Citrus Sinensis ID: 032328

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140---
Protein Sequence
MVMEILISLTLLFVGIAALVVIHVCVVGRAFRRGYEQSGFAQGGFKMISSDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVILKDGSSVSSDVAIELT
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHccccEEEEEcccccccccccccEEccccccccEEccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHccEEEEEccccccccccEEEEEHcccccccEEEEcccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MVMEILISLTLLFVGIAALVVIHVCVVGRafrrgyeqsgfaqggfkmissddlkqipcfeykaaadrgsspvdCVVCLenfrmgdkcrllpncrhsfhaQCIDswllktpicpicrtrvspskvGVILkdgssvssdvAIELT
Flexible Loop (DISEMBL)
MVMEILISLTLLFVGIAALVVIHVCVVGRAFRRGYEQSGFAQGGFKMISSDDLKQIPCFEYkaaadrgsspVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICrtrvspskvgvilkdgssvssdvaielt
Low Complexity Region (SEG)
MVMEILISLTLLFVGIAALVVIHVCVVGRAFRRGYEQSGFAQGGFKMISSDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVILKDGSSVSSDVAIELT
Disordered region (IsUnstruct)
**MEILISLTLLFVGIAALVVIHVCVVGRAFRRGYEQSGFAQGGFKMISSDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVIL***************
Disordered Region (DISOPRED)
MVMEILISLTLLFVGIAALVVIHVCVVGR************************KQIPCFEYKAA****SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTR*************************
Disordered Region (DISEMBL)
MVMEILISLTLLFVGIAALVVIHVCVVGRAFRRGYEQSGFAQGGFKMISSDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVILKDGSSVSSDVAIELT
Disordered Region (DISPRO)
MVMEILISLTLLFVGIAALVVIHVCVVGRAF***************MISSDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS***********************
Transmembrane Helix (TMHMM)
ooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVMEILISLTLLFVGIAALVVIHVCVVGRAFRRGYEQSGFAQGGFKMISSDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVILKDGSSVSSDVAIELT
Positional Conservation
no confident homologs detected

---

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	143	2.2.26 [Sep-21-2011]
Q9ZV51	181	RING-H2 finger protein AT	yes	no	0.503	0.397	0.472	6e-15
Q9ZV53	423	Putative RING-H2 finger p	no	no	0.447	0.151	0.5	4e-14
Q7X843	349	RING-H2 finger protein AT	no	no	0.482	0.197	0.478	9e-14
Q5XF85	432	E3 ubiquitin-protein liga	no	no	0.678	0.224	0.37	2e-13
Q940Q4	472	RING-H2 finger protein AT	no	no	0.426	0.129	0.508	2e-13
Q9FHG8	210	Putative RING-H2 finger p	no	no	0.783	0.533	0.317	4e-13
Q9M0C3	176	RING-H2 finger protein AT	no	no	0.454	0.369	0.485	5e-13
Q8L9W3	163	E3 ubiquitin-protein liga	no	no	0.846	0.742	0.317	8e-13
Q8GW38	369	RING-H2 finger protein AT	no	no	0.412	0.159	0.532	1e-12
Q8GT74	241	NEP1-interacting protein	no	no	0.538	0.319	0.392	3e-12

>sp|Q9ZV51|ATL56_ARATH RING-H2 finger protein ATL56 OS=Arabidopsis thaliana GN=ATL56 PE=2 SV=1

 Score = 79.7 bits (195), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 34/72 (47%), Positives = 45/72 (62%)

Query: 48  ISSDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL 107
           +SS  +K++P F++   +       DCVVC + FR G  CR LP C H FH +C+D+WLL
Sbjct: 84  LSSRFVKKLPQFKFSEPSTYTRYESDCVVCFDGFRQGQWCRNLPGCGHVFHRKCVDTWLL 143

Query: 108 KTPICPICRTRV 119
           K   CPICR RV
Sbjct: 144 KASTCPICRARV 155

Arabidopsis thaliana (taxid: 3702)

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

 Score = 77.0 bits (188), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 32/64 (50%), Positives = 40/64 (62%)

Query: 56  IPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPIC 115
           +P F YK+      SP DC VCL  F   DK RLLP C H+FH +CID+WLL    CP+C
Sbjct: 108 LPVFHYKSIVGLKISPFDCPVCLCEFETEDKLRLLPKCSHAFHVECIDTWLLSHSTCPLC 167

Query: 116 RTRV 119
           R+ +
Sbjct: 168 RSNL 171

May be involved in female gametophyte development.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 75.5 bits (184), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 33/69 (47%), Positives = 38/69 (55%)

Query: 56  IPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPIC 115
           +P F Y         P DC VCL  F   DK RLLP C H+FH  CID+WLL    CP+C
Sbjct: 189 LPVFLYGNVTISLEQPFDCAVCLNEFSDTDKLRLLPVCSHAFHLHCIDTWLLSNSTCPLC 248

Query: 116 RTRVSPSKV 124
           R  +S S V
Sbjct: 249 RRSLSTSNV 257

Arabidopsis thaliana (taxid: 3702)

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

 Score = 74.3 bits (181), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/100 (37%), Positives = 55/100 (55%), Gaps = 3/100 (3%)

Query: 35  YEQSGFAQGGFKMISSDDLKQIPCFEYKAAADRGSSP-VDCVVCLENFRMGDKCRLLPNC 93
           + +S  +   F  +    ++ +P F + A   +GS   +DC VCL  F   +  RLLP C
Sbjct: 85  FNRSTASSDRFSGLDKTAIESLPLFRFSAL--KGSKQGLDCSVCLSKFESVEILRLLPKC 142

Query: 94  RHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVILKDGSS 133
           RH+FH  CID WL +   CP+CR RVS  +   +L +G+S
Sbjct: 143 RHAFHIGCIDQWLEQHATCPLCRDRVSMEEDSSVLTNGNS 182

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|Q940Q4|ATL13_ARATH RING-H2 finger protein ATL13 OS=Arabidopsis thaliana GN=ATL13 PE=2 SV=2

 Score = 74.3 bits (181), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 31/61 (50%), Positives = 37/61 (60%)

Query: 56  IPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPIC 115
           +P F YK+     + P DC VCL  F   DK RLLP C H+FH  CID+WLL    CP+C
Sbjct: 116 LPVFHYKSIIGLKNYPFDCAVCLCEFETEDKLRLLPKCSHAFHMDCIDTWLLSHSTCPLC 175

Query: 116 R 116
           R
Sbjct: 176 R 176

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FHG8|ATL50_ARATH Putative RING-H2 finger protein ATL50 OS=Arabidopsis thaliana GN=ATL50 PE=3 SV=1

 Score = 73.2 bits (178), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 41/129 (31%), Positives = 58/129 (44%), Gaps = 17/129 (13%)

Query: 5   ILISLTLLFVGIAALVVIHVCV---------VGRAFRRGYEQSGFAQGGFKM-------- 47
           +L+ +TLL +      +IH+ V         +  A+    E S   QG ++         
Sbjct: 36  VLLYITLLSIIFFVAALIHLLVKFLHRPQTRLDDAYDGITESSTALQGRYQTRFNLHDAE 95

Query: 48  ISSDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL 107
           I    +  +P   YK          DC VCL  F   D+ RLLP C H+FH +CID+WLL
Sbjct: 96  IDQSFIDALPLLHYKTMIGLRHDLSDCAVCLREFTAEDELRLLPKCSHAFHVECIDTWLL 155

Query: 108 KTPICPICR 116
               CP+CR
Sbjct: 156 TNSTCPLCR 164

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M0C3|ATL14_ARATH RING-H2 finger protein ATL14 OS=Arabidopsis thaliana GN=ATL14 PE=2 SV=1

 Score = 73.2 bits (178), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 33/68 (48%), Positives = 46/68 (67%), Gaps = 3/68 (4%)

Query: 53  LKQIPCFEY-KAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPI 111
           +K++P F+Y + +++ G    DCVVC++ FR G  CR LP C H FH +C+D WL+K   
Sbjct: 95  VKRLPQFKYCEPSSEYGGD--DCVVCIDGFRQGQWCRKLPRCGHVFHRKCVDLWLIKVST 152

Query: 112 CPICRTRV 119
           CPICR RV
Sbjct: 153 CPICRDRV 160

Arabidopsis thaliana (taxid: 3702)

>sp|Q8L9W3|ATL23_ARATH E3 ubiquitin-protein ligase ATL23 OS=Arabidopsis thaliana GN=ATL23 PE=1 SV=2

 Score = 72.4 bits (176), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 40/126 (31%), Positives = 68/126 (53%), Gaps = 5/126 (3%)

Query: 1   MVMEILISLTLLFVGIAALVVIHVCVVGRAFRRGYEQSGFAQG----GFKMISSDDLKQI 56
           M+  + ++L L  VG+  + +I++ ++  + RR  E+  FA+       K +S  +L++I
Sbjct: 28  MIATVFMALLLPCVGMCIVFLIYLFLLWCSTRRRIERLRFAEPVKPVTGKGLSVLELEKI 87

Query: 57  PCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICR 116
           P    +  A    S  +C VCLE+   G   RL+P C H FH  C D+WL    +CP+CR
Sbjct: 88  PKLTGRELAVIARS-TECAVCLEDIESGQSTRLVPGCNHGFHQLCADTWLSNHTVCPVCR 146

Query: 117 TRVSPS 122
             ++P+
Sbjct: 147 AELAPN 152

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

 Score = 71.6 bits (174), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 33/62 (53%), Positives = 39/62 (62%), Gaps = 3/62 (4%)

Query: 56  IPCFEYKAAADRGS-SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPI 114
           +P F YK    +G+  P DC VCL  F   DK RLLPNC H+FH  CID+WLL    CP+
Sbjct: 127 LPVFLYKEI--KGTKEPFDCAVCLCEFSEDDKLRLLPNCSHAFHIDCIDTWLLSNSTCPL 184

Query: 115 CR 116
           CR
Sbjct: 185 CR 186

Arabidopsis thaliana (taxid: 3702)

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

 Score = 70.1 bits (170), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 31/79 (39%), Positives = 46/79 (58%), Gaps = 2/79 (2%)

Query: 40  FAQGGFKMISSDDLKQIP--CFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSF 97
           F  GG K ++ D +++IP          D   +   C VCL++F++G+  R LP+C H F
Sbjct: 160 FDTGGSKGLTGDLVEKIPKMTITGNNNTDASENTDSCSVCLQDFQLGETVRSLPHCHHMF 219

Query: 98  HAQCIDSWLLKTPICPICR 116
           H  CID+WLL+   CP+CR
Sbjct: 220 HLPCIDNWLLRHGSCPMCR 238

Intrinsic thylakoid membrane protein that fixes RPOT2 on the stromal side of the thylakoid membrane.

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	143
255540713	189	conserved hypothetical protein [Ricinus	0.993	0.751	0.62	3e-49
359491594	146	PREDICTED: RING-H2 finger protein ATL48-	0.979	0.958	0.639	9e-46
359488847	188	PREDICTED: E3 ubiquitin-protein ligase A	0.979	0.744	0.573	1e-39
255552618	200	zinc finger protein, putative [Ricinus c	0.972	0.695	0.524	3e-36
388501546	188	unknown [Lotus japonicus]	0.965	0.734	0.509	2e-31
413944251	172	putative RING zinc finger domain superfa	0.762	0.633	0.451	2e-21
326516304	148	predicted protein [Hordeum vulgare subsp	0.811	0.783	0.379	8e-21
242066104	157	hypothetical protein SORBIDRAFT_04g02906	0.797	0.726	0.4	1e-20
242095466	168	hypothetical protein SORBIDRAFT_10g00986	0.783	0.666	0.409	4e-20
357143605	150	PREDICTED: E3 ubiquitin-protein ligase A	0.797	0.76	0.385	6e-19

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

 Score =  199 bits (506), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 93/150 (62%), Positives = 116/150 (77%), Gaps = 8/150 (5%)

Query: 1   MVMEILISLTLLFVGIAALVVIHVCVVGRAFRRGYEQS--------GFAQGGFKMISSDD 52
           M MEI++S+ LLFVGIA LV IHVC+VGRAFRRGYE            ++ G K IS+++
Sbjct: 1   MAMEIIVSVVLLFVGIAVLVAIHVCIVGRAFRRGYETGQEIGPGSFSSSRYGIKKISNEE 60

Query: 53  LKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPIC 112
           LK +PCF+YKAA   GSS  DCVVCLENF +GDKC+LLPNC+HSFH+QCIDSWL+KTPIC
Sbjct: 61  LKNLPCFDYKAAEKEGSSSSDCVVCLENFNVGDKCKLLPNCKHSFHSQCIDSWLVKTPIC 120

Query: 113 PICRTRVSPSKVGVILKDGSSVSSDVAIEL 142
           PICRT V+  KVG++L+  SS+S  V +E+
Sbjct: 121 PICRTIVNTPKVGLVLRQESSISIAVGVEI 150

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  187 bits (476), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 94/147 (63%), Positives = 106/147 (72%), Gaps = 7/147 (4%)

Query: 3   MEILISLTLLFVGIAALVVIHVCVVGRAFRRGYEQSGFAQ----GGFKMISSDDLKQIPC 58
           MEI++SL LLFVGIA L+VIHVC+VGRAFRR Y      Q    GG  M S D+LK++PC
Sbjct: 1   MEIVVSLVLLFVGIAVLIVIHVCIVGRAFRRAYGNGAMVQRGGSGGLGM-SQDELKKLPC 59

Query: 59  FEYKAAA--DRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICR 116
           FEYKA A     +SPVDC VCLENFR GDKCRLLPNC+H FH+QCIDSWLLKTPICPICR
Sbjct: 60  FEYKAVALEKASNSPVDCAVCLENFRKGDKCRLLPNCKHFFHSQCIDSWLLKTPICPICR 119

Query: 117 TRVSPSKVGVILKDGSSVSSDVAIELT 143
           T  S  K+       S +S DV  ELT
Sbjct: 120 TCASTPKISTFSGQESGISRDVGAELT 146

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  167 bits (423), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 82/143 (57%), Positives = 99/143 (69%), Gaps = 3/143 (2%)

Query: 3   MEILISLTLLFVGIAALVVIHVCVVGRAFRRGYEQSGFAQGGFKMISS---DDLKQIPCF 59
           M I+ISL LLF+GI  LV+IHVC+VGRAFR G+      + G    +S   DDL ++PCF
Sbjct: 1   MAIVISLILLFLGIGVLVIIHVCIVGRAFRGGFGNGRMVERGNPRSTSMSLDDLDKLPCF 60

Query: 60  EYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRV 119
            ++A     SSPVDC VCL+NF+MGDKCRLLP C HSFHAQC+DSWLLKTPICPICRT  
Sbjct: 61  HFQAKEKGSSSPVDCAVCLDNFKMGDKCRLLPLCNHSFHAQCVDSWLLKTPICPICRTSA 120

Query: 120 SPSKVGVILKDGSSVSSDVAIEL 142
              K  ++  + SS  SD   EL
Sbjct: 121 DFRKGSLVSGEESSHFSDTGNEL 143

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  156 bits (394), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 76/145 (52%), Positives = 99/145 (68%), Gaps = 6/145 (4%)

Query: 3   MEILISLTLLFVGIAALVVIHVCVVGRAFRRGYEQ-----SGFAQGGFKMISSDDLKQIP 57
           M I++S+ LLFVGI  LV IH C++GR+FR          S  + G    IS+DDL+++P
Sbjct: 1   MAIVVSVILLFVGIGLLVFIHACIIGRSFRNNDPANDPTGSTDSPGRTTSISADDLEKLP 60

Query: 58  CFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRT 117
            F++ A   +GSSPVDC VCL+NFR GDKCRLLP C+HSFHAQC+D WLLKTPICPICR 
Sbjct: 61  SFDFIAKG-KGSSPVDCAVCLDNFRAGDKCRLLPICKHSFHAQCVDEWLLKTPICPICRA 119

Query: 118 RVSPSKVGVILKDGSSVSSDVAIEL 142
                +  V + + SS  SD +I++
Sbjct: 120 SAGSRRGSVAIGEESSHLSDTSIDM 144

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 77/151 (50%), Positives = 99/151 (65%), Gaps = 13/151 (8%)

Query: 1   MVMEILISLTLLFVGIAALVVIHVCVVGRAFRRGYEQSGF------AQGGFKMISSDDLK 54
           + M ++ISL L+FVG+  LV+IHVC+    F R    SG       A GG  M S  DL+
Sbjct: 13  LTMAVIISLVLIFVGLVFLVLIHVCL-SEWFSRTGGGSGGSMTERGANGGRSM-SKKDLE 70

Query: 55  QIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPI 114
           ++PC++Y A  +   SPVDC VCLEN   GDKCRLLP C+HSFHAQC+D+WLLKTPICPI
Sbjct: 71  KLPCYDYVAKDNSTCSPVDCAVCLENLTTGDKCRLLPVCKHSFHAQCVDTWLLKTPICPI 130

Query: 115 CRTRVSPSKVG---VILKDGSSVSSDVAIEL 142
           CR+    S  G    +++ GS  S +VAIE+
Sbjct: 131 CRSSAGSSHSGNQVQVVESGS--SRNVAIEM 159

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 56/124 (45%), Positives = 74/124 (59%), Gaps = 15/124 (12%)

Query: 6   LISLTLLFVGIAALVVIHVCVVGRAFRRGYEQSGFAQG------------GFKMISSDDL 53
           ++S+ LL  G+A ++V H+ VV  A  RG    G +Q             G + +SS +L
Sbjct: 9   ILSVVLLIAGVAVMLVAHILVVFWALLRGLGSRGSSQHAANQEERVEDGRGRRGLSSGEL 68

Query: 54  KQIPCFEY-KAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPIC 112
             +PC EY KAAAD  +   DC VCLE F  GD+CR LP C HSFHA+C+DSWL K+  C
Sbjct: 69  ATLPCHEYFKAAADGETG--DCAVCLEAFEAGDRCRQLPRCEHSFHAECVDSWLRKSSAC 126

Query: 113 PICR 116
           P+CR
Sbjct: 127 PVCR 130

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  105 bits (261), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 47/124 (37%), Positives = 75/124 (60%), Gaps = 8/124 (6%)

Query: 5   ILISLTLLFVGIAALVVIHVCVVGRAFRRGY--------EQSGFAQGGFKMISSDDLKQI 56
           + +S+  L  G+  ++ +HV V+  A RRG          +    QG    +++D+L ++
Sbjct: 4   MAVSVLFLIAGVVLMLALHVLVIVWAVRRGAVLRLRGAARERDREQGEATGLTADELGEL 63

Query: 57  PCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICR 116
           PC ++KAAA  G+   +C VCLE F+ GD+CR+LP C H FH QC+D+WL ++  CP+CR
Sbjct: 64  PCQDFKAAAVVGTGAGECAVCLEAFQGGDRCRVLPGCHHGFHTQCVDAWLRQSRRCPVCR 123

Query: 117 TRVS 120
             V+
Sbjct: 124 AEVA 127

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  104 bits (259), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 52/130 (40%), Positives = 81/130 (62%), Gaps = 16/130 (12%)

Query: 2   VMEILISLTLLFVGIAALVVIHVCVVGRAFRRGY-----------EQSGFAQGGFKMISS 50
           ++E+ +S+ LL  G+ A++V+HV +V  A RRG            E+    QG    +S 
Sbjct: 1   MVELTVSVLLLVAGVVAMLVLHVLIVVWALRRGVVLRAAASRRQDEERAAGQG----LSP 56

Query: 51  DDLKQIPCFEYK-AAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT 109
           +DL ++PC +++ + A  G++  +C VCLE F+ GD+CR+LP C H FHAQC+D WL K+
Sbjct: 57  EDLNELPCHDHECSKAGAGAAGAECAVCLEAFQAGDRCRVLPRCEHGFHAQCVDQWLRKS 116

Query: 110 PICPICRTRV 119
            +CP+CR  V
Sbjct: 117 RLCPVCRAEV 126

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  102 bits (255), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 52/127 (40%), Positives = 75/127 (59%), Gaps = 15/127 (11%)

Query: 6   LISLTLLFVGIAALVVIHVCVVGRAFRRG------------YEQSGFAQG-GFKMISSDD 52
           ++S+ LL VG++ ++ +H+ VV  A RRG             +Q     G G + +S  +
Sbjct: 7   ILSVALLIVGVSLMLAVHILVVFWALRRGLGSRDTGQHANHQDQERVEDGHGRRGLSPGE 66

Query: 53  LKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPIC 112
           L  +PC ++KAA   G +  DC VCLE F+ GD+CR LP C H FHA+C+DSWL K+  C
Sbjct: 67  LVTLPCHDFKAA--DGEAAGDCAVCLEAFQAGDRCRQLPRCEHCFHAECVDSWLRKSSKC 124

Query: 113 PICRTRV 119
           P+CR  V
Sbjct: 125 PVCRADV 131

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357143605|ref|XP_003572980.1| PREDICTED: E3 ubiquitin-protein ligase ATL23-like [Brachypodium distachyon]

 Score = 99.0 bits (245), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 49/127 (38%), Positives = 80/127 (62%), Gaps = 13/127 (10%)

Query: 5   ILISLTLLFVGIAALVVIHVCVVGRAFRRGYEQSGFAQ-----GGFKMISSDDLKQIPCF 59
           + +++ LL  G+A +  +HV VV  A RRG       +     GG   +++++++++PC 
Sbjct: 4   MTVAVLLLVAGVALMFALHVLVVVWAIRRGAASREARERAAAAGG---LTAEEIRELPCQ 60

Query: 60  EYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRV 119
           ++KA    G++   C VCLE  + GD+CR+LP C+H FHAQC+DSWL K+ +CP+CR  V
Sbjct: 61  DFKA----GATGECCAVCLEALQAGDRCRVLPGCQHGFHAQCVDSWLCKSRLCPVCRAVV 116

Query: 120 -SPSKVG 125
            +P + G
Sbjct: 117 QAPGRRG 123

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

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	143
TAIR|locus:2053994	181	AT2G18670 [Arabidopsis thalian	0.818	0.646	0.363	1.6e-17
TAIR|locus:2118651	176	AT4G30370 [Arabidopsis thalian	0.454	0.369	0.485	2.6e-15
TAIR|locus:2054049	423	MEE16 "maternal effect embryo	0.825	0.278	0.356	2.8e-15
TAIR|locus:2199902	369	AT1G23980 [Arabidopsis thalian	0.412	0.159	0.532	4.2e-15
TAIR|locus:2172550	210	AT5G57750 [Arabidopsis thalian	0.482	0.328	0.420	7.2e-15
TAIR|locus:2117622	200	RHA3B "RING-H2 finger A3B" [Ar	0.475	0.34	0.4	9.2e-15
TAIR|locus:2123558	432	AT4G28890 [Arabidopsis thalian	0.720	0.238	0.370	1.7e-14
TAIR|locus:2165735	163	AT5G42200 [Arabidopsis thalian	0.846	0.742	0.317	2.3e-14
TAIR|locus:2118666	472	AT4G30400 [Arabidopsis thalian	0.811	0.245	0.354	5.7e-14
WB|WBGene00007666	456	C18B12.4 [Caenorhabditis elega	0.706	0.221	0.382	6.8e-14

TAIR|locus:2053994 AT2G18670 [Arabidopsis thaliana (taxid:3702)]

 Score = 214 (80.4 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 44/121 (36%), Positives = 69/121 (57%)

Query:     1 MVMEILISLTLLFVGIAALVVIHVCV--VGRAFRRGYEQSGFAQGGFKMISSDDLKQIPC 58
             ++M  +  L L+ +GIA+++++ + +  + R  RR   +    Q     +SS  +K++P 
Sbjct:    37 VIMFSIFFLFLVLIGIASVLILPLLLSSLHRHHRR--RRRNRRQESSDGLSSRFVKKLPQ 94

Query:    59 FEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTR 118
             F++   +       DCVVC + FR G  CR LP C H FH +C+D+WLLK   CPICR R
Sbjct:    95 FKFSEPSTYTRYESDCVVCFDGFRQGQWCRNLPGCGHVFHRKCVDTWLLKASTCPICRAR 154

Query:   119 V 119
             V
Sbjct:   155 V 155

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2118651 AT4G30370 [Arabidopsis thaliana (taxid:3702)]

 Score = 193 (73.0 bits), Expect = 2.6e-15, P = 2.6e-15
 Identities = 33/68 (48%), Positives = 46/68 (67%)

Query:    53 LKQIPCFEY-KAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPI 111
             +K++P F+Y + +++ G    DCVVC++ FR G  CR LP C H FH +C+D WL+K   
Sbjct:    95 VKRLPQFKYCEPSSEYGGD--DCVVCIDGFRQGQWCRKLPRCGHVFHRKCVDLWLIKVST 152

Query:   112 CPICRTRV 119
             CPICR RV
Sbjct:   153 CPICRDRV 160

GO:0005634 "nucleus" evidence=ISM

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

GO:0010200 "response to chitin" evidence=IEP

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

 Score = 199 (75.1 bits), Expect = 2.8e-15, P = 2.8e-15
 Identities = 46/129 (35%), Positives = 68/129 (52%)

Query:     2 VMEILISLTLLFV--GIAALVVIHVCVVGRAFRRGYEQSGFA-QGGFKMI-----SSDD- 52
             ++ I+I L+++F   G+  ++V  +    R  R  Y  +  A QG  + +     S  D 
Sbjct:    43 ILLIIIILSIIFFISGLLHILVKFLLTPSRESREDYFDNVTALQGQLQQLFNLHDSGVDQ 102

Query:    53 --LKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP 110
               +  +P F YK+      SP DC VCL  F   DK RLLP C H+FH +CID+WLL   
Sbjct:   103 SLIDTLPVFHYKSIVGLKISPFDCPVCLCEFETEDKLRLLPKCSHAFHVECIDTWLLSHS 162

Query:   111 ICPICRTRV 119
              CP+CR+ +
Sbjct:   163 TCPLCRSNL 171

GO:0005634 "nucleus" evidence=ISM

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

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

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

 Score = 181 (68.8 bits), Expect = 4.2e-15, Sum P(2) = 4.2e-15
 Identities = 33/62 (53%), Positives = 39/62 (62%)

Query:    56 IPCFEYKAAADRGSS-PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPI 114
             +P F YK    +G+  P DC VCL  F   DK RLLPNC H+FH  CID+WLL    CP+
Sbjct:   127 LPVFLYKEI--KGTKEPFDCAVCLCEFSEDDKLRLLPNCSHAFHIDCIDTWLLSNSTCPL 184

Query:   115 CR 116
             CR
Sbjct:   185 CR 186

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2172550 AT5G57750 [Arabidopsis thaliana (taxid:3702)]

 Score = 169 (64.5 bits), Expect = 7.2e-15, Sum P(2) = 7.2e-15
 Identities = 29/69 (42%), Positives = 36/69 (52%)

Query:    48 ISSDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL 107
             I    +  +P   YK          DC VCL  F   D+ RLLP C H+FH +CID+WLL
Sbjct:    96 IDQSFIDALPLLHYKTMIGLRHDLSDCAVCLREFTAEDELRLLPKCSHAFHVECIDTWLL 155

Query:   108 KTPICPICR 116
                 CP+CR
Sbjct:   156 TNSTCPLCR 164

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

TAIR|locus:2117622 RHA3B "RING-H2 finger A3B" [Arabidopsis thaliana (taxid:3702)]

 Score = 157 (60.3 bits), Expect = 9.2e-15, Sum P(2) = 9.2e-15
 Identities = 30/75 (40%), Positives = 41/75 (54%)

Query:    49 SSDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK 108
             ++DDL   PC    +  D G S  +C +C+  F  G++ R+LP C H+FH  CID WL  
Sbjct:    95 AADDL---PC---SSVGD-GDSSTECAICITEFSEGEEIRILPLCSHAFHVACIDKWLTS 147

Query:   109 TPICPICRTRVSPSK 123
                CP CR  + P K
Sbjct:   148 RSSCPSCRRILVPVK 162

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0010200 "response to chitin" evidence=IEP

GO:0009693 "ethylene biosynthetic process" evidence=RCA

GO:0010286 "heat acclimation" evidence=RCA

GO:0015824 "proline transport" evidence=RCA

TAIR|locus:2123558 AT4G28890 [Arabidopsis thaliana (taxid:3702)]

 Score = 192 (72.6 bits), Expect = 1.7e-14, P = 1.7e-14
 Identities = 40/108 (37%), Positives = 59/108 (54%)

Query:    29 RAFRRG--YEQSGFAQGGFKMISSDDLKQIPCFEYKAAADRGSSP-VDCVVCLENFRMGD 85
             R  R+G  + +S  +   F  +    ++ +P F + A   +GS   +DC VCL  F   +
Sbjct:    77 RRLRQGIFFNRSTASSDRFSGLDKTAIESLPLFRFSAL--KGSKQGLDCSVCLSKFESVE 134

Query:    86 KCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVILKDGSS 133
               RLLP CRH+FH  CID WL +   CP+CR RVS  +   +L +G+S
Sbjct:   135 ILRLLPKCRHAFHIGCIDQWLEQHATCPLCRDRVSMEEDSSVLTNGNS 182

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0000041 "transition metal ion transport" evidence=RCA

GO:0048527 "lateral root development" evidence=RCA

GO:0048589 "developmental growth" evidence=RCA

GO:0048765 "root hair cell differentiation" evidence=RCA

GO:0048767 "root hair elongation" evidence=RCA

TAIR|locus:2165735 AT5G42200 [Arabidopsis thaliana (taxid:3702)]

 Score = 184 (69.8 bits), Expect = 2.3e-14, P = 2.3e-14
 Identities = 40/126 (31%), Positives = 68/126 (53%)

Query:     1 MVMEILISLTLLFVGIAALVVIHVCVVGRAFRRGYEQSGFAQG----GFKMISSDDLKQI 56
             M+  + ++L L  VG+  + +I++ ++  + RR  E+  FA+       K +S  +L++I
Sbjct:    28 MIATVFMALLLPCVGMCIVFLIYLFLLWCSTRRRIERLRFAEPVKPVTGKGLSVLELEKI 87

Query:    57 PCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICR 116
             P    +  A    S  +C VCLE+   G   RL+P C H FH  C D+WL    +CP+CR
Sbjct:    88 PKLTGRELAVIARS-TECAVCLEDIESGQSTRLVPGCNHGFHQLCADTWLSNHTVCPVCR 146

Query:   117 TRVSPS 122
               ++P+
Sbjct:   147 AELAPN 152

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

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

 Score = 188 (71.2 bits), Expect = 5.7e-14, P = 5.7e-14
 Identities = 45/127 (35%), Positives = 65/127 (51%)

Query:     2 VMEILISLTLLFV--GIAALVVIHVCVVGRAFRRGYEQSGFA-QGGFKMI-----SSDD- 52
             ++ I+I L+++F   G+  L+V  +       R  Y  +  A QG  + +     S  D 
Sbjct:    51 ILLIIIILSIIFFISGLLHLLVRFLLTPSSRDREDYFDNVTALQGQLQQLFHLHDSGVDQ 110

Query:    53 --LKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP 110
               +  +P F YK+     + P DC VCL  F   DK RLLP C H+FH  CID+WLL   
Sbjct:   111 SFIDTLPVFHYKSIIGLKNYPFDCAVCLCEFETEDKLRLLPKCSHAFHMDCIDTWLLSHS 170

Query:   111 ICPICRT 117
              CP+CR+
Sbjct:   171 TCPLCRS 177

GO:0005634 "nucleus" evidence=ISM

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

GO:0080167 "response to karrikin" evidence=IEP

WB|WBGene00007666 C18B12.4 [Caenorhabditis elegans (taxid:6239)]

 Score = 187 (70.9 bits), Expect = 6.8e-14, P = 6.8e-14
 Identities = 44/115 (38%), Positives = 63/115 (54%)

Query:     6 LISLTLLFVGIAALVVIHVCVVGRAFRRGYEQSGFAQGGFKMISSDDLKQIPCFEYKAAA 65
             LI   ++ V   AL +I +CV G   RR   +        + +S  +LK+IP  +Y+   
Sbjct:   191 LIPFLVVIVFCFALFLITLCVRGCVERRKLNK--------RRLSKRNLKKIPVKKYRL-- 240

Query:    66 DRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT-PICPICRTRV 119
               G  P  C +CLE+F  G+K R LP CRH FH  CID WL +T  ICP+C+ ++
Sbjct:   241 --GDDPDTCAICLESFASGEKLRHLP-CRHVFHCNCIDVWLTQTRKICPLCKRKI 292

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00016116001 SubName- Full=Chromosome chr17 scaffold_12, whole genome shotgun sequence; (148 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	143
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	3e-13
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	3e-13
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	6e-10
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	3e-07
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	6e-07
smart00184	40	smart00184, RING, Ring finger	1e-05
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	1e-05
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	2e-05
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	5e-04
COG5432	391	COG5432, RAD18, RING-finger-containing E3 ubiquiti	0.001
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	0.001
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	0.001
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	0.001

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

 Score = 59.7 bits (145), Expect = 3e-13
 Identities = 19/46 (41%), Positives = 29/46 (63%), Gaps = 1/46 (2%)

Query: 73  DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTR 118
           +C +CL+ F  G++  +LP C H FH +C+D WL  +  CP+CR  
Sbjct: 2   ECPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

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

 Score = 65.0 bits (158), Expect = 3e-13
 Identities = 28/63 (44%), Positives = 37/63 (58%), Gaps = 5/63 (7%)

Query: 60  EYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPI-CPICRTR 118
           E    AD+G   V+C +C+ NF   D+ R+LP C H FH  C+D WLL     CP+CRT 
Sbjct: 315 ERAVEADKG---VECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTA 370

Query: 119 VSP 121
           + P
Sbjct: 371 IPP 373

Length = 374

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

 Score = 50.9 bits (122), Expect = 6e-10
 Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 4/48 (8%)

Query: 73  DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPI-CPICRTRV 119
           +C +CLE FR   +  +L  C H F   CID WL      CP+CRT +
Sbjct: 1   ECPICLEEFR---EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 44.0 bits (104), Expect = 3e-07
 Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 3/48 (6%)

Query: 70  SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRT 117
             ++C +CL+  R      +L  C H F  +CI  +L K   CPICRT
Sbjct: 1   EELECPICLDLLR---DPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 44.0 bits (104), Expect = 6e-07
 Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 9/53 (16%)

Query: 73  DCVVCLENFRM--------GDKCRL-LPNCRHSFHAQCIDSWLLKTPICPICR 116
            C +C  +F          GD C +    C H+FH  CI  WL     CP+CR
Sbjct: 21  VCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73

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

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

 Score = 40.2 bits (94), Expect = 1e-05
 Identities = 17/43 (39%), Positives = 21/43 (48%), Gaps = 4/43 (9%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPI-CPIC 115
           C +CLE +       +LP C H+F   CI  WL      CPIC
Sbjct: 1   CPICLEEY--LKDPVILP-CGHTFCRSCIRKWLESGNNTCPIC 40

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

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

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 11/73 (15%)

Query: 53  LKQIP--CFEYKAAADRGSSPVDCVVCLENFRMGDK------CRLLPNCRHSFHAQCIDS 104
           LK IP    EY+   +R S   +C +C+E   + DK        +L NC H F  +CID 
Sbjct: 155 LKTIPSVLSEYEKLYNR-SKDKECAICMEK--VYDKEIKNMYFGILSNCNHVFCIECIDI 211

Query: 105 WLLKTPICPICRT 117
           W  +   CP+CRT
Sbjct: 212 WKKEKNTCPVCRT 224

Length = 238

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

 Score = 40.6 bits (95), Expect = 2e-05
 Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 1/44 (2%)

Query: 74  CVVCLENFRMGDKCRLL-PNCRHSFHAQCIDSWLLKTPICPICR 116
           C  C      GD+C ++   C H+FH  CI  WL    +CP+ R
Sbjct: 34  CPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDR 77

Length = 88

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

 Score = 38.4 bits (89), Expect = 5e-04
 Identities = 17/71 (23%), Positives = 25/71 (35%), Gaps = 9/71 (12%)

Query: 58  CFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPN---------CRHSFHAQCIDSWLLK 108
            +         +S   C +C++     D   L            C H  H  C+ +WL +
Sbjct: 274 MYPTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER 333

Query: 109 TPICPICRTRV 119
              CPICR  V
Sbjct: 334 QQTCPICRRPV 344

Length = 491

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

 Score = 37.8 bits (87), Expect = 0.001
 Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 4/43 (9%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICR 116
           C +C     +         C H+F + CI   L   P CP+CR
Sbjct: 28  CRICDCRISI----PCETTCGHTFCSLCIRRHLGTQPFCPVCR 66

Length = 391

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

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 4/37 (10%)

Query: 84  GDKCRL-LPNCRHSFHAQCIDSWLLKTP---ICPICR 116
           GD C L    C+H+FH  CI  WL       +CP+CR
Sbjct: 42  GDDCPLVWGKCKHNFHMHCILKWLATETSKGLCPMCR 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|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 9/55 (16%)

Query: 73   DCVVCLENFRMGDKCRLLPN-----CRHSFHAQCIDSWLLKT--PICPICRTRVS 120
            +C +C     M D  R LP+     C++ FH +C+  W   +    CP+CR+ ++
Sbjct: 1471 ECAICYSVLDMVD--RSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523

Length = 1525

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

 Score = 34.4 bits (79), Expect = 0.001
 Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 4/43 (9%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPI-CPIC 115
           C +CLE  +  D   +LP C H F ++CI SWL    + CP+C
Sbjct: 1   CPICLEEPK--DPVTILP-CGHLFCSKCILSWLESGNVTCPLC 40

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	143
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.89
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.77
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.63
PHA02929	238	N1R/p28-like protein; Provisional	99.62
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.57
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.53
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.53
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.53
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.5
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.41
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.4
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.36
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.36
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.31
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	99.31
PHA02926	242	zinc finger-like protein; Provisional	99.29
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.29
PF14634	44	zf-RING_5: zinc-RING finger domain	99.23
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.17
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.17
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.14
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	99.12
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	99.07
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	99.04
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	99.0
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.99
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.98
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.97
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.96
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.86
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.79
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.77
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.73
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.71
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.69
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.66
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.66
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.63
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.59
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.56
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.56
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.55
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.41
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	98.4
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.35
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	98.34
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.31
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.23
KOG4445	368	consensus Uncharacterized conserved protein, conta	98.16
KOG0825	1134	consensus PHD Zn-finger protein [General function	98.15
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	98.06
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.03
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.95
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	97.91
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.88
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.83
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.79
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.66
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.65
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	97.63
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.58
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.52
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	97.49
PHA02862	156	5L protein; Provisional	97.44
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	97.43
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	97.41
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	97.39
PHA02825	162	LAP/PHD finger-like protein; Provisional	97.38
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	97.34
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	97.27
KOG3039	303	consensus Uncharacterized conserved protein [Funct	97.26
PF04641	260	Rtf2: Rtf2 RING-finger	97.22
COG5236	493	Uncharacterized conserved protein, contains RING Z	97.22
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.22
PHA03096	284	p28-like protein; Provisional	97.11
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.05
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	97.05
KOG2660	331	consensus Locus-specific chromosome binding protei	97.05
COG5152	259	Uncharacterized conserved protein, contains RING a	97.03
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.96
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.92
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	96.79
KOG4739	233	consensus Uncharacterized protein involved in syna	96.74
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	96.69
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	96.64
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	96.63
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	96.58
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	96.35
COG5222	427	Uncharacterized conserved protein, contains RING Z	96.32
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	96.3
KOG3002	299	consensus Zn finger protein [General function pred	96.25
KOG1940	276	consensus Zn-finger protein [General function pred	96.11
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	96.08
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	96.02
KOG1001	674	consensus Helicase-like transcription factor HLTF/	96.01
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	95.6
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	95.29
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	95.15
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	94.93
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	94.62
KOG0298	1394	consensus DEAD box-containing helicase-like transc	94.56
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	94.41
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	94.34
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	94.07
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	94.05
KOG3053	293	consensus Uncharacterized conserved protein [Funct	93.76
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	93.72
KOG3899	381	consensus Uncharacterized conserved protein [Funct	93.44
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	93.36
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	93.26
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	93.1
KOG0269	839	consensus WD40 repeat-containing protein [Function	92.96
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	92.26
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	92.24
KOG3113	293	consensus Uncharacterized conserved protein [Funct	92.13
KOG1609	323	consensus Protein involved in mRNA turnover and st	91.95
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	91.45
PF02439	38	Adeno_E3_CR2: Adenovirus E3 region protein CR2; In	91.0
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	90.52
KOG0825	1134	consensus PHD Zn-finger protein [General function	90.03
PF14569	80	zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.	89.9
PF15050	133	SCIMP: SCIMP protein	89.87
TIGR00622	112	ssl1 transcription factor ssl1. This family is bas	89.57
PLN02189	1040	cellulose synthase	88.75
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	88.7
KOG3005	276	consensus GIY-YIG type nuclease [General function	87.87
PF12273	130	RCR: Chitin synthesis regulation, resistance to Co	87.84
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	87.77
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	87.17
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	87.06
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	86.81
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	86.75
PLN02400	1085	cellulose synthase	86.36
KOG4367	699	consensus Predicted Zn-finger protein [Function un	85.94
KOG1829	580	consensus Uncharacterized conserved protein, conta	85.11
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	84.95
PLN02436	1094	cellulose synthase A	84.66
KOG3842	429	consensus Adaptor protein Pellino [Signal transduc	84.51
PF02439	38	Adeno_E3_CR2: Adenovirus E3 region protein CR2; In	84.38
PLN02638	1079	cellulose synthase A (UDP-forming), catalytic subu	82.17
PF15102	146	TMEM154: TMEM154 protein family	81.08
COG5109	396	Uncharacterized conserved protein, contains RING Z	80.91
PF04423	54	Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IP	80.91
PF06024	101	DUF912: Nucleopolyhedrovirus protein of unknown fu	80.61
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	80.55
PF06844	68	DUF1244: Protein of unknown function (DUF1244); In	80.32

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

Probab=99.89  E-value=1.7e-23  Score=153.74  Aligned_cols=79  Identities=34%  Similarity=0.826  Sum_probs=69.6

Q ss_pred             CCCCCCChHHhhcCCeeeecccccCCCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCC-CccccCccCC
Q 032328           43 GGFKMISSDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPI-CPICRTRVSP  121 (143)
Q Consensus        43 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~-CP~CR~~i~~  121 (143)
                      .+..++.++.+.++|...|+..++.... +.|+||||+|++||++++|| |+|.||..||++||....+ ||+||+++..
T Consensus       202 ~~~~r~~k~~l~~~p~~~f~~~~~~~~~-~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~~  279 (348)
T KOG4628|consen  202 LRRNRLIKRLLKKLPVRTFTKGDDEDAT-DTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIRT  279 (348)
T ss_pred             hhhhhhHHHHHhhCCcEEeccccccCCC-ceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence            4556678899999999999997777655 89999999999999999999 9999999999999988755 9999998876


Q ss_pred             CC
Q 032328          122 SK  123 (143)
Q Consensus       122 ~~  123 (143)
                      ..
T Consensus       280 ~~  281 (348)
T KOG4628|consen  280 DS  281 (348)
T ss_pred             CC
Confidence            64

>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=99.77  E-value=1e-19  Score=97.39  Aligned_cols=44  Identities=48%  Similarity=1.183  Sum_probs=40.4

Q ss_pred             CccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCcccc
Q 032328           72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICR  116 (143)
Q Consensus        72 ~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR  116 (143)
                      ++|+||++++..++.+..++ |||.||.+|+.+|++.+.+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHhCCcCCccC
Confidence            47999999999999999999 999999999999999999999997

...

>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=99.63  E-value=3e-16  Score=92.51  Aligned_cols=46  Identities=35%  Similarity=0.850  Sum_probs=36.0

Q ss_pred             CCCccccccccccCC----------CeeeEcCCCCCcccHHhHHHHHhCCCCCcccc
Q 032328           70 SPVDCVVCLENFRMG----------DKCRLLPNCRHSFHAQCIDSWLLKTPICPICR  116 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~----------~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR  116 (143)
                      .++.|+||++++.+.          -.+...+ |||.||..||.+|++.+.+||+||
T Consensus        18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   18 ADDNCAICREPLEDPCPECQAPQDECPIVWGP-CGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CCSBETTTTSBTTSTTCCHHHCTTTS-EEEET-TSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             cCCcccccChhhhChhhhhcCCccccceEecc-cCCCEEHHHHHHHHhcCCcCCCCC
Confidence            455699999999332          2344445 999999999999999999999998

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

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.62  E-value=4.3e-16  Score=110.31  Aligned_cols=75  Identities=29%  Similarity=0.572  Sum_probs=54.3

Q ss_pred             CCChHHhhcCCeeeeccccc-CCCCCCccccccccccCCCe----eeEcCCCCCcccHHhHHHHHhCCCCCccccCccCC
Q 032328           47 MISSDDLKQIPCFEYKAAAD-RGSSPVDCVVCLENFRMGDK----CRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSP  121 (143)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~C~ICl~~~~~~~~----v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~  121 (143)
                      +..++-+..+|....+.... ..+.+.+|+||++.+.++..    +.+++.|+|.||.+||.+|+..+.+||+||.++..
T Consensus       149 ~~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~  228 (238)
T PHA02929        149 KNYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFIS  228 (238)
T ss_pred             chhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeE
Confidence            34555666677665443222 23457899999999876431    23444599999999999999999999999998874

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

Probab=99.57  E-value=1.9e-15  Score=111.11  Aligned_cols=52  Identities=35%  Similarity=0.875  Sum_probs=43.3

Q ss_pred             CCCCCccccccccccCCC----------eeeEcCCCCCcccHHhHHHHHhCCCCCccccCccC
Q 032328           68 GSSPVDCVVCLENFRMGD----------KCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS  120 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~----------~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~  120 (143)
                      .+.+..|+||++++-+.+          ....+| |||+||-+|++.|++++++||.||.++.
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            346788999999954333          335678 9999999999999999999999999954

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

Probab=99.53  E-value=7.9e-15  Score=101.87  Aligned_cols=66  Identities=30%  Similarity=0.596  Sum_probs=55.6

Q ss_pred             CCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC---CCCccccCccCCCCcceeecCCCCCCcc
Q 032328           68 GSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT---PICPICRTRVSPSKVGVILKDGSSVSSD  137 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~---~~CP~CR~~i~~~~~~~~~~~~~~~~~~  137 (143)
                      .....+|-|||+.-+++   +++. |||+||+.||-+|+..+   +.||+||..+..+++.++++.++....+
T Consensus        44 ~~~~FdCNICLd~akdP---VvTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYGrG~~~~~~  112 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDP---VVTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYGRGSKKPSD  112 (230)
T ss_pred             CCCceeeeeeccccCCC---EEee-cccceehHHHHHHHhhcCCCeeCCccccccccceEEeeeccCCCCCCC
Confidence            35677999999997664   5555 99999999999999864   4599999999999999999999865554

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

Probab=99.53  E-value=5.5e-15  Score=106.08  Aligned_cols=52  Identities=46%  Similarity=1.179  Sum_probs=47.1

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHh-CCCCCccccCccCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL-KTPICPICRTRVSP  121 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~-~~~~CP~CR~~i~~  121 (143)
                      ..+.+|+|||+.|..+|.++++| |+|.||..|++.|+. .+..||+||.++..
T Consensus       321 ~~GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         321 DKGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCCceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            45679999999999999999999 999999999999998 46779999998864

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.53  E-value=2.1e-14  Score=98.09  Aligned_cols=63  Identities=30%  Similarity=0.707  Sum_probs=51.8

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC----------------CCCCccccCccCCCCcceeecCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK----------------TPICPICRTRVSPSKVGVILKDGS  132 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~----------------~~~CP~CR~~i~~~~~~~~~~~~~  132 (143)
                      ..+.+|+||++.++++   .+++ |||.||+.||..|+..                ...||+||..+...++.++.+.+.
T Consensus        16 ~~~~~CpICld~~~dP---VvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiygrg~   91 (193)
T PLN03208         16 GGDFDCNICLDQVRDP---VVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIYGRGQ   91 (193)
T ss_pred             CCccCCccCCCcCCCc---EEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEeeccCC
Confidence            3567899999998765   5566 9999999999999842                346999999999999998888776


Q ss_pred             CCC
Q 032328          133 SVS  135 (143)
Q Consensus       133 ~~~  135 (143)
                      ...
T Consensus        92 ~~~   94 (193)
T PLN03208         92 KAP   94 (193)
T ss_pred             CCC
Confidence            544

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

Probab=99.50  E-value=1.9e-14  Score=102.77  Aligned_cols=53  Identities=38%  Similarity=0.779  Sum_probs=45.8

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG  125 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~  125 (143)
                      .....|.+||+...++   ..+| |||+||+.||..|...+..||+||......++.
T Consensus       237 ~a~~kC~LCLe~~~~p---SaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~pskvi  289 (293)
T KOG0317|consen  237 EATRKCSLCLENRSNP---SATP-CGHIFCWSCILEWCSEKAECPLCREKFQPSKVI  289 (293)
T ss_pred             CCCCceEEEecCCCCC---CcCc-CcchHHHHHHHHHHccccCCCcccccCCCccee
Confidence            4567899999997664   6677 999999999999999999999999999877643

>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=99.41  E-value=1.3e-13  Score=75.48  Aligned_cols=47  Identities=38%  Similarity=0.902  Sum_probs=39.1

Q ss_pred             CCccccccccccCCCeeeEcCCCCCc-ccHHhHHHHHhCCCCCccccCccCC
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHS-FHAQCIDSWLLKTPICPICRTRVSP  121 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~-FH~~Ci~~wl~~~~~CP~CR~~i~~  121 (143)
                      +..|.||++...   .+..+| |||. |+..|..+|+.....||+||+++..
T Consensus         2 ~~~C~iC~~~~~---~~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~   49 (50)
T PF13920_consen    2 DEECPICFENPR---DVVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIES   49 (50)
T ss_dssp             HSB-TTTSSSBS---SEEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred             cCCCccCCccCC---ceEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence            467999999944   357778 9998 9999999999999999999998863

...

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

Probab=99.40  E-value=2.5e-13  Score=80.94  Aligned_cols=53  Identities=32%  Similarity=0.685  Sum_probs=40.0

Q ss_pred             CCCccccccccccC--------CCe-eeEcCCCCCcccHHhHHHHHhC---CCCCccccCccCCC
Q 032328           70 SPVDCVVCLENFRM--------GDK-CRLLPNCRHSFHAQCIDSWLLK---TPICPICRTRVSPS  122 (143)
Q Consensus        70 ~~~~C~ICl~~~~~--------~~~-v~~l~~C~H~FH~~Ci~~wl~~---~~~CP~CR~~i~~~  122 (143)
                      .++.|.||...|+.        ++. -.++..|+|.||.+||.+|+..   +..||+||+++..+
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k   84 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFK   84 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeeeC
Confidence            37789999988852        222 2233469999999999999986   46799999987643

>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=99.36  E-value=5.8e-13  Score=69.17  Aligned_cols=39  Identities=44%  Similarity=1.138  Sum_probs=32.3

Q ss_pred             cccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccc
Q 032328           74 CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPIC  115 (143)
Q Consensus        74 C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~C  115 (143)
                      |+||++.+.+  .+..++ |||.|+++|+.+|++.+..||+|
T Consensus         1 C~iC~~~~~~--~~~~~~-CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTP-CGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECT-TSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC--cCEECC-CCCchhHHHHHHHHHCcCCCcCC
Confidence            8999999777  445566 99999999999999998899998

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

Probab=99.36  E-value=8.5e-13  Score=70.19  Aligned_cols=44  Identities=48%  Similarity=1.180  Sum_probs=36.4

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-CCCCccccCcc
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRV  119 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i  119 (143)
                      .|+||++.+  .+.+...+ |||.||..|+..|+.. ...||.||..+
T Consensus         1 ~C~iC~~~~--~~~~~~~~-C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEF--REPVVLLP-CGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhh--hCceEecC-CCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            499999998  34445555 9999999999999987 77799999864

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

Probab=99.31  E-value=1.1e-12  Score=103.85  Aligned_cols=53  Identities=38%  Similarity=0.885  Sum_probs=45.8

Q ss_pred             CCCCccccccccccCCCe--eeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCC
Q 032328           69 SSPVDCVVCLENFRMGDK--CRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~--v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      ..++.|+||+|++..+.+  ...+| |+|+||..|+..|++++++||.||..+...
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~~~~  343 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVLYDY  343 (543)
T ss_pred             hcCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhhhcc
Confidence            457889999999988655  67788 999999999999999999999999954443

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

Probab=99.31  E-value=1.1e-12  Score=76.21  Aligned_cols=54  Identities=30%  Similarity=0.659  Sum_probs=39.8

Q ss_pred             Cccccccccc-----------cCCCe-eeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcc
Q 032328           72 VDCVVCLENF-----------RMGDK-CRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG  125 (143)
Q Consensus        72 ~~C~ICl~~~-----------~~~~~-v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~  125 (143)
                      +.|+||...+           ..+++ ......|+|.||.+||.+||..+..||++|++....+.+
T Consensus        21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~~~~   86 (88)
T COG5194          21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLADGG   86 (88)
T ss_pred             chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEeccc
Confidence            5566666554           33333 333335999999999999999999999999998766543

>PHA02926 zinc finger-like protein; Provisional

Probab=99.29  E-value=2.3e-12  Score=89.22  Aligned_cols=54  Identities=35%  Similarity=0.703  Sum_probs=41.3

Q ss_pred             CCCCccccccccccCC-----CeeeEcCCCCCcccHHhHHHHHhCC------CCCccccCccCCC
Q 032328           69 SSPVDCVVCLENFRMG-----DKCRLLPNCRHSFHAQCIDSWLLKT------PICPICRTRVSPS  122 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~-----~~v~~l~~C~H~FH~~Ci~~wl~~~------~~CP~CR~~i~~~  122 (143)
                      +.+.+|+||+|..-+.     ....+++.|+|.||..||..|...+      .+||+||.....-
T Consensus       168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I  232 (242)
T PHA02926        168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNI  232 (242)
T ss_pred             cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeee
Confidence            5678999999986332     2234566699999999999999753      3599999987744

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

Probab=99.29  E-value=3.7e-12  Score=85.25  Aligned_cols=54  Identities=28%  Similarity=0.671  Sum_probs=44.3

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKV  124 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~  124 (143)
                      ..-..|+|||+.+.+...  +-++|||+||+.||+..++....||+||..|+.+..
T Consensus       129 ~~~~~CPiCl~~~sek~~--vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~  182 (187)
T KOG0320|consen  129 EGTYKCPICLDSVSEKVP--VSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQF  182 (187)
T ss_pred             ccccCCCceecchhhccc--cccccchhHHHHHHHHHHHhCCCCCCcccccchhhh
Confidence            445689999999877533  323599999999999999999999999998887644

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.23  E-value=1.1e-11  Score=65.92  Aligned_cols=44  Identities=34%  Similarity=0.831  Sum_probs=37.5

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccC
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRT  117 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~  117 (143)
                      .|.||+++|.++....+++ |||.|+..|+..+......||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~-CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTS-CGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcc-cCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            4899999996666667777 9999999999998866678999985

>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=99.17  E-value=1.7e-11  Score=64.27  Aligned_cols=39  Identities=46%  Similarity=1.094  Sum_probs=32.9

Q ss_pred             cccccccccCCCeeeEcCCCCCcccHHhHHHHHh--CCCCCccc
Q 032328           74 CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL--KTPICPIC  115 (143)
Q Consensus        74 C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~--~~~~CP~C  115 (143)
                      |+||++.+.++.  ..++ |||.||..|+.+|++  ....||+|
T Consensus         1 C~iC~~~~~~~~--~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPV--ILLP-CGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEE--EETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCCC--EEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence            899999987752  3666 999999999999998  46679998

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 ....

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

Probab=99.17  E-value=2.2e-11  Score=64.07  Aligned_cols=38  Identities=37%  Similarity=0.890  Sum_probs=29.4

Q ss_pred             cccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC----CCCccc
Q 032328           74 CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT----PICPIC  115 (143)
Q Consensus        74 C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~----~~CP~C  115 (143)
                      |+||++-|.++   ..++ |||.|+..||.+|.+..    ..||.|
T Consensus         1 CpiC~~~~~~P---v~l~-CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDP---VSLP-CGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSE---EE-S-SSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCc---cccC-CcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999986   6677 99999999999999763    359987

>smart00504 Ubox Modified RING finger domain

Probab=99.14  E-value=7.1e-11  Score=67.56  Aligned_cols=50  Identities=20%  Similarity=0.448  Sum_probs=42.9

Q ss_pred             CccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcc
Q 032328           72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG  125 (143)
Q Consensus        72 ~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~  125 (143)
                      ..|+||.+.+.++   ..++ |||.|+++||.+|+..+..||.|+.++...+..
T Consensus         2 ~~Cpi~~~~~~~P---v~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~   51 (63)
T smart00504        2 FLCPISLEVMKDP---VILP-SGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLI   51 (63)
T ss_pred             cCCcCCCCcCCCC---EECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCChhhce
Confidence            4699999999886   5667 999999999999999888999999998765443

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

>smart00184 RING Ring finger

Probab=99.12  E-value=7.1e-11  Score=60.57  Aligned_cols=38  Identities=45%  Similarity=1.094  Sum_probs=32.1

Q ss_pred             cccccccccCCCeeeEcCCCCCcccHHhHHHHHh-CCCCCccc
Q 032328           74 CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL-KTPICPIC  115 (143)
Q Consensus        74 C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~-~~~~CP~C  115 (143)
                      |+||++.   ......++ |||.||..|+..|+. ....||+|
T Consensus         1 C~iC~~~---~~~~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEE---LKDPVVLP-CGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccC---CCCcEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence            7899998   34557777 999999999999998 56779987

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)

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

Probab=99.07  E-value=3.4e-10  Score=86.37  Aligned_cols=51  Identities=37%  Similarity=0.969  Sum_probs=39.3

Q ss_pred             CCCccccccccccC--------------CCeeeEcCCCCCcccHHhHHHHHhC-CCCCccccCccCC
Q 032328           70 SPVDCVVCLENFRM--------------GDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSP  121 (143)
Q Consensus        70 ~~~~C~ICl~~~~~--------------~~~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~  121 (143)
                      ...+|+||+..+.-              ..+....| |.|+||..|+.+|... +-.||+||.++..
T Consensus       570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tP-C~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTP-CHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             ccccceEeccccceeeccCcchhhhhhhhccccccc-hHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            45689999988632              12234457 9999999999999994 5589999998753

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

Probab=99.04  E-value=9.8e-11  Score=71.47  Aligned_cols=56  Identities=23%  Similarity=0.585  Sum_probs=43.7

Q ss_pred             CCCccccccccc-------------cCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcc
Q 032328           70 SPVDCVVCLENF-------------RMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG  125 (143)
Q Consensus        70 ~~~~C~ICl~~~-------------~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~  125 (143)
                      .-+.|+||...+             ..++.......|+|.||..||.+|++.+..||+|.++...+.++
T Consensus        45 ~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~~qr~g  113 (114)
T KOG2930|consen   45 VVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWVFQRYG  113 (114)
T ss_pred             eechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcceeEeecC
Confidence            456799887543             23445555667999999999999999999999999988766544

>TIGR00599 rad18 DNA repair protein rad18

Probab=99.00  E-value=3.4e-10  Score=85.80  Aligned_cols=50  Identities=34%  Similarity=0.802  Sum_probs=42.9

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSK  123 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~  123 (143)
                      ....|+||++.+...   .+++ |||.||..|+..|+.....||+||..+....
T Consensus        25 ~~l~C~IC~d~~~~P---vitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~   74 (397)
T TIGR00599        25 TSLRCHICKDFFDVP---VLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQESK   74 (397)
T ss_pred             cccCCCcCchhhhCc---cCCC-CCCchhHHHHHHHHhCCCCCCCCCCcccccc
Confidence            467899999998765   4566 9999999999999998888999999987543

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

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

Probab=98.99  E-value=5.9e-11  Score=68.53  Aligned_cols=53  Identities=36%  Similarity=0.800  Sum_probs=37.9

Q ss_pred             CCCccccccccccC--------CCeee-EcCCCCCcccHHhHHHHHhCC---CCCccccCccCCC
Q 032328           70 SPVDCVVCLENFRM--------GDKCR-LLPNCRHSFHAQCIDSWLLKT---PICPICRTRVSPS  122 (143)
Q Consensus        70 ~~~~C~ICl~~~~~--------~~~v~-~l~~C~H~FH~~Ci~~wl~~~---~~CP~CR~~i~~~  122 (143)
                      .++.|.||.-+|..        +|... ++..|.|.||.+||.+|+...   ..||+||+++..+
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~~   83 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQFK   83 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEec
Confidence            34578888877743        23222 233599999999999999763   4599999987643

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

Probab=98.98  E-value=5.5e-10  Score=79.44  Aligned_cols=55  Identities=31%  Similarity=0.725  Sum_probs=45.5

Q ss_pred             CCCCCccccccccccCCC-------eeeEcCCCCCcccHHhHHHHHh--CCCCCccccCccCCCC
Q 032328           68 GSSPVDCVVCLENFRMGD-------KCRLLPNCRHSFHAQCIDSWLL--KTPICPICRTRVSPSK  123 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~-------~v~~l~~C~H~FH~~Ci~~wl~--~~~~CP~CR~~i~~~~  123 (143)
                      ..++..|+||-..+....       +...+. |+|.||..||+.|-.  ++++||.|+..++.+.
T Consensus       221 hl~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVdl~r  284 (328)
T KOG1734|consen  221 HLSDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKR  284 (328)
T ss_pred             CCCcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhhHhh
Confidence            346788999998886554       667787 999999999999974  5788999999998663

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

Probab=98.97  E-value=2.8e-10  Score=80.73  Aligned_cols=51  Identities=37%  Similarity=0.833  Sum_probs=43.1

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHH-HHhCCCC-CccccCccCCCCc
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDS-WLLKTPI-CPICRTRVSPSKV  124 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~-wl~~~~~-CP~CR~~i~~~~~  124 (143)
                      .+..|+||++.....   ..++ |||+||..||.. |-.++.. ||+||+.+..+++
T Consensus       214 ~d~kC~lC~e~~~~p---s~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v  266 (271)
T COG5574         214 ADYKCFLCLEEPEVP---SCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV  266 (271)
T ss_pred             cccceeeeecccCCc---cccc-ccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence            467899999995553   6777 999999999999 8777766 9999999988765

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

Probab=98.96  E-value=3.2e-10  Score=86.95  Aligned_cols=62  Identities=24%  Similarity=0.531  Sum_probs=48.3

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC-----CCCccccCccCCCCcceeecCCCCCCc
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT-----PICPICRTRVSPSKVGVILKDGSSVSS  136 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~-----~~CP~CR~~i~~~~~~~~~~~~~~~~~  136 (143)
                      +..|+|||++....   ..+ .|||+||..||-+++...     ..||+||..+...++.++.-....+..
T Consensus       186 ~~~CPICL~~~~~p---~~t-~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~~e~~qkke  252 (513)
T KOG2164|consen  186 DMQCPICLEPPSVP---VRT-NCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVFIEDDQKKE  252 (513)
T ss_pred             CCcCCcccCCCCcc---ccc-ccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeeeeeccccccH
Confidence            77899999994442   444 499999999999987543     469999999999888877766655443

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

Probab=98.86  E-value=2.5e-09  Score=58.02  Aligned_cols=42  Identities=26%  Similarity=0.823  Sum_probs=32.2

Q ss_pred             ccccccccccCCCeeeEcCCCC-----CcccHHhHHHHHhCC--CCCcccc
Q 032328           73 DCVVCLENFRMGDKCRLLPNCR-----HSFHAQCIDSWLLKT--PICPICR  116 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~-----H~FH~~Ci~~wl~~~--~~CP~CR  116 (143)
                      .|.||++. .+++...+.| |.     |.+|.+|+.+|+..+  .+||+|+
T Consensus         1 ~CrIC~~~-~~~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDE-GDEGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCC-CCCCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            48999993 3344455778 74     899999999999654  4799995

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

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

Probab=98.79  E-value=5.2e-09  Score=55.04  Aligned_cols=38  Identities=34%  Similarity=0.806  Sum_probs=22.1

Q ss_pred             cccccccccCCC-eeeEcCCCCCcccHHhHHHHHhCC----CCCc
Q 032328           74 CVVCLENFRMGD-KCRLLPNCRHSFHAQCIDSWLLKT----PICP  113 (143)
Q Consensus        74 C~ICl~~~~~~~-~v~~l~~C~H~FH~~Ci~~wl~~~----~~CP  113 (143)
                      |+||.+ |.+++ .-.+|+ |||.|+++|+.+++...    ..||
T Consensus         1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 75544 446688 99999999999999743    3476

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

Probab=98.77  E-value=4.1e-09  Score=77.81  Aligned_cols=50  Identities=36%  Similarity=0.806  Sum_probs=42.6

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCC-cccHHhHHHHHhCCCCCccccCccCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRH-SFHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H-~FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      .+..+|.||+.+   .....++| |.| +.|..|-+..-..+++||+||.++...
T Consensus       288 ~~gkeCVIClse---~rdt~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~l  338 (349)
T KOG4265|consen  288 ESGKECVICLSE---SRDTVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIEEL  338 (349)
T ss_pred             cCCCeeEEEecC---CcceEEec-chhhehhHhHHHHHHHhhcCCCccccchHhh
Confidence            446789999999   55569999 999 999999988766678899999999865

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.73  E-value=4.8e-09  Score=76.79  Aligned_cols=60  Identities=22%  Similarity=0.499  Sum_probs=43.3

Q ss_pred             CCcccccccc-ccCCCe-eeEcCCCCCcccHHhHHHHHhC-CCCCccccCccCCCCcceeecCC
Q 032328           71 PVDCVVCLEN-FRMGDK-CRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPSKVGVILKDG  131 (143)
Q Consensus        71 ~~~C~ICl~~-~~~~~~-v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~~~~~~~~~~~  131 (143)
                      +..||+|... |..++. +.+.+ |||.||..|++..+.. ...||.|+..+.........-+.
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~-CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr~q~F~D   65 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFRVQLFED   65 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCC-CCCcccHHHHHHHhcCCCCCCCCCCCccchhhcccccccc
Confidence            4689999986 333332 23334 9999999999996644 56799999999888766544433

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

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

Probab=98.71  E-value=4.5e-09  Score=77.09  Aligned_cols=51  Identities=33%  Similarity=0.822  Sum_probs=44.9

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcc
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG  125 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~  125 (143)
                      --.|.||.+-|..+   .+.| |+|.||.-||..+|..++.||.|+.++.+..+.
T Consensus        23 lLRC~IC~eyf~ip---~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr   73 (442)
T KOG0287|consen   23 LLRCGICFEYFNIP---MITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLR   73 (442)
T ss_pred             HHHHhHHHHHhcCc---eecc-ccchHHHHHHHHHhccCCCCCceecccchhhhh
Confidence            35799999999886   6777 999999999999999999999999998876543

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

Probab=98.69  E-value=9.8e-09  Score=73.96  Aligned_cols=48  Identities=29%  Similarity=0.665  Sum_probs=41.3

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCC
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      -..|-||-+.+..+   ..++ |||.||+-||...|..+..||+||.+.-+.
T Consensus        25 ~lrC~IC~~~i~ip---~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~~~es   72 (391)
T COG5432          25 MLRCRICDCRISIP---CETT-CGHTFCSLCIRRHLGTQPFCPVCREDPCES   72 (391)
T ss_pred             HHHhhhhhheeecc---eecc-cccchhHHHHHHHhcCCCCCccccccHHhh
Confidence            45799999998875   5555 999999999999999999999999876543

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

Probab=98.66  E-value=5.3e-09  Score=56.62  Aligned_cols=47  Identities=26%  Similarity=0.508  Sum_probs=35.6

Q ss_pred             CCCccccccccccCCCeeeEcCCCCC-cccHHhHHHHHh-CCCCCccccCccC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRH-SFHAQCIDSWLL-KTPICPICRTRVS  120 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H-~FH~~Ci~~wl~-~~~~CP~CR~~i~  120 (143)
                      ..++|.||.|.-.+    .++..||| +.+..|-.+.+. .+..||+||+++.
T Consensus         6 ~~dECTICye~pvd----sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    6 WSDECTICYEHPVD----SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             cccceeeeccCcch----HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            45899999998444    23334999 889999766555 6888999999875

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

Probab=98.66  E-value=3.9e-09  Score=61.57  Aligned_cols=51  Identities=25%  Similarity=0.686  Sum_probs=24.5

Q ss_pred             CCccccccccccCCCe--eeEcC--CCCCcccHHhHHHHHhC----C-------CCCccccCccCC
Q 032328           71 PVDCVVCLENFRMGDK--CRLLP--NCRHSFHAQCIDSWLLK----T-------PICPICRTRVSP  121 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~--v~~l~--~C~H~FH~~Ci~~wl~~----~-------~~CP~CR~~i~~  121 (143)
                      +.+|.||.+...+++.  ..+.+  .|++.||..|+.+|+..    +       ..||.|+.+|.-
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence            3579999998763322  23332  68999999999999963    1       249999998864

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

Probab=98.63  E-value=2.4e-08  Score=58.81  Aligned_cols=52  Identities=25%  Similarity=0.406  Sum_probs=40.5

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-CCCCccccCccCCCCcc
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPSKVG  125 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~~~~~  125 (143)
                      +...|+|+.+-|.++   ++++ +||.|.+.+|.+|+.. ...||+|+.++...++.
T Consensus         3 ~~f~CpIt~~lM~dP---Vi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~   55 (73)
T PF04564_consen    3 DEFLCPITGELMRDP---VILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSESDLI   55 (73)
T ss_dssp             GGGB-TTTSSB-SSE---EEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSE
T ss_pred             cccCCcCcCcHhhCc---eeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccce
Confidence            356799999999987   7777 9999999999999999 78899999999876543

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 ....

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

Probab=98.59  E-value=1.7e-08  Score=76.43  Aligned_cols=49  Identities=35%  Similarity=0.771  Sum_probs=39.2

Q ss_pred             CCCCccccccccccCCC-eeeEcCCCCCcccHHhHHHHHhCCCCCccccCccC
Q 032328           69 SSPVDCVVCLENFRMGD-KCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS  120 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~-~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~  120 (143)
                      .+.+.|++|||.+.+.- .+.... |.|.||-.|+..|..  .+||+||.-..
T Consensus       173 tELPTCpVCLERMD~s~~gi~t~~-c~Hsfh~~cl~~w~~--~scpvcR~~q~  222 (493)
T KOG0804|consen  173 TELPTCPVCLERMDSSTTGILTIL-CNHSFHCSCLMKWWD--SSCPVCRYCQS  222 (493)
T ss_pred             ccCCCcchhHhhcCccccceeeee-cccccchHHHhhccc--CcChhhhhhcC
Confidence            46678999999998753 344444 999999999999964  45999998766

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

Probab=98.56  E-value=1.8e-08  Score=82.38  Aligned_cols=52  Identities=23%  Similarity=0.816  Sum_probs=38.7

Q ss_pred             CCCCcccccccccc-CCCee--eEcCCCCCcccHHhHHHHHhC--CCCCccccCccC
Q 032328           69 SSPVDCVVCLENFR-MGDKC--RLLPNCRHSFHAQCIDSWLLK--TPICPICRTRVS  120 (143)
Q Consensus        69 ~~~~~C~ICl~~~~-~~~~v--~~l~~C~H~FH~~Ci~~wl~~--~~~CP~CR~~i~  120 (143)
                      +..++||||..-+. .+...  ...+.|+|-||..|+-.|+..  +.+||+||.+++
T Consensus      1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            56789999987765 22111  223358999999999999976  567999998775

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

Probab=98.56  E-value=2.4e-08  Score=74.41  Aligned_cols=52  Identities=23%  Similarity=0.717  Sum_probs=36.6

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC---CCCccccCccCCC
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT---PICPICRTRVSPS  122 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~---~~CP~CR~~i~~~  122 (143)
                      ...|.||.+-+.....+.-...|||+||..|+.+|+...   ..||.||-.+...
T Consensus         4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r   58 (465)
T KOG0827|consen    4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQER   58 (465)
T ss_pred             cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccce
Confidence            357999955444444444333599999999999999873   4699999444433

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

Probab=98.55  E-value=1.7e-08  Score=56.90  Aligned_cols=49  Identities=24%  Similarity=0.649  Sum_probs=24.8

Q ss_pred             CccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcc
Q 032328           72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG  125 (143)
Q Consensus        72 ~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~  125 (143)
                      -.|++|.+-++++   ..+..|.|.|++.|+..-+..  .||+|+.+...++++
T Consensus         8 LrCs~C~~~l~~p---v~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD~~   56 (65)
T PF14835_consen    8 LRCSICFDILKEP---VCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQDIQ   56 (65)
T ss_dssp             TS-SSS-S--SS----B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS--
T ss_pred             cCCcHHHHHhcCC---ceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHHHH
Confidence            4699999998875   445569999999999885543  499999998877654

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

Probab=98.41  E-value=1.2e-07  Score=69.45  Aligned_cols=44  Identities=39%  Similarity=0.884  Sum_probs=38.8

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCcccc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICR  116 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR  116 (143)
                      .+...|+||++.|.++   .++| |+|.||..|+..++.....||.||
T Consensus        11 ~~~~~C~iC~~~~~~p---~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr   54 (386)
T KOG2177|consen   11 QEELTCPICLEYFREP---VLLP-CGHNFCRACLTRSWEGPLSCPVCR   54 (386)
T ss_pred             cccccChhhHHHhhcC---cccc-ccchHhHHHHHHhcCCCcCCcccC
Confidence            3567899999999998   7777 999999999999988556799999

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

Probab=98.40  E-value=5.2e-08  Score=73.12  Aligned_cols=59  Identities=27%  Similarity=0.719  Sum_probs=44.5

Q ss_pred             CCCccccccccccC-CCeeeEcCCCCCcccHHhHHHHHhC--CCCCccccCccCCCCcceee
Q 032328           70 SPVDCVVCLENFRM-GDKCRLLPNCRHSFHAQCIDSWLLK--TPICPICRTRVSPSKVGVIL  128 (143)
Q Consensus        70 ~~~~C~ICl~~~~~-~~~v~~l~~C~H~FH~~Ci~~wl~~--~~~CP~CR~~i~~~~~~~~~  128 (143)
                      ....|+||++.+.. ++.....+.|||.|..+||+.|+-+  ...||.|........+...+
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~i~~e~   64 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQIRPEY   64 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHHHHHHHH
Confidence            45789999999974 5555555569999999999999953  24599998887765544433

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

Probab=98.35  E-value=2.2e-07  Score=67.31  Aligned_cols=49  Identities=22%  Similarity=0.534  Sum_probs=40.0

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC-CCCccccCccCCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT-PICPICRTRVSPS  122 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~-~~CP~CR~~i~~~  122 (143)
                      ...+|+||+....-+   ..++ |+|.||..||+.-.... .+||+||.++.+.
T Consensus         6 ~~~eC~IC~nt~n~P---v~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    6 KKKECLICYNTGNCP---VNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             cCCcceeeeccCCcC---cccc-ccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            356899999995554   6666 99999999999876664 5599999999866

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

Probab=98.34  E-value=1.3e-07  Score=71.07  Aligned_cols=59  Identities=27%  Similarity=0.678  Sum_probs=46.6

Q ss_pred             cCCCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC--CCCCccccCccCCCCcceee
Q 032328           66 DRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK--TPICPICRTRVSPSKVGVIL  128 (143)
Q Consensus        66 ~~~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~--~~~CP~CR~~i~~~~~~~~~  128 (143)
                      ++++.-+.|.||-|.   +..|.+.| |||..|..|+..|-..  .+.||.||.+|.-.+...+.
T Consensus       364 eMgsTFeLCKICaen---dKdvkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~viid  424 (563)
T KOG1785|consen  364 EMGSTFELCKICAEN---DKDVKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPVIID  424 (563)
T ss_pred             HccchHHHHHHhhcc---CCCccccc-ccchHHHHHHHhhcccCCCCCCCceeeEeccccceeee
Confidence            344555679999998   66778888 9999999999999855  46799999999866544443

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

Probab=98.31  E-value=1.9e-07  Score=74.97  Aligned_cols=53  Identities=23%  Similarity=0.619  Sum_probs=43.2

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-CCCCccccCccCCCCccee
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPSKVGVI  127 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~~~~~~~  127 (143)
                      --.|+.|-..+++    .+++.|||+||..|+..-+.. +..||.|...+...++..+
T Consensus       643 ~LkCs~Cn~R~Kd----~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I  696 (698)
T KOG0978|consen  643 LLKCSVCNTRWKD----AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHRI  696 (698)
T ss_pred             ceeCCCccCchhh----HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccccccc
Confidence            3479999988777    555569999999999998865 5679999999888776544

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

Probab=98.23  E-value=6.4e-07  Score=66.99  Aligned_cols=54  Identities=37%  Similarity=0.821  Sum_probs=41.2

Q ss_pred             CCCCccccccccccCCC----eeeEcCCCCCcccHHhHHHHHhC-------CCCCccccCccCCC
Q 032328           69 SSPVDCVVCLENFRMGD----KCRLLPNCRHSFHAQCIDSWLLK-------TPICPICRTRVSPS  122 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~----~v~~l~~C~H~FH~~Ci~~wl~~-------~~~CP~CR~~i~~~  122 (143)
                      ..+..|.||++...+..    -..++|+|.|.||..||..|-..       .+.||.||......
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v  223 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFV  223 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccc
Confidence            45778999999876532    12345779999999999999833       36799999887744

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

Probab=98.16  E-value=6.9e-07  Score=64.79  Aligned_cols=56  Identities=27%  Similarity=0.716  Sum_probs=45.6

Q ss_pred             CCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHh------------------C-----CCCCccccCccCCCCc
Q 032328           68 GSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL------------------K-----TPICPICRTRVSPSKV  124 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~------------------~-----~~~CP~CR~~i~~~~~  124 (143)
                      +.....|+|||--|.+++...+++ |.|.||..|+.++|.                  .     ...||+||..|..+..
T Consensus       112 n~p~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~~  190 (368)
T KOG4445|consen  112 NHPNGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEEN  190 (368)
T ss_pred             CCCCCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccccc
Confidence            345668999999999999888888 999999999998872                  1     1249999999987643

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

Probab=98.15  E-value=3.6e-07  Score=73.66  Aligned_cols=51  Identities=22%  Similarity=0.413  Sum_probs=42.3

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCC
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      ...|++|+..+.++......+ |+|.||.+|+..|-....+||+||.++...
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v  173 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGEFGEV  173 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhhhhee
Confidence            446888988877765555555 999999999999999999999999988754

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

Probab=98.06  E-value=2.6e-06  Score=72.84  Aligned_cols=66  Identities=26%  Similarity=0.629  Sum_probs=50.7

Q ss_pred             CCeeeecccccCCCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC----------CCCccccCccCCC
Q 032328           56 IPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT----------PICPICRTRVSPS  122 (143)
Q Consensus        56 ~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~----------~~CP~CR~~i~~~  122 (143)
                      +|-...+.++...+.++.|.||+.+--.....+.+. |+|+||.+|....|+++          -+||+|+.++.-.
T Consensus      3471 LPCl~Cdks~tkQD~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH~ 3546 (3738)
T KOG1428|consen 3471 LPCLHCDKSATKQDADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINHI 3546 (3738)
T ss_pred             ccccccChhhhhcccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhhH
Confidence            444444444555677889999999987777888887 99999999998866543          3599999988744

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

Probab=98.03  E-value=4.7e-07  Score=66.95  Aligned_cols=50  Identities=28%  Similarity=0.568  Sum_probs=41.7

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-CCCCccccCccCCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPS  122 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~~  122 (143)
                      .+..|+|||+-++..   +..+.|.|-||.+||..-+.. +..||.||+.+.+.
T Consensus        42 ~~v~c~icl~llk~t---mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Sk   92 (381)
T KOG0311|consen   42 IQVICPICLSLLKKT---MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSK   92 (381)
T ss_pred             hhhccHHHHHHHHhh---cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccc
Confidence            466899999998775   555579999999999888765 67799999998865

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

Probab=97.95  E-value=5.4e-06  Score=46.28  Aligned_cols=42  Identities=21%  Similarity=0.563  Sum_probs=26.9

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC--CCCCcc
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK--TPICPI  114 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~--~~~CP~  114 (143)
                      ....|+|.+..|+++   +....|||.|-++.|.+|++.  ...||+
T Consensus        10 ~~~~CPiT~~~~~~P---V~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFEDP---VKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SSE---EEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhhCC---cCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            456899999998874   333359999999999999944  445998

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

Probab=97.91  E-value=4.3e-06  Score=54.17  Aligned_cols=36  Identities=22%  Similarity=0.577  Sum_probs=30.7

Q ss_pred             CCCccccccccccCCCeeeEcCCCC------CcccHHhHHHHH
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCR------HSFHAQCIDSWL  106 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~------H~FH~~Ci~~wl  106 (143)
                      ...+|+||++.+.+++.++.++ ||      |+||.+|+.+|-
T Consensus        25 ~~~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~   66 (134)
T PF05883_consen   25 CTVECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWR   66 (134)
T ss_pred             cCeeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHH
Confidence            3578999999999977777777 65      999999999994

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.

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

Probab=97.88  E-value=5.7e-06  Score=62.20  Aligned_cols=50  Identities=32%  Similarity=0.756  Sum_probs=40.0

Q ss_pred             CCCccccccccccC-CCeeeEcCCCCCcccHHhHHHHHhCC--CCCccccCccC
Q 032328           70 SPVDCVVCLENFRM-GDKCRLLPNCRHSFHAQCIDSWLLKT--PICPICRTRVS  120 (143)
Q Consensus        70 ~~~~C~ICl~~~~~-~~~v~~l~~C~H~FH~~Ci~~wl~~~--~~CP~CR~~i~  120 (143)
                      .+-.|..|-+.+-. ++....+| |.|+||..|+...+..+  .+||.||+-..
T Consensus       364 ~~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~CrklrS  416 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCRKLRS  416 (518)
T ss_pred             HhhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHHHHHh
Confidence            34579999998854 45678888 99999999999999764  56999995444

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

Probab=97.83  E-value=1.1e-05  Score=61.73  Aligned_cols=49  Identities=33%  Similarity=0.741  Sum_probs=42.6

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSP  121 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~  121 (143)
                      ..+..|.||..-+..+   ..+| |||.|+..||++-+.....||.||.++..
T Consensus        82 ~sef~c~vc~~~l~~p---v~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   82 RSEFECCVCSRALYPP---VVTP-CGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cchhhhhhhHhhcCCC---cccc-ccccccHHHHHHHhccCCCCccccccccc
Confidence            4577899999888775   6677 99999999999988888889999999886

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

Probab=97.79  E-value=1.4e-05  Score=61.24  Aligned_cols=54  Identities=24%  Similarity=0.551  Sum_probs=44.0

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG  125 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~  125 (143)
                      ..+..|++|...+.++   .....|||.||..|+..|+..+..||.||.++......
T Consensus        19 ~~~l~C~~C~~vl~~p---~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~   72 (391)
T KOG0297|consen   19 DENLLCPICMSVLRDP---VQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEEL   72 (391)
T ss_pred             cccccCccccccccCC---CCCCCCCCcccccccchhhccCcCCcccccccchhhcc
Confidence            4567899999998885   22124999999999999999999999999988866433

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

Probab=97.66  E-value=4e-05  Score=40.97  Aligned_cols=45  Identities=29%  Similarity=0.617  Sum_probs=22.4

Q ss_pred             cccccccccCCCeeeEcC-CCCCcccHHhHHHHHh-CCCCCccccCcc
Q 032328           74 CVVCLENFRMGDKCRLLP-NCRHSFHAQCIDSWLL-KTPICPICRTRV  119 (143)
Q Consensus        74 C~ICl~~~~~~~~v~~l~-~C~H~FH~~Ci~~wl~-~~~~CP~CR~~i  119 (143)
                      |++|.+++...+. ...| .||+..+..|...-+. ....||-||++-
T Consensus         1 cp~C~e~~d~~d~-~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDK-DFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCT-T--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCC-ccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            7899999954332 3334 4899999999988775 477899999863

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

Probab=97.65  E-value=7.1e-05  Score=53.91  Aligned_cols=51  Identities=31%  Similarity=0.613  Sum_probs=38.0

Q ss_pred             CCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC--CCCCccccCccCC
Q 032328           68 GSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK--TPICPICRTRVSP  121 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~--~~~CP~CR~~i~~  121 (143)
                      ...+.+|++|-+.=..+  ....+ |||+||+.|+..-...  ..+||.|-.+...
T Consensus       236 ~t~~~~C~~Cg~~PtiP--~~~~~-C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~  288 (298)
T KOG2879|consen  236 GTSDTECPVCGEPPTIP--HVIGK-CGHIYCYYCIATSRLWDASFTCPLCGENVEP  288 (298)
T ss_pred             ccCCceeeccCCCCCCC--eeecc-ccceeehhhhhhhhcchhhcccCccCCCCcc
Confidence            46788999999883332  23334 9999999999886654  3689999887763

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

Probab=97.63  E-value=2.8e-05  Score=57.93  Aligned_cols=49  Identities=33%  Similarity=0.718  Sum_probs=35.0

Q ss_pred             cCCCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCC
Q 032328           66 DRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSP  121 (143)
Q Consensus        66 ~~~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~  121 (143)
                      .+.+..+.|.||+++..+   ...+| |||+-+  |.. .-+...+||+||+.+..
T Consensus       300 ~~~~~p~lcVVcl~e~~~---~~fvp-cGh~cc--ct~-cs~~l~~CPvCR~rI~~  348 (355)
T KOG1571|consen  300 RELPQPDLCVVCLDEPKS---AVFVP-CGHVCC--CTL-CSKHLPQCPVCRQRIRL  348 (355)
T ss_pred             cccCCCCceEEecCCccc---eeeec-CCcEEE--chH-HHhhCCCCchhHHHHHH
Confidence            344667889999999554   57788 999754  332 23445669999998764

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

Probab=97.58  E-value=7.7e-05  Score=52.33  Aligned_cols=51  Identities=29%  Similarity=0.703  Sum_probs=42.6

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC--------CCCccccCccCCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT--------PICPICRTRVSPS  122 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~--------~~CP~CR~~i~~~  122 (143)
                      -...|..|-..+.++|.++..  |-|.||++|+..|-..-        ..||-|..+|...
T Consensus        49 Y~pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp  107 (299)
T KOG3970|consen   49 YNPNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP  107 (299)
T ss_pred             CCCCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence            456799999999999998875  99999999999997541        3599999998755

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

Probab=97.52  E-value=8.7e-05  Score=55.34  Aligned_cols=50  Identities=26%  Similarity=0.510  Sum_probs=43.6

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      ++++.|+||...   +-.....| |+|.-|+.||.+.+...+.|=.|+..+...
T Consensus       420 sEd~lCpICyA~---pi~Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~~~  469 (489)
T KOG4692|consen  420 SEDNLCPICYAG---PINAVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVIDV  469 (489)
T ss_pred             cccccCcceecc---cchhhccC-CCCchHHHHHHHHHhcCCeeeEecceeeeh
Confidence            578889999987   55557788 999999999999999999999999988754

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

Probab=97.49  E-value=0.00063  Score=50.30  Aligned_cols=51  Identities=22%  Similarity=0.337  Sum_probs=38.9

Q ss_pred             CCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCC
Q 032328           68 GSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSP  121 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~  121 (143)
                      ..+...|++|+..-+.+-.+.+   -|=+||+.|+-.++...+.||+=-.+..-
T Consensus       297 ~~~~~~CpvClk~r~Nptvl~v---SGyVfCY~Ci~~Yv~~~~~CPVT~~p~~v  347 (357)
T KOG0826|consen  297 PPDREVCPVCLKKRQNPTVLEV---SGYVFCYPCIFSYVVNYGHCPVTGYPASV  347 (357)
T ss_pred             CCccccChhHHhccCCCceEEe---cceEEeHHHHHHHHHhcCCCCccCCcchH
Confidence            3567789999999666433222   58999999999999999999976555443

>PHA02862 5L protein; Provisional

Probab=97.44  E-value=0.00013  Score=47.70  Aligned_cols=49  Identities=20%  Similarity=0.491  Sum_probs=36.1

Q ss_pred             CCccccccccccCCCeeeEcC-CC---CCcccHHhHHHHHhC--CCCCccccCccCCCC
Q 032328           71 PVDCVVCLENFRMGDKCRLLP-NC---RHSFHAQCIDSWLLK--TPICPICRTRVSPSK  123 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~-~C---~H~FH~~Ci~~wl~~--~~~CP~CR~~i~~~~  123 (143)
                      .+.|=||.++-+++    ..| .|   ...-|.+|+.+|+..  +..||+|+.+...+.
T Consensus         2 ~diCWIC~~~~~e~----~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik~   56 (156)
T PHA02862          2 SDICWICNDVCDER----NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIKK   56 (156)
T ss_pred             CCEEEEecCcCCCC----cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEEE
Confidence            46799999985442    345 23   257899999999976  456999999887543

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

Probab=97.43  E-value=8.8e-05  Score=39.73  Aligned_cols=41  Identities=29%  Similarity=0.878  Sum_probs=26.4

Q ss_pred             cccccccccCCCeeeEcC-CCC---CcccHHhHHHHHhC--CCCCccc
Q 032328           74 CVVCLENFRMGDKCRLLP-NCR---HSFHAQCIDSWLLK--TPICPIC  115 (143)
Q Consensus        74 C~ICl~~~~~~~~v~~l~-~C~---H~FH~~Ci~~wl~~--~~~CP~C  115 (143)
                      |-||++.-.+++ ..+.| .|+   -.-|.+|+.+|+..  +.+|++|
T Consensus         1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            679998877655 34456 233   37899999999974  5669887

>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=97.41  E-value=6.2e-05  Score=47.23  Aligned_cols=33  Identities=27%  Similarity=0.664  Sum_probs=27.4

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHH
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCID  103 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~  103 (143)
                      +....|++|-..+.. ....+.| |||+||..|+.
T Consensus        76 ~~~~~C~vC~k~l~~-~~f~~~p-~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGN-SVFVVFP-CGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCC-ceEEEeC-CCeEEeccccc
Confidence            456779999999987 5566678 99999999985

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 [].

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

Probab=97.39  E-value=3.3e-05  Score=63.12  Aligned_cols=51  Identities=25%  Similarity=0.688  Sum_probs=39.6

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC-------CCCccccCcc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT-------PICPICRTRV  119 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~-------~~CP~CR~~i  119 (143)
                      ....+|.||.+.+...+.+--...|-|+||..||..|-...       -.||.|+...
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~  246 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVS  246 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchh
Confidence            45678999999998776655544588999999999998642       2399998443

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=97.38  E-value=0.0002  Score=47.74  Aligned_cols=51  Identities=20%  Similarity=0.585  Sum_probs=37.1

Q ss_pred             CCCCCccccccccccCCCeeeEcC-CCCC---cccHHhHHHHHhC--CCCCccccCccCCC
Q 032328           68 GSSPVDCVVCLENFRMGDKCRLLP-NCRH---SFHAQCIDSWLLK--TPICPICRTRVSPS  122 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~v~~l~-~C~H---~FH~~Ci~~wl~~--~~~CP~CR~~i~~~  122 (143)
                      ...+..|-||.++..+    -..| .|..   .-|.+|+.+|+..  ...||.|+.+....
T Consensus         5 s~~~~~CRIC~~~~~~----~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          5 SLMDKCCWICKDEYDV----VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCCCeeEecCCCCCC----ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            3467889999988432    1235 3544   5699999999976  45699999887654

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

Probab=97.34  E-value=3e-05  Score=56.26  Aligned_cols=42  Identities=29%  Similarity=0.750  Sum_probs=34.4

Q ss_pred             CCccccccccccCCCeeeEcCCCCC-cccHHhHHHHHhCCCCCccccCccC
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRH-SFHAQCIDSWLLKTPICPICRTRVS  120 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H-~FH~~Ci~~wl~~~~~CP~CR~~i~  120 (143)
                      +..|+||++.   +.....|+ ||| +-|.+|-...    ..||+||+.+.
T Consensus       300 ~~LC~ICmDa---P~DCvfLe-CGHmVtCt~CGkrm----~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDA---PRDCVFLE-CGHMVTCTKCGKRM----NECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcC---CcceEEee-cCcEEeehhhcccc----ccCchHHHHHH
Confidence            5679999999   66678888 999 7788898663    47999998764

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

Probab=97.27  E-value=7.3e-05  Score=49.84  Aligned_cols=30  Identities=37%  Similarity=0.853  Sum_probs=27.2

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccH
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHA   99 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~   99 (143)
                      .+..+|.||||++..++.+..|| |--+||+
T Consensus       175 ddkGECvICLEdL~~GdtIARLP-CLCIYHK  204 (205)
T KOG0801|consen  175 DDKGECVICLEDLEAGDTIARLP-CLCIYHK  204 (205)
T ss_pred             ccCCcEEEEhhhccCCCceeccc-eEEEeec
Confidence            45668999999999999999999 9999996

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.26  E-value=0.00047  Score=49.09  Aligned_cols=62  Identities=15%  Similarity=0.326  Sum_probs=52.6

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcceeecCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVILKDG  131 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~~~~~~~  131 (143)
                      ....|++|.+.+...-....|..|||+|..+|.+..+.....||+|-.++.+.++.....-|
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~LqrGG  281 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGLQRGG  281 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEeeeccc
Confidence            45679999999988777777766999999999999999999999999999988776655443

>PF04641 Rtf2: Rtf2 RING-finger

Probab=97.22  E-value=0.00065  Score=49.46  Aligned_cols=63  Identities=19%  Similarity=0.365  Sum_probs=49.3

Q ss_pred             CCCCCccccccccccCCCe-eeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcceeecCCC
Q 032328           68 GSSPVDCVVCLENFRMGDK-CRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVILKDGS  132 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~-v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~~~~~~~~  132 (143)
                      ......|||...+|..... +.+.| |||+|...++... .....||+|-.++...++..+.+.+.
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~-cG~V~s~~alke~-k~~~~Cp~c~~~f~~~DiI~Lnp~~e  173 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRP-CGCVFSEKALKEL-KKSKKCPVCGKPFTEEDIIPLNPPEE  173 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcC-CCCEeeHHHHHhh-cccccccccCCccccCCEEEecCCcc
Confidence            3456789999999965444 55556 9999999999996 33567999999999888777666555

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

Probab=97.22  E-value=0.0004  Score=51.78  Aligned_cols=61  Identities=25%  Similarity=0.537  Sum_probs=43.2

Q ss_pred             CCeeeecccccCCCCCCccccccccccCCCeeeEcCCCCCcccHHhHHH--HHhCCCCCccccCccC
Q 032328           56 IPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDS--WLLKTPICPICRTRVS  120 (143)
Q Consensus        56 ~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~--wl~~~~~CP~CR~~i~  120 (143)
                      -|.......++...+...|.||-+.+.-   ..++| |+|..|.-|--+  -|..++.||+||.+..
T Consensus        46 EPnlttsSaddtDEen~~C~ICA~~~TY---s~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE~e  108 (493)
T COG5236          46 EPNLTTSSADDTDEENMNCQICAGSTTY---SARYP-CGHQICHACAVRLRALYMQKGCPLCRTETE  108 (493)
T ss_pred             CCccccccccccccccceeEEecCCceE---EEecc-CCchHHHHHHHHHHHHHhccCCCccccccc
Confidence            3444444444445567789999998543   37788 999888888654  3456788999999865

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

Probab=97.22  E-value=0.00016  Score=56.67  Aligned_cols=52  Identities=23%  Similarity=0.554  Sum_probs=40.3

Q ss_pred             CCCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-----CCCCccccCccCCC
Q 032328           67 RGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-----TPICPICRTRVSPS  122 (143)
Q Consensus        67 ~~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-----~~~CP~CR~~i~~~  122 (143)
                      ++....+|.+|.++-++.   .... |.|.||+-|+..+...     +.+||.|...+..+
T Consensus       532 enk~~~~C~lc~d~aed~---i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD  588 (791)
T KOG1002|consen  532 ENKGEVECGLCHDPAEDY---IESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             cccCceeecccCChhhhh---Hhhh-hhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            345677899999996652   4444 9999999999988753     46799998887755

>PHA03096 p28-like protein; Provisional

Probab=97.11  E-value=0.00027  Score=51.91  Aligned_cols=48  Identities=27%  Similarity=0.577  Sum_probs=34.3

Q ss_pred             CccccccccccCC----CeeeEcCCCCCcccHHhHHHHHhCC------CCCccccCcc
Q 032328           72 VDCVVCLENFRMG----DKCRLLPNCRHSFHAQCIDSWLLKT------PICPICRTRV  119 (143)
Q Consensus        72 ~~C~ICl~~~~~~----~~v~~l~~C~H~FH~~Ci~~wl~~~------~~CP~CR~~i  119 (143)
                      ..|.||++.....    ..--.++.|.|.|+..|+..|-...      +.||.||.-+
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~~~~~  236 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRLNTVI  236 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccchhhHH
Confidence            6799999987643    2334567899999999999998542      2355555444

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.05  E-value=0.00054  Score=51.00  Aligned_cols=63  Identities=19%  Similarity=0.367  Sum_probs=42.0

Q ss_pred             CCCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHh-CCCCCccccCccCCCCcceeec
Q 032328           67 RGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL-KTPICPICRTRVSPSKVGVILK  129 (143)
Q Consensus        67 ~~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~-~~~~CP~CR~~i~~~~~~~~~~  129 (143)
                      ++++++.|+.|+|++...|+-..-..||-.-|.-|...--+ -+..||-||+...++.+.++.-
T Consensus        10 sedeed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~~~   73 (480)
T COG5175          10 SEDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYVTL   73 (480)
T ss_pred             cccccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeEEec
Confidence            34456779999999987766443223886444444433222 2566999999999988877654

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

Probab=97.05  E-value=0.0003  Score=51.23  Aligned_cols=49  Identities=22%  Similarity=0.477  Sum_probs=40.7

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSP  121 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~  121 (143)
                      .-...|-||-..|..+   ++. .|+|.||..|-..-+++...|++|-+....
T Consensus       239 ~~Pf~c~icr~~f~~p---Vvt-~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g  287 (313)
T KOG1813|consen  239 LLPFKCFICRKYFYRP---VVT-KCGHYFCEVCALKPYQKGEKCYVCSQQTHG  287 (313)
T ss_pred             cCCccccccccccccc---hhh-cCCceeehhhhccccccCCcceeccccccc
Confidence            4466799999999985   444 499999999998888888899999887653

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

Probab=97.05  E-value=0.00013  Score=53.89  Aligned_cols=51  Identities=22%  Similarity=0.582  Sum_probs=42.9

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      .....|.+|-.-+.+...+.   .|-|.||+.||...+.....||.|...+...
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            35678999999988764433   4999999999999999999999999888765

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

Probab=97.03  E-value=0.00026  Score=48.81  Aligned_cols=45  Identities=24%  Similarity=0.570  Sum_probs=36.7

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCcc
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRV  119 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i  119 (143)
                      ...|.||-.+|..+   ++. .|||.||..|...=.+.-..|-+|-...
T Consensus       196 PF~C~iCKkdy~sp---vvt-~CGH~FC~~Cai~~y~kg~~C~~Cgk~t  240 (259)
T COG5152         196 PFLCGICKKDYESP---VVT-ECGHSFCSLCAIRKYQKGDECGVCGKAT  240 (259)
T ss_pred             ceeehhchhhccch---hhh-hcchhHHHHHHHHHhccCCcceecchhh
Confidence            44799999999985   444 4999999999988777778899996543

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

Probab=96.96  E-value=0.00052  Score=52.15  Aligned_cols=39  Identities=28%  Similarity=0.703  Sum_probs=34.0

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK  108 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~  108 (143)
                      .....|.||+++.........+| |+|.||+.|...++..
T Consensus       182 ~slf~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~~  220 (445)
T KOG1814|consen  182 NSLFDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFTI  220 (445)
T ss_pred             hhcccceeeehhhcCcceeeecc-cchHHHHHHHHHHHHH
Confidence            45678999999988778889999 9999999999999853

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

Probab=96.92  E-value=3.1e-05  Score=58.23  Aligned_cols=53  Identities=23%  Similarity=0.525  Sum_probs=45.6

Q ss_pred             CCCccccccccccCC-CeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCC
Q 032328           70 SPVDCVVCLENFRMG-DKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSK  123 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~-~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~  123 (143)
                      ....|+||.+.++.. +++..+. |||.+|..|+.+|+.....||.||+++....
T Consensus       195 lv~sl~I~~~slK~~y~k~~~~~-~g~~~~~~kL~k~L~~~~kl~~~~rel~~~~  248 (465)
T KOG0827|consen  195 LVGSLSICFESLKQNYDKISAIV-CGHIYHHGKLSKWLATKRKLPSCRRELPKNG  248 (465)
T ss_pred             HHhhhHhhHHHHHHHHHHHHHHh-hcccchhhHHHHHHHHHHHhHHHHhhhhhhh
Confidence            345799999999887 6677776 9999999999999999888999999998653

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=96.79  E-value=0.0022  Score=35.06  Aligned_cols=41  Identities=27%  Similarity=0.652  Sum_probs=34.4

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCcc
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPI  114 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~  114 (143)
                      ....|++|-+.|.+++.+.+.|.||--+|+.|-+.    ...|-.
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~   44 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCIN   44 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEe
Confidence            45679999999999899999999999999999855    455644

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

Probab=96.74  E-value=0.00078  Score=47.85  Aligned_cols=53  Identities=25%  Similarity=0.608  Sum_probs=35.6

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcceeec
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVILK  129 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~~~~~  129 (143)
                      .|--|.-.=. ++....+- |+|+||..|...-  ....||+||..+.....+..++
T Consensus         5 hCn~C~~~~~-~~~f~LTa-C~HvfC~~C~k~~--~~~~C~lCkk~ir~i~l~~slp   57 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLTA-CRHVFCEPCLKAS--SPDVCPLCKKSIRIIQLNRSLP   57 (233)
T ss_pred             EeccccccCC-CCceeeee-chhhhhhhhcccC--Cccccccccceeeeeecccccc
Confidence            3555554433 56666665 9999999998652  2337999999977665554443

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

Probab=96.69  E-value=0.0013  Score=34.51  Aligned_cols=41  Identities=27%  Similarity=0.805  Sum_probs=23.1

Q ss_pred             cccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCC--CCccc
Q 032328           74 CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP--ICPIC  115 (143)
Q Consensus        74 C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~--~CP~C  115 (143)
                      |.+|-+-...|...... .|+=.+|..|+..++..+.  .||.|
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            56777776666443332 3888999999999998755  69987

; PDB: 3NW0_A 2CT0_A.

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

Probab=96.64  E-value=0.0015  Score=48.37  Aligned_cols=49  Identities=24%  Similarity=0.636  Sum_probs=37.7

Q ss_pred             CCccccccccccCC--CeeeEcCCCCCcccHHhHHHHHhC-CCCCccccCcc
Q 032328           71 PVDCVVCLENFRMG--DKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRV  119 (143)
Q Consensus        71 ~~~C~ICl~~~~~~--~~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i  119 (143)
                      -..|-||-++|..+  +.+.....|||.|+..|+...+.. ...||.||...
T Consensus         3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CCceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            35799999999765  344444459999999999876655 34599999996

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

Probab=96.63  E-value=0.0011  Score=54.62  Aligned_cols=42  Identities=26%  Similarity=0.638  Sum_probs=32.6

Q ss_pred             CccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCcc
Q 032328           72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRV  119 (143)
Q Consensus        72 ~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i  119 (143)
                      ..|..|-..++-+-.-.   .|||.||.+|+.   .....||.|+.+.
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            47999999877753322   399999999998   5557799998743

>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=96.58  E-value=0.0024  Score=42.58  Aligned_cols=52  Identities=31%  Similarity=0.664  Sum_probs=34.8

Q ss_pred             CCccccccccccCCCeeeEcC------C-----CCC-cccHHhHHHHHhC------------------------------
Q 032328           71 PVDCVVCLENFRMGDKCRLLP------N-----CRH-SFHAQCIDSWLLK------------------------------  108 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~------~-----C~H-~FH~~Ci~~wl~~------------------------------  108 (143)
                      +..|+||||-   +-+.+.|.      +     |+. .=|..|+++..+.                              
T Consensus         2 d~~CpICme~---PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (162)
T PF07800_consen    2 DVTCPICMEH---PHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQ   78 (162)
T ss_pred             CccCceeccC---CCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccccccccccc
Confidence            5679999998   44334443      1     444 3478899998631                              


Q ss_pred             -CCCCccccCccCCCCcc
Q 032328          109 -TPICPICRTRVSPSKVG  125 (143)
Q Consensus       109 -~~~CP~CR~~i~~~~~~  125 (143)
                       +..||+||.+|.-+.+.
T Consensus        79 ~~L~CPLCRG~V~GWtvv   96 (162)
T PF07800_consen   79 PELACPLCRGEVKGWTVV   96 (162)
T ss_pred             ccccCccccCceeceEEc
Confidence             12499999999877544

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.

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

Probab=96.35  E-value=0.003  Score=42.94  Aligned_cols=32  Identities=28%  Similarity=0.805  Sum_probs=26.1

Q ss_pred             CCCCcccHHhHHHHHhCC-----------CCCccccCccCCCC
Q 032328           92 NCRHSFHAQCIDSWLLKT-----------PICPICRTRVSPSK  123 (143)
Q Consensus        92 ~C~H~FH~~Ci~~wl~~~-----------~~CP~CR~~i~~~~  123 (143)
                      .||.-||.-|+..||+.-           ..||.|-.++..+.
T Consensus       189 qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKm  231 (234)
T KOG3268|consen  189 QCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKM  231 (234)
T ss_pred             ccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeec
Confidence            499999999999999641           35999999887653

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

Probab=96.32  E-value=0.0026  Score=46.73  Aligned_cols=43  Identities=33%  Similarity=0.692  Sum_probs=33.4

Q ss_pred             CccccccccccCCCeeeEcCCCCCcccHHhHHHHHh-CCCCCccccC
Q 032328           72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL-KTPICPICRT  117 (143)
Q Consensus        72 ~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~-~~~~CP~CR~  117 (143)
                      ..|+.|..-+...   ...|.|+|.||.+||..-|. ....||.|.+
T Consensus       275 LkCplc~~Llrnp---~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRNP---MKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhCc---ccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            4699998776554   44566999999999997664 5788999965

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

Probab=96.30  E-value=0.0019  Score=53.52  Aligned_cols=36  Identities=22%  Similarity=0.573  Sum_probs=28.9

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHH
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWL  106 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl  106 (143)
                      ..++.|.+|...+... .-.+-| |||.||++|+.+-.
T Consensus       815 ep~d~C~~C~~~ll~~-pF~vf~-CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  815 EPQDSCDHCGRPLLIK-PFYVFP-CGHCFHRDCLIRHV  850 (911)
T ss_pred             cCccchHHhcchhhcC-cceeee-ccchHHHHHHHHHH
Confidence            3567899999988764 445667 99999999998765

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

Probab=96.25  E-value=0.0026  Score=47.15  Aligned_cols=45  Identities=24%  Similarity=0.628  Sum_probs=35.3

Q ss_pred             CCCCccccccccccCCCeeeEcCCC--CCcccHHhHHHHHhCCCCCccccCccCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNC--RHSFHAQCIDSWLLKTPICPICRTRVSP  121 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C--~H~FH~~Ci~~wl~~~~~CP~CR~~i~~  121 (143)
                      .+-.+|+||.+.+..+    +.. |  ||+-|..|-.+   ....||.||.++..
T Consensus        46 ~~lleCPvC~~~l~~P----i~Q-C~nGHlaCssC~~~---~~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   46 LDLLDCPVCFNPLSPP----IFQ-CDNGHLACSSCRTK---VSNKCPTCRLPIGN   92 (299)
T ss_pred             hhhccCchhhccCccc----cee-cCCCcEehhhhhhh---hcccCCcccccccc
Confidence            4556899999999884    444 6  79999999863   35679999999883

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

Probab=96.11  E-value=0.0043  Score=45.34  Aligned_cols=46  Identities=26%  Similarity=0.732  Sum_probs=37.6

Q ss_pred             CCccccccccccCCCe-eeEcCCCCCcccHHhHHHHHhCCCCCccccC
Q 032328           71 PVDCVVCLENFRMGDK-CRLLPNCRHSFHAQCIDSWLLKTPICPICRT  117 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~-v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~  117 (143)
                      ...|+||.+.+-.... +..++ |||..|..|+........+||+|..
T Consensus       158 ~~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             cCCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc
Confidence            4449999999876544 44455 9999999999998888889999988

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

Probab=96.08  E-value=0.0029  Score=44.52  Aligned_cols=41  Identities=44%  Similarity=0.890  Sum_probs=33.5

Q ss_pred             cccccccccCCCeeeEcCCCCC-cccHHhHHHHHhCCCCCccccCccCCC
Q 032328           74 CVVCLENFRMGDKCRLLPNCRH-SFHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        74 C~ICl~~~~~~~~v~~l~~C~H-~FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      |-.|-+.   +..|..+| |.| ++|..|-..    ...||+|+....+.
T Consensus       161 Cr~C~~~---~~~VlllP-CrHl~lC~~C~~~----~~~CPiC~~~~~s~  202 (207)
T KOG1100|consen  161 CRKCGER---EATVLLLP-CRHLCLCGICDES----LRICPICRSPKTSS  202 (207)
T ss_pred             ceecCcC---CceEEeec-ccceEeccccccc----CccCCCCcChhhce
Confidence            8888888   78899999 998 888899865    35599999877654

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

Probab=96.02  E-value=0.0026  Score=46.83  Aligned_cols=43  Identities=37%  Similarity=0.854  Sum_probs=31.6

Q ss_pred             ccccccccccC-CCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCC
Q 032328           73 DCVVCLENFRM-GDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSP  121 (143)
Q Consensus        73 ~C~ICl~~~~~-~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~  121 (143)
                      -|.-|--.+.. +   ++.| |+|+||.+|-..  ...+.||+|-.++..
T Consensus        92 fCd~Cd~PI~IYG---RmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~Vqr  135 (389)
T KOG2932|consen   92 FCDRCDFPIAIYG---RMIP-CKHVFCLECARS--DSDKICPLCDDRVQR  135 (389)
T ss_pred             eecccCCcceeee---cccc-cchhhhhhhhhc--CccccCcCcccHHHH
Confidence            47777665442 2   5677 999999999865  446789999877764

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

Probab=96.01  E-value=0.0016  Score=53.27  Aligned_cols=49  Identities=24%  Similarity=0.625  Sum_probs=37.9

Q ss_pred             CccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC--CCCccccCccCCCCcc
Q 032328           72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT--PICPICRTRVSPSKVG  125 (143)
Q Consensus        72 ~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~--~~CP~CR~~i~~~~~~  125 (143)
                      ..|.||++    .+.....+ |+|.|+.+|+..-+...  ..||+||..+......
T Consensus       455 ~~c~ic~~----~~~~~it~-c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~  505 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITR-CGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLL  505 (674)
T ss_pred             cccccccc----cccceeec-ccchHHHHHHHhccccccCCCCcHHHHHHHHHHHh
Confidence            78999999    23345555 99999999999887653  3599999998876544

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

Probab=95.60  E-value=0.0082  Score=31.77  Aligned_cols=44  Identities=23%  Similarity=0.579  Sum_probs=25.4

Q ss_pred             ccccccccccCCCeeeEcCCC-CCcccHHhHHHHHhCCCCCccccCccCCC
Q 032328           73 DCVVCLENFRMGDKCRLLPNC-RHSFHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C-~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      .|.-|+-+   +...+.   | .|..+..|+...+.....||+|..++...
T Consensus         4 nCKsCWf~---~k~Li~---C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen    4 NCKSCWFA---NKGLIK---CSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             ---SS-S-----SSEEE----SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             cChhhhhc---CCCeee---ecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            46677766   333333   6 59999999999999999999999887643

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.

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=95.29  E-value=0.011  Score=32.38  Aligned_cols=46  Identities=30%  Similarity=0.597  Sum_probs=32.5

Q ss_pred             CccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCC
Q 032328           72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSK  123 (143)
Q Consensus        72 ~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~  123 (143)
                      ..|..|...   +.+-.++| |||+-+..|..-+  +-+-||.|-+++...+
T Consensus         8 ~~~~~~~~~---~~~~~~~p-CgH~I~~~~f~~~--rYngCPfC~~~~~~~~   53 (55)
T PF14447_consen    8 QPCVFCGFV---GTKGTVLP-CGHLICDNCFPGE--RYNGCPFCGTPFEFDD   53 (55)
T ss_pred             eeEEEcccc---cccccccc-ccceeeccccChh--hccCCCCCCCcccCCC
Confidence            446666665   34447788 9999988887653  3345999999887653

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

Probab=95.15  E-value=0.012  Score=48.27  Aligned_cols=40  Identities=25%  Similarity=0.663  Sum_probs=27.8

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCcc
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPI  114 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~  114 (143)
                      .|+||.-....--.+ -.. |+|..|..|...|+.....||-
T Consensus      1030 ~C~~C~l~V~gss~~-Cg~-C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1030 QCAICHLAVRGSSNF-CGT-CGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeeEeeEeeccchh-hcc-ccccccHHHHHHHHhcCCcCCC
Confidence            366665544332222 223 9999999999999999888883

>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=94.93  E-value=0.006  Score=43.45  Aligned_cols=67  Identities=22%  Similarity=0.429  Sum_probs=45.4

Q ss_pred             CCCcccccccc-ccCCC-eeeEcCCCCCcccHHhHHHHHhCC-CCCc--cccCccCCCCcceeecCCCCCCc
Q 032328           70 SPVDCVVCLEN-FRMGD-KCRLLPNCRHSFHAQCIDSWLLKT-PICP--ICRTRVSPSKVGVILKDGSSVSS  136 (143)
Q Consensus        70 ~~~~C~ICl~~-~~~~~-~v~~l~~C~H~FH~~Ci~~wl~~~-~~CP--~CR~~i~~~~~~~~~~~~~~~~~  136 (143)
                      .+..||+|-.+ |-.++ ++.+-|.|-|-.|.+|+++-+..- ..||  -|..-+-.........+....+.
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK~kf~~qtFeD~~vEk   80 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRKIKFIKQTFEDITVEK   80 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHHhcccccccchhhhhh
Confidence            45689999866 33444 445556799999999999999774 4599  88766665555544444444333

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

Probab=94.62  E-value=0.024  Score=45.56  Aligned_cols=57  Identities=26%  Similarity=0.702  Sum_probs=43.6

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcceeecCCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVILKDGSS  133 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~~~~~~~~~  133 (143)
                      ...+.|.||+++.    ..+..+ |.   |..|+..|+..+..||+|+..+..++..........
T Consensus       477 ~~~~~~~~~~~~~----~~~~~~-~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~~~~~~~~~~  533 (543)
T KOG0802|consen  477 EPNDVCAICYQEM----SARITP-CS---HALCLRKWLYVQEVCPLCHTYMKEDDFLSKNSSEST  533 (543)
T ss_pred             cccCcchHHHHHH----Hhcccc-cc---chhHHHhhhhhccccCCCchhhhcccccCccccccc
Confidence            4567899999998    225555 77   889999999999999999999887765544443333

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

Probab=94.56  E-value=0.011  Score=51.07  Aligned_cols=49  Identities=29%  Similarity=0.683  Sum_probs=39.1

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS  120 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~  120 (143)
                      .....|.||++.+.....+.  . |||.++..|...|+..+..||.|+....
T Consensus      1151 ~~~~~c~ic~dil~~~~~I~--~-cgh~~c~~c~~~~l~~~s~~~~~ksi~~ 1199 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRNQGGIA--G-CGHEPCCRCDELWLYASSRCPICKSIKG 1199 (1394)
T ss_pred             hcccchHHHHHHHHhcCCee--e-echhHhhhHHHHHHHHhccCcchhhhhh
Confidence            34558999999988433333  2 9999999999999999999999984443

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

Probab=94.41  E-value=0.035  Score=46.07  Aligned_cols=56  Identities=21%  Similarity=0.473  Sum_probs=41.4

Q ss_pred             CCCCCCccccccccccCCCeeeEcC-CCC---CcccHHhHHHHHhC--CCCCccccCccCCCC
Q 032328           67 RGSSPVDCVVCLENFRMGDKCRLLP-NCR---HSFHAQCIDSWLLK--TPICPICRTRVSPSK  123 (143)
Q Consensus        67 ~~~~~~~C~ICl~~~~~~~~v~~l~-~C~---H~FH~~Ci~~wl~~--~~~CP~CR~~i~~~~  123 (143)
                      .+.++..|-||..+=..++... .| +|.   ...|.+|+..|+..  ...|-+|+.+..-++
T Consensus         8 mN~d~~~CRICr~e~~~d~pLf-hPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~   69 (1175)
T COG5183           8 MNEDKRSCRICRTEDIRDDPLF-HPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKD   69 (1175)
T ss_pred             CCccchhceeecCCCCCCCcCc-ccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeee
Confidence            3456678999998866655544 45 342   47899999999976  456999999887654

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

Probab=94.34  E-value=0.04  Score=41.87  Aligned_cols=29  Identities=28%  Similarity=0.871  Sum_probs=21.1

Q ss_pred             CCCcccHHhHHHHHhC-------------CCCCccccCccCC
Q 032328           93 CRHSFHAQCIDSWLLK-------------TPICPICRTRVSP  121 (143)
Q Consensus        93 C~H~FH~~Ci~~wl~~-------------~~~CP~CR~~i~~  121 (143)
                      |.-+.|.+|+.+|+..             +-.||.||+..=.
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi  352 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI  352 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence            4456678999999843             2359999997643

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

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=94.07  E-value=0.045  Score=38.41  Aligned_cols=42  Identities=29%  Similarity=0.792  Sum_probs=30.8

Q ss_pred             CCCcccccccc-----ccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccC
Q 032328           70 SPVDCVVCLEN-----FRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRT  117 (143)
Q Consensus        70 ~~~~C~ICl~~-----~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~  117 (143)
                      .+..|.+|-++     |+. +.+...+.|+.+||++|..+     ..||.|-+
T Consensus       151 kGfiCe~C~~~~~IfPF~~-~~~~~C~~C~~v~H~~C~~~-----~~CpkC~R  197 (202)
T PF13901_consen  151 KGFICEICNSDDIIFPFQI-DTTVRCPKCKSVFHKSCFRK-----KSCPKCAR  197 (202)
T ss_pred             CCCCCccCCCCCCCCCCCC-CCeeeCCcCccccchhhcCC-----CCCCCcHh
Confidence            46788899753     233 35566667999999999962     66999954

>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=94.05  E-value=0.053  Score=29.38  Aligned_cols=43  Identities=26%  Similarity=0.523  Sum_probs=23.4

Q ss_pred             cccccccccCC------CeeeEcCCCCCcccHHhHHHHHhCCCCCcccc
Q 032328           74 CVVCLENFRMG------DKCRLLPNCRHSFHAQCIDSWLLKTPICPICR  116 (143)
Q Consensus        74 C~ICl~~~~~~------~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR  116 (143)
                      |.-|+.++..+      .....-|.|++.|+.+|=.---+.--+||-|-
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            55666666654      35677778999999999644334455699883

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.

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.76  E-value=0.031  Score=40.26  Aligned_cols=53  Identities=21%  Similarity=0.526  Sum_probs=35.7

Q ss_pred             CCCCccccccccccCCCee-eEcC-CC---CCcccHHhHHHHHhCC--------CCCccccCccCC
Q 032328           69 SSPVDCVVCLENFRMGDKC-RLLP-NC---RHSFHAQCIDSWLLKT--------PICPICRTRVSP  121 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v-~~l~-~C---~H~FH~~Ci~~wl~~~--------~~CP~CR~~i~~  121 (143)
                      ..+..|-||+.-=+++... -+.| .|   .|=-|..|+..|+..+        ..||-|+.+-..
T Consensus        18 e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYii   83 (293)
T KOG3053|consen   18 ELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYII   83 (293)
T ss_pred             ccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhee
Confidence            4556799999875443222 2345 23   3788999999999643        249999887653

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

Probab=93.72  E-value=0.34  Score=30.56  Aligned_cols=30  Identities=20%  Similarity=0.416  Sum_probs=21.1

Q ss_pred             eEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCC
Q 032328           88 RLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSK  123 (143)
Q Consensus        88 ~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~  123 (143)
                      ...|+|+|.      ...+.+...|+.|+++++.++
T Consensus        70 V~CP~C~K~------TKmLGr~D~CM~C~~pLTLd~   99 (114)
T PF11023_consen   70 VECPNCGKQ------TKMLGRVDACMHCKEPLTLDP   99 (114)
T ss_pred             eECCCCCCh------HhhhchhhccCcCCCcCccCc
Confidence            334567764      355666678999999999773

; GO: 0005887 integral to plasma membrane

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.44  E-value=0.047  Score=40.11  Aligned_cols=32  Identities=25%  Similarity=0.701  Sum_probs=24.5

Q ss_pred             CCCcccHHhHHHHHhC-------------CCCCccccCccCCCCc
Q 032328           93 CRHSFHAQCIDSWLLK-------------TPICPICRTRVSPSKV  124 (143)
Q Consensus        93 C~H~FH~~Ci~~wl~~-------------~~~CP~CR~~i~~~~~  124 (143)
                      |..+.|.+|+.+|+..             +-+||+||+..-..++
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~dv  369 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRDV  369 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEeee
Confidence            6678889999999843             3469999998765543

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

Probab=93.36  E-value=0.025  Score=45.75  Aligned_cols=43  Identities=21%  Similarity=0.563  Sum_probs=30.9

Q ss_pred             CccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccC
Q 032328           72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRT  117 (143)
Q Consensus        72 ~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~  117 (143)
                      -.|.||+..|-...-..+.+.|||.-|.+|+....  +.+|| |++
T Consensus        12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly--n~scp-~~~   54 (861)
T KOG3161|consen   12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY--NASCP-TKR   54 (861)
T ss_pred             hhchHHHHHHHHHhcCcccccccchHHHHHHHhHh--hccCC-CCc
Confidence            35999988876654444444699999999998743  45688 543

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

Probab=93.26  E-value=0.041  Score=40.32  Aligned_cols=56  Identities=20%  Similarity=0.466  Sum_probs=39.1

Q ss_pred             cccccccc-ccCCCeeeEcCCCCCcccHHhHHHHHhC-CCCCccccCccCCCCcceee
Q 032328           73 DCVVCLEN-FRMGDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPSKVGVIL  128 (143)
Q Consensus        73 ~C~ICl~~-~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~~~~~~~~  128 (143)
                      .|++|-.. |-.++.......|+|-.|.+|.+..+.. ...||-|-..+-.......+
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nfr~q~   59 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNNFRVQT   59 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhcccchhh
Confidence            48888755 3344433333349999999999998876 56799998877766555443

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

Probab=93.10  E-value=0.47  Score=36.39  Aligned_cols=53  Identities=21%  Similarity=0.281  Sum_probs=41.8

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC---CCCccccCccCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT---PICPICRTRVSPS  122 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~---~~CP~CR~~i~~~  122 (143)
                      ..-..|||=-++-.+++....+. |||+-.++-+.+..+..   ..||.|=.+-...
T Consensus       332 HSvF~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~e~~~~  387 (394)
T KOG2817|consen  332 HSVFICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYCPVEQLAS  387 (394)
T ss_pred             cceeecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCCCcccCHH
Confidence            34568999999988888888888 99999999999976552   4699995544433

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

Probab=92.96  E-value=0.078  Score=43.69  Aligned_cols=41  Identities=29%  Similarity=0.540  Sum_probs=31.3

Q ss_pred             CccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCcc
Q 032328           72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPI  114 (143)
Q Consensus        72 ~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~  114 (143)
                      -.|++|-..+..-+..  .+.|||.-|.+|+.+|+.....||.
T Consensus       780 ~~CtVC~~vi~G~~~~--c~~C~H~gH~sh~~sw~~~~s~ca~  820 (839)
T KOG0269|consen  780 AKCTVCDLVIRGVDVW--CQVCGHGGHDSHLKSWFFKASPCAK  820 (839)
T ss_pred             cCceeecceeeeeEee--cccccccccHHHHHHHHhcCCCCcc
Confidence            3688888775543222  2359999999999999999888876

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

Probab=92.26  E-value=0.14  Score=33.35  Aligned_cols=54  Identities=22%  Similarity=0.456  Sum_probs=37.7

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC---CCCCccccCccCCCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK---TPICPICRTRVSPSK  123 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~---~~~CP~CR~~i~~~~  123 (143)
                      .-.+|-||.|.-.++.-+.--..||=.-|.-|....++.   .+.||+|+....+..
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            456899999986665333222248887788887775554   577999999887653

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

Probab=92.24  E-value=0.053  Score=41.79  Aligned_cols=59  Identities=22%  Similarity=0.537  Sum_probs=38.2

Q ss_pred             CCCccccccccccCC-CeeeEcCCCCCcccHHhHHHHHhCC------CCCc--cccCccCCCCcceeec
Q 032328           70 SPVDCVVCLENFRMG-DKCRLLPNCRHSFHAQCIDSWLLKT------PICP--ICRTRVSPSKVGVILK  129 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~-~~v~~l~~C~H~FH~~Ci~~wl~~~------~~CP--~CR~~i~~~~~~~~~~  129 (143)
                      ....|.||..+.... +..... .|+|.|+.+|..+.+..+      ..||  .|...+........++
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~-~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~~c~~llt  212 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVL-KCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLESCRKLLT  212 (384)
T ss_pred             ccccCccCccccccHhhhHHHh-cccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHHHHhhhcC
Confidence            467899999555444 444434 599999999999988643      3464  3555555554444433

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.13  E-value=0.13  Score=37.11  Aligned_cols=59  Identities=17%  Similarity=0.270  Sum_probs=43.3

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcceeec
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVILK  129 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~~~~~  129 (143)
                      .....|+|=--+|........+-.|||+|-..-+.+.  ....|++|.......+...+-+
T Consensus       109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~dvIvlNg  167 (293)
T KOG3113|consen  109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDDVIVLNG  167 (293)
T ss_pred             cceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccCeEeeCC
Confidence            4456799998888776554444449999999988874  3567999999888876654433

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

Probab=91.95  E-value=0.11  Score=38.57  Aligned_cols=52  Identities=21%  Similarity=0.564  Sum_probs=36.7

Q ss_pred             CCccccccccccCCCe-eeEcC-CCC---CcccHHhHHHHHhC--CCCCccccCccCCC
Q 032328           71 PVDCVVCLENFRMGDK-CRLLP-NCR---HSFHAQCIDSWLLK--TPICPICRTRVSPS  122 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~-v~~l~-~C~---H~FH~~Ci~~wl~~--~~~CP~CR~~i~~~  122 (143)
                      +..|-||.++..+... ....| .|+   +..|..|+..|+..  +..|..|.......
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~  136 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV  136 (323)
T ss_pred             CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence            5789999998664332 23445 243   57799999999984  55699998766544

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

Probab=91.45  E-value=0.049  Score=44.49  Aligned_cols=50  Identities=24%  Similarity=0.705  Sum_probs=38.9

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC---CCCccccCccCCCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT---PICPICRTRVSPSK  123 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~---~~CP~CR~~i~~~~  123 (143)
                      ...+|+||++.+.++   ..+ .|.|.|+..|+..-+...   ..||+|+..+....
T Consensus        20 k~lEc~ic~~~~~~p---~~~-kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~s   72 (684)
T KOG4362|consen   20 KILECPICLEHVKEP---SLL-KCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKRS   72 (684)
T ss_pred             hhccCCceeEEeecc---chh-hhhHHHHhhhhhceeeccCccccchhhhhhhhhhh
Confidence            356899999999886   344 499999999988766543   45999998877553

>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=91.00  E-value=0.96  Score=22.81  Aligned_cols=22  Identities=14%  Similarity=0.285  Sum_probs=8.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 032328            4 EILISLTLLFVGIAALVVIHVC   25 (143)
Q Consensus         4 ~il~~~~~~~~~~~~~~~~~~~   25 (143)
                      +++.+++..+..+++.++++.|
T Consensus         7 aIIv~V~vg~~iiii~~~~YaC   28 (38)
T PF02439_consen    7 AIIVAVVVGMAIIIICMFYYAC   28 (38)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444433333333333

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.

>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length

Probab=90.52  E-value=0.65  Score=25.53  Aligned_cols=48  Identities=21%  Similarity=0.617  Sum_probs=34.8

Q ss_pred             CCccccccccccCCC-eeeEcCCCCC--cccHHhHHHHHhCCCCCccccCccCCCC
Q 032328           71 PVDCVVCLENFRMGD-KCRLLPNCRH--SFHAQCIDSWLLKTPICPICRTRVSPSK  123 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~-~v~~l~~C~H--~FH~~Ci~~wl~~~~~CP~CR~~i~~~~  123 (143)
                      ...|-.|-.++..+. ...+   |.+  .|+.+|.+..|  +..||.|-.++...+
T Consensus         5 rpnCE~C~~dLp~~s~~A~I---CSfECTFC~~C~e~~l--~~~CPNCgGelv~RP   55 (57)
T PF06906_consen    5 RPNCECCDKDLPPDSPEAYI---CSFECTFCADCAETML--NGVCPNCGGELVRRP   55 (57)
T ss_pred             CCCccccCCCCCCCCCcceE---EeEeCcccHHHHHHHh--cCcCcCCCCccccCC
Confidence            456778888877665 3333   664  89999999976  466999988877553

This family contains a number of conserved cysteine residues and its function is unknown.

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

Probab=90.03  E-value=0.26  Score=41.12  Aligned_cols=54  Identities=11%  Similarity=0.110  Sum_probs=37.6

Q ss_pred             CCCccccccccccC---CCeeeEcCCCCCcccHHhHHHHHhC------CCCCccccCccCCCC
Q 032328           70 SPVDCVVCLENFRM---GDKCRLLPNCRHSFHAQCIDSWLLK------TPICPICRTRVSPSK  123 (143)
Q Consensus        70 ~~~~C~ICl~~~~~---~~~v~~l~~C~H~FH~~Ci~~wl~~------~~~CP~CR~~i~~~~  123 (143)
                      ..+.|.+|.-++..   +..+..+.+|+|-||..||..|...      +-.|++|..-+..+.
T Consensus        95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWs  157 (1134)
T KOG0825|consen   95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWS  157 (1134)
T ss_pred             cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhh
Confidence            45568888877765   2233333369999999999999854      234899988776553

>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A

Probab=89.90  E-value=0.83  Score=26.91  Aligned_cols=67  Identities=19%  Similarity=0.370  Sum_probs=22.1

Q ss_pred             CCCcccccccccc---CCCeeeEcCCCCCcccHHhHHHHH-hCCCCCccccCccCCCCcceeecCCCCCCcc
Q 032328           70 SPVDCVVCLENFR---MGDKCRLLPNCRHSFHAQCIDSWL-LKTPICPICRTRVSPSKVGVILKDGSSVSSD  137 (143)
Q Consensus        70 ~~~~C~ICl~~~~---~~~~v~~l~~C~H~FH~~Ci~~wl-~~~~~CP~CR~~i~~~~~~~~~~~~~~~~~~  137 (143)
                      +...|.||-++.-   +++.....-.|+---++.|.+-=. ..++.||-|+.+...... .....+++.++|
T Consensus         8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~ykr~kg-sp~V~gDeeedd   78 (80)
T PF14569_consen    8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYKRHKG-SPRVEGDEEEDD   78 (80)
T ss_dssp             SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B----TT-----TTS-----
T ss_pred             CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcccccC-CCCCCCCccccC
Confidence            5678999999874   333322222466666778876433 346789999987775533 333444444444

>PF15050 SCIMP: SCIMP protein

Probab=89.87  E-value=0.97  Score=28.89  Aligned_cols=32  Identities=22%  Similarity=0.503  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhccCccc
Q 032328            5 ILISLTLLFVGIAALVVIHVCVVGRAFRRGYEQ   37 (143)
Q Consensus         5 il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   37 (143)
                      |++++.++++++++.+ +++|++++.+|+....
T Consensus        10 iiLAVaII~vS~~lgl-IlyCvcR~~lRqGkkw   41 (133)
T PF15050_consen   10 IILAVAIILVSVVLGL-ILYCVCRWQLRQGKKW   41 (133)
T ss_pred             HHHHHHHHHHHHHHHH-HHHHHHHHHHHccccc
Confidence            4555555555554433 3445555555555443

>TIGR00622 ssl1 transcription factor ssl1

Probab=89.57  E-value=0.49  Score=30.02  Aligned_cols=45  Identities=20%  Similarity=0.332  Sum_probs=34.9

Q ss_pred             CccccccccccCC----------CeeeEcCCCCCcccHHhHHHHHhCCCCCcccc
Q 032328           72 VDCVVCLENFRMG----------DKCRLLPNCRHSFHAQCIDSWLLKTPICPICR  116 (143)
Q Consensus        72 ~~C~ICl~~~~~~----------~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR  116 (143)
                      ..|.-|+..|.+.          ......+.|++.|+.+|=.-+-+.--+||-|-
T Consensus        56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~  110 (112)
T TIGR00622        56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI  110 (112)
T ss_pred             CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence            4699999988653          22344567999999999888877777899995

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

>PLN02189 cellulose synthase

Probab=88.75  E-value=0.78  Score=39.59  Aligned_cols=55  Identities=24%  Similarity=0.388  Sum_probs=36.9

Q ss_pred             CCCCcccccccccc---CCCeeeEcCCCCCcccHHhHHHH-HhCCCCCccccCccCCCC
Q 032328           69 SSPVDCVVCLENFR---MGDKCRLLPNCRHSFHAQCIDSW-LLKTPICPICRTRVSPSK  123 (143)
Q Consensus        69 ~~~~~C~ICl~~~~---~~~~v~~l~~C~H~FH~~Ci~~w-l~~~~~CP~CR~~i~~~~  123 (143)
                      .+...|.||-+++.   +++.-+....|+---|+.|.+-= -..++.||-|+++-..-+
T Consensus        32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~r~k   90 (1040)
T PLN02189         32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYKRLK   90 (1040)
T ss_pred             ccCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchhhcc
Confidence            35668999999974   44444443346665788888431 123678999999888544

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

Probab=88.70  E-value=0.47  Score=25.52  Aligned_cols=42  Identities=29%  Similarity=0.615  Sum_probs=16.2

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-----CCCCccccCc
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-----TPICPICRTR  118 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-----~~~CP~CR~~  118 (143)
                      .|+|....+..  .++-. .|.|.-+.+ ++.|+..     .-.||.|.++
T Consensus         4 ~CPls~~~i~~--P~Rg~-~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    4 RCPLSFQRIRI--PVRGK-NCKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             B-TTTSSB-SS--EEEET-T--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eCCCCCCEEEe--CccCC-cCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            57888777655  33444 488852211 2234432     2359999763

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.

>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]

Probab=87.87  E-value=0.22  Score=36.21  Aligned_cols=52  Identities=29%  Similarity=0.574  Sum_probs=36.5

Q ss_pred             CCCccccccccccCCCeeeE-cC--CCCCcccHHhHHHHHhC---------CCCCccccCccCC
Q 032328           70 SPVDCVVCLENFRMGDKCRL-LP--NCRHSFHAQCIDSWLLK---------TPICPICRTRVSP  121 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~-l~--~C~H~FH~~Ci~~wl~~---------~~~CP~CR~~i~~  121 (143)
                      ...+|.+|.+++.+.+..+. .+  .|+-.+|..|+..-+..         ...||.|++.+.-
T Consensus       181 ~~~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~w  244 (276)
T KOG3005|consen  181 LNVECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLSW  244 (276)
T ss_pred             cchhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceeeH
Confidence            34689999999954444333 22  68889999999984421         2459999986553

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

Probab=87.84  E-value=0.55  Score=30.50  Aligned_cols=7  Identities=29%  Similarity=0.178  Sum_probs=2.9

Q ss_pred             hhhccCc
Q 032328           29 RAFRRGY   35 (143)
Q Consensus        29 ~~~~~~~   35 (143)
                      ...||++
T Consensus        22 ~~rRR~r   28 (130)
T PF12273_consen   22 HNRRRRR   28 (130)
T ss_pred             HHHHHhh
Confidence            3444433

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

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

Probab=87.77  E-value=0.32  Score=34.22  Aligned_cols=47  Identities=26%  Similarity=0.585  Sum_probs=36.1

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCcc
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRV  119 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i  119 (143)
                      +-..|.+|..-...+   +....||=.+|..|+...+++...||-|..-+
T Consensus       180 nlk~Cn~Ch~LvIqg---~rCg~c~i~~h~~c~qty~q~~~~cphc~d~w  226 (235)
T KOG4718|consen  180 NLKNCNLCHCLVIQG---IRCGSCNIQYHRGCIQTYLQRRDICPHCGDLW  226 (235)
T ss_pred             HHHHHhHhHHHhhee---eccCcccchhhhHHHHHHhcccCcCCchhccc
Confidence            445799999876654   33334777899999999999999999995443

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

Probab=87.17  E-value=0.27  Score=37.92  Aligned_cols=46  Identities=22%  Similarity=0.408  Sum_probs=32.4

Q ss_pred             CCccccccccccC--CCeeeEcCCCCCcccHHhHHHHHhCCCCCccccC
Q 032328           71 PVDCVVCLENFRM--GDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRT  117 (143)
Q Consensus        71 ~~~C~ICl~~~~~--~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~  117 (143)
                      -..|+.|.-.++.  |=...... |||.|++.|...|...+..|..|-+
T Consensus       306 wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~~~~~~~~~r  353 (384)
T KOG1812|consen  306 WRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTHNGECYECCR  353 (384)
T ss_pred             cCcCcccceeeeecCCcceEEee-ccccchhhcCcchhhCCccccCccc
Confidence            4568888766543  33344455 9999999999999888777754433

>smart00249 PHD PHD zinc finger

Probab=87.06  E-value=0.56  Score=23.91  Aligned_cols=31  Identities=19%  Similarity=0.416  Sum_probs=21.0

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHH
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDS  104 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~  104 (143)
                      .|.+|...... +.++.-..|+..||..|+..
T Consensus         1 ~C~~C~~~~~~-~~~i~C~~C~~~~H~~C~~~   31 (47)
T smart00249        1 YCSVCGKPDDG-GELLQCDGCDRWYHQTCLGP   31 (47)
T ss_pred             CcccCCCcCCC-CCEEECCCCCchhhhhhCCC
Confidence            37788877633 33344335999999999854

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

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=86.81  E-value=0.45  Score=23.87  Aligned_cols=26  Identities=35%  Similarity=0.737  Sum_probs=14.7

Q ss_pred             ccccccccccCCCe-------eeEcCCCCCccc
Q 032328           73 DCVVCLENFRMGDK-------CRLLPNCRHSFH   98 (143)
Q Consensus        73 ~C~ICl~~~~~~~~-------v~~l~~C~H~FH   98 (143)
                      .|+-|...|..++.       ....+.|+|.|.
T Consensus         4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~   36 (37)
T PF13719_consen    4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR   36 (37)
T ss_pred             ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence            57777777754432       233345666664

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=86.75  E-value=0.25  Score=41.07  Aligned_cols=44  Identities=27%  Similarity=0.580  Sum_probs=31.5

Q ss_pred             CCCccccccccccC-C---CeeeEcCCCCCcccHHhHHHHHhCCCCCccc
Q 032328           70 SPVDCVVCLENFRM-G---DKCRLLPNCRHSFHAQCIDSWLLKTPICPIC  115 (143)
Q Consensus        70 ~~~~C~ICl~~~~~-~---~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~C  115 (143)
                      .+..|.-|.+.... +   +.+.+.. |||+||+.|+..-..++. |-.|
T Consensus       783 ~e~rc~~c~~~~l~~~~~~~~~~v~~-c~h~yhk~c~~~~~~~~~-~~~~  830 (846)
T KOG2066|consen  783 VEERCSSCFEPNLPSGAAFDSVVVFH-CGHMYHKECLMMESLRNA-CNIE  830 (846)
T ss_pred             ehhhhhhhcccccccCcccceeeEEE-ccchhhhcccccHHHhcc-cChh
Confidence            34579999988652 2   4556665 999999999987666654 5444

>PLN02400 cellulose synthase

Probab=86.36  E-value=1  Score=39.03  Aligned_cols=54  Identities=24%  Similarity=0.460  Sum_probs=35.1

Q ss_pred             CCCcccccccccc---CCCeeeEcCCCCCcccHHhHHH-HHhCCCCCccccCccCCCC
Q 032328           70 SPVDCVVCLENFR---MGDKCRLLPNCRHSFHAQCIDS-WLLKTPICPICRTRVSPSK  123 (143)
Q Consensus        70 ~~~~C~ICl~~~~---~~~~v~~l~~C~H~FH~~Ci~~-wl~~~~~CP~CR~~i~~~~  123 (143)
                      +...|.||-++..   +++.-+....|+-=-|+.|.+- .-..++.||-|+.+-..-+
T Consensus        35 ~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYkR~K   92 (1085)
T PLN02400         35 NGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYRRHK   92 (1085)
T ss_pred             CCceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCcccccc
Confidence            5568999999974   4444433334555478888842 1123678999999988553

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

Probab=85.94  E-value=0.41  Score=37.37  Aligned_cols=34  Identities=29%  Similarity=0.699  Sum_probs=28.6

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHh
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL  107 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~  107 (143)
                      ++-.|+||..-|.++   +++| |+|-.|.-|-..-+.
T Consensus         3 eelkc~vc~~f~~ep---iil~-c~h~lc~~ca~~~~~   36 (699)
T KOG4367|consen    3 EELKCPVCGSFYREP---IILP-CSHNLCQACARNILV   36 (699)
T ss_pred             ccccCceehhhccCc---eEee-cccHHHHHHHHhhcc
Confidence            456799999999887   8888 999999999876553

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

Probab=85.11  E-value=0.2  Score=40.48  Aligned_cols=53  Identities=30%  Similarity=0.715  Sum_probs=31.1

Q ss_pred             CCCCcccccccc-----ccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcc
Q 032328           69 SSPVDCVVCLEN-----FRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG  125 (143)
Q Consensus        69 ~~~~~C~ICl~~-----~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~  125 (143)
                      .....|.+|-..     |+ .+.++..-.|+++||++|...   ....||.|-+.-..++.+
T Consensus       509 ~~gfiCe~Cq~~~iiyPF~-~~~~~rC~~C~avfH~~C~~r---~s~~CPrC~R~q~r~~~~  566 (580)
T KOG1829|consen  509 GKGFICELCQHNDIIYPFE-TRNTRRCSTCLAVFHKKCLRR---KSPCCPRCERRQKRAEQG  566 (580)
T ss_pred             cCeeeeeeccCCCcccccc-cccceeHHHHHHHHHHHHHhc---cCCCCCchHHHHHHhhcc
Confidence            345678888211     22 223333334999999999855   234499996555444433

>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=84.95  E-value=0.59  Score=24.85  Aligned_cols=43  Identities=26%  Similarity=0.510  Sum_probs=28.0

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHh------CCCCCcccc
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL------KTPICPICR  116 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~------~~~~CP~CR  116 (143)
                      .|.||...-..+ .+..-..|+..||..|+..=..      ..-.||.|+
T Consensus         1 ~C~vC~~~~~~~-~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~   49 (51)
T PF00628_consen    1 YCPVCGQSDDDG-DMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR   49 (51)
T ss_dssp             EBTTTTSSCTTS-SEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred             eCcCCCCcCCCC-CeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence            388999844444 4444445999999999866432      134588775

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 the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....

>PLN02436 cellulose synthase A

Probab=84.66  E-value=1.8  Score=37.65  Aligned_cols=54  Identities=22%  Similarity=0.434  Sum_probs=36.3

Q ss_pred             CCCccccccccc---cCCCeeeEcCCCCCcccHHhHHHHH-hCCCCCccccCccCCCC
Q 032328           70 SPVDCVVCLENF---RMGDKCRLLPNCRHSFHAQCIDSWL-LKTPICPICRTRVSPSK  123 (143)
Q Consensus        70 ~~~~C~ICl~~~---~~~~~v~~l~~C~H~FH~~Ci~~wl-~~~~~CP~CR~~i~~~~  123 (143)
                      ....|.||-++.   .+++.-+....|+---|+.|.+-=- ..++.||-|+++-..-.
T Consensus        35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~r~k   92 (1094)
T PLN02436         35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYKRIK   92 (1094)
T ss_pred             CCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchhhcc
Confidence            456899999996   4455544433455557888884311 23677999999888443

>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]

Probab=84.51  E-value=1.7  Score=32.68  Aligned_cols=53  Identities=21%  Similarity=0.524  Sum_probs=35.6

Q ss_pred             CCCCccccccccc---------cCC-------CeeeEcCCCCCcccHHhHHHHHhC---------CCCCccccCccCCC
Q 032328           69 SSPVDCVVCLENF---------RMG-------DKCRLLPNCRHSFHAQCIDSWLLK---------TPICPICRTRVSPS  122 (143)
Q Consensus        69 ~~~~~C~ICl~~~---------~~~-------~~v~~l~~C~H~FH~~Ci~~wl~~---------~~~CP~CR~~i~~~  122 (143)
                      ....+|++|+..=         +.+       -.....| |||+.-.+=..-|-+.         +..||.|-..+.-+
T Consensus       339 ~~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~P-CGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge  416 (429)
T KOG3842|consen  339 QRERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNP-CGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGE  416 (429)
T ss_pred             cccCcCCeeeeecceeeeeccccceeEecCCCcccccCC-cccccchhhhhHhhcCcCCCccccccccCcchhhhhccC
Confidence            4567899999761         000       0112345 9999888888889754         34599998887754

>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=84.38  E-value=3.6  Score=20.76  Aligned_cols=28  Identities=11%  Similarity=0.199  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcc
Q 032328            6 LISLTLLFVGIAALVVIHVCVVGRAFRR   33 (143)
Q Consensus         6 l~~~~~~~~~~~~~~~~~~~~~~~~~~~   33 (143)
                      +..++.+.++++++.+..+++..++.+.
T Consensus         6 IaIIv~V~vg~~iiii~~~~YaCcykk~   33 (38)
T PF02439_consen    6 IAIIVAVVVGMAIIIICMFYYACCYKKH   33 (38)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHccc
Confidence            4445566666666666666665544443

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.

>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit

Probab=82.17  E-value=2.5  Score=36.78  Aligned_cols=54  Identities=20%  Similarity=0.407  Sum_probs=35.5

Q ss_pred             CCCcccccccccc---CCCeeeEcCCCCCcccHHhHHH-HHhCCCCCccccCccCCCC
Q 032328           70 SPVDCVVCLENFR---MGDKCRLLPNCRHSFHAQCIDS-WLLKTPICPICRTRVSPSK  123 (143)
Q Consensus        70 ~~~~C~ICl~~~~---~~~~v~~l~~C~H~FH~~Ci~~-wl~~~~~CP~CR~~i~~~~  123 (143)
                      +...|.||-++..   +|+.-+....|+-=-|+.|.+- .-..++.||-|+++-..-+
T Consensus        16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYkr~k   73 (1079)
T PLN02638         16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYKRHK   73 (1079)
T ss_pred             CCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchhhhc
Confidence            4568999999974   4444443334554478888843 1133678999999888544

>PF15102 TMEM154: TMEM154 protein family

Probab=81.08  E-value=0.48  Score=31.42  Aligned_cols=6  Identities=33%  Similarity=1.199  Sum_probs=2.6

Q ss_pred             HHHHHh
Q 032328          102 IDSWLL  107 (143)
Q Consensus       102 i~~wl~  107 (143)
                      +++|..
T Consensus       130 ldkwm~  135 (146)
T PF15102_consen  130 LDKWMN  135 (146)
T ss_pred             HHhHHH
Confidence            344543

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

Probab=80.91  E-value=1.3  Score=33.22  Aligned_cols=47  Identities=21%  Similarity=0.325  Sum_probs=35.4

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC---CCCCccccC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK---TPICPICRT  117 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~---~~~CP~CR~  117 (143)
                      .-..||+=-++-.+++....+. |||+--++-+++.-+.   ...||.|-.
T Consensus       335 s~FiCPVlKe~~t~ENpP~ml~-CgHVIskeal~~LS~nG~~~FKCPYCP~  384 (396)
T COG5109         335 SLFICPVLKELCTDENPPVMLE-CGHVISKEALSVLSQNGVLSFKCPYCPE  384 (396)
T ss_pred             ceeeccccHhhhcccCCCeeee-ccceeeHHHHHHHhhcCcEEeeCCCCCc
Confidence            4457998888877777777777 9999999999885433   345999943

>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association

Probab=80.91  E-value=0.58  Score=25.45  Aligned_cols=14  Identities=21%  Similarity=0.743  Sum_probs=7.5

Q ss_pred             CCCccccCccCCCC
Q 032328          110 PICPICRTRVSPSK  123 (143)
Q Consensus       110 ~~CP~CR~~i~~~~  123 (143)
                      ..||+|.+++....
T Consensus        21 ~~CPlC~r~l~~e~   34 (54)
T PF04423_consen   21 GCCPLCGRPLDEEH   34 (54)
T ss_dssp             EE-TTT--EE-HHH
T ss_pred             CcCCCCCCCCCHHH
Confidence            37999999988653

The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.

>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=80.61  E-value=0.96  Score=28.13  Aligned_cols=18  Identities=33%  Similarity=0.285  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 032328            6 LISLTLLFVGIAALVVIH   23 (143)
Q Consensus         6 l~~~~~~~~~~~~~~~~~   23 (143)
                      +++++.++.++.++..++
T Consensus        65 li~lls~v~IlVily~Iy   82 (101)
T PF06024_consen   65 LISLLSFVCILVILYAIY   82 (101)
T ss_pred             HHHHHHHHHHHHHHhhhe
Confidence            334444443333333333

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=80.55  E-value=0.93  Score=20.89  Aligned_cols=23  Identities=22%  Similarity=0.605  Sum_probs=11.4

Q ss_pred             ccccccccccCCCeeeEcCCCCCcc
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSF   97 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~F   97 (143)
                      .|+-|-.++...  ....|.|||.|
T Consensus         2 ~CP~C~~~V~~~--~~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCPECGAEVPES--AKFCPHCGYDF   24 (26)
T ss_pred             cCCCCcCCchhh--cCcCCCCCCCC
Confidence            356666554332  23334566665

Several members are annotated as putative helicases.

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

Probab=80.32  E-value=1.1  Score=25.48  Aligned_cols=12  Identities=25%  Similarity=0.919  Sum_probs=8.7

Q ss_pred             cccHHhHHHHHh
Q 032328           96 SFHAQCIDSWLL  107 (143)
Q Consensus        96 ~FH~~Ci~~wl~  107 (143)
                      -||+.|+.+|+.
T Consensus        11 gFCRNCLskWy~   22 (68)
T PF06844_consen   11 GFCRNCLSKWYR   22 (68)
T ss_dssp             S--HHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            499999999985

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	143
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		3e-09
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		2e-08
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		2e-06
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		1e-05
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		2e-05
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		9e-05
4ayc_B	138	Rnf8 Ring Domain Structure Length = 138		1e-04
4ayc_A	138	Rnf8 Ring Domain Structure Length = 138		1e-04
4epo_C	149	Crystal Structure Of Rnf8 Bound To The Ubc13MMS2 HE		2e-04

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 23/48 (47%), Positives = 29/48 (60%)
Query: 72  VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRV 119
           V+C VCL     G++ R LP C H FHA+C+D WL     CP+CR  V
Sbjct: 6   VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 49  SSDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK 108
           SS    Q+P + +    +  S    CVVC+ +F      R+LP C H FHA+C+D WL  
Sbjct: 2   SSGSSGQLPSYRFNPN-NHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKA 59
Query: 109 TPICPICRTRVSPS 122
              CPICR    PS
Sbjct: 60  NRTCPICRADSGPS 73

>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 = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 70  SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS 120
           S ++C VC E++ +G+  R LP C H FH  CI  WL +   CP+CR  ++
Sbjct: 14  SGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLT 63

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS 120
           C +CL     G+  R LP C H FH  C+D WL+    CPICR  + 
Sbjct: 17  CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIE 62

>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 = 2e-05,   Method: Compositional matrix adjust.
 Identities = 19/46 (41%), Positives = 29/46 (63%), Gaps = 1/46 (2%)
Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRV 119
           C VCLE+F+  D+  + P C+H+FH +C+  WL    +CP+C   V
Sbjct: 18  CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPV 62

>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 = 42.4 bits (98), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSP 121
           C +C   +  GD    LP C H FH  C+  WL K+  CP+CR    P
Sbjct: 43  CPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCMFPP 89

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 9/75 (12%)
Query: 69  SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVIL 128
            + + C++C E F       +  NC HSF + CI+ W+ +   CPICR  +      ++L
Sbjct: 51  ENELQCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVL 106
Query: 129 KDG-----SSVSSDV 138
            +      +++SS+V
Sbjct: 107 DNXINKMVNNLSSEV 121

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 69  SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVIL 128
            + + C++C E F       +  NC HSF + CI+ W+ +   CPICR  +      ++L
Sbjct: 51  ENELQCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVL 106
Query: 129 KD 130
            +
Sbjct: 107 DN 108

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 69  SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVIL 128
            + + C++C E F       +  NC HSF + CI+ W+ +   CPICR  +      ++L
Sbjct: 62  ENELQCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVL 117
Query: 129 KD 130
            +
Sbjct: 118 DN 119

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	143
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	2e-25
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	2e-21
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	6e-21
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	9e-19
2ect_A	78	Ring finger protein 126; metal binding protein, st	1e-17
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	3e-17
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	7e-16
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	5e-15
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	3e-13
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	1e-12
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	9e-12
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	1e-10
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	2e-10
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	4e-10
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	6e-10
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	3e-09
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	4e-09
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	1e-08
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-08
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	3e-08
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	8e-08
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	1e-07
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	1e-07
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	5e-07
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	6e-07
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	7e-07
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-06
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-05
3nw0_A	238	Non-structural maintenance of chromosomes element	2e-06
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	1e-05
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	2e-05
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	4e-05
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	5e-05
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	1e-04
1z6u_A	150	NP95-like ring finger protein isoform B; structura	1e-04
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	3e-04
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	4e-04
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	7e-04
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	9e-04

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

 Score = 91.2 bits (227), Expect = 2e-25
 Identities = 29/74 (39%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 49  SSDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK 108
           SS    Q+P + +    +  S    CVVC+ +F      R+LP C H FHA+C+D WL  
Sbjct: 2   SSGSSGQLPSYRFNPN-NHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKA 59

Query: 109 TPICPICRTRVSPS 122
              CPICR    PS
Sbjct: 60  NRTCPICRADSGPS 73

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

 Score = 81.2 bits (201), Expect = 2e-21
 Identities = 21/73 (28%), Positives = 30/73 (41%), Gaps = 1/73 (1%)

Query: 49  SSDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK 108
           S + +  +P              + C +C   +  GD    LP C H FH  C+  WL K
Sbjct: 18  SKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQK 76

Query: 109 TPICPICRTRVSP 121
           +  CP+CR    P
Sbjct: 77  SGTCPVCRCMFPP 89

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

 Score = 79.2 bits (196), Expect = 6e-21
 Identities = 23/49 (46%), Positives = 29/49 (59%)

Query: 71  PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRV 119
            V+C VCL     G++ R LP C H FHA+C+D WL     CP+CR  V
Sbjct: 5   GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 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 = 73.9 bits (182), Expect = 9e-19
 Identities = 20/50 (40%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 73  DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPS 122
            C +CL     G+  R LP C H FH  C+D WL+    CPICR  +   
Sbjct: 16  KCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQ 64

>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 = 70.9 bits (174), Expect = 1e-17
 Identities = 20/50 (40%), Positives = 30/50 (60%), Gaps = 1/50 (2%)

Query: 72  VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSP 121
           ++C VC E++ +G+  R LP C H FH  CI  WL +   CP+CR  ++ 
Sbjct: 16  LECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTG 64

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

 Score = 70.2 bits (172), Expect = 3e-17
 Identities = 19/50 (38%), Positives = 29/50 (58%), Gaps = 1/50 (2%)

Query: 73  DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPS 122
            C VCLE+F+  D+  + P C+H+FH +C+  WL    +CP+C   V   
Sbjct: 17  LCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQL 65

>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 = 66.1 bits (162), Expect = 7e-16
 Identities = 14/53 (26%), Positives = 20/53 (37%)

Query: 68  GSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS 120
            S    C +CLE+         +  C H  H  C +  L +   CP+C    S
Sbjct: 2   SSGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS 54

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

 Score = 64.5 bits (157), Expect = 5e-15
 Identities = 14/52 (26%), Positives = 24/52 (46%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG 125
           C+ C    +  D   +   C HSFH  C+  W+ +   CP+C+      ++G
Sbjct: 29  CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIG 80

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

 Score = 59.7 bits (145), Expect = 3e-13
 Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 3/47 (6%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS 120
           C +CLE+    +    LP C H+F   CI  W+ + P CP+C+  V 
Sbjct: 8   CPICLEDPS--NYSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVE 51

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

 Score = 58.6 bits (142), Expect = 1e-12
 Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 5/51 (9%)

Query: 73  DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSK 123
           +C +C++         +LP C HSF  +CID W  +   CPICR +++ + 
Sbjct: 17  ECCICMDGR----ADLILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGAN 62

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

 Score = 56.1 bits (135), Expect = 9e-12
 Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

Query: 63  AAADRGSSPVDCVVCLENFRMGDKCRLLP---NCRHSFHAQCIDSWLLKTPICPICRTRV 119
               R S  V C +C++ +    +   L     C H F +QC+   L     CP CR ++
Sbjct: 7   GTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66

Query: 120 SP 121
           + 
Sbjct: 67  NH 68

>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 = 52.9 bits (127), Expect = 1e-10
 Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 3/65 (4%)

Query: 63  AAADRGSSPVDCVVCLENFRMGDKCRLLP---NCRHSFHAQCIDSWLLKTPICPICRTRV 119
               R S  V C +C++ +    +   L     C H F +QC+   L     CP CR ++
Sbjct: 2   TTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61

Query: 120 SPSKV 124
           +  + 
Sbjct: 62  NHKRY 66

>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 = 56.3 bits (135), Expect = 2e-10
 Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 50  SDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK- 108
             D  ++   +Y+   + GS+   C +C EN +     ++ P C H     C+ SW    
Sbjct: 311 PQDHIKVTQEQYELYCEMGSTFQLCKICAENDK---DVKIEP-CGHLMCTSCLTSWQESE 366

Query: 109 TPICPICRTRVSPSKVGVI 127
              CP CR  +  ++  V+
Sbjct: 367 GQGCPFCRCEIKGTEPIVV 385

>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 = 52.6 bits (126), Expect = 4e-10
 Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 4/52 (7%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT-PICPICRTRVSPSKV 124
           C +C+E  R     RL P+C       CI  WL +    CP CR  +   ++
Sbjct: 25  CFICMEKLR---DARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLREL 73

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

 Score = 51.3 bits (123), Expect = 6e-10
 Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 3/56 (5%)

Query: 72  VDCVVCLENFR---MGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKV 124
           V C +C++ +       +  +   C H F +QC+   L     CP CR +++  + 
Sbjct: 4   VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY 59

>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 = 50.6 bits (120), Expect = 3e-09
 Identities = 12/50 (24%), Positives = 17/50 (34%)

Query: 76  VCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG 125
               +    +       C H+FH  CI  WL    +CP+        K G
Sbjct: 67  ANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYG 116

>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 = 49.8 bits (118), Expect = 4e-09
 Identities = 12/50 (24%), Positives = 17/50 (34%)

Query: 76  VCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG 125
               +    +       C H+FH  CI  WL    +CP+        K G
Sbjct: 56  ANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYG 105

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

 Score = 47.8 bits (114), Expect = 1e-08
 Identities = 11/50 (22%), Positives = 17/50 (34%), Gaps = 3/50 (6%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSK 123
           C +C            +  C H+F   CI      +  CP C   V  ++
Sbjct: 18  CSICKGYLI---DATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQ 64

>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 = 48.3 bits (115), Expect = 2e-08
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSK 123
           CV+C   F        +  C HSF   CI  +L  +  CPIC  +V  ++
Sbjct: 18  CVLCGGYFI---DATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTR 64

>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 = 46.8 bits (111), Expect = 3e-08
 Identities = 11/47 (23%), Positives = 14/47 (29%), Gaps = 5/47 (10%)

Query: 73  DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL--KTPICPICRT 117
            C +C      G  C     C    H  C+  +      P CP C  
Sbjct: 17  ICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCND 60

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

 Score = 46.0 bits (109), Expect = 8e-08
 Identities = 14/49 (28%), Positives = 18/49 (36%), Gaps = 4/49 (8%)

Query: 71  PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRV 119
           P  C +C + F+  +       CRH F   C       TP C IC    
Sbjct: 15  PFRCFICRQAFQ--NPVVT--KCRHYFCESCALEHFRATPRCYICDQPT 59

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

 Score = 45.9 bits (109), Expect = 1e-07
 Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 3/50 (6%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSK 123
           C +C E F       ++P C H++ + CI  +L     CP C   V+   
Sbjct: 25  CGICFEYFN---IAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPD 71

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

 Score = 47.0 bits (111), Expect = 1e-07
 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 4/57 (7%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVILKD 130
           C++C E F       +  NC HSF + CI+ W+ +   CPICR  +      ++L +
Sbjct: 67  CIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDN 119

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

 Score = 43.7 bits (103), Expect = 5e-07
 Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 4/52 (7%)

Query: 73  DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKV 124
           +C +CL+          LP C+H F   C+         C +CR  +    +
Sbjct: 17  ECAICLQTCVH---PVSLP-CKHVFCYLCVKGASWLGKRCALCRQEIPEDFL 64

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

 Score = 46.4 bits (109), Expect = 6e-07
 Identities = 15/74 (20%), Positives = 26/74 (35%), Gaps = 16/74 (21%)

Query: 72  VDCVVCLENFRMGDKCRLL----PNCRHSFHAQCIDSWLLKTP-----------ICPICR 116
           + C +C      G +  L+      C    HA C++ W                 CP C+
Sbjct: 309 LRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCK 368

Query: 117 TRVSPSKVGVILKD 130
            ++S +    +L D
Sbjct: 369 AKLS-TSFAALLND 381

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

 Score = 44.4 bits (104), Expect = 7e-07
 Identities = 14/64 (21%), Positives = 23/64 (35%), Gaps = 19/64 (29%)

Query: 73  DCVVCLENFRMG--------------DKCRLLPNCRHSFHAQCIDSWLLK-----TPICP 113
           DC++C+E   +                    L  C H+FH  C+ +         +  CP
Sbjct: 27  DCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCP 86

Query: 114 ICRT 117
            C+T
Sbjct: 87  SCKT 90

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

 Score = 44.4 bits (104), Expect = 1e-06
 Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 3/60 (5%)

Query: 65  ADRGSSPVDCVVCLENFRMGDKCRLLP---NCRHSFHAQCIDSWLLKTPICPICRTRVSP 121
              GS  V C +C++ +    +   L     C H F +QC+   L     CP CR +++ 
Sbjct: 1   GAMGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH 60

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

 Score = 41.3 bits (96), Expect = 1e-05
 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 3/74 (4%)

Query: 54  KQIPCFEYKAAADRGSSPVDCVVCLENFR---MGDKCRLLPNCRHSFHAQCIDSWLLKTP 110
           ++    +       GS  V C +C++ +       +  +   C H F +QC+   L    
Sbjct: 55  RKKINHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN 114

Query: 111 ICPICRTRVSPSKV 124
            CP CR +++  + 
Sbjct: 115 TCPTCRKKINHKRY 128

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

 Score = 44.7 bits (105), Expect = 2e-06
 Identities = 13/68 (19%), Positives = 20/68 (29%), Gaps = 11/68 (16%)

Query: 52  DLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWL--LKT 109
           +++Q     Y        +   C +C      G  C     C    H  C+  +      
Sbjct: 167 EMEQYIRETY------PDAVKICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAE 217

Query: 110 PICPICRT 117
           P CP C  
Sbjct: 218 PRCPHCND 225

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

 Score = 39.7 bits (93), Expect = 1e-05
 Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 7/55 (12%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVIL 128
           C  C    +     +LLP C H+  + C+++  ++   CPIC+           L
Sbjct: 9   CQQCQAEAK---CPKLLP-CLHTLCSGCLEASGMQ---CPICQAPWPLGADTPAL 56

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

 Score = 39.3 bits (92), Expect = 2e-05
 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 5/50 (10%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK--TPICPICRTRVSP 121
           C++C +         ++P C +S+  +CI + LL+     CP C      
Sbjct: 18  CLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS 64

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

 Score = 38.9 bits (90), Expect = 4e-05
 Identities = 13/60 (21%), Positives = 19/60 (31%), Gaps = 1/60 (1%)

Query: 66  DRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPSKV 124
           D    PV+C +C+E   + D       C +     C          +CP CR        
Sbjct: 6   DAKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPA 65

>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 = 39.5 bits (92), Expect = 5e-05
 Identities = 13/51 (25%), Positives = 19/51 (37%), Gaps = 5/51 (9%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKV 124
           C  C    R   +   L  C H F + C+    + T  CP+C T      +
Sbjct: 25  CSRCTNILR---EPVCLGGCEHIFCSNCVSDC-IGTG-CPVCYTPAWIQDL 70

>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 = 38.8 bits (90), Expect = 1e-04
 Identities = 12/51 (23%), Positives = 18/51 (35%), Gaps = 5/51 (9%)

Query: 73  DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPI-CPICRTRVSPS 122
            C+ C E      +      C+H+    C+D         CP CR  +  S
Sbjct: 54  QCICCQELVF---RPITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGRS 100

>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 = 38.8 bits (90), Expect = 1e-04
 Identities = 18/88 (20%), Positives = 28/88 (31%), Gaps = 18/88 (20%)

Query: 46  KMISSDDLKQIPCFEYKAAADRGSSPVD-------CVVCLENFRMGDKCRLLP---NCRH 95
            +I  D   Q    E  +    G + +        CV C E           P    C H
Sbjct: 46  HLIREDCQNQKLWDEVLSHLVEGPNFLKKLEQSFMCVCCQELVYQ-------PVTTECFH 98

Query: 96  SFHAQCID-SWLLKTPICPICRTRVSPS 122
           +    C+  S+  +   CP CR  +  +
Sbjct: 99  NVCKDCLQRSFKAQVFSCPACRHDLGQN 126

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

 Score = 36.6 bits (85), Expect = 3e-04
 Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 3/54 (5%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWL---LKTPICPICRTRVSPSKV 124
           C +C+E+F        L +C H+   QC++  L   +    CP C      + +
Sbjct: 18  CPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITSL 71

>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 = 37.6 bits (87), Expect = 4e-04
 Identities = 13/50 (26%), Positives = 19/50 (38%), Gaps = 4/50 (8%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCID-SWLLKTPICPICRTRVSPS 122
           C +CL+  +          C H F A CI  +       CP CR ++   
Sbjct: 57  CPICLDMLK---NTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSK 103

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

 Score = 35.1 bits (81), Expect = 7e-04
 Identities = 12/53 (22%), Positives = 17/53 (32%), Gaps = 5/53 (9%)

Query: 73  DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPSKV 124
            C  C               C H F   C+ + L   +P C  C+  +   KV
Sbjct: 17  KCEKCHLVLC----SPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDKV 65

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

 Score = 35.5 bits (82), Expect = 9e-04
 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 5/50 (10%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK--TPICPICRTRVSP 121
           C++C +         ++P C +S+  +CI + LL+     CP C      
Sbjct: 16  CLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS 62

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	143
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.87
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.8
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.77
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.76
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.76
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.76
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.75
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.69
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.69
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.69
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.68
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.68
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.68
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.67
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.66
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.65
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.65
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.62
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.61
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.61
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.6
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.59
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.58
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.57
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.56
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.55
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.54
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.54
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.53
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.52
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.52
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.51
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.5
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.48
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.48
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.47
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.46
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.45
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.43
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.42
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.42
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.41
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.38
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.37
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.36
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.36
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.36
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.35
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.34
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.34
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.32
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.31
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.31
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.31
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.3
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.26
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.2
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	99.2
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.14
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.13
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.11
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	99.1
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.08
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.08
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.06
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.99
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.98
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.92
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.82
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.8
3nw0_A	238	Non-structural maintenance of chromosomes element	98.68
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.61
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	97.07
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	97.05
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	96.8
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	96.07
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	95.83
1we9_A	64	PHD finger family protein; structural genomics, PH	95.48
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	95.18
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	95.17
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	94.96
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	94.88
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	94.85
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	94.83
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	94.73
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	94.56
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	94.48
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	94.48
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	93.86
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	93.64
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	93.63
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	93.62
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	93.38
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	93.32
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	93.29
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	93.14
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	92.99
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	92.42
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	92.25
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	91.52
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	91.32
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	90.95
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	90.71
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	90.58
2yt5_A	66	Metal-response element-binding transcription facto	90.45
1z60_A	59	TFIIH basal transcription factor complex P44 subun	90.36
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	90.27
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	90.23
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	90.09
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	88.43
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	88.29
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	87.63
1wem_A	76	Death associated transcription factor 1; structura	87.39
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	87.2
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	86.7
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	86.08
1weu_A	91	Inhibitor of growth family, member 4; structural g	85.62
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	82.86
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	82.58
1wfk_A	88	Zinc finger, FYVE domain containing 19; riken stru	82.1
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	81.95
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	81.94
1vfy_A	73	Phosphatidylinositol-3-phosphate binding FYVE doma	81.44
1wew_A	78	DNA-binding family protein; structural genomics, P	81.1
3a1b_A	159	DNA (cytosine-5)-methyltransferase 3A, histone H3;	80.99
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	80.79
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	80.64
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	80.23

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

Probab=99.87  E-value=5.5e-22  Score=121.38  Aligned_cols=83  Identities=25%  Similarity=0.565  Sum_probs=73.6

Q ss_pred             CCCCCCCCCCCChHHhhcCCeeeecccccCCCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccC
Q 032328           38 SGFAQGGFKMISSDDLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRT  117 (143)
Q Consensus        38 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~  117 (143)
                      .........+++++.+..+|...+.........+..|+||+++|..++.+..+| |||.||..||.+|+..+.+||+||.
T Consensus         7 ~~~~~~~~~~~s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~Cr~   85 (91)
T 2l0b_A            7 HHSHMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRC   85 (91)
T ss_dssp             CSCCSSCCCCCCHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTTCC
T ss_pred             cCCCCcCCCCCCHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCcCc
Confidence            345666788899999999999998876666667889999999999999999999 9999999999999999999999999


Q ss_pred             ccCC
Q 032328          118 RVSP  121 (143)
Q Consensus       118 ~i~~  121 (143)
                      ++..
T Consensus        86 ~~~~   89 (91)
T 2l0b_A           86 MFPP   89 (91)
T ss_dssp             BSSC
T ss_pred             cCCC
Confidence            8865

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

Probab=99.80  E-value=1.9e-20  Score=110.55  Aligned_cols=69  Identities=39%  Similarity=0.914  Sum_probs=58.1

Q ss_pred             HhhcCCeeeecccccCCCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCC
Q 032328           52 DLKQIPCFEYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        52 ~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      .+.++|..+++... ...++..|+||++++..++.+..++ |+|.||..|+.+|+..+.+||+||.++...
T Consensus         5 ~i~~lp~~~~~~~~-~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A            5 SSGQLPSYRFNPNN-HQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             CCSSCCCEEBCSSS-CSSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             hHhhCCcEEecCcc-ccCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            45567777766533 3346778999999999999999999 999999999999999999999999998765

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

Probab=99.77  E-value=2.9e-19  Score=99.23  Aligned_cols=51  Identities=45%  Similarity=1.108  Sum_probs=46.6

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS  120 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~  120 (143)
                      ++.+|+||++++..++.+..++.|||.||.+|+.+|+..+.+||+||.++.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            467899999999998888888779999999999999999999999999874

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

Probab=99.76  E-value=7.5e-19  Score=104.33  Aligned_cols=58  Identities=36%  Similarity=0.917  Sum_probs=51.8

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCccee
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVI  127 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~~~  127 (143)
                      .....|+||++.|..++.+..++ |+|.||..||.+|+..+.+||+||.++........
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   70 (78)
T 2ect_A           13 GSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATN   70 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSCCC
T ss_pred             CCCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCccCCcccCCC
Confidence            45678999999999988888888 99999999999999999999999999998765543

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

Probab=99.76  E-value=9.1e-19  Score=102.95  Aligned_cols=54  Identities=35%  Similarity=0.859  Sum_probs=49.0

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSK  123 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~  123 (143)
                      ..+..|+||++.+..++.+..++ |+|.||..|+.+|+..+.+||+||.++....
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA   66 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSSCC
T ss_pred             CCCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCccccccc
Confidence            45678999999999998888888 9999999999999999899999999997653

>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=99.76  E-value=8.8e-19  Score=101.67  Aligned_cols=54  Identities=37%  Similarity=0.970  Sum_probs=49.1

Q ss_pred             CCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCC
Q 032328           68 GSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      ......|+||++.+..++.+..++ |||.||..|+.+|+..+.+||+||..+...
T Consensus        11 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           11 EDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             TTCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             CCCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            346678999999999888888898 999999999999999999999999999875

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

Probab=99.75  E-value=4.6e-19  Score=106.06  Aligned_cols=55  Identities=24%  Similarity=0.621  Sum_probs=44.2

Q ss_pred             CCCccccccccccC-----------CCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCc
Q 032328           70 SPVDCVVCLENFRM-----------GDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKV  124 (143)
Q Consensus        70 ~~~~C~ICl~~~~~-----------~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~  124 (143)
                      +++.|+||++++.+           ++.++.++.|||.||.+||.+|+..+.+||+||+++..+++
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~~   79 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRI   79 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEEEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchhhc
Confidence            45668888887754           45556665699999999999999999999999999876643

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

Probab=99.69  E-value=1e-17  Score=97.52  Aligned_cols=57  Identities=25%  Similarity=0.601  Sum_probs=48.3

Q ss_pred             CCCCccccccccccCC----CeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcce
Q 032328           69 SSPVDCVVCLENFRMG----DKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGV  126 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~----~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~~  126 (143)
                      .++..|+||++.+.++    +.+..++ |||.||..|+.+|+..+.+||+||.++...++..
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   68 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHP   68 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSCCC
T ss_pred             CCCCCCcccChhhhccccccCCeEeCC-CCChHhHHHHHHHHHcCCCCCCCCCccChhheee
Confidence            4567899999998763    5556777 9999999999999999999999999999776554

>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=99.69  E-value=1.5e-17  Score=104.08  Aligned_cols=54  Identities=24%  Similarity=0.519  Sum_probs=45.0

Q ss_pred             CCCCccccccccccCC---------------CeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCC
Q 032328           69 SSPVDCVVCLENFRMG---------------DKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSK  123 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~---------------~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~  123 (143)
                      .+++.|+||++.|.+.               ..+..++ |+|.||.+||.+|+..+.+||+||+++..+.
T Consensus        35 ~~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~~~~  103 (106)
T 3dpl_R           35 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEFQK  103 (106)
T ss_dssp             SCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCCEEE
T ss_pred             CCCCCCccCChhHhCcCchhhccccccCCccceEeecc-cCcEECHHHHHHHHHcCCcCcCCCCcceeec
Confidence            3578899999998754               1355667 9999999999999999999999999976543

>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=99.69  E-value=2.1e-17  Score=91.60  Aligned_cols=50  Identities=30%  Similarity=0.725  Sum_probs=43.1

Q ss_pred             CCCccccccccccCC-CeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccC
Q 032328           70 SPVDCVVCLENFRMG-DKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS  120 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~-~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~  120 (143)
                      .+..|+||++.+.++ +.+..++ |||.||.+|+.+|+..+.+||+||.++.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLP-CGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECT-TSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecC-CCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            567899999999654 4466677 9999999999999999899999998874

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

Probab=99.68  E-value=2.7e-17  Score=97.85  Aligned_cols=56  Identities=21%  Similarity=0.500  Sum_probs=46.5

Q ss_pred             cCCCCCCccccccccccCCCeeeEcCCCC-----CcccHHhHHHHHhCC--CCCccccCccCCCC
Q 032328           66 DRGSSPVDCVVCLENFRMGDKCRLLPNCR-----HSFHAQCIDSWLLKT--PICPICRTRVSPSK  123 (143)
Q Consensus        66 ~~~~~~~~C~ICl~~~~~~~~v~~l~~C~-----H~FH~~Ci~~wl~~~--~~CP~CR~~i~~~~  123 (143)
                      ....++..|.||++++.+++.+ ++| |+     |.||.+||++|+..+  .+||+||.++....
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~   72 (80)
T 2d8s_A           10 ITPSSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMET   72 (80)
T ss_dssp             CCCTTSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCC
T ss_pred             CCCCCCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCc
Confidence            3345678899999999877766 578 86     999999999999875  48999999998664

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

Probab=99.68  E-value=1.4e-17  Score=94.94  Aligned_cols=56  Identities=23%  Similarity=0.588  Sum_probs=47.5

Q ss_pred             CCCccccccccccCC----CeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcce
Q 032328           70 SPVDCVVCLENFRMG----DKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGV  126 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~----~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~~  126 (143)
                      ++..|+||++.+.++    +.+..++ |||.||.+|+.+|+..+.+||+||.++...++..
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   61 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHP   61 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEET-TSCEEEHHHHHHHHHHCSBCTTTCCBCTTTCEEE
T ss_pred             CCCCCCccChhhhCccccCCCEEeCC-CCCchhHHHHHHHHHcCCCCCCCCccCCccceee
Confidence            467899999998753    4556677 9999999999999999899999999999876554

>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=99.68  E-value=8.3e-17  Score=102.01  Aligned_cols=54  Identities=28%  Similarity=0.647  Sum_probs=43.7

Q ss_pred             CCCccccccccccCCC---------------eeeEcCCCCCcccHHhHHHHH-----hCCCCCccccCccCCCCc
Q 032328           70 SPVDCVVCLENFRMGD---------------KCRLLPNCRHSFHAQCIDSWL-----LKTPICPICRTRVSPSKV  124 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~---------------~v~~l~~C~H~FH~~Ci~~wl-----~~~~~CP~CR~~i~~~~~  124 (143)
                      .++.|+||++.|..+.               .+..++ |+|.||.+||.+|+     ..+.+||+||..+.....
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~~g   97 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTG   97 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSS
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCC-CCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCCCC
Confidence            4568999999997643               334666 99999999999999     456789999999987643

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

Probab=99.67  E-value=1.8e-17  Score=96.28  Aligned_cols=57  Identities=30%  Similarity=0.743  Sum_probs=48.4

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcceeecC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVILKD  130 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~~~~~~  130 (143)
                      .+...|+||++.+.+    ..++ |||.||..|+.+|+..+..||+||.++...+.....++
T Consensus        13 ~~~~~C~IC~~~~~~----~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~   69 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGANESSGPSS   69 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEET-TTEEECHHHHHHSSCCCSSCHHHHHCTTCCCCCCCCCC
T ss_pred             CCCCCCeeCCcCccC----cccC-CCCcccHHHHHHHHHCcCcCCCcCCcccCCCccccCCC
Confidence            456789999999877    6677 99999999999999999999999999997765555443

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

Probab=99.66  E-value=6e-17  Score=93.68  Aligned_cols=52  Identities=27%  Similarity=0.668  Sum_probs=44.3

Q ss_pred             CCCCccccccccccCC----CeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCC
Q 032328           69 SSPVDCVVCLENFRMG----DKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSP  121 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~----~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~  121 (143)
                      .+...|+||++.+.+.    +.+..++ |||.||..|+..|+..+..||+||.++..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECS-SSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCC-CCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            4567899999998763    4446677 99999999999999998999999998864

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

Probab=99.65  E-value=1.6e-16  Score=92.81  Aligned_cols=56  Identities=20%  Similarity=0.399  Sum_probs=46.6

Q ss_pred             CCCCccccccccccCCCeeeEc-CCCCCcccHHhHHHHHhCCCCCccccCccCCCCcceee
Q 032328           69 SSPVDCVVCLENFRMGDKCRLL-PNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVIL  128 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l-~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~~~~  128 (143)
                      .+...|+||++.+.+.   ..+ + |||.||..||..|+..+..||+||..+...+.....
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~   69 (72)
T 2djb_A           13 TPYILCSICKGYLIDA---TTITE-CLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLSGP   69 (72)
T ss_dssp             CGGGSCTTTSSCCSSC---EECSS-SCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSCCCC
T ss_pred             CCCCCCCCCChHHHCc---CEECC-CCCHHHHHHHHHHHHcCCcCCCcCcccCcccccccC
Confidence            3567899999998874   444 6 999999999999999889999999999887655443

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

Probab=99.65  E-value=3.1e-17  Score=95.63  Aligned_cols=53  Identities=23%  Similarity=0.567  Sum_probs=45.1

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG  125 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~  125 (143)
                      .++..|+||++.+.+.   ..++ |||.||..|+..|+..+..||+||..+......
T Consensus        13 ~~~~~C~IC~~~~~~~---~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   65 (71)
T 2d8t_A           13 LTVPECAICLQTCVHP---VSLP-CKHVFCYLCVKGASWLGKRCALCRQEIPEDFLD   65 (71)
T ss_dssp             SSCCBCSSSSSBCSSE---EEET-TTEEEEHHHHHHCTTCSSBCSSSCCBCCHHHHS
T ss_pred             CCCCCCccCCcccCCC---EEcc-CCCHHHHHHHHHHHHCCCcCcCcCchhCHhhcc
Confidence            4567899999998664   5667 999999999999999999999999999865443

>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=99.62  E-value=3.4e-17  Score=103.80  Aligned_cols=56  Identities=25%  Similarity=0.568  Sum_probs=1.6

Q ss_pred             CCCCccccccccccCC-------------C--eeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcc
Q 032328           69 SSPVDCVVCLENFRMG-------------D--KCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG  125 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~-------------~--~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~  125 (143)
                      ..++.|+||+++|.+.             +  .+..++ |+|.||.+||.+|+..+.+||+||.++..+..+
T Consensus        46 ~~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~-C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~~k~g  116 (117)
T 4a0k_B           46 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEFQKYG  116 (117)
T ss_dssp             CCC---------------------------------------------------------------------
T ss_pred             CCCCcCeECChhhcCcChhhhcccccccccccccccCC-cCceEcHHHHHHHHHcCCcCCCCCCeeeeeccC
Confidence            3568899999999752             1  222235 999999999999999999999999998766543

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

Probab=99.61  E-value=4.9e-16  Score=89.67  Aligned_cols=50  Identities=34%  Similarity=0.849  Sum_probs=42.9

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      .+..|+||++.+.+  ....++ |||.||..|+.+|+..+.+||+||.++...
T Consensus         4 ~~~~C~IC~~~~~~--~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   53 (68)
T 1chc_A            4 VAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVESV   53 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCCE
T ss_pred             CCCCCeeCCccccC--CcEecC-CCCeeHHHHHHHHHhCcCcCcCCChhhHhh
Confidence            46789999999765  346677 999999999999999889999999998743

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

Probab=99.61  E-value=1.5e-15  Score=91.81  Aligned_cols=57  Identities=25%  Similarity=0.627  Sum_probs=47.4

Q ss_pred             CCCCccccccccccCCCe-eeEcCCCCCcccHHhHHHHHhCC---CCCccccCccCCCCcce
Q 032328           69 SSPVDCVVCLENFRMGDK-CRLLPNCRHSFHAQCIDSWLLKT---PICPICRTRVSPSKVGV  126 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~-v~~l~~C~H~FH~~Ci~~wl~~~---~~CP~CR~~i~~~~~~~  126 (143)
                      .+...|+||++.|.+.+. ...++ |||.||..|+.+|+..+   ..||+||..+...++..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~i~~   73 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRITSLTQ   73 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCSSTTT
T ss_pred             cCCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcccchhHHH
Confidence            456789999999988664 56677 99999999999999875   78999999988765443

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

Probab=99.60  E-value=1.5e-15  Score=88.80  Aligned_cols=52  Identities=27%  Similarity=0.593  Sum_probs=43.4

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHh---CCCCCccccCccCCCCc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL---KTPICPICRTRVSPSKV  124 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~---~~~~CP~CR~~i~~~~~  124 (143)
                      .+...|+||++.+.+.   ..++ |||.||..|+..|+.   ....||+||.++...++
T Consensus        18 ~~~~~C~IC~~~~~~~---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~   72 (73)
T 2ysl_A           18 QEEVICPICLDILQKP---VTID-CGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNAI   72 (73)
T ss_dssp             CCCCBCTTTCSBCSSE---EECT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCCC
T ss_pred             ccCCEeccCCcccCCe---EEcC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcccC
Confidence            4567899999998763   5567 999999999999997   45679999999987654

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

Probab=99.59  E-value=1.7e-15  Score=86.90  Aligned_cols=51  Identities=22%  Similarity=0.537  Sum_probs=42.8

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHh-CCCCCccccCccCCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL-KTPICPICRTRVSPSK  123 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~-~~~~CP~CR~~i~~~~  123 (143)
                      .+...|+||++.+.++   ..++ |||.||..|+.+|+. .+..||+||.++...+
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   64 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCSP---KQTE-CGHRFCESCMAALLSSSSPKCTACQESIVKDK   64 (66)
T ss_dssp             CCCEECTTTCCEESSC---CCCS-SSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTT
T ss_pred             CcCCCCCCCChHhcCe---eECC-CCCHHHHHHHHHHHHhCcCCCCCCCcCCChhh
Confidence            4567899999998875   3466 999999999999994 5678999999988764

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

Probab=99.58  E-value=1.7e-15  Score=88.84  Aligned_cols=52  Identities=23%  Similarity=0.646  Sum_probs=42.5

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC--CCCccccCccCCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT--PICPICRTRVSPSK  123 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~--~~CP~CR~~i~~~~  123 (143)
                      .+...|+||++.+.++   ..++.|||.||..||..|+..+  ..||+||.++...+
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           13 PDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             CGGGSCSSSCCCCTTC---EECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTT
T ss_pred             CCCCCCcCCChHHhCC---eEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCcc
Confidence            3567899999999875   4555599999999999999865  68999999866543

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

Probab=99.57  E-value=1.9e-15  Score=90.18  Aligned_cols=48  Identities=29%  Similarity=0.669  Sum_probs=42.1

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS  120 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~  120 (143)
                      .....|+||++.+.++   ..++ |||.||..|+.+|+.....||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQNP---VVTK-CRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCSE---EECT-TSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcCe---eEcc-CCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            4567899999998763   4567 9999999999999998899999999986

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

Probab=99.56  E-value=2.5e-15  Score=97.22  Aligned_cols=61  Identities=25%  Similarity=0.573  Sum_probs=50.6

Q ss_pred             CCCCccccccccccCC----CeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcceeecC
Q 032328           69 SSPVDCVVCLENFRMG----DKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVILKD  130 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~----~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~~~~~~  130 (143)
                      .+...|+||++.+.++    +.+..++ |||.||..||.+|+..+.+||+||..+...........
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l~~l~i~   69 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYIG   69 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCEEECBCS
T ss_pred             CCCCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcCccccccccccC
Confidence            3567899999998764    5556777 99999999999999999999999999998876554433

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

Probab=99.55  E-value=6.1e-15  Score=84.32  Aligned_cols=58  Identities=24%  Similarity=0.508  Sum_probs=45.8

Q ss_pred             CCCccccccc-cccCCCee-eEcCCCCCcccHHhHHHHHhC-CCCCccccCccCCCCcceee
Q 032328           70 SPVDCVVCLE-NFRMGDKC-RLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPSKVGVIL  128 (143)
Q Consensus        70 ~~~~C~ICl~-~~~~~~~v-~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~~~~~~~~  128 (143)
                      ++..|+||++ .+.++... ..++ |||.||..|+.+|+.. ...||+||..+...++....
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~   62 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQL   62 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCCEEEC
T ss_pred             CCCcCCcCCCCccCCCccCeecCC-CCCHhHHHHHHHHHHcCCCcCCCCCCccccccceeec
Confidence            3567999999 77765443 3456 9999999999999765 46799999999988776554

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

Probab=99.54  E-value=6.8e-15  Score=85.82  Aligned_cols=50  Identities=22%  Similarity=0.630  Sum_probs=42.7

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC--CCCccccCccCCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT--PICPICRTRVSPS  122 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~--~~CP~CR~~i~~~  122 (143)
                      ..+.|+||.+.+..++...   .|+|.||.+||.+||+.+  .+||+||.++..+
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            4578999999998765443   499999999999999887  7899999998755

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

Probab=99.54  E-value=3.3e-15  Score=97.71  Aligned_cols=49  Identities=35%  Similarity=0.896  Sum_probs=42.8

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCC
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSK  123 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~  123 (143)
                      +..|+||++.+.++   ..+| |||.||..||..|+..+.+||+||.++....
T Consensus        53 ~~~C~iC~~~~~~~---~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~  101 (138)
T 4ayc_A           53 ELQCIICSEYFIEA---VTLN-CAHSFCSYCINEWMKRKIECPICRKDIKSKT  101 (138)
T ss_dssp             HSBCTTTCSBCSSE---EEET-TSCEEEHHHHHHHTTTCSBCTTTCCBCCCEE
T ss_pred             cCCCcccCcccCCc---eECC-CCCCccHHHHHHHHHcCCcCCCCCCcCCCCC
Confidence            45799999998764   6677 9999999999999999999999999987653

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

Probab=99.53  E-value=1.6e-14  Score=86.48  Aligned_cols=53  Identities=28%  Similarity=0.565  Sum_probs=44.7

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC------CCCCccccCccCCCCcc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK------TPICPICRTRVSPSKVG  125 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~------~~~CP~CR~~i~~~~~~  125 (143)
                      .++..|+||++.+.++   ..++ |||.||..|+..|+..      ...||+||..+...+..
T Consensus        17 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~   75 (85)
T 2ecw_A           17 KEEVTCPICLELLKEP---VSAD-CNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLK   75 (85)
T ss_dssp             CTTTSCTTTCSCCSSC---EECT-TSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTCCE
T ss_pred             ccCCCCcCCChhhCcc---eeCC-CCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHhCC
Confidence            4567899999998775   5677 9999999999999987      66799999999876443

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

Probab=99.52  E-value=1.2e-14  Score=85.95  Aligned_cols=51  Identities=16%  Similarity=0.381  Sum_probs=43.9

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-CCCCccccCccCCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPSK  123 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~~~  123 (143)
                      .+...|+||++.+.++   ..++ |||.||+.||.+|+.. +.+||+||.++...+
T Consensus         6 ~~~~~C~IC~~~~~~P---v~~~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~   57 (78)
T 1t1h_A            6 PEYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLHAG   57 (78)
T ss_dssp             SSSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCC
T ss_pred             cccCCCCCccccccCC---EEcC-CCCeecHHHHHHHHHHCcCCCCCCcCCCChhh
Confidence            4567899999998875   5567 9999999999999987 788999999988654

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

Probab=99.52  E-value=5.2e-15  Score=87.69  Aligned_cols=51  Identities=29%  Similarity=0.550  Sum_probs=43.4

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-------CCCCccccCccCCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-------TPICPICRTRVSPSK  123 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-------~~~CP~CR~~i~~~~  123 (143)
                      .+...|+||++.+.++   ..++ |||.||..|+..|+..       ...||+||..+...+
T Consensus        10 ~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~   67 (79)
T 2egp_A           10 QEEVTCPICLELLTEP---LSLD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEH   67 (79)
T ss_dssp             CCCCEETTTTEECSSC---CCCS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSG
T ss_pred             ccCCCCcCCCcccCCe---eECC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhh
Confidence            4567899999998775   4567 9999999999999986       567999999998754

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

Probab=99.51  E-value=2.3e-14  Score=85.86  Aligned_cols=53  Identities=32%  Similarity=0.699  Sum_probs=44.5

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC------CCCCccccCccCCCCcc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK------TPICPICRTRVSPSKVG  125 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~------~~~CP~CR~~i~~~~~~  125 (143)
                      .+...|+||++.+.+.   ..++ |||.||..|+..|+..      ...||+||..+...+..
T Consensus        17 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~   75 (85)
T 2ecv_A           17 KEEVTCPICLELLTQP---LSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIR   75 (85)
T ss_dssp             CCCCCCTTTCSCCSSC---BCCS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSCC
T ss_pred             cCCCCCCCCCcccCCc---eeCC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhcC
Confidence            4567899999998775   5567 9999999999999977      77899999999876443

>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=99.50  E-value=7.8e-15  Score=90.88  Aligned_cols=51  Identities=29%  Similarity=0.742  Sum_probs=42.9

Q ss_pred             CCCccccccccccCCCeeeE-cCCCCCcccHHhHHHHHhCC-CCCccccCccCCCCc
Q 032328           70 SPVDCVVCLENFRMGDKCRL-LPNCRHSFHAQCIDSWLLKT-PICPICRTRVSPSKV  124 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~-l~~C~H~FH~~Ci~~wl~~~-~~CP~CR~~i~~~~~  124 (143)
                      +...|+||++.+.++   .. ++ |||.||..||..|+... ..||+||.++...++
T Consensus        21 ~~~~C~IC~~~~~~p---~~~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~l   73 (100)
T 3lrq_A           21 EVFRCFICMEKLRDA---RLCPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPLQLREL   73 (100)
T ss_dssp             HHTBCTTTCSBCSSE---EECTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGC
T ss_pred             CCCCCccCCccccCc---cccCC-CCChhhHHHHHHHHHHCcCCCCCCCCcCCHHHh
Confidence            456899999998763   44 66 99999999999999887 689999999976543

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

Probab=99.48  E-value=2.1e-14  Score=88.71  Aligned_cols=50  Identities=26%  Similarity=0.747  Sum_probs=42.6

Q ss_pred             CCCccccccccccCCCeeeEc-CCCCCcccHHhHHHHHhCCCCCccccCccCCCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLL-PNCRHSFHAQCIDSWLLKTPICPICRTRVSPSK  123 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l-~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~  123 (143)
                      +...|+||++.+.++   ..+ + |||.||..|+..|+..+..||+||..+...+
T Consensus        21 ~~~~C~IC~~~~~~p---~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   71 (99)
T 2y43_A           21 DLLRCGICFEYFNIA---MIIPQ-CSHNYCSLCIRKFLSYKTQCPTCCVTVTEPD   71 (99)
T ss_dssp             HHTBCTTTCSBCSSE---EECTT-TCCEEEHHHHHHHHTTCCBCTTTCCBCCGGG
T ss_pred             CCCCcccCChhhCCc---CEECC-CCCHhhHHHHHHHHHCCCCCCCCCCcCChhh
Confidence            356899999998863   444 6 9999999999999999899999999988643

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

Probab=99.48  E-value=5e-14  Score=79.97  Aligned_cols=43  Identities=28%  Similarity=0.630  Sum_probs=36.8

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHh---CCCCCccc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL---KTPICPIC  115 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~---~~~~CP~C  115 (143)
                      .++..|+||++.+.++   ..++ |||.||..||.+|+.   ....||+|
T Consensus        18 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           18 QEEVICPICLDILQKP---VTID-CGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCBCTTTCSBCSSC---EECT-TSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             ccCCCCCcCCchhCCe---EEeC-CCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            4567899999998875   5667 999999999999998   45689998

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

Probab=99.47  E-value=1.7e-14  Score=93.29  Aligned_cols=57  Identities=25%  Similarity=0.601  Sum_probs=47.6

Q ss_pred             CCCCccccccccccCC----CeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcce
Q 032328           69 SSPVDCVVCLENFRMG----DKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGV  126 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~----~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~~  126 (143)
                      .+...|+||++.+.+.    .....++ |||.||..|+.+|+..+.+||+||.++...++..
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~  130 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHP  130 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEET-TSBEEEHHHHHHHHHHCSBCTTTCCBCCGGGEEE
T ss_pred             CCCCCCCCCCCccccccccCcceEeCC-CCChhhHHHHHHHHHcCCCCCCCCCcCChhccee
Confidence            4567899999998753    3445666 9999999999999999999999999998876544

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

Probab=99.46  E-value=5.9e-14  Score=78.23  Aligned_cols=43  Identities=33%  Similarity=0.880  Sum_probs=36.1

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHh---CCCCCccc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL---KTPICPIC  115 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~---~~~~CP~C  115 (143)
                      .+...|+||++.+.++   ..++ |||.||..|+.+|+.   .+..||+|
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKEP---VIIE-CGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSSC---CCCS-SCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccCCCCccCCcccCcc---EeCC-CCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            4567899999999875   5567 999999999999954   56779998

>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=99.45  E-value=5e-14  Score=88.35  Aligned_cols=50  Identities=32%  Similarity=0.713  Sum_probs=42.6

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      ++..|+||++.+.++  +...+ |||.||..|+..|+..+..||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           14 PHLMCVLCGGYFIDA--TTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGTBCTTTSSBCSSE--EEETT-TCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             CcCCCccCChHHhCc--CEeCC-CCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            467899999998763  33336 999999999999999989999999998865

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

Probab=99.43  E-value=1.5e-13  Score=83.65  Aligned_cols=49  Identities=24%  Similarity=0.676  Sum_probs=40.8

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC--CCCccccCccC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT--PICPICRTRVS  120 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~--~~CP~CR~~i~  120 (143)
                      .+...|+||++.+.++   ..++.|||.||..||..|+...  ..||+||..+.
T Consensus        11 ~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           11 PDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CTTTEETTTTEECSSC---EECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CcCCCCCCCChhhcCc---eECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            4567899999999875   5555599999999999999653  58999999974

>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=99.42  E-value=1.1e-13  Score=88.77  Aligned_cols=48  Identities=23%  Similarity=0.537  Sum_probs=41.0

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCC-CCccccCccCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP-ICPICRTRVSP  121 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~-~CP~CR~~i~~  121 (143)
                      +...|+||++.+.++   ..++ |||.||..||..|+..+. .||+||..+..
T Consensus        51 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           51 ETFQCICCQELVFRP---ITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHTBCTTTSSBCSSE---EECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             cCCCCCcCChHHcCc---EEee-CCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            346799999998864   5567 999999999999998644 89999999976

>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=99.42  E-value=1.3e-13  Score=86.77  Aligned_cols=51  Identities=24%  Similarity=0.612  Sum_probs=42.7

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCC---CCccccCccCCCCcc
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP---ICPICRTRVSPSKVG  125 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~---~CP~CR~~i~~~~~~  125 (143)
                      ...|+||++.+.++   ..++ |||.||..|+..|+..+.   .||+||..+......
T Consensus        21 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~~   74 (112)
T 1jm7_A           21 ILECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQ   74 (112)
T ss_dssp             HTSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCB
T ss_pred             CCCCcccChhhcCe---EECC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhcC
Confidence            45799999998765   4467 999999999999998753   799999999876543

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

Probab=99.41  E-value=5.2e-13  Score=78.91  Aligned_cols=56  Identities=21%  Similarity=0.494  Sum_probs=43.3

Q ss_pred             CCCCccccccccccCCCeee-EcCCCCCcccHHhHHHHHhC-CCCCccccCccCCCCcc
Q 032328           69 SSPVDCVVCLENFRMGDKCR-LLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPSKVG  125 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~-~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~~~~~  125 (143)
                      .++..|+||++.+...+... .++ |||.||..|+..++.. ...||.||+.+......
T Consensus         9 ~~~~~CpICle~~~~~d~~~~p~~-CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~~   66 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPEDPAV   66 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTTCCSST-TSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSSC
T ss_pred             ccCCcCCccCccCccccccccccC-CCCCcCHHHHHHHHhcCCCCCCCCCCccCCCchh
Confidence            45678999999986543322 234 9999999999998754 56799999999987654

>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=99.38  E-value=2.2e-13  Score=91.45  Aligned_cols=49  Identities=29%  Similarity=0.647  Sum_probs=40.8

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-CCCCccccCccCCC
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPS  122 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~~  122 (143)
                      ...|+||++.+.++  +..++ |||.||..|+..|+.. +..||+||..+...
T Consensus        54 ~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  103 (165)
T 2ckl_B           54 ELMCPICLDMLKNT--MTTKE-CLHRFCADCIITALRSGNKECPTCRKKLVSK  103 (165)
T ss_dssp             HHBCTTTSSBCSSE--EEETT-TCCEEEHHHHHHHHHTTCCBCTTTCCBCCSG
T ss_pred             CCCCcccChHhhCc--CEeCC-CCChhHHHHHHHHHHhCcCCCCCCCCcCCCc
Confidence            45899999998863  33346 9999999999999987 77899999998643

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

Probab=99.37  E-value=2.1e-13  Score=75.64  Aligned_cols=50  Identities=24%  Similarity=0.566  Sum_probs=41.3

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG  125 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~  125 (143)
                      .+...|+||++.+.++   ..++ |||.||..|+..|   ...||+||..+.....+
T Consensus         4 ~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~~~   53 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGADT   53 (56)
T ss_dssp             CCCSSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCSSC
T ss_pred             ccCCCceEeCCccCCe---EEcC-CCCcccHHHHccC---CCCCCcCCcEeecCCcC
Confidence            3567899999999875   6677 9999999999874   56799999999876543

>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=99.36  E-value=2.4e-13  Score=86.55  Aligned_cols=51  Identities=25%  Similarity=0.547  Sum_probs=43.0

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCC-CCccccCccCCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP-ICPICRTRVSPSK  123 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~-~CP~CR~~i~~~~  123 (143)
                      .+...|+||++.+.++   ..++ |||.||..|+..|+.... .||+||..+....
T Consensus        16 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   67 (118)
T 3hct_A           16 ESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLENQ   67 (118)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCcCChhhcCe---EECC-cCChhhHHHHHHHHhhCCCCCCCCCCCcCHHh
Confidence            3567899999998775   5567 999999999999998755 8999999988653

>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=99.36  E-value=3.1e-13  Score=85.75  Aligned_cols=51  Identities=25%  Similarity=0.546  Sum_probs=43.1

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-CCCCccccCccCCCCcc
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPSKVG  125 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~~~~~  125 (143)
                      ...|+||++.+.++   ..++ |||.||..|+.+|+.. ...||+||.++...+..
T Consensus        23 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~   74 (116)
T 1rmd_A           23 SISCQICEHILADP---VETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE   74 (116)
T ss_dssp             HTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCB
T ss_pred             CCCCCCCCcHhcCc---EEcC-CCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhcc
Confidence            46799999998764   4567 9999999999999987 67899999999876543

>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=99.36  E-value=4.9e-13  Score=88.52  Aligned_cols=49  Identities=22%  Similarity=0.495  Sum_probs=41.9

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCC-CCccccCccCCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP-ICPICRTRVSPS  122 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~-~CP~CR~~i~~~  122 (143)
                      +...|+||++.+.++   ..++ |||.||..||..|+.... .||+||..+...
T Consensus        77 ~~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQP---VTTE-CFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSSE---EECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhcCC---EEcC-CCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            345799999998764   5577 999999999999998754 799999999876

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

Probab=99.35  E-value=4.2e-13  Score=76.41  Aligned_cols=48  Identities=21%  Similarity=0.485  Sum_probs=40.0

Q ss_pred             CCCccccccccccCCCeeeEc--CCCCCc-ccHHhHHHHHhCCCCCccccCccCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLL--PNCRHS-FHAQCIDSWLLKTPICPICRTRVSP  121 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l--~~C~H~-FH~~Ci~~wl~~~~~CP~CR~~i~~  121 (143)
                      ++..|+||++...+.   ..+  | |||. |+.+|+..|...+..||+||.++..
T Consensus         7 ~~~~C~IC~~~~~~~---~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~   57 (64)
T 2vje_A            7 AIEPCVICQGRPKNG---CIVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQM   57 (64)
T ss_dssp             GGSCCTTTSSSCSCE---EEEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCCE
T ss_pred             CcCCCCcCCCCCCCE---EEECCC-CCChhhHHHHHHHHHHcCCcCCCcCcchhc
Confidence            456899999985542   444  8 9998 8999999999988899999999863

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

Probab=99.34  E-value=4.7e-13  Score=100.15  Aligned_cols=52  Identities=29%  Similarity=0.682  Sum_probs=43.8

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHh-CCCCCccccCccCCCCc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL-KTPICPICRTRVSPSKV  124 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~-~~~~CP~CR~~i~~~~~  124 (143)
                      .....|+||++.+.+   ...+| |||.||..|+..|+. ....||+||.++.....
T Consensus       330 ~~~~~C~ICle~~~~---pv~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~~  382 (389)
T 2y1n_A          330 STFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP  382 (389)
T ss_dssp             TSSSBCTTTSSSBCC---EEEET-TCCEECHHHHHHHHHHTCSBCTTTCCBCCEEEE
T ss_pred             CCCCCCCccCcCCCC---eEEeC-CCChhhHHHHHHHHhcCCCCCCCCCCccCCcee
Confidence            345789999999765   36677 999999999999998 67889999999987643

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

Probab=99.34  E-value=3.4e-13  Score=76.55  Aligned_cols=50  Identities=20%  Similarity=0.329  Sum_probs=39.9

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCc-ccHHhHHHHHhCCCCCccccCccCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHS-FHAQCIDSWLLKTPICPICRTRVSP  121 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~-FH~~Ci~~wl~~~~~CP~CR~~i~~  121 (143)
                      ....|+||++...+. .+..+| |||. |+..|+..|......||+||.++..
T Consensus         6 ~~~~C~IC~~~~~~~-~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~   56 (63)
T 2vje_B            6 LLKPCSLCEKRPRDG-NIIHGR-TGHLVTCFHCARRLKKAGASCPICKKEIQL   56 (63)
T ss_dssp             GGSBCTTTSSSBSCE-EEEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCCE
T ss_pred             cCCCCcccCCcCCCe-EEEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhhc
Confidence            456899999985542 112238 9997 9999999999888899999999864

>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=99.32  E-value=2.9e-13  Score=85.70  Aligned_cols=48  Identities=38%  Similarity=0.780  Sum_probs=41.1

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-CCCCccccCccCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSP  121 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~  121 (143)
                      ++..|+||++.+.++   ..++ |||.||..|+..|+.. ...||+||..+..
T Consensus        14 ~~~~C~iC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           14 SECQCGICMEILVEP---VTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHBCTTTCSBCSSC---EECT-TSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCccCCcccCce---eEcC-CCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            356799999998875   6667 9999999999999976 6689999999864

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

Probab=99.31  E-value=1.6e-12  Score=78.09  Aligned_cols=52  Identities=17%  Similarity=0.129  Sum_probs=45.4

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKV  124 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~  124 (143)
                      .....|+||++-|.++   +.++ |||.|++.||..|+..+.+||+||.++....+
T Consensus        12 p~~~~CpI~~~~m~dP---V~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~l   63 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTDP---VRLP-SGTVMDRSIILRHLLNSPTDPFNRQMLTESML   63 (85)
T ss_dssp             CTTTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCGGGC
T ss_pred             chheECcccCchhcCC---eECC-CCCEECHHHHHHHHhcCCCCCCCcCCCChHhc
Confidence            4577899999999986   6677 99999999999999988899999999876543

>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=99.31  E-value=1.6e-12  Score=80.33  Aligned_cols=53  Identities=17%  Similarity=0.126  Sum_probs=46.3

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG  125 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~  125 (143)
                      .....|+||++-|.++   +.++ |||.|++.||..|+..+.+||+||.++...++.
T Consensus        27 p~~~~CpI~~~~m~dP---V~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~L~   79 (100)
T 2kre_A           27 PDEFRDPLMDTLMTDP---VRLP-SGTIMDRSIILRHLLNSPTDPFNRQTLTESMLE   79 (100)
T ss_dssp             STTTBCTTTCSBCSSE---EEET-TTEEEEHHHHHHHTTSCSBCSSSCCBCCTTSSE
T ss_pred             cHhhCCcCccCcccCC---eECC-CCCEEchHHHHHHHHcCCCCCCCCCCCChhhce
Confidence            4567899999999986   6777 999999999999999889999999999876543

>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=99.31  E-value=6.4e-13  Score=87.06  Aligned_cols=51  Identities=22%  Similarity=0.419  Sum_probs=42.4

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCC-CCccccCccCCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP-ICPICRTRVSPSK  123 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~-~CP~CR~~i~~~~  123 (143)
                      .+...|+||++.+.++   ..++ |||.||..||..|+.... .||+||.++...+
T Consensus        29 ~~~~~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   80 (141)
T 3knv_A           29 EAKYLCSACRNVLRRP---FQAQ-CGHRYCSFCLASILSSGPQNCAACVHEGIYEE   80 (141)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHGGGSCEECHHHHHTTCCCT
T ss_pred             CcCcCCCCCChhhcCc---EECC-CCCccCHHHHHHHHhcCCCCCCCCCCcccccc
Confidence            4567899999999876   5566 999999999999998654 7999999876543

>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=99.30  E-value=3.9e-12  Score=78.31  Aligned_cols=53  Identities=13%  Similarity=0.111  Sum_probs=46.0

Q ss_pred             CCCCccccccccccCCCeeeEcCCCC-CcccHHhHHHHHhCCCCCccccCccCCCCcc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCR-HSFHAQCIDSWLLKTPICPICRTRVSPSKVG  125 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~-H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~  125 (143)
                      .++..|+||++-|.++   ++++ || |.|++.||.+|+..+.+||+||.++....+.
T Consensus        20 p~~~~CpI~~~~m~dP---V~~~-cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~L~   73 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCDP---VVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIR   73 (98)
T ss_dssp             CTTTBCTTTCSBCSSE---EECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSE
T ss_pred             cHhcCCcCccccccCC---eECC-CCCeEECHHHHHHHHHhCCCCCCCCCCCChhhce
Confidence            4567899999999986   6677 99 9999999999999888999999999876543

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

Probab=99.26  E-value=1.5e-12  Score=82.68  Aligned_cols=48  Identities=25%  Similarity=0.547  Sum_probs=40.6

Q ss_pred             CCCccccccccccCCCeeeEc-CCCCCcccHHhHHHHHhCCCCCccccCccCCCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLL-PNCRHSFHAQCIDSWLLKTPICPICRTRVSPSK  123 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l-~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~  123 (143)
                      +...|+||++.+.++   ..+ + |||.||..||..|+.  ..||+||..+...+
T Consensus        21 ~~~~C~IC~~~~~~p---v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~   69 (117)
T 1jm7_B           21 KLLRCSRCTNILREP---VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAWIQD   69 (117)
T ss_dssp             HTTSCSSSCSCCSSC---BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCSCSS
T ss_pred             hCCCCCCCChHhhCc---cEeCC-CCCHHHHHHHHHHhc--CCCcCCCCcCcccc
Confidence            457899999999775   555 6 999999999999987  77999999986543

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

Probab=99.20  E-value=3.3e-12  Score=74.70  Aligned_cols=45  Identities=24%  Similarity=0.578  Sum_probs=37.6

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCc-ccHHhHHHHHhCCCCCccccCccCCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHS-FHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~-FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      ++..|+||++.+.+.   ..+| |||. ||..|+..|    ..||+||..+...
T Consensus        23 ~~~~C~iC~~~~~~~---~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~   68 (74)
T 4ic3_A           23 EEKLCKICMDRNIAI---VFVP-CGHLVTCKQCAEAV----DKCPMCYTVITFK   68 (74)
T ss_dssp             HHTBCTTTSSSBCCE---EEET-TCCBCCCHHHHTTC----SBCTTTCCBCSEE
T ss_pred             cCCCCCCCCCCCCCE---EEcC-CCChhHHHHhhhcC----ccCCCcCcCccCc
Confidence            346899999996653   6678 9998 999999998    7899999998754

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

Probab=99.20  E-value=3.3e-12  Score=93.60  Aligned_cols=54  Identities=24%  Similarity=0.640  Sum_probs=41.6

Q ss_pred             CCCCccccccccccCCCeee----EcCCCCCcccHHhHHHHHhCC-----------CCCccccCccCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCR----LLPNCRHSFHAQCIDSWLLKT-----------PICPICRTRVSPS  122 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~----~l~~C~H~FH~~Ci~~wl~~~-----------~~CP~CR~~i~~~  122 (143)
                      ....+|+||++.+.++..+.    ..+.|||.||..|+.+|++..           .+||+||.++...
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            45778999999988744333    223599999999999999752           4699999988743

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

Probab=99.14  E-value=3.4e-11  Score=69.24  Aligned_cols=46  Identities=39%  Similarity=0.812  Sum_probs=38.1

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCc-ccHHhHHHHHhCCCCCccccCccCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHS-FHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~-FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      .+...|.||++...+   +..+| |||. |+..|+..    ...||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i~~~   59 (68)
T 2ea5_A           13 ENSKDCVVCQNGTVN---WVLLP-CRHTCLCDGCVKY----FQQCPMCRQFVQES   59 (68)
T ss_dssp             CCSSCCSSSSSSCCC---CEETT-TTBCCSCTTHHHH----CSSCTTTCCCCCCE
T ss_pred             CCCCCCCCcCcCCCC---EEEEC-CCChhhhHHHHhc----CCCCCCCCcchhce
Confidence            456789999998544   57788 9998 99999984    47899999998864

>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=99.13  E-value=2e-11  Score=82.21  Aligned_cols=51  Identities=25%  Similarity=0.550  Sum_probs=42.8

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC-CCCccccCccCCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT-PICPICRTRVSPSK  123 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~-~~CP~CR~~i~~~~  123 (143)
                      .+...|+||++.+.++   +.++ |||.||..|+.+|+... ..||+||..+...+
T Consensus        16 ~~~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   67 (170)
T 3hcs_A           16 ESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLENQ   67 (170)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCChhhcCc---EECC-CCCHHHHHHHHHHHHhCCCCCCCCccCcchhh
Confidence            4567899999998875   5567 99999999999999764 48999999988653

>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=99.11  E-value=3.5e-11  Score=73.51  Aligned_cols=52  Identities=21%  Similarity=0.426  Sum_probs=41.0

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC------CCCcc--ccCc-cCCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT------PICPI--CRTR-VSPSK  123 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~------~~CP~--CR~~-i~~~~  123 (143)
                      .....|+||++.|.++   +.++.|||.|++.||..|+..+      .+||+  |+.. +...+
T Consensus         5 ~~~~~CPI~~~~~~dP---V~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~~~   65 (94)
T 2yu4_A            5 SSGFTCPITKEEMKKP---VKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSD   65 (94)
T ss_dssp             SSCCBCTTTCSBCSSE---EEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCGGG
T ss_pred             CcEeECcCcCchhcCC---EEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCHhh
Confidence            3567899999999874   4553499999999999999753      47999  9876 65443

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

Probab=99.10  E-value=6.6e-11  Score=66.27  Aligned_cols=50  Identities=22%  Similarity=0.620  Sum_probs=37.7

Q ss_pred             CCCCccccccccccCCCeeeEcC-CCCC---cccHHhHHHHHhC--CCCCccccCccCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLP-NCRH---SFHAQCIDSWLLK--TPICPICRTRVSP  121 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~-~C~H---~FH~~Ci~~wl~~--~~~CP~CR~~i~~  121 (143)
                      ++...|.||+++..  +.+ ++| .|+|   .||.+|+.+|+..  +.+||+||.++..
T Consensus         4 ~~~~~CrIC~~~~~--~~l-~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            4 EDVPVCWICNEELG--NER-FRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEECS--CCC-CCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCEeEEeecCCC--Cce-ecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            35678999999833  333 577 3445   9999999999975  5779999988753

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

Probab=99.08  E-value=5.5e-11  Score=69.62  Aligned_cols=44  Identities=25%  Similarity=0.609  Sum_probs=36.1

Q ss_pred             CCccccccccccCCCeeeEcCCCCCc-ccHHhHHHHHhCCCCCccccCccCCC
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHS-FHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~-FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      ...|+||++.+.+.   ..+| |||. ||..|+..    ...||+||.++...
T Consensus        25 ~~~C~IC~~~~~~~---~~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           25 EKLCKICMDRNIAI---VFVP-CGHLVTCKQCAEA----VDKCPMCYTVITFK   69 (75)
T ss_dssp             HHSCSSSCSSCCCB---CCSS-SCCCCBCHHHHHH----CSBCTTTCCBCCCC
T ss_pred             CCCCCcCCCCCCCE---EEec-CCCHHHHHHHhhC----CCCCccCCceecCc
Confidence            45799999997653   5677 9998 99999965    37899999998764

>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=99.08  E-value=6.4e-11  Score=85.20  Aligned_cols=51  Identities=14%  Similarity=0.259  Sum_probs=43.2

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC-CCCccccCccCCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT-PICPICRTRVSPSK  123 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~-~~CP~CR~~i~~~~  123 (143)
                      .....|+||++-|.++   ++++ |||.|++.||..|+... .+||+||.++...+
T Consensus       206 ~~~~~c~i~~~~~~dP---v~~~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~  257 (281)
T 2c2l_A          206 PDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQ  257 (281)
T ss_dssp             CSTTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCGGG
T ss_pred             CcccCCcCcCCHhcCC---eECC-CCCEECHHHHHHHHHHCCCCCcCCCCCCchhc
Confidence            4567899999999886   6677 99999999999999864 45999999997554

>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=99.06  E-value=2.7e-11  Score=73.96  Aligned_cols=55  Identities=16%  Similarity=0.561  Sum_probs=43.7

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC--------CCCCcc--ccCc--cCCCCcc
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK--------TPICPI--CRTR--VSPSKVG  125 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~--------~~~CP~--CR~~--i~~~~~~  125 (143)
                      +...|+||++++..++.+...+ |||.||..|+.+++..        ...||.  ||..  +....+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~-CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~~~i~   70 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQENEIE   70 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECHHHHH
T ss_pred             CCcCCcccCcccccccceEcCC-CCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCHHHHH
Confidence            4568999999998876666667 9999999999999853        236999  9998  6654443

>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=98.99  E-value=7.2e-11  Score=69.83  Aligned_cols=44  Identities=32%  Similarity=0.746  Sum_probs=36.9

Q ss_pred             CCccccccccccCCCeeeEcCCCCCc-ccHHhHHHHHhCCCCCccccCccCCC
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHS-FHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~-FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      +..|+||++...+   ...+| |||. |+..|+..|    ..||+||..+...
T Consensus        18 ~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~   62 (79)
T 2yho_A           18 AMLCMVCCEEEIN---STFCP-CGHTVCCESCAAQL----QSCPVCRSRVEHV   62 (79)
T ss_dssp             HTBCTTTSSSBCC---EEEET-TCBCCBCHHHHTTC----SBCTTTCCBCCEE
T ss_pred             CCEeEEeCcccCc---EEEEC-CCCHHHHHHHHHhc----CcCCCCCchhhCe
Confidence            4579999998654   47778 9998 999999876    4899999999875

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

Probab=98.98  E-value=2.3e-10  Score=77.39  Aligned_cols=52  Identities=13%  Similarity=0.258  Sum_probs=43.7

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC-CCCccccCccCCCCc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT-PICPICRTRVSPSKV  124 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~-~~CP~CR~~i~~~~~  124 (143)
                      .....|+||++-|.++   ++++ |||.|++.||..|+..+ .+||+||.++....+
T Consensus       104 p~~f~CPI~~elm~DP---V~~~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~L  156 (179)
T 2f42_A          104 PDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQL  156 (179)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGC
T ss_pred             cHhhcccCccccCCCC---eECC-CCCEECHHHHHHHHHhCCCCCCCCcCCCChhhC
Confidence            4567899999999985   6667 99999999999999864 469999999876543

>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=98.92  E-value=4.1e-10  Score=63.26  Aligned_cols=55  Identities=20%  Similarity=0.256  Sum_probs=45.4

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcceee
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVIL  128 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~~~~  128 (143)
                      ...|+|+++.+.++   .+.+.+||.|.+.||.+|+..+.+||+.+.++...++....
T Consensus         3 ~~~CpIs~~~m~dP---V~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~Lip~~   57 (61)
T 2bay_A            3 HMLCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEIV   57 (61)
T ss_dssp             -CCCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEECC
T ss_pred             eEEecCCCCCCCCC---EEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhhcEECc
Confidence            45799999999875   55523999999999999999888899999999887766543

>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=98.82  E-value=7.2e-10  Score=82.27  Aligned_cols=45  Identities=29%  Similarity=0.671  Sum_probs=37.8

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCc-ccHHhHHHHHhCCCCCccccCccCCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHS-FHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~-FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      ++..|+||++.+.+.   ..+| |||. ||..|+..|    ..||+||..+...
T Consensus       294 ~~~~C~IC~~~~~~~---v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i~~~  339 (345)
T 3t6p_A          294 EERTCKVCMDKEVSV---VFIP-CGHLVVCQECAPSL----RKCPICRGIIKGT  339 (345)
T ss_dssp             TTCBCTTTSSSBCCE---EEET-TCCEEECTTTGGGC----SBCTTTCCBCCEE
T ss_pred             CCCCCCccCCcCCce---EEcC-CCChhHhHHHHhcC----CcCCCCCCCccCe
Confidence            457899999997653   6678 9998 999999987    6799999998743

>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=98.80  E-value=1.9e-09  Score=76.56  Aligned_cols=52  Identities=21%  Similarity=0.446  Sum_probs=41.0

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC--CCCcc--ccCccCCCCc
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT--PICPI--CRTRVSPSKV  124 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~--~~CP~--CR~~i~~~~~  124 (143)
                      ....|+||++.|.++   +....|||.|++.||.+|+..+  ..||+  ||..+...+.
T Consensus       180 ~el~CPIcl~~f~DP---Vts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL  235 (267)
T 3htk_C          180 IELTCPITCKPYEAP---LISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDF  235 (267)
T ss_dssp             CCSBCTTTSSBCSSE---EEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGE
T ss_pred             eeeECcCccCcccCC---eeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhC
Confidence            455799999999774   3332399999999999999764  46999  9998876543

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

Probab=98.68  E-value=3.1e-08  Score=70.00  Aligned_cols=52  Identities=17%  Similarity=0.435  Sum_probs=43.2

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCC--CCccccCccCCCCc
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP--ICPICRTRVSPSKV  124 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~--~CP~CR~~i~~~~~  124 (143)
                      ....|+||.+-...+   ...+.|+|.||..|+..|++.+.  .||.|+..+.-+..
T Consensus       179 ~i~~C~iC~~iv~~g---~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~~  232 (238)
T 3nw0_A          179 AVKICNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIP  232 (238)
T ss_dssp             TCCBCTTTCSBCSSC---EECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCCC
T ss_pred             CCCcCcchhhHHhCC---cccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCC
Confidence            467899999998877   44455999999999999998754  79999999876643

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.61  E-value=4.1e-08  Score=59.46  Aligned_cols=48  Identities=27%  Similarity=0.555  Sum_probs=37.7

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-CCCCccccCccCCCC
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPSK  123 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~~~  123 (143)
                      -|.+|--++..  -.++.| |+|.|+.+|+..|.+. .+.||.||.++..-+
T Consensus         3 fC~~C~~Pi~i--ygRmIP-CkHvFCydCa~~~~~~~~k~Cp~C~~~V~rVe   51 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMIP-CKHVFCYDCAILHEKKGDKMCPGCSDPVQRIE   51 (101)
T ss_dssp             BCTTTCSBCSE--EEEEET-TCCEEEHHHHHHHHHTTCCBCTTTCCBCSEEE
T ss_pred             ecCccCCCeEE--Eeeecc-ccccHHHHHHHHHHhccCCCCcCcCCeeeeeE
Confidence            37777766543  347788 9999999999999854 688999999998653

>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=97.07  E-value=0.0017  Score=37.89  Aligned_cols=59  Identities=20%  Similarity=0.375  Sum_probs=36.4

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHH------------HhCC----CCCccccCccCCCCcceeecCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSW------------LLKT----PICPICRTRVSPSKVGVILKDGS  132 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~w------------l~~~----~~CP~CR~~i~~~~~~~~~~~~~  132 (143)
                      ..++.|.||-.- ..++...-. -|+-.||..|+.+.            +..+    =+||.|      ++++..+.+..
T Consensus        13 ~~D~~C~VC~~~-t~~~l~pCR-vC~RvfH~~CL~r~gy~~~~~a~e~~l~A~T~~GWSC~~C------enL~lLLtEeE   84 (89)
T 1wil_A           13 VNDEMCDVCEVW-TAESLFPCR-VCTRVFHDGCLRRMGYIQGDSAAEVTEMAHTETGWSCHYC------DNINLLLTEES   84 (89)
T ss_dssp             CCSCCCTTTCCC-CSSCCSSCS-SSSSCCCHHHHHHHTSCCCCCCCSCSCCCSSSSSCCCTTT------CCCCSSSCCCC
T ss_pred             CCCcccCccccc-cccceeccc-cccccccHhhcccccccccHHHHHHHHccCCCCCcccccc------chhhhhcchhh
Confidence            467889999732 223222222 38999999999996            2222    249999      44555555554


Q ss_pred             CCC
Q 032328          133 SVS  135 (143)
Q Consensus       133 ~~~  135 (143)
                      -.+
T Consensus        85 ~~~   87 (89)
T 1wil_A           85 GPS   87 (89)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            443

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=97.05  E-value=0.00075  Score=37.95  Aligned_cols=47  Identities=26%  Similarity=0.470  Sum_probs=34.4

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCC----CCccccCccC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP----ICPICRTRVS  120 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~----~CP~CR~~i~  120 (143)
                      ....|.||.+.   ++ +.....|...||..|+.+.+....    .||.|+....
T Consensus        11 ~~~~C~vC~~~---~~-ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~   61 (66)
T 2lri_C           11 PGARCGVCGDG---TD-VLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDVT   61 (66)
T ss_dssp             TTCCCTTTSCC---TT-CEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCCC
T ss_pred             CCCCcCCCCCC---Ce-EEECCCCCCceecccCCCccCcCCCCCEECccccCCCc
Confidence            45679999854   44 444446899999999998876543    4999976544

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=96.07  E-value=0.0047  Score=37.30  Aligned_cols=35  Identities=17%  Similarity=0.365  Sum_probs=25.4

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHH
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWL  106 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl  106 (143)
                      +..|.||.+.+..+....-++ |+|.|+..|+..+.
T Consensus         3 e~~C~~C~~~~~~~av~~C~~-C~~~~C~~Cl~~~h   37 (101)
T 2jun_A            3 KVLCQFCDQDPAQDAVKTCVT-CEVSYCDECLKATH   37 (101)
T ss_dssp             CCBCTTCCSSSCCBCCEEETT-TTEEECHHHHHHHS
T ss_pred             CCCCcCCCCCCCCCceEECCc-CChHHhHHHCHHHh
Confidence            467999998754333333366 99999999999843

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=95.83  E-value=0.0077  Score=33.14  Aligned_cols=46  Identities=28%  Similarity=0.636  Sum_probs=32.1

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC----CCCccccCc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT----PICPICRTR  118 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~----~~CP~CR~~  118 (143)
                      ..+..|.+|.+.   + .+.....|...||..|+..=+...    -.||.|+..
T Consensus         9 ~~~~~C~vC~~~---g-~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            9 DHQDYCEVCQQG---G-EIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             CCCSSCTTTSCC---S-SEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCCccCCCC---C-cEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            456789999874   3 344444588899999998754332    249999653

>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=95.48  E-value=0.0034  Score=34.82  Aligned_cols=50  Identities=24%  Similarity=0.481  Sum_probs=35.2

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHh-----CCCCCccccCc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL-----KTPICPICRTR  118 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~-----~~~~CP~CR~~  118 (143)
                      .+...|++|...+.++...+....|..=||..|+.--..     ....||.|+..
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            456789999999875555555446888999999854221     24569999764

>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=95.18  E-value=0.0061  Score=33.57  Aligned_cols=49  Identities=24%  Similarity=0.541  Sum_probs=32.8

Q ss_pred             CCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC----CCCccccCccC
Q 032328           68 GSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT----PICPICRTRVS  120 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~----~~CP~CR~~i~  120 (143)
                      ..++..|.+|.+.   ++ +.....|...||..|+.+=+...    -.||.|+....
T Consensus         6 d~~~~~C~vC~~~---g~-ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~   58 (61)
T 1mm2_A            6 DHHMEFCRVCKDG---GE-LLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPAL   58 (61)
T ss_dssp             CSSCSSCTTTCCC---SS-CBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTCC
T ss_pred             cCCCCcCCCCCCC---CC-EEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCchh
Confidence            3457789999864   33 33333588899999998644432    24999976543

>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=95.17  E-value=0.0036  Score=43.04  Aligned_cols=49  Identities=29%  Similarity=0.498  Sum_probs=35.3

Q ss_pred             CCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC----CCCccccCccC
Q 032328           68 GSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT----PICPICRTRVS  120 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~----~~CP~CR~~i~  120 (143)
                      ..+++.|.+|.+.   + .+.....|...||..|+.+-+...    -.||.|+..-.
T Consensus         4 d~~~~~C~~C~~~---g-~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~~   56 (207)
T 3u5n_A            4 DPNEDWCAVCQNG---G-DLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGK   56 (207)
T ss_dssp             CSSCSSBTTTCCC---E-EEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSSS
T ss_pred             CCCCCCCCCCCCC---C-ceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCccc
Confidence            3467789999865   3 345555688999999998766543    34999987544

>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=94.96  E-value=0.006  Score=41.09  Aligned_cols=47  Identities=28%  Similarity=0.518  Sum_probs=34.3

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC----CCCccccCccC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT----PICPICRTRVS  120 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~----~~CP~CR~~i~  120 (143)
                      +++.|.+|.+.   ++ +.....|...||..|+.+-+...    -.||.|+..-.
T Consensus         3 ~~~~C~~C~~~---g~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   53 (184)
T 3o36_A            3 NEDWCAVCQNG---GE-LLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSK   53 (184)
T ss_dssp             SCSSCTTTCCC---SS-CEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSSS
T ss_pred             CCCccccCCCC---Ce-eeecCCCCcccCccccCCCCCCCCCCCEECccccCccc
Confidence            56789999865   44 44444688999999998766543    34999987654

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=94.88  E-value=0.24  Score=29.12  Aligned_cols=54  Identities=22%  Similarity=0.385  Sum_probs=36.9

Q ss_pred             CCCcccccccccc---CCCeeeEcCCCCCcccHHhHHHHH-hCCCCCccccCccCCCC
Q 032328           70 SPVDCVVCLENFR---MGDKCRLLPNCRHSFHAQCIDSWL-LKTPICPICRTRVSPSK  123 (143)
Q Consensus        70 ~~~~C~ICl~~~~---~~~~v~~l~~C~H~FH~~Ci~~wl-~~~~~CP~CR~~i~~~~  123 (143)
                      ....|.||-+++-   +++.......|+---|+.|.+-=. ..++.||-|+.+....+
T Consensus        15 ~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCktrYkr~k   72 (93)
T 1weo_A           15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKRLR   72 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCCCT
T ss_pred             CCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhccCccccccCCcccccc
Confidence            5678999999963   233322222466667889987644 34788999999987553

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.85  E-value=0.0029  Score=34.25  Aligned_cols=46  Identities=30%  Similarity=0.737  Sum_probs=31.5

Q ss_pred             CCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCC----CCccccC
Q 032328           68 GSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP----ICPICRT  117 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~----~CP~CR~  117 (143)
                      ..++..|.+|.+.   ++ +.....|...||..|+.+=+...+    .||.|+.
T Consensus         6 ~~~~~~C~vC~~~---g~-ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            6 SGHEDFCSVCRKS---GQ-LLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             CSSCCSCSSSCCS---SC-CEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCCccCCCC---Ce-EEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            4467789999975   33 344446889999999986444322    3888854

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=94.83  E-value=0.008  Score=34.40  Aligned_cols=53  Identities=17%  Similarity=0.353  Sum_probs=36.2

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC----CCCCccccCccCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK----TPICPICRTRVSPS  122 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~----~~~CP~CR~~i~~~  122 (143)
                      .+...|.+|..... ++.++....|..-||..|+..-...    .-.||.|+..+...
T Consensus        16 ~~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~k~   72 (75)
T 2k16_A           16 NQIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKKD   72 (75)
T ss_dssp             CEEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHCSC
T ss_pred             CCCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchhhc
Confidence            45567999988754 3444444468899999999754432    34599998776543

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=94.73  E-value=0.014  Score=39.44  Aligned_cols=50  Identities=20%  Similarity=0.339  Sum_probs=36.0

Q ss_pred             CCccccccccccCCCe---eeEcCCCCCcccHHhHHH------HHh-----CCCCCccccCccC
Q 032328           71 PVDCVVCLENFRMGDK---CRLLPNCRHSFHAQCIDS------WLL-----KTPICPICRTRVS  120 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~---v~~l~~C~H~FH~~Ci~~------wl~-----~~~~CP~CR~~i~  120 (143)
                      +..|+||...|.+++.   ++....|..=||..|..-      -+.     ....||.|+..-.
T Consensus         2 G~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~~   65 (183)
T 3lqh_A            2 GNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHP   65 (183)
T ss_dssp             CCBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSSS
T ss_pred             cCcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCCC
Confidence            4579999999988763   555556999999999732      111     1567999987644

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=94.56  E-value=0.012  Score=34.94  Aligned_cols=54  Identities=13%  Similarity=0.362  Sum_probs=35.6

Q ss_pred             CCCCccccccccc-cCCCeeeEcCCCCCcccHHhHHHHHhC--CCCCccccCccCCC
Q 032328           69 SSPVDCVVCLENF-RMGDKCRLLPNCRHSFHAQCIDSWLLK--TPICPICRTRVSPS  122 (143)
Q Consensus        69 ~~~~~C~ICl~~~-~~~~~v~~l~~C~H~FH~~Ci~~wl~~--~~~CP~CR~~i~~~  122 (143)
                      .++..|.||.+.- .+++.+.....|.-.||..|+..=...  .-.||.|+......
T Consensus        23 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~~~~   79 (88)
T 2l43_A           23 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRARP   79 (88)
T ss_dssp             CCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHTTSC
T ss_pred             CCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCccchh
Confidence            4567899999763 233455555568889999999753222  23499997655443

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=94.48  E-value=0.023  Score=29.86  Aligned_cols=44  Identities=32%  Similarity=0.654  Sum_probs=29.2

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC----CCCccccC
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT----PICPICRT  117 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~----~~CP~CR~  117 (143)
                      .|.+|...-.. +.+..-..|...||..|+.+=+...    -.||.|+.
T Consensus         2 ~C~vC~~~~~~-~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGED-DKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCC-SCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCC-CCEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            48888876433 3444444688999999997644332    23999964

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=94.48  E-value=0.071  Score=34.40  Aligned_cols=47  Identities=26%  Similarity=0.464  Sum_probs=33.9

Q ss_pred             CCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHh-----------CCCCCccccCc
Q 032328           68 GSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL-----------KTPICPICRTR  118 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~-----------~~~~CP~CR~~  118 (143)
                      ...++.|.+|.+-   ++-+- ...|-..||..|+.+-+.           ..-.||.|+..
T Consensus        60 Dg~~d~C~vC~~G---G~Llc-CD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~~  117 (142)
T 2lbm_A           60 DGMDEQCRWCAEG---GNLIC-CDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPE  117 (142)
T ss_dssp             TSCBCSCSSSCCC---SSEEE-CSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCCC
T ss_pred             CCCCCeecccCCC---CcEEe-CCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccCc
Confidence            4567899999987   55443 334889999999997652           12359999743

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=93.86  E-value=0.025  Score=32.08  Aligned_cols=49  Identities=14%  Similarity=0.409  Sum_probs=32.9

Q ss_pred             CCCCccccccccc-cCCCeeeEcCCCCCcccHHhHHHHHhC--CCCCccccC
Q 032328           69 SSPVDCVVCLENF-RMGDKCRLLPNCRHSFHAQCIDSWLLK--TPICPICRT  117 (143)
Q Consensus        69 ~~~~~C~ICl~~~-~~~~~v~~l~~C~H~FH~~Ci~~wl~~--~~~CP~CR~  117 (143)
                      .++..|.||.+.- .+++.+.....|.-.||..|+..=...  .-.||.|+.
T Consensus        14 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~   65 (71)
T 2ku3_A           14 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQ   65 (71)
T ss_dssp             CSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcC
Confidence            4677899998763 334455555578899999999753211  224888864

>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=93.64  E-value=0.072  Score=29.58  Aligned_cols=35  Identities=20%  Similarity=0.499  Sum_probs=27.0

Q ss_pred             CCCCccccccccccCCCeeeEcC-CCCCcccHHhHH
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLP-NCRHSFHAQCID  103 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~-~C~H~FH~~Ci~  103 (143)
                      .....|++|...+.+++..+... .|.-=||..|+.
T Consensus         6 ~~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvg   41 (65)
T 2vpb_A            6 DPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTG   41 (65)
T ss_dssp             ---CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHT
T ss_pred             CCcCcCccCCCccCCCCCeEecccCccccCchhccC
Confidence            34568999999998877777766 688999999963

>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=93.63  E-value=0.16  Score=29.16  Aligned_cols=53  Identities=25%  Similarity=0.528  Sum_probs=35.0

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHH-----hCCCCCccccCccCCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWL-----LKTPICPICRTRVSPS  122 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl-----~~~~~CP~CR~~i~~~  122 (143)
                      .....| ||...+.++...+....|..=||..|+.--.     .....||.|+..-...
T Consensus        10 ~~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~~~~   67 (79)
T 1wep_A           10 LVPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFGPS   67 (79)
T ss_dssp             CCCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSCSC
T ss_pred             CCccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCcccccCCC
Confidence            345567 9999886444445544688899999984211     1245699998765443

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=93.62  E-value=0.022  Score=35.21  Aligned_cols=45  Identities=31%  Similarity=0.690  Sum_probs=31.0

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC----CCCccccC
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT----PICPICRT  117 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~----~~CP~CR~  117 (143)
                      .|.+|.+.-.+++.+..-..|...||..|+.+-+...    =.||.||.
T Consensus        63 ~C~vC~~~~~~~~~ll~Cd~C~~~yH~~Cl~p~l~~~P~~~W~C~~C~~  111 (112)
T 3v43_A           63 TCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRP  111 (112)
T ss_dssp             CBTTTCCCCCTTCCCEECTTTCCEECGGGCSSCCSSCCSSCCCCTTTSC
T ss_pred             ccccccCcCCCccceEEcCCCCCeeecccCCCCCCCCCCCCeECCCCCC
Confidence            6888887533334455555689999999997655442    24999975

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=93.38  E-value=0.028  Score=34.61  Aligned_cols=39  Identities=28%  Similarity=0.537  Sum_probs=27.2

Q ss_pred             CCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHh
Q 032328           68 GSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL  107 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~  107 (143)
                      ..+++.|.+|.+.-+.++ +..-..|+..||..|+...+.
T Consensus         4 ~~~~~~C~~C~~~g~~~~-ll~C~~C~~~~H~~Cl~~~~~   42 (111)
T 2ysm_A            4 GSSGANCAVCDSPGDLLD-QFFCTTCGQHYHGMCLDIAVT   42 (111)
T ss_dssp             CCCCSCBTTTCCCCCTTT-SEECSSSCCEECTTTTTCCCC
T ss_pred             CCCCCCCcCCCCCCCCcC-CeECCCCCCCcChHHhCCccc
Confidence            346788999988733222 233345999999999987664

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=93.32  E-value=0.056  Score=36.55  Aligned_cols=46  Identities=26%  Similarity=0.541  Sum_probs=31.6

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC----CCCCccccCccC
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK----TPICPICRTRVS  120 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~----~~~CP~CR~~i~  120 (143)
                      ++.|.+|.+.   ++ +.....|...||..|+.+=+..    .-.||.|+..-.
T Consensus         2 ~~~C~~C~~~---g~-ll~Cd~C~~~~H~~Cl~p~l~~~p~g~W~C~~C~~~~~   51 (189)
T 2ro1_A            2 ATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   51 (189)
T ss_dssp             CCCBTTTCCC---SS-CCCCTTTCCBCCSTTSTTCCSSCCCTTCCTTTTSCSCC
T ss_pred             CCcCccCCCC---Cc-eeECCCCCchhccccCCCCcccCCCCCCCCcCccCCCC
Confidence            4679999966   44 3333358889999999764433    224999987644

>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A

Probab=93.29  E-value=0.13  Score=32.53  Aligned_cols=48  Identities=25%  Similarity=0.475  Sum_probs=33.0

Q ss_pred             CCCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHH------h-----CCCCCccccCc
Q 032328           67 RGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWL------L-----KTPICPICRTR  118 (143)
Q Consensus        67 ~~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl------~-----~~~~CP~CR~~  118 (143)
                      +...++.|.+|-+-   ++ +.....|-..||.+|+.+-+      .     ..=.|++|+-.
T Consensus        53 ~Dg~~~~C~vC~dG---G~-LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~~  111 (129)
T 3ql9_A           53 SDGMDEQCRWCAEG---GN-LICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPE  111 (129)
T ss_dssp             TTSCBSSCTTTCCC---SE-EEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCCG
T ss_pred             CCCCCCcCeecCCC---Ce-eEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCCH
Confidence            34567789999976   43 33334588999999999752      1     12359999654

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=93.14  E-value=0.0057  Score=33.51  Aligned_cols=47  Identities=28%  Similarity=0.634  Sum_probs=32.7

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC----CCCccccCccC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT----PICPICRTRVS  120 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~----~~CP~CR~~i~  120 (143)
                      ++..|.+|...   ++ +.....|...||..|+.+=+...    -.||.|+....
T Consensus         4 ~~~~C~vC~~~---g~-ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~   54 (60)
T 2puy_A            4 HEDFCSVCRKS---GQ-LLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQML   54 (60)
T ss_dssp             CCSSCTTTCCC---SS-CEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHH
T ss_pred             CCCCCcCCCCC---Cc-EEEcCCCCcCEECCcCCCCcCCCCCCceEChhccChhh
Confidence            56789999975   43 34444688999999998644432    23999976544

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=92.99  E-value=0.056  Score=31.95  Aligned_cols=46  Identities=30%  Similarity=0.661  Sum_probs=32.7

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCC----CCccccCc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP----ICPICRTR  118 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~----~CP~CR~~  118 (143)
                      .+++.|.+|.+.   ++ +.....|.-.||..|+.+=+...+    .||.|+..
T Consensus        23 ~n~~~C~vC~~~---g~-LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~   72 (88)
T 1fp0_A           23 DSATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   72 (88)
T ss_dssp             SSSSCCSSSCSS---SC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCC
T ss_pred             CCCCcCcCcCCC---CC-EEECCCCCCceecccCCCCCCCCcCCCcCCccccCC
Confidence            467789999976   43 344445888999999977554422    49999754

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=92.42  E-value=0.022  Score=31.73  Aligned_cols=46  Identities=24%  Similarity=0.564  Sum_probs=31.9

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC----CCCccccCc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT----PICPICRTR  118 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~----~~CP~CR~~  118 (143)
                      .++..|.+|.+.   ++ +.....|...||..|+.+=+...    -.||.|+..
T Consensus         6 ~~~~~C~vC~~~---g~-ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~   55 (66)
T 1xwh_A            6 KNEDECAVCRDG---GE-LICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQA   55 (66)
T ss_dssp             SCCCSBSSSSCC---SS-CEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHT
T ss_pred             CCCCCCccCCCC---CC-EEEcCCCChhhcccccCCCcCcCCCCCeECccccCc
Confidence            357789999975   43 34444588899999998644432    249999653

>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=92.25  E-value=0.12  Score=42.99  Aligned_cols=53  Identities=15%  Similarity=0.154  Sum_probs=45.2

Q ss_pred             CCCCccccccccccCCCeeeEcCCCC-CcccHHhHHHHHhCCCCCccccCccCCCCcc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCR-HSFHAQCIDSWLLKTPICPICRTRVSPSKVG  125 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~-H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~  125 (143)
                      ++...|+|-++-|.++   +++| -| +.|-+..|.+|+..+.+||+=|.++...++.
T Consensus       889 P~~F~cPIs~~lM~DP---Vilp-sG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~li  942 (968)
T 3m62_A          889 PDEFLDPLMYTIMKDP---VILP-ASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVT  942 (968)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCE
T ss_pred             cHHhCCcchhhHHhCC---eEcC-CCCEEECHHHHHHHHhcCCCCCCCCCCCCccccc
Confidence            5667899999999987   7777 77 5899999999999999999999988866443

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=91.52  E-value=0.46  Score=29.11  Aligned_cols=34  Identities=21%  Similarity=0.426  Sum_probs=24.0

Q ss_pred             CCCccccccccc-----cCCCeeeEcCCCCCcccHHhHH
Q 032328           70 SPVDCVVCLENF-----RMGDKCRLLPNCRHSFHAQCID  103 (143)
Q Consensus        70 ~~~~C~ICl~~~-----~~~~~v~~l~~C~H~FH~~Ci~  103 (143)
                      ....|.+|+..-     ..++.+..-..|+..||..|+.
T Consensus         4 p~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~   42 (112)
T 3v43_A            4 PIPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLK   42 (112)
T ss_dssp             CCSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHT
T ss_pred             cCccccccCCchhhCcCCCchhceEhhhcCCCCCCchhc
Confidence            456799998753     1234455555699999999995

>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=91.32  E-value=0.02  Score=34.14  Aligned_cols=49  Identities=24%  Similarity=0.410  Sum_probs=33.4

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC----CCCccccCc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT----PICPICRTR  118 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~----~~CP~CR~~  118 (143)
                      .+...|.||...-.. +.+.....|...||..|+.+=+...    -.||.|+..
T Consensus        14 ~~~~~C~vC~~~~~~-~~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~   66 (92)
T 2e6r_A           14 IDSYICQVCSRGDED-DKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILA   66 (92)
T ss_dssp             CCCCCCSSSCCSGGG-GGCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHH
T ss_pred             cCCCCCccCCCcCCC-CCEEEcCCCCchhccccCCCCcccCCCCCcCCccCcCc
Confidence            355679999987433 3444444688999999998544332    239999764

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=90.95  E-value=0.11  Score=31.21  Aligned_cols=46  Identities=22%  Similarity=0.377  Sum_probs=30.0

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC---CCCCccccCc
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK---TPICPICRTR  118 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~---~~~CP~CR~~  118 (143)
                      ...| ||-.....+.. +....|.--||..|+..=...   ...||.|+..
T Consensus        28 ~vrC-iC~~~~~~~~m-i~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~~   76 (98)
T 2lv9_A           28 VTRC-ICGFTHDDGYM-ICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQPR   76 (98)
T ss_dssp             BCCC-TTSCCSCSSCE-EEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSSS
T ss_pred             CEEe-ECCCccCCCcE-EEcCCCCCcCcCcCCCCCccCCCCCEECCCCcCC
Confidence            3457 88877655543 444458999999998652222   2359999743

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2

Probab=90.71  E-value=0.044  Score=32.36  Aligned_cols=53  Identities=19%  Similarity=0.432  Sum_probs=36.5

Q ss_pred             CCCccccccccccC-CCeeeEcCCCCCcccHHhHHHHHh--------CCCCCccccCccCCC
Q 032328           70 SPVDCVVCLENFRM-GDKCRLLPNCRHSFHAQCIDSWLL--------KTPICPICRTRVSPS  122 (143)
Q Consensus        70 ~~~~C~ICl~~~~~-~~~v~~l~~C~H~FH~~Ci~~wl~--------~~~~CP~CR~~i~~~  122 (143)
                      .+..|.+|...-.. ++.+.....|...||..|+.+=+.        ..-.||.|+......
T Consensus        15 ~~~~C~vC~~~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~~~~~~~   76 (88)
T 1wev_A           15 MGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKRM   76 (88)
T ss_dssp             HCCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHCCS
T ss_pred             CCCcCCCCCCCCCCCCCceEECCCCCCeEcCccCCCcccccccCCCCCCeeCccccchhhhh
Confidence            35679999976433 244555557899999999987543        123499998766544

>2kgg_A Histone demethylase jarid1A; PHD finger, histone modification, leukemia, alternative splicing, chromatin regulator, developmental protein; NMR {Homo sapiens} PDB: 2kgi_A* 3gl6_A*

Probab=90.58  E-value=0.25  Score=25.95  Aligned_cols=44  Identities=18%  Similarity=0.291  Sum_probs=30.2

Q ss_pred             ccccccccccCCCeeeEcC-CCCCcccHHhHHHH----HhCCCCCcccc
Q 032328           73 DCVVCLENFRMGDKCRLLP-NCRHSFHAQCIDSW----LLKTPICPICR  116 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~-~C~H~FH~~Ci~~w----l~~~~~CP~CR  116 (143)
                      .|.+|...+.+++..+.-. .|..=||..|+.--    ...+..||.|+
T Consensus         4 ~cc~C~~p~~~~~~mI~Cd~~C~~WfH~~Cvgl~~~~~~~~~~~C~~C~   52 (52)
T 2kgg_A            4 AAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA   52 (52)
T ss_dssp             SCTTCCCCCCTTCCEEECTTTTCCEEETTTTTCCHHHHHHSCCCCSCC-
T ss_pred             cCCCCcCccCCCCcEEEeCCCCCccCcccccCCCccccCCCCEECCCCC
Confidence            4778988887666666655 58889999996421    12456799885

>2yt5_A Metal-response element-binding transcription factor 2; zinc-regulated factor 1, ZIRF1, metal-response element DNA-binding protein M96; NMR {Mus musculus}

Probab=90.45  E-value=0.18  Score=27.75  Aligned_cols=51  Identities=18%  Similarity=0.484  Sum_probs=34.3

Q ss_pred             CCCCcccccccccc-CCCeeeEcCCCCCcccHHhHHHHHh-------CCCCCccccCcc
Q 032328           69 SSPVDCVVCLENFR-MGDKCRLLPNCRHSFHAQCIDSWLL-------KTPICPICRTRV  119 (143)
Q Consensus        69 ~~~~~C~ICl~~~~-~~~~v~~l~~C~H~FH~~Ci~~wl~-------~~~~CP~CR~~i  119 (143)
                      .++..|.+|..... ++..+.....|...||..|+.+=+.       ..-.||.|+...
T Consensus         4 ~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~   62 (66)
T 2yt5_A            4 GSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFAT   62 (66)
T ss_dssp             CCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTT
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCcc
Confidence            45678999998643 2344555556889999999876331       223499986543

>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=90.36  E-value=0.23  Score=26.99  Aligned_cols=43  Identities=19%  Similarity=0.342  Sum_probs=31.4

Q ss_pred             CccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccc
Q 032328           72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPIC  115 (143)
Q Consensus        72 ~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~C  115 (143)
                      ..|--|...+.+. .....+.|++.|+.+|=.---..--+||-|
T Consensus        16 ~~C~~C~~~~~~~-~~y~C~~C~~~FC~dCD~fiHe~Lh~CPgC   58 (59)
T 1z60_A           16 RFCYGCQGELKDQ-HVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             CEETTTTEECTTS-EEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CcccccCcccCCC-ccEECCccCcCcccchhHHHHhhccCCcCC
Confidence            4599999998643 335567899999999975444445679988

>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=90.27  E-value=0.14  Score=33.91  Aligned_cols=48  Identities=17%  Similarity=0.517  Sum_probs=33.6

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHH-----hCCCCCccccCc
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWL-----LKTPICPICRTR  118 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl-----~~~~~CP~CR~~  118 (143)
                      +...| +|.....++...+....|..-||..|+.--.     ...-.||.|+..
T Consensus         7 ~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~   59 (174)
T 2ri7_A            7 TKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST   59 (174)
T ss_dssp             CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHH
T ss_pred             CCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcch
Confidence            45679 9998876555555555688999999984211     124569999864

>4gne_A Histone-lysine N-methyltransferase NSD3; zinc finger, transcription, nuclear protein, transf nuclear protein complex; 1.47A {Homo sapiens} PDB: 4gnd_A 4gnf_A 4gng_A*

Probab=90.23  E-value=0.26  Score=30.15  Aligned_cols=45  Identities=22%  Similarity=0.605  Sum_probs=29.2

Q ss_pred             CCCCCccccccccccCCCeeeEcC--CCCCcccHHhHHHHHhCCC----CCccccCc
Q 032328           68 GSSPVDCVVCLENFRMGDKCRLLP--NCRHSFHAQCIDSWLLKTP----ICPICRTR  118 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~v~~l~--~C~H~FH~~Ci~~wl~~~~----~CP~CR~~  118 (143)
                      ..+++.|.+|.+.   + .+..-.  .|...||..|+.  +...+    .||.|+-.
T Consensus        12 ~~~~~~C~~C~~~---G-~ll~CD~~~Cp~~fH~~Cl~--L~~~P~g~W~Cp~c~C~   62 (107)
T 4gne_A           12 QMHEDYCFQCGDG---G-ELVMCDKKDCPKAYHLLCLN--LTQPPYGKWECPWHQCD   62 (107)
T ss_dssp             CSSCSSCTTTCCC---S-EEEECCSTTCCCEECTGGGT--CSSCCSSCCCCGGGBCT
T ss_pred             CCCCCCCCcCCCC---C-cEeEECCCCCCcccccccCc--CCcCCCCCEECCCCCCC
Confidence            3567889999843   3 344433  487899999997  44322    38866533

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=90.09  E-value=0.045  Score=31.53  Aligned_cols=45  Identities=31%  Similarity=0.608  Sum_probs=28.1

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC-----CCCccccCc
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT-----PICPICRTR  118 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~-----~~CP~CR~~  118 (143)
                      .|.+|...-.. +.+..-..|...||..|+.+-+...     =.||.|+++
T Consensus        28 ~C~vC~~~~d~-~~ll~CD~C~~~yH~~Cl~PpL~~~P~g~~W~C~~C~~d   77 (77)
T 3shb_A           28 ACHLCGGRQDP-DKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND   77 (77)
T ss_dssp             SBTTTCCCSCG-GGEEECTTTCCEEETTTSSSCCSSCCSSSCCCCTTTC--
T ss_pred             cCCccCCCCCC-cceeEeCCCCCccCcccCCCcccCCCCCCceECcCcccc
Confidence            46677655322 3344444688999999998765442     359999753

>1wen_A Inhibitor of growth family, member 4; ING1-like protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.50.1.2 PDB: 1wes_A

Probab=88.43  E-value=0.58  Score=26.31  Aligned_cols=46  Identities=28%  Similarity=0.626  Sum_probs=28.8

Q ss_pred             CCCccccccccccCCCeeeEcCC--CC-CcccHHhHHHHHhC----CCCCccccCccC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPN--CR-HSFHAQCIDSWLLK----TPICPICRTRVS  120 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~--C~-H~FH~~Ci~~wl~~----~~~CP~CR~~i~  120 (143)
                      +...| ||-.... ++ ++....  |. .-||..|+.  +..    +-.||.|+..-.
T Consensus        15 ~~~~C-~C~~~~~-g~-MI~CD~~~C~~~wfH~~Cvg--l~~~p~g~w~Cp~C~~~~~   67 (71)
T 1wen_A           15 EPTYC-LCHQVSY-GE-MIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESG   67 (71)
T ss_dssp             SCCCS-TTCCCSC-SS-EECCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSCSS
T ss_pred             CCCEE-ECCCCCC-CC-EeEeeCCCCCCccEecccCC--cCcCCCCCEECCCCCcccc
Confidence            45568 8987643 33 333334  55 689999997  433    234999976543

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=88.29  E-value=0.14  Score=29.40  Aligned_cols=45  Identities=29%  Similarity=0.580  Sum_probs=29.6

Q ss_pred             CccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-----CCCCccccC
Q 032328           72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-----TPICPICRT  117 (143)
Q Consensus        72 ~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-----~~~CP~CR~  117 (143)
                      ..|.+|...-.. ..+..-..|...||..|+.+=+..     .=.||.|+.
T Consensus        27 c~C~vC~~~~~~-~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   76 (77)
T 2e6s_A           27 CSCRVCGGKHEP-NMQLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKT   76 (77)
T ss_dssp             SSCSSSCCCCCS-TTEEECSSSCCEEETTSSSSCCSSCCCSSCCCCTTTCC
T ss_pred             CCCcCcCCcCCC-CCEEEcCCCCccccccccCCCccCCCCCCCcCCcCccC
Confidence            378999865333 334444468899999999864433     224888864

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=87.63  E-value=0.43  Score=29.39  Aligned_cols=34  Identities=21%  Similarity=0.362  Sum_probs=23.4

Q ss_pred             Ccccccccccc------CCCeeeEcCCCCCcccHHhHHHH
Q 032328           72 VDCVVCLENFR------MGDKCRLLPNCRHSFHAQCIDSW  105 (143)
Q Consensus        72 ~~C~ICl~~~~------~~~~v~~l~~C~H~FH~~Ci~~w  105 (143)
                      +.|.+|+..-.      +++.+..-..|+..||..|+...
T Consensus         2 ~~C~~C~~~~~~n~k~g~~~~Li~C~~C~~~~H~~Cl~~~   41 (114)
T 2kwj_A            2 SYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFT   41 (114)
T ss_dssp             CCCSSSCCBTTBCTTTCCCCCCEECSSSCCEECTTTTTCC
T ss_pred             CcCccCCCCccccccCCCCCCCeEeCCCCCccchhhCCCh
Confidence            56999987541      12344544469999999998754

>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=87.39  E-value=0.27  Score=27.91  Aligned_cols=48  Identities=21%  Similarity=0.429  Sum_probs=31.4

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHH---------HhCCCCCccccCcc
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSW---------LLKTPICPICRTRV  119 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~w---------l~~~~~CP~CR~~i  119 (143)
                      +...| ||...+..+.. +....|..=||..|+.--         ......||.|+..-
T Consensus        15 ~~~~C-~C~~~~~~~~M-I~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~~   71 (76)
T 1wem_A           15 NALYC-ICRQPHNNRFM-ICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             TCCCS-TTCCCCCSSCE-EECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             CCCEE-ECCCccCCCCE-EEeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCcc
Confidence            34567 89888764333 333458899999998421         12457799997543

>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=87.20  E-value=1.4  Score=25.32  Aligned_cols=39  Identities=23%  Similarity=0.431  Sum_probs=29.7

Q ss_pred             CCCCccccccccccCCCeeeEcC-CCCCcccHHhHHHHHhC
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLP-NCRHSFHAQCIDSWLLK  108 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~-~C~H~FH~~Ci~~wl~~  108 (143)
                      ...-.|.+|.+.+++..-|. .| .=.|-||..|-+..+++
T Consensus        13 ~a~l~CtlC~erLEdtHFVQ-CPsv~~HkFCFpCsr~sIk~   52 (93)
T 2cs3_A           13 SGPLCCTICHERLEDTHFVQ-CPSVPSHKFCFPCSRESIKA   52 (93)
T ss_dssp             CCSCCCSSSCSCCSSTTSEE-CSSCSSCEECHHHHHHHHHH
T ss_pred             CCeeEeecchhhhccCceee-CCCccCCeeeccccHHHHHh
Confidence            45668999999998865544 33 33699999999998865

>3asl_A E3 ubiquitin-protein ligase UHRF1; histone reader module, epigenetic regulation, LI binding protein complex; 1.41A {Homo sapiens} PDB: 3sou_A 3sow_A* 3sox_A 3zvy_A 2lgg_A 2lgk_A* 2lgl_A 3t6r_A 3zvz_B

Probab=86.70  E-value=0.15  Score=28.72  Aligned_cols=45  Identities=31%  Similarity=0.614  Sum_probs=28.3

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-----CCCCccccCc
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-----TPICPICRTR  118 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-----~~~CP~CR~~  118 (143)
                      .|.+|...-. +..+..-..|...||..|+.+=+..     .=.||.|+.+
T Consensus        20 ~C~~C~~~~~-~~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~~   69 (70)
T 3asl_A           20 ACHLCGGRQD-PDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND   69 (70)
T ss_dssp             SBTTTCCCSC-GGGEEECTTTCCEEEGGGSSSCCSSCCSSSCCCCTTTSCC
T ss_pred             CCcCCCCcCC-CCCEEEcCCCCCceecccCCCCcCCCCCCCCcCCcCccCc
Confidence            4667775422 2344444468899999999854433     2249998753

>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens}

Probab=86.08  E-value=0.55  Score=28.51  Aligned_cols=50  Identities=20%  Similarity=0.418  Sum_probs=35.0

Q ss_pred             CCccccccccccCCCeeeEcC-CCCCcccHHhHHHH------H----hCCCCCccccCccC
Q 032328           71 PVDCVVCLENFRMGDKCRLLP-NCRHSFHAQCIDSW------L----LKTPICPICRTRVS  120 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~-~C~H~FH~~Ci~~w------l----~~~~~CP~CR~~i~  120 (143)
                      ...|.||...+.++...+... .|..=||..|+.-=      +    .....||.|+..-.
T Consensus         3 ~~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~~   63 (105)
T 2xb1_A            3 VYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTKE   63 (105)
T ss_dssp             CCBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTTT
T ss_pred             cCCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcCC
Confidence            357999999987766666554 58889999997421      1    02355999987644

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2

Probab=85.62  E-value=0.69  Score=27.38  Aligned_cols=45  Identities=29%  Similarity=0.636  Sum_probs=28.1

Q ss_pred             CCCccccccccccCCCeeeEcCC--CC-CcccHHhHHHHHhC----CCCCccccCcc
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPN--CR-HSFHAQCIDSWLLK----TPICPICRTRV  119 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~--C~-H~FH~~Ci~~wl~~----~~~CP~CR~~i  119 (143)
                      +...| ||-.... ++ ++....  |. .-||..|+.  +..    +-.||.|+..-
T Consensus        35 e~~yC-iC~~~~~-g~-MI~CD~~dC~~~WfH~~CVg--l~~~p~g~W~Cp~C~~~~   86 (91)
T 1weu_A           35 EPTYC-LCHQVSY-GE-MIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQES   86 (91)
T ss_dssp             CCBCS-TTCCBCC-SC-CCCCSCSSCSCCCCCSTTTT--CSSCCCSSCCCTTTCCCC
T ss_pred             CCcEE-ECCCCCC-CC-EeEecCCCCCCCCEecccCC--cCcCCCCCEECcCccCcC
Confidence            45567 9988643 32 233234  54 579999997  333    33599997643

>3c6w_A P28ING5, inhibitor of growth protein 5; chromatin, PHD, ING, epigenetics, alternative splicing, metal-binding, phosphoprotein, zinc; HET: M3L; 1.75A {Homo sapiens} PDB: 2pnx_A*

Probab=82.86  E-value=0.38  Score=26.00  Aligned_cols=43  Identities=33%  Similarity=0.675  Sum_probs=27.3

Q ss_pred             CCCccccccccccCCCeeeEcCC--CC-CcccHHhHHHHHhC----CCCCccccC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPN--CR-HSFHAQCIDSWLLK----TPICPICRT  117 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~--C~-H~FH~~Ci~~wl~~----~~~CP~CR~  117 (143)
                      +...| +|-+... + ..+....  |. .-||..|+.  +..    +-.||.|+.
T Consensus         8 e~~yC-~C~~~~~-g-~mi~CD~~~C~~~wfH~~Cvg--l~~~p~~~w~Cp~C~~   57 (59)
T 3c6w_A            8 EPTYC-LCHQVSY-G-EMIGCDNPDCPIEWFHFACVD--LTTKPKGKWFCPRCVQ   57 (59)
T ss_dssp             CCEET-TTTEECC-S-EEEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CCcEE-ECCCCCC-C-CeeEeeCCCCCCCCEecccCC--cccCCCCCEECcCccC
Confidence            44567 8987642 3 3444445  65 699999997  433    234998864

>2vnf_A ING 4, P29ING4, inhibitor of growth protein 4; acetylation, alternative splicing, anti-oncogene, cell cycle, coiled C nucleus, zinc, zinc-finger, ING4; HET: M3L; 1.76A {Homo sapiens} SCOP: g.50.1.2 PDB: 2k1j_A 2jmq_A 2qic_A*

Probab=82.58  E-value=0.37  Score=26.15  Aligned_cols=43  Identities=30%  Similarity=0.659  Sum_probs=26.6

Q ss_pred             CCCccccccccccCCCeeeEcCC--CC-CcccHHhHHHHHhC----CCCCccccC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPN--CR-HSFHAQCIDSWLLK----TPICPICRT  117 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~--C~-H~FH~~Ci~~wl~~----~~~CP~CR~  117 (143)
                      +...| ||..... + .++....  |. .-||..|+.  +..    +-.||.|+.
T Consensus         9 e~~~C-~C~~~~~-g-~mi~CD~cdC~~~wfH~~Cvg--l~~~p~g~w~C~~C~~   58 (60)
T 2vnf_A            9 EPTYC-LCHQVSY-G-EMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQ   58 (60)
T ss_dssp             CCEET-TTTEECC-S-EEEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CCCEE-ECCCcCC-C-CEEEeCCCCCCCceEehhcCC--CCcCCCCCEECcCccC
Confidence            44567 8987632 3 3343334  44 689999997  443    234998864

>1wfk_A Zinc finger, FYVE domain containing 19; riken structural genomics/proteomics initiative, RSGI, structural genomics, unknown function; NMR {Mus musculus} SCOP: g.50.1.1

Probab=82.10  E-value=1.4  Score=25.80  Aligned_cols=53  Identities=23%  Similarity=0.440  Sum_probs=34.0

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHh-------CCCCCccccCccCCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL-------KTPICPICRTRVSPS  122 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~-------~~~~CP~CR~~i~~~  122 (143)
                      +...|.+|...|..-..--....||++|+..|......       ....|-.|...+...
T Consensus         8 ~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~~~~lp~~g~~~~RVC~~C~~~l~~~   67 (88)
T 1wfk_A            8 MESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFSALVPRAGNTQQKVCKQCHTILTRG   67 (88)
T ss_dssp             CCSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCEEEEETTTTSEEEEECHHHHHHHHHC
T ss_pred             cCCCCcCcCCcccCccccccCCCCCCEEChhHcCCceeccccCCCcCEECHHHHHHHHhc
Confidence            45679999999875422222235999999999865321       123488886665543

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=81.95  E-value=0.21  Score=30.56  Aligned_cols=45  Identities=20%  Similarity=0.440  Sum_probs=29.1

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC----CCCccccCc
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT----PICPICRTR  118 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~----~~CP~CR~~  118 (143)
                      .|.+|...-.+ +.+..-..|...||..|+.+=+...    -.||.|+.-
T Consensus        56 ~C~~C~~~~~~-~~ll~Cd~C~~~yH~~Cl~ppl~~~P~g~W~C~~C~~c  104 (111)
T 2ysm_A           56 VCQNCKQSGED-SKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNCRIC  104 (111)
T ss_dssp             CCTTTCCCSCC-TTEEECSSSCCEEEGGGSSSCCSSCCSSCCCCHHHHCC
T ss_pred             cccccCccCCC-CCeeECCCCCcHHhHHhcCCccccCCCCCcCCcCCcCc
Confidence            57777766333 3344444689999999998644432    248888554

>3ask_A E3 ubiquitin-protein ligase UHRF1; histone reader modules, epigenetic regulation, trimethylaion of lysine residue, ligase-DNA binding protein; HET: M3L; 2.90A {Homo sapiens}

Probab=81.94  E-value=0.38  Score=33.41  Aligned_cols=45  Identities=31%  Similarity=0.625  Sum_probs=26.0

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC--C---CCCccccCc
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK--T---PICPICRTR  118 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~--~---~~CP~CR~~  118 (143)
                      .|.+|...-. +..+.....|...||..|+.+=+..  .   =.||.|+.+
T Consensus       176 ~C~vC~~~~~-~~~lL~CD~C~~~yH~~CL~PPL~~vP~G~~W~Cp~C~~~  225 (226)
T 3ask_A          176 ACHLCGGRQD-PDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND  225 (226)
T ss_dssp             SCSSSCCCCC---CCEECSSSCCEECSCC--CCCCSCCSSSCCCCGGGC--
T ss_pred             CCcCCCCCCC-CCCeEEcCCCCcceeCccCCCCcccCCCCCCCCCcCCcCc
Confidence            5888876422 2334444468899999999864433  2   249999653

>1vfy_A Phosphatidylinositol-3-phosphate binding FYVE domain of protein VPS27; endosome maturation, intracellular trafficking; 1.15A {Saccharomyces cerevisiae} SCOP: g.50.1.1

Probab=81.44  E-value=1.3  Score=24.82  Aligned_cols=33  Identities=15%  Similarity=0.430  Sum_probs=23.0

Q ss_pred             CccccccccccCCCeeeEcCCCCCcccHHhHHH
Q 032328           72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDS  104 (143)
Q Consensus        72 ~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~  104 (143)
                      ..|.+|...|..-..--....||++|+..|...
T Consensus        12 ~~C~~C~~~F~~~~RrHHCR~CG~v~C~~Cs~~   44 (73)
T 1vfy_A           12 DACMICSKKFSLLNRKHHCRSCGGVFCQEHSSN   44 (73)
T ss_dssp             SBCTTTCCBCBTTBCCEECTTTCCEECGGGSCE
T ss_pred             CcccCCCCccCCccccccCCCCCEEEcccccCC
Confidence            479999999875322122235999999999753

>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=81.10  E-value=0.8  Score=26.12  Aligned_cols=49  Identities=22%  Similarity=0.374  Sum_probs=30.8

Q ss_pred             CCCccccccccccCCCeeeEcC-CCCCcccHHhHHHHH---------hCCCCCccccCcc
Q 032328           70 SPVDCVVCLENFRMGDKCRLLP-NCRHSFHAQCIDSWL---------LKTPICPICRTRV  119 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~-~C~H~FH~~Ci~~wl---------~~~~~CP~CR~~i  119 (143)
                      ....| ||-.....+..|.--. .|..=||..|+.-=-         ..+..||.|+..-
T Consensus        15 ~~~~C-iC~~~~~~g~MI~CD~~~C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T 1wew_A           15 IKVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             CCEEe-ECCCcCCCCCEEEECCccCCccccCEEEccccccccccccCCCCEECCCCCccc
Confidence            45678 7988754443333320 488899999985311         1245699997653

>3a1b_A DNA (cytosine-5)-methyltransferase 3A, histone H3; zinc-finger, histone binding, chromosomal protein, DNA damag repair, DNA-binding, methylation; HET: DNA; 2.29A {Homo sapiens} PDB: 3a1a_A*

Probab=80.99  E-value=1.4  Score=28.79  Aligned_cols=37  Identities=19%  Similarity=0.468  Sum_probs=27.7

Q ss_pred             CCCCCccccccccccCCCeeeEcC--CCCCcccHHhHHHHHhC
Q 032328           68 GSSPVDCVVCLENFRMGDKCRLLP--NCRHSFHAQCIDSWLLK  108 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~v~~l~--~C~H~FH~~Ci~~wl~~  108 (143)
                      .+.+..|.||-+.    ..+....  .|...|+.+||..++..
T Consensus        76 DG~~~yC~wC~~G----g~l~~Cdn~~C~r~FC~~CI~~nvG~  114 (159)
T 3a1b_A           76 DGYQSYCTICCGG----REVLMCGNNNCCRCFCVECVDLLVGP  114 (159)
T ss_dssp             TSSBSSCTTTSCC----SEEEECSSTTTCCEEEHHHHHHHTCT
T ss_pred             CCCcceeeEecCC----CeEEeeCCCCCCCchhHHHHHHhcCH
Confidence            4457789999975    3445544  58899999999998743

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=80.79  E-value=1.5  Score=25.37  Aligned_cols=36  Identities=17%  Similarity=0.246  Sum_probs=25.2

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHH
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSW  105 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~w  105 (143)
                      +...|.+|...|..-..--....||++|+..|....
T Consensus        20 ~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~   55 (84)
T 1z2q_A           20 DAPACNGCGCVFTTTVRRHHCRNCGYVLCGDCSRHR   55 (84)
T ss_dssp             TCCBCTTTCCBCCTTSCCEECTTTCCEECTGGGCCE
T ss_pred             CCCCCcCcCCccccchhcccccCCCcEEChHHhCCe
Confidence            456799999998753222222359999999997653

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=80.64  E-value=1.5  Score=25.22  Aligned_cols=35  Identities=23%  Similarity=0.575  Sum_probs=24.6

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHH
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDS  104 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~  104 (143)
                      +...|.+|...|..-..--....||.+|+..|...
T Consensus        18 ~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~   52 (82)
T 2yw8_A           18 EATHCRQCEKEFSISRRKHHCRNCGHIFCNTCSSN   52 (82)
T ss_dssp             CCCBCTTTCCBCBTTBCCEECTTTCCEECSGGGCE
T ss_pred             cCCcccCcCCcccCccccccCCCCCCEEChHHhCC
Confidence            34579999999875322222235999999999865

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=80.23  E-value=0.098  Score=32.35  Aligned_cols=47  Identities=15%  Similarity=0.488  Sum_probs=30.2

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC----CCCccccCccC
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT----PICPICRTRVS  120 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~----~~CP~CR~~i~  120 (143)
                      .|.+|...-.++ .+..-..|...||..|+.+=+...    -.||.|+....
T Consensus        60 ~C~~C~~~~~~~-~ll~Cd~C~~~yH~~Cl~ppl~~~P~g~W~C~~C~~~~~  110 (114)
T 2kwj_A           60 SCILCGTSENDD-QLLFCDDCDRGYHMYCLNPPVAEPPEGSWSCHLCWELLK  110 (114)
T ss_dssp             CCTTTTCCTTTT-TEEECSSSCCEEETTTSSSCCSSCCSSCCCCHHHHHHHH
T ss_pred             ccCcccccCCCC-ceEEcCCCCccccccccCCCccCCCCCCeECccccchhh
Confidence            588887764333 344444689999999998644332    23888865443

---

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	143
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	1e-16
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	6e-11
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	4e-10
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	6e-10
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	2e-08
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	5e-08
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	9e-08
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	7e-07
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	2e-06
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	5e-06
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	6e-06
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	9e-06
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	5e-04
d1we9a_	64	g.50.1.2 (A:) PHD finger protein At5g26210 {Thale	6e-04
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	0.004

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 66.8 bits (163), Expect = 1e-16
 Identities = 23/48 (47%), Positives = 29/48 (60%)

Query: 72  VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRV 119
           V+C VCL     G++ R LP C H FHA+C+D WL     CP+CR  V
Sbjct: 6   VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 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 = 52.6 bits (126), Expect = 6e-11
 Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 3/47 (6%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS 120
           C +CLE+    +    LP C H+F   CI  W+ + P CP+C+  V 
Sbjct: 8   CPICLEDPS--NYSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVE 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 = 50.8 bits (121), Expect = 4e-10
 Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 60  EYKAAADRGSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWL-LKTPICPICRTR 118
           +Y+   + GS+   C +C EN +     ++ P C H     C+ SW   +   CP CR  
Sbjct: 12  QYELYCEMGSTFQLCKICAENDK---DVKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCE 67

Query: 119 VSPSKVGVI 127
           +  ++  V+
Sbjct: 68  IKGTEPIVV 76

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.7 bits (118), Expect = 6e-10
 Identities = 11/51 (21%), Positives = 18/51 (35%), Gaps = 1/51 (1%)

Query: 72  VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWL-LKTPICPICRTRVSP 121
           V+C +C+E   + D       C +     C       +  +CP CR     
Sbjct: 1   VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE 51

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.6 bits (108), Expect = 2e-08
 Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 7/49 (14%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPS 122
           C  C    +     +LLP C H+  + C+++  ++   CPIC+      
Sbjct: 9   CQQCQAEAK---CPKLLP-CLHTLCSGCLEASGMQ---CPICQAPWPLG 50

>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 = 45.2 bits (106), Expect = 5e-08
 Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 2/60 (3%)

Query: 73  DCVVCLENFRMGDKCRLLPN-CRHSFHAQCIDSWLLKTP-ICPICRTRVSPSKVGVILKD 130
            C  C          +L+ N C H+    C+D   ++    CP C T +  S   V L +
Sbjct: 5   GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQLFE 64

>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 = 44.7 bits (105), Expect = 9e-08
 Identities = 12/59 (20%), Positives = 18/59 (30%), Gaps = 14/59 (23%)

Query: 73  DCVVCLENFRMGDKCRLLPN--------------CRHSFHAQCIDSWLLKTPICPICRT 117
           +C +C  +                          C H+FH  CI  WL    +CP+   
Sbjct: 23  NCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 81

>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 = 42.6 bits (100), Expect = 7e-07
 Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 5/52 (9%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWL-LKTPICPICRTRVSPSKV 124
           C +C           +  +C+H F   CI   L +    CP CR    P+ +
Sbjct: 26  CQICEHIL----ADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDL 73

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.9 bits (97), Expect = 2e-06
 Identities = 10/49 (20%), Positives = 15/49 (30%), Gaps = 5/49 (10%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPI-----CPICRT 117
             +             L  C H+FH  C+ +            CP C+T
Sbjct: 42  SDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKT 90

>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 = 40.5 bits (94), Expect = 5e-06
 Identities = 12/51 (23%), Positives = 17/51 (33%), Gaps = 5/51 (9%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKV 124
           C  C    R       L  C H F + C+   +     CP+C T      +
Sbjct: 25  CSRCTNILRE---PVCLGGCEHIFCSNCVSDCI--GTGCPVCYTPAWIQDL 70

>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 = 40.4 bits (94), Expect = 6e-06
 Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 7/55 (12%)

Query: 73  DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWL---LKTPICPICRTRVSPSKV 124
           +C +CLE  +   +      C H F   C+   L        CP+C+  ++   +
Sbjct: 23  ECPICLELIK---EPVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL 73

>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 = 39.1 bits (90), Expect = 9e-06
 Identities = 10/50 (20%), Positives = 17/50 (34%), Gaps = 3/50 (6%)

Query: 74  CVVCLENF-RMGDKCRLLPNCRHSFHAQCIDSWLLKTPI--CPICRTRVS 120
           C +C E       +         + H  C+ +WL  +    C IC    +
Sbjct: 9   CWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN 58

>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 = 35.1 bits (80), Expect = 5e-04
 Identities = 9/58 (15%), Positives = 17/58 (29%), Gaps = 9/58 (15%)

Query: 69  SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWL--------LKTPICPICRTR 118
           S    C +CL  + +     +   C+  F   C+  ++             CP     
Sbjct: 3   SGSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACP 59

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 64

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 34.2 bits (78), Expect = 6e-04
 Identities = 13/59 (22%), Positives = 20/59 (33%), Gaps = 5/59 (8%)

Query: 69  SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP-----ICPICRTRVSPS 122
            S   C  C E++   +       C   FH +C+     +        CP C  +  PS
Sbjct: 4   GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKSGPS 62

>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 = 31.7 bits (71), Expect = 0.004
 Identities = 9/51 (17%), Positives = 18/51 (35%), Gaps = 3/51 (5%)

Query: 74  CVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKV 124
           C +  +  R        P  R  F    ++ ++  T   PI    +S  ++
Sbjct: 3   CAISGKVPRRPVLS---PKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEI 50

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	143
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.86
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.74
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.72
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.71
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.7
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.69
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.66
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.64
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.55
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.53
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.5
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.46
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.36
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.32
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.32
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.21
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.96
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	96.37
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	96.11
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	95.78
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	95.66
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	95.15
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	94.86
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	94.59
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	94.07
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	93.7
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	92.89
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	92.18
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	89.55
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	89.51
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	88.44
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	87.87
d2co8a2	36	Nedd9 interacting protein with calponin homology,	87.74
d1dvpa2	72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	84.03
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	83.77
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	83.67
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	83.66
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	82.74
d2dasa1	49	Zinc finger MYM-type protein 5 {Human (Homo sapien	82.42
d1vfya_	67	vps27p protein {Baker's yeast (Saccharomyces cerev	81.86
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	80.61

>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=99.86  E-value=1.1e-22  Score=111.45  Aligned_cols=51  Identities=45%  Similarity=1.108  Sum_probs=46.7

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVS  120 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~  120 (143)
                      ++.+|+||+++|.+++.+..++.|||.||.+|+.+|++.+.+||+||+++.
T Consensus         4 d~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            456799999999999999888779999999999999999999999999874

>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=99.74  E-value=6e-19  Score=100.70  Aligned_cols=50  Identities=34%  Similarity=0.849  Sum_probs=43.0

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      ..+.|+||++.+.+  .++.++ |||.||.+|+.+|++.+.+||+||.++...
T Consensus         4 ~~d~C~IC~~~~~~--~~~~~~-C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~~   53 (68)
T d1chca_           4 VAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVESV   53 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCCE
T ss_pred             CCCCCccCCcCccC--CcEEeC-CCCcCcHHHHHHHHHhCCcCCCCCcchHhh
Confidence            46789999999865  345677 999999999999999999999999988643

>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=99.72  E-value=1.1e-18  Score=94.42  Aligned_cols=50  Identities=20%  Similarity=0.505  Sum_probs=41.0

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-CCCCccccCccCCC
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPS  122 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~~  122 (143)
                      +|+||+++|..++.......|||.||.+|+.+|++. +.+||+||+++.++
T Consensus         2 eCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~d   52 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED   52 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSCC
T ss_pred             CCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCCC
Confidence            699999999877654443239999999999999986 45699999998753

>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=99.71  E-value=3e-18  Score=102.49  Aligned_cols=52  Identities=23%  Similarity=0.530  Sum_probs=43.3

Q ss_pred             CCCccccccccccCCC---------------eeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCC
Q 032328           70 SPVDCVVCLENFRMGD---------------KCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPS  122 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~---------------~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~  122 (143)
                      .++.|+||++++.+..               .+..++ |||.||.+||.+||+.+.+||+||+++..+
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   86 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEFQ   86 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCCEE
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCccccc
Confidence            5667999998886532               356666 999999999999999999999999998654

>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=99.70  E-value=2.5e-18  Score=100.77  Aligned_cols=54  Identities=30%  Similarity=0.644  Sum_probs=44.0

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-CCCCccccCccCCCCcce
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPSKVGV  126 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~~~~~~  126 (143)
                      +....|+||++.+.+   .+++| |||.||.+||..|+.. .++||+||.++.......
T Consensus        21 ~~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~i~   75 (79)
T d1fbva4          21 STFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIV   75 (79)
T ss_dssp             CCTTBCTTTSSSBCC---EECSS-SCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCCSS
T ss_pred             CCCCCCccCCCcCCC---eEEeC-CCCeeeHHHHHHHHHHCcCcCCCCCcCccCCceee
Confidence            344679999999765   46777 9999999999999975 567999999998765443

>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=99.69  E-value=1.6e-17  Score=93.82  Aligned_cols=57  Identities=23%  Similarity=0.458  Sum_probs=44.2

Q ss_pred             CCCccccccccccCC-C-eeeEcCCCCCcccHHhHHHHHhC-CCCCccccCccCCCCccee
Q 032328           70 SPVDCVVCLENFRMG-D-KCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPSKVGVI  127 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~-~-~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~~~~~~~  127 (143)
                      ++..|+||++.+..+ + .+.+++ |||.||.+||.+|+.. +..||+||..+...+.+..
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~~~~~   61 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQ   61 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCCEEE
T ss_pred             CCCCCCcCCceeecCCceEEEeCc-cChHhhHHHHHHHhCcCcCCCCCCCcCccccccccc
Confidence            467899999986433 3 334556 9999999999999965 5579999999987765544

>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=99.66  E-value=3.5e-17  Score=102.31  Aligned_cols=55  Identities=27%  Similarity=0.608  Sum_probs=43.0

Q ss_pred             CCCCccccccccccC---------------CCeeeEcCCCCCcccHHhHHHHHhCC-----CCCccccCccCCCCc
Q 032328           69 SSPVDCVVCLENFRM---------------GDKCRLLPNCRHSFHAQCIDSWLLKT-----PICPICRTRVSPSKV  124 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~---------------~~~v~~l~~C~H~FH~~Ci~~wl~~~-----~~CP~CR~~i~~~~~  124 (143)
                      ..++.|+||++++..               ...+..++ |||.||.+||..|+...     .+||+||+.+..+..
T Consensus        23 ~~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~~   97 (114)
T d1v87a_          23 APEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTG   97 (114)
T ss_dssp             CCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSS
T ss_pred             cccccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhcCcCCCCccccccchhccCcC
Confidence            346789999999853               23355666 99999999999999753     479999999877654

>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=99.64  E-value=2.8e-17  Score=90.08  Aligned_cols=53  Identities=21%  Similarity=0.263  Sum_probs=45.6

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcceee
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVGVIL  128 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~~~~  128 (143)
                      .|+||++.++++   ..++.|||.||++||.+|++.+.+||+||.++..+++..+.
T Consensus         2 ~C~Ic~~~~~~P---v~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dLipik   54 (56)
T d2baya1           2 LCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEIV   54 (56)
T ss_dssp             CCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEECC
T ss_pred             CCccCCchHHhc---CccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhceeCC
Confidence            599999998764   45556999999999999999999999999999988776543

>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=99.55  E-value=5e-16  Score=84.75  Aligned_cols=49  Identities=24%  Similarity=0.597  Sum_probs=40.5

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcc
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG  125 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~  125 (143)
                      ....|+||++.+.++   +.+| |||.||..|+.+|   +.+||+||.++......
T Consensus         5 ~~l~C~IC~~~~~~p---~~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~~~   53 (56)
T d1bora_           5 QFLRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGADT   53 (56)
T ss_dssp             CCSSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCSSC
T ss_pred             CCCCCcccCcccCCC---EEec-CCCHHhHHHHHcC---CCcCcCCCCcccCCCCC
Confidence            345899999999875   6778 9999999999765   56799999999876543

>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=99.53  E-value=2.8e-15  Score=88.58  Aligned_cols=50  Identities=26%  Similarity=0.554  Sum_probs=41.9

Q ss_pred             CccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-CCCCccccCccCCCCcc
Q 032328           72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPSKVG  125 (143)
Q Consensus        72 ~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~~~~~  125 (143)
                      ..|+||++.+.+.   .+++ |||.||+.||.+|++. ..+||.||.++...++.
T Consensus        24 l~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l~   74 (86)
T d1rmda2          24 ISCQICEHILADP---VETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE   74 (86)
T ss_dssp             TBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCB
T ss_pred             cCCccCCcchhcc---eecC-CCChhhHHHHHHHHhhCCCcCcccCCCCChhhcc
Confidence            5799999998774   6677 9999999999999974 46799999998766544

>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=99.50  E-value=7.8e-15  Score=89.86  Aligned_cols=50  Identities=24%  Similarity=0.637  Sum_probs=41.6

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC---CCCccccCccCCCCc
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT---PICPICRTRVSPSKV  124 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~---~~CP~CR~~i~~~~~  124 (143)
                      ...|+||++.+.++   ..++ |||.||..||..|+..+   ..||+||.++...+.
T Consensus        21 ~l~CpIC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l   73 (103)
T d1jm7a_          21 ILECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL   73 (103)
T ss_dssp             HTSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTC
T ss_pred             CcCCCccCchhCCe---EEcC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhC
Confidence            35699999999875   5567 99999999999999764   369999999976654

>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=99.46  E-value=2.1e-14  Score=79.49  Aligned_cols=53  Identities=19%  Similarity=0.408  Sum_probs=38.6

Q ss_pred             CCCCccccccccccCCCeeeE-cCCCCCcccHHhHHHHHhC--CCCCccccCccCC
Q 032328           69 SSPVDCVVCLENFRMGDKCRL-LPNCRHSFHAQCIDSWLLK--TPICPICRTRVSP  121 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~-l~~C~H~FH~~Ci~~wl~~--~~~CP~CR~~i~~  121 (143)
                      .+...|.||++++.++....- ...|+|.||..|+.+|+..  +.+||+||+++..
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            356789999999865422211 1124699999999999954  5679999998764

>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=99.36  E-value=8.2e-14  Score=84.32  Aligned_cols=49  Identities=24%  Similarity=0.550  Sum_probs=39.3

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCc
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKV  124 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~  124 (143)
                      ...|+||++.|.++   ..++.|||.||..||.+|+..  .||.||.++...+.
T Consensus        22 ~l~C~IC~~~~~~p---v~~~~CgH~fC~~Ci~~~~~~--~CP~Cr~~~~~~~l   70 (97)
T d1jm7b_          22 LLRCSRCTNILREP---VCLGGCEHIFCSNCVSDCIGT--GCPVCYTPAWIQDL   70 (97)
T ss_dssp             TTSCSSSCSCCSSC---BCCCSSSCCBCTTTGGGGTTT--BCSSSCCBCSCSSC
T ss_pred             cCCCccCCchhhcC---ceeCCCCCchhHHHHHHHHhc--cccccCCcCchhhC
Confidence            45799999999875   333339999999999999853  59999998876543

>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=99.32  E-value=5.8e-13  Score=77.70  Aligned_cols=52  Identities=13%  Similarity=0.258  Sum_probs=43.8

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC-CCCCccccCccCCCCc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK-TPICPICRTRVSPSKV  124 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~-~~~CP~CR~~i~~~~~  124 (143)
                      .++..|+||++-|.++   ..++ |||.|+..||.+|+.. +..||.||.++...++
T Consensus         5 P~~l~CpIc~~l~~dP---v~~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~l   57 (80)
T d2c2la2           5 PDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQL   57 (80)
T ss_dssp             CSTTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGC
T ss_pred             CccccCcCcCchhhhh---cccC-CcCeecHHHHHHHHhcCCccCCCcccccccccc
Confidence            4667899999999886   5677 9999999999999975 5579999999876543

>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=99.32  E-value=1e-12  Score=76.28  Aligned_cols=53  Identities=15%  Similarity=0.366  Sum_probs=44.9

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC-CCCccccCccCCCCcc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT-PICPICRTRVSPSKVG  125 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~-~~CP~CR~~i~~~~~~  125 (143)
                      .++..|+||++-|.++   ++++ |||.|++.||.+|+..+ ..||.||.++...++.
T Consensus         6 P~~l~CpIc~~~m~dP---V~~~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~l~   59 (78)
T d1t1ha_           6 PEYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLT   59 (78)
T ss_dssp             SSSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCE
T ss_pred             CccCCCcCcCchhhCc---eEcc-CCCcchHHHHHHHHHHCCCCCCcccccCCccccc
Confidence            4677899999999886   5677 99999999999999764 5699999998876543

>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=99.21  E-value=1e-11  Score=74.95  Aligned_cols=54  Identities=15%  Similarity=0.145  Sum_probs=46.0

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccccCccCCCCcc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICRTRVSPSKVG  125 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR~~i~~~~~~  125 (143)
                      .++..|+||.+-|.++   ++++.|||.|++.||.+|+..+..||+||.++...++.
T Consensus        20 P~~f~CPI~~~lm~dP---V~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L~   73 (98)
T d1wgma_          20 CDEFLDPIMSTLMCDP---VVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIR   73 (98)
T ss_dssp             CTTTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSE
T ss_pred             cHHhCCcCchhHHHHH---HhcccccchhhHHHHHHHHHhcCCcccccccccchhhc
Confidence            4678999999999986   67773456899999999999999999999999876554

>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=98.96  E-value=1.5e-10  Score=69.15  Aligned_cols=46  Identities=17%  Similarity=0.525  Sum_probs=37.1

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCC--------CCCcccc
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKT--------PICPICR  116 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~--------~~CP~CR  116 (143)
                      ....|+||++++..++.+..++ |+|.||.+|+..|+..+        ..||.|+
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCCcCccCCCcccCCceEEECC-CCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            4568999999998877777766 99999999999999531        2599854

>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=96.37  E-value=0.00085  Score=34.31  Aligned_cols=44  Identities=34%  Similarity=0.749  Sum_probs=31.0

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCC----CCccccC
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP----ICPICRT  117 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~----~CP~CR~  117 (143)
                      .|.||-..-.. +.+..-..|...||..|+..-+...+    .||.||.
T Consensus         2 ~C~vC~~~~~~-~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGED-DKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCC-SCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCC-CCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            48888766443 34455556999999999988665432    3999974

>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=96.11  E-value=0.0029  Score=35.26  Aligned_cols=36  Identities=22%  Similarity=0.408  Sum_probs=27.1

Q ss_pred             CCCCCccccccccccCCCeeeEcCCCCCcccHHhHHHH
Q 032328           68 GSSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSW  105 (143)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~w  105 (143)
                      -.++..|.|| +.+..++...-. -|+.+||..|+.+.
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            4567889999 777666544333 38899999999997

>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=95.78  E-value=0.019  Score=31.76  Aligned_cols=51  Identities=25%  Similarity=0.561  Sum_probs=34.6

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHH--HH-h--CCCCCccccCccCCC
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDS--WL-L--KTPICPICRTRVSPS  122 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~--wl-~--~~~~CP~CR~~i~~~  122 (143)
                      ...| ||...+..++..+....|+--||..|+..  .- .  .+..||.|+......
T Consensus        12 pv~C-iC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~gp~   67 (79)
T d1wepa_          12 PVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFGPS   67 (79)
T ss_dssp             CCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSCSC
T ss_pred             CeEe-ECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcCCc
Confidence            3445 99988776665565567999999999842  11 1  135699998765443

>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=95.66  E-value=0.0011  Score=35.19  Aligned_cols=47  Identities=26%  Similarity=0.581  Sum_probs=32.2

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhC----CCCCccccCcc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLK----TPICPICRTRV  119 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~----~~~CP~CR~~i  119 (143)
                      ...+.|.+|.+.   ++ ++.-..|.-.||..|+...+..    .-.||.|+..-
T Consensus         7 ~~~~~C~~C~~~---g~-lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           7 HHMEFCRVCKDG---GE-LLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---SS-CBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCcCCCcCCCCC---Ce-EEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            345679999864   43 3443458899999999765543    23499997553

>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=95.15  E-value=0.0067  Score=32.26  Aligned_cols=50  Identities=24%  Similarity=0.471  Sum_probs=36.5

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhHHHHH---h--CCCCCccccCc
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWL---L--KTPICPICRTR  118 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl---~--~~~~CP~CR~~  118 (143)
                      .....|.+|.+...+++.++.-..|+.-||..|+..=.   .  ....||.|+..
T Consensus         4 ~~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            35668999999887777666666799999999985311   1  23469999764

>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=94.86  E-value=0.0074  Score=32.76  Aligned_cols=46  Identities=28%  Similarity=0.632  Sum_probs=31.5

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCC----CCccccCccC
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTP----ICPICRTRVS  120 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~----~CP~CR~~i~  120 (143)
                      ...|.+|.+.   ++ +..-..|...||..|+.+.+...+    .||.|+..-.
T Consensus         7 c~~C~~C~~~---~~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   56 (70)
T d1fp0a1           7 ATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   56 (70)
T ss_dssp             SSCCSSSCSS---SC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             CCCCCCCCCc---CE-EEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCc
Confidence            4467777654   44 444446999999999998765533    3999965443

>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=94.59  E-value=0.017  Score=30.05  Aligned_cols=45  Identities=18%  Similarity=0.340  Sum_probs=33.1

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCccc
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPIC  115 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~C  115 (143)
                      ....|.-|..++.+ ..+...+.|++.|+.+|=.---+.--+||-|
T Consensus        14 ~~~~C~gC~~~l~~-~~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKD-QHVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTT-SEEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCC-CceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            34679999988865 4556677899999999964433444569988

>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=94.07  E-value=0.006  Score=34.61  Aligned_cols=52  Identities=19%  Similarity=0.455  Sum_probs=34.3

Q ss_pred             CCccccccccccC-CCeeeEcCCCCCcccHHhHHHHH-----hC---CCCCccccCccCCC
Q 032328           71 PVDCVVCLENFRM-GDKCRLLPNCRHSFHAQCIDSWL-----LK---TPICPICRTRVSPS  122 (143)
Q Consensus        71 ~~~C~ICl~~~~~-~~~v~~l~~C~H~FH~~Ci~~wl-----~~---~~~CP~CR~~i~~~  122 (143)
                      ...|.||...... +..++....|+..||..|+.+.+     ..   .-.||.|.......
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~~~~   76 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKRM   76 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHCCS
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchHhhh
Confidence            4569999875543 33455455699999999976432     11   34599997765544

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=93.70  E-value=0.25  Score=27.38  Aligned_cols=69  Identities=20%  Similarity=0.343  Sum_probs=43.0

Q ss_pred             CCCCccccccccccC---CCeeeEcCCCCCcccHHhHHHHH-hCCCCCccccCccCCCCcceeecCCCCCCccc
Q 032328           69 SSPVDCVVCLENFRM---GDKCRLLPNCRHSFHAQCIDSWL-LKTPICPICRTRVSPSKVGVILKDGSSVSSDV  138 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~---~~~v~~l~~C~H~FH~~Ci~~wl-~~~~~CP~CR~~i~~~~~~~~~~~~~~~~~~~  138 (143)
                      .+...|.||-+++-.   ++..+....|+---|+.|.+-=. ..++.||-|+.+....+.. ....++..+++.
T Consensus        14 ~~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Ykr~kgs-prv~gDe~e~~~   86 (93)
T d1weoa_          14 LDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKRLRGS-PRVEGDEDEEDI   86 (93)
T ss_dssp             CSSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCCCTTC-CCCTTSCCCCCS
T ss_pred             cccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhhhhcCC-CCCCCCcccccc
Confidence            356789999998743   33333322466667888986533 3478899999998765433 333444444443

>d1wesa_ g.50.1.2 (A:) PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD Inhibitor of growth protein 2, Ing2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.89  E-value=0.028  Score=30.52  Aligned_cols=44  Identities=30%  Similarity=0.625  Sum_probs=25.5

Q ss_pred             CCccccccccccCCCeeeEc-CCCC-CcccHHhHHHHHhC----CCCCccccCc
Q 032328           71 PVDCVVCLENFRMGDKCRLL-PNCR-HSFHAQCIDSWLLK----TPICPICRTR  118 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l-~~C~-H~FH~~Ci~~wl~~----~~~CP~CR~~  118 (143)
                      ...| ||.+... ++.+... ..|. .-||..|+.  +..    +-.||.|+..
T Consensus        16 ~~~C-iC~~~~~-~~~i~c~~~~C~~~wfH~~Cvg--l~~~p~~~w~C~~C~~~   65 (71)
T d1wesa_          16 PTYC-LCNQVSY-GEMIGCDNEQCPIEWFHFSCVS--LTYKPKGKWYCPKCRGD   65 (71)
T ss_dssp             CCCS-TTCCCCC-SSEECCSCTTCSCCCEETTTTT--CSSCCSSCCCCTTTSSC
T ss_pred             CCEE-EeCCCCC-CCEEEEECCCCCCcCccCccCC--CCcCCCCcEECcCCccc
Confidence            3456 8987643 2333332 1344 469999984  333    2349999754

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.18  E-value=0.032  Score=25.02  Aligned_cols=29  Identities=14%  Similarity=0.377  Sum_probs=24.1

Q ss_pred             CccccccccccCCCeeeEcCCCCCcccHHhH
Q 032328           72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCI  102 (143)
Q Consensus        72 ~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci  102 (143)
                      ..|+-|...+...|.|+.-  =+++||-+|.
T Consensus         3 g~Ca~C~~~I~~~e~VmRA--~~~VyHl~CF   31 (31)
T d1rutx3           3 GACSACGQSIPASELVMRA--QGNVYHLKCF   31 (31)
T ss_dssp             EECTTTCCEECTTSEEEEE--TTEEECGGGC
T ss_pred             cccccccCcCChhHhheec--ccceeeeccC
Confidence            3599999999998888876  3789999883

>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=89.55  E-value=0.15  Score=27.33  Aligned_cols=38  Identities=21%  Similarity=0.423  Sum_probs=29.0

Q ss_pred             CCCccccccccccCCCeeeEcC-CCCCcccHHhHHHHHhC
Q 032328           70 SPVDCVVCLENFRMGDKCRLLP-NCRHSFHAQCIDSWLLK  108 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~-~C~H~FH~~Ci~~wl~~  108 (143)
                      ..-.|.+|.+.+++..-|. .| .=+|-||..|-+..+++
T Consensus         7 ~~l~CtlC~erLEdtHFVQ-CPsv~~HkFCFpCsr~sik~   45 (80)
T d2cs3a1           7 GPLCCTICHERLEDTHFVQ-CPSVPSHKFCFPCSRESIKA   45 (80)
T ss_dssp             CSCCCSSSCSCCSSTTSEE-CSSCSSCEECHHHHHHHHHH
T ss_pred             CceeeeeehhhhcCCceEe-CCCCcCCceeccccHHHHHh
Confidence            4567999999998865544 33 23799999999998864

>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=89.51  E-value=0.25  Score=26.58  Aligned_cols=48  Identities=21%  Similarity=0.470  Sum_probs=30.5

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHhHH------HH---HhCCCCCccccCcc
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCID------SW---LLKTPICPICRTRV  119 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~------~w---l~~~~~CP~CR~~i  119 (143)
                      +...| ||-.....+ .++.-..|.--||..|+.      ..   ......||.|+..-
T Consensus        15 ~~~~C-iC~~~~~~~-~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~~   71 (76)
T d1wema_          15 NALYC-ICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             TCCCS-TTCCCCCSS-CEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             CcCEE-ECCCccCCC-eEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCcC
Confidence            34458 898775543 344444688899999982      11   12346799996543

>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=88.44  E-value=0.021  Score=28.90  Aligned_cols=44  Identities=18%  Similarity=0.500  Sum_probs=26.9

Q ss_pred             ccccccccccCCCeeeEcCCCCCcccHHhHHHHHhCCCCCcccc
Q 032328           73 DCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLLKTPICPICR  116 (143)
Q Consensus        73 ~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~~~~~CP~CR  116 (143)
                      .|.+|-.+|..-..-..-..||.+|+.+|....-.....|..|.
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C~   45 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQ   45 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhHh
Confidence            57888888765332233335999999999765433344576664

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.87  E-value=0.036  Score=25.51  Aligned_cols=28  Identities=21%  Similarity=0.565  Sum_probs=21.5

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHh
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQC  101 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~C  101 (143)
                      .-+.|.+|-+.+.+    +++...|-.||..|
T Consensus         7 tlEkC~~C~~~I~d----riLrA~Gk~yHP~C   34 (35)
T d2dloa1           7 TLEKCATCSQPILD----RILRAMGKAYHPGC   34 (35)
T ss_dssp             SCCBCTTTCCBCCS----CCEEETTEEECTTT
T ss_pred             HHHHHHHhchHHHH----HHHHHhCCCCCCCC
Confidence            35679999999877    44445788898887

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.74  E-value=0.17  Score=23.39  Aligned_cols=31  Identities=23%  Similarity=0.481  Sum_probs=21.7

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHhH
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQCI  102 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci  102 (143)
                      ...+.|.+|-.....-+.+..   =|+.||+.|.
T Consensus         6 g~~~~C~~C~K~VY~~Erl~a---~g~~yHk~CF   36 (36)
T d2co8a2           6 GAGDLCALCGEHLYVLERLCV---NGHFFHRSCF   36 (36)
T ss_dssp             CSSCBCSSSCCBCCTTTBCCB---TTBCCBTTTC
T ss_pred             CCCCcccccCCEEeeeeEEEe---cCcEeccccC
Confidence            456789999877655443332   4899999983

>d1dvpa2 g.50.1.1 (A:149-220) Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Hrs
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=84.03  E-value=0.32  Score=26.04  Aligned_cols=34  Identities=24%  Similarity=0.482  Sum_probs=24.1

Q ss_pred             CCccccccccccCCCeeeEcCCCCCcccHHhHHH
Q 032328           71 PVDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDS  104 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~  104 (143)
                      .+.|.+|-.+|..-..-..-..||++|+.+|...
T Consensus        13 ~~~C~~C~~~F~~~~rrhhCr~CG~~~C~~C~~~   46 (72)
T d1dvpa2          13 GRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAK   46 (72)
T ss_dssp             CSBCTTTCCBCCSSSCCEECTTTCCEECSTTSCE
T ss_pred             CCccccCCCcccCccccccccccCCeeChhhhCC
Confidence            3569999999875433233336999999999754

>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=83.77  E-value=0.71  Score=24.89  Aligned_cols=48  Identities=25%  Similarity=0.465  Sum_probs=30.4

Q ss_pred             CCccccccccccCCCeeeEc-CCCCCcccHHhHHH----HHh-----CCCCCccccCcc
Q 032328           71 PVDCVVCLENFRMGDKCRLL-PNCRHSFHAQCIDS----WLL-----KTPICPICRTRV  119 (143)
Q Consensus        71 ~~~C~ICl~~~~~~~~v~~l-~~C~H~FH~~Ci~~----wl~-----~~~~CP~CR~~i  119 (143)
                      ...| ||-.....+..+..- ..|..=||..|+.-    .-.     ....||.|+..-
T Consensus        16 ~~~C-~C~~~~~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T d1wewa_          16 KVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             ccEe-ECCCccCCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcC
Confidence            4568 899887655544332 14889999999831    101     125699997543

>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=83.67  E-value=0.23  Score=26.52  Aligned_cols=46  Identities=24%  Similarity=0.395  Sum_probs=31.6

Q ss_pred             CccccccccccCCCeeeEcCCCCCcccHHhHHHHHh----CCCCCccccCc
Q 032328           72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSWLL----KTPICPICRTR  118 (143)
Q Consensus        72 ~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~wl~----~~~~CP~CR~~  118 (143)
                      ..| ||.....+++.++.-..|..-||..|+..-..    ....||.|+..
T Consensus        17 ~~C-~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~~~~~~~~C~~C~~~   66 (72)
T d1weea_          17 VDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIEL   66 (72)
T ss_dssp             ECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHH
T ss_pred             EEe-eCCCCcCCCCeEEEeCCCCCcCchhhcCCccccCCCCcEECcCCcCc
Confidence            457 78877766666666667899999999754211    23459999654

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.66  E-value=0.35  Score=22.13  Aligned_cols=30  Identities=20%  Similarity=0.445  Sum_probs=21.4

Q ss_pred             CCCCccccccccccCCCeeeEcCCCCCcccHHh
Q 032328           69 SSPVDCVVCLENFRMGDKCRLLPNCRHSFHAQC  101 (143)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~C  101 (143)
                      ...+.|..|-.....-+.+..   =|+.||+.|
T Consensus         5 p~~~kC~~C~K~VY~~E~~~a---~g~~~Hk~C   34 (35)
T d2d8ya1           5 PARETCVECQKTVYPMERLLA---NQQVFHISC   34 (35)
T ss_dssp             SSSCBCTTTCCBCCTTSEEEC---SSSEEETTT
T ss_pred             CCCcccccCCCEEeeeeeEec---CCeehhhcc
Confidence            346789999887665444442   588999988

>d1g47a1 g.39.1.3 (A:1-35) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.74  E-value=0.29  Score=22.10  Aligned_cols=30  Identities=23%  Similarity=0.459  Sum_probs=24.5

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHh
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQC  101 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~C  101 (143)
                      ..-.|.-|-+-|.+.++++-.  =|-++|.+|
T Consensus         6 ~~~~C~RC~~gF~p~EkiVNS--nGEl~H~qC   35 (35)
T d1g47a1           6 ASATCERCKGGFAPAEKIVNS--NGELYHEQC   35 (35)
T ss_dssp             CCCBCSSSCCBCCSTTTCEEE--TTEEECTTT
T ss_pred             HHHHHHHHccCCCchHHhhcC--CCccccccC
Confidence            456799999999998888876  378888877

>d2dasa1 g.39.1.17 (A:8-56) Zinc finger MYM-type protein 5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: TRASH domain
domain: Zinc finger MYM-type protein 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.42  E-value=0.89  Score=22.05  Aligned_cols=36  Identities=19%  Similarity=0.537  Sum_probs=30.1

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHH-hHHHH
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQ-CIDSW  105 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~-Ci~~w  105 (143)
                      ....|+-|-..++.++.......+.|+||.. ||..+
T Consensus        12 ~~v~Ca~Ckk~lqKGQTAyqrkGs~~LFCSt~Cl~~~   48 (49)
T d2dasa1          12 AKITCANCKKPLQKGQTAYQRKGSAHLFCSTTCLSSF   48 (49)
T ss_dssp             SSCBCTTTCCBCCTTSCCEECTTCCCEESSHHHHHHH
T ss_pred             eEeEecccchHHhccchHHhhCCCcceeEcchhhccc
Confidence            4568999999999999988887788999974 88753

>d1vfya_ g.50.1.1 (A:) vps27p protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: vps27p protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.86  E-value=0.6  Score=24.49  Aligned_cols=34  Identities=15%  Similarity=0.385  Sum_probs=23.4

Q ss_pred             CccccccccccCCCeeeEcCCCCCcccHHhHHHH
Q 032328           72 VDCVVCLENFRMGDKCRLLPNCRHSFHAQCIDSW  105 (143)
Q Consensus        72 ~~C~ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~w  105 (143)
                      +.|.+|-.+|..-..--.-..||.+|+..|....
T Consensus         6 ~~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~   39 (67)
T d1vfya_           6 DACMICSKKFSLLNRKHHCRSCGGVFCQEHSSNS   39 (67)
T ss_dssp             SBCTTTCCBCBTTBCCEECTTTCCEECGGGSCEE
T ss_pred             cccccCCCcccCcccccccccCCCEecccccCCc
Confidence            4699999998653222222359999999997443

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=80.61  E-value=0.3  Score=23.47  Aligned_cols=29  Identities=21%  Similarity=0.399  Sum_probs=22.2

Q ss_pred             CCCccccccccccCCCeeeEcCCCCCcccHHh
Q 032328           70 SPVDCVVCLENFRMGDKCRLLPNCRHSFHAQC  101 (143)
Q Consensus        70 ~~~~C~ICl~~~~~~~~v~~l~~C~H~FH~~C  101 (143)
                      ..+.|+.|-.....-+.+..   =|+.||+.|
T Consensus        14 ~~~kC~~C~k~VY~~E~~~~---~g~~~Hk~C   42 (43)
T d1b8ta3          14 GSDGCPRCGQAVYAAEKVIG---AGKSWHKSC   42 (43)
T ss_dssp             CCEECTTTSCEECSSSCEEE---TTEEECTTT
T ss_pred             CCCcCccCCCEeeHHHHhhc---CCCccccCC
Confidence            35789999988766665544   589999988