Citrus Sinensis ID: 028584

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------
Protein Sequence
MAGMLPGVECARRRRIHQSGGGCSSASDGLAPTWSSMSMSMSRRSSFCLYTSSHESHHTSSISSLRSIINQACEDEQLAGVAREAKERLDERLGTQRKSSDSNSRQNGKESSVLMNINKSTVLHTQVFGSKKSGSKRFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAASSAD
Secondary Structure (PSIPRED)
cccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccHHHcccHHHHHHHHHHHHHcccccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccccccHHHHHHcccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHHHccccccccccccccccccccccccccccccccEEcccccccccccccHHHHHHHHccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccEEEHHHcccccEEEEccccccHcHHHHHHHHHHcccccccccHccccccccccc
Coil and Loop (DISEMBL)
magmlpgveCARRrrihqsgggcssasdglaptwssmsmsmsrrssfclytssheshhtssISSLRSIINQACEDEQLAGVAREAKERLDerlgtqrkssdsnsrqngkessvLMNINKSTVLHTqvfgskksgskrfswsklsWKACEQEECAIClerfkvgdtlvhlpcahrfharcllpwlatnahncpccrmqildpaassad
Flexible Loop (DISEMBL)
MAGMLPGVECARRRRihqsgggcssasdgLAPTWSSMSMSMSRRSSFCLYTSSHESHHTSSISSLRSIINQACEDEQLAGVAREAKErlderlgtqrkssdsnsrqngkessvlmninkSTVLHTQvfgskksgskrfSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAASSAD
Low Complexity Region (SEG)
MAGMLPGVECARRRRIHQSGGGCSSASDGLAPTWssmsmsmsrrssFCLYTssheshhtssisslrsiiNQACEDEQLAGVAREAKERLDERLGTQRKSSDSNSRQNGKESSVLMNINKSTVLHTQVfgskksgskrfswskLSWKACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAASSAD
Disordered region (IsUnstruct)
************************************************************************************************************************TVLHTQVFG******KRFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL********
Disordered Region (DISOPRED)
*AGMLPGVECA*******************************************************************************************************************************************EECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCR************
Disordered Region (DISEMBL)
MAGMLPGVECARRRR*************GLAPTWSSMSMSMSRRSSFCL***************LRSIINQACEDEQLAGVARE**************************SSVLMNINKSTVLHTQV****************SWKACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAASSAD
Disordered Region (DISPRO)
******************************************************ESHHTSSISSLRSIINQACEDEQLAGVAREAKERLDERL*******************************************RFSW****WKACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI*********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAGMLPGVECARRRRIHQSGGGCSSASDGLAPTWSSMSMSMSRRSSFCLYTSSHESHHTSSISSLRSIINQACEDEQLAGVAREAKERLDERLGTQRKSSDSNSRQNGKESSVLMNINKSTVLHTQVFGSKKSGSKRFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAASSAD
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	207	2.2.26 [Sep-21-2011]
Q4KLR8	784	E3 ubiquitin-protein liga	N/A	no	0.458	0.121	0.358	3e-10
Q5SSZ7	913	E3 ubiquitin-protein liga	yes	no	0.458	0.104	0.339	8e-10
Q08D68	853	E3 ubiquitin-protein liga	yes	no	0.227	0.055	0.541	1e-09
A5WWA0	868	E3 ubiquitin-protein liga	yes	no	0.227	0.054	0.541	2e-09
Q9C1X4	513	Uncharacterized RING fing	yes	no	0.246	0.099	0.471	3e-09
O54965	381	E3 ubiquitin-protein liga	no	no	0.260	0.141	0.425	4e-09
Q66HG0	380	E3 ubiquitin-protein liga	no	no	0.260	0.142	0.425	5e-09
Q9ULT6	936	E3 ubiquitin-protein liga	yes	no	0.458	0.101	0.330	6e-09
Q90972	381	E3 ubiquitin-protein liga	yes	no	0.294	0.160	0.387	6e-09
Q9R1W3	683	E3 ubiquitin-protein liga	no	no	0.256	0.077	0.472	9e-09

>sp|Q4KLR8|ZNRF3_XENLA E3 ubiquitin-protein ligase ZNRF3 OS=Xenopus laevis GN=znrf3 PE=2 SV=1

 Score = 65.5 bits (158), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 38/106 (35%), Positives = 56/106 (52%), Gaps = 11/106 (10%)

Query: 96  QRKSSDSNSRQNGKESSVLMNINKSTVLHTQVFGSKKSGSKRFSWSKL-SWKACEQEECA 154
           QR+S +S +R         M +     + T+ F +K   S+  S   L +  +    +CA
Sbjct: 153 QRRSQNSMNR---------MAVQALEKMETRKFKAKGKVSREGSCGGLDTLSSSSISDCA 203

Query: 155 ICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD 200
           ICLE++  G+ L  +PC HRFH RC+ PWL  N H CP CR  I++
Sbjct: 204 ICLEKYIDGEELRVIPCTHRFHKRCVDPWLLQN-HTCPHCRHNIIE 248

E3 ubiquitin-protein ligase that acts as a negative regulator of the Wnt signaling pathway by mediating the ubiquitination and subsequent degradation of Wnt receptor complex components.
Xenopus laevis (taxid: 8355)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|Q5SSZ7|ZNRF3_MOUSE E3 ubiquitin-protein ligase ZNRF3 OS=Mus musculus GN=Znrf3 PE=2 SV=1

 Score = 63.5 bits (153), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 36/106 (33%), Positives = 56/106 (52%), Gaps = 11/106 (10%)

Query: 96  QRKSSDSNSRQNGKESSVLMNINKSTVLHTQVFGSKKSGSKRFSWSKL-SWKACEQEECA 154
           QR+S +S +R         + +     + T+ F SK  G +  S   L +  +    +CA
Sbjct: 241 QRRSQNSMNR---------LAVQALEKMETRKFNSKSKGRREGSCGALDTLSSGSTSDCA 291

Query: 155 ICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD 200
           ICLE++  G+ L  +PC HRFH +C+ PWL  + H CP CR  I++
Sbjct: 292 ICLEKYIDGEELRVIPCTHRFHRKCVDPWLLQH-HTCPHCRHNIIE 336

Mus musculus (taxid: 10090)

>sp|Q08D68|ZNRF3_XENTR E3 ubiquitin-protein ligase ZNRF3 OS=Xenopus tropicalis GN=znrf3 PE=2 SV=1

 Score = 62.8 bits (151), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 26/48 (54%), Positives = 33/48 (68%), Gaps = 1/48 (2%)

Query: 153 CAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD 200
           CAICLE++  G+ L  +PC HRFH RC+ PWL  N H CP CR  I++
Sbjct: 266 CAICLEKYIDGEELRVIPCTHRFHKRCVDPWLLQN-HTCPHCRHNIIE 312

E3 ubiquitin-protein ligase that acts as a negative regulator of the Wnt signaling pathway by mediating the ubiquitination and subsequent degradation of Wnt receptor complex components (By similarity).

Xenopus tropicalis (taxid: 8364)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|A5WWA0|ZNRF3_DANRE E3 ubiquitin-protein ligase ZNRF3 OS=Danio rerio GN=znrf3 PE=3 SV=2

 Score = 62.8 bits (151), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 26/48 (54%), Positives = 34/48 (70%), Gaps = 1/48 (2%)

Query: 153 CAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD 200
           CAICLE++  G+ L  +PCAHRFH +C+ PWL  + H CP CR  I+D
Sbjct: 267 CAICLEKYIDGEELRVIPCAHRFHKKCVDPWLLQH-HTCPHCRHNIID 313

E3 ubiquitin-protein ligase that acts as a negative regulator of the Wnt signaling pathway by mediating the ubiquitination and subsequent degradation of Wnt receptor complex components.

Danio rerio (taxid: 7955)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9C1X4|YKW3_SCHPO Uncharacterized RING finger protein P32A8.03c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAP32A8.03c PE=4 SV=1

 Score = 62.0 bits (149), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 32/53 (60%), Gaps = 2/53 (3%)

Query: 149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDP 201
           E+ EC IC+E FK+ D ++ LPC H FH  C+ PWL  N   C  CR  + DP
Sbjct: 392 EEGECTICMEMFKINDDVIQLPCKHYFHENCIKPWLRVNG-TCAICRAPV-DP 442

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|O54965|RNF13_MOUSE E3 ubiquitin-protein ligase RNF13 OS=Mus musculus GN=Rnf13 PE=1 SV=2

 Score = 61.2 bits (147), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 34/54 (62%)

Query: 146 KACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL 199
           K  E + CAICLE ++ GD L  LPC+H +H +C+ PWL      CP C+ +++
Sbjct: 233 KGDEYDVCAICLEEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKTCPVCKQKVV 286

E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q66HG0|RNF13_RAT E3 ubiquitin-protein ligase RNF13 OS=Rattus norvegicus GN=Rnf13 PE=2 SV=1

 Score = 61.2 bits (147), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 34/54 (62%)

Query: 146 KACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL 199
           K  E + CAICLE ++ GD L  LPC+H +H +C+ PWL      CP C+ +++
Sbjct: 233 KGDEYDVCAICLEEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKTCPVCKQKVV 286

E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation.

Rattus norvegicus (taxid: 10116)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9ULT6|ZNRF3_HUMAN E3 ubiquitin-protein ligase ZNRF3 OS=Homo sapiens GN=ZNRF3 PE=1 SV=3

 Score = 60.8 bits (146), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 35/106 (33%), Positives = 56/106 (52%), Gaps = 11/106 (10%)

Query: 96  QRKSSDSNSRQNGKESSVLMNINKSTVLHTQVFGSKKSGSKRFS-WSKLSWKACEQEECA 154
           QR+S +S +R         + +     + T+ F SK  G +  S  +  +  +    +CA
Sbjct: 244 QRRSQNSMNR---------LAVQALEKMETRKFNSKSKGRREGSCGALDTLSSSSTSDCA 294

Query: 155 ICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD 200
           ICLE++  G+ L  +PC HRFH +C+ PWL  + H CP CR  I++
Sbjct: 295 ICLEKYIDGEELRVIPCTHRFHRKCVDPWLLQH-HTCPHCRHNIIE 339

Homo sapiens (taxid: 9606)

>sp|Q90972|RNF13_CHICK E3 ubiquitin-protein ligase RNF13 OS=Gallus gallus GN=RNF13 PE=1 SV=1

 Score = 60.8 bits (146), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 38/62 (61%), Gaps = 1/62 (1%)

Query: 146 KACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAASS 205
           K  E + CAICL+ ++ GD L  LPC+H +H +C+ PWL      CP C+ +++ P+   
Sbjct: 233 KGDEYDVCAICLDEYEDGDKLRILPCSHAYHCKCVDPWLTKTKKTCPVCKQKVV-PSQGD 291

Query: 206 AD 207
           +D
Sbjct: 292 SD 293

E3 ubiquitin-protein ligase. May play a role in controlling cell proliferation, including that of muscle cells.

Gallus gallus (taxid: 9031)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9R1W3|RN103_MOUSE E3 ubiquitin-protein ligase RNF103 OS=Mus musculus GN=Rnf103 PE=2 SV=2

 Score = 60.5 bits (145), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 26/55 (47%), Positives = 32/55 (58%), Gaps = 2/55 (3%)

Query: 143 LSWKA--CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCR 195
           L+W A      EC +CLE F+ G  L+ LPC H FH  C++ WLA   H CP CR
Sbjct: 607 LTWPAGTLHCTECVVCLENFENGCLLMGLPCGHVFHQNCIVMWLAGGRHCCPVCR 661

Acts as an E2-dependent E3 ubiquitin-protein ligase, probably involved in the ER-associated protein degradation pathway.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	207
225463022	193	PREDICTED: E3 ubiquitin-protein ligase a	0.908	0.974	0.658	4e-63
147794470	193	hypothetical protein VITISV_034074 [Viti	0.908	0.974	0.653	4e-62
224142453	190	predicted protein [Populus trichocarpa]	0.869	0.947	0.591	2e-57
224091643	202	predicted protein [Populus trichocarpa]	0.898	0.920	0.535	5e-55
351721935	202	uncharacterized protein LOC100527583 [Gl	0.898	0.920	0.547	3e-50
388500058	183	unknown [Lotus japonicus]	0.864	0.978	0.562	8e-48
449442999	201	PREDICTED: E3 ubiquitin-protein ligase R	0.927	0.955	0.514	5e-45
388508966	183	unknown [Lotus japonicus]	0.864	0.978	0.557	2e-44
297832042	195	zinc finger family protein [Arabidopsis	0.913	0.969	0.470	4e-41
18397866	196	RING/U-box domain-containing protein [Ar	0.908	0.959	0.475	3e-39

>gi|225463022|ref|XP_002266038.1| PREDICTED: E3 ubiquitin-protein ligase arkadia-like isoform 1 [Vitis vinifera]

 Score =  246 bits (628), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 133/202 (65%), Positives = 154/202 (76%), Gaps = 14/202 (6%)

Query: 1   MAGMLPGVECARRRRIHQSGGGCSSASDGLAPTWSSMSMSMSRRSSFCLYTSSHESHHTS 60
           MAGMLPGVECARRRR HQSGG CS +     PT +    +  RRSSFCLYTS+HE+HH +
Sbjct: 1   MAGMLPGVECARRRRFHQSGG-CSDS-----PTVAVHGCT--RRSSFCLYTSNHENHHAT 52

Query: 61  SISSL-RSIINQACEDEQLAGVAREAKERLDERLGTQRKSSDSNSRQNGKESSVLMNINK 119
           S SS+ RS++NQA  DE+L GVAREAKERLDERL TQRKS  +  R   KES  +++   
Sbjct: 53  SSSSMQRSVLNQAYSDEKLGGVAREAKERLDERLRTQRKSEPT--RNKSKESLRIVDGRA 110

Query: 120 STV--LHTQVFGSKKSGSKRFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRFHA 177
             V  L T+VFGSK+SGSKRFSW KLSWKA +Q ECAICLE FK G++LVHLPCAHRFH+
Sbjct: 111 MVVGELQTEVFGSKRSGSKRFSWGKLSWKASDQVECAICLEGFKAGESLVHLPCAHRFHS 170

Query: 178 RCLLPWLATNAHNCPCCRMQIL 199
           RCL+PWL TNAH CPCCRM I 
Sbjct: 171 RCLMPWLETNAH-CPCCRMGIF 191

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147794470|emb|CAN73727.1| hypothetical protein VITISV_034074 [Vitis vinifera]

 Score =  243 bits (619), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 132/202 (65%), Positives = 153/202 (75%), Gaps = 14/202 (6%)

Query: 1   MAGMLPGVECARRRRIHQSGGGCSSASDGLAPTWSSMSMSMSRRSSFCLYTSSHESHHTS 60
           MAGMLPGVECARRRR HQSGG CS +     PT +    +  RRSSFCLYTS+HE+HH +
Sbjct: 1   MAGMLPGVECARRRRFHQSGG-CSDS-----PTVAVHGCT--RRSSFCLYTSNHENHHAT 52

Query: 61  SISSL-RSIINQACEDEQLAGVAREAKERLDERLGTQRKSSDSNSRQNGKESSVLMNINK 119
           S SS+ RS++NQA  DE+L GVAREAKERLDERL TQRKS  +  R   KES  +++   
Sbjct: 53  SSSSMQRSVLNQAYSDEKLGGVAREAKERLDERLRTQRKSEPT--RNKSKESLRIVDGRA 110

Query: 120 STV--LHTQVFGSKKSGSKRFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRFHA 177
             V  L T+VFGSK+SGSKRFSW KLSWKA +Q ECAICLE FK G++LVHLPCAHRFH+
Sbjct: 111 MVVGELQTEVFGSKRSGSKRFSWGKLSWKASDQVECAICLEGFKAGESLVHLPCAHRFHS 170

Query: 178 RCLLPWLATNAHNCPCCRMQIL 199
           RCL+PWL TNAH CPC RM I 
Sbjct: 171 RCLMPWLETNAH-CPCXRMGIF 191

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224142453|ref|XP_002324572.1| predicted protein [Populus trichocarpa] gi|222866006|gb|EEF03137.1| predicted protein [Populus trichocarpa]

 Score =  228 bits (580), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 120/203 (59%), Positives = 142/203 (69%), Gaps = 23/203 (11%)

Query: 1   MAGMLPGVECARRRRIHQSGGGCSSASDGLAPTWSSMSMSMSRRSSFCLYTSSHESHHTS 60
           MAGMLPGVECARRRR HQSG    + + G    WS       R+ SFCLYTSSHES+H S
Sbjct: 1   MAGMLPGVECARRRRFHQSGDSLGAPAHG----WS-------RKPSFCLYTSSHESYHGS 49

Query: 61  SISSLRSIINQACEDEQLAGVAREAKERLDERLGTQRK-----SSDSNSRQNGKESSVLM 115
             S  RS+ +QA EDE+L GVAREAKERLDERL  Q+K     +S  N R     S VL 
Sbjct: 50  VSSLQRSVSSQAYEDEKLGGVAREAKERLDERLRLQKKKTAETTSTGNLRDVDGRSMVLG 109

Query: 116 NINKSTVLHTQVFGSKKSGSKRFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRF 175
                  L  +V+G+K+SGSKRF+W+KLSWKA +Q+EC ICL+RFK G+TLVHLPCAHR+
Sbjct: 110 E------LQMEVYGTKRSGSKRFNWAKLSWKAADQDECTICLDRFKSGETLVHLPCAHRY 163

Query: 176 HARCLLPWLATNAHNCPCCRMQI 198
           H RCL+PWL  N H CPCCRM+I
Sbjct: 164 HPRCLVPWLENNGH-CPCCRMEI 185

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224091643|ref|XP_002309314.1| predicted protein [Populus trichocarpa] gi|222855290|gb|EEE92837.1| predicted protein [Populus trichocarpa]

 Score =  219 bits (558), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 112/209 (53%), Positives = 142/209 (67%), Gaps = 23/209 (11%)

Query: 1   MAGMLPGVECARRRRIHQSGGGCSSASDGLAPTWSSMSMSMSRRSSFCLYTSSHESHHTS 60
           MAG+LPGVECARRRR H+SG    + + G    W+       RR SFCLYTSSHE+HH S
Sbjct: 1   MAGVLPGVECARRRRFHRSGDSLGAPAHG----WT-------RRPSFCLYTSSHENHHGS 49

Query: 61  SISSLRSIINQACEDEQLAGVAREAKERLDERLGTQRKSSDSNSRQNG-------KESSV 113
             S  RSI+NQA EDE+L GVA+EAKERLDERL  Q+K  +   +          K +  
Sbjct: 50  ISSLQRSILNQAYEDEKLGGVAKEAKERLDERLRMQKKKPEITRKTMASAQFIWHKSTGN 109

Query: 114 LMNINKSTV----LHTQVFGSKKSGSKRFSWSKLSWKACEQEECAICLERFKVGDTLVHL 169
           L  ++  ++    L  +V+G K+SGSKR+ W+KLSWKA +Q+EC ICL+RFK G+TLVHL
Sbjct: 110 LRGVDGRSMVPGELQMEVYGPKRSGSKRYKWAKLSWKAADQDECTICLDRFKSGETLVHL 169

Query: 170 PCAHRFHARCLLPWLATNAHNCPCCRMQI 198
           PCAHR+H +CL+PWL  N   CPCCRM+I
Sbjct: 170 PCAHRYHPKCLVPWLENNG-QCPCCRMEI 197

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351721935|ref|NP_001238250.1| uncharacterized protein LOC100527583 [Glycine max] gi|255632685|gb|ACU16694.1| unknown [Glycine max]

 Score =  203 bits (517), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 109/199 (54%), Positives = 133/199 (66%), Gaps = 13/199 (6%)

Query: 1   MAGMLPGVECARRRRIHQSGGGCSSASDGLAPTWSSMSMSMSRRSSFCLYTSSHESHHTS 60
           MAGMLPGVECARRRR+H+     S++    A T         RRSSFCLYTS+HE   + 
Sbjct: 15  MAGMLPGVECARRRRLHRCLDSNSTSLTSHAST---------RRSSFCLYTSNHECRLSL 65

Query: 61  SISSLRSIINQACEDEQLAGVAREAKERLDERLGTQRKSSDSNSRQNGKESSVLMNINKS 120
           S S  RS++ Q   DE + GV REAK+RLD++    R S   N RQN  +  V     + 
Sbjct: 66  SSSLQRSMLYQPHPDENMGGVVREAKQRLDDKFRAHRNSE--NKRQNSTKC-VEGRRTRI 122

Query: 121 TVLHTQVFGSKKSGSKRFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRFHARCL 180
              HT+V+GSKKSGS+RFSW+K SWKA EQE+CA+CLE F+VG+TL+HLPCAHRFH RCL
Sbjct: 123 AEFHTEVYGSKKSGSRRFSWTKWSWKASEQEDCAVCLESFRVGETLIHLPCAHRFHDRCL 182

Query: 181 LPWLATNAHNCPCCRMQIL 199
            PWL  N+H CPCCR  I 
Sbjct: 183 KPWLENNSH-CPCCRTTIF 200

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388500058|gb|AFK38095.1| unknown [Lotus japonicus]

 Score =  195 bits (496), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 113/201 (56%), Positives = 137/201 (68%), Gaps = 22/201 (10%)

Query: 1   MAGMLPGVECARRRRIHQSGGGCSSASDG--LAPTWSSMSMSMSRRSSFCLYTSSHESHH 58
           MAGMLPGVE ARRRR H+SGG      DG  LAP       + +RRSSFCLY S+HES  
Sbjct: 1   MAGMLPGVESARRRRFHKSGG----CLDGPLLAP------HNPTRRSSFCLYASNHESRI 50

Query: 59  TSSISSLRSIINQACEDEQLAGVAREAKERLDERLGTQRKSSDSNSRQNGKESSVLMNIN 118
           +SS S  R ++ QA  DE L G AREAK RLD++   QR  S++NS +  + S       
Sbjct: 51  SSSSSLQRGLLYQAHLDESLGGAAREAKHRLDDKFRAQR-VSETNSVEERRRSL------ 103

Query: 119 KSTVLHTQVFGSKKSGSKRFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRFHAR 178
               L T+ +GS+KSGS+RFSWSKLSWKA EQE+CA+CLE F+ G+TL+ LPCAHRFH+R
Sbjct: 104 --GELGTETYGSRKSGSRRFSWSKLSWKASEQEDCAVCLETFRNGETLIPLPCAHRFHSR 161

Query: 179 CLLPWLATNAHNCPCCRMQIL 199
           CL PWL  N+H CPCCR  IL
Sbjct: 162 CLKPWLENNSH-CPCCRTTIL 181

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449442999|ref|XP_004139268.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like [Cucumis sativus] gi|449493673|ref|XP_004159405.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like [Cucumis sativus]

 Score =  186 bits (472), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 108/210 (51%), Positives = 141/210 (67%), Gaps = 18/210 (8%)

Query: 1   MAGMLPGVECARRRRIHQSGGGCSSASDGLAPTWSSMSMSMSRRSSFCLYTSSHESHHTS 60
           MAGMLPGVECARRRR HQS     ++SD  +P  +  S S +RR SFCLYTS+ + H  S
Sbjct: 1   MAGMLPGVECARRRRFHQS----INSSD--SPFTAGKSGS-TRRPSFCLYTSNRDFHLIS 53

Query: 61  SISSLRS-IINQACEDEQLAGVAREAKERLDERLGTQRKSSDSNSRQN-----GKESSVL 114
           S SS +  + NQA ++++L  +AREAKERLDERL T RK  +S  + N     GKES   
Sbjct: 54  SSSSQQRSLTNQAYQNDKLGEIAREAKERLDERLRTHRKPENSRKKNNNEEVKGKESREK 113

Query: 115 MNINKSTVLHTQVFGSKKSGSKRFSWSK--LSWKACEQEECAICLERFKVGDTLVHLPCA 172
            N  K  + +T+  G ++   KRFSW +  + WKA EQEEC++CLERF++ + L+HLPCA
Sbjct: 114 NNGEKKEMKNTK--GKEEETKKRFSWGRKLMKWKASEQEECSVCLERFRLSEPLLHLPCA 171

Query: 173 HRFHARCLLPWLATNAHNCPCCRMQILDPA 202
           H+FH+ CL+PWL  NAH CPCCR  I  P+
Sbjct: 172 HKFHSTCLVPWLQANAH-CPCCRFPIAVPS 200

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388508966|gb|AFK42549.1| unknown [Lotus japonicus]

 Score =  184 bits (468), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 112/201 (55%), Positives = 136/201 (67%), Gaps = 22/201 (10%)

Query: 1   MAGMLPGVECARRRRIHQSGGGCSSASDG--LAPTWSSMSMSMSRRSSFCLYTSSHESHH 58
           MAGMLPGVE ARRRR H+SGG      DG  LAP  S+      RRSSFCLY S++ES  
Sbjct: 1   MAGMLPGVESARRRRFHKSGG----CLDGPLLAPHNST------RRSSFCLYASNNESRI 50

Query: 59  TSSISSLRSIINQACEDEQLAGVAREAKERLDERLGTQRKSSDSNSRQNGKESSVLMNIN 118
           +SS S  R ++ QA  DE L G AREAK RLD++   QR  S++NS +  + S       
Sbjct: 51  SSSSSLQRGLLYQAHLDESLGGAAREAKHRLDDKFRAQR-VSETNSVEERRRSL------ 103

Query: 119 KSTVLHTQVFGSKKSGSKRFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRFHAR 178
               L T+ +GS+KSGS+RFSWSKLSWKA EQE+CA+CLE  + G+TL+ LPCAHRFH+R
Sbjct: 104 --GELGTETYGSRKSGSRRFSWSKLSWKASEQEDCAVCLETIRNGETLIPLPCAHRFHSR 161

Query: 179 CLLPWLATNAHNCPCCRMQIL 199
           CL PWL  N+H CPCCR  IL
Sbjct: 162 CLKPWLENNSH-CPCCRTTIL 181

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297832042|ref|XP_002883903.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata] gi|297329743|gb|EFH60162.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  173 bits (439), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 97/206 (47%), Positives = 127/206 (61%), Gaps = 17/206 (8%)

Query: 1   MAGMLPGVECARRRRIHQSGGGCSSASDGLAPTWSSMSMSMSRRSSFCLYTSSHESHHTS 60
           MAGMLPGVECARRRR H       S +  +A   ++     +RR SF LYT++HESH   
Sbjct: 1   MAGMLPGVECARRRRFHGGAPPIESTNTAVA---AAAGHVWTRRPSFSLYTTNHESHQAH 57

Query: 61  SISSLRSIINQAC---EDEQLAGVAREAKERLDERLGTQRKSSDSNSRQNGKESSVLMNI 117
              S RS+ N++     DE+L G A+EAK+RL+ERL   R++     RQNGK+    +  
Sbjct: 58  VSFSERSVRNKSYGEDNDEKLDGAAKEAKKRLNERLRIPRRT-----RQNGKDKGNKLEQ 112

Query: 118 NKST---VLHTQVFGSKKSGSKRFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHR 174
            K      L T+V G KKS  +   W K  W+  EQ++CAICL++FK G+TLVHLPCAH+
Sbjct: 113 GKGKPPGALPTEVVGLKKSRGRLIEWFK--WRVREQQDCAICLDQFKKGETLVHLPCAHK 170

Query: 175 FHARCLLPWLATNAHNCPCCRMQILD 200
           FH+ CLLPWL TN + CP CR  I +
Sbjct: 171 FHSLCLLPWLDTNVY-CPYCRTDIWN 195

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18397866|ref|NP_565376.1| RING/U-box domain-containing protein [Arabidopsis thaliana] gi|20197705|gb|AAD17402.2| putative RING-H2 zinc finger protein [Arabidopsis thaliana] gi|21594677|gb|AAM66032.1| putative RING-H2 zinc finger protein [Arabidopsis thaliana] gi|66865916|gb|AAY57592.1| RING finger family protein [Arabidopsis thaliana] gi|149944335|gb|ABR46210.1| At2g15580 [Arabidopsis thaliana] gi|222423846|dbj|BAH19888.1| AT2G15580 [Arabidopsis thaliana] gi|330251325|gb|AEC06419.1| RING/U-box domain-containing protein [Arabidopsis thaliana]

 Score =  167 bits (423), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 97/204 (47%), Positives = 124/204 (60%), Gaps = 16/204 (7%)

Query: 1   MAGMLPGVECARRRRIHQSGGGCSSASDGLAPTWSSMSMSMSRRSSFCLYTSSHESHHTS 60
           MAGMLPGVECARRRR H  GG     S   A   ++     +RR SF LYT++HESH   
Sbjct: 1   MAGMLPGVECARRRRFH--GGAPPIESSNTASVAAAAGHVWTRRPSFSLYTTNHESHQAH 58

Query: 61  SISSLRSIINQAC---EDEQLAGVAREAKERLDERLGTQRKSSDSNSRQNGKESSVLMNI 117
              S RS+ N++     DE+L G A+EAK+RL++RL    ++     RQNGK+    +  
Sbjct: 59  VSFSERSVRNKSYGEDNDEKLDGAAKEAKQRLNKRLRIPPRT-----RQNGKDKGNKLEQ 113

Query: 118 NKSTVL---HTQVFGSKKSGSKRFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHR 174
            K   L    T+V G KKS  +   W K   +  EQ++CAICL+RFK G+TLVHLPCAH+
Sbjct: 114 GKGKPLGDLPTEVVGLKKSRGRLMEWFKR--RVREQQDCAICLDRFKKGETLVHLPCAHK 171

Query: 175 FHARCLLPWLATNAHNCPCCRMQI 198
           FH+ CLLPWL TN + CP CR  I
Sbjct: 172 FHSICLLPWLDTNVY-CPYCRTDI 194

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	207
TAIR|locus:2053583	196	AT2G15580 [Arabidopsis thalian	0.908	0.959	0.392	2.1e-29
TAIR|locus:2010582	634	AT1G04790 [Arabidopsis thalian	0.231	0.075	0.510	3.4e-12
TAIR|locus:2007273	250	AT1G49850 [Arabidopsis thalian	0.236	0.196	0.54	6.4e-12
UNIPROTKB|E1BBM5	295	RNF167 "Uncharacterized protei	0.256	0.179	0.433	8.8e-12
MGI|MGI:1917760	347	Rnf167 "ring finger protein 16	0.256	0.152	0.452	9.5e-12
RGD|1305972	349	Rnf167 "ring finger protein 16	0.256	0.151	0.452	9.7e-12
UNIPROTKB|I3L0L6	315	RNF167 "E3 ubiquitin-protein l	0.256	0.168	0.433	1.3e-11
UNIPROTKB|Q9H6Y7	350	RNF167 "E3 ubiquitin-protein l	0.256	0.151	0.433	2.1e-11
UNIPROTKB|F1RFY0	350	RNF167 "Uncharacterized protei	0.256	0.151	0.433	2.1e-11
TAIR|locus:2147152	310	AIP2 "ABI3-interacting protein	0.227	0.151	0.48	7.3e-11

TAIR|locus:2053583 AT2G15580 [Arabidopsis thaliana (taxid:3702)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 80/204 (39%), Positives = 100/204 (49%)

Query:     1 MAGMLPGVECARRRRIHQSGGGCSSASDGLAPTWXXXXXXXXXXXXFCLYTXXXXXXXXX 60
             MAGMLPGVECARRRR H  GG     S   A               F LYT         
Sbjct:     1 MAGMLPGVECARRRRFH--GGAPPIESSNTASVAAAAGHVWTRRPSFSLYTTNHESHQAH 58

Query:    61 XXXXXXXXXNQAC---EDEQLAGVAREAKERLDERLGTQRKSSDSNSRQNGKESSVLMNI 117
                      N++     DE+L G A+EAK+RL++RL    ++     RQNGK+    +  
Sbjct:    59 VSFSERSVRNKSYGEDNDEKLDGAAKEAKQRLNKRLRIPPRT-----RQNGKDKGNKLEQ 113

Query:   118 NKSTVLHTQVXXXXXXXXXXXXXXXLSW---KACEQEECAICLERFKVGDTLVHLPCAHR 174
              K   L                   + W   +  EQ++CAICL+RFK G+TLVHLPCAH+
Sbjct:   114 GKGKPLGD--LPTEVVGLKKSRGRLMEWFKRRVREQQDCAICLDRFKKGETLVHLPCAHK 171

Query:   175 FHARCLLPWLATNAHNCPCCRMQI 198
             FH+ CLLPWL TN + CP CR  I
Sbjct:   172 FHSICLLPWLDTNVY-CPYCRTDI 194

GO:0005634 "nucleus" evidence=ISM

GO:0005739 "mitochondrion" evidence=ISM

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

TAIR|locus:2010582 AT1G04790 [Arabidopsis thaliana (taxid:3702)]

 Score = 156 (60.0 bits), Expect = 3.4e-12, Sum P(2) = 3.4e-12
 Identities = 25/49 (51%), Positives = 33/49 (67%)

Query:   150 QEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
             QE C ICLE  K+GDT+ HLPC H+FH  C+ PWL   + +CP C+  +
Sbjct:   586 QETCVICLETPKIGDTIRHLPCLHKFHKDCIDPWLG-RSKSCPVCKSSV 633

GO:0005634 "nucleus" evidence=ISM

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

GO:0006635 "fatty acid beta-oxidation" evidence=RCA

GO:0016558 "protein import into peroxisome matrix" evidence=RCA

TAIR|locus:2007273 AT1G49850 [Arabidopsis thaliana (taxid:3702)]

 Score = 161 (61.7 bits), Expect = 6.4e-12, P = 6.4e-12
 Identities = 27/50 (54%), Positives = 32/50 (64%)

Query:   149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
             E  +C+ICLE F  GD L+ LPC H FH+ CL PWL     +CPCCR  I
Sbjct:   199 EMRDCSICLESFTKGDMLISLPCTHSFHSSCLNPWLRA-CGDCPCCRRAI 247

GO:0005634 "nucleus" evidence=ISM

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

UNIPROTKB|E1BBM5 RNF167 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 146 (56.5 bits), Expect = 8.8e-12, Sum P(2) = 8.8e-12
 Identities = 23/53 (43%), Positives = 33/53 (62%)

Query:   146 KACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
             K  + + CAICL+ ++ GD L  LPCAH +H+RC+ PWL      CP C+  +
Sbjct:   169 KGDQYDVCAICLDEYEDGDKLRVLPCAHAYHSRCVDPWLTQTRKTCPICKQPV 221

GO:0008270 "zinc ion binding" evidence=IEA

MGI|MGI:1917760 Rnf167 "ring finger protein 167" [Mus musculus (taxid:10090)]

 Score = 149 (57.5 bits), Expect = 9.5e-12, Sum P(2) = 9.5e-12
 Identities = 24/53 (45%), Positives = 33/53 (62%)

Query:   146 KACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
             K  E + CAICL+ ++ GD L  LPCAH +H+RC+ PWL      CP C+  +
Sbjct:   223 KGDEYDVCAICLDEYEDGDKLRVLPCAHAYHSRCVDPWLTQTRKTCPICKQPV 275

GO:0000209 "protein polyubiquitination" evidence=ISO

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

GO:0005737 "cytoplasm" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0045786 "negative regulation of cell cycle" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

RGD|1305972 Rnf167 "ring finger protein 167" [Rattus norvegicus (taxid:10116)]

 Score = 149 (57.5 bits), Expect = 9.7e-12, Sum P(2) = 9.7e-12
 Identities = 24/53 (45%), Positives = 33/53 (62%)

Query:   146 KACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
             K  E + CAICL+ ++ GD L  LPCAH +H+RC+ PWL      CP C+  +
Sbjct:   223 KGDEYDVCAICLDEYEDGDKLRILPCAHAYHSRCVDPWLTQTRKTCPICKQPV 275

GO:0000209 "protein polyubiquitination" evidence=IEA;ISO

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

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0012505 "endomembrane system" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0045786 "negative regulation of cell cycle" evidence=IEA;ISO

UNIPROTKB|I3L0L6 RNF167 "E3 ubiquitin-protein ligase RNF167" [Homo sapiens (taxid:9606)]

 Score = 146 (56.5 bits), Expect = 1.3e-11, Sum P(2) = 1.3e-11
 Identities = 23/53 (43%), Positives = 33/53 (62%)

Query:   146 KACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
             K  + + CAICL+ ++ GD L  LPCAH +H+RC+ PWL      CP C+  +
Sbjct:   188 KGDQYDVCAICLDEYEDGDKLRVLPCAHAYHSRCVDPWLTQTRKTCPICKQPV 240

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q9H6Y7 RNF167 "E3 ubiquitin-protein ligase RNF167" [Homo sapiens (taxid:9606)]

 Score = 146 (56.5 bits), Expect = 2.1e-11, Sum P(2) = 2.1e-11
 Identities = 23/53 (43%), Positives = 33/53 (62%)

Query:   146 KACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
             K  + + CAICL+ ++ GD L  LPCAH +H+RC+ PWL      CP C+  +
Sbjct:   223 KGDQYDVCAICLDEYEDGDKLRVLPCAHAYHSRCVDPWLTQTRKTCPICKQPV 275

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0012505 "endomembrane system" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

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

GO:0045786 "negative regulation of cell cycle" evidence=IMP

GO:0005737 "cytoplasm" evidence=IDA

GO:0000209 "protein polyubiquitination" evidence=IDA

UNIPROTKB|F1RFY0 RNF167 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 146 (56.5 bits), Expect = 2.1e-11, Sum P(2) = 2.1e-11
 Identities = 23/53 (43%), Positives = 33/53 (62%)

Query:   146 KACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
             K  + + CAICL+ ++ GD L  LPCAH +H+RC+ PWL      CP C+  +
Sbjct:   223 KGDQYDVCAICLDEYEDGDRLRVLPCAHAYHSRCVDPWLTQTRKTCPICKQPV 275

GO:0045786 "negative regulation of cell cycle" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0000209 "protein polyubiquitination" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2147152 AIP2 "ABI3-interacting protein 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 138 (53.6 bits), Expect = 7.3e-11, Sum P(2) = 7.3e-11
 Identities = 24/50 (48%), Positives = 30/50 (60%)

Query:   150 QEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHN-CPCCRMQI 198
             + EC IC E   +GD +  LPC H FH  CL PWL  + HN CP CR ++
Sbjct:   227 EAECCICKENLVIGDKMQELPCKHTFHPPCLKPWL--DEHNSCPICRHEL 274

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0005515 "protein binding" evidence=IPI

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

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

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

GO:0009788 "negative regulation of abscisic acid mediated signaling pathway" evidence=IMP

GO:0006865 "amino acid transport" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.XVIII.3410.1 hypothetical protein (185 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	207
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	3e-12
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	8e-12
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	6e-10
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	2e-07
smart00184	40	smart00184, RING, Ring finger	1e-06
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	1e-06
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	2e-05
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	1e-04
pfam05883	135	pfam05883, Baculo_RING, Baculovirus U-box/Ring-lik	2e-04
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	0.003

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

 Score = 58.6 bits (142), Expect = 3e-12
 Identities = 22/45 (48%), Positives = 30/45 (66%), Gaps = 1/45 (2%)

Query: 151 EECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCR 195
           +EC ICL+ F+ G+ +V LPC H FH  CL  WL ++ + CP CR
Sbjct: 1   DECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSS-NTCPLCR 44

Length = 46

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

 Score = 62.7 bits (152), Expect = 8e-12
 Identities = 24/50 (48%), Positives = 28/50 (56%)

Query: 152 ECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDP 201
           ECAIC+  F   D L  LPC HRFH  C+  WL   ++ CP CR  I  P
Sbjct: 325 ECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPPP 374

Length = 374

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

 Score = 52.4 bits (126), Expect = 6e-10
 Identities = 21/47 (44%), Positives = 27/47 (57%), Gaps = 2/47 (4%)

Query: 152 ECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
           EC ICLE F+  + +V LPC H F   C+  WL +  + CP CR  I
Sbjct: 1   ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 50.8 bits (121), Expect = 2e-07
 Identities = 33/91 (36%), Positives = 41/91 (45%), Gaps = 13/91 (14%)

Query: 119  KSTVLHTQVFGSKKSGSKRFS---WSK-LSWKACEQEECAICLERFKVGDTLVHLP---- 170
            KS +   Q    KK+GS       W K +  K    EECAIC     + D    LP    
Sbjct: 1434 KSWINLRQNEMIKKNGSFMDLLGLWKKNIDEKFSGHEECAICYSVLDMVDR--SLPSKRC 1491

Query: 171  --CAHRFHARCLLPWLAT-NAHNCPCCRMQI 198
              C ++FH RCL  W A+    NCP CR +I
Sbjct: 1492 ATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522

Length = 1525

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

 Score = 43.7 bits (103), Expect = 1e-06
 Identities = 17/42 (40%), Positives = 21/42 (50%), Gaps = 2/42 (4%)

Query: 153 CAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCC 194
           C ICLE +      V LPC H F   C+  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|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger)

 Score = 43.6 bits (103), Expect = 1e-06
 Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 3/48 (6%)

Query: 149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRM 196
           E+ EC ICL+  +  D +V  PC H F   C+L +L      CP CR 
Sbjct: 1   EELECPICLDLLR--DPVVLTPCGHVFCRECILRYLKKK-SKCPICRT 45

Length = 45

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

 Score = 40.1 bits (94), Expect = 2e-05
 Identities = 19/42 (45%), Positives = 24/42 (57%), Gaps = 2/42 (4%)

Query: 153 CAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCC 194
           C ICLE  K   T+  LPC H F ++C+L WL +    CP C
Sbjct: 1   CPICLEEPKDPVTI--LPCGHLFCSKCILSWLESGNVTCPLC 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|221705 pfam12678, zf-rbx1, RING-H2 zinc finger

 Score = 38.9 bits (91), Expect = 1e-04
 Identities = 21/58 (36%), Positives = 24/58 (41%), Gaps = 11/58 (18%)

Query: 148 CEQEECAICLERFKV--------GD--TLVHLPCAHRFHARCLLPWLATNAHNCPCCR 195
            E + CAIC   F          GD   +V   C H FH  C+  WL T    CP CR
Sbjct: 17  IEDDVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRN-TCPLCR 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|218794 pfam05883, Baculo_RING, Baculovirus U-box/Ring-like domain

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 16/51 (31%), Positives = 19/51 (37%), Gaps = 7/51 (13%)

Query: 145 WKACEQEECAICLERFKVGDTLVHLPCA------HRFHARCLLPWLATNAH 189
           W  C  E CAICL+R    D +V +           FHA C   W      
Sbjct: 22  WPRCTVE-CAICLDRINDNDGVVAVTDGGTLNLEKMFHAECDKRWKRERKR 71

This family consists of several Baculovirus proteins of around 130 residues in length. 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. Length = 135

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

 Score = 35.2 bits (81), Expect = 0.003
 Identities = 23/64 (35%), Positives = 26/64 (40%), Gaps = 12/64 (18%)

Query: 144 SWKACEQEECAICLERFK--------VGD--TLVHLPCAHRFHARCLLPWLATNAHN--C 191
           +W     + C IC   F          GD   LV   C H FH  C+L WLAT      C
Sbjct: 15  TWDTPSDDVCGICRVSFDGTCPQCKFPGDDCPLVWGKCKHNFHMHCILKWLATETSKGLC 74

Query: 192 PCCR 195
           P CR
Sbjct: 75  PMCR 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	207
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.47
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.46
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.18
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.16
PHA02929	238	N1R/p28-like protein; Provisional	99.05
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	98.97
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	98.97
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	98.94
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.93
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.92
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.91
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.9
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.85
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.83
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.77
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.74
PF14634	44	zf-RING_5: zinc-RING finger domain	98.67
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.67
PHA02926	242	zinc finger-like protein; Provisional	98.66
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.64
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.63
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.54
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.46
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.44
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.41
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.37
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.32
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.22
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.15
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.15
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.14
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.13
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.13
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.12
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.11
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.05
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.05
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.04
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.04
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.89
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.85
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.85
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.72
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.68
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.6
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.44
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.39
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.36
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.33
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.22
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.21
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.17
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.16
KOG2660	331	consensus Locus-specific chromosome binding protei	97.05
KOG0297	391	consensus TNF receptor-associated factor [Signal t	96.94
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.94
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.87
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	96.75
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.61
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.39
COG5152	259	Uncharacterized conserved protein, contains RING a	96.38
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	96.15
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.05
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.93
COG5222	427	Uncharacterized conserved protein, contains RING Z	95.89
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	95.81
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.77
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	95.7
KOG1002	791	consensus Nucleotide excision repair protein RAD16	95.61
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	95.56
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	95.54
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	95.32
PHA02862	156	5L protein; Provisional	95.24
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.15
PHA02825	162	LAP/PHD finger-like protein; Provisional	94.92
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	94.7
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	94.53
COG5175	480	MOT2 Transcriptional repressor [Transcription]	94.5
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	94.47
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	94.2
PF04641	260	Rtf2: Rtf2 RING-finger	94.2
KOG3039	303	consensus Uncharacterized conserved protein [Funct	94.11
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	94.01
COG5236	493	Uncharacterized conserved protein, contains RING Z	93.95
PHA03096	284	p28-like protein; Provisional	93.84
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	93.5
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	93.2
KOG1001	674	consensus Helicase-like transcription factor HLTF/	92.66
KOG1940	276	consensus Zn-finger protein [General function pred	92.63
KOG3002	299	consensus Zn finger protein [General function pred	92.61
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	92.4
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	92.32
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	92.11
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	91.01
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	90.11
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	90.04
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	89.45
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	89.18
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	88.0
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	87.86
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	87.56
KOG3053	293	consensus Uncharacterized conserved protein [Funct	86.63
KOG0298	1394	consensus DEAD box-containing helicase-like transc	86.55
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	86.36
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	85.09
KOG1609	323	consensus Protein involved in mRNA turnover and st	84.84
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	84.68
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	83.33
COG5109	396	Uncharacterized conserved protein, contains RING Z	83.2
KOG3899	381	consensus Uncharacterized conserved protein [Funct	80.61
KOG3842	429	consensus Adaptor protein Pellino [Signal transduc	80.01

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

Probab=99.47  E-value=3.6e-14  Score=126.11  Aligned_cols=73  Identities=34%  Similarity=0.796  Sum_probs=58.7

Q ss_pred             hhhccccceeecccCCCCcccccccccccccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccC
Q 028584          118 NKSTVLHTQVFGSKKSGSKRFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQ  197 (207)
Q Consensus       118 ~~~~~l~~~~~~~k~~~~~~~~~~~~~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~  197 (207)
                      +.++++|..+|.......             ....|+||+|+|..+++++.|||.|.||..||++||......||+|+.+
T Consensus       210 ~~l~~~p~~~f~~~~~~~-------------~~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~d  276 (348)
T KOG4628|consen  210 RLLKKLPVRTFTKGDDED-------------ATDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRD  276 (348)
T ss_pred             HHHhhCCcEEeccccccC-------------CCceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCc
Confidence            346677777776654332             1258999999999999999999999999999999999886469999998


Q ss_pred             ccCCCC
Q 028584          198 ILDPAA  203 (207)
Q Consensus       198 l~~~~~  203 (207)
                      +.....
T Consensus       277 i~~~~~  282 (348)
T KOG4628|consen  277 IRTDSG  282 (348)
T ss_pred             CCCCCC
Confidence            865443

>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=99.46  E-value=2.6e-14  Score=91.11  Aligned_cols=43  Identities=53%  Similarity=1.302  Sum_probs=39.7

Q ss_pred             cccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcc
Q 028584          152 ECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCR  195 (207)
Q Consensus       152 ~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR  195 (207)
                      +|+||++.|..++.++.++|+|.||..||..|++.+. +||+||
T Consensus         2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~-~CP~CR   44 (44)
T PF13639_consen    2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNN-SCPVCR   44 (44)
T ss_dssp             CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSS-B-TTTH
T ss_pred             CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCC-cCCccC
Confidence            5999999998888999999999999999999999987 999997

...

>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=99.18  E-value=1.6e-11  Score=86.73  Aligned_cols=45  Identities=42%  Similarity=0.985  Sum_probs=35.7

Q ss_pred             cccccccccccccC----------CeeEEcCCCCcccHHhHHHHHhcCCCCCCCcc
Q 028584          150 QEECAICLERFKVG----------DTLVHLPCAHRFHARCLLPWLATNAHNCPCCR  195 (207)
Q Consensus       150 ~~~C~ICle~~~~~----------~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR  195 (207)
                      ++.|+||++.|...          ..+...+|+|.||..||.+|++.+. +||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~-~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNN-TCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSS-B-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCC-cCCCCC
Confidence            34499999999432          2455568999999999999999988 999997

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=99.16  E-value=2.1e-11  Score=105.86  Aligned_cols=55  Identities=45%  Similarity=0.950  Sum_probs=47.9

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      .....+|+||++.|..++.++.|||.|.||..|+++|+......||+||.+++++
T Consensus       320 a~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPPp  374 (374)
T COG5540         320 ADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPPP  374 (374)
T ss_pred             cCCCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCCC
Confidence            3456789999999999999999999999999999999984444899999998753

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.05  E-value=1.4e-10  Score=98.92  Aligned_cols=52  Identities=29%  Similarity=0.737  Sum_probs=41.8

Q ss_pred             cccccccccccccccCCe-----eEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVGDT-----LVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~-----~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ..+.+|+||++.+..++.     .+.++|+|.||..||.+|+.... +||+||..+..
T Consensus       172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~-tCPlCR~~~~~  228 (238)
T PHA02929        172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKN-TCPVCRTPFIS  228 (238)
T ss_pred             CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCC-CCCCCCCEeeE
Confidence            346789999999875431     23456999999999999999877 99999988753

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

Probab=98.97  E-value=3.7e-10  Score=97.58  Aligned_cols=50  Identities=32%  Similarity=0.776  Sum_probs=43.7

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      .....|.+|++...++   ..+||||+||+.||..|..... .||+||..+.+.
T Consensus       237 ~a~~kC~LCLe~~~~p---SaTpCGHiFCWsCI~~w~~ek~-eCPlCR~~~~ps  286 (293)
T KOG0317|consen  237 EATRKCSLCLENRSNP---SATPCGHIFCWSCILEWCSEKA-ECPLCREKFQPS  286 (293)
T ss_pred             CCCCceEEEecCCCCC---CcCcCcchHHHHHHHHHHcccc-CCCcccccCCCc
Confidence            4557899999998765   7889999999999999999887 899999988654

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

Probab=98.97  E-value=3.6e-10  Score=100.61  Aligned_cols=52  Identities=35%  Similarity=0.897  Sum_probs=43.9

Q ss_pred             ccccccccccccc-cccC---------CeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          147 ACEQEECAICLER-FKVG---------DTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       147 ~~~~~~C~ICle~-~~~~---------~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      .+++..|.||+++ |..+         .++..|||||.||..|++.|++.++ +||+||.++.
T Consensus       284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQ-TCPICr~p~i  345 (491)
T COG5243         284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQ-TCPICRRPVI  345 (491)
T ss_pred             cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhcc-CCCcccCccc
Confidence            3567889999999 4443         2467899999999999999999998 9999999964

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=98.94  E-value=6.5e-10  Score=91.70  Aligned_cols=51  Identities=25%  Similarity=0.696  Sum_probs=41.0

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcC---------------CCCCCCcccCccC
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATN---------------AHNCPCCRMQILD  200 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~---------------~~~CP~CR~~l~~  200 (207)
                      ..++.+|+||++.+.++   +.++|+|.||+.||..|+...               ...||+||..+..
T Consensus        15 ~~~~~~CpICld~~~dP---VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~   80 (193)
T PLN03208         15 SGGDFDCNICLDQVRDP---VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE   80 (193)
T ss_pred             CCCccCCccCCCcCCCc---EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence            34567899999998755   778899999999999998531               1379999998753

>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=98.93  E-value=5.3e-10  Score=72.98  Aligned_cols=46  Identities=41%  Similarity=0.881  Sum_probs=38.4

Q ss_pred             cccccccccccccCCeeEEcCCCCc-ccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          150 QEECAICLERFKVGDTLVHLPCAHR-FHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       150 ~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      +..|.||++...   .++.+||+|. ||..|+..|+.... .||+||.+|.
T Consensus         2 ~~~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~~-~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPR---DVVLLPCGHLCFCEECAERLLKRKK-KCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBS---SEEEETTCEEEEEHHHHHHHHHTTS-BBTTTTBB-S
T ss_pred             cCCCccCCccCC---ceEEeCCCChHHHHHHhHHhcccCC-CCCcCChhhc
Confidence            467999999865   4688899999 99999999999776 9999999874

...

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

Probab=98.92  E-value=7.9e-10  Score=69.95  Aligned_cols=39  Identities=44%  Similarity=0.958  Sum_probs=30.8

Q ss_pred             ccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCC---CCCCc
Q 028584          153 CAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAH---NCPCC  194 (207)
Q Consensus       153 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~---~CP~C  194 (207)
                      |+||++.|.++   +.|+|||.||..||..|++....   .||.|
T Consensus         1 CpiC~~~~~~P---v~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDP---VSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSE---EE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCc---cccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999866   89999999999999999986542   69987

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

Probab=98.91  E-value=1.1e-09  Score=67.99  Aligned_cols=39  Identities=38%  Similarity=1.058  Sum_probs=32.8

Q ss_pred             ccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCc
Q 028584          153 CAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCC  194 (207)
Q Consensus       153 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~C  194 (207)
                      |+||++.+.+  .++.++|||.||..|+..|++.+. .||+|
T Consensus         1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~~~-~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEKNP-KCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHCTS-B-TTT
T ss_pred             CCCCCCcccC--cCEECCCCCchhHHHHHHHHHCcC-CCcCC
Confidence            8999999874  557889999999999999999965 99998

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

Probab=98.90  E-value=1.6e-09  Score=67.28  Aligned_cols=45  Identities=47%  Similarity=1.146  Sum_probs=36.3

Q ss_pred             cccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCc
Q 028584          152 ECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI  198 (207)
Q Consensus       152 ~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l  198 (207)
                      .|+||++.+.  +.....+|+|.||..|+..|+......||.|+..+
T Consensus         1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhh--CceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            4999999983  34455569999999999999997333899998754

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

Probab=98.85  E-value=2.4e-09  Score=77.39  Aligned_cols=59  Identities=36%  Similarity=0.814  Sum_probs=45.0

Q ss_pred             cccccccccccccccccccccC---------C-eeEEcCCCCcccHHhHHHHHhcC--CCCCCCcccCccC
Q 028584          142 KLSWKACEQEECAICLERFKVG---------D-TLVHLPCAHRFHARCLLPWLATN--AHNCPCCRMQILD  200 (207)
Q Consensus       142 ~~~~~~~~~~~C~ICle~~~~~---------~-~~~~lpC~H~Fh~~Ci~~wl~~~--~~~CP~CR~~l~~  200 (207)
                      .+.|+..+++.|.||...|...         + .++.-.|+|.||..||.+|+...  +..||+||+++.-
T Consensus        13 ~W~Wd~~~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~   83 (85)
T PF12861_consen   13 TWKWDVANDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF   83 (85)
T ss_pred             EEEEecCCCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence            3456666788999999998741         2 23344599999999999999964  2489999998753

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

Probab=98.83  E-value=2.2e-09  Score=90.24  Aligned_cols=51  Identities=33%  Similarity=0.683  Sum_probs=41.9

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCC--CCCCCcccCccCC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNA--HNCPCCRMQILDP  201 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~--~~CP~CR~~l~~~  201 (207)
                      ....+|.||++.-+++   ++..|||.||+-||.+|++...  ..||+|+..|...
T Consensus        45 ~~~FdCNICLd~akdP---VvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~   97 (230)
T KOG0823|consen   45 GGFFDCNICLDLAKDP---VVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSID   97 (230)
T ss_pred             CCceeeeeeccccCCC---EEeecccceehHHHHHHHhhcCCCeeCCccccccccc
Confidence            4567899999997755   6777999999999999999654  3799999887543

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

Probab=98.77  E-value=5.3e-09  Score=84.86  Aligned_cols=50  Identities=30%  Similarity=0.687  Sum_probs=41.6

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ....|+|||+.+... .++...|||+||..||...++... .||+|+..|..
T Consensus       130 ~~~~CPiCl~~~sek-~~vsTkCGHvFC~~Cik~alk~~~-~CP~C~kkIt~  179 (187)
T KOG0320|consen  130 GTYKCPICLDSVSEK-VPVSTKCGHVFCSQCIKDALKNTN-KCPTCRKKITH  179 (187)
T ss_pred             cccCCCceecchhhc-cccccccchhHHHHHHHHHHHhCC-CCCCcccccch
Confidence            457799999999743 335578999999999999999988 99999986643

>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=98.74  E-value=9.7e-09  Score=63.95  Aligned_cols=40  Identities=45%  Similarity=1.138  Sum_probs=33.6

Q ss_pred             ccccccccccCCeeEEcCCCCcccHHhHHHHHh-cCCCCCCCc
Q 028584          153 CAICLERFKVGDTLVHLPCAHRFHARCLLPWLA-TNAHNCPCC  194 (207)
Q Consensus       153 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~-~~~~~CP~C  194 (207)
                      |+||++.+..+  ...++|+|.||..||..|+. .....||+|
T Consensus         1 C~iC~~~~~~~--~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDP--VILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSE--EEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCC--CEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            89999998744  35889999999999999999 333489988

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 ....

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.67  E-value=1.7e-08  Score=64.20  Aligned_cols=44  Identities=30%  Similarity=0.754  Sum_probs=36.6

Q ss_pred             cccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCccc
Q 028584          152 ECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRM  196 (207)
Q Consensus       152 ~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~  196 (207)
                      .|.||++.|........++|+|+||..|+..+..... .||+|+.
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~-~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSV-KCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCC-CCcCCCC
Confidence            3999999995555788889999999999999883333 8999974

>smart00504 Ubox Modified RING finger domain

Probab=98.67  E-value=2.8e-08  Score=67.15  Aligned_cols=45  Identities=27%  Similarity=0.467  Sum_probs=39.9

Q ss_pred             ccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          151 EECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       151 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ..|+||.+.+.++   +.++|||+|+..||..|+..+. +||+|+.++.
T Consensus         2 ~~Cpi~~~~~~~P---v~~~~G~v~~~~~i~~~~~~~~-~cP~~~~~~~   46 (63)
T smart00504        2 FLCPISLEVMKDP---VILPSGQTYERRAIEKWLLSHG-TDPVTGQPLT   46 (63)
T ss_pred             cCCcCCCCcCCCC---EECCCCCEEeHHHHHHHHHHCC-CCCCCcCCCC
Confidence            4599999999865   7789999999999999999865 9999998774

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

>PHA02926 zinc finger-like protein; Provisional

Probab=98.66  E-value=1.6e-08  Score=84.92  Aligned_cols=54  Identities=31%  Similarity=0.706  Sum_probs=39.4

Q ss_pred             ccccccccccccccccC-----CeeEEc-CCCCcccHHhHHHHHhcCC-----CCCCCcccCccC
Q 028584          147 ACEQEECAICLERFKVG-----DTLVHL-PCAHRFHARCLLPWLATNA-----HNCPCCRMQILD  200 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~-----~~~~~l-pC~H~Fh~~Ci~~wl~~~~-----~~CP~CR~~l~~  200 (207)
                      ...+.+|+||++..-..     .....| +|+|.||..||..|.....     ..||+||..+..
T Consensus       167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~  231 (242)
T PHA02926        167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN  231 (242)
T ss_pred             ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence            34568899999986432     112344 6999999999999998531     269999987753

>smart00184 RING Ring finger

Probab=98.64  E-value=2.9e-08  Score=59.42  Aligned_cols=39  Identities=46%  Similarity=1.161  Sum_probs=32.3

Q ss_pred             ccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCc
Q 028584          153 CAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCC  194 (207)
Q Consensus       153 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~C  194 (207)
                      |+||++...   .++.++|+|.||..|+..|+......||+|
T Consensus         1 C~iC~~~~~---~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELK---DPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCC---CcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            789998843   558889999999999999998443379987

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)

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

Probab=98.63  E-value=1.2e-08  Score=96.52  Aligned_cols=52  Identities=40%  Similarity=0.952  Sum_probs=44.6

Q ss_pred             ccccccccccccccccCCe--eEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          147 ACEQEECAICLERFKVGDT--LVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~--~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ...+..|+||++.+..+..  ...|+|+|.||..|+..|++..+ +||+||..+.
T Consensus       288 ~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~q-tCP~CR~~~~  341 (543)
T KOG0802|consen  288 ALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQ-TCPTCRTVLY  341 (543)
T ss_pred             hhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhC-cCCcchhhhh
Confidence            3457889999999987543  68899999999999999999987 9999998544

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.54  E-value=4.8e-08  Score=88.95  Aligned_cols=49  Identities=31%  Similarity=0.685  Sum_probs=42.2

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .....|+||++.|..+   +.++|+|.||..||..|+.... .||+|+..+..
T Consensus        24 e~~l~C~IC~d~~~~P---vitpCgH~FCs~CI~~~l~~~~-~CP~Cr~~~~~   72 (397)
T TIGR00599        24 DTSLRCHICKDFFDVP---VLTSCSHTFCSLCIRRCLSNQP-KCPLCRAEDQE   72 (397)
T ss_pred             ccccCCCcCchhhhCc---cCCCCCCchhHHHHHHHHhCCC-CCCCCCCcccc
Confidence            3557899999999755   6789999999999999998876 89999998764

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

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

Probab=98.46  E-value=1.1e-07  Score=67.66  Aligned_cols=51  Identities=31%  Similarity=0.654  Sum_probs=39.0

Q ss_pred             ccccccccccccc------------CCeeEEc-CCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          150 QEECAICLERFKV------------GDTLVHL-PCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       150 ~~~C~ICle~~~~------------~~~~~~l-pC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      .+.|+||...|..            ++.++.. .|.|.||.-||.+||.+++ .||+++++++..
T Consensus        20 id~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~-~CPld~q~w~~~   83 (88)
T COG5194          20 IDVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKG-VCPLDRQTWVLA   83 (88)
T ss_pred             cchhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCC-CCCCCCceeEEe
Confidence            3668888876643            1233333 4999999999999999987 999999988643

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

Probab=98.44  E-value=1.2e-07  Score=70.45  Aligned_cols=50  Identities=30%  Similarity=0.654  Sum_probs=38.9

Q ss_pred             cccccccccccccc-------------CCeeEEc-CCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          149 EQEECAICLERFKV-------------GDTLVHL-PCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       149 ~~~~C~ICle~~~~-------------~~~~~~l-pC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ..+.|+||...+-+             ++..+.. .|.|.||.-||.+||++++ .||+|..+..
T Consensus        45 ~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~-vCPLdn~eW~  108 (114)
T KOG2930|consen   45 VVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRN-VCPLDNKEWV  108 (114)
T ss_pred             eechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcC-cCCCcCccee
Confidence            56779999876532             2334444 4999999999999999998 9999987764

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

Probab=98.41  E-value=2e-07  Score=59.22  Aligned_cols=39  Identities=36%  Similarity=0.834  Sum_probs=23.0

Q ss_pred             cccccccccc-CCeeEEcCCCCcccHHhHHHHHhcC---CCCCC
Q 028584          153 CAICLERFKV-GDTLVHLPCAHRFHARCLLPWLATN---AHNCP  192 (207)
Q Consensus       153 C~ICle~~~~-~~~~~~lpC~H~Fh~~Ci~~wl~~~---~~~CP  192 (207)
                      |+||.+ |.. .+.++.|+|||+|+.+||..++..+   .+.||
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 654 3457889999999999999999865   23676

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

Probab=98.37  E-value=1.3e-07  Score=83.65  Aligned_cols=49  Identities=29%  Similarity=0.833  Sum_probs=43.2

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      .-..|.||.++|..+   +++||+|.||..||..+|..+. .||.|+.++.+.
T Consensus        22 ~lLRC~IC~eyf~ip---~itpCsHtfCSlCIR~~L~~~p-~CP~C~~~~~Es   70 (442)
T KOG0287|consen   22 DLLRCGICFEYFNIP---MITPCSHTFCSLCIRKFLSYKP-QCPTCCVTVTES   70 (442)
T ss_pred             HHHHHhHHHHHhcCc---eeccccchHHHHHHHHHhccCC-CCCceecccchh
Confidence            456799999999876   8899999999999999998887 999999887653

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

Probab=98.32  E-value=2.6e-07  Score=79.18  Aligned_cols=51  Identities=33%  Similarity=0.755  Sum_probs=41.9

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHH-HHhcCCCCCCCcccCccCCC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLP-WLATNAHNCPCCRMQILDPA  202 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~-wl~~~~~~CP~CR~~l~~~~  202 (207)
                      .+..|.||++....+   ..++|+|+||..||.. |-......||+||+.+.+..
T Consensus       214 ~d~kC~lC~e~~~~p---s~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~  265 (271)
T COG5574         214 ADYKCFLCLEEPEVP---SCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK  265 (271)
T ss_pred             cccceeeeecccCCc---ccccccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence            467899999997644   8889999999999999 86666546999999887653

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

Probab=98.22  E-value=6.8e-07  Score=82.40  Aligned_cols=54  Identities=31%  Similarity=0.829  Sum_probs=40.8

Q ss_pred             ccccccccccccccccC---C-----------eeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          147 ACEQEECAICLERFKVG---D-----------TLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~---~-----------~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ......|+||+.++.--   .           .-+..||.|+||..|+..|...-+-.||+||.++++
T Consensus       568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            34566899999886431   0           133569999999999999998543389999998864

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

Probab=98.15  E-value=1.4e-06  Score=61.28  Aligned_cols=49  Identities=24%  Similarity=0.443  Sum_probs=37.7

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      +...|+|+.+.|.++   +.+++||.|...||..|+..+..+||+|+.++..
T Consensus         3 ~~f~CpIt~~lM~dP---Vi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~   51 (73)
T PF04564_consen    3 DEFLCPITGELMRDP---VILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE   51 (73)
T ss_dssp             GGGB-TTTSSB-SSE---EEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred             cccCCcCcCcHhhCc---eeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence            456799999999866   8899999999999999999944499999887754

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 ....

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.15  E-value=1.7e-06  Score=76.25  Aligned_cols=51  Identities=18%  Similarity=0.516  Sum_probs=37.5

Q ss_pred             cccccccccc-cccCC-eeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          150 QEECAICLER-FKVGD-TLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       150 ~~~C~ICle~-~~~~~-~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      +..|+||... +.+++ .+.+.+|||.||..|+...+......||.|+.++..
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk   55 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRK   55 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence            4679999995 33333 223337999999999999876655589999987754

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).

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

Probab=98.14  E-value=9.9e-07  Score=76.77  Aligned_cols=48  Identities=29%  Similarity=0.648  Sum_probs=41.6

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .-..|-||-+.|..+   ..++|+|.||..||...|..+. .||+||.+..+
T Consensus        24 s~lrC~IC~~~i~ip---~~TtCgHtFCslCIR~hL~~qp-~CP~Cr~~~~e   71 (391)
T COG5432          24 SMLRCRICDCRISIP---CETTCGHTFCSLCIRRHLGTQP-FCPVCREDPCE   71 (391)
T ss_pred             hHHHhhhhhheeecc---eecccccchhHHHHHHHhcCCC-CCccccccHHh
Confidence            345799999999866   7889999999999999999887 99999987653

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

Probab=98.13  E-value=2.4e-06  Score=55.73  Aligned_cols=43  Identities=26%  Similarity=0.730  Sum_probs=33.0

Q ss_pred             cccccccccccCCeeEEcCCC-----CcccHHhHHHHHhcCC-CCCCCcc
Q 028584          152 ECAICLERFKVGDTLVHLPCA-----HRFHARCLLPWLATNA-HNCPCCR  195 (207)
Q Consensus       152 ~C~ICle~~~~~~~~~~lpC~-----H~Fh~~Ci~~wl~~~~-~~CP~CR  195 (207)
                      .|.||++. ..++.....||.     |.||..|+.+|+.... .+||+|+
T Consensus         1 ~CrIC~~~-~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDE-GDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCC-CCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            38999983 334456678974     7899999999997653 3899994

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

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

Probab=98.13  E-value=1.2e-06  Score=81.05  Aligned_cols=48  Identities=38%  Similarity=0.758  Sum_probs=39.0

Q ss_pred             cccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCC----CCCCCcccCccC
Q 028584          150 QEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNA----HNCPCCRMQILD  200 (207)
Q Consensus       150 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~----~~CP~CR~~l~~  200 (207)
                      +..|+||++....+   ..+.|||+||..||-.++....    ..||+|+..|..
T Consensus       186 ~~~CPICL~~~~~p---~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~  237 (513)
T KOG2164|consen  186 DMQCPICLEPPSVP---VRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL  237 (513)
T ss_pred             CCcCCcccCCCCcc---cccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence            67899999997654   5666999999999988877552    279999988765

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

Probab=98.12  E-value=1e-06  Score=73.89  Aligned_cols=45  Identities=42%  Similarity=0.876  Sum_probs=39.1

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcc
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCR  195 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR  195 (207)
                      ..+...|+||++.|..+   ..++|+|.||..|+..++. ....||.||
T Consensus        10 ~~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr   54 (386)
T KOG2177|consen   10 LQEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE-GPLSCPVCR   54 (386)
T ss_pred             ccccccChhhHHHhhcC---ccccccchHhHHHHHHhcC-CCcCCcccC
Confidence            34677899999999876   8899999999999999988 334899999

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

Probab=98.11  E-value=5.1e-07  Score=63.72  Aligned_cols=56  Identities=39%  Similarity=0.856  Sum_probs=40.9

Q ss_pred             ccccccccccccccccccccC---------CeeEEcC-CCCcccHHhHHHHHhcCC--CCCCCcccCcc
Q 028584          143 LSWKACEQEECAICLERFKVG---------DTLVHLP-CAHRFHARCLLPWLATNA--HNCPCCRMQIL  199 (207)
Q Consensus       143 ~~~~~~~~~~C~ICle~~~~~---------~~~~~lp-C~H~Fh~~Ci~~wl~~~~--~~CP~CR~~l~  199 (207)
                      +.|+..+ +.|.||.-.|...         +.+.++. |.|.||..||.+|+....  ..||+||+++.
T Consensus        14 wtW~~~~-e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   14 WTWDAPD-ETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             EEEcCCC-CccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            3444433 4899999888641         3344443 999999999999998543  38999999875

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

Probab=98.05  E-value=6.9e-07  Score=79.42  Aligned_cols=58  Identities=29%  Similarity=0.609  Sum_probs=45.9

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCCCCCCCC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAASSAD  207 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~~~~~~d  207 (207)
                      ..+..|+||+..+...  +....|.|.||..||..-+...+..||.||..+........|
T Consensus        41 ~~~v~c~icl~llk~t--mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr~D   98 (381)
T KOG0311|consen   41 DIQVICPICLSLLKKT--MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLRID   98 (381)
T ss_pred             hhhhccHHHHHHHHhh--cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCCCC
Confidence            3557799999999743  344459999999999999987777999999988776654443

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

Probab=98.05  E-value=1.5e-06  Score=85.32  Aligned_cols=50  Identities=48%  Similarity=1.068  Sum_probs=39.5

Q ss_pred             ccccccccccccccc-cCCeeEEcC------CCCcccHHhHHHHHhcCC-CCCCCcccCcc
Q 028584          147 ACEQEECAICLERFK-VGDTLVHLP------CAHRFHARCLLPWLATNA-HNCPCCRMQIL  199 (207)
Q Consensus       147 ~~~~~~C~ICle~~~-~~~~~~~lp------C~H~Fh~~Ci~~wl~~~~-~~CP~CR~~l~  199 (207)
                      .....+|+||+..+. ..   +.+|      |.|.||..|+.+|+.... .+||+||.++.
T Consensus      1466 fsG~eECaICYsvL~~vd---r~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1466 FSGHEECAICYSVLDMVD---RSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             cCCcchhhHHHHHHHHHh---ccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            357789999999876 22   2333      899999999999999654 48999998764

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

Probab=98.04  E-value=8.2e-07  Score=62.14  Aligned_cols=50  Identities=30%  Similarity=0.695  Sum_probs=23.3

Q ss_pred             cccccccccccc-cCCeeEEc----CCCCcccHHhHHHHHhcC---C-------CCCCCcccCcc
Q 028584          150 QEECAICLERFK-VGDTLVHL----PCAHRFHARCLLPWLATN---A-------HNCPCCRMQIL  199 (207)
Q Consensus       150 ~~~C~ICle~~~-~~~~~~~l----pC~H~Fh~~Ci~~wl~~~---~-------~~CP~CR~~l~  199 (207)
                      +..|.||+..+. .++.+..+    .|+..||..||..||...   .       ..||.|+.+|.
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~   66 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS   66 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence            356999999876 33222221    489999999999998842   1       15999998874

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

Probab=98.04  E-value=1e-06  Score=75.87  Aligned_cols=54  Identities=26%  Similarity=0.658  Sum_probs=42.1

Q ss_pred             cccccccccccccccCC-------eeEEcCCCCcccHHhHHHHHhcCC-CCCCCcccCccCC
Q 028584          148 CEQEECAICLERFKVGD-------TLVHLPCAHRFHARCLLPWLATNA-HNCPCCRMQILDP  201 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~-------~~~~lpC~H~Fh~~Ci~~wl~~~~-~~CP~CR~~l~~~  201 (207)
                      .++..|+||-..+....       +.-.|.|+|+||..||.-|-.-.+ ++||.|+..+...
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~  283 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLK  283 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHh
Confidence            35677999998876543       567889999999999999965332 3999998877543

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

Probab=97.89  E-value=4.1e-06  Score=76.52  Aligned_cols=50  Identities=34%  Similarity=0.905  Sum_probs=39.2

Q ss_pred             ccccccccccccccccCC-eeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          147 ACEQEECAICLERFKVGD-TLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~-~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ..+.++|+||++.+...- .++...|.|.||..|+..|...   +||+||....
T Consensus       172 ~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~~---scpvcR~~q~  222 (493)
T KOG0804|consen  172 LTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWDS---SCPVCRYCQS  222 (493)
T ss_pred             cccCCCcchhHhhcCccccceeeeecccccchHHHhhcccC---cChhhhhhcC
Confidence            457789999999987542 3345569999999999999643   8999997654

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

Probab=97.85  E-value=6.7e-06  Score=71.84  Aligned_cols=48  Identities=29%  Similarity=0.631  Sum_probs=39.8

Q ss_pred             cccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          150 QEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       150 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ..+|+||+....-   ++.|+|+|.||..||+--.......|++||.+|..
T Consensus         7 ~~eC~IC~nt~n~---Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids   54 (324)
T KOG0824|consen    7 KKECLICYNTGNC---PVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDS   54 (324)
T ss_pred             CCcceeeeccCCc---CccccccchhhhhhhcchhhcCCCCCceecCCCCc
Confidence            4679999998754   48899999999999987776665479999998864

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

Probab=97.85  E-value=9.3e-06  Score=72.41  Aligned_cols=49  Identities=35%  Similarity=0.689  Sum_probs=40.1

Q ss_pred             cccccccccccccccCCeeEEcCCCCc-ccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHR-FHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ....+|.||+.+..+   ...|||.|. .|..|.+..--..+ .||+||++|.+
T Consensus       288 ~~gkeCVIClse~rd---t~vLPCRHLCLCs~Ca~~Lr~q~n-~CPICRqpi~~  337 (349)
T KOG4265|consen  288 ESGKECVICLSESRD---TVVLPCRHLCLCSGCAKSLRYQTN-NCPICRQPIEE  337 (349)
T ss_pred             cCCCeeEEEecCCcc---eEEecchhhehhHhHHHHHHHhhc-CCCccccchHh
Confidence            346789999999764   489999997 89999988765555 89999998864

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

Probab=97.72  E-value=2e-05  Score=66.48  Aligned_cols=62  Identities=31%  Similarity=0.644  Sum_probs=48.8

Q ss_pred             cccccccccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCC-------CCCCCcccCccCCC
Q 028584          140 WSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNA-------HNCPCCRMQILDPA  202 (207)
Q Consensus       140 ~~~~~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~-------~~CP~CR~~l~~~~  202 (207)
                      +..|..+.+....|.+|-..+..++++ .|-|-|.||++|+..|...-.       ..||.|..+|+++.
T Consensus        40 YLqWL~DsDY~pNC~LC~t~La~gdt~-RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~  108 (299)
T KOG3970|consen   40 YLQWLQDSDYNPNCRLCNTPLASGDTT-RLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPI  108 (299)
T ss_pred             HHHHHhhcCCCCCCceeCCccccCcce-eehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCc
Confidence            445555677788899999999988654 556999999999999966421       27999999998764

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

Probab=97.68  E-value=1.8e-05  Score=71.28  Aligned_cols=48  Identities=31%  Similarity=0.889  Sum_probs=36.3

Q ss_pred             ccccccccccccCCeeEEcC-CCCcccHHhHHHHHhcCCC--CCCCcccCc
Q 028584          151 EECAICLERFKVGDTLVHLP-CAHRFHARCLLPWLATNAH--NCPCCRMQI  198 (207)
Q Consensus       151 ~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~wl~~~~~--~CP~CR~~l  198 (207)
                      ..|.||.+.+.+...+.-+. |||+||..|+..|+.....  .||+|+-.+
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~   55 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL   55 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence            56999965555544555554 9999999999999996542  799998433

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

Probab=97.60  E-value=1.4e-05  Score=53.09  Aligned_cols=46  Identities=33%  Similarity=0.590  Sum_probs=34.9

Q ss_pred             ccccccccccccCCeeEEcCCCCc-ccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          151 EECAICLERFKVGDTLVHLPCAHR-FHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       151 ~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      .+|.||++.-.+.   +...|+|. .|.+|-.+.++.....||+||++|.
T Consensus         8 dECTICye~pvds---VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    8 DECTICYEHPVDS---VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             cceeeeccCcchH---HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            6799999875432   44569997 8999987776633339999999874

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

Probab=97.44  E-value=6.2e-05  Score=67.60  Aligned_cols=52  Identities=31%  Similarity=0.810  Sum_probs=38.2

Q ss_pred             cccccccccccccccCC----eeEEcC-CCCcccHHhHHHHHhcCC------CCCCCcccCcc
Q 028584          148 CEQEECAICLERFKVGD----TLVHLP-CAHRFHARCLLPWLATNA------HNCPCCRMQIL  199 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~----~~~~lp-C~H~Fh~~Ci~~wl~~~~------~~CP~CR~~l~  199 (207)
                      ..+..|.||++.+....    ...+|| |.|.||..||..|-....      +.||+||....
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS  221 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence            45778999999876431    123445 999999999999974322      38999997653

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

Probab=97.39  E-value=4.3e-05  Score=74.09  Aligned_cols=53  Identities=21%  Similarity=0.399  Sum_probs=43.7

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .+....|++|+..+.+.......+|+|.||..||..|-...+ +||+||..+..
T Consensus       120 ~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aq-TCPiDR~EF~~  172 (1134)
T KOG0825|consen  120 THVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQ-TCPVDRGEFGE  172 (1134)
T ss_pred             hhhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcc-cCchhhhhhhe
Confidence            356678999999988654455567999999999999999887 99999987653

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

Probab=97.36  E-value=5.8e-05  Score=72.91  Aligned_cols=50  Identities=28%  Similarity=0.612  Sum_probs=40.8

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      .-..|++|-..+.+-   ++..|+|.||..|+.+-+......||.|...|.+.
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            446799999877643   55669999999999999997766999998887654

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

Probab=97.33  E-value=4e-05  Score=52.57  Aligned_cols=45  Identities=24%  Similarity=0.654  Sum_probs=22.6

Q ss_pred             cccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          150 QEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       150 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      -..|++|.+.+..+  +....|.|+||..||..-+.  . .||+|+.+..
T Consensus         7 lLrCs~C~~~l~~p--v~l~~CeH~fCs~Ci~~~~~--~-~CPvC~~Paw   51 (65)
T PF14835_consen    7 LLRCSICFDILKEP--VCLGGCEHIFCSSCIRDCIG--S-ECPVCHTPAW   51 (65)
T ss_dssp             TTS-SSS-S--SS---B---SSS--B-TTTGGGGTT--T-B-SSS--B-S
T ss_pred             hcCCcHHHHHhcCC--ceeccCccHHHHHHhHHhcC--C-CCCCcCChHH
Confidence            35699999999754  34456999999999977443  2 6999987653

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

Probab=97.22  E-value=0.00016  Score=66.19  Aligned_cols=51  Identities=29%  Similarity=0.666  Sum_probs=43.1

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCCC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPA  202 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~~  202 (207)
                      ..+..|.||+..|..+   +.+||||.||..||.+-+.... .||.||..+...+
T Consensus        82 ~sef~c~vc~~~l~~p---v~tpcghs~c~~Cl~r~ld~~~-~cp~Cr~~l~e~~  132 (398)
T KOG4159|consen   82 RSEFECCVCSRALYPP---VVTPCGHSFCLECLDRSLDQET-ECPLCRDELVELP  132 (398)
T ss_pred             cchhhhhhhHhhcCCC---ccccccccccHHHHHHHhccCC-CCcccccccccch
Confidence            4667899999999765   7789999999999999777665 9999999987643

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

Probab=97.21  E-value=0.00012  Score=66.37  Aligned_cols=49  Identities=33%  Similarity=0.788  Sum_probs=37.9

Q ss_pred             ccccccccccccCCeeEEcCCCCcccHHhHHHHHhcC-CCCCCCcccCccCCC
Q 028584          151 EECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATN-AHNCPCCRMQILDPA  202 (207)
Q Consensus       151 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~-~~~CP~CR~~l~~~~  202 (207)
                      ..|-||-+.=   ..+.+-||||..|..|+..|-... ..+||+||.+|...+
T Consensus       370 eLCKICaend---KdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte  419 (563)
T KOG1785|consen  370 ELCKICAEND---KDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTE  419 (563)
T ss_pred             HHHHHhhccC---CCcccccccchHHHHHHHhhcccCCCCCCCceeeEecccc
Confidence            3599998762   245666899999999999998654 349999999886543

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

Probab=97.17  E-value=0.00013  Score=63.99  Aligned_cols=52  Identities=31%  Similarity=0.659  Sum_probs=42.0

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhc------------------CC----CCCCCcccCccC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLAT------------------NA----HNCPCCRMQILD  200 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~------------------~~----~~CP~CR~~l~~  200 (207)
                      ..-.|.||+--|..++..+.++|.|.||..|+.++|..                  -.    .+||+||..|..
T Consensus       114 p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~  187 (368)
T KOG4445|consen  114 PNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI  187 (368)
T ss_pred             CCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence            34569999999999888999999999999999877542                  11    279999988763

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

Probab=97.16  E-value=0.00031  Score=63.86  Aligned_cols=47  Identities=32%  Similarity=0.909  Sum_probs=37.0

Q ss_pred             cccccccccccccC--CeeEEcCCCCcccHHhHHHHHhcCC-CCCCCccc
Q 028584          150 QEECAICLERFKVG--DTLVHLPCAHRFHARCLLPWLATNA-HNCPCCRM  196 (207)
Q Consensus       150 ~~~C~ICle~~~~~--~~~~~lpC~H~Fh~~Ci~~wl~~~~-~~CP~CR~  196 (207)
                      ..+|+||++.+...  ..++.+.|+|.|...||+.|+.+.. ..||.|..
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~   53 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSG   53 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCC
Confidence            46799999987643  3566777999999999999996332 37999965

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

Probab=97.05  E-value=0.00013  Score=64.48  Aligned_cols=52  Identities=21%  Similarity=0.537  Sum_probs=42.2

Q ss_pred             cccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          146 KACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       146 ~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      +......|.+|-.+|.+.  ..+..|-|.||+.||...|...+ .||.|...|..
T Consensus        11 ~~n~~itC~LC~GYliDA--TTI~eCLHTFCkSCivk~l~~~~-~CP~C~i~ih~   62 (331)
T KOG2660|consen   11 ELNPHITCRLCGGYLIDA--TTITECLHTFCKSCIVKYLEESK-YCPTCDIVIHK   62 (331)
T ss_pred             hcccceehhhccceeecc--hhHHHHHHHHHHHHHHHHHHHhc-cCCccceeccC
Confidence            345667899999999854  33445999999999999999977 99999876643

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

Probab=96.94  E-value=0.00046  Score=63.15  Aligned_cols=51  Identities=35%  Similarity=0.770  Sum_probs=42.4

Q ss_pred             ccccccccccccccccCCeeEE-cCCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          147 ACEQEECAICLERFKVGDTLVH-LPCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~-lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      ..++..|+||...+.++   .. ..|+|.||..|+..|+..+. .||.|+..+...
T Consensus        18 ~~~~l~C~~C~~vl~~p---~~~~~cgh~fC~~C~~~~~~~~~-~cp~~~~~~~~~   69 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDP---VQTTTCGHRFCAGCLLESLSNHQ-KCPVCRQELTQA   69 (391)
T ss_pred             CcccccCccccccccCC---CCCCCCCCcccccccchhhccCc-CCcccccccchh
Confidence            45668899999999865   33 58999999999999999965 999998877543

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

Probab=96.94  E-value=0.00032  Score=63.53  Aligned_cols=50  Identities=38%  Similarity=0.820  Sum_probs=40.6

Q ss_pred             cccccccccccccccc-CCeeEEcCCCCcccHHhHHHHHhcCC-CCCCCccc
Q 028584          147 ACEQEECAICLERFKV-GDTLVHLPCAHRFHARCLLPWLATNA-HNCPCCRM  196 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~-~~~~~~lpC~H~Fh~~Ci~~wl~~~~-~~CP~CR~  196 (207)
                      ..-+..|..|-+.+-. ++.+..|||.|+||..|+.+.|.++. .+||.||.
T Consensus       362 ~e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  362 EETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             HHHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            3456679999998754 35778899999999999999998765 38999983

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

Probab=96.87  E-value=0.0012  Score=57.21  Aligned_cols=51  Identities=22%  Similarity=0.462  Sum_probs=38.7

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcC-CCCCCCcccCcc
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATN-AHNCPCCRMQIL  199 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~-~~~CP~CR~~l~  199 (207)
                      ...+.+|++|.+.-..+  .+..+|+|+||+.||..-+... .++||.|-.++.
T Consensus       236 ~t~~~~C~~Cg~~PtiP--~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  236 GTSDTECPVCGEPPTIP--HVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             ccCCceeeccCCCCCCC--eeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            34678899999885533  3556799999999998766533 249999988776

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

Probab=96.75  E-value=0.0011  Score=44.55  Aligned_cols=43  Identities=26%  Similarity=0.634  Sum_probs=28.6

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCC-CCCCC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNA-HNCPC  193 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~-~~CP~  193 (207)
                      ....|+|.+..|.+  .++...|+|.|-+..|..|+..+. ..||+
T Consensus        10 ~~~~CPiT~~~~~~--PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFED--PVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SS--EEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhhC--CcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            34679999999984  466668999999999999994332 37998

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

Probab=96.61  E-value=0.0011  Score=59.49  Aligned_cols=49  Identities=27%  Similarity=0.600  Sum_probs=41.7

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ..++..|+||+-.-.   ..+..||+|.-|+.||.+.+.+.+ .|-+|+..+.
T Consensus       419 ~sEd~lCpICyA~pi---~Avf~PC~H~SC~~CI~qHlmN~k-~CFfCktTv~  467 (489)
T KOG4692|consen  419 DSEDNLCPICYAGPI---NAVFAPCSHRSCYGCITQHLMNCK-RCFFCKTTVI  467 (489)
T ss_pred             CcccccCcceecccc---hhhccCCCCchHHHHHHHHHhcCC-eeeEecceee
Confidence            357888999997643   347889999999999999999987 9999998776

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

Probab=96.39  E-value=0.0014  Score=42.58  Aligned_cols=45  Identities=24%  Similarity=0.591  Sum_probs=22.2

Q ss_pred             ccccccccccCCeeEEcC--CCCcccHHhHHHHHhcCCCCCCCcccCc
Q 028584          153 CAICLERFKVGDTLVHLP--CAHRFHARCLLPWLATNAHNCPCCRMQI  198 (207)
Q Consensus       153 C~ICle~~~~~~~~~~lp--C~H~Fh~~Ci~~wl~~~~~~CP~CR~~l  198 (207)
                      |++|.+++... ....+|  |++.+|..|+...+......||-||.+.
T Consensus         1 cp~C~e~~d~~-d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDET-DKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CC-CTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccC-CCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            78999988432 223445  8999999999998864334999999764

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

Probab=96.38  E-value=0.0012  Score=54.97  Aligned_cols=44  Identities=23%  Similarity=0.554  Sum_probs=37.8

Q ss_pred             ccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCc
Q 028584          151 EECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI  198 (207)
Q Consensus       151 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l  198 (207)
                      ..|.||-++|..+   +...|||.||..|...-++... .|-+|....
T Consensus       197 F~C~iCKkdy~sp---vvt~CGH~FC~~Cai~~y~kg~-~C~~Cgk~t  240 (259)
T COG5152         197 FLCGICKKDYESP---VVTECGHSFCSLCAIRKYQKGD-ECGVCGKAT  240 (259)
T ss_pred             eeehhchhhccch---hhhhcchhHHHHHHHHHhccCC-cceecchhh
Confidence            3799999999866   7888999999999988888876 999997644

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

Probab=96.15  E-value=0.0038  Score=64.49  Aligned_cols=53  Identities=26%  Similarity=0.607  Sum_probs=41.5

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCC--------C-CCCCcccCcc
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNA--------H-NCPCCRMQIL  199 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~--------~-~CP~CR~~l~  199 (207)
                      .+.++.|.||+.+--.....+.|.|+|+||..|....|++.=        + .||+|..+|.
T Consensus      3483 QD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             cccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            456778999998755555778999999999999988776531        1 7999988763

>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=96.05  E-value=0.0026  Score=46.88  Aligned_cols=34  Identities=26%  Similarity=0.694  Sum_probs=28.7

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHH
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLL  181 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~  181 (207)
                      ..+...|++|...|.+ ......||+|.||..|+.
T Consensus        75 i~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   75 ITESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             ECCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence            3466779999999986 477888999999999975

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 [].

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

Probab=95.93  E-value=0.0097  Score=53.45  Aligned_cols=47  Identities=32%  Similarity=0.659  Sum_probs=34.5

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ......|.||++...+   .+.+||||.-|  |..-- +... .||+||..|..
T Consensus       302 ~~~p~lcVVcl~e~~~---~~fvpcGh~cc--ct~cs-~~l~-~CPvCR~rI~~  348 (355)
T KOG1571|consen  302 LPQPDLCVVCLDEPKS---AVFVPCGHVCC--CTLCS-KHLP-QCPVCRQRIRL  348 (355)
T ss_pred             cCCCCceEEecCCccc---eeeecCCcEEE--chHHH-hhCC-CCchhHHHHHH
Confidence            4466779999998764   58999999876  65432 2333 79999987754

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

Probab=95.89  E-value=0.0053  Score=54.11  Aligned_cols=43  Identities=26%  Similarity=0.681  Sum_probs=36.1

Q ss_pred             ccccccccccccCCeeEEcC-CCCcccHHhHHHHHhcCCCCCCCccc
Q 028584          151 EECAICLERFKVGDTLVHLP-CAHRFHARCLLPWLATNAHNCPCCRM  196 (207)
Q Consensus       151 ~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~wl~~~~~~CP~CR~  196 (207)
                      ..|+.|-..+.++   ..++ |+|.||..||..-|....+.||.|..
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            6799999999865   5556 89999999999887766679999954

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

Probab=95.81  E-value=0.0049  Score=39.67  Aligned_cols=41  Identities=32%  Similarity=0.807  Sum_probs=27.2

Q ss_pred             ccccccccccCCeeEEcCCC--C---cccHHhHHHHHhcCC-CCCCCc
Q 028584          153 CAICLERFKVGDTLVHLPCA--H---RFHARCLLPWLATNA-HNCPCC  194 (207)
Q Consensus       153 C~ICle~~~~~~~~~~lpC~--H---~Fh~~Ci~~wl~~~~-~~CP~C  194 (207)
                      |-||++.-...+ ....||.  -   ..|..|+..|+.... ..|++|
T Consensus         1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            678998866543 4567763  3   689999999998543 379887

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

Probab=95.77  E-value=0.0071  Score=55.23  Aligned_cols=48  Identities=27%  Similarity=0.613  Sum_probs=38.0

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCC-------CCCCCccc
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNA-------HNCPCCRM  196 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~-------~~CP~CR~  196 (207)
                      ....|.||++...-....+.+||+|+||..|+..++....       -.||-+..
T Consensus       183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             hcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            4567999999987557889999999999999999877432       16876643

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

Probab=95.70  E-value=0.0041  Score=54.55  Aligned_cols=45  Identities=29%  Similarity=0.509  Sum_probs=38.8

Q ss_pred             ccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          151 EECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       151 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ..|-||.++|..+   ++..|+|.||..|...-++... .|++|...+-
T Consensus       242 f~c~icr~~f~~p---Vvt~c~h~fc~~ca~~~~qk~~-~c~vC~~~t~  286 (313)
T KOG1813|consen  242 FKCFICRKYFYRP---VVTKCGHYFCEVCALKPYQKGE-KCYVCSQQTH  286 (313)
T ss_pred             ccccccccccccc---hhhcCCceeehhhhccccccCC-cceecccccc
Confidence            3599999999876   8888999999999988888876 9999987654

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

Probab=95.61  E-value=0.0055  Score=57.68  Aligned_cols=51  Identities=22%  Similarity=0.638  Sum_probs=39.1

Q ss_pred             cccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhc----CCCCCCCcccCcc
Q 028584          146 KACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLAT----NAHNCPCCRMQIL  199 (207)
Q Consensus       146 ~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~----~~~~CP~CR~~l~  199 (207)
                      +..++..|.+|-+.-++.   +...|.|.||..|+.+++..    .+.+||.|.-.+.
T Consensus       532 enk~~~~C~lc~d~aed~---i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls  586 (791)
T KOG1002|consen  532 ENKGEVECGLCHDPAEDY---IESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS  586 (791)
T ss_pred             cccCceeecccCChhhhh---HhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence            455778899999886543   67789999999999888663    2248999976653

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

Probab=95.56  E-value=0.0063  Score=59.90  Aligned_cols=50  Identities=32%  Similarity=0.783  Sum_probs=36.9

Q ss_pred             ccccccccccccccccCCeeEE-cCCCCcccHHhHHHHHhcCCC------CCCCccc
Q 028584          147 ACEQEECAICLERFKVGDTLVH-LPCAHRFHARCLLPWLATNAH------NCPCCRM  196 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~-lpC~H~Fh~~Ci~~wl~~~~~------~CP~CR~  196 (207)
                      .....+|.||++.+.....+-. -.|.|+||..||..|..+...      .||.|+.
T Consensus       188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs  244 (950)
T KOG1952|consen  188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS  244 (950)
T ss_pred             hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence            4567789999999875432211 238999999999999875321      6999984

>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=95.54  E-value=0.0072  Score=47.36  Aligned_cols=37  Identities=30%  Similarity=0.594  Sum_probs=30.3

Q ss_pred             cccccccccccccCCeeEEcCCC------CcccHHhHHHHHhc
Q 028584          150 QEECAICLERFKVGDTLVHLPCA------HRFHARCLLPWLAT  186 (207)
Q Consensus       150 ~~~C~ICle~~~~~~~~~~lpC~------H~Fh~~Ci~~wl~~  186 (207)
                      ..+|.||++.+.+++.++.++|+      |.||..|+.+|-..
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~   68 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRE   68 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhh
Confidence            46799999999885678888875      66999999999443

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.

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

Probab=95.32  E-value=0.005  Score=49.75  Aligned_cols=29  Identities=45%  Similarity=1.044  Sum_probs=26.6

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccH
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHA  177 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~  177 (207)
                      +.-+|.||+|++..++++..|||-.+||+
T Consensus       176 dkGECvICLEdL~~GdtIARLPCLCIYHK  204 (205)
T KOG0801|consen  176 DKGECVICLEDLEAGDTIARLPCLCIYHK  204 (205)
T ss_pred             cCCcEEEEhhhccCCCceeccceEEEeec
Confidence            45679999999999999999999999996

>PHA02862 5L protein; Provisional

Probab=95.24  E-value=0.016  Score=46.02  Aligned_cols=45  Identities=20%  Similarity=0.583  Sum_probs=33.6

Q ss_pred             ccccccccccccCCeeEEcCCC-----CcccHHhHHHHHhcCC-CCCCCcccCcc
Q 028584          151 EECAICLERFKVGDTLVHLPCA-----HRFHARCLLPWLATNA-HNCPCCRMQIL  199 (207)
Q Consensus       151 ~~C~ICle~~~~~~~~~~lpC~-----H~Fh~~Ci~~wl~~~~-~~CP~CR~~l~  199 (207)
                      +.|-||.+.-.+.    .-||.     ...|..|+.+|+.... ..|++|+.+..
T Consensus         3 diCWIC~~~~~e~----~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~   53 (156)
T PHA02862          3 DICWICNDVCDER----NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN   53 (156)
T ss_pred             CEEEEecCcCCCC----cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence            5699999984322    35764     3599999999998554 38999998764

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

Probab=95.15  E-value=0.012  Score=51.30  Aligned_cols=48  Identities=31%  Similarity=0.636  Sum_probs=39.4

Q ss_pred             ccccccccccccCC---eeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCc
Q 028584          151 EECAICLERFKVGD---TLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI  198 (207)
Q Consensus       151 ~~C~ICle~~~~~~---~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l  198 (207)
                      ..|-||-++|...+   .+..|.|+|.||..|+...+....-.||+||...
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            46999999998763   4566779999999999888776655899999874

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=94.92  E-value=0.023  Score=45.73  Aligned_cols=48  Identities=27%  Similarity=0.606  Sum_probs=35.3

Q ss_pred             cccccccccccccccCCeeEEcCCCC-----cccHHhHHHHHhcCC-CCCCCcccCcc
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAH-----RFHARCLLPWLATNA-HNCPCCRMQIL  199 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H-----~Fh~~Ci~~wl~~~~-~~CP~CR~~l~  199 (207)
                      ..+..|-||.+.-.+    ...||..     ..|..|+.+|+.... ..|++|..+..
T Consensus         6 ~~~~~CRIC~~~~~~----~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~   59 (162)
T PHA02825          6 LMDKCCWICKDEYDV----VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN   59 (162)
T ss_pred             CCCCeeEecCCCCCC----ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence            456779999987431    2357644     469999999998654 38999998764

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

Probab=94.70  E-value=0.0054  Score=53.81  Aligned_cols=42  Identities=33%  Similarity=0.751  Sum_probs=32.9

Q ss_pred             cccccccccccccCCeeEEcCCCCc-ccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          150 QEECAICLERFKVGDTLVHLPCAHR-FHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       150 ~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ...|.||++.-.   ..+.|+|||. -|..|-+..    + .||+||+-|+
T Consensus       300 ~~LC~ICmDaP~---DCvfLeCGHmVtCt~CGkrm----~-eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPR---DCVFLECGHMVTCTKCGKRM----N-ECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCc---ceEEeecCcEEeehhhcccc----c-cCchHHHHHH
Confidence            677999998754   5589999995 688887654    2 7999998664

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

Probab=94.53  E-value=0.026  Score=50.32  Aligned_cols=46  Identities=20%  Similarity=0.507  Sum_probs=35.9

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcc
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCR  195 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR  195 (207)
                      ..+...|+||+....++ .+ ...-|-+||+.|+...+.+.+ .||+=.
T Consensus       297 ~~~~~~CpvClk~r~Np-tv-l~vSGyVfCY~Ci~~Yv~~~~-~CPVT~  342 (357)
T KOG0826|consen  297 PPDREVCPVCLKKRQNP-TV-LEVSGYVFCYPCIFSYVVNYG-HCPVTG  342 (357)
T ss_pred             CCccccChhHHhccCCC-ce-EEecceEEeHHHHHHHHHhcC-CCCccC
Confidence            44667899999998765 22 223699999999999999887 999743

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=94.50  E-value=0.025  Score=50.80  Aligned_cols=53  Identities=23%  Similarity=0.521  Sum_probs=38.6

Q ss_pred             ccccccccccccccccCCee-EEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          147 ACEQEECAICLERFKVGDTL-VHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~-~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      .++++.|++|++.+...++- .--|||...|..|+...-+.-+..||-||....
T Consensus        11 edeed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~   64 (480)
T COG5175          11 EDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYD   64 (480)
T ss_pred             ccccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcc
Confidence            34556699999988765432 234689999999988776654459999997654

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=94.47  E-value=0.024  Score=37.70  Aligned_cols=44  Identities=23%  Similarity=0.427  Sum_probs=31.4

Q ss_pred             ccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          151 EECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       151 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ..|..|...-.   +-+.+||+|..+..|..-+  .-+ -||+|..++..
T Consensus         8 ~~~~~~~~~~~---~~~~~pCgH~I~~~~f~~~--rYn-gCPfC~~~~~~   51 (55)
T PF14447_consen    8 QPCVFCGFVGT---KGTVLPCGHLICDNCFPGE--RYN-GCPFCGTPFEF   51 (55)
T ss_pred             eeEEEcccccc---ccccccccceeeccccChh--hcc-CCCCCCCcccC
Confidence            44666655533   3478899999999998664  233 79999988754

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

Probab=94.20  E-value=0.032  Score=45.86  Aligned_cols=34  Identities=32%  Similarity=0.770  Sum_probs=26.2

Q ss_pred             EcCCCCcccHHhHHHHHhcC-----C-----CCCCCcccCccCC
Q 028584          168 HLPCAHRFHARCLLPWLATN-----A-----HNCPCCRMQILDP  201 (207)
Q Consensus       168 ~lpC~H~Fh~~Ci~~wl~~~-----~-----~~CP~CR~~l~~~  201 (207)
                      ...|+.-||.-|+..||..-     +     ..||+|..++..+
T Consensus       187 N~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK  230 (234)
T KOG3268|consen  187 NIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK  230 (234)
T ss_pred             ccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence            34599999999999998741     1     1699999887543

>PF04641 Rtf2: Rtf2 RING-finger

Probab=94.20  E-value=0.051  Score=47.03  Aligned_cols=50  Identities=20%  Similarity=0.414  Sum_probs=38.0

Q ss_pred             cccccccccccccccCCeeE-EcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          148 CEQEECAICLERFKVGDTLV-HLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~-~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      .....|||....|......+ ..||||+|...+|...- ... .||+|-.++.
T Consensus       111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~-~Cp~c~~~f~  161 (260)
T PF04641_consen  111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSK-KCPVCGKPFT  161 (260)
T ss_pred             CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccc-cccccCCccc
Confidence            45678999999995443444 45899999999999973 233 8999988765

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.11  E-value=0.05  Score=46.85  Aligned_cols=51  Identities=14%  Similarity=0.274  Sum_probs=42.2

Q ss_pred             ccccccccccccccCCeeEEc-CCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          149 EQEECAICLERFKVGDTLVHL-PCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ....|+||.+.+.+.-....| ||+|+|+..|.+..+.... .||+|-.++.+
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~-v~pv~d~plkd  271 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDM-VDPVTDKPLKD  271 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccc-cccCCCCcCcc
Confidence            556899999999876555555 6999999999999988877 99999876654

>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO)

Probab=94.01  E-value=0.024  Score=35.81  Aligned_cols=42  Identities=26%  Similarity=0.735  Sum_probs=23.0

Q ss_pred             ccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCC-CCCCc
Q 028584          153 CAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAH-NCPCC  194 (207)
Q Consensus       153 C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~-~CP~C  194 (207)
                      |.+|-+....+..-....|+-.+|..|+..++..... .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            6778887766632222248889999999999886653 59987

; PDB: 3NW0_A 2CT0_A.

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

Probab=93.95  E-value=0.059  Score=48.55  Aligned_cols=48  Identities=27%  Similarity=0.616  Sum_probs=36.9

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHH--HhcCCCCCCCcccCcc
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPW--LATNAHNCPCCRMQIL  199 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~w--l~~~~~~CP~CR~~l~  199 (207)
                      .+...|-||-+.+.   -...+||+|..|..|..+.  |.... .||+||.+..
T Consensus        59 Een~~C~ICA~~~T---Ys~~~PC~H~~CH~Ca~RlRALY~~K-~C~~CrTE~e  108 (493)
T COG5236          59 EENMNCQICAGSTT---YSARYPCGHQICHACAVRLRALYMQK-GCPLCRTETE  108 (493)
T ss_pred             cccceeEEecCCce---EEEeccCCchHHHHHHHHHHHHHhcc-CCCccccccc
Confidence            45567999998764   4578899999999998654  44444 8999998653

>PHA03096 p28-like protein; Provisional

Probab=93.84  E-value=0.033  Score=49.04  Aligned_cols=45  Identities=29%  Similarity=0.538  Sum_probs=31.0

Q ss_pred             ccccccccccccCC----eeEEcC-CCCcccHHhHHHHHhcCC--CCCCCcc
Q 028584          151 EECAICLERFKVGD----TLVHLP-CAHRFHARCLLPWLATNA--HNCPCCR  195 (207)
Q Consensus       151 ~~C~ICle~~~~~~----~~~~lp-C~H~Fh~~Ci~~wl~~~~--~~CP~CR  195 (207)
                      ..|.||++......    .-..|+ |.|.||..|+..|-....  .+||.|+
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~  230 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENR  230 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCcccc
Confidence            56999999765421    223455 999999999999976443  1444443

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

Probab=93.50  E-value=0.067  Score=52.95  Aligned_cols=42  Identities=29%  Similarity=0.843  Sum_probs=32.7

Q ss_pred             ccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCc
Q 028584          151 EECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI  198 (207)
Q Consensus       151 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l  198 (207)
                      ..|.+|--.+..+  .++..|+|.||..|+.   .+. ..||.|+.++
T Consensus       841 skCs~C~~~LdlP--~VhF~CgHsyHqhC~e---~~~-~~CP~C~~e~  882 (933)
T KOG2114|consen  841 SKCSACEGTLDLP--FVHFLCGHSYHQHCLE---DKE-DKCPKCLPEL  882 (933)
T ss_pred             eeecccCCccccc--eeeeecccHHHHHhhc---cCc-ccCCccchhh
Confidence            4599999888744  5677799999999998   233 4899998643

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

Probab=93.20  E-value=0.066  Score=48.78  Aligned_cols=51  Identities=20%  Similarity=0.362  Sum_probs=42.4

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCC--CCCCCcccCcc
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNA--HNCPCCRMQIL  199 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~--~~CP~CR~~l~  199 (207)
                      ....|||=-+.-.+.+.++.|.|||+...+-|.+......  +.||+|-.+..
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~~  385 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQL  385 (394)
T ss_pred             ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcccC
Confidence            3457999888877778899999999999999999888776  68999965543

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

Probab=92.66  E-value=0.045  Score=53.50  Aligned_cols=46  Identities=28%  Similarity=0.725  Sum_probs=37.2

Q ss_pred             ccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCC-CCCCcccCccC
Q 028584          151 EECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAH-NCPCCRMQILD  200 (207)
Q Consensus       151 ~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~-~CP~CR~~l~~  200 (207)
                      ..|.||++ .   +..+..+|+|.||..|+..-+..... .||.||..+..
T Consensus       455 ~~c~ic~~-~---~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~  501 (674)
T KOG1001|consen  455 HWCHICCD-L---DSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKE  501 (674)
T ss_pred             cccccccc-c---ccceeecccchHHHHHHHhccccccCCCCcHHHHHHHH
Confidence            78999999 2   45678889999999999988875543 59999976643

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

Probab=92.63  E-value=0.063  Score=47.00  Aligned_cols=47  Identities=28%  Similarity=0.623  Sum_probs=37.9

Q ss_pred             ccccccccccccccCC-eeEEcCCCCcccHHhHHHHHhcCCCCCCCccc
Q 028584          149 EQEECAICLERFKVGD-TLVHLPCAHRFHARCLLPWLATNAHNCPCCRM  196 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~-~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~  196 (207)
                      ....|+||.+.+.... .+..++|+|..|..|+......+ -+||+|..
T Consensus       157 ~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~  204 (276)
T KOG1940|consen  157 SEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK  204 (276)
T ss_pred             ccCCCchhHHHhccccccCCccCcccchHHHHHHHHhccC-CCCCcccc
Confidence            3445999999876543 55678899999999999988877 49999987

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

Probab=92.61  E-value=0.07  Score=47.29  Aligned_cols=44  Identities=23%  Similarity=0.645  Sum_probs=33.6

Q ss_pred             cccccccccccccccCCeeEEcCC--CCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          148 CEQEECAICLERFKVGDTLVHLPC--AHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC--~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      .+-.+|+||.+.+..+    +..|  ||..|..|-.+   ..+ .||.||.++.
T Consensus        46 ~~lleCPvC~~~l~~P----i~QC~nGHlaCssC~~~---~~~-~CP~Cr~~~g   91 (299)
T KOG3002|consen   46 LDLLDCPVCFNPLSPP----IFQCDNGHLACSSCRTK---VSN-KCPTCRLPIG   91 (299)
T ss_pred             hhhccCchhhccCccc----ceecCCCcEehhhhhhh---hcc-cCCccccccc
Confidence            3557799999999765    3346  79999999754   344 8999998875

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

Probab=92.40  E-value=0.13  Score=40.39  Aligned_cols=51  Identities=24%  Similarity=0.486  Sum_probs=38.5

Q ss_pred             ccccccccccccccCCeeEEc-C---CCCcccHHhHHHHHhcCC--CCCCCcccCccCCC
Q 028584          149 EQEECAICLERFKVGDTLVHL-P---CAHRFHARCLLPWLATNA--HNCPCCRMQILDPA  202 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~l-p---C~H~Fh~~Ci~~wl~~~~--~~CP~CR~~l~~~~  202 (207)
                      .-.+|.||.+...+.   ..| |   ||-..|..|....++..+  ++||.|+..+-...
T Consensus        79 ~lYeCnIC~etS~ee---~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   79 KLYECNICKETSAEE---RFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS  135 (140)
T ss_pred             CceeccCcccccchh---hcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence            346799999987654   344 3   899999999988777544  48999999886443

>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=92.32  E-value=0.13  Score=41.47  Aligned_cols=34  Identities=32%  Similarity=0.597  Sum_probs=22.5

Q ss_pred             ccccccccccccccCCeeEEcCC------------C-CcccHHhHHHHHh
Q 028584          149 EQEECAICLERFKVGDTLVHLPC------------A-HRFHARCLLPWLA  185 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC------------~-H~Fh~~Ci~~wl~  185 (207)
                      ++..|+||++.-.+.   +.|-|            + ..-|..||+++.+
T Consensus         1 ed~~CpICme~PHNA---VLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    1 EDVTCPICMEHPHNA---VLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CCccCceeccCCCce---EEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            356799999985543   44433            2 2357899998754

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.

>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]

Probab=92.11  E-value=0.089  Score=45.22  Aligned_cols=47  Identities=26%  Similarity=0.692  Sum_probs=35.5

Q ss_pred             ccccccccccc-cccCCe-eEEcC-CCCcccHHhHHHHHhcCCCCCC--Ccc
Q 028584          149 EQEECAICLER-FKVGDT-LVHLP-CAHRFHARCLLPWLATNAHNCP--CCR  195 (207)
Q Consensus       149 ~~~~C~ICle~-~~~~~~-~~~lp-C~H~Fh~~Ci~~wl~~~~~~CP--~CR  195 (207)
                      .+..|+||..+ +-+++. +.+-| |-|..|.+|+++.|......||  -|-
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~   60 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCG   60 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHH
Confidence            45679999975 334443 33335 9999999999999998877899  564

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

Probab=91.01  E-value=0.015  Score=52.83  Aligned_cols=51  Identities=31%  Similarity=0.637  Sum_probs=42.9

Q ss_pred             ccccccccccccccC-CeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          149 EQEECAICLERFKVG-DTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       149 ~~~~C~ICle~~~~~-~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      -...|+||.+.+... +++..+.|+|.+|..||..|+.+.. .||.|+.++..
T Consensus       195 lv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~-kl~~~~rel~~  246 (465)
T KOG0827|consen  195 LVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKR-KLPSCRRELPK  246 (465)
T ss_pred             HHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHH-HhHHHHhhhhh
Confidence            345799999998865 5666778999999999999999876 99999988753

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=90.11  E-value=0.33  Score=32.22  Aligned_cols=33  Identities=33%  Similarity=0.807  Sum_probs=27.5

Q ss_pred             cccccccccccccCCeeEEcC-CCCcccHHhHHH
Q 028584          150 QEECAICLERFKVGDTLVHLP-CAHRFHARCLLP  182 (207)
Q Consensus       150 ~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~  182 (207)
                      ...|.+|-+.|.+++.+++-| |+-.+|..|+..
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            456999999998777777766 999999999765

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

Probab=90.04  E-value=0.23  Score=44.24  Aligned_cols=45  Identities=22%  Similarity=0.479  Sum_probs=30.4

Q ss_pred             cccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          150 QEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       150 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ...|.-|--.+..  --+.+||.|+||.+|...-  .. +.||.|-..|.
T Consensus        90 VHfCd~Cd~PI~I--YGRmIPCkHvFCl~CAr~~--~d-K~Cp~C~d~Vq  134 (389)
T KOG2932|consen   90 VHFCDRCDFPIAI--YGRMIPCKHVFCLECARSD--SD-KICPLCDDRVQ  134 (389)
T ss_pred             eEeecccCCccee--eecccccchhhhhhhhhcC--cc-ccCcCcccHHH
Confidence            4567777655432  2356799999999997542  22 38999976553

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

Probab=89.45  E-value=0.19  Score=50.04  Aligned_cols=38  Identities=26%  Similarity=0.633  Sum_probs=30.1

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHh
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLA  185 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~  185 (207)
                      ...++.|.+|...+... .....||+|.||+.||.+-..
T Consensus       814 ~ep~d~C~~C~~~ll~~-pF~vf~CgH~FH~~Cl~~~v~  851 (911)
T KOG2034|consen  814 LEPQDSCDHCGRPLLIK-PFYVFPCGHCFHRDCLIRHVL  851 (911)
T ss_pred             ecCccchHHhcchhhcC-cceeeeccchHHHHHHHHHHH
Confidence            34667899999988753 667779999999999977643

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

Probab=89.18  E-value=0.25  Score=44.84  Aligned_cols=29  Identities=28%  Similarity=0.827  Sum_probs=23.4

Q ss_pred             CCCcccHHhHHHHHhcCC------------CCCCCcccCcc
Q 028584          171 CAHRFHARCLLPWLATNA------------HNCPCCRMQIL  199 (207)
Q Consensus       171 C~H~Fh~~Ci~~wl~~~~------------~~CP~CR~~l~  199 (207)
                      |...+|.+|+-+||...+            ..||.||+.+.
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC  351 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC  351 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence            567789999999988643            17999999864

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

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

Probab=88.00  E-value=0.28  Score=41.28  Aligned_cols=39  Identities=36%  Similarity=0.686  Sum_probs=28.8

Q ss_pred             ccccccccccCCeeEEcCCCC-cccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          153 CAICLERFKVGDTLVHLPCAH-RFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       153 C~ICle~~~~~~~~~~lpC~H-~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      |-+|-+.   +..+..+||.| .+|..|-..    -. .||+|+....
T Consensus       161 Cr~C~~~---~~~VlllPCrHl~lC~~C~~~----~~-~CPiC~~~~~  200 (207)
T KOG1100|consen  161 CRKCGER---EATVLLLPCRHLCLCGICDES----LR-ICPICRSPKT  200 (207)
T ss_pred             ceecCcC---CceEEeecccceEeccccccc----Cc-cCCCCcChhh
Confidence            7777766   34788899998 488888643    22 7999987654

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

Probab=87.86  E-value=0.2  Score=48.46  Aligned_cols=40  Identities=33%  Similarity=0.681  Sum_probs=30.2

Q ss_pred             cccccccccccccCC-eeEEcCCCCcccHHhHHHHHhcCCCCCC
Q 028584          150 QEECAICLERFKVGD-TLVHLPCAHRFHARCLLPWLATNAHNCP  192 (207)
Q Consensus       150 ~~~C~ICle~~~~~~-~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP  192 (207)
                      -..|.||+..|.+.. ..+.+-|+|..|..|+.... +.  +||
T Consensus        11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly-n~--scp   51 (861)
T KOG3161|consen   11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY-NA--SCP   51 (861)
T ss_pred             HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHh-hc--cCC
Confidence            356999998887642 45667799999999997754 22  788

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

Probab=87.56  E-value=0.34  Score=47.78  Aligned_cols=26  Identities=31%  Similarity=0.814  Sum_probs=22.9

Q ss_pred             EEcCCCCcccHHhHHHHHhcCCCCCCC
Q 028584          167 VHLPCAHRFHARCLLPWLATNAHNCPC  193 (207)
Q Consensus       167 ~~lpC~H~Fh~~Ci~~wl~~~~~~CP~  193 (207)
                      +-..|+|+.|.+|...|+.... .||.
T Consensus      1044 ~Cg~C~Hv~H~sc~~eWf~~gd-~Cps 1069 (1081)
T KOG0309|consen 1044 FCGTCGHVGHTSCMMEWFRTGD-VCPS 1069 (1081)
T ss_pred             hhccccccccHHHHHHHHhcCC-cCCC
Confidence            3456999999999999999987 9986

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.63  E-value=0.31  Score=42.26  Aligned_cols=51  Identities=24%  Similarity=0.604  Sum_probs=35.4

Q ss_pred             ccccccccccccccCCee-EEcCC-----CCcccHHhHHHHHhcCC-------CCCCCcccCcc
Q 028584          149 EQEECAICLERFKVGDTL-VHLPC-----AHRFHARCLLPWLATNA-------HNCPCCRMQIL  199 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~-~~lpC-----~H~Fh~~Ci~~wl~~~~-------~~CP~CR~~l~  199 (207)
                      .+..|=||+..=+++... -+-||     .|+.|..|+..|+..++       ..||.|+.+..
T Consensus        19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi   82 (293)
T KOG3053|consen   19 LERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI   82 (293)
T ss_pred             cceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence            455688999875543111 12366     47899999999998643       16999998654

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

Probab=86.55  E-value=0.24  Score=51.15  Aligned_cols=47  Identities=28%  Similarity=0.616  Sum_probs=38.4

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQ  197 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~  197 (207)
                      .....|.||.+.+.+- . .+..|+|.+|..|+..|+..+. .||.|...
T Consensus      1151 ~~~~~c~ic~dil~~~-~-~I~~cgh~~c~~c~~~~l~~~s-~~~~~ksi 1197 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRNQ-G-GIAGCGHEPCCRCDELWLYASS-RCPICKSI 1197 (1394)
T ss_pred             hcccchHHHHHHHHhc-C-CeeeechhHhhhHHHHHHHHhc-cCcchhhh
Confidence            4556899999998732 2 4455999999999999999988 99999743

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

Probab=86.36  E-value=0.28  Score=44.96  Aligned_cols=39  Identities=31%  Similarity=0.664  Sum_probs=27.9

Q ss_pred             ccccccccccccccC-CeeEEcCCCCcccHHhHHHHHhcC
Q 028584          149 EQEECAICLERFKVG-DTLVHLPCAHRFHARCLLPWLATN  187 (207)
Q Consensus       149 ~~~~C~ICle~~~~~-~~~~~lpC~H~Fh~~Ci~~wl~~~  187 (207)
                      ...+|.||+...... +......|+|.||..|+.+.+...
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~  184 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK  184 (384)
T ss_pred             ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh
Confidence            456799999444333 333345699999999999988743

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

Probab=85.09  E-value=0.24  Score=48.32  Aligned_cols=46  Identities=35%  Similarity=0.691  Sum_probs=36.9

Q ss_pred             cccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCC--CCCCCcccCc
Q 028584          150 QEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNA--HNCPCCRMQI  198 (207)
Q Consensus       150 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~--~~CP~CR~~l  198 (207)
                      ..+|+||...+..+   +.+.|.|.|+..|+..-|...+  ..||+|+..+
T Consensus        21 ~lEc~ic~~~~~~p---~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~   68 (684)
T KOG4362|consen   21 ILECPICLEHVKEP---SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDI   68 (684)
T ss_pred             hccCCceeEEeecc---chhhhhHHHHhhhhhceeeccCccccchhhhhhh
Confidence            46799999998866   7788999999999977666443  3799998654

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

Probab=84.84  E-value=0.67  Score=40.22  Aligned_cols=51  Identities=25%  Similarity=0.638  Sum_probs=36.2

Q ss_pred             ccccccccccccccCCe-eEEcCCC-----CcccHHhHHHHHhcCC-CCCCCcccCcc
Q 028584          149 EQEECAICLERFKVGDT-LVHLPCA-----HRFHARCLLPWLATNA-HNCPCCRMQIL  199 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~-~~~lpC~-----H~Fh~~Ci~~wl~~~~-~~CP~CR~~l~  199 (207)
                      ++..|-||..+...... ....||.     ...|..|+..|+...+ ..|.+|.....
T Consensus        77 ~~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~  134 (323)
T KOG1609|consen   77 SGPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI  134 (323)
T ss_pred             CCCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence            35789999997653321 4566764     3479999999998443 38999987554

>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=84.68  E-value=0.3  Score=31.62  Aligned_cols=43  Identities=26%  Similarity=0.566  Sum_probs=24.9

Q ss_pred             cccccccccccCCeeEEcCC-CCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          152 ECAICLERFKVGDTLVHLPC-AHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       152 ~C~ICle~~~~~~~~~~lpC-~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .|--|+-...     ..+.| .|..|..|+...+.... .||+|..+++.
T Consensus         4 nCKsCWf~~k-----~Li~C~dHYLCl~CLt~ml~~s~-~C~iC~~~LPt   47 (50)
T PF03854_consen    4 NCKSCWFANK-----GLIKCSDHYLCLNCLTLMLSRSD-RCPICGKPLPT   47 (50)
T ss_dssp             ---SS-S--S-----SEEE-SS-EEEHHHHHHT-SSSS-EETTTTEE---
T ss_pred             cChhhhhcCC-----CeeeecchhHHHHHHHHHhcccc-CCCcccCcCcc
Confidence            3666664432     23456 59999999999998887 99999988754

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.

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

Probab=83.33  E-value=0.77  Score=45.71  Aligned_cols=50  Identities=24%  Similarity=0.697  Sum_probs=37.4

Q ss_pred             ccccccccccccccCCeeEEcCCCCc-----ccHHhHHHHHhcCC-CCCCCcccCcc
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHR-----FHARCLLPWLATNA-HNCPCCRMQIL  199 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~-----Fh~~Ci~~wl~~~~-~~CP~CR~~l~  199 (207)
                      ++..|-||..+=.. +.+..-||...     .|.+|+.+|+.... ..|-+|+.++.
T Consensus        11 d~~~CRICr~e~~~-d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~   66 (1175)
T COG5183          11 DKRSCRICRTEDIR-DDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK   66 (1175)
T ss_pred             cchhceeecCCCCC-CCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence            55789999987543 34455677654     89999999999654 37999998764

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

Probab=83.20  E-value=1.3  Score=39.54  Aligned_cols=48  Identities=21%  Similarity=0.343  Sum_probs=37.5

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCC--CCCCCccc
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNA--HNCPCCRM  196 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~--~~CP~CR~  196 (207)
                      ....||+=-+.-.+++.++.|.|+|+.-..-+...-+++.  +.||+|-.
T Consensus       335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~  384 (396)
T COG5109         335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPE  384 (396)
T ss_pred             ceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCc
Confidence            3457988777766667788999999999999988766554  48999953

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=80.61  E-value=0.97  Score=40.03  Aligned_cols=29  Identities=24%  Similarity=0.634  Sum_probs=22.9

Q ss_pred             CCCcccHHhHHHHHhcCC------------CCCCCcccCcc
Q 028584          171 CAHRFHARCLLPWLATNA------------HNCPCCRMQIL  199 (207)
Q Consensus       171 C~H~Fh~~Ci~~wl~~~~------------~~CP~CR~~l~  199 (207)
                      |...+|.+|+.+|+....            .+||.||+++.
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            567799999999986432            28999998774

>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]

Probab=80.01  E-value=5.3  Score=35.88  Aligned_cols=116  Identities=16%  Similarity=0.222  Sum_probs=59.3

Q ss_pred             HHHHHHHHHHHhccccCCCCCCCCCCCCcchhhhchhhhccccceeecccCCCCcccccccccccccccccccccccccc
Q 028584           82 AREAKERLDERLGTQRKSSDSNSRQNGKESSVLMNINKSTVLHTQVFGSKKSGSKRFSWSKLSWKACEQEECAICLERFK  161 (207)
Q Consensus        82 ~~Ea~erL~erl~~~~~~~~~~~~~~~~e~~~~~~~~~~~~l~~~~~~~k~~~~~~~~~~~~~~~~~~~~~C~ICle~~~  161 (207)
                      .+...|.|.+++.+.+-.-+..-.|-..  ....+...+..-|..+|-.-..-.-...|...+.....+.+|++|+..-.
T Consensus       275 t~k~lE~~~~~iNA~RPQCPVglnTL~~--P~~~~~~~~~~~QP~vYl~CGHV~G~H~WG~~e~~g~~~r~CPmC~~~gp  352 (429)
T KOG3842|consen  275 TMKHLEALRQEINAARPQCPVGLNTLAF--PSKRRKRVVDEKQPWVYLNCGHVHGYHNWGVRENTGQRERECPMCRVVGP  352 (429)
T ss_pred             cHHHHHHHHHHHhccCCCCCcccceeec--ccccccccccccCCeEEEeccccccccccccccccCcccCcCCeeeeecc
Confidence            3566778888888777554321000000  00001111222222233332222222234444444456778999987521


Q ss_pred             c---------------C-CeeEEcCCCCcccHHhHHHHHhcCC--------CCCCCcccCcc
Q 028584          162 V---------------G-DTLVHLPCAHRFHARCLLPWLATNA--------HNCPCCRMQIL  199 (207)
Q Consensus       162 ~---------------~-~~~~~lpC~H~Fh~~Ci~~wl~~~~--------~~CP~CR~~l~  199 (207)
                      .               + -.-..-||+|+--..-..-|-+..-        ..||+|-..+.
T Consensus       353 ~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~  414 (429)
T KOG3842|consen  353 YVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLA  414 (429)
T ss_pred             eeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhc
Confidence            1               0 0122458999988888888866422        27999977654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	207
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		1e-06
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		1e-06
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		4e-05
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		8e-05
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		3e-04
2ecn_A	70	Solution Structure Of The Ring Domain Of The Human		3e-04

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 150 QEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAASSA 206
            E CA+CLE FK  D L   PC H FH +CL+ WL      CP C M +L  A  S 
Sbjct: 15  HELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRK-VCPLCNMPVLQLAQLSG 70

>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 = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 152 ECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
           EC +C E + +G+++  LPC H FH  C++PWL  +  +CP CR  +
Sbjct: 17  ECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQH-DSCPVCRKSL 62

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 152 ECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
           +C ICL   + G+ +  LPC H FH  C+  WL TN   CP CR+ I
Sbjct: 16  KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNK-KCPICRVDI 61

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCR 195
           EQ  C +C+  F+    L  LPC H FHA+C+  WL  N   CP CR
Sbjct: 22  EQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKAN-RTCPICR 67

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 2/49 (4%)
Query: 152 ECAICLERFKVGDTLVHLP-CAHRFHARCLLPWLATNAHNCPCCRMQIL 199
           ECA+CL   + G+    LP C H FHA C+  WL +++  CP CR+ ++
Sbjct: 7   ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHS-TCPLCRLTVV 54

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAASSA 206
           ++EEC IC++    G   + LPCAH F  +C+  W +    NCP CR+Q+     SS 
Sbjct: 14  DEEECCICMD----GRADLILPCAHSFCQKCIDKW-SDRHRNCPICRLQMTGANESSG 66

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	207
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	2e-18
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	3e-17
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	3e-17
2ect_A	78	Ring finger protein 126; metal binding protein, st	2e-16
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	3e-16
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	3e-14
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	3e-13
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	1e-12
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	3e-12
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	1e-09
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-09
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	4e-09
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	1e-08
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	1e-08
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	1e-08
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	3e-08
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	1e-07
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	1e-07
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	2e-07
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	4e-07
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	7e-07
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	3e-06
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	3e-06
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	3e-06
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	3e-06
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	1e-05
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	2e-05
1z6u_A	150	NP95-like ring finger protein isoform B; structura	3e-05
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	4e-05
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	2e-04
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	3e-04
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	4e-04
3nw0_A	238	Non-structural maintenance of chromosomes element	4e-04
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	4e-04
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	4e-04
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	6e-04

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

 Score = 75.2 bits (185), Expect = 2e-18
 Identities = 26/58 (44%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAASSA 206
             E CA+CLE FK  D L   PC H FH +CL+ WL      CP C M +L  A  S 
Sbjct: 14  LHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRK-VCPLCNMPVLQLAQLSG 70

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

 Score = 72.8 bits (179), Expect = 3e-17
 Identities = 19/65 (29%), Positives = 26/65 (40%), Gaps = 1/65 (1%)

Query: 137 RFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRM 196
               ++      ++  C IC   +  GD    LPC H FH  C+  WL  +   CP CR 
Sbjct: 27  EILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKS-GTCPVCRC 85

Query: 197 QILDP 201
               P
Sbjct: 86  MFPPP 90

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

 Score = 72.0 bits (177), Expect = 3e-17
 Identities = 23/58 (39%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAASSA 206
            +E+C ICL   + G+ +  LPC H FH  C+  WL TN   CP CR+ I     S +
Sbjct: 13  TEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNK-KCPICRVDIEAQLPSES 69

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

 Score = 69.8 bits (171), Expect = 2e-16
 Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAASS 205
              EC +C E + +G+++  LPC H FH  C++PWL  +  +CP CR  +     ++
Sbjct: 14  SGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQH-DSCPVCRKSLTGQNTAT 69

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

 Score = 69.3 bits (170), Expect = 3e-16
 Identities = 21/56 (37%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAA 203
            EQ  C +C+  F+    L  LPC H FHA+C+  WL  N   CP CR      + 
Sbjct: 21  SEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANR-TCPICRADSGPSSG 75

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

 Score = 64.3 bits (157), Expect = 3e-14
 Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 5/58 (8%)

Query: 149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAASSA 206
           ++EEC IC++        + LPCAH F  +C+  W   +  NCP CR+Q+     SS 
Sbjct: 14  DEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRH-RNCPICRLQMTGANESSG 66

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

 Score = 60.7 bits (148), Expect = 3e-13
 Identities = 20/52 (38%), Positives = 31/52 (59%), Gaps = 2/52 (3%)

Query: 149 EQEECAICLERFKVGDTLVHLP-CAHRFHARCLLPWLATNAHNCPCCRMQIL 199
           +  ECA+CL   + G+    LP C H FHA C+  WL +++  CP CR+ ++
Sbjct: 4   DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHS-TCPLCRLTVV 54

>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 = 1e-12
 Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 3/52 (5%)

Query: 147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
           A   E C ICLE     +  + LPC H F   C+  W+  N   CP C++ +
Sbjct: 2   ATVAERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQN-PTCPLCKVPV 50

>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 = 58.4 bits (142), Expect = 3e-12
 Identities = 16/47 (34%), Positives = 18/47 (38%), Gaps = 2/47 (4%)

Query: 150 QEECAICLERFKVGDTLVH-LPCAHRFHARCLLPWLATNAHNCPCCR 195
              C ICLE       + H LPC H  H  C    L    + CP C 
Sbjct: 5   SSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEG-YRCPLCS 50

>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 = 55.5 bits (133), Expect = 1e-09
 Identities = 18/83 (21%), Positives = 28/83 (33%), Gaps = 5/83 (6%)

Query: 116 NINKSTVLHTQVFGSKKSGSKRFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRF 175
           N + + +         K   +++            + C IC E  K    +   PC H  
Sbjct: 300 NPDLTGLCEPTPQDHIKVTQEQYE--LYCEMGSTFQLCKICAENDK---DVKIEPCGHLM 354

Query: 176 HARCLLPWLATNAHNCPCCRMQI 198
              CL  W  +    CP CR +I
Sbjct: 355 CTSCLTSWQESEGQGCPFCRCEI 377

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

 Score = 51.5 bits (123), Expect = 2e-09
 Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 5/51 (9%)

Query: 152 ECAICLERFK----VGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
            C IC++ +      G  +V   C H F ++CL   L    + CP CR +I
Sbjct: 17  SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA-NTCPTCRKKI 66

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

 Score = 54.5 bits (130), Expect = 4e-09
 Identities = 23/133 (17%), Positives = 38/133 (28%), Gaps = 21/133 (15%)

Query: 90  DERLGTQRKSSDSNSRQNGKESSVLMNINKSTVLHTQVFGSKKSGSKRFSWSKLSWKACE 149
            E +   R            E ++  N+    +     F             KL  +  E
Sbjct: 254 TEEVARLRHVLSDGLSNWDSEMNIHKNL--LRMFDLCYFPMPDWSDGP----KLDEEDNE 307

Query: 150 QEECAICLERFKVGDTLV-----HLPCAHRFHARCLLPWLATNAH----------NCPCC 194
           +  C IC      G  +      +  C  + HA CL  W  T              CP C
Sbjct: 308 ELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFC 367

Query: 195 RMQILDPAASSAD 207
           + ++    A+  +
Sbjct: 368 KAKLSTSFAALLN 380

>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 = 49.1 bits (117), Expect = 1e-08
 Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 5/51 (9%)

Query: 152 ECAICLERFK----VGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
            C IC++ +      G  +V   C H F ++CL   L    + CP CR +I
Sbjct: 12  SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA-NTCPTCRKKI 61

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

 Score = 49.0 bits (117), Expect = 1e-08
 Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 5/51 (9%)

Query: 152 ECAICLERFK----VGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
            C IC++ +      G  +V   C H F ++CL   L    + CP CR +I
Sbjct: 5   SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA-NTCPTCRKKI 54

>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 = 49.9 bits (119), Expect = 1e-08
 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 2/51 (3%)

Query: 148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
            E   C IC+E+ +  D  +   C+      C+  WL      CP CR  +
Sbjct: 20  AEVFRCFICMEKLR--DARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPL 68

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

 Score = 48.4 bits (115), Expect = 3e-08
 Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 2/46 (4%)

Query: 151 EECAICLERFKVGDTLVHLP-CAHRFHARCLLPWLATNAHNCPCCR 195
           + C  C    K  D +V    C H FH  C+  W+  N + CP C+
Sbjct: 27  DACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQN-NRCPLCQ 71

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

 Score = 46.3 bits (110), Expect = 1e-07
 Identities = 11/51 (21%), Positives = 17/51 (33%), Gaps = 3/51 (5%)

Query: 148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
                C+IC       D      C H F   C++     +   CP C + +
Sbjct: 13  TPYILCSICKGYLI--DATTITECLHTFCKSCIVRHFYYSNR-CPKCNIVV 60

>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 = 47.7 bits (113), Expect = 1e-07
 Identities = 14/65 (21%), Positives = 19/65 (29%), Gaps = 3/65 (4%)

Query: 131 KKSGSKRFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHN 190
           K   +    +     K  E  +C  C E        +   C H     CL         +
Sbjct: 33  KDRPASGSPFQLFLSKVEETFQCICCQELVF---RPITTVCQHNVCKDCLDRSFRAQVFS 89

Query: 191 CPCCR 195
           CP CR
Sbjct: 90  CPACR 94

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

 Score = 45.6 bits (108), Expect = 2e-07
 Identities = 17/50 (34%), Positives = 20/50 (40%), Gaps = 4/50 (8%)

Query: 149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
              ECAICL+        V LPC H F   C+          C  CR +I
Sbjct: 14  TVPECAICLQTCVHP---VSLPCKHVFCYLCVKGASWLG-KRCALCRQEI 59

>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 = 44.9 bits (106), Expect = 4e-07
 Identities = 11/46 (23%), Positives = 16/46 (34%), Gaps = 3/46 (6%)

Query: 151 EECAICLERFKVGDTLVHLPCAHRFHARCLLPWLAT-NAHNCPCCR 195
           + C IC      G +     C  R H  C+  +  +     CP C 
Sbjct: 16  KICNICHSLLIQGQSC--ETCGIRMHLPCVAKYFQSNAEPRCPHCN 59

>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 = 45.2 bits (107), Expect = 7e-07
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 152 ECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDP 201
            C +C   F   D    + C H F   C++ +L T+ + CP C +Q+   
Sbjct: 17  MCVLCGGYFI--DATTIIECLHSFCKTCIVRYLETSKY-CPICDVQVHKT 63

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

 Score = 44.1 bits (103), Expect = 3e-06
 Identities = 17/69 (24%), Positives = 24/69 (34%), Gaps = 19/69 (27%)

Query: 146 KACEQEECAICLERFKVGD---------------TLVHLPCAHRFHARCLLPWL----AT 186
           K   +E+C IC+E+  V                       C+H FH  CLL         
Sbjct: 21  KVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKD 80

Query: 187 NAHNCPCCR 195
            +  CP C+
Sbjct: 81  GSLQCPSCK 89

>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 = 43.7 bits (103), Expect = 3e-06
 Identities = 14/59 (23%), Positives = 21/59 (35%), Gaps = 3/59 (5%)

Query: 148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAASSA 206
             + +C IC+E        V LPC H     C    +   +  CP CR ++        
Sbjct: 13  LSECQCGICMEILV---EPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSSWTRYHT 68

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

 Score = 42.9 bits (101), Expect = 3e-06
 Identities = 12/47 (25%), Positives = 14/47 (29%), Gaps = 4/47 (8%)

Query: 152 ECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
            C IC + F+     V   C H F   C L         C  C    
Sbjct: 17  RCFICRQAFQNP---VVTKCRHYFCESCALEHFRAT-PRCYICDQPT 59

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

 Score = 42.5 bits (100), Expect = 3e-06
 Identities = 11/50 (22%), Positives = 20/50 (40%), Gaps = 3/50 (6%)

Query: 149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
           ++ +C  C              C HRF   C+   L++++  C  C+  I
Sbjct: 14  DKYKCEKCHLVLCSP---KQTECGHRFCESCMAALLSSSSPKCTACQESI 60

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

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 21/69 (30%), Positives = 28/69 (40%), Gaps = 4/69 (5%)

Query: 130 SKKSGSKRFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAH 189
            K    K    S ++     + +C IC E F      V L CAH F + C+  W+     
Sbjct: 44  EKMQAQKEEVLSHMNDVLENELQCIICSEYFIEA---VTLNCAHSFCSYCINEWMKRK-I 99

Query: 190 NCPCCRMQI 198
            CP CR  I
Sbjct: 100 ECPICRKDI 108

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

 Score = 40.5 bits (94), Expect = 2e-05
 Identities = 11/53 (20%), Positives = 19/53 (35%), Gaps = 1/53 (1%)

Query: 149 EQEECAICLERFKVGD-TLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD 200
           +  EC +C+E  ++ D       C ++    C           CP CR    +
Sbjct: 10  DPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE 62

>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 = 41.5 bits (97), Expect = 3e-05
 Identities = 12/48 (25%), Positives = 14/48 (29%), Gaps = 3/48 (6%)

Query: 148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCR 195
            +   C  C E        V   C H     CL         +CP CR
Sbjct: 76  EQSFMCVCCQELVYQP---VTTECFHNVCKDCLQRSFKAQVFSCPACR 120

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

 Score = 38.9 bits (91), Expect = 4e-05
 Identities = 14/55 (25%), Positives = 18/55 (32%), Gaps = 7/55 (12%)

Query: 152 ECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAASSA 206
            C  C    K       LPC H   + C    L  +   CP C+      A + A
Sbjct: 8   RCQQCQAEAK---CPKLLPCLHTLCSGC----LEASGMQCPICQAPWPLGADTPA 55

>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 = 39.6 bits (92), Expect = 2e-04
 Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 2/46 (4%)

Query: 153 CAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
           C ICL+  K  +T+    C HRF A C++  L +    CP CR ++
Sbjct: 57  CPICLDMLK--NTMTTKECLHRFCADCIITALRSGNKECPTCRKKL 100

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

 Score = 37.8 bits (88), Expect = 3e-04
 Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 3/57 (5%)

Query: 152 ECAICLERFKVGDTL-VHLPCAHRFHARCLLPWLATNAHN--CPCCRMQILDPAASS 205
           EC IC+E F         L C H    +CL   LA++ +   CP C       + + 
Sbjct: 17  ECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITSLTQ 73

>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 = 37.9 bits (87), Expect = 4e-04
 Identities = 13/49 (26%), Positives = 15/49 (30%), Gaps = 2/49 (4%)

Query: 148 CEQEECAICLERFKVGDTLVHLP-CAHRFHARCLLPWLATNAHNCPCCR 195
               EC          +  V    C H FH  C+  WL T    CP   
Sbjct: 49  DLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTR-QVCPLDN 96

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

 Score = 39.3 bits (91), Expect = 4e-04
 Identities = 11/45 (24%), Positives = 14/45 (31%), Gaps = 3/45 (6%)

Query: 152 ECAICLERFKVGDTLVHLPCAHRFHARCLLPWLAT-NAHNCPCCR 195
            C IC      G       C  R H  C+  +  +     CP C 
Sbjct: 182 ICNICHSLLIQGQ--SCETCGIRMHLPCVAKYFQSNAEPRCPHCN 224

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

 Score = 38.2 bits (88), Expect = 4e-04
 Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 5/57 (8%)

Query: 146 KACEQEECAICLERFK----VGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
                  C IC++ +      G  +V   C H F ++CL   L  NA+ CP CR +I
Sbjct: 3   MGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSL-KNANTCPTCRKKI 58

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

 Score = 37.9 bits (88), Expect = 4e-04
 Identities = 15/44 (34%), Positives = 19/44 (43%), Gaps = 3/44 (6%)

Query: 152 ECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCR 195
           EC ICL   +     V  PC HRF   C++  +    H CP   
Sbjct: 20  ECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDN 60

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

 Score = 37.5 bits (86), Expect = 6e-04
 Identities = 20/97 (20%), Positives = 29/97 (29%), Gaps = 18/97 (18%)

Query: 115 MNINKSTVLHTQVFGSKKSGSKRFSWSKL-SWKACEQEECAICLERFKVGD--------- 164
           +             G K+   K+++   L +W     + CAIC                 
Sbjct: 13  LYFQGGGRGTNSGAGKKRFEVKKWNAVALWAWDIVV-DNCAICRNHIMDLCIECQANQAS 71

Query: 165 ------TLVHLPCAHRFHARCLLPWLATNAHNCPCCR 195
                 T+    C H FH  C+  WL T    CP   
Sbjct: 72  ATSEECTVAWGVCNHAFHFHCISRWLKTRQV-CPLDN 107

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	207
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.58
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.56
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.49
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.48
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.45
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.43
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.37
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.35
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.35
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.35
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.32
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.3
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.3
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.27
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.27
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.27
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.26
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.26
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.25
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.25
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.25
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.24
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.22
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.21
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.19
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.19
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.19
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.18
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.18
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.18
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.17
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.15
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.14
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.13
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.12
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.11
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.11
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.08
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.07
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.06
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.05
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.03
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.02
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.02
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.01
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.97
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.96
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.95
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.95
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.93
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.92
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.88
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.86
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.84
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.82
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.81
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.79
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.78
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.78
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.73
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.68
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.67
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.61
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.56
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.53
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.5
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.47
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.33
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.29
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.21
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.18
3nw0_A	238	Non-structural maintenance of chromosomes element	97.5
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	94.92
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	94.43
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	93.2
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	92.27
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	85.37
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	84.01
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	83.29
1we9_A	64	PHD finger family protein; structural genomics, PH	82.5
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	82.37
1wem_A	76	Death associated transcription factor 1; structura	82.35

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

Probab=99.58  E-value=2.7e-15  Score=108.58  Aligned_cols=76  Identities=25%  Similarity=0.577  Sum_probs=61.0

Q ss_pred             hhhhchhhhccccceeecccCCCCcccccccccccccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCC
Q 028584          112 SVLMNINKSTVLHTQVFGSKKSGSKRFSWSKLSWKACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNC  191 (207)
Q Consensus       112 ~~~~~~~~~~~l~~~~~~~k~~~~~~~~~~~~~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~C  191 (207)
                      ......+.+..||..++......            ..++..|+||++.|..++.++.++|+|.||..||..|+..+. +|
T Consensus        14 ~~~~s~~~i~~lp~~~~~~~~~~------------~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~-~C   80 (91)
T 2l0b_A           14 NPPASKESIDALPEILVTEDHGA------------VGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSG-TC   80 (91)
T ss_dssp             CCCCCHHHHHTSCEEECCTTCSS------------SSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTC-BC
T ss_pred             CCCCCHHHHHhCCCeeecccccc------------cCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCC-cC
Confidence            44455666888888776654321            235678999999999888889999999999999999999877 99


Q ss_pred             CCcccCccC
Q 028584          192 PCCRMQILD  200 (207)
Q Consensus       192 P~CR~~l~~  200 (207)
                      |+||..+..
T Consensus        81 P~Cr~~~~~   89 (91)
T 2l0b_A           81 PVCRCMFPP   89 (91)
T ss_dssp             TTTCCBSSC
T ss_pred             cCcCccCCC
Confidence            999998864

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

Probab=99.56  E-value=3.1e-15  Score=104.05  Aligned_cols=52  Identities=40%  Similarity=0.903  Sum_probs=47.2

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      ++..|+||++.|..++.++.++|+|.||..||..|+..+. +||+||.++.+.
T Consensus        22 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~-~CP~Cr~~~~~~   73 (75)
T 1x4j_A           22 EQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANR-TCPICRADSGPS   73 (75)
T ss_dssp             SCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCS-SCTTTCCCCCCC
T ss_pred             CCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCC-cCcCcCCcCCCC
Confidence            5678999999999888889999999999999999999887 999999988654

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

Probab=99.49  E-value=3e-14  Score=98.55  Aligned_cols=54  Identities=46%  Similarity=0.966  Sum_probs=48.0

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCCC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPA  202 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~~  202 (207)
                      ..+..|+||++.|..+..+..++|+|.||..||..|+..+. +||+||.++....
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~-~CP~Cr~~~~~~~   66 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRK-VCPLCNMPVLQLA   66 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCS-BCTTTCCBCSSCC
T ss_pred             CCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCC-cCCCcCccccccc
Confidence            45678999999999888888899999999999999999887 9999999987543

>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=99.48  E-value=4.5e-14  Score=96.40  Aligned_cols=56  Identities=39%  Similarity=0.894  Sum_probs=48.6

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCCCC
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAA  203 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~~~  203 (207)
                      ......|+||++.|..++.++.++|+|.||..||..|+..+. +||+||..|.....
T Consensus        11 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~~~   66 (69)
T 2kiz_A           11 EDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNK-KCPICRVDIEAQLP   66 (69)
T ss_dssp             TTCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCS-BCTTTCSBSCSCCC
T ss_pred             CCCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCC-CCcCcCccccCcCC
Confidence            345678999999998777888999999999999999999887 99999999875443

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

Probab=99.45  E-value=2.9e-14  Score=93.08  Aligned_cols=50  Identities=40%  Similarity=1.054  Sum_probs=44.9

Q ss_pred             ccccccccccccccCCeeEEcC-CCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          149 EQEECAICLERFKVGDTLVHLP-CAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ++..|+||++.|..++.+..++ |+|.||..||..|+..+. +||+||.++.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~-~CP~Cr~~~~   54 (55)
T 1iym_A            4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHS-TCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCC-SCSSSCCCSC
T ss_pred             CCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCC-cCcCCCCEeE
Confidence            4567999999999887888888 999999999999998876 9999998874

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

Probab=99.43  E-value=8.8e-14  Score=97.13  Aligned_cols=53  Identities=36%  Similarity=1.019  Sum_probs=47.0

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      .+...|+||++.|..+..+..++|+|.||..||..|+.... +||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~   65 (78)
T 2ect_A           13 GSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHD-SCPVCRKSLTGQ   65 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTC-SCTTTCCCCCCS
T ss_pred             CCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCC-cCcCcCCccCCc
Confidence            45678999999999887888899999999999999998876 999999988654

>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=99.37  E-value=4.2e-13  Score=87.35  Aligned_cols=50  Identities=30%  Similarity=0.616  Sum_probs=43.0

Q ss_pred             ccccccccccccccC-CeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          149 EQEECAICLERFKVG-DTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       149 ~~~~C~ICle~~~~~-~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ++..|+||++.|.++ +.++.++|+|.||..||..|+.... +||+||..+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGY-RCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTC-CCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCC-cCCCCCCcCC
Confidence            456799999999653 3578889999999999999999886 9999998874

>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=99.35  E-value=6.5e-13  Score=99.10  Aligned_cols=54  Identities=30%  Similarity=0.709  Sum_probs=41.7

Q ss_pred             ccccccccccccccCC---------------eeEEcCCCCcccHHhHHHHHhc----CCCCCCCcccCccCCC
Q 028584          149 EQEECAICLERFKVGD---------------TLVHLPCAHRFHARCLLPWLAT----NAHNCPCCRMQILDPA  202 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~---------------~~~~lpC~H~Fh~~Ci~~wl~~----~~~~CP~CR~~l~~~~  202 (207)
                      .+..|+||++.|..+.               .+..++|+|.||..||..|+..    ...+||+||..+....
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~~   96 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKT   96 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCS
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCCC
Confidence            3457999999996542               3447889999999999999953    1238999999886543

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

Probab=99.35  E-value=4.5e-13  Score=91.52  Aligned_cols=53  Identities=28%  Similarity=0.655  Sum_probs=45.5

Q ss_pred             cccccccccccccccC----CeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          148 CEQEECAICLERFKVG----DTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~----~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      .++..|+||++.|.++    +.++.++|+|.||..||..|+.... +||+||..+...
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~   64 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINHK   64 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCS-BCTTTCCBCCCC
T ss_pred             CCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCC-CCCCCCCccChh
Confidence            4567899999998763    4567889999999999999999887 999999988754

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

Probab=99.35  E-value=5.5e-13  Score=90.36  Aligned_cols=52  Identities=29%  Similarity=0.671  Sum_probs=44.2

Q ss_pred             cccccccccccccccC----CeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVG----DTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~----~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .+...|+||++.|.++    ..++.++|+|.||..||..|+.... .||+||.+|..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~   68 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINH   68 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCS-SCTTTCCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCC-CCCCCCCccCc
Confidence            4567899999999753    3457889999999999999999876 99999998753

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

Probab=99.32  E-value=8.2e-13  Score=93.55  Aligned_cols=51  Identities=33%  Similarity=0.752  Sum_probs=41.4

Q ss_pred             cccccccccccccc-----------CCeeEEcC-CCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          149 EQEECAICLERFKV-----------GDTLVHLP-CAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       149 ~~~~C~ICle~~~~-----------~~~~~~lp-C~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ++..|+||++.|..           ++.++.++ |+|.||..||.+|+..+. +||+||.++..
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~~~~   76 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNN-RCPLCQQDWVV   76 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCC-BCTTTCCBCCE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCC-CCCCcCCCcch
Confidence            55669999988854           34455555 999999999999999887 99999998753

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

Probab=99.30  E-value=1.2e-12  Score=87.43  Aligned_cols=52  Identities=29%  Similarity=0.666  Sum_probs=44.0

Q ss_pred             ccccccccccccccC----CeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          149 EQEECAICLERFKVG----DTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       149 ~~~~C~ICle~~~~~----~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      ++..|+||++.+.++    +.++.++|+|.||..|+..|+..+. .||+||.++...
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~   57 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINHK   57 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCS-BCTTTCCBCTTT
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCC-CCCCCCccCCcc
Confidence            346799999999753    3557889999999999999999876 999999988653

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

Probab=99.30  E-value=3.1e-12  Score=88.14  Aligned_cols=50  Identities=20%  Similarity=0.537  Sum_probs=42.6

Q ss_pred             cccccccccccccccCCeeEEc-CCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          148 CEQEECAICLERFKVGDTLVHL-PCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      .+...|+||++.|.++   +.+ +|+|.||..||..|+.... .||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~-~CP~Cr~~~~~~   63 (72)
T 2djb_A           13 TPYILCSICKGYLIDA---TTITECLHTFCKSCIVRHFYYSN-RCPKCNIVVHQT   63 (72)
T ss_dssp             CGGGSCTTTSSCCSSC---EECSSSCCEECHHHHHHHHHHCS-SCTTTCCCCCSS
T ss_pred             CCCCCCCCCChHHHCc---CEECCCCCHHHHHHHHHHHHcCC-cCCCcCcccCcc
Confidence            4567899999999754   555 9999999999999998876 999999988654

>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=99.27  E-value=2.2e-12  Score=96.24  Aligned_cols=50  Identities=30%  Similarity=0.553  Sum_probs=42.5

Q ss_pred             ccccccccccccccC---------------CeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          149 EQEECAICLERFKVG---------------DTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       149 ~~~~C~ICle~~~~~---------------~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ++..|+||++.|...               ..++.++|+|.||..||..||..+. +||+||.++.
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~-~CP~Cr~~~~  100 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQ-VCPLDNREWE  100 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCS-BCSSSCSBCC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCC-cCcCCCCcce
Confidence            567799999998754               1366789999999999999999877 9999999864

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

Probab=99.27  E-value=3.4e-12  Score=90.61  Aligned_cols=55  Identities=25%  Similarity=0.613  Sum_probs=44.9

Q ss_pred             cccccccccccccccccCCeeEEcCCC-----CcccHHhHHHHHhcCC-CCCCCcccCccCC
Q 028584          146 KACEQEECAICLERFKVGDTLVHLPCA-----HRFHARCLLPWLATNA-HNCPCCRMQILDP  201 (207)
Q Consensus       146 ~~~~~~~C~ICle~~~~~~~~~~lpC~-----H~Fh~~Ci~~wl~~~~-~~CP~CR~~l~~~  201 (207)
                      ...++..|.||+++|.+++.+ ++||.     |.||..||.+|+..+. .+||+||..+...
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~l-~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~   71 (80)
T 2d8s_A           11 TPSSQDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIME   71 (80)
T ss_dssp             CCTTSCCCSSSCCCCCSSSCE-ECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCC
T ss_pred             CCCCCCCCeEcCccccCCCee-EeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecC
Confidence            445677899999999866555 68996     9999999999999753 3899999988643

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

Probab=99.27  E-value=1.1e-12  Score=90.08  Aligned_cols=48  Identities=35%  Similarity=0.613  Sum_probs=41.8

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      .+...|+||++.+.++   +.++|+|.||..||..|+.... .||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~~---~~~~CgH~fC~~Ci~~~~~~~~-~CP~Cr~~~~   60 (71)
T 2d8t_A           13 LTVPECAICLQTCVHP---VSLPCKHVFCYLCVKGASWLGK-RCALCRQEIP   60 (71)
T ss_dssp             SSCCBCSSSSSBCSSE---EEETTTEEEEHHHHHHCTTCSS-BCSSSCCBCC
T ss_pred             CCCCCCccCCcccCCC---EEccCCCHHHHHHHHHHHHCCC-cCcCcCchhC
Confidence            3567899999999754   7789999999999999998876 9999999875

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

Probab=99.26  E-value=4.9e-12  Score=86.86  Aligned_cols=52  Identities=27%  Similarity=0.637  Sum_probs=42.3

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhc--CCCCCCCcccCccCC
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLAT--NAHNCPCCRMQILDP  201 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~--~~~~CP~CR~~l~~~  201 (207)
                      ..+...|+||++.|.++   +.++|+|.||..||..|+..  ....||+||..+...
T Consensus        17 ~~~~~~C~IC~~~~~~~---~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           17 LQEEVICPICLDILQKP---VTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCCCBCTTTCSBCSSE---EECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCC
T ss_pred             CccCCEeccCCcccCCe---EEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcc
Confidence            34567899999999743   67799999999999999973  223899999988654

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

Probab=99.26  E-value=3.2e-12  Score=86.74  Aligned_cols=49  Identities=35%  Similarity=0.838  Sum_probs=42.1

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ....|+||++.+.+  .++.++|+|.||..|+..|+..+. +||+||.++..
T Consensus         4 ~~~~C~IC~~~~~~--~~~~~~C~H~fc~~Ci~~~~~~~~-~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNP-TCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETTTTEEESTTHHHHHHHHSC-STTTTCCCCCC
T ss_pred             CCCCCeeCCccccC--CcEecCCCCeeHHHHHHHHHhCcC-cCcCCChhhHh
Confidence            45679999999864  357889999999999999999886 99999988753

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

Probab=99.25  E-value=4.9e-12  Score=87.71  Aligned_cols=51  Identities=25%  Similarity=0.671  Sum_probs=42.8

Q ss_pred             cccccccccccccccCCeeEEcC-CCCcccHHhHHHHHhcCC-CCCCCcccCccCC
Q 028584          148 CEQEECAICLERFKVGDTLVHLP-CAHRFHARCLLPWLATNA-HNCPCCRMQILDP  201 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~wl~~~~-~~CP~CR~~l~~~  201 (207)
                      .++..|+||++.|.++   +.++ |+|.||..||..|+.... ..||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~   65 (74)
T 2yur_A           13 PDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSP   65 (74)
T ss_dssp             CGGGSCSSSCCCCTTC---EECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCT
T ss_pred             CCCCCCcCCChHHhCC---eEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCc
Confidence            4567899999999865   7799 999999999999998652 3899999986543

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

Probab=99.25  E-value=4.4e-12  Score=85.81  Aligned_cols=51  Identities=22%  Similarity=0.565  Sum_probs=42.2

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      .+...|+||++.+.++   +.++|+|.||..||..|+......||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCSP---KQTECGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCCEECTTTCCEESSC---CCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             CcCCCCCCCChHhcCe---eECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            4567899999999765   55899999999999999964434899999988654

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

Probab=99.25  E-value=4.6e-12  Score=89.11  Aligned_cols=48  Identities=25%  Similarity=0.469  Sum_probs=41.8

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      .....|+||++.|.++   +.++|+|.||..||..|+.... .||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~-~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQNP---VVTKCRHYFCESCALEHFRATP-RCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCSE---EECTTSCEEEHHHHHHHHHHCS-BCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcCe---eEccCCCHhHHHHHHHHHHCCC-cCCCcCcccc
Confidence            3567899999999754   6789999999999999998876 9999999875

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

Probab=99.24  E-value=7e-12  Score=88.89  Aligned_cols=54  Identities=31%  Similarity=0.571  Sum_probs=44.5

Q ss_pred             cccccccccccccccCCe-eEEcCCCCcccHHhHHHHHhcC--CCCCCCcccCccCC
Q 028584          148 CEQEECAICLERFKVGDT-LVHLPCAHRFHARCLLPWLATN--AHNCPCCRMQILDP  201 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~-~~~lpC~H~Fh~~Ci~~wl~~~--~~~CP~CR~~l~~~  201 (207)
                      .+...|+||++.|.+.+. ++.++|+|.||..||..|+...  ...||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             cCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            456789999999986543 6888999999999999999976  23899999987543

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

Probab=99.22  E-value=2.7e-12  Score=99.37  Aligned_cols=48  Identities=38%  Similarity=0.874  Sum_probs=41.8

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ++..|+||++.|.++   +.+||+|.||..||..|+.... .||+||.++..
T Consensus        52 ~~~~C~iC~~~~~~~---~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~   99 (138)
T 4ayc_A           52 NELQCIICSEYFIEA---VTLNCAHSFCSYCINEWMKRKI-ECPICRKDIKS   99 (138)
T ss_dssp             HHSBCTTTCSBCSSE---EEETTSCEEEHHHHHHHTTTCS-BCTTTCCBCCC
T ss_pred             ccCCCcccCcccCCc---eECCCCCCccHHHHHHHHHcCC-cCCCCCCcCCC
Confidence            446799999999754   7789999999999999998877 99999998853

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

Probab=99.21  E-value=2.7e-12  Score=87.70  Aligned_cols=49  Identities=39%  Similarity=0.970  Sum_probs=42.4

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      .+...|+||++.+.+    +.++|+|.||..||..|+.... .||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~   61 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHR-NCPICRLQMTGA   61 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEETTTEEECHHHHHHSSCCCS-SCHHHHHCTTCC
T ss_pred             CCCCCCeeCCcCccC----cccCCCCcccHHHHHHHHHCcC-cCCCcCCcccCC
Confidence            356789999999874    7889999999999999998766 999999988754

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

Probab=99.19  E-value=1.1e-11  Score=86.42  Aligned_cols=50  Identities=24%  Similarity=0.461  Sum_probs=42.4

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .+...|+||++.|.++   +.++|+|.||..||..|+.....+||+||..+..
T Consensus         6 ~~~~~C~IC~~~~~~P---v~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~   55 (78)
T 1t1h_A            6 PEYFRCPISLELMKDP---VIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSSCTTTSCCCSSE---EEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             cccCCCCCccccccCC---EEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCCh
Confidence            4567899999999754   6789999999999999998734499999998754

>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=99.19  E-value=7.1e-12  Score=91.91  Aligned_cols=50  Identities=26%  Similarity=0.630  Sum_probs=42.4

Q ss_pred             cccccccccccccccCCeeEE-cCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVGDTLVH-LPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~-lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .+...|+||++.|.++   +. ++|+|.||..||..|+......||+||.++..
T Consensus        20 ~~~~~C~IC~~~~~~p---~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (100)
T 3lrq_A           20 AEVFRCFICMEKLRDA---RLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQL   70 (100)
T ss_dssp             HHHTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCCCCCccCCccccCc---cccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCH
Confidence            4667899999999743   56 89999999999999999873389999998753

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

Probab=99.19  E-value=2.4e-11  Score=81.29  Aligned_cols=45  Identities=31%  Similarity=0.716  Sum_probs=37.6

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhc--CCCCCCCc
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLAT--NAHNCPCC  194 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~--~~~~CP~C  194 (207)
                      ..++..|+||++.|.++   +.++|+|.||..||..|+..  ....||+|
T Consensus        17 ~~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           17 LQEEVICPICLDILQKP---VTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCBCTTTCSBCSSC---EECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             CccCCCCCcCCchhCCe---EEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            34667899999999865   77899999999999999984  22389998

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

Probab=99.18  E-value=2.3e-11  Score=85.24  Aligned_cols=51  Identities=35%  Similarity=0.652  Sum_probs=42.6

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcC-----CCCCCCcccCccCC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATN-----AHNCPCCRMQILDP  201 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~-----~~~CP~CR~~l~~~  201 (207)
                      .+...|+||++.|.++   +.++|+|.||..||..|+...     ...||+||..+...
T Consensus        17 ~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           17 KEEVTCPICLELLKEP---VSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             CTTTSCTTTCSCCSSC---EECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTT
T ss_pred             ccCCCCcCCChhhCcc---eeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHH
Confidence            3567899999999765   678999999999999999982     23899999988643

>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=99.18  E-value=1.5e-11  Score=93.19  Aligned_cols=50  Identities=24%  Similarity=0.490  Sum_probs=42.8

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .+...|+||++.|.++   +.++|+|.||..||..|+......||+||..+..
T Consensus        50 ~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           50 EETFQCICCQELVFRP---ITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHHTBCTTTSSBCSSE---EECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             ccCCCCCcCChHHcCc---EEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            3567899999999754   7789999999999999998554589999998865

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

Probab=99.18  E-value=2.2e-11  Score=87.36  Aligned_cols=50  Identities=24%  Similarity=0.625  Sum_probs=42.3

Q ss_pred             ccccccccccccccccCCeeEEcC-CCCcccHHhHHHHHhcCC-CCCCCcccCcc
Q 028584          147 ACEQEECAICLERFKVGDTLVHLP-CAHRFHARCLLPWLATNA-HNCPCCRMQIL  199 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~wl~~~~-~~CP~CR~~l~  199 (207)
                      ..++..|+||++.|.++   +.++ |+|.||..||..|+.... ..||+||..+.
T Consensus        10 ~~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           10 IPDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CCTTTEETTTTEECSSC---EECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CCcCCCCCCCChhhcCc---eECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            34668899999999865   7889 999999999999997543 48999999874

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

Probab=99.17  E-value=2.1e-11  Score=82.18  Aligned_cols=53  Identities=21%  Similarity=0.547  Sum_probs=42.3

Q ss_pred             cccccccccc-ccccCCe-eEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          149 EQEECAICLE-RFKVGDT-LVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       149 ~~~~C~ICle-~~~~~~~-~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      ++..|+||++ .|.++.. .+.++|||.||..||..|+......||+||..+...
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   56 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccc
Confidence            3567999999 7876543 356799999999999999876544899999988643

>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=99.15  E-value=4e-12  Score=96.51  Aligned_cols=54  Identities=30%  Similarity=0.605  Sum_probs=2.7

Q ss_pred             cccccccccccccccccccCC---------------eeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          144 SWKACEQEECAICLERFKVGD---------------TLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       144 ~~~~~~~~~C~ICle~~~~~~---------------~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      .|+. +++.|+||++.|....               .++.++|+|.||..||.+||..+. +||+||.++.
T Consensus        43 ~wd~-~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~-~CP~Cr~~~~  111 (117)
T 4a0k_B           43 AWDI-VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQ-VCPLDNREWE  111 (117)
T ss_dssp             EECC-CC----------------------------------------------------------------
T ss_pred             eecC-CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCC-cCCCCCCeee
Confidence            3444 5578999999997521               233458999999999999999987 9999999864

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

Probab=99.14  E-value=2.6e-11  Score=84.97  Aligned_cols=50  Identities=32%  Similarity=0.706  Sum_probs=42.2

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhc------CCCCCCCcccCccCC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLAT------NAHNCPCCRMQILDP  201 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~------~~~~CP~CR~~l~~~  201 (207)
                      .+...|+||++.|.++   +.++|+|.||..|+..|+..      .. .||+||..+...
T Consensus        17 ~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~~~-~CP~Cr~~~~~~   72 (85)
T 2ecv_A           17 KEEVTCPICLELLTQP---LSLDCGHSFCQACLTANHKKSMLDKGES-SCPVCRISYQPE   72 (85)
T ss_dssp             CCCCCCTTTCSCCSSC---BCCSSSCCBCTTHHHHHHHHHHHTTSCC-CCTTTCCSSCSS
T ss_pred             cCCCCCCCCCcccCCc---eeCCCCCHHHHHHHHHHHHHhhcCCCCC-cCCCCCCccCHH
Confidence            3567899999999765   66799999999999999987      44 999999988643

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

Probab=99.13  E-value=8.1e-12  Score=86.92  Aligned_cols=50  Identities=26%  Similarity=0.559  Sum_probs=41.9

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcC------CCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATN------AHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~------~~~CP~CR~~l~~  200 (207)
                      .++..|+||++.|.++   +.++|+|.||..||..|+...      ...||+||..+..
T Consensus        10 ~~~~~C~IC~~~~~~p---~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A           10 QEEVTCPICLELLTEP---LSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             CCCCEETTTTEECSSC---CCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCS
T ss_pred             ccCCCCcCCCcccCCe---eECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCH
Confidence            4567899999999765   668999999999999999862      2389999998864

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

Probab=99.12  E-value=2.5e-11  Score=88.36  Aligned_cols=49  Identities=24%  Similarity=0.790  Sum_probs=41.5

Q ss_pred             cccccccccccccccCCeeEEc-CCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVGDTLVHL-PCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .+...|+||++.|.++   +.+ +|+|.||..||..|+.... .||+||..+..
T Consensus        20 ~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~-~CP~Cr~~~~~   69 (99)
T 2y43_A           20 DDLLRCGICFEYFNIA---MIIPQCSHNYCSLCIRKFLSYKT-QCPTCCVTVTE   69 (99)
T ss_dssp             HHHTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHHTTCC-BCTTTCCBCCG
T ss_pred             CCCCCcccCChhhCCc---CEECCCCCHhhHHHHHHHHHCCC-CCCCCCCcCCh
Confidence            3567899999999753   555 8999999999999999776 99999998753

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

Probab=99.11  E-value=3.2e-11  Score=91.14  Aligned_cols=52  Identities=29%  Similarity=0.667  Sum_probs=44.5

Q ss_pred             ccccccccccccccC----CeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          149 EQEECAICLERFKVG----DTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       149 ~~~~C~ICle~~~~~----~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      ++..|+||++.|.++    ..++.++|+|.||..||..|+.... +||+||..+...
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~   61 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINHK   61 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCS-BCTTTCCBCTTT
T ss_pred             CCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCC-CCCCCCCcCccc
Confidence            557799999999754    4558889999999999999999887 999999988643

>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=99.11  E-value=3.4e-11  Score=89.10  Aligned_cols=50  Identities=26%  Similarity=0.651  Sum_probs=42.4

Q ss_pred             ccccccccccccccccCCeeEEc-CCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          147 ACEQEECAICLERFKVGDTLVHL-PCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ..++..|+||++.|.++   +.+ +|+|.||..||..|+.... .||+||..+..
T Consensus        12 ~~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~-~CP~Cr~~~~~   62 (108)
T 2ckl_A           12 LNPHLMCVLCGGYFIDA---TTIIECLHSFCKTCIVRYLETSK-YCPICDVQVHK   62 (108)
T ss_dssp             HGGGTBCTTTSSBCSSE---EEETTTCCEEEHHHHHHHHTSCS-BCTTTCCBSCS
T ss_pred             cCCcCCCccCChHHhCc---CEeCCCCChhhHHHHHHHHHhCC-cCcCCCccccc
Confidence            34667899999999743   555 9999999999999999876 99999998864

>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=99.08  E-value=6.3e-11  Score=93.24  Aligned_cols=50  Identities=24%  Similarity=0.500  Sum_probs=43.0

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      +...|+||++.|.++   +.++|+|.||..||..|+......||+||..+...
T Consensus        77 ~~~~C~IC~~~~~~p---v~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQP---VTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSSE---EECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhcCC---EEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            557799999999754   67899999999999999997655899999998754

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

Probab=99.07  E-value=5.2e-11  Score=77.96  Aligned_cols=44  Identities=32%  Similarity=0.863  Sum_probs=36.4

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhc--CCCCCCCc
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLAT--NAHNCPCC  194 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~--~~~~CP~C  194 (207)
                      .+...|+||++.+.++   +.++|+|.||..||..|+..  ....||+|
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKEP---VIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSSC---CCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccCCCCccCCcccCcc---EeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            4567899999999865   66899999999999999654  23489998

>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=99.06  E-value=2.1e-11  Score=91.11  Aligned_cols=49  Identities=29%  Similarity=0.691  Sum_probs=42.0

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      .++..|+||++.|.++   +.++|+|.||..||..|+......||+||..+.
T Consensus        13 ~~~~~C~iC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   61 (115)
T 3l11_A           13 LSECQCGICMEILVEP---VTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVS   61 (115)
T ss_dssp             HHHHBCTTTCSBCSSC---EECTTSCEECHHHHCCCCCTTTSBCTTTCCBCH
T ss_pred             CCCCCCccCCcccCce---eEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccC
Confidence            3567899999999765   778999999999999999874458999999875

>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=99.05  E-value=6.1e-11  Score=94.05  Aligned_cols=51  Identities=33%  Similarity=0.800  Sum_probs=41.5

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .+...|+||++.|.+  .+..++|+|.||..||..|+......||+||..+..
T Consensus        52 ~~~~~C~IC~~~~~~--p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           52 HSELMCPICLDMLKN--TMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHHBCTTTSSBCSS--EEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCCcccChHhhC--cCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            356789999999974  344459999999999999999744489999998853

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

Probab=99.03  E-value=1.8e-10  Score=80.61  Aligned_cols=51  Identities=25%  Similarity=0.542  Sum_probs=41.2

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCC-CCCCCcccCcc
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNA-HNCPCCRMQIL  199 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~-~~CP~CR~~l~  199 (207)
                      ......|+||.+.|..++  .-..|+|.||..||.+||+... .+||+|+.++.
T Consensus        12 ~~~i~~C~IC~~~i~~g~--~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~   63 (74)
T 2ct0_A           12 PDAVKICNICHSLLIQGQ--SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWP   63 (74)
T ss_dssp             SSSSCBCSSSCCBCSSSE--ECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCC
T ss_pred             cCCCCcCcchhhHcccCC--ccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCC
Confidence            345678999999998653  2227999999999999998762 39999999875

>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=99.02  E-value=1.5e-10  Score=86.58  Aligned_cols=50  Identities=28%  Similarity=0.603  Sum_probs=42.3

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .+...|+||++.|.++   +.++|+|.||..||..|+......||+||..+..
T Consensus        21 ~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (116)
T 1rmd_A           21 VKSISCQICEHILADP---VETSCKHLFCRICILRCLKVMGSYCPSCRYPCFP   70 (116)
T ss_dssp             HHHTBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             cCCCCCCCCCcHhcCc---EEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCH
Confidence            4567899999999754   6689999999999999999743499999998764

>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=99.02  E-value=1.1e-10  Score=87.77  Aligned_cols=50  Identities=32%  Similarity=0.761  Sum_probs=42.6

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .+...|+||++.|.++   +.++|+|.||..||..|+......||+||..+..
T Consensus        16 ~~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   65 (118)
T 3hct_A           16 ESKYECPICLMALREA---VQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLE   65 (118)
T ss_dssp             CGGGBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCCcCChhhcCe---EECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCH
Confidence            4567899999999754   7789999999999999998764489999998754

>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=99.01  E-value=1.2e-10  Score=86.06  Aligned_cols=50  Identities=36%  Similarity=0.707  Sum_probs=41.5

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCC--CCCCCcccCccCC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNA--HNCPCCRMQILDP  201 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~--~~CP~CR~~l~~~  201 (207)
                      +...|+||++.|.++   +.++|+|.||..||..|+....  ..||+||..+...
T Consensus        20 ~~~~C~IC~~~~~~p---~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (112)
T 1jm7_A           20 KILECPICLELIKEP---VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (112)
T ss_dssp             HHTSCSSSCCCCSSC---CBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             CCCCCcccChhhcCe---EECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHh
Confidence            456799999999765   5689999999999999998642  3899999988643

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

Probab=98.97  E-value=1.4e-10  Score=90.38  Aligned_cols=50  Identities=22%  Similarity=0.553  Sum_probs=42.5

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ..+...|+||++.|.++   +.++|+|.||..||..|+......||+||.++.
T Consensus        28 l~~~~~C~IC~~~~~~p---v~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~   77 (141)
T 3knv_A           28 LEAKYLCSACRNVLRRP---FQAQCGHRYCSFCLASILSSGPQNCAACVHEGI   77 (141)
T ss_dssp             CCGGGBCTTTCSBCSSE---EECTTSCEEEHHHHHHHGGGSCEECHHHHHTTC
T ss_pred             CCcCcCCCCCChhhcCc---EECCCCCccCHHHHHHHHhcCCCCCCCCCCccc
Confidence            34667899999999765   678999999999999999866558999999764

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

Probab=98.96  E-value=4.1e-10  Score=80.38  Aligned_cols=48  Identities=15%  Similarity=0.126  Sum_probs=42.6

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      .+...|+||++.|.++   +.++|||.|+..||..|+.... +||+|+.++.
T Consensus        12 p~~~~CpI~~~~m~dP---V~~~cGhtf~r~~I~~~l~~~~-~cP~~~~~l~   59 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTDP---VRLPSGTVMDRSIILRHLLNSP-TDPFNRQMLT   59 (85)
T ss_dssp             CTTTBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHCS-BCTTTCCBCC
T ss_pred             chheECcccCchhcCC---eECCCCCEECHHHHHHHHhcCC-CCCCCcCCCC
Confidence            3567899999999866   8899999999999999999765 9999998875

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

Probab=98.95  E-value=2.7e-10  Score=80.31  Aligned_cols=53  Identities=21%  Similarity=0.552  Sum_probs=40.7

Q ss_pred             cccccccccccccccCCeeEEc--CCCCcccHHhHHHHHhcCCCCCCCcccCccCC
Q 028584          148 CEQEECAICLERFKVGDTLVHL--PCAHRFHARCLLPWLATNAHNCPCCRMQILDP  201 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~l--pC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~  201 (207)
                      .++..|+||++.+...+ +..+  +|||.||..|+..++......||.||..+...
T Consensus         9 ~~~~~CpICle~~~~~d-~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~   63 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDD-INFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED   63 (78)
T ss_dssp             CCCCBCTTTCCBCCTTT-TTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSC
T ss_pred             ccCCcCCccCccCcccc-ccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCC
Confidence            46678999999886432 2334  49999999999999865445899999988643

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

Probab=98.95  E-value=3.2e-10  Score=85.59  Aligned_cols=52  Identities=29%  Similarity=0.671  Sum_probs=44.0

Q ss_pred             cccccccccccccccC----CeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVG----DTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~----~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .+...|+||++.|..+    ..++.++|+|.||..||.+|+.... +||+||.++..
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~  125 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINH  125 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCS-BCTTTCCBCCG
T ss_pred             CCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCC-CCCCCCCcCCh
Confidence            4567799999998753    3457889999999999999999887 99999998864

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2

Probab=98.93  E-value=9.6e-10  Score=80.61  Aligned_cols=49  Identities=16%  Similarity=0.142  Sum_probs=43.1

Q ss_pred             cccccccccccccccCCeeEEcCCC-CcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCA-HRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~-H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .++..|+||++.|.++   +.++|+ |.|+..||..|+.... +||+|+.++..
T Consensus        20 p~~~~CpI~~~~m~dP---V~~~cG~htf~r~cI~~~l~~~~-~cP~~~~~l~~   69 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCDP---VVLPSSRVTVDRSTIARHLLSDQ-TDPFNRSPLTM   69 (98)
T ss_dssp             CTTTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHTTTSC-BCTTTCSBCCT
T ss_pred             cHhcCCcCccccccCC---eECCCCCeEECHHHHHHHHHhCC-CCCCCCCCCCh
Confidence            4567899999999866   889999 9999999999998765 99999998764

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=98.92  E-value=5.1e-10  Score=82.39  Aligned_cols=49  Identities=14%  Similarity=0.145  Sum_probs=43.2

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .+...|+||++.|.++   +.++|||.|+..||..|+.... +||+|+.++..
T Consensus        27 p~~~~CpI~~~~m~dP---V~~~cGhtf~r~~I~~~l~~~~-~cP~~~~~l~~   75 (100)
T 2kre_A           27 PDEFRDPLMDTLMTDP---VRLPSGTIMDRSIILRHLLNSP-TDPFNRQTLTE   75 (100)
T ss_dssp             STTTBCTTTCSBCSSE---EEETTTEEEEHHHHHHHTTSCS-BCSSSCCBCCT
T ss_pred             cHhhCCcCccCcccCC---eECCCCCEEchHHHHHHHHcCC-CCCCCCCCCCh
Confidence            4678899999999866   8889999999999999998765 99999998764

>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A

Probab=98.88  E-value=7.8e-10  Score=74.78  Aligned_cols=47  Identities=32%  Similarity=0.528  Sum_probs=39.2

Q ss_pred             ccccccccccccccCCeeEEc--CCCCc-ccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          149 EQEECAICLERFKVGDTLVHL--PCAHR-FHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~l--pC~H~-Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ++..|.||++.+.+.   +.+  ||+|. ||..|+..|+..+. .||+||.++.
T Consensus         7 ~~~~C~IC~~~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~~-~CPiCR~~i~   56 (64)
T 2vje_A            7 AIEPCVICQGRPKNG---CIVHGKTGHLMACFTCAKKLKKRNK-PCPVCRQPIQ   56 (64)
T ss_dssp             GGSCCTTTSSSCSCE---EEEETTEEEEEECHHHHHHHHHTTC-CCTTTCCCCC
T ss_pred             CcCCCCcCCCCCCCE---EEECCCCCChhhHHHHHHHHHHcCC-cCCCcCcchh
Confidence            556799999987643   444  99999 89999999998776 9999999874

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

Probab=98.86  E-value=4.8e-10  Score=73.69  Aligned_cols=48  Identities=27%  Similarity=0.506  Sum_probs=39.5

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCCC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPA  202 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~~  202 (207)
                      .+...|+||++.|.++   +.++|+|.||..|+..|   .. .||+||..+..+.
T Consensus         4 ~~~~~C~IC~~~~~~p---~~l~CgH~fC~~Ci~~~---~~-~CP~Cr~~~~~~~   51 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCP---KLLPCLHTLCSGCLEAS---GM-QCPICQAPWPLGA   51 (56)
T ss_dssp             CCCSSCSSSCSSCBCC---SCSTTSCCSBTTTCSSS---SS-SCSSCCSSSSCCS
T ss_pred             ccCCCceEeCCccCCe---EEcCCCCcccHHHHccC---CC-CCCcCCcEeecCC
Confidence            3567799999999865   77899999999999774   33 8999999887543

>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=98.84  E-value=1.4e-09  Score=91.56  Aligned_cols=50  Identities=14%  Similarity=0.117  Sum_probs=43.3

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ......|+||++.|.++   ++++|||+||..||..|+..+..+||+|+.++.
T Consensus       205 ~~~~~~c~i~~~~~~dP---v~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~  254 (281)
T 2c2l_A          205 IPDYLCGKISFELMREP---CITPSGITYDRKDIEEHLQRVGHFNPVTRSPLT  254 (281)
T ss_dssp             CCSTTBCTTTCSBCSSE---EECSSCCEEETTHHHHHHHHTCSSCTTTCCCCC
T ss_pred             CCcccCCcCcCCHhcCC---eECCCCCEECHHHHHHHHHHCCCCCcCCCCCCc
Confidence            34677899999999866   889999999999999999976536999999875

>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=98.82  E-value=5e-10  Score=84.06  Aligned_cols=47  Identities=23%  Similarity=0.550  Sum_probs=40.3

Q ss_pred             cccccccccccccccCCeeEEc-CCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVGDTLVHL-PCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .+...|+||++.|.++   +.+ +|+|.||..||..|+.  . .||+||..+..
T Consensus        20 ~~~~~C~IC~~~~~~p---v~~~~CgH~fC~~Ci~~~~~--~-~CP~Cr~~~~~   67 (117)
T 1jm7_B           20 EKLLRCSRCTNILREP---VCLGGCEHIFCSNCVSDCIG--T-GCPVCYTPAWI   67 (117)
T ss_dssp             HHTTSCSSSCSCCSSC---BCCCSSSCCBCTTTGGGGTT--T-BCSSSCCBCSC
T ss_pred             hhCCCCCCCChHhhCc---cEeCCCCCHHHHHHHHHHhc--C-CCcCCCCcCcc
Confidence            4567899999999765   667 8999999999999987  4 89999998853

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B*

Probab=98.81  E-value=1.7e-09  Score=72.93  Aligned_cols=49  Identities=24%  Similarity=0.530  Sum_probs=39.5

Q ss_pred             ccccccccccccccCCeeEEcCCCCc-ccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHR-FHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ....|.||++.+.+. .++.+||+|. ||..|+..|...+. .||+||.++.
T Consensus         6 ~~~~C~IC~~~~~~~-~~~~~pCgH~~~C~~C~~~~~~~~~-~CPiCR~~i~   55 (63)
T 2vje_B            6 LLKPCSLCEKRPRDG-NIIHGRTGHLVTCFHCARRLKKAGA-SCPICKKEIQ   55 (63)
T ss_dssp             GGSBCTTTSSSBSCE-EEEETTEEEEEECHHHHHHHHHTTC-BCTTTCCBCC
T ss_pred             cCCCCcccCCcCCCe-EEEecCCCCHhHHHHHHHHHHHhCC-cCCCcCchhh
Confidence            456799999987643 2334599998 99999999988775 9999999874

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=98.79  E-value=1.1e-09  Score=76.04  Aligned_cols=43  Identities=33%  Similarity=0.763  Sum_probs=37.1

Q ss_pred             ccccccccccccccCCeeEEcCCCCc-ccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHR-FHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ++..|+||++.+.+   ++.+||+|. ||..|+..|    . .||+||..+.
T Consensus        23 ~~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~----~-~CP~Cr~~i~   66 (74)
T 4ic3_A           23 EEKLCKICMDRNIA---IVFVPCGHLVTCKQCAEAV----D-KCPMCYTVIT   66 (74)
T ss_dssp             HHTBCTTTSSSBCC---EEEETTCCBCCCHHHHTTC----S-BCTTTCCBCS
T ss_pred             cCCCCCCCCCCCCC---EEEcCCCChhHHHHhhhcC----c-cCCCcCcCcc
Confidence            55679999999864   478899999 999999998    3 8999999875

>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=98.78  E-value=2.5e-09  Score=85.00  Aligned_cols=51  Identities=31%  Similarity=0.738  Sum_probs=43.0

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ..+...|+||++.|.++   +.++|+|.||..||..|+......||+||..+..
T Consensus        15 ~~~~~~C~IC~~~~~~p---v~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   65 (170)
T 3hcs_A           15 LESKYECPICLMALREA---VQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLE   65 (170)
T ss_dssp             CCGGGBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCCCCCChhhcCc---EECCCCCHHHHHHHHHHHHhCCCCCCCCccCcch
Confidence            34667899999999755   6789999999999999998654489999988754

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

Probab=98.78  E-value=3.1e-09  Score=95.31  Aligned_cols=48  Identities=33%  Similarity=0.761  Sum_probs=40.3

Q ss_pred             cccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          150 QEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       150 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ...|+||++.+.+   ++.+||+|.||..|+..|+......||+||.++..
T Consensus       332 ~~~C~ICle~~~~---pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~  379 (389)
T 2y1n_A          332 FQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKG  379 (389)
T ss_dssp             SSBCTTTSSSBCC---EEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCE
T ss_pred             CCCCCccCcCCCC---eEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCC
Confidence            3679999999864   48899999999999999998433399999998764

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.73  E-value=6.1e-09  Score=75.46  Aligned_cols=46  Identities=22%  Similarity=0.502  Sum_probs=38.6

Q ss_pred             ccccccccccccccCCeeEEcC-CCCcccHHhHHHHHhcC-----CCCCCC--cccC
Q 028584          149 EQEECAICLERFKVGDTLVHLP-CAHRFHARCLLPWLATN-----AHNCPC--CRMQ  197 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~wl~~~-----~~~CP~--CR~~  197 (207)
                      +...|+||++.|.++   +.++ |||.|+..||..|+..+     ..+||+  |+..
T Consensus         6 ~~~~CPI~~~~~~dP---V~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            6 SGFTCPITKEEMKKP---VKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             SCCBCTTTCSBCSSE---EEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             cEeECcCcCchhcCC---EEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            557799999999865   7785 99999999999999864     238999  9855

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=98.68  E-value=1.1e-08  Score=82.80  Aligned_cols=50  Identities=14%  Similarity=0.108  Sum_probs=42.9

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ..+...|+||++.|.++   +.++|||.|+..||..|+..+..+||+|+.++.
T Consensus       103 ip~~f~CPI~~elm~DP---V~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~  152 (179)
T 2f42_A          103 IPDYLCGKISFELMREP---CITPSGITYDRKDIEEHLQRVGHFDPVTRSPLT  152 (179)
T ss_dssp             CCGGGBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CcHhhcccCccccCCCC---eECCCCCEECHHHHHHHHHhCCCCCCCCcCCCC
Confidence            34678899999999865   888999999999999999875437999998875

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.67  E-value=4.2e-09  Score=73.02  Aligned_cols=44  Identities=32%  Similarity=0.657  Sum_probs=36.3

Q ss_pred             ccccccccccccccCCeeEEcCCCCc-ccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHR-FHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ++..|+||++.+.+.   +.+||+|. ||..|+..+    . .||+||.++..
T Consensus        24 ~~~~C~IC~~~~~~~---~~~pCgH~~~C~~C~~~~----~-~CP~Cr~~i~~   68 (75)
T 2ecg_A           24 EEKLCKICMDRNIAI---VFVPCGHLVTCKQCAEAV----D-KCPMCYTVITF   68 (75)
T ss_dssp             HHHSCSSSCSSCCCB---CCSSSCCCCBCHHHHHHC----S-BCTTTCCBCCC
T ss_pred             CCCCCCcCCCCCCCE---EEecCCCHHHHHHHhhCC----C-CCccCCceecC
Confidence            456799999998654   77899999 999999642    3 89999998864

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.61  E-value=2.7e-08  Score=68.04  Aligned_cols=46  Identities=26%  Similarity=0.648  Sum_probs=37.4

Q ss_pred             ccccccccccccccccCCeeEEcCCCCc-ccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHR-FHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ..+...|.||++.+.+   ++.+||+|. ||..|+..    .. .||+||..|..
T Consensus        12 ~~~~~~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~----~~-~CP~CR~~i~~   58 (68)
T 2ea5_A           12 EENSKDCVVCQNGTVN---WVLLPCRHTCLCDGCVKY----FQ-QCPMCRQFVQE   58 (68)
T ss_dssp             CCCSSCCSSSSSSCCC---CEETTTTBCCSCTTHHHH----CS-SCTTTCCCCCC
T ss_pred             CCCCCCCCCcCcCCCC---EEEECCCChhhhHHHHhc----CC-CCCCCCcchhc
Confidence            3456789999998764   588999999 99999984    23 89999998854

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

Probab=98.56  E-value=1.1e-08  Score=90.40  Aligned_cols=52  Identities=29%  Similarity=0.666  Sum_probs=39.9

Q ss_pred             cccccccccccccccCCeeE-----EcCCCCcccHHhHHHHHhcCC----------CCCCCcccCcc
Q 028584          148 CEQEECAICLERFKVGDTLV-----HLPCAHRFHARCLLPWLATNA----------HNCPCCRMQIL  199 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~-----~lpC~H~Fh~~Ci~~wl~~~~----------~~CP~CR~~l~  199 (207)
                      ....+|+||+..+.++..+.     ..+|+|.||..||.+||....          ..||+||.+|.
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs  372 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLS  372 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEE
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCC
Confidence            45678999999988732221     246999999999999998531          16999999875

>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=98.53  E-value=4.3e-08  Score=70.59  Aligned_cols=49  Identities=27%  Similarity=0.583  Sum_probs=38.7

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcC-------CCCCCC--cccC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATN-------AHNCPC--CRMQ  197 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~-------~~~CP~--CR~~  197 (207)
                      +..+|+||++++..++.+...+|+|.||..||..++...       ...||.  |+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            346799999999876544445799999999999998742       127999  9987

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.50  E-value=7.6e-08  Score=64.36  Aligned_cols=50  Identities=24%  Similarity=0.559  Sum_probs=37.8

Q ss_pred             ccccccccccccccccCCeeEEcCCC--C---cccHHhHHHHHhcC-CCCCCCcccCcc
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCA--H---RFHARCLLPWLATN-AHNCPCCRMQIL  199 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~--H---~Fh~~Ci~~wl~~~-~~~CP~CR~~l~  199 (207)
                      ..+...|.||++...  +.+ .+||.  +   .||..||.+|+... +.+||+|+.++.
T Consensus         3 ~~~~~~CrIC~~~~~--~~l-~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            3 DEDVPVCWICNEELG--NER-FRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             TCSCCEETTTTEECS--CCC-CCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCEeEEeecCCC--Cce-ecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            345678999999743  233 58864  4   89999999999852 348999998875

>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=98.47  E-value=2.8e-08  Score=69.83  Aligned_cols=43  Identities=28%  Similarity=0.638  Sum_probs=36.0

Q ss_pred             ccccccccccccccCCeeEEcCCCCc-ccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHR-FHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ++..|.||++.+.+   ++.+||+|. ||..|+..|    . .||+||..+.
T Consensus        17 ~~~~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~~----~-~CP~Cr~~i~   60 (79)
T 2yho_A           17 EAMLCMVCCEEEIN---STFCPCGHTVCCESCAAQL----Q-SCPVCRSRVE   60 (79)
T ss_dssp             HHTBCTTTSSSBCC---EEEETTCBCCBCHHHHTTC----S-BCTTTCCBCC
T ss_pred             CCCEeEEeCcccCc---EEEECCCCHHHHHHHHHhc----C-cCCCCCchhh
Confidence            45679999998764   488999999 999999876    2 8999998774

>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=98.33  E-value=9.3e-08  Score=84.63  Aligned_cols=44  Identities=30%  Similarity=0.753  Sum_probs=38.0

Q ss_pred             cccccccccccccccCCeeEEcCCCCc-ccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHR-FHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~-Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      .++..|+||++.+.+   ++.+||+|. ||..|+..|    . .||+||.++.
T Consensus       293 ~~~~~C~IC~~~~~~---~v~lpCgH~~fC~~C~~~~----~-~CP~CR~~i~  337 (345)
T 3t6p_A          293 QEERTCKVCMDKEVS---VVFIPCGHLVVCQECAPSL----R-KCPICRGIIK  337 (345)
T ss_dssp             HTTCBCTTTSSSBCC---EEEETTCCEEECTTTGGGC----S-BCTTTCCBCC
T ss_pred             cCCCCCCccCCcCCc---eEEcCCCChhHhHHHHhcC----C-cCCCCCCCcc
Confidence            466789999999864   478899999 999999988    3 8999999875

>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=98.29  E-value=2.9e-07  Score=78.48  Aligned_cols=50  Identities=20%  Similarity=0.478  Sum_probs=40.4

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCC-CCCCC--cccCcc
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNA-HNCPC--CRMQIL  199 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~-~~CP~--CR~~l~  199 (207)
                      .....|+||++.|.++  ++.+.|||.||..||..|+..+. ..||+  |+..+.
T Consensus       179 ~~el~CPIcl~~f~DP--Vts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~  231 (267)
T 3htk_C          179 KIELTCPITCKPYEAP--LISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVS  231 (267)
T ss_dssp             BCCSBCTTTSSBCSSE--EEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEEC
T ss_pred             ceeeECcCccCcccCC--eeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCc
Confidence            4667899999999754  44458999999999999998643 37999  998664

>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=98.21  E-value=4.7e-07  Score=60.61  Aligned_cols=45  Identities=18%  Similarity=0.129  Sum_probs=39.3

Q ss_pred             ccccccccccccCCeeEEc-CCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          151 EECAICLERFKVGDTLVHL-PCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       151 ~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ..|+||++.+.++   +.+ +|||+|...||.+|+..+. +||+.+.++.
T Consensus         4 ~~CpIs~~~m~dP---V~~~~sG~~yer~~I~~~l~~~~-~cP~t~~~L~   49 (61)
T 2bay_A            4 MLCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTG-NDPITNEPLS   49 (61)
T ss_dssp             CCCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHS-BCTTTCCBCC
T ss_pred             EEecCCCCCCCCC---EEeCCCCcEEcHHHHHHHHHhCC-CCcCCcCCCC
Confidence            4699999999854   666 8999999999999999876 8999998774

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.18  E-value=1.3e-06  Score=63.86  Aligned_cols=46  Identities=24%  Similarity=0.444  Sum_probs=38.3

Q ss_pred             cccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          152 ECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       152 ~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      .|.+|--.|.  ...+.+||.|+||.+|+..|.+.....||.|+.+|.
T Consensus         3 fC~~C~~Pi~--iygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~   48 (101)
T 3vk6_A            3 FCDKCGLPIK--VYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQ   48 (101)
T ss_dssp             BCTTTCSBCS--EEEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCS
T ss_pred             ecCccCCCeE--EEeeeccccccHHHHHHHHHHhccCCCCcCcCCeee
Confidence            4888887775  356788999999999999998765559999998875

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

Probab=97.50  E-value=0.0001  Score=61.81  Aligned_cols=49  Identities=27%  Similarity=0.590  Sum_probs=39.7

Q ss_pred             ccccccccccccccCCeeEEcC-CCCcccHHhHHHHHhcCC-CCCCCcccCccC
Q 028584          149 EQEECAICLERFKVGDTLVHLP-CAHRFHARCLLPWLATNA-HNCPCCRMQILD  200 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~wl~~~~-~~CP~CR~~l~~  200 (207)
                      ....|.||.+.+..+   ..-+ |+|.||..|+..|++... ..||.|+..+..
T Consensus       179 ~i~~C~iC~~iv~~g---~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~  229 (238)
T 3nw0_A          179 AVKICNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPH  229 (238)
T ss_dssp             TCCBCTTTCSBCSSC---EECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCS
T ss_pred             CCCcCcchhhHHhCC---cccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCC
Confidence            467899999998866   3333 999999999999998643 489999998864

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=94.43  E-value=0.025  Score=40.31  Aligned_cols=35  Identities=17%  Similarity=0.359  Sum_probs=25.6

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHH
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPW  183 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~w  183 (207)
                      ++..|.||.+.+..+....-+.|+|.||..|+..+
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETTTTEEECHHHHHHH
T ss_pred             CCCCCcCCCCCCCCCceEECCcCChHHhHHHCHHH
Confidence            45679999986433223333899999999999983

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=93.20  E-value=0.061  Score=36.07  Aligned_cols=50  Identities=26%  Similarity=0.565  Sum_probs=33.6

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCC---CCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNA---HNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~---~~CP~CR~~l~~  200 (207)
                      .....|.||.+.   ++.+.=-.|...||..|+.+.+....   -.||.|.....+
T Consensus        10 ~~~~~C~vC~~~---~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~p   62 (66)
T 2lri_C           10 APGARCGVCGDG---TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDVTP   62 (66)
T ss_dssp             CTTCCCTTTSCC---TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCCCC
T ss_pred             CCCCCcCCCCCC---CeEEECCCCCCceecccCCCccCcCCCCCEECccccCCCcc
Confidence            345679999753   33222224899999999988776543   279999865543

>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=92.27  E-value=0.081  Score=37.31  Aligned_cols=33  Identities=27%  Similarity=0.636  Sum_probs=23.9

Q ss_pred             ccccccccccccccccCCeeEEcC---CCCcccHHhHHHH
Q 028584          147 ACEQEECAICLERFKVGDTLVHLP---CAHRFHARCLLPW  183 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lp---C~H~Fh~~Ci~~w  183 (207)
                      ...+..|.||-.. ..+   ..+|   |+-+||..|+.+.
T Consensus        12 ~~~D~~C~VC~~~-t~~---~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           12 VVNDEMCDVCEVW-TAE---SLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCSCCCTTTCCC-CSS---CCSSCSSSSSCCCHHHHHHH
T ss_pred             CCCCcccCccccc-ccc---ceeccccccccccHhhcccc
Confidence            3467889999633 333   3455   7899999999996

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=85.37  E-value=0.35  Score=31.55  Aligned_cols=48  Identities=25%  Similarity=0.701  Sum_probs=31.3

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCC---CCCCCcccC
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNA---HNCPCCRMQ  197 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~---~~CP~CR~~  197 (207)
                      ...+..|.||...   ++.+.--.|...||..|+.+-+....   -.||.|...
T Consensus         8 ~~~~~~C~vC~~~---g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            8 TDHQDYCEVCQQG---GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             SCCCSSCTTTSCC---SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCCCccCCCC---CcEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            4466779999873   32222224889999999987443221   279999653

>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=84.01  E-value=0.93  Score=28.44  Aligned_cols=44  Identities=20%  Similarity=0.310  Sum_probs=28.2

Q ss_pred             cccccccccccCCeeEEc--CCCCcccHHhHHHH---HhcCCCCCCCcc
Q 028584          152 ECAICLERFKVGDTLVHL--PCAHRFHARCLLPW---LATNAHNCPCCR  195 (207)
Q Consensus       152 ~C~ICle~~~~~~~~~~l--pC~H~Fh~~Ci~~w---l~~~~~~CP~CR  195 (207)
                      .|.||...+..+...+.-  .|...||..|+.--   .......||.|+
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            377888887544444443  38889999998422   112334899985

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=83.29  E-value=0.22  Score=33.65  Aligned_cols=50  Identities=22%  Similarity=0.408  Sum_probs=32.8

Q ss_pred             ccccccccccccccCCeeEEc-CCCCcccHHhHHHHHhcC---CCCCCCcccCcc
Q 028584          149 EQEECAICLERFKVGDTLVHL-PCAHRFHARCLLPWLATN---AHNCPCCRMQIL  199 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~wl~~~---~~~CP~CR~~l~  199 (207)
                      +...|.||..... ++.++.- .|...||..|+..-....   ...||.|...+.
T Consensus        17 ~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~   70 (75)
T 2k16_A           17 QIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIK   70 (75)
T ss_dssp             EEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHC
T ss_pred             CCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchh
Confidence            4556999987653 3334433 389999999996543321   237999976553

>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=82.50  E-value=0.6  Score=30.43  Aligned_cols=49  Identities=22%  Similarity=0.549  Sum_probs=33.1

Q ss_pred             cccccccccccccccCCeeEEc-CCCCcccHHhHHHHHh----cCCCCCCCccc
Q 028584          148 CEQEECAICLERFKVGDTLVHL-PCAHRFHARCLLPWLA----TNAHNCPCCRM  196 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~wl~----~~~~~CP~CR~  196 (207)
                      .+...|+||...+.++..++.- .|...||..|+.--..    .....||.|+.
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~   57 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcC
Confidence            3556799999887544444443 4999999999854322    12248999965

>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=82.37  E-value=0.97  Score=30.81  Aligned_cols=49  Identities=20%  Similarity=0.525  Sum_probs=30.9

Q ss_pred             ccccccccccccccCCeeEEc-CCCCcccHHhHHHHHh----cCCCCCCCcccCc
Q 028584          149 EQEECAICLERFKVGDTLVHL-PCAHRFHARCLLPWLA----TNAHNCPCCRMQI  198 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~wl~----~~~~~CP~CR~~l  198 (207)
                      +...| ||...+.....++.- .|..+||..|+.--..    .....||.|+...
T Consensus        11 ~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A           11 VPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             CccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            33446 998877433344443 4999999999943211    1224899998654

>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2

Probab=82.35  E-value=0.42  Score=32.39  Aligned_cols=48  Identities=21%  Similarity=0.408  Sum_probs=29.9

Q ss_pred             cccccccccccccCCeeEEc-CCCCcccHHhHHHHH--------hcCCCCCCCcccCcc
Q 028584          150 QEECAICLERFKVGDTLVHL-PCAHRFHARCLLPWL--------ATNAHNCPCCRMQIL  199 (207)
Q Consensus       150 ~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~wl--------~~~~~~CP~CR~~l~  199 (207)
                      ...| ||....... .++.- .|..+||..|+.--.        ......||.|+..-.
T Consensus        16 ~~~C-~C~~~~~~~-~MI~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~~~   72 (76)
T 1wem_A           16 ALYC-ICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILSG   72 (76)
T ss_dssp             CCCS-TTCCCCCSS-CEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHSC
T ss_pred             CCEE-ECCCccCCC-CEEEeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCccC
Confidence            3456 898876532 33333 499999999993211        112348999976443

---

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	207
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	4e-13
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	4e-11
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	5e-11
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	9e-10
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	2e-08
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	6e-08
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	5e-07
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	1e-06
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	4e-06
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	2e-05
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	6e-05
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	4e-04
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	5e-04
d1t1ha_	78	g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cre	0.002

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 59.5 bits (144), Expect = 4e-13
 Identities = 20/52 (38%), Positives = 30/52 (57%), Gaps = 2/52 (3%)

Query: 149 EQEECAICLERFKVGDTLVHLP-CAHRFHARCLLPWLATNAHNCPCCRMQIL 199
           +  ECA+CL   + G+    LP C H FHA C+  WL ++   CP CR+ ++
Sbjct: 4   DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSH-STCPLCRLTVV 54

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 54.6 bits (131), Expect = 4e-11
 Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 3/52 (5%)

Query: 147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
           A   E C ICLE     +  + LPC H F   C+  W+  N   CP C++ +
Sbjct: 2   ATVAERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQN-PTCPLCKVPV 50

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (131), Expect = 5e-11
 Identities = 16/50 (32%), Positives = 20/50 (40%), Gaps = 3/50 (6%)

Query: 149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
             + C IC E  K    +   PC H     CL  W  +    CP CR +I
Sbjct: 22  TFQLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 68

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 9e-10
 Identities = 11/52 (21%), Positives = 17/52 (32%), Gaps = 2/52 (3%)

Query: 149 EQEECAICLERFKVGDTLVHL--PCAHRFHARCLLPWLATNAHNCPCCRMQI 198
           + + C  C        +L  +   C H     C+       A NCP C   +
Sbjct: 2   DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

>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 = 47.0 bits (111), Expect = 2e-08
 Identities = 11/48 (22%), Positives = 17/48 (35%), Gaps = 1/48 (2%)

Query: 152 ECAICLERFKVGDT-LVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
           EC +C+E  ++ D       C ++    C           CP CR   
Sbjct: 2   ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPY 49

>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 = 46.7 bits (110), Expect = 6e-08
 Identities = 16/70 (22%), Positives = 21/70 (30%), Gaps = 17/70 (24%)

Query: 141 SKLSWKACEQEECAICLERF---------------KVGDTLVHLPCAHRFHARCLLPWLA 185
           +  +W     + CAIC                       T+    C H FH  C+  WL 
Sbjct: 13  ALWAWDIVV-DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLK 71

Query: 186 TNAHNCPCCR 195
           T    CP   
Sbjct: 72  TR-QVCPLDN 80

>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 = 43.3 bits (102), Expect = 5e-07
 Identities = 12/47 (25%), Positives = 14/47 (29%), Gaps = 7/47 (14%)

Query: 152 ECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
            C  C    K       LPC H   + CL          CP C+   
Sbjct: 8   RCQQCQAEAKCP---KLLPCLHTLCSGCLEASGMQ----CPICQAPW 47

>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 = 43.0 bits (101), Expect = 1e-06
 Identities = 14/46 (30%), Positives = 15/46 (32%), Gaps = 3/46 (6%)

Query: 153 CAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
           C IC          V   C H F   C+L  L      CP CR   
Sbjct: 26  CQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPC 68

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 4e-06
 Identities = 18/52 (34%), Positives = 21/52 (40%), Gaps = 5/52 (9%)

Query: 149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLAT--NAHNCPCCRMQI 198
           +  EC ICLE  K     V   C H F   C+L  L        CP C+  I
Sbjct: 20  KILECPICLELIK---EPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 68

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 38.7 bits (89), Expect = 2e-05
 Identities = 11/53 (20%), Positives = 15/53 (28%), Gaps = 3/53 (5%)

Query: 149 EQEECAICLERFKVGDTL--VHLPCAHRFHARCLLPWLATNAHN-CPCCRMQI 198
           +   C IC E                   H  CL  WL  + +  C  C +  
Sbjct: 5   DVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVY 57

>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 = 38.5 bits (89), Expect = 6e-05
 Identities = 10/54 (18%), Positives = 14/54 (25%), Gaps = 7/54 (12%)

Query: 149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHN-------CPCCR 195
               C +CL  + V        C   F   CL  ++             CP   
Sbjct: 4   GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA 57

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (83), Expect = 4e-04
 Identities = 9/43 (20%), Positives = 15/43 (34%), Gaps = 2/43 (4%)

Query: 149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNC 191
           +   C+ C    +    L    C H F + C+   + T    C
Sbjct: 21  KLLRCSRCTNILREPVCL--GGCEHIFCSNCVSDCIGTGCPVC 61

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.2 bits (82), Expect = 5e-04
 Identities = 17/72 (23%), Positives = 24/72 (33%), Gaps = 19/72 (26%)

Query: 146 KACEQEECAICLERFKV---------------GDTLVHLPCAHRFHARCLLPWLATNAHN 190
           K   +E+C IC+E+  V                       C+H FH  CLL        +
Sbjct: 21  KVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKD 80

Query: 191 ----CPCCRMQI 198
               CP C+   
Sbjct: 81  GSLQCPSCKTIY 92

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 78

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 33.9 bits (77), Expect = 0.002
 Identities = 10/46 (21%), Positives = 15/46 (32%), Gaps = 3/46 (6%)

Query: 153 CAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQI 198
           C I LE  K     V +     +    +  WL      CP  +  +
Sbjct: 11  CPISLELMK---DPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETL 53

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	207
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.57
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.4
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.37
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.35
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.35
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.32
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.3
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.24
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.14
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.13
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.08
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.07
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.04
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.95
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.9
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.69
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.41
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	90.35
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	90.21
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	90.14
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	89.5
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	86.39
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	83.19
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	82.55

>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=99.57  E-value=3.8e-16  Score=101.99  Aligned_cols=50  Identities=40%  Similarity=1.054  Sum_probs=44.8

Q ss_pred             ccccccccccccccCCeeEEcC-CCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          149 EQEECAICLERFKVGDTLVHLP-CAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lp-C~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ++.+|+||++.|..++.+..++ |+|.||..||.+|+..++ +||+||.+|+
T Consensus         4 d~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~-~CP~CR~~i~   54 (55)
T d1iyma_           4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHS-TCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCC-SCSSSCCCSC
T ss_pred             CCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCC-cCCCCCCEeE
Confidence            4567999999999888888875 999999999999999887 9999999875

>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=99.40  E-value=5.8e-14  Score=94.95  Aligned_cols=47  Identities=36%  Similarity=0.884  Sum_probs=41.2

Q ss_pred             cccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          150 QEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       150 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      .+.|+||++.|.+  .++.++|+|.||..||.+|++.+. +||+||.++.
T Consensus         5 ~d~C~IC~~~~~~--~~~~~~C~H~Fc~~Ci~~w~~~~~-~CP~CR~~i~   51 (68)
T d1chca_           5 AERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNP-TCPLCKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCCCS--CEEETTTTEEESTTHHHHHHHHSC-STTTTCCCCC
T ss_pred             CCCCccCCcCccC--CcEEeCCCCcCcHHHHHHHHHhCC-cCCCCCcchH
Confidence            4569999999963  456789999999999999999887 9999999874

>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=99.37  E-value=5.2e-14  Score=90.53  Aligned_cols=49  Identities=22%  Similarity=0.594  Sum_probs=40.8

Q ss_pred             cccccccccccCCe-eEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          152 ECAICLERFKVGDT-LVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       152 ~C~ICle~~~~~~~-~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      +|+||+++|..++. +..++|+|.||..|+.+|+...+.+||+||.++.+
T Consensus         2 eCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            59999999976543 44568999999999999998765479999998864

>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=99.35  E-value=3.7e-13  Score=93.58  Aligned_cols=51  Identities=31%  Similarity=0.719  Sum_probs=42.5

Q ss_pred             cccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCCCC
Q 028584          150 QEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAA  203 (207)
Q Consensus       150 ~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~~~  203 (207)
                      ...|+||++.+.+   ++.++|+|.||..||..|+..+...||+||..|.....
T Consensus        23 ~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~   73 (79)
T d1fbva4          23 FQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP   73 (79)
T ss_dssp             TTBCTTTSSSBCC---EECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCC
T ss_pred             CCCCccCCCcCCC---eEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCce
Confidence            3469999999864   48899999999999999998654489999999976543

>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=99.35  E-value=3.1e-13  Score=90.62  Aligned_cols=52  Identities=21%  Similarity=0.475  Sum_probs=41.4

Q ss_pred             ccccccccccccccC-C-eeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          149 EQEECAICLERFKVG-D-TLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       149 ~~~~C~ICle~~~~~-~-~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ++..|+||++.+..+ + .+..++|+|.||..||..|+......||+||.++..
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~   55 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRK   55 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSS
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCccc
Confidence            467899999976433 2 345678999999999999997655489999998854

>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=99.32  E-value=4.1e-13  Score=95.07  Aligned_cols=50  Identities=30%  Similarity=0.553  Sum_probs=41.7

Q ss_pred             ccccccccccccccCC---------------eeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          149 EQEECAICLERFKVGD---------------TLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~---------------~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      .++.|+||++.+....               .+..++|+|.||..||.+||+.++ +||+||.++.
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~~~   84 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQ-VCPLDNREWE   84 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCS-BCSSSCSBCC
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCC-cCCCCCCccc
Confidence            4456999998876531               367789999999999999999987 9999999874

>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=99.30  E-value=1e-12  Score=96.71  Aligned_cols=54  Identities=30%  Similarity=0.679  Sum_probs=41.9

Q ss_pred             ccccccccccccccC---------------CeeEEcCCCCcccHHhHHHHHhcCC----CCCCCcccCccCCC
Q 028584          149 EQEECAICLERFKVG---------------DTLVHLPCAHRFHARCLLPWLATNA----HNCPCCRMQILDPA  202 (207)
Q Consensus       149 ~~~~C~ICle~~~~~---------------~~~~~lpC~H~Fh~~Ci~~wl~~~~----~~CP~CR~~l~~~~  202 (207)
                      .+..|+||++.|...               ..+..++|+|.||..||..|+...+    .+||+||..+....
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~   96 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKT   96 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCS
T ss_pred             ccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccCc
Confidence            345799999988542               2456778999999999999998643    27999998876543

>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=99.24  E-value=1.3e-12  Score=92.36  Aligned_cols=50  Identities=28%  Similarity=0.603  Sum_probs=42.3

Q ss_pred             cccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          148 CEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .+...|+||++.|.++   +.++|+|.||..||..|++.....||+||.++..
T Consensus        21 ~~~l~C~IC~~~~~~p---v~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~   70 (86)
T d1rmda2          21 VKSISCQICEHILADP---VETSCKHLFCRICILRCLKVMGSYCPSCRYPCFP   70 (86)
T ss_dssp             HHHTBCTTTCSBCSSE---EECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             ccCcCCccCCcchhcc---eecCCCChhhHHHHHHHHhhCCCcCcccCCCCCh
Confidence            3556799999999754   7889999999999999998665489999998754

>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=99.14  E-value=3.2e-12  Score=83.26  Aligned_cols=48  Identities=27%  Similarity=0.509  Sum_probs=39.5

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccCCCC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILDPAA  203 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~~~~  203 (207)
                      +...|+||++.|.++   +.+||+|.||..||..|   .. +||+||.++...+.
T Consensus         5 ~~l~C~IC~~~~~~p---~~lpCgH~fC~~Ci~~~---~~-~CP~Cr~~~~~~~~   52 (56)
T d1bora_           5 QFLRCQQCQAEAKCP---KLLPCLHTLCSGCLEAS---GM-QCPICQAPWPLGAD   52 (56)
T ss_dssp             CCSSCSSSCSSCBCC---SCSTTSCCSBTTTCSSS---SS-SCSSCCSSSSCCSS
T ss_pred             CCCCCcccCcccCCC---EEecCCCHHhHHHHHcC---CC-cCcCCCCcccCCCC
Confidence            345799999999765   77899999999999765   33 89999999976544

>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=99.13  E-value=9.3e-12  Score=90.17  Aligned_cols=49  Identities=37%  Similarity=0.728  Sum_probs=41.2

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCC--CCCCCcccCccC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNA--HNCPCCRMQILD  200 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~--~~CP~CR~~l~~  200 (207)
                      +...|+||++.|.++   +.++|+|.||..||..|+....  ..||+||.++..
T Consensus        20 ~~l~CpIC~~~~~~p---v~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (103)
T d1jm7a_          20 KILECPICLELIKEP---VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (103)
T ss_dssp             HHTSCSSSCCCCSSC---CBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             cCcCCCccCchhCCe---EEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCCh
Confidence            446799999999765   6789999999999999997653  379999998854

>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=99.08  E-value=2.3e-11  Score=78.96  Aligned_cols=45  Identities=18%  Similarity=0.115  Sum_probs=38.8

Q ss_pred             cccccccccccCCeeEEc-CCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          152 ECAICLERFKVGDTLVHL-PCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       152 ~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      .|+||++.|.++   +.+ .|||.||.+||.+|+..+. +||+||.++..
T Consensus         2 ~C~Ic~~~~~~P---v~~~~cGh~fc~~cI~~~l~~~~-~CP~c~~~l~~   47 (56)
T d2baya1           2 LCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTG-NDPITNEPLSI   47 (56)
T ss_dssp             CCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHS-BCTTTCCBCCG
T ss_pred             CCccCCchHHhc---CccCCCCCcccHHHHHHHHhhcc-CCCccCCcCCH
Confidence            499999999754   555 5999999999999999987 99999988753

>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=99.07  E-value=3.4e-11  Score=83.35  Aligned_cols=50  Identities=14%  Similarity=0.117  Sum_probs=43.1

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCcc
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQIL  199 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~  199 (207)
                      ..++..|+||++.|.++   +.++|||.||..||..|+......||+|+.++.
T Consensus         4 iP~~l~CpIc~~l~~dP---v~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~   53 (80)
T d2c2la2           4 IPDYLCGKISFELMREP---CITPSGITYDRKDIEEHLQRVGHFNPVTRSPLT   53 (80)
T ss_dssp             CCSTTBCTTTCSBCSSE---EECSSCCEEETTHHHHHHHHTCSSCTTTCCCCC
T ss_pred             CCccccCcCcCchhhhh---cccCCcCeecHHHHHHHHhcCCccCCCcccccc
Confidence            34678899999999865   788999999999999999876558999998774

>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=99.04  E-value=6.3e-11  Score=81.51  Aligned_cols=51  Identities=24%  Similarity=0.437  Sum_probs=43.4

Q ss_pred             ccccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ..++..|+||++.|.++   +.++|||.||..||..|+..+...||.|+.++..
T Consensus         5 iP~~l~CpIc~~~m~dP---V~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~   55 (78)
T d1t1ha_           5 FPEYFRCPISLELMKDP---VIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             CSSSSSCTTTSCCCSSE---EEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             CCccCCCcCcCchhhCc---eEccCCCcchHHHHHHHHHHCCCCCCcccccCCc
Confidence            34678899999999865   6789999999999999998765479999988754

>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=98.95  E-value=1.9e-10  Score=75.26  Aligned_cols=50  Identities=24%  Similarity=0.523  Sum_probs=38.3

Q ss_pred             ccccccccccccccccCCeeEEcCC-----CCcccHHhHHHHHhc-CCCCCCCcccCcc
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPC-----AHRFHARCLLPWLAT-NAHNCPCCRMQIL  199 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC-----~H~Fh~~Ci~~wl~~-~~~~CP~CR~~l~  199 (207)
                      +.+...|.||++.+..+   ...||     +|.||..||..|+.. .+.+||+||+++.
T Consensus         3 ded~~~C~IC~~~~~~~---~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           3 DEDVPVCWICNEELGNE---RFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             TCSCCEETTTTEECSCC---CCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCCccCCccCCCc---eeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            44667899999988644   33444     599999999999964 3348999999874

>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=98.90  E-value=9.7e-11  Score=83.77  Aligned_cols=47  Identities=19%  Similarity=0.496  Sum_probs=38.0

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      +...|+||++.|.++  +...+|+|.||..||..|+.  + .||.||.++..
T Consensus        21 ~~l~C~IC~~~~~~p--v~~~~CgH~fC~~Ci~~~~~--~-~CP~Cr~~~~~   67 (97)
T d1jm7b_          21 KLLRCSRCTNILREP--VCLGGCEHIFCSNCVSDCIG--T-GCPVCYTPAWI   67 (97)
T ss_dssp             HTTSCSSSCSCCSSC--BCCCSSSCCBCTTTGGGGTT--T-BCSSSCCBCSC
T ss_pred             hcCCCccCCchhhcC--ceeCCCCCchhHHHHHHHHh--c-cccccCCcCch
Confidence            556799999999755  23347999999999999983  3 69999987754

>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=98.69  E-value=4.8e-09  Score=75.13  Aligned_cols=50  Identities=18%  Similarity=0.155  Sum_probs=42.5

Q ss_pred             ccccccccccccccccCCeeEEcCCC-CcccHHhHHHHHhcCCCCCCCcccCccC
Q 028584          147 ACEQEECAICLERFKVGDTLVHLPCA-HRFHARCLLPWLATNAHNCPCCRMQILD  200 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lpC~-H~Fh~~Ci~~wl~~~~~~CP~CR~~l~~  200 (207)
                      ..++..|+||++.|.++   ++++|+ |.|+..||..|+..+. .||+|+.++..
T Consensus        19 ~P~~f~CPI~~~lm~dP---V~~~~~~~ty~r~~I~~~l~~~~-~~P~~~~~l~~   69 (98)
T d1wgma_          19 ACDEFLDPIMSTLMCDP---VVLPSSRVTVDRSTIARHLLSDQ-TDPFNRSPLTM   69 (98)
T ss_dssp             CCTTTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHTTTSC-BCTTTCSBCCT
T ss_pred             CcHHhCCcCchhHHHHH---HhcccccchhhHHHHHHHHHhcC-Ccccccccccc
Confidence            34678899999999866   888865 5899999999998876 99999998754

>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=98.41  E-value=2.7e-08  Score=69.96  Aligned_cols=47  Identities=21%  Similarity=0.498  Sum_probs=37.1

Q ss_pred             ccccccccccccccCCeeEEcCCCCcccHHhHHHHHhcC----C---CCCCCcc
Q 028584          149 EQEECAICLERFKVGDTLVHLPCAHRFHARCLLPWLATN----A---HNCPCCR  195 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~lpC~H~Fh~~Ci~~wl~~~----~---~~CP~CR  195 (207)
                      ....|+||++++...+.+..++|+|.||..||..|+...    .   -.||.|.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            346799999999876666677899999999999998742    1   1599864

>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=90.35  E-value=0.048  Score=32.71  Aligned_cols=44  Identities=32%  Similarity=0.726  Sum_probs=29.1

Q ss_pred             cccccccccccCCeeEEc-CCCCcccHHhHHHHHhcCC---CCCCCccc
Q 028584          152 ECAICLERFKVGDTLVHL-PCAHRFHARCLLPWLATNA---HNCPCCRM  196 (207)
Q Consensus       152 ~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~wl~~~~---~~CP~CR~  196 (207)
                      .|.||...-.. +.++.= .|...||..|+.+-+....   -.||.|+.
T Consensus         2 ~C~vC~~~~~~-~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGED-DKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCC-SCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCC-CCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            48888765432 233333 4999999999987654332   26999974

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=90.21  E-value=0.039  Score=36.30  Aligned_cols=49  Identities=16%  Similarity=0.501  Sum_probs=31.0

Q ss_pred             cccccccccccccccCCeeEEcC---CCCcccHHhHHH----HHhc----CCCCCCCcccCc
Q 028584          148 CEQEECAICLERFKVGDTLVHLP---CAHRFHARCLLP----WLAT----NAHNCPCCRMQI  198 (207)
Q Consensus       148 ~~~~~C~ICle~~~~~~~~~~lp---C~H~Fh~~Ci~~----wl~~----~~~~CP~CR~~l  198 (207)
                      .+...| ||......+ ..+...   |..+||..|+.-    ....    ....||.|+..-
T Consensus        14 ~~~~~C-~C~~~~~~~-~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T d1wewa_          14 EIKVRC-VCGNSLETD-SMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCCCCC-SSCCCCCCS-CEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             CCccEe-ECCCccCCC-cEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcC
Confidence            344567 998876543 445563   999999999832    1000    114899997544

>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=90.14  E-value=0.074  Score=35.65  Aligned_cols=33  Identities=30%  Similarity=0.752  Sum_probs=25.5

Q ss_pred             ccccccccccccccccCCeeEEcC---CCCcccHHhHHHH
Q 028584          147 ACEQEECAICLERFKVGDTLVHLP---CAHRFHARCLLPW  183 (207)
Q Consensus       147 ~~~~~~C~ICle~~~~~~~~~~lp---C~H~Fh~~Ci~~w  183 (207)
                      ...+..|.|| +.|...   ..+|   |+.+||..|+.+.
T Consensus        12 v~~D~mC~vC-~v~t~~---~l~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          12 VVNDEMCDVC-EVWTAE---SLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCSCCCTTT-CCCCSS---CCSSCSSSSSCCCHHHHHHH
T ss_pred             CCcCcccccc-Cccccc---ceecceeecchhhHHHHHHh
Confidence            3467789999 666654   3456   7899999999997

>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=89.50  E-value=0.02  Score=36.15  Aligned_cols=49  Identities=22%  Similarity=0.575  Sum_probs=33.0

Q ss_pred             ccccccccccccccCCeeEEc-CCCCcccHHhHHHHHh---c-CCCCCCCcccC
Q 028584          149 EQEECAICLERFKVGDTLVHL-PCAHRFHARCLLPWLA---T-NAHNCPCCRMQ  197 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~wl~---~-~~~~CP~CR~~  197 (207)
                      ....|.||......++.++.= .|+..||..|+..-..   . ....||.|+..
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            345799999877665544443 4999999999953211   1 22489999754

>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=86.39  E-value=0.62  Score=30.17  Aligned_cols=49  Identities=18%  Similarity=0.462  Sum_probs=30.9

Q ss_pred             ccccccccccccCCeeEEc-CCCCcccHHhHHH--H-Hhc-CCCCCCCcccCcc
Q 028584          151 EECAICLERFKVGDTLVHL-PCAHRFHARCLLP--W-LAT-NAHNCPCCRMQIL  199 (207)
Q Consensus       151 ~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~--w-l~~-~~~~CP~CR~~l~  199 (207)
                      ..+.||...+......+.= .|.-.||..|+..  . +.. ....||.|+....
T Consensus        12 pv~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~g   65 (79)
T d1wepa_          12 PVYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CCCSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             CeEeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcC
Confidence            3445998876544444443 4999999999942  1 222 1248999986543

>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=83.19  E-value=0.5  Score=30.10  Aligned_cols=47  Identities=23%  Similarity=0.545  Sum_probs=28.6

Q ss_pred             ccccccccccccccCCeeEEc-CCCCcccHHhHH------HHH--hcCCCCCCCcccC
Q 028584          149 EQEECAICLERFKVGDTLVHL-PCAHRFHARCLL------PWL--ATNAHNCPCCRMQ  197 (207)
Q Consensus       149 ~~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~------~wl--~~~~~~CP~CR~~  197 (207)
                      +...| ||......+ .++.= .|.-.||..|+.      ..+  ......||.|+..
T Consensus        15 ~~~~C-iC~~~~~~~-~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~   70 (76)
T d1wema_          15 NALYC-ICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             TCCCS-TTCCCCCSS-CEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             CcCEE-ECCCccCCC-eEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCc
Confidence            34457 898765433 34333 489999999982      111  1222489999654

>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=82.55  E-value=0.21  Score=31.15  Aligned_cols=43  Identities=23%  Similarity=0.517  Sum_probs=28.7

Q ss_pred             cccccccccccccCCeeEEc-CCCCcccHHhHHHHHhcCCCCCCCc
Q 028584          150 QEECAICLERFKVGDTLVHL-PCAHRFHARCLLPWLATNAHNCPCC  194 (207)
Q Consensus       150 ~~~C~ICle~~~~~~~~~~l-pC~H~Fh~~Ci~~wl~~~~~~CP~C  194 (207)
                      ...|--|+..|.+. ....- .|++.||.+|-.- +...-..||.|
T Consensus        15 ~~~C~gC~~~l~~~-~~y~C~~C~~~FC~dCD~f-iHe~lh~CpgC   58 (59)
T d1z60a1          15 ERFCYGCQGELKDQ-HVYVCAVCQNVFCVDCDVF-VHDSLHSCPGC   58 (59)
T ss_dssp             CCEETTTTEECTTS-EEECCTTTTCCBCHHHHHT-TTTTSCSSSTT
T ss_pred             CCCccCCCCcCCCC-ceEECcCCCCccccccchh-hhhhhcCCCCC
Confidence            45699999988643 23333 3999999999533 22222379988