~~~  129 (192)
                      .+...|+||++.+..+   ..++ |||.||..||..|+.   .+..||+||+++....
T Consensus        18 ~~~~~C~IC~~~~~~~---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           18 QEEVICPICLDILQKP---VTID-CGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCCBCTTTCSBCSSE---EECT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             ccCCEeccCCcccCCe---EEcC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            4567899999998643   4567 999999999999997   3557999999986543

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

Probab=99.36  E-value=2.7e-13  Score=99.20  Aligned_cols=48  Identities=33%  Similarity=0.922  Sum_probs=41.6

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSR  128 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  128 (192)
                      +..|+||++.|..+   ..++ |||.||..||..|+..+.+||+||.++...
T Consensus        53 ~~~C~iC~~~~~~~---~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           53 ELQCIICSEYFIEA---VTLN-CAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             HSBCTTTCSBCSSE---EEET-TSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             cCCCcccCcccCCc---eECC-CCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            45799999998654   5577 999999999999999999999999998654

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

Probab=99.34  E-value=8.2e-13  Score=86.37  Aligned_cols=51  Identities=25%  Similarity=0.707  Sum_probs=41.1

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC--CCCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN--PNCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~--~~CP~Cr~~~~~~  128 (192)
                      .+...|+||++.|..+   ..++.|||.||..||..|+..+  .+||+||+++...
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~   65 (74)
T 2yur_A           13 PDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSP   65 (74)
T ss_dssp             CGGGSCSSSCCCCTTC---EECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCT
T ss_pred             CCCCCCcCCChHHhCC---eEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCc
Confidence            4567899999999764   4455599999999999999765  6899999976443

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

Probab=99.34  E-value=7.4e-13  Score=86.46  Aligned_cols=51  Identities=25%  Similarity=0.707  Sum_probs=42.1

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC--CCCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN--PNCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~--~~CP~Cr~~~~~~  128 (192)
                      ....+|+||++.+..+..+.  . |+|.||..||.+||+++  .+||+||+++...
T Consensus        13 ~~i~~C~IC~~~i~~g~~C~--~-C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~   65 (74)
T 2ct0_A           13 DAVKICNICHSLLIQGQSCE--T-CGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE   65 (74)
T ss_dssp             SSSCBCSSSCCBCSSSEECS--S-SCCEECHHHHHHHSTTCSSCCCTTTCSCCCSC
T ss_pred             CCCCcCcchhhHcccCCccC--C-CCchhhHHHHHHHHHhcCCCCCCCCcCcCCCC
Confidence            34567999999998764333  4 99999999999999887  7899999998654

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

Probab=99.32  E-value=1.4e-12  Score=85.93  Aligned_cols=51  Identities=14%  Similarity=0.428  Sum_probs=42.7

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~  129 (192)
                      .+...|+||++.|..+   ..++ |||.||..||..|+.. +.+||+||.++....
T Consensus         6 ~~~~~C~IC~~~~~~P---v~~~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~   57 (78)
T 1t1h_A            6 PEYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLHAG   57 (78)
T ss_dssp             SSSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCC
T ss_pred             cccCCCCCccccccCC---EEcC-CCCeecHHHHHHHHHHCcCCCCCCcCCCChhh
Confidence            4567899999998654   4467 9999999999999987 778999999986543

>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=99.31  E-value=7.5e-13  Score=91.62  Aligned_cols=51  Identities=24%  Similarity=0.667  Sum_probs=42.0

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC-CCCcccccccccCC
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN-PNCPICRSTANSRR  129 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~-~~CP~Cr~~~~~~~  129 (192)
                      +...|+||++.|..+  +..++ |||.||..||..|+..+ .+||+||.++....
T Consensus        21 ~~~~C~IC~~~~~~p--~~~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (100)
T 3lrq_A           21 EVFRCFICMEKLRDA--RLCPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRE   72 (100)
T ss_dssp             HHTBCTTTCSBCSSE--EECTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCCCCccCCccccCc--cccCC-CCChhhHHHHHHHHHHCcCCCCCCCCcCCHHH
Confidence            456799999998653  33367 99999999999999887 68999999986644

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

Probab=99.30  E-value=8.4e-13  Score=95.16  Aligned_cols=54  Identities=30%  Similarity=0.708  Sum_probs=45.6

Q ss_pred             CCCCcccccCccccCC----CceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKG----DKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      .+...|+||++.|..+    ..+..++ |||.||..||..|+..+.+||+||+.+....
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKR   62 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBCTTTC
T ss_pred             CCCCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcCcccc
Confidence            4567899999998653    4456677 9999999999999999999999999987654

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

Probab=99.30  E-value=2.5e-12  Score=85.67  Aligned_cols=50  Identities=28%  Similarity=0.672  Sum_probs=42.2

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC------CCCCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT------NPNCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~------~~~CP~Cr~~~~~~  128 (192)
                      .+...|+||++.+..+   ..++ |||.||..|+..|+..      ...||+||..+...
T Consensus        17 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           17 KEEVTCPICLELLKEP---VSAD-CNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             CTTTSCTTTCSCCSSC---EECT-TSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTT
T ss_pred             ccCCCCcCCChhhCcc---eeCC-CCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHH
Confidence            4567899999998665   4577 9999999999999987      56799999988654

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

Probab=99.29  E-value=2e-12  Score=82.25  Aligned_cols=52  Identities=23%  Similarity=0.551  Sum_probs=41.2

Q ss_pred             CCcccccCc-cccCCCce-EEcCCCCCcccHHhHHHHHcC-CCCCcccccccccCC
Q 040080           77 PIECAVCLD-KFNKGDKC-RLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRR  129 (192)
Q Consensus        77 ~~~C~IC~~-~~~~~~~~-~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~  129 (192)
                      +..|+||++ .+..+... ..++ |||.||..||..|+.. +..||+||.++....
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   57 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKSN   57 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCC
T ss_pred             CCcCCcCCCCccCCCccCeecCC-CCCHhHHHHHHHHHHcCCCcCCCCCCcccccc
Confidence            567999999 77665433 3466 9999999999999765 467999999987644

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

Probab=99.28  E-value=2.8e-12  Score=85.41  Aligned_cols=51  Identities=27%  Similarity=0.711  Sum_probs=42.4

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC------CCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT------NPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~------~~~CP~Cr~~~~~~~  129 (192)
                      .+...|+||++.+..+   ..++ |||.||..|+..|+..      ...||+||..+....
T Consensus        17 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~   73 (85)
T 2ecv_A           17 KEEVTCPICLELLTQP---LSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPEN   73 (85)
T ss_dssp             CCCCCCTTTCSCCSSC---BCCS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSS
T ss_pred             cCCCCCCCCCcccCCc---eeCC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHh
Confidence            4567899999998664   4467 9999999999999977      678999999987643

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

Probab=99.28  E-value=2.3e-12  Score=88.77  Aligned_cols=49  Identities=24%  Similarity=0.729  Sum_probs=41.2

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSR  128 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  128 (192)
                      ...|+||++.|..+  +...+ |||.||..||..|+..+.+||+||..+...
T Consensus        22 ~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   70 (99)
T 2y43_A           22 LLRCGICFEYFNIA--MIIPQ-CSHNYCSLCIRKFLSYKTQCPTCCVTVTEP   70 (99)
T ss_dssp             HTBCTTTCSBCSSE--EECTT-TCCEEEHHHHHHHHTTCCBCTTTCCBCCGG
T ss_pred             CCCcccCChhhCCc--CEECC-CCCHhhHHHHHHHHHCCCCCCCCCCcCChh
Confidence            56799999998653  33336 999999999999999889999999998753

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

Probab=99.27  E-value=8.9e-13  Score=86.96  Aligned_cols=50  Identities=22%  Similarity=0.614  Sum_probs=41.8

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-------CCCCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-------NPNCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-------~~~CP~Cr~~~~~~  128 (192)
                      .+...|+||++.|..+   ..++ |||.||..||..|+..       ...||+||.++...
T Consensus        10 ~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~   66 (79)
T 2egp_A           10 QEEVTCPICLELLTEP---LSLD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFE   66 (79)
T ss_dssp             CCCCEETTTTEECSSC---CCCS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSS
T ss_pred             ccCCCCcCCCcccCCe---eECC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHh
Confidence            4567899999999765   3467 9999999999999986       56799999998654

>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=99.27  E-value=3.2e-12  Score=89.47  Aligned_cols=51  Identities=27%  Similarity=0.670  Sum_probs=42.6

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  128 (192)
                      .+...|+||++.+..  .+...+ |||.||..||..|+..+.+||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           13 NPHLMCVLCGGYFID--ATTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGGTBCTTTSSBCSS--EEEETT-TCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             CCcCCCccCChHHhC--cCEeCC-CCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            346779999999855  344447 999999999999999999999999998754

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

Probab=99.26  E-value=5.7e-12  Score=79.59  Aligned_cols=43  Identities=28%  Similarity=0.719  Sum_probs=36.1

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHc---CCCCCccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLL---TNPNCPIC  121 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~---~~~~CP~C  121 (192)
                      .+...|+||++.+..+   ..++ |||.||..||..|+.   .+.+||+|
T Consensus        18 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           18 QEEVICPICLDILQKP---VTID-CGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCBCTTTCSBCSSC---EECT-TSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             ccCCCCCcCCchhCCe---EEeC-CCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            4567899999998754   4567 999999999999997   45679998

>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=99.24  E-value=4.7e-12  Score=90.78  Aligned_cols=48  Identities=21%  Similarity=0.555  Sum_probs=40.4

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCC-CCccccccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNP-NCPICRSTANS  127 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~-~CP~Cr~~~~~  127 (192)
                      +...|+||++.|..+   ..++ |||.||..||..|+..+. .||+||.++..
T Consensus        51 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           51 ETFQCICCQELVFRP---ITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHTBCTTTSSBCSSE---EECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             cCCCCCcCChHHcCc---EEee-CCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            356799999998654   4567 999999999999998644 89999999976

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

Probab=99.22  E-value=7.6e-12  Score=84.93  Aligned_cols=49  Identities=24%  Similarity=0.727  Sum_probs=40.3

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC--CCCcccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN--PNCPICRSTAN  126 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~--~~CP~Cr~~~~  126 (192)
                      .+...|+||++.|..+   ..++.|||.||..||..|+..+  ..||+||.++.
T Consensus        11 ~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           11 PDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CTTTEETTTTEECSSC---EECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CcCCCCCCCChhhcCc---eECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            5567899999999765   4455599999999999999653  57999999874

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

Probab=99.22  E-value=8.3e-12  Score=77.34  Aligned_cols=43  Identities=28%  Similarity=0.893  Sum_probs=35.5

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHc---CCCCCccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLL---TNPNCPIC  121 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~---~~~~CP~C  121 (192)
                      .+...|+||++.+..+   ..++ |||.||..||..|+.   .+.+||+|
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKEP---VIIE-CGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSSC---CCCS-SCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccCCCCccCCcccCcc---EeCC-CCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            4567899999999765   4467 999999999999954   46679998

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

Probab=99.22  E-value=4.9e-12  Score=91.09  Aligned_cols=54  Identities=30%  Similarity=0.708  Sum_probs=44.7

Q ss_pred             CCCCcccccCccccCC----CceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKG----DKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      .+...|+||++.+...    .....++ |||.||..||.+|+..+++||+||+++..+.
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~  127 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKR  127 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEET-TSBEEEHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCCCccccccccCcceEeCC-CCChhhHHHHHHHHHcCCCCCCCCCcCChhc
Confidence            4567899999998642    3345667 9999999999999999999999999987654

>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=99.20  E-value=9.7e-12  Score=87.30  Aligned_cols=50  Identities=26%  Similarity=0.693  Sum_probs=41.3

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCC---CCcccccccccCCC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNP---NCPICRSTANSRRF  130 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~---~CP~Cr~~~~~~~~  130 (192)
                      ...|+||++.+..+   ..++ |||.||..||..|+..+.   +||+||.++.....
T Consensus        21 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~   73 (112)
T 1jm7_A           21 ILECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL   73 (112)
T ss_dssp             HTSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTC
T ss_pred             CCCCcccChhhcCe---EECC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhc
Confidence            45799999998665   3467 999999999999998754   79999999876543

>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=99.19  E-value=1.1e-11  Score=93.20  Aligned_cols=50  Identities=34%  Similarity=0.732  Sum_probs=41.2

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCcccccccccC
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSR  128 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~  128 (192)
                      ....|+||++.|..  .+..++ |||.||..||..|+.. +..||+||.++...
T Consensus        53 ~~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  103 (165)
T 2ckl_B           53 SELMCPICLDMLKN--TMTTKE-CLHRFCADCIITALRSGNKECPTCRKKLVSK  103 (165)
T ss_dssp             HHHBCTTTSSBCSS--EEEETT-TCCEEEHHHHHHHHHTTCCBCTTTCCBCCSG
T ss_pred             CCCCCcccChHhhC--cCEeCC-CCChhHHHHHHHHHHhCcCCCCCCCCcCCCc
Confidence            34579999999865  344447 9999999999999987 77899999998543

>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=99.19  E-value=7.1e-12  Score=89.16  Aligned_cols=50  Identities=24%  Similarity=0.554  Sum_probs=42.2

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCC-CCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNP-NCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~-~CP~Cr~~~~~~  128 (192)
                      .+...|+||++.+..+   ..++ |||.||..||..|+..+. +||+||.++...
T Consensus        16 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           16 ESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCcCChhhcCe---EECC-cCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            5567899999998654   4567 999999999999998754 899999998764

>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=99.15  E-value=1.9e-11  Score=90.57  Aligned_cols=49  Identities=18%  Similarity=0.507  Sum_probs=41.2

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCC-CCcccccccccC
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNP-NCPICRSTANSR  128 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~-~CP~Cr~~~~~~  128 (192)
                      +...|+||++.|..+   ..++ |||.||..||..|+.... +||+||.++...
T Consensus        77 ~~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQP---VTTE-CFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSSE---EECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhcCC---EEcC-CCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            346799999998654   4477 999999999999998754 799999998765

>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=99.12  E-value=3e-11  Score=85.53  Aligned_cols=50  Identities=24%  Similarity=0.545  Sum_probs=41.9

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCcccccccccCCC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRRF  130 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~~  130 (192)
                      ...|+||++.+..+   ..++ |||.||..||..|+.. +.+||+||.++.....
T Consensus        23 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   73 (116)
T 1rmd_A           23 SISCQICEHILADP---VETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPTDL   73 (116)
T ss_dssp             HTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGC
T ss_pred             CCCCCCCCcHhcCc---EEcC-CCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhc
Confidence            56799999998654   4467 9999999999999987 6789999999876543

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

Probab=99.11  E-value=4e-11  Score=80.48  Aligned_cols=50  Identities=14%  Similarity=0.163  Sum_probs=43.6

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  128 (192)
                      .+...|+||++.|..+   ..++ |||.|+..||..|+..+.+||+||.++...
T Consensus        12 p~~~~CpI~~~~m~dP---V~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~   61 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTDP---VRLP-SGTVMDRSIILRHLLNSPTDPFNRQMLTES   61 (85)
T ss_dssp             CTTTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             chheECcccCchhcCC---eECC-CCCEECHHHHHHHHhcCCCCCCCcCCCChH
Confidence            4567899999999765   5677 999999999999999888999999988654

>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=99.11  E-value=1.4e-11  Score=87.10  Aligned_cols=48  Identities=29%  Similarity=0.750  Sum_probs=40.6

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCccccccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANS  127 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~  127 (192)
                      ++..|+||++.+..+   ..++ |||.||..||..|+.. +..||+||..+..
T Consensus        14 ~~~~C~iC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           14 SECQCGICMEILVEP---VTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHBCTTTCSBCSSC---EECT-TSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCccCCcccCce---eEcC-CCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            356799999998654   4567 9999999999999977 6679999999864

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

Probab=99.09  E-value=1.5e-10  Score=76.39  Aligned_cols=54  Identities=22%  Similarity=0.491  Sum_probs=41.3

Q ss_pred             CCCCcccccCccccCCCceE-EcCCCCCcccHHhHHHHHcC-CCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCR-LLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~-~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~  129 (192)
                      .++..|+||++.+...+... .++ |||.||..|+..|+.. +..||+||+++..+.
T Consensus         9 ~~~~~CpICle~~~~~d~~~~p~~-CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~   64 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPEDP   64 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTTCCSST-TSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCS
T ss_pred             ccCCcCCccCccCccccccccccC-CCCCcCHHHHHHHHhcCCCCCCCCCCccCCCc
Confidence            45678999999886432222 235 9999999999998754 567999999987654

>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=99.09  E-value=5.4e-11  Score=82.25  Aligned_cols=51  Identities=16%  Similarity=0.164  Sum_probs=43.9

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      .+...|+||++.|..+   ..++ |||.|+..||..|+..+.+||+||.++....
T Consensus        27 p~~~~CpI~~~~m~dP---V~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~   77 (100)
T 2kre_A           27 PDEFRDPLMDTLMTDP---VRLP-SGTIMDRSIILRHLLNSPTDPFNRQTLTESM   77 (100)
T ss_dssp             STTTBCTTTCSBCSSE---EEET-TTEEEEHHHHHHHTTSCSBCSSSCCBCCTTS
T ss_pred             cHhhCCcCccCcccCC---eECC-CCCEEchHHHHHHHHcCCCCCCCCCCCChhh
Confidence            4567899999999765   5577 9999999999999998889999999987543

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

Probab=99.07  E-value=9e-11  Score=80.83  Aligned_cols=51  Identities=14%  Similarity=0.176  Sum_probs=43.8

Q ss_pred             CCCCcccccCccccCCCceEEcCCCC-CcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICN-HSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~-H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      .+.+.|+||++.|..+   ..++ || |.|+..||..|+..+.+||+||.++....
T Consensus        20 p~~~~CpI~~~~m~dP---V~~~-cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~   71 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCDP---VVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQ   71 (98)
T ss_dssp             CTTTBCTTTCSBCSSE---EECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTT
T ss_pred             cHhcCCcCccccccCC---eECC-CCCeEECHHHHHHHHHhCCCCCCCCCCCChhh
Confidence            4567899999999765   5577 99 99999999999998889999999987643

>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=99.06  E-value=5.1e-11  Score=75.69  Aligned_cols=48  Identities=21%  Similarity=0.507  Sum_probs=39.6

Q ss_pred             CCCcccccCccccCCCceEEc--CCCCCc-ccHHhHHHHHcCCCCCccccccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLL--PICNHS-FHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~--~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      ++..|+||++...+.   ..+  | |||. |+..|+..|...+..||+||+++..
T Consensus         7 ~~~~C~IC~~~~~~~---~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~   57 (64)
T 2vje_A            7 AIEPCVICQGRPKNG---CIVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQM   57 (64)
T ss_dssp             GGSCCTTTSSSCSCE---EEEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCCE
T ss_pred             CcCCCCcCCCCCCCE---EEECCC-CCChhhHHHHHHHHHHcCCcCCCcCcchhc
Confidence            456799999986432   444  8 9999 8999999999888899999998853

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B*

Probab=99.05  E-value=5.1e-11  Score=75.44  Aligned_cols=51  Identities=18%  Similarity=0.369  Sum_probs=39.8

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCc-ccHHhHHHHHcCCCCCccccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHS-FHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      .....|.||++...+. .+..+| |||. ||..|+..|...+..||+||+++..
T Consensus         5 ~~~~~C~IC~~~~~~~-~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~   56 (63)
T 2vje_B            5 NLLKPCSLCEKRPRDG-NIIHGR-TGHLVTCFHCARRLKKAGASCPICKKEIQL   56 (63)
T ss_dssp             GGGSBCTTTSSSBSCE-EEEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCCE
T ss_pred             CcCCCCcccCCcCCCe-EEEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhhc
Confidence            3456799999986432 122238 9998 9999999999888899999998853

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

Probab=99.04  E-value=5.7e-11  Score=87.13  Aligned_cols=49  Identities=20%  Similarity=0.548  Sum_probs=40.9

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCC-CCccccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNP-NCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~-~CP~Cr~~~~~  127 (192)
                      .+...|+||++.+..+   ..++ |||.||..||..|+.... +||+||.++..
T Consensus        29 ~~~~~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   78 (141)
T 3knv_A           29 EAKYLCSACRNVLRRP---FQAQ-CGHRYCSFCLASILSSGPQNCAACVHEGIY   78 (141)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHGGGSCEECHHHHHTTCC
T ss_pred             CcCcCCCCCChhhcCc---EECC-CCCccCHHHHHHHHhcCCCCCCCCCCcccc
Confidence            4567899999998665   4467 999999999999998654 79999998743

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

Probab=99.03  E-value=1.2e-10  Score=98.13  Aligned_cols=49  Identities=22%  Similarity=0.723  Sum_probs=41.5

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHc-CCCCCcccccccccC
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLL-TNPNCPICRSTANSR  128 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~~  128 (192)
                      ....|+||++.+..   ...+| |||.||..|+..|+. .+.+||+||+++...
T Consensus       331 ~~~~C~ICle~~~~---pv~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          331 TFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SSSBCTTTSSSBCC---EEEET-TCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCCCccCcCCCC---eEEeC-CCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            34689999999744   36678 999999999999998 678899999998664

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

Probab=99.03  E-value=7.6e-11  Score=72.82  Aligned_cols=47  Identities=28%  Similarity=0.639  Sum_probs=38.7

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  128 (192)
                      .+...|+||++.|..+   ..++ |||.||..|+..|   ...||+||+.+...
T Consensus         4 ~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCCSSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             ccCCCceEeCCccCCe---EEcC-CCCcccHHHHccC---CCCCCcCCcEeecC
Confidence            4567799999999765   5577 9999999999884   56799999988654

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

Probab=99.00  E-value=9.7e-11  Score=83.09  Aligned_cols=47  Identities=26%  Similarity=0.651  Sum_probs=39.3

Q ss_pred             CCCcccccCccccCCCceEEc-CCCCCcccHHhHHHHHcCCCCCcccccccccC
Q 040080           76 SPIECAVCLDKFNKGDKCRLL-PICNHSFHAQCVDAWLLTNPNCPICRSTANSR  128 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~-~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  128 (192)
                      +...|+||++.|..+   ..+ + |||.||..||..|+.  ..||+||..+...
T Consensus        21 ~~~~C~IC~~~~~~p---v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~   68 (117)
T 1jm7_B           21 KLLRCSRCTNILREP---VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAWIQ   68 (117)
T ss_dssp             HTTSCSSSCSCCSSC---BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCSCS
T ss_pred             hCCCCCCCChHhhCc---cEeCC-CCCHHHHHHHHHHhc--CCCcCCCCcCccc
Confidence            356799999999665   445 6 999999999999987  7899999998543

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

Probab=98.98  E-value=1.1e-10  Score=96.22  Aligned_cols=54  Identities=22%  Similarity=0.621  Sum_probs=41.0

Q ss_pred             CCCCcccccCccccCCCceE----EcCCCCCcccHHhHHHHHcCC-----------CCCcccccccccC
Q 040080           75 SSPIECAVCLDKFNKGDKCR----LLPICNHSFHAQCVDAWLLTN-----------PNCPICRSTANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~----~~~~C~H~fh~~Ci~~wl~~~-----------~~CP~Cr~~~~~~  128 (192)
                      ....+|+||++.+.....+.    ..+.|+|.||..|+.+|+++.           .+||+||+++..+
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~s  374 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTS  374 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCcc
Confidence            45678999999987633222    123499999999999999752           4699999998643

>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=98.92  E-value=3.9e-10  Score=84.96  Aligned_cols=51  Identities=24%  Similarity=0.518  Sum_probs=42.4

Q ss_pred             CCCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC-CCCcccccccccC
Q 040080           74 GSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN-PNCPICRSTANSR  128 (192)
Q Consensus        74 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~-~~CP~Cr~~~~~~  128 (192)
                      ..+...|+||++.+..+   ..++ |||.||..||..|+..+ .+||+||.++...
T Consensus        15 ~~~~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           15 LESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             CCGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCChhhcCc---EECC-CCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            35567899999998665   4467 99999999999999764 4899999988764

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

Probab=98.92  E-value=2.5e-10  Score=74.50  Aligned_cols=43  Identities=28%  Similarity=0.705  Sum_probs=36.4

Q ss_pred             CCcccccCccccCCCceEEcCCCCCc-ccHHhHHHHHcCCCCCccccccccc
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHS-FHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      ...|+||++.+..   ...+| |||. ||..|+..|    ..||+||+++..
T Consensus        24 ~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           24 EKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HTBCTTTSSSBCC---EEEET-TCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             CCCCCCCCCCCCC---EEEcC-CCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            4579999998744   35678 9999 999999998    789999998864

>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=98.85  E-value=1.3e-09  Score=87.61  Aligned_cols=51  Identities=10%  Similarity=0.215  Sum_probs=42.4

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~  129 (192)
                      .....|+||++.|..+   ..++ |||.||..||..|+.. +.+||+||.++....
T Consensus       206 ~~~~~c~i~~~~~~dP---v~~~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~  257 (281)
T 2c2l_A          206 PDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQ  257 (281)
T ss_dssp             CSTTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCGGG
T ss_pred             CcccCCcCcCCHhcCC---eECC-CCCEECHHHHHHHHHHCCCCCcCCCCCCchhc
Confidence            4577899999999665   5577 9999999999999976 445999999986543

>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=98.83  E-value=8e-10  Score=75.40  Aligned_cols=51  Identities=20%  Similarity=0.505  Sum_probs=39.4

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC------CCCcc--cccc-cccC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN------PNCPI--CRST-ANSR  128 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~------~~CP~--Cr~~-~~~~  128 (192)
                      .....|+||++.|..+  + .++.|||.|+..||..|+..+      .+||+  |+.. +...
T Consensus         5 ~~~~~CPI~~~~~~dP--V-~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~~   64 (94)
T 2yu4_A            5 SSGFTCPITKEEMKKP--V-KNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKS   64 (94)
T ss_dssp             SSCCBCTTTCSBCSSE--E-EESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCGG
T ss_pred             CcEeECcCcCchhcCC--E-EcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCHh
Confidence            3467899999999654  3 343399999999999999764      47999  9876 5443

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.79  E-value=3.5e-09  Score=66.21  Aligned_cols=49  Identities=24%  Similarity=0.687  Sum_probs=37.5

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCC-----cccHHhHHHHHcC--CCCCccccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNH-----SFHAQCVDAWLLT--NPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H-----~fh~~Ci~~wl~~--~~~CP~Cr~~~~~  127 (192)
                      .+...|.||++...  +.. .+| |.+     .||..|+..|+..  +.+||+||.++..
T Consensus         4 ~~~~~CrIC~~~~~--~~l-~~P-C~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            4 EDVPVCWICNEELG--NER-FRA-CGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEECS--CCC-CCS-CCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCEeEEeecCCC--Cce-ecC-cCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            45668999999843  233 466 664     8999999999965  5779999998753

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.76  E-value=2.9e-09  Score=69.46  Aligned_cols=43  Identities=28%  Similarity=0.682  Sum_probs=35.0

Q ss_pred             CCcccccCccccCCCceEEcCCCCCc-ccHHhHHHHHcCCCCCccccccccc
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHS-FHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      ...|+||++.+...   ..+| |||. ||..|+..    ...||+||.++..
T Consensus        25 ~~~C~IC~~~~~~~---~~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i~~   68 (75)
T 2ecg_A           25 EKLCKICMDRNIAI---VFVP-CGHLVTCKQCAEA----VDKCPMCYTVITF   68 (75)
T ss_dssp             HHSCSSSCSSCCCB---CCSS-SCCCCBCHHHHHH----CSBCTTTCCBCCC
T ss_pred             CCCCCcCCCCCCCE---EEec-CCCHHHHHHHhhC----CCCCccCCceecC
Confidence            45699999987543   5578 9999 99999965    3689999998865

>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=6.3e-09  Score=66.69  Aligned_cols=45  Identities=31%  Similarity=0.764  Sum_probs=37.0

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCc-ccHHhHHHHHcCCCCCccccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHS-FHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      .+...|.||++...   .+..+| |||. ||..|+..    ...||+||+++..
T Consensus        13 ~~~~~C~IC~~~~~---~~v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i~~   58 (68)
T 2ea5_A           13 ENSKDCVVCQNGTV---NWVLLP-CRHTCLCDGCVKY----FQQCPMCRQFVQE   58 (68)
T ss_dssp             CCSSCCSSSSSSCC---CCEETT-TTBCCSCTTHHHH----CSSCTTTCCCCCC
T ss_pred             CCCCCCCCcCcCCC---CEEEEC-CCChhhhHHHHhc----CCCCCCCCcchhc
Confidence            44678999999853   457788 9999 99999984    4689999998865

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

Probab=98.74  E-value=4e-09  Score=80.00  Aligned_cols=51  Identities=10%  Similarity=0.184  Sum_probs=42.4

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC-CCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN-PNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~-~~CP~Cr~~~~~~~  129 (192)
                      .....||||++.|..+   ..++ |||.|+..||..|+..+ .+||+|+.++....
T Consensus       104 p~~f~CPI~~elm~DP---V~~~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~  155 (179)
T 2f42_A          104 PDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQ  155 (179)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             cHhhcccCccccCCCC---eECC-CCCEECHHHHHHHHHhCCCCCCCCcCCCChhh
Confidence            5677899999999765   5567 99999999999999763 57999999886543

>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=98.73  E-value=4.2e-09  Score=71.65  Aligned_cols=51  Identities=18%  Similarity=0.541  Sum_probs=40.4

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC--------CCCCcc--cccc--ccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT--------NPNCPI--CRST--ANS  127 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--------~~~CP~--Cr~~--~~~  127 (192)
                      +...|+||++.+..+..+...+ |||.||..|+..|+..        .-.||.  |+..  +..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~-CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~   66 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQE   66 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECH
T ss_pred             CCcCCcccCcccccccceEcCC-CCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCH
Confidence            4567999999987765555557 9999999999999863        135999  9988  544

>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=98.64  E-value=6.9e-09  Score=68.48  Aligned_cols=44  Identities=27%  Similarity=0.742  Sum_probs=36.2

Q ss_pred             CCcccccCccccCCCceEEcCCCCCc-ccHHhHHHHHcCCCCCcccccccccC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHS-FHAQCVDAWLLTNPNCPICRSTANSR  128 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~~  128 (192)
                      ...|+||++.+.   ....+| |||. ||..|+..|    ..||+||.++...
T Consensus        18 ~~~C~IC~~~~~---~~v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~   62 (79)
T 2yho_A           18 AMLCMVCCEEEI---NSTFCP-CGHTVCCESCAAQL----QSCPVCRSRVEHV   62 (79)
T ss_dssp             HTBCTTTSSSBC---CEEEET-TCBCCBCHHHHTTC----SBCTTTCCBCCEE
T ss_pred             CCEeEEeCcccC---cEEEEC-CCCHHHHHHHHHhc----CcCCCCCchhhCe
Confidence            457999999864   346778 9999 999999887    3899999988654

>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=98.58  E-value=1.6e-08  Score=63.36  Aligned_cols=51  Identities=12%  Similarity=0.156  Sum_probs=41.8

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCCC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRF  130 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~  130 (192)
                      ...|+||++.+.++  +...+ |||.|...||.+|+..+.+||+++.++.....
T Consensus         3 ~~~CpIs~~~m~dP--V~~~~-sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~L   53 (61)
T 2bay_A            3 HMLCAISGKVPRRP--VLSPK-SRTIFEKSLLEQYVKDTGNDPITNEPLSIEEI   53 (61)
T ss_dssp             -CCCTTTCSCCSSE--EEETT-TTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGC
T ss_pred             eEEecCCCCCCCCC--EEeCC-CCcEEcHHHHHHHHHhCCCCcCCcCCCChhhc
Confidence            35799999999754  33326 99999999999999988889999999876553

>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=98.56  E-value=3.8e-08  Score=78.46  Aligned_cols=53  Identities=21%  Similarity=0.530  Sum_probs=42.0

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC--CCCcc--cccccccCCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN--PNCPI--CRSTANSRRF  130 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~--~~CP~--Cr~~~~~~~~  130 (192)
                      .....||||++.|..  .+.... |||.|+..||..|+..+  .+||+  ||..+.....
T Consensus       179 ~~el~CPIcl~~f~D--PVts~~-CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL  235 (267)
T 3htk_C          179 KIELTCPITCKPYEA--PLISRK-CNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDF  235 (267)
T ss_dssp             BCCSBCTTTSSBCSS--EEEESS-SCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGE
T ss_pred             ceeeECcCccCcccC--CeeeCC-CCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhC
Confidence            345679999999955  454456 99999999999999764  46999  9998866543

>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=98.49  E-value=2.1e-08  Score=83.59  Aligned_cols=44  Identities=32%  Similarity=0.796  Sum_probs=37.0

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCc-ccHHhHHHHHcCCCCCccccccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHS-FHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      +...|+||++.+..   ...+| |||. ||..|+..|    ..||+||.++..
T Consensus       294 ~~~~C~IC~~~~~~---~v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          294 EERTCKVCMDKEVS---VVFIP-CGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             TTCBCTTTSSSBCC---EEEET-TCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             CCCCCCccCCcCCc---eEEcC-CCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            35679999999754   35678 9999 999999988    679999998864

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

Probab=98.29  E-value=4.6e-07  Score=61.50  Aligned_cols=46  Identities=24%  Similarity=0.508  Sum_probs=37.5

Q ss_pred             cccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCccccccccc
Q 040080           79 ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANS  127 (192)
Q Consensus        79 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~  127 (192)
                      .|.+|--.+.  ...+..| |+|+||.+|+..|.++ .++||.|+.++..
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            4788877763  3457788 9999999999999855 6889999998854

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

Probab=98.28  E-value=1e-06  Score=69.76  Aligned_cols=51  Identities=22%  Similarity=0.531  Sum_probs=41.1

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCC--CCcccccccccCC
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNP--NCPICRSTANSRR  129 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~--~CP~Cr~~~~~~~  129 (192)
                      ....|.||.+-+..+.   .-+.|+|.||..|+..|++++.  .||.|+..|....
T Consensus       179 ~i~~C~iC~~iv~~g~---~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~  231 (238)
T 3nw0_A          179 AVKICNICHSLLIQGQ---SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEI  231 (238)
T ss_dssp             TCCBCTTTCSBCSSCE---ECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCC
T ss_pred             CCCcCcchhhHHhCCc---ccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCC
Confidence            4678999999987662   2334999999999999998754  7999999986653

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

Probab=95.88  E-value=0.0066  Score=38.09  Aligned_cols=48  Identities=23%  Similarity=0.409  Sum_probs=34.0

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC----CCCcccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN----PNCPICRSTAN  126 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP~Cr~~~~  126 (192)
                      .....|.||.+.   ++. ..-..|...||..|+++.+..-    -.||.|.....
T Consensus        10 ~~~~~C~vC~~~---~~l-l~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~   61 (66)
T 2lri_C           10 APGARCGVCGDG---TDV-LRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDVT   61 (66)
T ss_dssp             CTTCCCTTTSCC---TTC-EECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCCC
T ss_pred             CCCCCcCCCCCC---CeE-EECCCCCCceecccCCCccCcCCCCCEECccccCCCc
Confidence            345679999854   443 3334499999999999887653    24999976543

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=95.11  E-value=0.017  Score=38.88  Aligned_cols=34  Identities=18%  Similarity=0.427  Sum_probs=25.2

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHH
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAW  111 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w  111 (192)
                      +..|.||.+.+.......-+. |+|.||..|+..+
T Consensus         3 e~~C~~C~~~~~~~av~~C~~-C~~~~C~~Cl~~~   36 (101)
T 2jun_A            3 KVLCQFCDQDPAQDAVKTCVT-CEVSYCDECLKAT   36 (101)
T ss_dssp             CCBCTTCCSSSCCBCCEEETT-TTEEECHHHHHHH
T ss_pred             CCCCcCCCCCCCCCceEECCc-CChHHhHHHCHHH
Confidence            467999998653332333377 9999999999984

>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=93.99  E-value=0.018  Score=35.56  Aligned_cols=50  Identities=22%  Similarity=0.536  Sum_probs=33.9

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHc-----CCCCCcccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLL-----TNPNCPICRST  124 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-----~~~~CP~Cr~~  124 (192)
                      .+...|+||...+..+...+.-..|...||..|+.--..     ..-.||.|+..
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            445679999998865444444445999999999864221     23459999763

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=93.35  E-value=0.027  Score=35.91  Aligned_cols=52  Identities=19%  Similarity=0.335  Sum_probs=35.2

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC----CCCCccccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT----NPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~~~~  127 (192)
                      .+...|.||..... +...+.-..|...||..|+..-...    .-.||.|+..+..
T Consensus        16 ~~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~k   71 (75)
T 2k16_A           16 NQIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKK   71 (75)
T ss_dssp             CEEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHCS
T ss_pred             CCCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchhh
Confidence            44556999988753 3334444459999999999764432    2349999887654

>2l2t_A Receptor tyrosine-protein kinase ERBB-4; transmembrane dimer, membrane domain, membrane protei; NMR {Homo sapiens}

Probab=93.16  E-value=0.19  Score=28.69  Aligned_cols=27  Identities=19%  Similarity=0.011  Sum_probs=13.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 040080            3 MAIIISVIFLFLGIGALIFIHVCIVAR   29 (192)
Q Consensus         3 ~~iil~~~~~~~~i~~l~~~~~~~~~~   29 (192)
                      .+|+.+++..+++++++.+..++++++
T Consensus        10 ~aIA~gVVgGv~~v~ii~~~~~~~~RR   36 (44)
T 2l2t_A           10 PLIAAGVIGGLFILVIVGLTFAVYVRR   36 (44)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             ceEEEeehHHHHHHHHHHHHHHHHhhh
Confidence            355666665455555544444344433

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

Probab=91.81  E-value=0.11  Score=31.70  Aligned_cols=45  Identities=27%  Similarity=0.620  Sum_probs=31.3

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC----CCCCccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT----NPNCPICRS  123 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~  123 (192)
                      ..+..|.+|...   + .+..-..|...||..|+..-+..    .-.||.|+.
T Consensus         9 ~~~~~C~vC~~~---g-~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A            9 DHQDYCEVCQQG---G-EIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CCCSSCTTTSCC---S-SEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCCccCCCC---C-cEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            446679999873   3 33444449999999999875533    234999975

>2ks1_B Epidermal growth factor receptor; ERBB1, ERBB2, transmembrane, heterodimer, complex, tyrosine receptor, bicelles, transferase; NMR {Homo sapiens}

Probab=91.51  E-value=0.17  Score=28.93  Aligned_cols=23  Identities=9%  Similarity=-0.063  Sum_probs=9.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 040080            5 IIISVIFLFLGIGALIFIHVCIV   27 (192)
Q Consensus         5 iil~~~~~~~~i~~l~~~~~~~~   27 (192)
                      |+.+++..+++++++++..++++
T Consensus        13 IA~gVVgGv~~~~ii~~~~~~~~   35 (44)
T 2ks1_B           13 IATGMVGALLLLLVVALGIGLFM   35 (44)
T ss_dssp             STHHHHHHHHHHHHHHHHHHHHH
T ss_pred             EEeehhHHHHHHHHHHHHHHHHh
Confidence            44455544444444444333333

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=91.50  E-value=0.079  Score=39.89  Aligned_cols=48  Identities=19%  Similarity=0.405  Sum_probs=33.9

Q ss_pred             CcccccCccccCCCc---eEEcCCCCCcccHHhHHH------HHc-----CCCCCccccccc
Q 040080           78 IECAVCLDKFNKGDK---CRLLPICNHSFHAQCVDA------WLL-----TNPNCPICRSTA  125 (192)
Q Consensus        78 ~~C~IC~~~~~~~~~---~~~~~~C~H~fh~~Ci~~------wl~-----~~~~CP~Cr~~~  125 (192)
                      ..|+||...|..++.   .+.-..|...||..|+.-      -+.     ..-.||.|+..-
T Consensus         3 ~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~   64 (183)
T 3lqh_A            3 NFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERH   64 (183)
T ss_dssp             CBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSS
T ss_pred             CcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCC
Confidence            459999999987752   444445999999999842      111     145799998754

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=90.93  E-value=0.038  Score=33.21  Aligned_cols=45  Identities=29%  Similarity=0.578  Sum_probs=30.6

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC----CCCCccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT----NPNCPICRS  123 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~  123 (192)
                      ..+..|.+|...   +..+. -..|...||..|+.+-+..    .-.||.|+.
T Consensus         7 ~~~~~C~vC~~~---g~ll~-Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            7 GHEDFCSVCRKS---GQLLM-CDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SSCCSCSSSCCS---SCCEE-CSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCccCCCC---CeEEE-cCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            456679999875   43333 3349999999999865433    223988864

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=90.70  E-value=0.12  Score=30.22  Aligned_cols=44  Identities=34%  Similarity=0.687  Sum_probs=28.4

Q ss_pred             cccccCccccCCCceEEcCCCCCcccHHhHHHHHcC----CCCCccccc
Q 040080           79 ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT----NPNCPICRS  123 (192)
Q Consensus        79 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~  123 (192)
                      .|.||...-..+ .+..-..|...||..|+.+=+..    .-.||.|+.
T Consensus         2 ~C~vC~~~~~~~-~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCC-CEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            488888754333 33333449999999999754433    224999964

>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=90.46  E-value=0.34  Score=31.58  Aligned_cols=35  Identities=20%  Similarity=0.409  Sum_probs=22.8

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHH
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAW  111 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w  111 (192)
                      ..+..|.||-.- ...+.... ..|+-+||..|+.+-
T Consensus        13 ~~D~~C~VC~~~-t~~~l~pC-RvC~RvfH~~CL~r~   47 (89)
T 1wil_A           13 VNDEMCDVCEVW-TAESLFPC-RVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTTCCC-CSSCCSSC-SSSSSCCCHHHHHHH
T ss_pred             CCCcccCccccc-cccceecc-ccccccccHhhcccc
Confidence            346679999742 22222222 239999999999985

>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=90.33  E-value=0.071  Score=32.63  Aligned_cols=47  Identities=30%  Similarity=0.558  Sum_probs=31.3

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC----CCCCccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT----NPNCPICRSTA  125 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~~  125 (192)
                      .....|.+|...   ++. ..-..|...||..|+.+-+..    .-.||.|+...
T Consensus         7 ~~~~~C~vC~~~---g~l-l~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            7 HHMEFCRVCKDG---GEL-LCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---SSC-BCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCCcCCCCCCC---CCE-EEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            456679999863   333 333349999999999864433    22499997643

>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=90.02  E-value=0.45  Score=30.47  Aligned_cols=51  Identities=24%  Similarity=0.548  Sum_probs=32.3

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHH---Hc--CCCCCccccccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAW---LL--TNPNCPICRSTANS  127 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w---l~--~~~~CP~Cr~~~~~  127 (192)
                      ....| ||...+......+.-..|...||..|+.--   ..  ..-.||.|+....+
T Consensus        11 ~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~~~   66 (79)
T 1wep_A           11 VPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFGP   66 (79)
T ss_dssp             CCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSCS
T ss_pred             CccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCcccccCC
Confidence            34456 898887533344444449999999999421   11  23459999876543

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=89.82  E-value=0.071  Score=39.94  Aligned_cols=47  Identities=28%  Similarity=0.510  Sum_probs=32.7

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC----CCCCcccccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT----NPNCPICRSTAN  126 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~~~  126 (192)
                      ++..|.+|...   ++. ..-..|...||..|+.+-+..    .-.||.|+..-.
T Consensus         3 ~~~~C~~C~~~---g~l-l~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   53 (184)
T 3o36_A            3 NEDWCAVCQNG---GEL-LCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSK   53 (184)
T ss_dssp             SCSSCTTTCCC---SSC-EECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSSS
T ss_pred             CCCccccCCCC---Cee-eecCCCCcccCccccCCCCCCCCCCCEECccccCccc
Confidence            35679999854   443 333449999999999876654    234999987543

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=89.81  E-value=0.05  Score=33.14  Aligned_cols=48  Identities=27%  Similarity=0.515  Sum_probs=32.8

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC----CCCCccccccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT----NPNCPICRSTANS  127 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~~~~  127 (192)
                      .+..|.+|...   +..+. -..|...||..|+.+=+..    .-.||.|......
T Consensus         4 ~~~~C~vC~~~---g~ll~-Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~~   55 (60)
T 2puy_A            4 HEDFCSVCRKS---GQLLM-CDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQMLK   55 (60)
T ss_dssp             CCSSCTTTCCC---SSCEE-CSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHHH
T ss_pred             CCCCCcCCCCC---CcEEE-cCCCCcCEECCcCCCCcCCCCCCceEChhccChhhc
Confidence            35679999874   43333 3349999999999864433    2249999876544

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=89.78  E-value=0.054  Score=41.43  Aligned_cols=47  Identities=30%  Similarity=0.511  Sum_probs=33.1

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC----CCCccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN----PNCPICRSTA  125 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP~Cr~~~  125 (192)
                      ..+..|.+|...   + .+..-..|...||..|+.+-+...    -.||.|+..-
T Consensus         5 ~~~~~C~~C~~~---g-~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            5 PNEDWCAVCQNG---G-DLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             SSCSSBTTTCCC---E-EEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCCCCC---C-ceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            445679999854   3 344444599999999998766542    3499998744

>2jwa_A Receptor tyrosine-protein kinase ERBB-2; transmembrane helix dimer, protein kinase receptor membrane domain, ATP-binding, glycoprotein; NMR {Homo sapiens} PDB: 2ks1_A

Probab=89.38  E-value=0.81  Score=26.01  Aligned_cols=7  Identities=43%  Similarity=0.411  Sum_probs=2.9

Q ss_pred             HHHHHHH
Q 040080            5 IIISVIF   11 (192)
Q Consensus         5 iil~~~~   11 (192)
                      |+.+++.
T Consensus        14 Ia~~vVG   20 (44)
T 2jwa_A           14 IISAVVG   20 (44)
T ss_dssp             HHHHHHH
T ss_pred             hHHHHHH
Confidence            4444444

>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=88.62  E-value=0.46  Score=27.86  Aligned_cols=44  Identities=18%  Similarity=0.260  Sum_probs=28.6

Q ss_pred             cccccCccccCCCceEEcC-CCCCcccHHhHHHH----HcCCCCCcccc
Q 040080           79 ECAVCLDKFNKGDKCRLLP-ICNHSFHAQCVDAW----LLTNPNCPICR  122 (192)
Q Consensus        79 ~C~IC~~~~~~~~~~~~~~-~C~H~fh~~Ci~~w----l~~~~~CP~Cr  122 (192)
                      .|.+|...+..+...+.-. .|...||..|+.--    ...+-.||.|+
T Consensus         4 ~cc~C~~p~~~~~~mI~Cd~~C~~WfH~~Cvgl~~~~~~~~~~~C~~C~   52 (52)
T 2kgg_A            4 AAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA   52 (52)
T ss_dssp             SCTTCCCCCCTTCCEEECTTTTCCEEETTTTTCCHHHHHHSCCCCSCC-
T ss_pred             cCCCCcCccCCCCcEEEeCCCCCccCcccccCCCccccCCCCEECCCCC
Confidence            4788888876554444444 48889999998421    12355688885

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=88.21  E-value=0.25  Score=31.17  Aligned_cols=50  Identities=18%  Similarity=0.475  Sum_probs=33.0

Q ss_pred             CCCCcccccCccc-cCCCceEEcCCCCCcccHHhHHHHHcC--CCCCcccccc
Q 040080           75 SSPIECAVCLDKF-NKGDKCRLLPICNHSFHAQCVDAWLLT--NPNCPICRST  124 (192)
Q Consensus        75 ~~~~~C~IC~~~~-~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~  124 (192)
                      .+...|.||...- ...+.+..-..|.-.||..|+..-..-  .-.||.|+..
T Consensus        14 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~~   66 (71)
T 2ku3_A           14 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQS   66 (71)
T ss_dssp             CSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcCc
Confidence            4567799998753 233445554559999999999753211  2349999763

>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=88.12  E-value=0.45  Score=29.42  Aligned_cols=34  Identities=24%  Similarity=0.607  Sum_probs=25.2

Q ss_pred             CCCcccccCccccCCCceEEcC-CCCCcccHHhHH
Q 040080           76 SPIECAVCLDKFNKGDKCRLLP-ICNHSFHAQCVD  109 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~-~C~H~fh~~Ci~  109 (192)
                      ....|++|...+......+.-. .|.-.||..|+.
T Consensus         7 ~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvg   41 (65)
T 2vpb_A            7 PVYPCGICTNEVNDDQDAILCEASCQKWFHRICTG   41 (65)
T ss_dssp             --CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHT
T ss_pred             CcCcCccCCCccCCCCCeEecccCccccCchhccC
Confidence            3456999999987665555544 599999999983

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=87.94  E-value=0.2  Score=33.64  Aligned_cols=45  Identities=18%  Similarity=0.305  Sum_probs=29.8

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC---CCCCccccc
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT---NPNCPICRS  123 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~  123 (192)
                      ...| ||......+..+.--. |.-.||..|+..=...   .-.||.|+.
T Consensus        28 ~vrC-iC~~~~~~~~mi~Cd~-C~~w~H~~C~~~~~~~~p~~w~C~~C~~   75 (98)
T 2lv9_A           28 VTRC-ICGFTHDDGYMICCDK-CSVWQHIDCMGIDRQHIPDTYLCERCQP   75 (98)
T ss_dssp             BCCC-TTSCCSCSSCEEEBTT-TCBEEETTTTTCCTTSCCSSBCCTTTSS
T ss_pred             CEEe-ECCCccCCCcEEEcCC-CCCcCcCcCCCCCccCCCCCEECCCCcC
Confidence            3457 8987765554444444 9999999998653222   235999974

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

Probab=87.64  E-value=3  Score=27.36  Aligned_cols=52  Identities=19%  Similarity=0.372  Sum_probs=34.9

Q ss_pred             CCCcccccCccccCC---CceEEcCCCCCcccHHhHHHHHcC-CCCCccccccccc
Q 040080           76 SPIECAVCLDKFNKG---DKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANS  127 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~---~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~  127 (192)
                      ....|.||-+.+...   +.-..--.|+--.|..|++-=.+. ++.||-|++....
T Consensus        15 ~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCktrYkr   70 (93)
T 1weo_A           15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKR   70 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCC
T ss_pred             CCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhccCccccccCCcccc
Confidence            456799999986422   211111227777899999754443 7789999998753

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=87.48  E-value=0.38  Score=31.67  Aligned_cols=46  Identities=28%  Similarity=0.584  Sum_probs=32.1

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC----CCCCcccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT----NPNCPICRST  124 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~  124 (192)
                      .....|.+|...   ++. ..-..|.-.||..|+.+=+..    .-.||.|+..
T Consensus        23 ~n~~~C~vC~~~---g~L-L~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~   72 (88)
T 1fp0_A           23 DSATICRVCQKP---GDL-VMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   72 (88)
T ss_dssp             SSSSCCSSSCSS---SCC-EECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCC
T ss_pred             CCCCcCcCcCCC---CCE-EECCCCCCceecccCCCCCCCCcCCCcCCccccCC
Confidence            456679999975   433 333348899999999775544    2249999864

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=87.43  E-value=0.21  Score=34.12  Aligned_cols=47  Identities=30%  Similarity=0.582  Sum_probs=30.9

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC----CCCCcccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT----NPNCPICR  122 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr  122 (192)
                      .++..|.||.+.-...+.+.-.. |+..||..|+...+..    .-.||.|+
T Consensus         5 ~~~~~C~~C~~~g~~~~ll~C~~-C~~~~H~~Cl~~~~~~~~~~~W~C~~C~   55 (111)
T 2ysm_A            5 SSGANCAVCDSPGDLLDQFFCTT-CGQHYHGMCLDIAVTPLKRAGWQCPECK   55 (111)
T ss_dssp             CCCSCBTTTCCCCCTTTSEECSS-SCCEECTTTTTCCCCTTTSTTCCCTTTC
T ss_pred             CCCCCCcCCCCCCCCcCCeECCC-CCCCcChHHhCCccccccccCccCCcCC
Confidence            45678999988733222244344 9999999999876642    22377664

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=87.00  E-value=0.2  Score=31.00  Aligned_cols=46  Identities=30%  Similarity=0.564  Sum_probs=31.2

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC----CCCCcccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT----NPNCPICRST  124 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~  124 (192)
                      ..+..|.||...   ++. ..-..|...||..|+.+-+..    .-.||.|...
T Consensus         6 ~~~~~C~vC~~~---g~l-l~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~   55 (66)
T 1xwh_A            6 KNEDECAVCRDG---GEL-ICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQA   55 (66)
T ss_dssp             SCCCSBSSSSCC---SSC-EECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHT
T ss_pred             CCCCCCccCCCC---CCE-EEcCCCChhhcccccCCCcCcCCCCCeECccccCc
Confidence            346679999864   433 333349999999999864433    2249999753

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=86.57  E-value=0.29  Score=32.20  Aligned_cols=53  Identities=17%  Similarity=0.441  Sum_probs=34.5

Q ss_pred             CCCCcccccCccc-cCCCceEEcCCCCCcccHHhHHHHHcC--CCCCccccccccc
Q 040080           75 SSPIECAVCLDKF-NKGDKCRLLPICNHSFHAQCVDAWLLT--NPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~-~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~~  127 (192)
                      .++..|.||...- ...+.+..-..|.-.||..|+..-+.-  .-.||.|......
T Consensus        23 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~~~   78 (88)
T 2l43_A           23 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRAR   78 (88)
T ss_dssp             CCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHTTS
T ss_pred             CCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCccch
Confidence            4566799999753 222344444559999999999753211  2349999876543

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=86.17  E-value=0.21  Score=34.33  Aligned_cols=45  Identities=31%  Similarity=0.659  Sum_probs=29.9

Q ss_pred             cccccCccccCCCceEEcCCCCCcccHHhHHHHHcC----CCCCccccc
Q 040080           79 ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT----NPNCPICRS  123 (192)
Q Consensus        79 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~  123 (192)
                      .|.||...-.....+..-..|...||..|+.+-+..    .-.||.|+.
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            578887653333344444459999999999765544    234999975

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

Probab=86.01  E-value=0.94  Score=32.51  Aligned_cols=46  Identities=22%  Similarity=0.484  Sum_probs=32.5

Q ss_pred             CCCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHc-----------CCCCCccccc
Q 040080           74 GSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLL-----------TNPNCPICRS  123 (192)
Q Consensus        74 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-----------~~~~CP~Cr~  123 (192)
                      ...+..|.+|.+-   ++. ..-..|...||..||.+=+.           ..-.||.|+.
T Consensus        60 Dg~~d~C~vC~~G---G~L-lcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~  116 (142)
T 2lbm_A           60 DGMDEQCRWCAEG---GNL-ICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHP  116 (142)
T ss_dssp             TSCBCSCSSSCCC---SSE-EECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCC
T ss_pred             CCCCCeecccCCC---CcE-EeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccC
Confidence            3456779999975   443 33344999999999997552           1335999974

>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=85.48  E-value=0.62  Score=43.40  Aligned_cols=51  Identities=14%  Similarity=0.212  Sum_probs=42.7

Q ss_pred             CCCCcccccCccccCCCceEEcCCCC-CcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICN-HSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~-H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      .+.+.|||-++-|.++   ..+| -| +.|-..+|..|+.++.+||.=|.++....
T Consensus       889 P~~F~cPIs~~lM~DP---Vilp-sG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~  940 (968)
T 3m62_A          889 PDEFLDPLMYTIMKDP---VILP-ASKMNIDRSTIKAHLLSDSTDPFNRMPLKLED  940 (968)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGG
T ss_pred             cHHhCCcchhhHHhCC---eEcC-CCCEEECHHHHHHHHhcCCCCCCCCCCCCccc
Confidence            5577899999998665   5577 76 58999999999999999999999887643

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=85.23  E-value=0.6  Score=30.10  Aligned_cols=40  Identities=18%  Similarity=0.468  Sum_probs=30.1

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT  114 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~  114 (192)
                      .....|.+|.+.++...-+..-..=+|.||..|-+..+++
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            4456799999999876544433335799999999998865

>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=85.23  E-value=0.48  Score=30.03  Aligned_cols=48  Identities=23%  Similarity=0.422  Sum_probs=30.8

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHH---------HcCCCCCcccccccc
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAW---------LLTNPNCPICRSTAN  126 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w---------l~~~~~CP~Cr~~~~  126 (192)
                      ...| ||...+..+..+.-- .|...||..|+.--         ....-.||.|+..-.
T Consensus        16 ~~~C-~C~~~~~~~~MI~Cd-~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~~~   72 (76)
T 1wem_A           16 ALYC-ICRQPHNNRFMICCD-RCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILSG   72 (76)
T ss_dssp             CCCS-TTCCCCCSSCEEECS-SSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHSC
T ss_pred             CCEE-ECCCccCCCCEEEeC-CCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCccC
Confidence            3456 898876543333333 49999999998421         123566999987543

>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=84.30  E-value=0.29  Score=30.07  Aligned_cols=52  Identities=15%  Similarity=0.454  Sum_probs=34.2

Q ss_pred             CCCCcccccCccccC-CCceEEcCCCCCcccHHhHHHHHc-------CCCCCcccccccc
Q 040080           75 SSPIECAVCLDKFNK-GDKCRLLPICNHSFHAQCVDAWLL-------TNPNCPICRSTAN  126 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~-~~~~~~~~~C~H~fh~~Ci~~wl~-------~~~~CP~Cr~~~~  126 (192)
                      .++..|.||...... ...+..-..|.-.||..|+.+=+.       ..-.||.|+....
T Consensus         4 ~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~~   63 (66)
T 2yt5_A            4 GSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFATT   63 (66)
T ss_dssp             CCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTTS
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCccc
Confidence            345679999976432 234444455999999999986331       2335999976543

>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=82.93  E-value=0.15  Score=33.89  Aligned_cols=50  Identities=22%  Similarity=0.376  Sum_probs=32.7

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC----CCCCccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT----NPNCPICRSTA  125 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~~  125 (192)
                      .+...|.||...-... .+..-..|...||..|+.+=+..    .-.||.|+..-
T Consensus        14 ~~~~~C~vC~~~~~~~-~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~~   67 (92)
T 2e6r_A           14 IDSYICQVCSRGDEDD-KLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILAE   67 (92)
T ss_dssp             CCCCCCSSSCCSGGGG-GCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHHH
T ss_pred             cCCCCCccCCCcCCCC-CEEEcCCCCchhccccCCCCcccCCCCCcCCccCcCcc
Confidence            3455799999764322 33444449999999999753433    22499997643

>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=82.90  E-value=0.68  Score=34.03  Aligned_cols=48  Identities=23%  Similarity=0.534  Sum_probs=31.6

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHH--H---cCCCCCcccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAW--L---LTNPNCPICRST  124 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w--l---~~~~~CP~Cr~~  124 (192)
                      +...| +|......+...+.-..|...||..|+.--  -   ...-.||.|+..
T Consensus         7 ~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~   59 (174)
T 2ri7_A            7 TKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST   59 (174)
T ss_dssp             CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHH
T ss_pred             CCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcch
Confidence            34568 999876544434444459999999999421  1   123459999874

>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=82.42  E-value=0.74  Score=31.23  Aligned_cols=51  Identities=24%  Similarity=0.498  Sum_probs=33.6

Q ss_pred             CCcccccCccccCCCceEEcC-CCCCcccHHhHHHH------H--c--CCCCCccccccccc
Q 040080           77 PIECAVCLDKFNKGDKCRLLP-ICNHSFHAQCVDAW------L--L--TNPNCPICRSTANS  127 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~-~C~H~fh~~Ci~~w------l--~--~~~~CP~Cr~~~~~  127 (192)
                      ...|.||...+......+.-. .|...||..|+.-=      +  .  ..-.||.|+.....
T Consensus         3 ~~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~~~   64 (105)
T 2xb1_A            3 VYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTKEG   64 (105)
T ss_dssp             CCBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTTTT
T ss_pred             cCCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcCCC
Confidence            346999999986554444432 48999999998411      1  0  23459999886543

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=82.05  E-value=0.28  Score=36.97  Aligned_cols=45  Identities=27%  Similarity=0.558  Sum_probs=30.4

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC----CCCCccccccc
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT----NPNCPICRSTA  125 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~~  125 (192)
                      +..|.+|...   ++.+..-. |...||..|+.+=+..    .-.||.|+...
T Consensus         2 ~~~C~~C~~~---g~ll~Cd~-C~~~~H~~Cl~p~l~~~p~g~W~C~~C~~~~   50 (189)
T 2ro1_A            2 ATICRVCQKP---GDLVMCNQ-CEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   50 (189)
T ss_dssp             CCCBTTTCCC---SSCCCCTT-TCCBCCSTTSTTCCSSCCCTTCCTTTTSCSC
T ss_pred             CCcCccCCCC---CceeECCC-CCchhccccCCCCcccCCCCCCCCcCccCCC
Confidence            3569999865   43333333 8899999999764433    22499998763

>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=81.90  E-value=0.82  Score=30.26  Aligned_cols=46  Identities=30%  Similarity=0.591  Sum_probs=28.0

Q ss_pred             CCCcccccCccccCCCceEEcCC--CC-CcccHHhHHHHHcC----CCCCcccccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPI--CN-HSFHAQCVDAWLLT----NPNCPICRSTAN  126 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~--C~-H~fh~~Ci~~wl~~----~~~CP~Cr~~~~  126 (192)
                      +...| ||..... +. .+.-..  |. ..||..|+.  +..    +-.||.|+....
T Consensus        35 e~~yC-iC~~~~~-g~-MI~CD~~dC~~~WfH~~CVg--l~~~p~g~W~Cp~C~~~~~   87 (91)
T 1weu_A           35 EPTYC-LCHQVSY-GE-MIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESG   87 (91)
T ss_dssp             CCBCS-TTCCBCC-SC-CCCCSCSSCSCCCCCSTTTT--CSSCCCSSCCCTTTCCCCS
T ss_pred             CCcEE-ECCCCCC-CC-EeEecCCCCCCCCEecccCC--cCcCCCCCEECcCccCcCC
Confidence            34557 9988643 32 222233  55 689999997  332    234999987543

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=81.83  E-value=2.2  Score=29.00  Aligned_cols=46  Identities=22%  Similarity=0.391  Sum_probs=28.0

Q ss_pred             CCcccccCccc-----cCCCceEEcCCCCCcccHHhHHH------HHc-CCCCCcccc
Q 040080           77 PIECAVCLDKF-----NKGDKCRLLPICNHSFHAQCVDA------WLL-TNPNCPICR  122 (192)
Q Consensus        77 ~~~C~IC~~~~-----~~~~~~~~~~~C~H~fh~~Ci~~------wl~-~~~~CP~Cr  122 (192)
                      ...|.+|+..-     ..++.+..-..|+..||..|+..      .+. ..-.||.|+
T Consensus         5 ~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   62 (112)
T 3v43_A            5 IPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLKFSPELTVRVKALRWQCIECK   62 (112)
T ss_dssp             CSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHTCCHHHHHHHHTSCCCCTTTC
T ss_pred             CccccccCCchhhCcCCCchhceEhhhcCCCCCCchhcCCHHHHHHhhccccccccCC
Confidence            45699998752     11223444444999999999952      222 234477775

>1iij_A ERBB-2 receptor protein-tyrosine kinase; alpha-helix-PI-bulge-alpha-helix, signaling protein; NMR {Synthetic} SCOP: j.35.1.1

Probab=81.65  E-value=0.65  Score=25.05  Aligned_cols=15  Identities=27%  Similarity=0.166  Sum_probs=6.7

Q ss_pred             HHHHHHHHHHHHHHH
Q 040080            4 AIIISVIFLFLGIGA   18 (192)
Q Consensus         4 ~iil~~~~~~~~i~~   18 (192)
                      +|+.+++.+++.+++
T Consensus         9 sIaagVvglll~vii   23 (35)
T 1iij_A            9 FIIATVVGVLLFLIL   23 (35)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             EeHHHHHHHHHHHHH
Confidence            455555553333333

>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=81.54  E-value=1.3  Score=27.84  Aligned_cols=46  Identities=30%  Similarity=0.580  Sum_probs=28.3

Q ss_pred             CCCcccccCccccCCCceEEcCC--CC-CcccHHhHHHHHcC----CCCCcccccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPI--CN-HSFHAQCVDAWLLT----NPNCPICRSTAN  126 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~--C~-H~fh~~Ci~~wl~~----~~~CP~Cr~~~~  126 (192)
                      +...| ||..... + ..+.-..  |. ..||..|+.  +..    +-.||.|+..-.
T Consensus        15 ~~~~C-~C~~~~~-g-~MI~CD~~~C~~~wfH~~Cvg--l~~~p~g~w~Cp~C~~~~~   67 (71)
T 1wen_A           15 EPTYC-LCHQVSY-G-EMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESG   67 (71)
T ss_dssp             SCCCS-TTCCCSC-S-SEECCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSCSS
T ss_pred             CCCEE-ECCCCCC-C-CEeEeeCCCCCCccEecccCC--cCcCCCCCEECCCCCcccc
Confidence            34557 8987642 3 3333333  55 689999997  333    234999977543

>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=81.29  E-value=0.45  Score=29.67  Aligned_cols=47  Identities=21%  Similarity=0.472  Sum_probs=29.7

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHc---CCCCCccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLL---TNPNCPICRS  123 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~---~~~~CP~Cr~  123 (192)
                      .+...| ||..... +...+.-..|...||..|+.---.   ..-.||.|+.
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            445568 9988765 333343344999999999864211   1335998864

>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=81.16  E-value=0.55  Score=30.00  Aligned_cols=49  Identities=27%  Similarity=0.448  Sum_probs=30.1

Q ss_pred             CCCcccccCccccCCCceEEc-CCCCCcccHHhHHHHH---------cCCCCCccccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLL-PICNHSFHAQCVDAWL---------LTNPNCPICRSTA  125 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~-~~C~H~fh~~Ci~~wl---------~~~~~CP~Cr~~~  125 (192)
                      ....| ||-.....+.-+.-- +.|...||..|+.---         ..+-.||.|+..-
T Consensus        15 ~~~~C-iC~~~~~~g~MI~CD~~~C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T 1wew_A           15 IKVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             CCEEe-ECCCcCCCCCEEEECCccCCccccCEEEccccccccccccCCCCEECCCCCccc
Confidence            34557 788874444333333 1499999999985311         1234599998754

>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=81.04  E-value=0.34  Score=30.44  Aligned_cols=49  Identities=18%  Similarity=0.346  Sum_probs=31.5

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHH----cCCCCCccccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWL----LTNPNCPICRSTA  125 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl----~~~~~CP~Cr~~~  125 (192)
                      ....| ||......+...+.-..|...||..|+.---    ...-.||.|+..-
T Consensus        15 ~~~~C-~C~~~~~~g~~mI~Cd~C~~W~H~~Cvg~~~~~~~~~~~~C~~C~~~~   67 (72)
T 1wee_A           15 WKVDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELS   67 (72)
T ss_dssp             SEECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHHC
T ss_pred             cceEe-eCCCccCCCCcEEECCCCCCccCCeeeccCccccCCCcEECCCccCCC
Confidence            34558 7988765554344444599999999986421    1234599998644

>4gne_A Histone-lysine N-methyltransferase NSD3; zinc finger, transcription, nuclear protein, transf nuclear protein complex; 1.47A {Homo sapiens} PDB: 4gnd_A 4gnf_A 4gng_A*

Probab=80.46  E-value=1.8  Score=29.52  Aligned_cols=51  Identities=24%  Similarity=0.427  Sum_probs=33.0

Q ss_pred             CCCCCCCcccccCccccCCCceEEcC--CCCCcccHHhHHHHHcCC----CCCcccccccccC
Q 040080           72 SKGSSPIECAVCLDKFNKGDKCRLLP--ICNHSFHAQCVDAWLLTN----PNCPICRSTANSR  128 (192)
Q Consensus        72 ~~~~~~~~C~IC~~~~~~~~~~~~~~--~C~H~fh~~Ci~~wl~~~----~~CP~Cr~~~~~~  128 (192)
                      .+...+..|.+|.+.   + .+..-.  .|...||..|+.  |...    -.||.|+.....+
T Consensus        10 ~~~~~~~~C~~C~~~---G-~ll~CD~~~Cp~~fH~~Cl~--L~~~P~g~W~Cp~c~C~~C~k   66 (107)
T 4gne_A           10 PKQMHEDYCFQCGDG---G-ELVMCDKKDCPKAYHLLCLN--LTQPPYGKWECPWHQCDECSS   66 (107)
T ss_dssp             CCCSSCSSCTTTCCC---S-EEEECCSTTCCCEECTGGGT--CSSCCSSCCCCGGGBCTTTCS
T ss_pred             CcCCCCCCCCcCCCC---C-cEeEECCCCCCcccccccCc--CCcCCCCCEECCCCCCCcCCC
Confidence            334567779999842   3 333332  488999999997  4432    2499887766544

---

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	192
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	3e-17
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-11
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	1e-09
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	2e-09
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-08
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	1e-08
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	2e-07
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	7e-07
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	4e-06
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	1e-05
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	6e-05
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	1e-04
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	2e-04
d1we9a_	64	g.50.1.2 (A:) PHD finger protein At5g26210 {Thale	0.004

>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 = 69.9 bits (171), Expect = 3e-17
 Identities = 25/47 (53%), Positives = 33/47 (70%)

Query: 78  IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRST 124
           +ECAVCL +   G++ R LP C H FHA+CVD WL ++  CP+CR T
Sbjct: 6   VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLT 52

>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 = 55.7 bits (134), Expect = 1e-11
 Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 5/66 (7%)

Query: 79  ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRFGEESSRFS 138
            C +CL+  +  +    LP C H+F   C+  W+  NP CP+C+    S     ES   S
Sbjct: 7   RCPICLEDPS--NYSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVESVVHTIESD--S 61

Query: 139 DIDVEL 144
           +   +L
Sbjct: 62  EFGDQL 67

>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 = 50.1 bits (119), Expect = 1e-09
 Identities = 11/47 (23%), Positives = 16/47 (34%), Gaps = 1/47 (2%)

Query: 78  IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRS 123
           +EC +C++     D       C +     C        N  CP CR 
Sbjct: 1   VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRK 47

>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 = 50.5 bits (120), Expect = 2e-09
 Identities = 14/66 (21%), Positives = 22/66 (33%), Gaps = 14/66 (21%)

Query: 79  ECAVCLDKFNKGDKCRLLPI--------------CNHSFHAQCVDAWLLTNPNCPICRST 124
            CA+C +                           CNH+FH  C+  WL T   CP+    
Sbjct: 23  NCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 82

Query: 125 ANSRRF 130
              +++
Sbjct: 83  WEFQKY 88

>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 = 48.1 bits (114), Expect = 1e-08
 Identities = 13/57 (22%), Positives = 21/57 (36%), Gaps = 5/57 (8%)

Query: 74  GSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN-PNCPICRSTANSRR 129
           GS+   C +C +        ++ P C H     C+ +W  +    CP CR       
Sbjct: 20  GSTFQLCKICAEND---KDVKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE 72

>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 = 47.5 bits (112), Expect = 1e-08
 Identities = 12/54 (22%), Positives = 18/54 (33%), Gaps = 2/54 (3%)

Query: 79  ECAVCLDKFNKGDKCRLLPI-CNHSFHAQCVDAWLLTNPN-CPICRSTANSRRF 130
            C  C     +    +L+   C H+    CVD   +     CP C +      F
Sbjct: 5   GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNF 58

>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 = 44.1 bits (104), Expect = 2e-07
 Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 7/46 (15%)

Query: 78  IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRS 123
           + C  C  +       +LLP C H+  + C++A       CPIC++
Sbjct: 7   LRCQQCQAEA---KCPKLLP-CLHTLCSGCLEAS---GMQCPICQA 45

>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 = 43.9 bits (102), Expect = 7e-07
 Identities = 19/94 (20%), Positives = 32/94 (34%), Gaps = 24/94 (25%)

Query: 49  SIGSTSMSRDDVEKLPCYEYLAKSKGSSPIECAVCLD--------------KFNKGDKCR 94
           S GS+      + K     Y  + K +   +C +C++              K        
Sbjct: 2   SSGSSGEPEQVIRK-----YTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVG 56

Query: 95  LLPICNHSFHAQCVDAWLLTNPN-----CPICRS 123
            L  C+H+FH  C+ A            CP C++
Sbjct: 57  RLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKT 90

>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 = 40.6 bits (94), Expect = 4e-06
 Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 3/52 (5%)

Query: 80  CAVCLDKF-NKGDKCRLLPICNHSFHAQCVDAWLLTNPN--CPICRSTANSR 128
           C +C ++  N+  +         + H  C+  WL  + N  C IC    N+R
Sbjct: 9   CWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNTR 60

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.9 bits (93), Expect = 1e-05
 Identities = 12/52 (23%), Positives = 16/52 (30%), Gaps = 5/52 (9%)

Query: 78  IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWL-LTNPNCPICRSTANSR 128
           I C +C           +   C H F   C+   L +    CP CR      
Sbjct: 24  ISCQICEHIL----ADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPT 71

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

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

 Score = 38.5 bits (89), Expect = 6e-05
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 7/54 (12%)

Query: 78  IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPN---CPICRSTANSR 128
           +EC +CL+   +         C+H F   C+   L        CP+C++    R
Sbjct: 22  LECPICLELIKE---PVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR 71

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 1e-04
 Identities = 9/56 (16%), Positives = 17/56 (30%), Gaps = 9/56 (16%)

Query: 75  SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT--------NPNCPICR 122
           S    C +CL ++       +   C   F   C+  ++            +CP   
Sbjct: 3   SGSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAA 57

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (85), Expect = 2e-04
 Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 5/53 (9%)

Query: 78  IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRF 130
           + C+ C +      +   L  C H F + CV   +     CP+C + A  +  
Sbjct: 23  LRCSRCTNIL---REPVCLGGCEHIFCSNCVSDCI--GTGCPVCYTPAWIQDL 70

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 64

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]

 Score = 32.3 bits (73), Expect = 0.004
 Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 6/57 (10%)

Query: 72  SKGSSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPN-----CPICRS 123
           S GSS  +C  C + +   +      +C   FH +CV        +     CP C +
Sbjct: 2   SSGSS-GQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN 57

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	192
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.75
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.6
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.58
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.56
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.52
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.51
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.46
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.41
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.33
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.29
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.29
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.24
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.14
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.09
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.08
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.95
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.64
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	95.15
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	94.19
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	93.37
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	93.26
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	93.15
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	91.9
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	87.53
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	86.92
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	86.73
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	86.03
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	85.73
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	82.7
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	82.1
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	81.57

>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=99.75  E-value=2.1e-19  Score=109.89  Aligned_cols=52  Identities=48%  Similarity=1.141  Sum_probs=46.6

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTAN  126 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~  126 (192)
                      +++.+|+||+++|..++.+..++.|+|.||..||.+|++++++||+||+++.
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            3456799999999998888887669999999999999999999999999874

>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=99.60  E-value=2.1e-16  Score=100.55  Aligned_cols=49  Identities=33%  Similarity=0.897  Sum_probs=42.1

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANS  127 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~  127 (192)
                      ...+|+||++.+..  .+..++ |||.||..||..|++.+.+||+||+++..
T Consensus         4 ~~d~C~IC~~~~~~--~~~~~~-C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~   52 (68)
T d1chca_           4 VAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCccCCcCccC--CcEEeC-CCCcCcHHHHHHHHHhCCcCCCCCcchHh
Confidence            45679999999854  456677 99999999999999999999999998754

>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=99.58  E-value=5.6e-16  Score=103.49  Aligned_cols=52  Identities=27%  Similarity=0.563  Sum_probs=42.9

Q ss_pred             CCCcccccCccccCCC---------------ceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccC
Q 040080           76 SPIECAVCLDKFNKGD---------------KCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSR  128 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~---------------~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~  128 (192)
                      ....|+||++.+....               .+..++ |||.||..||.+||..+++||+||+++...
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   86 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEFQ   86 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCCEE
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCccccc
Confidence            3556999999886532               245567 999999999999999999999999998654

>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=99.56  E-value=3.6e-16  Score=94.25  Aligned_cols=48  Identities=23%  Similarity=0.481  Sum_probs=39.8

Q ss_pred             cccccCccccCCCceE-EcCCCCCcccHHhHHHHHcC-CCCCccccccccc
Q 040080           79 ECAVCLDKFNKGDKCR-LLPICNHSFHAQCVDAWLLT-NPNCPICRSTANS  127 (192)
Q Consensus        79 ~C~IC~~~~~~~~~~~-~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~  127 (192)
                      +|+||+++|..++... .++ |||.||..|+..|+.. +.+||+||+++..
T Consensus         2 eCpICl~~~~~~~~~~~~~~-CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSS-SSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecC-CCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            6999999997665443 346 9999999999999986 4569999998864

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=3.3e-15  Score=104.27  Aligned_cols=54  Identities=26%  Similarity=0.662  Sum_probs=41.5

Q ss_pred             CCCCcccccCccccCC---------------CceEEcCCCCCcccHHhHHHHHcCC-----CCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKG---------------DKCRLLPICNHSFHAQCVDAWLLTN-----PNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~---------------~~~~~~~~C~H~fh~~Ci~~wl~~~-----~~CP~Cr~~~~~~~  129 (192)
                      ..+..|+||++.+...               ..+.+++ |||+||..||..|+..+     .+||+||+.+..+.
T Consensus        23 ~~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~   96 (114)
T d1v87a_          23 APEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKT   96 (114)
T ss_dssp             CCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCS
T ss_pred             cccccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhcCcCCCCccccccchhccCc
Confidence            3456799999998542               2345566 99999999999999753     47999999886553

>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=99.51  E-value=6.9e-15  Score=92.55  Aligned_cols=53  Identities=23%  Similarity=0.526  Sum_probs=40.8

Q ss_pred             CCCcccccCccccCC-C-ceEEcCCCCCcccHHhHHHHHcC-CCCCcccccccccCC
Q 040080           76 SPIECAVCLDKFNKG-D-KCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRR  129 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~-~-~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~  129 (192)
                      ++..|+||++.+..+ + .+..++ |||.||..||..|+.+ +.+||+||+++....
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            356799999976432 2 334556 9999999999999966 567999999886543

>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=99.46  E-value=2.3e-14  Score=93.55  Aligned_cols=49  Identities=22%  Similarity=0.726  Sum_probs=40.7

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCcccccccccCC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRR  129 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~  129 (192)
                      ...|+||++.+..   .+.++ |||.||..||..|+.. +++||+||..+....
T Consensus        23 ~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~   72 (79)
T d1fbva4          23 FQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE   72 (79)
T ss_dssp             TTBCTTTSSSBCC---EECSS-SCCEECHHHHHHHHHTTCCSCTTTCCCCCCCC
T ss_pred             CCCCccCCCcCCC---eEEeC-CCCeeeHHHHHHHHHHCcCcCCCCCcCccCCc
Confidence            4569999998754   46677 9999999999999975 567999999997543

>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=99.41  E-value=2.1e-14  Score=87.65  Aligned_cols=49  Identities=16%  Similarity=0.238  Sum_probs=41.4

Q ss_pred             cccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCCC
Q 040080           79 ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRF  130 (192)
Q Consensus        79 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~  130 (192)
                      .|+||++.+..+   ..++.|||.||..||.+|++++++||+||.++...+.
T Consensus         2 ~C~Ic~~~~~~P---v~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dL   50 (56)
T d2baya1           2 LCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEI   50 (56)
T ss_dssp             CCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGC
T ss_pred             CCccCCchHHhc---CccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhc
Confidence            599999998654   3444499999999999999999999999999877654

>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=99.33  E-value=3.9e-13  Score=88.79  Aligned_cols=49  Identities=24%  Similarity=0.542  Sum_probs=40.8

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCcccccccccCC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRR  129 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~  129 (192)
                      ...|+||++.+..+   ..++ |||.||..||..|++. +.+||+||.++....
T Consensus        23 ~l~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~   72 (86)
T d1rmda2          23 SISCQICEHILADP---VETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (86)
T ss_dssp             HTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CcCCccCCcchhcc---eecC-CCChhhHHHHHHHHhhCCCcCcccCCCCChhh
Confidence            35699999998654   5677 9999999999999975 567999999987654

>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=99.29  E-value=2.6e-13  Score=82.54  Aligned_cols=47  Identities=28%  Similarity=0.655  Sum_probs=38.4

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      ...+|+||++.+..+   +.++ |||.||..||..|   +.+||+||+++....
T Consensus         5 ~~l~C~IC~~~~~~p---~~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T d1bora_           5 QFLRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCSSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             CCCCCcccCcccCCC---EEec-CCCHHhHHHHHcC---CCcCcCCCCcccCCC
Confidence            345899999998765   5678 9999999999865   567999999986543

>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=99.29  E-value=8.4e-13  Score=90.23  Aligned_cols=50  Identities=26%  Similarity=0.700  Sum_probs=41.0

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC---CCCcccccccccCCC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN---PNCPICRSTANSRRF  130 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~---~~CP~Cr~~~~~~~~  130 (192)
                      ...|+||++.|..+   ..++ |||.||..||..|+..+   ..||+||.++.....
T Consensus        21 ~l~CpIC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l   73 (103)
T d1jm7a_          21 ILECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL   73 (103)
T ss_dssp             HTSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTC
T ss_pred             CcCCCccCchhCCe---EEcC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhC
Confidence            45699999999765   4467 99999999999999764   369999999876543

>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=99.24  E-value=2.3e-12  Score=79.43  Aligned_cols=52  Identities=21%  Similarity=0.464  Sum_probs=38.4

Q ss_pred             CCCCcccccCccccCCCce--EEcCCCCCcccHHhHHHHHcC--CCCCccccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKC--RLLPICNHSFHAQCVDAWLLT--NPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~--~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~~  127 (192)
                      .+...|.||++.+......  .... |+|.||..||..|+..  +.+||+||+++..
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~-c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTG-ELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSS-GGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCccCCccCCCceeEecccCC-CCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            4567799999988654221  1122 5699999999999954  5689999998754

>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=99.14  E-value=5.8e-12  Score=85.01  Aligned_cols=48  Identities=25%  Similarity=0.614  Sum_probs=38.5

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCC
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRR  129 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~  129 (192)
                      ...|+||++.|..+  +...+ |||.||..||..|+.  +.||.||.++....
T Consensus        22 ~l~C~IC~~~~~~p--v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~   69 (97)
T d1jm7b_          22 LLRCSRCTNILREP--VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAWIQD   69 (97)
T ss_dssp             TTSCSSSCSCCSSC--BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCSCSS
T ss_pred             cCCCccCCchhhcC--ceeCC-CCCchhHHHHHHHHh--ccccccCCcCchhh
Confidence            45799999999665  33345 999999999999984  46999999886544

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.09  E-value=2.7e-11  Score=78.75  Aligned_cols=51  Identities=10%  Similarity=0.215  Sum_probs=42.3

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~  129 (192)
                      .++..|+||++.|..+   ..++ |||.|+..||..|+.. +.+||.||.++....
T Consensus         5 P~~l~CpIc~~l~~dP---v~~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~   56 (80)
T d2c2la2           5 PDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQ   56 (80)
T ss_dssp             CSTTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCGGG
T ss_pred             CccccCcCcCchhhhh---cccC-CcCeecHHHHHHHHhcCCccCCCccccccccc
Confidence            3567899999999665   4577 9999999999999975 567999999886543

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

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

Probab=99.08  E-value=4.4e-11  Score=77.32  Aligned_cols=51  Identities=14%  Similarity=0.428  Sum_probs=42.5

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC-CCCCcccccccccCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT-NPNCPICRSTANSRR  129 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~  129 (192)
                      .++..|+||++.|.++   ..++ |||.|+..||..|+.. +..||.|+.++....
T Consensus         6 P~~l~CpIc~~~m~dP---V~~~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~   57 (78)
T d1t1ha_           6 PEYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLHAG   57 (78)
T ss_dssp             SSSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCC
T ss_pred             CccCCCcCcCchhhCc---eEcc-CCCcchHHHHHHHHHHCCCCCCcccccCCccc
Confidence            4578899999999665   4567 9999999999999976 456999999887644

>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=98.95  E-value=2.8e-10  Score=76.66  Aligned_cols=53  Identities=13%  Similarity=0.161  Sum_probs=43.6

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCcccccccccCCC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRSTANSRRF  130 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~  130 (192)
                      .+.+.|+||++.|.++   .+++.|||.|+..||..|+..+.+||+||.++.....
T Consensus        20 P~~f~CPI~~~lm~dP---V~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L   72 (98)
T d1wgma_          20 CDEFLDPIMSTLMCDP---VVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQI   72 (98)
T ss_dssp             CTTTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTS
T ss_pred             cHHhCCcCchhHHHHH---HhcccccchhhHHHHHHHHHhcCCcccccccccchhh
Confidence            3468899999999665   5677355689999999999999999999999876543

>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=98.64  E-value=4.3e-09  Score=69.98  Aligned_cols=47  Identities=17%  Similarity=0.494  Sum_probs=36.5

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC--------CCCccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN--------PNCPICRS  123 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~--------~~CP~Cr~  123 (192)
                      ...+|+||++++...+.+..++ |+|.||..|+..|+..+        -+||.|+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCcCccCCCcccCCceEEECC-CCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            4567999999987665556566 99999999999999631        24998654

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

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.15  E-value=0.004  Score=35.36  Aligned_cols=44  Identities=32%  Similarity=0.643  Sum_probs=30.2

Q ss_pred             cccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC----CCCccccc
Q 040080           79 ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN----PNCPICRS  123 (192)
Q Consensus        79 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP~Cr~  123 (192)
                      .|.||...-..+. +..-..|...||..|+.+-+...    -.||.||.
T Consensus         2 ~C~vC~~~~~~~~-~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDK-LILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSC-CEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCC-EEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            4888876644433 34444499999999998866442    23999975

>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=94.19  E-value=0.0082  Score=35.66  Aligned_cols=49  Identities=22%  Similarity=0.533  Sum_probs=34.1

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHH---c--CCCCCcccccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWL---L--TNPNCPICRST  124 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl---~--~~~~CP~Cr~~  124 (192)
                      ....|.+|......+...+.-..|+..||..|+..=.   .  .+-.||.|+..
T Consensus         5 ~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            4567999998876665545444599999999995311   1  13459999864

>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=93.37  E-value=0.023  Score=34.34  Aligned_cols=45  Identities=27%  Similarity=0.522  Sum_probs=30.4

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCC----CCCccccccc
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTN----PNCPICRSTA  125 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP~Cr~~~  125 (192)
                      ...|.+|...   ++.+.-- .|...||..|+.+.+...    -.||.|+...
T Consensus         7 c~~C~~C~~~---~~ll~Cd-~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           7 ATICRVCQKP---GDLVMCN-QCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             SSCCSSSCSS---SCCEECT-TSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCCCCc---CEEEECC-CCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            4457777643   4443333 499999999999876542    2399997644

>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=93.26  E-value=0.036  Score=34.39  Aligned_cols=35  Identities=20%  Similarity=0.540  Sum_probs=25.2

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHH
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAW  111 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w  111 (192)
                      ..+..|.|| +.+........ ..|+-+||..|+.+-
T Consensus        13 ~~D~mC~vC-~v~t~~~l~pC-RvCtRv~H~~CL~r~   47 (89)
T d1wila_          13 VNDEMCDVC-EVWTAESLFPC-RVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTT-CCCCSSCCSSC-SSSSSCCCHHHHHHH
T ss_pred             CcCcccccc-Ccccccceecc-eeecchhhHHHHHHh
Confidence            456779999 66655543322 239999999999985

>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=93.15  E-value=0.0085  Score=35.31  Aligned_cols=47  Identities=30%  Similarity=0.558  Sum_probs=31.3

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC----CCCCccccccc
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT----NPNCPICRSTA  125 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~~  125 (192)
                      .....|.+|.+.   ++.+.- ..|.-.||..|+...+..    .-.||.|+...
T Consensus         7 ~~~~~C~~C~~~---g~lv~C-d~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           7 HHMEFCRVCKDG---GELLCC-DTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---SSCBCC-SSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCcCCCcCCCCC---CeEEEe-CCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            344569999864   433333 349999999999765543    22499997643

>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=91.90  E-value=0.38  Score=29.24  Aligned_cols=48  Identities=21%  Similarity=0.447  Sum_probs=31.4

Q ss_pred             ccccCccccCCCceEEcCCCCCcccHHhHH--HHH-cC--CCCCccccccccc
Q 040080           80 CAVCLDKFNKGDKCRLLPICNHSFHAQCVD--AWL-LT--NPNCPICRSTANS  127 (192)
Q Consensus        80 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~--~wl-~~--~~~CP~Cr~~~~~  127 (192)
                      +-||...+......+.-..|.-.||..|+.  ..- ..  +-.||.|+....+
T Consensus        14 ~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~gp   66 (79)
T d1wepa_          14 YCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFGP   66 (79)
T ss_dssp             CSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSCS
T ss_pred             EeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcCC
Confidence            449998766554444445599999999994  221 22  3469999875433

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Death associated transcription factor 1, Datf1 (DIO-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.53  E-value=0.42  Score=28.58  Aligned_cols=47  Identities=23%  Similarity=0.470  Sum_probs=29.4

Q ss_pred             CCcccccCccccCCCceEEcCCCCCcccHHhHH------HH---HcCCCCCccccccc
Q 040080           77 PIECAVCLDKFNKGDKCRLLPICNHSFHAQCVD------AW---LLTNPNCPICRSTA  125 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~------~w---l~~~~~CP~Cr~~~  125 (192)
                      ...| ||......+. .+.-..|.-.||..|+.      ..   ....-.||.|+..-
T Consensus        16 ~~~C-iC~~~~~~~~-mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~~   71 (76)
T d1wema_          16 ALYC-ICRQPHNNRF-MICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             CCCS-TTCCCCCSSC-EEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             cCEE-ECCCccCCCe-EEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCcC
Confidence            3447 8887654443 34444499999999982      11   12245799997644

>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=86.92  E-value=0.14  Score=31.84  Aligned_cols=51  Identities=18%  Similarity=0.404  Sum_probs=32.8

Q ss_pred             CCcccccCccccC-CCceEEcCCCCCcccHHhHHHHH-----cC---CCCCccccccccc
Q 040080           77 PIECAVCLDKFNK-GDKCRLLPICNHSFHAQCVDAWL-----LT---NPNCPICRSTANS  127 (192)
Q Consensus        77 ~~~C~IC~~~~~~-~~~~~~~~~C~H~fh~~Ci~~wl-----~~---~~~CP~Cr~~~~~  127 (192)
                      ...|.||...... ...++.-..|...||..|+.+.+     ..   .-.||.|......
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~~~   75 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKR   75 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHCC
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchHhh
Confidence            4569999875433 23444444599999999986432     11   2359999775543

>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=86.73  E-value=0.22  Score=29.75  Aligned_cols=40  Identities=18%  Similarity=0.468  Sum_probs=29.8

Q ss_pred             CCCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcC
Q 040080           75 SSPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLT  114 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~  114 (192)
                      .....|.+|.+.+++..-+..-..=+|.||..|-+..+++
T Consensus         6 ~~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~   45 (80)
T d2cs3a1           6 SGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   45 (80)
T ss_dssp             CCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CCceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHh
Confidence            3456799999999876544433335799999999998865

>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=86.03  E-value=0.04  Score=31.15  Aligned_cols=45  Identities=18%  Similarity=0.407  Sum_probs=28.2

Q ss_pred             cccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccccc
Q 040080           79 ECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPICRS  123 (192)
Q Consensus        79 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~  123 (192)
                      .|.+|...|.....--.-..||.+|+..|....-.....|..|..
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            488888888644322223349999999997655444556888854

>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=85.73  E-value=0.2  Score=28.92  Aligned_cols=45  Identities=18%  Similarity=0.401  Sum_probs=30.5

Q ss_pred             CCCcccccCccccCCCceEEcCCCCCcccHHhHHHHHcCCCCCccc
Q 040080           76 SPIECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLLTNPNCPIC  121 (192)
Q Consensus        76 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~C  121 (192)
                      ....|--|...+... ....-+.|++.|+.+|-.---.+-..||-|
T Consensus        14 ~~~~C~gC~~~l~~~-~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKDQ-HVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTTS-EEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCCC-ceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            356799999888544 334456699999999965422333459988

>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=82.70  E-value=0.12  Score=30.97  Aligned_cols=47  Identities=19%  Similarity=0.396  Sum_probs=31.1

Q ss_pred             CcccccCccccCCCceEEcCCCCCcccHHhHHHHHc----CCCCCccccccc
Q 040080           78 IECAVCLDKFNKGDKCRLLPICNHSFHAQCVDAWLL----TNPNCPICRSTA  125 (192)
Q Consensus        78 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~----~~~~CP~Cr~~~  125 (192)
                      ..| ||......+...+.-..|...||..|+..-..    ..-.||.|+..-
T Consensus        17 ~~C-~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~~~~~~~~C~~C~~~~   67 (72)
T d1weea_          17 VDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELS   67 (72)
T ss_dssp             ECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHHC
T ss_pred             EEe-eCCCCcCCCCeEEEeCCCCCcCchhhcCCccccCCCCcEECcCCcCcC
Confidence            347 78876655655555556999999999854211    133599997754

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=82.10  E-value=2.7  Score=25.80  Aligned_cols=53  Identities=19%  Similarity=0.342  Sum_probs=35.3

Q ss_pred             CCCCcccccCccccCC---CceEEcCCCCCcccHHhHHHHH-cCCCCCccccccccc
Q 040080           75 SSPIECAVCLDKFNKG---DKCRLLPICNHSFHAQCVDAWL-LTNPNCPICRSTANS  127 (192)
Q Consensus        75 ~~~~~C~IC~~~~~~~---~~~~~~~~C~H~fh~~Ci~~wl-~~~~~CP~Cr~~~~~  127 (192)
                      .....|.||-+.+...   +....--.|+--.|..|..-=. ..++.||.|++....
T Consensus        14 ~~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Ykr   70 (93)
T d1weoa_          14 LDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKR   70 (93)
T ss_dssp             CSSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCC
T ss_pred             cccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhhh
Confidence            3456799999987532   2211122277778999987444 347789999998754

>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=81.57  E-value=0.74  Score=27.73  Aligned_cols=49  Identities=27%  Similarity=0.476  Sum_probs=30.5

Q ss_pred             CCcccccCccccCCCceEEc-CCCCCcccHHhHHH----HHc-----CCCCCcccccccc
Q 040080           77 PIECAVCLDKFNKGDKCRLL-PICNHSFHAQCVDA----WLL-----TNPNCPICRSTAN  126 (192)
Q Consensus        77 ~~~C~IC~~~~~~~~~~~~~-~~C~H~fh~~Ci~~----wl~-----~~~~CP~Cr~~~~  126 (192)
                      ...| ||......+..+... ..|...||..|+.-    +-.     ..-.||.|+..-.
T Consensus        16 ~~~C-~C~~~~~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~~   74 (78)
T d1wewa_          16 KVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSG   74 (78)
T ss_dssp             CCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCCS
T ss_pred             ccEe-ECCCccCCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcCC
Confidence            3457 899877654444332 14999999999831    100     1245999987543