Citrus Sinensis ID: 044318

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-----
Protein Sequence
LYQVSSDFAMAMALQEQERLATIESESSNEDDDGSEVNGANGYDYFECDGFDTFEAAGLQFLEGQDSNYSDDDDEIMDDDDELELDVDELTYEELIALGEFIGQEKRGLSLNQISTCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNNAITSKL
Secondary Structure (PSIPRED)
cccccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHccccccccccHHHHHHcccEEEcccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHccccHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHcccccccccHHHHHHHccccEEccccccccccccEEEEEEEEcccccEEEEEccccccHHHHHHHHHHHHcccccEEEEEcccccccccEEEcc
Coil and Loop (DISEMBL)
LYQVSSDFAMAMALQEQERLATIesessnedddgsevngangydyfecdgfdtfeAAGLqflegqdsnysddddeimddddeleldvdeLTYEELIALGEFigqekrglslNQISTClhacksppadgtksgidrcvICQVEYEEGESIVALLPCEHLYHSECISNWLqikkicpicsteasppknhnnaitskl
Flexible Loop (DISEMBL)
LYQVSSDFAMAMALQEQERLATIesessnedddgseVNGANGYDYFECDGFDTFEAAGLQFLEGQDSNYSDDDDEIMDDDDELELDVDELTYEELIALGEFIGQEKRGLSLNQISTCLHACKsppadgtksgIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICsteasppknhnnaitskl
Low Complexity Region (SEG)
LYQVSSDFAMAMALQEQERLATIesessnedddgseVNGANGYDYFECDGFDTFEAAGLQFLEGQDSNYSddddeimddddeleldvdeltyeelIALGEFIGQEKRGLSLNQISTCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNNAITSKL
Disordered region (IsUnstruct)
***************************************ANGYDYFECDGFDTFEAAGLQFLE*******************LELDVDELTYEELIALGEFIGQEKRGLSLNQISTCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICS*****************
Disordered Region (DISOPRED)
*****SD************************************************************************DDELELDVDELTYEELIALGEFIGQEKRGLSLNQISTCLHAC*************RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPIC******************
Disordered Region (DISEMBL)
LYQVSSDFAMAMALQEQER****************EVNGANGYDYFECDGFDTFEAAGLQFLEGQDSNYSDDDDEIMDDDDELELDVDELTYEELIALGEFIGQEKRGLSLNQISTCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNNAITSKL
Disordered Region (DISPRO)
**QVSSDFAMAMALQEQE****************************ECDGFDTFEAAGLQFLEGQDSNYSDDDDEIMDDDDELELDVDELTYEELIALGEFIGQEKRGLSLNQISTCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASP******A*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
LYQVSSDFAMAMALQEQERLATIESESSNEDDDGSEVNGANGYDYFECDGFDTFEAAGLQFLEGQDSNYSDDDDEIMDDDDELELDVDELTYEELIALGEFIGQEKRGLSLNQISTCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNNAITSKL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	195	2.2.26 [Sep-21-2011]
Q9LT17	340	E3 ubiquitin ligase BIG B	no	no	0.497	0.285	0.505	1e-23
Q8L649	248	E3 ubiquitin ligase BIG B	no	no	0.497	0.391	0.484	5e-20
Q7L0R7	432	RING finger protein 44 OS	yes	no	0.528	0.238	0.345	8e-10
Q4V7B8	350	RING finger protein 44 OS	yes	no	0.497	0.277	0.355	3e-09
Q5R476	986	E3 ubiquitin-protein liga	no	no	0.451	0.089	0.363	3e-09
Q3UHJ8	407	RING finger protein 44 OS	no	no	0.497	0.238	0.355	3e-09
Q9H0F5	515	RING finger protein 38 OS	no	no	0.497	0.188	0.336	9e-09
Q08CG8	448	RING finger protein 44 OS	no	no	0.482	0.209	0.327	2e-08
Q90ZT7	923	E3 ubiquitin-protein liga	N/A	no	0.451	0.095	0.336	2e-08
Q0V9R0	954	E3 ubiquitin-protein liga	no	no	0.451	0.092	0.336	2e-08

>sp|Q9LT17|BBR_ARATH E3 ubiquitin ligase BIG BROTHER-related OS=Arabidopsis thaliana GN=BBR PE=2 SV=1

 Score =  109 bits (273), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 50/99 (50%), Positives = 72/99 (72%), Gaps = 2/99 (2%)

Query: 84  ELDVDELTYEELIALGEFIGQEKRGLSLNQISTCLHACKSPPADGTKSGIDRCVICQVEY 143
           E+D DEL+YEEL+ALG+ +G E RGLS + I++ L + +    D      + CVIC+++Y
Sbjct: 237 EMDPDELSYEELLALGDIVGTESRGLSADTIAS-LPSKRYKEGDNQNGTNESCVICRLDY 295

Query: 144 EEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS 182
           E+ E ++ LLPC+H YHSECI+NWL+I K+CP+CS E S
Sbjct: 296 EDDEDLI-LLPCKHSYHSECINNWLKINKVCPVCSAEVS 333

E3 ubiquitin-ligase probably involved in organ size regulation.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|Q8L649|BB_ARATH E3 ubiquitin ligase BIG BROTHER OS=Arabidopsis thaliana GN=BB PE=1 SV=1

 Score = 97.4 bits (241), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 48/99 (48%), Positives = 64/99 (64%), Gaps = 2/99 (2%)

Query: 84  ELDVDELTYEELIALGEFIGQEKRGLSLNQISTC-LHACKSPPADGTKSGIDRCVICQVE 142
           ++D D +TYEEL+ LGE +G E RGLS   I T      K       K   +RCVICQ++
Sbjct: 144 DIDPDTMTYEELVELGEAVGTESRGLSQELIETLPTKKYKFGSIFSRKRAGERCVICQLK 203

Query: 143 YEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEA 181
           Y+ GE  + L PC+H+YHSECIS WL I K+CP+C++E 
Sbjct: 204 YKIGERQMNL-PCKHVYHSECISKWLSINKVCPVCNSEV 241

E3 ubiquitin-ligase that limits organ size, and possibly seed size, in a dose-dependent manner. Negatively regulates the duration of cell proliferation in leaves and petals independently of the major phytohormones (e.g. auxin, cytokinin, gibberellin, brassinosteroids, ethylene, abscisic acid, jasmonic acid), probably by targeting growth stimulators for degradation.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q7L0R7|RNF44_HUMAN RING finger protein 44 OS=Homo sapiens GN=RNF44 PE=2 SV=1

 Score = 63.5 bits (153), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 38/110 (34%), Positives = 59/110 (53%), Gaps = 7/110 (6%)

Query: 77  MDDDDELELDVDEL---TYEELIALGEFIGQEK-RGLSLNQISTCLHACKSPPADGTKSG 132
           M     L+LDVD++    YE L+ L E +G  K RGL+   I        +P  D  +S 
Sbjct: 319 MGPTISLDLDVDDVEMENYEALLNLAERLGDAKPRGLTKADIEQLPSYRFNP--DSHQSE 376

Query: 133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS 182
              CV+C  ++E    ++ +LPC H +H++C+  WL+  + CPIC  +AS
Sbjct: 377 QTLCVVCFSDFE-ARQLLRVLPCNHEFHTKCVDKWLKANRTCPICRADAS 425

Homo sapiens (taxid: 9606)

>sp|Q4V7B8|RNF44_RAT RING finger protein 44 OS=Rattus norvegicus GN=Rnf44 PE=2 SV=1

 Score = 61.6 bits (148), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 37/104 (35%), Positives = 59/104 (56%), Gaps = 7/104 (6%)

Query: 83  LELDVDEL---TYEELIALGEFIGQEK-RGLSLNQISTCLHACKSPPADGTKSGIDRCVI 138
           L+LDVD++    YE L+ L E +G  K RGL+   I        +P  D  +S    CV+
Sbjct: 243 LDLDVDDVEMENYEALLNLAERLGDAKPRGLTKADIEQLPSYRFNP--DSHQSEQTLCVV 300

Query: 139 CQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS 182
           C  ++E  + ++ +LPC H +H++C+  WL+  + CPIC  +AS
Sbjct: 301 CFSDFEVRQ-LLRVLPCNHEFHAKCVDKWLKANRTCPICRADAS 343

Rattus norvegicus (taxid: 10116)

>sp|Q5R476|RN111_PONAB E3 ubiquitin-protein ligase Arkadia OS=Pongo abelii GN=RNF111 PE=2 SV=1

 Score = 61.6 bits (148), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 36/99 (36%), Positives = 45/99 (45%), Gaps = 11/99 (11%)

Query: 92  YEELIALGEFIGQEKRGLSLNQISTC----------LHACKSPPADGTKSGIDRCVICQV 141
           +EELI L E +G   RG S   I  C          LH  +       +   ++C IC  
Sbjct: 880 FEELIHLEERLGNVNRGASQGTIERCTYPHKYKKRKLHCKQDGEEGTEEDTEEKCTICLS 939

Query: 142 EYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTE 180
             EEGE  V  LPC HL+H  C+  WL   K CPIC  +
Sbjct: 940 ILEEGED-VRRLPCMHLFHQVCVDQWLITNKKCPICRVD 977

Acts in the NODAL pathway of mesoderm patterning during embryonic development. Acts downstream AXIN1 as an E3 ubiquitin-protein ligase which promotes the ubiquitination of inhibitory SMADs such as SMAD7, induces their proteasomal degradation and thereby enhances the transcriptional activity of TGF-beta and BMP. Activates Smad3/Smad4-dependent transcription by triggering signal-induced SnoN degradation.

Pongo abelii (taxid: 9601)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q3UHJ8|RNF44_MOUSE RING finger protein 44 OS=Mus musculus GN=Rnf44 PE=2 SV=1

 Score = 61.6 bits (148), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 37/104 (35%), Positives = 59/104 (56%), Gaps = 7/104 (6%)

Query: 83  LELDVDEL---TYEELIALGEFIGQEK-RGLSLNQISTCLHACKSPPADGTKSGIDRCVI 138
           L+LDVD++    YE L+ L E +G  K RGL+   I        +P  D  +S    CV+
Sbjct: 300 LDLDVDDVEMENYEALLNLAERLGDAKPRGLTKADIEQLPSYRFNP--DSHQSEQTLCVV 357

Query: 139 CQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS 182
           C  ++E  + ++ +LPC H +H++C+  WL+  + CPIC  +AS
Sbjct: 358 CFSDFEVRQ-LLRVLPCNHEFHAKCVDKWLKANRTCPICRADAS 400

Mus musculus (taxid: 10090)

>sp|Q9H0F5|RNF38_HUMAN RING finger protein 38 OS=Homo sapiens GN=RNF38 PE=1 SV=4

 Score = 60.1 bits (144), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 35/104 (33%), Positives = 58/104 (55%), Gaps = 7/104 (6%)

Query: 83  LELDVDE---LTYEELIALGEFIGQEK-RGLSLNQISTCLHACKSPPADGTKSGIDRCVI 138
            ELDV++     YE L+ L E +G+ K RGL+   I        +P  +  +S    CV+
Sbjct: 408 FELDVEDGEVENYEALLNLAERLGEAKPRGLTKADIEQLPSYRFNP--NNHQSEQTLCVV 465

Query: 139 CQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS 182
           C  ++E  + ++ +LPC H +H++C+  WL+  + CPIC  +AS
Sbjct: 466 CMCDFESRQ-LLRVLPCNHEFHAKCVDKWLKANRTCPICRADAS 508

Homo sapiens (taxid: 9606)

>sp|Q08CG8|RNF44_DANRE RING finger protein 44 OS=Danio rerio GN=rnf44 PE=2 SV=1

 Score = 59.3 bits (142), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 35/107 (32%), Positives = 60/107 (56%), Gaps = 13/107 (12%)

Query: 83  LELDVDEL---TYEELIALGEFIGQEK-RGLS---LNQISTCLHACKSPPADGTKSGIDR 135
           L+LDVD++    YE L+ L E +G+ K RGL+   + Q+ +          +  +S    
Sbjct: 341 LDLDVDDVEMENYEALLNLAERLGEAKPRGLTKADIEQLPSYRFNL-----ENHQSEQTL 395

Query: 136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS 182
           CV+C  ++E    ++ +LPC H +H++C+  WL+  + CPIC  +AS
Sbjct: 396 CVVCFSDFE-SRQLLRVLPCNHEFHAKCVDKWLKTNRTCPICRADAS 441

Danio rerio (taxid: 7955)

>sp|Q90ZT7|R111A_XENLA E3 ubiquitin-protein ligase arkadia-A (Fragment) OS=Xenopus laevis GN=rnf111-a PE=2 SV=1

 Score = 58.9 bits (141), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/107 (33%), Positives = 46/107 (42%), Gaps = 19/107 (17%)

Query: 92  YEELIALGEFIGQEKRGLSLNQISTC------------------LHACKSPPADGTKSGI 133
           +EELI L E +G   RG S   I  C                  LH+ +       +   
Sbjct: 809 FEELIHLEERLGNVNRGASQGTIERCTYPHKYKKVSTDWFSQRKLHSKQDGEEAPEEDTE 868

Query: 134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTE 180
           ++C IC    EEGE  V  LPC HL+H  C+  WL   K CPIC  +
Sbjct: 869 EKCTICLSILEEGED-VRRLPCMHLFHQVCVDQWLITNKKCPICRVD 914

Acts in the nodal-related pathway of mesoderm patterning during embryonic development. Enhances signaling of the subset of TGF-beta factors responsible for the formation of dorso-anterior tissues of Spemann's organizer. May act as an E3 ubiquitin-protein ligase, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates.

Xenopus laevis (taxid: 8355)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q0V9R0|RN111_XENTR E3 ubiquitin-protein ligase arkadia OS=Xenopus tropicalis GN=rnf111 PE=2 SV=1

 Score = 58.9 bits (141), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/107 (33%), Positives = 46/107 (42%), Gaps = 19/107 (17%)

Query: 92  YEELIALGEFIGQEKRGLSLNQISTC------------------LHACKSPPADGTKSGI 133
           +EELI L E +G   RG S   I  C                  LH+ +       +   
Sbjct: 840 FEELIHLEERLGNVNRGASQGTIERCTYPHKYEKVSTDWFSQRKLHSKQDGEEATEEDTE 899

Query: 134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTE 180
           ++C IC    EEGE  V  LPC HL+H  C+  WL   K CPIC  +
Sbjct: 900 EKCTICLSILEEGED-VRRLPCMHLFHQVCVDQWLITNKKCPICRVD 945

Acts in the nodal-related pathway of mesoderm patterning during embryonic development. Enhances signaling of the subset of TGF-beta factors responsible for the formation of dorso-anterior tissues of Spemann's organizer. May act as an E3 ubiquitin-protein ligase, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates.

Xenopus tropicalis (taxid: 8364)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	195
255558630	213	ring finger protein, putative [Ricinus c	0.876	0.802	0.533	1e-38
224084916	208	predicted protein [Populus trichocarpa]	0.912	0.855	0.551	2e-38
224063048	210	predicted protein [Populus trichocarpa]	0.876	0.814	0.549	2e-37
357463511	211	RING finger protein [Medicago truncatula	0.943	0.872	0.54	2e-37
449533741	217	PREDICTED: uncharacterized LOC101217935	0.933	0.838	0.505	3e-37
449464174	217	PREDICTED: uncharacterized protein LOC10	0.933	0.838	0.505	3e-37
302141791	188	unnamed protein product [Vitis vinifera]	0.810	0.840	0.5	4e-34
356552703	205	PREDICTED: E3 ubiquitin ligase BIG BROTH	0.482	0.458	0.697	1e-30
356547497	203	PREDICTED: E3 ubiquitin ligase BIG BROTH	0.887	0.852	0.529	2e-30
351722283	202	uncharacterized protein LOC100526881 [Gl	0.917	0.886	0.510	2e-30

>gi|255558630|ref|XP_002520340.1| ring finger protein, putative [Ricinus communis] gi|223540559|gb|EEF42126.1| ring finger protein, putative [Ricinus communis]

 Score =  165 bits (417), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 104/195 (53%), Positives = 131/195 (67%), Gaps = 24/195 (12%)

Query: 1   LYQVSSDFAMAMALQEQERLATIESESSNEDDDGSEV---------NGANGYDYFECDGF 51
           L QV SDFA+AMALQ QE    + +   +E ++ +E          NG N Y++FE    
Sbjct: 29  LNQVRSDFAIAMALQNQESAFNVLTSIESESEEDNEESEDFSSEENNGINDYEFFE---- 84

Query: 52  DTFEAAGLQFLEGQDSNYSDDDDEIMDDDDELELDVDELTYEELIALGEFIGQEKRGLSL 111
               +  L+FLEGQDSN  +D +E  DD D      DEL+YEEL+ALGEFIG+EKRGLS+
Sbjct: 85  ----SQDLEFLEGQDSNSDEDMEEEEDDID-----PDELSYEELLALGEFIGEEKRGLSI 135

Query: 112 NQISTCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK 171
            +IS CL+  K    +  KS IDRCVICQVEY+ GE +V+LLPC+H YHSECI NWLQ+K
Sbjct: 136 EEISKCLNPSKYKSVEN-KSEIDRCVICQVEYQGGEPLVSLLPCQHPYHSECIINWLQVK 194

Query: 172 KICPICSTE-ASPPK 185
           KICPIC+TE +S PK
Sbjct: 195 KICPICTTEVSSSPK 209

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224084916|ref|XP_002307448.1| predicted protein [Populus trichocarpa] gi|222856897|gb|EEE94444.1| predicted protein [Populus trichocarpa]

 Score =  164 bits (414), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 107/194 (55%), Positives = 140/194 (72%), Gaps = 16/194 (8%)

Query: 1   LYQVSSDFAMAMALQEQER----LATIESESSNED-DDGSEVN---GANGYDYFECDGFD 52
           L QV  D A+AM LQEQER    L TIES+S+ E+ D+ S ++   G N Y++F+   F+
Sbjct: 18  LEQVHPDNAIAMVLQEQERAFTILTTIESDSNKEESDEASSIDSNEGGNDYEFFQSLEFE 77

Query: 53  TFEAAGLQFLEGQDSNYSDDDDEIMDDDDELELDVDELTYEELIALGEFIGQEKRGLSLN 112
               + ++F   Q+   SD D+++ +++DE E+D+DEL+YEELIALGEFIGQEKRGLS+N
Sbjct: 78  ----SEMEF--QQEGQDSDSDEDMEEEEDEDEIDLDELSYEELIALGEFIGQEKRGLSVN 131

Query: 113 QISTCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKK 172
           +ISTCLH  K       K+G DRCVICQ+EYEE ES+VA L C+H YHSEC++ WLQI K
Sbjct: 132 EISTCLHPWKYRSL-ANKTGTDRCVICQMEYEEDESLVA-LSCDHPYHSECLTKWLQINK 189

Query: 173 ICPICSTEASPPKN 186
           ICPICSTE S P+N
Sbjct: 190 ICPICSTEVSSPRN 203

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224063048|ref|XP_002300971.1| predicted protein [Populus trichocarpa] gi|222842697|gb|EEE80244.1| predicted protein [Populus trichocarpa]

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 106/193 (54%), Positives = 134/193 (69%), Gaps = 22/193 (11%)

Query: 1   LYQVSSDFAMAMALQEQER----LATIESESSNEDDDGSEVN--GA--NGYDYFECDGFD 52
           L QV SDFA+AM LQEQER    L +IES+S+ E+ D +  +  GA  N Y++F+   F+
Sbjct: 27  LEQVHSDFAIAMVLQEQERAFTILTSIESDSNEEESDEASSSESGADDNDYEFFQSHEFE 86

Query: 53  TFEAAGLQFL-EGQDSNYSDDDDEIMDDDDELELDVDELTYEELIALGEFIGQEKRGLSL 111
           +     ++FL EG+DSN  +D +E   D        DEL+YE+LIALGEF+GQEKRGLS 
Sbjct: 87  S----EMEFLQEGEDSNSDEDMEEDEVD-------PDELSYEDLIALGEFVGQEKRGLSR 135

Query: 112 NQISTCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK 171
           N+ISTCL  CK      +K+G DRCVICQ+EYEE ES+VA L C+H YH ECI+NWLQI 
Sbjct: 136 NEISTCLRPCKYESL-ASKTGTDRCVICQMEYEEDESLVA-LSCDHPYHPECIANWLQIN 193

Query: 172 KICPICSTEASPP 184
           KICPIC+TE S P
Sbjct: 194 KICPICTTEVSSP 206

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357463511|ref|XP_003602037.1| RING finger protein [Medicago truncatula] gi|355491085|gb|AES72288.1| RING finger protein [Medicago truncatula]

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 108/200 (54%), Positives = 130/200 (65%), Gaps = 16/200 (8%)

Query: 1   LYQVSSDFAMAMALQEQE-------RLATIESESSNEDDDGSEVNGANG-YDYFECDGFD 52
           L +VSSDF +A+ LQEQE        LATIESES  +  D S  N   G  D+     F+
Sbjct: 18  LEEVSSDFVLAIGLQEQELERTTFTNLATIESESDEDISDSSFSNDDIGDADFSFSQEFE 77

Query: 53  TFEAAGLQFLEGQDSNYSDDDDEIMDDDDELELDV--DELTYEELIALGEFIGQEKRGLS 110
           T     LQF+E + SN  DDDD   D+ +  E +V  DEL+YEELI LG FIG+EKRGL 
Sbjct: 78  T----DLQFVEDEGSNIDDDDDYEDDEMELEEDEVDPDELSYEELIELGNFIGEEKRGLP 133

Query: 111 LNQISTCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI 170
            N+IS+CLH   S  A+ T SGIDRCVICQ+EYEEGES+VA L C+H YH++CIS WLQI
Sbjct: 134 ANEISSCLHPYTSKIAEST-SGIDRCVICQIEYEEGESLVA-LHCDHPYHTDCISKWLQI 191

Query: 171 KKICPICSTEASPPKNHNNA 190
           KK+CPICS E S      N 
Sbjct: 192 KKVCPICSNEVSTTNKAKNT 211

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449533741|ref|XP_004173830.1| PREDICTED: uncharacterized LOC101217935 [Cucumis sativus]

 Score =  160 bits (405), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 98/194 (50%), Positives = 126/194 (64%), Gaps = 12/194 (6%)

Query: 3   QVSSDFAMAMALQEQER------LATIESESSNEDDDGSEVNGANGYDYFECDGFDTFEA 56
           QV++D  MA+A+Q+QE       L TI S+S  E+D+ S+ N  NG D            
Sbjct: 28  QVNTDLIMALAMQQQEHEMAYTTLETIASDS--EEDENSDSNSNNGLDTNATSQRQEL-V 84

Query: 57  AGLQFLEG-QDSNYSDDDDEIMDDDDELELDVDELTYEELIALGEFIGQEKRGLSLNQIS 115
           +   FLE  +++   +DD E  +D D    D+DELTYEELIALGEFIG+EKRGL +N+I 
Sbjct: 85  SRWAFLEDDEETTDGNDDMEEDEDGDFEGFDLDELTYEELIALGEFIGEEKRGLPINEIP 144

Query: 116 TCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICP 175
           +CLH+ K    +  +SGIDRCVICQVEY++GE + A LPCEH YHSECI  WLQIK++CP
Sbjct: 145 SCLHSSKFQTIEN-RSGIDRCVICQVEYDDGEELAA-LPCEHPYHSECIGEWLQIKRVCP 202

Query: 176 ICSTEASPPKNHNN 189
           IC TE S P    N
Sbjct: 203 ICGTEVSSPNGSKN 216

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449464174|ref|XP_004149804.1| PREDICTED: uncharacterized protein LOC101217935 [Cucumis sativus]

 Score =  160 bits (404), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 98/194 (50%), Positives = 126/194 (64%), Gaps = 12/194 (6%)

Query: 3   QVSSDFAMAMALQEQER------LATIESESSNEDDDGSEVNGANGYDYFECDGFDTFEA 56
           QV++D  MA+A+Q+QE       L TI S+S  E+D+ S+ N  NG D            
Sbjct: 28  QVNTDLIMALAMQQQEHELAYTTLETIASDS--EEDENSDSNSNNGLDTNATSQRQEL-V 84

Query: 57  AGLQFLEG-QDSNYSDDDDEIMDDDDELELDVDELTYEELIALGEFIGQEKRGLSLNQIS 115
           +   FLE  +++   +DD E  +D D    D+DELTYEELIALGEFIG+EKRGL +N+I 
Sbjct: 85  SRWAFLEDDEETTDGNDDMEEDEDGDFEGFDLDELTYEELIALGEFIGEEKRGLPINEIP 144

Query: 116 TCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICP 175
           +CLH+ K    +  +SGIDRCVICQVEY++GE + A LPCEH YHSECI  WLQIK++CP
Sbjct: 145 SCLHSSKFQTIEN-RSGIDRCVICQVEYDDGEELAA-LPCEHPYHSECIGEWLQIKRVCP 202

Query: 176 ICSTEASPPKNHNN 189
           IC TE S P    N
Sbjct: 203 ICGTEVSSPNGSKN 216

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302141791|emb|CBI18994.3| unnamed protein product [Vitis vinifera]

 Score =  149 bits (377), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 95/190 (50%), Positives = 121/190 (63%), Gaps = 32/190 (16%)

Query: 1   LYQVSSDFAMAMALQEQER------LATIESESSNEDDDGSEVNGANGYDYFECDGFDTF 54
           L QV+SDFA+A+ALQEQER      L TI   +S+E +  S     +             
Sbjct: 20  LNQVASDFALAIALQEQERRAFTTLLPTIFQTNSDELESDSSDETDDD------------ 67

Query: 55  EAAGLQFLEGQDSNYSDDDDEIMDDDDELELDVDELTYEELIALGEFIGQEKRGLSLNQI 114
                +FLEG+ SN SD D   M++DD   +D D+L+YEELIALGE +G+E RGLS+ +I
Sbjct: 68  -EDEDKFLEGEGSN-SDQD---MEEDD---IDPDQLSYEELIALGEIVGEESRGLSMEEI 119

Query: 115 STCL--HACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKK 172
           S  L  + C S     +K+ +DRCVICQVEYEE E +VAL PCEH YH++CI+ WLQIKK
Sbjct: 120 SASLRPYTCHSL---RSKTAVDRCVICQVEYEEEEKLVAL-PCEHPYHADCITKWLQIKK 175

Query: 173 ICPICSTEAS 182
            CPICSTE S
Sbjct: 176 TCPICSTEVS 185

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356552703|ref|XP_003544702.1| PREDICTED: E3 ubiquitin ligase BIG BROTHER-like [Glycine max]

 Score =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 67/96 (69%), Positives = 79/96 (82%), Gaps = 2/96 (2%)

Query: 90  LTYEELIALGEFIGQEKRGLSLNQISTCLHACKSPPADGTKSGIDRCVICQVEYEEGESI 149
           LTYEELI LG+FIGQEKRGLS ++I +CLH+     A+  KSGIDRCVICQVEYEEGES+
Sbjct: 109 LTYEELIELGDFIGQEKRGLSAHEICSCLHSHTFHSAEN-KSGIDRCVICQVEYEEGESL 167

Query: 150 VALLPCEHLYHSECISNWLQIKKICPICSTEASPPK 185
           VA + CEH YH++CIS WLQIKK+CPIC+ E S PK
Sbjct: 168 VA-IQCEHPYHTDCISKWLQIKKVCPICNIEISAPK 202

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356547497|ref|XP_003542148.1| PREDICTED: E3 ubiquitin ligase BIG BROTHER-like [Glycine max]

 Score =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 98/185 (52%), Positives = 126/185 (68%), Gaps = 12/185 (6%)

Query: 5   SSDFAMAMALQEQE----RLATIESESSNEDDDGSEVNGANGYDYFECDGFDTFEAAGLQ 60
           S++F +   LQEQ       A+ ESE+  E     + +     D+F    F++     LQ
Sbjct: 24  SNNFVLEHNLQEQSGTFTTFASFESETEGESS-FDDNDYDGDADFFLSQEFES----ELQ 78

Query: 61  FLEGQDSNYSDDDDEIMDDDDELELDVDELTYEELIALGEFIGQEKRGLSLNQISTCLHA 120
           FLE + SNY++DDD   +D +E ++DVDELTYEELI LG+FIGQEKRGLS ++I +CLH 
Sbjct: 79  FLESEGSNYNNDDDN-DEDMEEDDIDVDELTYEELIELGDFIGQEKRGLSAHEICSCLHI 137

Query: 121 CKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTE 180
                A+  KSGIDRCVICQVEYEEGE +VA + CEH YH++CIS WLQIKK+CPIC+TE
Sbjct: 138 HIFHSAEN-KSGIDRCVICQVEYEEGEPLVA-IQCEHPYHTDCISKWLQIKKVCPICNTE 195

Query: 181 ASPPK 185
            S PK
Sbjct: 196 ISAPK 200

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351722283|ref|NP_001235447.1| uncharacterized protein LOC100526881 [Glycine max] gi|255631050|gb|ACU15889.1| unknown [Glycine max]

 Score =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 99/194 (51%), Positives = 127/194 (65%), Gaps = 15/194 (7%)

Query: 1   LYQVSSDFAMAMALQEQER----LATIESESSNE-DDDGSEVNGANGYDYFECDGFDTFE 55
           L +V  DF +AM++QEQER    L+TIESES     D   + +     D+     F+T  
Sbjct: 18  LEEVDFDFILAMSMQEQEREFTMLSTIESESDEYLSDSSIDNDDDGDPDFIASQEFET-- 75

Query: 56  AAGLQFLEGQDSNYSDDDDEIMDDDDELELDVDELTYEELIALGEFIGQEKRGLSLNQIS 115
              L+FLEG+ S+  D+D E+ +D+     D DEL+YEEL+ L EFIG+E RGLS N+IS
Sbjct: 76  --DLRFLEGEGSDDDDEDMEMEEDEI----DPDELSYEELMELEEFIGEETRGLSANEIS 129

Query: 116 TCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICP 175
            CL+      A+ +KSGIDRCVICQVEYEEGE++VA L CEH YHS+CI  WLQIKK+CP
Sbjct: 130 LCLYPYTCQCAE-SKSGIDRCVICQVEYEEGEALVA-LQCEHPYHSDCIRKWLQIKKVCP 187

Query: 176 ICSTEASPPKNHNN 189
           IC  E S P   +N
Sbjct: 188 ICGNEVSTPNLASN 201

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	195
TAIR|locus:2075641	210	AT3G47180 [Arabidopsis thalian	0.897	0.833	0.411	6.4e-28
TAIR|locus:2092271	340	AT3G19910 [Arabidopsis thalian	0.435	0.25	0.471	3e-24
TAIR|locus:504955576	248	BB "BIG BROTHER" [Arabidopsis	0.466	0.366	0.457	5.3e-17
TAIR|locus:2145086	280	AT5G52140 [Arabidopsis thalian	0.410	0.285	0.38	1.3e-13
TAIR|locus:2027804	367	AT1G73760 [Arabidopsis thalian	0.425	0.226	0.425	4.8e-12
TAIR|locus:2124271	666	MBR2 "MED25 BINDING RING-H2 PR	0.435	0.127	0.390	9.3e-12
TAIR|locus:2019150	249	AT1G74620 [Arabidopsis thalian	0.297	0.232	0.466	1e-11
TAIR|locus:2086305	486	AT3G15070 [Arabidopsis thalian	0.435	0.174	0.395	1.9e-11
TAIR|locus:2159634	525	AT5G10650 [Arabidopsis thalian	0.461	0.171	0.350	5.9e-11
UNIPROTKB|C9IY58	232	RNF13 "E3 ubiquitin-protein li	0.358	0.301	0.378	1.5e-10

TAIR|locus:2075641 AT3G47180 [Arabidopsis thaliana (taxid:3702)]

 Score = 312 (114.9 bits), Expect = 6.4e-28, P = 6.4e-28
 Identities = 74/180 (41%), Positives = 97/180 (53%)

Query:     3 QVSSDFAMAMALQEQERLATIXXXXXXXXXXXXXVNGANGYDYFECDGFDTFEAAGLQFL 62
             Q +S FA AM       ++ I             +N  N Y+YF+ +GF   E    +FL
Sbjct:    34 QANSHFAHAMHDSSPSMISMIESDEESEDEEE--IN-ENYYEYFDSNGFGVDEDEINEFL 90

Query:    63 EGQDSNYSXXXXXXXXXXXXXXXXXXXXXXXXXIALGEFIGQEKRGLSLNQISTCLHACK 122
             E Q+SN S                         IALG+FIG E RGL+  +ISTCL+A  
Sbjct:    91 EDQESN-SNLEEEDDFLEEEDEIDPDQLSYEELIALGDFIGVENRGLTPIEISTCLNA-S 148

Query:   123 SPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS 182
             +      K+ IDRCV+CQ+E+EE ES+V L PC+H YHSECI+ WL+ KKICPIC +E S
Sbjct:   149 TYVFSHNKNEIDRCVVCQMEFEERESLVVLRPCDHPYHSECITKWLETKKICPICCSEPS 208

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2092271 AT3G19910 [Arabidopsis thaliana (taxid:3702)]

 Score = 233 (87.1 bits), Expect = 3.0e-24, Sum P(2) = 3.0e-24
 Identities = 41/87 (47%), Positives = 61/87 (70%)

Query:    96 IALGEFIGQEKRGLSLNQISTCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPC 155
             +ALG+ +G E RGLS + I++ L + +    D      + CVIC+++YE+ E ++ LLPC
Sbjct:   249 LALGDIVGTESRGLSADTIAS-LPSKRYKEGDNQNGTNESCVICRLDYEDDEDLI-LLPC 306

Query:   156 EHLYHSECISNWLQIKKICPICSTEAS 182
             +H YHSECI+NWL+I K+CP+CS E S
Sbjct:   307 KHSYHSECINNWLKINKVCPVCSAEVS 333

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:504955576 BB "BIG BROTHER" [Arabidopsis thaliana (taxid:3702)]

 Score = 209 (78.6 bits), Expect = 5.3e-17, P = 5.3e-17
 Identities = 43/94 (45%), Positives = 56/94 (59%)

Query:    96 IALGEFIGQEKRGLSLNQISTC-LHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLP 154
             + LGE +G E RGLS   I T      K       K   +RCVICQ++Y+ GE  + L P
Sbjct:   156 VELGEAVGTESRGLSQELIETLPTKKYKFGSIFSRKRAGERCVICQLKYKIGERQMNL-P 214

Query:   155 CEHLYHSECISNWLQIKKICPICSTEA-SPPKNH 187
             C+H+YHSECIS WL I K+CP+C++E    P  H
Sbjct:   215 CKHVYHSECISKWLSINKVCPVCNSEVFGEPSIH 248

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0031624 "ubiquitin conjugating enzyme binding" evidence=IPI

GO:0046621 "negative regulation of organ growth" evidence=IMP

GO:0048437 "floral organ development" evidence=IMP

GO:0051865 "protein autoubiquitination" evidence=IDA

TAIR|locus:2145086 AT5G52140 [Arabidopsis thaliana (taxid:3702)]

 Score = 161 (61.7 bits), Expect = 1.3e-13, Sum P(2) = 1.3e-13
 Identities = 38/100 (38%), Positives = 52/100 (52%)

Query:    98 LGEFIGQEKRGLSLNQIST--------------CLHACKSPPADGTKSGIDRCVICQVEY 143
             LG+ +G   +GLS  +IS               CLH  K   AD ++     C IC +EY
Sbjct:   187 LGDSVGDVGKGLSQERISRLRTHKYGTKTKSWYCLHMKKKFVADDSQ-----CSICLMEY 241

Query:   144 EEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASP 183
              +G+ I  L PC+H+YH +CIS WL+  K+C IC  E  P
Sbjct:   242 AKGDKITTL-PCKHIYHKDCISQWLKQNKVCCICKAEVYP 280

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2027804 AT1G73760 [Arabidopsis thaliana (taxid:3702)]

 Score = 168 (64.2 bits), Expect = 4.8e-12, P = 4.8e-12
 Identities = 37/87 (42%), Positives = 48/87 (55%)

Query:    96 IALGEFIGQEKRGLSLNQISTCLHACKSPPADGTKSGIDR-CVICQVEYEEGESIVALLP 154
             + LGE IG    GL+  QI +CL   K    D T +  DR C+ICQ EYE  +  V  L 
Sbjct:   280 LELGERIGHVNTGLTEKQIKSCLRKVKPCRQDTTVA--DRKCIICQDEYEAKDE-VGELR 336

Query:   155 CEHLYHSECISNWLQIKKICPICSTEA 181
             C H +H +C++ WL  K  CP+C T A
Sbjct:   337 CGHRFHIDCVNQWLVRKNSCPVCKTMA 363

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2124271 MBR2 "MED25 BINDING RING-H2 PROTEIN 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 170 (64.9 bits), Expect = 9.3e-12, P = 9.3e-12
 Identities = 34/87 (39%), Positives = 48/87 (55%)

Query:    96 IALGEFIGQEKRGLSLNQISTCLHACK-SPPADGTKSGIDRCVICQVEYEEGESIVALLP 154
             +ALGE IG    GLS   I   +   K +  A G+   ++ C +CQ EY EG+ +   L 
Sbjct:   578 LALGERIGDVSTGLSEEVILKVMKQHKHTSSAAGSHQDMEPCCVCQEEYAEGDDL-GTLG 636

Query:   155 CEHLYHSECISNWLQIKKICPICSTEA 181
             C H +H+ C+  WL +K +CPIC T A
Sbjct:   637 CGHEFHTACVKQWLMLKNLCPICKTVA 663

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2019150 AT1G74620 [Arabidopsis thaliana (taxid:3702)]

 Score = 159 (61.0 bits), Expect = 1.0e-11, P = 1.0e-11
 Identities = 28/60 (46%), Positives = 39/60 (65%)

Query:   136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNNAITSKL 195
             C IC  +Y EG SIVA LPC+H +H +CI+ WLQ+  +CP+C   +S PK+  +   S L
Sbjct:   183 CAICMEDYIEGSSIVAKLPCDHEFHGDCINKWLQLNHMCPLC--RSSIPKDVKSGYQSCL 240

GO:0005737 "cytoplasm" evidence=ISM

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

TAIR|locus:2086305 AT3G15070 [Arabidopsis thaliana (taxid:3702)]

 Score = 165 (63.1 bits), Expect = 1.9e-11, P = 1.9e-11
 Identities = 36/91 (39%), Positives = 48/91 (52%)

Query:    96 IALGEFIGQEKRGLSLNQISTCLHACKSPPA---DGTKSGI--DRCVICQVEYEEGESIV 150
             +AL + IG  K GLS   +   L    S      +G  + +  D C ICQ  Y+  E  +
Sbjct:   383 LALSDQIGTVKTGLSSEDVKELLKRRTSTRINLEEGPSTDLETDSCTICQENYKN-EDKI 441

Query:   151 ALLPCEHLYHSECISNWLQIKKICPICSTEA 181
             A L C H YH+EC+  WL IK +CPIC +EA
Sbjct:   442 ATLDCMHKYHAECLKKWLVIKNVCPICKSEA 472

GO:0005737 "cytoplasm" evidence=ISM

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

TAIR|locus:2159634 AT5G10650 [Arabidopsis thaliana (taxid:3702)]

 Score = 161 (61.7 bits), Expect = 5.9e-11, P = 5.9e-11
 Identities = 34/97 (35%), Positives = 49/97 (50%)

Query:    96 IALGEFIGQEKRGLSLNQISTCLHACKSPPADGT------KSGIDRCVICQVEYEEGESI 149
             +ALG+ +G     LS   +S  L        D T      K    +C ICQ EY +G+ +
Sbjct:   429 LALGDKMGTVSTALSEEALSRSLKQSIYQETDETGSISLYKDDDIKCSICQEEYVDGDEL 488

Query:   150 VALLPCEHLYHSECISNWLQIKKICPICSTEASPPKN 186
                +PC+H+YH  C+  WL++K  CPIC T A   K+
Sbjct:   489 -GTIPCQHMYHVSCVQQWLRMKNWCPICKTSAEEEKS 524

GO:0005634 "nucleus" evidence=ISM

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

GO:0006914 "autophagy" evidence=RCA

GO:0007165 "signal transduction" evidence=RCA

GO:0009755 "hormone-mediated signaling pathway" evidence=RCA

GO:0010260 "organ senescence" evidence=RCA

UNIPROTKB|C9IY58 RNF13 "E3 ubiquitin-protein ligase RNF13" [Homo sapiens (taxid:9606)]

 Score = 148 (57.2 bits), Expect = 1.5e-10, P = 1.5e-10
 Identities = 28/74 (37%), Positives = 41/74 (55%)

Query:   122 KSPPADGTKSG--IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWL-QIKKICPICS 178
             K  P    K G   D C IC  EYE+G+ +  +LPC H YH +C+  WL + KK CP+C 
Sbjct:   105 KKLPVHKFKKGDEYDVCAICLDEYEDGDKL-RILPCSHAYHCKCVDPWLTKTKKTCPVCK 163

Query:   179 TEASPPKNHNNAIT 192
              +  P +  +++ T
Sbjct:   164 QKVVPSQGDSDSDT 177

GO:0008270 "zinc ion binding" 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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	195
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	5e-13
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	5e-09
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	9e-09
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	2e-08
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	5e-08
smart00184	40	smart00184, RING, Ring finger	5e-07
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	1e-06
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	2e-05
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	3e-05
pfam13920	49	pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RI	0.001

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

 Score = 60.5 bits (147), Expect = 5e-13
 Identities = 21/47 (44%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTE 180
           D C IC  E+E GE +V +LPC H++H EC+  WL+    CP+C   
Sbjct: 1   DECPICLDEFEPGEEVV-VLPCGHVFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

>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 = 49.8 bits (119), Expect = 5e-09
 Identities = 20/46 (43%), Positives = 25/46 (54%), Gaps = 4/46 (8%)

Query: 136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKI-CPICSTE 180
           C IC  E+ E    V LLPC H++   CI  WL+  K  CP+C T 
Sbjct: 2   CPICLEEFRE---PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44

Length = 45

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

 Score = 50.1 bits (120), Expect = 9e-09
 Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 9/53 (16%)

Query: 134 DRCVICQVEYEE---------GESIVALLPCEHLYHSECISNWLQIKKICPIC 177
           D C IC+  ++           +  V    C H +H  CIS WL+ +  CP+C
Sbjct: 20  DVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLC 72

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

 Score = 52.7 bits (126), Expect = 2e-08
 Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 3/54 (5%)

Query: 132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKI-CPICSTEASPP 184
           G++ C IC   + + + +  L PC+H +H  C+  WL      CP+C T   PP
Sbjct: 323 GVE-CAICMSNFIKNDRLRVL-PCDHRFHVGCVDKWLLGYSNKCPVCRTAIPPP 374

Length = 374

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

 Score = 47.1 bits (112), Expect = 5e-08
 Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 3/45 (6%)

Query: 133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPIC 177
              C IC    +     V L PC H++  ECI  +L+ K  CPIC
Sbjct: 2   ELECPIC---LDLLRDPVVLTPCGHVFCRECILRYLKKKSKCPIC 43

Length = 45

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

 Score = 44.4 bits (105), Expect = 5e-07
 Identities = 17/43 (39%), Positives = 20/43 (46%), Gaps = 4/43 (9%)

Query: 136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKI-CPIC 177
           C IC    EE      +LPC H +   CI  WL+     CPIC
Sbjct: 1   CPIC---LEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40

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

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

 Score = 44.4 bits (105), Expect = 1e-06
 Identities = 17/60 (28%), Positives = 21/60 (35%), Gaps = 12/60 (20%)

Query: 133 IDRCVICQVEYEE------------GESIVALLPCEHLYHSECISNWLQIKKICPICSTE 180
           ID C IC+                  E  V    C H +H  CI  WL  K +CP+    
Sbjct: 20  IDVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQT 79

Length = 88

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

 Score = 39.8 bits (93), Expect = 2e-05
 Identities = 18/43 (41%), Positives = 27/43 (62%), Gaps = 4/43 (9%)

Query: 136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKI-CPIC 177
           C IC  E ++    V +LPC HL+ S+CI +WL+   + CP+C
Sbjct: 1   CPICLEEPKD---PVTILPCGHLFCSKCILSWLESGNVTCPLC 40

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

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

 Score = 43.4 bits (102), Expect = 3e-05
 Identities = 13/25 (52%), Positives = 18/25 (72%)

Query: 153 LPCEHLYHSECISNWLQIKKICPIC 177
           LPC H+ H  C+ NWL+ ++ CPIC
Sbjct: 316 LPCGHILHLHCLKNWLERQQTCPIC 340

Length = 491

>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger)

 Score = 35.0 bits (81), Expect = 0.001
 Identities = 20/45 (44%), Positives = 20/45 (44%), Gaps = 6/45 (13%)

Query: 134 DRCVICQVEYEEGESIVALLPCEHL-YHSECISNWLQIKKICPIC 177
           D CVIC     E    V  LPC HL    EC       KK CPIC
Sbjct: 3   DLCVICL----ERPRNVVFLPCGHLCLCEECAKRLRSKKK-CPIC 42

Length = 49

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	195
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.63
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.63
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.45
PHA02929	238	N1R/p28-like protein; Provisional	99.43
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.43
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.26
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.2
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.19
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.18
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.17
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.15
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.15
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.15
PHA02926	242	zinc finger-like protein; Provisional	99.12
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.11
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.01
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.01
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.96
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.96
PF14634	44	zf-RING_5: zinc-RING finger domain	98.95
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.93
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.89
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.83
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.76
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.75
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.74
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.69
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.67
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.66
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.66
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.55
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.49
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.48
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.47
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.46
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.45
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.35
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.35
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.26
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.21
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.2
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.19
KOG0825	1134	consensus PHD Zn-finger protein [General function	98.14
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.14
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.09
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.01
KOG4445	368	consensus Uncharacterized conserved protein, conta	98.01
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.98
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.91
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.88
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.69
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.68
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.63
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.63
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.52
KOG2660	331	consensus Locus-specific chromosome binding protei	97.51
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.47
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.33
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.22
KOG3039	303	consensus Uncharacterized conserved protein [Funct	97.18
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.05
PF04641	260	Rtf2: Rtf2 RING-finger	97.03
COG5152	259	Uncharacterized conserved protein, contains RING a	97.03
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	96.97
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.91
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.9
PHA02825	162	LAP/PHD finger-like protein; Provisional	96.8
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	96.76
PHA02862	156	5L protein; Provisional	96.75
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.72
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.64
KOG1002	791	consensus Nucleotide excision repair protein RAD16	96.64
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.62
COG5236	493	Uncharacterized conserved protein, contains RING Z	96.45
KOG4739	233	consensus Uncharacterized protein involved in syna	96.44
PHA03096	284	p28-like protein; Provisional	96.36
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	96.35
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	96.34
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.33
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	96.26
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.16
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	96.01
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	95.93
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	95.81
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.67
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	95.65
KOG1940	276	consensus Zn-finger protein [General function pred	95.46
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	95.3
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	94.75
KOG3002	299	consensus Zn finger protein [General function pred	94.68
KOG1001	674	consensus Helicase-like transcription factor HLTF/	94.61
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	94.51
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	94.42
COG5175	480	MOT2 Transcriptional repressor [Transcription]	94.39
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	94.26
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	94.26
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	94.12
COG5222	427	Uncharacterized conserved protein, contains RING Z	94.0
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	93.99
KOG3053	293	consensus Uncharacterized conserved protein [Funct	93.39
KOG0298	1394	consensus DEAD box-containing helicase-like transc	92.94
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	92.88
KOG3899	381	consensus Uncharacterized conserved protein [Funct	92.64
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	92.23
KOG1609	323	consensus Protein involved in mRNA turnover and st	91.26
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	90.81
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	90.54
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	90.43
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	90.23
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	90.11
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	89.27
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	88.42
KOG1829	580	consensus Uncharacterized conserved protein, conta	87.52
KOG0825	1134	consensus PHD Zn-finger protein [General function	86.42
PF14569	80	zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.	86.16
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	85.95
KOG2068	327	consensus MOT2 transcription factor [Transcription	85.35
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	84.97
KOG3113	293	consensus Uncharacterized conserved protein [Funct	84.27
PF15295	132	CCDC50_N: Coiled-coil domain-containing protein 50	84.13
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	83.88
KOG0269	839	consensus WD40 repeat-containing protein [Function	82.94
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	82.71
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	82.55
PLN02189	1040	cellulose synthase	81.46
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	81.33
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	81.26
KOG3842	429	consensus Adaptor protein Pellino [Signal transduc	81.09
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	81.02
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	80.75
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	80.24

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

Probab=99.63  E-value=3e-16  Score=135.96  Aligned_cols=79  Identities=28%  Similarity=0.691  Sum_probs=65.7

Q ss_pred             CCCCHHHHHhhcCcccCCCCCCCCCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCC-CCCccccccCCCC
Q 044318          107 RGLSLNQISTCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKK-ICPICSTEASPPK  185 (195)
Q Consensus       107 ~gls~~~i~~~l~~~~~~~~~~~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~-sCPvCR~~l~~~~  185 (195)
                      ..+.+..+ +.++..+|......... ..|+||+++|+.+++++.| ||+|.||..||..||...+ .||+||+.+....
T Consensus       205 ~r~~k~~l-~~~p~~~f~~~~~~~~~-~~CaIClEdY~~GdklRiL-PC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~  281 (348)
T KOG4628|consen  205 NRLIKRLL-KKLPVRTFTKGDDEDAT-DTCAICLEDYEKGDKLRIL-PCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDS  281 (348)
T ss_pred             hhhHHHHH-hhCCcEEeccccccCCC-ceEEEeecccccCCeeeEe-cCCCchhhccchhhHhhcCccCCCCCCcCCCCC
Confidence            35566666 88898999887744444 8999999999999999999 9999999999999997775 5999999887665


Q ss_pred             CCC
Q 044318          186 NHN  188 (195)
Q Consensus       186 ~~~  188 (195)
                      ...
T Consensus       282 ~~~  284 (348)
T KOG4628|consen  282 GSE  284 (348)
T ss_pred             CCC
Confidence            543

>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=99.63  E-value=1.5e-16  Score=99.20  Aligned_cols=44  Identities=48%  Similarity=1.260  Sum_probs=39.8

Q ss_pred             cccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccc
Q 044318          134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICS  178 (195)
Q Consensus       134 ~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR  178 (195)
                      +.|+||++.|..++.++.+ +|+|.||..||.+|++.+++||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKL-PCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEE-TTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEc-cCCCeeCHHHHHHHHHhCCcCCccC
Confidence            4799999999888888888 8999999999999999999999997

...

>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=99.45  E-value=8.4e-14  Score=96.02  Aligned_cols=47  Identities=38%  Similarity=0.978  Sum_probs=37.2

Q ss_pred             CCcccccccccccCC---------ceeEEecCccceechhhHHHHhhcCCCCCccc
Q 044318          132 GIDRCVICQVEYEEG---------ESIVALLPCEHLYHSECISNWLQIKKICPICS  178 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~---------~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR  178 (195)
                      ..+.|+||++.|...         +..+.+.+|||.||..||.+||+.+.+||+||
T Consensus        18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            355699999999432         23345558999999999999999999999998

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=99.43  E-value=9.4e-14  Score=115.47  Aligned_cols=78  Identities=24%  Similarity=0.433  Sum_probs=57.2

Q ss_pred             cCCCCCHHHHHhhcCcccCCCCC-CCCCCCcccccccccccCCc----eeEEecCccceechhhHHHHhhcCCCCCcccc
Q 044318          105 EKRGLSLNQISTCLHACKSPPAD-GTKSGIDRCVICQVEYEEGE----SIVALLPCEHLYHSECISNWLQIKKICPICST  179 (195)
Q Consensus       105 ~~~gls~~~i~~~l~~~~~~~~~-~~~~~~~~C~ICl~~f~~~~----~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~  179 (195)
                      .+.+.....+ ..+|........ .......+|+||++.+..+.    .+.++++|+|.||..||.+|++.+.+||+||.
T Consensus       146 ~k~~~~~~~i-~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~  224 (238)
T PHA02929        146 KKGKNYKKFL-KTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRT  224 (238)
T ss_pred             HhcchhHHHH-HhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCC
Confidence            3455566666 677766544322 13345689999999986543    23456689999999999999999999999999


Q ss_pred             ccCC
Q 044318          180 EASP  183 (195)
Q Consensus       180 ~l~~  183 (195)
                      ++..
T Consensus       225 ~~~~  228 (238)
T PHA02929        225 PFIS  228 (238)
T ss_pred             EeeE
Confidence            8763

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

Probab=99.43  E-value=8.1e-14  Score=117.71  Aligned_cols=54  Identities=31%  Similarity=0.899  Sum_probs=48.4

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhh-cCCCCCccccccCCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ-IKKICPICSTEASPP  184 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~-~~~sCPvCR~~l~~~  184 (195)
                      ...+.+|+|||+.|..+++++++ ||.|.||..||.+|+. .+..||+||++++++
T Consensus       320 a~~GveCaICms~fiK~d~~~vl-PC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPPp  374 (374)
T COG5540         320 ADKGVECAICMSNFIKNDRLRVL-PCDHRFHVGCVDKWLLGYSNKCPVCRTAIPPP  374 (374)
T ss_pred             cCCCceEEEEhhhhcccceEEEe-ccCceechhHHHHHHhhhcccCCccCCCCCCC
Confidence            33568999999999999998888 9999999999999997 678999999999864

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

Probab=99.26  E-value=2.8e-12  Score=107.84  Aligned_cols=54  Identities=26%  Similarity=0.700  Sum_probs=46.6

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCC
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKN  186 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~  186 (195)
                      .......|.|||+....+    ..+||||+||+.||..|...+..||+||..+.+...
T Consensus       235 i~~a~~kC~LCLe~~~~p----SaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskv  288 (293)
T KOG0317|consen  235 IPEATRKCSLCLENRSNP----SATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKV  288 (293)
T ss_pred             CCCCCCceEEEecCCCCC----CcCcCcchHHHHHHHHHHccccCCCcccccCCCcce
Confidence            455678999999998776    556999999999999999999999999999877653

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

Probab=99.20  E-value=9e-12  Score=98.23  Aligned_cols=56  Identities=27%  Similarity=0.568  Sum_probs=46.8

Q ss_pred             CCCCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCC
Q 044318          128 GTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPK  185 (195)
Q Consensus       128 ~~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~  185 (195)
                      ..+.+...|+|||..+.....  +-++|||+||..||+..++....||+||++|..+.
T Consensus       126 ~~~~~~~~CPiCl~~~sek~~--vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~  181 (187)
T KOG0320|consen  126 LRKEGTYKCPICLDSVSEKVP--VSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQ  181 (187)
T ss_pred             cccccccCCCceecchhhccc--cccccchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence            456677999999999876533  43599999999999999999999999999876553

>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=99.19  E-value=1.4e-11  Score=78.64  Aligned_cols=46  Identities=39%  Similarity=0.850  Sum_probs=37.8

Q ss_pred             CcccccccccccCCceeEEecCccce-echhhHHHHhhcCCCCCccccccC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHL-YHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~-FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      ...|+||++....   ++. .||||. ||..|+.+|++....||+||+++.
T Consensus         2 ~~~C~iC~~~~~~---~~~-~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRD---VVL-LPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSS---EEE-ETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCc---eEE-eCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            4689999998654   344 499999 999999999999999999999875

...

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

Probab=99.18  E-value=1.2e-11  Score=107.17  Aligned_cols=52  Identities=33%  Similarity=0.842  Sum_probs=42.9

Q ss_pred             CCCCccccccccc-ccCCc---------eeEEecCccceechhhHHHHhhcCCCCCccccccC
Q 044318          130 KSGIDRCVICQVE-YEEGE---------SIVALLPCEHLYHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       130 ~~~~~~C~ICl~~-f~~~~---------~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      ..++..|.|||++ |..+.         +..+| ||||++|.+|++.|+.+..+||+||.++.
T Consensus       284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrL-pCGHilHl~CLknW~ERqQTCPICr~p~i  345 (491)
T COG5243         284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRL-PCGHILHLHCLKNWLERQQTCPICRRPVI  345 (491)
T ss_pred             cCCCCeEEEecccccCCCCccCcccccCCcccc-cccceeeHHHHHHHHHhccCCCcccCccc
Confidence            5567899999999 44331         23566 99999999999999999999999999953

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.17  E-value=1.4e-11  Score=99.02  Aligned_cols=50  Identities=28%  Similarity=0.685  Sum_probs=40.8

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhc----------------CCCCCccccccCCCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI----------------KKICPICSTEASPPK  185 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~----------------~~sCPvCR~~l~~~~  185 (195)
                      +...|+||++.++.+    ++++|||.||+.||.+|+..                ...||+||..+....
T Consensus        17 ~~~~CpICld~~~dP----VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~   82 (193)
T PLN03208         17 GDFDCNICLDQVRDP----VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT   82 (193)
T ss_pred             CccCCccCCCcCCCc----EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence            567899999998776    34589999999999999852                247999999886543

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

Probab=99.15  E-value=1.5e-11  Score=100.68  Aligned_cols=53  Identities=32%  Similarity=0.716  Sum_probs=43.5

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHHhhcC---CCCCccccccCCCC
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK---KICPICSTEASPPK  185 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~---~sCPvCR~~l~~~~  185 (195)
                      .......|.|||+.-+++    +++.|||.||+.||.+||..+   +.||+||..+...+
T Consensus        43 ~~~~~FdCNICLd~akdP----VvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~   98 (230)
T KOG0823|consen   43 RDGGFFDCNICLDLAKDP----VVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT   98 (230)
T ss_pred             CCCCceeeeeeccccCCC----EEeecccceehHHHHHHHhhcCCCeeCCccccccccce
Confidence            356778999999997776    445799999999999999754   57999999886554

>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=99.15  E-value=3.6e-11  Score=72.87  Aligned_cols=39  Identities=38%  Similarity=0.997  Sum_probs=32.2

Q ss_pred             cccccccccCCceeEEecCccceechhhHHHHhhcCCCCCcc
Q 044318          136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPIC  177 (195)
Q Consensus       136 C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvC  177 (195)
                      |+||++.+..+  ++.+ +|||.||..||.+|++.+.+||+|
T Consensus         1 C~iC~~~~~~~--~~~~-~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRDP--VVVT-PCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SSE--EEEC-TTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccCc--CEEC-CCCCchhHHHHHHHHHCcCCCcCC
Confidence            89999988773  3344 999999999999999999999998

>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=99.15  E-value=2.6e-11  Score=74.13  Aligned_cols=44  Identities=45%  Similarity=1.106  Sum_probs=35.9

Q ss_pred             ccccccccccCCceeEEecCccceechhhHHHHhhc-CCCCCcccccc
Q 044318          135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-KKICPICSTEA  181 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-~~sCPvCR~~l  181 (195)
                      .|+||++.+..   ...+++|+|.||..|+..|++. ...||+||..+
T Consensus         1 ~C~iC~~~~~~---~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFRE---PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhC---ceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            59999999832   2344479999999999999987 77899999764

>PHA02926 zinc finger-like protein; Provisional

Probab=99.12  E-value=2.8e-11  Score=98.71  Aligned_cols=53  Identities=28%  Similarity=0.577  Sum_probs=41.6

Q ss_pred             CCCCcccccccccccCC-----ceeEEecCccceechhhHHHHhhcC------CCCCccccccC
Q 044318          130 KSGIDRCVICQVEYEEG-----ESIVALLPCEHLYHSECISNWLQIK------KICPICSTEAS  182 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~-----~~~~~L~~C~H~FH~~CI~~Wl~~~------~sCPvCR~~l~  182 (195)
                      ...+.+|+|||+....+     ...+.|.+|+|.||..||..|.+.+      ++||+||..+.
T Consensus       167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            44578999999886332     2345677999999999999999753      46999999775

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

Probab=99.11  E-value=4.3e-11  Score=84.13  Aligned_cols=52  Identities=29%  Similarity=0.700  Sum_probs=40.1

Q ss_pred             CCcccccccccccCC--------c-eeEEecCccceechhhHHHHhhc---CCCCCccccccCC
Q 044318          132 GIDRCVICQVEYEEG--------E-SIVALLPCEHLYHSECISNWLQI---KKICPICSTEASP  183 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~--------~-~~~~L~~C~H~FH~~CI~~Wl~~---~~sCPvCR~~l~~  183 (195)
                      .++.|.||...|...        + -..++..|+|.||..||.+|+..   +..||+||+++.-
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~   83 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF   83 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence            378899999988621        1 12344589999999999999975   4789999998753

>smart00504 Ubox Modified RING finger domain

Probab=99.01  E-value=2.8e-10  Score=75.42  Aligned_cols=52  Identities=19%  Similarity=0.315  Sum_probs=43.5

Q ss_pred             cccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCCCCc
Q 044318          134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNN  189 (195)
Q Consensus       134 ~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~  189 (195)
                      ..|+||+..+.++    ++.+|||+|++.||.+|++.+.+||+|+.++......++
T Consensus         2 ~~Cpi~~~~~~~P----v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~   53 (63)
T smart00504        2 FLCPISLEVMKDP----VILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPN   53 (63)
T ss_pred             cCCcCCCCcCCCC----EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeC
Confidence            4699999999886    334999999999999999888999999998866554443

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

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

Probab=99.01  E-value=2.4e-10  Score=70.51  Aligned_cols=38  Identities=32%  Similarity=0.826  Sum_probs=29.3

Q ss_pred             cccccccccCCceeEEecCccceechhhHHHHhhcC----CCCCcc
Q 044318          136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK----KICPIC  177 (195)
Q Consensus       136 C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~----~sCPvC  177 (195)
                      |+||++.|..+   +.| +|||.||..||.+|++..    ..||.|
T Consensus         1 CpiC~~~~~~P---v~l-~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDP---VSL-PCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSE---EE--SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCc---ccc-CCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999987   344 999999999999999654    369988

>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.96  E-value=5.3e-10  Score=68.16  Aligned_cols=39  Identities=38%  Similarity=1.065  Sum_probs=33.3

Q ss_pred             cccccccccCCceeEEecCccceechhhHHHHhh--cCCCCCcc
Q 044318          136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQ--IKKICPIC  177 (195)
Q Consensus       136 C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~--~~~sCPvC  177 (195)
                      |+||++.+..+.   .+++|||.||..||.+|++  ....||+|
T Consensus         1 C~iC~~~~~~~~---~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPV---ILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEE---EETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCCC---EEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            899999987763   3459999999999999998  55689998

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

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

Probab=98.96  E-value=3e-10  Score=78.31  Aligned_cols=52  Identities=33%  Similarity=0.720  Sum_probs=39.1

Q ss_pred             Cccccccccccc-----------CCc-eeEEecCccceechhhHHHHhhcCCCCCccccccCCC
Q 044318          133 IDRCVICQVEYE-----------EGE-SIVALLPCEHLYHSECISNWLQIKKICPICSTEASPP  184 (195)
Q Consensus       133 ~~~C~ICl~~f~-----------~~~-~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~  184 (195)
                      .+.|.||...|.           .++ -.++...|.|.||..||.+||..++.||+||+++.-.
T Consensus        20 id~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~   83 (88)
T COG5194          20 IDVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLA   83 (88)
T ss_pred             cchhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEe
Confidence            466676665543           222 3344557999999999999999999999999987543

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.95  E-value=4.7e-10  Score=69.75  Aligned_cols=44  Identities=30%  Similarity=0.741  Sum_probs=36.1

Q ss_pred             ccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCcccc
Q 044318          135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICST  179 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~  179 (195)
                      .|+||+..|...... .+++|||+||..||..+......||+||+
T Consensus         1 ~C~~C~~~~~~~~~~-~l~~CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRP-RLTSCGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCe-EEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            499999999443344 44599999999999999866789999985

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

Probab=98.93  E-value=3.2e-10  Score=104.93  Aligned_cols=55  Identities=29%  Similarity=0.748  Sum_probs=45.5

Q ss_pred             CCCcccccccccccCCce--eEEecCccceechhhHHHHhhcCCCCCccccccCCCCC
Q 044318          131 SGIDRCVICQVEYEEGES--IVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKN  186 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~--~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~  186 (195)
                      .....|+||++.+..+..  ..++ +|+|+||..|+..|+++..+||+||..+.....
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL-~C~Hifh~~CL~~W~er~qtCP~CR~~~~~~~~  345 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRL-PCGHIFHDSCLRSWFERQQTCPTCRTVLYDYVL  345 (543)
T ss_pred             hcCCeeeeechhhcccccccccee-ecccchHHHHHHHHHHHhCcCCcchhhhhcccc
Confidence            347899999999977543  4466 999999999999999999999999996654443

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.89  E-value=6.1e-10  Score=98.87  Aligned_cols=56  Identities=30%  Similarity=0.599  Sum_probs=46.1

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCCCCc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNN  189 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~  189 (195)
                      ......|+||+..|..+    ++++|+|.||..||..|+.....||+||..+.......+
T Consensus        23 Le~~l~C~IC~d~~~~P----vitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~N   78 (397)
T TIGR00599        23 LDTSLRCHICKDFFDVP----VLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSN   78 (397)
T ss_pred             cccccCCCcCchhhhCc----cCCCCCCchhHHHHHHHHhCCCCCCCCCCccccccCccc
Confidence            33567999999999776    345999999999999999988899999998876544443

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

>smart00184 RING Ring finger

Probab=98.83  E-value=2.3e-09  Score=63.14  Aligned_cols=38  Identities=45%  Similarity=1.100  Sum_probs=31.1

Q ss_pred             cccccccccCCceeEEecCccceechhhHHHHhh-cCCCCCcc
Q 044318          136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQ-IKKICPIC  177 (195)
Q Consensus       136 C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~-~~~sCPvC  177 (195)
                      |+||+....   ..+.+ +|+|.||..|+..|++ ....||+|
T Consensus         1 C~iC~~~~~---~~~~~-~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELK---DPVVL-PCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCC---CcEEe-cCCChHHHHHHHHHHHhCcCCCCCC
Confidence            789988833   33445 9999999999999998 66789998

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

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

Probab=98.76  E-value=1.1e-09  Score=94.16  Aligned_cols=57  Identities=32%  Similarity=0.661  Sum_probs=50.5

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCCCCcccc
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNNAIT  192 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~~~~  192 (195)
                      ....|.||.+.|..+    +++||+|.||.-||+..|..+..||.|+.++..+.+..+.+.
T Consensus        22 ~lLRC~IC~eyf~ip----~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n~il   78 (442)
T KOG0287|consen   22 DLLRCGICFEYFNIP----MITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNNRIL   78 (442)
T ss_pred             HHHHHhHHHHHhcCc----eeccccchHHHHHHHHHhccCCCCCceecccchhhhhhhhHH
Confidence            456899999999988    778999999999999999999999999999988877766554

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

Probab=98.75  E-value=2.5e-09  Score=95.68  Aligned_cols=53  Identities=32%  Similarity=0.895  Sum_probs=41.9

Q ss_pred             CCCcccccccccccCCce-------------eEEecCccceechhhHHHHhh-cCCCCCccccccCC
Q 044318          131 SGIDRCVICQVEYEEGES-------------IVALLPCEHLYHSECISNWLQ-IKKICPICSTEASP  183 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~-------------~~~L~~C~H~FH~~CI~~Wl~-~~~sCPvCR~~l~~  183 (195)
                      .....|+|||..+.-...             -.+++||.|+||..|+.+|+. .+-.||+||.++++
T Consensus       569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            345689999998743211             146679999999999999998 56699999999875

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

Probab=98.74  E-value=4.5e-09  Score=94.61  Aligned_cols=52  Identities=21%  Similarity=0.448  Sum_probs=42.6

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhcC-----CCCCccccccCCCCCCC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK-----KICPICSTEASPPKNHN  188 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~-----~sCPvCR~~l~~~~~~~  188 (195)
                      ...||||++....+    .++.|||+||..||-++|...     +.||+||..+..++..+
T Consensus       186 ~~~CPICL~~~~~p----~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~p  242 (513)
T KOG2164|consen  186 DMQCPICLEPPSVP----VRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLP  242 (513)
T ss_pred             CCcCCcccCCCCcc----cccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceee
Confidence            67899999987665    556899999999999988644     68999999988765544

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

Probab=98.69  E-value=6.7e-09  Score=86.65  Aligned_cols=52  Identities=31%  Similarity=0.688  Sum_probs=42.1

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHH-HhhcCCC-CCccccccCCCCC
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISN-WLQIKKI-CPICSTEASPPKN  186 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~-Wl~~~~s-CPvCR~~l~~~~~  186 (195)
                      .++..|+||++.....    ..++|||+||..||.. |-+.+.- ||+||+.+.++..
T Consensus       213 ~~d~kC~lC~e~~~~p----s~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v  266 (271)
T COG5574         213 LADYKCFLCLEEPEVP----SCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV  266 (271)
T ss_pred             ccccceeeeecccCCc----ccccccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence            3577899999887665    3459999999999999 8876654 9999998877643

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

Probab=98.67  E-value=9.2e-09  Score=86.09  Aligned_cols=74  Identities=19%  Similarity=0.487  Sum_probs=54.0

Q ss_pred             hhcCcccCCCCCCCCCCCcccccccccccCCc-------eeEEecCccceechhhHHHHh--hcCCCCCccccccCCCCC
Q 044318          116 TCLHACKSPPADGTKSGIDRCVICQVEYEEGE-------SIVALLPCEHLYHSECISNWL--QIKKICPICSTEASPPKN  186 (195)
Q Consensus       116 ~~l~~~~~~~~~~~~~~~~~C~ICl~~f~~~~-------~~~~L~~C~H~FH~~CI~~Wl--~~~~sCPvCR~~l~~~~~  186 (195)
                      ..+.-..-...+.+...+..|+||-..+....       .+..| .|+|+||..||+.|-  ..+.+||.|+.++-.+..
T Consensus       207 s~iGfYs~~glPtkhl~d~vCaVCg~~~~~s~~eegvienty~L-sCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~rm  285 (328)
T KOG1734|consen  207 STIGFYSPSGLPTKHLSDSVCAVCGQQIDVSVDEEGVIENTYKL-SCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRM  285 (328)
T ss_pred             HHhcccCCCCCCCCCCCcchhHhhcchheeecchhhhhhhheee-ecccchHHHhhhhheeecCCCCCchHHHHhhHhhh
Confidence            33333333444445567789999998886554       56778 899999999999998  466799999998876655


Q ss_pred             CCcc
Q 044318          187 HNNA  190 (195)
Q Consensus       187 ~~~~  190 (195)
                      ..+|
T Consensus       286 fsnp  289 (328)
T KOG1734|consen  286 FSNP  289 (328)
T ss_pred             ccCc
Confidence            5443

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

Probab=98.66  E-value=3.5e-09  Score=72.44  Aligned_cols=51  Identities=25%  Similarity=0.698  Sum_probs=38.4

Q ss_pred             CCcccccccccccCC---------ceeEEecCccceechhhHHHHhhcC---CCCCccccccC
Q 044318          132 GIDRCVICQVEYEEG---------ESIVALLPCEHLYHSECISNWLQIK---KICPICSTEAS  182 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~---------~~~~~L~~C~H~FH~~CI~~Wl~~~---~sCPvCR~~l~  182 (195)
                      ..+.|.||...|...         +-..++..|.|.||..||.+|+...   ..||+||+.+.
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            445899999988632         1122344699999999999999653   67999998764

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

Probab=98.66  E-value=1.6e-08  Score=62.59  Aligned_cols=38  Identities=29%  Similarity=0.835  Sum_probs=22.4

Q ss_pred             cccccccccCCce-eEEecCccceechhhHHHHhhcC----CCCC
Q 044318          136 CVICQVEYEEGES-IVALLPCEHLYHSECISNWLQIK----KICP  175 (195)
Q Consensus       136 C~ICl~~f~~~~~-~~~L~~C~H~FH~~CI~~Wl~~~----~sCP  175 (195)
                      |+||.+ |...+. .++| +|||+|++.||.+|++..    ..||
T Consensus         1 CpIc~e-~~~~~n~P~~L-~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVL-PCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE--SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEE-eCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 866443 4556 899999999999999743    3576

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

Probab=98.55  E-value=3.2e-08  Score=71.50  Aligned_cols=53  Identities=34%  Similarity=0.738  Sum_probs=41.1

Q ss_pred             CCCCccccccccccc-------------CCceeEEecCccceechhhHHHHhhcCCCCCccccccC
Q 044318          130 KSGIDRCVICQVEYE-------------EGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~-------------~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      +...+.|+||..-+-             ..+-.+....|.|.||..||.+||++++.||+|.++..
T Consensus        43 Di~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~  108 (114)
T KOG2930|consen   43 DIVVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWV  108 (114)
T ss_pred             eeeechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCccee
Confidence            445678888875431             23344566689999999999999999999999988764

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

Probab=98.49  E-value=6.2e-08  Score=66.61  Aligned_cols=53  Identities=23%  Similarity=0.313  Sum_probs=39.9

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhc-CCCCCccccccCCCCCCCc
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-KKICPICSTEASPPKNHNN  189 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-~~sCPvCR~~l~~~~~~~~  189 (195)
                      ...|+|+.+-+.++    ++++|||.|.+.||.+|++. +.+||+|+.++......++
T Consensus         4 ~f~CpIt~~lM~dP----Vi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn   57 (73)
T PF04564_consen    4 EFLCPITGELMRDP----VILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPN   57 (73)
T ss_dssp             GGB-TTTSSB-SSE----EEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-
T ss_pred             ccCCcCcCcHhhCc----eeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceEC
Confidence            46899999999887    44599999999999999988 8899999998877655444

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 ....

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

Probab=98.48  E-value=9.7e-08  Score=60.77  Aligned_cols=42  Identities=38%  Similarity=0.985  Sum_probs=31.4

Q ss_pred             ccccccccccCCceeEEecCcc-----ceechhhHHHHhhcC--CCCCccc
Q 044318          135 RCVICQVEYEEGESIVALLPCE-----HLYHSECISNWLQIK--KICPICS  178 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~~C~-----H~FH~~CI~~Wl~~~--~sCPvCR  178 (195)
                      .|.||+.....++. ... ||.     |.+|..||.+|+..+  .+||+|+
T Consensus         1 ~CrIC~~~~~~~~~-l~~-PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEGDEGDP-LVS-PCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCCCCCCCe-eEe-ccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            48999984334433 344 885     899999999999544  5899995

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

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

Probab=98.47  E-value=4.3e-08  Score=66.96  Aligned_cols=50  Identities=32%  Similarity=0.594  Sum_probs=23.9

Q ss_pred             Cccccccccccc-CCcee-EEe--cCccceechhhHHHHhhc-----------CCCCCccccccC
Q 044318          133 IDRCVICQVEYE-EGESI-VAL--LPCEHLYHSECISNWLQI-----------KKICPICSTEAS  182 (195)
Q Consensus       133 ~~~C~ICl~~f~-~~~~~-~~L--~~C~H~FH~~CI~~Wl~~-----------~~sCPvCR~~l~  182 (195)
                      ...|.||+..+. .+... .+.  ..|++.||..||.+||..           .+.||.|+++|.
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~   66 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS   66 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence            358999999876 33221 222  269999999999999952           136999999875

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.46  E-value=1.3e-07  Score=81.37  Aligned_cols=54  Identities=17%  Similarity=0.383  Sum_probs=39.5

Q ss_pred             Ccccccccccc-cCCc-eeEEecCccceechhhHHHHh-hcCCCCCccccccCCCCCC
Q 044318          133 IDRCVICQVEY-EEGE-SIVALLPCEHLYHSECISNWL-QIKKICPICSTEASPPKNH  187 (195)
Q Consensus       133 ~~~C~ICl~~f-~~~~-~~~~L~~C~H~FH~~CI~~Wl-~~~~sCPvCR~~l~~~~~~  187 (195)
                      ...||||...- ..+. .+.+. +|||.||..||...| .....||.|+..+......
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr   59 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFR   59 (309)
T ss_pred             CCCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhcCCCCCCCCCCCccchhhcc
Confidence            46899999863 3333 22333 799999999999966 5557899999988766533

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

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

Probab=98.45  E-value=4.8e-08  Score=82.70  Aligned_cols=51  Identities=25%  Similarity=0.624  Sum_probs=44.3

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKN  186 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~  186 (195)
                      ....|-||-..|..+    .+++|||.||.-||+..|..+..||+||.+......
T Consensus        24 s~lrC~IC~~~i~ip----~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~esrl   74 (391)
T COG5432          24 SMLRCRICDCRISIP----CETTCGHTFCSLCIRRHLGTQPFCPVCREDPCESRL   74 (391)
T ss_pred             hHHHhhhhhheeecc----eecccccchhHHHHHHHhcCCCCCccccccHHhhhc
Confidence            457899999998887    668999999999999999999999999987655443

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

Probab=98.35  E-value=1e-07  Score=63.52  Aligned_cols=53  Identities=36%  Similarity=0.638  Sum_probs=25.8

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCCCCcc
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNNA  190 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~~  190 (195)
                      .-.|++|...++.+   +.+..|.|.||..||..-+..  .||+|+++.-..+...|.
T Consensus         7 lLrCs~C~~~l~~p---v~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD~~~Nr   59 (65)
T PF14835_consen    7 LLRCSICFDILKEP---VCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQDIQINR   59 (65)
T ss_dssp             TTS-SSS-S--SS----B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS----H
T ss_pred             hcCCcHHHHHhcCC---ceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHHHHhhh
Confidence            35799999998876   345599999999999886553  499999988766655443

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

Probab=98.35  E-value=1e-07  Score=91.05  Aligned_cols=54  Identities=24%  Similarity=0.688  Sum_probs=40.6

Q ss_pred             CCCCCcccccccccccCCc---eeEEecCccceechhhHHHHhhcC--CCCCccccccC
Q 044318          129 TKSGIDRCVICQVEYEEGE---SIVALLPCEHLYHSECISNWLQIK--KICPICSTEAS  182 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~---~~~~L~~C~H~FH~~CI~~Wl~~~--~sCPvCR~~l~  182 (195)
                      ...+.++|+||...+..-+   .-.+++.|.|.||..||.+|++..  .+||+||..++
T Consensus      1465 ~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1465 KFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             hcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            4567899999997764111   112344799999999999999765  67999998764

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

Probab=98.26  E-value=2.8e-07  Score=76.28  Aligned_cols=46  Identities=28%  Similarity=0.626  Sum_probs=39.4

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCcccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICST  179 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~  179 (195)
                      ......|+||++.|..+   .. ++|+|.||..||..|+.....||.||.
T Consensus        10 ~~~~~~C~iC~~~~~~p---~~-l~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   10 LQEELTCPICLEYFREP---VL-LPCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             ccccccChhhHHHhhcC---cc-ccccchHhHHHHHHhcCCCcCCcccCC
Confidence            34667999999999988   34 499999999999999986678999994

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

Probab=98.21  E-value=4.5e-07  Score=79.42  Aligned_cols=53  Identities=23%  Similarity=0.684  Sum_probs=39.1

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcC---CCCCccccccCCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK---KICPICSTEASPP  184 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~---~sCPvCR~~l~~~  184 (195)
                      ....|.||-..+.....+..+-.|||+||..|+.+|+...   +.||+||-.+...
T Consensus         3 i~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r   58 (465)
T KOG0827|consen    3 IMAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQER   58 (465)
T ss_pred             ccceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccce
Confidence            3568999954444444566664699999999999999753   5799999555443

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

Probab=98.20  E-value=6.3e-07  Score=78.39  Aligned_cols=54  Identities=31%  Similarity=0.629  Sum_probs=41.7

Q ss_pred             CCCCcccccccccccCCc----eeEEecCccceechhhHHHHh--hc-----CCCCCccccccCC
Q 044318          130 KSGIDRCVICQVEYEEGE----SIVALLPCEHLYHSECISNWL--QI-----KKICPICSTEASP  183 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~----~~~~L~~C~H~FH~~CI~~Wl--~~-----~~sCPvCR~~l~~  183 (195)
                      +.....|.|||+......    ..+.|++|.|.||..||..|-  ++     .+.||.||....-
T Consensus       158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~  222 (344)
T KOG1039|consen  158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSF  222 (344)
T ss_pred             ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcccc
Confidence            356789999999975543    234556899999999999999  34     4789999976543

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

Probab=98.19  E-value=8.1e-07  Score=79.09  Aligned_cols=49  Identities=22%  Similarity=0.733  Sum_probs=39.1

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      +-.+|||||+........+..+.|.|.||-.|+.+|.  ..+||+||.-..
T Consensus       174 ELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~  222 (493)
T KOG0804|consen  174 ELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS  222 (493)
T ss_pred             cCCCcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC
Confidence            4579999999986655444444899999999999994  468999997655

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

Probab=98.14  E-value=3.3e-07  Score=86.15  Aligned_cols=52  Identities=17%  Similarity=0.426  Sum_probs=44.6

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCC
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASP  183 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~  183 (195)
                      .....|+||+..|.++...... +|+|+||..||..|-+...+||+||..+..
T Consensus       121 ~~~~~CP~Ci~s~~DqL~~~~k-~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~  172 (1134)
T KOG0825|consen  121 HVENQCPNCLKSCNDQLEESEK-HTAHYFCEECVGSWSRCAQTCPVDRGEFGE  172 (1134)
T ss_pred             hhhhhhhHHHHHHHHHhhcccc-ccccccHHHHhhhhhhhcccCchhhhhhhe
Confidence            3456899999999887666666 899999999999999999999999987643

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

Probab=98.14  E-value=1.2e-06  Score=76.10  Aligned_cols=49  Identities=33%  Similarity=0.655  Sum_probs=40.1

Q ss_pred             CCCcccccccccccCCceeEEecCccc-eechhhHHHHhhcCCCCCccccccCC
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEH-LYHSECISNWLQIKKICPICSTEASP  183 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H-~FH~~CI~~Wl~~~~sCPvCR~~l~~  183 (195)
                      +...+|+|||.+-++-   .+| ||.| ..|..|.+...-+++.||+||+++..
T Consensus       288 ~~gkeCVIClse~rdt---~vL-PCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~  337 (349)
T KOG4265|consen  288 ESGKECVICLSESRDT---VVL-PCRHLCLCSGCAKSLRYQTNNCPICRQPIEE  337 (349)
T ss_pred             cCCCeeEEEecCCcce---EEe-cchhhehhHhHHHHHHHhhcCCCccccchHh
Confidence            4477999999986654   445 9999 58999998877788999999998754

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

Probab=98.09  E-value=8.5e-07  Score=83.33  Aligned_cols=52  Identities=19%  Similarity=0.701  Sum_probs=42.7

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhh-cCCCCCccccccCCCCCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ-IKKICPICSTEASPPKNH  187 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~-~~~sCPvCR~~l~~~~~~  187 (195)
                      +--.|+.|-..+++.    +++.|+|+||..||..-+. +.+.||.|.+.+.+.+..
T Consensus       642 ~~LkCs~Cn~R~Kd~----vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~  694 (698)
T KOG0978|consen  642 ELLKCSVCNTRWKDA----VITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVH  694 (698)
T ss_pred             hceeCCCccCchhhH----HHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccccc
Confidence            456899999887765    5569999999999999985 568899999988776543

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

Probab=98.01  E-value=2e-06  Score=73.16  Aligned_cols=52  Identities=23%  Similarity=0.435  Sum_probs=41.6

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcC-CCCCccccccCCCCCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK-KICPICSTEASPPKNH  187 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~-~sCPvCR~~l~~~~~~  187 (195)
                      ...+|+||+..-..+   +.| +|+|.||.-||+.-.+.. ++||+||.++.+....
T Consensus         6 ~~~eC~IC~nt~n~P---v~l-~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i~~   58 (324)
T KOG0824|consen    6 KKKECLICYNTGNCP---VNL-YCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTIDF   58 (324)
T ss_pred             cCCcceeeeccCCcC---ccc-cccchhhhhhhcchhhcCCCCCceecCCCCcchhc
Confidence            467899999886555   455 999999999999877654 5699999999766443

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

Probab=98.01  E-value=1.8e-06  Score=73.45  Aligned_cols=56  Identities=21%  Similarity=0.661  Sum_probs=45.3

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHHhhc-----------------------CCCCCccccccCCCC
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-----------------------KKICPICSTEASPPK  185 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-----------------------~~sCPvCR~~l~~~~  185 (195)
                      .......|+|||..|..+...++. +|-|+||..|+.++|..                       ...||+||.++.-..
T Consensus       111 nn~p~gqCvICLygfa~~~~ft~T-~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~  189 (368)
T KOG4445|consen  111 NNHPNGQCVICLYGFASSPAFTVT-ACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEE  189 (368)
T ss_pred             CCCCCCceEEEEEeecCCCceeee-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccc
Confidence            455678999999999988877777 99999999999887741                       236999999886443

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

Probab=97.98  E-value=1.5e-06  Score=55.90  Aligned_cols=46  Identities=26%  Similarity=0.569  Sum_probs=35.9

Q ss_pred             CcccccccccccCCceeEEecCccc-eechhhHHHHh-hcCCCCCccccccC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEH-LYHSECISNWL-QIKKICPICSTEAS  182 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H-~FH~~CI~~Wl-~~~~sCPvCR~~l~  182 (195)
                      .++|.||++.-.+.    +|..||| ..|..|-.+.+ ..+..||+||+++.
T Consensus         7 ~dECTICye~pvds----VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    7 SDECTICYEHPVDS----VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             ccceeeeccCcchH----HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            48999999876554    5568999 47889965555 47899999999874

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

Probab=97.91  E-value=6e-06  Score=72.90  Aligned_cols=49  Identities=41%  Similarity=0.895  Sum_probs=38.2

Q ss_pred             Cccccccccccc-CCceeEEecCccceechhhHHHHhhc--CCCCCcccccc
Q 044318          133 IDRCVICQVEYE-EGESIVALLPCEHLYHSECISNWLQI--KKICPICSTEA  181 (195)
Q Consensus       133 ~~~C~ICl~~f~-~~~~~~~L~~C~H~FH~~CI~~Wl~~--~~sCPvCR~~l  181 (195)
                      .-.|+||+..|. .++.....+.|||.|...||++||.+  +..||.|..+.
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka   55 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA   55 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence            468999999985 34444444599999999999999952  35799998654

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

Probab=97.88  E-value=1.3e-06  Score=75.79  Aligned_cols=55  Identities=20%  Similarity=0.386  Sum_probs=43.1

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhc-CCCCCccccccCCCCCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-KKICPICSTEASPPKNH  187 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-~~sCPvCR~~l~~~~~~  187 (195)
                      ......|+|||.-++..   +....|.|.||..||..-++. .+.||.||+.+.++...
T Consensus        40 ~~~~v~c~icl~llk~t---mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsL   95 (381)
T KOG0311|consen   40 FDIQVICPICLSLLKKT---MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSL   95 (381)
T ss_pred             hhhhhccHHHHHHHHhh---cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccC
Confidence            34568999999987654   222379999999999998864 57899999999876543

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

Probab=97.69  E-value=2.1e-05  Score=78.20  Aligned_cols=66  Identities=26%  Similarity=0.619  Sum_probs=53.1

Q ss_pred             hhcCcccCCCCCCCCCCCcccccccccccCCceeEEecCccceechhhHHHHhhcC----------CCCCccccccC
Q 044318          116 TCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK----------KICPICSTEAS  182 (195)
Q Consensus       116 ~~l~~~~~~~~~~~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~----------~sCPvCR~~l~  182 (195)
                      ..+|-...+.......+++.|.||+.+-......+.| .|+|+||..|.++-|.++          -+||+|+.++.
T Consensus      3469 ~CLPCl~Cdks~tkQD~DDmCmICFTE~L~AAP~IqL-~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3469 HCLPCLHCDKSATKQDADDMCMICFTEALSAAPAIQL-DCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             hcccccccChhhhhcccCceEEEEehhhhCCCcceec-CCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            5677777666666777889999999887777788888 999999999997766543          27999998874

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

Probab=97.68  E-value=2.6e-05  Score=51.15  Aligned_cols=43  Identities=26%  Similarity=0.552  Sum_probs=28.7

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhc--CCCCCc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI--KKICPI  176 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~--~~sCPv  176 (195)
                      .-...|||.+..|+++  ++.. .|+|+|-+..|.+|++.  ...||+
T Consensus         9 ~~~~~CPiT~~~~~~P--V~s~-~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen    9 TISLKCPITLQPFEDP--VKSK-KCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             B--SB-TTTSSB-SSE--EEES-SS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             EeccCCCCcCChhhCC--cCcC-CCCCeecHHHHHHHHHhcCCCCCCC
Confidence            3467899999999876  3444 89999999999999943  457998

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

Probab=97.63  E-value=2.5e-05  Score=64.26  Aligned_cols=63  Identities=29%  Similarity=0.604  Sum_probs=51.6

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhc--------CCCCCccccccCCCCCCCcccccCC
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI--------KKICPICSTEASPPKNHNNAITSKL  195 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~--------~~sCPvCR~~l~~~~~~~~~~~~~l  195 (195)
                      .-...|..|-..+..++.++ | .|-|.||..|+..|-..        .-.||.|..++.++.....|+.++|
T Consensus        48 DY~pNC~LC~t~La~gdt~R-L-vCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva~aL  118 (299)
T KOG3970|consen   48 DYNPNCRLCNTPLASGDTTR-L-VCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVSPVAEAL  118 (299)
T ss_pred             CCCCCCceeCCccccCccee-e-hhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccchhHHHH
Confidence            34678999998888887654 4 79999999999999853        2369999999999999888887654

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

Probab=97.63  E-value=3.4e-05  Score=68.84  Aligned_cols=51  Identities=25%  Similarity=0.575  Sum_probs=43.6

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCC
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASP  183 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~  183 (195)
                      .......|.||+..+..+   +. +||||.||..||.+-+.....||.||..+..
T Consensus        80 ~~~sef~c~vc~~~l~~p---v~-tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   80 EIRSEFECCVCSRALYPP---VV-TPCGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cccchhhhhhhHhhcCCC---cc-ccccccccHHHHHHHhccCCCCccccccccc
Confidence            345678999999998776   34 4999999999999988888999999998875

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

Probab=97.52  E-value=6.9e-05  Score=67.01  Aligned_cols=55  Identities=20%  Similarity=0.458  Sum_probs=45.4

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNH  187 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~  187 (195)
                      ...+..|+||+..+.++-..   +.|||.||..|+..|+..+..||.|+..+......
T Consensus        18 ~~~~l~C~~C~~vl~~p~~~---~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~   72 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDPVQT---TTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEEL   72 (391)
T ss_pred             CcccccCccccccccCCCCC---CCCCCcccccccchhhccCcCCcccccccchhhcc
Confidence            45678999999999887321   38999999999999999999999999887655444

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

Probab=97.51  E-value=2.1e-05  Score=67.77  Aligned_cols=57  Identities=21%  Similarity=0.459  Sum_probs=45.0

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCCCCc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNN  189 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~  189 (195)
                      ...-..|.+|-..|.+...   .+-|-|.||+.||.+.|...+.||+|...+-......+
T Consensus        12 ~n~~itC~LC~GYliDATT---I~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t~pl~n   68 (331)
T KOG2660|consen   12 LNPHITCRLCGGYLIDATT---ITECLHTFCKSCIVKYLEESKYCPTCDIVIHKTHPLLN   68 (331)
T ss_pred             cccceehhhccceeecchh---HHHHHHHHHHHHHHHHHHHhccCCccceeccCcccccc
Confidence            3456799999988877633   23799999999999999999999999987755443333

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

Probab=97.47  E-value=3.8e-05  Score=67.67  Aligned_cols=47  Identities=30%  Similarity=0.715  Sum_probs=37.6

Q ss_pred             CCcccccccccccC-CceeEEecCccceechhhHHHHhhcC--CCCCcccc
Q 044318          132 GIDRCVICQVEYEE-GESIVALLPCEHLYHSECISNWLQIK--KICPICST  179 (195)
Q Consensus       132 ~~~~C~ICl~~f~~-~~~~~~L~~C~H~FH~~CI~~Wl~~~--~sCPvCR~  179 (195)
                      -.-.|..|-+.+-. ++.+..| ||.|+||..|+...|.++  .+||.||+
T Consensus       364 ~~L~Cg~CGe~~Glk~e~LqAL-pCsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNERLQAL-PCSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             HhhhhhhhhhhhcCCccccccc-chhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            34679999888743 3456667 999999999999999654  68999994

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

Probab=97.33  E-value=0.00022  Score=60.29  Aligned_cols=51  Identities=22%  Similarity=0.473  Sum_probs=39.7

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHHhhc--CCCCCccccccC
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI--KKICPICSTEAS  182 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~--~~sCPvCR~~l~  182 (195)
                      ......+|++|-+.-..+-   ...+|+|+||.-||..-+..  ..+||.|..++.
T Consensus       235 ~~t~~~~C~~Cg~~PtiP~---~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  235 TGTSDTECPVCGEPPTIPH---VIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cccCCceeeccCCCCCCCe---eeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            4567789999988765552   23389999999999887754  478999998776

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

Probab=97.22  E-value=0.00011  Score=65.11  Aligned_cols=49  Identities=27%  Similarity=0.756  Sum_probs=37.5

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhc--CCCCCccccccCCCC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI--KKICPICSTEASPPK  185 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~--~~sCPvCR~~l~~~~  185 (195)
                      -.-|-||-+.=+   .+... ||||..|..||..|-..  ..+||.||..+....
T Consensus       369 FeLCKICaendK---dvkIE-PCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte  419 (563)
T KOG1785|consen  369 FELCKICAENDK---DVKIE-PCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTE  419 (563)
T ss_pred             HHHHHHhhccCC---Ccccc-cccchHHHHHHHhhcccCCCCCCCceeeEecccc
Confidence            467999976522   23344 99999999999999744  468999999987654

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.18  E-value=0.00033  Score=58.42  Aligned_cols=55  Identities=13%  Similarity=0.253  Sum_probs=49.8

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKN  186 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~  186 (195)
                      ....|+||...+.+.-.+..|-||||+|+.+|+.+.++.-..||+|-.++...+.
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdi  274 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDI  274 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccce
Confidence            5678999999999998899999999999999999999999999999998876654

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

Probab=97.05  E-value=0.00039  Score=43.88  Aligned_cols=45  Identities=22%  Similarity=0.507  Sum_probs=23.5

Q ss_pred             cccccccccC-CceeEEecCccceechhhHHHHhh-cCCCCCcccccc
Q 044318          136 CVICQVEYEE-GESIVALLPCEHLYHSECISNWLQ-IKKICPICSTEA  181 (195)
Q Consensus       136 C~ICl~~f~~-~~~~~~L~~C~H~FH~~CI~~Wl~-~~~sCPvCR~~l  181 (195)
                      |++|.+.+.. +..+... +|++.+|..|...-++ ..+.||-||++.
T Consensus         1 cp~C~e~~d~~d~~~~PC-~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPC-ECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SS-TTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccC-cCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            7899999833 3344445 7899999999998886 478999999864

>PF04641 Rtf2: Rtf2 RING-finger

Probab=97.03  E-value=0.00065  Score=57.51  Aligned_cols=56  Identities=20%  Similarity=0.467  Sum_probs=46.1

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKN  186 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~  186 (195)
                      ......|||....|......+.+.+|||+|...+|..- +....||+|-.++...+.
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~f~~~Di  165 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKPFTEEDI  165 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCccccCCE
Confidence            45667999999999777777788899999999999996 345679999999875543

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

Probab=97.03  E-value=0.0002  Score=58.01  Aligned_cols=45  Identities=27%  Similarity=0.550  Sum_probs=38.8

Q ss_pred             cccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccC
Q 044318          134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       134 ~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      ..|.||-.+|+.+    +.+.|||.||..|..+-++....|-+|.+...
T Consensus       197 F~C~iCKkdy~sp----vvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~  241 (259)
T COG5152         197 FLCGICKKDYESP----VVTECGHSFCSLCAIRKYQKGDECGVCGKATY  241 (259)
T ss_pred             eeehhchhhccch----hhhhcchhHHHHHHHHHhccCCcceecchhhc
Confidence            4899999999987    44589999999999988888899999987543

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

Probab=96.97  E-value=0.00073  Score=42.46  Aligned_cols=40  Identities=35%  Similarity=0.956  Sum_probs=26.9

Q ss_pred             cccccccccCCceeEEecCcc-----ceechhhHHHHhh--cCCCCCcc
Q 044318          136 CVICQVEYEEGESIVALLPCE-----HLYHSECISNWLQ--IKKICPIC  177 (195)
Q Consensus       136 C~ICl~~f~~~~~~~~L~~C~-----H~FH~~CI~~Wl~--~~~sCPvC  177 (195)
                      |-||++.-.....++  .||+     -..|..||.+|+.  .+.+|++|
T Consensus         1 CrIC~~~~~~~~~li--~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDEPLI--SPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS-EE---SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCCcee--cccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            779998876655333  3664     3789999999996  45679988

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

Probab=96.91  E-value=0.00047  Score=58.85  Aligned_cols=47  Identities=21%  Similarity=0.487  Sum_probs=40.0

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASP  183 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~  183 (195)
                      ...|-||...|..+    +.+.|+|.||..|...=++....|++|.+....
T Consensus       241 Pf~c~icr~~f~~p----Vvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g  287 (313)
T KOG1813|consen  241 PFKCFICRKYFYRP----VVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG  287 (313)
T ss_pred             Cccccccccccccc----hhhcCCceeehhhhccccccCCcceeccccccc
Confidence            35699999999987    445999999999999888888999999876643

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

Probab=96.90  E-value=0.0004  Score=59.21  Aligned_cols=43  Identities=28%  Similarity=0.569  Sum_probs=32.2

Q ss_pred             CcccccccccccCCceeEEecCccc-eechhhHHHHhhcCCCCCccccccCC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEH-LYHSECISNWLQIKKICPICSTEASP  183 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H-~FH~~CI~~Wl~~~~sCPvCR~~l~~  183 (195)
                      ..-|.|||....+   ++.| +||| +-|..|-+..    +.||+||+.+..
T Consensus       300 ~~LC~ICmDaP~D---CvfL-eCGHmVtCt~CGkrm----~eCPICRqyi~r  343 (350)
T KOG4275|consen  300 RRLCAICMDAPRD---CVFL-ECGHMVTCTKCGKRM----NECPICRQYIVR  343 (350)
T ss_pred             HHHHHHHhcCCcc---eEEe-ecCcEEeehhhcccc----ccCchHHHHHHH
Confidence            5679999987544   4555 9999 5688887553    489999987653

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=96.80  E-value=0.00088  Score=52.45  Aligned_cols=51  Identities=27%  Similarity=0.638  Sum_probs=35.5

Q ss_pred             CCCCcccccccccccCCceeEEecCccc---eechhhHHHHhhc--CCCCCccccccCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEH---LYHSECISNWLQI--KKICPICSTEASP  183 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H---~FH~~CI~~Wl~~--~~sCPvCR~~l~~  183 (195)
                      ......|-||.++-..  ..... .|..   ..|..|+.+|+..  ..+||+|+++..-
T Consensus         5 s~~~~~CRIC~~~~~~--~~~PC-~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i   60 (162)
T PHA02825          5 SLMDKCCWICKDEYDV--VTNYC-NCKNENKIVHKECLEEWINTSKNKSCKICNGPYNI   60 (162)
T ss_pred             CCCCCeeEecCCCCCC--ccCCc-ccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEE
Confidence            4567799999988432  22222 3444   5699999999964  4679999987653

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

Probab=96.76  E-value=0.00072  Score=51.58  Aligned_cols=45  Identities=16%  Similarity=0.448  Sum_probs=34.2

Q ss_pred             CcccccccccccCCceeEEecCcc------ceechhhHHHHhhcCCCCCccc
Q 044318          133 IDRCVICQVEYEEGESIVALLPCE------HLYHSECISNWLQIKKICPICS  178 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~------H~FH~~CI~~Wl~~~~sCPvCR  178 (195)
                      ..+|.||++.+.....++.+ +|+      |.||..|+.+|-+.++.=|.=|
T Consensus        26 ~~EC~IC~~~I~~~~GvV~v-t~~g~lnLEkmfc~~C~~rw~~~~~rDPfnR   76 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYV-TDGGTLNLEKMFCADCDKRWRRERNRDPFNR   76 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEE-ecCCeehHHHHHHHHHHHHHHhhccCCCccc
Confidence            67999999999885556666 675      8999999999955444445544

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.

>PHA02862 5L protein; Provisional

Probab=96.75  E-value=0.00089  Score=51.59  Aligned_cols=46  Identities=30%  Similarity=0.653  Sum_probs=34.1

Q ss_pred             CcccccccccccCCceeEEecCcc-----ceechhhHHHHhhc--CCCCCccccccCC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCE-----HLYHSECISNWLQI--KKICPICSTEASP  183 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~-----H~FH~~CI~~Wl~~--~~sCPvCR~~l~~  183 (195)
                      .+.|-||+..-.+.  .   .||.     ...|..||.+|++.  +..||+|+.+..-
T Consensus         2 ~diCWIC~~~~~e~--~---~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I   54 (156)
T PHA02862          2 SDICWICNDVCDER--N---NFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI   54 (156)
T ss_pred             CCEEEEecCcCCCC--c---ccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence            46799999885433  2   2554     56899999999964  4689999987643

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

Probab=96.72  E-value=0.00097  Score=48.16  Aligned_cols=34  Identities=26%  Similarity=0.709  Sum_probs=26.7

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHH
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECIS  165 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~  165 (195)
                      -.....|++|-..+..+ ...+. ||||+||..|+.
T Consensus        75 i~~~~~C~vC~k~l~~~-~f~~~-p~~~v~H~~C~~  108 (109)
T PF10367_consen   75 ITESTKCSVCGKPLGNS-VFVVF-PCGHVVHYSCIK  108 (109)
T ss_pred             ECCCCCccCcCCcCCCc-eEEEe-CCCeEEeccccc
Confidence            34567899999998774 34444 999999999985

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 [].

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

Probab=96.64  E-value=0.00095  Score=58.39  Aligned_cols=51  Identities=27%  Similarity=0.459  Sum_probs=42.2

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCC
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASP  183 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~  183 (195)
                      ...++..|+||...-...    +..||+|.-|..||.+-+.+.+.|=.|++.+..
T Consensus       418 p~sEd~lCpICyA~pi~A----vf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  418 PDSEDNLCPICYAGPINA----VFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             CCcccccCcceecccchh----hccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            346778999998664333    446999999999999999999999999998864

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

Probab=96.64  E-value=0.00079  Score=61.63  Aligned_cols=52  Identities=23%  Similarity=0.542  Sum_probs=39.7

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHHhhc-----CCCCCccccccCCC
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-----KKICPICSTEASPP  184 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-----~~sCPvCR~~l~~~  184 (195)
                      ...+...|.+|-+.-++.    ....|.|.||+-||.+++..     +-+||+|...+.-.
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----IESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             cccCceeecccCChhhhh----HhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            455677999998775543    33489999999999998843     35899998877544

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

Probab=96.62  E-value=0.0011  Score=58.84  Aligned_cols=48  Identities=25%  Similarity=0.573  Sum_probs=37.7

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhc--------CCCCCccccc
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI--------KKICPICSTE  180 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~--------~~sCPvCR~~  180 (195)
                      ....|.||++........+.+ ||+|+||+.|+..++..        .-.||-++-.
T Consensus       183 slf~C~ICf~e~~G~~c~~~l-pC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~  238 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFL-PCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG  238 (445)
T ss_pred             hcccceeeehhhcCcceeeec-ccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence            457899999998766666666 99999999999999953        2368877653

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

Probab=96.45  E-value=0.0024  Score=55.82  Aligned_cols=56  Identities=32%  Similarity=0.584  Sum_probs=40.8

Q ss_pred             CCCCCCCCCCCcccccccccccCCceeEEecCccceechhhHHHH--hhcCCCCCccccccC
Q 044318          123 SPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNW--LQIKKICPICSTEAS  182 (195)
Q Consensus       123 ~~~~~~~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~W--l~~~~sCPvCR~~l~  182 (195)
                      .......++.+..|.||...+.-    ..++||+|..|-.|..+.  |...+.||+||+..-
T Consensus        51 tsSaddtDEen~~C~ICA~~~TY----s~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e  108 (493)
T COG5236          51 TSSADDTDEENMNCQICAGSTTY----SARYPCGHQICHACAVRLRALYMQKGCPLCRTETE  108 (493)
T ss_pred             cccccccccccceeEEecCCceE----EEeccCCchHHHHHHHHHHHHHhccCCCccccccc
Confidence            33334567778899999876543    244599999999997553  456789999998653

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

Probab=96.44  E-value=0.0012  Score=54.80  Aligned_cols=51  Identities=18%  Similarity=0.507  Sum_probs=34.2

Q ss_pred             ccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCCCCc
Q 044318          135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNN  189 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~  189 (195)
                      .|.-|...-. +.... |+.|+|+||..|...-.  ...||+||+.+.......+
T Consensus         5 hCn~C~~~~~-~~~f~-LTaC~HvfC~~C~k~~~--~~~C~lCkk~ir~i~l~~s   55 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFF-LTACRHVFCEPCLKASS--PDVCPLCKKSIRIIQLNRS   55 (233)
T ss_pred             EeccccccCC-CCcee-eeechhhhhhhhcccCC--ccccccccceeeeeecccc
Confidence            4666654433 44444 44999999999986632  2289999998765554443

>PHA03096 p28-like protein; Provisional

Probab=96.36  E-value=0.0014  Score=56.28  Aligned_cols=48  Identities=19%  Similarity=0.254  Sum_probs=35.1

Q ss_pred             cccccccccccCC----ceeEEecCccceechhhHHHHhhcC------CCCCcccccc
Q 044318          134 DRCVICQVEYEEG----ESIVALLPCEHLYHSECISNWLQIK------KICPICSTEA  181 (195)
Q Consensus       134 ~~C~ICl~~f~~~----~~~~~L~~C~H~FH~~CI~~Wl~~~------~sCPvCR~~l  181 (195)
                      ..|.||++.....    .....|..|.|.||..||..|...+      +.||.|+..+
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            7899999987543    2345677899999999999999543      3455555544

>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=96.35  E-value=0.0022  Score=40.20  Aligned_cols=32  Identities=25%  Similarity=0.651  Sum_probs=23.2

Q ss_pred             cCcc-ceechhhHHHHhhcCCCCCccccccCCC
Q 044318          153 LPCE-HLYHSECISNWLQIKKICPICSTEASPP  184 (195)
Q Consensus       153 ~~C~-H~FH~~CI~~Wl~~~~sCPvCR~~l~~~  184 (195)
                      ..|. |+.|..|+...+.....||+|..+++..
T Consensus        16 i~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen   16 IKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             EE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             eeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            3686 9999999999999999999999998754

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.

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

Probab=96.34  E-value=0.0018  Score=50.90  Aligned_cols=32  Identities=41%  Similarity=0.876  Sum_probs=28.4

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceech
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHS  161 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~  161 (195)
                      .....-+|+||++++..++.+.+| ||-.+||+
T Consensus       173 L~ddkGECvICLEdL~~GdtIARL-PCLCIYHK  204 (205)
T KOG0801|consen  173 LKDDKGECVICLEDLEAGDTIARL-PCLCIYHK  204 (205)
T ss_pred             hcccCCcEEEEhhhccCCCceecc-ceEEEeec
Confidence            345667999999999999999999 99999997

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

Probab=96.33  E-value=0.00018  Score=63.47  Aligned_cols=53  Identities=30%  Similarity=0.606  Sum_probs=45.0

Q ss_pred             CCCCcccccccccccCC-ceeEEecCccceechhhHHHHhhcCCCCCccccccCC
Q 044318          130 KSGIDRCVICQVEYEEG-ESIVALLPCEHLYHSECISNWLQIKKICPICSTEASP  183 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~-~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~  183 (195)
                      ......|+||...++.. +.+..+ .|||.+|.+||.+||.....||.||+.+.-
T Consensus       193 ~slv~sl~I~~~slK~~y~k~~~~-~~g~~~~~~kL~k~L~~~~kl~~~~rel~~  246 (465)
T KOG0827|consen  193 SSLVGSLSICFESLKQNYDKISAI-VCGHIYHHGKLSKWLATKRKLPSCRRELPK  246 (465)
T ss_pred             HHHHhhhHhhHHHHHHHHHHHHHH-hhcccchhhHHHHHHHHHHHhHHHHhhhhh
Confidence            44567899999998765 556666 899999999999999999999999998864

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

Probab=96.26  E-value=0.0023  Score=61.39  Aligned_cols=49  Identities=24%  Similarity=0.697  Sum_probs=39.4

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhcC-------CCCCcccc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK-------KICPICST  179 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~-------~sCPvCR~  179 (195)
                      ....+|.||.+.+.....+-....|-|+||..||.+|-+..       ..||.|..
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs  244 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS  244 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence            35689999999998776655555789999999999998642       36999984

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

Probab=96.16  E-value=0.0025  Score=55.79  Aligned_cols=46  Identities=26%  Similarity=0.610  Sum_probs=32.3

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      ..-...|+||+......    ...||||.-|  |..-- +.-.+||+||..+.
T Consensus       302 ~~~p~lcVVcl~e~~~~----~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI~  347 (355)
T KOG1571|consen  302 LPQPDLCVVCLDEPKSA----VFVPCGHVCC--CTLCS-KHLPQCPVCRQRIR  347 (355)
T ss_pred             cCCCCceEEecCCccce----eeecCCcEEE--chHHH-hhCCCCchhHHHHH
Confidence            33457899999987763    3349999865  65443 33455999998774

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

Probab=96.01  E-value=0.0039  Score=49.83  Aligned_cols=31  Identities=29%  Similarity=0.792  Sum_probs=25.6

Q ss_pred             CccceechhhHHHHhhcC-----------CCCCccccccCCC
Q 044318          154 PCEHLYHSECISNWLQIK-----------KICPICSTEASPP  184 (195)
Q Consensus       154 ~C~H~FH~~CI~~Wl~~~-----------~sCPvCR~~l~~~  184 (195)
                      .||..||.-||..||+.-           +.||.|..++.-+
T Consensus       189 qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK  230 (234)
T KOG3268|consen  189 QCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK  230 (234)
T ss_pred             ccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence            799999999999999631           4699999887543

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

Probab=95.93  E-value=0.0044  Score=38.17  Aligned_cols=41  Identities=22%  Similarity=0.693  Sum_probs=23.2

Q ss_pred             cccccccccCCceeEEecCccceechhhHHHHhhcCC--CCCcc
Q 044318          136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKK--ICPIC  177 (195)
Q Consensus       136 C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~--sCPvC  177 (195)
                      |.+|.+-...+...... .|+=.+|..|+..+++...  .||.|
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            67787777666333222 4888999999999997665  79988

; PDB: 3NW0_A 2CT0_A.

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=95.81  E-value=0.0061  Score=39.45  Aligned_cols=46  Identities=30%  Similarity=0.632  Sum_probs=31.1

Q ss_pred             cccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCC
Q 044318          134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPK  185 (195)
Q Consensus       134 ~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~  185 (195)
                      ..|..|...   +.+-+.+ ||+|..+..|..-+  +-+-||+|.+++...+
T Consensus         8 ~~~~~~~~~---~~~~~~~-pCgH~I~~~~f~~~--rYngCPfC~~~~~~~~   53 (55)
T PF14447_consen    8 QPCVFCGFV---GTKGTVL-PCGHLICDNCFPGE--RYNGCPFCGTPFEFDD   53 (55)
T ss_pred             eeEEEcccc---ccccccc-cccceeeccccChh--hccCCCCCCCcccCCC
Confidence            345555433   2222344 99999999997654  4567999999886553

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

Probab=95.67  E-value=0.0062  Score=52.11  Aligned_cols=49  Identities=29%  Similarity=0.710  Sum_probs=38.0

Q ss_pred             CcccccccccccCC--ceeEEecCccceechhhHHHHhhcC-CCCCcccccc
Q 044318          133 IDRCVICQVEYEEG--ESIVALLPCEHLYHSECISNWLQIK-KICPICSTEA  181 (195)
Q Consensus       133 ~~~C~ICl~~f~~~--~~~~~L~~C~H~FH~~CI~~Wl~~~-~sCPvCR~~l  181 (195)
                      ...|-||-.+|...  ..+...+.|||.||..|+.+.+... ..||.||...
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  3333334899999999998887554 5799999885

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

Probab=95.65  E-value=0.0092  Score=51.76  Aligned_cols=48  Identities=17%  Similarity=0.361  Sum_probs=37.7

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCcccccc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEA  181 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l  181 (195)
                      .....|+||+....++.   ++..-|-+||..||.++++.++.||+=..++
T Consensus       298 ~~~~~CpvClk~r~Npt---vl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~  345 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPT---VLEVSGYVFCYPCIFSYVVNYGHCPVTGYPA  345 (357)
T ss_pred             CccccChhHHhccCCCc---eEEecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence            34568999998876653   3324689999999999999999999865544

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

Probab=95.46  E-value=0.0059  Score=52.09  Aligned_cols=47  Identities=30%  Similarity=0.538  Sum_probs=38.3

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCcccc
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICST  179 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~  179 (195)
                      ...||||.+.+..........+|||.-|..|+.......-+||+|.+
T Consensus       158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             cCCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence            34499999888666554444599999999999999877799999987

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

Probab=95.30  E-value=0.0083  Score=57.70  Aligned_cols=43  Identities=28%  Similarity=0.761  Sum_probs=33.6

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCcccccc
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEA  181 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l  181 (195)
                      ...|.+|-..+..+  .+-. .|||.||..|+.   .....||-|+..+
T Consensus       840 ~skCs~C~~~LdlP--~VhF-~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTLDLP--FVHF-LCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCccccc--eeee-ecccHHHHHhhc---cCcccCCccchhh
Confidence            35899998887766  2333 799999999998   4567899998743

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

Probab=94.75  E-value=0.022  Score=43.35  Aligned_cols=55  Identities=20%  Similarity=0.445  Sum_probs=42.9

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhc---CCCCCccccccCCCCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI---KKICPICSTEASPPKN  186 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~---~~sCPvCR~~l~~~~~  186 (195)
                      ...+|-||.+...+...+..---||-..|..|-...|+.   ...||+|++.+.+...
T Consensus        79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~~  136 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSSS  136 (140)
T ss_pred             CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccccc
Confidence            778999999987776554433248999999998887764   5689999999887654

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

Probab=94.68  E-value=0.019  Score=49.63  Aligned_cols=45  Identities=22%  Similarity=0.566  Sum_probs=36.0

Q ss_pred             CCCCcccccccccccCCceeEEecCc--cceechhhHHHHhhcCCCCCccccccC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPC--EHLYHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C--~H~FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      .....+||||...+..+    .. .|  ||.-|..|-.   +..+.||.||.++.
T Consensus        45 ~~~lleCPvC~~~l~~P----i~-QC~nGHlaCssC~~---~~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   45 DLDLLDCPVCFNPLSPP----IF-QCDNGHLACSSCRT---KVSNKCPTCRLPIG   91 (299)
T ss_pred             chhhccCchhhccCccc----ce-ecCCCcEehhhhhh---hhcccCCccccccc
Confidence            44567999999999887    33 56  7999999975   45778999998886

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

Probab=94.61  E-value=0.0076  Score=57.49  Aligned_cols=50  Identities=26%  Similarity=0.518  Sum_probs=37.7

Q ss_pred             cccccccccccCCceeEEecCccceechhhHHHHhhcC--CCCCccccccCCCCCCC
Q 044318          134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK--KICPICSTEASPPKNHN  188 (195)
Q Consensus       134 ~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~--~sCPvCR~~l~~~~~~~  188 (195)
                      ..|.||++    .+.... ++|+|.||..|+..-+...  ..||+||..+.......
T Consensus       455 ~~c~ic~~----~~~~~i-t~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s  506 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFI-TRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLS  506 (674)
T ss_pred             cccccccc----ccccee-ecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhh
Confidence            89999998    233333 4899999999999988543  36999998876554443

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=94.51  E-value=0.049  Score=35.16  Aligned_cols=44  Identities=27%  Similarity=0.668  Sum_probs=35.2

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCc--ccc
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPI--CST  179 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPv--CR~  179 (195)
                      ....|++|-..|+.++.+++.+.|+-.||+.|..+    .+.|-+  |..
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~~~c~~   49 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCINYSCGT   49 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEeccCCC
Confidence            46789999999998888888888999999999654    555654  544

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

Probab=94.42  E-value=0.032  Score=43.74  Aligned_cols=51  Identities=25%  Similarity=0.541  Sum_probs=33.6

Q ss_pred             CcccccccccccCCceeEEecCc------------cc-eechhhHHHHhhc-----------------------------
Q 044318          133 IDRCVICQVEYEEGESIVALLPC------------EH-LYHSECISNWLQI-----------------------------  170 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C------------~H-~FH~~CI~~Wl~~-----------------------------  170 (195)
                      ...|+|||+---+.    +|+-|            +- .-|..||.+.-+.                             
T Consensus         2 d~~CpICme~PHNA----VLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (162)
T PF07800_consen    2 DVTCPICMEHPHNA----VLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQE   77 (162)
T ss_pred             CccCceeccCCCce----EEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccc
Confidence            46899999874443    22233            32 2478899887641                             


Q ss_pred             --CCCCCccccccCCCCCC
Q 044318          171 --KKICPICSTEASPPKNH  187 (195)
Q Consensus       171 --~~sCPvCR~~l~~~~~~  187 (195)
                        +..||+||..|..+...
T Consensus        78 ~~~L~CPLCRG~V~GWtvv   96 (162)
T PF07800_consen   78 QPELACPLCRGEVKGWTVV   96 (162)
T ss_pred             cccccCccccCceeceEEc
Confidence              12599999999876544

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.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=94.39  E-value=0.024  Score=49.56  Aligned_cols=55  Identities=20%  Similarity=0.391  Sum_probs=37.8

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhh-cCCCCCccccccCCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ-IKKICPICSTEASPP  184 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~-~~~sCPvCR~~l~~~  184 (195)
                      ..+.+.|+.|++.+...++--.-.+||-..|.-|...--+ .++.||-||+.....
T Consensus        11 edeed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~de   66 (480)
T COG5175          11 EDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDE   66 (480)
T ss_pred             ccccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcccc
Confidence            4456679999999866554322238998888888655432 457899999866543

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

Probab=94.26  E-value=0.025  Score=50.02  Aligned_cols=29  Identities=28%  Similarity=0.826  Sum_probs=22.1

Q ss_pred             ccceechhhHHHHhhc-------------CCCCCccccccCC
Q 044318          155 CEHLYHSECISNWLQI-------------KKICPICSTEASP  183 (195)
Q Consensus       155 C~H~FH~~CI~~Wl~~-------------~~sCPvCR~~l~~  183 (195)
                      |.-..|.+|+.+|+..             +..||+||+++.-
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi  352 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI  352 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence            4556788999999943             3479999998753

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

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

Probab=94.26  E-value=0.018  Score=55.71  Aligned_cols=38  Identities=21%  Similarity=0.482  Sum_probs=29.6

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHHh
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWL  168 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl  168 (195)
                      .-...+.|.+|...+..... .+ .||||.||++||.+-.
T Consensus       813 v~ep~d~C~~C~~~ll~~pF-~v-f~CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  813 VLEPQDSCDHCGRPLLIKPF-YV-FPCGHCFHRDCLIRHV  850 (911)
T ss_pred             EecCccchHHhcchhhcCcc-ee-eeccchHHHHHHHHHH
Confidence            34578999999998876633 33 4899999999997655

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

Probab=94.12  E-value=0.025  Score=48.84  Aligned_cols=45  Identities=27%  Similarity=0.704  Sum_probs=30.6

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      .-.|.-|--.+.  -..+++ ||.|+||.+|...  ..-+.||.|--+|.
T Consensus        90 VHfCd~Cd~PI~--IYGRmI-PCkHvFCl~CAr~--~~dK~Cp~C~d~Vq  134 (389)
T KOG2932|consen   90 VHFCDRCDFPIA--IYGRMI-PCKHVFCLECARS--DSDKICPLCDDRVQ  134 (389)
T ss_pred             eEeecccCCcce--eeeccc-ccchhhhhhhhhc--CccccCcCcccHHH
Confidence            456777754432  233444 9999999999754  33578999976654

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

Probab=94.00  E-value=0.026  Score=48.61  Aligned_cols=44  Identities=27%  Similarity=0.565  Sum_probs=34.2

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHh-hcCCCCCcccc
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWL-QIKKICPICST  179 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl-~~~~sCPvCR~  179 (195)
                      ...|+.|..-++.+-+   ..-|+|.||.+||...| .....||.|.+
T Consensus       274 ~LkCplc~~Llrnp~k---T~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         274 SLKCPLCHCLLRNPMK---TPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             cccCcchhhhhhCccc---CccccchHHHHHHhhhhhhccccCCCccc
Confidence            3789999887776632   23689999999999777 45689999954

>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=93.99  E-value=0.039  Score=47.20  Aligned_cols=51  Identities=16%  Similarity=0.393  Sum_probs=38.0

Q ss_pred             ccccccccc-cCCceeEEecCccceechhhHHHHhh-cCCCCCccccccCCCC
Q 044318          135 RCVICQVEY-EEGESIVALLPCEHLYHSECISNWLQ-IKKICPICSTEASPPK  185 (195)
Q Consensus       135 ~C~ICl~~f-~~~~~~~~L~~C~H~FH~~CI~~Wl~-~~~sCPvCR~~l~~~~  185 (195)
                      .|++|.... ..++...+..+|+|..|..|+...+. ....||.|.+.+.-.+
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~n   54 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNN   54 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhcc
Confidence            599998664 44444444459999999999999885 4578999987665443

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.39  E-value=0.027  Score=47.41  Aligned_cols=54  Identities=30%  Similarity=0.612  Sum_probs=36.5

Q ss_pred             CCCCCcccccccccccCCceeEEecCc-----cceechhhHHHHhhcC--------CCCCccccccC
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPC-----EHLYHSECISNWLQIK--------KICPICSTEAS  182 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C-----~H~FH~~CI~~Wl~~~--------~sCPvCR~~l~  182 (195)
                      ....+..|=||+..=++.......-||     .|..|..||..|+-.+        -+||.|+++..
T Consensus        16 ~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi   82 (293)
T KOG3053|consen   16 NQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI   82 (293)
T ss_pred             ccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence            355667899999875554322111255     3889999999999322        26999998754

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

Probab=92.94  E-value=0.025  Score=56.76  Aligned_cols=45  Identities=29%  Similarity=0.569  Sum_probs=37.5

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCcccc
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICST  179 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~  179 (195)
                      ....|.||+........  + ..|||.||..|+..|+..+..||+|+.
T Consensus      1152 ~~~~c~ic~dil~~~~~--I-~~cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGG--I-AGCGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred             cccchHHHHHHHHhcCC--e-eeechhHhhhHHHHHHHHhccCcchhh
Confidence            45589999998874322  2 379999999999999999999999984

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

Probab=92.88  E-value=0.049  Score=52.14  Aligned_cols=24  Identities=29%  Similarity=0.948  Sum_probs=22.1

Q ss_pred             cCccceechhhHHHHhhcCCCCCc
Q 044318          153 LPCEHLYHSECISNWLQIKKICPI  176 (195)
Q Consensus       153 ~~C~H~FH~~CI~~Wl~~~~sCPv  176 (195)
                      ..|+|+-|..|.+.|+.....||.
T Consensus      1046 g~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1046 GTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             ccccccccHHHHHHHHhcCCcCCC
Confidence            379999999999999999999985

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.64  E-value=0.051  Score=46.64  Aligned_cols=29  Identities=21%  Similarity=0.590  Sum_probs=22.8

Q ss_pred             ccceechhhHHHHhh-------------cCCCCCccccccCC
Q 044318          155 CEHLYHSECISNWLQ-------------IKKICPICSTEASP  183 (195)
Q Consensus       155 C~H~FH~~CI~~Wl~-------------~~~sCPvCR~~l~~  183 (195)
                      |....|.+||.+|+.             .+.+||+||+.+.-
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci  366 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCI  366 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEE
Confidence            667788999999984             34589999998753

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

Probab=92.23  E-value=0.11  Score=46.35  Aligned_cols=48  Identities=17%  Similarity=0.408  Sum_probs=39.2

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcC---CCCCccccc
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK---KICPICSTE  180 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~---~sCPvCR~~  180 (195)
                      ....|||=.+.-.+.....+| .|||+..++-|.+..+..   ..||.|=..
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L-~CGHVISkdAlnrLS~ng~~sfKCPYCP~e  383 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMML-ICGHVISKDALNRLSKNGSQSFKCPYCPVE  383 (394)
T ss_pred             ceeecccchhhccCCCCCeee-eccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence            567899988777777777888 899999999999988654   479999543

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

Probab=91.26  E-value=0.1  Score=44.50  Aligned_cols=53  Identities=26%  Similarity=0.610  Sum_probs=36.8

Q ss_pred             CCcccccccccccCCceeEEecCcc-----ceechhhHHHHhh--cCCCCCccccccCCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCE-----HLYHSECISNWLQ--IKKICPICSTEASPP  184 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~-----H~FH~~CI~~Wl~--~~~sCPvCR~~l~~~  184 (195)
                      ....|-||............+.||.     +..|..|+..|+.  .+..|.+|.......
T Consensus        77 ~~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~  136 (323)
T KOG1609|consen   77 SGPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV  136 (323)
T ss_pred             CCCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence            3578999998765432111223664     5679999999997  556899998865544

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

Probab=90.81  E-value=0.17  Score=41.62  Aligned_cols=40  Identities=33%  Similarity=0.814  Sum_probs=27.4

Q ss_pred             cccccccccCCceeEEecCccc-eechhhHHHHhhcCCCCCccccccCC
Q 044318          136 CVICQVEYEEGESIVALLPCEH-LYHSECISNWLQIKKICPICSTEASP  183 (195)
Q Consensus       136 C~ICl~~f~~~~~~~~L~~C~H-~FH~~CI~~Wl~~~~sCPvCR~~l~~  183 (195)
                      |-+|-+.   ...+ .+.||.| .+|..|-..    .+.||+|+.....
T Consensus       161 Cr~C~~~---~~~V-lllPCrHl~lC~~C~~~----~~~CPiC~~~~~s  201 (207)
T KOG1100|consen  161 CRKCGER---EATV-LLLPCRHLCLCGICDES----LRICPICRSPKTS  201 (207)
T ss_pred             ceecCcC---CceE-EeecccceEeccccccc----CccCCCCcChhhc
Confidence            7777543   3334 4459998 689999754    4569999976543

>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=90.54  E-value=0.12  Score=43.35  Aligned_cols=50  Identities=20%  Similarity=0.499  Sum_probs=36.0

Q ss_pred             CCcccccccccc-cCCceeEEecC-ccceechhhHHHHhhc-CCCCC--cccccc
Q 044318          132 GIDRCVICQVEY-EEGESIVALLP-CEHLYHSECISNWLQI-KKICP--ICSTEA  181 (195)
Q Consensus       132 ~~~~C~ICl~~f-~~~~~~~~L~~-C~H~FH~~CI~~Wl~~-~~sCP--vCR~~l  181 (195)
                      ....||||..+. ..++...-..| |-|..|..|+.+-|.. ...||  -|.+-+
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL   63 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL   63 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence            456899999775 34443333335 9999999999999965 46899  786644

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

Probab=90.43  E-value=0.05  Score=51.66  Aligned_cols=47  Identities=28%  Similarity=0.724  Sum_probs=37.2

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhc---CCCCCccccccC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI---KKICPICSTEAS  182 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~---~~sCPvCR~~l~  182 (195)
                      ...+|+||+..+..+    .++.|-|.|+..|+..-|..   ...||+|+..+.
T Consensus        20 k~lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e   69 (684)
T KOG4362|consen   20 KILECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIE   69 (684)
T ss_pred             hhccCCceeEEeecc----chhhhhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence            347899999998887    45599999999998776643   457999996554

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

Probab=90.23  E-value=0.11  Score=46.59  Aligned_cols=41  Identities=29%  Similarity=0.656  Sum_probs=29.5

Q ss_pred             CCCCcccccccccccCC-ceeEEecCccceechhhHHHHhhcC
Q 044318          130 KSGIDRCVICQVEYEEG-ESIVALLPCEHLYHSECISNWLQIK  171 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~-~~~~~L~~C~H~FH~~CI~~Wl~~~  171 (195)
                      ......|.||+...... ....+. .|+|.||.+|+.+.+..+
T Consensus       143 ~~~~~~C~iC~~e~~~~~~~f~~~-~C~H~fC~~C~k~~iev~  184 (384)
T KOG1812|consen  143 KLPKEECGICFVEDPEAEDMFSVL-KCGHRFCKDCVKQHIEVK  184 (384)
T ss_pred             ccccccCccCccccccHhhhHHHh-cccchhhhHHhHHHhhhh
Confidence            33567999999555444 333344 899999999999888643

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

Probab=90.11  E-value=0.077  Score=49.99  Aligned_cols=40  Identities=23%  Similarity=0.419  Sum_probs=30.5

Q ss_pred             cccccccccccCCceeEEecCccceechhhHHHHhhcCCCCC
Q 044318          134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICP  175 (195)
Q Consensus       134 ~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCP  175 (195)
                      ..|.||+..|......-+.+.|||+.|..|+....+  .+||
T Consensus        12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn--~scp   51 (861)
T KOG3161|consen   12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN--ASCP   51 (861)
T ss_pred             hhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh--ccCC
Confidence            469999999876654444448999999999988654  4566

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

Probab=89.27  E-value=0.29  Score=47.46  Aligned_cols=53  Identities=28%  Similarity=0.700  Sum_probs=37.5

Q ss_pred             CCCCcccccccccccCCceeEEecCcc-----ceechhhHHHHhhcC--CCCCccccccCCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCE-----HLYHSECISNWLQIK--KICPICSTEASPP  184 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~-----H~FH~~CI~~Wl~~~--~sCPvCR~~l~~~  184 (195)
                      ......|-||..+=..++.+-  -||+     ...|.+|+.+|+..+  +.|-+|+.++.-+
T Consensus         9 N~d~~~CRICr~e~~~d~pLf--hPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk   68 (1175)
T COG5183           9 NEDKRSCRICRTEDIRDDPLF--HPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFK   68 (1175)
T ss_pred             CccchhceeecCCCCCCCcCc--ccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeee
Confidence            345589999997765554432  2444     457999999999644  5799999877543

>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=88.42  E-value=0.38  Score=30.43  Aligned_cols=43  Identities=26%  Similarity=0.522  Sum_probs=19.6

Q ss_pred             cccccccccccCCceeEEecCccceechhhHHHHhhc-----CCCCCccccc
Q 044318          134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-----KKICPICSTE  180 (195)
Q Consensus       134 ~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-----~~sCPvCR~~  180 (195)
                      ..|+|....+..+  ++.. .|.|.-|.+ +..|+..     .-.||+|.++
T Consensus         3 L~CPls~~~i~~P--~Rg~-~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRIP--VRGK-NCKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SSE--EEET-T--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEeC--ccCC-cCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            3688888777665  3333 899975543 4556632     2469999864

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.

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

Probab=87.52  E-value=0.18  Score=47.23  Aligned_cols=44  Identities=23%  Similarity=0.578  Sum_probs=28.8

Q ss_pred             CCccccccccc-----ccCCceeEEecCccceechhhHHHHhhcCCCCCcccc
Q 044318          132 GIDRCVICQVE-----YEEGESIVALLPCEHLYHSECISNWLQIKKICPICST  179 (195)
Q Consensus       132 ~~~~C~ICl~~-----f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~  179 (195)
                      ....|.||...     |. .+.++....|+++||+.|+..   .+.-||.|-+
T Consensus       510 ~gfiCe~Cq~~~iiyPF~-~~~~~rC~~C~avfH~~C~~r---~s~~CPrC~R  558 (580)
T KOG1829|consen  510 KGFICELCQHNDIIYPFE-TRNTRRCSTCLAVFHKKCLRR---KSPCCPRCER  558 (580)
T ss_pred             CeeeeeeccCCCcccccc-cccceeHHHHHHHHHHHHHhc---cCCCCCchHH
Confidence            45678888532     33 233344447999999999765   3334999943

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

Probab=86.42  E-value=0.34  Score=46.81  Aligned_cols=55  Identities=9%  Similarity=0.069  Sum_probs=38.1

Q ss_pred             CCcccccccccccCCce-eEEe--cCccceechhhHHHHhhc------CCCCCccccccCCCCC
Q 044318          132 GIDRCVICQVEYEEGES-IVAL--LPCEHLYHSECISNWLQI------KKICPICSTEASPPKN  186 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~-~~~L--~~C~H~FH~~CI~~Wl~~------~~sCPvCR~~l~~~~~  186 (195)
                      ....|.||...+..... ...+  -.|+|-||..||..|..+      +-.|++|..-|..+..
T Consensus        95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR  158 (1134)
T KOG0825|consen   95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSR  158 (1134)
T ss_pred             cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhh
Confidence            45678888877766321 1222  249999999999999943      3568999887765543

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

Probab=86.16  E-value=1  Score=31.22  Aligned_cols=60  Identities=23%  Similarity=0.388  Sum_probs=23.7

Q ss_pred             CCCccccccccccc---CCceeEEecCccceechhhHHHHhh-cCCCCCccccccCCCCCCCcc
Q 044318          131 SGIDRCVICQVEYE---EGESIVALLPCEHLYHSECISNWLQ-IKKICPICSTEASPPKNHNNA  190 (195)
Q Consensus       131 ~~~~~C~ICl~~f~---~~~~~~~L~~C~H~FH~~CI~~Wl~-~~~sCPvCR~~l~~~~~~~~~  190 (195)
                      .....|-||-+.+-   .++..+....|+-..|+.|..-=.+ .+..||.|+++....+..+..
T Consensus         7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~ykr~kgsp~V   70 (80)
T PF14569_consen    7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYKRHKGSPRV   70 (80)
T ss_dssp             -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B----TT----
T ss_pred             cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcccccCCCCC
Confidence            35678999988873   4455555557888899999865443 457899999988766655543

>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=85.95  E-value=0.83  Score=29.16  Aligned_cols=43  Identities=23%  Similarity=0.517  Sum_probs=22.2

Q ss_pred             cccccccccCC------ceeEEecCccceechhhHHHHhhcCCCCCccc
Q 044318          136 CVICQVEYEEG------ESIVALLPCEHLYHSECISNWLQIKKICPICS  178 (195)
Q Consensus       136 C~ICl~~f~~~------~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR  178 (195)
                      |--|+..|..+      ....+.+.|++.||.+|=.--=..-..||-|-
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            55577777654      23456668999999999433223346799884

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.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=85.35  E-value=0.76  Score=40.12  Aligned_cols=52  Identities=17%  Similarity=0.352  Sum_probs=39.0

Q ss_pred             CcccccccccccCCc-eeEEecCccceechhhHHHHhhcCCCCCccccccCCCC
Q 044318          133 IDRCVICQVEYEEGE-SIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPK  185 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~-~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~  185 (195)
                      ...|+||-+...... ..... +|+|..|..|+..-...+.+||.||++.....
T Consensus       249 ~~s~p~~~~~~~~~d~~~lP~-~~~~~~~l~~~~t~~~~~~~~~~~rk~~~~~t  301 (327)
T KOG2068|consen  249 PPSCPICYEDLDLTDSNFLPC-PCGFRLCLFCHKTISDGDGRCPGCRKPYERNT  301 (327)
T ss_pred             CCCCCCCCCcccccccccccc-cccccchhhhhhcccccCCCCCccCCccccCc
Confidence            478999998763332 33334 78888888999888888999999997665443

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

Probab=84.97  E-value=0.47  Score=39.05  Aligned_cols=49  Identities=29%  Similarity=0.704  Sum_probs=38.1

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASP  183 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~  183 (195)
                      ....|.+|..-...+   +....|+-.||..|+..+++....||.|.--++.
T Consensus       180 nlk~Cn~Ch~LvIqg---~rCg~c~i~~h~~c~qty~q~~~~cphc~d~w~h  228 (235)
T KOG4718|consen  180 NLKNCNLCHCLVIQG---IRCGSCNIQYHRGCIQTYLQRRDICPHCGDLWTH  228 (235)
T ss_pred             HHHHHhHhHHHhhee---eccCcccchhhhHHHHHHhcccCcCCchhcccCc
Confidence            456899998776555   2333788899999999999999999999654443

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.27  E-value=1  Score=38.02  Aligned_cols=53  Identities=13%  Similarity=0.296  Sum_probs=40.7

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKN  186 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~  186 (195)
                      ....|+|---.+...-....+.+|||+|-..-+.+.  ...+|++|...+...+.
T Consensus       110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~dv  162 (293)
T KOG3113|consen  110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDDV  162 (293)
T ss_pred             ceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccCe
Confidence            446799987777766666677799999988887773  36789999998876543

>PF15295 CCDC50_N: Coiled-coil domain-containing protein 50 N-terminus

Probab=84.13  E-value=0.6  Score=35.62  Aligned_cols=20  Identities=45%  Similarity=0.282  Sum_probs=16.6

Q ss_pred             ccchHHHHHHHHHHHHhhhh
Q 044318            3 QVSSDFAMAMALQEQERLAT   22 (195)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~   22 (195)
                      .|.-|++||.-||+||+-.+
T Consensus        22 ~V~EDgaLA~~LQeqEIe~h   41 (132)
T PF15295_consen   22 AVLEDGALAHRLQEQEIEHH   41 (132)
T ss_pred             HHhhhHHHHHHHHHHHHHHH
Confidence            36789999999999998433

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=83.88  E-value=0.83  Score=37.24  Aligned_cols=42  Identities=26%  Similarity=0.720  Sum_probs=30.2

Q ss_pred             CCccccccccc-----ccCCceeEEecCccceechhhHHHHhhcCCCCCcccc
Q 044318          132 GIDRCVICQVE-----YEEGESIVALLPCEHLYHSECISNWLQIKKICPICST  179 (195)
Q Consensus       132 ~~~~C~ICl~~-----f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~  179 (195)
                      .+..|-||-..     |.. +.++....|+-+||+.|..+     ..||-|.+
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     223 24555668999999999862     67999954

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

Probab=82.94  E-value=0.92  Score=43.67  Aligned_cols=41  Identities=20%  Similarity=0.441  Sum_probs=30.4

Q ss_pred             cccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCc
Q 044318          134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPI  176 (195)
Q Consensus       134 ~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPv  176 (195)
                      ..|.+|--.++.  .......|+|.-|..|+.+|+..+..||.
T Consensus       780 ~~CtVC~~vi~G--~~~~c~~C~H~gH~sh~~sw~~~~s~ca~  820 (839)
T KOG0269|consen  780 AKCTVCDLVIRG--VDVWCQVCGHGGHDSHLKSWFFKASPCAK  820 (839)
T ss_pred             cCceeecceeee--eEeecccccccccHHHHHHHHhcCCCCcc
Confidence            467788655432  22334479999999999999998888876

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

Probab=82.71  E-value=0.62  Score=42.39  Aligned_cols=39  Identities=33%  Similarity=0.722  Sum_probs=30.9

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK  171 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~  171 (195)
                      ......|.||.+.+..  .+..+ .|+|.||..|+...+..+
T Consensus        67 ~~~~~~c~ic~~~~~~--~~~~~-~c~H~~c~~cw~~yl~~k  105 (444)
T KOG1815|consen   67 KKGDVQCGICVESYDG--EIIGL-GCGHPFCPPCWTGYLGTK  105 (444)
T ss_pred             CCccccCCcccCCCcc--hhhhc-CCCcHHHHHHHHHHhhhe
Confidence            4566899999999866  33444 899999999999999643

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

Probab=82.55  E-value=1.9  Score=28.05  Aligned_cols=47  Identities=19%  Similarity=0.528  Sum_probs=31.9

Q ss_pred             cccccccccccCCceeEEecCcc--ceechhhHHHHhhcCCCCCccccccCCC
Q 044318          134 DRCVICQVEYEEGESIVALLPCE--HLYHSECISNWLQIKKICPICSTEASPP  184 (195)
Q Consensus       134 ~~C~ICl~~f~~~~~~~~L~~C~--H~FH~~CI~~Wl~~~~sCPvCR~~l~~~  184 (195)
                      ..|-.|-.++.....-..  -|.  ..||..|....|  ++.||.|...+...
T Consensus         6 pnCE~C~~dLp~~s~~A~--ICSfECTFC~~C~e~~l--~~~CPNCgGelv~R   54 (57)
T PF06906_consen    6 PNCECCDKDLPPDSPEAY--ICSFECTFCADCAETML--NGVCPNCGGELVRR   54 (57)
T ss_pred             CCccccCCCCCCCCCcce--EEeEeCcccHHHHHHHh--cCcCcCCCCccccC
Confidence            346667666655432222  355  479999999876  78899999887654

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

>PLN02189 cellulose synthase

Probab=81.46  E-value=2.1  Score=42.84  Aligned_cols=61  Identities=23%  Similarity=0.339  Sum_probs=43.4

Q ss_pred             CCCCccccccccccc---CCceeEEecCccceechhhHHHHh-hcCCCCCccccccCCCCCCCcc
Q 044318          130 KSGIDRCVICQVEYE---EGESIVALLPCEHLYHSECISNWL-QIKKICPICSTEASPPKNHNNA  190 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~---~~~~~~~L~~C~H~FH~~CI~~Wl-~~~~sCPvCR~~l~~~~~~~~~  190 (195)
                      ......|.||-+.+.   .++..+...-|+-..|+.|.+-=. ..+..||.|+++....+..+..
T Consensus        31 ~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~r~kgs~~v   95 (1040)
T PLN02189         31 NLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYKRLKGSPRV   95 (1040)
T ss_pred             cccCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchhhccCCCCc
Confidence            335569999998873   455566665699999999994322 2356899999998866655443

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

Probab=81.33  E-value=0.62  Score=44.99  Aligned_cols=44  Identities=32%  Similarity=0.603  Sum_probs=31.5

Q ss_pred             CcccccccccccCC----ceeEEecCccceechhhHHHHhhcCCCCCccc
Q 044318          133 IDRCVICQVEYEEG----ESIVALLPCEHLYHSECISNWLQIKKICPICS  178 (195)
Q Consensus       133 ~~~C~ICl~~f~~~----~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR  178 (195)
                      ...|.-|+......    ..++++ .|+|.||+.|+..-.-+++ |-.|.
T Consensus       784 e~rc~~c~~~~l~~~~~~~~~~v~-~c~h~yhk~c~~~~~~~~~-~~~~~  831 (846)
T KOG2066|consen  784 EERCSSCFEPNLPSGAAFDSVVVF-HCGHMYHKECLMMESLRNA-CNIES  831 (846)
T ss_pred             hhhhhhhcccccccCcccceeeEE-EccchhhhcccccHHHhcc-cChhh
Confidence            45899998876432    345666 9999999999987765444 66654

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

Probab=81.26  E-value=0.94  Score=40.59  Aligned_cols=45  Identities=22%  Similarity=0.507  Sum_probs=33.3

Q ss_pred             CCcccccccccccCCc--eeEEecCccceechhhHHHHhhcCCCCCcc
Q 044318          132 GIDRCVICQVEYEEGE--SIVALLPCEHLYHSECISNWLQIKKICPIC  177 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~--~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvC  177 (195)
                      ....|++|...+.-..  .-... .|||.||..|...|......|.-|
T Consensus       305 ~wr~CpkC~~~ie~~~GCnhm~C-rC~~~fcy~C~~~~~~~~~~~~~~  351 (384)
T KOG1812|consen  305 RWRQCPKCKFMIELSEGCNHMTC-RCGHQFCYMCGGDWKTHNGECYEC  351 (384)
T ss_pred             hcCcCcccceeeeecCCcceEEe-eccccchhhcCcchhhCCccccCc
Confidence            3568999987764433  22444 599999999999998877777555

>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]

Probab=81.09  E-value=1.5  Score=38.25  Aligned_cols=55  Identities=27%  Similarity=0.648  Sum_probs=36.8

Q ss_pred             CCccccccccccc---------------CCceeEEecCccceechhhHHHHhhc---------CCCCCccccccCCCCC
Q 044318          132 GIDRCVICQVEYE---------------EGESIVALLPCEHLYHSECISNWLQI---------KKICPICSTEASPPKN  186 (195)
Q Consensus       132 ~~~~C~ICl~~f~---------------~~~~~~~L~~C~H~FH~~CI~~Wl~~---------~~sCPvCR~~l~~~~~  186 (195)
                      ...+|++|+..-.               .+.......||||+--..-..-|.+.         +..||.|-+.+.....
T Consensus       340 ~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge~~  418 (429)
T KOG3842|consen  340 RERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGEQG  418 (429)
T ss_pred             ccCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhccCCc
Confidence            4679999986411               11111244589998888888888864         3479999887765443

>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=81.02  E-value=2.3  Score=26.71  Aligned_cols=40  Identities=20%  Similarity=0.540  Sum_probs=28.7

Q ss_pred             cccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCC
Q 044318          136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPK  185 (195)
Q Consensus       136 C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~  185 (195)
                      |..|...+.....++.  .-+..||..|+        +|-.|+++|....
T Consensus         1 C~~C~~~I~~~~~~~~--~~~~~~H~~Cf--------~C~~C~~~l~~~~   40 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIK--AMGKFWHPECF--------KCSKCGKPLNDGD   40 (58)
T ss_dssp             BTTTSSBESSSSEEEE--ETTEEEETTTS--------BETTTTCBTTTSS
T ss_pred             CCCCCCCccCcEEEEE--eCCcEEEcccc--------ccCCCCCccCCCe
Confidence            6778888776554332  46788999886        6899988886553

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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....

>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=80.75  E-value=1.6  Score=27.02  Aligned_cols=44  Identities=23%  Similarity=0.587  Sum_probs=29.9

Q ss_pred             ccccccccccCCceeEEecCccceechhhHHHHhh------cCCCCCcccc
Q 044318          135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ------IKKICPICST  179 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~------~~~sCPvCR~  179 (195)
                      .|.||...- ....++.--.|+..||..|+..-..      ..-.||.|+.
T Consensus         1 ~C~vC~~~~-~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~   50 (51)
T PF00628_consen    1 YCPVCGQSD-DDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP   50 (51)
T ss_dssp             EBTTTTSSC-TTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred             eCcCCCCcC-CCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence            488998843 3344444558999999999865442      2357888864

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 ....

>smart00249 PHD PHD zinc finger

Probab=80.24  E-value=1.2  Score=26.23  Aligned_cols=31  Identities=23%  Similarity=0.700  Sum_probs=21.7

Q ss_pred             ccccccccccCCceeEEecCccceechhhHHH
Q 044318          135 RCVICQVEYEEGESIVALLPCEHLYHSECISN  166 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~  166 (195)
                      .|.+|.... .+..++.-..|...||..|+..
T Consensus         1 ~C~~C~~~~-~~~~~i~C~~C~~~~H~~C~~~   31 (47)
T smart00249        1 YCSVCGKPD-DGGELLQCDGCDRWYHQTCLGP   31 (47)
T ss_pred             CcccCCCcC-CCCCEEECCCCCchhhhhhCCC
Confidence            377887765 3334444447999999999854

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	195
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		2e-07
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		7e-06
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		8e-06
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		8e-06
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		6e-05
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		8e-05
2y43_A	99	Rad18 Ubiquitin Ligase Ring Domain Structure Length		7e-04
4a0k_B	117	Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp		7e-04
1u6g_B	108	Crystal Structure Of The Cand1-Cul1-Roc1 Complex Le		9e-04

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 32/48 (66%), Gaps = 1/48 (2%)
Query: 136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASP 183
           CV+C  ++E  + ++ +LPC H +H++C+  WL+  + CPIC  ++ P
Sbjct: 26  CVVCMCDFESRQ-LLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGP 72

>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 = 47.0 bits (110), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 9/61 (14%)
Query: 131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPIC-------STEASP 183
           SG++ C +C+ +Y  GES V  LPC HL+H  CI  WL+    CP+C       +T  +P
Sbjct: 14  SGLE-CPVCKEDYALGES-VRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATNP 71
Query: 184 P 184
           P
Sbjct: 72  P 72

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 22/46 (47%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTE 180
           +C IC    EEGE  V  LPC HL+H  C+  WL   K CPIC  +
Sbjct: 16  KCTICLSILEEGED-VRRLPCMHLFHQVCVDQWLITNKKCPICRVD 60

>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 = 46.6 bits (109), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPP 184
           C IC  EY +G+ +   LPC H +H  C+S WLQ    CP+C     PP
Sbjct: 43  CPICCSEYVKGD-VATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFPPP 90

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 13/44 (29%), Positives = 30/44 (68%), Gaps = 1/44 (2%)
Query: 136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICST 179
           C +C  +++  + +  + PC+H +H +C+  WL+++K+CP+C+ 
Sbjct: 18  CAVCLEDFKPRDEL-GICPCKHAFHRKCLIKWLEVRKVCPLCNM 60

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 17/42 (40%), Positives = 23/42 (54%)
Query: 136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPIC 177
           C +C  E E+GE    L  C H +H+EC+  WL     CP+C
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLC 49

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 31/74 (41%)
Query: 122 KSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEA 181
           + PP       ID  + C + +E     + +  C H Y S CI  +L  K  CP C    
Sbjct: 8   RWPPGLAVMKTIDDLLRCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTV 67
Query: 182 SPPKNHNNAITSKL 195
           + P   NN I  +L
Sbjct: 68  TEPDLKNNRILDEL 81

>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic Site Containing Dna-Duplex Length = 117

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 133 IDRCVICQVEYEEG---ESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPK 185
           +D C+ CQ         E  VA   C H +H  CIS WL+ +++CP+ + E    K
Sbjct: 59  MDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQK 114

>pdb|1U6G|B Chain B, Crystal Structure Of The Cand1-Cul1-Roc1 Complex Length = 108

Iteration: 1
 Score = 40.0 bits (92), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 133 IDRCVICQVEYEEG---ESIVALLPCEHLYHSECISNWLQIKKICPI 176
           +D C+ CQ         E  VA   C H +H  CIS WL+ +++CP+
Sbjct: 50  MDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 96

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	195
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	3e-16
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	8e-16
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	2e-15
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	7e-15
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	5e-14
2ect_A	78	Ring finger protein 126; metal binding protein, st	1e-13
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	4e-12
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	7e-12
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	8e-12
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	3e-11
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	4e-11
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	6e-11
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	3e-10
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	8e-07
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	9e-07
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	1e-06
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	1e-06
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	3e-06
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	3e-06
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	7e-06
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	7e-06
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-05
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	8e-05
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	2e-05
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	2e-05
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	2e-05
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	2e-05
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	2e-04
1we9_A	64	PHD finger family protein; structural genomics, PH	7e-04
3nw0_A	238	Non-structural maintenance of chromosomes element	8e-04

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

 Score = 69.7 bits (171), Expect = 3e-16
 Identities = 22/59 (37%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 126 ADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPP 184
             G       C IC  EY +G+ +   LPC H +H  C+S WLQ    CP+C     PP
Sbjct: 33  DHGAVGQEMCCPICCSEYVKGD-VATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFPPP 90

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

 Score = 67.7 bits (166), Expect = 8e-16
 Identities = 18/58 (31%), Positives = 35/58 (60%), Gaps = 1/58 (1%)

Query: 126 ADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASP 183
            +  +S    CV+C  ++E  + ++ +LPC H +H++C+  WL+  + CPIC  ++ P
Sbjct: 16  PNNHQSEQTLCVVCMCDFESRQ-LLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGP 72

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

 Score = 66.7 bits (163), Expect = 2e-15
 Identities = 13/56 (23%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNN 189
           + C +C  +++  +  + + PC+H +H +C+  WL+++K+CP+C+         + 
Sbjct: 16  ELCAVCLEDFKPRDE-LGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLSG 70

>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 = 65.5 bits (160), Expect = 7e-15
 Identities = 25/66 (37%), Positives = 32/66 (48%), Gaps = 2/66 (3%)

Query: 122 KSPPADGTKSGID-RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTE 180
           K    +GT+   + +C IC    EEGE  V  LPC HL+H  C+  WL   K CPIC  +
Sbjct: 2   KQDGEEGTEEDTEEKCTICLSILEEGED-VRRLPCMHLFHQVCVDQWLITNKKCPICRVD 60

Query: 181 ASPPKN 186
                 
Sbjct: 61  IEAQLP 66

>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 = 62.7 bits (153), Expect = 5e-14
 Identities = 18/52 (34%), Positives = 24/52 (46%)

Query: 131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS 182
           SG   C IC  +      +  +LPC HL H  C    L+    CP+CS  +S
Sbjct: 3   SGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS 54

>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 = 62.4 bits (152), Expect = 1e-13
 Identities = 26/72 (36%), Positives = 37/72 (51%), Gaps = 11/72 (15%)

Query: 123 SPPADGTKSGIDR---CVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPIC-- 177
           S  + GT+  +     C +C+ +Y  GES V  LPC HL+H  CI  WL+    CP+C  
Sbjct: 2   SSGSSGTEEHVGSGLECPVCKEDYALGES-VRQLPCNHLFHDSCIVPWLEQHDSCPVCRK 60

Query: 178 -----STEASPP 184
                +T  +PP
Sbjct: 61  SLTGQNTATNPP 72

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

 Score = 58.4 bits (141), Expect = 4e-12
 Identities = 15/44 (34%), Positives = 26/44 (59%)

Query: 134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPIC 177
           D C+ CQ E ++ + +V    C H +H+ C+S W++    CP+C
Sbjct: 27  DACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLC 70

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

 Score = 56.8 bits (138), Expect = 7e-12
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 128 GTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPIC 177
               G++ C +C  E E+GE    L  C H +H+EC+  WL     CP+C
Sbjct: 1   AMDDGVE-CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLC 49

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

 Score = 57.2 bits (138), Expect = 8e-12
 Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 3/64 (4%)

Query: 123 SPPADGTKSGIDRCVICQVEYEE---GESIVALLPCEHLYHSECISNWLQIKKICPICST 179
           S       SG   C IC   Y E      ++    C H++ S+C+ + L+    CP C  
Sbjct: 5   SSGTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 64

Query: 180 EASP 183
           + + 
Sbjct: 65  KINH 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 = 56.0 bits (135), Expect = 3e-11
 Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 3/63 (4%)

Query: 130 KSGIDRCVICQVEYEE---GESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKN 186
            SG   C IC   Y E      ++    C H++ S+C+ + L+    CP C  + +  + 
Sbjct: 7   PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY 66

Query: 187 HNN 189
           H  
Sbjct: 67  HPI 69

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

 Score = 55.5 bits (134), Expect = 4e-11
 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 3/57 (5%)

Query: 136 CVICQVEYEE---GESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNN 189
           C IC   Y E      ++    C H++ S+C+ + L+    CP C  + +  + H  
Sbjct: 6   CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI 62

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

 Score = 55.1 bits (133), Expect = 6e-11
 Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 3/44 (6%)

Query: 134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPIC 177
           +RC IC  +          LPC H +   CI+ W++    CP+C
Sbjct: 6   ERCPICLEDPSNY---SMALPCLHAFCYVCITRWIRQNPTCPLC 46

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

 Score = 53.2 bits (128), Expect = 3e-10
 Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 5/44 (11%)

Query: 134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPIC 177
           + C IC     +G + + +LPC H +  +CI  W    + CPIC
Sbjct: 16  EECCICM----DGRADL-ILPCAHSFCQKCIDKWSDRHRNCPIC 54

>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 = 45.2 bits (106), Expect = 8e-07
 Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 14/60 (23%)

Query: 132 GIDRCVICQV--------------EYEEGESIVALLPCEHLYHSECISNWLQIKKICPIC 177
            +D C IC+                    E  VA   C H +H  CIS WL+ +++CP+ 
Sbjct: 36  VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLD 95

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

 Score = 44.0 bits (104), Expect = 9e-07
 Identities = 12/55 (21%), Positives = 19/55 (34%), Gaps = 4/55 (7%)

Query: 123 SPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPIC 177
           S         +  C IC             LPC+H++   C+     + K C +C
Sbjct: 5   SSGNTAPSLTVPECAICLQTCVH----PVSLPCKHVFCYLCVKGASWLGKRCALC 55

>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 = 43.8 bits (103), Expect = 1e-06
 Identities = 10/51 (19%), Positives = 18/51 (35%), Gaps = 5/51 (9%)

Query: 132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI--KKICPICSTE 180
            +  C IC   +       +   C    H  C++ + Q   +  CP C+  
Sbjct: 14  AVKICNIC---HSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDY 61

>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 = 44.5 bits (104), Expect = 1e-06
 Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 14/60 (23%)

Query: 132 GIDRCVICQV--------------EYEEGESIVALLPCEHLYHSECISNWLQIKKICPIC 177
            +D C IC+                    E  VA   C H +H  CIS WL+ +++CP+ 
Sbjct: 47  VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLD 106

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

 Score = 42.8 bits (101), Expect = 3e-06
 Identities = 10/46 (21%), Positives = 15/46 (32%), Gaps = 3/46 (6%)

Query: 135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTE 180
            C IC+    +      +  C H +   CI         CP C+  
Sbjct: 17  LCSICKGYLIDA---TTITECLHTFCKSCIVRHFYYSNRCPKCNIV 59

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

 Score = 42.9 bits (101), Expect = 3e-06
 Identities = 13/61 (21%), Positives = 21/61 (34%), Gaps = 4/61 (6%)

Query: 135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNNAITSK 194
           RC IC+  ++       +  C H +   C     +    C IC        N    + +K
Sbjct: 17  RCFICRQAFQNP----VVTKCRHYFCESCALEHFRATPRCYICDQPTGGIFNPAKELMAK 72

Query: 195 L 195
           L
Sbjct: 73  L 73

>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 = 42.5 bits (100), Expect = 7e-06
 Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 3/55 (5%)

Query: 135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNN 189
            CV+C   + +      ++ C H +   CI  +L+  K CPIC  +    +   N
Sbjct: 17  MCVLCGGYFID---ATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLN 68

>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 = 42.2 bits (99), Expect = 7e-06
 Identities = 15/62 (24%), Positives = 21/62 (33%), Gaps = 4/62 (6%)

Query: 135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKK-ICPICSTEASPPKNHNNAITS 193
           RC IC    E+         C  L    CI  WL  ++  CP C       +  N     
Sbjct: 24  RCFIC---MEKLRDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVNCRWAE 80

Query: 194 KL 195
           ++
Sbjct: 81  EV 82

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

 Score = 42.1 bits (98), Expect = 2e-05
 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 3/57 (5%)

Query: 136 CVICQVEYEEGES---IVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNN 189
           C IC   Y E      ++    C H++ S+C+ + L+    CP C  + +  + H  
Sbjct: 10  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI 66

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

 Score = 40.2 bits (93), Expect = 8e-05
 Identities = 10/43 (23%), Positives = 20/43 (46%)

Query: 135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPIC 177
            C+    E  +   ++    C H++ S+C+ + L+    CP C
Sbjct: 77  ICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTC 119

>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 = 43.2 bits (101), Expect = 2e-05
 Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 5/56 (8%)

Query: 131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-KKICPICSTEASPPK 185
           S    C IC     E +  V + PC HL  + C+++W +   + CP C  E    +
Sbjct: 330 STFQLCKICA----ENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE 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 = 41.4 bits (96), Expect = 2e-05
 Identities = 12/65 (18%), Positives = 18/65 (27%), Gaps = 19/65 (29%)

Query: 134 DRCVICQVEYEEG--------------ESIVALLPCEHLYHSECISNWLQIK-----KIC 174
           + C+IC  +                    +  L  C H +H  C+              C
Sbjct: 26  EDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQC 85

Query: 175 PICST 179
           P C T
Sbjct: 86  PSCKT 90

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

 Score = 40.9 bits (96), Expect = 2e-05
 Identities = 18/55 (32%), Positives = 23/55 (41%), Gaps = 3/55 (5%)

Query: 135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNN 189
           RC IC   +      + +  C H Y S CI  +L  K  CP C    + P   NN
Sbjct: 24  RCGICFEYFNIA---MIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLKNN 75

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

 Score = 42.9 bits (100), Expect = 2e-05
 Identities = 15/80 (18%), Positives = 23/80 (28%), Gaps = 15/80 (18%)

Query: 120 ACKSPPADGTKSGIDRCVICQVEYEEGESIVAL----LPCEHLYHSECISNWLQ------ 169
               P  D   +   RC IC     +G  +  +      C    H+ C+  W +      
Sbjct: 295 WSDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGK 354

Query: 170 -----IKKICPICSTEASPP 184
                    CP C  + S  
Sbjct: 355 TFLEVSFGQCPFCKAKLSTS 374

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

 Score = 38.0 bits (88), Expect = 2e-04
 Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 9/65 (13%)

Query: 123 SPPADGTKSGIDRCVICQVEYEEGESIVALLPCE-----HLYHSECISNWLQIK--KICP 175
           S     T S  D C IC  E ++   ++   PC      H  H  C+  W++    + C 
Sbjct: 5   SSGTSITPSSQDICRICHCEGDDESPLIT--PCHCTGSLHFVHQACLQQWIKSSDTRCCE 62

Query: 176 ICSTE 180
           +C  E
Sbjct: 63  LCKYE 67

>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 Length = 64

 Score = 35.6 bits (82), Expect = 7e-04
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 5/61 (8%)

Query: 128 GTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECI----SNWLQIKK-ICPICSTEAS 182
           G+     +C  C   Y   E  +    CE  +H +C+    +    IK+  CP CS ++ 
Sbjct: 1   GSSGSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKSG 60

Query: 183 P 183
           P
Sbjct: 61  P 61

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

 Score = 38.2 bits (88), Expect = 8e-04
 Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 5/52 (9%)

Query: 131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI--KKICPICSTE 180
             +  C IC     +G+S      C    H  C++ + Q   +  CP C+  
Sbjct: 178 DAVKICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCNDY 226

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	195
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.76
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.68
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.64
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.64
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.63
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.61
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.59
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.59
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.58
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.52
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.52
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.51
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.5
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.5
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.48
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.48
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.46
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.45
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.43
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.42
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.42
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.41
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.41
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.41
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.41
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.41
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.4
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.4
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.4
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.39
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.38
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.35
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.35
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.33
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.31
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.31
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.31
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.29
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.28
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.25
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.25
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.25
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.23
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.2
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.2
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.19
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.19
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.19
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.19
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.18
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.18
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.17
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.14
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.11
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.1
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.08
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.05
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.02
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.96
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.95
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.94
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.89
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.89
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.83
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.79
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.77
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.76
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.75
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.74
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.65
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.4
3nw0_A	238	Non-structural maintenance of chromosomes element	98.3
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	97.04
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	95.71
1we9_A	64	PHD finger family protein; structural genomics, PH	95.49
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.48
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	93.64
2yt5_A	66	Metal-response element-binding transcription facto	92.74
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	92.7
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	92.53
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	92.06
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	92.04
1wee_A	72	PHD finger family protein; structural genomics, PH	91.82
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	91.81
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	91.78
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	91.73
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	91.42
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	90.89
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	90.8
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	90.57
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	90.03
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	89.77
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	89.68
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	89.39
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	88.99
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	88.67
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	88.54
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	88.38
1wem_A	76	Death associated transcription factor 1; structura	88.06
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	88.04
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	87.9
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	87.55
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	87.47
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	87.34
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	86.82
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	86.7
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	86.5
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	86.16
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	85.95
1y02_A	120	CARP2, FYVE-ring finger protein sakura; zinc-bindi	85.64
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	85.23
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	84.98
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	84.77
1weu_A	91	Inhibitor of growth family, member 4; structural g	83.46
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	83.36
1wew_A	78	DNA-binding family protein; structural genomics, P	83.32
1wfk_A	88	Zinc finger, FYVE domain containing 19; riken stru	82.68
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	82.6
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	81.91
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	80.73
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	80.72
2rsd_A	68	E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant	80.5
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	80.39

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

Probab=99.76  E-value=1.7e-18  Score=122.88  Aligned_cols=79  Identities=30%  Similarity=0.597  Sum_probs=69.0

Q ss_pred             CccCCCCCHHHHHhhcCcccCCCCCCCCCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccC
Q 044318          103 GQEKRGLSLNQISTCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       103 g~~~~gls~~~i~~~l~~~~~~~~~~~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      +...+|++.+.+ ..++...+............|+||++.|..+..++.+ +|+|.||..||.+|++.+.+||+||+.+.
T Consensus        11 ~~~~~~~s~~~i-~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l-~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   88 (91)
T 2l0b_A           11 MVANPPASKESI-DALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATEL-PCHHYFHKPCVSIWLQKSGTCPVCRCMFP   88 (91)
T ss_dssp             SSCCCCCCHHHH-HTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEE-TTTEEEEHHHHHHHHTTTCBCTTTCCBSS
T ss_pred             CcCCCCCCHHHH-HhCCCeeecccccccCCCCCCcccChhhcCCCcEEec-CCCChHHHHHHHHHHHcCCcCcCcCccCC
Confidence            445678999999 8999888877665666778999999999988888888 89999999999999999999999999886


Q ss_pred             C
Q 044318          183 P  183 (195)
Q Consensus       183 ~  183 (195)
                      +
T Consensus        89 ~   89 (91)
T 2l0b_A           89 P   89 (91)
T ss_dssp             C
T ss_pred             C
Confidence            5

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

Probab=99.68  E-value=3.2e-17  Score=111.87  Aligned_cols=68  Identities=29%  Similarity=0.844  Sum_probs=56.2

Q ss_pred             hhcCcccCCCCCCCCCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCC
Q 044318          116 TCLHACKSPPADGTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPK  185 (195)
Q Consensus       116 ~~l~~~~~~~~~~~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~  185 (195)
                      ..++..++.... .......|+||++.|..+..++.+ +|+|.||..||.+|++.+.+||+||+.+.+..
T Consensus         7 ~~lp~~~~~~~~-~~~~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~   74 (75)
T 1x4j_A            7 GQLPSYRFNPNN-HQSEQTLCVVCMCDFESRQLLRVL-PCNHEFHAKCVDKWLKANRTCPICRADSGPSS   74 (75)
T ss_dssp             SSCCCEEBCSSS-CSSSCCEETTTTEECCBTCEEEEE-TTTEEEETTHHHHHHHHCSSCTTTCCCCCCCC
T ss_pred             hhCCcEEecCcc-ccCCCCCCeECCcccCCCCeEEEE-CCCCHhHHHHHHHHHHcCCcCcCcCCcCCCCC
Confidence            455666665543 455678999999999988887888 89999999999999999999999999987653

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

Probab=99.64  E-value=4.2e-16  Score=106.86  Aligned_cols=61  Identities=33%  Similarity=0.818  Sum_probs=52.1

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCCCCcc
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNNA  190 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~~  190 (195)
                      .......|+||++.|..+..++.+ +|+|.||..||.+|++.+.+||+||+.+......+++
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~-~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~   71 (78)
T 2ect_A           11 HVGSGLECPVCKEDYALGESVRQL-PCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATNP   71 (78)
T ss_dssp             TSSSSCCCTTTTSCCCTTSCEEEC-TTSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSCCCC
T ss_pred             cCCCCCCCeeCCccccCCCCEEEe-CCCCeecHHHHHHHHHcCCcCcCcCCccCCcccCCCC
Confidence            344567999999999988777777 9999999999999999999999999999876655443

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

Probab=99.64  E-value=5e-16  Score=105.46  Aligned_cols=60  Identities=22%  Similarity=0.746  Sum_probs=51.7

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCCCCcc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNNA  190 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~~  190 (195)
                      ......|+||++.|..+..++.+ +|+|.||..||.+|++.+.+||+||+++........+
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~   71 (74)
T 2ep4_A           12 LNLHELCAVCLEDFKPRDELGIC-PCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLSGP   71 (74)
T ss_dssp             CCCSCBCSSSCCBCCSSSCEEEE-TTTEEEEHHHHHHHHHHCSBCTTTCCBCSSCCSCCCS
T ss_pred             CCCCCCCcCCCcccCCCCcEEEc-CCCCEecHHHHHHHHHcCCcCCCcCcccccccccCCC
Confidence            44567999999999988888877 9999999999999999999999999999776555443

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

Probab=99.63  E-value=2.7e-16  Score=100.74  Aligned_cols=52  Identities=33%  Similarity=0.780  Sum_probs=46.1

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccC
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      .....|+||++.|..++.++.+++|+|.||..||.+|++.+.+||+||+++.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            3567899999999988887888449999999999999999999999998874

>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=99.61  E-value=1e-15  Score=102.52  Aligned_cols=56  Identities=38%  Similarity=0.902  Sum_probs=48.5

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCC
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPK  185 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~  185 (195)
                      .......|+||++.|..+..++.+ +|+|.||..||.+|++.+.+||+||+.+....
T Consensus        10 ~~~~~~~C~IC~~~~~~~~~~~~~-~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   65 (69)
T 2kiz_A           10 EEDTEEKCTICLSILEEGEDVRRL-PCMHLFHQVCVDQWLITNKKCPICRVDIEAQL   65 (69)
T ss_dssp             STTCCCSBTTTTBCCCSSSCEEEC-TTSCEEEHHHHHHHHHHCSBCTTTCSBSCSCC
T ss_pred             cCCCCCCCeeCCccccCCCcEEEe-CCCCHHHHHHHHHHHHcCCCCcCcCccccCcC
Confidence            345667899999999877777777 99999999999999999999999999987543

>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=99.59  E-value=1e-15  Score=97.92  Aligned_cols=52  Identities=35%  Similarity=0.756  Sum_probs=43.9

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccC
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      .....|+||++.|..+.....+++|+|.||..||.+|++.+.+||+||+++.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            3 SGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             SCCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            3567899999999765544444599999999999999999999999999875

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

Probab=99.59  E-value=1.7e-15  Score=105.14  Aligned_cols=53  Identities=28%  Similarity=0.762  Sum_probs=43.9

Q ss_pred             CCCcccccccccccC-----------CceeEEecCccceechhhHHHHhhcCCCCCccccccCC
Q 044318          131 SGIDRCVICQVEYEE-----------GESIVALLPCEHLYHSECISNWLQIKKICPICSTEASP  183 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~-----------~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~  183 (195)
                      .....|+||++.|..           ++.++.+++|+|.||..||.+|++.+++||+||+++..
T Consensus        13 ~~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   76 (81)
T 2ecl_A           13 VECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVV   76 (81)
T ss_dssp             CCCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCE
T ss_pred             CCCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcch
Confidence            356778888888854           34566675799999999999999999999999998754

>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=99.58  E-value=2.8e-15  Score=109.84  Aligned_cols=56  Identities=21%  Similarity=0.463  Sum_probs=44.3

Q ss_pred             CCcccccccccccCCc--------------eeEEecCccceechhhHHHHh-----hcCCCCCccccccCCCCCC
Q 044318          132 GIDRCVICQVEYEEGE--------------SIVALLPCEHLYHSECISNWL-----QIKKICPICSTEASPPKNH  187 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~--------------~~~~L~~C~H~FH~~CI~~Wl-----~~~~sCPvCR~~l~~~~~~  187 (195)
                      ....|+||++.|..+.              .++.+++|+|.||..||..|+     +.+.+||+||+.+......
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~~g~   98 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGT   98 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSSS
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCCCCC
Confidence            3569999999996643              344455999999999999999     4567999999988755443

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

Probab=99.52  E-value=5.8e-15  Score=99.06  Aligned_cols=57  Identities=32%  Similarity=0.676  Sum_probs=46.8

Q ss_pred             CCCCcccccccccccCC----ceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCCC
Q 044318          130 KSGIDRCVICQVEYEEG----ESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNH  187 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~----~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~  187 (195)
                      ......|+||++.|..+    ..++.+ +|||.||..||.+|++.+.+||+||+.+......
T Consensus         7 ~~~~~~C~IC~~~~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   67 (71)
T 3ng2_A            7 PSGTVSCPICMDGYSEIVQNGRLIVST-ECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYH   67 (71)
T ss_dssp             CTTCCBCTTTCCBHHHHHTTTCCEEEC-TTSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSCC
T ss_pred             CCCCCCCcccChhhhccccccCCeEeC-CCCChHhHHHHHHHHHcCCCCCCCCCccChhhee
Confidence            44678999999998664    333444 9999999999999999999999999999866543

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

Probab=99.52  E-value=9.5e-15  Score=97.25  Aligned_cols=54  Identities=31%  Similarity=0.671  Sum_probs=44.4

Q ss_pred             CCCCCcccccccccccCC----ceeEEecCccceechhhHHHHhhcCCCCCccccccCC
Q 044318          129 TKSGIDRCVICQVEYEEG----ESIVALLPCEHLYHSECISNWLQIKKICPICSTEASP  183 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~----~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~  183 (195)
                      .......|+||++.|...    ..++.+ +|||.||..||.+|++.+.+||+||+.+..
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           11 RPSGTVSCPICMDGYSEIVQNGRLIVST-ECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CTTCCCCCTTTCCCHHHHTTTTCCEEEC-SSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCCCcccCccccccccccCCeEeC-CCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            345678899999999764    223444 999999999999999999999999998754

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

Probab=99.51  E-value=2.2e-14  Score=99.58  Aligned_cols=65  Identities=26%  Similarity=0.620  Sum_probs=50.1

Q ss_pred             CCCCCCCCCCCcccccccccccCCceeEEecCcc-----ceechhhHHHHhhcC--CCCCccccccCCCCCCCc
Q 044318          123 SPPADGTKSGIDRCVICQVEYEEGESIVALLPCE-----HLYHSECISNWLQIK--KICPICSTEASPPKNHNN  189 (195)
Q Consensus       123 ~~~~~~~~~~~~~C~ICl~~f~~~~~~~~L~~C~-----H~FH~~CI~~Wl~~~--~sCPvCR~~l~~~~~~~~  189 (195)
                      +............|.||++.|..+..+ .+ ||+     |.||..||.+|+..+  .+||+||..+.......+
T Consensus         5 ~s~~s~~~~~~~~C~IC~~~~~~~~~l-~~-pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~~~~P   76 (80)
T 2d8s_A            5 SSGTSITPSSQDICRICHCEGDDESPL-IT-PCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMETKLSG   76 (80)
T ss_dssp             CCCCCCCCTTSCCCSSSCCCCCSSSCE-EC-SSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCCCSCC
T ss_pred             cCCCCCCCCCCCCCeEcCccccCCCee-Ee-ccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCcccCC
Confidence            333344556678999999999877665 35 896     999999999999766  489999999976654433

>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=99.50  E-value=1.4e-14  Score=105.75  Aligned_cols=51  Identities=33%  Similarity=0.735  Sum_probs=42.3

Q ss_pred             CCcccccccccccCCc--------------eeEEecCccceechhhHHHHhhcCCCCCccccccC
Q 044318          132 GIDRCVICQVEYEEGE--------------SIVALLPCEHLYHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~--------------~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      ..+.|+||++.|...-              ..+.+++|+|.||..||.+||+.+.+||+||+.+.
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            5688999999997541              12344499999999999999999999999999864

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

Probab=99.50  E-value=3.6e-14  Score=95.92  Aligned_cols=58  Identities=17%  Similarity=0.411  Sum_probs=47.9

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCCCCcc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNNA  190 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~~  190 (195)
                      ......|+||++.|..+   +.+++|||.||..||.+|++.+.+||+||+.+.......++
T Consensus        12 ~~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~   69 (72)
T 2djb_A           12 LTPYILCSICKGYLIDA---TTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLSGP   69 (72)
T ss_dssp             CCGGGSCTTTSSCCSSC---EECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSCCCC
T ss_pred             cCCCCCCCCCChHHHCc---CEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCcccccccC
Confidence            34567899999999875   33449999999999999999999999999999876655543

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

Probab=99.48  E-value=1.4e-14  Score=95.01  Aligned_cols=53  Identities=28%  Similarity=0.669  Sum_probs=44.2

Q ss_pred             CCcccccccccccCC----ceeEEecCccceechhhHHHHhhcCCCCCccccccCCCC
Q 044318          132 GIDRCVICQVEYEEG----ESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPK  185 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~----~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~  185 (195)
                      +...|+||++.|..+    ..++.+ +|||.||..||.+|++.+.+||+||+++....
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   58 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVST-ECGHVFCSQCLRDSLKNANTCPTCRKKINHKR   58 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEE-TTSCEEEHHHHHHHHHHCSBCTTTCCBCTTTC
T ss_pred             CCCCCCccChhhhCccccCCCEEeC-CCCCchhHHHHHHHHHcCCCCCCCCccCCccc
Confidence            457899999999753    333455 99999999999999999999999999987653

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

Probab=99.48  E-value=3.5e-14  Score=95.69  Aligned_cols=52  Identities=25%  Similarity=0.596  Sum_probs=44.0

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCC
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPP  184 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~  184 (195)
                      .......|+||++.+...   +.+ +|+|.||..||.+|++.+.+||+||+.+...
T Consensus        11 ~~~~~~~C~IC~~~~~~~---~~~-~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   62 (71)
T 2d8t_A           11 PSLTVPECAICLQTCVHP---VSL-PCKHVFCYLCVKGASWLGKRCALCRQEIPED   62 (71)
T ss_dssp             SSSSCCBCSSSSSBCSSE---EEE-TTTEEEEHHHHHHCTTCSSBCSSSCCBCCHH
T ss_pred             cCCCCCCCccCCcccCCC---EEc-cCCCHHHHHHHHHHHHCCCcCcCcCchhCHh
Confidence            344667899999998765   445 9999999999999999999999999988643

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

Probab=99.46  E-value=4.7e-14  Score=94.56  Aligned_cols=51  Identities=27%  Similarity=0.780  Sum_probs=44.2

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPK  185 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~  185 (195)
                      ......|+||++.+..    +.+ +|+|.||..||.+|++.+.+||+||+++....
T Consensus        12 ~~~~~~C~IC~~~~~~----~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           12 LTDEEECCICMDGRAD----LIL-PCAHSFCQKCIDKWSDRHRNCPICRLQMTGAN   62 (70)
T ss_dssp             CCCCCCCSSSCCSCCS----EEE-TTTEEECHHHHHHSSCCCSSCHHHHHCTTCCC
T ss_pred             CCCCCCCeeCCcCccC----ccc-CCCCcccHHHHHHHHHCcCcCCCcCCcccCCC
Confidence            4456799999999876    455 99999999999999999999999999987554

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

Probab=99.45  E-value=5.8e-14  Score=93.53  Aligned_cols=50  Identities=30%  Similarity=0.784  Sum_probs=42.5

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCC
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASP  183 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~  183 (195)
                      .....|+||++.+..+  .+.+ +|||.||..||.+|++.+.+||+||+++..
T Consensus         3 ~~~~~C~IC~~~~~~~--~~~~-~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            3 TVAERCPICLEDPSNY--SMAL-PCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCCSSCCSCCCSC--EEET-TTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCCeeCCccccCC--cEec-CCCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            3467899999998754  2344 999999999999999999999999998864

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

Probab=99.43  E-value=2.5e-13  Score=94.57  Aligned_cols=56  Identities=25%  Similarity=0.511  Sum_probs=45.3

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHHhhcC---CCCCccccccCCC
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK---KICPICSTEASPP  184 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~---~sCPvCR~~l~~~  184 (195)
                      .......|+||++.|.......++++|||.||..||.+|++.+   ..||+||+.+...
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           11 ALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CCCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             hccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            3445678999999998865423334999999999999999875   7899999988654

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

Probab=99.42  E-value=6.8e-14  Score=106.17  Aligned_cols=48  Identities=35%  Similarity=0.839  Sum_probs=41.7

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPP  184 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~  184 (195)
                      ...|+||++.|..+   +.+ +|||.||..||..|+..+.+||+||+++...
T Consensus        53 ~~~C~iC~~~~~~~---~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           53 ELQCIICSEYFIEA---VTL-NCAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             HSBCTTTCSBCSSE---EEE-TTSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             cCCCcccCcccCCc---eEC-CCCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            35799999999765   345 9999999999999999999999999998654

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

Probab=99.42  E-value=2.8e-13  Score=92.08  Aligned_cols=53  Identities=28%  Similarity=0.636  Sum_probs=43.1

Q ss_pred             CCCCcccccccccccCCceeEEecC-ccceechhhHHHHhhcC--CCCCccccccCCCCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLP-CEHLYHSECISNWLQIK--KICPICSTEASPPKN  186 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~-C~H~FH~~CI~~Wl~~~--~sCPvCR~~l~~~~~  186 (195)
                      ......|+||++.|..+   +.+ + |||.||..||..|++.+  .+||+||+++...+.
T Consensus        12 ~~~~~~C~IC~~~~~~p---~~~-~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~~   67 (74)
T 2yur_A           12 IPDELLCLICKDIMTDA---VVI-PCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA   67 (74)
T ss_dssp             SCGGGSCSSSCCCCTTC---EEC-SSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTTT
T ss_pred             CCCCCCCcCCChHHhCC---eEc-CCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCccc
Confidence            34567899999999876   334 7 99999999999999865  689999998665443

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

Probab=99.41  E-value=2e-13  Score=94.09  Aligned_cols=59  Identities=20%  Similarity=0.460  Sum_probs=48.0

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhc------CCCCCccccccCCCCCCCcccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI------KKICPICSTEASPPKNHNNAIT  192 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~------~~sCPvCR~~l~~~~~~~~~~~  192 (195)
                      ......|+||++.|..+   +. ++|||.||..||..|++.      ...||+||+.+......++...
T Consensus        16 ~~~~~~C~IC~~~~~~p---~~-~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~n~~l   80 (85)
T 2ecv_A           16 VKEEVTCPICLELLTQP---LS-LDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRPNRHV   80 (85)
T ss_dssp             CCCCCCCTTTCSCCSSC---BC-CSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSCCCSCCC
T ss_pred             ccCCCCCCCCCcccCCc---ee-CCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhcCccHHH
Confidence            34567999999999775   23 499999999999999977      7899999999987666655443

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

Probab=99.41  E-value=1.6e-13  Score=94.62  Aligned_cols=49  Identities=22%  Similarity=0.577  Sum_probs=42.3

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      ......|+||+..|..+   +. ++|||.||..||.+|++...+||+||+.+.
T Consensus        12 ~~~~~~C~IC~~~~~~p---~~-~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           12 EEIPFRCFICRQAFQNP---VV-TKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCCSBCSSSCSBCCSE---EE-CTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCCcCCCchhcCe---eE-ccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            34567899999999775   33 499999999999999999999999999986

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

Probab=99.41  E-value=2.5e-13  Score=93.62  Aligned_cols=58  Identities=24%  Similarity=0.399  Sum_probs=46.9

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhc------CCCCCccccccCCCCCCCccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI------KKICPICSTEASPPKNHNNAI  191 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~------~~sCPvCR~~l~~~~~~~~~~  191 (195)
                      ......|+||+..|..+   +. ++|+|.||..||..|+..      ...||+||..+......++..
T Consensus        16 ~~~~~~C~IC~~~~~~p---~~-~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~n~~   79 (85)
T 2ecw_A           16 IKEEVTCPICLELLKEP---VS-ADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLKPNLH   79 (85)
T ss_dssp             CCTTTSCTTTCSCCSSC---EE-CTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTCCEECSC
T ss_pred             CccCCCCcCCChhhCcc---ee-CCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHhCCcCHH
Confidence            34567999999999876   23 499999999999999987      678999999998765554443

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

Probab=99.41  E-value=6.1e-14  Score=95.89  Aligned_cols=58  Identities=26%  Similarity=0.404  Sum_probs=46.5

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhc-------CCCCCccccccCCCCCCCccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-------KKICPICSTEASPPKNHNNAI  191 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-------~~sCPvCR~~l~~~~~~~~~~  191 (195)
                      ......|+||++.|..+   +. ++|||.||..||.+|++.       ...||+||..+......++..
T Consensus         9 ~~~~~~C~IC~~~~~~p---~~-l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~n~~   73 (79)
T 2egp_A            9 VQEEVTCPICLELLTEP---LS-LDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHLQANQH   73 (79)
T ss_dssp             CCCCCEETTTTEECSSC---CC-CSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSGGGTCSS
T ss_pred             cccCCCCcCCCcccCCe---eE-CCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhhCCcCHH
Confidence            34568899999999876   23 499999999999999976       578999999998765544443

>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=99.41  E-value=2.5e-14  Score=106.16  Aligned_cols=52  Identities=33%  Similarity=0.697  Sum_probs=1.2

Q ss_pred             CCcccccccccccCCc--------------eeEEecCccceechhhHHHHhhcCCCCCccccccCC
Q 044318          132 GIDRCVICQVEYEEGE--------------SIVALLPCEHLYHSECISNWLQIKKICPICSTEASP  183 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~--------------~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~  183 (195)
                      ..+.|+||++.|....              ..+.+++|+|.||..||.+||+.+.+||+||+++..
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~  112 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEF  112 (117)
T ss_dssp             CC----------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeeee
Confidence            5689999999997531              123335899999999999999999999999998653

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

Probab=99.40  E-value=1.2e-13  Score=94.55  Aligned_cols=55  Identities=22%  Similarity=0.355  Sum_probs=45.6

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhc-CCCCCccccccCCCCCCCc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-KKICPICSTEASPPKNHNN  189 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-~~sCPvCR~~l~~~~~~~~  189 (195)
                      .....|+||++.|..+   +.+ +|||.||..||.+|++. +.+||+||+++......++
T Consensus         6 ~~~~~C~IC~~~~~~P---v~~-~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~l~~n   61 (78)
T 1t1h_A            6 PEYFRCPISLELMKDP---VIV-STGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPN   61 (78)
T ss_dssp             SSSSSCTTTSCCCSSE---EEE-TTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEEC
T ss_pred             cccCCCCCccccccCC---EEc-CCCCeecHHHHHHHHHHCcCCCCCCcCCCChhhCccC
Confidence            4567999999999876   334 99999999999999987 7899999999976655444

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

Probab=99.40  E-value=2.1e-13  Score=90.54  Aligned_cols=52  Identities=17%  Similarity=0.409  Sum_probs=42.9

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHh-hcCCCCCccccccCCCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWL-QIKKICPICSTEASPPK  185 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl-~~~~sCPvCR~~l~~~~  185 (195)
                      ......|+||++.+..+    +.++|||.||..||.+|+ +...+||+||+++....
T Consensus        12 ~~~~~~C~IC~~~~~~p----~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   64 (66)
T 2ecy_A           12 VEDKYKCEKCHLVLCSP----KQTECGHRFCESCMAALLSSSSPKCTACQESIVKDK   64 (66)
T ss_dssp             CCCCEECTTTCCEESSC----CCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTT
T ss_pred             CCcCCCCCCCChHhcCe----eECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhh
Confidence            34567899999999876    224999999999999999 45678999999987653

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

Probab=99.40  E-value=4.7e-13  Score=90.18  Aligned_cols=52  Identities=23%  Similarity=0.421  Sum_probs=42.7

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhh---cCCCCCccccccCCCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ---IKKICPICSTEASPPK  185 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~---~~~sCPvCR~~l~~~~  185 (195)
                      ......|+||++.|..+   +.+ +|||.||..||..|++   ....||+||+.+....
T Consensus        17 ~~~~~~C~IC~~~~~~~---~~~-~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           17 LQEEVICPICLDILQKP---VTI-DCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCCCBCTTTCSBCSSE---EEC-TTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             CccCCEeccCCcccCCe---EEc-CCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            44567999999998864   344 9999999999999996   4568999999886543

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

Probab=99.39  E-value=1.7e-13  Score=90.69  Aligned_cols=55  Identities=18%  Similarity=0.401  Sum_probs=43.8

Q ss_pred             Ccccccccc-cccCCceeEEecCccceechhhHHHHhhc-CCCCCccccccCCCCCC
Q 044318          133 IDRCVICQV-EYEEGESIVALLPCEHLYHSECISNWLQI-KKICPICSTEASPPKNH  187 (195)
Q Consensus       133 ~~~C~ICl~-~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-~~sCPvCR~~l~~~~~~  187 (195)
                      ...|+||++ .|..+.....+++|||.||..||.+|+.. ...||+||+.+......
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~   59 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFR   59 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCCE
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccccce
Confidence            568999999 77776554444599999999999999754 46899999998765443

>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=99.38  E-value=6.5e-14  Score=100.72  Aligned_cols=53  Identities=25%  Similarity=0.541  Sum_probs=43.7

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcC-CCCCccccccCCCCCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK-KICPICSTEASPPKNH  187 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~-~sCPvCR~~l~~~~~~  187 (195)
                      ....|+||++.|..+   +.+++|||.||..||.+|++.+ .+||+||+++......
T Consensus        21 ~~~~C~IC~~~~~~p---~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~l~   74 (100)
T 3lrq_A           21 EVFRCFICMEKLRDA---RLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELV   74 (100)
T ss_dssp             HHTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCE
T ss_pred             CCCCCccCCccccCc---cccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHHHhH
Confidence            357899999999764   3425999999999999999887 6999999998755443

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

Probab=99.35  E-value=6.3e-13  Score=90.89  Aligned_cols=57  Identities=21%  Similarity=0.459  Sum_probs=46.1

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHHhhcC--CCCCccccccCCCCCCC
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK--KICPICSTEASPPKNHN  188 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~--~sCPvCR~~l~~~~~~~  188 (195)
                      -......|+||.+.|..+..   ...|+|.||..||.+||+.+  .+||+||+.+.......
T Consensus        11 y~~~i~~C~IC~~~i~~g~~---C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~~~~   69 (74)
T 2ct0_A           11 YPDAVKICNICHSLLIQGQS---CETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIPKS   69 (74)
T ss_dssp             CSSSSCBCSSSCCBCSSSEE---CSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCCCCC
T ss_pred             ccCCCCcCcchhhHcccCCc---cCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCCCCC
Confidence            34566899999999987643   23899999999999999887  89999999987554443

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

Probab=99.35  E-value=1.5e-13  Score=98.24  Aligned_cols=52  Identities=31%  Similarity=0.685  Sum_probs=43.5

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCCC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNH  187 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~  187 (195)
                      ...|+||++.|..+   +.+++|||.||..||..|+..+.+||+||..+......
T Consensus        22 ~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~l~   73 (99)
T 2y43_A           22 LLRCGICFEYFNIA---MIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLK   73 (99)
T ss_dssp             HTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCE
T ss_pred             CCCcccCChhhCCc---CEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCChhhCC
Confidence            46899999999874   23348999999999999999999999999998764443

>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=99.33  E-value=9.5e-13  Score=97.86  Aligned_cols=48  Identities=19%  Similarity=0.481  Sum_probs=40.8

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcC-CCCCccccccCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK-KICPICSTEASP  183 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~-~sCPvCR~~l~~  183 (195)
                      ....|+||+..|..+   +.+ +|||.||..||..|+..+ ..||+||+.+..
T Consensus        51 ~~~~C~IC~~~~~~p---~~~-~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           51 ETFQCICCQELVFRP---ITT-VCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHTBCTTTSSBCSSE---EEC-TTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             cCCCCCcCChHHcCc---EEe-eCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            346899999999865   344 999999999999999855 499999999976

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

Probab=99.31  E-value=6.9e-13  Score=98.58  Aligned_cols=55  Identities=31%  Similarity=0.668  Sum_probs=45.8

Q ss_pred             CCCcccccccccccCC----ceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCC
Q 044318          131 SGIDRCVICQVEYEEG----ESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKN  186 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~----~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~  186 (195)
                      .....|+||++.|..+    ..++.+ +|||.||..||.+|++.+.+||+||+.+.....
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l   63 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVST-ECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   63 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEE-TTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCE
T ss_pred             CCCCCCcccChhhhCccccccCeEec-CCCChhhHHHHHHHHHhCCCCCCCCCcCccccc
Confidence            3567899999999764    333455 999999999999999999999999999876544

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

Probab=99.31  E-value=8.9e-13  Score=92.84  Aligned_cols=49  Identities=29%  Similarity=0.632  Sum_probs=41.0

Q ss_pred             CCCCcccccccccccCCceeEEecC-ccceechhhHHHHhhcC--CCCCccccccC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLP-CEHLYHSECISNWLQIK--KICPICSTEAS  182 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~-C~H~FH~~CI~~Wl~~~--~sCPvCR~~l~  182 (195)
                      ......|+||++.|..+   +.+ + |||.||..||..|+..+  ..||+||..+.
T Consensus        10 ~~~~~~C~IC~~~~~~p---~~~-~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           10 IPDELLCLICKDIMTDA---VVI-PCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CCTTTEETTTTEECSSC---EEC-TTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CCcCCCCCCCChhhcCc---eEC-CCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            44568999999999876   344 8 99999999999999644  58999999874

>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=99.31  E-value=8.4e-13  Score=95.96  Aligned_cols=53  Identities=26%  Similarity=0.605  Sum_probs=43.3

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhcCC---CCCccccccCCCCCCCc
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKK---ICPICSTEASPPKNHNN  189 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~---sCPvCR~~l~~~~~~~~  189 (195)
                      ...|+||++.|..+    +.++|||.||..||..|+..+.   .||+||..+.......+
T Consensus        21 ~~~C~IC~~~~~~p----~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~~~~   76 (112)
T 1jm7_A           21 ILECPICLELIKEP----VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQES   76 (112)
T ss_dssp             HTSCSSSCCCCSSC----CBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCC
T ss_pred             CCCCcccChhhcCe----EECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhcCcc
Confidence            45899999999776    2249999999999999998654   89999999887655444

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

Probab=99.29  E-value=5e-12  Score=82.92  Aligned_cols=44  Identities=25%  Similarity=0.491  Sum_probs=37.2

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhh---cCCCCCcc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ---IKKICPIC  177 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~---~~~sCPvC  177 (195)
                      ......|+||++.|..+   +.+ +|||.||..||.+|++   ...+||+|
T Consensus        17 ~~~~~~C~IC~~~~~~p---~~~-~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           17 LQEEVICPICLDILQKP---VTI-DCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCBCTTTCSBCSSC---EEC-TTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             CccCCCCCcCCchhCCe---EEe-CCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            44667999999999875   344 9999999999999997   45689998

>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=99.28  E-value=1.5e-12  Score=94.53  Aligned_cols=50  Identities=26%  Similarity=0.688  Sum_probs=42.9

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPP  184 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~  184 (195)
                      ....|+||+..|..+   +.+++|||.||..||..|+..+.+||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           14 PHLMCVLCGGYFIDA---TTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGTBCTTTSSBCSSE---EEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             CcCCCccCChHHhCc---CEeCCCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            457899999999764   33349999999999999999999999999998764

>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=99.25  E-value=3.3e-12  Score=99.38  Aligned_cols=49  Identities=24%  Similarity=0.511  Sum_probs=41.2

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhc-CCCCCccccccCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-KKICPICSTEASP  183 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-~~sCPvCR~~l~~  183 (195)
                      ....|+||+..|..+   +.+++|||.||..||..|+.. +..||+||..+..
T Consensus        53 ~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           53 SELMCPICLDMLKNT---MTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHBCTTTSSBCSSE---EEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCcccChHhhCc---CEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            345899999999874   333499999999999999987 7889999999854

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

Probab=99.25  E-value=5.8e-12  Score=80.93  Aligned_cols=44  Identities=25%  Similarity=0.719  Sum_probs=36.5

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHh---hcCCCCCcc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWL---QIKKICPIC  177 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl---~~~~sCPvC  177 (195)
                      ......|+||++.+..+    ++++|||.||..||.+|+   +.+.+||+|
T Consensus        12 ~~~~~~C~IC~~~~~~p----~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           12 LQVEASCSVCLEYLKEP----VIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             SCCCCBCSSSCCBCSSC----CCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cccCCCCccCCcccCcc----EeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            34567999999999876    334999999999999995   456789998

>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=99.25  E-value=2.3e-12  Score=99.26  Aligned_cols=48  Identities=23%  Similarity=0.467  Sum_probs=41.3

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhcCC-CCCccccccCCC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKK-ICPICSTEASPP  184 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~-sCPvCR~~l~~~  184 (195)
                      ...|+||++.|..+   +. ++|||.||..||..|+.... .||+||..+...
T Consensus        78 ~~~C~IC~~~~~~p---v~-~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           78 SFMCVCCQELVYQP---VT-TECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HTBCTTTSSBCSSE---EE-CTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CCEeecCChhhcCC---EE-cCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            46899999999876   23 49999999999999998764 899999999866

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

Probab=99.23  E-value=2.4e-12  Score=95.58  Aligned_cols=55  Identities=31%  Similarity=0.670  Sum_probs=44.9

Q ss_pred             CCCCcccccccccccCC----ceeEEecCccceechhhHHHHhhcCCCCCccccccCCCC
Q 044318          130 KSGIDRCVICQVEYEEG----ESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPK  185 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~----~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~  185 (195)
                      ......|+||++.|...    ...+.+ +|||.||..||.+|++.+++||+||+.+....
T Consensus        69 ~~~~~~C~iC~~~~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~  127 (133)
T 4ap4_A           69 GSGTVSCPICMDGYSEIVQNGRLIVST-ECGHVFCSQCLRDSLKNANTCPTCRKKINHKR  127 (133)
T ss_dssp             SSSSCBCTTTCCBHHHHHHTTCCEEEE-TTSBEEEHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCCCCccccccccCcceEeC-CCCChhhHHHHHHHHHcCCCCCCCCCcCChhc
Confidence            34567899999998753    223444 99999999999999999999999999987543

>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=99.20  E-value=7.6e-12  Score=90.18  Aligned_cols=55  Identities=11%  Similarity=0.006  Sum_probs=46.9

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCCCCc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNN  189 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~  189 (195)
                      .....|+||+..|.++    +.++|||.|++.||.+|+..+.+||+||.++......++
T Consensus        27 p~~~~CpI~~~~m~dP----V~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~L~pn   81 (100)
T 2kre_A           27 PDEFRDPLMDTLMTDP----VRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESMLEPV   81 (100)
T ss_dssp             STTTBCTTTCSBCSSE----EEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCTTSSEEC
T ss_pred             cHhhCCcCccCcccCC----eECCCCCEEchHHHHHHHHcCCCCCCCCCCCChhhceEC
Confidence            3567999999999987    334899999999999999988999999999987655544

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

Probab=99.20  E-value=5.5e-12  Score=88.17  Aligned_cols=55  Identities=11%  Similarity=-0.012  Sum_probs=46.4

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCCCCc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNN  189 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~  189 (195)
                      .....|+||++.|.++    +.++|||.|++.||.+|+..+.+||+||.++......++
T Consensus        12 p~~~~CpI~~~~m~dP----V~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~l~pn   66 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTDP----VRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTESMLEPV   66 (85)
T ss_dssp             CTTTBCTTTCSBCSSE----EECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGGGCEEC
T ss_pred             chheECcccCchhcCC----eECCCCCEECHHHHHHHHhcCCCCCCCcCCCChHhcchH
Confidence            3568999999999987    445899999999999999988999999999876554443

>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=99.19  E-value=4.4e-12  Score=92.96  Aligned_cols=48  Identities=29%  Similarity=0.611  Sum_probs=40.8

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhc-CCCCCccccccCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-KKICPICSTEASP  183 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-~~sCPvCR~~l~~  183 (195)
                      ....|+||+..|..+   +.+ +|||.||..||..|+.. ...||+||+.+..
T Consensus        14 ~~~~C~iC~~~~~~p---~~~-~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           14 SECQCGICMEILVEP---VTL-PCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHBCTTTCSBCSSC---EEC-TTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCccCCcccCce---eEc-CCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            456899999999875   344 99999999999999976 6789999998853

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

Probab=99.19  E-value=1.7e-11  Score=84.50  Aligned_cols=57  Identities=16%  Similarity=0.275  Sum_probs=42.9

Q ss_pred             CCCCcccccccccccCCcee-EEecCccceechhhHHHHhh-cCCCCCccccccCCCCCC
Q 044318          130 KSGIDRCVICQVEYEEGESI-VALLPCEHLYHSECISNWLQ-IKKICPICSTEASPPKNH  187 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~-~~L~~C~H~FH~~CI~~Wl~-~~~sCPvCR~~l~~~~~~  187 (195)
                      ......|+||++.+...+.. ..+ +|||.||..||..|+. ....||+||+++......
T Consensus         8 ~~~~~~CpICle~~~~~d~~~~p~-~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~~   66 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEIDDINFFPC-TCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAV   66 (78)
T ss_dssp             CCCCCBCTTTCCBCCTTTTTCCSS-TTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSSC
T ss_pred             cccCCcCCccCccCcccccccccc-CCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCchh
Confidence            34567899999988643322 222 5999999999999984 457899999998765543

>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=99.19  E-value=4.9e-12  Score=93.33  Aligned_cols=52  Identities=23%  Similarity=0.473  Sum_probs=43.4

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCC-CCCccccccCCCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKK-ICPICSTEASPPK  185 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~-sCPvCR~~l~~~~  185 (195)
                      ......|+||+..|..+   +.+ +|||.||..||..|++.+. +||+||..+....
T Consensus        15 ~~~~~~C~IC~~~~~~p---~~~-~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   67 (118)
T 3hct_A           15 LESKYECPICLMALREA---VQT-PCGHRFCKACIIKSIRDAGHKCPVDNEILLENQ   67 (118)
T ss_dssp             CCGGGBCTTTCSBCSSE---EEC-TTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCcCChhhcCe---EEC-CcCChhhHHHHHHHHhhCCCCCCCCCCCcCHHh
Confidence            44567999999999876   344 9999999999999998765 9999999987643

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

Probab=99.19  E-value=9.5e-12  Score=80.17  Aligned_cols=49  Identities=33%  Similarity=0.566  Sum_probs=40.2

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCC
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKN  186 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~  186 (195)
                      .....|+||+..|..+    +.++|||.||..||..|   ...||+||+.+..+..
T Consensus         4 ~~~~~C~IC~~~~~~p----~~l~CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~~   52 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCP----KLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGAD   52 (56)
T ss_dssp             CCCSSCSSSCSSCBCC----SCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCCSS
T ss_pred             ccCCCceEeCCccCCe----EEcCCCCcccHHHHccC---CCCCCcCCcEeecCCc
Confidence            4567899999999876    33499999999999885   6789999999876543

>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=99.18  E-value=8e-12  Score=91.69  Aligned_cols=50  Identities=28%  Similarity=0.618  Sum_probs=42.1

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhc-CCCCCccccccCCCCC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-KKICPICSTEASPPKN  186 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-~~sCPvCR~~l~~~~~  186 (195)
                      ...|+||++.|..+   +. ++|||.||..||.+|++. ..+||+||.++.....
T Consensus        23 ~~~C~IC~~~~~~p---~~-~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   73 (116)
T 1rmd_A           23 SISCQICEHILADP---VE-TSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDL   73 (116)
T ss_dssp             HTBCTTTCSBCSSE---EE-CTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGC
T ss_pred             CCCCCCCCcHhcCc---EE-cCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhc
Confidence            46899999999765   33 499999999999999986 6799999999876543

>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=99.18  E-value=6.3e-12  Score=92.59  Aligned_cols=52  Identities=33%  Similarity=0.615  Sum_probs=43.1

Q ss_pred             CCcccccccccccCCceeEEec-CccceechhhHHHHhhcCCCCCccccccCCCCCCCc
Q 044318          132 GIDRCVICQVEYEEGESIVALL-PCEHLYHSECISNWLQIKKICPICSTEASPPKNHNN  189 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~-~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~  189 (195)
                      ....|+||+..|..+    +.+ +|||.||..||..|+.  ..||+||..+......++
T Consensus        21 ~~~~C~IC~~~~~~p----v~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~~~~n   73 (117)
T 1jm7_B           21 KLLRCSRCTNILREP----VCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKIN   73 (117)
T ss_dssp             HTTSCSSSCSCCSSC----BCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCCCC
T ss_pred             hCCCCCCCChHhhCc----cEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCcccccccc
Confidence            357899999999876    334 8999999999999998  889999999866555444

>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=99.17  E-value=1.4e-11  Score=88.42  Aligned_cols=55  Identities=13%  Similarity=0.026  Sum_probs=46.9

Q ss_pred             CCCcccccccccccCCceeEEecCcc-ceechhhHHHHhhcCCCCCccccccCCCCCCCc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCE-HLYHSECISNWLQIKKICPICSTEASPPKNHNN  189 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~-H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~  189 (195)
                      .....|+||++.|+++    +.++|| |.|++.||.+||..+.+||+||.++......++
T Consensus        20 p~~~~CpI~~~~m~dP----V~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~L~pn   75 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCDP----VVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPN   75 (98)
T ss_dssp             CTTTBCTTTCSBCSSE----EECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEEC
T ss_pred             cHhcCCcCccccccCC----eECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChhhceEc
Confidence            3567999999999987    445999 999999999999988999999999987655544

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

Probab=99.14  E-value=2e-11  Score=80.88  Aligned_cols=49  Identities=29%  Similarity=0.554  Sum_probs=40.2

Q ss_pred             CCcccccccccccCCceeEEecCccce-echhhHHHHhhcCCCCCccccccC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHL-YHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~-FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      ....|+||++.+.+.  +...+||||. ||..|+..|++.++.||+||+++.
T Consensus         7 ~~~~C~IC~~~~~~~--~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            7 AIEPCVICQGRPKNG--CIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             GGSCCTTTSSSCSCE--EEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CcCCCCcCCCCCCCE--EEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            456899999987654  2212399999 899999999998999999999874

>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=99.11  E-value=2.2e-11  Score=92.89  Aligned_cols=51  Identities=22%  Similarity=0.389  Sum_probs=42.2

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCC-CCCccccccCCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKK-ICPICSTEASPP  184 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~-sCPvCR~~l~~~  184 (195)
                      ......|+||+..|..+   +.+ +|||.||..||.+|++... +||+||.++...
T Consensus        28 l~~~~~C~IC~~~~~~p---v~~-~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   79 (141)
T 3knv_A           28 LEAKYLCSACRNVLRRP---FQA-QCGHRYCSFCLASILSSGPQNCAACVHEGIYE   79 (141)
T ss_dssp             CCGGGBCTTTCSBCSSE---EEC-TTSCEEEHHHHHHHGGGSCEECHHHHHTTCCC
T ss_pred             CCcCcCCCCCChhhcCc---EEC-CCCCccCHHHHHHHHhcCCCCCCCCCCccccc
Confidence            34567999999999877   334 9999999999999998665 899999987543

>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=99.10  E-value=3.3e-11  Score=79.55  Aligned_cols=50  Identities=22%  Similarity=0.463  Sum_probs=40.7

Q ss_pred             CCCcccccccccccCCceeEEecCccce-echhhHHHHhhcCCCCCccccccC
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHL-YHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~-FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      .....|+||++.+.+.  +....||||. ||..|+.+|.+..+.||+||+++.
T Consensus         5 ~~~~~C~IC~~~~~~~--~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            5 NLLKPCSLCEKRPRDG--NIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GGGSBCTTTSSSBSCE--EEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             CcCCCCcccCCcCCCe--EEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            3457899999986554  2233499998 999999999988899999999874

>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=99.08  E-value=6.3e-11  Score=103.86  Aligned_cols=48  Identities=27%  Similarity=0.704  Sum_probs=41.0

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhh-cCCCCCccccccCCC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ-IKKICPICSTEASPP  184 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~-~~~sCPvCR~~l~~~  184 (195)
                      ...|+||++.+...   +. +||||.||..||..|+. .+.+||+||+++...
T Consensus       332 ~~~C~ICle~~~~p---v~-lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          332 FQLCKICAENDKDV---KI-EPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SSBCTTTSSSBCCE---EE-ETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCCccCcCCCCe---EE-eCCCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            47899999998654   33 49999999999999998 788999999988654

>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=99.05  E-value=9.7e-11  Score=97.03  Aligned_cols=56  Identities=16%  Similarity=0.090  Sum_probs=45.5

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcC-CCCCccccccCCCCCCCc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK-KICPICSTEASPPKNHNN  189 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~-~sCPvCR~~l~~~~~~~~  189 (195)
                      ......|+||++.|.++    +.++|||.||..||.+|+..+ .+||+||.++......++
T Consensus       205 ~~~~~~c~i~~~~~~dP----v~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~l~~n  261 (281)
T 2c2l_A          205 IPDYLCGKISFELMREP----CITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPN  261 (281)
T ss_dssp             CCSTTBCTTTCSBCSSE----EECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEEC
T ss_pred             CCcccCCcCcCCHhcCC----eECCCCCEECHHHHHHHHHHCCCCCcCCCCCCchhcCccc
Confidence            34567899999999987    445999999999999999764 459999999976555444

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

Probab=99.02  E-value=7.8e-11  Score=80.03  Aligned_cols=43  Identities=30%  Similarity=0.572  Sum_probs=36.3

Q ss_pred             CcccccccccccCCceeEEecCccce-echhhHHHHhhcCCCCCccccccCC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHL-YHSECISNWLQIKKICPICSTEASP  183 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~-FH~~CI~~Wl~~~~sCPvCR~~l~~  183 (195)
                      ...|+||++.+...   +.+ ||||. ||..|+..|    ..||+||+.+..
T Consensus        24 ~~~C~iC~~~~~~~---~~~-pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           24 EKLCKICMDRNIAI---VFV-PCGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HTBCTTTSSSBCCE---EEE-TTCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             CCCCCCCCCCCCCE---EEc-CCCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            46899999987664   344 99999 999999999    889999998754

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

Probab=98.96  E-value=1.3e-10  Score=82.56  Aligned_cols=56  Identities=23%  Similarity=0.404  Sum_probs=42.5

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhcC------CCCCc--cccc-cCCCCCCCc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK------KICPI--CSTE-ASPPKNHNN  189 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~------~sCPv--CR~~-l~~~~~~~~  189 (195)
                      .....|+||+..|.++   +.+..|||.|++.||..||..+      .+||+  |+.. +......++
T Consensus         5 ~~~~~CPI~~~~~~dP---V~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~~~L~pn   69 (94)
T 2yu4_A            5 SSGFTCPITKEEMKKP---VKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSDLIQD   69 (94)
T ss_dssp             SSCCBCTTTCSBCSSE---EEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCGGGEEEC
T ss_pred             CcEeECcCcCchhcCC---EEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCHhhCcCC
Confidence            3467899999999886   3341499999999999999754      48999  9876 655444433

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

Probab=98.95  E-value=1.2e-10  Score=100.28  Aligned_cols=55  Identities=24%  Similarity=0.564  Sum_probs=41.8

Q ss_pred             CCCCcccccccccccCCcee----EEecCccceechhhHHHHhhcC-----------CCCCccccccCCC
Q 044318          130 KSGIDRCVICQVEYEEGESI----VALLPCEHLYHSECISNWLQIK-----------KICPICSTEASPP  184 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~----~~L~~C~H~FH~~CI~~Wl~~~-----------~sCPvCR~~l~~~  184 (195)
                      .....+|+||++.+..+..+    -..++|+|.||..||.+||+..           ++||+||+++..+
T Consensus       305 ee~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~s  374 (381)
T 3k1l_B          305 DNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTS  374 (381)
T ss_dssp             CCSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGG
T ss_pred             ccCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCcc
Confidence            34677999999998763221    1123799999999999999752           5799999988643

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

Probab=98.94  E-value=2.4e-10  Score=89.08  Aligned_cols=52  Identities=23%  Similarity=0.483  Sum_probs=43.2

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcC-CCCCccccccCCCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK-KICPICSTEASPPK  185 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~-~sCPvCR~~l~~~~  185 (195)
                      ......|+||+..|..+   +.+ +|||.||..||.+|++.+ .+||+||..+....
T Consensus        15 ~~~~~~C~IC~~~~~~p---v~~-~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   67 (170)
T 3hcs_A           15 LESKYECPICLMALREA---VQT-PCGHRFCKACIIKSIRDAGHKCPVDNEILLENQ   67 (170)
T ss_dssp             CCGGGBCTTTCSBCSSE---EEC-TTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCCChhhcCc---EEC-CCCCHHHHHHHHHHHHhCCCCCCCCccCcchhh
Confidence            44567999999999876   334 999999999999999765 49999999987643

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

Probab=98.89  E-value=5e-10  Score=88.62  Aligned_cols=55  Identities=16%  Similarity=0.094  Sum_probs=45.2

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhcC-CCCCccccccCCCCCCCc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK-KICPICSTEASPPKNHNN  189 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~-~sCPvCR~~l~~~~~~~~  189 (195)
                      .....||||+..|.++    +.++|||.|+..||..|+..+ .+||+||.++......++
T Consensus       104 p~~f~CPI~~elm~DP----V~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~L~pN  159 (179)
T 2f42_A          104 PDYLCGKISFELMREP----CITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPN  159 (179)
T ss_dssp             CGGGBCTTTCSBCSSE----EECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEEC
T ss_pred             cHhhcccCccccCCCC----eECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChhhCcch
Confidence            4667999999999987    334999999999999999764 479999999876655544

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

Probab=98.89  E-value=7.2e-10  Score=75.28  Aligned_cols=44  Identities=27%  Similarity=0.569  Sum_probs=35.9

Q ss_pred             CcccccccccccCCceeEEecCccce-echhhHHHHhhcCCCCCccccccCCC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHL-YHSECISNWLQIKKICPICSTEASPP  184 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~-FH~~CI~~Wl~~~~sCPvCR~~l~~~  184 (195)
                      ...|+||++.+...    +++||||. ||..|+..    ...||+||.++...
T Consensus        25 ~~~C~IC~~~~~~~----~~~pCgH~~~C~~C~~~----~~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           25 EKLCKICMDRNIAI----VFVPCGHLVTCKQCAEA----VDKCPMCYTVITFK   69 (75)
T ss_dssp             HHSCSSSCSSCCCB----CCSSSCCCCBCHHHHHH----CSBCTTTCCBCCCC
T ss_pred             CCCCCcCCCCCCCE----EEecCCCHHHHHHHhhC----CCCCccCCceecCc
Confidence            35799999998765    44599999 99999965    37899999988653

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

Probab=98.83  E-value=3.8e-09  Score=70.66  Aligned_cols=48  Identities=27%  Similarity=0.650  Sum_probs=38.2

Q ss_pred             CCCCCcccccccccccCCceeEEecCccce-echhhHHHHhhcCCCCCccccccCCC
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHL-YHSECISNWLQIKKICPICSTEASPP  184 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~-FH~~CI~~Wl~~~~sCPvCR~~l~~~  184 (195)
                      .......|+||++.+...    +++||||. ||..|+..    ...||+||+.+...
T Consensus        11 ~~~~~~~C~IC~~~~~~~----v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~~~   59 (68)
T 2ea5_A           11 SEENSKDCVVCQNGTVNW----VLLPCRHTCLCDGCVKY----FQQCPMCRQFVQES   59 (68)
T ss_dssp             SCCCSSCCSSSSSSCCCC----EETTTTBCCSCTTHHHH----CSSCTTTCCCCCCE
T ss_pred             cCCCCCCCCCcCcCCCCE----EEECCCChhhhHHHHhc----CCCCCCCCcchhce
Confidence            344567899999987654    55599999 99999984    47899999988653

>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=98.79  E-value=1.5e-09  Score=74.77  Aligned_cols=44  Identities=23%  Similarity=0.636  Sum_probs=35.6

Q ss_pred             CcccccccccccCCceeEEecCccce-echhhHHHHhhcCCCCCccccccCCC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHL-YHSECISNWLQIKKICPICSTEASPP  184 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~-FH~~CI~~Wl~~~~sCPvCR~~l~~~  184 (195)
                      ...|+||++.+...    +++||||. ||..|+..|    ..||+||.++...
T Consensus        18 ~~~C~IC~~~~~~~----v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~~   62 (79)
T 2yho_A           18 AMLCMVCCEEEINS----TFCPCGHTVCCESCAAQL----QSCPVCRSRVEHV   62 (79)
T ss_dssp             HTBCTTTSSSBCCE----EEETTCBCCBCHHHHTTC----SBCTTTCCBCCEE
T ss_pred             CCEeEEeCcccCcE----EEECCCCHHHHHHHHHhc----CcCCCCCchhhCe
Confidence            35899999887653    44499999 999999987    3899999987643

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

Probab=98.77  E-value=3.8e-09  Score=74.60  Aligned_cols=48  Identities=21%  Similarity=0.684  Sum_probs=38.5

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcC--------CCCCc--cccc
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK--------KICPI--CSTE  180 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~--------~sCPv--CR~~  180 (195)
                      ....|+||++.+..+..+. +.+|||.||..||..|+..+        ..||.  ||..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~-l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTT-IAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEE-ETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceE-cCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            4568999999987765444 43899999999999999632        37999  9987

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

Probab=98.76  E-value=4.8e-09  Score=68.59  Aligned_cols=50  Identities=28%  Similarity=0.642  Sum_probs=37.8

Q ss_pred             CCCCcccccccccccCCceeEEecCcc--c---eechhhHHHHhhc--CCCCCccccccCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCE--H---LYHSECISNWLQI--KKICPICSTEASP  183 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~--H---~FH~~CI~~Wl~~--~~sCPvCR~~l~~  183 (195)
                      ......|.||+....  +.+ .+ ||.  |   .||..||.+|+..  +.+||+||.++..
T Consensus         3 ~~~~~~CrIC~~~~~--~~l-~~-PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            3 DEDVPVCWICNEELG--NER-FR-ACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             TCSCCEETTTTEECS--CCC-CC-SCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCEeEEeecCCC--Cce-ec-CcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            346678999998743  333 34 765  4   9999999999964  5789999998753

>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=98.75  E-value=1.2e-09  Score=91.03  Aligned_cols=57  Identities=26%  Similarity=0.430  Sum_probs=45.0

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcC--CCCCc--cccccCCCCCCCc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK--KICPI--CSTEASPPKNHNN  189 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~--~sCPv--CR~~l~~~~~~~~  189 (195)
                      ......||||+..|..+  ++. ..|||.||+.||..|++.+  .+||+  ||+.+......++
T Consensus       178 ~~~el~CPIcl~~f~DP--Vts-~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL~pN  238 (267)
T 3htk_C          178 GKIELTCPITCKPYEAP--LIS-RKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFVRD  238 (267)
T ss_dssp             SBCCSBCTTTSSBCSSE--EEE-SSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGEEEC
T ss_pred             CceeeECcCccCcccCC--eee-CCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhCCcC
Confidence            34567899999999887  222 3899999999999999764  47999  9998876655444

>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=98.74  E-value=2.6e-09  Score=70.07  Aligned_cols=53  Identities=11%  Similarity=0.081  Sum_probs=44.1

Q ss_pred             CcccccccccccCCceeEEec-CccceechhhHHHHhhcCCCCCccccccCCCCCCCc
Q 044318          133 IDRCVICQVEYEEGESIVALL-PCEHLYHSECISNWLQIKKICPICSTEASPPKNHNN  189 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~-~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~  189 (195)
                      ...|+||++.+.++    ++. +|||+|.+.||.+|++.+++||+++.++......+.
T Consensus         3 ~~~CpIs~~~m~dP----V~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~Lip~   56 (61)
T 2bay_A            3 HMLCAISGKVPRRP----VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEI   56 (61)
T ss_dssp             -CCCTTTCSCCSSE----EEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEEC
T ss_pred             eEEecCCCCCCCCC----EEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhhcEEC
Confidence            35799999999876    333 899999999999999988899999999976655443

>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=98.65  E-value=8.6e-09  Score=89.23  Aligned_cols=44  Identities=30%  Similarity=0.635  Sum_probs=36.9

Q ss_pred             CCcccccccccccCCceeEEecCccce-echhhHHHHhhcCCCCCccccccCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHL-YHSECISNWLQIKKICPICSTEASP  183 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~-FH~~CI~~Wl~~~~sCPvCR~~l~~  183 (195)
                      ....|+||++.+...   +.+ ||||. ||..|+..|    ..||+||.++..
T Consensus       294 ~~~~C~IC~~~~~~~---v~l-pCgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          294 EERTCKVCMDKEVSV---VFI-PCGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             TTCBCTTTSSSBCCE---EEE-TTCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             CCCCCCccCCcCCce---EEc-CCCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            356899999998764   344 99999 999999998    789999998753

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.40  E-value=2e-07  Score=66.53  Aligned_cols=46  Identities=24%  Similarity=0.528  Sum_probs=36.6

Q ss_pred             ccccccccccCCceeEEecCccceechhhHHHHhh-cCCCCCccccccCC
Q 044318          135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ-IKKICPICSTEASP  183 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~-~~~sCPvCR~~l~~  183 (195)
                      -|.+|--.+..  ..+++ ||+|+||.+|+..|.+ ..++||+|+.++..
T Consensus         3 fC~~C~~Pi~i--ygRmI-PCkHvFCydCa~~~~~~~~k~Cp~C~~~V~r   49 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMI-PCKHVFCYDCAILHEKKGDKMCPGCSDPVQR   49 (101)
T ss_dssp             BCTTTCSBCSE--EEEEE-TTCCEEEHHHHHHHHHTTCCBCTTTCCBCSE
T ss_pred             ecCccCCCeEE--Eeeec-cccccHHHHHHHHHHhccCCCCcCcCCeeee
Confidence            48888766544  34555 9999999999999985 46899999998864

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

Probab=98.30  E-value=7.9e-07  Score=73.18  Aligned_cols=53  Identities=21%  Similarity=0.474  Sum_probs=42.9

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcCC--CCCccccccCCCCCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKK--ICPICSTEASPPKNH  187 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~--sCPvCR~~l~~~~~~  187 (195)
                      ....|.||.+-+..+   .....|+|.||..|+.+|++.+.  .||.|+..++.....
T Consensus       179 ~i~~C~iC~~iv~~g---~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~~~  233 (238)
T 3nw0_A          179 AVKICNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIPK  233 (238)
T ss_dssp             TCCBCTTTCSBCSSC---EECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCCCC
T ss_pred             CCCcCcchhhHHhCC---cccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCC
Confidence            478999999998876   33435999999999999997654  899999988765433

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=95.71  E-value=0.013  Score=38.51  Aligned_cols=49  Identities=18%  Similarity=0.359  Sum_probs=35.2

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcC----CCCCccccccC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK----KICPICSTEAS  182 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~----~sCPvCR~~l~  182 (195)
                      ......|.||...   + .++..-.|...||..|+...|...    -.||.|+....
T Consensus         9 ~~~~~~C~vC~~~---~-~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~   61 (66)
T 2lri_C            9 LAPGARCGVCGDG---T-DVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDVT   61 (66)
T ss_dssp             CCTTCCCTTTSCC---T-TCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCCC
T ss_pred             CCCCCCcCCCCCC---C-eEEECCCCCCceecccCCCccCcCCCCCEECccccCCCc
Confidence            3455789999743   3 344455799999999999887543    47999986543

>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=95.49  E-value=0.0093  Score=38.53  Aligned_cols=51  Identities=24%  Similarity=0.518  Sum_probs=37.3

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhh-----cCCCCCccccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ-----IKKICPICSTE  180 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~-----~~~sCPvCR~~  180 (195)
                      ......|+||...+......+..-.|...||..|+.--..     ..-.||.|+.+
T Consensus         3 ~~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            3 SGSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             CSSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            3456789999998865555566568999999999864332     34579999764

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=95.48  E-value=0.0085  Score=41.88  Aligned_cols=35  Identities=20%  Similarity=0.458  Sum_probs=25.8

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHH-Hh
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISN-WL  168 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~-Wl  168 (195)
                      ...|.||.+.+.......-+ .|+|.||..|+.. |.
T Consensus         3 e~~C~~C~~~~~~~av~~C~-~C~~~~C~~Cl~~~h~   38 (101)
T 2jun_A            3 KVLCQFCDQDPAQDAVKTCV-TCEVSYCDECLKATHP   38 (101)
T ss_dssp             CCBCTTCCSSSCCBCCEEET-TTTEEECHHHHHHHSC
T ss_pred             CCCCcCCCCCCCCCceEECC-cCChHHhHHHCHHHhc
Confidence            46899999875433333335 9999999999998 54

>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=93.64  E-value=0.082  Score=36.27  Aligned_cols=37  Identities=14%  Similarity=0.479  Sum_probs=24.7

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHH
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNW  167 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~W  167 (195)
                      ....++.|.||- .|...+.. ..--|+-+||..||.+-
T Consensus        11 ~~~~D~~C~VC~-~~t~~~l~-pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           11 PVVNDEMCDVCE-VWTAESLF-PCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCSCCCTTTC-CCCSSCCS-SCSSSSSCCCHHHHHHH
T ss_pred             CCCCCcccCccc-ccccccee-ccccccccccHhhcccc
Confidence            344678999994 44444221 12247899999999996

>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=92.74  E-value=0.06  Score=34.76  Aligned_cols=54  Identities=26%  Similarity=0.529  Sum_probs=37.3

Q ss_pred             CCCCccccccccccc-CCceeEEecCccceechhhHHHHhh-------cCCCCCccccccCC
Q 044318          130 KSGIDRCVICQVEYE-EGESIVALLPCEHLYHSECISNWLQ-------IKKICPICSTEASP  183 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~-~~~~~~~L~~C~H~FH~~CI~~Wl~-------~~~sCPvCR~~l~~  183 (195)
                      ......|.||..... ....++..-.|.-.||..|+..-+.       ..-.||.|+.....
T Consensus         3 ~~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~~~   64 (66)
T 2yt5_A            3 SGSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFATTT   64 (66)
T ss_dssp             CCCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTTSC
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCcccc
Confidence            446678999997753 2344555558999999999986442       23479999765543

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=92.70  E-value=0.053  Score=35.98  Aligned_cols=54  Identities=20%  Similarity=0.506  Sum_probs=37.5

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhh----cCCCCCccccccCCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ----IKKICPICSTEASPP  184 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~----~~~sCPvCR~~l~~~  184 (195)
                      ......|.||..... +..++..-.|.-.||..|+..-..    ..-.||.|+..+...
T Consensus        15 ~~~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~k~   72 (75)
T 2k16_A           15 GNQIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKKD   72 (75)
T ss_dssp             SCEEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHCSC
T ss_pred             CCCCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchhhc
Confidence            334567999987753 444555557999999999976543    234799998876543

>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=92.53  E-value=0.076  Score=41.62  Aligned_cols=49  Identities=20%  Similarity=0.515  Sum_probs=36.0

Q ss_pred             CcccccccccccCCce---eEEecCccceechhhHHHH------hh-----cCCCCCcccccc
Q 044318          133 IDRCVICQVEYEEGES---IVALLPCEHLYHSECISNW------LQ-----IKKICPICSTEA  181 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~---~~~L~~C~H~FH~~CI~~W------l~-----~~~sCPvCR~~l  181 (195)
                      +..|+||...|..++.   .+..-.|...||..|+.--      +.     ..-.||.|+..-
T Consensus         2 G~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~   64 (183)
T 3lqh_A            2 GNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERH   64 (183)
T ss_dssp             CCBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSS
T ss_pred             cCcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCC
Confidence            3469999999987763   5666689999999997431      11     156899998754

>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=92.06  E-value=0.11  Score=32.10  Aligned_cols=44  Identities=20%  Similarity=0.396  Sum_probs=32.1

Q ss_pred             ccccccccccCCceeEEec-CccceechhhHHHHh----hcCCCCCccc
Q 044318          135 RCVICQVEYEEGESIVALL-PCEHLYHSECISNWL----QIKKICPICS  178 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~-~C~H~FH~~CI~~Wl----~~~~sCPvCR  178 (195)
                      .|.||...+..+...+..- .|...||..|+.--.    ..+..||.|+
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            5789998887666666665 699999999975322    2456899985

>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=92.04  E-value=0.048  Score=38.87  Aligned_cols=50  Identities=18%  Similarity=0.474  Sum_probs=35.6

Q ss_pred             CcccccccccccCCceeEEec-CccceechhhHHHHh----------hcCCCCCccccccC
Q 044318          133 IDRCVICQVEYEEGESIVALL-PCEHLYHSECISNWL----------QIKKICPICSTEAS  182 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~-~C~H~FH~~CI~~Wl----------~~~~sCPvCR~~l~  182 (195)
                      ...|+||...+......+..- .|...||..|+.---          ..+-.||.|+....
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            467999999986655555554 689999999974221          13457999987543

>1wee_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=91.82  E-value=0.082  Score=34.87  Aligned_cols=53  Identities=25%  Similarity=0.426  Sum_probs=36.1

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHh----hcCCCCCccccccCC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWL----QIKKICPICSTEASP  183 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl----~~~~sCPvCR~~l~~  183 (195)
                      ......| ||......+...+..-.|...||..|+.---    .....||.|+..-.+
T Consensus        13 ~~~~~~C-~C~~~~~~g~~mI~Cd~C~~W~H~~Cvg~~~~~~~~~~~~C~~C~~~~~p   69 (72)
T 1wee_A           13 DNWKVDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELSGP   69 (72)
T ss_dssp             CSSEECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHHCSS
T ss_pred             CCcceEe-eCCCccCCCCcEEECCCCCCccCCeeeccCccccCCCcEECCCccCCCCC
Confidence            3345578 7988766665556666899999999986432    234579999865433

>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=91.81  E-value=0.3  Score=33.75  Aligned_cols=58  Identities=22%  Similarity=0.328  Sum_probs=41.5

Q ss_pred             CCCccccccccccc---CCceeEEecCccceechhhHHHHh-hcCCCCCccccccCCCCCCC
Q 044318          131 SGIDRCVICQVEYE---EGESIVALLPCEHLYHSECISNWL-QIKKICPICSTEASPPKNHN  188 (195)
Q Consensus       131 ~~~~~C~ICl~~f~---~~~~~~~L~~C~H~FH~~CI~~Wl-~~~~sCPvCR~~l~~~~~~~  188 (195)
                      .....|.||-..+-   +++..+....|+-..|+.|..-=. ..+..||.|+++....+..+
T Consensus        14 ~~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCktrYkr~kgsp   75 (93)
T 1weo_A           14 LDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKRLRGSP   75 (93)
T ss_dssp             CSSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCCCTTCC
T ss_pred             cCCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhccCccccccCCccccccCCC
Confidence            35679999998863   344444445788889999986554 45678999999997554443

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=91.78  E-value=0.15  Score=32.61  Aligned_cols=47  Identities=32%  Similarity=0.652  Sum_probs=33.4

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhh----cCCCCCccccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ----IKKICPICSTE  180 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~----~~~sCPvCR~~  180 (195)
                      ......|.||...   + .++..-.|...||..|+..-+.    ..-.||.|+..
T Consensus         8 ~~~~~~C~vC~~~---g-~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            8 TDHQDYCEVCQQG---G-EIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             SCCCSSCTTTSCC---S-SEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCCCccCCCC---C-cEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            4456789999863   3 3444457889999999987553    23479999753

>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=91.73  E-value=0.29  Score=32.73  Aligned_cols=50  Identities=18%  Similarity=0.397  Sum_probs=34.5

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhh-----cCCCCCcccccc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ-----IKKICPICSTEA  181 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~-----~~~sCPvCR~~l  181 (195)
                      .....| ||...+......+..-.|...||..|+.--..     ..-.||.|+...
T Consensus        10 ~~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A           10 LVPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             CCccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            344566 99888754555555558999999999853221     345799998654

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=91.42  E-value=0.064  Score=33.64  Aligned_cols=47  Identities=28%  Similarity=0.706  Sum_probs=32.8

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHHhhc----CCCCCcccc
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI----KKICPICST  179 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~----~~sCPvCR~  179 (195)
                      .......|.||...   + .++....|...||..|+..-+..    .-.||.|+.
T Consensus         5 ~~~~~~~C~vC~~~---g-~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            5 SSGHEDFCSVCRKS---G-QLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             CCSSCCSCSSSCCS---S-CCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             cCCCCCCCccCCCC---C-eEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            45567789999864   3 34444579999999999865532    235888864

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=90.89  E-value=0.41  Score=33.02  Aligned_cols=50  Identities=26%  Similarity=0.535  Sum_probs=35.0

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHHhhc----CCCCCccccccC
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI----KKICPICSTEAS  182 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~----~~sCPvCR~~l~  182 (195)
                      .......|.||...   + .+...-.|.-.||..|+..=+..    .-.||.|+..-.
T Consensus        21 ~d~n~~~C~vC~~~---g-~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~~   74 (88)
T 1fp0_A           21 LDDSATICRVCQKP---G-DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   74 (88)
T ss_dssp             SSSSSSCCSSSCSS---S-CCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             cCCCCCcCcCcCCC---C-CEEECCCCCCceecccCCCCCCCCcCCCcCCccccCCCc
Confidence            34566789999854   3 34444578899999999776543    347999986543

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=90.80  E-value=0.13  Score=40.65  Aligned_cols=49  Identities=22%  Similarity=0.525  Sum_probs=34.9

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhc----CCCCCccccccC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI----KKICPICSTEAS  182 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~----~~sCPvCR~~l~  182 (195)
                      ......|.+|...    ..+...-.|...||..|+...+..    .-.||.|+..-.
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----GDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGK   56 (207)
T ss_dssp             CSSCSSBTTTCCC----EEEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSSS
T ss_pred             CCCCCCCCCCCCC----CceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCccc
Confidence            3456789999743    335555579999999999876643    247999987543

>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=90.57  E-value=0.11  Score=33.18  Aligned_cols=48  Identities=25%  Similarity=0.642  Sum_probs=32.6

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhc----CCCCCcccccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI----KKICPICSTEA  181 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~----~~sCPvCR~~l  181 (195)
                      ......|.||...   + .++..-.|...||..|+..-+..    .-.||.|+...
T Consensus         6 d~~~~~C~vC~~~---g-~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            6 DHHMEFCRVCKDG---G-ELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             CSSCSSCTTTCCC---S-SCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             cCCCCcCCCCCCC---C-CEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            4456789999753   2 33333468899999999865532    34699997643

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=90.03  E-value=0.2  Score=30.55  Aligned_cols=44  Identities=25%  Similarity=0.631  Sum_probs=29.7

Q ss_pred             ccccccccccCCceeEEecCccceechhhHHHHhhc----CCCCCcccc
Q 044318          135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI----KKICPICST  179 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~----~~sCPvCR~  179 (195)
                      .|.||...-..+ .++..-.|...||..|+..=+..    .-.||.|+.
T Consensus         2 ~C~vC~~~~~~~-~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCC-CEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            588897654333 34444589999999999754432    236999975

>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=89.77  E-value=0.21  Score=35.45  Aligned_cols=48  Identities=21%  Similarity=0.423  Sum_probs=31.9

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhc----CCCCCccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI----KKICPICS  178 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~----~~sCPvCR  178 (195)
                      ......|.||...-.. ..++.-..|+..||..||..++..    .-.||.|+
T Consensus         4 ~~~~~~C~~C~~~g~~-~~ll~C~~C~~~~H~~Cl~~~~~~~~~~~W~C~~C~   55 (111)
T 2ysm_A            4 GSSGANCAVCDSPGDL-LDQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPECK   55 (111)
T ss_dssp             CCCCSCBTTTCCCCCT-TTSEECSSSCCEECTTTTTCCCCTTTSTTCCCTTTC
T ss_pred             CCCCCCCcCCCCCCCC-cCCeECCCCCCCcChHHhCCccccccccCccCCcCC
Confidence            4567889999876322 223444589999999999877642    23466553

>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=89.68  E-value=0.19  Score=38.86  Aligned_cols=47  Identities=28%  Similarity=0.630  Sum_probs=33.7

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhc----CCCCCccccccC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI----KKICPICSTEAS  182 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~----~~sCPvCR~~l~  182 (195)
                      ....|.||...   ++ +...-.|...||..|+..-+..    .-.||.|+..-.
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            45679999844   33 4444579999999999776643    347999987543

>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=89.39  E-value=0.28  Score=31.81  Aligned_cols=49  Identities=18%  Similarity=0.405  Sum_probs=33.8

Q ss_pred             CCCCcccccccccccCCceeEEec-CccceechhhHHHHhh----------cCCCCCccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALL-PCEHLYHSECISNWLQ----------IKKICPICS  178 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~-~C~H~FH~~CI~~Wl~----------~~~sCPvCR  178 (195)
                      ......|++|...+......+..- .|.-.||..|+.---.          ..-.||.|+
T Consensus         5 ~~~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvglt~~~~~~l~~e~~~~w~C~~C~   64 (65)
T 2vpb_A            5 SDPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTCM   64 (65)
T ss_dssp             ----CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHTCCHHHHHHHHHCTTEEECCHHHH
T ss_pred             CCCcCcCccCCCccCCCCCeEecccCccccCchhccCCCHHHHHHhhccCCCcEECcCcc
Confidence            445678999999988777777776 7999999999732211          134688885

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=88.99  E-value=0.28  Score=33.71  Aligned_cols=55  Identities=20%  Similarity=0.306  Sum_probs=37.1

Q ss_pred             CCCCcccccccccc-cCCceeEEecCccceechhhHHHHhh--cCCCCCccccccCCC
Q 044318          130 KSGIDRCVICQVEY-EEGESIVALLPCEHLYHSECISNWLQ--IKKICPICSTEASPP  184 (195)
Q Consensus       130 ~~~~~~C~ICl~~f-~~~~~~~~L~~C~H~FH~~CI~~Wl~--~~~sCPvCR~~l~~~  184 (195)
                      ......|.||...- .....++..-.|.-.||..|+..-+.  ..-.||.|+......
T Consensus        22 ~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~~~~   79 (88)
T 2l43_A           22 IDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRARP   79 (88)
T ss_dssp             CCCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHTTSC
T ss_pred             CCCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCccchh
Confidence            34567899998753 23335555557889999999975432  234799998765444

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=88.67  E-value=0.23  Score=35.51  Aligned_cols=45  Identities=24%  Similarity=0.560  Sum_probs=31.0

Q ss_pred             ccccccccccCCceeEEecCccceechhhHHHHhhc----CCCCCcccc
Q 044318          135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI----KKICPICST  179 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~----~~sCPvCR~  179 (195)
                      .|.||...-.....+...-.|...||..|+..-|..    .-.||.|+.
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            678887643333345555579999999999765543    247999975

>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=88.54  E-value=0.23  Score=47.98  Aligned_cols=55  Identities=11%  Similarity=-0.005  Sum_probs=45.3

Q ss_pred             CCCcccccccccccCCceeEEecCcc-ceechhhHHHHhhcCCCCCccccccCCCCCCCc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCE-HLYHSECISNWLQIKKICPICSTEASPPKNHNN  189 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~-H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~  189 (195)
                      .....|||-++-+.++    +.+|-| +.|-+.+|.+|+..+.+||+=|.++......++
T Consensus       889 P~~F~cPIs~~lM~DP----VilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~liPN  944 (968)
T 3m62_A          889 PDEFLDPLMYTIMKDP----VILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPN  944 (968)
T ss_dssp             CGGGBCTTTCSBCSSE----EECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEEC
T ss_pred             cHHhCCcchhhHHhCC----eEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCCccccccc
Confidence            3567899999998887    334887 689999999999999999999999986655544

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=88.38  E-value=0.46  Score=33.17  Aligned_cols=46  Identities=24%  Similarity=0.594  Sum_probs=31.2

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhc---CCCCCcccc
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI---KKICPICST  179 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~---~~sCPvCR~  179 (195)
                      ....| ||......+ .++..-.|.-.||..|+..=+..   .-.||.|+.
T Consensus        27 d~vrC-iC~~~~~~~-~mi~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~   75 (98)
T 2lv9_A           27 DVTRC-ICGFTHDDG-YMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQP   75 (98)
T ss_dssp             CBCCC-TTSCCSCSS-CEEEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSS
T ss_pred             CCEEe-ECCCccCCC-cEEEcCCCCCcCcCcCCCCCccCCCCCEECCCCcC
Confidence            34567 897765544 44555589999999998653322   347999974

>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=88.06  E-value=0.35  Score=31.98  Aligned_cols=48  Identities=23%  Similarity=0.542  Sum_probs=32.5

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHh---------hcCCCCCccccccC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWL---------QIKKICPICSTEAS  182 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl---------~~~~sCPvCR~~l~  182 (195)
                      ...| ||...+.. ...+..-.|...||..|+.--.         .....||.|+..-.
T Consensus        16 ~~~C-~C~~~~~~-~~MI~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~~~   72 (76)
T 1wem_A           16 ALYC-ICRQPHNN-RFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILSG   72 (76)
T ss_dssp             CCCS-TTCCCCCS-SCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHSC
T ss_pred             CCEE-ECCCccCC-CCEEEeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCccC
Confidence            4556 89887653 3445555899999999984321         24578999986543

>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=88.04  E-value=0.18  Score=34.59  Aligned_cols=50  Identities=24%  Similarity=0.577  Sum_probs=35.2

Q ss_pred             CcccccccccccC-CceeEEecCccceechhhHHHHhh--------cCCCCCccccccC
Q 044318          133 IDRCVICQVEYEE-GESIVALLPCEHLYHSECISNWLQ--------IKKICPICSTEAS  182 (195)
Q Consensus       133 ~~~C~ICl~~f~~-~~~~~~L~~C~H~FH~~CI~~Wl~--------~~~sCPvCR~~l~  182 (195)
                      ...|.||...-.. ...++..-.|...||..|+..-|.        ..-.||.|+....
T Consensus        16 ~~~C~vC~~~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~~~~~   74 (88)
T 1wev_A           16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMK   74 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHC
T ss_pred             CCcCCCCCCCCCCCCCceEECCCCCCeEcCccCCCcccccccCCCCCCeeCccccchhh
Confidence            4679999876432 234555557999999999987553        2357999977554

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=87.90  E-value=0.24  Score=32.01  Aligned_cols=48  Identities=23%  Similarity=0.567  Sum_probs=33.5

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhc----CCCCCcccccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI----KKICPICSTEA  181 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~----~~sCPvCR~~l  181 (195)
                      ......|.||...   + .++..-.|...||..|+..-+..    .-.||.|+..-
T Consensus         5 ~~~~~~C~vC~~~---g-~ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~~   56 (66)
T 1xwh_A            5 QKNEDECAVCRDG---G-ELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQAT   56 (66)
T ss_dssp             CSCCCSBSSSSCC---S-SCEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHTC
T ss_pred             CCCCCCCccCCCC---C-CEEEcCCCChhhcccccCCCcCcCCCCCeECccccCcc
Confidence            3457789999854   3 34444478999999999865532    34699997643

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=87.55  E-value=0.73  Score=34.56  Aligned_cols=46  Identities=20%  Similarity=0.434  Sum_probs=33.6

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhh-----------cCCCCCcccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ-----------IKKICPICST  179 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~-----------~~~sCPvCR~  179 (195)
                      +.....|.||...    -.+...-.|...||..||.+-+.           ..-.||+|+.
T Consensus        60 Dg~~d~C~vC~~G----G~LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~  116 (142)
T 2lbm_A           60 DGMDEQCRWCAEG----GNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHP  116 (142)
T ss_dssp             TSCBCSCSSSCCC----SSEEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCC
T ss_pred             CCCCCeecccCCC----CcEEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccC
Confidence            4567899999854    33455558999999999997652           2347999974

>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=87.47  E-value=1  Score=30.63  Aligned_cols=41  Identities=20%  Similarity=0.313  Sum_probs=31.1

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI  170 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~  170 (195)
                      ......|.+|.+.+++...+..-..=.|.||..|-+..++.
T Consensus        12 ~~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~   52 (93)
T 2cs3_A           12 NSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   52 (93)
T ss_dssp             SCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CCCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHh
Confidence            45667899999999887654422234799999999998864

>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=87.34  E-value=0.16  Score=38.87  Aligned_cols=49  Identities=22%  Similarity=0.568  Sum_probs=34.3

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHh-----hcCCCCCccccc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWL-----QIKKICPICSTE  180 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl-----~~~~sCPvCR~~  180 (195)
                      .....| ||......+...+..-.|...||..|+.--.     ...-.||.|+..
T Consensus         6 ~~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~   59 (174)
T 2ri7_A            6 DTKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST   59 (174)
T ss_dssp             -CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHH
T ss_pred             CCCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcch
Confidence            355678 9998875555556666899999999985322     234579999864

>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC, structural genom type zinc finger, protein binding, zinc ION binding; 1.85A {Homo sapiens}

Probab=86.82  E-value=0.31  Score=31.84  Aligned_cols=48  Identities=19%  Similarity=0.499  Sum_probs=32.5

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhh---cCCCCCcccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ---IKKICPICST  179 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~---~~~sCPvCR~  179 (195)
                      ......| ||..... +...+..-.|...||..|+.---.   ..-.||.|+.
T Consensus        16 ~~~~~~C-iC~~~~~-~~~MIqCd~C~~WfH~~Cvgi~~~~~~~~~~C~~C~~   66 (68)
T 3o70_A           16 FQGLVTC-FCMKPFA-GRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRD   66 (68)
T ss_dssp             TTTCCCS-TTCCCCT-TCCEEECTTTCCEEETTTTTCCTTSCCSSCCCHHHHT
T ss_pred             CCCceEe-ECCCcCC-CCCEEECCCCCccccccccCcCcccCCCcEECCCCCC
Confidence            3455678 9987765 444555557999999999854321   3357999864

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=86.70  E-value=0.95  Score=32.19  Aligned_cols=35  Identities=20%  Similarity=0.450  Sum_probs=25.3

Q ss_pred             CCcccccccccc-----cCCceeEEecCccceechhhHHH
Q 044318          132 GIDRCVICQVEY-----EEGESIVALLPCEHLYHSECISN  166 (195)
Q Consensus       132 ~~~~C~ICl~~f-----~~~~~~~~L~~C~H~FH~~CI~~  166 (195)
                      ....|.+|+..=     ..++.++.-..|+..||..||..
T Consensus         4 p~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~~   43 (112)
T 3v43_A            4 PIPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLKF   43 (112)
T ss_dssp             CCSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHTC
T ss_pred             cCccccccCCchhhCcCCCchhceEhhhcCCCCCCchhcC
Confidence            457899998752     12345666668999999999953

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=86.50  E-value=0.18  Score=31.97  Aligned_cols=47  Identities=28%  Similarity=0.687  Sum_probs=33.0

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhc----CCCCCcccccc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI----KKICPICSTEA  181 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~----~~sCPvCR~~l  181 (195)
                      .....|.||...   + .++..-.|...||..|+..-+..    .-.||.|+...
T Consensus         3 ~~~~~C~vC~~~---g-~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   53 (60)
T 2puy_A            3 IHEDFCSVCRKS---G-QLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQM   53 (60)
T ss_dssp             CCCSSCTTTCCC---S-SCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHH
T ss_pred             CCCCCCcCCCCC---C-cEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccChh
Confidence            346789999864   3 34444579999999999865532    34699997654

>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=86.16  E-value=0.3  Score=32.04  Aligned_cols=44  Identities=20%  Similarity=0.527  Sum_probs=28.2

Q ss_pred             ccccccccccCCceeEEecCccceechhhHHHHhhc-----CCCCCcccc
Q 044318          135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-----KKICPICST  179 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-----~~sCPvCR~  179 (195)
                      .|.||...- .+..++.--.|...||..||..=|..     .-.||.|+.
T Consensus        20 ~C~~C~~~~-~~~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   68 (70)
T 3asl_A           20 ACHLCGGRQ-DPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   68 (70)
T ss_dssp             SBTTTCCCS-CGGGEEECTTTCCEEEGGGSSSCCSSCCSSSCCCCTTTSC
T ss_pred             CCcCCCCcC-CCCCEEEcCCCCCceecccCCCCcCCCCCCCCcCCcCccC
Confidence            455666432 23344444578999999999854432     337999975

>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=85.95  E-value=0.46  Score=34.01  Aligned_cols=34  Identities=21%  Similarity=0.384  Sum_probs=24.6

Q ss_pred             ccccccccccc------CCceeEEecCccceechhhHHHH
Q 044318          134 DRCVICQVEYE------EGESIVALLPCEHLYHSECISNW  167 (195)
Q Consensus       134 ~~C~ICl~~f~------~~~~~~~L~~C~H~FH~~CI~~W  167 (195)
                      ..|.||+..-.      .+..++.-..|+..||..||..+
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            57999987642      12355555689999999999765

>1y02_A CARP2, FYVE-ring finger protein sakura; zinc-binding module, phosphoinositide binding, caspase regulation, metal binding protein; 1.80A {Homo sapiens} SCOP: a.140.2.1 g.50.1.1

Probab=85.64  E-value=0.18  Score=36.89  Aligned_cols=52  Identities=15%  Similarity=0.343  Sum_probs=33.5

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCcccccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEA  181 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l  181 (195)
                      ......|.+|...|..-..---...||.+||..|........+.|-.|-..+
T Consensus        16 d~~~~~C~~C~~~Fs~~~RkHHCR~CG~ifC~~Cs~~~~~~vRVC~~C~~~~   67 (120)
T 1y02_A           16 TGLEPSCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQRFR   67 (120)
T ss_dssp             ----CCCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHHHHH
T ss_pred             ccccCcccCcCCccccccccccCCCCCCeeCHHHhCCCCCCceECHHHHHHH
Confidence            3445689999999965433333448999999999888776677888886543

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=85.23  E-value=0.31  Score=32.18  Aligned_cols=51  Identities=20%  Similarity=0.306  Sum_probs=35.1

Q ss_pred             CCCCcccccccccc-cCCceeEEecCccceechhhHHHHh--hcCCCCCccccc
Q 044318          130 KSGIDRCVICQVEY-EEGESIVALLPCEHLYHSECISNWL--QIKKICPICSTE  180 (195)
Q Consensus       130 ~~~~~~C~ICl~~f-~~~~~~~~L~~C~H~FH~~CI~~Wl--~~~~sCPvCR~~  180 (195)
                      ......|.||...- .....++..-.|.-.||..|+..-.  ...-.||.|+..
T Consensus        13 ~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~~   66 (71)
T 2ku3_A           13 IDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQS   66 (71)
T ss_dssp             CCSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcCc
Confidence            45678899998763 3344555556899999999997533  223469999754

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=84.98  E-value=0.38  Score=32.24  Aligned_cols=44  Identities=27%  Similarity=0.520  Sum_probs=29.2

Q ss_pred             ccccccccccCCceeEEecCccceechhhHHHHhhc-----CCCCCcccc
Q 044318          135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-----KKICPICST  179 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-----~~sCPvCR~  179 (195)
                      .|.||...-. +..++..-.|...||..|+..=|..     .-.||.|+.
T Consensus        28 ~C~vC~~~~~-~~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   76 (77)
T 2e6s_A           28 SCRVCGGKHE-PNMQLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKT   76 (77)
T ss_dssp             SCSSSCCCCC-STTEEECSSSCCEEETTSSSSCCSSCCCSSCCCCTTTCC
T ss_pred             CCcCcCCcCC-CCCEEEcCCCCccccccccCCCccCCCCCCCcCCcCccC
Confidence            6778875432 3344444589999999999854432     236999864

>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=84.77  E-value=0.27  Score=34.06  Aligned_cols=50  Identities=22%  Similarity=0.375  Sum_probs=33.9

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhc----CCCCCccccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI----KKICPICSTE  180 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~----~~sCPvCR~~  180 (195)
                      ......|.||...-.. ..++..-.|...||..|+..=+..    .-.||.|+..
T Consensus        13 ~~~~~~C~vC~~~~~~-~~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~   66 (92)
T 2e6r_A           13 FIDSYICQVCSRGDED-DKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILA   66 (92)
T ss_dssp             CCCCCCCSSSCCSGGG-GGCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHH
T ss_pred             ccCCCCCccCCCcCCC-CCEEEcCCCCchhccccCCCCcccCCCCCcCCccCcCc
Confidence            3345679999876432 344445589999999999754432    3469999764

>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=83.46  E-value=0.82  Score=31.66  Aligned_cols=46  Identities=28%  Similarity=0.658  Sum_probs=28.7

Q ss_pred             CCcccccccccccCCceeEEecC--cc-ceechhhHHHHhh----cCCCCCccccccC
Q 044318          132 GIDRCVICQVEYEEGESIVALLP--CE-HLYHSECISNWLQ----IKKICPICSTEAS  182 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~--C~-H~FH~~CI~~Wl~----~~~sCPvCR~~l~  182 (195)
                      ....| ||..... + .++..-.  |. ..||..|+.  |.    .+-.||.|+..-.
T Consensus        35 e~~yC-iC~~~~~-g-~MI~CD~~dC~~~WfH~~CVg--l~~~p~g~W~Cp~C~~~~~   87 (91)
T 1weu_A           35 EPTYC-LCHQVSY-G-EMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESG   87 (91)
T ss_dssp             CCBCS-TTCCBCC-S-CCCCCSCSSCSCCCCCSTTTT--CSSCCCSSCCCTTTCCCCS
T ss_pred             CCcEE-ECCCCCC-C-CEeEecCCCCCCCCEecccCC--cCcCCCCCEECcCccCcCC
Confidence            44567 9987643 3 2232324  55 689999996  32    2347999986543

>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=83.36  E-value=1.7  Score=31.97  Aligned_cols=46  Identities=20%  Similarity=0.441  Sum_probs=32.3

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHh------h-----cCCCCCcccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWL------Q-----IKKICPICST  179 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl------~-----~~~sCPvCR~  179 (195)
                      +.....|.||...    ..+...-.|-..||..||.+-+      +     ..-.|++|+-
T Consensus        54 Dg~~~~C~vC~dG----G~LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~  110 (129)
T 3ql9_A           54 DGMDEQCRWCAEG----GNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHP  110 (129)
T ss_dssp             TSCBSSCTTTCCC----SEEEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCC
T ss_pred             CCCCCcCeecCCC----CeeEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCC
Confidence            4456779999744    3444445789999999999752      1     2257999964

>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=83.32  E-value=0.7  Score=30.79  Aligned_cols=49  Identities=22%  Similarity=0.396  Sum_probs=32.4

Q ss_pred             CCcccccccccccCCceeEEec--CccceechhhHHHHhh---------cCCCCCccccccC
Q 044318          132 GIDRCVICQVEYEEGESIVALL--PCEHLYHSECISNWLQ---------IKKICPICSTEAS  182 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~--~C~H~FH~~CI~~Wl~---------~~~sCPvCR~~l~  182 (195)
                      ....| ||-.....+ ..+..-  .|...||..|+.---.         .+-.||.|+..-.
T Consensus        15 ~~~~C-iC~~~~~~g-~MI~CD~~~C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~~~   74 (78)
T 1wew_A           15 IKVRC-VCGNSLETD-SMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSG   74 (78)
T ss_dssp             CCCCC-SSCCCCCCS-CEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCCS
T ss_pred             CCEEe-ECCCcCCCC-CEEEECCccCCccccCEEEccccccccccccCCCCEECCCCCcccC
Confidence            45667 788774333 455554  6999999999853221         2457999986543

>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=82.68  E-value=1.6  Score=29.80  Aligned_cols=53  Identities=21%  Similarity=0.375  Sum_probs=36.4

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhh-------cCCCCCccccccC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ-------IKKICPICSTEAS  182 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~-------~~~sCPvCR~~l~  182 (195)
                      ......|.+|...|..-..-.-.-.||++||..|....+.       ..+.|-.|-..+.
T Consensus         6 ~~~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~~~~lp~~g~~~~RVC~~C~~~l~   65 (88)
T 1wfk_A            6 SGMESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFSALVPRAGNTQQKVCKQCHTILT   65 (88)
T ss_dssp             CCCCSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCEEEEETTTTSEEEEECHHHHHHHH
T ss_pred             CCcCCCCcCcCCcccCccccccCCCCCCEEChhHcCCceeccccCCCcCEECHHHHHHHH
Confidence            4456789999999975543333447999999999876432       2356877765543

>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=82.60  E-value=2.1  Score=28.05  Aligned_cols=46  Identities=28%  Similarity=0.658  Sum_probs=29.1

Q ss_pred             CCcccccccccccCCceeEEecC--cc-ceechhhHHHHhh----cCCCCCccccccC
Q 044318          132 GIDRCVICQVEYEEGESIVALLP--CE-HLYHSECISNWLQ----IKKICPICSTEAS  182 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~--C~-H~FH~~CI~~Wl~----~~~sCPvCR~~l~  182 (195)
                      ....| ||..... + .++..-.  |. ..||..|+.  |.    .+-.||.|+..-.
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-G-EMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESG   67 (71)
T ss_dssp             SCCCS-TTCCCSC-S-SEECCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSCSS
T ss_pred             CCCEE-ECCCCCC-C-CEeEeeCCCCCCccEecccCC--cCcCCCCCEECCCCCcccc
Confidence            44567 8987643 3 3333334  66 699999997  32    2347999986543

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=81.91  E-value=0.53  Score=31.54  Aligned_cols=44  Identities=20%  Similarity=0.522  Sum_probs=28.0

Q ss_pred             ccccccccccCCceeEEecCccceechhhHHHHhhc----C-CCCCcccc
Q 044318          135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI----K-KICPICST  179 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~----~-~sCPvCR~  179 (195)
                      .|.||...- ....++..-.|...||..|+..-|..    . -.||.|+.
T Consensus        28 ~C~vC~~~~-d~~~ll~CD~C~~~yH~~Cl~PpL~~~P~g~~W~C~~C~~   76 (77)
T 3shb_A           28 ACHLCGGRQ-DPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   76 (77)
T ss_dssp             SBTTTCCCS-CGGGEEECTTTCCEEETTTSSSCCSSCCSSSCCCCTTTC-
T ss_pred             cCCccCCCC-CCcceeEeCCCCCccCcccCCCcccCCCCCCceECcCccc
Confidence            455665443 22344444578999999999876532    2 46999975

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=80.73  E-value=0.49  Score=36.93  Aligned_cols=45  Identities=29%  Similarity=0.606  Sum_probs=30.8

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhc----CCCCCcccccc
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI----KKICPICSTEA  181 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~----~~sCPvCR~~l  181 (195)
                      ...|.+|...   ++ +.....|...||..|+..=+..    .-.||.|+..-
T Consensus         2 ~~~C~~C~~~---g~-ll~Cd~C~~~~H~~Cl~p~l~~~p~g~W~C~~C~~~~   50 (189)
T 2ro1_A            2 ATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   50 (189)
T ss_dssp             CCCBTTTCCC---SS-CCCCTTTCCBCCSTTSTTCCSSCCCTTCCTTTTSCSC
T ss_pred             CCcCccCCCC---Cc-eeECCCCCchhccccCCCCcccCCCCCCCCcCccCCC
Confidence            4679999844   32 3333468899999999765532    34699998653

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=80.72  E-value=1.5  Score=29.42  Aligned_cols=53  Identities=23%  Similarity=0.466  Sum_probs=35.5

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhh------cCCCCCccccccC
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ------IKKICPICSTEAS  182 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~------~~~sCPvCR~~l~  182 (195)
                      +.....|.+|...|..-..-.-.-.||.+||..|....+.      ..+.|-.|-..+.
T Consensus        16 d~~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~~~l~~~~~~~RVC~~C~~~l~   74 (82)
T 2yw8_A           16 DDEATHCRQCEKEFSISRRKHHCRNCGHIFCNTCSSNELALPSYPKPVRVCDSCHTLLL   74 (82)
T ss_dssp             CCCCCBCTTTCCBCBTTBCCEECTTTCCEECSGGGCEEECCTTCSSCEEECHHHHHHTT
T ss_pred             CccCCcccCcCCcccCccccccCCCCCCEEChHHhCCeeecCCCCCcCEECHHHHHHHH
Confidence            4456789999999975443333447999999999876542      1235666655443

>2rsd_A E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant homeodomain (PHD), histone binding; NMR {Oryza sativa japonica group}

Probab=80.50  E-value=0.36  Score=31.38  Aligned_cols=45  Identities=20%  Similarity=0.420  Sum_probs=27.4

Q ss_pred             CcccccccccccCCceeEEec--CccceechhhHHHHh---h-----cCCCCCcccc
Q 044318          133 IDRCVICQVEYEEGESIVALL--PCEHLYHSECISNWL---Q-----IKKICPICST  179 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~--~C~H~FH~~CI~~Wl---~-----~~~sCPvCR~  179 (195)
                      ...| ||-.....+. .+..-  .|...||..|+.---   .     .+-.||.||.
T Consensus        10 ~v~C-~C~~~~~~g~-mI~CD~~~C~~W~H~~Cvgi~~~~~~~~~~p~~~~C~~Cr~   64 (68)
T 2rsd_A           10 KVRC-ICSSTMVNDS-MIQCEDQRCQVWQHLNCVLIPDKPGESAEVPPVFYCELCRL   64 (68)
T ss_dssp             EECC-TTCCCSCCSC-EEECSCTTTCEEEETTTSCCCSSTTSCCCCCSSCCCHHHHH
T ss_pred             CEEe-ECCCCcCCCC-EEEECCCCCCCeEchhhCCCCcccccccCCCCcEECcCccC
Confidence            3456 7866554443 33332  488999999983211   0     1357999974

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=80.39  E-value=2.8  Score=28.17  Aligned_cols=54  Identities=11%  Similarity=0.279  Sum_probs=36.4

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHHhh--------cCCCCCccccccC
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQ--------IKKICPICSTEAS  182 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~--------~~~sCPvCR~~l~  182 (195)
                      .+.....|.+|...|..-..-.-.-.||++||..|....+.        ..+.|-.|-..+.
T Consensus        17 pd~~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~   78 (84)
T 1z2q_A           17 EDEDAPACNGCGCVFTTTVRRHHCRNCGYVLCGDCSRHRAAIPMRGITEPERVCDACYLALR   78 (84)
T ss_dssp             CTTTCCBCTTTCCBCCTTSCCEECTTTCCEECTGGGCCEEEETTTTEEEEEECCHHHHHHHH
T ss_pred             cCCCCCCCcCcCCccccchhcccccCCCcEEChHHhCCeEeccCCCCCCCCEECHHHHHHHh
Confidence            34567799999999975443333447999999999876531        2246777655443

---

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	195
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	2e-13
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	2e-10
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	2e-10
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	9e-08
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	1e-07
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	9e-07
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	4e-06
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	5e-05
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	1e-04
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	2e-04
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	0.001
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	0.002
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	0.003
d1we9a_	64	g.50.1.2 (A:) PHD finger protein At5g26210 {Thale	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 = 59.9 bits (145), Expect = 2e-13
 Identities = 17/44 (38%), Positives = 23/44 (52%)

Query: 134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPIC 177
             C +C  E E+GE    L  C H +H+EC+  WL     CP+C
Sbjct: 6   VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLC 49

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 2e-10
 Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 14/65 (21%)

Query: 130 KSGIDRCVICQVEYEEGE--------------SIVALLPCEHLYHSECISNWLQIKKICP 175
              +D C IC+    +                  VA   C H +H  CIS WL+ +++CP
Sbjct: 18  DIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCP 77

Query: 176 ICSTE 180
           + + E
Sbjct: 78  LDNRE 82

>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 = 52.3 bits (125), Expect = 2e-10
 Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 3/47 (6%)

Query: 134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTE 180
           +RC IC  +          LPC H +   CI+ W++    CP+C   
Sbjct: 6   ERCPICLEDPSNY---SMALPCLHAFCYVCITRWIRQNPTCPLCKVP 49

>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 = 45.8 bits (108), Expect = 9e-08
 Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 5/51 (9%)

Query: 131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK-KICPICSTE 180
           S    C IC    ++    V + PC HL  + C+++W + + + CP C  E
Sbjct: 21  STFQLCKICAENDKD----VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCE 67

>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 = 44.3 bits (104), Expect = 1e-07
 Identities = 8/46 (17%), Positives = 13/46 (28%), Gaps = 1/46 (2%)

Query: 136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK-KICPICSTE 180
           C +C    E  +       C +     C       +  +CP C   
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKP 48

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.2 bits (99), Expect = 9e-07
 Identities = 16/52 (30%), Positives = 19/52 (36%), Gaps = 7/52 (13%)

Query: 135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKN 186
           RC  CQ E +       LLPC H   S C+         CPIC        +
Sbjct: 8   RCQQCQAEAKC----PKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGAD 52

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 4e-06
 Identities = 10/49 (20%), Positives = 15/49 (30%), Gaps = 2/49 (4%)

Query: 134 DRCVICQVEYEEGESIVALL-PCEHLYHSECISNWLQIKK-ICPICSTE 180
             C  C+       S+  ++  C H     C+          CP C T 
Sbjct: 4   QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTP 52

>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 = 38.5 bits (89), Expect = 5e-05
 Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 7/64 (10%)

Query: 135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKK---ICPICSTEASPPKNHNNAI 191
            C IC    +E         C+H++   C+   L  KK    CP+C  + +      +  
Sbjct: 23  ECPICLELIKE----PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTR 78

Query: 192 TSKL 195
            S+L
Sbjct: 79  FSQL 82

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.7 bits (86), Expect = 1e-04
 Identities = 9/51 (17%), Positives = 14/51 (27%), Gaps = 5/51 (9%)

Query: 134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKI-----CPICST 179
               +   +      +  L  C H +H  C+              CP C T
Sbjct: 40  GYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKT 90

>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 = 35.6 bits (81), Expect = 2e-04
 Identities = 13/48 (27%), Positives = 15/48 (31%), Gaps = 3/48 (6%)

Query: 136 CVICQVEYEEG-ESIVALLPCEHLYHSECISNWLQIKKI--CPICSTE 180
           C IC  E                  H  C+S WL I +   C IC   
Sbjct: 9   CWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVV 56

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.8 bits (79), Expect = 0.001
 Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 2/63 (3%)

Query: 133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNNAIT 192
           +++ + C          V L  CEH++ S C+S+ +     CP+C T A       N   
Sbjct: 19  LEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTG--CPVCYTPAWIQDLKINRQL 76

Query: 193 SKL 195
             +
Sbjct: 77  DSM 79

>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 = 33.9 bits (77), Expect = 0.002
 Identities = 10/56 (17%), Positives = 23/56 (41%), Gaps = 9/56 (16%)

Query: 131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKI--------CPICS 178
           SG   C +C  EY   +    +  C+ ++ + C+  ++++           CP  +
Sbjct: 3   SGSSGCKLCLGEYPVEQMTT-IAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA 57

>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 = 33.3 bits (76), Expect = 0.003
 Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 5/49 (10%)

Query: 136 CVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK-KICPICSTEASP 183
           C IC+    +         C+HL+   CI   L++    CP C     P
Sbjct: 26  CQICEHILAD----PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFP 70

>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 = 32.7 bits (74), Expect = 0.004
 Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 5/61 (8%)

Query: 128 GTKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKK-----ICPICSTEAS 182
           G+     +C  C   Y   E  +    CE  +H +C+       +      CP CS ++ 
Sbjct: 1   GSSGSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKSG 60

Query: 183 P 183
           P
Sbjct: 61  P 61

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	195
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.74
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.6
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.56
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.54
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.53
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.51
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.49
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.42
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.4
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.4
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.36
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.3
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.23
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.2
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.18
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.01
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.72
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	96.03
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	94.85
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	94.67
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	92.65
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	92.61
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	92.4
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	92.29
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	92.13
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	91.27
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	90.29
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	90.2
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	88.43
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	88.16
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	87.98
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	81.71

>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=99.74  E-value=5.8e-19  Score=112.92  Aligned_cols=51  Identities=33%  Similarity=0.792  Sum_probs=46.7

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      ...+|+||++.|..++.++.+++|+|.||..||.+|++.+++||+||++|.
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            456799999999999988888789999999999999999999999999874

>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=99.60  E-value=3.2e-16  Score=103.97  Aligned_cols=49  Identities=31%  Similarity=0.790  Sum_probs=42.0

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASP  183 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~  183 (195)
                      ..+.|+||++.|..+  ++. ++|||.||..||.+|++.+++||+||+++..
T Consensus         4 ~~d~C~IC~~~~~~~--~~~-~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~   52 (68)
T d1chca_           4 VAERCPICLEDPSNY--SMA-LPCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCSC--EEE-TTTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCccCCcCccCC--cEE-eCCCCcCcHHHHHHHHHhCCcCCCCCcchHh
Confidence            567899999998654  333 4999999999999999999999999998753

>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=99.56  E-value=3.1e-16  Score=98.78  Aligned_cols=49  Identities=16%  Similarity=0.317  Sum_probs=41.3

Q ss_pred             ccccccccccCCceeEEecCccceechhhHHHHhhc-CCCCCccccccCC
Q 044318          135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-KKICPICSTEASP  183 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-~~sCPvCR~~l~~  183 (195)
                      +|+||++.|..+.....+++|||.||..||.+|++. +++||+||+++..
T Consensus         2 eCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            699999999876655455599999999999999986 4579999998854

>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=99.54  E-value=1.7e-15  Score=105.30  Aligned_cols=51  Identities=33%  Similarity=0.723  Sum_probs=41.7

Q ss_pred             CCcccccccccccCCce--------------eEEecCccceechhhHHHHhhcCCCCCccccccC
Q 044318          132 GIDRCVICQVEYEEGES--------------IVALLPCEHLYHSECISNWLQIKKICPICSTEAS  182 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~--------------~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~  182 (195)
                      ..+.|+||++.+.....              .+.+++|+|+||..||.+||+.+++||+||+++.
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~   84 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE   84 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCCcCCCCCCccc
Confidence            45679999988865321              2344599999999999999999999999999874

>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=99.53  E-value=3.5e-15  Score=108.04  Aligned_cols=57  Identities=21%  Similarity=0.430  Sum_probs=43.5

Q ss_pred             CCcccccccccccCC--------------ceeEEecCccceechhhHHHHhhcC-----CCCCccccccCCCCCCC
Q 044318          132 GIDRCVICQVEYEEG--------------ESIVALLPCEHLYHSECISNWLQIK-----KICPICSTEASPPKNHN  188 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~--------------~~~~~L~~C~H~FH~~CI~~Wl~~~-----~sCPvCR~~l~~~~~~~  188 (195)
                      ....|+||++.+...              ...+.+++|+|.||..||..||+.+     .+||+||+.+..+....
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~~~q   99 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQ   99 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSSSC
T ss_pred             ccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccCcCCC
Confidence            356899999988542              2345556999999999999999743     47999999886664433

>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=99.51  E-value=3.9e-15  Score=97.79  Aligned_cols=54  Identities=17%  Similarity=0.333  Sum_probs=41.6

Q ss_pred             CCcccccccccccC-CceeEEecCccceechhhHHHHhhc-CCCCCccccccCCCC
Q 044318          132 GIDRCVICQVEYEE-GESIVALLPCEHLYHSECISNWLQI-KKICPICSTEASPPK  185 (195)
Q Consensus       132 ~~~~C~ICl~~f~~-~~~~~~L~~C~H~FH~~CI~~Wl~~-~~sCPvCR~~l~~~~  185 (195)
                      +...|+||++.+.. +.....+++|||.||..||.+|++. +++||+||+++....
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~   57 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSN   57 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCccccc
Confidence            35789999998643 3333344599999999999999954 568999999886544

>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=99.49  E-value=1.4e-14  Score=98.71  Aligned_cols=50  Identities=26%  Similarity=0.684  Sum_probs=41.0

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhc-CCCCCccccccCCCCC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-KKICPICSTEASPPKN  186 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-~~sCPvCR~~l~~~~~  186 (195)
                      ...|+||++.+...   +. ++|||.||..||..|+.. +++||+||+.+.....
T Consensus        23 ~~~C~IC~~~~~~~---~~-~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~   73 (79)
T d1fbva4          23 FQLCKICAENDKDV---KI-EPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP   73 (79)
T ss_dssp             TTBCTTTSSSBCCE---EC-SSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCC
T ss_pred             CCCCccCCCcCCCe---EE-eCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCce
Confidence            35799999988653   34 499999999999999974 5789999999976543

>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=99.42  E-value=2.2e-14  Score=91.45  Aligned_cols=49  Identities=12%  Similarity=0.121  Sum_probs=42.1

Q ss_pred             ccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCC
Q 044318          135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKN  186 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~  186 (195)
                      .|+||++.++++   +.++.|||+||+.||.+|++.+++||+||+++...+.
T Consensus         2 ~C~Ic~~~~~~P---v~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dL   50 (56)
T d2baya1           2 LCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEI   50 (56)
T ss_dssp             CCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGC
T ss_pred             CCccCCchHHhc---CccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhc
Confidence            599999999876   3344699999999999999999999999999876544

>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=99.40  E-value=5.6e-14  Score=97.16  Aligned_cols=51  Identities=27%  Similarity=0.608  Sum_probs=42.0

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhc-CCCCCccccccCCCCCC
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-KKICPICSTEASPPKNH  187 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-~~sCPvCR~~l~~~~~~  187 (195)
                      ...|+||++.|..+   +. ++|||.||..||.+|++. ..+||+||.++......
T Consensus        23 ~l~C~IC~~~~~~p---v~-~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l~   74 (86)
T d1rmda2          23 SISCQICEHILADP---VE-TSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE   74 (86)
T ss_dssp             HTBCTTTCSBCSSE---EE-CTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCB
T ss_pred             CcCCccCCcchhcc---ee-cCCCChhhHHHHHHHHhhCCCcCcccCCCCChhhcc
Confidence            35799999998776   33 599999999999999974 46899999998765544

>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=99.40  E-value=5.1e-14  Score=100.22  Aligned_cols=52  Identities=23%  Similarity=0.572  Sum_probs=42.5

Q ss_pred             cccccccccccCCceeEEecCccceechhhHHHHhhcC---CCCCccccccCCCCCCCc
Q 044318          134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK---KICPICSTEASPPKNHNN  189 (195)
Q Consensus       134 ~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~---~sCPvCR~~l~~~~~~~~  189 (195)
                      ..|+||++.|..+    +.++|||.||..||..|++..   ..||+||+++......++
T Consensus        22 l~CpIC~~~~~~p----v~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l~~n   76 (103)
T d1jm7a_          22 LECPICLELIKEP----VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQES   76 (103)
T ss_dssp             TSCSSSCCCCSSC----CBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCC
T ss_pred             cCCCccCchhCCe----EEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhCCcC
Confidence            4799999999876    334999999999999999765   379999999976655444

>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=99.36  E-value=1.2e-13  Score=88.03  Aligned_cols=49  Identities=33%  Similarity=0.583  Sum_probs=40.2

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNH  187 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~  187 (195)
                      ....|+||++.|..+    ++++|||.||..||.+|   +.+||+||++++.....
T Consensus         5 ~~l~C~IC~~~~~~p----~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~~~   53 (56)
T d1bora_           5 QFLRCQQCQAEAKCP----KLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGADT   53 (56)
T ss_dssp             CCSSCSSSCSSCBCC----SCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCCSSC
T ss_pred             CCCCCcccCcccCCC----EEecCCCHHhHHHHHcC---CCcCcCCCCcccCCCCC
Confidence            345899999999876    33599999999999876   67899999999766443

>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=99.30  E-value=2.1e-13  Score=95.91  Aligned_cols=53  Identities=34%  Similarity=0.612  Sum_probs=42.7

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCccccccCCCCCCCcc
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICSTEASPPKNHNNA  190 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~~  190 (195)
                      ...|+||++.|..+   +.+++|||.||..||.+|+.  ..||+||.++......++.
T Consensus        22 ~l~C~IC~~~~~~p---v~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~l~~n~   74 (97)
T d1jm7b_          22 LLRCSRCTNILREP---VCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKINR   74 (97)
T ss_dssp             TTSCSSSCSCCSSC---BCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCCCCH
T ss_pred             cCCCccCCchhhcC---ceeCCCCCchhHHHHHHHHh--ccccccCCcCchhhCcccH
Confidence            45899999999877   23448999999999999985  4599999998776665543

>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=99.23  E-value=2.8e-12  Score=82.44  Aligned_cols=54  Identities=22%  Similarity=0.447  Sum_probs=39.2

Q ss_pred             CCCCcccccccccccCCceeE-EecCccceechhhHHHHhh--cCCCCCccccccCC
Q 044318          130 KSGIDRCVICQVEYEEGESIV-ALLPCEHLYHSECISNWLQ--IKKICPICSTEASP  183 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~-~L~~C~H~FH~~CI~~Wl~--~~~sCPvCR~~l~~  183 (195)
                      ......|.||++.+....... ....|+|.||..||.+|+.  .+.+||+||+++..
T Consensus         3 ded~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           3 DEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             TCSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            446678999999886542210 1113569999999999995  45689999998753

>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=99.20  E-value=4.8e-12  Score=85.38  Aligned_cols=55  Identities=22%  Similarity=0.345  Sum_probs=45.7

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhcC-CCCCccccccCCCCCCCc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK-KICPICSTEASPPKNHNN  189 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~-~sCPvCR~~l~~~~~~~~  189 (195)
                      .....|+||++.|.++   +++ +|||.||+.||.+|++.+ ..||.|+.++......++
T Consensus         6 P~~l~CpIc~~~m~dP---V~~-~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~l~pN   61 (78)
T d1t1ha_           6 PEYFRCPISLELMKDP---VIV-STGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPN   61 (78)
T ss_dssp             SSSSSCTTTSCCCSSE---EEE-TTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEEC
T ss_pred             CccCCCcCcCchhhCc---eEc-cCCCcchHHHHHHHHHHCCCCCCcccccCCcccccch
Confidence            3567899999999887   345 999999999999999765 679999999987655544

>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=99.18  E-value=4.5e-12  Score=85.95  Aligned_cols=54  Identities=17%  Similarity=0.107  Sum_probs=44.0

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhc-CCCCCccccccCCCCCCCc
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI-KKICPICSTEASPPKNHNN  189 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~-~~sCPvCR~~l~~~~~~~~  189 (195)
                      ....|+||++-|.++    +.++|||.||..||.+|+.. +.+||+||.++......++
T Consensus         6 ~~l~CpIc~~l~~dP----v~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~l~pN   60 (80)
T d2c2la2           6 DYLCGKISFELMREP----CITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPN   60 (80)
T ss_dssp             STTBCTTTCSBCSSE----EECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEEC
T ss_pred             ccccCcCcCchhhhh----cccCCcCeecHHHHHHHHhcCCccCCCccccccccccccH
Confidence            567899999999887    33499999999999999965 5679999998876554443

>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=99.01  E-value=1e-10  Score=82.27  Aligned_cols=56  Identities=14%  Similarity=0.039  Sum_probs=46.6

Q ss_pred             CCCcccccccccccCCceeEEecCcc-ceechhhHHHHhhcCCCCCccccccCCCCCCCcc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCE-HLYHSECISNWLQIKKICPICSTEASPPKNHNNA  190 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~-H~FH~~CI~~Wl~~~~sCPvCR~~l~~~~~~~~~  190 (195)
                      .....|+||+.-|.++   +++ +|+ |.|++.||.+||+.+.+||+||.++......++.
T Consensus        20 P~~f~CPI~~~lm~dP---V~~-~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L~pN~   76 (98)
T d1wgma_          20 CDEFLDPIMSTLMCDP---VVL-PSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPNT   76 (98)
T ss_dssp             CTTTBCTTTCSBCSSE---EEC-TTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEECH
T ss_pred             cHHhCCcCchhHHHHH---Hhc-ccccchhhHHHHHHHHHhcCCcccccccccchhhcchH
Confidence            3568999999999987   334 666 5899999999999999999999999877665554

>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=98.72  E-value=3.3e-09  Score=73.27  Aligned_cols=48  Identities=21%  Similarity=0.587  Sum_probs=37.4

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhcC--------CCCCcccc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK--------KICPICST  179 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~--------~sCPvCR~  179 (195)
                      .+...|+||++.+...+.+..+ +|+|.||..||..|++.+        -+||.|+-
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           3 SGSSGCKLCLGEYPVEQMTTIA-QCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEET-TTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCCcCccCCCcccCCceEEEC-CCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            4567999999999765555544 899999999999999532        25998653

>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=96.03  E-value=0.0018  Score=40.39  Aligned_cols=52  Identities=23%  Similarity=0.528  Sum_probs=37.9

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHh---h--cCCCCCcccccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWL---Q--IKKICPICSTEA  181 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl---~--~~~sCPvCR~~l  181 (195)
                      ......|.||..........+..-.|+..||..|+..-.   .  ..-.||.|+..-
T Consensus         3 ~~~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~~   59 (64)
T d1we9a_           3 SGSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKS   59 (64)
T ss_dssp             CSSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTT
T ss_pred             CCCCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCcC
Confidence            345678999998877766666666899999999985321   1  235799998643

>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=94.85  E-value=0.0072  Score=35.78  Aligned_cols=44  Identities=25%  Similarity=0.629  Sum_probs=31.5

Q ss_pred             ccccccccccCCceeEEecCccceechhhHHHHhhcC----CCCCcccc
Q 044318          135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIK----KICPICST  179 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~----~sCPvCR~  179 (195)
                      .|.||...-.. ..++.--.|...||..|+..-+...    -.||.||.
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            68899765433 3445555899999999998876432    36999974

>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=94.67  E-value=0.019  Score=36.26  Aligned_cols=50  Identities=26%  Similarity=0.525  Sum_probs=33.2

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhc----CCCCCccccccCCCC
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI----KKICPICSTEASPPK  185 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~----~~sCPvCR~~l~~~~  185 (195)
                      ....|.||..   .+ .++..-.|...||..|+...+..    .-.||.|+..-....
T Consensus         6 ~c~~C~~C~~---~~-~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~~~~   59 (70)
T d1fp0a1           6 SATICRVCQK---PG-DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKE   59 (70)
T ss_dssp             SSSCCSSSCS---SS-CCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCSSCC
T ss_pred             CCCCCCCCCC---cC-EEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCccCc
Confidence            3445666653   33 34455589999999999987743    246999976554443

>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=92.65  E-value=0.025  Score=37.09  Aligned_cols=50  Identities=24%  Similarity=0.533  Sum_probs=33.9

Q ss_pred             CcccccccccccC-CceeEEecCccceechhhHHHHhh-----c---CCCCCccccccC
Q 044318          133 IDRCVICQVEYEE-GESIVALLPCEHLYHSECISNWLQ-----I---KKICPICSTEAS  182 (195)
Q Consensus       133 ~~~C~ICl~~f~~-~~~~~~L~~C~H~FH~~CI~~Wl~-----~---~~sCPvCR~~l~  182 (195)
                      ...|.||...... ...++..-.|...||..|+...+.     .   .-.||.|+....
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~~   74 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMK   74 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHC
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchHh
Confidence            3569999865433 334555558999999999875431     1   347999976543

>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=92.61  E-value=0.024  Score=34.77  Aligned_cols=48  Identities=25%  Similarity=0.642  Sum_probs=32.6

Q ss_pred             CCCCcccccccccccCCceeEEecCccceechhhHHHHhhc----CCCCCcccccc
Q 044318          130 KSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI----KKICPICSTEA  181 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~----~~sCPvCR~~l  181 (195)
                      ......|.||...   + .++..-.|.-.||..||...+..    .-.||.|+...
T Consensus         6 d~~~~~C~~C~~~---g-~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           6 DHHMEFCRVCKDG---G-ELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             CSSCSSCTTTCCC---S-SCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             cCCcCCCcCCCCC---C-eEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            3445679999742   3 34444478999999999766643    34699997543

>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=92.40  E-value=0.048  Score=35.58  Aligned_cols=37  Identities=14%  Similarity=0.447  Sum_probs=26.8

Q ss_pred             CCCCCcccccccccccCCceeEEecCccceechhhHHHH
Q 044318          129 TKSGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNW  167 (195)
Q Consensus       129 ~~~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~W  167 (195)
                      ....+..|.|| ..|...... ..--|+-+||..|+.+.
T Consensus        11 ~v~~D~mC~vC-~v~t~~~l~-pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          11 PVVNDEMCDVC-EVWTAESLF-PCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCSCCCTTT-CCCCSSCCS-SCSSSSSCCCHHHHHHH
T ss_pred             CCCcCcccccc-Cccccccee-cceeecchhhHHHHHHh
Confidence            35567899999 677665432 22247899999999986

>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=92.29  E-value=0.14  Score=32.72  Aligned_cols=49  Identities=16%  Similarity=0.371  Sum_probs=33.7

Q ss_pred             cccccccccccCCceeEEecCccceechhhHHH--Hh-h--cCCCCCccccccC
Q 044318          134 DRCVICQVEYEEGESIVALLPCEHLYHSECISN--WL-Q--IKKICPICSTEAS  182 (195)
Q Consensus       134 ~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~--Wl-~--~~~sCPvCR~~l~  182 (195)
                      ..|.||...+......+..-.|.-.||..|+.-  .. .  .+-.||.|+....
T Consensus        12 pv~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~g   65 (79)
T d1wepa_          12 PVYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CCCSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             CeEeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcC
Confidence            445599887766555566668999999999842  11 1  2357999987543

>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=92.13  E-value=0.012  Score=35.17  Aligned_cols=45  Identities=18%  Similarity=0.483  Sum_probs=31.6

Q ss_pred             ccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCcccc
Q 044318          135 RCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPICST  179 (195)
Q Consensus       135 ~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvCR~  179 (195)
                      .|.+|...|..-..-..--.||.+||..|....-+..+.|..|.+
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C~~   46 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQR   46 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhHhh
Confidence            588999888665443444479999999998877666678888854

>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=91.27  E-value=0.26  Score=32.19  Aligned_cols=62  Identities=21%  Similarity=0.299  Sum_probs=44.4

Q ss_pred             CCCCccccccccccc---CCceeEEecCccceechhhHHHHh-hcCCCCCccccccCCCCCCCccc
Q 044318          130 KSGIDRCVICQVEYE---EGESIVALLPCEHLYHSECISNWL-QIKKICPICSTEASPPKNHNNAI  191 (195)
Q Consensus       130 ~~~~~~C~ICl~~f~---~~~~~~~L~~C~H~FH~~CI~~Wl-~~~~sCPvCR~~l~~~~~~~~~~  191 (195)
                      ......|-||-+.+-   +++..+..--|+-..|+.|..-=. ..+..||.|+++....+..+.+.
T Consensus        13 ~~~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Ykr~kgsprv~   78 (93)
T d1weoa_          13 NLDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKRLRGSPRVE   78 (93)
T ss_dssp             CCSSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCCCTTCCCCT
T ss_pred             hcccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhhhhcCCCCCC
Confidence            345678999998873   344445555688889999986444 45678999999998776665443

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=90.29  E-value=0.063  Score=34.36  Aligned_cols=49  Identities=20%  Similarity=0.393  Sum_probs=31.0

Q ss_pred             CCcccccccccccCCceeEEec--CccceechhhHHH----Hhh-----cCCCCCccccccC
Q 044318          132 GIDRCVICQVEYEEGESIVALL--PCEHLYHSECISN----WLQ-----IKKICPICSTEAS  182 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~--~C~H~FH~~CI~~----Wl~-----~~~sCPvCR~~l~  182 (195)
                      ....| ||......+. .+.+-  .|...||..|+.-    +..     ..-.||.|+..-.
T Consensus        15 ~~~~C-~C~~~~~~~~-~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~~   74 (78)
T d1wewa_          15 IKVRC-VCGNSLETDS-MIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSG   74 (78)
T ss_dssp             CCCCC-SSCCCCCCSC-EEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCCS
T ss_pred             CccEe-ECCCccCCCc-EEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcCC
Confidence            34567 8988765543 33442  4999999999832    111     1357999986543

>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=90.20  E-value=0.053  Score=34.10  Aligned_cols=48  Identities=25%  Similarity=0.450  Sum_probs=33.5

Q ss_pred             cccccccccccCCceeEEecCccceechhhHHHHh----hcCCCCCccccccC
Q 044318          134 DRCVICQVEYEEGESIVALLPCEHLYHSECISNWL----QIKKICPICSTEAS  182 (195)
Q Consensus       134 ~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl----~~~~sCPvCR~~l~  182 (195)
                      ..| ||......+..++....|...||..|+..-.    .....||.|+..-.
T Consensus        17 ~~C-~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~~~~~~~~C~~C~~~~~   68 (72)
T d1weea_          17 VDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELSG   68 (72)
T ss_dssp             ECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHHCS
T ss_pred             EEe-eCCCCcCCCCeEEEeCCCCCcCchhhcCCccccCCCCcEECcCCcCcCC
Confidence            457 7877666666666666899999999985422    13357999976543

>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=88.43  E-value=0.29  Score=30.60  Aligned_cols=47  Identities=23%  Similarity=0.557  Sum_probs=30.7

Q ss_pred             CcccccccccccCCceeEEecCccceechhhHH----HH-----hhcCCCCCcccccc
Q 044318          133 IDRCVICQVEYEEGESIVALLPCEHLYHSECIS----NW-----LQIKKICPICSTEA  181 (195)
Q Consensus       133 ~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~----~W-----l~~~~sCPvCR~~l  181 (195)
                      ...| ||......+ .++..-.|.-.||..|+.    ..     ......||.|+...
T Consensus        16 ~~~C-iC~~~~~~~-~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~~   71 (76)
T d1wema_          16 ALYC-ICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             CCCS-TTCCCCCSS-CEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             cCEE-ECCCccCCC-eEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCcC
Confidence            3457 897765443 345555899999999982    11     12346899997554

>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=88.16  E-value=0.14  Score=31.17  Aligned_cols=45  Identities=22%  Similarity=0.474  Sum_probs=32.4

Q ss_pred             CCcccccccccccCCceeEEecCccceechhhHHHHhhcCCCCCcc
Q 044318          132 GIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQIKKICPIC  177 (195)
Q Consensus       132 ~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~~~sCPvC  177 (195)
                      ....|--|+..+.+. .+.....|++.||.+|=.--=..-..||-|
T Consensus        14 ~~~~C~gC~~~l~~~-~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKDQ-HVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTTS-EEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCCC-ceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            456799999888654 345566899999999954322444689988

>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=87.98  E-value=0.34  Score=30.47  Aligned_cols=40  Identities=20%  Similarity=0.314  Sum_probs=29.9

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhHHHHhhc
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECISNWLQI  170 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI~~Wl~~  170 (195)
                      .....|.+|.+.+++...+..--.=+|.||..|-+..++.
T Consensus         6 ~~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~   45 (80)
T d2cs3a1           6 SGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   45 (80)
T ss_dssp             CCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CCceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHh
Confidence            3457899999999887654322224799999999998864

>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=81.71  E-value=0.72  Score=26.02  Aligned_cols=31  Identities=23%  Similarity=0.552  Sum_probs=24.1

Q ss_pred             CCCcccccccccccCCceeEEecCccceechhhH
Q 044318          131 SGIDRCVICQVEYEEGESIVALLPCEHLYHSECI  164 (195)
Q Consensus       131 ~~~~~C~ICl~~f~~~~~~~~L~~C~H~FH~~CI  164 (195)
                      ...+.|+.|-...-.-+++.   -=|+.||+.|.
T Consensus        13 g~~~kC~~C~k~VY~~E~~~---~~g~~~Hk~CF   43 (43)
T d1b8ta3          13 GGSDGCPRCGQAVYAAEKVI---GAGKSWHKSCF   43 (43)
T ss_dssp             CCCEECTTTSCEECSSSCEE---ETTEEECTTTC
T ss_pred             CCCCcCccCCCEeeHHHHhh---cCCCccccCCC
Confidence            35688999998887777655   34899999983