Citrus Sinensis ID: 043807

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240--
Protein Sequence
TLAIVAYHLIVKYLMMRRRLRSERLIISRSSQTLHQFAKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTSGEAANLPNYKIMITSCLDVVSLATSIEDKQQLLATTLKRSLSMDECSNYVIVRLQNHDHIMCKQEGDDDYDQSCSSSSSFTARSMKQLDRVSSRVVRSFSQLRIGSRSSSTKANGNFLPC
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHccccEEEEcccccccccccccccEEccccccccEEccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccccccccccEEEEccccccccccccccccccccccccccHHHHHHHHcccccccEEEccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHccEEEEEcccccccccccccEEEEHHccccccEEEEcccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccEEccccccccccccccccccccccccccEEEcccccccccccccccccccHHHcccccccHHHHHcHHHHHHHHHHHcccccccccccccccccccccc
Coil and Loop (DISEMBL)
TLAIVAYHLIVKYLMMRRRLRSERLIISRSSQTLHQFAKGIEEKVLLTIPILAysakdcklfrvdQSECVIclgeledgemvrllpscrhaFHVQCIGNwllghticpvcrspvadqpkstsgeaanlpnykimITSCLDVVSLATSIEDKQQLLATTLKRSLSMDECSNYVIVRLQnhdhimckqegdddydqscsssssfTARSMKQLDRVSSRVVRSfsqlrigsrssstkangnflpc
Flexible Loop (DISEMBL)
TLAIVAYHLIVKYLMMRRRLRSERLIISRSSQTLHQFAKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTSGEAANLPNYKIMITSCLDVVSLATSIEDKQQLLATTlkrslsmdECSNYVIVRLQNHDHIMCKQEGDDDYDQSCSSSSSFtarsmkqldrvssrvvrsfsqlrigsrssstkangnflpc
Low Complexity Region (SEG)
TLAIVAYHLIVKYLMMrrrlrserliisrssQTLHQFAKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTSGEAANLPNYKIMITSCLDVVSLATSIEDKQQLLATTLKRSLSMDECSNYVIVRLQNHDHIMCKQEGdddydqscsssssFTARSMKQLDrvssrvvrsFSQLRIGSRSSSTKANGNFLPC
Disordered region (IsUnstruct)
**AIVAYHLIVKYLMMRRRLRSERLIISRSSQTLHQFAKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSP*************NLPNYKIMITSCLDVVSLATSIEDKQQLLATTLKRSLSMDECSNYVIVRLQNHDHIMC**********************************************************
Disordered Region (DISOPRED)
TLAIVAYHLIVKYLMMR***************************VLLTIPILAYSAKD****RVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV******************************************************************************************************************************P*
Disordered Region (DISEMBL)
TLAIVAYHLIVKYLMMRRRLRSERLIISRSSQTLHQFAKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV********GEAANLPNYKIMITSCLDVVSLATSIEDKQQLLATTLKRSLSMDECSNYVIVRLQNHDHIMCKQE********************************SFSQLRIGSRSSSTKANGNFLPC
Disordered Region (DISPRO)
TLAIVAYHLIVKYLMMRRR*******************KGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD******************************************************************************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
TLAIVAYHLIVKYLMMRRRLRSERLIISRSSQTLHQFAKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTSGEAANLPNYKIMITSCLDVVSLATSIEDKQQLLATTLKRSLSMDECSNYVIVRLQNHDHIMCKQEGDDDYDQSCSSSSSFTARSMKQLDRVSSRVVRSFSQLRIGSRSSSTKANGNFLPC
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	242	2.2.26 [Sep-21-2011]
Q9FLC6	176	RING-H2 finger protein AT	yes	no	0.347	0.477	0.420	4e-17
Q8LGA5	368	E3 ubiquitin-protein liga	no	no	0.330	0.217	0.462	6e-17
Q8W571	323	RING-H2 finger protein AT	no	no	0.367	0.275	0.450	1e-16
Q8RXX9	398	E3 ubiquitin-protein liga	no	no	0.371	0.226	0.433	2e-16
P0C035	310	RING-H2 finger protein AT	no	no	0.450	0.351	0.353	3e-16
Q9SG96	181	RING-H2 finger protein AT	no	no	0.322	0.430	0.451	3e-15
Q67YI6	411	RING-H2 finger protein AT	no	no	0.611	0.360	0.284	6e-15
Q9LF64	362	RING-H2 finger protein AT	no	no	0.495	0.331	0.335	7e-15
Q9ZV53	423	Putative RING-H2 finger p	no	no	0.425	0.243	0.342	9e-15
Q9LUL6	204	Putative RING-H2 finger p	no	no	0.293	0.348	0.493	1e-14

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

 Score = 88.2 bits (217), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 37/88 (42%), Positives = 55/88 (62%), Gaps = 4/88 (4%)

Query: 36  QFAKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQ 95
             AKGI+++ L  IP+ +YS +     ++  +EC+ICLG+  +GE VR+LP C H FHV+
Sbjct: 84  NVAKGIKKRALKVIPVDSYSPE----LKMKATECLICLGDFVEGETVRVLPKCNHGFHVK 139

Query: 96  CIGNWLLGHTICPVCRSPVADQPKSTSG 123
           CI  WLL H+ CP CR  + +     +G
Sbjct: 140 CIDTWLLSHSSCPTCRQSLLEHQTPANG 167

Arabidopsis thaliana (taxid: 3702)

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

 Score = 87.8 bits (216), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 37/80 (46%), Positives = 47/80 (58%)

Query: 38  AKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCI 97
           A+G++ + + T P   YS    +       EC ICL E ED E +RLLP C H FH  CI
Sbjct: 93  ARGLDAETIETFPTFVYSEVKTQKIGKGALECAICLNEFEDDETLRLLPKCDHVFHPHCI 152

Query: 98  GNWLLGHTICPVCRSPVADQ 117
           G WL GH  CPVCR+ +A+Q
Sbjct: 153 GAWLQGHVTCPVCRTNLAEQ 172

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

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score = 86.7 bits (213), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 41/91 (45%), Positives = 53/91 (58%), Gaps = 2/91 (2%)

Query: 40  GIEEKVLLTIPILAYSA-KDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIG 98
           G++  V+ + P+ AYS+ K+ K+   D  EC ICL ELED E VRLLP C H FH+ CI 
Sbjct: 95  GLDNAVVESFPVFAYSSVKESKIGSKDL-ECAICLNELEDHETVRLLPICNHLFHIDCID 153

Query: 99  NWLLGHTICPVCRSPVADQPKSTSGEAANLP 129
            WL  H  CPVCRS +  +      E   +P
Sbjct: 154 TWLYSHATCPVCRSNLTAKSNKPGDEDDGVP 184

Arabidopsis thaliana (taxid: 3702)

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

 Score = 86.7 bits (213), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 39/90 (43%), Positives = 52/90 (57%)

Query: 28  SRSSQTLHQFAKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPS 87
           +RS  T++  A+G++  V+ T P   YS    +     + EC ICL E ED E +RLLP 
Sbjct: 87  ARSRATVNAAARGLDVSVVETFPTFLYSDVKTQKLGKGELECAICLNEFEDDETLRLLPK 146

Query: 88  CRHAFHVQCIGNWLLGHTICPVCRSPVADQ 117
           C H FH  CI  WL  H  CPVCR+ +A+Q
Sbjct: 147 CDHVFHPHCIDAWLEAHVTCPVCRANLAEQ 176

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

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|P0C035|ATL60_ARATH RING-H2 finger protein ATL60 OS=Arabidopsis thaliana GN=ATL60 PE=2 SV=1

 Score = 85.5 bits (210), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 41/116 (35%), Positives = 63/116 (54%), Gaps = 7/116 (6%)

Query: 15  MMRRRLRSERLIISRSSQ-TLHQFAKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICL 73
           ++ R  R  R + ++S +  LH    G++ K+L +I ++ +   D K    D  EC +CL
Sbjct: 71  VIGRNPRRRRFVFAQSQEDPLHN--AGLDSKILQSIHVVVFKCTDFK----DGLECAVCL 124

Query: 74  GELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTSGEAANLP 129
            +L DG+  R+LP C H FHV CI  W   H+ CP+CR+ V     +T G +  LP
Sbjct: 125 SDLVDGDKARVLPRCNHGFHVDCIDMWFQSHSTCPLCRNTVGSVEDTTHGGSEGLP 180

Arabidopsis thaliana (taxid: 3702)

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

 Score = 82.0 bits (201), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 37/82 (45%), Positives = 53/82 (64%), Gaps = 4/82 (4%)

Query: 38  AKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCI 97
           A G++++ L  IP+  Y +    +  +  +EC+ICLG+ EDGE VR+LP C H FHV+CI
Sbjct: 86  ATGLKKQALKQIPVGLYGSG---IIDMKATECLICLGDFEDGEKVRVLPKCNHGFHVRCI 142

Query: 98  GNWLLGHTICPVCR-SPVADQP 118
             WLL  + CP CR S + +QP
Sbjct: 143 DTWLLSRSSCPTCRQSLLLEQP 164

Arabidopsis thaliana (taxid: 3702)

>sp|Q67YI6|ATL65_ARATH RING-H2 finger protein ATL65 OS=Arabidopsis thaliana GN=ATL65 PE=2 SV=2

 Score = 81.3 bits (199), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 53/186 (28%), Positives = 81/186 (43%), Gaps = 38/186 (20%)

Query: 40  GIEEKVLLTIPILAYSAKDC-------KLFRVDQSECVICLGELEDGEMVRLLPSCRHAF 92
           G+++ V+ T+P+  YSA  C       K    +  +C +CL E E+G+ VR LP C HAF
Sbjct: 120 GLDDSVIKTLPLFLYSAAACTGKPAVGKTSAANCRDCAVCLLEFEEGDYVRTLPLCFHAF 179

Query: 93  HVQCIGNWLLGHTICPVCRSPVADQPKSTSGEAANLPNYKIMITSCLDVVSLATSIEDKQ 152
           H++CI  WL  H  CP+CR                        T+ L    + T +    
Sbjct: 180 HLECIDEWLRSHPNCPLCR------------------------TAILGSAGVLTPMSPFV 215

Query: 153 QLLATTLKRSLSMDECSNYVIVRLQ------NHDHIMCKQEGDDDYDQSCSSSSSFTARS 206
            L+A  ++ SL  DE +N +I+R +      N + I      D +   S    SS     
Sbjct: 216 PLMAPRIRPSLD-DEENNAIIIRGEITPSRSNWNTIAADTTNDQEIRASVEEQSSPAISR 274

Query: 207 MKQLDR 212
            ++L R
Sbjct: 275 FRELKR 280

Arabidopsis thaliana (taxid: 3702)

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

 Score = 80.9 bits (198), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 45/134 (33%), Positives = 70/134 (52%), Gaps = 14/134 (10%)

Query: 2   LAIVAYH-LIVKYLMMRRRLRSERLI--------ISRSSQTLHQFAKGIEEKVLLTIPIL 52
           L +V+Y+ LI KY     +  S   +           S+Q +     G+ E ++ +I + 
Sbjct: 69  LILVSYYTLISKYCHRHHQTSSSETLNLNHNGEGFFSSTQRISTNGDGLNESMIKSITVY 128

Query: 53  AYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRS 112
            Y + D     VD S+C +CL E E+ E +RLLP C HAFH+ CI  WL  H+ CP+CR+
Sbjct: 129 KYKSGDG---FVDGSDCSVCLSEFEENESLRLLPKCNHAFHLPCIDTWLKSHSNCPLCRA 185

Query: 113 PVA--DQPKSTSGE 124
            V   + P ++ G+
Sbjct: 186 FVTGVNNPTASVGQ 199

Arabidopsis thaliana (taxid: 3702)

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

 Score = 80.5 bits (197), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 38/111 (34%), Positives = 62/111 (55%), Gaps = 8/111 (7%)

Query: 8   HLIVKYLMMRRRLRSERLIISRSS------QTLHQFAKGIEEKVLLTIPILAYSAKDCKL 61
           H++VK+L+   R   E    + ++      Q  +    G+++ ++ T+P+  Y  K    
Sbjct: 61  HILVKFLLTPSRESREDYFDNVTALQGQLQQLFNLHDSGVDQSLIDTLPVFHY--KSIVG 118

Query: 62  FRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRS 112
            ++   +C +CL E E  + +RLLP C HAFHV+CI  WLL H+ CP+CRS
Sbjct: 119 LKISPFDCPVCLCEFETEDKLRLLPKCSHAFHVECIDTWLLSHSTCPLCRS 169

May be involved in female gametophyte development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LUL6|ATL61_ARATH Putative RING-H2 finger protein ATL61 OS=Arabidopsis thaliana GN=ATL61 PE=3 SV=1

 Score = 80.5 bits (197), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 37/75 (49%), Positives = 50/75 (66%), Gaps = 4/75 (5%)

Query: 40  GIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGN 99
           GI+  VL +IPI+ ++ KD K       ECV+CL EL DG+  R+LPSC H FHV+CI +
Sbjct: 63  GIKPYVLRSIPIVDFNTKDFKYVL----ECVVCLSELADGDKARVLPSCDHWFHVECIDS 118

Query: 100 WLLGHTICPVCRSPV 114
           WL  ++ CP+CR  V
Sbjct: 119 WLQSNSTCPICRKRV 133

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	242
147799195	269	hypothetical protein VITISV_030410 [Viti	0.884	0.795	0.378	7e-34
255556794	329	RING-H2 finger protein ATL3C, putative [	0.533	0.392	0.468	5e-23
413944084	421	putative RING zinc finger domain superfa	0.400	0.230	0.420	8e-16
338808408	299	ring-H2 zinc finger protein, partial [Ze	0.409	0.331	0.419	1e-15
12003386	256	Avr9/Cf-9 rapidly elicited protein 132 [	0.338	0.320	0.430	2e-15
326525004	297	predicted protein [Hordeum vulgare subsp	0.454	0.370	0.388	2e-15
357512053	361	RING finger protein [Medicago truncatula	0.334	0.224	0.469	2e-15
255559693	208	RING-H2 finger protein ATL3C, putative [	0.380	0.442	0.416	2e-15
168251077	298	ring-H2 zinc finger protein [Zea mays]	0.413	0.335	0.378	2e-15
15239062	176	RING-H2 finger protein ATL73 [Arabidopsi	0.347	0.477	0.420	2e-15

>gi|147799195|emb|CAN65773.1| hypothetical protein VITISV_030410 [Vitis vinifera]

 Score =  149 bits (377), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 92/243 (37%), Positives = 133/243 (54%), Gaps = 29/243 (11%)

Query: 1   TLAIVAYHLIVKYLMMRRRLRSERLIISRSSQTLHQFAKGIEEKVLLTIPILAYSAKDCK 60
           +L IV YHL++    +RR+     L+    S    + + G++ K+L TIPIL+YS K   
Sbjct: 29  SLVIVVYHLVIVKYCLRRQADPRPLL----SAPRXRLSTGVDAKILETIPILSYSKKKGL 84

Query: 61  LFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA----- 115
           LF  DQSEC +CL ELED + VRLLPSC HAFH+ CI  W +GHT CP+CRSPV      
Sbjct: 85  LFHADQSECAVCLAELEDDDXVRLLPSCHHAFHITCIDEWFVGHTNCPLCRSPVTAVLSL 144

Query: 116 ----------DQPKST-SGEAANLPNYKIMITSCLDVVSLATSIEDKQQLLATTLKRSLS 164
                     ++P +    + +N  +  + +  C   V     ++ K + +   LKRSLS
Sbjct: 145 SNAIEEGNGFNRPTAQFQHQRSNGSDLGLQLRHCESCV---LHMDGKPRPVMAGLKRSLS 201

Query: 165 MDECSNYVIVRLQNHDHIMCKQEGDDDYDQSCSSSSSFTARSMKQLDRVSSRVVRSFSQL 224
           M +  +YVI+ +Q       ++            S S+ ARSM+QLDR SS + RS+S+L
Sbjct: 202 MGQ--SYVIIDIQR----ESERASSSSSKAILGRSRSYKARSMRQLDRASSTLRRSYSRL 255

Query: 225 RIG 227
           R+G
Sbjct: 256 RMG 258

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255556794|ref|XP_002519430.1| RING-H2 finger protein ATL3C, putative [Ricinus communis] gi|223541293|gb|EEF42844.1| RING-H2 finger protein ATL3C, putative [Ricinus communis]

 Score =  114 bits (284), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 66/141 (46%), Positives = 82/141 (58%), Gaps = 12/141 (8%)

Query: 1   TLAIVAYHLIVKYLMMRRRLRSERLIISRSSQTL--HQFAKGIEEKVLLTIPILAYSAKD 58
           ++ I AYHL++    +RRR    R I +  S T+   +   G+EE VL  IPIL YS  D
Sbjct: 29  SMIIAAYHLLLVRFCIRRR----RSITTNDSFTIPVQEMRTGVEEDVLKAIPILLYSKVD 84

Query: 59  CKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQP 118
                 DQ+ECVICLGELEDG+ VR LP+C H FHV CI  WL  HT CP+CR+P+    
Sbjct: 85  H-----DQTECVICLGELEDGDKVRSLPNCGHVFHVPCIDGWLSAHTNCPICRAPIVSS- 138

Query: 119 KSTSGEAANLPNYKIMITSCL 139
                 AA+ PN    ITS L
Sbjct: 139 PPPPAAAASTPNSDHHITSVL 159

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413944084|gb|AFW76733.1| putative RING zinc finger domain superfamily protein [Zea mays]

 Score = 89.7 bits (221), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 45/107 (42%), Positives = 60/107 (56%), Gaps = 10/107 (9%)

Query: 25  LIISRSSQTLHQFAKGIEEKVLLTIPILAYSAKDCKLFRVDQS----ECVICLGELEDGE 80
           L +SR  +   Q  +G++  V+ + P + Y+  D +  RV       EC +CL E ED E
Sbjct: 100 LALSRQEERNQQ--RGLDPAVVASFPTMRYA--DARELRVGGKDAALECAVCLSEFEDDE 155

Query: 81  MVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTSGEAAN 127
            +RLLPSC HAFH  CIG WL GH  CPVCR  +   P+  +GEA  
Sbjct: 156 ELRLLPSCSHAFHPDCIGEWLAGHVTCPVCRCNL--DPEEPAGEATG 200

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|338808408|gb|AEJ07912.1| ring-H2 zinc finger protein, partial [Zea luxurians]

 Score = 89.4 bits (220), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 44/105 (41%), Positives = 63/105 (60%), Gaps = 6/105 (5%)

Query: 25  LIISRSSQTLHQFAKGIEEKVLLTIPILAYS-AKDCKLFRVDQS-ECVICLGELEDGEMV 82
           L +SR  Q   Q  +G++  V+ + P + Y+ A++ ++   D + EC +CL E ED E +
Sbjct: 41  LALSRQEQRNQQ--RGLDPAVVASFPTMRYADARELRVGGKDAALECAVCLSEFEDDEEL 98

Query: 83  RLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTSGEAAN 127
           RLLP+C HAFH  CIG WL GH  CPVCR  +   P+  +GEA  
Sbjct: 99  RLLPNCSHAFHPDCIGEWLAGHVTCPVCRCNL--DPEEPAGEATG 141

Source: Zea luxurians

Species: Zea luxurians

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|12003386|gb|AAG43550.1|AF211532_1 Avr9/Cf-9 rapidly elicited protein 132 [Nicotiana tabacum]

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 37/86 (43%), Positives = 55/86 (63%), Gaps = 4/86 (4%)

Query: 32  QTLHQFAKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHA 91
           Q ++   +G++  VL TIP++ ++ KD K    D  EC +CL E+ +GE  R+LP C H 
Sbjct: 73  QEVNVLRRGLDPSVLKTIPVVPFNMKDFK----DGLECSVCLSEVSEGENTRVLPKCNHG 128

Query: 92  FHVQCIGNWLLGHTICPVCRSPVADQ 117
           FHV CI  W   H+ CP+CR+PV++Q
Sbjct: 129 FHVDCIDMWFHSHSTCPLCRNPVSEQ 154

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326525004|dbj|BAK04438.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score = 89.0 bits (219), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 49/126 (38%), Positives = 63/126 (50%), Gaps = 16/126 (12%)

Query: 2   LAIVAYHLIVKYLMMRRRLRSERLIISRSSQTLH-------QFAKGIEEKVLLTIPILAY 54
           LA V YH    YL + RR   +     R S +L          A+G++  VL  +P+  Y
Sbjct: 57  LAFVLYH----YLTVSRRGVRDGTGTERGSPSLRVGAASASGVAQGVDPVVLRALPVTLY 112

Query: 55  SAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV 114
            AKD      D  EC +CL EL DGE  R LP C H FH +C+  WL  H  CP+CR  V
Sbjct: 113 RAKDF----ADALECAVCLAELSDGEAARFLPKCGHGFHAECVDLWLHSHPTCPLCRVDV 168

Query: 115 ADQPKS 120
            D+P +
Sbjct: 169 -DKPDA 173

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357512053|ref|XP_003626315.1| RING finger protein [Medicago truncatula] gi|87240525|gb|ABD32383.1| Zinc finger, RING-type [Medicago truncatula] gi|355501330|gb|AES82533.1| RING finger protein [Medicago truncatula]

 Score = 88.6 bits (218), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/81 (46%), Positives = 48/81 (59%)

Query: 38  AKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCI 97
           A+G++  V+ T PIL YS         D  EC +CL E ED E +RL+P C H FH +CI
Sbjct: 89  ARGLDPSVIETFPILEYSEVKIHKIGKDVLECAVCLMEFEDTETLRLIPKCDHVFHPECI 148

Query: 98  GNWLLGHTICPVCRSPVADQP 118
             WL  HT CPVCR+ +  QP
Sbjct: 149 DEWLSSHTTCPVCRANLVPQP 169

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255559693|ref|XP_002520866.1| RING-H2 finger protein ATL3C, putative [Ricinus communis] gi|223539997|gb|EEF41575.1| RING-H2 finger protein ATL3C, putative [Ricinus communis]

 Score = 88.6 bits (218), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 40/96 (41%), Positives = 56/96 (58%), Gaps = 4/96 (4%)

Query: 38  AKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCI 97
           A G+++  L  IP++ Y A   ++   D   C ICLGE  DGE VR+LP C H FHV+CI
Sbjct: 88  ATGLKKSALRQIPVVIYGAAGIQIIATD---CAICLGEFSDGEKVRVLPKCNHGFHVRCI 144

Query: 98  GNWLLGHTICPVCRSPVADQPKSTSGEAANLPNYKI 133
             WL  H+ CP CR  + +QP   + +A   P+ +I
Sbjct: 145 DTWLGSHSSCPTCRQSLLEQPAPGNSDATE-PDVEI 179

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|168251077|gb|ACA21860.1| ring-H2 zinc finger protein [Zea mays]

 Score = 88.6 bits (218), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 42/111 (37%), Positives = 57/111 (51%), Gaps = 11/111 (9%)

Query: 13  YLMMRRRLRSERLIISRSSQTLHQFA-------KGIEEKVLLTIPILAYSAKDCKLFRVD 65
           YL  +R L +  L+   S  +   F        +G+   VL ++P+  Y +   K    D
Sbjct: 38  YLYAKRYLGANPLLAPSSPSSRFLFVAASPLPQRGLPASVLQSLPVTVYGSPGGK----D 93

Query: 66  QSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD 116
             EC +CL E+ DGE VR LP C H FHV+CI  W   H  CP+CR+PV D
Sbjct: 94  ALECAVCLSEVGDGEKVRTLPKCSHGFHVECIDMWFHSHDTCPLCRAPVGD 144

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15239062|ref|NP_196147.1| RING-H2 finger protein ATL73 [Arabidopsis thaliana] gi|68565292|sp|Q9FLC6.1|ATL73_ARATH RecName: Full=RING-H2 finger protein ATL73; Flags: Precursor gi|10176740|dbj|BAB09971.1| RING zinc finger protein-like [Arabidopsis thaliana] gi|332003467|gb|AED90850.1| RING-H2 finger protein ATL73 [Arabidopsis thaliana]

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 37/88 (42%), Positives = 55/88 (62%), Gaps = 4/88 (4%)

Query: 36  QFAKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQ 95
             AKGI+++ L  IP+ +YS +     ++  +EC+ICLG+  +GE VR+LP C H FHV+
Sbjct: 84  NVAKGIKKRALKVIPVDSYSPE----LKMKATECLICLGDFVEGETVRVLPKCNHGFHVK 139

Query: 96  CIGNWLLGHTICPVCRSPVADQPKSTSG 123
           CI  WLL H+ CP CR  + +     +G
Sbjct: 140 CIDTWLLSHSSCPTCRQSLLEHQTPANG 167

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	242
TAIR|locus:2140069	323	AT4G40070 [Arabidopsis thalian	0.367	0.275	0.450	1.6e-17
TAIR|locus:2153554	176	DAF "DEFECTIVE IN ANTHER DEHIS	0.338	0.465	0.430	1.6e-17
TAIR|locus:2085914	411	AT3G18930 [Arabidopsis thalian	0.309	0.182	0.402	7.2e-17
TAIR|locus:2146330	368	CNI1 "carbon/nitrogen insensit	0.330	0.217	0.462	1.3e-16
TAIR|locus:505006547	367	AT4G33565 [Arabidopsis thalian	0.384	0.253	0.385	2.9e-16
TAIR|locus:2103162	181	DAFL1 "DAF-Like gene 1" [Arabi	0.322	0.430	0.451	3.7e-16
TAIR|locus:2197026	310	AT1G53820 [Arabidopsis thalian	0.355	0.277	0.388	4.1e-16
TAIR|locus:2090980	204	AT3G14320 [Arabidopsis thalian	0.334	0.397	0.458	4.7e-16
TAIR|locus:2028506	251	AT1G49220 [Arabidopsis thalian	0.347	0.334	0.430	7.7e-16
TAIR|locus:2096309	398	ATL6 "Arabidopsis toxicos en l	0.347	0.211	0.465	8.3e-16

TAIR|locus:2140069 AT4G40070 [Arabidopsis thaliana (taxid:3702)]

 Score = 214 (80.4 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 41/91 (45%), Positives = 53/91 (58%)

Query:    40 GIEEKVLLTIPILAYSA-KDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIG 98
             G++  V+ + P+ AYS+ K+ K+   D  EC ICL ELED E VRLLP C H FH+ CI 
Sbjct:    95 GLDNAVVESFPVFAYSSVKESKIGSKDL-ECAICLNELEDHETVRLLPICNHLFHIDCID 153

Query:    99 NWLLGHTICPVCRSPVADQPKSTSGEAANLP 129
              WL  H  CPVCRS +  +      E   +P
Sbjct:   154 TWLYSHATCPVCRSNLTAKSNKPGDEDDGVP 184

GO:0005576 "extracellular region" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 214 (80.4 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 37/86 (43%), Positives = 55/86 (63%)

Query:    38 AKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCI 97
             AKGI+++ L  IP+ +YS +     ++  +EC+ICLG+  +GE VR+LP C H FHV+CI
Sbjct:    86 AKGIKKRALKVIPVDSYSPE----LKMKATECLICLGDFVEGETVRVLPKCNHGFHVKCI 141

Query:    98 GNWLLGHTICPVCRSPVADQPKSTSG 123
               WLL H+ CP CR  + +     +G
Sbjct:   142 DTWLLSHSSCPTCRQSLLEHQTPANG 167

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

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

 Score = 186 (70.5 bits), Expect = 7.2e-17, Sum P(2) = 7.2e-17
 Identities = 33/82 (40%), Positives = 49/82 (59%)

Query:    40 GIEEKVLLTIPILAYSAKDC-------KLFRVDQSECVICLGELEDGEMVRLLPSCRHAF 92
             G+++ V+ T+P+  YSA  C       K    +  +C +CL E E+G+ VR LP C HAF
Sbjct:   120 GLDDSVIKTLPLFLYSAAACTGKPAVGKTSAANCRDCAVCLLEFEEGDYVRTLPLCFHAF 179

Query:    93 HVQCIGNWLLGHTICPVCRSPV 114
             H++CI  WL  H  CP+CR+ +
Sbjct:   180 HLECIDEWLRSHPNCPLCRTAI 201

GO:0005634 "nucleus" evidence=ISM

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

GO:0009693 "ethylene biosynthetic process" evidence=RCA

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

 Score = 209 (78.6 bits), Expect = 1.3e-16, P = 1.3e-16
 Identities = 37/80 (46%), Positives = 47/80 (58%)

Query:    38 AKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCI 97
             A+G++ + + T P   YS    +       EC ICL E ED E +RLLP C H FH  CI
Sbjct:    93 ARGLDAETIETFPTFVYSEVKTQKIGKGALECAICLNEFEDDETLRLLPKCDHVFHPHCI 152

Query:    98 GNWLLGHTICPVCRSPVADQ 117
             G WL GH  CPVCR+ +A+Q
Sbjct:   153 GAWLQGHVTCPVCRTNLAEQ 172

GO:0005576 "extracellular region" evidence=ISM

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

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

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

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

GO:0016020 "membrane" evidence=IDA

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

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

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

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

GO:0007165 "signal transduction" evidence=RCA

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

GO:0009611 "response to wounding" evidence=RCA

GO:0009693 "ethylene biosynthetic process" evidence=RCA

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

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

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

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

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

GO:0035556 "intracellular signal transduction" evidence=RCA

GO:0042538 "hyperosmotic salinity response" evidence=RCA

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

 Score = 206 (77.6 bits), Expect = 2.9e-16, P = 2.9e-16
 Identities = 37/96 (38%), Positives = 55/96 (57%)

Query:    40 GIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGN 99
             G+   V+ +I +  YS KD     V+ ++C +CL E E+ E +RLLP C+HAFH+ CI  
Sbjct:   191 GLNPTVISSIKVCQYSKKDGV---VEGTDCSVCLSEFEEEETLRLLPKCKHAFHLYCIDT 247

Query:   100 WLLGHTICPVCRSPVADQPKSTSGEAANLPNYKIMI 135
             WL  HT CP+CR+P+ +        +  L    +MI
Sbjct:   248 WLRSHTNCPLCRAPIVEANTMIDDHSEGLEEISVMI 283

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

GO:0005886 "plasma membrane" evidence=IDA

TAIR|locus:2103162 DAFL1 "DAF-Like gene 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 201 (75.8 bits), Expect = 3.7e-16, P = 3.7e-16
 Identities = 37/82 (45%), Positives = 53/82 (64%)

Query:    38 AKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCI 97
             A G++++ L  IP+  Y +    +  +  +EC+ICLG+ EDGE VR+LP C H FHV+CI
Sbjct:    86 ATGLKKQALKQIPVGLYGSG---IIDMKATECLICLGDFEDGEKVRVLPKCNHGFHVRCI 142

Query:    98 GNWLLGHTICPVCR-SPVADQP 118
               WLL  + CP CR S + +QP
Sbjct:   143 DTWLLSRSSCPTCRQSLLLEQP 164

GO:0005634 "nucleus" evidence=ISM

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

GO:0010413 "glucuronoxylan metabolic process" evidence=RCA

GO:0045492 "xylan biosynthetic process" evidence=RCA

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

 Score = 201 (75.8 bits), Expect = 4.1e-16, P = 4.1e-16
 Identities = 35/90 (38%), Positives = 51/90 (56%)

Query:    40 GIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGN 99
             G++ K+L +I ++ +   D K    D  EC +CL +L DG+  R+LP C H FHV CI  
Sbjct:    95 GLDSKILQSIHVVVFKCTDFK----DGLECAVCLSDLVDGDKARVLPRCNHGFHVDCIDM 150

Query:   100 WLLGHTICPVCRSPVADQPKSTSGEAANLP 129
             W   H+ CP+CR+ V     +T G +  LP
Sbjct:   151 WFQSHSTCPLCRNTVGSVEDTTHGGSEGLP 180

GO:0005634 "nucleus" evidence=ISM

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

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

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 39/85 (45%), Positives = 53/85 (62%)

Query:    40 GIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGN 99
             GI+  VL +IPI+ ++ KD K       ECV+CL EL DG+  R+LPSC H FHV+CI +
Sbjct:    63 GIKPYVLRSIPIVDFNTKDFKYVL----ECVVCLSELADGDKARVLPSCDHWFHVECIDS 118

Query:   100 WLLGHTICPVCRSPVADQPKSTSGE 124
             WL  ++ CP+CR  V  +   T  E
Sbjct:   119 WLQSNSTCPICRKRVCLKQSRTRPE 143

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

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

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 37/86 (43%), Positives = 53/86 (61%)

Query:    39 KGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIG 98
             KGI++K L   P+++YS  +  L  +D+ ECVICL +   GE +RLLP C H FHV+CI 
Sbjct:   107 KGIKKKALRMFPVVSYSP-EMNLPGLDE-ECVICLSDFVSGEQLRLLPKCNHGFHVRCID 164

Query:    99 NWLLGHTICPVCRSPVADQPKSTSGE 124
              WL  H  CP CR+ + +  +   G+
Sbjct:   165 KWLQQHLTCPKCRNCLVETCQKILGD 190

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

TAIR|locus:2096309 ATL6 "Arabidopsis toxicos en levadura 6" [Arabidopsis thaliana (taxid:3702)]

 Score = 203 (76.5 bits), Expect = 8.3e-16, P = 8.3e-16
 Identities = 40/86 (46%), Positives = 52/86 (60%)

Query:    33 TLHQFAKGIEEKVLLTIPILAYS-AKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHA 91
             T++  A+G++  V+ T P   YS  K  KL +  + EC ICL E ED E +RLLP C H 
Sbjct:    92 TVNAAARGLDVSVVETFPTFLYSDVKTQKLGK-GELECAICLNEFEDDETLRLLPKCDHV 150

Query:    92 FHVQCIGNWLLGHTICPVCRSPVADQ 117
             FH  CI  WL  H  CPVCR+ +A+Q
Sbjct:   151 FHPHCIDAWLEAHVTCPVCRANLAEQ 176

GO:0005576 "extracellular region" evidence=ISM

GO:0008270 "zinc ion binding" evidence=ISS

GO:0005886 "plasma membrane" evidence=IDA

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

GO:0016567 "protein ubiquitination" evidence=IDA

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

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

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

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

GO:0035556 "intracellular signal transduction" 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

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

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.XIX.1626.1 hypothetical protein (150 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	242
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	1e-12
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	3e-11
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	4e-09
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	1e-06
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	7e-06
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	9e-06
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	3e-05
smart00184	40	smart00184, RING, Ring finger	5e-05
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	8e-05
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	7e-04
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	0.004

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

 Score = 60.1 bits (146), Expect = 1e-12
 Identities = 24/46 (52%), Positives = 29/46 (63%), Gaps = 1/46 (2%)

Query: 68  ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSP 113
           EC ICL E E GE V +LP C H FH +C+  WL     CP+CR+P
Sbjct: 2   ECPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

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

 Score = 61.9 bits (150), Expect = 3e-11
 Identities = 22/48 (45%), Positives = 31/48 (64%), Gaps = 2/48 (4%)

Query: 68  ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTI-CPVCRSPV 114
           EC IC+      + +R+LP C H FHV C+  WLLG++  CPVCR+ +
Sbjct: 325 ECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAI 371

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 = 50.9 bits (122), Expect = 4e-09
 Identities = 20/48 (41%), Positives = 25/48 (52%), Gaps = 4/48 (8%)

Query: 68  ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWL-LGHTICPVCRSPV 114
           EC ICL E  +     +L  C H F   CI  WL  G   CP+CR+P+
Sbjct: 1   ECPICLEEFRE---PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 44.7 bits (106), Expect = 1e-06
 Identities = 16/52 (30%), Positives = 21/52 (40%), Gaps = 9/52 (17%)

Query: 69  CVICLGELED---------GEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCR 111
           C IC    +           +   +   C HAFH+ CI  WL     CP+CR
Sbjct: 22  CAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73

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

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

 Score = 45.5 bits (108), Expect = 7e-06
 Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 5/74 (6%)

Query: 44  KVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVR----LLPSCRHAFHVQCIGN 99
           K L TIP +    +       D+ EC IC+ ++ D E+      +L +C H F ++CI  
Sbjct: 153 KFLKTIPSVLSEYEKLYNRSKDK-ECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDI 211

Query: 100 WLLGHTICPVCRSP 113
           W      CPVCR+P
Sbjct: 212 WKKEKNTCPVCRTP 225

Length = 238

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

 Score = 45.7 bits (108), Expect = 9e-06
 Identities = 26/93 (27%), Positives = 37/93 (39%), Gaps = 14/93 (15%)

Query: 69  CVICLGEL-----------EDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ 117
           C IC+ E+            D    RL   C H  H+ C+ NWL     CP+CR PV   
Sbjct: 290 CTICMDEMFHPDHEPLPRGLDMTPKRL--PCGHILHLHCLKNWLERQQTCPICRRPVIFD 347

Query: 118 PKSTSGEAANLPNYKIM-ITSCLDVVSLATSIE 149
             S +  + N+ N +I       D     T++ 
Sbjct: 348 QSSPTPASPNVRNTQIATQVPNPDNTPTTTAVP 380

Length = 491

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

 Score = 39.8 bits (93), Expect = 3e-05
 Identities = 20/48 (41%), Positives = 27/48 (56%), Gaps = 3/48 (6%)

Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRS 112
           ++ EC ICL  L D   V L P C H F  +CI  +L   + CP+CR+
Sbjct: 1   EELECPICLDLLRD--PVVLTP-CGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 39.0 bits (91), Expect = 5e-05
 Identities = 17/43 (39%), Positives = 20/43 (46%), Gaps = 4/43 (9%)

Query: 69  CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTI-CPVC 110
           C ICL E    +   +LP C H F   CI  WL      CP+C
Sbjct: 1   CPICLEEYL--KDPVILP-CGHTFCRSCIRKWLESGNNTCPIC 40

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

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

 Score = 39.8 bits (93), Expect = 8e-05
 Identities = 16/46 (34%), Positives = 19/46 (41%), Gaps = 1/46 (2%)

Query: 69  CVIC-LGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSP 113
           C  C  G     E   +   C HAFH  CI  WL    +CP+ R  
Sbjct: 34  CPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQT 79

Length = 88

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

 Score = 40.4 bits (94), Expect = 7e-04
 Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 9/52 (17%)

Query: 68   ECVICLGELEDGEMVRLLPS-----CRHAFHVQCIGNWLL--GHTICPVCRS 112
            EC IC   L+  +  R LPS     C++ FH +C+  W      + CP+CRS
Sbjct: 1471 ECAICYSVLDMVD--RSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRS 1520

Length = 1525

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

 Score = 35.2 bits (81), Expect = 0.004
 Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 3/31 (9%)

Query: 84  LLPSCRHAFHVQCIGNWLLGHT---ICPVCR 111
           +   C+H FH+ CI  WL   T   +CP+CR
Sbjct: 48  VWGKCKHNFHMHCILKWLATETSKGLCPMCR 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	242
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.71
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.48
PHA02929	238	N1R/p28-like protein; Provisional	99.33
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.31
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.29
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.2
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.0
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	98.97
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.96
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	98.94
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.93
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.92
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.9
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.85
PHA02926	242	zinc finger-like protein; Provisional	98.84
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.79
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.72
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.72
KOG4445	368	consensus Uncharacterized conserved protein, conta	98.71
PF14634	44	zf-RING_5: zinc-RING finger domain	98.71
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.7
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.66
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.62
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.58
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.51
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.51
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.42
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.38
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.3
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.25
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.22
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.22
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.16
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.15
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.11
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.09
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.08
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.06
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.05
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.02
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.95
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.85
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.74
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.64
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.59
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.55
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.41
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.26
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.23
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.22
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.19
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.08
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.04
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.03
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	96.91
KOG2660	331	consensus Locus-specific chromosome binding protei	96.88
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.7
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.7
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.63
KOG1002	791	consensus Nucleotide excision repair protein RAD16	96.61
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.52
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	96.48
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	96.48
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	96.33
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	96.26
PHA02862	156	5L protein; Provisional	96.23
COG5152	259	Uncharacterized conserved protein, contains RING a	96.22
KOG3039	303	consensus Uncharacterized conserved protein [Funct	96.13
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	95.98
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	95.92
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.86
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	95.82
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.52
PHA03096	284	p28-like protein; Provisional	95.36
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	95.29
PHA02825	162	LAP/PHD finger-like protein; Provisional	95.17
PF04641	260	Rtf2: Rtf2 RING-finger	95.09
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	95.04
COG5236	493	Uncharacterized conserved protein, contains RING Z	94.83
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	94.43
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	94.41
KOG4739	233	consensus Uncharacterized protein involved in syna	94.13
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	94.1
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	93.97
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	93.76
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	93.7
COG5222	427	Uncharacterized conserved protein, contains RING Z	93.37
COG5175	480	MOT2 Transcriptional repressor [Transcription]	93.28
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	93.22
KOG1940	276	consensus Zn-finger protein [General function pred	92.99
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	92.47
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	90.99
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	90.93
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	90.92
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	90.8
KOG1001	674	consensus Helicase-like transcription factor HLTF/	90.73
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	90.05
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	89.34
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	88.26
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	87.87
KOG0298	1394	consensus DEAD box-containing helicase-like transc	87.48
KOG3053	293	consensus Uncharacterized conserved protein [Funct	87.18
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	86.73
KOG1609	323	consensus Protein involved in mRNA turnover and st	85.93
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	84.93
KOG3899	381	consensus Uncharacterized conserved protein [Funct	84.93
KOG3002	299	consensus Zn finger protein [General function pred	84.84
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	82.46
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	82.12
KOG4367	699	consensus Predicted Zn-finger protein [Function un	81.11
KOG0269	839	consensus WD40 repeat-containing protein [Function	80.19

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

Probab=99.71  E-value=2.5e-17  Score=149.92  Aligned_cols=79  Identities=32%  Similarity=0.799  Sum_probs=67.2

Q ss_pred             hcCCCCHHHHhcCCceeeecccccccccCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCC-CCCCCCcCCC
Q 043807           37 FAKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHT-ICPVCRSPVA  115 (242)
Q Consensus        37 ~~~gl~~~~i~~lp~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~-~CP~CR~~i~  115 (242)
                      ...++.+..++++|...|...+...  .. ..|+||+|+|..|++++.|| |+|.||..||+.||..+. .||+|+..+.
T Consensus       203 ~~~r~~k~~l~~~p~~~f~~~~~~~--~~-~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~  278 (348)
T KOG4628|consen  203 RRNRLIKRLLKKLPVRTFTKGDDED--AT-DTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIR  278 (348)
T ss_pred             hhhhhHHHHHhhCCcEEeccccccC--CC-ceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCC
Confidence            4557889999999999999987332  12 69999999999999999999 999999999999998875 5999999886


Q ss_pred             CCCC
Q 043807          116 DQPK  119 (242)
Q Consensus       116 ~~~~  119 (242)
                      ....
T Consensus       279 ~~~~  282 (348)
T KOG4628|consen  279 TDSG  282 (348)
T ss_pred             CCCC
Confidence            5543

>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=99.48  E-value=9.4e-15  Score=95.38  Aligned_cols=44  Identities=59%  Similarity=1.232  Sum_probs=40.0

Q ss_pred             ceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCC
Q 043807           67 SECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCR  111 (242)
Q Consensus        67 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR  111 (242)
                      ++|+||++.|..++.+..++ |+|.||.+||..|++.+.+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHhCCcCCccC
Confidence            37999999998888899998 999999999999999999999997

...

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.33  E-value=1.1e-12  Score=114.74  Aligned_cols=79  Identities=32%  Similarity=0.633  Sum_probs=60.7

Q ss_pred             hcCCCCHHHHhcCCceeeecccccccccCCceeeeecccccCCc----eeeecCCCCccccHhHHHHHHhcCCCCCCCCc
Q 043807           37 FAKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGE----MVRLLPSCRHAFHVQCIGNWLLGHTICPVCRS  112 (242)
Q Consensus        37 ~~~gl~~~~i~~lp~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~----~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~  112 (242)
                      ...|.....++.+|.+........ ....+.+|+||++.+.+++    .+.+++.|+|.||..||.+|+..+.+||+||.
T Consensus       146 ~k~~~~~~~i~~lp~vl~~~e~~~-~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~  224 (238)
T PHA02929        146 KKGKNYKKFLKTIPSVLSEYEKLY-NRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRT  224 (238)
T ss_pred             HhcchhHHHHHhcchhhhhhhhhh-cCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCC
Confidence            356778999999999875544321 1234679999999987643    13355569999999999999999999999999


Q ss_pred             CCCC
Q 043807          113 PVAD  116 (242)
Q Consensus       113 ~i~~  116 (242)
                      .+..
T Consensus       225 ~~~~  228 (238)
T PHA02929        225 PFIS  228 (238)
T ss_pred             EeeE
Confidence            8753

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

Probab=99.31  E-value=3.5e-12  Score=115.96  Aligned_cols=71  Identities=28%  Similarity=0.679  Sum_probs=52.2

Q ss_pred             CHHHHhcCCceeeecccccccccCCceeeeeccc-ccCC---------ceeeecCCCCccccHhHHHHHHhcCCCCCCCC
Q 043807           42 EEKVLLTIPILAYSAKDCKLFRVDQSECVICLGE-LEDG---------EMVRLLPSCRHAFHVQCIGNWLLGHTICPVCR  111 (242)
Q Consensus        42 ~~~~i~~lp~~~~~~~~~~~~~~~~~~C~ICl~~-~~~~---------~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR  111 (242)
                      .++.-+.+|.+.....     ..++..|.||+++ |..+         .++..+| |||+||..|+..|++++.+||+||
T Consensus       268 ~kdl~~~~~t~t~eql-----~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr  341 (491)
T COG5243         268 TKDLNAMYPTATEEQL-----TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICR  341 (491)
T ss_pred             hhHHHhhcchhhhhhh-----cCCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCccc
Confidence            3444445554443333     2467899999999 4443         2567888 999999999999999999999999


Q ss_pred             cCCCCCC
Q 043807          112 SPVADQP  118 (242)
Q Consensus       112 ~~i~~~~  118 (242)
                      .++..+.
T Consensus       342 ~p~ifd~  348 (491)
T COG5243         342 RPVIFDQ  348 (491)
T ss_pred             Ccccccc
Confidence            9954443

>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=99.29  E-value=2.4e-12  Score=93.20  Aligned_cols=48  Identities=40%  Similarity=0.955  Sum_probs=36.7

Q ss_pred             cCCceeeeecccccCC---------ceeeecCCCCccccHhHHHHHHhcCCCCCCCC
Q 043807           64 VDQSECVICLGELEDG---------EMVRLLPSCRHAFHVQCIGNWLLGHTICPVCR  111 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~---------~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR  111 (242)
                      ..+..|+||++.|.+.         +....+..|||.||..||.+||+.+.+||+||
T Consensus        17 ~~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   17 IADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             SCCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CcCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            3456799999999432         23333434999999999999999999999997

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=99.20  E-value=1.3e-11  Score=109.65  Aligned_cols=52  Identities=40%  Similarity=1.016  Sum_probs=46.9

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHh-cCCCCCCCCcCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL-GHTICPVCRSPVAD  116 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~i~~  116 (242)
                      ....+|+|||+.|..++.++++| |.|.||..|+++|+. -+..||+||.++++
T Consensus       321 ~~GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         321 DKGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCCceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            34578999999999999999999 999999999999998 46789999999864

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

Probab=99.00  E-value=3.1e-10  Score=83.85  Aligned_cols=52  Identities=31%  Similarity=0.744  Sum_probs=41.5

Q ss_pred             CCceeeeecccccC---------CceeeecCCCCccccHhHHHHHHhc---CCCCCCCCcCCCC
Q 043807           65 DQSECVICLGELED---------GEMVRLLPSCRHAFHVQCIGNWLLG---HTICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~---------~~~~~~lp~C~H~Fh~~Ci~~wl~~---~~~CP~CR~~i~~  116 (242)
                      .++.|.||...|..         ++...++..|+|.||..||.+|+..   +..||+||+++..
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~   83 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF   83 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence            47899999999863         2334455569999999999999984   5789999998753

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

Probab=98.97  E-value=3.9e-10  Score=99.84  Aligned_cols=50  Identities=28%  Similarity=0.711  Sum_probs=43.2

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      .....|.+||+...++   ..+| |||+||..||..|......||+||..+.+.
T Consensus       237 ~a~~kC~LCLe~~~~p---SaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~ps  286 (293)
T KOG0317|consen  237 EATRKCSLCLENRSNP---SATP-CGHIFCWSCILEWCSEKAECPLCREKFQPS  286 (293)
T ss_pred             CCCCceEEEecCCCCC---CcCc-CcchHHHHHHHHHHccccCCCcccccCCCc
Confidence            3457899999998774   4666 999999999999999999999999988654

>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=98.96  E-value=3.8e-10  Score=75.48  Aligned_cols=46  Identities=41%  Similarity=0.948  Sum_probs=39.2

Q ss_pred             CceeeeecccccCCceeeecCCCCcc-ccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           66 QSECVICLGELEDGEMVRLLPSCRHA-FHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      +..|.||++....   +.++| |||. ||..|+..|+.....||+||+++.
T Consensus         2 ~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRD---VVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSS---EEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCc---eEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            4589999999765   67777 9999 999999999999999999999874

...

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=98.94  E-value=7.2e-10  Score=93.72  Aligned_cols=50  Identities=34%  Similarity=0.789  Sum_probs=40.6

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc----------------CCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG----------------HTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----------------~~~CP~CR~~i~~~  117 (242)
                      .++.+|+||++.+.++   ++++ |||.||..||..|+..                ...||+||..+...
T Consensus        16 ~~~~~CpICld~~~dP---VvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~   81 (193)
T PLN03208         16 GGDFDCNICLDQVRDP---VVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEA   81 (193)
T ss_pred             CCccCCccCCCcCCCc---EEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChh
Confidence            3567899999998764   4566 9999999999999852                35799999998653

>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=98.93  E-value=5.5e-10  Score=70.94  Aligned_cols=39  Identities=49%  Similarity=1.070  Sum_probs=32.7

Q ss_pred             eeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCC
Q 043807           69 CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVC  110 (242)
Q Consensus        69 C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~C  110 (242)
                      |+||++.+.+  .+..++ |||.||..||.+|++.+..||+|
T Consensus         1 C~iC~~~~~~--~~~~~~-CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTP-CGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECT-TSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC--cCEECC-CCCchhHHHHHHHHHCcCCCcCC
Confidence            8999999886  245666 99999999999999999999998

>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=98.92  E-value=9.2e-10  Score=70.24  Aligned_cols=44  Identities=52%  Similarity=1.206  Sum_probs=36.2

Q ss_pred             eeeeecccccCCceeeecCCCCccccHhHHHHHHhc-CCCCCCCCcCC
Q 043807           68 ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG-HTICPVCRSPV  114 (242)
Q Consensus        68 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~i  114 (242)
                      .|+||++.+.  +.+...+ |+|.||..|+..|+.. +..||+|+..+
T Consensus         1 ~C~iC~~~~~--~~~~~~~-C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFR--EPVVLLP-CGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhh--CceEecC-CCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            4999999983  2344555 9999999999999987 77899998764

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

Probab=98.90  E-value=1e-09  Score=94.52  Aligned_cols=50  Identities=32%  Similarity=0.669  Sum_probs=41.3

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc---CCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG---HTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~---~~~CP~CR~~i~~~  117 (242)
                      ....+|.|||+.-+++   +++. |||.||..||.+||..   ...||+|+..+...
T Consensus        45 ~~~FdCNICLd~akdP---VvTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~   97 (230)
T KOG0823|consen   45 GGFFDCNICLDLAKDP---VVTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSID   97 (230)
T ss_pred             CCceeeeeeccccCCC---EEee-cccceehHHHHHHHhhcCCCeeCCccccccccc
Confidence            4668999999998874   4555 9999999999999974   45799999988554

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

Probab=98.85  E-value=1.5e-09  Score=90.10  Aligned_cols=54  Identities=31%  Similarity=0.696  Sum_probs=44.0

Q ss_pred             ccccCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           61 LFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        61 ~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      ........|+|||+.+...  +.+-.+|||+||..||..-++....||+|++.|..
T Consensus       126 ~~~~~~~~CPiCl~~~sek--~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~  179 (187)
T KOG0320|consen  126 LRKEGTYKCPICLDSVSEK--VPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH  179 (187)
T ss_pred             cccccccCCCceecchhhc--cccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence            3444567899999999864  33434699999999999999999999999987753

>PHA02926 zinc finger-like protein; Provisional

Probab=98.84  E-value=1.9e-09  Score=92.58  Aligned_cols=54  Identities=31%  Similarity=0.734  Sum_probs=41.6

Q ss_pred             cCCceeeeecccccC-----CceeeecCCCCccccHhHHHHHHhcC------CCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELED-----GEMVRLLPSCRHAFHVQCIGNWLLGH------TICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~-----~~~~~~lp~C~H~Fh~~Ci~~wl~~~------~~CP~CR~~i~~~  117 (242)
                      ..+.+|+||++..-+     +....+++.|+|.||..||..|...+      .+||+||..+...
T Consensus       168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I  232 (242)
T PHA02926        168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNI  232 (242)
T ss_pred             cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeee
Confidence            356789999998633     22345677799999999999999743      4599999987544

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

Probab=98.79  E-value=4.2e-09  Score=68.19  Aligned_cols=38  Identities=37%  Similarity=0.830  Sum_probs=28.9

Q ss_pred             eeeecccccCCceeeecCCCCccccHhHHHHHHhcC----CCCCCC
Q 043807           69 CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGH----TICPVC  110 (242)
Q Consensus        69 C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~C  110 (242)
                      |+||++.|.+   .+.++ |||.||..||..|++..    ..||.|
T Consensus         1 CpiC~~~~~~---Pv~l~-CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKD---PVSLP-CGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SS---EEE-S-SSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCC---ccccC-CcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            8999999988   45676 99999999999999753    469987

>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=98.72  E-value=7.9e-09  Score=65.95  Aligned_cols=39  Identities=51%  Similarity=1.209  Sum_probs=33.5

Q ss_pred             eeeecccccCCceeeecCCCCccccHhHHHHHHh--cCCCCCCC
Q 043807           69 CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL--GHTICPVC  110 (242)
Q Consensus        69 C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~--~~~~CP~C  110 (242)
                      |+||++.+..+  ..+++ |||.||..||.+|+.  ....||+|
T Consensus         1 C~iC~~~~~~~--~~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDP--VILLP-CGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSE--EEETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCC--CEEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence            89999998864  34666 999999999999998  56789998

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

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

Probab=98.72  E-value=7.7e-09  Score=74.99  Aligned_cols=53  Identities=30%  Similarity=0.599  Sum_probs=41.6

Q ss_pred             CCceeeeecccccC------------CceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           65 DQSECVICLGELED------------GEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        65 ~~~~C~ICl~~~~~------------~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      .-+.|+||...|.+            ++.+.+...|.|.||..||.+||..+..||++|+++...
T Consensus        19 ~id~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~   83 (88)
T COG5194          19 PIDVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLA   83 (88)
T ss_pred             ccchhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEe
Confidence            34678888776632            344555556999999999999999999999999988543

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

Probab=98.71  E-value=9.2e-09  Score=91.57  Aligned_cols=114  Identities=23%  Similarity=0.466  Sum_probs=79.6

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc-----------------------CCCCCCCCcCCCCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG-----------------------HTICPVCRSPVADQPKS  120 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-----------------------~~~CP~CR~~i~~~~~~  120 (242)
                      ....+|+|||..|.+++.+.+++ |.|.||..|+..+|..                       ...||+||..|..... 
T Consensus       113 ~p~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~~-  190 (368)
T KOG4445|consen  113 HPNGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEEN-  190 (368)
T ss_pred             CCCCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccccc-
Confidence            45678999999999999888887 9999999999876631                       2369999999965533 


Q ss_pred             CCcccCCCCCCcccccccccccccccchHHHHHHHHhhhhcccccCCCceeEEEeccCCcccccccCCCCC
Q 043807          121 TSGEAANLPNYKIMITSCLDVVSLATSIEDKQQLLATTLKRSLSMDECSNYVIVRLQNHDHIMCKQEGDDD  191 (242)
Q Consensus       121 ~~~~~~~~p~~~~~~~~~~~~~s~~~~~e~~q~~~~~~~~Rs~s~~~~~~~~i~d~~~~~~~~~~~~~~d~  191 (242)
                       ..+.+..|.+.......     ...++..++..+ ..+.|+.+-|.     |||+++++.-+..+++..|
T Consensus       191 -slk~a~~Pt~~l~~~~~-----~~eslrq~~~r~-~ly~~qk~rg~-----iid~~ae~~a~~~ies~~d  249 (368)
T KOG4445|consen  191 -SLKIAEFPTYPMELYQP-----SAESLRQQEERK-RLYQRQQERGG-----IIDLEAERPAPAEPESAVD  249 (368)
T ss_pred             -ceeccCCCccccccCcc-----cHHHHHHHHHHH-HHHHHHhhcCc-----eEeeeccCCCCCCchhHHH
Confidence             34455566665544322     111233344445 77777777776     9999998766666665544

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.71  E-value=1.1e-08  Score=66.73  Aligned_cols=44  Identities=30%  Similarity=0.737  Sum_probs=37.3

Q ss_pred             eeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCc
Q 043807           68 ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRS  112 (242)
Q Consensus        68 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~  112 (242)
                      .|.||++.|.+.....+++ |||+||..|+..+......||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~-CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTS-CGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcc-cCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            4899999995555677776 9999999999999866789999984

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

Probab=98.70  E-value=7.8e-09  Score=100.64  Aligned_cols=51  Identities=37%  Similarity=0.949  Sum_probs=44.2

Q ss_pred             cCCceeeeecccccCCce--eeecCCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGEM--VRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~--~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      ..+..|+||++.+..+..  +..++ |+|+||..|+..|+++..+||+||..+.
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~~  341 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVLY  341 (543)
T ss_pred             hcCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhhh
Confidence            346789999999987654  67887 9999999999999999999999999543

>smart00504 Ubox Modified RING finger domain

Probab=98.66  E-value=2.3e-08  Score=69.40  Aligned_cols=45  Identities=31%  Similarity=0.614  Sum_probs=39.8

Q ss_pred             ceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           67 SECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        67 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      ..|+||++.+.++   ++++ |||+|+..||..|+..+.+||+|+.++.
T Consensus         2 ~~Cpi~~~~~~~P---v~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~   46 (63)
T smart00504        2 FLCPISLEVMKDP---VILP-SGQTYERRAIEKWLLSHGTDPVTGQPLT   46 (63)
T ss_pred             cCCcCCCCcCCCC---EECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence            5799999999874   4666 9999999999999998899999998874

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

>smart00184 RING Ring finger

Probab=98.62  E-value=2.8e-08  Score=61.10  Aligned_cols=38  Identities=50%  Similarity=1.205  Sum_probs=32.0

Q ss_pred             eeeecccccCCceeeecCCCCccccHhHHHHHHh-cCCCCCCC
Q 043807           69 CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL-GHTICPVC  110 (242)
Q Consensus        69 C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~C  110 (242)
                      |+||++...   ....++ |+|.||..|+..|+. .+..||+|
T Consensus         1 C~iC~~~~~---~~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELK---DPVVLP-CGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCC---CcEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence            789999843   366776 999999999999998 66789987

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

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

Probab=98.58  E-value=1.1e-08  Score=73.51  Aligned_cols=54  Identities=30%  Similarity=0.692  Sum_probs=42.1

Q ss_pred             cccCCceeeeecccccC---------CceeeecCCCCccccHhHHHHHHhc---CCCCCCCCcCCC
Q 043807           62 FRVDQSECVICLGELED---------GEMVRLLPSCRHAFHVQCIGNWLLG---HTICPVCRSPVA  115 (242)
Q Consensus        62 ~~~~~~~C~ICl~~~~~---------~~~~~~lp~C~H~Fh~~Ci~~wl~~---~~~CP~CR~~i~  115 (242)
                      -...++.|.||...|..         ++.+.++..|.|.||..||.+|+..   +..||+||..+.
T Consensus        16 W~~~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   16 WDAPDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             EcCCCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            34566799999999853         3444555569999999999999964   567999999874

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.51  E-value=7.3e-08  Score=90.10  Aligned_cols=50  Identities=28%  Similarity=0.599  Sum_probs=42.6

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      .....|+||++.|..+   ++++ |||.||..||..|+.....||+|+..+...
T Consensus        24 e~~l~C~IC~d~~~~P---vitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~   73 (397)
T TIGR00599        24 DTSLRCHICKDFFDVP---VLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQES   73 (397)
T ss_pred             ccccCCCcCchhhhCc---cCCC-CCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence            4567899999999764   4566 999999999999999888999999988643

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

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

Probab=98.51  E-value=4.2e-08  Score=74.53  Aligned_cols=67  Identities=25%  Similarity=0.550  Sum_probs=48.8

Q ss_pred             ceeeecccccccccCCceeeeecccc-------------cCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           51 ILAYSAKDCKLFRVDQSECVICLGEL-------------EDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        51 ~~~~~~~~~~~~~~~~~~C~ICl~~~-------------~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      ..++.....-.-+...+.|+||..-+             ..++.++....|.|.||..||.+||+.+..||+|.+++..+
T Consensus        31 lKKWnAvAlWaWDi~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~~q  110 (114)
T KOG2930|consen   31 LKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWVFQ  110 (114)
T ss_pred             EeeeeeeeeeeeeeeechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcceeEe
Confidence            33444444334445567899987654             23455666667999999999999999999999999887544

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

Probab=98.42  E-value=2.2e-07  Score=87.67  Aligned_cols=52  Identities=40%  Similarity=0.969  Sum_probs=39.9

Q ss_pred             cCCceeeeecccccC---C-----------ceeeecCCCCccccHhHHHHHHhc-CCCCCCCCcCCCC
Q 043807           64 VDQSECVICLGELED---G-----------EMVRLLPSCRHAFHVQCIGNWLLG-HTICPVCRSPVAD  116 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~---~-----------~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~i~~  116 (242)
                      ....+|+||+..+.-   +           ....+.| |.|+||..|+.+|+.. +-.||+||.++++
T Consensus       569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tP-C~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTP-CHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             hccccceEeccccceeeccCcchhhhhhhhccccccc-hHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            345689999998742   1           1133456 9999999999999994 5599999999864

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

Probab=98.38  E-value=1.8e-07  Score=82.17  Aligned_cols=49  Identities=33%  Similarity=0.743  Sum_probs=40.7

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHH-HHhcCCC-CCCCCcCCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGN-WLLGHTI-CPVCRSPVADQ  117 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~-wl~~~~~-CP~CR~~i~~~  117 (242)
                      .+..|+||++....   ...++ |||+||..||.. |-..+.. ||+||+...++
T Consensus       214 ~d~kC~lC~e~~~~---ps~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk  264 (271)
T COG5574         214 ADYKCFLCLEEPEV---PSCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPK  264 (271)
T ss_pred             cccceeeeecccCC---ccccc-ccchhhHHHHHHHHHhhccccCchhhhhccch
Confidence            46789999999876   45666 999999999999 9877665 99999987654

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

Probab=98.30  E-value=1.5e-07  Score=82.78  Aligned_cols=52  Identities=29%  Similarity=0.718  Sum_probs=42.0

Q ss_pred             cCCceeeeecccccCCc-------eeeecCCCCccccHhHHHHHHh--cCCCCCCCCcCCCC
Q 043807           64 VDQSECVICLGELEDGE-------MVRLLPSCRHAFHVQCIGNWLL--GHTICPVCRSPVAD  116 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~-------~~~~lp~C~H~Fh~~Ci~~wl~--~~~~CP~CR~~i~~  116 (242)
                      .++..|+||-..+....       ..-.+. |+|+||..||..|..  .+++||.|++.+.-
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVdl  282 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVDL  282 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhhH
Confidence            46678999999875443       456676 999999999999975  57899999988743

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

Probab=98.25  E-value=6.3e-07  Score=58.27  Aligned_cols=38  Identities=29%  Similarity=0.669  Sum_probs=22.3

Q ss_pred             eeeecccccCC-ceeeecCCCCccccHhHHHHHHhcC----CCCC
Q 043807           69 CVICLGELEDG-EMVRLLPSCRHAFHVQCIGNWLLGH----TICP  108 (242)
Q Consensus        69 C~ICl~~~~~~-~~~~~lp~C~H~Fh~~Ci~~wl~~~----~~CP  108 (242)
                      |+||.+ |..+ ....+|+ |||+|+.+||.+|+..+    ..||
T Consensus         1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 7554 4567788 99999999999999743    3566

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

Probab=98.22  E-value=3.3e-07  Score=83.42  Aligned_cols=61  Identities=31%  Similarity=0.562  Sum_probs=46.4

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHh-cCCCCCCCCcCCCCCCCCCCcccCCCCCCc
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL-GHTICPVCRSPVADQPKSTSGEAANLPNYK  132 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~i~~~~~~~~~~~~~~p~~~  132 (242)
                      ..+..|+|||+.+...   +..+.|.|.||.+||..-++ .+..||.||..+...     ..+...|+++
T Consensus        41 ~~~v~c~icl~llk~t---mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Sk-----rsLr~Dp~fd  102 (381)
T KOG0311|consen   41 DIQVICPICLSLLKKT---MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSK-----RSLRIDPNFD  102 (381)
T ss_pred             hhhhccHHHHHHHHhh---cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccc-----ccCCCCccHH
Confidence            4567899999999763   44457999999999988776 578999999988655     3334455554

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

Probab=98.22  E-value=6e-07  Score=85.16  Aligned_cols=47  Identities=30%  Similarity=0.575  Sum_probs=38.0

Q ss_pred             CceeeeecccccCCceeeecCCCCccccHhHHHHHHhc-----CCCCCCCCcCCCC
Q 043807           66 QSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG-----HTICPVCRSPVAD  116 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-----~~~CP~CR~~i~~  116 (242)
                      +..|+|||+.....   ..+ .|||+||..||.++|..     ...||+|+..|..
T Consensus       186 ~~~CPICL~~~~~p---~~t-~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~  237 (513)
T KOG2164|consen  186 DMQCPICLEPPSVP---VRT-NCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL  237 (513)
T ss_pred             CCcCCcccCCCCcc---ccc-ccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence            67899999997653   233 49999999999998863     3579999998865

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

Probab=98.16  E-value=1.6e-06  Score=57.97  Aligned_cols=42  Identities=31%  Similarity=0.793  Sum_probs=32.3

Q ss_pred             eeeeecccccCCceeeecCCCC-----ccccHhHHHHHHhc--CCCCCCCC
Q 043807           68 ECVICLGELEDGEMVRLLPSCR-----HAFHVQCIGNWLLG--HTICPVCR  111 (242)
Q Consensus        68 ~C~ICl~~~~~~~~~~~lp~C~-----H~Fh~~Ci~~wl~~--~~~CP~CR  111 (242)
                      .|.||++.. .++...+.| |.     |.+|..|+.+|+..  +.+||+|+
T Consensus         1 ~CrIC~~~~-~~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEG-DEGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCCC-CCCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            489999933 344455777 85     89999999999964  45899995

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

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

Probab=98.15  E-value=6.7e-07  Score=81.05  Aligned_cols=49  Identities=31%  Similarity=0.677  Sum_probs=41.9

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      .-..|.||.+.|..+   .++| |+|.||.-||..+|..+..||.|+.++.+.
T Consensus        22 ~lLRC~IC~eyf~ip---~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~Es   70 (442)
T KOG0287|consen   22 DLLRCGICFEYFNIP---MITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTES   70 (442)
T ss_pred             HHHHHhHHHHHhcCc---eecc-ccchHHHHHHHHHhccCCCCCceecccchh
Confidence            346799999999863   4556 999999999999999999999999887543

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

Probab=98.11  E-value=4.5e-07  Score=65.02  Aligned_cols=50  Identities=40%  Similarity=0.943  Sum_probs=23.5

Q ss_pred             Cceeeeeccccc-CCce-eeecC--CCCccccHhHHHHHHhc---C--------CCCCCCCcCCC
Q 043807           66 QSECVICLGELE-DGEM-VRLLP--SCRHAFHVQCIGNWLLG---H--------TICPVCRSPVA  115 (242)
Q Consensus        66 ~~~C~ICl~~~~-~~~~-~~~lp--~C~H~Fh~~Ci~~wl~~---~--------~~CP~CR~~i~  115 (242)
                      +.+|.||+..+. .++. ..+.+  .|++.||..||.+||..   .        ..||.|+.+|.
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            458999999876 3322 22332  69999999999999962   1        25999998774

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.09  E-value=2.4e-06  Score=77.29  Aligned_cols=53  Identities=21%  Similarity=0.552  Sum_probs=38.5

Q ss_pred             CCceeeeeccc-ccCCc-eeeecCCCCccccHhHHHHHH-hcCCCCCCCCcCCCCCC
Q 043807           65 DQSECVICLGE-LEDGE-MVRLLPSCRHAFHVQCIGNWL-LGHTICPVCRSPVADQP  118 (242)
Q Consensus        65 ~~~~C~ICl~~-~~~~~-~~~~lp~C~H~Fh~~Ci~~wl-~~~~~CP~CR~~i~~~~  118 (242)
                      ++..|+||... +..++ .+.+. .|||.||..|++..+ .....||.|+..+....
T Consensus         2 d~~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~   57 (309)
T TIGR00570         2 DDQGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFVRGSGSCPECDTPLRKNN   57 (309)
T ss_pred             CCCCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence            34689999995 33333 33333 499999999999965 45668999998886544

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=98.08  E-value=1.5e-06  Score=77.49  Aligned_cols=48  Identities=29%  Similarity=0.603  Sum_probs=40.6

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      .-..|.||-+.|..+    ++..|||.||.-||..+|..+..||+||.+..+
T Consensus        24 s~lrC~IC~~~i~ip----~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~e   71 (391)
T COG5432          24 SMLRCRICDCRISIP----CETTCGHTFCSLCIRRHLGTQPFCPVCREDPCE   71 (391)
T ss_pred             hHHHhhhhhheeecc----eecccccchhHHHHHHHhcCCCCCccccccHHh
Confidence            346799999999853    444599999999999999999999999987644

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

Probab=98.06  E-value=2.6e-06  Score=61.45  Aligned_cols=48  Identities=27%  Similarity=0.496  Sum_probs=37.2

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc-CCCCCCCCcCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG-HTICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~i~~  116 (242)
                      +...|+|+.+.+.+   .++++ +||.|.+.||..|+.. +.+||+|+.++..
T Consensus         3 ~~f~CpIt~~lM~d---PVi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~   51 (73)
T PF04564_consen    3 DEFLCPITGELMRD---PVILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSE   51 (73)
T ss_dssp             GGGB-TTTSSB-SS---EEEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred             cccCCcCcCcHhhC---ceeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence            45789999999988   45677 9999999999999998 8899999988753

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 ....

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

Probab=98.05  E-value=1.6e-06  Score=75.19  Aligned_cols=44  Identities=39%  Similarity=0.841  Sum_probs=39.0

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCR  111 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR  111 (242)
                      .+...|+||++.|..+   .+++ |+|.||..|+..|+.....||.||
T Consensus        11 ~~~~~C~iC~~~~~~p---~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr   54 (386)
T KOG2177|consen   11 QEELTCPICLEYFREP---VLLP-CGHNFCRACLTRSWEGPLSCPVCR   54 (386)
T ss_pred             cccccChhhHHHhhcC---cccc-ccchHhHHHHHHhcCCCcCCcccC
Confidence            4677999999999986   6777 999999999999988667899999

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

Probab=98.02  E-value=1.2e-06  Score=88.04  Aligned_cols=52  Identities=29%  Similarity=0.821  Sum_probs=39.2

Q ss_pred             cCCceeeeecccccCCc---eeeecCCCCccccHhHHHHHHh--cCCCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGE---MVRLLPSCRHAFHVQCIGNWLL--GHTICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~---~~~~lp~C~H~Fh~~Ci~~wl~--~~~~CP~CR~~i~  115 (242)
                      .+..+|+||+..+..-+   .-...+.|.|.||..|+.+|++  .+.+||+||..++
T Consensus      1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            35678999999875211   1123346999999999999997  4678999998774

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

Probab=97.95  E-value=4.6e-06  Score=76.87  Aligned_cols=47  Identities=30%  Similarity=0.868  Sum_probs=36.0

Q ss_pred             CceeeeecccccCCceeeecCCCCccccHhHHHHHHhc---CCCCCCCCc
Q 043807           66 QSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG---HTICPVCRS  112 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~---~~~CP~CR~  112 (242)
                      ...|.||.+.+.....+.-+..|||+||..|+.+|+..   +..||+|+-
T Consensus         4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~i   53 (465)
T KOG0827|consen    4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQI   53 (465)
T ss_pred             cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceee
Confidence            35899996655544444444459999999999999984   468999993

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

Probab=97.85  E-value=1.3e-05  Score=73.36  Aligned_cols=48  Identities=40%  Similarity=0.914  Sum_probs=41.5

Q ss_pred             CCceeeeecccccCCceeeecCCCCcc-ccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHA-FHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      ...+|.||+.+..+   +.+|| |-|. .|..|.+...-++..||+||.++..
T Consensus       289 ~gkeCVIClse~rd---t~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~  337 (349)
T KOG4265|consen  289 SGKECVICLSESRD---TVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIEE  337 (349)
T ss_pred             CCCeeEEEecCCcc---eEEec-chhhehhHhHHHHHHHhhcCCCccccchHh
Confidence            35689999999876   77898 9997 9999999877778899999999854

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

Probab=97.74  E-value=1e-05  Score=75.74  Aligned_cols=48  Identities=29%  Similarity=0.822  Sum_probs=38.2

Q ss_pred             CCceeeeecccccCCc-eeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           65 DQSECVICLGELEDGE-MVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~-~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      +-.+|+|||+-+.... .++... |.|.||..|+..|..  .+||+||....
T Consensus       174 ELPTCpVCLERMD~s~~gi~t~~-c~Hsfh~~cl~~w~~--~scpvcR~~q~  222 (493)
T KOG0804|consen  174 ELPTCPVCLERMDSSTTGILTIL-CNHSFHCSCLMKWWD--SSCPVCRYCQS  222 (493)
T ss_pred             cCCCcchhHhhcCccccceeeee-cccccchHHHhhccc--CcChhhhhhcC
Confidence            4568999999987653 344555 999999999999964  68999997654

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

Probab=97.64  E-value=1.3e-05  Score=54.24  Aligned_cols=46  Identities=33%  Similarity=0.710  Sum_probs=35.9

Q ss_pred             CceeeeecccccCCceeeecCCCCcc-ccHhHHHHHHh-cCCCCCCCCcCCC
Q 043807           66 QSECVICLGELEDGEMVRLLPSCRHA-FHVQCIGNWLL-GHTICPVCRSPVA  115 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~-~~~~CP~CR~~i~  115 (242)
                      +.+|.||++.-.+.    ++-.|||. .|..|-.+.++ .+..||+||+++.
T Consensus         7 ~dECTICye~pvds----VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    7 SDECTICYEHPVDS----VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             ccceeeeccCcchH----HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            37899999986653    33349997 88899776555 7889999999874

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

Probab=97.59  E-value=4.3e-05  Score=70.45  Aligned_cols=53  Identities=32%  Similarity=0.852  Sum_probs=40.6

Q ss_pred             CCceeeeecccccCCc----eeeecCCCCccccHhHHHHHHh--c-----CCCCCCCCcCCCCC
Q 043807           65 DQSECVICLGELEDGE----MVRLLPSCRHAFHVQCIGNWLL--G-----HTICPVCRSPVADQ  117 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~----~~~~lp~C~H~Fh~~Ci~~wl~--~-----~~~CP~CR~~i~~~  117 (242)
                      .+..|.||++.+.+..    ....+|+|.|.||..||..|-.  +     .+.||.||......
T Consensus       160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v  223 (344)
T KOG1039|consen  160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFV  223 (344)
T ss_pred             ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccc
Confidence            4678999999876532    1334577999999999999983  3     57899999876443

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

Probab=97.55  E-value=1.9e-05  Score=55.38  Aligned_cols=47  Identities=34%  Similarity=0.721  Sum_probs=23.9

Q ss_pred             CceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           66 QSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      -..|++|.+.+..+   +.+..|.|+||..||..-+.  ..||+|+.+...+
T Consensus         7 lLrCs~C~~~l~~p---v~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~q   53 (65)
T PF14835_consen    7 LLRCSICFDILKEP---VCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQ   53 (65)
T ss_dssp             TTS-SSS-S--SS----B---SSS--B-TTTGGGGTT--TB-SSS--B-S-S
T ss_pred             hcCCcHHHHHhcCC---ceeccCccHHHHHHhHHhcC--CCCCCcCChHHHH
Confidence            35799999999874   33446999999999988554  4599998876443

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

Probab=97.41  E-value=2.5e-05  Score=77.46  Aligned_cols=50  Identities=26%  Similarity=0.534  Sum_probs=40.9

Q ss_pred             CceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           66 QSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      ...|++|+..+.+.......+ |+|+||..||..|-+.-.+||+||..+..
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~  172 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGEFGE  172 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhhhhe
Confidence            456888888887665444555 99999999999999999999999987643

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

Probab=97.26  E-value=0.00015  Score=65.15  Aligned_cols=48  Identities=31%  Similarity=0.609  Sum_probs=37.9

Q ss_pred             CceeeeecccccCCceeeecCCCCccccHhHHHHHHh-cCCCCCCCCcCCCCC
Q 043807           66 QSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL-GHTICPVCRSPVADQ  117 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~i~~~  117 (242)
                      ..+|+||+....-+   +.++ |+|.||..||..-.+ ...+|++||.+|...
T Consensus         7 ~~eC~IC~nt~n~P---v~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    7 KKECLICYNTGNCP---VNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             CCcceeeeccCCcC---cccc-ccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            45899999986553   4555 999999999987655 456799999998653

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

Probab=97.23  E-value=0.00023  Score=66.28  Aligned_cols=48  Identities=33%  Similarity=0.764  Sum_probs=37.8

Q ss_pred             CceeeeecccccC-CceeeecCCCCccccHhHHHHHHhc--CCCCCCCCcC
Q 043807           66 QSECVICLGELED-GEMVRLLPSCRHAFHVQCIGNWLLG--HTICPVCRSP  113 (242)
Q Consensus        66 ~~~C~ICl~~~~~-~~~~~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~CR~~  113 (242)
                      ...|+||++.+.. ++...+.+.|||.|-..||.+||.+  ...||.|...
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k   54 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK   54 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence            4689999998864 4555556679999999999999953  3579999753

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

Probab=97.22  E-value=0.0001  Score=73.10  Aligned_cols=48  Identities=21%  Similarity=0.641  Sum_probs=39.0

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHh-cCCCCCCCCcCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL-GHTICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~i~~  116 (242)
                      .-..|++|-..+.+   + +++.|||+||..|+...+. ++..||.|.+.|..
T Consensus       642 ~~LkCs~Cn~R~Kd---~-vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga  690 (698)
T KOG0978|consen  642 ELLKCSVCNTRWKD---A-VITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA  690 (698)
T ss_pred             hceeCCCccCchhh---H-HHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence            34689999987775   3 4446999999999999886 57899999998854

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

Probab=97.19  E-value=0.00032  Score=60.71  Aligned_cols=54  Identities=26%  Similarity=0.621  Sum_probs=44.7

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc--------CCCCCCCCcCCCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG--------HTICPVCRSPVADQPK  119 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~--------~~~CP~CR~~i~~~~~  119 (242)
                      +....|..|-..+..++.+++.  |.|.||.+|+++|-..        ...||.|..+|++...
T Consensus        48 DY~pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~N  109 (299)
T KOG3970|consen   48 DYNPNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPIN  109 (299)
T ss_pred             CCCCCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCcc
Confidence            3556799999999999988764  9999999999999752        3579999999976543

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

Probab=97.08  E-value=0.00017  Score=66.96  Aligned_cols=46  Identities=30%  Similarity=0.816  Sum_probs=37.3

Q ss_pred             ceeeeecccccCCceeeecCCCCccccHhHHHHHHhc--CCCCCCCCcCCCC
Q 043807           67 SECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG--HTICPVCRSPVAD  116 (242)
Q Consensus        67 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~CR~~i~~  116 (242)
                      .-|-||-+.-++   +..-| |||..|..|+..|-..  ..+||.||..|--
T Consensus       370 eLCKICaendKd---vkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG  417 (563)
T KOG1785|consen  370 ELCKICAENDKD---VKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG  417 (563)
T ss_pred             HHHHHhhccCCC---ccccc-ccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence            359999887544   67777 9999999999999843  5789999998743

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

Probab=97.04  E-value=0.00033  Score=65.93  Aligned_cols=51  Identities=31%  Similarity=0.664  Sum_probs=42.6

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      ..+..|++|...+.++-.  .. .|||.||..|+..|+..+..||.|+..+...
T Consensus        19 ~~~l~C~~C~~vl~~p~~--~~-~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~   69 (391)
T KOG0297|consen   19 DENLLCPICMSVLRDPVQ--TT-TCGHRFCAGCLLESLSNHQKCPVCRQELTQA   69 (391)
T ss_pred             cccccCccccccccCCCC--CC-CCCCcccccccchhhccCcCCcccccccchh
Confidence            466899999999988622  12 5999999999999999999999998877544

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

Probab=97.03  E-value=0.0003  Score=66.11  Aligned_cols=49  Identities=31%  Similarity=0.736  Sum_probs=42.3

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      ..+..|.||+..+..+   +++| |||.||..||++-+.....||.||..+..
T Consensus        82 ~sef~c~vc~~~l~~p---v~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   82 RSEFECCVCSRALYPP---VVTP-CGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cchhhhhhhHhhcCCC---cccc-ccccccHHHHHHHhccCCCCccccccccc
Confidence            4567899999998764   4666 99999999999988888999999999875

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

Probab=96.91  E-value=0.00039  Score=47.87  Aligned_cols=42  Identities=33%  Similarity=0.628  Sum_probs=27.7

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHh--cCCCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL--GHTICPV  109 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~--~~~~CP~  109 (242)
                      -...|+|.+..|.++  ++-. .|+|.|-+..|.+|+.  ....||+
T Consensus        10 ~~~~CPiT~~~~~~P--V~s~-~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFEDP--VKSK-KCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SSE--EEES-SS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhhCC--cCcC-CCCCeecHHHHHHHHHhcCCCCCCC
Confidence            456899999999875  4444 4999999999999994  3557998

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

Probab=96.88  E-value=0.00024  Score=64.46  Aligned_cols=51  Identities=27%  Similarity=0.621  Sum_probs=42.3

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      .....|.+|-..|-+...   .+.|-|.||+.||..+|..+..||.|...+-..
T Consensus        13 n~~itC~LC~GYliDATT---I~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   13 NPHITCRLCGGYLIDATT---ITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             ccceehhhccceeecchh---HHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            355689999999987533   336999999999999999999999999877544

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

Probab=96.70  E-value=0.0029  Score=56.28  Aligned_cols=50  Identities=24%  Similarity=0.495  Sum_probs=38.6

Q ss_pred             ccCCceeeeecccccCCceeeecCCCCccccHhHHHHHHh--cCCCCCCCCcCCC
Q 043807           63 RVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL--GHTICPVCRSPVA  115 (242)
Q Consensus        63 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~--~~~~CP~CR~~i~  115 (242)
                      ...+.+|++|.+.-..+  .... +|+|+||..||..-+.  ...+||.|..+..
T Consensus       236 ~t~~~~C~~Cg~~PtiP--~~~~-~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  236 GTSDTECPVCGEPPTIP--HVIG-KCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             ccCCceeeccCCCCCCC--eeec-cccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            35678999999987665  2333 4999999999987654  3579999988775

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

Probab=96.70  E-value=0.0012  Score=60.58  Aligned_cols=46  Identities=30%  Similarity=0.650  Sum_probs=34.2

Q ss_pred             ccCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           63 RVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        63 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      ......|.||+++..+   ...+| |||.-|  |..-. +....||+||..|.
T Consensus       302 ~~~p~lcVVcl~e~~~---~~fvp-cGh~cc--ct~cs-~~l~~CPvCR~rI~  347 (355)
T KOG1571|consen  302 LPQPDLCVVCLDEPKS---AVFVP-CGHVCC--CTLCS-KHLPQCPVCRQRIR  347 (355)
T ss_pred             cCCCCceEEecCCccc---eeeec-CCcEEE--chHHH-hhCCCCchhHHHHH
Confidence            3456789999999876   66777 999966  66543 23456999998774

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

Probab=96.63  E-value=0.0011  Score=60.85  Aligned_cols=67  Identities=22%  Similarity=0.422  Sum_probs=47.7

Q ss_pred             HhcCCceeeecccccccccCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           46 LLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        46 i~~lp~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      +..+|..+...........++..|+||+..--.   .+..| |+|.-|..||.+.+.+.+.|=.|+..+..
T Consensus       402 ~~~l~~~~~~~~~~~lp~sEd~lCpICyA~pi~---Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  402 SSQLPERKEESFNKDLPDSEDNLCPICYAGPIN---AVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             HhhcchhhHHhhcCCCCCcccccCcceecccch---hhccC-CCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            334444333333322334567889999876432   45666 99999999999999999999999988764

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

Probab=96.61  E-value=0.0013  Score=63.32  Aligned_cols=55  Identities=25%  Similarity=0.551  Sum_probs=41.9

Q ss_pred             ccCCceeeeecccccCCceeeecCCCCccccHhHHHHHHh-----cCCCCCCCCcCCCCCCCCC
Q 043807           63 RVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL-----GHTICPVCRSPVADQPKST  121 (242)
Q Consensus        63 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-----~~~~CP~CR~~i~~~~~~~  121 (242)
                      +.+...|.+|.+.-++   ..... |.|.||+-||.++..     .+.+||.|...+.-....+
T Consensus       533 nk~~~~C~lc~d~aed---~i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~  592 (791)
T KOG1002|consen  533 NKGEVECGLCHDPAED---YIESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEP  592 (791)
T ss_pred             ccCceeecccCChhhh---hHhhh-hhHHHHHHHHHHHHHhhhcccCCCCccccccccccccch
Confidence            3456789999998765   33444 999999999988875     3679999998886654433

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

Probab=96.52  E-value=0.00078  Score=62.54  Aligned_cols=49  Identities=31%  Similarity=0.703  Sum_probs=38.8

Q ss_pred             CCceeeeecccccC-CceeeecCCCCccccHhHHHHHHhcC--CCCCCCCcCC
Q 043807           65 DQSECVICLGELED-GEMVRLLPSCRHAFHVQCIGNWLLGH--TICPVCRSPV  114 (242)
Q Consensus        65 ~~~~C~ICl~~~~~-~~~~~~lp~C~H~Fh~~Ci~~wl~~~--~~CP~CR~~i  114 (242)
                      -+..|..|-+.+.. ++..--+| |.|+||..|+...|.++  .+||.||+-.
T Consensus       364 ~~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Crklr  415 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCRKLR  415 (518)
T ss_pred             HhhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHHHHH
Confidence            35679999998754 34566787 99999999999999754  6899999433

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

Probab=96.48  E-value=0.0011  Score=53.23  Aligned_cols=38  Identities=21%  Similarity=0.528  Sum_probs=30.7

Q ss_pred             CceeeeecccccCCceeeecCCCC------ccccHhHHHHHHhcC
Q 043807           66 QSECVICLGELEDGEMVRLLPSCR------HAFHVQCIGNWLLGH  104 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~~~~~lp~C~------H~Fh~~Ci~~wl~~~  104 (242)
                      ..+|+||++.+...+.++.++ ||      |.||..|+.+|-+.+
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~~~~   69 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWRRER   69 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHHhhc
Confidence            568999999998855577776 76      889999999995433

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=96.48  E-value=0.0012  Score=54.53  Aligned_cols=41  Identities=41%  Similarity=0.886  Sum_probs=31.9

Q ss_pred             CceeeecccccccccCCceeeeecccccCCceeeecCCCCccccH
Q 043807           50 PILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHV   94 (242)
Q Consensus        50 p~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~   94 (242)
                      |.+.|..+.   ...+..+|.|||+++..++.+..|| |-.+||+
T Consensus       164 PrlsYNdDV---L~ddkGECvICLEdL~~GdtIARLP-CLCIYHK  204 (205)
T KOG0801|consen  164 PRLSYNDDV---LKDDKGECVICLEDLEAGDTIARLP-CLCIYHK  204 (205)
T ss_pred             cccccccch---hcccCCcEEEEhhhccCCCceeccc-eEEEeec
Confidence            444454443   2245678999999999999999999 9999996

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

Probab=96.33  E-value=0.0024  Score=64.26  Aligned_cols=51  Identities=33%  Similarity=0.716  Sum_probs=39.3

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc-------CCCCCCCCcCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG-------HTICPVCRSPV  114 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-------~~~CP~CR~~i  114 (242)
                      ....+|.||++.+.....+.-...|.|+||..||..|-+.       .-.||.|....
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~  246 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVS  246 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchh
Confidence            3567899999999876555444469999999999999864       22599998433

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

Probab=96.26  E-value=0.0026  Score=42.00  Aligned_cols=40  Identities=38%  Similarity=0.978  Sum_probs=27.1

Q ss_pred             eeeecccccCCceeeecCCCC-----ccccHhHHHHHHh--cCCCCCCC
Q 043807           69 CVICLGELEDGEMVRLLPSCR-----HAFHVQCIGNWLL--GHTICPVC  110 (242)
Q Consensus        69 C~ICl~~~~~~~~~~~lp~C~-----H~Fh~~Ci~~wl~--~~~~CP~C  110 (242)
                      |-||++.-.+++ ..+.| |.     ...|..|+..|+.  .+..|++|
T Consensus         1 CrIC~~~~~~~~-~li~p-C~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISP-CRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-S-SS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecc-cccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            779999877655 33455 65     3789999999997  45679887

>PHA02862 5L protein; Provisional

Probab=96.23  E-value=0.0046  Score=50.15  Aligned_cols=46  Identities=20%  Similarity=0.559  Sum_probs=35.3

Q ss_pred             ceeeeecccccCCceeeecCCCC-----ccccHhHHHHHHh--cCCCCCCCCcCCCCC
Q 043807           67 SECVICLGELEDGEMVRLLPSCR-----HAFHVQCIGNWLL--GHTICPVCRSPVADQ  117 (242)
Q Consensus        67 ~~C~ICl~~~~~~~~~~~lp~C~-----H~Fh~~Ci~~wl~--~~~~CP~CR~~i~~~  117 (242)
                      ..|-||+++-.++    ..| |.     ...|..|+.+|++  ++..|++|+.++.-.
T Consensus         3 diCWIC~~~~~e~----~~P-C~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik   55 (156)
T PHA02862          3 DICWICNDVCDER----NNF-CGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK   55 (156)
T ss_pred             CEEEEecCcCCCC----ccc-ccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence            5799999986443    344 65     4699999999997  456899999887543

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

Probab=96.22  E-value=0.0018  Score=55.21  Aligned_cols=44  Identities=25%  Similarity=0.455  Sum_probs=37.8

Q ss_pred             ceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCC
Q 043807           67 SECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV  114 (242)
Q Consensus        67 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i  114 (242)
                      ..|.||-.+|..+   ++. .|||.||..|...-++....|-+|.+..
T Consensus       197 F~C~iCKkdy~sp---vvt-~CGH~FC~~Cai~~y~kg~~C~~Cgk~t  240 (259)
T COG5152         197 FLCGICKKDYESP---VVT-ECGHSFCSLCAIRKYQKGDECGVCGKAT  240 (259)
T ss_pred             eeehhchhhccch---hhh-hcchhHHHHHHHHHhccCCcceecchhh
Confidence            5799999999874   344 4999999999999999999999998754

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.13  E-value=0.0072  Score=53.14  Aligned_cols=53  Identities=17%  Similarity=0.368  Sum_probs=45.7

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      ....|+||.+.+.......+|..|||+|+.+|..+.+..-..||+|-.++.+.
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdr  272 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDR  272 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCccc
Confidence            34679999999988776777767999999999999999999999998888554

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

Probab=95.98  E-value=0.0063  Score=64.45  Aligned_cols=69  Identities=25%  Similarity=0.512  Sum_probs=46.8

Q ss_pred             HHhcCCceeeecccccccccCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc----------CCCCCCCCcCC
Q 043807           45 VLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG----------HTICPVCRSPV  114 (242)
Q Consensus        45 ~i~~lp~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----------~~~CP~CR~~i  114 (242)
                      ...-||-+..+....  ..+.++.|.||..+--.......+. |+|+||..|...-|.+          --.||+|..+|
T Consensus      3467 EE~CLPCl~Cdks~t--kQD~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~I 3543 (3738)
T KOG1428|consen 3467 EEHCLPCLHCDKSAT--KQDADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKI 3543 (3738)
T ss_pred             hhhcccccccChhhh--hcccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchh
Confidence            334467766554442  3456778999998765444455665 9999999999765432          13699999887


Q ss_pred             CC
Q 043807          115 AD  116 (242)
Q Consensus       115 ~~  116 (242)
                      ..
T Consensus      3544 nH 3545 (3738)
T KOG1428|consen 3544 NH 3545 (3738)
T ss_pred             hh
Confidence            43

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

Probab=95.92  E-value=0.003  Score=47.78  Aligned_cols=33  Identities=27%  Similarity=0.784  Sum_probs=27.4

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHH
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIG   98 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~   98 (242)
                      .++..|++|...+.. ..+.+.| |||+||..|+.
T Consensus        76 ~~~~~C~vC~k~l~~-~~f~~~p-~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGN-SVFVVFP-CGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCC-ceEEEeC-CCeEEeccccc
Confidence            355689999999977 5677777 99999999975

Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].

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

Probab=95.86  E-value=0.0061  Score=57.03  Aligned_cols=48  Identities=25%  Similarity=0.618  Sum_probs=39.0

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc--------CCCCCCCCcC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG--------HTICPVCRSP  113 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~--------~~~CP~CR~~  113 (242)
                      .-..|.||+++.........+| |+|+||+.|+..++..        .-.||-+...
T Consensus       183 slf~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~  238 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG  238 (445)
T ss_pred             hcccceeeehhhcCcceeeecc-cchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence            4468999999998778888998 9999999999999852        2358776543

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

Probab=95.82  E-value=0.0033  Score=56.46  Aligned_cols=45  Identities=22%  Similarity=0.373  Sum_probs=38.5

Q ss_pred             ceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           67 SECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        67 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      ..|-||...|..+   ++. .|+|.||..|...-++....|++|...+.
T Consensus       242 f~c~icr~~f~~p---Vvt-~c~h~fc~~ca~~~~qk~~~c~vC~~~t~  286 (313)
T KOG1813|consen  242 FKCFICRKYFYRP---VVT-KCGHYFCEVCALKPYQKGEKCYVCSQQTH  286 (313)
T ss_pred             ccccccccccccc---hhh-cCCceeehhhhccccccCCcceecccccc
Confidence            4699999999875   344 49999999999999998899999987663

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

Probab=95.52  E-value=0.0079  Score=39.92  Aligned_cols=45  Identities=27%  Similarity=0.555  Sum_probs=22.3

Q ss_pred             eeeecccccCCc-eeeecCCCCccccHhHHHHHHh-cCCCCCCCCcCC
Q 043807           69 CVICLGELEDGE-MVRLLPSCRHAFHVQCIGNWLL-GHTICPVCRSPV  114 (242)
Q Consensus        69 C~ICl~~~~~~~-~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~i  114 (242)
                      |++|.+++...+ .+.-- .|++.+|..|...-+. .+..||-||.+.
T Consensus         1 cp~C~e~~d~~d~~~~PC-~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPC-ECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SS-TTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccC-cCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            788999884433 22223 4999999999888775 578999999864

>PHA03096 p28-like protein; Provisional

Probab=95.36  E-value=0.0081  Score=54.24  Aligned_cols=46  Identities=26%  Similarity=0.596  Sum_probs=33.5

Q ss_pred             ceeeeecccccC----CceeeecCCCCccccHhHHHHHHhc---CCCCCCCCc
Q 043807           67 SECVICLGELED----GEMVRLLPSCRHAFHVQCIGNWLLG---HTICPVCRS  112 (242)
Q Consensus        67 ~~C~ICl~~~~~----~~~~~~lp~C~H~Fh~~Ci~~wl~~---~~~CP~CR~  112 (242)
                      -.|.||++....    +.....++.|.|.||..|+..|...   ..+||.||.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            479999998653    2245577789999999999999863   234555543

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

Probab=95.29  E-value=0.017  Score=52.61  Aligned_cols=48  Identities=25%  Similarity=0.514  Sum_probs=37.8

Q ss_pred             ccCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcC
Q 043807           63 RVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSP  113 (242)
Q Consensus        63 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~  113 (242)
                      ..+...|+||+.....+..  +. .-|-+||..||..++..+..||+=..+
T Consensus       297 ~~~~~~CpvClk~r~Nptv--l~-vSGyVfCY~Ci~~Yv~~~~~CPVT~~p  344 (357)
T KOG0826|consen  297 PPDREVCPVCLKKRQNPTV--LE-VSGYVFCYPCIFSYVVNYGHCPVTGYP  344 (357)
T ss_pred             CCccccChhHHhccCCCce--EE-ecceEEeHHHHHHHHHhcCCCCccCCc
Confidence            3456789999999887632  22 279999999999999999999985443

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=95.17  E-value=0.023  Score=46.86  Aligned_cols=50  Identities=22%  Similarity=0.636  Sum_probs=35.9

Q ss_pred             cCCceeeeecccccCCceeeecC-CCCc---cccHhHHHHHHhc--CCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLP-SCRH---AFHVQCIGNWLLG--HTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp-~C~H---~Fh~~Ci~~wl~~--~~~CP~CR~~i~~~  117 (242)
                      ..+..|-||.++-..  .  ..| .|..   ..|..|+..|+..  ...|++|+.++...
T Consensus         6 ~~~~~CRIC~~~~~~--~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          6 LMDKCCWICKDEYDV--V--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCCeeEecCCCCCC--c--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            356789999988542  1  234 2434   5799999999974  56899999987544

>PF04641 Rtf2: Rtf2 RING-finger

Probab=95.09  E-value=0.034  Score=49.47  Aligned_cols=52  Identities=19%  Similarity=0.411  Sum_probs=40.8

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      .....|+|...+|.....++.+-+|||+|...+|.+-- ....||+|-.++..
T Consensus       111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~  162 (260)
T PF04641_consen  111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTE  162 (260)
T ss_pred             CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCcccc
Confidence            45678999999996555555554599999999999963 35679999998863

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

Probab=95.04  E-value=0.015  Score=48.79  Aligned_cols=31  Identities=39%  Similarity=1.006  Sum_probs=25.3

Q ss_pred             CCCccccHhHHHHHHhcC-----------CCCCCCCcCCCCC
Q 043807           87 SCRHAFHVQCIGNWLLGH-----------TICPVCRSPVADQ  117 (242)
Q Consensus        87 ~C~H~Fh~~Ci~~wl~~~-----------~~CP~CR~~i~~~  117 (242)
                      .||.-||.-|+..||+.-           ..||+|..++.-+
T Consensus       189 qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK  230 (234)
T KOG3268|consen  189 QCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK  230 (234)
T ss_pred             ccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence            499999999999999741           2599999888544

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

Probab=94.83  E-value=0.028  Score=51.78  Aligned_cols=70  Identities=26%  Similarity=0.456  Sum_probs=47.3

Q ss_pred             CHHHHhcCCceeeecccccccccCCceeeeecccccCCceeeecCCCCccccHhHHHHH--HhcCCCCCCCCcCCCCC
Q 043807           42 EEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNW--LLGHTICPVCRSPVADQ  117 (242)
Q Consensus        42 ~~~~i~~lp~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w--l~~~~~CP~CR~~i~~~  117 (242)
                      .+..+..-|.+.-+.++  ..+++...|.||-+.+.-   ..++| |+|..|.-|.-..  |-....||+||..+...
T Consensus        39 kKNnlsaEPnlttsSad--dtDEen~~C~ICA~~~TY---s~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE~e~V  110 (493)
T COG5236          39 KKNNLSAEPNLTTSSAD--DTDEENMNCQICAGSTTY---SARYP-CGHQICHACAVRLRALYMQKGCPLCRTETEAV  110 (493)
T ss_pred             cccccccCCcccccccc--ccccccceeEEecCCceE---EEecc-CCchHHHHHHHHHHHHHhccCCCccccccceE
Confidence            33444445554444443  233455679999998754   56777 9999999998643  34678999999887543

>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=94.43  E-value=0.021  Score=36.92  Aligned_cols=41  Identities=22%  Similarity=0.629  Sum_probs=22.9

Q ss_pred             eeeecccccCCceeeecCCCCccccHhHHHHHHhcCC--CCCCC
Q 043807           69 CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHT--ICPVC  110 (242)
Q Consensus        69 C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~--~CP~C  110 (242)
                      |.+|.+.+..|...... .|+=.+|..|+..+++...  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~-~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNR-DCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS---S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCC-ccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            66777777766333222 4888999999999998654  79987

; PDB: 3NW0_A 2CT0_A.

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

Probab=94.41  E-value=0.028  Score=50.45  Aligned_cols=47  Identities=30%  Similarity=0.758  Sum_probs=37.8

Q ss_pred             ceeeeecccccCCc---eeeecCCCCccccHhHHHHHHhc-CCCCCCCCcCC
Q 043807           67 SECVICLGELEDGE---MVRLLPSCRHAFHVQCIGNWLLG-HTICPVCRSPV  114 (242)
Q Consensus        67 ~~C~ICl~~~~~~~---~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~i  114 (242)
                      ..|-||-++|...+   .++++. |||.||..|+...+.. ...||.||.+.
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~-c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLK-CGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccc-cCceehHhHHHHHhcCceeeccCCCCcc
Confidence            57999999997653   455565 9999999999887764 45799999985

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

Probab=94.13  E-value=0.018  Score=50.45  Aligned_cols=47  Identities=23%  Similarity=0.592  Sum_probs=33.6

Q ss_pred             eeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCCC
Q 043807           68 ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQP  118 (242)
Q Consensus        68 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~~  118 (242)
                      .|-.|..--. ++...++. |+|+||..|...-  ....||+|+.++....
T Consensus         5 hCn~C~~~~~-~~~f~LTa-C~HvfC~~C~k~~--~~~~C~lCkk~ir~i~   51 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLTA-CRHVFCEPCLKAS--SPDVCPLCKKSIRIIQ   51 (233)
T ss_pred             EeccccccCC-CCceeeee-chhhhhhhhcccC--Cccccccccceeeeee
Confidence            5777766554 55666665 9999999998652  2338999999875443

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=94.10  E-value=0.053  Score=36.85  Aligned_cols=41  Identities=22%  Similarity=0.622  Sum_probs=32.9

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPV  109 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~  109 (242)
                      ....|.+|-+.|.+++.+++.|.|+-.+|+.|...    ...|-.
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~   44 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCIN   44 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEe
Confidence            34689999999987777888899999999999654    345544

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

Probab=93.97  E-value=0.028  Score=57.11  Aligned_cols=36  Identities=28%  Similarity=0.523  Sum_probs=28.7

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHH
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWL  101 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl  101 (242)
                      ..+..|.+|...+... ...+-| |||.||.+||.+-.
T Consensus       815 ep~d~C~~C~~~ll~~-pF~vf~-CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  815 EPQDSCDHCGRPLLIK-PFYVFP-CGHCFHRDCLIRHV  850 (911)
T ss_pred             cCccchHHhcchhhcC-cceeee-ccchHHHHHHHHHH
Confidence            4567899999988653 455667 99999999998754

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=93.76  E-value=0.044  Score=37.32  Aligned_cols=46  Identities=26%  Similarity=0.516  Sum_probs=32.9

Q ss_pred             CceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           66 QSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      ...|..|...-..   -.++| |+|..+..|...+  +-.-||+|..++...
T Consensus         7 ~~~~~~~~~~~~~---~~~~p-CgH~I~~~~f~~~--rYngCPfC~~~~~~~   52 (55)
T PF14447_consen    7 EQPCVFCGFVGTK---GTVLP-CGHLICDNCFPGE--RYNGCPFCGTPFEFD   52 (55)
T ss_pred             ceeEEEccccccc---ccccc-ccceeeccccChh--hccCCCCCCCcccCC
Confidence            3457666655332   45677 9999999998764  456799999988543

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

Probab=93.70  E-value=0.035  Score=56.20  Aligned_cols=41  Identities=29%  Similarity=0.699  Sum_probs=33.2

Q ss_pred             CceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCc
Q 043807           66 QSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRS  112 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~  112 (242)
                      ...|..|-..+.-+  .+.-. |||.||..|+.   .....||.|+.
T Consensus       840 ~skCs~C~~~LdlP--~VhF~-CgHsyHqhC~e---~~~~~CP~C~~  880 (933)
T KOG2114|consen  840 VSKCSACEGTLDLP--FVHFL-CGHSYHQHCLE---DKEDKCPKCLP  880 (933)
T ss_pred             eeeecccCCccccc--eeeee-cccHHHHHhhc---cCcccCCccch
Confidence            36899999998875  44444 99999999998   45678999976

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

Probab=93.37  E-value=0.044  Score=49.57  Aligned_cols=43  Identities=35%  Similarity=0.753  Sum_probs=35.1

Q ss_pred             ceeeeecccccCCceeeecCCCCccccHhHHHHHHh-cCCCCCCCCc
Q 043807           67 SECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL-GHTICPVCRS  112 (242)
Q Consensus        67 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~  112 (242)
                      ..|+.|...+..+   ..++.|+|.||..||..-|. .-..||.|..
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            6899999988774   33467999999999987665 5678999976

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=93.28  E-value=0.056  Score=49.70  Aligned_cols=52  Identities=21%  Similarity=0.485  Sum_probs=37.4

Q ss_pred             CCceeeeecccccCCc-eeeecCCCCccccHhHHHHHHh-cCCCCCCCCcCCCCC
Q 043807           65 DQSECVICLGELEDGE-MVRLLPSCRHAFHVQCIGNWLL-GHTICPVCRSPVADQ  117 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~-~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~i~~~  117 (242)
                      +++-|+.|++++...+ ...-.+ ||-..|..|...--+ .+..||.||....+.
T Consensus        13 eed~cplcie~mditdknf~pc~-cgy~ic~fc~~~irq~lngrcpacrr~y~de   66 (480)
T COG5175          13 EEDYCPLCIEPMDITDKNFFPCP-CGYQICQFCYNNIRQNLNGRCPACRRKYDDE   66 (480)
T ss_pred             ccccCcccccccccccCCcccCC-cccHHHHHHHHHHHhhccCCChHhhhhcccc
Confidence            3445999999987655 344455 999888888765432 367899999977544

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

Probab=93.22  E-value=0.014  Score=52.53  Aligned_cols=42  Identities=29%  Similarity=0.714  Sum_probs=31.9

Q ss_pred             CceeeeecccccCCceeeecCCCCcc-ccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           66 QSECVICLGELEDGEMVRLLPSCRHA-FHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      +.-|+||++...+   ...|+ |||. -|..|-..    -..||+||+-+.
T Consensus       300 ~~LC~ICmDaP~D---CvfLe-CGHmVtCt~CGkr----m~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPRD---CVFLE-CGHMVTCTKCGKR----MNECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCcc---eEEee-cCcEEeehhhccc----cccCchHHHHHH
Confidence            5679999998765   67887 9996 67777544    348999998653

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

Probab=92.99  E-value=0.053  Score=48.73  Aligned_cols=46  Identities=26%  Similarity=0.562  Sum_probs=37.4

Q ss_pred             CceeeeecccccCCc-eeeecCCCCccccHhHHHHHHhcCCCCCCCCc
Q 043807           66 QSECVICLGELEDGE-MVRLLPSCRHAFHVQCIGNWLLGHTICPVCRS  112 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~-~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~  112 (242)
                      ...|+||.+.+.... .+.+++ |||..|..|+......+.+||+|.+
T Consensus       158 ~~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             cCCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc
Confidence            345999999876554 345565 9999999999998887899999988

>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=92.47  E-value=0.05  Score=35.94  Aligned_cols=43  Identities=26%  Similarity=0.677  Sum_probs=25.1

Q ss_pred             eeeeecccccCCceeeecCCCC-ccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           68 ECVICLGELEDGEMVRLLPSCR-HAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        68 ~C~ICl~~~~~~~~~~~lp~C~-H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      .|--|+-....     +.. |. |..|..|+...+.....||+|..+++.
T Consensus         4 nCKsCWf~~k~-----Li~-C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen    4 NCKSCWFANKG-----LIK-CSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             ---SS-S--SS-----EEE--SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             cChhhhhcCCC-----eee-ecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            45556554432     222 66 999999999999999999999998864

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.

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

Probab=90.99  E-value=0.22  Score=41.13  Aligned_cols=34  Identities=24%  Similarity=0.565  Sum_probs=22.2

Q ss_pred             CceeeeecccccCCceeeecC------C-----CCc-cccHhHHHHHHh
Q 043807           66 QSECVICLGELEDGEMVRLLP------S-----CRH-AFHVQCIGNWLL  102 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~~~~~lp------~-----C~H-~Fh~~Ci~~wl~  102 (242)
                      +..|+|||+--.+   .++|.      .     |+- .-|..|++++-+
T Consensus         2 d~~CpICme~PHN---AVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    2 DVTCPICMEHPHN---AVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CccCceeccCCCc---eEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            5689999998654   22333      0     442 357899998754

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.

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

Probab=90.93  E-value=0.012  Score=54.73  Aligned_cols=51  Identities=22%  Similarity=0.539  Sum_probs=41.8

Q ss_pred             CCceeeeecccccCC-ceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           65 DQSECVICLGELEDG-EMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~-~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      -...|+||...+... +.+..+. |||.+|.+||.+||.....||.|+..+..
T Consensus       195 lv~sl~I~~~slK~~y~k~~~~~-~g~~~~~~kL~k~L~~~~kl~~~~rel~~  246 (465)
T KOG0827|consen  195 LVGSLSICFESLKQNYDKISAIV-CGHIYHHGKLSKWLATKRKLPSCRRELPK  246 (465)
T ss_pred             HHhhhHhhHHHHHHHHHHHHHHh-hcccchhhHHHHHHHHHHHhHHHHhhhhh
Confidence            345799999998765 4455554 99999999999999988899999988753

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

Probab=90.92  E-value=0.34  Score=45.14  Aligned_cols=28  Identities=36%  Similarity=1.155  Sum_probs=21.2

Q ss_pred             CCccccHhHHHHHHh-------------cCCCCCCCCcCCC
Q 043807           88 CRHAFHVQCIGNWLL-------------GHTICPVCRSPVA  115 (242)
Q Consensus        88 C~H~Fh~~Ci~~wl~-------------~~~~CP~CR~~i~  115 (242)
                      |.-.+|.+|+.+|+.             ++..||+||+.+.
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC  351 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC  351 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence            445678899999874             3457999999874

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

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

Probab=90.80  E-value=0.16  Score=51.09  Aligned_cols=41  Identities=24%  Similarity=0.580  Sum_probs=30.3

Q ss_pred             ceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCC
Q 043807           67 SECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPV  109 (242)
Q Consensus        67 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~  109 (242)
                      ..|+||.-.+.. ....... |+|+.|.+|...|+.....||.
T Consensus      1029 ~~C~~C~l~V~g-ss~~Cg~-C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1029 FQCAICHLAVRG-SSNFCGT-CGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeeeEeeEeec-cchhhcc-ccccccHHHHHHHHhcCCcCCC
Confidence            346666555543 2233444 9999999999999999999997

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

Probab=90.73  E-value=0.089  Score=52.93  Aligned_cols=45  Identities=29%  Similarity=0.736  Sum_probs=34.6

Q ss_pred             ceeeeecccccCCceeeecCCCCccccHhHHHHHHhc--CCCCCCCCcCCCC
Q 043807           67 SECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG--HTICPVCRSPVAD  116 (242)
Q Consensus        67 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~CR~~i~~  116 (242)
                      ..|.||++ .   +.+...+ |+|.||..|+..-+..  ...||+||..+..
T Consensus       455 ~~c~ic~~-~---~~~~it~-c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~  501 (674)
T KOG1001|consen  455 HWCHICCD-L---DSFFITR-CGHDFCVECLKKSIQQSENAPCPLCRNVLKE  501 (674)
T ss_pred             cccccccc-c---ccceeec-ccchHHHHHHHhccccccCCCCcHHHHHHHH
Confidence            79999999 2   3355555 9999999999887753  3469999987643

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

Probab=90.05  E-value=0.29  Score=49.71  Aligned_cols=55  Identities=22%  Similarity=0.568  Sum_probs=40.5

Q ss_pred             cccCCceeeeecccccCCceeeecCCCC-----ccccHhHHHHHHhc--CCCCCCCCcCCCCCC
Q 043807           62 FRVDQSECVICLGELEDGEMVRLLPSCR-----HAFHVQCIGNWLLG--HTICPVCRSPVADQP  118 (242)
Q Consensus        62 ~~~~~~~C~ICl~~~~~~~~~~~lp~C~-----H~Fh~~Ci~~wl~~--~~~CP~CR~~i~~~~  118 (242)
                      .++++..|.||..+-..++.. ..| |.     ...|.+|+.+|+..  ...|-+|+.++..+.
T Consensus         8 mN~d~~~CRICr~e~~~d~pL-fhP-CKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~   69 (1175)
T COG5183           8 MNEDKRSCRICRTEDIRDDPL-FHP-CKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKD   69 (1175)
T ss_pred             CCccchhceeecCCCCCCCcC-ccc-ccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeee
Confidence            345668999999987665533 444 65     35999999999973  567999998875443

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

Probab=89.34  E-value=0.18  Score=45.94  Aligned_cols=43  Identities=30%  Similarity=0.724  Sum_probs=30.4

Q ss_pred             ceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCC
Q 043807           67 SECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV  114 (242)
Q Consensus        67 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i  114 (242)
                      -.|--|--.+..  .-+.+| |.|+||.+|...  ..-+.||.|-..+
T Consensus        91 HfCd~Cd~PI~I--YGRmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   91 HFCDRCDFPIAI--YGRMIP-CKHVFCLECARS--DSDKICPLCDDRV  133 (389)
T ss_pred             EeecccCCccee--eecccc-cchhhhhhhhhc--CccccCcCcccHH
Confidence            347777665542  346777 999999999854  2356899997665

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

Probab=88.26  E-value=0.38  Score=38.66  Aligned_cols=52  Identities=21%  Similarity=0.492  Sum_probs=37.4

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHh---cCCCCCCCCcCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL---GHTICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~---~~~~CP~CR~~i~~  116 (242)
                      .-.+|-||.+.-.+..-..--..||-..|.-|....|+   .+..||+|+.++-.
T Consensus        79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs  133 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS  133 (140)
T ss_pred             CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence            34689999998765321111114999999999987765   47889999998843

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

Probab=87.87  E-value=0.42  Score=44.80  Aligned_cols=47  Identities=17%  Similarity=0.311  Sum_probs=37.3

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcC---CCCCCCCc
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGH---TICPVCRS  112 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~---~~CP~CR~  112 (242)
                      .-..|||=.+.-.+.+.+..+. |||+..++-|.+..++.   ..||+|-.
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~  382 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYCPV  382 (394)
T ss_pred             ceeecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence            3467999888777777788887 99999999999977643   47999943

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

Probab=87.48  E-value=0.15  Score=53.99  Aligned_cols=48  Identities=29%  Similarity=0.666  Sum_probs=38.4

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      ....|.||++.+..-..+  . .|||.+|..|+..|+..+..||.|.....
T Consensus      1152 ~~~~c~ic~dil~~~~~I--~-~cgh~~c~~c~~~~l~~~s~~~~~ksi~~ 1199 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGI--A-GCGHEPCCRCDELWLYASSRCPICKSIKG 1199 (1394)
T ss_pred             cccchHHHHHHHHhcCCe--e-eechhHhhhHHHHHHHHhccCcchhhhhh
Confidence            345899999998742222  2 49999999999999999999999985443

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.18  E-value=0.24  Score=44.00  Aligned_cols=56  Identities=25%  Similarity=0.576  Sum_probs=39.3

Q ss_pred             cCCceeeeecccccCCcee-eecCCCC-----ccccHhHHHHHHhc--------CCCCCCCCcCCCCCCCC
Q 043807           64 VDQSECVICLGELEDGEMV-RLLPSCR-----HAFHVQCIGNWLLG--------HTICPVCRSPVADQPKS  120 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~-~~lp~C~-----H~Fh~~Ci~~wl~~--------~~~CP~CR~~i~~~~~~  120 (242)
                      +.+..|-||+..=++.... -+.| |-     |..|..|+..|+..        ...||.|+.......+.
T Consensus        18 e~eR~CWiCF~TdeDn~~a~WV~P-CrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~   87 (293)
T KOG3053|consen   18 ELERCCWICFATDEDNRLAAWVHP-CRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQ   87 (293)
T ss_pred             ccceeEEEEeccCcccchhhhccc-ccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccc
Confidence            4566799999986654322 3445 64     78999999999952        23699999987555443

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

Probab=86.73  E-value=0.3  Score=43.00  Aligned_cols=48  Identities=19%  Similarity=0.601  Sum_probs=35.8

Q ss_pred             CCceeeeeccc-ccCCc-eeeecCCCCccccHhHHHHHHhc-CCCCC--CCCc
Q 043807           65 DQSECVICLGE-LEDGE-MVRLLPSCRHAFHVQCIGNWLLG-HTICP--VCRS  112 (242)
Q Consensus        65 ~~~~C~ICl~~-~~~~~-~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP--~CR~  112 (242)
                      .+..|+||..+ |-.++ .+.+-|.|.|..|..|++.-+.. ...||  -|-.
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~k   61 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGK   61 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHH
Confidence            45689999986 33344 55555679999999999998864 56799  5754

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

Probab=85.93  E-value=0.49  Score=42.31  Aligned_cols=51  Identities=27%  Similarity=0.686  Sum_probs=37.1

Q ss_pred             CceeeeecccccCCce-eeecCCCC-----ccccHhHHHHHHh--cCCCCCCCCcCCCCC
Q 043807           66 QSECVICLGELEDGEM-VRLLPSCR-----HAFHVQCIGNWLL--GHTICPVCRSPVADQ  117 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~~-~~~lp~C~-----H~Fh~~Ci~~wl~--~~~~CP~CR~~i~~~  117 (242)
                      +..|-||..+...... ....| |.     +..|..|+..|+.  .+..|.+|.......
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~p-C~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~  136 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISP-CSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV  136 (323)
T ss_pred             CCcEEEEecccccccccccccC-ccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence            4689999998754321 23444 65     5689999999997  677899998866443

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

Probab=84.93  E-value=0.45  Score=41.08  Aligned_cols=38  Identities=45%  Similarity=0.878  Sum_probs=28.5

Q ss_pred             eeeecccccCCceeeecCCCCcc-ccHhHHHHHHhcCCCCCCCCcCC
Q 043807           69 CVICLGELEDGEMVRLLPSCRHA-FHVQCIGNWLLGHTICPVCRSPV  114 (242)
Q Consensus        69 C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~i  114 (242)
                      |-+|.+.=   ..+.++| |.|. +|..|-..    -..||+|+.+.
T Consensus       161 Cr~C~~~~---~~VlllP-CrHl~lC~~C~~~----~~~CPiC~~~~  199 (207)
T KOG1100|consen  161 CRKCGERE---ATVLLLP-CRHLCLCGICDES----LRICPICRSPK  199 (207)
T ss_pred             ceecCcCC---ceEEeec-ccceEeccccccc----CccCCCCcChh
Confidence            77777663   3488888 9986 89999754    35699998765

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.93  E-value=0.5  Score=42.76  Aligned_cols=28  Identities=29%  Similarity=0.870  Sum_probs=22.2

Q ss_pred             CCccccHhHHHHHHh-------------cCCCCCCCCcCCC
Q 043807           88 CRHAFHVQCIGNWLL-------------GHTICPVCRSPVA  115 (242)
Q Consensus        88 C~H~Fh~~Ci~~wl~-------------~~~~CP~CR~~i~  115 (242)
                      |.-.+|..|+.+|+.             ++-+||+||+.+.
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            556788999998874             3558999999874

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

Probab=84.84  E-value=0.71  Score=42.09  Aligned_cols=46  Identities=24%  Similarity=0.550  Sum_probs=33.7

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      +-.+|+||.+.+..+  +.... =||..|..|-.+   ....||.||.++..
T Consensus        47 ~lleCPvC~~~l~~P--i~QC~-nGHlaCssC~~~---~~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   47 DLLDCPVCFNPLSPP--IFQCD-NGHLACSSCRTK---VSNKCPTCRLPIGN   92 (299)
T ss_pred             hhccCchhhccCccc--ceecC-CCcEehhhhhhh---hcccCCcccccccc
Confidence            456899999999876  22222 368888888653   46789999988864

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

Probab=82.46  E-value=0.47  Score=44.67  Aligned_cols=37  Identities=32%  Similarity=0.686  Sum_probs=27.5

Q ss_pred             CCceeeeecccc-cCCceeeecCCCCccccHhHHHHHHh
Q 043807           65 DQSECVICLGEL-EDGEMVRLLPSCRHAFHVQCIGNWLL  102 (242)
Q Consensus        65 ~~~~C~ICl~~~-~~~~~~~~lp~C~H~Fh~~Ci~~wl~  102 (242)
                      ....|.||..+. ...+...+. .|+|.||.+|+.+.+.
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~-~C~H~fC~~C~k~~ie  182 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVL-KCGHRFCKDCVKQHIE  182 (384)
T ss_pred             ccccCccCccccccHhhhHHHh-cccchhhhHHhHHHhh
Confidence            456899999544 443445445 4999999999998886

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

Probab=82.12  E-value=1.1  Score=40.44  Aligned_cols=48  Identities=19%  Similarity=0.554  Sum_probs=34.5

Q ss_pred             eeeeeccc-ccCCceeeecCCCCccccHhHHHHHHh-cCCCCCCCCcCCC
Q 043807           68 ECVICLGE-LEDGEMVRLLPSCRHAFHVQCIGNWLL-GHTICPVCRSPVA  115 (242)
Q Consensus        68 ~C~ICl~~-~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~i~  115 (242)
                      .|++|-.. |..++-......|+|..|..|++..+. +...||.|-..+.
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLR   51 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILR   51 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhh
Confidence            48888764 444443333335999999999999886 4568999976653

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

Probab=81.11  E-value=0.91  Score=43.30  Aligned_cols=34  Identities=26%  Similarity=0.656  Sum_probs=28.1

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHh
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL  102 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~  102 (242)
                      ++..|+||..-|.++   ..+| |+|..|..|...-+.
T Consensus         3 eelkc~vc~~f~~ep---iil~-c~h~lc~~ca~~~~~   36 (699)
T KOG4367|consen    3 EELKCPVCGSFYREP---IILP-CSHNLCQACARNILV   36 (699)
T ss_pred             ccccCceehhhccCc---eEee-cccHHHHHHHHhhcc
Confidence            567899999999874   5777 999999999876543

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

Probab=80.19  E-value=1.5  Score=44.28  Aligned_cols=44  Identities=18%  Similarity=0.470  Sum_probs=33.7

Q ss_pred             ceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCC--CCc
Q 043807           67 SECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPV--CRS  112 (242)
Q Consensus        67 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~--CR~  112 (242)
                      ..|.+|-..+..-  ....+.|+|.-|..|+..|+..+..||.  |-.
T Consensus       780 ~~CtVC~~vi~G~--~~~c~~C~H~gH~sh~~sw~~~~s~ca~~~C~~  825 (839)
T KOG0269|consen  780 AKCTVCDLVIRGV--DVWCQVCGHGGHDSHLKSWFFKASPCAKSICPH  825 (839)
T ss_pred             cCceeecceeeee--EeecccccccccHHHHHHHHhcCCCCccccCCc
Confidence            4689998877642  2233469999999999999998888877  543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	242
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		7e-12
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		2e-07
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		2e-07
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		6e-07
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		5e-04

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 27/50 (54%), Positives = 32/50 (64%)
Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV 114
           D  EC +CL ELEDGE  R LP C H FH +C+  WL  H+ CP+CR  V
Sbjct: 4   DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/55 (47%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 68  ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTS 122
           +C ICL  LE+GE VR LP C H FH  C+  WL+ +  CP+CR  +  Q  S S
Sbjct: 16  KCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQLPSES 69

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 33/48 (68%), Gaps = 1/48 (2%)
Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRS 112
           +Q+ CV+C+ + E  +++R+LP C H FH +C+  WL  +  CP+CR+
Sbjct: 22  EQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRA 68

>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring Finger) Domain Of Ring Finger Protein 126 Length = 78

Iteration: 1
 Score = 50.8 bits (120), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 25/55 (45%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 68  ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTS 122
           EC +C  +   GE VR LP C H FH  CI  WL  H  CPVCR  +  Q  +T+
Sbjct: 17  ECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATN 70

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 17/46 (36%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 69  CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV 114
           C +CL + +  + + + P C+HAFH +C+  WL    +CP+C  PV
Sbjct: 18  CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPV 62

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	242
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	1e-24
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	8e-24
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	2e-21
2ect_A	78	Ring finger protein 126; metal binding protein, st	2e-19
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	5e-19
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	1e-18
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	5e-17
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	1e-14
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	2e-14
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	2e-12
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	4e-09
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	4e-09
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	6e-09
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	7e-09
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	1e-08
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	1e-08
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	3e-08
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	9e-08
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	4e-07
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	6e-07
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	1e-06
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	1e-06
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	3e-06
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	5e-06
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	2e-05
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	2e-05
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-05
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	3e-05
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	4e-05
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	4e-04
3nw0_A	238	Non-structural maintenance of chromosomes element	6e-04

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

 Score = 91.9 bits (229), Expect = 1e-24
 Identities = 27/50 (54%), Positives = 32/50 (64%)

Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV 114
           D  EC +CL ELEDGE  R LP C H FH +C+  WL  H+ CP+CR  V
Sbjct: 4   DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

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

 Score = 90.1 bits (224), Expect = 8e-24
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 4/75 (5%)

Query: 44  KVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG 103
                +P   ++  + +    +Q+ CV+C+ + E  +++R+LP C H FH +C+  WL  
Sbjct: 4   GSSGQLPSYRFNPNNHQ---SEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKA 59

Query: 104 HTICPVCRSPVADQP 118
           +  CP+CR+      
Sbjct: 60  NRTCPICRADSGPSS 74

>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 = 83.6 bits (207), Expect = 2e-21
 Identities = 26/58 (44%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTS 122
            + +C ICL  LE+GE VR LP C H FH  C+  WL+ +  CP+CR  +  Q  S S
Sbjct: 13  TEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQLPSES 69

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

 Score = 79.0 bits (195), Expect = 2e-19
 Identities = 25/62 (40%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTSGE 124
              EC +C  +   GE VR LP C H FH  CI  WL  H  CPVCR  +  Q  +T+  
Sbjct: 14  SGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATNPP 72

Query: 125 AA 126
             
Sbjct: 73  GL 74

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

 Score = 77.5 bits (191), Expect = 5e-19
 Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTSGE 124
               C +CL + +  + + + P C+HAFH +C+  WL    +CP+C  PV    + +   
Sbjct: 14  LHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLSGPS 72

Query: 125 AA 126
           + 
Sbjct: 73  SG 74

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

 Score = 77.0 bits (190), Expect = 1e-18
 Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 3/72 (4%)

Query: 43  EKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL 102
           ++ +  +P +  +          +  C IC  E   G++   LP C H FH  C+  WL 
Sbjct: 19  KESIDALPEILVTEDHGA--VGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQ 75

Query: 103 GHTICPVCRSPV 114
               CPVCR   
Sbjct: 76  KSGTCPVCRCMF 87

>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 = 71.5 bits (176), Expect = 5e-17
 Identities = 15/50 (30%), Positives = 21/50 (42%)

Query: 66  QSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA 115
            S C ICL ++    +V  +  C H  H  C    L     CP+C  P +
Sbjct: 5   SSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS 54

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

 Score = 66.1 bits (161), Expect = 1e-14
 Identities = 13/45 (28%), Positives = 23/45 (51%)

Query: 69  CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSP 113
           C+ C  E +  + V +   C H+FH  C+  W+  +  CP+C+  
Sbjct: 29  CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQD 73

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

 Score = 65.1 bits (159), Expect = 2e-14
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTSGE 124
           D+ EC IC+    DG    +LP C H+F  +CI  W   H  CP+CR  +    +S+   
Sbjct: 14  DEEECCICM----DGRADLILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGANESSGPS 68

Query: 125 AA 126
           + 
Sbjct: 69  SG 70

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

 Score = 60.1 bits (146), Expect = 2e-12
 Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 3/60 (5%)

Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTSGE 124
               C ICL +  +      LP C HAF   CI  W+  +  CP+C+ PV     +   +
Sbjct: 4   VAERCPICLEDPSNY--SMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVESVVHTIESD 60

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

 Score = 51.8 bits (124), Expect = 4e-09
 Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 4/51 (7%)

Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL-GHTICPVCRSPV 114
           +   C IC+ +L D    RL P C       CI  WL      CP CR+P+
Sbjct: 21  EVFRCFICMEKLRD---ARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPL 68

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

 Score = 50.7 bits (121), Expect = 4e-09
 Identities = 14/50 (28%), Positives = 19/50 (38%), Gaps = 3/50 (6%)

Query: 68  ECVICLGELEDGEMVRLLPS---CRHAFHVQCIGNWLLGHTICPVCRSPV 114
            C IC+    +      L     C H F  QC+ + L     CP CR  +
Sbjct: 17  SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66

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

 Score = 50.2 bits (120), Expect = 6e-09
 Identities = 14/50 (28%), Positives = 19/50 (38%), Gaps = 3/50 (6%)

Query: 68  ECVICLGELEDGEMVRLLPS---CRHAFHVQCIGNWLLGHTICPVCRSPV 114
            C IC+    +      L     C H F  QC+ + L     CP CR  +
Sbjct: 5   SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54

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

 Score = 50.2 bits (120), Expect = 7e-09
 Identities = 14/50 (28%), Positives = 19/50 (38%), Gaps = 3/50 (6%)

Query: 68  ECVICLGELEDGEMVRLLPS---CRHAFHVQCIGNWLLGHTICPVCRSPV 114
            C IC+    +      L     C H F  QC+ + L     CP CR  +
Sbjct: 12  SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61

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

 Score = 51.0 bits (121), Expect = 1e-08
 Identities = 19/87 (21%), Positives = 30/87 (34%), Gaps = 23/87 (26%)

Query: 68  ECVICLGELEDG--------------EMVRLLPSCRHAFHVQCIGNWL-----LGHTICP 108
           +C+IC+ +L                  +V  L  C HAFH+ C+          G   CP
Sbjct: 27  DCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCP 86

Query: 109 VCRSPV----ADQPKSTSGEAANLPNY 131
            C++        QP        + P+ 
Sbjct: 87  SCKTIYGEKTGTQPWGKMEVFRSGPSS 113

>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 = 50.6 bits (120), Expect = 1e-08
 Identities = 14/60 (23%), Positives = 19/60 (31%), Gaps = 4/60 (6%)

Query: 58  DCKLFRVDQSECV----ICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSP 113
           +C + R    +               E       C HAFH  CI  WL    +CP+    
Sbjct: 39  NCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 98

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

 Score = 49.8 bits (118), Expect = 3e-08
 Identities = 14/61 (22%), Positives = 19/61 (31%), Gaps = 4/61 (6%)

Query: 57  KDCKLFRVDQSECV----ICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRS 112
            +C + R    +               E       C HAFH  CI  WL    +CP+   
Sbjct: 49  DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 108

Query: 113 P 113
            
Sbjct: 109 E 109

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

 Score = 47.1 bits (112), Expect = 9e-08
 Identities = 14/65 (21%), Positives = 22/65 (33%), Gaps = 4/65 (6%)

Query: 53  AYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRS 112
           +  +       +   EC ICL        V L   C+H F   C+         C +CR 
Sbjct: 2   SSGSSGNTAPSLTVPECAICLQTCVHP--VSL--PCKHVFCYLCVKGASWLGKRCALCRQ 57

Query: 113 PVADQ 117
            + + 
Sbjct: 58  EIPED 62

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

 Score = 45.3 bits (107), Expect = 4e-07
 Identities = 11/48 (22%), Positives = 17/48 (35%), Gaps = 5/48 (10%)

Query: 68  ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGH--TICPVCRSP 113
            C IC   L  G   +   +C    H+ C+  +   +    CP C   
Sbjct: 17  ICNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDY 61

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

 Score = 44.7 bits (106), Expect = 6e-07
 Identities = 15/47 (31%), Positives = 16/47 (34%), Gaps = 3/47 (6%)

Query: 68  ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV 114
            C IC G L D      +  C H F   CI         CP C   V
Sbjct: 17  LCSICKGYLIDATT---ITECLHTFCKSCIVRHFYYSNRCPKCNIVV 60

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

 Score = 47.9 bits (113), Expect = 1e-06
 Identities = 17/86 (19%), Positives = 28/86 (32%), Gaps = 16/86 (18%)

Query: 46  LLTIPILAYSAKDCKLFRVD-QSECVICLGELEDGEMVRLL----PSCRHAFHVQCIGNW 100
           L   P+  +S         + +  C IC     DG  V L+      C    H  C+  W
Sbjct: 287 LCYFPMPDWSDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEW 346

Query: 101 L-----------LGHTICPVCRSPVA 115
                       +    CP C++ ++
Sbjct: 347 FKTLMDGKTFLEVSFGQCPFCKAKLS 372

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

 Score = 44.1 bits (104), Expect = 1e-06
 Identities = 11/47 (23%), Positives = 16/47 (34%), Gaps = 4/47 (8%)

Query: 68  ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV 114
            C IC    ++     ++  CRH F   C          C +C  P 
Sbjct: 17  RCFICRQAFQNP----VVTKCRHYFCESCALEHFRATPRCYICDQPT 59

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

 Score = 43.2 bits (101), Expect = 3e-06
 Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 1/55 (1%)

Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL-GHTICPVCRSPVADQP 118
           D  EC +C+  LE  ++     +C +     C        + +CP CR P  + P
Sbjct: 10  DPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDP 64

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

 Score = 45.5 bits (107), Expect = 5e-06
 Identities = 14/54 (25%), Positives = 20/54 (37%), Gaps = 5/54 (9%)

Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHT-ICPVCRSPVADQ 117
               C IC    +D   V++ P C H     C+ +W       CP CR  +   
Sbjct: 331 TFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGT 380

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

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 14/46 (30%), Positives = 18/46 (39%), Gaps = 3/46 (6%)

Query: 69  CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV 114
           C IC           ++P C H +   CI  +L   T CP C   V
Sbjct: 25  CGICFEYFNIA---MIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTV 67

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

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 4/53 (7%)

Query: 68  ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKS 120
           +C+IC     +     +  +C H+F   CI  W+     CP+CR  +  +  S
Sbjct: 66  QCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYS 114

>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 = 41.7 bits (98), Expect = 2e-05
 Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 3/47 (6%)

Query: 68  ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV 114
            CV+C G   D      +  C H+F   CI  +L     CP+C   V
Sbjct: 17  MCVLCGGYFIDATT---IIECLHSFCKTCIVRYLETSKYCPICDVQV 60

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

 Score = 41.7 bits (97), Expect = 3e-05
 Identities = 14/50 (28%), Positives = 19/50 (38%), Gaps = 3/50 (6%)

Query: 68  ECVICLGELEDGEMVRLLP---SCRHAFHVQCIGNWLLGHTICPVCRSPV 114
            C IC+    +      L     C H F  QC+ + L     CP CR  +
Sbjct: 9   SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 58

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

 Score = 39.7 bits (93), Expect = 4e-05
 Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 5/57 (8%)

Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL--GHTICPVCRSPVADQPK 119
           D+  C+IC   + D     ++P C +++  +CI   LL      CP C         
Sbjct: 14  DELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA 67

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

 Score = 37.8 bits (88), Expect = 4e-04
 Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 5/57 (8%)

Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL--GHTICPVCRSPVADQPK 119
           D+  C+IC   + D     ++P C +++  +CI   LL      CP C         
Sbjct: 12  DELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA 65

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

 Score = 38.9 bits (90), Expect = 6e-04
 Identities = 11/48 (22%), Positives = 17/48 (35%), Gaps = 5/48 (10%)

Query: 68  ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGH--TICPVCRSP 113
            C IC   L  G+      +C    H+ C+  +   +    CP C   
Sbjct: 182 ICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCNDY 226

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	242
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.7
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.63
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.52
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.52
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.5
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.49
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.46
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.41
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.4
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.37
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.35
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.35
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.33
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.32
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.31
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.3
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.28
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.27
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.25
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.24
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.24
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.23
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.21
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.21
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.2
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.19
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.18
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.18
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.17
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.17
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.13
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.13
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.13
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.12
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.11
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.1
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.08
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.07
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.06
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.05
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.02
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.99
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.97
1z6u_A	150	NP95-like ring finger protein isoform B; structura	98.96
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.94
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	98.93
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.92
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.91
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.91
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.91
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.91
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.89
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.86
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.83
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.82
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.82
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.75
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.68
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.68
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.67
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.63
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.58
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.57
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.57
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.51
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.49
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.46
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.33
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.29
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.25
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.0
3nw0_A	238	Non-structural maintenance of chromosomes element	97.93
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	95.75
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	94.3
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	93.8
1we9_A	64	PHD finger family protein; structural genomics, PH	88.12
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	84.57
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	83.63
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	83.11
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	82.49
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	82.42
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	81.92
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	80.93
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	80.63
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	80.47

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

Probab=99.70  E-value=1.6e-17  Score=123.59  Aligned_cols=80  Identities=25%  Similarity=0.520  Sum_probs=69.2

Q ss_pred             hhhhcCCCCHHHHhcCCceeeecccccccccCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcC
Q 043807           34 LHQFAKGIEEKVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSP  113 (242)
Q Consensus        34 ~~~~~~gl~~~~i~~lp~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~  113 (242)
                      ......|++++.++.||.+.+.....  ....+..|+||++.|..++.++.++ |+|.||..||..|+..+.+||+||..
T Consensus        10 ~~~~~~~~s~~~i~~lp~~~~~~~~~--~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~Cr~~   86 (91)
T 2l0b_A           10 HMVANPPASKESIDALPEILVTEDHG--AVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCM   86 (91)
T ss_dssp             CSSCCCCCCHHHHHTSCEEECCTTCS--SSSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTTCCB
T ss_pred             CCcCCCCCCHHHHHhCCCeeeccccc--ccCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCcCcc
Confidence            34567899999999999998876552  2346678999999999988888898 99999999999999999999999998


Q ss_pred             CCC
Q 043807          114 VAD  116 (242)
Q Consensus       114 i~~  116 (242)
                      +..
T Consensus        87 ~~~   89 (91)
T 2l0b_A           87 FPP   89 (91)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            864

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

Probab=99.63  E-value=9e-17  Score=114.89  Aligned_cols=70  Identities=29%  Similarity=0.849  Sum_probs=59.5

Q ss_pred             HHHhcCCceeeecccccccccCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           44 KVLLTIPILAYSAKDCKLFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        44 ~~i~~lp~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      +.++.||.+.+....   ...++..|+||++.|..++.++.++ |+|.||..||..|+..+.+||+||..+...
T Consensus         4 ~~i~~lp~~~~~~~~---~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A            4 GSSGQLPSYRFNPNN---HQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             CCCSSCCCEEBCSSS---CSSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             hhHhhCCcEEecCcc---ccCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            356788998887654   2346678999999999988888998 999999999999999999999999988643

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

Probab=99.52  E-value=6e-15  Score=98.86  Aligned_cols=52  Identities=52%  Similarity=1.155  Sum_probs=46.6

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      +++..|+||++.|..++.+..++.|+|.||..||.+|++.+.+||+||..+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            3567899999999988878888679999999999999999999999999874

>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=99.52  E-value=1.1e-14  Score=102.07  Aligned_cols=55  Identities=44%  Similarity=0.983  Sum_probs=48.4

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPK  119 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~~~  119 (242)
                      ..+..|+||++.|..++.++.++ |+|.||..||..|+..+.+||+||..+....+
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   66 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQLP   66 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCSCCC
T ss_pred             CCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccCcCC
Confidence            45678999999998877788888 99999999999999999999999999876543

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

Probab=99.50  E-value=2.2e-14  Score=101.91  Aligned_cols=54  Identities=31%  Similarity=0.856  Sum_probs=48.2

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQP  118 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~~  118 (242)
                      ..+..|+||++.|..+..+.+++ |+|.||..||..|+..+.+||+||..+....
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA   66 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSSCC
T ss_pred             CCCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCccccccc
Confidence            45678999999999888888888 9999999999999999899999999986543

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

Probab=99.49  E-value=3.2e-14  Score=102.04  Aligned_cols=55  Identities=44%  Similarity=0.879  Sum_probs=48.7

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPK  119 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~~~  119 (242)
                      ..+..|+||++.|..+..+..++ |+|.||..||..|+..+.+||+||..+.....
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   67 (78)
T 2ect_A           13 GSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNT   67 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCCCCSCS
T ss_pred             CCCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCccCCccc
Confidence            45678999999999888888888 99999999999999999999999999876543

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

Probab=99.46  E-value=2.4e-14  Score=104.17  Aligned_cols=53  Identities=28%  Similarity=0.710  Sum_probs=43.4

Q ss_pred             cCCceeeeecccccC-----------CceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           64 VDQSECVICLGELED-----------GEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~-----------~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      .++..|+||++.|.+           ++.+++++.|+|.||..||.+|+..+.+||+||.++..
T Consensus        13 ~~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   76 (81)
T 2ecl_A           13 VECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVV   76 (81)
T ss_dssp             CCCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCE
T ss_pred             CCCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcch
Confidence            355679999998854           34455665699999999999999999999999998753

>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=99.41  E-value=9.3e-14  Score=106.41  Aligned_cols=67  Identities=27%  Similarity=0.564  Sum_probs=51.1

Q ss_pred             cCCceeeecccccccccCCceeeeecccccCC--------------c-eeeecCCCCccccHhHHHHHHhcCCCCCCCCc
Q 043807           48 TIPILAYSAKDCKLFRVDQSECVICLGELEDG--------------E-MVRLLPSCRHAFHVQCIGNWLLGHTICPVCRS  112 (242)
Q Consensus        48 ~lp~~~~~~~~~~~~~~~~~~C~ICl~~~~~~--------------~-~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~  112 (242)
                      .+...++..........++..|+||++.|...              + .++.++ |+|.||..||..||..+.+||+||.
T Consensus        19 r~~ik~~~~v~~w~~d~~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~Cr~   97 (106)
T 3dpl_R           19 RFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNR   97 (106)
T ss_dssp             SEEEEEEEEEEEEEESSCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCS
T ss_pred             ceeEEEEEEeeEeecCCCCCCCccCChhHhCcCchhhccccccCCccceEeecc-cCcEECHHHHHHHHHcCCcCcCCCC
Confidence            34444455554444556778999999999754              1 245565 9999999999999999999999999


Q ss_pred             CCC
Q 043807          113 PVA  115 (242)
Q Consensus       113 ~i~  115 (242)
                      .+.
T Consensus        98 ~~~  100 (106)
T 3dpl_R           98 EWE  100 (106)
T ss_dssp             BCC
T ss_pred             cce
Confidence            874

>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=99.40  E-value=1.4e-13  Score=91.96  Aligned_cols=50  Identities=32%  Similarity=0.796  Sum_probs=43.0

Q ss_pred             CCceeeeecccccCCc-eeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           65 DQSECVICLGELEDGE-MVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~-~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      .+..|+||++.|..++ .+..++ |+|.||..||..|+..+.+||+||..+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLP-CGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECT-TSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecC-CCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            4578999999996543 466676 9999999999999998899999999874

>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=99.37  E-value=4.2e-13  Score=102.92  Aligned_cols=52  Identities=31%  Similarity=0.767  Sum_probs=42.0

Q ss_pred             CCceeeeecccccCCc---------------eeeecCCCCccccHhHHHHHH-----hcCCCCCCCCcCCCCC
Q 043807           65 DQSECVICLGELEDGE---------------MVRLLPSCRHAFHVQCIGNWL-----LGHTICPVCRSPVADQ  117 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~---------------~~~~lp~C~H~Fh~~Ci~~wl-----~~~~~CP~CR~~i~~~  117 (242)
                      .+..|+||++.|..+.               .+.+++ |+|.||..||..|+     ..+.+||+||..+...
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCC-CCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            4568999999996643               233566 99999999999999     4577999999988654

>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=2.6e-13  Score=94.49  Aligned_cols=51  Identities=25%  Similarity=0.651  Sum_probs=43.5

Q ss_pred             cCCceeeeecccccCC----ceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDG----EMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~----~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      .+...|+||++.|.++    ..+.+++ |||.||..||..|+..+..||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   67 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKIN   67 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECS-SSCEEEHHHHHHHHHHCSSCTTTCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCC-CCChhcHHHHHHHHHcCCCCCCCCCccC
Confidence            4567899999998753    3346676 9999999999999999999999999885

>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=2.7e-13  Score=95.13  Aligned_cols=53  Identities=25%  Similarity=0.639  Sum_probs=44.7

Q ss_pred             cCCceeeeecccccCC----ceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDG----EMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~----~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      .++..|+||++.+.++    +.+..++ |||.||..||..|+..+.+||+||..+...
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   64 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCCC
T ss_pred             CCCCCCcccChhhhccccccCCeEeCC-CCChHhHHHHHHHHHcCCCCCCCCCccChh
Confidence            4567899999998653    4446676 999999999999999999999999998643

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

Probab=99.33  E-value=1.3e-13  Score=107.41  Aligned_cols=68  Identities=25%  Similarity=0.522  Sum_probs=9.2

Q ss_pred             CCceeeecccccccccCCceeeeecccccCC--------------ceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCC
Q 043807           49 IPILAYSAKDCKLFRVDQSECVICLGELEDG--------------EMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV  114 (242)
Q Consensus        49 lp~~~~~~~~~~~~~~~~~~C~ICl~~~~~~--------------~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i  114 (242)
                      +...++........+..+..|+||++.|...              +..++++.|+|.||..||..||..+.+||+||.++
T Consensus        31 ~~ikkw~ava~w~wd~~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~  110 (117)
T 4a0k_B           31 FEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREW  110 (117)
T ss_dssp             EEEEEEEEEEEEEECCCC--------------------------------------------------------------
T ss_pred             eEEEEEEEEEEEeecCCCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCee
Confidence            3344455554444556778999999999752              22333334999999999999999999999999987


Q ss_pred             CC
Q 043807          115 AD  116 (242)
Q Consensus       115 ~~  116 (242)
                      ..
T Consensus       111 ~~  112 (117)
T 4a0k_B          111 EF  112 (117)
T ss_dssp             --
T ss_pred             ee
Confidence            43

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

Probab=99.32  E-value=4e-13  Score=92.14  Aligned_cols=52  Identities=25%  Similarity=0.648  Sum_probs=43.6

Q ss_pred             CCceeeeecccccCC----ceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           65 DQSECVICLGELEDG----EMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~----~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      ++..|+||++.+.++    +.+..++ |||.||..||..|+..+.+||+||..+...
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   57 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   57 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEET-TSCEEEHHHHHHHHHHCSBCTTTCCBCTTT
T ss_pred             CCCCCCccChhhhCccccCCCEEeCC-CCCchhHHHHHHHHHcCCCCCCCCccCCcc
Confidence            456899999998753    3446676 999999999999999999999999988643

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

Probab=99.31  E-value=1.8e-12  Score=91.65  Aligned_cols=52  Identities=29%  Similarity=0.544  Sum_probs=43.2

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQP  118 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~~  118 (242)
                      .+...|+||++.+.++  +.+++ |||.||..||..|+..+..||+||..+....
T Consensus        13 ~~~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   64 (72)
T 2djb_A           13 TPYILCSICKGYLIDA--TTITE-CLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQ   64 (72)
T ss_dssp             CGGGSCTTTSSCCSSC--EECSS-SCCEECHHHHHHHHHHCSSCTTTCCCCCSSC
T ss_pred             CCCCCCCCCChHHHCc--CEECC-CCCHHHHHHHHHHHHcCCcCCCcCcccCccc
Confidence            3567899999999863  33346 9999999999999998999999999986543

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

Probab=99.30  E-value=1.4e-12  Score=90.84  Aligned_cols=49  Identities=37%  Similarity=0.870  Sum_probs=42.6

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      .+..|+||++.+.++  +..++ |||.||..||..|+..+.+||+||..+..
T Consensus         4 ~~~~C~IC~~~~~~~--~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSNY--SMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCSC--EEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCeeCCccccCC--cEecC-CCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            456899999998753  46777 99999999999999999999999998853

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

Probab=99.28  E-value=1.5e-12  Score=91.86  Aligned_cols=49  Identities=29%  Similarity=0.649  Sum_probs=42.5

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      .++..|+||++.+.+   .+.++ |+|.||..||..|+..+..||+||..+..
T Consensus        13 ~~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (71)
T 2d8t_A           13 LTVPECAICLQTCVH---PVSLP-CKHVFCYLCVKGASWLGKRCALCRQEIPE   61 (71)
T ss_dssp             SSCCBCSSSSSBCSS---EEEET-TTEEEEHHHHHHCTTCSSBCSSSCCBCCH
T ss_pred             CCCCCCccCCcccCC---CEEcc-CCCHHHHHHHHHHHHCCCcCcCcCchhCH
Confidence            456789999999976   45667 99999999999999999999999998853

>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=92.92  Aligned_cols=53  Identities=26%  Similarity=0.669  Sum_probs=44.0

Q ss_pred             cCCceeeeecccccCCceeeecCCCC-----ccccHhHHHHHHhcC--CCCCCCCcCCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCR-----HAFHVQCIGNWLLGH--TICPVCRSPVADQP  118 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~-----H~Fh~~Ci~~wl~~~--~~CP~CR~~i~~~~  118 (242)
                      .++..|.||+++|..++.+ ++| |.     |.||..||++|+..+  .+||+||..+....
T Consensus        13 ~~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~   72 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMET   72 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCC
T ss_pred             CCCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCc
Confidence            4567899999999876655 577 96     999999999999864  58999999986554

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

Probab=99.25  E-value=1.4e-12  Score=91.49  Aligned_cols=49  Identities=39%  Similarity=0.968  Sum_probs=42.9

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      .+...|+||++.+..    ..++ |+|.||..||..|+..+..||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~----~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   61 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGA   61 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEET-TTEEECHHHHHHSSCCCSSCHHHHHCTTCC
T ss_pred             CCCCCCeeCCcCccC----cccC-CCCcccHHHHHHHHHCcCcCCCcCCcccCC
Confidence            356789999999876    5676 999999999999999999999999998644

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

Probab=99.24  E-value=6.9e-12  Score=88.40  Aligned_cols=50  Identities=30%  Similarity=0.690  Sum_probs=41.9

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHh---cCCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL---GHTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~---~~~~CP~CR~~i~~~  117 (242)
                      .++..|+||++.+.+   ...++ |||.||..||..|+.   .+..||+||..+...
T Consensus        18 ~~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           18 QEEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCCBCTTTCSBCSS---EEECT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCC
T ss_pred             ccCCEeccCCcccCC---eEEcC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcc
Confidence            456789999999985   45666 999999999999996   466899999988543

>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=5e-12  Score=92.11  Aligned_cols=52  Identities=27%  Similarity=0.638  Sum_probs=44.1

Q ss_pred             cCCceeeeecccccCCce-eeecCCCCccccHhHHHHHHhcC---CCCCCCCcCCCC
Q 043807           64 VDQSECVICLGELEDGEM-VRLLPSCRHAFHVQCIGNWLLGH---TICPVCRSPVAD  116 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~-~~~lp~C~H~Fh~~Ci~~wl~~~---~~CP~CR~~i~~  116 (242)
                      .+...|+||++.|...+. +++++ |||.||..||..|+..+   ..||+||..+..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   68 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRI   68 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCC
T ss_pred             cCCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcccc
Confidence            456789999999987654 66776 99999999999999875   799999998754

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

Probab=99.23  E-value=6.9e-12  Score=90.54  Aligned_cols=48  Identities=23%  Similarity=0.533  Sum_probs=41.9

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      .....|+||++.|.+   .++++ |||.||..||..|+.....||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQN---PVVTK-CRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCS---EEECT-TSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcC---eeEcc-CCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            355789999999976   44676 9999999999999999999999999884

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

Probab=99.21  E-value=3.7e-12  Score=101.27  Aligned_cols=47  Identities=30%  Similarity=0.846  Sum_probs=41.5

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      ++..|+||++.|.+   +++++ |||.||..||..|+..+.+||+||.++.
T Consensus        52 ~~~~C~iC~~~~~~---~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   98 (138)
T 4ayc_A           52 NELQCIICSEYFIE---AVTLN-CAHSFCSYCINEWMKRKIECPICRKDIK   98 (138)
T ss_dssp             HHSBCTTTCSBCSS---EEEET-TSCEEEHHHHHHHTTTCSBCTTTCCBCC
T ss_pred             ccCCCcccCcccCC---ceECC-CCCCccHHHHHHHHHcCCcCCCCCCcCC
Confidence            34689999999976   45677 9999999999999999999999999884

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

Probab=99.21  E-value=1.3e-11  Score=87.87  Aligned_cols=49  Identities=29%  Similarity=0.698  Sum_probs=40.7

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcC--CCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGH--TICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~--~~CP~CR~~i~  115 (242)
                      .++..|+||++.|.++   +.++.|||.||..||..|+..+  ..||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   63 (74)
T 2yur_A           13 PDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   63 (74)
T ss_dssp             CGGGSCSSSCCCCTTC---EECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSC
T ss_pred             CCCCCCcCCChHHhCC---eEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCC
Confidence            3567899999999874   3455599999999999999865  68999999764

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

Probab=99.20  E-value=1.1e-11  Score=86.06  Aligned_cols=50  Identities=22%  Similarity=0.514  Sum_probs=41.5

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHH-hcCCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWL-LGHTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl-~~~~~CP~CR~~i~~~  117 (242)
                      .+...|+||++.+.++   ..++ |||.||..||..|+ ..+..||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCSP---KQTE-CGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCCEECTTTCCEESSC---CCCS-SSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             CcCCCCCCCChHhcCe---eECC-CCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            4567899999999864   3356 99999999999999 4667999999988543

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

Probab=99.19  E-value=2.1e-11  Score=87.45  Aligned_cols=52  Identities=21%  Similarity=0.541  Sum_probs=43.1

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcC--CCCCCCCcCCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGH--TICPVCRSPVADQP  118 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~--~~CP~CR~~i~~~~  118 (242)
                      +....|+||++.|..++...   .|+|.||..||.+||+.+  .+||+||..+....
T Consensus        13 ~~i~~C~IC~~~i~~g~~C~---~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~   66 (74)
T 2ct0_A           13 DAVKICNICHSLLIQGQSCE---TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEI   66 (74)
T ss_dssp             SSSCBCSSSCCBCSSSEECS---SSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCC
T ss_pred             CCCCcCcchhhHcccCCccC---CCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCC
Confidence            44578999999998764332   599999999999999877  89999999986543

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

Probab=99.18  E-value=2.3e-11  Score=87.61  Aligned_cols=50  Identities=30%  Similarity=0.616  Sum_probs=42.5

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc------CCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG------HTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~------~~~CP~CR~~i~~~  117 (242)
                      .+...|+||++.+.++   ..++ |||.||..||..|+..      ...||+||..+...
T Consensus        17 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecv_A           17 KEEVTCPICLELLTQP---LSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPE   72 (85)
T ss_dssp             CCCCCCTTTCSCCSSC---BCCS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSS
T ss_pred             cCCCCCCCCCcccCCc---eeCC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHH
Confidence            4567899999999764   4566 9999999999999986      78999999998653

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

Probab=99.18  E-value=2e-11  Score=87.99  Aligned_cols=50  Identities=32%  Similarity=0.607  Sum_probs=42.5

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc------CCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG------HTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~------~~~CP~CR~~i~~~  117 (242)
                      .++..|+||++.|.++   .+++ |||.||..||..|+..      ...||+||..+...
T Consensus        17 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           17 KEEVTCPICLELLKEP---VSAD-CNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             CTTTSCTTTCSCCSSC---EECT-TSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTT
T ss_pred             ccCCCCcCCChhhCcc---eeCC-CCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHH
Confidence            4567899999999874   3676 9999999999999987      77899999988643

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

Probab=99.17  E-value=8.1e-12  Score=89.26  Aligned_cols=49  Identities=29%  Similarity=0.531  Sum_probs=41.8

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc-------CCCCCCCCcCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG-------HTICPVCRSPVAD  116 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-------~~~CP~CR~~i~~  116 (242)
                      .++..|+||++.|.++   +.++ |||.||..||..|+..       ...||+||..+..
T Consensus        10 ~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A           10 QEEVTCPICLELLTEP---LSLD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             CCCCEETTTTEECSSC---CCCS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCS
T ss_pred             ccCCCCcCCCcccCCe---eECC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCH
Confidence            4567899999999864   4566 9999999999999986       6789999999864

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

Probab=99.17  E-value=1.8e-11  Score=87.54  Aligned_cols=49  Identities=20%  Similarity=0.472  Sum_probs=42.1

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc-CCCCCCCCcCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG-HTICPVCRSPVAD  116 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~i~~  116 (242)
                      .++..|+||++.|.+   .+.++ |||.||..||..|+.. +.+||+||..+..
T Consensus         6 ~~~~~C~IC~~~~~~---Pv~~~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~   55 (78)
T 1t1h_A            6 PEYFRCPISLELMKD---PVIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSSCTTTSCCCSS---EEEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             cccCCCCCccccccC---CEEcC-CCCeecHHHHHHHHHHCcCCCCCCcCCCCh
Confidence            456799999999986   34566 9999999999999986 7899999998853

>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=99.13  E-value=1.6e-11  Score=92.44  Aligned_cols=47  Identities=36%  Similarity=0.899  Sum_probs=40.8

Q ss_pred             CCceeeeecccccCCceeee-cCCCCccccHhHHHHHHhcC-CCCCCCCcCCC
Q 043807           65 DQSECVICLGELEDGEMVRL-LPSCRHAFHVQCIGNWLLGH-TICPVCRSPVA  115 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~-lp~C~H~Fh~~Ci~~wl~~~-~~CP~CR~~i~  115 (242)
                      ++..|+||++.|.+   .+. ++ |||.||..||..|+... ..||+||.++.
T Consensus        21 ~~~~C~IC~~~~~~---p~~~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~   69 (100)
T 3lrq_A           21 EVFRCFICMEKLRD---ARLCPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPLQ   69 (100)
T ss_dssp             HHTBCTTTCSBCSS---EEECTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCccCCccccC---ccccCC-CCChhhHHHHHHHHHHCcCCCCCCCCcCC
Confidence            45789999999986   345 66 99999999999999977 69999999884

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

Probab=99.13  E-value=3.6e-11  Score=82.53  Aligned_cols=43  Identities=33%  Similarity=0.737  Sum_probs=36.7

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHh---cCCCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL---GHTICPVC  110 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~---~~~~CP~C  110 (242)
                      .++..|+||++.|.++   ++++ |||.||..||..|+.   .+..||+|
T Consensus        18 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           18 QEEVICPICLDILQKP---VTID-CGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCBCTTTCSBCSSC---EECT-TSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             ccCCCCCcCCchhCCe---EEeC-CCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            4567899999999863   4566 999999999999998   46689998

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

Probab=99.13  E-value=2.7e-11  Score=83.77  Aligned_cols=52  Identities=19%  Similarity=0.535  Sum_probs=41.1

Q ss_pred             CCceeeeecc-cccCCcee-eecCCCCccccHhHHHHHHhc-CCCCCCCCcCCCCC
Q 043807           65 DQSECVICLG-ELEDGEMV-RLLPSCRHAFHVQCIGNWLLG-HTICPVCRSPVADQ  117 (242)
Q Consensus        65 ~~~~C~ICl~-~~~~~~~~-~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~i~~~  117 (242)
                      ++..|+||++ .+.++... ..++ |||.||..||..|+.. ...||+||..+...
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   56 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCcCCcCCCCccCCCccCeecCC-CCCHhHHHHHHHHHHcCCCcCCCCCCccccc
Confidence            4568999999 77766443 3455 9999999999999764 56899999988543

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

Probab=99.12  E-value=1.8e-11  Score=95.23  Aligned_cols=53  Identities=25%  Similarity=0.639  Sum_probs=44.9

Q ss_pred             cCCceeeeecccccCC----ceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDG----EMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~----~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      .++..|+||++.|.++    +.++.++ |||.||..||.+|+..+.+||+||..+...
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   61 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   61 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBCTTT
T ss_pred             CCCCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcCccc
Confidence            4567899999999753    3446776 999999999999999999999999998644

>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=2.9e-11  Score=91.93  Aligned_cols=50  Identities=30%  Similarity=0.693  Sum_probs=42.3

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      .++..|+||++.|.++  +.+++ |||.||..||..|+..+..||+||..+..
T Consensus        13 ~~~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   62 (108)
T 2ckl_A           13 NPHLMCVLCGGYFIDA--TTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVHK   62 (108)
T ss_dssp             GGGTBCTTTSSBCSSE--EEETT-TCCEEEHHHHHHHHTSCSBCTTTCCBSCS
T ss_pred             CCcCCCccCChHHhCc--CEeCC-CCChhhHHHHHHHHHhCCcCcCCCccccc
Confidence            3567899999999763  33346 99999999999999999999999998854

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

Probab=99.10  E-value=3.1e-11  Score=90.33  Aligned_cols=48  Identities=31%  Similarity=0.710  Sum_probs=40.9

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      +...|+||++.|.+   .+.++.|||.||..||..|+..+..||+||..+.
T Consensus        21 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   68 (99)
T 2y43_A           21 DLLRCGICFEYFNI---AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVT   68 (99)
T ss_dssp             HHTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCC
T ss_pred             CCCCcccCChhhCC---cCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCC
Confidence            45689999999986   3444239999999999999999999999999885

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

Probab=99.08  E-value=7.3e-11  Score=86.91  Aligned_cols=49  Identities=29%  Similarity=0.702  Sum_probs=40.6

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc--CCCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG--HTICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~CR~~i~  115 (242)
                      .++..|+||++.|.++   +.++.|||.||..||..|+..  +..||+||..+.
T Consensus        11 ~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           11 PDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CTTTEETTTTEECSSC---EECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CcCCCCCCCChhhcCc---eECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            4668999999999864   455559999999999999974  369999999873

>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=99.07  E-value=1.1e-10  Score=95.06  Aligned_cols=76  Identities=24%  Similarity=0.322  Sum_probs=52.9

Q ss_pred             hcCCCCHHHHhcCCceeeeccccc----ccccCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc-CCCCCCCC
Q 043807           37 FAKGIEEKVLLTIPILAYSAKDCK----LFRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG-HTICPVCR  111 (242)
Q Consensus        37 ~~~gl~~~~i~~lp~~~~~~~~~~----~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR  111 (242)
                      ...+++...+...|...+......    ........|+||++.|.++  +.+++ |||.||..||..|+.. +..||+||
T Consensus        21 ~~~~l~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr   97 (165)
T 2ckl_B           21 KTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNT--MTTKE-CLHRFCADCIITALRSGNKECPTCR   97 (165)
T ss_dssp             CCCCCCHHHHHCCCCCCCCSCCEEC----CCHHHHBCTTTSSBCSSE--EEETT-TCCEEEHHHHHHHHHTTCCBCTTTC
T ss_pred             ccccCCHHHHhcCchhhhccccccccchhhCCCCCCCcccChHhhCc--CEeCC-CCChhHHHHHHHHHHhCcCCCCCCC
Confidence            345667777766655433332211    1112345899999999863  43446 9999999999999986 78899999


Q ss_pred             cCCC
Q 043807          112 SPVA  115 (242)
Q Consensus       112 ~~i~  115 (242)
                      ..+.
T Consensus        98 ~~~~  101 (165)
T 2ckl_B           98 KKLV  101 (165)
T ss_dssp             CBCC
T ss_pred             CcCC
Confidence            9885

>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=99.06  E-value=7.9e-11  Score=91.65  Aligned_cols=48  Identities=19%  Similarity=0.492  Sum_probs=40.7

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcC-CCCCCCCcCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGH-TICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~-~~CP~CR~~i~~  116 (242)
                      ++..|+||++.|.+   .+.++ |||.||..||..|+..+ ..||+||..+..
T Consensus        51 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           51 ETFQCICCQELVFR---PITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHTBCTTTSSBCSS---EEECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             cCCCCCcCChHHcC---cEEee-CCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            45689999999986   45666 99999999999999854 499999999854

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

Probab=99.05  E-value=9.8e-11  Score=78.66  Aligned_cols=43  Identities=33%  Similarity=0.834  Sum_probs=36.0

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHH---hcCCCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWL---LGHTICPVC  110 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl---~~~~~CP~C  110 (242)
                      .+...|+||++.+.++   +.++ |||.||..||..|+   ..+..||+|
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKEP---VIIE-CGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSSC---CCCS-SCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccCCCCccCCcccCcc---EeCC-CCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            4567899999999874   4566 99999999999995   456789998

>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=99.02  E-value=2e-10  Score=87.32  Aligned_cols=48  Identities=27%  Similarity=0.639  Sum_probs=40.0

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcC---CCCCCCCcCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGH---TICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~---~~CP~CR~~i~~  116 (242)
                      +...|+||++.+.++   ..++ |||.||..||..|+..+   ..||+||..+..
T Consensus        20 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (112)
T 1jm7_A           20 KILECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (112)
T ss_dssp             HHTSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             CCCCCcccChhhcCe---EECC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCH
Confidence            346899999999764   3466 99999999999999865   489999998864

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

Probab=98.99  E-value=1.2e-10  Score=90.54  Aligned_cols=52  Identities=25%  Similarity=0.641  Sum_probs=43.5

Q ss_pred             cCCceeeeecccccCC----ceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           64 VDQSECVICLGELEDG----EMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~----~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      .+...|+||++.|...    ...+.++ |||.||..||..|+..+.+||+||..+..
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~  125 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINH  125 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEET-TSBEEEHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCCCCCCccccccccCcceEeCC-CCChhhHHHHHHHHHcCCCCCCCCCcCCh
Confidence            4567899999998752    2345666 99999999999999999999999998854

>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=98.97  E-value=5.6e-11  Score=91.26  Aligned_cols=47  Identities=30%  Similarity=0.699  Sum_probs=40.4

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc-CCCCCCCCcCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG-HTICPVCRSPVA  115 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~i~  115 (242)
                      ++..|+||++.|..   .+.++ |||.||..||..|+.. +..||+||..+.
T Consensus        14 ~~~~C~iC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   61 (115)
T 3l11_A           14 SECQCGICMEILVE---PVTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRVS   61 (115)
T ss_dssp             HHHBCTTTCSBCSS---CEECT-TSCEECHHHHCCCCCTTTSBCTTTCCBCH
T ss_pred             CCCCCccCCcccCc---eeEcC-CCCHHhHHHHHHHHhHCcCCCCCCCcccC
Confidence            45789999999986   34566 9999999999999976 678999999885

>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=98.96  E-value=3.3e-10  Score=91.50  Aligned_cols=49  Identities=20%  Similarity=0.477  Sum_probs=41.2

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCC-CCCCCCcCCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHT-ICPVCRSPVADQ  117 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~-~CP~CR~~i~~~  117 (242)
                      +...|+||++.|.+   .+.++ |||.||..||..|+.... .||+||..+...
T Consensus        77 ~~~~C~IC~~~~~~---pv~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQ---PVTTE-CFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSS---EEECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhcC---CEEcC-CCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            45689999999986   44576 999999999999998654 899999998644

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

Probab=98.94  E-value=5.2e-10  Score=81.91  Aligned_cols=48  Identities=19%  Similarity=0.117  Sum_probs=42.7

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      .++..|+||++.|.+   .++++ |||.|+..||..|+..+.+||+|+.++.
T Consensus        12 p~~~~CpI~~~~m~d---PV~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~   59 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTD---PVRLP-SGTVMDRSIILRHLLNSPTDPFNRQMLT   59 (85)
T ss_dssp             CTTTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCC
T ss_pred             chheECcccCchhcC---CeECC-CCCEECHHHHHHHHhcCCCCCCCcCCCC
Confidence            356889999999987   56777 9999999999999998899999998874

>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=98.93  E-value=3.1e-10  Score=87.68  Aligned_cols=48  Identities=31%  Similarity=0.560  Sum_probs=40.8

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCC-CCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHT-ICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~-~CP~CR~~i~  115 (242)
                      .++..|+||++.+.++   +.++ |||.||..||..|+.... .||+||..+.
T Consensus        16 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   64 (118)
T 3hct_A           16 ESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILL   64 (118)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCC
T ss_pred             CCCCCCCcCChhhcCe---EECC-cCChhhHHHHHHHHhhCCCCCCCCCCCcC
Confidence            4567899999999863   4566 999999999999998654 9999999884

>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=98.92  E-value=4e-10  Score=78.16  Aligned_cols=47  Identities=28%  Similarity=0.605  Sum_probs=40.0

Q ss_pred             CCceeeeecccccCCceeeec--CCCCcc-ccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           65 DQSECVICLGELEDGEMVRLL--PSCRHA-FHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~l--p~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      ++..|.||++.+.+   ..++  | |||. ||..|+..|+..+..||+||.++.
T Consensus         7 ~~~~C~IC~~~~~~---~~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            7 AIEPCVICQGRPKN---GCIVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             GGSCCTTTSSSCSC---EEEEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CcCCCCcCCCCCCC---EEEECCC-CCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            45689999999875   3343  7 9999 899999999998899999999884

>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=98.91  E-value=6.2e-10  Score=84.07  Aligned_cols=49  Identities=18%  Similarity=0.144  Sum_probs=43.2

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      .++..|+||++.|.+   +++++ |||.|+..||..|+..+.+||+|+.++..
T Consensus        27 p~~~~CpI~~~~m~d---PV~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   75 (100)
T 2kre_A           27 PDEFRDPLMDTLMTD---PVRLP-SGTIMDRSIILRHLLNSPTDPFNRQTLTE   75 (100)
T ss_dssp             STTTBCTTTCSBCSS---EEEET-TTEEEEHHHHHHHTTSCSBCSSSCCBCCT
T ss_pred             cHhhCCcCccCcccC---CeECC-CCCEEchHHHHHHHHcCCCCCCCCCCCCh
Confidence            456889999999997   45677 99999999999999988999999998853

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

Probab=98.91  E-value=6.9e-10  Score=80.18  Aligned_cols=53  Identities=25%  Similarity=0.537  Sum_probs=40.9

Q ss_pred             cCCceeeeecccccCCcee-eecCCCCccccHhHHHHHHh-cCCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDGEMV-RLLPSCRHAFHVQCIGNWLL-GHTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~-~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~i~~~  117 (242)
                      .++..|+||++.+...+.. .-++ |||.||..|+..|+. .+..||+||..+...
T Consensus         9 ~~~~~CpICle~~~~~d~~~~p~~-CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~   63 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPED   63 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTTCCSST-TSCCCCHHHHHHHTTSSCSBCTTTCCBCSSC
T ss_pred             ccCCcCCccCccCccccccccccC-CCCCcCHHHHHHHHhcCCCCCCCCCCccCCC
Confidence            4667899999998643322 2233 999999999999874 467899999998654

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

Probab=98.91  E-value=5.7e-10  Score=85.69  Aligned_cols=48  Identities=33%  Similarity=0.591  Sum_probs=40.9

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc-CCCCCCCCcCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG-HTICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~i~~  116 (242)
                      ++..|+||++.+.+   .+.++ |||.||..||..|+.. +..||+||..+..
T Consensus        22 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (116)
T 1rmd_A           22 KSISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFP   70 (116)
T ss_dssp             HHTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCCCCCCCCcHhcC---cEEcC-CCCcccHHHHHHHHhHCcCcCCCCCCCCCH
Confidence            35689999999976   34566 9999999999999986 7799999998853

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

Probab=98.91  E-value=3e-10  Score=76.59  Aligned_cols=47  Identities=28%  Similarity=0.635  Sum_probs=39.1

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      .+...|+||++.|.++   ++++ |||.||..||..|   ...||+||..+...
T Consensus         4 ~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCCSSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             ccCCCceEeCCccCCe---EEcC-CCCcccHHHHccC---CCCCCcCCcEeecC
Confidence            4567899999999864   5677 9999999999884   56899999988654

>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=98.89  E-value=1.2e-09  Score=82.11  Aligned_cols=48  Identities=25%  Similarity=0.248  Sum_probs=42.6

Q ss_pred             cCCceeeeecccccCCceeeecCCCC-ccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCR-HAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~-H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      .++..|+||++.|.+   .++++ || |.|++.||..|+..+.+||+|+.++.
T Consensus        20 p~~~~CpI~~~~m~d---PV~~~-cG~htf~r~cI~~~l~~~~~cP~~~~~l~   68 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCD---PVVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPLT   68 (98)
T ss_dssp             CTTTBCTTTCSBCSS---EEECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBCC
T ss_pred             cHhcCCcCccccccC---CeECC-CCCeEECHHHHHHHHHhCCCCCCCCCCCC
Confidence            356889999999997   45677 99 99999999999998899999999885

>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=98.86  E-value=7e-10  Score=88.74  Aligned_cols=50  Identities=18%  Similarity=0.348  Sum_probs=41.6

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcC-CCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGH-TICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~-~~CP~CR~~i~~~  117 (242)
                      .++..|+||++.|.++   +.++ |||.||..||..|+... ..||+||.++...
T Consensus        29 ~~~~~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   79 (141)
T 3knv_A           29 EAKYLCSACRNVLRRP---FQAQ-CGHRYCSFCLASILSSGPQNCAACVHEGIYE   79 (141)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHGGGSCEECHHHHHTTCCC
T ss_pred             CcCcCCCCCChhhcCc---EECC-CCCccCHHHHHHHHhcCCCCCCCCCCccccc
Confidence            4667999999999874   4566 99999999999999865 4899999987543

>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=98.83  E-value=1.2e-09  Score=75.52  Aligned_cols=49  Identities=18%  Similarity=0.403  Sum_probs=39.6

Q ss_pred             CCceeeeecccccCCceeeecCCCCcc-ccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHA-FHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      ....|.||++...+. .+..+| |||. ||..|+..|...+..||+||.++.
T Consensus         6 ~~~~C~IC~~~~~~~-~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            6 LLKPCSLCEKRPRDG-NIIHGR-TGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GGSBCTTTSSSBSCE-EEEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             cCCCCcccCCcCCCe-EEEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            456899999987652 122237 9998 999999999988889999999884

>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=1e-09  Score=84.59  Aligned_cols=45  Identities=31%  Similarity=0.671  Sum_probs=38.9

Q ss_pred             CCceeeeecccccCCceeeec-CCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           65 DQSECVICLGELEDGEMVRLL-PSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~l-p~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      +...|+||++.|.++   +.+ + |||.||..||..|+.  ..||+||..+.
T Consensus        21 ~~~~C~IC~~~~~~p---v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~   66 (117)
T 1jm7_B           21 KLLRCSRCTNILREP---VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAW   66 (117)
T ss_dssp             HTTSCSSSCSCCSSC---BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCS
T ss_pred             hCCCCCCCChHhhCc---cEeCC-CCCHHHHHHHHHHhc--CCCcCCCCcCc
Confidence            467899999999874   455 6 999999999999997  78999999874

>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=98.82  E-value=1.8e-09  Score=99.43  Aligned_cols=47  Identities=30%  Similarity=0.747  Sum_probs=41.1

Q ss_pred             CceeeeecccccCCceeeecCCCCccccHhHHHHHHh-cCCCCCCCCcCCCC
Q 043807           66 QSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL-GHTICPVCRSPVAD  116 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~i~~  116 (242)
                      ...|+||++.+.+   ++.+| |||.||..|+..|+. .+..||+||.++..
T Consensus       332 ~~~C~ICle~~~~---pv~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~  379 (389)
T 2y1n_A          332 FQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKG  379 (389)
T ss_dssp             SSBCTTTSSSBCC---EEEET-TCCEECHHHHHHHHHHTCSBCTTTCCBCCE
T ss_pred             CCCCCccCcCCCC---eEEeC-CCChhhHHHHHHHHhcCCCCCCCCCCccCC
Confidence            4689999999865   56677 999999999999998 78899999998854

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

Probab=98.75  E-value=1.8e-09  Score=76.78  Aligned_cols=44  Identities=25%  Similarity=0.635  Sum_probs=37.6

Q ss_pred             CCceeeeecccccCCceeeecCCCCcc-ccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHA-FHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      ++..|+||++.+.+   +..+| |||. ||..|+..|    ..||+||..+..
T Consensus        23 ~~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           23 EEKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HHTBCTTTSSSBCC---EEEET-TCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             cCCCCCCCCCCCCC---EEEcC-CCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            45689999999876   56677 9999 999999999    789999998853

>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=98.68  E-value=7.8e-09  Score=89.68  Aligned_cols=48  Identities=21%  Similarity=0.243  Sum_probs=41.0

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc-CCCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG-HTICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~i~  115 (242)
                      .....|+||++.|.+   +++++ |||.||..||..|+.. ..+||+||.++.
T Consensus       206 ~~~~~c~i~~~~~~d---Pv~~~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~~  254 (281)
T 2c2l_A          206 PDYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLT  254 (281)
T ss_dssp             CSTTBCTTTCSBCSS---EEECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCC
T ss_pred             CcccCCcCcCCHhcC---CeECC-CCCEECHHHHHHHHHHCCCCCcCCCCCCc
Confidence            356789999999987   45677 9999999999999985 445999999884

>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=98.68  E-value=7.9e-09  Score=76.84  Aligned_cols=47  Identities=19%  Similarity=0.393  Sum_probs=38.6

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcC------CCCCC--CCcC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGH------TICPV--CRSP  113 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~------~~CP~--CR~~  113 (242)
                      ..+..|+||++.|.+   +++++.|||.|+..||..|+..+      .+||+  |+..
T Consensus         5 ~~~~~CPI~~~~~~d---PV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            5 SSGFTCPITKEEMKK---PVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             SSCCBCTTTCSBCSS---EEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             CcEeECcCcCchhcC---CEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            456789999999987   44553499999999999999753      58999  8765

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

Probab=98.67  E-value=3.6e-09  Score=95.67  Aligned_cols=52  Identities=25%  Similarity=0.600  Sum_probs=39.7

Q ss_pred             cCCceeeeecccccCCcee----eecCCCCccccHhHHHHHHhcC-----------CCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGEMV----RLLPSCRHAFHVQCIGNWLLGH-----------TICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~----~~lp~C~H~Fh~~Ci~~wl~~~-----------~~CP~CR~~i~  115 (242)
                      ....+|+||++.+.++..+    -..+.|+|.||..||.+||+..           .+||+||.++.
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            4567899999999873222    1223599999999999999742           46999999874

>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=98.63  E-value=1.2e-08  Score=83.38  Aligned_cols=49  Identities=31%  Similarity=0.572  Sum_probs=41.1

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcC-CCCCCCCcCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGH-TICPVCRSPVAD  116 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~-~~CP~CR~~i~~  116 (242)
                      .+...|+||++.|.++   +.++ |||.||..||..|+... ..||+||..+..
T Consensus        16 ~~~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   65 (170)
T 3hcs_A           16 ESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLE   65 (170)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCCCCChhhcCc---EECC-CCCHHHHHHHHHHHHhCCCCCCCCccCcch
Confidence            4567999999999874   4566 99999999999999754 499999998854

>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=98.58  E-value=2.1e-08  Score=74.17  Aligned_cols=48  Identities=27%  Similarity=0.654  Sum_probs=39.6

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc--------CCCCCC--CCcC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG--------HTICPV--CRSP  113 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~--------~~~CP~--CR~~  113 (242)
                      +...|+||++.+..++.+.+.+ |||.||..|+..|+..        ...||.  |+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~-CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCC-CCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            4568999999998776666666 9999999999999863        247999  9876

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

Probab=98.57  E-value=4e-08  Score=68.88  Aligned_cols=46  Identities=33%  Similarity=0.796  Sum_probs=38.2

Q ss_pred             cCCceeeeecccccCCceeeecCCCCcc-ccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHA-FHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      .+...|.||++...+   +.++| |||. ||..|+..    ...||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i~~~   59 (68)
T 2ea5_A           13 ENSKDCVVCQNGTVN---WVLLP-CRHTCLCDGCVKY----FQQCPMCRQFVQES   59 (68)
T ss_dssp             CCSSCCSSSSSSCCC---CEETT-TTBCCSCTTHHHH----CSSCTTTCCCCCCE
T ss_pred             CCCCCCCCcCcCCCC---EEEEC-CCChhhhHHHHhc----CCCCCCCCcchhce
Confidence            456789999998765   66788 9999 99999984    47899999988643

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

Probab=98.57  E-value=2.5e-08  Score=70.87  Aligned_cols=44  Identities=25%  Similarity=0.640  Sum_probs=36.3

Q ss_pred             CCceeeeecccccCCceeeecCCCCcc-ccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHA-FHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      ++..|+||++.+.+   +..+| |||. ||..|+..    ...||+||.++..
T Consensus        24 ~~~~C~IC~~~~~~---~~~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i~~   68 (75)
T 2ecg_A           24 EEKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEA----VDKCPMCYTVITF   68 (75)
T ss_dssp             HHHSCSSSCSSCCC---BCCSS-SCCCCBCHHHHHH----CSBCTTTCCBCCC
T ss_pred             CCCCCCcCCCCCCC---EEEec-CCCHHHHHHHhhC----CCCCccCCceecC
Confidence            34689999999876   55677 9999 99999965    3789999998854

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

Probab=98.51  E-value=5e-08  Score=81.05  Aligned_cols=48  Identities=21%  Similarity=0.230  Sum_probs=40.8

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcC-CCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGH-TICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~-~~CP~CR~~i~  115 (242)
                      .....|+||++.|.+   +++++ |||.|+..||..|+..+ .+||+|+.++.
T Consensus       104 p~~f~CPI~~elm~D---PV~~~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l~  152 (179)
T 2f42_A          104 PDYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFDPVTRSPLT  152 (179)
T ss_dssp             CGGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             cHhhcccCccccCCC---CeECC-CCCEECHHHHHHHHHhCCCCCCCCcCCCC
Confidence            456789999999997   45667 99999999999999864 47999998874

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

Probab=98.49  E-value=7.6e-08  Score=65.96  Aligned_cols=48  Identities=29%  Similarity=0.615  Sum_probs=37.1

Q ss_pred             cCCceeeeecccccCCceeeecCCCC--c---cccHhHHHHHHhc--CCCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCR--H---AFHVQCIGNWLLG--HTICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~--H---~Fh~~Ci~~wl~~--~~~CP~CR~~i~  115 (242)
                      .+...|.||+++..  +.. ++| |.  |   .||..||.+|+..  +.+||+|+..+.
T Consensus         4 ~~~~~CrIC~~~~~--~~l-~~P-C~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            4 EDVPVCWICNEELG--NER-FRA-CGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECS--CCC-CCS-CCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCEeEEeecCCC--Cce-ecC-cCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            45678999999843  223 566 65  4   8999999999963  689999998874

>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=98.46  E-value=3.8e-08  Score=70.98  Aligned_cols=44  Identities=32%  Similarity=0.738  Sum_probs=36.9

Q ss_pred             CCceeeeecccccCCceeeecCCCCcc-ccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHA-FHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      ++..|.||++.+.+   +..+| |||. ||..|+..|    ..||+||..+..
T Consensus        17 ~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~   61 (79)
T 2yho_A           17 EAMLCMVCCEEEIN---STFCP-CGHTVCCESCAAQL----QSCPVCRSRVEH   61 (79)
T ss_dssp             HHTBCTTTSSSBCC---EEEET-TCBCCBCHHHHTTC----SBCTTTCCBCCE
T ss_pred             CCCEeEEeCcccCc---EEEEC-CCCHHHHHHHHHhc----CcCCCCCchhhC
Confidence            34589999998875   66777 9999 999999987    389999998854

>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=98.33  E-value=1.3e-07  Score=82.73  Aligned_cols=48  Identities=29%  Similarity=0.485  Sum_probs=39.4

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcC--CCCCC--CCcCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGH--TICPV--CRSPVA  115 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~--~~CP~--CR~~i~  115 (242)
                      ....|+||++.|.++  |+... |||.||+.||..|+..+  ..||+  |+..+.
T Consensus       180 ~el~CPIcl~~f~DP--Vts~~-CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~  231 (267)
T 3htk_C          180 IELTCPITCKPYEAP--LISRK-CNHVFDRDGIQNYLQGYTTRDCPQAACSQVVS  231 (267)
T ss_dssp             CCSBCTTTSSBCSSE--EEESS-SCCEEEHHHHHHHSTTCSCEECSGGGCSCEEC
T ss_pred             eeeECcCccCcccCC--eeeCC-CCCcccHHHHHHHHHhCCCCCCCcccccCcCc
Confidence            456799999999875  43345 99999999999999754  57999  999764

>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=98.29  E-value=1.3e-07  Score=85.95  Aligned_cols=44  Identities=25%  Similarity=0.764  Sum_probs=38.0

Q ss_pred             cCCceeeeecccccCCceeeecCCCCcc-ccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHA-FHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      .++..|+||++.+..   +..+| |||. ||..|+..|    ..||+||..+.
T Consensus       293 ~~~~~C~IC~~~~~~---~v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i~  337 (345)
T 3t6p_A          293 QEERTCKVCMDKEVS---VVFIP-CGHLVVCQECAPSL----RKCPICRGIIK  337 (345)
T ss_dssp             HTTCBCTTTSSSBCC---EEEET-TCCEEECTTTGGGC----SBCTTTCCBCC
T ss_pred             cCCCCCCccCCcCCc---eEEcC-CCChhHhHHHHhcC----CcCCCCCCCcc
Confidence            356789999999876   56677 9999 999999998    68999999885

>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=98.25  E-value=3.5e-07  Score=62.77  Aligned_cols=47  Identities=17%  Similarity=0.233  Sum_probs=40.2

Q ss_pred             ceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           67 SECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        67 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      ..|+||++.+.++   ++++.|||.|.+.||.+|+..+.+||+++.++..
T Consensus         4 ~~CpIs~~~m~dP---V~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~   50 (61)
T 2bay_A            4 MLCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSI   50 (61)
T ss_dssp             CCCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCG
T ss_pred             EEecCCCCCCCCC---EEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCCh
Confidence            5799999999874   4552499999999999999988889999998854

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.00  E-value=3.7e-06  Score=63.00  Aligned_cols=47  Identities=30%  Similarity=0.641  Sum_probs=38.5

Q ss_pred             eeeeecccccCCceeeecCCCCccccHhHHHHHHh-cCCCCCCCCcCCCCC
Q 043807           68 ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL-GHTICPVCRSPVADQ  117 (242)
Q Consensus        68 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~i~~~  117 (242)
                      .|.+|--.+.  ...+.+| |+|+||.+|+..|.+ ...+||.|+.++...
T Consensus         3 fC~~C~~Pi~--iygRmIP-CkHvFCydCa~~~~~~~~k~Cp~C~~~V~rV   50 (101)
T 3vk6_A            3 FCDKCGLPIK--VYGRMIP-CKHVFCYDCAILHEKKGDKMCPGCSDPVQRI   50 (101)
T ss_dssp             BCTTTCSBCS--EEEEEET-TCCEEEHHHHHHHHHTTCCBCTTTCCBCSEE
T ss_pred             ecCccCCCeE--EEeeecc-ccccHHHHHHHHHHhccCCCCcCcCCeeeee
Confidence            4777777765  3577888 999999999999985 568999999998544

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

Probab=97.93  E-value=7e-06  Score=70.92  Aligned_cols=52  Identities=21%  Similarity=0.515  Sum_probs=42.0

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcC--CCCCCCCcCCCCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGH--TICPVCRSPVADQPK  119 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~--~~CP~CR~~i~~~~~  119 (242)
                      ....|.||.+.+..+  . ..+.|+|.||..|+..|++.+  ..||.|+..|+...+
T Consensus       179 ~i~~C~iC~~iv~~g--~-~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~~  232 (238)
T 3nw0_A          179 AVKICNICHSLLIQG--Q-SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIP  232 (238)
T ss_dssp             TCCBCTTTCSBCSSC--E-ECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCCC
T ss_pred             CCCcCcchhhHHhCC--c-ccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCC
Confidence            356899999999876  3 333599999999999999764  489999999876543

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=94.30  E-value=0.022  Score=41.68  Aligned_cols=35  Identities=11%  Similarity=0.405  Sum_probs=25.3

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHH
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNW  100 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w  100 (242)
                      ++..|.||++.+..+-...-+. |+|.||..|+..|
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~-C~~~~C~~Cl~~~   36 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVT-CEVSYCDECLKAT   36 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETT-TTEEECHHHHHHH
T ss_pred             CCCCCcCCCCCCCCCceEECCc-CChHHhHHHCHHH
Confidence            3568999998753322233365 9999999999983

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=93.80  E-value=0.043  Score=37.72  Aligned_cols=47  Identities=23%  Similarity=0.386  Sum_probs=33.8

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc----CCCCCCCCcCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG----HTICPVCRSPV  114 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~CR~~i  114 (242)
                      .....|.||.+.   ++ +..-..|...||..|+...|..    .-.||.|....
T Consensus        10 ~~~~~C~vC~~~---~~-ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           10 APGARCGVCGDG---TD-VLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             CTTCCCTTTSCC---TT-CEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCCcCCCCCC---Ce-EEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            345679999753   33 4444569999999999887754    33799997654

>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=88.12  E-value=0.096  Score=35.29  Aligned_cols=50  Identities=20%  Similarity=0.370  Sum_probs=34.0

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHh-----cCCCCCCCCcC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL-----GHTICPVCRSP  113 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-----~~~~CP~CR~~  113 (242)
                      .+...|+||...+.++...+....|..-||..|+.--..     ....||.|+..
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            355679999998864443333335999999999854221     35679999753

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=84.57  E-value=0.4  Score=32.11  Aligned_cols=45  Identities=31%  Similarity=0.719  Sum_probs=31.6

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHh----cCCCCCCCCc
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL----GHTICPVCRS  112 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~----~~~~CP~CR~  112 (242)
                      ..+..|.||...   ++ +.....|...||..|+..-+.    ..-.||.|..
T Consensus         9 ~~~~~C~vC~~~---g~-ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A            9 DHQDYCEVCQQG---GE-IILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CCCSSCTTTSCC---SS-EEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCCccCCCC---Cc-EEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            456789999873   23 444456989999999987543    2346999965

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=83.63  E-value=0.27  Score=40.82  Aligned_cols=47  Identities=26%  Similarity=0.528  Sum_probs=33.8

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc----CCCCCCCCcCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG----HTICPVCRSPV  114 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~CR~~i  114 (242)
                      ..+..|.+|...    ..+.....|...||..|+.+.+..    .-.||.|+..-
T Consensus         5 ~~~~~C~~C~~~----g~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            5 PNEDWCAVCQNG----GDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             SSCSSBTTTCCC----EEEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCCCCC----CceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            456679999854    235555569999999999776543    34699998654

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=83.11  E-value=0.25  Score=40.18  Aligned_cols=46  Identities=28%  Similarity=0.636  Sum_probs=33.0

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc----CCCCCCCCcCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG----HTICPVCRSPV  114 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~CR~~i  114 (242)
                      ++..|.||...   ++ +.....|...||..|+..-+..    .-.||.|+..-
T Consensus         3 ~~~~C~~C~~~---g~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            3 NEDWCAVCQNG---GE-LLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             SCSSCTTTCCC---SS-CEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCccccCCCC---Ce-eeecCCCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            45679999854   33 4455569999999999775543    34699998754

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=82.49  E-value=0.46  Score=39.04  Aligned_cols=48  Identities=19%  Similarity=0.340  Sum_probs=34.1

Q ss_pred             ceeeeecccccCCce---eeecCCCCccccHhHHHH------HHh-----cCCCCCCCCcCC
Q 043807           67 SECVICLGELEDGEM---VRLLPSCRHAFHVQCIGN------WLL-----GHTICPVCRSPV  114 (242)
Q Consensus        67 ~~C~ICl~~~~~~~~---~~~lp~C~H~Fh~~Ci~~------wl~-----~~~~CP~CR~~i  114 (242)
                      ..|+||...+.+++.   .+....|...||..|+.-      -+.     ....||.|+..-
T Consensus         3 ~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~   64 (183)
T 3lqh_A            3 NFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERH   64 (183)
T ss_dssp             CBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSS
T ss_pred             CcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCC
Confidence            369999999987652   334445999999999842      111     267999998753

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=82.42  E-value=0.36  Score=33.43  Aligned_cols=50  Identities=20%  Similarity=0.395  Sum_probs=33.7

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHh----cCCCCCCCCcCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL----GHTICPVCRSPVA  115 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~----~~~~CP~CR~~i~  115 (242)
                      +...|.||..... ++..+....|...||..|+..-..    ..-.||.|+..+.
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            3456999988764 333444445999999999975443    2456999976553

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=81.92  E-value=0.64  Score=29.64  Aligned_cols=44  Identities=32%  Similarity=0.707  Sum_probs=28.8

Q ss_pred             eeeeecccccCCceeeecCCCCccccHhHHHHHHhc----CCCCCCCCc
Q 043807           68 ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG----HTICPVCRS  112 (242)
Q Consensus        68 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~CR~  112 (242)
                      .|.||...-..+ .+..-..|...||..|+..=+..    .-.||.|+.
T Consensus         2 ~C~vC~~~~~~~-~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCC-CEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            588888764333 34444469999999999753332    235888864

>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=80.93  E-value=1.1  Score=32.19  Aligned_cols=35  Identities=20%  Similarity=0.442  Sum_probs=23.3

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHH
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNW  100 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w  100 (242)
                      ..+..|.||-.-- .++....- -|+-+||..|+.+-
T Consensus        13 ~~D~~C~VC~~~t-~~~l~pCR-vC~RvfH~~CL~r~   47 (89)
T 1wil_A           13 VNDEMCDVCEVWT-AESLFPCR-VCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTTCCCC-SSCCSSCS-SSSSCCCHHHHHHH
T ss_pred             CCCcccCcccccc-ccceeccc-cccccccHhhcccc
Confidence            4677899997432 22222222 39999999999985

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=80.63  E-value=2.5  Score=30.64  Aligned_cols=52  Identities=21%  Similarity=0.464  Sum_probs=37.4

Q ss_pred             CCceeeeeccccc---CCceeeecCCCCccccHhHHHHH-HhcCCCCCCCCcCCCC
Q 043807           65 DQSECVICLGELE---DGEMVRLLPSCRHAFHVQCIGNW-LLGHTICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~---~~~~~~~lp~C~H~Fh~~Ci~~w-l~~~~~CP~CR~~i~~  116 (242)
                      ....|.||-+++.   +++..+..-.|+--.|+.|++-= -..+..||.|+..+..
T Consensus        15 ~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCktrYkr   70 (93)
T 1weo_A           15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKR   70 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCC
T ss_pred             CCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhccCccccccCCcccc
Confidence            4468999999863   33434333458888999999643 3468899999998853

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A

Probab=80.47  E-value=0.39  Score=32.14  Aligned_cols=47  Identities=26%  Similarity=0.675  Sum_probs=31.4

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc----CCCCCCCCcCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG----HTICPVCRSPV  114 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~CR~~i  114 (242)
                      ..+..|.||.+.   ++ +..-..|...||..|+..-+..    .-.||.|....
T Consensus         7 ~~~~~C~vC~~~---g~-ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            7 HHMEFCRVCKDG---GE-LLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---SS-CBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCCcCCCCCCC---CC-EEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            456679999863   22 3344458899999999854432    33599997643

---

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	242
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	2e-17
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-10
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	6e-10
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	9e-09
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	4e-08
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	4e-08
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	9e-08
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	8e-06
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	1e-05
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	2e-04
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	2e-04
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	9e-04
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	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 = 71.8 bits (176), Expect = 2e-17
 Identities = 27/50 (54%), Positives = 32/50 (64%)

Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV 114
           D  EC +CL ELEDGE  R LP C H FH +C+  WL  H+ CP+CR  V
Sbjct: 4   DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 53.8 bits (129), Expect = 1e-10
 Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 3/47 (6%)

Query: 68  ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV 114
            C ICL +  +  M      C HAF   CI  W+  +  CP+C+ PV
Sbjct: 7   RCPICLEDPSNYSMA---LPCLHAFCYVCITRWIRQNPTCPLCKVPV 50

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.3 bits (122), Expect = 6e-10
 Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 1/50 (2%)

Query: 68  ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWL-LGHTICPVCRSPVAD 116
           EC +C+  LE  ++     +C +     C        + +CP CR P  +
Sbjct: 2   ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE 51

>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 = 48.6 bits (115), Expect = 9e-09
 Identities = 12/52 (23%), Positives = 18/52 (34%), Gaps = 2/52 (3%)

Query: 65  DQSECVICLGELEDGEMVRLLP-SCRHAFHVQCIGNWL-LGHTICPVCRSPV 114
           D   C  C         ++L+   C H     C+      G   CP C +P+
Sbjct: 2   DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

>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 = 47.4 bits (112), Expect = 4e-08
 Identities = 15/64 (23%), Positives = 20/64 (31%), Gaps = 14/64 (21%)

Query: 64  VDQSECVICLGELEDGEMVRLLP--------------SCRHAFHVQCIGNWLLGHTICPV 109
           +    C IC   + D  +                    C HAFH  CI  WL    +CP+
Sbjct: 19  IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 78

Query: 110 CRSP 113
               
Sbjct: 79  DNRE 82

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.9 bits (111), Expect = 4e-08
 Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 5/51 (9%)

Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWL-LGHTICPVCRSPV 114
               C IC    +D   V++ P C H     C+ +W       CP CR  +
Sbjct: 22  TFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEI 68

>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 = 45.6 bits (108), Expect = 9e-08
 Identities = 13/55 (23%), Positives = 21/55 (38%), Gaps = 7/55 (12%)

Query: 68  ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPKSTS 122
            C  C  E +     +LLP C H     C+         CP+C++P      + +
Sbjct: 8   RCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGADTPA 55

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 40.2 bits (93), Expect = 8e-06
 Identities = 13/52 (25%), Positives = 18/52 (34%), Gaps = 3/52 (5%)

Query: 65  DQSECVICLGELEDGEMVRLLPS-CRHAFHVQCIGNWL--LGHTICPVCRSP 113
           D   C IC  EL +        +      H  C+  WL    +T C +C   
Sbjct: 5   DVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVV 56

>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 = 41.6 bits (96), Expect = 1e-05
 Identities = 15/69 (21%), Positives = 22/69 (31%), Gaps = 9/69 (13%)

Query: 62  FRVDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWL-----LGHTICPVCRS---- 112
             V      +   +     +V  L  C HAFH+ C+          G   CP C++    
Sbjct: 35  LAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGE 94

Query: 113 PVADQPKST 121
               QP   
Sbjct: 95  KTGTQPWGK 103

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 2e-04
 Identities = 13/57 (22%), Positives = 20/57 (35%), Gaps = 9/57 (15%)

Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTI--------CPVCRSP 113
             S C +CLGE    +M  +   C+  F   C+  ++             CP    P
Sbjct: 4   GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACP 59

>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 = 37.4 bits (86), Expect = 2e-04
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 7/50 (14%)

Query: 68  ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWL---LGHTICPVCRSPV 114
           EC ICL  +++         C H F   C+   L    G + CP+C++ +
Sbjct: 23  ECPICLELIKE---PVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 68

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.3 bits (81), Expect = 9e-04
 Identities = 16/47 (34%), Positives = 19/47 (40%), Gaps = 5/47 (10%)

Query: 69  CVICLGELEDGEMVRLLPSCRHAFHVQCIGNWL-LGHTICPVCRSPV 114
           C IC   L D         C+H F   CI   L +  + CP CR P 
Sbjct: 26  CQICEHILADPVETS----CKHLFCRICILRCLKVMGSYCPSCRYPC 68

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.4 bits (78), Expect = 0.002
 Identities = 14/50 (28%), Positives = 18/50 (36%), Gaps = 5/50 (10%)

Query: 65  DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPV 114
               C  C   L        L  C H F   C+ + +   T CPVC +P 
Sbjct: 21  KLLRCSRCTNILR---EPVCLGGCEHIFCSNCVSDCI--GTGCPVCYTPA 65

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	242
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.65
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.46
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.45
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.42
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.35
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.32
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.31
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.22
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.15
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.13
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.12
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.07
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.97
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.94
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.93
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.78
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.51
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	91.42
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	87.57
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	86.2
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	86.18
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	85.53
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	84.35
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	82.41
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	82.35

>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=99.65  E-value=2.4e-17  Score=110.42  Aligned_cols=52  Identities=52%  Similarity=1.155  Sum_probs=46.9

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      +++.+|+||+++|..++.+..++.|+|.||..||.+|++.+.+||+||.++.
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            3556899999999998888888779999999999999999999999999874

>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=99.46  E-value=1.5e-14  Score=105.41  Aligned_cols=54  Identities=30%  Similarity=0.631  Sum_probs=43.9

Q ss_pred             cccCCceeeeecccccCCc---------------eeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           62 FRVDQSECVICLGELEDGE---------------MVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        62 ~~~~~~~C~ICl~~~~~~~---------------~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      .+..+..|+||++.+....               .+..++ |||.||..||.+||+.+.+||+||+++..
T Consensus        17 ~d~~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   85 (88)
T d3dplr1          17 WDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEF   85 (88)
T ss_dssp             ESSCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCCE
T ss_pred             ecCCCCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCcccc
Confidence            3456678999999886532               245566 99999999999999999999999998853

>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=99.45  E-value=2.5e-14  Score=99.28  Aligned_cols=48  Identities=38%  Similarity=0.885  Sum_probs=41.6

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      ....|+||++.|.++  ++.++ |||.||..||..|++.+.+||+||.++.
T Consensus         4 ~~d~C~IC~~~~~~~--~~~~~-C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           4 VAERCPICLEDPSNY--SMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCCSSCCSCCCSC--EEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCCccCCcCccCC--cEEeC-CCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            345799999999753  56677 9999999999999999999999999874

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=2.2e-14  Score=94.56  Aligned_cols=50  Identities=24%  Similarity=0.563  Sum_probs=40.6

Q ss_pred             ceeeeecccccCCceeeecCCCCccccHhHHHHHHhc-CCCCCCCCcCCCC
Q 043807           67 SECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG-HTICPVCRSPVAD  116 (242)
Q Consensus        67 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~i~~  116 (242)
                      .+|+||+++|..++....+..|||.||..||.+|+.. +..||+||+++.+
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            3799999999876654333349999999999999985 5579999999864

>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=99.35  E-value=4.7e-13  Score=101.30  Aligned_cols=52  Identities=29%  Similarity=0.729  Sum_probs=40.5

Q ss_pred             CCceeeeecccccCC---------------ceeeecCCCCccccHhHHHHHHhc-----CCCCCCCCcCCCCC
Q 043807           65 DQSECVICLGELEDG---------------EMVRLLPSCRHAFHVQCIGNWLLG-----HTICPVCRSPVADQ  117 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~---------------~~~~~lp~C~H~Fh~~Ci~~wl~~-----~~~CP~CR~~i~~~  117 (242)
                      .+..|+||++.|...               ..+.+++ |+|.||..||..||..     +.+||+||..+...
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             ccccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            456899999987532               2345565 9999999999999974     34799999988554

>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=99.32  E-value=3.6e-13  Score=92.52  Aligned_cols=51  Identities=20%  Similarity=0.481  Sum_probs=39.7

Q ss_pred             CCceeeeecccccC-Cc-eeeecCCCCccccHhHHHHHHhc-CCCCCCCCcCCCC
Q 043807           65 DQSECVICLGELED-GE-MVRLLPSCRHAFHVQCIGNWLLG-HTICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~-~~-~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~i~~  116 (242)
                      ++..|+||++.+.. ++ .+.+++ |||.||..||..|+.. +..||+||..+..
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~   55 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRK   55 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSS
T ss_pred             CCCCCCcCCceeecCCceEEEeCc-cChHhhHHHHHHHhCcCcCCCCCCCcCccc
Confidence            46789999998643 23 334555 9999999999999964 5689999998853

>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=99.31  E-value=7.6e-13  Score=94.31  Aligned_cols=48  Identities=29%  Similarity=0.732  Sum_probs=40.8

Q ss_pred             CceeeeecccccCCceeeecCCCCccccHhHHHHHHh-cCCCCCCCCcCCCCC
Q 043807           66 QSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL-GHTICPVCRSPVADQ  117 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~i~~~  117 (242)
                      ...|+||++.+.+   +++++ |||.||..||..|+. ++.+||+||..+...
T Consensus        23 ~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~   71 (79)
T d1fbva4          23 FQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGT   71 (79)
T ss_dssp             TTBCTTTSSSBCC---EECSS-SCCEECHHHHHHHHHTTCCSCTTTCCCCCCC
T ss_pred             CCCCccCCCcCCC---eEEeC-CCCeeeHHHHHHHHHHCcCcCCCCCcCccCC
Confidence            3579999999875   66777 999999999999997 457899999999644

>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=99.22  E-value=1.5e-12  Score=86.83  Aligned_cols=47  Identities=17%  Similarity=0.253  Sum_probs=40.6

Q ss_pred             eeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCC
Q 043807           68 ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        68 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~  117 (242)
                      .|+||++.+.+   .++++.|||.||..||.+|++.+.+||+||.++...
T Consensus         2 ~C~Ic~~~~~~---Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~   48 (56)
T d2baya1           2 LCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   48 (56)
T ss_dssp             CCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             CCccCCchHHh---cCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHH
Confidence            59999999986   345556999999999999999999999999988543

>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=99.15  E-value=3.3e-12  Score=85.20  Aligned_cols=48  Identities=27%  Similarity=0.625  Sum_probs=39.6

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVADQPK  119 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~~~~  119 (242)
                      +...|+||++.|.+   .++++ |||.||..||.+|   +..||+||.++.....
T Consensus         5 ~~l~C~IC~~~~~~---p~~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~~   52 (56)
T d1bora_           5 QFLRCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGAD   52 (56)
T ss_dssp             CCSSCSSSCSSCBC---CSCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCSS
T ss_pred             CCCCCcccCcccCC---CEEec-CCCHHhHHHHHcC---CCcCcCCCCcccCCCC
Confidence            34689999999976   45677 9999999999876   6689999999975543

>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=99.13  E-value=1.2e-11  Score=89.45  Aligned_cols=47  Identities=34%  Similarity=0.599  Sum_probs=40.0

Q ss_pred             CceeeeecccccCCceeeecCCCCccccHhHHHHHHh-cCCCCCCCCcCCCC
Q 043807           66 QSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLL-GHTICPVCRSPVAD  116 (242)
Q Consensus        66 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~i~~  116 (242)
                      ...|+||++.+.+   +++++ |||.||..||.+|++ ++..||+||.++..
T Consensus        23 ~l~C~IC~~~~~~---pv~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~   70 (86)
T d1rmda2          23 SISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFP   70 (86)
T ss_dssp             HTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CcCCccCCcchhc---ceecC-CCChhhHHHHHHHHhhCCCcCcccCCCCCh
Confidence            4589999999976   56777 999999999999997 45689999998753

>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=99.12  E-value=1.8e-11  Score=90.92  Aligned_cols=48  Identities=27%  Similarity=0.639  Sum_probs=39.7

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcC---CCCCCCCcCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGH---TICPVCRSPVAD  116 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~---~~CP~CR~~i~~  116 (242)
                      ....|+||++.|.++   +.++ |||.||..||..|+...   ..||+||.++..
T Consensus        20 ~~l~CpIC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (103)
T d1jm7a_          20 KILECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (103)
T ss_dssp             HHTSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             cCcCCCccCchhCCe---EEcC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcCCh
Confidence            346899999999874   4566 99999999999999754   479999998853

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=99.07  E-value=3.5e-11  Score=80.93  Aligned_cols=52  Identities=25%  Similarity=0.491  Sum_probs=38.6

Q ss_pred             cCCceeeeecccccCCceee-ecCCCCccccHhHHHHHHh--cCCCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGEMVR-LLPSCRHAFHVQCIGNWLL--GHTICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~-~lp~C~H~Fh~~Ci~~wl~--~~~~CP~CR~~i~  115 (242)
                      ++...|.||++++..+.... ....|+|.||..||..|+.  .+.+||+||+++.
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            45678999999887542211 1112569999999999995  5678999999874

>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=98.97  E-value=7.3e-11  Score=86.68  Aligned_cols=46  Identities=33%  Similarity=0.658  Sum_probs=37.6

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVA  115 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~  115 (242)
                      ....|+||++.|.++  +...+ |||.||..||..|+.  ..||.||.++.
T Consensus        21 ~~l~C~IC~~~~~~p--v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~   66 (97)
T d1jm7b_          21 KLLRCSRCTNILREP--VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAW   66 (97)
T ss_dssp             HTTSCSSSCSCCSSC--BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCS
T ss_pred             hcCCCccCCchhhcC--ceeCC-CCCchhHHHHHHHHh--ccccccCCcCc
Confidence            456899999999875  33345 999999999999985  45999998874

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.94  E-value=3.2e-10  Score=79.84  Aligned_cols=49  Identities=20%  Similarity=0.474  Sum_probs=41.7

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc-CCCCCCCCcCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG-HTICPVCRSPVAD  116 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~i~~  116 (242)
                      .++..|+||++.|.++   ++++ |||.||..||..|+.. ...||.|+.++..
T Consensus         6 P~~l~CpIc~~~m~dP---V~~~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~   55 (78)
T d1t1ha_           6 PEYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             CccCCCcCcCchhhCc---eEcc-CCCcchHHHHHHHHHHCCCCCCcccccCCc
Confidence            4678999999999874   5677 9999999999999976 4679999998754

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.93  E-value=3e-10  Score=80.42  Aligned_cols=48  Identities=21%  Similarity=0.245  Sum_probs=41.0

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc-CCCCCCCCcCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG-HTICPVCRSPVA  115 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~i~  115 (242)
                      .++..|+||++.|.++   ++++ |||.||..||..|+.. +..||+|+.++.
T Consensus         5 P~~l~CpIc~~l~~dP---v~~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l~   53 (80)
T d2c2la2           5 PDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLT   53 (80)
T ss_dssp             CSTTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCC
T ss_pred             CccccCcCcCchhhhh---cccC-CcCeecHHHHHHHHhcCCccCCCcccccc
Confidence            4678999999999874   5676 9999999999999974 568999999874

>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=98.78  E-value=2.3e-09  Score=78.88  Aligned_cols=50  Identities=28%  Similarity=0.266  Sum_probs=42.6

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCCCcCCCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVCRSPVAD  116 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~i~~  116 (242)
                      .++..|+||++.|.+   +++++.|+|.|++.||..||..+..||+|+.++..
T Consensus        20 P~~f~CPI~~~lm~d---PV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~   69 (98)
T d1wgma_          20 CDEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             CTTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             cHHhCCcCchhHHHH---HHhcccccchhhHHHHHHHHHhcCCcccccccccc
Confidence            357899999999998   56777455689999999999999999999998853

>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=98.51  E-value=2.4e-08  Score=72.20  Aligned_cols=48  Identities=27%  Similarity=0.634  Sum_probs=38.1

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc--------CCCCCCCCcC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG--------HTICPVCRSP  113 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~--------~~~CP~CR~~  113 (242)
                      +...|+||++++...+.+.+++ |+|.||..|+..|+..        ...||.|..+
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~   59 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACP   59 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCS
T ss_pred             CCCcCccCCCcccCCceEEECC-CCCEeCCcCHHHHHHHHHhcCCccccCCcCCCCC
Confidence            4568999999998766666666 9999999999999962        1259987543

>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=91.42  E-value=0.035  Score=34.25  Aligned_cols=44  Identities=32%  Similarity=0.707  Sum_probs=30.5

Q ss_pred             eeeeecccccCCceeeecCCCCccccHhHHHHHHhc----CCCCCCCCc
Q 043807           68 ECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG----HTICPVCRS  112 (242)
Q Consensus        68 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~CR~  112 (242)
                      .|.||...-..+ .+..-..|...||..|+..-+..    .-.||.|+.
T Consensus         2 ~C~vC~~~~~~~-~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCC-CEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            588887665443 34445569999999999876543    235888864

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.57  E-value=0.2  Score=32.82  Aligned_cols=46  Identities=22%  Similarity=0.554  Sum_probs=30.8

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc----CCCCCCCCcCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG----HTICPVCRSPV  114 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~CR~~i  114 (242)
                      ....|.||...   ++ +..-..|...||..|+...+..    .-.||.|+...
T Consensus         6 ~c~~C~~C~~~---~~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           6 SATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             SSSCCSSSCSS---SC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCCCCCc---CE-EEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            34457777643   33 4444469999999999877643    33699996544

>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=86.20  E-value=0.17  Score=32.44  Aligned_cols=49  Identities=20%  Similarity=0.396  Sum_probs=35.3

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHH---Hh--cCCCCCCCCcC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNW---LL--GHTICPVCRSP  113 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w---l~--~~~~CP~CR~~  113 (242)
                      ....|.||.....+++..+.-..|+..||..|+..-   ..  ....||.|+..
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            456899999988776554555569999999999531   11  34679999753

>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=86.18  E-value=0.16  Score=32.56  Aligned_cols=45  Identities=31%  Similarity=0.544  Sum_probs=31.9

Q ss_pred             CCceeeeecccccCCceeeecCCCCccccHhHHHHHHhcCCCCCCC
Q 043807           65 DQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLGHTICPVC  110 (242)
Q Consensus        65 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~C  110 (242)
                      ....|.-|+..+.+. .+...+.|++.||.+|=.---..-.+||-|
T Consensus        14 ~~~~C~gC~~~l~~~-~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKDQ-HVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTTS-EEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCCC-ceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            346799999988653 445566799999999954322334579987

>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=85.53  E-value=0.22  Score=33.99  Aligned_cols=35  Identities=20%  Similarity=0.520  Sum_probs=25.9

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHH
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNW  100 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w  100 (242)
                      ..+..|.|| +.|........- -|+.+||..|+.+-
T Consensus        13 ~~D~mC~vC-~v~t~~~l~pCR-vCtRv~H~~CL~r~   47 (89)
T d1wila_          13 VNDEMCDVC-EVWTAESLFPCR-VCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTT-CCCCSSCCSSCS-SSSSCCCHHHHHHH
T ss_pred             CcCcccccc-Ccccccceecce-eecchhhHHHHHHh
Confidence            467789999 777665443322 38999999999885

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=84.35  E-value=1.8  Score=29.45  Aligned_cols=53  Identities=21%  Similarity=0.463  Sum_probs=38.0

Q ss_pred             CCceeeeeccccc---CCceeeecCCCCccccHhHHHH-HHhcCCCCCCCCcCCCCC
Q 043807           65 DQSECVICLGELE---DGEMVRLLPSCRHAFHVQCIGN-WLLGHTICPVCRSPVADQ  117 (242)
Q Consensus        65 ~~~~C~ICl~~~~---~~~~~~~lp~C~H~Fh~~Ci~~-wl~~~~~CP~CR~~i~~~  117 (242)
                      ....|.||-+.+.   +++..+-...|+--.|+.|..- +-..+..||.|+..+...
T Consensus        15 ~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Ykr~   71 (93)
T d1weoa_          15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKRL   71 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCCC
T ss_pred             ccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhhhh
Confidence            4568999999874   3444443445888899999964 335688999999887543

>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=82.41  E-value=0.56  Score=31.20  Aligned_cols=47  Identities=21%  Similarity=0.467  Sum_probs=31.5

Q ss_pred             ceeeeecccccCCceeeecCCCCccccHhHHHH--H-Hh--cCCCCCCCCcCC
Q 043807           67 SECVICLGELEDGEMVRLLPSCRHAFHVQCIGN--W-LL--GHTICPVCRSPV  114 (242)
Q Consensus        67 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~--w-l~--~~~~CP~CR~~i  114 (242)
                      .-| ||...+..++..+....|.-.||..|+..  . ..  .+..||.|+...
T Consensus        13 v~C-iC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~   64 (79)
T d1wepa_          13 VYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             eEe-ECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCc
Confidence            346 89987665544444456999999999941  1 11  246899998654

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.35  E-value=0.11  Score=33.16  Aligned_cols=47  Identities=26%  Similarity=0.675  Sum_probs=31.3

Q ss_pred             cCCceeeeecccccCCceeeecCCCCccccHhHHHHHHhc----CCCCCCCCcCC
Q 043807           64 VDQSECVICLGELEDGEMVRLLPSCRHAFHVQCIGNWLLG----HTICPVCRSPV  114 (242)
Q Consensus        64 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~CR~~i  114 (242)
                      ..+..|.||.+.   ++ ++.-..|.-.||..|+...+..    .-.||.|+...
T Consensus         7 ~~~~~C~~C~~~---g~-lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           7 HHMEFCRVCKDG---GE-LLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---SS-CBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCcCCCcCCCCC---Ce-EEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            344579999753   33 3344458999999999765542    34699997543