Citrus Sinensis ID: 029544

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-
Protein Sequence
MWGSGMNLITTVIGFGMSAAFIVFICTRIICRRIRGVESRPMFEIESGIDLEQPAPGHRINGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPLGRKHAREATFSMAQAVDSPETSINHSRQWLLTHLGHPEVNGNNQGHLHSVPGN
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHcccEEEEcccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHccEEEEEccccccccccEEEEEEcccccccEEEEcccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccccc
Coil and Loop (DISEMBL)
MWGSGMNLITTVIGFGMSAAFIVFICTRIICRrirgvesrpmfeiesgidleqpapghringlepVLVAAIPTMKFNQEAFKSVEDAECSiclgeyqdkevlrimpqcghsfhLACIDIWLrkkttcpvcrlplqdplgrkhaREATFSMaqavdspetsinhSRQWLLThlghpevngnnqghlhsvpgn
Flexible Loop (DISEMBL)
MWGSGMNLITTVIGFGMSAAFIVFICTRIICRRIRGVESRPMFEIESGIDLEQPAPGHRINGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPLGRKHAREATFSMaqavdspetSINHSRQWLLTHLGHPevngnnqghlhsvpgn
Low Complexity Region (SEG)
MWGSGMNLITTVIGFGMSAAFIVFictriicrrirGVESRPMFEIESGIDLEQPAPGHRINGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPLGRKHAREATFSMAQAVDSPETSINHSRQWLLTHLGHPEVNGNNQGHLHSVPGN
Disordered region (IsUnstruct)
****GMNLITTVIGFGMSAAFIVFICTRIICRRIRGVESRPMFEIESGIDLEQPAPGHRINGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD*****************************QWLLTHL*******************
Disordered Region (DISOPRED)
***SGMNLITTVIGFGMSAAFIVFICTRIICRRIR*******************************LVAAIPTMKFNQE******DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL*********************************************************
Disordered Region (DISEMBL)
MWGSGMNLITTVIGFGMSAAFIVFICTRIICRRIRGVESRPMFEIESGIDLEQPAPGHRINGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPLGRKHAREATFSMA***********HSRQWLLTHLGHPEVNGNNQGHLHSVPGN
Disordered Region (DISPRO)
*WGSGMNLITTVIGFGMSAAFIVFICTRIICRRIRG************************NGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL*********************************************************
Transmembrane Helix (TMHMM)
oooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MWGSGMNLITTVIGFGMSAAFIVFICTRIICRRIRGVESRPMFEIESGIDLEQPAPGHRINGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPLGRKHAREATFSMAQAVDSPETSINHSRQWLLTHLGHPEVNGNNQGHLHSVPGN
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	191	2.2.26 [Sep-21-2011]
O82353	214	RING-H2 finger protein AT	no	no	0.691	0.616	0.331	3e-16
Q9SN28	236	RING-H2 finger protein AT	no	no	0.591	0.478	0.367	1e-15
Q9SN27	225	E3 ubiquitin-protein liga	no	no	0.371	0.315	0.493	1e-15
P93823	381	RING-H2 finger protein AT	no	no	0.633	0.317	0.337	1e-15
O64762	302	RING-H2 finger protein AT	no	no	0.649	0.410	0.310	2e-15
Q5XF85	432	E3 ubiquitin-protein liga	no	no	0.654	0.289	0.310	5e-15
Q9LM69	197	RING-H2 finger protein AT	no	no	0.413	0.401	0.430	7e-15
Q9SL78	390	Putative RING-H2 finger p	no	no	0.413	0.202	0.392	1e-14
Q9SK92	381	E3 ubiquitin-protein liga	no	no	0.795	0.398	0.304	2e-14
Q9LSW9	375	RING-H2 finger protein AT	no	no	0.403	0.205	0.388	2e-14

>sp|O82353|ATL67_ARATH RING-H2 finger protein ATL67 OS=Arabidopsis thaliana GN=ATL67 PE=2 SV=1

 Score = 84.7 bits (208), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 55/166 (33%), Positives = 78/166 (46%), Gaps = 34/166 (20%)

Query: 4   SGMNLITTVIGFGMSAAFIV-------------FICTRIICRRIRGVES----------- 39
           +G +   T +GFG S A  +             +IC R   RR   VES           
Sbjct: 24  AGNHSYLTTLGFGYSIAIALGFLVLLSTVLLSSYICCRDSRRRTTAVESTGDRGGSVILP 83

Query: 40  RPMFEIESGIDLEQPAPGHRINGLEPVLVAAIPTMKFNQEAFKSVED-------AECSIC 92
           R +F  E   D E    G  + GL+  ++ + P   F+++   +  D         CSIC
Sbjct: 84  RIIFVAEE--DNEDLEAGDVVVGLDQAVINSYPKFHFSKDTSAASSDGFGGGGDTTCSIC 141

Query: 93  LGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCR-LPLQDP 137
           L EY++ E+LR+MP+C H FHL C+D WL+   +CPVCR  PL  P
Sbjct: 142 LCEYKEAEMLRMMPECKHYFHLCCLDAWLKLNGSCPVCRNSPLPTP 187

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SN28|ATL7_ARATH RING-H2 finger protein ATL7 OS=Arabidopsis thaliana GN=ATL7 PE=2 SV=1

 Score = 82.8 bits (203), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 43/117 (36%), Positives = 65/117 (55%), Gaps = 4/117 (3%)

Query: 62  GLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWL 121
           GL   +   +P + + +E+F  V+D++CS+CLG+YQ +E L+ MP CGH+FH+ CID+WL
Sbjct: 86  GLSKDIREMLPVVIY-KESFI-VKDSQCSVCLGDYQAEEKLQQMPSCGHTFHMECIDLWL 143

Query: 122 RKKTTCPVCRLPL--QDPLGRKHAREATFSMAQAVDSPETSINHSRQWLLTHLGHPE 176
              TTCP+CRL L  +  L   H      S  +  +  E S     Q     + H +
Sbjct: 144 TSHTTCPLCRLSLIPKPSLDLSHQSTEIVSSIENSNGGEASTQPDSQSATEAISHTD 200

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SN27|ATL59_ARATH E3 ubiquitin-protein ligase ATL59 OS=Arabidopsis thaliana GN=ATL59 PE=1 SV=1

 Score = 82.8 bits (203), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 36/73 (49%), Positives = 52/73 (71%), Gaps = 2/73 (2%)

Query: 62  GLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWL 121
           GL   +   +P + + +E+F +V D +CS+CLG+YQ +E L+ MP CGH+FH+ CID+WL
Sbjct: 72  GLSKDIREMLPIVIY-KESF-TVNDTQCSVCLGDYQAEEKLQQMPSCGHTFHMECIDLWL 129

Query: 122 RKKTTCPVCRLPL 134
              TTCP+CRL L
Sbjct: 130 TSHTTCPLCRLSL 142

E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8, UBC10, UBC11, and UBC34 in vitro.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|P93823|ATL1_ARATH RING-H2 finger protein ATL1 OS=Arabidopsis thaliana GN=ATL1 PE=2 SV=1

 Score = 82.4 bits (202), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 52/154 (33%), Positives = 77/154 (50%), Gaps = 33/154 (21%)

Query: 58  HRIN-GLEPVLVAAIPTMKFNQ------EAFKSVEDAECSICLGEYQDKEVLRIMPQCGH 110
           H +N GL+   + AIP  KF +      E  +S    ECS+CL E+Q+ E LRI+P C H
Sbjct: 96  HEVNRGLDESAIRAIPVFKFKKRDVVAGEEDQSKNSQECSVCLNEFQEDEKLRIIPNCCH 155

Query: 111 SFHLACIDIWLRKKTTCPVCRLPLQDPLGRKHAREATFSMA--QAVDSPETSINHSR--- 165
            FH+ CIDIWL+    CP+CR  +        + EA+F++    A  SP  +  HSR   
Sbjct: 156 VFHIDCIDIWLQGNANCPLCRTSV--------SCEASFTLDLISAPSSPRENSPHSRNRN 207

Query: 166 -----------QWLLTHLGHPEVNGNNQGHLHSV 188
                       +++  LG    NGNN+  + ++
Sbjct: 208 LEPGLVLGGDDDFVVIELGAS--NGNNRESVRNI 239

Arabidopsis thaliana (taxid: 3702)

>sp|O64762|ATL38_ARATH RING-H2 finger protein ATL38 OS=Arabidopsis thaliana GN=ATL38 PE=2 SV=1

 Score = 82.0 bits (201), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 40/129 (31%), Positives = 69/129 (53%), Gaps = 5/129 (3%)

Query: 8   LITTVIGFGMSAAFIVFICTRIICRRIRGVESRPMFEIESGIDLEQPAPGHRINGLEPVL 67
           L+ T+I F +    +  +C R   R+    ES   F   +  D+E       + GL+  +
Sbjct: 16  LVITIILFAIFIVGLASVCFRWTSRQFYSQESINPF---TDSDVESRTSITAVRGLDEAI 72

Query: 68  VAAIPTMKFNQ--EAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT 125
           + + PT  +++  E    +   EC++C+ E++D E LR+MP+C H FH  C+ +WL   +
Sbjct: 73  INSFPTFLYSEVKERRIGIGGVECAVCICEFEDHETLRLMPECCHVFHADCVSVWLSDHS 132

Query: 126 TCPVCRLPL 134
           TCP+CR+ L
Sbjct: 133 TCPLCRVDL 141

Arabidopsis thaliana (taxid: 3702)

>sp|Q5XF85|ATL42_ARATH E3 ubiquitin-protein ligase ATL42 OS=Arabidopsis thaliana GN=ATL42 PE=1 SV=2

 Score = 80.9 bits (198), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 72/132 (54%), Gaps = 7/132 (5%)

Query: 5   GMNLITTVIGFGMSAAFIVFI---CTRIICRRIRGVESRPMFEIESGIDLEQP-APGHRI 60
            + ++T V+    +  F++ +   C  I  R   G   R    +  GI   +  A   R 
Sbjct: 36  SLAVVTGVLAIMFALTFVLLVYAKCCHIDLRSGSGDRRRHDRRLRQGIFFNRSTASSDRF 95

Query: 61  NGLEPVLVAAIPTMKFNQEAFK-SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDI 119
           +GL+   + ++P  +F+  A K S +  +CS+CL +++  E+LR++P+C H+FH+ CID 
Sbjct: 96  SGLDKTAIESLPLFRFS--ALKGSKQGLDCSVCLSKFESVEILRLLPKCRHAFHIGCIDQ 153

Query: 120 WLRKKTTCPVCR 131
           WL +  TCP+CR
Sbjct: 154 WLEQHATCPLCR 165

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

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9LM69|ATL80_ARATH RING-H2 finger protein ATL80 OS=Arabidopsis thaliana GN=ATL80 PE=1 SV=1

 Score = 80.5 bits (197), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 34/79 (43%), Positives = 52/79 (65%)

Query: 53  QPAPGHRINGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSF 112
           QP       GL+  ++ ++P + F+ E+ +S + AEC+ICL E+   + LR++PQCGH F
Sbjct: 75  QPPVAAANKGLKKKVLQSLPKLTFSPESPESEKFAECAICLAEFSAGDELRVLPQCGHGF 134

Query: 113 HLACIDIWLRKKTTCPVCR 131
           H+ACID WL   ++CP CR
Sbjct: 135 HVACIDTWLGSHSSCPSCR 153

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SL78|ATL12_ARATH Putative RING-H2 finger protein ATL12 OS=Arabidopsis thaliana GN=ATL12 PE=3 SV=1

 Score = 79.7 bits (195), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 33/84 (39%), Positives = 57/84 (67%), Gaps = 5/84 (5%)

Query: 59  RINGLEPVLVAAIPTMKFNQEAFKSVEDA-ECSICLGEYQDKEVLRIMPQCGHSFHLACI 117
           R +GL+   + ++P  +F+  A K ++   ECS+CL +++D E+LR++P+C H+FH+ CI
Sbjct: 95  RFSGLDKKAIESLPFFRFS--ALKGLKQGLECSVCLSKFEDVEILRLLPKCRHAFHIGCI 152

Query: 118 DIWLRKKTTCPVC--RLPLQDPLG 139
           D WL +  TCP+C  R+ ++D L 
Sbjct: 153 DQWLEQHATCPLCRNRVNIEDDLS 176

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SK92|ATL15_ARATH E3 ubiquitin-protein ligase ATL15 OS=Arabidopsis thaliana GN=ATL15 PE=1 SV=1

 Score = 79.3 bits (194), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 52/171 (30%), Positives = 80/171 (46%), Gaps = 19/171 (11%)

Query: 10  TTVIGFGMSAAFIVFICTRIICRRIRGVESRPMFEIESGIDLEQPAPGHRIN-------G 62
           T +I   + + F    C  +  RR          +   G+D     PG+ +N       G
Sbjct: 39  TAIIMIVLVSVFFALGCISVYMRRC--------LQHALGMD-SGGGPGNWLNVRQTTEPG 89

Query: 63  LEPVLVAAIPTMKFNQEAFKSV--EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIW 120
           L+  ++   PT  ++      +  E  EC +CL E++D E LR++PQC H FH  CID W
Sbjct: 90  LDASVIETFPTFPYSTVKTLRIGKEALECPVCLNEFEDDETLRLIPQCCHVFHPGCIDAW 149

Query: 121 LRKKTTCPVCRLPLQDPLGRKHARE-ATFSMAQAVDSPETSINHSRQWLLT 170
           LR +TTCP+CR  L    G   + E    +     +S  T I+ +R+ +LT
Sbjct: 150 LRSQTTCPLCRANLVPVPGESVSSEIPGLARETGQNSLRTPIDDNRKRVLT 200

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

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9LSW9|ATL16_ARATH RING-H2 finger protein ATL16 OS=Arabidopsis thaliana GN=ATL16 PE=2 SV=1

 Score = 79.0 bits (193), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/90 (38%), Positives = 50/90 (55%), Gaps = 13/90 (14%)

Query: 55  APGHRINGLEPVLVAAIPTMKFNQEAFKS-------------VEDAECSICLGEYQDKEV 101
           +P  R  GL+  ++ AIP  KF +   ++                 ECS+CL E+QD+E 
Sbjct: 91  SPELRSRGLDESVIRAIPIFKFKKRYDQNDGVFTGEGEEEEEKRSQECSVCLSEFQDEEK 150

Query: 102 LRIMPQCGHSFHLACIDIWLRKKTTCPVCR 131
           LRI+P C H FH+ CID+WL+    CP+CR
Sbjct: 151 LRIIPNCSHLFHIDCIDVWLQNNANCPLCR 180

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	191
255541456	201	ring finger protein, putative [Ricinus c	0.989	0.940	0.696	2e-73
147781800	224	hypothetical protein VITISV_011419 [Viti	0.963	0.821	0.715	7e-73
225453756	201	PREDICTED: RING-H2 finger protein ATL7 [	0.963	0.915	0.715	2e-72
224063957	197	predicted protein [Populus trichocarpa]	0.963	0.934	0.666	1e-67
224130156	230	predicted protein [Populus trichocarpa]	0.989	0.821	0.579	1e-65
449454614	203	PREDICTED: RING-H2 finger protein ATL54-	0.994	0.935	0.642	1e-64
359807415	193	uncharacterized protein LOC100780922 [Gl	0.827	0.818	0.656	1e-56
356568327	193	PREDICTED: RING-H2 finger protein ATL51-	0.827	0.818	0.656	1e-56
357507109	190	RING finger protein [Medicago truncatula	0.837	0.842	0.639	1e-56
217072448	187	unknown [Medicago truncatula]	0.837	0.855	0.627	3e-55

>gi|255541456|ref|XP_002511792.1| ring finger protein, putative [Ricinus communis] gi|223548972|gb|EEF50461.1| ring finger protein, putative [Ricinus communis]

 Score =  280 bits (716), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 133/191 (69%), Positives = 157/191 (82%), Gaps = 2/191 (1%)

Query: 1   MWGSGMNLITTVIGFGMSAAFIVFICTRIICRRIRGVESRPMFEIESGIDLEQPAPGHRI 60
           M GSGMNLITTVIGFGMSA FIVF+CTRIIC R+R  ESR  FE+ES IDL+QP   H+I
Sbjct: 1   MLGSGMNLITTVIGFGMSATFIVFVCTRIICGRLRASESRQTFELESRIDLDQPE--HQI 58

Query: 61  NGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIW 120
           +GLEPV+VAAIPTMKFN+EAF +VEDA+CSICLGEYQ+KEVLRIMP+CGH+FHL+CID+W
Sbjct: 59  SGLEPVMVAAIPTMKFNREAFTAVEDAQCSICLGEYQEKEVLRIMPKCGHNFHLSCIDVW 118

Query: 121 LRKKTTCPVCRLPLQDPLGRKHAREATFSMAQAVDSPETSINHSRQWLLTHLGHPEVNGN 180
           LRK++TCPVCR P+QD L  KH R+AT SM +++DSPETS  HSRQWLL        N +
Sbjct: 119 LRKQSTCPVCRFPIQDTLEAKHMRQATMSMVRSIDSPETSTEHSRQWLLPGPDRSMGNAS 178

Query: 181 NQGHLHSVPGN 191
           NQ HL  V G+
Sbjct: 179 NQEHLVPVSGS 189

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147781800|emb|CAN65442.1| hypothetical protein VITISV_011419 [Vitis vinifera]

 Score =  278 bits (711), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 133/186 (71%), Positives = 152/186 (81%), Gaps = 2/186 (1%)

Query: 5   GMNLITTVIGFGMSAAFIVFICTRIICRRIRGVESRPMFEIESGIDLEQPAPGHRINGLE 64
           GMNLITTVIGFGMSA FIVF+CTR+IC R+RGVESR MFEI+S IDLEQP   HRI+GLE
Sbjct: 27  GMNLITTVIGFGMSATFIVFVCTRLICGRLRGVESRQMFEIDSRIDLEQPE--HRISGLE 84

Query: 65  PVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK 124
           PV+VAAIPTMKFN+EAF SVEDA+CSICLGEYQ+KEVLRIMP+CGH+FHL+CID+WLRK+
Sbjct: 85  PVMVAAIPTMKFNREAFSSVEDAQCSICLGEYQEKEVLRIMPKCGHNFHLSCIDVWLRKQ 144

Query: 125 TTCPVCRLPLQDPLGRKHAREATFSMAQAVDSPETSINHSRQWLLTHLGHPEVNGNNQGH 184
           +TCPVCRL LQD    KH R   F  AQ+VDSPE S++ S QWLL        NG NQ H
Sbjct: 145 STCPVCRLSLQDSFETKHVRPEAFDTAQSVDSPEISVDRSHQWLLPGPERSVENGTNQVH 204

Query: 185 LHSVPG 190
             S+PG
Sbjct: 205 HESIPG 210

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225453756|ref|XP_002270058.1| PREDICTED: RING-H2 finger protein ATL7 [Vitis vinifera] gi|296089077|emb|CBI38780.3| unnamed protein product [Vitis vinifera]

 Score =  277 bits (708), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 133/186 (71%), Positives = 152/186 (81%), Gaps = 2/186 (1%)

Query: 5   GMNLITTVIGFGMSAAFIVFICTRIICRRIRGVESRPMFEIESGIDLEQPAPGHRINGLE 64
           GMNLITTVIGFGMSA FIVF+CTR+IC R+RGVESR MFEI+S IDLEQP   HRI+GLE
Sbjct: 4   GMNLITTVIGFGMSATFIVFVCTRLICGRLRGVESRQMFEIDSRIDLEQPE--HRISGLE 61

Query: 65  PVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK 124
           PV+VAAIPTMKFN+EAF SVEDA+CSICLGEYQ+KEVLRIMP+CGH+FHL+CID+WLRK+
Sbjct: 62  PVMVAAIPTMKFNREAFSSVEDAQCSICLGEYQEKEVLRIMPKCGHNFHLSCIDVWLRKQ 121

Query: 125 TTCPVCRLPLQDPLGRKHAREATFSMAQAVDSPETSINHSRQWLLTHLGHPEVNGNNQGH 184
           +TCPVCRL LQD    KH R   F  AQ+VDSPE S++ S QWLL        NG NQ H
Sbjct: 122 STCPVCRLSLQDSFETKHVRPEAFDTAQSVDSPEISVDRSHQWLLPGPERSVENGTNQVH 181

Query: 185 LHSVPG 190
             S+PG
Sbjct: 182 HESIPG 187

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224063957|ref|XP_002301320.1| predicted protein [Populus trichocarpa] gi|222843046|gb|EEE80593.1| predicted protein [Populus trichocarpa]

 Score =  261 bits (666), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 124/186 (66%), Positives = 142/186 (76%), Gaps = 2/186 (1%)

Query: 6   MNLITTVIGFGMSAAFIVFICTRIICRRIRGVESRPMFEIESGIDLEQPAPGHRINGLEP 65
           MNLITT IGFGMSA FIVF+C RIIC RIRG ESR MFEIES ID EQP   HRI GLEP
Sbjct: 1   MNLITTAIGFGMSATFIVFVCARIICGRIRGTESRQMFEIESRIDPEQPE--HRIGGLEP 58

Query: 66  VLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT 125
           VL+AAIPT++F  E F S EDA+CSICLGEYQ+KEVLRIMP CGH+FHL+CID+WLRK++
Sbjct: 59  VLLAAIPTLRFTHEEFSSAEDAQCSICLGEYQEKEVLRIMPGCGHNFHLSCIDVWLRKQS 118

Query: 126 TCPVCRLPLQDPLGRKHAREATFSMAQAVDSPETSINHSRQWLLTHLGHPEVNGNNQGHL 185
           TCPVCR P+QD    KH R+   SM Q++DSP+T    SRQWLL        N +N+ HL
Sbjct: 119 TCPVCRFPIQDSFEAKHMRQTAISMVQSIDSPDTRSEQSRQWLLPSYQGSAGNHSNERHL 178

Query: 186 HSVPGN 191
             VPGN
Sbjct: 179 DPVPGN 184

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224130156|ref|XP_002320766.1| predicted protein [Populus trichocarpa] gi|222861539|gb|EEE99081.1| predicted protein [Populus trichocarpa]

 Score =  254 bits (649), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 127/219 (57%), Positives = 148/219 (67%), Gaps = 30/219 (13%)

Query: 1   MWGSGMNLITTVIGFGMSAAFIVFICTRIICRRIRGVESRPMFEIESGIDLEQPAPGHRI 60
           M+ + MNL TTVIGFGMS  FIVF+CTRIIC R+RG ESR M EIES ID+EQP   H I
Sbjct: 1   MFDAAMNLTTTVIGFGMSVTFIVFVCTRIICGRLRGAESRQMLEIESRIDIEQPE--HGI 58

Query: 61  NGLEPVLVAAIPTMKFNQEAFKSVEDAE----------------------------CSIC 92
           +GLEPVLVAAIPT++F +EAF S EDA+                            CSIC
Sbjct: 59  SGLEPVLVAAIPTLRFTREAFSSAEDAQVFTLFSITGKQSFSPVIDQGAFSSLLASCSIC 118

Query: 93  LGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPLGRKHAREATFSMAQ 152
           LGEYQ+KEVLRIMP+CGH+FHL+CID WLRK +TCPVCR  +QD    KH R+A  SM Q
Sbjct: 119 LGEYQEKEVLRIMPKCGHNFHLSCIDEWLRKHSTCPVCRFQIQDSFKAKHMRQAAISMVQ 178

Query: 153 AVDSPETSINHSRQWLLTHLGHPEVNGNNQGHLHSVPGN 191
           ++DSP+T   HSRQWLL    H   N +NQ HL  VPGN
Sbjct: 179 SIDSPDTPSEHSRQWLLPSYQHQAGNHSNQRHLDPVPGN 217

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449454614|ref|XP_004145049.1| PREDICTED: RING-H2 finger protein ATL54-like [Cucumis sativus] gi|449472490|ref|XP_004153610.1| PREDICTED: RING-H2 finger protein ATL54-like [Cucumis sativus] gi|449516541|ref|XP_004165305.1| PREDICTED: RING-H2 finger protein ATL54-like [Cucumis sativus]

 Score =  251 bits (640), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 124/193 (64%), Positives = 146/193 (75%), Gaps = 3/193 (1%)

Query: 1   MWGSGMNLITTVIGFGMSAAFIVFICTRIICRRIRGVESR-PMFEIESGIDLEQPAPGHR 59
           M GSGMNLITTVIGFGMSA FIVF+CTRIIC R+R  +S  P +EIES +DLEQ  P  R
Sbjct: 1   MTGSGMNLITTVIGFGMSATFIVFVCTRIICGRLRSAQSNTPNYEIESRLDLEQ-QPESR 59

Query: 60  INGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDI 119
            +GLEPVL+AAIPTM F++EAF S+EDA+CSICLGEY++KEVLRIMP+CGHSFHL CID+
Sbjct: 60  ASGLEPVLIAAIPTMTFDREAFSSIEDAQCSICLGEYEEKEVLRIMPKCGHSFHLTCIDV 119

Query: 120 WLRKKTTCPVCRLPLQDPLGRKHAREATFSMAQAVDSPETSIN-HSRQWLLTHLGHPEVN 178
           WLRK++TCPVCRLPLQD    K AR  T S  Q+ D  E S + HS+ WLL      E N
Sbjct: 120 WLRKQSTCPVCRLPLQDSFRTKPARPMTVSRDQSFDGSEISTDHHSQHWLLPGPNRSEGN 179

Query: 179 GNNQGHLHSVPGN 191
            +NQ  L  +P N
Sbjct: 180 TSNQSQLQPIPVN 192

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359807415|ref|NP_001240876.1| uncharacterized protein LOC100780922 [Glycine max] gi|255641268|gb|ACU20911.1| unknown [Glycine max]

 Score =  224 bits (572), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 107/163 (65%), Positives = 132/163 (80%), Gaps = 5/163 (3%)

Query: 1   MWGSGMNLITTVIGFGMSAAFIVFICTRIICRRIRG-VESRPMFEIESGIDLEQPAPGHR 59
           M GSG NL+TTVIGFGMSA FIVF+CTRIIC R+RG VESR M+EIES IDLEQP   H 
Sbjct: 1   MLGSGTNLVTTVIGFGMSATFIVFVCTRIICGRLRGGVESRMMYEIESRIDLEQPE--HH 58

Query: 60  ING--LEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACI 117
           +N    +PVL+ AIPT+KFNQEAF S+E  +C ICL +Y+++EVLRIMP+CGH+FHL+CI
Sbjct: 59  VNDPDSDPVLLDAIPTLKFNQEAFSSLEHTQCVICLADYKEREVLRIMPKCGHTFHLSCI 118

Query: 118 DIWLRKKTTCPVCRLPLQDPLGRKHAREATFSMAQAVDSPETS 160
           DIWLRK++TCPVCRLPL++    KH R  TF+M+Q++D   TS
Sbjct: 119 DIWLRKQSTCPVCRLPLKNSSETKHVRPVTFTMSQSLDESHTS 161

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356568327|ref|XP_003552363.1| PREDICTED: RING-H2 finger protein ATL51-like [Glycine max]

 Score =  224 bits (571), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 107/163 (65%), Positives = 132/163 (80%), Gaps = 5/163 (3%)

Query: 1   MWGSGMNLITTVIGFGMSAAFIVFICTRIICRRIRG-VESRPMFEIESGIDLEQPAPGHR 59
           M GSG NL+TTVIGFGMSA FIVF+CTRIIC R+RG VESR M+EIES ID+EQP   H 
Sbjct: 1   MLGSGTNLVTTVIGFGMSATFIVFVCTRIICGRLRGGVESRMMYEIESRIDMEQPE--HH 58

Query: 60  INGLE--PVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACI 117
           +N  E  PVL+ AIPT+KFNQEAF S+E  +C ICL +Y+++EVLRIMP+CGH+FHL+CI
Sbjct: 59  VNDPESDPVLLDAIPTLKFNQEAFSSLEHTQCVICLADYREREVLRIMPKCGHTFHLSCI 118

Query: 118 DIWLRKKTTCPVCRLPLQDPLGRKHAREATFSMAQAVDSPETS 160
           DIWLRK++TCPVCRLPL++    KH R  TF+M+Q++D   TS
Sbjct: 119 DIWLRKQSTCPVCRLPLKNSSETKHVRPVTFTMSQSLDESHTS 161

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357507109|ref|XP_003623843.1| RING finger protein [Medicago truncatula] gi|124360239|gb|ABN08252.1| Zinc finger, RING-type [Medicago truncatula] gi|124360861|gb|ABN08833.1| Zinc finger, RING-type [Medicago truncatula] gi|355498858|gb|AES80061.1| RING finger protein [Medicago truncatula] gi|388496154|gb|AFK36143.1| unknown [Medicago truncatula]

 Score =  224 bits (571), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 103/161 (63%), Positives = 128/161 (79%), Gaps = 1/161 (0%)

Query: 1   MWGSGMNLITTVIGFGMSAAFIVFICTRIICRRIRG-VESRPMFEIESGIDLEQPAPGHR 59
           M GSG NL+TTVIGFGMSA FIVF+CTRIIC R+RG VESR M+EIES  D+EQP     
Sbjct: 1   MLGSGTNLVTTVIGFGMSATFIVFVCTRIICGRLRGGVESRMMYEIESRYDIEQPEHHGN 60

Query: 60  INGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDI 119
             G EPVL+ AIPT+KFNQEAF ++ED +C ICL +Y+++E+LRIMP+CGH+FHL+CIDI
Sbjct: 61  DPGTEPVLIEAIPTLKFNQEAFSAIEDTQCVICLADYKEREILRIMPKCGHTFHLSCIDI 120

Query: 120 WLRKKTTCPVCRLPLQDPLGRKHAREATFSMAQAVDSPETS 160
           WLRK++TCPVCRLPL++    KH R  TF+M+Q +D    S
Sbjct: 121 WLRKQSTCPVCRLPLKNSSETKHVRPVTFTMSQPLDESHAS 161

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217072448|gb|ACJ84584.1| unknown [Medicago truncatula]

 Score =  220 bits (560), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 101/161 (62%), Positives = 127/161 (78%), Gaps = 1/161 (0%)

Query: 1   MWGSGMNLITTVIGFGMSAAFIVFICTRIICRRIRG-VESRPMFEIESGIDLEQPAPGHR 59
           M GSG NL+TTVIGFGMSA FIVF+CTRIIC R+ G VESR M+EIES  D+EQP     
Sbjct: 1   MLGSGTNLVTTVIGFGMSATFIVFVCTRIICGRLGGGVESRMMYEIESRYDIEQPEHHGN 60

Query: 60  INGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDI 119
             G EPVL+ AIPT+KFNQEAF ++ED +C ICL +Y+++E+LRIMP+CGH+FHL+CIDI
Sbjct: 61  DPGTEPVLIEAIPTLKFNQEAFSAIEDTQCVICLADYKEREILRIMPKCGHTFHLSCIDI 120

Query: 120 WLRKKTTCPVCRLPLQDPLGRKHAREATFSMAQAVDSPETS 160
           WL+K++TCPVCRLPL++    KH R  TF+M+Q +D    S
Sbjct: 121 WLKKQSTCPVCRLPLKNSSETKHVRPVTFTMSQPLDESHAS 161

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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	191
TAIR|locus:2090980	204	AT3G14320 [Arabidopsis thalian	0.356	0.333	0.442	4.8e-17
TAIR|locus:2124695	236	AT4G10150 [Arabidopsis thalian	0.591	0.478	0.367	5.3e-17
TAIR|locus:505006547	367	AT4G33565 [Arabidopsis thalian	0.476	0.247	0.380	7.7e-17
TAIR|locus:2124700	225	AT4G10160 [Arabidopsis thalian	0.371	0.315	0.493	1.1e-16
TAIR|locus:2007008	261	AT1G33480 [Arabidopsis thalian	0.554	0.406	0.384	3.7e-16
TAIR|locus:2825708	197	AT1G20823 [Arabidopsis thalian	0.445	0.431	0.413	3.7e-16
TAIR|locus:2081740	257	ATL5 "AtL5" [Arabidopsis thali	0.544	0.404	0.317	6e-16
TAIR|locus:2089398	304	ATL2 "TOXICOS EN LEVADURA 2" [	0.612	0.384	0.341	8.1e-16
TAIR|locus:2018334	381	AT1G04360 [Arabidopsis thalian	0.523	0.262	0.393	9.3e-16
TAIR|locus:2062008	227	AT2G47560 [Arabidopsis thalian	0.413	0.348	0.4	9.8e-16

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

 Score = 188 (71.2 bits), Expect = 4.8e-17, Sum P(2) = 4.8e-17
 Identities = 31/70 (44%), Positives = 46/70 (65%)

Query:    62 GLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWL 121
             G++P ++ +IP + FN + FK V   EC +CL E  D +  R++P C H FH+ CID WL
Sbjct:    63 GIKPYVLRSIPIVDFNTKDFKYV--LECVVCLSELADGDKARVLPSCDHWFHVECIDSWL 120

Query:   122 RKKTTCPVCR 131
             +  +TCP+CR
Sbjct:   121 QSNSTCPICR 130

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

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

 Score = 209 (78.6 bits), Expect = 5.3e-17, P = 5.3e-17
 Identities = 43/117 (36%), Positives = 65/117 (55%)

Query:    62 GLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWL 121
             GL   +   +P + + +E+F  V+D++CS+CLG+YQ +E L+ MP CGH+FH+ CID+WL
Sbjct:    86 GLSKDIREMLPVVIY-KESF-IVKDSQCSVCLGDYQAEEKLQQMPSCGHTFHMECIDLWL 143

Query:   122 RKKTTCPVCRLPL--QDPLGRKHAREATFSMAQAVDSPETSINHSRQWLLTHLGHPE 176
                TTCP+CRL L  +  L   H      S  +  +  E S     Q     + H +
Sbjct:   144 TSHTTCPLCRLSLIPKPSLDLSHQSTEIVSSIENSNGGEASTQPDSQSATEAISHTD 200

GO:0005634 "nucleus" evidence=ISM

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

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

 Score = 211 (79.3 bits), Expect = 7.7e-17, P = 7.7e-17
 Identities = 35/92 (38%), Positives = 61/92 (66%)

Query:    43 FEIESGIDLEQPAPGHRINGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVL 102
             F+  + + ++ P    R  GL P ++++I   +++++    VE  +CS+CL E++++E L
Sbjct:   172 FDGPAPVIVDHPIWHIRTIGLNPTVISSIKVCQYSKKD-GVVEGTDCSVCLSEFEEEETL 230

Query:   103 RIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL 134
             R++P+C H+FHL CID WLR  T CP+CR P+
Sbjct:   231 RLLPKCKHAFHLYCIDTWLRSHTNCPLCRAPI 262

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:2124700 AT4G10160 [Arabidopsis thaliana (taxid:3702)]

 Score = 206 (77.6 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 36/73 (49%), Positives = 52/73 (71%)

Query:    62 GLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWL 121
             GL   +   +P + + +E+F +V D +CS+CLG+YQ +E L+ MP CGH+FH+ CID+WL
Sbjct:    72 GLSKDIREMLPIVIY-KESF-TVNDTQCSVCLGDYQAEEKLQQMPSCGHTFHMECIDLWL 129

Query:   122 RKKTTCPVCRLPL 134
                TTCP+CRL L
Sbjct:   130 TSHTTCPLCRLSL 142

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

TAIR|locus:2007008 AT1G33480 [Arabidopsis thaliana (taxid:3702)]

 Score = 201 (75.8 bits), Expect = 3.7e-16, P = 3.7e-16
 Identities = 45/117 (38%), Positives = 70/117 (59%)

Query:    56 PGHRIN----GLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHS 111
             PG+ ++    GL   L   +P + F +E+F +V D++CS+CLG+YQ  + L+ +P C H+
Sbjct:    65 PGNSLSTIELGLSKELREMLPIVVF-KESF-TVMDSQCSVCLGDYQPNDKLQQIPVCKHT 122

Query:   112 FHLACIDIWLRKKTTCPVCRLPLQDPLGRKHAREATFSMA---QAVDS-PETS-INH 163
             FH+ CID+WL   TTCP+CRL L     R+   +   S+    + V S PE+  +NH
Sbjct:   123 FHMDCIDLWLTSHTTCPLCRLALIPSRSRQSQDDPVPSLVSPDEEVSSQPESEPVNH 179

GO:0005634 "nucleus" evidence=ISM

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

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

 Score = 201 (75.8 bits), Expect = 3.7e-16, P = 3.7e-16
 Identities = 36/87 (41%), Positives = 55/87 (63%)

Query:    47 SGIDLEQPAP--GHRINGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRI 104
             SG   + P P       GL+  ++ ++P + F+ E+ +S + AEC+ICL E+   + LR+
Sbjct:    67 SGSQTQSPQPPVAAANKGLKKKVLQSLPKLTFSPESPESEKFAECAICLAEFSAGDELRV 126

Query:   105 MPQCGHSFHLACIDIWLRKKTTCPVCR 131
             +PQCGH FH+ACID WL   ++CP CR
Sbjct:   127 LPQCGHGFHVACIDTWLGSHSSCPSCR 153

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

GO:0009507 "chloroplast" evidence=ISM

GO:0010200 "response to chitin" evidence=IEP

TAIR|locus:2081740 ATL5 "AtL5" [Arabidopsis thaliana (taxid:3702)]

 Score = 199 (75.1 bits), Expect = 6.0e-16, P = 6.0e-16
 Identities = 34/107 (31%), Positives = 63/107 (58%)

Query:    60 INGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDI 119
             ++ L+P ++  IP   ++ +  +S  + ECS+CL E+++ +  R++P+CGH FH+ CID 
Sbjct:    85 LSPLDPTVLEKIPIFVYSVKTHESPLE-ECSVCLSEFEEDDEGRVLPKCGHVFHVDCIDT 143

Query:   120 WLRKKTTCPVCRLPLQ--DPLGRKHAREATFSMAQAVDSPETSINHS 164
             W R +++CP+CR P+Q   P+       A F   + ++  E   + S
Sbjct:   144 WFRSRSSCPLCRAPVQPAQPVTEPEPVAAVFPSVKPIEDTEAGSSSS 190

GO:0005634 "nucleus" evidence=ISM

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

GO:0006461 "protein complex assembly" evidence=TAS

GO:0016020 "membrane" evidence=ISS

TAIR|locus:2089398 ATL2 "TOXICOS EN LEVADURA 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 198 (74.8 bits), Expect = 8.1e-16, P = 8.1e-16
 Identities = 42/123 (34%), Positives = 68/123 (55%)

Query:    62 GLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWL 121
             GL+P ++ ++P   F+ E  K  +  EC++CL E+++ E  R++P C H+FH+ CID+W 
Sbjct:    94 GLDPNVIKSLPVFTFSDETHK--DPIECAVCLSEFEESETGRVLPNCQHTFHVDCIDMWF 151

Query:   122 RKKTTCPVCRLPLQDPLGRKHAREATF-SMAQAVDS-PETSINHSRQWLLTHLGHPEVNG 179
                +TCP+CR  ++   G +    A    +  AVDS P   I  S    LT    P  +G
Sbjct:   152 HSHSTCPLCRSLVESLAGIESTAAAREREVVIAVDSDPVLVIEPSSSSGLTD--EPHGSG 209

Query:   180 NNQ 182
             ++Q
Sbjct:   210 SSQ 212

GO:0005634 "nucleus" evidence=ISM

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

GO:0006952 "defense response" evidence=IDA

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

GO:0000165 "MAPK cascade" evidence=RCA

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

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009595 "detection of biotic stimulus" evidence=RCA

GO:0009611 "response to wounding" evidence=RCA

GO:0009612 "response to mechanical stimulus" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

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

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=RCA

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

GO:0031348 "negative regulation of defense response" evidence=RCA

GO:0035556 "intracellular signal transduction" evidence=RCA

GO:0042742 "defense response to bacterium" evidence=RCA

GO:0043900 "regulation of multi-organism process" evidence=RCA

GO:0050832 "defense response to fungus" evidence=RCA

TAIR|locus:2018334 AT1G04360 [Arabidopsis thaliana (taxid:3702)]

 Score = 202 (76.2 bits), Expect = 9.3e-16, P = 9.3e-16
 Identities = 46/117 (39%), Positives = 64/117 (54%)

Query:    58 HRIN-GLEPVLVAAIPTMKFNQ------EAFKSVEDAECSICLGEYQDKEVLRIMPQCGH 110
             H +N GL+   + AIP  KF +      E  +S    ECS+CL E+Q+ E LRI+P C H
Sbjct:    96 HEVNRGLDESAIRAIPVFKFKKRDVVAGEEDQSKNSQECSVCLNEFQEDEKLRIIPNCCH 155

Query:   111 SFHLACIDIWLRKKTTCPVCRLPLQDPLGRKHAREATFSM--AQAVDSPETSINHSR 165
              FH+ CIDIWL+    CP+CR  +        + EA+F++    A  SP  +  HSR
Sbjct:   156 VFHIDCIDIWLQGNANCPLCRTSV--------SCEASFTLDLISAPSSPRENSPHSR 204

GO:0005634 "nucleus" evidence=ISM

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

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

 Score = 197 (74.4 bits), Expect = 9.8e-16, P = 9.8e-16
 Identities = 32/80 (40%), Positives = 53/80 (66%)

Query:    59 RINGLEPVLVAAIPTMKFNQEAFKSVEDAE-CSICLGEYQDKEVLRIMPQCGHSFHLACI 117
             R   L+  ++  IP   ++ +     E+ E CS+CL E+++++  R++P+CGHSFH+ CI
Sbjct:    77 RDQALDQAVLDKIPIFVYSSKNPPPPEEKEECSVCLSEFEEEDEGRLLPKCGHSFHVDCI 136

Query:   118 DIWLRKKTTCPVCRLPLQDP 137
             D W R ++TCP+CR P+Q P
Sbjct:   137 DTWFRSRSTCPLCRAPVQPP 156

GO:0005634 "nucleus" evidence=ISM

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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: GSVIVG00026250001 SubName- Full=Chromosome chr15 scaffold_37, whole genome shotgun sequence; (201 aa) (Vitis vinifera)

Predicted Functional Partners:

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

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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	191
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	3e-14
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	3e-13
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	8e-12
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	5e-10
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	7e-09
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	4e-08
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	6e-08
smart00184	40	smart00184, RING, Ring finger	1e-07
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	9e-06
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	2e-04
PHA02926	242	PHA02926, PHA02926, zinc finger-like protein; Prov	3e-04
COG5432	391	COG5432, RAD18, RING-finger-containing E3 ubiquiti	5e-04
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	6e-04
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	0.001
TIGR00599	397	TIGR00599, rad18, DNA repair protein rad18	0.002
pfam11793	70	pfam11793, FANCL_C, FANCL C-terminal domain	0.004

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

 Score = 63.6 bits (155), Expect = 3e-14
 Identities = 23/44 (52%), Positives = 30/44 (68%), Gaps = 1/44 (2%)

Query: 88  ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCR 131
           EC ICL E++  E + ++P CGH FH  C+D WLR   TCP+CR
Sbjct: 2   ECPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLCR 44

Length = 46

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

 Score = 65.2 bits (159), Expect = 3e-13
 Identities = 25/60 (41%), Positives = 37/60 (61%), Gaps = 4/60 (6%)

Query: 78  QEAFKSVEDAECSICLGEYQDKEV----LRIMPQCGHSFHLACIDIWLRKKTTCPVCRLP 133
           ++ +   +D EC+IC+ +  DKE+      I+  C H F + CIDIW ++K TCPVCR P
Sbjct: 166 EKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTP 225

Length = 238

>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 = 57.1 bits (138), Expect = 8e-12
 Identities = 22/48 (45%), Positives = 31/48 (64%), Gaps = 4/48 (8%)

Query: 88  ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPL 134
           EC ICL E+++     ++  CGH F  +CID WL+  K TCP+CR P+
Sbjct: 1   ECPICLEEFREP---VVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 53.2 bits (128), Expect = 5e-10
 Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 9/58 (15%)

Query: 83  SVEDAECSICLGEYQDKEVLRIMP---------QCGHSFHLACIDIWLRKKTTCPVCR 131
            +ED  C+IC   +         P         +CGH+FHL CI  WL+ + TCP+CR
Sbjct: 16  DIEDDVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73

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

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

 Score = 49.4 bits (118), Expect = 7e-09
 Identities = 22/47 (46%), Positives = 28/47 (59%), Gaps = 3/47 (6%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCR 131
           E+ EC ICL   +D  VL     CGH F   CI  +L+KK+ CP+CR
Sbjct: 1   EELECPICLDLLRDPVVL---TPCGHVFCRECILRYLKKKSKCPICR 44

Length = 45

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

 Score = 51.9 bits (124), Expect = 4e-08
 Identities = 32/119 (26%), Positives = 48/119 (40%), Gaps = 25/119 (21%)

Query: 21  FIVFICTRIICRRIRGVESRPMFEIESGIDLEQPAPGHRING-LEPVLVAAIPTMKFNQE 79
           F + +  +I             F         +  P     G L+P+ +          E
Sbjct: 279 FNIILEIQIN--------FDVGFYSS-----SEAIPTTTTKGSLKPLSIERA------VE 319

Query: 80  AFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK-KTTCPVCRLPLQDP 137
           A K VE   C+IC+  +   + LR++P C H FH+ C+D WL      CPVCR  +  P
Sbjct: 320 ADKGVE---CAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPPP 374

Length = 374

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

 Score = 51.1 bits (122), Expect = 6e-08
 Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 9/58 (15%)

Query: 86  DAECSICLGEY------QDKEVLRIMPQ---CGHSFHLACIDIWLRKKTTCPVCRLPL 134
           D  C+IC+ E            L + P+   CGH  HL C+  WL ++ TCP+CR P+
Sbjct: 287 DRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPV 344

Length = 491

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

 Score = 45.6 bits (108), Expect = 1e-07
 Identities = 20/43 (46%), Positives = 24/43 (55%), Gaps = 4/43 (9%)

Query: 89  CSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT-TCPVC 130
           C ICL EY       I+P CGH+F  +CI  WL     TCP+C
Sbjct: 1   CPICLEEYLKD--PVILP-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|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger)

 Score = 40.9 bits (96), Expect = 9e-06
 Identities = 20/43 (46%), Positives = 24/43 (55%), Gaps = 4/43 (9%)

Query: 89  CSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVC 130
           C ICL E   K+ + I+P CGH F   CI  WL     TCP+C
Sbjct: 1   CPICLEEP--KDPVTILP-CGHLFCSKCILSWLESGNVTCPLC 40

The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway. Length = 40

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

 Score = 40.8 bits (95), Expect = 2e-04
 Identities = 17/58 (29%), Positives = 24/58 (41%), Gaps = 7/58 (12%)

Query: 79   EAFKSVEDAECSIC---LGEYQDKEVLRIMPQCGHSFHLACIDIWLRK--KTTCPVCR 131
            E F   E  EC+IC   L         +    C + FH  C+  W     ++ CP+CR
Sbjct: 1464 EKFSGHE--ECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCR 1519

Length = 1525

>gnl|CDD|165237 PHA02926, PHA02926, zinc finger-like protein; Provisional

 Score = 40.0 bits (93), Expect = 3e-04
 Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 11/65 (16%)

Query: 78  QEAFKSVEDAECSICL-----GEYQDKEVLRIMPQCGHSFHLACIDIWLRKK------TT 126
           ++ ++  ++ EC IC         ++     ++  C H F + CI+IW R +        
Sbjct: 162 EDVYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDN 221

Query: 127 CPVCR 131
           CP+CR
Sbjct: 222 CPICR 226

Length = 242

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

 Score = 39.7 bits (92), Expect = 5e-04
 Identities = 16/53 (30%), Positives = 21/53 (39%), Gaps = 4/53 (7%)

Query: 89  CSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPLGRK 141
           C IC      +  +     CGH+F   CI   L  +  CPVCR    +   R 
Sbjct: 28  CRIC----DCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCESRLRG 76

Length = 391

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

 Score = 37.1 bits (86), Expect = 6e-04
 Identities = 12/28 (42%), Positives = 14/28 (50%)

Query: 108 CGHSFHLACIDIWLRKKTTCPVCRLPLQ 135
           C H+FH  CI  WL  K  CP+ R    
Sbjct: 54  CNHAFHDHCIYRWLDTKGVCPLDRQTWV 81

Length = 88

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

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 13/28 (46%), Positives = 19/28 (67%), Gaps = 3/28 (10%)

Query: 107 QCGHSFHLACIDIWLRKKTT---CPVCR 131
           +C H+FH+ CI  WL  +T+   CP+CR
Sbjct: 51  KCKHNFHMHCILKWLATETSKGLCPMCR 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

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

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 4/53 (7%)

Query: 89  CSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPLGRK 141
           C IC  ++ D  VL     C H+F   CI   L  +  CP+CR   Q+   R 
Sbjct: 29  CHIC-KDFFDVPVL---TSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRS 77

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

>gnl|CDD|204746 pfam11793, FANCL_C, FANCL C-terminal domain

 Score = 34.3 bits (79), Expect = 0.004
 Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 15/63 (23%)

Query: 88  ECSICLGEYQDKEVLRIM----PQCGHSFHLACIDIWLRKKT-----------TCPVCRL 132
           EC IC     D   +  +    P+CG  FH+AC+  WLR              TCP C+ 
Sbjct: 4   ECGICYAYRLDGGEIPDISCDNPKCGLPFHIACLYEWLRTLRDSRQSFNVSFGTCPYCKA 63

Query: 133 PLQ 135
            + 
Sbjct: 64  KIS 66

This domain is found at the C-terminus of the Fancl protein in humans which is the putative E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2. Length = 70

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	191
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.79
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.51
PHA02929	238	N1R/p28-like protein; Provisional	99.38
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.29
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.26
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.25
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.19
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.16
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.13
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.11
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.09
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.04
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.02
PHA02926	242	zinc finger-like protein; Provisional	99.0
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.92
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.92
PF14634	44	zf-RING_5: zinc-RING finger domain	98.85
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.83
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.82
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.79
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.77
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.68
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.59
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.59
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.55
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.5
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.49
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.48
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.34
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.33
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.33
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.31
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.24
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.23
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.21
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.18
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.11
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.11
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.11
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.08
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.07
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.05
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.04
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.99
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.97
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.93
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.88
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.68
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.61
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.57
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.51
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.47
KOG2660	331	consensus Locus-specific chromosome binding protei	97.43
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.34
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	97.33
COG5152	259	Uncharacterized conserved protein, contains RING a	97.29
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.28
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.27
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.08
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.08
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.0
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.97
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.87
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	96.8
KOG3039	303	consensus Uncharacterized conserved protein [Funct	96.78
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.69
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.46
PF04641	260	Rtf2: Rtf2 RING-finger	96.43
PHA02862	156	5L protein; Provisional	96.37
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.34
PHA02825	162	LAP/PHD finger-like protein; Provisional	96.29
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	96.29
COG5236	493	Uncharacterized conserved protein, contains RING Z	96.26
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	96.24
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.0
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	95.9
KOG4739	233	consensus Uncharacterized protein involved in syna	95.9
PHA03096	284	p28-like protein; Provisional	95.86
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.66
COG5222	427	Uncharacterized conserved protein, contains RING Z	95.59
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	95.56
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	95.43
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	95.38
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	95.02
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	95.0
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	94.93
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	94.42
KOG1001	674	consensus Helicase-like transcription factor HLTF/	94.28
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	94.27
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	94.16
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	94.06
KOG1940	276	consensus Zn-finger protein [General function pred	93.85
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	93.84
PF02439	38	Adeno_E3_CR2: Adenovirus E3 region protein CR2; In	93.41
PF05393	94	Hum_adeno_E3A: Human adenovirus early E3A glycopro	93.15
KOG3002	299	consensus Zn finger protein [General function pred	93.11
COG5175	480	MOT2 Transcriptional repressor [Transcription]	92.78
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	92.74
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	92.52
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	92.35
KOG0298	1394	consensus DEAD box-containing helicase-like transc	92.31
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	92.08
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	92.02
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	91.52
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	90.21
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	90.15
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	89.88
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	89.42
KOG4367	699	consensus Predicted Zn-finger protein [Function un	89.29
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	89.04
KOG3113	293	consensus Uncharacterized conserved protein [Funct	88.69
KOG3053	293	consensus Uncharacterized conserved protein [Funct	88.62
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	88.6
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	88.48
PF01102	122	Glycophorin_A: Glycophorin A; InterPro: IPR001195	88.1
KOG3899	381	consensus Uncharacterized conserved protein [Funct	87.87
PF06024	101	DUF912: Nucleopolyhedrovirus protein of unknown fu	84.71
PF02439	38	Adeno_E3_CR2: Adenovirus E3 region protein CR2; In	83.52
PF00558	81	Vpu: Vpu protein; InterPro: IPR008187 The Human im	83.24
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	82.35
KOG0825	1134	consensus PHD Zn-finger protein [General function	81.22
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	81.03

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

Probab=99.79  E-value=3.6e-19  Score=144.36  Aligned_cols=87  Identities=36%  Similarity=0.767  Sum_probs=73.3

Q ss_pred             CCCCCHHHHhhCCCccccccccCCCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCc-cccccccccCCC
Q 029544           60 INGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTT-CPVCRLPLQDPL  138 (191)
Q Consensus        60 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~-CP~Cr~~~~~~~  138 (191)
                      ...+.+..++.+|..++......... ..|+||+|+|..++.++.|| |+|.||..||++||.++.+ ||+||.++....
T Consensus       204 ~~r~~k~~l~~~p~~~f~~~~~~~~~-~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~  281 (348)
T KOG4628|consen  204 RNRLIKRLLKKLPVRTFTKGDDEDAT-DTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDS  281 (348)
T ss_pred             hhhhHHHHHhhCCcEEeccccccCCC-ceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCCCCC
Confidence            35677888999999999876655544 78999999999999999998 9999999999999998865 999999998887


Q ss_pred             CCCCcccccc
Q 029544          139 GRKHAREATF  148 (191)
Q Consensus       139 ~~~~~~~~~~  148 (191)
                      +.....+.+.
T Consensus       282 ~~~~~~e~tp  291 (348)
T KOG4628|consen  282 GSEPVSEDTP  291 (348)
T ss_pred             CCCCccCCCc
Confidence            7766555333

>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=99.51  E-value=5.2e-15  Score=86.40  Aligned_cols=43  Identities=53%  Similarity=1.328  Sum_probs=39.4

Q ss_pred             cCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCcccccc
Q 029544           88 ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCR  131 (191)
Q Consensus        88 ~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr  131 (191)
                      +|+||++.+.....+..++ |+|.||.+|+.+|+..+.+||+||
T Consensus         2 ~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    2 ECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHhCCcCCccC
Confidence            6999999999888888887 999999999999999989999997

...

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.38  E-value=4e-13  Score=104.80  Aligned_cols=77  Identities=36%  Similarity=0.816  Sum_probs=57.1

Q ss_pred             CCCCCHHHHhhCCCccccccc-cCCCCCCcCcccccccccCcc----EEEcCCCCCcccHhhHHHHhcCCCccccccccc
Q 029544           60 INGLEPVLVAAIPTMKFNQEA-FKSVEDAECSICLGEYQDKEV----LRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL  134 (191)
Q Consensus        60 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~C~IC~~~~~~~~~----~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~  134 (191)
                      ..+..+..+..+|.....-+. .....+.+|+||++.+.++..    ...+++|+|.||..||.+|+..+.+||+||..+
T Consensus       147 k~~~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~  226 (238)
T PHA02929        147 KGKNYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPF  226 (238)
T ss_pred             hcchhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEe
Confidence            345567778888877544222 233456789999998776431    234557999999999999999999999999987


Q ss_pred             cC
Q 029544          135 QD  136 (191)
Q Consensus       135 ~~  136 (191)
                      ..
T Consensus       227 ~~  228 (238)
T PHA02929        227 IS  228 (238)
T ss_pred             eE
Confidence            64

>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=2.5e-12  Score=83.10  Aligned_cols=45  Identities=42%  Similarity=1.037  Sum_probs=35.1

Q ss_pred             CCcCcccccccccC----------ccEEEcCCCCCcccHhhHHHHhcCCCcccccc
Q 029544           86 DAECSICLGEYQDK----------EVLRIMPQCGHSFHLACIDIWLRKKTTCPVCR  131 (191)
Q Consensus        86 ~~~C~IC~~~~~~~----------~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr  131 (191)
                      +..|+||++.+.++          ..+... .|+|.||..||.+|+..+.+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~-~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWG-PCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEE-TTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEec-ccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            44599999999432          233334 5999999999999999999999997

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 ....

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

Probab=99.26  E-value=5.2e-12  Score=99.31  Aligned_cols=53  Identities=32%  Similarity=0.745  Sum_probs=46.7

Q ss_pred             CCCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCCC
Q 029544           82 KSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPL  138 (191)
Q Consensus        82 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~~  138 (191)
                      ..+....|.+|++...++..+    +|||+||+.||..|...+..||+||..+...+
T Consensus       235 i~~a~~kC~LCLe~~~~pSaT----pCGHiFCWsCI~~w~~ek~eCPlCR~~~~psk  287 (293)
T KOG0317|consen  235 IPEATRKCSLCLENRSNPSAT----PCGHIFCWSCILEWCSEKAECPLCREKFQPSK  287 (293)
T ss_pred             CCCCCCceEEEecCCCCCCcC----cCcchHHHHHHHHHHccccCCCcccccCCCcc
Confidence            345677899999999999888    89999999999999999889999999887543

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.25  E-value=8.9e-12  Score=93.66  Aligned_cols=54  Identities=35%  Similarity=0.772  Sum_probs=43.5

Q ss_pred             CCCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC----------------CCccccccccccCCCC
Q 029544           82 KSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK----------------KTTCPVCRLPLQDPLG  139 (191)
Q Consensus        82 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~----------------~~~CP~Cr~~~~~~~~  139 (191)
                      +..++.+|+||++.+.++..+    .|||.||..||..|+..                ...||+||..+....-
T Consensus        14 ~~~~~~~CpICld~~~dPVvT----~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~L   83 (193)
T PLN03208         14 DSGGDFDCNICLDQVRDPVVT----LCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATL   83 (193)
T ss_pred             cCCCccCCccCCCcCCCcEEc----CCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcE
Confidence            334578899999999888665    69999999999999852                2469999999976543

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

Probab=99.19  E-value=4.9e-11  Score=96.69  Aligned_cols=52  Identities=38%  Similarity=1.060  Sum_probs=42.0

Q ss_pred             CCCCCcCcccccc-cccC---------ccEEEcCCCCCcccHhhHHHHhcCCCcccccccccc
Q 029544           83 SVEDAECSICLGE-YQDK---------EVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ  135 (191)
Q Consensus        83 ~~~~~~C~IC~~~-~~~~---------~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~  135 (191)
                      ...|..|.||+++ +..+         ....++| |||++|.+|++.|++++.+||.||.++.
T Consensus       284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~i  345 (491)
T COG5243         284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPVI  345 (491)
T ss_pred             cCCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCccc
Confidence            4567889999999 4433         1223565 9999999999999999999999999954

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

Probab=99.16  E-value=1.7e-11  Score=96.94  Aligned_cols=50  Identities=40%  Similarity=1.115  Sum_probs=44.7

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-CCCccccccccccC
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQD  136 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-~~~~CP~Cr~~~~~  136 (191)
                      .-+|+||+++|...++++.+| |.|.||..|+++|+. -+..||+||.+++.
T Consensus       323 GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         323 GVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            467999999999888999997 999999999999998 55679999998864

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

Probab=99.13  E-value=1e-10  Score=89.54  Aligned_cols=54  Identities=31%  Similarity=0.656  Sum_probs=45.8

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC---CCccccccccccCCCCC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK---KTTCPVCRLPLQDPLGR  140 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~---~~~CP~Cr~~~~~~~~~  140 (191)
                      ....++|.|||+.-++++.+    .|||.||+-||-+|+..   .+.||+||..+...+-.
T Consensus        44 ~~~~FdCNICLd~akdPVvT----lCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vv  100 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDPVVT----LCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVV  100 (230)
T ss_pred             CCCceeeeeeccccCCCEEe----ecccceehHHHHHHHhhcCCCeeCCccccccccceEE
Confidence            45678999999999999888    79999999999999983   34599999998876543

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

Probab=99.11  E-value=3.8e-11  Score=88.24  Aligned_cols=55  Identities=29%  Similarity=0.702  Sum_probs=45.1

Q ss_pred             cCCCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           81 FKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        81 ~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      ...+....|+|||+.+.....+.  .+|||+||+.||+..++....||+|++.+...
T Consensus       126 ~~~~~~~~CPiCl~~~sek~~vs--TkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k  180 (187)
T KOG0320|consen  126 LRKEGTYKCPICLDSVSEKVPVS--TKCGHVFCSQCIKDALKNTNKCPTCRKKITHK  180 (187)
T ss_pred             cccccccCCCceecchhhccccc--cccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence            34456688999999998776431  27999999999999999999999999877643

>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A

Probab=99.09  E-value=5e-11  Score=71.34  Aligned_cols=46  Identities=41%  Similarity=1.012  Sum_probs=37.7

Q ss_pred             CCcCcccccccccCccEEEcCCCCCc-ccHhhHHHHhcCCCcccccccccc
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHS-FHLACIDIWLRKKTTCPVCRLPLQ  135 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~-f~~~Ci~~wl~~~~~CP~Cr~~~~  135 (191)
                      +..|.||++...+....    +|||. ||..|+..|+.....||+||.++.
T Consensus         2 ~~~C~iC~~~~~~~~~~----pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRDVVLL----PCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSSEEEE----TTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCceEEe----CCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            46799999987764444    69999 999999999999999999999875

...

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

Probab=99.04  E-value=8e-11  Score=66.72  Aligned_cols=39  Identities=51%  Similarity=1.171  Sum_probs=31.7

Q ss_pred             CcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccc
Q 029544           89 CSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVC  130 (191)
Q Consensus        89 C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~C  130 (191)
                      |+||++.+.++..  .+ +|||.||..|+.+|+..+..||+|
T Consensus         1 C~iC~~~~~~~~~--~~-~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRDPVV--VT-PCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SSEEE--EC-TTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccCcCE--EC-CCCCchhHHHHHHHHHCcCCCcCC
Confidence            7899999988532  23 699999999999999998889987

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

Probab=99.02  E-value=1.4e-10  Score=66.71  Aligned_cols=38  Identities=39%  Similarity=1.014  Sum_probs=30.2

Q ss_pred             CcccccccccCccEEEcCCCCCcccHhhHHHHhcCC----Cccccc
Q 029544           89 CSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK----TTCPVC  130 (191)
Q Consensus        89 C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~----~~CP~C  130 (191)
                      |+||++.|.++..+    +|||.||..||..|+...    ..||.|
T Consensus         1 CpiC~~~~~~Pv~l----~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDPVSL----PCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSEEE-----SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCcccc----CCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999999988    899999999999999843    359987

>PHA02926 zinc finger-like protein; Provisional

Probab=99.00  E-value=2.1e-10  Score=87.39  Aligned_cols=56  Identities=30%  Similarity=0.864  Sum_probs=42.1

Q ss_pred             CCCCCCcCcccccccccC-----ccEEEcCCCCCcccHhhHHHHhcCC------CccccccccccCC
Q 029544           82 KSVEDAECSICLGEYQDK-----EVLRIMPQCGHSFHLACIDIWLRKK------TTCPVCRLPLQDP  137 (191)
Q Consensus        82 ~~~~~~~C~IC~~~~~~~-----~~~~~~~~C~H~f~~~Ci~~wl~~~------~~CP~Cr~~~~~~  137 (191)
                      ....+.+|+||++....+     .....+++|+|.||..||..|...+      .+||+||..+...
T Consensus       166 ~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I  232 (242)
T PHA02926        166 RVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNI  232 (242)
T ss_pred             hccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeee
Confidence            345667899999986432     2334566899999999999998742      3599999887643

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

Probab=98.92  E-value=6.2e-10  Score=72.76  Aligned_cols=50  Identities=38%  Similarity=0.907  Sum_probs=38.0

Q ss_pred             CCCcCcccccccccCc----------cEEEcCCCCCcccHhhHHHHhcC---CCcccccccccc
Q 029544           85 EDAECSICLGEYQDKE----------VLRIMPQCGHSFHLACIDIWLRK---KTTCPVCRLPLQ  135 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~----------~~~~~~~C~H~f~~~Ci~~wl~~---~~~CP~Cr~~~~  135 (191)
                      ++..|.||+..|...-          .+ ....|+|.||.+||.+|+..   +..||+||+++.
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cpl-v~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~   82 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPL-VWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK   82 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCce-eeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence            4678999998887321          22 22369999999999999985   356999999875

>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=7.6e-10  Score=63.99  Aligned_cols=44  Identities=55%  Similarity=1.315  Sum_probs=35.2

Q ss_pred             cCcccccccccCccEEEcCCCCCcccHhhHHHHhcC-CCccccccccc
Q 029544           88 ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK-KTTCPVCRLPL  134 (191)
Q Consensus        88 ~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~-~~~CP~Cr~~~  134 (191)
                      .|+||++.+.....+  . +|+|.||..|+..|+.. ...||+|+..+
T Consensus         1 ~C~iC~~~~~~~~~~--~-~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFREPVVL--L-PCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhCceEe--c-CCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            499999998443333  3 49999999999999986 66799999754

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.85  E-value=2.4e-09  Score=62.21  Aligned_cols=44  Identities=34%  Similarity=0.902  Sum_probs=35.8

Q ss_pred             cCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccc
Q 029544           88 ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRL  132 (191)
Q Consensus        88 ~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~  132 (191)
                      .|++|++.|........+ +|||+||..|+..+......||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~-~CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLT-SCGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEc-ccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            499999999555555556 49999999999999856667999984

>smart00504 Ubox Modified RING finger domain

Probab=98.83  E-value=2.5e-09  Score=66.88  Aligned_cols=46  Identities=30%  Similarity=0.541  Sum_probs=40.6

Q ss_pred             CcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccC
Q 029544           87 AECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        87 ~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      ..|+||.+.+.++..+    +|||+|+..||.+|+..+..||+|+.++..
T Consensus         2 ~~Cpi~~~~~~~Pv~~----~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~   47 (63)
T smart00504        2 FLCPISLEVMKDPVIL----PSGQTYERRAIEKWLLSHGTDPVTGQPLTH   47 (63)
T ss_pred             cCCcCCCCcCCCCEEC----CCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence            4699999999998555    699999999999999988889999988753

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

>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=98.82  E-value=1.6e-09  Score=61.99  Aligned_cols=39  Identities=41%  Similarity=1.140  Sum_probs=32.9

Q ss_pred             CcccccccccCccEEEcCCCCCcccHhhHHHHhc--CCCccccc
Q 029544           89 CSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR--KKTTCPVC  130 (191)
Q Consensus        89 C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~--~~~~CP~C  130 (191)
                      |+||++.+..+.  ..+ +|+|.||..|+.+|+.  ....||+|
T Consensus         1 C~iC~~~~~~~~--~~~-~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPV--ILL-PCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEE--EET-TTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCCC--EEe-cCCCcchHHHHHHHHHhcCCccCCcC
Confidence            789999998887  233 6999999999999998  55569987

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

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

Probab=98.79  E-value=4.1e-09  Score=92.42  Aligned_cols=53  Identities=38%  Similarity=0.876  Sum_probs=43.2

Q ss_pred             CCCCcCcccccccccCcc--EEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           84 VEDAECSICLGEYQDKEV--LRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~--~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      ..+..|+||++.+..+..  ..++ +|+|+||..|+..|+++..+||+||..+...
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL-~C~Hifh~~CL~~W~er~qtCP~CR~~~~~~  343 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRL-PCGHIFHDSCLRSWFERQQTCPTCRTVLYDY  343 (543)
T ss_pred             hcCCeeeeechhhcccccccccee-ecccchHHHHHHHHHHHhCcCCcchhhhhcc
Confidence            447789999999988532  3344 5999999999999999999999999955443

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.77  E-value=4.5e-09  Score=87.81  Aligned_cols=51  Identities=27%  Similarity=0.614  Sum_probs=44.3

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      ......|+||++.|..+..+    +|+|.||..|+..|+.....||+|+..+...
T Consensus        23 Le~~l~C~IC~d~~~~Pvit----pCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~   73 (397)
T TIGR00599        23 LDTSLRCHICKDFFDVPVLT----SCSHTFCSLCIRRCLSNQPKCPLCRAEDQES   73 (397)
T ss_pred             cccccCCCcCchhhhCccCC----CCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence            34567899999999988765    6999999999999999888899999988753

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

>smart00184 RING Ring finger

Probab=98.68  E-value=1.3e-08  Score=56.66  Aligned_cols=38  Identities=53%  Similarity=1.276  Sum_probs=30.5

Q ss_pred             CcccccccccCccEEEcCCCCCcccHhhHHHHhc-CCCccccc
Q 029544           89 CSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVC  130 (191)
Q Consensus        89 C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-~~~~CP~C  130 (191)
                      |+||++.......+    +|+|.||..|++.|+. ....||+|
T Consensus         1 C~iC~~~~~~~~~~----~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELKDPVVL----PCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCCCcEEe----cCCChHHHHHHHHHHHhCcCCCCCC
Confidence            78999885444344    5999999999999998 55669987

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)

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

Probab=98.59  E-value=1.2e-08  Score=82.17  Aligned_cols=51  Identities=25%  Similarity=0.622  Sum_probs=46.0

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCCCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPLG  139 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~~~  139 (191)
                      .-..|.||.+.|..+..+    +|+|.||..||+.+|..+..||.|+.++.+..-
T Consensus        22 ~lLRC~IC~eyf~ip~it----pCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~L   72 (442)
T KOG0287|consen   22 DLLRCGICFEYFNIPMIT----PCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDL   72 (442)
T ss_pred             HHHHHhHHHHHhcCceec----cccchHHHHHHHHHhccCCCCCceecccchhhh
Confidence            456799999999999888    799999999999999999999999999987644

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

Probab=98.59  E-value=2e-08  Score=78.33  Aligned_cols=50  Identities=38%  Similarity=0.868  Sum_probs=42.4

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHH-HhcCCCc-cccccccccCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDI-WLRKKTT-CPVCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~-wl~~~~~-CP~Cr~~~~~~  137 (191)
                      ..+..|+||++....+..+    +|||+||..||.. |-.++.. ||+||+.....
T Consensus       213 ~~d~kC~lC~e~~~~ps~t----~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk  264 (271)
T COG5574         213 LADYKCFLCLEEPEVPSCT----PCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPK  264 (271)
T ss_pred             ccccceeeeecccCCcccc----cccchhhHHHHHHHHHhhccccCchhhhhccch
Confidence            3478899999999988888    7999999999999 8766665 99999876543

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

Probab=98.55  E-value=3.7e-08  Score=83.29  Aligned_cols=47  Identities=32%  Similarity=0.678  Sum_probs=40.6

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC-----CCccccccccccC
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK-----KTTCPVCRLPLQD  136 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~-----~~~CP~Cr~~~~~  136 (191)
                      +..|+||++....+..+    .|||+||..||.+++..     ...||+|+..+..
T Consensus       186 ~~~CPICL~~~~~p~~t----~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~  237 (513)
T KOG2164|consen  186 DMQCPICLEPPSVPVRT----NCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL  237 (513)
T ss_pred             CCcCCcccCCCCccccc----ccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence            67899999998888877    79999999999998863     3459999998876

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

Probab=98.50  E-value=7.3e-08  Score=61.55  Aligned_cols=30  Identities=40%  Similarity=0.786  Sum_probs=27.7

Q ss_pred             CCCCcccHhhHHHHhcCCCccccccccccC
Q 029544          107 QCGHSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus       107 ~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      .|+|.||.+||.+||..+..||++|+++.-
T Consensus        53 ~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~   82 (88)
T COG5194          53 VCNHAFHDHCIYRWLDTKGVCPLDRQTWVL   82 (88)
T ss_pred             ecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence            599999999999999999999999998754

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

Probab=98.49  E-value=3.2e-08  Score=78.20  Aligned_cols=52  Identities=29%  Similarity=0.469  Sum_probs=45.6

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCCCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPLG  139 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~~~  139 (191)
                      ..-..|-||-+.+..+..+    .|||.||..||+..|..+..||+||.+..+...
T Consensus        23 Ds~lrC~IC~~~i~ip~~T----tCgHtFCslCIR~hL~~qp~CP~Cr~~~~esrl   74 (391)
T COG5432          23 DSMLRCRICDCRISIPCET----TCGHTFCSLCIRRHLGTQPFCPVCREDPCESRL   74 (391)
T ss_pred             hhHHHhhhhhheeecceec----ccccchhHHHHHHHhcCCCCCccccccHHhhhc
Confidence            3456799999999998888    799999999999999999999999998876543

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

Probab=98.48  E-value=3e-08  Score=62.77  Aligned_cols=50  Identities=36%  Similarity=0.784  Sum_probs=36.4

Q ss_pred             CCCcCcccccccccCc----------cEEEcCCCCCcccHhhHHHHhcC---CCcccccccccc
Q 029544           85 EDAECSICLGEYQDKE----------VLRIMPQCGHSFHLACIDIWLRK---KTTCPVCRLPLQ  135 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~----------~~~~~~~C~H~f~~~Ci~~wl~~---~~~CP~Cr~~~~  135 (191)
                      .+..|.||.-.|...-          .+ +...|.|.||..||.+|+..   +..||+||+.+.
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPL-v~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGDDCPL-VWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCCCCcc-HHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            4457999988876321          22 22259999999999999973   345999998774

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

Probab=98.34  E-value=2.9e-07  Score=59.36  Aligned_cols=49  Identities=29%  Similarity=0.571  Sum_probs=39.1

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC-CCccccccccccCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK-KTTCPVCRLPLQDP  137 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~-~~~CP~Cr~~~~~~  137 (191)
                      +.+.|+|+.+.+.++..+    ++||.|...||..|+.. +..||+|+.++...
T Consensus         3 ~~f~CpIt~~lM~dPVi~----~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~   52 (73)
T PF04564_consen    3 DEFLCPITGELMRDPVIL----PSGHTYERSAIERWLEQNGGTDPFTRQPLSES   52 (73)
T ss_dssp             GGGB-TTTSSB-SSEEEE----TTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred             cccCCcCcCcHhhCceeC----CcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence            356899999999999888    79999999999999998 88899999888753

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 ....

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

Probab=98.33  E-value=3.5e-07  Score=52.56  Aligned_cols=33  Identities=33%  Similarity=0.857  Sum_probs=20.1

Q ss_pred             CcccccccccCc-cEEEcCCCCCcccHhhHHHHhcC
Q 029544           89 CSICLGEYQDKE-VLRIMPQCGHSFHLACIDIWLRK  123 (191)
Q Consensus        89 C~IC~~~~~~~~-~~~~~~~C~H~f~~~Ci~~wl~~  123 (191)
                      |+||.+ +.+.. .-.+|+ |||.||.+|+++++..
T Consensus         1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~   34 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKK   34 (43)
T ss_dssp             -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH
T ss_pred             CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhc
Confidence            899999 76533 334565 9999999999999873

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

Probab=98.33  E-value=1.4e-07  Score=73.86  Aligned_cols=51  Identities=31%  Similarity=0.661  Sum_probs=41.0

Q ss_pred             CCCcCcccccccccCc-------cEEEcCCCCCcccHhhHHHHhc--CCCccccccccccC
Q 029544           85 EDAECSICLGEYQDKE-------VLRIMPQCGHSFHLACIDIWLR--KKTTCPVCRLPLQD  136 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~-------~~~~~~~C~H~f~~~Ci~~wl~--~~~~CP~Cr~~~~~  136 (191)
                      ++..|+||-..+....       .+..+. |+|+||..||+-|..  ++.+||.|+..+..
T Consensus       223 ~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVdl  282 (328)
T KOG1734|consen  223 SDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVDL  282 (328)
T ss_pred             CcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhhH
Confidence            4667999998876554       555664 999999999999976  66789999987754

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.31  E-value=5.2e-07  Score=72.85  Aligned_cols=52  Identities=29%  Similarity=0.735  Sum_probs=37.9

Q ss_pred             CCcCcccccc-cccCc-cEEEcCCCCCcccHhhHHHHhc-CCCccccccccccCCC
Q 029544           86 DAECSICLGE-YQDKE-VLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQDPL  138 (191)
Q Consensus        86 ~~~C~IC~~~-~~~~~-~~~~~~~C~H~f~~~Ci~~wl~-~~~~CP~Cr~~~~~~~  138 (191)
                      +..|++|... +.++. .+.+. .|||.||..|+...+. ....||.|+.++....
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~   57 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFVRGSGSCPECDTPLRKNN   57 (309)
T ss_pred             CCCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence            4579999995 33333 33333 4999999999999765 4456999998887543

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).

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

Probab=98.24  E-value=3.4e-07  Score=77.09  Aligned_cols=51  Identities=33%  Similarity=0.815  Sum_probs=37.4

Q ss_pred             CCcCcccccccccCccE-------------EEcCCCCCcccHhhHHHHhc-CCCccccccccccC
Q 029544           86 DAECSICLGEYQDKEVL-------------RIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQD  136 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~-------------~~~~~C~H~f~~~Ci~~wl~-~~~~CP~Cr~~~~~  136 (191)
                      ...|+||+..+.--.+.             ..+.+|.|+||..|+.+|.. .+-.||+||.++..
T Consensus       571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            45699999876521100             12225999999999999998 44479999998853

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

Probab=98.23  E-value=3.3e-07  Score=56.54  Aligned_cols=47  Identities=32%  Similarity=0.665  Sum_probs=24.8

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      -..|++|.+.+.++..+.   .|.|+||..|+..-+.  ..||+|+.+....
T Consensus         7 lLrCs~C~~~l~~pv~l~---~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~q   53 (65)
T PF14835_consen    7 LLRCSICFDILKEPVCLG---GCEHIFCSSCIRDCIG--SECPVCHTPAWIQ   53 (65)
T ss_dssp             TTS-SSS-S--SS-B------SSS--B-TTTGGGGTT--TB-SSS--B-S-S
T ss_pred             hcCCcHHHHHhcCCceec---cCccHHHHHHhHHhcC--CCCCCcCChHHHH
Confidence            457999999999997665   7999999999988654  3499999876543

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

Probab=98.21  E-value=6.2e-07  Score=74.79  Aligned_cols=51  Identities=31%  Similarity=0.775  Sum_probs=40.1

Q ss_pred             CCCCCCcCcccccccccCc-cEEEcCCCCCcccHhhHHHHhcCCCcccccccccc
Q 029544           82 KSVEDAECSICLGEYQDKE-VLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ  135 (191)
Q Consensus        82 ~~~~~~~C~IC~~~~~~~~-~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~  135 (191)
                      ...+..+|+|||+.+.... .+... .|.|.||..|+..|.  ..+||+||.-..
T Consensus       171 ~~tELPTCpVCLERMD~s~~gi~t~-~c~Hsfh~~cl~~w~--~~scpvcR~~q~  222 (493)
T KOG0804|consen  171 GLTELPTCPVCLERMDSSTTGILTI-LCNHSFHCSCLMKWW--DSSCPVCRYCQS  222 (493)
T ss_pred             CcccCCCcchhHhhcCccccceeee-ecccccchHHHhhcc--cCcChhhhhhcC
Confidence            4456678999999998776 22333 599999999999995  467999997665

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

Probab=98.18  E-value=1.2e-06  Score=51.87  Aligned_cols=42  Identities=29%  Similarity=0.831  Sum_probs=30.6

Q ss_pred             cCcccccccccCccEEEcCCCC-----CcccHhhHHHHhcC--CCcccccc
Q 029544           88 ECSICLGEYQDKEVLRIMPQCG-----HSFHLACIDIWLRK--KTTCPVCR  131 (191)
Q Consensus        88 ~C~IC~~~~~~~~~~~~~~~C~-----H~f~~~Ci~~wl~~--~~~CP~Cr  131 (191)
                      .|.||++...+. .....| |.     |.+|..|+.+|+..  +..||+|+
T Consensus         1 ~CrIC~~~~~~~-~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEGDEG-DPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCCCCCC-CeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            389999833333 333565 85     88999999999964  44799995

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

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

Probab=98.11  E-value=1.3e-06  Score=71.10  Aligned_cols=53  Identities=34%  Similarity=0.731  Sum_probs=43.6

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCc-ccHhhHHHHhcCCCccccccccccCCCCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHS-FHLACIDIWLRKKTTCPVCRLPLQDPLGR  140 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~-f~~~Ci~~wl~~~~~CP~Cr~~~~~~~~~  140 (191)
                      ++..+|.||+.+..+...+    +|.|. .|..|.+..-.+++.||+||+++.+....
T Consensus       288 ~~gkeCVIClse~rdt~vL----PCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ll~i  341 (349)
T KOG4265|consen  288 ESGKECVICLSESRDTVVL----PCRHLCLCSGCAKSLRYQTNNCPICRQPIEELLEI  341 (349)
T ss_pred             cCCCeeEEEecCCcceEEe----cchhhehhHhHHHHHHHhhcCCCccccchHhhhee
Confidence            4467899999988776555    69996 89999999877889999999999876543

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

Probab=98.11  E-value=7.6e-07  Score=78.75  Aligned_cols=49  Identities=27%  Similarity=0.731  Sum_probs=42.8

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-CCCccccccccccCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQDP  137 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-~~~~CP~Cr~~~~~~  137 (191)
                      ....|+.|-..+.+...+    .|+|.||..|+...+. ++..||.|...|...
T Consensus       642 ~~LkCs~Cn~R~Kd~vI~----kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan  691 (698)
T KOG0978|consen  642 ELLKCSVCNTRWKDAVIT----KCGHVFCEECVQTRYETRQRKCPKCNAAFGAN  691 (698)
T ss_pred             hceeCCCccCchhhHHHH----hcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence            456799999999988877    8999999999999887 677899999998754

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

Probab=98.11  E-value=6.4e-07  Score=53.08  Aligned_cols=47  Identities=34%  Similarity=0.770  Sum_probs=37.5

Q ss_pred             CCcCcccccccccCccEEEcCCCCCc-ccHhhHHHHhc-CCCccccccccccC
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHS-FHLACIDIWLR-KKTTCPVCRLPLQD  136 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~-f~~~Ci~~wl~-~~~~CP~Cr~~~~~  136 (191)
                      +.+|.||++...+...-    -|||. .|..|-.+.++ .+..||+||+++..
T Consensus         7 ~dECTICye~pvdsVlY----tCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~d   55 (62)
T KOG4172|consen    7 SDECTICYEHPVDSVLY----TCGHMCMCYACGLRLKKALHGCCPICRAPIKD   55 (62)
T ss_pred             ccceeeeccCcchHHHH----HcchHHhHHHHHHHHHHccCCcCcchhhHHHH
Confidence            36899999987776655    69996 89999776665 67789999998753

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

Probab=98.08  E-value=1.3e-06  Score=58.67  Aligned_cols=29  Identities=34%  Similarity=0.950  Sum_probs=26.7

Q ss_pred             CCCCcccHhhHHHHhcCCCcccccccccc
Q 029544          107 QCGHSFHLACIDIWLRKKTTCPVCRLPLQ  135 (191)
Q Consensus       107 ~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~  135 (191)
                      .|+|.||..||.+||+....||+|.++..
T Consensus        80 ~CNHaFH~hCisrWlktr~vCPLdn~eW~  108 (114)
T KOG2930|consen   80 VCNHAFHFHCISRWLKTRNVCPLDNKEWV  108 (114)
T ss_pred             ecchHHHHHHHHHHHhhcCcCCCcCccee
Confidence            59999999999999999999999988754

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

Probab=98.07  E-value=1.6e-06  Score=69.85  Aligned_cols=46  Identities=37%  Similarity=0.839  Sum_probs=38.5

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccc
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRL  132 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~  132 (191)
                      ..+...|+||++.|..+..+    +|+|.||..|+..++.....||.||.
T Consensus        10 ~~~~~~C~iC~~~~~~p~~l----~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   10 LQEELTCPICLEYFREPVLL----PCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             ccccccChhhHHHhhcCccc----cccchHhHHHHHHhcCCCcCCcccCC
Confidence            34677899999999999333    59999999999999885556999993

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

Probab=98.05  E-value=1.4e-06  Score=78.55  Aligned_cols=53  Identities=25%  Similarity=0.669  Sum_probs=39.0

Q ss_pred             CCCCCcCccccccccc---CccEEEcCCCCCcccHhhHHHHhc--CCCcccccccccc
Q 029544           83 SVEDAECSICLGEYQD---KEVLRIMPQCGHSFHLACIDIWLR--KKTTCPVCRLPLQ  135 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~---~~~~~~~~~C~H~f~~~Ci~~wl~--~~~~CP~Cr~~~~  135 (191)
                      .+...+|+||+..+.-   ...-.+.+.|.|.||..|+-+|+.  .+++||+||..++
T Consensus      1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            3556789999987651   112233446999999999999998  4556999997764

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

Probab=98.04  E-value=1.3e-06  Score=55.87  Aligned_cols=50  Identities=36%  Similarity=0.923  Sum_probs=23.0

Q ss_pred             CCcCcccccccc-cCcc-EEEc--CCCCCcccHhhHHHHhcC---C--------Ccccccccccc
Q 029544           86 DAECSICLGEYQ-DKEV-LRIM--PQCGHSFHLACIDIWLRK---K--------TTCPVCRLPLQ  135 (191)
Q Consensus        86 ~~~C~IC~~~~~-~~~~-~~~~--~~C~H~f~~~Ci~~wl~~---~--------~~CP~Cr~~~~  135 (191)
                      +.+|.||+.... .+.. ....  +.|++.||..|+.+|+..   .        ..||.|+.++.
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            357999999865 2221 1222  369999999999999871   1        13999998875

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

Probab=97.99  E-value=6.4e-07  Score=72.71  Aligned_cols=51  Identities=31%  Similarity=0.612  Sum_probs=42.0

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-CCCccccccccccCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-~~~~CP~Cr~~~~~~  137 (191)
                      ..+..|+||++.++....+.   .|.|.||.+||..-+. .++.||.||+.+...
T Consensus        41 ~~~v~c~icl~llk~tmttk---eClhrfc~~ci~~a~r~gn~ecptcRk~l~Sk   92 (381)
T KOG0311|consen   41 DIQVICPICLSLLKKTMTTK---ECLHRFCFDCIWKALRSGNNECPTCRKKLVSK   92 (381)
T ss_pred             hhhhccHHHHHHHHhhcccH---HHHHHHHHHHHHHHHHhcCCCCchHHhhcccc
Confidence            34678999999998776654   7999999999988877 566799999988653

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

Probab=97.97  E-value=2.9e-06  Score=69.73  Aligned_cols=49  Identities=37%  Similarity=0.970  Sum_probs=35.9

Q ss_pred             CcCcccccccccCccEEEcCCCCCcccHhhHHHHhc---CCCcccccccccc
Q 029544           87 AECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR---KKTTCPVCRLPLQ  135 (191)
Q Consensus        87 ~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~---~~~~CP~Cr~~~~  135 (191)
                      -.|.||.+-+.....+.-...|||+||..|+.+|+.   .+..||.|+-.+.
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~   56 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQ   56 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeeccc
Confidence            369999666555555544435999999999999998   3357999994333

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

Probab=97.93  E-value=5e-06  Score=68.47  Aligned_cols=52  Identities=38%  Similarity=1.003  Sum_probs=40.7

Q ss_pred             CCCCcCcccccccccCc----cEEEcCCCCCcccHhhHHHHhc--C-----CCcccccccccc
Q 029544           84 VEDAECSICLGEYQDKE----VLRIMPQCGHSFHLACIDIWLR--K-----KTTCPVCRLPLQ  135 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~----~~~~~~~C~H~f~~~Ci~~wl~--~-----~~~CP~Cr~~~~  135 (191)
                      ..+..|.||++......    ...++|+|.|.||..||..|-.  +     .+.||.||....
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS  221 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence            45778999999876654    2345678999999999999973  3     467999997654

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

Probab=97.88  E-value=6.2e-06  Score=65.73  Aligned_cols=50  Identities=34%  Similarity=0.685  Sum_probs=40.2

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-CCCccccccccccCCCC
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQDPLG  139 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-~~~~CP~Cr~~~~~~~~  139 (191)
                      ..+|+||+....-+..+    .|+|.||..||+--.. ....|++||.++.+.-.
T Consensus         7 ~~eC~IC~nt~n~Pv~l----~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i~   57 (324)
T KOG0824|consen    7 KKECLICYNTGNCPVNL----YCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTID   57 (324)
T ss_pred             CCcceeeeccCCcCccc----cccchhhhhhhcchhhcCCCCCceecCCCCcchh
Confidence            44799999988877555    6999999999987665 44559999999986543

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

Probab=97.68  E-value=8.1e-06  Score=72.44  Aligned_cols=52  Identities=27%  Similarity=0.504  Sum_probs=42.4

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCCC
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPL  138 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~~  138 (191)
                      ...|++|+..+.+....... .|+|.||..|+..|-....+||+||..|....
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k-~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~  174 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEK-HTAHYFCEECVGSWSRCAQTCPVDRGEFGEVK  174 (1134)
T ss_pred             hhhhhHHHHHHHHHhhcccc-ccccccHHHHhhhhhhhcccCchhhhhhheee
Confidence            34588888887776555444 49999999999999999999999999887653

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

Probab=97.61  E-value=3.9e-05  Score=64.51  Aligned_cols=50  Identities=38%  Similarity=0.772  Sum_probs=44.5

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      ..++.|.||+..+..+..+    +|||.||..|+.+-+.....||.||..+.+.
T Consensus        82 ~sef~c~vc~~~l~~pv~t----pcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e~  131 (398)
T KOG4159|consen   82 RSEFECCVCSRALYPPVVT----PCGHSFCLECLDRSLDQETECPLCRDELVEL  131 (398)
T ss_pred             cchhhhhhhHhhcCCCccc----cccccccHHHHHHHhccCCCCcccccccccc
Confidence            5678899999999999888    7999999999999888777799999999864

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

Probab=97.57  E-value=3.9e-05  Score=46.88  Aligned_cols=42  Identities=29%  Similarity=0.670  Sum_probs=28.7

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc--CCCcccc
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR--KKTTCPV  129 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~--~~~~CP~  129 (191)
                      -...|+|.+..|.++....   .|+|.|-++.|.+|+.  ....||+
T Consensus        10 ~~~~CPiT~~~~~~PV~s~---~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFEDPVKSK---KCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SSEEEES---SS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhhCCcCcC---CCCCeecHHHHHHHHHhcCCCCCCC
Confidence            4567999999999987654   6999999999999994  3445998

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

Probab=97.51  E-value=3e-05  Score=61.87  Aligned_cols=54  Identities=28%  Similarity=0.733  Sum_probs=42.9

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-----------------------CCCccccccccccCCCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-----------------------KKTTCPVCRLPLQDPLG  139 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-----------------------~~~~CP~Cr~~~~~~~~  139 (191)
                      ....|+|||.-|.......+++ |.|.||..|+.++|.                       ....||+||..+.....
T Consensus       114 p~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~~  190 (368)
T KOG4445|consen  114 PNGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEEN  190 (368)
T ss_pred             CCCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccccc
Confidence            3567999999999998777776 999999999987764                       11249999998875443

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

Probab=97.47  E-value=6.7e-05  Score=62.23  Aligned_cols=49  Identities=41%  Similarity=0.897  Sum_probs=37.0

Q ss_pred             CCcCcccccccccCccEE-EcCCCCCcccHhhHHHHhcC--CCccccccccc
Q 029544           86 DAECSICLGEYQDKEVLR-IMPQCGHSFHLACIDIWLRK--KTTCPVCRLPL  134 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~-~~~~C~H~f~~~Ci~~wl~~--~~~CP~Cr~~~  134 (191)
                      ...|+||++.+..+...+ ..+.|||.|..+||+.|+.+  ...||.|...-
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka   55 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA   55 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence            457999999988665332 34469999999999999962  22499998643

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

Probab=97.43  E-value=2.4e-05  Score=63.26  Aligned_cols=51  Identities=25%  Similarity=0.668  Sum_probs=44.3

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      .....|.+|-..+.++..+.   .|-|.||+.||..++...+.||.|...+...
T Consensus        13 n~~itC~LC~GYliDATTI~---eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   13 NPHITCRLCGGYLIDATTIT---ECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             ccceehhhccceeecchhHH---HHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            34567999999999987775   7999999999999999999999999877654

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

Probab=97.34  E-value=0.00013  Score=61.73  Aligned_cols=54  Identities=31%  Similarity=0.633  Sum_probs=45.7

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCCCC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPLG  139 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~~~  139 (191)
                      ..++..|++|...+.++...  . .|||.||..|+..|+..+..||.|+..+.....
T Consensus        18 ~~~~l~C~~C~~vl~~p~~~--~-~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~   71 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDPVQT--T-TCGHRFCAGCLLESLSNHQKCPVCRQELTQAEE   71 (391)
T ss_pred             CcccccCccccccccCCCCC--C-CCCCcccccccchhhccCcCCcccccccchhhc
Confidence            35667899999999999874  1 699999999999999998899999887775543

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

Probab=97.33  E-value=0.00055  Score=55.42  Aligned_cols=48  Identities=29%  Similarity=0.593  Sum_probs=39.2

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL  134 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~  134 (191)
                      .....|++|+....++..+.   --|-+||+.|+..++..+..||+=..+.
T Consensus       298 ~~~~~CpvClk~r~Nptvl~---vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~  345 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPTVLE---VSGYVFCYPCIFSYVVNYGHCPVTGYPA  345 (357)
T ss_pred             CccccChhHHhccCCCceEE---ecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence            34557999999988887663   2689999999999999999999865544

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

Probab=97.29  E-value=9.2e-05  Score=55.79  Aligned_cols=46  Identities=33%  Similarity=0.619  Sum_probs=40.8

Q ss_pred             CcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccC
Q 029544           87 AECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        87 ~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      +.|.||-.+|..++.+    .|||.||..|...-+.....|-+|.+....
T Consensus       197 F~C~iCKkdy~spvvt----~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G  242 (259)
T COG5152         197 FLCGICKKDYESPVVT----ECGHSFCSLCAIRKYQKGDECGVCGKATYG  242 (259)
T ss_pred             eeehhchhhccchhhh----hcchhHHHHHHHHHhccCCcceecchhhcc
Confidence            4699999999999888    899999999999888888889999876543

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

Probab=97.28  E-value=0.00018  Score=56.79  Aligned_cols=49  Identities=29%  Similarity=0.623  Sum_probs=39.5

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc--CCCcccccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR--KKTTCPVCRLPLQ  135 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~--~~~~CP~Cr~~~~  135 (191)
                      ..+.+|++|-+.-..|....   +|+|+||+.|+..-..  ...+||.|..+..
T Consensus       237 t~~~~C~~Cg~~PtiP~~~~---~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  237 TSDTECPVCGEPPTIPHVIG---KCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cCCceeeccCCCCCCCeeec---cccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            45678999999888776663   5999999999988765  3467999987665

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

Probab=97.27  E-value=0.00012  Score=60.78  Aligned_cols=46  Identities=33%  Similarity=0.871  Sum_probs=35.1

Q ss_pred             cCcccccccccCccEEEcCCCCCcccHhhHHHHhcC--CCccccccccccCC
Q 029544           88 ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK--KTTCPVCRLPLQDP  137 (191)
Q Consensus        88 ~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~--~~~CP~Cr~~~~~~  137 (191)
                      -|-||-+.-++   +.+- +|||..|..|+..|-..  ...||.||.++...
T Consensus       371 LCKICaendKd---vkIE-PCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGt  418 (563)
T KOG1785|consen  371 LCKICAENDKD---VKIE-PCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGT  418 (563)
T ss_pred             HHHHhhccCCC---cccc-cccchHHHHHHHhhcccCCCCCCCceeeEeccc
Confidence            39999886443   3334 59999999999999753  56799999987643

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

Probab=97.08  E-value=0.00045  Score=56.52  Aligned_cols=50  Identities=26%  Similarity=0.520  Sum_probs=42.8

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      +.++..|+||+-.-.+....    +|+|.-|+.||.+.+.+.+.|=.|+..+..
T Consensus       419 ~sEd~lCpICyA~pi~Avf~----PC~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  419 DSEDNLCPICYAGPINAVFA----PCSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             CcccccCcceecccchhhcc----CCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            36677899999876666555    799999999999999999999999988764

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

Probab=97.08  E-value=0.00023  Score=60.99  Aligned_cols=50  Identities=30%  Similarity=0.674  Sum_probs=41.4

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-----CCCccccccccccCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-----KKTTCPVCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-----~~~~CP~Cr~~~~~~  137 (191)
                      .+...|.+|-+.-++....    .|.|.||..|+.+++.     .+-+||+|...+.-.
T Consensus       534 k~~~~C~lc~d~aed~i~s----~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD  588 (791)
T KOG1002|consen  534 KGEVECGLCHDPAEDYIES----SCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             cCceeecccCChhhhhHhh----hhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            4556799999998888888    7999999999999876     345699998877654

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

Probab=97.00  E-value=0.00049  Score=65.16  Aligned_cols=66  Identities=27%  Similarity=0.630  Sum_probs=46.4

Q ss_pred             hCCCccccccccCCCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCC----------CccccccccccC
Q 029544           70 AIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK----------TTCPVCRLPLQD  136 (191)
Q Consensus        70 ~~~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~----------~~CP~Cr~~~~~  136 (191)
                      -+|-+...+.......+.-|.||+.+--.......+. |+|+||..|.+..|.+.          -+||+|+.++..
T Consensus      3470 CLPCl~Cdks~tkQD~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3470 CLPCLHCDKSATKQDADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred             cccccccChhhhhcccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence            3555555444444456778999998866666666665 99999999987665522          249999987763

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

Probab=96.97  E-value=0.00029  Score=56.23  Aligned_cols=48  Identities=27%  Similarity=0.510  Sum_probs=42.1

Q ss_pred             CcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCCC
Q 029544           87 AECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPL  138 (191)
Q Consensus        87 ~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~~  138 (191)
                      +.|-||...|..++..    .|+|.||..|...-++....|.+|.+.+....
T Consensus       242 f~c~icr~~f~~pVvt----~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~  289 (313)
T KOG1813|consen  242 FKCFICRKYFYRPVVT----KCGHYFCEVCALKPYQKGEKCYVCSQQTHGSF  289 (313)
T ss_pred             ccccccccccccchhh----cCCceeehhhhccccccCCcceeccccccccc
Confidence            4599999999999988    89999999999888888888999988776543

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

Probab=96.87  E-value=0.00015  Score=59.37  Aligned_cols=46  Identities=28%  Similarity=0.607  Sum_probs=33.5

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      .....|.||++...+...+    +|||..|  |..-.. ....||+||..+..
T Consensus       303 ~~p~lcVVcl~e~~~~~fv----pcGh~cc--ct~cs~-~l~~CPvCR~rI~~  348 (355)
T KOG1571|consen  303 PQPDLCVVCLDEPKSAVFV----PCGHVCC--CTLCSK-HLPQCPVCRQRIRL  348 (355)
T ss_pred             CCCCceEEecCCccceeee----cCCcEEE--chHHHh-hCCCCchhHHHHHH
Confidence            3455699999999887777    7999877  654432 23449999987653

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

Probab=96.80  E-value=0.0012  Score=50.93  Aligned_cols=51  Identities=24%  Similarity=0.623  Sum_probs=41.0

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC--------CCccccccccccCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK--------KTTCPVCRLPLQDP  137 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~--------~~~CP~Cr~~~~~~  137 (191)
                      ....|..|-..+..++.++.  -|.|.||.+|+.+|-..        ...||-|..++...
T Consensus        49 Y~pNC~LC~t~La~gdt~RL--vCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp  107 (299)
T KOG3970|consen   49 YNPNCRLCNTPLASGDTTRL--VCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP  107 (299)
T ss_pred             CCCCCceeCCccccCcceee--hhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence            45569999999998887754  49999999999999652        23499999988755

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.78  E-value=0.0014  Score=51.21  Aligned_cols=53  Identities=21%  Similarity=0.394  Sum_probs=47.2

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCCC
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPL  138 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~~  138 (191)
                      .+.|++|.+.+.+......+.+|||+|+.+|.+.++.....||+|-.++.+..
T Consensus       221 ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrd  273 (303)
T KOG3039|consen  221 RYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRD  273 (303)
T ss_pred             ceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccc
Confidence            45699999999999988888889999999999999999899999998887653

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

Probab=96.69  E-value=0.00064  Score=56.31  Aligned_cols=49  Identities=35%  Similarity=0.756  Sum_probs=37.7

Q ss_pred             CCCcCcccccccccC-ccEEEcCCCCCcccHhhHHHHhcCC--Cccccccccc
Q 029544           85 EDAECSICLGEYQDK-EVLRIMPQCGHSFHLACIDIWLRKK--TTCPVCRLPL  134 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~-~~~~~~~~C~H~f~~~Ci~~wl~~~--~~CP~Cr~~~  134 (191)
                      -+..|..|-+.+... +.+.-+| |.|+||..|+.+++.++  .+||.||+-.
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            355699999988754 3555665 99999999999999744  4599999433

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

Probab=96.46  E-value=0.0018  Score=54.11  Aligned_cols=48  Identities=23%  Similarity=0.634  Sum_probs=37.8

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc--------CCCcccccccc
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR--------KKTTCPVCRLP  133 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~--------~~~~CP~Cr~~  133 (191)
                      .-..|.||++..........+| |+|+||..|+..++.        +.-.||-+...
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            3567999999988878888887 999999999999976        22248776643

>PF04641 Rtf2: Rtf2 RING-finger

Probab=96.43  E-value=0.0039  Score=49.93  Aligned_cols=54  Identities=24%  Similarity=0.492  Sum_probs=43.9

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      ....+.|||....|........+.+|||+|...++.+.- ....||+|-.++...
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~  163 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEE  163 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccC
Confidence            355678999999997777676666799999999999973 355699999998754

>PHA02862 5L protein; Provisional

Probab=96.37  E-value=0.0026  Score=45.73  Aligned_cols=46  Identities=26%  Similarity=0.771  Sum_probs=33.8

Q ss_pred             CcCcccccccccCccEEEcCCCC-----CcccHhhHHHHhc--CCCccccccccccCC
Q 029544           87 AECSICLGEYQDKEVLRIMPQCG-----HSFHLACIDIWLR--KKTTCPVCRLPLQDP  137 (191)
Q Consensus        87 ~~C~IC~~~~~~~~~~~~~~~C~-----H~f~~~Ci~~wl~--~~~~CP~Cr~~~~~~  137 (191)
                      ..|-||.+.-.+..    - +|.     ..-|.+|+.+|+.  ++..|++|+.++.-.
T Consensus         3 diCWIC~~~~~e~~----~-PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik   55 (156)
T PHA02862          3 DICWICNDVCDERN----N-FCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK   55 (156)
T ss_pred             CEEEEecCcCCCCc----c-cccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence            46999999854432    2 354     4589999999997  444599999988643

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

Probab=96.34  E-value=0.0036  Score=36.58  Aligned_cols=45  Identities=27%  Similarity=0.637  Sum_probs=22.0

Q ss_pred             CcccccccccCc-cEEEcCCCCCcccHhhHHHHhc-CCCccccccccc
Q 029544           89 CSICLGEYQDKE-VLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPL  134 (191)
Q Consensus        89 C~IC~~~~~~~~-~~~~~~~C~H~f~~~Ci~~wl~-~~~~CP~Cr~~~  134 (191)
                      |++|.+.+.... ...-- +|++..|..|+...+. ....||-||.++
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            678888874332 22222 5899999999999886 467799999875

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=96.29  E-value=0.004  Score=45.59  Aligned_cols=49  Identities=27%  Similarity=0.663  Sum_probs=34.8

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCC-----cccHhhHHHHhcC--CCccccccccccCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGH-----SFHLACIDIWLRK--KTTCPVCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H-----~f~~~Ci~~wl~~--~~~CP~Cr~~~~~~  137 (191)
                      ..+..|-||.+.....  .  . +|.-     .-|.+|+++|+..  ...|++|+.++.-.
T Consensus         6 ~~~~~CRIC~~~~~~~--~--~-PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          6 LMDKCCWICKDEYDVV--T--N-YCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCCeeEecCCCCCCc--c--C-CcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            3566899999885421  1  2 3554     4599999999984  44599999988644

>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=96.29  E-value=0.0016  Score=46.33  Aligned_cols=35  Identities=23%  Similarity=0.585  Sum_probs=26.8

Q ss_pred             CCcCcccccccccCccEEEcCCCC------CcccHhhHHHHh
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCG------HSFHLACIDIWL  121 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~------H~f~~~Ci~~wl  121 (191)
                      ..+|.||++.+.+...+..++ |+      |.||.+|+++|-
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~   66 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWR   66 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHH
Confidence            567999999998833444443 55      789999999994

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.

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

Probab=96.26  E-value=0.0029  Score=51.75  Aligned_cols=66  Identities=26%  Similarity=0.503  Sum_probs=46.6

Q ss_pred             HHHhhCCCccccccccCCCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHH--hcCCCcccccccccc
Q 029544           66 VLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIW--LRKKTTCPVCRLPLQ  135 (191)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w--l~~~~~CP~Cr~~~~  135 (191)
                      ..+..-|..........+++...|.||-+.+.-...+    +|+|..|.-|..+.  |...+.||+||....
T Consensus        41 NnlsaEPnlttsSaddtDEen~~C~ICA~~~TYs~~~----PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e  108 (493)
T COG5236          41 NNLSAEPNLTTSSADDTDEENMNCQICAGSTTYSARY----PCGHQICHACAVRLRALYMQKGCPLCRTETE  108 (493)
T ss_pred             cccccCCccccccccccccccceeEEecCCceEEEec----cCCchHHHHHHHHHHHHHhccCCCccccccc
Confidence            3445556665555555666677899999876544444    69999999997543  557788999997654

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

Probab=96.24  E-value=0.0016  Score=47.63  Aligned_cols=41  Identities=24%  Similarity=0.678  Sum_probs=30.6

Q ss_pred             CCccccccccCCCCCCcCcccccccccCccEEEcCCCCCcccH
Q 029544           72 PTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHL  114 (191)
Q Consensus        72 ~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~  114 (191)
                      |.+.|++.. ......+|.||++++..+..+.++| |-.+||+
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            344454322 2344568999999999999999998 9999886

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

Probab=96.00  E-value=0.0011  Score=53.00  Aligned_cols=43  Identities=30%  Similarity=0.687  Sum_probs=33.8

Q ss_pred             CCcCcccccccccCccEEEcCCCCC-cccHhhHHHHhcCCCccccccccccC
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGH-SFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H-~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      +.-|.||++...+-..+    .||| +-|.+|-+..    +.||+||+.+..
T Consensus       300 ~~LC~ICmDaP~DCvfL----eCGHmVtCt~CGkrm----~eCPICRqyi~r  343 (350)
T KOG4275|consen  300 RRLCAICMDAPRDCVFL----ECGHMVTCTKCGKRM----NECPICRQYIVR  343 (350)
T ss_pred             HHHHHHHhcCCcceEEe----ecCcEEeehhhcccc----ccCchHHHHHHH
Confidence            55699999988777666    7999 5788887553    479999987653

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

Probab=95.90  E-value=0.0051  Score=55.67  Aligned_cols=52  Identities=31%  Similarity=0.665  Sum_probs=40.4

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC-------CCcccccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK-------KTTCPVCRLPLQ  135 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~-------~~~CP~Cr~~~~  135 (191)
                      ....+|.||++.+.....+.....|.|+||..||..|-.+       .-.||.|.....
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~  247 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK  247 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence            3456799999999887777655569999999999999762       224999985443

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

Probab=95.90  E-value=0.0029  Score=49.32  Aligned_cols=46  Identities=20%  Similarity=0.579  Sum_probs=32.3

Q ss_pred             cCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           88 ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        88 ~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      .|.-|...-. +.....+ .|+|+||..|...-  ....||+|+.++...
T Consensus         5 hCn~C~~~~~-~~~f~LT-aC~HvfC~~C~k~~--~~~~C~lCkk~ir~i   50 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLT-ACRHVFCEPCLKAS--SPDVCPLCKKSIRII   50 (233)
T ss_pred             EeccccccCC-CCceeee-echhhhhhhhcccC--Cccccccccceeeee
Confidence            4777766544 5666556 59999999997553  222799999986543

>PHA03096 p28-like protein; Provisional

Probab=95.86  E-value=0.0039  Score=50.39  Aligned_cols=36  Identities=33%  Similarity=0.793  Sum_probs=28.4

Q ss_pred             CcCcccccccccCc----cEEEcCCCCCcccHhhHHHHhc
Q 029544           87 AECSICLGEYQDKE----VLRIMPQCGHSFHLACIDIWLR  122 (191)
Q Consensus        87 ~~C~IC~~~~~~~~----~~~~~~~C~H~f~~~Ci~~wl~  122 (191)
                      ..|.||++......    .-..++.|.|.||..|+..|-.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~  218 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMT  218 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHH
Confidence            57999999866432    2235668999999999999976

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

Probab=95.66  E-value=0.0074  Score=49.08  Aligned_cols=48  Identities=29%  Similarity=0.738  Sum_probs=37.0

Q ss_pred             CcCcccccccccC--ccEEEcCCCCCcccHhhHHHHhcCCC-ccccccccc
Q 029544           87 AECSICLGEYQDK--EVLRIMPQCGHSFHLACIDIWLRKKT-TCPVCRLPL  134 (191)
Q Consensus        87 ~~C~IC~~~~~~~--~~~~~~~~C~H~f~~~Ci~~wl~~~~-~CP~Cr~~~  134 (191)
                      ..|-||-++|...  ........|||.||..|+...+.... .||.||.+.
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            4699999999865  33333336999999999998877444 499999986

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

Probab=95.59  E-value=0.0063  Score=48.90  Aligned_cols=43  Identities=30%  Similarity=0.681  Sum_probs=36.4

Q ss_pred             CcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-CCCccccccc
Q 029544           87 AECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRL  132 (191)
Q Consensus        87 ~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-~~~~CP~Cr~  132 (191)
                      ..|+.|-..+.++..+   +.|+|.||.+||...|. ....||.|..
T Consensus       275 LkCplc~~Llrnp~kT---~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRNPMKT---PCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhCcccC---ccccchHHHHHHhhhhhhccccCCCccc
Confidence            6799999999888776   37999999999997765 6667999976

>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=95.56  E-value=0.0058  Score=41.82  Aligned_cols=33  Identities=33%  Similarity=0.870  Sum_probs=25.7

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHH
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACID  118 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~  118 (191)
                      .+...|++|-..+.++. ..+.| |||.||..|+.
T Consensus        76 ~~~~~C~vC~k~l~~~~-f~~~p-~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGNSV-FVVFP-CGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCCce-EEEeC-CCeEEeccccc
Confidence            44667999999998854 33454 99999999975

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

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

Probab=95.43  E-value=0.015  Score=33.33  Aligned_cols=41  Identities=22%  Similarity=0.637  Sum_probs=22.4

Q ss_pred             CcccccccccCccEEEcCCCCCcccHhhHHHHhcCCC--ccccc
Q 029544           89 CSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT--TCPVC  130 (191)
Q Consensus        89 C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~--~CP~C  130 (191)
                      |.+|.+....+..-... .|+-.+|..|+..++....  .||.|
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            55677666665544211 4888999999999998555  69987

; PDB: 3NW0_A 2CT0_A.

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

Probab=95.38  E-value=0.014  Score=34.03  Aligned_cols=40  Identities=38%  Similarity=1.008  Sum_probs=25.7

Q ss_pred             CcccccccccCccEEEcCCCC--C---cccHhhHHHHhc--CCCccccc
Q 029544           89 CSICLGEYQDKEVLRIMPQCG--H---SFHLACIDIWLR--KKTTCPVC  130 (191)
Q Consensus        89 C~IC~~~~~~~~~~~~~~~C~--H---~f~~~Ci~~wl~--~~~~CP~C  130 (191)
                      |-||++.-.+...+ +.| |.  -   ..|.+|+.+|+.  ....|++|
T Consensus         1 CrIC~~~~~~~~~l-i~p-C~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDEPL-ISP-CRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS-E-E-S-SS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCCce-ecc-cccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            67899887665533 233 64  2   579999999998  45568887

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=95.02  E-value=0.014  Score=35.02  Aligned_cols=43  Identities=28%  Similarity=0.536  Sum_probs=29.9

Q ss_pred             cCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccC
Q 029544           88 ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        88 ~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      .|..|...-.....+    +|+|..|..|+.-+  +-+.||+|..++..
T Consensus         9 ~~~~~~~~~~~~~~~----pCgH~I~~~~f~~~--rYngCPfC~~~~~~   51 (55)
T PF14447_consen    9 PCVFCGFVGTKGTVL----PCGHLICDNCFPGE--RYNGCPFCGTPFEF   51 (55)
T ss_pred             eEEEccccccccccc----cccceeeccccChh--hccCCCCCCCcccC
Confidence            466665544444344    69999999997654  44679999988754

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

Probab=95.00  E-value=0.011  Score=53.57  Aligned_cols=42  Identities=38%  Similarity=0.822  Sum_probs=33.8

Q ss_pred             CcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccc
Q 029544           87 AECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL  134 (191)
Q Consensus        87 ~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~  134 (191)
                      ..|..|-..+..|...-   .|||.||.+|+.   .....||-|+.++
T Consensus       841 skCs~C~~~LdlP~VhF---~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  841 SKCSACEGTLDLPFVHF---LCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeecccCCccccceeee---ecccHHHHHhhc---cCcccCCccchhh
Confidence            47999999988876443   699999999998   3455699999744

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

Probab=94.93  E-value=0.023  Score=47.36  Aligned_cols=28  Identities=32%  Similarity=0.913  Sum_probs=21.0

Q ss_pred             CCCcccHhhHHHHhc-------------CCCcccccccccc
Q 029544          108 CGHSFHLACIDIWLR-------------KKTTCPVCRLPLQ  135 (191)
Q Consensus       108 C~H~f~~~Ci~~wl~-------------~~~~CP~Cr~~~~  135 (191)
                      |....|.+|+-+|+.             .+-.||+||+.+-
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC  351 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC  351 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence            445678999998875             2335999999875

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

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

Probab=94.42  E-value=0.032  Score=40.84  Aligned_cols=59  Identities=27%  Similarity=0.563  Sum_probs=40.0

Q ss_pred             CCcCcccccccccCccEEEcC--------CCCCc-ccHhhHHHHhcC-------------------------------CC
Q 029544           86 DAECSICLGEYQDKEVLRIMP--------QCGHS-FHLACIDIWLRK-------------------------------KT  125 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~--------~C~H~-f~~~Ci~~wl~~-------------------------------~~  125 (191)
                      +..|+|||+.-.+.+.+.-..        -|+.. -|..|++++-+.                               .-
T Consensus         2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L   81 (162)
T PF07800_consen    2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPEL   81 (162)
T ss_pred             CccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccccc
Confidence            567999999998887774211        25543 467899988530                               12


Q ss_pred             ccccccccccCCCCCCCcc
Q 029544          126 TCPVCRLPLQDPLGRKHAR  144 (191)
Q Consensus       126 ~CP~Cr~~~~~~~~~~~~~  144 (191)
                      .||+||..+...+.+..+.
T Consensus        82 ~CPLCRG~V~GWtvve~AR  100 (162)
T PF07800_consen   82 ACPLCRGEVKGWTVVEPAR  100 (162)
T ss_pred             cCccccCceeceEEchHHH
Confidence            3999999988766554433

The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.

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

Probab=94.28  E-value=0.019  Score=51.90  Aligned_cols=46  Identities=28%  Similarity=0.766  Sum_probs=35.4

Q ss_pred             CcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCC--CccccccccccCC
Q 029544           87 AECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK--TTCPVCRLPLQDP  137 (191)
Q Consensus        87 ~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~--~~CP~Cr~~~~~~  137 (191)
                      ..|.+|++ ......+    .|+|.||..|+...+...  ..||.||..+...
T Consensus       455 ~~c~ic~~-~~~~~it----~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~  502 (674)
T KOG1001|consen  455 HWCHICCD-LDSFFIT----RCGHDFCVECLKKSIQQSENAPCPLCRNVLKEK  502 (674)
T ss_pred             cccccccc-cccceee----cccchHHHHHHHhccccccCCCCcHHHHHHHHH
Confidence            68999999 3443344    699999999999988732  2499999877654

>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=94.27  E-value=0.011  Score=46.19  Aligned_cols=54  Identities=28%  Similarity=0.676  Sum_probs=39.6

Q ss_pred             CCCCcCcccccc-ccc-CccEEEcCCCCCcccHhhHHHHhcCC-Cccc--cccccccCC
Q 029544           84 VEDAECSICLGE-YQD-KEVLRIMPQCGHSFHLACIDIWLRKK-TTCP--VCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~-~~~-~~~~~~~~~C~H~f~~~Ci~~wl~~~-~~CP--~Cr~~~~~~  137 (191)
                      ..+..|++|-.+ |-+ ...+.+.|.|.|..|.+|.++.+... ..||  -|.+.+...
T Consensus         8 ~~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK~   66 (314)
T COG5220           8 MEDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRKI   66 (314)
T ss_pred             hhcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHHh
Confidence            346689999875 334 44555666799999999999998744 4598  887766543

>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=94.16  E-value=0.032  Score=32.28  Aligned_cols=44  Identities=30%  Similarity=0.843  Sum_probs=25.5

Q ss_pred             cCcccccccccCccEEEcCCCC-CcccHhhHHHHhcCCCccccccccccCC
Q 029544           88 ECSICLGEYQDKEVLRIMPQCG-HSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        88 ~C~IC~~~~~~~~~~~~~~~C~-H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      .|--|+-.  +...+    .|. |..|..|+...+.....||+|..+++..
T Consensus         4 nCKsCWf~--~k~Li----~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen    4 NCKSCWFA--NKGLI----KCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             ---SS-S----SSEE----E-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             cChhhhhc--CCCee----eecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            36666643  33444    475 8999999999999999999999988643

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.

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

Probab=94.06  E-value=0.039  Score=39.18  Aligned_cols=54  Identities=26%  Similarity=0.525  Sum_probs=39.9

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc---CCCccccccccccCCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR---KKTTCPVCRLPLQDPL  138 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~---~~~~CP~Cr~~~~~~~  138 (191)
                      .-.+|.||.+...+...+.----||-..|..|....|+   .+..||+|+.++..+.
T Consensus        79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS  135 (140)
T ss_pred             CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence            56789999998766554432224999999999877666   5567999999887654

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

Probab=93.85  E-value=0.034  Score=44.64  Aligned_cols=46  Identities=26%  Similarity=0.516  Sum_probs=37.1

Q ss_pred             CcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccc
Q 029544           87 AECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRL  132 (191)
Q Consensus        87 ~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~  132 (191)
                      ..|+||.+.+..........+|||..|..|+......+-.||+|.+
T Consensus       159 ~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  159 FNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             CCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence            3499999987766544333369999999999999887788999998

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

Probab=93.84  E-value=0.034  Score=41.46  Aligned_cols=30  Identities=43%  Similarity=1.100  Sum_probs=24.0

Q ss_pred             CCCCcccHhhHHHHhcC-----CC------ccccccccccC
Q 029544          107 QCGHSFHLACIDIWLRK-----KT------TCPVCRLPLQD  136 (191)
Q Consensus       107 ~C~H~f~~~Ci~~wl~~-----~~------~CP~Cr~~~~~  136 (191)
                      +||.-||.-|+..||..     +.      .||.|-.++..
T Consensus       189 qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pial  229 (234)
T KOG3268|consen  189 QCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIAL  229 (234)
T ss_pred             ccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCccee
Confidence            69999999999999872     11      39999887753

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

Probab=93.41  E-value=0.26  Score=27.17  Aligned_cols=30  Identities=13%  Similarity=0.182  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Q 029544            8 LITTVIGFGMSAAFIVFICTRIICRRIRGV   37 (191)
Q Consensus         8 ~v~~~i~~~~~~~li~~~~~~~~~~r~~~~   37 (191)
                      .+.++.+++++++++++.+..+.|++++.+
T Consensus         5 ~IaIIv~V~vg~~iiii~~~~YaCcykk~~   34 (38)
T PF02439_consen    5 TIAIIVAVVVGMAIIIICMFYYACCYKKHR   34 (38)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHcccc
Confidence            344445555555555555444445544433

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

>PF05393 Hum_adeno_E3A: Human adenovirus early E3A glycoprotein; InterPro: IPR008652 This family consists of several early glycoproteins (E3A), from human adenovirus type 2

Probab=93.15  E-value=0.3  Score=32.11  Aligned_cols=24  Identities=25%  Similarity=0.692  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHhhccccCCCCccc
Q 029544           21 FIVFICTRIICRRIRGVESRPMFE   44 (191)
Q Consensus        21 li~~~~~~~~~~r~~~~~~r~~~~   44 (191)
                      |++.++..++||+-|++.+|+.++
T Consensus        44 Fil~VilwfvCC~kRkrsRrPIYr   67 (94)
T PF05393_consen   44 FILLVILWFVCCKKRKRSRRPIYR   67 (94)
T ss_pred             HHHHHHHHHHHHHHhhhccCCccc
Confidence            333444555677777777666544

; GO: 0016021 integral to membrane

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

Probab=93.11  E-value=0.06  Score=43.96  Aligned_cols=47  Identities=23%  Similarity=0.602  Sum_probs=36.7

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      -+-.+|+||.+.+..+..-.   +=||.-|..|-.+   ..+.||.||.++..
T Consensus        46 ~~lleCPvC~~~l~~Pi~QC---~nGHlaCssC~~~---~~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   46 LDLLDCPVCFNPLSPPIFQC---DNGHLACSSCRTK---VSNKCPTCRLPIGN   92 (299)
T ss_pred             hhhccCchhhccCcccceec---CCCcEehhhhhhh---hcccCCcccccccc
Confidence            34568999999999886652   3479999999653   45679999999983

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=92.78  E-value=0.078  Score=43.54  Aligned_cols=52  Identities=19%  Similarity=0.445  Sum_probs=34.9

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-CCCccccccccccCC
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQDP  137 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-~~~~CP~Cr~~~~~~  137 (191)
                      +.-|+.|++.+...+.-..-=+||-..|.-|+...-+ -+..||-||+.+.+.
T Consensus        14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~de   66 (480)
T COG5175          14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDE   66 (480)
T ss_pred             cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcccc
Confidence            3349999998876543322115998888888765433 234599999877644

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

Probab=92.74  E-value=0.007  Score=50.29  Aligned_cols=51  Identities=27%  Similarity=0.625  Sum_probs=40.9

Q ss_pred             CCcCcccccccccC-ccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           86 DAECSICLGEYQDK-EVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        86 ~~~C~IC~~~~~~~-~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      ...|+||.+.+... ..+..+ -|||.+|..|+.+|+.....||.|+..+...
T Consensus       196 v~sl~I~~~slK~~y~k~~~~-~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~  247 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAI-VCGHIYHHGKLSKWLATKRKLPSCRRELPKN  247 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHH-hhcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence            34699999988765 333333 4999999999999999988899999988643

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=92.52  E-value=0.19  Score=30.08  Aligned_cols=34  Identities=24%  Similarity=0.812  Sum_probs=29.4

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHH
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDI  119 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~  119 (191)
                      ...|.+|-+.|.+...+.+-|.|+-.+|..|++.
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            4569999999988777778888999999999765

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

Probab=92.35  E-value=0.057  Score=43.75  Aligned_cols=29  Identities=31%  Similarity=0.827  Sum_probs=21.1

Q ss_pred             EEcCCCCCcccHhhHHHHhcCCCccccccccc
Q 029544          103 RIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL  134 (191)
Q Consensus       103 ~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~  134 (191)
                      +.+ +|.|+||.+|...  ...+.||.|-..+
T Consensus       105 RmI-PCkHvFCl~CAr~--~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen  105 RMI-PCKHVFCLECARS--DSDKICPLCDDRV  133 (389)
T ss_pred             ccc-ccchhhhhhhhhc--CccccCcCcccHH
Confidence            344 5999999999754  3456798887654

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

Probab=92.31  E-value=0.037  Score=52.48  Aligned_cols=47  Identities=28%  Similarity=0.735  Sum_probs=38.7

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccc
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL  134 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~  134 (191)
                      ....|.||++.+.+-..+.   .|||.+|..|...|+..+..||.|+...
T Consensus      1152 ~~~~c~ic~dil~~~~~I~---~cgh~~c~~c~~~~l~~~s~~~~~ksi~ 1198 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGIA---GCGHEPCCRCDELWLYASSRCPICKSIK 1198 (1394)
T ss_pred             cccchHHHHHHHHhcCCee---eechhHhhhHHHHHHHHhccCcchhhhh
Confidence            3457999999998443333   6999999999999999999999999544

>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=92.08  E-value=0.13  Score=41.38  Aligned_cols=50  Identities=24%  Similarity=0.691  Sum_probs=35.6

Q ss_pred             cCcccccc-cccCccEEEcCCCCCcccHhhHHHHhcC-CCccccccccccCC
Q 029544           88 ECSICLGE-YQDKEVLRIMPQCGHSFHLACIDIWLRK-KTTCPVCRLPLQDP  137 (191)
Q Consensus        88 ~C~IC~~~-~~~~~~~~~~~~C~H~f~~~Ci~~wl~~-~~~CP~Cr~~~~~~  137 (191)
                      .|++|-.+ |.++.......+|+|..|.+|....+.. ...||.|...+...
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~   53 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKN   53 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhc
Confidence            48888764 4455433333359999999999998874 44699998777544

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

Probab=92.02  E-value=0.046  Score=48.40  Aligned_cols=44  Identities=25%  Similarity=0.659  Sum_probs=32.3

Q ss_pred             CcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCcccccccc
Q 029544           87 AECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLP  133 (191)
Q Consensus        87 ~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~  133 (191)
                      ..|.||+..|......-+.+.|||..|.+|+....  +.+|| |+++
T Consensus        12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly--n~scp-~~~D   55 (861)
T KOG3161|consen   12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY--NASCP-TKRD   55 (861)
T ss_pred             hhchHHHHHHHHHhcCcccccccchHHHHHHHhHh--hccCC-CCcc
Confidence            45999988887665554444799999999998754  45688 6543

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

Probab=91.52  E-value=0.055  Score=48.48  Aligned_cols=51  Identities=25%  Similarity=0.650  Sum_probs=40.0

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCC---CccccccccccCCCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK---TTCPVCRLPLQDPLG  139 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~---~~CP~Cr~~~~~~~~  139 (191)
                      -..+|+||...+.++..+    .|.|.||..|+..-+...   ..||+|+..+.....
T Consensus        20 k~lEc~ic~~~~~~p~~~----kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~s~   73 (684)
T KOG4362|consen   20 KILECPICLEHVKEPSLL----KCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKRSL   73 (684)
T ss_pred             hhccCCceeEEeeccchh----hhhHHHHhhhhhceeeccCccccchhhhhhhhhhhc
Confidence            356899999999999666    799999999987766533   459999977765433

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

Probab=90.21  E-value=0.15  Score=46.78  Aligned_cols=36  Identities=25%  Similarity=0.552  Sum_probs=26.8

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHh
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWL  121 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl  121 (191)
                      +.+..|.+|...+...-.. +- +|||.||.+|+.+-.
T Consensus       815 ep~d~C~~C~~~ll~~pF~-vf-~CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  815 EPQDSCDHCGRPLLIKPFY-VF-PCGHCFHRDCLIRHV  850 (911)
T ss_pred             cCccchHHhcchhhcCcce-ee-eccchHHHHHHHHHH
Confidence            5567899999887654322 33 599999999997654

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

Probab=90.15  E-value=0.27  Score=44.94  Aligned_cols=53  Identities=21%  Similarity=0.491  Sum_probs=37.7

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCC-----cccHhhHHHHhc--CCCccccccccccCCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGH-----SFHLACIDIWLR--KKTTCPVCRLPLQDPL  138 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H-----~f~~~Ci~~wl~--~~~~CP~Cr~~~~~~~  138 (191)
                      +++..|.||..+-..+..+-.  +|..     ..|.+|+.+|+.  ....|-+|+.++.-.+
T Consensus        10 ~d~~~CRICr~e~~~d~pLfh--PCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~   69 (1175)
T COG5183          10 EDKRSCRICRTEDIRDDPLFH--PCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKD   69 (1175)
T ss_pred             ccchhceeecCCCCCCCcCcc--cccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeee
Confidence            445789999987655554422  3553     389999999998  3445999999886543

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

Probab=89.88  E-value=0.31  Score=28.89  Aligned_cols=43  Identities=23%  Similarity=0.538  Sum_probs=21.5

Q ss_pred             CcccccccccCc------cEEEcCCCCCcccHhhHHHHhcCCCcccccc
Q 029544           89 CSICLGEYQDKE------VLRIMPQCGHSFHLACIDIWLRKKTTCPVCR  131 (191)
Q Consensus        89 C~IC~~~~~~~~------~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr  131 (191)
                      |--|+..+....      ....-+.|++.||.+|=.-.-..-..||-|.
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~   50 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE   50 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence            444555555542      3345568999999999544334556699884

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

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

Probab=89.42  E-value=0.22  Score=29.37  Aligned_cols=43  Identities=21%  Similarity=0.539  Sum_probs=19.1

Q ss_pred             CcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-----CCCcccccccc
Q 029544           87 AECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-----KKTTCPVCRLP  133 (191)
Q Consensus        87 ~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-----~~~~CP~Cr~~  133 (191)
                      ..|++....+..+.+-.   .|.|.-|.+ ++.|+.     ..-.||+|.++
T Consensus         3 L~CPls~~~i~~P~Rg~---~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRIPVRGK---NCKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SSEEEET---T--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEeCccCC---cCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            46888888887765543   699985433 233443     22359999863

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.

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

Probab=89.29  E-value=0.21  Score=42.43  Aligned_cols=35  Identities=29%  Similarity=0.636  Sum_probs=30.1

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR  122 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~  122 (191)
                      +++..|+||..-|.++..+    +|+|..|..|....+.
T Consensus         2 eeelkc~vc~~f~~epiil----~c~h~lc~~ca~~~~~   36 (699)
T KOG4367|consen    2 EEELKCPVCGSFYREPIIL----PCSHNLCQACARNILV   36 (699)
T ss_pred             cccccCceehhhccCceEe----ecccHHHHHHHHhhcc
Confidence            3567899999999999888    7999999999886654

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

Probab=89.04  E-value=0.17  Score=42.89  Aligned_cols=37  Identities=27%  Similarity=0.741  Sum_probs=26.9

Q ss_pred             CCCcCcccccccccC-ccEEEcCCCCCcccHhhHHHHhc
Q 029544           85 EDAECSICLGEYQDK-EVLRIMPQCGHSFHLACIDIWLR  122 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~-~~~~~~~~C~H~f~~~Ci~~wl~  122 (191)
                      ...+|.||..+.... .... ...|+|.||.+|+.+.+.
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~-~~~C~H~fC~~C~k~~ie  182 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFS-VLKCGHRFCKDCVKQHIE  182 (384)
T ss_pred             ccccCccCccccccHhhhHH-HhcccchhhhHHhHHHhh
Confidence            456799999544433 3333 336999999999999887

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.69  E-value=0.43  Score=37.72  Aligned_cols=52  Identities=21%  Similarity=0.312  Sum_probs=41.3

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPL  138 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~~  138 (191)
                      ..+.|+|---.+........+.+|||+|-..-+.+.  ....|++|...+....
T Consensus       110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~d  161 (293)
T KOG3113|consen  110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDD  161 (293)
T ss_pred             ceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccC
Confidence            346799988888877766666689999999998885  4677999999887654

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.62  E-value=0.21  Score=39.51  Aligned_cols=52  Identities=23%  Similarity=0.625  Sum_probs=35.8

Q ss_pred             CCCCcCcccccccccCccE-EEcCCCC-----CcccHhhHHHHhcCC--------CccccccccccC
Q 029544           84 VEDAECSICLGEYQDKEVL-RIMPQCG-----HSFHLACIDIWLRKK--------TTCPVCRLPLQD  136 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~-~~~~~C~-----H~f~~~Ci~~wl~~~--------~~CP~Cr~~~~~  136 (191)
                      +.+..|-||+..=++.... .+- +|.     |.-|..|+..|+..+        -.||.|+.++..
T Consensus        18 e~eR~CWiCF~TdeDn~~a~WV~-PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYii   83 (293)
T KOG3053|consen   18 ELERCCWICFATDEDNRLAAWVH-PCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYII   83 (293)
T ss_pred             ccceeEEEEeccCcccchhhhcc-cccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhee
Confidence            4456689999875554333 233 363     779999999999732        249999987753

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

Probab=88.60  E-value=0.29  Score=44.40  Aligned_cols=42  Identities=29%  Similarity=0.692  Sum_probs=29.0

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCcccc
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPV  129 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~  129 (191)
                      ...|.||--.......+ .. .|+|+.|.+|..+|+.....||.
T Consensus      1028 ~~~C~~C~l~V~gss~~-Cg-~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1028 TFQCAICHLAVRGSSNF-CG-TCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeeeeEeeEeeccchh-hc-cccccccHHHHHHHHhcCCcCCC
Confidence            34566665444332222 22 59999999999999998888874

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

Probab=88.48  E-value=0.36  Score=40.51  Aligned_cols=49  Identities=16%  Similarity=0.414  Sum_probs=36.2

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCC---ccccccccc
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT---TCPVCRLPL  134 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~---~CP~Cr~~~  134 (191)
                      .-+.|||=.+.-.+...-..+. |||+.+.+-+.+...+..   .||.|-...
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~e~  384 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYCPVEQ  384 (394)
T ss_pred             ceeecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence            3567998777766555555554 999999999999887544   599995433

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

Probab=88.10  E-value=1  Score=31.79  Aligned_cols=29  Identities=21%  Similarity=0.280  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Q 029544            8 LITTVIGFGMSAAFIVFICTRIICRRIRGV   37 (191)
Q Consensus         8 ~v~~~i~~~~~~~li~~~~~~~~~~r~~~~   37 (191)
                      ++.++++++.+++++++ ++.|+++|++++
T Consensus        66 i~~Ii~gv~aGvIg~Il-li~y~irR~~Kk   94 (122)
T PF01102_consen   66 IIGIIFGVMAGVIGIIL-LISYCIRRLRKK   94 (122)
T ss_dssp             HHHHHHHHHHHHHHHHH-HHHHHHHHHS--
T ss_pred             eeehhHHHHHHHHHHHH-HHHHHHHHHhcc
Confidence            34444454444444333 344444444443

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

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.87  E-value=0.27  Score=39.66  Aligned_cols=29  Identities=21%  Similarity=0.531  Sum_probs=22.6

Q ss_pred             CCCcccHhhHHHHhc-------------CCCccccccccccC
Q 029544          108 CGHSFHLACIDIWLR-------------KKTTCPVCRLPLQD  136 (191)
Q Consensus       108 C~H~f~~~Ci~~wl~-------------~~~~CP~Cr~~~~~  136 (191)
                      |....|.+|+.+|+.             ++-+||+||+.+--
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci  366 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCI  366 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEE
Confidence            566788999998874             34569999998764

>PF06024 DUF912: Nucleopolyhedrovirus protein of unknown function (DUF912); InterPro: IPR009261 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf78; it is a family of uncharacterised viral proteins

Probab=84.71  E-value=0.4  Score=32.69  Aligned_cols=14  Identities=14%  Similarity=0.337  Sum_probs=6.2

Q ss_pred             chhHHHHHHHHHHH
Q 029544            5 GMNLITTVIGFGMS   18 (191)
Q Consensus         5 ~~~~v~~~i~~~~~   18 (191)
                      +..+++.++++++.
T Consensus        61 ~~iili~lls~v~I   74 (101)
T PF06024_consen   61 GNIILISLLSFVCI   74 (101)
T ss_pred             ccchHHHHHHHHHH
Confidence            34444444444443

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

Probab=83.52  E-value=4.6  Score=22.28  Aligned_cols=32  Identities=13%  Similarity=0.050  Sum_probs=23.1

Q ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 029544            5 GMNLITTVIGFGMSAAFIVFICTRIICRRIRG   36 (191)
Q Consensus         5 ~~~~v~~~i~~~~~~~li~~~~~~~~~~r~~~   36 (191)
                      -..++..+++.++.+++++++++..+.+..+.
T Consensus         5 ~IaIIv~V~vg~~iiii~~~~YaCcykk~~~~   36 (38)
T PF02439_consen    5 TIAIIVAVVVGMAIIIICMFYYACCYKKHRRQ   36 (38)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHcccccc
Confidence            34577777777777888888888887776643

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

>PF00558 Vpu: Vpu protein; InterPro: IPR008187 The Human immunodeficiency virus 1 (HIV-1) Vpu protein acts in the degradation of CD4 in the endoplasmic reticulum and in the enhancement of virion release from the plasma membrane of infected cells []

Probab=83.24  E-value=1.3  Score=28.87  Aligned_cols=10  Identities=30%  Similarity=0.415  Sum_probs=3.9

Q ss_pred             CCCCCCCCHH
Q 029544           57 GHRINGLEPV   66 (191)
Q Consensus        57 ~~~~~~~~~~   66 (191)
                      +...+|-...
T Consensus        54 GnES~Gd~Ee   63 (81)
T PF00558_consen   54 GNESDGDEEE   63 (81)
T ss_dssp             HCTTTTCCHH
T ss_pred             CCCCCCcHHH
Confidence            3334444333

; GO: 0019076 release of virus from host; PDB: 2JPX_A 1PI8_A 2GOH_A 2GOF_A 1PI7_A 1PJE_A 1VPU_A 2K7Y_A.

>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=82.35  E-value=0.79  Score=39.61  Aligned_cols=36  Identities=31%  Similarity=0.720  Sum_probs=29.0

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR  122 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~  122 (191)
                      ....+|.||.+.+..  .+..+ .|+|.||..|+..++.
T Consensus        68 ~~~~~c~ic~~~~~~--~~~~~-~c~H~~c~~cw~~yl~  103 (444)
T KOG1815|consen   68 KGDVQCGICVESYDG--EIIGL-GCGHPFCPPCWTGYLG  103 (444)
T ss_pred             CccccCCcccCCCcc--hhhhc-CCCcHHHHHHHHHHhh
Confidence            456789999999887  33334 5999999999999987

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

Probab=81.22  E-value=0.94  Score=41.45  Aligned_cols=55  Identities=13%  Similarity=0.077  Sum_probs=37.0

Q ss_pred             CCCcCcccccccccCc---cEEEcCCCCCcccHhhHHHHhc------CCCccccccccccCCCC
Q 029544           85 EDAECSICLGEYQDKE---VLRIMPQCGHSFHLACIDIWLR------KKTTCPVCRLPLQDPLG  139 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~---~~~~~~~C~H~f~~~Ci~~wl~------~~~~CP~Cr~~~~~~~~  139 (191)
                      ....|.+|...+..+.   -.-.+..|+|.||..||..|..      .+-.|++|..-|.....
T Consensus        95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR  158 (1134)
T KOG0825|consen   95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSR  158 (1134)
T ss_pred             cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhh
Confidence            3456888888777632   1111225999999999999986      23348899887765433

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

Probab=81.03  E-value=0.63  Score=36.02  Aligned_cols=40  Identities=28%  Similarity=0.716  Sum_probs=27.4

Q ss_pred             CcccccccccCccEEEcCCCCC-cccHhhHHHHhcCCCccccccccccC
Q 029544           89 CSICLGEYQDKEVLRIMPQCGH-SFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        89 C~IC~~~~~~~~~~~~~~~C~H-~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      |-.|.+.-.   .+..+| |.| .+|..|-..    -..||+|+.....
T Consensus       161 Cr~C~~~~~---~VlllP-CrHl~lC~~C~~~----~~~CPiC~~~~~s  201 (207)
T KOG1100|consen  161 CRKCGEREA---TVLLLP-CRHLCLCGICDES----LRICPICRSPKTS  201 (207)
T ss_pred             ceecCcCCc---eEEeec-ccceEeccccccc----CccCCCCcChhhc
Confidence            888886533   344454 998 588889643    3559999976543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	191
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		4e-11
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		4e-10
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		2e-07
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		2e-05
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		4e-05
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		4e-05
2ecn_A	70	Solution Structure Of The Ring Domain Of The Human		5e-04
2y43_A	99	Rad18 Ubiquitin Ligase Ring Domain Structure Length		9e-04

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 34/47 (72%)
Query: 88  ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL 134
           EC++CL E +D E  R +P+CGH FH  C+D+WL   +TCP+CRL +
Sbjct: 7   ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 40/61 (65%), Gaps = 2/61 (3%)
Query: 71  IPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVC 130
           +P+ +FN    +S E   C +C+ +++ +++LR++P C H FH  C+D WL+   TCP+C
Sbjct: 9   LPSYRFNPNNHQS-EQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPIC 66
Query: 131 R 131
           R
Sbjct: 67  R 67

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 68  VAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTC 127
           + A+P +   ++     ++  C IC  EY   +V   +P C H FH  C+ IWL+K  TC
Sbjct: 22  IDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTC 80
Query: 128 PVCRLPLQDPL 138
           PVCR     PL
Sbjct: 81  PVCRCMFPPPL 91

>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 = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 88  ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL 134
           EC +C  +Y   E +R +P C H FH +CI  WL +  +CPVCR  L
Sbjct: 17  ECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL 62

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 88  ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPL 138
           +C+ICL   ++ E +R +P C H FH  C+D WL     CP+CR+ ++  L
Sbjct: 16  KCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQL 65

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 17/46 (36%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 89  CSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL 134
           C++CL +++ ++ L I P C H+FH  C+  WL  +  CP+C +P+
Sbjct: 18  CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPV 62

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 84  VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL 134
            ++ EC IC+    D     I+P C HSF   CID W  +   CP+CRL +
Sbjct: 13  TDEEECCICM----DGRADLILP-CAHSFCQKCIDKWSDRHRNCPICRLQM 58

>pdb|2Y43|A Chain A, Rad18 Ubiquitin Ligase Ring Domain Structure Length = 99

Iteration: 1
 Score = 40.0 bits (92), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 25/89 (28%), Positives = 43/89 (48%), Gaps = 13/89 (14%)
Query: 82  KSVEDA-ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPLGR 140
           K+++D   C IC   +    +  I+PQC H++   CI  +L  KT CP C + + +P  +
Sbjct: 17  KTIDDLLRCGICFEYFN---IAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLK 73
Query: 141 KHAREATFSMAQAVDSPETSINHSRQWLL 169
            +         + +D    S+N +R  LL
Sbjct: 74  NN---------RILDELVKSLNFARNHLL 93

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	191
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	4e-28
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	1e-26
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	2e-26
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	8e-23
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	9e-21
2ect_A	78	Ring finger protein 126; metal binding protein, st	4e-20
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	4e-18
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	6e-17
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	7e-17
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	2e-16
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	3e-14
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	1e-13
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	4e-13
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	6e-13
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	7e-12
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	2e-11
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	3e-11
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	5e-11
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	5e-11
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-10
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-05
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	1e-10
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	6e-10
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	1e-09
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	1e-09
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	6e-09
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	8e-09
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	5e-08
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	7e-08
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	8e-08
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	9e-08
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	1e-07
1z6u_A	150	NP95-like ring finger protein isoform B; structura	1e-07
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	2e-07
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	3e-07
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	8e-07
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	1e-06
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	1e-06
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	1e-06
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	2e-06
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	2e-06
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	5e-06
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	5e-06
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	6e-06
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	8e-06
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	8e-06
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	1e-05
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	2e-05
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	3e-05
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	5e-05
3nw0_A	238	Non-structural maintenance of chromosomes element	5e-05
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	1e-04
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	1e-04
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	3e-04
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	3e-04

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

 Score = 99.7 bits (249), Expect = 4e-28
 Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 68  VAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTC 127
              +P+ +FN    +S E   C +C+ +++ +++LR++P C H FH  C+D WL+   TC
Sbjct: 6   SGQLPSYRFNPNNHQS-EQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTC 63

Query: 128 PVCRLPLQDPLG 139
           P+CR       G
Sbjct: 64  PICRADSGPSSG 75

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

 Score = 96.3 bits (240), Expect = 1e-26
 Identities = 26/71 (36%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 68  VAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTC 127
           + A+P +   ++     ++  C IC  EY   +V   +P C H FH  C+ IWL+K  TC
Sbjct: 22  IDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTC 80

Query: 128 PVCRLPLQDPL 138
           PVCR     PL
Sbjct: 81  PVCRCMFPPPL 91

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

 Score = 94.6 bits (236), Expect = 2e-26
 Identities = 24/50 (48%), Positives = 35/50 (70%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL 134
           +  EC++CL E +D E  R +P+CGH FH  C+D+WL   +TCP+CRL +
Sbjct: 4   DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>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 = 85.9 bits (213), Expect = 8e-23
 Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPL 138
            + +C+ICL   ++ E +R +P C H FH  C+D WL     CP+CR+ ++  L
Sbjct: 13  TEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQL 65

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

 Score = 80.6 bits (199), Expect = 9e-21
 Identities = 17/50 (34%), Positives = 30/50 (60%), Gaps = 1/50 (2%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL 134
               C++CL +++ ++ L I P C H+FH  C+  WL  +  CP+C +P+
Sbjct: 14  LHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPV 62

>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 = 4e-20
 Identities = 21/50 (42%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL 134
              EC +C  +Y   E +R +P C H FH +CI  WL +  +CPVCR  L
Sbjct: 14  SGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL 62

>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 = 73.1 bits (180), Expect = 4e-18
 Identities = 16/52 (30%), Positives = 24/52 (46%)

Query: 83  SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL 134
           S   + C ICL +     V+  +  CGH  H  C +  L++   CP+C  P 
Sbjct: 2   SSGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPS 53

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

 Score = 70.5 bits (173), Expect = 6e-17
 Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 5/53 (9%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP 137
           ++ EC IC+    D     I+P C HSF   CID W  +   CP+CRL +   
Sbjct: 14  DEEECCICM----DGRADLILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGA 61

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

 Score = 70.5 bits (173), Expect = 7e-17
 Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 3/54 (5%)

Query: 83  SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD 136
           +     C ICL +  +  +      C H+F   CI  W+R+  TCP+C++P++ 
Sbjct: 2   ATVAERCPICLEDPSNYSMA---LPCLHAFCYVCITRWIRQNPTCPLCKVPVES 52

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

 Score = 69.5 bits (170), Expect = 2e-16
 Identities = 13/54 (24%), Positives = 27/54 (50%)

Query: 82  KSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ 135
           +      C  C  E + ++ + +  +C HSFH  C+ +W+++   CP+C+    
Sbjct: 22  RVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWV 75

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

 Score = 63.8 bits (155), Expect = 3e-14
 Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 3/61 (4%)

Query: 77  NQEAFKSVEDAECSICLGEYQDKEVLRIMP---QCGHSFHLACIDIWLRKKTTCPVCRLP 133
           +    +      C IC+  Y +      +    +CGH F   C+   L+   TCP CR  
Sbjct: 6   SGTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKK 65

Query: 134 L 134
           +
Sbjct: 66  I 66

>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 = 63.0 bits (153), Expect = 1e-13
 Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 4/52 (7%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK-KTTCPVCRLPLQ 135
           E   C IC+ + +D    R+ P C      +CI  WL + +  CP CR PLQ
Sbjct: 21  EVFRCFICMEKLRDA---RLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQ 69

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

 Score = 60.6 bits (147), Expect = 4e-13
 Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 3/54 (5%)

Query: 85  EDAECSICLGEYQDKEVLRIMP---QCGHSFHLACIDIWLRKKTTCPVCRLPLQ 135
               C IC+  Y +      +    +CGH F   C+   L+   TCP CR  + 
Sbjct: 2   AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN 55

>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 = 60.2 bits (146), Expect = 6e-13
 Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 3/51 (5%)

Query: 88  ECSICLGEYQDKEVLRIMPQ---CGHSFHLACIDIWLRKKTTCPVCRLPLQ 135
            C IC+  Y +      +     CGH F   C+   L+   TCP CR  + 
Sbjct: 12  SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN 62

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

 Score = 57.5 bits (139), Expect = 7e-12
 Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 3/51 (5%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ 135
               CSIC G   D   +    +C H+F  +CI         CP C + + 
Sbjct: 14  PYILCSICKGYLIDATTI---TECLHTFCKSCIVRHFYYSNRCPKCNIVVH 61

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

 Score = 56.4 bits (136), Expect = 2e-11
 Identities = 14/58 (24%), Positives = 20/58 (34%), Gaps = 4/58 (6%)

Query: 79  EAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD 136
               S+   EC+ICL        L     C H F   C+         C +CR  + +
Sbjct: 8   NTAPSLTVPECAICLQTCVHPVSLP----CKHVFCYLCVKGASWLGKRCALCRQEIPE 61

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

 Score = 56.0 bits (135), Expect = 3e-11
 Identities = 13/51 (25%), Positives = 18/51 (35%), Gaps = 4/51 (7%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ 135
               C IC   +Q+  V +    C H F  +C     R    C +C  P  
Sbjct: 14  IPFRCFICRQAFQNPVVTK----CRHYFCESCALEHFRATPRCYICDQPTG 60

>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 = 56.4 bits (136), Expect = 5e-11
 Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 3/53 (5%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP 137
               C +C G + D   +    +C HSF   CI  +L     CP+C + +   
Sbjct: 14  PHLMCVLCGGYFIDATTI---IECLHSFCKTCIVRYLETSKYCPICDVQVHKT 63

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

 Score = 55.9 bits (135), Expect = 5e-11
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 3/53 (5%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP 137
           +   C IC   +       I+PQC H++   CI  +L  KT CP C + + +P
Sbjct: 21  DLLRCGICFEYFNIA---MIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEP 70

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

 Score = 55.9 bits (134), Expect = 1e-10
 Identities = 16/85 (18%), Positives = 27/85 (31%), Gaps = 3/85 (3%)

Query: 85  EDAECSICLGEYQDKEVLRIMP---QCGHSFHLACIDIWLRKKTTCPVCRLPLQDPLGRK 141
               C IC+  Y +      +    +CGH F   C+   L+   TCP CR  +       
Sbjct: 6   GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHP 65

Query: 142 HAREATFSMAQAVDSPETSINHSRQ 166
               +            + I  + +
Sbjct: 66  IYIGSGTVSCPICMDGYSEIVQNGR 90

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

 Score = 42.1 bits (98), Expect = 1e-05
 Identities = 16/62 (25%), Positives = 22/62 (35%), Gaps = 3/62 (4%)

Query: 73  TMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQ---CGHSFHLACIDIWLRKKTTCPV 129
             K     +       C IC+  Y +      +     CGH F   C+   L+   TCP 
Sbjct: 59  NHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPT 118

Query: 130 CR 131
           CR
Sbjct: 119 CR 120

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

 Score = 56.2 bits (135), Expect = 1e-10
 Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 4/53 (7%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP 137
            + +C IC   + +     +   C HSF   CI+ W+++K  CP+CR  ++  
Sbjct: 63  NELQCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDIKSK 111

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A Length = 106

 Score = 53.3 bits (127), Expect = 6e-10
 Identities = 12/47 (25%), Positives = 18/47 (38%)

Query: 89  CSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ 135
           C         +E       C H+FH  CI  WL+ +  CP+     +
Sbjct: 54  CQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE 100

>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 = 52.9 bits (126), Expect = 1e-09
 Identities = 17/73 (23%), Positives = 26/73 (35%), Gaps = 16/73 (21%)

Query: 75  KFNQEAFKS--VEDAECSIC--------------LGEYQDKEVLRIMPQCGHSFHLACID 118
           K+N  A  +  +    C+IC                    +E       C H+FH  CI 
Sbjct: 35  KWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCIS 94

Query: 119 IWLRKKTTCPVCR 131
            WL+ +  CP+  
Sbjct: 95  RWLKTRQVCPLDN 107

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

 Score = 55.6 bits (133), Expect = 1e-09
 Identities = 13/73 (17%), Positives = 24/73 (32%), Gaps = 15/73 (20%)

Query: 82  KSVEDAECSICLGEYQDKEVLRIM----PQCGHSFHLACIDIWLRKKT-----------T 126
           +  E+  C+IC     D   + ++     +C    H  C++ W +               
Sbjct: 304 EDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQ 363

Query: 127 CPVCRLPLQDPLG 139
           CP C+  L     
Sbjct: 364 CPFCKAKLSTSFA 376

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

 Score = 51.1 bits (122), Expect = 6e-09
 Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 5/73 (6%)

Query: 74  MKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT-TCPVCRL 132
           M   ++A  S+ + +C IC+    +   L     C H+    C    + K +  CP CR 
Sbjct: 3   MALPKDAIPSLSECQCGICMEILVEPVTL----PCNHTLCKPCFQSTVEKASLCCPFCRR 58

Query: 133 PLQDPLGRKHARE 145
            +         R 
Sbjct: 59  RVSSWTRYHTRRN 71

>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 = 50.6 bits (120), Expect = 8e-09
 Identities = 16/80 (20%), Positives = 27/80 (33%), Gaps = 19/80 (23%)

Query: 79  EAFKSVEDAECSICLGEYQDK--------------EVLRIMPQCGHSFHLACIDIWLRKK 124
           E  K   + +C IC+ +                   V+  + +C H+FHL C+       
Sbjct: 18  EELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNG 77

Query: 125 T-----TCPVCRLPLQDPLG 139
                  CP C+    +  G
Sbjct: 78  NKDGSLQCPSCKTIYGEKTG 97

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

 Score = 48.8 bits (116), Expect = 5e-08
 Identities = 13/54 (24%), Positives = 18/54 (33%), Gaps = 5/54 (9%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT-TCPVCRLPLQDP 137
           E  +C  C               C H+    C+D   R +  +CP CR  L   
Sbjct: 51  ETFQCICCQELVFRPITT----VCQHNVCKDCLDRSFRAQVFSCPACRYDLGRS 100

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

 Score = 47.4 bits (113), Expect = 7e-08
 Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT---TCPVCR 131
           E  EC IC+  + ++++   +  CGH+    C++  L        CP C 
Sbjct: 14  EVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCS 63

>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 = 50.1 bits (119), Expect = 8e-08
 Identities = 15/67 (22%), Positives = 26/67 (38%), Gaps = 5/67 (7%)

Query: 71  IPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT-TCPV 129
           +   ++            C IC    +D   ++I P CGH    +C+  W   +   CP 
Sbjct: 317 VTQEQYELYCEMGSTFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPF 372

Query: 130 CRLPLQD 136
           CR  ++ 
Sbjct: 373 CRCEIKG 379

>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 = 46.5 bits (110), Expect = 9e-08
 Identities = 11/49 (22%), Positives = 17/49 (34%), Gaps = 5/49 (10%)

Query: 88  ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR--KKTTCPVCRLPL 134
            C+IC       +       CG   HL C+  + +   +  CP C    
Sbjct: 17  ICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYW 62

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

 Score = 47.6 bits (113), Expect = 1e-07
 Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 5/51 (9%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ 135
           +   CS C    ++   L     C H F   C+   +   T CPVC  P  
Sbjct: 21  KLLRCSRCTNILREPVCL---GGCEHIFCSNCVSDCI--GTGCPVCYTPAW 66

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

 Score = 48.1 bits (114), Expect = 1e-07
 Identities = 10/52 (19%), Positives = 18/52 (34%), Gaps = 5/52 (9%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT-TCPVCRLPLQ 135
           +   C  C           +  +C H+    C+    + +  +CP CR  L 
Sbjct: 77  QSFMCVCCQELVYQP----VTTECFHNVCKDCLQRSFKAQVFSCPACRHDLG 124

>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 = 45.9 bits (109), Expect = 2e-07
 Identities = 18/58 (31%), Positives = 24/58 (41%), Gaps = 7/58 (12%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT--TCPVCR--LPLQDPL 138
           ++  C IC     D  V+   P CG+S+   CI   L +    TCP C       D L
Sbjct: 14  DELLCLICKDIMTDAVVI---PCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDAL 68

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

 Score = 44.8 bits (106), Expect = 3e-07
 Identities = 12/55 (21%), Positives = 20/55 (36%), Gaps = 9/55 (16%)

Query: 85  EDAECSICLGEYQDKEVLR--IMPQCGHSFHLACIDIWLRKKT-TCPVCRLPLQD 136
           +  +C  C        VL      +CGH F  +C+   L   +  C  C+  +  
Sbjct: 14  DKYKCEKCH------LVLCSPKQTECGHRFCESCMAALLSSSSPKCTACQESIVK 62

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

 Score = 45.1 bits (107), Expect = 8e-07
 Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 7/54 (12%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK---TTCPVCRLPLQ 135
           +  EC ICL   ++     +  +C H F   C+   L +K   + CP+C+  + 
Sbjct: 20  KILECPICLELIKEP----VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDIT 69

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

 Score = 43.9 bits (104), Expect = 1e-06
 Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 10/59 (16%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK------TTCPVCRLPLQDP 137
           E+  C ICL   ++     +   C HSF  ACI +             CPVCR+P    
Sbjct: 18  EEVTCPICLELLKEP----VSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG 72

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

 Score = 44.4 bits (105), Expect = 1e-06
 Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 5/49 (10%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT--TCPVCR 131
           ++  C IC     D  V+   P CG+S+   CI   L +    TCP C 
Sbjct: 12  DELLCLICKDIMTDAVVI---PCCGNSYCDECIRTALLESDEHTCPTCH 57

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

 Score = 45.7 bits (108), Expect = 1e-06
 Identities = 16/52 (30%), Positives = 20/52 (38%), Gaps = 4/52 (7%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT-TCPVCRLPLQ 135
            +  C ICL   ++        +C H F   CI   LR     CP CR  L 
Sbjct: 53  SELMCPICLDMLKN---TMTTKECLHRFCADCIITALRSGNKECPTCRKKLV 101

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

 Score = 43.1 bits (102), Expect = 2e-06
 Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 7/54 (12%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK---TTCPVCRLPLQ 135
           E+  C ICL   Q      +   CGH+F L CI            CP+C+  ++
Sbjct: 19  EEVICPICLDILQKP----VTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVR 68

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

 Score = 42.3 bits (100), Expect = 2e-06
 Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 7/50 (14%)

Query: 88  ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP 137
            C  C  E +  ++L     C H+    C++        CP+C+ P    
Sbjct: 8   RCQQCQAEAKCPKLL----PCLHTLCSGCLE---ASGMQCPICQAPWPLG 50

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

 Score = 41.9 bits (99), Expect = 5e-06
 Identities = 17/60 (28%), Positives = 24/60 (40%), Gaps = 11/60 (18%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTT-------CPVCRLPLQDP 137
           E+  C ICL    +     +   CGHS   ACI +  ++  T       CPVC +     
Sbjct: 11  EEVTCPICLELLTEP----LSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFE 66

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 65

 Score = 41.9 bits (98), Expect = 5e-06
 Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 6/67 (8%)

Query: 84  VEDAECSICLGE-YQDKEVLRIMPQCGHSFHLACID-IWLRKKTTCPVCRLPLQDPLGRK 141
           ++D  C  C    Y++  +  ++  CGH+   +C+D +++R    CP C  PL+    + 
Sbjct: 1   MDDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLR----KS 56

Query: 142 HAREATF 148
           + R   F
Sbjct: 57  NFRVQLF 63

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

 Score = 41.2 bits (97), Expect = 6e-06
 Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 7/49 (14%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIW---LRKKTTCPVC 130
            +A CS+CL   ++     ++ +CGH+F  ACI  W   L +   CPVC
Sbjct: 14  VEASCSVCLEYLKE----PVIIECGHNFCKACITRWWEDLERDFPCPVC 58

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

 Score = 42.5 bits (100), Expect = 8e-06
 Identities = 19/55 (34%), Positives = 21/55 (38%), Gaps = 9/55 (16%)

Query: 84  VEDAECSICLGEYQDKEVLR--IMPQCGHSFHLACIDIWLRKKT-TCPVCRLPLQ 135
               EC ICL        LR  +   CGH F  ACI   +R     CPV    L 
Sbjct: 16  ESKYECPICL------MALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILL 64

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

 Score = 42.2 bits (99), Expect = 8e-06
 Identities = 16/53 (30%), Positives = 20/53 (37%), Gaps = 5/53 (9%)

Query: 84  VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQ 135
           V+   C IC     D     +   C H F   CI   L+   + CP CR P  
Sbjct: 21  VKSISCQICEHILADP----VETSCKHLFCRICILRCLKVMGSYCPSCRYPCF 69

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

 Score = 41.1 bits (97), Expect = 1e-05
 Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 16/62 (25%)

Query: 85  EDAECSICLGEYQDKEVLRIMP---QCGHSFHLACIDIWLRKK------TTCPVCRLPLQ 135
           E+  C ICL            P    CGHSF  AC+    +K       ++CPVCR+  Q
Sbjct: 18  EEVTCPICLELLTQ-------PLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQ 70

Query: 136 DP 137
             
Sbjct: 71  PE 72

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 63

 Score = 40.1 bits (94), Expect = 2e-05
 Identities = 16/49 (32%), Positives = 20/49 (40%), Gaps = 7/49 (14%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIW---LRKKTTCPVC 130
           E+  C ICL   Q      +   CGH+F L CI            CP+C
Sbjct: 19  EEVICPICLDILQK----PVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63

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

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 19/55 (34%), Positives = 21/55 (38%), Gaps = 9/55 (16%)

Query: 84  VEDAECSICLGEYQDKEVLR--IMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQ 135
               EC ICL        LR  +   CGH F  ACI   +R     CPV    L 
Sbjct: 16  ESKYECPICL------MALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILL 64

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

 Score = 39.3 bits (91), Expect = 5e-05
 Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 1/61 (1%)

Query: 77  NQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACI-DIWLRKKTTCPVCRLPLQ 135
           ++      +  EC +C+   +  ++      CG+     C   I   +   CP CR P  
Sbjct: 2   SRSPDAKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYP 61

Query: 136 D 136
           +
Sbjct: 62  E 62

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

 Score = 41.6 bits (97), Expect = 5e-05
 Identities = 8/39 (20%), Positives = 14/39 (35%), Gaps = 2/39 (5%)

Query: 106 PQCGHSFHLACIDIWLRK--KTTCPVCRLPLQDPLGRKH 142
             CG   HL C+  + +   +  CP C       + +  
Sbjct: 197 ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIPKVF 235

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 94

 Score = 38.7 bits (90), Expect = 1e-04
 Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 9/59 (15%)

Query: 88  ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT--------TCPVCRLPLQDPL 138
            C +CLGEY  +++   + QC   F   C+  ++            +CP    P Q  L
Sbjct: 7   GCKLCLGEYPVEQMTT-IAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHL 64

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

 Score = 37.7 bits (88), Expect = 1e-04
 Identities = 7/46 (15%), Positives = 18/46 (39%), Gaps = 3/46 (6%)

Query: 89  CSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL 134
           C+I     +   +    P+    F  + ++ +++     P+   PL
Sbjct: 6   CAISGKVPRRPVLS---PKSRTIFEKSLLEQYVKDTGNDPITNEPL 48

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 37.2 bits (86), Expect = 3e-04
 Identities = 16/65 (24%), Positives = 22/65 (33%), Gaps = 9/65 (13%)

Query: 78  QEAFKSVEDAECSICLGEYQDKEVLRIMPQCG-----HSFHLACIDIWL--RKKTTCPVC 130
             +        C IC  E  D+  L I P C      H  H AC+  W+       C +C
Sbjct: 7   GTSITPSSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELC 64

Query: 131 RLPLQ 135
           +    
Sbjct: 65  KYEFI 69

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

 Score = 38.6 bits (89), Expect = 3e-04
 Identities = 14/56 (25%), Positives = 16/56 (28%), Gaps = 9/56 (16%)

Query: 85  EDAECSICLGEYQDKEVLR--IMPQCGHSFHLACIDIWLRKKT-TCPVCRLPLQDP 137
               CS C        VLR     QCGH +   C+   L      C  C       
Sbjct: 30  AKYLCSACR------NVLRRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYE 79

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	191
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.72
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.62
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.55
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.55
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.54
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.53
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.53
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.48
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.45
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.42
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.4
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.39
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.39
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.38
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.36
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.36
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.35
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.35
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.34
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.34
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.34
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.32
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.31
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.3
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.3
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.26
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.26
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.25
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.25
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.25
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.25
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.24
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.23
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.22
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.19
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.19
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.18
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.18
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.18
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.12
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.12
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.12
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.1
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.1
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.1
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.09
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.08
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.06
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.06
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.06
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.05
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.03
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.96
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.95
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.92
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.92
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.89
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.87
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.83
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.82
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.78
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.75
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.74
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.72
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.71
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.64
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.6
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.6
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.48
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.36
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.18
3nw0_A	238	Non-structural maintenance of chromosomes element	97.93
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	96.84
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.4
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	94.71
1we9_A	64	PHD finger family protein; structural genomics, PH	91.69
2l2t_A	44	Receptor tyrosine-protein kinase ERBB-4; transmemb	91.46
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	91.03
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	88.86
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	88.7
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	88.67
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	88.58
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	87.25
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	86.7
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	86.31
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	86.3
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	85.53
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	84.99
1z60_A	59	TFIIH basal transcription factor complex P44 subun	84.79
2jwa_A	44	Receptor tyrosine-protein kinase ERBB-2; transmemb	84.73
1y02_A	120	CARP2, FYVE-ring finger protein sakura; zinc-bindi	84.5
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	84.46
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	84.13
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	84.03
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	83.97
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	83.55
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	82.45
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	81.89
1wem_A	76	Death associated transcription factor 1; structura	81.8
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	81.18
1wee_A	72	PHD finger family protein; structural genomics, PH	80.92
2klu_A	70	T-cell surface glycoprotein CD4; cell membrane, di	80.09
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	80.02

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

Probab=99.72  E-value=1.5e-17  Score=111.46  Aligned_cols=80  Identities=30%  Similarity=0.607  Sum_probs=70.2

Q ss_pred             CCCCCCCCCHHHHhhCCCccccccccCCCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCcccccccccc
Q 029544           56 PGHRINGLEPVLVAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ  135 (191)
Q Consensus        56 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~  135 (191)
                      ......++++..++.+|...+.........+..|+||++.+..+.....++ |+|.||..||..|+..+..||+||..+.
T Consensus        10 ~~~~~~~~s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   88 (91)
T 2l0b_A           10 HMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCMFP   88 (91)
T ss_dssp             CSSCCCCCCHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTTCCBSS
T ss_pred             CCcCCCCCCHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCcCccCC
Confidence            466778999999999999888766656667788999999999888887887 9999999999999999999999999886


Q ss_pred             C
Q 029544          136 D  136 (191)
Q Consensus       136 ~  136 (191)
                      .
T Consensus        89 ~   89 (91)
T 2l0b_A           89 P   89 (91)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.62  E-value=1e-16  Score=103.39  Aligned_cols=68  Identities=32%  Similarity=0.954  Sum_probs=55.0

Q ss_pred             HhhCCCccccccccCCCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           68 VAAIPTMKFNQEAFKSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        68 ~~~~~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      ++.+|..++.... ...++..|+||++.+..+..+..++ |+|.||..|+.+|+..+..||+||+++...
T Consensus         6 i~~lp~~~~~~~~-~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A            6 SGQLPSYRFNPNN-HQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             CSSCCCEEBCSSS-CSSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             HhhCCcEEecCcc-ccCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            3456666665332 3346678999999999988877886 999999999999999888999999988754

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

Probab=99.55  E-value=3e-15  Score=90.54  Aligned_cols=52  Identities=46%  Similarity=1.177  Sum_probs=45.5

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCcccccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ  135 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~  135 (191)
                      +++..|+||++.+..+.....++.|+|.||..|+.+|+..+.+||+||.++.
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            3566899999999988777777669999999999999999999999998764

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

Probab=99.55  E-value=5.1e-15  Score=95.05  Aligned_cols=55  Identities=31%  Similarity=0.869  Sum_probs=48.4

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCCC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPL  138 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~~  138 (191)
                      ...+..|+||++.+..+..+..++ |+|.||..||.+|+..+..||+||..+....
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2ep4_A           12 LNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA   66 (74)
T ss_dssp             CCCSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSSCC
T ss_pred             CCCCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCccccccc
Confidence            345678999999999988888887 9999999999999998889999999987543

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

Probab=99.54  E-value=6.4e-15  Score=95.53  Aligned_cols=55  Identities=38%  Similarity=0.853  Sum_probs=48.3

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCCC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPL  138 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~~  138 (191)
                      ......|+||++.|..+..+..++ |+|.||..||.+|+..+..||+||..+....
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (78)
T 2ect_A           12 VGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQN   66 (78)
T ss_dssp             SSSSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCCCCSC
T ss_pred             CCCCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCccCCcc
Confidence            345678999999999888887786 9999999999999998899999999987653

>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=99.53  E-value=9.3e-15  Score=92.53  Aligned_cols=55  Identities=36%  Similarity=0.939  Sum_probs=47.6

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCCC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPL  138 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~~  138 (191)
                      ......|+||++.+........++ |+|.||..|+.+|+..+..||+||..+....
T Consensus        11 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   65 (69)
T 2kiz_A           11 EDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQL   65 (69)
T ss_dssp             TTCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCSCC
T ss_pred             CCCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccCcC
Confidence            345678999999998877777776 9999999999999998889999999987653

>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=99.53  E-value=1.6e-14  Score=100.42  Aligned_cols=64  Identities=23%  Similarity=0.554  Sum_probs=49.0

Q ss_pred             CCCcCcccccccccCc---------------cEEEcCCCCCcccHhhHHHHh-----cCCCccccccccccCCCCCCCcc
Q 029544           85 EDAECSICLGEYQDKE---------------VLRIMPQCGHSFHLACIDIWL-----RKKTTCPVCRLPLQDPLGRKHAR  144 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~---------------~~~~~~~C~H~f~~~Ci~~wl-----~~~~~CP~Cr~~~~~~~~~~~~~  144 (191)
                      .+..|+||++.|..+.               ....+ +|+|.||..||.+|+     ..+..||+||..+....+.++..
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~-~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~~g~qp~g  102 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLT-KCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPWG  102 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEES-SSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSSSCTTS
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecC-CCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCCCCCCCCC
Confidence            4568999999997653               22344 599999999999999     45678999999998877666555


Q ss_pred             ccccc
Q 029544          145 EATFS  149 (191)
Q Consensus       145 ~~~~~  149 (191)
                      .+...
T Consensus       103 ~m~~~  107 (114)
T 1v87_A          103 KMEVF  107 (114)
T ss_dssp             SCCCS
T ss_pred             eEEEE
Confidence            54443

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

Probab=99.48  E-value=2.2e-14  Score=93.83  Aligned_cols=52  Identities=29%  Similarity=0.823  Sum_probs=41.7

Q ss_pred             CCCcCccccccccc-----------CccEEEcCCCCCcccHhhHHHHhcCCCccccccccccC
Q 029544           85 EDAECSICLGEYQD-----------KEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        85 ~~~~C~IC~~~~~~-----------~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      ++..|+||++.+.+           ...++.+++|+|.||..||.+|+..+.+||+||+++..
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   76 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVV   76 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcch
Confidence            45668888888854           33344555699999999999999999999999998753

>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=99.45  E-value=4.7e-14  Score=85.17  Aligned_cols=51  Identities=29%  Similarity=0.772  Sum_probs=42.0

Q ss_pred             CCCCcCcccccccccCc-cEEEcCCCCCcccHhhHHHHhcCCCcccccccccc
Q 029544           84 VEDAECSICLGEYQDKE-VLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ  135 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~-~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~  135 (191)
                      ..+..|+||++.+.+.. ....+ +|+|.||..|+.+|+..+..||+||..+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            3 SGSSGCPICLEDIHTSRVVAHVL-PCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             SCCCSCTTTCCCCCTTTSCEEEC-TTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCCcCcccChhhcCCCcCeEec-CCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            34668999999997643 34455 49999999999999998899999998764

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

Probab=99.42  E-value=7.4e-14  Score=88.70  Aligned_cols=53  Identities=28%  Similarity=0.744  Sum_probs=44.1

Q ss_pred             CCCCcCcccccccccC----ccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           84 VEDAECSICLGEYQDK----EVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~----~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      .++..|+||++.+.++    .....+ +|||.||..|+.+|+..+..||+||..+...
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVST-ECGHVFCSQCLRDSLKNANTCPTCRKKINHK   64 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEEC-TTSCEEEHHHHHHHHHHCSBCTTTCCBCCCC
T ss_pred             CCCCCCcccChhhhccccccCCeEeC-CCCChHhHHHHHHHHHcCCCCCCCCCccChh
Confidence            4577899999999875    333445 5999999999999999889999999988754

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

Probab=99.40  E-value=1.3e-13  Score=87.69  Aligned_cols=49  Identities=27%  Similarity=0.581  Sum_probs=43.1

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      .+...|+||++.+.++..+    +|+|.||..|+..|+..+..||+||..+..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~----~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (71)
T 2d8t_A           13 LTVPECAICLQTCVHPVSL----PCKHVFCYLCVKGASWLGKRCALCRQEIPE   61 (71)
T ss_dssp             SSCCBCSSSSSBCSSEEEE----TTTEEEEHHHHHHCTTCSSBCSSSCCBCCH
T ss_pred             CCCCCCccCCcccCCCEEc----cCCCHHHHHHHHHHHHCCCcCcCcCchhCH
Confidence            4567899999999887555    699999999999999988999999998864

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

Probab=99.39  E-value=8.8e-14  Score=87.76  Aligned_cols=53  Identities=28%  Similarity=0.736  Sum_probs=43.2

Q ss_pred             CCCCCcCcccccccccCc----cEEEcCCCCCcccHhhHHHHhcCCCccccccccccC
Q 029544           83 SVEDAECSICLGEYQDKE----VLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~----~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      ..+...|+||++.+.++.    ....+ +|+|.||..|+..|+..+..||+||..+..
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           12 PSGTVSCPICMDGYSEIVQNGRLIVST-ECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             TTCCCCCTTTCCCHHHHTTTTCCEEEC-SSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCCcccCccccccccccCCeEeC-CCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            345678999999998752    22345 599999999999999988899999998753

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

Probab=99.39  E-value=2.1e-13  Score=87.00  Aligned_cols=53  Identities=26%  Similarity=0.554  Sum_probs=44.1

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCCC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPL  138 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~~  138 (191)
                      ..+...|+||++.+.++..+  + +|+|.||..||..|+..+..||+||..+....
T Consensus        12 ~~~~~~C~IC~~~~~~p~~~--~-~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   64 (72)
T 2djb_A           12 LTPYILCSICKGYLIDATTI--T-ECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQ   64 (72)
T ss_dssp             CCGGGSCTTTSSCCSSCEEC--S-SSCCEECHHHHHHHHHHCSSCTTTCCCCCSSC
T ss_pred             cCCCCCCCCCChHHHCcCEE--C-CCCCHHHHHHHHHHHHcCCcCCCcCcccCccc
Confidence            34567899999999886443  2 59999999999999998889999999987543

>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=99.38  E-value=3.3e-13  Score=92.48  Aligned_cols=51  Identities=27%  Similarity=0.684  Sum_probs=42.2

Q ss_pred             CCCCcCcccccccccCc---------------cEEEcCCCCCcccHhhHHHHhcCCCcccccccccc
Q 029544           84 VEDAECSICLGEYQDKE---------------VLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ  135 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~---------------~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~  135 (191)
                      .++..|+||++.|....               .+..+ +|+|.||..||.+|+..+.+||+||.++.
T Consensus        35 ~~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~-~C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           35 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWG-VCNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             SCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEE-TTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCCCccCChhHhCcCchhhccccccCCccceEeec-ccCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            35678999999988652               23445 59999999999999999999999999864

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

Probab=99.36  E-value=2e-13  Score=84.82  Aligned_cols=52  Identities=29%  Similarity=0.751  Sum_probs=42.8

Q ss_pred             CCCcCcccccccccC----ccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           85 EDAECSICLGEYQDK----EVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~----~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      ++..|+||++.+.++    .....+ +|||.||..|+.+|+..+..||+||..+...
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   57 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVST-ECGHVFCSQCLRDSLKNANTCPTCRKKINHK   57 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEE-TTSCEEEHHHHHHHHHHCSBCTTTCCBCTTT
T ss_pred             CCCCCCccChhhhCccccCCCEEeC-CCCCchhHHHHHHHHHcCCCCCCCCccCCcc
Confidence            456899999999875    223344 5999999999999999888999999988754

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

Probab=99.36  E-value=6e-13  Score=86.58  Aligned_cols=55  Identities=29%  Similarity=0.696  Sum_probs=44.3

Q ss_pred             CCCCCCcCcccccccccCccEEEcCCCC-----CcccHhhHHHHhcCC--CccccccccccCCC
Q 029544           82 KSVEDAECSICLGEYQDKEVLRIMPQCG-----HSFHLACIDIWLRKK--TTCPVCRLPLQDPL  138 (191)
Q Consensus        82 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~-----H~f~~~Ci~~wl~~~--~~CP~Cr~~~~~~~  138 (191)
                      ...++..|.||++++.+...+ ++| |+     |.||..||++|+..+  .+||+||..+....
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~   72 (80)
T 2d8s_A           11 TPSSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMET   72 (80)
T ss_dssp             CCTTSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCC
T ss_pred             CCCCCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCc
Confidence            334567899999999876666 466 96     999999999999855  48999999987544

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

Probab=99.35  E-value=4.1e-13  Score=85.08  Aligned_cols=50  Identities=38%  Similarity=0.967  Sum_probs=42.6

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPL  138 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~~  138 (191)
                      .+...|+||++.+.+    ..+ +|+|.||..|+.+|+..+..||+||..+....
T Consensus        13 ~~~~~C~IC~~~~~~----~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LIL-PCAHSFCQKCIDKWSDRHRNCPICRLQMTGAN   62 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEE-TTTEEECHHHHHHSSCCCSSCHHHHHCTTCCC
T ss_pred             CCCCCCeeCCcCccC----ccc-CCCCcccHHHHHHHHHCcCcCCCcCCcccCCC
Confidence            456789999999887    334 59999999999999998899999999887543

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

Probab=99.35  E-value=8.2e-13  Score=82.76  Aligned_cols=50  Identities=20%  Similarity=0.524  Sum_probs=42.9

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-CCCccccccccccCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-~~~~CP~Cr~~~~~~  137 (191)
                      .+...|+||++.+.++..+    +|||.||..|+..|+. ....||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCSPKQT----ECGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCCEECTTTCCEESSCCCC----SSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             CcCCCCCCCChHhcCeeEC----CCCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            4567899999999988776    6999999999999995 566799999988653

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

Probab=99.34  E-value=8.7e-13  Score=84.16  Aligned_cols=51  Identities=31%  Similarity=0.693  Sum_probs=42.6

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc---CCCccccccccccCC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR---KKTTCPVCRLPLQDP  137 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~---~~~~CP~Cr~~~~~~  137 (191)
                      ..+...|+||++.+.++..+    +|||.||..|+..|+.   ....||+||..+...
T Consensus        17 ~~~~~~C~IC~~~~~~~~~~----~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           17 LQEEVICPICLDILQKPVTI----DCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCCCBCTTTCSBCSSEEEC----TTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCC
T ss_pred             CccCCEeccCCcccCCeEEc----CCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcc
Confidence            45677899999999976655    6999999999999997   455799999988653

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

Probab=99.34  E-value=4.8e-13  Score=87.25  Aligned_cols=49  Identities=27%  Similarity=0.542  Sum_probs=42.8

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCcccccccccc
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ  135 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~  135 (191)
                      ......|+||++.+.++..+    +|+|.||..|+..|+.....||+||..+.
T Consensus        12 ~~~~~~C~IC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           12 EEIPFRCFICRQAFQNPVVT----KCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCCSBCSSSCSBCCSEEEC----TTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCCcCCCchhcCeeEc----cCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            34567899999999887544    69999999999999998889999999986

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

Probab=99.34  E-value=4.5e-13  Score=85.96  Aligned_cols=50  Identities=30%  Similarity=0.584  Sum_probs=42.3

Q ss_pred             CCCCCcCcccccccccCccEEEcCC-CCCcccHhhHHHHhcCC--CccccccccccC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQ-CGHSFHLACIDIWLRKK--TTCPVCRLPLQD  136 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~-C~H~f~~~Ci~~wl~~~--~~CP~Cr~~~~~  136 (191)
                      ..+...|+||++.+.++..+    + |||.||..||..|+..+  ..||+||..+..
T Consensus        12 ~~~~~~C~IC~~~~~~p~~~----~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A           12 IPDELLCLICKDIMTDAVVI----PCCGNSYCDECIRTALLESDEHTCPTCHQNDVS   64 (74)
T ss_dssp             SCGGGSCSSSCCCCTTCEEC----SSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCC
T ss_pred             CCCCCCCcCCChHHhCCeEc----CCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCC
Confidence            34567899999999988776    6 99999999999999854  679999997653

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

Probab=99.32  E-value=5.8e-13  Score=95.61  Aligned_cols=48  Identities=33%  Similarity=0.929  Sum_probs=42.5

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      ++..|+||++.+.++..+    +|||.||..||..|+..+..||+||.++..
T Consensus        52 ~~~~C~iC~~~~~~~~~~----~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           52 NELQCIICSEYFIEAVTL----NCAHSFCSYCINEWMKRKIECPICRKDIKS   99 (138)
T ss_dssp             HHSBCTTTCSBCSSEEEE----TTSCEEEHHHHHHHTTTCSBCTTTCCBCCC
T ss_pred             ccCCCcccCcccCCceEC----CCCCCccHHHHHHHHHcCCcCCCCCCcCCC
Confidence            356799999999987665    699999999999999999999999998854

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

Probab=99.31  E-value=7.1e-13  Score=83.46  Aligned_cols=49  Identities=33%  Similarity=0.933  Sum_probs=41.4

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      .+..|+||++.+.++.  ..+ +|||.||..|+..|+..+..||+||..+..
T Consensus         4 ~~~~C~IC~~~~~~~~--~~~-~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSNYS--MAL-PCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCSCE--EET-TTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCeeCCccccCCc--Eec-CCCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            4567999999988653  344 599999999999999988899999998864

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

Probab=99.30  E-value=3.9e-12  Score=83.96  Aligned_cols=54  Identities=24%  Similarity=0.686  Sum_probs=43.7

Q ss_pred             CCCCCcCcccccccccCcc-EEEcCCCCCcccHhhHHHHhcCC---CccccccccccCC
Q 029544           83 SVEDAECSICLGEYQDKEV-LRIMPQCGHSFHLACIDIWLRKK---TTCPVCRLPLQDP  137 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~-~~~~~~C~H~f~~~Ci~~wl~~~---~~CP~Cr~~~~~~  137 (191)
                      ..+...|+||++.+.+... ...+ +|||.||..|+..|+..+   ..||+||..+...
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~-~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           12 LREVLECPICMESFTEEQLRPKLL-HCGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CCSCCBCTTTCCBCCTTSSCEEEC-SSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             ccCCCCCccCCccccccCCCeEEC-CCCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            3556789999999998553 3445 599999999999999865   6799999987653

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

Probab=99.30  E-value=1.7e-12  Score=83.97  Aligned_cols=50  Identities=26%  Similarity=0.523  Sum_probs=43.7

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC-CCccccccccccCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK-KTTCPVCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~-~~~CP~Cr~~~~~~  137 (191)
                      .+...|+||++.+.++..+    +|||.||..||..|+.. +..||+||..+...
T Consensus         6 ~~~~~C~IC~~~~~~Pv~~----~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~   56 (78)
T 1t1h_A            6 PEYFRCPISLELMKDPVIV----STGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             SSSSSCTTTSCCCSSEEEE----TTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             cccCCCCCccccccCCEEc----CCCCeecHHHHHHHHHHCcCCCCCCcCCCChh
Confidence            4577899999999998766    69999999999999986 77899999988643

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

Probab=99.26  E-value=1.5e-12  Score=84.36  Aligned_cols=50  Identities=36%  Similarity=0.775  Sum_probs=43.2

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC-------CCccccccccccC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK-------KTTCPVCRLPLQD  136 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~-------~~~CP~Cr~~~~~  136 (191)
                      ..+...|+||++.+.++..+    +|||.||..|+..|+..       ...||+||..+..
T Consensus         9 ~~~~~~C~IC~~~~~~p~~l----~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A            9 VQEEVTCPICLELLTEPLSL----DCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             CCCCCEETTTTEECSSCCCC----SSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCS
T ss_pred             cccCCCCcCCCcccCCeeEC----CCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCH
Confidence            34677899999999988776    69999999999999986       5679999998864

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

Probab=99.26  E-value=4.4e-12  Score=78.62  Aligned_cols=45  Identities=38%  Similarity=0.774  Sum_probs=38.1

Q ss_pred             CCCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc---CCCccccc
Q 029544           82 KSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR---KKTTCPVC  130 (191)
Q Consensus        82 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~---~~~~CP~C  130 (191)
                      ...++..|+||++.+.++..+    +|||.||..||.+|+.   ....||+|
T Consensus        16 ~~~~~~~C~IC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           16 KLQEEVICPICLDILQKPVTI----DCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCCBCTTTCSBCSSCEEC----TTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             hCccCCCCCcCCchhCCeEEe----CCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            345677899999999987666    6999999999999998   45579998

>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=99.25  E-value=6.8e-13  Score=92.24  Aligned_cols=52  Identities=27%  Similarity=0.675  Sum_probs=1.5

Q ss_pred             CCCCcCcccccccccCcc--------------EEEcCCCCCcccHhhHHHHhcCCCcccccccccc
Q 029544           84 VEDAECSICLGEYQDKEV--------------LRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ  135 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~--------------~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~  135 (191)
                      ..+..|+||++.|..+..              ....++|+|.||..||.+|+..+.+||+||.++.
T Consensus        46 ~~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~  111 (117)
T 4a0k_B           46 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  111 (117)
T ss_dssp             CCC---------------------------------------------------------------
T ss_pred             CCCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeee
Confidence            346789999999976321              1222259999999999999999999999999864

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

Probab=99.25  E-value=5.1e-12  Score=78.84  Aligned_cols=52  Identities=27%  Similarity=0.776  Sum_probs=40.9

Q ss_pred             CCcCccccc-ccccCccEEEcCCCCCcccHhhHHHHhcC-CCccccccccccCC
Q 029544           86 DAECSICLG-EYQDKEVLRIMPQCGHSFHLACIDIWLRK-KTTCPVCRLPLQDP  137 (191)
Q Consensus        86 ~~~C~IC~~-~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~-~~~CP~Cr~~~~~~  137 (191)
                      +..|+||++ .+.++.....+.+|||.||..|+.+|+.. ...||+||..+...
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   56 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccc
Confidence            567999999 88887643322259999999999999764 45699999988654

>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=99.25  E-value=1.8e-12  Score=87.97  Aligned_cols=50  Identities=34%  Similarity=0.796  Sum_probs=42.1

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCC-CccccccccccC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK-TTCPVCRLPLQD  136 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~-~~CP~Cr~~~~~  136 (191)
                      .+...|+||++.+.++..+  + +|||.||..||..|+... ..||+||.++..
T Consensus        20 ~~~~~C~IC~~~~~~p~~~--~-~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (100)
T 3lrq_A           20 AEVFRCFICMEKLRDARLC--P-HCSKLCCFSCIRRWLTEQRAQCPHCRAPLQL   70 (100)
T ss_dssp             HHHTBCTTTCSBCSSEEEC--T-TTCCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCCCCCccCCccccCcccc--C-CCCChhhHHHHHHHHHHCcCCCCCCCCcCCH
Confidence            3467899999999886551  2 699999999999999977 689999999864

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

Probab=99.25  E-value=4.4e-12  Score=83.01  Aligned_cols=51  Identities=37%  Similarity=0.762  Sum_probs=42.9

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC------CCccccccccccCC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK------KTTCPVCRLPLQDP  137 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~------~~~CP~Cr~~~~~~  137 (191)
                      ..++..|+||++.+.++..+    +|+|.||..|+..|+..      ...||+||..+...
T Consensus        16 ~~~~~~C~IC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           16 IKEEVTCPICLELLKEPVSA----DCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             CCTTTSCTTTCSCCSSCEEC----TTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTT
T ss_pred             CccCCCCcCCChhhCcceeC----CCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHH
Confidence            34567899999999988644    69999999999999986      66799999988643

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

Probab=99.24  E-value=6.9e-12  Score=82.07  Aligned_cols=50  Identities=40%  Similarity=0.850  Sum_probs=43.2

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC------CCccccccccccC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK------KTTCPVCRLPLQD  136 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~------~~~CP~Cr~~~~~  136 (191)
                      ..+...|+||++.+.++..+    +|+|.||..|+..|+..      ...||+||..+..
T Consensus        16 ~~~~~~C~IC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecv_A           16 VKEEVTCPICLELLTQPLSL----DCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQP   71 (85)
T ss_dssp             CCCCCCCTTTCSCCSSCBCC----SSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCS
T ss_pred             ccCCCCCCCCCcccCCceeC----CCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCH
Confidence            34567899999999987666    69999999999999976      6779999998875

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

Probab=99.23  E-value=4.5e-12  Score=84.54  Aligned_cols=50  Identities=30%  Similarity=0.584  Sum_probs=42.4

Q ss_pred             CCCCCCcCcccccccccCccEEEcCC-CCCcccHhhHHHHhcC--CCcccccccccc
Q 029544           82 KSVEDAECSICLGEYQDKEVLRIMPQ-CGHSFHLACIDIWLRK--KTTCPVCRLPLQ  135 (191)
Q Consensus        82 ~~~~~~~C~IC~~~~~~~~~~~~~~~-C~H~f~~~Ci~~wl~~--~~~CP~Cr~~~~  135 (191)
                      ...++..|+||++.+.++..+    + |||.||..||..|+..  ...||+||..+.
T Consensus         9 ~~~~~~~C~IC~~~~~~p~~~----~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A            9 PIPDELLCLICKDIMTDAVVI----PCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CCCTTTEETTTTEECSSCEEC----TTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             cCCcCCCCCCCChhhcCceEC----CCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            345678899999999988766    7 9999999999999973  357999999874

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

Probab=99.22  E-value=8.8e-12  Score=75.78  Aligned_cols=43  Identities=40%  Similarity=1.031  Sum_probs=36.7

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc---CCCccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR---KKTTCPVC  130 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~---~~~~CP~C  130 (191)
                      .+...|+||++.+.++..+    +|+|.||..||..|+.   ....||+|
T Consensus        13 ~~~~~C~IC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKEPVII----ECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSSCCCC----SSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccCCCCccCCcccCccEeC----CCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            4567899999999998665    6999999999999954   55679998

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

Probab=99.19  E-value=7.7e-12  Score=88.55  Aligned_cols=54  Identities=28%  Similarity=0.717  Sum_probs=44.5

Q ss_pred             CCCCcCcccccccccC----ccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCCC
Q 029544           84 VEDAECSICLGEYQDK----EVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPL  138 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~----~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~~  138 (191)
                      .+...|+||++.+.++    .....+ +|||.||..||.+|+..+..||+||..+....
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVST-ECGHVFCSQCLRDSLKNANTCPTCRKKINHKR   62 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEE-TTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTC
T ss_pred             CCCCCCcccChhhhCccccccCeEec-CCCChhhHHHHHHHHHhCCCCCCCCCcCcccc
Confidence            3567899999999876    223344 59999999999999999999999999987543

>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=1.9e-11  Score=77.98  Aligned_cols=50  Identities=22%  Similarity=0.561  Sum_probs=41.5

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCC--CccccccccccCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK--TTCPVCRLPLQDP  137 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~--~~CP~Cr~~~~~~  137 (191)
                      ....|+||++.+..+....   .|+|.||..||.+|+..+  .+||+||.++...
T Consensus        14 ~i~~C~IC~~~i~~g~~C~---~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~   65 (74)
T 2ct0_A           14 AVKICNICHSLLIQGQSCE---TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE   65 (74)
T ss_dssp             SSCBCSSSCCBCSSSEECS---SSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSC
T ss_pred             CCCcCcchhhHcccCCccC---CCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCC
Confidence            4567999999998665432   699999999999999876  7899999888644

>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=99.18  E-value=7.8e-12  Score=85.90  Aligned_cols=51  Identities=27%  Similarity=0.709  Sum_probs=43.2

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      .++..|+||++.+.++..+  . +|||.||..|+..|+..+..||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~p~~~--~-~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           13 NPHLMCVLCGGYFIDATTI--I-ECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGGTBCTTTSSBCSSEEEE--T-TTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             CCcCCCccCChHHhCcCEe--C-CCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            3567899999999876443  2 5999999999999999889999999998754

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

Probab=99.18  E-value=8.8e-12  Score=87.73  Aligned_cols=48  Identities=27%  Similarity=0.567  Sum_probs=41.5

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCC-ccccccccccC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT-TCPVCRLPLQD  136 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~-~CP~Cr~~~~~  136 (191)
                      +...|+||++.+.++..+    +|||.||..||..|+..+. .||+||..+..
T Consensus        51 ~~~~C~IC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           51 ETFQCICCQELVFRPITT----VCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHTBCTTTSSBCSSEEEC----TTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             cCCCCCcCChHHcCcEEe----eCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            456899999999988666    6999999999999998544 89999999875

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

Probab=99.18  E-value=8.6e-12  Score=84.32  Aligned_cols=49  Identities=29%  Similarity=0.733  Sum_probs=41.9

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      +...|+||++.+.++..+  . +|||.||..|+..|+..+..||+||..+..
T Consensus        21 ~~~~C~IC~~~~~~p~~~--~-~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           21 DLLRCGICFEYFNIAMII--P-QCSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HHTBCTTTCSBCSSEEEC--T-TTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCCcccCChhhCCcCEE--C-CCCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            456899999999886433  2 599999999999999988899999998875

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

Probab=99.12  E-value=5.8e-12  Score=87.50  Aligned_cols=49  Identities=24%  Similarity=0.687  Sum_probs=42.0

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC-CCccccccccccC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK-KTTCPVCRLPLQD  136 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~-~~~CP~Cr~~~~~  136 (191)
                      .++..|+||++.+.++..+    +|||.||..|+..|+.. ...||+||..+..
T Consensus        13 ~~~~~C~iC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           13 LSECQCGICMEILVEPVTL----PCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHHBCTTTCSBCSSCEEC----TTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCCccCCcccCceeEc----CCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            3467899999999987766    69999999999999976 6679999998863

>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=99.12  E-value=3e-11  Score=83.23  Aligned_cols=49  Identities=29%  Similarity=0.647  Sum_probs=41.9

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCC---ccccccccccCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT---TCPVCRLPLQDP  137 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~---~CP~Cr~~~~~~  137 (191)
                      +...|+||++.+.++..+    +|||.||..|+..|+..+.   .||+||..+...
T Consensus        20 ~~~~C~IC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (112)
T 1jm7_A           20 KILECPICLELIKEPVST----KCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (112)
T ss_dssp             HHTSCSSSCCCCSSCCBC----TTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             CCCCCcccChhhcCeEEC----CCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHh
Confidence            356799999999988776    6999999999999998654   799999988754

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

Probab=99.12  E-value=1.2e-10  Score=75.30  Aligned_cols=55  Identities=20%  Similarity=0.489  Sum_probs=41.1

Q ss_pred             CCCCCcCcccccccccCc-cEEEcCCCCCcccHhhHHHHhc-CCCccccccccccCCC
Q 029544           83 SVEDAECSICLGEYQDKE-VLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQDPL  138 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~-~~~~~~~C~H~f~~~Ci~~wl~-~~~~CP~Cr~~~~~~~  138 (191)
                      .+++..|+||++.+.... ...-+ +|||.||..|+..++. ....||.||..+....
T Consensus         8 ~~~~~~CpICle~~~~~d~~~~p~-~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~   64 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEIDDINFFPC-TCGYQICRFCWHRIRTDENGLCPACRKPYPEDP   64 (78)
T ss_dssp             CCCCCBCTTTCCBCCTTTTTCCSS-TTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCS
T ss_pred             cccCCcCCccCccCcccccccccc-CCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCc
Confidence            356778999999886432 22212 3999999999999875 4567999999987643

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

Probab=99.10  E-value=3.4e-11  Score=87.54  Aligned_cols=49  Identities=20%  Similarity=0.489  Sum_probs=42.4

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCC-ccccccccccCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT-TCPVCRLPLQDP  137 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~-~CP~Cr~~~~~~  137 (191)
                      +...|+||++.+.++..+    +|||.||..||..|+.... .||+||..+...
T Consensus        77 ~~~~C~IC~~~~~~pv~~----~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQPVTT----ECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSSEEEC----TTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhcCCEEc----CCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            456899999999988765    6999999999999998654 799999998765

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

Probab=99.10  E-value=6.2e-11  Score=80.30  Aligned_cols=50  Identities=18%  Similarity=0.110  Sum_probs=45.3

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      .+.+.|+||++.|.++..+    +|||.||..||..|+..+.+||+|+.++...
T Consensus        27 p~~~~CpI~~~~m~dPV~~----~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~   76 (100)
T 2kre_A           27 PDEFRDPLMDTLMTDPVRL----PSGTIMDRSIILRHLLNSPTDPFNRQTLTES   76 (100)
T ss_dssp             STTTBCTTTCSBCSSEEEE----TTTEEEEHHHHHHHTTSCSBCSSSCCBCCTT
T ss_pred             cHhhCCcCccCcccCCeEC----CCCCEEchHHHHHHHHcCCCCCCCCCCCChh
Confidence            4578899999999999888    7999999999999999888999999988653

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

Probab=99.10  E-value=4.3e-11  Score=78.70  Aligned_cols=49  Identities=18%  Similarity=0.098  Sum_probs=44.3

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      .+.+.|+||++.|.++..+    +|||.||..||..|+..+.+||+|+.++..
T Consensus        12 p~~~~CpI~~~~m~dPV~~----~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   60 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTDPVRL----PSGTVMDRSIILRHLLNSPTDPFNRQMLTE   60 (85)
T ss_dssp             CTTTBCTTTCSBCSSEEEC----TTSCEEEHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             chheECcccCchhcCCeEC----CCCCEECHHHHHHHHhcCCCCCCCcCCCCh
Confidence            4578899999999999887    799999999999999988899999988764

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

Probab=99.09  E-value=2.2e-11  Score=85.01  Aligned_cols=51  Identities=33%  Similarity=0.563  Sum_probs=43.1

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCC-ccccccccccCC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT-TCPVCRLPLQDP  137 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~-~CP~Cr~~~~~~  137 (191)
                      ..+...|+||++.+.++..+    +|||.||..||..|+.... .||+||..+...
T Consensus        15 ~~~~~~C~IC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           15 LESKYECPICLMALREAVQT----PCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             CCGGGBCTTTCSBCSSEEEC----TTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCcCChhhcCeEEC----CcCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            34567899999999988554    6999999999999998655 899999988753

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

Probab=99.08  E-value=8.8e-11  Score=79.26  Aligned_cols=50  Identities=22%  Similarity=0.128  Sum_probs=45.0

Q ss_pred             CCCCcCcccccccccCccEEEcCCCC-CcccHhhHHHHhcCCCccccccccccCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCG-HSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~-H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      .+++.|+||++.|.++..+    +|| |.||..||..|+..+.+||+||.++...
T Consensus        20 p~~~~CpI~~~~m~dPV~~----~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~   70 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCDPVVL----PSSRVTVDRSTIARHLLSDQTDPFNRSPLTMD   70 (98)
T ss_dssp             CTTTBCTTTCSBCSSEEEC----TTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTT
T ss_pred             cHhcCCcCccccccCCeEC----CCCCeEECHHHHHHHHHhCCCCCCCCCCCChh
Confidence            4578899999999999887    799 9999999999999888999999988753

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

Probab=99.06  E-value=4.8e-11  Score=85.85  Aligned_cols=51  Identities=24%  Similarity=0.387  Sum_probs=43.0

Q ss_pred             CCCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCC-ccccccccccC
Q 029544           82 KSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT-TCPVCRLPLQD  136 (191)
Q Consensus        82 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~-~CP~Cr~~~~~  136 (191)
                      ...+...|+||++.+.++..+    +|||.||..||..|+.... .||+||.++..
T Consensus        27 ~l~~~~~C~IC~~~~~~pv~~----~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   78 (141)
T 3knv_A           27 KLEAKYLCSACRNVLRRPFQA----QCGHRYCSFCLASILSSGPQNCAACVHEGIY   78 (141)
T ss_dssp             GCCGGGBCTTTCSBCSSEEEC----TTSCEEEHHHHHHHGGGSCEECHHHHHTTCC
T ss_pred             cCCcCcCCCCCChhhcCcEEC----CCCCccCHHHHHHHHhcCCCCCCCCCCcccc
Confidence            445678899999999998665    6999999999999998554 79999998643

>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=99.06  E-value=5.4e-11  Score=87.70  Aligned_cols=49  Identities=33%  Similarity=0.679  Sum_probs=40.9

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC-CCccccccccccC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK-KTTCPVCRLPLQD  136 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~-~~~CP~Cr~~~~~  136 (191)
                      +...|+||++.+.++..+  + +|||.||..||..|+.. +..||+||..+..
T Consensus        53 ~~~~C~IC~~~~~~p~~~--~-~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           53 SELMCPICLDMLKNTMTT--K-ECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHBCTTTSSBCSSEEEE--T-TTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCcccChHhhCcCEe--C-CCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            456899999999986433  3 59999999999999986 6779999999854

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

Probab=99.06  E-value=5.7e-11  Score=71.90  Aligned_cols=48  Identities=23%  Similarity=0.566  Sum_probs=39.9

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPL  138 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~~  138 (191)
                      .+...|+||++.+.++..+    +|||.||..|+..|   ...||+||..+....
T Consensus         4 ~~~~~C~IC~~~~~~p~~l----~CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCPKLL----PCLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCCSSCSSSCSSCBCCSCS----TTSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             ccCCCceEeCCccCCeEEc----CCCCcccHHHHccC---CCCCCcCCcEeecCC
Confidence            4567899999999988666    69999999998773   567999999887543

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

Probab=99.05  E-value=4.1e-11  Score=84.75  Aligned_cols=53  Identities=28%  Similarity=0.744  Sum_probs=43.3

Q ss_pred             CCCCcCcccccccccC----ccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           84 VEDAECSICLGEYQDK----EVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~----~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      .+...|+||++.+.++    .....+ +|||.||..|+.+|+..+.+||+||.++...
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  126 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVST-ECGHVFCSQCLRDSLKNANTCPTCRKKINHK  126 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEE-TTSBEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCCccccccccCcceEeC-CCCChhhHHHHHHHHHcCCCCCCCCCcCChh
Confidence            4567899999998865    222344 5999999999999999999999999988643

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

Probab=99.03  E-value=7e-11  Score=82.07  Aligned_cols=49  Identities=31%  Similarity=0.587  Sum_probs=42.2

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC-CCccccccccccCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK-KTTCPVCRLPLQDP  137 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~-~~~CP~Cr~~~~~~  137 (191)
                      +...|+||++.+.++..+    +|||.||..||..|+.. ...||+||..+...
T Consensus        22 ~~~~C~IC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (116)
T 1rmd_A           22 KSISCQICEHILADPVET----SCKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (116)
T ss_dssp             HHTBCTTTCSBCSSEEEC----TTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCcHhcCcEEc----CCCCcccHHHHHHHHhHCcCcCCCCCCCCCHh
Confidence            356799999999887665    69999999999999986 67899999998753

>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=98.96  E-value=3.3e-10  Score=93.46  Aligned_cols=49  Identities=27%  Similarity=0.720  Sum_probs=41.8

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-CCCccccccccccCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQDP  137 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-~~~~CP~Cr~~~~~~  137 (191)
                      ....|+||++.+.++..+    +|||.||..|+..|+. ....||+||..+...
T Consensus       331 ~~~~C~ICle~~~~pv~l----pCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          331 TFQLCKICAENDKDVKIE----PCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SSSBCTTTSSSBCCEEEE----TTCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCCCccCcCCCCeEEe----CCCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            346899999999876555    6999999999999998 678899999988653

>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=98.95  E-value=2e-10  Score=71.36  Aligned_cols=49  Identities=29%  Similarity=0.640  Sum_probs=39.9

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCc-ccHhhHHHHhcCCCcccccccccc
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHS-FHLACIDIWLRKKTTCPVCRLPLQ  135 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~-f~~~Ci~~wl~~~~~CP~Cr~~~~  135 (191)
                      ++..|.||++...+...+ .+| |||. ||..|+..|...+..||+||.++.
T Consensus         7 ~~~~C~IC~~~~~~~~~~-~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            7 AIEPCVICQGRPKNGCIV-HGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             GGSCCTTTSSSCSCEEEE-ETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CcCCCCcCCCCCCCEEEE-CCC-CCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            455799999987765321 235 9999 899999999988888999999875

>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=98.92  E-value=3.5e-10  Score=78.67  Aligned_cols=48  Identities=29%  Similarity=0.555  Sum_probs=40.6

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      .+...|+||++.+.++..+.   +|||.||..||..|+.  ..||+||..+..
T Consensus        20 ~~~~~C~IC~~~~~~pv~~~---~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~   67 (117)
T 1jm7_B           20 EKLLRCSRCTNILREPVCLG---GCEHIFCSNCVSDCIG--TGCPVCYTPAWI   67 (117)
T ss_dssp             HHTTSCSSSCSCCSSCBCCC---SSSCCBCTTTGGGGTT--TBCSSSCCBCSC
T ss_pred             hhCCCCCCCChHhhCccEeC---CCCCHHHHHHHHHHhc--CCCcCCCCcCcc
Confidence            34678999999998876542   5999999999999987  779999999854

>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=98.92  E-value=3.1e-10  Score=70.30  Aligned_cols=50  Identities=22%  Similarity=0.471  Sum_probs=40.1

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCc-ccHhhHHHHhcCCCccccccccccC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHS-FHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~-f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      ....|.||++...+...+ .+| |||. ||..|+..|......||+||.++..
T Consensus         6 ~~~~C~IC~~~~~~~~~~-~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~   56 (63)
T 2vje_B            6 LLKPCSLCEKRPRDGNII-HGR-TGHLVTCFHCARRLKKAGASCPICKKEIQL   56 (63)
T ss_dssp             GGSBCTTTSSSBSCEEEE-ETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCCE
T ss_pred             cCCCCcccCCcCCCeEEE-ecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhhc
Confidence            355799999987665422 245 9998 9999999999888889999998853

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

Probab=98.89  E-value=3.5e-10  Score=72.34  Aligned_cols=44  Identities=25%  Similarity=0.603  Sum_probs=37.9

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCc-ccHhhHHHHhcCCCccccccccccC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHS-FHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~-f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      ++..|+||++.+.++..+    +|||. ||..|+..|    ..||+||..+..
T Consensus        23 ~~~~C~iC~~~~~~~~~~----pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           23 EEKLCKICMDRNIAIVFV----PCGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HHTBCTTTSSSBCCEEEE----TTCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             cCCCCCCCCCCCCCEEEc----CCCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            456799999998887666    69999 999999988    789999998864

>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=98.87  E-value=7.3e-10  Score=74.13  Aligned_cols=46  Identities=22%  Similarity=0.487  Sum_probs=39.9

Q ss_pred             CCCCcCcccccccccCccEEEcCC-CCCcccHhhHHHHhcCC------Ccccc--cccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQ-CGHSFHLACIDIWLRKK------TTCPV--CRLP  133 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~-C~H~f~~~Ci~~wl~~~------~~CP~--Cr~~  133 (191)
                      ...+.|+||++.|.++..+    + |||.||..||..|+..+      ..||+  |+..
T Consensus         5 ~~~~~CPI~~~~~~dPV~~----~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            5 SSGFTCPITKEEMKKPVKN----KVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             SSCCBCTTTCSBCSSEEEE----SSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             CcEeECcCcCchhcCCEEc----CCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            4567899999999998877    5 99999999999999854      47999  9866

>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=98.83  E-value=8.1e-10  Score=81.71  Aligned_cols=52  Identities=33%  Similarity=0.554  Sum_probs=43.3

Q ss_pred             CCCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCC-CccccccccccCC
Q 029544           82 KSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK-TTCPVCRLPLQDP  137 (191)
Q Consensus        82 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~-~~CP~Cr~~~~~~  137 (191)
                      ...+...|+||++.+.++..+    +|||.||..|+..|+... ..||+||..+...
T Consensus        14 ~~~~~~~C~IC~~~~~~pv~~----~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           14 PLESKYECPICLMALREAVQT----PCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             CCCGGGBCTTTCSBCSSEEEC----TTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCCChhhcCcEEC----CCCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            345677899999999988654    699999999999999754 4899999988653

>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=98.82  E-value=1.4e-09  Score=86.08  Aligned_cols=50  Identities=18%  Similarity=0.215  Sum_probs=43.1

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC-CCccccccccccC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK-KTTCPVCRLPLQD  136 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~-~~~CP~Cr~~~~~  136 (191)
                      ....+.|+||++.+.+++.+    +|||.||..||..|+.. +.+||+||.++..
T Consensus       205 ~~~~~~c~i~~~~~~dPv~~----~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          205 IPDYLCGKISFELMREPCIT----PSGITYDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             CCSTTBCTTTCSBCSSEEEC----SSCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CCcccCCcCcCCHhcCCeEC----CCCCEECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            34578899999999999887    79999999999999985 4459999998864

>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=98.78  E-value=3.7e-09  Score=70.59  Aligned_cols=49  Identities=27%  Similarity=0.698  Sum_probs=39.9

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC--------CCcccc--cccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK--------KTTCPV--CRLP  133 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~--------~~~CP~--Cr~~  133 (191)
                      .+...|+||++.+..+..+...+ |+|.||..||..++..        ...||.  |+..
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~l~~-CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            3 SGSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCCcCCcccCcccccccceEcCC-CCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            35678999999998877665554 9999999999999862        236999  9987

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

Probab=98.75  E-value=1.6e-09  Score=87.45  Aligned_cols=54  Identities=24%  Similarity=0.622  Sum_probs=40.8

Q ss_pred             CCCCcCcccccccccCccE----EEcCCCCCcccHhhHHHHhcCC-----------CccccccccccCC
Q 029544           84 VEDAECSICLGEYQDKEVL----RIMPQCGHSFHLACIDIWLRKK-----------TTCPVCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~----~~~~~C~H~f~~~Ci~~wl~~~-----------~~CP~Cr~~~~~~  137 (191)
                      +...+|+||++.+.+...+    ...+.|+|.||..|+.+|+...           ..||.||.++..+
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~s  374 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTS  374 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCcc
Confidence            4567899999998873322    2233699999999999999732           3599999988644

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

Probab=98.74  E-value=5.2e-09  Score=66.92  Aligned_cols=45  Identities=24%  Similarity=0.585  Sum_probs=37.3

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCc-ccHhhHHHHhcCCCccccccccccCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHS-FHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~-f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      ++..|+||++.+.++..+    +|||. ||..|+...    ..||+||.++...
T Consensus        24 ~~~~C~IC~~~~~~~~~~----pCgH~~~C~~C~~~~----~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           24 EEKLCKICMDRNIAIVFV----PCGHLVTCKQCAEAV----DKCPMCYTVITFK   69 (75)
T ss_dssp             HHHSCSSSCSSCCCBCCS----SSCCCCBCHHHHHHC----SBCTTTCCBCCCC
T ss_pred             CCCCCCcCCCCCCCEEEe----cCCCHHHHHHHhhCC----CCCccCCceecCc
Confidence            345799999999887766    69999 999999653    6799999988653

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

Probab=98.72  E-value=4.2e-09  Score=78.31  Aligned_cols=51  Identities=18%  Similarity=0.210  Sum_probs=43.7

Q ss_pred             CCCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC-CCccccccccccC
Q 029544           82 KSVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK-KTTCPVCRLPLQD  136 (191)
Q Consensus        82 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~-~~~CP~Cr~~~~~  136 (191)
                      .....+.|+||++.|.+|..+    +|||.||..||..|+.. ..+||+|+.++..
T Consensus       102 ~ip~~f~CPI~~elm~DPV~~----~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~  153 (179)
T 2f42_A          102 EIPDYLCGKISFELMREPCIT----PSGITYDRKDIEEHLQRVGHFDPVTRSPLTQ  153 (179)
T ss_dssp             CCCGGGBCTTTCSBCSSEEEC----TTSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCcHhhcccCccccCCCCeEC----CCCCEECHHHHHHHHHhCCCCCCCCcCCCCh
Confidence            345678899999999999877    79999999999999985 3469999988864

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

Probab=98.71  E-value=6.9e-09  Score=65.15  Aligned_cols=47  Identities=23%  Similarity=0.635  Sum_probs=37.4

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCc-ccHhhHHHHhcCCCccccccccccCC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHS-FHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~-f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      ..+...|.||++...+...+    +|+|. ||..|+..    ...||+||..+...
T Consensus        12 ~~~~~~C~IC~~~~~~~v~~----pCgH~~~C~~C~~~----~~~CP~CR~~i~~~   59 (68)
T 2ea5_A           12 EENSKDCVVCQNGTVNWVLL----PCRHTCLCDGCVKY----FQQCPMCRQFVQES   59 (68)
T ss_dssp             CCCSSCCSSSSSSCCCCEET----TTTBCCSCTTHHHH----CSSCTTTCCCCCCE
T ss_pred             CCCCCCCCCcCcCCCCEEEE----CCCChhhhHHHHhc----CCCCCCCCcchhce
Confidence            34567899999987765444    69999 99999984    36799999988754

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

Probab=98.64  E-value=2.5e-08  Score=60.97  Aligned_cols=48  Identities=27%  Similarity=0.740  Sum_probs=36.5

Q ss_pred             CCCCcCcccccccccCccEEEcCCCC--C---cccHhhHHHHhc--CCCcccccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCG--H---SFHLACIDIWLR--KKTTCPVCRLPLQ  135 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~--H---~f~~~Ci~~wl~--~~~~CP~Cr~~~~  135 (191)
                      ++...|.||++...++  + .+| |.  +   .||..|+.+|+.  .+.+||+|+..+.
T Consensus         4 ~~~~~CrIC~~~~~~~--l-~~P-C~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            4 EDVPVCWICNEELGNE--R-FRA-CGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCC--C-CCS-CCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCEeEEeecCCCCc--e-ecC-cCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            4566899999985443  2 344 65  4   899999999997  3577999998875

>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=98.60  E-value=1.1e-08  Score=66.15  Aligned_cols=45  Identities=29%  Similarity=0.672  Sum_probs=37.1

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCc-ccHhhHHHHhcCCCccccccccccCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHS-FHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~-f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      +...|+||++.+.+...+    +|||. ||..|+..|    ..||+||..+...
T Consensus        17 ~~~~C~IC~~~~~~~v~~----pCgH~~~C~~C~~~~----~~CP~Cr~~i~~~   62 (79)
T 2yho_A           17 EAMLCMVCCEEEINSTFC----PCGHTVCCESCAAQL----QSCPVCRSRVEHV   62 (79)
T ss_dssp             HHTBCTTTSSSBCCEEEE----TTCBCCBCHHHHTTC----SBCTTTCCBCCEE
T ss_pred             CCCEeEEeCcccCcEEEE----CCCCHHHHHHHHHhc----CcCCCCCchhhCe
Confidence            345799999998876555    69999 999999877    4899999988753

>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=98.60  E-value=1.7e-08  Score=78.86  Aligned_cols=50  Identities=24%  Similarity=0.500  Sum_probs=41.5

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCC--Ccccc--ccccccC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK--TTCPV--CRLPLQD  136 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~--~~CP~--Cr~~~~~  136 (191)
                      .....|+||++.|.++....   .|||.||..||..|+..+  ..||+  |+..+..
T Consensus       179 ~~el~CPIcl~~f~DPVts~---~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~  232 (267)
T 3htk_C          179 KIELTCPITCKPYEAPLISR---KCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSM  232 (267)
T ss_dssp             BCCSBCTTTSSBCSSEEEES---SSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECG
T ss_pred             ceeeECcCccCcccCCeeeC---CCCCcccHHHHHHHHHhCCCCCCCcccccCcCch
Confidence            34567999999999997642   699999999999999854  46999  9997754

>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=98.48  E-value=3e-08  Score=81.06  Aligned_cols=45  Identities=24%  Similarity=0.683  Sum_probs=38.7

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCc-ccHhhHHHHhcCCCccccccccccC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHS-FHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~-f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      .++..|+||++.+.++..+    +|||. ||..|+..|    ..||+||..+..
T Consensus       293 ~~~~~C~IC~~~~~~~v~l----pCgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          293 QEERTCKVCMDKEVSVVFI----PCGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             HTTCBCTTTSSSBCCEEEE----TTCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             cCCCCCCccCCcCCceEEc----CCCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            3567899999999887666    69999 999999988    679999998864

>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=98.36  E-value=1e-07  Score=58.42  Aligned_cols=49  Identities=14%  Similarity=0.251  Sum_probs=40.7

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      .+.|+||++.+.++...   +++||.|...||.+|+..+..||+.+.++...
T Consensus         3 ~~~CpIs~~~m~dPV~~---~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~   51 (61)
T 2bay_A            3 HMLCAISGKVPRRPVLS---PKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   51 (61)
T ss_dssp             -CCCTTTCSCCSSEEEE---TTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             eEEecCCCCCCCCCEEe---CCCCcEEcHHHHHHHHHhCCCCcCCcCCCChh
Confidence            35799999999987443   24999999999999999878899999888643

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.18  E-value=1.1e-06  Score=58.29  Aligned_cols=47  Identities=28%  Similarity=0.559  Sum_probs=35.5

Q ss_pred             cCcccccccccCccEEEcCCCCCcccHhhHHHHhc-CCCccccccccccCC
Q 029544           88 ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQDP  137 (191)
Q Consensus        88 ~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-~~~~CP~Cr~~~~~~  137 (191)
                      .|.+|--.+..  .-+.+| |+|+||.+|+..|.+ ..+.||.|+.++...
T Consensus         3 fC~~C~~Pi~i--ygRmIP-CkHvFCydCa~~~~~~~~k~Cp~C~~~V~rV   50 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMIP-CKHVFCYDCAILHEKKGDKMCPGCSDPVQRI   50 (101)
T ss_dssp             BCTTTCSBCSE--EEEEET-TCCEEEHHHHHHHHHTTCCBCTTTCCBCSEE
T ss_pred             ecCccCCCeEE--Eeeecc-ccccHHHHHHHHHHhccCCCCcCcCCeeeee
Confidence            36777655543  334454 999999999999975 567899999988754

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

Probab=97.93  E-value=9.3e-06  Score=63.00  Aligned_cols=50  Identities=22%  Similarity=0.559  Sum_probs=40.4

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCC--ccccccccccCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT--TCPVCRLPLQDP  137 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~--~CP~Cr~~~~~~  137 (191)
                      ....|.||.+....+...   +.|+|.||..|+..|+..+.  .||.|+..+...
T Consensus       179 ~i~~C~iC~~iv~~g~~C---~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          179 AVKICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             TCCBCTTTCSBCSSCEEC---SSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSC
T ss_pred             CCCcCcchhhHHhCCccc---CccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCC
Confidence            366799999998876444   25999999999999998544  799999987654

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=95.40  E-value=0.0096  Score=39.38  Aligned_cols=35  Identities=20%  Similarity=0.422  Sum_probs=25.5

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHH
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIW  120 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w  120 (191)
                      ++..|.||.+.+..+....-+ .|+|.||..|+..+
T Consensus         2 ee~~C~~C~~~~~~~av~~C~-~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCV-TCEVSYCDECLKAT   36 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEET-TTTEEECHHHHHHH
T ss_pred             CCCCCcCCCCCCCCCceEECC-cCChHHhHHHCHHH
Confidence            356799999875433333334 59999999999984

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=94.71  E-value=0.039  Score=33.73  Aligned_cols=47  Identities=23%  Similarity=0.490  Sum_probs=32.6

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCC----Cccccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK----TTCPVCRLPL  134 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~----~~CP~Cr~~~  134 (191)
                      .....|.||.+.   +..+ .-..|...||..|+.+.+...    -.||.|....
T Consensus        10 ~~~~~C~vC~~~---~~ll-~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           10 APGARCGVCGDG---TDVL-RCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             CTTCCCTTTSCC---TTCE-ECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCCcCCCCCC---CeEE-ECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            445679999753   3333 334689999999998877633    3599997543

>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=91.69  E-value=0.092  Score=31.62  Aligned_cols=50  Identities=26%  Similarity=0.514  Sum_probs=33.6

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-----CCCcccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-----KKTTCPVCRLP  133 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-----~~~~CP~Cr~~  133 (191)
                      .+...|++|...+.+....+.-..|...||..|+.--..     ....||.|+..
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            456679999988865444444446888999999753221     33459999753

>2l2t_A Receptor tyrosine-protein kinase ERBB-4; transmembrane dimer, membrane domain, membrane protei; NMR {Homo sapiens}

Probab=91.46  E-value=0.71  Score=25.63  Aligned_cols=8  Identities=25%  Similarity=0.289  Sum_probs=3.0

Q ss_pred             HHHHHhhc
Q 029544           27 TRIICRRI   34 (191)
Q Consensus        27 ~~~~~~r~   34 (191)
                      ..++.+|+
T Consensus        30 ~~~~~RRR   37 (44)
T 2l2t_A           30 FAVYVRRK   37 (44)
T ss_dssp             HHHHHHTT
T ss_pred             HHHHhhhh
Confidence            33333333

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=91.03  E-value=0.2  Score=29.86  Aligned_cols=45  Identities=24%  Similarity=0.654  Sum_probs=30.9

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC----CCccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK----KTTCPVCRL  132 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~----~~~CP~Cr~  132 (191)
                      .++..|.+|...   + .+..-..|...||..|+..-+..    .-.||.|+.
T Consensus         9 ~~~~~C~vC~~~---g-~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A            9 DHQDYCEVCQQG---G-EIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CCCSSCTTTSCC---S-SEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCCccCCCC---C-cEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            456679999873   3 33334468889999999875442    234999975

>1wil_A KIAA1045 protein; ring finger domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: g.50.1.3

Probab=88.86  E-value=1.1  Score=28.52  Aligned_cols=35  Identities=23%  Similarity=0.488  Sum_probs=22.9

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHH
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIW  120 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w  120 (191)
                      ..+..|.||-.-- ......-- -|+-+||..|+.+-
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            3677899997432 22222111 48999999999986

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=88.70  E-value=0.14  Score=31.78  Aligned_cols=52  Identities=17%  Similarity=0.359  Sum_probs=34.5

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC----CCccccccccccCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK----KTTCPVCRLPLQDP  137 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~----~~~CP~Cr~~~~~~  137 (191)
                      +...|.+|..... +..+.....|...||..|+..-...    .-.||.|+..+...
T Consensus        17 ~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~k~   72 (75)
T 2k16_A           17 QIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKKD   72 (75)
T ss_dssp             EEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHCSC
T ss_pred             CCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchhhc
Confidence            4456999987754 3333334458889999998754432    33599998776543

>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=88.67  E-value=0.15  Score=30.47  Aligned_cols=47  Identities=28%  Similarity=0.625  Sum_probs=30.7

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC----CCccccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK----KTTCPVCRLPL  134 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~----~~~CP~Cr~~~  134 (191)
                      .++..|.+|.+.   +..+ .-..|...||..|+.+-+..    .-.||.|+...
T Consensus         7 ~~~~~C~vC~~~---g~ll-~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            7 HHMEFCRVCKDG---GELL-CCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---SSCB-CCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCCcCCCCCCC---CCEE-EcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            456679999863   2333 23358889999999864442    23499997543

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=88.58  E-value=1.2  Score=28.08  Aligned_cols=39  Identities=18%  Similarity=0.390  Sum_probs=30.1

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR  122 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~  122 (191)
                      .....|.+|.+.+++...+..-..=.|.||..|-+..++
T Consensus        13 ~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk   51 (93)
T 2cs3_A           13 SGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIK   51 (93)
T ss_dssp             CCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHH
T ss_pred             CCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHH
Confidence            456789999999999888732112268999999998887

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=87.25  E-value=0.37  Score=27.41  Aligned_cols=44  Identities=27%  Similarity=0.782  Sum_probs=28.3

Q ss_pred             cCcccccccccCccEEEcCCCCCcccHhhHHHHhcC----CCccccccc
Q 029544           88 ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK----KTTCPVCRL  132 (191)
Q Consensus        88 ~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~----~~~CP~Cr~  132 (191)
                      .|.+|...-.....+ .-..|...||..|+.+=+..    .-.||.|+.
T Consensus         2 ~C~vC~~~~~~~~ll-~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDDKLI-LCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCE-ECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCEE-ECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            378887654433344 33358899999999764442    224998864

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=86.70  E-value=0.48  Score=30.49  Aligned_cols=52  Identities=27%  Similarity=0.481  Sum_probs=34.5

Q ss_pred             CCCCcCccccccc-ccCccEEEcCCCCCcccHhhHHHHhc--CCCcccccccccc
Q 029544           84 VEDAECSICLGEY-QDKEVLRIMPQCGHSFHLACIDIWLR--KKTTCPVCRLPLQ  135 (191)
Q Consensus        84 ~~~~~C~IC~~~~-~~~~~~~~~~~C~H~f~~~Ci~~wl~--~~~~CP~Cr~~~~  135 (191)
                      .++..|.||...- .+...+.....|.-.||..|+..-..  ..-.||.|.....
T Consensus        23 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~~   77 (88)
T 2l43_A           23 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRA   77 (88)
T ss_dssp             CCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHTT
T ss_pred             CCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCccc
Confidence            4567899999753 23334444456888999999975432  2334999976543

>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=86.31  E-value=0.24  Score=37.08  Aligned_cols=47  Identities=26%  Similarity=0.439  Sum_probs=32.6

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC----CCccccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK----KTTCPVCRLPL  134 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~----~~~CP~Cr~~~  134 (191)
                      .++..|.+|...   + .+.....|...||..|+.+-+..    .-.||.|+..-
T Consensus         5 ~~~~~C~~C~~~---g-~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            5 PNEDWCAVCQNG---G-DLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             SSCSSBTTTCCC---E-EEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCCCCC---C-ceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            456679999853   2 24444468899999999776552    23599998644

>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=86.30  E-value=0.23  Score=36.45  Aligned_cols=46  Identities=28%  Similarity=0.585  Sum_probs=31.7

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC----CCccccccccc
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK----KTTCPVCRLPL  134 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~----~~~CP~Cr~~~  134 (191)
                      ++..|.+|.+.   +..+ ....|...||..|+.+-+..    .-.||.|+..-
T Consensus         3 ~~~~C~~C~~~---g~ll-~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            3 NEDWCAVCQNG---GELL-CCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             SCSSCTTTCCC---SSCE-ECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCccccCCCC---Ceee-ecCCCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            45679999854   3333 33458899999998776553    23499998644

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=85.53  E-value=0.35  Score=29.28  Aligned_cols=46  Identities=30%  Similarity=0.698  Sum_probs=31.2

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC----CCcccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK----KTTCPVCRLP  133 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~----~~~CP~Cr~~  133 (191)
                      .++..|.+|.+.   +..+ .-..|...||..|+.+-+..    .-.||.|...
T Consensus         6 ~~~~~C~vC~~~---g~ll-~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~   55 (66)
T 1xwh_A            6 KNEDECAVCRDG---GELI-CCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQA   55 (66)
T ss_dssp             SCCCSBSSSSCC---SSCE-ECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHT
T ss_pred             CCCCCCccCCCC---CCEE-EcCCCChhhcccccCCCcCcCCCCCeECccccCc
Confidence            456779999864   3333 33358889999999864442    2349999754

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=84.99  E-value=0.15  Score=30.28  Aligned_cols=48  Identities=27%  Similarity=0.699  Sum_probs=32.0

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC----CCcccccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK----KTTCPVCRLPLQ  135 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~----~~~CP~Cr~~~~  135 (191)
                      .++..|.+|...   +..+ .-..|...||..|+.+-+..    .-.||.|.....
T Consensus         3 ~~~~~C~vC~~~---g~ll-~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~   54 (60)
T 2puy_A            3 IHEDFCSVCRKS---GQLL-MCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQML   54 (60)
T ss_dssp             CCCSSCTTTCCC---SSCE-ECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHH
T ss_pred             CCCCCCcCCCCC---CcEE-EcCCCCcCEECCcCCCCcCCCCCCceEChhccChhh
Confidence            356679999874   3333 33358889999999865442    234999976554

>1z60_A TFIIH basal transcription factor complex P44 subunit; basic transcription factor, zinc binding protein, ring finger; NMR {Homo sapiens} SCOP: g.49.1.2

Probab=84.79  E-value=0.65  Score=27.56  Aligned_cols=43  Identities=26%  Similarity=0.583  Sum_probs=30.6

Q ss_pred             CcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccc
Q 029544           87 AECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVC  130 (191)
Q Consensus        87 ~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~C  130 (191)
                      ..|-.|...+.+.. ...-+.|++.||.+|=.-.-..-..||-|
T Consensus        16 ~~C~~C~~~~~~~~-~y~C~~C~~~FC~dCD~fiHe~Lh~CPgC   58 (59)
T 1z60_A           16 RFCYGCQGELKDQH-VYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             CEETTTTEECTTSE-EECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CcccccCcccCCCc-cEECCccCcCcccchhHHHHhhccCCcCC
Confidence            35888998886433 23456899999999954444455679988

>2jwa_A Receptor tyrosine-protein kinase ERBB-2; transmembrane helix dimer, protein kinase receptor membrane domain, ATP-binding, glycoprotein; NMR {Homo sapiens} PDB: 2ks1_A

Probab=84.73  E-value=3.5  Score=22.78  Aligned_cols=7  Identities=43%  Similarity=1.047  Sum_probs=2.7

Q ss_pred             HHHHHHH
Q 029544            8 LITTVIG   14 (191)
Q Consensus         8 ~v~~~i~   14 (191)
                      +..++++
T Consensus        14 Ia~~vVG   20 (44)
T 2jwa_A           14 IISAVVG   20 (44)
T ss_dssp             HHHHHHH
T ss_pred             hHHHHHH
Confidence            3333344

>1y02_A CARP2, FYVE-ring finger protein sakura; zinc-binding module, phosphoinositide binding, caspase regulation, metal binding protein; 1.80A {Homo sapiens} SCOP: a.140.2.1 g.50.1.1

Probab=84.50  E-value=0.18  Score=34.52  Aligned_cols=51  Identities=14%  Similarity=0.360  Sum_probs=33.6

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCcccccccccc
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ  135 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~  135 (191)
                      ....|..|...|..-..-.....||.+||..|..........|-.|...+.
T Consensus        18 ~~~~C~~C~~~Fs~~~RkHHCR~CG~ifC~~Cs~~~~~~vRVC~~C~~~~~   68 (120)
T 1y02_A           18 LEPSCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQRFRA   68 (120)
T ss_dssp             --CCCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHHHHHH
T ss_pred             ccCcccCcCCccccccccccCCCCCCeeCHHHhCCCCCCceECHHHHHHHh
Confidence            345799999988765444444479999999997665555667888876543

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=84.46  E-value=0.61  Score=28.71  Aligned_cols=51  Identities=27%  Similarity=0.494  Sum_probs=33.5

Q ss_pred             CCCCCcCccccccc-ccCccEEEcCCCCCcccHhhHHHHhc--CCCcccccccc
Q 029544           83 SVEDAECSICLGEY-QDKEVLRIMPQCGHSFHLACIDIWLR--KKTTCPVCRLP  133 (191)
Q Consensus        83 ~~~~~~C~IC~~~~-~~~~~~~~~~~C~H~f~~~Ci~~wl~--~~~~CP~Cr~~  133 (191)
                      ..++..|.||...- .+...+..-..|.-.||..|+..-..  ..-.||.|+..
T Consensus        13 ~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~~   66 (71)
T 2ku3_A           13 IDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQS   66 (71)
T ss_dssp             CCSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcCc
Confidence            34567799998753 33344445556889999999875332  22348888653

>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2

Probab=84.13  E-value=1.7  Score=27.14  Aligned_cols=51  Identities=22%  Similarity=0.439  Sum_probs=32.4

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHH---h--cCCCccccccccccC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIW---L--RKKTTCPVCRLPLQD  136 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w---l--~~~~~CP~Cr~~~~~  136 (191)
                      +...| ||...+......+....|...||..|+.--   .  .....||.|+.....
T Consensus        11 ~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~~~   66 (79)
T 1wep_A           11 VPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFGP   66 (79)
T ss_dssp             CCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSCS
T ss_pred             CccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCcccccCC
Confidence            34456 898877534334344458899999998421   1  134569999876543

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=84.03  E-value=0.2  Score=29.30  Aligned_cols=45  Identities=29%  Similarity=0.691  Sum_probs=29.6

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC----CCccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK----KTTCPVCRL  132 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~----~~~CP~Cr~  132 (191)
                      .++..|.+|...   +..+ .-..|...||..|+.+-+..    .-.||.|..
T Consensus         7 ~~~~~C~vC~~~---g~ll-~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            7 GHEDFCSVCRKS---GQLL-MCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SSCCSCSSSCCS---SCCE-ECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCccCCCC---CeEE-EcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            456679999874   3333 33358889999999865442    223888853

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*

Probab=83.97  E-value=0.95  Score=27.30  Aligned_cols=34  Identities=26%  Similarity=0.505  Sum_probs=25.0

Q ss_pred             CCCCcCcccccccccCccEEEcC-CCCCcccHhhH
Q 029544           84 VEDAECSICLGEYQDKEVLRIMP-QCGHSFHLACI  117 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~-~C~H~f~~~Ci  117 (191)
                      .....|.+|...+......+... .|.-.||..|+
T Consensus         6 ~~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cv   40 (65)
T 2vpb_A            6 DPVYPCGICTNEVNDDQDAILCEASCQKWFHRICT   40 (65)
T ss_dssp             ---CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHH
T ss_pred             CCcCcCccCCCccCCCCCeEecccCccccCchhcc
Confidence            44567999999987766665554 68889999997

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A

Probab=83.55  E-value=0.72  Score=42.26  Aligned_cols=51  Identities=18%  Similarity=0.215  Sum_probs=43.9

Q ss_pred             CCCCCCcCcccccccccCccEEEcCCCC-CcccHhhHHHHhcCCCccccccccccC
Q 029544           82 KSVEDAECSICLGEYQDKEVLRIMPQCG-HSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        82 ~~~~~~~C~IC~~~~~~~~~~~~~~~C~-H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      ...+.+.|+|-++.+.+|+.+    +-| +.|-..+|.+|+..+.+||+=|.++..
T Consensus       887 ~iP~~F~cPIs~~lM~DPVil----psG~~TydR~~I~~wl~~~~tdP~Tr~~L~~  938 (968)
T 3m62_A          887 DVPDEFLDPLMYTIMKDPVIL----PASKMNIDRSTIKAHLLSDSTDPFNRMPLKL  938 (968)
T ss_dssp             CSCGGGBCTTTCSBCSSEEEC----TTTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCcHHhCCcchhhHHhCCeEc----CCCCEEECHHHHHHHHhcCCCCCCCCCCCCc
Confidence            335567899999999999888    687 589999999999998899999988864

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=82.45  E-value=1.7  Score=27.50  Aligned_cols=37  Identities=14%  Similarity=0.225  Sum_probs=27.0

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHH
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIW  120 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w  120 (191)
                      .+...|.+|...|..-..-..-..||++||..|....
T Consensus        19 ~~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~   55 (84)
T 1z2q_A           19 EDAPACNGCGCVFTTTVRRHHCRNCGYVLCGDCSRHR   55 (84)
T ss_dssp             TTCCBCTTTCCBCCTTSCCEECTTTCCEECTGGGCCE
T ss_pred             CCCCCCcCcCCccccchhcccccCCCcEEChHHhCCe
Confidence            3455799999998765444344479999999997553

>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=81.89  E-value=0.62  Score=30.20  Aligned_cols=49  Identities=24%  Similarity=0.611  Sum_probs=32.9

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC----CCcccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK----KTTCPVCRLP  133 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~----~~~CP~Cr~~  133 (191)
                      .++..|.||...-.....+ ....|...||..|+.+-+..    .-.||.|...
T Consensus        14 ~~~~~C~vC~~~~~~~~ll-~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~   66 (92)
T 2e6r_A           14 IDSYICQVCSRGDEDDKLL-FCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILA   66 (92)
T ss_dssp             CCCCCCSSSCCSGGGGGCE-ECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHH
T ss_pred             cCCCCCccCCCcCCCCCEE-EcCCCCchhccccCCCCcccCCCCCcCCccCcCc
Confidence            3456799999865443344 33358899999999754432    2349999764

>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2

Probab=81.80  E-value=0.91  Score=28.11  Aligned_cols=48  Identities=23%  Similarity=0.508  Sum_probs=31.2

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHH---------hcCCCcccccccccc
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIW---------LRKKTTCPVCRLPLQ  135 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w---------l~~~~~CP~Cr~~~~  135 (191)
                      ...| ||.........+. -..|...||..|+.--         ......||.|+..-.
T Consensus        16 ~~~C-~C~~~~~~~~MI~-Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~~~   72 (76)
T 1wem_A           16 ALYC-ICRQPHNNRFMIC-CDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILSG   72 (76)
T ss_dssp             CCCS-TTCCCCCSSCEEE-CSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHSC
T ss_pred             CCEE-ECCCccCCCCEEE-eCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCccC
Confidence            4557 8988766444443 3358899999997421         124566999986543

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=81.18  E-value=0.74  Score=30.17  Aligned_cols=45  Identities=22%  Similarity=0.437  Sum_probs=30.2

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc---CCCccccccc
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR---KKTTCPVCRL  132 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~---~~~~CP~Cr~  132 (191)
                      ...| ||......+..+. ...|...||..|+..-..   ..-.||.|+.
T Consensus        28 ~vrC-iC~~~~~~~~mi~-Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~   75 (98)
T 2lv9_A           28 VTRC-ICGFTHDDGYMIC-CDKCSVWQHIDCMGIDRQHIPDTYLCERCQP   75 (98)
T ss_dssp             BCCC-TTSCCSCSSCEEE-BTTTCBEEETTTTTCCTTSCCSSBCCTTTSS
T ss_pred             CEEe-ECCCccCCCcEEE-cCCCCCcCcCcCCCCCccCCCCCEECCCCcC
Confidence            3457 8887766655553 335889999999865322   2345999973

>1wee_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=80.92  E-value=0.47  Score=29.19  Aligned_cols=49  Identities=27%  Similarity=0.358  Sum_probs=31.3

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHh----cCCCccccccccc
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWL----RKKTTCPVCRLPL  134 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl----~~~~~CP~Cr~~~  134 (191)
                      +...| ||......+...+....|...||..|+.--.    .....||.|+..-
T Consensus        15 ~~~~C-~C~~~~~~g~~mI~Cd~C~~W~H~~Cvg~~~~~~~~~~~~C~~C~~~~   67 (72)
T 1wee_A           15 WKVDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELS   67 (72)
T ss_dssp             SEECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHHC
T ss_pred             cceEe-eCCCccCCCCcEEECCCCCCccCCeeeccCccccCCCcEECCCccCCC
Confidence            44568 7988765554343444588899999975321    2334599997644

>2klu_A T-cell surface glycoprotein CD4; cell membrane, disulfide bond, HOST- virus interaction, immune response, immunoglobulin domain, lipoprotein; NMR {Homo sapiens}

Probab=80.09  E-value=3.5  Score=24.81  Aligned_cols=15  Identities=13%  Similarity=0.107  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHHHHHH
Q 029544           11 TVIGFGMSAAFIVFI   25 (191)
Q Consensus        11 ~~i~~~~~~~li~~~   25 (191)
                      ++++.++++++++.+
T Consensus        12 ivlGg~~~lll~~gl   26 (70)
T 2klu_A           12 IVLGGVAGLLLFIGL   26 (70)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHH
Confidence            455555554433333

>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A*

Probab=80.02  E-value=1.2  Score=32.17  Aligned_cols=49  Identities=20%  Similarity=0.471  Sum_probs=32.4

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHh-----cCCCcccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWL-----RKKTTCPVCRLP  133 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl-----~~~~~CP~Cr~~  133 (191)
                      .+...| +|...............|...||..|+.--.     ...-.||.|+..
T Consensus         6 ~~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~   59 (174)
T 2ri7_A            6 DTKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST   59 (174)
T ss_dssp             -CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHH
T ss_pred             CCCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcch
Confidence            455678 9998765444444444688999999984211     234569999864

---

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	191
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	8e-20
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	2e-14
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	2e-11
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	4e-11
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	9e-11
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	2e-10
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	5e-09
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	7e-09
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	1e-08
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	2e-08
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	2e-08
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	1e-06
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	2e-06
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	3e-05

>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 = 76.4 bits (188), Expect = 8e-20
 Identities = 24/50 (48%), Positives = 35/50 (70%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL 134
           +  EC++CL E +D E  R +P+CGH FH  C+D+WL   +TCP+CRL +
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 = 63.0 bits (153), Expect = 2e-14
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 3/49 (6%)

Query: 88  ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD 136
            C ICL +  +  +      C H+F   CI  W+R+  TCP+C++P++ 
Sbjct: 7   RCPICLEDPSNYSMA---LPCLHAFCYVCITRWIRQNPTCPLCKVPVES 52

>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 = 54.8 bits (131), Expect = 2e-11
 Identities = 17/66 (25%), Positives = 27/66 (40%), Gaps = 6/66 (9%)

Query: 85  EDAECSICLGEYQDKEVLRIMP-QCGHSFHLACIDIWLR-KKTTCPVCRLPLQDPLGRKH 142
           +D  C  C         L++M   CGH+   +C+D+        CP C  PL+    + +
Sbjct: 2   DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLR----KSN 57

Query: 143 AREATF 148
            R   F
Sbjct: 58  FRVQLF 63

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.8 bits (131), Expect = 4e-11
 Identities = 15/67 (22%), Positives = 23/67 (34%), Gaps = 14/67 (20%)

Query: 83  SVEDAECSICLGEYQDKEVLRIMPQ--------------CGHSFHLACIDIWLRKKTTCP 128
            +    C+IC     D  +     Q              C H+FH  CI  WL+ +  CP
Sbjct: 18  DIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCP 77

Query: 129 VCRLPLQ 135
           +     +
Sbjct: 78  LDNREWE 84

>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 = 52.8 bits (126), Expect = 9e-11
 Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 1/50 (2%)

Query: 88  ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTT-CPVCRLPLQD 136
           EC +C+   +  ++      CG+     C       +   CP CR P  +
Sbjct: 2   ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE 51

>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 = 52.7 bits (126), Expect = 2e-10
 Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 5/52 (9%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT-TCPVCRLPLQ 135
               C IC    +D   ++I P CGH    +C+  W   +   CP CR  ++
Sbjct: 22  TFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIK 69

>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 = 48.3 bits (115), Expect = 5e-09
 Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 7/50 (14%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPL 134
           +   C  C  E +     +++P C H+    C++        CP+C+ P 
Sbjct: 5   QFLRCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPW 47

>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 = 49.6 bits (117), Expect = 7e-09
 Identities = 16/82 (19%), Positives = 28/82 (34%), Gaps = 19/82 (23%)

Query: 79  EAFKSVEDAECSICLGEYQD--------------KEVLRIMPQCGHSFHLACIDIWLRKK 124
           E  K   + +C IC+ +                   V+  + +C H+FHL C+       
Sbjct: 18  EELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNG 77

Query: 125 T-----TCPVCRLPLQDPLGRK 141
                  CP C+    +  G +
Sbjct: 78  NKDGSLQCPSCKTIYGEKTGTQ 99

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.0 bits (114), Expect = 1e-08
 Identities = 16/53 (30%), Positives = 20/53 (37%), Gaps = 5/53 (9%)

Query: 84  VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQ 135
           V+   C IC     D     +   C H F   CI   L+   + CP CR P  
Sbjct: 21  VKSISCQICEHILAD----PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCF 69

>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 = 48.1 bits (114), Expect = 2e-08
 Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 7/54 (12%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWL---RKKTTCPVCRLPLQ 135
           +  EC ICL   ++    +    C H F   C+   L   +  + CP+C+  + 
Sbjct: 20  KILECPICLELIKEPVSTK----CDHIFCKFCMLKLLNQKKGPSQCPLCKNDIT 69

>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 = 46.8 bits (110), Expect = 2e-08
 Identities = 11/54 (20%), Positives = 19/54 (35%), Gaps = 3/54 (5%)

Query: 85  EDAECSICLGEYQDKEVLRIMPQ-CGHSFHLACIDIWLRKK--TTCPVCRLPLQ 135
           +   C IC  E  ++            + H +C+  WL     T C +C +   
Sbjct: 5   DVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN 58

>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 = 43.2 bits (101), Expect = 1e-06
 Identities = 16/65 (24%), Positives = 23/65 (35%), Gaps = 6/65 (9%)

Query: 72  PTMKFNQEAFKSVEDA-ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVC 130
                ++ A   +E    CS C    ++   L     C H F   C+   +   T CPVC
Sbjct: 7   GAWAHSRAALDRLEKLLRCSRCTNILREPVCL---GGCEHIFCSNCVSDCI--GTGCPVC 61

Query: 131 RLPLQ 135
             P  
Sbjct: 62  YTPAW 66

>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 = 42.8 bits (100), Expect = 2e-06
 Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 9/64 (14%)

Query: 83  SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKT--------TCPVCRLPL 134
           S   + C +CLGEY  +++   + QC   F   C+  ++            +CP    P 
Sbjct: 2   SSGSSGCKLCLGEYPVEQMTT-IAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPK 60

Query: 135 QDPL 138
           Q  L
Sbjct: 61  QGHL 64

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.2 bits (88), Expect = 3e-05
 Identities = 7/47 (14%), Positives = 18/47 (38%), Gaps = 3/47 (6%)

Query: 89  CSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ 135
           C+I     +      + P+    F  + ++ +++     P+   PL 
Sbjct: 3   CAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLS 46

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	191
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.69
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.5
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.49
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.46
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.42
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.39
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.38
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.3
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.28
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.27
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.24
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.15
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.13
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.1
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.1
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.85
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.62
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	94.39
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	92.86
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	89.42
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	89.07
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	88.32
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	88.08
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	87.34
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	87.15
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	87.01
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	86.86
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	86.09
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	85.33
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	83.45
d1wfka_	88	Zinc finger FYVE domain containing protein 19 {Mou	80.86

>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=99.69  E-value=7e-18  Score=100.78  Aligned_cols=52  Identities=46%  Similarity=1.177  Sum_probs=46.5

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCcccccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ  135 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~  135 (191)
                      +++.+|+||++.|..+..+..++.|+|.||..|+.+|+..+.+||+||+++.
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            3456799999999998888877779999999999999999999999998774

>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=99.50  E-value=1.1e-14  Score=99.57  Aligned_cols=63  Identities=24%  Similarity=0.566  Sum_probs=46.3

Q ss_pred             CCCCcCcccccccccC---------------ccEEEcCCCCCcccHhhHHHHhcC-----CCccccccccccCCCCCCCc
Q 029544           84 VEDAECSICLGEYQDK---------------EVLRIMPQCGHSFHLACIDIWLRK-----KTTCPVCRLPLQDPLGRKHA  143 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~---------------~~~~~~~~C~H~f~~~Ci~~wl~~-----~~~CP~Cr~~~~~~~~~~~~  143 (191)
                      ..+..|+||++.+..+               ..+..+ +|+|.||..||..|+..     +.+||+||..+....+.++.
T Consensus        23 ~~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~-~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~~~qP~  101 (114)
T d1v87a_          23 APEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLT-KCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPW  101 (114)
T ss_dssp             CCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEES-SSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSSSCTT
T ss_pred             cccccccchhheecccccccccccccccccccceEEC-CCCChhhHHHHHHHHHhcCcCCCCccccccchhccCcCCCCC
Confidence            3466799999987542               223344 59999999999999973     34799999999877665554


Q ss_pred             cccc
Q 029544          144 REAT  147 (191)
Q Consensus       144 ~~~~  147 (191)
                      .++.
T Consensus       102 ~~~~  105 (114)
T d1v87a_         102 GKME  105 (114)
T ss_dssp             SSCC
T ss_pred             Ccee
Confidence            4443

>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=99.49  E-value=5.2e-15  Score=87.09  Aligned_cols=49  Identities=22%  Similarity=0.558  Sum_probs=39.9

Q ss_pred             cCcccccccccCccEEEcCCCCCcccHhhHHHHhcC-CCccccccccccC
Q 029544           88 ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK-KTTCPVCRLPLQD  136 (191)
Q Consensus        88 ~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~-~~~CP~Cr~~~~~  136 (191)
                      +|+||+++|........+.+|||.||..|+.+|+.. +..||+||+++.+
T Consensus         2 eCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            699999999876544333359999999999999985 4469999999864

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=99.46  E-value=9.8e-15  Score=90.77  Aligned_cols=48  Identities=33%  Similarity=0.965  Sum_probs=40.5

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccC
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~  136 (191)
                      ..+|+||++.+.++.  +.+ +|||.||..|+.+|+..+.+||+||.++..
T Consensus         5 ~d~C~IC~~~~~~~~--~~~-~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~   52 (68)
T d1chca_           5 AERCPICLEDPSNYS--MAL-PCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCSSCCSCCCSCE--EET-TTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCccCCcCccCCc--EEe-CCCCcCcHHHHHHHHHhCCcCCCCCcchHh
Confidence            456999999997653  345 599999999999999999999999998753

>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=99.42  E-value=6.7e-14  Score=91.29  Aligned_cols=50  Identities=28%  Similarity=0.677  Sum_probs=40.6

Q ss_pred             CCCcCcccccccccCc---------------cEEEcCCCCCcccHhhHHHHhcCCCcccccccccc
Q 029544           85 EDAECSICLGEYQDKE---------------VLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQ  135 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~---------------~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~  135 (191)
                      .+..|+||++.+....               .+..+ +|+|.||..||.+||..+.+||+||+++.
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~   84 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWG-VCNHAFHFHCISRWLKTRQVCPLDNREWE   84 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEE-TTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEc-cccCcccHHHHHHHHHHCCcCCCCCCccc
Confidence            4556999998876532               23345 49999999999999999999999999875

>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=99.39  E-value=1.2e-13  Score=85.00  Aligned_cols=52  Identities=27%  Similarity=0.700  Sum_probs=39.7

Q ss_pred             CCCcCcccccccccC-c-cEEEcCCCCCcccHhhHHHHhcC-CCccccccccccCC
Q 029544           85 EDAECSICLGEYQDK-E-VLRIMPQCGHSFHLACIDIWLRK-KTTCPVCRLPLQDP  137 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~-~-~~~~~~~C~H~f~~~Ci~~wl~~-~~~CP~Cr~~~~~~  137 (191)
                      ++..|+||++.+..+ . ....+ +|||.||..||.+|+.. +..||+||.++...
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~-~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEEC-TTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCCCCcCCceeecCCceEEEeC-ccChHhhHHHHHHHhCcCcCCCCCCCcCcccc
Confidence            456899999986433 2 33344 59999999999999964 55799999988643

>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=99.38  E-value=1.6e-13  Score=87.56  Aligned_cols=49  Identities=27%  Similarity=0.702  Sum_probs=40.6

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-CCCccccccccccCCC
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQDPL  138 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-~~~~CP~Cr~~~~~~~  138 (191)
                      ...|+||++.+.++..+    +|||.||..|+..|+. +++.||+||..+....
T Consensus        23 ~~~C~IC~~~~~~~~~~----~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~   72 (79)
T d1fbva4          23 FQLCKICAENDKDVKIE----PCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE   72 (79)
T ss_dssp             TTBCTTTSSSBCCEECS----SSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCC
T ss_pred             CCCCccCCCcCCCeEEe----CCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCc
Confidence            45699999998875444    5999999999999997 4567999999997544

>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=99.30  E-value=4.9e-13  Score=86.37  Aligned_cols=48  Identities=31%  Similarity=0.593  Sum_probs=41.1

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-CCCccccccccccCC
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQDP  137 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-~~~~CP~Cr~~~~~~  137 (191)
                      ...|+||++.+.++..+    +|||.||..||.+|+. .+..||+||.++...
T Consensus        23 ~l~C~IC~~~~~~pv~~----~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~   71 (86)
T d1rmda2          23 SISCQICEHILADPVET----SCKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (86)
T ss_dssp             HTBCTTTCSBCSSEEEC----TTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CcCCccCCcchhcceec----CCCChhhHHHHHHHHhhCCCcCcccCCCCChh
Confidence            45799999999988666    6999999999999997 456799999988654

>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=99.28  E-value=4.8e-13  Score=79.51  Aligned_cols=47  Identities=23%  Similarity=0.577  Sum_probs=39.4

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDPL  138 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~~  138 (191)
                      +...|+||++.+.++..+    +|||.||..|+.+|   +..||+||.++....
T Consensus         5 ~~l~C~IC~~~~~~p~~l----pCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T d1bora_           5 QFLRCQQCQAEAKCPKLL----PCLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCSSCSSSCSSCBCCSCS----TTSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             CCCCCcccCcccCCCEEe----cCCCHHhHHHHHcC---CCcCcCCCCcccCCC
Confidence            456899999999988766    69999999999765   567999999987543

>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=99.27  E-value=3.8e-13  Score=80.15  Aligned_cols=47  Identities=15%  Similarity=0.264  Sum_probs=41.3

Q ss_pred             cCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           88 ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        88 ~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      .|+||++.+.++..+   +.|||.||.+||.+|+..+..||+||.++...
T Consensus         2 ~C~Ic~~~~~~Pv~~---~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~   48 (56)
T d2baya1           2 LCAISGKVPRRPVLS---PKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   48 (56)
T ss_dssp             CCTTTCSCCSSEEEE---TTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             CCccCCchHHhcCcc---CCCCCcccHHHHHHHHhhccCCCccCCcCCHH
Confidence            599999999988655   25999999999999999999999999988643

>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=99.24  E-value=1.8e-12  Score=86.83  Aligned_cols=48  Identities=29%  Similarity=0.676  Sum_probs=40.9

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCC---CccccccccccC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK---TTCPVCRLPLQD  136 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~---~~CP~Cr~~~~~  136 (191)
                      ....|+||++.+.++..+    +|||.||..||..|+...   ..||+||.++..
T Consensus        20 ~~l~CpIC~~~~~~pv~~----~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (103)
T d1jm7a_          20 KILECPICLELIKEPVST----KCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (103)
T ss_dssp             HHTSCSSSCCCCSSCCBC----TTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             cCcCCCccCchhCCeEEc----CCCCchhhHHHHHHHHHCCCCCcCcCCCCcCCh
Confidence            346799999999998776    699999999999999754   369999998864

>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=99.15  E-value=1.3e-11  Score=74.44  Aligned_cols=53  Identities=21%  Similarity=0.488  Sum_probs=39.3

Q ss_pred             CCCCCcCcccccccccCccEE-EcCCCCCcccHhhHHHHhc--CCCcccccccccc
Q 029544           83 SVEDAECSICLGEYQDKEVLR-IMPQCGHSFHLACIDIWLR--KKTTCPVCRLPLQ  135 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~-~~~~C~H~f~~~Ci~~wl~--~~~~CP~Cr~~~~  135 (191)
                      +++...|.||++.+.+..... ....|+|.||..||.+|+.  .+.+||+||+++.
T Consensus         3 ded~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           3 DEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             TCSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            346678999999887664441 0112459999999999996  4567999999875

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.13  E-value=1.9e-11  Score=77.53  Aligned_cols=51  Identities=25%  Similarity=0.494  Sum_probs=43.9

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC-CCccccccccccCC
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK-KTTCPVCRLPLQDP  137 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~-~~~CP~Cr~~~~~~  137 (191)
                      ..+++.|+||++.|.++..+    +|||.||..||..|+.. ...||.|+.++...
T Consensus         5 iP~~l~CpIc~~~m~dPV~~----~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~   56 (78)
T d1t1ha_           5 FPEYFRCPISLELMKDPVIV----STGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             CSSSSSCTTTSCCCSSEEEE----TTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             CCccCCCcCcCchhhCceEc----cCCCcchHHHHHHHHHHCCCCCCcccccCCcc
Confidence            34678999999999999776    79999999999999975 45699999988653

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.10  E-value=1.7e-11  Score=78.16  Aligned_cols=49  Identities=18%  Similarity=0.202  Sum_probs=42.5

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-CCCccccccccccC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-KKTTCPVCRLPLQD  136 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-~~~~CP~Cr~~~~~  136 (191)
                      .+++.|+||++.|.++..+    +|||.||..||.+|+. .+..||.|+.++..
T Consensus         5 P~~l~CpIc~~l~~dPv~~----~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~   54 (80)
T d2c2la2           5 PDYLCGKISFELMREPCIT----PSGITYDRKDIEEHLQRVGHFNPVTRSPLTQ   54 (80)
T ss_dssp             CSTTBCTTTCSBCSSEEEC----SSCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CccccCcCcCchhhhhccc----CCcCeecHHHHHHHHhcCCccCCCccccccc
Confidence            4678899999999999766    7999999999999997 45579999998754

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.10  E-value=1.1e-11  Score=81.97  Aligned_cols=48  Identities=29%  Similarity=0.567  Sum_probs=39.6

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccccccCC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      +...|+||++.|.++..+.   +|||.||..||.+|+.  ..||.||.++...
T Consensus        21 ~~l~C~IC~~~~~~pv~~~---~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~   68 (97)
T d1jm7b_          21 KLLRCSRCTNILREPVCLG---GCEHIFCSNCVSDCIG--TGCPVCYTPAWIQ   68 (97)
T ss_dssp             HTTSCSSSCSCCSSCBCCC---SSSCCBCTTTGGGGTT--TBCSSSCCBCSCS
T ss_pred             hcCCCccCCchhhcCceeC---CCCCchhHHHHHHHHh--ccccccCCcCchh
Confidence            3568999999999886542   6999999999999984  4599999887643

>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=98.85  E-value=1.1e-09  Score=72.20  Aligned_cols=50  Identities=22%  Similarity=0.128  Sum_probs=43.5

Q ss_pred             CCCCcCcccccccccCccEEEcCCCC-CcccHhhHHHHhcCCCccccccccccCC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCG-HSFHLACIDIWLRKKTTCPVCRLPLQDP  137 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~-H~f~~~Ci~~wl~~~~~CP~Cr~~~~~~  137 (191)
                      .+++.|+||.+.|.+++.+    +|+ |.|+..||..|+..+..||+|+.++...
T Consensus        20 P~~f~CPI~~~lm~dPV~~----~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~   70 (98)
T d1wgma_          20 CDEFLDPIMSTLMCDPVVL----PSSRVTVDRSTIARHLLSDQTDPFNRSPLTMD   70 (98)
T ss_dssp             CTTTBCTTTCSBCSSEEEC----TTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTT
T ss_pred             cHHhCCcCchhHHHHHHhc----ccccchhhHHHHHHHHHhcCCcccccccccch
Confidence            4578999999999999877    565 5899999999999999999999988653

>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=98.62  E-value=9.2e-09  Score=67.03  Aligned_cols=48  Identities=27%  Similarity=0.664  Sum_probs=36.9

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC--------CCccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK--------KTTCPVCRL  132 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~--------~~~CP~Cr~  132 (191)
                      .....|+||++++........+ +|+|.||.+||..|+..        .-.||.|+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           3 SGSSGCKLCLGEYPVEQMTTIA-QCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEET-TTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCCcCccCCCcccCCceEEEC-CCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            3456799999999776666555 49999999999999862        124998654

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=94.39  E-value=0.0095  Score=34.65  Aligned_cols=50  Identities=26%  Similarity=0.522  Sum_probs=35.0

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-----CCCccccccccc
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-----KKTTCPVCRLPL  134 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-----~~~~CP~Cr~~~  134 (191)
                      ....|.+|.....+....+.-..|+..||..|+..-..     ..-.||.|+..-
T Consensus         5 ~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~~   59 (64)
T d1we9a_           5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKS   59 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTT
T ss_pred             CCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCcC
Confidence            45579999988777665555557999999999853211     334599998543

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.86  E-value=0.026  Score=31.03  Aligned_cols=44  Identities=27%  Similarity=0.760  Sum_probs=29.6

Q ss_pred             cCcccccccccCccEEEcCCCCCcccHhhHHHHhcCC----Cccccccc
Q 029544           88 ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK----TTCPVCRL  132 (191)
Q Consensus        88 ~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~----~~CP~Cr~  132 (191)
                      .|.||...-.....+ .-..|...||..|+..-+...    -.||.|+.
T Consensus         2 ~C~vC~~~~~~~~~i-~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDKLI-LCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCE-ECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCCEE-EcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            478887654444444 344699999999998765532    24998874

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.42  E-value=0.42  Score=27.81  Aligned_cols=38  Identities=18%  Similarity=0.409  Sum_probs=29.0

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR  122 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~  122 (191)
                      ....|.+|.+.+++...+..-.-=+|.||..|-+..++
T Consensus         7 ~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik   44 (80)
T d2cs3a1           7 GPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIK   44 (80)
T ss_dssp             CSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHH
T ss_pred             CceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHH
Confidence            34679999999999887732111269999999998886

>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=89.07  E-value=0.13  Score=29.02  Aligned_cols=44  Identities=27%  Similarity=0.603  Sum_probs=31.5

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccc
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVC  130 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~C  130 (191)
                      ...|.-|...+.+... ..-+.|++.||.+|=.-.-..-..||-|
T Consensus        15 ~~~C~gC~~~l~~~~~-y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          15 ERFCYGCQGELKDQHV-YVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             CCEETTTTEECTTSEE-ECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCccCCCCcCCCCce-EECcCCCCccccccchhhhhhhcCCCCC
Confidence            4568899888765533 4456799999999965443455679988

>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=88.32  E-value=0.079  Score=30.20  Aligned_cols=47  Identities=28%  Similarity=0.625  Sum_probs=30.3

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcC----CCccccccccc
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRK----KTTCPVCRLPL  134 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~----~~~CP~Cr~~~  134 (191)
                      .++..|.+|.+.   +..+ .-..|.-.||..|+...+..    .-.||.|+..-
T Consensus         7 ~~~~~C~~C~~~---g~lv-~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           7 HHMEFCRVCKDG---GELL-CCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---SSCB-CCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCcCCCcCCCCC---CeEE-EeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            345569999853   3333 33358889999998755542    23499997543

>d1y02a2 g.50.1.1 (A:20-70) Rififylin (FYVE-RING finger protein Sakura) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Rififylin (FYVE-RING finger protein Sakura)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.08  E-value=0.043  Score=30.33  Aligned_cols=45  Identities=16%  Similarity=0.452  Sum_probs=28.7

Q ss_pred             cCcccccccccCccEEEcCCCCCcccHhhHHHHhcCCCccccccc
Q 029544           88 ECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKKTTCPVCRL  132 (191)
Q Consensus        88 ~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~~~CP~Cr~  132 (191)
                      .|.+|...|..-..-..-..||.+||..|....-.....|..|..
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C~~   46 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQR   46 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhHhh
Confidence            477888877755443344479999999997554444556777753

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=87.34  E-value=0.17  Score=30.19  Aligned_cols=50  Identities=20%  Similarity=0.544  Sum_probs=31.0

Q ss_pred             CCCcCcccccccccCccEEEc-CCCCCcccHhhHHH----Hhc-----CCCcccccccccc
Q 029544           85 EDAECSICLGEYQDKEVLRIM-PQCGHSFHLACIDI----WLR-----KKTTCPVCRLPLQ  135 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~-~~C~H~f~~~Ci~~----wl~-----~~~~CP~Cr~~~~  135 (191)
                      +...| ||.........+..- ..|...||..|+.-    +..     ....||.|+..-.
T Consensus        15 ~~~~C-~C~~~~~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~~   74 (78)
T d1wewa_          15 IKVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSG   74 (78)
T ss_dssp             CCCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCCS
T ss_pred             CccEe-ECCCccCCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcCC
Confidence            34567 899877655444321 14899999999831    101     1345999986543

>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=87.15  E-value=0.23  Score=29.93  Aligned_cols=36  Identities=22%  Similarity=0.591  Sum_probs=24.9

Q ss_pred             CCCCCcCcccccccccCccEEEcCCCCCcccHhhHHHH
Q 029544           83 SVEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIW  120 (191)
Q Consensus        83 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w  120 (191)
                      ..++..|.|| +.+........- -|+-+||..|+.+.
T Consensus        12 v~~D~mC~vC-~v~t~~~l~pCR-vCtRv~H~~CL~r~   47 (89)
T d1wila_          12 VVNDEMCDVC-EVWTAESLFPCR-VCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCSCCCTTT-CCCCSSCCSSCS-SSSSCCCHHHHHHH
T ss_pred             CCcCcccccc-Ccccccceecce-eecchhhHHHHHHh
Confidence            3467789999 555544433111 38899999999987

>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=87.01  E-value=1.1  Score=26.49  Aligned_cols=49  Identities=18%  Similarity=0.361  Sum_probs=31.9

Q ss_pred             cCcccccccccCccEEEcCCCCCcccHhhHH---HHhc--CCCccccccccccC
Q 029544           88 ECSICLGEYQDKEVLRIMPQCGHSFHLACID---IWLR--KKTTCPVCRLPLQD  136 (191)
Q Consensus        88 ~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~---~wl~--~~~~CP~Cr~~~~~  136 (191)
                      .+.||...+......+.-..|.-.||..|+.   .-..  .+-.||.|+.....
T Consensus        13 v~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~gp   66 (79)
T d1wepa_          13 VYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFGP   66 (79)
T ss_dssp             CCSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSCS
T ss_pred             eEeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcCC
Confidence            3448988766554444455699999999984   1111  23569999865543

>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=86.86  E-value=0.24  Score=28.88  Aligned_cols=45  Identities=24%  Similarity=0.597  Sum_probs=29.2

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHHhcCC----Cccccccccc
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLRKK----TTCPVCRLPL  134 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~~~----~~CP~Cr~~~  134 (191)
                      ...|.+|.+   .+..+ .-..|...||..|+.+.+...    -.||.|+...
T Consensus         7 c~~C~~C~~---~~~ll-~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           7 ATICRVCQK---PGDLV-MCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             SSCCSSSCS---SSCCE-ECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCCCC---cCEEE-ECCCCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            345667754   23333 334699999999998776532    2499997544

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Death associated transcription factor 1, Datf1 (DIO-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.09  E-value=0.51  Score=27.63  Aligned_cols=50  Identities=20%  Similarity=0.465  Sum_probs=31.2

Q ss_pred             CCCcCcccccccccCccEEEcCCCCCcccHhhHH----H-----HhcCCCccccccccccC
Q 029544           85 EDAECSICLGEYQDKEVLRIMPQCGHSFHLACID----I-----WLRKKTTCPVCRLPLQD  136 (191)
Q Consensus        85 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~----~-----wl~~~~~CP~Cr~~~~~  136 (191)
                      +...| ||.........+ .-..|.-.||..|+.    .     .......||.|+....+
T Consensus        15 ~~~~C-iC~~~~~~~~mi-~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~~~p   73 (76)
T d1wema_          15 NALYC-ICRQPHNNRFMI-CCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILSGP   73 (76)
T ss_dssp             TCCCS-TTCCCCCSSCEE-ECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHSCS
T ss_pred             CcCEE-ECCCccCCCeEE-EECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCcCCC
Confidence            33457 888766554444 333588899999982    1     11234679999765443

>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At1g33420
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=85.33  E-value=0.11  Score=30.50  Aligned_cols=49  Identities=27%  Similarity=0.382  Sum_probs=31.9

Q ss_pred             CCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc----CCCcccccccccc
Q 029544           86 DAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR----KKTTCPVCRLPLQ  135 (191)
Q Consensus        86 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~----~~~~CP~Cr~~~~  135 (191)
                      ...| ||.........+..-..|...||..|+..-..    ....||.|+..-.
T Consensus        16 ~~~C-~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~~~~~~~~C~~C~~~~~   68 (72)
T d1weea_          16 KVDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELSG   68 (72)
T ss_dssp             EECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHHCS
T ss_pred             eEEe-eCCCCcCCCCeEEEeCCCCCcCchhhcCCccccCCCCcEECcCCcCcCC
Confidence            3457 78876666655555556889999999754222    3345999976543

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.45  E-value=0.23  Score=30.27  Aligned_cols=50  Identities=16%  Similarity=0.345  Sum_probs=32.3

Q ss_pred             CCcCccccccccc-CccEEEcCCCCCcccHhhHHHHhc--------CCCcccccccccc
Q 029544           86 DAECSICLGEYQD-KEVLRIMPQCGHSFHLACIDIWLR--------KKTTCPVCRLPLQ  135 (191)
Q Consensus        86 ~~~C~IC~~~~~~-~~~~~~~~~C~H~f~~~Ci~~wl~--------~~~~CP~Cr~~~~  135 (191)
                      ...|.||...... ...+..-..|...||..|+.+.+.        ..-.||.|.....
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~~   74 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMK   74 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHC
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchHh
Confidence            4469999865432 334444446999999999764321        1345999986544

>d1wfka_ g.50.1.1 (A:) Zinc finger FYVE domain containing protein 19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Zinc finger FYVE domain containing protein 19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.86  E-value=0.14  Score=31.56  Aligned_cols=53  Identities=17%  Similarity=0.354  Sum_probs=36.4

Q ss_pred             CCCCcCcccccccccCccEEEcCCCCCcccHhhHHHHhc-------CCCccccccccccC
Q 029544           84 VEDAECSICLGEYQDKEVLRIMPQCGHSFHLACIDIWLR-------KKTTCPVCRLPLQD  136 (191)
Q Consensus        84 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~wl~-------~~~~CP~Cr~~~~~  136 (191)
                      ..+..|.+|...|..-..-..-..||-+||..|......       ..+.|..|-..+..
T Consensus         7 ~~~s~C~~C~~~Fs~~~rrhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~~   66 (88)
T d1wfka_           7 GMESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFSALVPRAGNTQQKVCKQCHTILTR   66 (88)
T ss_dssp             CCCSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCEEEEETTTTSEEEEECHHHHHHHHH
T ss_pred             cccCcCcccCchhccccccccccccChhhChHHhCCccccCCCCCCCCeECHHHHHHHHh
Confidence            345679999999876555444557999999999865533       12348888655543