Citrus Sinensis ID: 042258

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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--
Protein Sequence
LWLLVSLYCYAVEVVIWLILERRNPWSGSLIDIMIPDPDVRFTLKLAAVETGNWLSGLIQKFRGDSEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNLELDV
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEccHHHHcccccccccccccccccccccccccHHHHccccEEEEcccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHcccccccccccccccccccHHHHHHHHHcccccccccccHHHHHHHccEEEEEccccccccccccEEEHHHccccccEEccccccccccHHHHHHHHHcccccccccccccccccccc
Coil and Loop (DISEMBL)
LWLLVSLYCYAVEVVIWLILErrnpwsgslidimipdpdvRFTLKLAAVETGNWLSGLIQKFrgdseetqglcpqelpvslpqmsykngetemtsntdcaiclddfiegetcksfpecnhifHLHCIDQWLkhrlncpvcrnplcrnleldv
Flexible Loop (DISEMBL)
LWLLVSLYCYAVEVVIWLILERRNPWSGSLIDIMIPDPDVRFTLKLAAVETGNWLSGLIQKFRGDSEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRnplcrnleldv
Low Complexity Region (SEG)
LWLLVSLYCYAVEVVIWLILERRNPWSGSLIDIMIPDPDVRFTLKLAAVETGNWLSGLIQKFRGDSEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNLELDV
Disordered region (IsUnstruct)
*WLLVSLYCYAVEVVIWLILERRNPWSGSLIDIMIPDPDVRFTLKLAAVETGNWLSGLIQKFR********************************NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNL****
Disordered Region (DISOPRED)
LWLLVSLYCYAVEVVIWLILERRNPWSGSLIDIMIPDPDVRFTLKLAAVET*************************LPVSLPQMSYKNG****TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL********
Disordered Region (DISEMBL)
LWLLVSLYCYAVEVVIWLILERRNPWSGSLIDIMIPDPDVRFTLKLAAVETGNWLSGLIQKFRGDSEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNLELDV
Disordered Region (DISPRO)
LWLLVSLYCYAVEVVIWLILERRNPWSGSLIDIMIPDPDVRFTLKLAAVETGNWLSGLIQKFRGDSEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLC*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
LWLLVSLYCYAVEVVIWLILERRNPWSGSLIDIMIPDPDVRFTLKLAAVETGNWLSGLIQKFRGDSEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNLELDV
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	152	2.2.26 [Sep-21-2011]
Q8GT74	241	NEP1-interacting protein	yes	no	0.796	0.502	0.312	5e-13
Q9SG96	181	RING-H2 finger protein AT	no	no	0.638	0.535	0.375	5e-12
Q9SJJ7	237	RING-H2 finger protein AT	no	no	0.401	0.257	0.476	5e-12
Q9LZV8	159	RING-H2 finger protein AT	no	no	0.519	0.496	0.419	6e-12
O22755	185	RING-H2 finger protein AT	no	no	0.625	0.513	0.378	6e-12
Q9FKX5	221	NEP1-interacting protein-	no	no	0.5	0.343	0.4	7e-12
Q9DBU5	667	E3 ubiquitin-protein liga	yes	no	0.519	0.118	0.345	9e-12
Q9LF64	362	RING-H2 finger protein AT	no	no	0.401	0.168	0.467	2e-11
Q6NML0	225	E3 ubiquitin-protein liga	no	no	0.407	0.275	0.451	2e-11
Q9FLC6	176	RING-H2 finger protein AT	no	no	0.506	0.437	0.437	2e-11

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

 Score = 73.2 bits (178), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 45/144 (31%), Positives = 71/144 (49%), Gaps = 23/144 (15%)

Query: 8   YCYAVEVVIWL-----ILERRNPWSGSLIDIMIPDPDVRFTLKLAAVETGNWLSGLIQKF 62
           + Y ++V++ L     + ER  P   S +   +   D  F    +  +TG          
Sbjct: 114 FLYLIDVIVSLLSGRLVRERIGPAMLSAVQSQMGAVDTAFDDHTSLFDTGG--------- 164

Query: 63  RGDSEETQGLCPQELPVSLPQMSYK-NGETEMTSNTD-CAICLDDFIEGETCKSFPECNH 120
                 ++GL   +L   +P+M+   N  T+ + NTD C++CL DF  GET +S P C+H
Sbjct: 165 ------SKGL-TGDLVEKIPKMTITGNNNTDASENTDSCSVCLQDFQLGETVRSLPHCHH 217

Query: 121 IFHLHCIDQWLKHRLNCPVCRNPL 144
           +FHL CID WL    +CP+CR  +
Sbjct: 218 MFHLPCIDNWLLRHGSCPMCRRDI 241

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

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

 Score = 70.1 bits (170), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 39/104 (37%), Positives = 54/104 (51%), Gaps = 7/104 (6%)

Query: 41  RFTLKLAAVETGNWLSGLIQKFRGDSEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCA 100
           RFT         N  + L +       + Q L  +++PV L    Y +G  +M + T+C 
Sbjct: 63  RFTSDDQVSNASNANANLGRLAAATGLKKQAL--KQIPVGL----YGSGIIDMKA-TECL 115

Query: 101 ICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           ICL DF +GE  +  P+CNH FH+ CID WL  R +CP CR  L
Sbjct: 116 ICLGDFEDGEKVRVLPKCNHGFHVRCIDTWLLSRSSCPTCRQSL 159

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SJJ7|ATL57_ARATH RING-H2 finger protein ATL57 OS=Arabidopsis thaliana GN=ATL57 PE=2 SV=1

 Score = 70.1 bits (170), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 30/63 (47%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 80  SLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPV 139
           SLP   Y     +   N DC ICL DF EGET K  P C H+FH+ C+D WL   + CP+
Sbjct: 123 SLPVYRYTKAAKQ--RNEDCVICLSDFEEGETVKVIPHCGHVFHVDCVDTWLSSYVTCPL 180

Query: 140 CRN 142
           CR+
Sbjct: 181 CRS 183

Arabidopsis thaliana (taxid: 3702)

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

 Score = 69.7 bits (169), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 34/81 (41%), Positives = 47/81 (58%), Gaps = 2/81 (2%)

Query: 64  GDSEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFH 123
           G   +  GL  +EL    P   Y +GE ++ + T+CAICL +F +GE  +  P CNH FH
Sbjct: 72  GTVADRAGLKKRELK-KFPVAEYGSGEVKIAA-TECAICLGEFADGERVRVLPPCNHSFH 129

Query: 124 LHCIDQWLKHRLNCPVCRNPL 144
           + CID WL    +CP CR+ L
Sbjct: 130 MSCIDTWLVSHSSCPNCRHSL 150

Arabidopsis thaliana (taxid: 3702)

>sp|O22755|ATL44_ARATH RING-H2 finger protein ATL44 OS=Arabidopsis thaliana GN=ATL44 PE=2 SV=1

 Score = 69.7 bits (169), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 39/103 (37%), Positives = 52/103 (50%), Gaps = 8/103 (7%)

Query: 46  LAAVETGNWLSGLIQKFRGDSEETQGLCPQELPVSLPQMSYKNGET------EMTSNTDC 99
           LAAV    WL        GDS        ++   SLP+ ++   E+      E   +T+C
Sbjct: 45  LAAVVRCAWLRRFTAG--GDSPSPNKGLKKKALQSLPRSTFTAAESTSGAAAEEGDSTEC 102

Query: 100 AICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRN 142
           AICL DF +GE  +  P C H FH+ CID+WL  R +CP CR 
Sbjct: 103 AICLTDFADGEEIRVLPLCGHSFHVECIDKWLVSRSSCPSCRR 145

Arabidopsis thaliana (taxid: 3702)

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

 Score = 69.7 bits (169), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 32/80 (40%), Positives = 49/80 (61%), Gaps = 4/80 (5%)

Query: 65  DSEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHL 124
           D+  ++GL    L   +P++   +   E+ S   C++CL DF  GET +S P C+H+FHL
Sbjct: 146 DTAISKGLTGDSLN-RIPKVRITDTSPEIVS---CSVCLQDFQVGETVRSLPHCHHMFHL 201

Query: 125 HCIDQWLKHRLNCPVCRNPL 144
            CID+WL+   +CP+CR  L
Sbjct: 202 PCIDKWLRRHASCPLCRRHL 221

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q9DBU5|RNF6_MOUSE E3 ubiquitin-protein ligase RNF6 OS=Mus musculus GN=Rnf6 PE=1 SV=1

 Score = 69.3 bits (168), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 2/81 (2%)

Query: 64  GDSEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFH 123
           GD +  +GL  +++  +L   SY+    +      C++C+ D++ G   +  P C H FH
Sbjct: 580 GDDDPIRGLTKEQID-NLSTRSYEQDGVDSELGKVCSVCISDYVAGNKLRQLP-CLHEFH 637

Query: 124 LHCIDQWLKHRLNCPVCRNPL 144
           +HCID+WL     CPVCR P+
Sbjct: 638 IHCIDRWLSENCTCPVCRRPV 658

E3 ubiquitin-protein ligase mediating 'Lys-48'-linked polyubiquitination of LIMK1 and its subsequent targeting to the proteasome for degradation. Negatively regulates axonal outgrowth through regulation of the LIMK1 turnover. Mediates 'Lys-6' and 'Lys-27'-linked polyubiquitination of AR/androgen receptor thereby modulating its transcriptional activity. May also bind DNA and function as a transcriptional regulator.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9LF64|ATL52_ARATH RING-H2 finger protein ATL52 OS=Arabidopsis thaliana GN=ATL52 PE=2 SV=1

 Score = 68.2 bits (165), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 29/62 (46%), Positives = 40/62 (64%), Gaps = 1/62 (1%)

Query: 80  SLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPV 139
           S+    YK+G+      +DC++CL +F E E+ +  P+CNH FHL CID WLK   NCP+
Sbjct: 124 SITVYKYKSGDG-FVDGSDCSVCLSEFEENESLRLLPKCNHAFHLPCIDTWLKSHSNCPL 182

Query: 140 CR 141
           CR
Sbjct: 183 CR 184

Arabidopsis thaliana (taxid: 3702)

>sp|Q6NML0|ATL76_ARATH E3 ubiquitin-protein ligase ATL76 OS=Arabidopsis thaliana GN=ATL76 PE=1 SV=1

 Score = 68.2 bits (165), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 28/62 (45%), Positives = 37/62 (59%)

Query: 81  LPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVC 140
            P +SY           +C ICL DF+ GE  +  P+CNH FH+ CID+WL+H L CP C
Sbjct: 117 FPVVSYSREMNLPGIGEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQHHLTCPKC 176

Query: 141 RN 142
           R+
Sbjct: 177 RH 178

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|Q9FLC6|ATL73_ARATH RING-H2 finger protein ATL73 OS=Arabidopsis thaliana GN=ATL73 PE=2 SV=1

 Score = 68.2 bits (165), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 35/80 (43%), Positives = 50/80 (62%), Gaps = 3/80 (3%)

Query: 65  DSEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHL 124
           ++   +G+  + L V +P  SY + E +M + T+C ICL DF+EGET +  P+CNH FH+
Sbjct: 82  NANVAKGIKKRALKV-IPVDSY-SPELKMKA-TECLICLGDFVEGETVRVLPKCNHGFHV 138

Query: 125 HCIDQWLKHRLNCPVCRNPL 144
            CID WL    +CP CR  L
Sbjct: 139 KCIDTWLLSHSSCPTCRQSL 158

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	152
449466635	162	PREDICTED: putative RING-H2 finger prote	0.434	0.407	0.484	5e-13
242095466	168	hypothetical protein SORBIDRAFT_10g00986	0.611	0.553	0.385	7e-12
357454085	219	RING finger family protein [Medicago tru	0.592	0.410	0.434	7e-12
147858036	209	hypothetical protein VITISV_003141 [Viti	0.414	0.301	0.507	1e-11
255581815	150	protein with unknown function [Ricinus c	0.809	0.82	0.340	2e-11
255565501	254	zinc finger protein, putative [Ricinus c	0.460	0.275	0.506	2e-11
224054252	183	predicted protein [Populus trichocarpa]	0.467	0.387	0.486	2e-11
255564226	239	RING-H2 finger protein ATL3L, putative [	0.480	0.305	0.460	2e-11
413925756	235	putative RING zinc finger domain superfa	0.703	0.455	0.330	3e-11
297737435	264	unnamed protein product [Vitis vinifera]	0.644	0.371	0.323	3e-11

>gi|449466635|ref|XP_004151031.1| PREDICTED: putative RING-H2 finger protein ATL53-like [Cucumis sativus] gi|449521203|ref|XP_004167619.1| PREDICTED: putative RING-H2 finger protein ATL53-like [Cucumis sativus]

 Score = 79.3 bits (194), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 32/66 (48%), Positives = 43/66 (65%)

Query: 79  VSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCP 138
           +S     Y  G   +  N DC+ICLD+F EGE C+  P+C H+FH  CID+WL +  NCP
Sbjct: 87  ISTRLFQYGVGGGVIGKNADCSICLDEFTEGEICRMLPKCKHVFHRFCIDRWLPNERNCP 146

Query: 139 VCRNPL 144
           VCR+P+
Sbjct: 147 VCRSPV 152

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 = 75.5 bits (184), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 37/96 (38%), Positives = 51/96 (53%), Gaps = 3/96 (3%)

Query: 46  LAAVETGNWLSGLIQKFRGDSEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDD 105
           L + +TG   +   Q+   D    +GL P EL V+LP   +K  + E     DCA+CL+ 
Sbjct: 36  LGSRDTGQHANHQDQERVEDGHGRRGLSPGEL-VTLPCHDFKAADGEAAG--DCAVCLEA 92

Query: 106 FIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCR 141
           F  G+ C+  P C H FH  C+D WL+    CPVCR
Sbjct: 93  FQAGDRCRQLPRCEHCFHAECVDSWLRKSSKCPVCR 128

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357454085|ref|XP_003597323.1| RING finger family protein [Medicago truncatula] gi|355486371|gb|AES67574.1| RING finger family protein [Medicago truncatula]

 Score = 75.5 bits (184), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 43/99 (43%), Positives = 57/99 (57%), Gaps = 9/99 (9%)

Query: 53  NWLSGLIQKFRGDSEETQGLCPQELPV--SLPQMSYKNGET-EMTSNTDCAICLDDFIEG 109
           NW+ G   +F  +S +   L   EL +  SLP   +K  E  EMT N DCAICL +F  G
Sbjct: 92  NWIEG---QFHDESIQGSDL---ELSIINSLPMYQFKKNEAQEMTINVDCAICLGEFEGG 145

Query: 110 ETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNL 148
           E  K  P CNH FH+ CID+W +   +CP+CR+ + R L
Sbjct: 146 ELLKLLPNCNHGFHVSCIDKWFQLHSSCPLCRSRVYRVL 184

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147858036|emb|CAN80353.1| hypothetical protein VITISV_003141 [Vitis vinifera]

 Score = 74.7 bits (182), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 32/63 (50%), Positives = 41/63 (65%)

Query: 80  SLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPV 139
           SLP   +K  E    SNTDCA+CL +F EGE  K  P C+H+FH+ CID W +   NCP+
Sbjct: 41  SLPIAQFKKNEGPSHSNTDCAVCLGEFEEGEFLKHLPNCSHVFHIPCIDTWFESHSNCPL 100

Query: 140 CRN 142
           CR+
Sbjct: 101 CRS 103

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255581815|ref|XP_002531708.1| protein with unknown function [Ricinus communis] gi|223528651|gb|EEF30667.1| protein with unknown function [Ricinus communis]

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 45/132 (34%), Positives = 65/132 (49%), Gaps = 9/132 (6%)

Query: 11  AVEVVIWLILERRNPWSGSLIDIMIPDPDVRFTLKLAAVETGNWLSGLIQKFRGDSEETQ 70
           A + + WL   RRN   G  +          F L L + E  + L  L+ K    S+ T+
Sbjct: 25  ACKCIFWLQFGRRNLDLGHGLR---SSQHRSFLLSLRSHEYLDILQWLVDK----SKATR 77

Query: 71  GLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQW 130
           G     +   LP + Y + E ++     C ICL+D+++ E C+  P C H+FH HCI+QW
Sbjct: 78  G--QYAIDNLLPTVIYGDNEMKIPEFEVCVICLEDYMDRELCRILPSCRHMFHSHCIEQW 135

Query: 131 LKHRLNCPVCRN 142
           LK  L CP CR 
Sbjct: 136 LKWNLTCPTCRG 147

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255565501|ref|XP_002523741.1| zinc finger protein, putative [Ricinus communis] gi|223537045|gb|EEF38681.1| zinc finger protein, putative [Ricinus communis]

 Score = 73.6 bits (179), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/73 (50%), Positives = 47/73 (64%), Gaps = 3/73 (4%)

Query: 70  QGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQ 129
           +GL P E+  SLP  SY +GE +     +CA+CL +F E ET KS P C H+FHL CI+ 
Sbjct: 106 KGLDP-EVIKSLPVYSYYHGEAKY--QIECAVCLGEFEEKETVKSIPYCKHMFHLECIET 162

Query: 130 WLKHRLNCPVCRN 142
           WLK  + CPVCR 
Sbjct: 163 WLKLHVTCPVCRG 175

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224054252|ref|XP_002298167.1| predicted protein [Populus trichocarpa] gi|222845425|gb|EEE82972.1| predicted protein [Populus trichocarpa]

 Score = 73.6 bits (179), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 36/74 (48%), Positives = 48/74 (64%), Gaps = 3/74 (4%)

Query: 69  TQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCID 128
           T+GL PQ +  SLP  SY +G+ +     +CAICL +F E E  K  P+C+H+FHL CID
Sbjct: 61  TRGLDPQVVN-SLPVYSYYHGDVKY--QIECAICLGEFEEKEAVKMIPKCHHVFHLQCID 117

Query: 129 QWLKHRLNCPVCRN 142
            WL+  + CPVCR 
Sbjct: 118 TWLEMHVTCPVCRG 131

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255564226|ref|XP_002523110.1| RING-H2 finger protein ATL3L, putative [Ricinus communis] gi|223537672|gb|EEF39295.1| RING-H2 finger protein ATL3L, putative [Ricinus communis]

 Score = 73.6 bits (179), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 35/76 (46%), Positives = 50/76 (65%), Gaps = 3/76 (3%)

Query: 69  TQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCID 128
           +QGL P  L +SLP + Y + +T   S  +CA+CL +F+EGE  +  P+CNH FH+ CID
Sbjct: 82  SQGLDPSVL-LSLPVLVYTS-KTHYRS-LECAVCLSEFVEGEKGRVLPKCNHTFHIPCID 138

Query: 129 QWLKHRLNCPVCRNPL 144
            W +   NCP+CR P+
Sbjct: 139 MWFRSHSNCPLCRAPI 154

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413925756|gb|AFW65688.1| putative RING zinc finger domain superfamily protein [Zea mays]

 Score = 73.6 bits (179), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 37/112 (33%), Positives = 57/112 (50%), Gaps = 5/112 (4%)

Query: 37  DPDVRFTL--KLAAVETGNWLSGLIQKFRGDSEETQGLCPQELPVSLPQMSYKNGETEMT 94
           DP V+  +  ++ A ++ +    L   F   + + +G+ P     +LP M++        
Sbjct: 125 DPAVQSAVDSQMNAADSQDMAPTLADMFETGAADAKGM-PAAAVAALPIMAFTEHTVADG 183

Query: 95  SN--TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           S     C++CL DF  GET +S PEC H FHL CID WL    +CP+CR  +
Sbjct: 184 SGEPIGCSVCLQDFEAGETARSLPECGHTFHLPCIDVWLLRHASCPLCRRAV 235

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 73.2 bits (178), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 34/105 (32%), Positives = 54/105 (51%), Gaps = 7/105 (6%)

Query: 47  AAVETGNWLSGLIQKFRGDSEE------TQGLCPQELPVSLPQMSYKNGETEMTSNTDCA 100
           A ++   W    ++   G++E+       +GL P      LP+ ++ +   EM +   C 
Sbjct: 158 AVLKAYQWQISTLETNYGETEDFYNISGAKGL-PHNFIEKLPKSNFCHSNAEMYNEISCT 216

Query: 101 ICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLC 145
           ICL DF +GE  +  P C H FH+ C+DQWL    +CP+CR  +C
Sbjct: 217 ICLQDFKDGEMTRGLPSCRHYFHMECVDQWLTLHGSCPMCRKDVC 261

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	152
TAIR|locus:2207066	413	AT1G72220 [Arabidopsis thalian	0.467	0.171	0.438	7.8e-15
TAIR|locus:2011491	178	AT1G53010 [Arabidopsis thalian	0.921	0.786	0.298	1.4e-14
TAIR|locus:505006547	367	AT4G33565 [Arabidopsis thalian	0.526	0.217	0.435	1.8e-14
TAIR|locus:2057861	237	AT2G27940 [Arabidopsis thalian	0.513	0.329	0.439	7.9e-14
TAIR|locus:2181032	159	DAFL2 "DAF-Like gene 2" [Arabi	0.519	0.496	0.419	7.9e-14
TAIR|locus:2028406	225	AT1G49210 [Arabidopsis thalian	0.513	0.346	0.405	1e-13
TAIR|locus:2153554	176	DAF "DEFECTIVE IN ANTHER DEHIS	0.473	0.409	0.466	1e-13
RGD|1306092	663	Rnf6 "ring finger protein (C3H	0.519	0.119	0.345	1.2e-13
MGI|MGI:1921382	667	Rnf6 "ring finger protein (C3H	0.519	0.118	0.345	1.6e-13
TAIR|locus:2028506	251	AT1G49220 [Arabidopsis thalian	0.513	0.310	0.421	2.1e-13

TAIR|locus:2207066 AT1G72220 [Arabidopsis thaliana (taxid:3702)]

 Score = 180 (68.4 bits), Expect = 7.8e-15, Sum P(2) = 7.8e-15
 Identities = 32/73 (43%), Positives = 45/73 (61%)

Query:    69 TQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCID 128
             T GL  Q +  S+   +YK G+  +   TDC +CL++F E E+ +  P+CNH FH+ CID
Sbjct:   149 TTGL-QQSIINSITICNYKRGDG-LIERTDCPVCLNEFEEDESLRLLPKCNHAFHISCID 206

Query:   129 QWLKHRLNCPVCR 141
              WL    NCP+CR
Sbjct:   207 TWLSSHTNCPLCR 219

GO:0005634 "nucleus" evidence=ISM

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

GO:0010413 "glucuronoxylan metabolic process" evidence=RCA

GO:0045492 "xylan biosynthetic process" evidence=RCA

TAIR|locus:2011491 AT1G53010 [Arabidopsis thaliana (taxid:3702)]

 Score = 186 (70.5 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 45/151 (29%), Positives = 84/151 (55%)

Query:     3 LLVSLYCYAVEVVIWLILER-RNPWSGSLIDIMIPDPDVRFTLKLAAVETGNWL--SGL- 58
             L+V +   A+ +VI++I++    P+ G+ +D+ + +  V+   + A + T + +  +GL 
Sbjct:    27 LVVLIATSALILVIYVIIDCILRPFLGTCLDLDL-EIGVQRGQQRARIVTYHTIISTGLR 85

Query:    59 IQKFRGDSEETQGLCPQELPVSLPQM-----SYKNGETEMTSNTDCAICLDDFIEGETCK 113
             +  F  + ++ +GL    +   LP++     +++  E +   + +CAICL  ++  E C+
Sbjct:    86 LPDFEREGKK-RGLKQSVIETLLPKLLVGQGNHEEDEEKSLESRECAICLSGYVVNEECR 144

Query:   114 SFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
              FP C HI+H  CID WLK+ L CP CR  L
Sbjct:   145 VFPVCRHIYHALCIDAWLKNHLTCPTCRKDL 175

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

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

 Score = 190 (71.9 bits), Expect = 1.8e-14, P = 1.8e-14
 Identities = 37/85 (43%), Positives = 51/85 (60%)

Query:    69 TQGLCPQELP-VSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCI 127
             T GL P  +  + + Q S K+G  E    TDC++CL +F E ET +  P+C H FHL+CI
Sbjct:   189 TIGLNPTVISSIKVCQYSKKDGVVE---GTDCSVCLSEFEEEETLRLLPKCKHAFHLYCI 245

Query:   128 DQWLKHRLNCPVCRNPLCR-NLELD 151
             D WL+   NCP+CR P+   N  +D
Sbjct:   246 DTWLRSHTNCPLCRAPIVEANTMID 270

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

GO:0005886 "plasma membrane" evidence=IDA

TAIR|locus:2057861 AT2G27940 [Arabidopsis thaliana (taxid:3702)]

 Score = 179 (68.1 bits), Expect = 7.9e-14, P = 7.9e-14
 Identities = 36/82 (43%), Positives = 46/82 (56%)

Query:    70 QGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQ 129
             +GL  Q +  SLP   Y     +   N DC ICL DF EGET K  P C H+FH+ C+D 
Sbjct:   114 RGLDSQAVR-SLPVYRYTKAAKQR--NEDCVICLSDFEEGETVKVIPHCGHVFHVDCVDT 170

Query:   130 WLKHRLNCPVCR-NPLCRNLEL 150
             WL   + CP+CR N L  + +L
Sbjct:   171 WLSSYVTCPLCRSNQLFSDKDL 192

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

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

 Score = 179 (68.1 bits), Expect = 7.9e-14, P = 7.9e-14
 Identities = 34/81 (41%), Positives = 47/81 (58%)

Query:    64 GDSEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFH 123
             G   +  GL  +EL    P   Y +GE ++ + T+CAICL +F +GE  +  P CNH FH
Sbjct:    72 GTVADRAGLKKRELK-KFPVAEYGSGEVKIAA-TECAICLGEFADGERVRVLPPCNHSFH 129

Query:   124 LHCIDQWLKHRLNCPVCRNPL 144
             + CID WL    +CP CR+ L
Sbjct:   130 MSCIDTWLVSHSSCPNCRHSL 150

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

TAIR|locus:2028406 AT1G49210 [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 1.0e-13, P = 1.0e-13
 Identities = 32/79 (40%), Positives = 45/79 (56%)

Query:    66 SEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLH 125
             S   +G+  + L +  P +SY           +C ICL DF+ GE  +  P+CNH FH+ 
Sbjct:   103 SSSNKGIKKKALRM-FPVVSYSREMNLPGIGEECVICLSDFVSGEQLRLLPKCNHGFHVR 161

Query:   126 CIDQWLKHRLNCPVCRNPL 144
             CID+WL+H L CP CR+ L
Sbjct:   162 CIDKWLQHHLTCPKCRHCL 180

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

TAIR|locus:2153554 DAF "DEFECTIVE IN ANTHER DEHISCENCE1- ( DAD1-) Activating Factor" [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 1.0e-13, P = 1.0e-13
 Identities = 35/75 (46%), Positives = 48/75 (64%)

Query:    70 QGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQ 129
             +G+  + L V +P  SY + E +M + T+C ICL DF+EGET +  P+CNH FH+ CID 
Sbjct:    87 KGIKKRALKV-IPVDSY-SPELKMKA-TECLICLGDFVEGETVRVLPKCNHGFHVKCIDT 143

Query:   130 WLKHRLNCPVCRNPL 144
             WL    +CP CR  L
Sbjct:   144 WLLSHSSCPTCRQSL 158

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

RGD|1306092 Rnf6 "ring finger protein (C3H2C3 type) 6" [Rattus norvegicus (taxid:10116)]

 Score = 174 (66.3 bits), Expect = 1.2e-13, Sum P(2) = 1.2e-13
 Identities = 28/81 (34%), Positives = 45/81 (55%)

Query:    64 GDSEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFH 123
             GD +  +GL  +++  +L   SY+    +      C++C+ D++ G   +  P C H FH
Sbjct:   576 GDDDPIRGLTKEQID-NLSTRSYEQSAVDSELGKVCSVCISDYVAGNKLRQLP-CLHEFH 633

Query:   124 LHCIDQWLKHRLNCPVCRNPL 144
             +HCID+WL     CPVCR P+
Sbjct:   634 IHCIDRWLSENCTCPVCRRPV 654

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=ISO

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

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

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

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=ISO

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=ISO

GO:0016605 "PML body" evidence=ISO

GO:0030424 "axon" evidence=ISO

GO:0030517 "negative regulation of axon extension" evidence=ISO

GO:0044314 "protein K27-linked ubiquitination" evidence=ISO

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISO

GO:0050681 "androgen receptor binding" evidence=ISO

GO:0060765 "regulation of androgen receptor signaling pathway" evidence=ISO

GO:0070936 "protein K48-linked ubiquitination" evidence=ISO

GO:0085020 "protein K6-linked ubiquitination" evidence=ISO

MGI|MGI:1921382 Rnf6 "ring finger protein (C3H2C3 type) 6" [Mus musculus (taxid:10090)]

 Score = 172 (65.6 bits), Expect = 1.6e-13, Sum P(2) = 1.6e-13
 Identities = 28/81 (34%), Positives = 45/81 (55%)

Query:    64 GDSEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFH 123
             GD +  +GL  +++  +L   SY+    +      C++C+ D++ G   +  P C H FH
Sbjct:   580 GDDDPIRGLTKEQID-NLSTRSYEQDGVDSELGKVCSVCISDYVAGNKLRQLP-CLHEFH 637

Query:   124 LHCIDQWLKHRLNCPVCRNPL 144
             +HCID+WL     CPVCR P+
Sbjct:   638 IHCIDRWLSENCTCPVCRRPV 658

GO:0003677 "DNA binding" evidence=IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO;IDA

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

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IDA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0016605 "PML body" evidence=IDA

GO:0016874 "ligase activity" evidence=IEA

GO:0030424 "axon" evidence=IDA

GO:0030517 "negative regulation of axon extension" evidence=IGI;IMP

GO:0042995 "cell projection" evidence=IEA

GO:0044314 "protein K27-linked ubiquitination" evidence=ISO

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISO;IDA

GO:0046872 "metal ion binding" evidence=IEA

GO:0050681 "androgen receptor binding" evidence=ISO

GO:0060765 "regulation of androgen receptor signaling pathway" evidence=ISO

GO:0070936 "protein K48-linked ubiquitination" evidence=IMP

GO:0085020 "protein K6-linked ubiquitination" evidence=ISO

TAIR|locus:2028506 AT1G49220 [Arabidopsis thaliana (taxid:3702)]

 Score = 175 (66.7 bits), Expect = 2.1e-13, P = 2.1e-13
 Identities = 35/83 (42%), Positives = 50/83 (60%)

Query:    63 RGDSEETQGLCPQELPVSLPQMSYKNGETEMTS-NTDCAICLDDFIEGETCKSFPECNHI 121
             RG S +  G+  + L +  P +SY + E  +   + +C ICL DF+ GE  +  P+CNH 
Sbjct:   102 RGSSNK--GIKKKALRM-FPVVSY-SPEMNLPGLDEECVICLSDFVSGEQLRLLPKCNHG 157

Query:   122 FHLHCIDQWLKHRLNCPVCRNPL 144
             FH+ CID+WL+  L CP CRN L
Sbjct:   158 FHVRCIDKWLQQHLTCPKCRNCL 180

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	152
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	3e-13
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	5e-13
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	1e-11
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	7e-10
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	2e-09
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	3e-09
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	9e-07
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	4e-06
smart00184	40	smart00184, RING, Ring finger	2e-05
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	3e-04
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	0.001
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	0.004

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

 Score = 65.4 bits (159), Expect = 3e-13
 Identities = 21/54 (38%), Positives = 33/54 (61%), Gaps = 2/54 (3%)

Query: 92  EMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWL-KHRLNCPVCRNPL 144
           E     +CAIC+ +FI+ +  +  P C+H FH+ C+D+WL  +   CPVCR  +
Sbjct: 319 EADKGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAI 371

Length = 374

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

 Score = 59.3 bits (144), Expect = 5e-13
 Identities = 22/46 (47%), Positives = 29/46 (63%), Gaps = 1/46 (2%)

Query: 98  DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNP 143
           +C ICLD+F  GE     P C H+FH  C+D+WL+    CP+CR P
Sbjct: 2   ECPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

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

 Score = 56.7 bits (137), Expect = 1e-11
 Identities = 24/53 (45%), Positives = 29/53 (54%), Gaps = 9/53 (16%)

Query: 98  DCAICLDDFIE--------GETCK-SFPECNHIFHLHCIDQWLKHRLNCPVCR 141
            CAIC + F          G+ C   + EC H FHLHCI +WLK R  CP+CR
Sbjct: 21  VCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73

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

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

 Score = 51.3 bits (123), Expect = 7e-10
 Identities = 20/48 (41%), Positives = 27/48 (56%), Gaps = 4/48 (8%)

Query: 98  DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR-LNCPVCRNPL 144
           +C ICL++F E         C H+F   CID+WLK     CP+CR P+
Sbjct: 1   ECPICLEEFRE---PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 53.6 bits (129), Expect = 2e-09
 Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 4/50 (8%)

Query: 98  DCAICLDDFIEGETCKSF----PECNHIFHLHCIDQWLKHRLNCPVCRNP 143
           +CAIC++   + E    +      CNH+F + CID W K +  CPVCR P
Sbjct: 176 ECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTP 225

Length = 238

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

 Score = 53.8 bits (129), Expect = 3e-09
 Identities = 25/71 (35%), Positives = 34/71 (47%), Gaps = 13/71 (18%)

Query: 86  YKNGETEMTSNTD--CAICLDDFIE----------GETCKSFPECNHIFHLHCIDQWLKH 133
           Y     E  +N+D  C IC+D+               T K  P C HI HLHC+  WL+ 
Sbjct: 275 YPTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLER 333

Query: 134 RLNCPVCRNPL 144
           +  CP+CR P+
Sbjct: 334 QQTCPICRRPV 344

Length = 491

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

 Score = 44.1 bits (104), Expect = 9e-07
 Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 99  CAICLDDFIEGETCK-SFPECNHIFHLHCIDQWLKHRLNCPVCRNP 143
           C  C      G+ C   +  CNH FH HCI +WL  +  CP+ R  
Sbjct: 34  CPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQT 79

Length = 88

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

 Score = 41.3 bits (97), Expect = 4e-06
 Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 3/47 (6%)

Query: 95  SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCR 141
              +C ICLD             C H+F   CI ++LK +  CP+CR
Sbjct: 1   EELECPICLDLLR---DPVVLTPCGHVFCRECILRYLKKKSKCPICR 44

Length = 45

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

 Score = 39.4 bits (92), Expect = 2e-05
 Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 4/43 (9%)

Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK-HRLNCPVC 140
           C ICL++++          C H F   CI +WL+     CP+C
Sbjct: 1   CPICLEEYL---KDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40

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

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

 Score = 39.7 bits (92), Expect = 3e-04
 Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 11/63 (17%)

Query: 87   KNGETEMTSNTDCAIC------LDDFIEGETCKSFPECNHIFHLHCIDQWLK--HRLNCP 138
            KN + + + + +CAIC      +D  +  + C     C + FH  C+ +W     R NCP
Sbjct: 1460 KNIDEKFSGHEECAICYSVLDMVDRSLPSKRC---ATCKNKFHTRCLYKWFASSARSNCP 1516

Query: 139  VCR 141
            +CR
Sbjct: 1517 LCR 1519

Length = 1525

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

 Score = 34.8 bits (80), Expect = 0.001
 Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 4/43 (9%)

Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR-LNCPVC 140
           C ICL++  +     +   C H+F   CI  WL+   + CP+C
Sbjct: 1   CPICLEEPKD---PVTILPCGHLFCSKCILSWLESGNVTCPLC 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|193335 pfam12861, zf-Apc11, Anaphase-promoting complex subunit 11 RING-H2 finger

 Score = 34.0 bits (78), Expect = 0.004
 Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 3/27 (11%)

Query: 118 CNHIFHLHCIDQWLKHRLN---CPVCR 141
           C H FH+HCI +WL    +   CP+CR
Sbjct: 52  CKHNFHMHCILKWLATETSKGLCPMCR 78

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	152
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.66
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.62
PHA02929	238	N1R/p28-like protein; Provisional	99.41
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.4
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.39
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.23
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.17
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.17
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.17
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.16
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.12
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.11
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.1
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.09
PHA02926	242	zinc finger-like protein; Provisional	99.08
PF14634	44	zf-RING_5: zinc-RING finger domain	98.98
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.95
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.93
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.88
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.82
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.82
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.78
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.74
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.67
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.65
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.61
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.56
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.55
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.51
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.5
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.45
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.44
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.41
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.39
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.39
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.37
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.3
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.3
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.25
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.24
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.21
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.18
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	98.06
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.06
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.95
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.93
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.91
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.74
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.7
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.67
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.67
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.63
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.62
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.42
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.38
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.35
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.25
KOG2660	331	consensus Locus-specific chromosome binding protei	97.18
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.17
COG5152	259	Uncharacterized conserved protein, contains RING a	97.11
PHA02862	156	5L protein; Provisional	97.0
KOG3039	303	consensus Uncharacterized conserved protein [Funct	96.89
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	96.84
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	96.79
COG5236	493	Uncharacterized conserved protein, contains RING Z	96.77
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	96.75
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.71
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.65
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	96.54
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.53
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	96.47
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	96.39
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.38
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	96.35
PHA02825	162	LAP/PHD finger-like protein; Provisional	96.3
PHA03096	284	p28-like protein; Provisional	96.26
KOG1002	791	consensus Nucleotide excision repair protein RAD16	96.23
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	96.16
KOG4739	233	consensus Uncharacterized protein involved in syna	96.03
PF04641	260	Rtf2: Rtf2 RING-finger	95.92
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	95.8
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	95.77
COG5222	427	Uncharacterized conserved protein, contains RING Z	95.76
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	95.72
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	95.71
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.65
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.54
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	95.51
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	95.42
KOG1940	276	consensus Zn-finger protein [General function pred	95.15
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	94.88
KOG3002	299	consensus Zn finger protein [General function pred	94.84
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	94.28
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	94.15
KOG3053	293	consensus Uncharacterized conserved protein [Funct	93.95
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	93.92
KOG1001	674	consensus Helicase-like transcription factor HLTF/	93.81
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	93.61
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	93.38
COG5175	480	MOT2 Transcriptional repressor [Transcription]	93.09
KOG0298	1394	consensus DEAD box-containing helicase-like transc	92.76
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	92.56
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	92.51
KOG3899	381	consensus Uncharacterized conserved protein [Funct	92.28
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	92.05
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	91.46
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	89.75
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	89.71
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	86.85
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	86.75
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	86.71
KOG1609	323	consensus Protein involved in mRNA turnover and st	86.48
KOG4367	699	consensus Predicted Zn-finger protein [Function un	86.36
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	86.0
KOG0269	839	consensus WD40 repeat-containing protein [Function	85.38
COG5109	396	Uncharacterized conserved protein, contains RING Z	84.59
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	84.03
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	83.57
TIGR00622	112	ssl1 transcription factor ssl1. This family is bas	82.85
KOG0825	1134	consensus PHD Zn-finger protein [General function	82.76
PF06844	68	DUF1244: Protein of unknown function (DUF1244); In	82.07
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	81.97
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	81.38
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	80.47

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

Probab=99.66  E-value=8.6e-17  Score=126.56  Aligned_cols=81  Identities=33%  Similarity=0.818  Sum_probs=67.4

Q ss_pred             CCCCCCCCccccCCCceeecCCCCCCCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCC-CCCCCcCccCcc
Q 042258           68 ETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR-LNCPVCRNPLCR  146 (152)
Q Consensus        68 ~~~~~~~~~i~~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~-~~CP~CR~~l~~  146 (152)
                      ...++.+..+. ++|..++......... ..|+||+++|..|++++.|| |+|.||..||++||... ..||+||.++.+
T Consensus       203 ~~~r~~k~~l~-~~p~~~f~~~~~~~~~-~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~~  279 (348)
T KOG4628|consen  203 RRNRLIKRLLK-KLPVRTFTKGDDEDAT-DTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIRT  279 (348)
T ss_pred             hhhhhHHHHHh-hCCcEEeccccccCCC-ceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence            44556666677 9999999877744443 68999999999999999999 99999999999999876 559999999988


Q ss_pred             CCCCC
Q 042258          147 NLELD  151 (152)
Q Consensus       147 ~~~~~  151 (152)
                      ....+
T Consensus       280 ~~~~~  284 (348)
T KOG4628|consen  280 DSGSE  284 (348)
T ss_pred             CCCCC
Confidence            76653

>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=1.2e-16  Score=90.91  Aligned_cols=44  Identities=50%  Similarity=1.308  Sum_probs=40.0

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCR  141 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR  141 (152)
                      .+|+||++++..++.+..++ |||.||.+|+.+|++++.+||+||
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            36999999998888889998 999999999999999999999997

...

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.41  E-value=1.3e-13  Score=104.20  Aligned_cols=67  Identities=31%  Similarity=0.831  Sum_probs=49.2

Q ss_pred             CCCceeecCCCC-CCCCCccCccccccccCCC----eeeecCCCCccccHHhHHHHHhCCCCCCCcCccCcc
Q 042258           80 SLPQMSYKNGET-EMTSNTDCAICLDDFIEGE----TCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCR  146 (152)
Q Consensus        80 ~lp~~~~~~~~~-~~~~~~~C~IC~~~~~~~~----~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~  146 (152)
                      .+|.....-... ....+.+|+||++.+.+++    ....+++|+|.||..||.+|+..+.+||+||.++..
T Consensus       157 ~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~  228 (238)
T PHA02929        157 TIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFIS  228 (238)
T ss_pred             hcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeE
Confidence            666665432221 2234588999999986543    123555699999999999999999999999998763

>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=99.40  E-value=3.1e-13  Score=84.92  Aligned_cols=46  Identities=46%  Similarity=1.097  Sum_probs=35.4

Q ss_pred             CccCccccccccCC---------CeeeecCCCCccccHHhHHHHHhCCCCCCCcC
Q 042258           96 NTDCAICLDDFIEG---------ETCKSFPECNHIFHLHCIDQWLKHRLNCPVCR  141 (152)
Q Consensus        96 ~~~C~IC~~~~~~~---------~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR  141 (152)
                      +..|+||++.+.+.         +-...+++|||.||..||.+||..+.+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            35699999999432         12233444999999999999999999999998

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

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

Probab=99.39  E-value=2.5e-13  Score=104.27  Aligned_cols=53  Identities=38%  Similarity=1.028  Sum_probs=47.5

Q ss_pred             CCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHh-CCCCCCCcCccCcc
Q 042258           93 MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK-HRLNCPVCRNPLCR  146 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~-~~~~CP~CR~~l~~  146 (152)
                      ...+-+|+|||+.|..++.++++| |+|.||..|+.+|+. -+..||+||.+++.
T Consensus       320 a~~GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         320 ADKGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             cCCCceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            345578999999998888999999 999999999999998 57889999999875

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

Probab=99.23  E-value=3.3e-12  Score=100.56  Aligned_cols=51  Identities=43%  Similarity=1.184  Sum_probs=42.4

Q ss_pred             CCCccCccccccccCCC----------eeeecCCCCccccHHhHHHHHhCCCCCCCcCccCc
Q 042258           94 TSNTDCAICLDDFIEGE----------TCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLC  145 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~----------~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~  145 (152)
                      .++..|.||++++-...          ....+| |||.+|.+|+..|++++.+||.||.++.
T Consensus       285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~i  345 (491)
T COG5243         285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPVI  345 (491)
T ss_pred             CCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCccc
Confidence            45578999999953321          346788 9999999999999999999999999854

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.17  E-value=3.5e-11  Score=87.92  Aligned_cols=49  Identities=33%  Similarity=0.826  Sum_probs=39.8

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC----------------CCCCCCcCccCccC
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH----------------RLNCPVCRNPLCRN  147 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----------------~~~CP~CR~~l~~~  147 (152)
                      +..+|+||++.+.++   ..++ |||.||..||.+|+..                ...||+||+++...
T Consensus        17 ~~~~CpICld~~~dP---VvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~   81 (193)
T PLN03208         17 GDFDCNICLDQVRDP---VVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEA   81 (193)
T ss_pred             CccCCccCCCcCCCc---EEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChh
Confidence            457899999998554   5566 9999999999999852                35799999998654

>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=99.17  E-value=2.4e-11  Score=70.77  Aligned_cols=46  Identities=33%  Similarity=0.959  Sum_probs=38.3

Q ss_pred             CccCccccccccCCCeeeecCCCCcc-ccHHhHHHHHhCCCCCCCcCccCc
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHI-FHLHCIDQWLKHRLNCPVCRNPLC  145 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~CP~CR~~l~  145 (152)
                      +..|.||++...   ....+| |||. |+..|+..|+.+...||+||+++.
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            357999999863   456777 9999 999999999999999999999875

...

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

Probab=99.17  E-value=5.1e-11  Score=91.13  Aligned_cols=48  Identities=31%  Similarity=0.902  Sum_probs=42.0

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      ...|.+|++..+++   ..+| |||+||..||..|...+..||+||.+...+
T Consensus       239 ~~kC~LCLe~~~~p---SaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~ps  286 (293)
T KOG0317|consen  239 TRKCSLCLENRSNP---SATP-CGHIFCWSCILEWCSEKAECPLCREKFQPS  286 (293)
T ss_pred             CCceEEEecCCCCC---CcCc-CcchHHHHHHHHHHccccCCCcccccCCCc
Confidence            37899999987554   5677 999999999999999999999999987654

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

Probab=99.16  E-value=2.5e-11  Score=77.42  Aligned_cols=51  Identities=37%  Similarity=0.912  Sum_probs=38.8

Q ss_pred             CCccCccccccccC--------CCe-eeecCCCCccccHHhHHHHHhC---CCCCCCcCccCc
Q 042258           95 SNTDCAICLDDFIE--------GET-CKSFPECNHIFHLHCIDQWLKH---RLNCPVCRNPLC  145 (152)
Q Consensus        95 ~~~~C~IC~~~~~~--------~~~-~~~l~~C~H~fh~~Ci~~wl~~---~~~CP~CR~~l~  145 (152)
                      .++.|.||...|..        ++. ..+..+|+|.||..||.+|+.+   +..||+||++..
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~   82 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK   82 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence            35779999888853        122 2334469999999999999986   578999999764

>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=99.12  E-value=7.4e-11  Score=66.22  Aligned_cols=44  Identities=48%  Similarity=1.278  Sum_probs=35.7

Q ss_pred             cCccccccccCCCeeeecCCCCccccHHhHHHHHhC-CCCCCCcCccC
Q 042258           98 DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPL  144 (152)
Q Consensus        98 ~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l  144 (152)
                      +|+||++.+.  +.....+ |||.||..|+..|+.. +..||+||..+
T Consensus         1 ~C~iC~~~~~--~~~~~~~-C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFR--EPVVLLP-CGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhh--CceEecC-CCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            4999999982  2333444 9999999999999997 78899999864

>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=99.11  E-value=7.5e-11  Score=65.17  Aligned_cols=39  Identities=41%  Similarity=1.078  Sum_probs=31.7

Q ss_pred             CccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCc
Q 042258           99 CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVC  140 (152)
Q Consensus        99 C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~C  140 (152)
                      |+||++.+.+  .+..++ |||.||..|+.+|++.+..||+|
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            7999998855  234565 99999999999999999999998

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

Probab=99.10  E-value=6.2e-11  Score=84.91  Aligned_cols=51  Identities=33%  Similarity=0.750  Sum_probs=42.4

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCC
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNL  148 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~  148 (152)
                      ...|+|||+.+.....  +-.+|||+||+.||...+++...||+||+.+..+.
T Consensus       131 ~~~CPiCl~~~sek~~--vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~  181 (187)
T KOG0320|consen  131 TYKCPICLDSVSEKVP--VSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQ  181 (187)
T ss_pred             ccCCCceecchhhccc--cccccchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence            3889999999865432  33459999999999999999999999999877654

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

Probab=99.09  E-value=6.4e-11  Score=88.14  Aligned_cols=53  Identities=32%  Similarity=0.708  Sum_probs=42.5

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC---CCCCCCcCccCccCCCC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH---RLNCPVCRNPLCRNLEL  150 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---~~~CP~CR~~l~~~~~~  150 (152)
                      ....+|.||++.-+++   +++. |||.||..||.+||..   ++.||+||..+..+..|
T Consensus        45 ~~~FdCNICLd~akdP---VvTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vv  100 (230)
T KOG0823|consen   45 GGFFDCNICLDLAKDP---VVTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVV  100 (230)
T ss_pred             CCceeeeeeccccCCC---EEee-cccceehHHHHHHHhhcCCCeeCCccccccccceEE
Confidence            3448999999986444   5566 9999999999999985   56799999998776543

>PHA02926 zinc finger-like protein; Provisional

Probab=99.08  E-value=8.2e-11  Score=87.20  Aligned_cols=53  Identities=32%  Similarity=0.849  Sum_probs=40.3

Q ss_pred             CCCCccCccccccccCC-----CeeeecCCCCccccHHhHHHHHhCC------CCCCCcCccCc
Q 042258           93 MTSNTDCAICLDDFIEG-----ETCKSFPECNHIFHLHCIDQWLKHR------LNCPVCRNPLC  145 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~-----~~~~~l~~C~H~fh~~Ci~~wl~~~------~~CP~CR~~l~  145 (152)
                      .+.+.+|+||++..-..     .....+++|+|.||..||..|.+.+      .+||+||..+.
T Consensus       167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            34458899999986322     2235677799999999999998753      45999998764

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.98  E-value=5.1e-10  Score=63.42  Aligned_cols=44  Identities=30%  Similarity=0.865  Sum_probs=37.0

Q ss_pred             cCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCc
Q 042258           98 DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRN  142 (152)
Q Consensus        98 ~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~  142 (152)
                      .|++|++.+........++ |||.|+..|+..+......||+||+
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            4999999995545566676 9999999999999866789999985

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

Probab=98.95  E-value=5.8e-10  Score=62.58  Aligned_cols=38  Identities=42%  Similarity=1.042  Sum_probs=28.7

Q ss_pred             CccccccccCCCeeeecCCCCccccHHhHHHHHhCC----CCCCCc
Q 042258           99 CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR----LNCPVC  140 (152)
Q Consensus        99 C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~----~~CP~C  140 (152)
                      |+||++.|.++   ..++ |||.|+..||.+|.+..    ..||.|
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            89999999554   7787 99999999999999763    469987

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

Probab=98.93  E-value=3e-10  Score=95.78  Aligned_cols=53  Identities=38%  Similarity=0.947  Sum_probs=44.7

Q ss_pred             CCCccCccccccccCCCe--eeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           94 TSNTDCAICLDDFIEGET--CKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~--~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      ..+..|+||++.+..+.+  ...++ |+|.||..|+..|++.+.+||.||..+...
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            345789999999977544  56788 999999999999999999999999955443

>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=98.88  E-value=1.2e-09  Score=60.79  Aligned_cols=39  Identities=38%  Similarity=1.114  Sum_probs=32.5

Q ss_pred             CccccccccCCCeeeecCCCCccccHHhHHHHHh--CCCCCCCc
Q 042258           99 CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK--HRLNCPVC  140 (152)
Q Consensus        99 C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~--~~~~CP~C  140 (152)
                      |+||++.+..+.  ..++ |||.||..|+.+|++  ....||+|
T Consensus         1 C~iC~~~~~~~~--~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPV--ILLP-CGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEE--EETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCCC--EEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence            789999985542  3566 999999999999998  56789998

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 ....

>smart00504 Ubox Modified RING finger domain

Probab=98.82  E-value=5e-09  Score=63.51  Aligned_cols=46  Identities=24%  Similarity=0.473  Sum_probs=39.9

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCcc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCR  146 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~  146 (152)
                      ..|+||.+.+.++   ..++ |||.|++.||.+|+..+..||+|+.++..
T Consensus         2 ~~Cpi~~~~~~~P---v~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~~   47 (63)
T smart00504        2 FLCPISLEVMKDP---VILP-SGQTYERRAIEKWLLSHGTDPVTGQPLTH   47 (63)
T ss_pred             cCCcCCCCcCCCC---EECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence            3699999998765   5566 99999999999999998999999998854

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

>smart00184 RING Ring finger

Probab=98.82  E-value=4.3e-09  Score=56.90  Aligned_cols=38  Identities=42%  Similarity=1.161  Sum_probs=31.7

Q ss_pred             CccccccccCCCeeeecCCCCccccHHhHHHHHh-CCCCCCCc
Q 042258           99 CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK-HRLNCPVC  140 (152)
Q Consensus        99 C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~-~~~~CP~C  140 (152)
                      |+||++..   .....++ |+|.||..|+..|+. .+..||+|
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            78998883   4456677 999999999999998 67779987

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)

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

Probab=98.78  E-value=5.4e-09  Score=65.33  Aligned_cols=29  Identities=45%  Similarity=0.956  Sum_probs=26.6

Q ss_pred             CCCCccccHHhHHHHHhCCCCCCCcCccC
Q 042258          116 PECNHIFHLHCIDQWLKHRLNCPVCRNPL  144 (152)
Q Consensus       116 ~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l  144 (152)
                      ..|+|.||..||.+||.++..||++|++.
T Consensus        52 G~CnHaFH~HCI~rWL~Tk~~CPld~q~w   80 (88)
T COG5194          52 GVCNHAFHDHCIYRWLDTKGVCPLDRQTW   80 (88)
T ss_pred             EecchHHHHHHHHHHHhhCCCCCCCCcee
Confidence            34999999999999999999999999864

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.74  E-value=8e-09  Score=83.53  Aligned_cols=49  Identities=31%  Similarity=0.613  Sum_probs=41.5

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCcc
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCR  146 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~  146 (152)
                      .....|+||.+.|...   ..++ |||.||..||..|+.....||+||..+..
T Consensus        24 e~~l~C~IC~d~~~~P---vitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~   72 (397)
T TIGR00599        24 DTSLRCHICKDFFDVP---VLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQE   72 (397)
T ss_pred             ccccCCCcCchhhhCc---cCCC-CCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence            3447899999999654   4566 99999999999999998899999998764

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

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

Probab=98.67  E-value=3.6e-09  Score=65.57  Aligned_cols=50  Identities=36%  Similarity=0.827  Sum_probs=36.0

Q ss_pred             CccCccccccccC--------CCe-eeecCCCCccccHHhHHHHHhC---CCCCCCcCccCc
Q 042258           96 NTDCAICLDDFIE--------GET-CKSFPECNHIFHLHCIDQWLKH---RLNCPVCRNPLC  145 (152)
Q Consensus        96 ~~~C~IC~~~~~~--------~~~-~~~l~~C~H~fh~~Ci~~wl~~---~~~CP~CR~~l~  145 (152)
                      +++|.||.-.|..        ++. ..++..|.|.||..||.+|+..   +..||+||+...
T Consensus        20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            3578888877743        122 1233459999999999999975   567999998653

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

Probab=98.65  E-value=9.4e-09  Score=83.84  Aligned_cols=49  Identities=43%  Similarity=0.973  Sum_probs=38.6

Q ss_pred             ccCccccccccCC---C-----------eeeecCCCCccccHHhHHHHHhC-CCCCCCcCccCcc
Q 042258           97 TDCAICLDDFIEG---E-----------TCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCR  146 (152)
Q Consensus        97 ~~C~IC~~~~~~~---~-----------~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~  146 (152)
                      .+|+|||....-.   .           ....+| |+|+||..|+.+|+.+ +-.||+||.+|+.
T Consensus       572 ~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tP-C~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  572 NDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTP-CHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             ccceEeccccceeeccCcchhhhhhhhccccccc-hHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            6899999987321   1           123346 9999999999999996 4599999999874

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

Probab=98.61  E-value=9e-09  Score=78.28  Aligned_cols=50  Identities=30%  Similarity=0.778  Sum_probs=40.2

Q ss_pred             CCccCccccccccCCC-------eeeecCCCCccccHHhHHHHH--hCCCCCCCcCccCc
Q 042258           95 SNTDCAICLDDFIEGE-------TCKSFPECNHIFHLHCIDQWL--KHRLNCPVCRNPLC  145 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~-------~~~~l~~C~H~fh~~Ci~~wl--~~~~~CP~CR~~l~  145 (152)
                      ++..|++|-..+....       +.-.+. |+|.||..||..|-  .++.+||.|+..+.
T Consensus       223 ~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVd  281 (328)
T KOG1734|consen  223 SDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVD  281 (328)
T ss_pred             CcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhh
Confidence            3467999998886544       455677 99999999999995  46889999998653

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

Probab=98.56  E-value=2e-08  Score=87.29  Aligned_cols=53  Identities=30%  Similarity=0.839  Sum_probs=40.7

Q ss_pred             CCCCccCccccccccC-CCe--eeecCCCCccccHHhHHHHHhC--CCCCCCcCccCc
Q 042258           93 MTSNTDCAICLDDFIE-GET--CKSFPECNHIFHLHCIDQWLKH--RLNCPVCRNPLC  145 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~-~~~--~~~l~~C~H~fh~~Ci~~wl~~--~~~CP~CR~~l~  145 (152)
                      .++.++|+||+.-+.. +..  -...+.|.|.||..|+.+|++.  +++||+||.+++
T Consensus      1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            3455899999988852 111  1245569999999999999986  678999998875

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

Probab=98.55  E-value=3.3e-08  Score=75.05  Aligned_cols=48  Identities=31%  Similarity=0.872  Sum_probs=39.2

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHH-HHhCCCC-CCCcCccCccC
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQ-WLKHRLN-CPVCRNPLCRN  147 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~-wl~~~~~-CP~CR~~l~~~  147 (152)
                      +..|+||++.....   ..++ |||+||..||.. |-..+.. ||+||+...-+
T Consensus       215 d~kC~lC~e~~~~p---s~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk  264 (271)
T COG5574         215 DYKCFLCLEEPEVP---SCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPK  264 (271)
T ss_pred             ccceeeeecccCCc---cccc-ccchhhHHHHHHHHHhhccccCchhhhhccch
Confidence            47899999987443   5677 999999999999 9776665 99999976544

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

Probab=98.51  E-value=1.3e-08  Score=63.36  Aligned_cols=52  Identities=31%  Similarity=0.838  Sum_probs=25.5

Q ss_pred             ccCcccccccc-CCCe-eeec--CCCCccccHHhHHHHHhC-----------CCCCCCcCccCccCC
Q 042258           97 TDCAICLDDFI-EGET-CKSF--PECNHIFHLHCIDQWLKH-----------RLNCPVCRNPLCRNL  148 (152)
Q Consensus        97 ~~C~IC~~~~~-~~~~-~~~l--~~C~H~fh~~Ci~~wl~~-----------~~~CP~CR~~l~~~~  148 (152)
                      .+|.||++... +++. ....  ++|+..||..|+.+||..           ...||.|++++.-++
T Consensus         3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~~   69 (70)
T PF11793_consen    3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWSF   69 (70)
T ss_dssp             -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGGG
T ss_pred             CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEec
Confidence            57999999875 3322 1222  369999999999999963           134999999886543

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

Probab=98.50  E-value=1.1e-07  Score=55.02  Aligned_cols=42  Identities=26%  Similarity=0.822  Sum_probs=32.1

Q ss_pred             cCccccccccCCCeeeecCCCC-----ccccHHhHHHHHhC--CCCCCCcC
Q 042258           98 DCAICLDDFIEGETCKSFPECN-----HIFHLHCIDQWLKH--RLNCPVCR  141 (152)
Q Consensus        98 ~C~IC~~~~~~~~~~~~l~~C~-----H~fh~~Ci~~wl~~--~~~CP~CR  141 (152)
                      .|-||++. .+++.....| |.     |.+|.+|+.+|+..  +.+||+|+
T Consensus         1 ~CrIC~~~-~~~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDE-GDEGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCC-CCCCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            38899983 3344445677 85     88999999999965  45899995

Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.45  E-value=1.8e-07  Score=73.16  Aligned_cols=50  Identities=24%  Similarity=0.507  Sum_probs=36.5

Q ss_pred             ccCccccccc-cCCC-eeeecCCCCccccHHhHHHHHh-CCCCCCCcCccCccC
Q 042258           97 TDCAICLDDF-IEGE-TCKSFPECNHIFHLHCIDQWLK-HRLNCPVCRNPLCRN  147 (152)
Q Consensus        97 ~~C~IC~~~~-~~~~-~~~~l~~C~H~fh~~Ci~~wl~-~~~~CP~CR~~l~~~  147 (152)
                      ..||+|...- ..+. .....+ |||.||..|+...+. ....||.|+.++...
T Consensus         4 ~~CP~Ck~~~y~np~~kl~i~~-CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~   56 (309)
T TIGR00570         4 QGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGSGSCPECDTPLRKN   56 (309)
T ss_pred             CCCCcCCCCCccCcccccccCC-CCCcccHHHHHHHhcCCCCCCCCCCCccchh
Confidence            5799999852 2322 223334 999999999999654 467899999887664

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

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

Probab=98.44  E-value=7.3e-08  Score=75.59  Aligned_cols=47  Identities=30%  Similarity=0.720  Sum_probs=41.5

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      ..|.||.+.|..+   ..+| |+|.||.-||...|..+..||.|+.++..+
T Consensus        24 LRC~IC~eyf~ip---~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~Es   70 (442)
T KOG0287|consen   24 LRCGICFEYFNIP---MITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTES   70 (442)
T ss_pred             HHHhHHHHHhcCc---eecc-ccchHHHHHHHHHhccCCCCCceecccchh
Confidence            7899999999665   5566 999999999999999999999999887653

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

Probab=98.41  E-value=1.4e-07  Score=76.37  Aligned_cols=47  Identities=32%  Similarity=0.796  Sum_probs=38.9

Q ss_pred             CccCccccccccCCC-eeeecCCCCccccHHhHHHHHhCCCCCCCcCccCc
Q 042258           96 NTDCAICLDDFIEGE-TCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLC  145 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~-~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~  145 (152)
                      -.+|++|++.+.... .+.... |.|.||..|+.+|  ...+||+||.-..
T Consensus       175 LPTCpVCLERMD~s~~gi~t~~-c~Hsfh~~cl~~w--~~~scpvcR~~q~  222 (493)
T KOG0804|consen  175 LPTCPVCLERMDSSTTGILTIL-CNHSFHCSCLMKW--WDSSCPVCRYCQS  222 (493)
T ss_pred             CCCcchhHhhcCccccceeeee-cccccchHHHhhc--ccCcChhhhhhcC
Confidence            378999999996643 445556 9999999999999  7789999998655

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

Probab=98.39  E-value=1.7e-07  Score=72.16  Aligned_cols=47  Identities=32%  Similarity=0.620  Sum_probs=40.5

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCcc
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCR  146 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~  146 (152)
                      -..|-||.+.++.+   ..++ |||.||.-||...|.++.-||+||.+...
T Consensus        25 ~lrC~IC~~~i~ip---~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~~~e   71 (391)
T COG5432          25 MLRCRICDCRISIP---CETT-CGHTFCSLCIRRHLGTQPFCPVCREDPCE   71 (391)
T ss_pred             HHHhhhhhheeecc---eecc-cccchhHHHHHHHhcCCCCCccccccHHh
Confidence            36799999998665   4455 99999999999999999999999987654

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

Probab=98.39  E-value=2.5e-07  Score=52.02  Aligned_cols=38  Identities=34%  Similarity=0.915  Sum_probs=22.2

Q ss_pred             CccccccccCCC-eeeecCCCCccccHHhHHHHHhCC----CCCC
Q 042258           99 CAICLDDFIEGE-TCKSFPECNHIFHLHCIDQWLKHR----LNCP  138 (152)
Q Consensus        99 C~IC~~~~~~~~-~~~~l~~C~H~fh~~Ci~~wl~~~----~~CP  138 (152)
                      |+||.+ +.+.+ ....|+ |||.|+.+|+.+++.++    ..||
T Consensus         1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 75544 356788 99999999999998843    3566

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

Probab=98.37  E-value=2.3e-07  Score=73.19  Aligned_cols=54  Identities=31%  Similarity=0.730  Sum_probs=45.1

Q ss_pred             CCCccCccccccccCCCeeeecCCCCcc-ccHHhHHHHHhCCCCCCCcCccCccCCCCC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHI-FHLHCIDQWLKHRLNCPVCRNPLCRNLELD  151 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~CP~CR~~l~~~~~~~  151 (152)
                      .++.+|.||+++-+   ....|| |.|. .|..|.....-.+..||+||.++.+.++|-
T Consensus       288 ~~gkeCVIClse~r---dt~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ll~i~  342 (349)
T KOG4265|consen  288 ESGKECVICLSESR---DTVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIEELLEIY  342 (349)
T ss_pred             cCCCeeEEEecCCc---ceEEec-chhhehhHhHHHHHHHhhcCCCccccchHhhheec
Confidence            34589999999874   457888 9995 899999997667888999999999988874

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

Probab=98.30  E-value=3.7e-07  Score=75.03  Aligned_cols=47  Identities=32%  Similarity=0.695  Sum_probs=37.3

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-----CCCCCCcCccCcc
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-----RLNCPVCRNPLCR  146 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-----~~~CP~CR~~l~~  146 (152)
                      +..||||+++...+   ..+. |||+||..||-+.+..     ...||+||..+..
T Consensus       186 ~~~CPICL~~~~~p---~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~  237 (513)
T KOG2164|consen  186 DMQCPICLEPPSVP---VRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL  237 (513)
T ss_pred             CCcCCcccCCCCcc---cccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence            57899999987554   3344 9999999999888764     4679999987754

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

Probab=98.30  E-value=5.8e-07  Score=56.29  Aligned_cols=49  Identities=22%  Similarity=0.457  Sum_probs=37.6

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-CCCCCCcCccCccC
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCRN  147 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~~  147 (152)
                      ....|+|+.+-+.++   ..++ +||.|.+.||..|+.. ...||.|+.++...
T Consensus         3 ~~f~CpIt~~lM~dP---Vi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~   52 (73)
T PF04564_consen    3 DEFLCPITGELMRDP---VILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSES   52 (73)
T ss_dssp             GGGB-TTTSSB-SSE---EEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred             cccCCcCcCcHhhCc---eeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence            446799999999654   6677 9999999999999998 88999999988764

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 ....

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

Probab=98.25  E-value=6.8e-07  Score=58.64  Aligned_cols=47  Identities=40%  Similarity=0.985  Sum_probs=35.8

Q ss_pred             ccCccccccccC-------C-----Ce-eeecCCCCccccHHhHHHHHhCCCCCCCcCcc
Q 042258           97 TDCAICLDDFIE-------G-----ET-CKSFPECNHIFHLHCIDQWLKHRLNCPVCRNP  143 (152)
Q Consensus        97 ~~C~IC~~~~~~-------~-----~~-~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~  143 (152)
                      ..|+||...+-+       +     +. ...=..|+|.||..||.+||+++..||+|.++
T Consensus        47 DnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~e  106 (114)
T KOG2930|consen   47 DNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKE  106 (114)
T ss_pred             chhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcc
Confidence            679999876622       1     11 12223499999999999999999999999875

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

Probab=98.24  E-value=5.9e-07  Score=71.60  Aligned_cols=50  Identities=32%  Similarity=0.838  Sum_probs=37.6

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhC---CCCCCCcCccCc
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH---RLNCPVCRNPLC  145 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---~~~CP~CR~~l~  145 (152)
                      ...|.||.+-+.....+.....|||+||..|+.+|+..   +..||.|+-.+.
T Consensus         4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~   56 (465)
T KOG0827|consen    4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQ   56 (465)
T ss_pred             cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeeccc
Confidence            45799995555455555555569999999999999986   368999994433

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

Probab=98.21  E-value=2.4e-07  Score=55.90  Aligned_cols=43  Identities=37%  Similarity=0.869  Sum_probs=22.2

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL  144 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l  144 (152)
                      ..|++|.+.++.+   ..+..|.|+||+.||..-+.  ..||+|+.+.
T Consensus         8 LrCs~C~~~l~~p---v~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Pa   50 (65)
T PF14835_consen    8 LRCSICFDILKEP---VCLGGCEHIFCSSCIRDCIG--SECPVCHTPA   50 (65)
T ss_dssp             TS-SSS-S--SS----B---SSS--B-TTTGGGGTT--TB-SSS--B-
T ss_pred             cCCcHHHHHhcCC---ceeccCccHHHHHHhHHhcC--CCCCCcCChH
Confidence            5699999998554   44566999999999988544  3599999875

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

Probab=98.18  E-value=7.8e-07  Score=68.22  Aligned_cols=44  Identities=39%  Similarity=0.868  Sum_probs=38.1

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRN  142 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~  142 (152)
                      ....|+||++.|..+   ..++ |+|.||..|+..+......||.||.
T Consensus        12 ~~~~C~iC~~~~~~p---~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   12 EELTCPICLEYFREP---VLLP-CGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             ccccChhhHHHhhcC---cccc-ccchHhHHHHHHhcCCCcCCcccCC
Confidence            447899999999877   6677 9999999999999886678999993

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

Probab=98.06  E-value=2.9e-06  Score=68.09  Aligned_cols=48  Identities=35%  Similarity=0.994  Sum_probs=38.4

Q ss_pred             CccCccccccccC-CCeeeecCCCCccccHHhHHHHHhC--CCCCCCcCcc
Q 042258           96 NTDCAICLDDFIE-GETCKSFPECNHIFHLHCIDQWLKH--RLNCPVCRNP  143 (152)
Q Consensus        96 ~~~C~IC~~~~~~-~~~~~~l~~C~H~fh~~Ci~~wl~~--~~~CP~CR~~  143 (152)
                      +.+|+||++++.. ++...+.+.|||.|...||.+||.+  ...||.|..+
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k   54 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK   54 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence            4689999999964 4555555569999999999999964  4569999764

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

Probab=98.06  E-value=4.8e-07  Score=71.34  Aligned_cols=54  Identities=31%  Similarity=0.613  Sum_probs=44.3

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-CCCCCCcCccCccCCCCC
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCRNLELD  151 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~~~~~~  151 (152)
                      ....|+||++-++.   .++.+.|.|.||..||..-++. .+.||.||+.+.++.++.
T Consensus        42 ~~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr   96 (381)
T KOG0311|consen   42 IQVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLR   96 (381)
T ss_pred             hhhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCC
Confidence            44679999998844   3566779999999999998875 789999999998876653

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

Probab=97.95  E-value=2.6e-06  Score=72.95  Aligned_cols=49  Identities=20%  Similarity=0.666  Sum_probs=40.1

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-CCCCCCcCccCccC
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCRN  147 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~~  147 (152)
                      .-..|+.|-..+++.    ++++|+|.||..|+.+-+.. +..||.|.+++..+
T Consensus       642 ~~LkCs~Cn~R~Kd~----vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan  691 (698)
T KOG0978|consen  642 ELLKCSVCNTRWKDA----VITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAN  691 (698)
T ss_pred             hceeCCCccCchhhH----HHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence            336899999887653    45569999999999999985 77899999988654

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

Probab=97.93  E-value=2e-06  Score=50.10  Aligned_cols=46  Identities=26%  Similarity=0.698  Sum_probs=34.5

Q ss_pred             ccCccccccccCCCeeeecCCCCcc-ccHHhHHHHHh-CCCCCCCcCccCcc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHI-FHLHCIDQWLK-HRLNCPVCRNPLCR  146 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~-~~~~CP~CR~~l~~  146 (152)
                      .+|.||++.-.+.    ++-.|||+ +|-+|..+..+ .+..||+||+++..
T Consensus         8 dECTICye~pvds----VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~d   55 (62)
T KOG4172|consen    8 DECTICYEHPVDS----VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKD   55 (62)
T ss_pred             cceeeeccCcchH----HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHH
Confidence            7899999886443    33349996 78889655444 68899999998753

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

Probab=97.91  E-value=1.9e-06  Score=73.96  Aligned_cols=50  Identities=22%  Similarity=0.478  Sum_probs=40.3

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      ..|++|+..+.++......+ |+|.||..|+..|-+.-.+||+||..+.+-
T Consensus       124 ~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v  173 (1134)
T KOG0825|consen  124 NQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGEFGEV  173 (1134)
T ss_pred             hhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhhhhee
Confidence            56888888776654433444 999999999999999999999999987654

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

Probab=97.74  E-value=1.6e-05  Score=61.71  Aligned_cols=50  Identities=28%  Similarity=0.610  Sum_probs=40.5

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-CCCCCCcCccCccCCC
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCRNLE  149 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~~~~  149 (152)
                      ..+|+||+....-+   ..++ |+|.||--||..-..+ ..+|++||.++..++.
T Consensus         7 ~~eC~IC~nt~n~P---v~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids~i~   57 (324)
T KOG0824|consen    7 KKECLICYNTGNCP---VNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDSTID   57 (324)
T ss_pred             CCcceeeeccCCcC---cccc-ccchhhhhhhcchhhcCCCCCceecCCCCcchh
Confidence            36799999876444   5566 9999999999987766 5569999999988764

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

Probab=97.70  E-value=1.8e-05  Score=63.11  Aligned_cols=51  Identities=37%  Similarity=0.959  Sum_probs=38.8

Q ss_pred             CCCccCccccccccCCC----eeeecCCCCccccHHhHHHHHh--C-----CCCCCCcCccC
Q 042258           94 TSNTDCAICLDDFIEGE----TCKSFPECNHIFHLHCIDQWLK--H-----RLNCPVCRNPL  144 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~----~~~~l~~C~H~fh~~Ci~~wl~--~-----~~~CP~CR~~l  144 (152)
                      ..+.+|.||++..-...    ....+|+|.|.||..||..|-.  .     ++.||.||...
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s  220 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPS  220 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence            34578999999875432    1234577999999999999973  3     57899999754

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

Probab=97.67  E-value=1.4e-05  Score=62.03  Aligned_cols=51  Identities=31%  Similarity=0.790  Sum_probs=42.0

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-----------------------CCCCCCcCccCcc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-----------------------RLNCPVCRNPLCR  146 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-----------------------~~~CP~CR~~l~~  146 (152)
                      ..-.|.||+-.|.++....+++ |.|.||..|+.+.|..                       ...||+||..+..
T Consensus       114 p~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~  187 (368)
T KOG4445|consen  114 PNGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI  187 (368)
T ss_pred             CCCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence            3357999999999988888888 9999999999988731                       2349999998754

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

Probab=97.67  E-value=2.6e-05  Score=63.45  Aligned_cols=51  Identities=31%  Similarity=0.791  Sum_probs=43.0

Q ss_pred             CCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           93 MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      ...+.+|.||+.-+..+   +.+| |||.||..||.+-+.....||.||.++...
T Consensus        81 ~~sef~c~vc~~~l~~p---v~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l~e~  131 (398)
T KOG4159|consen   81 IRSEFECCVCSRALYPP---VVTP-CGHSFCLECLDRSLDQETECPLCRDELVEL  131 (398)
T ss_pred             ccchhhhhhhHhhcCCC---cccc-ccccccHHHHHHHhccCCCCcccccccccc
Confidence            35568899998888444   6677 999999999999888889999999998864

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

Probab=97.63  E-value=3.8e-05  Score=62.59  Aligned_cols=54  Identities=31%  Similarity=0.650  Sum_probs=44.3

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCCCC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNLEL  150 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~~~  150 (152)
                      ..+..|++|+..+.++-.  .. .|||.||..|+.+|+..+..||.|+.++....++
T Consensus        19 ~~~l~C~~C~~vl~~p~~--~~-~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~   72 (391)
T KOG0297|consen   19 DENLLCPICMSVLRDPVQ--TT-TCGHRFCAGCLLESLSNHQKCPVCRQELTQAEEL   72 (391)
T ss_pred             cccccCccccccccCCCC--CC-CCCCcccccccchhhccCcCCcccccccchhhcc
Confidence            455789999999977622  13 4999999999999999999999999988766544

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

Probab=97.62  E-value=1.9e-05  Score=63.48  Aligned_cols=50  Identities=26%  Similarity=0.691  Sum_probs=39.3

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhC--CCCCCCcCccCccCCCC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH--RLNCPVCRNPLCRNLEL  150 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~--~~~CP~CR~~l~~~~~~  150 (152)
                      .-|.||-+.-   ..+..-| |||..|..|+..|-..  ..+||.||.++.-...|
T Consensus       370 eLCKICaend---KdvkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~v  421 (563)
T KOG1785|consen  370 ELCKICAEND---KDVKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPV  421 (563)
T ss_pred             HHHHHhhccC---CCccccc-ccchHHHHHHHhhcccCCCCCCCceeeEeccccce
Confidence            6799998763   4456667 9999999999999754  57899999988654443

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

Probab=97.42  E-value=8.6e-05  Score=44.20  Aligned_cols=41  Identities=29%  Similarity=0.626  Sum_probs=26.7

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhC--CCCCCC
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH--RLNCPV  139 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~--~~~CP~  139 (152)
                      ...|+|.+..|.++   ....+|||.|-++.|.+++++  ...||+
T Consensus        11 ~~~CPiT~~~~~~P---V~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   11 SLKCPITLQPFEDP---VKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             -SB-TTTSSB-SSE---EEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             ccCCCCcCChhhCC---cCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            37899999998654   333359999999999999944  556998

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

Probab=97.38  E-value=5.5e-05  Score=60.72  Aligned_cols=44  Identities=36%  Similarity=0.926  Sum_probs=36.8

Q ss_pred             ccCccccccccC-CCeeeecCCCCccccHHhHHHHHhC--CCCCCCcC
Q 042258           97 TDCAICLDDFIE-GETCKSFPECNHIFHLHCIDQWLKH--RLNCPVCR  141 (152)
Q Consensus        97 ~~C~IC~~~~~~-~~~~~~l~~C~H~fh~~Ci~~wl~~--~~~CP~CR  141 (152)
                      ..|..|-+.+-- ++....+| |.|+||..|+...|.+  ..+||.||
T Consensus       366 L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Cr  412 (518)
T KOG1941|consen  366 LYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCR  412 (518)
T ss_pred             hhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHH
Confidence            679999887743 45677888 9999999999999976  56899998

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

Probab=97.35  E-value=0.00013  Score=66.70  Aligned_cols=65  Identities=29%  Similarity=0.786  Sum_probs=51.0

Q ss_pred             CCCceeecCCCCCCCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCC----------CCCCCcCccCc
Q 042258           80 SLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR----------LNCPVCRNPLC  145 (152)
Q Consensus        80 ~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~----------~~CP~CR~~l~  145 (152)
                      -||-+.-.+.......+..|.||..+-......+.+. |+|+||..|...-|.++          -+||+|+.++-
T Consensus      3470 CLPCl~Cdks~tkQD~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3470 CLPCLHCDKSATKQDADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             cccccccChhhhhcccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            6777776665555566788999998876667788898 99999999998877652          46999998763

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

Probab=97.25  E-value=0.00041  Score=55.19  Aligned_cols=48  Identities=27%  Similarity=0.562  Sum_probs=39.5

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCc
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLC  145 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~  145 (152)
                      +++..|+||+..-...   ...| |+|.=|..||.+.+.+.+.|=.|++.+.
T Consensus       420 sEd~lCpICyA~pi~A---vf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~  467 (489)
T KOG4692|consen  420 SEDNLCPICYAGPINA---VFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVI  467 (489)
T ss_pred             cccccCcceecccchh---hccC-CCCchHHHHHHHHHhcCCeeeEecceee
Confidence            4557899998764332   4556 9999999999999999999999998665

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

Probab=97.18  E-value=7.8e-05  Score=58.54  Aligned_cols=50  Identities=28%  Similarity=0.688  Sum_probs=40.9

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      ...+|.+|-..|.+...   ...|-|.||+.||.+.|.....||.|...+-..
T Consensus        14 ~~itC~LC~GYliDATT---I~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   14 PHITCRLCGGYLIDATT---ITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             cceehhhccceeecchh---HHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            44789999999977533   334999999999999999999999998766443

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

Probab=97.17  E-value=0.00036  Score=39.92  Aligned_cols=45  Identities=24%  Similarity=0.633  Sum_probs=22.6

Q ss_pred             CccccccccC-CCeeeecCCCCccccHHhHHHHHh-CCCCCCCcCccC
Q 042258           99 CAICLDDFIE-GETCKSFPECNHIFHLHCIDQWLK-HRLNCPVCRNPL  144 (152)
Q Consensus        99 C~IC~~~~~~-~~~~~~l~~C~H~fh~~Ci~~wl~-~~~~CP~CR~~l  144 (152)
                      |++|.+++.. +....-.+ ||+.++..|...-+. ....||.||.+.
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            7899999843 23334455 899999999888776 478899999863

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

Probab=97.11  E-value=0.00016  Score=53.15  Aligned_cols=50  Identities=22%  Similarity=0.419  Sum_probs=41.2

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCCCC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNLEL  150 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~~~  150 (152)
                      ..|.||.+.|..+   ++.. |||.||..|...-++....|-+|-+...-.+-|
T Consensus       197 F~C~iCKkdy~sp---vvt~-CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~f~V  246 (259)
T COG5152         197 FLCGICKKDYESP---VVTE-CGHSFCSLCAIRKYQKGDECGVCGKATYGRFWV  246 (259)
T ss_pred             eeehhchhhccch---hhhh-cchhHHHHHHHHHhccCCcceecchhhccceeH
Confidence            4799999999654   5565 999999999999889999999998876655443

>PHA02862 5L protein; Provisional

Probab=97.00  E-value=0.00061  Score=47.66  Aligned_cols=43  Identities=26%  Similarity=0.716  Sum_probs=32.4

Q ss_pred             ccCccccccccCCCeeeecCCCC-----ccccHHhHHHHHhC--CCCCCCcCccC
Q 042258           97 TDCAICLDDFIEGETCKSFPECN-----HIFHLHCIDQWLKH--RLNCPVCRNPL  144 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~-----H~fh~~Ci~~wl~~--~~~CP~CR~~l  144 (152)
                      ..|=||.++-.++    ..| |+     ...|.+|+.+|+..  +..|++|+.+.
T Consensus         3 diCWIC~~~~~e~----~~P-C~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY   52 (156)
T PHA02862          3 DICWICNDVCDER----NNF-CGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKY   52 (156)
T ss_pred             CEEEEecCcCCCC----ccc-ccccCcchhHHHHHHHHHHhcCCCcCccCCCCeE
Confidence            5699999885332    234 54     47999999999975  56799999865

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.89  E-value=0.00095  Score=50.70  Aligned_cols=54  Identities=17%  Similarity=0.423  Sum_probs=48.3

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCC
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNL  148 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~  148 (152)
                      ....|++|.+.+.+.-.+..|.+|||+|+.+|+.+.++....||+|-.++.+.-
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrd  273 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRD  273 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccc
Confidence            347899999999988888888889999999999999999999999999887653

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

Probab=96.84  E-value=0.00049  Score=60.01  Aligned_cols=48  Identities=31%  Similarity=0.874  Sum_probs=39.9

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhCC-------CCCCCcCcc
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR-------LNCPVCRNP  143 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~-------~~CP~CR~~  143 (152)
                      ..+|.||++.+...+.+.....|-|+||..||.+|-+..       =.||.|...
T Consensus       191 ~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv  245 (950)
T KOG1952|consen  191 KYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSV  245 (950)
T ss_pred             ceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccch
Confidence            389999999998888877777799999999999997641       249999843

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

Probab=96.79  E-value=0.0015  Score=49.06  Aligned_cols=51  Identities=25%  Similarity=0.813  Sum_probs=41.2

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhC--------CCCCCCcCccCccCC
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH--------RLNCPVCRNPLCRNL  148 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~--------~~~CP~CR~~l~~~~  148 (152)
                      ...|..|-..+..++.++ +- |-|.||-+|+..|-..        ...||.|..++....
T Consensus        50 ~pNC~LC~t~La~gdt~R-Lv-CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~  108 (299)
T KOG3970|consen   50 NPNCRLCNTPLASGDTTR-LV-CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPI  108 (299)
T ss_pred             CCCCceeCCccccCccee-eh-hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCc
Confidence            356999999998877655 55 9999999999999753        456999999887654

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

Probab=96.77  E-value=0.0023  Score=50.93  Aligned_cols=58  Identities=24%  Similarity=0.636  Sum_probs=41.3

Q ss_pred             CceeecCCCCCCCCCccCccccccccCCCeeeecCCCCccccHHhHHHH--HhCCCCCCCcCcc
Q 042258           82 PQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQW--LKHRLNCPVCRNP  143 (152)
Q Consensus        82 p~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~w--l~~~~~CP~CR~~  143 (152)
                      |............++..|.||-+.+   .....+| |+|..|-.|..+.  |.+++.||+||.+
T Consensus        47 PnlttsSaddtDEen~~C~ICA~~~---TYs~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE  106 (493)
T COG5236          47 PNLTTSSADDTDEENMNCQICAGST---TYSARYP-CGHQICHACAVRLRALYMQKGCPLCRTE  106 (493)
T ss_pred             CccccccccccccccceeEEecCCc---eEEEecc-CCchHHHHHHHHHHHHHhccCCCccccc
Confidence            3333333333344557899998776   3446677 9999999997664  5679999999985

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

Probab=96.75  E-value=0.00089  Score=46.41  Aligned_cols=36  Identities=19%  Similarity=0.580  Sum_probs=29.4

Q ss_pred             ccCccccccccCCCeeeecCCCC------ccccHHhHHHHHhC
Q 042258           97 TDCAICLDDFIEGETCKSFPECN------HIFHLHCIDQWLKH  133 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~------H~fh~~Ci~~wl~~  133 (152)
                      .+|.||++.+.+.++++..+ ||      |+||.+|+.+|-+.
T Consensus        27 ~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~~~   68 (134)
T PF05883_consen   27 VECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWRRE   68 (134)
T ss_pred             eeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHHhh
Confidence            57999999998856677666 65      88999999999443

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.

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

Probab=96.71  E-value=0.0022  Score=49.43  Aligned_cols=49  Identities=27%  Similarity=0.615  Sum_probs=36.1

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC--CCCCCCcCccCc
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH--RLNCPVCRNPLC  145 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~--~~~CP~CR~~l~  145 (152)
                      ..+.+|++|-+.--.+   -...+|+|+||-.|+..-...  +.+||.|-.+..
T Consensus       237 t~~~~C~~Cg~~PtiP---~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  237 TSDTECPVCGEPPTIP---HVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cCCceeeccCCCCCCC---eeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            3457899997764222   233349999999999987654  578999988765

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

Probab=96.65  E-value=0.00072  Score=52.51  Aligned_cols=48  Identities=23%  Similarity=0.427  Sum_probs=40.2

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNL  148 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~  148 (152)
                      ..|-||...|..+   ++.. |+|.||..|...-++....|++|.+..-..+
T Consensus       242 f~c~icr~~f~~p---Vvt~-c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~  289 (313)
T KOG1813|consen  242 FKCFICRKYFYRP---VVTK-CGHYFCEVCALKPYQKGEKCYVCSQQTHGSF  289 (313)
T ss_pred             ccccccccccccc---hhhc-CCceeehhhhccccccCCcceeccccccccc
Confidence            5699999999665   4554 9999999999998889999999998765443

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

Probab=96.54  E-value=0.0016  Score=47.24  Aligned_cols=51  Identities=27%  Similarity=0.769  Sum_probs=33.9

Q ss_pred             cCccccccccCCC---eeeecCCCCccccHHhHHHHHhC-----------CCCCCCcCccCccCC
Q 042258           98 DCAICLDDFIEGE---TCKSFPECNHIFHLHCIDQWLKH-----------RLNCPVCRNPLCRNL  148 (152)
Q Consensus        98 ~C~IC~~~~~~~~---~~~~l~~C~H~fh~~Ci~~wl~~-----------~~~CP~CR~~l~~~~  148 (152)
                      .|.||+..-.+|.   .+..-..||..||.-|+..||+.           -..||.|..++.-++
T Consensus       167 ~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKm  231 (234)
T KOG3268|consen  167 ACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKM  231 (234)
T ss_pred             cccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeec
Confidence            4666655433331   11222249999999999999974           134999999887654

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

Probab=96.53  E-value=0.0011  Score=43.94  Aligned_cols=34  Identities=32%  Similarity=0.826  Sum_probs=27.0

Q ss_pred             CCCCccCccccccccCCCeeeecCCCCccccHHhHH
Q 042258           93 MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCID  128 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~  128 (152)
                      ...+..|++|-..+.. ......| |||.||..|+.
T Consensus        75 i~~~~~C~vC~k~l~~-~~f~~~p-~~~v~H~~C~~  108 (109)
T PF10367_consen   75 ITESTKCSVCGKPLGN-SVFVVFP-CGHVVHYSCIK  108 (109)
T ss_pred             ECCCCCccCcCCcCCC-ceEEEeC-CCeEEeccccc
Confidence            3445779999999866 4556677 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 [].

>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=96.47  E-value=0.0021  Score=35.97  Aligned_cols=41  Identities=32%  Similarity=0.920  Sum_probs=23.7

Q ss_pred             CccccccccCCCeeeecCCCCccccHHhHHHHHhCCC--CCCCc
Q 042258           99 CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRL--NCPVC  140 (152)
Q Consensus        99 C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~--~CP~C  140 (152)
                      |.+|.+-.-.|....... |+-.+|..|+..+++...  .||.|
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            667777766665544334 999999999999998755  79987

; PDB: 3NW0_A 2CT0_A.

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

Probab=96.39  E-value=0.011  Score=47.54  Aligned_cols=28  Identities=32%  Similarity=1.181  Sum_probs=22.4

Q ss_pred             CCccccHHhHHHHHhC-------------CCCCCCcCccCc
Q 042258          118 CNHIFHLHCIDQWLKH-------------RLNCPVCRNPLC  145 (152)
Q Consensus       118 C~H~fh~~Ci~~wl~~-------------~~~CP~CR~~l~  145 (152)
                      |.-++|.+|+.+|+..             +-.||+||+++.
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC  351 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC  351 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence            5667899999999853             345999999864

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

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

Probab=96.38  E-value=0.0016  Score=51.84  Aligned_cols=50  Identities=32%  Similarity=0.636  Sum_probs=34.6

Q ss_pred             CCCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCC
Q 042258           92 EMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNL  148 (152)
Q Consensus        92 ~~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~  148 (152)
                      ..+....|.||+++..+   ...+| |||.-|  |..-- +...+||+||..+...+
T Consensus       301 ~~~~p~lcVVcl~e~~~---~~fvp-cGh~cc--ct~cs-~~l~~CPvCR~rI~~~~  350 (355)
T KOG1571|consen  301 ELPQPDLCVVCLDEPKS---AVFVP-CGHVCC--CTLCS-KHLPQCPVCRQRIRLVR  350 (355)
T ss_pred             ccCCCCceEEecCCccc---eeeec-CCcEEE--chHHH-hhCCCCchhHHHHHHHH
Confidence            34455789999998744   56788 999866  54432 23445999999876543

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

Probab=96.35  E-value=0.0024  Score=36.44  Aligned_cols=40  Identities=33%  Similarity=0.903  Sum_probs=26.0

Q ss_pred             CccccccccCCCeeeecCCCC-----ccccHHhHHHHHh--CCCCCCCc
Q 042258           99 CAICLDDFIEGETCKSFPECN-----HIFHLHCIDQWLK--HRLNCPVC  140 (152)
Q Consensus        99 C~IC~~~~~~~~~~~~l~~C~-----H~fh~~Ci~~wl~--~~~~CP~C  140 (152)
                      |-||++.-.+.+ ....| |+     ...|.+|+.+|+.  .+..|++|
T Consensus         1 CrIC~~~~~~~~-~li~p-C~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISP-CRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-S-SS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecc-cccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            678988865544 23445 64     2789999999998  45679887

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=96.30  E-value=0.0045  Score=44.11  Aligned_cols=45  Identities=29%  Similarity=0.834  Sum_probs=33.2

Q ss_pred             CCccCccccccccCCCeeeecCCCCc-----cccHHhHHHHHhC--CCCCCCcCccC
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNH-----IFHLHCIDQWLKH--RLNCPVCRNPL  144 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H-----~fh~~Ci~~wl~~--~~~CP~CR~~l  144 (152)
                      .+..|-||.++-.+  .  ..| |..     ..|.+|+.+|+..  ..+|+.|+++.
T Consensus         7 ~~~~CRIC~~~~~~--~--~~P-C~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y   58 (162)
T PHA02825          7 MDKCCWICKDEYDV--V--TNY-CNCKNENKIVHKECLEEWINTSKNKSCKICNGPY   58 (162)
T ss_pred             CCCeeEecCCCCCC--c--cCC-cccCCCchHHHHHHHHHHHhcCCCCcccccCCeE
Confidence            44789999888432  2  234 654     5699999999985  56799999864

>PHA03096 p28-like protein; Provisional

Probab=96.26  E-value=0.0023  Score=50.04  Aligned_cols=37  Identities=27%  Similarity=0.702  Sum_probs=29.3

Q ss_pred             ccCccccccccCC----CeeeecCCCCccccHHhHHHHHhC
Q 042258           97 TDCAICLDDFIEG----ETCKSFPECNHIFHLHCIDQWLKH  133 (152)
Q Consensus        97 ~~C~IC~~~~~~~----~~~~~l~~C~H~fh~~Ci~~wl~~  133 (152)
                      ..|.||++.....    ..-..++.|.|.||..|+..|...
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~  219 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTE  219 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHh
Confidence            5799999987542    234567889999999999999764

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

Probab=96.23  E-value=0.0017  Score=54.25  Aligned_cols=48  Identities=27%  Similarity=0.730  Sum_probs=36.4

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-----CCCCCCcCccCc
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-----RLNCPVCRNPLC  145 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-----~~~CP~CR~~l~  145 (152)
                      .+..+|.+|.+.-++   .+... |.|.||+.|+..+...     +-+||.|...|.
T Consensus       534 k~~~~C~lc~d~aed---~i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls  586 (791)
T KOG1002|consen  534 KGEVECGLCHDPAED---YIESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS  586 (791)
T ss_pred             cCceeecccCChhhh---hHhhh-hhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence            344789999887533   35555 9999999999888753     578999987664

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

Probab=96.16  E-value=0.0018  Score=46.20  Aligned_cols=27  Identities=41%  Similarity=0.978  Sum_probs=25.2

Q ss_pred             ccCccccccccCCCeeeecCCCCccccH
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHL  124 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~  124 (152)
                      -+|.||++++..++.+..|| |-.+||+
T Consensus       178 GECvICLEdL~~GdtIARLP-CLCIYHK  204 (205)
T KOG0801|consen  178 GECVICLEDLEAGDTIARLP-CLCIYHK  204 (205)
T ss_pred             CcEEEEhhhccCCCceeccc-eEEEeec
Confidence            68999999999999999999 9999996

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

Probab=96.03  E-value=0.003  Score=47.79  Aligned_cols=43  Identities=21%  Similarity=0.559  Sum_probs=29.8

Q ss_pred             cCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccC
Q 042258           98 DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL  144 (152)
Q Consensus        98 ~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l  144 (152)
                      .|.-|...-. +.....+. |+|+||..|...-  ....||+|++++
T Consensus         5 hCn~C~~~~~-~~~f~LTa-C~HvfC~~C~k~~--~~~~C~lCkk~i   47 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLTA-CRHVFCEPCLKAS--SPDVCPLCKKSI   47 (233)
T ss_pred             EeccccccCC-CCceeeee-chhhhhhhhcccC--Ccccccccccee
Confidence            3666765544 44545555 9999999997662  223899999974

>PF04641 Rtf2: Rtf2 RING-finger

Probab=95.92  E-value=0.031  Score=43.23  Aligned_cols=53  Identities=19%  Similarity=0.481  Sum_probs=41.3

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      .....|||...+|........+-+|||+|...++..- .....||+|-.++...
T Consensus       111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~f~~~  163 (260)
T PF04641_consen  111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKPFTEE  163 (260)
T ss_pred             CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCccccC
Confidence            3448899999999655556666559999999999996 3366799999887643

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=95.80  E-value=0.015  Score=34.05  Aligned_cols=34  Identities=26%  Similarity=0.771  Sum_probs=29.5

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHH
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQ  129 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~  129 (152)
                      +..|++|-+.|..++.+.+.|.||-.+|+.|-.+
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            4679999999998888888999999999999544

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

Probab=95.77  E-value=0.00041  Score=55.76  Aligned_cols=51  Identities=25%  Similarity=0.643  Sum_probs=44.1

Q ss_pred             ccCccccccccCC-CeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCC
Q 042258           97 TDCAICLDDFIEG-ETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNL  148 (152)
Q Consensus        97 ~~C~IC~~~~~~~-~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~  148 (152)
                      ..|+||...++.. +.+..+. |||.+|..|+.+||.+...||-|+++|....
T Consensus       197 ~sl~I~~~slK~~y~k~~~~~-~g~~~~~~kL~k~L~~~~kl~~~~rel~~~~  248 (465)
T KOG0827|consen  197 GSLSICFESLKQNYDKISAIV-CGHIYHHGKLSKWLATKRKLPSCRRELPKNG  248 (465)
T ss_pred             hhhHhhHHHHHHHHHHHHHHh-hcccchhhHHHHHHHHHHHhHHHHhhhhhhh
Confidence            6799999998765 5566676 9999999999999999999999999987653

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

Probab=95.76  E-value=0.022  Score=44.62  Aligned_cols=43  Identities=28%  Similarity=0.623  Sum_probs=34.7

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHh-CCCCCCCcCc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK-HRLNCPVCRN  142 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~-~~~~CP~CR~  142 (152)
                      ..|+.|..-+.+.   ..++.|+|.||.+||..-|. ....||.|.+
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   34567999999999997765 5678999976

>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=95.72  E-value=0.0038  Score=35.41  Aligned_cols=31  Identities=32%  Similarity=0.890  Sum_probs=22.6

Q ss_pred             C-CccccHHhHHHHHhCCCCCCCcCccCccCC
Q 042258          118 C-NHIFHLHCIDQWLKHRLNCPVCRNPLCRNL  148 (152)
Q Consensus       118 C-~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~  148 (152)
                      | .|..|..|+...+..+..||+|..+|+.++
T Consensus        18 C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtki   49 (50)
T PF03854_consen   18 CSDHYLCLNCLTLMLSRSDRCPICGKPLPTKI   49 (50)
T ss_dssp             -SS-EEEHHHHHHT-SSSSEETTTTEE----S
T ss_pred             ecchhHHHHHHHHHhccccCCCcccCcCcccc
Confidence            5 599999999999999999999999999875

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.

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

Probab=95.71  E-value=0.018  Score=45.59  Aligned_cols=46  Identities=22%  Similarity=0.486  Sum_probs=36.4

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCcc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNP  143 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~  143 (152)
                      ....|++|+....++   .++.--|-+||-.|+.+.+.+.+.||+=..+
T Consensus       299 ~~~~CpvClk~r~Np---tvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p  344 (357)
T KOG0826|consen  299 DREVCPVCLKKRQNP---TVLEVSGYVFCYPCIFSYVVNYGHCPVTGYP  344 (357)
T ss_pred             ccccChhHHhccCCC---ceEEecceEEeHHHHHHHHHhcCCCCccCCc
Confidence            348899999987554   2333269999999999999999999986544

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

Probab=95.65  E-value=0.0078  Score=47.11  Aligned_cols=47  Identities=28%  Similarity=0.804  Sum_probs=37.4

Q ss_pred             ccCccccccccCCC--e-eeecCCCCccccHHhHHHHHhC-CCCCCCcCccC
Q 042258           97 TDCAICLDDFIEGE--T-CKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPL  144 (152)
Q Consensus        97 ~~C~IC~~~~~~~~--~-~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l  144 (152)
                      ..|-||-++|+..+  . .+.+ +|||.++..|+.+.+.. ...||.||...
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l-~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVL-KCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCccc-ccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            57999999998753  3 3445 49999999999998876 45799999873

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

Probab=95.54  E-value=0.0084  Score=48.71  Aligned_cols=45  Identities=29%  Similarity=0.783  Sum_probs=34.0

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhC--------CCCCCCcCc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH--------RLNCPVCRN  142 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~--------~~~CP~CR~  142 (152)
                      ..|.||+++.....-...+| |+|+||+.|+...+..        .-.||-+.-
T Consensus       185 f~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  185 FDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             ccceeeehhhcCcceeeecc-cchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            68999999964445556677 9999999999998753        334776543

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

Probab=95.51  E-value=0.0017  Score=50.54  Aligned_cols=43  Identities=33%  Similarity=0.796  Sum_probs=32.7

Q ss_pred             CccCccccccccCCCeeeecCCCCcc-ccHHhHHHHHhCCCCCCCcCccCcc
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHI-FHLHCIDQWLKHRLNCPVCRNPLCR  146 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~CP~CR~~l~~  146 (152)
                      +.-|.||++.-   ..+..|+ |||. -|..|...    -..||+||+.+.+
T Consensus       300 ~~LC~ICmDaP---~DCvfLe-CGHmVtCt~CGkr----m~eCPICRqyi~r  343 (350)
T KOG4275|consen  300 RRLCAICMDAP---RDCVFLE-CGHMVTCTKCGKR----MNECPICRQYIVR  343 (350)
T ss_pred             HHHHHHHhcCC---cceEEee-cCcEEeehhhccc----cccCchHHHHHHH
Confidence            46799999875   5677888 9995 56777655    3489999987754

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=95.42  E-value=0.0069  Score=35.50  Aligned_cols=44  Identities=23%  Similarity=0.508  Sum_probs=30.4

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCcc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCR  146 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~  146 (152)
                      ..|..|...-   ..-..+| |||+.+..|-.-+  +-+.||.|-+++..
T Consensus         8 ~~~~~~~~~~---~~~~~~p-CgH~I~~~~f~~~--rYngCPfC~~~~~~   51 (55)
T PF14447_consen    8 QPCVFCGFVG---TKGTVLP-CGHLICDNCFPGE--RYNGCPFCGTPFEF   51 (55)
T ss_pred             eeEEEccccc---ccccccc-ccceeeccccChh--hccCCCCCCCcccC
Confidence            3466565442   2225566 9999999996554  67889999988754

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

Probab=95.15  E-value=0.013  Score=45.52  Aligned_cols=45  Identities=22%  Similarity=0.703  Sum_probs=36.7

Q ss_pred             ccCccccccccCCCe-eeecCCCCccccHHhHHHHHhCCCCCCCcCc
Q 042258           97 TDCAICLDDFIEGET-CKSFPECNHIFHLHCIDQWLKHRLNCPVCRN  142 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~-~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~  142 (152)
                      ..|+||.+.+-.... +..++ |||..|..|...-...+-.||+|.+
T Consensus       159 ~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  159 FNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             CCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc
Confidence            449999988866544 44565 9999999999998877899999988

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

Probab=94.88  E-value=0.0091  Score=52.44  Aligned_cols=43  Identities=28%  Similarity=0.716  Sum_probs=33.4

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLC  145 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~  145 (152)
                      ..|..|-..+.-+  ..... |||.||..|+.   .+...||-|+.++-
T Consensus       841 skCs~C~~~LdlP--~VhF~-CgHsyHqhC~e---~~~~~CP~C~~e~~  883 (933)
T KOG2114|consen  841 SKCSACEGTLDLP--FVHFL-CGHSYHQHCLE---DKEDKCPKCLPELR  883 (933)
T ss_pred             eeecccCCccccc--eeeee-cccHHHHHhhc---cCcccCCccchhhh
Confidence            6899998887443  23344 99999999998   57788999988543

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

Probab=94.84  E-value=0.018  Score=45.36  Aligned_cols=41  Identities=29%  Similarity=0.797  Sum_probs=33.2

Q ss_pred             ccCccccccccCCCeeeecCCC--CccccHHhHHHHHhCCCCCCCcCccCc
Q 042258           97 TDCAICLDDFIEGETCKSFPEC--NHIFHLHCIDQWLKHRLNCPVCRNPLC  145 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C--~H~fh~~Ci~~wl~~~~~CP~CR~~l~  145 (152)
                      .+||||.+.+..+    ... |  ||..|..|-.+   .+..||.||-++.
T Consensus        49 leCPvC~~~l~~P----i~Q-C~nGHlaCssC~~~---~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   49 LDCPVCFNPLSPP----IFQ-CDNGHLACSSCRTK---VSNKCPTCRLPIG   91 (299)
T ss_pred             ccCchhhccCccc----cee-cCCCcEehhhhhhh---hcccCCccccccc
Confidence            7899999998665    333 5  79999999764   4788999999886

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

Probab=94.28  E-value=0.061  Score=43.61  Aligned_cols=49  Identities=16%  Similarity=0.406  Sum_probs=37.8

Q ss_pred             CCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCC---CCCCCcCc
Q 042258           93 MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR---LNCPVCRN  142 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~---~~CP~CR~  142 (152)
                      -.+...|||=.+.-.+......+. |||+..++-+.+..++.   ..||.|=.
T Consensus       331 fHSvF~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~  382 (394)
T KOG2817|consen  331 FHSVFICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYCPV  382 (394)
T ss_pred             ccceeecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence            344578999877766655667787 99999999999987763   46999943

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

Probab=94.15  E-value=0.022  Score=50.31  Aligned_cols=37  Identities=24%  Similarity=0.607  Sum_probs=29.3

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHh
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK  132 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~  132 (152)
                      ..++.|.+|...+... .-...| |||.||++|+.+-..
T Consensus       815 ep~d~C~~C~~~ll~~-pF~vf~-CgH~FH~~Cl~~~v~  851 (911)
T KOG2034|consen  815 EPQDSCDHCGRPLLIK-PFYVFP-CGHCFHRDCLIRHVL  851 (911)
T ss_pred             cCccchHHhcchhhcC-cceeee-ccchHHHHHHHHHHH
Confidence            4557899999888664 445677 999999999988753

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.95  E-value=0.025  Score=43.35  Aligned_cols=49  Identities=22%  Similarity=0.710  Sum_probs=35.0

Q ss_pred             CCccCccccccccCCCee-eecCCC-----CccccHHhHHHHHhCC--------CCCCCcCccC
Q 042258           95 SNTDCAICLDDFIEGETC-KSFPEC-----NHIFHLHCIDQWLKHR--------LNCPVCRNPL  144 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~-~~l~~C-----~H~fh~~Ci~~wl~~~--------~~CP~CR~~l  144 (152)
                      .+.-|-||+..-++.... .+.| |     .|..|..|+..|+..+        -+||.|+++.
T Consensus        19 ~eR~CWiCF~TdeDn~~a~WV~P-CrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY   81 (293)
T KOG3053|consen   19 LERCCWICFATDEDNRLAAWVHP-CRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY   81 (293)
T ss_pred             cceeEEEEeccCcccchhhhccc-ccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence            446799999876554322 3445 6     4889999999999642        3499999864

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

Probab=93.92  E-value=0.045  Score=37.91  Aligned_cols=54  Identities=22%  Similarity=0.385  Sum_probs=37.0

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHh---CCCCCCCcCccCccCC
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK---HRLNCPVCRNPLCRNL  148 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~---~~~~CP~CR~~l~~~~  148 (152)
                      .-.+|.||.+.-.+..-+.--.-||-..|..|-....+   ....||+|++.+.++-
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            34789999887544332222223899999998655444   3788999999887653

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

Probab=93.81  E-value=0.025  Score=49.36  Aligned_cols=46  Identities=30%  Similarity=0.688  Sum_probs=35.8

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhC--CCCCCCcCccCccC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH--RLNCPVCRNPLCRN  147 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~--~~~CP~CR~~l~~~  147 (152)
                      ..|.+|++    .+.....+ |+|.||..|+.+-+..  ...||.||..+..+
T Consensus       455 ~~c~ic~~----~~~~~it~-c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~  502 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITR-CGHDFCVECLKKSIQQSENAPCPLCRNVLKEK  502 (674)
T ss_pred             cccccccc----cccceeec-ccchHHHHHHHhccccccCCCCcHHHHHHHHH
Confidence            68999998    24445566 9999999999888764  34699999876543

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

Probab=93.61  E-value=0.042  Score=48.02  Aligned_cols=24  Identities=29%  Similarity=0.844  Sum_probs=21.6

Q ss_pred             CCCCccccHHhHHHHHhCCCCCCC
Q 042258          116 PECNHIFHLHCIDQWLKHRLNCPV  139 (152)
Q Consensus       116 ~~C~H~fh~~Ci~~wl~~~~~CP~  139 (152)
                      ..|+|..|..|...|+++...||.
T Consensus      1046 g~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1046 GTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             ccccccccHHHHHHHHhcCCcCCC
Confidence            349999999999999999999984

>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=93.38  E-value=0.076  Score=41.41  Aligned_cols=49  Identities=24%  Similarity=0.525  Sum_probs=34.6

Q ss_pred             cCccccccc-cCCCe-eeecCCCCccccHHhHHHHHhC-CCCCCCcCccCccC
Q 042258           98 DCAICLDDF-IEGET-CKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCRN  147 (152)
Q Consensus        98 ~C~IC~~~~-~~~~~-~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~~  147 (152)
                      .|++|...- -.++- ..+-+ |+|..|.+|+..-+.. ...||.|...+..+
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~-C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~   53 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINE-CGHRLCESCVDRIFSLGPAQCPECMVILRKN   53 (300)
T ss_pred             CCcccccceecCccceeeecc-ccchHHHHHHHHHHhcCCCCCCcccchhhhc
Confidence            488886543 33332 22334 9999999999998865 66899998766543

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=93.09  E-value=0.071  Score=42.59  Aligned_cols=49  Identities=18%  Similarity=0.507  Sum_probs=35.6

Q ss_pred             ccCccccccccCCC-eeeecCCCCccccHHhHHHHHhC-CCCCCCcCccCcc
Q 042258           97 TDCAICLDDFIEGE-TCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCR  146 (152)
Q Consensus        97 ~~C~IC~~~~~~~~-~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~  146 (152)
                      .-|+.|++++...+ ...-.+ ||...|..|-..--++ +..||.||+...+
T Consensus        15 d~cplcie~mditdknf~pc~-cgy~ic~fc~~~irq~lngrcpacrr~y~d   65 (480)
T COG5175          15 DYCPLCIEPMDITDKNFFPCP-CGYQICQFCYNNIRQNLNGRCPACRRKYDD   65 (480)
T ss_pred             ccCcccccccccccCCcccCC-cccHHHHHHHHHHHhhccCCChHhhhhccc
Confidence            45999999997544 344566 9999999995553333 7889999986543

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

Probab=92.76  E-value=0.035  Score=50.91  Aligned_cols=44  Identities=30%  Similarity=0.671  Sum_probs=36.2

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCc
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRN  142 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~  142 (152)
                      ...|.||.+.+.....  ... |||.+|..|...|+..+..||.|+.
T Consensus      1153 ~~~c~ic~dil~~~~~--I~~-cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1153 HFVCEICLDILRNQGG--IAG-CGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred             ccchHHHHHHHHhcCC--eee-echhHhhhHHHHHHHHhccCcchhh
Confidence            3579999999864322  233 9999999999999999999999974

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

Probab=92.56  E-value=0.062  Score=40.24  Aligned_cols=44  Identities=30%  Similarity=0.696  Sum_probs=31.9

Q ss_pred             CccccccccCCCeeeecCCCCc-cccHHhHHHHHhCCCCCCCcCccCccCCCC
Q 042258           99 CAICLDDFIEGETCKSFPECNH-IFHLHCIDQWLKHRLNCPVCRNPLCRNLEL  150 (152)
Q Consensus        99 C~IC~~~~~~~~~~~~l~~C~H-~fh~~Ci~~wl~~~~~CP~CR~~l~~~~~~  150 (152)
                      |-.|-+.   +..+..+| |.| .+|..|-..    -..||+|+....+.+.|
T Consensus       161 Cr~C~~~---~~~VlllP-CrHl~lC~~C~~~----~~~CPiC~~~~~s~~~v  205 (207)
T KOG1100|consen  161 CRKCGER---EATVLLLP-CRHLCLCGICDES----LRICPICRSPKTSSVEV  205 (207)
T ss_pred             ceecCcC---CceEEeec-ccceEeccccccc----CccCCCCcChhhceeec
Confidence            7777654   35577788 998 577888654    35599999988776654

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

Probab=92.51  E-value=0.13  Score=36.77  Aligned_cols=35  Identities=26%  Similarity=0.819  Sum_probs=22.2

Q ss_pred             CccCccccccccCC---------CeeeecCCCCc-cccHHhHHHHH
Q 042258           96 NTDCAICLDDFIEG---------ETCKSFPECNH-IFHLHCIDQWL  131 (152)
Q Consensus        96 ~~~C~IC~~~~~~~---------~~~~~l~~C~H-~fh~~Ci~~wl  131 (152)
                      +-.|+|||+.--+.         .+++-.. |+. .-|.+|+++.-
T Consensus         2 d~~CpICme~PHNAVLLlCSS~~kgcRpym-c~Ts~rhSNCLdqfk   46 (162)
T PF07800_consen    2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYM-CDTSYRHSNCLDQFK   46 (162)
T ss_pred             CccCceeccCCCceEEEEeccccCCccccc-cCCccchhHHHHHHH
Confidence            35799999886443         1223233 554 45889999974

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.

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.28  E-value=0.079  Score=41.47  Aligned_cols=28  Identities=29%  Similarity=0.890  Sum_probs=22.8

Q ss_pred             CCccccHHhHHHHHhC-------------CCCCCCcCccCc
Q 042258          118 CNHIFHLHCIDQWLKH-------------RLNCPVCRNPLC  145 (152)
Q Consensus       118 C~H~fh~~Ci~~wl~~-------------~~~CP~CR~~l~  145 (152)
                      |...+|.+|+.+|+..             +-+||+||+++.
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fc  365 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFC  365 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceE
Confidence            6778999999999742             567999999864

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

Probab=92.05  E-value=0.13  Score=45.37  Aligned_cols=48  Identities=23%  Similarity=0.644  Sum_probs=34.9

Q ss_pred             CccCccccccccCCCeeeecCCCCc-----cccHHhHHHHHhC--CCCCCCcCccCc
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNH-----IFHLHCIDQWLKH--RLNCPVCRNPLC  145 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H-----~fh~~Ci~~wl~~--~~~CP~CR~~l~  145 (152)
                      ...|-||..+=..+ .....| |..     ..|.+|+.+|+..  ...|-+|+++..
T Consensus        12 ~~~CRICr~e~~~d-~pLfhP-CKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~   66 (1175)
T COG5183          12 KRSCRICRTEDIRD-DPLFHP-CKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK   66 (1175)
T ss_pred             chhceeecCCCCCC-CcCccc-ccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence            37899998875333 334445 653     5899999999985  556999998653

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

Probab=91.46  E-value=0.071  Score=42.03  Aligned_cols=44  Identities=25%  Similarity=0.605  Sum_probs=30.3

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLC  145 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~  145 (152)
                      -.|.-|-..+..  .-+..| |.|+||.+|...  ...+.||.|-.++.
T Consensus        91 HfCd~Cd~PI~I--YGRmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~Vq  134 (389)
T KOG2932|consen   91 HFCDRCDFPIAI--YGRMIP-CKHVFCLECARS--DSDKICPLCDDRVQ  134 (389)
T ss_pred             EeecccCCccee--eecccc-cchhhhhhhhhc--CccccCcCcccHHH
Confidence            457777555422  124566 999999999765  34678999977654

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

Probab=89.75  E-value=0.33  Score=28.08  Aligned_cols=43  Identities=28%  Similarity=0.623  Sum_probs=22.5

Q ss_pred             CccccccccCC------CeeeecCCCCccccHHhHHHHHhCCCCCCCcC
Q 042258           99 CAICLDDFIEG------ETCKSFPECNHIFHLHCIDQWLKHRLNCPVCR  141 (152)
Q Consensus        99 C~IC~~~~~~~------~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR  141 (152)
                      |.-|...|..+      ...-..++|++.|+.+|=.--=..-..||-|-
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~   50 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE   50 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence            55566666553      23456778999999999554323456799884

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

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

Probab=89.71  E-value=0.19  Score=37.52  Aligned_cols=42  Identities=33%  Similarity=0.773  Sum_probs=35.4

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCR  141 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR  141 (152)
                      ..|.+|..-...+   +....||-.+|..|+...++....||.|.
T Consensus       182 k~Cn~Ch~LvIqg---~rCg~c~i~~h~~c~qty~q~~~~cphc~  223 (235)
T KOG4718|consen  182 KNCNLCHCLVIQG---IRCGSCNIQYHRGCIQTYLQRRDICPHCG  223 (235)
T ss_pred             HHHhHhHHHhhee---eccCcccchhhhHHHHHHhcccCcCCchh
Confidence            6899999887665   33445999999999999999999999994

>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=86.85  E-value=0.32  Score=37.16  Aligned_cols=47  Identities=26%  Similarity=0.670  Sum_probs=34.3

Q ss_pred             CccCccccccc-cCCC-eeeecCCCCccccHHhHHHHHhC-CCCCC--CcCc
Q 042258           96 NTDCAICLDDF-IEGE-TCKSFPECNHIFHLHCIDQWLKH-RLNCP--VCRN  142 (152)
Q Consensus        96 ~~~C~IC~~~~-~~~~-~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP--~CR~  142 (152)
                      +..||+|..+- ..++ ....-|.|-|.+|.+|+++-+.. ...||  -|.+
T Consensus        10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~k   61 (314)
T COG5220          10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGK   61 (314)
T ss_pred             cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHH
Confidence            35799997653 3333 34455669999999999998876 56799  7754

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

Probab=86.75  E-value=0.23  Score=42.87  Aligned_cols=43  Identities=26%  Similarity=0.567  Sum_probs=31.3

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRN  142 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~  142 (152)
                      ..|.||+..|-.....-+.+.|||..|+.|+..-  -+.+|| |+.
T Consensus        12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~   54 (861)
T KOG3161|consen   12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKR   54 (861)
T ss_pred             hhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCc
Confidence            5699999888665544444459999999999886  355677 443

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

Probab=86.71  E-value=0.25  Score=40.39  Aligned_cols=37  Identities=24%  Similarity=0.618  Sum_probs=27.0

Q ss_pred             CccCccccccccCC-CeeeecCCCCccccHHhHHHHHhC
Q 042258           96 NTDCAICLDDFIEG-ETCKSFPECNHIFHLHCIDQWLKH  133 (152)
Q Consensus        96 ~~~C~IC~~~~~~~-~~~~~l~~C~H~fh~~Ci~~wl~~  133 (152)
                      ..+|.||..+.... +... ..+|+|.||.+|..+.+..
T Consensus       146 ~~~C~iC~~e~~~~~~~f~-~~~C~H~fC~~C~k~~iev  183 (384)
T KOG1812|consen  146 KEECGICFVEDPEAEDMFS-VLKCGHRFCKDCVKQHIEV  183 (384)
T ss_pred             cccCccCccccccHhhhHH-HhcccchhhhHHhHHHhhh
Confidence            47899999555443 3334 4459999999999988763

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

Probab=86.48  E-value=0.69  Score=36.14  Aligned_cols=47  Identities=23%  Similarity=0.718  Sum_probs=33.3

Q ss_pred             ccCccccccccCCCe-eeecCCCC-----ccccHHhHHHHHh--CCCCCCCcCccC
Q 042258           97 TDCAICLDDFIEGET-CKSFPECN-----HIFHLHCIDQWLK--HRLNCPVCRNPL  144 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~-~~~l~~C~-----H~fh~~Ci~~wl~--~~~~CP~CR~~l  144 (152)
                      ..|-||..+...... ....| |.     +..|+.|+..|+.  +...|..|....
T Consensus        79 ~~cRIc~~~~~~~~~~~l~~p-C~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~  133 (323)
T KOG1609|consen   79 PICRICHEEDEESNGLLLISP-CSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFF  133 (323)
T ss_pred             CcEEEEecccccccccccccC-ccccCcHHHHHHHHHHhhhccccCeeeecccccc
Confidence            679999987643221 23344 64     4689999999998  567799997744

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

Probab=86.36  E-value=0.41  Score=39.67  Aligned_cols=34  Identities=24%  Similarity=0.532  Sum_probs=27.8

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHh
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK  132 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~  132 (152)
                      +...|+||..-|.++   +.+| |+|..|..|...-+.
T Consensus         3 eelkc~vc~~f~~ep---iil~-c~h~lc~~ca~~~~~   36 (699)
T KOG4367|consen    3 EELKCPVCGSFYREP---IILP-CSHNLCQACARNILV   36 (699)
T ss_pred             ccccCceehhhccCc---eEee-cccHHHHHHHHhhcc
Confidence            346799999988554   8898 999999999886554

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

Probab=86.00  E-value=0.21  Score=43.46  Aligned_cols=46  Identities=28%  Similarity=0.826  Sum_probs=35.6

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhC---CCCCCCcCccCcc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH---RLNCPVCRNPLCR  146 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---~~~CP~CR~~l~~  146 (152)
                      .+|+||...+..+    .+.+|.|.|+..|+..-+..   ...||+|+..+..
T Consensus        22 lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK   70 (684)
T KOG4362|consen   22 LECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEK   70 (684)
T ss_pred             ccCCceeEEeecc----chhhhhHHHHhhhhhceeeccCccccchhhhhhhhh
Confidence            6799999998775    34459999999998776653   5679999876543

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

Probab=85.38  E-value=1  Score=39.64  Aligned_cols=41  Identities=20%  Similarity=0.398  Sum_probs=29.3

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPV  139 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~  139 (152)
                      ..|.+|-..+ .|..+. .+.|||.-|..|+.+|+...+.||.
T Consensus       780 ~~CtVC~~vi-~G~~~~-c~~C~H~gH~sh~~sw~~~~s~ca~  820 (839)
T KOG0269|consen  780 AKCTVCDLVI-RGVDVW-CQVCGHGGHDSHLKSWFFKASPCAK  820 (839)
T ss_pred             cCceeeccee-eeeEee-cccccccccHHHHHHHHhcCCCCcc
Confidence            3577775554 222323 3459999999999999998887766

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

Probab=84.59  E-value=1.3  Score=35.28  Aligned_cols=61  Identities=15%  Similarity=0.302  Sum_probs=38.2

Q ss_pred             CCCceeecCCCCCCCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC---CCCCCCcC
Q 042258           80 SLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH---RLNCPVCR  141 (152)
Q Consensus        80 ~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---~~~CP~CR  141 (152)
                      .||-...........+-..||+=.+.--+......+. |||+.-.+-++...++   +..||.|-
T Consensus       320 eLP~eIklp~~~hfHs~FiCPVlKe~~t~ENpP~ml~-CgHVIskeal~~LS~nG~~~FKCPYCP  383 (396)
T COG5109         320 ELPMEIKLPKGRHFHSLFICPVLKELCTDENPPVMLE-CGHVISKEALSVLSQNGVLSFKCPYCP  383 (396)
T ss_pred             CCceEEecCCcccccceeeccccHhhhcccCCCeeee-ccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence            4444444333333344477988655433323344555 9999999999997665   45699994

>smart00249 PHD PHD zinc finger

Probab=84.03  E-value=0.86  Score=24.60  Aligned_cols=31  Identities=19%  Similarity=0.580  Sum_probs=22.1

Q ss_pred             cCccccccccCCCeeeecCCCCccccHHhHHH
Q 042258           98 DCAICLDDFIEGETCKSFPECNHIFHLHCIDQ  129 (152)
Q Consensus        98 ~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~  129 (152)
                      .|.+|.... .++..+....|+..||..|+..
T Consensus         1 ~C~~C~~~~-~~~~~i~C~~C~~~~H~~C~~~   31 (47)
T smart00249        1 YCSVCGKPD-DGGELLQCDGCDRWYHQTCLGP   31 (47)
T ss_pred             CcccCCCcC-CCCCEEECCCCCchhhhhhCCC
Confidence            377887765 3445555556999999999765

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

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=83.57  E-value=1  Score=33.53  Aligned_cols=40  Identities=35%  Similarity=0.871  Sum_probs=28.2

Q ss_pred             ccCcccccc-----ccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCc
Q 042258           97 TDCAICLDD-----FIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRN  142 (152)
Q Consensus        97 ~~C~IC~~~-----~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~  142 (152)
                      ..|-+|-+.     |+. +.+...++|+..||..|..     +..||-|.+
T Consensus       153 fiCe~C~~~~~IfPF~~-~~~~~C~~C~~v~H~~C~~-----~~~CpkC~R  197 (202)
T PF13901_consen  153 FICEICNSDDIIFPFQI-DTTVRCPKCKSVFHKSCFR-----KKSCPKCAR  197 (202)
T ss_pred             CCCccCCCCCCCCCCCC-CCeeeCCcCccccchhhcC-----CCCCCCcHh
Confidence            567788642     111 3566777899999999955     277999954

>TIGR00622 ssl1 transcription factor ssl1

Probab=82.85  E-value=2.2  Score=28.82  Aligned_cols=46  Identities=20%  Similarity=0.356  Sum_probs=34.6

Q ss_pred             ccCccccccccCC----------CeeeecCCCCccccHHhHHHHHhCCCCCCCcCc
Q 042258           97 TDCAICLDDFIEG----------ETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRN  142 (152)
Q Consensus        97 ~~C~IC~~~~~~~----------~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~  142 (152)
                      ..|--|...|..+          ...-..++|++.|+.+|=..+-..-..||.|..
T Consensus        56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~~  111 (112)
T TIGR00622        56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCIH  111 (112)
T ss_pred             CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCCC
Confidence            4699999988542          122346679999999998887677778999963

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

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

Probab=82.76  E-value=0.81  Score=40.59  Aligned_cols=48  Identities=6%  Similarity=0.113  Sum_probs=33.7

Q ss_pred             ccCccccccccCCC---eeeecCCCCccccHHhHHHHHhC------CCCCCCcCccC
Q 042258           97 TDCAICLDDFIEGE---TCKSFPECNHIFHLHCIDQWLKH------RLNCPVCRNPL  144 (152)
Q Consensus        97 ~~C~IC~~~~~~~~---~~~~l~~C~H~fh~~Ci~~wl~~------~~~CP~CR~~l  144 (152)
                      ..|.+|..+++.+.   ...-+..|+|.+|-.||..|...      +-.|++|..-+
T Consensus        97 ~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci  153 (1134)
T KOG0825|consen   97 DTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV  153 (1134)
T ss_pred             cccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence            56888888777632   22223349999999999999864      44588887644

>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length

Probab=82.07  E-value=0.87  Score=27.68  Aligned_cols=11  Identities=27%  Similarity=1.147  Sum_probs=8.4

Q ss_pred             ccHHhHHHHHh
Q 042258          122 FHLHCIDQWLK  132 (152)
Q Consensus       122 fh~~Ci~~wl~  132 (152)
                      ||++|+.+|+.
T Consensus        12 FCRNCLskWy~   22 (68)
T PF06844_consen   12 FCRNCLSKWYR   22 (68)
T ss_dssp             --HHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999985

The function of this family is unknown.; PDB: 2O35_A 3FYB_B.

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

Probab=81.97  E-value=1.3  Score=37.77  Aligned_cols=44  Identities=30%  Similarity=0.836  Sum_probs=35.1

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNL  148 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~  148 (152)
                      ..|.+|+...    ..+..+ |.   |..|+.+|+..+..||+|+..+..+.
T Consensus       480 ~~~~~~~~~~----~~~~~~-~~---~~~~l~~~~~~~~~~pl~~~~~~~~~  523 (543)
T KOG0802|consen  480 DVCAICYQEM----SARITP-CS---HALCLRKWLYVQEVCPLCHTYMKEDD  523 (543)
T ss_pred             CcchHHHHHH----Hhcccc-cc---chhHHHhhhhhccccCCCchhhhccc
Confidence            6799998887    224455 77   99999999999999999988766544

>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=81.38  E-value=1  Score=22.25  Aligned_cols=23  Identities=30%  Similarity=0.596  Sum_probs=12.5

Q ss_pred             cCccccccccCCCeeeecCCCCccc
Q 042258           98 DCAICLDDFIEGETCKSFPECNHIF  122 (152)
Q Consensus        98 ~C~IC~~~~~~~~~~~~l~~C~H~f  122 (152)
                      .|+-|.......  ....|-|||.|
T Consensus         2 ~CP~C~~~V~~~--~~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCPECGAEVPES--AKFCPHCGYDF   24 (26)
T ss_pred             cCCCCcCCchhh--cCcCCCCCCCC
Confidence            466666665332  23445577766

Several members are annotated as putative helicases.

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=80.47  E-value=1.1  Score=23.91  Aligned_cols=26  Identities=27%  Similarity=0.696  Sum_probs=16.8

Q ss_pred             cCccccccccCCCe-------eeecCCCCcccc
Q 042258           98 DCAICLDDFIEGET-------CKSFPECNHIFH  123 (152)
Q Consensus        98 ~C~IC~~~~~~~~~-------~~~l~~C~H~fh  123 (152)
                      +|+-|...|..++.       -...+.|+|.|.
T Consensus         4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~   36 (37)
T PF13719_consen    4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR   36 (37)
T ss_pred             ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence            58888888855332       234556888874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	152
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		1e-07
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		1e-07
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		2e-06
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		1e-05
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		3e-05
4ayc_B	138	Rnf8 Ring Domain Structure Length = 138		1e-04
4ayc_A	138	Rnf8 Ring Domain Structure Length = 138		1e-04
4epo_C	149	Crystal Structure Of Rnf8 Bound To The Ubc13MMS2 HE		1e-04
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 = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 27/49 (55%)
Query: 93  MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCR 141
           M    +CA+CL +  +GE  +  P C H FH  C+D WL     CP+CR
Sbjct: 2   MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50

>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 = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 90  ETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           E  + S  +C +C +D+  GE+ +  P CNH+FH  CI  WL+   +CPVCR  L
Sbjct: 9   EEHVGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL 62

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 85  SYK-NGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCR 141
           SY+ N     +  T C +C+ DF   +  +  P CNH FH  C+D+WLK    CP+CR
Sbjct: 11  SYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICR 67

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/43 (48%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCR 141
           C ICL    EGE  +  P C H+FH  C+DQWL     CP+CR
Sbjct: 17  CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICR 58

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 80  SLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPV 139
           +LP++        +     C IC  ++++G+     P C+H FH  C+  WL+    CPV
Sbjct: 24  ALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPV 82
Query: 140 CR 141
           CR
Sbjct: 83  CR 84

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           C IC + FIE  T      C H F  +CI++W+K ++ CP+CR  +
Sbjct: 56  CIICSEYFIEAVTLN----CAHSFCSYCINEWMKRKIECPICRKDI 97

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 27/46 (58%), Gaps = 4/46 (8%)
Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           C IC + FIE  T      C H F  +CI++W+K ++ CP+CR  +
Sbjct: 56  CIICSEYFIEAVTLN----CAHSFCSYCINEWMKRKIECPICRKDI 97

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 4/47 (8%)
Query: 98  DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
            C IC + FIE  T      C H F  +CI++W+K ++ CP+CR  +
Sbjct: 66  QCIICSEYFIEAVTLN----CAHSFCSYCINEWMKRKIECPICRKDI 108

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 91  TEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
            E+  +  CA+CL+DF   +     P C H FH  C+ +WL+ R  CP+C  P+
Sbjct: 10  KELNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPV 62

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	152
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	9e-21
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	4e-20
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	7e-20
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	5e-19
2ect_A	78	Ring finger protein 126; metal binding protein, st	2e-18
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	2e-18
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	2e-17
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	2e-14
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-13
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	4e-13
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	4e-13
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	9e-13
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	1e-12
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	7e-12
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	2e-11
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	4e-11
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	1e-10
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	1e-10
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	1e-09
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	2e-09
3nw0_A	238	Non-structural maintenance of chromosomes element	2e-09
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	4e-09
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	6e-09
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-08
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	7e-09
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	8e-09
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	8e-09
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	4e-08
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	1e-07
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	1e-06
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	1e-06
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	7e-06
1z6u_A	150	NP95-like ring finger protein isoform B; structura	5e-05
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	5e-05
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	8e-05
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	2e-04
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	2e-04
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	2e-04
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	6e-04
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	7e-04

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

 Score = 80.1 bits (198), Expect = 9e-21
 Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 80  SLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPV 139
           +LP++        +     C IC  ++++G+     P C+H FH  C+  WL+    CPV
Sbjct: 24  ALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPV 82

Query: 140 CRNPL 144
           CR   
Sbjct: 83  CRCMF 87

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

 Score = 77.8 bits (192), Expect = 4e-20
 Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 2/65 (3%)

Query: 80  SLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPV 139
            LP   +     + +  T C +C+ DF   +  +  P CNH FH  C+D+WLK    CP+
Sbjct: 8   QLPSYRFNPNNHQ-SEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPI 65

Query: 140 CRNPL 144
           CR   
Sbjct: 66  CRADS 70

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

 Score = 76.9 bits (190), Expect = 7e-20
 Identities = 19/48 (39%), Positives = 27/48 (56%)

Query: 97  TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
            +CA+CL +  +GE  +  P C H FH  C+D WL     CP+CR  +
Sbjct: 6   VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>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 = 74.6 bits (184), Expect = 5e-19
 Identities = 15/51 (29%), Positives = 23/51 (45%)

Query: 94  TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           + ++ C ICL+D            C H+ H  C ++ LK    CP+C  P 
Sbjct: 3   SGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPS 53

>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 = 74.0 bits (182), Expect = 2e-18
 Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 1/56 (1%)

Query: 90  ETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLC 145
           E  + S  +C +C +D+  GE+ +  P CNH+FH  CI  WL+   +CPVCR  L 
Sbjct: 9   EEHVGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLT 63

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

 Score = 73.3 bits (180), Expect = 2e-18
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 92  EMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNLELD 151
           E+  +  CA+CL+DF   +     P C H FH  C+ +WL+ R  CP+C  P+ +  +L 
Sbjct: 11  ELNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLS 69

>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 = 70.9 bits (174), Expect = 2e-17
 Identities = 23/58 (39%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 87  KNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
               TE  +   C ICL    EGE  +  P C H+FH  C+DQWL     CP+CR  +
Sbjct: 5   GEEGTEEDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDI 61

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

 Score = 63.4 bits (154), Expect = 2e-14
 Identities = 14/49 (28%), Positives = 22/49 (44%)

Query: 96  NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
              C  C  +  + +    + ECNH FH  C+  W+K    CP+C+   
Sbjct: 26  MDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDW 74

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

 Score = 60.3 bits (146), Expect = 2e-13
 Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 3/58 (5%)

Query: 90  ETEMTSNTDCAICLDDFIEGETCKSFP---ECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
               +    C IC+D + E           EC H+F   C+   LK+   CP CR  +
Sbjct: 9   GLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66

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

 Score = 59.7 bits (145), Expect = 4e-13
 Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 5/56 (8%)

Query: 92  EMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN 147
           ++T   +C IC+D   +         C H F   CID+W     NCP+CR  +   
Sbjct: 11  QLTDEEECCICMDGRADLIL-----PCAHSFCQKCIDKWSDRHRNCPICRLQMTGA 61

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

 Score = 59.7 bits (145), Expect = 4e-13
 Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 3/46 (6%)

Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           C ICL+D            C H F   CI +W++    CP+C+ P+
Sbjct: 8   CPICLEDPSNYSMA---LPCLHAFCYVCITRWIRQNPTCPLCKVPV 50

>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 = 58.7 bits (142), Expect = 9e-13
 Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 3/57 (5%)

Query: 94  TSNTDCAICLDDFIEGETCKSFP---ECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN 147
           +    C IC+D + E           EC H+F   C+   LK+   CP CR  +   
Sbjct: 8   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 64

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

 Score = 58.2 bits (141), Expect = 1e-12
 Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 3/56 (5%)

Query: 95  SNTDCAICLDDFIEGETCKSFP---ECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN 147
           +   C IC+D + E           EC H+F   C+   LK+   CP CR  +   
Sbjct: 2   AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 57

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

 Score = 56.5 bits (136), Expect = 7e-12
 Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 5/62 (8%)

Query: 85  SYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLN--CPVCRN 142
                ET   +   C IC    I+G++C     C    HL C+ ++ +      CP C +
Sbjct: 4   GSSGRETYPDAVKICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCND 60

Query: 143 PL 144
             
Sbjct: 61  YW 62

>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 = 56.4 bits (135), Expect = 2e-11
 Identities = 17/54 (31%), Positives = 22/54 (40%)

Query: 90  ETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNP 143
              M    +C          E   ++  CNH FH HCI +WLK R  CP+    
Sbjct: 45  NHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 98

>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 = 56.0 bits (134), Expect = 4e-11
 Identities = 17/54 (31%), Positives = 22/54 (40%)

Query: 90  ETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNP 143
              M    +C          E   ++  CNH FH HCI +WLK R  CP+    
Sbjct: 56  NHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 109

>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 = 54.1 bits (130), Expect = 1e-10
 Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 4/54 (7%)

Query: 92  EMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWL-KHRLNCPVCRNPL 144
            +     C IC++   +   C   P C+ +    CI +WL + R  CP CR PL
Sbjct: 18  SIAEVFRCFICMEKLRDARLC---PHCSKLCCFSCIRRWLTEQRAQCPHCRAPL 68

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

 Score = 53.6 bits (129), Expect = 1e-10
 Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 3/54 (5%)

Query: 91  TEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           +E+T    C+IC    I+     +  EC H F   CI +   +   CP C   +
Sbjct: 10  SELTPYILCSICKGYLID---ATTITECLHTFCKSCIVRHFYYSNRCPKCNIVV 60

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

 Score = 51.8 bits (123), Expect = 1e-09
 Identities = 15/76 (19%), Positives = 24/76 (31%), Gaps = 19/76 (25%)

Query: 90  ETEMTSNTDCAICLDDFIEG--------------ETCKSFPECNHIFHLHCIDQWLKH-- 133
           E ++    DC IC++                          +C+H FHL C+     +  
Sbjct: 19  ELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGN 78

Query: 134 ---RLNCPVCRNPLCR 146
               L CP C+     
Sbjct: 79  KDGSLQCPSCKTIYGE 94

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

 Score = 50.6 bits (121), Expect = 2e-09
 Identities = 12/45 (26%), Positives = 15/45 (33%), Gaps = 4/45 (8%)

Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNP 143
           C IC   F      K    C H F   C  +  +    C +C  P
Sbjct: 18  CFICRQAFQNPVVTK----CRHYFCESCALEHFRATPRCYICDQP 58

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

 Score = 53.6 bits (128), Expect = 2e-09
 Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 5/49 (10%)

Query: 98  DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLN--CPVCRNPL 144
            C IC    I+G++C     C    HL C+ ++ +      CP C +  
Sbjct: 182 ICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYW 227

>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 = 50.2 bits (120), Expect = 4e-09
 Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 3/54 (5%)

Query: 91  TEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           TE+  +  C +C   FI+     +  EC H F   CI ++L+    CP+C   +
Sbjct: 10  TELNPHLMCVLCGGYFID---ATTIIECLHSFCKTCIVRYLETSKYCPICDVQV 60

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

 Score = 50.6 bits (120), Expect = 6e-09
 Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 3/59 (5%)

Query: 92  EMTSNTDCAICLDDFIEGETCKSFP---ECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN 147
             +    C IC+D + E           EC H+F   C+   LK+   CP CR  +   
Sbjct: 3   MGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 61

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

 Score = 49.0 bits (116), Expect = 2e-08
 Identities = 15/81 (18%), Positives = 27/81 (33%), Gaps = 1/81 (1%)

Query: 68  ETQGLCPQE-LPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHC 126
           +    CP     ++  +       +   S   C     + ++        EC H+F   C
Sbjct: 46  KNANTCPTCRKKINHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQC 105

Query: 127 IDQWLKHRLNCPVCRNPLCRN 147
           +   LK+   CP CR  +   
Sbjct: 106 LRDSLKNANTCPTCRKKINHK 126

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

 Score = 48.7 bits (116), Expect = 7e-09
 Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 4/47 (8%)

Query: 98  DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           +CAICL   +   +      C H+F   C+         C +CR  +
Sbjct: 17  ECAICLQTCVHPVSLP----CKHVFCYLCVKGASWLGKRCALCRQEI 59

>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 = 52.1 bits (124), Expect = 8e-09
 Identities = 14/83 (16%), Positives = 26/83 (31%), Gaps = 7/83 (8%)

Query: 66  SEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLH 125
           +   +      + V+  Q  Y+      ++   C IC ++            C H+    
Sbjct: 304 TGLCEPTPQDHIKVT--QEQYELYCEMGSTFQLCKICAEND----KDVKIEPCGHLMCTS 357

Query: 126 CIDQWL-KHRLNCPVCRNPLCRN 147
           C+  W       CP CR  +   
Sbjct: 358 CLTSWQESEGQGCPFCRCEIKGT 380

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

 Score = 50.4 bits (120), Expect = 8e-09
 Identities = 18/46 (39%), Positives = 27/46 (58%), Gaps = 4/46 (8%)

Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           C IC + FIE  T      C H F  +CI++W+K ++ CP+CR  +
Sbjct: 67  CIICSEYFIEAVTL----NCAHSFCSYCINEWMKRKIECPICRKDI 108

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

 Score = 47.5 bits (113), Expect = 4e-08
 Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 3/48 (6%)

Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCR 146
           C IC + F         P+C+H +   CI ++L ++  CP C   +  
Sbjct: 25  CGICFEYFNI---AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTE 69

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

 Score = 48.3 bits (114), Expect = 1e-07
 Identities = 14/72 (19%), Positives = 22/72 (30%), Gaps = 15/72 (20%)

Query: 88  NGETEMTSNTDCAICLDDFIEGETCKSF----PECNHIFHLHCIDQWLK----------- 132
             + E      C IC    ++G           +C    H  C+++W K           
Sbjct: 300 KLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEV 359

Query: 133 HRLNCPVCRNPL 144
               CP C+  L
Sbjct: 360 SFGQCPFCKAKL 371

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

 Score = 44.2 bits (104), Expect = 1e-06
 Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 5/54 (9%)

Query: 98  DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR-LNCPVCRNPLCRNLEL 150
            C  C +      T      C H     C+D+  + +  +CP CR  L R+  +
Sbjct: 54  QCICCQELVFRPITT----VCQHNVCKDCLDRSFRAQVFSCPACRYDLGRSYAM 103

>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 = 43.7 bits (103), Expect = 1e-06
 Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 10/58 (17%)

Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNP-----LCRNLELD 151
           C+ C +   E         C HIF  +C+   +     CPVC  P     L  N +LD
Sbjct: 25  CSRCTNILRE---PVCLGGCEHIFCSNCVSDCIGTG--CPVCYTPAWIQDLKINRQLD 77

>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 = 42.7 bits (100), Expect = 7e-06
 Identities = 18/53 (33%), Positives = 20/53 (37%), Gaps = 4/53 (7%)

Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLN-CPVCRNPLCRNLEL 150
           C ICLD         +  EC H F   CI   L+     CP CR  L     L
Sbjct: 57  CPICLDMLKN---TMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSL 106

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

 Score = 40.0 bits (93), Expect = 5e-05
 Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 5/53 (9%)

Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR-LNCPVCRNPLCRNLEL 150
           C  C +   +  T     EC H     C+ +  K +  +CP CR+ L +N  +
Sbjct: 81  CVCCQELVYQPVT----TECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYIM 129

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

 Score = 39.5 bits (92), Expect = 5e-05
 Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 5/48 (10%)

Query: 98  DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR-LNCPVCRNPL 144
            C IC++  +E  T      CNH     C    ++   L CP CR  +
Sbjct: 17  QCGICMEILVEPVTL----PCNHTLCKPCFQSTVEKASLCCPFCRRRV 60

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

 Score = 37.8 bits (88), Expect = 8e-05
 Identities = 10/51 (19%), Positives = 16/51 (31%), Gaps = 5/51 (9%)

Query: 98  DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK-HRLNCPVCRNPLCRN 147
            C  C       +      EC H F   C+   L      C  C+  + ++
Sbjct: 17  KCEKCHLVLCSPKQT----ECGHRFCESCMAALLSSSSPKCTACQESIVKD 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 = 37.0 bits (86), Expect = 2e-04
 Identities = 12/45 (26%), Positives = 15/45 (33%), Gaps = 5/45 (11%)

Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWL--KHRLNCPVCR 141
           C IC D   +       P C + +   CI   L       CP C 
Sbjct: 18  CLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCH 59

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

 Score = 37.8 bits (88), Expect = 2e-04
 Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 18/63 (28%)

Query: 99  CAICLDDFIEGETCKSFP---ECNHIFHLHCIDQWLKHR---LNCPVCRNP-----LCRN 147
           C ICL+   E       P   +C+HIF   C+ + L  +     CP+C+N      L  +
Sbjct: 24  CPICLELIKE-------PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQES 76

Query: 148 LEL 150
              
Sbjct: 77  TRF 79

>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 Length = 94

 Score = 37.1 bits (86), Expect = 2e-04
 Identities = 10/48 (20%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 98  DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLC 145
            C +CL ++   E   +  +C  IF   C+ Q+++  +   +     C
Sbjct: 7   GCKLCLGEY-PVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISC 53

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A Length = 61

 Score = 35.4 bits (82), Expect = 6e-04
 Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 3/46 (6%)

Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           CAI              P+   IF    ++Q++K   N P+   PL
Sbjct: 6   CAISGKVPRRPVLS---PKSRTIFEKSLLEQYVKDTGNDPITNEPL 48

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

 Score = 35.4 bits (82), Expect = 7e-04
 Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 13/51 (25%)

Query: 99  CAICLDDFIEGETCKSFP---ECNHIFHLHCIDQWLKHR---LNCPVCRNP 143
           C ICLD   +       P   +C H F L CI Q  +       CP+C+  
Sbjct: 23  CPICLDILQK-------PVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTS 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	152
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.77
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.72
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.66
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.65
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.63
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.59
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.56
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.54
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.52
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.51
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.5
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.47
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.47
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.45
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.45
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.45
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.44
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.42
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.4
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.4
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.39
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.39
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.38
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.38
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.38
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.35
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.33
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.32
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.31
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.31
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.31
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.3
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.3
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.29
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.28
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.27
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.26
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.25
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.24
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.22
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	99.22
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.2
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.18
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.17
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.16
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.16
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.14
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.13
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.12
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.12
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.11
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.09
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.08
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.08
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.08
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.03
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.0
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.98
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.9
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.9
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.88
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.88
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.85
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.75
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.75
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.74
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.74
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.58
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.54
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.5
3nw0_A	238	Non-structural maintenance of chromosomes element	98.25
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.14
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	97.56
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	96.1
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	94.89
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	94.76
1we9_A	64	PHD finger family protein; structural genomics, PH	94.53
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	93.53
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	92.61
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	92.56
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	92.55
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	91.14
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	90.94
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	90.75
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	90.47
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	90.45
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	90.11
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	89.19
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	88.34
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	88.17
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	88.14
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	87.27
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	86.43
1weu_A	91	Inhibitor of growth family, member 4; structural g	86.37
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	85.75
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	85.65
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	85.26
1z60_A	59	TFIIH basal transcription factor complex P44 subun	84.66
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	84.53
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	83.88
1wew_A	78	DNA-binding family protein; structural genomics, P	83.66
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	82.55
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	82.28
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	81.95
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	81.13
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	80.6

>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=4e-19  Score=115.38  Aligned_cols=79  Identities=24%  Similarity=0.666  Sum_probs=67.9

Q ss_pred             CCCCCCCCCccccCCCceeecCCCCCCCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCcc
Q 042258           67 EETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCR  146 (152)
Q Consensus        67 ~~~~~~~~~~i~~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~  146 (152)
                      ....+++++.+. .||...+............|+||++.+..++.+..++ |||.||..||.+|+..+.+||+||+++..
T Consensus        12 ~~~~~~s~~~i~-~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           12 VANPPASKESID-ALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCMFPP   89 (91)
T ss_dssp             SCCCCCCHHHHH-TSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTTCCBSSC
T ss_pred             cCCCCCCHHHHH-hCCCeeecccccccCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCcCccCCC
Confidence            455677777777 9999988876655556688999999999888888898 99999999999999999999999999876


Q ss_pred             C
Q 042258          147 N  147 (152)
Q Consensus       147 ~  147 (152)
                      .
T Consensus        90 ~   90 (91)
T 2l0b_A           90 P   90 (91)
T ss_dssp             C
T ss_pred             C
Confidence            5

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

Probab=99.72  E-value=5.5e-18  Score=106.01  Aligned_cols=70  Identities=31%  Similarity=0.772  Sum_probs=58.9

Q ss_pred             CccccCCCceeecCCCCCCCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           75 QELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        75 ~~i~~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      ..+. ++|..++.... .......|+||++.+..++.+..++ |+|.||..||.+|+..+.+||+||+++...
T Consensus         4 ~~i~-~lp~~~~~~~~-~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A            4 GSSG-QLPSYRFNPNN-HQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             CCCS-SCCCEEBCSSS-CSSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             hhHh-hCCcEEecCcc-ccCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            3344 88888887654 3345578999999999888888898 999999999999999999999999998764

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

Probab=99.66  E-value=7e-17  Score=94.92  Aligned_cols=51  Identities=37%  Similarity=1.024  Sum_probs=45.8

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLC  145 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~  145 (152)
                      ++.+|+||++.+..++....+++|||.||..|+.+|++++.+||+||+++.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            446899999999888877788779999999999999999999999999874

>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=99.65  E-value=1.9e-16  Score=97.26  Aligned_cols=57  Identities=39%  Similarity=0.936  Sum_probs=50.0

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCCCCC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNLELD  151 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~~~~  151 (152)
                      .....|+||++.+..++.+..++ |||.||..|+.+|+..+.+||+||+++...+..+
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   68 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQLPSE   68 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCSCCCCC
T ss_pred             CCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccCcCCCC
Confidence            34478999999998877888888 9999999999999999999999999998876543

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

Probab=99.63  E-value=3.3e-16  Score=97.49  Aligned_cols=56  Identities=36%  Similarity=0.856  Sum_probs=49.4

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCCCC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNLEL  150 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~~~  150 (152)
                      .....|+||++.+..+..+..++ |+|.||..||.+|++.+.+||+||+++.....+
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   68 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQL   68 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSSCCSC
T ss_pred             CCCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCccccccccc
Confidence            34578999999998888888888 999999999999999999999999999876554

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

Probab=99.59  E-value=1.2e-15  Score=95.87  Aligned_cols=54  Identities=41%  Similarity=1.010  Sum_probs=47.8

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNL  148 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~  148 (152)
                      ....+|+||++.|..+..+..++ |+|.||..||.+|+..+.+||+||+++....
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (78)
T 2ect_A           13 GSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQN   66 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCCCCSC
T ss_pred             CCCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCccCCcc
Confidence            34478999999998888778888 9999999999999999999999999987654

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

Probab=99.56  E-value=1e-15  Score=97.21  Aligned_cols=51  Identities=31%  Similarity=0.806  Sum_probs=41.6

Q ss_pred             CccCccccccccC-----------CCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCcc
Q 042258           96 NTDCAICLDDFIE-----------GETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCR  146 (152)
Q Consensus        96 ~~~C~IC~~~~~~-----------~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~  146 (152)
                      +..|+||++.+.+           ++.++.+++|+|.||..||.+|+..+.+||+||+++..
T Consensus        15 ~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   76 (81)
T 2ecl_A           15 CDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVV   76 (81)
T ss_dssp             CSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCE
T ss_pred             CCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcch
Confidence            4568888887754           34456666699999999999999999999999998754

>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=99.54  E-value=3.3e-15  Score=87.58  Aligned_cols=50  Identities=32%  Similarity=0.908  Sum_probs=42.5

Q ss_pred             CCccCccccccccCCC-eeeecCCCCccccHHhHHHHHhCCCCCCCcCccCc
Q 042258           95 SNTDCAICLDDFIEGE-TCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLC  145 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~-~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~  145 (152)
                      ....|+||++.+.+++ ....++ |+|.||..|+.+|+..+.+||+||+++.
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            3468999999996644 456666 9999999999999999999999999874

>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=6.9e-15  Score=90.54  Aligned_cols=54  Identities=30%  Similarity=0.706  Sum_probs=44.8

Q ss_pred             CCCccCccccccccCC----CeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCC
Q 042258           94 TSNTDCAICLDDFIEG----ETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNL  148 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~----~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~  148 (152)
                      .....|+||++.+.+.    +....++ |||.||..|+.+|+..+.+||+||+++..+-
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   65 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKR   65 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCCCS
T ss_pred             CCCCCCcccChhhhccccccCCeEeCC-CCChHhHHHHHHHHHcCCCCCCCCCccChhh
Confidence            3457899999998653    3445666 9999999999999999999999999987653

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

Probab=99.51  E-value=1.2e-14  Score=88.86  Aligned_cols=52  Identities=31%  Similarity=0.742  Sum_probs=43.5

Q ss_pred             CCCccCccccccccCC----CeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCcc
Q 042258           94 TSNTDCAICLDDFIEG----ETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCR  146 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~----~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~  146 (152)
                      .....|+||++.+.+.    +.+..++ |||.||..|+.+|+..+..||+||+++..
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            3457899999999653    3345666 99999999999999999999999999865

>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=99.50  E-value=2.1e-14  Score=96.34  Aligned_cols=53  Identities=26%  Similarity=0.676  Sum_probs=41.8

Q ss_pred             CCccCccccccccCCC---------------eeeecCCCCccccHHhHHHHH-----hCCCCCCCcCccCccCC
Q 042258           95 SNTDCAICLDDFIEGE---------------TCKSFPECNHIFHLHCIDQWL-----KHRLNCPVCRNPLCRNL  148 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~---------------~~~~l~~C~H~fh~~Ci~~wl-----~~~~~CP~CR~~l~~~~  148 (152)
                      .+..|+||++.|..+.               .+..++ |+|.||..||.+|+     ..+.+||+||+.+..+.
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            3468999999996543               223555 99999999999999     45779999999887654

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

Probab=99.47  E-value=1.5e-14  Score=87.10  Aligned_cols=51  Identities=31%  Similarity=0.732  Sum_probs=43.1

Q ss_pred             CccCccccccccCC----CeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           96 NTDCAICLDDFIEG----ETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        96 ~~~C~IC~~~~~~~----~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      ..+|+||++.+.++    +.+..++ |||.||..|+.+|+..+.+||+||+++..+
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   57 (64)
T 2xeu_A            3 MVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   57 (64)
T ss_dssp             CCBCTTTCCBHHHHHHTTCCEEEET-TSCEEEHHHHHHHHHHCSBCTTTCCBCTTT
T ss_pred             CCCCCccChhhhCccccCCCEEeCC-CCCchhHHHHHHHHHcCCCCCCCCccCCcc
Confidence            36799999999653    3445666 999999999999999999999999998764

>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=99.47  E-value=3.6e-14  Score=94.38  Aligned_cols=49  Identities=41%  Similarity=0.844  Sum_probs=40.7

Q ss_pred             CCccCccccccccCC-------------C--eeeecCCCCccccHHhHHHHHhCCCCCCCcCccC
Q 042258           95 SNTDCAICLDDFIEG-------------E--TCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL  144 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~-------------~--~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l  144 (152)
                      .+..|+||++.|...             +  .+..++ |+|.||..||.+||..+.+||+||+++
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~   99 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREW   99 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecc-cCcEECHHHHHHHHHcCCcCcCCCCcc
Confidence            447899999998754             1  244465 999999999999999999999999984

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

Probab=99.45  E-value=1.2e-13  Score=85.41  Aligned_cols=54  Identities=28%  Similarity=0.557  Sum_probs=44.2

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCCCC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNLEL  150 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~~~  150 (152)
                      .....|+||++.+.+.   ..+.+|||.||..||..|+..+..||+||+++...-.+
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   66 (72)
T 2djb_A           13 TPYILCSICKGYLIDA---TTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPL   66 (72)
T ss_dssp             CGGGSCTTTSSCCSSC---EECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSC
T ss_pred             CCCCCCCCCChHHHCc---CEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCccccc
Confidence            3457899999998653   45523999999999999999999999999998765443

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

Probab=99.45  E-value=6e-14  Score=88.79  Aligned_cols=54  Identities=26%  Similarity=0.631  Sum_probs=44.0

Q ss_pred             CCCccCccccccccCCCeeeecCCCC-----ccccHHhHHHHHhCC--CCCCCcCccCccCCC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECN-----HIFHLHCIDQWLKHR--LNCPVCRNPLCRNLE  149 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~-----H~fh~~Ci~~wl~~~--~~CP~CR~~l~~~~~  149 (152)
                      .....|.||++++..++.+ .+| |+     |.||..||.+|+..+  .+||+||+++.....
T Consensus        13 ~~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~~   73 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMETK   73 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCCC
T ss_pred             CCCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCcc
Confidence            4457899999999776665 577 96     999999999999865  589999999875443

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

Probab=99.45  E-value=3.2e-14  Score=87.42  Aligned_cols=51  Identities=37%  Similarity=0.914  Sum_probs=43.8

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCCC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNLE  149 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~~  149 (152)
                      .....|+||++.+.+    ..++ |||.||..|+.+|+..+..||+||+++.....
T Consensus        13 ~~~~~C~IC~~~~~~----~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   63 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGANE   63 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEET-TTEEECHHHHHHSSCCCSSCHHHHHCTTCCCC
T ss_pred             CCCCCCeeCCcCccC----cccC-CCCcccHHHHHHHHHCcCcCCCcCCcccCCCc
Confidence            345789999999865    5677 99999999999999999999999999886543

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

Probab=99.44  E-value=6.5e-14  Score=86.43  Aligned_cols=49  Identities=29%  Similarity=0.716  Sum_probs=42.3

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      ....|+||++.+.+.   ..++ |||.||..|+.+|+..+..||+||+++...
T Consensus        14 ~~~~C~IC~~~~~~~---~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   62 (71)
T 2d8t_A           14 TVPECAICLQTCVHP---VSLP-CKHVFCYLCVKGASWLGKRCALCRQEIPED   62 (71)
T ss_dssp             SCCBCSSSSSBCSSE---EEET-TTEEEEHHHHHHCTTCSSBCSSSCCBCCHH
T ss_pred             CCCCCccCCcccCCC---EEcc-CCCHHHHHHHHHHHHCCCcCcCcCchhCHh
Confidence            447899999998553   5677 999999999999999999999999998754

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

Probab=99.42  E-value=9.4e-14  Score=84.79  Aligned_cols=50  Identities=32%  Similarity=0.855  Sum_probs=42.1

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      .+..|+||++.+.++  ...++ |||.||..|+.+|+..+.+||+||+++...
T Consensus         4 ~~~~C~IC~~~~~~~--~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   53 (68)
T 1chc_A            4 VAERCPICLEDPSNY--SMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVESV   53 (68)
T ss_dssp             CCCCCSSCCSCCCSC--EEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCCE
T ss_pred             CCCCCeeCCccccCC--cEecC-CCCeeHHHHHHHHHhCcCcCcCCChhhHhh
Confidence            346799999998543  35677 999999999999999999999999988653

>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=3.2e-13  Score=86.28  Aligned_cols=53  Identities=25%  Similarity=0.651  Sum_probs=43.8

Q ss_pred             CCCccCccccccccCCCe-eeecCCCCccccHHhHHHHHhCC---CCCCCcCccCccC
Q 042258           94 TSNTDCAICLDDFIEGET-CKSFPECNHIFHLHCIDQWLKHR---LNCPVCRNPLCRN  147 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~-~~~l~~C~H~fh~~Ci~~wl~~~---~~CP~CR~~l~~~  147 (152)
                      .....|+||++.+.+.+. ...++ |||.||..|+..|+..+   ..||+||+++...
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             cCCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            345789999999977554 56677 99999999999999875   7899999977543

>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=99.40  E-value=1.4e-14  Score=97.83  Aligned_cols=50  Identities=38%  Similarity=0.874  Sum_probs=0.9

Q ss_pred             CCccCccccccccCC-------------Ce-eeecCCCCccccHHhHHHHHhCCCCCCCcCccC
Q 042258           95 SNTDCAICLDDFIEG-------------ET-CKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL  144 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~-------------~~-~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l  144 (152)
                      .+..|+||++.|...             +. .+.+++|+|.||..||.+||..+.+||+||+++
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~  110 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREW  110 (117)
T ss_dssp             CC--------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCee
Confidence            447899999999652             11 222234999999999999999999999999984

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

Probab=99.39  E-value=4.3e-13  Score=81.47  Aligned_cols=50  Identities=20%  Similarity=0.527  Sum_probs=41.4

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHh-CCCCCCCcCccCccC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK-HRLNCPVCRNPLCRN  147 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~-~~~~CP~CR~~l~~~  147 (152)
                      .....|+||++.+.++   ..++ |||.||..|+.+|+. .+..||+||+++..+
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            3457899999999665   3466 999999999999995 577899999998764

>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=4.2e-13  Score=84.76  Aligned_cols=48  Identities=23%  Similarity=0.505  Sum_probs=41.3

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCcc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCR  146 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~  146 (152)
                      ....|+||++.+.++   ..++ |||.||..|+..|+.....||+||+++..
T Consensus        14 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (81)
T 2csy_A           14 IPFRCFICRQAFQNP---VVTK-CRHYFCESCALEHFRATPRCYICDQPTGG   61 (81)
T ss_dssp             CCSBCSSSCSBCCSE---EECT-TSCEEEHHHHHHHHHHCSBCSSSCCBCCS
T ss_pred             CCCCCcCCCchhcCe---eEcc-CCCHhHHHHHHHHHHCCCcCCCcCccccc
Confidence            347899999998553   4576 99999999999999999999999999863

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

Probab=99.38  E-value=4.1e-13  Score=83.50  Aligned_cols=50  Identities=24%  Similarity=0.524  Sum_probs=41.1

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCC--CCCCCcCccCcc
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR--LNCPVCRNPLCR  146 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~--~~CP~CR~~l~~  146 (152)
                      .....|+||++.+.++   ..++.|||.||..||..|+..+  ..||+||+++..
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A           13 PDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS   64 (74)
T ss_dssp             CGGGSCSSSCCCCTTC---EECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCC
T ss_pred             CCCCCCcCCChHHhCC---eEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCC
Confidence            3457899999999664   4465599999999999999865  689999998654

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

Probab=99.38  E-value=7e-13  Score=81.89  Aligned_cols=50  Identities=32%  Similarity=0.711  Sum_probs=41.2

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHh---CCCCCCCcCccCccC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK---HRLNCPVCRNPLCRN  147 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~---~~~~CP~CR~~l~~~  147 (152)
                      .....|+||++.+.+   ...++ |||.||..|+..|+.   ....||+||+++..+
T Consensus        18 ~~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           18 QEEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCCBCTTTCSBCSS---EEECT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCC
T ss_pred             ccCCEeccCCcccCC---eEEcC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcc
Confidence            445789999999864   35566 999999999999997   466899999998654

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

Probab=99.38  E-value=2.7e-13  Score=94.06  Aligned_cols=46  Identities=37%  Similarity=1.023  Sum_probs=40.7

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCcc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCR  146 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~  146 (152)
                      ..|+||++.+.+   ...++ |||.||..||..|+..+.+||+||+++..
T Consensus        54 ~~C~iC~~~~~~---~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           54 LQCIICSEYFIE---AVTLN-CAHSFCSYCINEWMKRKIECPICRKDIKS   99 (138)
T ss_dssp             SBCTTTCSBCSS---EEEET-TSCEEEHHHHHHHTTTCSBCTTTCCBCCC
T ss_pred             CCCcccCcccCC---ceECC-CCCCccHHHHHHHHHcCCcCCCCCCcCCC
Confidence            579999999955   36677 99999999999999999999999998864

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

Probab=99.35  E-value=8.1e-13  Score=82.73  Aligned_cols=51  Identities=18%  Similarity=0.419  Sum_probs=42.7

Q ss_pred             CCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-CCCCCCcCccCccC
Q 042258           93 MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCRN  147 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~~  147 (152)
                      ......|+||++.+.++   ..++ |||.||..||.+|+.. +.+||+||+++...
T Consensus         5 ~~~~~~C~IC~~~~~~P---v~~~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~   56 (78)
T 1t1h_A            5 FPEYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             CSSSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             CcccCCCCCccccccCC---EEcC-CCCeecHHHHHHHHHHCcCCCCCCcCCCChh
Confidence            34557899999999654   5567 9999999999999987 78899999988643

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

Probab=99.33  E-value=3e-12  Score=80.98  Aligned_cols=50  Identities=38%  Similarity=0.696  Sum_probs=42.0

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC------CCCCCCcCccCccC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH------RLNCPVCRNPLCRN  147 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~------~~~CP~CR~~l~~~  147 (152)
                      .....|+||++.+.++   ..++ |||.||..|+..|+..      ...||+||.++...
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            3457899999998665   4677 9999999999999987      67899999988653

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

Probab=99.32  E-value=1.3e-12  Score=81.24  Aligned_cols=48  Identities=27%  Similarity=0.782  Sum_probs=41.0

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCC--CCCCCcCccCccC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR--LNCPVCRNPLCRN  147 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~--~~CP~CR~~l~~~  147 (152)
                      .+|+||.+.+..++.+.   .|+|.||..||.+||+++  .+||+||++....
T Consensus        16 ~~C~IC~~~i~~g~~C~---~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~   65 (74)
T 2ct0_A           16 KICNICHSLLIQGQSCE---TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE   65 (74)
T ss_dssp             CBCSSSCCBCSSSEECS---SSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSC
T ss_pred             CcCcchhhHcccCCccC---CCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCC
Confidence            78999999998764433   599999999999999987  8999999987644

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

Probab=99.31  E-value=1.5e-12  Score=78.84  Aligned_cols=51  Identities=24%  Similarity=0.558  Sum_probs=40.3

Q ss_pred             CccCccccc-cccCCCee-eecCCCCccccHHhHHHHHhC-CCCCCCcCccCccC
Q 042258           96 NTDCAICLD-DFIEGETC-KSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCRN  147 (152)
Q Consensus        96 ~~~C~IC~~-~~~~~~~~-~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~~  147 (152)
                      +..|+||++ .+.++... ..++ |||.||..|+.+|+.+ +..||+||+++..+
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   56 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCcCCcCCCCccCCCccCeecCC-CCCHhHHHHHHHHHHcCCCcCCCCCCccccc
Confidence            357999999 77665443 3455 9999999999999765 56899999998654

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

Probab=99.31  E-value=8.6e-13  Score=90.07  Aligned_cols=53  Identities=30%  Similarity=0.733  Sum_probs=44.4

Q ss_pred             CCCccCccccccccCC----CeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           94 TSNTDCAICLDDFIEG----ETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~----~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      .+..+|+||++.+.++    +....++ |||.||..||.+|+..+.+||+||+++..+
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   61 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   61 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBCTTT
T ss_pred             CCCCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcCccc
Confidence            3457899999999653    3446676 999999999999999999999999988754

>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=1.1e-12  Score=86.12  Aligned_cols=48  Identities=29%  Similarity=0.810  Sum_probs=40.6

Q ss_pred             CccCccccccccCCCeeee-cCCCCccccHHhHHHHHhCC-CCCCCcCccCccC
Q 042258           96 NTDCAICLDDFIEGETCKS-FPECNHIFHLHCIDQWLKHR-LNCPVCRNPLCRN  147 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~-l~~C~H~fh~~Ci~~wl~~~-~~CP~CR~~l~~~  147 (152)
                      ...|+||++.+.+   ... ++ |||.||..||.+|+..+ ..||+||+++...
T Consensus        22 ~~~C~IC~~~~~~---p~~~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (100)
T 3lrq_A           22 VFRCFICMEKLRD---ARLCPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPLQLR   71 (100)
T ss_dssp             HTBCTTTCSBCSS---EEECTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CCCCccCCccccC---ccccCC-CCChhhHHHHHHHHHHCcCCCCCCCCcCCHH
Confidence            3679999999954   355 66 99999999999999987 6999999998643

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

Probab=99.30  E-value=7.5e-13  Score=82.91  Aligned_cols=49  Identities=31%  Similarity=0.613  Sum_probs=41.2

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-------CCCCCCcCccCcc
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-------RLNCPVCRNPLCR  146 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-------~~~CP~CR~~l~~  146 (152)
                      .....|+||++.+.++   ..++ |||.||..|+..|+..       ...||+||.++..
T Consensus        10 ~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A           10 QEEVTCPICLELLTEP---LSLD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             CCCCEETTTTEECSSC---CCCS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCS
T ss_pred             ccCCCCcCCCcccCCe---eECC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCH
Confidence            3457899999999664   4567 9999999999999986       6789999998864

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

Probab=99.30  E-value=4e-12  Score=80.38  Aligned_cols=50  Identities=30%  Similarity=0.660  Sum_probs=41.8

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC------CCCCCCcCccCccC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH------RLNCPVCRNPLCRN  147 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~------~~~CP~CR~~l~~~  147 (152)
                      .....|+||++.+.+.   ..++ |||.||..|+..|+..      ...||+||..+...
T Consensus        17 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecv_A           17 KEEVTCPICLELLTQP---LSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPE   72 (85)
T ss_dssp             CCCCCCTTTCSCCSSC---BCCS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSS
T ss_pred             cCCCCCCCCCcccCCc---eeCC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHH
Confidence            3457899999999664   4566 9999999999999987      78999999988753

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

Probab=99.29  E-value=1.8e-12  Score=84.80  Aligned_cols=48  Identities=27%  Similarity=0.706  Sum_probs=40.8

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCcc
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCR  146 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~  146 (152)
                      ...|+||++.+.++   ..+++|||.||..|+..|+..+..||+||.++..
T Consensus        22 ~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           22 LLRCGICFEYFNIA---MIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCcccCChhhCCc---CEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            36899999999653   4553499999999999999999999999998864

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

Probab=99.28  E-value=6.4e-12  Score=75.48  Aligned_cols=43  Identities=35%  Similarity=0.763  Sum_probs=36.2

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHh---CCCCCCCc
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK---HRLNCPVC  140 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~---~~~~CP~C  140 (152)
                      .....|+||++.+.++   ..++ |||.||..||.+|+.   ....||+|
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            4457899999999654   5566 999999999999998   46689998

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

Probab=99.27  E-value=6e-12  Score=81.11  Aligned_cols=49  Identities=24%  Similarity=0.540  Sum_probs=40.3

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC--CCCCCCcCccCc
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH--RLNCPVCRNPLC  145 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~--~~~CP~CR~~l~  145 (152)
                      .....|+||++.+.++   ..++.|||.||..||..|+..  ...||+||.++.
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            4557899999999664   456559999999999999974  468999999973

>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=99.26  E-value=3e-12  Score=85.08  Aligned_cols=49  Identities=27%  Similarity=0.697  Sum_probs=42.0

Q ss_pred             CCccCccccccccCCCeeeec-CCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           95 SNTDCAICLDDFIEGETCKSF-PECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l-~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      ....|+||++.+.++   ..+ + |||.||..||..|+..+..||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~p---~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           14 PHLMCVLCGGYFIDA---TTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGTBCTTTSSBCSSE---EEETT-TCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             CcCCCccCChHHhCc---CEeCC-CCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            447899999998553   455 6 999999999999999999999999998764

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

Probab=99.25  E-value=7.9e-12  Score=73.64  Aligned_cols=43  Identities=33%  Similarity=0.899  Sum_probs=35.5

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHH---hCCCCCCCc
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWL---KHRLNCPVC  140 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl---~~~~~CP~C  140 (152)
                      .....|+||++.+.++   ..++ |||.||..||.+|+   ..+..||+|
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            3457899999999765   4566 99999999999995   457789998

>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=7.5e-12  Score=85.09  Aligned_cols=47  Identities=26%  Similarity=0.644  Sum_probs=40.0

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhCC-CCCCCcCccCcc
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR-LNCPVCRNPLCR  146 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~-~~CP~CR~~l~~  146 (152)
                      ...|+||++.+.++   ..++ |||.||..||..|+..+ ..||+||+++..
T Consensus        52 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           52 TFQCICCQELVFRP---ITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HTBCTTTSSBCSSE---EECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             CCCCCcCChHHcCc---EEee-CCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            36799999999653   5677 99999999999999854 489999999876

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

Probab=99.22  E-value=4.7e-12  Score=86.35  Aligned_cols=53  Identities=30%  Similarity=0.733  Sum_probs=44.0

Q ss_pred             CCCccCccccccccCC----CeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           94 TSNTDCAICLDDFIEG----ETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~----~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      .....|+||++.+...    .....++ |||.||..|+.+|+..+++||+||+++..+
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  126 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK  126 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEET-TSBEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCCccccccccCcceEeCC-CCChhhHHHHHHHHHcCCCCCCCCCcCChh
Confidence            3457899999998652    2335566 999999999999999999999999998765

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

Probab=99.22  E-value=2.8e-12  Score=100.22  Aligned_cols=56  Identities=23%  Similarity=0.644  Sum_probs=43.6

Q ss_pred             CCCccCccccccccCCCee----eecCCCCccccHHhHHHHHhCC-----------CCCCCcCccCccCCC
Q 042258           94 TSNTDCAICLDDFIEGETC----KSFPECNHIFHLHCIDQWLKHR-----------LNCPVCRNPLCRNLE  149 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~----~~l~~C~H~fh~~Ci~~wl~~~-----------~~CP~CR~~l~~~~~  149 (152)
                      ....+|+||++.+.++..+    ...++|+|.||..|+.+|+++.           .+||+||+++..+++
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~sf~  376 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTSFA  376 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGGGG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCccHH
Confidence            3457899999999873222    2234699999999999999752           469999999998875

>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=1e-11  Score=82.67  Aligned_cols=47  Identities=34%  Similarity=0.842  Sum_probs=39.6

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCC---CCCCcCccCccC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRL---NCPVCRNPLCRN  147 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~---~CP~CR~~l~~~  147 (152)
                      ..|+||++.+.++   ..++ |||.||..|+..|+..+.   .||+||.++...
T Consensus        22 ~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (112)
T 1jm7_A           22 LECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (112)
T ss_dssp             TSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             CCCcccChhhcCe---EECC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHh
Confidence            5799999998654   4466 999999999999998754   899999988753

>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=99.18  E-value=1.5e-11  Score=87.51  Aligned_cols=49  Identities=37%  Similarity=0.697  Sum_probs=40.3

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-CCCCCCcCccCcc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCR  146 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~  146 (152)
                      ....|+||++.+.++   ..+.+|||.||..||..|+.. +..||+||.++..
T Consensus        53 ~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           53 SELMCPICLDMLKNT---MTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHBCTTTSSBCSSE---EEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCcccChHhhCc---CEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            346899999998653   444239999999999999997 7889999999853

>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=99.17  E-value=1.7e-11  Score=86.16  Aligned_cols=48  Identities=25%  Similarity=0.593  Sum_probs=40.9

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCC-CCCCcCccCccC
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRL-NCPVCRNPLCRN  147 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~-~CP~CR~~l~~~  147 (152)
                      ...|+||++.+.++   ..++ |||.||..||..|+.... .||+||.++...
T Consensus        78 ~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           78 SFMCVCCQELVYQP---VTTE-CFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HTBCTTTSSBCSSE---EECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CCEeecCChhhcCC---EEcC-CCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            36899999998554   5577 999999999999998754 899999998865

>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=99.16  E-value=1.2e-11  Score=83.50  Aligned_cols=50  Identities=34%  Similarity=0.626  Sum_probs=41.8

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCC-CCCCcCccCccC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRL-NCPVCRNPLCRN  147 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~-~CP~CR~~l~~~  147 (152)
                      .....|+||++.+.++   ..++ |||.||..||.+|+..+. .||+||.++...
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            4457899999998654   5566 999999999999998765 999999988753

>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=99.16  E-value=4.7e-12  Score=84.99  Aligned_cols=46  Identities=30%  Similarity=0.852  Sum_probs=39.8

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-CCCCCCcCccCc
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLC  145 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~  145 (152)
                      +..|+||++.+.++   ..++ |||.||..|+..|+.. +..||+||.++.
T Consensus        15 ~~~C~iC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   61 (115)
T 3l11_A           15 ECQCGICMEILVEP---VTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRVS   61 (115)
T ss_dssp             HHBCTTTCSBCSSC---EECT-TSCEECHHHHCCCCCTTTSBCTTTCCBCH
T ss_pred             CCCCccCCcccCce---eEcC-CCCHHhHHHHHHHHhHCcCCCCCCCcccC
Confidence            47899999999654   5677 9999999999999976 678999999875

>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=99.14  E-value=1.8e-11  Score=74.06  Aligned_cols=50  Identities=26%  Similarity=0.546  Sum_probs=41.0

Q ss_pred             CCccCccccccccCCCeeeec--CCCCcc-ccHHhHHHHHhCCCCCCCcCccCccCC
Q 042258           95 SNTDCAICLDDFIEGETCKSF--PECNHI-FHLHCIDQWLKHRLNCPVCRNPLCRNL  148 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l--~~C~H~-fh~~Ci~~wl~~~~~CP~CR~~l~~~~  148 (152)
                      .+..|+||++...+.   ..+  | |||. |+..|+..|...+..||+||+++....
T Consensus         7 ~~~~C~IC~~~~~~~---~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~~i   59 (64)
T 2vje_A            7 AIEPCVICQGRPKNG---CIVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQMIV   59 (64)
T ss_dssp             GGSCCTTTSSSCSCE---EEEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCCEEE
T ss_pred             CcCCCCcCCCCCCCE---EEECCC-CCChhhHHHHHHHHHHcCCcCCCcCcchhceE
Confidence            346799999987443   333  7 9999 899999999999999999999986543

>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=99.13  E-value=3.6e-11  Score=95.91  Aligned_cols=51  Identities=25%  Similarity=0.670  Sum_probs=43.3

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHh-CCCCCCCcCccCccCCCC
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK-HRLNCPVCRNPLCRNLEL  150 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~-~~~~CP~CR~~l~~~~~~  150 (152)
                      ...|+||++.+.+   ...++ |||.||..|+..|+. .+.+||+||+++.....+
T Consensus       332 ~~~C~ICle~~~~---pv~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~~i  383 (389)
T 2y1n_A          332 FQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPI  383 (389)
T ss_dssp             SSBCTTTSSSBCC---EEEET-TCCEECHHHHHHHHHHTCSBCTTTCCBCCEEEEC
T ss_pred             CCCCCccCcCCCC---eEEeC-CCChhhHHHHHHHHhcCCCCCCCCCCccCCceeE
Confidence            3689999999844   46677 999999999999999 788999999998876544

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

Probab=99.12  E-value=5e-11  Score=76.03  Aligned_cols=51  Identities=12%  Similarity=0.088  Sum_probs=43.8

Q ss_pred             CCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           93 MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      .+....|+||++.+.++   ..++ |||.|++.||.+|+..+.+||+||.++...
T Consensus        11 ~p~~~~CpI~~~~m~dP---V~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~   61 (85)
T 2kr4_A           11 APDEFRDPLMDTLMTDP---VRLP-SGTVMDRSIILRHLLNSPTDPFNRQMLTES   61 (85)
T ss_dssp             CCTTTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CchheECcccCchhcCC---eECC-CCCEECHHHHHHHHhcCCCCCCCcCCCChH
Confidence            34557899999999664   6677 999999999999999889999999988654

>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=3.5e-11  Score=80.78  Aligned_cols=48  Identities=31%  Similarity=0.648  Sum_probs=40.7

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-CCCCCCcCccCccC
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCRN  147 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~~  147 (152)
                      ...|+||++.+.++   ..++ |||.||..||.+|+.. ...||+||+++...
T Consensus        23 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (116)
T 1rmd_A           23 SISCQICEHILADP---VETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (116)
T ss_dssp             HTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCcHhcCc---EEcC-CCCcccHHHHHHHHhHCcCcCCCCCCCCCHh
Confidence            36899999998553   5566 9999999999999986 77999999998753

>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=99.11  E-value=6e-11  Score=77.94  Aligned_cols=51  Identities=14%  Similarity=0.111  Sum_probs=44.1

Q ss_pred             CCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           93 MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      .+....|+||++.|.++   ..++ |||.|++.||.+|+..+.+||+||.++...
T Consensus        26 ~p~~~~CpI~~~~m~dP---V~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~   76 (100)
T 2kre_A           26 APDEFRDPLMDTLMTDP---VRLP-SGTIMDRSIILRHLLNSPTDPFNRQTLTES   76 (100)
T ss_dssp             CSTTTBCTTTCSBCSSE---EEET-TTEEEEHHHHHHHTTSCSBCSSSCCBCCTT
T ss_pred             CcHhhCCcCccCcccCC---eECC-CCCEEchHHHHHHHHcCCCCCCCCCCCChh
Confidence            34558899999999665   6677 999999999999999899999999998754

>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=1.4e-10  Score=72.78  Aligned_cols=54  Identities=17%  Similarity=0.462  Sum_probs=40.4

Q ss_pred             CCCccCccccccccCCCe-eeecCCCCccccHHhHHHHHhC-CCCCCCcCccCccCC
Q 042258           94 TSNTDCAICLDDFIEGET-CKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCRNL  148 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~-~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~~~  148 (152)
                      ....+|+||++.+...+. ...++ |||.||..|+..++.. ...||.||+++....
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            344789999998854322 22234 9999999999998754 678999999887643

>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=99.08  E-value=3.6e-11  Score=72.46  Aligned_cols=51  Identities=20%  Similarity=0.483  Sum_probs=40.4

Q ss_pred             CccCccccccccCCCeeeecCCCCcc-ccHHhHHHHHhCCCCCCCcCccCccCC
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHI-FHLHCIDQWLKHRLNCPVCRNPLCRNL  148 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~CP~CR~~l~~~~  148 (152)
                      ...|.||++...+. .+..+| |||. |+..|+..|...+..||+||+++....
T Consensus         7 ~~~C~IC~~~~~~~-~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~~i   58 (63)
T 2vje_B            7 LKPCSLCEKRPRDG-NIIHGR-TGHLVTCFHCARRLKKAGASCPICKKEIQLVI   58 (63)
T ss_dssp             GSBCTTTSSSBSCE-EEEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCCEEE
T ss_pred             CCCCcccCCcCCCe-EEEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhhceE
Confidence            36799999986442 112237 9998 999999999988899999999986543

>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=99.08  E-value=1.3e-10  Score=75.98  Aligned_cols=50  Identities=16%  Similarity=0.121  Sum_probs=43.4

Q ss_pred             CCCccCccccccccCCCeeeecCCCC-ccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECN-HIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~-H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      +....|+||++.|.++   ..++ || |.|++.||.+|+..+.+||+||.++...
T Consensus        20 p~~~~CpI~~~~m~dP---V~~~-cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~   70 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCDP---VVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPLTMD   70 (98)
T ss_dssp             CTTTBCTTTCSBCSSE---EECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBCCTT
T ss_pred             cHhcCCcCccccccCC---eECC-CCCeEECHHHHHHHHHhCCCCCCCCCCCChh
Confidence            4557899999999665   6677 99 9999999999999989999999998754

>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=99.08  E-value=2.4e-11  Score=84.62  Aligned_cols=49  Identities=18%  Similarity=0.425  Sum_probs=40.5

Q ss_pred             CCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCC-CCCCcCccCc
Q 042258           93 MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRL-NCPVCRNPLC  145 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~-~CP~CR~~l~  145 (152)
                      ......|+||++.+.++   ..++ |||.||..||.+|+.... .||+||.++.
T Consensus        28 l~~~~~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~   77 (141)
T 3knv_A           28 LEAKYLCSACRNVLRRP---FQAQ-CGHRYCSFCLASILSSGPQNCAACVHEGI   77 (141)
T ss_dssp             CCGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHGGGSCEECHHHHHTTC
T ss_pred             CCcCcCCCCCChhhcCc---EECC-CCCccCHHHHHHHHhcCCCCCCCCCCccc
Confidence            34557899999999665   5566 999999999999998654 8999999763

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

Probab=99.03  E-value=6.2e-11  Score=73.59  Aligned_cols=47  Identities=26%  Similarity=0.631  Sum_probs=39.2

Q ss_pred             CccCccccccccCCCeeeecCCCCcc-ccHHhHHHHHhCCCCCCCcCccCccCCCC
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHI-FHLHCIDQWLKHRLNCPVCRNPLCRNLEL  150 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~CP~CR~~l~~~~~~  150 (152)
                      ...|+||++.+.+   ...+| |||. ||..|+..|    ..||+||+++.....+
T Consensus        24 ~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~~~i   71 (74)
T 4ic3_A           24 EKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEAV----DKCPMCYTVITFKQKI   71 (74)
T ss_dssp             HTBCTTTSSSBCC---EEEET-TCCBCCCHHHHTTC----SBCTTTCCBCSEEEEC
T ss_pred             CCCCCCCCCCCCC---EEEcC-CCChhHHHHhhhcC----ccCCCcCcCccCcEEE
Confidence            3679999998744   46677 9999 999999998    8999999998876543

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

Probab=99.00  E-value=1.1e-10  Score=68.65  Aligned_cols=46  Identities=24%  Similarity=0.601  Sum_probs=38.0

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      ....|+||++.+.+.   ..++ |||.||..|+..|   ...||+||+++...
T Consensus         5 ~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T 1bor_A            5 QFLRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCSSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             cCCCceEeCCccCCe---EEcC-CCCcccHHHHccC---CCCCCcCCcEeecC
Confidence            346799999999764   5677 9999999999884   67899999988643

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

Probab=98.98  E-value=1e-10  Score=78.68  Aligned_cols=45  Identities=29%  Similarity=0.691  Sum_probs=38.5

Q ss_pred             CccCccccccccCCCeeeec-CCCCccccHHhHHHHHhCCCCCCCcCccCcc
Q 042258           96 NTDCAICLDDFIEGETCKSF-PECNHIFHLHCIDQWLKHRLNCPVCRNPLCR  146 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l-~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~  146 (152)
                      ...|+||++.+.++   ..+ + |||.||..||..|+.  ..||+||.++..
T Consensus        22 ~~~C~IC~~~~~~p---v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~   67 (117)
T 1jm7_B           22 LLRCSRCTNILREP---VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAWI   67 (117)
T ss_dssp             TTSCSSSCSCCSSC---BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCSC
T ss_pred             CCCCCCCChHhhCc---cEeCC-CCCHHHHHHHHHHhc--CCCcCCCCcCcc
Confidence            36799999999654   556 5 999999999999987  889999998854

>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=98.90  E-value=5.4e-10  Score=79.69  Aligned_cols=50  Identities=34%  Similarity=0.642  Sum_probs=41.7

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCC-CCCCCcCccCccC
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR-LNCPVCRNPLCRN  147 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~-~~CP~CR~~l~~~  147 (152)
                      .....|+||++.+.++   ..++ |||.||..|+.+|+..+ ..||+||.++..+
T Consensus        16 ~~~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           16 ESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCChhhcCc---EECC-CCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            4557899999999654   5576 99999999999999864 4999999988764

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.90  E-value=8.1e-10  Score=68.60  Aligned_cols=47  Identities=26%  Similarity=0.635  Sum_probs=38.1

Q ss_pred             CccCccccccccCCCeeeecCCCCcc-ccHHhHHHHHhCCCCCCCcCccCccCCCC
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHI-FHLHCIDQWLKHRLNCPVCRNPLCRNLEL  150 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~CP~CR~~l~~~~~~  150 (152)
                      ...|+||++.+.+   ...+| |||. ||..|+..    ...||+||+++.....|
T Consensus        25 ~~~C~IC~~~~~~---~~~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i~~~~~i   72 (75)
T 2ecg_A           25 EKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEA----VDKCPMCYTVITFKQKI   72 (75)
T ss_dssp             HHSCSSSCSSCCC---BCCSS-SCCCCBCHHHHHH----CSBCTTTCCBCCCCCBC
T ss_pred             CCCCCcCCCCCCC---EEEec-CCCHHHHHHHhhC----CCCCccCCceecCcEEE
Confidence            3679999998754   35577 9999 99999965    47899999999876654

>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=98.88  E-value=8.2e-10  Score=83.90  Aligned_cols=51  Identities=20%  Similarity=0.234  Sum_probs=42.0

Q ss_pred             CCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-CCCCCCcCccCccC
Q 042258           93 MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCRN  147 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~~  147 (152)
                      .+....|+||++.+.++   .+++ |||.||+.||..|+.. ..+||+||.++...
T Consensus       205 ~~~~~~c~i~~~~~~dP---v~~~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~  256 (281)
T 2c2l_A          205 IPDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQE  256 (281)
T ss_dssp             CCSTTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCGG
T ss_pred             CCcccCCcCcCCHhcCC---eECC-CCCEECHHHHHHHHHHCCCCCcCCCCCCchh
Confidence            34557899999999664   6677 9999999999999986 44599999998643

>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=98.88  E-value=9e-10  Score=71.39  Aligned_cols=47  Identities=21%  Similarity=0.504  Sum_probs=38.2

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCC------CCCCC--cCcc
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR------LNCPV--CRNP  143 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~------~~CP~--CR~~  143 (152)
                      .....|+||++.|.++   ..++.|||.|++.||..|+..+      .+||+  |+..
T Consensus         5 ~~~~~CPI~~~~~~dP---V~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            5 SSGFTCPITKEEMKKP---VKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             SSCCBCTTTCSBCSSE---EEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             CcEeECcCcCchhcCC---EEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            3457899999999654   5564599999999999999753      58999  9866

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.85  E-value=2e-09  Score=65.67  Aligned_cols=48  Identities=25%  Similarity=0.711  Sum_probs=39.0

Q ss_pred             CCccCccccccccCCCeeeecCCCCcc-ccHHhHHHHHhCCCCCCCcCccCccCCCC
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHI-FHLHCIDQWLKHRLNCPVCRNPLCRNLEL  150 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~CP~CR~~l~~~~~~  150 (152)
                      ....|.||++...+   +..+| |||. ||..|+..    ...||+||+++...+.+
T Consensus        14 ~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i~~~~~i   62 (68)
T 2ea5_A           14 NSKDCVVCQNGTVN---WVLLP-CRHTCLCDGCVKY----FQQCPMCRQFVQESFAL   62 (68)
T ss_dssp             CSSCCSSSSSSCCC---CEETT-TTBCCSCTTHHHH----CSSCTTTCCCCCCEECC
T ss_pred             CCCCCCCcCcCCCC---EEEEC-CCChhhhHHHHhc----CCCCCCCCcchhceEEe
Confidence            34679999998744   46677 9999 99999985    57899999999876654

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

Probab=98.75  E-value=4.9e-09  Score=75.53  Aligned_cols=51  Identities=20%  Similarity=0.227  Sum_probs=42.2

Q ss_pred             CCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCC-CCCCCcCccCccC
Q 042258           93 MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR-LNCPVCRNPLCRN  147 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~-~~CP~CR~~l~~~  147 (152)
                      .+....|+||++.|.++   ..++ |||.|++.||..|+..+ .+||+||.++...
T Consensus       103 ip~~f~CPI~~elm~DP---V~~~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~  154 (179)
T 2f42_A          103 IPDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFDPVTRSPLTQD  154 (179)
T ss_dssp             CCGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CcHhhcccCccccCCCC---eECC-CCCEECHHHHHHHHHhCCCCCCCCcCCCChh
Confidence            45558899999999654   6677 99999999999999863 4699999988654

>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=98.75  E-value=2.5e-09  Score=67.17  Aligned_cols=44  Identities=30%  Similarity=0.668  Sum_probs=36.5

Q ss_pred             ccCccccccccCCCeeeecCCCCcc-ccHHhHHHHHhCCCCCCCcCccCccCC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHI-FHLHCIDQWLKHRLNCPVCRNPLCRNL  148 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~CP~CR~~l~~~~  148 (152)
                      ..|+||++.+.+   ...+| |||. ||..|+..|    ..||+||.++....
T Consensus        19 ~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~~   63 (79)
T 2yho_A           19 MLCMVCCEEEIN---STFCP-CGHTVCCESCAAQL----QSCPVCRSRVEHVQ   63 (79)
T ss_dssp             TBCTTTSSSBCC---EEEET-TCBCCBCHHHHTTC----SBCTTTCCBCCEEE
T ss_pred             CEeEEeCcccCc---EEEEC-CCCHHHHHHHHHhc----CcCCCCCchhhCeE
Confidence            579999998743   46677 9999 999999886    49999999887654

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.74  E-value=6.8e-09  Score=61.82  Aligned_cols=47  Identities=23%  Similarity=0.588  Sum_probs=36.2

Q ss_pred             CCccCccccccccCCCeeeecCCCC--c---cccHHhHHHHHhC--CCCCCCcCccCc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECN--H---IFHLHCIDQWLKH--RLNCPVCRNPLC  145 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~--H---~fh~~Ci~~wl~~--~~~CP~CR~~l~  145 (152)
                      ....|.||+++.  ++.. .+| |.  |   .||..|+.+|+..  +.+||+||+++.
T Consensus         5 ~~~~CrIC~~~~--~~~l-~~P-C~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            5 DVPVCWICNEEL--GNER-FRA-CGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             SCCEETTTTEEC--SCCC-CCS-CCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCEeEEeecCC--CCce-ecC-cCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            447899999873  2233 466 65  3   8999999999974  678999999875

>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=98.74  E-value=6.9e-09  Score=67.02  Aligned_cols=48  Identities=23%  Similarity=0.708  Sum_probs=38.2

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC--------CCCCCC--cCcc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH--------RLNCPV--CRNP  143 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~--------~~~CP~--CR~~  143 (152)
                      ...+|+||++.+..++.....+ |||.||..|+..++..        ...||.  |+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~-CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCC-CCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            3467999999987665544445 9999999999999863        247999  9987

>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=98.58  E-value=8.4e-09  Score=81.38  Aligned_cols=48  Identities=23%  Similarity=0.702  Sum_probs=39.6

Q ss_pred             CCccCccccccccCCCeeeecCCCCcc-ccHHhHHHHHhCCCCCCCcCccCccCCCC
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHI-FHLHCIDQWLKHRLNCPVCRNPLCRNLEL  150 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~CP~CR~~l~~~~~~  150 (152)
                      ....|+||++.+.+   ...+| |||. ||..|+..|    ..||+||.++.....+
T Consensus       294 ~~~~C~IC~~~~~~---~v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i~~~~~i  342 (345)
T 3t6p_A          294 EERTCKVCMDKEVS---VVFIP-CGHLVVCQECAPSL----RKCPICRGIIKGTVRT  342 (345)
T ss_dssp             TTCBCTTTSSSBCC---EEEET-TCCEEECTTTGGGC----SBCTTTCCBCCEEEEC
T ss_pred             CCCCCCccCCcCCc---eEEcC-CCChhHhHHHHhcC----CcCCCCCCCccCeEEe
Confidence            34689999999844   46677 9999 999999988    7899999998876543

>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=98.54  E-value=2.9e-08  Score=75.13  Aligned_cols=49  Identities=22%  Similarity=0.503  Sum_probs=38.9

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCC--CCCCC--cCccCcc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR--LNCPV--CRNPLCR  146 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~--~~CP~--CR~~l~~  146 (152)
                      ....|+||++.|.++   ....+|||.|++.||..|+..+  ..||+  ||..+..
T Consensus       180 ~el~CPIcl~~f~DP---Vts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~  232 (267)
T 3htk_C          180 IELTCPITCKPYEAP---LISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSM  232 (267)
T ss_dssp             CCSBCTTTSSBCSSE---EEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECG
T ss_pred             eeeECcCccCcccCC---eeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCch
Confidence            347899999999654   3332499999999999999864  47999  9997654

>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=98.50  E-value=3.4e-08  Score=58.91  Aligned_cols=49  Identities=24%  Similarity=0.284  Sum_probs=41.1

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNL  148 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~  148 (152)
                      ..|+||.+.+.++   ..++++||.|.+.||.+|+..+.+||+.+.+|..+-
T Consensus         4 ~~CpIs~~~m~dP---V~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~   52 (61)
T 2bay_A            4 MLCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEE   52 (61)
T ss_dssp             CCCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGG
T ss_pred             EEecCCCCCCCCC---EEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhh
Confidence            5699999999654   555249999999999999998888999999987654

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

Probab=98.25  E-value=1.2e-06  Score=65.72  Aligned_cols=49  Identities=27%  Similarity=0.661  Sum_probs=39.7

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhCC--CCCCCcCccCccC
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR--LNCPVCRNPLCRN  147 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~--~~CP~CR~~l~~~  147 (152)
                      -..|.||.+-...+.   ..+.|+|.||..|+.+|++++  ..||.|+.+.+..
T Consensus       180 i~~C~iC~~iv~~g~---~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          180 VKICNICHSLLIQGQ---SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             CCBCTTTCSBCSSCE---ECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSC
T ss_pred             CCcCcchhhHHhCCc---ccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCC
Confidence            378999999987663   344599999999999999875  4899999976544

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

Probab=98.14  E-value=1.7e-06  Score=55.93  Aligned_cols=46  Identities=28%  Similarity=0.561  Sum_probs=36.3

Q ss_pred             cCccccccccCCCeeeecCCCCccccHHhHHHHHh-CCCCCCCcCccCcc
Q 042258           98 DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK-HRLNCPVCRNPLCR  146 (152)
Q Consensus        98 ~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~-~~~~CP~CR~~l~~  146 (152)
                      .|++|--.+..  ..+..| |+|.||.+|+..|.. +.++||.|+.++.+
T Consensus         3 fC~~C~~Pi~i--ygRmIP-CkHvFCydCa~~~~~~~~k~Cp~C~~~V~r   49 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMIP-CKHVFCYDCAILHEKKGDKMCPGCSDPVQR   49 (101)
T ss_dssp             BCTTTCSBCSE--EEEEET-TCCEEEHHHHHHHHHTTCCBCTTTCCBCSE
T ss_pred             ecCccCCCeEE--Eeeecc-ccccHHHHHHHHHHhccCCCCcCcCCeeee
Confidence            47788666533  346777 999999999999985 47899999998754

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

Probab=96.10  E-value=0.0053  Score=36.67  Aligned_cols=46  Identities=24%  Similarity=0.550  Sum_probs=34.2

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCC----CCCCCcCccC
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR----LNCPVCRNPL  144 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~----~~CP~CR~~l  144 (152)
                      .+..|.||.+.    ..+.....|...||..|+.+.+...    =.||.|++..
T Consensus        11 ~~~~C~vC~~~----~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           11 PGARCGVCGDG----TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             TTCCCTTTSCC----TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCcCCCCCC----CeEEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            44679999743    3455566799999999999887653    3699998653

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=94.89  E-value=0.023  Score=36.25  Aligned_cols=34  Identities=15%  Similarity=0.359  Sum_probs=24.2

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHH-HH
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQ-WL  131 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~-wl  131 (152)
                      ..|.||.+.+.......-+. |+|.|+..|+.. |.
T Consensus         4 ~~C~~C~~~~~~~av~~C~~-C~~~~C~~Cl~~~h~   38 (101)
T 2jun_A            4 VLCQFCDQDPAQDAVKTCVT-CEVSYCDECLKATHP   38 (101)
T ss_dssp             CBCTTCCSSSCCBCCEEETT-TTEEECHHHHHHHSC
T ss_pred             CCCcCCCCCCCCCceEECCc-CChHHhHHHCHHHhc
Confidence            56999997643322223366 999999999998 53

>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=94.76  E-value=0.01  Score=42.59  Aligned_cols=50  Identities=16%  Similarity=0.400  Sum_probs=36.8

Q ss_pred             CccCccccccccCCC---eeeecCCCCccccHHhHHH------HHh-----CCCCCCCcCccCc
Q 042258           96 NTDCAICLDDFIEGE---TCKSFPECNHIFHLHCIDQ------WLK-----HRLNCPVCRNPLC  145 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~---~~~~l~~C~H~fh~~Ci~~------wl~-----~~~~CP~CR~~l~  145 (152)
                      +..|+||...+.+++   ..+....|...||..|+.-      -+.     ..-.||.|+..-.
T Consensus         2 G~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~~   65 (183)
T 3lqh_A            2 GNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHP   65 (183)
T ss_dssp             CCBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSSS
T ss_pred             cCcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCCC
Confidence            356999999987765   3677777999999999742      111     1568999987644

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=94.53  E-value=0.0053  Score=36.20  Aligned_cols=49  Identities=24%  Similarity=0.571  Sum_probs=35.9

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHh-----CCCCCCCcCcc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK-----HRLNCPVCRNP  143 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~-----~~~~CP~CR~~  143 (152)
                      +...|++|...+.++...+....|...||..|+.--..     ..-.||.|+.+
T Consensus         5 e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            44679999988765566666667999999999864321     34569999764

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

Probab=93.53  E-value=0.061  Score=31.33  Aligned_cols=46  Identities=20%  Similarity=0.639  Sum_probs=33.0

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC----CCCCCCcCcc
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH----RLNCPVCRNP  143 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~~~CP~CR~~  143 (152)
                      ..+..|.+|...    ..+.....|...||..|+..-+..    .=.||.|++.
T Consensus         9 ~~~~~C~vC~~~----g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            9 DHQDYCEVCQQG----GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             CCCSSCTTTSCC----SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCCccCCCC----CcEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            344679999763    345555669999999999985543    3359999764

>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=92.61  E-value=0.11  Score=30.79  Aligned_cols=34  Identities=21%  Similarity=0.533  Sum_probs=27.2

Q ss_pred             CCccCccccccccCCCeeeecC-CCCccccHHhHH
Q 042258           95 SNTDCAICLDDFIEGETCKSFP-ECNHIFHLHCID  128 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~-~C~H~fh~~Ci~  128 (152)
                      ....|.+|...+.+++..+... .|.-.||..|+.
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            3467999999987777777776 799999999974

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=92.56  E-value=0.052  Score=32.85  Aligned_cols=51  Identities=20%  Similarity=0.472  Sum_probs=36.7

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC----CCCCCCcCccCcc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH----RLNCPVCRNPLCR  146 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~~~CP~CR~~l~~  146 (152)
                      ....|.+|.... +++..+....|...||..|+..-...    .-.||.|+..+.+
T Consensus        17 ~~~~C~~C~~~~-~~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~k   71 (75)
T 2k16_A           17 QIWICPGCNKPD-DGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKK   71 (75)
T ss_dssp             EEECBTTTTBCC-SSCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHCS
T ss_pred             CCcCCCCCCCCC-CCCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchhh
Confidence            336699997764 44556666679999999999765432    3469999877654

>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=92.55  E-value=0.17  Score=30.87  Aligned_cols=47  Identities=19%  Similarity=0.464  Sum_probs=33.6

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHh-----CCCCCCCcCccC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK-----HRLNCPVCRNPL  144 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~-----~~~~CP~CR~~l  144 (152)
                      ..| ||...+..+...+....|...||..|+.---.     ....||.|+...
T Consensus        13 ~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A           13 VYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             cEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            457 89887754555666667999999999853211     356799998764

>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=91.14  E-value=0.05  Score=31.73  Aligned_cols=49  Identities=24%  Similarity=0.609  Sum_probs=33.7

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC----CCCCCCcCccCcc
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH----RLNCPVCRNPLCR  146 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~~~CP~CR~~l~~  146 (152)
                      ..+..|.+|.+.    ..+.....|...||..|+.+-+..    .=.||.|+....+
T Consensus         7 ~~~~~C~vC~~~----g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~k   59 (61)
T 1mm2_A            7 HHMEFCRVCKDG----GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPALK   59 (61)
T ss_dssp             SSCSSCTTTCCC----SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTCCT
T ss_pred             CCCCcCCCCCCC----CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCchhc
Confidence            344679999752    344455569999999999865443    2359999876543

>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=90.94  E-value=0.071  Score=29.97  Aligned_cols=44  Identities=16%  Similarity=0.328  Sum_probs=31.5

Q ss_pred             cCccccccccCCCeeeecC-CCCccccHHhHHHHH----hCCCCCCCcC
Q 042258           98 DCAICLDDFIEGETCKSFP-ECNHIFHLHCIDQWL----KHRLNCPVCR  141 (152)
Q Consensus        98 ~C~IC~~~~~~~~~~~~l~-~C~H~fh~~Ci~~wl----~~~~~CP~CR  141 (152)
                      .|.+|...+.+++..+... .|...||..|+.--.    .....||.|+
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            4788988886666666666 699999999975321    2567799885

>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=90.75  E-value=0.085  Score=37.44  Aligned_cols=46  Identities=26%  Similarity=0.602  Sum_probs=33.4

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC----CCCCCCcCccC
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH----RLNCPVCRNPL  144 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~~~CP~CR~~l  144 (152)
                      .+..|.+|...    ..+.....|...||..|+.+-+..    .-.||.|+..-
T Consensus         3 ~~~~C~~C~~~----g~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            3 NEDWCAVCQNG----GELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             SCSSCTTTCCC----SSCEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCccccCCCC----CeeeecCCCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            44679999743    335566679999999998876654    23599998754

>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=90.47  E-value=0.11  Score=37.64  Aligned_cols=47  Identities=26%  Similarity=0.521  Sum_probs=34.6

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC----CCCCCCcCccCc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH----RLNCPVCRNPLC  145 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~~~CP~CR~~l~  145 (152)
                      .+..|.+|...    ..+.....|...||..|+.+-+..    .-.||.|+..-.
T Consensus         6 ~~~~C~~C~~~----g~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~~   56 (207)
T 3u5n_A            6 NEDWCAVCQNG----GDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGK   56 (207)
T ss_dssp             SCSSBTTTCCC----EEEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSSS
T ss_pred             CCCCCCCCCCC----CceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCccc
Confidence            44679999743    456667779999999999876654    235999987543

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=90.45  E-value=0.18  Score=28.00  Aligned_cols=44  Identities=30%  Similarity=0.696  Sum_probs=30.1

Q ss_pred             cCccccccccCCCeeeecCCCCccccHHhHHHHHhC----CCCCCCcCc
Q 042258           98 DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH----RLNCPVCRN  142 (152)
Q Consensus        98 ~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~~~CP~CR~  142 (152)
                      .|.+|...-. ++.+.....|...||..|+.+=+..    .=.||.|+.
T Consensus         2 ~C~vC~~~~~-~~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGE-DDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSC-CSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCC-CCCEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            4888876532 3345556669999999999764443    234999975

>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=90.11  E-value=1  Score=27.95  Aligned_cols=36  Identities=17%  Similarity=0.525  Sum_probs=23.3

Q ss_pred             CCCCccCccccccccCCCeeeecCCCCccccHHhHHHH
Q 042258           93 MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQW  130 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~w  130 (152)
                      ...+..|.||-. +..++.. -.-.|+-+||..|+.+-
T Consensus        12 ~~~D~~C~VC~~-~t~~~l~-pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           12 VVNDEMCDVCEV-WTAESLF-PCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCSCCCTTTCC-CCSSCCS-SCSSSSSCCCHHHHHHH
T ss_pred             CCCCcccCcccc-cccccee-ccccccccccHhhcccc
Confidence            345678999952 3232221 12238999999999996

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=89.19  E-value=0.15  Score=32.00  Aligned_cols=52  Identities=21%  Similarity=0.392  Sum_probs=35.0

Q ss_pred             CCccCccccccc-cCCCeeeecCCCCccccHHhHHHHHh--CCCCCCCcCccCcc
Q 042258           95 SNTDCAICLDDF-IEGETCKSFPECNHIFHLHCIDQWLK--HRLNCPVCRNPLCR  146 (152)
Q Consensus        95 ~~~~C~IC~~~~-~~~~~~~~l~~C~H~fh~~Ci~~wl~--~~~~CP~CR~~l~~  146 (152)
                      .+..|.||...- .+...+.....|.-.||..|+..-+.  ..=.||.|......
T Consensus        24 ~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~~~   78 (88)
T 2l43_A           24 EDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRAR   78 (88)
T ss_dssp             CCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHTTS
T ss_pred             CCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCccch
Confidence            447899998653 23345666667999999999986332  13359999765443

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=88.34  E-value=0.13  Score=33.66  Aligned_cols=46  Identities=26%  Similarity=0.588  Sum_probs=31.7

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhC----CCCCCCcCc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH----RLNCPVCRN  142 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~~~CP~CR~  142 (152)
                      ..|.+|...-.+++.+.....|...||..|+.+-|..    .=.||.|+.
T Consensus        62 ~~C~vC~~~~~~~~~ll~Cd~C~~~yH~~Cl~p~l~~~P~~~W~C~~C~~  111 (112)
T 3v43_A           62 KTCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRP  111 (112)
T ss_dssp             CCBTTTCCCCCTTCCCEECTTTCCEECGGGCSSCCSSCCSSCCCCTTTSC
T ss_pred             CccccccCcCCCccceEEcCCCCCeeecccCCCCCCCCCCCCeECCCCCC
Confidence            3688887643333455556669999999998765543    235999975

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=88.17  E-value=0.35  Score=30.35  Aligned_cols=48  Identities=25%  Similarity=0.496  Sum_probs=33.9

Q ss_pred             CCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC----CCCCCCcCccCc
Q 042258           94 TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH----RLNCPVCRNPLC  145 (152)
Q Consensus        94 ~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~~~CP~CR~~l~  145 (152)
                      ..+..|.+|...    ..+.....|.-.||..|+.+=+..    .=.||.|+....
T Consensus        23 ~n~~~C~vC~~~----g~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~~   74 (88)
T 1fp0_A           23 DSATICRVCQKP----GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   74 (88)
T ss_dssp             SSSSCCSSSCSS----SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             CCCCcCcCcCCC----CCEEECCCCCCceecccCCCCCCCCcCCCcCCccccCCCc
Confidence            344679999864    344556669999999999876544    235999986543

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=88.14  E-value=0.029  Score=32.57  Aligned_cols=49  Identities=24%  Similarity=0.672  Sum_probs=33.6

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC----CCCCCCcCccCccC
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH----RLNCPVCRNPLCRN  147 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~~~CP~CR~~l~~~  147 (152)
                      .+..|.+|...    ..+.....|...||..|+.+=+..    .-.||.|+.....+
T Consensus         4 ~~~~C~vC~~~----g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~~~   56 (60)
T 2puy_A            4 HEDFCSVCRKS----GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQMLKK   56 (60)
T ss_dssp             CCSSCTTTCCC----SSCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHHHT
T ss_pred             CCCCCcCCCCC----CcEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccChhhch
Confidence            34679999764    344555569999999999865443    23499997765443

>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=87.27  E-value=1.9  Score=27.02  Aligned_cols=51  Identities=24%  Similarity=0.434  Sum_probs=36.2

Q ss_pred             CCccCccccccccC---CCeeeecCCCCccccHHhHHHHHh-CCCCCCCcCccCc
Q 042258           95 SNTDCAICLDDFIE---GETCKSFPECNHIFHLHCIDQWLK-HRLNCPVCRNPLC  145 (152)
Q Consensus        95 ~~~~C~IC~~~~~~---~~~~~~l~~C~H~fh~~Ci~~wl~-~~~~CP~CR~~l~  145 (152)
                      ....|.||-+..-.   ++.......|+--.|+.|..-=.+ .+..||.|++...
T Consensus        15 ~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCktrYk   69 (93)
T 1weo_A           15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYK   69 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCC
T ss_pred             CCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhccCccccccCCccc
Confidence            34689999988632   333333344788899999875444 4889999999875

>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=86.43  E-value=0.3  Score=31.55  Aligned_cols=48  Identities=17%  Similarity=0.425  Sum_probs=33.8

Q ss_pred             ccCccccccccCCCeeeecC-CCCccccHHhHHHHH----------hCCCCCCCcCccC
Q 042258           97 TDCAICLDDFIEGETCKSFP-ECNHIFHLHCIDQWL----------KHRLNCPVCRNPL  144 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~-~C~H~fh~~Ci~~wl----------~~~~~CP~CR~~l  144 (152)
                      ..|.+|...+.+....+... .|...||..|+.---          ...-.||.|+..-
T Consensus         4 ~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~   62 (105)
T 2xb1_A            4 YPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTK   62 (105)
T ss_dssp             CBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTT
T ss_pred             CCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcC
Confidence            56999999986655555554 699999999975221          0245699998653

>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=86.37  E-value=1.4  Score=27.73  Aligned_cols=44  Identities=27%  Similarity=0.656  Sum_probs=28.9

Q ss_pred             ccCccccccccCCCeeeecCC--CC-ccccHHhHHHHHhC----CCCCCCcCccCc
Q 042258           97 TDCAICLDDFIEGETCKSFPE--CN-HIFHLHCIDQWLKH----RLNCPVCRNPLC  145 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~--C~-H~fh~~Ci~~wl~~----~~~CP~CR~~l~  145 (152)
                      ..| ||.... .+ ..+....  |. ..||..|+.  |..    .-.||.|+....
T Consensus        37 ~yC-iC~~~~-~g-~MI~CD~~dC~~~WfH~~CVg--l~~~p~g~W~Cp~C~~~~~   87 (91)
T 1weu_A           37 TYC-LCHQVS-YG-EMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESG   87 (91)
T ss_dssp             BCS-TTCCBC-CS-CCCCCSCSSCSCCCCCSTTTT--CSSCCCSSCCCTTTCCCCS
T ss_pred             cEE-ECCCCC-CC-CEeEecCCCCCCCCEecccCC--cCcCCCCCEECcCccCcCC
Confidence            557 997754 33 3444555  55 689999987  332    446999987644

>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=85.75  E-value=0.76  Score=40.62  Aligned_cols=51  Identities=14%  Similarity=0.072  Sum_probs=42.5

Q ss_pred             CCCCccCccccccccCCCeeeecCCCC-ccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           93 MTSNTDCAICLDDFIEGETCKSFPECN-HIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~~~~~~l~~C~-H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      .+....|||-.+-+.++   ..+| -| +.|-+.+|.+|+.++.+||.=|.+|...
T Consensus       888 iP~~F~cPIs~~lM~DP---Vilp-sG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~  939 (968)
T 3m62_A          888 VPDEFLDPLMYTIMKDP---VILP-ASKMNIDRSTIKAHLLSDSTDPFNRMPLKLE  939 (968)
T ss_dssp             SCGGGBCTTTCSBCSSE---EECT-TTCCEEEHHHHHHHHTTCCBCTTTCCBCCGG
T ss_pred             CcHHhCCcchhhHHhCC---eEcC-CCCEEECHHHHHHHHhcCCCCCCCCCCCCcc
Confidence            45557899999988654   6677 66 6899999999999999999999988754

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=85.65  E-value=0.079  Score=30.23  Aligned_cols=44  Identities=27%  Similarity=0.714  Sum_probs=30.1

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC----CCCCCCcCc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH----RLNCPVCRN  142 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~~~CP~CR~  142 (152)
                      .+..|.+|...    ..+.....|...||..|+.+-+..    .-.||.|++
T Consensus         8 ~~~~C~vC~~~----g~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            8 HEDFCSVCRKS----GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SCCSCSSSCCS----SCCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCccCCCC----CeEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            44679999864    344555569999999999865443    224887754

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=85.26  E-value=0.083  Score=31.22  Aligned_cols=45  Identities=27%  Similarity=0.688  Sum_probs=31.6

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC----CCCCCCcCcc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH----RLNCPVCRNP  143 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~~~CP~CR~~  143 (152)
                      .+..|.+|...    ..+.....|...||..|+.+-+..    .=.||.|...
T Consensus         7 ~~~~C~vC~~~----g~ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~   55 (66)
T 1xwh_A            7 NEDECAVCRDG----GELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQA   55 (66)
T ss_dssp             CCCSBSSSSCC----SSCEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHT
T ss_pred             CCCCCccCCCC----CCEEEcCCCChhhcccccCCCcCcCCCCCeECccccCc
Confidence            44679999853    344555669999999999864443    2349998764

>1z60_A TFIIH basal transcription factor complex P44 subunit; basic transcription factor, zinc binding protein, ring finger; NMR {Homo sapiens} SCOP: g.49.1.2

Probab=84.66  E-value=0.83  Score=26.40  Aligned_cols=43  Identities=19%  Similarity=0.428  Sum_probs=31.0

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVC  140 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~C  140 (152)
                      ..|-.|...+.+. ..-..++|++.|+.+|=.---..=..||.|
T Consensus        16 ~~C~~C~~~~~~~-~~y~C~~C~~~FC~dCD~fiHe~Lh~CPgC   58 (59)
T 1z60_A           16 RFCYGCQGELKDQ-HVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             CEETTTTEECTTS-EEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CcccccCcccCCC-ccEECCccCcCcccchhHHHHhhccCCcCC
Confidence            4599999988543 334577899999999955533345679988

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=84.53  E-value=2.2  Score=27.56  Aligned_cols=34  Identities=24%  Similarity=0.452  Sum_probs=24.1

Q ss_pred             CCccCccccccc-----cCCCeeeecCCCCccccHHhHH
Q 042258           95 SNTDCAICLDDF-----IEGETCKSFPECNHIFHLHCID  128 (152)
Q Consensus        95 ~~~~C~IC~~~~-----~~~~~~~~l~~C~H~fh~~Ci~  128 (152)
                      ....|.+|+..-     ..++.++.-..|+..||..|+.
T Consensus         4 p~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~   42 (112)
T 3v43_A            4 PIPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLK   42 (112)
T ss_dssp             CCSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHT
T ss_pred             cCccccccCCchhhCcCCCchhceEhhhcCCCCCCchhc
Confidence            345799998652     1234566666799999999995

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

Probab=83.88  E-value=2  Score=29.27  Aligned_cols=45  Identities=20%  Similarity=0.497  Sum_probs=33.0

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHh-----------CCCCCCCcCcc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK-----------HRLNCPVCRNP  143 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~-----------~~~~CP~CR~~  143 (152)
                      .+..|.+|.+.    ..+.....|-..||..|+.+=+.           ..=.||+|+.+
T Consensus        62 ~~d~C~vC~~G----G~LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~~  117 (142)
T 2lbm_A           62 MDEQCRWCAEG----GNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPE  117 (142)
T ss_dssp             CBCSCSSSCCC----SSEEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCCC
T ss_pred             CCCeecccCCC----CcEEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccCc
Confidence            44779999754    45556667999999999997653           13369999864

>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=83.66  E-value=0.54  Score=28.56  Aligned_cols=47  Identities=19%  Similarity=0.436  Sum_probs=31.5

Q ss_pred             ccCccccccccCCCeeeecC--CCCccccHHhHHHHHh---------CCCCCCCcCccCc
Q 042258           97 TDCAICLDDFIEGETCKSFP--ECNHIFHLHCIDQWLK---------HRLNCPVCRNPLC  145 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~--~C~H~fh~~Ci~~wl~---------~~~~CP~CR~~l~  145 (152)
                      ..| ||-.....+ ..+...  .|...||..|+.---.         ....||.|+..-.
T Consensus        17 ~~C-iC~~~~~~g-~MI~CD~~~C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~~~   74 (78)
T 1wew_A           17 VRC-VCGNSLETD-SMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSG   74 (78)
T ss_dssp             CCC-SSCCCCCCS-CEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCCS
T ss_pred             EEe-ECCCcCCCC-CEEEECCccCCccccCEEEccccccccccccCCCCEECCCCCcccC
Confidence            568 798774443 455555  6999999999864211         2556999976543

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=82.55  E-value=0.61  Score=29.65  Aligned_cols=45  Identities=22%  Similarity=0.428  Sum_probs=31.1

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhC---CCCCCCcCcc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH---RLNCPVCRNP  143 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---~~~CP~CR~~  143 (152)
                      ..| ||-..... ..++....|.-.||..|+..=+..   .-.||.|+..
T Consensus        29 vrC-iC~~~~~~-~~mi~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~~   76 (98)
T 2lv9_A           29 TRC-ICGFTHDD-GYMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQPR   76 (98)
T ss_dssp             CCC-TTSCCSCS-SCEEEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSSS
T ss_pred             EEe-ECCCccCC-CcEEEcCCCCCcCcCcCCCCCccCCCCCEECCCCcCC
Confidence            457 78766544 345666679999999998763322   3469999753

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=82.28  E-value=0.28  Score=35.07  Aligned_cols=43  Identities=26%  Similarity=0.581  Sum_probs=30.2

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhC----CCCCCCcCcc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH----RLNCPVCRNP  143 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~~~CP~CR~~  143 (152)
                      ..|.+|.+.    ..+.....|...||..|+.+=+..    .-.||.|+..
T Consensus         3 ~~C~~C~~~----g~ll~Cd~C~~~~H~~Cl~p~l~~~p~g~W~C~~C~~~   49 (189)
T 2ro1_A            3 TICRVCQKP----GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   49 (189)
T ss_dssp             CCBTTTCCC----SSCCCCTTTCCBCCSTTSTTCCSSCCCTTCCTTTTSCS
T ss_pred             CcCccCCCC----CceeECCCCCchhccccCCCCcccCCCCCCCCcCccCC
Confidence            569999754    234445568999999999764443    2359999865

>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=81.95  E-value=0.22  Score=29.59  Aligned_cols=46  Identities=26%  Similarity=0.650  Sum_probs=31.1

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHh---CCCCCCCcCc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK---HRLNCPVCRN  142 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~---~~~~CP~CR~  142 (152)
                      ....| ||..... ++..+....|...||..|+.---.   ..-.||.|+.
T Consensus        18 ~~~~C-iC~~~~~-~~~MIqCd~C~~WfH~~Cvgi~~~~~~~~~~C~~C~~   66 (68)
T 3o70_A           18 GLVTC-FCMKPFA-GRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRD   66 (68)
T ss_dssp             TCCCS-TTCCCCT-TCCEEECTTTCCEEETTTTTCCTTSCCSSCCCHHHHT
T ss_pred             CceEe-ECCCcCC-CCCEEECCCCCccccccccCcCcccCCCcEECCCCCC
Confidence            33568 9987654 555666667999999999864221   2456888864

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=81.13  E-value=0.25  Score=30.18  Aligned_cols=44  Identities=32%  Similarity=0.722  Sum_probs=29.2

Q ss_pred             cCccccccccCCCeeeecCCCCccccHHhHHHHHhC----C-CCCCCcCc
Q 042258           98 DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH----R-LNCPVCRN  142 (152)
Q Consensus        98 ~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~-~~CP~CR~  142 (152)
                      .|.+|...- +++.+.....|...||..|+.+-|..    . =.||.|++
T Consensus        28 ~C~vC~~~~-d~~~ll~CD~C~~~yH~~Cl~PpL~~~P~g~~W~C~~C~~   76 (77)
T 3shb_A           28 ACHLCGGRQ-DPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   76 (77)
T ss_dssp             SBTTTCCCS-CGGGEEECTTTCCEEETTTSSSCCSSCCSSSCCCCTTTC-
T ss_pred             cCCccCCCC-CCcceeEeCCCCCccCcccCCCcccCCCCCCceECcCccc
Confidence            466665543 33445556669999999999876553    2 36999975

>3asl_A E3 ubiquitin-protein ligase UHRF1; histone reader module, epigenetic regulation, LI binding protein complex; 1.41A {Homo sapiens} PDB: 3sou_A 3sow_A* 3sox_A 3zvy_A 2lgg_A 2lgk_A* 2lgl_A 3t6r_A 3zvz_B

Probab=80.60  E-value=0.38  Score=28.71  Aligned_cols=45  Identities=31%  Similarity=0.706  Sum_probs=29.7

Q ss_pred             cCccccccccCCCeeeecCCCCccccHHhHHHHHhC-----CCCCCCcCcc
Q 042258           98 DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-----RLNCPVCRNP  143 (152)
Q Consensus        98 ~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-----~~~CP~CR~~  143 (152)
                      .|.+|...- ++..+.....|...||..|+.+=|..     .=.||.|+.+
T Consensus        20 ~C~~C~~~~-~~~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~~   69 (70)
T 3asl_A           20 ACHLCGGRQ-DPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND   69 (70)
T ss_dssp             SBTTTCCCS-CGGGEEECTTTCCEEEGGGSSSCCSSCCSSSCCCCTTTSCC
T ss_pred             CCcCCCCcC-CCCCEEEcCCCCCceecccCCCCcCCCCCCCCcCCcCccCc
Confidence            466776542 23455556679999999999865443     2359999753

---

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	152
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	9e-17
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	2e-12
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	2e-09
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	5e-09
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	6e-09
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	8e-09
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	2e-08
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	4e-07
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	5e-07
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	2e-06
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	2e-06
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	2e-05
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	7e-05
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	5e-04

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 67.6 bits (165), Expect = 9e-17
 Identities = 20/52 (38%), Positives = 28/52 (53%)

Query: 93  MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           M    +CA+CL +  +GE  +  P C H FH  C+D WL     CP+CR  +
Sbjct: 2   MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 56.9 bits (137), Expect = 2e-12
 Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 3/51 (5%)

Query: 94  TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           T    C ICL+D            C H F   CI +W++    CP+C+ P+
Sbjct: 3   TVAERCPICLEDPSNYSMA---LPCLHAFCYVCITRWIRQNPTCPLCKVPV 50

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 2e-09
 Identities = 18/60 (30%), Positives = 25/60 (41%), Gaps = 14/60 (23%)

Query: 98  DCAICLDDFIEGETCKSFPE--------------CNHIFHLHCIDQWLKHRLNCPVCRNP 143
           +CAIC +  ++        +              CNH FH HCI +WLK R  CP+    
Sbjct: 23  NCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 82

>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 = 48.9 bits (115), Expect = 5e-09
 Identities = 14/83 (16%), Positives = 29/83 (34%)

Query: 64  GDSEETQGLCPQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFH 123
           G+ E+      +EL V+  +      E    ++    +     +         +C+H FH
Sbjct: 7   GEPEQVIRKYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFH 66

Query: 124 LHCIDQWLKHRLNCPVCRNPLCR 146
           L C+     +       + P C+
Sbjct: 67  LLCLLAMYCNGNKDGSLQCPSCK 89

>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 = 47.9 bits (113), Expect = 6e-09
 Identities = 12/52 (23%), Positives = 16/52 (30%), Gaps = 2/52 (3%)

Query: 98  DCAICLDDFIEGETCKSFP-ECNHIFHLHCIDQWLKHRLN-CPVCRNPLCRN 147
            C  C        + K     C H     C+D         CP C  PL ++
Sbjct: 5   GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS 56

>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 = 47.7 bits (113), Expect = 8e-09
 Identities = 16/80 (20%), Positives = 31/80 (38%), Gaps = 6/80 (7%)

Query: 74  PQELPVSLPQMSYKNGETEMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH 133
           PQ+  + + Q  Y+      ++   C IC ++  + +       C H+    C+  W + 
Sbjct: 2   PQDH-IKVTQEQYELYCEMGSTFQLCKICAENDKDVKIEP----CGHLMCTSCLTSWQES 56

Query: 134 RLN-CPVCRNPLCRNLELDV 152
               CP CR  +     + V
Sbjct: 57  EGQGCPFCRCEIKGTEPIVV 76

>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 = 45.5 bits (107), Expect = 2e-08
 Identities = 9/48 (18%), Positives = 16/48 (33%), Gaps = 1/48 (2%)

Query: 98  DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR-LNCPVCRNPL 144
           +C +C++     +       C +     C  +        CP CR P 
Sbjct: 2   ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPY 49

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

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.6 bits (100), Expect = 4e-07
 Identities = 9/46 (19%), Positives = 16/46 (34%), Gaps = 7/46 (15%)

Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           C  C  +    +       C H     C++      + CP+C+ P 
Sbjct: 9   CQQCQAEAKCPKLLP----CLHTLCSGCLEAS---GMQCPICQAPW 47

>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 = 43.5 bits (102), Expect = 5e-07
 Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 7/59 (11%)

Query: 92  EMTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLN---CPVCRNPLCRN 147
            M    +C ICL+   E  + K    C+HIF   C+ + L  +     CP+C+N + + 
Sbjct: 17  AMQKILECPICLELIKEPVSTK----CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR 71

>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 = 41.0 bits (95), Expect = 2e-06
 Identities = 9/48 (18%), Positives = 13/48 (27%), Gaps = 3/48 (6%)

Query: 99  CAICLDDFIEG-ETCKSFPECNHIFHLHCIDQWLKHR--LNCPVCRNP 143
           C IC ++                  H  C+  WL       C +C   
Sbjct: 9   CWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVV 56

>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 = 41.4 bits (97), Expect = 2e-06
 Identities = 15/50 (30%), Positives = 18/50 (36%), Gaps = 5/50 (10%)

Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK-HRLNCPVCRNPLCRN 147
           C IC     +         C H+F   CI + LK     CP CR P    
Sbjct: 26  CQICEHILADPVETS----CKHLFCRICILRCLKVMGSYCPSCRYPCFPT 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 = 38.9 bits (90), Expect = 2e-05
 Identities = 13/66 (19%), Positives = 30/66 (45%), Gaps = 9/66 (13%)

Query: 94  TSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK--------HRLNCPVCRNPLC 145
           + ++ C +CL ++   E   +  +C  IF   C+ Q+++          ++CP    P  
Sbjct: 3   SGSSGCKLCLGEY-PVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ 61

Query: 146 RNLELD 151
            +L+ +
Sbjct: 62  GHLQEN 67

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.5 bits (86), Expect = 7e-05
 Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 5/46 (10%)

Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           C+ C +   E         C HIF  +C+   +     CPVC  P 
Sbjct: 25  CSRCTNILREPVCL---GGCEHIFCSNCVSDCIGTG--CPVCYTPA 65

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 34.3 bits (78), Expect = 5e-04
 Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 3/46 (6%)

Query: 99  CAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPL 144
           CAI              P+   IF    ++Q++K   N P+   PL
Sbjct: 3   CAISGKVPRRPVLS---PKSRTIFEKSLLEQYVKDTGNDPITNEPL 45

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	152
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.77
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.59
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.57
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.54
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.53
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.5
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.47
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.41
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.31
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.29
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.27
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.18
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.14
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.13
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.11
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.95
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.68
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	95.48
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	93.03
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	92.57
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	92.57
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	91.81
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	91.72
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	90.8
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	88.62
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	83.32
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	81.92
d2o35a1	79	Hypothetical protein SMc04008 {Rhizobium meliloti	80.63

>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=99.77  E-value=9.8e-20  Score=106.22  Aligned_cols=51  Identities=37%  Similarity=1.024  Sum_probs=46.5

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLC  145 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~  145 (152)
                      ++.+|+||+++|..++.+..++.|+|.||..|+.+|++++.+||+||+++.
T Consensus         4 d~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            446799999999998888888779999999999999999999999999874

>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=99.59  E-value=3.5e-16  Score=94.74  Aligned_cols=49  Identities=33%  Similarity=0.888  Sum_probs=41.7

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCcc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCR  146 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~  146 (152)
                      ..++|+||++.+.+.  ...++ |||.||..|+.+|++.+.+||+||+++..
T Consensus         4 ~~d~C~IC~~~~~~~--~~~~~-C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~   52 (68)
T d1chca_           4 VAERCPICLEDPSNY--SMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCSC--EEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCccCCcCccCC--cEEeC-CCCcCcHHHHHHHHHhCCcCCCCCcchHh
Confidence            457799999998543  44566 99999999999999999999999998753

>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=99.57  E-value=4e-16  Score=89.61  Aligned_cols=48  Identities=19%  Similarity=0.517  Sum_probs=39.8

Q ss_pred             cCccccccccCCCeee-ecCCCCccccHHhHHHHHhC-CCCCCCcCccCcc
Q 042258           98 DCAICLDDFIEGETCK-SFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCR  146 (152)
Q Consensus        98 ~C~IC~~~~~~~~~~~-~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~  146 (152)
                      +|+||+++|..++... .++ |||.||..|+.+|+.+ +.+||+||+++.+
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            6999999997665433 445 9999999999999986 4579999999865

>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=99.54  E-value=2.6e-15  Score=93.41  Aligned_cols=50  Identities=26%  Similarity=0.700  Sum_probs=42.1

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-CCCCCCcCccCccCCCC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCRNLEL  150 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~~~~~  150 (152)
                      ..|+||++.+.+   .+.++ |||.||..||..|+.. +..||+||.++...-.|
T Consensus        24 ~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~i   74 (79)
T d1fbva4          24 QLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPI   74 (79)
T ss_dssp             TBCTTTSSSBCC---EECSS-SCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCCS
T ss_pred             CCCccCCCcCCC---eEEeC-CCCeeeHHHHHHHHHHCcCcCCCCCcCccCCcee
Confidence            569999998844   46777 9999999999999985 57899999999876554

>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=99.53  E-value=3.8e-15  Score=94.46  Aligned_cols=50  Identities=38%  Similarity=0.763  Sum_probs=40.4

Q ss_pred             CCccCccccccccCCC---------------eeeecCCCCccccHHhHHHHHhCCCCCCCcCccCc
Q 042258           95 SNTDCAICLDDFIEGE---------------TCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLC  145 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~---------------~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~  145 (152)
                      .+..|+||++.+.+..               .+..++ |||.||..||.+||+.+.+||+||++..
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~   84 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWE   84 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCccc
Confidence            3466999998885432               234556 9999999999999999999999999864

>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=99.50  E-value=8.1e-15  Score=87.81  Aligned_cols=51  Identities=24%  Similarity=0.539  Sum_probs=39.7

Q ss_pred             CccCccccccccCC-C-eeeecCCCCccccHHhHHHHHhC-CCCCCCcCccCccC
Q 042258           96 NTDCAICLDDFIEG-E-TCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCRN  147 (152)
Q Consensus        96 ~~~C~IC~~~~~~~-~-~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~~  147 (152)
                      +..|+||++.+..+ + ....++ |||.||..||.+|+.+ +.+||+||+++..+
T Consensus         3 d~~CpIC~~~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_           3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCCCcCCceeecCCceEEEeCc-cChHhhHHHHHHHhCcCcCCCCCCCcCcccc
Confidence            46799999986433 2 234455 9999999999999965 56899999998654

>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=99.47  E-value=1.9e-14  Score=95.15  Aligned_cols=53  Identities=26%  Similarity=0.658  Sum_probs=40.7

Q ss_pred             CCccCccccccccCC---------------CeeeecCCCCccccHHhHHHHHhC-----CCCCCCcCccCccCC
Q 042258           95 SNTDCAICLDDFIEG---------------ETCKSFPECNHIFHLHCIDQWLKH-----RLNCPVCRNPLCRNL  148 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~---------------~~~~~l~~C~H~fh~~Ci~~wl~~-----~~~CP~CR~~l~~~~  148 (152)
                      .+..|+||++.+...               ..+..++ |+|.||..||..|+..     +.+||+||+.+..+.
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~   96 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKT   96 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCS
T ss_pred             ccccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhcCcCCCCccccccchhccCc
Confidence            346799999998542               1234455 9999999999999974     347999999886654

>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=2.4e-14  Score=83.23  Aligned_cols=48  Identities=25%  Similarity=0.294  Sum_probs=41.4

Q ss_pred             cCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCC
Q 042258           98 DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNL  148 (152)
Q Consensus        98 ~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~  148 (152)
                      .|+||++.+.++   ..+++|||.||.+||.+|+..+++||+||+++..+-
T Consensus         2 ~C~Ic~~~~~~P---v~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~d   49 (56)
T d2baya1           2 LCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEE   49 (56)
T ss_dssp             CCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGG
T ss_pred             CCccCCchHHhc---CccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHh
Confidence            599999998543   556569999999999999999999999999987654

>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=99.31  E-value=6.8e-13  Score=83.36  Aligned_cols=46  Identities=33%  Similarity=0.655  Sum_probs=39.1

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-CCCCCCcCccCcc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCR  146 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~  146 (152)
                      ..|+||++.+.+   ...++ |||.||..||.+|++. +..||.||.++..
T Consensus        24 l~C~IC~~~~~~---pv~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~   70 (86)
T d1rmda2          24 ISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFP   70 (86)
T ss_dssp             TBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             cCCccCCcchhc---ceecC-CCChhhHHHHHHHHhhCCCcCcccCCCCCh
Confidence            579999999854   46677 9999999999999974 5689999998764

>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=7.6e-13  Score=85.90  Aligned_cols=46  Identities=35%  Similarity=0.858  Sum_probs=38.9

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCC---CCCCCcCccCcc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR---LNCPVCRNPLCR  146 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~---~~CP~CR~~l~~  146 (152)
                      ..|+||++.+.++   ..++ |||.||..||..|+..+   ..||+||.++..
T Consensus        22 l~CpIC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (103)
T d1jm7a_          22 LECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (103)
T ss_dssp             TSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             cCCCccCchhCCe---EEcC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcCCh
Confidence            5699999999654   5567 99999999999999764   479999998864

>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=99.27  E-value=4.6e-13  Score=77.60  Aligned_cols=46  Identities=24%  Similarity=0.633  Sum_probs=38.5

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccCCC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRNLE  149 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~~~  149 (152)
                      .+|+||++.+.++   +.++ |||.||..|+.+|   +.+||+||+++..+..
T Consensus         7 l~C~IC~~~~~~p---~~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~~   52 (56)
T d1bora_           7 LRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGAD   52 (56)
T ss_dssp             SSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCSS
T ss_pred             CCCcccCcccCCC---EEec-CCCHHhHHHHHcC---CCcCcCCCCcccCCCC
Confidence            6899999999664   5677 9999999999865   6789999999876543

>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=99.18  E-value=1e-11  Score=72.73  Aligned_cols=51  Identities=18%  Similarity=0.379  Sum_probs=37.1

Q ss_pred             CCccCccccccccCCCee-eecCCCCccccHHhHHHHHh--CCCCCCCcCccCc
Q 042258           95 SNTDCAICLDDFIEGETC-KSFPECNHIFHLHCIDQWLK--HRLNCPVCRNPLC  145 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~-~~l~~C~H~fh~~Ci~~wl~--~~~~CP~CR~~l~  145 (152)
                      +...|.||++.+.+.... ....+|+|.||..|+.+|+.  ++.+||+||+++.
T Consensus         5 d~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           5 DVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             SCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            446799999987553211 11122569999999999995  4668999999864

>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=99.14  E-value=1.6e-11  Score=76.00  Aligned_cols=51  Identities=20%  Similarity=0.234  Sum_probs=42.5

Q ss_pred             CCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-CCCCCCcCccCccC
Q 042258           93 MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCRN  147 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~~  147 (152)
                      .+....|+||++-|.++   ..++ |||.|+..||.+|+.. +..||.||.++...
T Consensus         4 iP~~l~CpIc~~l~~dP---v~~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~   55 (80)
T d2c2la2           4 IPDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQE   55 (80)
T ss_dssp             CCSTTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCGG
T ss_pred             CCccccCcCcCchhhhh---cccC-CcCeecHHHHHHHHhcCCccCCCcccccccc
Confidence            45668899999999664   5677 9999999999999974 66899999988643

>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=99.13  E-value=4.7e-12  Score=81.17  Aligned_cols=45  Identities=29%  Similarity=0.707  Sum_probs=36.8

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCcc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCR  146 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~  146 (152)
                      ..|+||++.|.++   ..++.|||.||..||.+|+.  ..||.||.++..
T Consensus        23 l~C~IC~~~~~~p---v~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~   67 (97)
T d1jm7b_          23 LRCSRCTNILREP---VCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWI   67 (97)
T ss_dssp             TSCSSSCSCCSSC---BCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSC
T ss_pred             CCCccCCchhhcC---ceeCCCCCchhHHHHHHHHh--ccccccCCcCch
Confidence            5799999999665   44434999999999999985  459999987754

>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=99.11  E-value=3.4e-11  Score=74.05  Aligned_cols=51  Identities=18%  Similarity=0.419  Sum_probs=42.6

Q ss_pred             CCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC-CCCCCCcCccCccC
Q 042258           93 MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH-RLNCPVCRNPLCRN  147 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-~~~CP~CR~~l~~~  147 (152)
                      .+....|+||++.|.++   ..++ |||.|++.||.+|+.. ...||.|+.++...
T Consensus         5 iP~~l~CpIc~~~m~dP---V~~~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~   56 (78)
T d1t1ha_           5 FPEYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             CSSSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             CCccCCCcCcCchhhCc---eEcc-CCCcchHHHHHHHHHHCCCCCCcccccCCcc
Confidence            45668899999999654   5677 9999999999999986 46799999988653

>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=4.9e-10  Score=71.72  Aligned_cols=52  Identities=15%  Similarity=0.110  Sum_probs=43.4

Q ss_pred             CCCCccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCcCccCccC
Q 042258           93 MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVCRNPLCRN  147 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~CR~~l~~~  147 (152)
                      .+....|+||.+-|.++   .+++.|||.|++.||.+|+..+..||+||.++...
T Consensus        19 ~P~~f~CPI~~~lm~dP---V~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~   70 (98)
T d1wgma_          19 ACDEFLDPIMSTLMCDP---VVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMD   70 (98)
T ss_dssp             CCTTTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTT
T ss_pred             CcHHhCCcCchhHHHHH---HhcccccchhhHHHHHHHHHhcCCcccccccccch
Confidence            45568899999999665   67773456899999999999999999999998753

>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=98.68  E-value=4.3e-09  Score=66.45  Aligned_cols=47  Identities=21%  Similarity=0.630  Sum_probs=36.1

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHhC--------CCCCCCcCc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH--------RLNCPVCRN  142 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~--------~~~CP~CR~  142 (152)
                      +..+|+||++++...+....++ |+|.||..|+..|+..        .-.||.|+-
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            4478999999987655555555 9999999999999963        125998653

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

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.48  E-value=0.0038  Score=33.74  Aligned_cols=44  Identities=32%  Similarity=0.725  Sum_probs=31.8

Q ss_pred             cCccccccccCCCeeeecCCCCccccHHhHHHHHhCC----CCCCCcCc
Q 042258           98 DCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR----LNCPVCRN  142 (152)
Q Consensus        98 ~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~----~~CP~CR~  142 (152)
                      .|.||...- ++..++....|...||.+|+.+-+...    =.||.||.
T Consensus         2 ~C~vC~~~~-~~~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKG-EDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSS-CCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCC-CCCCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            488887654 334556667799999999999876542    24999975

>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=93.03  E-value=0.024  Score=31.83  Aligned_cols=49  Identities=24%  Similarity=0.571  Sum_probs=35.9

Q ss_pred             CCccCccccccccCCCeeeecCCCCccccHHhHHHHHh-----CCCCCCCcCcc
Q 042258           95 SNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLK-----HRLNCPVCRNP  143 (152)
Q Consensus        95 ~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~-----~~~~CP~CR~~  143 (152)
                      ....|.+|.....+++..+....|+..||..|+..-..     ..-.||.|+..
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            34679999988766666667777999999999863211     24569999764

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.57  E-value=0.026  Score=32.39  Aligned_cols=44  Identities=25%  Similarity=0.533  Sum_probs=31.4

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHHHHHhCC----CCCCCcCccC
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHR----LNCPVCRNPL  144 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~----~~CP~CR~~l  144 (152)
                      ..|.+|.+.    ..+.....|...||..|+.+.+...    =.||.|+...
T Consensus         8 ~~C~~C~~~----~~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           8 TICRVCQKP----GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             SCCSSSCSS----SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCCCc----CEEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            457777542    3456666799999999999877543    3499997644

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

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: TFIIH p44 subunit cysteine-rich domain
domain: TFIIH p44 subunit cysteine-rich domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.57  E-value=0.055  Score=29.95  Aligned_cols=44  Identities=18%  Similarity=0.446  Sum_probs=32.4

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhCCCCCCCc
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKHRLNCPVC  140 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~CP~C  140 (152)
                      ...|.-|...+.+ +.....++|++.|+.+|=.--=..-..||.|
T Consensus        15 ~~~C~gC~~~l~~-~~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          15 ERFCYGCQGELKD-QHVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             CCEETTTTEECTT-SEEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCccCCCCcCCC-CceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            3579999988855 4556678899999999955433345679988

>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=91.81  E-value=0.28  Score=28.39  Aligned_cols=48  Identities=17%  Similarity=0.339  Sum_probs=33.4

Q ss_pred             cCccccccccCCCeeeecCCCCccccHHhHHH--HH-h--CCCCCCCcCccCc
Q 042258           98 DCAICLDDFIEGETCKSFPECNHIFHLHCIDQ--WL-K--HRLNCPVCRNPLC  145 (152)
Q Consensus        98 ~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~--wl-~--~~~~CP~CR~~l~  145 (152)
                      .+-||...+..++..+....|.-.||..|+..  .- .  .+-.||.|+...-
T Consensus        13 v~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~g   65 (79)
T d1wepa_          13 VYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CCSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             eEeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcC
Confidence            34489887665555667777999999999852  11 1  2467999987543

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.72  E-value=0.017  Score=32.26  Aligned_cols=46  Identities=26%  Similarity=0.632  Sum_probs=32.4

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhC----CCCCCCcCccCc
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH----RLNCPVCRNPLC  145 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~~~CP~CR~~l~  145 (152)
                      ...|.+|.+.    ..++....|.-.||..|+..-+..    .-.||.|+.+..
T Consensus         9 ~~~C~~C~~~----g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~~   58 (61)
T d1mm2a_           9 MEFCRVCKDG----GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPAL   58 (61)
T ss_dssp             CSSCTTTCCC----SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTCC
T ss_pred             cCCCcCCCCC----CeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCccc
Confidence            3569999742    345556669999999998765543    335999987654

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.80  E-value=0.14  Score=30.16  Aligned_cols=36  Identities=17%  Similarity=0.576  Sum_probs=25.0

Q ss_pred             CCCCccCccccccccCCCeeeecCCCCccccHHhHHHH
Q 042258           93 MTSNTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQW  130 (152)
Q Consensus        93 ~~~~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~w  130 (152)
                      ..++..|.|| +.+...+.. -.--|+-+||..|+.+-
T Consensus        12 v~~D~mC~vC-~v~t~~~l~-pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          12 VVNDEMCDVC-EVWTAESLF-PCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCSCCCTTT-CCCCSSCCS-SCSSSSSCCCHHHHHHH
T ss_pred             CCcCcccccc-Cccccccee-cceeecchhhHHHHHHh
Confidence            4566889999 666443332 12238899999999997

>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=88.62  E-value=0.67  Score=27.32  Aligned_cols=52  Identities=25%  Similarity=0.456  Sum_probs=36.6

Q ss_pred             CCccCccccccccC---CCeeeecCCCCccccHHhHHHHHh-CCCCCCCcCccCcc
Q 042258           95 SNTDCAICLDDFIE---GETCKSFPECNHIFHLHCIDQWLK-HRLNCPVCRNPLCR  146 (152)
Q Consensus        95 ~~~~C~IC~~~~~~---~~~~~~l~~C~H~fh~~Ci~~wl~-~~~~CP~CR~~l~~  146 (152)
                      ....|.||-+..-.   ++.......|+--.|+.|..-=.+ .++.||.|+++..+
T Consensus        15 ~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Ykr   70 (93)
T d1weoa_          15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKR   70 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCC
T ss_pred             ccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhhh
Confidence            44679999888743   333344445888899999765443 58899999987654

>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=83.32  E-value=1.4  Score=24.88  Aligned_cols=38  Identities=18%  Similarity=0.347  Sum_probs=28.3

Q ss_pred             CccCccccccccCCCeeeecCCCCccccHHhHHHHHhC
Q 042258           96 NTDCAICLDDFIEGETCKSFPECNHIFHLHCIDQWLKH  133 (152)
Q Consensus        96 ~~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~  133 (152)
                      ...|.+|.+.+++..-+..-.-=+|.||-.|-...++.
T Consensus         8 ~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~   45 (80)
T d2cs3a1           8 PLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   45 (80)
T ss_dssp             SCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             ceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHh
Confidence            37799999999776544332224799999999888764

>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=81.92  E-value=0.83  Score=25.78  Aligned_cols=45  Identities=22%  Similarity=0.482  Sum_probs=30.3

Q ss_pred             ccCccccccccCCCeeeecCCCCccccHHhHH------HH---HhCCCCCCCcCcc
Q 042258           97 TDCAICLDDFIEGETCKSFPECNHIFHLHCID------QW---LKHRLNCPVCRNP  143 (152)
Q Consensus        97 ~~C~IC~~~~~~~~~~~~l~~C~H~fh~~Ci~------~w---l~~~~~CP~CR~~  143 (152)
                      ..| ||...... ..++....|.-.||..|+.      ..   ....-.||.|+..
T Consensus        17 ~~C-iC~~~~~~-~~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~   70 (76)
T d1wema_          17 LYC-ICRQPHNN-RFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             CCS-TTCCCCCS-SCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             CEE-ECCCccCC-CeEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCc
Confidence            457 89766533 4456667799999999983      11   1235789999654

>d2o35a1 a.293.1.1 (A:2-80) Hypothetical protein SMc04008 {Rhizobium meliloti [TaxId: 382]}

class: All alpha proteins
fold: SMc04008-like
superfamily: SMc04008-like
family: SMc04008-like
domain: Hypothetical protein SMc04008
species: Rhizobium meliloti [TaxId: 382]

Probab=80.63  E-value=0.33  Score=28.06  Aligned_cols=11  Identities=27%  Similarity=1.123  Sum_probs=10.3

Q ss_pred             ccHHhHHHHHh
Q 042258          122 FHLHCIDQWLK  132 (152)
Q Consensus       122 fh~~Ci~~wl~  132 (152)
                      ||+.|+.+|+.
T Consensus        40 FCRNCLskWy~   50 (79)
T d2o35a1          40 FCRNCLSNWYR   50 (79)
T ss_dssp             CCHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999985